Full

CHEM 212/213:
INORGANIC
CHEMISTRY
Chip Nataro
Lafayette College
Lafayette College: CHEM 212/213
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This text was compiled on 01/12/2023

TABLE OF CONTENTS
Licensing
1: Atoms
1.1: Mass Spectrometry
1.2: Rutherford's Atom
1.3: Bohr's Atom
1.4: Hydrogen Atom
1.5: Slater Rules
2: Molecules
2.1: Front Matter
TitlePage
InfoPage
Table of Contents
2.2: Molecular Shapes
2.3: The VSEPR Model
2.4: Hybrid Orbitals
2.5: Molecular Orbitals
2.5.1: Molecular Shape and Molecular Polarity
2.5.2: Prelude to Molecular Orbital Theory
2.5.3: Constructing Molecular Orbitals from Atomic Orbitals
2.5.4: Orbital Symmetry
2.5.5: Molecular Orbital Diagrams
2.5.6: π Orbitals and Diatomic Molecules
2.5.7: Orbital Filling
2.5.8: δ orbitals
2.6: The Range of Bonding
2.7: Advanced Bonding
2.7.1: Symmetry Elements and Operations
2.7.2: Point Groups
2.7.2.1: Other Groups
2.7.2.2: Groups of Low and High Symmetry
2.7.3: Ligand Group Orbitals and Generator Functions
2.7.4: Expanded Octets and Molecular Orbitals
2.8: Nuclear Magnetic Resonance (NMR)
2.8.1: The Origin of the NMR Signal
2.8.2: Chemical Equivalence
2.8.3: The 1H-NMR experiment
2.8.4: Spin-Spin Coupling
2.8.5: The Basis for Differences in Chemical Shift
Index
Glossary
1 https://chem.libretexts.org/@go/page/294076
3: Solid state
3.1: Prelude to Metals and Alloys
3.2: Unit Cells and Crystal Structures
3.3: Crystal Structures of Metals
3.4: Conduction in Metals
3.5: Atomic Orbitals and Magnetism
3.6: Ferro-, Ferri- and Antiferromagnetism
3.7: Hard and Soft Magnets
3.8: Defects in Metallic Crystals
3.9: X-ray Crystallography
3.10: Miller Indices (hkl)
3.11: Powder X-ray Diffraction
3.12: Prelude to Ionic and Covalent Solids - Structures
3.13: Close-packing and Interstitial Sites
3.14: Structures Related to NaCl and NiAs
3.15: Tetrahedral Structures
3.16: Layered Structures and Intercalation Reactions
3.17: Ionic Radii and Radius Ratios
3.18: Structure Maps
3.19: Energetics of Crystalline Solids- The Ionic Model
3.20: Born-Haber Cycles for NaCl and Silver Halides
3.21: Lattice Energies and Solubility
3.22: Spinel, Perovskite, and Rutile Structures
3.23: Kapustinskii Equation
4: Acid-Base Theories
4.1: Bronsted-Lowry acids and bases
4.2: Lewis Acids and Bases
4.3: Acidity of the Hexaaqua Ions
4.4: Hard-soft Acids and Bases
4.5: Quantitative Measures of Hardness and Softness
5: Coordination Chemistry
5.1: Introduction to Coordination Chemistry
5.2: Ligands and Nomenclature
5.3: Coordination Numbers and Geometry
5.4: Bonding with d-orbitals
5.5: Isomers
5.5.1: Structural Isomers - Ionization Isomerism in Transition Metal Complexes
5.5.2: Structural Isomers - Geometric Isomerism in Transition Metal Complexes
5.5.3: Stereoisomers - Optical Isomerism in Transition Metal Complexes
5.5.4: Structural Isomers - Linkage Isomerism in Transition Metal Complexes
5.6: Crystal Field Theory
5.6.1: Crystal Field Theory
5.6.2: Colors of Coordination Complexes
5.6.3: Crystal Field Stabilization Energy
5.6.4: Factors That Affect the Magnitude of Δo
5.6.5: Jahn-Teller Distortions
5.6.6: Magnetic Moments of Transition Metals
5.6.7: Magnetism
5.6.8: Thermodynamics and Structural Consequences of d-Orbital Splitting
5.7: Ligand Field Theory
5.8: Ligand Exchange Reactions (Thermodynamics)
5.9: Electronic Spectra of Coordination Compounds
6: Bioinorganic Chemistry
6.1: Biological Signi cance of Iron, Zinc, Copper, Molybdenum, Cobalt, Chromium, Vanadium, and Nickel
6.2: Introduction to Amino Acids and Proteins
6.3: Redox Reactions
6.3.1: Introduction to Redox Reactions
6.3.2: Balancing Redox Reactions
6.3.3: Electrochemical Potentials
6.3.4: Prelude to Redox Stability and Redox Reactions
6.3.5: Latimer and Frost Diagrams
6.3.6: Pourbaix Diagrams
6.4: Associative Ligand Substitution
6.5: Dissociative Ligand Substitution
6.6: Biological Signi cance of Iron, Zinc, Copper, Molybdenum, Cobalt, Chromium, Vanadium, and Nickel
6.7: Ferrodoxins, Hydrogenases, and Nitrogenases - Metal-Sul de Proteins
6.7.1: Iron-sulfur Proteins and Models
6.7.2: Iron-sulfur Proteins and Models (Part 2)
6.8: Overview of Hemoglobin and Myoglobin
6.8.1: Myoglobin, Hemoglobin, and their Ligands
6.8.2: Oxygen Transport by the Proteins Myoglobin and Hemoglobin
Index
Glossary
Glossary
Detailed Licensing
Licensing
A detailed breakdown of this resource's licensing can be found in Back Matter/Detailed Licensing.
CHAPTER OVERVIEW
1: Atoms
1.3: Bohr's Atom
1.4: Hydrogen Atom
1.5: Slater Rules
1: Atoms is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
1
Mass spectrometry (MS) is a powerful analytical technique widely used by chemists, biologists, medical researchers, and
environmental and forensic scientists, among others. With MS, we are looking at the mass of a molecule, or of different fragments
of that molecule.
The basics of a mass spectrometry experiment

There are many different types of MS instruments, but they all have the same three essential components. First, there is an
ionization source, where the molecule is given a positive electrical charge, either by removing an electron or by adding a proton.
Depending on the ionization method used, the ionized molecule may or may not break apart into a population of smaller fragments.
In the figure below, some of the sample molecules remain whole, while others fragment into smaller pieces.
Next in line there is a mass analyzer, where the cationic fragments are separated according to their mass.
Finally, there is a detector, which detects and quantifies the separated ions.
One of the more common types of MS techniques used in the organic laboratory is electron ionization. In the ionization source,
the sample molecule is bombarded by a high-energy electron beam, which has the effect of knocking a valence electron off of the
molecule to form a radical cation. Because a great deal of energy is transferred by this bombardment process, the radical cation
quickly begins to break up into smaller fragments, some of which are positively charged and some of which are neutral. The neutral
fragments are either adsorbed onto the walls of the chamber or are removed by a vacuum source. In the mass analyzer component,
the positively charged fragments and any remaining unfragmented molecular ions are accelerated down a tube by an electric field.
(Image from Wikipedia Commons)
1.1.1 https://chem.libretexts.org/@go/page/294676
This tube is curved, and the ions are deflected by a strong magnetic field. Ions of different mass to charge (m/z) ratios are deflected
to a different extent, resulting in a ‘sorting’ of ions by mass (virtually all ions have charges of z = +1, so sorting by the mass to
charge ratio is the same thing as sorting by mass). A detector at the end of the curved flight tube records and quantifies the sorted
ions.
Looking at mass spectra

Below is typical output for an electron-ionization MS experiment (MS data in the section is derived from the Spectral Database for
Organic Compounds, a free, web-based service provided by AIST in Japan.
The sample is acetone. On the horizontal axis is the value for m/z (as we stated above, the charge z is almost always +1, so in
practice this is the same as mass). On the vertical axis is the relative abundance of each ion detected. On this scale, the most
abundant ion, called the base peak, is set to 100%, and all other peaks are recorded relative to this value. For acetone, the base
peak is at m/z = 43 - we will discuss the formation of this fragment a bit later. The molecular weight of acetone is 58, so we can
identify the peak at m/z = 58 as that corresponding to the molecular ion peak, or parent peak. Notice that there is a small peak at
m/z = 59: this is referred to as the M+1 peak. How can there be an ion that has a greater mass than the molecular ion? Simple: a
small fraction - about 1.1% - of all carbon atoms in nature are actually the 13C rather than the 12C isotope. The 13C isotope is, of
course, heavier than 12C by 1 mass unit. In addition, about 0.015% of all hydrogen atoms are actually deuterium, the 2H isotope. So
the M+1 peak represents those few acetone molecules in the sample which contained either a 13C or 2H.
Molecules with lots of oxygen atoms sometimes show a small M+2 peak (2 m/z units greater than the parent peak) in their mass
spectra, due to the presence of a small amount of 18O (the most abundant isotope of oxygen is 16O). Because there are two
abundant isotopes of both chlorine (about 75% 35Cl and 25% 37Cl) and bromine (about 50% 79Br and 50% 81Br), chlorinated and
brominated compounds have very large and recognizable M+2 peaks. Fragments containing both isotopes of Br can be seen in the
mass spectrum of ethyl bromide:
Much of the utility in electron-ionization MS comes from the fact that the radical cations generated in the electron-bombardment
process tend to fragment in predictable ways. Detailed analysis of the typical fragmentation patterns of different functional groups
is beyond the scope of this text, but it is worthwhile to see a few representative examples, even if we don’t attempt to understand
the exact process by which the fragmentation occurs. We saw, for example, that the base peak in the mass spectrum of acetone is
m/z = 43. This is the result of cleavage at the ‘alpha’ position - in other words, at the carbon-carbon bond adjacent to the carbonyl.
Alpha cleavage results in the formation of an acylium ion (which accounts for the base peak at m/z = 43) and a methyl radical,
which is neutral and therefore not detected.
After the parent peak and the base peak, the next largest peak, at a relative abundance of 23%, is at m/z = 15. This, as you might
expect, is the result of formation of a methyl cation, in addition to an acyl radical (which is neutral and not detected).
You can see many more actual examples of mass spectra in the Spectral Database for Organic Compounds
Exercise 1.1
Predict some signals that you would expect to see in a mass spectrum of 2-chloropropane.
Answer
There are two isotopes of Cl, Cl-35 and Cl-37.

The molecular ion appears at 78 which would contain Cl-35 and the peak at 80 contains Cl-37.
This pattern can be quite indicative of a fragment still containing a chlorine atom.
The next major peak grouping occurs at 63 and 65. The relative abundance values of the peaks and the difference of 2 in
terms of mass suggest that there is still a chlorine atom in this fragment. The difference in mass from the molecular ion is 15,
which based on the molecular formula can only be accounted for by the loss of a CH3 unit. This suggests that these two
peaks are due to the fragments CH3CH-35Cl and CH3CH-37Cl.
There is a cluster of peaks around 40. This is a little tougher to interpret. Thinking about the starting molecule, one might
consider breaking the C-Cl bond. That would give a fragment of H3CCHCH3 which would have a mass of 43 matching the
highest intensity peak.
The mass of chlorine on the periodic table is closer to 35 than 37 indicating that the Cl-35 isotope is more abundant that Cl-
37. This can also be seen in the molecular ion. One might consider saying that the peak at 41 is just due to the other isotope
of chlorine. However, the peak at 43 does not contain chlorine and the relative ratio of 43 to 41 does not support the presence
of chlorine. It is much more likely that the peak at 41 is due to loss of two hydrogen atoms from the fragment with a mass of
43. Which specific hydrogen atoms is well beyond the scope of this course, so we will just say the fragment is C3H5.
The final major peak has a mass of 27. This would correspond to a fragment of C2H3.
The spectrum was obtained from SDBSWeb. (National Institute of Advanced Industrial Science and Technology, 1/18/21).
Gas Chromatography - Mass Spectrometry

Quite often, mass spectrometry is used in conjunction with a separation technique called gas chromatography (GC). The combined
GC-MS procedure is very useful when dealing with a sample that is a mixture of two or more different compounds, because the
various compounds are separated from one another before being subjected individually to MS analysis. We will not go into the
details of gas chromatography here, although if you are taking an organic laboratory course you might well get a chance to try your
hand at GC, and you will almost certainly be exposed to the conceptually analogous techniques of thin layer and column
chromatography. Suffice it to say that in GC, a very small amount of a liquid sample is vaporized, injected into a long, coiled metal
column, and pushed though the column by helium gas. Along the way, different compounds in the sample stick to the walls of the
column to different extents, and thus travel at different speeds and emerge separately from the end of the column. In GC-MS, each
purified compound is sent directly from the end of GC column into the MS instrument, so in the end we get a separate mass
spectrum for each of the compounds in the original mixed sample. Because a compound's MS spectrum is a very reliable and
reproducible 'fingerprint', we can instruct the instrument to search an MS database and identify each compound in the sample.
Gas chromatography-mass spectrometry (GC-MS) schematic

(Image from Wikipedia by K. Murray)
The extremely high sensitivity of modern GC-MS instrumentation makes it possible to detect and identify very small trace amounts
of organic compounds. GC-MS is being used increasingly by environmental chemists to detect the presence of harmful organic
contaminants in food and water samples. Airport security screeners also use high-speed GC-MS instruments to look for residue
from bomb-making chemicals on checked luggage.
Contributors
Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris)
This page titled 1.1: Mass Spectrometry is shared under a CC BY-NC-SA license and was authored, remixed, and/or curated by Tim Soderberg.
Learning Objectives
Introduce the initial attempts to explain the structure of atoms.
The Gold Foil Experiment

In 1911, Rutherford and coworkers Hans Geiger and Ernest Marsden initiated a series of groundbreaking experiments that would
completely change the accepted model of the atom. They bombarded very thin sheets of gold foil with fast moving alpha particles.
Alpha particles, a type of natural radioactive particle, are positively charged particles with a mass about four times that of a
hydrogen atom.
Figure 1.2.1 : (A) The experimental setup for Rutherford's gold foil experiment: A radioactive element that emitted alpha particles
was directed toward a thin sheet of gold foil that was surrounded by a screen which would allow detection of the deflected
particles. (B) According to the plum pudding model (top) all of the alpha particles should have passed through the gold foil with
little or no deflection. Rutherford found that a small percentage of alpha particles were deflected at large angles, which could be
explained by an atom with a very small, dense, positively-charged nucleus at its center (bottom).
According to the accepted atomic model, in which an atom's mass and charge are uniformly distributed throughout the atom, the
scientists expected that all of the alpha particles would pass through the gold foil with only a slight deflection or none at all.
Surprisingly, while most of the alpha particles were indeed undeflected, a very small percentage (about 1 in 8000 particles)
bounced off the gold foil at very large angles. Some were even redirected back toward the source. No prior knowledge had
prepared them for this discovery. In a famous quote, Rutherford exclaimed that it was "as if you had fired a 15-inch [artillery] shell
at a piece of tissue and it came back and hit you."
Rutherford needed to come up with an entirely new model of the atom in order to explain his results. Because the vast majority of
the alpha particles had passed through the gold, he reasoned that most of the atom was empty space. In contrast, the particles that
were highly deflected must have experienced a tremendously powerful force within the atom. He concluded that all of the positive
charge and the majority of the mass of the atom must be concentrated in a very small space in the atom's interior, which he called
the nucleus. The nucleus is the tiny, dense, central core of the atom and is composed of protons and neutrons.
Rutherford's atomic model became known as the nuclear model. Most of the α -particles were not scattered; they passed
unchanged through the thin metal foil. Some of the few that were scattered were scattered in the backward direction; i.e. they
recoiled. This backward scattering requires that the foil contain heavy particles. When an α-particle hits one of these heavy
particles it simply recoils backward, just like a ball thrown at a brick wall. Since most of the α -particles don’t get scattered, the
heavy particles (the nuclei of the atoms) must occupy only a very small region of the total space of the atom. Most of the space
must be empty or occupied by very low-mass particles. These low-mass particles are the electrons that surround the nucleus. It is
worth emphasizing just how small the nucleus is compared to the rest of the atom. If we could blow up an atom to be the size of a
large professional football stadium, the nucleus would be about the size of a marble.
Rutherford's Failed Planetary Atom

There are some basic problems with the Rutherford model. The Coulomb force that exists between oppositely charge particles
means that a positive nucleus and negative electrons should attract each other, and the atom should collapse. To prevent the
collapse, the electron was postulated to be orbiting the positive nucleus. The Coulomb force (discussed below) is used to change
the direction of the velocity, just as a string pulls a ball in a circular orbit around your head or the gravitational force holds the
moon in orbit around the Earth. The origin for this hypothesis that suggests this perspective is plausible is the similarity of gravity
and Coulombic interactions. The expression for the force of gravity between two masses (Newton's Law of gravity) is
m1 m2
Fgravity ∝ (1.2.1)
r2
with m and m representing the mass of object 1 and 2, respectively and r representing the distance between the objects centers
1 2
The expression for the Coulomb force between two charged species is
Q1 Q2
FC oulomb ∝ (1.2.2)
2
r
with Q and Q representing the charge of object 1 and 2, respectively and r representing the distance between the objects centers.
1 2
However, this analogy has a problem too. An electron going around in a circle is constantly being accelerated because its velocity
vector is changing. A charged particle that is being accelerated emits radiation. This property is essentially how a radio transmitter
works. A power supply drives electrons up and down a wire and thus transmits energy (electromagnetic radiation) that your radio
receiver picks up. The radio then plays the music for you that is encoded in the waveform of the radiated energy.
Figure 1.2.2 : The classical death spiral of an electron around a nucleus. (CC BY-NC; Ümit Kaya)
If the orbiting electron is generating radiation, it is losing energy. If an orbiting particle loses energy, the radius of the orbit
decreases. To conserve angular momentum, the frequency of the orbiting electron increases. The frequency increases continuously
as the electron collapses toward the nucleus. Since the frequency of the rotating electron and the frequency of the radiation that is
emitted are the same, both change continuously to produce a continuous spectrum and not the observed discrete lines. Furthermore,
if one calculates how long it takes for this collapse to occur, one finds that it takes about 10‑ seconds. This means that nothing in
1l
the world based on the structure of atoms could exist for longer than about 10 seconds. Clearly something is terribly wrong with
−11
this classical picture, which means that something was missing at that time from the known laws of physics.
Conservative Forces can be explained with Potentials
A conservative force is dependent only on the position of the object. If a force is conservative, it is possible to assign a
numerical value for the potential at any point. When an object moves from one location to another, the force changes the
potential energy of the object by an amount that does not depend on the path taken. The potential can be constructed as simple
derivatives for 1-D forces:
dV
F =−
dx
or as gradients in 3-D forces
F = −∇V
where ∇ is the vector of partial derivatives

∂ ∂ ∂
∇ =( , , )
∂x ∂y ∂z
The most familiar conservative forces are gravity and Coloumbic forces.
The Coulomb force law (Equation 1.2.2) comes from the corresponding Coulomb potential (sometimes call electrostatic potential)
kQ1 Q2
V (r) = (1.2.3)
r
and it can be easily verified that the Coulombic force from this interaction (F (r) is
dV
F (r) = − (1.2.4)
dr
As r is varied, the energy will change, so that we have an example of a potential energy curve V (r) (Figure 1.2.2; lef t). If Q and 1
Q are the same sign, then the curve which is a purely repulsive potential, i.e., the energy increases monotonically as the charges
2
are brought together and decreases monotonically as they are separated. From this, it is easy to see that like charges (charges of the
same sign) repel each other.
V(r) V(r)
r r
Repulsive Coulomb Potential Attractive Coulomb Potential
Figure 1.2.3 : Potential energy curve for the Coulomb interactions between two charges of same sign (left) and opposite signs
(right). (CC BY-NC; Ümit Kaya)
If the charges are of opposite sign, then the curve appears roughly Figure 1.2.2; right and this is a purely attractive potential.
Thus, the energy decreases as the charges are brought together, implying that opposite charges attract.
Contributors and Attributions

CK-12 Foundation by Sharon Bewick, Richard Parsons, Therese Forsythe, Shonna Robinson, and Jean Dupon.
Mark Tuckerman (New York University)
David M. Hanson, Erica Harvey, Robert Sweeney, Theresa Julia Zielinski ("Quantum States of Atoms and Molecules")
Template:Contriboundless
1.2: Rutherford's Atom is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
1.3: Bohr's Atom
Review Necessary Skills

Relate the wavelength (λ) and frequency (ν) of light to the velocity of light (c) (c = λν) and to the energy of a photon (E) (E = hν = hc/λ).
Find help using c = λν and lots of problems here on ChemTeam.
Find help using E = hν = hc/λ and lots of problems here on ChemTeam.
Relate charge, distance, and electrostatic potential energy using Coulomb’s law (U = k q1 x q2/r) qualitatively.
Here is an interactive simulation.
Coulomb's law
Here is a review in the context of atoms with some problems.
Describe what happens to molecules when they interact with electromagnetic radiation.
What happens to molecules at different wavelengths? See NO2 in this simulation. Don't worry if this doesn't look familiar, it is just a
reminder that IR, microwave, and UV light all interact with molecules differently.
Experiments that can't be explained without quantization of energy or position

Electron diffraction
Photoelectric effect Atomic line spectra
(see demo below or go to PheT)
(see demo below or go to PheT) (see demo below or go to PheT)
Click to Run or Click to Run or Click to Run

Download (Needs Download (Needs
Java!) Java!)
Double-slit experiment
(see demo or go to PheT)
Click to Run or
Download (Needs
Java!)
So what does this mean for atoms? The Bohr model and particle-in-a-box.
Bohr's Model of the Hydrogen Atom
The Danish scientist, Niels Bohr, introduced the first theory that quantized the energy of electrons in atoms.
Although Bohr's reasoning relies on classical concepts and hence, is not a correct explanation, the reasoning
is interesting, and so we examine this model for its historical significance. This is now referred to as "Old
Quantum Theory", while the "New Quantum Theory" is that described by the Schrodinger equation, and that
will be described a bit later. Below, the story of Bohr's model will be described. Another way to tell the story
is here.
Bohr's Condition of a Stable Orbit: Bohr imagined that electrons were in circular orbit around a nucleus. He applied classical mechanics to
rationalize that if the electron of charge, -e, were to be in a stable orbit around a nucleus of opposite charge, +e, then the electrostatic attractive
force (Fe) between the electron and nucleus must be exactly opposed by the outward centripetal force (Fo) created by the electron's circular
orbit. (We can ignore any gravitational force because it is relatively weak.)
Where the electrostatic attractive force F and centripetal force F are,
e o
2
(+e)(−e) e
Fe = =− (1.3.1)
2 2
r r
2
me v
Fo = (1.3.2)
r
For a stable orbit to exist F + F = 0, or,

e o
Fo = −Fe (1.3.3)
2 2
me v e
= (1.3.4)
r r2
Bohr's Calculation of the Electron's Energy: Bohr could calculate the total energy of the electron, again using classical mechanics. The total
energy of a system is the sum of the kinetic energy (KE, energy of motion of the electron) and the potential energy (PE, from the electrostatic
attraction, F and the distance, r).
e
1
2
KE = me v (1.3.5)
2
2 2
e e
P E = rFe = r( − ) =− (1.3.6)
2
r r
If total Energy (E) is equal to the sum of KE and PE,

2
1 e
2
E = KE + P E = me v − (1.3.7)
2 r
This expression can be simplified by first solving equation (4) for m ev

2
=
e
r
and substituting into equation 7.
2 2 2 2
1 e 2 e 1 e e
E = ( )− ( ) =− ( ) =− (1.3.8)
2 r 2 r 2 r 2r
Now we see that energy of the electron, E, can be calculated if we know the distance, r, at which the electron is orbiting. This is a good time to
remind ourselves that we also know, from Planck's work, that E = hν . This reminds us that the electron is a wave with frequency, ν , in units of
sec-1. So, we could also write,
2
e
E =− = hν (1.3.9)
2r
Bohr's Quantization, and Equations for Radius, r, and Velocity, v: Bohr knew that electrons must have stable orbits, otherwise the electrons
would fall into the nucleus. Bohr was familiar with Maxwell's theory of classical electromagnetism and knew that in a classical theory, the
orbiting electron should radiate energy away and eventually collapse into the nucleus (E is given off as r decreases). He circumvented this
problem by following Planck's idea underlying blackbody radiation and positing that the orbital angular momentum p = m vr of the electron e
could only take on specific values. He proposed those values to be units of , where h is Planck's constant. Bohr's proposal was,
2π
h
h
me vr = n (1.3.10)
2π
where n is the first quantum number and can have values of any integer (n = 1, 2, 3...). This relationship can be rearranged to find the velocity,
v,
h
v=n (1.3.11)
me r2π
This implies that only certain velocities are allowed, since only certain values of n are allowed. This expression for v can be substituted into the
2
condition of a stable orbit (using a rearranged version of equation 4, (m v = e

2 e
r
) to give equation 12. Ultimately, this allows us to find how
the radius, r , depends on the the quantum number, n, as shown in equation 13.
h 2
me (n ) 2 2 2 2 2
me r2π me n h n h e
= = = (1.3.12)
2 2 2 2 2
r 4me r π 4me r π r
This expression can be rearranged to solve for r ,

2 2
n h
r = (1.3.13)
2 2
4 π me e K
K is the Coulomb constant which is needed for unit conversion and has a value of
2
9 Nm
K = 8.9875517923x10 2
C
This expression shows Bohr's assumption that there are discrete distances where the electron can orbit, as the values or r are restricted by the
integer values of n. The relationship between n and E is found by substitution of the equation for r into equation 8 or 9.
2 2 2 2 2 4 2
e K e K4 π me e K 2 π me e 2 K
E =− =− =− (1.3.14)
2
n2 h 2 2 2 2
2n h n h
2( )
4 π 2 me e 2 K
This expression shows that energy is quantized, as like values of v and r , the energy depends on the integer value, n.
Exercise 1.3.1
Show how you would find the Bohr radius, velocity, and energy of an electron in the first shell of a hydrogen atom.
Answer
2 2
n h
r =
2 2
4π me e K
2 −34 2
1 (6.626070x10 )
r =
2 −31 −19 2 9
4(3.141592654 ) (9.10938356x10 )(1.602176634x10 ) (8.9875517923x10 )
−67 2 2
(4.390480364x10 )J s
r =
−57 2
(8.296805693x10 )kgN m
−11
r = 5.292x 10 m
h
v=n
me r2π
−34
6.626070x10
v=1
−31 −11
(9.10938356x10 )(5.292x10 )2(3.141592654)
−34
6.626070x10 Js
v=
−40
3.028926207x10 kgm
6
v = 2.19x 10 m/s
2 4 2
2π me e 2 K
E =−
2 2
n h
2 −31 −19 4 9 2
2(3.141592654 ) (9.10938356x10 )(1.602176634x10 ) (8.9875517923x10 )
E =−
2 −34 2
1 (6.626070x10 )
−85 4 4
9.570687085x10 kgN m
E =− 2
−67 2
4.390480367x10 J s
−18
E = −2.1799x 10 J
Hydrogen Absorption and Emission Spectra
When a high-voltage electrical discharge is passed through a sample of hydrogen gas (H2) at low pressure, the result is individual isolated
hydrogen atoms that emit a red light. Unlike blackbody radiation, the color of the light emitted by the hydrogen atoms does not depend greatly
on the temperature of the gas in the tube. When the emitted light is passed through a prism, only a few narrow lines of particular wavelengths,
called a line spectrum, are observed rather than a continuous range of wavelengths (Figure 1.3.1). The light emitted by hydrogen atoms is red
because, of its four characteristic lines, the most intense line in its spectrum is in the red portion of the visible spectrum, at 656 nm.
Figure 1.3.1: The Emission of Light by Hydrogen Atoms. (left) A sample of excited hydrogen atoms emits a characteristic red light. (bottom)
When the light emitted by a sample of excited hydrogen atoms is split into its component wavelengths by a prism, four characteristic violet,
blue, green, and red emission lines can be observed, the most intense of which is at 656 nm. (top) An diagram showing extended regions of the
electromagnetic spectrum and the hydrogen line spectra that are observed.
In 1885, a Swiss mathematics teacher, Johann Balmer (1825–1898), showed that the frequencies of the lines observed in the visible region of
the hydrogen line spectrum fit a simple equation that can be expressed as follows:
1 1
ν = constant ( − ) (1.3.15)
2 2
2 n
where n = 3, 4, 5, 6. As a result, these lines are known as the Balmer series. The Swedish physicist Johannes Rydberg (1854–1919)
subsequently restated and expanded Balmer’s result in the Rydberg equation:
1 1 1
= Rh ( − ) (1.3.16)
2 2
λ n m
where n and m are positive integers, m > n , and R the Rydberg constant, has a value of 1.09737 × 107 m−1. Like Balmer’s equation,
h
Rydberg’s simple equation described the wavelengths of the visible lines in the emission spectrum of hydrogen (with n = 2, m = 3, 4, 5,…).
More important, Rydberg’s equation also predicted the wavelengths of other series of lines that would be observed in the emission spectrum of
hydrogen: one in the ultraviolet (n = 1, m = 2, 3, 4,…) and one in the infrared (n = 3, m = 4, 5, 6).
Exercise 1.3.2
Solve the Rydberg Equation for a line where m = 3 and n = 1 . In what region of the electromagnetic spectrum does this appear, and which
series is this?
Answer
1
1 1
= Rh ( − )
λ 2 2
n m
1
1 1
7 −1
= 1.09737x 10 m ( − )
λ 2 2
1 3
1 −1
= 9754400 m
λ
−7
λ = 1.03x 10 m = 102.5nm
This is in the Ultra-violet region.
Sources
The Bohr Theory of the Hydrogen Atom
Line Spectra and the Bohr Model
1.3: Bohr's Atom is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
1.4: Hydrogen Atom
Atomic Spectra
When gaseous hydrogen in a glass tube is excited by a 5000-volt electrical discharge, four lines are observed in the visible part of
the emission spectrum: red at 656.3 nm, blue-green at 486.1 nm, blue violet at 434.1 nm and violet at 410.2 nm:
Figure 1.4.1 : Visible spectrum of atomic hydrogen.

Other series of lines have been observed in the ultraviolet and infrared regions. Rydberg (1890) found that all the lines of the
atomic hydrogen spectrum could be fitted to a single formula
1 1 1
= R( − ), n1 = 1, 2, 3..., n2 > n1 (1.4.1)
2 2
λ n n
1 2
where R , known as the Rydberg constant, has the value 109, 677 cm-1 for hydrogen. The reciprocal of wavelength, in units of cm-
1
, is in general use by spectroscopists. This unit is also designated wavenumbers, since it represents the number of wavelengths per
cm. The Balmer series of spectral lines in the visible region, shown in Figure 1.4.1 , correspond to the values
n = 2, n = 3, 4, 5 and 6 . The lines with n = 1 in the ultraviolet make up the Lyman series. The line with n = 2 , designated
1 2 1 2
the Lyman alpha, has the longest wavelength (lowest wavenumber) in this series, with 1/λ = 82.258 cm-1 or λ = 121.57 nm.
Other atomic species have line spectra, which can be used as a "fingerprint" to identify the element. However, no atom other than
hydrogen has a simple relation analogous to Equation 1.4.1 for its spectral frequencies. Bohr in 1913 proposed that all atomic
spectral lines arise from transitions between discrete energy levels, giving a photon such that
hc
ΔE = hν = (1.4.2)
λ
This is called the Bohr frequency condition. We now understand that the atomic transition energy ΔE is equal to the energy of a
photon, as proposed earlier by Planck and Einstein.
The Bohr Atom

The nuclear model proposed by Rutherford in 1911 pictures the atom as a heavy, positively-charged nucleus, around which much
lighter, negatively-charged electrons circulate, much like planets in the Solar system. This model is however completely untenable
from the standpoint of classical electromagnetic theory, for an accelerating electron (circular motion represents an acceleration)
should radiate away its energy. In fact, a hydrogen atom should exist for no longer than 5 × 10 sec, time enough for the
−11
electron's death spiral into the nucleus. This is one of the worst quantitative predictions in the history of physics. It has been called
the Hindenberg disaster on an atomic level. (Recall that the Hindenberg, a hydrogen-filled dirigible, crashed and burned in a
famous disaster in 1937.)
Bohr sought to avoid an atomic catastrophe by proposing that certain orbits of the electron around the nucleus could be exempted
from classical electrodynamics and remain stable. The Bohr model was quantitatively successful for the hydrogen atom, as we shall
now show.
We recall that the attraction between two opposite charges, such as the electron and proton, is given by Coulomb's law
2
⎧ e
⎪
⎪
⎪− (gaussian units)
2
r
F =⎨ 2
(1.4.3)
e
⎪
⎪
⎩−
⎪ (SI units)
2
4πϵ0 r
We prefer to use the Gaussian system in applications to atomic phenomena. Since the Coulomb attraction is a central force
(dependent only on r), the potential energy is related by
dV (r)
F =− (1.4.4)
dr
We find therefore, for the mutual potential energy of a proton and electron,
2
e
V (r) = − (1.4.5)
r
Bohr considered an electron in a circular orbit of radius r around the proton. To remain in this orbit, the electron must be
experiencing a centripetal acceleration
2
v
a =− (1.4.6)
r
where v is the speed of the electron. Using Equations 1.4.4 and 1.4.6 in Newton's second law, we find
2 2
e mv
= (1.4.7)
2
r r
where m is the mass of the electron. For simplicity, we assume that the proton mass is infinite (actually m ≈ 1836m ) so that the p e
proton's position remains fixed. We will later correct for this approximation by introducing reduced mass. The energy of the
hydrogen atom is the sum of the kinetic and potential energies:
2
1 2
e
E = T +V = mv − (1.4.8)
2 r
Using Equation 1.4.7 , we see that

1 1
T =− V and E = V = −T (1.4.9)
2 2
This is the form of the virial theorem for a force law varying as r . Note that the energy of a bound atom is negative, since it is
−2
lower than the energy of the separated electron and proton, which is taken to be zero.
For further progress, we need some restriction on the possible values of r or v . This is where we can introduce the quantization of
angular momentum L = r × p . Since p is perpendicular to r , we can write simply
L = rp = mvr (1.4.10)
Using Equation 1.4.9, we find also that

2
L
r = (1.4.11)
2
me
We introduce angular momentum quantization, writing

L = nℏ, n = 1, 2... (1.4.12)
excluding n = 0 , since the electron would then not be in a circular orbit. The allowed orbital radii are then given by
2
rn = n a0 (1.4.13)
where
2
ℏ −11
a0 ≡
2
= 5.29 × 10 m = 0.529 Å (1.4.14)
me
which is known as the Bohr radius. The corresponding energy is

2 4
e me
En = − =− , n = 1, 2... (1.4.15)
2a0 n2 2ℏ 2 n2
Rydberg's formula (Equation 1.4.1) can now be deduced from the Bohr model. We have
2 4
hc 2π me 1 1
= En2 − En1 = ( − ) (1.4.16)
2 2 2
λ h n n
1 2
and the Rydbeg constant can be identified as
2 4
2π me −1
R = ≈ 109, 737 cm (1.4.17)
3
h c
The slight discrepency with the experimental value for hydrogen (109, 677) is due to the finite proton mass. This will be corrected
later.
The Bohr model can be readily extended to hydrogenlike ions, systems in which a single electron orbits a nucleus of arbitrary
atomic number Z . Thus Z = 1 for hydrogen, Z = 2 for He , Z = 3 for Li , and so on. The Coulomb potential 1.4.5
+ ++
generalizes to
2
Ze
V (r) = − , (1.4.18)
r
the radius of the orbit (Equation 1.4.13) becomes

2
n a0
rn = (1.4.19)
Z
and the energy Equation 1.4.15 becomes

2 2
Z e
En = − (1.4.20)
2
2a0 n
De Broglie's proposal that electrons can have wavelike properties was actually inspired by the Bohr atomic model. Since
nh
L = rp = nℏ = (1.4.21)
2π
we find
nh
2πr = = nλ (1.4.22)
p
Therefore, each allowed orbit traces out an integral number of de Broglie wavelengths.
Wilson (1915) and Sommerfeld (1916) generalized Bohr's formula for the allowed orbits to
∮ p dr = nh, n = 1, 2... (1.4.23)
The Sommerfeld-Wilson quantum conditions Equation 1.4.23 reduce to Bohr's results for circular orbits, but allow, in addition,
elliptical orbits along which the momentum p is variable. According to Kepler's first law of planetary motion, the orbits of planets
are ellipses with the Sun at one focus. Figure 1.4.2 shows the generalization of the Bohr theory for hydrogen, including the
elliptical orbits. The lowest energy state n = 1 is still a circular orbit. But n = 2 allows an elliptical orbit in addition to the circular
one; n = 3 has three possible orbits, and so on. The energy still depends on n alone, so that the elliptical orbits represent
degenerate states. Atomic spectroscopy shows in fact that energy levels with n > 1 consist of multiple states, as implied by the
splitting of atomic lines by an electric field (Stark effect) or a magnetic field (Zeeman effect). Some of these generalized orbits are
drawn schematically in Figure 1.4.2.
Figure 1.4.1 : Elliptical orbits with the same energy and quantized angular momentum in Bohr-Sommerfield orbits for n = 1, 2, 3
(not to scale). (Public Domain; Pieter Kuiper)

The Bohr model was an important first step in the historical development of quantum mechanics. It introduced the quantization of
atomic energy levels and gave quantitative agreement with the atomic hydrogen spectrum. With the Sommerfeld-Wilson
generalization, it accounted as well for the degeneracy of hydrogen energy levels. Although the Bohr model was able to sidestep
the atomic "Hindenberg disaster," it cannot avoid what we might call the "Heisenberg disaster." By this we mean that the
assumption of well-defined electronic orbits around a nucleus is completely contrary to the basic premises of quantum mechanics.
Another flaw in the Bohr picture is that the angular momenta are all too large by one unit, for example, the ground state actually
has zero orbital angular momentum (rather than ℏ ).
The assumption of well-defined electronic orbits around a nucleus in the Bohr atom is
completely contrary to the basic premises of quantum mechanics.
Quantum Mechanics of Hydrogenlike Atoms

In contrast to the particle in a box and the harmonic oscillator, the hydrogen atom is a real physical system that can be treated
exactly by quantum mechanics. In addition to their inherent significance, these solutions suggest prototypes for atomic orbitals
used in approximate treatments of complex atoms and molecules.
For an electron in the field of a nucleus of charge +Ze , the Schrӧdinger equation can be written
2 2
ℏ 2
Ze
{− ∇ − } ψ(r) = Eψ(r) (1.4.24)
2m r
It is convenient to introduce atomic units in which length is measured in bohrs:

2
ℏ −11
a0 = = 5.29 × 10 m ≡ 1 bohr (1.4.25)
me2
and energy in hartrees:

2
e −18
= 4.358 × 10 J = 27.211 eV ≡ 1 hartree (1.4.26)
a0
Electron volts (eV) are a convenient unit for atomic energies. One eV is defined as the energy an electron gains when accelerated
across a potential difference of 1 volt. The ground state of the hydrogen atom has an energy of −1/2 hartree or −13.6 eV.
Conversion to atomic units is equivalent to setting
ℏ =e =m =1 (1.4.27)
in all formulas containing these constants. Rewriting the Schrӧdinger equation in atomic units, we have
1 2
Z
{− ∇ − } ψ(r) = Eψ(r) (1.4.28)
2 r
Since the potential energy is spherically symmetrical (a function of r alone), it is obviously advantageous to treat this problem in
spherical polar coordinates r, θ, ϕ. Expressing the Laplacian operator in these coordinates [cf. Eq (6-20)],
2
1 1 ∂ 2
∂ 1 ∂ ∂ 1 ∂
− { r + sin θ + } (1.4.29)
2 2 2 2 2
2 r ∂r ∂r r sin θ ∂θ ∂θ r sin θ ∂ϕ
Z
× ψ(r, θ, ϕ) − ψ(r, θ, ϕ) = Eψ(r, θ, ϕ)
r
2
Equation 1.4.29 shows that the second and third terms in the Laplacian represent the angular momentum operator ^
L . Clearly,
Equation 1.4.29 will have separable solutions of the form
ψ(r, θ, ϕ) = R(r)Yℓm (θ, ϕ) (1.4.30)
Substituting Equation 1.4.30 into Equation 1.4.29 and using the angular momentum eigenvalue Equation Equation ??? , we obtain
an ordinary differential equation for the radial function R(r) :
1 d d ℓ(ℓ + 1) Z
2
{− r + − } R(r) = ER(r) (1.4.31)
2r2 dr dr 2r2 r
Note that in the domain of the variable r, the angular momentum contribution ℓ(ℓ + 1)/2r acts as an effective addition to the 2
potential energy. It can be identified with centrifugal force, which pulls the electron outward, in opposition to the Coulomb
attraction. Carrying out the successive differentiations in Equation 1.4.32 and simplifying, we obtain
1 1 Z ℓ(ℓ + 1)
′′ ′
R (r) + R (r) + [ − + E] R(r) = 0 (1.4.32)
2
2 r r 2r
another second-order linear differential equation with non-constant coefficients. It is again useful to explore the asymptotic
solutions to Equation 1.4.32, as r → ∞ . In the asymptotic approximation,
′′
R (r) − 2r|E|R(r) ≈ 0 (1.4.33)
having noted that the energy E is negative for bound states. Solutions to Equation 1.4.33 are
±√2|E|r
R(r) ≈ const e (1.4.34)
We reject the positive exponential on physical grounds, since R(r) → ∞ as r → ∞ , in violation of the requirement that the
wavefunction must be finite everywhere. Choosing the negative exponential and setting E = −Z /2 the ground state energy in the 2
Bohr theory (in atomic units), we obtain

−Zr
R(r) ≈ const e (1.4.35)
It turns out, very fortunately, that this asymptotic approximation is also an exact solution of the Schrӧdinger equation (Equation \
(\ref{29}\)) with ℓ = 0 , just what happened for the harmonic-oscillator problem in Chap. 5. The solutions to Equation 1.4.32,
designated R (r), are labeled by n , known as the principal quantum number, as well as by the angular momentum ℓ , which is a
nℓ
parameter in the radial equation. The solution in Equation 1.4.35 corresponds to R (r). This should be normalized according to 10
the condition
∞
2 2
∫ [ R10 (r)] r dr = 1 (1.4.36)
0
A useful definite integral is

∞
n!
n −αr
∫ r e dr = (1.4.37)
n+1
0 α
The normalized radial function is thereby given by

3/2 −Zr
R10 (r) = 2 Z e (1.4.38)
Since this function is nodeless, we identify it with the ground state of the hydrogenlike atom. Multipyling Equation 1.4.38 by the
− −
spherical harmonic Y = 1/√4π, we obtain the total wavefunction (Equation 1.4.30)
00
3 1/2
Z
−Zr
ψ100 (r, θ, ϕ) = ( ) e (1.4.39)
π
This is conventionally designated as the 1s function ψ 1s (r) .

Integrals in spherical-polar coordinates over a spherically-symmetrical integrand (like the 1s orbital) can be significantly
simplified. We can do the reduction
∞ π 2π ∞
2 2
∫ ∫ ∫ f (r) r sin θ dr dθ dϕ = ∫ f (r) 4π r dr (1.4.40)
0 0 0 0
since integration over θ and ϕ gives 4π , the total solid angle of a sphere. The normalization of the 1s wavefunction can thus be
written as
∞
2 2
∫ [ ψ1s (r)] 4π r dr = 1 (1.4.41)
0
Hydrogen Atom Ground State

There are a number of different ways of representing hydrogen-atom wavefunctions graphically. We will illustrate some of these
for the 1s ground state. In atomic units,
1 −r
ψ1s (r) = −e (1.4.42)
√π
is a decreasing exponential function of a single variable r, and is simply plotted in Figure 3.
Figure 1.4.3 . Wavefunctions for 1s and 2s orbitals for atomic hydrogen. The 2s-wavefunction (scaled by a factor of 2) has a node at
r = 2 bohr. Taken from voh.chem.ucla.edu/vohtar/wint.../lecture3.html
Figure 1.4.3 gives a somewhat more pictorial representation, a three-dimensional contour plot of ψ 1s (r) as a function of x and y in
the x, y -plane.
Figure 1.4.4 : Contour map of 1s orbital in the x -, y -plane. Taken from winter.group.shef.ac.uk/orbit...s/wave-fn.html
According to Born's interpretation of the wavefunction, the probability per unit volume of finding the electron at the point
(r, θ, ϕ) is equal to the square of the normalized wavefunction
2
1 −2r
ρ1s (r) = [ ψ1s (r)] = e (1.4.43)
π
This is represented in Figure 5 by a scatter plot describing a possible sequence of observations of the electron position. Although
results of individual measurements are not predictable, a statistical pattern does emerge after a sufficiently large number of
measurements.
Figure 1.4.5 : Scatter plot of electron position measurements in hydrogen 1s orbital. Taken from winter.group.shef.ac.uk/orbit...sity-
dots.html
The probability density is normalized such that
∞
2
∫ ρ1s (r) 4π r dr = 1 (1.4.44)
0
In some ways ρ(r) does not provide the best description of the electron distribution, since the region around r = 0 , where the
wavefunction has its largest values, is a relatively small fraction of the volume accessible to the electron. Larger radii r represent
larger physical regions since, in spherical polar coordinates, a value of r is associated with a shell of volume 4π r dr. A more 2
significant measure is therefore the radial distribution function

2 2
D1s (r) = 4π r [ ψ1s (r)] (1.4.45)
which represents the probability density within the entire shell of radius r, normalized such that
∞
∫ D1s (r) dr = 1 (1.4.46)

0
The functions ρ (r) and D

1s 1s (r) are both shown in Figure 1.4.6. Remarkably, the 1s RDF has its maximum at r = a , equal to the
0
radius of the first Bohr orbit
Figure 1.4.6 : The wavefunction and probability distribution as functions of r for the n = 1 level of the H atom. The functions and
the radius r are in atomic units in this and succeeding figures. Image used with permisison (Bader).
Atomic Orbitals
The general solution for R nℓ (r) has a rather complicated form which we give without proof:
ℓ −ρ/2
2Zr
2ℓ+1
Rnℓ (r) = Nnℓ ρ L (ρ)e ρ ≡ (1.4.47)
n+ℓ
n
Here L is an associated Laguerre polynomial and N , a normalizing constant. The angular momentum quantum number ℓ is by
α
β nℓ
convention designated by a code: s for ℓ = 0 , p for ℓ = 1 , d for ℓ = 2 , f for ℓ = 3 , g for ℓ = 4 , and so on. The first four letters
come from an old classification scheme for atomic spectral lines: sharp, principal, diffuse and fundamental. Although these
designations have long since outlived their original significance, they remain in general use. The solutions of the hydrogenic
Schrӧdinger equation
in spherical polar coordinates can now be written in full
ψnℓm (r, θ, ϕ) = Rnℓ (r)Yℓm (θ, ϕ) (1.4.48)
n = 1, 2... ℓ = 0, 1... n − 1 m = 0, ±1, ±2... ± ℓ
where Y are the spherical harmonics tabulated in Chap. 6. Table 1 below enumerates all the hydrogenic functions we will
ℓm
actually need. These are called hydrogenic atomic orbitals, in anticipation of their later applications to the structure of atoms and
molecules.
Table 1. Real hydrogenic functions in atomic units.
1
−r
ψ1s = e (1.4.49)
−
√π
1 r
−r/2
ψ2s = (1 − )e (1.4.50)
−−
2 √2π 2
1
−r/2
ψ2p = ze (1.4.51)
z −−
4 √2π
ψ2p , ψ2p analogous (1.4.52)

x y
1
2 −r/3
ψ3s = (27 − 18r + 2 r )e (1.4.53)
−−
81 √3π
–
√2
−r/3
ψ3p = (6 − r)z e (1.4.54)
z −
81 √π
ψ3p , ψ3p analogous (1.4.55)

x y
1
2 2 −r/3
ψ3d = (3 z − r )e (1.4.56)
z2 −−
81 √6π
–
√2
−r/3
ψ3d = zx e (1.4.57)
zx −
81 √π
ψ3d , ψ3d analogous (1.4.58)

yz xy
1
2 2 −r/3
ψ3d = (x − y )e (1.4.59)
x2 − y 2 −
81 √π
The energy levels for a hydrogenic system are given by

2
Z
En = − hartrees (1.4.60)
2n2
and depends on the principal quantum number alone. Considering all the allowed values of ℓ and m, the level E has a degeneracy n
of n . Figure 7 shows an energy level diagram for hydrogen (Z = 1) . For E ≥ 0 , the energy is a continuum, since the electron is
2
in fact a free particle. The continuum represents states of an electron and proton in interaction, but not bound into a stable atom.
Figure 1.4.7 also shows some of the transitions which make up the Lyman series in the ultraviolet and the Balmer series in the
visible region.
Figure 1.4.7 : Energy levels of atomic hydrogen. Taken from http://eilat.sci.brooklyn.cuny.edu/c...hws/hw2d_c.htm
The ns orbitals are all spherically symmetrical, being associated with a constant angular factor, the spherical harmonic
−−
Y00 = 1/ √4π . They have n − 1 radial nodes—spherical shells on which the wavefunction equals zero. The 1s ground state is
nodeless and the number of nodes increases with energy, in a pattern now familiar from our study of the particle-in-a-box and
harmonic oscillator. The 2s orbital, with its radial node at r = 2 bohr, is also shown in Figure 1.4.3.
p- and d-Orbitals
The lowest-energy solutions deviating from spherical symmetry are the 2p-orbitals. Using Equations 1.4.47, 1.4.48 and the ℓ =1
spherical harmonics, we find three degenerate eigenfunctions:

1 −r/2
ψ210 (r, θ, ϕ) = −− re cos θ (1.4.61)
4 √2π
and
1 −r/2 ±iϕ
ψ21±1 (r, θ, ϕ) = ∓ −− re sin θe (1.4.62)
4 √2π
The function ψ 210 is real and contains the factor r cos θ, which is equal to the cartesian variable z . In chemical applications, this is
designated as a 2pz orbital:
1 −r/2
ψ2p = −− ze (1.4.63)
z
4 √2π
A contour plot is shown in Figure 1.4.8. Note that this function is cylindrically-symmetrical about the z -axis with a node in the x,
y -plane. The ψ 21±1 are complex functions and not as easy to represent graphically. Their angular dependence is that of the
spherical harmonics Y 1±1 , shown in Figure 6-4. As noted in Chap. 4, any linear combination of degenerate eigenfunctions is an
equally-valid alternative eigenfunction. Making use of the Euler formulas for sine and cosine
iϕ −iϕ iϕ −iϕ
e +e e −e
cos ϕ = and sin ϕ = (1.4.64)
2 2
and noting that the combinations sin θ cos ϕ and sin θ sin ϕ correspond to the cartesian variables x and y , respectively, we can
define the alternative 2p orbitals
1 1
−r/2
ψ2p = (ψ21−1 − ψ211 ) = xe (1.4.65)
x – −−
√2 4 √2π
and
i 1
−r/2
ψ2p =− (ψ21−1 + ψ211 ) = ye (1.4.66)
y – −−
√2 4 √2π
Clearly, these have the same shape as the 2pz-orbital, but are oriented along the x- and y -axes, respectively. The threefold
degeneracy of the p-orbitals is very clearly shown by the geometric equivalence the functions 2px, 2py and 2pz, which is not
obvious for the spherical harmonics. The functions listed in Table 1 are, in fact, the real forms for all atomic orbitals, which are
more useful in chemical applications. All higher p-orbitals have analogous functional forms x f (r), y f (r) and z f (r) and are
likewise 3-fold degenerate.
Figure 1.4.8 : Contour plot of 2pz orbital. (Bader).
The orbital ψ is, like ψ

320 210 , a real function. It is known in chemistry as the d -orbital and can be expressed as a cartesian factor
z
2
times a function of r:
2 2
ψ3d 2
= ψ320 = (3 z − r )f (r) (1.4.67)
z
A contour plot is shown in Figure 1.4.9. This function is also cylindrically symmetric about the z -axis with two angular nodes—the
conical surfaces with 3z − r = 0 . The remaining four 3d orbitals are complex functions containing the spherical harmonics Y
2 2
2±1
and Y pictured in Figure 6-4. We can again construct real functions from linear combinations, the result being four
2±2
geometrically equivalent "four-leaf clover" functions with two perpendicular planar nodes. These orbitals are designated
d 2
x −y
, d
2 , d and d . Two of them are shown in Figure 9. The d orbital has a different shape. However, it can be expressed
xy zx yz z
2
in terms of two non-standard d-orbitals, d and d

z
2 . The latter functions, along with d
−x
2
y
2
−z
2 add to zero and thus constitute a
2
x −y
2
linearly dependent set. Two combinations of these three functions can be chosen as independent eigenfunctions.
Figure 1.4.8 : Contour plot of 3d xy orbital.
Summary
The atomic orbitals listed in Table 1 are illustrated in Figure 1.4.20. Blue and red indicate, respectively, positive and negative
regions of the wavefunctions (the radial nodes of the 2s and 3s orbitals are obscured). These pictures are intended as stylized
representations of atomic orbitals and should not be interpreted as quantitatively accurate.
Figure 1.4.20 : Hydrogenic atomic orbitals. Taken from www.chemcomp.com/journal/molorbs.htm
The electron charge distribution in an orbital ψ nℓm (r) is given by
2
ρ(r) = | ψnℓm (r)| (1.4.68)
which for the s-orbitals is a function of r alone. The radial distribution function can be defined, even for orbitals containing angular
dependence, by
2 2
Dnℓ (r) = r [ Rnℓ (r)] (1.4.69)
This represents the electron density in a shell of radius r, including all values of the angular variables θ , ϕ . Figure 1.4.11 shows
plots of the RDF for the first few hydrogen orbitals.
Figure 1.4.22 : Some radial distribution functions.

Seymour Blinder (Professor Emeritus of Chemistry and Physics at the University of Michigan, Ann Arbor)
Integrated by Daniel SantaLucia (Chemistry student at Hope College, Holland MI)
1.4: Hydrogen Atom is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
1.5: Slater Rules
Learning Objective
To quantify the shielding effect experienced by atomic electrons.
We have previously described the concepts of electron shielding, orbital penetration and effective nuclear charge, but we did so in a
qualitative manner. In this section, we explore one model for quantitatively estimating the impact of electron shielding, and then
use that to calculate the effective nuclear charge experienced by an electron in an atom. The model we will use is known as Slater's
Rules (J.C. Slater, Phys Rev 1930, 36, 57).
Slater's Rules
The general principle behind Slater's Rule is that the actual charge felt by an electron is equal to what you'd expect the charge to be
from a certain number of protons, but minus a certain amount of charge from other electrons. Slater's rules allow you to estimate
the effective nuclear charge Z ef ffrom the real number of protons in the nucleus and the effective shielding of electrons in each
orbital "shell" (e.g., to compare the effective nuclear charge and shielding 3d and 4s in transition metals). Slater's rules are fairly
simple and produce fairly accurate predictions of things like the electron configurations and ionization energies.
Slater's Rules
Step 1: Write the electron configuration of the atom in the following form:
(1s) (2s, 2p) (3s, 3p) (3d) (4s, 4p) (4d) (4f) (5s, 5p) . . .
Step 2: Identify the electron of interest, and ignore all electrons in higher groups (to the right in the list from Step 1). These
do not shield electrons in lower groups
Step 3: Slater's Rules is now broken into two cases:
the shielding experienced by an s- or p- electron,
electrons within same group shield 0.35, except the 1s which shield 0.30
electrons within the n-1 group shield 0.85
electrons within the n-2 or lower groups shield 1.00
the shielding experienced by nd or nf valence electrons
electrons within same group shield 0.35
electrons within the lower groups shield 1.00
These rules are summarized in Figure 1.5.1 and Table 1.5.1.

s and p
electrons
0.35
0.85
1.00
1.00
n-3 n-2 n-1 n

1.00
1.00
1.00
0.35
d and f
electrons
Figure 1.5.1 : Graphical depiction of Slater's rules with shielding constants indicated. (CC BY-NC; Ümit Kaya)
Shielding happens when electrons in lower valence shells (or the same valence shell) provide a repulsive force to valence electrons,
thereby "negating" some of the attractive force from the positive nucleus. Electrons really close to the atom (n-2 or lower) pretty
much just look like protons, so they completely negate. As electrons get closer to the electron of interest, some more complex
interactions happen that reduce this shielding.
Table 1.5.1 : Slater's Rules for calculating shieldings
Electrons in group(s) with
Electrons in group(s) with Electrons in all group(s)
Other electrons in the same principal quantum number
Group principal quantum number with principal quantum
group n and azimuthal quantum
n-1 number < n-1
number < l
[1s] 0.30 - - -
[ns,np] 0.35 - 0.85 1
[nd] or [nf] 0.35 1 1 1
The shielding numbers in Table 1.5.1 were derived semi-empirically (i.e., derived from experiments) as opposed to theoretical
calculations. This is because quantum mechanics makes calculating shielding effects quite difficult, which is outside the scope of
this Module.
Calculating S
Sum together the contributions as described in the appropriate rule above to obtain an estimate of the shielding constant, S , which
is found by totaling the screening by all electrons except the one in question.
S = ∑ ni Si (1.5.1)
where
ni is the number of electrons in a specific shell and subshell and
Si is the shielding of the electrons subject to Slater's rules (Table 1.5.1)
Electrons of Nitrogen Atoms

What is the shielding constant experienced by a 2p electron in the nitrogen atom?
Given: Nitrogen (N)
Asked for: S , the shielding constant, for a 2p electron (Equation 1.5.1)
Strategy:
A. Determine the electron configuration of nitrogen, then write it in the appropriate form.
B. Use the appropriate Slater Rules (Table 1.5.1) to calculate the shielding constant for the electron.
Step A N: 1s2 2s2 2p3
N: (1s2)(2s2,2p3)
Step B
There are 4 other electrons in the same ns, np group @ 0.35: (2s2,2p3).
There are 2 electrons in the n-1 groups @ 0.85: (1s2)
S[2p] = 0.85(2) + 0.35(4) = 3.10

 
the 1s electrons the 2s and 2p electrons
As Table 1.5.1 indicates,

the 1s electrons shield the other 2p electron to 0.85 "charges".
the 2s and 2p electrons shield the other 2p electron equally at 0.35 "charges".
Electrons of Bromine Atoms
What is the shielding constant experienced by a valence p-electron in the bromine atom?
Answer
There are 6 other electrons in the same ns, np group.
There are 18 electrons in the n-1 groups: (3s, 3p and 3d)
There are 10 electrons in the n-2 and lower groups: (1s, 2s and 2p)
S = 6(0.35) + 18(0.85) + 10(1.00) = 27.4
Electrons of Bromine Atoms
What is the shielding constant experienced by a 3d electron in the bromine atom?

Given: Bromine (Br)
Asked for: S , the shielding constant, for a 3d electron
Strategy:
A. Determine the electron configuration of bromine, then write it in the appropriate form.
B. Use the appropriate Slater Rules (Table 1.5.1) to calculate the shielding constant for the electron.
Step A Br: 1s2 2s2 2p6 3s2 3p6 4s2 3d10 4p5
Br: (1s2)(2s2,2p6)(3s2,3p6)(3d10)(4s2,4p5)
Step B
There are 9 other electrons in the same ns, np group @ 0.35: (3s2,3p6)
There are 18 other lower group elements electrons in the same nd, nf group @ 1: (1s2)(2s2,2p6)
Ignore the group to the right of the 3d electrons; these do not contribute to the shielding constant @ 0. (4s2,4p5)
S[3d] = 1.00(18) + 0.35(9) = 21.15
Electrons of Copper Atoms

What is the shielding constant experienced by a valence d-electron in the copper atom?
Answer
S = 21.15
Calculating Zeff
One set of estimates for the effective nuclear charge (Z ) was presented in Figure 2.5.1. Previously, we qualitatively described
ef f
Zef f
as being less than the actual nuclear charge (Z ) because of the repulsive interaction between core and valence electrons. We
can quantitatively represent this difference between Z and Z as follows:
ef f
S = Z − Zef f (1.5.2)
Rearranging this formula to solve for Z ef f we obtain:
Zef f = Z − S (1.5.3)
We can then substitute the shielding constant obtained using Equation 1.5.3 to calculate an estimate of Z ef f for the corresponding
atomic electron.
Example 1.5.3: The Effective Charge of p Electrons of Boron Atoms
What is the effective nuclear charge experienced by a valence p- electron in boron?

Given: Boron (B)
Asked for: Z ef f for a valence p- electron
Strategy:
A. Determine the electron configuration of boron and identify the electron of interest.
B. Use the appropriate Slater Rule to calculate the shielding constant for the electron.
C. Use the Periodic Table to determine the actual nuclear charge for boron.
D. Determine the effective nuclear constant.
Solution:
Step A B: 1s2 2s2 2p1 . The valence p- electron in boron resides in the 2p subshell.
B: (1s2)(2s2,2p1)
Step B S[2p] = 1.00(0) + 0.85(2) + 0.35(2) = 2.40
Step C Z = 5
Step D Using Equation 1.5.3, Z ef f = 2.60
Exercise 1.5.3
What is the effective nuclear charge experienced by a valence d-electron in copper?
Answer
Zef f = 7.85
Summary
Slater's Rules can be used as a model of shielding. This permits us to quantify both the amount of shielding experienced by an
electron and the resulting effective nuclear charge. Others performed better optimizations of Z using variational Hartree-Fock
ef f
methods. For example, Clementi and Raimondi published "Atomic Screening Constants from SCF Functions." J Chem Phys (1963)
38, 2686–2689.
References
James L. Reed, "The Genius of Slater's Rules" , J. Chem. Educ., 1999, 76 (6), p 802
David Tudela, "Slater's rules and electron configurations", J. Chem. Educ., 1993, 70 (11), p 956
Kimberley A. Waldron, Erin M. Fehringer, Amy E. Streeb, Jennifer E. Trosky and Joshua J. Pearson, "Screening Percentages
Based on Slater Effective Nuclear Charge as a Versatile Tool for Teaching Periodic Trends", J. Chem. Educ., 2001, 78 (5), p 635

Brett McCollum (Mount Royal University)
1.5: Slater Rules is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
2.1: Front Matter
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2: Molecules
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This text was compiled on 01/12/2023

TABLE OF CONTENTS
2.1: Front Matter

TitlePage
InfoPage
Table of Contents


2.5.8: δ orbitals

2.7.2: Point Groups

Index
Glossary
The Lewis electron-pair approach described previously can be used to predict the number and types of bonds between the atoms in
a substance, and it indicates which atoms have lone pairs of electrons. This approach gives no information about the actual
arrangement of atoms in space, however.
Molecular Geometry
The specific three dimensional arrangement of atoms in molecules is referred to as molecular geometry. We also define molecular
geometry as the positions of the atomic nuclei in a molecule. There are various instrumental techniques such as X-Ray
crystallography and other experimental techniques which can be used to tell us where the atoms are located in a molecule. Using
advanced techniques, very complicated structures for proteins, enzymes, DNA, and RNA have been determined. Molecular
geometry is associated with the chemistry of vision, smell, taste, drug reactions, and enzyme controlled reactions to name a few.
Example 2.2.1: Carbon Tetrachloride
The Lewis structure of carbon tetrachloride provides information about connectivities, provides information about valence
orbitals, and provides information about bond character.
However, the Lewis structure provides no information about the shape of the molecule, which is defined by the bond angles
and the bond lengths. For carbon tetrachloride, each C-Cl bond length is 1.78Å and each Cl-C-Cl bond angle is 109.5°. Hence,
carbon tetrachloride is tetrahedral in structure:
Molecular Geometries of AB molecules n
Molecular geometry is associated with the specific orientation of bonding atoms. A careful analysis of electron distributions in
orbitals will usually result in correct molecular geometry determinations. In addition, the simple writing of Lewis diagrams can also
provide important clues for the determination of molecular geometry. Molecular shapes, or geometries, are critical to molecular
recognition and function. Table 2.2.1 shows some examples of geometries where a central atom A is bonded to two or more X
atoms. As indicated in several of the geometries below, non-bonding electrons E can strongly influence the molecular geometry of
the molecule; this is discussed in more details in Section 9.2.
Table 2.2.1 :
6 5 4 3 2
AX6 AX5 AX4 AX3 AX2
octahedral trigonal bipyramidal tetrahedral trigonal planar linear
1 lone pair of electrons
6 5 4 3 2
AX5E AX4E AX3E AX2E AXE
square pyramidal distorted tetrahedron pyramidal nonlinear linear
2 lone pairs of electrons
AX4E2 AX3E2 AX2E2 AXE2
square planar T-shaped bent linear
These structures can generally be predicted, when A is a nonmetal, using the "valence-shell electron-pair repulsion model (VSEPR)
discussed in the next section.

Mike Blaber (Florida State University)
Robyn Rindge (Class of '98) who now works for PDI Dreamworks (look for his name in the credits of Shrek2.). Robyn drew
these rotating molecules using Infini-D (MetaCreations).
Paul Groves, chemistry teacher at South Pasadena High School and Chemmy Bear
2.2: Molecular Shapes is shared under a CC BY-NC-SA license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To use the VSEPR model to predict molecular geometries.
To predict whether a molecule has a dipole moment.
The Lewis electron-pair approach can be used to predict the number and types of bonds between the atoms in a substance, and it
indicates which atoms have lone pairs of electrons. This approach gives no information about the actual arrangement of atoms in
space, however. We continue our discussion of structure and bonding by introducing the valence-shell electron-pair repulsion
(VSEPR) model (pronounced “vesper”), which can be used to predict the shapes of many molecules and polyatomic ions. Keep in
mind, however, that the VSEPR model, like any model, is a limited representation of reality; the model provides no information
about bond lengths or the presence of multiple bonds.
The VSEPR Model

The VSEPR model can predict the structure of nearly any molecule or polyatomic ion in which the central atom is a nonmetal, as
well as the structures of many molecules and polyatomic ions with a central metal atom. The premise of the VSEPR theory is that
electron pairs located in bonds and lone pairs repel each other and will therefore adopt the geometry that places electron pairs as far
apart from each other as possible. This theory is very simplistic and does not account for the subtleties of orbital interactions that
influence molecular shapes; however, the simple VSEPR counting procedure accurately predicts the three-dimensional structures of
a large number of compounds, which cannot be predicted using the Lewis electron-pair approach.
Figure 2.3.1 : Common Structures for Molecules and Polyatomic Ions That Consist of a Central Atom Bonded to Two or Three
Other Atoms. (CC BY-NC-SA; anonymous)
We can use the VSEPR model to predict the geometry of most polyatomic molecules and ions by focusing only on the number of
electron pairs around the central atom, ignoring all other valence electrons present. According to this model, valence electrons in
the Lewis structure form groups, which may consist of a single bond, a double bond, a triple bond, a lone pair of electrons, or even
a single unpaired electron, which in the VSEPR model is counted as a lone pair. Because electrons repel each other
electrostatically, the most stable arrangement of electron groups (i.e., the one with the lowest energy) is the one that minimizes
repulsions. Groups are positioned around the central atom in a way that produces the molecular structure with the lowest energy, as
illustrated in Figures 2.3.1 and 2.3.2.
Figure 2.3.2 : Electron Geometries for Species with Two to Six Electron Groups. Groups are placed around the central atom in a
way that produces a molecular structure with the lowest energy, that is, the one that minimizes repulsions. (CC BY-NC-SA;
anonymous)
In the VSEPR model, the molecule or polyatomic ion is given an AXmEn designation, where A is the central atom, X is a bonded
atom, E is a nonbonding valence electron group (usually a lone pair of electrons), and m and n are integers. Each group around the
central atom is designated as a bonding pair (BP) or lone (nonbonding) pair (LP). From the BP and LP interactions we can predict
both the relative positions of the atoms and the angles between the bonds, called the bond angles. Using this information, we can
describe the molecular geometry, the arrangement of the bonded atoms in a molecule or polyatomic ion.
VESPR Produce to predict Molecular geometry
This VESPR procedure is summarized as follows:

1. Draw the Lewis electron structure of the molecule or polyatomic ion.
2. Determine the electron group arrangement around the central atom that minimizes repulsions.
3. Assign an AXmEn designation; then identify the LP–LP, LP–BP, or BP–BP interactions and predict deviations from ideal
bond angles.
4. Describe the molecular geometry.
We will illustrate the use of this procedure with several examples, beginning with atoms with two electron groups. In our
discussion we will refer to Figure 2.3.2 and Figure 2.3.3, which summarize the common molecular geometries and idealized bond
angles of molecules and ions with two to six electron groups.
Figure 2.3.3 : Common Molecular Geometries for Species with Two to Six Electron Groups. Lone pairs are shown using a dashed
line. (CC BY-NC-SA; anonymous)
Two Electron Groups
Our first example is a molecule with two bonded atoms and no lone pairs of electrons, BeH . 2
AX2 Molecules: BeH2

1. The central atom, beryllium, contributes two valence electrons, and each hydrogen atom contributes one. The Lewis electron
structure is
Figure 2.3.2 that the arrangement that minimizes repulsions places the groups 180° apart. (CC BY-NC-SA; anonymous)
3. Both groups around the central atom are bonding pairs (BP). Thus BeH2 is designated as AX2.
4. From Figure 2.3.3 we see that with two bonding pairs, the molecular geometry that minimizes repulsions in BeH2 is linear.
AX2 Molecules: CO2
1. The central atom, carbon, contributes four valence electrons, and each oxygen atom contributes six. The Lewis electron
structure is
2. The carbon atom forms two double bonds. Each double bond is a group, so there are two electron groups around the central
atom. Like BeH2, the arrangement that minimizes repulsions places the groups 180° apart.
3. Once again, both groups around the central atom are bonding pairs (BP), so CO2 is designated as AX2.
4. VSEPR only recognizes groups around the central atom. Thus the lone pairs on the oxygen atoms do not influence the
molecular geometry. With two bonding pairs on the central atom and no lone pairs, the molecular geometry of CO2 is linear
(Figure 2.3.3). The structure of CO is shown in Figure 2.3.1.
2
Three Electron Groups

AX3 Molecules: BCl3
1. The central atom, boron, contributes three valence electrons, and each chlorine atom contributes seven valence electrons.
The Lewis electron structure is
Figure 2.3.2 ): (CC BY-NC-SA; anonymous)

3. All electron groups are bonding pairs (BP), so the structure is designated as AX3.
4. From Figure 2.3.3 we see that with three bonding pairs around the central atom, the molecular geometry of BCl3 is trigonal
planar, as shown in Figure 2.3.2.
AX3 Molecules: CO32−
1. The central atom, carbon, has four valence electrons, and each oxygen atom has six valence electrons. As you learned
previously, the Lewis electron structure of one of three resonance forms is represented as
Figure 2.3.2 ).
3. All electron groups are bonding pairs (BP). With three bonding groups around the central atom, the structure is designated as
AX3.
4. We see from Figure 2.3.3 that the molecular geometry of CO32− is trigonal planar with bond angles of 120°.
In our next example we encounter the effects of lone pairs and multiple bonds on molecular geometry for the first time.
AX2E Molecules: SO2

1. The central atom, sulfur, has 6 valence electrons, as does each oxygen atom. With 18 valence electrons, the Lewis electron
structure is shown below.

3. There are two bonding pairs and one lone pair, so the structure is designated as AX2E. This designation has a total of three
electron pairs, two X and one E. Because a lone pair is not shared by two nuclei, it occupies more space near the central atom
than a bonding pair (Figure 2.3.4). Thus bonding pairs and lone pairs repel each other electrostatically in the order BP–BP <
LP–BP < LP–LP. In SO2, we have one BP–BP interaction and two LP–BP interactions.
4. The molecular geometry is described only by the positions of the nuclei, not by the positions of the lone pairs. Thus with
two nuclei and one lone pair the shape is bent, or V shaped, which can be viewed as a trigonal planar arrangement with a
missing vertex (Figures 2.3.2 and 2.3.3). The O-S-O bond angle is expected to be less than 120° because of the extra space
taken up by the lone pair.
Figure 2.3.4 : The Difference in the Space Occupied by a Lone Pair of Electrons and by a Bonding Pair. (CC BY-NC-SA;
anonymous)
As with SO2, this composite model of electron distribution and negative electrostatic potential in ammonia shows that a lone
pair of electrons occupies a larger region of space around the nitrogen atom than does a bonding pair of electrons that is shared
with a hydrogen atom.
Like lone pairs of electrons, multiple bonds occupy more space around the central atom than a single bond, which can cause other
bond angles to be somewhat smaller than expected. This is because a multiple bond has a higher electron density than a single
bond, so its electrons occupy more space than those of a single bond. For example, in a molecule such as CH2O (AX3), whose
structure is shown below, the double bond repels the single bonds more strongly than the single bonds repel each other. This causes
a deviation from ideal geometry (an H–C–H bond angle of 116.5° rather than 120°).
Four Electron Groups

One of the limitations of Lewis structures is that they depict molecules and ions in only two dimensions. With four electron groups,
we must learn to show molecules and ions in three dimensions.
AX4 Molecules: CH4
1. The central atom, carbon, contributes four valence electrons, and each hydrogen atom has one valence electron, so the full
Lewis electron structure is
2. There are four electron groups around the central atom. As shown in Figure 2.3.2, repulsions are minimized by placing the
groups in the corners of a tetrahedron with bond angles of 109.5°.
3. All electron groups are bonding pairs, so the structure is designated as AX4.
4. With four bonding pairs, the molecular geometry of methane is tetrahedral (Figure 2.3.3).
AX3E Molecules: NH3

1. In ammonia, the central atom, nitrogen, has five valence electrons and each hydrogen donates one valence electron,
producing the Lewis electron structure
2. There are four electron groups around nitrogen, three bonding pairs and one lone pair. Repulsions are minimized by
directing each hydrogen atom and the lone pair to the corners of a tetrahedron.
3. With three bonding pairs and one lone pair, the structure is designated as AX3E. This designation has a total of four electron
pairs, three X and one E. We expect the LP–BP interactions to cause the bonding pair angles to deviate significantly from the
angles of a perfect tetrahedron.
4. There are three nuclei and one lone pair, so the molecular geometry is trigonal pyramidal. In essence, this is a tetrahedron
with a vertex missing (Figure 2.3.3). However, the H–N–H bond angles are less than the ideal angle of 109.5° because of LP–
BP repulsions (Figure 2.3.3 and Figure 2.3.4).
AX2E2 Molecules: H2O

1. Oxygen has six valence electrons and each hydrogen has one valence electron, producing the Lewis electron structure
Figure 2.3.2 : (CC BY-NC-SA; anonymous)

3. With two bonding pairs and two lone pairs, the structure is designated as AX2E2 with a total of four electron pairs. Due to
LP–LP, LP–BP, and BP–BP interactions, we expect a significant deviation from idealized tetrahedral angles.
4. With two hydrogen atoms and two lone pairs of electrons, the structure has significant lone pair interactions. There are two
nuclei about the central atom, so the molecular shape is bent, or V shaped, with an H–O–H angle that is even less than the H–
N–H angles in NH3, as we would expect because of the presence of two lone pairs of electrons on the central atom rather than
one. This molecular shape is essentially a tetrahedron with two missing vertices.
Five Electron Groups

In previous examples it did not matter where we placed the electron groups because all positions were equivalent. In some cases,
however, the positions are not equivalent. We encounter this situation for the first time with five electron groups.
AX5 Molecules: PCl5
1. Phosphorus has five valence electrons and each chlorine has seven valence electrons, so the Lewis electron structure of PCl5
is

3. All electron groups are bonding pairs, so the structure is designated as AX5. There are no lone pair interactions.
4. The molecular geometry of PCl5 is trigonal bipyramidal, as shown in Figure 2.3.3. The molecule has three atoms in a plane
in equatorial positions and two atoms above and below the plane in axial positions. The three equatorial positions are
separated by 120° from one another, and the two axial positions are at 90° to the equatorial plane. The axial and equatorial
positions are not chemically equivalent, as we will see in our next example.
AX4E Molecules: SF4

1. The sulfur atom has six valence electrons and each fluorine has seven valence electrons, so the Lewis electron structure is
With an expanded valence, this species is an exception to the octet rule.

2. There are five groups around sulfur, four bonding pairs and one lone pair. With five electron groups, the lowest energy
arrangement is a trigonal bipyramid, as shown in Figure 2.3.2.
3. We designate SF4 as AX4E; it has a total of five electron pairs. However, because the axial and equatorial positions are not
chemically equivalent, where do we place the lone pair? If we place the lone pair in the axial position, we have three LP–BP
repulsions at 90°. If we place it in the equatorial position, we have two 90° LP–BP repulsions at 90°. With fewer 90° LP–BP
repulsions, we can predict that the structure with the lone pair of electrons in the equatorial position is more stable than the one
with the lone pair in the axial position. We also expect a deviation from ideal geometry because a lone pair of electrons
occupies more space than a bonding pair.
Figure 2.3.5 : Illustration of the Area Shared by Two Electron Pairs versus the Angle between Them
At 90°, the two electron pairs share a relatively large region of space, which leads to strong repulsive electron–electron
interactions.
4. With four nuclei and one lone pair of electrons, the molecular structure is based on a trigonal bipyramid with a missing
equatorial vertex; it is described as a seesaw. The Faxial–S–Faxial angle is 173° rather than 180° because of the lone pair of
electrons in the equatorial plane.
AX3E2 Molecules: BrF3
1. The bromine atom has seven valence electrons, and each fluorine has seven valence electrons, so the Lewis electron
structure is
Once again, we have a compound that is an exception to the octet rule.

2. There are five groups around the central atom, three bonding pairs and two lone pairs. We again direct the groups toward the
vertices of a trigonal bipyramid.
3. With three bonding pairs and two lone pairs, the structural designation is AX3E2 with a total of five electron pairs. Because
the axial and equatorial positions are not equivalent, we must decide how to arrange the groups to minimize repulsions. If we
place both lone pairs in the axial positions, we have six LP–BP repulsions at 90°. If both are in the equatorial positions, we
have four LP–BP repulsions at 90°. If one lone pair is axial and the other equatorial, we have one LP–LP repulsion at 90° and
three LP–BP repulsions at 90°:
Structure (c) can be eliminated because it has a LP–LP interaction at 90°. Structure (b), with fewer LP–BP repulsions at 90°
than (a), is lower in energy. However, we predict a deviation in bond angles because of the presence of the two lone pairs of
electrons.
4. The three nuclei in BrF3 determine its molecular structure, which is described as T shaped. This is essentially a trigonal
bipyramid that is missing two equatorial vertices. The Faxial–Br–Faxial angle is 172°, less than 180° because of LP–BP
repulsions (Figure 2.3.2.1).
Because lone pairs occupy more space around the central atom than bonding pairs, electrostatic repulsions are more
important for lone pairs than for bonding pairs.
AX2E3 Molecules: I3−

1. Each iodine atom contributes seven electrons and the negative charge one, so the Lewis electron structure is
2. There are five electron groups about the central atom in I3−, two bonding pairs and three lone pairs. To minimize repulsions,
the groups are directed to the corners of a trigonal bipyramid.
3. With two bonding pairs and three lone pairs, I3− has a total of five electron pairs and is designated as AX2E3. We must now
decide how to arrange the lone pairs of electrons in a trigonal bipyramid in a way that minimizes repulsions. Placing them in
the axial positions eliminates 90° LP–LP repulsions and minimizes the number of 90° LP–BP repulsions.
The three lone pairs of electrons have equivalent interactions with the three iodine atoms, so we do not expect any deviations in
bonding angles.
4. With three nuclei and three lone pairs of electrons, the molecular geometry of I3− is linear. This can be described as a
trigonal bipyramid with three equatorial vertices missing. The ion has an I–I–I angle of 180°, as expected.
Six Electron Groups

Six electron groups form an octahedron, a polyhedron made of identical equilateral triangles and six identical vertices (Figure
2.3.2.)
AX6 Molecules: SF6
1. The central atom, sulfur, contributes six valence electrons, and each fluorine atom has seven valence electrons, so the Lewis
electron structure is
With an expanded valence, this species is an exception to the octet rule.

2. There are six electron groups around the central atom, each a bonding pair. We see from Figure 2.3.2 that the geometry that
minimizes repulsions is octahedral.
3. With only bonding pairs, SF6 is designated as AX6. All positions are chemically equivalent, so all electronic interactions are
equivalent.
4. There are six nuclei, so the molecular geometry of SF6 is octahedral.
AX5E Molecules: BrF5

1. The central atom, bromine, has seven valence electrons, as does each fluorine, so the Lewis electron structure is
With its expanded valence, this species is an exception to the octet rule.
2. There are six electron groups around the Br, five bonding pairs and one lone pair. Placing five F atoms around Br while
minimizing BP–BP and LP–BP repulsions gives the following structure:
3. With five bonding pairs and one lone pair, BrF5 is designated as AX5E; it has a total of six electron pairs. The BrF5 structure
has four fluorine atoms in a plane in an equatorial position and one fluorine atom and the lone pair of electrons in the axial
positions. We expect all Faxial–Br–Fequatorial angles to be less than 90° because of the lone pair of electrons, which occupies
more space than the bonding electron pairs.
4. With five nuclei surrounding the central atom, the molecular structure is based on an octahedron with a vertex missing. This
molecular structure is square pyramidal. The Faxial–B–Fequatorial angles are 85.1°, less than 90° because of LP–BP repulsions.
AX4E2 Molecules: ICl4−

1. The central atom, iodine, contributes seven electrons. Each chlorine contributes seven, and there is a single negative charge.
The Lewis electron structure is
2. There are six electron groups around the central atom, four bonding pairs and two lone pairs. The structure that minimizes
LP–LP, LP–BP, and BP–BP repulsions is
3. ICl4− is designated as AX4E2 and has a total of six electron pairs. Although there are lone pairs of electrons, with four
bonding electron pairs in the equatorial plane and the lone pairs of electrons in the axial positions, all LP–BP repulsions are the
same. Therefore, we do not expect any deviation in the Cl–I–Cl bond angles.
4. With five nuclei, the ICl4− ion forms a molecular structure that is square planar, an octahedron with two opposite vertices
missing.
The relationship between the number of electron groups around a central atom, the number of lone pairs of electrons, and the
molecular geometry is summarized in Figure 2.3.6.
Figure 2.3.6 : Overview of Molecular Geometries
Example 2.3.1
Using the VSEPR model, predict the molecular geometry of each molecule or ion.
1. PF5 (phosphorus pentafluoride, a catalyst used in certain organic reactions)
2. H3O+ (hydronium ion)
Given: two chemical species
Asked for: molecular geometry
Strategy:
A. Draw the Lewis electron structure of the molecule or polyatomic ion.
B. Determine the electron group arrangement around the central atom that minimizes repulsions.
C. Assign an AXmEn designation; then identify the LP–LP, LP–BP, or BP–BP interactions and predict deviations in bond
angles.
D. Describe the molecular geometry.
Solution:
1. A The central atom, P, has five valence electrons and each fluorine has seven valence electrons, so the Lewis structure of
PF5 is
C All electron groups are bonding pairs, so PF5 is designated as AX5. Notice that this gives a total of five electron pairs.
With no lone pair repulsions, we do not expect any bond angles to deviate from the ideal.
D The PF5 molecule has five nuclei and no lone pairs of electrons, so its molecular geometry is trigonal bipyramidal.
2. A The central atom, O, has six valence electrons, and each H atom contributes one valence electron. Subtracting one
electron for the positive charge gives a total of eight valence electrons, so the Lewis electron structure is
B There are four electron groups around oxygen, three bonding pairs and one lone pair. Like NH3, repulsions are minimized
by directing each hydrogen atom and the lone pair to the corners of a tetrahedron.
C With three bonding pairs and one lone pair, the structure is designated as AX3E and has a total of four electron pairs
(three X and one E). We expect the LP–BP interactions to cause the bonding pair angles to deviate significantly from the
angles of a perfect tetrahedron.
D There are three nuclei and one lone pair, so the molecular geometry is trigonal pyramidal, in essence a tetrahedron
missing a vertex. However, the H–O–H bond angles are less than the ideal angle of 109.5° because of LP–BP repulsions:
Exercise 2.3.1
Using the VSEPR model, predict the molecular geometry of each molecule or ion.
a. XeO3
b. PF6−
c. NO2+
Answer a
trigonal pyramidal
Answer b
octahedral
Answer c
linear
Example 2.3.2
Predict the molecular geometry of each molecule.

1. XeF2
2. SnCl2
Given: two chemical compounds
Strategy:
Use the strategy given in Example2.3.1.
Solution:
1. A Xenon contributes eight electrons and each fluorine seven valence electrons, so the Lewis electron structure is
B There are five electron groups around the central atom, two bonding pairs and three lone pairs. Repulsions are minimized
by placing the groups in the corners of a trigonal bipyramid.
C From B, XeF2 is designated as AX2E3 and has a total of five electron pairs (two X and three E). With three lone pairs
about the central atom, we can arrange the two F atoms in three possible ways: both F atoms can be axial, one can be axial
and one equatorial, or both can be equatorial:
The structure with the lowest energy is the one that minimizes LP–LP repulsions. Both (b) and (c) have two 90° LP–LP
interactions, whereas structure (a) has none. Thus both F atoms are in the axial positions, like the two iodine atoms around
the central iodine in I3−. All LP–BP interactions are equivalent, so we do not expect a deviation from an ideal 180° in the
F–Xe–F bond angle.
D With two nuclei about the central atom, the molecular geometry of XeF2 is linear. It is a trigonal bipyramid with three
missing equatorial vertices.
2. A The tin atom donates 4 valence electrons and each chlorine atom donates 7 valence electrons. With 18 valence electrons,
the Lewis electron structure is
B There are three electron groups around the central atom, two bonding groups and one lone pair of electrons. To minimize
repulsions the three groups are initially placed at 120° angles from each other.
C From B we designate SnCl2 as AX2E. It has a total of three electron pairs, two X and one E. Because the lone pair of
electrons occupies more space than the bonding pairs, we expect a decrease in the Cl–Sn–Cl bond angle due to increased
LP–BP repulsions.
D With two nuclei around the central atom and one lone pair of electrons, the molecular geometry of SnCl2 is bent, like
SO2, but with a Cl–Sn–Cl bond angle of 95°. The molecular geometry can be described as a trigonal planar arrangement
with one vertex missing.
Exercise 2.3.2
Predict the molecular geometry of each molecule.

a. SO3
b. XeF4
Answer a
trigonal planar
Answer b
square planar
Molecules with No Single Central Atom

The VSEPR model can be used to predict the structure of somewhat more complex molecules with no single central atom by
treating them as linked AXmEn fragments. We will demonstrate with methyl isocyanate (CH3–N=C=O), a volatile and highly toxic
molecule that is used to produce the pesticide Sevin. In 1984, large quantities of Sevin were accidentally released in Bhopal, India,
when water leaked into storage tanks. The resulting highly exothermic reaction caused a rapid increase in pressure that ruptured the
tanks, releasing large amounts of methyl isocyanate that killed approximately 3800 people and wholly or partially disabled about
50,000 others. In addition, there was significant damage to livestock and crops.
We can treat methyl isocyanate as linked AXmEn fragments beginning with the carbon atom at the left, which is connected to three
H atoms and one N atom by single bonds. The four bonds around carbon mean that it must be surrounded by four bonding electron
pairs in a configuration similar to AX4. We can therefore predict the CH3–N portion of the molecule to be roughly tetrahedral,
similar to methane:
The nitrogen atom is connected to one carbon by a single bond and to the other carbon by a double bond, producing a total of three
bonds, C–N=C. For nitrogen to have an octet of electrons, it must also have a lone pair:
Because multiple bonds are not shown in the VSEPR model, the nitrogen is effectively surrounded by three electron pairs. Thus
according to the VSEPR model, the C–N=C fragment should be bent with an angle less than 120°.
The carbon in the –N=C=O fragment is doubly bonded to both nitrogen and oxygen, which in the VSEPR model gives carbon a
total of two electron pairs. The N=C=O angle should therefore be 180°, or linear. The three fragments combine to give the
following structure:
Figure 2.3.7 ).
Figure 2.3.7 : The Experimentally Determined Structure of Methyl Isocyanate
Certain patterns are seen in the structures of moderately complex molecules. For example, carbon atoms with four bonds (such as
the carbon on the left in methyl isocyanate) are generally tetrahedral. Similarly, the carbon atom on the right has two double bonds
that are similar to those in CO2, so its geometry, like that of CO2, is linear. Recognizing similarities to simpler molecules will help
you predict the molecular geometries of more complex molecules.
Example 2.3.3
Use the VSEPR model to predict the molecular geometry of propyne (H3C–C≡CH), a gas with some anesthetic properties.
Given: chemical compound
Strategy:
Count the number of electron groups around each carbon, recognizing that in the VSEPR model, a multiple bond counts as a
single group. Use Figure 2.3.3 to determine the molecular geometry around each carbon atom and then deduce the structure of
the molecule as a whole.
Solution:
Because the carbon atom on the left is bonded to four other atoms, we know that it is approximately tetrahedral. The next two
carbon atoms share a triple bond, and each has an additional single bond. Because a multiple bond is counted as a single bond
in the VSEPR model, each carbon atom behaves as if it had two electron groups. This means that both of these carbons are
linear, with C–C≡C and C≡C–H angles of 180°.
Exercise 2.3.3
Predict the geometry of allene (H2C=C=CH2), a compound with narcotic properties that is used to make more complex organic
molecules.
Answer
The terminal carbon atoms are trigonal planar, the central carbon is linear, and the C–C–C angle is 180°.
Molecular Dipole Moments

You previously learned how to calculate the dipole moments of simple diatomic molecules. In more complex molecules with polar
covalent bonds, the three-dimensional geometry and the compound’s symmetry determine whether there is a net dipole moment.
Mathematically, dipole moments are vectors; they possess both a magnitude and a direction. The dipole moment of a molecule is
therefore the vector sum of the dipole moments of the individual bonds in the molecule. If the individual bond dipole moments
cancel one another, there is no net dipole moment. Such is the case for CO2, a linear molecule (Figure 2.3.8a). Each C–O bond in
CO2 is polar, yet experiments show that the CO2 molecule has no dipole moment. Because the two C–O bond dipoles in CO2 are
equal in magnitude and oriented at 180° to each other, they cancel. As a result, the CO2 molecule has no net dipole moment even
though it has a substantial separation of charge. In contrast, the H2O molecule is not linear (Figure 2.3.8b); it is bent in three-
dimensional space, so the dipole moments do not cancel each other. Thus a molecule such as H2O has a net dipole moment. We
expect the concentration of negative charge to be on the oxygen, the more electronegative atom, and positive charge on the two
hydrogens. This charge polarization allows H2O to hydrogen-bond to other polarized or charged species, including other water
molecules.
Figure 2.3.8 : How Individual Bond Dipole Moments Are Added Together to Give an Overall Molecular Dipole Moment for Two
Triatomic Molecules with Different Structures. (a) In CO2, the C–O bond dipoles are equal in magnitude but oriented in opposite
directions (at 180°). Their vector sum is zero, so CO2 therefore has no net dipole. (b) In H2O, the O–H bond dipoles are also equal
in magnitude, but they are oriented at 104.5° to each other. Hence the vector sum is not zero, and H2O has a net dipole moment.
Other examples of molecules with polar bonds are shown in Figure 2.3.9. In molecular geometries that are highly symmetrical
(most notably tetrahedral and square planar, trigonal bipyramidal, and octahedral), individual bond dipole moments completely
cancel, and there is no net dipole moment. Although a molecule like CHCl3 is best described as tetrahedral, the atoms bonded to
carbon are not identical. Consequently, the bond dipole moments cannot cancel one another, and the molecule has a dipole moment.
Due to the arrangement of the bonds in molecules that have V-shaped, trigonal pyramidal, seesaw, T-shaped, and square pyramidal
geometries, the bond dipole moments cannot cancel one another. Consequently, molecules with these geometries always have a
nonzero dipole moment.
Figure 2.3.9 : Molecules with Polar Bonds. Individual bond dipole moments are indicated in red. Due to their different three-
dimensional structures, some molecules with polar bonds have a net dipole moment (HCl, CH2O, NH3, and CHCl3), indicated in
blue, whereas others do not because the bond dipole moments cancel (BCl3, CCl4, PF5, and SF6).
Molecules with asymmetrical charge distributions have a net dipole moment.
Example 2.3.4
Which molecule(s) has a net dipole moment?

a. H S
2
b. NHF 2
c. BF 3
Given: three chemical compounds

Asked for: net dipole moment
Strategy:
For each three-dimensional molecular geometry, predict whether the bond dipoles cancel. If they do not, then the molecule has
a net dipole moment.
Solution:
1. The total number of electrons around the central atom, S, is eight, which gives four electron pairs. Two of these electron
pairs are bonding pairs and two are lone pairs, so the molecular geometry of H S is bent (Figure 2.3.6). The bond dipoles
2
cannot cancel one another, so the molecule has a net dipole moment.
2. Difluoroamine has a trigonal pyramidal molecular geometry. Because there is one hydrogen and two fluorines, and because
of the lone pair of electrons on nitrogen, the molecule is not symmetrical, and the bond dipoles of NHF2 cannot cancel one
another. This means that NHF2 has a net dipole moment. We expect polarization from the two fluorine atoms, the most
electronegative atoms in the periodic table, to have a greater affect on the net dipole moment than polarization from the
lone pair of electrons on nitrogen.
3. The molecular geometry of BF3 is trigonal planar. Because all the B–F bonds are equal and the molecule is highly
symmetrical, the dipoles cancel one another in three-dimensional space. Thus BF3 has a net dipole moment of zero:
Exercise 2.3.4
Which molecule(s) has a net dipole moment?

CH Cl
3
SO
3
XeO
3
Answer
CH Cl
3
and XeO
3
Summary
Lewis electron structures give no information about molecular geometry, the arrangement of bonded atoms in a molecule or
polyatomic ion, which is crucial to understanding the chemistry of a molecule. The valence-shell electron-pair repulsion
(VSEPR) model allows us to predict which of the possible structures is actually observed in most cases. It is based on the
assumption that pairs of electrons occupy space, and the lowest-energy structure is the one that minimizes electron pair–electron
pair repulsions. In the VSEPR model, the molecule or polyatomic ion is given an AXmEn designation, where A is the central atom,
X is a bonded atom, E is a nonbonding valence electron group (usually a lone pair of electrons), and m and n are integers. Each
group around the central atom is designated as a bonding pair (BP) or lone (nonbonding) pair (LP). From the BP and LP
interactions we can predict both the relative positions of the atoms and the angles between the bonds, called the bond angles. From
this we can describe the molecular geometry. The VSEPR model can be used to predict the shapes of many molecules and
polyatomic ions, but it gives no information about bond lengths and the presence of multiple bonds. A combination of VSEPR and
a bonding model, such as Lewis electron structures, is necessary to understand the presence of multiple bonds.
Molecules with polar covalent bonds can have a dipole moment, an asymmetrical distribution of charge that results in a tendency
for molecules to align themselves in an applied electric field. Any diatomic molecule with a polar covalent bond has a dipole
moment, but in polyatomic molecules, the presence or absence of a net dipole moment depends on the structure. For some highly
symmetrical structures, the individual bond dipole moments cancel one another, giving a dipole moment of zero.
2.3: The VSEPR Model is shared under a CC BY-NC-SA license and was authored, remixed, and/or curated by LibreTexts.
The localized valence bond theory uses a process called hybridization, in which atomic orbitals that are similar in energy but not
equivalent are combined mathematically to produce sets of equivalent orbitals that are properly oriented to form bonds. These new
combinations are called hybrid atomic orbitals because they are produced by combining (hybridizing) two or more atomic orbitals
from the same atom.
Hybridization of s and p Orbitals

In BeH2, we can generate two equivalent orbitals by combining the 2s orbital of beryllium and any one of the three degenerate 2p
orbitals. By taking the sum and the difference of Be 2s and 2pz atomic orbitals, for example, we produce two new orbitals with
major and minor lobes oriented along the z-axes, as shown in Figure 2.4.1.
Figure 2.4.1 : The position of the atomic nucleus with respect to an sp hybrid orbital. The nucleus is actually located slightly inside
the minor lobe, not at the node separating the major and minor lobes.
Because the difference A − B can also be written as A + (−B), in Figure 2.4.2 and subsequent figures we have reversed the phase(s)
of the orbital being subtracted, which is the same as multiplying it by −1 and adding. This gives us Equation 2.4.2, where the value
1
is needed mathematically to indicate that the 2s and 2p orbitals contribute equally to each hybrid orbital.
√2
1
sp = – (2s + 2 pz ) (2.4.1)
√2
and
1
sp = – (2s − 2 pz ) (2.4.2)
√2
Figure 2.4.2 : The Formation of sp Hybrid Orbitals. Taking the sum and difference of an ns and an np atomic orbital where n = 2
gives two equivalent sp hybrid orbitals oriented at 180° to each other.
The nucleus resides just inside the minor lobe of each orbital. In this case, the new orbitals are called sp hybrids because they are
formed from one s and one p orbital. The two new orbitals are equivalent in energy, and their energy is between the energy values
associated with pure s and p orbitals, as illustrated in this diagram:
Figure 2.4.3 . each sp orbital on Be has the correct orientation for the major lobes to overlap with the 1s atomic orbital of an H
atom. The formation of two energetically equivalent Be–H bonds produces a linear BeH molecule. Thus valence bond theory
2
does what neither the Lewis electron structure nor the VSEPR model is able to do; it explains why the bonds in BeH are 2
equivalent in energy and why BeH has a linear geometry.

2
Figure 2.4.3 : Explanation of the Bonding in BeH2 Using sp Hybrid Orbitals. Each singly occupied sp hybrid orbital on beryllium
can form an electron-pair bond with the singly occupied 1s orbital of a hydrogen atom. Because the two sp hybrid orbitals are
oriented at a 180° angle, the BeH2 molecule is linear.
Because both promotion and hybridization require an input of energy, the formation of a set of singly occupied hybrid atomic
orbitals is energetically uphill. The overall process of forming a compound with hybrid orbitals will be energetically favorable only
if the amount of energy released by the formation of covalent bonds is greater than the amount of energy used to form the hybrid
orbitals (Figure 2.4.4). As we will see, some compounds are highly unstable or do not exist because the amount of energy required
to form hybrid orbitals is greater than the amount of energy that would be released by the formation of additional bonds.
Figure 2.4.4 : A Hypothetical Stepwise Process for the Formation of BeH2 from a Gaseous Be Atom and Two Gaseous H Atoms.
The promotion of an electron from the 2s orbital of beryllium to one of the 2p orbitals is energetically uphill. The overall process of
forming a BeH2 molecule from a Be atom and two H atoms will therefore be energetically favorable only if the amount of energy
released by the formation of the two Be–H bonds is greater than the amount of energy required for promotion and hybridization.
The concept of hybridization also explains why boron, with a 2s22p1 valence electron configuration, forms three bonds with
fluorine to produce BF3, as predicted by the Lewis and VSEPR approaches. With only a single unpaired electron in its ground state,
boron should form only a single covalent bond. By the promotion of one of its 2s electrons to an unoccupied 2p orbital, however,
followed by the hybridization of the three singly occupied orbitals (the 2s and two 2p orbitals), boron acquires a set of three
equivalent hybrid orbitals with one electron each, as shown here:
Figure 2.4.5 ). Because the hybrid atomic orbitals are formed from one s and two p orbitals, boron is said to be sp2 hybridized
(pronounced “s-p-two” or “s-p-squared”). The singly occupied sp2 hybrid atomic orbitals can overlap with the singly occupied
orbitals on each of the three F atoms to form a trigonal planar structure with three energetically equivalent B–F bonds.
Figure 2.4.5 : Formation of sp2 Hybrid Orbitals. Combining one ns and two np atomic orbitals gives three equivalent sp2 hybrid
orbitals in a trigonal planar arrangement; that is, oriented at 120° to one another.
Looking at the 2s22p2 valence electron configuration of carbon, we might expect carbon to use its two unpaired 2p electrons to
form compounds with only two covalent bonds. We know, however, that carbon typically forms compounds with four covalent
bonds. We can explain this apparent discrepancy by the hybridization of the 2s orbital and the three 2p orbitals on carbon to give a
set of four degenerate sp3 (“s-p-three” or “s-p-cubed”) hybrid orbitals, each with a single electron:
Figure 2.4.6 ). Like all the hybridized orbitals discussed earlier, the sp3 hybrid atomic orbitals are predicted to be equal in energy.
Thus, methane (CH4) is a tetrahedral molecule with four equivalent C-H bonds.
Figure 2.4.6 : Formation of sp3 Hybrid Orbitals. Combining one ns and three np atomic orbitals results in four sp3 hybrid orbitals
oriented at 109.5° to one another in a tetrahedral arrangement.
In addition to explaining why some elements form more bonds than would be expected based on their valence electron
configurations, and why the bonds formed are equal in energy, valence bond theory explains why these compounds are so stable:
the amount of energy released increases with the number of bonds formed. In the case of carbon, for example, much more energy is
released in the formation of four bonds than two, so compounds of carbon with four bonds tend to be more stable than those with
only two. Carbon does form compounds with only two covalent bonds (such as CH2 or CF2), but these species are highly reactive,
unstable intermediates that only form in certain chemical reactions.
Valence bond theory explains the number of bonds formed in a compound and the relative
bond strengths.
The bonding in molecules such as NH3 or H2O, which have lone pairs on the central atom, can also be described in terms of hybrid
atomic orbitals. In NH3, for example, N, with a 2s22p3 valence electron configuration, can hybridize its 2s and 2p orbitals to
produce four sp3 hybrid orbitals. Placing five valence electrons in the four hybrid orbitals, we obtain three that are singly occupied
and one with a pair of electrons:
The three singly occupied sp3 lobes can form bonds with three H atoms, while the fourth orbital accommodates the lone pair of
electrons. Similarly, H2O has an sp3 hybridized oxygen atom that uses two singly occupied sp3 lobes to bond to two H atoms, and
two to accommodate the two lone pairs predicted by the VSEPR model. Such descriptions explain the approximately tetrahedral
distribution of electron pairs on the central atom in NH3 and H2O. Unfortunately, however, recent experimental evidence indicates
that in NH3 and H2O, the hybridized orbitals are not entirely equivalent in energy, making this bonding model an active area of
research.
Example 2.4.1
Use the VSEPR model to predict the number of electron pairs and molecular geometry in each compound and then describe the
hybridization and bonding of all atoms except hydrogen.
a. H2S
b. CHCl3
Given: two chemical compounds
Asked for: number of electron pairs and molecular geometry, hybridization, and bonding
Strategy:
A. Using the VSEPR approach to determine the number of electron pairs and the molecular geometry of the molecule.
B. From the valence electron configuration of the central atom, predict the number and type of hybrid orbitals that can be
produced. Fill these hybrid orbitals with the total number of valence electrons around the central atom and describe the
hybridization.
Solution:
1. A H2S has four electron pairs around the sulfur atom with two bonded atoms, so the VSEPR model predicts a molecular
geometry that is bent, or V shaped. B Sulfur has a 3s23p4 valence electron configuration with six electrons, but by
hybridizing its 3s and 3p orbitals, it can produce four sp3 hybrids. If the six valence electrons are placed in these orbitals,
two have electron pairs and two are singly occupied. The two sp3 hybrid orbitals that are singly occupied are used to form
S–H bonds, whereas the other two have lone pairs of electrons. Together, the four sp3 hybrid orbitals produce an
approximately tetrahedral arrangement of electron pairs, which agrees with the molecular geometry predicted by the
VSEPR model.
2. A The CHCl3 molecule has four valence electrons around the central atom. In the VSEPR model, the carbon atom has four
electron pairs, and the molecular geometry is tetrahedral. B Carbon has a 2s22p2 valence electron configuration. By
hybridizing its 2s and 2p orbitals, it can form four sp3 hybridized orbitals that are equal in energy. Eight electrons around
the central atom (four from C, one from H, and one from each of the three Cl atoms) fill three sp3 hybrid orbitals to form
C–Cl bonds, and one forms a C–H bond. Similarly, the Cl atoms, with seven electrons each in their 3s and 3p valence
subshells, can be viewed as sp3 hybridized. Each Cl atom uses a singly occupied sp3 hybrid orbital to form a C–Cl bond and
three hybrid orbitals to accommodate lone pairs.
Exercise 2.4.1
Use the VSEPR model to predict the number of electron pairs and molecular geometry in each compound and then describe the
hybridization and bonding of all atoms except hydrogen.
a. the BF4− ion
b. hydrazine (H2N–NH2)
Answer a
B is sp3 hybridized; F is also sp3 hybridized so it can accommodate one B–F bond and three lone pairs. The molecular
geometry is tetrahedral.
Answer b
Each N atom is sp3 hybridized and uses one sp3 hybrid orbital to form the N–N bond, two to form N–H bonds, and one to
accommodate a lone pair. The molecular geometry about each N is trigonal pyramidal.
The number of hybrid orbitals used by the central atom is the same as the number of electron pairs around the central atom.
Summary
Hybridization increases the overlap of bonding orbitals and explains the molecular geometries of many species whose geometry
cannot be explained using a VSEPR approach. The localized bonding model (called valence bond theory) assumes that covalent
bonds are formed when atomic orbitals overlap and that the strength of a covalent bond is proportional to the amount of overlap. It
also assumes that atoms use combinations of atomic orbitals (hybrids) to maximize the overlap with adjacent atoms. The formation
of hybrid atomic orbitals can be viewed as occurring via promotion of an electron from a filled ns2 subshell to an empty np
valence orbital, followed by hybridization, the combination of the orbitals to give a new set of (usually) equivalent orbitals that are
oriented properly to form bonds. The combination of an ns and an np orbital gives rise to two equivalent sp hybrids oriented at
180°, whereas the combination of an ns and two or three np orbitals produces three equivalent sp2 hybrids or four equivalent sp3
hybrids, respectively. The spatial orientation of the hybrid atomic orbitals is consistent with the geometries predicted using the
VSEPR model.
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SECTION OVERVIEW
2.5.8: δ orbitals
2.5: Molecular Orbitals is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
Learning Objectives
To calculate the percent ionic character of a covalent polar bond
Previously, we described the two idealized extremes of chemical bonding:

ionic bonding—in which one or more electrons are transferred completely from one atom to another, and the resulting ions are
held together by purely electrostatic forces—and
covalent bonding, in which electrons are shared equally between two atoms.
Most compounds, however, have polar covalent bonds, which means that electrons are shared unequally between the bonded
atoms. Figure 2.5.1.1 compares the electron distribution in a polar covalent bond with those in an ideally covalent and an ideally
ionic bond. Recall that a lowercase Greek delta (δ ) is used to indicate that a bonded atom possesses a partial positive charge,
indicated by δ , or a partial negative charge, indicated by δ , and a bond between two atoms that possess partial charges is a polar
+ −
bond.
Figure 2.5.1.1 : The Electron Distribution in a Nonpolar Covalent Bond, a Polar Covalent Bond, and an Ionic Bond Using Lewis
Electron Structures. In a purely covalent bond (a), the bonding electrons are shared equally between the atoms. In a purely ionic
bond (c), an electron has been transferred completely from one atom to the other. A polar covalent bond (b) is intermediate between
the two extremes: the bonding electrons are shared unequally between the two atoms, and the electron distribution is asymmetrical
with the electron density being greater around the more electronegative atom. Electron-rich (negatively charged) regions are shown
in blue; electron-poor (positively charged) regions are shown in red.
Bond Polarity
The polarity of a bond—the extent to which it is polar—is determined largely by the relative electronegativities of the bonded
atoms. Electronegativity (χ) was defined as the ability of an atom in a molecule or an ion to attract electrons to itself. Thus there is
a direct correlation between electronegativity and bond polarity. A bond is nonpolar if the bonded atoms have equal
electronegativities. If the electronegativities of the bonded atoms are not equal, however, the bond is polarized toward the more
electronegative atom. A bond in which the electronegativity of B (χ ) is greater than the electronegativity of A (χ ), for example,
B A
is indicated with the partial negative charge on the more electronegative atom:
less electronegative more electronegative
A − B
+ −
δ δ
One way of estimating the ionic character of a bond—that is, the magnitude of the charge separation in a polar covalent bond—is
to calculate the difference in electronegativity between the two atoms:
Δχ = χB − χA .
To predict the polarity of the bonds in Cl2, HCl, and NaCl, for example, we look at the electronegativities of the relevant atoms
(Table A2): χ = 3.16 , χ = 2.20, and χ = 0.93. Cl must be nonpolar because the electronegativity difference (Δχ) is zero;
Cl H Na 2
hence the two chlorine atoms share the bonding electrons equally. In NaCl, Δχ is 2.23. This high value is typical of an ionic
compound (Δχ ≥≈ 1.5 ) and means that the valence electron of sodium has been completely transferred to chlorine to form Na+
and Cl− ions. In HCl, however, Δχ is only 0.96. The bonding electrons are more strongly attracted to the more electronegative
chlorine atom, and so the charge distribution is
2.5.1.1 https://chem.libretexts.org/@go/page/294867
+ −
δ δ
H − Cl
Remember that electronegativities are difficult to measure precisely and different definitions produce slightly different numbers. In
practice, the polarity of a bond is usually estimated rather than calculated.
Bond polarity and ionic character increase with an increasing difference in electronegativity.
As with bond energies, the electronegativity of an atom depends to some extent on its chemical environment. It is therefore
unlikely that the reported electronegativities of a chlorine atom in NaCl, Cl , ClF , and HClO would be exactly the same.
2 5 4
Dipole Moments
The asymmetrical charge distribution in a polar substance such as HCl produces a dipole moment where Qr in meters (m). is
abbreviated by the Greek letter mu (μ ). The dipole moment is defined as the product of the partial charge Q on the bonded atoms
and the distance r between the partial charges:
μ = Qr (2.5.1.1)
where Q is measured in coulombs (C ) and r in meters. The unit for dipole moments is the debye (D):
−30
1 D = 3.3356 × 10 C ⋅m (2.5.1.2)
When a molecule with a dipole moment is placed in an electric field, it tends to orient itself with the electric field because of its
asymmetrical charge distribution (Figure 2.5.1.2).
Figure 2.5.1.2 : Molecules That Possess a Dipole Moment Partially Align Themselves with an Applied Electric Field In the absence
of a field (a), theHClmolecules are randomly oriented. When an electric field is applied (b), the molecules tend to align themselves
with the field, such that the positive end of the molecular dipole points toward the negative terminal and vice versa.
We can measure the partial charges on the atoms in a molecule such as HCl using Equation 2.5.1.1. If the bonding in HCl were
purely ionic, an electron would be transferred from H to Cl, so there would be a full +1 charge on the H atom and a full −1 charge
on the Cl atom. The dipole moment of HCl is 1.109 D, as determined by measuring the extent of its alignment in an electric field,
and the reported gas-phase H–Cl distance is 127.5 pm. Hence the charge on each atom is
μ
Q =
r
−30 1 pm
3.3356 × 10 C ⋅ m 1
= 1.109 D ( )( )( )
−12
1 D 127.8 pm 10 m
−20
= 2.901 × 10 C
By dividing this calculated value by the charge on a single electron (1.6022 × 10−19 C), we find that the electron distribution inHCl
is asymmetric and that effectively it appears that there is a net negative charge on the Cl of about −0.18, effectively corresponding
to about 0.18 e−. This certainly does not mean that there is a fraction of an electron on the Cl atom, but that the distribution of
electron probability favors the Cl atom side of the molecule by about this amount.
−20
2.901 × 10 C
−
= 0.1811 e
−19
1.6022 × 10 C
To form a neutral compound, the charge on the H atom must be equal but opposite. Thus the measured dipole moment of HCl
indicates that the H–Cl bond has approximately 18% ionic character (0.1811 × 100), or 82% covalent character. Instead of writing
HCl as
+ −
δ δ
H − Cl
we can therefore indicate the charge separation quantitatively as

+ −
0.18δ 0.18δ
H − Cl
Our calculated results are in agreement with the electronegativity difference between hydrogen and chlorine (χ H = 2.20 and
χCl= 3.16 ) so
χC l − χH = 0.96 (2.5.1.3)
This is a value well within the range for polar covalent bonds. We indicate the dipole moment by writing an arrow above the
molecule.Mathematically, dipole moments are vectors, and they possess both a magnitude and a direction. The dipole moment of a
molecule is the vector sum of the dipoles of the individual bonds. In HCl, for example, the dipole moment is indicated as follows:
The arrow shows the direction of electron flow by pointing toward the more electronegative atom.
A warning about Dipole Moment arrows
As the figure above shows, we represent dipole moments by an arrow with a length proportional to μ and pointing from the
positive charge to the negative charge. However, the opposite convention is still widely used especially among physicists.
The charge on the atoms of many substances in the gas phase can be calculated using measured dipole moments and bond
distances. Figure 2.5.1.2 shows a plot of the percent ionic character versus the difference in electronegativity of the bonded atoms
for several substances. According to the graph, the bonding in species such as N aC l and C sF is substantially less than 100%
(g) (g)
ionic in character. As the gas condenses into a solid, however, dipole–dipole interactions between polarized species increase the
charge separations. In the crystal, therefore, an electron is transferred from the metal to the nonmetal, and these substances behave
like classic ionic compounds. The data in Figure 2.5.1.2 show that diatomic species with an electronegativity difference of less
than 1.5 are less than 50% ionic in character, which is consistent with our earlier description of these species as containing polar
covalent bonds. The use of dipole moments to determine the ionic character of a polar bond is illustrated in Example 2.5.1.1.
Figure 2.5.1.2 : A Plot of the Percent Ionic Character of a Bond as Determined from Measured Dipole Moments versus the
Difference in Electronegativity of the Bonded Atoms. In the gas phase, even CsF, which has the largest possible difference in
electronegativity between atoms, is not 100% ionic. Solid CsF, however, is best viewed as 100% ionic because of the additional
electrostatic interactions in the lattice.
Example 2.5.1.1: percent ionic character
In the gas phase, NaCl has a dipole moment of 9.001 D and an Na–Cl distance of 236.1 pm. Calculate the percent ionic
character in NaCl.
Given: chemical species, dipole moment, and internuclear distance
Asked for: percent ionic character
Strategy:
A. Compute the charge on each atom using the information given and Equation 2.5.1.1
B. Find the percent ionic character from the ratio of the actual charge to the charge of a single electron.
Solution:
A The charge on each atom is given by
μ
Q =
r
−30
3.3356 × 10 C ⋅ m 1 1 pm
= 9.001 D ( )( )( )
−12
236.1 pm 10 m
1 D
−19
= 1.272 × 10 C
Thus NaCl behaves as if it had charges of 1.272 × 10−19 C on each atom separated by 236.1 pm.
B The percent ionic character is given by the ratio of the actual charge to the charge of a single electron (the charge expected
for the complete transfer of one electron):
−19
1.272 × 10 C
ionic character = ( ) (100)
−19
1.6022 × 10 C
= 79.39% ≃ 79%
Exercise 2.5.1.1
In the gas phase, silver chloride (AgCl) has a dipole moment of 6.08 D and an Ag–Cl distance of 228.1 pm. What is the
percent ionic character in silver chloride?
Answer
55.5%
Summary
Bond polarity and ionic character increase with an increasing difference in electronegativity.
μ = Qr
Compounds with polar covalent bonds have electrons that are shared unequally between the bonded atoms. The polarity of such a
bond is determined largely by the relative electronegativites of the bonded atoms. The asymmetrical charge distribution in a polar
substance produces a dipole moment, which is the product of the partial charges on the bonded atoms and the distance between
them.

Modified by Joshua Halpern (Howard University)
2.5.1: Molecular Shape and Molecular Polarity is shared under a CC BY-NC-SA license and was authored, remixed, and/or curated by LibreTexts.
Valence bond (VB) theory gave us a qualitative picture of chemical bonding, which was useful for predicting the shapes of
molecules, bond strengths, etc. It fails to describe some bonding situations accurately because it ignores the wave nature of the
electrons. Molecular orbital (MO) theory has the potential to be more quantitative. With it we can also get a picture of where the
electrons are in the molecule, as shown in the image at the right. This can help us understand patterns of bonding and reactivity that
are otherwise difficult to explain.
Although MO theory in principle gives us a way to calculate the energies and wavefunctions of electrons in molecules very
precisely, usually we settle for simplified models. These models do not give very accurate orbital and bond energies, but they do
explain concepts such as resonance (e.g., in the ferrocene, C10H10Fe, molecule) that are hard to represent otherwise. We can get
more accurate energies from MO theory using computational methods. While MO theory is more correct than VB theory and can
be very accurate in predicting the properties of molecules, it is also rather complicated even for fairly simple molecules. For
example, you should be able to draw the VB pictures for CO, NH3, and benzene, but we will find that these are increasingly
challenging with MO theory.
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Molecular orbital theory involves solving (approximately) the Schrödinger equation for the electrons in a molecule. To review from
Chapter 1, this is a differential equation in which the first and second terms on the right represent the kinetic and potential energies:
2
ℏ
2
Eψ = − ∇ ψ +V ψ (2.5.3.1)
2μ
While the Schrödinger equation can be solved analytically for the hydrogen atom, the potential energy function V becomes more
complicated - and the equation can then only be solved numerically - when there are many (mutually repulsive) electrons in a
molecule. So as a first approximation we will assume that the s, p, d, f, etc. orbitals of the atoms that make up the molecule are
good solutions to the Schrödinger equation. We can then allow these wavefunctions to interfere constructively and destructively as
we bring the atoms together to make bonds. In this way, we use the atomic orbitals (AO) as our basis for constructing MO's.
LCAO-MO = linear combination of atomic orbitals. In physics, this is called this the tight binding approximation.
We have actually seen linear combinations of atomic orbitals before when we constructed hybrid orbitals. The basic rules we
developed for hybridization also apply here: orbitals are added with scalar coefficients (c) in such a way that the resulting orbitals
are orthogonal and normalized. The difference is that in the MO case, the atomic orbitals come from different atoms.
The linear combination of atomic orbitals always gives back the same number of molecular orbitals. So if we start with two atomic
orbitals (e.g., an s and a pz orbital as shown in Fig. 2.5.3.1), we end up with two molecular orbitals. When atomic orbitals add in
phase, we get constructive interference and a lower energy orbital. When they add out of phase, we get a node and the resulting
orbital has higher energy. The lower energy MOs are bonding and higher energy MOs are antibonding. Note that the antibonding
orbital is raised in energy MORE than the bonding orbital is lowered in energy. A mnemonic for remembering this is
ABIMABTBIB (a-BIM-ab-ta-bib) which stands for AntiBonding Is More AntiBonding Than Bonding Is Bonding.
Figure 2.5.3.1 : Sigma bonding and antibonding combinations of an s and p orbital

Molecular orbitals are also called wavefunctions (ψ), because they are solutions to the Schrödinger equation for the molecule. The
atomic orbitals (also called basis functions) are labeled as φ's, for example, φ1s and φ3pz or simply as φ1and φ2.
In principle, we need to solve the Schrödinger equation for all the orbitals in a molecule, and then fill them up with pairs of
electrons as we do for the orbitals in atoms. In practice we are really interested only in the MOs that derive from the valence
orbitals of the constituent atoms, because these are the orbitals that are involved in bonding. We are especially interested in the
frontier orbitals, i.e., the highest occupied molecular orbital (the HOMO) and the lowest unoccupied molecular orbital (the
LUMO). Filled orbitals that are much lower in energy (i.e., core orbitals) do not contribute to bonding, and empty orbitals at higher
energy likewise do not contribute. Those orbitals are however important in photochemistry and spectroscopy, which involve
electronic transitions from occupied to empty orbitals.
As an example of the LCAO-MO approach we can construct two MO's (ψ1 and ψ2) of the HCl molecule from two AO's φ1and φ2
(Fig. 2.1.1). To make these two linear combinations, we write:
Ψ1 = c1 φ1 + c2 φ2 (2.5.3.2)
and
Ψ2 = c1 φ1 − c2 φ2 (2.5.3.3)
The coefficients c1 and c2 will be equal (or nearly so) when the two AOs from which they are constructed are the same, e.g., when
two hydrogen 1s orbitals combine to make bonding and antibonding MOs in H2. They will be unequal when there is an energy
difference between the AOs, for example when a hydrogen 1s orbital and a chlorine 3p orbital combine to make a polar H-Cl bond.
Nodes:
The wavefunctions φ and ψ are amplitudes that are related to the probability of finding the electron at some point in space. They
have lobes with (+) or (-) signs, which we indicate by shading or color. Wherever the wavefunction changes sign we have a node.
As you can see in Fig. 2.5.3.1, nodes in MOs result from destructive interference of (+) and (-) wavefunctions. Generally, the more
nodes, the higher the energy of the orbital.
In the example above we have drawn a simplified picture of the Cl 3pz orbital and the resulting MOs, leaving out the radial node.
Recall that 2p orbitals have no radial nodes, 3p orbitals have one, as illustrated in Fig. 2.5.3.3. 4p orbitals have two radial nodes,
and so on. The MOs we make by combining the AOs have these nodes too.
Figure 2.5.3.3 : Nodal structure of 2p and 3p orbitals
Normalization:
We square the wave functions to get probabilities, which are always positve or zero. So if an electron is in orbital φ1, the
probability of finding it at point xyz is the square[1] of φ1(x,y,z). The total probability does not change when we combine AOs to
make MOs, so for the simple case of combining φ1 and φ2 to make ψ1and ψ2,
2 2 2 2
Ψ +Ψ =φ +φ (2.5.3.4)
1 2 1 2
Overlap integral:
The spatial overlap between two atomic orbitals φ1 and φ2 is described by the overlap integral S,
S12 = ∫ φ1 ∗ φ2 dτ (2.5.3.5)
where the integration is over all space dτ = dxdydz .
Figure 2.5.3.4 : The wavefunctions of atomic orbitals decrease exponentially with distance. Orbital overlap is non-zero when two
atoms are close together, as illustrated for 1s orbitals in the upper figure. The lower figure shows orbitals that are too far away to
interact. In this case both S and β are close to zero.
Energies of bonding and antibonding MOs:

The energies of bonding and antibonding orbitals depend strongly on the distance between atoms. This is illustrated in Fig. 2.1.5
for the hydrogen molecule, H2. At very long distances, there is essentially no difference in energy between the in-phase and out-of-
phase combinations of H 1s orbitals. As they get closer, the in-phase (bonding) combination drops in energy because electrons are
shared between the two positively charged nuclei. The energy reaches a minimum at the equilibrium bond distance (0.74 Å) and
then rises again as the nuclei get closer together. The antibonding combination has a node between the nuclei so its energy rises
continuously as the atoms are brought together.
Figure 2.5.3.5 : Energy as a function of distance for the bonding and antibonding orbitals of the H2 molecule
At the equilibrium bond distance, the energies of the bonding and antibonding molecular orbitals (ψ1, ψ2) are lower and higher,
respectively, than the energies of the atomic basis orbitals φ1 and φ2. This is shown in Fig. 2.5.3.6 for the MO’s of the H2 molecule.
Figure 2.5.3.6 : Molecular orbital energy diagram for the H2 molecule

The energy of an electron in one of the atomic orbitals is α, the Coulomb integral.
α =∫ φ1 H φ1 dτ (2.5.3.6)
where H is the Hamiltonian operator. Essentially, α represents the ionization energy of an electron in atomic orbital φ1 or φ2.
The energy difference between an electron in the AO’s and the MO’s is determined by the exchange integral β,
β =∫ φ1 H φ2 dτ (2.5.3.7)
β is an important quantity, because it tells us about the bonding energy of the molecule, and also the difference in energy between
bonding and antibonding orbitals. Calculating β is not straightforward for multi-electron molecules because we cannot solve the
Schrödinger equation analytically for the wavefunctions. We can however make some approximations to calculate the energies and
wavefunctions numerically. In the Hückel approximation, which can be used to obtain approximate solutions for π molecular
orbitals in organic molecules, we simplify the math by taking S=0 and setting H=0 for any p-orbitals that are not adjacent to each
other. The extended Hückel method,[2] developed by Roald Hoffmann, and other semi-empirical methods can be used to rapidly
obtain relative orbital energies, approximate wavefunctions, and degeneracies of molecular orbitals for a wide variety of molecules
and extended solids. More sophisticated ab initio methods are now readily available in software packages and can be used to
compute accurate orbital energies for molecules and solids.
We can get the coefficients c1 and c2 for the hydrogen molecule by applying the normalization criterion:
−−−−−−−
Φ1 = (φ1 + φ2 )/(√ 2(1 + S) )(bonding orbital) (2.5.3.8)
and
−−−−−−−
Φ2 = (φ1 − φ2 )/(√ 2(1 − S) )(antibonding orbital) (2.5.3.9)
In the case where S≈0, we can eliminate the 1-S terms and both coefficients become 1/√2
Note that the bonding orbital in the MO diagram of H2 is stabilized by an energy β/1+S and the antibonding orbital is destabilized
by β/1-S. That is, the antibonding orbital goes up in energy more than the bonding orbital goes down. This means that H2 (ψ12ψ20)
is energetically more stable than two H atoms, but He2 with four electrons (ψ12ψ22) is unstable relative to two He atoms.
Bond order: In any MO diagram, the bond order can be calculated as ½ ( # of bonding electrons - # of antibonding electrons). For
H2 the bond order is 1, and for He2the bond order is zero.
Heteronuclear case (e.g., HCl) - Polar bonds

Here we introduce an electronegativity difference between the two atoms making the chemical bond. The energy of an electron in
the H 1s orbital is higher (it is easier to ionize) than the electron in the chlorine 3pz orbital. This results in a larger energy difference
between the resulting molecular orbitals ψ1 and ψ2, as shown in Fig. 2.5.3.7. The bigger the electronegativity difference between
atomic orbitals (the larger Δα is) the more “φ2 character” the bonding orbital has, i.e., the more it resembles the Cl 3pz orbital in
this case. This is consistent with the idea that H-Cl has a polar single bond: the two electrons reside in a bonding molecular orbital
that is primarily localized on the Cl atom.
Figure 2.5.3.7 : Molecular orbital energy diagram for the HCl molecule
The antibonding orbital (empty) has more H-character. The bond order is again 1 because there are two electrons in the bonding
orbital and none in the antibonding orbital.
Extreme case - Ionic bonding (NaF): very large Δα
In this case, there is not much mixing between the AO’s because their energies are far apart (Fig. 2.5.3.8). The two bonding
electrons are localized on the F atom , so we can write the molecule as Na+F-. Note that if we were to excite an electron from ψ1 to
ψ2 using light, the resulting electronic configuration would be (ψ11ψ21) and we would have Na0F0. This is called a charge transfer
transition.
Figure 2.5.3.8 : Molecular orbital energy diagram illustrating ionic bonding in the NaF molecule
Summary of molecular orbital theory so far:

• Add and subtract AO wavefunctions to make MOs. Two AOs → two MOs. More generally, the total number of MOs equals the
number of AO basis orbitals.
• We showed the simplest case (only two basis orbitals). More accurate calculations use a much larger basis set (more AOs) and
solve for the matrix of c’s that gives the lowest total energy, using mathematically friendly approximations of the potential energy
function that is part of the Hamiltonian operator H.
• More nodes → higher energy MO
• Bond order = ½ ( # of bonding electrons - # of antibonding electrons)
• Bond polarity emerges in the MO picture as orbital “character.”
• AOs that are far apart in energy do not interact much when they combine to make MOs.
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The MO picture for a molecule gets complicated when many valence AOs are involved. We can simplify the problem enormously
by noting (without proof here) that orbitals of different symmetry with respect to the molecule do not interact. The symmetry
operations of a molecule (which can include rotations, mirror planes, inversion centers, etc.), and the symmetry classes of bonds
and orbitals in molecules, can be rigorously defined according to group theory. Here we will take a simple approach to this
problem based on our intuitive understanding of the symmetry of three-dimensional objects as illustrated in Fig. 2.5.4.1.
Figure 2.5.4.1 : Example of σ symmetry.

AO’s must have the same nodal symmetry (as defined by the molecular symmetry operations), or their overlap is zero.
For example, in the HCl molecule, there is a unique symmetry axis →, which is typically defined as the Cartesian z-axis, as shown
in Fig. 2.5.4.2.
Figure 2.5.4.2 : Orbitals of σ and π symmetry do not interact.

We can see from this figure that the H 1s orbital is unchanged by a 180° rotation about the bond axis. However, the same rotation
inverts the sign of the Cl 3pywavefunction. Because these two orbitals have different symmetries, the Cl 3py orbital is nonbonding
and doesn’t interact with the H 1s. The same is true of the Cl 3pxorbital. The px and py orbitals have π symmetry (nodal plane
containing the bonding axis) and are labeled πnb in the MO energy level diagram, Fig. 2.5.4.3. In contrast, the H 1s and Cl 3pz
orbitals both have σ symmetry, which is also the symmetry of the clay pot shown in Fig. 2.5.4.1. Because these orbitals have the
same symmetry (in the point group of the molecule), they can make the bonding and antibonding combinations shown in Fig. 2.1.1.
The MO diagram of HCl that includes all the valence orbitals of the Cl atom is shown in Fig. 2.5.4.3. Two of the Cl valence
orbitals (3px and 3py) have the wrong symmetry to interact with the H 1s orbital. The Cl 3s orbital has the same (σ) symmetry as H
1s, but it is much lower in energy so there is little orbital interaction. The energy of the Cl 3s orbital is thus affected only slightly by
forming the molecule. The pairs of electrons in the πnb and σnb orbitals are therefore non-bonding.
Figure 2.5.4.3 : Energy level diagram of the HCl molecule showing MOs derived from the valence AOs.
Note that the MO result in Fig. 2.5.4.3 (1 bond and three pairs of nonbonding electrons) is the same as we would get from valence
bond theory for HCl. The nonbonding orbitals are localized on the Cl atom, just as we would surmise from the valence bond
picture.
In order to differentiate it from the σ bonding orbital, the σ antibonding orbital, which is empty in this case, is designated with an
asterisk.
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Learning Objectives
Make sure you thoroughly understand the following essential ideas
Describe the essential difference between a sigma and a pi molecular orbital.
Define bond order, and state its significance.
Construct a "molecular orbital diagram" of the kind shown in this lesson for a simple diatomic molecule, and indicate
whether the molecule or its positive and negative ions should be stable.
Molecular Orbital Diagrams

This scheme of bonding and antibonding orbitals is usually depicted by a molecular orbital diagram such as the one shown here for
the dihydrogen ion H2+. Atomic valence electrons (shown in boxes on the left and right) fill the lower-energy molecular orbitals
before the higher ones, just as is the case for atomic orbitals. Thus, the single electron in this simplest of all molecules goes into the
bonding orbital, leaving the antibonding orbital empty.
Since any orbital can hold a maximum of two electrons, the bonding orbital in H2+is only half-full. This single electron is
nevertheless enough to lower the potential energy of one mole of hydrogen nuclei pairs by 270 kJ— quite enough to make them
stick together and behave like a distinct molecular species. Although H2+ is stable in this energetic sense, it happens to be an
extremely reactive molecule— so much so that it even reacts with itself, so these ions are not commonly encountered in everyday
chemistry.
Dihydrogen
If one electron in the bonding orbital is conducive to bond formation, might two electrons be even better? We can arrange this by
combining two hydrogen atoms-- two nuclei, and two electrons. Both electrons will enter the bonding orbital, as depicted in the
Figure.
We recall that one electron lowered the potential energy of the two nuclei by 270 kJ/mole, so we might expect two electrons to
produce twice this much stabilization, or 540 kJ/mole.
Bond order is defined as the difference between the number of electron pairs occupying bonding and nonbonding orbitals in the
molecule. A bond order of unity corresponds to a conventional "single bond".
Experimentally, one finds that it takes only 452 kJ to break apart a mole of hydrogen molecules. The reason the potential energy
was not lowered by the full amount is that the presence of two electrons in the same orbital gives rise to a repulsion that acts
against the stabilization. This is exactly the same effect we saw in comparing the ionization energies of the hydrogen and helium
atoms.
Dihelium
With two electrons we are still ahead, so let’s try for three. The dihelium positive ion is a three-electron molecule. We can think of
it as containing two helium nuclei and three electrons. This molecule is stable, but not as stable as dihydrogen; the energy required
to break He2+ is 301 kJ/mole. The reason for this should be obvious; two electrons were accommodated in the bonding orbital, but
the third electron must go into the next higher slot— which turns out to be the sigma antibonding orbital. The presence of an
electron in this orbital, as we have seen, gives rise to a repulsive component which acts against, and partially cancels out, the
attractive effect of the filled bonding orbital.
Taking our building-up process one step further, we can look at the possibilities of combining to helium atoms to form dihelium.
You should now be able to predict that He2 cannot be a stable molecule; the reason, of course, is that we now have four electrons—
two in the bonding orbital, and two in the antibonding orbital. The one orbital almost exactly cancels out the effect of the other.
Experimentally, the bond energy of dihelium is only .084 kJ/mol; this is not enough to hold the two atoms together in the presence
of random thermal motion at ordinary temperatures, so dihelium dissociates as quickly as it is formed, and is therefore not a distinct
chemical species.
Diatomic molecules containing second-row atoms

The four simplest molecules we have examined so far involve molecular orbitals that derived from two 1s atomic orbitals. If we
wish to extend our model to larger atoms, we will have to contend with higher atomic orbitals as well. One greatly simplifying
principle here is that only the valence-shell orbitals need to be considered. Inner atomic orbitals such as 1s are deep within the atom
and well-shielded from the electric field of a neighboring nucleus, so that these orbitals largely retain their atomic character when
bonds are formed.
Dilithium
For example, when lithium, whose configuration is 1s22s1, bonds with itself to form Li2, we can forget about the 1s atomic orbitals
and consider only the σ bonding and antibonding orbitals. Since there are not enough electrons to populate the antibonding orbital,
the attractive forces win out and we have a stable molecule.
The bond energy of dilithium is 110 kJ/mole; notice that this value is less than half of the 270 kJ bond energy in dihydrogen, which
also has two electrons in a bonding orbital. The reason, of course, is that the 2s orbital of Li is much farther from its nucleus than is
the 1s orbital of H, and this is equally true for the corresponding molecular orbitals. It is a general rule, then, that the larger the
parent atom, the less stable will be the corresponding diatomic molecule.
Lithium hydride
All the molecules we have considered thus far are homonuclear; they are made up of one kind of atom. As an example of a
heteronuclear molecule, let’s take a look at a very simple example— lithium hydride. Lithium hydride is a stable, though highly
reactive molecule. The diagram shows how the molecular orbitals in lithium hydride can be related to the atomic orbitals of the
parent atoms. One thing that makes this diagram look different from the ones we have seen previously is that the parent atomic
orbitals have widely differing energies; the greater nuclear charge of lithium reduces the energy of its 1s orbital to a value well
below that of the 1s hydrogen orbital.
There are two occupied atomic orbitals on the lithium atom, and only one on the hydrogen. With which of the lithium orbitals does
the hydrogen 1s orbital interact? The lithium 1s orbital is the lowest-energy orbital on the diagram. Because this orbital is so small
and retains its electrons so tightly, it does not contribute to bonding; we need consider only the 2s orbital of lithium which
combines with the 1s orbital of hydrogen to form the usual pair of sigma bonding and antibonding orbitals. Of the four electrons in
lithium and hydrogen, two are retained in the lithium 1s orbital, and the two remaining ones reside in the σ orbital that constitutes
the Li–H covalent bond.
The resulting molecule is 243 kJ/mole more stable than the parent atoms. As we might expect, the bond energy of the heteronuclear
molecule is very close to the average of the energies of the corresponding homonuclear molecules. Actually, it turns out that the
correct way to make this comparison is to take the geometric mean, rather than the arithmetic mean, of the two bond energies. The
geometric mean is simply the square root of the product of the two energies.
The geometric mean of the H2 and Li2 bond energies is 213 kJ/mole, so it appears that the lithium hydride molecule is 30 kJ/mole
more stable than it “is supposed” to be. This is attributed to the fact that the electrons in the 2σ bonding orbital are not equally
shared between the two nuclei; the orbital is skewed slightly so that the electrons are attracted somewhat more to the hydrogen
atom. This bond polarity, which we considered in some detail near the beginning of our study of covalent bonding, arises from the
greater electron-attracting power of hydrogen— a consequence of the very small size of this atom. The electrons can be at a lower
potential energy if they are slightly closer to the hydrogen end of the lithium hydride molecule. It is worth pointing out, however,
that the electrons are, on the average, also closer to the lithium nucleus, compared to where they would be in the 2s orbital of the
isolated lithium atom. So it appears that everyone gains and no one loses here!

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π orbitals
The molecules we have considered thus far are composed of atoms that have no more than four electrons each; our molecular
orbitals have therefore been derived from s-type atomic orbitals only. If we wish to apply our model to molecules involving larger
atoms, we must take a close look at the way in which p-type orbitals interact as well. Although two atomic p orbitals will be
expected to split into bonding and antibonding orbitals just as before, it turns out that the extent of this splitting, and thus the
relative energies of the resulting molecular orbitals, depend very much on the nature of the particular p orbital that is involved.
You will recall that there are three possible p orbitals for any value of the principal quantum number. You should also recall that p
orbitals are not spherical like s orbitals, but are elongated, and thus possess definite directional properties. The three p orbitals
correspond to the three directions of Cartesian space, and are frequently designated px, py, and pz, to indicate the axis along which
the orbital is aligned. Of course, in the free atom, where no coordinate system is defined, all directions are equivalent, and so are
the p orbitals. But when the atom is near another atom, the electric field due to that other atom acts as a point of reference that
defines a set of directions. The line of centers between the two nuclei is conventionally taken as the x axis. If this direction is
represented horizontally on a sheet of paper, then the y axis is in the vertical direction and the z axis would be normal to the page.
These directional differences lead to the formation of two different classes of molecular orbitals. The above figure shows how two
px atomic orbitals interact. In many ways the resulting molecular orbitals are similar to what we got when s atomic orbitals
combined; the bonding orbital has a large electron density in the region between the two nuclei, and thus corresponds to the lower
potential energy. In the out-of-phase combination, most of the electron density is away from the internuclear region, and as before,
there is a surface exactly halfway between the nuclei that corresponds to zero electron density. This is clearly an antibonding
orbital— again, in general shape, very much like the kind we saw in hydrogen and similar molecules. Like the ones derived from s-
atomic orbitals, these molecular orbitals are σ (sigma) orbitals.
Sigma orbitals are cylindrically symmetric with respect to the line of centers of the nuclei; this means that if you could look down
this line of centers, the electron density would be the same in all directions.
orbitals, we get the bonding and antibonding pairs that we would expect, but the resulting molecular orbitals have a different
symmetry: rather than being rotationally symmetric about the line of centers, these orbitals extend in both perpendicular directions
from this line of centers. Orbitals having this more complicated symmetry are called π (pi) orbitals. There are two of them, πy and
πz differing only in orientation, but otherwise completely equivalent.
The different geometric properties of the π and σ orbitals causes the latter orbitals to split more than the π orbitals, so that the σ*
antibonding orbital always has the highest energy. The σ bonding orbital can be either higher or lower than the π bonding orbitals,
depending on the particular atom.
Second-Row Diatomics
If we combine the splitting schemes for the 2s and 2p orbitals, we can predict bond order in all of the diatomic molecules and ions
composed of elements in the first complete row of the periodic table. Remember that only the valence orbitals of the atoms need be
considered; as we saw in the cases of lithium hydride and dilithium, the inner orbitals remain tightly bound and retain their
localized atomic character.
Valence bond theory fails for a number of the second row diatomics, most famously for O2, where it predicts a diamagnetic (no
unpaired electrons), doubly bonded molecule with four lone pairs. O2 does have a double bond, but it is paramagneric (having two
unpaired electrons in the ground state), a property that can be explained by the MO picture. We can construct the MO energy level
diagrams for these molecules as follows:
We get the simpler diatomic MO picture on the right when the 2s and 2p AOs are well separated in energy, as they are for O, F, and
Ne. The picture on the left results from mixing of the σ2s and σ2p MO’s, which are close in energy for Li2, Be2, B2, C2, and N2. The
effect of this mixing is to push the σ2s* down in energy and the σ2pup, to the point where the pπ orbitals are below the σ2p.
Asymmetric diatomic molecules and ions such as CO, NO, and NO+ also have the ordering of energy levels shown on the left
because of sp mixing. A good animation of the molecular orbitals in the CO molecule can be found on the University of Liverpool
Structure and Bonding website.
Dicarbon
Carbon has four outer-shell electrons, two 2s and two 2p. For two carbon atoms, we therefore have a total of eight electrons, which
can be accommodated in the first four molecular orbitals. The lowest two are the 2s-derived bonding and antibonding pair, so the
“first” four electrons make no net contribution to bonding. The other four electrons go into the pair of pibonding orbitals, and there
are no more electrons for the antibonding orbitals— so we would expect the dicarbon molecule to be stable, and it is. (But being
extremely reactive, it is known only in the gas phase.)
You will recall that one pair of electrons shared between two atoms constitutes a “single” chemical bond; this is Lewis’ original
definition of the covalent bond. In C2 there are two paris of electrons in the π bonding orbitals, so we have what amounts to a
double bond here; in other words, the bond order in dicarbon is two.
Dioxygen
The electron configuration of oxygen is 1s22s22p4. In O2, therefore, we need to accommodate twelve valence electrons (six from
each oxygen atom) in molecular orbitals. As you can see from the diagram, this places two electrons in antibonding orbitals. Each
of these electrons occupies a separate π* orbital because this leads to less electron-electron repulsion (Hund's Rule).
The bond energy of molecular oxygen is 498 kJ/mole. This is smaller than the 945 kJ bond energy of N2— not surprising,
considering that oxygen has two electrons in an antibonding orbital, compared to nitrogen’s one.
The two unpaired electrons of the dioxygen molecule give this substance an unusual and distinctive property: O2 is paramagnetic.
The paramagnetism of oxygen can readily be demonstrated by pouring liquid O2 between the poles of a strong permanent magnet;
the liquid stream is trapped by the field and fills up the space between the poles.
Since molecular oxygen contains two electrons in an antibonding orbital, it might be possible to make the molecule more stable by
removing one of these electrons, thus increasing the ratio of bonding to antibonding electrons in the molecule. Just as we would
expect, and in accord with our model, O2+ has a bond energy higher than that of neutral dioxygen; removing the one electron
actually gives us a more stable molecule. This constitutes a very good test of our model of bonding and antibonding orbitals. In the
same way, adding an electron to O2 results in a weakening of the bond, as evidenced by the lower bond energy of O2–. The bond
energy in this ion is not known, but the length of the bond is greater, and this is indicative of a lower bond energy. These two
dioxygen ions, by the way, are highly reactive and can be observed only in the gas phase.
Why don't we get sp-orbital mixing for O2 and F2? The reason has to do with the energies of the orbitals, which are not drawn to
scale in the simple picture above. As we move across the second row of the periodic table from Li to F, we are progressively adding
protons to the nucleus. The 2s orbital, which has finite amplitude at the nucleus, "feels" the increased nuclear charge more than the
2p orbital. This means that as we progress across the periodic table (and also, as we will see later, when we move down the periodic
table), the energy difference between the s and p orbitals increases. As the 2s and 2p energies become farther apart in energy,
there is less interaction between the orbitals (i.e., less mixing).
A plot of orbital energies is shown below. Because of the very large energy difference between the 1s and 2s/2p orbitals, we plot
them on different energy scales, with the 1s to the left and the 2s/2p to the right. For elements at the left side of the 2nd period (Li,
Be, B) the 2s and 2p energies are only a few eV apart. The energy difference becomes very large - more than 20 electron volts - for
O and F. Since single bond energies are typically about 3-4 eV, this energy difference would be very large on the scale of our MO
diagrams. For all the elements in the 2nd row of the periodic table, the 1s (core) orbitals are very low in energy compared to the
2s/2p (valence) orbitals, so we don't need to consider them in drawing our MO diagrams.
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MO’s are filled from the bottom according to the Aufbau principle and Hund’s rule, as we learned for atomic orbitals.
Question: what is the quantum mechanical basis of Hund’s rule?
Consider the case of two degenerate orbitals, such as the π or π* orbitals in a second-row diatomic molecule. If these orbitals
each contain one electron, their spins can be parallel (as preferred by Hund's rule) or antiparallel. The Pauli exclusion principle
says that no two electrons in an orbital can have the same set of quantum numbers (n, l, ml, ms). That means that, in the parallel
case, the Pauli principle prevents the electrons from ever visiting each other's orbitals. In the antiparallel case, they are free to
come and go because they have different ms quantum numbers. However, having two electrons in the same orbital is
energetically unfavorable because like charges repel. Thus, the parallel arrangement, thanks to the Pauli principle, has lower
energy.
For O2 (12 valence electrons), we get the MO energy diagram below. The shapes of the molecular orbitals are shown at the right.
This energy ordering of MOs correctly predicts two unpaired electrons in the π* orbital and a net bond order of two (8 bonding
electrons and 4 antibonding electrons). This is consistent with the experimentally observed paramagnetism of the oxygen molecule.
Other interesting predictions of the MO theory for second-row diatomics are that the C2 molecule has a bond order of 2 and that the
B2 molecule has two unpaired electrons (both verified experimentally).
We can also predict (using the O2, F2, Ne2 diagram above) that NO has a bond order of 2.5, and CO has a bond order of 3.
The symbols "g" and "u" in the orbital labels, which we only include in the case of centrosymmetric molecules, refer to their
symmetry with respect to inversion. Gerade (g) orbitals are symmetric, meaning that inversion through the center leaves the orbital
unchanged. Ungerade (u) means that the sign of the orbital is reversed by the inversion operation. Because g and u orbitals have
different symmetries, they have zero overlap with each other. As we will see below, factoring orbitals according to g and u
symmetry simplifies the task of constructing molecular orbitals in more complicated molecules, such as butadiene and benzene.
The orbital shapes shown above were computed using a one-electron model of the molecule, as we did for hydrogen-like AOs to
get the shapes of s, p, and d-orbitals. To get accurate MO energies and diagrams for multi-electron molecules (i.e. all real
molecules), we must include the fact that electrons are “correlated,” i.e. that they avoid each other in molecules because of their
negative charge. This problem cannot be solved analytically, and is solved approximately in numerical calculations by using
density functional theory (DFT)
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2.5.8: δ orbitals
Inorganic compounds use s, p, d and f orbitals to make bonding and antibonding combinations. These combinations result in σ, π,
and δ bonds (and antibonds). The previous sections presented σ and π bonds. In inorganic chemistry, π bonds can be made from p-
and/or d-orbitals. δ bonds are more rare and occur by face-to-face overlap of d-orbitals, as in the ion Re2Cl82-. The fact that the Cl
atoms are eclipsed in this anion is evidence of δ bonding.
Figure 2.5.8.1 : The octachlorodirhenate(III) anion, [Re2Cl8]2−, which has a quadruple Re-Re bond.[3]
Some possible σ (top row), π (bottom row), and δ bonding combinations (right) of s, p, and d orbitals are sketched below. In each
case, we can make bonding or antibonding combinations, depending on the signs of the AO wavefunctions. Because pπ-pπ bonding
involves sideways overlap of p-orbitals, it is most commonly observed with second-row elements (C, N, O). π-bonded compounds
of heavier elements are rare because the larger cores of the atoms prevent good π-overlap. For this reason, compounds containing
C=C double bonds are very common, but those with Si=Si bonds are rare. This does not mean that there is no π-bonding in
inorganic chemistry and we will further examine this in a later section. While known, δ bonds are generally quite weak compared
to σ and π bonds. Compounds with metal-metal δ bonds occur in the middle of the transition series.
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In general chemistry we learned that bonding between atoms can classified as range of possible bonding between ionic bonds
(fully charge transfer) and covalent bonds (fully shared electrons). When two atoms of slightly differing electronegativities come
together to form a covalent bond, one atom attracts the electrons more than the other; this is called a polar covalent bond. However,
simple “ionic” and “covalent” bonding are idealized concepts and most bonds exist on a two-dimensional continuum described by
the van Arkel-Ketelaar Triangle (Figure 2.6.1).
Figure 2.6.1 : van Arkel-Ketelaar Triangle plots the difference in electronegativity (Δχ) and the average electronegativity in a bond
(∑ χ ). the top region is where bonds are mostly ionic, the lower left region is where bonding is metallic, and the lower right region
is where the bonding is covalent.
Bond triangles or van Arkel–Ketelaar triangles (named after Anton Eduard van Arkel and J. A. A. Ketelaar) are triangles used for
showing different compounds in varying degrees of ionic, metallic and covalent bonding. In 1941 van Arkel recognized three
extreme materials and associated bonding types. Using 36 main group elements, such as metals, metalloids and non-metals, he
placed ionic, metallic and covalent bonds on the corners of an equilateral triangle, as well as suggested intermediate species. The
bond triangle shows that chemical bonds are not just particular bonds of a specific type. Rather, bond types are interconnected and
different compounds have varying degrees of different bonding character (for example, polar covalent bonds).
A1 What is the van Arkel-Ketelaar Trian…

Trian…
Video 2.6.1 : What is the van Arkel-Ketelaar Triangle of Bonding?

Using electronegativity - two compound average electronegativity on x-axis of Figure 2.6.1.
χA + χB
∑χ = (2.6.1)
2
and electronegativity difference on y-axis,

Δχ = | χA − χB | (2.6.2)
we can rate the dominant bond between the compounds. On the right side of Figure 2.6.1 (from ionic to covalent) should be
compounds with varying difference in electronegativity. The compounds with equal electronegativity, such as Cl (chlorine) are
2
placed in the covalent corner, while the ionic corner has compounds with large electronegativity difference, such as NaCl (table
salt). The bottom side (from metallic to covalent) contains compounds with varying degree of directionality in the bond. At one
extreme is metallic bonds with delocalized bonding and at the other are covalent bonds in which the orbitals overlap in a particular
direction. The left side (from ionic to metallic) is meant for delocalized bonds with varying electronegativity difference.
The Three Extremes in bonding

In general:
Metallic bonds have low Δχ and low average ∑ χ.
Ionic bonds have moderate-to-high Δχ and moderate values of average ∑ χ.
Covalent bonds have moderate to high average ∑ χ and can exist with moderately low Δχ.
Example 2.6.1
Use the tables of electronegativities and Figure 2.6.1 to estimate the following values
difference in electronegativity (Δχ)
average electronegativity in a bond (∑ χ)
percent ionic character
likely bond type
for the selected compounds:
a. AsH (e.g., in arsine AsH )
b. SrLi
c. KF.
Solution
a: AsH
The electronegativity of As is 2.18
The electronegativity of H is 2.22
Using Equations 2.6.1 and 2.6.2:
χA + χB
∑χ =
2
2.18 + 2.22
=
2
= 2.2
Δχ = χA − χB
= 2.18 − 2.22
= 0.04
From Figure 2.6.1, the bond is fairly nonpolar and has a low ionic character (10% or less)
The bonding is in the middle of a covalent bond and a metallic bond
b: SrLi
The electronegativity of Sr is 0.95
The electronegativity of Li is 0.98
χA + χB
∑χ =
2
0.95 + 0.98
=
2
= 0.965
Δχ = χA − χB
= 0.98 − 0.95
= 0.025
From Figure 2.6.1, the bond is fairly nonpolar and has a low ionic character (~3% or less)
The bonding is likely metallic.
c: KF
The electronegativity of K is 0.82
The electronegativity of F is 3.98
χA + χB
∑χ =
2
0.82 + 3.98
=
2
= 2.4
Δχ = χA − χB
= |0.82 − 3.98|
= 3.16
From Figure 2.6.1, the bond is fairly polar and has a high ionic character (~75%)
The bonding is likely ionic.
Exercise 2.6.1
Contrast the bonding of NaCl and silicon tetrafluoride.
Answer
NaCl is an ionic crystal structure, and an electrolyte when dissolved in water; Δχ = 1.58, average ∑ χ = 1.79 , while
silicon tetrafluoride is covalent (molecular, non-polar gas; Δχ = 2.08, average ∑ χ = 2.94.

Jim Clark (Chemguide.co.uk)
Daniel James Berger
Wikipedia
Ed Vitz (Kutztown University), John W. Moore (UW-Madison), Justin Shorb (Hope College), Xavier Prat-Resina (University of
Minnesota Rochester), Tim Wendorff, and Adam Hahn.
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SECTION OVERVIEW
2.7.2: Point Groups

2.7: Advanced Bonding is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
Introduction
The symmetry of a molecule consists of symmetry
operations and symmetry elements. A symmetry
operation is an operation that is performed to a
molecule which leaves it indistinguishable and
superimposable on the original position. Symmetry
operations are performed with respect to symmetry
elements (points, lines, or planes).
An example of a symmetry operation is a
180° rotation of a water molecule in which the
resulting position of the molecule is indistinguishable Figure 2.7.1.1 : An example of a symmetry operation is a 180° rotation
where the resulting position is indistinguishable from the original. A 180°
from the original position (see Figure 2.7.1.1). In this
rotation is called a C2 operation; the axis of rotation is the symmetry
example, the symmetry operation is the rotation and
element.
the symmetry element is the axis of rotation.
There are five types of symmetry
operations: identity, reflection, inversion,
proper rotation, and improper rotation. The symmetry elements that correspond to the five types of symmetry operations are
listed in Table 2.7.1.1.
Table 2.7.1.1 : Table of elements and operations
S
y
m
Element Operation
b
o
l
Identity identity E
C
Proper rotation rotation by (360/n)o
n
Reflection reflection in a plane σ
Inversion inversion of a point at (x,y,z) to (-x,-y,-z) i
rotation by (360/n)o, followed by reflection in the plane perpendicular S

Improper rotation
to the rotation axis n
Symmetry Operations and Elements

Identity (E)
All molecules have the identity element. The identity operation is doing nothing to the molecule (it doesn't rotate, reflect, or
invert...it just is).
Proper Rotation and Proper Axis (Cn)

A "proper" rotation is just a simple rotation operation about an axis. The symbol for any proper rotation or proper axis is C(360/n),
where n is the degree of rotation. Thus, a 180° rotation is a C2 rotation around a C2 axis, and a 120° rotation is a C3 rotation about a
C3 axis.
PRINCIPLE AXIS: The principle axis of a molecule is the highest order proper rotation axis, in other words, the largest
value of n. For example, if a molecule had C2 and C4 axes, the C4 is the principle axis.
Reflection and Symmetry Planes (σ)
Mirror planes are symmetry planes within the molecule. A reflection operation occurs with respect to a plane of symmetry. There
are three classes of symmetry elements:
1. σh (horizontal): horizontal planes are perpendicular to principal axis
2. σv (vertical): vertical planes are parallel to the principal axis
3. σd (dihedral): dihedral planes are parallel to the principle axis and bisect two C2 axes
Inversion and Inversion Center (i)

The inversion operation requires a point of symmetry (a center of symmetry within a molecule). In other words, a point at the
center of the molecule that can transform (x,y,z) into (-x,-y,-z) coordinate. Structures of tetrahedron, triangles, and pentagons lack
an inversion center.
Improper rotation (Sn)

Improper rotation is a combination of a rotation with respect to an axis of rotation (Cn), followed by a reflection through a plane
perpendicular to that Cn axis. In short, an Sn operation is equivalent to Cn followed by σ . h
References
1. Introduction to Molecular Symmetry by J. S Ogden
2. Inorganic Chemistry by Catherine Housecroft And Alan G. Sharpe.
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SECTION OVERVIEW
2.7.2: Point Groups
Introduction
A Point Group describes all the symmetry operations that can be performed on a molecule that result in a conformation
indistinguishable from the original. Point groups are used in Group Theory, the mathematical analysis of groups, to determine
properties such as a molecule's molecular orbitals.
Assigning Point Groups

While a point group contains all of the symmetry operations that can be performed on a given molecule, it is not necessary to
identify all of these operations to determine the molecule's overall point group. Instead, a molecule's point group can be determined
by following a set of steps which analyze the presence (or absence) of particular symmetry elements.
Steps for assigning a molecule's point group:

1. Determine if the molecule has an infinite rotation axis.
2. If yes, determine if there is an inversion center. If no, find the highest order rotation axis, Cn, and continue.
3. If the molecule does not contain a rotation axis, look for either a mirror plane or an inversion center. If you find at least one
rotation axis, look for multiple rotation axes where the n value is greater than 2.
4. Determine if the molecule has any C2 axes perpendicular to the principal Cn axis. If so, then there are n such C2 axes, and
the molecule is in the D set of point groups. If not, it is in either the C or S set of point groups.
5. Determine if the molecule has a horizontal mirror plane (σh) perpendicular to the principal Cn axis. If so, the molecule is
either in the Cnh or Dnh set of point groups.
6. Determine if the molecule has a vertical mirror plane (σv) containing the principal Cn axis. If so, the molecule is either in
the Cnv or Dnd set of point groups. If not, and if the molecule has n perpendicular C2 axes, then it is part of the Dn set of
point groups.
7. Determine if there is an improper rotation axis, S2n, collinear with the principal Cn axis. If so, the molecule is in the S2n
point group. The S2n point group is extremely unlikely to appear in this course. If not, the molecule is in the Cn point group.
Figure 2.7.2.1: Decision tree for
determining a molecule's point group (CC-BY-NC-SA; Chip Nataro)
Example 2.7.2.1
Find the point group of borane (BH3).
Answer
Solution
1. Borane does not have an infinite rotation axis.
2. Highest order rotation axis: C3
3. There are not multiple axes with n greater than 2.
4. There are 3 C2 axes perpendicular to the principal axis
5. There is a horizontal mirror plane (σh)
Borane is in the D3h point group.
See Also
Symmetry Challenge
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D Groups
The D set of point groups are classified as Dnh, Dnd, or Dn, where n refers to the principal axis of rotation. Overall, the D groups are
characterized by the presence of n C2 axes perpendicular to the principal Cn axis. Further classification of a molecule in the D
groups depends on the presence of horizontal or vertical/dihedral mirror planes.
Group Description Example
n perpendicular C2 axes, and a horizontal

Dnh benzene, C6H6 is D6h
mirror plane (σh)
n perpendicular C2 axes, and a vertical mirror

Dnd propadiene, C3H4 is D2d
plane (σv)
Dn n perpendicular C2 axes, no mirror planes [Co(en)3]3+ is D3
C Groups
The C set of point groups are classified as Cnh, Cnv, or Cn, where n refers to the principal axis of rotation. The C set of groups are
characterized by the absence of n C2 axes perpendicular to the principal Cn axis. Further classification of a molecule in the C
groups depends on the presence of horizontal or vertical/dihedral mirror planes.
horizontal mirror plane (σh) perpendicular to

Cnh boric acid, H3BO3 is C3h
the principal Cn axis
vertical mirror plane (σv) containing the

Cnv ammonia, NH3 is C3v
principal Cn axis
Cn no mirror planes P(C6H5)3 is C3
S Groups
The S set of point groups are classified as S2n, where n refers to the principal axis of rotation. The S set of groups are characterized
by the absence of n C2 axes perpendicular to the principal Cn axis, as well as the absence of horizontal and vertical/dihedral mirror
planes. However, there is an improper rotation (or a rotation-reflection) axis collinear with the principal Cn axis.
improper rotation (or a rotation-reflection) axis

S2n 12-crown-4 is S4
collinear with the principal Cn axis
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Low Symmetry Point Groups

Low symmetry point groups include the C1, Cs, and Ci groups
C1 only the identity operation (E) CHFClBr
only the identity operation (E) and one mirror

Cs C2H2ClBr
plane
only the identity operation (E) and a center of

Ci C2H2Cl2Br
inversion (i)
High Symmetry Point Groups

High symmetry point groups include the Td, Oh, Ih, C∞v, and D∞h groups. The table below describes their characteristic symmetry
operations. The full set of symmetry operations included in the point group is described in the corresponding character table.
linear molecule with an infinite number of

C∞v HBr
rotation axes and vertical mirror planes (σv)
linear molecule with an infinite number of

rotation axes, vertical mirror planes (σv),
D∞h CO2
perpendicular C2 axes, a horizontal mirror
plane (σh), and an inversion center (i)
typically have tetrahedral geometry, with 4 C4

Td axes, 3 C2 axes, 3 S4 axes, and 6 dihedral CH4
mirror planes (σd)
typically have octahedral geometry, with 3 C4

Oh axes, 4 C3 axes, and an inversion center (i) as SF6
characteristic symmetry operations
typically have an icosahedral structure, with 6

Ih B12H122-
C5 axes as characteristic symmetry operations
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So far we have examined the Molecular Orbital (MO) diagrams for diatomic molecules. These molecules can be classified in two
different groups, those that contain hydrogen (and thus only have the hydrogen 1s orbital available to make MOs) and those that do
not. For the second group, the general diagram developed in previous sections containing σ- and π-bonding and antibonding MOs
will generally apply, although there can be subtle differences for heteronuclear diatomics that contain atoms with vastly different
electroneagitivity values. The number of diatomic molecules is incredibly small compared to the number of molecules containing
three or more atoms. It would be impractical to create and refer to general MO diagrams for all of the different possible
combinations, so developing a method to quickly develop MO diagrams for these larger molecules is highly desirable. The method
described will use group theory to do just that. For our purposes, we are only going to consider molecules that have a central atom
surrounded by either hydrogen or a halide (which can be treated like hydrogen but with three lone pair). In other words, there will
be no π-bonding in these molecules. While this again is a relatively small subset of all known molecules, it will provide a basis for
the development and understanding of MO diagrams. As this course is not entirely dedicated to MO diagrams, it makes sense to
take this limited approach. Larger molecules with π-bonding (and in some cases δ-bonding) requires advanced computational
methods to develop MO diagrams.
The starting point to this approach is drawing a proper three-dimensional structure of the molecule of interest. From there, the point
group of the molecule must be determined. Once the symmetry of the molecule is known, the symmetry of the central atom’s
atomic orbitals (AOs) can be described using the appropriate symmetry labels. These are found in what is known as a character
table and will be called the generator functions. The ligand group orbitals (LGOs) are then derived using a graphical approach.
Combination of the generator functions and LGOs in an appropriate way gives the desired MO diagram. Using this technique,
you should be able to quickly (albeit crudely) derive an MO diagram to help understand the symmetry and relative energy of the
frontier orbitals, often the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), the
orbitals most responsible for chemical reactivity and spectroscopy. At this point, this approach likely seems somewhat vague at
best. Rather than continue in a long narrative of the process, it is likely more effective to work through an example. This example
will work through several steps that will be summarized at the end.
Step 1 - Drawing the structure and determining the hybridization of the central atom
Exercise 2.7.3.1
Using VSEPR, draw the three-dimensional structure of methane (CH4).
Answer
Exercise 2.7.3.2
What orbitals need to be used for hybridzation of the central carbon atom?
Answer
The carbon would be classified as AX4E0 since it is bonded to the four hydrogen atoms and has no lone pair. Based on this
the carbon would have to be sp3 hybridized, which means you will need to account for the s- and all three p-orbitals on the
carbon atom.
Step 2 - Determine the point group of the molecule and assign the generator functions
Exercise 2.7.3.3
What is the point group of methane?
Answer
Methane does not have an infinite rotation axis.
There is at least one rotation axis (in fact several). The highest order rotation axis is C3, which can be thought of as any C-H
bond. While not important for this application, there are also several C2 axes that pass between two C-H bonds.
There are not 6 C5 axes.

There are 4 C3 axes as each of the C-H bonds is a C3 axis.
There is not an inversion center (it would have to be the unique carbon atom, and none of the hydrogen atoms have another
hydrogen atoms directly across from it).
There are 6 σ.
The point group of methane is Td.
At this point we need to turn to the character table for the point group of methane. Character tables have many uses, most of which
are not applicable to this course. As such, character tables have a lot of information that will will not find necessary. Shown below
are two different representations for the character table for the Td point group. The first is the full character table while the second
is an abbreviated character table that will be more useful for our purposes.
Linear Quadratic
Td E 8 C3 3 C2 6 S4 6 σd
Functions Functions
A1 +1 +1 +1 +1 +1 x2 + y2 + z2
A2 +1 +1 +1 -1 -1
(2z2-x2-y2, x2-
E +2 -1 +2 0 0
y2)
T1 +3 0 -1 +1 -1 (Rx, Ry, Rz)
T2 +3 0 -1 -1 +1 (x, y, z) (xy, xz, yz)
Table 2.7.3.1: Full character table for the Td point group.

You may notice that this point group has an improper rotation (even though we did not find it when assigning the point group) and
that the mirror planes are designated as σd. While significant and useful, there is much more information here than we need. The
abbreviated character table will give us all of the information that is necessary. The table has been contracted to include on the
symmetry labels (beneath Td) and the corresponding orbitals that go with those labels. Note that some of the labels do not
correspond to orbitals. The Orbitals column in the abbreviated character table corresponds to the Linear Functions column above.
The (x, y, z) translates to the (px, py, pz). The s orbital is always assigned to the row that only contains values of +1 beneath the
symmetry operations. That is not significant for our purposes, but worth mentioning.
Td Orbitals
A1 s
A2
T1
T2 (px, py, pz)
Table 2.7.3.2: Abbreviated character table for the Td point group.
Exercise 2.7.3.4
What are the symmetry labels for the orbitals on carbon used to make methane.
Answer
s - a1
px - t2
py - t2
pz - t2
These are now our generator functions for making the LGOs. Note that the convention is a switch to lower case when
assigning symmetry to orbitals.
Step 3 - Making the LGOs

Now that we have the generator functions, we can make the LGOs. This is done pictorially essentially asking the questions "What
would the hydrogen 1s orbitals have to look like in order to interact in a constructive way with the carbon orbital in question?' To
do this, it is very important to define the axes of your molecule before you start considering potential interactions. Due to the high
symmetry of the molecule we will slightly break from convention in order to maximize orbital interactions. In group theory, the
principle axis is always assigned as the z-axis, but in this case, we will assign the axes to the C2 axes in the molecule. To begin
with, let's consider the s-orbital of carbon which is labeled a1. The s-orbital is a sphere with the same sign for the wave function in
all directions (Fig. 2.7.3.1).
Figure 2.7.3.1: The a1 orbital for the carbon atom in methane.

Once the axes and the orbital on carbon are drawn we want to consider what the signs for the wave functions on each hydrogen
atom would have to be in order to have constructive overlap. In this case, the symmetric a1 orbital of carbon will be able to interact
with all of the hydrogen atoms in a constructive manner is they have the same sign for their wave functions (Fig. 2.7.3.2). This
generates a LGO for the hydrogen atoms that has a1 symmetry. Although it is comprised of AOs from four hydrogen atoms, we
now treat this as a single orbital for all of the hydrogen atoms hence the LGO designation.
Figure 2.7.3.2: The LGO for the hydrogen atoms that has a1 symmetry with the carbon generator function depicted on the axes.
The p-orbitals for the carbon atom all have the same symmetry label (t2). One important consequence of this is that the orbitals are
degenerate (equal in energy). While you would likely expect this for an isolated carbon atom, in compounds it is possible that the
orbitals are no longer degenerate based on the shape of the molecule. The introduction of p-orbitals into our pictorial method adds
one additional complication, p-orbitals are not symmetric and each lobe has a different sign for the wave function. In addition, p-
orbitals also posses a nodal plane, a plane in which the probability of finding an electron is zero. In developing the LGO that
matches with the pz-orbital, these factors must be considered. For the pz-orbital, the nodal plane is the xy plane. So, any hydrogen
atoms that lie in the xy plane would be unable to interact with the carbon atom. That leads to an LGO that matches with the pz-
orbital as shown below (Fig. 2.7.3.3).
Figure 2.7.3.3: The LGO for the hydrogen atoms that has t2 symmetry with the carbon generator function depicted on the axes.
None of the hydrogen atoms are in the xy plane, so they are all capable of interacting. Notice that the change in sign of the carbon
pz-orbital impacts the way the orbitals on the hydrogen atoms are represented, but does not impact the ability of those hydrogen
atoms to interact.
Exercise 2.7.3.5
Using the remaining basis functions, sketch the rest of the LGOs for the hydrogen atoms in methane.
Answer
For the px-orbital, the nodal plane is the yz plane. Once again none of the hydrogen atoms are in this plane so they can all
interact. The LGO is depicted below. Again, the p-orbital of carbon does not point directly at any of the hydrogen atoms,
but they are still capable of interacting.
For the py-orbital, the nodal plane is the xz plane. Once again there are no hydrogen atoms that are unable to interact. This
is a consequence of our decision to maximize the interactions possible in this highly symmetric molecule. The LGO is
depicted below.
Step 4 - Constructing the MO diagram

The final step in the process is to construct the MO diagram for the molecule. Before we start constructing the MO diagram there is
one final crucial question to be considered, are the atomic orbitals similar enough in energy to interact? We have actually done this
to some extent already by ignoring the 1s orbital on carbon as being too low in energy to interact. Compare the energy of the
valence orbitals of the atoms that are interacting and if that difference is 15 eV or less, they are close enough in energy. Like many
'rules' you have learned in chemistry, the 15 eV difference is not absolute, but is a reasonable guideline. In the case of methane, all
of the orbitals are close enough in energy to interact.
Atomic
Element 1s 2s 2p 3s 3p 4s 4p
Number
1 H -13.6
2 He -24.5
3 Li -5.5
4 Be -9.3
5 B -14.0 -8.3
6 C -19.5 -10.7
7 N -25.5 -13.1
8 O -32.4 -15.9
9 F -46.4 -18.7
10 Ne -48.5 -21.6
11 Na -5.2
12 Mg -7.7
13 Al -11.3 -6.0
14 Si -15.0 -7.8
15 P -18.7 -10.0
16 S -20.7 -12.0
17 Cl -25.3 -13.7
18 Ar -29.3 -15.9
19 K -4.3
20 Ca -6.1
30 Zn -9.4
31 Ga -12.6 -6.0
32 Ge -15.6 -7.6
33 As -17.6 -9.1
34 Se -20.8 -11.0
35 Br -24.1 -12.5
36 Kr -27.5 -14.3
Table 2.7.3.3: Energy (eV) for valence orbitals of atoms from J.G. Verkade, A Pictorial Approach to Molecular Bonding and
Vibrations, Springer-Verlag, New York, 1997, p. 69.
Building the MO diagram is similar to how it was done for diatomic molecules (Fig. 2.7.3.4). The central atom is placed on one
side and the outer atoms, as a group, are placed on the other. The relative orbital energies are approximated based on the values in
Table 2.7.3.3, in this case the hydrogen LGOs fall between the a1 and t2 orbitals for carbon. The hydrogen LGOs are depicted as
being degenerate since they are all derived from hydrogen 1s orbitals. The molecular orbitals are drawn between the carbon and
hydrogen atoms. The a1 atomic orbital on carbon has a matching a1 LGO from hydrogen and so these orbitals can combine to give
a bonding MO and an antibonding MO. As the carbon a1 orbital is the lowest energy AO in this system it leads to the lowest energy
MO. Recall that ABIMABTBIB, so it is not surprising that the lowest energy bonding orbital would give the highest energy
antibonding orbital. Again, this is a rough guideline and not always the case. Dashed lines are often added to link orbitals with the
same symmetry label. This is useful, but with more complex molecules can make the diagrams difficult to read. Finally, there are
orbitals with t2 symmetry on both the carbon atom and from the hydrogen LGOs. Again, these can combine to give three
degenerate bonding MOs and three degenerate antibonding MOs. The exact placement of these orbitals is not critical, however, the
bonding orbitals should be lower in energy than the AO and LGOs and the antibonding should be higher. The eight valence
electrons are added to the system using standard electron configuration principles (Aufbau, Paulii exclusion and Hund's rule).
Figure 2.7.3.4: The MO diagram for CH4.
For this system the bond order= 8−0
2
= 4 . Notice that while this agrees with your original structure, the MO diagram shows
something very different. The lowest energy bonding MO (a1 which is depicted in c) involves all five atoms sharing two electrons,
not the carbon atom and one hydrogen atom sharing. The same would be true for the bonding t2 orbitals, more than 2 atoms are
involved. In addition it would be worth noting that the HOMO would be a t2 orbital (remember they are degenerate so a specific
one can not be distinguished) and the LUMO would be a t2 antibonding orbital.
How did we do?

Our pictorial method is qualitative but does a reasonable job of predicting the MO diagram. A more quantitative method would be
to use computational methods to derive a more accurate MO diagram for this methane. The orbitals and their energies as calculated
by WebMO are presented below (Table 2.7.3.4). Overall our MO diagram looks pretty good. We see that the bonding a1 orbital is
approximately 5 eV lower in energy than the carbon a1 orbital. The a1* orbital is almost 40 eV higher in energy than the a1 LGO.
This is an excellent representation of the ABIMABTBIB principle. A similar trend is noted for the t2 orbitals in which the bonding
MOs are approximately 1.7 eV lower in energy than the LGOs and the t2* orbitals are approximately 14 eV higher in energy than
the carbon 2p orbitals.
(Table 2.7.3.4 ). The MOs for CH4 as calculated and displayed by WebMO. The data for CF4 was imported into WebMO from the
NIST Webbook as a computed 3-D structure and calculations were performed using B3LYP-6-31G(d). The same perspective of the
molecule is used throughout.
Symmetry Label Orbital(s) Energy (eV)
a1* 26.479
t2* 3.649
t2 -15.334
a1 -24.545
Step
2.7.3: Ligand Group Orbitals and Generator Functions is shared under a not declared license and was authored, remixed, and/or curated by
LibreTexts.
In organic chemistry the octet rule is closer to a law; do not make more than four bonds to carbon! However, once you start dealing
with atoms in the third row of the periodic table, the octet rule becomes a bit more of a guideline. Consider the common anion,
hexfluorophospate, PF6- (Figure 2.7.4.1), in which we draw the phosphorous atom with six bonds giving it an apparently electron
count of 12.
Figure 2.7.4.1 . The structure of the hexafluorophosphate anion.

The bonding in these types of systems is a bit more involved and to fully appreciate it we must consider the molecular orbital
diagram for such a molecule. This will be done using the same techniques as were used in the previous section, but some
adjustments will need to be made as we progress from the Lewis structure to the molecular orbital diagram.
Exercise 2.7.4.1
Using VSEPR, draw the three-dimensional structure of sulfur tetrafluoride (SF4).
Answer
Sulfur has 6 valence electrons and fluorine has 7 giving a total of 34 electrons in this molecule.
To start, you would draw bonds between sulfur and each of the fluorine atoms which would use 8 of the 34 electrons.
As fluorine is more electronegative, the next step would be to give each fluorine 3 lone pair in order to fill their octets. This
will use 26 of the remaining electrons. At this point you might be tempted to stop as the sulfur atom and all of the fluorine
atoms have an octet.
The problem is that this structure only accounts for 32 of our 34 electrons. As fluorine is an element in the 2nd row, we will
not add the missing electrons to any of the fluorine atoms. That leaves sulfur as the only option. Checking the formal
charge on each of the atoms supports this placement.
Formal Charge = number of valence electrons - (2 x number of lone pair + number of bonds)
FCF = 7 - (2(3) + 1) = 0
FCS = 6 - (2(1) + 4) = 0
This makes the sulfur AX4E1 so the structure is going to be based on AX5E0 which is trigonal bipyramidal.
There are two possible options for the structure, but the rules for VSEPR say that the lone pair should be as far away from
other electrons as possible. In this structure that would be one of the equatorial positions and so the structure on the right
(see-saw) is the correct one.
Exercise 2.7.4.2
What orbitals need to be considered for hybridization on the central sulfur atom?
Answer
We need a total of 5 hybrid orbitals to account for the 4 fluorine atoms and the lone pair. That means we need to incorporate
a d-orbital which will give sp3d hybridization. The particular d-orbital that is used would be the dz2 orbital.
Step 2 - Determine the point group of the molecule and assign the generator functions
Exercise 2.7.4.3
What is the point group of sulfur hexafluoride?
Answer
SF4 does not have an infinite rotation axis.
There one rotation axis passing through the lone pair which is C2.

The are no perpendicular C2 axes.
There is not an S4 axis.
There is not a perpendicular mirror plane.
There are however two mirror planes.
The point group of SF4 is C2v.
Once again we need the character table for the point group of SF4. Shown below are two different representations for the character
table for the C2v point group. The first is the full character table. Although we ignored it in the methane example, this does include
the d-orbital needed for hybridization. In the abbreviated character table the d-orbital has just been incorporated.
Quadratic
C2v E C2 σv (xz) σv (yz) Linear Functions
Functions
A1 +1 +1 +1 +1 z x2, y2, z2
A2 +1 +1 -1 -1 Rz xy
B1 +1 -1 +1 -1 x, Ry xz
B2 +1 -1 -1 +1 z, Rx yz
Table 2.7.4.1: Full character table for the C2v point group.
C2v Orbitals
A1 s, pz, dz2
A2
B1 px
B2 py
Table 2.7.4.2: Abbreviated character table for the C2v point group.
Exercise 2.7.4.4
What are the symmetry labels for the orbitals on sulfur used to make SF4.
Answer
s - a1
px - b1
py - b2
pz - a1
dz2 - a1
Before making the LGOs, we need to assign axis labels to the molecule. While there are many ways to do this, the proper
convention is to assign the principle axis to be the z-axis (Figure 2.7.4.2).
Figure 2.7.4.2 . Assignment of the axes in SF4.

As mentioned in the previous section, we can treat terminal halides using this method. To make the pictures less cluttered, the
halides will be represented just as the hydrogen atoms were and we will ignore the lone pair on the fluorine atoms. Based on the
assigned axes above, the LGOs can be drawn to match the orbitals on the sulfur atom (Figure 2.7.4.3).
Figure 2.7.4.3 . LGOs in SF4.
Step 3a - A few new twists

Before we go to step 4, we have a little bit of extra work to do. There are two features in this molecule that we have not dealt with
before, the lone pair and the use of d-orbitals. Let's begin with the lone pair as this is something that could be encountered in
molecules that do not break the octet rule. We know that this molecule has a lone pair on the sulfur atom. That lone pair has to be
accounted for and must occupy one of the orbitals we considered as our basis functions. The question is, which orbital? The best
option would be an orbital on the central atom that has no symmetry matched LGO. An example of this would be if all of the outer
atoms in a molecule were sitting in the nodal plane of a p-orbital. We do not have that case in this example, so now we need to dig
a little deeper. Our next best option is to consider all of the atomic orbitals of the central atom and ask which has the least amount
of direct interaction with a LGO. The s-orbital on sulfur has interaction with all four fluorine atoms so it is not a good candidate.
The p-orbitals all have interactions with two fluorine atoms, so they are slightly better options. In looking closer at the p-orbitals
we see that the px orbital has very direct overlap with two fluorine atoms; the orbital is pointing directly at two atoms and both
lobes interact. This is greater than the overlap of the py orbital in which the LGO does not lie directly on the y-axis. However, both
lobes of the py orbital are interacting with the LGO. The pz orbital is somewhat similar in that the LGO does not lie along the z-
axis. However, for this orbital, only one lobe of the sulfur pz is interacting with the LGO. So, given the options for the location of
the lone pair, pz > py > px > s, we must assign the pz (a1) orbital to be the one with the lone pair. You may have noticed that
the dz2 was not considered in the previous discussion. That is because the dz2 orbital is not accessible energetically. It is too high in
energy to participate in any meaningful bonding in this molecule. While, we draw an LGO that would match this orbital, we do not
consider any possible bonding or antibonding interaction between the LGO and the dz2 orbital. This is going to become very critical
in the next step.

In looking at the orbital energies from the previous section, we see that the 2s orbital of fluorine is MUCH lower in energy than the
2p of fluorine or the 3s and 3p of sulfur. It will not interact and does not need to be considered for this diagram. The 2p orbitals of
fluorine fall between the 3s and 3p orbitals of sulfur. We will be bringing together a total of eight orbitals. Why only eight? Let's
consider each of the combinations above (Figure 2.7.4.3).
Remember, we are ignoring the extra lone pairs on fluorine so that leaves a total of 12 orbitals that will not be shown in
our diagram.
The s-orbital (a1) from sulfur and the corresponding LGO will make a bonding and antibonding set.
The px orbital (b1) orbital from sulfur and the corresponding LGO will make a bonding and antibonding set.
The py orbital (b2) orbital from sulfur and the corresponding LGO will make a bonding and antibonding set.
The pz orbital (a1) has been assigned as the orbital holding the lone pair so we ignore the LGO it could interact with. Note
that this does not mean that the fluorine orbitals do not contribute to this orbital, but for the purpose of constructing the
MO diagram we will ignore any contribution.
The dz2 orbital (a1) of sulfur is not energetically accessible so we do not include it, but we do consider the LGO that
would interact with it.
In sketching the MO diagram, the s-orbital of sulfur is the lowest energy orbital depicted and as such will give the lowest energy
bonding MO and likely the highest energy antibonding MO. We will have two a1 orbitals that will be labeled as non-bonding (nb),
one for the pz orbital with the lone pair, and one for the LGO that would match the dz2 orbital. As we are considering the orbitals to
be localized on specific atoms, we will not change their energy from that of the atomic orbital from which they are derived. That
leaves the b1 and b2 orbitals that will make a bonding and antibonding set. At first glance, you might expect these to be degenerate
as they both are derived from p-orbitals on sulfur and the corresponding LGOs. However, upon examining the pictures
above, (Figure 2.7.4.3), it might be expected that the b1 bonding orbital might be slightly lower in energy than the b2 since there is
a more direct overlap between the sulfur orbital and the LGO. For now we will treat the orbitals as being degenerate. This would
lead to a MO diagram as pictured below (Figure 2.7.4.4).
(Figure 2.7.4.4 ). MO diagram for SF4.

Overall, this would give a bond order= = 3 which is quite different from the Lewis structure. The bonding in structures of p-
6−0
block elements with 'expanded' octets is not as straightforward as the Lewis structure might suggest. There are filled bonding
orbitals that involve more than two atoms. There are also significant ionic contributions to what is typically drawn as covalent
bonds.
How did we do?

Our MO diagram was generated using a pictorial method. Using computational methods it is possible to derive a more accurate
MO diagram for this molecule. Show below are the orbitals and their energies as calculated by WebMO (Table 2.7.4.3). Overall
our MO diagram looks pretty good. We see a VERY slight difference in the energy of the b1 and b2 bonding orbitals. This
difference is more pronounced in the antibonding orbitals. Based on the ABIMABTBIB principle, it is not surprising that we see a
greater difference in the antibonding orbitals. So our approximation of the b1 and b2 orbitals as being degenerate is not
unreasonable for the bonding MOs but not accurate for the antibonding.
You may also notice that all of the fluorine contributions are from p-orbitals. The 2s orbital of fluorine is much too low in energy to
participate in these interactions. So the only orbital involved in bonding with the sulfur would be the p-orbital pointing directly at
the sulfur atom. This justifies our treatment of the fluorine as being hydrogen-like. Again, we are ignoring any possible π-bonding
interactions in this molecule.
We also estimated that the a1 (nb) would not change in energy much from the atomic orbitals they were derived from. The energy
for the a1 (nb) derived from the sulfur pz is -12.049 eV which compares very favorably to the value of -12.0 eV for the 3p orbital of
sulfur found in the previous page. For the a1 (nb) LGO, the energy was calculated to be -17.853 eV which is slightly higher than the
-18.7 eV listed for the 2p orbitals of fluorine. Again, while not completely accurate, our pictorial method did a fairly reasonable job
of generating the MO diagram.
(Table 2.7.4.3 ). The MOs for SF4 (ignoring the lone pairs) as calculated and displayed by WebMO. The data for SF4 was
imported into WebMO from the NIST Webbook as a computed 3-D structure and calculations were performed using B3LYP-6-
31G(d).
Orbital Label Energy (eV)
a1* 0.517
b1* -1.950
b2* -4.083
a1 (nb) -12.049
a1 (nb) -17.853
b2 -18.559
b1 -18.697
a1 -20.655
2.7.4: Expanded Octets and Molecular Orbitals is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
SECTION OVERVIEW
2.8: Nuclear Magnetic Resonance (NMR) is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
The Magnetic Moment
Nuclear magnetic resonance spectroscopy is an incredibly powerful tool for inorganic chemists because it allows us to analyze the
connectivity of atoms in molecules. The basis for NMR is the observation that many atomic nuclei generate their own magnetic
field, or magnetic moment, as they spin about their axes. Not all nuclei have a magnetic moment. Fortunately for inorganic
chemists, though, hydrogen ( H ), the C isotope of carbon, the F isotope of fluorine, and the P isotope of phosphorus all
1 13 19 31
have magnetic moments and therefore can be observed by NMR – they are, in other words, NMR-active. Other nuclei - such as the
common C and O isotopes of carbon and oxygen - do not have magnetic moments, and cannot be directly observed by NMR.
12 16
Still other nuclei such as the hydrogen isotope deuterium ( H ) and nitrogen ( N ) have magnetic moments and are NMR-active,
2 14
but the nature of their magnetic moments is such that analysis of these nuclei by NMR is more complex.
In practice it is H and C nuclei that are most commonly observed by NMR spectroscopy. The fundamentals of interpreting H
1 13 1
NMR are covered in organic chemistry and as such will not be a focus of this course. However, the principles behind H 1
NMR apply to other nuclei, so H NMR will be used in much of the discussion. The terms ‘proton’ and ‘hydrogen’ are used
1
interchangeably when discussing because the H nucleus is just a single proton.

1
Table 2.8.1.1 : Some examples of magnetic and nonmagnetic nuclei relevant to inorganic chemistry.
Magnetic Nuclei Nonmagnetic Nuclei
1 12
H C
2 16
H O
13 32
C S
14 35
N Cl
19
F
31
P
Spin States and the Magnetic Transition

When a sample of an inorganic compound is sitting in a flask on a laboratory bench, the magnetic moments of all of its nuclei are
randomly oriented. However, when the same sample is placed within the field of a very strong superconducting magnet (this field
is referred to by NMR spectroscopists as the applied field, abbreviated B ) each nucleus will assume one of two possible quantum
0
spin states. In the +½ spin state, the magnetic moment is aligned with the direction of B , while in the -½ spin state it is aligned
0
opposed to the direction of B . 0
The +½ spin state is slightly lower in energy than the -½ state, and the energy gap between them, which we will call ΔE, depends
upon the strength of B : a stronger applied field results in a larger ΔE. For a large population of inorganic molecules in an applied
0
field, slightly more than half of the protons will occupy the lower energy +½ spin state, while slightly less than half will occupy the
higher energy -½ spin state. It is this population difference (between the two spin states) that is exploited by NMR, and the
difference increases with the strength of the applied magnetic field.
At this point, we need to look a little more closely at how a nucleus spins in an applied magnetic field. You may have see a toy
spinning top. When a top slows down a little and the spin axis is no longer completely vertical, it begins to exhibit precessional
motion, as the spin axis rotates slowly around the vertical. In the same way, a nucleus spinning in an applied magnetic field also
exhibits precessional motion about a vertical axis. It is this axis (which is either parallel or antiparallel to B ) that defines the
0
proton’s magnetic moment.
Watch the first minute or so of this video of spinning tops: look for the precessional motion
The frequency of precession (also called the Larmour frequency, abbreviated ν ) is simply the number of times per second that the
L
nucleus precesses in a complete circle. The precessional frequency increases with the strength of B0 .
If a nucleus that is precessing in an applied magnetic field is exposed to electromagnetic radiation of a frequency ν that matches its
precessional frequency ν , we have a condition called resonance. In the resonance condition, a nucleus in the lower-energy +½
L
spin state (aligned with B0 ) will transition (flip) to the higher energy –½ spin state (opposed to B0 ). In doing so, it will absorb
radiation at this resonance frequency n - and this frequency corresponds to ΔE, the energy difference between the two spin states.
With the strong magnetic fields generated by the superconducting magnets used in modern NMR instruments, the resonance
frequency for protons falls within the radio-wave range, anywhere from 100 MHz to 800 MHz depending on the strength of the
magnet.
Recall that photons of electromagnetic radiation of a given frequency correspond to energy (E) given by E = hν , where h is
Plank's constant and ν is the frequency in waves per second, or Hz. Now, we know that in NMR, the energy gap ΔE between the
+½ and -½ spin states of a proton in a strong magnetic field corresponds to the energy associated with radiation in the radio
frequency (Rf) region of the spectrum. By detecting the frequency of radiation that is absorbed, we can gain information about the
chemical environment of the nucleus.
Contributors
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Soderberg.
The frequency of radiation absorbed by a proton (or any other nucleus) during a spin transition in an NMR experiment is called its
'resonance frequency'. If all nuclei in all inorganic molecules had the same resonance frequency, NMR spectroscopy but would not
be terribly useful for chemists. Fortunately for us, however, resonance frequencies are not uniform for different nuclei in a
molecule - rather, the resonance frequency varies according to the electronic environment that a given nucleus inhabits. In methyl
acetate, for example, there are two distinct ‘sets’ of protons.
The three methyl acetate protons labeled Ha above have a different resonance frequency compared to the three Hb protons, because
the two sets of protons are in non-identical electronic environments: the Ha protons are on a carbon next to a carbonyl
(C=O) carbon, while the Hb protons or on a carbon next to the an oxygen. In the terminology of NMR, all three Ha protons are
chemically equivalent to each other, as are all three Hb protons. The Ha protons are, however, chemically nonequivalent to the
Hb protons. As a consequence, the resonance frequency of the Ha protons is different from that of the Hb protons. For now, do not
worry about why the different electronic environment gives rise to different resonance frequencies - we will get to that soon.
The ability to recognize chemical equivalancy and nonequivalency among atoms in a molecule will be central to understanding
NMR. Each of the molecules below contains only one set of chemically equivalent protons: all six protons on benzene, for
example, are equivalent to each other and have the same resonance frequency in an NMR experiment. Notice that any description
of the bonding and position of one proton in benzene applies to all five other protons as well.
Acetaldehyde contains two sets of chemically equivalent protons, just like our previous example of methyl acetate, and again in
each case the resonance frequency of the Ha protons will be different from that of the Hb proton. A description of the bonding and
position of the Hb proton does not apply to the three Ha protons: Hb is bonded to an sp2-hybridized carbonyl carbon while the
Ha protons are bonded to an sp3-hybridized methyl carbon.
Note that while all four aromatic protons in 1,4-dimethylbenzene are chemically equivalent, its constitutional isomer 1,2
dimethylbenzene has two sets of aromatic protons in addition to the six methyl (H ) protons. The 1,3-substituted isomer, on the
a
other hand, has three sets of aromatic protons.
In 1,2-dimethylbenzene, both Hb protons are adjacent to a methyl substituent, while both Hc protons are two carbons away. In 1,3-
dimethylbenzene, Hb is situated between two methyl groups, the two Hc protons are one carbon away from a methyl group, and
Hd is two carbons away from a methyl group.
As you have probably already realized, chemical equivalence or non-equivalence in NMR is closely related to symmetry. Different
planes of symmetry in the three isomers of dimethylbenzene lead to different patterns of equivalence.
Contributors
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Soderberg.
In an NMR experiment, a sample compound (we'll again use methyl acetate as our example) is placed inside a very strong applied
magnetic field (B ) generated by a superconducting magnet in the instrument.
0
At first, the magnetic moments of (slightly more than) half of the protons in the sample are aligned with B , and half are aligned
0
against B . Then, the sample is exposed to a range of radio frequencies. Out of all of the frequencies which hit the sample, only
0
two - the resonance frequencies for Ha and Hb - are absorbed, causing those protons which are aligned with B to 'spin flip' so that
0
they align themselves against B . When the 'flipped' protons flip back down to their ground state, they emit energy, again in the
0
form of radio-frequency radiation. The NMR instrument detects and records the frequency and intensity of this radiation, making
using of a mathematical technique known as a 'Fourier Transform'.
In most cases, a sample being analyzed by NMR is in solution. If we use a common laboratory solvent (diethyl ether, acetone,
dichloromethane, ethanol, water, etc.) to dissolve our NMR sample, however, we run into a problem – there many more solvent
protons in solution than there are sample protons, so the signals from the sample protons will be overwhelmed. To get around this
problem, we use special NMR solvents in which all protons have been replaced by deuterium. Deuterium is NMR-active, but its
resonance frequency is far outside of the range in which protons absorb, so it is `invisible` in 1H-NMR. Some common NMR
solvents are shown below.
Common NMR solvents
Note that this is not necessarily a problem when looking at nuclei such as 31P. Very few solvents contain phosphorus so there is no
chance for the phosphorus signals to be overwhelmed by signals from the solvent. However, most spectra are still obtained in
deuterated solvents because the instruments often rely on a deutrerium signal to fine tune the signal and a proton spectrum is often
obtained along with spectra for other nuclei.
It should also be noted that when conducting an NMR experiment, the operator chooses which nucleus is being observed. As
mentioned previously, the resonance frequency of deuterium is significantly different than that of protons. One could choose to
observe a proton spectrum of a sample or the deuterium spectrum of the same sample, but not both at the same time. There are
some very specialized experiments that do allow the observation of two different nuclei in the same experiment, but that is beyond
the score of this course. If the 31P spectrum of a sample is obtained, the presence of protons in the solvent will not have an impact
on the spectrum. This does not mean that different nuclei (e.g. phosphorus and proton) do not influence each other as we will see
when we discuss coupling.
Let's look at an actual 1H-NMR spectrum for methyl acetate. The vertical axis corresponds to intensity of absorbance, the
horizontal axis to frequency. However, you will notice right away that a) there is no y-axis line or units drawn in the figure, and b)
the x-axis units are not Hz, which you would expect for a frequency scale. Both of these mysteries will become clear very soon.
We see three absorbance signals: two of these correspond to Ha and Hb (don't worry yet which is which), while the peak at the far
right of the spectrum corresponds to the 12 chemically equivalent protons in tetramethylsilane (TMS), a standard reference
compound that was added to our sample.
First, let's talk about the x-axis. The 'ppm' label stands for 'parts per million', and simply tells us that the two sets of equivalent
protons in our methyl acetate sample have resonance frequencies about 2.0 and 3.6 parts per million higher than the resonance
frequency of the TMS protons, which we are using as our reference standard. This is referred to as their chemical shift.
The reason for using a relative value (chemical shift expressed in ppm) rather than the actual resonance frequency (expressed in
Hz) is that every NMR instrument will have a different magnetic field strength, so the actual value of resonance frequencies
expressed in Hz will be different on different instruments - remember that ΔE for the magnetic transition of a nucleus depends upon
the strength of the externally applied magnetic field. However, the resonance frequency values relative to the TMS standard will
always be the same, regardless of the strength of the applied field. For example, if the resonance frequency for the TMS protons in
a given NMR instrument is exactly 300 MHz (300 million Hz), then a chemical shift of 2.0 ppm corresponds to an actual resonance
frequency of 300,000,600 Hz (2 parts per million of 300 million is 600). In another instrument (with a stronger magnet) where the
resonance frequency for TMS protons is 400 MHz, a chemical shift of 2.0 ppm corresponds to a resonance frequency of
400,000,800 Hz.
A frequently used symbolic designation for chemical shift in ppm is the lower-case Greek letter δ. Most protons in organic
compounds have chemical shift values between 0 and 10 ppm relative to TMS, although values below 0 ppm and up to 12 ppm and
above are occasionally observed. By convention, the left-hand side of an NMR spectrum (higher chemical shift) is called
downfield, and the right-hand direction is called upfield.
In modern research-grade NMR instruments, it is no longer necessary to actually add TMS to the sample: the computer simply
calculates where the TMS signal should be, based on resonance frequencies of the solvent. So, from now on you will not see a
TMS peak on NMR spectra - but the 0 ppm point on the x-axis will always be defined as the resonance frequency of TMS protons.
A Chemical Shift Analogy
If you are having trouble understanding the concept of chemical shift and why it is used in NMR,
try this analogy: imagine that you have a job where you travel frequently to various planets, each
of which has a different gravitational eld strength. Although your body mass remains constant,
your measured weight is variable - the same scale may show that you weigh 60 kg on one planet,
and 75 kg on another. You want to be able to keep track your body mass in a meaningful,
reproducible way, so you choose an object to use as a standard: a heavy iron bar, for example.
You record the weight of the iron bar and yourself on your home planet, and nd that the iron
bar weighs 50 kg and you weigh 60 kg. You are 20 percent (or pph, parts per hundred) heavier
than the bar. The next day you travel (with the iron bar in your suitcase) to another planet and
nd that the bar weighs 62.5 kg, and you weigh 75 kg. Although your measured weight is
different, you are still 20% heavier than the bar: you have a 'weight shift' of 20 pph relative to the
iron bar, no matter what planet you are on.
We have already pointed out that, on our spectrum of methyl acetate, there is there is no y-axis scale indicated. With y-axis data it
is relative values, rather than absolute values, that are important in NMR. The computer in an NMR instrument can be instructed to
mathematically integrate the area under a signal or group of signals. The signal integration process is very useful, because in 1H-
NMR spectroscopy the area under a signal is proportional to the number of protons to which the signal corresponds. When we
instruct the computer to integrate the areas under the Ha and Hb signals in our methyl acetate spectrum, we find that they have
approximately the same area. This makes sense, because each signal corresponds to a set of three equivalent protons.
Be careful not to assume that you can correlate apparent peak height to number of protons - depending on the spectrum, relative
peak heights will not always be the same as relative peak areas, and it is the relative areas that are meaningful. Because it is
difficult to compare relative peak area by eye, we rely on the instrument's computer to do the calculations. Note also that in the
spectrum above the signal for TMS represents 12 protons and yet is appears to be similar to the signals for the methyl acetate. The
intensity of the signals is also dependent on the concentration of the species in solution. Without careful sample preparation, it is
extremely unlikely that the concentration of TMS is the same as that of the methyl acetate meaning that there can not be a direct
comparison of their signals.
Take a look next at the spectrum of 1,4-dimethylbenzene:
As we discussed earlier, this molecule has two sets of equivalent protons: the six methyl Ha protons and the four aromatic
Hb protons. When we instruct the instrument to integrate the areas under the two signals, we find that the area under the peak at 2.6
ppm is 1.5 times greater than the area under the peak at 7.4 ppm. The ratio 1.5 to 1 is of course the same as the ratio 6 to 4. This
integration information (along with the actual chemical shift values, which we'll discuss soon) tells us that the peak at 7.4 ppm must
correspond to Hb, and the peak at 2.6 ppm to Ha.
Contributors
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Soderberg.
The 1H-NMR spectra that we have seen so far (of methyl acetate and 1,4-dimethylbenzene) are somewhat unusual in the sense that
in both of these molecules, each set of protons generates a single NMR signal. In fact, the 1H-NMR spectra of most molecules
contain signals that are 'split' into two or more sub-peaks. Rather than being a complication, however, this splitting behavior is
actually very useful because it provides us with more information about our sample molecule.
Consider the spectrum for 1,1,2-trichloroethane. In this and in many spectra to follow, we show enlargements of individual signals
so that the signal splitting patterns are recognizable.
The signal at 3.96 ppm, corresponding to the two Ha protons, is split into two subpeaks of equal height (and area) – this is referred
to as a doublet. The Hb signal at 5.76 ppm, on the other hand, is split into three sub-peaks, with the middle peak higher than the two
outside peaks - if we were to integrate each subpeak, we would see that the area under the middle peak is twice that of each of the
outside peaks. This is called a triplet.
The source of signal splitting is a phenomenon called spin-spin coupling, a term that describes the magnetic interactions between
neighboring, non-equivalent NMR-active nuclei. (The terms 'splitting' and 'coupling' are often used interchangeably when
discussing NMR.) In our 1,1,2 trichloromethane example, the Ha and Hb protons are spin-coupled to each other. Here's how it
works, looking first at the Ha signal: in addition to being shielded by nearby valence electrons, each of the Ha protons is also
influenced by the small magnetic field generated by Hb next door (remember, each spinning proton is like a tiny magnet). The
magnetic moment of Hb will be aligned with B0 in slightly more than half of the molecules in the sample, while in the remaining
molecules it will be opposed to B0. The Beff ‘felt’ by Ha is a slightly weaker if Hb is aligned against B0, or slightly stronger if Hb is
aligned with B0. In other words, in half of the molecules Ha is shielded by Hb (thus the NMR signal is shifted slightly upfield) and
in the other half Ha is deshielded by Hb (and the NMR signal shifted slightly downfield). What would otherwise be a single Ha peak
has been split into two sub-peaks (a doublet), one upfield and one downfield of the original signal. These ideas an be illustrated by
a splitting diagram, as shown below.
Now, let's think about the Hb signal. The magnetic environment experienced by Hb is influenced by the fields of both neighboring
Ha protons, which we will call Ha1 and Ha2. There are four possibilities here, each of which is equally probable. First, the magnetic
fields of both Ha1 and Ha2 could be aligned with B0, which would deshield Hb, shifting its NMR signal slightly downfield. Second,
both the Ha1 and Ha2 magnetic fields could be aligned opposed to B0, which would shield Hb, shifting its resonance signal slightly
upfield. Third and fourth, Ha1 could be with B0 and Ha2 opposed, or Ha1 opposed to B0 and Ha2 with B0. In each of the last two
cases, the shielding effect of one Ha proton would cancel the deshielding effect of the other, and the chemical shift of Hb would be
unchanged.
So in the end, the signal for Hb is a triplet, with the middle peak twice as large as the two outer peaks because there are two ways
that Ha1 and Ha2 can cancel each other out.
While this coupling most often occurs between the same nuclei as seen in the proton spectrum above, nuclei of different atoms will
couple if they are in close enough proximity. For example, if the 13C NMR spectrum of 1,1,2-trichloroethane were obtained, there
would be two signals. Since the carbon atoms are not equivalent, they would couple each other. In practice this is not typically a
concern due to the low natural abundance of 13C. The carbon signals would also couple with the protons making for a very
complex signal. As many molecules contain multiple protons, we often seek to eliminate this complication. In this case,
the 13C{1H} NMR spectrum would be obtained. The {1H} indicates proton decoupling which means irradiating the sample with a
frequency such that the protons become 'invisible' and no coupling to them is seen. Running decoupled spectra is very common for
non-hydrogen nuclei.
Video tutorials: proton NMR spectroscopy
Video of an actual NMR experiment
Contributors
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We come now to the question of why nonequivalent protons have different resonance frequencies and thus different chemical
shifts. The chemical shift of a given proton is determined primarily by interactions with the nearby electrons. The most important
thing to understand is that when electrons are subjected to an external magnetic field, they form their own small induced magnetic
fields in opposition to the external field.
Consider the methane molecule (C H ) in which the four equivalent protons have a chemical shift of 0.23 ppm. The valence
4
electrons around the methyl carbon, when subjected to B0, generate their own very small induced magnetic field that opposes B0.
This induced field, to a small but significant degree, shields the nearby protons from experiencing the full force of B0, an effect
known as local diamagnetic shielding. In other words, the methane protons do not quite experience the full force of B0 - what they
experience is called Beff, or the effective field, which is slightly weaker than B0 due to the influence of the nearby electrons.
Because Beff is slightly weaker than B0, the resonance frequency (and thus the chemical shift) of the methane proton is slightly
lower than what it would be if it did not have electrons nearby and was feeling the full force of B0. (You should note that the figure
above is not to scale: the applied field is generated by a superconducting magnet and is extremely strong, while the opposing
induced field from the electrons is comparatively very small.)
Now consider methyl fluoride, CH3F, in which the protons have a chemical shift of 4.26 ppm, significantly higher than that of
methane. This is caused by something called the deshielding effect. Recall that fluorine is very electronegative: it pulls electrons
towards itself, effectively decreasing the electron density around each of the protons. For the protons, being in a lower electron
density environment means less diamagnetic shielding, which in turn means a greater overall exposure to B0, a stronger Beff, and a
higher resonance frequency. Put another way, the fluorine, by pulling electron density away from the protons, is deshielding them,
leaving them more exposed to B0. As the electronegativity of the substituent increases, so does the extent of deshielding, and so
does the chemical shift. This is evident when we look at the chemical shifts of methane and three halomethane compounds
(remember that electronegativity increases as we move up a column in the periodic table, so fluorine is the most electronegative
and bromine the least).
CH4 CH3Br CH3Cl CH3F
0.23 ppm 2.68 ppm 3.05 ppm 4.26 ppm
Table 2.4.4.1. 1H NMR chemical shifts for CH3X compounds.

To a large extent, then, we can predict trends in chemical shift by considering how much deshielding is taking place near a proton.
The chemical shift of trichloromethane (common name chloroform) is, as expected, higher than that of dichloromethane, which is
in turn higher than that of chloromethane.
CH4 CH3Cl CH2Cl2 CHCl3
0.23 ppm 3.05 ppm 5.30 ppm 7.26 ppm
Table 2.4.4.2. 1H NMR chemical shifts for CH4-nCln compounds.

The deshielding effect of an electronegative substituent diminishes significantly with increasing distance.
Contributors
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CHAPTER OVERVIEW
Back Matter
Index
Glossary
1
Index
A L sp2 hybrid orbital
antibonding Linear 2.4: Hybrid Orbitals
2.5.5: Molecular Orbital Diagrams 2.3: The VSEPR Model sp3 hybrid orbital
B M sp3d hybrid orbital
bent Magnetic Moment
2.3: The VSEPR Model 2.8.1: The Origin of the NMR Signal
sp3d2 hybrid orbital
bond angle metallic bonding
2.3: The VSEPR Model 2.6: The Range of Bonding
spectroscopy
bond order Molecular Geometry 2.8.2: Chemical Equivalence
2.5.5: Molecular Orbital Diagrams 2.2: Molecular Shapes 2.8.3: The 1H-NMR experiment
Bond Polarity molecular orbital 2.8.4: Spin-Spin Coupling
2.5.1: Molecular Shape and Molecular Polarity 2.5.5: Molecular Orbital Diagrams 2.8.5: The Basis for Differences in Chemical Shift
bonding molecular orbital Molecular orbital diagram square pyramidal
2.5.5: Molecular Orbital Diagrams 2.5.5: Molecular Orbital Diagrams 2.3: The VSEPR Model
symmetry elements
C N 2.7.1: Symmetry Elements and Operations
Chemical Equivalence NMR symmetry operations

2.8.2: Chemical Equivalence 2.8.1: The Origin of the NMR Signal
chemical shift 2.8.2: Chemical Equivalence
2.8.3: The 1H-NMR experiment T
Tetrahedral
D 2.2: Molecular Shapes
debye (unit) O trigonal bipyramidal
2.5.1: Molecular Shape and Molecular Polarity Octahedral 2.3: The VSEPR Model
diamagnetic 2.3: The VSEPR Model Trigonal Planar
diamagnetic anisotropy P trigonal pyramidal
2.8.5: The Basis for Differences in Chemical Shift paramagnetic 2.3: The VSEPR Model
diamagnetic deshielding 2.5.5: Molecular Orbital Diagrams
2.8.5: The Basis for Differences in Chemical Shift polar covalent bond V
diamagnetic shielding 2.5.1: Molecular Shape and Molecular Polarity Valence Bond Theory
dipole moment S valence shell electron pair repulsion
seesaw theory
2.3: The VSEPR Model 2.3: The VSEPR Model
H Solvents VSEPR
2.8.3: The 1H-NMR experiment 2.3: The VSEPR Model
hybrid orbital
sp hybrid orbital
hybridization
Glossary
Sample Word 1 | Sample Definition 1
CHAPTER OVERVIEW
3: Solid state
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1
In the chemistry of molecular compounds, we are accustomed to the idea that properties depend strongly on structure. For example
we can rationalize the polarity of the water molecule based on its shape. We also know that two molecules with the same
composition (e.g., ethanol and dimethyl ether) have very different properties based on the bonding arrangements of atoms. It should
come as no surprise that the properties of extended solids are also connected to their structures, and so to understand what they do
we should begin with their crystal structures. Most of the metals in the periodic table have relatively simple structures and so this is
a good place to begin.
Over 2/3 of the elements in the periodic table exist in their pure form as metals. All elemental metals (except the three - Cs, Ga, Hg - that are
liquid) are crystalline solids at room temperature, and most have one of three simple crystal structures.
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Crystals can be thought of as repeating patterns, much like wallpaper or bathroom tiles, but in three dimensions. The fundamental
repeating unit of the crystal is called the unit cell. It is a three dimensional shape that can be repeated over and over by unit
translations to fill space (and leave minimal gaps) in the structure. Some possible unit cells are shown in the tiling pattern at the
right, along with arrows that indicate unit translation vectors. In three dimensions, the hexagonal or rhombic unit cells of this
pattern would be replaced by three dimensional boxes that would stack together to fill all space. As shown in the figure, the origin
of the unit cell is arbitrary. The same set of boxes will fill all space no matter where we define the origin of the lattice. We will see
that pure metals typically have very simple crystal structures with cubic or hexagonal unit cells. However the crystal structures of
alloys can be quite complicated.
When considering the crystal structures of metals and alloys, it is not sufficient to think of each atom and its neighboring ligands as
an isolated system. Instead, think of the entire metallic crystal as a network of atoms connected by a sea of shared valence
electrons. The electrons are delocalized because there are not enough of them to fill each "bond" between atoms with an electron
pair. For example, in the crystal structures of s-block and p-block metals, each atom has either 8 or 12 nearest neighbors, but the
maximum number of s + p electrons is 8. Thus, there are not enough to put two electrons between each pair of atoms. Transition
metals can also use their d-orbitals in bonding, but again there are never enough electrons to completely fill all the "bonds."
Possible unit cells in a periodic tile pattern. The arrows connect translationally equivalent points (lattice points) in the pattern.
The atoms in a metal lattice arrange themselves in a certain pattern which can be represented as a 3D box structure known as the
unit cell which repeats across the entire metal.
Simple Cubic Body Centered Cubic Face Centered Cubic Hexagonal Close Packed
1 atom/cell 2 atoms/cell 4 atoms/cell 2 atoms/cell
Metal atoms can be approximated as spheres, and therefore are not 100 % efficient in packing, the same way a stack of cannonballs
has some empty spaces between the balls. Different unit cells have different packing efficiencies. The number of atoms that is
included in the unit cell only includes the fractions of atoms inside of the box. Atoms on the corners of the unit cell count as ⅛ of
an atom, atoms on a face count as ½, an atom in the center counts as a full atom. Using this, let's calculate the number of atoms in a
simple cubic unit cell, a face centered cubic (fcc) unit cell, and a body centered cubic (bcc) unit cell.
Simple Cubic:
8 corner atoms × ⅛ = 1 atom/cell. The packing in this structure is not efficient (52%) and so this structure type is very rare for
metals.
Body Centered Cubic, bcc:
(8 corner atoms × ⅛) + (1 center atom × 1)= 2 atoms/cell. The packing is more efficient (68%) and the structure is a common one
for alkali metals and early transition metals. Alloys such as brass (CuZn) also adopt these structures.
Face Centered Cubic, fcc (also called Cubic Close Packed, ccp):
(8 corner atoms × ⅛)+ (6 face atoms × ½)= 4 atoms/cell. This structure, along with its hexagonal relative (hcp), has the most
efficient packing (74%). Many metals adopt either the fcc or hcp structure.
Hexagonal Close Packed, hcp:
Like the fcc structure, the packing density of hcp is 74%.
The unit cell of a bcc metal contains two atoms.
Calculating the packing fraction. The packing fractions of the crystal structures shown above can be calculated by dividing the
volume of the atoms in the cell by the volume of the cell itself. The volume of the atoms in the cell is equal to the number of
atoms/cell times the volume of a sphere, (4/3)πr3. The volume of the cubic cells is found by cubing the side length. As an example,
let's calculate the packing efficiency of a simple cubic unit cell. As we saw earlier in the section, a simple cubic unit cell contains
one atom. The side length of the simple cubic unit cell is 2r, since the centers of each atom occupy the corners of the unit cell.
4 3
(1 atom) × ( )π r
3
Packing efficiency = = 0.523 (3.2.1)
3
(2r)
The same method can be applied to bcc and fcc structures.
Face-centered cubic stack of cannonballs.
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Crystal structures
Most metals and alloys crystallize in one of three very common structures: body-centered cubic (bcc), hexagonal close packed
(hcp), or cubic close packed (ccp, also called face centered cubic, fcc). In all three structures the coordination number of the metal
atoms (i.e., the number of equidistant nearest neighbors) is rather high: 8 for bcc, and 12 for hcp and ccp. We can contrast this with
the low coordination numbers (i.e., low valences - like 2 for O, 3 for N, or 4 for C) found in nonmetals. Atoms in metallic crystals
have a tendency to pack in dense arrangments that fill space efficiently.
Periodic trends in structure and metallic behavior

Remember where we find the metallic elements in the periodic table - everywhere except the upper right corner. This means that as
we go down a group in the p-block (let's say, group IVA, the carbon group, or group VA, the nitrogen group), the properties of the
elements gradually change from nonmetals to metalloids to metals. The carbon group nicely illustrates the transition. Starting at the
top, the element carbon has two stable allotropes - graphite and diamond. In each one, the valence of carbon atoms is exactly
satisfied by making four electron pair bonds to neighboring atoms. In graphite, each carbon has three nearest neighbors, and so
there are two single bonds and one double bond. In diamond, there are four nearest neighbors situated at the vertices of a
tetrahedron, and so there is a single bond to each one.
The two elements right under carbon (silicon and germanium) in the periodic table also have the diamond structure (recall that
these elements cannot make double bonds to themselves easily, so there is no graphite allotrope for Si or Ge). While diamond is a
good insulator, both silicon and germanium are semiconductors (i.e., metalloids). Mechanically, they are hard like diamond. Like
carbon, each atom of Si and Ge satisfies its valence of four by making single bonds to four nearest neighbors.
The next element under germanium is tin (Sn). Tin has two allotropes, one with the diamond structure, and one with a slightly
distorted bcc structure. The latter has metallic properties (metallic luster, malleability), and conductivity about 109 times higher
than Si. Finally, lead (Pb), the element under Sn, has the ccp structure, and also is metallic. Note the trends in coordination number
and conducting properties:
Element Structure Coord. no. Conductivity
C graphite, diamond 3, 4 semimetal, insulator
Si diamond 4 semiconductor
Ge diamond 4 semiconductor
Sn diamond, distorted bcc 4, 8 semiconductor, metal
Pb ccp 12 metal
The elements C, Si, and Ge obey the octet rule, and we can easily identify the electron pair bonds in their structures. Sn and Pb, on
the other hand, adopt structures with high coordination numbers. They do not have enough valence electrons to make electron pair
bonds to each neighbor (this is a common feature of metals). What happens in this case is that the valence electrons become
"smeared out" or delocalized over all the atoms in the crystal. It is best to think of the bonding in metals as a crystalline
arrangement of positively charged cores with a "sea" of shared valence electrons gluing the structure together. Because the
electrons are not localized in any particular bond between atoms, they can move in an electric field, which is why metals conduct
electricity well. Another way to describe the bonding in metals is nondirectional. That is, an atom's nearest neighbors surround it in
every direction, rather than in a few particular directions (like at the corners of a tetrahedron, as we found for diamond). Nonmetals
(insulators and semiconductors), on the other hand, have directional bonding. Because the bonding is non-directional and
coordination numbers are high, it is relatively easy to deform the coordination sphere (i.e., break or stretch bonds) than it is in the
case of a nonmetal. This is why elements like Pb are much more malleable than C, Si, or Ge.
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In metals, the valence electrons are in molecular orbitals that extend over the entire crystal lattice. Metals are almost always
crystalline and the individual crystal grains are typically micron size. This means that the spatial extent of the orbitals is very large
compared to the size of the atoms or the unit cell. The diagram shows a generic plot of electron energy vs. density of states for a
metal such as Na, Cu, or Ag. In these cases, there are N orbitals for N electrons, and each orbital can accommodate two electrons.
Therefore the Fermi level, which corresponds to the energy of the highest occupied MO at zero temperature, is somewhere in the
middle of the band of orbitals. The energy level spacing between orbitals is very small compared to the thermal energy kT, so we
can think of the orbitals as forming a continuous band.
Classically, if the electrons in this band were free to be thermally excited, we would expect them to have a specific heat of 3R per
mole of electrons. However, experimentally we observe that Cp is only about 0.02 R per mole. This suggests that only about 1% of
the electrons in the metal can be thermally excited at room temperature. However, essentially all of the valence electrons are free to
move in the crystal and contribute to electrical conduction. To understand this apparent paradox, we need to recall that the electrons
exist in quantized energy levels.
Because of quantization, electrons in metals have a Fermi-Dirac distribution of energies. In this distribution, most of the electrons
are spin-paired, although the individual electrons in these pairs can be quite far apart since the orbitals extend over the entire
crystal. A relatively small number of electrons at the top of the Fermi sea are unpaired by thermal excitation. This is the origin of
the Pauli paramagnetism of metals.
How fast are electrons traveling in a typical metal? Because of the bell shape of the E vs. DOS curve, most of the electrons have
E ≈ EF. At the midpoint energy (EF) of the band, the MO's have one node for every two atoms. We can calculate the de Broglie
wavelength as twice the distance between nodes and thus:
λ = 4a at the midpoint of the band.
where a is the interatomic spacing. Since a typical value of a is about 2 Å, we obtain the de Broglie wavelength λ ≈ 8 Å.
Using the de Broglie relation p = h/λ, we can write:
h
p = = me vF (3.4.1)
λ
where me is the mass of the electron and vF is the velocity of electrons with energy EF.
−34
(6.62×10 Js)
Solving for VF =
h
me λ
we obtain v
F = −31 −10
6
= 1.0 × 10 m/s
(9.1×10 kg)(8×10 m)
Experimental values of vF are 1.07 x 106 and 1.39 x 106 m/s for Na and Ag, respectively, so our approximations are pretty good.
How fast are electrons moving in metals? Really, really fast!! 1,000,000 meters per second! This is about 1/300 the speed of light,
and about 3000 times the speed of sound in air (3 x 102 m/s).
However, the drift velocity of electrons in metals - the speed at which electrons move in applied electric field - is quite slow, on
the order of 0.0001 m/s, or .01 cm/s. You can easily outrun an electron drifting in a metal, even if you have been drinking all night
and have been personally reduced to a very slow crawl.
In order to understand the great disparity between the Fermi velocity and the drift velocity of electrons in metals, we need to
consider a picture for the scattering of electrons, and their acceleration in an electric field, as shown at the left. If we apply a
voltage across a metal (e.g., a metal wire), the electrons are subjected to an electric field E, which is the voltage divided by the
length of the wire. This electric field exerts a force on the electron, causing it to accelerate. However, the electron is frequently
scattered, mostly by phonons (lattice vibrations). Each time the electron is scattered its acceleration starts all over again. The time
between scattering events is τ and the distance the electrons travel between scattering events is the mean free path, λ. (Note that
this is NOT the same λ as the de Broglie wavelength, they just unfortunately have the same symbol!)
We can write the force on the electron as:
me vdrift
F = eE = me a = (3.4.2)
τ
In this equation, a is the acceleration in the electric field, me is the mass, and vdrift is the drift velocity of the electron.
Experimentally, the mean free path is typically obtained by measuring the scattering time. For an electron in Cu metal at 300 K, the
scattering time τ is about 2 x 10-14 s. From this we can calculate the mean free path as:
6 −14
λ = vavg τ ≈ vF τ = (1 × 10 m/s)(2 × 10 ) = 40nm (3.4.3)
The mean free path (40 nm = 400 Å) is quite long compared to the interatomic spacing (2 Å). To put it in perspective, if the
interatomic spacing were scaled to the length of a football (0.3 m), the mean free path would be over half the length of the football
field (60 m). Thus an electron travels a fairly long way between scattering events and scarcely notices the atomic structure of the
metal in which it is traveling.
To summarize, electrons are traveling in metals at the Fermi velocity vF, which is very, very fast (106 m/s), but the flux of electrons
is the same in all directions. That is, they are going nowhere fast. In an electric field, a very small but directional drift velocity is
superimposed on this fast random motion of valence electrons.
From F = ma, we obtain the acceleration (a) as:We can calculate the drift velocity of electrons as the acceleration in the electric
field times the scattering time:
F eE
a= = (3.4.4)
me me
And thus,
eEτ
vdrift = aτ = (3.4.5)
me
If we divide both sides of this equation by the magnitude of the electric field (E), we obtain the mobility (μ):
vdrift eτ
μ = = (3.4.6)
E me
μ has units of velocity/field = cm/s / V/cm = cm2/Vs

An important consequence of the calculation of vdrift is Ohm's Law, V = iR. From the equations above, we can see that the drift
velocity increases linearly with the applied electric field. The drift velocity (cm/s) is proportional to the current (i, coul/s), and the
electric field (E, V/cm) is proportional to the voltage (V):
Current (i) = nevdrift × area (3.4.7)
Voltage (V) = E × length (3.4.8)
Here n is the density of valence electrons (#/cm3) and e is the charge of the electron (coul). Combining these equations with our
equation for vdrift we obtain:
me (
V = i( ) area) = iR (3.4.9)
2
ne τ length
Thus, V = iR, where R is the combination of the two terms in parentheses. The first of these is the resistivity, ρ, and the second is a
geometrical factor.
The conductivity (σ) of a metal, which is the inverse of ρ, is proportional to μ, which in turn is proportional to τ (and λ):
2
ne τ
σ = neμ = (3.4.10)
me
We can use this equation to work out the conductivity of a specific metal (Cu), for which n = 8.5 x 1022 cm-3 and τ = 2 x 10-14 s.
Putting in the numbers for me and e, we obtain σ = 7 x 105 Ω-1 cm-1 for Cu, in good agreement with the measured value (6 x 105
Ω-1cm-1).
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The MO picture we developed in Section 6.4 helps us rationalize the electrical conductivity of Na (3s1), but what about Mg, which
(as an atom in the gas phase) has a 3s2 electronic configuration? The two valence electrons are spin-paired in atomic Mg, as they
are in the helium atom (1s2). When the 3s orbitals of Mg combine to form a band, we would expect the band to be completely
filled, since Mg has two electrons per orbital. By this reasoning, solid Mg should be an insulator. But Mg has all the properties of a
metal: high electrical and thermal conductivity, metallic luster, malleability, etc. In this case the 3s and 3p bands are sufficiently
broad (because of strong orbital overlap between Mg atoms) that they form a continuous band. This band, which contains a total of
four orbitals (one 3s and three 3p) per atom, is only partially filled by the two valence electrons.
Another way to think about this is to consider the hybridization of the 3s and 3p electrons in Mg. Hybridization requires
promotion from the 3s23p0 ground state of an Mg atom to a 3s13p1 excited state. The promotion energy (+264 kJ/mol) is more
than offset by the bonding energy (-410 kJ/mol), the energy released when gaseous atoms in the excited state condense to form the
metallic solid. The heat of vaporization, or the cohesive energy of a metal, is the difference between the bonding energy and the
promotion energy. Experimentally, we can measure the vaporization energy (+146 kJ/mol) and the promotion energy and use them
to calculate the bonding energy. From this we learn that each s or p electron is worth about 200 kJ/mol in bonding energy. The
concepts of promotion energy and bonding energy are very useful in rationalizing periodic trends in the bond strengths and
magnetic properties of metals, which are described below.
The cohesive energy of Mg metal is the difference between the bonding and promotion energies. The ground state of a gas phase Mg atom is
[Ar]3s2, but it can be promoted to the [Ar]3s13p1 state, which is 264 kJ/mol above the ground state. Mg uses two electrons per atom to make
bonds, and the sublimation energy of the metal is 146 kJ/mol.
Filling of the 3d and 4s,4p bands

In the 3d series, we see magnetic behavior for elements and alloys between Cr and Ni. Past Ni, the elements (Cu, Zn, Ga,...) are no
longer magnetic and they are very good electrical conductors, implying that their valence electrons are highly delocalized. We can
understand this behavior by considering the overlap of 4s, 4p, and 3d orbitals, all of which are close in energy. The 4s and 4p have
strong overlap and form a broad, continuous band. On the other hand, the 3d electrons are contracted and form a relatively narrow
band. Progressing from the early 3d elements (Sc, Ti, V), we begin to fill the 3d orbitals, which are not yet so contracted that they
cannot contribute to bonding. Thus, the valence electrons in Sc, Ti, and V are all spin-paired, except for a small number near the
Fermi level that give rise to a weak Pauli paramagnetism. Moving across the 3d series to the magnetic elements (Fe, Co, Ni), the d-
orbitals are now so contracted that their electrons unpair and we see cooperative ordering of spins (ferromagnetism and
antiferromagnetism). Referring to the band diagram at the right, the 3d band is only partially filled and the Fermi level cuts through
it. For Cu, Zn, and Ga, the 3d orbitals are even more contracted and the 3d band is thus more narrow, but now it is completely filled
and the Fermi level is in the 4s,4p band. The strong orbital overlap in these bands results in spin pairing and a high degree of
electron delocalization. Consequently, metals in this part of the periodic table (Cu, Ag) are diamagnetic and are among the best
electrical conductors at room temperature. Finally, at Ge, the 4s,4p band is completely filled and the solid is a semiconductor.
Progressive filling of the 3d and 4s,4p bands going across the periodic table from Sc to Ge.
Materials are classified as diamagnetic if they contain no unpaired electrons. Diamagnetic substances are very weakly repelled
from an inhomogeneous magnetic field. Molecules or ions that have unpaired spins are paramagnetic and are attracted to a magnet,
i.e., they move towards the high field region of an inhomogeneous field. This attractive force results from the alignment of spins
with the field, but in the case of paramagnetism each molecule acts independently. In metals, alloys, oxides, and other solid state
compounds, the unpaired spins interact strongly with each other and can order spontaneously, resulting in the cooperative magnetic
phenomena described below.
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The magnetism of metals and other materials are determined by the orbital and spin motions of the unpaired electrons and the way
in which unpaired electrons align with each other. All magnetic substances are paramagnetic at sufficiently high temperature,
where the thermal energy (kT) exceeds the interaction energy between spins on neighboring atoms. Below a certain critical
temperature, spins can adopt different kinds of ordered arrangements.
A pictorial description of the ordering of spins in ferromagnetism, antiferromagnetism, ferrimagnetism, and paramagnetism
Let's begin by considering an individual atom in the bcc structure of iron metal. Fe is in group VIIIb of the periodic table, so it has
eight valence electrons. The atom is promoted to the 4s13d7 state in order to make bonds. A localized picture of the d-electrons for
an individual iron atom might look like this:
Since each unpaired electron has a spin moment of 1/2, the total spin angular momentum, S, for this atom is:
S =3
1
2
=
3
2
(in units of h/2π)
We can think of each Fe atom in the solid as a little bar magnet with a spin-only moment S of 3/2. The spin moments of neigboring
atoms can align in parallel (↑ ↑), antiparallel (↑ ↓), or random fashion. In bcc Fe, the tendency is to align parallel because of the
positive sign of the exchange interaction. This results in ferromagnetic ordering, in which all the spins within a magnetic domain
(typically hundreds of unit cells in width) have the same orientation, as shown in the figure at the right. Conversely, a negative
exchange interaction between neighboring atoms in bcc Cr results in antiferromagnetic ordering. A third arrangement,
ferrimagnetic ordering, results from an antiparallel alignment of spins on neighboring atoms when the magnetic moments of the
neighbors are unequal. In this case, the spin moments do not cancel and there is a net magnetization. The ordering mechanism is
like that of an antiferromagnetic solid, but the magnetic properties resemble those of a ferromagnet. Ferrimagnetic ordering is most
common in metal oxides.
Magnetization and susceptibility

The magnetic susceptibility, χ, of a solid depends on the ordering of spins. Paramagnetic, ferromagnetic, antiferromagnetic, and
ferrimagnetic solids all have χ > 0, but the magnitude of their susceptibility varies with the kind of ordering and with temperature.
We will see these kinds of magnetic ordering primarily among the 3d and 4f elements and their alloys and compounds. For
example, Fe, Co, Ni, Nd2Fe14B, SmCo5, and YCo5 are all ferromagnets, Cr and MnO are antiferromagnets, and Fe3O4 and
CoFe2O4 are ferrimagnets. Diamagnetic compounds have a weak negative susceptibility (χ < 0).
Definitions
H = applied magnetic field (units: Henry (H))
B = induced magnetic field in a material (units: Tesla (T))
M = magnetization, which represents the magnetic moments within a material in the presence of an external field H.
Magnetic susceptibility χ = M/H
Usually, χ is given in molar units in the cgs system:
χM = molar susceptibility (units: cm3/mol)
Typical values of χM:
Compound Type of Magnetism χ at 300K (cm3/mol)
SiO2 Diamagnetic - 3 x 10-4
Pt metal Pauli paramagnetic + 2 x 10-4
Gd2(SO4)3.8H2O Paramagnetic + 5 x 10-2
Ni-Fe alloy Ferromagnetic + 104 - 106
To correlate χ with the number of unpaired electrons in a compound, we first correct for the small diamagnetic contribution of the
core electrons:
corr obs diamagnetic cores
χ =χ −χ (3.6.1)
Susceptibility of paramagnets
For a paramagnetic substance,
C
corr
χ = (3.6.2)
M
T
The inverse relationship between the magnetic susceptibility and T, the absolute temperature, is called Curie's Law, and the
proportionality constant C is the Curie constant:
NA
2
C = μ (3.6.3)
ef f
3kB
Note that C is not a "constant" in the usual sense, because it depends on µeff, the effective magnetic moment of the molecule or
ion, which in turn depends on its number of unpaired electrons:
−−−−−−−
μef f = √ n(n + 2) μB (3.6.4)
Curie law behavior of a paramagnet. A plot of 1/χ vs. absolute temperature is a straight line, with a slope of 1/C and an intercept of zero.
Here µB is the Bohr magneton, a physical constant defined as µB = eh/4πme = 9.274 x 10-21 erg/gauss (in cgs units).
In cgs units, we can combine physical constants,
NA
2
μ = .125 (3.6.5)
B
3kB
Combining these equations, we obtain

.125 μef f
corr 2
χ = ( ) (3.6.6)
M
T μB
These equations relate the molar susceptibility, a bulk quantity that can be measured with a magnetometer, to µeff, a quantity that
can be calculated from the number of unpaired electrons, n. Two important points to note about this formula are:
The magnetic susceptibility is inversely proportional to the absolute temperature, with a proportionality constant C (Curie's
Law)
So far we are talking only about paramagnetic substances, where there is no interaction between neighboring atoms.
Number of unpaired electrons per atom, determined from Curie constants of transition metals and their 1:1 alloys.
Returning to the isolated Fe atom with its three unpaired electrons, we can measure the Curie constant for iron metal (above the
temperature of its transition to a paramagnetic solid) and compare it to the calculation of µeff. Since n = 3, we calculate:
−−−−−
μef f = √(3)(5)μB = 3.87 μB (3.6.7)
The plot at the right shows the number of unpaired electrons per atom, calculated from measured Curie constants, for the magnetic
elements and 1:1 alloys in the 3d series. The plot peaks at a value of 2.4 spins per atom, slightly lower than we calculated for an
isolated iron atom. This reflects that fact that there is some pairing of d-electrons, i.e., that they do contribute somewhat to bonding
in this part of the periodic table.
Susceptibility of ferro-, ferri-, and antiferromagnets

Below a certain critical temperature, the spins of a solid paramagnetic substance order and the susceptibility deviates from simple
Curie-law behavior. Because the ordering depends on the short-range exchange interaction, this critical temperature varies widely.
Metals and alloys in the 3d series tend to have high critical temperatures because the atoms are directly bonded to each other and
the interaction is strong. For example, Fe and Co have critical temperatures (also called the Curie temperature, Tc, for
ferromagnetic substances) of 1043 and 1400 K, respectively. The Curie temperature is determined by the strength of the magnetic
exchange interaction and by the number of unpaired electrons per atom. The number of unpaired electrons peaks between Fe and
Co as the d-band is filled, and the exchange interaction is stronger for Co than for Fe. In contrast to ferromagnetic metals and
alloys, paramagnetic salts of transition metal ions typically have critical temperatures below 1K because the magnetic ions are not
directly bonded to each other and thus their spins are very weakly coupled in the solid state. For example, in gadolinium sulfate, the
paramagnetic Gd3+ ions are isolated from each other by SO42- ions.
Magnetic susceptibility vs temperature (Kelvin) for ferrimagnetic, ferromagnetic, and antiferromagnetic materials
Above the critical temperature TC, ferromagnetic compounds become paramagnetic and obey the Curie-Weiss law:
C
χ = (3.6.8)
T − Tc
This is similar to the Curie law, except that the plot of 1/χ vs. T is shifted to a positive intercept TC on the temperature axis. This
reflects the fact that ferromagnetic materials (in their paramagnetic state) have a greater tendency for their spins to align in a
magnetic field than an ordinary paramagnet in which the spins do not interact with each other. Ferrimagnets follow the same kind
of ordering behavior. Typical plots of χ vs. T and 1/χ vs. T for ferro-/ferrimagnets are shown above and below.
Plots of 1/χ vs. T for ferromagnets, ferrimagnets, and antiferromagnets.
Antiferromagnetic solids are also paramagnetic above a critical temperature, which is called the Néel temperature, TN. For
antiferromagnets, χ reaches a maximum at TN and is smaller at higher temperature (where the paramagnetic spins are further
disordered by thermal energy) and at lower temperature (where the spins pair up). Typically, antiferromagnets retain some positive
susceptibility even at very low temperature because of canting of their paired spins. However the maximum value of χ is much
lower for an antiferromagnet than it is for a ferro- or ferrimagnet. The Curie-Weiss law is also modified for an antiferromagnet,
reflecting the tendency of spins (in the paramagnetic state above TN) to resist parallel ordering. A plot of 1/χ vs. T intercepts the
temperature axis at a negative temperature, -θ, and the Curie-Weiss law becomes:
C
χ = (3.6.9)
T +θ
Ordering of spins below TC

Below TC, the spins align spontaneously in ferro- and ferrimagnets. Complex magnetization behavior is observed that depends on
the history of the sample. For example, if a ferromagnetic material is cooled in the absence of an applied magnetic field, it forms a
mosaic structure of magnetic domains that each have internally aligned spins. However, neighboring domains tend to align the
opposite way in order to minimize the total energy of the system. This is illustrated in the figure at the left for a Nd-Fe-B magnet.
The sample consists of 5-10 µm wide crystal grains that can be easily distinguished by the sharp boundaries in the image. Within
each grain are a series of lighter and darker stripes (imaged by using the optical Kerr effect) that are ferromagnetic domains with
opposite orientations. Averaged over the whole sample, these domains have random orientation so the net magnetization is zero.
Microcrystalline grains within a piece of Nd2Fe14B (the alloy used in neodymium magnets) with magnetic domains made visible with a Kerr
microscope. The domains are the light and dark stripes visible within each grain.
When a sample like this one is magnetized (i.e., exposed to a strong magnetic field), the domain walls move and the favorably
aligned domains grow at the expense of those with the opposite orientation. This transformation can be seen in real time in the Kerr
microscope. The domain walls are typically hundreds of atoms wide, so movement of a domain wall involves a cooperative tilting
of spin orientation (analogous to "the wave" in a sports stadium) and is a relatively low energy process.
The movement of domain walls in a grain of silicon steel is driven in this movie by increasing the external magnetic field in the "downward"
direction, and is imaged using a Kerr microscope. White areas are domains with their magnetization directed up, dark areas - which eventually
comprise the entire grain - are domains with their magnetization directed down.
The process of magnetization moves the solid away from its lowest energy state (random domain orientation), so magnetization
involves input of energy. When the external magnetic field is removed, the domain walls relax somewhat, but the solid (especially
in the case of a "hard" magnet) can retain much of its magnetization. If you have ever magnetized a nail or a paper clip by using a
permanent magnet, what you were doing was moving the walls of the magnetic domains inside the ferromagnet. The object
thereafter retains the "memory" of its magnetization. However, annealing a permanent magnet destroys the magnetization by
returning the system to its lowest energy state in which all the magnetic domains cancel each other.
Rotation of orientation and increase in size of magnetic domains in response to an externally applied magnetic field.
Magnetic hysteresis. Cycling a ferro- or ferrimagnetic material in a magnetic field results in hysteresis in the magnetization of the
material, as shown in the figure at the left. At the beginning, the magnetization is zero, but it begins to rise rapidly as the magnetic
field is applied. At high field, the magnetic domains are aligned and the magnetization is said to be saturated. When the field is
removed, a certain remanent magnetization (indicated as the point Br on the graph) is retained, i.e., the material is magnetized.
Applying a field in the opposite direction begins to orient the magnetic domains in the other direction, and at a field Hc (the
coercive field), the magnetization of the sample is reduced to zero. Eventually the material reaches saturation in the opposite
direction, and when the field is removed again, it has remanent magnetization Br, but in the opposite direction. As the field
continues to reverse, the magnet follows the hysteresis loop as indicated by the arrows. The area of colored region inside the loop is
proportional to the magnetic work done in each cycle. When the field cycles rapidly (for example, in the core of a transformer, or in
read-write cycles of a magnetic disk) this work is turned into heat.
Magnetization of a ferro- or ferrimagnet vs. applied magnetic field H. Starting at the origin, the upward curve is the initial magnetization curve.
The downward curve after saturation, along with the lower return curve, form the main loop. The intercepts Hc and Br are the coercivity and
remanent magnetization.
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Whether a ferro- or ferrimagnetic material is a hard or a soft magnet depends on the strength of the magnetic field needed to align
the magnetic domains. This property is characterized by Hc, the coercivity. Hard magnets have a high coercivity (Hc), and thus
retain their magnetization in the absence of an applied field, whereas soft magnets have low values.
The figure at the right compares hysteresis loops for hard and soft magnets. Recall that the energy dissipated in magnetizing and
demagnetizing the material is proportional to the area of the hysteresis loop. We can see that soft magnets, while they can achieve a
high value of Bsat, dissipate relatively little energy in the loop. This makes soft magnets preferable for use in transformer cores,
where the field is switched rapidly. Permalloy, an alloy consisting of about 20% Fe and 80% Ni, is a soft magnet that has very high
magnetic permeability µ (i.e., a large maximum slope of the B vs. H curve) and a very narrow hysteresis loop.
Some materials, such as iron metal, can exist as either hard or soft magnets. Whether bcc iron is a hard or soft magnet depends on
the crystal grain size. When crystal grains in iron are sub-micron size, and comparable to the size of the magnetic domains, then the
magnetic domains are pinned by crystal grain boundaries. When the magnetic domains are pinned a stronger coercive magnetic
field needs to be applied to cause them to re-align. When iron is annealed, the crystal grains grow and the magnetic domains
become more free to align with applied magnetic fields. This decreases the coercive field and the material becomes a soft magnet.
Hysteresis loops comparing a hard magnet (iron-silicon steel) to a soft magnet (permalloy) on the same scale. Hc for permallloy is 0.05 Oe, about
10 times lower than that of the hard magnet. The remanent magnetizations of the two materials are comparable.
Hard magnets such as CrO2, γ-Fe2O3, and cobalt ferrite (CoFe2O4) are used in magnetic recording media, where the high coercivity
allows them to retain the magnetization state (read as a logical 0 or 1) of a magnetic bit over long periods of time. Hard magnets are
also used in disk drives, refrigerator magnets, electric motors and other applications. Drive motors for hybrid and electric vehicles
such as the Toyota Prius use the hard magnet Nd2Fe14B (also used to make strong refrigerator magnets) and require 1 kilogram (2.2
pounds) of neodymium.[6]. A high-resolution transmission electron microscope image of Nd2Fe14B is shown below and compared
to the crystal structure with the unit cell marked.
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“Crystals are like people, it is the defects in them which tend to make them interesting!” - Colin Humphreys.
Metals, by virtue of their non-directional bonding, are more energetically tolerant of defects than are covalent network or ionic
solids. Because there is no strong preference for one atomic position over another, the energy of a metallic crystal is not greatly
impaired by the vacancy of a single atom or by the dislocation of a group of atoms. These kinds of "mistakes" in the packing of
metal atoms within crystals are collectively called defects. The deformability of metals is the direct result of defects in the crystal
structure. Defects in metals such as Al and Fe are responsible for the three orders of magnitude difference between the yield stress
of annealed polycrystalline samples (i.e., normal articles of commerce) and perfect single crystals.
Grains and grain boundaries in a polycrystalline material
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X-ray Crystallography is a scientific method used to determine the arrangement of atoms of a crystalline solid in three dimensional
space. This technique takes advantage of the interatomic spacing of most crystalline solids by employing them as a diffraction
gradient for x-ray light, which has wavelengths on the order of 1 angstrom (10-8 cm).
Introduction
In 1895, Wilhelm Rontgen discovered X-rays. The nature of X-rays, whether they were particles or electromagnetic radiation, was
a topic of debate until 1912. If the wave idea was correct, researchers knew that the wavelength of this light would need to be on
the order of 1 Angstrom (Å) (10-8 cm). Diffraction and measurement of such small wavelengths would require a gradient with
spacing on the same order of magnitude as the light.
In 1912, Max von Laue, at the University of Munich in Germany, postulated that atoms in a crystal lattice had a regular, periodic
structure with interatomic distances on the order of 1 Å. Without having any evidence to support his claim on the periodic
arrangements of atoms in a lattice, he further postulated that the crystalline structure can be used to diffract X-rays, much like a
gradient in an infrared spectrometer can diffract infrared light. His postulate was based on the following assumptions: the atomic
lattice of a crystal is periodic, X-rays are electromagnetic radiation, and the interatomic distance of a crystal are on the same order
of magnitude as X-ray light. Laue's predictions were confirmed when two researchers: Friedrich and Knipping, successfully
photographed the diffraction pattern associated with the X-ray radiation of crystalline CuSO4 • 5 H2O. The science of X-ray
crystallography was born.
The arrangement of the atoms needs to be in an ordered, periodic structure in order for them to diffract the X-ray beams. A series of
mathematical calculations is then used to produce a diffraction pattern that is characteristic to the particular arrangement of atoms
in that crystal. X-ray crystallography remains to this day the primary tool used by researchers in characterizing the structure and
bonding of organometallic compounds.
Diffraction
Diffraction is a phenomena that occurs when light encounters an obstacle. The waves of light can either bend around the obstacle,
or in the case of a slit, can travel through the slits. The resulting diffraction pattern will show areas of constructive interference,
where two waves interact in phase, and destructive interference, where two waves interact out of phase. Calculation of the phase
difference can be explained by examining Figure 1 below.
In the figure below, two parallel waves, BD and AH are striking a gradient at an angle θ . The incident wave BD travels farther
o
than AH by a distance of CD before reaching the gradient. The scattered wave (depicted below the gradient) HF, travels father than
the scattered wave DE by a distance of HG. So the total path difference between path AHGF and BCDE is CD - HG. To observe a
wave of high intensity (one created through constructive interference), the difference CD - HG must equal to an integer number of
wavelengths to be observed at the angle psi, C D − H G = nλ , where λ is the wavelength of the light. Applying some basic
trigonometric properties, the following two equations can be shown about the lines:
C D = x cos(θo) (3.9.1)
and
H G = x cos(θ) (3.9.2)
where x is the distance between the points where the diffraction repeats. Combining the two equations,
x(cos θo − cos θ) = nλ (3.9.3)
Bragg's Law
Diffraction of an X-ray beam, occurs when the light interacts with the electron cloud surrounding the atoms of the crystalline solid.
Due to the periodic crystalline structure of a solid, it is possible to describe it as a series of planes with an equal interplaner
distance. As an X-ray's beam hits the surface of the crystal at an angle, θ, some of the light will be diffracted at that same angle
away from the solid (Figure 2). The remainder of the light will travel into the crystal and some of that light will interact with the
second plane of atoms. Some of the light will be diffracted at an angle θ, and the remainder will travel deeper into the solid. This
process will repeat for the many planes in the crystal. The X-ray beams travel different pathlengths before hitting the various planes
of the crystal, so after diffraction, the beams will interact constructively only if the path length difference is equal to an integer
number of wavelengths (just like in the normal diffraction case above). In the figure below, the difference in path lengths of the
beam striking the first plane and the beam striking the second plane is equal to BG + GF. So, the two diffracted beams will
constructively interfere (be in phase) only if BG + GF = nλ . Basic trigonometry will tell us that the two segments are equal to
one another with the interplaner distance times the sine of the angle θ. So we get:
BG = BC = d sin θ (3.9.4)
Thus,
2d sin θ = nλ (3.9.5)
This equation is known as Bragg's Law, discovered in 1912. {C}{C}Bragg's Law relates the distance between two planes in a
crystal and the angle of reflection to the X-ray wavelength. The X-rays that are diffracted off the crystal have to be in-phase in
order to signal. Only certain angles that satisfy the following condition will register:
nλ
sin θ = (3.9.6)
2d
For historical reasons, the resulting diffraction spectrum is represented as intensity vs. 2θ.
Instrument Components
The main components of an X-ray instrument are similar to those of many optical spectroscopic instruments. These include a
source, a device to select and restrict the wavelengths used for measurement, a holder for the sample, a detector, and a signal
converter and readout. However, for X-ray diffraction; only a source, sample holder, and signal converter/readout are required.
The Source
X-ray tubes provides a means for generating X-ray radiation in most analytical instruments. An evacuated tube houses a tungsten
filament which acts as a cathode opposite to a much larger, water cooled anode made of copper with a metal plate on it. The metal
plate can be made of any of the following metals: chromium, tungsten, copper, rhodium, silver, cobalt, and iron. A high voltage is
passed through the filament and high energy electrons are produced. The machine needs some way of controlling the intensity and
wavelength of the resulting light. The intensity of the light can be controlled by adjusting the amount of current passing through the
filament; essentially acting as a temperature control. The wavelength of the light is controlled by setting the proper accelerating
voltage of the electrons. The voltage placed across the system will determine the energy of the electrons traveling towards the
anode. X-rays are produced when the electrons hit the target metal. Because the energy of light is inversely proportional to
wavelength (E = hc = h(1/λ ), controlling the energy, controls the wavelength of the X-ray beam.
X-ray Filter
Monochromators and filters are used to produce monochromatic X-ray light. This narrow wavelength range is essential for
diffraction calculations. For instance, a zirconium filter can be used to cut out unwanted wavelengths from a molybdenum metal
target (see figure 4). The molybdenum target will produce X-rays with two wavelengths. A zirconium filter can be used to absorb
the unwanted emission with wavelength Kβ, while allowing the desired wavelength, Kα to pass through.
Signal Converter
In x-ray diffraction, the detector is a transducer that counts the number of photons that collide into it. This photon counter gives a
digital readout in number of photons per unit time.
References
1. Skoog, D . A.; Holler, F. J.; Stanley R. C.; Principles of Instrumental Analysis; Thomson Brooks/Cole: Belmont CA, 2007.
2. Sands, D. E.; Introduction to Crystallography; Dover Publications, Inc.; New York, 1975
3. Drenth, Jan. Principles of Protein x-ray Crystallography, 3rd edition. 2007, Springer Science + Business Media, LLC. pg. 14.
4. Rhodes, Gale. Crystallography Made Crystal Clear, 3rd edition. 2006, Elsevier Inc. pg. 33, 55 - 57.
5. Actual experimentation done of APS Kinase D63N Penicillium Chrysogenum.

Roman Kazantsev (UC Davis) and Michelle Towles (UC Davis)
3.9: X-ray Crystallography is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
The orientation of a surface or a crystal plane may be defined by considering how the plane (or indeed any parallel plane) intersects
the main crystallographic axes of the solid. The application of a set of rules leads to the assignment of the Miller Indices (hkl),
which are a set of numbers which quantify the intercepts and thus may be used to uniquely identify the plane or surface.
The following treatment of the procedure used to assign the Miller Indices is a simplified one and only a cubic crystal system (one
having a cubic unit cell with dimensions a x a x a ) will be considered.
The procedure is most easily illustrated using an example so we will first consider the following surface/plane:
Step 1: Identify the intercepts on the x- , y- and z- axes.

In this case the intercept on the x-axis is at x = a ( at the point (a,0,0) ), but the surface is parallel to the y- and z-axes - strictly
therefore there is no intercept on these two axes but we shall consider the intercept to be at infinity (∞) for the special case where
the plane is parallel to an axis. The intercepts on the x- , y- and z-axes are thus a , ∞ , ∞.
Step 2: Specify the intercepts in fractional co-ordinates
Co-ordinates are converted to fractional co-ordinates by dividing by the respective cell-dimension - for example, a point (x,y,z) in a
unit cell of dimensions a x b x c has fractional co-ordinates of (x/a , y/b , z/c). In the case of a cubic unit cell each co-ordinate will
simply be divided by the cubic cell constant, a. This gives
Fractional Intercepts = a/a , ∞/a, ∞/a i.e. 1 , ∞ , ∞.
Step 3: Take the reciprocals of the fractional intercepts
This final manipulation generates the Miller Indices which (by convention) should then be specified without being separated by any
commas or other symbols. The Miller Indices are also enclosed within standard brackets (….) when one is specifying a unique
surface such as that being considered here.
The reciprocals of 1 and ∞ are 1 and 0 respectively, thus yielding Miller Indices (100).
So the surface/plane illustrated is the (100) plane of the cubic crystal.
Other Examples
1. The (110) surface
Assignment
Intercepts: a , a , ∞
Fractional intercepts: 1 , 1 , ∞
Miller Indices: (110)
Assignment
Intercepts: a , a , a
Fractional intercepts: 1 , 1 , 1
The (100), (110) and (111) surfaces considered above are the so-called low index surfaces of a cubic crystal system (the "low"
refers to the Miller indices being small numbers - 0 or 1 in this case). These surfaces have a particular importance but there an
infinite number of other planes that may be defined using Miller index notation. We shall just look at one more …
Assignment
Intercepts: ½ a , a , ∞
Fractional intercepts: ½ , 1 , ∞
Further notes:
i. in some instances the Miller indices are best multiplied or divided through by a common number in order to simplify them by,
for example, removing a common factor. This operation of multiplication simply generates a parallel plane which is at a
different distance from the origin of the particular unit cell being considered. e.g. (200) is transformed to (100) by dividing
through by 2 .
ii. if any of the intercepts are at negative values on the axes then the negative sign will carry through into the Miller indices; in
¯
¯¯
such cases the negative sign is actually denoted by overstriking the relevant number. e.g. (00-1) is instead denoted by (001)
iii. in the hcp crystal system there are four principal axes; this leads to four Miller Indices e.g. you may see articles referring to an
hcp (0001) surface. It is worth noting, however, that the intercepts on the first three axes are necessarily related and not
completely independent; consequently the values of the first three Miller indices are also linked by a simple mathematical
relationship.

Roger Nix (Queen Mary, University of London)
This page titled 3.10: Miller Indices (hkl) is shared under a not declared license and was authored, remixed, and/or curated by Roger Nix.
When an X-ray is shined on a crystal, it diffracts in a pattern characteristic of the structure. In powder X-ray diffraction, the
diffraction pattern is obtained from a powder of the material, rather than an individual crystal. Powder diffraction is often easier
and more convenient than single crystal diffraction since it does not require individual crystals be made. Powder X-ray diffraction
(XRD) also obtains a diffraction pattern for the bulk material of a crystalline solid, rather than of a single crystal, which doesn't
necessarily represent the overall material. A diffraction pattern plots intensity against the angle of the detector, 2θ.
Introduction
Since most materials have unique diffraction patterns, compounds can be identified by using a database of diffraction patterns. The
purity of a sample can also be determined from its diffraction pattern, as well as the composition of any impurities present. A
diffraction pattern can also be used to determine and refine the lattice parameters of a crystal structure. A theoretical structure can
also be refined using a method known as Rietveld refinement. The particle size of the powder can also be determined by using the
Scherrer formula, which relates the particle size to the peak width. The Scherrer fomula is
0.9λ
t = −−−−−−−− (3.11.1)
2 2
√B − Bs cos θ
M
with
λ is the x-ray wavelength,
BM is the observed peak width,
B Sis the peak width of a crystalline standard, and
θ is the angle of diffraction.
To the left is an example XRD pattern for Ba 24 Ge100 . The x axis is 2θ and the y axis is the intensity.
References
1. Dann, S.E. Reactions and Characterization of SOLIDS. Royal Society of Chemistry, USA (2002).
2. Skoog, D.A.; Holler, F.J.; Crouch, S.R. Principles of Instrumental Analysis. Sixth Edition, Thomson Brooks/Cole, USA (2007).

Jason Grebenkemper
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As we noted in our discussion of metal and alloy structures, there is an intimate connection between the structures and the physical
properties of materials. As we "graduate" from simple metal structures based on sphere packings to more complex structures, we
find that this is still true. In this section we will try to systematize the structures of inorganic solids - metal oxides, halides, sulfides,
and related compounds - and develop some rules for which structures to expect based on electronegativity differences, hard-soft
acid-base rules, and other periodic trends. We will see that many of these structures are related to the sphere packings that we
learned about previously.
The morphology of twinned crystals of iron pyrite (FeS2) is related to the underlying cubic symmetry of the unit cell. Like NaCl, the pyrite crystal
structure can be thought of as a face-centered cubic array of anions (S22-) with cations (Fe2+) occupying all the octahedral holes.
Inorganic solids often have simple crystal structures, and some of these structures are adopted by large families of ionic or covalent
compounds. Examples of the most common structures include NaCl, CsCl, NiAs, zincblende, wurtzite, fluorite, perovskite, rutile,
and spinel. We will develop these structures systematically from the close packed and non-close packed lattices. Some layered
structures, such as CdCl2 and CdI2, can be thought of as relatives of simple ionic lattices with some atoms "missing."
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Many common inorganic crystals have structures that are related to cubic close packed (face-centered cubic) or hexagonal close
packed sphere packings. These packing lattices contain two types of sites or "holes" that the interstitial atoms fill, and the
coordination geometry of these sites is either tetrahedral or octahedral. An interstitial atom filling a tetrahedral hole is
coordinated to four packing atoms, and an atom filling an octahedral hole is coordinated to six packing atoms. In both the
hexagonal close packed and cubic close packed lattices, there is one octahedral hole and two tetrahedral holes per packing atom.
Question: Would anions or cations be better as packing atoms?
We might expect that anions, which are often larger than cations, would be better suited to the positions of packing atoms. While
this is often true, there are many examples of structures in which cations are the packing atoms, and others in which the distinction
is arbitrary. The NaCl structure is a good example of the latter.
One octahedral and one tetrahedral site in a face-centered cubic unit cell. Each cell contains four packing atoms (gray), four octahedral sites
(pink), and eight tetrahedral sites (blue).
In the NaCl structure, shown on the right, the green spheres are the Cl- ions and the gray spheres are the Na+ ions. The octahedral
holes in a face-centered cubic lattice can be found at fractional coordinates (1/2 1/2 1/2), (1/2 0 0), (0 1/2 0), and (0 0 1/2). There
are four of these holes per cell, and they are filled by the chloride ions. The packing atoms (Na+) have coordinates (0 0 0), (0 1/2
1/2), (1/2 1/2 0), and (1/2 0 1/2). Note that each of the Na+ positions is related to a Cl- position by a translation of (1/2 0 0).
Another way of stating this is that the structure consists of two interpenetrating fcc lattices, which are related to each other by a
translation of half the unit cell along any of the three Cartesian axes. We could have equivalently placed the Cl ions at the fcc lattice
points and the Na ions in the octahedral holes by simply translating the origin of the unit cell by (1/2 0 0). Thus the distinction
between packing and interstitial atoms in this case is arbitrary.
Crystal structure of NaCl. Both the Na+ and Cl- ions are octahedrally coordinated.
NaCl is interesting in that it is a three-dimensional checkerboard, and thus there are no NaCl "molecules" that exist in the structure.
When this structure was originally solved (in 1913 by using X-ray diffraction) by W. L. Bragg, his interpretation met resistance by
chemists who thought that precise integer stoichiometries were a consequence of the valency of atoms in molecules. The German
chemist Pfeiffer noted in 1915 that ‘the ordinary notion of valency didn’t seem to apply’, and fourteen years later, the influential
chemist Armstrong still found Bragg’s proposed structure of sodium chloride ‘more than repugnant to the common sense, not
chemical cricket’! Nevertheless, Bragg and his father, W. H. Bragg, persevered and used the then-new technique of X-ray
diffraction to determine the structures of a number of other compounds, including diamond, zincblende, calcium fluoride, and other
alkali halides. These experiments gave chemists their first real look at the atomic structure of solids, and laid the groundwork for
X-ray diffraction experiments that later elucidated the structures of DNA, proteins, and many other compounds. For their work on
X-ray diffraction the Braggs received the Nobel prize in Physics in 1915.
The lattice dimensions and positions of atoms in crystals such as NaCl are inferred from diffraction patterns.
Since each type of atom in the NaCl structure forms a face-centered cubic lattice, there are four Na and four Cl atoms per NaCl unit
cell. It is because of this ratio that NaCl has a 1:1 stoichiometry. The shaded green and gray bipyramidal structures in the NaCl
lattice show that the Na+ ions are coordinated to six Cl- ions, and vice versa. The NaCl structure can be alternatively drawn as a
stacking of close-packed layer planes, AcBaCbAcBa... along the body diagonal of the unit cell. Here the uppercase letters represent
the packing atoms, and the lower case letters are the interstitial atoms. This layered packing is illustrated below:
NaCl structure
------------ A
- - -c- - - -
------------ B
- - -a- - - -
------------ C
- - -b- - - -
------------ A
- - -c- - - -
------------ B
- - -a- - - -
------------ C
- - -b- - - -
------------ A
Note that both the packing atoms and interstitials are stacked in the sequence A-B-C-A-B-C..., in keeping with the fact that each
forms a cubic close-packed lattice.
The NaCl structure is fairly common among ionic compounds:
Alkali Halides (except CsCl, CsBr, and CsI)
Transition Metal Monoxides (TiO, VO,..., NiO)
Alkali Earth Oxides and Sulfides (MgO, CaO, BaS... except BeO and MgTe)
Carbides and Nitrides (TiC, TiN, ZrC, NbC) -these are very stable refractory, interstitial alloys (metallic)
A number of other inorganic crystal structures are formed (at least conceptually) by filling octahedral and/or tetrahedral holes in
close-packed lattices. The figure at the right shows some of the most common structures (fluorite, halite, zincblende) as well as a
rather rare one (Li3Bi) that derive from the fcc lattice. From the hcp lattice, we can make the NiAs and wurzite structures, which
are the hexagonal relatives of NaCl and zincblende, respectively.
An alternative and very convenient way to represent inorganic crystal structures (especially complex structures such as Li3Bi) is to
draw the unit cell in slices along one of the unit cell axes. This kind of representation is shown at the left for the fcc lattice and the
NaCl structure. Since all atoms in these structures have z-coordinates of either 0 or 1/2, only those sections need to be drawn in
order to describe the contents of the unit cell. It is a useful exercise to draw some of the fcc compound structures (above) in
sections.
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There are a number of compounds that have structures similar to that of NaCl, but have a lower symmetry (usually imposed by the
geometry of the anion) than NaCl itself. These compounds include:
FeS2 (pyrite, "fools gold"): S22- (disulfide) and Fe2+
CaC2 (a salt-like carbide): Ca2+ and linear C22- anions
CaCO3 (calcite, limestone, marble): Ca2+ and triangular CO32-.
The rhombohedral unit cell of the calcite crystal structure. The hexagonal c-axis is shown.
The calcite (CaCO3) crystal structure is shown above. Triangular CO32- ions fill octahedral holes between the Ca2+ ions (black
spheres) in a distorted NaCl lattice. As in NaCl, each ion is coordinated by six of the other kind. From this image we can see why
the CaCO3 structure has a lower symmetry than that of NaCl. The fourfold rotation symmetry of the NaCl unit cell is lost when the
spherical Cl- ions are replaced by triangular CO32- ions. Because of this symmetry lowering, transparent crystals calcite are
birefringent, as illustrated below.
Calcite crystals are birefringent, meaning that their refractive indices are different along the two principal crystal directions. This gives rise to the
phenomenon of double refraction.
NiAs structure
The NaCl structure can be described a face-centered cubic lattice with all of the octahedral holes filled. What if we start with a
hexagonal-close packed lattice rather than a face-centered cubic lattice?
Nickel arsenide crystal structure. The Ni6As trigonal prisms are shaded gray. One octahedron of six As atoms surrounding a Ni atom is shown in
the center of the figure.
This is the structure adopted by NiAs and many other transition metal sulfides, phosphides, and arsenides. The cations are shown in
gray while the anions are light blue in the figure at the right. The cations are in octahedral coordination, so each cation is
coordinated to six anions. The anions are also coordinated to six cations, but they occupy trigonal prismatic sites. In terms of layer
stacking, the NiAs structure is AcBcAcBc..., where the A and B sites (the hcp lattice) are occupied by the As atoms, and the c sites,
which are eclipsed along the layer stacking axis, are occupied by Ni. Unlike the NaCl structure, where the anion and cation sites are
interchangeable, NiAs has unique anion and cation sites. The layer stacking sequence for NiAs is shown below:
------------ A
- - -c- - - -
------------ B
- - -c- - - -
------------ A
- - -c- - - -
------------ B
- - -c- - - -
The NiAs structure cannot be adopted by ionic compounds because of the eclipsing cations, because the cation-cation repulsions
would be internally destabilizing for an ionic compound. This structure is mainly adopted by covalent and polar covalent MX
compounds, typically with "soft" X anions (S, Se, P, As,....) and low-valent transition metal cations. For example, some compounds
with the NiAs structure are: MS, MSe, MTe (M=Ti, V, Fe, Co, Ni). Often these are nonstoichiometric or complex stoichiometries
with ordered vacancies (Cr7S8, Fe7S8).
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In ccp and hcp lattices, there are two tetrahedral holes per packing atom. A stoichiometry of either M2X or MX2 gives a structure
that fills all tetrahedral sites, while an MX structure fills only half of the sites. An example of an MX2 structure is fluorite, CaF2,
whose structure is shown in the figure at the left. The packing atom in fluorite is Ca2+ and the structure is composed of three
interpenetrating fcc lattices. It should be noted that the Ca2+ ion (gray spheres) as a packing atom defies our "rule" that anions are
larger than cations and therefore must be the packing atoms. The fluorite structure is common for ionic MX2 (MgF2, ZrO2, etc.)
and M2X compounds (Li2O). In contrast, the hcp relative of the fluorite structure is quite rare because of unfavorable close contacts
between like-charged ions.
The fluorite (CaF2) crystal structure showing the coordination environments of the Ca and F atoms
In terms of geometry, Ca2+ is in cubic coordination with eight F- neighbors, and the fluoride ions are tetrahedrally coordinated by
four Ca2+ ions. The 8:4 coordination geometry is consistent with the 1:2 Ca:F stoichiometry; in all crystal structures the ratio of the
coordination numbers is the inverse of the stoichiometric ratio. The three interpenetrating fcc lattices have Ca at 0,0,0 , 1/2,1/2,0 ,
etc....F at 1/4,1/4,1/4 , 3/4,3/4,1/4 , etc... and F at 3/4,3/4,3/4 , 1/4,1/4/3/4 , etc.
Looking more closely at the tetrahedral sites in fluorite, we see that they fall into two distinct groups: T+ and T-. If a tetrahedron is
oriented with a vertex pointing upwards along the stacking axis, the site is T+. Likewise, a tetrahedron with a vertex oriented
downward is T-. The alternation of T+ and T- sites allows for efficient packing of ions in the structure. The layer stacking sequence
in this structure (including fluoride ions in the T+ and T- sites) is:
------------ A
- - -b- - - T+
- - -a- - - T-
------------ B
- - -c- - - T+
- - -b- - - T-
------------ C
- - -a- - - T+
- - -c- - - T-
------------ A
- - -b- - - T+
- - -a- - - T-
Polyhedral view of the fluorite crystal structure, showing T+ and T- Ca4F tetrahedra. The Ca2+ ions are stacked ABCABC... along the body
diagonal of the unit cell, which is the vertical direction in this image.
Tetrahedrally bonded compounds with a 1:1 stoichiometry (MX compounds) have only half of the tetrahedral sites (either the T+ or
T- sites) filled. In this case, both the M and the X atoms are tetrahedrally coordinated. The zincblende and wurtzite structures of
ZnS are 1:1 tetrahedral structures based on fcc and hcp lattices, respectively. Both structures are favored by p-block compounds
that follow the octet rule, and these compounds are usually semiconductors or insulators. The zincblende structure, shown below,
can be thought of as two interpenetrating fcc lattices, one of anions and one of cations, offset from each other by a translation of 1/4
along the body diagonal of the unit cell. Examples of compounds with the zincblende structure include CuCl, CuI, ZnSe, HgS,
BeS, CdTe, AlP, GaP, SnSb, CSi, and diamond. Additionally, the compound CuInSe2 is zincblende in an ordered, doubled unit cell
(the chalcopyrite structure). The solid solution compounds CuIn1-xGaxSe2 with this structure are among the most widely studied
materials for use in efficient thin film photovoltaic cells. Using ZnS as a representative of zincblende, the coordination of both Zn
and S atoms is tetrahedral. The layer sequence, which is AbBcCaAbBcC..., results in non-planar, six-membered ZnS rings
which allows for a relatively long distance between opposite atoms in the ring. The sequence of close-packed layers in zincblende,
filling only the T+ sites and leaving the T- sites empty, is shown below:
------------ A
- - -b- - - T+
- - - - - - T-
------------ B
- - -c- - - T+
- - - - - - T-
------------ C
- - -a- - - T+
- - - - - - T-
The zincblende unit cell
The wurtzite structure is a close relative of zinc blende, based on filling half the tetrahedral holes in the hcp lattice. Like
zincblende, wurtzite contains planes of fused six-membered rings in the chair conformation. Unlike zincblende, however, the rings
joining these planes contain non-planar, six-membered rings. The structure aligns the anions so that they are directly above the
cations in the structure, a less favorable situation sterically but a more favorable one in terms of electrostatics. As a result, the
wurtzite structure tends to favor more polar or ionic compounds (e.g., ZnO, NH4+F-) than the zincblende structure. As with
zincblende, both ions are in tetrahedral (4:4) coordination and there are typically eight valence electrons in the MX compound.
Examples of compounds with this structure include: BeO, ZnO, MnS, CdSe, MgTe, AlN, and NH4F. The layered structure of
wurtzite is AbBaAbB and the layer sequence with T+ sites filled is illustrated below:
------------ A
- - -b- - - T+
- - - - - - T-
------------ B
- - -a- - - T+
- - - - - - T-
------------ A
- - -b- - - T+
- - - - - - T-
------------ B
The chair and boat conformations of six-membered ZnS rings in the wurtzite structure.
An interesting consequence of the layer stacking in the wurtzite structure is that the crystals are polar. When cleaved along the c-
axis (the stacking axis), crystals of ZnO, ZnS, and GaN have one negatively charged face and an opposite positively charged face.
An applied electric field interacts with the crystal dipole, resulting in compression or elongation of the lattice along this direction.
For this reason crystals of compounds in the wurtzite structure are typically piezoelectric (increasing the pressure on the material
generates a voltage in the material).
Some compounds are diamorphic and can have either the zincblende or wurtzite structure. Examples of these compounds that have
intermediate polarities include CdS and ZnS. SiO2 exists in polymorphs (crystobalite and tridymite) that resemble zincblende and
wurtzite with O atoms midway between each of the Si atoms. The zincblende and wurtzite structures have efficient packing
arrangements for tetrahedrally bonded networks and are commonly found in compounds that have tetrahedral bonding. Water, for
example, has a tetrahedral hydrogen bonding network and is wurtzite-type. The undistorted wurtzite and zinc blende structures are
typically found for AX compounds with eight valence electrons, which follow the octet rule. AX compounds with nine or ten
electrons such as GaSe and GaAs crystallize in distorted variants of the wurtzite structure. In GaSe, the extra electrons form lone
pairs and this creates layers in the structure, as can be seen in the figure below. To the right of GaSe, the structures of As, Sb, and
SbAs show an ever further breakdown of the structure into layers as more valence electrons are added.
Hexagonal ice is the most stable polymorph of ice, which is obtained upon freezing at 1 atmosphere pressure. This polymorph (ice-
I) has a hcp wurtzite-type structure. Looking at the structure shown at the right, we see that there are irregular arrangements of the
O-H---O bonds. In the structure, hydrogen bonding enforces the tetrahedral coordination of each water molecule, resulting in a
relatively open structure that is less dense than liquid water. For this reason, ice floats in water.
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Layered structures are characterized by strong (and typically covalent) bonding between atoms in two dimensions and weaker
bonding in the third. A broad range of compounds including metal halides, oxides, sulfides, selenides, borides, nitrides, carbides,
and allotropes of some pure elements (B, C, P, As) exist in layered forms. Structurally, the simplest of these structures (for example
binary metal halides and sulfides) can be described as having some fraction of the octahedral and/or tetrahedral sites are filled in
the fcc and hcp lattices. For example, the CdCl2 structure is formed by filling all the octahedral sites in alternate layers of the fcc
lattice, and the CdI2 structure is the relative of this structure in the hcp lattice.
In the CdCl2 structure, the stacking sequence of anion layers is ABCABC...
In the CdI2 structure, the anion stacking sequence is ABAB..., and all the cations are eclipsed along the stacking axis.
Comparison of the CdCl2 (left) and CdI2 (right) crystal structures
These are examples of 6-3 structures, because the cations are coordinated by an octahedron of six anions, and the anions are
coordinated by three cations to make a trigonal pyramid (like NH3). Another way to describe these structures is to say that the MX6
octahedra each share six edges in the MX2 sheets.
Polyhedral drawing of one layer of the CdCl2 or CdI2 structure showing edge-sharing MX6 octahedra
Because these structures place the packing atoms (the anions) in direct van der Waals contact, they are most stable for relatively
covalent compounds. Otherwise, the electrostatic repulsion between contacting anions would destabilize the structure energetically.
More ionic MX2 compounds tend to adopt the fluorite (CaF2) or rutile (TiO2) structures, which are not layered.
Despite the fact that these two structure types are the same at the level of nearest and next-nearest neighbor ions, the CdI2 structure
is much more common than the CdCl2 structure.
CdCl2 structure:
MCl2 (M = Mg, Mn, Fe, Co, Ni, Zn, Cd)
NiBr2, NiI2, ZnBr2, ZnI2
CdI2 structure:
MCl2 (M = Ti, V)
MBr2 (M = Mg, Fe, Co, Cd)
MI2 (M = Mg, Ca, Ti, V, Mn, Fe, Co, Cd, Ge, Pb, Th)
M(OH)2 (M = Mg, Ca, Mn, Fe, Co, Ni, Cd)
MS2 (M = Ti, Zr, Sn, Ta, Pt)
MSe2 (M = Ti, Zr, Sn, V, Pt)
MTe2 (M = Ti, Co, Ni, Rh, Pd, Pt)
Physically, layered compounds are soft and slippery, because the layer planes slide past each other easily. For example, graphite,
MoS2, and talc (a silicate) are layered compounds that are used widely as lubricants and lubricant additives.
An important reaction of layered compounds is intercalation. In intercalation reactions, guest molecules and ions enter the
galleries that separate the sheets, usually with expansion of the lattice along the stacking axis. This reaction is typically reversible if
it does not perturb the bonding within the sheets. Often the driving force for intercalation is a redox reaction, i.e., electron
transfer between the host and guest. For example, lithium metal reacts with TiS2, MoS2, and graphite to produce LiTiS2, LixMoS2
(x < 1), and LiC6. In these compounds, lithium is ionized to Li+ and the sheets are negatively charged. Oxidizing agents such as
Br2, FeCl3, and AsF5 also react with graphite. In the resulting intercalation compounds, the sheets are positively charged and the
intercalated species are anionic.
Intercalation reactions are especially important for electrochemical energy storage in secondary batteries, such as lithium ion
batteries, nickel-metal hydride batteries, and nickel-cadmium batteries. The reversible nature of the intercalation reaction allows
the electrodes to be charged and discharged up to several thousand times without losing their mechanical integrity. In lithium ion
batteries, the negative electrode material is typically graphite, which is intercalated by lithium to make LiC6. Several different
oxides and phosphates containing redox active transition metal ions (Mn, Fe, Co, Ni) are used as the positive electrode materials.
Oxidative or reductive intercalation involves the placement of anions or cations between sheets.
Lithium ion batteries based on CoO2 were first described in 1980[1] by John B. Goodenough's research group at Oxford. In batteries
based on CoO2, which has the CdI2 structure, the positive electrode half-reaction is:
+ −
LiCoO ⇋ Li CoO + xLi + xe (3.16.1)
2 1 −x 2
The negative electrode half reaction is:

+ −
xLi + xe + xC ⇋ xLiC (3.16.2)
6 6
The battery is fully charged when the positive electrode is in the CoO2 form and the negative electrode is in the LiC6 form.
Discharge involves the motion of Li+ ions through the electrolyte, forming LixCoO2 and graphite at the two electrodes.
Blue plaque erected by the Royal Society of Chemistry commemorating the development of cathode materials for the lithium-ion battery
Crystal structure of LiCoO2[2]
The lithium ion battery is a "rocking chair" battery, so named because charging and discharging involve moving Li+ ions from one
side to the other. CoO2 is one example of a positive electrode material that has been used in lithium ion batteries. It has a high
energy density, but batteries based on CoO2 have poor thermal stability. Safer materials include lithium iron phosphate (LiFePO4),
and LiMO2 (M = a mixture of Co, Mn, and Ni). These batteries are used widely in laptop computers, portable electronics, cellular
telephones, cordless tools, and electric and hybrid vehicles.
A similar intercalation reaction occurs in nickel-cadmium batteries and nickel-metal hydride batteries, except in this case the
reaction involves the movement of protons in and out of the Ni(OH)2 lattice, which has the CdI2 structure:
− −
NiO(OH) + H O + e ⟶ Ni (OH) + OH (3.16.3)
2 2
There are many layered compounds that cannot be intercalated by redox reactions, typically because some other stable product is
formed. For example, the reaction of layered CdI2 with Li produces LiI (NaCl structure) and Cd metal.
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Atoms in crystals are held together by electrostatic forces, van der Waals interactions, and covalent bonding. It follows that
arrangements of atoms that can maximize the strength of these attractive interactions should be most favorable and lead to the most
commonly observed crystal structures.
Radius ratio rules

Early crystallographers had trouble solving the structures of inorganic solids using X-ray diffraction because some of the
mathematical tools for analyzing the data had not yet been developed. Once a trial structure was proposed, it was relatively easy to
calculate the diffraction pattern, but it was difficult to go the other way (from the diffraction pattern to the structure) if nothing was
known a priori about the arrangement of atoms in the unit cell. It was (and still is!) important to develop some guidelines for
guessing the coordination numbers and bonding geometries of atoms in crystals. The first such rules were proposed by Linus
Pauling, who considered how one might pack together oppositely charged spheres of different radii. Pauling proposed from
geometric considerations that the quality of the "fit" depended on the radius ratio of the anion and the cation.
Atomic and Ionic Radii. Note that cations are always smaller than the neutral atom (pink) of the same element, whereas anions are larger. Going
from left to right across any row of the periodic table, neutral atoms and cations contract in size because of increasing nuclear charge. (click for
larger image)
The basic idea of radius ratio rules is illustrated at the right. We consider that the anion is the packing atom in the crystal and the
smaller cation fills interstitial sites ("holes"). Cations will find arrangements in which they can contact the largest number of
anions. If the cation can touch all of its nearest neighbor anions, as shown at the right for a small cation in contact with larger
anions, then the fit is good. If the cation is too small for a given site, that coordination number will be unstable and it will prefer a
lower coordination structure. The table below gives the ranges of cation/anion radius ratios that give the best fit for a given
coordination geometry.
Critical Radius Ratio. This diagram is for coordination number six: 4 anions in the plane are shown, 1 is above the plane and 1 is below. The
stability limit is at rC/rA = 0.414
Coordination number Geometry ρ = rcation/ranion
2 linear 0 - 0.155
3 triangular 0.155 - 0.225
4 tetrahedral 0.225 - 0.414
4 square planar 0.414 - 0.732
6 octahedral 0.414 - 0.732
8 cubic 0.732 - 1.0
12 cuboctahedral 1.0
There are unfortunately several challenges with using this idea to predict crystal structures:
We don't know the radii of individual ions
Atoms in crystals are not really ions - there is a varying degree of covalency depending electronegativity differences
Bond distances (and therefore ionic radii) depend on bond strength and coordination number (remember Pauling's rule D(n) =
D(1) - 0.6 log n)
Ionic radii depend on oxidation state (higher charge => smaller cation size, larger anion size)
We can build up a table of ionic radii by assuming that the bond length is the sum of the radii (r+ + r-) if the ions are in contact in
the crystal. Consider for example the compounds MgX and MnX, where X = O, S, Se. All of these compounds crystallize in the
NaCl structure:
For the two larger anions (S2- and Se2-), the unit cell dimensions are the same for both cations. This suggests that the anions are in
contact in these structures. From geometric considerations, the anion radius in this case is given by:
r_{_}= \frac{r_{MX}}{\sqrt{2}}
and thus the radii of the S2- and Se2- ions are 1.84 and 1.93 Å, respectively. Once the sizes of these anions are fixed, we can obtain
a self-consistent set of cation and anion radii from the lattice constants of many MX compounds.
How well does this model work? Let's consider the structures of tetravalent metal oxides (MO2), using Pauling radii and the
predictions of the radius ratio model:
Oxide MO2 Radius ratio Predicted coord. no. Observed coord no. (structure)
CO2 ~0.1 2 2 (linear molecule)
SiO2 0.32 4 4 (various tetrahedral structures)
GeO2 0.43 4 4 (silica-like structures)
" 0.54 6 6 (rutile)
TiO2 0.59 6 6 (rutile)
ZrO2 0.68 6 7 (baddleyite)
" 0.77 8 8 (fluorite)
ThO2 0.95 8 8 (fluorite)
Note that cations have different radii depending on their coordination numbers, and thus different radius ratios are calculated for
Ge4+ with coordination numbers 4 and 6, and for Zr4+ with coordination numbers 6 and 8.
For this series of oxides, the model appears to work quite well. The correct coordination number is predicted in all cases, and
borderline cases such as GeO2 and ZrO2 are found in structures with different coordination numbers. The model also correctly
predicts the structures of BeF2 (SiO2 type), MgF2 (rutile), and CaF2 (fluorite).
What about the alkali halides NaCl, KBr, LiI, CsF, etc.? All of them have the NaCl structure except for CsCl, CsBr, and CsI, which
have the CsCl (8-8) structure. In this case the radius ratio model fails rather badly. The Li+ salts LiBr and LiI are predicted to have
tetrahedral structures, and KF is predicted to have an 8-8 structure like CsCl. We can try adjusting the radii (e.g., making the
cations larger and anions smaller), but the best we can do with the alkali halides is predict about half of their structures correctly.
Since the alkali halides are clearly ionic compounds, this failure suggests that there is something very wrong with the radius ratio
model, and its success with MO2 compounds was coincidental.
In addition to the radius ratio rule, Linus Pauling developed other useful rules that are helpful in rationalizing and also predicting
the structures of inorganic compounds. Pauling's rules[1] state that:
Stable structures are locally electroneutral. For example, in the structure of the double perovskite Sr2FeMoO6, MO6 (M =
Fe2+, Mo6+) octahedra share all their vertices, and Sr2+ ions fill the cubooctahedral cavities that are flanked by eight MO6
octahedra.[2] Each O2- ion is coordinated to one Fe2+ and one Mo6+ ion in order to achieve local electroneutrality, and thus the
FeO6 and MoO6 octahedra alternate in the structure.
Cation-cation repulsion should be minimized. Anion polyhedra can share vertices (as in the perovskite structure) without any
energetic penalty. Shared polyhedral edges, and especially shared faces, cause cation-cation repulsion and should be avoided.
For example, in rutile, the most stable polymorph of TiO2, the TiO6 octahedra share vertices and two opposite edges, forming
ribbons in the structure. In anatase TiO2, each octahedron shares four edges so the anatase polymorph is less thermodynamically
stable.
Highly charged cations in anion polyhedra tend not to share edges or even vertices, especially when the coordination number
is low. For example, in orthosilicates such as olivine (M2SiO4), there are isolated SiO44- tetrahedra.
Structure of olivine. M (Mg or Fe) = blue spheres, Si = pink tetrahedra, O = red spheres.
As we will soon see, all of Pauling's rules are justified on the basis of lattice energy considerations. In ionic compounds, the
arrangement of atoms that maximizes anion-cation interactions while minimizing cation-cation and anion-anion contacts is
energetically the best.
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Structure maps, which plot structures against properties such electronegativity, are more consistent than radius ratio rules in
correctly predicting coordination numbers and crystal structures. One of the early examples of this approach was published by
Mooser and Pearson in 1959.[3]
A Mooser-Pearson diagram maps crystal structures according to the average principal quantum numbers of the atoms and their
electronegativity difference. The basic ideas behind such a plot are:
The greater the electronegativity difference, the more ionic is the compound. Higher ionicity results in higher coordination
numbers because anions like to surround cations (and vice versa).
Higher principal quantum numbers result in less s-p hybridization, less directional bonding, and therefore higher coordination
number. We saw this trend before with the structures of elements in group IV: descending the group the coordination number
increases progressively from 3-4 (carbon) to 12 (Pb).
The lines in the Mooser-Pearson diagram separate MX compounds with CsCl, NaCl, and tetrahedral (wurtzite and zincblende)
structures. Note that wurtzite has higher ionicity than zincblende in the plot, consistent with our discussion of the "boat" and
"chair" ring structures in Chapter 8. Diamorphic compounds tend to fall on the boundaries. On the whole, the Mooser-Pearson
diagram makes far fewer errors in predicting structures than the radius ratio rule. There are similar diagrams for MX2 structures, in
which the order of ionicity is CaF2 (8:4 coordination) > rutile (6:3) > silica structures (4:2).
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Many ionic compounds have simple structures. Because the forces holding the atoms together are primarily electrostatic, we can
calculate the cohesive energy of the crystal lattice with good accuracy. Interesting questions to ask about these lattice energy
calculations are:
How accurate are lattice energy calculations?
What do they teach us about the chemical bonds in ionic crystals?
Can we use lattice energies to predict properties such as solubility, stability, and reactivity?
Can we use lattice energies to predict the crystal structures of ionic compounds?
Let's start by looking at the forces that hold ionic lattices together. There are mainly two kinds of force that determine the energy of
an ionic bond.
The NaCl crystal structure is the archetype for calculating lattice energies and computing enthalpies of formation from Born-Haber cycles.
1) Electrostatic Force of attraction and repulsion (Coulomb's Law): Two ions with charges z+ and z-, separated by a distance r,
experience a force F:
2
e z+ z−
F =− (3.19.1)
2
4πε0 r
where
e = 1.6022×10−19 C
4 π ε0 = 1.112×10−10 C²/(J m)
This force is attractive for ions of opposite charge.
The electrostatic potential energy, Eelec, is then given by
r 2
e z+ z−
Eelec ∫ F (r)dr = (3.19.2)
∞ 4πε0 r
The sign of Eelec is negative for the attractive interaction between a cation and an anion. That is, the closer oppositely charged ions
approach each other, the lower the potential energy.
2) Closed-shell repulsion. When electrons in the closed shells of one ion overlap with those of another ion, there is a repulsive
force comes from the Pauli exclusion principle. A third electron cannot enter an orbital that already contains two electrons. This
force is short range, and is typically modeled as falling off exponentially or with a high power of the distance r between atoms. For
example, in the Born approximation, B is a constant and ρ is a number with units of length, which is usually empirically
determined from compressibility data. A typical value of ρ is 0.345 Å.
−r
Erepulsion = Bexp( ) (3.19.3)
ρ
The energy of the ionic bond between two atoms is then calculated as the combination of net electrostatic and the closed-shell
repulsion energies, as shown in the figure at the right. Note that for the moment we are ignoring the attractive van der Waals energy
between ions, which we will explain below. For a pair of ions, the equilibrium distance between ions is determined by the
minimum in the total energy curve. At this distance, the net force on each ion is zero.
Electrostatic energy of a crystal lattice

We can use these equations to calculate the lattice energy of a crystal by summing up the interactions between all pairs of ions.
Because the closed-shell repulsion force is short range, this term is typically calculated only for interactions between neighboring
ions. However, the Coulomb force is long range, and must be calculated over the entire crystal. This problem was first solved in
1918 by Erwin Madelung, a German physicist.[4]
Consider an ion in the NaCl structure labeled "O" in the diagram at the right. We can see that the nearest neighbor interactions (+ -)
with ions labeled "1" are attractive, the next nearest neighbor interactions (- - and + +) are repulsive, and so on. In the NaCl
structure, counting from the ion in the center of the unit cell, there are 6 nearest neighbors (on the faces of the cube), 12 next
nearest neighbors (on the edges of the cube), 8 in the next shell (at the vertices of the cube), and so on. Their distances from ion "0"
increase progressively: ro, √2 ro, √3 ro, and so on, where ro is the nearest neighbor distance.
We can now write the electrostatic energy at ion "O" as:
2 2 2
e z+ z− e z+ z− e z+ z−
Eelec = −6 + 12 −8 +… (3.19.4)
– –
4πε0 ro 4πε0 √2ro 4πε0 √3r
o
Factoring out constants and the nearest-neighbor bond distance ro we obtain:

2
e z+ z− 12 8 6
Eelec = (6 − + − + …) (3.19.5)
– – –
4πε0 ro √2 √3 √4
Where the sum in parentheses, which is unitless, slowly converges to a value of A = 1.74756. Generalizing this formula for any
three-dimensional ionic crystal we get a function:
2
e z+ z−
Eelec = NA (3.19.6)
4πε0 ro
where N is Avogadro's number (because we are calculating energy per mole of ions) and A is called the Madelung constant. The
Madelung constant depends only on the geometrical arrangement of the ions and so it varies between different types of crystal
structures, but within a given structure type it does not change. Thus MgO and NaCl have the same Madelung constant because
they both have the NaCl structure. We will see more about the Madelung constant in an upcoming section.
The Madelung constant is calculated by summing up electrostatic interactions with ion labeled 0 in the expanding spheres method. Each number
designates the order in which it is summed. For example, ions labeled 1 represent the six nearest neighbors (attractive interaction), ions labeled 2
are the 12 next nearest neighbors (repulsive interaction) and so on. Note that if the sum is carried out over shells 1-2-3..., it converges very slowly,
but there are mathematical methods for summing it which give a rapidly converging series.
Total lattice energy of a crystal

Having in hand a formula for the electrostatic energy, we can now add in the closed-shell repulsion term to obtain an equation that
gives us the total lattice energy.
2
e z+ z− −r
EL = N A + N Bexp( ) (3.19.7)
4πε0 ro ρ
At the equilibrium bond distance, the forces on all the ions are zero, and we can use this fact to eliminate the constant B:
dE
[ ]r=r =0 (3.19.8)
o
dr
Expressed this way, EL is a negative number (because z+ and z- have opposite signs). It represents the energy change for forming
one mole of solid salt from one mole of the gaseous ions, separated initially at an infinite distance.
Lithium fluoride (shown here as a large single crystal in a beaker of water) is the only alkali halide that is not freely soluble in water. The lattice
energy of LiF is the most negative of the alkali fluorides because Li+ and F- are both small ions and EL is proportional to 1/r0.
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Now that we have an equation for the lattice energy of an ionic crystal, we can ask the question of how accurate it is. Remember,
we made several approximations in arriving at this formula. We assumed that the lattice was completely ionic, we ignored the van
der Waals attractive energy of the ions, and we assumed that there was no covalent contribution to the bonding.
Let's consider the lattice energy of table salt (NaCl)
+ −
Na + Cl ⟶ NaCl
(g) (g) (s)
To calculate the lattice energy, we lump together the physical constants:

kJ Aq1 q2 .345
EL ( ) = (1389.3) (1 − ) (3.20.1)
mol ro ro
where ro is expressed in Å. Now we can calculate the lattice energy for NaCl using ro = 2.814 Å, as:
1.7476 .345 kJ
EL = −(1389.3) (1 − ) = −766.5 (3.20.2)
2.814 2.814 mol
We can alternatively construct a Born-Haber cycle for the formation of NaCl from the elements and calculate the lattice energy as
the "missing" term in the cycle.
S= Sublimation energy of Na(s)

IP= Ionization potential of Na(g)
D= Bond dissocation energy of Cl2(g)
EA= Electron affinity of Cl(g)
EL=Lattice energy of NaCl
R= Gas constant
T= Absolute temperature
From Hess' Law: ΔH f = s+
1
2
D + I P + EA + EL − 2RT = −396
mol
kJ
Here we have to subtract 2RT to convert our cycle of energies to a cycle of enthalpies, because we are compressing two moles of
gas in making NaCl(s) and PΔV = ΔnRT, where Δn = -2.
Experimentally ΔHf for NaCl is -411 kJ/mol
Because all the other numbers in the cycle are known accurately, the error in our calculation is only about 15 kJ (about 2% of EL).
The result is promising because we neglected the van der Waals term.
But....how did we get away with neglecting the van der Waals term?
This is because we used energy minimization to obtain the repulsion energy in the Born-Mayer equation. If we underestimate the
attractive energy of the crystal lattice, the energy minimization criterion ensures that the repulsion energy is underestimated as well.
The two errors partially compensate, so the overall error in the calculation is small.
We can do better by explicitly including the short-range van der Waals attractive energy between ions. The table below shows
results of more detailed lattice energy calculations for ionic fluorides in which the van der Waals term is explicitly included. The
errors in this case are only about 1% of EL.
Compound Calculated Lattice Energy (kJ/mol) Experimental EL from Born-Haber Cycle
MgF2 (rutile structure) -2,920 -2,908
CaF2 (fluorite structure) -2,586 -2,611
BaF2 (fluorite structure) -2,326 -2,368
Silver Halides
It is interesting to repeat this exercise for the silver halides, which have either the NaCl structure (AgF, AgCl, AgBr) or zincblende
structure (AgI).
Silver Halide Calculated Cycle Difference (kJ/mol)
AgF -920 -954 34
AgCl -833 -908 75
AgBr -816 -900 84
AgI -778 -883 105
Looking at the table, we see that the error is small for AgF and becomes progressively larger for the heavier silver halides.
However we are still obtaining answers within about 12% error even for AgI. Should we interpret the good agreement with values
calculated from the ionic model to mean that these compounds are ionic? Clearly, this description is inappropriate for AgI, where
the electronegativity difference Δχ is only 0.6 (compare this value to 0.4 for a C-H bond, which we typically view as non-polar).
A drop of siver nitrate solution, when added to a dilute hydrochloric acid solution, results in the immediate formation of a white silver chloride
precipitate. This reaction is used as a qualitative test for the presence of halide ions in solutions. The covalent bonding contribution to the lattice
energies of AgCl, AgBr, and AgI makes these salts sparingly soluble in water.
Again, we can interpret the fortuitous agreement between the calculated and experimentally obtained energies in terms of
compensating errors. Our lattice energy calculation overestimates the ionic contribution in the case of the heavier silver halides, but
underestimates the covalent contribution. Of these compounds, only AgF is soluble in water and should be thought of as an ionic
compound. The others are progressively more insoluble in water (Ksp is 10-10, 10-13, and 10-16 for AgCl, AgBr, and AgI), reflecting
increasing covalency as Δχ decreases.
The moral of the story is that simple lattice energy calculations based on the ionic model work well, but they do not necessarily
imply that the compounds are ionic!
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Lattice energies can also help predict compound solubilities. Let's consider a Born-Haber cycle for dissolving a salt in water. We
can imagine this as the sum of two processes: (1) the vaporization of the salt to produce gaseous ions, characterized by the lattice
enthalpy, and (2) the hydration of those ions to produce the solution. The enthalpy change for the overall process is the sum of
those two steps. We know that the entropy change for dissolution of a solid is positive, so the solubility depends on the enthalpy
change for the overall process.
Here we need to consider the trends in both the lattice energy EL and the hydration energy EH. The lattice energy depends on the
sum of the anion and cation radii (r+ + r-), whereas the hydration energy has separate anion and cation terms. Generally the
solvation of small ions (typically cations) dominates the hydration energy because of the 1/r2 dependence.
1
EL α (3.21.1)
r+ + r−
1 1
EH α + (3.21.2)
2 2
r+ r−
For salts that contain large anions, EL doesn't change much as r+ changes. That is because the anion dominates the r+ + r- term in
the denominator of the formula for EL. On the other hand, EH changes substantially with r+, especially for small cations.
As a result, sulfate salts of small divalent cations, such as MgSO4 (epsom salts), are soluble, whereas the lower hydration energy of
Ba2+ in BaSO4 makes that salt insoluble (Ksp = 10-10).
Left: EL diagram for sulfate salts. The large SO42- ion is size-mismatched to small cations such as Mg2+, which have large hydration energies,
resulting soluble salts. With larger cations such as Ba2+, which have lower EH, the lattice energy exceeds the solvation enthalpy and the salts are
insoluble.. Right: In the case of small anions such as F- and OH-, the lattice energy dominates with small cations such as transition metal ions
(TMn+), Mg2+, and Li+. Anion-cation size mismatch occurs with larger cations, such as Cs+ and Ba2+, which make soluble fluoride salts.
For small anions, EL is more sensitive to r+, whereas EH does not depend on r+ as strongly. For fluorides and hydroxides, LiF is
slightly soluble whereas CsF is very soluble, and Mg(OH)2 is insoluble whereas Ba(OH)2 is very soluble.
Putting both trends together, we see that low solubility is most often encountered when the anion and cation match well in their
sizes, especially when one or both are multiply charged.
Space-filling models showing the van der Waals surfaces of Ba2+ and SO42-. The similarity in size of the two ions contributes to the low solubility
of BaSO4 in water.
Combining all our conclusions about solubility, we note the following trends:
1) Increasing size mismatch between the anion and cation leads to greater solubility, so CsF and LiI are the most soluble alkali
halides.
2) Increasing covalency leads to lower solubility in the salts (due to larger EL. For example, AgF, AgCl, AgBr, and AgI exhibit
progressively lower solubility because of increasing covalency.
AgF > AgCl > AgBr > AgI
3) Increasing the charge on the anion lowers the solubility because the increase in EL is large relative to the increase in EH.
4) Small, polyvalent cations (having large EH) make soluble salts with large, univalent anions such as I-, NO3-, ClO4-, PF6-, and
acetate.
Examples: Salts of transition metal and lanthanide ions
Ln3+: Nitrate salts are soluble, but oxides and hydroxides are insoluble.
Fe3+: Perchlorate is soluble, but sulfate is insoluble.
5) Multiple charged anions such as O2-, S2-, PO43-, and SO42- make insoluble salts with most M2+, M3+, and M4+ metals.
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There are three more structures, which are derived from close-packed lattices, that are particularly important because of the
material properties of their compounds. These are the spinel structure, on which ferrites and other magnetic oxides are based, the
perovskite structure, which is adopted by ferroelectric and superconducting oxides, and the rutile structure, which is a common
binary 6:3 structure adopted by oxides and fluorides.
The spinel structure is formulated MM'2X4, where M and M' are tetrahedrally and octahedrally coordinated cations, respectively,
and X is an anion (typically O or F). The structure is named after the mineral MgAl2O4, and oxide spinels have the general formula
AB2O4.
In the normal spinel structure, there is a close-packed array of anions. The A-site cations fill 1/8 of the tetrahedral holes and the B-
site cations fill 1/2 of the octahedral holes. A polyhedral view of the normal spinel unit cell is shown at the left, and a simplified
view (with the contents of the back half of the cell removed for clarity) is shown above. Each unit cell contains eight formula units
and has a composition A8B16O32.
Inverse spinels have a closely related structure (with the same large unit cell) in which the A-site ions and half of the B-site ions
switch places. Inverse spinels are thus formulated B(AB)O4, where the AB ions in parentheses occupy octahedral sites, and the
other B ions are on tetrahedral sites. There are also mixed spinels, which are intermediate between the normal and inverse spinel
structure.
Some spinel and inverse spinel AB combinations are:
A2+B3+, e.g., MgAl2O4 (normal spinel)
A4+B2+, e.g., Pb3O4 = PbII(PbIIPbIV)O4 (inverse spinel)
A6+B+, e.g., Na2WO4 (normal spinel)
Many magnetic oxides, such as Fe3O4 and CoFe2O4, are spinels.
Normal vs. inverse spinel structure

For transition metal oxide spinels, the choice of the normal vs. inverse spinel structure is driven primarily by the crystal field
stabilization energy (CFSE) of ions in the tetrahedral and octahedral sites. For spinels that contain 3d elements such as Cr, Mn, Fe,
Co, and Ni, the electron configuration is typically high spin because O2- is a weak field ligand. We will learn more about these
terms in the next section.
Ferrites are compounds of general formula MIIFe2O4. We can see that magnetite is one example of a ferrite (with M = Fe). Other
divalent metals (M = Mg, Mn, Co, Ni, Zn) also form ferrites. Ferrites can be normal or inverse spinels, or mixed spinels, depending
on the CFSE of the MII ion. Based on their CFSE, Fe2+, Co2+, and Ni2+ all have a strong preference for the octahedral site, so those
compounds are all inverse spinels. ZnFe2O4 is a normal spinel because the small Zn2+ ion (d10) fits more easily into the tetrahedral
site than Fe3+ (d5), and both ions have zero CFSE. MgFe2O4 and MnFe2O4, in which all ions have zero CFSE and no site
preference, are mixed spinels. Chromite spinels, MIICr2O4, are always normal spinels because the d3 Cr3+ ion has a strong
preference for the octahedral site.
Examples of normal and inverse spinel structures:
MgAl2O4 is a normal spinel since both Mg2+ and Al3+ are non-transition metal ions and thus CFSE = 0. The more highly
charged Al3+ ion prefers the octahedral site, where it is surrounded by six negatively charged oxygen atoms.
Mn3O4 is a normal spinel since the Mn2+ ion is a high spin d5 system with zero CFSE. The two Mn3+ ions are high spin d4
with higher CFSE on the octahedral sites (3/5 ΔO) than on the tetrahedral site (2/5 Δt ~ 1/5 ΔO).
Fe3O4 is an inverse spinel since the Fe3+ ion is a high spin d5 system with zero CFSE. Fe2+ is a high spin d6 system with
more CFSE on an octahedral site than on a tetrahedral one.
NiFe2O4 is again an inverse spinel since Ni2+ (a d8 ion) prefers the octahedral site and the CFSE of Fe3+ (a d5 ion) is zero.
FeCr2O4 is a normal spinel since Fe2+ is high spin d6 ion with C F SE = [4( ) − 2( )]Δ = Δ on an octahedral site,
2
5
3
5
o
2
5
o
and Cr3+ is a d3 ion with CFSE = 3(2/5) ΔO = 6/5 ΔO. Hence it is more energetically favorable for Cr3+ to occupy both of the
octahedral sites.
Co3O4 is a normal spinel. Even in the presence of weak field oxo ligands, Co3+ is a low spin d6 ion with very high CFSE on
the octahedral sites, because of the high charge and small size of the Co3+ ion. Hence the Co3+ ions occupy both octahedral
sites, and Co2+ occupies the tetrahedral site.
Magnetism of ferrite spinels

Ferrite spinels are of technological interest because of their magnetic ordering, which can be ferrimagnetic or antiferromagnetic
depending on the structure (normal or inverse) and the nature of the metal ions. Fe3O4, CoFe2O4, and NiFe2O4 are all inverse
spinels and are ferrimagnets. The latter two compounds are used in magnetic recording media and as deflection magnets,
respectively.
Illustration of antiferromagnetic superexchange between two transition metal cations through a shared oxygen atom.
In order to understand the magnetism of ferrites, we need to think about how the unpaired spins of metal ions are coupled in oxides.
If an oxide ion is shared by two metal ions, it can mediate the coupling of spins by superexchange as shown at the right. The
coupling can be antiferromagnetic, as shown, or ferromagnetic, depending on the orbital filling and the symmetry of the orbitals
involved. The Goodenough-Kanamori rules predict the local magnetic ordering (ferromagnetic vs. antiferromagnetic) that results
from superexchange coupling of the electron spins of transition metal ions. For ferrites, the strongest coupling is between ions on
neighboring tetrahedral and octahedral sites, and the ordering of spins between these two sites is reliably antiferromagnetic.
Because all the tetrahedral and octahedral sites in a spinel or inverse spinel crystal are coupled together identically, it works out that
ions on the tetrahedral sites will all have one orientation (e.g., spin down) and ions on all the octahedral sites will have the opposite
orientation (e.g., spin up). If the number of spins on the two sites is the same, then the solid will be antiferromagnetic. However, if
the number of spins is unequal (as in the case of Fe3O4, CoFe2O4, and NiFe2O4) then the solid will be ferrimagnetic. This is
illustrated above for Fe3O4. The spins on the Fe3+ sites cancel, because half of them are up and half are down. However, the four
unpaired electrons on the Fe2+ ions are all aligned the same way in the crystal, so the compound is ferrimagnetic.
Perovskites are ternary oxides of general formula ABO3. More generally, the perovskite formula is ABX3, where the anion X can
be O, N, or halogen. The A ions are typically large ions such as Sr2+, Ba2+, Rb+, or a lanthanide 3+ ion, and the B ions are smaller
transition metal ions such as Ti4+, Nb5+, Ru4+, etc. The mineral after which the structure is named has the formula CaTiO3.
The perovskite structure has simple cubic symmetry, but is related to the fcc lattice in the sense that the A site cations and the three
O atoms comprise a fcc lattice. The B-site cations fill 1/4 of the octahedral holes and are surrounded by six oxide anions.
ABX3 perovskite structure. A, B, and X are white, blue, and red, respectively.
The coordination of the A ions in perovsite and the arrangement of BO6 octahedra is best understood by looking at the ReO3
structure, which is the same structure but with the A-site cations removed. In the polyhedral representation of the structure shown
at the right, it can be seen that the octahedra share all their vertices but do not share any octahedral edges. This makes the ReO3 and
perovskite structures flexible, like three-dimensional wine racks, in that the octahedra can rotate and tilt cooperatively. Eight such
octahedra surround a large cuboctahedral cavity, which is the site of the A ions in the perovskite structure. Cations in these sites
are coordinated by 12 oxide ions, as expected from the relationship between the perovskite and fcc lattices.
Polyhedral representation of the ReO3 structure showing the large cuboctahedral cavity that is surrounded by 12 oxygen atoms
Because the A-site is empty in the ReO3 structure, compounds with that structure can be reversibly intercalated by small ions such
as Li+ or H+, which then occupy sites in the cuboctahedral cavity. For example, smart windows that darken in bright sunlight
contain the electrochromic material WO3, which has the ReO3 structure. In the sunlight, a photovoltaic cell drives the reductive
intercalation of WO3 according to the reaction:
+ −
xH + xe + WO ⇋ Hx WO (3.22.1)
3 3
WO3 is a light yellow compound containing d0 W(VI). In contrast, HxWO3, which is mixed-valent W(V)-W(VI) = d1-d0, has a
deep blue color. Such coloration is typical of mixed-valence transition metal complexes because their d-electrons can be excited to
delocalized conduction band levels by red light. Because the electrochemical intercalation-deintercalation process is powered by a
solar cell, the tint of the windows can adjust automatically to the level of sunlight.
Ferroelectric perovskites
The flexibility of the network of corner-sharing BO6 octahedra is also very important in ferroelectric oxides that have the
perovskite structure. In some perovsites with small B-site cations, such as Ti4+ and Nb5+, the cation is too small to fit
symmetrically in the BO6 octahedron. The octahedron distorts, allowing the cation to move off-center. These distortions can be
tetragonal (as in the example shown at the right), rhombohedral, or orthorhombic, depending on whether the cation moves
towards a vertex, face, or edge of the BO6 octahedron. Moving the cation off-center in the octahedron creates an electric dipole. In
ferroelectrics, these dipoles align in neighboring unit cells through cooperative rotation and tilting of octahedra. The crystal thus
acquires a net electrical polarization.
Tetragonal distortion of the perovskite unit cell in the ferroelectric oxide PZT, PbTixZr1-x
Ferroelectricity behaves analogously to ferromagnetism, except that the polarization is electrical rather than magnetic. In both
cases, there is a critical temperature (Tc) above which the spontaneous polarization of the crystal disappears. Below Tc, the
electric polarization of a ferroelectric can be switched with a coercive field, and hysteresis loop of polarization vs. field resembles
that of a ferromagnet. Above Tc, the crystal is paraelectric and has a high dielectric permittivity.
Ferroelectric and paraelectric oxides (along with piezoelectrics and pyroelectrics) have a wide variety of applications as switches,
actuators, transducers, and dielectrics for capacitors. Ferroelectric capacitors are important in memory devices (FRAM) and in
the tuning circuits of cellular telephones. Multiferroics, which are materials that are simultaneously ferroelectric and
ferromagnetic, are rare and are being now intensively researched because of their potential applications in electrically adressable
magnetic memory.
Halide perovskites (ABX3, X = Cl, Br, I) can be made by combining salts of monovalent A ions (A+ = Cs+, NH4+, RNH3+) and
divalent metal salts such as PbCl2 or PbI2. These compounds have sparked recent interest as light absorbers for thin film solar
cells that produce electricity from sunlight. Lead and tin halide perovskites can be grown as thin films from solution precursors or
by thermal evaporation at relatively low temperatures. In some lead halide perovskites, the mobility of electrons and holes is very
high, comparable to that of more expensive III-V semiconductors such as GaAs, which must be grown as very pure single crystals
at high temperatures for use in solar cells. Because of their high carrier mobility, some lead halide perovskites are also
electroluminescent and are of interest as inexpensive materials for light-emitting diodes (LEDs).
Tin and lead halide perovskites were first studied in the 1990s as materials for thin film electronics,[4] and more recently as light
absorbers in dye-sensitized solar cells. Soon after the results on dye-sensitized perovskite cells were reported, it was discovered that
halide perovskites could also be used in thin film solid state solar cells. The structures of these solar cells are shown schematically
at the right. The highest reported solar power conversion efficiencies of perovskite solar cells have jumped from 3.8% in 2009 [5] to
10.2% in 2012[6] and a certified 20.1% in 2014.[7]. The highest performing cells to date contain divalent lead in the perovskite B
cation site and a mixture of methylammonium and formamidinium ions in the perovskite A cation site.
a) Solar cell architecture in which a lead halide perovskite absorber coats a layer of nanocrystalline anatase TiO2. b) Thin-film solar cell, with a
layer of lead halide perovskite sandwiched between two selective contacts. c) Charge generation and extraction in the sensitized architecture and
d) in the thin-film architecture.
Despite their very impressive efficiency, perovskite solar cells are stable for relatively short periods of time and are sensitive to air
and moisture. Current research is focused on understanding the degradation mechanisms of these solar cells and improving their
stability under operating conditions.
The rutile structure is an important MX2 (X = O, F) structure. It is a 6:3 structure, in which the cations are octahedrally
coordinated by anions, and as such is intermediate in polarity between the CaF2 (8:4) and SiO2 (4:2) structures. The mineral rutile
is one of the polymorphs of TiO2, the others (anatase and brookite) also being 6:3 structures.
The rutile structure can be described as a distorted version of the NiAs structure with half the cations removed. Recall that
compounds with the NiAs structure were typically metallic because the metal ions are eclipsed along the stacking axis and thus are
in relatively close contact. In rutile, the MO6 octahedra share edges along the tetragonal c-axis, and so some rutile oxides, such as
NbO2, RuO2 and IrO2, are also metallic because of d-orbital overlap along that axis. These compounds are important as
electrolyzer catalysts and catalyst supports because they combine high catalytic activity with good electronic conductivity.
View down the tetragonal c-axis of the rutile lattice, showing edge-sharing MO6 octahedra.
Rutile TiO2, because of its high refractive index, is the base pigment for white paint. It is a wide bandgap semiconductor that has
also been extensively researched as an electrode for water splitting solar cells and as a photocatalyst (primarily as the anatase
polymorph) for degradation of pollutants in air and water. Self-cleaning glass exploits the photocatalytic properties of a thin film of
TiO2 to remove oily substances from the glass surface and improve the wetting properties of the glass.
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From the discussion above, it is clear that the lattice energy, EL, of an ionic crystal can be calculated with reasonable accuracy if the
structure is known. But how can we calculate EL for a new or hypothetical compound of unknown structure? Recall that the
reduced Madelung constant is about the same for different crystal structures. Russian chemist A. F. Kapustinskii recognized this
fact and devised a formula that allows one to calculate EL for any compound if we know the univalent radii of the constituent ions.
[5]
The Madelung constant, A, is proportional to the number of ions (n) in formula unit, so dividing by the n gives similar values as
shown in the table below:
A/n ~ invariant
Structure A/n
NaCl 0.874
CsCl 0.882
Rutile 0.803
Fluorite 0.800
Kapustinskii noticed that the difference in ionic radii between M+ and M2+ (the monovalent vs. divalent radius) largely
compensates for the differences in A/n between monovalent (NaCl, CsCl) and divalent (rutile, CaF2) structures. He thus arrived at a
lattice energy formula using an average Madelung constant, corrected to monovalent radii. In the Kapustinskii formula, the lattice
energy (kJ/mol) is given by:
1213.8 z+ z− n 0.345
EL = (1 − ) (3.23.1)
r+ + r− r+ + r−
Here the sum of the monovalent radii is used in place of ro, the bond distance in the Born-Mayer equation. The beauty of this
formula is that it requires no knowledge of the structure of the compound. Therefore it can be used, in combination with Born-
Haber cycles, to predict the stability of unknown compounds. As we show below, this is a broadly useful tool in guiding syntheses
and predicting the reactivity of inorganic solids.
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CHAPTER OVERVIEW
4: Acid-Base Theories
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1
We’ll begin our discussion of acid-base chemistry with a couple of essential definitions. The first of these was proposed in 1923 by
the Danish chemist Johannes Brønsted and the English chemist Thomas Lowry, and has come to be known as the Brønsted-Lowry
definition of acidity and basicity. An acid, by the Brønsted-Lowry definition, is a species which acts as a proton donor (i.e., it
gives away an H+), while a base is a proton (H+) acceptor. One of the most familiar examples of a Brønsted-Lowry acid-base
reaction is between hydrochloric acid and hydroxide ion:
In this reaction, a proton is transferred from HCl (the acid, or proton donor) to hydroxide ion (the base, or proton acceptor). As we
learned in the previous chapter, curved arrows depict the movement of electrons in this bond-breaking and bond-forming process.
After a Brønsted-Lowry acid donates a proton, what remains is called the conjugate base. Chloride ion is thus the conjugate base
of hydrochloric acid. Conversely, when a Brønsted-Lowry base accepts a proton it is converted into its conjugate acid form: water
is thus the conjugate acid of hydroxide ion.
Here is an organic acid-base reaction between acetic acid and methylamine:
In the reverse of this reaction, acetate ion is the base and methylammonium ion (protonated methylamine) is the acid.
For now, let’s just consider one common property of bases: in order to act as a base, a molecule must have a reactive pair of
electrons. In all of the acid-base reactions we’ll see in this chapter, the basic species has an atom with a lone pair of electrons.
When methylamine acts as a base, for example, the lone pair of electrons on the nitrogen atom is used to form a new bond to a
proton. A negative charge often (but not always!) indicates that a structure (in this case, an anion) is likely to act as a base.
Clearly, methylammonium ion cannot act as a base – it does not have a reactive pair of electrons with which to accept a proton.
In summary,
A Brønsted-Lowry acid is a proton (hydrogen ion) donor.
A Brønsted-Lowry base is a proton (hydrogen ion) acceptor.
When a Brønsted acid HA dissociates in water, it increases the concentration of hydrogen ions in the solution, H+; conversely,
Brønsted bases dissociate by taking a proton from the solvent (water) to generate OH-.
Acid dissociation
− +
H A(aq) ⇌ A +H (4.1.1)
(aq) (aq)
Acid Ionization Constant:

− +
[A ][ H ]
Ka = (4.1.2)
[H A]
Base dissociation:
+ −
B(aq) + H2 O(l) ⇌ H B + OH (4.1.3)
(aq) (aq)
Base Ionization Constant

+ −
[H B ][OH ]
Kb = (4.1.4)
[B]
The determination of a substance as a Brønsted-Lowry acid or base can only be done by observing the reaction. In the case of the
H2O it is a base in the first case and an acid in the second case.
Water does not need to be involved in a Bronsted-Lowry reaction. In general, for an acid HA and a base Z, we have
− +
HA + Z ⇌ A + HZ (4.1.5)
A Donates H to form HZ+.

Z Accepts H from A which forms HZ+
A– becomes conjugate base of HA and in the reverse reaction it accepts a H from HZ to recreate HA in order to remain in
equilibrium
HZ+ becomes a conjugate acid of Z and in the reverse reaction it donates a H to A– recreating Z in order to remain in
equilibrium
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Learning Objectives
Explain the Lewis model of acid-base chemistry
Write equations for the formation of adducts and complex ions
Perform equilibrium calculations involving formation constants
In 1923, G. N. Lewis proposed a generalized definition of acid-base behavior in which acids and bases are identified by their ability
to accept or to donate a pair of electrons and form a coordinate covalent bond.
A coordinate covalent bond (or dative bond) occurs when one of the atoms in the bond provides both bonding electrons. For
example, a coordinate covalent bond occurs when a water molecule combines with a hydrogen ion to form a hydronium ion. A
coordinate covalent bond also results when an ammonia molecule combines with a hydrogen ion to form an ammonium ion. Both
of these equations are shown here.
Definition: Lewis Acids and Bases

A Lewis acid is any species (molecule or ion) that can accept a pair of electrons, and a Lewis base is any species (molecule or
ion) that can donate a pair of electrons.
A Lewis acid-base reaction occurs when a base donates a pair of electrons to an acid. A Lewis acid-base adduct, a compound that
contains a coordinate covalent bond between the Lewis acid and the Lewis base, is formed. The following equations illustrate the
general application of the Lewis concept.
The boron atom in boron trifluoride, BF3, has only six electrons in its valence shell. Being short of the preferred octet, BF3 is a very
good Lewis acid and reacts with many Lewis bases; a fluoride ion is the Lewis base in this reaction, donating one of its lone pairs:
In the following reaction, each of two ammonia molecules, Lewis bases, donates a pair of electrons to a silver ion, the Lewis acid:
Nonmetal oxides act as Lewis acids and react with oxide ions, Lewis bases, to form oxyanions:
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Many Lewis acid-base reactions are displacement reactions in which one Lewis base displaces another Lewis base from an acid-
base adduct, or in which one Lewis acid displaces another Lewis acid:
The last displacement reaction shows how the reaction of a Brønsted-Lowry acid with a base fits into the Lewis concept. A
Brønsted-Lowry acid such as HCl is an acid-base adduct according to the Lewis concept, and proton transfer occurs because a
more stable acid-base adduct is formed. Thus, although the definitions of acids and bases in the two theories are quite different, the
theories overlap considerably.
Many slightly soluble ionic solids dissolve when the concentration of the metal ion in solution is decreased through the formation
of complex (polyatomic) ions in a Lewis acid-base reaction. For example, silver chloride dissolves in a solution of ammonia
because the silver ion reacts with ammonia to form the complex ion [Ag(NH3)2]+. The Lewis structure of the [Ag(NH3)2]+ ion is:
The equations for the dissolution of AgCl in a solution of NH3 are:

+ −
AgCl(s) ⟶ Ag (aq) + Cl (aq) (4.2.1)
+ +
Ag (aq) + 2 NH (aq) ⟶ [Ag (NH ) ] (aq) (4.2.2)
3 3 2
+ −
Net: AgCl(s) + 2 NH (aq) ⟶ [Ag (NH ) ] (aq) + Cl (aq) (4.2.3)
3 3 2
Aluminum hydroxide dissolves in a solution of sodium hydroxide or another strong base because of the formation of the complex
ion Al(OH) . The Lewis structure of the Al(OH) ion is:
−
4
−

The equations for the dissolution are:
3+ −
[Al (OH) ](s) ⟶ Al (aq) + 3 OH (aq) (4.2.4)
3
3+ − −
Al (aq) + 4 OH (aq) ⟶ [Al (OH) ] (aq) (4.2.5)
4
− −
Net: [Al (OH) ](s) + OH (aq) ⟶ [Al (OH) ] (aq) (4.2.6)
3 4
Mercury(II) sulfide dissolves in a solution of sodium sulfide because HgS reacts with the S2– ion:
2+ 2−
HgS(s) ⟶ Hg (aq) + S (aq) (4.2.7)
2+ 2− 2−
Hg (aq) + 2 S (aq) ⟶ [ HgS ] (aq) (4.2.8)
2
2− 2−
Net: HgS(s) + S (aq) ⟶ [ HgS ] (aq) (4.2.9)
2
A complex ion consists of a central atom, typically a transition metal cation, surrounded by ions, or molecules called ligands. These
ligands can be neutral molecules like H2O or NH3, or ions such as CN– or OH–. Often, the ligands act as Lewis bases, donating a
pair of electrons to the central atom. The ligands aggregate themselves around the central atom, creating a new ion with a charge
equal to the sum of the charges and, most often, a transitional metal ion. This more complex arrangement is why the resulting ion is
called a complex ion. The complex ion formed in these reactions cannot be predicted; it must be determined experimentally. The
types of bonds formed in complex ions are called coordinate covalent bonds, as electrons from the ligands are being shared with the
central atom. Because of this, complex ions are sometimes referred to as coordination complexes. This will be studied further in
upcoming chapters.
The equilibrium constant for the reaction of the components of a complex ion to form the complex ion in solution is called a
−
formation constant (Kf) (sometimes called a stability constant). For example, the complex ion [Cu(CN) ] is shown here: 2
It forms by the reaction:

+ − −
Cu (aq) + 2 CN (aq) ⇌ [Cu(CN) ] (aq) (4.2.10)
2
At equilibrium:
−
[Cu(CN) ]
2
Kf = Q = (4.2.11)
+ − 2
[ Cu ] [ CN ]
The inverse of the formation constant is the dissociation constant (Kd), the equilibrium constant for the decomposition of a complex
ion into its components in solution. We will work with dissociation constants further in the exercises for this section. Table E4 and
Table 4.2.1 are tables of formation constants. In general, the larger the formation constant, the more stable the complex; however,
as in the case of Ksp values, the stoichiometry of the compound must be considered.
Table 4.2.1 : Common Complex Ions by Decreasing Formation Constants
Substance Kf at 25 °C
[Cd(CN) ]
4
2−
3 × 1018
[Ag (NH ) ]
3 2
+
1.7 × 107
[AlF ]
6
3−
7 × 1019
As an example of dissolution by complex ion formation, let us consider what happens when we add aqueous ammonia to a mixture
of silver chloride and water. Silver chloride dissolves slightly in water, giving a small concentration of Ag+ ([Ag+] = 1.3 × 10–5 M):
+ −
AgCl(s) ⇌ Ag (aq) + Cl (aq) (4.2.12)
However, if NH3 is present in the water, the complex ion, [Ag(NH 3

) ]
2
+
, can form according to the equation:
+ +
Ag (aq) + 2 NH (aq) ⇌ [Ag (NH ) ] (aq) (4.2.13)
3 3 2
with

+
[Ag (NH ) ]
3 2 7
Kf = = 1.7 × 10 (4.2.14)
+ 2
[ Ag ] [ NH ]
3
The large size of this formation constant indicates that most of the free silver ions produced by the dissolution of AgCl combine
with NH3 to form [Ag(NH ) ] . As a consequence, the concentration of silver ions, [Ag+], is reduced, and the reaction quotient
+
3 2
for the dissolution of silver chloride, [Ag+][Cl–], falls below the solubility product of AgCl:
+ −
Q = [ Ag ][ Cl ] < Ksp (4.2.15)
More silver chloride then dissolves. If the concentration of ammonia is great enough, all of the silver chloride dissolves.
Example 4.2.1: Dissociation of a Complex Ion

+
Calculate the concentration of the silver ion in a solution that initially is 0.10 M with respect to [Ag(NH 3
) ]
2
.
Solution
We use the familiar path to solve this problem:
1. Determine the direction of change. The complex ion [Ag(NH 3

) ]
2
+
is in equilibrium with its components, as represented by
the equation:
+ +
Ag (aq) + 2 NH (aq) ⇌ [Ag (NH ) ] (aq) (4.2.16)
3 3 2
We write the equilibrium as a formation reaction because Table 4.2.1 lists formation constants for complex ions. Before
0.10
equilibrium, the reaction quotient is larger than the equilibrium constant (Kf = 1.7 x 107), and Q = =∞ (it is infinitely
0 ×0
large), so the reaction shifts to the left to reach equilibrium.
This page titled 4.2: Lewis Acids and Bases is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
15.2: Lewis Acids and Bases by OpenStax is licensed CC BY 4.0. Original source: https://openstax.org/details/books/chemistry-2e.

This page explains why complex ions of the type [M(H2O)6]n+ are acidic.
The Charge Distribution within Complex Ion

The pH of solutions containing hexaaqua ions vary a lot from one metal to another (assuming you are comparing solutions of equal
concentrations). However, the underlying explanation is the same for all of them. We'll take the hexaaquairon(III) ion,
[Fe(H2O)6]3+ as typical. The structure of the ion is:
Each of the six water molecules are attached to the central iron(III) ion via a coordinate bond using one of the lone pairs on the
oxygen. We'll choose one of these water molecules at random (it doesn't make any difference which one!), and look at the bonding
in a bit more detail - showing all the bonds around the oxygen. Imagine for the moment that the 3+ charge is located entirely on the
iron.
When the lone pairs on the oxygen atoms form coordinate bonds with the iron, there is obviously a movement of electrons towards
the iron. That has an effect on the electrons in the O-H bonds. These electrons, in turn, get pulled towards the oxygen even more
than usual. That leaves the hydrogen nuclei more exposed than normal. The overall effect is that each of the hydrogen atoms is
more positive than it is in ordinary water molecules. The 3+ charge is no longer located entirely on the iron but spread out over the
whole ion - much of it on the hydrogen atoms.
The effect of dissolving this ion in water

The hydrogen atoms attached to the water ligands are sufficiently positive that they can be pulled off in a reaction involving water
molecules in the solution. The first stage of this process is:
3 + 2 + +
Fe(H O) +H O −
↽⇀
− Fe(H O) (OH) +H O (4.3.1)
2 6 2 2 5 3
The complex ion is acting as an (Arrhenius) acid by donating a hydrogen ion to water molecules in the solution. The water is, of
course, acting as a (Arrhenius) base by accepting the hydrogen ion. Because of the confusing presence of water from two different
sources (the ligands and the solution), it is easier to simplify Equation 4.3.1:
3 + 2 + +
[Fe(H O) ] (aq) ⇌ [Fe(H O) (OH)] (aq) + H (aq) (4.3.2)
2 6 2 5
However, if you write it like this, remember that the hydrogen ion is not just falling off the complex ion. It is being pulled off by a
water molecule in the solution. Whenever you write "H (aq) " what you really mean is a hydroxonium ion, H3O+.
+
The hexaaquairon(III) ion is quite strongly acidic giving solutions with a pH around 1.5, depending on concentration. You can get
further loss of hydrogen ions as well, from a second and a third water molecule since the complex ion is a polyprotic acid.
Losing a second hydrogen ion:
2 + + +
[Fe(H O) (OH)] (aq) ⇌ [Fe(H O) (OH) ] (aq) + H (aq) (4.3.3)
2 5 2 4 2
and a third one:
+ +
[Fe(H O) (OH) ] (aq) ⇌ [Fe(H O) (OH) ](s) + H (aq) (4.3.4)
2 4 2 2 3 4
This time you end up with a neutral complex and because it has no charge, it does not dissolve to any extent in water, and a
precipitate is formed.
In practice
What do you actually get in solution if you dissolve an iron(III) salt in water? In fact you get a mixture of all the complexes that
you have seen in the equations above. These reactions are all equilibrium, so everything will be present. The proportions depend on
how concentrated the solution is.
The color of the solution is very variable and depends in part on the concentration of the solution. Dilute solutions containing
iron(III) ions can be pale yellow. More concentrated ones are much more orange, and may even produce some orange precipitate.
None of these colors represents the true color of the [Fe(H2O)6]3+ ion - which is a very pale lilac color and is only really easy to see
in solids containing the ion.
Looking at the equilibrium showing the loss of the first hydrogen ion:
3 + 2 + +
Fe(H O) +H O −
↽⇀
− Fe(H O) (OH) +H O (4.3.5)
2 6 2 2 5 3
 
pale lilac orange
The color of the new complex ion on the right-hand side is so strong that it completely masks the color of the hexaaqua ion. In
concentrated solutions, the equilibrium position will be even further to the right-hand side (Le Chatelier's Principle), and so the
color darkens. You will also get significant loss of other hydrogen ions (Equation 4.3.3 and 4.3.4) leading to some formation of the
neutral complex and thus some precipitate.
The position of this equilibrium can be shifted by adding extra hydrogen ions from a concentrated acid (e.g., by adding
concentrated nitric acid to a solution of iron(III) nitrate). The new hydrogen ions push the position of the equilibrium to the left so
that you can see the color of the hexaaqua ion. This is slightly easier to follow if you write the simplified version of the equilibrium
(Equation 4.3.2).
3+ Ions are More Acidic than 2+ ions

Solutions containing 3+ hexaaqua ions tend to have pH in the range from 1 to 3. Solutions containing 2+ ions have higher pH -
typically around 5 - 6, although they can go down to about 3. Remember that the reason that these ions are acidic is because of
the pull of the electrons towards the positive central ion. An ion with 3+ charges on it is going to pull the electrons more
strongly than one with only 2+ charges.
In 3+ ions, the electrons in the O-H bonds will be pulled further away from the hydrogen atoms than in 2+ ions. That means
that the hydrogen atoms in the water ligands will have a greater positive charge in a 3+ ion, and so will be more attracted to
water molecules in the solution. If they are more attracted, they will be more readily lost - and so the 3+ ions are more acidic.
The Effect of ionic radius on acidity

If you have ions of the same charge, it seems reasonable that the smaller the volume this charge is packed into, the greater the
distorting effect on the electrons in the O-H bonds. Ions with the same charge but in a smaller volume (a higher charge density)
would be expected to be more acidic. You would therefore expect to find that the smaller the radius of the metal ion, the stronger
the acid. Unfortunately, it's not that simple!
Almost every data source that you refer to quotes different values for ionic radii. This is because the radius of a metal ion varies
depending on what negative ion it is associated with. We are interested in what happens when the metal ion is bonded to water
ligands. Whatever values we take are unlikely to represent the real situation. In the graphs which follow, values for ionic radii from
two common sources were used so that you can see the difference it makes to the argument.
If it is true that the smaller the ionic radius, the stronger the acidity of the hexaaqua ion, you would expect some sort of regular
increase in pKa (showing weaker acids) as ionic radius increases. The following graphs plot pKa against ionic radii for the 2+ ions
of the elements in the first transition series from vanadium to copper. The first graph plots pKa against ionic radii taken from
Chemistry Data Book by Stark and Wallace.
There is a trend for several of the ions, but it is completely broken by vanadium and chromium. The second graph uses ionic radii
taken from the Nuffield Advanced Science Book of Data.
There probably is a relationship between ionic radius and acid strength. The problem is that there are other more important effects
operating as well (quite apart from differences in charge) that can completely swamp the effect of the changes in ionic radius. You
have to look in far more detail at the bonding in the hexaaqua ions and the product ions.

This page titled 4.3: Acidity of the Hexaaqua Ions is shared under a not declared license and was authored, remixed, and/or curated by Jim Clark.
The Hard Soft Acid Base Principle is a Conceptual Tool for Thinking About Patterns of Lewis acid
base Reactivity
The explanation of the trends in metal distribution, halide salt solubility, and preferred metal coordination patterns is rooted in
Arland, Chatt, and Davies' observation that Lewis acids and bases could be classified into two groups based on their propensity to
form stable compounds with one another (e.g. acids in a class tend to form more stable adducts with bases in the same class than
they did with bases in the other).1 Arland, Chatt, and Davies somewhat boringly termed these groups class a and class b but today
they are known by Ralph Pearson's name for them. Pearson called the class a acids and bases hard and class b acids and bases soft.
These terms reflect how "soft" these substance's electron clouds are towards distortion or, in other words, their polarizability
(Figure 4.4.1). Pearson terms acids and bases which are relatively polarizable soft and those which are difficult to polarize hard.
Figure 4.4.1: Polarizability refers to the ease with which a substance's electron cloud may be distorted under the action of an
electric field. An fragment's polarizability determines the degree to which its electron cloud is distorted by A.) an Ion and B.) a
polar molecule to induce a dipole moment. The figure is taken from (and the caption expanded from) Cox, Kelly and Dana Reusser
"Polarizability" in
https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Supplemental_Modules_(Physical_
and_Theoretical_Chemistry)/Physical_Properties_of_Matter/Atomic_and_Molecular_Properties/Intermolecular_Forces/Specific_I
nteractions/Polarizability
Recognizing Hard and Soft Acids and Bases

Hard acids and bases come in two varieties:
1. hard acid and base sites which possess few valence electrons and for which polarization therefore involves distorting core
electrons, which are difficult to distort because they are close to the nucleus and experience a high nuclear charge. The most
common examples of such substances are Lewis acids hard acids towards the left of the periodic table.
2. hard acids and base sites with a high charge density (highly charged relative to size) and/or which are electron deficient. In
these cases polarization involves distorting electrons that already experience strong unshielded electrostatic interactions.
Soft acids and bases also come in two varieties
1. soft acids and bases which posses many valence electrons and so are more readily polarized. In consequence, all other tings
being equal, soft acids and bases are more likely to be found towards the middle or right of the periodic table.
2. soft acids and bases with little charge density and/or which are relatively electron rich.
Note that the hard-soft classification should not be thought of as if all hard acids and bases are equally hard and all soft acids and
bases equally soft. There is a graduation in hardness and softness and a number of intermediate acids and bases which do not fit
neatly in either category. With this caveat in mind, representative hard, soft, and borderline acids are given below. Notice how
they illustrate the trends just outlined.
As expected, hard acids tend to be found towards the left side of the periodic table and involve higher oxidation states and/or
electron donating substituents while soft acids are more common to the right of the periodic table and involve lower oxidation
states and/or electron donating substituents.
Illustrative hard, soft, and borderline bases are given below. Again, notice how these substances illustrate the general trends.
Qualitative Estimation of the Relative Hardness and Softness of Lewis Acids and Bases
As can be seen from the examples above, hard acids are relatively electron-poor and hard bases electron-rich since they have
comparatively
small frontier orbitals, reflective of their relatively small atom/ion/fragment sizes
high (for acids) or low (for bases) oxidation states on the base atom, reflected in a large positive formal charge (for acids) or
negative formal charge (for bases)
low polarizability, due to loss or gain of substantial numbers of electrons, or the localization of
positive charge on an electropositive element or an atom bearing electron-withdrawing substituents
negative charge on an electronegative element or an atom bearing electron-donating substituents
In contrast to hard acids and bases soft acids are relatively electron-rich and soft bases larger and more electron poor since
they have comparatively
large frontier orbitals, reflective of their relatively large atom/ion/fragment sizes
low oxidation states, often resulting in small or nonexistent atomic charges
high polarizability, as might be expected of species in which electron-electron repulsions are lower and electrons are spread
over a large volume. Sometimes this is indicated by
positive charge on an electronegative element or an atom bearing electron-donating substituents
negative charge on an electropositive element or an atom bearing electron-withdrawing substituents
Exercise 4.4.1
Rank the acid or bases in each set in increasing order of expected hardness?
(a) Cr2+ and Cr3+
(b) H+, Cs+, and Tl+
(c) SCN- (acting as a base at N) and SCN- (acting as a base at S)
(d) AlF3, AlH3, AlMe3
(e) The side chains of the following proteinogenic amino acids
Answer
(a) Cr2+ < Cr3+ All other things being equal, hardness increases with oxidation state.
(b) Tl+ < Cs+ < H+ The order reflects Cs+ and Tl+'s larger size relative to H+ (which doesn't possess any electrons that can
be polarized anyway) and that Tl+ still possesses two valence electrons while Cs+ possesses none.
(c) SCN- (acting as a base at S) < SCN- (acting as a base at N) The order reflects that N is more elctronegative than S and
possesses a more negative formal charge of -1.
(d) AlH3 < AlMe3, AlF3 The hardness increases as the substituents on the Lewis acid Al center become less electron
donating and more electron withdrawing (and, incidentally, harder bases) as their electronegativity increases in the order H-
< CH3- < F-. Note that the order of electron donating ability for H- and CH3- is the opposite observed for carbocations, for
which hyperconjugation plays a larger role.
(e) Sec < Cys < Ser The hardness increases as the electronegativity of the Lewis base chalcogen increases on going from a
selenol to a thiol to an alcohol.
The Hard-Soft Acid-Base Principle (HSAB Principle)

The Hard-Soft acid-base principle (HSAB Principle) explains patterns in Lewis acid-base reactivity in terms of a like reacts
with like preference. Both thermodynamically and kinetically hard acids prefer hard bases and soft acids soft bases. Specifically,
Thermodynamically, hard acids form stronger acid-base complexes with hard bases while soft acids form stronger complexes
with soft bases.
Kinetically, hard acids/electrophiles react more quickly with hard bases/nucleophiles while soft acids/electrophiles react more
quickly with soft bases/neucleophiles
Applications of the HSAB principle include
1. Predicting the equilibrium or speed of Lewis acid-base metathesis and displacement reactions. In a Lewis acid-base
metathesis reaction the acids and bases swap partners
(4.4.1)
For example, the equilibrium position of the metathesis reaction between TlF and K2S favors the products:
(4.4.2)
consistent with the HSAB's hard-hard and soft-soft preference.
(4.4.3)
The HSAB principle also allows for prediction of the position of displacement reactions, in which a Lewis acid or base forms
an adduct using a base or acid from an existing Lewis acid-base complex. In these reactions, the displacement of acid or base
from the reactant complex to may be thought of as a sort of metathesis reaction, one in which in the unbound acid or base
switches places with one in the complex. For example, the reaction between HI and methylmercury cation
HI + HgSCH3+ ⇌ CH3SHgI + H+
(4.4.4)
involves displacement of an iodide from HI to give CH3HgI. The position of the equilibrium favors CH3HgI since both
CH3Hg+ and I- are both soft, while H+ is a hard acid.
(4.4.5)
Exercise 4.4.2
Predict the position of equilibrium for the following reaction.
Answer
The equilibrium will favor the reactants (K<1) since the hard-hard and soft-soft interactions in the reactants are more stable
than the hard-soft interactions in the products.
Exercise 4.4.3
Predict whether K for the following equilibria will be <<1, ~1, or >>1.
a. 2H F + (C H3 H g)2 S ⇌ 2C H3 H gF + H2 S
b. Ag(N H 3)
+
2
+ 2P H3 ⇌ Ag(P H3 )
+
2
+ 2N H3
c. Ag(P H +
3 )2 + 2 H3 B − S H2 ⇌ 2 H3 B − P H3 + Ag(S H2 )
+
d. H3B − N H3 + F3 B − S H2 ⇌ H3 B − S H2 + F3 B − N H3
Answer
a. K< < 1 since the reactant adducts are hard-hard and soft-soft while the products involve hard-soft interactions
b. K>>1 since the reactant complex, diamine silver(I) is a complex of a hard base, NH3, with the soft acid, Ag+, while the
product is a complex of the same soft acid with the soft base phosphine.
c. K~1 since all the adducts amongst the reactants and products involve soft acids and bases
d. K>>1 since BH3 is a softer acid than BF3 so it will form a stronger complex with the softer base H2S while the harder
BF3 forms a stronger complex with the harder base NH3.
2. Predicting the relative strengths of a given set of Lewis acids or bases towards a particular substrate. Consider, for
example, the relative strengths of a BH3, BMe3, and BF3 towards group 15 hydrides like NH3, PH3, and AsH3. Of the
boranes listed, the hardest acid BF3 is the strongest acid towards the hard base NH3 while BH3 is the strongest towards
AsH3.†
Exercise 4.4.4
Which acid will form the most stable complex with CO - BH3, BF3, or BMe3?
Answer
BH3. Since CO forms complexes primarily through its carbon lone pair it is a soft base and so will form the strongest
complex with the softest Lewis acid.
The Theoretical Interpretation of the Hard Soft Acid-Base Principle is that hard-hard preferences
reflect superior electrostatic stabilization while soft-soft preferences reflect superior covalent
stabilization.
The hard-hard and soft-soft preferences in Lewis acid-base interactions reflect that
The lone pair of a hard base is strongly stabilized electrostatically by a hard acid
The lone pair of a soft base is strongly stabilized by forming a covalent bond with a soft acid
The lone pair of a hard or soft base is comparatively weakly stabilized by an acid opposite to it in hardness or softness since the
overall electrostatic and covalent stabilization of the adduct is comparatively weak.
To see why this is the case it is helpful to divide the contributions to the interaction energy between an acid and a base as follows:
(4.4.6)
Of the three contributions to the interaction energy, only the ionic and covalent terms directly relate to the hardness of the
interacting acid and base. One approach to thinking about how hardness influences the ionic and covalent contributions is to
consider the frontier orbitals involved in the acid-base interaction. This is sometimes done through the use of the Salem-Klopman
equation,1,* although in the treatment which follows a more qualitative approach will be employed.
Both hard acids and bases will have comparatively low energy HOMO levels and high energy LUMO levels, with a
correspondingly high HOMO-LUMO gap. In contrast, soft acids and bases will have comparatively high-energy HOMO levels and
low-energy LUMO levels, giving a comparatively smaller HOMO-LUMO gap.
Given this, consider the frontier orbital interactions involved in the formation of an acid-base complex for the possible cases, as
illustrated schematically below.
The large gap in energy between hard bases’ highly stabilized HOMO lone pairs and the high energy LUMO of hard acids ensures
that in hard acid-hard base adducts the dominant stabilizing interaction will involve electrostatic attraction between the
base lone pair and the electropositive Lewis acid center. Fortunately, since the electron clouds in hard bases are relatively dense
and electron rich while hard Lewis acids are highly charged and small these electrostatic interactions are strong.
In contrast, in soft acid-soft base adducts the dominant stabilizing interaction will be covalent. This is because the small gap in
energy between a soft base HOMO and soft acid LUMO enables the formation of a well-stabilized bonding orbital with significant
electron density between the acid and base.
The orbitals interactions between hard acids and soft bases and soft acids and hard bases are intermediate between the hard acid-
hard base and soft acid-soft base cases.
This means that the adducts are stable relative to free acid and base – just not as well stabilized as in the hard acid and hard base
case. In the case of hard acids and soft bases the hard acids are less able to stabilize the soft bases’ relatively diffuse electron pair
electrostatically and there isn’t as much covalent stabilization as in adducts of soft acids and bases due to hard acid’s high energy.
References
1. Ahrland, S.; Chatt, J.; Davies, N. R., The relative affinities of ligand atoms for acceptor molecules and ions. Quarterly Reviews,
Chemical Society 1958, 12 (3), 265-276.
2. Pearson, R. G., Hard and Soft Acids and Bases. Journal of the American Chemical Society 1963, 85 (22), 3533-3539.
3. Fleming, I., Molecular orbitals and organic chemical reactions. Reference ed.; Wiley: Hoboken, N.J., 2010.
Notes
* Despite the fruitfulness of this observation, in general it is important to reduce the potential for observer bias by checking
observations like these against compounds reported in the chemical literature and databases like the Inorganic Crystal Structure and
Cambridge Crystallographic Databases.
** These are very soluble in water, to the point where some solutions are perhaps better described as solutions of water in the
halide.
† This can be predicted based on the relative hardness of BF3, BR3, and BH3 in the list of hard and soft acids. However, for those of
you who may be confused as to why H is considered a better electron donor for the purposes of softening a Lewis acid center while
alkyl groups are better electron donors for the purposes of stabilizing carbocations in organic chemistry, the dominant effect is the
lower electronegativity of H relative to carbon (in CH3). The effect of electron donation due to hyperconjugation isn't as great for
thermodynamically stable bases like BX3/BR3.
†† For more on the Salem-Klopman equation see Fleming, I., Molecular orbitals and organic chemical reactions. Reference ed.;
Wiley: Hoboken, N.J., 2010; pp. 138-143.

Stephen M. Contakes (Westmont College)
4.4: Hard-soft Acids and Bases is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
Pearson Absolute Hardness is a useful metric of hardness based on orbital energies
The recognition that hard acids and bases possess a large HOMO-LUMO gap suggests that the gap size itself might serve as a
useful index of hardness. The basis for this idea may be found by considering Pearson’s definition of absolute hardness, η.1
Pearson's absolute hardness, η, is half the second derivative of a species energy with respect to changes in total number of
electrons, Ne
−
2
1 d E
′
P earson s absolute hardness = η = (4.5.1)
2
2 dN
e−
(in eV )
and, since acid and bases’ hardness and softness are inversely related, Pearson’s absolute softness, σ, is just the inverse of hardness
1
′
P earson s sof tness = (4.5.2)
η
Of these, Pearson’s absolute hardness is related to the Mulliken definition of electronegativity as the first derivative of a species
energy with respect to changes in total number of electrons.
dE
M ulliken electronegativity = χ = (4.5.3)
dNe−
(in eV )
Operationally, both the Pearson hardness and Mulliken electronegativity are approximated in terms of the energies associated with
unit changes in the number of electrons – i.e. in terms of ionization energies and electronegativities. Specifically,
I E– EA
′
P earson s absolute hardness = η ≈ (4.5.4)
2
I E + EA
M ulliken electronegativity = χ ≈ (4.5.5)
2
where I E and EA are in eV
The connection between Pearson’s absolute hardness/softness and the HOMO-LUMO gap then follows from Koopman’s theorem,
in which the ionization energy (IE) is just the opposite of the HOMO energy.
I E = −EH OMO (4.5.6)
Similarly, the electron affinity (EA), defined as the opposite of the energy released on absorption of an electron, may be taken as an
approximation of the LUMO energy.
ELUMO ≈ −EA (4.5.7)
So Pearson’s absolute hardness is just half the HOMO-LUMO gap (band gap) size in electron volts
′
ELUMO – EH OMO
P earson s absolute hardness, η ≈ (4.5.8)
2
where all values are given in eV
and the Mulliken electronegativity is just the average of the HOMO and LUMO energies (~Fermi energy):
ELUMO + EH OMO
M ulliken electronegativity, χ ≈ − (4.5.9)
2
where all values are given in eV
The relationships between the Pearson absolute hardness, Mulliken electronegativity, and HOMO and LUMO energies are depicted
schematically for the group 1A monocations in Figure 4.5.1.
Figure 4.5.1 . Relationships between Pearson absolute hardness, Mulliken electronegativity, and HOMO and LUMO energies for
the group 1A monocations.
Values of the Pearson hardness and Mulliken electronegativity for several acids and bases are given in Table 4.5.1. The values in
the table confirm the expected trends, showing an increase in hardness with size (down a group), with increasing charge, and as
substituent electronegativity increases for a series of isolobal ions.
Table 4.5.1 : Pearson Absolute Hardness and Related Parameters for Selected Acids and Bases.2 Taken from Pearson, R. G., Absolute
electronegativity and hardness: application to inorganic chemistry. Inorganic Chemistry 1988, 27 (4), 734-740.
E
l
e
c
t
r
o
n
A
f
f
i
n
Species Ionization Energy, IE or I (eV) Mulliken Electronegativity, χ (eV) Pearson Absolute Hardness, η (eV)
i
t
y
,
E
A
o
r
A
(
e
V
)
Selected Acids
Group 1A monocations
5
.
Li+ 75.64 40.52 35.12
3
9
5
.
Na+ 47.29 26.21 21.08
1
4
4
.
K+ 31.63 17.99 13.64
3
4
4
.
Rb+ 27.28 15.77 11.55
1
8
3
.
Cs+ 25.1 14.5 10.6
8
9
Group 11 monocations
7
.
Cu+ 20.29 14.01 6.28
7
3
7
.
Ag+ 21.49 14.53 6.96
5
8
9
.
Au+ 20.5 14.9 5.6
2
3
Isoelectronic Row 3 Metal Cations
5
.
Na+ 47.29 26.21 21.08
1
4
1
5
Mg2+ 80.14 . 47.59 32.55
0
4
2
8
Al3+ 119.99 . 74.22 45.77
4
5
Changes with Transition Metal Ion Charge
1
6
Fe2+ 30.65 . 23.42 7.24
1
8
3
0
Fe3+ 54.8 . 42.73 12.08
6
5
1
7
Co2+ 33.50 . 25.28 8.22
0
6
2
2
Co3+ 51.3 42.4 8.9
.
5
Boron trihalides
-
3
BF3 15.81 6.2 9.7
.
5
0
.
BCl3 11.60 5.97 5.64
3
3
0
.
BBr3 10.51 5.67 4.85
8
2
-
3
CO2 13.8 5.0 8.8
.
8
0
.
CS2 10.08 5.35 5.56
6
2
Selected Bases
Group 17 monoanions (taken to be identical to the free atom values; for arguments as to why this is reasonable see Pearson, R. G., Inorg. Chem.
1988, 27 (4), 734-740.)
3
.
F- 17.42 10.41 7.01
4
0
3
.
Cl- 13.01 8.31 4.70
6
2
3
.
Br- 11.84 7.60 4.24
3
6
3
.
I- 10.45 6.76 3.70
0
6
Group 15 hydrides
-
5
NH3 10.7 2.6 8.2
.
6
-
1
PH3 10.0 4.1 6.0
.
9
Trimethylpnictides
-
4
NMe3 7.8 1.5 6.3
.
8
-
3
PMe3 8.6 2.8 5.9
.
1
-
2
AsMe3 8.7 3.0 5.7
.
7
Group 16 hydrides
-
6
H2O 12.6 3.1 9.5
.
4
-
2
H2S 10.5 4.2 6.2
.
1
Phosphorous trihalides
-
1
PF3 12.3 5.7 6.7
.
0
0
PC13 10.2 . 5.5 4.7
8
1
PBr3 9.9 . 5.6 4.2
6
Drago-Wayland Acid-Base Parameters allow for estimation of the electrostatic and covalent
contributions to the enthalpy of formation of a Lewis acid-base adduct.
Although Pearson hardness values are a useful metric of acid and bases' hardness, they cannot easily be used to estimate the Lewis
acid-base interaction energy. This is not the case for the EC model developed by Drago and Wayland.3 In the Drago and
Wayland's EC Model the enthalpy of formation of an acid base adduct, AB,
A + B ⇌ AB ΔHAB adduct (4.5.10)
from the acid (A) and base (B) can be calculated as the sum of products of electrostatic (E) and covalent (C) factors that reflect the
propensity of the acid and base to engage in strong electrostatic and covalent interactions with one another:
−ΔHAB adduct = EA EB + CA CB (4.5.11)
where EA and CA are the electrostatic and covalent parameters for the acid and EB and CB the electrostatic and covalent parameters
for the base given in units of kcal½ mol-½. E and C parameters for selected acids and bases are given in Table 4.5.2.
Table 4.5.2 : E and C Parameters for selected Lewis acids and bases according to the ECW model.4,5 Taken from Vogel, G. C.; Drago, R. S.,
The ECW Model. Journal of Chemical Education 1996, 73 (8), 701 and Drago, R. S. A modern approach to acid-base chemistry. Journal of
Chemical Education 1974, 51 (5), 300 (for BF3).
Species E (kcal½ mol-½) C (kcal½ mol-½) W (kcal mol-1) C/E
Acids
I2 0.5† 2† 0 4
ICl 2.92 1.66 0 0.57
H2O 1.31 0.78 0 0.59
SO2 0.51 1.56 0 3.1
HCCl3 (chloroform) 1.56 0.44 0 0.28
(CH3)3COH 1.07 0.69 0 0.65
(CF3)3COH 3.06 1.88 -0.87 0.61
2.27 1.07 0 0.47
2.23 1.03 0 0.46
2.30 1.11 0 0.48
1.38 0.68 0 0.49
BF3 1.62 9.88 6.10
B(CH3)3 2.90 3.60 0 1.2
Al(CH3)3 8.66 3.68 0 0.43
Ga(C2H5)3 6.95 1.48 0 0.21
In(CH3)3 6.60 2.15 0 0.33
Zn[N(Si(CH3)3)]2 2.75 2.32 0 0.84
Cd[N(Si(CH3)3)]2 2.50 1.83 0 0.73
Bases
NH3 2.31 2.04 0.88
CH3NH2 2.16 3.13 1.4
(CH3)2NH 1.80 4.21 2.3
(CH3)3N 1.21 5.61 4.6
1.78 3.54 2.0
Species E (kcal½ mol-½) C (kcal½ mol-½) W (kcal mol-1) C/E
1.81 3.73 2.0
1.53 2.94 1.9
CH3CN 1.64 0.71 0.43
ClCH2CN 1.67 0.33 0.20
CH3C(O)CH3 1.74 1.26 0.72
(C2H5)2O 1.80 1.63 0.91
1.64 2.18 1.3
1.63 0.95 0.58

(EtOAc)
2.35† 1.31 0.56
(CH3)2S 0.25 3.75 15
(CH3CH2)2S 0.24 3.92† 15
0.26 4.07 16
(CH3)2Se 0.05 4.24 83
(CH3)2SO 2.4 1.47 0.61
(CH3)3P 0.25 5.81 24
(CH3O)3P 0.13 4.83 37
(C6H5)3PO 2.59 1.67 0.64
(C6H5)3PS 0.35 3.65 10
C6H6 0.70 0.45 0.64
† These values were fixed to parameterize the rest of the E and C parameters.
Trends in the relative values of C and E for the acids and bases in Table 4.5.2 are very roughly consistent with the trends in
hardness and softness outlined earlier. However, the parameters suggest that some trends in hardness reflect changes in species
ability to engage in ionic interactions while others reflect changes in species ability to engage in strong covalent interactions. For
example, CB for the dimethylchalcogenides increases steadily from 1.5 to 4.25 kcal½ mol-½ on going from Me2O to Me2Se while
EB decreases from 1.68 to 0.05 kcal½ mol-½, suggesting that electrostatic and covalent factors are both involved in a decreases in
base hardness down group 16. However, in the case of phosphines and amines it appears that electrostatic factors are primarily
responsible for the decrease in hardness down group 15. On going from Me3N to Me3P, CB only increases slighly from 5.61 to 5.81
kcal½ mol-½while EB decreases from 1.21 to 0.25 kcal½ mol-½- i.e. to 20% of the Me3N value.
However, some species tend to have very high values for both E and C, reflecting their ability to engage in strong electrostatic and
covalent interactions while others have small values for both, reflecting their relative stability as free species in solution.
As can be seen by comparing the acids and bases listed in the absolute hardness table (Table 4.5.1) and the EC parameters table
(Table 4.5.2) The EC model has primarily been applied to organic and main group organometallic acids and bases. However, a
variety of extensions have been proposed that enable its wider applicability.
Since the simple EC model only includes electrostatic and covalent considerations and thus ignores steric, lattice energy, and other
contributions to the interaction energy. Thus it is only useful for analyzing the interaction energies of sterically unhindered adducts
in which solvation energy and other contributions to the overall interaction energy are insignificant. However, additional
refinements of the model attempt to extend its usefulness by accomodating various factors, such as
Steric strain. Specifically, Hancock and Martell6 introduced a D parameter to account for any additional steric strain introduced
on adduct formation,* giving
−ΔHAB adduct = EA EB + CA CB − DA DB (4.5.12)
Charge transfer on adduct formation. As discussed in section 6.4.2 the formation of a Lewis acid base complex results in a net
transfer of electron density from the electron donor (base) to the acceptor (acid). Drago and Wong7 extended the EC model to
include that charge transfer by adding what they called receptance factors that account for the acid's ability to receive electron
density (RA) and transference factors that account for the base's ability to donate electron density (TB), giving
−ΔHAB adduct = EA EB + CA CB + RA TB (4.5.13)
This extension of the EC model is called the electrostatic-covalent-transfer or ECT model. Notably, it has been applied
successfully to adducts involving ions, for which the RATB term can account for as much as 31% of the interaction energy.
Any constant energy term, such as the energy needed to cleave a dimer in order to make the Lewis acid (e.g. Al2Cl6 → 2AlCl3).
Drago and Vogel4 extended the EC model to accommodate these constant energy terms, which they designated W. The resulting
model is called the ECW model for which
− Δ HAB adduct = EA EB + CA CB + W (4.5.14)
where W = WA + WB
A simple application of EC and extended EC models is that they allow the enthalpy of adduct formation to be calculated. These
enthalpy calculations based on the EC model are consistent with the superior interaction energy of hard-hard and soft-soft
interactions compared to hard-soft ones. Consider, for example, the transfer of I2 between BF3 and InMe3. H3N-BF3 and H3N-
InMe3.
H3 N − BF3 + I nM e3 ⇌ BF3 + H3 N − I nM e3 (4.5.15)
Since H3N is a hard base and BF3 and InMe3 harder and softer acids, respectively, the equilibrium us expected to favor the reactant,
H3N-BF3. Assuming the equilbrium is enthalpically driven this qualitative analysis is consistent with the expected endothermic
enthalpy of the reaction, as may be seen from the calculated enthalpies of adduct formation for both H3N-BF3 and H3N-InMe3.
For H3N-BF3:
−ΔHH N −BF3 = EBF EN H + CBF CN H (4.5.16)
3 3 3 3 3
−ΔHH N −BF3 = (1.62)(2.31) + (9.88)(2.04) (4.5.17)

3
− Δ HH N −BF3 = 3.74 kcal/mol + 20.1 kcal/mol = 23.8 kcal/mol (4.5.18)

3
ΔHH N −BF3 = −23.8 kcal/mol (4.5.19)

3
For H3N-InMe3:
− Δ HH N −InM e3 = EInMe EN H + CInMe CN H (4.5.20)
3 3 3 3 3
− Δ HH N −InM e3 = (6.6)(2.31) + (2.15)(2.04) (4.5.21)

3
− Δ HH N −InM e3 = 15.25 kcal/mol + 4.39 kcal/mol = 19.63 kcal/mol (4.5.22)

3
ΔHH N −InM e3 = −19.63 kcal/mol (4.5.23)

3
So H3N-BF3 is enthalpically favored by -4.2 kcal/mol [=-23.8 kcal/mol - (-19.63 kcal/mol) according to Hess' Law].
In addition to their utility for estimating enthalpies of Lewis acid-base complex formation, EC and related models serve as a useful
tool for estimating the relative importance of ionic, covalent, and steric factors in complex formation. Specifically,
The relative contributions of ionic and covalent factors can be calculated directly as from the E and C terms. This can provide
insight into why some complexes are more stable than others. Such calculations reveal that the hard-hard adduct H3N-BF3 is
favored over the hard-soft adduct H3N-InMe3 because of the strong covalent interaction holding together H3N-BF3. The
covalent term accounts for 84% of energy of the H3N-BF3 interaction and is largely lost on formation of H3N-InMe3, for which
it contributes only 22% of the interaction energy. When the electrostatic term is accounted for it can be seen that the formation
of H3N-InMe3 from H3N-BF3 is disfavored since it would result in a loss of 15.7 kcal/mol of covalent stabilization that would
be incompletely compensated for by a gain of 11.5 kcal/mol of electrostatic stabilization.
The role of other contributions to the bonding in a Lewis acid-base complex may be estimated from the discrepancy between
experimental and EC model calculated stabilization energies. This is because the EC parameters assume sigma bonding and so
any deviation between the calculated and experimental enthalpies of complex formation can be attributed to non-sigma
contributions.
This is done explicitly in extensions of the EC model. For instance, in the case of the Hancock and Martell, ECT, and ECW
extensions of the EC model the contribution of the steric, charge transfer, and constant energy factors (like dimer
dissociation) are directly computed in the model.
Comparisons of the difference between the energies calculated using ordinary EC parameters and the observed enthalpies
has also been used as an estimate of the
steric strain energy in strained adducts, which exhibit a less exothermic heat of adduct formation than expected
π-backbonding energy in adducts which are capable of such interactions and exhibit a more exothermic heat of
formation than expected.8-10

For examples see (a) Drago, R. S., The interpretation of reactivity in chemical and biological systems with the E and C
model. Coordination Chemistry Reviews 1980, 33 (3), 251-277; (b) Drago, R. S.; Bilgrien, C. J., Inductive transfer and
coordination of ligands in metal—metal bonded systems. Polyhedron 1988, 7 (16), 1453-1468; (c) Drago, R. S., The
question of a synergistic metal-metal interaction leading to .pi.-back-bond stabilization in dirhodium tetrabutyrate adducts.
Inorganic Chemistry 1982, 21 (4), 1697-1698.
The role of electrostatic, covalent, and other contributions to the spectroscopic behavior of Lewis acid-base complexes can be
assessed similarly using specialized versions of the ECW or ECT model that allow for calculation of changes in spectroscopic
parameters on adduct formation - e.g. OH stretching frequencies. Details are beyond the scope of this text but may be found in
the original literature;11 for example Drago, R. S.; Vogel, G. C. JACS 1992, 114 (24), 9527-9532; Vogel, G. C.; Drago, R. S., J.
Chem. Educ. 1996, 73 (8), 701; Drago, R. S.; Wong, N. M., J. Chem. Educ. 1996, 73 (2), 123.).
Pearson Softness Parameters have been proposed as a means of calculating the equilibrium
constant for formation of a Lewis acid-base adduct, although they are more commonly used to
estimate metal toxicity
Pearson also proposed a softness parameter that can be used to estimate the thermodynamics of Lewis acid base complex
formation, this time in the form fo the equilibrium constant for
K
A + B ⇌ AB (4.5.24)
for which Pearson proposed
logK = SA SB + σa σB (4.5.25)
where S_A and S_B are acid and base parameters related to the strength of the acid-base interaction and σ and σ are acid and
A B
base parameters related to softness. This approach hasn't found as wide acceptance in studies of chemical reactivity as the Drago-
Wayland and absolute hardness parameters. However, because the toxicity of metal ions' sometimes depends on their propensity to
bind soft Lewis bases in living systems, the softness parameter's which Pearson and Mawby subsequently proposed based on the
relative energies of metal flourine and metal iodine bonds12 has been widely used as a tool for predicting metal ion toxicity.13
References
1. Pearson, R. G., Absolute electronegativity and absolute hardness of Lewis acids and bases. Journal of the American Chemical
Society 1985, 107 (24), 6801-6806.
2. Pearson, R. G., Absolute electronegativity and hardness: application to inorganic chemistry. Inorganic Chemistry 1988, 27 (4),
734-740.
3. Drago, R. S.; Wayland, B. B., A Double-Scale Equation for Correlating Enthalpies of Lewis Acid-Base Interactions. Journal of
the American Chemical Society 1965, 87 (16), 3571-3577.
4. Vogel, G. C.; Drago, R. S., The ECW Model. Journal of Chemical Education 1996, 73 (8), 701.
5. Drago, R. S. A modern approach to acid-base chemistry. Journal of Chemical Education 1974, 51 (5), 300
6. Hancock, R. D.; Martell, A. E., Hard and Soft Acid-Base Behavior in Aqueous Solution: Steric Effects Make Some Metal Ions
Hard: A Quantitative Scale of Hardness-Softness for Acids and Bases. Journal of Chemical Education 1996, 73 (7), 654.
7. Drago, R. S.; Wong, N. M., The Role of Electron-Density Transfer and Electronegativity in Understanding Chemical Reactivity
and Bonding. Journal of Chemical Education 1996, 73 (2), 123.
8. Drago, R. S., The interpretation of reactivity in chemical and biological systems with the E and C model. Coordination
Chemistry Reviews 1980, 33 (3), 251-277.
9. Drago, R. S.; Bilgrien, C. J., Inductive transfer and coordination of ligands in metal—metal bonded systems. Polyhedron 1988, 7
(16), 1453-1468.
10. Drago, R. S., The question of a synergistic metal-metal interaction leading to .pi.-back-bond stabilization in dirhodium
tetrabutyrate adducts. Inorganic Chemistry 1982, 21 (4), 1697-1698.
11. Drago, R. S.; Vogel, G. C., Interpretation of spectroscopic changes upon adduct formation and their use to determine
electrostatic and covalent (E and C) parameters. Journal of the American Chemical Society 1992, 114 (24), 9527-9532.
12. Pearson, R. G.; Mawby, R. J. The Nature of Metal-Halogen Bonds in Gutmann, V. Halogen Chemistry, vol. 3. Academic Press:
London, 1967, pp. 55-84.
13. Kinraide, T. B. Improved Scales for Metal Ion Softness and Toxicity Environmental Toxicology and Chemistry 2009, 28 (3),
525-533.
Notes
* More precisely, the D parameters account for the difference in steric strain in the adduct relative to a water adduct of the Lewis
acid.
Contributors
Stephen Contakes (Westmont College, USA)
4.5: Quantitative Measures of Hardness and Softness is shared under a not declared license and was authored, remixed, and/or curated by
LibreTexts.
CHAPTER OVERVIEW
5: Coordination Chemistry
5.5: Isomers
5.6.7: Magnetism
5: Coordination Chemistry is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
1
Coordination chemistry is the study of the compounds that form between metals and ligands, where a ligand is any molecule or
ion that binds to the metal. A metal complex is the unit containing the metal bound to its ligands. For example, [PtCl2(NH3)2] is the
neutral metal complex where the Pt(II) metal is bound to two Cl ligands and two NH3 ligands. If a complex is charged, it is called a
complex ion (ex. [Pt(NH3)4]+2 is a complex cation). A complex ion is stabilized by formation of a coordination compound with
ions of opposite charge (ex. [Pt(NH3)4]Cl2). It is convention to write the formula of a complex or complex ion inside of square
brackets, while counterions are written outside of the brackets. In this convention, it is understood that ligands inside the brackets
are bound directly to the metal, in the metal's first coordination sphere (a.k.a inner coordination sphere). Ions written outside of the
brackets are assumed to be in the second coordination sphere, and they are not directly bound to the metal.
Neutral Complex: [CoCl3(NH3)3]
Complex Cation: [Co(NH3)6]3+
Complex Anion: [CoCl4(NH3)2]-
Coordination Compound: K4[Fe(CN)6]
A common metal complex is [Ag(NH3)2]+ formed when Ag+ ions are mixed with neutral ammonia molecules.
+ +
Ag + 2N H3 → [Ag(N H3 )2 ] (5.1.1)
3-
A complex [Ag(S2O3)2] is formed between silver ions and negative thiosulfate ions:
+ 2− 3−
Ag + 2 S2 O → [Ag(S2 O3 )2 ] (5.1.2)
3
How did the study of coordination compounds started?

The coordination chemistry was pioneered by Nobel Prize winner Alfred Werner (1866-1919). He received the Nobel Prize in 1913
for his coordination theory of transition metal-amine complexes. At the start of the 20th century, inorganic chemistry was not a
prominant field until Werner studied the metal-amine complexes of cobalt. Werner recognized the existence of several forms of
cobalt-ammonia chloride. These compounds have different color and other characteristics. The chemical formula has three chloride
ions per mole, but the number of chloride ions that precipitate with Ag+ ions per formula was not always three. He thought only
ionized chloride ions will form precipitate with silver ion. In the following table, the number below the Ionized Cl- is the number
of ionized chloride ions per formula. To distinguish ionized chloride from the coordinated chloride, Werner formulated the
Complex formula and explained structure of the cobalt complexes.
Table 5.1.1 : Proposed Structure of Cobalt Ammonia Complexes from Number of Ionized Chloride
Solid Color Ionized Cl- Complex formula
CoCl36NH3 Yellow 3 [Co(NH3)6]Cl3
CoCl35NH3 Purple 2 [Co(NH3)5Cl]Cl2
CoCl34NH3 Green 1 trans-[Co(NH3)4Cl2]Cl
CoCl34NH3 Violet 1 cis-[Co(NH3)4Cl2]Cl
The structures of the complexes were proposed based on a coordination number of 6. The six ligands can be ammonia or chloride.
Two different structures were proposed for the last two compounds, the trans- compound has two chloride ions on opposite vertices
of an octahedral, whereas the the two chloride ions are adjacent to each other in the cis- compound. The cis- and trans- compounds
are known as geometric isomers. Isomers will be the focus of a later section.
Classification of ligands
The discussion of the cobalt complexes above suggests that there are two types of chlorides in the [Co(NH3)5Cl]Cl2 and cis-/trans-
[Co(NH3)4Cl2]Cl complexes. In comparing the formula and the amounts of ionized Cl- listed in Table 5.1.1, the outer sphere
chlorides must be the ionizable ones. The reason the inner sphere ligands are not ionizable is because there is significant covalent
character in the bond with the cobalt. Even though we call these inner sphere ligands chloride (or more properly chloro) ligands,
they are not Cl-, but rather better thought of as being Co-Cl.
In order to account for this difference, we will use the Covalent Bond Classification (CBC) method for thinking about ligands. In
this system, ligands are classified as either being X-type (one-electron donors) or L-type (two-electron donors). In order to
determine if a ligand is an X-type or L-type ligand, perform a thought experiment in which you remove the ligand from the metal
as a neutral atom or molecule.
Example 5.1.1
Consider the complex cation, [Co(NH3)5Cl]2+. What types of ligands are NH3 and Cl?
NH3
There are three possible ways you could think of breaking the Co-N bond. One could consider homolytic cleavage (one
electron goes with Co and one with N) or heterolytic cleavage (one atom takes both electrons). The homolytic cleavage option
is shown in the middle results in the formation of NH3+. Our goal is to remove the ligand as a neutral species, so this is not the
correct option. If both electrons in the bond go with the nitrogen, there is no charge on the outgoing ligand. When considering
the two heterolytic cleavage options, the pair of electrons can either go with the nitrogen (left) or Co (right). Only one of these
options (the one on the left) results in the formation of the neutral NH3 molecule. As such, NH3 is a two-electron donor and
therefore a L-type ligand.
It is important to note two things before we move on to our consideration of chloride. First, even though there are four bonds to
the nitrogen atom in the initial Co-NH3, we do not put a positive charge on the nitrogen. While the nitrogen atom bound to
cobalt is certainly less electron rich than the nitrogen atom in an uncoordinated ammonia molecule, if we think back on our
discussion of the acidity of hexaaqua species, the charge is difficult to localize and so we ignore it. This will be true for all
metal complexes. Second, no charge is shown on any of the cobalt species as accounting for charge on the ligand will likely be
more straightforward.
Cl
Similar to our treatment of NH3, there are three ways to consider removing the chloride. In this case, both heterolytic cleavage
options (left and right) result in a charged chlorine species so these are not the correct option. However homolytic cleavage
(center) of the Co-Cl bond results in a neutral chlorine atom. So the chloride ligand is a X-type ligand.
Why do we need to classify the different ligand types? Doing so is going to help us in determining the valence of the metal.
Valence is somewhat similar to oxidation state, but there are subtle differences. The main difference is that valence accounts for
both the overall charge on the complex and the number of X-type ligands in the complex. The emphasis with valence is once again
on the idea that the metal needs to provide electrons to make covalent bonds to some ligands. To determine the valence of a metal
use the following equation:
valence - number of X-type ligands = overall charge on the complex
Example 5.1.2
Determine the valence of cobalt in [Co(NH3)5Cl]2+.
Previously we determined that the cobalt in this complex has one X-type ligand, the chloride. The complex has an overall
+2 charge. Based on the equation above, the valence of the cobalt would be +3 or Co(III).
Had you followed traditional oxidation state rules, you should have arrived at the same conclusion. These rules would have
treated the chloride as Cl- and accounted for the remainder of the charge by oxidizing the cobalt. While a subtle difference, the
results of experiments in which Ag+ is added to [Co(NH3)5Cl]2+ clearly indicate that the chloride is not ionizable and therefore
should not be treated as Cl-. While similar, the idea of valence emphasizes the covalent nature of the Co-Cl bond.
Exercise 5.1.1
Determine the valence of cobalt in [Co(NH3)4Cl2]Cl.
Answer
While the amounts have changed, the NH3 ligands are still L-type and the Cl ligands are X-type.
The valence on cobalt is (valence - 2 = +1) or Co(III) just like in the previous example.

Chung (Peter) Chieh (Professor Emeritus, Chemistry @ University of Waterloo)
5.1: Introduction to Coordination Chemistry is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
Ligand Denticity
Ligands can also be classified based on whether they bind to the metal center through a single site on the ligand or whether they
bind at multiple sites. Ligands which bind through only a single site are called monodentate at the Latin word for tooth; in contrast
those those which bind through multiple sites are called chelating after the Greek χαλϵ for “claw”. These relationships are
summarized in Figure 5.2.1.
Figure 5.2.1 . (A) Ammonia is monodentate ligand while (B) ethylene diamine is a chelating ligand owing to its capacity to bind
metals via its two amine functional groups. (C) Chelating ligands act like a Lobster claw in attaching to the metal via multiple sites.
The lobster claw image is adapted from https://www.clipart.email/download/1127636.html. Otherwise this work by Stephen
Contakes is licensed under a Creative Commons Attribution 4.0 International License.
Following naturally from the classification of non-chelating ligands as monodentate, chelating ligands are further classified
according to the number of sites which they can use to bind a metal center. This number of binding sites is called the denticity and
ligands are referred to as monodentate (non chelating), bidentate, tridentate, etc. based on the number of sites available. Ligands
with two binding sites have a denticity of two and are said to be bidentate; those with three are tridentate, four tetradentate, and so
on. To illustrate this classification system examples of chelating ligands classified according to denticity are given in Figure 5.2.2.
Figure 5.2.2 . A selection of chelating ligands classified according to denticity. this work by Stephen Contakes is licensed under a
Creative Commons Attribution 4.0 International License.
The classification of several of the ligands in Figure 5.2.2 requires a bit of explanation, specifically as to why the denticity of the
carboxylate-containing ligands is less than the total number of lone-pair bearing oxygen and nitrogen atoms present. This is
because only one of the carboxylate oxygen atoms is counted. Only one is counted because in most cases only one oxygen binds to
a metal at any given time. When that oxygen is bound the other oxygen faces away from the metal, as depicted for the iron complex
shown in Figure 5.2.3A. Because only one oxygen per carboxylate typically binds only one is counted when assigning a ligand's
denticity.
Although only one carboxylate oxygen usually binds to a metal it is still possible to bind a metal using both oxygen atoms. As
shown in Figure 5.2.3B complexes in which both carboxylates bind to a metal are known, and in fact are common in the active
sites of some enzymes. It is just that the binding of both oxygen atoms gives a strained four-membered ring that is usually unstable.
Figure 5.2.3 . (A) Only one oxygen per carboxylate counts towards the denticity of EDTA since on binding the other oxygen
generally points away from the metal center, as in the structure of Fe(EDTA)-. This does not mean that both oxygens of a
carboxylate can never both bind to metal centers in a complex. (B) Structures in which both oxygens of a carboxylate side chain
bind to a metal are sometimes found in the active sites of some of the nonheme iron enzymes your body uses to break down amino
acids. this work by Stephen Contakes is licensed under a Creative Commons Attribution 4.0 International License.
As was the case for carboxylate groups above, sometimes the classification of a group's denticity is based on experimental
knowledge of their common binding modes. Carboxylates might commonly act as monodentate ligands but dithiocarbamates more
commonly bind metals through both sulfur atoms (Figure 5.2.4) and are classified as bidentate.
Figure 5.2.4 . As in this complex, dithiocarbamates commonly bind metals through both sulfur atoms. Consequently,
dithiocarbamates are classified as bidentate. this work by Stephen Contakes is licensed under a Creative Commons Attribution 4.0
International License.
Because of these factors it is technically more correct to say that carboxylates usually act as monodentate ligands and
dithiocarbamates bidentate ones than it is to say that carboxylates are monodentate ligands and dithiocarbamates bidentate ones. So
in other words the ligand classifications presented here are just represent common binding modes.
Exercise 5.2.1
Determine the denticity of each ligand in the list below and classify them as monodentate, tridentate, etc.
Answer
(a) bidentate
(b) tridentate
(c) bidentate
(d) tridentate (only the lower N on each ring has a lone pair that can be used to bind the metal)
(e) hexadentate (remember that each carboxylate only counts as one point of attachment)
(f) bidentate
(g) monodentate (through the lone pair on the isocyanide C)
(h) bidentate
This experimentally-based classification of dithiocarbamates as bidentate and carboxylates as monodentate can be confusing to a
beginner. Fortunately, such experimentally based classifications are embedded in the lists of common monodentate ligands are
given in Table 5.2.1 and common chelating ligands in Table 5.2.2.
A perusal of the ligands in Table 5.2.1 reveals that several can bind to a metal in multiple ways. For example, thiocyanate, SCN-
can bind metal's through its S or N atoms. Such ligands are called ambidentate ligands. When naming an ambidentate ligand the
atom through which it attaches to the metal is commonly specified after the ligand name using the italicized element symbol or,
more formally a κ followed by the italicized element symbol.
Table 5.2.1 . Common monodentate ligands. Most chemists still prefer common names over the IUPAC ones.
Ligand Ligand Type Common name IUPAC name
H X hydrido hydrido
F X fluoro fluorido
Cl X chloro chlorido
Br X bromo bromido
I X iodo iodido
cyanido or cyanido-κ C or
M-CN X cyano
cyanido-C
RNC L alkyl or aryl isocyanide alkyl or aryl isocyanide
N3 X azido azido
M-SCN X thiocyanato thiocyanato-κ S or thiocyanato-S
M-NCS X isothiocyanato thiocyanato-κ N or thiocyanato-N
CH3CO2 X acetato ethanoato
N X3 nitrido nitrido
NH X2 imido azanediido
NH2 X amido azanido
NH3 L ammine ammine
alkylamine, dialkylamine, alkylamine, dialkylamine,

RNH2, R2NH, R3N L trialkalyamine trialkalyamine
(e.g. methylamine for CH3NH2) (e.g. methylamine for CH3NH2)
L piperidine piperidine
piperidine, abbreviated pip
L pyridine pyridine
pyridine, abbreviated py
CH3CN
L acetonitrile acetonitrile
acetonitrile, abbreviated MeCN
P X3 phosphido phosphido
PH3 L phosphine phosphane
trialkylphosphine (e.g. trialkylphosphane (e.g.

PR3 L
trimethylphosphine for Me3P) trimethylphosphane for Me3P)
triarylphosphine (e.g. triarylphosphine (e.g.

PAr3 L
triphenylphosphine for Ph3P) triphenylphosphane for Ph3P)
O X2 oxo oxido
OH X hydroxo hydroxido
H2O L aqua aqua
S X2 sulfo sulfo
HS X hydrosulfido hydrosulfido
alkanethiolate (e.g. ethanthiolate

RS X thioalkanoate
for EtS-)
NO X nitrosyl nitrosyl
CO L carbonyl carbonyl
CS L thiocarbonyl thiocarbonyl
M-NO2 L nitro or nitrito-N nitrito-κ N or nitrito-N
M-ONO X nitrito or nitrito-O nitrito-κ O or nitrito-O
Table 5.2.2 . Common chelating ligands organized by denticity. Most chemists use the common names and abbreviations to
describe these ligands.
structure
or representative/parent
abbreviation structure
Common Ligand name IUPAC ligand name Ligand Type
(if applicable) (shown in the ionization
state in which they bind
to a metal)
bidentate ligands
acetylacetonato 2,4-pentanediono acac LX
bpy
2,2'-bipyridine 2,2'-bipyridine L2
or bipy
dialkyldithiocarbamato dialkylcarbamodithiolato R2NCS2- or dtc LX
diphenylphosphinoethane Ethane-1,2-
or 1,2- diylbis(diphenylphosphane dppe L2
(diphenylphosphino)ethane )
ethylenediamine Ethane-1,2-diamine en L2
ethylenedithiolato Ethane-1,2-dithiolato C2H2S22- X2
N,N'-diphenyl-2,4-
nacnac nacnac LX
pentanediiminato
oxalato oxalato ox X2
1,10-phenanthroline
1,10-phenanthroline phen or o-phen L2
or o-phenanthroline
tridentate ligands
triazacyclononane 1,3,7-triazacyclononane tacn L3
diethylenetriamine 1,4,7-triazaheptane dien L3
pyrazoylborato hydrotris(pyrazo-1-
Tp L2X
(scorpionate) yl)borato
12,22:26,32-terpyridine
or 2,6-bis(2-
terpyridine
pyridyl)pyridine, tpy or terpy L3
or 2,2';6',2"-terpyridine
tripyridyl, 2,2′:6′,2″-
terpyridine
tetradentate ligands
, ', β''-
β β , ', β''-tris(2-
β β
tren L4
triaminotriethylamine aminoethyl)amine
triethylenetetramine 1,4,7,10-tetraazadecane trien L4
variable and generally not

corroles cor or Cor L2X2
used
1,4,7,10-
12-crown-4 12-crown-4 L4
tetraoxacyclododecane
1,4,8,11-tetramethyl-
tetramethylcyclam 1,4,8,11- TMC or cyclam L4
tetraazacyclotetradecane
1,4,8,11-
cyclam cyclam L4
tetraazacyclotetradecane
1,4,7,10-
cyclen cyclen L4
tetraazacyclododecane
1-pyridin-2-yl-N,N-
tris(2-pyridylmethyl)amine bis(pyridin-2- tpa or TPA L4
ylmethyl)methanamine
variable and generally not variable, usually a

phthalocyanines L2X2
used modified Pc
variable, usually a
variable and generally not modified por, Por, or P
porphyrins L2X2
used (e.g. TPP =
tetraphenylporphyrin)
2,2'-
salen ethylenebis(nitrilomethylid salen L2X2
ene)diphenoxido
pentadentate ligands
1,4,7,10,13-
Pentaoxacyclopentadecane
1,4,7,10,13-
tetraethylenepentamine tepa or TEPA L5
pentaazatridecane
hexadentate ligands
1,4,7,10,13,16-
hexaoxacyclooctadecane
2,1,1-crypt
4,7,13,18-Tetraoxa-1,10- or [2.1.1]-cryptand
2,1,1-cryptand L6
diazabicyclo[8.5.5]icosane kryptofix 211
and variations thereof
2,2′,2″,2‴-(Ethane-1,2-
ethylenediaminetetraaceto EDTA, edta, Y4- L2X4
diyldinitrilo)tetraaceto
heptadentate ligands
2,2,1-crypt
4,7,13,16,21-pentaoxa-
or [2.2.1]-cryptand
2,2,1-cryptand 1,10-diazabicyclo[8 L7
kryptofix 221
.8.5]icosane
octadentate ligands
2,2,2-crypt
4,7,13,16,21,24-Hexaoxa-
or [2.2.2]-cryptand
2,2,2-cryptand 1,10-diazabicy L8
kryptofix 222
clo[8.8.8]hexacosan
pentetato acid or 2-[bis[2-
diethylenetriaminepentaace [bis(carboxylatomethyl)am DTPA L3X5
tato or DTPA ino]ethyl]amino]acetato
1,4,7,10-
DOTA or tetraxetan Tetraazacyclododecane- Dota, DOTA L4X4
1,4,7,10-tetraacetic acid
Rules for Naming Coordination Compounds

There are well-established rules for both naming and writing the formulae of coordination compounds. The purpose of these rules
is to facilitate clear and precise communication among chemists. As with all such rules some are more burdensome than others to
employ and some serve more crucial roles in the communication process while others are more peripheral.
Coordination Complexes are named as the ligand derivatives of a metal

A variety of systems have been used for naming coordination compounds since the development of the discipline in the time of
Alfred Werner. In this section the most common approaches as they are currently used by practicing chemists will be described.
Those who need a more thorough and accurate acquaintance with the full IUPAC nomenclature rules are encouraged to consult the
IUPAC brief guide to inorganic nomenclature followed by complete guidelines, commonly known as the IUPAC red book. The
systems for naming coordination compounds used at present are additive, meaning that they consider coordination compounds as
comprised of a central metal to which are added ligands. To specify the structure and bonding in this metal-ligand complex then
involves
1. When there are several different ways of attaching the metal and ligands, specifying the structural or stereoisomer
2. systematically listing the ligands in a way that, as necessary, conveys information about how they are linked to the metal and
their stereochemistry
3. providing the identity of the metal and its valence, or if the valence is unclear, at least the overall charge on the complex
4. specifying any counterions present
Since the stereochemistry of coordination compounds forms is the subject subsequent sections, in this section it will be addressed
by simply giving the prefixes that designate stereochemistry as if they were self-evident. Do not worry about these for now. They
will make sense after you have learned more about stereochemistry in the next sections. At that time, you can go back over the
examples in this section to solidify your understanding of how to name coordination compounds.
Before going into these rules it is worth pointing out a few things.
1. It is easiest to learn these rules by starting with one or two of the rules, learning how to apply them, and then adding additional
rules one at a time.
2. The rules also assume some familiarity with common coordination geometries and patterns of isomerism in metal complexes.
Again, we will learn more about these in a later section. For now it is safe to assume
complexes in which the metal has a coordination number of six are octahedral
complexes in which the metal has a coordination number of five are trigonal bipyramidal
complexes in which PtII , PdII , or RhI, or IrI have a coordination number of four are square planar
other complexes in which the metal has a coordination number of four are tetrahedral
Like all assumptions these don't always work in real life but they should be good enough for now.
Rule 1: If ions are present, name the cation first, followed by the anion.
Examples:
K2[PtIICl4]: potassium tetrachloroplatinate(2- or II)
[CoIII(NH3)6](NO3)3: hexaamminecobalt(3+ or III) nitrate
[CoIII(NH3)6][CrIII(C2O4)3]: hexaamminecobalt(3+ or III) tris(oxalato)chromate(3- or III)
You may notice two unusual features in these name. First, there are two numbers in parentheses. Second, in a few
places the name of the metal seems to have changed to end in -ate. Both of these will be addressed in later rules.
Rule 2: When multiple isomers are possible, designate the particular isomer in italics at the front of the name of each
complex
When a complex might exist as one of two stereosisomers prefixes are commonly used to designate which isomer is present. The
most common cases are listed in Table 5.2.3.
Table5.2.3 . Prefixes used to specify isomerism about a metal center when naming and writing coordination compounds' formulae.
Type of isomerism Graphical reminder Prefixes
Geometric, cis- , trans- cis- or trans-
Geometric, fac- /mer- fac- or mer-
Enantiomers, Λ-, Δ - Λ - or Δ -
Examples of how isomerism about a metal center is designated are given in Figure 5.2.5.
Figure 5.2.5 . Application of nomenclature rules for stereosimerism about a metal.1

There are a number of other cases where it might be advisable to specify the stereochemistry of a complex. These cases involve
specifying
the coordination geometry about a metal center (octahedral, trigonal prismatic, tetrahedral, square planar, etc. )
the geometry cannot be unambigouously described by a single cis/trans or fac/mer relaionship of ligands
These cases may also be handled by using a designator to specify the coordination geometry and, as necessary, giving the position
of ligated atoms in terms of designated numbered positions for that geometry. See the IUPAC red book for details as such cases fall
outside the scope of this course.
Rule 3: Specify the identity, number, and as appropriate, isomerism of the ligands present in alphabetical order by
ligand name.
Before specifying the metal, the ligands are written as prefixes of the metal.
In specifying the ligands several rules are followed.
1. The ligands are written in alphabetical order by the ligand name only; symbols are not considered and prefixes do not count in
determining alphabetical order.
Example: In the name of the complex ion [Co(NH)3Cl]2+, pentamminechlorocobalt(II), the ammine ligand is named before
the chloro ligand because the order is alphabetical by the ligand name by virtue of which ammine comes before chloro.
2. Prefixes are used to indicate the number of each ligand present. Specifically, di-, tri-, tetra- , penta-, hexa-, etc. prefixes are
used to indicate multiple ligands of the same type EXCEPT when the ligand is polydentate or its name already has a di-, tri-,
tetra- etc. In that case bis-,tris-, tetrakis-, etc. are used instead. These prefix rules are summarized in Table 5.2.3.
Table 5.2.3 . Prefixes used to specify the number of a given ligand present.
prefix used when the ligand is polydentate or

Number of identical ligands prefix used when the ligand name is simple
its name already has a di-, tri-, tetra- etc.
2 di- bis-
3 tri- tris-
4 tetra- tetrakis-
5 penta- pentakis-
6 hexa- hexakis-
7 hepta- heptakis-
8 octa- octakis-
9 nona- nonakis-
10 deca- decakis-
An example of the application of the prefix rule is given in Figure 5.2.6.
Figure 5.2.6 . Example of the use of prefixes to specify the number of ligands of each type in a complex.1
3. Ligand names are based on their charge
L-type ligand names are the same as the names of their neutral compounds with two caveats
i. names that involve spaces should either be put in parentheses or the spaces should be eliminated (preferred)
Example: cis-dichlorobis(dimethyl sulfoxide)platinum(II) or cis-dichlorobis(dimethylsulfoxide)platinum(II)
ii. A few ligands are given common names.
H2O = aqua
NH3 = ammine (notice that there ate two n's)
CO = carbonyl
CS = thiocarbonyl
NO = nitrosyl
For X-type ligands, the ending is typically changed to end in an -”o”
Examples: Cl = chloro, NH2 = amido, N3 = azido
Caveat: some X-type ligands have common names that may also be used
Examples:
I = iodo or iodino
CN = cyano or cyanido
O = oxo or oxido
The IUPAC and common names of many ligands are given in Tables 5.2.1. and 5.2.2.
4. When an ambidentate ligand is present the atom through which it is bound to the metal is indicated by giving either its element
symbol or a κ and its element symbol in italics after the ligand name
Example:
M-SCN is thiocyanato-S or thiocyanato-κ S
M-NCS = thiocyanato-N or thiocyanato-κ N
The use of κ and an element symbol to indicate how a ligand and metal are linked is called a k-term. More complex k-
terms might also involve specifying the atoms by number, though their use is outside the scope of this text.
5. As appropriate, additional information about the way a ligand is bound to the metal center and/or its stereochemistry is
specified using a prefix. The prefixes to provide linkage and stereochemistry for ligands are given in Table5.2.4.
Table5.2.4 . Prefixes used to specify ligands' isomerism when naming and writing coordination compounds' formulae. Some of
these types of isomerism will be discussed in later pages.
Type of isomerism Graphical reminder Prefixes
κ
n
where n is the number of attached atoms;
used when the attached atoms are not directly
when a multidentate ligand binds through less
connected by a chemical bond. The metal-
than the full number of atoms
ligand bonding usually involves σ -type
coordination.
μ
n where n is the number of atoms bridged.
bridging ligands
The number n is usually omitted when n =2.
chelating ligand ring twist λ - or δ -
A example showing how the nomenclature rule is applied to a ligand that can have two coordination modes is given in Figure
5.2.7.
Figure 5.2.7 . Use of the κ notation to specify the number of attached groups in a multidentate ligand.
6. If desired, parentheses may be used to delineate a ligand name to make it easier to identify in the name. This can be particularly
helpful when the name contains a lot of information to keep track of. An example is given in Figure 5.2.8.
Figure 5.2.8 . When naming the complex shown cis-diaquabis(ethylenediamine)chromium(III) nitrate is easier to read than cis-
diaquabisethylenediaminechromium(III) nitrate.
Rule 4: Specify the identity of the metal

In neutral and cationic complexes the metal's name is used directly
- e.g. as in hexammineruthenium(III) for [Ru(NH3)6]3+
In anionic complexes, -ate replaces -ium, -en, or –ese or adds to the metal name.
e.g. as in hexachloromanganate(IV) for [MnCl6]2-
In anionic complexes of some metals a Latin-derived name is used instead of the element's English name. These names are
given in Table 5.2.5.
Table 5.2.5 . Latin terms for Select Metal Ions. Redrawn from this page describing the nomenclature of coordination
complexes.
Transition Metal Latin
Copper Cuprate
Gold Aurate
Iron Ferrate
Lead Plumbate
Silver Argentate
Tin Stannate
An example of the application of the metal naming rules is given in Figure \sf{\PageIndex{9}}\).
Figure 5.2.9 . Example of the application of the metal specification rules to a cationic and anionic platinum
complexes.1
Rule 5: Specify the valence of the metal.

Two different systems are used to specify the valence of the metal.
1. In the Stock system the metal's valence is indicated in Roman numerals after the metal name.
Examples:
[CoCl(NH3)5]Cl2 = pentamminechlorocobalt(III) chloride
[PtBr2(bpy)] = bipyridinedibromoplatinium(II)
K[Ag(SCN)2] = potassium di-S-thiocyanatoargentate(I)
2. In the Ewing-Bassett system the charge on the complex is specified in Arabic numerals after the complex name. This provides
a way of specifying a complex even when the valence of the metal isn't known and, in cases where it is known, the value of the
metal's valence may be inferred from the complex ion's charge.
[CoCl(NH3)5]Cl2 = pentamminechlorocobalt(2+) chloride
[PtBr2(bpy)] = bipyridinedibromoplatinium(0)
K[Ag(SCN)2] = potassium di-S-thiocyanatoargentate(1-)
Exercise 5.2.2. Assigning metal valence in a complex
In order to name a complex in the Stock system it is necessary to assign a valence to the metal.
For this reason it is important to be able to assign the valence of a metal in a complex. Remember the relationship
valence - number of X-type ligands = total charge on the complex
Assign the valence of the metal in the following real and hypothetical complexes.
a. K3[Fe(CN)6]
b. K2[PtCl4]
c. [MnCl(por)]
d. [Ru(bpy)3]Cl2
e. [PdCl2(dppe)]
Answer for K3[Fe(CN)6].

This contains [Fe(CN)6]3-; so valence - 6 (for 6 CN-) = -3 (the complexes' charge) so valence = +3 or Fe3+.
Answer for K2[PtCl4].
This contains [PtCl4]2-; so valence - 4 (for 4 Cl) = -2 (the complexes' charge) so valence = +2 or Pt2+.
Answer for [MnCl(por)].
valence - 2 (for por a which is L2X2; see table 9.2.2) - 1 (for Cl) = 0 (the complexes' charge) so valence = +3 or
Mn3+.
Answer [Ru(bpy)3]Cl2.
This contains [Ru(bpy)3]2+; so valence - 0 (for bpy which is L2) = +2 (the complexes' charge) so valence = +2 or
Ru2+.
Answer [PdCl2(dppe)].
valence - 2 (for 2 Cl) - 0 (for dppe which is L2) = 0 (the complexes' charge) so valence = +2 or Pd2+.
Exercise 5.2.3: Simple Nomenclature Problems.
Name the following compounds in both the Stock and Ewing-Bassett systems:
a. [Ru(NH3)6](NO3)3
b. K2[PtCl4]
c. K[Ag(CN)2]
d. Cs[CuBrCl2F]
e. [Cu(acac)2]
f. K4[Fe(CN)6]
g. trans-[Cu(en)2(NO2)2] (the N is bound to Cu)
h. cis-IrCl2(CO)(PPh3) (ignore stereochemistry)
i. IrCl(PPh3)
Answer
Ewing-Bassett
Complex Stock system name
System name
hexammineruthenium( hexammineruthenium(
a [Ru(NH3)6](NO3)3
III) nitrate 3+) nitrate
potassium potassium
b K2[PtCl4]
tetrachloroplatinate(II) tetrachloroplatinate(2-)
potassium potassium
c K[Ag(CN)2]
dicyanoargentate(I) dicyanoargentate(1-)
cesium cesium
d Cs2[CuBrCl2F] bromodichloroflouroc bromodichloroflouroc
uprate(II) uprate(2-)
bis(acetylacetonato)co bis(acetylacetonato)co
e [Cu(acac)2]
pper(II) pper(0)
potassium potassium
hexacyanoferrate(II) hexacyanoferrate(4-)
f K4[Fe(CN)6] or potassium or potassium
hexacyanidoferrrate(II hexacyanidoferrrate(4-
) )
bis(ethylenediamine)b
bis(ethylenediamine)bi
trans- isnitrocopper(II) or
snitrocopper(0) or
g [Cu(en)2(NO2)2] (the bis(ethylenediamine)b
bis(ethylenediamine)bi
N is bound to Cu) is(nitrito-
s(nitrito-κ N)copper(0)
κ N)copper(II)
cis- cis-
dichlorocarbonyltriph dichlorocarbonyltriphe
enylphosphineiridium( nylphosphineiridium(0
I) )
h cis-IrCl2(CO)(PPh3)
or cis- or cis-
dichloro(carbonyl) dichloro(carbonyl)
(triphenylphosphine)ir (triphenylphosphine)ir
idium(I) idium(0)
chlorotris(triphenylph chlorotris(triphenylph
i IrCl(PPh3)
osphine)iridium(I) osphine)iridium(0)
Exercise 5.2.8
Draw structural formulae for the following compounds and ions. You may assume that
complexes in which the metal has a coordination number of six are octahedral
complexes in which the metal has a coordination number of five are trigonal bipyramidal
complexes in which PtII , PdII , or RhI, or IrI have a coordination number of four are square planar
other complexes in which the metal has a coordination number of four will be tetrahedral
a. (2,2'-bipyridine)tetracyanoruthenium(2-)
b. sodium tetrachloroalumnate (note that since Al is a main group metal with a generally fixed oxidation state no oxidation
state is given)
c. carbonylhydridotris(triphenylphosphine)rhodium(I) (the ligands in this complex occupy sterically preferred positions)
d. bromotrichlorocobaltate(III)
e. sodium tris(oxalato)cobalt(III)
f. fac-(1,10-phenanthroline)tricarbonylchlororhenium(I)
g. mer-triaquatrichlorochromium(III)
h. trans-dichlorobis(ethylenediamine)platinum(IV)
Answers
a
f
Note 5.2.1: Sometimes the most helpful name to give a compound is 42.
Even though the IUPAC nomenclature rules permit specification of even the most complex structures, it is often much easier
and more effective to supply a numbered structure that can be referred to instead of the IUPAC name. Consider bis{[(μμ-2-
mercaptoethyl)(2-mercaptoethyl)-methylthioethylaminato (2-)]Nickel(II)}. Which is easier, to expect readers and hearers to
work out the structure from that name or to just refer them to compound 42 in Figure 5.2.10.
Figure 5.2.10 . Structure of bis{[(μ-2-mercaptoethyl)(2-mercaptoethyl)-methylthioethylaminato (2-)]Nickel(II)}. The authors
of the synthesis of this compound in Inorganic syntheses2 may have had to figure out an IUPAC name for this compound but if
you have this scheme in your paper and your instructor is OK with it you can just call it 42.
References
1. Haas, K. Naming Transition Metal
Complexes. https://chem.libretexts.org/Courses/Saint_Mary's_College%2C_Notre_Dame%2C_IN/CHEM_342%3A_Bio-
inorganic_Chemistry/Readings/Week_2%3A_Introduction_to_Metal-
Ligand_Interactions_and_Biomolecules/2.1_Transition_metal_complexes/2.1.6%3A_Naming_Transition_Metal_Complexes
2. The structure and name is taken from Choudhury, S. B.; Allan, C. B.; Maroney, M.; Wodward, A. D.; Lucas, C. R. Inorg.
Synth. 1998, 32, 98-107.

Stephen Contakes, Westmont College, to whom comments, corrections, and criticisms should be addressed.
with some examples taken from Naming Transition Metal Complexes by Kathryn Haas.
Consistent with the policy for original artwork made as part of this project, all unlabeled drawings of chemical structures are by
Stephen Contakes and licensed under a Creative Commons Attribution 4.0 International License.
5.2: Ligands and Nomenclature is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
The total number of points of attachment to the central element is termed the coordination number and this can vary from 2 to as
many as 16, but is usually 6. In simple terms, the coordination number of a complex is influenced by the relative sizes of the metal
ion and the ligands and by electronic factors, such as charge which is dependent on the electronic configuration of the metal ion.
Introduction
Based on the radius ratio, it can be seen that the bigger the charge on the central ion, the more attraction there will be for negatively
charged ligands, however at the same time, the bigger the charge the smaller the ion becomes which then limits the number of
groups able to coordinate. It is important to recognize that every geometry has a specific coordination number, but every complex
wish a specific coordination number will have a choice of several possible geometries (i.e., there is not a one-to-one
correspondance between coordination number and geometry).
Coordination Number 2
This arrangement is not very common for first row transition metal ion complexes and some of the best known examples are for
Silver(I). In this case we have a low charge and an ion at the right hand side of the d-block indicating smaller size
Figure 1: The linear [Ag(NH3)2]+ ion
Once again, this is not very common for first row transition metal ions. Examples with three different geometries have been
identified:
Trigonal planar Geometry: Well known for main group species like CO32- etc., this geometry has the four atoms in a plane
with the bond angles between the ligands at 120 degrees.
Figure 2: The Trigonal planar [Cu(CN)3]2- system

Trigonal pyramid Geometry: More common with main group ions.
T-shaped: The first example of a rare T-shaped molecule was found in 1977.
Two different geometries are possible. The tetrahedron is the more common while the square planar is found almost exclusively
with metal ions having a d8 electronic configuration.
Tetrahedral Geometry:
Figure 3: [CoCl2pyr2]
Square Planar Geometry: This is fairly common with Rh(I), Ir(I), Pd(II) and Pt(II) compounds.
Figure 4: cisplatin - cis-[PtCl2(NH3)2]
Square pyramid Geometry: Oxovanadium salts (Vanadyl, VO2+) often show square pyramidal geometry, for example,
[VO(acac)2]. Note that the Vanadium(IV) can be considered coordinatively unsaturated and addition of pyridine leads to the
formation of an octahedral complex.
Trigonal Bipyramid Geometry: The structure of [Cr(en)3][Ni(CN)5] • 1.5 H2O was reported in 1968 to be a remarkable
example of a complex exhibiting both types of geometry in the same crystal. The reaction of cyanide ion with Ni2+ proceeds via
several steps:
2+ −
Ni + 2C N → N i(C N )2 (5.3.1)
− 2−
N i(C N )2 + 2C N → [N i(C N )4 ] (5.3.2)
orange-red
2− − 3−
[N i(C N )4 ] + CN → [N i(C N )5 ] (5.3.3)
deep red
Figure 5: [Ni(CN)5]3-
Hexagonal planar Geometry: Unknown for first row transition metal ions, although the arrangement of six groups in a plane
is found in some higher coordination number geometries.
Trigonal prism Geometry: Most trigonal prismatic compounds have three bidentate ligands such as dithiolates or oxalates and
few are known for first row transition metal ions.
Octahedral (Oh): The most common geometry found for first row transition metal ions, including all aqua ions. In some cases
distortions are observed and these can sometimes be explained in terms of the Jahn-Teller Theorem which we will discuss later.
Figure 6: [Co(en)3]Cl3(left) and [CoCO3(NH3)5]+ (right)
Not very common for 1st row complexes and the energy difference between the structures seems small and distortions occur so that
prediction of the closest "idealized" shape is generally difficult. Three geometries are possible:
Capped octahedron (C3v) Geometry
Figure 7: K3[NbOF6]
Capped trigonal prism (C2v)
Pentagonal Bipyramid (D5h)
Figure 8: bis-[(tert-butylacac)2(DMSO)di-oxoUranium]
Dodecahedron (D2d) Geometry

Cube (Oh) Geometry
Square antiprism (D4d) Geometry
Hexagonal bipyramid (D6h) Geometry
Three-face centered trigonal prism (D3h) Geometry
Bicapped square antiprism (D4d) Geometry
All-faced capped trigonal prism (D3h) Geometry: This is not a common stereochemistry.
Figure 9: aqua-(12-crown-4)-tris(nitrato-O,O')-cerium(III) (12-crown-4) solvate and (15-crown-5)-tris(nitrato-O,O')-cerium(III)

the Cerium ion is 11 coordinate.
cuboctahedron (Oh) Geometry
Figure 10: Ceric ammonium nitrate -(NH4)2Ce(NO3)6

Prof. Robert J. Lancashire (The Department of Chemistry, University of the West Indies)
5.3: Coordination Numbers and Geometry is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
While electrons in s and p orbitals tend to form strong bonds, d-electron bonds can be strong or weak. There are two important
periodic trends that are related to orbital size and orbital overlap. As we move across the periodic table ( Sc - Ti - V - Cr - Fe ), the
d orbitals contract because of increasing nuclear charge. Moving down the periodic table ( V - Nb - Ta ), the d orbitals expand
because of the increase in principal quantum number. These trends explain the distinct behavior of the 3d elements relative to those
in the 4d and 5d series. In the 3d series, the contraction of orbitals affects the ability of the d electrons to contribute to bonding. Past
V in the first row of the transition metals, the 3d electrons become much less effective in bonding because they overlap weakly
with their neighbors. Weak overlap of 3d orbitals gives narrow d-bands and results in the emergence of magnetic properties as
discussed below.
Schematic representation of the sizes of different orbitals of Cr and W. In the first transition series, shielding of the 3d orbitals is poor. Therefore
the 4s and 4p orbitals are more effective in bonding than the 3d. In the third transition series, the situation is reversed. The increased nuclear
charge is felt most strongly by the 6s, which takes on the character of an inert electron pair. The 5d orbitals are well shielded by the complete n=4
shell so they have good orbital overlap with neighboring atoms.
In the 4d and 5d series, a plot of cohesive energy vs. number of valence electrons (below left) has a "volcano" shape that is peaked
at the elements Mo and W (5s14d5 and 6s15d5, respectively). The number of bonding electrons, and therefore the bonding energy,
increases steadily going from Rb to Mo in the 4d series, and from Cs to W in the 5d series. Mo and W have the most bonding
energy because they can use all six of their valence electrons in bonding without promotion. Elements past Mo and W have more d
electrons, but some of them are spin paired and so some promotion energy is needed to prepare these electrons for bonding. For
example, Pt metal must be promoted from the 6s15d9 atomic ground state to 6s15d76p2 in order to make six bonds per atom, and the
energy cost of promoting electrons from the 5d to the 6p orbitals is reflected in the net bonding energy. Because of their strong
bonding energy, elements in the middle of the 4d and 5d series have very high melting points. We do not see magnetism in the 4d
or 5d metals or their alloys because orbital overlap is strong and the bonding energy exceeds the electron pairing energy.
The heat of vaporization (the cohesive energy) of metals in the 3d and 5d series, measured at the melting point of the metal.
The 3d elements (Sc through Zn) are distinctly different from the 4d and 5d elements in their bonding (and consequently in their
magnetic properties). In the 3d series, we see the expected increase in cohesive energy going from Ca (4s2) to Sc (4s23d1) to Ti
(4s23d2) to V (4s23d3), but then something very odd happens. The 3d series has a "crater" in the cohesive energy plot where there
was a peak in the 5d series. The cohesive energy actually decreases going from V to Mn, even though the number of valence
electrons is increasing. We can explain this effect by remembering that the 3d orbitals are progressively contracting as more
protons are added to the nucleus. For elements beyond V, the orbital overlap is so poor that the 3d electrons are no longer effective
in bonding, and the valence electrons begin to unpair. At this point the elements become magnetic. Depending on the way the spins
order, metals and alloys in this part of the periodic table can be ferromagnetic (spins on neighboring atoms aligned parallel, as in
the case of Fe or Ni) or antiferromagnetic (spins on neighboring atoms antiparallel, as in the case of Mn). We have seen the trade-
off between orbital overlap and magnetism before (in Chapter 5) in the context of paramagnetic transition metal complexes. It is
worth recalling that this behavior is predicted in the energy vs. distance diagram of the hydrogen atom (from Chapter 2). At short
interatomic distances (or with strong overlap between atomic orbitals), the spins of the electrons pair and a bond is formed.
Unpairing the electrons becomes favorable at larger interatomic distances where the overlap between orbitals is poor.
With strong overlap between orbitals of neighboring atoms, the bonding energy exceeds the pairing energy and electrons spin-pair. With weaker
overlap, bonding is weak and spins unpair, resulting in magnetic behavior.
Interestingly, many alloys of the 4f elements (the lanthanides) are also magnetic because the 4f orbitals, like the 3d orbitals, are
poorly shielded from the nuclear charge and are ineffective in bonding. Strong permanent magnets often contain alloys of Nd, Sm,
or Y, usually with magnetic 3d elements such as Fe and Co.
Because the 4f orbitals are contracted and not very effective in bonding, other physical properties of the lanthanides can also be
affected. For example, it has been proposed that oxides of the 4f elements have weak surface interactions with polar molecules such
as water because of f-orbital contraction. Experimentally, CeO2, Er2O3, and Ho2O3 are observed to be hydrophobic, whereas main
group and early transition metal oxides (e.g., Al2O3, SiO2, TiO2) are quite hydrophilic.[1]
5.4: Bonding with d-orbitals is shared under a CC BY-SA license and was authored, remixed, and/or curated by LibreTexts.
6.7: Atomic Orbitals and Magnetism by Chemistry 310 is licensed CC BY-SA 4.0. Original source:
SECTION OVERVIEW
5.5: Isomers
There are several types of this isomerism frequently encountered in coordination chemistry and the following represents some of
them. Isomers that contain the same number of atoms of each kind but differ in which atoms are bonded to one another are called
structural isomers, which differ in structure or bond type. For inorganic complexes, there are three types of structural isomers:
ionization, coordination, and linkage and two types of stereoisomers: geometric and optical.
Structural isomers, as their name implies, differ in their structure or bonding, which are separate from stereoisomers that differ in
the spatial arrangement of the ligands are attached, but still have the bonding properties. The different chemical formulas in
structural isomers are caused either by a difference in what ligands are bonded to the central atoms or how the individual ligands
are bonded to the central atoms. When determining a structural isomer, you look at: (1) the ligands that are bonded to the central
metal, and (2) which atom of the ligands attach to the central metal. Below is a quick look at the different types of structural
isomers. The highlighted ions are the ions that switch or change somehow to make the type of structural isomer it is.
5.5: Isomers is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
Coordination isomerism is a form of structural isomerism in which the composition of the complex ion varies. In a coordination
isomer the total ratio of ligand to metal remains the same, but the ligands attached to a specific metal ion change. Ionization
isomers can be thought of as occurring because of the formation of different ions in solution.
Introduction
Ionization isomers are identical except for a ligand has exchanged places with an anion or neutral molecule that was originally
outside the coordination complex. The central ion and the other ligands are identical. For example, an octahedral isomer will have
five ligands that are identical, but the sixth will differ. The non-matching ligand in one compound will be outside of the
coordination sphere of the other compound. Because the anion or molecule outside the coordination sphere is different, the
chemical properties of these isomers is different.
Figure 5.5.1.1 : Two Ionization isomers. The two isomers differ only which ligands are actually bound to the center metal. These
two isomers are called pentaaquabromocobaltate(II) chloride and pentaaquachlorocobaltate(II) bromide.
The difference between the ionization isomers can be view within the context of the ions generated when each are dissolved in
solution.
For example, when pentaaquabromocobaltate(II)chloride is dissolved in water, C l ions are generated: −
+ +
C oBr(H2 O)5 C l(s) → C oBr(H2 O) (aq) + C l (aq) (5.5.1.1)
5
whereas when pentaaquachlorocobaltate(II)bromide is dissolved, Br ions are generated: −
+ +
C oC l(H2 O)5 Br(s) → C oC l(H2 O) (aq) + Br (aq). (5.5.1.2)
5
Note
If one dissolved [P tBr(N H 3 )3 ]N O2 and [P t(N O 2 )(N H3 )3 ]Br into solution, then two different set of ions will be general.
Dissolving [P t(N O 2 )(N H3 )3 ]Br in aqueous solution would have the following reaction
+ −
[P tBr(N H3 )3 ]N O2 (s) → [P tBr(N H3 )3 ] (aq) + N O (aq) (5.5.1.3)
2
Dissolving of [P t(N O 2 )(N H3 )3 ]Br in aqueous solution would be

+ −
[P t(N O2 )(N H3 )3 ]Br(s) → [P t(N O2 )(N H3 )3 ] (aq) + Br (aq) (5.5.1.4)
Notice that these two ionization isomers differ in that one ion is directly attached to the central metal, but the other is not.
Equations 5.5.1.3 and 5.5.1.4 are valid under the assumption that the platinum-ligand bonds of the complexes are do not break
and allow other ligands (e.g., water) to bind.
Example 5.5.1.1
Are [Cr(NH 3
) (OSO )]Br
5 3
and [Cr(NH 3
) Br] SO
5 4
coordination isomers?
Solution
First, we need confirm that each compound has the same number of atoms of the respective elements (this requires viewing
both cations and anions of each compound).
number of atoms in
Element number of atoms in [Cr(NH 3
) Br] SO
5 4
[Cr(NH ) (OSO )]Br
3 5 3
Cr 1 1
number of atoms in
Element number of atoms in [Cr(NH 3
) Br] SO
5 4
[Cr(NH ) (OSO )]Br
3 5 3
N 5 5
H 15 15
O 4 4
S 1 1
Br 1 1
Now, let's look at what these two compounds look like (Figure 5.5.1.2). The sulfate group is a ligand with a dative bond to the
chromium atom and the bromine atom is a counter ion (\ce{[Cr(NH3)5(OSO3)]Br}\). For [Cr(NH ) Br]SO , this is the the 3 5 4
reverse.
Figure 5.5.1.2 : [Cr(NH

3
) ( OSO )]Br
5 3
(left) and [Cr(NH 3
) Br]SO
5 4
(right) are coordination isomers.
Yes, [Cr(NH 3
) (OSO )]Br
5 3
and [Cr(NH 3
) Br] SO
5 4
are coordination isomers.
Exercise 5.5.1.1
Are [Co(NH3)5(SO4)]Br and [Co(NH3)5Br]SO4 ionization isomers?
Answer
In the first isomer, SO4 is attached to the Cobalt and is part of the complex ion (the cation), with Br as the anion. In the
second isomer, Br is attached to the cobalt as part of the complex and SO4 is acting as the anion.
A hydrate isomer is a specific kind of ionization isomer where a water molecule is one of the molecules that exchanges places.
Solvate or Hydrate Isomerization: A Special kind of Ionization Isomer

A very similar type of isomerism results from replacement of a coordinated group by a solvent molecule (Solvate Isomerism).
In the case of water, this is called Hydrate Isomerism. The best known example of this occurs for chromium chloride
"CrCl3.6H2O" which may contain 4, 5, or 6 coordinated water molecules.
[C rC l2 (H2 O)4 ]C l ⋅ 2 H2 O : bright-green colored
[C rC l(H2 O)5 ]C l2 ⋅ H2 O : grey-green colored
[C r(H2 O)6 ]C l3 : violet colored
These isomers have very different chemical properties and on reaction with AgN O to test for C l ions, would find 1, 2, and
3
−
3 C l ions in solution respectively.

−

5.5.1: Structural Isomers - Ionization Isomerism in Transition Metal Complexes is shared under a not declared license and was authored, remixed,
and/or curated by LibreTexts.
Geometric Isomers are isomers that differ in the arrangement of the ligands around the metal or the central atom. In other words,
these isomers differ from each other based on where the ligands are placed in the coordinate compound. This will be much easier to
understand as examples will be considered. There are 2 main types of geometric isomers:
Cis-Trans Isomers (referencing the spatial arrangement of two species)
Mer-Fac Isomers (referencing the spatial arrangement of three species)
Cis-Trans Isomers
Cis-Trans Isomers are isomers that differ in the arrangement of two ligands in square planar and octahedral geometry. Cis isomers
are isomers where the two ligands are 90 degrees apart from one another in relation to the central molecule. This is because Cis
isomers have a bond angle of 90o, between two same atoms. Trans isomers, on the other hand, are isomers where the two ligands
are on opposite sides in a molecule because trans isomers have a bond angle of 180o, between the two same atoms. When naming
cis or trans isomers, the name begins either with cis or trans, whichever applies, followed by a hyphen and then the name of a
molecule. For example a cis isomer of CoCl2F2 would be called cis-CoCl2F2. Finally, the last thing to keep in mind when
examining cis and trans isomers is that only square planar and octahedral geometries can have cis or trans isomers. Examples of
both isomers are provided below.
Example 5.5.2.1: cis Isomer
CoCl2F2:
(Color scheme: pink=cobalt, blue=fluorine, green=chlorine)
This above is an example of the molecule cis-CoCl2F2 or cis-dichlorodifluorocobalt (IV). The molecule pictured above is a cis
isomer because both fluorine and chlorine ligands, respectively, are on the same side of the molecule. Additionally, one can
approximate that the bond angle between each of the chlorine atoms and between each of the fluorine atoms is 90o.
Isomer
CoCl2F2:
(Color scheme: pink=cobalt, blue=fluorine, green=chlorine)
(Note, the differences in the length of the bond between the two pictures are not intentional and have nothing to do with cis-
trans isomerism)
This above is an example of the molecule trans-CoCl2F2 or trans-dichlorodifluorocobalt (IV).
We know the above molecule is a trans isomer because the two same chlorine atoms and the two same fluorine atoms are
opposite each other. Furthermore, the bond angle between the two chlorine atoms and between the two fluorine atoms is 180o.
The above examples were all for square planar geometry but as the examples below illustrate, cis-trans isomerism can also
occur in octahedral geometry. Both the molecules below are isomers of the molecule SCl2F4 (color scheme: yellow=sulfur,
blue=fluorine, green=chlorine).
Example 5.5.2.3: Octahedral cis Isomer
SCl2F4:
We know this isomer above is a cis isomer because both the chlorine ligands are on the same side and the bond angle between
the chlorine atoms appears to be 90o.
Example 5.5.2.4: Octahedral trans Isomer
SCl2F4:
The isomer above is a trans isomer because the chlorine ligands are on opposite sides and the bond angle between the chlorine
atoms is 180o. All other isomers are essentially just rotations of these two isomers. Once again when trying to find cis and trans
isomers look at the arrangement of the ligands. If two same ligands are on the same side, it is a cis isomer and if the ligands are
on opposite sides, it is a trans isomer. Another way to tell the isomers apart is the bond angles: cis isomers have a 90o bond
angle whereas trans isomers have a 180o bond angle.
Mer-Fac Isomers
Mer-Fac isomers are easier to notice than cis-trans isomers in the sense that they only exist in octahedral geometry. Just like cis-
trans isomers, mer-fac isomers are determined based on whether or not the ligands exist on the same side. Instead of dealing with 2
ligands, mer-fac isomers deal with 3 ligands. If the 3 ligands are all on the same side, the isomer is called a fac-isomer. Another
way to identify fac isomers is to look at the bond angle between the ligands because fac isomers have a 90o bond angle between
each of the 3 atoms. The mer isomer on the other hand is where only 2 of the 3 ligands are on the same side. In mer isomers, there
exists a 90o-90o-180o bond angle between the 3 same ligands. In terms of nomenclature, mer-fac isomers follow the same rule as
cis-trans isomers where you put the isomer type, followed by a hyphen, followed by the molecular formula. Examples have been
provided below.
Example 5.5.2.5: fac Isomer
Below is an example of the fac isomer, fac-CoCl3F3:
(note the color scheme: pink=cobalt, green=chlorine, blue=fluorine)

Through the 2d version, it is easier to see how the ligands are all on the same side. Nonetheless, in the 3D version, one can
observe that the bond angle between the 3 same ligands is 90o, thus making this isomer a fac-isomer.
Example 5.5.2.6: mer Isomer
Below is an example of the mer isomer, mer-CoCl3F3:
(note the color scheme: pink=cobalt, green=chlorine, blue=fluorine)
Its hard to tell in the 3D version but in the 2D version, one can easily tell how the same ligands are not on the same side.
Additionally, one can approximate that the bond angle between the three chlorine atoms and between the three fluorine
atoms is 90o-90o-180o, thus making the above molecule a mer isomer.

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has
Optical activity refers to whether or not a compound has optical isomers. A coordinate compound that is optically active
optical isomers and a coordinate compound that is not optically active does not have optical isomers. As
we will discuss later, optical isomers have the unique property of rotating light. When light is shot
through a polarimeter, optical isomers can rotate the light so it comes out in a different direction on the
other end. Armed with the knowledge of symmetry and mirror images, optical isomers should not be
very difficult. There are two ways optical isomers can be determined: using mirror images or using
planes of symmetry.
Optical isomers do not exhibit symmetry and do not have identical mirror images. Let's go through a quick review of symmetry and
mirror images. A mirror image of an object is that object flipped or the way the object would look in front of a mirror. For
example, the mirror image of your left hand would be your right hand. Symmetry on the other hand refers to when an object looks
exactly the same when sliced in a certain direction with a plane. For example imagine the shape of a square. No matter in what
direction it is sliced, the two resulting images will be the same.
Method 1: The "Mirror Image Method"

The mirror images method uses a mirror image of the molecule to determined whether optical isomers exist or not. If the mirror
image can be rotated in such a way that it looks identical to the original molecule, then the molecule is said to be superimposable
and has no optical isomers. On the other hand, if the mirror image cannot be rotated in any way such that it looks identical to the
original molecule, then the molecule is said to be non-superimposable and the molecule has optical isomers. Once again, if the
mirror image is superimposable, then no optical isomers but if the mirror image is non-superimposable, then optical isomers exist.
Definition: Non-superimposable
Non-superimposable means the structure cannot be rotated in a way that one can be put on top of another. This means that no
matter how the structure is rotated, it cannot be put on top of another with all points matching. An example of this is your
hands. Both left and right hands are identical, but they cannot be put on top of each other with all points matching.
The examples you are most likely to need occur in octahedral complexes which contain bidentate ligands - ions like
[N i(N H C H C H N H ) ]
2 2 2 2 3 or [C r(C O ) ] . The diagram below shows a simplified view of one of these ions. Essentially,
2+
2 4 3
3−
they all have the same shape - all that differs is the nature of the "headphones".
A substance with no plane of symmetry is going to have optical isomers - one of which is the mirror image of the other. One of the
isomers will rotate the plane of polarization of plane polarised light clockwise; the other rotates it counter-clockwise. In this case,
the two isomers are:
You may be able to see that there is no way of rotating the second isomer in space so that it looks exactly the same as the first one.
As long as you draw the isomers carefully, with the second one a true reflection of the first, the two structures will be different.
Method 2: The "Plane of Symmetry Method"

The plane of symmetry method uses symmetry, as it's name indicates, to identify optical isomers. In this method, one tries to see if
such a plane exists which when cut through the coordinate compound produces two exact images. In other words, one looks for the
existence of a plane of symmetry within the coordinate compound. If a plane of symmetry exists, then no optical isomers exist. On
the other hand, if there is no plane of symmetry, the coordinate compound has optical isomers. Furthermore, if a plane of symmetry
exists around the central atom, then that molecule is called achiral but if a plane of symmetry does not exist around the central
molecule, then that molecule has chiral center.
Example 5.5.3.1: CHBrClF
Consider the tetrahedral molecule, CHBrClF (note the color scheme: grey=carbon, white=hydrogen, green=chlorine,
blue=fluorine, red=bromine)
Is this molecule optically active? In other words, does this molecule have optical isomers?
Solution
First take the Mirror-image method. The mirror image of the molecule is:
Note that this mirror image is not superimposable. In other words, the mirror image above cannot be rotated in any such way
that it looks identical to the original molecule. Remember, if the mirror image is not superimposable, then optical isomers exist.
Thus we know that this molecule has optical isomers.
Let's try approaching this problem using the symmetry method. If we take the original molecule and draw an axis or plane of
symmetry down the middle, this is what we get:
Since the left side is not identical to the right, this molecule does not have a symmetrical center and thus can be called
chiral.Additionally, because it does not have a symmetrical center, we can conclude that this molecule has optical isomers. In
general, when dealing with a tetrahedral molecule that has 4 different ligands, optical isomers will exist most of the time.
No matter which method you use, the answer will end up being the same.
Optical isomers because they have no plane of symmetry. In the organic case, for tetrahedral complexes, this is fairly easy to
recognize the possibility of this by looking for a center atom with four different things attached to it. Unfortunately, this is not quite
so easy with more complicated geometries!
Example 5.5.3.1: fac−FeCl 3

F
3
This time we will be analyzing the octahedral compound fac-FeCl3F3. Is this molecule optically active?
(note the color scheme: orange=iron, blue=fluorine, green=chlorine):

Solution
If we try to attempt this problem using the mirror image method, we notice that the mirror image is essentially identical to the
original molecule. In other words, the mirror image can be placed on top of the original molecule and is thus superimposable.
Since the mirror image is superimposable, this molecule does not have any optical isomers. Let's attempt this same problem
using the symmetry method. If we draw an axis or plane of symmetry, this is what we get:
Since the left side is identical to the right side, this molecule has a symmetrical center and is an achiral molecule. Thus, it has
no optical isomers.
What is a Polarimeter?
A polarimeter is a scientific instrument used to measure the angle of rotation caused by passing polarized light through an optically
active substance. Some chemical substances are optically active, and polarized (uni-directional) light will rotate either to the left
(counter-clockwise) or right (clockwise) when passed through these substances. The amount by which the light is rotated is known
as the angle of rotation. The angle of rotation is basically known as observed angle.
Figure 5.5.3.1 : Schematic of a polarimeter showing the principles behind it's operation. Unpolarized light is passed through a
polarizing filter before traveling through a sample. The degree of rotation of polarization is determined by a second, rotatable filter.
(CC AS 3.0; Kaidor).
The polarimeter is made up of a polarizer (#3 on Figure 5.5.3.1) and an analyzer (#7 on Figure 5.5.3.1). The polarizer allows only
those light waves which move in a single plane. This causes the light to become plane polarized. When the analyzer is also placed
in a similar position it allows the light waves coming from the polarizer to pass through it. When it is rotated through the right
angle no waves can pass through the right angle and the field appears to be dark. If now a glass tube containing an optically active
solution is placed between the polarizer and analyzer the light now rotates through the plane of polarization through a certain angle,
the analyzer will have to be rotated in same angle.
Nomenclature of Optical Isomers

Various methods have been used to denote the absolute configuration of optical isomers such as R or S, Λ or Δ, or C and A. The
IUPAC rules suggest that for general octahedral complexes C/A scheme is convenient to use and that for bis and tris bidentate
complexes the absolute configuration be designated Λ (left-handed) and Δ (right-handed).
Priorities are assigned for mononuclear coordination systems based on the standard sequence rules developed for enantiomeric
carbon compounds by Cahn, Ingold and Prelog (CIP rules). These rules use the coordinating atom to arrange the ligands into a
priority order such that the highest atomic number gives the highest priority number (smallest CIP number). For example the
hypothetical complex [Co Cl Br I NH3 NO2 SCN]2- would assign the I- as 1, Br as 2, Cl as 3, SCN as 4, NO2 as 5 and NH3 as 6.
Figure 5.5.3.2 : Here is one isomer where the I and Cl, and Br and NO2 were found to be trans- to each other.
The reference axis for an octahedral center is that axis containing the ligating atom of CIP priority 1 and the trans ligating atom of
lowest possible priority (highest numerical value). The atoms in the coordination plane perpendicular to the reference axis are
viewed from the ligand having that highest priority (CIP priority 1) and the clockwise and anticlockwise sequences of priority
numbers are compared. The structure is assigned the symbol C or A, according to whether the clockwise (C) or anticlockwise (A)
sequence is lower at the first point of difference. In the example shown below this would be C (Figure 5.5.3.3).
Figure 5.5.3.3 . Reference axes for assigning group priority.
Isomers with bidentate ligands

Bidentate ligands bind very tightly to a metal because they form two bonds with it, rather than just one. We will investigate this
further in a later section. The spatial relationship between the metal and the two atoms connected to it from the same ligand forms a
plane. If more than one bidentate ligand is connected to the metal, the relative orientation of one plane to another creates the
possibility of mirror images. A complex containing three bidentate ligands can take on the shape of a left-handed propeller or a
right-handed propeller.
These shapes are alternatively described as a left-handed screw and a right handed screw. If you can picture turning the shape so
that it screws into the page behind it, which direction would you turn the screwdriver? If you would twist the screwdriver
clockwise, then you have a right handed screw. If you would twist the screwdriver counter-clockwise, then you have a left handed
screw. The two optical isomers of [Co(en)3]3+ have identical chemical properties and just denoting their absolute configuration
does NOT give any information regarding the direction in which they rotate plane-polarised light. This can ONLY be determined
from measurement and then the isomers are further distinguished by using the prefixes (-) and (+) depending on whether they rotate
left or right.
Figure 5.5.3.3 : left-handed Λ isomer (left) and right-handed Δ isomer (right)

To add to the confusion, when measured at the sodium D line (589 nm), the tris(1,2-diaminoethane)M(III) complexes (M= Rh(III)
and Co(III)) with IDENTICAL absolute configuration, rotate plane polarized light in OPPOSITE directions! The left-handed (Λ)-
[Co(en)3]3+ isomer gives a rotation to the right and therefore corresponds to the (+) isomer. Since the successful resolution of an
entirely inorganic ion (containing no C atoms) (hexol) only a handful of truly inorganic complexes have been isolated as their
optical isomers e.g. (NH4)2Pt(S5)3.2H2O.
For tetrahedral complexes, R and S would be used in a similar method to tetrahedral Carbon species and although it is predicted
that tetrahedral complexes with 4 different ligands should be able to give rise to optical isomers, in general they are too labile and
can not be isolated.

5.5.3: Stereoisomers - Optical Isomerism in Transition Metal Complexes is shared under a not declared license and was authored, remixed, and/or
curated by LibreTexts.
Linkage isomerism occurs with ambidentate ligands that are capable of coordinating in more than one way. The best known cases
involve the monodentate ligands: SC N /N C S and N O /ON O . The only difference is what atoms the molecular ligands
− − −
2
−
bind to the central ion. The ligand(s) must have more than one donor atom, but bind to ion in only one place. For example, the
(NO2-) ion is a ligand can bind to the central atom through the nitrogen or the oxygen atom, but cannot bind to the central atom
with both oxygen and nitrogen at once, in which case it would be called a polydentate rather than an ambidentate ligand.
Figure 5.5.4.1 : Linkage Isomerism in the N O ligand. This occurs when a particular ligand is capable of coordinating to a metal in
2
two different and distinct ways.
The names used to specify the changed ligands are changed as well. For example, the (NO2-) ion is called nitro when it binds with
the N atom and is called nitrito when it binds with the O atom.
Example 5.5.4.1: Nitro- vs. Nitrito- Linkage Isomers
The cationic cobalt complex [Co(NH3)5(NO2)]Cl2 exists in two separable linkage isomers of the complex ion:
[Co(NH3)5(NO2)]2+.
(left) The nitro isomer (Co-NO2) and (right) the nitrito isomer (Co-ONO)
When donation is from nitrogen to a metal center, the complex is known as a nitro- complex and when donation is from one
oxygen to a metal center, the complex is known as a nitrito- complex.
[C o(ON O)(N H3 )5 ]C l : the nitrito isomer -O attached
[C o(N O2 )(N H3 )5 ]C l : the nitro isomer - N attached.
The formula of the complex is unchanged, but the properties of the complex may differ.
Another example of an ambidentate ligans is thiocyanate, SCN−, which can attach at either the sulfur atom or the nitrogen atom.
Such compounds give rise to linkage isomerism. Polyfunctional ligands can bond to a metal center through different ligand atoms
to form various isomers. Other ligands that give rise to linkage isomers include selenocyanate, SeCN− – isoselenocyanate, NCSe−
and sulfite, SO32−.
Exercise 5.5.4.1
Sketch the linkage isomers of [FeCl5(SCN)]3-.
Answer
In the first isomer, the ligand bonds to the metal through the nitrogen atom. In the second isomer, the ligand bonds to the
metal through the sulfur atom. It's easier to see it:
5.5.4: Structural Isomers - Linkage Isomerism in Transition Metal Complexes is shared under a not declared license and was authored, remixed,
SECTION OVERVIEW
One of the most striking characteristics of transition-metal complexes is the wide range of colors they exhibit. Crystal field theory
(CFT) is a bonding model that explains many important properties of transition-metal complexes, including their colors,
magnetism, structures, stability, and reactivity. The central assumption of CFT is that metal–ligand interactions are purely
electrostatic in nature.
5.6.7: Magnetism
5.6: Crystal Field Theory is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
Crystal field theory (CFT) describes the breaking of orbital degeneracy in transition metal complexes due to the presence of ligands. CFT
qualitatively describes the strength of the metal-ligand bonds. Based on the strength of the metal-ligand bonds, the energy of the system is altered.
This may lead to a change in magnetic properties as well as color. This theory was developed by Hans Bethe and John Hasbrouck van Vleck.
Basic Concept
In Crystal Field Theory, it is assumed that the ions are simple point charges (a simplification). When applied to alkali metal ions containing a
symmetric sphere of charge, calculations of bond energies are generally quite successful. The approach taken uses classical potential energy
equations that take into account the attractive and repulsive interactions between charged particles (that is, Coulomb's Law interactions).
q1 q2
E ∝ (5.6.1.1)
r
with
E the bond energy between the charges and
q1 and q are the charges of the interacting ions and
2
r is the distance separating them.
This approach leads to the correct prediction that large cations of low charge, such as K and N a , should form few coordination compounds. For
+ +
transition metal cations that contain varying numbers of d electrons in orbitals that are NOT spherically symmetric, however, the situation is quite
different. The shape and occupation of these d-orbitals then becomes important in an accurate description of the bond energy and properties of the
transition metal compound.
Description of d-Orbitals
To understand CFT, one must understand the description of the lobes:
dxy: lobes lie in-between the x and the y axes.
dxz: lobes lie in-between the x and the z axes.
dyz: lobes lie in-between the y and the z axes.
dx2-y2: lobes lie on the x and y axes.
dz2: there are two lobes on the z axes and there is a donut shape ring that lies on the xy plane around the other two lobes.
Figure 5.6.1.1 : Spatial arrangement of ligands in the an octahedral ligand field with respect to the five d-orbitals.
Octahedral Complexes
When examining a single transition metal ion, the five d-orbitals have the same energy (Figure 5.6.1.2). When ligands approach the metal ion, some
experience more opposition from the d-orbital electrons than others based on the geometric structure of the molecule. Since ligands approach from
different directions, not all d-orbitals interact directly. These interactions, however, create a splitting due to the electrostatic environment.
For example, consider a molecule with octahedral geometry. Ligands approach the metal ion along the x, y , and z axes. Therefore, the electrons in
the d and d
z2 orbitals (which lie along these axes) experience greater repulsion. It requires more energy to have an electron in these orbitals
x2 −y 2
than it would to put an electron in one of the other orbitals. This causes a splitting in the energy levels of the d-orbitals. This is known as crystal
field splitting. For octahedral complexes, crystal field splitting is denoted by Δ (or Δ ). Any orbital that has a lobe on the axes moves to a higher
o oct
energy level. The energies of the d and d

z
2 orbitals increase due to greater interactions with the ligands. The d , d , and d orbitals decrease
2
x −y
2
xy xz yz
in energy with respect to the normal energy level and become more stable. This means that in an octahedral, the energy levels of e are higher (by g
0.6∆o) while t are lower (by 0.4∆o). It should be noted that the labels t2g and eg come from group theory and the octahedral point group. The
2g
energy difference between the t and e orbitals dictates the energy that the complex will absorb causing electrons to move from one level to the
2g g
next. For transition metal complexes, the absorbed energy is typically in the visible part of the spectrum and thus this will determine the color of the
complex. Whether the complex is paramagnetic or diamagnetic will be determined by the spin state. If there are unpaired electrons, the complex is
paramagnetic; if all electrons are paired, the complex is diamagnetic.
Figure 5.6.1.2 : (a) Distributing a charge of −6 uniformly over a spherical surface surrounding a metal ion causes the energy of all five d orbitals to
increase due to electrostatic repulsions, but the five d orbitals remain degenerate. Placing a charge of −1 at each vertex of an octahedron causes the d
orbitals to split into two groups with different energies: the dx2−y2 and dz2 orbitals increase in energy, while the, dxy, dxz, and dyz orbitals decrease in
energy. The average energy of the five d orbitals is the same as for a spherical distribution of a −6 charge, however. Attractive electrostatic
interactions between the negatively charged ligands and the positively charged metal ion (far right) cause all five d orbitals to decrease in energy but
does not affect the splittings of the orbitals. (b) The two eg orbitals (left) point directly at the six negatively charged ligands, which increases their
energy compared with a spherical distribution of negative charge. In contrast, the three t2g orbitals (right) point between the negatively charged
ligands, which decreases their energy compared with a spherical distribution of charge.
Electrons in Orbitals
According to the Aufbau principle, electrons are filled from lower to higher energy orbitals (Figure 5.6.1.3). For the octahedral case above, this
corresponds to the dxy, dxz, and dyz orbitals. Following Hund's rule, electrons are filled in order to have the highest number of unpaired electrons. For
example, if one had a d3 complex, there would be three unpaired electrons. If one were to add an electron, however, it has the ability to fill a higher
energy orbital ( dz² or dx²-y²) or pair with an electron residing in the dxy, dxz, or dyz orbitals. This pairing of the electrons requires energy (spin pairing
energy). If the pairing energy is less than the crystal field splitting energy, ∆₀, then the next electron will go into the dxy, dxz, or dyz orbitals due to
stability. This situation allows for the least amount of unpaired electrons, and is known as low spin. If the pairing energy is greater than ∆₀, then the
next electron will go into the dz² or dx²-y² orbitals as an unpaired electron. This situation allows for the most number of unpaired electrons, and is
known as high spin. Ligands that cause a transition metal to have a small crystal field splitting, which leads to high spin, are called weak-field
ligands. Ligands that produce a large crystal field splitting, which leads to low spin, are called strong field ligands.
Figure 5.6.1.3 : Low Spin, Strong Field (∆o˃P) High Spin, Weak Field (∆o˂P)Splitting for a d complex under a strong field (left) and a weak field
4
(right). The strong field is a low spin complex, while the weak field is a high spin complex.
As mentioned above, CFT is based primarily on symmetry of ligands around a central metal/ion and how this anisotropic (properties depending on
direction) ligand field affects the metal's atomic orbitals; the energies of which may increase, decrease or not be affected at all. Once the ligands'
electrons interact with the electrons of the d-orbitals, the electrostatic interactions cause the energy levels of the d-orbital to fluctuate depending on
the orientation and the nature of the ligands. For example, the valence and the strength of the ligands determine splitting; the higher the valence or
the stronger the ligand, the larger the splitting. Ligands are classified as strong or weak based on the spectrochemical series:
I < Br < Cl < SCN < F < OH < ox< ONO < H2O < SCN < EDTA < NH3 < en < NO2 < CN
Note that SCN and NO2 ligands are represented twice in the above spectrochemical series since there are two different Lewis base sites (e.g., free
electron pairs to share) on each ligand (e.g., for the SCN ligand, the electron pair on the sulfur or the nitrogen can form the bond to a metal). The
specific atom that binds in such ligands is underlined.
Tetrahedral Complexes
In a tetrahedral complex, there are four ligands attached to the central metal. The d orbitals also split into two different energy levels. The top three
consist of the d , d , and d orbitals. The bottom two consist of the d
xy xz yz and d orbitals. The reason for this is due to poor orbital overlap
2
x −y
2
z
2
between the metal and the ligand orbitals. The orbitals are directed on the axes, while the ligands are not.
Figure 5.6.1.5 : (a) Tetraheral ligand field surrounding a central transition metal (blue sphere). (b) Splitting of the degenerate d-orbitals (without a
ligand field) due to an octahedral ligand field (left diagram) and the tetrahedral field (right diagram).
The difference in the splitting energy is tetrahedral splitting constant (Δ ), which less than (Δ ) for the same ligands:
t o
Δt = 0.44 Δo (5.6.1.2)
Consequentially, Δ is typically smaller than the spin pairing energy, so tetrahedral complexes are usually high spin. As seen with octahedral
t
compounds, the labels for the groups of orbitals, t2 and e in this case, come from group theory and the tetrahedral point group.
Square Planar Complexes

In a square planar, there are four ligands as well. However, the difference is that the electrons of the ligands are only attracted to the xy plane. Any
orbital in the xy plane has a higher energy level (Figure 5.6.1.6). There are four different energy levels for the square planar (from the highest energy
level to the lowest energy level): dx2-y2, dxy, dz2, and both dxz and dyz.
Figure 5.6.1.6 : Splitting of the degenerate d-orbitals (without a ligand field) due to an square planar ligand field.
The splitting energy (from highest orbital to lowest orbital) is Δ sp and tends to be larger then Δ o
Δsp = 1.74 Δo (5.6.1.3)
Moreover, Δ sp is also larger than the pairing energy, so the square planar complexes are usually low spin complexes.
Exercise 5.6.1.1
For the complex ion [Fe(Cl)6]3- determine the number of d-electrons for Fe, sketch the d-orbital energy levels and the distribution of d electrons
among them, list the number of lone electrons, and label whether the complex is paramagnetic or diamagnetic.
Answer
Step 1: Determine the valence of Fe. Here it is Fe(III). Based on its electron configuration, Fe(III) has 5 d-electrons. Step 2: Determine the
geometry of the ion. Here it is an octahedral which means the energy splitting should look like:
Step 3: Decide whether the ligand induces is a strong or weak field spin by looking at the spectrochemical series. Cl- is a weak field ligand
(i.e., it induces high spin complexes). Therefore, electrons will likely fill all orbitals before being paired.
Step four: Count the number of lone electrons. Here, there are 5 electrons. Step five: The five unpaired electrons means this complex ion is
paramagnetic (and strongly so).
Exercise 5.6.1.2
A tetrahedral complex absorbs at 545 nm. Estimate the octahedral crystal field splitting (Δ ) for an octahedral compound of the same metal
o
with the same ligands? What would be the color of the complex?
Answer
hc
Δt = (5.6.1.4)
λ
−34 8
(6.626 × 10 J ⋅ s)(3 × 10 m/s)
−19
Δt = = 3.65 × 10 J (5.6.1.5)
−9
545 × 10 m
However, the tetrahedral splitting (Δ ) is ~4/9 that of the octahedral splitting (Δ ).

t o
Δt = 0.44 Δo (5.6.1.6)
−19
Δt 3.65 × 10 J −18
Δo = = = 8.30 × 10 J (5.6.1.7)
0.44 0.44
This is the energy needed to promote one electron in one complex. Often the crystal field splitting is given per mole, which requires this
number to be multiplied by Avogadro's Number (6.022 × 10 ). 23
This complex appears red, since it absorbs in the complementary green color (determined via the color wheel).
Electronic Structure of Coordination Complexes
Video:
Exercise 5.6.1.3
For each of the following, sketch the d-orbital energy levels and the distribution of d electrons among them, state the geometry, list the number
of d-electrons, list the number of lone electrons, and label whether they are paramagnetic or dimagnetic:
1. [Ti(H2O)6]2+
2. [NiCl4]2-
3. [CoF6]3- (also state whether this is low or high spin)
4. [Co(NH3)6]3+ (also state whether this is low or high spin)
Answer
1. octahedral, 2, 2, paramagnetic
2. tetrahedral, 8, 2, paramagnetic (see Octahedral vs. Tetrahedral Geometries)
3. octahedral, 6, 4, paramagnetic, high spin
4. octahedral, 6, 0, diamagnetic, low spin

Asadullah Awan (UCD), Hong Truong (UCD)
5.6.1: Crystal Field Theory is shared under a CC BY-NC-SA license and was authored, remixed, and/or curated by LibreTexts.
The color for a coordination complex can be predicted using the Crystal Field Theory (CFT). Knowing the color can have a number
of useful applications, such as the creation of pigments for dyes in the textile industry. The tendency for coordination complexes to
display such a wide array of colors is merely coincidental; their absorption energies happen to fall within range of the visible light
spectrum. Chemists and physicists often study the color of a substance not to understand its sheer appearance, but because color is
an indicator of a chemical's physical proprieties on the atomic level.
The Electromagnetic Spectrum

The electromagnetic spectrum (EM) spectrum is made up of photons of different wavelengths. Photons, unique in displaying the
properties of both waves and particles, create visible light and colors in a small portion of the EM spectrum. This visible light
portion has wavelengths in approximately the 400-700 nanometer range (a nanometer, “nm,” is 10-9 meters). Each specific
wavelength corresponds to a different color (Figure 5.6.2.1), and when all the wavelengths are present, it appears as white light.
Figure 5.6.2.1 : A linear representation of the visible light spectrum. (Public Domain; Gringer via Wikipedia)
The wavelength and frequency of a wave are inversely proportional: as one increases, the other decreases; this is a consequence of
all light traveling at the same speed.
−1
λ =ν (5.6.2.1)
Because of this relationship, blue light has a much higher frequency and more energy than red light. In general, photons to the
right of the EM spectrum have increasingly higher energy than photons to the left.
Perceiving Color
Color is perceived in two ways, through additive mixing, where different colors are made by combining different colors of light,
and through subtractive mixing, where different wavelengths of light are taken out so that the light is no longer pure white. For
colors of coordination complexes, subtractive mixing is considered. As shown in Figure 5.6.2.2, the idea behind subtractive mixing
is that white light (which is made from all the colors mixed together) interacts with an object. The object absorbs some of the light,
and then reflects or transmits (or both, depending on the object) the rest of the light, which contacts the eye. The object is perceived
as whichever color is not absorbed. In Figure 5.6.2.2, white light (simplified as green, red, and blue bands) is shone through a
solution. The solution absorbs the red and green wavelengths; however, the blue light is reflected and passes through, so the
solution appears blue. This procedure takes place whenever an object displays visible color. If none of the light is absorbed, and all
is reflected back off, the object appears white; if all of the light is absorbed, and there is none left to reflect or transmit through, the
object appears black.
Figure 5.6.2.2 : Subtractive mixing
Colors of Coordination Complexes: Crystal Field Splitting

When ligands attach to a transition metal to form a coordination complex, electrons in the d orbital split into high energy and low
energy orbitals. The difference in energy of the two levels is denoted as ∆, and it is a characteristic a property both of the metal and
the ligands. This is illustrated in Figure 5.6.2.3; the "o" subscript on the ∆ indicates that the complex has octahedral geometry.
Figure 5.6.2.3 : d-Orbitals Splitting in an octahedral ligand field. (CC BY-SA-NC; anonymous by request)
If ∆o is large, and much energy is required to promote electrons into the high energy orbitals, the electrons will instead pair in the
lower energy orbitals, resulting in a "low spin" complex (Figure 5.6.2.4A); however, if ∆o is small, and it takes little energy to
occupy the higher orbitals, the electrons will do so, and remain unpaired (until there are more than five electrons), resulting in a
“high spin” complex (Figure 5.6.2.4B). Different ligands are associated with either high or low spin —a "strong field" ligand
results in a large ∆o and a low spin configuration, while a "weak field" ligand results in a small ∆o and a high spin configuration.
For more details, see the Crystal Field Theory (CFT) page.
Figure 5.6.2.4A : Low Spin, Strong Field (Δ o > P ). (CC BY-SA-NC; anonymous
by request)
Figure 5.6.2.4B : High Spin, Weak Field (Δ o < P ). (CC BY-SA-NC; anonymous
by request)
A photon equal to the energy difference ∆o can be absorbed, promoting an electron to the higher energy level. As certain
wavelengths are absorbed in this process, subtractive color mixing occurs and the coordination complex solution becomes colored.
If the ions have a noble gas configuration, and have no unpaired electrons, the solutions appear colorless; in reality, they still have a
measured energy and absorb certain wavelengths of light, but these wavelengths are not in the visible portion of the EM spectrum
and no color is perceived by the eye.
In general, a larger Δ indicates that higher energy photons are absorbed, and the solution appears further to the left on the EM
o
spectrum shown in Figure 5.6.2.1. This relationship is described in the equation

Δo = hc/λ (5.6.2.2)
where h and c are constants, and λ is the wavelength of light absorbed.

Using a color wheel can be useful for determining what color a solution will appear based on what wavelengths it absorbs (Figure
5.6.2.6). If a complex absorbs a particular color, it will have the appearance of whatever color is directly opposite it on the wheel.
For example, if a complex is known to absorb photons in the orange range, it can be concluded that the solution will look blue. This
concept can be used in reverse to determine ∆ for a complex from the color of its solution.
Figure 5.6.2.5
Relating the Colors of Coordination Complexes to the Spectrochemical Series

According to the Crystal Field Theory, ligands that have smaller Δ) values are considered "weak field" and will absorb lower-
energy light with longer λ values (ie a "red shift"). Ligands that have larger Δ) values are considered "strong field" and will absorb
higher-energy light with shorter λ values (ie a "blue shift"). This relates to the colors seen in a coordination complex. Weaker-
field ligands induce the absorption of longer wavelength (lower frequency=lower energy) light than stronger-field ligands since
their respective Δ values are smaller than the electron pairing energy.
o
The energy difference, Δ , determines the color of the coordination complex. According to the spectrochemical series, the high
o
spin ligands are considered "weak field," and absorb longer wavelengths of light (weak Δ ), while complexes with low spin
o
ligands absorb light of greater frequency (high Δ ). The color seen is the complementary color of the color associated with the
o
absorbed wavelength. To predict which possible colors and their corresponding wavelengths are absorbed, the spectrochemical
series can be used:
(Strong field/large Δ0/low spin) (weak field/ small Δ0/high spin)
CO, NO, CN>NO2>en>py≈NH3>EDTA>SCN>H2O>ONO>ox>OH>F>SCN>Cl>Br>I
Exercise 5.6.2.1
If a solution with a dissolved octahedral complex appears yellow to the eye, what wavelength of light does it absorb? Is this
complex expected to be low spin or high spin?
Answer
A solution that looks yellow absorbs light that is violet, which is roughly 410 nm from the color wheel. Since it absorbs
high energy, the electrons must be raised to a higher level, and Δ is high, so the complex is likely to be low spin
o
Exercise 5.6.2.2
An octahedral metal complex absorbs light with wavelength 535 nm. What is the crystal field splitting Δo for the complex?
What color is it to the eye?
Answer
To solve this question, we need to use the equation
hc
Δo =
λ
with
h is Planck’s constant and is 6.625 × 10−34
J⋅s and c is the speed of light and is 2.998 × 108
m/s.
Note: the fact that the complex is octahedral makes no impact when solving this problem. Although the splitting is different
for complexes of different structures, the mechanics of solving the problem are identical.
It is also important to remember that 1 nm is equal to 1 × 10
−9
meters. With all this information, the final equation looks
like this:
−34 8
(6.625 × 10 J ⋅ s)(2.998 × 10 m/s)
Δo = = 3.712 J/molecule
1m
(535nm) ( )
9
1 × 10 nm
It is not necessary to use any equations to solve the second part of the problem. Light that is 535 nm is green, and because
green light is absorbed, the complex appears red (refer to Figures 5.6.2.1and 5.6.2.6for this information).
Exercise 5.6.2.3
There are two solutions, one orange and one blue. Both solutions are known to be made up of a cobalt complex; however, one
has chloride ions as ligands, while the other has ammonia ligands. Which solution is expected to be orange?
Answer
In order to solve this problem, it is necessary to know the relative strengths of the ligands involved. A sample ligand
strength list is given here, but see Crystal Field Splitting for a more complete list:
CN > en > NH3 > H2O > F >SCN > Cl
From this information, it is clear that NH3 is a stronger ligand than Cl, which means that the complex involving NH3 has a
greater ∆, and the complex will be low spin. Because of the larger ∆, the electrons absorb higher energy photons, and the
solution will have the appearance of a lower energy color. Since orange light is less energetic than blue light, the NH3
containing solution is predicted to be orange
References
1. Cox, P. A. Instant Notes Inorganic Chemistry. Second ed. Grand Rapids: Garland, Incorporated, 2004.
2. Nassau, Kurt. The Physics and Chemistry of Color : The Fifteen Causes of Color. Second ed. New York: Wiley-Interscience,
2001.
3. Petrucci, Ralph H., William S. Harwood, and Geoff E. Herring. General Chemistry : Principles and Modern Applications. Ninth
ed. Upper Saddle River: Prentice Hall PTR, 2006.
4. Petrucci, Ralph H., Carey Bissonnette, F. Geoffrey Herring, Jeffrey D. Madura. General Chemistry: Principles and Modern
Applications. Tenth Ed. Upper Saddle River: Pearson Education, Inc. 2011.

Deyu Wang (UCD)
5.6.2: Colors of Coordination Complexes is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
A consequence of Crystal Field Theory is that the distribution of electrons in the d orbitals may lead to net stabilization (decrease in
energy) of some complexes depending on the specific ligand field geometry and metal d-electron configurations. It is a simple
matter to calculate this stabilization since all that is needed is the electron configuration and knowledge of the splitting patterns.
Definition: Crystal Field Stabilization Energy

The Crystal Field Stabilization Energy is defined as the energy of the electron configuration in the ligand field minus the
energy of the electronic configuration in the isotropic field.
C F SE = ΔE = Eligand field − Eisotropic field (5.6.3.1)
The CSFE will depend on multiple factors including:

Geometry (which changes the d-orbital splitting patterns)
Number of d-electrons
Spin Pairing Energy
Ligand character (via Spectrochemical Series)
For an octahedral complex, an electron in the more stable t subset is treated as contributing −2/5Δ whereas an electron in the
2g o
higher energy e subset contributes to a destabilization of +3/5Δ . The final answer is then expressed as a multiple of the crystal
g o
field splitting parameter Δ . If any electrons are paired within a single orbital, then the term P is used to represent the spin pairing
o
energy.
Example 5.6.3.1: CFSE for a high Spin d complex 7
What is the Crystal Field Stabilization Energy for a high spin d octahedral complex?
7
Solution
The splitting pattern and electron configuration for both isotropic and octahedral ligand fields are compared below.
The energy of the isotropic field (E isotropic field) is
Eisotropic field = 7 × 0 + 2P = 2P
The energy of the octahedral ligand field E ligand field is
Eligand field = (5 × −2/5 Δo ) + (2 × 3/5 Δo ) + 2P = −4/5 Δo + 2P
So via Equation 5.6.3.1, the CFSE is

C F SE = Eligand field − Eisotropic field
= (−4/5 Δo + 2P ) − 2P
= −4/5Δo
Notice that the Spin pairing Energy falls out in this case (and will when calculating the CFSE of high spin complexes) since the
number of paired electrons in the ligand field is the same as that in isotropic field of the free metal ion.
Exercise 5.6.3.1
What is the Crystal Field Stabilization Energy for a low spin d octahedral complex? 7
Answer
The splitting pattern and electron configuration for both isotropic and octahedral ligand fields are compared below.
The energy of the isotropic field is the same as calculated for the high spin configuration in Example 1:
Eisotropic field = 7 × 0 + 2P = 2P
The energy of the octahedral ligand\) field E ligand field is

Eligand field = (6 × −2/5Δo ) + (1 × 3/5Δo ) + 3P
= −9/5Δo + 3P
So via Equation 5.6.3.1, the CFSE is

C F SE = Eligand field − Eisotropic field
= (−9/5Δo + 3P ) − 2P
= −9/5Δo + P
Adding in the pairing energy since it will require extra energy to pair up one extra group of electrons. This appears more a more
stable configuration than the high spin d configuration in Example 5.6.3.1, but we have then to take into consideration the Pairing
7
energy P to know definitely, which varies between 200 − 400 kJ mol depending on the metal. −1
Table 5.6.3.1 : Crystal Field Stabilization Energies (CFSE) for high and low spin octahedral complexes
Total d- Crystal Field Stabilization
Isotropic Field Octahedral Complex
electrons Energy
High Spin Low Spin
Eisotropic fie ld Configuration Eligand fie ld Configuration Eligand fie ld High Spin Low Spin
d0 0 t2g 0e 0
g 0 t2g
0e 0
g 0 0 0
d1 0 t2g 1e 0
g -2/5 Δ o t2g eg
1 0 -2/5 Δ o -2/5 Δ o -2/5 Δ o
d2 0 t2g 2e 0
g -4/5 Δ o t2g
2e 0
g -4/5 Δ o -4/5 Δ o -4/5 Δ o
d3 0 t2g 3e 0
g -6/5 Δ o t2g
3e 0
g -6/5 Δ o -6/5 Δ o -6/5 Δ o
d4 0 t2g 3e 1
g -3/5 Δ o t2g eg
4 0 -8/5 Δ + Po -3/5 Δ o -8/5 Δ + P
o
d5 0 t2g 3e 2
g 0Δ o t2g
5e 0
g -10/5 Δ + 2P o 0Δ o -10/5 Δ + 2P
o
d6 P t2g 4e 2
g -2/5 Δ + P o t2g
6e 0
g -12/5 Δ + 3P o -2/5 Δ o -12/5 Δ + P
o
d7 2P t2g 5e 2
g -4/5 Δ + 2P o t2g eg
6 1 -9/5 Δ + 3P o -4/5 Δ o -9/5 Δ + P
o
d8 3P t2g 6e 2
g -6/5 Δ + 3P o t2g eg
6 2 -6/5 Δ + 3P o -6/5 Δ o -6/5 Δ o
d9 4P t2g 6e 3
g -3/5 Δ + 4P o t2g
6e 3
g -3/5 Δ + 4P o -3/5 Δ o -3/5 Δ o
d10 5P t2g 6e 4
g 0 Δ + 5P
o t2g
6e 4
g 0 Δ + 5P
o 0 0
P is the spin pairing energy and represents the energy required to pair up electrons within the same orbital. For a given metal ion P
(pairing energy) is constant, but it does not vary with ligand and oxidation state of the metal ion).
Octahedral Preference
Similar CFSE values can be constructed for non-octahedral ligand field geometries once the knowledge of the d-orbital splitting is
known and the electron configuration within those orbitals known, e.g., the tetrahedral complexes in Table 5.6.3.2. These energies
geoemtries can then be contrasted to the octahedral CFSE to calculate a thermodynamic preference (Enthalpy-wise) for a metal-
ligand combination to favor the octahedral geometry. This is quantified via a Octahedral Site Preference Energy defined below.
Definition: Octahedral Site Preference Energies

The Octahedral Site Preference Energy (OSPE) is defined as the difference of CFSE energies for a non-octahedral complex and
the octahedral complex. For comparing the preference of forming an octahedral ligand field vs. a tetrahedral ligand field, the
OSPE is thus:
OSP E = C F S E(oct) − C F S E(tet) (5.6.3.2)
The OSPE quantifies the preference of a complex to exhibit an octahedral geometry vs. a tetrahedral geometry.
Note: the conversion between Δ and Δ used for these calculations is:
o t
4
Δt ≈ Δo (5.6.3.3)
9
which is applicable for comparing octahedral and tetrahedral complexes that involve same ligands only.
Table 5.6.3.2: Octahedral Site Preference Energies (OSPE)
OSPE (for high spin
Total d-electrons CFSE(Octahedral) CFSE(Tetrahedral)
complexes)**
High Spin Low Spin Configuration Always High Spin*
d0 0Δ o 0Δ o e0 0Δ t 0Δ o
d1 -2/5 Δ o -2/5 Δ o e1 -3/5 Δ t -6/45 Δ o
d2 -4/5 Δ o -4/5 Δ o e2 -6/5 Δ t -12/45 Δ o
d3 -6/5 Δ o -6/5 Δ o e2t21 -4/5 Δ t -38/45 Δ o
d4 -3/5 Δ o -8/5 Δ + P
o e2t22 -2/5 Δ t -19/45 Δ o
d5 0Δ o -10/5 Δ + 2P
o e2t23 0Δ t 0Δ o
d6 -2/5 Δ o -12/5 Δ + P
o e3t23 -3/5 Δ t -6/45 Δ o
d7 -4/5 Δ o -9/5 Δ + P
o e4t23 -6/5 Δ t -12/45 Δ o
d8 -6/5 Δ o -6/5 Δ o e4t24 -4/5 Δ t -38/45 Δ o
d9 -3/5 Δ o -3/5 Δ o e4t25 -2/5 Δ t -19/45 Δ o
d10 0 0 e4t26 0Δ t 0Δ o
P is the spin pairing energy and represents the energy required to pair up electrons within the same orbital.
Tetrahedral complexes are always high spin since the splitting is appreciably smaller than P (Equation 5.6.3.3).
After conversion with Equation 5.6.3.3. The data in Tables 5.6.3.1 and 5.6.3.2 are represented graphically by the curves in Figure
5.6.3.1 below for the high spin complexes only. The low spin complexes require knowledge of P to graph.
Figure 5.6.3.1 : Crystal Field Stabilization Energies for both octahedral fields (C F SE ) and tetrahedral fields (C F SE ).
oct tet
Octahedral Site Preference Energies (OSPE) are in yellow. This is for high spin complexes.
From a simple inspection of Figure 5.6.3.1, the following observations can be made:
The OSPE is small in d , d , d , d , d complexes and other factors influence the stability of the complexes including steric
1 2 5 6 7
factors
The OSPE is large in d and d complexes which strongly favor octahedral geometries
3 8
Applications
The "double-humped" curve in Figure 5.6.3.1 is found for various properties of the first-row transition metals, including Hydration
and Lattice energies of the M(II) ions, ionic radii as well as the stability of M(II) complexes. This suggests that these properties are
somehow related to Crystal Field effects.
In the case of Hydration Energies describing the complexation of water ligands to a bare metal ion:
2+ 2+
M (g) + H2 O → [M (OH2 )6 ] (aq) (5.6.3.4)
Table 5.6.3.3 and Figure 5.6.3.1 shows this type of curve. Note that in any series of this type not all the data are available since a
number of ions are not very stable in the M(II) state.
Table 5.6.3.3: Hydration energies of M 2+
ions
M ΔH°/kJmol-1 M ΔH°/kJmol-1
Ca -2469 Fe -2840
Sc no stable 2+ ion Co -2910
Ti -2729 Ni -2993
>V -2777 Cu -2996
Cr -2792 Zn -2928
Mn -2733
Graphically the data in Table 2 can be represented by:
Figure 5.6.3.2 : hydration energies of M 2+
ions

5.6.3: Crystal Field Stabilization Energy is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
The magnitude of Δo dictates whether a complex with four, five, six, or seven d electrons is high spin or low spin, which affects its
magnetic properties, structure, and reactivity. Large values of Δo (i.e., Δo > P) yield a low-spin complex, whereas small values of
Δo (i.e., Δo < P) produce a high-spin complex. The magnitude of Δo depends on three factors: the valence of the metal, the principal
quantum number of the metal (and thus its location in the periodic table), and the nature of the ligand(s). Values of Δo for some
representative transition-metal complexes are given in Table 5.6.4.1.
Table 5.6.4.1 : Crystal Field Splitting Energies for Some Octahedral (Δo)* and Tetrahedral (Δt) Transition-Metal Complexes
Octahedral Tetrahedral
Δo (cm−1) Octahedral Complexes Δo (cm−1) Δt (cm−1)
Complexes Complexes
[Ti(H2O)6]3+ 20,300 [Fe(CN)6]4− 32,800 VCl4 9010
[V(H2O)6]2+ 12,600 [Fe(CN)6]3− 35,000 [CoCl4]2− 3300
[V(H2O)6]3+ 18,900 [CoF6]3− 13,000 [CoBr4]2− 2900
[CrCl6]3− 13,000 [Co(H2O)6]2+ 9300 [CoI4]2− 2700
[Cr(H2O)6]2+ 13,900 [Co(H2O)6]3+ 27,000
[Cr(H2O)6]3+ 17,400 [Co(NH3)6]3+ 22,900
[Cr(NH3)6]3+ 21,500 [Co(CN)6]3− 34,800
[Cr(CN)6]3− 26,600 [Ni(H2O)6]2+ 8500
Cr(CO)6 34,150 [Ni(NH3)6]2+ 10,800
[MnCl6]4− 7500 [RhCl6]3− 20,400
[Mn(H2O)6]2+ 8500 [Rh(H2O)6]3+ 27,000
[MnCl6]3− 20,000 [Rh(NH3)6]3+ 34,000
[Mn(H2O)6]3+ 21,000 [Rh(CN)6]3− 45,500
[Fe(H2O)6]2+ 10,400 [IrCl6]3− 25,000
[Fe(H2O)6]3+ 14,300 [Ir(NH3)6]3+ 41,000
*Energies obtained by spectroscopic measurements are often given in units of wave numbers (cm−1); the wave number is the reciprocal of the
wavelength of the corresponding electromagnetic radiation expressed in centimeters: 1 cm−1 = 11.96 J/mol.
Source of data: Duward F. Shriver, Peter W. Atkins, and Cooper H. Langford, Inorganic Chemistry, 2nd ed. (New York: W. H.
Freeman and Company, 1994).
Factor 1: Valence of the Metal

Increasing the valence of a metal ion has two effects: the radius of the metal decreases, and ligands are more strongly attracted to it.
Both factors decrease the metal–ligand distance, which in turn causes the ligands to interact more strongly with the d-orbitals.
Consequently, the magnitude of Δo increases as the valence of the metal increases. Typically, Δo for a M(III) is about 50% greater
than for the M(II) of the same metal; for example, for [V(H2O)6]2+, Δo = 11,800 cm−1; for [V(H2O)6]3+, Δo = 17,850 cm−1.
Factor 2: Principal Quantum Number of the Metal

For a series of complexes of metals from the same group in the periodic table with the same charge and the same ligands, the
magnitude of Δo increases with increasing principal quantum number: Δo (3d) < Δo (4d) < Δo (5d). The data for hexaammine
complexes of the trivalent Group 9 metals illustrate this point:
[Co(NH3)6]3+: Δo = 22,900 cm−1
[Rh(NH3)6]3+: Δo = 34,100 cm−1
[Ir(NH3)6]3+: Δo = 40,000 cm−1
The increase in Δo with increasing principal quantum number is due to the larger radius of valence orbitals down a column. In
addition, repulsive ligand–ligand interactions are most important for smaller metal ions. Relatively speaking, this results in shorter
M–L distances and stronger d orbital–ligand interactions.
Factor 3: The Nature of the Ligands

Experimentally, it is found that the Δo observed for a series of complexes of the same metal ion depends strongly on the nature of
the ligands. For a series of chemically similar ligands, the magnitude of Δo decreases as the size of the donor atom increases. For
example, Δo values for halide complexes generally decrease in the order F > Cl > Br > I because smaller, more localized charges,
such as we see for F, interact more strongly with the d-orbitals of the metal. In addition, a small neutral ligand with a highly
localized lone pair, such as NH3, results in significantly larger Δo values than might be expected. Because the lone pair points
directly at the metal ion, the electron density along the M–L axis is greater than for a spherical anion such as F. The experimentally
observed order of the crystal field splitting energies produced by different ligands is called the spectrochemical series which was
presented in a previous section.
5.6.4: Factors That Affect the Magnitude of Δo is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
The Jahn-Teller effect is a geometric distortion of a non-linear molecular system that reduces its symmetry and energy. This
distortion is typically observed among octahedral complexes where the two axial bonds can be shorter or longer than those of the
equatorial bonds. This effect can also be observed in tetrahedral compounds. This effect is dependent on the electronic state of the
system.
Introduction
In 1937, Hermann Jahn and Edward Teller postulated a theorem stating that "stability and degeneracy are not possible
simultaneously unless the molecule is a linear one," in regards to its electronic state.[1] This leads to a break in degeneracy which
stabilizes the molecule and by consequence, reduces its symmetry. Since 1937, the theorem has been revised which Housecroft and
Sharpe have eloquently phrased as "any non-linear molecular system in a degenerate electronic state will be unstable and will
undergo distortion to form a system of lower symmetry and lower energy, thereby removing the degeneracy."[2] This is most
commonly observed with transition metal octahedral complexes, however, it can be observed in tetrahedral compounds as well.
For a given octahedral complex, the five d atomic orbitals are split into two degenerate sets when constructing a molecular orbital
diagram. These are represented by the sets' symmetry labels: t (d , d , d ) and e (d and d
2g xz yz xy g z
). When a molecule
2 2
x −y
2
possesses a degenerate electronic ground state, it will distort to remove the degeneracy and form a lower energy (and by
consequence, lower symmetry) system. The octahedral complex will either elongate or compress the z ligand bonds as shown in
Figure 5.6.5.1 below:
Figure 5.6.5.1 : Jahn-Teller distortions for an octahedral complex.

When an octahedral complex exhibits elongation, the axial bonds are longer than the equatorial bonds. For a compression, it is the
reverse; the equatorial bonds are longer than the axial bonds. Elongation and compression effects are dictated by the amount of
overlap between the metal and ligand orbitals. Thus, this distortion varies greatly depending on the type of metal and ligands. In
general, the stronger the metal-ligand orbital interactions are, the greater the chance for a Jahn-Teller effect to be observed.
Elongation
Elongation Jahn-Teller distortions occur when the degeneracy is broken by the stabilization (lowering in energy) of the d orbitals
with a z component, while the orbitals without a z component are destabilized (higher in energy) as shown in Figure 5.6.5.2 below:
Figure 5.6.5.2 : Illustration of tetragonal distortion (elongation) for an octahedral complex.
This is due to the d and d
xy orbitals having greater overlap with the ligand orbitals, resulting in the orbitals being higher in
2
x −y
2
energy. Since the d 2

x −y
orbital is antibonding, it is expected to increase in energy due to elongation. The d orbital is still
2
xy
nonbonding, but is destabilized due to the interactions. Jahn-Teller elongations are well-documented for copper(II) octahedral
compounds. A classic example is that of copper(II) fluoride as shown in Figure 5.6.5.3.
Figure 5.6.5.3 : Structure of octahedral copper(II) fluoride.[3]

Notice that the two axial bonds are both elongated and the four shorter equatorial bonds are the same length as each other.
According the theorem, the orbital degeneracy is eliminated by distortion, making the molecule more stable based on the model
presented in Figure 5.6.5.2.
Compression
Compression Jahn-Teller distortions occur when the degeneracy is broken by the stabilization (lowering in energy) of the d orbitals
without a z component, while the orbitals with a z component are destabilized (higher in energy) as shown in Figure 5.6.5.4 below:
Figure 5.6.5.4 : Illustration of tetragonal distortion (compression) for an octahedral complex.
This is due to the z-component d orbitals having greater overlap with the ligand orbitals, resulting in the orbitals being higher in
energy. Since the dz2 orbital is antibonding, it is expected to increase in energy due to compression. The dxz and dyz orbitals are still
nonbonding, but are destabilized due to the interactions.
Electronic Configurations
For Jahn-Teller effects to occur in transition metals there must be degeneracy in either the t2g or eg orbitals. The electronic states of
octahedral complexes depend on the number of d-electrons and the splitting energy, Δ. When Δ is large and is greater than the
energy required to pair electrons, electrons pair in t2g before occupying eg. On the other hand, when Delta small and is less than
the pairing energy, electrons will occupy eg before pairing in t2g. The Δ of an octahedral complex is dictated by the chemical
environment (ligand identity), and the identity and charge of the metal ion. If there electron configurations for any d-electron count
is different depending on Δ, the configuration with more paired electrons is called low spin while the one with more unpaired
electrons is called high spin.
The electron configurations diagrams for d1 through d10 with large and small δ are illustrated in the figures below. Notice that the
electron configurations for d1, d2, d3, d8, d9, and d10 are the same no matter what the magnitude of Δ. Low spin and high spin
configurations exist only for the electron counts d4, d5, d6, and d7.
Large Δ
Figure 5.6.5.5 (below) shows the various electronic configurations for octahedral complexes with large Δ, including the low-spin
configurations of d4, d5, d6, and d7:
Figure 5.6.5.5 : Electron configuration diagram of octahedral complexes (red indicates no degeneracies possible, thus no Jahn-
Teller effects).
The figure illustrates the electron configurations in the case of large Δ. The electron configurations highlighted in red (d3, low spin
d6, d8, and d10) do not exhibit Jahn-Teller distortions. On the other hand d1, d2, low spin d4, low spin d5, low spin d7, and d9, would
be expected to exhibit Jhan-Teller distortion. These electronic configurations correspond to a variety of transition metals. Some
common examples include Cr3+, Co3+, and Ni2+.
Small Δ
Figure 5.6.5.6 (below) shows the various electronic configurations for octahedral complexes with small Δ, including the high-spin
configurations of d4, d5, d6, and d7::
Figure 5.6.5.6 : High spin octahedral coordination diagram (red indicates no degeneracies possible, thus no Jahn-Teller effects).
The figure illustrates the electron configurations in the case of small Δ. The electron configurations highlighted in red (d3, high
spin d5, d8, and d10) do not exhibit Jahn-Teller distortions. In general, degenerate electronic states occupying the e orbital set tend
g
to show stronger Jahn-Teller effects. This is primarily caused by the occupation of these high energy orbitals. Since the system is
more stable with a lower energy configuration, the degeneracy of the eg set is broken, the symmetry is reduced, and occupations at
lower energy orbitals occur.
Spectroscopic Observation
Jahn-Teller distortions can be observed using a variety of spectroscopic techniques. In UV-VIS absorption spectroscopy, distortion
causes splitting of bands in the spectrum due to a reduction in symmetry (Oh to D4h). Consider a hypothetical molecule with
octahedral symmetry showing a single absorption band. If the molecule were to undergo Jahn-Teller distortion, the number of
bands would increase as shown in Figure 5.6.5.7 below:
Figure 5.6.5.7 : Hypothetical absorption spectra of an octahedral molecule (left) and the same molecule with Jahn-Teller elongation
(right). The red arrows indicate electronic transitions.
A similar phenomenon can be seen with IR and Raman vibrational spectroscopy. The number of vibrational modes for a molecule
can be calculated using the 3n - 6 rule (or 3n - 5 for linear geometry) rule. If a molecule exhibits an Oh symmetry point group, it
will have fewer bands than that of a Jahn-Teller distorted molecule with D4h symmetry. Thus, one could observe Jahn-Teller effects
through either IR or Raman techniques. This effect can also be observed in EPR experiments as long as there is at least one
unpaired electron.
Table 5.6.5.1: Examples of Jahn-Teller distorted complexes
CuBr2 4 Br at 240 pm 2 Br at 318 pm
CuCl2 4 Cl at 230 pm 2 Cl at 295 pm
CuCl 2.2H 2O 2 O at 193 pm 2 Cl at 228 pm 2 Cl at 295 pm
CsCuCl3 4 Cl at 230 pm 2 Cl at 265 pm
CuF2 4 F at 193 pm 2 F at 227 pm
CuSO4.4NH3.H2O 4 N at 205 pm 1 O at 259 pm 1 O at 337 pm
K2CuF4 4 F at 191 pm 2 F at 237 pm
KCuAlF6 2 F at 188 pm 4 F at 220 pm
CrF2 4 F at 200 pm 2 F at 243 pm
KCrF3 4 F at 214 pm 2 F at 200 pm
MnF3 2 F at 209 pm 2 F at 191 pm 2 F at 179 pm
The Jahn-Teller Theorem predicts that distortions should occur for any degenerate state, including degeneracy of the t2g level,
however distortions in bond lengths are much more distinctive when the degenerate electrons are in the eg level.
References
1. Jahn, H. A.; Teller, E. Proc. R. Soc. London A, 1937, 161, 220-235. DOI: 10.1098/rspa.1937.0142
2. Housecroft, C.; Sharpe, A. G. Inorganic Chemistry. Prentice Hall, 3rd Ed., 2008, p. 644. ISBN: 978-0-13-175553-6
3. Billy, C.; Haendler, H. A. J. Am. Chem. Soc., 1957, 79, 1049–1051. DOI: 10.1021/ja01562a011
References
Janes, R.; Moore, E. A. Metal-ligand bonding. The Open University, 2004, p. 23. ISBN 0-85404-979-7
P.T.Miller, P.G.Lenhert and M.D.Joesten, Inorg. Chem., 11, 2221, 1972.
J.S.Wood, C.P.Keijzers and R.O.Day, Acta Crystallogr., Sect.C (Cr. Str. Comm.), 40, 404, 1984.
M.D.Joesten, M.S.Hussain and P.G.Lenhert, Inorg. Chem., 9, 151, 1970.
Practice Questions
1. Why do d3 complexes not show Jahn-Teller distortions?
2. Does the spin system (high spin v. low spin) of a molecule play a role in Jahn-Teller effects?
3. What spectroscopic method would one utilize in order to observe Jahn-Teller distortions in a diamagnetic molecule?
4. What spectroscopic method(s) would one utilize in order to observe Jahn-Teller distortions in a paramagnetic molecule?
5. Why are Jahn-Teller effects most prevalent in inorganic (transition metal) compounds?
Answers
1. Complexes with d3 electron configurations do not show Jahn-Teller distortions because there is no ground state degeneracy.
2. Yes. Examining the d5 electron configuration, one finds that the high spin scenario contains all singly occupied d orbitals (no
degeneracy). However, the low spin d5 electron configuration shows degeneracy, which then leads to possible Jahn-Teller
effects.
3. UV-VIS absorption spectroscopy is one of the most common techniques for observing these effects. In general, it is independent
of magnetism (diamagnetic v. paramagnetic). Thus, one would see the effect in the spectrum of UV-VIS absorption analysis.
Note that EPR requires at least one unpaired electron, and therefore not EPR active.
4. Inorganic, specifically transition metal, complexes are most prevalent in showing Jahn-Teller distortions due to the availability
of d orbitals. The most common geometry that the Jahn-Teller effect is observed is in octahedral complexes (see Figures 2, 4, 5
and 6 above) due to the splitting of d orbitals into two degenerate sets. Due to stabilization, the degeneracies are removed,
making a lower symmetry and lower energy molecule.
5. In addition to UV-VIS absorption, one can also employ EPR spectroscopy if a molecule possesses and unpaired electron.

Kamran Ghiassi (UC Davis)
5.6.5: Jahn-Teller Distortions is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
Magnetic moments are often used in conjunction with electronic spectra to gain information about the valence and stereochemistry
of the central metal atom in coordination complexes. A common laboratory procedure for the determination of the magnetic
moment for a complex is the Gouy method which involves weighing a sample of the complex in the presence and absence of a
magnetic field and observing the difference in weight. A template is provided for the calculations involved.
For first row transition metal ions in the free ion state, i.e. isolated ions in a vacuum, all 5 of the 3d orbitals are degenerate.
A simple crystal field theory approach to the bonding in these ions assumes that when they form octahedral complexes, the energy
of the d orbitals are no longer degenerate but are split such that two orbitals, the dx2-y2 and the dz2 (eg subset) are at higher energy
than the dxy, dxz, dyz orbitals (the t2g subset).
For octahedral ions with between 4 and 7 d electrons, this gives rise to 2 possible arrangements called either high spin/weak field or
low spin/strong field respectively. The energy gap is dependent on the position of the coordinated ligands in the
SPECTROCHEMICAL SERIES.
Note
A good starting point is to assume that all Co(III), d6 complexes are octahedral and LOW spin, i.e. t2g6.
In tetrahedral complexes, the energy levels of the orbitals are again split, such that the energy of two orbitals, the d and the 2
x −y
2
dz
(e subset) are now at lower energy (more favored) than the remaining three d , d , d (the t subset) which are destabilized.
2
xy xz yz 2
Tetrahedral complexes are ALL high spin since the difference between the 2 subsets of
energies of the orbitals is much smaller than is found in octahedral complexes.
The usual relationship quoted between them is:
4
Δtet ≈ Δoct (5.6.6.1)
9
Square planar complexes are less common than tetrahedral and d8 e.g. Ni(II), Pd(II), Pt(II), etc, have a strong propensity to
form square planar complexes. As with octahedral complexes, the energy gap between the d and d is Δ and these are
xy 2
x −y
2
oct
considered strong field / low spin hence they are all diamagnetic, μ=0 Bohr Magneton (B.M.)
The formula used to calculate the spin-only magnetic moment can be written in two forms; the first based on the number of
unpaired electrons, n, and the second based on the electron spin quantum number, S . Since for each unpaired electron, n = 1 and
S = 1/2 then the two formulae are related and the answer obtained must be identical.
−−−−−−−
μso = √ n(n + 2) (5.6.6.2)
−−−−−−−−
μso = √ 4S(S + 1) (5.6.6.3)
Comparison of calculated spin-only magnetic moments with experimental data for some octahedral complexes
Metal Config μso / B.M. μobs / B.M.
Ti(III) d1 (t2g1) √3 = 1.73 1.6-1.7
V(III) d2 (t2g2) √8 = 2.83 2.7-2.9
Cr(III) d3 (t2g3) √15 = 3.88 3.7-3.9
Cr(II) d4 high spin (t2g3 eg1) √24 = 4.90 4.7-4.9
Cr(II) d4 low spin (t2g4) √8 = 2.83 3.2-3.3
Mn(II)/ Fe(III) d5 high spin (t2g3 eg2) √35 = 5.92 5.6-6.1
Mn(II)/ Fe(III) d5 low spin (t2g5) √3 = 1.73 1.8-2.1
Fe(II) d6 high spin (t2g4 eg2) √24 = 4.90 5.1-5.7
Metal Config μso / B.M. μobs / B.M.
Co(III) d6 low spin (t2g6) 0 0
Co(II) d7 high spin (t2g5 eg2) √15 = 3.88 4.3-5.2
Co(II) d7 low spin (t2g6 eg1) √3 = 1.73 1.8
Ni(II) d8 (t2g6 eg2) √8 = 2.83 2.9-3.3
Cu(II) d9 (t2g6 eg3) √3 = 1.73 1.7-2.2
Comparison of calculated spin-only magnetic moments with experimental data for some tetrahedral complexes
Ion Config μso / B.M. μobs / B.M.
Cr(V) d1 (e1) √3 = 1.73 1.7-1.8
Cr(IV) / Mn(V) d2 (e2) √8 = 2.83 2.6 - 2.8
Fe(V) d3 (e2 t21) √15 = 3.88 3.6-3.7
- d4 (e2 t22) √24 = 4.90 -
Mn(II) d5 (e2 t23) √35 = 5.92 5.9-6.2
Fe(II) d6 (e3 t23) √24 = 4.90 5.3-5.5
Co(II) d7 (e4 t23) √15 = 3.88 4.2-4.8
Ni(II) d8 (e4 t24) √8 = 2.83 3.7-4.0
Cu(II) d9 (e4 t25) √3 = 1.73 -

5.6.6: Magnetic Moments of Transition Metals is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
5.6.7: Magnetism
Movement of an electrical charge (which is the basis of electric currents) generates a magnetic field in a material. Magnetism is
therefore a characteristic property of all materials that contain electrically charged particles and for most purposes can be
considered to be entirely of electronic origin.
Figure 5.6.7.1 : The Right Hand Rule for an induced magnetic field
In an atom, the magnetic field is due to the coupled spin and orbital magnetic moments associated with the motion of electrons. The
spin magnetic moment is due to the precession of the electrons about their own axes whereas the orbital magnetic moment is due to
the motion of electrons around the nucleus. The resultant combination of the spin and orbital magnetic moments of the constituent
atoms of a material gives rise to the observed magnetic properties.
Historically, magnetism has been recognized for thousands of years. An account, that is probably apochryphal, tells of a shepherd
called Magnes in Crete who around 900 B.C discovered the naturally occurring magnet lodestone (a form of the the spinel
magnetite, Fe3O4) in a region later named Magnesia. Supposedly while he was walking over a deposit, the lodestone pulled the
nails out of his sandals and the metal tip from his staff.
The Classical Theory of Magnetism

The classical theory of magnetism was well developed before quantum mechanics. Lenz's Law states that when a substance is
placed within a magnetic field, H , the field within the substance, B , differs from H by the induced field, 4πI, which is
proportional to the intensity of magnetization, I . That is;
B = H + 4πI (5.6.7.1)
where B is the magnetic field within the substance and H is the applied magnetic field and I is the intensity of magnetization
Lenz's Law (1834)

Lenz's Law can also be written as
B 4πI
=1+ (5.6.7.2)
H H
or
B
= 1 + 4πκ (5.6.7.3)
H
where
B/H is called the magnetic permeability of the material and
κ is the magnetic susceptibility per unit volume, (I/H)
By definition, κ in a vacuum is zero, so under those conditions the equation would reduce to B = H . It is usually more convenient
to measure mass than volume and the mass susceptibility, χ , is related to the volume susceptibility, κ , through the density.
g
κ
χ = (5.6.7.4)
g
ρ
where ρ is the density.
Finally to get our measured quantity on a basis that can be related to atomic properties, we convert to molar susceptibility
χm = χg × RM M (5.6.7.5)
Since this value includes the underlying diamagnetism of paired electrons, it is necessary to correct for the diamagnetic portion of
χm to get a corrected paramagnetic susceptibility.
′
χm = χm + χdia (5.6.7.6)
Examples of these corrections are tabulated below.

Table 5.6.7.1 : Table of Diamagnetic Corrections (Pascal's constants, 10-6 c.g.s. units)
Ion DC Ion DC
Na+ 6.8 Co2+ 12.8
K+ 14.9 Co3+ 12.8
NH4+ 13.3 Ni2+ 12.8
Hg2+ 40 VO2+ 12.5
Fe2+ 12.8 Mn3+ 12.5
Fe3+ 12.8 Cr3+ 12.5
Cu2+ 12.8 Cl- 23.4
Br- 34.6 SO42- 40.1
I- 50.6 OH- 12
NO3- 18.9 C2O42- 34
ClO4- 32 OAc- 31.5
IO4- 51.9 pyr 49.2
CN- 13 Me-pyr 60
NCS- 26.2 Acac- 62.5
H2O 13 en 46.3
EDTA4- ~150 urea 33.4
these can be converted to S.I units of m3 mol-1 by multiplying by 4 π x 10-7

There are numerous methods for measuring magnetic susceptibilities, including, the Gouy, Evans and Faraday methods. These
all depend on measuring the force exerted upon a sample when it is placed in a magnetic field. The more paramagnetic the sample,
the more strongly it will be drawn toward the more intense part of the field.
Determination of Magnetic Susceptibility

The Gouy Method: The underlying theory of the Gouy method is described here and a form for calculating the magnetic
moment from the collected data is available as well.
The Evans method: The Evans balance measures the change in current required to keep a pair of suspended magnets in place
or balanced after the interaction of the magnetic field with the sample. The Evans balance differs from that of the Gouy in that,
in the former the permanent magnets are suspended and the position of the sample is kept constant while in the latter the
position of the magnet is constant and the sample is suspended between the magnets.
Orbital contribution to magnetic moments

From a quantum mechanics viewpoint, the magnetic moment is dependent on both spin and orbital angular momentum
contributions. The spin-only formula used last year was given as:
−−−−−−−−
μs.o. = √ 4S(S + 1) (5.6.7.7)
and this can be modified to include the orbital angular momentum

−−−−−−−−−−−−−−−−−
μS+L = √ 4S(S + 1) + L(L + 1) (5.6.7.8)
An orbital angular momentum contribution is expected when the ground term is triply degenerate (i.e. a triplet state). These show
temperature dependence as well.
In order for an electron to contribute to the orbital angular momentum the orbital in which it resides must be able to transform into
an exactly identical and degenerate orbital by a simple rotation (it is the rotation of the electrons that induces the orbital
contribution). For example, in an octahedral complex the degenerate t2g set of orbitals (dxz,dyx,dyz) can be interconverted by a 90o
rotation. However the orbitals in the eg subset (dz2,dx2-y2) cannot be interconverted by rotation about any axis as the orbital shapes
are different; therefore an electron in the eg set does not contribute to the orbital angular momentum and is said to be quenched. In
the free ion case the electrons can be transformed between any of the orbitals as they are all degenerate, but there will still be
partial orbital quenching as the orbitals are not identical.
Electrons in the t2g set do not always contribute to the orbital angular moment. For example in the d3, t2g3 case, an electron in the
dxz orbital cannot by rotation be placed in the dyz orbital as the orbital already has an electron of the same spin. This process is also
called quenching.
Tetrahedral complexes can be treated in a similar way with the exception that we fill the e orbitals first, and the electrons in these
do not contribute to the orbital angular momentum. The tables in the links below give a list of all d1 to d9 configurations including
high and low spin complexes and a statement of whether or not a direct orbital contribution is expected.
Octahedral complexes
Tetrahedral complexes

5.6.7: Magnetism is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
The energy level splitting of the d-orbitals due to their interaction with the ligands in a complex has important structural and
thermodynamic effects on the chemistry of transition-metal complexes. Although these two types of effects are interrelated, they
are considered separately here.
Structural Effects
There are two major kinds of structural effects: effects on the ionic radii of metal ions with regular octahedral or tetrahedral
geometries, and structural distortions observed for specific electron configurations.
Ionic Radii
Figure 5.6.8.1 is a plot of the ionic radii of the divalent fourth-period metal ions versus atomic number. The dashed line represents
the behavior predicted based on the effects of screening and variation in effective nuclear charge (Zeff), assuming a spherical
distribution of the 3d electrons. Because these radii are based on the structures of octahedral complexes and Cr2+ and Cu2+ do not
form truly octahedral complexes, the points for these ions are shown as open circles.
Figure 5.6.8.1 : The Effect of d-Orbital Splittings on the Radii of the Divalent Ions of the Fourth-Period Metals. Only Ca2+(d0),
Mn2+ (high-spin d5), and Zn2+ (d10) lie on the smooth dashed curve. All other divalent ions fall below this curve because they have
asymmetrical distributions of d electrons. To explain why an asymmetrical distribution of d electrons makes a metal ion smaller
than expected, consider the Ti2+ ion, which has a d2 configuration with both electrons in the t2g orbitals. Because the t2g orbitals are
directed between the ligands, the two d-electrons are unable to shield the ligands from the nuclear charge. Consequently, the
ligands experience a higher effective nuclear charge than predicted, the metal–ligand distance is unusually short, and the ionic
radius is smaller than expected. If instead the two electrons were distributed uniformly over all five d orbitals, they would be much
more effective at screening the ligands from the nuclear charge, making the metal–ligand distances longer and giving the metal a
larger ionic radius.
A similar effect is observed for the V2+ ion, which has a d3 configuration. Because the three electrons in the t2g orbitals provide
essentially no shielding of the ligands from the metal, the ligands experience the full increase of +1 in nuclear charge that occurs
from Ti2+ to V2+. Consequently, the observed ionic radius of the V2+ ion is significantly smaller than that of the Ti2+ ion.
Skipping the Cr2+ ion for the moment, consider the d5 Mn2+ ion. Because the nuclear charge increases by +2 from V2+ to Mn2+,
Mn2+ might be expected to be smaller than V2+. The two electrons added from V2+ to Mn2+ occupy the eg orbitals, however, which
are oriented directly toward the six ligands. Because these electrons are localized directly between the metal ion and the ligands,
they are effective at screening the ligands from the increased nuclear charge. As a result, the ionic radius actually increases
significantly from V2+ to Mn2+, despite the higher nuclear charge of the latter.
The same effects are observed in the second half of the first-row transition metals. In the Fe2+, Co2+, and Ni2+ ions, the extra
electrons are added successively to the t2g orbitals, resulting in increasingly poor shielding of the ligands from the nuclei and in
abnormally small ionic radii. Skipping over Cu2+, adding the last two electrons causes a significant increase in the ionic radius of
Zn2+, despite its greater nuclear charge.
The Jahn–Teller Effect

Because simple octahedral complexes are not observed for the Cr2+ and Cu2+ ions, only estimated values for their radii are shown
in Figure 5.6.8.1. Since both Cr2+ and Cu2+ ions have electron configurations with an odd number of electrons in the eg orbitals.
Because the single electron (in the case of Cr2+) or the third electron (in the case of Cu2+) can occupy either one of two degenerate
eg orbitals, both systems have degenerate ground states. The Jahn–Teller theorem states that such non-linear systems are not stable;
they undergo a distortion that makes the complex less symmetrical and splits the degenerate states, which decreases the energy of
the system. The distortion and resulting decrease in energy are collectively referred to as the Jahn–Teller effect. Neither the nature
of the distortion nor its magnitude is specified, and in fact, they are difficult to predict. In principle, Jahn–Teller distortions are
possible for many transition-metal ions; in practice, however, they are observed only for systems with an odd number of electrons
in the eg orbitals, such as the Cr2+ and Cu2+ ions.
Consider an octahedral Cu2+ complex, [Cu(H2O)6]2+, which is elongated along the z axis. As indicated in Figure 5.6.8.2, this kind
of distortion splits both the eg and t2g sets of orbitals. Because the axial ligands interact most strongly with the dz2 orbital, the
splitting of the eg set (δ1) is significantly larger than the splitting of the t2g set (δ2), but both δ1 and δ2 are much, much smaller than
the Δo. This splitting does not change the centerpoint of the energy within each set, so a Jahn–Teller distortion results in no net
change in energy for a filled or half-filled set of orbitals. If, however, the eg set contains one electron (as in the d4 ions, Cr2+ and
Mn3+) or three electrons (as in the d9 ion, Cu2+), the distortion decreases the energy of the system. For Cu2+, for example, the
change in energy after distortion is 2(−δ1/2) + 1(δ1/2) = −δ1/2. For Cu2+ complexes, the observed distortion is always an elongation
along the z axis by as much as 50 pm; in fact, many Cu2+ complexes are distorted to the extent that they are effectively square
planar. In contrast, the distortion observed for most Cr2+ complexes is a compression along the z axis. In both cases, however, the
net effect is the same: the distorted system is more stable than the undistorted system.
Jahn–Teller distortions are most important for d9 and high-spin d4 complexes; the distorted system is more stable than the
undistorted one.
Figure 5.6.8.2 : The Jahn–Teller Effect

Increasing the axial metal–ligand distances in an octahedral d9 complex is an example of a Jahn–Teller distortion, which causes the
degenerate pair of eg orbitals to split in energy by an amount δ1; δ1 and δ2 are much smaller than Δo. As a result, the distorted
system is more stable (lower in energy) than the undistorted complex by δ1/2.
Thermodynamic Effects
As previously noted, crystal field splitting energies (CFSEs) can be as large as several hundred kilojoules per mole, which is the
same magnitude as the strength of many chemical bonds or the energy change in most chemical reactions. Consequently, CFSEs
are important factors in determining the magnitude of hydration energies, lattice energies, and other thermodynamic properties of
the transition metals.
Hydration Energies
The hydration energy of a metal ion is defined as the change in enthalpy for the following reaction:
2+ 2+
M + H2 O(l) → M (5.6.8.1)
(g) (aq)
Although hydration energies cannot be measured directly, they can be calculated from experimentally measured quantities using
thermochemical cycles. In Figure 5.6.8.3a, a plot of the hydration energies of the fourth-period metal dications versus atomic
number forms a curve with two valleys. Note the relationship between the plot in Figure 5.6.8.3a and the plot of ionic radii in
Figure 5.6.8.1 the overall shapes are essentially identical, and only the three cations with spherically symmetrical distributions of d
electrons (Ca2+, Mn2+, and Zn2+) lie on the dashed lines. In Figure 5.6.8.3a, the dashed line corresponds to hydration energies
calculated based solely on electrostatic interactions. Subtracting the CFSE values for the [M(H2O)6]2+ ions from the experimentally
determined hydration energies gives the points shown as open circles, which lie very near the calculated curve. Therefore, CFSEs
are primarily responsible for the differences between the measured and calculated values of hydration energies.
Figure 5.6.8.3 : Thermochemical Effects of d-Orbital Splittings. (a) A plot of the hydration energies of the divalent fourth-period
metal ions versus atomic number (solid circles) shows large deviations from the smooth curve calculated, assuming a spherical
distribution of d electrons (dashed line). Correcting for CFSE gives the points shown as open circles, which, except for Ti2+ and
Cr2+, are close to the calculated values. The apparent deviations for these ions are caused by the fact that solutions of the Ti2+ ion in
water are not stable, and Cr2+ does not form truly octahedral complexes. (b) A plot of the lattice energies for the fourth-period
metal dichlorides versus atomic number shows similar deviations from the smooth curve calculated, assuming a spherical
distribution of d electrons (dashed lines), again illustrating the importance of CFSEs.
Lattice Energies
Values of the lattice energies for the fourth-period metal dichlorides are plotted against atomic number in part (b) of Figure 5.6.8.3.
Recall that the lattice energy is defined as the negative of the enthalpy change for the reaction below. Like hydration energies,
lattice energies are determined indirectly from a thermochemical cycle.
2+ −
M (g) + 2C l (g) → M C l2 (s) (5.6.8.2)
The shape of the lattice-energy curve is essentially the mirror image of the hydration-energy curve in part (a) of Figure 5.6.8.3,
with only Ca2+, Mn2+, and Zn2+ lying on the smooth curve. It is not surprising that the explanation for the deviations from the
curve is exactly the same as for the hydration energy data: all the transition-metal dichlorides, except MnCl2 and ZnCl2, are more
stable than expected due to CFSE.
Summary
Distorting an octahedral complex by moving opposite ligands away from the metal produces a tetragonal or square planar
arrangement, in which interactions with equatorial ligands become stronger. Because none of the d orbitals points directly at the
ligands in a tetrahedral complex, these complexes have smaller values of the crystal field splitting energy Δt. The crystal field
stabilization energy (CFSE) is the additional stabilization of a complex due to placing electrons in the lower-energy set of d
orbitals. CFSE explains the unusual curves seen in plots of ionic radii, hydration energies, and lattice energies versus atomic
number. The Jahn–Teller theorem states that a non-linear molecule with a spatially degenerate electronic ground state undergoes a
geometrical distortion to remove the degeneracy and lower the overall energy of the system.
5.6.8: Thermodynamics and Structural Consequences of d-Orbital Splitting is shared under a CC BY-NC-SA license and was authored, remixed,
Ligand Field Theory (LFT) can be considered an extension of Crystal Field Theory such that all levels of covalent interactions can
be incorporated into the model. LFT describes the bonding, orbital arrangement, and other characteristics of coordination
complexes. It represents an application of molecular orbital theory to transition metal complexes. A transition
metal has nine valence atomic orbitals: five nd, one (n+1)s, and three (n+1)p orbitals. These orbitals are of appropriate energy to
form bonding interaction with ligands. The LFT analysis is highly dependent on the geometry of the complex, but will begin by
examining octahedral complexes.
Treatment of the bonding in LFT is generally done using molecular orbital theory. A qualitative approach using generator functions
and LGOs can be applied to these compounds just as we did previously. For the purpose of this discussion, we will consider the
octahedral complex ion [Co(NH3)6]3+. There are several assumptions that we must make in this approach.
1. The 4s, 4p and 3d orbitals are of the correct energy to interact with the nitrogen donor atoms of the NH3 ligands.
2. As the NH3 ligands are L-type ligands and will not participate in any π-bonding with the cobalt, we can treat the nitrogen atoms
as though they were hydrogen atoms. This means our MO diagram will not account for any N-H bonding. As there are 18 N-H
bonds in the complex, it certainly simplifies matters by choosing to ignore this.
The geometry of the complex has already been specified and the structure of the complex is depicted below (Figure 5.7.1).
Figure 5.7.1 . Structure and assigned axes for [Co(NH3)6]3+.
Exercise 5.7.1
Using rules for VSEPR, what orbitals need to be used for hybridization of the central cobalt atom? Be as specific as possible
about the orbitals.
Answer
The cobalt would be treated as AX6E0 and so would be sp3d2 hybridized.
The orbitals involved would be the 4s, 4p and two of the 3d orbitals. For the 3d orbitals, we can decide which ones to
involve based on the assigned axes. As we are making σ-bonds, the orbitals involved must be pointing at the incoming
ligands. In this geometry that means we much use the dz2 and dx2-y2 orbitals.
Step 2 - Determine the point group of the complex and assign the generator functions
The molecule is octahedral and so the point group is Oh. The Oh character table is rather robust and so only the abbreviated version
will appear here.
Oh Orbitals
A1g s
A2g
Eg dz2, dx2-y2
T1g
T2g dxy, dyz, dxz
A1u
A2u
Eu
T1u px. py, pz
T2u
Exercise 5.7.2
What are the symmetry labels for the cobalt orbitals used to make [Co(NH3)6]3+?.
Answer
s - a1g
px - t1u
py - t1u
pz - t1u
dz2 - eg
dx2-y2 - eg

As we have done previously, we will consider all of the potential interactions between the metal orbitals and ligand orbitals using a
pictorial method. Based on the axes assigned above, the matching LGOs can be drawn as shown (Figure 5.7.2).
Figure 5.7.2 . LGOs [Co(NH3)6]3+.

Previously when we were building MO diagrams we would start by looking at the orbital energies. In this case, doing this is a little
more complicated. One complication is that the ligand is NH3 and so we can not just use the orbital energy for nitrogen. Another
complication is that the orbital energies for transition metals in various valence states are not as readily available. However, we can
make some reasonable approximations. From WebMO, the orbital energies for Co(III) are 3d (-12.12 eV), 4s (-8.10 eV), and 4p
(-5.290 eV). The lone pair in NH3 would be the HOMO and from WebMO the energy of this orbital was calculated to be -13.702
eV. The general trend here is that the ligand orbitals are lower in energy than the metal orbitals. Once again we match the symmetry
labels and if there is a match on the metal and the LGOs, we make bonding and antibonding orbitals. The t2g orbitals on the metal
do not have a match among the LGOs and so they will make non-bonding orbitals that do not change in energy much from the
original metal d-orbitals. The rest of the metal orbitals have a match with the LGOs and so we get the diagram below (Figure
5.7.3).
Figure 5.7.3 . MO diagram for [Co(NH3)6]3+.
This diagram likely raises a number of questions. One likely question would be the ordering of the bonding MOs. The eg orbitals
on the cobalt are the lowest energy, and yet they make the highest energy bonding MOs. Recall from our previous discussion that
d-orbitals are not terribly good at forming bonding interactions. The s- and p-orbitals are much better at interacting with the
incoming ligands and as such, give rise to lower energy bonding MOs. The a1g orbital is based on the 4s orbital of cobalt which is
lower in energy than the 4p orbitals which are t1u. Somewhat similar logic can be applied to the antibonding orbitals. Since the
eg orbitals are not very good at forming bonding interactions, their antibonding interactions (eg*) will not be quite as high in
energy. The ordering of the a1g* and t1u* orbitals is a bit more difficult to rationalize. However, when considering the electron
configuration of a cobalt atom ([Ar] 4s2 3d7), the 4p orbitals are unoccupied. In fact, it may have seemed a bit odd to even consider
these orbitals in the hybridization. They are certainly higher in energy and as the t1u* orbitals are more localized on the cobalt, this
could cause them to be higher in energy than the a1g* orbital.
Another subtle point is that the d-orbital splitting that was previously discussed is found in this diagram. The MOs are labeled as
t2g and eg*. The eg* is slightly different than what we saw in the discussion on crystal field theory. However, these orbitals are
closer in energy to the metal d-orbitals and as such are mostly metal d-orbital in character. It is common practice to refer to the
t2g and eg* orbitals show in this diagram as the metal d-orbitals but realize there is antibonding character to the eg* orbitals. In
addition, this compound is drawn as being Low Spin, with the t2g completely occupied and the eg* unoccupied. Just building the
MO diagram there is no way to make that distinction. Looking at the spectrochemical series we see that NH3 is towards the strong
field end of the series so a Low Spin configuration is not unreasonable.
How did we do?

The calculations are a bit more involved for this complex. There are a total of 51 MOs for this complex cation, 18 from the 18
hydrogen atoms, 24 from the six nitrogen atoms and 9 from the cobalt. Pictorially, the 18 lowest energy MOs are mostly N-H in
nature and will be ignored for this discussion. As there are multiple degenerate levels in the MO diagram, one representative orbital
will be shown. The energy for the cobalt orbitals was calculated to be -13.180 eV (3d), -9.210 eV (4s) and -5.290 eV (4p). The
energy of the HOMO for NH3 was calculated to be -13.684 eV. This supports the idea that the orbitals from the ligands are lower in
energy that those of the metal.
a1g t1u eg t2g eg* a1g* t1u*
-15.2 eV -13.9 eV -13.8 eV -13.2 eV -12.5 eV 20.7 eV 24.795 eV
Overall this isn't a bad match to our pictorial method. Overall the pictures help to visualize the orbitals and the energies do make
sense with our rough approximations. The a1g, t1u and eg orbitals are all lower in energy than the HOMO of NH3. The t2g orbitals
are very similar to the energy of the 3d orbitals of cobalt. The eg* orbitals are slightly higher in energy than the t2g orbitals. The
energy difference from this very rough calculation corresponds to an absorption of light with a wavelength of 1700 nm. While well
outside the visible range and much larger than the actual value of approximately 470 nm displayed by the yellow [Co(NH3)6]3+,
this is a rough estimate made from fairly low level calculations.
Why did we choose NH3?

The choice of NH3 might seem a bit odd at first. Certainly a halide even with three lone pair would have been easier to deal with
than NH3. The choice of NH3 was not by chance. The NH3 ligand is purely σ-donating to the cobalt through the lone pair on the
nitrogen atom. There are no other lone pair that could be donated to the cobalt to form and kind of π-bonding interaction. Although
you may not think of halides as making π-bonds, the lone pair on the halides are capable of interacting in a π-bonding manner with
an atom capable of accepting electrons. And it just so happens that the t2g orbitals of a transition metal are of the proper symmetry
and energy to interact with ligands capable of donating electrons to give a π-bonding interaction. While we would still draw a
single bond (M-Cl) and not a double bond (M=Cl), we should appreciate that there is possibly some π-bonding interaction
occurring in a M-Cl bond. In fact, all of the weak field ligands are capable of this sort of interaction to some extent.
An explanation for strong field ligands is also based on π-bonding arguments. However, in the case of strong field ligands, it is the
metal that is providing the electrons in the π-bonding interaction. This interaction is a bit tougher to deal with. Unlike say the halide
ligands, we never draw lone pair on metals. This means it is not always readily apparent that there are electrons on the metal
available for π-bonding. However, as long as the metal does not have a d0 configuration, we can consider that there are electrons in
the t2g orbitals that could be used for π-bonding. Even harder to visualize is how is the ligand going to be accepting these electrons.
As we saw for weak field ligands, the key is that the ligand must have an orbital of the right symmetry and energy to be able to
interact with a metal t2g orbital. These orbitals are not readily apparent for many ligands. Consider the CO ligand which is called a
carbonyl ligand (similar to an organic carbonyl, R2C=O but there are no groups on the carbon atom and so we draw a C≡O). The π-
bonding interaction between the carbonyl and the metal involves the π* orbital of CO Figure 5.7.4. Consider first the CO portion
depicted. The orbitals are not drawn along the C-O bond axis. This tells us that we are dealing with some type of π-orbital. In the
top half of the picture, the orbital is blue on the carbon atom and white on the oxygen atom. And these lobes point away from each
other. The combination of the direction and the sign change indicate that this is a π* orbital. In addition (although it is a bit subtle in
this picture), the lobes on the carbon atom are larger than the lobes on the oxygen atom. Antibonding orbitals are more localized on
the LEAST electronegative atom where as bonding orbitals are localized on the more electronegative atom. This π* orbital of CO
has the right symmetry and energy to give a boding interaction with a metal d-orbital. But way, we said this was a π* orbital. It
is...with respect to the carbon-oxygen bond. However, the interaction is bonding (as noted by the interaction of lobes with the same
sign) with respect to the metal-carbon bond. In general, strong field ligands will share this ability to act as π-acceptors.
Figure 5.7.4 . π interaction between a metal and a carbonyl ligand.

How does this impact our diagram for the metal d-orbitals? In both cases we consider the ligands to be interacting with the t2g
orbitals of the metal. In the case of a weak field ligand, the filled orbitals of the π-donating ligand are at a lower energy than the
t2g orbitals. The ligand orbitals and the t2g orbitals interact to give π-bonding and π-antibonding orbitals. The π-antibonding orbitals
will be more localized on the metal and they will get pushed up in energy relative to the starting t2g orbitals. This will make them
closer in energy to the eg orbitals and therefore decrease Δo. With strong field ligands, the metal t2g orbitals are lower in energy
than the π-accepting orbitals of the ligands. These orbitals interact to give π-bonding and π-antibonding (with respect to the M-L)
orbitals. The π-bonding orbital will go down in energy and be more metal in character. The moves it further away from the
eg orbitals and thus increases Δo. These interactions are illustrated below Figure 5.7.5).
Figure 5.7.5 . π interactions between a metal and its ligands (B: [M(II)I6]4-; A: [M(II)(H2O)6]2+; C: [M(II)(CN)6]4-).

5.7: Ligand Field Theory is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
Replacing aqua ligands with ammine ligands
If you add ammonia solution to a solution containing hexaaquacopper(II) ions, [Cu(H2O)6]2+, four of the water molecules are
eventually replaced by ammonia molecules to give [Cu(NH3)4(H2O)2]2+. This can be written as an equilibrium reaction to show the
overall effect:
2 + 2 +
[Cu(H O) ] + 4 NH −
↽⇀
− [Cu(NH ) (H O) ] +4 H O (5.8.1)
2 6 3 3 4 2 2 2
In fact, the water molecules get replaced one at a time, and so this is made up of a series of part-reactions:
2 + 2 +
[Cu(H O) ] + NH −
↽⇀
− [Cu(NH )(H O) ] +H O (5.8.2)
2 6 3 3 2 5 2
2 + 2 +
[Cu(NH )(H O) ] + NH −
↽⇀
− [Cu(NH ) (H O) ] +H O (5.8.3)
3 2 5 3 3 2 2 4 2
2 + 2 +
[Cu(NH ) (H O) ] + NH −
↽⇀
− [Cu(NH ) (H O) ] +H O (5.8.4)
3 2 2 4 3 3 3 2 3 2
2 + 2 +
[Cu(NH ) (H O) ] + NH −
↽⇀
− [Cu(NH ) (H O) ] +H O (5.8.5)
3 3 2 3 3 3 4 2 2 2
Although this can look a bit daunting at first sight, all that is happening is that first you have one, then two, then three, then four
water molecules in total replaced by four ammine ligands.
Individual stability constants

Let's take a closer look at the first of these equilibria (Equation 5.8.2). Like any other equilibrium, this one has an equilibrium
constant, K - except that in this case, we call it a stability constant. Because this is the first water molecule to be replaced, we call
c
it K and is given by this expression:

1
2 +
[ [Cu(NH )(H O) ] ]
3 2 5
K1 = (5.8.6)
2 +
[ [Cu(H O) ] ][ NH ]
2 6 3
There are two points of possible confusion here - one minor, one more important!
First, the square brackets have changed their meaning! Square brackets are often used to keep everything in a complex ion
together and tidy. Here, they have reverted to their other use, which implies concentrations in mol dm-3.
In order to avoid complete confusion, the square brackets keeping the complexes together have been removed entirely.
More importantly, if you compare the equilibrium constant expression with the equation, you will see that the water on the
right-hand side hasn't been included. That is normal practice with these expressions.
Because everything is dissolved in water, the water is present as a huge excess. Generating a little bit more during the reaction
is going to make no effective difference to the total concentration of the water in terms of moles of water per dm3.
The concentration of the water is approximately constant. The equilibrium constant is defined so that you avoid having an extra
unnecessary constant in the expression.
With that out of the way, let's go back to where we were - but introduce a value for K1:
The value of the equilibrium constant is fairly large, suggesting that there is a strong tendency to form the ion containing an
ammonia molecule. A high value of a stability constant shows that the ion is easily formed. Each of the other equilibria above also
has its own stability constant, K2, K3 and K4. For example, K2 is given by:
The ion with two ammonias is even more stable than the ion with one ammonia. You could keep plugging away at this and come up
with the following table of stability constants:
ion Kn value (mol-1 dm3) log Kn
[Cu(NH3)(H2O)5]2+ K1 1.78 x 104 4.25
[Cu(NH3)2(H2O)4]2+ K2 4.07 x 103 3.61
[Cu(NH3)3(H2O)3]2+ K3 9.55 x 102 2.98
[Cu(NH3)4(H2O)2]2+ K4 1.74 x 102 2.24
You will often find these values quoted as log K1 or whatever. All this does is tidy the numbers up so that you can see the patterns
more easily. The ions keep on getting more stable as you replace up to 4 water molecules, but notice that the equilibrium constants
are gradually getting smaller as you replace more and more water ligands. This is common with individual stability constants.
Overall Formation constants

The overall stability constant is simply the equilibrium constant for the total reaction:
It is given by this expression:
You can see that overall this is a very large equilibrium constant, implying a high tendency for the ammonia ligands to replace the
water ligands. The "log" value is 13.1. This overall value is found by multiplying together all the individual values of K1, K2 and so
on. To find out why that works, write down expressions for all the individual values (the first two are done for you above), and then
multiply those expressions together. You will find that all the terms for the intermediate ions cancel out to leave you with the
expression for the overall stability constant.
Summary
Whether you are looking at the replacement of individual water molecules or an overall reaction producing the final complex ion, a
stability constant is simply the equilibrium constant for the reaction you are looking at. The larger the value of the stability
constant, the further the reaction lies to the right. That implies that complex ions with large stability constants are more stable than
ones with smaller ones.
Stability constants and entropy - the chelate effect

The chelate effect is an effect which happens when you replace water (or other simple ligands) around the central metal ion by
multidentate ligands like 1,2-diaminoethane (en) or EDTA. Compare what happens if you replace two water ligands around a
[Cu(H2O)6]2+ ion with either 2 ammonia ligands or one en ligand.
Chelates are much more stable than complex ions formed from simple monodentate ligands. The overall stability constants for the
two ions are:
ion log K
[Cu(NH3)2(H2O)4]2+ 7.86
[Cu(H2O)4(en)]2+ 10.6
The reaction with the 1,2-diaminoethane could eventually go on to produce a complex ion [Cu(en)3]2+. The overall stability
constant for this (as log K) is 18.7. Another copper-based chelate comes from the reaction with EDTA. This also has a high stability
constant - log K is 18.8. However many examples you take, you always find that a chelated complex is more stable than one with
only monodentate ligands. This is known as the chelate effect.
The reason for the chelate effect

If you compare the two equilibria below, the one with the en has the higher equilibrium (stability) constant (for values, see above).
The enthalpy changes of the two reactions are fairly similar. You might expect this because in each case you are breaking two
bonds between copper and oxygen atoms and replacing them by two bonds between copper and nitrogen atoms. However, when
considering the reverse reaction there is a bit of a difference in enthalpy. If one Cu-N bond breaks, the NH3 ligand can be replaced
by a water ligand. However, for en to leave, both Cu-N bonds to the ligand must be broken. If only one Cu-N bond to en is broken,
the unbound nitrogen atom remains in close proximity to the copper atom, making it very likely that it will just reform the Cu-N
bond.
Another factor in the chelate effect is the difference has to do with the entropy change during each reaction.
Entropy is most easily thought of as a measure of disorder. Any change which increases the amount of disorder increases the
tendency of a reaction to happen.
If you look again at the two equiilbria, you might notice that the en equilibrium does lead to an increase in the entropy. There are
only two species on the left-hand side of the equation, but three on the right.
You can obviously get more entropy out of three species than out of only two. Compare that with the other equilibrium. In this
case, there is no change in the total number of species before and after reaction, and so no useful contribution to an increase in
entropy.
In the case of the complex with EDTA, the increase in entropy is very pronounced.
Here, we are increasing the number of species present from two on the left-hand side to seven on the right. You can get a major
amount of increase in disorder by making this change.
Reversing this last change is going to be far more difficult in entropy terms. You would have to move from a highly disordered
state to a much more ordered one. That isn't so likely to happen, and so the copper-EDTA complex is very stable.
Summary
Complexes involving multidentate ligands are more stable than those with only monodentate ligands. The underlying reason for
this is that each multidentate ligand displaces more than one water molecule. This leads to an increase in the number of species
present in the system, and therefore an increase in entropy. An increase in entropy makes the formation of the chelated complex
more favorable.

This page titled 5.8: Ligand Exchange Reactions (Thermodynamics) is shared under a not declared license and was authored, remixed, and/or
curated by Jim Clark.
Term Splitting for Octahedral d2 metal complexes
At first glance, one might think that there is only one possible transition for the d-electrons in an octahedral compound with a
d2 configuration when it absorbs light. That transition would be one of the electrons in a t2g orbital raising in energy to one of the
eg orbitals. One example of this is shown below (Figure 5.9.1). This might lead you to think there is only one band (peak) in the
visible absorption spectrum for d2 complexes, but that is not the case. In order to explain the additional bands, there would have to
be other possible transitions. Perhaps you might think that since the electrons in the t2g orbitals are equal in energy either of them
could move to the eg. Similarly, the eg orbitals are degenerate, so the electron could go to either of those orbitals. That could give
multiple transitions, but they would all be the same energy as the one depicted.
Figure 5.9.1 . A possible transition for an electron in the t2g orbital of a d2 system.
What other transitions would be possible? The state shown above depicts the ground state electron configuration of a d2 system.
Remember back to general chemistry, the ground state follows Hund's rule in that the electrons are spread out and have the same
spin. There are multiple possible excited states and these do not have to abide by Hund's rule, but they still must follow the
Pauli exclusion principle. Several possible excited state configurations are shown below (Figure 5.9.2).
Figure 5.9.2 . Additional possible excited states for a d2 system.

To help keep track of all of the possible transitions, we use Term Symbols. Term Symbols are a method of accounting for electron-
electron interactions in an atom. They are derived from the quantum numbers, in particular the values of ml and ms, associated with
the electrons of interest. These term symbols take the form 2S+1LJ, where S represents the total spin angular momentum, L specifies
the total orbital angular momentum, and J refers to the total angular momentum. How do we get these term symbols? The value of
S comes from the sum of the ms values for the electrons under consideration. As has typically been the case since general
chemistry, the first electron we place is spin up or + . So for the ground state shown in (Figure 5.9.1) the value of S would be +1.
1
The value of 2S+1 is called the multiplicity and in this example the multiplicity would equal three. This is referred to as a triplet or
triplet state. The value of L comes from the sum of the ml values. In the case above we are looking at d-orbitals. The possible
ml values are +2, +1, 0, -1 and -2. Standard practice is to begin filling the orbital with the highest value of ml working to the lowest
value. So for the ground state d2 system, one electron would have a ml or +2 and the other would be +1 giving a total of +3 as the
value for L. However, L is not represented by this value, but rather a letter. This system is very similar to that used for the naming
of atomic orbitals; an atomic orbital with an l value of 0 is an s-orbital while a term symbol with a L value of 0 would be an S term.
This follows the same order as we learned for atomic orbitals, but it is very easy to get L values greater than 3, so after S, P, D, F
the order proceeds G, H, K, I, etc. So far, this would make our ground state term for the d2 system a 3F term. The final value in the
term symbol is J (which is why the letter J was skipped in the list above). This value comes from combinations of L and S.
The term symbols just described are known as free ion terms. This means we would be thinking about a d2 metal ion in the gas
phase. Things change a bit when you consider a metal with ligands. We move from the free ion terms to symbols that come from
group theory. We also now have to deal with a wide range of ligands from weak field to strong field. As the ligands impact the
separation of the t2g and eg orbitals, they should have an impact on the absorption of the complex. Doing much more with Term
symbols is beyond the scope of this course. However, they do appear in the discussion below so it is important you have some
appreciation of their source.
Selection Rules
In most cases the ligand field strength is in between the very weak and very strong case, and thus, we could expect very
complicated spectra. Fortunately, nature does not make things quite as complicated, because not all possible electron transitions are
quantum-mechanically allowed. The allowed transitions are defined by two rules: The spin selection rule and the Laporte rule.
The spin selection rule states that only transitions are allowed in which the total spin quantum number S does not change. Another
way to say this is that only transitions between states with the same multiplicity are allowed. For example, it would be allowed to
excite an electron from a triplet term to another triplet term, but not from a triplet term to a doublet or singlet term.
The Laporte rule state that transitions are only allowed when there is a change of parity. To fully appreciate this, we must define the
terms gerade (symmetric with respect to inversion) and ungerade (not symmetric with respect to inversion). In thinking about this
in terms of atomic orbitals, s-orbitals are completely spherical and as such are gerade. While it might take a little more to visualize
it, d-orbitals are also gerade. On the other hand, p-orbitals, with the lobes having different signs are ungerade. This means that
transitions between d-orbitals should not be allowed by the Laporte rule. However, in an octahedral geometry, it is possible that
some terms may have a change in parity. So overall, a transition from a gerade (g) to an ungerade (u)-term and vice versa is
possible, but not a transition from a g-term to another g-term, or the transition from a u-term to another u-term. For example the
transition from a T2g to a T1u term would be allowed, but not the transition from a T2g to a T1g term.
Tanabe-Sugano diagram of a d2 octahedral complex

In order to provide a somewhat quantitative way of representing the possible transitions for electrons in an octahedral compound,
Tanabe-Sugano diagrams were developed (Figure 5.9.3). The y-axis is energy divide by B, the Racah parameter. The Racah
parameter is a quantum-mechanical energy unit for the electromagnetic interactions between the electrons. It is chosen because it
provides “handy” numbers. Also on the y-axis one can find the free ion terms. The ground state is the lowest energy term. The x-
axis is a measurement of the ligand field strength also given in terms of the Racah parameter. At 0, there are no ligands so we use
the free ion terms. As the values on the x-axis increase so does the ligand field strength so weak-field ligands are towards the origin
and strong field ligands are further away.
Figure 5.9.3 . Tanabe-Sugano diagram for d2 octahedral complexes.

You can see that some lines coming from the free ion terms in the diagram are bent, and some are straight. Bending of lines occurs
when two terms interact with each other because they are close in energy and have the same symmetry. This is again an analogy to
orbitals. Like orbitals interact when they have the same symmetry and similar energy, terms interact when they have the same
symmetry and the same energy. The closer the terms come to the point where they cross, the stronger their interactions, because
their energies become more and more similar. The interactions lead to the fact that the terms bend away from each other, leading to
bent curves. This means that curves for two terms of the same symmetry type will bend away in a Tanabe-Sugano diagram and
never cross. For example the terms for the two 1A1g terms (in red above) bend away from each other and do not cross.
Next, let us think about which electron transitions would be allowed under the consideration of the spin selection and the Laporte
rule. We notice that in the symmetry labels the “g” for gerade has been omitted. This is a common simplification made in the
literature but all the terms shown are “g” terms. What does this mean for the allowance of electron transitions? It suggests that no
electron transition should be allowed, and that would imply that the complex could not absorb light. The Laporte selection rule
however does not hold strictly. It only says that the probability of the electron-transition is reduced, however, not forbidden. This
means that an absorption band that disobeys the Laporte rule will have lower intensity compared to one that follows the Laporte
rule, but it still can be observed. The spin-selection rule, however, holds strictly, and transitions between terms of different spin
multiplicity are strictly forbidden, meaning that they have near zero probability to occur. Overall, we can therefore excite an
electron from the 3T1 ground state to other triplet terms, namely the 3T2, 3T1 and the 3A2 terms.
Tanabe-Sugano diagram of d3 octahedral complexes

Now, let us have a look at the Tanabe-Sugano diagram for a d3 system in an octahedral ligand field (Figure 5.9.4). What is the
ground term? We can see the term designation on the horizontal line reads “4A2”, therefore this term is the ground term. How many
electron transitions from the ground state should we expect? To answer this question we need to count the number of other quartet
terms. There is the 4T2, the 4T1, and the 4T1. Thus, there are overall three electron transitions possible.

Now let us look at the Tanabe-Sugano diagram for d4 octahedral complexes (Figure 5.9.5). You can see that this diagram is
separated into two parts separated by a vertical line. The line indicates the ligand field strength at which the complex changes from
a low sping complex to a high spin complex. At lower ligand field strengths, the ground term is a 5E term. At higher field strength
the ground term is a 3T term. For a high spin complex there is only one allowed transition because there is only one other quintet
term, namely the 5T2 term. For the low spin complex, there are four transitions because there are four other triplet terms.
Tananbe-Sugano diagram of d5 octahedral complexes

The Tanabe-Sugano diagram for d5 octahedral complexes is divided into two parts separated by a vertical line (Figure 5.9.6). The
left part reflects that high spin and the right part the low spin complex. The high spin ground state is a sextet term, and the low spin
ground state is a doublet term. For the high-spin complex there are no other sextet terms, meaning that there is no electron
transition possible. Hence, high-spin octahedral d5-complexes are nearly colorless. An example for that is the hexaaqua manganese
(2+) complex. A solution of this complex is near colorless, only very slightly pinkish. The slight color is because spin-forbidden
transitions can occur albeit at a very low probability. For a d5-low spin complex there are three additional doublet states, and thus
there are three electron transitions possible.

The next diagram is the one for the d6 electron configuration (Figure 5.9.7). Again, the diagram is separated into parts for high and
low spin complexes. There are dotted lines in the diagram. They indicate the terms that have a different spin multiplicity than the
ground term. This way we can more easily see how many electron transitions are allowed. The ground term for the high-spin
complex is the quintet 5T2 term. The ground term for the low spin complex is a 1A1 term. There is only transition allowed for the
high-spin comples because the 5E term is the only other quintet term. There are two transitions possible for the low-spin case
because there are two additional singlet terms, namely the 1T1 and the 1T2.

Next, is the Tanabe-Sugano diagram for d7 octahedral complexes (Figure 5.9.8). In this case, the high spin complex has a 4T1
ground term, and the low spin complex has a 2E ground term. There are two other quartet terms, and two other doublet terms,
hence there are two electrons transitions for the high-spin complex, and two for the low spin complex.

Finally, we will examine the Tanabe-Sugano diagram for octahedral complexes with d8 electron configuration (Figure 5.9.9). For
this electron configuration, there are no high and low spin complexes possible, therefore, the Tanabe-Sugano diagram is no longer
divided into two parts. There is a single ground term of the type 3A2. There are three other triplet states, namely the 3T2 and two
3
T1 terms. Therefore, there are three electron transitions possible.

You might wonder where are the Tanabe-Sugano diagrams for d1, d9, and d10? For d1 there are no electron-electron interactions,
thus a simple orbital picture is sufficient. The 2D term splits into T2g and Eg terms, and there is only one electron transition
possible. The d9 electron configuration is the “hole-analog” of the d1 electron configuration. It has also just one 2D term which
splits into a T2g and an Eg term in the octahedral ligand field. Therefore, also in this case there is only one electron transition from
the T2g into the Eg term possible. In the case of d10 the orbitals are filled, and there is only the 1S term which does not split in an
octahedral ligand field. Therefore, there are no electron transitions in this case.
Finally, it should be mentioned that it is also possible to construct Tanabe-Sugano diagrams for other shapes such as the tetrahedral
shape, but we will not discuss these further here.
Charge Transfer Transitions
Figure 8.2.19 d-d transitions

We are still not done with our electronic spectra. Thus, far we have only considered transitions of d-electrons between d-orbitals,
and their terms. They are called d-d transitions. However, there are also so-called charge transfer transitions possible, that are not d-
d transitions. We can easily see that there must be other transitions but d-d transitions when we look at the color of d10 and d0 ions.
For those, the are no d-d transitions possible. Therefore, they all should be colorless. However, that is not always true. Some of
these ions are indeed colorless, but some are not. For example, Zn2+, a d10 ion are always colorless in complexes, but not Cu(I)
which is also d10. While tetrakis(acetonitrile)copper (+) is colorless, bis(phenanthrene) copper(+) is dark orange. Similar is true for
d0 ions. While TiF4 and TiCl4 are colorless, TiBr4 is orange, and TiI4 is brown. Some d0 species are even extremely colorful, for
example permanganate with Mn7+ which is extremely purple, and dichromate with Cr(VI) which is bright orange.
Figure 8.2.20 Charge-transfer transitions

The explanation of these phenomena are charge-transfer transitions. There are two types of charge-transfer transitions, the ligand-
to-metal (LCMT) and the metal-to-ligand (MLCT) charge transfer transitions. For the ligand-to-metal transitions, electrons from
bonding σ and π-orbitals get excited into metal d-orbitals in the ligand field, for example the t2g and the eg orbitals in an octahedral
complex. If the energy difference between the σ/π-orbitals and the d-orbitals is small enough, then this electron-transition is
associated with the absorption of visible light. The transition is called a ligand-to-metal transition because the ligand σ/π-orbitals
are mostly located at the ligands, while the metal-d-orbitals in a ligand field are mostly located at the metal. Vice versa, the metal-
to-ligand transition involves the transition of an electron from metal d-orbitals in a ligand field to ligand π*-orbitals. This
essentially moves electron density from the metal to the ligand, hance the name ligand-to-metal-charge transfer transition. If the
energy-difference between the ligand π* and the metal orbitals is small enough, then the absorption occurs in the visible range.
Charge-transfer transitions are usually both spin- and Laporte allowed, hence if they occur the color is often very intense. How can
we distinguish between d-d and charge transfer transitions? Charge transfer transitions often change in energy as the solvent
polarity is varied (solvatochromic) as there is a change in polarity of the complex associated with the charge transfer transition.
This can be used to distinguish between d-d transitions and charge-transfer bands.
LMCT Transitions
Can we predict when the energy windows between the bonding molecular orbitals and the metal d-orbitals are small enough so that
LMCT transitions in the visible can take place? Generally, it would be desirable if the energy of the metal orbitals was as low as
possible and the energy of the bonding ligand orbitals are as high as possible. The energy of metal d-orbitals decreases with
increasing positive charge at the metal because the effective nuclear charge on the metal increases. This means that very high
oxidation states favor an LMCT transition. The d-orbitals should have few or no electrons, so that electrons can be promoted into
the orbitals, and orbital energy increase due to electron-electron repulsion is minimized. Examples are Mn(VII), Cr(VI), and Ti(IV).
The energy of MOs from bonding ligand orbitals increases when the ligand orbitals have high energy this is typically the case for
π-donor ligand with negative charge.
Figure 8.2.21 The properties of the metal ion and ligands in MnO4- (Attribution: Pradana Aumars / CC
(https://commons.wikimedia.org/wiki/F...entrations.jpg))
Examples of ligands are oxo- and halo ligands. This explains for example the LMCT transitions in permanganate. The Mn is in the
very high oxidation state +7, and the ligands are are oxo-ligands wich are π-donors with a 2- negative charge. The transitions are
both Laporte and spin-allowed leading to very high intensity of light absorption, and thus color.
MLCT Transitions
What are favorable metal ion and ligand properties for a metal-to-ligand transition, then? In this case we would like to keep the
energy of the metal orbitals as high as possible so that the energy difference between a metal d-orbital and a π*-orbital is
minimized. This is accomplished when the positive charge at the metal ion is small, and there are many d-electrons that can repel
each other, thereby increasing orbital energies, for examples Cu(I).
Figure 8.2.22 bis(phenanthroline) copper(+)
The ligand should be a π-acceptor with low-lying π*-orbitals, for example phenanthroline, CN-, SCN-, and CO. For instance, the
bis(phenanthroline) copper(+) is dark-orange and has a MCLT absorption band a 458 nm. Also, the MLCT transfer is both spin and
Laporte-allowed.
It should be mentioned that some complexes allow for both metal-to-ligand and ligand to metal transitions. For example, in the
Cr(CO)6 complex the σ-orbitals are high enough and the π*-orbitals are low enough in energy to allow for light absorption in the
visible range. Finally, also intraligand bands are possible when the ligand is a chromophore.
Dr. Kai Landskron (Lehigh University). If you like this textbook, please consider to make a donation to support the author's
research at Lehigh University: Click Here to Donate.
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This page titled 5.9: Electronic Spectra of Coordination Compounds is shared under a not declared license and was authored, remixed, and/or
curated by Kai Landskron.
CHAPTER OVERVIEW
6: Bioinorganic Chemistry
6.1: Biological Significance of Iron, Zinc, Copper, Molybdenum, Cobalt, Chromium, Vanadium, and Nickel
6.6: Biological Significance of Iron, Zinc, Copper, Molybdenum, Cobalt, Chromium, Vanadium, and Nickel
6.7: Ferrodoxins, Hydrogenases, and Nitrogenases - Metal-Sulfide Proteins
6: Bioinorganic Chemistry is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
1
6.1: Biological Significance of Iron, Zinc, Copper, Molybdenum, Cobalt, Chromium,
Vanadium, and Nickel
The transition metals are among the least abundant metal ions in sea water from which contemporary organisms are thought to have
evolved (Table 1.1).1-5 For many of the metals, the concentration in human blood plasma greatly exceeds that in sea water. Such
data indicate the importance of mechanisms for accumulation, storage, and transport of transition metals and zinc in living
organisms.
Table 1.1: Concentrations of transition metals and zinc in sea water and human plasma.a*Data from References 1 - 5 and 12
Element Sea Water (M) x 108 Human Plasma (M) x 108
Fe 0.005 - 2 2230
Zn 8.0 1720
Cu 1.0 1650
Mo 10.0 1000
Co 0.7 0.0025
Cr 0.4 5.5
V 4.0 17.7
Mn 0.7 10.9
Ni 0.5 4.4
The metals are generally found either bound directly to proteins, found in cofactors, or part of clusters that are in turn bound by
a protein. The ligands usually contain O, N, S, or C donor atoms. Proteins with transition metals are most commonly associated
with the catalysis involving the intramolecular or intermolecular rearrangement of electrons. Although the redox properties of the
metals are important in many of the reactions, in others the metal appears to contribute to the structure of the active state, e.g., zinc
in the Cu-Zn dismutases and some of the iron in the photosynthetic reaction center. Sometimes equivalent reactions are catalyzed
by proteins with different metal centers; the metal binding sites and proteins have evolved separately for each type of metal center.
Iron is the most common transition metal in biology.6,7 Its use has created a dependence that has survived the appearance of
dioxygen in the atmosphere ca. 2.5 billion years ago, and the concomitant conversion of ferrous ion to ferric ion and insoluble rust.
All plants, animals, and bacteria use iron, except for a lactobacillus that appears to maintain high concentrations of manganese
instead of iron. The processes and reactions in which iron participates are crucial to the survival of terrestrial organisms, and
include ribonucleotide reduction (DNA synthesis), energy production (respiration), energy conversion (photosynthesis), nitrogen
reduction, oxygen transport (respiration, muscle contraction), and oxygenation (e.g., steroid synthesis, solubilization and
detoxification of aromatic compounds). Among the transition metals used in living organisms, iron is the most abundant in the
environment. Whether this fact alone explains the biological predominance of iron or whether specific features of iron chemistry
contribute is not clear.
Many of the other transition metals participate in reactions equivalent to those involving iron, and can sometimes substitute for
iron, albeit less effectively, in natural Fe-proteins. Additional biological reactions are unique to nonferrous transition metals.
Zinc is relatively abundant in biological materials.8,9 The major location of zinc in the body is metallothionein, which also binds
copper, chromium, mercury, and other metals. Among the other well-characterized zinc proteins are the Cu-Zn superoxide
dismutases (other forms have Fe or Mn), carbonic anhydrase (an abundant protein in red blood cells responsible for maintaining the
pH of the blood), alcohol dehydrogenase, and a variety of hydrolases involved in the metabolism of sugars, proteins, and nucleic
acids. Zinc is a common element in nucleic-acid polymerases and transcription factors, where its role is considered to be structural
rather than catalytic. Interestingly, zinc enhances the stereoselectivity of the polymerization of nucleotides under reaction
conditions designed to simulate the environment for prebiotic reactions. Recently a group of nucleic-acid binding proteins, with a
repeated sequence containing the amino acids cysteine and histidine, were shown to bind as many as eleven zinc atoms necessary
for protein function (transcribing DNA to RNA).10 Zinc plays a structural role, forming the peptide into multiple domains or "zinc
fingers" by means of coordination to cysteine and histidine. A survey of the sequences of many nucleic-acid binding proteins
shows that many of them have the common motif required to form zinc fingers. Other zinc-finger proteins called steroid receptors
bind both steroids such as progesterone and the progesterone gene DNA . Much of the zinc in animals and plants has no known
function, but it may be maintaining the structures of proteins that activate and deactivate genes.11
Copper and iron proteins participate in many of the same biological reactions:
1. reversible binding of dioxygen, e.g., hemocyanin (Cu), hemerythrin (Fe), and hemoglobin (Fe);
2. activation of dioxygen, e.g., dopamine hydroxylase (Cu) (important in the synthesis of the hormone epinephrine), tyrosinases
(Cu), and catechol dioxygenases (Fe);
3. electron transfer, e.g., plastocyanins (Cu), ferredoxins, and c-type cytochromes (Fe);
4. dismutation of superoxide by Cu or Fe as the redox-active metal (superoxide dismutases).
The two metal ions also function in concert in proteins such as cytochrome oxidase, which catalyzes the transfer of four electrons
to dioxygen to form water during respiration. Whether any types of biological reactions are unique to copper proteins is not clear.
However, use of stored iron is reduced by copper deficiency, which suggests that iron metabolism may depend on copper proteins,
such as the serum protein ceruloplasmin, which can function as a ferroxidase, and the cellular protein ascorbic acid oxidase, which
also is a ferrireductase.
Cobalt is found in vitamin B12 , its only apparent biological site.12 The vitamin is a cyano complex, but a methyl or methylene
group replaces CN in native enzymes. Vitamin-B12 deficiency causes the severe disease of pernicious anemia in humans, which
indicates the critical role of cobalt. The most common type of reaction in which cobalamin enzymes participate results in the
reciprocal exchange of hydrogen atoms if they are on adjacent carbon atoms, yet not with hydrogen in solvent water:
(An important exception is the ribonucleotide reductase from some bacteria and lower plants, which converts ribonucleotides to the
DNA precursors, deoxyribonucleotides, a reaction in which a sugar -OH is replaced by -H. Note that ribonucleotide reductases
catalyzing the same reaction in higher organisms and viruses are proteins with an oxo-bridged dimeric iron center.) The cobalt in
vitamin B12 is coordinated to five N atoms, four contributed by a tetrapyrrole (corrin); the sixth ligand is C, provided either by C5
of deoxyadenosine in enzymes such as methylmalonyl-CoA mutase (fatty acid metabolism) or by a methyl group in the enzyme
that synthesizes the amino acid methionine in bacteria.
Nickel is a component of a hydrolase (urease), of hydrogenase, of CO dehydrogenase, and of S-methyl CoM reductase, which
catalyzes the terminal step in methane production by methanogenic bacteria. All the Ni-proteins known to date are from plants or
bacteria.13,14 However, about 50 years elapsed between the crystallization of jack-bean urease in 1925 and the identification of the
nickel component in the plant protein. Thus it is premature to exclude the possibility of Ni-proteins in animals. Despite the small
number of characterized Ni-proteins, it is clear that many different environments exist, from apparently direct coordination to
protein ligands (urease) to the tetrapyrrole F430 in methylreductase and the multiple metal sites of Ni and Fe-S in a hydrogenase
from the bacterium Desulfovibrio gigas. Specific environments for nickel are also indicated for nucleic acids (or nucleic acid-
binding proteins), since nickel activates the gene for hydrogenase.15
Manganese plays a critical role in oxygen evolution catalyzed by the proteins of the photosynthetic reaction center. The superoxide
dismutase of bacteria and mitochondria, as well as pyruvate carboxylase in mammals, are also manganese proteins.16,17 How the
multiple manganese atoms of the photosynthetic reaction center participate in the removal of four electrons and protons from water
is the subject of intense investigation by spectroscopists, synthetic inorganic chemists, and molecular biologists.17
Vanadium and chromium have several features in common, from a bioinorganic viewpoint.18a First, both metals are present in only
small amounts in most organisms. Second, the biological roles of each remain largely unknown.18 Finally, each has served as a
probe to characterize the sites of other metals, such as iron and zinc. Vanadium is required for normal health, and could act in vivo
either as a metal cation or as a phosphate analogue, depending on the oxidation state, V(lV) or V(V), respectively. Vanadium in a
sea squirt (tunicate), a primitive vertebrate, is concentrated in blood cells, apparently as the major cellular transition metal, but
whether it participates in the transport of dioxygen (as iron and copper do) is not known. In proteins, vanadium is a cofactor in an
algal bromoperoxidase and in certain prokaryotic nitrogenases. Chromium imbalance affects sugar metabolism and has been
associated with the glucose tolerance factor in animals. But little is known about the structure of the factor or of any other specific
chromium complexes from plants, animals, or bacteria.
Molybdenum proteins catalyze the reduction of nitrogen and nitrate, as well as the oxidation of aldehydes, purines, and sulfite.19
Few Mo-proteins are known compared to those involving other transition metals. Nitrogenases, which also contain iron, have been
the focus of intense investigations by bioinorganic chemists and biologists; the iron is found in a cluster with molybdenum (the
iron-molybdenum cofactor, or FeMoCo) and in an iron-sulfur center (Chapter 7). Interestingly, certain bacteria (Azotobacter) have
alternative nitrogenases, which are produced when molybdenum is deficient and which contain vanadium and iron or only iron. All
other known Mo-proteins are also Fe-proteins with iron centers, such as tetrapyrroles (heme and chlorins), Fe-sulfur clusters, and,
apparently, non-heme/non-sulfur iron. Some Mo-proteins contain additional cofactors such as the Havins, e.g., in xanthine oxidase
and aldehyde oxidase. The number of redox centers in some Mo-proteins exceeds the number of electrons transferred; reasons for
this are unknown currently.
6.1: Biological Significance of Iron, Zinc, Copper, Molybdenum, Cobalt, Chromium, Vanadium, and Nickel is shared under a not declared license
and was authored, remixed, and/or curated by LibreTexts.
Proteins are polymers of amino acids, linked by amide groups known as peptide bonds. An amino acid can be thought of as
having two components: a 'backbone', or 'main chain', composed of an ammonium group (H3N+-C), an 'alpha-carbon' bonded to the
nitrogen atom, a carboxylate (COO-), and a variable 'side chain' (in green below) bonded to the alpha-carbon (Figure 6.2.1).
(Figure 6.2.1 ). Structures of amino acids.

There are twenty different side chains in naturally occurring amino acids, and it is the identity of the side chain that determines the
identity of the amino acid: for example, if the side chain is a -CH3 group, the amino acid is alanine, and if the side chain is a -
CH2OH group, the amino acid is serine. Many amino acid side chains contain a functional group (the side chain of serine, for
example, contains a primary alcohol), while others, like alanine, lack a functional group, and contain only a simple hydrocarbon
group.
The two 'hooks' on an amino acid monomer are the ammonium and carboxylate groups. Proteins (polymers of ~50 amino acids or
more) and peptides (shorter polymers) are formed when the amino group of one amino acid monomer reacts with the carboxylate
carbon of another amino acid to form an amide linkage, which in protein terminology is a peptide bond. Which amino acids are
linked, and in what order - the protein sequence - is what distinguishes one protein from another. This sequence is coded for by an
organism's DNA. Protein sequences are written in the ammonium terminal (N-terminal) to carboxylate terminal (C-terminal)
direction, with either three-letter or single-letter abbreviations for the amino acids. Below is a four amino acid peptide with the
sequence "cysteine - histidine - glutamate - methionine". Using the single-letter code, the sequence is abbreviated CHEM (Figure
6.2.2).
Figure 6.2.2 . The CHEM peptide.

When an amino acid is incorporated into a protein it loses a molecule of water and what remains is called a residue of
the original amino acid. Thus we might refer to the 'glutamate residue' at position 3 of the CHEM peptide above.
Once a protein polymer is constructed, it in many cases folds up very specifically into a three-dimensional structure, which often
includes one or more 'binding pockets' in which other molecules can be bound. It is this shape of this folded structure, and the
precise arrangement of the functional groups within the structure (especially in the area of the binding pocket) that determines the
function of the protein.
Enzymes are proteins which catalyze biochemical reactions. One or more reacting molecules - often called substrates - become
bound in the active site pocket of an enzyme, where the actual reaction takes place. Receptors are proteins that bind specifically to
one or more molecules - referred to as ligands - to initiate a biochemical process. For example, we saw in the introduction to this
chapter that the TrpVI receptor in mammalian tissues binds capsaicin (from hot chili peppers) in its binding pocket and initiates a
heat/pain signal which is sent to the brain.

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SECTION OVERVIEW
6.3.1: Introduction to Redox Reactions is shared under a CC BY-SA license and was authored, remixed, and/or curated by LibreTexts.
In studying redox chemistry, it is important to remember balancing electrochemical reactions. Simple redox reactions (for example,
H2 + I2 → 2 HI) can be balanced by inspection, but for more complex reactions it is helpful to have a systematic method. There are
many different methods for doing this. The focus in this section will be on the ion-electron method allows one to balance redox
reactions regardless of their complexity and allows for identification of the species changing valence states in the reaction. We
illustrate this method with two examples.
Example 1:
I- is oxidized to IO3- by MnO4-, which is reduced to Mn2+.
How can this reaction be balanced? In the ion-electron method we follow a series of four steps:
Step 1A: Write out the (unbalanced) reaction and identify the elements that are undergoing redox.
MnO4- + I- → IO3- + Mn2+ (The elements undergoing redox are Mn and I)
Step 1B: Separate the reaction into two half reactions, balancing the element undergoing redox in each.
MnO4- → Mn2+
I- → IO3-
Step 2A: Balance the oxygen atoms by adding water to one side of each half reaction.
MnO4-→ Mn2+ + 4H2O

3H2O + I- → IO3-
Step 2B: Balance the hydrogen atoms by adding H+ ions.
8H+ + MnO4-→ Mn2+ + 4H2O
The left side has a net charge of +7 and the right side has a net charge of +2
3H2O + I- → IO3- + 6H+
The left side has a net charge of -1 and the right side has a net charge of +5
Step 2C: Balance the overall charge by adding electrons
8H+ + 5e- + MnO4-→ Mn2+ + 4H2O
The left side has a charge of +2 while the right side has a charge of +2. They are balanced.
3H2O + I- → IO3- + 6H+ + 6e-
The left side has a charge of -1 while the right side has a charge of -1. They are balanced.
Note: We did not need to explicitly determine the oxidation states of Mn or I to arrive at the correct number of electrons in each
half reaction.
Step 3: Combine the half reactions so that there are equal numbers of electrons on the left and right sides
6 (8H+ + 5e- + MnO4-→ Mn2+ + 4H2O)

5 (3H2O + I- → IO3- + 6H+ + 6e-)
48H+ + 30e- + 15H2O + 6MnO4- + 5I- → 5IO3- + 6Mn2+ + 24H2O + 30e- + 30H+
Cancel the H+, electrons, and water:
48H+ + 30e- + 15H2O + 6MnO4- + 5I- → 5IO3- + 6Mn2+ + 24H2O + 30e- + 30H+
The overall balanced reaction is therefore:
18H+ + 6MnO4- + 5I- → 5IO3- + 6Mn2+ + 9H2O
Check your work by making sure that all elements and charges are balanced.
Step 4: If the reaction occurs under basic conditions, we add OH- to each side to cancel H+
18H+ + 18OH- + 6MnO4- + 5I- → 5IO3- + 6Mn2+ + 9H2O + 18OH-
The 18H+ + 18OH- will become 18H2O so the overall balanced reaction is:
9H2O + 6MnO4- + 5I- → 5IO3- + 6Mn2+ + 18OH-
Again, it is a good idea to check and make sure that all of the elements are balanced, and that the charge is the same on both sides.
If this is not the case, you need to find the error in one of the earlier steps.
Example 2:
Redox reaction of S2O32- and H2O2
S2O32- + H2O2 → S4O62- + H2O
Which elements are undergoing redox? S and O
Step 1: Write out half reactions, balancing the element undergoing redox
2S2O32- → S4O62-
H2O2 → 2H2O
Step 2A: Balance oxygen (already balanced)

Step 2B: Balance hydrogen:
2S2O32- → S4O62-
H2O2 + 2H+ → 2H2O
Step 2C: Balance charge by adding electrons:
2S2O32- → S4O62- + 2e-

H2O2 + 2H+ + 2e- → 2H2O
Step 3: Combine the half reactions so that there are equal numbers of electrons on the left and right sides (already equal)
Overall balanced reaction:
2S2O32- + H2O2 + 2H+ → S4O62- + 2H2O
Note that again, we did not need to know the valence states of S or O in the reactants and products in order to balance the reaction.
In this case, assigning the valence states is a bit complex, because S4O62- contains sulfur in more than one valence state.
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In electrochemical cells, or in redox reactions that happen in solution, the thermodynamic driving force can be measured as the cell
potential. Chemical reactions are spontaneous in the direction of -ΔG, which is also the direction in which the cell potential
(defined as Ecathode - Eanode) is positive. A cell operating in the spontaneous direction (for example, a battery that is discharging) is
called a galvanic cell. A cell that is being driven in the non-spontaneous direction is called an electrolytic cell. For example, let
us consider the reaction of hydrogen and oxygen to make water:
2H +O =2 H O (6.3.3.1)
2(g) 2(g) 2 (l)
Thermodynamically, this reaction is spontaneous in the direction shown and has an overall standard free energy change (ΔG°) of
-237 kJ per mole of water produced.
When this reaction occurs electrochemically in the spontaneous direction (e.g., in a hydrogen-air fuel cell), the two half cell
reactions that occur are:
Anode: H 2(g)
⟶ 2H
+
(aq)
+2 e
−
Cathode: O 2(g)
+4 H
+
(aq)
+4 e
−
⟶ 2H O
2 (l)
Here the anode is the negative electrode and the cathode is the positive electrode; under conditions of very low current density
(where there are minimal resistive losses and kinetic overpotentials), the potential difference we would measure between the two
electrodes would be 1.229 V.
In an electrolytic cell, this reaction is run in reverse. That is, we put in electrical energy to split water into hydrogen and oxygen
molecules. In this case, the half reactions (and their standard potentials) reverse. O2(g) bubbles form at the anode and H2(g) is
formed at the cathode. Now the anode is the positive electrode and the cathode is negative. Electrons are extracted from the
substance at the anode (water) and pumped into the solution at the cathode to make hydrogen. An animation of the cathode half
reaction is shown below.
In both galvanic and electrolytic cells, oxidation occurs at the anode and reduction occurs at the cathode.
Half-cell potentials
As noted above, the equilibrium voltage of an electrochemical cell is proportional to the free energy change of the reaction.
Because electrochemical reactions can be broken up into two half-reactions, it follows that the potentials of half reactions (like free
energies) can be added and subtracted to give an overall value for the reaction. If we take the standard hydrogen electrode as our
reference, i.e., if we assign it a value of zero volts, we can measure all the other half cells against it and thus obtain the voltage of
each one. This allows us to rank redox couples according to their standard reduction potentials (or more simply their standard
potentials), as shown in the table below.
Note that when we construct an electrochemical cell and calculate the voltage, we simply take the difference between the half cell
potentials and do not worry about the number of electrons in the reaction. For example, for the displacement reaction in which
silver ions are reduced by copper metal, the reaction is:
+ 2 +
2 Ag + Cu =2 Ag + Cu
(aq) (s) (s) (aq)
The two half-cell reactions are:

+ −
Ag +e = Ag(s) + 0.80V
(aq)
2+ −
Cu + 2e = C u(s) + 0.34V
(aq)
and the standard potential E o

= +0.80 − 0.34V = +0.46V
The reason we don't need to multiply the Ag potential by 2 is that Eo is a measure of the free energy change per electron. Dividing
the free energy change by the number of electrons (see below) makes Eo an intensive property (like pressure, temperature, etc.).
Relationship between E and ΔG. For systems that are in equilibrium, ΔG = −nF E , where n is number of moles of
o o
cell
electrons per mole of products and F is the Faraday constant, ~96485 C/mol. Here the o symbol indicates that the substances
involved in the reaction are in their standard states. For example, for the water electrolysis reaction, the standard states would be
pure liquid water, H+ at 1M concentration (or more precisely, at unit activity), and O2 and H2(g) at 1 atmosphere pressure.
More generally (at any concentration or pressure), ΔG = −nF E , where
o
RT
E =E − ∗ lnQ (6.3.3.2)
nF
,
or at 298 K
0.0592
o
E =E − ∗ log Q (6.3.3.3)
n
where Q is the concentration ratio of products over reactants, raised to the powers of their coefficients in the reaction. This equation
(in either form) is called the Nernst equation. The second term in the equation, when multiplied by -nF, is RT*lnQ. This is the free
energy difference between ΔG and ΔG°. We can think of this as an entropic term that takes into account the positive entropy
change of dilution, or the negative entropy change of concentrating a reactant or product, relative to its standard state.
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In redox reactions, one element or compound is reduced (gains electrons) and another is oxidized (loses electrons). In terms of
everyday life, redox reactions occur all of the time around us. For example, the metabolism of sugars to CO2, which stores energy
in the form of ATP, is a redox reaction. Another example of redox is fire or combustion, such as in a car engine. In a car engine,
hydrocarbons in the fuel are oxidized to carbon dioxide and water, while oxygen is reduced to water. Corrosion (i.e. the formation
of rust on iron) is a redox reaction involving oxidation of a metal.
Different valence states of vanadium in acidic solution. From left to right the valence goes from +5 to +2. These four valencen states form the
basis of the vanadium flow battery, a storage device for electricity generated from sunlight and wind.[1]
Oxidation-reduction reactions are important to understanding inorganic chemistry for several reasons:
Transition metals can have multiple valence states
Main group elements (N, halogens, O, S...) also have multiple valence states and important redox chemistry
Many inorganic compounds catalyze redox reactions (which are especially useful in industrial and biological applications)
Energy conversion and storage technologies (solar water splitting, batteries, electrolyzers, fuel cells) rely on inorganic redox
reactions and catalysis
Electrochemistry provides a way to measure equilibrium constants for dissolution/precipitation, complexation, and other
reactions.
Reaction mechanisms often involve changes in the valence states of metals.
Not all oxidizers and reducers are created equal. The electrochemical series ranks substances according to their oxidizing and
reducing power, i.e., their standard electrode potential. Strong oxidizing agents are typically compounds with elements in high
valence states or with high electronegativity, which gain electrons in the redox reaction. Examples of strong oxidizers include
hydrogen peroxide, permanganate (Mn(VII)), and osmium tetroxide (Os(VIII)). Reducing agents are typically electropositive
elements such as hydrogen, lithium, sodium, iron, and aluminum, which lose electrons in redox reactions. Hydrides (compounds
that contain hydrogen in the formal -1 valence state), such as sodium hydride, sodium borohydride and lithium aluminum hydride,
are often used as reducing agents.
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There are a few different types of redox stability diagrams, two of which are known as Latimer diagrams and Frost diagrams. Each
of these diagrams contains similar information, but one representation may be more useful in a given situation than the others.
Latimer and Frost diagrams help predict stability relative to higher and lower valence states, usually at one fixed pH. A third type
of diagram, a Pourbaix diagram, helps understand pH-dependent equilibria, which are often coupled to solubility equilibria and
corrosion (which will be talked about more later).
Latimer diagrams:
Latimer diagrams are the oldest and most compact way to represent electrochemical equilibria for substances that have multiple
valence states. Electrochemical potential values are written for successive redox reactions (from highest to lowest oxidation state),
typically under standard conditions in either strong acid ([H+] = 1 M, pH 0) or strong base ([OH-] = 1 M, pH 14). The valence
states of successive substances in a Latimer diagram can differ by one or more electrons. Valence states for the element undergoing
redox are typically determined by difference; we assign the oxygen atoms a valence state of -2 and the hydrogen atoms avalence
state of +1.
Example:
Mn in Acid
The Latimer diagram for Mn illustrates its standard reduction potentials (in 1 M acid) in valence states from +7 to 0.
The Latimer diagram compresses into shorthand notation all the standard potentials for redox reactions of the element Mn. For
example, the entry that connects Mn2+ and Mn gives the potential for the half-cell reaction:
Mn
2 +
(aq)
+2 e
−
⟶ Mn
(s)
E1/2° = -1.18V
and the entry connecting Mn4+ and Mn3+ represents the reaction:
MnO
2(s)
+4 H
+
(aq)
−
+e ⟶ Mn
3 +
(aq)
+2 H O
2 (l)
, :E1/2° = +0.95V
We can also calculate values for multi-electron reactions by first adding ΔG°(=-nFE°) values and then dividing by the total
number of electrons
For example, for the 5-electron reduction of MnO4- to Mn2+, we write
1(0.564) + 1(0.274) + 1(4.27) + 1(0.95) + 1(1.51)
o
E = = +1.51V (6.3.5.1)
5
and for the three-electron reduction of MnO4-(aq) to MnO2(s),

1(0.564) + 1(0.274) + 1(4.27)
o
E = = +1.70V (6.3.5.2)
3
Remember to divide by the number of electrons involved in the valence number change (5 and 3 for the above equations).
Thermodynamically stable and unstable oxidation states
An unstable species on a Latimer diagram will have a lower standard potential to the left than to the right.
Example:
\(\ce{2MnO4^{3-} -> MnO2 + MnO4^{2-}}\ ) the MnO43- species is unstable
E
o
= +4.27 − 0.274 = 3.997V (spontaneous disproportionation)
Which Mn species are unstable with respect to disproportionation?
MnO43- 5+ → 6+,4+
Mn3+ 3+ → 4+,2+
So stable species are: MnO4-, MnO42-, MnO2, Mn2+, and Mn0.
But MnO42- is also unstable - why?
2 −
MnO ⟶ MnO
4 2
2 MnO
2 −
4
⟶ 2 MnO
−
4
+ MnO
2
E° = 2.272 - 0.564 = +1.708 V
Moral: All possible disproportionation reactions must be considered in order to determine stability (this is often more convenient
with a Frost diagram).
Note
Thermodynamically unstable ions can be quite stable kinetically. For example, most N-containing molecules (NO2, NO, N2H4)
are unstable relative to the elements (O2, N2, H2), but they are still quite stable kinetically.
Frost diagrams:
In a Frost diagram, we plot ΔG°⁄F (= nE°) vs. valence number. The zero valence state is assigned a nE° value of zero.[2]
Stable and unstable oxidation states can be easily identified in the plot. Unstable compounds are higher on the plot than the line
connecting their neighbors. Note that this is simply a graphical representation of what we did with the Latimer diagram to
determine which valence states were stable and unstable.
The standard potential for any electrochemical reaction is given by the slope of the line connecting the two species on a Frost
diagram. For example, the line connecting Mn3+ and MnO2 on the Frost diagram has a slope of +0.95, the standard potential of
MnO2 reduction to Mn3+. This is the number that is written above the arrow in the Latimer diagram for Mn. Multielectron
potentials can be calculated easily by connecting the dots in a Frost diagram.
A Frost diagram:
Contains the same information as in a Latimer diagram, but graphically shows stability and oxidizing power.
The lowest species on the diagram are the most stable (Mn2+, MnO2)
The highest species on diagram are the strongest oxidizers (MnO4-)
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Pourbaix Diagrams plot electrochemical stability for different redox states of an element as a function of pH. These diagrams are
essentially phase diagrams that map the conditions of potential and pH (most typically in aqueous solutions) where different redox
species are stable. The lines in Pourbaix diagrams represent redox and acid-base reactions, and are the parts of the diagram where
two species can exist in equilibrium. For example, in the Pourbaix diagram for Fe below, the horizontal line between the Fe3+ and
Fe2+ regions represents the reaction Fe + e =Fe , which has a standard potential of +0.77 V. While we could use standard
3 +
(aq)
− 2 +
(aq)
potentials for all these lines, in practice Pourbaix diagrams are usually plotted for lower ion concentrations (often 1 mM) that are
more relevant to corrosion and electrochemical experiments.
Example: Iron Pourbaix diagram
Areas in the Pourbaix diagram mark regions where a single species (Fe2+(aq), Fe3O4(s), etc.) is stable. More stable species tend to
occupy larger areas.
Lines mark places where two species exist in equilibrium.
Pure redox reactions are horizontal lines - these reactions are not pH-dependent
Pure acid-base reactions are vertical lines - these do not depend on potential
Reactions that are both acid-base and redox have a slope of -0.0592 V/pH x # H+⁄# e-)
Figure 6.3.6.1 : Pourbaix diagram for iron at ionic concentrations of 1.0 mM. (CC BY-SA 3.0 Unported; Metallos via Wikipedia)
Examples of equilibria in the iron Pourbaix diagram (numbered on the plot):
1. Fe 2 +
+2 e
−
⟶ Fe
(s)
(pure redox reaction - no pH dependence)
2. Fe 3 +
+e
−
⟶ Fe
2 +
(pure redox reaction - no pH dependence)
3. 2 Fe 3 +
+ 3 H O ⟶ Fe O
2 2
+6 H
3(s)
(pure acid-base, no redox)
+
4. 2 Fe 2 +
+ 3 H O ⟶ Fe O
2 2 3(s)
+6 H
+ −
+2 e (slope = -59.2 x 6/2 = -178 mV/pH)
5. 2 Fe 3
O
4(s)
+H O ⟶ 2 H
2
+
+2 e
−
(slope = -59.2 x 2/2 = -59.2 mV/pH)
The water redox lines have special significance on a Pourbaix diagram for an element such as iron. Recall that liquid water is stable
only in the region between the dotted lines. Below the H2 line, water is unstable relative to hydrogen gas, and above the O2 line,
water is unstable with respect to oxygen. For active metals such as Fe, the region where the pure element is stable is typically
below the H2 line. This means that iron metal is unstable in contact with water, undergoing reactions:
Fe
(s)
+2 H
+
⟶ Fe
2 +
(aq)
+H
2
(in acid)
fe
(s)
+ 2 H O ⟶ Fe(OH)
2 2(s)
+H
2
(in base)
Iron (and most other metals) are also thermodynamically unstable in air-saturated water, where the potential of the solution is close
to the O2 line in the Pourbaix diagram. Here the spontaneous reactions are:
4 Fe
(s)
+3 O
2
+ 12 H
+
⟶ 4 Fe
3 +
+6 H O
2
(in acid)
\(\ce{4Fe_{(s)} + 3O2 -> 2Fe2O3_{(s)} (in base)

Corrosion and passivation. It certainly sounds bad for our friend Fe: unstable in water, no matter what the pH or potential. Given
enough time, it will all turn into rust. But iron (and other active metals) can corrode, or can be stabilized against corrosion,
depending on the conditions. Because our civilization is dependent on the use of active metals such as Fe, Al, Zn, Ti, Cr... for
practically everything, it is important to understand this, and we can do so by referring to the Pourbaix diagram.
The corrosion of iron (and other active metals such as Al) is indeed rapid in parts of the Pourbaix diagram where the element is
oxidized to a soluble, ionic product such as Fe3+(aq) or Al3+(aq). However, solids such as Fe2O3, and especially Al2O3, form a
protective coating on the metal that greatly impedes the corrosion reaction. This phenomenon is called passivation.
Draw a vertical line through the iron Pourbaix diagram at the pH of tap water (about 6) and you will discover something
interesting: at slightly acidic pH, iron is quite unstable with respect to corrosion by the reaction:
+ 2 +
Fe +2 H ⟶ Fe +H (6.3.6.1)
(s) (aq) 2
but only in water that contains relatively little oxygen, i.e., in solutions where the potential is near the H2 line. Saturating the water
with air or oxygen moves the system closer to the O2 line, where the most stable species is Fe2O3 and the corrosion reaction is:
4 Fe +3 O ⟶ 2 Fe O (6.3.6.2)
(s) 2 2 3(s)
This oxidation reaction is orders of magnitude slower because the oxide that is formed passivates the surface. Therefore iron
corrodes much more slowly in oxygenated solutions.
More generally, iron (and other active metals) are passivated whenever they oxidize to produce a solid product, and corrode
whenever the product is ionic and soluble. This behavior can be summed up on the color-coded Pourbaix diagram below. The red
and green regions represent conditions under which oxidation of iron produces soluble and insoluble products, respectively.
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A very common reaction for metal complexes is ligand substitution in which one ligand is exchanged with another. There are two
common mechanisms for ligand substitution reactions the first of which is called the associative mechanism. In this mechanism the
incoming ligand approaches the complex before departure of the leaving ligand. How can we spot an associative mechanism in
experimental data, and what are some of the consequences of this mechanism?
The prototypical mechanism of associative ligand substitution. The first step is rate-determining. A typical mechanism for
associative ligand substitution is shown above. Let’s begin by examining the kinetics of the reaction.
Reaction kinetics are commonly used to elucidate reaction mechanisms, and ligand substitution is no exception. Different
mechanisms of substitution may follow different rate laws, so plotting the dependence of reaction rate on concentration of the
species involved in the reaction often allows us to distinguish mechanisms. Associative substitution’s rate law depends on the
concentrations of both starting materials.
d d
Ln M – L + Li → Ln M – Li + L (6.4.1)
i
d[ Ln M – L ]
d i
= rate = k1 [ Ln M – L ][ L ] (6.4.2)
dt
The easiest way to determine this rate law is to use pseudo-first-order conditions. Although the rate law is second order overall, if
we could somehow render the concentration of the incoming ligand unchanging, the reaction would appear first order. The
observed rate constant under these conditions reflects the consistency of the incoming ligand’s concentration (k = k [L ] , where
obs 1
i
both k and [Li] are constants). How can we make the concentration of the incoming ligand invariant, you ask? We can drown the
1
reaction in ligand to achieve this. The small amount of the incoming ligand actually used up in the reaction has a negligible effect
on the concentration of the “sea” of starting ligand we began with. The observed rate is equal to k [L M – L ], as shown by the
obs n
d
purple trace below. By determining k at a variety of [L ] values, we can isolate k , the rate constant for the slow step. The red
obs
i
1
trace below at right shows the idea.
Associative substitution under pseudo-first-order conditions. The reaction is “swamped out” with incoming ligand.
In many cases, the red trace ends up with a non-zero y-intercept…curious, if we limit ourselves to the simple mechanism shown in
the first figure of this post. A non-zero intercept suggests a more complex mechanism. We need to add a new term (called k for s
reasons to become clear shortly) to our first set of equations:

d
rate = (k1 [ Li ] + ks )[ Ln M – L ] (6.4.3)
kobs = k1 [ Li ] + ks (6.4.4)
The full rate law suggests that some other step (with rate ks[LnM–Ld]) independent of incoming ligand is involved in the
mechanism. To explain this observation, we can invoke the solvent as a reactant. Solvent can associate with the complex first in a
slow step, then incoming ligand can displace the solvent in a fast step. Solvent concentration doesn’t enter the rate law because,
well, it’s drowning the reactants and its concentration undergoes negligible change! An example of this mechanism iis shown
below.
Associative substitution with solvent participation—a head-scratching mechanism for many an organometallic grad student!
As an aside, it’s worth mentioning that the entropy of activation of associative substitution is typically negative. Entropy decreases
as the incoming ligand and complex come together in the rate-determining step.
Dr. Michael Evans (Georgia Tech)
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Evans.
The second mechanism for ligand substitution is the dissociative mechanism. In the slow step with positive entropy of activation,
the departing ligand leaves, generating a coordinatively unsaturated intermediate. The incoming ligand then enters the coordination
sphere of the metal to generate the product. The reverse of the first step, re-coordination of the departing ligand (rate constant k–1),
is often competitive with dissociation.
A general scheme for dissociative ligand substitution. There’s more to the intermediate than meets the eye!
Let’s begin with the general situation in which k and k are similar in magnitude. Since k is rate limiting, k is assumed to be
1 –1 1 2
much larger than k and k . Most importantly, we need to assume that variation in the concentration of the unsaturated
1 –1
intermediate is essentially zero. This is called the steady state approximation, and it allows us to set up an equation that relates
reaction rate to observable concentrations Hold onto that for a second; first, we can use step 2 to establish a preliminary rate
expression.
rate = k2 [ Ln M – ◊][Li] (1)
Of course, the unsaturated complex is present in very small concentration and is unmeasurable, so this equation doesn’t help us
much. We need to remove the concentration of the unmeasurable intermediate from (1), and the steady state approximation helps us
do this. We can express variation in the concentration of the unsaturated intermediate as (processes that make it) minus (processes
that destroy it), multiplying by an arbitrary time length to make the units work out. All of that equals zero, according to the steady
state approximation. Since Δt must not be zero, the other factor, the collection of terms, must equal zero.
d d
Δ[LnM – ◊] = 0 = (k1[LnM – L ]– k– 1[LnM – ◊][ L ]– k2 [LnM – ◊][Li])Δt (2)
0 = k1 [LnM – Ld]– k−1 [LnM – ◊][Ld]– k2 [LnM – ◊][Li] (3)
Rearranging to solve for [LnM–◊], we arrive at the following.

[LnM – Ld ]
[LnM – ◊] = k1 (4)
(k−1 [ Ld ] + k2 [Li]
Finally, substituting into equation (1) we reach a verifiable rate equation.

[LnM – Ld][Li]
rate = k2 k1 (5)
(k−1 [ Ld ] + k2 [Li]
When k –1 is negligibly small, (5) reduces to the familiar equation (6), typical of dissociative reactions like SN1.
rate = k1 [LnM – Ld ] (6)
Unlike the associative rate law, this rate does not depend on the concentration of incoming ligand. For reactions that are better
described by (5), we can drown the reaction in incoming ligand to make k [Li] far greater than k [Ld] , essentially forcing the
2 −1
reaction to fit equation (6).

In general, introducing structural features that either stabilize the unsaturated intermediate or destabilize the starting complex can
encourage dissociative substitution. Both of these strategies lower the activation barrier for the reaction. Other, quirky ways to
encourage dissociation include photochemical methods, oxidation/reduction, and ligand abstraction.

Dr. Michael Evans (Georgia Tech)
This page titled 6.5: Dissociative Ligand Substitution is shared under a not declared license and was authored, remixed, and/or curated by Michael
Evans.
6.6: Biological Significance of Iron, Zinc, Copper, Molybdenum, Cobalt, Chromium,
Vanadium, and Nickel
The transition metals and zinc are among the least abundant metal ions in sea water from which contemporary organisms are
thought to have evolved.1-5 For many metals, the concentration in human blood plasma, while still very low, greatly exceeds that in
sea water (Table 6.6.1). Such data indicate the importance of mechanisms for accumulation, storage, and transport of transition
metals in living organisms.
Table 6.6.1. Concentrations of transition metals and zinc in sea water and human plasma.a*Data from References 1 - 5 and 12
Element Sea Water (M) x 108 Human Plasma (M) x 108
Fe 0.005 - 2 2230
Zn 8.0 1720
Cu 1.0 1650
Mo 10.0 1000
Co 0.7 0.0025
Cr 0.4 5.5
V 4.0 17.7
Mn 0.7 10.9
Ni 0.5 4.4
The metals are generally found either bound directly to proteins, in cofactors, or in clusters that are in turn bound to proteins; the
ligands usually have O, N, S, or C donor atoms. Proteins with which transition metals are most commonly associated catalyze the
intramolecular or intermolecular rearrangement of electrons. Although the redox properties of the metals are important in many of
the reactions, in others the metal appears to contribute to the structure of the active state, e.g., zinc in the Cu-Zn dismutases and
some of the iron in the photosynthetic reaction center. Sometimes equivalent reactions are catalyzed by proteins with different
metal centers; the metal binding sites and proteins have evolved separately for each type of metal center.
Iron is the most common transition metal in biology.6,7 Its use has created a dependence that has survived the appearance of
dioxygen in the atmosphere ca. 2.5 billion years ago, and the concomitant conversion of ferrous ion to ferric ion and insoluble rust.
All plants, animals, and bacteria use iron, except for a lactobacillus that appears to maintain high concentrations of manganese
instead of iron. The processes and reactions in which iron participates are crucial to the survival of terrestrial organisms, and
include ribonucleotide reduction (DNA synthesis), energy production (respiration), energy conversion (photosynthesis), nitrogen
reduction, oxygen transport (respiration, muscle contraction), and oxygenation (e.g., steroid synthesis, solubilization and
detoxification of aromatic compounds). Among the transition metals used in living organisms, iron is the most abundant in the
environment. Whether this fact alone explains the biological predominance of iron or whether specific features of iron chemistry
contribute is not clear.
Many of the other transition metals participate in reactions equivalent to those involving iron, and can sometimes substitute for
iron, albeit less effectively, in natural Fe-proteins. Additional biological reactions are unique to nonferrous transition metals.
Zinc is relatively abundant in biological materials.8,9 The major location of zinc in the body is metallothionein, which also binds
copper, chromium, mercury, and other metals. Among the other well-characterized zinc proteins are the Cu-Zn superoxide
dismutases (other forms have Fe or Mn), carbonic anhydrase (an abundant protein in red blood cells responsible for maintaining the
pH of the blood), alcohol dehydrogenase, and a variety of hydrolases involved in the metabolism of sugars, proteins, and nucleic
acids. Zinc is a common element in nucleic-acid polymerases and transcription factors, where its role is considered to be structural
rather than catalytic. Interestingly, zinc enhances the selectivity of the polymerization of nucleotides under reaction conditions
designed to simulate the environment for prebiotic reactions. Recently a group of nucleic-acid binding proteins, with a repeated
sequence containing the amino acids cysteine and histidine, were shown to bind as many as eleven zinc atoms necessary for protein
function (transcribing DNA to RNA).10 Zinc plays a structural role, forming the peptide into multiple domains or "zinc fingers" by
means of coordination to cysteine and histidine. A survey of the sequences of many nucleic-acid binding proteins shows that many
of them have the common motif required to form zinc fingers. Other zinc-finger proteins called steroid receptors bind both steroids
such as progesterone and the progesterone gene DNA . Much of the zinc in animals and plants has no known function, but it may
be maintaining the structures of proteins that activate and deactivate genes.11
Copper and iron proteins participate in many of the same biological reactions:
1. reversible binding of dioxygen, e.g., hemocyanin (Cu), hemerythrin (Fe), and hemoglobin (Fe);
2. activation of dioxygen, e.g., dopamine hydroxylase (Cu) (important in the synthesis of the hormone epinephrine), tyrosinases
(Cu), and catechol dioxygenases (Fe);
3. electron transfer, e.g., plastocyanins (Cu), ferredoxins, and c-type cytochromes (Fe);
4. dismutation of superoxide by Cu or Fe as the redox-active metal (superoxide dismutases).
The two metal ions also function in concert in proteins such as cytochrome oxidase, which catalyzes the transfer of four electrons
to dioxygen to form water during respiration. Whether any types of biological reactions are unique to copper proteins is not clear.
However, use of stored iron is reduced by copper deficiency, which suggests that iron metabolism may depend on copper proteins,
such as the serum protein ceruloplasmin, which can function as a ferroxidase, and the cellular protein ascorbic acid oxidase, which
also is a ferrireductase.
Cobalt is found in vitamin B12 , its only apparent biological site.12 The vitamin is a cyano complex, but a methyl or methylene
group replaces the cyano ligand in native enzymes. Vitamin-B12 deficiency causes the severe disease of pernicious anemia in
humans, which indicates the critical role of cobalt. The most common type of reaction in which cobalamin enzymes participate
results in the reciprocal exchange of hydrogen atoms if they are on adjacent carbon atoms, yet not with hydrogen in solvent water:
Nickel is a component of a hydrolase (urease), of hydrogenase, of CO dehydrogenase, and of S-methyl CoM reductase, which
catalyzes the terminal step in methane production by methanogenic bacteria. All the Ni-proteins known to date are from plants or
bacteria.13,14 However, about 50 years elapsed between the crystallization of jack-bean urease in 1925 and the identification of the
nickel component in the plant protein. Thus it is premature to exclude the possibility of Ni-proteins in animals. Despite the small
number of characterized Ni-proteins, it is clear that many different environments exist, from apparently direct coordination to
protein ligands (urease) to the tetrapyrrole F430 in methylreductase and the multiple metal sites of Ni and Fe-S in a hydrogenase
from the bacterium Desulfovibrio gigas. Specific environments for nickel are also indicated for nucleic acids (or nucleic acid-
binding proteins), since nickel activates the gene for hydrogenase.15
Manganese plays a critical role in oxygen evolution catalyzed by the proteins of the photosynthetic reaction center. The superoxide
dismutase of bacteria and mitochondria, as well as pyruvate carboxylase in mammals, are also manganese proteins.16,17 How the
multiple manganese atoms of the photosynthetic reaction center participate in the removal of four electrons and protons from water
is the subject of intense investigation by spectroscopists, synthetic inorganic chemists, and molecular biologists.17
Vanadium and chromium have several features in common, from a bioinorganic viewpoint.18a First, both metals are present in only
small amounts in most organisms. Second, the biological roles of each remain largely unknown.18 Finally, each has served as a
probe to characterize the sites of other metals, such as iron and zinc. Vanadium is required for normal health, and could act in vivo
either as a metal cation or as a phosphate analogue, depending on the oxidation state, V(lV) or V(V), respectively. Vanadium in a
sea squirt (tunicate), a primitive vertebrate (Figure 1.2B), is concentrated in blood cells, apparently as the major cellular transition
metal, but whether it participates in the transport of dioxygen (as iron and copper do) is not known. In proteins, vanadium is a
cofactor in an algal bromoperoxidase and in certain prokaryotic nitrogenases. Chromium imbalance affects sugar metabolism and
has been associated with the glucose tolerance factor in animals. But little is known about the structure of the factor or of any other
specific chromium complexes from plants, animals, or bacteria.
Molybdenum proteins catalyze the reduction of nitrogen and nitrate, as well as the oxidation of aldehydes, purines, and sulfite.19
Few Mo-proteins are known compared to those involving other transition metals. Nitrogenases, which also contain iron, have been
the focus of intense investigations by bioinorganic chemists and biologists; the iron is found in a cluster with molybdenum (the
iron-molybdenum cofactor, or FeMoCo) and in an iron-sulfur center (Chapter 7). Interestingly, certain bacteria (Azotobacter) have
alternative nitrogenases, which are produced when molybdenum is deficient and which contain vanadium and iron or only iron. All
other known Mo-proteins are also Fe-proteins with iron centers, such as tetrapyrroles (heme and chlorins), Fe-sulfur clusters, and,
apparently, non-heme/non-sulfur iron. Some Mo-proteins contain additional cofactors such as the Havins, e.g., in xanthine oxidase
and aldehyde oxidase. The number of redox centers in some Mo-proteins exceeds the number of electrons transferred; reasons for
this are unknown currently.
6.6: Biological Significance of Iron, Zinc, Copper, Molybdenum, Cobalt, Chromium, Vanadium, and Nickel is shared under a not declared license
and was authored, remixed, and/or curated by LibreTexts.
SECTION OVERVIEW
6.7: Ferrodoxins, Hydrogenases, and Nitrogenases - Metal-Sulfide Proteins
Transition-metal/sulfide sites, especially those containing iron, are present in all forms of life and are found at the active centers of
a wide variety of redox and catalytic proteins. These proteins include simple soluble electron-transfer agents (the ferredoxins),
membrane-bound components of electron-transfer chains, and some of the most complex metalloenzymes, such as nitrogenase,
hydrogenase, and xanthine oxidase. In this chapter we first review the chemistry of the Fe-S sites that occur in relatively simple
rubredoxins and ferredoxins, and make note of the ubiquity of these sites in other metalloenzymes. We use these relatively simple
systems to show the usefulness of spectroscopy and model-system studies for deducing bioinorganic structure and reactivity. We
then direct our attention to the hydrogenase and nitrogenase enzyme systems, both of which use transition-metalsulfur clusters to
activate and evolve molecular hydrogen.
References
1. F. Armstrong, in A. G. Sykes, ed., Advances in Inorganic and Bioinorganic Mechanisms, Vol. I, Academic Press, 1982.
2. H. Beinert and S. P. J. Albracht, Biochim. Biophys. Acta 683 (1982), 245.
3. A. V. Xavier, J. J. G. Moura, and I. Moura, in J. B. Goodenough et al., eds., Structure and Bonding, Springer-Verlag, 43 (1981),
187-213.
4. D. C. Yoch and R. P. Carithers, Microbiol. Rev. 43 (1979), 384.
5. H. B. Dunford et aI., eds., The Biological Chemistry of Iron: A Look at the Metabolism of Iron and Its Subsequent Uses in
Living Organisms, Reidel, 1981.
6. R. K. Thauer and P. Schönheit, in Reference 8, p. 329.
7. A. Bezkorovainy, Biochemistry of Nonheme Iron, Plenum, 1980, pp. 343-393.
8. T. G. Spiro, ed., Iron-Sulfur Proteins, Wiley-Interscience, 1985.
9. W. Lovenberg, ed., Iron-Sulfur Proteins, Vol. I, Academic Press, 1973.
10. Reference 9, Vol. II, Academic Press, 1973.
11. Reference 10, Vol. III, Academic Press, 1977.
12. Nomenclature, Eur. J. Biochem. 93 (1979), 427.
13. Nomenclature, Biochim. Biophys. Acta 549 (1979), 101.
14. C. F. Yocum, J. N. Sadow, and A. San Pietro, in Reference 9, p. 112.
15. B. B. Buchanan, in Reference 9, p. 129.
16. T. P. Singer and R. R. Ramsay, in A. N. Martonosi, ed., The Enzymes of Biological Membranes, Plenum, 1985, pp. 301-332.
17. T. Yagi, H. Inokuchi, and K. Kimura, Acc. Chem. Res. 16 (1983), 2; Y. Higuchi et al., J. Mol. Biol. 172 (1984), 109.
18. R. Lemberg and J. Barrett, Cytochromes, Academic Press, 1973.
19. H. Beinert, in Reference 9, p. 1.
20. K. K. Rao and D. O. Hall, in G. V. Leigh, ed., Evolution of Metalloenzymes, Metalloproteins, and Related Materials, 1977, p.
39.
21. D. O. Hall, R. Cammack, and K. K. Rao, Nature 233 (1977), 136.
22. T. Ohnishi and J. C. Salerno, in Reference 8, p. 285.
23. F. A. Cotton and G. Wilkinson, Advanced Inorganic Chemistry, Wiley, 1980.
24. D. E. McRee et al., J. Biol. Chem. 261 (1986), 10277.
25. S. J. N. Burgmayer and E. I. Stiefel, J. Chem. Educ. 62 (1985), 943.
26. W. Lovenberg and B. E. Sobel, Proc. Natl. Acad. Sci. USA 54 (1965), 193.
27. E. T. Lode and M. J. Coon, in Reference 9, pp. 173-191.
28. I. C. Gunsalus and J. D. Lipscomb, in Reference 11, p. 151.
29. R. W. Estabrook et al., in Reference 9.
30. I. Moura et al., Biochem. Biophys. Res. Commun. 75 (1977), 1037.
31. I. Moura et al., J. Biol. Chem. 255 (1980), 2493. a) J. LeGall et al., Biochemistry 27 (1988), 1636.
32. K. D. Watenpaugh, L. C. Sieker, and L. H. Jensen, J. Mol. Biol. 138 (1980), 615.
33. E. T. Adman et al., J. Mol. Biol. 112 (1977), 113. a) C. D. Stout, in Reference 8, p. 97.
34. K. D. Watenpaugh et al., Acta Cryst. B29 (1973), 943.
35. R. G. Shulman et al., Proc. Natl. Acad. Sci. USA 72 (1975), 4003.
36. R. G. Shulman et al., J. Mol. Biol. 124 (1978), 305.
37. W. D. Phillips et al., Nature 227 (1970), 574.
38. J. C. Rivoal et aI., Biochim. Biophys. Acta 493 (1977), 122.
39. D. E. Bennett and M. K. Johnson, Biochim. Biophys. Acta 911 (1987), 71. a) M. S. Gebhard et al.,J. Am. Chem. Soc. 112 (1990),
2217. b) K. D. Butcher, M. S. Gebhard, and E. I. Solomon, Inorg. Chem. 29 (1990), 2067.
40. M. C. W. Evans, in Reference 8, p. 249.
41. W. A. Eaton and W. J. Lovenberg, J. Am. Chem. Soc. 92 (1970), 7195.
42. M. K. Johnson, A. E. Robinson, and A. J. Thomson, in Reference 8, p. 367.
43. P. J. Stephens et aI., Proc. Natl. Acad. Sci. USA 75 (1978), 5273.
44. J. Peisach et al., J. Biol. Chem. 246 (1971), 5877.
45. P. M. Champion and A. J. Siever, J. Chem. Phys. 66 (1977), 1819; D. Coucouvanis et al., J. Am. Chem Soc. 101 (1979), 3392.
46. R. Cammack, D. S. Patil, and V. M. Fernandez, Biochem. Soc. Trans. 13 (1985), 572.
47. B. L. Trumpower, Biochim. Biophys. Acta 639 (1981), 129.
48. H. Beinert, Biochem. Soc. Trans. 13 (1985), 542.
49. G. Palmer, Biochem. Soc. Trans. 13 (1985), 548.
50. R. Malkin and A. J. Bearden, Biochim. Biophys. Acta 505 (1978), 147.
51. C. E. Johnson, J. Inorg. Biochem. 28 (1986), 207.
52. E. Münck and T. A. Kent, Hyperfine Interactions 27 (1986), 161.
53. K. K. Rao et al., Biochem. J. 129 (1972), 1063.
54. I. Bertini and C. Luchinat, eds., NMR of Paramagnetic Molecules in Biological Systems, Benjamin/ Cummings, 1986.
55. G. N. La Mar, W. D. Horrocks, Jr., and R. H. Holm, NMR of Paramagnetic Molecules, Academic Press, 1973.
56. M. T. Werth et al., J. Am. Chem. Soc. 109 (1987), 273.
57. T. G. Spiro et al., in Reference 8, p. 407. a) T. V. Long and T. M. Loehr, J. Am. Chem. Soc. 92 (1970), 6384.
58. G. Christou, B. Ridge, and H. N. Rydon, J. Chem. Soc. Chem. Commun. (1979), 20.
59. S. W. May and J.-Y. Kuo, Biochemistry 17 (1978), 3333.
60. S. W. May et al., Biochemistry 23 (1984), 2187.
61. P. Saint-Martin et al., Proc. Natl. Acad. Sci. USA 85 (1988), 9378.
62. R. W. Lane et al., Proc. Natl. Acad. Sci. USA 72 (1975), 2868.
63. R. W. Lane et al., J. Am. Chem. Soc. 99 (1977), 84.
64. D. G. Holah and D. Coucouvanis, J. Am. Chem. Soc. 97 (1975), 6917.
65. D. Coucouvanis et al., J. Am. Chem. Soc. 93 (1976), 5721.
66. M. Millar et al., lnorg. Chem. 21 (1982), 4105.
67. S. A. Koch and L. E. Madia, J. Am. Chem. Soc. 105 (1983), 5944.
68. M. Millar, S. A. Koch, and R. Fikar, lnorg. Chim. Acta 88 (1984), L15.
69. J. C. Deaton et al., J. Am. Chem. Soc. 110 (1988), 6241.
70. D. B. Knaff, Trends Biochem. Sci. 13 (1988), 461. a) T. Tsukihara et al., J. Biochem. 90 (1981), 1763.
71. D. R. Ort and N. E. Good, Trends Biochem. Sci. 13 (1988), 467.
72. V. Massey, in Reference 9, p. 301.
73. M. K. Johnson et al., J. Biol. Chem. 260 (1985), 7368.
74. J. C. Salerno et al., J. Biol. Chem. 254 (1979), 4828.
75. T. P. Singer, M. Gutman, and V. Massey, in Reference 9, p. 225.
76. H. Twilfer, F.-H. Bernhardt, and K. Gersonde, Eur. J. Biochem. 119 (1981), 595.
77. L. Petersson, R. Cammack, and K. Krishna Rao, Biochim. Biophys. Acta 622 (1980), 18.
78. B.-K. Teo and R. G. Shulman, in Reference 8, p. 343.
79. T. Tsukihara et al., in K. Kimura, ed., Molecular Evolution, Protein Polymorphism and the Neutral Theory, Japan Scientific
Societies Press and Springer-Verlag, 1982, p. 299.
80. T. Tsukihara et al., BioSystems 15 (1982), 243.
81. D. Petering and G. Palmer, Arch. Biochem. Biophys. 141 (1970), 456.
82. J. F. Gibson et aI., Proc. Natl. Acad. Sci. USA 56 (1966), 987.
83. W. A. Eaton et al., Proc. Natl. Acad. Soc. USA 68 (1971), 3015. a) L. B. Dugad et al., Biochemistry 29 (1990), 2663.
84. J. Rawlings, O. Siiman, and H. B. Gray, Proc. Natl. Acad. Sci. USA 71 (1974), 125.
85. I. Salmeen and G. Palmer, Arch. Biochem. Biophys. 150 (1972), 767.
86. J. J. Mayerle et al., Proc. Natl. Acad. Sci. USA 70 (1973), 2429.
87. J. L. Markley et al., Science 240 (1988), 908. a) L. Banci, I. Bertini, and C. Luchinat, Structure and Bonding 72 (1990), 113.
88. V. K. Yachandra et al., J. Am. Chem. Soc. 105 (1983), 6462.
89. S. Hwa, R. S. Czernuszewicz, and T. G. Spiro, J. Am. Chem. Soc. 111 (1989), 3496.
90. S. Hwa et al., J. Am. Chem. Soc. 111 (1989), 3505.
91. J. R. Rieske, D. H. MacLennan, and R. Coleman, Biochem. Biophys. Res. Commun. 15 (1964), 338.
92. W. D. Bonner, Jr., and R. C. Prince, FEBS Lett. 177 (1984), 47.
93. J. F. Cline et al., J. Biol. Chem. 260 (1985), 3251.
94. H.-T. Tsang et al., Biochemistry 28 (1989), 7233.
95. R. C. Prince, S. J. G. Linkletter, and P. L. Dutton, Biochem. Biophys. Acta 635 (1981), 132.
96. J. G. Reynolds and R. H. Holm, lnorg. Chem. 19 (1980), 3257; 20 (1981), 1873. a) J. J. Mayerle et al., J. Am. Chem. Soc. 97
(1977), 1032. b) Y. Do, E. D. Simhon, and R. H. Holm, lnorg. Chem. 22 (1983), 3809. c) S. Han, R. Czernuszewicz, and T. G.
Spiro, lnorg. Chem. 25 (1986), 2276. d) H. Strasdeit, B. Krebs, and G. Henkel, lnorg. Chim. Acta 89 (1989), LII.
97. P. K. Mascharak et al., J. Am. Chem. Soc. 103 (1981), 6110.
98. P. Beardwood et al., J. Chem. Soc. Dalton Trans. (1982), 2015.
100. P. Beardwood and J. F. Gibson, J. Chem. Soc. Chem. Commun. 102 (1985), 490 and 1345.
101. L. C. Sieker, E. Adman, and L. H. Jensen, Nature 235 (1971), 40.
102. J. M. Berg, K. O. Hodgson, and R. H. Holm, J. Am. Chem. Soc. 101 (1970), 4586.
103. P. J. Stephens et al., Proc. Natl. Acad. Sci. USA 82 (1985), 5661.
104. M. W. W. Adams and L. E. Mortenson, in Reference 235a.
105. L. W. Lim et al., J. Biol. Chem. 261 (1986), 15 and 140.
106. J. C. Salerno et al., Biochem. Biophys. Res. Commun. 73 (1976), 833.
107. G. Strahs and J. Kraut, J. Mol. Biol. 35 (1968), 503.
108. C. W. Carter, Jr., et al., Proc. Natl. Acad. Sci. USA 69 (1972), 3526.
109. C. W. Carter, Jr., et al., J. Biol. Chem. 249 (1974), 4212.
110. K. Fukuyama, J. Mol. Biol. 199 (1988), 183. a) K. Fukuyama et al., J. Mol. Biol. 210 (1989), 383.
111. G. H. Stout et al., Proc. Natl. Acad. Sci. USA 85 (1988), 1020.
112. C. D. Stout, J. Biol. Chem. 263 (1988), 9256.
113. A. H. Robbins and C. D. Stout, Proc. Natl. Acad. Sci. USA 86 (1989), 3639.
114. E. T. Adman, L. C. Sieker, and L. H. Jensen, J. Biol. Chem. 248 (1973), 3987.
115. R. C. Prince and M. W. W. Adams, J. Biol. Chem. 262 (1987), 5125.
116. L. E. Mortenson, R. C. Valentine, and J. E. Carnahan, Biochem. Biophys. Res. Commun. 7 (1962), 448.
117. W. Lovenberg, B. B. Buchanan, and J. C. Rabinowitz, J. Biol. Chem. 254 (1979), 4499.
118. R. Mathews et al., J. Biol. Chem. 249 (1974), 4326.
119. A. J. Thomson, in P. M. Harrison, ed., Metalloproteins, Part I: Metal Proteins with Redox Roles, Verlag Chemie, 1985, pp. 79-
120.
120. R. Cammack, Biochem. Biophys. Res. Commun. 54 (1973), 548.
121. M. J. Carney et al., Inorg. Chem. 27 (1988), 346.
122. M. J. Carney et al., J. Am. Chem. Soc. 110 (1988), 6084.
123. L. Noodleman, D. A. Case, and A. Aizman, J. Am. Chem. Soc. 110 (1988), 1001.
124. L. Noodleman, Inorg. Chem. 27 (1988), 3677.
125. J.-M. Moulis, J. Meyer, and M. Lutz, Biochemistry 23 (1984), 6605. a) W. D. Phillips and M. Poe, in Reference 10, p. 255. b) E.
L. Packer et al., J. Biol. Chem. 252 (1977), 2245. c) J. Bertini et al., Inorg. Chem. 29 (1990), 1874. d) B.-K. Teo et al., J. Am.
Chem. Soc. 101 (1979), 5624.
126. T. Herskovitz et al., Proc. Natl. Acad. Sci. USA 69 (1972), 2437.
127. B. A. Averill et al., J. Am. Chem. Soc. 95 (1973), 3523.
128. J. M. Berg and R. H. Holm, in Reference 8, p. I.
129. G. B. Wang, M. A. Bobrick, and R. H. Holm, Inorg. Chem. 17 (1978), 578.
131. A. Müller and N. Schladerbeck, Chimia 39 (1985), 23.
132. A. Müller, N. Schladerbeck, and H. Bagge, Chimia 39 (1985), 24.
133. S. Rutchik, S. Kim, and M. A. Walters, Inorg. Chem. 27 (1988), 1513.
134. W. E. Cleland et al., J. Am. Chem. Soc. 105 (1983), 6021.
135. M. G. Kanatzidis et al., J. Am. Chem. Soc. 106 (1984), 4500.
136. M. G. Kanatzidis et al., Inorg. Chem. 22 (1983), 179.
137. R. E. Johnson et al., J. Am. Chem. Soc. 105 (1983), 7280.
138. M. G. Kanatzidis et al., J. Am. Chem. Soc. 107 (1985), 4925. a) K. S. Hagen, J. G. Reynolds, and R. H. Holm, J. Am. Chem.
Soc. 103 (1981), 4054. b) G. Christou and C. D. Gamer, J. Chem. Soc. Dalton Trans. (1979), 1093. c) M. J. Carney et al., Inorg.
Chem. 27 (1988), 346. d) P. Barbaro et al., J. Am. Chem. Soc. 112 (1990), 7238.
139. E. J. Laskowski et al., J. Am. Chem. Soc. 100 (1978), 5322.
140. E.1. Laskowski et al., J. Am. Chem. Soc. 101 (1979), 6562.
141. T. O'Sullivan and M. Millar, J. Am. Chem. Soc. 107 (1985), 4096.
142. M. Millar, private communication.
143. T. D. P. Stack and R. H. Holm, J. Am. Chem. Soc. 110 (1989), 2484. a) T. D. P. Stack, M. J. Carney, and R. H. Holm, J. Am.
Chem. Soc. 111 (1989), 1670. b) S. Ciurli et al., J. Am. Chem. Soc. 112 (1990), 2654. c) P. R. Challen et al., J. Am. Chem. Soc.
112 (1990), 2455.
144. L. Que, Jr., R. H. Holm, and L. E. Mortenson, J. Am. Chem. Soc. 97 (1975), 463.
145. N. R. Bastian et al., in Reference 10, p. 227.
146. H. Beinert and A. J. Thomson, Arch. Biochem. Biophys. 222 (1983), 333.
147. M. H. Emptage et al., J. Biol. Chem. 255 (1980), 1793.
148. W. W. Sweeney, J. C. Rabinowitz, and D. C. Yoch, J. Biol. Chem. 250 (1985), 7842.
149. B. A. Averill, J. R. Bal, and W. H. Orme-Johnson, J. Am. Chem. Soc. 100 (1978), 3034.
150. C. D. Stout, Nature 279 (1979), 83.
151. D. Ghosh et al., J. Biol. Chem. 256 (1981), 4185.
152. D. Ghosh et al., J. Mol. Biol. 158 (1982), 73.
153. M. K. Johnson et al., J. Am. Chem. Soc. 105 (1983), 6671.
154. H. Beinert and A. J. Thomson, Arch. Biochem. Biophys. 222 (1983), 333.
155. M. R. Antonio et al., J. Biol. Chem. 257 (1982), 6646.
156. E. Miinck, in Reference 8, p. 147.
157. C. E. Johnson, J. Inorg. Biochem. 207 (1986), 28.
158. B. H. Huynh et al., J. Biol. Chem. 255 (1980), 3242.
159. J. J. G. Moura et al., J. Biol. Chem. 257 (1982), 6259. a) H. Beinert and M. C. Kennedy, Eur. J. Biochem. 186 (1989), 1865.
160. C. R. Kissinger et al., J. Am. Chem. Soc. 110 (1988), 8721. a) S. Ciurli and R. H. Holm, Inorg. Chem. 28 (1989), 1685.
161. T. A. Kent et al., J. Biol. Chem. 260 (1985), 6871.
162. A. H. Robbins and C. D. Stout, J. Biol. Chem. 260 (1985), 2328.
164. M. C. Kennedy et al., J. Biol. Chem. 258 (1983), 11098.
165. J. TeIser et al., J. Biol. Chem. 261 (1986), 4840.
166. D. H. Flint, M. H. Emptage, and J. R. Guest, J. Inorg. Biochem. 36 (1989), 306. a) R. L. Switzer, BioFactors 2 (1989), 77.
167. H. Beinert et al., Proc. Natl. Acad. Sci. USA 80 (1983), 393.
169. T. R. Halbert et al., J. Am. Chem. Soc. 106 (1984),1849.
170. G. N. George and S. J. George, Trends Biochem. Sci. 13 (1988), 369. a) I. Moura et al., J. Am. Chem. Soc. 108 (1986), 349. b)
K. K. Surerus et al., J. Am. Chem. Soc. 109 (1987), 3805. c) R. C. Conover et al., J. Am. Chem. Soc. 112 (1990), 4562. d) J. K.
Money, J. C. Huffman, and G. Christou, Inorg. Chem. 27 (1988), 507.
171. B. H. Huynh et al., Proc. Natl. Acad. Sci. USA 81 (1984), 3728.
172. T. R. Hawkes and B. E. Smith, Biochem. J. 223 (1984), 783.
173. M. A. Whitener et al., J. Am. Chem. Soc. 108 (1986), 5607.
174. K. S. Hagen and R. H. Holm, J. Am. Chem. Soc. 104 (1982), 5496.
175. K. S. Hagen, A. D. Watson, and R. H. Holm, J. Am. Chem. Soc. 105 (1983), 3905. a) J.-J. Girard et al., J. Am. Chem. Soc. 106
(1984), 5941.
176. M. C. Kennedy et al., J. Biol. Chem. 259 (1984), 14463. a) H. Strasdeit, B. Krebs, and G. Henkel, Inorg. Chem. 23 (1983),
1816.
177. M. G. Kanatzidis et al., J. Chem. Soc. Chem. Commun. (1984), 356.
178. M. G. Kanatzidis, A. Salifoglou, and D. Coucouvanis, J. Am. Chem. Soc. 107 (1985), 3358; Inorg. Chem. 25 (1986), 2460.
179. S. Pohl and W. Saak, Angew. Chem. Int. Ed. Engl. 23 (1984), 907. a) S. A. AI-Ahmand et al., Inorg. Chem. 29 (1990), 927.
180. F. Cecconi, C. A. Ghilardi, and S. Midolini, J. Chem. Soc. Chem. Commun. (1981), 640.
181. A. Agresti et al., Inorg. Chem. 24 (1985), 689.
182. K. S. Hagen, J. M. Berg, and R. H. Holm, Inorg. Chim. Acta 45 (1980), L17. a) B. S. Snyder and R. H. Holm, Inorg. Chem. 27
(1988), 1816. b) B. S. Synder et al., Inorg. Chem. 27 (1988), 595. c) M. S. Reynolds and R. H. Holm, Inorg. Chem. 27 (1988),
4494. d) B. S. Snyder and R. H. Holm, Inorg. Chem. 29 (1990), 274.
183. I. Noda, B. S. Snyder, and R. H. Holm, Inorg. Chem. 25 (1986), 3851. a) J.-F. You, B. S. Snyder, and R. H. Holm, J. Am. Chem.
Soc. 110 (1988), 6589. b) J.-F. You et al., J. Am. Chem. Soc. 112 (1990), 1067. c) W. R. Hagen, A. J. Pierik, and C. Veeger, J.
Chem. Soc., Faraday Trans. I 85 (1989), 4083.
184. E. I. Stiefel et al., Adv. Chem. Ser. 162 (1977), 353. a) I. Moura and J. J. G. Moura, in Reference 5, p. 179. b) J. R. Lancaster,
Jr., ed., The Bioinorganic Chemistry of Nickel, VCH Publishers, 1988. c) H. J. Grande et al., in Reference 5, p. 193. d M. W. W.
Adams, L. E. Mortenson, and J.-S. Chen, Biochim. Biophys. Acta 594 (1981), 105. e) J. LeGall and H. D. Peck, Jr., in Reference
5, p. 207. f) J. LeGall et al., in Reference 8, p. 177. g) S. P. Ballantine and D. H. Boxer, Eur. J. Biochem. 156 (1986), 276. h) W.
H. Onne-Johnson and N. R. Onne-Johnson, in Reference 8, p. 67.
185. B. Bowien and H. G. Schlegel, Annu. Rev. Microbiol. 35 (1981), 401.
186. C. R. Bowers and D. P. Weitekamp, J. Am. Chem. Soc. 109 (1987), 5541.
187. T. C. Eisenschmid et al., J. Am. Chem. Soc. 109 (1987), 8089.
188. M. W. W. Adams et al., Biochimie 68 (1986), 35.
189. R. Cammack, V. M. Fernandez, and K. Schneider, in Reference 184b, p. 167. 189a. M. W. W. Adams, Biochem. Biophys. Acta
1020 (1990),115.
190. H. J. Grande et al., Eur. J. Biochem. 136 (1983), 201.
191. M. W. W. Adams and L. E. Mortenson, J. Biol. Chem. 259 (1984), 7045.
192. S. W. Ragsdale and L. G. L. Ljungdahl, Arch. Microbial. 139 (1984), 361.
193. C. R. Woese, Microbial. Rev. 81 (1987), 221.
194. M. W. W. Adams, E. Eccleston, and J. B. Howard, Proc. Natl. Acad. Sci. USA 86 (1989), 4932.
195. D. S. Patil et al., J. Am. Chem. Soc. 110 (1988), 8533.
196. A. T. Kowal, M. W. W. Adams, and M. K. Johnson, J. Biol. Chem. 264 (1989), 4342.
197. W. R. Hagen et al., FEBS Lett. 203 (1986), 59.
198. I. C. Zambrano et al., J. Biol. Chem. 264 (1989), 20974.
199. M. W. W. Adams, J. Biol. Chem. 262 (1987), 15054.
200. T. V. Morgan, R. C. Prince, and L. E. Mortenson, FEBS Lett. 206 (1986), 4.
202. F. M. Rusnak et al., J. Biol. Chem. 262 (1987), 38.
203. G. Wang et al., J. Biol. Chem. 259 (1984), 14328.
204. J. Telser et al., J. Biol. Chem. 262 (1987), 6589.
205. J. Telser et al., J. Biol. Chem. 261 (1986), 15536.
206. H. Thomann, M. Bernardo, and M. W. W. Adams, J. Am. Chem. Soc. 113 (1991), 7044.
207. A. J. Thomson et al., Biochem. J. 227 (1985), 333.
208. K. A. Macor et al., J. Biol. Chem. 282 (1987), 9945.
209. G. N. George et al., Biochem. J. 259 (1989), 597.
210. R. Cammack, Adv. Inorg. Chem. 32 (1988), 297.
211. J. J. G. Moura et al., in Reference 5, p. 191.
212. J. R. Lancaster, FEBS Lett. 115 (1980), 285.
213. M. Teixeira et al., J. Biol. Chem. 260 (1985), 8942.
214. J. W. Van der Zwaan et al., FEBS Lett. 179 (1985), 271.
215. M. K. Eidsness, R. J. Sullivan, and R. A. Scott, in Reference 184b, p. 73.
216. M. K. Eidsness et al., Proc. Natl. Acad. Sci. USA 86 (1989), 147.
217. P. A. Lindahl et al., J. Am. Chem. Soc. 106 (1984), 3062.
218. R. A. Scott et al., J. Am. Chem. Soc. 106 (1984), 6864.
219. S. P. J. Albracht et al., Biochim. Biophys. Acta 874 (1986), 116.
220. A. Chapman et al., FEBS Lett. 242 (1988), 134.
221. S. L. Tau et al., J. Am. Chem. Soc. 106 (1984), 3064.
222. G. J. Kubas et al., J. Am. Chem. Soc. 106 (1984), 451.
223. G. J. Kubas and R. R. Ryan, Polyhedron 5 (1986), 473.
224. G. J. Kubas et al., J. Am. Chem. Soc. 108 (1986), 7000.
225. M. Rakowski DuBois et al., J. Am. Chem. Soc. 102 (1980), 7456.
226. C. Bianchini et al., Inorg. Chem. 25 (1986), 4617.
227. W. Tremel et al., Inorg. Chem. 27 (1988), 3886.
228. W. Tremel and G. Henkel, Inorg. Chem. 27 (1988), 3896.
229. I. Dance, Polyhedron 5 (1986), 1037; P. J. Blower and J. R. Dilworth, Coord. Chem. Rev. 76 (1987), 121.
230. C. L. Coyle and E. I. Stiefel, in Reference 184b, p. 1.
231. M. Kumar et al., J. Am Chem. Soc. 111 (1989), 5974.
232. M. Kumar et al., J. Am. Chem. Soc. 111 (1989), 8323.
233. T. H. Blackburn, in W. E. Krumbein, ed., Microbial Geochemistry, Blackwell Scientific, 1983, p. 63.
234. J. R. Postgate, Fundamentals of Nitrogen Fixation, Cambridge University Press, 1982.
235. R. W. F. Hardy, Treatise on Dinitrogen Fixation, Wiley, 1979, Section I. a) T. G. Spiro, ed., Molybdenum Enzymes, Wiley-
Interscience, 1985.
236. W. J. Brill, NATO Adv. Sci. Inst., Ser. A 63 (1983), 231.
237. R. Haselkorn, Annu. Rev. Microbial. 40 (1986), 525.
238. A. C. Robinson, D. R. Dean, and B. K. Burgess, J. Biol. Chem. 262 (1987), 14327.
239. P. J. Stephens, in Reference 235a, p. 117.
240. A. H. Gibson and W. E. Newton, eds., Current Perspectives in Nitrogen Fixation, Australian Academy of Science, 1981.
241. E. I. Stiefel, in W. E. Newton and C. Rodriquez-Barrucco, eds., in Recent Progress in Nitrogen Fixation, Academic Press, 1977,
p. 69.
242. C. Veeger and W. E. Newton, eds., Advances in Nitrogen Fixation Research, Nijhoff/Junk, 1984.
243. H. J. Evans, P. J. Bottomley, and W. E. Newton, eds., Nitrogen Fixation Research Progress, Martinus Nijhoff, 1985. a) A.
Braaksma et al., in Reference 5, p. 223. b) B. H. Huynh, E. Münck, and W. H. Orme-Johnson, in Reference 5, p. 241.
244. E. I. Stiefel, in Reference 240, p. 55.
245. R. V. Hageman and R. H. Burris, Proc. Natl. Acad. Sci. USA 75 (1978), 2699.
246. V. Sundaresan and F. M. Ausubel, J. Biol. Chem. 256 (1981), 2808. a) R. P. Hausinger and J. B. Howard, J. Biol. Chem. 258
(1983), 13486. b) M. M. Georgiadis, P. Chakrabarti, and D. C. Rees, SSRL Annual Report (1989), p. 94.
247. L. E. Mortenson, M. N. Walker, and G. A. Walker, in W. E. Newton and C. J. Nyman, eds., Proceedings of the First
International Conference on Nitrogen Fixation, Washington State University Press (1976), p. 117.
248. W. H. Orme-Johnson et al., in W. E. Newton, J. R. Postgate, and C. Rodriguez Barrucco, eds., Recent Developments in Nitrogen
Fixation, Academic Press, 1977, p. 131.
249. G. D. Watt and J. W. McDonald, Biochemistry 24 (1985), 7226.
251. L. Noodleman et al., J. Am. Chem. Soc. 107 (1985), 3418.
252. G. D. Watt, Z.-C. Wang, and R. R. Knotts, Biochemistry 25 (1986),8156; J. Cordewener et al., Eur. J. Biochem. 148 (1985),
499.
253. L. E. Mortenson and R. N. F. Thorneley, Annu. Rev. Biochem. 48 (1979), 387.
254. A. V. Kulikov et al., Dokl. Akad. Nauk SSR 262 (1981), 1177.
255. R. N. F. Thorneley and D. J. Lowe, in Reference 235, p. 221. a) F. A. Schultz, S. F. Gheller, and W. E. Newton, Proc. Int. Symp.
Redox Mech. Interfacial Prop. Mol. Biol. Importance 3 (1988), 203.
256. B. K. Burgess and W. E. Newton, in A. Müller and W. E. Newton, eds., Nitrogen Fixation: The Chemical-Biochemical-Genetic
Interface, Plenum, 1983, p. 83.
257. E. I. Stiefel and S. P. Cramer, in Reference 235, p. 88.
258. V. Shah and W. J. Brill, Proc. Natl. Acad. Sci. USA 74 (1977), 3249.
259. S. D. Conradson et al., J. Am. Chem. Soc. 109 (1987), 7507. a) P. A. McLean et al., Biochemistry 28 (1989), 9402. b) D. A.
Wink et al., Biochemistry 28 (1989), 9407.
260. M. A. Walters, S. K. Chapman, and W. H. Orme-Johnson, Polyhedron 5 (1986), 561.
261. P. A. McLean and R. A. Dixon, Nature 292 (1981), 655.
262. P. A. McLean and B. E. Smith, Biochem. J. 211 (1983), 589.
263. T. R. Hawkes, P. A. McLean, and B. E. Smith, Biochem. J. 217 (1984), 317.
264. T. R. Hoover et al., Biochemistry 27 (1988), 3647.
265. T. R. Hoover et al., Biochemistry 28 (1989), 2768. a) J. Liang et al., Biochemistry 29 (1990), 8377. b) M. S. Madden et al.,
Proc. Natl. Acad. Sci. USA 87 (1990), 6517.
266. A. C. Robinson, D. Dean, and B. K. Burgess, J. Biol. Chem. 262 (1989), 14327. a) A. C. Robinson et al., J. Biol. Chem. 264
(1989), 10088. b) D. J. Scott et al., Nature 343 (1990), 188. c) H. M. Kent et al., Biochem. J. 264 (1989), 257.
267. W. R. Hagen et al., Eur. J. Biochem. 169 (1987), 457.
268. P. A. McLean et al., J. Biol. Chem. 262 (1987), 12900.
269. P. A. Lindahl et al., J. Biol. Chem. 263 (1988), 19442.
270. G. D. Watt, A. Burns, and D. L. Tennent, Biochemistry 20 (1981), 7272; G. D. Watt and Z. C. Wang, Biochemistry 25 (1986),
5196.
271. R. Zimmermann et al., Biochim. Biophys. Acta. 537 (1978), 185.
272. D. M. Kurtz et al., Proc. Natl. Acad. Sci. USA 76 (1979), 4986.
273. R. A. Venters et al., J. Am. Chem. Soc. 108 (1986), 3487. a) J. Bolin, in P. M. Gresshoff, L. E. Roth, G. Stacey, and W. E.
Newton, eds., Nitrogen Fixation: Achievements and Objectives, Chapman and Hall, 1990, p. 111.
274. B. M. Hoffman, J. E. Roberts, and W. H. Orme-Johnson, J. Am. Chern. Soc. 104 (1982), 860.
275. A. E. True et al., J. Am. Chem. Soc. 110 (1988), 1935. a) A. E. True et al., J. Am. Chem. Soc. 112 (1990), 651.
276. G. N. George et aI., Biochem. J. 262 (1989), 349.
277. W. B. Mims and J. Peisach, in R. G. Shulman, ed., Biological Applications of Magnetic Resonance, Academic Press, 1980, p.
221.
278. W. H. Orme-Johnson et al., in Reference 8, p. 79.
279. H. Thomann et al., J. Am. Chem. Soc. 109 (1987), 7913.
280. H. Thomann et al., Proc. Natl. Acad. Sci. USA, 88 (1991), 6620.
281. B. H. Huynh, E. Munck, and W. H. Orme-Johnson, Biochim. Biophys. Acta 527 (1979), 192.
282. B. H. Huynh et aI., Biochim. Biophys. Acta 623 (1980), 124.
283. E. Münck et al., Biochim. Biophys. Acta 400 (1975), 32. a) W. E. Newton et al., Biochem. Biophys. Res. Commun. 162 (1989),
882.
284. S. D. Conradson, B. K. Burgess, and R. H. Holm, J. Biol. Chem. 263 (1988), 13743.
285. W. R. Dunham et aI., Eur. J. Biochem. 146 (1985), 497.
286. S. P. Cramer et al., J. Am. Chem. Soc. 100 (1978), 3398.
287. M. K. Eidsness et al., J. Am. Chem. Soc. 108 (1986), 2746.
288. S. D. Conradson et aI., J. Am. Chem. Soc. 107 (1985), 7935; Reference 259.
289. B. Hedman et al., J. Am. Chem. Soc. 110 (1988), 3798.
290. M. R. Antonio et al., J. Am. Chem. Soc. 104 (1982), 4703.
291. J. M. Arber et al., Biochem. J. 252 (1988), 421.
292. M. S. Weininger and L. E. Mortenson, Proc. Natl. Acad. Sci. USA 79 (1982), 378.
293. N. I. Sosfenov et al., Dokl. Akad. Nauk. SSSR 291 (1986), 1123.
294. T. Yamane et al., J. Biol. Chem. 257 (1982), 1221.
295. A. M. Flank et aI., J. Am. Chem. Soc. 108 (1986), 1049.
296. J. F. Rubinson et aI., Biochemistry 24 (1985), 273.
297. E. I. Stiefel, Proc. Natl. Acad. Sci. USA 70 (1973), 988.
298. K. L. Hadfield and W. A. Bulen, Biochemistry 8 (1969), 5103.
299. F. B. Simpson and R. Burris, Science 224 (1984), 1095.
300. B. K. Burgess et al., Biochemistry 20 (1981), 5140.
301. S. Wherland et aI., Biochemistry 20 (1981), 5132.
302. J. H. Guth and R. H. Burris, Biochemistry 22 (1983), 5111.
303. Z.-c. Wang and G. D. Watt, Proc. Natl. Acad. Sci. USA 81 (1984), 376.
304. B. E. Smith et al., Phil. Trans. Roy. Soc. London B317 (1987), 131.
305. R. N. F. Thorneley, R. R. Eady, and D. J. Lowe, Nature 272 (1978), 557.
306. S. Wherland et al., Biochemistry 20 (1981), 5132.
307. B. K. Burgess et al., Biochemistry 20 (1981), 5140.
308. H. Bortels, Arch. Mikrobiol. 1 (1930), 333.
309. R. C. Bray, Quart. Rev. Biophys. 21 (1988), 299.
310. H. Bortels, Zentbl. Bakt. Parasiten Abt. II 95 (1935), 193.
311. C. E. McKenna, J. R. Benemann, and T. G. Traylor, Biochem. Biophys. Res. Commun. 41 (1970), 1501.
312. R. C. Burns, W. H. Fuchsman, and R. W. F. Hardy, Biochem. Biophys. Res. Commun. 42 (1971), 353.
313. J. R. Benemann et al., Biochim. Biophys. Acta 264 (1972), 25.
314. P. E. Bishop, D. M. L. Jarlenski, and D. R. Hetherington, Proc. Natl. Acad. Sci. USA 77 (1980), 7342.
315. P. E. Bishop et al., Science 232 (1986), 92.
316. B. J. Hales, D. J. Langosch, and E. E. Case, J. Biol. Chem. 261 (1986), 15301.
317. B. J. Hales et al., Biochemistry 26 (1987), 1795.
318. J. Morningstar et al., Biochemistry 26 (1987), 1795.
319. R. L. Robson et al., Nature 322 (1986), 388.
320. R. R. Eady et al., Biochem. J. 244 (1987), 197.
321. M. J. Dilworth et al., Nature 327 (1987), 167.
322. R. N. Pau, Trends Biochem. Res. 14 (1989), 186; P. E. Bishop and R. D. Joerger, Annu. Rev. Plant Physiol. Plant Mol. Biol. 41
(1990), 109.
323. J. E. Morningstar and B. J. Hales, J. Am. Chem. Soc. 109 (1987), 6854.
324. J. M. Arber et al., Nature 372 (1987), 325.
325. G. N. George et al., J: Am. Chem. Soc. 110 (1988), 4057.
326. R. R. Eady et al., Recueil des Travaus Chim. des Pays-Bas 106 (1987), 175.
327. M. J. Carney et al., J. Am. Chem. Soc. 108 (1986), 3519.
328. R. H. Holm, Chem. Soc. Rev. (1981), 455.
329. G. Christou and C. D. Gamer, J. Chem. Soc. Dalton Trans. (1980), 2354.
330. C. D. Gamer et al., Phil. Trans. Roy. Soc. Land. A308 (1982), 159. a). R. H. Holm and E. D. Simhon, in Reference 235a, p. 1.
331. W. H. Armstrong, P. K. Mascharak, and R. H. Holm, Inorg. Chem. 21 (1982),1699.
332. R. E. Palermo and R. H. Holm, J. Am. Chem. Soc. 105 (1983), 4310. a) D. Coucouvanis, E. D. Simhon, and N. C. Baenziger, J.
Am. Chem. Soc. 102 (1980), 6644. b) G. D. Friesen et al., Inorg. Chem. 22 (1983), 2203. c) P. Stremple, N. C. Baenziger, and D.
Coucouvanis, J. Am. Chem. Soc. 103 (1981), 4601. d) D. Coucouvanis et al., J. Am. Chem. Soc. 102 (1980), 1732. e) A. Müller
et al., Inorg. Chim. Acta 148 (1988), 11. f) A. Müller et al., Angew. Chem. Int. Ed. Engl. 21 (1982), 860. g) D. Coucouvanis et
al., Inorg. Chem. 27 (1988), 4066. h) P. A. Eldridge et al., J. Am. Chem. Soc. 110 (1988), 5573. i) K. S. Bose et al., J. Am.
Chem. Soc. 111 (1989), 8953. j) J. A. Kovacs, J. K. Bashkin, and R. H. Holm, Polyhedron 6 (1987), 1445.
333. R. D. Sanner et al., J. Am. Chem. Soc. 98 (1972), 8351. a) M. B. O'Regan et al., J. Am. Chem. Soc. 112 (1990), 4331.
334. G. Pez, P. Apgar, and R. K. Crissey, J. Am. Chem. Soc. 104 (1982), 462.
335. K. Jones et al., J. Am. Chem. Soc. 98 (1976), 74.
336. G. J. Leigh, J. Mol. Catal. 47 (1988), 363.
337. R. A. Henderson, G. J. Leigh, and C. J. Pickett, Adv. Inorg. Chem. Radiochem. 27 (1984), 198. a) M. Hidai and Y. Mizobe, in P.
S. Braterman, ed., Reactions of Coordinated Ligands, Plenum, 2 (1989),53. b) T. Yoshida et al., J. Am. Chem. Soc. 110 (1988),
4872. c) T. Yoshida, T. Adachi, and T. Ueda, Pure Appl. Chem. 62 (1990), 1127.
338. D. Sellmann et al., Angew. Chem. Int. Ed. Engl. 28 (1989), 1271.
339. A. E. Shilov, in M. Gratzel, ed., Energy Resources through Chemistry and Catalysis, Academic Press, 1983, p. 533.
340. W. E. Newton et al., Inorg. Chem. 19 (1980), 1997.
341. T. R. Halbert, W.-H. Pan, and E. I. Stiefel, J. Am. Chem. Soc. 105 (1983), 5476.
342. M. Rakowski DuBois et al., J. Am. Chem. Soc. 101 (1979), 5245.
343. R. H. Crabtree, Inorg. Chim. Acta 125 (1986), 27.
344. W. B. Mims and J. Peisach, in J. Berliner and J. Reuben, eds., Biological Magnetic Resonance, Plenum, 3 (1981), 213.
345. T. Yamane et al., J. Biol. Chem. 257 (1982), 1221.
346. D. C. Rees and J. B. Howard, J. Biol. Chem. 2587 (1983), 12733.
347. R. B. Frankel et al., J. de Physique 37 (1976), C6.
348. C. E. Johnson, J. Appl. Phys. 42 (1971), 1325.
349. P. Middleton et al., Eur. J. Biochem. 88 (1978), 135.
350. K. Tagawa and D. I. Amon, Biochim. Biophys. Acta 153 (1968), 602.
351. G. Palmer, R. H. Sands, and L. E. Mortenson, Biochim. Biophys. Acta 23 (1966), 357.
352. R. H. Sands and W. R. Dunham, Quart. Rev. Biophys. 4 (1975), 443.
353. R. Cammack, in M. J. Allen and P. N. R. Usherwood, eds., Charge and Field Effects in Biosystems, Abacus Press, 1984, p. 41.
354. J. Cardenas, L. E. Mortenson, and D. C. Yoch, Biochim. Biophys. Acta 434 (1976), 244.
355. R. Cammack, M. J. Barber, and R. C. Bray, Biochem. J. 157 (1976), 469.
356. R. C. Bray, in The Enzymes, 3d ed., 12 (1975), 299.
357. J. A. Fee et al., J. Biol. Chem. 259 (1984), 124.
358. R. N. Mullinger et al., Biochem. J. 151 (1975), 75.
359. R. Cammack et al., Biochim. Biophys. Acta 490 (1977), 311.
360. F. A. Armstrong et al., FEBS Lett. 234 (1988), 107.
361. W. R. Hagen et al., Biochim. Biophys. Acta 828 (1985), 369.
362. E. deGryse, N. Glandsdorff, and A. Piérard, Arch. Microbiol. 117 (1978), 189.
363. V. M. Fernandez, E. C. Hatchikian, and R. Cammack, Biochim. Biophys. Acta 832 (1985), 69.
364. V. Niviére, Biochem. Biophys. Res. Commun. 139 (1986), 658.
365. M. Teixeira et al., Biochimie 68 (1986), 75.
366. D. J. Lowe, B. E. Smith, and R. R. Eady, in N. S. Subba Rao, ed., Recent Advances in Biological Nitrogen Fixation, Arnold,
1980, p. 34.
367. R. C. Bums, R. D. Holsten, and R. W. F. Hardy, Biochem. Biophys. Res. Commun. 39 (1970), 90.
368. M. G. Yates and K. Planque, Eur. J. Biochem. 60 (1975), 467.
369. T. C. Huang, W. G. Zumft, and L. E. Mortenson, J. Bact. 113 (1973), 884.
370. P. C. Hallenback, P. J. Kostel, and J. R. Benemann, Eur. J. Biochem. 98 (1979), 275.
371. S. Norlund, U. Erikson, and H. Baltscheffsky, Biochim. Biophys. Acta 504 (1978), 248.
372. B. K. Burgess et al., in Reference 242.
373. S. D. Conradson et aI., J. Am. Chem. Soc. 109 (1987), 7507.
374. S. A. Vaughn and B. K. Burgess, Biochemistry 28 (1989), 419.
375. R. W. Miller and R. R. Eady, Biochim. Biophys. Acta 952 (1988), 290.
376. B. K. Burgess, in Reference 235a, p. 161.
377. B. J. Hales et al., Biochemistry 25 (1986), 7251.
378. M. M. Georgiadis et al., Science 257 (1992), 1653.
379. J. T. Bolin et al., in P. M. Greshoff et al., eds., Nitrogen Fixation: Achievements and Objectives, Chapman and Hall, 1990, p.
117.
380. J. Kim and D. C. Rees, Science 257 (1992), 1677.
381. J. Kim and D. C. Rees, Nature 360 (1992), 553.
382. For allowing us to see and quote their work prior to publication, we are grateful to Prof. M. W. W. Adams, Prof. B. K. Burgess,
Dr. R. Cammack, Prof. D. Coucouvanis, Prof. S. P. Cramer, Dr. S. J. George, Prof. J. N. Enemark, Prof. J. Lancaster, Dr.
Michelle Millar, Prof. M. Maroney, Prof. W. E. Newton, Prof. D. C. Rees, Prof. Dieter Sellman, Prof. A. E. Shilov, Dr. Barry E.
Smith, Dr. R. N. F. Thorneley, and Prof. G. D. Watt. We thank Pat Deuel for her superb efforts under difficult circumstances in
the preparation of this manuscript.

Edward I. Stiefel (Exxon Research and Engineering Company)
Graham N. George (Exxon Research and Engineering Company)
6.7: Ferrodoxins, Hydrogenases, and Nitrogenases - Metal-Sulfide Proteins is shared under a not declared license and was authored, remixed,
Iron sulfide proteins involved in electron transfer are called ferredoxins and rubredoxins.* The ferredoxins were discovered first,
and were originally classified as bacterial (containing Fe4S4 clusters) and plant (containing Fe2S2 clusters) ferredoxins. This
classification is now recognized as being not generally useful, since both Fe2S2 and Fe4S4 ferredoxins are found in plants,14,15
animals,2,6,16 and bacteria.4 Ferredoxins are distinguished from rubredoxins by their possession of acid-labile sulfide; i.e., an
inorganic S2- ion that forms H2S gas upon denaturation at low pH. Rubredoxins have no acid-labile sulfide, and generally have a
single iron in a more or less isolated site. Despite their lack of acid-labile sulfide, rubredoxins are included in this chapter because
they have sequences much like those of the ferredoxins, and because their simple mononuclear Fe2+ and Fe3+ sites provide
convenient illustrations of key structural and spectroscopic features.
In most ferredoxins, and in all rubredoxins, the protein ligands are cysteines, which provide four thiolate donors to the 1Fe, 2Fe, or
4Fe center. Additionally, the existence of 3Fe centers and of Fe-S sites that contain a second metal (i.e., heteronuclear clusters)
make the Fe-S class a broad and multifunctional one.
Simple cytochromes and simple iron-sulfide proteins are similar, in that both can undergo one-electron transfer processes that are
generally uncoupled from proton-, atom-, or group-transfer processes. Some of these proteins, such as cytochrome c3 from
Desulfovibrio with four hemes17 or ferredoxin from Clostridium pasteurianum with two Fe4S4 centers,6 can transfer more than one
electron, because they have multiple copies of a one-electron transfer group. The cytochromes were discovered in 1886 by
McMunn,18 and their role in metabolism was discovered in the 1920s by Keilin (Chapter 6). The intense optical absorbance of
these heme-containing proteins contributed singularly to their discovery and biochemical characterization. In contrast, the iron-
sulfur proteins, although red to red-brown, absorb far more weakly in the visible region than do the cytochromes. Their presence is
sometimes obscured by the cytochromes, and their frequent air instability made their initial recognition and isolation more difficult.
It was not until the early 1960s that discoveries by several research groups19 led to the isolation, recognition, and characterization
of the ferredoxins. The use of EPR spectroscopy and its application to biological systems had a profoundly stimulating effect on the
field (see below).
Although cytochromes were discovered first, the ferredoxins are likely to be the older proteins from an evolutionary perspective.20
Ferredoxins have relatively low-molecular-weight polypeptide chains, require no organic prosthetic group, and often lack the more
complex amino acids. In fact, the amino-acid composition in clostridial ferredoxin is close to that found in certain meteorites.21
The various Fe-S sites found in electron-transfer proteins (ferredoxins) are also found in many enzymes,6,11,22.23 where these
centers are involved in intraor interprotein electron transfer. For example, sulfite reductase contains a siroheme and an Fe4S4
center,24 which are strongly coupled and involved in the sixelectron reduction of SO32- to H2S. Xanthine oxidase (see Figure 7.1)
has two identical subunits, each containing two different Fe2S2 sites plus molybdenum and FAD sites. In xanthine oxidase, the
Mo(VI) site carries out the two-electron oxidation of xanthine to uric acid, being reduced to Mo(IV) in the process.25 The Mo(VI)
site is regenerated by transferring electrons, one at a time, to the Fe2S2 and flavin sites, thereby readying the Mo site for the next
equivalent of xanthine. Although the Fe2S2 sites do not directly participate in substrate reactions, they are essential to the overall
functioning of the enzyme system. The Fe2S2 centers in xanthine oxidase play the same simple electron-transfer role as the Fe2S2
ferredoxins play in photosynthesis.
Figure 7.1 - A schematic drawing of xanthine oxidase illustrating the Mo, flavin, and Fe2S2 sites and interaction of the enzyme with
substrate and oxidant(s).
Structurally, all the iron-sulfur sites characterized to date are built up of (approximately) tetrahedral iron units (see Figure 7.2). In
rubredoxins the single iron atom is bound in tetrahedral coordination by four thiolate ligands provided by cysteine side chains. In
two-iron ferredoxins the Fe2S2 site consists of two tetrahedra doubly bridged through a pair of sulfide ions, i.e., Fe2(μ -S)2, with 2
the tetrahedral coordination of each Fe completed by two cysteine thiolates. In four-iron or eight-iron ferredoxins, the 'thiocubane'
Fe4S4 cluster consists of four tetrahedra sharing edges with triply bridging S2- ions, i.e., Fe4(μ -S)4, with each Fe completing its
3
tetrahedron by binding to a single cysteine thiolate. Finally, for Fe3S4 clusters, which are now being found in more and more
proteins, the well-established structure has one triply bridging and three doubly bridging sulfide ions, Fe3(μ -S)(μ S)3. The Fe3S4
3 2
unit can be thought of as derived from the 'thiocubane' Fe4S4 unit by the removal of a single iron atom.
In what follows we will introduce these structures in the order 1Fe, 2Fe, 4Fe, and 3Fe. For each, we will first discuss the
physiological role(s) of the particular proteins, then the structural features, followed by the spectroscopic properties and model
systems.
Figure 7.2 - Structural systematics of Fe-S units found in proteins: (A) rubredoxin single Fe center; (B) Fe2S2 unit; (C) Fe4S4 unit;
(d) Fe3S4 unit.
* For review articles, see References 1-11. For a discussion of nomenclature, see References 12 and 13.
6.7.1: Iron-sulfur Proteins and Models is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
Rubredoxin Model Systems
The simple mononuclear tetrahedral site of Rd has been chemically modeled in both its reduced and its oxidized forms. The
bidentate o-xylyl-α ,α '-dithiolate ligand forms bis complexes of Fe(II) and Fe(III) that have spectroscopic features quite similar to
those of the protein.62,63 The preparative procedure is relatively straightforward (Equation 7.1).
(7.1)
The UV-visible-NIR spectra, Mössbauer spectra, and magnetic susceptibility differ only slightly from those of oxidized and
reduced rubredoxins.
The monodentate benzenethiolate (thiophenolate) ligand, C6H5S-, similarly forms the ferrous Fe(SC6H5)42- complex.64,65 Although
for some time it was felt that the oxidized form, Fe(SC6H5)4-, was inherently unstable, the sterically hindered monothiolate ligand
2,3,5,6-tetramethylbenzenethiolate was found to form66-68 a stable, quite symmetric Fe(III) tetrathiolate anion. Armed with this
information, the preparation of the tetrakis(benzenethiolate) Fe(III) complex was reinvestigated, and the complex successfully
synthesized67 (Equation 7.2).
(7.2)
The Fe(III) and Fe(II) tetrathiolate species now serve as excellent structural models for the Fe sites of both oxidized and reduced
Rd.69
The structural parameters for the oxidized rubredoxin analogues are very similar to those of the oxidized Rd iron site. The reduced
complexes reveal a lengthening of the average Fe-S bond from 2.27 to 2.36 Å, consistent with the change in oxidation state from
ferric to ferrous. The addition of an electron has a more profound structural effect in this single-iron center than in some of the
multiiron clusters, where electrons are more delocalized.
Clearly, for the single-Fe sites, the dominant structural feature is their near-tetrahedral tetrathiolate coordination. The dominant
electronic structural feature is the presence of high-spin Fe3+ and Fe2+ sites. The important mode of chemical reactivity is a simple
one-electron transfer. Each of these features carries over to the 2Fe, 4Fe, and 3Fe sites discussed below.
Fe2S2 Ferredoxins
The simple 2Fe-2S proteins are sometimes referred to as "plant" or "plant-type" ferredoxins. The protein from spinach, which
serves as an electron acceptor in the photosynthetic apparatus,14,15,50,70 was among the first to be wellcharacterized and widely
studied, and could be considered the prototypical 2Fe-2S ferredoxin, However, 2Fe-2S proteins are also well-known in bacteria.4
The protein from the cyanobacterium (blue-green alga) Spirulina platensis has been structurally elucidated by x-ray
crystallography.47 Putidaredoxin, from Pseudomonas putida, which serves as a donor to the P-450 camphor monooxygenase
system, has been extensively studied.28 Fe2S2 centers are also well-established in mammalian proteins. Adrenodoxin29 serves as the
electron donor to the P-450 monooxygenase system that carries out the 11-β-hydroxylation of steroids, The so-called "Rieske
proteins" are found in the bc1 complex of mitochondria47 as well as in the bd complex of the photosynthetic apparatus of plants.71
In addition, Fe2S2 centers are well-known constituents of such redox proteins as xanthine oxidase,25,72 CO oxidase,25 succinate
dehydrogenase,73-75 and putidamonooxin.76 Table 7.1 lists some of the Fe2S2 proteins and their properties.
The x-ray crystal structure of only the single 2Fe-2S protein mentioned above has been determined;70a the 2Fe-2S ferredoxin from
the blue-green alga Spirulina platensis6,22,47,77,78 shows significant sequence identity with chloroplast ferredoxins typical of higher
plants.79,80 As Figure 7.8 shows, the Fe2S2 unit in this 11-kDa protein is bound by Cys-41, Cys-46, Cys-49, and Cys-79, The
binuclear iron cluster is found in a largely hydrophobic region of the protein, but is within 5 Å of the protein surface.6 The sulfur
atoms of the cluster, both inorganic and cysteinyl, are hydrogen-bonded to six peptide NH groups and one serine OH group, which
presumably stabilize the cluster/protein complex, The serine involved in the H-bonding, Ser-40, is conserved in all plant and algal
2Fe-2S ferredoxins sequenced, which implies that it plays a crucial structural or functional role.
Figure 7.8 - The x-ray crystal structure of the Fe2S2 ferredoxin from Spirulina platensis.70a
The structure of the 2Fe-2S core in Figure 7.2 reveals a tetrahedron of S ligands surrounding each Fe atom. The two tetrahedra
share an edge defined by the two bridging sulfide ions, and the core structure is designated Fe2(μ -S)2. Fe-S distances and angles
2
cannot be measured accurately in the structure at the present 2.5-Å resolution;70a so we will later discuss these details in terms of
model compounds.
The Fe2S2 center shows nicely how spectroscopy can be used to deduce the structure of an active site. Indeed, in this case the now
well-established active-site structure was deduced by a combination of chemical, spectroscopic, and magnetic methods, and the site
was successfully modeled long before the first protein crystallographic study was reported. The presence of acid-labile, inorganic
sulfide is a key feature of both the Fe2S2 and the Fe4S4 centers. The 1:1 stoichiometry between iron and acid-labile sulfide was
eventually established analytically for Fe2S2 centers.9-11 Care must be taken to ensure that both the protein and its active-site
complement are homogeneous. Although protein homogeneity is usually established by electrophoretic methods, these methods
may not distinguish between pure proteins and those with absent or incomplete active centers. Fortunately, absorption at 420 nm is
due solely to the Fe2S2 cluster, whereas the 275-nm absorption is dominated by the protein. Therefore a good criterion for active-
site saturation and homogeneity is the ratio of the absorbances at 420 and 275 nm, A420 nm/A275 nm, which is ~0.48 for pure spinach
ferredoxin.81 Once homogeneous protein is obtained, the Fe2S2 composition of the "plant" ferredoxins can be correctly deduced
analytically.
The Fe2S2 center displays two redox states that differ by a single electron. The potential range for the couple is -250 to -420 mV,
revealing the highly reducing nature of the ferredoxin. The correct structure of the Fe2S2 center was first proposed in 1966 based on
EPR studies.82 The reduced state of the cluster shows a rhombic EPR signal with g values of 1.88, 1.94, and 2.04 (Figure 7.6B)
characteristic of an S = center. The oxidized state is EPR-silent. The weakness of the sulfur ligand field causes the iron atoms to
1
be high-spin. But how can two sulfur-ligated iron atoms, each with a tendency to be high-spin, produce a state with a single
unpaired electron?
The individual Fe atoms in the Fe2S2 cluster resemble those in rubredoxin quite closely. The two redox states of the Fe2S2 protein
correspond to an Fe3+-Fe3+ and an Fe3+-Fe2+ pair, respectively, as shown in Figure 7.9. In the all-ferric oxidized state, the two Fe3+
sites are antiferromagnetically coupled; i.e., the spins of the five d electrons on the two iron atoms are oppositely aligned, such that
their pairing produces an effective S = 0, diamagnetic ground state. In the reduced form, a single unpaired electron is present,
because the S = Fe3+ and S = 2 Fe2+ sites are antiferromagnetically coupled, leaving one net unpaired spin and an S = ground
5
2
1
state. The profound difference between the electronic properties of rubredoxin and Fe2S2 ferredoxin arises because the latter has
two Fe atoms in close proximity, which allows for their magnetic coupling.
Figure 7.9 - Redox states of Fe2S2 proteins: (A) reduced; (B) oxidized.
Strong support for the spin-coupling model in Fe2S2 ferredoxins comes from a detailed analysis of their absorption and circular
dichroism spectra.83 As with rubredoxin (see Figure 7.5), we expect no low-energy spin-allowed d-d bands for the ferric site in
either the oxidized or the reduced state. Indeed, the oxidized state containing all Fe3+ shows no low-energy bands; the reduced state
containing a single Fe2+ displays low-energy, low-intensity bands in the region 4,000-9,000 cm-1, in close analogy to the situation
in reduced rubredoxin. The combined EPR and optical spectra leave little doubt about the structural assignment: two coupled high-
spin ferric ions in the oxidized state, and coupled high-spin ferric and ferrous ions in the reduced state. Moreover, the spectra are
consistent only with a localized model, i.e., one in which the Fe(II) site is associated with a single iron.83,83a The Fe2S2 site is
inherently asymmetric, and inequivalence of the Fe(llI) sites is spectroscopically detectable in the all-ferric oxidized form.84 In fact,
the localized valence trapping is present in reduced model compounds that contain no ligand asymmetry.
Mössbauer spectra provide additional and striking confirmation of the structural assignment. The spectrum of the oxidized
ferredoxin (Figure 7.7) resembles strongly that of oxidized rubredoxin, indicating the presence of high-spin Fe3+, even though the
net spin is zero. In the reduced form, the Mössbauer spectrum involves the superposition of signals from a high-spin Fe2+ and a
high-spin Fe3+, i.e., a reduced and an oxidized rubredoxin, respectively. Clearly, the simplest interpretation of this result consistent
with the S = spin state required by the EPR is the localized Fe2+-Fe3+ antiferromagnetic coupling model discussed above.
1
NMR studies of oxidized Fe2S2 proteins reveal broad isotropically shifted resonances for the CH2 protons of the cysteine ligands.85
Despite the coupling of the irons, the net magnetism at room temperature is sufficient to lead to large contact shifts (-30 to -40 ppm
downfield from TMS). The assignment of the resonance was confirmed with the synthesis and spectroscopic analysis of model
compounds.86 Extensive NMR studies of the Fe2S2 proteins have been reported.87,87a
Resonance Raman spectra of Fe2S2 sites88,89,90 reveal many bands attributable to Fe-S stretching. Detailed assignments have been
presented for the four bridging and four terminal Fe-S modes. A strong band at 390 cm-1, which shifts on 34S sulfide labeling, is
assigned to the A1g "breathing" mode; another band at 275 cm-1 is assigned to B3u symmetry in point group D2h.57,88 Spectroscopic
differences in the terminal, Fe-S(Cys) stretches between plant ferredoxins and adrenodoxin (which also differ somewhat in redox
potential) seem to reflect different conformations of the cysteine ligands in the two classes. Evidence for asymmetry of the iron
atoms is found in the intensity of the resonance enhancement of certain modes.
Rieske Centers
Within the class of Fe2S2 ferredoxins there is a subclass called the Rieske proteins, or the Rieske centers.47,91,92 The Rieske iron-
sulfur centers are found in proteins isolated from mitochondria and related redox chains.47,92 In addition, the phthalate dioxygenase
system from Pseudomonas cepacia93,94 contains one Fe2S2 Rieske center as well as one additional nonheme Fe atom. Although the
Rieske centers appear to contain an Fe2S2 core, there is extensive evidence for nonsulfur ligands coordinated to at least one of the
Fe atoms. The proposed model in Scheme (7.3) has two imidazole ligands bound to one Fe atom. The nitrogen atoms are seen in
ENDOR (Electron Nuclear Double Resonance) experiments,93 and are manifest in EXAFS spectra, which are consistent with the
presence of a low-Z (atomic number) ligand bound to iron.94 The potentials for the Rieske proteins range from +350 to -150 mV,47
in contrast to the plant-type Fe2S2 centers, which range from -250 to -450 mV. The strong dependence of redox potential on pH95
suggests a possible role in coupling protonand electron-transfer processes.
(7.3)
Fe2S2 Models
Although spectroscopic studies led to the correct deduction of the structure of the Fe2S2 core, the synthesis of model compounds
containing this core provided unequivocal confirmation. The model compounds allowed detailed structural analysis unavailable for
the proteins. Moreover, by using a uniform set of peripheral ligands, properties inherent to the Fe2S2 core could be discerned.
Figure 7.10: Preparative schemes leading to complexes containing the Fe2S2 core.128
The Fe2S2 core has been synthesized by several routes86,96,96a,b,c,d (see Figure 7.10). For example, the reaction of Fe(SR)42-, the
ferrous rubredoxin model, with elemental sulfur produces the complex Fe2S2(SR)42-. In this reaction the sulfur presumably oxidizes
the Fe2+ to Fe3+, being reduced to sulfide in the process. The Fe2S2 core has been prepared with a variety of peripheral S-donor
ligands. Metrical details for Fe2S2(SC6H4-p-CH3)42- are given in Table 7.3. Notable distances are the Fe-S (bridging) distance of
2.20 Å, the Fe-S (terminal) distance of 2.31 Å, and the Fe-Fe distance of 2.69 Å.
Table 7.3: Structural parameters for F e
2 S2 (SC6 H4
2−
− p − C H3 )
4
. a) Data from Reference 211.
Atomsa Distance Å Atomsa Anglea
Fe-Fe 2.691 (1) Fe-S-Fe 75.3
Fe-S1 (bridge) 2.200 (1) S-Fe-S 104.6
Fe-S2 (bridge) 2.202 (1) S-Fe-S 115.1
Fe-S3 2.312 (1) S-Fe-S 105.4
To date, all analogue systems structurally characterized contain the Fe3+-Fe3+ fully oxidized form. Attempts to isolate the Fe3+-Fe2+
form have so far failed. However, the mixed-valence Fe2S2 form can be generated and trapped by freezing for spectroscopic
examination.97,98 Mössbauer spectroscopy reveals the presence of distinct Fe2+ and Fe3+ ions, as found in the proteins, clearly
showing that "trapped" valence states are an inherent characteristic of the Fe2S22+ core and are not enforced by the protein.97,98
The existence of noncysteine-bound Fe2S2 cores in Rieske-type proteins has led to attempts to synthesize complexes with oxygen
and nitrogen ligands.99-101 Characterized species include Fe2S2(OC6H5)42-, Fe2S2(OC6H4-p-CH3)42-, Fe2S2(C4H4N)42-, and
Fe2S2(L)22-, where L is a bidentate ligand.
(7.4)
The potentially tridentate ligand
(7.5)
acts in a bidentate fashion, binding through S and O but not N.
No Fe2S2 complexes containing mixed S,N terminal ligands, such as those suggested for the Rieske site, have been prepared. The
Se2- bridged analogue has been prepared for some of the complexes.102,103
6.7.2: Iron-sulfur Proteins and Models (Part 2) is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
Fe4S4 Ferredoxins (including HiPIPs)
We now turn our attention to proteins containing the Fe4S4 center. Historically, within this class a strong distinction was made
between the "ferredoxins," which are low-potential (as low as -600 mV in chloroplasts) iron-sulfur proteins, and the "HiPIPs" =
High Potential Iron Proteins, which have positive redox potentials (as high as +350 mV in photosynthetic bacteria). Although the
HiPIP designation is still useful, proteins of both high and low potential are considered ferredoxins, whose key defining feature is
the presence of iron and acid-labile sulfide.13
The Fe4S4 proteins participate in numerous electron-transfer functions in bacteria, and in some organisms (such as Clostridium) are
the immediate electron donors for the nitrogenase and/or hydrogenase enzymes. The function of the HiPIPs seems obscure at
present. In addition, Fe4S4 centers have been shown or postulated to occur in numerous microbial, plant, and mammalian redox
enzymes, including nitrate reductase,104 sulfite reductase,24 trimethylamine dehydrogenase,105 succinate dehydrogenase,73,106
hydrogenase, and, possibly, in altered forms, nitrogenase. Table 7.1 lists some of the Fe4S4 ferredoxins and their properties.
In the Fe2S2 ferredoxins, combined spectroscopic, analytical, and model-system work led to an unequivocal assignment of the
structural nature of the active site long before the crystallography was done. In contrast, for Fe4S4 systems and in particular the
8Fe-8S = 2Fe4S4 systems from bacteria, the initial chemical suggestions were fallacious, and even the number and stoichiometry of
the clusters were in doubt. In these cases, crystallography provided the definitive structural information.
The first indication of the presence of the "thiocubane" structure came in 1968, when a 4-Å resolution study107 indicated a compact
cluster of potentially tetrahedral Fe4 shape in the HiPIP from Chromatium vinosum. This finding did not lead to much excitement,
since it was not yet appreciated that HiPIPs and ferredoxins were structurally similar. In 1972, the high-resolution structure solution
of both Chromatium HiPIP108 and the 8Fe ferredoxin from Peptococcus aerogenes (formerly Microbacter aerogenes)101 confirmed
the presence of virtually identical thiocubane clusters in the two proteins.108 Moreover, the structures for both oxidized and reduced
HiPIP were deduced, and these revealed that the Fe4S4 cluster remained intact during the redox interconversion.109 Subsequently,
four-iron clusters have been crystallographically confirmed in an Fe4S4 ferredoxin from Bacillus thermoproteolyticus,110,110a in
Azotobacter vinelandii ferredoxin I (also previously called Shethna Fe-S protein II), which also contains a 3Fe-4S cluster,111,112 in
the active form of aconitase,113 and in sulfite reductase, where the cluster is probably bridged by cysteine sulfur to a siroheme.
In all the proteins characterized to date, the Fe4S4 clusters adopt the thiocubane structure,108 which is discussed at greater length in
the section on models. The clusters are usually bound to their proteins by four cysteine residues. As shown in Figure 7.11, in the P.
aerogenes protein the two Fe4S4 clusters are bound by cysteines numbered 8, 11, 14, 18, 35, 38, 41, and 45.101,114 The presence of
the Cys-x-x-Cys unit is again apparent. However, this sequence seems prominent in all Fe-S proteins, and so is not specific for a
particular Fe-S site. At first glance one might expect one cluster to be bound by cysteines 8,11,14, and 18, the other by cysteines
35, 38, 41, and 45. Actually, one cluster is bound by cysteines 8, 11, 14, and 45, the other by cysteines 35, 38, 41, and 18. The
binding of a given cluster by cysteine residues from different portions of the polypeptide chain apparently helps stabilize the
tertiary structure of the protein and brings the two clusters into relatively close proximity, the center-center distance being 12 Å.114
Figure 7.11 - The x-ray crystal structures of (A) Chromatium vinosum HiPIP108 and (B) the 8Fe-8S ferredoxin from Peptococcus
aerogenes.101
The C. pasteurianum protein displays weak magnetic coupling, which leads to an unusual EPR spectrum115 consistent with the 12-
Å cluster-cluster separation. However, the redox potentials for the two sites seem virtually identical at -412 mV, thus allowing the
8Fe ferredoxin to deliver two electrons at this low redox potential.115 Significant sequence identity indicates the likelihood that
other 8Fe ferredoxins, such as the well-studied one from C. pasteurianum,116-118 have quite similar structures.
The thiocubane unit of Fe4S4 proteins can exist in proteins in at least three stable oxidation states. This so-called three-state
modeI74,109,119,120 contrasts dramatically with the situation for Rd(1Fe), Fe2S2, and Fe3S4 systems, in which only two oxidation
states are accessible through simple electron transfer for each center. For the thiocubane structure, the three accessible states can be
designated Fe4S43+, Fe4S42+, and Fe4S4+, corresponding to [Fe(III)2Fe(II)], [Fe(III)2Fe(II)2], and [Fe(III)Fe(II)3] valence-state
combinations, respectively. It is crucial to note that, in sharp contrast to the Fe2S2 and Fe3S4 sites, the oxidation states are not
localized in the Fe4S4 clusters. In most cases, each Fe atom behaves as if it had the same average oxidation level as the other Fe
atoms in the cluster. The redox interconversion of the Fe4S4 sites is shown in Figure 7.12. The Fe4S43+ ⇌ Fe4S42+ couple is the
high-potential redox couple characteristic of HiPIPs; the Fe4S42+ ⇌ Fe4S4+ couple is responsible for the low-potential process
characteristic of the classical ferredoxins. In any given protein under physiological conditions, only one of the two redox couples
appears to be accessible and functional.
Figure 7.12 - The redox interconversions of Fe4S4 sites illustrating the three-state model. The states are found in (A) oxidized
HiPIP; (B) reduced HiPIP and oxidized ferredoxin; (C) reduced ferredoxin.
Both the Fe4S4+ and the Fe4S43+ states of the thiocubane cluster are paramagnetic and display characteristic EPR spectra (Figure
7.6C,D). The Fe4S43+ site in reduced ferredoxins46,48,49,119 displays a rhombic EPR signal (Figure 7.6C) with g = 1.88, 1.92, and
2.06. The oxidized form of low-potential ferredoxins is EPR-silent, and attempts to "superoxidize" it to achieve the Fe4S43+ state
invariably lead to irreversible cluster decomposition, probably through a 3Fe-4S structure. The Fe4S43+ signal is usually referred to
as the HiPIP signal (Figure 7.6D) and shows distinct g values at 2.04(g ) and 2.10(g ); it is present in oxidized HiPIP but absent in
⊥ ∥
reduced HiPIP.46,119 Reduction of HiPIP to a "super-reduced" state apparently occurs under partially denaturing conditions in
aqueous DMSO.108 The observed axial EPR signal with g = 1.94 and 2.05 is assigned to the Fe4S4+ state characteristic of reduced
ferredoxins. This result108 is consistent with structural and spectroscopic identity of the HiPIP and Fd sites, as required by the
three-state model of the Fe4S4 proteins (Figure 7.12).
In Fe4S4 centers at each level of oxidation, electronic transitions give rise to characteristic visible and UV spectra, although the
delocalized nature of the electronic states makes detailed assignment difficult. MCD spectra of clusters in the three states of
oxidation are clearly distinguishable from each other and from MCD of Fe2S2 clusters.43,119 MCD, magnetic susceptibility, and
Mössbauer spectra provide evidence that the S = state, whose EPR signal is so distinct in reduced ferredoxins, may coexist at
1
higher T with S = 3
2
and perhaps even higher spin states. Indeed, recent studies with model systems121,122 and theoretical
treatments123,124 clearly support the ability of the Fe4S4 cluster to display a number of spin states that are in labile equilibria, which
are influenced, perhaps quite subtly, by local structural conditions. The iron protein of nitrogenase also displays this behavior.
The Mössbauer spectra of Fe4S4 centers of ferredoxins reveal the equivalence of the Fe sites, and quadrupole splittings and isomer
shifts at averaged values for the particular combination of oxidation states present.3,51,52 Representative spectra are shown in Figure
7.7. Magnetic coupling is seen for the paramagnetic states.
Resonance Raman spectra (and IR spectra) have been extensively investigated in C. pasteurianum ferredoxin and in model
compounds.57,125 Selective labeling of either thiolate sulfur or sulfide sulfur with 34S allows modes associated with the Fe4S4 core
to be distinguished from modes associated with the FeSR ligands. The band at 351 cm-1 is assigned to Fe-SR stretching, and Fe4S4
modes occur at 248 and 334 cm-1 in reduced ferredoxin from C. pasteurianum. There is little difference between the oxidized and
reduced spectra, although an extra band at 277 cm-1 seems present in the oxidized protein. The Fe4Se4 substituted protein has also
been studied.125
As in the 1Fe and 2Fe proteins, 1H NMR spectra reveal resonances from contact-shifted-CH2-groups of cysteinyl residues.125a
However, unlike the other proteins, where all states are at least weakly magnetic, only the reduced ferredoxin and the oxidized
HiPIP states show contact shifts.87a,125a,b,c
EXAFS studies on proteins and on model compounds clearly identify the Fe-S distance of ~2.35 Å and an Fe-Fe distance of 2.7 Å.
These distances, as expected, vary only slightly with state of oxidation.125d
Fe4S4 Models
Judging from the ease with which models of Fe4S4 are prepared under a variety of conditions and their relative stability, the
Fe4S42+ core structure seems to be a relatively stable entity, a local thermodynamic minimum in the multitude of possible iron-
sulfide-thiolate complexes. The initial preparation and structural characterization126,127 of the models showed that synthetic
chemistry can duplicate the biological centers in far-simpler chemical systems, which can be more easily studied in great detail.
The general synthetic scheme for Fe-S clusters is shown in Figure 7.13. Many different synthetic procedures can be used to obtain
complexes with the Fe4S4 core.126-138,138a,b The multitude of preparative procedures is consistent with the notion that the Fe4S42+
core is the most stable entity present and "spontaneously self-assembles" when not limited by stoichiometric constraints.
Figure 7.13 - Preparative schemes leading to complexes containing the Fe4S4 core.128
The thiocubane structure can be viewed as two interpenetrating tetrahedra of 4Fe and 4S atoms. The 4S tetrahedra are the larger,
since the S-S distance is ~3.5 Å, compared with the Fe-Fe distance of ~2.7 Å. The S4 tetrahedron encloses ~2.3 times as much
volume as does the Fe4 tetrahedron.128 Key distances and angles for Fe4S4(SCH2C6H5)42- given in Table 7.4 are extremely similar
to those found in oxidized ferredoxin and reduced HiPIP centers in proteins.127
Table 7.4 - Structural parameters for Fe4S4(SCH2C6H5)42-.

a) Data from References 126 and 127.
Atomsa Average Distances Number of Bonds Type
Fe(1)-S(3) 2.310 (3) 8 Sulfide
Fe(1)-S(2) 2.239 (4) 4 Sulfide
Fe(1)-S(5) 2.251 ( 3) 4 Thiolate
Fe(1)-Fe(2) 2.776 (10) 2
Fe-Fe(other) 2.732 (5) 4
Atomsa Average Distances Number of Bonds Type
Fe-S-Fe 73.8 (3) 12
S-Fe-S 104.1 (2) 12 Sulfide-Fe-Sulfide
S-Fe-S 111.7-117.3 12 Sulfide-Fe-Thiolate
The idealized symmetry of Fe4S42+ model systems is that of a regular tetrahedron, i.e., Td. Though the distortion of the cube is quite
pronounced, all known examples of the Fe4S2+ core show distortion, which lowers the symmetry at least to D2d. In most Fe4S2+
core structures, this distortion involves a tetragonal compression, which leaves four short and eight long Fe-S bonds.
Complexes with non-S-donor peripheral ligands have been prepared and studied. The halide complexes Fe4S4X42- (X = CI-, Br-, I-)
have been prepared, and serve as useful starting points for further syntheses.129-133 The complex Fe4S4(OC6H5)42- can be
prepared134 from the tetrachloride (or tetrathiolate) thiocubane by reaction with NaOC6H5 (or HOC6H5). There are a few examples
of synthetic Fe4S42+ cores in which the peripheral ligands are not identical. For example, Fe4S4Cl2(OC6H5)22- and
Fe4S4Cl2(SC6H5)22- have structures characterized by D2d symmetry.135 The complexes Fe4S4(SC6H5)2[S2CN(C2H5)2]2- and
Fe4S4(SC6H4OH)42- are similarly asymmetric, containing both four- and five-coordinate iron.136-138 The presence of five-
coordinate iron in the Fe4S4 cluster is notable, since it offers a possible mode of reactivity for the cluster wherever it plays a
catalytic role (such as in aconitase). Complexes with Fe4Se2+ and Fe4Te42+ cores have also been prepared.138c,d
One structural analysis of Fe4S4(SC6H5)43-, which contains the reduced Fe4S4+ core, revealed a tetragonal elongation139 in the solid
state. In contrast, analysis of Fe4S4(SCH2C6H5)43- revealed a distorted structure possessing C2v symmetry.102 It would appear that
the Fe4S4+ clusters maintain the thiocubane structure, but are nevertheless highly deformable. Interestingly, when the solidstate C2v
structure, Fe4S4(SCH2C6H5)43-, is investigated in solution, its spectroscopic and magnetic behavior change to resemble closely
those of the Fe4S4(SC6H5)43- cluster,140 which does not change on dissolution. The simplest interpretation assigns the elongated
tetragonal structure as the preferred form for Fe4S4+ cores with deformation of sufficiently low energy that crystal packing (or, by
inference, protein binding forces) could control the nature of the distortions in specific compounds.128 The elongated tetragonal
structure has four long and eight short bonds in the core structure. The terminal (thiolate) ligands are 0.03-0.05 Å longer in the
reduced structure, consistent with the presence of 3Fe(ll) and 1Fe(III) in the reduced form, compared to 2Fe(II) and 2Fe(III) in the
oxidized form. There is no evidence for any valence localization.128
The oxidized Fe4S43+ core defied isolation and crystallization in a molecular complex prior to the use of sterically hindered thiolate
ligands. With 2,4,6 tris(isopropyl)phenylthiolate, the Fe4S4L4- complex could be isolated and characterized.141 The structure is a
tetragonally compressed thiocubane with average Fe-S and Fe-SR distances 0.02 and 0.04 Å shorter than the corresponding
distances in the Fe4S4L42- complex. Again, there is no evidence for Fe inequivalence or more profound structural distortion in this
3Fe(III)-1Fe(II) cluster. Clearly, the Fe4S4 clusters have highly delocalized bonding.
Evidence from model systems using sterically hindered thiolate ligands indicates the existence of an Fe4S44+, i.e., all-ferric fully
oxidized cube.142 The existence of the complete series Fe4S4[(Cy)3C6H2S]4n (Cy =cyclohexyl; n = 0, -1, -2, -3) is implied by
reversible electrochemical measurements. Clearly, five different states of the Fe4S4 core—including the (at least) transient fully
oxidized state and the all-ferrous fully reduced state—may have stable existence. Although only the central three states have been
shown to exist in biological contexts, one must not rule out the possible existence of the others under certain circumstances.
Recently, specifically designed tridentate ligands have been synthesized that bind tightly to three of the four Fe atoms in the
thiocubane structure.143,143a,b The remaining Fe atom can then be treated with a range of reagents to produce a series of subsite-
differentiated derivatives and variously bridged double-cubane units. These derivatives illustrate the potential to synthesize
complexes that mimic the more unusual features of Fe4S4 centers that are bound specifically and asymmetrically to protein sites.
The recently synthesized complex ion [(Cl3Fe4S4)2S]4-, containing two Fe4S4 units bridged by a single S2- ligand, illustrates the
potential coupling of known clusters into larger aggregates.143c
The model-system work has made an important contribution to our understanding of the Fe4S4 centers. The existence of three
states, the exchange of ligands, the redox properties, the metrical details of the basic Fe4S4 unit, and the subtleties of structural
distortion can each be addressed through the study of models in comparison with the native proteins.
Core Extrusion/Cluster Displacement Reactions
Synthetic model-system work led to the realization that the cluster cores can exist outside the protein and undergo relatively facile
ligand-exchange reactions.128 This behavior of the purely inorganic complexes allowed core extrusion reactions128,144 to be
developed. The basic assumption behind these reactions is that the cluster core retains its integrity when it is substituted by low-
MW thiolates, especially aryl thiolates, which replace the cysteinyl ligands that bind it to the protein. In order to free the cluster
from the protein, one must at least partially denature the protein, usually by using ~80 percent aqueous solution of a polar aprotic
solvent, such as DMSO or HMPA. The resulting inorganic clusters can be identified and quantified by measurement of their
characteristic electronic absorption or NMR spectra. An alternative approach involves transferal of the unknown cluster in question
to an apoprotein that binds a cluster of known type.145
Since the 1Fe, 2Fe, and 4Fe sites are each usually bound to the protein by four cysteine residues, it is perhaps not surprising that
there have been reports58 of interconversion of cluster types bound to a given protein. Specifically, in 90 percent aqueous DMSO,
the single Fe site in rubredoxin from C. pasteurianum is converted to an Fe4S4 cluster by the addition of sodium sulfide, ferrous
chloride, and ferric chloride in ratio 4:2:1. Presumably the spacing and geometric disposition of the cysteines are suitable to bind a
single Fe or the Fe4S4 cluster, which is readily formed under the reaction conditions. Another example of cluster rearrangement
involves the three-iron center discussed below that does not extrude as an Fe3S4 center. Rather, at least under certain conditions,
the Fe3Sx center rearranges to form Fe2S2 centers.146 The facile interconversion of the Fe clusters demonstrated the lability of Fe-S
systems, and indicates that caution must be exercised in interpreting the results of cluster-displacement reactions.
Fe3S4 Centers
Three-iron centers are a comparatively recent finding,119,146 and the full scope of their distribution is not yet known. Although they
have now been confirmed in dozens of proteins, it often remains uncertain what physiological role these centers play. Indeed, since
Fe3S4 centers can be produced as an artifact upon oxidation of Fe4S4 centers, it has been suggested that 3Fe centers may not be
truly physiological, and could be side products of aerobic protein isolation. This caveat notwithstanding, the 3Fe sites are being
found in more and more proteins and enzymes. Their physiological raison d' être may be more subtle than that of their 1, 2, and
4Fe cousins; we should certainly try to find out more about them. Some proteins containing Fe3S4 centers are listed in Table 7.1.
The 3Fe center was first recognized147 in the protein ferredoxin I from the anaerobic nitrogen-fixing bacterium Azotobacter
vinelandii. The protein is called Av FdI for short. It is instructive to sketch historically the evolution of our understanding of this
protein. Av ferredoxin I was reported to have 6 to 8 Fe atoms and was first thought to resemble the clostridial 8Fe ferredoxins.
However, unlike the clostridial protein, the Av FdI clusters appeared to have two quite different redox couples at +320 and -420
mV. Although it might have been thought that this protein contained one HiPIP-type and one Fd- or "ferredoxin"-type Fe4S4
cluster, the protein as isolated had an EPR signal with g = 2.01, which differed significantly (Figure 7.6) from that of an oxidized
HiPIP or a reduced Fd.148 Cluster extrusion reactions also seemed to indicate the presence of an unusual cluster type.149
Fortunately, the protein was crystallized, and could be studied by x-ray diffraction. Unfortunately, the initial conclusions150 and
subsequent revisions151,152 of the crystal-structure analysis have proven to be wrong, teaching us in the process that protein x-ray
crystallography, taken alone, does not always provide definitive results. Specifically, the first crystallographic report suggested the
presence of a conventional Fe4S4 cluster and a smaller packet of electron density that was assigned as a 2Fe-2S center.150 However,
upon further refinement, and following the formulation of the 3Fe center by Mössbauer spectroscopy,147 a 3Fe-3S center was
identified and refined.151,152 The "refined" Fe3S3 center was a six-membered alternating iron-sulfide ring with an open, almost flat,
twistedboat conformation (Figure 7. 14). The Fe-Fe separation of 4.1 Å and the structural type was unprecedented, and did not
agree with the results of resonance Raman spectroscopy,153 with x-ray absorption spectroscopy on the native protein or on samples
from which the Fe4S4 center was removed,103 or even with stoichiometry, which eventually led to the reformulation154 of the
cluster as Fe3S4. The x-ray absorption studies (EXAFS) clearly led to the assignment of a 2.7-Å Fe-Fe distance for the 3Fe
cluster.103
Figure 7.14 - Fe3Sn structures: (A) open Fe3S3 structure proposed from initial x-ray studies (now shown to be in error); (B) the
thiocubane fragment structure believed present in most Fe3S4 proteins; (C) open Fe3S4 structure (not found to date).
In parallel with the studies on Av FdI, two additional proteins played key roles in the resolution of the nature of the Fe3 cluster.
These are FdII from Desulfovibrio gigas and aconitase from beef heart. Each contains (under certain conditions) only Fe3S4 sites,
thus enabling more definitive structural, stoichiometric, and spectral information to be acquired. Studies on these proteins using
EXAFS,155 Mössbauer,52,156,157 EPR,146 and resonance Raman (to which we will return briefly) clearly favor the closed structure
shown in Figure 7.14C. Indeed, x-ray crystallography on aconitase by the same group that did the initial x-ray work on Av FdII
revealed the compact structure in agreement with the spectroscopy.20
In 1988 the structural error in the crystallography of Av FdI was found by two groups, and a new refinement in a corrected space
group led to a structure in agreement with the spectroscopy.111,112 The Fe3S4 cluster has the apoFe thiocubane structure, with each
iron atom bound to the protein by a single cysteinyl thiolate. Clearly, even x-ray crystallography is potentially fallible, and its
findings must be critically integrated with the data from other techniques in arriving at full structural definition of metalloenzyme
sites.
The studies on the ferredoxins from D. gigas present an interesting lesson on the lability of the Fe-S cluster systems. Two distinct
proteins from D. gigas, FdI and FdII, contain the same polypeptide chain (6 kDa) in different states of aggregation,158,159 Whereas
FdI is a trimer containing three Fe4S4 clusters, FdII is a tetramer that contains four Fe3S4 clusters. The ferredoxins differ in their
redox potentials and appear to have different metabolic functions in D. gigas. The oxidation of D. gigas FdI with Fe(CN)63- leads
to FdII, and treatment of FdII with iron salts leads to FdI. The D. gigas system reveals the lability and interconvertibility of Fe-S
clusters. The recently reported160 crystal structure of D. gigas FdII shown in Figure 7.15 confirms the partial (apoFe) thiocubane
Fe3S4 center. The iron atoms are ligated by three cysteinyl residues from protein side chains. The cube missing an iron is now
firmly established as a viable structural type.
Figure 7.15 - The x-ray crystal structure of D.gigas FdII, illustrating the Fe4S4 and Fe3S4 centers in this protein.160
The aconitase system presents yet another fascinating story.159a Aconitase is a key enzyme in the Krebs cycle, catalyzing the
conversion of citrate and isocitrate through the intermediacy of cis-aconitate, as shown in Equation (7.6).
(7.6)
2+
This is a hydrolytic nonredox process, and for some time it was thought that aconitase was a simple Fe protein wherein the
ferrous iron was involved in the Lewis-acid function of facilitating the hydrolytic reaction. Indeed, aconitase is inactive when
isolated from mitochondria, and requires the addition of Fe2+ to achieve activity.
Surprisingly, the isolated aconitase was found by analysis and Mossbauer spectroscopy to possess an Fe3S4 site in its inactive
form.161 Low-resolution crystallographic study supports the presence of an apo-Fe thiocubane, Fe3S4 structure in aconitase.162
Resonance Raman163 and EXAFS103,155 studies clearly fingerprint the Fe3S4 cluster. The current hypothesis for aconitase activation
involves the Fe3S4 thiocubane fragment reacting with Fe2+ to complete the cube, which is the active form of the enzyme.164 Recent
crystallographic studies113 confirm the presence of a complete cube in the activated aconitase. The dimensions and positioning of
the Fe3S4 and Fe4S4 centers in the cube are virtually identical. The added Fe2+ iron atom is ligated by a water (or hydroxide) ligand,
consistent with the absence of any cysteine residues near the exchangeable iron. Since this water (or a hydroxide) is also present in
the Fe3S4 system, one wonders whether a small ion such as Na+ might be present in the Fe3S4 aconitase system.
Questions of detailed mechanism for aconitase remain open. ENDOR spectroscopy165 shows that both substrate and water (or OH-)
can bind at the cluster. Does one of its Fe-atom vertices play the Lewis-acid role necessary for aconitase activity? Is the Fe3S4 ⇌
Fe4S4 conversion a redox- or iron-activated switch, which works as a control system for the activity of aconitase? These and other
questions will continue to be asked. If aconitase is indeed an Fe-S enzyme with an iron-triggered control mechanism, it may be
representative of a large class of Fe3/Fe4 proteins. Other hydrolytic enzymes containing similar Fe-S centers have recently been
reported.166,166a
Spectroscopically, the Fe3S4 center is distinct and clearly distinguishable from 1Fe, 2Fe, and 4Fe centers. The center is EPR-active
in its oxidized form, displaying a signal (Figure 7.6) with g = 1.97, 2.00, and 2.06 (D. gigas FdII).158 The Mössbauer spectrum
(Figure 7.7) shows a single quadrupole doublet with ΔQ = 0.53 nm/s and isomer shift of 0.27 nm, suggesting the now familiar
highspin iron electronic structure.158,159 In its reduced form, the center becomes EPR-silent, but the Mössbauer spectrum now
reveals two quadrupole doublets of intensity ratio 2:1. The suggestion of the presence of a 3Fe center was first made based on this
observation.147 The picture of the reduced Fe3S4 state that has emerged involves a coupled, delocalized Fe2+/Fe3+ unit responsible
for the outer doublet, with a single Fe3+ unit responsible for the inner doublet of half the intensity. The oxidized state contains all
Fe3+ ions, which are coupled in the trinuclear center.
EXAFS studies were consistent and unequivocal in finding an Fe-Fe distance of ~2.7 Å in all putative Fe3S4 proteins.103,155,167
Resonance Raman spectra compared with those of other proteins and of model compounds with known structures168,169 for other
metals also favored the structure of Figure 7.14B. Clearly, what has been termed the spectroscopic imperative170 has been crucial in
the successful elucidation of the 3Fe structure. An interesting excursion has led to isolation of what are presumed to be ZnFe3S4,
CoFe3S4, and NiFe3S4 thiocubane structures by adding Zn2+, Co2+, or Ni2+, respectively, to proteins containing reduced Fe3S4
cores.170a,b,c These modified proteins provide interesting electronic structural insights and, potentially, new catalytic capabilities.
Fe3 Model Systems

To date, the Fe3S4 center is the only structurally characterized biological iron-sulfide center that does not have an analogue in
synthetic Fe chemistry. In fact, the closest structural analogue21,170d is found in the Mo3S44+ or V3S43+ core in clusters such as
Mo3S4(SCH2CH2S)32-, whose structure is shown in Figure 7.16.
Figure 7.16 - The x-ray crystal structure of Mo3S4(SCH2CH2S)32-. (From Reference 10a.)
The resonance Raman spectrum169 of this complex bears a close resemblance to that of the D. gigas ferredoxin II. Since the
vibrational bands responsible for the resonance Raman spectrum are not strongly dependent on the electronic properties, it is not
surprising that an analogue with a different metal can be identified using this technique.
In synthetic Fe chemistry, although there is no precise structural analogue, it is instructive to consider three types of trinuclear and
one hexanuclear center in relation to the three-iron biocenter.
The trinuclear cluster Fe3S[(SCH2)C6H4]32- is prepared171,172 by the reaction of FeCI3, C6H4(CH2SH)2, Na+OCH3-, and p-CH3-
C6H4-SH in CH3OH. As shown in Figure 7.17A, this cluster has, like the biocluster, a single triply bridging sulfide ion but, unlike
the biocluster, it uses the sulfur atoms of the ethane 1,2-dithiolate as doubly bridging, as well as terminal, groups. The inorganic
ring Fe3(SR)3S63- (X = CI, Br) has a planar Fe3(SR)3 core, which resembles the now-discredited structure for Av FdI173 (Figure 7.
14A).
Figure 7.17 - The x-ray crystal structures of trinuclear Fe complexes: (A) Fe3S4(SR)43-; (B) Fe3S[(SCH2)2C6H4]32-. (Data from
References 171, 172, 174, 175.)
The complex Fe3S4(SR)43- is prepared174,175 by reaction of Fe(SR)42- with sulfur. The x-ray-determined structure reveals two
tetrahedra sharing a vertex with the linear Fe-Fe-Fe array shown in Figure 7.17B. This complex has distinctive EPR, Mössbauer,
and NMR spectra that allow it to be readily identified174,175,175a Interestingly, after the complex was reported, a study of
(denatured) aconitase at high pH (>9.5) revealed that the thiocubane fragment Fe3S4 site in that enzyme rearranged to adopt a
structure that was spectroscopically almost identical with that of the linear complex.176 Although the state may not have any
physiological significance, it does show that Fe-S clusters different from the common (conventional) ones already discussed could
be important in proteins under certain physiological conditions or in certain organisms; i.e., iron centers first identified
synthetically may yet prove to be present in biological systems.
A synthetic cluster that displays features related to the biological Fe3S4 cluster is the hexanuclear cluster Fe6S9(SR)24- shown in
Figure 7.18. This cluster contains two Fe3S4 units bridged through their diiron edges by a unique quadruply bridging S2- ion (μ - 4
S2-) and by two additional μ S2- bridges. The inability of synthetic chemists to isolate an Fe3S4 analogue may indicate that in
2
proteins this unit requires strong binding. Significant sequestration by the protein may be needed to stabilize the Fe3S4 unit against
oligomerization through sulfide bridges or, alternatively, rearrangement to the stable Fe4S4 center.
Figure 7.18 - The x-ray crystal structure176a,b of Fe6S9(SR)24- .
Fe-S Chemistry: Comments and New Structures

The first successful model system for an iron-sulfur protein was an analogue of the Fe4S4 system, i.e., the system with the largest
presently established biological Fe cluster. The reactions used to synthesize the cluster shown in Figure 7.13 are said to involve
self-assembly, meaning that starting materials are simply mixed together, and thermodynamic control causes the cluster to assemble
in its stable form. Interestingly, the Fe4S4-containing proteins, such as those of C. pasteurianum, are considered to be among the
most ancient of proteins. Perhaps on the anaerobic primordial Earth, Fe-S clusters self-assembled in the presence of protein ligands
to form the progenitors of the modem ferredoxins.
Much progress has been made in synthetic chemistry, and it is clear that both understanding and control of Fe-S chemistry are
continuing to grow. New preparations for known clusters continue to be found, and new clusters continue to be synthesized,
Although many of the new clusters appear to be abiological, we should not ignore them or their potential. They add to our
understanding of Fe-S chemistry in general, and serve as starting points in the study of heteronuclear clusters, There is also the
distinct possibility that one or more of these synthetic clusters represent an existing biological site that has not yet been identified in
an isolated system.
Among the "nonbiological" structures that have been synthesized are complexes with Fe6S63+/2+ cores177,178 including the
thioprismanes,108,109,177-179 the octahedron/cube Fe6S83+ cores,180,181 the Fe6S92- cores176a,b discussed above, the adamantane-like
Fe6(SR)104- complexes related to Zn and Cu structures in metallothioneins,182 basket Fe6S62+/Fe6S6+ cores,182a,b,c,d monocapped
prismatic Fe7S63+ cores,183 the cube/octahedron Fe8S65+ cores,179 and the circular Na+-binding Fe18S3010- unit.183a,b Representative
ions are shown in Figure 7.19. Some of these cores are stabilized by distinctly nonbiological phosphine ligands. Nevertheless, one
should not a priori eliminate any of these structures from a possible biological presence. Indeed, recently a novel, apparently six-
iron protein from Desulfovibio gigas has been suggested183c to have the thioprismane core structure first found in model
compounds.
Figure 7.19 - Structures of "to date nonbiological" Fe-S clusters: (A) the thioprismane structure;177 (B) basket-handle structure;182a
(C) monocapped prismatic structure;183 (D) adamantane structure;182 (E) circular Fe18S3010- core unit.183a,b
Detection of Fe-S Sites

Several recent reviews have concentrated on the ways in which the various Fe-S centers can be identified in newly isolated
proteins.5,6,184 It is instructive to summarize the central techniques used in the identification of active sites. Optical spectra are
usually quite distinctive, but they are broad and of relatively low intensity, and can be obscured or uninterpretable in complex
systems. MCD spectra can give useful electronic information, especially when the temperature dependence is measured. EPR
spectra, when they are observed, are distinctive, and are usually sufficiently sharp to be useful even in complex systems.
Mössbauer and resonance Raman spectroscopies have each been applied with good effect when they can be deconvoluted, and
NMR and magnetic susceptibility have given important information in some simple, lower-MW protein systems. X-ray absorption
spectra, especially EXAFS, give accurate Fe-S and Fe-Fe distances when a single type of Fe atom is present. Analytical and
extrusion data complement the spectroscopic and magnetic information. Extrusion data must be viewed with considerable caution,
because of possible cluster-rearrangement reactions. Even x-ray crystallography has led to incorrect or poorly refined structures. In
general, no one technique can unequivocally identify a site except in the very simplest systems, and there is continued need for
synergistic and collaborative application of complementary techniques to a given system.
Redox Behavior
Figure 7.20 shows the ranges of redox behavior known for Fe-S centers. Clearly, the Fe-S systems can carry out low-potential
processes. The rubredoxins cover the mid-potential range, and the HiPIPs are active in the high-potential region. The lack of
extensive Fe-S proteins in the positive potential region may reflect their instability under oxidizing conditions and their preemption
by Mn, Cu, or heme-iron sites (such as in cytochrome c), which function in this region.
Figure 7.20 - A schematic diagram of the redox potential of the various FeS centers in comparison with other known redox centers.
SECTION OVERVIEW
6.8: Overview of Hemoglobin and Myoglobin is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
Hemoglobin:
1st. protein whose molecular weight was determined
1st protein to be assigned a specific function - dioxygen transport
has a prosthetic group (non-amino acid) heme group (protoporphyrin IX with a ferrous ion) covalently attached to the protein.
The heme group binds dioxygen.
1st protein in which a point mutation (single base pair charge) causes a single amino acid change in the protein, marking the
start of molecular medicine
1st protein with high resolution x-ray structure
theory for dioxygen binding explain control of enzyme activity
the binding of dioxygen is regulated by binding of H+, CO2, and bisphosphoglcyerate which bind to sites (allosteric) distant
from oxygen binding site.
crystals of deoxy-Hb shatter on binding dioxygen, indicating significant conformational changes on binding.
Figure 6.8.1.1. The heme group contains protoporphyrin IX, with four tetrapyrrole rings linked by methene bridges. Attached to
the tetrapyrrole structure are four methyl, two vinyl, and two proprionate groups. These can be arranged in 15 ways, only one (IX)
occurs in biological systems.
The heme fits into a hydrophobic crevice in the proteins with the proprionate groups exposed to solvent. The Fe2+ ion is
coordinated to 4 N's on the 4 pyrrole rings, The 5th ligand is a supplied by proximal His (the 8th amino acid on helix F) of the
protein. In the absence of dioxygen, the 6 ligand is missing. and the geometry of the complex is square pyramidal with the Fe above
the plane of the heme ring. A distal His (E7) is on the opposite side of the heme ring, but too far to coordinate with the Fe. When
dioxgen binds, it occupies the 6th coordination site and pulls the Fe into the plane of the ring, leading to octahedral geometry. CO,
NO, and H2S also bind to the 6th site, but with higher affinity than dioxygen, which can lead to CO poisoning. The distal His keeps
these ligands (including dioxygen) bound in a bent, non-optimal geometry. This minimizes the chances of CO poisoning.
Myoglobin
Myoglobin is a relatively small protein that contains 150 amino acids.
Mb is extremely compact, and consists of 75% alpha helical structure.
The interior amino acids are almost entirely nonpolar. The only polar amino acids found completely buried are the two His
(proximal and distal) found at the active site of dioxygen binding.
Figure 6.8.1.2. The skeletal structure of the heme prosthetic group found within the structure of myoglobin. The porphyrin ring
contains four pyrrole nitrogens bound to a ferrous (Fe(II)) ion center. There are six coordination sites in the Fe(II) ion; four are
occupied by the pyrrole nitrogens, one is occupied by a proximal histidine, one site can be occupied by a dioxygen molecule (not
shown).
Difference between Hb and Mb
Hb is a tetramer of two α and two β subunits held together by IMF's (an example of quarternary protein structure), and 4 bound
hemes, each of which can bind a dioxygen. In a fetus, two other subunits make up Hb (two zeta - ζand two epsilion - ε subunits -
analogous to the two αand two β subunits, respectively). This changes in fetuses to two α and two γ subunits. Fetal Hb has higher
affinity for dioxygen than adult Hb. Mb is a single polypeptide chains which has higher affinity for dioxygen than Hb.
The α and β chains are similar to Mb, which is unexpected since only 24 of 141 residues in the α and β chains of Hb are identical to
amino acids in Mb. This suggests that different sequences can fold to similar structures. The globin fold of Mb and each chain of
Hb is common to vertebrates and must be nature's design for dioxygen carriers. A comparison of the sequence of Hb from 60
species show much variability of amino acids, with only 9 identical amino founds. These must be important for structure/function.
All internal changes are conservative (e.g. changing a nonpolar for a nonpolar amino acid). Not even Pro's are conserved,
suggesting there are different ways to break helices. The two active site His are conserved, as is Gly B6 (required for a reverse
turn).
This page titled 6.8.1: Myoglobin, Hemoglobin, and their Ligands is shared under a CC BY-NC-SA license and was authored, remixed, and/or
curated by Henry Jakubowski.
Oxygen Transport
Many microorganisms and most animals obtain energy by respiration, the oxidation of organic or inorganic molecules by O2. At
25°C, however, the concentration of dissolved oxygen in water in contact with air is only about 0.25 mM. Because of their high
surface area-to-volume ratio, aerobic microorganisms can obtain enough oxygen for respiration by passive diffusion of O2 through
the cell membrane. As the size of an organism increases, however, its volume increases much more rapidly than its surface area,
and the need for oxygen depends on its volume. Consequently, as a multicellular organism grows larger, its need for O2 rapidly
outstrips the supply available through diffusion. Unless a transport system is available to provide an adequate supply of oxygen for
the interior cells, organisms that contain more than a few cells cannot exist. In addition, O2 is such a powerful oxidant that the
oxidation reactions used to obtain metabolic energy must be carefully controlled to avoid releasing so much heat that the water in
the cell boils. Consequently, in higher-level organisms, the respiratory apparatus is located in internal compartments called
mitochondria, which are the power plants of a cell. Oxygen must therefore be transported not only to a cell but also to the proper
compartment within a cell.
Myoglobin and Hemoglobin

Myoglobin is a relatively small protein that contains 150 amino acids. The functional unit of myoglobin is an iron–porphyrin
complex that is embedded in the protein (Figure 4.2.1). In myoglobin, the heme iron is five-coordinate, with only a single histidine
imidazole ligand from the protein (called the proximal histidine because it is near the iron) in addition to the four nitrogen atoms of
the porphyrin. A second histidine imidazole (the distal histidine because it is more distant from the iron) is located on the other side
of the heme group, too far from the iron to be bonded to it. Consequently, the iron atom has a vacant coordination site, which is
where O2 binds.
Figure 6.8.2.1. The Structure of Deoxymyoglobin, Showing the Heme Group. The iron in deoxymyoglobin is five-coordinate,
with one histidine imidazole ligand from the protein. Oxygen binds at the vacant site on iron.
In the ferrous form (deoxymyoglobin), the iron is five-coordinate and high spin. Because high-spin Fe2+ is too large to fit into the
“hole” in the center of the porphyrin, it is about 60 pm above the plane of the porphyrin. When O2 binds to deoxymyoglobin to
form oxymyoglobin, the iron is converted from five-coordinate (high spin) to six-coordinate (low spin; Figure 4.2.2). Because low-
spin Fe2+ and Fe3+ are smaller than high-spin Fe2+, the iron atom moves into the plane of the porphyrin ring to form an octahedral
complex. The O2 pressure at which half of the molecules in a solution of myoglobin are bound to O2 (P1/2) is about 1 mm Hg (1.3 ×
10−3 atm).
Figure 6.8.2.2. Oxygen Binding to Myoglobin and Hemoglobin. (a) The Fe2+ ion in deoxymyoglobin is high spin, which makes
it too large to fit into the “hole” in the center of the porphyrin. (b) When O2 binds to deoxymyoglobin, the iron is converted to low-
spin Fe3+, which is smaller, allowing the iron to move into the plane of the four nitrogen atoms of the porphyrin to form an
octahedral complex.
Hemoglobin consists of two subunits of 141 amino acids and two subunits of 146 amino acids, both similar to myoglobin; it is
called a tetramer because of its four subunits. Because hemoglobin has very different O2-binding properties, however, it is not
simply a “super myoglobin” that can carry four O2 molecules simultaneously (one per heme group). The shape of the O2-binding
curve of myoglobin can be described mathematically by the following equilibrium:
M b O2 ⇌ M b + O2 (6.8.2.1)
[M b] [ O2 ]
Kdiss = (6.8.2.2)
[M b O2 ]
The O2-binding curve of hemoglobin is S shaped (Figure 4.2.3). As shown in the curves, at low oxygen pressures, the affinity of
deoxyhemoglobin for O2 is substantially lower than that of myoglobin, whereas at high O2 pressures the two proteins have
comparable O2 affinities. The physiological consequences of unusual S-shaped O2-binding curve of hemoglobin are enormous. In
the lungs, where O2 pressure is highest, the high oxygen affinity of deoxyhemoglobin allows it to be completely loaded with O2,
giving four O2 molecules per hemoglobin. In the tissues, however, where the oxygen pressure is much lower, the decreased oxygen
affinity of hemoglobin allows it to release O2, resulting in a net transfer of oxygen to myoglobin.
Figure 4.2.3: The O2-Binding Curves of Myoglobin and Hemoglobin. Plots of Y (fractional saturation) vs L (pO2) are hyperbolic
for Mb, but sigmoidal for Hb, suggesting cooperative binding of oxygen to Hb (binding of the first oxygen facilitates binding of
second, etc).
The S-shaped O2-binding curve of hemoglobin is due to a phenomenon called cooperativity, in which the affinity of one heme for
O2 depends on whether the other hemes are already bound to O2. Cooperativity in hemoglobin requires an interaction between the
four heme groups in the hemoglobin tetramer, even though they are more than 3000 pm apart, and depends on the change in
structure of the heme group that occurs with oxygen binding. The structures of deoxyhemoglobin and oxyhemoglobin are slightly
different, and as a result, deoxyhemoglobin has a much lower O2 affinity than myoglobin, whereas the O2 affinity of
oxyhemoglobin is essentially identical to that of oxymyoglobin. Binding of the first two O2 molecules to deoxyhemoglobin causes
the overall structure of the protein to change to that of oxyhemoglobin; consequently, the last two heme groups have a much higher
affinity for O2 than the first two.
The affinity of Hb, but not of Mb, for dioxygen depends on pH. This is called the Bohr effect, after the father of Neils Bohr, who
discovered it.
Figure 4.2.4: The Bohr Effect
Decreasing pH shifts the oxygen binding curves to the right (to decreased oxygen affinity). Increased [H+] will cause protonation of
basic side chains. In the pH range for the Bohr effect, the mostly likely side chain to get protonated is His (pKa around 6), which
then becomes charged. The mostly likely candidate for protonation is His 146 (on the β chain - CH3) which can then form a salt
bridge with Asp 94 of the β(FG1) chain. This salt bridge stabilizes the positive charge on the His and raises its pKa compared to the
oxyHb state. Carbon dioxide binds covalently to the N-terminus to form a negatively charge carbamate which forms a salt bridge
with Arg 141 on the alpha chain. BPG, a strongly negatively charged ligand, binds in a pocket lined with Lys 82, His 2, and His
143 (all on the beta chain). It fits into a cavity present between the β subunits of the Hb tetramer in the T state. Notice all these
allosteric effectors lead to the formation of more salt bridges which stabilize the T or deoxy state. The central cavity where BPG
binds between the β subunits become much smaller on oxygen binding and the shift to the oxy or R state. Hence BPG is extruded
from the cavity.
The binding of H+ and CO2 helps shift the equilibrium to deoxyHb which faciliates dumping of oxygen to the tissue. It is in
respiring tissues that CO2 and H+ levels are high. CO2 is produced from the oxidation of glucose through glycolysis and the Krebs
cycle. In addition, high levels of CO2 increase H+ levels through the following equilibrium:
+ −
H2 O + CO2 ⇌ H2 CO3 ⇌ H + HCO (6.8.2.3)
3
In addition, H+ increases due to production of weak acids such as pyruvic acid in glycolysis .
Hb, by binding CO2 and H+, in addition to O2, serves an additional function: it removes excess CO2 and H+ from the tissues where
they build up. When deoxyHb with bound H+ and CO2 reaches the lungs, they leave as O2 builds and deoxyHb is converted to
oxyHb.
Contributors
Prof. Henry Jakubowski (College of St. Benedict/St. John's University)
Contributed by OpenStax, General Biology at OpenStax CNX
Dr. Kevin Ahern and Dr. Indira Rajagopal (Oregon State University)
6.8.2: Oxygen Transport by the Proteins Myoglobin and Hemoglobin is shared under a not declared license and was authored, remixed, and/or
curated by LibreTexts.
Index
A chiral dissociation
achiral 5.5.3: Stereoisomers - Optical Isomerism in 6.5: Dissociative Ligand Substitution
Transition Metal Complexes dissociation constant
5.5.3: Stereoisomers - Optical Isomerism in
Transition Metal Complexes chiral center 4.2: Lewis Acids and Bases
Acidity 5.5.3: Stereoisomers - Optical Isomerism in Dissociative Ligand Substitution
Transition Metal Complexes
4.3: Acidity of the Hexaaqua Ions 6.5: Dissociative Ligand Substitution
Cis isomers Dodecahedron
active site
5.5.2: Structural Isomers - Geometric Isomerism in
6.2: Introduction to Amino Acids and Proteins 5.3: Coordination Numbers and Geometry
ambidentate ligands complex ion Dodecahedron Geometry
5.5.4: Structural Isomers - Linkage Isomerism in 5.3: Coordination Numbers and Geometry
Transition Metal Complexes 4.3: Acidity of the Hexaaqua Ions Drago and Wayland's EC Model
Amino Acids compression 4.5: Quantitative Measures of Hardness and Softness
6.2: Introduction to Amino Acids and Proteins 5.6.5: Jahn-Teller Distortions
ammine ligands conservative forces E
5.8: Ligand Exchange Reactions (Thermodynamics) 1.2: Rutherford's Atom electromagnetic spectrum
antibonding coordinate compound 5.6.2: Colors of Coordination Complexes
2.5.5: Molecular Orbital Diagrams 5.5.3: Stereoisomers - Optical Isomerism in electron ionization
aqua ligands Transition Metal Complexes 1.1: Mass Spectrometry
5.8: Ligand Exchange Reactions (Thermodynamics) coordinate covalent bond electronegativity (Mulliken)
Associative Substitution 4.2: Lewis Acids and Bases 4.5: Quantitative Measures of Hardness and Softness
6.4: Associative Ligand Substitution coordination complex Electronic Configurations
5.6.2: Colors of Coordination Complexes 5.6.5: Jahn-Teller Distortions
B Coordination Complexes electrospray ionization
base peak 5.6.2: Colors of Coordination Complexes 1.1: Mass Spectrometry
1.1: Mass Spectrometry coordination compounds Elongation
bent 5.1: Introduction to Coordination Chemistry 5.6.5: Jahn-Teller Distortions
2.3: The VSEPR Model coordination number Enzymes
Berry pseudorotation 5.3: Coordination Numbers and Geometry 6.2: Introduction to Amino Acids and Proteins
6.4: Associative Ligand Substitution Coulombic force
Bicapped square antiprism geometry 1.2: Rutherford's Atom F
5.3: Coordination Numbers and Geometry crystal field splitting fluorite (structure)
birefringence 5.6.3: Crystal Field Stabilization Energy
3.14: Structures Related to NaCl and NiAs crystal field stabilization energy formation constant
Bohr Atom 5.6.3: Crystal Field Stabilization Energy
1.2: Rutherford's Atom crystal field theory Formation constants
Bohr model 5.6: Crystal Field Theory
1.2: Rutherford's Atom 5.6.2: Colors of Coordination Complexes
bond angle 6.5: Dissociative Ligand Substitution G
2.3: The VSEPR Model Cube geometric isomers
bond order 5.3: Coordination Numbers and Geometry 5.5.2: Structural Isomers - Geometric Isomerism in
2.5.5: Molecular Orbital Diagrams Cube geometry Transition Metal Complexes
Bond Polarity 5.3: Coordination Numbers and Geometry
2.5.1: Molecular Shape and Molecular Polarity cuboctahedron geometry H
bonding molecular orbital 5.3: Coordination Numbers and Geometry Hexaaqua Ions
Bragg equation D Hexagonal bipyramid
debye (unit) 5.3: Coordination Numbers and Geometry
2.5.1: Molecular Shape and Molecular Polarity Hexagonal bipyramid geometry
C diamagnetic 5.3: Coordination Numbers and Geometry
Capped octahedron 2.5.5: Molecular Orbital Diagrams Hexagonal planar Geometry
5.3: Coordination Numbers and Geometry diamagnetic anisotropy 5.3: Coordination Numbers and Geometry
Capped trigonal prism 2.8.5: The Basis for Differences in Chemical Shift high spin
5.3: Coordination Numbers and Geometry diamagnetic deshielding 5.6.3: Crystal Field Stabilization Energy
chelate effect 2.8.5: The Basis for Differences in Chemical Shift 5.6.5: Jahn-Teller Distortions
5.8: Ligand Exchange Reactions (Thermodynamics) diamagnetic shielding hybrid orbital
Chemical Equivalence 2.8.5: The Basis for Differences in Chemical Shift 2.4: Hybrid Orbitals
2.8.2: Chemical Equivalence dipole moment hybridization
chemical shift 2.3: The VSEPR Model 2.4: Hybrid Orbitals
2.8.5: The Basis for Differences in Chemical Shift 2.5.1: Molecular Shape and Molecular Polarity hydrate isomer
Dissocative Substitution 5.5.1: Structural Isomers - Ionization Isomerism in
6.5: Dissociative Ligand Substitution Transition Metal Complexes
hydration Mirror Image Method proteomics
5.6.3: Crystal Field Stabilization Energy 5.5.3: Stereoisomers - Optical Isomerism in 1.1: Mass Spectrometry
I Molecular Geometry R
Ionic Radius radical cation
molecular ion peak 1.1: Mass Spectrometry
ionization isomerism radius
5.5.1: Structural Isomers - Ionization Isomerism in
molecular ions 4.3: Acidity of the Hexaaqua Ions
Transition Metal Complexes 1.1: Mass Spectrometry
rate law
isomerism molecular orbital 6.4: Associative Ligand Substitution
5.5.4: Structural Isomers - Linkage Isomerism in 2.5.5: Molecular Orbital Diagrams
Reaction Kinetics
Transition Metal Complexes Molecular orbital diagram 6.4: Associative Ligand Substitution
isomers 2.5.5: Molecular Orbital Diagrams 6.5: Dissociative Ligand Substitution
5.5: Isomers
N S
NMR seesaw
K 2.8.1: The Origin of the NMR Signal
Kapustinskii equation 2.8.3: The 1H-NMR experiment
soft ionization
2.8.4: Spin-Spin Coupling 1.1: Mass Spectrometry
2.8.5: The Basis for Differences in Chemical Shift Solvents
L 2.8.3: The 1H-NMR experiment
Lancashire
O sp hybrid orbital
Octahedral 2.4: Hybrid Orbitals
5.6.5: Jahn-Teller Distortions 2.3: The VSEPR Model sp2 hybrid orbital
5.3: Coordination Numbers and Geometry 2.4: Hybrid Orbitals
Lenz's Law
5.6.7: Magnetism
Octahedral Preference sp3 hybrid orbital
5.6.3: Crystal Field Stabilization Energy 2.4: Hybrid Orbitals
Lewis Acid
Octahedral Site Preference Energy sp3d hybrid orbital
5.6.3: Crystal Field Stabilization Energy 2.4: Hybrid Orbitals
Lewis base
Optical Isomers sp3d2 hybrid orbital
5.5.3: Stereoisomers - Optical Isomerism in 2.4: Hybrid Orbitals
ligand Transition Metal Complexes
4.2: Lewis Acids and Bases spectrochemical series
optical isomers (complex ions) 5.6.2: Colors of Coordination Complexes
6.5: Dissociative Ligand Substitution 5.5.3: Stereoisomers - Optical Isomerism in spectroscopy
Ligand Exchange Reactions 2.8.1: The Origin of the NMR Signal
organometallic 2.8.2: Chemical Equivalence
6.4: Associative Ligand Substitution 2.8.3: The 1H-NMR experiment
Linear
low spin P 2.8.5: The Basis for Differences in Chemical Shift
spin pairing energy
5.6.3: Crystal Field Stabilization Energy paramagnetic
5.6.5: Jahn-Teller Distortions 2.5.5: Molecular Orbital Diagrams
Square antiprism
parent peak
M 1.1: Mass Spectrometry
Square antiprism geometry
M+1 peak (mass spec) Pearson's absolute hardness
1.1: Mass Spectrometry 4.5: Quantitative Measures of Hardness and Softness
Square Planar Geometry
M+2 peak (mass spec) Pentagonal Bipyramid
1.1: Mass Spectrometry 5.3: Coordination Numbers and Geometry
Square pyramid Geometry
Magnetic Moment peptide bond
2.8.1: The Origin of the NMR Signal 6.2: Introduction to Amino Acids and Proteins
square pyramidal
magnetic moments Plane of Symmetry Method
5.6.6: Magnetic Moments of Transition Metals 5.5.3: Stereoisomers - Optical Isomerism in
Transition Metal Complexes stability constants
magnetic permeability 5.8: Ligand Exchange Reactions (Thermodynamics)
5.6.7: Magnetism
polar covalent bond
2.5.1: Molecular Shape and Molecular Polarity steady state approximation
magnetism 6.5: Dissociative Ligand Substitution
5.6.7: Magnetism
polarimeter
5.5.3: Stereoisomers - Optical Isomerism in stereochemistry
mass spectrometry Transition Metal Complexes 6.4: Associative Ligand Substitution
1.1: Mass Spectrometry 6.5: Dissociative Ligand Substitution
Polarimetry
McLafferty rearrangement 5.5.3: Stereoisomers - Optical Isomerism in stereoisomers
1.1: Mass Spectrometry Transition Metal Complexes 5.5: Isomers
metallic bonding Pourbaix diagrams structural isomers
2.6: The Range of Bonding 6.3.6: Pourbaix Diagrams 5.5: Isomers
miller indicies proteins 5.5.4: Structural Isomers - Linkage Isomerism in
3.10: Miller Indices (hkl) Transition Metal Complexes
substitution Trans Isomers Trigonal pyramid Geometry
6.4: Associative Ligand Substitution 5.5.2: Structural Isomers - Geometric Isomerism in 5.3: Coordination Numbers and Geometry
substrate Transition Metal Complexes trigonal pyramidal
6.2: Introduction to Amino Acids and Proteins Transition Metal Complexes 2.3: The VSEPR Model
symmetry elements 5.5.1: Structural Isomers - Ionization Isomerism in
U
symmetry operations Transition Metal Complexes Unsaturated Intermediate
2.7.1: Symmetry Elements and Operations 5.5.4: Structural Isomers - Linkage Isomerism in 6.5: Dissociative Ligand Substitution
T Trigonal Bipyramid Geometry V
Tetrahedral Valence Bond Theory
trigonal bipyramidal
2.3: The VSEPR Model 2.3: The VSEPR Model
Trigonal Planar valence shell electron pair repulsion
Tetrahedral Geometry
5.3: Coordination Numbers and Geometry 2.3: The VSEPR Model theory
Trigonal planar Geometry 2.3: The VSEPR Model
thermodynamics
5.8: Ligand Exchange Reactions (Thermodynamics) 5.3: Coordination Numbers and Geometry VSEPR
Trigonal prism Geometry 2.3: The VSEPR Model
Glossary
Glossary
Detailed Licensing
Overview
Title: CHEM 212/213: Inorganic Chemistry (Nataro)
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By Page
CHEM 212/213: Inorganic Chemistry (Nataro) - Undeclared 2.6: The Range of Bonding - CC BY-SA 4.0
Front Matter - Undeclared 2.7: Advanced Bonding - Undeclared
TitlePage - Undeclared 2.7.1: Symmetry Elements and Operations -
InfoPage - Undeclared Undeclared
Table of Contents - Undeclared 2.7.2: Point Groups - Undeclared
Licensing - Undeclared 2.7.2.1: Other Groups - Undeclared
1: Atoms - Undeclared 2.7.2.2: Groups of Low and High Symmetry -
Undeclared
1.1: Mass Spectrometry - CC BY-NC-SA 4.0
1.2: Rutherford's Atom - Undeclared 2.7.3: Ligand Group Orbitals and Generator
1.3: Bohr's Atom - Undeclared Functions - Undeclared
1.4: Hydrogen Atom - Undeclared 2.7.4: Expanded Octets and Molecular Orbitals -
1.5: Slater Rules - Undeclared Undeclared
2: Molecules - Undeclared 2.8: Nuclear Magnetic Resonance (NMR) -
2.1: Front Matter - Undeclared Undeclared
TitlePage - Undeclared 2.8.1: The Origin of the NMR Signal - CC BY-

Table of Contents - Undeclared NC-SA 4.0
InfoPage - Undeclared 2.8.2: Chemical Equivalence - CC BY-NC-SA 4.0
2.8.3: The 1H-NMR experiment - CC BY-NC-SA
2.2: Molecular Shapes - CC BY-NC-SA 4.0
4.0
2.3: The VSEPR Model - CC BY-NC-SA 4.0
2.8.4: Spin-Spin Coupling - CC BY-NC-SA 4.0
2.4: Hybrid Orbitals - CC BY-NC-SA 4.0
2.5: Molecular Orbitals - Undeclared
- CC BY-NC-SA 4.0
2.5.1: Molecular Shape and Molecular Polarity -
Back Matter - Undeclared
CC BY-NC-SA 4.0
Index - Undeclared
2.5.2: Prelude to Molecular Orbital Theory -
Glossary - Undeclared
Undeclared
2.5.3: Constructing Molecular Orbitals from 3: Solid state - Undeclared
Atomic Orbitals - CC BY-SA 4.0 3.1: Prelude to Metals and Alloys - Undeclared
2.5.4: Orbital Symmetry - CC BY-SA 4.0 3.2: Unit Cells and Crystal Structures - CC BY-SA 4.0
2.5.5: Molecular Orbital Diagrams - CC BY-SA 3.3: Crystal Structures of Metals - CC BY-SA 4.0
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BY-SA 4.0 3.6: Ferro-, Ferri- and Antiferromagnetism - CC BY-
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3.8: Defects in Metallic Crystals - CC BY-SA 4.0
3.9: X-ray Crystallography - Undeclared 5.6.4: Factors That Affect the Magnitude of Δo -
3.10: Miller Indices (hkl) - Undeclared Undeclared
3.11: Powder X-ray Diffraction - Undeclared 5.6.5: Jahn-Teller Distortions - Undeclared
3.12: Prelude to Ionic and Covalent Solids - 5.6.6: Magnetic Moments of Transition Metals -
Structures - Undeclared Undeclared
3.13: Close-packing and Interstitial Sites - CC BY-SA 5.6.7: Magnetism - Undeclared
4.0 5.6.8: Thermodynamics and Structural
3.14: Structures Related to NaCl and NiAs - CC BY- Consequences of d-Orbital Splitting - CC BY-NC-
SA 4.0 SA 4.0
3.15: Tetrahedral Structures - CC BY-SA 4.0 5.7: Ligand Field Theory - Undeclared
3.16: Layered Structures and Intercalation Reactions - 5.8: Ligand Exchange Reactions (Thermodynamics) -
CC BY-SA 4.0 Undeclared
3.17: Ionic Radii and Radius Ratios - CC BY-SA 4.0 5.9: Electronic Spectra of Coordination Compounds -
3.18: Structure Maps - CC BY-SA 4.0 Undeclared
3.19: Energetics of Crystalline Solids- The Ionic 6: Bioinorganic Chemistry - Undeclared
Model - CC BY-SA 4.0
6.1: Biological Significance of Iron, Zinc, Copper,
Molybdenum, Cobalt, Chromium, Vanadium, and
- CC BY-SA 4.0
Nickel - Undeclared
3.21: Lattice Energies and Solubility - CC BY-SA 4.0
6.2: Introduction to Amino Acids and Proteins - CC
3.22: Spinel, Perovskite, and Rutile Structures - CC
BY-NC-SA 4.0
BY-SA 4.0
6.3: Redox Reactions - Undeclared
3.23: Kapustinskii Equation - CC BY-SA 4.0
6.3.1: Introduction to Redox Reactions - CC BY-
4: Acid-Base Theories - Undeclared
SA 4.0
4.1: Bronsted-Lowry acids and bases - Undeclared
6.3.2: Balancing Redox Reactions - CC BY-SA 4.0
4.2: Lewis Acids and Bases - CC BY 4.0
6.3.3: Electrochemical Potentials - CC BY-SA 4.0
4.3: Acidity of the Hexaaqua Ions - Undeclared
6.3.4: Prelude to Redox Stability and Redox
4.4: Hard-soft Acids and Bases - Undeclared
Reactions - Undeclared
6.3.5: Latimer and Frost Diagrams - CC BY-SA 4.0
- Undeclared
6.3.6: Pourbaix Diagrams - CC BY-SA 4.0
5: Coordination Chemistry - Undeclared 6.4: Associative Ligand Substitution - Undeclared
5.1: Introduction to Coordination Chemistry - 6.5: Dissociative Ligand Substitution - Undeclared
Undeclared 6.6: Biological Significance of Iron, Zinc, Copper,
5.2: Ligands and Nomenclature - Undeclared Molybdenum, Cobalt, Chromium, Vanadium, and
5.3: Coordination Numbers and Geometry - Nickel - Undeclared
Undeclared 6.7: Ferrodoxins, Hydrogenases, and Nitrogenases -
5.4: Bonding with d-orbitals - CC BY-SA 4.0 Metal-Sulfide Proteins - Undeclared
5.5: Isomers - Undeclared 6.7.1: Iron-sulfur Proteins and Models -
5.5.1: Structural Isomers - Ionization Isomerism in Undeclared
Transition Metal Complexes - Undeclared 6.7.2: Iron-sulfur Proteins and Models (Part 2) -
5.5.2: Structural Isomers - Geometric Isomerism Undeclared
in Transition Metal Complexes - Undeclared 6.7.3: Iron-sulfur Proteins and Models (Part 3) -
5.5.3: Stereoisomers - Optical Isomerism in Undeclared
Transition Metal Complexes - Undeclared 6.7.4: Iron-sulfur Proteins and Models (Part 4) -
5.5.4: Structural Isomers - Linkage Isomerism in Undeclared
Transition Metal Complexes - Undeclared 6.8: Overview of Hemoglobin and Myoglobin -
5.6: Crystal Field Theory - Undeclared Undeclared
5.6.1: Crystal Field Theory - CC BY-NC-SA 4.0 6.8.1: Myoglobin, Hemoglobin, and their Ligands
5.6.2: Colors of Coordination Complexes - - CC BY-NC-SA 4.0
Undeclared 6.8.2: Oxygen Transport by the Proteins
5.6.3: Crystal Field Stabilization Energy - Myoglobin and Hemoglobin - Undeclared
Undeclared
Back Matter - Undeclared
Index - Undeclared Detailed Licensing - Undeclared

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CHEM 212/213:

This text was compiled on 01/12/2023

The basics of a mass spectrometry experiment

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Looking at mass spectra

There are two isotopes of Cl, Cl-35 and Cl-37.

Gas Chromatography - Mass Spectrometry

Gas chromatography-mass spectrometry (GC-MS) schematic

The Gold Foil Experiment

Rutherford's Failed Planetary Atom

Conservative Forces can be explained with Potentials

or as gradients in 3-D forces

where ∇ is the vector of partial derivatives

Repulsive Coulomb Potential Attractive Coulomb Potential

Contributors and Attributions

Review Necessary Skills

Experiments that can't be explained without quantization of energy or position

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For a stable orbit to exist F + F = 0, or,

If total Energy (E) is equal to the sum of KE and PE,

This expression can be simplified by first solving equation (4) for m ev

condition of a stable orbit (using a rearranged version of equation 4, (m v = e

This expression can be rearranged to solve for r ,

This is in the Ultra-violet region.

Figure 1.4.1 : Visible spectrum of atomic hydrogen.

The Bohr Atom

Using Equation 1.4.7 , we see that

Using Equation 1.4.9, we find also that

We introduce angular momentum quantization, writing

which is known as the Bohr radius. The corresponding energy is

the radius of the orbit (Equation 1.4.13) becomes

and the energy Equation 1.4.15 becomes

∮ p dr = nh, n = 1, 2... (1.4.23)

(not to scale). (Public Domain; Pieter Kuiper)

Quantum Mechanics of Hydrogenlike Atoms

It is convenient to introduce atomic units in which length is measured in bohrs:

and energy in hartrees:

ψ(r, θ, ϕ) = R(r)Yℓm (θ, ϕ) (1.4.30)

Bohr theory (in atomic units), we obtain

A useful definite integral is

The normalized radial function is thereby given by

This is conventionally designated as the 1s function ψ 1s (r) .

Hydrogen Atom Ground State

is a decreasing exponential function of a single variable r, and is simply plotted in Figure 3.

significant measure is therefore the radial distribution function

∫ D1s (r) dr = 1 (1.4.46)

The functions ρ (r) and D

radius of the first Bohr orbit

n = 1, 2... ℓ = 0, 1... n − 1 m = 0, ±1, ±2... ± ℓ

ψ2p , ψ2p analogous (1.4.52)

ψ3p , ψ3p analogous (1.4.55)

ψ3d , ψ3d analogous (1.4.58)

The energy levels for a hydrogenic system are given by

spherical harmonics, we find three degenerate eigenfunctions:

The orbital ψ is, like ψ

in terms of two non-standard d-orbitals, d and d

Figure 1.4.8 : Contour plot of 3d xy orbital.

Figure 1.4.22 : Some radial distribution functions.

Contributors and Attributions

These rules are summarized in Figure 1.5.1 and Table 1.5.1.