Organic Chemistry, Second Edition

Janice Gorzynski Smith

University of Hawai’i

Chapter 1
Structure & Bonding
Prepared by Rabi Ann Musah
State University of New York at Albany

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
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 Chapter 1 Topics

• Atomic structure and the periodic table.

• Bonding – Ionic, covalent.
• Bond polarity – electronegativity.
• Lewis structures – octet rule.
• Formal charge on each atom.
• Empirical, molecular and structural formulas.
• Isomers
• Resonance structures.
• Hybridization and geometry.

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 Structure and Bonding
Atomic Structure:

 The nucleus contains positively charged protons and

uncharged neutrons.
 The electron cloud is composed of negatively charged
electrons. 3
 Structure and Bonding
Isotopes: Figure 1.1 A comparison of two isotopes of carbon

(Same number of protons)

(Different number of neutrons)

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 Structure and Bonding

• Elements in the same row are similar in size but

size decreases going to the right.

• Elements in the same column have similar

electronic and chemical properties but become
more metallic going down the family.

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 Structure and Bonding
The Periodic Table: Figure 1.2 A periodic table of the common
elements seen in organic chemistry

Most common atoms in organic are C, H, N & O.

Other common atoms are the halogens, P & S.

S orbitals P orbitals
Be

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 Structure and Bonding

Rules for sequentially adding electrons:

• Aufbau principle: orbitals fill in order of

increasing energy, lowest to highest.
• Pauli exclusion principle: only two electrons
are allowed to occupy each orbital and the spins
must be paired.
• Hund’s Rule: when filling orbitals of equal
energy (degenerate), one electron is added to
each orbital of equal energy until all have one
electron. The three 2p orbitals are degenerate.

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 Structure and Bonding
Atomic Orbitals:
• An s orbital has a sphere of electron density and is lower
in energy than the other orbitals of the same shell.
• A p orbital has a dumbbell shape and contains a node of
electron density at the nucleus. It is higher in energy
than an s orbital. There are three p orbitals in the same
shell.

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 Structure and Bonding
Since there is only one orbital in the first shell, and each orbital can
hold a maximum of two electrons, there are two elements in the first
row, H and He. Rows represent the major energy levels.

Each element in the second row of the periodic table has four orbitals
available to accept electrons: one 2s orbital, and three 2p orbitals,
therefore the second row elements are limited to 8 electrons.

Atomic orbitals of Carbon

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 Structure and Bonding
Second Row Elements: filling the 2nd major energy level.
• Since each of the four orbitals available in the second
shell can hold two electrons, there is a maximum
capacity of eight electrons for elements in the second
row. Each atom has an increasing number of electrons.
• The second row of the periodic chart consists of eight
elements, obtained by adding electrons to the 2s and
three 2p orbitals.
(The electronic configuration of C = 1s22s22p2 )

S orbitals P orbitals
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 Structure and Bonding
Review of Bonding:

• Bonding joins of two atoms in a stable arrangement

using only valence electrons. Valence electrons are
outer shell electrons.
• Through bonding, atoms attain a complete outer shell
configuration which is like a noble gas.
• Covalent bonds result from the sharing of electrons
between two elements.
• Ionic bonds result from the transfer of electrons from
one element to another.
• Polarity of a bond depends upon the electronegativity
and size of the atoms forming the bond. 11
 Structure and Bonding
Figure 1.3 Summary: The usual number of bonds of common neutral atoms

Valence electrons are outer shell electrons used

in bonding.
Valence is the combining capacity (number of
bonds) to an atom in producing a neutral
structure.

Valence electrons 1 4 5 6 7
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 Ionic Bonding – electron transfer
• An ionic bond generally occurs when an element on
the far left side of the periodic table combines with an
element on the far right side, ignoring noble gases.
• A positively charged cation formed from the element
on the left side attracts a negatively charged anion
formed from the element on the right side. An example
is sodium chloride, NaCl.

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 Covalent Bonding – electron sharing
Bonding in Molecular Hydrogen (H2):

• Hydrogen forms one covalent bond.

• When two hydrogen atoms are joined in a NONPOLAR
covalent bond, each has a filled valence shell of two
electrons. It is nonpolar due to equal sharing of e’s.

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 Structure and Bonding
Electronegativity and Bond Polarity (see Figure 1.16):
Electronegativity is a measure of the attraction of an
atom for electrons in a bond.
Electronegativity values for some common elements:

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 Electronegativity and Bond Polarity

Electronegativity values are used as a guideline to

indicate whether the electrons in a bond are equally
shared or unequally shared between two atoms.
When electrons are equally shared, the bond is
nonpolar. When differences in electronegativity
result in unequal sharing of electrons, the bond is
polar, and is said to have a “separation of charge” or
a “dipole”.

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 Electronegativity and Bond Polarity
• A carbon—carbon bond is nonpolar. The same is true
whenever two different atoms having similar
electronegativities are bonded together.
• C—H bonds have very slight polarity and are
considered to be nonpolar because the electronegativity
difference between C (2.5) and H (2.2) is small.
Bonding between atoms of different electronegativity
values results in unequal sharing of electrons.

Example: In the C—O bond, the electrons are pulled

away from C (2.5) toward O (3.4), the element of higher
electronegativity. The bond is polar, or polar covalent.
The bond is said to have dipole; that is, separation of
charge.
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 Electronegativity and Bond Polarity

d+ means the
indicated atom is
electron deficient.
d- means the
indicated atom is
electron rich.

The direction of polarity in a bond is indicated by an

arrow with the head of the arrow pointing towards the
more electronegative element. The tail of the arrow,
with a perpendicular line drawn through it, is drawn at
the less electronegative element.
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 Structure and Bonding
Lewis Structures:
Lewis structures are electron dot representations for
molecules. There are three general rules for drawing
Lewis structures:
1. Draw all and only the valence electrons.
2. Give every second-row element an octet of electrons,
if possible.
3. Give each hydrogen only two electrons.

In a Lewis structure, a solid

line indicates a two-electron 19
covalent bond.
 Structure and Bonding

• Second row elements can have no more than eight

electrons around them. For neutral molecules, this has
two consequences:
 Atoms with one, two, or three valence electrons form one,
two, or three bonds, respectively, in neutral molecules.
 Atoms with four or more valence electrons form enough
bonds to give an octet. This results in the following
equation for elements with 4 or more valence e’s:

 When second-row elements form fewer than four bonds

their octets consist of both bonding (shared) and
nonbonding (unshared) electrons. Unshared electrons are
also called lone pairs. e.g. :NH3 20
 Structure and Bonding
Formal Charge:
• Formal charge is the charge assigned to individual atoms in a
Lewis structure.
• By calculating formal charge, we determine how the number
of electrons around a particular atom compares to its number
of valence electrons. Formal charge is calculated as follows:

• The number of electrons “owned” by an atom is determined

by its number of bonds and lone pairs.
• An atom “owns” all of its unshared electrons and half of its
shared electrons.
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 Structure and Bonding
In formal charge calculation, the number of electrons
“owned” by an atom is shown in these examples:
Example 1

Example 3

Example 2

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Structure and Bonding

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 Structure and Bonding
Exceptions to the Octet Rule:
Elements in Groups 2A and 3A

Elements in the Third Row

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 Structure and Bonding
Drawing Organic Molecules: Condensed Structures
• All atoms are drawn, but the two-electron bond lines are
generally omitted.
• Atoms are usually drawn next to the atoms to which they are
bonded.
• Parentheses are used around similar groups bonded to the
same atom.
• Lone pairs are omitted.

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Examples of Condensed Structures (see Fig.1.5):

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Examples of Condensed Structures
Containing a C=O Double Bond (see Fig. 1.6):

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 Structure and Bonding
Skeletal Structures:
• Assume there is a carbon atom at the junction of any two
lines or at the end of any line.
• Assume there are enough hydrogens around each carbon
to make it tetravalent.
• Draw in all heteroatoms and hydrogens directly bonded to
them.

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 Structure and Bonding

Examples of Skeletal (LINE) Structures (see Figure 1.7):

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 Structure and Bonding
Words of Caution Regarding Interpretation of Skeletal
Structures…
• A charge on a carbon atom takes the place of one hydrogen
atom.
• The charge determines the number of lone pairs. Negatively
charged carbon atoms have one lone pair and positively
charged carbon atoms have none.

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 Structure and Bonding
Isomers:
In drawing a Lewis structure for a molecule with several
atoms, sometimes more than one arrangement of atoms
is possible for a given molecular formula.
Example:

Both are valid Lewis structures and both molecules exist.

These two compounds are called isomers.
Isomers are different molecules having the same
molecular formula. Ethanol and dimethyl ether are
constitutional isomers. 31
 Structure and Bonding
Resonance:
Some molecules cannot be adequately represented by a single
Lewis structure. For example, two valid Lewis structures can
be drawn for the anion (HCONH)¯. One structure has a
negatively charged N atom and a C=O double bond; the other
has a negatively charged O atom and a C=N double bond.

These structures are called resonance structures or resonance

forms. A double headed arrow is used to separate the two
resonance structures. Only electrons are moved.

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 Structure and Bonding
Introduction to Resonance Theory:
Regarding the two resonance forms of (HCONH)¯ shown
below, it should be noted that:

• Neither resonance structure is an accurate representation

for (HCONH)¯. The true structure is a composite of both
resonance forms and is called a resonance hybrid.
• The hybrid shows characteristics of both structures.
• Resonance allows certain electron pairs to be delocalized
over two or more atoms, and this delocalization adds
stability.
• A molecule with two or more resonance forms is said to be
resonance stabilized. The more forms-THE MORE STABLE 33
 Structure and Bonding
Resonance Theory continued:
The following basic principles of resonance theory should
be kept in mind:

1. Resonance structures are not real. An individual

resonance structure does not accurately represent the
structure of a molecule or ion. Only the hybrid does.
2. Resonance structures are not in equilibrium with each
other. There is no movement of electrons from one form
to another. BUT WE TREAT THEM AS IF THEY DO!
3. Resonance structures are not isomers. Two isomers
differ in the arrangement of both atoms and electrons,
whereas resonance structures differ only in the
arrangement of electrons.
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 Structure and Bonding
Drawing Resonance Structures:
Rule [1]: Two resonance structures differ in the position of multiple
bonds and nonbonded electrons. The placement of atoms and
single bonds always stays the same.

Rule [2]: Two resonance structures must have the same number
of unpaired electrons.

35
 Structure and Bonding
Drawing Resonance Structures:
Rule [3]: Resonance structures must be valid Lewis structures.
Hydrogen must have two electrons and no second-row element
can have more than eight electrons.

36
 Structure and Bonding
Drawing Resonance Structures:
• Curved arrow notation is a convention that is used to show how
electron position differs between the two resonance forms.
• Curved arrow notation shows the movement of an electron pair.
The tail of the arrow always begins at the electron pair, either in a
bond or lone pair. The head points to where the electron pair
“moves.”
Example 1:

Example 2:

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 Structure and Bonding
Resonance Structure Examples:

Equivalent structures:

Nonequivalent structures:

In the two examples above, a lone pair is located on

an atom directly bonded to a double bond.
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 Structure and Bonding

Resonance Structure Examples:

In the above examples, an atom bearing a (+) charge

is bonded either to a double bond or an atom with a
lone pair.
39
 Structure and Bonding
Resonance Hybrids:
• A resonance hybrid is a composite of all possible
resonance structures. In the resonance hybrid, the
electron pairs drawn in different locations in
individual resonance forms are delocalized.
• When two resonance structures are different, the
hybrid looks more like the “better” resonance
structure. The “better” resonance structure is called
the major contributor to the hybrid, and all others are
minor contributors.
• The hybrid is a weighted average of the contributing
resonance structures.

40
 Structure and Bonding
Resonance Hybrids:
A “better” resonance structure is one that has more bonds
and fewer charges.

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 Structure and Bonding
Determining Molecular Shape:
Two variables define a molecule’s structure: bond length
and bond angle.
• Bond length decreases across a row of the periodic
table as the size of the atom decreases.

• Bond length increases down a column of the

periodic table as the size of an atom increases.

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Structure and Bonding

43
 Structure and Bonding
Bond Angle:
• The number of groups surrounding a particular
atom determines its geometry. A group is either an
atom or a lone pair of electrons.
• The most stable arrangement keeps the electrons
as far away from each other as possible (negative
repulsion). This is shown by the Valence Shell
Electron Pair Repulsion (VSEPR) theory.

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 Structure and Bonding
Bond Angle:

When two groups are around an atom with no

lone pairs:

45
 Structure and Bonding
Bond Angle:

When three groups are around an atom with no

lone pairs:

46
 Structure and Bonding
Bond Angle:

When four groups are around an atom:

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 Structure and Bonding
Example: water

In water (H2O), two of the four groups attached to the

central O atom are lone pairs. The two H atoms and
two lone pairs around O point to the corners of a
tetrahedron. The H-O-H bond angle of 105° is close to
the theoretical tetrahedral bond angle of 109.5°. Water
has a bent shape, because the two groups around
oxygen are lone pairs of electrons.

48
 Structure and Bonding
A Nonbonded Pair of Electrons is Counted as a “Group”:
Example: ammonia
In ammonia (NH3), one of the four groups attached to
the central N atom is a lone pair. The three H atoms
and the lone pair point to the corners of a tetrahedron.
The H-N-H bond angle of 107° is close to the theoretical
tetrahedral bond angle of 109.5°. This shape is referred
to as a trigonal pyramid.

49
 Structure and Bonding
Drawing Three Dimensional Wedge Structures:

• A solid line is used for a bond in the plane.

• A wedge is used for a bond in front of the plane.
• A dashed line is used for a bond behind the plane.

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 Structure and Bonding
Drawing Three Dimensional Wedge Structures:
The molecule can be turned in many different ways,
generating many equivalent representations. All of
the following are acceptable drawings for CH4.

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 Structure and Bonding
Drawing Three Dimensional Structures:
Note that wedges and dashes are used for groups
that are really aligned one behind another. It does
not matter in the following two drawings whether the
wedge or dash is skewed to the left or right, because
the two H atoms are really aligned.

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 Structure and Bonding
Orbitals and Bonding: Hydrogen
When the 1s orbital of one H atom overlaps with the 1s
orbital of another H atom, a sigma () bond that
concentrates electron density between the two nuclei is
formed.
This bond is cylindrically symmetrical because the
electrons forming the bond are distributed symmetrically
about an imaginary line connecting the two nuclei.

Atomic orbitals Molecular orbital

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 Structure and Bonding
Orbitals and Bonding: Methane

Carbon has two core electrons, plus four valence electrons.

To fill atomic orbitals in the most stable arrangement,
electrons are placed in the orbitals of lowest energy. For
carbon, this places two in the 2s orbital and one each in 2p
orbitals.

The lowest energy arrangement of electrons for an

atom is called its ground state.
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 Structure and Bonding
Orbitals and Bonding: Methane
There is a second possibility. Promotion of an electron from a
2s to a vacant 2p orbital would form four unpaired electrons
for bonding. This process requires energy because it moves
an electron to a higher energy orbital. This higher energy
electron configuration is called an electronically excited state.

But this description is still not adequate to account for the

observed bonding in methane. Using the atomic orbitals after
excitation above, carbon would form two different types of
bonds: three with 2p orbitals and one with a 2s orbital. 55
 Structure and Bonding
Orbitals and Bonding: Methane
To solve this dilemma, chemists have proposed that atoms
like carbon do not use pure s and pure p orbitals in forming
bonds. Instead, atoms use a set of new orbitals called hybrid
orbitals.
Hybridization is the combination of two or more atomic
orbitals to form the same number of hybrid orbitals, each new
of the orbitals having the same shape and energy.

56
 Structure and Bonding
Shape and Orientation of sp3 Hybrid Orbitals:
The mixing of a spherical 2s orbital and three dumbbell shaped
2p orbitals together produces four hybrid orbitals, each having
one large lobe and one small lobe (see Figure 1.8).

The four hybrid orbitals are oriented towards the corners of a

tetrahedron, and form four equivalent bonds.

57
 Structure and Bonding
Bonding Using sp3 Hybrid Orbitals:

Each bond in CH4 is formed by overlap of an sp3 hybrid

orbital of carbon with a 1s orbital of hydrogen. These
four bonds point to the corners of a tetrahedron.

Figure 1.9 Bonding in CH4

using sp3 hybrid orbitals

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 Structure and Bonding
Other Hybridization Patterns (see Figures 1.10 and 1.11):
• One 2s orbital and three 2p orbitals form four sp3 hybrid
orbitals.
• One 2s orbital and two 2p orbitals form three sp2 hybrid
orbitals.
• One 2s orbital and one 2p orbital form two sp hybrid orbitals.

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Hybridization & Bonding in Organic Molecules

60
 Structure and Bonding
Hybridization and Bonding in Organic Molecules:

Making a model of ethane illustrates one

additional feature about its structure.
Rotation occurs around the central C—C
 bond.

61
 Structure and Bonding
Hybridization and Bonding in Organic Molecules:

Each carbon is trigonal and

planar.
Each carbon is sp2 hybridized

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Hybridization & Bonding in Organic Molecules

63
 Structure and Bonding
Hybridization and Bonding in Organic Molecules:

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 Structure and Bonding
Hybridization and Bonding in Organic Molecules:

From Figure 1.14

Summary of Bonding in Acetylene

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 Structure and Bonding
Summary of Covalent Bonding Seen in Carbon Compounds
(from Figure 1.15)

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 Structure and Bonding
Hybrids: Bond Length and Bond Strength:
• As the number of electrons between two nuclei
increases, bonds become shorter and stronger.
• Thus, triple bonds are shorter and stronger than
double bonds, which are shorter and stronger than
single bonds.

67
 Structure and Bonding

Bond Length and Bond Strength:

• The length and strength of C—H bonds vary depending
on the hybridization of the carbon atom.

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Structure and Bonding

69
 Structure and Bonding
Bond Length and Bond Strength:

70
 Structure and Bonding
Bond Length and Bond Strength:
Note:
• As the percent s-character increases, a hybrid orbital holds
its electrons closer to the nucleus, and the bond becomes
shorter and stronger.
• Although sp3, sp2 and sp hybrid orbitals are similar in
shape, they are different in size.

71
 Structure and Bonding
Polarity of Molecules (see Figure 1.17):
Use the following two-step procedure to determine if a
molecule has a net dipole:
1. Use electronegativity differences to identify all of the
polar bonds and the directions of the bond dipoles.
2. Determine the geometry around individual atoms by
counting groups, and decide if individual dipoles
cancel or reinforce each other in space.
Electrostatic potential plot of CH3Cl

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 Structure and Bonding
Polarity of Molecules:
A polar molecule has either one polar bond, or two or more
bond dipoles that reinforce each other. An example is water:

A nonpolar molecule has either no polar bonds, or two or

more bond dipoles that cancel. An example is carbon dioxide:

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Organic Chemistry, Second Edition

Janice Gorzynski Smith

University of Hawai’i

End Chapter 1
Prepared by Rabi Ann Musah
State University of New York at Albany

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
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