Molecule

A molecule is a group of two or more atoms that are held together

by attractive forces known as chemical bonds; depending on
context, the term may or may not include ions that satisfy this
criterion.[4][5][6][7][8] In quantum physics, organic chemistry, and
biochemistry, the distinction from ions is dropped and molecule is
often used when referring to polyatomic ions.

A molecule may be homonuclear, that is, it consists of atoms of

one chemical element, e.g. two atoms in the oxygen molecule
(O2); or it may be heteronuclear, a chemical compound composed
of more than one element, e.g. water (two hydrogen atoms and one
oxygen atom; H2O). In the kinetic theory of gases, the term Atomic force microscopy (AFM)
molecule is often used for any gaseous particle regardless of its image of a PTCDA molecule, in
composition. This relaxes the requirement that a molecule contains which the five six-carbon rings are
visible.[1]
two or more atoms, since the noble gases are individual atoms.[9]
Atoms and complexes connected by non-covalent interactions,
such as hydrogen bonds or ionic bonds, are typically not
considered single molecules.[10]

Concepts similar to molecules have been discussed since ancient

times, but modern investigation into the nature of molecules and
their bonds began in the 17th century. Refined over time by
scientists such as Robert Boyle, Amedeo Avogadro, Jean Perrin,
and Linus Pauling, the study of molecules is today known as
molecular physics or molecular chemistry.

Etymology A scanning tunneling microscopy

image of pentacene molecules,
According to Merriam-Webster and the Online Etymology which consist of linear chains of five
Dictionary, the word "molecule" derives from the Latin "moles" or carbon rings.[2]
small unit of mass. The word is derived from French molécule
(1678), from Neo-Latin molecula, diminutive of Latin moles
"mass, barrier". The word, which until the late 18th century was used only in Latin form, became popular
after being used in works of philosophy by Descartes.[11][12]

History
The definition of the molecule has evolved as knowledge of the
structure of molecules has increased. Earlier definitions were less
precise, defining molecules as the smallest particles of pure
chemical substances that still retain their composition and
chemical properties.[13] This definition often breaks down since
many substances in ordinary experience, such as rocks, salts, and
AFM image of 1,5,9-trioxo-13-
metals, are composed of large crystalline networks of chemically
azatriangulene and its chemical
bonded atoms or ions, but are not made of discrete molecules. structure.[3]

The modern concept of molecules can be traced back towards pre-

scientific and Greek philosophers such as Leucippus and Democritus who argued that all the universe is
composed of atoms and voids. Circa 450 BC Empedocles imagined fundamental elements (fire ( ),
earth ( ), air ( ), and water ( )) and "forces" of attraction and repulsion allowing the elements to
interact.

A fifth element, the incorruptible quintessence aether, was considered to be the fundamental building
block of the heavenly bodies. The viewpoint of Leucippus and Empedocles, along with the aether, was
accepted by Aristotle and passed to medieval and renaissance Europe.

In a more concrete manner, however, the concept of aggregates or units of bonded atoms, i.e.
"molecules", traces its origins to Robert Boyle's 1661 hypothesis, in his famous treatise The Sceptical
Chymist, that matter is composed of clusters of particles and that chemical change results from the
rearrangement of the clusters. Boyle argued that matter's basic elements consisted of various sorts and
sizes of particles, called "corpuscles", which were capable of arranging themselves into groups. In 1789,
William Higgins published views on what he called combinations of "ultimate" particles, which
foreshadowed the concept of valency bonds. If, for example, according to Higgins, the force between the
ultimate particle of oxygen and the ultimate particle of nitrogen were 6, then the strength of the force
would be divided accordingly, and similarly for the other combinations of ultimate particles.

Amedeo Avogadro created the word "molecule".[14] His 1811 paper "Essay on Determining the Relative
Masses of the Elementary Molecules of Bodies", he essentially states, i.e. according to Partington's A
Short History of Chemistry, that:[15]

The smallest particles of gases are not necessarily simple atoms, but are made up of a certain
number of these atoms united by attraction to form a single molecule.

In coordination with these concepts, in 1833 the French chemist Marc Antoine Auguste Gaudin presented
a clear account of Avogadro's hypothesis,[16] regarding atomic weights, by making use of "volume
diagrams", which clearly show both semi-correct molecular geometries, such as a linear water molecule,
and correct molecular formulas, such as H2O:
 Marc Antoine Auguste Gaudin's volume diagrams of
molecules in the gas phase (1833)

In 1917, an unknown American undergraduate chemical engineer named Linus Pauling was learning the
Dalton hook-and-eye bonding method, which was the mainstream description of bonds between atoms at
the time. Pauling, however, was not satisfied with this method and looked to the newly emerging field of
quantum physics for a new method. In 1926, French physicist Jean Perrin received the Nobel Prize in
physics for proving, conclusively, the existence of molecules. He did this by calculating the Avogadro
constant using three different methods, all involving liquid phase systems. First, he used a gamboge soap-
like emulsion, second by doing experimental work on Brownian motion, and third by confirming
Einstein's theory of particle rotation in the liquid phase.[17]

In 1927, the physicists Fritz London and Walter Heitler applied the new quantum mechanics to the deal
with the saturable, nondynamic forces of attraction and repulsion, i.e., exchange forces, of the hydrogen
molecule. Their valence bond treatment of this problem, in their joint paper,[18] was a landmark in that it
brought chemistry under quantum mechanics. Their work was an influence on Pauling, who had just
received his doctorate and visited Heitler and London in Zürich on a Guggenheim Fellowship.

Subsequently, in 1931, building on the work of Heitler and London and on theories found in Lewis'
famous article, Pauling published his ground-breaking article "The Nature of the Chemical Bond"[19] in
which he used quantum mechanics to calculate properties and structures of molecules, such as angles
between bonds and rotation about bonds. On these concepts, Pauling developed hybridization theory to
account for bonds in molecules such as CH4, in which four sp³ hybridised orbitals are overlapped by
hydrogen's 1s orbital, yielding four sigma (σ) bonds. The four bonds are of the same length and strength,
which yields a molecular structure as shown below:

A schematic presentation of
hybrid orbitals overlapping
hydrogens' s orbitals

Molecular science
The science of molecules is called molecular chemistry or molecular physics, depending on whether the
focus is on chemistry or physics. Molecular chemistry deals with the laws governing the interaction
between molecules that results in the formation and breakage of chemical bonds, while molecular physics
deals with the laws governing their structure and properties. In practice, however, this distinction is
vague. In molecular sciences, a molecule consists of a stable system (bound state) composed of two or
more atoms. Polyatomic ions may sometimes be usefully thought of as electrically charged molecules.
The term unstable molecule is used for very reactive species, i.e., short-lived assemblies (resonances) of
electrons and nuclei, such as radicals, molecular ions, Rydberg molecules, transition states, van der Waals
complexes, or systems of colliding atoms as in Bose–Einstein condensate.

Prevalence
Molecules as components of matter are common. They also make up most of the oceans and atmosphere.
Most organic substances are molecules. The substances of life are molecules, e.g. proteins, the amino
acids of which they are composed, the nucleic acids (DNA and RNA), sugars, carbohydrates, fats, and
vitamins. The nutrient minerals are generally ionic compounds, thus they are not molecules, e.g. iron
sulfate.

However, the majority of familiar solid substances on Earth are made partly or completely of crystals or
ionic compounds, which are not made of molecules. These include all of the minerals that make up the
substance of the Earth, sand, clay, pebbles, rocks, boulders, bedrock, the molten interior, and the core of
the Earth. All of these contain many chemical bonds, but are not made of identifiable molecules.

No typical molecule can be defined for salts nor for covalent crystals, although these are often composed
of repeating unit cells that extend either in a plane, e.g. graphene; or three-dimensionally e.g. diamond,
quartz, sodium chloride. The theme of repeated unit-cellular-structure also holds for most metals which
are condensed phases with metallic bonding. Thus solid metals are not made of molecules. In glasses,
which are solids that exist in a vitreous disordered state, the atoms are held together by chemical bonds
with no presence of any definable molecule, nor any of the regularity of repeating unit-cellular-structure
that characterizes salts, covalent crystals, and metals.

Bonding
Molecules are generally held together by covalent bonding. Several non-metallic elements exist only as
molecules in the environment either in compounds or as homonuclear molecules, not as free atoms: for
example, hydrogen.

While some people say a metallic crystal can be considered a single giant molecule held together by
metallic bonding,[20] others point out that metals behave very differently than molecules.[21]

Covalent
A covalent bond is a chemical bond that involves the sharing of
electron pairs between atoms. These electron pairs are termed
shared pairs or bonding pairs, and the stable balance of attractive
and repulsive forces between atoms, when they share electrons, is
termed covalent bonding.[22]
A covalent bond forming H2 (right)
where two hydrogen atoms share
Ionic the two electrons
Ionic bonding is a type of
chemical bond that
involves the electrostatic attraction between oppositely charged
ions, and is the primary interaction occurring in ionic compounds.
The ions are atoms that have lost one or more electrons (termed
Sodium and fluorine undergoing a cations) and atoms that have gained one or more electrons (termed
redox reaction to form sodium anions).[23] This transfer of electrons is termed electrovalence in
fluoride. Sodium loses its outer
contrast to covalence. In the simplest case, the cation is a metal
electron to give it a stable electron
configuration, and this electron
atom and the anion is a nonmetal atom, but these ions can be of a
enters the fluorine atom more complicated nature, e.g. molecular ions like NH4+ or SO42−.
exothermically. At normal temperatures and pressures, ionic bonding mostly
creates solids (or occasionally liquids) without separate
identifiable molecules, but the vaporization/sublimation of such
materials does produce separate molecules where electrons are still transferred fully enough for the bonds
to be considered ionic rather than covalent.

Molecular size
Most molecules are far too small to be seen with the naked eye, although molecules of many polymers
can reach macroscopic sizes, including biopolymers such as DNA. Molecules commonly used as building
blocks for organic synthesis have a dimension of a few angstroms (Å) to several dozen Å, or around one
billionth of a meter. Single molecules cannot usually be observed by light (as noted above), but small
molecules and even the outlines of individual atoms may be traced in some circumstances by use of an
atomic force microscope. Some of the largest molecules are macromolecules or supermolecules.

The smallest molecule is the diatomic hydrogen (H2), with a bond length of 0.74 Å.[24]

Effective molecular radius is the size a molecule displays in solution.[25][26] The table of permselectivity
for different substances contains examples.

Molecular formulas

Chemical formula types

The chemical formula for a molecule uses one line of chemical element symbols, numbers, and
sometimes also other symbols, such as parentheses, dashes, brackets, and plus (+) and minus (−) signs.
These are limited to one typographic line of symbols, which may include subscripts and superscripts.

A compound's empirical formula is a very simple type of chemical formula.[27] It is the simplest integer
ratio of the chemical elements that constitute it.[28] For example, water is always composed of a 2:1 ratio
of hydrogen to oxygen atoms, and ethanol (ethyl alcohol) is always composed of carbon, hydrogen, and
oxygen in a 2:6:1 ratio. However, this does not determine the kind of molecule uniquely – dimethyl ether
has the same ratios as ethanol, for instance. Molecules with the same atoms in different arrangements are
called isomers. Also carbohydrates, for example, have the same ratio (carbon:hydrogen:oxygen= 1:2:1)
(and thus the same empirical formula) but different total numbers of atoms in the molecule.

The molecular formula reflects the exact number of atoms that compose the molecule and so
characterizes different molecules. However different isomers can have the same atomic composition
while being different molecules.

The empirical formula is often the same as the molecular formula but not always. For example, the
molecule acetylene has molecular formula C2H2, but the simplest integer ratio of elements is CH.

The molecular mass can be calculated from the chemical formula and is expressed in conventional atomic
mass units equal to 1/12 of the mass of a neutral carbon-12 (12C isotope) atom. For network solids, the
term formula unit is used in stoichiometric calculations.

Structural formula
For molecules with a complicated 3-
dimensional structure, especially
involving atoms bonded to four
different substituents, a simple
molecular formula or even semi-
structural chemical formula may not
be enough to completely specify the 3D (left and center) and 2D (right) representations of the terpenoid
molecule atisane
molecule. In this case, a graphical
type of formula called a structural
formula may be needed. Structural formulas may in turn be represented with a one-dimensional chemical
name, but such chemical nomenclature requires many words and terms which are not part of chemical
formulas.

Molecular geometry
Molecules have fixed equilibrium geometries—bond lengths and angles— about which they continuously
oscillate through vibrational and rotational motions. A pure substance is composed of molecules with the
same average geometrical structure. The chemical formula and the structure of a molecule are the two
important factors that determine its properties, particularly its reactivity. Isomers share a chemical
 formula but normally have very different properties because of their
different structures. Stereoisomers, a particular type of isomer, may have
very similar physico-chemical properties and at the same time different
biochemical activities.

Molecular spectroscopy

Structure and STM image

of a "cyanostar" dendrimer
molecule.[29]
Hydrogen can be removed from individual
H2TPP molecules by applying excess voltage to
Molecular spectroscopy deals with the response the tip of a scanning tunneling microscope
(spectrum) of molecules interacting with probing (STM, a); this removal alters the current-voltage
(I-V) curves of TPP molecules, measured using
signals of known energy (or frequency, according to the
the same STM tip, from diode like (red curve in
Planck relation). Molecules have quantized energy b) to resistor like (green curve). Image (c) shows
levels that can be analyzed by detecting the molecule's a row of TPP, H2TPP and TPP molecules. While
energy exchange through absorbance or emission.[31] scanning image (d), excess voltage was applied
Spectroscopy does not generally refer to diffraction to H2TPP at the black dot, which instantly
studies where particles such as neutrons, electrons, or removed hydrogen, as shown in the bottom part
high energy X-rays interact with a regular arrangement of (d) and in the rescan image (e). Such
manipulations can be used in single-molecule
of molecules (as in a crystal).
electronics.[30]
Microwave spectroscopy commonly measures changes
in the rotation of molecules, and can be used to identify
molecules in outer space. Infrared spectroscopy measures the vibration of molecules, including
stretching, bending or twisting motions. It is commonly used to identify the kinds of bonds or functional
groups in molecules. Changes in the arrangements of electrons yield absorption or emission lines in
ultraviolet, visible or near infrared light, and result in colour. Nuclear resonance spectroscopy measures
the environment of particular nuclei in the molecule, and can be used to characterise the numbers of
atoms in different positions in a molecule.

Theoretical aspects
The study of molecules by molecular physics and theoretical chemistry is largely based on quantum
mechanics and is essential for the understanding of the chemical bond. The simplest of molecules is the
hydrogen molecule-ion, H2+, and the simplest of all the chemical bonds is the one-electron bond. H2+ is
composed of two positively charged protons and one negatively charged electron, which means that the
Schrödinger equation for the system can be solved more easily due to the lack of electron–electron
repulsion. With the development of fast digital computers, approximate solutions for more complicated
molecules became possible and are one of the main aspects of computational chemistry.

When trying to define rigorously whether an arrangement of atoms is sufficiently stable to be considered
a molecule, IUPAC suggests that it "must correspond to a depression on the potential energy surface that
is deep enough to confine at least one vibrational state".[4] This definition does not depend on the nature
of the interaction between the atoms, but only on the strength of the interaction. In fact, it includes
weakly bound species that would not traditionally be considered molecules, such as the helium dimer,
He2, which has one vibrational bound state[32] and is so loosely bound that it is only likely to be observed
at very low temperatures.

Whether or not an arrangement of atoms is sufficiently stable to be considered a molecule is inherently an

operational definition. Philosophically, therefore, a molecule is not a fundamental entity (in contrast, for
instance, to an elementary particle); rather, the concept of a molecule is the chemist's way of making a
useful statement about the strengths of atomic-scale interactions in the world that we observe.

See also
Atom
Chemical polarity
Chemical structure
Covalent bond
Diatomic molecule
List of compounds
List of interstellar and circumstellar molecules
Molecular biology
Molecular design software
Molecular engineering
Molecular geometry
Molecular Hamiltonian
Molecular ion
Molecular modelling
Molecular promiscuity
Molecular orbital
Non-covalent bonding
Periodic systems of small molecules
Small molecule
Comparison of software for molecular mechanics modeling
Van der Waals molecule
World Wide Molecular Matrix

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External links
Molecule of the Month – School of Chemistry, University of Bristol (http://www.chm.bris.ac.u
k/motm/motm.htm)

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