Molecule

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"Molecules" and "Molecular" redirect here. For other uses, see Molecules (journal) and Molecular
(game).

Atomic force microscopy (AFM) image of a PTCDA molecule, in which the five six-carbon rings are visible.[1]

A scanning tunneling microscopyimage of pentacene molecules, which consist of linear chains of five carbon
rings.[2]

AFM image of 1,5,9-trioxo-13-azatriangulene and its chemical structure.[3]

A molecule is an electrically neutral group of two or more atoms held together by chemical
bonds.[4][5][6][7][8] Molecules are distinguished from ions by their lack of electrical charge. However,
in quantum physics, organic chemistry, and biochemistry, the term molecule is often used less
strictly, also being applied to polyatomic ions.
In the kinetic theory of gases, the term molecule is often used for any gaseous particle regardless of
its composition. According to this definition, noble gas atoms are considered molecules as they are
monatomic molecules.[9]
A molecule may be homonuclear, that is, it consists of atoms of one chemical element, as
with oxygen (O2); or it may be heteronuclear, a chemical compound composed of more than one
element, as with water(H2O). Atoms and complexes connected by non-covalent interactions, such
as hydrogen bonds or ionic bonds, are generally not considered single molecules.[10]
Molecules as components of matter are common in organic substances (and therefore
biochemistry). They also make up most of the oceans and atmosphere. However, the majority of
familiar solid substances on Earth, including most of the minerals that make up the crust, mantle,
and core of the Earth, contain many chemical bonds, but are not made of identifiable molecules.
Also, no typical molecule can be defined for ionic crystals (salts) and covalent crystals (network
solids), although these are often composed of repeating unit cells that extend either in a plane (such
as in graphene) or three-dimensionally (such as in diamond, quartz, or sodium chloride). The theme
of repeated unit-cellular-structure also holds for most condensed phases with metallic bonding,
which means that solid metals are also not made of molecules. In glasses(solids that exist in a
vitreous disordered state), atoms may also be held together by chemical bonds with no presence of
any definable molecule, nor any of the regularity of repeating units that characterizes crystals.

Contents

 1Molecular science
 2History and etymology
 3Bonding
o 3.1Covalent
o 3.2Ionic
 4Molecular size
 5Molecular formulas
o 5.1Chemical formula types
o 5.2Structural formula
 6Molecular geometry
 7Molecular spectroscopy
 8Theoretical aspects
 9See also
 10References
 11External links

Molecular science[edit]
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.
History and etymology[edit]
Main article: History of molecular theory
According to Merriam-Webster and the Online Etymology Dictionary, the word "molecule" derives
from the Latin "moles" or small unit of mass.

 Molecule (1794) – "extremely minute particle", from

French molécule (1678), from New Latin molecula, diminutive of
Latin moles "mass, barrier". A vague meaning at first; the vogue for
the word (used until the late 18th century only in Latin form) can be
traced to the philosophy of Descartes.[11][12]
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 metals,
are composed of large crystalline networks of chemically bonded atoms or ions, but are not made of
discrete molecules.

Bonding[edit]
Molecules are held together by either covalent bonding or ionic bonding. Several types of non-metal
elements exist only as molecules in the environment. For example, hydrogen only exists as
hydrogen molecule. A molecule of a compound is made out of two or more elements.[14]
Covalent[edit]
Main article: Covalent bonding

A covalent bond forming H2 (right) where two hydrogen atoms share the two electrons
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.[15]
Ionic[edit]
Main article: Ionic bonding

Sodium and fluorine undergoing a redox reaction to form sodium fluoride. Sodium loses its outer electron to
give it a stable electron configuration, and this electron enters the fluorine atom exothermically.
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 cations) and atoms that have gained one or more electrons
(termed anions).[16] This transfer of electrons is termed electrovalence in contrast to covalence. In the
simplest case, the cation is a metal atom and the anion is a nonmetal atom, but these ions can be of
a more complicated nature, e.g. molecular ions like NH4+ or SO42−. Basically, an ionic bond is the
transfer of electrons from a metal to a non-metal for both atoms to obtain a full valence shell.

Molecular size[edit]
Most molecules are far too small to be seen with the naked eye, but there are exceptions. DNA,
a macromolecule, can reach macroscopic sizes, as can molecules of many polymers. 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.[17]
Effective molecular radius is the size a molecule displays in solution.[18][19] The table of permselectivity
for different substances contains examples.

Molecular formulas[edit]
Chemical formula types[edit]
Main article: Chemical formula
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.[20] It is the
simplest integer ratio of the chemical elements that constitute it.[21] For example, water is always
composed of a 2:1 ratio of hydrogen to oxygen atoms, and ethyl alcohol or ethanol 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[edit]
Main article: Structural formula
3D (left and center) and 2D (right) representations of the terpenoidmolecule atisane
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 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[edit]
Main article: Molecular geometry

Structure and STM image of a "cyanostar" dendrimermolecule.[22]

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[edit]
Main article: Spectroscopy
Hydrogen can be removed from individual H2TPP molecules by applying excess voltage to the tip of a scanning
tunneling microscope (STM, a); this removal alters the current-voltage (I-V) curves of TPP molecules,
measured using the same STM tip, from diode like (red curve in b) to resistor like (green curve). Image (c)
shows a row of TPP, H2TPP and TPP molecules. While scanning image (d), excess voltage was applied to
H2TPP at the black dot, which instantly removed hydrogen, as shown in the bottom part of (d) and in the rescan
image (e). Such manipulations can be used in single-molecule electronics.[23]
Molecular spectroscopy deals with the response (spectrum) of molecules interacting with probing
signals of known energy (or frequency, according to Planck's formula). Molecules have quantized
energy levels that can be analyzed by detecting the molecule's energy exchange
through absorbance or emission.[24] Spectroscopy does not generally refer to diffractionstudies where
particles such as neutrons, electrons, or high energy X-rays interact with a regular arrangement of
molecules (as in a crystal).
Microwave spectroscopy commonly measures changes in the rotation of molecules, and can be
used to identify molecules in outer space. Infrared spectroscopy measures changes in 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 actually 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[edit]
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[25] 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[edit]
 Atom
 Chemical polarity
 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 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

 Chemistry portal
 Molecular and cell biology portal

 Physics portal

References[edit]
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