Molecule

For the scientific journal, see Molecules (journal).

Atomic force microscopy image of a PTCDA molecule, which contains five carbon rings in a non-linear arrangement.

A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings.

A molecule (/ˈmɒlɪkjuːl/ from Latin moles "mass") is an electrically neutral group of two or more atoms held together by chemical bonds. 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 in fact monoatomic molecules.

A molecule may be homonuclear, that is, it consists of atoms of a single 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 bonds such as hydrogen bonds or ionic bonds are generally not considered single molecules.

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 without presence of any definable molecule, but also without any of the regularity of repeating units that characterizes crystals.

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.

History and etymology

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 Fr. molécule (1678), from modern 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.

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. 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.

Molecular size

Arrangement of polyvinylidene fluoride molecules in a nanofiber – transmission electron microscopy image.

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. 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.

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

Molecular formulas

Chemical formula types

Main article: Chemical formula

The chemical formula for a molecule uses a single 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 a single typographic line of symbols, which may include subscripts and superscripts.

A compound's empirical formula is a very simple type of chemical formula. It is the simplest integer ratio of the chemical elements that constitute it. 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

Main article: Structural formula

3D (left and center) and 2D (right) representations of the terpenoid molecule 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

Main article: Molecular geometry

Structure and STM image of a "cyanostar" dendrimer molecule.

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 isomers, may have very similar physico-chemical properties and at the same time different biochemical activities.

Molecular spectroscopy

Main article: Spectroscopy

Hydrogen can be removed from individual H₂TPP molecules by applying excess voltage to the tip of a scanning tunneling microscope (STAM, 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 re-scan image (e). Such manipulations can be used in single-molecule electronics.

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. Spectroscopy does not generally refer to diffraction studies where particles such as neutrons, electrons, or high energy X-rays interact with a regular arrangement of molecules (as in a crystal).

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". 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 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
• Van der Waals molecule
• Diatomic molecule
• Small molecule
• Chemical polarity
• Molecular geometry
• Covalent bond
• Noncovalent bonding
• list of compounds for a list of chemical compounds
• List of molecules in interstellar space
• Software for molecular mechanics modeling
• Molecular Hamiltonian
• Molecular ion
• Molecular orbital
• Molecular modelling
• Molecular design software
• WorldWide Molecular Matrix
• Periodic Systems of Small Molecules

External links

• Molecule of the Month – School of Chemistry, University of Bristol