In science, a molecule is the smallest particle of a pure chemical substance that still retains its chemical composition and properties. A molecule consists of two or more atoms joined by shared pairs of electrons in a chemical bond. It may consist of atoms of the same chemical element, as with oxygen (O₂), or of different elements, as with water (H₂O). Abstractly, a single atom may be considered a molecule, as it is when referred to collectively with molecules of multiple atoms, but in practice the use of the word molecule is usually confined to chemical compounds, of multiple atoms.

A substance that consists of molecules is a molecular substance or molecular compound.

Figure 1. 3D (left and center) and 2D (right) representations of the terpenoid, atisane . In the 3D model on the left, carbon atoms are represented by gray spheres, white spheres represent the hydrogen atoms and the cylinders represent the bonds. The model is enveloped in a "mesh" representation of the molecular surface, colored by areas of positive (red) and negative (blue) electric charge. In the 3D model (center), the light-blue spheres represent carbon atoms, the white spheres are hydrogen atoms, and the cylinders in between the atoms correspond to single-bonds.

Most molecules are much too small to be seen with the naked eye, but there are exceptions. DNA, a macromolecule, can reach macroscopic sizes.

A property of molecules is the integer ratio of the elements that constitute the compound, the empirical formula. For example, in their pure forms, water is always composed of a 2:1 ratio of hydrogen to oxygen, 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 ratio as ethanol, for instance. Molecules with the same atoms in different arrangements are called isomers.

Chemical formula on the other hand reflects the exact number of atoms that compose a molecule. The molecular mass is calculated from the chemical formula and is expressed in conventional units equal to 1/12 from the mass of a ¹²C isotope atom.

Molecules have fixed equilibrium geometries—bond lengths and angles—that are dictated by the laws of quantum mechanics. A pure substance is composed of molecules with the same 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 very different biochemical activities.

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