Polyatomic molecules are electrically neutral groups of three or more atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their lack of electrical charge. 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 the presence of any definable molecule, but also without any of the regularity of repeating units that characterizes crystals.
Molecular Chemistry and Molecular Physics
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 result in the formation and breakage of chemical bonds. 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) comprising two or more atoms. 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. Molecules that exhibit stereoisomerism may have very similar physico-chemical properties and at the same time different biochemical activities. A compound's empirical formula 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. 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. For instance, dimethyl ether has the same ratios as ethanol. Molecules with the same atoms in different arrangements are called isomers. For example, carbohydrates 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.
Molecular and Empirical Formulas
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. For example, carbon dioxide Figure 1 is written CO2, having three atoms. Water Figure 2, H2O, also has three atoms, but a different molecular shape than carbon dioxide. Propane Figure 3 is a trimer of carbon bonded to hydrogen, as seen in the illustration. Sulfur exists as many different allotropes, but the most common is S8 seen as the closed chain structure in Figure 4.