The interactions described so far are not limited to molecules of any specific composition. However, there is one important intermolecular interaction specific to molecules containing an oxygen, nitrogen, or fluorine atom that is attached to a hydrogen atom. This interaction is the hydrogen bond, an interaction of the form A―H···B, where A and B are atoms of any of the three elements mentioned above and the hydrogen atom lies on a straight line between the nuclei of A and B. A hydrogen bond is about 10 times as strong as the other interactions described above, and when present it dominates all other types of intermolecular interaction. It is responsible, for example, for the existence of water as a liquid at normal temperatures; because of its low molar mass, water would be expected to be a gas. The hydrogen bond is also responsible for the existence as solids of many organic molecules containing hydroxyl groups (―OH); the sugars glucose and sucrose are examples.

Many interpretations of the hydrogen bond have been proposed. One that fits into the general scheme of this article is to think of the A―H unit as being composed of an A atomic orbital and a hydrogen 1s orbital and to consider a lone pair of electrons on B as occupying a B orbital. When the three atoms are aligned, these three orbitals can form three molecular orbitals: one bonding, one largely nonbonding, and one antibonding. There are four electrons to accommodate (two from the original A―H bond and two from the lone pair). They occupy the bonding and nonbonding orbitals, leaving the antibonding orbital vacant. Hence, the net effect is to lower the energy of the AHB grouping and thus to constitute an intermolecular bond. Once again, on encountering the hydrogen bond, one encounters a twist in the conventional attitude; the question raised by this interpretation is not why such a bond occurs but why it does not occur more generally. The explanation lies in the small size of the hydrogen atom, which enables the balance of energies in the molecular orbital scheme to be favourable to bonding.

Hydrogen bonding occurs to atoms other than nitrogen, oxygen, and fluorine if they carry a negative charge and hence are rich in readily available electrons. Thus, hydrogen bonding is one of the principal mechanisms of hydration of anions in aqueous solution (the bonding of H₂O molecules to the solute species) and hence contributes to the ability of water to act as a good solvent for ionic compounds. It also contributes to the hydration of organic compounds containing oxygen or nitrogen atoms and thus accounts for the much greater aqueous solubility of alcohols than hydrocarbons.

Hydrogen bonds are of great significance in determining the structure of biologically significant compounds, most notably proteins and deoxyribonucleic acid (DNA). An important feature of the structure of proteins (which are polypeptides, or polymers formed from amino acids) is the existence of the peptide link, the group ―CO―NH―, which appears between each pair of adjacent amino acids. This link provides an NH group that can form a hydrogen bond to a suitable acceptor atom and an oxygen atom, which can act as a suitable receptor. Therefore, a peptide link provides the two essential ingredients of a hydrogen bond. The keying together of such peptide groups by hydrogen bonding of the type shown in Figure 17 was examined in detail by Pauling and Robert Corey, who formulated a set of rules, the Pauling-Corey rules, for its implementation. The implication of these rules is the existence of two types of structure for a polypeptide, which is either a helical form (the α helix) or a pleated sheet form (the β-pleated sheet). All polypeptides have one structure or the other and often have alternating regions of each. Since the properties and behaviour of an enzyme molecule (a particular class of polypeptides) are determined by its shape and, in particular, by the shape of the region where the molecule it acts on needs to attach, it follows that hydrogen bonds are centrally important to the functions of life.

Hydrogen bonds are also responsible for the transmission of genetic information from one generation to another, for they are responsible for the specific keying together of cytosine with guanine and thymine with adenine moieties that characterizes the structure of the DNA double helix.

Ionic solids

The structures of ionic solids have already been described in some detail. They consist of individual ions that are stacked together in such a way that the assembly has the lowest possible energy. These ions may be monatomic (as in sodium chloride, which consists of Na⁺ and Cl⁻ ions) or the ions may themselves be covalently bonded polyatomic species. An example of the latter is ammonium nitrate, in which the cation is NH₄⁺ and the anion is NO₃⁻; the N―H and N―O bonds within the ions are covalent. Ionic compounds are generally hard and brittle and have high melting points.