As the name "hydrogen bond" implies, one part of the bond involves a hydrogen atom. The hydrogen must be attached to a strongly electronegative heteroatom, such as oxygen or nitrogen, which is called the hydrogen-bond donor. This electronegative element attracts the electron cloud from around the hydrogen nucleus and, by decentralizing the cloud, leaves the atom with a positive partial charge. Because of the small size of hydrogen relative to other atoms and molecules, the resulting charge, though only partial, nevertheless represents a large charge density. A hydrogen bond results when this strong positive charge density attracts a lone pair of electrons on another heteroatom, which becomes the hydrogen-bond acceptor.
The hydrogen bond is not like a simple attraction between point charges, however. It possesses some degree of orientational preference, and can be shown to have some of the characteristics of a covalent bond. This covalency tends to be more extreme when acceptors bind hydrogens from more electronegative donors.
Strong covalency in a hydrogen bond begs the question, to which molecule or atom does the hydrogen nucleus belong, as well as which should be labelled "donor" and which called "acceptor." According to chemical convention, the donor generally is that atom to which, on separation of donor and acceptor, the retention of the hydrogen nucleus (or proton) would cause no increase in the atom's positive charge. The acceptor meanwhile is the atom or molecule that would become more positive by retaining the positively charged proton.
The most ubiquitous, and perhaps simplest, example of a hydrogen bond is found between water molecules. In a discrete water molecule, water has two hydrogen atoms and one oxygen atom. Two molecules of water can form a hydrogen bond between them. The oxygen of one water molecule has two lone pairs of electrons, each of which can form a hydrogen bond with hydrogens on two other water molecules. This can repeat so that every water molecule is H-bonded with four other molecules (two through its two lone pairs, and two through its two hydrogen atoms.)
Were the bond strengths more equivalent, one might instead find the atoms of two interacting water molecules partitioned into two polyatomic ions of opposite charge, specifically hydroxide and hydronium.
Hydrogen bonding also plays an important role in determining the three-dimensional structures adopted by proteins and nucleic acids. In these macromolecules, bonding between parts of the same macromolecule cause it to fold into a specific shape, which helps determine the molecule's physiological or biochemical role. The double helical structure of DNA, for example, is due largely to hydrogen bonding between the base pairs, which link one complementary strand to the other and enable replication.
In proteins, hydrogen bonds form between the backbone oxygens and amide hydrogens. When the spacing of the amino acid residues participating in a hydrogen bond occurs regularly between positions i and i+4, an alpha helix is formed. When the spacing is less, between positions i and i+3, then a 310 helix is formed. When two strands are joined by hydrogen bonds involving alternating residues on each participating strand, a beta sheet is formed.(See also protein folding).