Hydrogen bond

A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, like nitrogen, oxygen or fluorine (thus the name "hydrogen bond", which must not be confused with a covalent bond to hydrogen). The hydrogen must be covalently bonded to another electronegative atom to create the bond. These bonds can occur between molecules (intermolecularly), or within different parts of a single molecule (intramolecularly).^[2] The hydrogen bond (5 to 30 kJ/mole) is stronger than a van der Waals interaction, but weaker than covalent or ionic bonds. This type of bond occurs in both inorganic molecules such as water and organic molecules such as DNA.

Intermolecular hydrogen bonding is responsible for the high boiling point of water (100 °C). This is because of the strong hydrogen bond, as opposed to other group 16 hydrides. Intramolecular hydrogen bonding is partly responsible for the secondary, tertiary, and quaternary structures of proteins and nucleic acids.

Bonding

A hydrogen atom attached to a relatively electronegative atom is a hydrogen bond donor. This electronegative atom is usually fluorine, oxygen, or nitrogen. An electronegative atom such as fluorine, oxygen, or nitrogen is a hydrogen bond acceptor, regardless of whether it is bonded to a hydrogen atom or not. An example of a hydrogen bond donor is ethanol, which has a hydrogen bonded to oxygen; an example of a hydrogen bond acceptor which does not have a hydrogen atom bonded to it is the oxygen atom on diethyl ether.

Examples of hydrogen bond donating (donors) and hydrogen bond accepting groups (acceptors)

Carboxylic acids often form dimers in vapor phase.

A hydrogen attached to carbon can also participate in hydrogen bonding when the carbon atom is bound to electronegative atoms, as is the case in chloroform, CHCl₃. The electronegative atom 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 often described as an electrostatic dipole-dipole interaction. However, it also has some features of covalent bonding: it is directional, strong, produces interatomic distances shorter than sum of van der Waals radii, and usually involves a limited number of interaction partners, which can be interpreted as a kind of valence. These covalent features are more significant when acceptors bind hydrogens from more electronegative donors.

The partially covalent nature of a hydrogen bond raises the questions: "To which molecule or atom does the hydrogen nucleus belong?" and "Which should be labeled 'donor' and which 'acceptor'?" Usually, this is easy to determine simply based on interatomic distances in the X—H^...Y system: X—H distance is typically ~110 pm, whereas H^...Y distance is ~160 to 200 pm. Liquids that display hydrogen bonding are called associated liquids.

The length of hydrogen bonds depends on bond strength, temperature, and pressure. The bond strength itself is dependent on temperature, pressure, bond angle, and environment (usually characterized by local dielectric constant).

Hydrogen bonds in DNA and proteins

Hydrogen bonding between guanine and cytosine, one of two types of base pairs in DNA.

Hydrogen bonding also plays an important role in determining the three-dimensional structures adopted by proteins and nucleic bases. 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 the secondary structure of 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. Hydrogen bonds also play a part in forming the tertiary structure of protein through interaction of R-groups.