Hydrogen bond

A hydrogen bond in chemistry and biochemistry is a type of intermolecular force between chargeslocated on different molecules or different parts of one large molecule. Although stronger than most other intermolecular forces, hydrogen bonds are much weaker than both the ionic and covalent bond.

As the name 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. This electronegative element has the effect of removing the electron cloud surrounding the hydrogen nucleus, leaving the atom with a positive partial charge[?]. Because the hydrogen atom is small on the molecular scale, this partial charge represents a very strong charge density. A hydrogen bond involves the positive proton (hydrogen nucleus) becoming attracted to a lone pair of negatively charged electrons on another heteroatom, the hydrogen bond acceptor.

Despite the implications of the above description, the hydrogen bond is not a simple electrostatic attraction. It possesses some degree of directionality, and can be shown to have some of the characteristics of a covalent. This covalency is stronger the more electronegative the donor atom is, and hence is seen most strongly in the molecule hydrogen fluoride (HF).

Generally speaking, the donor is that atom to which, in the absence of the hydrogen bond, the attachment of the hydrogen atom would not increase the positive formal charge on the molecule, whereas attaching the hydrogen to the acceptor atom would leave that portion of the molecule with a positive formal charge (dipole).

The most ubiquitous, and perhaps simplest, example of a hydrogen bond is found in the interaction among 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 2 lone pairs, and two through its 2 hydrogen atoms.)

H-O-H^...O-H₂

Liquid water's high boiling point is due to the high number of hydrogen bonds each molecule can have relative to its low molecular mass. Water is unique because its oxygen atom has 2 lone pairs and 2 hydrogen atoms, meaning that the total number of bonds of a water molecule is 4. (For example, hydrogen fluoride - which has 2 lone pairs on the F atom but only one H atom - can have a total of only 2 bonds.)

H-F^...H-F^...H-F

In solid water (i.e., ice), the crystalline lattice is dominated by a regular array of hydrogen bonds which space the water molecules farther apart than they are in liquid water. This accounts for water's decrease in density upon freezing. In other words, the presence of hydrogen bonds enables ice to float, because this spacing causes ice to be less dense than liquid water.

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.

H-O^- H₃O⁺

Indeed, in pure water under conditions of standard temperature and pressure, this latter formulation is applicable only rarely, on average but once in every 10^-14 times (which is the value of the dissociation constant for water under such conditions).

Hydrogen bonding also plays an important role in determining the three-dimensional structures adopted by proteins and nucleic acids (see protein folding problem[?]). In these macromolecules, intramolecular hydrogen bonding between groups in the same protein or nucleic acid molecule cause the molecule to fold into specific shapes, thus affecting molecular function.

For example, the classic double helix of DNA is due to the presence of hydrogen bonds between the bases of the nucleic acids in each strand of the helix.

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.