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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 pairA lone pair is an electron pair without bonding or sharing with other atoms. It often exhibits a negative polar character with its high charge density. It is used in the formation of dative bonds, for example, the creation of the hydronium, HO+, ion occur 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 nucleusThe nucleus atomic nucleus is the center of an atom. It is composed of one or more protons and usually some neutrons as well. The number of protons in an atom's nucleus is called the atomic number, and determines which element the atom is (for example hyd 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 protonFor alternative meanings see proton (disambiguation). Proton Classification Subatomic particle Fermion Hadron Baryon Nucleon Proton Properties Mass: 938 MeV/ c2 Electric Charge: 1. 6 × 10−19 C Spin: 1/2 In physics, the proton is a subatomic particle) 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 waterDrinking water This article focuses on water as we experience it every day. The water (molecule) article describes water from a scientific and technical perspective. Water is an abundant substance on Earth. It exists in many forms, such as sea, rain, and 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.)
In iceIce is the solid form of water. The phase transition occurs when liquid water is cooled below 0 °C (273. 15 K, 32 °F) at standard atmospheric pressure. Ice can be formed at higher temperatures in pressurized environments, and water will remain a liquid or, 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.
Indeed, in pure water under conditions of standard temperature and pressure, this latter formulation is applicable only rarely; on average about one in every 107 molecules gives up a proton to another water molecule, in accordance with 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. 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).
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