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A hydrogen bond is the attractive force between the hydrogen attached to an electronegative atom of one molecule and an electronegative atom of a different molecule. Usually the electronegative atom is oxygen, nitrogen, or fluorine, which has a partial negative charge. The hydrogen then has the partial positive charge. It should not be confused with a covalent bond. It is not a true bond but a particularly strong dipole-dipole force. The hydrogen bond is stronger than a van der Waals interaction, but weaker than covalent or ionic bonds.
Hydrogen bonds in water
|The most ubiquitous and perhaps simplest example of a hydrogen bond is found between water molecules. In a discrete water molecule, there are two hydrogen atoms and one oxygen atom. Two molecules of water can form a hydrogen bond between them; the simplest case, when only two molecules are present, is called the water dimer and is often used as a model system. When more molecules are present, as is the case with liquid water, more bonds are possible because the oxygen of one water molecule has two lone pairs of electrons, each of which can form a hydrogen bond with a hydrogen on another water molecule. This can repeat such that every water molecule is H-bonded with up to four other molecules, as shown in the figure (two through its two lone pairs, and two through its two hydrogen atoms). Hydrogen bonding strongly affects the crystal structure of ice, helping to create an open hexagonal lattice. The density of ice is less than the density of water at the same temperature; thus, the solid phase of water floats on the liquid, unlike most other substances. Liquid water's high boiling point is due to the high number of hydrogen bonds each molecule can form, relative to its low molecular mass. Owing to the difficulty of breaking these bonds, water has a very high boiling point, melting point, and viscosity compared to otherwise similar liquids not conjoined by hydrogen bonds. Water is unique because its oxygen atom has two lone pairs and two hydrogen atoms, meaning that the total number of bonds of a water molecule is up to four. For example, hydrogen fluoride—which has three lone pairs on the F atom but only one H atom—can form only two bonds; (ammonia has the opposite problem: three hydrogen atoms but only one lone pair).
Hydrogen bonds in nucleic acids
In RNA, hydrogen bonds occur in all forms of base pairing, in canonical Watson-Crick ones, as depicted in the picture on the right, in GU wobble ones, in noncanonical ones, and they also happen in many other motifs and tertiary interactions, like base triples, quadruplexes, A-Minor motifs and ribose zippers.