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The canonical Watson-Crick base pairs, G:C and A:T/U as well as most of the non-canonical ones are stabilized by two or more (e.g. 3 in the case of G:C cWW) hydrogen bonds. Justifiably, a significant amount of research on non-canonical base pairs has been carried out towards bench-marking their strengths (interaction energies) and (geometric ...
An ubiquitous example of a hydrogen bond is found between water molecules. In a discrete water molecule, there are two hydrogen atoms and one oxygen atom. The simplest case is a pair of water molecules with one hydrogen bond between them, which is called the water dimer and is often used as a model system. When more molecules are present, as is ...
Purines form hydrogen bonds to pyrimidines, with adenine bonding only to thymine in two hydrogen bonds, and cytosine bonding only to guanine in three hydrogen bonds. This arrangement of two nucleotides binding together across the double helix (from six-carbon ring to six-carbon ring) is called a Watson-Crick base pair.
An additional type of bond is a "non-bond", indicated with ., to indicate that two parts are not bonded together. For example, aqueous sodium chloride may be written as [Na+].[Cl-] to show the dissociation. An aromatic "one and a half" bond may be indicated with :; see § Aromaticity below.
For hydrocarbons, the DBE (or IHD) tells us the number of rings and/or extra bonds in a non-saturated structure, which equals the number of hydrogen pairs that are required to make the structure saturated, simply because joining two elements to form a ring or adding one extra bond (e.g., a single bond changed to a double bond) in a structure reduces the need for two H's.
The A–T pairing is based on two hydrogen bonds, while the C–G pairing is based on three. In both cases, the hydrogen bonds are between the amine and carbonyl groups on the complementary bases. Nucleobases such as adenine, guanine, xanthine , hypoxanthine , purine, 2,6-diaminopurine , and 6,8-diaminopurine may have formed in outer space as ...
Alternate hydrogen bonding patterns, such as the wobble base pair and Hoogsteen base pair, also occur—particularly in RNA—giving rise to complex and functional tertiary structures. Importantly, pairing is the mechanism by which codons on messenger RNA molecules are recognized by anticodons on transfer RNA during protein translation .
Examples are the transition metals where the non-bonding pairs do not influence molecular geometry and are said to be stereochemically inactive. In molecular orbital theory (fully delocalized canonical orbitals or localized in some form), the concept of a lone pair is less distinct, as the correspondence between an orbital and components of a ...