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The general notation for hydrogen bonding is Dn−H···Ac, where the solid line represents a polar covalent bond, and the dotted or dashed line indicates the hydrogen bond. [6] The most frequent donor and acceptor atoms are nitrogen (N), oxygen (O), and fluorine (F), due to their high electronegativity and ability to engage in stronger ...
The hydrogen bonding of β-strands need not be perfect, but can exhibit localized disruptions known as β-bulges. The hydrogen bonds lie roughly in the plane of the sheet, with the peptide carbonyl groups pointing in alternating directions with successive residues; for comparison, successive carbonyls point in the same direction in the alpha helix.
Secondary structure is defined by hydrogen bonding, so the exact definition of a hydrogen bond is critical. The standard hydrogen-bond definition for secondary structure is that of DSSP, which is a purely electrostatic model. It assigns charges of ±q 1 ≈ 0.42e to the carbonyl carbon and oxygen, respectively, and charges of ±q 2 ≈ 0.20e to ...
In chemistry, dimerization is the process of joining two identical or similar molecular entities by bonds. The resulting bonds can be either strong or weak. Many symmetrical chemical species are described as dimers, even when the monomer is unknown or highly unstable. [1] The term homodimer is used when the two subunits are identical (e.g.
The first theoretical study of the water dimer was an ab initio calculation published in 1968 by Morokuma and Pedersen. [10] Since then, the water dimer has been the focus of sustained interest by theoretical chemists concerned with hydrogen bonding—a search of the CAS database up to 2006 returns over 1100 related references (73 of them in 2005).
Hydrogen bonds contribute to the stability of ion pairs with e.g. protonated ammonium ions, and with anions is formed by deprotonation as in the case of carboxylate, phosphate etc; then the association constants depend on the pH. Entropic driving forces for ion pairing (in absence of significant H-bonding contributions) are also found in ...
According to one definition, a turn is a structural motif where the C α atoms of two residues separated by a few (usually 1 to 5) peptide bonds are close (less than 7 Å [0.70 nm]). [1] The proximity of the terminal C α atoms often correlates with formation of an inter main chain hydrogen bond between the corresponding residues. Such hydrogen ...
Hydrogen bonds of the form A--H•••B occur when A and B are two highly electronegative atoms (usually N, O or F) such that A forms a highly polar covalent bond with H so that H has a partial positive charge, and B has a lone pair of electrons which is attracted to this partial positive charge and forms a hydrogen bond. [23]: 702 Hydrogen ...