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Alanyl dipeptide potential‐derived net atomic charges and bond dipoles, and their variation with molecular conformation
Author(s) -
Williams Donald E.
Publication year - 1990
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360291005
Subject(s) - chemistry , dipeptide , conformational isomerism , dipole , electronegativity , crystallography , atomic charge , bond length , molecular geometry , molecule , computational chemistry , molecular physics , crystal structure , biochemistry , organic chemistry , amino acid
The elctric potential around the alanyl dipeptide in various conformations was calculated from ab initio 6–31G wave functions. Seven conformations were selected to correspond to calculated local energy minima of the isolated molecule. Five additional conformations were selected corresponding to the alanylalanine crystal structure and the polypeptide conformations in a right‐handed α‐helix, left‐handed α‐helix, parallel β‐sheet, and anti‐parallel β‐sheet. The electric potential surrounding each conformer was fitted with either net charges at atomic sites or dipolles at bond sites by least squares. Either choice reproduced the electric potential with relative rms deviations of 1.9–4.8%. Values for net atomic charges or bond dipoles were usually in line with expectations based on electronegativity. The imino and carbonyl groups showed their expected polarities, although there were considerable deviations from zero group charge. Net atomic charges on and near the α‐carbon changed substantially with the conformation angles; bond dipoles around the α‐carbon showed analogous behavior.