Alanyl dipeptide potential‐derived net atomic charges and bond dipoles, and their variation with molecular conformation

Abstract

AbstractThe 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.