Do the neighboring residues in a polypeptide affect the electron distribution of an amino acid significantly? A quantitative study using the quantum theory of atoms in molecules (QTAIM)

Geometries, as well as bond and atomic properties obtained with the atoms-in-molecules theory applied on B3LYP/6-31++G**//B3LYP/6-31G** charge densities, of the N-formyl amides of the nine tripeptides obtained by combining glycine, alanine, and serine around a central glycine residue were analyzed to check how the properties of the central residue are modified by other amino acids bonded to it. All of the molecules were optimized from an alpha-helix conformation that was also displayed by the optimized structure. Significant variations of the geometry (especially remarkable for dihedral angles) and atomic properties of the central glycine residue are observed when it is attached to a serine residue whose side chain is involved in a hydrogen bond.