Bader's electron density analysis of hydrogen bonding in secondary structural elements of protein

Abstract

The hydrogen-bonding (H-bonding) interactions in α-helical and β-sheet model peptides have been studied by using the atoms-in-molecule (AIM) approach. The relative importance of NH···O and CH···O H-bonding interactions in the different secondary elements such as α-helix, parallel, and antiparallel β-sheets have been assessed. The electron density values at the NH···O bond are higher than those of the CH···O bonds in the α-helical conformation. The electron density values at the H-bonded critical points (HBCPs) corresponding to NH···O and CH···O interactions are nearly equal in the parallel β-sheet of the order of 10^-3 au, whereas in the case of antiparallel β-sheets, ρ(r_c) values for NH···O and CH···O interactions are of the order of 10^-2 and 10^-3 au, respectively. It is interesting to point out here that the weakening of NH···O interactions in the parallel β-sheet arrangement is evident from the AIM analysis. This is concomitant with the increase in the NH···O distance in the parallel β-sheet conformation. In addition to the clear description of H-bonding by electron density at the HBCP, possible good linear relationships between the electron density at ring critical points (RCP) and stabilization energy (SE) have been observed corresponding to the various β-sheet conformations.