On the van der Waals interactions and the stability of polypeptide chains in helical conformations

摘要: In this work, we aim to investigate the contribution of van der Waals (vdW) interactions stability polypeptides in helical conformations studying infinitely long chains alanine and glycine with density functional theory. To account for vdW interactions, have used interatomic pairwise dispersion approach proposed by Tkatchenko–Scheffler (TS), TS self-consistent screening (SCS) that self-consistently includes long-range electrostatic effects (TS + SCS), D2 D3 methods Grimme et al., Langreth–Lundqvist procedure treats nonlocally correlation part approximation exchange-correlation (xc) (called DF). First, tested performance these strategies a set representative hydrogen bonded dimers. Next, studied polyalanine polyglicine π-helix, α-helix, -helix, 27, polyproline-II fully extended structure. We found DF methodology combination modified version Becke exchange (optB86b), D2, D3, TS, TS + SCS Perdew–Burke–Ernzerhof xc functional, describe fairly well dimer association energies. Furthermore, method predict very similar stabilities even though describing is different one D2/D3 TS/TS + SCS. doubles π α helices if are taken into account. © 2015 Wiley Periodicals, Inc.