Conformation dynamics in peptides: quantum chemical calculations and molecular dynamics simulations on N-acetylalanyl- N'-methylamide

Abstract

The preferred conformations of N-acetylalanyl- N'-methylamide were determined by means of ab initio quantum chemical and empirical force field calculations. The stability order of these conformations in solution was estimated using a quantum chemical reaction field model. The various conformers were the starting point for molecular dynamics calculations in the vacuum and in solution using the gromos force field. The vacuum simulations demonstrate that the minimum conformations have to be considered as part of larger regions of conformational flexibility. Simulation in aqueous solution shows significant changes of the contributions of the various conformations exhibiting the α-helical arrangement as important structure which does not occur in the gas phase.