Isomerization of a Peptidic Fragment Studied Theoretically in Vacuum and in Explicit Water Solvent at Finite Temperature

Abstract

The cis?trans isomerization of N-methylacetamide, a molecular model of the polypeptide chain, is examined via umbrella sampling Car?Parrinello MD and classical MD, in both gas and solution phases at 300 K. A new analysis of the C(O)?N bond interconversion and a full examination of the solvent shell structure are presented. Copyright © 2004 American Chemical Society.