Ab initio and empirical model MD simulation studies of solvent effects on the properties of N-methylacetamide along a cis-trans isomerization pathway.

The properties of N-methylacetamide along a cis-trans isomerization pathway described by twisting about the C(O)-N bond are examined at finite temperature both in vacuo and in explicit water solvent. Two distinctly different theoretical descriptions, an ab initio (DFT-BLYP) and an empirical (CHARMM22) model, are studied in order to permit an assessment of the dominant forces active in the system. An analysis of the solvent structure at equilibrium and changes in solvation structure accompanying isomerization is, therefore, given for each model. Many-body polarization effects absent under CHARMM22 but present in the ab initio model are found to have a profound influence on the system. The electronic structure of the NMA molecule predicted by the ab initio method along the reaction coordinate is examined in order to shed further light on changes in peptide "partial-double" bond character [C(O)-N] as isomerization takes place. A new statistical-mechanical interpretation of the entropy change during a chemical reaction is presented to help interpret the thermochemistry of the simple reaction.