Ab Initio MD studies of hydrogen bonding in water and peptidic fragments
Glenn Martyna, IBM Research, Yorktown Heights, NY

Liquid water is a ubiquitous solvent whose importance cannot be underestimated. However, much remains unknown about the radial and angular structure of this hydrogen bonding liquid both at room temperature and physiological temperatures. Therefore, large scale ab inito MD simulations have been performed to examine neat water and a novel analysis of the results yields insight into the hydrogen bonding patterns and changes in these patterns induced by temperature. N-methylacetamide or NMA, CH3-CO-NH-CH3,is of interest as a model of the peptide linkage. Its behavior at points along the cis-trans isomerization pathway contributes to our understanding of the nonprolyl peptide C(O)-N bond, a ubiquitous structural proteinaceous element that can be involved in the rate-limiting steps of protein restructuring. Measurement of the radial and angular dependence of the solvation shell structure of NMA(aq) is helpful in elucidating the effect of water solvent on protein function and is now feasible experimentally, making theoretical structural studies particularly relevant. Increasingly powerful computing platforms and algorithms, now, permit, for the first time, an ``ab initio'' computational study of NMA in vacuum and in explicit water solvent at finite temperature to address these issues. A pictorial description of the amide group emerges that enhances our understanding of chemical bonding, and a detailed analysis of NMA(aq) provides structural data for comparison to anticipated new experiments.

Electronic Structure in Chemistry I

The Preliminary Program for 37th Middle Atlantic Regional Meeting (May 22-25, 2005)