The structure of pure liquid water and solvent
effects on the cis-trans isomerization of a
model peptidic fragment, N-methylacetamide:
ab initio and empirical model simulation studies
Dr. Yves MANTZ
Department of Chemistry and
Applied Biosciences ETH Zurich
CH-6900 Lugano, Switzerland
Lundi 22 mai 2006, 11 heures
Salle RAPHAEL 1 - site d'Ivry-sur-Seine
Liquid water's structure is important to understand and is currently a
vigorous topic of debate in the literature. In this presentation,
structural correlations in liquid water are systematically examined using
increasingly realistic theoretical models, including empirical rigid,
empirical polarizable, empirical flexible with classical and quantum
nuclei, and ab initio (DFT-BLYP) with classical nuclei at 300 and 353 K
and quantum nuclei at 300 K.
The results obtained from well-converged Car-Parrinello MD and MD
simulations support a (traditional) tetrahedral model of liquid water and
provide a useful benchmark for the study of solvated N-methylacetamide
(NMA), a simple molecular model of the peptide linkage in proteins.
Because of its small size, NMA is amenable to study by high
resolution/accuracy experimental and theoretical techniques that are not
easily applicable to large systems. Two distinctly different theoretical
descriptions, an ab initio (DFT-BLYP) and an empirical (CHARMM22) model,
of NMA in explicit water solvent are employed to characterize the solvent
structure at equilibrium and changes in solvation structure accompanying
the cis-trans isomerization of NMA. Additionally, the thermodynamic,
structural, and electronic properties of NMA along a preselected
isomerization pathway, i.e., the torsional twist angle about the peptidic
C(O)-N bond, are probed by performing both umbrella-sampling CPMD and MD
as well as static calculations. An electronic restructuring of the peptide
bond is revealed using state-of-the-art analysis tools, namely ELF and
Wannier functions, shedding further light on (changes in) the peptide
partial-double bond in proteins.