title: Ensemble of transition state structures for the cis-trans isomerization of N-methylacetamide.
abstract: The cis-trans isomerization of N-methylacetamide (NMA), a model peptidic fragment, is studied theoretically in vacuo and in explicit water solvent at 300 K using the metadynamics technique. The computed cis-trans free energy difference is very similar for NMA(g) and NMA(aq), in agreement with experimental measurements of population ratios and theoretical studies at 0 K. By exploiting the flexibility in the definition of a pair of recently introduced collective variables (Branduardi, D.; Gervasio, F. L.; Parrinello, M. J. Chem. Phys. 2007, 126, 054103), an ensemble of transition state structures is generated at finite temperature for both NMA(g) and NMA(aq), as verified by computing committor distribution functions. Ensemble members of NMA(g) are shown to have correlated values of the backbone dihedral angle and a second dihedral angle involving the amide hydrogen atom. The dynamical character of these structures is preserved in the presence of solvent, whose influence on the committor functions can be modeled using effective friction/noise terms.
authors.affiliation: Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland. yves.mantz@netl.doe.gov
authors.forename: Yves A
authors.initials: YA
authors.lastname: Mantz
authors.forename: Davide
authors.initials: D
authors.lastname: Branduardi
authors.forename: Giovanni
authors.initials: G
authors.lastname: Bussi
authors.forename: Michele
authors.initials: M
authors.lastname: Parrinello
mesh_terms: D000081:Acetamides / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D012996:Solutions; D013237:Stereoisomerism; D014867:Water / Q000737:chemistry
chemical_list: D000081:Acetamides; D012996:Solutions; D014867:Water; C018595:N-methylacetamide