title: Application of Adaptive QM/MM Methods to Molecular Dynamics Simulations of Aqueous Systems.
abstract: The difference-based adaptive solvation quantum mechanics/molecular mechanics (adQM/MM) method (J. Chem. Theory Comput.2009, 5, 2212) as implemented in the Amber software was applied to the study of several chemical processes in solution. The adQM/MM method is based on an efficient selection scheme that enables quantum-mechanical treatment of the active region of a molecular system in solution taking explicitly into account diffusion of solvent molecules between the QM and the MM regions. Specifically, adQM/MM molecular dynamics simulations are carried out to characterize (1) the free energy profiles of halide exchange SN2 reactions in water, (2) the hydration structure of the Cl(-) ion, and (3) the solvation structure of the zwitterionic form of glycine in water. A comparison is made with the results obtained using standard MM and QM/MM methods as well as with the available fully QM and experimental data. In all cases, it is shown that the adaptive QM/MM simulations provide a physically realistic description of the system of interest.
authors.affiliation: Department of Chemistry and Biochemistry and ‡San Diego Supercomputer Center, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States.
authors.forename: Kyoyeon
authors.initials: K
authors.lastname: Park
authors.affiliation: Department of Chemistry and Biochemistry and ‡San Diego Supercomputer Center, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States.
authors.forename: Andreas W
authors.initials: AW
authors.lastname: Götz
authors.affiliation: Department of Chemistry and Biochemistry and ‡San Diego Supercomputer Center, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States.
authors.forename: Ross C
authors.initials: RC
authors.lastname: Walker
authors.affiliation: Department of Chemistry and Biochemistry and ‡San Diego Supercomputer Center, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States.
authors.forename: Francesco
authors.initials: F
authors.lastname: Paesani