title: Exploring Potential Energy Surfaces of Large Systems with Artificial Force Induced Reaction Method in Combination with ONIOM and Microiteration.
abstract: Development of efficient methods for finding chemical reaction pathways has been one of the central subjects of theoretical chemistry. Recently, the artificial force induced reaction (AFIR) method enabled automated search for associative reaction pathways between multiple reactant molecules and has been applied to reactions involving a few tens of atoms. To expand its applicability to large systems, we combined it with the geometrical microiteration technique. With this extension, full optimization of transition state structures of enzymatic reactions in the protein became possible within the QM/MM framework. Performance of the microiteration-AFIR method was tested for a single water catalyzed Aldol reaction in (H2O)299 cluster and for an enzymatic reaction of the isopenicillin N synthase, where the potential energy surfaces were calculated by the ONIOM(QM/MM) method. These numerical tests demonstrated that the present method is promising in predicting reaction pathways that take place within an active site (consisting of tens of atoms) in a very large environment such as protein and solution.
authors.affiliation: Department of Chemistry, Faculty of Science, Hokkaido University , Sapporo 060-0810, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Maeda
authors.affiliation: Fukui Institute for Fundamental Chemistry, Kyoto University , Kyoto 606-8103, Japan.
authors.forename: Erika
authors.initials: E
authors.lastname: Abe
authors.affiliation: Fukui Institute for Fundamental Chemistry, Kyoto University , Kyoto 606-8103, Japan.
authors.forename: Miho
authors.initials: M
authors.lastname: Hatanaka
authors.affiliation: Department of Chemistry, Faculty of Science, Hokkaido University , Sapporo 060-0810, Japan.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Taketsugu
authors.affiliation: Fukui Institute for Fundamental Chemistry, Kyoto University , Kyoto 606-8103, Japan.|Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University , Atlanta, Georgia 30322, United States.
authors.forename: Keiji
authors.initials: K
authors.lastname: Morokuma