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.
ASJC Scopus subject areas
- Computer Science Applications
- Physical and Theoretical Chemistry