title: Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvation.
abstract: Fragment Molecular Orbital based-Molecular Dynamics (FMO-MD, Komeiji et al., Chem Phys Lett 2003, 372, 342) is an ab initio MD method suitable for large molecular systems. Here, FMO-MD was implemented to conduct full quantum simulations of chemical reactions in explicit solvation. Several FMO-MD simulations were performed for a sphere of water to find a suitable simulation protocol. It was found that annealing of the initial configuration by a classical MD brought the subsequent FMO-MD trajectory to faster stabilization, and also that use of bond constraint in the FMO-MD heating stage effectively reduced the computation time. Then, the blue moon ensemble method (Sprik and Ciccotti, J Chem Phys 1998, 109, 7737) was implemented and was tested by calculating free energy profiles of the Menschutkin reaction (H3N + CH3Cl --> +H3NCH3 + Cl-) in the presence and absence of the solvent water via FMO-MD. The obtained free energy profiles were consistent with the Hammond postulate in that stabilization of the product by the solvent, namely hydration of Cl-, shifted the transition state to the reactant-side. Based on these FMO-MD results, plans for further improvement of the method are discussed.
authors.affiliation: CREST Project, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan. y-komeiji@aist.go.jp
authors.forename: Yuto
authors.initials: Y
authors.lastname: Komeiji
authors.forename: Takeshi
authors.initials: T
authors.lastname: Ishikawa
authors.forename: Yuji
authors.initials: Y
authors.lastname: Mochizuki
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Yamataka
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Nakano
mesh_terms: D003198:Computer Simulation; D007700:Kinetics; D008956:Models, Chemical; D011789:Quantum Theory; D012995:Solubility; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D012997:Solvents; D014867:Water