Premium
Fragment Molecular Orbital method‐based Molecular Dynamics (FMO‐MD) as a simulator for chemical reactions in explicit solvation
Author(s) -
Komeiji Yuto,
Ishikawa Takeshi,
Mochizuki Yuji,
Yamataka Hiroshi,
Nakano Tatsuya
Publication year - 2008
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21025
Subject(s) - fragment molecular orbital , molecular dynamics , solvation , chemistry , molecular orbital , computational chemistry , qm/mm , molecule , organic chemistry
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 (H 3 N + CH 3 Cl → + H 3 NCH 3 + 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. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009