Fragment Molecular Orbital method‐based Molecular Dynamics (FMO‐MD) as a simulator for chemical reactions in explicit solvation

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. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009

[1]  Kazuo Kitaura,et al.  Second order Møller-Plesset perturbation theory based upon the fragment molecular orbital method. , 2004, The Journal of chemical physics.

[2]  Mark S. Gordon,et al.  The Effective Fragment Potential Method: A QM-Based MM Approach to Modeling Environmental Effects in Chemistry , 2001 .

[3]  Nino Russo,et al.  Solvation effects on reaction profiles by the polarizable continuum model coupled with the Gaussian density functional method , 1998 .

[4]  Hajime Hirao,et al.  Transition-state optimization by the free energy gradient method : Application to aqueous-phase Menshutkin reaction between ammonia and methyl chloride , 2001 .

[5]  Mark S. Gordon,et al.  Solvation of the Menshutkin Reaction: A Rigorous Test of the Effective Fragment Method , 1999 .

[6]  Takeshi Ishikawa,et al.  How does an S(N)2 reaction take place in solution? Full ab initio MD simulations for the hydrolysis of the methyl diazonium ion. , 2008, Journal of the American Chemical Society.

[7]  J E Leffler,et al.  Parameters for the Description of Transition States. , 1953, Science.

[8]  Kenneth B. Wiberg,et al.  Solvent Effects on Methyl Transfer Reactions. 1. The Menshutkin Reaction , 1999 .

[9]  Kaori Fukuzawa,et al.  Fragment molecular orbital method: use of approximate electrostatic potential , 2002 .

[10]  R A Sayle,et al.  RASMOL: biomolecular graphics for all. , 1995, Trends in biochemical sciences.

[11]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[12]  Mark S. Gordon,et al.  Solvent Effects on the SN2 Reaction: Application of the Density Functional Theory-Based Effective Fragment Potential Method , 2005 .

[13]  Jiali Gao,et al.  A priori computation of a solvent-enhanced SN2 reaction profile in water : the Menshutkin reaction , 1991 .

[14]  Emili Besalú,et al.  Analysis of the changes on the potential energy surface of Menshutkin reactions induced by external perturbations , 1996 .

[15]  M. Klein,et al.  Nosé-Hoover chains : the canonical ensemble via continuous dynamics , 1992 .

[16]  H. C. Andersen.  Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations , 1983 .

[17]  Fumio Hirata,et al.  RISM-SCF study of the free-energy profile of the Menshutkin-type reaction NH3+CH3Cl→NH3CH3++Cl− in aqueous solution , 1999 .

[18]  Takeshi Ishikawa,et al.  A fully quantum mechanical simulation study on the lowest n-π* state of hydrated formaldehyde , 2007 .

[19]  Yuichi Inadomi,et al.  PEACH 4 with ABINIT-MP: a general platform for classical and quantum simulations of biological molecules. , 2004, Computational biology and chemistry.

[20]  Mark E. Tuckerman,et al.  Explicit reversible integrators for extended systems dynamics , 1996 .

[21]  Kazuo Kitaura,et al.  The three-body fragment molecular orbital method for accurate calculations of large systems , 2006 .

[22]  Kazuo Kitaura,et al.  The importance of three-body terms in the fragment molecular orbital method. , 2004, The Journal of chemical physics.

[23]  Yuto Komeiji.  Implementation of the blue moon ensemble method , 2007 .

[24]  André Melo,et al.  Unusual solvent effect on a SN2 reaction. A quantum-mechanical and kinetic study of the Menshutkin reaction between 2-amino-1-methylbenzimidazole and iodomethane in the gas phase and in acetonitrile. , 2006, The journal of physical chemistry. B.

[25]  Yuichi Inadomi,et al.  Fragment molecular orbital method: application to molecular dynamics simulation, ‘ab initio FMO-MD’ , 2003 .

[26]  Yuto Komeiji,et al.  Fragment molecular orbital method: analytical energy gradients , 2001 .

[27]  Umpei Nagashima,et al.  A parallelized integral-direct second-order Møller–Plesset perturbation theory method with a fragment molecular orbital scheme , 2004 .

[28]  George S. Hammond,et al.  A Correlation of Reaction Rates , 1955 .

[29]  G. Ciccotti,et al.  Constrained reaction coordinate dynamics for the simulation of rare events , 1989 .

[30]  Michiel Sprik,et al.  Free energy from constrained molecular dynamics , 1998 .

[31]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[32]  Miquel Solà,et al.  Analysis of Solvent Effects on the Menshutkin Reaction , 1991 .

[33]  Makoto Taiji,et al.  Fast and accurate molecular dynamics simulation of a protein using a special‐purpose computer , 1997 .

[34]  Peter A. Kollman,et al.  Gradient SHAKE: An improved method for constrained energy minimization in macromolecular simulations , 1995 .

[35]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[36]  Yuto Komeiji,et al.  Change in a protein's electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin , 2007, J. Comput. Chem..

[37]  Yutaka Akiyama,et al.  Fragment molecular orbital method: application to polypeptides , 2000 .

[38]  Yuji Mochizuki,et al.  Large scale MP2 calculations with fragment molecular orbital scheme , 2004 .