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231223s2009 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.21025
|2 doi
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|a pubmed24n0599.xml
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|a DE-627
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|a eng
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|a Komeiji, Yuto
|e verfasserin
|4 aut
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|a Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvation
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|c 2009
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|a Text
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|a ƒaComputermedien
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|a ƒa Online-Ressource
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|a Date Completed 19.12.2008
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|a Date Revised 21.11.2013
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|a published: Print
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|a Citation Status MEDLINE
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|a Copyright 2008 Wiley Periodicals, Inc.
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|a 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
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|a Journal Article
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|a Research Support, Non-U.S. Gov't
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|a Solvents
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|a Water
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|a 059QF0KO0R
|2 NLM
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|a Ishikawa, Takeshi
|e verfasserin
|4 aut
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|a Mochizuki, Yuji
|e verfasserin
|4 aut
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|a Yamataka, Hiroshi
|e verfasserin
|4 aut
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|a Nakano, Tatsuya
|e verfasserin
|4 aut
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 30(2009), 1 vom: 15. Jan., Seite 40-50
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
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|g volume:30
|g year:2009
|g number:1
|g day:15
|g month:01
|g pages:40-50
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|u http://dx.doi.org/10.1002/jcc.21025
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