Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method

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• 作者：Hiroya Nakata ; Dmitri G. Fedorov ; Takeshi Nagata ; Kazuo Kitaura ; Shinichiro Nakamura
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2015
• 出版时间：July 14, 2015
• 年：2015
• 卷：11
• 期：7
• 页码：3053-3064
• 全文大小：687K
• ISSN：1549-9626

文摘

The fully analytic first and second derivatives of the energy in the frozen domain formulation of the fragment molecular orbital (FMO) were developed and applied to locate transition states and determine vibrational contributions to free energies. The development is focused on the frozen domain with dimers (FDD) model. The intrinsic reaction coordinate method was interfaced with FMO. Simulations of IR and Raman spectra were enabled using FMO/FDD by developing the calculation of intensities. The accuracy is evaluated for S_N2 reactions in explicit solvent, and for the free binding energies of a protein鈥搇igand complex of the Trp cage protein (PDB: 1L2Y). FMO/FDD is applied to study the keto鈥揺nol tautomeric reaction of phosphoglycolohydroxamic acid and the triosephosphate isomerase (PDB: 7TIM), and the role of amino acid residue fragments in the reaction is discussed.