title: Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method.
abstract: 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(N)2 reactions in explicit solvent, and for the free binding energies of a protein-ligand complex of the Trp cage protein (PDB: 1L2Y ). FMO/FDD is applied to study the keto-enol tautomeric reaction of phosphoglycolohydroxamic acid and the triosephosphate isomerase (PDB: 7TIM ), and the role of amino acid residue fragments in the reaction is discussed.
authors.affiliation: Department of Biomolecular Engineering, Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.|Research Cluster for Innovation, RIKEN , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.|Japan Society for the Promotion of Science , Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan.
authors.forename: Hiroya
authors.initials: H
authors.lastname: Nakata
authors.affiliation: Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology , 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.
authors.forename: Dmitri G
authors.initials: DG
authors.lastname: Fedorov
authors.affiliation: Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology , 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.|Graduate School of System Informatics, Kobe University , 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Nagata
authors.affiliation: Graduate School of System Informatics, Kobe University , 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan.
authors.forename: Kazuo
authors.initials: K
authors.lastname: Kitaura
authors.affiliation: Research Cluster for Innovation, RIKEN , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
authors.forename: Shinichiro
authors.initials: S
authors.lastname: Nakamura
mesh_terms: D006877:Hydroxamic Acids / Q000737:chemistry* / Q000378:metabolism; D011789:Quantum Theory; D014305:Triose-Phosphate Isomerase / Q000737:chemistry* / Q000378:metabolism
chemical_list: D006877:Hydroxamic Acids; C008886:phosphoglycolohydroxamate; D014305:Triose-Phosphate Isomerase