DEVELOPMENT OF MULTILEVEL FRAGMENT MOLECULAR ORBITAL METHOD

• Project/Area Number: 20350004
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Physical chemistry
• Research Institution: Kyoto University
• Principal Investigator: KITAURA Kazuo Kyoto University, 薬学研究科, 教授 (30132723)
• Co-Investigator(Kenkyū-buntansha): NAKANISHI Isao 近畿大学, 薬学部, 教授 (10362576)
• Project Period (FY): 2008 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥19,370,000 (Direct Cost: ¥14,900,000、Indirect Cost: ¥4,470,000); Fiscal Year 2010: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000); Fiscal Year 2009: ¥7,410,000 (Direct Cost: ¥5,700,000、Indirect Cost: ¥1,710,000); Fiscal Year 2008: ¥8,320,000 (Direct Cost: ¥6,400,000、Indirect Cost: ¥1,920,000)
• Keywords: 生体高分子 / 電子状態計算法 / フラグメント分子軌道法 / 量子・古典融合法 / 溶媒の連続誘電体モデル / 電子状態計算 / FMO法 / 分子シミュレーション

Research Abstract

We have develped the multilevel fragment molecular orbital method in which effective fragment potential (EFP), molecular mechanics (MM), and polarizable continuum solvent model (PCM) have been interfaced with the the fragment molecular orbital (FMO) method. The method facilitates geometry optimizations and molecular dynamics simulations of large molecular systems and is expected to be usuful in simulation studies of biomolecules.

Research Products

• [Journal Article] Systematic Study of the Embedding Potential Description in the Fragment Molecular Orbital Method (2010)
  • Author(s): D.G.Fedorov, L.V.Slipchenko, K.Kitaura
  • Journal Title: J.Phys.Chem.A Volume: 114 Pages: 8742-8753
  • Peer Reviewed
• [Journal Article] A combined effective potential-fragment molecular orbital method. I. The energy expression and initial applications (2009)
  • Author(s): T.Nagata, D.G.Fedorov, K.Kitaura, M.S.Gordon
  • Journal Title: J.Chem.Phys. 131 Pages: 24101-24112
  • Peer Reviewed
• [Journal Article] A combined effective potential-fragment molecular orbital method. I. The energy expression and initial applications (2009)
  • Author(s): T.Nagata, D.G.Fedorov, K.Kitaura, M.S.Gordon
  • Journal Title: J.Chem.Phys. 13 Pages: 24101-24112
  • Peer Reviewed
• [Journal Article] The role of the exchange in the embedding electrostatic potential for the fragment molecular orbital method (2009)
  • Author(s): D.G.Fedorov, K.Kitaura
  • Journal Title: J.Chem.Phys. 13 Pages: 171106-171109
  • Peer Reviewed
• [Journal Article] Derivatives of the approximated electrostatic potentials in the fragment molecular orbital method (2009)
  • Author(s): Takeshi Nagata, Dmitri G. Fedorov, Kazuo Kitaura
  • Journal Title: Chem. Phys. Lett. (in press)
  • Peer Reviewed
• [Journal Article] A combined effective fragment potential-fragment molecular orbital method II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin
  • Author(s): T.Nagata, D.G.Fedorov, T.Sawada, K.Kitaura, M.S.Gordon
  • Journal Title: J.Chem.Phys. 134 in press
  • Peer Reviewed
• [Journal Article] Fully analytic gradient in the fragment molecular orbital method
  • Author(s): T.Nagata, K.Brorsen, D.G.Fedorov, K.Kitaura, M.S.Gordon
  • Journal Title: J.Cehm.Phys. 134 in press
  • Peer Reviewed
• [Journal Article] A combined effective fragment potential-fragment molecular orbital method II.Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin
  • Author(s): T.Nagata, D.G.Fedorov, T.Sawada, K.Kitaura, M.S.Gordon
  • Journal Title: J.Chem.Phys. Volume: 134(印刷中)
  • Peer Reviewed
• [Journal Article] Fully analytic gradient in the fragment molecular orbital method
  • Author(s): T.Nagata, K.Brorsen, D.G.Fedorov, K.Kitaura, M.S.Gordon
  • Journal Title: J.Chem.Phys. Volume: 134(印刷中)
  • Peer Reviewed
• [Presentation] Geometry Optimization of Protein-Ligand Complexes using the Fragment Molecular Orbital Method Combined with Molecular Mechanics (2010)
  • Author(s): Kazuo Kitaura
  • Organizer: Pacifichem 2010
  • Place of Presentation: Honololu.
  • Year and Date: 2010-12-16
• [Presentation] Geometry Optimization of Protein-Ligand Complexes using the Fragment Molecular Orbital Method Combined with Molecular Mechanics (2010)
  • Author(s): Kazuo Kitaura
  • Organizer: Pacifichem 2010
  • Place of Presentation: Honolulu Convension Center(Honolulu, USA)
  • Year and Date: 2010-12-16
• [Presentation] Binding free energy calculations of protein-ligand complexes using the fragment molecular orbital method combined with continuum solvent model (2009)
  • Author(s): Kazuo Kitaura
  • Organizer: 238^<th> ACS National Meeting
  • Place of Presentation: Washinton DC.
  • Year and Date: 2009-08-19
• [Presentation] Binding free energy calculations of protein-ligand complexes using the fragment molecular orbital method combined with continuum solvent model (2009)
  • Author(s): Kazuo Kitaura
  • Organizer: 238th ACS National Meeting
  • Place of Presentation: Washintongton DC. USA
  • Year and Date: 2009-08-19
• [Presentation] Electronic structure calculations of proteins using the fragment molecular orbital method (2008)
  • Author(s): 北浦和夫
  • Organizer: TSRC workshop on Many-Body Interactions : From Quantum Mechanics to Force Fields
  • Place of Presentation: Telluride. USA
  • Year and Date: 2008-07-10
• [Book] Detailed Electronic Structure Studies Revealing the Nature of Protein-Ligand Binding, in "The Fragment Molecular Orbital Method : Practical Applications to Large Molecular Systems",(D.G. Fedorov, K.Kitaura (Eds.))(Boca Raton) (2009)
  • Author(s): I.Nakanishi, D.G.Fedorov, K.Kitaura
  • Publisher: CRC press
• [Book] Theoretical Background of the fragment Molecular Orbital (FMO) Method and Its Implementation in GAMESS, in "The Fragment Molecular Orbital Method : Practical Application to Large Molecular Systems",(D.G.Fedorov, K.Kitaura(Eds.)) (2009)
  • Author(s): D.G.Fedorov, K.Kitaura
  • Publisher: CRC press
• [Book] The fragment molecular orbital method : Practical applications to large molecular systems (2009)
  • Author(s): D.G.Fedorov, K.Kitaura 編
  • Total Pages: 276
  • Publisher: CRC Press
• [Remarks] ホームページ等