Development of an intramolecular basis set superposition error correction and its applications to biomolecules

• Project/Area Number: 19550028
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Physical chemistry
• Research Institution: National Institute of Advanced Industrial Science and Technology
• Principal Investigator: FEDOROV Dmitri National Institute of Advanced Industrial Science and Technology, 計算科学研究部門, 主任研究員 (60357879)
• Project Period (FY): 2007 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2008: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2007: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
• Keywords: 化学反応 / FMO / AFO / zeolite / GAMESS / BSSE / TDDFT / 励起状態 / heparin

Research Abstract

研究成果の概要:巨大分子用量子化学計算法(FMO 法)の開発を続けて、励起状態に拡張し、分子結晶と共有結合結晶の為新機能を開発し、溶媒中等の構造最適化を行える様にした。応用として、螺旋多糖heparin の水和電子状態と分子結晶quinacridone の電子励起又はzeolite における小分子吸着過程を調べた。基底関数重ね合わせ誤差補正法のプログラムを開発した。

Research Products

• [Journal Article] Derivatives of the approximated electrostatic potentials in the fragment molecular orbital method (2009)
  • Author(s): T. Nagata, D. G. Fedorov, K. Kitaura
  • Journal Title: Chem. Phys.Lett 475 Pages: 124-131
• [Journal Article] Excited state geometry optimizations by time-dependent density functional theory based on the fragment molecular orbital method (2009)
  • Author(s): M. Chiba, D. G. Fedorov, T. Nagata, K. Kitaura
  • Journal Title: Chem. Phys. Lett 474 Pages: 227-232
• [Journal Article] Structural and interaction analysis of helical heparin oligosaccharides with the fragment molecular orbital method (2009)
  • Author(s): T. Sawada, D. G. Fedorov, K. Kitaura
  • Journal Title: Int.J. Quant. Chem 109 Pages: 2033-2045
• [Journal Article] Excited state geometry optimizations by time-dependent density functional theory based on the fragment molecular orbital method (2009)
  • Author(s): M. Chiba, D. G. Fedorov, T. Nagata, K. Kitaura
  • Journal Title: Chem. Phys. Lett. 474 Pages: 227-232
  • Peer Reviewed
• [Journal Article] Derivatives of the approximated electrostatic potentials in the Fragment Molecular Orbital method (2009)
  • Author(s): T. Nagata, D. G. Fedorov, K. Kitaura
  • Journal Title: Chem. Phys. Lett. 475 Pages: 124-131
  • Peer Reviewed
• [Journal Article] Structural and interaction analysis of helical heparin oligosaccharides with the fragment molecular orbital method (2009)
  • Author(s): T. Sawada, D. G. Fedorov, K. Kitaura
  • Journal Title: Int. J. Quant. Chem. 109 Pages: 2033-2045
  • Peer Reviewed
• [Journal Article] Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation (2009)
  • Author(s): H. Li, D. G. Fedorov, T. Nagata, K. Kitaura, J. H. Jensen, M. S. Gordon
  • Journal Title: J. Comp. Chem. (in press)
  • Peer Reviewed
• [Journal Article] A Combined Effective Fragment 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. (in press)
  • Peer Reviewed
• [Journal Article] Analytic gradient for the adaptive frozen orbital bond detachment in the fragment molecular orbital method (2009)
  • Author(s): D. G. Fedorov, P. V. Avramov, J. H. Jensend, K. Kitaura
  • Journal Title: Chem. Phys. Lett. (in press)
  • Peer Reviewed
• [Journal Article] Covalent Bond Fragmentation Suitable To Describe Solids in the Fragment Molecular Orbital Method (2008)
  • Author(s): D. G. Fedorov, J. H. Jensen, R. C. Deka, K. Kitaura
  • Journal Title: J.Phys. Chem A 112 Pages: 11808-11816
• [Journal Article] Theoretical Analysis of the Intermolecular Interaction Effects on the Excitation Energy of Organic Pigments: Solid State Quinacridone (2008)
  • Author(s): H. Fukunaga, D. G. Fedorov, M. Chiba, K. Nii, K. Kitaura
  • Journal Title: J. Phys. Chem A 112 Pages: 10887-10894
• [Journal Article] Polarizable continuum model with the fragment molecular orbital-based time-dependent density functional theory (2008)
  • Author(s): M. Chiba, D. G. Fedorov, K. Kitaura
  • Journal Title: J. Comp. Chem 29 Pages: 2667-2676
• [Journal Article] Polarizable continuum model with the fragment molecular orbital-based time-dependent density functional theory (2008)
  • Author(s): M. Chiba, D. G. Fedorov, K. Kitaura
  • Journal Title: J. Comp. Chem. 29 Pages: 2667-2676
  • Peer Reviewed
• [Journal Article] Theoretical Analysis of the Intermolecular Interaction Effects on the Excitation Energy of Organic Pigments : Solid State Quinacridone (2008)
  • Author(s): H. Fukunaga, D. G. Fedorov, M. Chiba, K. Nii, K. Kitaura
  • Journal Title: J. Phys. Chem. A 112 Pages: 10887-10894
  • Peer Reviewed
• [Journal Article] Covalent Bond Fragmentation Suitable To Describe Solids in the Fragment Molecular Orbital Method (2008)
  • Author(s): D. G. Fedorov, J. H. Jensen, R. C. Deka, K. Kitanra
  • Journal Title: J. Phys. Chem. A 112 Pages: 11808-11816
  • Peer Reviewed
• [Journal Article] Time-dependent density functional theory based upon the fragment molecular orbital method (2007)
  • Author(s): M. Chiba, D. G. Fedorov, K. Kitaura
  • Journal Title: .Chem. Phys 127 Pages: 104108-104108
• [Journal Article] Time-dependent density functional theory with the multilayer fragment molecular orbital method (2007)
  • Author(s): M. Chiba, D. G. Fedorov, K. Kitaura
  • Journal Title: Chem. Phys.Lett 444 Pages: 346-350
• [Journal Article] Extending the Power of Quantum Chemistry toLarge Systems with the Fragment Molecular Orbital Method (2007)
  • Author(s): D. G. Fedorov, K. Kitaura
  • Journal Title: J. Phys. Chem A 111 Pages: 6904-6914
• [Journal Article] Extending the Power of Quantum Chemistry to Large Systems with the Fragment Molecular Orbital Method (2007)
  • Author(s): D.G.Fedorov, K.Kitaura
  • Journal Title: J.Phys.Chem.A 111 Pages: 6904-6914
  • Peer Reviewed
• [Journal Article] Time-dependent density functional theory with the multilayer fragment molecular orbital method (2007)
  • Author(s): M.Chiba, D.G.Fedorov, K.Kitaura
  • Journal Title: Chem.Phys.Lett 444 Pages: 346-350
  • Peer Reviewed
• [Journal Article] Time-dependent denasity functional theory based upon the fragment mole cular orbital method (2007)
  • Author(s): M.Chiba, D.G.Fedorov, K.Kitaura
  • Journal Title: J.Chem.Phys 127
  • Peer Reviewed
• [Journal Article] A Combined Effective Fragment Potential -Fragment Molecular Orbital Method. I. The Energy Expression and Initial Applications.
  • Author(s): T. Nagata, D. G. Fedorov, K. Kitaura, M. S. Gordon
  • Journal Title: J. Chem. Phys., in press Pages: 0-0
• [Journal Article] Energy gradients in combined frag-ment molecular orbital and polarizable continuum model (FMO/PCM) calculation.
  • Author(s): H. Li, D. G. Fedorov, T. Nagata, K.Kitaura, J. H. Jensen, M. S. Gordon
  • Journal Title: J. Comp. Chem., in press Pages: 0-0
• [Presentation] faujasite zeolite に於ける小分子吸着過程の量子化学計算 (2009)
  • Author(s): D. G. Fedorov, 北浦和夫
  • Organizer: 日本化学会
  • Place of Presentation: 船橋市
  • Year and Date: 2009-03-29
• [Presentation] faujasite zeolite に於ける小分子吸着過程の量子化学計算 (2009)
  • Author(s): D. G. Fedorov , 北浦和夫
  • Organizer: 日本化学会
  • Place of Presentation: 船橋
• [Presentation] Ab initio level treatment of surfaces and solids in the framework of the fragment molecular orbital method (2009)
  • Author(s): D. G. Fedorov, K. Kitaura
  • Organizer: Simulations and dynamics for nanoscale and biological systems
  • Place of Presentation: Tokyo
• [Presentation] FMO法のGAMESSへの実装 (2008)
  • Author(s): D. G. Fedorov
  • Organizer: FMO symposium
  • Place of Presentation: 東京
  • Year and Date: 2008-09-21
• [Presentation] Quantum-Mechanical Calculations of Proteins : Why and How (2008)
  • Author(s): D. G. Fedorov, K. Kitaura
  • Organizer: WATOC2008
  • Place of Presentation: Sydney, Australia
  • Year and Date: 2008-09-16
• [Presentation] Large scale quantum-mechanical calculations with FMO (2008)
  • Author(s): D. G. Fedorov, K. Kitaura
  • Organizer: MSBSM2008
  • Place of Presentation: Tokyo
  • Year and Date: 2008-06-19
• [Presentation] Quantum-Mechanical Calculations of Proteins: Why and How (2008)
  • Author(s): D. G. Fedorov, K. Kitaura
  • Organizer: WATOC2008
  • Place of Presentation: Sydney (Australia)
• [Presentation] Large scale quantum-mechanical calculations with FMO, (2008)
  • Author(s): D. G. Fedorov, K. Kitaura
  • Organizer: MSBSM2008
  • Place of Presentation: Tokyo
• [Presentation] 巨大分子用量子化学計算法の開発とその適用 (2008)
  • Author(s): D. G. Fedorov , 北浦和夫
  • Organizer: 第六回産総研・豊田中研計算科学研究交流会
  • Place of Presentation: 裾野市
• [Presentation] FMO 法のGAMESS への実装 (2008)
  • Author(s): D. G. Fedorov
  • Organizer: FMO symposium
  • Place of Presentation: 東京
• [Presentation] Large Scale Quantum-Mechanical Calculations with the Fragment Molecular Orbital Method (2008)
  • Author(s): D. G. Fedorov, K. Kitaura
  • Organizer: CSW2008
  • Place of Presentation: Tsukuba
• [Presentation] Density functional theory for large systems (2007)
  • Author(s): D. G. Fedorov, K. Kitaura
  • Organizer: DFT2007
  • Place of Presentation: Amsterdam(Netherlands)
• [Presentation] Density functional theory for large systems (2007)
  • Author(s): D.G.Fedorov, K.Kitaura
  • Organizer: DFT2007
  • Place of Presentation: Amsterdam, Netherlands
• [Book] Theoretical Background of the Fragment Molecular Orbital (FMO) Method and Its Implementation in GAMESS. in The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems (2009)
  • Author(s): D. G. Fedorov, K. Kitaura
  • Publisher: CRC Press,Boca Raton, FL
• [Book] The Fragment Molecular Orbital - Based Time-Dependent DensityFunctional Theory for Excited States inLarge Systems. in The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems (2009)
  • Author(s): M. Chiba, D. G. Fedorov, K. Kitaura
  • Publisher: CRC Press, Boca Raton, FL
• [Book] Theoretical Background of the Fragment Molecular Orbital (FMO) Method and Its Implementation in GAMESS. In : The Fragmeat Molecular Orbital Method : Practical Applications to Large Molecular Systems(D. G. Fedorov, K. Kitaura, Eds.) (2009)
  • Author(s): D. G. Fedorov, K. Kitaura
  • Publisher: CRC press(in press)
• [Book] The Fragment Molecular Orbital-Based Time-Dependent Density Functional Theory for Excited States in Large Systems. In : The Fragment Molecular Orbital Method : Practical Applications to Large Molecular Systems(D. G. Fedorov, K. Kitaura, Eds.) (2009)
  • Author(s): M. Chiba, D. G. Fedorov, K. Kitaura
  • Publisher: CRC press(in press)
• [Remarks]
  • URL: http://staff.aist.go.jp/d.g.fedorov/