• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Free energy calculation of molecular assemblies

Research Project

Project/Area Number 18066020
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Science and Engineering
Research InstitutionNagoya University (2008-2009)
Institute for Molecular Science (2006-2007)

Principal Investigator

OKAZAKI Susumu  Nagoya University, 大学院・工学研究科, 教授 (70194339)

Co-Investigator(Kenkyū-buntansha) YAMADA Atsushi  名古屋大学, 大学院・工学研究科, 助教 (10390676)
三浦 伸一  分子科学研究所, 計算分子科学研究系, 助手 (10282865)
Project Period (FY) 2006 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥16,600,000 (Direct Cost: ¥16,600,000)
Fiscal Year 2009: ¥2,700,000 (Direct Cost: ¥2,700,000)
Fiscal Year 2008: ¥5,100,000 (Direct Cost: ¥5,100,000)
Fiscal Year 2007: ¥5,100,000 (Direct Cost: ¥5,100,000)
Fiscal Year 2006: ¥3,700,000 (Direct Cost: ¥3,700,000)
Keywords分子動力学 / 化学反応 / 溶液・コロイド / 理論化学 / 分子動力学法 / 自由エネルギー / 量子ダイナミクス / ミセル / プロトン移動 / (D)分子動力学 / (E)化学反応 / (H)溶液・コロイド / (P)理論化学 / 熱力学積分法 / 球状ミセル / 可溶化反応 / 量子古典混合系近似 / 量子効果 / プロトン移動反応 / マイクロエマルジョン / 付加反応
Research Abstract

Materials consist of numerous molecules, and chemical reactions take place in these molecular assemblies. In this study, computer simulations have been performed in order to elucidate molecular behaviors of chemical reactions from a microscopic view. We focus on two chemical reactions : (1) solubilization, which is represented by a phenomenon that a detergent removes dirt, from a microscopic view, insertion of a solute molecule into a spherical micelle core, and (2) proton transfer reaction, which is a transfer of a nucleus of a hydrogen atom.

Report

(6 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report   Self-evaluation Report ( PDF )
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • Research Products

    (34 results)

All 2010 2009 2008 2007 2006

All Journal Article (13 results) (of which Peer Reviewed: 12 results) Presentation (21 results)

  • [Journal Article] A quantum equation of motion for chemical reaction systems on an adiabatic double-well potential surface in solution based on the framework of mixed quantum-classical molecular dynamics2008

    • Author(s)
      A. Yamada, S. Okazaki
    • Journal Title

      J. Chem. Phys. 128

    • NAID

      120005510925

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] A quantum equation of motion for chemical reaction systems on an adiabatic double-well potential surface in solution based on the framework of mixed quantum-classical molecular dynamics2008

    • Author(s)
      A.Yamada and S.Okazaki
    • Journal Title

      J.Chem.Phys. 128

    • NAID

      120005510925

    • Related Report
      2008 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Structure and thermal fluctuation of one-dimensional AgO chains on Ag (110) surfaces studied with density functional theory and Monte Carlo simulations2008

    • Author(s)
      I. Nakai, Y. Matsumoto, N. Takagi and S. Okazaki
    • Journal Title

      J. Chem. Phys 129

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Quantum Equation of Motion for Chemical Reaction Systems on an Adiabatic Double-well Potential Surface in Solution based on the Framework of Mixed Quantum-Classical Molecular Dynamics2008

    • Author(s)
      A. Yamada and S. Okazaki
    • Journal Title

      J. Chem. Phys. 128

      Pages: 0445071-8

    • NAID

      120005510925

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Free energy of water permeation into hydrophobic core of sodium dodecyl sulfate micelle by molecular dynamics calculation2007

    • Author(s)
      N. Yoshii, S. Okazaki
    • Journal Title

      J. Chem. Phys. 126

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Electrostatic potential gap at the interface between triethylamine and water phases studied by molecular dynamics simulation2007

    • Author(s)
      S. Kajimoto, N. Yoshii, J. Hobley, H. Fukumura, S. Okazaki
    • Journal Title

      Chem. Phys. Lett. 448

      Pages: 70-74

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] A molecular dynamics study of structure and dynamics of surfactant molecules in SDS spherical micelle2007

    • Author(s)
      N. Yoshii, S. Okazaki
    • Journal Title

      Condens. Matt. Phys. 4

      Pages: 573-578

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Free energy of water permeation into hydrophobic core of sodium dodecyl sulfate micelle by molecular dynamics calculation2007

    • Author(s)
      N.Yoshii and S.Okazaki
    • Journal Title

      J.Chem.Phys. 126

    • Related Report
      2008 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Electrostatic potential gap at the interface between triethylamine and water phases studied by molecular dynamics simulation2007

    • Author(s)
      S.Kajimoto, N.Yoshii, J.Hobley, H.Fukumura, and S.Okazaki
    • Journal Title

      Chem.Phys.Lett. 448

      Pages: 70-74

    • Related Report
      2008 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] A molecular dynamics study of structure and dynamics of surfactant molecules in SDS spherical micelle2007

    • Author(s)
      N.Yoshii and S.Okazaki
    • Journal Title

      Condens.Matt.Phys. 4

      Pages: 573-578

    • Related Report
      2008 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Electrostatic potential gap at the interface between triethyla mine and water phases studied by molecular dynamics simulation2007

    • Author(s)
      S. Kajimoto, N. Yoshii, J. Hobley, H. Fukumura and S. Okazaki
    • Journal Title

      Chem. Phys. Lett. 448

      Pages: 70-74

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A molecular dynamics study of structure and dynamics of surfactant molecules in SDS spherical micelle2007

    • Author(s)
      N. Yoshii and S. Okazaki
    • Journal Title

      Condens. Matt. Phys. 10

      Pages: 573-578

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Free energy of water permeation into hydrophobic core of sodium dodecyl sulfate micelle by molecular dynamics calculation2007

    • Author(s)
      N.Yoshii, S.Okazaki
    • Journal Title

      J Chem. Phys. 126

      Pages: 0961011-3

    • Related Report
      2006 Annual Research Report
  • [Presentation] Molecular Dynamics Calculation for Biomembrane2010

    • Author(s)
      S. Okazaki
    • Organizer
      Fifty Years of Biophysics Research at Nagoya University
    • Place of Presentation
      Nagoya
    • Related Report
      2009 Final Research Report
  • [Presentation] Mixed Quantum-Classical Molecular Dynamics Simulation of Intramolecular One-Dimensional Proton Transfer Reaction in Solution2010

    • Author(s)
      A. Yamada, S. Okazaki
    • Organizer
      International Symposium on Molecular Theory for Real Systems
    • Place of Presentation
      Kyoto
    • Related Report
      2009 Final Research Report
  • [Presentation] Molecular dynamics study of lipid bilayer modeling plasma membrane of normal/leukemic lymphocytes2009

    • Author(s)
      Y. Andoh, S. Okazaki
    • Organizer
      FOMMS 2009
    • Place of Presentation
      Blaine, USA
    • Related Report
      2009 Final Research Report
  • [Presentation] Free energy based molecular dynamics study of a spherical micelle - structural stability and solubilization by it2009

    • Author(s)
      K. Fujimoto, M. Kitabata, N. Yoshii, S. Okazaki
    • Organizer
      FOMMS 2009
    • Place of Presentation
      Blaine, USA
    • Related Report
      2009 Final Research Report
  • [Presentation] 溶液中の分子内プロトン移動反応に対する量子古典混合系分子動力学シミュレーション2009

    • Author(s)
      山田篤志、岡崎進
    • Organizer
      第32回溶液化学シンポジウム
    • Place of Presentation
      新潟コンベンションセンター
    • Related Report
      2009 Annual Research Report
  • [Presentation] 極性分子のSDSミセルへの可溶化自由エネルギー計算2009

    • Author(s)
      藤本和士、吉井範行、岡崎進
    • Organizer
      第23回分子シミュレーション討論会
    • Place of Presentation
      名古屋市中小企業振興会館
    • Related Report
      2009 Annual Research Report
  • [Presentation] Mixed Quantum-Classical Molecular Dynamics Simulation of Intramolecular Proton Transfer Reaction in Solution : One-Dimensional Quantization Model Study2009

    • Author(s)
      A.Yamada, S.Okazaki
    • Organizer
      The 69th Okazaki Conference on "New Frontier in Quantum Chemical Dynamics"
    • Place of Presentation
      Okazaki Conference Center
    • Related Report
      2009 Annual Research Report
  • [Presentation] Molecular Dynamics Calculation for Biomembrane2009

    • Author(s)
      Susumu Okazaki
    • Organizer
      Fifty Years of Biophysics Research at Nagoya University
    • Place of Presentation
      Nagoya University
    • Related Report
      2009 Annual Research Report
  • [Presentation] A Mixed Quantum-Classical Molecular Dynamics Approach to Proton Transfer Reaction of a Solute Molecule in Solution2008

    • Author(s)
      S. Okazaki, A. Yamada
    • Organizer
      15th International Conference on the Properties of Water and Steam (ICPWS)
    • Place of Presentation
      Berlin, Germany
    • Related Report
      2009 Final Research Report 2008 Self-evaluation Report
  • [Presentation] A Molecular Dynamics Study of Stability of SDS Micelle in Water and Solubilization of Solute Molecule by It2008

    • Author(s)
      S. Okazaki, N. Yoshii, K. Fujimoto
    • Organizer
      EMLG/JMLG Annual Meeting 2008
    • Place of Presentation
      Lisbon, Portugal
    • Related Report
      2009 Final Research Report 2008 Self-evaluation Report
  • [Presentation] Molecular dynamics study of micelle formation in water and solubilization of solute molecules by it2008

    • Author(s)
      S. Okazaki
    • Organizer
      International Symposium on Multi-scale Simulations of Biological and Soft Materials (MSBSM2008)
    • Place of Presentation
      Tokyo
    • Related Report
      2009 Final Research Report 2008 Self-evaluation Report
  • [Presentation] Molecular dynamics study of micelle formation in water and solubilization of solute molecules by it2008

    • Author(s)
      Susumu Okazaki
    • Organizer
      International Symposium on Multi-scale Simulations of Biological and Soft Materials (MSBSM 2008)
    • Place of Presentation
      Akihabara Convention Hall
    • Related Report
      2008 Annual Research Report
  • [Presentation] A Molecular Dynamics Study of Stability of SDS Micelle in Water and Solubilization of Solute Molecule by2008

    • Author(s)
      S. Okazaki, N. Yoshii, K. Fujimoto
    • Organizer
      EMLG/JMLG Annual Meeting 2008
    • Place of Presentation
      Fundacao Calouste Gulbenkian, Lisbon
    • Related Report
      2008 Annual Research Report
  • [Presentation] A Mixed Quantum-Classical Molecular Dynamics Approach to Proton Transfer Reaction of a Solute Molecule in Solution2008

    • Author(s)
      S. Okazaki, A. Yamada
    • Organizer
      15 th International Conference on the Properties of Water and Steam (ICPWS)
    • Place of Presentation
      Radisson SAS Hotel, Berlin
    • Related Report
      2008 Annual Research Report
  • [Presentation] ミセルの構造安定性と可溶化の分子動力学シミュレーション-自由エネルギー計算の立場から2008

    • Author(s)
      藤太和士、吉井範行、岡崎進
    • Organizer
      第22回分子シミュレーション討論会
    • Place of Presentation
      岡山大学
    • Related Report
      2008 Annual Research Report
  • [Presentation] A Molecular Dynamics Study of Free Energy of Micelle Formation in Water2007

    • Author(s)
      N. Yoshii, S. Okazaki
    • Organizer
      62nd Calorimetry Conference held jointly with The Japan Society of Calorimetry and Thermal Analysis(Calcon 2007)
    • Place of Presentation
      Hawaii
    • Related Report
      2009 Final Research Report 2008 Self-evaluation Report
  • [Presentation] A Molecular Dynamics Study of Free Energy of Micelle Formation in Water2007

    • Author(s)
      N. Yoshii and S. Okazaki
    • Organizer
      62nd Calorimetry Conference held jointly with The Japan Society of Calorimetry and Thermal Analysis
    • Place of Presentation
      Hawaii, USA
    • Related Report
      2007 Annual Research Report
  • [Presentation] A quantum dynamics simulation for proton transfer reaction in solution based upon a diabatic surface hopping method2006

    • Author(s)
      S. Okazaki, A. Yamada
    • Organizer
      12th International Conference on Retinal Proteins (ICRP) Satelite Meeting in Nagoya "Structure, Function & Evolution of Rhodopsins: Meachanisms of Proton Transfer and Color Tuning"
    • Place of Presentation
      Nagoya
    • Year and Date
      2006-06-12
    • Related Report
      2009 Final Research Report
  • [Presentation] A Quantum Molecular Dynamics Study of Energy Relaxation and Decoherence of Solute Vibration in Solution2006

    • Author(s)
      S. Okazaki
    • Organizer
      20th International Conference on Raman Spectroscopy(ICORS 2006)
    • Place of Presentation
      Yokohama
    • Related Report
      2009 Final Research Report 2008 Self-evaluation Report
  • [Presentation] A Molecular Dynamics Study of the Free Energy of Micelle Formation for SDS in Water and its Size Distribution2006

    • Author(s)
      N. Yoshii, S. Okazaki
    • Organizer
      16th Symposium on Thermophysical Properties
    • Place of Presentation
      Boulder, USA
    • Related Report
      2009 Final Research Report 2008 Self-evaluation Report
  • [Presentation] A quantum dynamics simulation for proton transfer reaction in solution based upon a diabatic surface hopping method2006

    • Author(s)
      S.Okazaki and A.Yamada
    • Organizer
      12th International Conference on Retinal Proteins (ICRP) Satelite Meeting in Nagoya "Structure, Function & Evolution of Rhodopsins : Meachanisms of Proton Transfer and Color Tuning"
    • Place of Presentation
      Nagoya
    • Related Report
      2008 Self-evaluation Report

URL: 

Published: 2006-04-01   Modified: 2018-03-28  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi