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

Novel approach to obtain enzymatic reaction mechanisms on the free energy surface

Research Project

Project/Area Number 23550021
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Physical chemistry
Research InstitutionOsaka Prefecture University

Principal Investigator

ASADA Toshio  大阪府立大学, 理学(系)研究科(研究院), 准教授 (10285314)

Project Period (FY) 2011 – 2013
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Fiscal Year 2013: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2012: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2011: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000)
Keywords分子動力学法 / 自由エネルギー勾配法 / 反応経路最適化 / QM/MM法 / 凝縮系 / 化学反応メカニズム / 応答核 / 自由エネルギー / Charge Response Kernel / 原子分極 / 分子動力学シミュレーション / プログラム開発 / Nudged Elastic Band法 / QM/MM 法 / 自由エネルギー面 / 構造最適化
Research Abstract

Most of the reactions can be observed in the molecular assembly such as liquid or biological systems. In order to design new functional molecules, the theoretical investigations are necessary to explore hidden inter-molecular interactions. In this research, new theoretical approaches and a computational program have been developed. Reasonable charge polarization of the molecules can be evaluated very quickly compared to the expensive quantum mechanical calculation. Using our techniques, the optimized reaction path in the molecular assemble can be obtained, and the impressive future development of the functional molecular design are provided.

Report

(4 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Research-status Report
  • 2011 Research-status Report
  • Research Products

    (44 results)

All 2013 2012 2011 Other

All Journal Article (7 results) (of which Peer Reviewed: 7 results) Presentation (34 results) (of which Invited: 5 results) Remarks (3 results)

  • [Journal Article] Theoretical Investigation of the Reaction Mechanism of ClONO2 + HCl → HNO3 + Cl2 on (H2O)n (n = 0-3) Cluster2013

    • Author(s)
      T.Asada, T.Okajima, and S.Koseki
    • Journal Title

      Journal of Physical Chemistry A

      Volume: 117 Issue: 33 Pages: 7928-7938

    • DOI

      10.1021/jp406175j

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Spin Orbit Coupling Analyses of the Geometrical Effects on Phosphorescence in Ir(ppy)3 and Its Derivatives2013

    • Author(s)
      Koseki; Na-oya Kamata, Toshio Asada, Shigeyuki Yagi, Hiroyuki Nakazumi Takeshi Matsushita
    • Journal Title

      Journal of Physical Chemistry C

      Volume: on line Issue: 10 Pages: 5314-5327

    • DOI

      10.1021/jp312032s

    • Related Report
      2013 Annual Research Report 2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] A minimal implementation of the AMBER-PAICS interface for Ab initio FMO-QM/MM-MD simulation.2013

    • Author(s)
      Takuya Okamoto
    • Journal Title

      Bulletin of the Chemical Society of Japan

      Volume: 86(2) Issue: 5 Pages: 210-222

    • DOI

      10.1002/jcc.21678

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] QM/MM investigation on the degradation mechanism of the electron transporting layer2011

    • Author(s)
      T.Asada, K.Ohta, T.Matsushita and S.Koseki
    • Journal Title

      Theo.Chem.Acc

      Volume: 130 Issue: 2-3 Pages: 439-448

    • DOI

      10.1007/s00214-011-1020-y

    • Related Report
      2013 Final Research Report 2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Reaction path optimization and vibrational frequency analysis via ab initio QM/MM free energy gradient (FEG) method : Application to Isomerization Process of Glycine in Aqueous Solution2011

    • Author(s)
      N.Takenaka, Y.Kitamura, Y.Koyano, T.Asada, and M.Nagaoka
    • Journal Title

      Theo.Chem.Acc

      Volume: 130 Issue: 2-3 Pages: 215-226

    • DOI

      10.1007/s00214-011-0962-4

    • Related Report
      2013 Final Research Report 2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Toward a New Approach for Determination of Solute's Charge Distribition to Analyze Interatomic Electrostatic Interactions in QM/MM Simulations2011

    • Author(s)
      K.Yamada, Y.Koyano, T.Okamoto, T.Asada, N.Koga, and M.Nagaoka
    • Journal Title

      J.Comp.Chem

      Volume: 32 Issue: 14 Pages: 3092-3104

    • DOI

      10.1002/jcc.21893

    • Related Report
      2013 Final Research Report 2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Ab initio electron correlation studies of the intracluster reaction NO^+ (H_2O)_n → H_3O^+(H_2O)_<n-2> (HONO) at n=4 and 52011

    • Author(s)
      T.Asada, S.Koseki and M.Nagaoka
    • Journal Title

      Phys.Chem.Chem.Phys

      Volume: 13 Issue: 4 Pages: 1590-1596

    • DOI

      10.1039/c0cp01077d

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Presentation] QM/MM 法を用いた自由エネルギー安定構造の探索法2013

    • Author(s)
      麻田俊雄
    • Organizer
      第7回分子科学討論会 2013
    • Place of Presentation
      京都テルサ, 京都
    • Year and Date
      2013-09-18
    • Related Report
      2013 Final Research Report
  • [Presentation] Theoretical Study of Charge Transfer Process in Condenced Matter2013

    • Author(s)
      T.Asada
    • Organizer
      The 5th International Conference at the 2012 OCARINA Annual International Meeting
    • Place of Presentation
      大阪市立大学, 大阪
    • Year and Date
      2013-03-04
    • Related Report
      2013 Final Research Report
    • Invited
  • [Presentation] OLEDに用いられ白金錯体の燐光過程に関する理論的研究2013

    • Author(s)
      小関史朗、鍵田侑希、麻田俊雄
    • Organizer
      第16回理論化学討論会
    • Place of Presentation
      福岡
    • Related Report
      2013 Annual Research Report
  • [Presentation] 除草剤;光科学系IIの電子伝達阻害剤の機能解析2013

    • Author(s)
      田中絢子、硯智史、麻田俊雄、川上恵典、梅名泰史、沈建仁、宮原郁子、神谷信夫
    • Organizer
      第13回日本蛋白質科学会
    • Place of Presentation
      鳥取
    • Related Report
      2013 Annual Research Report
  • [Presentation] QM/MM 法を用いた自由エネルギー安定構造の探索法2013

    • Author(s)
      麻田俊雄
    • Organizer
      第7回分子科学討論会2013
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] シロール分子のアモルファス相中における電子移動度の理論的解析2013

    • Author(s)
      前田昂太郎,麻田俊雄,小関史朗
    • Organizer
      第7回分子科学討論会2013
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] 白金錯体における燐光過程の理論的再検討2013

    • Author(s)
      小関史朗,麻田俊雄,松下武司
    • Organizer
      第7回分子科学討論会2013
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] Efficient algorithm to optimize structures and reaction paths on free energy surface using QM/MM MD simulation2013

    • Author(s)
      Toshio Asada
    • Organizer
      5th JCS International Symposium on Theoretical Chemistry
    • Place of Presentation
      奈良
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Theoretical Study of Charge Transfer Process in Condenced Matter2013

    • Author(s)
      Toshio Asada
    • Organizer
      The 5th International Conference as the 2012 OCARINA Annual International Meeting
    • Place of Presentation
      大阪
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] 自由エネルギー面上の反応経路の探索2012

    • Author(s)
      麻田俊雄
    • Organizer
      第6回分子科学討論会 2012
    • Place of Presentation
      東京大学, 東京
    • Year and Date
      2012-09-18
    • Related Report
      2013 Final Research Report
  • [Presentation] Efficient Optimization algorithm of reaction pathway on free energy surface using QM/MM MD simulation2012

    • Author(s)
      T.Asada, K.Sakurai, S.Koseki
    • Organizer
      Advances in Quantum Chemistry : Interfacing Electronic Structure with Dynamics
    • Place of Presentation
      University of Minnesota , 米国
    • Year and Date
      2012-06-20
    • Related Report
      2013 Final Research Report
  • [Presentation] Computational Approach to the Optimization Method of the Reaction Pathway on the Free Energy Surface2012

    • Author(s)
      T.Asada, K.Sakurai, M.Nagaoka
    • Organizer
      JST International Synposium on Multi-Scale Simulation of Condensed-phase Reacting System
    • Place of Presentation
      名古屋大学, 名古屋
    • Year and Date
      2012-05-12
    • Related Report
      2013 Final Research Report
  • [Presentation] Optimization Method of Reaction Pathway on Free Energy Surface for Decarboxylation Reaction of Propylene Carbonate2012

    • Author(s)
      Toshio Asada, Kohji Sakurai, and Shiro Koseki
    • Organizer
      14th International Congress of Quantum Chemistry
    • Place of Presentation
      Boulder, Colorado, USA
    • Related Report
      2012 Research-status Report
  • [Presentation] Theoretical Studies on Phosphorescent Pt and Ir Complexes2012

    • Author(s)
      Shiro Koseki, Na-oya Kamata, Yuhki Kagita,Toshio Asada, and Takeshi Matsushita
    • Organizer
      14th International Congress of Quantum Chemistry
    • Place of Presentation
      Boulder, Colorado, USA
    • Related Report
      2012 Research-status Report
  • [Presentation] Efficient optimization algorithm of reaction pathway on free energy surface using QM/MM MD simulation2012

    • Author(s)
      Toshio Asada, Kohji Sakurai, and Shiro Koseki
    • Organizer
      Advances in Quantum Chemistry: Interfacing Electronic Structure with Dynamics
    • Place of Presentation
      Minnesota, Minneapolis, USA
    • Related Report
      2012 Research-status Report
  • [Presentation] 自由エネルギー面上の反応経路の探索2012

    • Author(s)
      麻田俊雄
    • Organizer
      分子科学討論会2012
    • Place of Presentation
      東京
    • Related Report
      2012 Research-status Report
  • [Presentation] Computational Approach to the Optimization Method of the Reaction Pathway on the Free Energy Surface2012

    • Author(s)
      T.Asada, K.Sakurai, M.Nagaoka
    • Organizer
      JST International Synposium on Multi-Scale Simulation of Condensed-phase Reacting System
    • Place of Presentation
      仙台
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] 有機 EL 材料分子における燐光過程の理論的考察2012

    • Author(s)
      小関 史朗、鎌田 尚也、鍵田 侑希、麻田 俊雄
    • Organizer
      第15回理論化学討論会
    • Place of Presentation
      仙台
    • Related Report
      2012 Research-status Report
  • [Presentation] QM/MM MD 法を用いたリチウム電池の正極における電解液分解反応に関する理論的解析2012

    • Author(s)
      櫻井 耕司、麻田 俊雄、小関 史朗
    • Organizer
      第15回理論化学討論会
    • Place of Presentation
      仙台
    • Related Report
      2012 Research-status Report
  • [Presentation] ab initio QM/MM-MD シミュレーションを用いた自由エネルギー面上の反応経路最適化2011

    • Author(s)
      麻田俊雄
    • Organizer
      CAC フォーラム 1 泊研修会
    • Place of Presentation
      リゾーピア熱海, 静岡
    • Year and Date
      2011-10-06
    • Related Report
      2013 Final Research Report
    • Invited
  • [Presentation] Charge Response Kernel を用いた ab initio QM/MMMD 法による自由エネルギー最適化の理論的研究2011

    • Author(s)
      麻田俊雄, 竹中規雄, 小谷野哲之, 長岡正隆, 小関史朗
    • Organizer
      第5回分子科学討論会 2011
    • Place of Presentation
      北海道大学, 札幌
    • Year and Date
      2011-09-21
    • Related Report
      2013 Final Research Report
  • [Presentation] Theoretical investigation of inhibitor mechanism in trypsin-BPTI using ab initio QM/MM-MD simulation2011

    • Author(s)
      T.Asada, N.Takenaka, S.Koseki, M.Nagaoka
    • Organizer
      WATOC2011
    • Place of Presentation
      Santiago de Compostela , スペイン
    • Year and Date
      2011-07-22
    • Related Report
      2013 Final Research Report
  • [Presentation] リチウムイオン電池中における電解液分解反応の理論的研究2011

    • Author(s)
      櫻井耕司,麻田俊雄,小関史朗
    • Organizer
      第14回理論化学討論会
    • Place of Presentation
      岡山大学
    • Related Report
      2011 Research-status Report
  • [Presentation] イリジウム錯体の燐光過程における理論的研究2011

    • Author(s)
      鎌田尚也,麻田俊雄,小関史朗
    • Organizer
      第14回理論化学討論会
    • Place of Presentation
      岡山大学
    • Related Report
      2011 Research-status Report
  • [Presentation] 白金錯体を用いた燐光発光材料の配位子および置換基効果の理論的解析2011

    • Author(s)
      鍵田侑希,麻田俊雄,小関史朗
    • Organizer
      第14回理論化学討論会
    • Place of Presentation
      岡山大学
    • Related Report
      2011 Research-status Report
  • [Presentation] QM/MM 法を用いたClass C β-ラクタマーゼにおけるアシル化反応の理論的解析2011

    • Author(s)
      岡島利幸,麻田俊雄,小関史朗
    • Organizer
      第14回理論化学討論会
    • Place of Presentation
      岡山大学
    • Related Report
      2011 Research-status Report
  • [Presentation] Theoretical investigation of inhibitor mechanism in trypsin-BPTI using ab initio QM/MM-MD simulation2011

    • Author(s)
      T.Asada, N.Takenaka, S.Koseki, M.Nagaoka
    • Organizer
      WATOC2011
    • Place of Presentation
      Santiago de compostela, Spain
    • Related Report
      2011 Research-status Report
  • [Presentation] リチウムイオン電池の電解質分解反応の自由エネルギー解析2011

    • Author(s)
      櫻井耕司,麻田俊雄,長岡正隆
    • Organizer
      計算分子科学研究拠点第二回研究会
    • Place of Presentation
      理化学研究所神戸
    • Related Report
      2011 Research-status Report
  • [Presentation] QM/MM 法を用いたリチウムイオン電池の電解液分解反応に関する理論的研究2011

    • Author(s)
      櫻井耕司,麻田俊雄,小関史朗
    • Organizer
      第5回分子科学討論会2011
    • Place of Presentation
      札幌
    • Related Report
      2011 Research-status Report
  • [Presentation] 白金錯体を用いた赤色燐光発光材料の理論設計2011

    • Author(s)
      鍵田侑希,麻田俊雄,小関史朗
    • Organizer
      第5回分子科学討論会2011
    • Place of Presentation
      札幌
    • Related Report
      2011 Research-status Report
  • [Presentation] β-ラクタマーゼの自由エネルギー面上におけるアシル化反応の理論的解析2011

    • Author(s)
      岡島利幸,麻田俊雄,小関史朗
    • Organizer
      第5回分子科学討論会2011
    • Place of Presentation
      札幌
    • Related Report
      2011 Research-status Report
  • [Presentation] Charge Response Kernel を用いたab initio QM/MMMD法による自由エネルギー最適化の理論的研究2011

    • Author(s)
      麻田俊雄,竹中規雄,小谷野哲之,長岡正隆,小関史朗
    • Organizer
      第5回分子科学討論会2011
    • Place of Presentation
      札幌
    • Related Report
      2011 Research-status Report
  • [Presentation] 青色燐光イリジウム錯体に関する理論的研究、第5回分子科学討論会20112011

    • Author(s)
      鎌田尚也,麻田俊雄,小関史朗
    • Organizer
      第5回分子科学討論会2011
    • Place of Presentation
      札幌
    • Related Report
      2011 Research-status Report
  • [Presentation] ab initio QM/MM-MDシミュレーションを用いた自由エネルギー面上の反応経路最適化2011

    • Author(s)
      麻田俊雄
    • Organizer
      CACフォーラム一泊研修会(招待講演)
    • Place of Presentation
      リゾートピア熱海
    • Related Report
      2011 Research-status Report
  • [Remarks]

    • URL

      http://fock.c.s.osakafu-u.ac.jp/~asada

    • Related Report
      2013 Final Research Report
  • [Remarks]

    • URL

      http://fock.c.s.osakafu-u.ac.jp/~asada/paper.html

    • Related Report
      2011 Research-status Report
  • [Remarks]

    • URL

      http://fock.c.s.osakafu-u.ac.jp/~asada/conference.html

    • Related Report
      2011 Research-status Report

URL: 

Published: 2011-08-05   Modified: 2019-07-29  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi