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Computational Chemistry of pH-dependent Activated Complex -From Development of Micro-constant pH Method to Transition State Control-

Research Project

Project/Area Number 16KT0053
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeMulti-year Fund
Section特設分野
Research Field Transition State Control
Research InstitutionNagoya University

Principal Investigator

Nagaoka Masataka  名古屋大学, 情報学研究科, 教授 (50201679)

Research Collaborator Kitamura Yukichi  
Project Period (FY) 2016-07-19 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥18,200,000 (Direct Cost: ¥14,000,000、Indirect Cost: ¥4,200,000)
Fiscal Year 2018: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2017: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Fiscal Year 2016: ¥7,150,000 (Direct Cost: ¥5,500,000、Indirect Cost: ¥1,650,000)
KeywordspH依存活性錯合体 / ミクロ定pH-MS法 / ミクロ定pH‐MS法 / 遷移状態制御
Outline of Final Research Achievements

A purpose of our study is to establish new molecular simulation method (the micro constant pH-MS method) that able to effectively take account of a pH (an index of the hydrogen ion concentration) change under solution and in vivo crowded environment. We have developed the micro constant pH-MS method based on discrete protonation state transition model. Furthermore, we improved it by an introduction of quantum mechanics method into this method. As well as organic molecules and protein, pH dependent chemical characteristic and their motions in the inorganic compound such as the metal complex were clarified from a microscopic viewpoint by applying our technique.

Academic Significance and Societal Importance of the Research Achievements

従来の定pH法では考慮が難しかった微視的な溶媒和構造について、本手法では、溶媒として全原子モデルを使用することが可能であり、溶媒の配向性やエンタルピー変化などの微視的な溶媒効果を考慮することが可能となった。また、溶質分子を量子化学計算的に記述することで、金属錯体系や複数の滴定可能サイトを含む複合的な系に適用可能となり、今後の将来的な応用研究において極めて重要な成果が得られた。

Report

(4 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (11 results)

All 2018 2017 2016

All Journal Article (4 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 2 results) Presentation (7 results) (of which Int'l Joint Research: 2 results)

  • [Journal Article] Microscopic Origin of Different Hydration Pattern of Paranitrophenol and Its Anion: A Study Combining Multiconfigurational Calculations and the Free Energy Gradient Method2018

    • Author(s)
      C. Bistafa, Y. Kitamura, M. Nagaoka, S. Canuto
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 122 Issue: 39 Pages: 9202-9209

    • DOI

      10.1021/acs.jpcb.8b06439

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] A Cost-Effective Method for Free-Energy Minimization in Complex Systems with Elaborated Ab Initio Potentials2018

    • Author(s)
      C. Bistafa, Y. Kitamura, M. T. C. Martins-Costa, M. Nagaoka, M. F. Ruiz-Lopez
    • Journal Title

      Journal of Chemical Theory and Computation

      Volume: 14 Issue: 6 Pages: 3262-3271

    • DOI

      10.1021/acs.jctc.8b00271

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Probing the Most Stable Isomer of Zirconium Bis(phenoxy-imine) Cation: A Computational Investigation2018

    • Author(s)
      S. Soumen, M. Takayanagi, K. Matsumoto, S. K. Sankaran, Y. Tanaka, N. Koga, M. Nagaoka
    • Journal Title

      The Journal of Physical Chemistry A

      Volume: 122 Issue: 8 Pages: 2198-2208

    • DOI

      10.1021/acs.jpca.7b10999

    • Related Report
      2017 Research-status Report
  • [Journal Article] Role of the Counteranion in the Reaction Mechanism of Propylene Polymerization Catalyzed by a (Pyridylamido)hafnium(IV) Complex2018

    • Author(s)
      K. Matsumoto, M.Takayanagi, S. K. Sankaran, N. Koga, M. Nagaoka
    • Journal Title

      Organometallics

      Volume: 37 Issue: 3 Pages: 343-349

    • DOI

      10.1021/acs.organomet.7b00767

    • Related Report
      2017 Research-status Report
  • [Presentation] ゼロエネルギー差条件を満たす配置選択法に基づいた定 pH 法の理論的研究:グルタミン酸水溶液系への適用2018

    • Author(s)
      北村 勇吉、長岡 正隆
    • Organizer
      第32回分子シミュレーション討論会
    • Related Report
      2018 Annual Research Report
  • [Presentation] アルミニウム水溶液における凝集過程の理論的解明-その初期過程とpH依存性-2018

    • Author(s)
      吉田正一、北村勇吉、長岡正隆
    • Organizer
      第12回分子科学討論会 2018福岡
    • Related Report
      2018 Annual Research Report
  • [Presentation] A Computational Investigation for Determining the Most Stable Isomer of Zirconium bis(phenoxy-imine) Cation2017

    • Author(s)
      S.Saha, K.Matsumoto, M.Takayanagi, S.K.Sankaran, N.Koga, M.Nagaoka
    • Organizer
      Asia-Pacific Conference of Theoretical and Computational Chemistry
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] How structural changes affect the paranitrophenol spectrum in aqueous solution: Insights from multiconfigurational calculations and the free energy gradient method2017

    • Author(s)
      C. Bistafa, Y. Kitamura, M. Nagaoka, S. Canuto
    • Organizer
      第11回分子科学討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] Hf錯体のイオン対活性種による立体規則性重合機構の理論的研究2017

    • Author(s)
      松本健太郎, S.K.Sankaran, 高柳昌芳, 古賀伸明, 長岡正隆
    • Organizer
      第11回分子科学討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] The Electronic Transitions of Paranitrophenol and Paranitrophenolate in Gas and Water: A Study Combining Ab Initio Multiconfigurational Calculations and the Free Energy Gradient Method2016

    • Author(s)
      Carlos Bistafa, Yukichi Kitamura, Masataka Nagaoka, Sylvio Canuto
    • Organizer
      Japan-France-Spain Joint-Symposium on Theoretical and Computational Science of Complex Systems
    • Place of Presentation
      Fukui Institute for Fundmental Chemistry
    • Year and Date
      2016-10-26
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] エネルギー揺らぎの制御スキームを導入した定pH分子シミュレーション法の開発2016

    • Author(s)
      北村勇吉、長岡正隆
    • Organizer
      第10回分子科学討論会
    • Place of Presentation
      神戸ファッションマート
    • Year and Date
      2016-09-13
    • Related Report
      2016 Research-status Report

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Published: 2016-07-20   Modified: 2023-03-08  

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