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Exploration of quantum effects on proton transfer reactions in biomolecules via the determination of reaction pathways

Research Project

Project/Area Number 15K17815
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Physical chemistry
Research InstitutionKyushu University

Principal Investigator

Mizukami Wataru  九州大学, 総合理工学研究院, 助教 (10732969)

Project Period (FY) 2015-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2017: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2016: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2015: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
Keywords量子化学 / ポテンシャル曲面 / 機械学習 / 核の量子効果 / ONIOM / インスタントン / ガウス過程 / ポテンシャル面 / 量子ダイナミクス / 拡散モンテカルロ / 水素移動反応 / 反応経路 / 分子力場 / QM/MM / 分極可能力場 / 第一原理計算 / 量子モンテカルロ法
Outline of Final Research Achievements

We developed the following two methods for constructing quantitative potential energy surfaces (PESs) in condensed phase to quantitatively describe proton transfer reactions in enzymes: The Indirect Gradient Enhanced Kriging method, which is a Gaussian process algorithm with information of forces, was utilized to reduce the number of quantum chemical calculations for PES constructions; the ONIOM approach was used to incorporate environmental effects to our highly accurate LASSO potentials. Moreover, we performed anharmonic vibrational spectrum analysis of an osmolyte molecule TMAO using a PES where density functional theory calculations were hybridized with accurate electron-correlation calculations.

Academic Significance and Societal Importance of the Research Achievements

量子力学的効果を生命が利用していることが様々な研究から示唆されており、いくつかの酵素反応などでは律速段階の反応がトンネル効果によって進むということがわかってきている。しかし、その過程や量子効果を活かすためのメカニズムを分子・原子レベルで明らかにすることはいまもって難しい課題となっている。本研究成果は、コンピュータ・シミュレーションを利用したプロトン移動反応の定量的記述に必要な要素技術を構築したものである。プロトンを用いた量子生命現象の詳細解明に繋がると期待される。

Report

(5 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (11 results)

All 2018 2017 2016 2015 Other

All Int'l Joint Research (1 results) Journal Article (2 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 2 results,  Acknowledgement Compliant: 2 results) Presentation (8 results) (of which Int'l Joint Research: 2 results,  Invited: 4 results)

  • [Int'l Joint Research] Max Planck Institute(Germany)

    • Related Report
      2016 Research-status Report
  • [Journal Article] Unveiling the amphiphilic nature of TMAO by vibrational sum frequency generation spectroscopy2016

    • Author(s)
      Tatsuhiko Ohto, Ellen H. G. Backus, Wataru Mizukami, Johannes Hunger, Mischa Bonn and Yuki Nagata
    • Journal Title

      J. Phys. Chem. C

      Volume: 120 Issue: 31 Pages: 17435-17443

    • DOI

      10.1021/acs.jpcc.6b04852

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Relativistic Internally Contracted Multireference Electron Correlation Methods2015

    • Author(s)
      Toru Shiozak and Wataru Mizukami
    • Journal Title

      Journal of Chemical Theory and Computation

      Volume: 11 Issue: 10 Pages: 4733-4739

    • DOI

      10.1021/acs.jctc.5b00754

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Presentation] 第一原理振動状態理論の開発:生体分子における量子現象解明を目指して2018

    • Author(s)
      水上 渉
    • Organizer
      QIQBセミナー
    • Related Report
      2018 Annual Research Report
  • [Presentation] H2Oを介したO2-I-間の電荷移動励起についての理論的研究2018

    • Author(s)
      水上渉,薮下彰啓 , 原田明,青木百合子
    • Organizer
      第12回分子科学討論会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 精密振動状態理論: 理論はどこまで精確になったか?2017

    • Author(s)
      水上 渉
    • Organizer
      第4回電子状態理論シンポジウム
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 振動波動関数理論によるC-H振動の解読: 「凝縮系の理論化学」を機とする共同研究2017

    • Author(s)
      水上 渉
    • Organizer
      凝縮系の理論化学2018
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 少数原子系の精密理論振動分光2017

    • Author(s)
      水上 渉
    • Organizer
      北大理論化学研究会:実践理論化学の最前線
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 振動状態理論と半大域ポテンシャルの構築2016

    • Author(s)
      水上 渉
    • Organizer
      凝縮系の理論化学
    • Place of Presentation
      琉球大学
    • Year and Date
      2016-03-10
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] Modeling molecular interactions in halogen-bonding cocrystal2016

    • Author(s)
      Wataru Mizukami and Yuriko Aoki
    • Organizer
      International Symposium on Multi-scale Simulation of Condensed-phase Reacting Systems ( MSCRS2016)
    • Place of Presentation
      Nagoya University, Nagoya, Japan
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Analysis and modeling of molecular interactions in halogen-bonded cocrystal2015

    • Author(s)
      Mizukami, Wataru; Matsubara, Ken; Aoki, Yuriko
    • Organizer
      The 51st Symposium on Theoretical Chemistry
    • Place of Presentation
      ドイツ
    • Year and Date
      2015-09-20
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research

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Published: 2015-04-16   Modified: 2020-03-30  

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