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Development of electron transfer dynamics theory of biological systems highly incorporating solvent response

Research Project

Project/Area Number 19H02677
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 32010:Fundamental physical chemistry-related
Research InstitutionNagoya University (2022)
Kyushu University (2019-2021)

Principal Investigator

Yoshida Norio  名古屋大学, 情報学研究科, 教授 (10390650)

Co-Investigator(Kenkyū-buntansha) 山口 毅  名古屋大学, 工学研究科, 助教 (80345917)
中野 晴之  九州大学, 理学研究院, 教授 (90251363)
Project Period (FY) 2019-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥17,420,000 (Direct Cost: ¥13,400,000、Indirect Cost: ¥4,020,000)
Fiscal Year 2022: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
Fiscal Year 2021: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
Fiscal Year 2020: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2019: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Keywords積分方程式理論 / 電子移動 / エネルギー移動 / 溶媒和ダイナミックス / 分極応答理論 / 溶媒和ダイナミックス理論
Outline of Research at the Start

生体系の電子移動過程においては、電子供与体および受容体をとりまく生体分子や溶媒分子といった環境のさまざまな性質が反応性に影響を与える。特に水分子の分布や配向の変化そして分極といった応答は電子移動の反応性を支配する重要な要因である。
本研究では、分子性液体の積分方程式理論を基盤として、電子状態理論および溶媒和ダイナミクス理論を組み合わせることで、高度に溶媒の応答を考慮した溶液内および生体内電子移動反応理論を構築する。この理論を用いて、生体内電子移動過程における電子状態変化と溶媒和ダイナミクスの相関を明らかにする。

Outline of Final Research Achievements

Electron transfer reactions in biological systems are among the most important elementary biological processes and play a central role in biological functions such as respiratory metabolism and photosynthesis. In such processes, changes in the distribution and orientation of water molecules and their response to electron polarization are important factors governing reactivity. In this study, we focused on the response of water molecules as solvents and developed a new theoretical method and its application. First, we proposed a solvent polarizable 3D-RISM theory that can describe solvent polarization. Based on this theory, we proposed a non-equilibrium free energy formalism, a dynamical solvation theory, and a hybrid method that integrates these theories with quantum chemical methods, and applied them to biomolecules.

Academic Significance and Societal Importance of the Research Achievements

溶液中の電子移動反応は、重要な化学反応の一つであり、さまざま化学・物理・生物学的過程に関与している。特に生体系においては呼吸代謝や光合成といった機構において中心的な役割を果たしている。溶液中や生体内の電子移動過程においては、電子供与体および受容体をとりまく生体分子や溶媒分子といった環境の性質が反応性に影響を与える。特に水分子の分布や配向の変化そして電子分極といった“応答”は電子移動の反応性を支配する重要な要因である。本研究では液体の統計力学理論を基盤とし、電子移動反応における溶媒の応答を統合的に扱うことのできる理論を構築し、生体関連分子へ適用することでその有効性を示した。

Report

(5 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • Research Products

    (43 results)

All 2023 2022 2021 2020 2019 Other

All Int'l Joint Research (3 results) Journal Article (19 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 19 results,  Open Access: 1 results) Presentation (19 results) (of which Int'l Joint Research: 14 results,  Invited: 18 results) Remarks (2 results)

  • [Int'l Joint Research] Kasetsart University(タイ)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Chiang Mai University(タイ)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Kasetsart University(タイ)

    • Related Report
      2019 Annual Research Report
  • [Journal Article] Phase equilibrium of three-component liquid systems composed of water, alcohol, and sodium chloride studied by the reference interaction-site model integral equation theory2023

    • Author(s)
      Yamaguchi Tsuyoshi、Chong Song-Ho、Yoshida Norio
    • Journal Title

      The Journal of Chemical Physics

      Volume: 158 Issue: 8 Pages: 084502-084502

    • DOI

      10.1063/5.0142256

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical Analysis of the Role of Water in Ligand Binding to Cucurbit[n]uril of Different Sizes2023

    • Author(s)
      Chiangraeng Natthiti、Nakano Haruyuki、Nimmanpipug Piyarat、Yoshida Norio
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 127 Issue: 16 Pages: 3651-3662

    • DOI

      10.1021/acs.jpcb.3c00343

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Application of the reference interaction site model self-consistent field method based on the Dirac-Hartree-Fock wave function to a chemical reaction2023

    • Author(s)
      Kanemaru K、Watanabe Y、Yoshida N、Nakano H
    • Journal Title

      IOP Conference Series: Materials Science and Engineering

      Volume: 1280 Issue: 1 Pages: 012002-012002

    • DOI

      10.1088/1757-899x/1280/1/012002

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Solvent effects in four‐component relativistic electronic structure theory based on the reference interaction‐site model2022

    • Author(s)
      Kanemaru Kodai、Watanabe Yoshihiro、Yoshida Norio、Nakano Haruyuki
    • Journal Title

      Journal of Computational Chemistry

      Volume: 44 Issue: 1 Pages: 5-14

    • DOI

      10.1002/jcc.27009

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Study of phase equilibria and thermodynamic properties of liquid mixtures using the integral equation theory: Application to water and alcohol mixtures2022

    • Author(s)
      Yamaguchi Tsuyoshi、Chong Song-Ho、Yoshida Norio
    • Journal Title

      The Journal of Chemical Physics

      Volume: 157 Issue: 23 Pages: 234502-234502

    • DOI

      10.1063/5.0131475

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Implementation of solvent polarization in three-dimensional reference interaction-site model self-consistent field theory2022

    • Author(s)
      Yoshida Norio、Yamaguchi Tsuyoshi、Nakano Haruyuki
    • Journal Title

      Chemical Physics Letters

      Volume: 797 Pages: 139579-139579

    • DOI

      10.1016/j.cplett.2022.139579

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Decoupling between Solvent Viscosity and Diffusion of a Small Solute Induced by Self-Motion2021

    • Author(s)
      Yamaguchi Tsuyoshi
    • Journal Title

      The Journal of Physical Chemistry Letters

      Volume: 12 Issue: 32 Pages: 7696-7700

    • DOI

      10.1021/acs.jpclett.1c02219

    • NAID

      120007190687

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Solvation dynamics in electronically polarizable solvents: Theoretical treatment using solvent-polarizable three-dimensional reference interaction-site model theory combined with time-dependent density functional theory2021

    • Author(s)
      Yamaguchi Tsuyoshi、Yoshida Norio
    • Journal Title

      The Journal of Chemical Physics

      Volume: 154 Issue: 4 Pages: 044504-044504

    • DOI

      10.1063/5.0036289

    • NAID

      120007169516

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A computational method to simulate global conformational changes of proteins induced by cosolvent2021

    • Author(s)
      Tanimoto Shoichi、Tamura Koichi、Hayashi Shigehiko、Yoshida Norio、Nakano Haruyuki
    • Journal Title

      Journal of Computational Chemistry

      Volume: 42 Issue: 8 Pages: 552-563

    • DOI

      10.1002/jcc.26481

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular dynamics simulation study on the isomerization reaction in a solvent with slow structural relaxation2021

    • Author(s)
      Yamaguchi Tsuyoshi
    • Journal Title

      Chemical Physics

      Volume: 542 Pages: 111056-111056

    • DOI

      10.1016/j.chemphys.2020.111056

    • NAID

      120007163644

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Nonequilibrium free-energy profile of charge-transfer reaction in polarizable solvent studied using solvent-polarizable three-dimensional reference interaction-site model theory2020

    • Author(s)
      Yamaguchi Tsuyoshi、Yoshida Norio
    • Journal Title

      The Journal of Chemical Physics

      Volume: 153 Issue: 3 Pages: 034502-034502

    • DOI

      10.1063/5.0013083

    • NAID

      120006948933

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Development of a solvent-polarizable three-dimensional reference interaction-site model theory2020

    • Author(s)
      Yoshida Norio、Yamaguchi Tsuyoshi
    • Journal Title

      The Journal of Chemical Physics

      Volume: 152 Issue: 11 Pages: 114108-114108

    • DOI

      10.1063/5.0004173

    • NAID

      120006869620

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Three-Dimensional Reference Interaction Site Model Self-Consistent Field Study on the Coordination Structure and Excitation Spectra of Cu(II)-Water Complexes in Aqueous Solution2019

    • Author(s)
      Yang Chen、Watanabe Yoshihiro、Yoshida Norio、Nakano Haruyuki
    • Journal Title

      The Journal of Physical Chemistry A

      Volume: 未定 Issue: 15 Pages: 3344-3354

    • DOI

      10.1021/acs.jpca.9b01364

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Implementation of state-averaged MCSCF method to RISM- and 3D-RISM-SCF schemes2019

    • Author(s)
      Okamoto Daisuke、Watanabe Yoshihiro、Yoshida Norio、Nakano Haruyuki
    • Journal Title

      Chemical Physics Letters

      Volume: 730 Pages: 179-185

    • DOI

      10.1016/j.cplett.2019.05.051

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] β-sheet elasticity of peptide self-assembly mimic, PSAM, with a graftedsequence characterized by comprehensive analyses ofisomorphous crystals2019

    • Author(s)
      Hideki Fujiwara, Kenta Hongo, Yuki Hori, Norio Yoshida, *Koki Makabe
    • Journal Title

      Journal of Molecular Liquids

      Volume: 290 Pages: 111161-111161

    • DOI

      10.1016/j.molliq.2019.111161

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Relation between Anharmonicity of Free-Energy Profile and Spectroscopy in Solvation Dynamics: Differences in Spectral Broadening and Peak Shift in Transient Hole-Burning Spectroscopy Studied by Equilibrium Molecular Dynamics Simulation2019

    • Author(s)
      Yamaguchi Tsuyoshi、Yoshida Norio、Nishiyama Katsura
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 123 Issue: 32 Pages: 7036-7042

    • DOI

      10.1021/acs.jpcb.9b04711

    • NAID

      120006765143

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Effect of Molecular Orientational Correlations on Solvation Free Energy Computed by Reference Interaction Site Model Theory2019

    • Author(s)
      Tanimoto Shoichi、Yoshida Norio、Yamaguchi Tsuyoshi、Ten-no Seiichiro L.、Nakano Haruyuki
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: 59 Issue: 9 Pages: 3770-3781

    • DOI

      10.1021/acs.jcim.9b00330

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Effects of Water Addition on a Catalytic Fluorination of Dienamine2019

    • Author(s)
      Kuraoku Daiki、Yonamine Tsunaki、Koja Genta、Yoshida Norio、Arimitsu Satoru、Higashi Masahiro
    • Journal Title

      Molecules

      Volume: 24 Issue: 19 Pages: 3428-3428

    • DOI

      10.3390/molecules24193428

    • NAID

      120006800746

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Distinct ionic adsorption sites in defective Prussian blue: a 3D-RISM study2019

    • Author(s)
      Ruankaew Nirun、Yoshida Norio、Watanabe Yoshihiro、Nakayama Akira、Nakano Haruyuki、Phongphanphanee Saree
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 21 Issue: 40 Pages: 22569-22576

    • DOI

      10.1039/c9cp04355a

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Presentation] Molecular Solvation Theory for Material Design2023

    • Author(s)
      Norio Yoshida
    • Organizer
      Asia Pacific Conference of Theoretical and Computational Chemistry
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Recent developments in molecular solvation theory2023

    • Author(s)
      Norio Yoshida
    • Organizer
      StudyCamp 2022
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 3D-RISM理論を基盤としたマルチスケール手法の開発と展開2022

    • Author(s)
      吉田紀生
    • Organizer
      電気化学界面シミュレーションコンソーシアム
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Development of a hybrid method based on 3D-RISM theory for biomolecules2022

    • Author(s)
      Norio Yoshida
    • Organizer
      The 25th international annual symposium on computational science and engineering
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Theoretical study of protein structure and function based on the solvation theory of biomolecules2022

    • Author(s)
      吉田紀生
    • Organizer
      第22回日本蛋白質科学会年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Development of solvent-polarizable 3D-RISM theory2022

    • Author(s)
      Norio Yoshida, Tsuyoshi Yamaguchi
    • Organizer
      The World Association of Theoretical and Computational Chemists 2020
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 生体分子の溶媒和統計力学理論によるタンパク質機能解析への展開2022

    • Author(s)
      吉田紀生
    • Organizer
      物性研短期研究会2020「理論タンパク質物性科学の最前線:理論と実験の密な協働」
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Development of theory of solvation and fluctuation of biomolecule2022

    • Author(s)
      Norio Yoshida
    • Organizer
      Joint Meeting of the 20th KIAS Conference on "Protein Structure and Function" and The 7th Korean-Polish Conference on "Protein Folding: Theoretical and Experimental Approaches"
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Development of Dynamic Solvation Theory for Biomolecules2022

    • Author(s)
      Norio Yoshida
    • Organizer
      日本生物物理学会年会2022
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Development of a hybrid method of three-dimensional reference interaction-site model theory and quantum chemical electronic structure theory for biomoleculese2022

    • Author(s)
      Norio Yoshida
    • Organizer
      International Congress on Pure & Applied Chemistry Kota Kinabalu 2022
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Molecular Solvation Theory for Material Design2022

    • Author(s)
      Norio Yoshida
    • Organizer
      2022 International Conference on Materials Research and Innovation
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ensity functional theory of molecular liquids for biophysics and chemical physics2021

    • Author(s)
      Norio Yoshida
    • Organizer
      3rd International Conference on Materials Research and Innovation
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Development of a hybrid method of three-dimensional reference interaction-site model theory and quantum chemical electronic structure theory for biomolecules2021

    • Author(s)
      Norio Yoshida
    • Organizer
      Pacifichem 2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] MULTI-SCALE IMPLEMENTATION OF 3D-RISM TO THE ELECTRONIC STRUCTURE THEORY BEING APPLICABLE FOR SOLVATED BIOMOLECULES.2020

    • Author(s)
      Norio Yoshida
    • Organizer
      Biophysical Society 64th Annual Meeting
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Development of Multiscale Method for Nano-Bio Materials Design Based on Statistical Mechanics Theory of Molecular Liquids2019

    • Author(s)
      Norio Yoshida
    • Organizer
      International Conference on Materials Research and Innovation 2020
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Understanding Biological Processes in Solution Based on the Statistical Mechanics Theory of Liquids2019

    • Author(s)
      Norio Yoshida
    • Organizer
      The 10th Toyota RIKEN International Workshop on Science of Life Phenomena Woven by Water and Biomolecules
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Understanding Biological Processes in Solution Based on the Statistical Mechanics Theory of Liquids2019

    • Author(s)
      Norio Yoshida
    • Organizer
      10th International Conference of the Asian Consortium on Computational Materials Science (ACCMS-10)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Understanding Biological Processes in Solution Based on the Statistical Mechanics Theory of Liquids2019

    • Author(s)
      Norio Yoshida
    • Organizer
      The 23th international annual symposium on computational science and engineering (ANSCSE23)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 水とイオンが駆動する生体分子機能の統計力学2019

    • Author(s)
      吉田紀生
    • Organizer
      有機・生体分子構造・物性研究会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Remarks] Yoshida Group home page

    • URL

      https://sites.google.com/view/yoshida-group/home

    • Related Report
      2022 Annual Research Report
  • [Remarks] Yoshida Group web-page/Research Topics

    • URL

      https://sites.google.com/view/yoshida-group/research?authuser=0

    • Related Report
      2021 Annual Research Report

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Published: 2019-04-18   Modified: 2024-01-30  

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