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Real-time analyses of proton-coupled electron transfer reactions : Quantal cumulant dynamics

Research Project

Project/Area Number 20750004
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Physical chemistry
Research InstitutionUniversity of Hyogo

Principal Investigator

SHIGETA Yasuteru  University of Hyogo, 大学院・生命理学研究科, 准教授 (80376483)

Project Period (FY) 2008 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Fiscal Year 2009: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2008: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Keywords量子動力学 / 電子移動 / 水素移動 / 集団運動 / PCET / 量子効果 / キュミュラント動力学 / 電子移動反応 / プロトン移動反応 / 量子ゆらぎ / 熱ゆらぎ / 協同効果 / 同位体効果
Research Abstract

The aim of the proposal is a real-time analysis of proton-coupled electron and electron-coupled proton transfer reactions. We develop a novel quantum dynamics method based on Heisenberg' equation of the motion, which is referred as QCD method, and QM/MM molecular dynamics methods. (1) We perform QM/MM molecular dynamics simulation of pyrene-deoxyuridine in protonic and non-protonic solvent environment. Solvent molecules, which are hydrogen-bonded to a solute molecule, enhance the electron transfer reaction activity. Moreover, another solvent molecule assist to form a bridged structure of pyrene and deoxyuridine groups that results in the enhancement of the electron transfer. (2) In order to enlarge the applicability of the QCD method, we develop the distribution function based method and the techniques for the calculation of quantum correlation functions. We applied it to investigate quantum isotope effects on the proton transfer reactions in a guanine-cytosine base pair. (3) We also performed the first principle analysis of electron-coupled proton transfer reaction in protein environment and found that multiple protonic states play a key role in proton transport process across membrane proteins.

Report

(3 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • Research Products

    (54 results)

All 2010 2009 2008 Other

All Journal Article (22 results) (of which Peer Reviewed: 10 results) Presentation (27 results) Book (4 results) Remarks (1 results)

  • [Journal Article] Effects of Mercury (II) on Structural Properties, Electronic Structure and UV Absorption Spectra of Thymine-Mercury (II)-Thymine Nucleobase Pair Containing Duplex2010

    • Author(s)
      H. Miyachi, T. Matsui, Y. Shigeta, K. Hirao
    • Journal Title

      Physical Chemistry Chemical Physics 12

      Pages: 909-917

    • Related Report
      2009 Final Research Report
  • [Journal Article] Effects of Mercury (II) on Structural Properties, Electronic Structure and UV Absorption Spectra of Thymine-Mercury (II)-Thymine Nucleobase Pair Containing Duplex2010

    • Author(s)
      H.Miyachi, T.Matsui, Y.Shigeta, K.Hirao
    • Journal Title

      Physical Chemistry Chemical Physics 12

      Pages: 909-917

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Theory Including Quantum Effects and Thermal Fluctuations2009

    • Author(s)
      Y. Shigeta
    • Journal Title

      Bulletin of the Chemical Society of Japan 82

      Pages: 1323-1340

    • NAID

      10027169701

    • Related Report
      2009 Final Research Report
  • [Journal Article] Sequence-dependent Proton-transfer Reaction in Stacked GC Pair II: The Origin of Stabilities of Proton-transfer Products2009

    • Author(s)
      T. Matsui, T. Sato, Y. Shigeta, K. Hirao
    • Journal Title

      Chemical Physics Letters 478

      Pages: 238-242

    • Related Report
      2009 Final Research Report
  • [Journal Article] Theoretical Studies on Sulfur and Metal Cation (Cu(II), Ni(II), Pd(II), and Pt(II))-Containing Artificial DNA2009

    • Author(s)
      T. Matsui, H. Miyachi, Y. Nakanishi, Y. Shigeta Y. Kitagawa, M. Okumura, K. Hirao
    • Journal Title

      Journal of Physical Chemistry B 113

      Pages: 12790-12795

    • Related Report
      2009 Final Research Report
  • [Journal Article] Sequence Dependent Proton-transfer Reaction in Stacked GC Pair I: The Possibility of Proton-transfer Reactions2009

    • Author(s)
      T. Matsui, T. Sato, Y. Shigeta
    • Journal Title

      International Journal of Quantum Chemistry 109

      Pages: 2168-2177

    • Related Report
      2009 Final Research Report
  • [Journal Article] Effects of Hydrogen-Bonding Environments on Protonation States around the Entrance of Proton Transfer Pathways in Cytochrome c Oxidase2009

    • Author(s)
      K. Kamiya, Y. Shigeta, A. Oshiyama
    • Journal Title

      AIP Conference issue 1102

      Pages: 257-261

    • Related Report
      2009 Final Research Report
  • [Journal Article] Molecular theory including quantum effects and thermal fluctuations2009

    • Author(s)
      Y.Shigeta
    • Journal Title

      Bulletin of the Chemical Society of Japan (Award Accounts) 82

      Pages: 1323-1340

    • NAID

      10027169701

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Sequence-dependent proton-transfer reaction in stacked GC pair II : Theorigin of stabilities of proton-transfer products2009

    • Author(s)
      T.Matsui, T.Sato, Y.Shigeta, K.Hirao
    • Journal Title

      Journal of Physical Chemistry B 113

      Pages: 12790-12795

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Sequence dependent proton-transfer reaction in stacked GC pair I : The possibility of proton-transfer reactions2009

    • Author(s)
      T.Matsui, T.Sato, Y.Shigeta
    • Journal Title

      International Journal of Quantum Chemistry 109

      Pages: 2168-2177

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Effects of Hydrogen-Bonding Environments on Protonation States around the Entrance of Proton Transfer Pathways in Cytochrome c Oxidase2009

    • Author(s)
      K. Kamiya
    • Journal Title

      AIP conference proceedings, AIP conference proceedings 1102

      Pages: 257-261

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Quantal Cumulant Dynamics for Dissipative Tunneling, selected papers from ICNAAM 2007 and2008

    • Author(s)
      Y. Shigeta
    • Journal Title

      AIP Conference Issue 963,1046

    • Related Report
      2009 Final Research Report
  • [Journal Article] Structural Origin of Copper Ion Containing Artificial DNA: A Density Functional Study2008

    • Author(s)
      T. Matsui, H. Miyachi, T. Sato, Y. Shigeta, K. Hirao
    • Journal Title

      Journal of Physical Chemistry B 112

      Pages: 16960-16965

    • Related Report
      2009 Final Research Report
  • [Journal Article] Correlation Functions in Quantized Hamilton Dynamics and Quantal Cumulant Dynamics2008

    • Author(s)
      Y.V. Pereverzev, A. Pereverzev, Y. Shigeta, O.V. Prezhdo
    • Journal Title

      Journal of Chemical Physics 129

      Pages: 144104-7

    • Related Report
      2009 Final Research Report
  • [Journal Article] Dynamic Quantum Isotope Effects on Multiple Proton Transfer Reactions2008

    • Author(s)
      Y. Shigeta, H. Miyachi, T. Matsui, K. Hirao
    • Journal Title

      Bulletin of the Chemical Society of Japan 81

      Pages: 1230-1240

    • NAID

      10024330696

    • Related Report
      2009 Final Research Report
  • [Journal Article] Quantal Cumulant Dynamics III: A Quantum Confinement Under a Magnetic Field2008

    • Author(s)
      Y. Shigeta
    • Journal Title

      Chemical Physics Letters 461

      Pages: 310-315

    • Related Report
      2009 Final Research Report
  • [Journal Article] Distribution Function in Quantal Cumulant Dynamics2008

    • Author(s)
      Y. Shigeta
    • Journal Title

      Journal of Chemical Physics 128

      Pages: 161103-4

    • NAID

      120007138823

    • Related Report
      2009 Final Research Report
  • [Journal Article] Structural origin of copper ion containing artificial DNA : a density functional study2008

    • Author(s)
      T. Matsui
    • Journal Title

      Journal of Physical Chemistry B 112

      Pages: 16960-16965

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Correlation functions in quantized Hamilton dynamics and quantal cumulant dynamics2008

    • Author(s)
      Y. Pereverzev
    • Journal Title

      Journal of Chemical Physics 129

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Distribution function in quantal cumulant dynamics2008

    • Author(s)
      Y. Shigeta
    • Journal Title

      Journal of Chemical Physics 128

    • NAID

      120007138823

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Quantal cumulant dynamics III : A quantum confinement under a magnetic field2008

    • Author(s)
      Y. Shigeta
    • Journal Title

      Chemical Physics Letters 461

      Pages: 310-315

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamic quantum isotope effects on multiple proton transfer reactions2008

    • Author(s)
      Y. Shigeta
    • Journal Title

      Bulletin of the Chemical Society of Japan 81

      Pages: 1230-1240

    • NAID

      10024330696

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Presentation] Structural Stability of Artificial DNA: Theoretical Study2010

    • Author(s)
      Y. Shigeta
    • Organizer
      第4回ACCMS-VO国際会議
    • Place of Presentation
      東北大学
    • Year and Date
      2010-01-17
    • Related Report
      2009 Final Research Report
  • [Presentation] Structural Stability of Artificial DNA : Theoretical Study2010

    • Author(s)
      Y.Shigeta
    • Organizer
      第4回ACCMS-VO国際会議
    • Place of Presentation
      東北大学・仙台
    • Year and Date
      2010-01-17
    • Related Report
      2009 Annual Research Report
  • [Presentation] 金属蛋白質の触媒反応の理論解析2009

    • Author(s)
      重田育照、神谷克政
    • Organizer
      第47回生物物理学会年会
    • Place of Presentation
      徳島文理大学・アスティとくしま
    • Year and Date
      2009-10-31
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] Energetics at an entrance part of proton transfer pathway2009

    • Author(s)
      Y.Shigeta
    • Organizer
      3rd. International Conference of Computational Science
    • Place of Presentation
      Bali, Indonesia
    • Year and Date
      2009-10-28
    • Related Report
      2009 Annual Research Report
  • [Presentation] Electron conduction of metal containing artificial DNA2009

    • Author(s)
      Y.Shigeta, T.Matsui
    • Organizer
      International Conference of Computational Methods in Sciences and Engineering 2009
    • Place of Presentation
      Rhodes, Greece
    • Year and Date
      2009-10-02
    • Related Report
      2009 Annual Research Report
  • [Presentation] Side-on型配位遷移金属錯体の反応解析2009

    • Author(s)
      重田育照、宮地秀明
    • Organizer
      第104回触媒討論会
    • Place of Presentation
      宮崎大学
    • Year and Date
      2009-09-29
    • Related Report
      2009 Final Research Report
  • [Presentation] Side-on型配位遷移金属錯体の反応解析2009

    • Author(s)
      重田育照、宮地秀明
    • Organizer
      第104回触媒討論会
    • Place of Presentation
      シーガイヤ・宮崎大学
    • Year and Date
      2009-09-28
    • Related Report
      2009 Annual Research Report
  • [Presentation] Energy Compensation Mechanism for Protonation States of a Asp-His Pair at entrance of D pathway in Cytochrome c Oxidase2009

    • Author(s)
      Y.Shigeta, K.Kamiya
    • Organizer
      International Meeting of Metalloprotein Functions
    • Place of Presentation
      University of Hyogo
    • Year and Date
      2009-07-31
    • Related Report
      2009 Annual Research Report
  • [Presentation] 蛋白質の立体構造・電子状態・生物機能の間の相関関係の研究2009

    • Author(s)
      神谷克政、重田育照
    • Organizer
      第64回日本物理学会年次大会
    • Place of Presentation
      立教大学
    • Year and Date
      2009-03-28
    • Related Report
      2009 Final Research Report
  • [Presentation] 量子ゆらぎの熱ゆらぎと動的分子理論2009

    • Author(s)
      Y. Shigeta
    • Organizer
      第89回日本化学会年会
    • Place of Presentation
      日本大学・船橋キャンパス
    • Year and Date
      2009-03-28
    • Related Report
      2008 Annual Research Report
  • [Presentation] 蛋白質の立体構造・電子状態・生物機能の間の相関関係の研究2009

    • Author(s)
      K. Kamiya
    • Organizer
      第64回日本物理学会年次大会
    • Place of Presentation
      立教大学・池袋キャンパス
    • Year and Date
      2009-03-28
    • Related Report
      2008 Annual Research Report
  • [Presentation] 量子ゆらぎと熱ゆらぎの動的分子理論2009

    • Author(s)
      重田育照
    • Organizer
      第89回日本化学会年会
    • Place of Presentation
      日本大学船橋キャンパス
    • Year and Date
      2009-03-27
    • Related Report
      2009 Final Research Report
  • [Presentation] Structural Stability of Artificial DNA: Theoretical Study2009

    • Author(s)
      Y. Shigeta
    • Organizer
      第3回ACCMS-VO国際会議
    • Place of Presentation
      東北大学
    • Year and Date
      2009-02-17
    • Related Report
      2009 Final Research Report
  • [Presentation] Structural Stability of Artificial DNA : Theoretical Study2009

    • Author(s)
      Y. Shigeta
    • Organizer
      第3回ACCMS-VO国際会議
    • Place of Presentation
      東北大学・仙台
    • Year and Date
      2009-02-17
    • Related Report
      2008 Annual Research Report
  • [Presentation] Energetics at an Entrance Part of Proton Transfer Pathway2009

    • Author(s)
      Y. Shigeta
    • Organizer
      3rd. International Conference of Computational Science [INVITED]
    • Place of Presentation
      Indonesia
    • Related Report
      2009 Final Research Report
  • [Presentation] Electron Conduction of Metal Containing Artificial DNA2009

    • Author(s)
      Y. Shigeta
    • Organizer
      International Conference of Computational Methods in Sciences and Engineering 2009 [INVITED]
    • Place of Presentation
      Greece
    • Related Report
      2009 Final Research Report
  • [Presentation] Energy Compensation Mechanism for Protonation States of a Asp-His Pair at Entrance of D pathway in Cytochrome c Oxidase2009

    • Author(s)
      Y. Shigeta
    • Organizer
      International Meeting of Metalloprotein Functions [INVITED]
    • Place of Presentation
      Japan
    • Related Report
      2009 Final Research Report
  • [Presentation] Global and local structure of cisplatin and DNA base pair complex : a theoretical study2008

    • Author(s)
      T. Matsui
    • Organizer
      2nd World Conference on Ehrlich II
    • Place of Presentation
      ニュルンベルグ・独国
    • Year and Date
      2008-10-05
    • Related Report
      2008 Annual Research Report
  • [Presentation] A novel proton transfer through peptide group in protein2008

    • Author(s)
      K. Kamiya
    • Organizer
      Theory and Application in Computational Chemis try 2008
    • Place of Presentation
      上海・中国
    • Year and Date
      2008-09-27
    • Related Report
      2008 Annual Research Report
  • [Presentation] Quantum dynamics in terms of cumulant2008

    • Author(s)
      Y. Shigeta
    • Organizer
      Theory and Application in Computational Chemistry 2008
    • Place of Presentation
      上海・中国
    • Year and Date
      2008-09-25
    • Related Report
      2008 Annual Research Report
  • [Presentation] 金属イオンを含む人工DN Aの理論的研究2008

    • Author(s)
      T. Matsui
    • Organizer
      第2回分子科学討論会
    • Place of Presentation
      福岡サンパレス
    • Year and Date
      2008-09-24
    • Related Report
      2009 Final Research Report
  • [Presentation] 金属イオンを含む人工DNAの理論的研究2008

    • Author(s)
      T. Matsui
    • Organizer
      第2回分子科学討論会
    • Place of Presentation
      福岡・サンパレス
    • Year and Date
      2008-09-24
    • Related Report
      2008 Annual Research Report
  • [Presentation] Quantum mechanics in terms of cumulant2008

    • Author(s)
      Y. Shigeta
    • Organizer
      13^<th>Quantum systems in chemistry and physics
    • Place of Presentation
      ミシガン州立大学・ランシング・米国
    • Year and Date
      2008-07-05
    • Related Report
      2008 Annual Research Report
  • [Presentation] キュミュラントによる量子動力学2008

    • Author(s)
      重田育照
    • Organizer
      第11回理論化学討論会
    • Place of Presentation
      慶応大学
    • Year and Date
      2008-05-22
    • Related Report
      2009 Final Research Report
  • [Presentation] キュミュラントによる量子動力学2008

    • Author(s)
      Y. Shigeta
    • Organizer
      第11回理論化学討論会
    • Place of Presentation
      慶応大学・日吉キャンパス
    • Year and Date
      2008-05-22
    • Related Report
      2008 Annual Research Report
  • [Presentation] Quantum Dynamics in Terms of Cumulant2008

    • Author(s)
      Y. Shigeta
    • Organizer
      Theory and Application in Computational Chemistry 2008 [INVITED]
    • Place of Presentation
      China
    • Related Report
      2009 Final Research Report
  • [Presentation] Quantum Mechanics in Terms of Cumulant2008

    • Author(s)
      Y. Shigeta
    • Organizer
      13th Quantum Systems in Chemistry and Physics [INVITED]
    • Place of Presentation
      USA
    • Related Report
      2009 Final Research Report
  • [Book] Quantum Theory in Terms of Cumulant Variables2009

    • Author(s)
      Y. Shigeta, H. Miyachi, T. Matsui, N. Yokoyama, K. Hirao
    • Publisher
      Springer
    • Related Report
      2009 Final Research Report
  • [Book] Quantum Theory in Terms of Cumulant Variables Advances in the Theory of Atomic and Molecular Systems, Conceptual and Computational Advances in Quantum Chemistry, chapter 21.2009

    • Author(s)
      Y.Shigeta, H.Miyachi, T.Matsui, N.Yokoyama, K.Hirao
    • Total Pages
      31
    • Publisher
      Springer
    • Related Report
      2009 Annual Research Report
  • [Book] Single-reference Methods for Excited States in Molecules and Polymers2008

    • Author(s)
      S. Hirata, P. -D. Fan, T. Shiozaki, Y. Shigeta
    • Publisher
      Springer
    • Related Report
      2009 Final Research Report
  • [Book] "Single-reference methods for excited states in molecules and polymers" Book chapter of Challenges and Advances in Computational Chemistry and Physics Vol 5, Ed. J. Lesczynski2008

    • Author(s)
      S. Hirata, P.-D. Fan, T. Shiozak i, Y. Shigeta
    • Total Pages
      50
    • Publisher
      Springer
    • Related Report
      2008 Annual Research Report
  • [Remarks]

    • URL

      http://www.sci.u-hyogo.ac.jp/life/GCOE/japanese/pico_intro/shigeta/Site/Home.html

    • Related Report
      2009 Final Research Report

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Published: 2008-04-01   Modified: 2016-04-21  

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