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2015 Fiscal Year Annual Research Report

DNAの協同的分子認識機構解明のための電子相関効果を導入した量子化学解析法と応用

Research Project

Project/Area Number 23245005
Research InstitutionKyushu University

Principal Investigator

青木 百合子  九州大学, 総合理工学研究科(研究院), 教授 (10211690)

Project Period (FY) 2011-04-01 – 2016-03-31
Keywords量子化学 / DNA / 電子状態 / 構造最適化 / 導電性
Outline of Annual Research Achievements

本課題は、DNAに対し、超効率的にグローバルミニマムな安定構造を決定し、その電子状態を高精度に求めることにより生体内で起こる諸現象を精密に解明し、生体機能をミクロな立場から機能設計できる方法を構築することを目的としている。
そのために、申請者らがオリジナルに開発してきたElongation法に、安定構造、基底状態、電子相関効果を正確に得る手法を導入し、DNAを代表する生体系の生理機能を分子レベルで解明できる方法を展開している。特に本年はDNAとタンパク質等との相互作用を効率よく得られる手法の展開としてIntermediate electrostatic field法によるElongation法を開発した。外部分子の電荷のもとでDNAを伸長できるようにすることで、計算精度と効率が改善されることが分かった。
機能を設計する上で重要なElongation-構造最適化法の開発について、従来の全系に対するダイレクトな構造最適化計算によって得られた構造よりも、さらに安定な点を効率的に探しうる可能性が示唆された。また、Hartree-Fock法レベルを超えて、電子相関効果を含めるためにHF+LMP2 法のレベルでの開発を行ない、効率よく電子相関効果の影響が得られるように開発している。さらに、機能性を評価するために、開殻系の効率的電子状態計算法も開発する一方で、Elongation法と分子動力学法との結合を本格的におこない、溶媒中での構造最適化が可能となるよう発展させた。DNAは系が巨大過ぎて膨大な計算時間を要するため、糖鎖を用いたテスト計算を行なった。

Research Progress Status

27年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

27年度が最終年度であるため、記入しない。

  • Research Products

    (24 results)

All 2016 2015 Other

All Int'l Joint Research (2 results) Journal Article (8 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 8 results,  Acknowledgement Compliant: 1 results) Presentation (14 results) (of which Int'l Joint Research: 9 results,  Invited: 4 results)

  • [Int'l Joint Research] Jagiellonian University/Faculty of Chemistry(ポーランド)

    • Country Name
      POLAND
    • Counterpart Institution
      Jagiellonian University/Faculty of Chemistry
  • [Int'l Joint Research] South China Normal University/Faculty of Chemistry&Environment(中国)

    • Country Name
      CHINA
    • Counterpart Institution
      South China Normal University/Faculty of Chemistry&Environment
  • [Journal Article] An efficient unrestricted PCM-elongation method for large high-spin polymer/dendrimer systems2016

    • Author(s)
      Xun Zhu, Yuuichi Orimoto, and Yuriko Aoki
    • Journal Title

      Z. Phys. Chem.

      Volume: 印刷中 Pages: 印刷中

    • DOI

      10.1515/zpch-2015-0722

    • Peer Reviewed
  • [Journal Article] Theoretical investigation of the pressure-induced insulator-to-metal-to-insulator transitions in one-dimensional bis(dimethylglyoximato) platinum(II), Pt(dmg)22015

    • Author(s)
      Kai Liu, Yuuichi Orimoto, and Yuriko Aoki
    • Journal Title

      Polyhedron

      Volume: 87 Pages: 141-146

    • DOI

      10.1016/j.poly.2014.11.013

    • Peer Reviewed
  • [Journal Article] Ab initio O(N) elongation-counterpoise method for BSSE-corrected interaction energy analyses in biosystems2015

    • Author(s)
      Yuuici Orimoto, Ryohei Yamamoto, Peng Xie, Kai Liu, Akira Imamura, and Yuriko Aoki
    • Journal Title

      J. Chem. Phys.

      Volume: 142 Pages: 104111(1-11)

    • DOI

      10.1063/1.4913931

    • Peer Reviewed
  • [Journal Article] Intermediate electrostatic field for the generalized elongation method2015

    • Author(s)
      Kai Liu, Jacek Korchowiec, and Yuriko Aoki
    • Journal Title

      ChemPhysChem

      Volume: 16 Pages: 1551-1556

    • DOI

      10.1002/cphc.201402901

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Development of minimized mixing molecular orbital method for designing organic ferromagnets2015

    • Author(s)
      Xun Zhu, and Yuriko Aok
    • Journal Title

      J. Comput. Chem.

      Volume: 36 Pages: 1232-1239

    • DOI

      10.1002/jcc.23915

    • Peer Reviewed
  • [Journal Article] Interaction of OH- with Xylan and Its Hydrated Complexes: Structures and Molecular Dynamics Study Using Elongation Method2015

    • Author(s)
      Lin Jin, Kai Liu, and Yuriko Aoki
    • Journal Title

      J. Mol. Model.

      Volume: 21 Pages: 117(1-10)

    • DOI

      10.1007/s00894-015-2666-5

    • Peer Reviewed
  • [Journal Article] Elongation method for electronic structure calculations of random DNA sequences2015

    • Author(s)
      Yuuichi Orimoto, Kai Liu, and Yuriko Aoki
    • Journal Title

      J. Comput. Chem.

      Volume: 36 Pages: 2103-2113

    • DOI

      10.1002/jcc.24047

    • Peer Reviewed
  • [Journal Article] Efficient prediction of high spin ground state stability in organic polyradicals under solvent effects2015

    • Author(s)
      Xun Zhu, and Yuriko Aoki
    • Journal Title

      Chem. Phys. Lett.

      Volume: 637 Pages: 143-147

    • DOI

      10.1016/j.cplett.2015.07.060

    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] Linear Scaling Method for Large Systems and its Applications to Nano-Bio Systems2015

    • Author(s)
      Yuriko Aoki
    • Organizer
      The 6th JCS International Symposium on Theoretical Chemistry (JCS-2015)
    • Place of Presentation
      Bratislava (Slovak Republic)
    • Year and Date
      2015-10-11 – 2015-10-15
    • Int'l Joint Research / Invited
  • [Presentation] Computational functional design of artificial DNAs: application of elongation method and through-space/bond interaction analysis2015

    • Author(s)
      Yuuichi Orimoto, and Yuriko Aoki
    • Organizer
      第42回国際核酸化学シンポジウム
    • Place of Presentation
      イーグレ姫路 (兵庫県姫路市)
    • Year and Date
      2015-09-23 – 2015-09-25
    • Int'l Joint Research
  • [Presentation] Analysis and modeling of molecular interactions in halogen-bonded cocrystal2015

    • Author(s)
      Wataru Mizukami, Ken Matsubara, and Yuriko Aoki
    • Organizer
      51st Symposium on Theoretical Chemistry(STC2015)
    • Place of Presentation
      Potsdam (Germany)
    • Year and Date
      2015-09-20 – 2015-09-24
    • Int'l Joint Research
  • [Presentation] 開殻分安定スピン状態予測のための結合性最Mixing(NB-MM)MO-ELG法2015

    • Author(s)
      Xun Zhu, and Yuriko Aoki
    • Organizer
      第9回分子化学討論会
    • Place of Presentation
      東京工業大学 (東京都目黒区)
    • Year and Date
      2015-09-16 – 2015-09-19
  • [Presentation] 相互作解析によるハロゲン結合をベースとした共結晶成過程の理解2015

    • Author(s)
      Ken Matsubara, Wataru Mizukami, and Yuriko Aoki
    • Organizer
      第9回分子化学討論会
    • Place of Presentation
      東京工業大学 (東京都目黒区)
    • Year and Date
      2015-09-16 – 2015-09-19
  • [Presentation] 大規模原子分子系に向けた効率的Elongation法の展開と応用2015

    • Author(s)
      Yuriko Aoki, Kai Liu, Wataru Mizukami, and Yuuichi Orimoto
    • Organizer
      第9回分子化学討論会
    • Place of Presentation
      東京工業大学 (東京都目黒区)
    • Year and Date
      2015-09-16 – 2015-09-19
  • [Presentation] 光電変換ワイヤの効率的理論設計法と応用2015

    • Author(s)
      Kouhei Kato, Yuuichi Orimoto, and Yuriko Aoki
    • Organizer
      第9回分子化学討論会
    • Place of Presentation
      東京工業大学 (東京都目黒区)
    • Year and Date
      2015-09-16 – 2015-09-19
  • [Presentation] 機能性人工核酸の理論的分子設計~導電性・強磁性・非線形光学特性~2015

    • Author(s)
      Yuuichi Orimoto, and Yuriko Aoki
    • Organizer
      第9回分子化学討論会
    • Place of Presentation
      東京工業大学 (東京都目黒区)
    • Year and Date
      2015-09-16 – 2015-09-19
  • [Presentation] An efficient quantum chemical approach for material design2015

    • Author(s)
      Yuriko Aoki
    • Organizer
      2015 International Symposium for Advanced Materials Research (ISAMR 2015)
    • Place of Presentation
      Sun Moon Lake (Taiwan)
    • Year and Date
      2015-08-16 – 2015-08-20
    • Int'l Joint Research / Invited
  • [Presentation] Theoretical design for NLO polymers2015

    • Author(s)
      Yuriko Aoki
    • Organizer
      2015 International Symposium for Advanced Materials Research (ISAMR 2015)
    • Place of Presentation
      Sun Moon Lake (Taiwan)
    • Year and Date
      2015-08-16 – 2015-08-20
    • Int'l Joint Research
  • [Presentation] Highly efficient electronic structure calculations of biomaterials for their functional design2015

    • Author(s)
      Yuuichi Orimoto, and Yuriko Aoki
    • Organizer
      2015 International Symposium for Advanced Materials Research (ISAMR 2015)
    • Place of Presentation
      Sun Moon Lake (Taiwan)
    • Year and Date
      2015-08-16 – 2015-08-20
    • Int'l Joint Research
  • [Presentation] Interaction of OH- with Xylan and Its Hydrated Complexes: Structures and Molecular Dynamics Study Using Elongation Method2015

    • Author(s)
      Lin Jin, and Yuriko Aoki
    • Organizer
      2015 International Symposium for Advanced Materials Research (ISAMR 2015)
    • Place of Presentation
      Sun Moon Lake (Taiwan)
    • Year and Date
      2015-08-16 – 2015-08-20
    • Int'l Joint Research
  • [Presentation] Elongation Method for Functional Design of Nano-Baio Systems2015

    • Author(s)
      Yuriko Aoki
    • Organizer
      The 15th International Congress of Quantum Chemistry (ICQC)
    • Place of Presentation
      Beijing (China)
    • Year and Date
      2015-06-08 – 2015-06-13
    • Int'l Joint Research / Invited
  • [Presentation] Efficient NLO Calculations by Elongation Method2015

    • Author(s)
      Yuriko Aoki
    • Organizer
      The 15th International Congress of Quantum Chemistry (ICQC) Satellite Meeting
    • Place of Presentation
      Nanjing (China)
    • Year and Date
      2015-06-01 – 2015-06-06
    • Int'l Joint Research / Invited

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Published: 2017-01-06  

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