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2017 Fiscal Year Annual Research Report

超分子・生体分子の自己集合機構の理解のための量子シミュレーション手法の高度化

Publicly Offered Research

Project AreaDynamical ordering of biomolecular systems for creation of integrated functions
Project/Area Number 16H00780
Research InstitutionYokohama City University

Principal Investigator

立川 仁典  横浜市立大学, 生命ナノシステム科学研究科(八景キャンパス), 教授 (00267410)

Project Period (FY) 2016-04-01 – 2018-03-31
Keywords量子シミュレーション / 超分子自己集合 / 歯車状両親媒性分子 / タンパク質 / 溶媒効果
Outline of Annual Research Achievements

本研究課題では、超分子・生体分子における自己集合機構の解明を目指し、我々が構築してきた量子シミュレーション手法を高度化させ、領域内での実験グループとの密な議論に基づき、量子化学計算の立場からこの課題に挑む。具体的には1.量子シミュレーション手法の高度化と、それによる2.超分子・生体分子の自己集合機構の解明に向けた計算を実現した。
1.量子シミュレーション手法の高度化: (1A) 階層的手法の実装 QM/MM 法やPCM法などを高度化することにより、溶媒効果を考慮した計算を可能とした。(1B) 効率的サンプリング手法の実装 マルチプルタイムステップの導入により、幅広い空間・時間スケールでのサンプリングを試みた。
2.超分子・生体分子の自己集合機構の解明に向けて: (2A) 歯車状両親媒性分子の超分子自己集合 歯車状両親媒性分子の立方体超分子の安定性に対する溶媒効果・置換基効果、アダマンタン内包による四面体への自己集合機構、を系統的に探った。(2B) 低障壁水素結合(LBHB)たんぱく質の高次構造転移 光活性黄色タンパク質(PYP)において、LBHB付近の水素結合の振動状態に着目し、水素の量子効果、溶媒効果、温度効果を含めた大規模ONIOM計算を実現した。
以上により、我々の理論手法と実験研究者との有機的な結びつきによる共同研究も具体的に実施し、いくつかは既に投稿論文として発表しており、当該領域の研究推進に大きく貢献したものと自負している。

Research Progress Status

29年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

29年度が最終年度であるため、記入しない。

  • Research Products

    (27 results)

All 2018 2017 Other

All Journal Article (15 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 15 results,  Open Access: 2 results) Presentation (11 results) (of which Int'l Joint Research: 10 results,  Invited: 7 results) Remarks (1 results)

  • [Journal Article] Quantum dynamics calculations for e + ?+?LiH?→?Li + ?+?[H ? ;? e + ] dissociative positron attachment using a pseudopotential model2018

    • Author(s)
      Suzuki Kento、Takayanagi Toshiyuki、Kita Yukiumi、Tachikawa Masanori、Oyamada Takayuki
    • Journal Title

      Computational and Theoretical Chemistry

      Volume: 1123 Pages: 135~141

    • DOI

      10.1016/j.comptc.2017.11.023

    • Peer Reviewed
  • [Journal Article] Quantum fluctuations of a fullerene cage modulate its internal magnetic environment2018

    • Author(s)
      Kawatsu Tsutomu、Tachikawa Masanori
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 20 Pages: 1673~1684

    • DOI

      10.1039/C7CP06401B

    • Peer Reviewed
  • [Journal Article] Reaction mechanism of hydrogen-tritium exchange reactions between several organic and HTO molecules: a role of the second HTO2018

    • Author(s)
      Udagawa Taro、Tachikawa Masanori
    • Journal Title

      RSC Advances

      Volume: 8 Pages: 3878~3888

    • DOI

      10.1039/C7RA13110K

    • Peer Reviewed / Open Access
  • [Journal Article] Strong Hydrogen Bonds at the Interface between Proton-Donating and -Accepting Self-Assembled Monolayers on Au(111)2018

    • Author(s)
      Kato Hiroyuki S.、Yoshimoto Shinya、Ueda Akira、Yamamoto Susumu、Kanematsu Yusuke、Tachikawa Masanori、Mori Hatsumi、Yoshinobu Jun、Matsuda Iwao
    • Journal Title

      Langmuir

      Volume: 34 Pages: 2189~2197

    • DOI

      10.1021/acs.langmuir.7b03451

    • Peer Reviewed
  • [Journal Article] Hyperthermostable cube-shaped assembly in water2018

    • Author(s)
      Zhan Yi-Yang、Ogata Kazuho、Kojima Tatsuo、Koide Takuya、Ishii Kentaro、Mashiko Takako、Tachikawa Masanori、Uchiyama Susumu、Hiraoka Shuichi
    • Journal Title

      Communications Chemistry

      Volume: 1 Pages: 14-1 - 14-4

    • DOI

      10.1038/s42004-018-0014-2

    • Peer Reviewed
  • [Journal Article] Semi-quantitative evaluation of molecular meshing via surface analysis with varying probe radii2018

    • Author(s)
      Tanaka Naru、Zhan Yi-Yang、Ozawa Yuka、Kojima Tatsuo、Koide Takuya、Mashiko Takako、Nagashima Umpei、Tachikawa Masanori、Hiraoka Shuichi
    • Journal Title

      Chemical Communications

      Volume: 54 Pages: 3335~3338

    • DOI

      10.1039/c8cc00695d

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Programed dynamical ordering in self-organization processes of a nanocube: a molecular dynamics study2018

    • Author(s)
      Harada Ryuhei、Mashiko Takako、Tachikawa Masanori、Hiraoka Shuichi、Shigeta Yasuteru
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 20 Pages: 9115~9122

    • DOI

      10.1039/C8CP00284C

    • Peer Reviewed
  • [Journal Article] Theoretical study on substituent and solvent effects for nanocubes formed with gear-shaped amphiphile molecules2017

    • Author(s)
      Mashiko T.、Hiraoka S.、Nagashima U.、Tachikawa M.
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 19 Pages: 1627~1631

    • DOI

      10.1039/C6CP07754D

    • Peer Reviewed
  • [Journal Article] Unusual H/D isotope effect in isomerization and keto?enol tautomerism reactions of pyruvic acid: nuclear quantum effect restricts some rotational isomerization reactions2017

    • Author(s)
      Udagawa Taro、Sugiura Keita、Suzuki Kimichi、Tachikawa Masanori
    • Journal Title

      RSC Advances

      Volume: 7 Pages: 9328~9337

    • DOI

      10.1039/C6RA28271G

    • Peer Reviewed / Open Access
  • [Journal Article] Asymmetric hydrogen bonding in formic acid?nitric acid dimer observed by quantum molecular dynamics simulations2017

    • Author(s)
      Ngaojampa Chanisorn、Kawatsu Tsutomu、Oba Yuki、Kungwan Nawee、Tachikawa Masanori
    • Journal Title

      Theoretical Chemistry Accounts

      Volume: 136 Pages: 30-1~30-10

    • DOI

      10.1007/s00214-017-2057-3

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Multicomponent DFT study of geometrical H/D isotope effect on hydrogen-bonded organic conductor, κ-H 3 (Cat EDT-ST) 22017

    • Author(s)
      Yamamoto Kaichi、Kanematsu Yusuke、Nagashima Umpei、Ueda Akira、Mori Hatsumi、Tachikawa Masanori
    • Journal Title

      Chemical Physics Letters

      Volume: 674 Pages: 168~172

    • DOI

      http://dx.doi.org/10.1016/j.cplett.2017.02.073

    • Peer Reviewed
  • [Journal Article] Quantum dynamics study on the binding of a positron to vibrationally excited states of hydrogen cyanide molecule2017

    • Author(s)
      Takayanagi Toshiyuki、Suzuki Kento、Yoshida Takahiko、Kita Yukiumi、Tachikawa Masanori
    • Journal Title

      Chemical Physics Letters

      Volume: 675 Pages: 118~123

    • DOI

      http://dx.doi.org/10.1016/j.cplett.2017.03.025

    • Peer Reviewed
  • [Journal Article] Solvent Dependence of Double Proton Transfer in the Formic Acid?Formamidine Complex: Path Integral Molecular Dynamics Investigation2017

    • Author(s)
      Kungwan Nawee、Ngaojampa Chanisorn、Ogata Yudai、Kawatsu Tsutomu、Oba Yuki、Kawashima Yukio、Tachikawa Masanori
    • Journal Title

      The Journal of Physical Chemistry A

      Volume: 121 Pages: 7324~7334

    • DOI

      10.1021/acs.jpca.7b07010

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] The Effect of Solvent and Coordination Environment of Metal Source on the Self-Assembly Pathway of a Pd(II)-Mediated Coordination Capsule2017

    • Author(s)
      Kai Shumpei、Sakuma Yui、Mashiko Takako、Kojima Tatsuo、Tachikawa Masanori、Hiraoka Shuichi
    • Journal Title

      Inorganic Chemistry

      Volume: 56 Pages: 12652~12663

    • DOI

      10.1021/acs.inorgchem.7b02152

    • Peer Reviewed
  • [Journal Article] Quantitative Analysis of Self-Assembly Process of a Pd2L4 Cage Consisting of Rigid Ditopic Ligands2017

    • Author(s)
      Kai Shumpei、Mart?-Centelles Vicente、Sakuma Yui、Mashiko Takako、Kojima Tatsuo、Nagashima Umpei、Tachikawa Masanori、Lusby Paul J.、Hiraoka Shuichi
    • Journal Title

      Chemistry - A European Journal

      Volume: 24 Pages: 663~671

    • DOI

      10.1002/chem.201704285

    • Peer Reviewed / Int'l Joint Research
  • [Presentation] 日本化学会 第98春季年会 (2018)2018

    • Author(s)
      Masanori Tachikawa
    • Organizer
      歯車状両親媒性分子からなるナノキューブの安定性に関する理論的研究
    • Invited
  • [Presentation] Theoretical study on substituent and solvent effects for nanocube formed with gear-shaped amphiphile molecules2017

    • Author(s)
      Masanori Tachikawa
    • Organizer
      5th International Symposium on Dynamical Ordering of Biomolecular Systems for Creation of Integrated Functions
    • Int'l Joint Research / Invited
  • [Presentation] Theoretical study on substituent and solvent effects for nanocube formed with gear-shaped amphiphile molecules2017

    • Author(s)
      Masanori Tachikawa
    • Organizer
      Frontier Bioorganization Forum 2017
    • Int'l Joint Research / Invited
  • [Presentation] A multicomponent QM study of H_2 dissociation on small aluminum cluster2017

    • Author(s)
      Masanori Tachikawa
    • Organizer
      INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE
    • Int'l Joint Research
  • [Presentation] First-principles study on the binding of a positron to polyatomic molecules2017

    • Author(s)
      Masanori Tachikawa
    • Organizer
      XIX International Workshop on Low-Energy Positron and Positronium Physics XX International Symposium on Electron-Molecule Collisions and Swarms
    • Int'l Joint Research
  • [Presentation] Path integral simulation on hyperfine coupling constants of muoniated and hydrogenated acetone radicals2017

    • Author(s)
      Masanori Tachikawa
    • Organizer
      30th International Conference on Photonic Electronic and Atomic Collisions
    • Int'l Joint Research
  • [Presentation] Theoretical study on substituent and solvent effects for nanocube formed with gear-shaped amphiphile molecules2017

    • Author(s)
      Masanori Tachikawa
    • Organizer
      The 9th Conference of the Asian Consortium on Computational Materials Science
    • Int'l Joint Research / Invited
  • [Presentation] Nuclear quantum effect on hydrogen fluoride trimer by ab initio path integral molecular dynamics simulation2017

    • Author(s)
      Masanori Tachikawa
    • Organizer
      11th European Conference on Theoretical and Computational Chemistry
    • Int'l Joint Research
  • [Presentation] Ab initio theoretical study of the effect of molecular vibrations on the positron-binding to polyatomic molecules2017

    • Author(s)
      Masanori Tachikawa
    • Organizer
      12th International Workshop on Positron and Positronium Chemistry
    • Int'l Joint Research / Invited
  • [Presentation] Path Integral Simulation for Hydrogen bonded systems: Protonic quantum nature and its isotope effects2017

    • Author(s)
      Masanori Tachikawa
    • Organizer
      3rd Japan-Korea Joint Symposium on Hydrogen in Materials
    • Int'l Joint Research / Invited
  • [Presentation] Ab initio study of the effect of molecular vibrations on the positron-binding to polyatomic molecules2017

    • Author(s)
      Masanori Tachikawa
    • Organizer
      8th Asia-Pacific Conference of Theoretical and Computational Chemistry
    • Int'l Joint Research / Invited
  • [Remarks] 横浜市立大学量子物理化学研究室

    • URL

      http://www-user.yokohama-cu.ac.jp/~tachi/

URL: 

Published: 2018-12-17  

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