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

• Project Area: Dynamical ordering of biomolecular systems for creation of integrated functions
• Project/Area Number: 16H00780
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Science and Engineering
• Research Institution: Yokohama 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
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000); Fiscal Year 2017: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000); Fiscal Year 2016: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
• 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

• [Journal Article] Quantum dynamics calculations for e + ?+?LiH?→?Li + ?+?[H ? ;? e + ] dissociative positron attachment using a pseudopotential model (2018)
  • 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 environment (2018)
  • Author(s): Kawatsu Tsutomu、Tachikawa Masanori
  • Journal Title: Physical Chemistry Chemical Physics Volume: 20 Issue: 3 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 HTO (2018)
  • Author(s): Udagawa Taro、Tachikawa Masanori
  • Journal Title: RSC Advances Volume: 8 Issue: 7 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 Issue: 5 Pages: 2189-2197
  • DOI: 10.1021/acs.langmuir.7b03451
  • Peer Reviewed
• [Journal Article] Hyperthermostable cube-shaped assembly in water (2018)
  • 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 Issue: 1 Pages: 14-14
  • DOI: 10.1038/s42004-018-0014-2
  • Peer Reviewed / Open Access
• [Journal Article] Semi-quantitative evaluation of molecular meshing via surface analysis with varying probe radii (2018)
  • 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 Issue: 27 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 study (2018)
  • Author(s): Harada Ryuhei、Mashiko Takako、Tachikawa Masanori、Hiraoka Shuichi、Shigeta Yasuteru
  • Journal Title: Physical Chemistry Chemical Physics Volume: 20 Issue: 14 Pages: 9115-9122
  • DOI: 10.1039/c8cp00284c
  • Peer Reviewed
• [Journal Article] Theoretical study on substituent and solvent effects for nanocube formed with gear-shaped amphiphile molecules (2017)
  • Author(s): T. Mashiko, S. Hiraoka, U, Nagashima, and M. Tachikawa,
  • Journal Title: Phys. Chem. Chem. Phys. Volume: 19 Issue: 2 Pages: 191627-1631
  • DOI: 10.1039/c6cp07754d
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Unusual H/D isotope effect in isomerization and keto-enol tautomerism reactions of pyruvic acid: Nuclear quantum effect restricts some rotational isomerization reactions (2017)
  • Author(s): Taro Udagawa, Keita Sugiura, Kimichi Suzuki, Masanori Tachikawa
  • Journal Title: RSC Advances Volume: 7 Issue: 15 Pages: 9328-9337
  • DOI: 10.1039/c6ra28271g
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Asymmetric hydrogen bonding in formic acid?nitric acid dimer observed by quantum molecular dynamics simulations (2017)
  • Author(s): Ngaojampa Chanisorn、Kawatsu Tsutomu、Oba Yuki、Kungwan Nawee、Tachikawa Masanori
  • Journal Title: Theoretical Chemistry Accounts Volume: 136 Issue: 3
  • 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-H3(Cat-EDT-ST)2 (2017)
  • Author(s): K. Yamamoto, Y. Kanematsu, U. Nagashima, A. Ueda, H. Mori, M. Tachikawa
  • Journal Title: Chem. Phys. Lett. Volume: 674 Pages: 168-172
  • DOI: 10.1016/j.cplett.2017.02.073
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Quantum dynamics study on the binding of a positron to vibrationally excited states of hydrogen cyanide molecule (2017)
  • Author(s): Toshiyuki Takayanagi, Kento Suzuki, Takahiko Yoshida, Yukiumi Kita, Masanori Tachikawa
  • Journal Title: Chem. Phys. Lett. Volume: 675 Pages: 118-123
  • DOI: 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 Investigation (2017)
  • 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 Issue: 39 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 Capsule (2017)
  • Author(s): Kai Shumpei、Sakuma Yui、Mashiko Takako、Kojima Tatsuo、Tachikawa Masanori、Hiraoka Shuichi
  • Journal Title: Inorganic Chemistry Volume: 56 Issue: 20 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 Ligands (2017)
  • 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 Issue: 3 Pages: 663-671
  • DOI: 10.1002/chem.201704285
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Quantum dynamics study on the binding of a positron to vibrationally excited states of hydrogen cyanide molecule (2017)
  • Author(s): T. Takayanagi, K. Suzuki, T. Yoshida, Y. Kita, and M. Tachikawa,
  • Journal Title: Chem. Phys. Lett. Volume: in press
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Multicomponent DFT study of geometrical H/D isotope effect on hydrogen-bonded organic conductor, κ-H3(Cat EDT-ST)2 (2017)
  • Author(s): K. Yamamoto, Y. Kanematsu, U. Nagashima, A. Ueda, H. Mori, and M. Tachikawa,
  • Journal Title: Chem. Phys. Lett. Volume: in press
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Asymmetric hydrogen bonding in formic acid-nitric acid dimer observed by quantum molecular dynamics simulations (2017)
  • Author(s): Chanisorn Ngaojampa, Tsutomu Kawatsu, Yuki Oba, Nawee Kungwan, and M. Tachikawa,
  • Journal Title: Theor. Chem. Acc. Volume: in press
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Unusual H/D isotope effect in isomerization and keto-enol tautomerism reactions of pyruvic acid: Nuclear quantum effect restricts some rotational isomerization reactions (2017)
  • Author(s): T. Udagawa, K. Sugiura, K. Suzuki, and M. Tachikawa,
  • Journal Title: RSC Advances Volume: in press
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Effects of vibrational anharmonicity and inter-mode couplings on the binding energy of a positron to molecules (2017)
  • Author(s): Y. Kita and M. Tachikawa,
  • Journal Title: AIP Conf. Proc. Volume: in press
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Nuclear quantum effect and H/D isotope effect on F + (H2O)n → FH + (H2O)n-1OH (n = 1-3) reactions (2016)
  • Author(s): T. Udagawa and M. Tachikawa,
  • Journal Title: J. Chem. Phys. Volume: 145 Issue: 16 Pages: 164310-164310
  • DOI: 10.1063/1.4966162
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Theoretical study of H/D isotope effect on phase transition of hydrogen-bonded organic conductor κ-H3(Cat-EDT-TTF)2 (2016)
  • Author(s): K. Yamamoto, Y. Kanematsu, U. Nagashima, A. Ueda, H. Mori, M. Tachikawa
  • Journal Title: Phys. Chem. Chem. Phys. Volume: 18 Issue: 43 Pages: 29673-29680
  • DOI: 10.1039/c6cp05414e
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] QM/MM Study on Sialyltransferase Reaction Mechanism (2016)
  • Author(s): Y. Hamada, Y. Kanematsu, and M. Tachikawa,
  • Journal Title: Biochemistry Volume: 55 Issue: 40 Pages: 5764-5771
  • DOI: 10.1021/acs.biochem.6b00267
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Aminooxy-naphthylpropionic acid and its derivatives are inhibitors of auxin biosynthesis targeting Trp aminotransferase: Structure-activity relationships (2016)
  • Author(s): M. Narukawa-Nara, A. Nakamura, K. Kikuzato, Y. Kakei, A. Sato, Y. Mitani, Y. Yamasaki-Kokudo, T. Ishii, KI. Hayashi, T. Asami, T. Ogura, S. Yoshida, S. Fujioka, T. Kamakura, T. Kawatsu, M. Tachikawa, K. Soeno, and Y. Shimada,
  • Journal Title: The Plant Journal Volume: 87 Issue: 3 Pages: 245-257
  • DOI: 10.1111/tpj.13197
  • Peer Reviewed / Open Access
• [Journal Article] A path integral molecular dynamics study of the hyperfine coupling constants of the muoniated and hydrogenated acetone radicals (2016)
  • Author(s): Y. Oba, T. Kawatsu, and M. Tachikawa,
  • Journal Title: J. Chem. Phys. Volume: 145 Issue: 6
  • DOI: 10.1063/1.4960077
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Can low-barrier hydrogen bond exist in systems with second row elements? An ab initio path integral molecular dynamics study for deprotonated hydrogen sulfide dimer (2016)
  • Author(s): Y. Ogata, T. Kawatsu, and M. Tachikawa,
  • Journal Title: Theor. Chem. Acc. Volume: 135 Issue: 8
  • DOI: 10.1007/s00214-016-1958-x
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Positron Binding Properties of Glycine and Its Aqueous Complexes (2016)
  • Author(s): M. Nummela, H. Raebiger, D. Yoshida, and M. Tachikawa,
  • Journal Title: J. Phys. Chem. A Volume: 120 Issue: 23 Pages: 4037-4042
  • DOI: 10.1021/acs.jpca.6b01780
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Inverse Ubbelohde Effect in the Short Hydrogen Bond of Photosystem II: Relation between H/D Isotope Effect and Symmetry in Potential Energy Profile (2016)
  • Author(s): Y. Kanematsu, Y. Takano, and M. Tachikawa,
  • Journal Title: J. Comput. Chem. Volume: 37 Issue: 23 Pages: 2140-2145
  • DOI: 10.1002/jcc.24438
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Theoretical study of a positron-attachment to vibrational excited states for non-polar carbon disulfide molecule (2016)
  • Author(s): Y. Takeda, Y. Kita, and M. Tachikawa,
  • Journal Title: Eur. Phys. J. D Volume: 70 Issue: 6
  • DOI: 10.1140/epjd/e2016-70140-7
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Thermal Dependence on Structures of Muoniated and Hydrogenated Acetone Radicals (2016)
  • Author(s): Y. Oba, T. Kawatsu, and M. Tachikawa,
  • Journal Title: AIP Conf. Proc. Volume: 179 Pages: 020022-020022
  • DOI: 10.1063/1.4968648
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Analysis of exponent values of Gaussian-type functions on quantum protons and deuterons in charged or polarized systems (2016)
  • Author(s): M. Hashimoto, T. Ishimoto, M. Tachikawa, and T. Udagawa,
  • Journal Title: Int. J. Quant. Chem. Volume: 116 Issue: 12 Pages: 961-967
  • DOI: 10.1002/qua.25117
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Vibrational analysis on the revised potential energy curve of the low-barrier hydrogen bond in photoactive yellow protein (2015)
  • Author(s): Yusuke Kanematsu, Hironari Kamikubo, Mikio Kataoka, Masanori Tachikawa
  • Journal Title: Computational and Structural Biotechnology Journal Volume: 14 Pages: 16-19
  • DOI: 10.1016/j.csbj.2015.10.003
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [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 molecules (2017)
  • Author(s): Masanori Tachikawa
  • Organizer: The 5th International Symposium on Dynamical Ordering of Biomolecular Systems for Creation of Integrated Functions
  • Place of Presentation: The University of Tokyo, Komaba, Japan
  • Year and Date: 2017-01-21
  • Int'l Joint Research / Invited
• [Presentation] Theoretical study on substituent and solvent effects for nanocube formed with gear-shaped amphiphile molecules (2017)
  • 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 molecules (2017)
  • 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 cluster (2017)
  • 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 molecules (2017)
  • 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 radicals (2017)
  • 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 molecules (2017)
  • 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 simulation (2017)
  • 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 molecules (2017)
  • 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 effects (2017)
  • 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 molecules (2017)
  • Author(s): Masanori Tachikawa
  • Organizer: 8th Asia-Pacific Conference of Theoretical and Computational Chemistry
  • Int'l Joint Research / Invited
• [Presentation] Quantum Monte Carlo calculation of Positron-attached Polyatomic Molecules (2016)
  • Author(s): Masanori Tachikawa
  • Organizer: 14th International Workshop on Slow Positron Beam Techniques & Applications (SLOPOS14)
  • Place of Presentation: Matsue, Japan
  • Year and Date: 2016-05-22
  • Int'l Joint Research / Invited
• [Presentation] Path Integral Simulation for Hydrogen bonded systems: Protonic quantum nature and its isotope effects (2016)
  • Author(s): Masanori Tachikawa
  • Organizer: Thai-Japan Symposium in Chemistry
  • Place of Presentation: Chiang Mai University, Thailand
  • Int'l Joint Research / Invited
• [Presentation] Path integral simulation on muoniated acetone radical (2016)
  • Author(s): Masanori Tachikawa
  • Organizer: The International Symposium of Quantum Beam Science
  • Place of Presentation: Ibaraki University, Japan
  • Int'l Joint Research / Invited
• [Presentation] Path integral simulation on muoniated acetone radical (2016)
  • Author(s): Masanori Tachikawa
  • Organizer: The 11th General Meeting of ACCMS-VO
  • Place of Presentation: Tohoku University, Japan
  • 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/
• [Remarks] 横浜市立大学量子物理化学研究室（立川研究室）
  • URL: http://www-user.yokohama-cu.ac.jp/~tachi/