量子シミュレーション手法の深化による超分子および生体分子の自己集合機構の解明

2014 Fiscal Year Annual Research Report

• Project Area: Dynamical ordering of biomolecular systems for creation of integrated functions
• Project/Area Number: 26102539
• 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, 教授 (00267410)
• Project Period (FY): 2014-04-01 – 2016-03-31
• Keywords: 量子シミュレーション / 溶媒効果 / 歯車状両親媒性分子 / 超分子自己集合 / 低障壁水素結合 / たんぱく質

Outline of Annual Research Achievements

メタノール溶媒中のナノキューブ崩壊過程：　平岡らは、メチル基を持つ歯車状両親媒性分子(1)が、25%含水メタノール溶媒中で一義的に立方体（16）に自己集合することを見出した。一方でメチル基を全て水素原子に置き換えた分子2や、純粋なメタノール溶媒中での分子１や２は自己集合をしないことも見出した。本研究では自己集合が見られないメタノール溶媒中の26の立方体構造崩壊過程を分子動力学計算により追った。その結果、16は立方体構造を保持するが、26の立方体構造は崩壊することが分かった。崩壊過程を詳細に調べると、ナノカプセルはまずメタノール分子がピリジル基のスタッキングをほどき、そこに出来た隙間からメタノール分子が内部に入り込み、一分子解離して崩壊することが確認出来た。これは、26では16に比べてピリジル基の三重スタッキングが外れやすく、また水溶媒とは異なりメタノール溶媒ではナノカプセルに溶媒和するためである。
タンパク質中の低障壁水素結合に関する理論的解析：　 Photoactive Yellow Protein (PYP) は、中性子散乱の実験により、特にGlu46とp-coumaric acidの間では、OH結合距離が通常よりも大幅に伸長した低障壁水素結合を形成している。本研究では上記の水素結合の特性に関する知見を得るために、水素原子核の量子揺らぎを考慮できる手法として近年我々が開発したONIOM (MC_QM:MM)法を用いた量子化学計算を行った。その結果、核の量子揺らぎによって、実験で観測されたのと同様な結合伸長が起きることが実証された。また水素の化学シフトとH/D同位体シフトを計算して実験値と比較したところ、先に述べた大きな結合伸長を伴うモデルではなく、活性サイト周りの静電的環境が先とは異なる条件を仮定した、一般的な水素結合を有するモデルの計算値が実験値と最も良く一致することが分かった。

Current Status of Research Progress

1: Research has progressed more than it was originally planned.

Reason

プログラムの改良により、領域内での多くの共同研究を手掛けることができ、さらに具体的計算結果を得ることができた。またその成果をいくつかの査読付き論文として報告することもできたので、当初の計画以上に進展している。

Strategy for Future Research Activity

今まで以上にプログラムを洗練させるとともに、共同研究を含め、さらなる応用計算を実施していきたい。

Research Products

• [Journal Article] Performance Test of Multicomponent Quantum Mechanical Calculation with Polarizable Continuum Model for Proton Chemical Shift (2015)
  • Author(s): Y. Kanematsu and M. Tachikawa
  • Journal Title: J. Phys. Chem. A Volume: 119 Pages: 4933-4938
  • DOI: 10.1021/jp512877a
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Ferromagnetic spin coupling in the chromium dimer cation: Measurements by photodissociation spectroscopy combined with coupled-cluster calculations (2015)
  • Author(s): K. Egashira, Y. Yamada, Y. Kita, and M. Tachikawa
  • Journal Title: J. Chem. Phys. Volume: 142 Pages: 054309(4pages)
  • DOI: 10.1063/1.4907197
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Why does deuterium substitution lead to the contraction of X...Pi distance? Origin of the reverse Ubbelohde effect in XH...Pi interaction (2015)
  • Author(s): T. Udagawa and M. Tachikawa
  • Journal Title: Theor. Chem. Acc. Volume: なし
  • DOI: 10.1007/s00214-015-1633-7
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Molecular dynamics simulations of self-assembled nanocubes in methanol (2015)
  • Author(s): T. Mashiko, K. Yamada, S. Hiraoka, U. Nagashima, and M. Tachikawa
  • Journal Title: Mol. Sim. Volume: なし
  • DOI: 10.1080/08927022.2014.940523
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Quantum simulation for muoniated and deuterated methyl radicals in implicit water solvent: combined ab initio path integral molecular dynamics and the polarizable continuum model simulation study (2015)
  • Author(s): K. Yamada, Y. Kawashima, and M. Tachikawa
  • Journal Title: Mol. Sim. Volume: なし
  • DOI: 10.1080/08927022.2014.938070
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Theoretical analysis of geometry and NMR isotope shift in hydrogen-bonding center of photoactive yellow protein by combination of multicomponent quantum mechanics and ONIOM scheme (2014)
  • Author(s): Y. Kanematsu and M. Tachikawa
  • Journal Title: J. Chem. Phys Volume: 141 Pages: 185101 (8ps)
  • DOI: 10.1063/1.4900987
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Is the structure of hydroxide dihydrate OH-(H2O)2? : An ab initio path integral molecular dynamics study (2014)
  • Author(s): Y. Ogata, Y. Kawashima, K. Takahashi, and M. Tachikawa
  • Journal Title: Theor. Chem. Acc. Volume: 134 Pages: 1587-1582
  • DOI: 10.1007/s00214-014-1587-1
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Nuclear quantum effect and temperature dependency on the hydrogen-bonded structure of 7-azaindole dimer (2014)
  • Author(s): N. Kungwana, Y. Ogata, S. Hannongbua, and M. Tachikawa
  • Journal Title: Theor. Chem. Acc. Volume: 133 Pages: 1553-1562
  • DOI: 10.1007/s00214-014-1553-y
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] H/D isotope effect on structures, binding energies, and basis set superposition errors in F-(H2O)n (n = 1-3) clusters (2014)
  • Author(s): T. Udagawa, T. Ishimoto, and M. Tachikawa
  • Journal Title: Chem. Phys. Volume: 441 Pages: 101-108
  • DOI: 10.1016/j.chemphys.2014.07.014
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Positron-attachment to acetonitrile, acetaldehyde, and acetone molecules: Vibrational enhancement of positron affinities with configuration interaction level of multi-component molecular orbital approach (2014)
  • Author(s): M. Tachikawa
  • Journal Title: J. Phys.: Conf. Ser. Volume: 488 Pages: 012053 (7ps)
  • DOI: 10.1088/1742-6596/488/1/012053
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Theoretical prediction of the binding of a positron to a formaldehyde molecule using a first-principles calculation (2014)
  • Author(s): Y. Yamada, Y. Kita, and M. Tachikawa
  • Journal Title: Phys. Rev. A Volume: 89 Pages: 062711 (5ps)
  • DOI: 10.1103/PhysRevA.89.062711
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Multi-component molecular orbital study on positron attachment to alkali-metal hydride molecules: nature of chemical bonding and dissociation limits of [LiH; e+] (2014)
  • Author(s): T. Oyamada and M. Tachikawa
  • Journal Title: Eur. Phys. J. D Volume: 68 Pages: 231-239
  • DOI: 10.1140/epjd/e2014-40708-4
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Electron-nucleus correlation functional for multicomponent density-functional theory (2014)
  • Author(s): T. Udagawa, T. Tsuneda, and M. Tachikawa
  • Journal Title: Phys. Rev. A Volume: 89 Pages: 052519 (5ps)
  • DOI: 10.1103/PhysRevA.89.052519
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Development of multicomponent hybrid density functional theory with polarizable continuum model for the analysis of nuclear quantum effect and solvent effect on NMR chemical shift (2014)
  • Author(s): Y. Kanematsu and M. Tachikawa
  • Journal Title: J. Chem. Phys. Volume: 140 Pages: 164111 (7ps)
  • DOI: 10.1063/1.4872006
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Accurate prediction of hyperfine coupling constants in muoniated and hydrogenated ethyl radicals: ab initio path integral simulation study with density functional theory method (2014)
  • Author(s): K. Yamada, Y. Kawashima, and M. Tachikawa
  • Journal Title: J. Chem. Theor. Comput. Volume: 10 Pages: 2005-2015
  • DOI: 10.1021/ct500027z
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Theoretical investigation of the binding of a positron to vibrational excited states of hydrogen cyanide molecule (2014)
  • Author(s): Y. Kita and M. Tachikawa
  • Journal Title: Eur. Phys. J. D Volume: 68 Pages: 116-122
  • DOI: 10.1140/epjd/e2014-40799-9
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Quantum Monte Carlo and high-level ab initio molecular orbital investigation of dissociation channels of the positronic alkali-metal hydrides, [XH;e+] (X = Li, Na, and K) (2014)
  • Author(s): Y. Yamada, Y. Kita, M. Tachikawa, M. Towler, and R. J. Needs
  • Journal Title: Eur. Phys. J. D Volume: 68 Pages: 63-68
  • DOI: 10.1140/epjd/e2014-40734-2
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Theoretical investigation of a positron binding to an aspartame molecule using the ab initio multicomponent molecular orbital approach (2014)
  • Author(s): Y. Oba and M. Tachikawa
  • Journal Title: Int. J. Quant. Chem. Volume: 114 Pages: 1146-1149
  • DOI: 10.1002/qua.24641
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] An Ab Initio Path Integral Molecular Dynamics Study of the Nuclear Quantum Effect on Out-of-plane Ring Deformation of Hydrogen Maleate Anion (2014)
  • Author(s): Y. Kawashima and M. Tachikawa
  • Journal Title: J. Chem. Theor. Comput. Volume: 10 Pages: 153-163
  • DOI: 10.1021/ct4007986
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Why is N...Be distance of NH3H+...DBeH shorter than that of NH3D+...HBeH? Paradoxical geometrical isotope effects for partially isotope-substituted dihydrogen-bonded isotopomers (2014)
  • Author(s): T. Udagawa and M. Tachikawa
  • Journal Title: J. Comput. Chem. (Communication) Volume: 35 Pages: 271-274
  • DOI: 10.1002/jcc.23505
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Muon-Electron Hyperfine Coupling Constants of Muoniated Ethyl Radical: a Path Integral Simulation Study with Semiempirical Molecular Orbital Method (2014)
  • Author(s): K. Yamada, Y. Kawashima, and M. Tachikawa
  • Journal Title: Chin. J. Phys. Volume: 52 Pages: 126-137
  • Peer Reviewed / Acknowledgement Compliant
• [Presentation] Positron-attachment to small molecules : Vibrational enhancement of positron affinities with configuration interaction level of multi-component molecular orbital approach (2015)
  • Author(s): Masanori Tachikawa
  • Organizer: The International Conference of Computational Methods in Sciences and Engineering 2015 (ICCMSE 2015)
  • Place of Presentation: Athens, Greece, Metropolitan
  • Year and Date: 2015-03-20 – 2015-03-23
  • Invited
• [Presentation] First-principles calculation for positron binding to molecules (2014)
  • Author(s): Masanori Tachikawa
  • Organizer: XIXth Quantum Systems in Chemistry, Physics and Biology (QSCP2014)
  • Place of Presentation: Tamsui, Taipei, Taiwan
  • Year and Date: 2014-11-11 – 2014-11-17
  • Invited
• [Presentation] First-principles calculation for positron binding to molecules (2014)
  • Author(s): Masanori Tachikawa
  • Organizer: 10th Congress of the World Association of Theoretical and Computational Chemists (WATOC2014)
  • Place of Presentation: Santiago, Chile
  • Year and Date: 2014-10-07 – 2014-10-11
• [Presentation] First-principles calculation for positron binding to molecules (2014)
  • Author(s): Masanori Tachikawa
  • Organizer: 9th Congress on Electronic Structure: Principles and Applications. ESPA 2014
  • Place of Presentation: Badajoz,Spain
  • Year and Date: 2014-07-02 – 2014-07-04
  • Invited
• [Presentation] Multi-component molecular theory for hydrogen-bonded systems and positronic compounds (2014)
  • Author(s): Masanori Tachikawa
  • Organizer: 5th French-Japanese Workshop on Computational Methods in Chemistry
  • Place of Presentation: Strasbourg, France
  • Year and Date: 2014-06-30 – 2014-07-01
  • Invited
• [Remarks] 横浜市立大学 立川研究室
  • URL: http://www-user.yokohama-cu.ac.jp/~tachi/