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

• Project Area: Dynamical ordering of biomolecular systems for creation of integrated functions
• Project/Area Number: 26102539
• 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, 教授 (00267410)
• Project Period (FY): 2014-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥6,760,000 (Direct Cost: ¥5,200,000、Indirect Cost: ¥1,560,000); Fiscal Year 2015: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000); Fiscal Year 2014: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
• 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 / 光活性黄色タンパク質 / たんぱく質

Outline of Annual Research Achievements

超分子・生体分子の量子化学計算により、領域内共同研究の研究成果を挙げただけでなく、若手の会やサイエンスカフェなどによるアウトリーチ活動も積極的に参画し、本新学術研究領域の推進に貢献してきた。以下、代表的な研究成果として、本領域研究計画班メンバーとの３件の共同研究成果を述べる。
平岡教授との共同研究：　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。一方で純粋なメタノール溶媒中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16の立方体構造崩壊過程を長時間分子動力学計算により追った。その結果、短時間分子動力学計算でみられた水素置換基の立方体構造崩壊と類似した崩壊過程を示すことがわかった。
上久保准教授との共同研究：　上久保らは、Photoactive Yellow Protein (PYP) におけるGlu46とp-coumaric acidの間で、低障壁水素結合を形成していることを見出した。昨年度、ONIOM (MC_QM:MM)法を用いた量子化学計算を行うことで、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を実証した。本年度、大規模な非調和振動計算を実施することにより、構造に関する同位体効果（幾何学的同位体効果）を再現することにも成功した。
加藤教授、神谷講師との共同研究：　加藤、神谷らは、methyl-α-D-glucopyranosideの円偏光二色性(CD)スペクトルのH/D同位体シフトを実験的に見出した。そこで我々は、当初研究計画にはなかったものの、ONIOM (MC_QM:MM)法を用いた量子化学計算を行うことで、その発現機構を解明した。

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

• [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: in press
  • 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
• [Journal Article] Isotope effect on the circular dichroism spectrum of methylα-D-glucopyranoside in aqueous solution (2015)
  • Author(s): Y. Kanematsu, Y. Kamiya, K. Matsuo, K. Gekko, K. Kato, and M. Tachikawa
  • Journal Title: Scientific Report Volume: 5 Issue: 1 Pages: 17900-17900
  • DOI: 10.1038/srep17900
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Theoretical vibrational spectra of OH-(H2O)2: Effect of quantum distribution and vibrational coupling (2015)
  • Author(s): Y. Ogata, Y. Kawashima, K. Takahashi, and M. Tachikawa
  • Journal Title: Phys. Chem. Chem. Phys. Volume: 17 Issue: 38 Pages: 25505-25515
  • DOI: 10.1039/c5cp03632a
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Multicomponent molecular orbital-climbing image-nudged elastic band method to analyze chemical reactions including nuclear quantum effect: Application to hydrogen transfer reaction (2015)
  • Author(s): T. Udagawa, K. Suzuki, and M. Tachikawa
  • Journal Title: Chem Phys Chem Volume: 16 Issue: 15 Pages: 3156-3160
  • DOI: 10.1002/cphc.201500498
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Effects of monohydration on an adenine-thymine base pair (2015)
  • Author(s): S. Watanabe, Y. Ogata, T. Kawatsu, Y. Kawashima, and M. Tachikawa
  • Journal Title: Theor. Chem. Acc. Volume: 134 Issue: 7 Pages: 84-84
  • DOI: 10.1007/s00214-015-1686-7
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] H/D isotope effect on charge-inverted hydrogen-bonded systems: Systematic classification of three different types in H3XH...YH3 (X = C, Si, or Ge, and Y = B, Al, or Ga) with multicomponent calculation (2015)
  • Author(s): T. Udagawa and M. Tachikawa
  • Journal Title: J. Comput. Chem. Volume: 36 Issue: 22 Pages: 1647-1654
  • DOI: 10.1002/jcc.23978
  • Peer Reviewed / Acknowledgement Compliant
• [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: なし Issue: 20 Pages: 4933-4938
  • DOI: 10.1021/jp512877a
  • 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 Issue: 3
  • DOI: 10.1007/s00214-015-1633-7
  • 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 Issue: 5
  • DOI: 10.1063/1.4907197
  • 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 Issue: 10-12 Pages: 832-839
  • 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 Issue: 18
  • 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 Issue: 1 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 Issue: 9 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 Issue: 1 Pages: 012053-012053
  • DOI: 10.1088/1742-6596/488/1/012053
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Molecular Dynamics Simulations of Self-Assembled Nanocubes in Methanol (2014)
  • Author(s): T. Mashiko, K. Yamada, S. Hiraoka, U. Nagashima, and M. Tachikawa
  • Journal Title: Molecular Simulation Volume: - Issue: 10-12 Pages: 845-849
  • DOI: 10.1080/08927022.2014.940523
  • Peer Reviewed / Open Access
• [Journal Article] Theoretical prediction of the binding of a positron to a formaldehyde molecule using a first-principles calculation (2014)
  • Author(s): Yurika Yamada, Yukiumi Kita, and Masanori Tachikawa
  • Journal Title: Phys. Rev. A Volume: 89, 062711 Issue: 6 Pages: 5-5
  • DOI: 10.1103/physreva.89.062711
  • Peer Reviewed
• [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 Issue: 8 Pages: 231-239
  • DOI: 10.1140/epjd/e2014-40708-4
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Electron-nucleus correlation functional for multi-component density functional theory (2014)
  • Author(s): T. Udagawa, T. Tsuneda, and M. Tachikawa
  • Journal Title: Phys. Rev. A Volume: 89 Issue: 5
  • 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 Issue: 16
  • DOI: 10.1063/1.4872006
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Accurate Prediction of Hyperfine Coupling Constant in Muoniated and Hydrogenated Ethyl Radicals: Ab Initio Path Integral Simulation Study with Density Functional Theory Method (2014)
  • Author(s): K. Yamada, Y. Kawashima, M. Tachikawa
  • Journal Title: J. Chem. Theory. Comput. Volume: 10 Issue: 5 Pages: 2005-2015
  • DOI: 10.1021/ct500027z
  • Peer Reviewed
• [Journal Article] Theoretical investigation of the binding of a positron to vibrational excited states of hydrogen cyanide molecule (2014)
  • Author(s): Yukiumi Kita and Masanori Tachikawa
  • Journal Title: Euro. Phys. J. D Volume: 68, 116 Issue: 5 Pages: 7-7
  • DOI: 10.1140/epjd/e2014-40799-9
  • Peer Reviewed
• [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): Yurika Yamada, Yukiumi Kita, Masanori Tachikawa, Mike D. Towler, and Richard J. Needs
  • Journal Title: Euro. Phys. J. D Volume: 68 Issue: 3 Pages: 6-6
  • DOI: 10.1140/epjd/e2014-40734-2
  • Peer Reviewed
• [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 Issue: 17 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 (2014)
  • Author(s): Y. Kawashima, M. Tachikawa
  • Journal Title: J. Chem. Theory Comp. Volume: 10 Issue: 1 Pages: 153-163
  • DOI: 10.1021/ct4007986
  • Peer Reviewed
• [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 Issue: 4 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] Path integral simulation on muoniated radicals (2016)
  • Author(s): Masanori Tachikawa
  • Organizer: The International Conference of Computational Methods in Sciences andEngineering (ICCMSE 2016)
  • Place of Presentation: Athens, Greece
  • Year and Date: 2016-03-17
  • Int'l Joint Research / Invited
• [Presentation] Path integral simulation on muoniated acetone radical (2016)
  • Author(s): Masanori Tachikawa
  • Organizer: Seventh Asia-Pacific Conference of Theoretical and Computational Chemistry (APCTCC7)
  • Place of Presentation: Kaohsiung, Taiwan
  • Year and Date: 2016-01-25
  • Int'l Joint Research / Invited
• [Presentation] Path integral simulation on muoniated acetone radical (2016)
  • Author(s): Masanori Tachikawa
  • Organizer: International USMM &CMSI Workshop
  • Place of Presentation: Hongo, Tokyo
  • Year and Date: 2016-01-05
  • Int'l Joint Research
• [Presentation] Quantum Monte Carlo calculation of Positron-attached Polyatomic Molecules (2015)
  • Author(s): Masanori Tachikawa
  • Organizer: The International Chemical Congress of Pacific Basin Societies 2015 (PACIFICHEM 2015)
  • Place of Presentation: Honolulu, Hawaii, USA
  • Year and Date: 2015-12-15
  • Int'l Joint Research / Invited
• [Presentation] First-principles Calculation for Positron Binding to Molecules (2015)
  • Author(s): Masanori Tachikawa
  • Organizer: 6th JCS, International Symposium on Theoretical Chemistry
  • Place of Presentation: Smolenice Castle, Slovakia
  • Year and Date: 2015-10-11
  • Int'l Joint Research / Invited
• [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] 横浜市立大学量子物理化学研究室（立川研究室）
  • URL: http://www-user.yokohama-cu.ac.jp/~tachi/
• [Remarks] 横浜市立大学 立川研究室
  • URL: http://www-user.yokohama-cu.ac.jp/~tachi/