Details of the Researcher

PHOTO

Hideaki Takahashi
Section
Graduate School of Science
Job title
Associate Professor
Degree

Research Areas 1

  • Natural sciences / Bio-, chemical, and soft-matter physics /

Awards 1

  1. 学術賞

    2007/11　分子シミュレーション学会　「量子化学と統計力学の融合による凝縮系の化学過程の自由エネルギー計算と反応機構の研究」

Papers 78

  1. Kinetic energy density functional based on electron distribution on the energy coordinate to describe covalent bond Invited Peer-reviewed

    Hideaki Takahashi

    Electronic Structure　7　(2)　025003-025003　2025/04/17

    Publisher: IOP Publishing

    DOI： 10.1088/2516-1075/adca7a 　

    eISSN： 2516-1075

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    Abstract The development of kinetic energy functional (KEF) is known as one of the most difficult subjects in the electronic density functional theory (DFT). In particular, the sound description of chemical bonds using a KEF is a matter of great significance in the field of theoretical physics and chemistry. It is well known, however, that the Thomas–Fermi (TF) model or the TF model corrected with a generalized gradient approximation (GGA) cannot realize the bound state of a covalent bond in general. In this work, a new KEF is developed on the basis of the novel DFT (Takahashi 2018 J. Phys. B: At. Mol. Opt. Phys. 51 055102) that utilizes the electron distribution on the energy coordinate as the fundamental variable. It is demonstrated for an H2 molecule that the bound state can be realized by the KEF by virtue of the property of the electron density on the energy coordinate. The mechanism underlying the formation of the bound state is the same as that for the realization of the static correlation in the exchange energy described with the new DFT. We also developed a method termed potential gradient approximation (PGA) to make a correction to the TF model instead of the GGA approach. The functional with the PGA correction is used to describe the dissociation of the double bond in an ethene molecule.

  2. Comparison of optimized effective potential with inverse Kohn–Sham method for Hartree–Fock exchange energy Peer-reviewed

    Hideaki Takahashi

    The Journal of Chemical Physics　161　(10)　2024/09/11

    Publisher: AIP Publishing

    DOI： 10.1063/5.0221906 　

    ISSN： 0021-9606

    eISSN： 1089-7690

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    The inverse Kohn–Sham (inv-KS) density-functional theory for the electron density of the Hartree–Fock (HF) wave function was revisited within the context of the optimized effective potential (HF-OEP). First, we clarify the relationship between the inv-KS and the HF-OEP within the framework of the potential-functional theory. The similarities and the differences of the approaches are then discussed on the basis of their methodological details, which motivates comparisons of the wave function provided by each method. Next, the real-space grid implementations of the inv-KS and the HF-OEP are addressed for the comparisons. The total HF energies EHF[{φiinv-KS}] for the wave functions φiinv-KS on the effective potentials optimized by the inv-KS are computed for a set of small molecules. It is found that the mean absolute deviation (MAD) of EHF[{φiinv-KS}] from the HF energy is clearly smaller than the MAD of EHF[{φiOEP}], demonstrating that the inv-KS is advantageous in constructing the detailed structure of the exchange potential υx as compared with the HF-OEP. The inv-KS method is also applied to an ortho-benzyne radical known as a strongly correlated polyatomic molecule. It is revealed that the spin populations on the atomic sites computed by the UHF calculation can be faithfully reproduced by the wave functions on the inv-KS potential.

  3. Orbital-free QM/MM simulation combined with a theory of solutions Peer-reviewed

    Hideaki Takahashi

    The Journal of Chemical Physics　159　(12)　2023/09/28

    Publisher: AIP Publishing

    DOI： 10.1063/5.0160465 　

    ISSN： 0021-9606

    eISSN： 1089-7690

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    In a recent study, we developed a kinetic-energy density functional that can be utilized in orbital-free quantum mechanical/molecular mechanical (OF-QM/MM) simulations. The functional includes the nonlocal term constructed from the response function of the reference system of the QM solute. The present work provides a method to combine the OF-QM/MM with a theory of solutions based on the energy representation to compute the solvation free energy of the QM solute in solution. The method is applied to the calculation of the solvation free energy Δμ of a QM water solute in an MM water solvent. It is demonstrated that Δμ is computed as −7.7 kcal/mol, in good agreement with an experimental value of −6.3 kcal/mol. We also develop a theory to map the free energy δμ due to electron density polarization onto the coordinate space of electrons. The free energy density obtained by the free-energy mapping for the QM water clarifies that each hydrogen atom makes a positive contribution (+34.7 kcal/mol) to δμ, and the oxygen atom gives the negative free energy (−71.7 kcal/mol). It is shown that the small polarization free energy −2.4 kcal/mol is generated as a result of the cancellation of these counteracting energies. These analyses are made possible by the OF-QM/MM approach combined with a statistical theory of solutions.

  4. Development of nonlocal kinetic-energy density functional for the hybrid QM/MM interaction Peer-reviewed

    Hideaki Takahashi

    The Journal of Chemical Physics　158　(1)　2023/01/03

    Publisher: AIP Publishing

    DOI： 10.1063/5.0128147 　

    ISSN： 0021-9606

    eISSN： 1089-7690

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    Development of the electronic kinetic-energy density functional is a subject of major interest in theoretical physics and chemistry. In this work, the nonlocal kinetic-energy functional is developed in terms of the response function for the molecular system to realize the orbital free density-functional theory (OF-DFT) to be utilized in the hybrid QM/MM (quantum mechanical/molecular mechanical) method. The present approach shows a clear contrast to the previous functionals where the homogeneous electron gas serves as a reference to build the response function. As a benchmark test, we apply the method to a QM water molecule in a dimer system and that embedded in a condensed environment to make comparisons with the results given by the QM/MM calculations employing the Kohn–Sham DFT. It was found that the energetics and the polarization density of the QM solute under the influence of the MM environment can be adequately reproduced with our approach. This work suggests the potential ability of the kinetic-energy functional based on the response functions for the molecular reference systems.

  5. Errata: Development of Kinetic Energy Density Functional Using Response Function Defined on the Energy Coordinate Peer-reviewed

    Hideaki Takahashi

    International Journal of Quantum Chemistry　122　(20)　2022/08/06

    Publisher: Wiley

    DOI： 10.1002/qua.26992 　

    ISSN： 0020-7608

    eISSN： 1097-461X

  6. Development of kinetic energy density functional using response function defined on the energy coordinate Peer-reviewed

    Hideaki Takahashi

    International Journal of Quantum Chemistry　122　(20)　2022/07/07

    Publisher: Wiley

    DOI： 10.1002/qua.26969 　

    ISSN： 0020-7608

    eISSN： 1097-461X

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    Abstract A kinetic energy functional was developed within the framework of the density‐functional theory (DFT) based on the energy electron density for the purpose of realizing the orbital‐free DFT. The functional includes the nonlocal term described with the linear‐response function (LRF) of a reference system. As a notable feature of the present approach, the LRF is represented on the energy coordinate ϵ defined for each system of interest. In addition, an atomic system is taken as a reference system for the construction of the LRF, which shows a clear difference from the conventional approach based on the homogeneous electron gas. The explicit form of the functional was formulated by means of the Taylor series expansion of the kinetic energy. The functional was applied to the calculations of the kinetic energies of the pseudo atoms that mimics H, He, Ne, and Ar. Explicitly, the kinetic energy of each atom was computed using the functional with respect to the variation of the valence charge Zv of each atom. In these calculations, the electron density n optimized by the Kohn‐Sham DFT was adopted as an argument of the functional. It was found that the results are in excellent agreements with those given by the Kohn‐Sham DFT. We also devised a method to perform the self‐consistent field calculation utilizing the functional . The method was applied to the computation of the radial distribution functions of the electrons in the pseudo Ne and Ar atoms. It was demonstrated that the results reasonably agree with those yielded by the Kohn‐Sham DFT.

  7. Development of static correlation functional using electron distribution on the energy coordinate Peer-reviewed

    Hideaki Takahashi

    Journal of Physics B: Atomic, Molecular and Optical Physics　53　(24)　245101-245101　2020/12/28

    Publisher: IOP Publishing

    DOI： 10.1088/1361-6455/abc45e 　

    ISSN： 0953-4075

    eISSN： 1361-6455

  8. Large-Scale Parallel Implementation of Hartree-Fock Exchange Energy on Real-Space Grids Using 3D-Parallel Fast Fourier Transform Peer-reviewed

    Hideaki Takahashi, Shun Sakuraba, Akihiro Morita

    JOURNAL OF CHEMICAL INFORMATION AND MODELING　60　(3)　1376-1389　2020/03

    DOI： 10.1021/acs.jcim.9b01063 　

    ISSN： 1549-9596

    eISSN： 1549-960X

  9. Role of the Photosystem II as an Environment in the Oxidation Free Energy of the Mn Cluster from S<inf>1</inf> to S<inf>2</inf> Peer-reviewed

    Hideaki Takahashi, Daiki Suzuoka, Shun Sakuraba, Akihiro Morita

    Journal of Physical Chemistry B　123　7081-7091　2019/08/22

    DOI： 10.1021/acs.jpcb.9b03831 　

    ISSN： 1520-6106

  10. Calculation of solvation free energy utilizing a constrained QM/MM approach combined with a theory of solutions Peer-reviewed

    Hideaki Takahashi, Hiroyuki Kambe, Akihiro Morita

    Journal of Chemical Physics　150　2019/03/21

    DOI： 10.1063/1.5089199 　

    ISSN： 0021-9606

  11. Free energy analyses for the ATP hydrolysis in aqueous solution by large-scale QM/MM simulations combined with a theory of solutions Peer-reviewed

    Hideaki Takahashi

    The Role of Water in ATP Hydrolysis Energy Transduction by Protein Machinery　3-23　2018/05/07

    DOI： 10.1007/978-981-10-8459-1_1 　

  12. A simple and effective solution to the constrained QM/MM simulations Peer-reviewed

    Hideaki Takahashi, Hiroyuki Kambe, Akihiro Morita

    Journal of Chemical Physics　148　(13)　2018/04/07

    Publisher: American Institute of Physics Inc.

    DOI： 10.1063/1.5019874 　

    ISSN： 0021-9606

  13. Density-functional theory based on the electron distribution on the energy coordinate Peer-reviewed

    Hideaki Takahashi

    Journal of Physics B: Atomic, Molecular and Optical Physics　51　(5)　055102-055102　2018/02/12

    Publisher: Institute of Physics Publishing

    DOI： 10.1088/1361-6455/aaaa0d 　

    ISSN： 1361-6455 0953-4075

    eISSN： 1361-6455

  14. Drastic Compensation of Electronic and Solvation Effects on ATP Hydrolysis Revealed through Large-Scale QM/MM Simulations Combined with a Theory of Solutions Peer-reviewed

    Hideaki Takahashi, Satoru Umino, Yuji Miki, Ryosuke Ishizuka, Shu Maeda, Akihiro Morita, Makoto Suzuki, Nobuyuki Matubayasi

    JOURNAL OF PHYSICAL CHEMISTRY B　121　(10)　2279-2287　2017/03

    DOI： 10.1021/acs.jpcb.7b00637 　

    ISSN： 1520-6106

  15. A QM/MM study on the correlation between the polarisations of pi and sigma electrons in a hydrated benzene Peer-reviewed

    Daiki Suzuoka, Hideaki Takahashi, Akihiro Morita

    MOLECULAR SIMULATION　43　(13-16)　1209-1217　2017

    DOI： 10.1080/08927022.2017.1350661 　

    ISSN： 0892-7022

    eISSN： 1029-0435

  16. Condensed phase QM/MM simulations utilizing the exchange core functions to describe exchange repulsions at the QM boundary region Peer-reviewed

    Satoru Umino, Hideaki Takahashi, Akihiro Morita

    JOURNAL OF CHEMICAL PHYSICS　145　(8)　084107　2016/08

    DOI： 10.1063/1.4961373 　

    ISSN： 0021-9606

    eISSN： 1089-7690

  17. Construction of exchange repulsion in terms of the wave functions at QM/MM boundary region Peer-reviewed

    Hideaki Takahashi, Satoru Umino, Akihiro Morita

    JOURNAL OF CHEMICAL PHYSICS　143　(8)　084104　2015/08

    DOI： 10.1063/1.4928762 　

    ISSN： 0021-9606

    eISSN： 1089-7690

  18. Why is Benzene Soluble in Water? Role of OH/pi Interaction in Solvation Peer-reviewed

    Hideaki Takahashi, Daiki Suzuoka, Akihiro Morita

    JOURNAL OF CHEMICAL THEORY AND COMPUTATION　11　(3)　1181-1194　2015/03

    DOI： 10.1021/ct501133u 　

    ISSN： 1549-9618

    eISSN： 1549-9626

  19. Development of a Massively Parallel QM/MM Approach Combined with a Theory of Solutions

    Takahashi, Hideaki Matubayasi, Nobuyuki

    Challenges and Advances in Computational Chemistry and Physics　21　153-196　2015/01/01

    Publisher: Springer

    DOI： 10.1007/978-3-319-21626-3_6 　

    ISSN： 2542-4491

  20. Computation of the free energy due to electron density fluctuation of a solute in solution: A QM/MM method with perturbation approach combined with a theory of solutions Peer-reviewed

    Daiki Suzuoka, Hideaki Takahashi, Akihiro Morita

    JOURNAL OF CHEMICAL PHYSICS　140　(13)　134111　2014/04

    DOI： 10.1063/1.4870037 　

    ISSN： 0021-9606

    eISSN： 1089-7690

  21. Reply to "Comment on 'Surface Acidity of Water Probed by Free Energy Calculation for Trimethylamine Protonation'"

    Yusuke Tabe, Nobuaki Kikkawa, Hideaki Takahashi, Akihiro Morita

    JOURNAL OF PHYSICAL CHEMISTRY C　118　(5)　2895-2895　2014/02

    DOI： 10.1021/jp5005083 　

    ISSN： 1932-7447

  22. 3P132 On the Hydration Dynamics and Energetics of Alkali halide and Phosphate Ions by Dielectric Relaxation Spectroscopy and Molecular Dynamics(07. Water & Hydration & Electrolyte,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

    Mogami George, Ishimori Kazuki, Matubayasi Nobuyuki, Takahashi Hideaki, Suzuki Makoto

    Seibutsu Butsuri　54　(1)　S270　2014

    Publisher: The Biophysical Society of Japan General Incorporated Association

    DOI： 10.2142/biophys.54.S270_6 　

  23. Surface Acidity of Water Probed by Free Energy Calculation for Trimethylamine Protonation Peer-reviewed

    Yusuke Tabe, Nobuaki Kikkawa, Hideaki Takahashi, Akihiro Morita

    JOURNAL OF PHYSICAL CHEMISTRY C　118　(2)　977-988　2014/01

    DOI： 10.1021/jp4078882 　

    ISSN： 1932-7447

  24. QM/MM法と溶液の理論の融合による凝縮系の化学過程の自由エネルギー計算(17)-凝縮系の第一原理計算の方法論について- Invited

    高橋英明

    分子シミュレーション研究会会誌「アンサンブル」　16　(1)　51-54　2014/01

    Publisher:

    DOI： 10.11436/mssj.16.51 　

    ISSN： 1884-6750

  25. QM/MM法と溶液の理論の融合による凝縮系の化学過程の自由エネルギー計算(18)-凝縮系の第一原理計算の方法論について- Invited

    高橋英明

    分子シミュレーション研究会会誌「アンサンブル」　61　49-48　2013/01

  26. Development of a methodology to compute solvation free energies on the basis of the theory of energy representation for solutions represented with a polarizable force field Peer-reviewed

    Daiki Suzuoka, Hideaki Takahashi, Tatsuya Ishiyama, Akihiro Morita

    JOURNAL OF CHEMICAL PHYSICS　137　(21)　214503　2012/12

    DOI： 10.1063/1.4769075 　

    ISSN： 0021-9606

    eISSN： 1089-7690

  27. Origin of Vibrational Spectroscopic Response at Ice Surface Peer-reviewed

    Tatsuya Ishiyama, Hideaki Takahashi, Akihiro Morita

    JOURNAL OF PHYSICAL CHEMISTRY LETTERS　3　(20)　3001-3006　2012/10

    DOI： 10.1021/jz3012723 　

    ISSN： 1948-7185

  28. Molecular dynamics simulations of surface-specific bonding of the hydrogen network of water: A solution to the low sum-frequency spectra Peer-reviewed

    Tatsuya Ishiyama, Hideaki Takahashi, Akihiro Morita

    PHYSICAL REVIEW B　86　(3)　035408　2012/07

    DOI： 10.1103/PhysRevB.86.035408 　

    ISSN： 1098-0121

  29. Simple and exact approach to the electronic polarization effect on the solvation free energy: Formulation for quantum-mechanical/molecular-mechanical system and its applications to aqueous solutions Peer-reviewed

    Hideaki Takahashi, Atsushi Omi, Akihiro Morita, Nobuyuki Matubayasi

    JOURNAL OF CHEMICAL PHYSICS　136　(21)　214503　2012/06

    DOI： 10.1063/1.4722347 　

    ISSN： 0021-9606

    eISSN： 1089-7690

  30. Vibrational spectrum at a water surface: a hybrid quantum mechanics/molecular mechanics molecular dynamics approach Peer-reviewed

    Tatsuya Ishiyama, Hideaki Takahashi, Akihiro Morita

    JOURNAL OF PHYSICS-CONDENSED MATTER　24　(12)　124107　2012/03

    DOI： 10.1088/0953-8984/24/12/124107 　

    ISSN： 0953-8984

  31. Free-energy analysis of the electron-density fluctuation in the quantum-mechanical/molecular-mechanical simulation combined with the theory of energy representation Peer-reviewed

    Nobuyuki Matubayasi, Hideaki Takahashi

    JOURNAL OF CHEMICAL PHYSICS　136　(4)　044505　2012/01

    DOI： 10.1063/1.3677184 　

    ISSN： 0021-9606

    eISSN： 1089-7690

  32. Electron Donor Solvent Effects on the (Hyper) Polarizabilities of a Solute Presenting Singlet Diradical Character

    Hideaki Takahashi, Kazuki Kubota, Hitoshi Fukui, Sean Bonness, Kyohei Yoneda, Ryohei Kishi, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek, Masayoshi Nakano

    INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2009 (ICCMSE 2009)　1504　899-902　2012

    DOI： 10.1063/1.4771840 　

    ISSN： 0094-243X

  33. The QM/MM-ER Studies for the Origin of the Antioxidative Properties of MCI-186 in Aqueous Solutions Peer-reviewed

    Hideaki Takahashi, Yuichi Iwata, Ryohei Kishi, Masayoshi Nakano

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY　111　(7-8)　1748-1762　2011/06

    DOI： 10.1002/qua.22814 　

    ISSN： 0020-7608

  34. Energetic Origin of Proton Affinity to the Air/Water Interface Peer-reviewed

    Hideaki Takahashi, Kunihiro Maruyama, Yasuhito Karino, Akihiro Morita, Masayoshi Nakano, Pavel Jungwirth, Nobuyuki Matubayasi

    JOURNAL OF PHYSICAL CHEMISTRY B　115　(16)　4745-4751　2011/04

    DOI： 10.1021/jp2015676 　

    ISSN： 1520-6106

  35. The Exchange-Energy Density Functional Based on the Modified Becke-Roussel Model Peer-reviewed

    Hideaki Takahashi, Ryohei Kishi, Masayoshi Nakano

    JOURNAL OF CHEMICAL THEORY AND COMPUTATION　6　(3)　647-661　2010/03

    DOI： 10.1021/ct900416x 　

    ISSN： 1549-9618

    eISSN： 1549-9626

  36. Development of a Quantum Chemical Method Combined with a Theory of Solutions-Free-Energy Calculation for Chemical Reactions by Condensed Phase Simulations

    Hideaki Takahashi, Nobuyuki Matubayasi, Masayoshi Nakano

    ADVANCES IN QUANTUM CHEMISTRY, VOL 59　59　283-351　2010

    DOI： 10.1016/S0065-3276(10)59009-9 　

    ISSN： 0065-3276

  37. Hydration effects on the reaction with an open-shell transition state: QM/MM-ER study for the dehydration reaction of alcohol in hot water Peer-reviewed

    Hideaki Takahashi, Fumihiro Miki, Hajime Ohno, Ryohei Kishi, Suguru Ohta, Shin-ichi Furukawa, Masayoshi Nakano

    JOURNAL OF MATHEMATICAL CHEMISTRY　46　(3)　781-794　2009/10

    DOI： 10.1007/s10910-009-9544-2 　

    ISSN： 0259-9791

    eISSN： 1572-8897

  38. Electron donor solvent effects on the (hyepr)polarizabilities of a singlet diradical molecule involving a boron atom (vol 477, pg 309, 2009)

    Kazuki Kubota, Hideaki Takahashi, Hitoshi Fukui, Sean Bonness, Kyohei Yoneda, Ryohei Kishi, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek, Masayoshi Nakano

    CHEMICAL PHYSICS LETTERS　479　(1-3)　171-171　2009/09

    DOI： 10.1016/j.cplett.2009.08.003 　

    ISSN： 0009-2614

  39. A quantum chemical approach to biological reaction with a theory of solutions

    Hideaki Takahashi

    FRONTIERS IN BIOSCIENCE-LANDMARK　14　1745-1760　2009/01

    DOI： 10.2741/3337 　

    ISSN： 1093-9946

    eISSN： 1093-4715

  40. A Novel Quantum Chemical Approach to the Computation of the Solvation Free Energy of a Biological Molecule with Structural Flexibility

    Hideaki Takahashi, Yuichi Iwata, Ryohei Kishi, Masayoshi Nakano

    COMPUTATIONAL METHODS IN SCIENCE AND ENGINEERING, VOL 2　1148　338-341　2009

    DOI： 10.1063/1.3225309 　

    ISSN： 0094-243X

  41. Computation of the free energy change associated with one-electron reduction of coenzyme immersed in water: A novel approach within the framework of the quantum mechanical/molecular mechanical method combined with the theory of energy representation Peer-reviewed

    Hideaki Takahashi, Hajime Ohno, Ryohei Kishi, Masayoshi Nakano, Nobuyuki Matubayasi

    JOURNAL OF CHEMICAL PHYSICS　129　(20)　2008/11

    DOI： 10.1063/1.3026506 　

    ISSN： 0021-9606

    eISSN： 1089-7690

  42. Computation of the reduction free energy of coenzyme in aqueous solution by the QM/MM-ER method Peer-reviewed

    Hideaki Takahashi, Hajime Ohno, Ryohei Kishi, Masayoshi Nakano, Nobuyuki Matubayasi

    CHEMICAL PHYSICS LETTERS　456　(4-6)　176-180　2008/05

    DOI： 10.1016/j.cplett.2008.03.038 　

    ISSN： 0009-2614

  43. Investigation of the dominant hydration structures among the ionic species in aqueous solution: Novel quantum mechanics/molecular mechanics simulations combined with the theory of energy representation Peer-reviewed

    Hideaki Takahashi, Hajime Ohno, Toshihiko Yamauchi, Ryohei Kishi, Shin-ichi Furukawa, Masayoshi Nakano, Nobuyuki Matubayasi

    JOURNAL OF CHEMICAL PHYSICS　128　(6)　2008/02

    DOI： 10.1063/1.2825600 　

    ISSN： 0021-9606

    eISSN： 1089-7690

  44. A Quantum Chemical Approach to Free Energy Calculation for Chemical Reactions in Condensed System: Combination of a Quantum Chemical Method with a Theory of Statistical Mechanics

    Hideaki Takahashi, Nobuyuki Matubayasi, Masayoshi Nakano

    Challenges and Advances in Computational Chemistry and Physics　6　455-505　2008/01/01

    DOI： 10.1007/978-1-4020-8270-2_17 　

    ISSN： 2542-4491

  45. Computation of the Reduction Free Energy of Coenzyme in Water: A Novel Approach within the Framework of the QM/MM-ER Method

    Hideaki Takahashi, Hajime Ohno, Ryohei Kishi, Shin-ichi Furukawa, Masayoshi Nakano

    SELECTED PAPERS FROM ICNAAM 2007 AND ICCMSE 2007　1046　56-59　2008

    DOI： 10.1063/1.2997315 　

    ISSN： 0094-243X

  46. Molecular orientation effects on two-photon absorption spectra of dimer systems

    Suguru Ohta, Masayoshi Nakano, Masahito Nate, Ryohei Kishi, Hideaki Takahashi

    CHEMICAL PHYSICS LETTERS　448　(1-3)　99-105　2007/11

    DOI： 10.1016/j.cplett.2007.09.057 　

    ISSN： 0009-2614

  47. Chemical equilibrium of formaldehyde and methanediol in hot water: Free-energy analysis of the solvent effect

    Nobuyuki Matubayasi, Saiko Morooka, Masaru Nakahara, Hideaki Takahashi

    JOURNAL OF MOLECULAR LIQUIDS　134　(1-3)　58-63　2007/05

    DOI： 10.1016/j.molliq.2006.12.002 　

    ISSN： 0167-7322

  48. Novel quantum mechanical/molecular mechanical method combined with the theory of energy representation: Free energy calculation for the Beckmann rearrangement promoted by proton transfers in the supercritical water

    Hideaki Takahashi, Kohsuke Tanabe, Masataka Aketa, Ryohei Kishi, Shin-ichi Furukawa, Masayoshi Nakano

    JOURNAL OF CHEMICAL PHYSICS　126　(8)　2007/02

    DOI： 10.1063/1.2566834 　

    ISSN： 0021-9606

    eISSN： 1089-7690

  49. Multi-scale simulations for materials and life sciences Peer-reviewed

    Frederic Castet, Benoit Champagne, Masayoshi Nakano, Hideaki Takahashi

    COMPUTATION IN MODERN SCIENCE AND ENGINEERING VOL 2, PTS A AND B　2　285-+　2007

    ISSN： 0094-243X

  50. Computational study on the relative acidity of acetic acid by the QM/MM method combined with the theory of energy representation

    Takumi Hori, Hideaki Takahashi, Shin-ichi Furukawa, Masayoshi Nakano, Weitao Yang

    JOURNAL OF PHYSICAL CHEMISTRY B　111　(3)　581-588　2007/01

    DOI： 10.1021/jp066334d 　

    ISSN： 1520-6106

  51. A QM/MM study combined with the theory of energy representation: Solvation free energies for anti/syn acetic acids in aqueous solution

    T Hori, H Takahashi, M Nakano, T Nitta, WT Yang

    CHEMICAL PHYSICS LETTERS　419　(1-3)　240-244　2006/02

    DOI： 10.1016/j.cplett.2005.11.096 　

    ISSN： 0009-2614

  52. A novel quantum chemical approach to the free energy calculation for the one-electron reduction of coenzyme in solution and biological system Peer-reviewed

    Hideaki Takahashi, Hajime Ohno, Ryohei Kishi, Suguru Ohta, Shin-ichi Furukawa, Masayoshi Nakano

    RECENT PROGRESS IN COMPUTATIONAL SCIENCES AND ENGINEERING, VOLS 7A AND 7B　7A-B　1533-1535　2006

    ISSN： 1573-4196

  53. Hybrid quantum mechanical/molecular mechanical approach to enzymatic reactions by utilizing the real-space grid technique

    T Hori, H Takahashi, T Nitta

    JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY　4　(3)　867-882　2005/09

    DOI： 10.1142/S0219633605001799 　

    ISSN： 0219-6336

    eISSN： 1793-6888

  54. A novel quantum mechanical/molecular mechanical approach to the free energy calculation for isomerization of glycine in aqueous solution

    H Takahashi, Y Kawashima, T Nitta, N Matubayasi

    JOURNAL OF CHEMICAL PHYSICS　123　(12)　2005/09

    DOI： 10.1063/1.2008234 　

    ISSN： 0021-9606

    eISSN： 1089-7690

  55. Quantum chemical calculations of third-order nonlinear optical properties for organic open-shell systems: Nitronyl nitroxide radicals and several pi-conjugated systems having unique structures. Peer-reviewed

    S. Yamada, M. Nakano, R. Kishi, S. Ohta, S. Furukawa, H. Takahashi, K. Yamaguchi

    Advances in Computational Methods in Sciences and Engineering 2005, Vols 4 A & 4 B　4A-4B　1158-1161　2005

    ISSN： 1573-4196

  56. Free energy calculation for the reaction that proceeds via singlet biradical transition state: Dehydration reaction of alcohol in hot water Peer-reviewed

    Hideaki Takahashi, Hajime Ohno, Ryohei Kishi, Suguru Ohta, Shin-Ichi Furukawa, Masayoshi Nakano

    Advances in Computational Methods in Sciences and Engineering 2005, Vols 4 A & 4 B　4A-4B　1167-1171　2005

    ISSN： 1573-4196

  57. An application of the novel quantum mechanical/molecular mechanical method combined with the theory of energy representation: An ionic dissociation of a water molecule in the supercritical water

    H Takahashi, W Satou, T Hori, T Nitta

    JOURNAL OF CHEMICAL PHYSICS　122　(4)　2005/01

    DOI： 10.1063/1.1839858 　

    ISSN： 0021-9606

    eISSN： 1089-7690

  58. A quantum chemical approach to the free energy calculations in condensed systems: The QM/MM method combined with the theory of energy representation

    H Takahashi, N Matubayasi, M Nakahara, T Nitta

    JOURNAL OF CHEMICAL PHYSICS　121　(9)　3989-3999　2004/09

    DOI： 10.1063/1.1774981 　

    ISSN： 0021-9606

    eISSN： 1089-7690

  59. Quantum mechanical/molecular mechanical studies of a novel reaction catalyzed by proton transfers in ambient and supercritical states of water

    H Takahashi, H Hashimoto, T Nitta

    JOURNAL OF CHEMICAL PHYSICS　119　(15)　7964-7971　2003/10

    DOI： 10.1063/1.1610440 　

    ISSN： 0021-9606

  60. Hybrid quantum chemical studies for the methanol formation reaction assisted by the proton transfer mechanism in supercritical water: CH3Cl+nH(2)O -&gt; CH3OH+HCl+(n-1)H2O

    T Hori, H Takahashi, T Nitta

    JOURNAL OF CHEMICAL PHYSICS　119　(16)　8492-8499　2003/10

    DOI： 10.1063/1.1611175 　

    ISSN： 0021-9606

    eISSN： 1089-7690

  61. A real-space-grid QM/MM study on the ionic/radical association reaction in aqueous phase: HCHO+OH -&gt; HCHO-OH

    H Takahashi, S Takei, T Hori, T Nitta

    JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM　632　185-195　2003/08

    DOI： 10.1016/S0166-1280(03)00298-7 　

    ISSN： 0166-1280

  62. Hybrid QM/MM molecular dynamics simulations for an ionic S(N)2 reaction in the supercritical water: OH-+CH3Cl -&gt; CH3OH+Cl-

    T Hori, H Takahashi, T Nitta

    JOURNAL OF COMPUTATIONAL CHEMISTRY　24　(2)　209-221　2003/01

    DOI： 10.1002/jcc.10134 　

    ISSN： 0192-8651

    eISSN： 1096-987X

  63. Ethanol oxidation reactions catalyzed by water molecules: CH3CH2OH+nH(2)O -&gt; CH3CHO+H-2+nH(2)O (n = 0, 1, 2)

    H Takahashi, S Hisaoka, T Nitta

    CHEMICAL PHYSICS LETTERS　363　(1-2)　80-86　2002/09

    DOI： 10.1016/S0009-2614(02)01142-9 　

    ISSN： 0009-2614

  64. Chemical modification of rutile TiO2(110) surface by ab initio calculations for the purpose of CO2 adsorption

    H Takahashi, K Yuki, T Nitta

    FLUID PHASE EQUILIBRIA　194　153-160　2002/03

    DOI： 10.1016/S0378-3812(01)00775-0 　

    ISSN： 0378-3812

  65. A hybrid QM/MM method employing real space grids for QM water in the TIP4P water solvents

    H Takahashi, T Hori, H Hashimoto, T Nitta

    JOURNAL OF COMPUTATIONAL CHEMISTRY　22　(12)　1252-1261　2001/09

    DOI： 10.1002/jcc.1082 　

    ISSN： 0192-8651

    eISSN： 1096-987X

  66. Real space ab initio molecular dynamics simulations for the reactions of OH radical/OH anion with formaldehyde

    H Takahashi, T Hori, T Wakabayashi, T Nitta

    JOURNAL OF PHYSICAL CHEMISTRY A　105　(17)　4351-4358　2001/05

    DOI： 10.1021/jp004348s 　

    ISSN： 1089-5639

  67. Ab initio molecular dynamics simulations of an OH radical /OH anion with a solvated formaldehyde molecule Peer-reviewed

    H Takahashi, T Hori, T Wakabayashi, T Nitta

    FOUNDATIONS OF MOLECULAR MODELING AND SIMULATION　97　(325)　280-282　2001

    ISSN： 0065-8812

  68. Chemical modification of MgO(001) surface by utilizing energy decomposition analyses for the purpose of CO2 adsorption

    H Takahashi, K Okuda, T Nitta

    BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN　73　(2)　315-319　2000/02

    DOI： 10.1246/bcsj.73.315 　

    ISSN： 0009-2673

    eISSN： 1348-0634

  69. A density functional study for hydrogen bond energy by employing real space grids Peer-reviewed

    Hideaki Takahashi, Takumi Hori, Tadafumi Wakabayashi, Tomoshige Nitta

    Chemistry Letters　(3)　222-223　2000

    Publisher: Chemical Society of Japan

    DOI： 10.1246/cl.2000.222 　

    ISSN： 0366-7022

  70. Density functional theory without the Born-Oppenheimer approximation and its application

    Y. Shigeta, H. Takahashi, S. Yamanaka, M. Mitani, H. Nagao, K. Yamaguchi

    International Journal of Quantum Chemistry　70　(4-5)　659-669　1998/12/01

    DOI： 10.1002/(sici)1097-461x(1998)70:4/5<659::aid-qua12>3.0.co;2-y 　

    ISSN： 0020-7608

  71. A wavepacket analysis of the statistical behaviour of molecules that penetrate a slit-shaped micropore

    H Takahashi, T Wakabayashi, T Nitta

    CHEMICAL PHYSICS LETTERS　294　(1-3)　95-102　1998/09

    DOI： 10.1016/S0009-2614(98)00840-9 　

    ISSN： 0009-2614

  72. Effect of the shape of simulation box on the Van der Waals loop of a Lennard-Jones fluid

    H Takahashi, A Nakamura, T Nitta

    CHEMICAL PHYSICS LETTERS　282　(2)　128-132　1998/01

    DOI： 10.1016/S0009-2614(97)01251-7 　

    ISSN： 0009-2614

  73. Three dimensional wavepacket simulation on the H atom scattering for the full reaction CF3H+Ar(P-3)-&gt; CF3*+H+Ar

    H Takahashi, T Kasai, K Yamaguchi, HH Loesch

    ISRAEL JOURNAL OF CHEMISTRY　37　(4)　359-365　1997

    DOI： 10.1002/ijch.199700041 　

    ISSN： 0021-2148

  74. Wavepacket dynamics in the full reaction of CF3H+Ar(P-3)-&gt;CF3*+H+Ar: Quantum interference for the H-end orientation

    H Takahashi, T Kasai, K Yamaguchi

    CHEMICAL PHYSICS LETTERS　264　(1-2)　44-50　1997/01

    DOI： 10.1016/S0009-2614(96)01297-3 　

    ISSN： 0009-2614

  75. Wave packet simulation on the cage effect in the full scattering: CF3H+Ar(P-3)-&gt;CF3*+H+Ar

    H Takahashi, T Kasai, K Yamaguchi

    CHEMISTRY LETTERS　(9)　793-794　1996

    DOI： 10.1246/cl.1996.793 　

    ISSN： 0366-7022

    eISSN： 1348-0715

  76. Orientation dependence of the electronic coupling in the energy transfer reaction CF<inf>3</inf>H + Ar(3P) → CF<inf>3</inf>* + Ar + H

    Hideaki Takahashi, Hiroshi Ohoyama, Toshio Kasai, Masayoshi Nakano, Kizashi Yamaguchi

    Journal of Physical Chemistry　99　(37)　13600-13605　1995/12/01

    DOI： 10.1021/j100037a005 　

    ISSN： 0022-3654

  77. ORIENTATION DEPENDENCE OF TRANSITION MATRIX-ELEMENTS FOR ENERGY-TRANSFER REACTION CF3H+AR(P-3)-]CF3-ASTERISK+AR+H Peer-reviewed

    H TAKAHASHI, H OHOYAMA, T KASAI, K KUWATA, M NAKANO, K YAMAGUCHI

    CHEMISTRY LETTERS　(11)　1985-1988　1994/11

    ISSN： 0366-7022

    eISSN： 1348-0715

  78. A THEORETICAL-STUDY ON THE ELECTRON-EXCHANGE MECHANISM IN THE CF3H+AR(P-3)-]CF3-ASTERISK+H+AR REACTION

    H TAKAHASHI, H OHOYAMA, T KASAI, K KUWATA, M NAKANO, K YAMAGUCHI

    CHEMICAL PHYSICS LETTERS　224　(5-6)　445-450　1994/07

    DOI： 10.1016/0009-2614(94)00576-1 　

    ISSN： 0009-2614

Show all ︎Show first 5

Misc. 68

  1. Generation of Aromatic (Dehydro) benzoannulene Dications Stabilized by Platinum Catecholate Complexes

    Kazukuni Tahara, Hiroyoshi Kozuma, Varadhachari Venkatesh, Eri Ryomura, Hirokazu Miyoshi, Keigo Nakamachi, Ryohei Kishi, Hideaki Takahashi, Masayoshi Nakano, Yoshito Tobe

    CHEMPLUSCHEM　82　(7)　1052-1056　2017/07

    DOI： 10.1002/cplu.201700018 　

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  2. QM/MM法と溶液の理論の融合による凝縮系の化学過程の自由エネルギー計算 (17) Peer-reviewed

    高橋 英明

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    13　(1)　33-36　2012/04/01

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    高橋 英明

    13　(1)　33-36　2012/01/01

  6. One- and Two-Photon Absorptions in Open-Shell Singlet Systems

    Masayoshi Nakano, Kyohei Yoneda, Ryohei Kishi, Hideaki Takahashi, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek

    INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2009 (ICCMSE 2009)　1504　136-142　2012

    DOI： 10.1063/1.4771708 　

    ISSN： 0094-243X

  7. Theoretical Aspects on the Evaluation and Interpretation of the Third-Order Nonlinear Optical Properties of Diradical Compounds

    Benoit Champagne, Edith Botek, Akihiro Shimizu, Takashi Kubo, Kenji Kamada, Koji Ohta, Ryohei Kishi, Hitoshi Fukui, Hideaki Takahashi, Masayoshi Nakano

    INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2009 (ICCMSE 2009)　1504　844-847　2012

    DOI： 10.1063/1.4771826 　

    ISSN： 0094-243X

  8. QM/MM法と溶液の理論の融合による凝縮系の化学過程の自由エネルギー計算 (13)

    高橋 英明

    13　(1)　33-36　2011/10/01

  9. QM/MM法と溶液の理論の融合による凝縮系の化学過程の自由エネルギー計算 (12)

    高橋 英明

    13　(1)　33-36　2011/01/01

    Publisher: 分子シミュレーション研究会

    DOI： 10.11436/mssj.13.33 　

    ISSN： 1884-6750

  10. QM/MM法と溶液の理論の融合による凝縮系の化学過程の自由エネルギー計算 (11)

    高橋 英明

    12　(4)　8-11　2010/10/01

    Publisher: 分子シミュレーション研究会

    DOI： 10.11436/mssj.12.4_8 　

    ISSN： 1884-6750

  11. QM/MM法と溶液の理論の融合による凝縮系の化学過程の自由エネルギー計算 (10)

    高橋 英明

    12　(3)　22-25　2010/07/01

    Publisher: 分子シミュレーション研究会

    DOI： 10.11436/mssj.12.3_22 　

    ISSN： 1884-6750

  12. QM/MM法と溶液の理論の融合による凝縮系の化学過程の自由エネルギー計算 (9)

    高橋 英明

    12　(2)　36-39　2010/04/01

    Publisher: 分子シミュレーション研究会

    DOI： 10.11436/mssj.12.2_36 　

    ISSN： 1884-6750

  13. Exciton Recurrence Motion in Double-Ring Molecular Aggregates Induced by Two-Mode Circular-Polarized Laser Field

    Takuya Minami, Kyohei Yoneda, Ryohei Kishi, Hideaki Takahashi, Masayoshi Nakano

    JOURNAL OF PHYSICAL CHEMISTRY C　114　(13)　6067-6076　2010/04

    DOI： 10.1021/jp908373k 　

    ISSN： 1932-7447

  14. Signature of multiradical character in second hyperpolarizabilities of rectangular graphene nanoflakes

    Hiroshi Nagai, Masayoshi Nakano, Kyohei Yoneda, Ryohei Kishi, Hideaki Takahashi, Akihiro Shimizu, Takashi Kubo, Kenji Kamada, Koji Ohta, Edith Botek, Benoit Champagne

    CHEMICAL PHYSICS LETTERS　489　(4-6)　212-218　2010/04

    DOI： 10.1016/j.cplett.2010.03.013 　

    ISSN： 0009-2614

  15. Singlet Diradical Character from Experiment

    Kenji Kamada, Koji Ohta, Akihiro Shimizu, Takashi Kubo, Ryohei Kishi, Hideaki Takahashi, Edith Botek, Benoit Champagne, Masayoshi Nakano

    JOURNAL OF PHYSICAL CHEMISTRY LETTERS　1　(6)　937-940　2010/03

    DOI： 10.1021/jz100155s 　

    ISSN： 1948-7185

  16. Long-range corrected density functional theory study on static second hyperpolarizabilities of singlet diradical systems

    Ryohei Kishi, Sean Bonness, Kyohei Yoneda, Hideaki Takahashi, Masayoshi Nakano, Edith Botek, Benoit Champagne, Takashi Kubo, Kenji Kamada, Koji Ohta, Takao Tsuneda

    JOURNAL OF CHEMICAL PHYSICS　132　(9)　2010/03

    DOI： 10.1063/1.3332707 　

    ISSN： 0021-9606

    eISSN： 1089-7690

  17. Ab initio MO-CI based quantum master equation approach: Exciton dynamics of weakly and strongly coupled J-type aggregates

    Ryohei Kishi, Masayoshi Nakano, Takuya Minami, Hitoshi Fukui, Hiroshi Nagai, Kyohei Yoneda, Hideaki Takahashi

    SYNTHETIC METALS　159　(21-22)　2194-2197　2009/11

    DOI： 10.1016/j.synthmet.2009.09.023 　

    ISSN： 0379-6779

  18. Control of third-order nonlinear optical properties of singlet diradical square planar metal complexes involving o-semiquinonato type ligands

    H. Fukui, H. Nagai, R. Kishi, T. Minami, H. Takahashi, T. Kubo, M. Nakano

    SYNTHETIC METALS　159　(21-22)　2416-2418　2009/11

    DOI： 10.1016/j.synthmet.2009.08.028 　

    ISSN： 0379-6779

  19. Third-order nonlinear optical properties of open-shell singlet molecular aggregates composed of diphenalenyl diradicals

    M. Nakano, H. Fukui, H. Nagai, T. Minami, R. Kishi, H. Takahashi

    SYNTHETIC METALS　159　(21-22)　2413-2415　2009/11

    DOI： 10.1016/j.synthmet.2009.07.035 　

    ISSN： 0379-6779

  20. Third-order nonlinear optical properties of trigonal, rhombic and bow-tie graphene nanoflakes with strong structural dependence of diradical character

    Kyohei Yoneda, Masayoshi Nakano, Ryohei Kishi, Hideaki Takahashi, Akihiro Shimizu, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek

    CHEMICAL PHYSICS LETTERS　480　(4-6)　278-283　2009/10

    DOI： 10.1016/j.cplett.2009.09.047 　

    ISSN： 0009-2614

    eISSN： 1873-4448

  21. Remarkable two-photon absorption in open-shell singlet systems

    Masayoshi Nakano, Kyohei Yoneda, Ryohei Kishi, Hideaki Takahashi, Takashi Kubo, Kenji Kamada, Koji Ohta, Edith Botek, Benoit Champagne

    JOURNAL OF CHEMICAL PHYSICS　131　(11)　2009/09

    DOI： 10.1063/1.3225202 　

    ISSN： 0021-9606

  22. Electron donor solvent effects on the (hyper)polarizabilities of a singlet diradical molecule involving a boron atom

    Kazuki Kubota, Hideaki Takahashi, Hitoshi Fukui, Sean Bonness, Kyohei Yoneda, Ryohei Kishi, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek, Masayoshi Nakano

    CHEMICAL PHYSICS LETTERS　477　(4-6)　309-314　2009/08

    DOI： 10.1016/j.cplett.2009.07.022 　

    ISSN： 0009-2614

  23. Theoretical study on third-order nonlinear optical properties in hexagonal graphene nanoflakes: Edge shape effect

    Hiroshi Nagai, Masayoshi Nakano, Kyohei Yoneda, Hitoshi Fukui, Takuya Minami, Sean Bonness, Ryohei Kishi, Hideaki Takahashi, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek

    CHEMICAL PHYSICS LETTERS　477　(4-6)　355-359　2009/08

    DOI： 10.1016/j.cplett.2009.07.035 　

    ISSN： 0009-2614

  24. Theoretical Study on Exciton Recurrence Motion in Anthracene Dimer Using the Ab Initio MO-CI Based Quantum Master Equation Approach

    Ryohei Kishi, Masayoshi Nakano, Takuya Minami, Hitoshi Fukui, Hiroshi Nagai, Kyohei Yoneda, Hideaki Takahashi

    JOURNAL OF PHYSICAL CHEMISTRY A　113　(18)　5455-5462　2009/05

    DOI： 10.1021/jp8111588 　

    ISSN： 1089-5639

  25. Theoretical study on open-shell nonlinear optical molecular systems and a development of a novel computational scheme of exciton dynamics

    Masayoshi Nakano, Ryohei Kishi, Hitoshi Fukui, Takuya Minami, Hiroshi Nagai, Kyohei Yoneda, Sean Bonness, Hideaki Takahashi

    International Journal of Nanoscience　8　123-129　2009/02/01

    ISSN： 0219-581X

  26. Quantum Master Equation Approach to Exciton Recurrence Motion in Ring-Shaped Aggregate Complexes Induced by Linear- and Circular-Polarized Laser Fields

    Takuya Minami, Hitoshi Fukui, Hiroshi Nagai, Kyohei Yoneda, Ryohei Kishi, Hideaki Takahashi, Masayoshi Nakano

    JOURNAL OF PHYSICAL CHEMISTRY C　113　(8)　3332-3338　2009/02

    DOI： 10.1021/jp8096555 　

    ISSN： 1932-7447

  27. Third-Order Nonlinear Optical Properties of Open-Shell Systems: Diradical Character and Spin State Dependences

    Masayoshi Nakano, Hitoshi Fukui, Hiroshi Nagai, Takuya Minami, Ryohei Kishi, Hideaki Takahashi, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek

    COMPUTATIONAL METHODS IN SCIENCE AND ENGINEERING, VOL 1　1108　43-+　2009

    DOI： 10.1063/1.3117140 　

    ISSN： 0094-243X

  28. Quantum Master Equation Approach to Exciton Recurrence Motion in a Ring-Shaped Aggregate Complex Induced by Circular-Polarized Laser Field

    Takuya Minami, Hitoshi Fukui, Hiroshi Nagai, Kyohei Yoneda, Ryohei Kishi, Hideaki Takahashi, Masayoshi Nakano

    COMPUTATIONAL METHODS IN SCIENCE AND ENGINEERING, VOL 2　1148　330-333　2009

    DOI： 10.1063/1.3225307 　

    ISSN： 0094-243X

  29. Theoretical study of third-order nonlinear optical properties in square nanographenes with open-shell singlet ground states

    Masayoshi Nakano, Hiroshi Nagai, Hitoshi Fukui, Kyohei Yoneda, Ryohei Kishi, Hideaki Takahashi, Akihiro Shimizu, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek

    CHEMICAL PHYSICS LETTERS　467　(1-3)　120-125　2008/12

    DOI： 10.1016/j.cplett.2008.10.084 　

    ISSN： 0009-2614

  30. Exciton Dynamics of Molecular Aggregate Systems Composed of Triangular Lattice Units: Structural Dependence of Exciton Migration and Recurrence

    Takuya Minami, Masayoshi Nakano, Hitoshi Fukui, Hiroshi Nagai, Ryohei Kishi, Hideaki Takahashi

    JOURNAL OF PHYSICAL CHEMISTRY C　112　(42)　16675-16681　2008/10

    DOI： 10.1021/jp805328k 　

    ISSN： 1932-7447

  31. Theoretical study on second hyperpolarizabilities of singlet diradical square planar nickel complexes involving o-semiquinonato type ligands

    Hitoshi Fukui, Ryohei Kishi, Takuya Minami, Hiroshi Nagai, Hideaki Takahashi, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek, Masayoshi Nakano

    JOURNAL OF PHYSICAL CHEMISTRY A　112　(36)　8423-8429　2008/09

    DOI： 10.1021/jp804400s 　

    ISSN： 1089-5639

  32. A novel dynamic exciton expression based on the ab initio MO CI based quantum master equation approach

    Masayoshi Nakano, Ryohei Kishi, Takuya Minami, Hitoshi Fukui, Hiroshi Nagai, Kyohei Yoneda, Hideaki Takahashi

    CHEMICAL PHYSICS LETTERS　460　(1-3)　370-374　2008/07

    DOI： 10.1016/j.cplett.2008.05.100 　

    ISSN： 0009-2614

    eISSN： 1873-4448

  33. Core molecule dependence of energy migration in phenylacetylene nanostar dendrimers: Ab initio molecular orbital-configuration interaction based quantum master equation study

    Ryohei Kishi, Takuya Minami, Hitoshi Fukui, Hideaki Takahashi, Masayoshi Nakano

    JOURNAL OF CHEMICAL PHYSICS　128　(24)　2008/06

    DOI： 10.1063/1.2939244 　

    ISSN： 0021-9606

  34. Cooperative effects in static polarizabilities and second hyperpolarizabilities of hydrogen-bonded 4-pyridones

    Ryohei Kishi, Shin-ya Umezaki, Hitoshi Fukui, Takuya Minami, Kazuki Kubota, Hideaki Takahashi, Masayoshi Nakano

    CHEMICAL PHYSICS LETTERS　454　(1-3)　91-96　2008/03

    DOI： 10.1016/j.cplett.2008.01.083 　

    ISSN： 0009-2614

  35. Intermolecular interaction effects on the second hyperpolarizability of open-shell singlet diphenalenyl radical dimer

    Masayoshi Nakano, Akihito Takebe, Ryohei Kishi, Hitoshi Fukui, Takuya Minami, Kazuki Kubota, Hideaki Takahashi, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek

    CHEMICAL PHYSICS LETTERS　454　(1-3)　97-104　2008/03

    DOI： 10.1016/j.cplett.2008.01.084 　

    ISSN： 0009-2614

  36. Theoretical study on the second hyperpolarizability of open-shell singlet one-dimensional systems with a charged defect

    Akihito Takebe, Masayoshi Nakano, Ryohei Kishi, Masahito Nate, Hideaki Takahashi, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek

    CHEMICAL PHYSICS LETTERS　451　(1-3)　111-115　2008/01

    DOI： 10.1016/j.cplett.2007.11.086 　

    ISSN： 0009-2614

    eISSN： 1873-4448

  37. Spin State Dependence of Second Hyperpolarizabilities of Zethrenes

    Masayoshi Nakano, Ryohei Kishi, Akihito Takebe, Masahito Nate, Hideaki Takahashi, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek

    SELECTED PAPERS FROM ICNAAM 2007 AND ICCMSE 2007　1046　15-+　2008

    DOI： 10.1063/1.2997302 　

    ISSN： 0094-243X

  38. Finite-field spin-flip configuration interaction calculation of the second hyperpolarizabilities of singlet diradical systems

    Ryohei Kishi, Masayoshi Nakano, Suguru Ohta, Akihito Takebe, Masahito Nate, Hideaki Takahashi, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek

    JOURNAL OF CHEMICAL THEORY AND COMPUTATION　3　(5)　1699-1707　2007/09

    DOI： 10.1021/ct700118q 　

    ISSN： 1549-9618

  39. Second hyperpolarizabilities of singlet polycyclic diphenalenyl radicals: Effects of the nature of the central heterocyclic ring and substitution to diphenalenyl rings

    Masayoshi Nakano, Nozomi Nakagawa, Ryohei Kishi, Suguru Ohta, Masahito Nate, Hideaki Takahashi, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek, Yasushi Morita, Kazuhiro Nakasuji, Kizashi Yamaguchi

    JOURNAL OF PHYSICAL CHEMISTRY A　111　(37)　9102-9110　2007/09

    DOI： 10.1021/jp0734676 　

    ISSN： 1089-5639

  40. Molecular simulation study on adsorption of methanol/water mixtures in mesoporous silicas modified pore surface silylation

    Naoki Aoyama, Tsukasa Yoshihara, Shin-ichi Furukawa, Tomoshige Nitta, Hideaki Takahashi, Masayoshi Nakano

    FLUID PHASE EQUILIBRIA　257　(2)　212-216　2007/08

    DOI： 10.1016/j.fluid.2007.01.039 　

    ISSN： 0378-3812

  41. Non-equilibrium molecular dynamics simulation study on permeation phenomena of LJ particles in slit-shaped membranes with periodic belt-like heterogeneous surfaces

    Ken-ichiro Yonemori, Atsushi Takitani, Shin-ichi Furukawa, Tomoshige Nitta, Hideaki Takahashi, Masayoshi Nakano

    FLUID PHASE EQUILIBRIA　257　(2)　190-194　2007/08

    DOI： 10.1016/j.fluid.2007.01.030 　

    ISSN： 0378-3812

  42. Relationship between third-order nonlinear optical properties and magnetic interactions in open-shell systems: A new paradigm for nonlinear optics

    Masayoshi Nakano, Ryohei Kishi, Suguru Ohta, Hideaki Takahashi, Takashi Kubo, Kenji Kamada, Koji Ohta, Edith Botek, Benoit Champagne

    PHYSICAL REVIEW LETTERS　99　(3)　2007/07

    DOI： 10.1103/PhysRevLett.99.033001 　

    ISSN： 0031-9007

  43. First and second hyperpolarizabilities of donor-acceptor disubstituted diphenalenyl radical systems

    Masayoshi Nakano, Suguru Ohta, Kazuya Tokushima, Ryohei Kishi, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek, Hideaki Takahashi

    CHEMICAL PHYSICS LETTERS　443　(1-3)　95-101　2007/07

    DOI： 10.1016/j.cplett.2007.05.104 　

    ISSN： 0009-2614

  44. Theoretical study on the second hyperpolarizabilities of phenalenyl radical systems involving acetylene and vinylene linkers: Diradical character and spin multiplicity dependences

    Suguru Ohta, Masayoshi Nakano, Takashi Kubo, Kenji Kamada, Koji Ohta, Ryohei Kishi, Nozomi Nakagawa, Benoit Champagne, Edith Botek, Akihito Takebe, Shin-ya Umezaki, Masahito Nate, Hideaki Takahashi, Shin-ichi Furukawa, Yasushi Morita, Kazuhiro Nakasuji, Kizashi Yamaguchi

    JOURNAL OF PHYSICAL CHEMISTRY A　111　(18)　3633-3641　2007/05

    DOI： 10.1021/jp0713662 　

    ISSN： 1089-5639

  45. Multi-scale simulations for materials and life sciences

    Frederic Caster, Benoit Champagne, Masayoshi Nakano, Hideaki Takahashi

    COMPUTATIONAL METHODS IN SCIENCE AND ENGINEERING VOL 1　963　350-+　2007

    DOI： 10.1063/1.2836062 　

    ISSN： 0094-243X

  46. Multi-scale simulations for materials and life sciences

    Frederic Caster, Benoit Champagne, Masayoshi Nakano, Hideaki Takahashi

    COMPUTATIONAL METHODS IN SCIENCE AND ENGINEERING VOL 1　963　350-+　2007

    DOI： 10.1063/1.2827019 　

    ISSN： 0094-243X

  47. Strong two-photon absorption of singlet diradical hydrocarbons

    Kenji Kamada, Koji Ohta, Takashi Kubo, Akihiro Shimizu, Yasushi Morita, Kazuhiro Nakasuji, Ryohei Kishi, Suguru Ohta, Shin-ichi Furukawa, Hideaki Takahashi, Masayoshi Nakano

    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION　46　(19)　3544-3546　2007

    DOI： 10.1002/anie.200605061 　

    ISSN： 1433-7851

  48. Second hyperpolarizabilities (gamma) of 1,3-dipole systems: Diradical character dependence of gamma

    Masayoshi Nakano, Ryohei Kishi, Akihito Takebe, Masahito Nate, Hideaki Takahashi, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek

    COMPUTATION IN MODERN SCIENCE AND ENGINEERING VOL 2, PTS A AND B　2　102-+　2007

    DOI： 10.1063/1.2835915 　

    ISSN： 0094-243X

  49. Exciton recurrence motion in aggregate systems in the presence of quantized optical fields

    Masayoshi Nakano, Suguru Ohta, Ryohei Kishi, Masahito Nate, Hideaki Takahashi, Shin-Ichi Furukawa, Hiroya Nitta, Kizashi Yamaguchi

    JOURNAL OF CHEMICAL PHYSICS　125　(23)　2006/12

    DOI： 10.1063/1.2390695 　

    ISSN： 0021-9606

  50. Second hyperpolarizabilities (gamma) of open-shell singlet one-dimensional systems: Intersite interaction effects on the average diradical character and size dependences of gamma

    Masayoshi Nakano, Akihito Takebe, Ryohei Kishi, Suguru Ohta, Masahito Nate, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek, Hideaki Takahashi, Shin-ichi Furukawa, Yasushi Morita, Kazuhiro Nakasuji

    CHEMICAL PHYSICS LETTERS　432　(4-6)　473-479　2006/12

    DOI： 10.1016/j.cplett.2006.10.082 　

    ISSN： 0009-2614

    eISSN： 1873-4448

  51. Second hyperpolarizabilities of polycyclic diphenalenyl radicals: Effects of para/ortho-quinoid structures and central ring modification

    Masayoshi Nakano, Nozomi Nakagawa, Suguru Ohta, Ryohei Kishi, Takashi Kubo, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek, Hideaki Takahashi, Shin-ichi Furukawa, Yasushi Morita, Kazuhiro Nakasuji, Kizashi Yamaguchi

    CHEMICAL PHYSICS LETTERS　429　(1-3)　174-179　2006/09

    DOI： 10.1016/j.cplett.2006.07.065 　

    ISSN： 0009-2614

  52. Origin of the enhancement of the second hyperpolarizability of singlet diradical systems with intermediate diradical character

    Masayoshi Nakano, Ryohei Kishi, Suguru Ohta, Akihito Takebe, Hideaki Takahashi, Shin-ichi Furukawa, Takashi Kubo, Yasushi Morita, Kazuhiro Nakasuji, Kizashi Yamaguchi, Kenji Kamada, Koji Ohta, Benoit Champagne, Edith Botek

    JOURNAL OF CHEMICAL PHYSICS　125　(7)　2006/08

    DOI： 10.1063/1.2213974 　

    ISSN： 0021-9606

    eISSN： 1089-7690

  53. Monte Carlo wavefunction approach to the dissipative quantum-phase dynamics of two-component Bose-Einstein condensates

    M Nakano, S Ohta, R Kishi, H Takahashi, S Furukawa

    EUROPEAN PHYSICAL JOURNAL D　38　(3)　523-532　2006/06

    DOI： 10.1140/epjd/e2006-00049-7 　

    ISSN： 1434-6060

  54. Theoretical study on the second hyperpolarizabilities of tetrathiafulvalene (TTF) and tetrathiapentalene (TTP) using highly correlated ab initio MO and the density functional theory methods

    S Yamada, M Nakano, R Kishi, S Ohta, H Takahashi, S Furukawa, T Nitta, K Yamaguchi

    SYNTHETIC METALS　156　(5-6)　375-378　2006/03

    DOI： 10.1016/j.synthmet.2005.12.016 　

    ISSN： 0379-6779

  55. Second hyperpolarizability of phenalenyl radical system involving acetylene pi-conjugated bridge

    S Ohta, M Nakano, T Kubo, K Kamada, K Ohta, R Kishi, N Nakagawa, B Champagne, E Botek, SY Umezaki, A Takebe, H Takahashi, SI Furukawa, Y Morita, K Nakasuji, K Yamaguchi

    CHEMICAL PHYSICS LETTERS　420　(4-6)　432-437　2006/03

    DOI： 10.1016/j.cplett.2006.01.022 　

    ISSN： 0009-2614

  56. Second hyperpolarizabilities (gamma) of bisimidazole and bistriazole benzenes: Diradical character, charged state, and spin state dependences

    M Nakano, R Kishi, N Nakagawa, S Ohta, H Takahashi, SI Furukawa, K Kamada, K Ohta, B Champagne, E Botek, S Yamada, K Yamaguchi

    JOURNAL OF PHYSICAL CHEMISTRY A　110　(12)　4238-4243　2006/03

    DOI： 10.1021/jp056672z 　

    ISSN： 1089-5639

  57. Monte Carlo wavefunction approach to the exciton dynamics of molecular aggregates with exciton-phonon coupling

    S Ohta, M Nakano, R Kishi, H Takahashi, S Furukawa

    CHEMICAL PHYSICS LETTERS　419　(1-3)　70-74　2006/02

    DOI： 10.1016/j.cplett.2005.11.052 　

    ISSN： 0009-2614

  58. Intermolecular interaction effects on second hyperpolarizabilities of clusters including charged species

    Masayoshi Nakano, Ryohei Kishi, Nozomi Nakagawa, Suguru Ohta, Hideaki Takahashi, Shin Ichi Furukawa

    Journal of Computational Methods in Sciences and Engineering　6　211-222　2006/01/01

    ISSN： 1472-7978

  59. Second hyperpolarizabilities of polycyclic aromatic hydrocarbons involving phenalenyl radical units

    M Nakano, T Kubo, K Kamada, K Ohta, R Kishi, S Ohta, N Nakagawa, H Takahashi, S Furukawa, Y Morita, K Nakasuji, K Yamaguchi

    CHEMICAL PHYSICS LETTERS　418　(1-3)　142-147　2006/01

    DOI： 10.1016/j.cplett.2005.10.109 　

    ISSN： 0009-2614

  60. Molecular simulation study on adsorption of methanol/water mixed gases in mesoporous silicas with surface modification

    Shin-Ichi Furukawa, Naoki Aoyama, Toshihiro Nishiumi, Tomoshige Nitta, Hideaki Takahashi, Masayoshi Nakano

    Kagaku Kogaku Ronbunshu　32　(1)　18-24　2006

    DOI： 10.1252/kakoronbunshu.32.18 　

    ISSN： 0386-216X 1349-9203

  61. Quantum-phase dynamics of two-component Bose-Einstein condensates: Collapse-revival of macroscopic superposition states

    M Nakano, R Kishi, S Ohta, H Takahashi, S Furukawa, K Yamaguchi

    PHYSICA B-CONDENSED MATTER　370　(1-4)　110-120　2005/12

    DOI： 10.1016/j.physb.2005.09.004 　

    ISSN： 0921-4526

  62. The Development and Application of Non-Periodic Ab Initio Molecular Dynamics Code Employing the Real Space Grids

    Hori Takumi, Takahashi Hideaki, Nitta Tomoshige

    Journal of Chemical Software　13　(1)　21-28　2001

    Publisher: Society of Computer Chemistry, Japan

    DOI： 10.14827/jccj1999.13.21 　

    ISSN： 1344-9826

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    We have developed a novel code for non-periodic ab initio molecular dynamics based on density functional method employing real space grids and simulated the SN2 reaction of CH3Cl and OH- in gas phase. In particular in this paper, we describe the details of the code. Furthermore, we have parallelized the code by using MPI (Message Passing Interface) and illustrated the efficiency of the real space grid method for the parallel computing.

  63. Molecular Dynamics Simulations on Disintegration of a Charged Liquid Thread

    ISHII Hiroki, FUNAKAWA Tomoya, YAMAGUCHI Manabu, FURUKAWA Shinichi, TAKAHASHI Hideaki, NITTA Tomoshige

    9　169-172　2000/12/11

    ISSN： 1341-6030

  64. Experimental determination of the dipole moment of HCl dimer using an electrostatic hexapole field

    K Imura, T Kasai, H Ohoyama, H Takahashi, R Naaman

    CHEMICAL PHYSICS LETTERS　259　(3-4)　356-360　1996/09

    DOI： 10.1016/0009-2614(96)00757-9 　

    ISSN： 0009-2614

  65. Alignment and orientation effects for the indirect ionization of CH<inf>3</inf>Cl in the |111〉 rotational state by fast electron impact

    T. Kasai, T. Matsunami, H. Takahashi, T. Fukawa, H. Ohoyama, K. Kuwata

    Journal of Physical Chemistry　99　(37)　13597-13599　1995/12/01

    DOI： 10.1021/j100037a004 　

    ISSN： 0022-3654

  66. A theoretical study on the steric effect of the electronic coupling in the energy transfer reaction using ab initio CASSI method.

    高橋英明, 大山浩, 笠井俊夫, 中野雅由, 山口兆

    日本化学会講演予稿集　69th　(1)　1995

    ISSN： 0285-7626

  67. A theoretical study on relationship between shape of molecular orbital and stereo-reactivity in energy transfer reactions.

    TAKAHASHI H, OHOYAMA H, KASAI T, KUWATA K, NAKANO M, YAMAGUCHI K

    Atomic Collision Research in Japan. Progress Report　(20)　1994

  68. Theoretical Study on the Steric Effects in the energy transfer reaction.

    高橋英明, 大山浩, 笠井俊夫, 桑田敬治, 中野雅由, 山口兆

    化学反応討論会講演要旨集　10th　1994

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Presentations 1

  1. Massively Parallel Implementation of the QM/MM Approach Combined with a Theory of Solutions International-presentation Invited

    TAKAHASHI Hideaki

    International Conference of the Molecular Simulation (ICMS)　2013/11/13

Research Projects 13

  1. Development of the nonlocal kinetic-energy density functional utilizing the response function on the energy coordinate as its kernel

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (C)

    Institution: Tohoku University

    2022/04/01 - 2025/03/31

  2. Development of the hybrid density functional theory on the real-space grid method and its implementation on massively parallel computers

    Takahashi Hideaki

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (C)

    Institution: Tohoku University

    2017/04/01 - 2020/03/31

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    In this subject we developed two types of implementation of the Hartree－Fock(HF) exchange energy using the real-space grid approach to achieve high efficiency in the parallel execution of the hybrid exchange functional in the density functional theory. We first reduce the problem of calculating the HF exchange energy to the solution of the Poisson equation presented on the discrete real-space grids. Then, the Poisson equations for the electrostatic potentials of the products of the orbital pairs were solved iteratively through the conjugate gradient (CG) method where the operation of Laplacian was parallelized by domain decomposition scheme. In the other approach, we adapted the three-dimensional fast Fourier transform (FFT), referred to as PFFT, to solve the Poisson equations. It was shown in the benchmark tests that the parallel execution with the FFT approach is faster than that using the CG method because a larger bandwidth can be made available in the parallel execution of FFT.

  3. Theory of Structure and Functions of Liquid and Polymer Interfaces

    Morita Akihiro, TAKAHASHI Hideaki, JOUTSUKA Tatsuya

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    Institution: Tohoku University

    2013/06/28 - 2018/03/31

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    We have advanced the theory and computational analysis of interfaces in collaboration with experimental groups. The achivement in this project includes many subjects, including the theoretical analysis of 2-D SFG spectroscopy, efficient computationaly analysis of difference spectra, calculation of chi3 effect in SFG/SHG spectroscopy, reliable assignment of SFG spectra of ice surface, modeling of alkyl C-H vibrations. We also elucidated the hidden barrier in the ion transport through liquid-liquid interfaces, which accounts for retarded kinetics of ion transport.

  4. Development of an exchange functional on the basis of the electron density defined on the energy coordinate

    TAKAHASHI Hideaki

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Challenging Exploratory Research

    Institution: Tohoku University

    2013/04/01 - 2015/03/31

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    The current DFT suffers from two major problems. The first one is referred to as the static correlation error and the other is known as the self-interaction error. The former error increases drastically in the dissociation limit of a chemical bond and the latter manifests itself in a system with excess electrons. To solve these problems we introduced a concept of the energy electron density by projecting the electron density on the energy coordinate defined as the electrostatic potential formed by the nuclei in the system. Then, a novel exchange functional was developed on the basis of the energy electron density. To examine the efficiency of the method we applied this functional to the calculation of the potential energy curves for diatomic molecules. It turns out that the PEC for these molecules can be adequately computed with the comparable accuracy as the current exchange functional based on GGA approximations.

  5. 量子化学計算によるタンパク質中のＡＴＰの加水分解反応の自由エネルギー解析

    高橋 英明

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 新学術領域研究(研究領域提案型)

    Institution: 東北大学

    2011/04/01 - 2013/03/31

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    ATPの加水分解の自由エネルギーは生体におけるエネルギーの通貨であり、その自由エネルギーを解析することは分子生物学や物理化学における最も重要な課題の一つである。ATPの加水分解の自由エネルギーを理論計算によって得るには、量子化学と統計力学に関わる問題を同時に解決する必要がある。量子化学における問題として、水溶液あるいはタンパク質中のATPの電子密度揺らぎをいかに再現するかという問題がある。ATPは水溶液において最大で4価までの余剰電子を有し、これらは水という極性分子の運動によって著しく揺さぶられるので、電子揺らぎを再現することはATP加水分解の自由エネルギー計算にとって本質的に重要である。これは、溶媒を連続誘電体で扱う方法や平均場近似では再現できない。また、これには電子揺らぎに起因する自由エネルギーを統計力学に基いていかに計算するかという問題が付随する。 前年度までの研究によって、我々は、溶質であるATPを量子化学的に扱い、溶媒としての水を古典力学的に記述するハイブリッド型の第一原理計算分子動力学法(QM/MM法)と溶液の理論を組み合わせることによって、電子揺らぎの自由エネルギーを厳密に計算する方法を開発した。より具体的には溶質の電子分極に起因する系全体のエネルギーの分布関数を基本変数として、電子揺らぎの自由エネルギー汎関数を構築した。この方法をATPのモデル分子であるピロリン酸の加水分解反応に適用した。0価および1価のピロリン酸については、加水分解の実験値を極めて良好に再現したが、2価および3価については、計算値が実験値から10 kcal/mol以上も外れてしまった。これは、主に反応の始状態において、ピロリン酸から周囲の水分子への電荷移動の効果が現在の我々のモデルでは再現できていないことが主要な原因であると考えられる。

  6. 量子化学計算による水溶液、及びタンパク質中のATPのプロトン親和性に関する研究

    高橋 英明

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 新学術領域研究(研究領域提案型)

    2009 - 2011

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    本研究の目的は、多くのタンパク質の機能発現のエネルギー源であるATPの加水分解に伴う自由エネルギー変化を量子化学と分子シミュレーションの方法によって計算し、得られた自由エネルギー変化に対する水和の影響を定量的に明らかにすることである。ATP分子はそれなりの大きさを持つので、溶液中でその分子構造が顕著に揺らぐことが予想される。従って、我々がこれまでに開発してきた方法、つまりQM/MM-ER法を拡張することによって、溶液中で溶質の構造が揺らぐことによる自由エネルギーへの寄与を考慮する必要がある。本年度は、これを実施する為に以下に述べるような方法論の大幅な単純化を行った。溶液におけるQM系の電子密度の揺らぎは、QM-MM間の多体の相互作用に由来する。ところが、エネルギー表示の理論は、溶質-溶媒間相互作用が2体的であることを前提にしているので、これをエネルギー表示の理論の枠組みで計算するには工夫が必要である。新規な方法では分子の電子分極に関わる全ての相互作用の和をとり、これに一つのエネルギー座標を与えてエネルギー分布関数を構築する。この分布関数によれば、近似的な汎関数を用いることなく正確に自由エネルギーを定式化することが可能である。本方法のベンチマークテストとして、水の溶媒和自由エネルギーを計算すると、本方法が実験値を極めて良い精度で再現することが分かった。また重要なことに、この方法をベースにして分子構造が揺らぐ系へ式を拡張できる。現在、その為のプログラム開発を実行中である。

  7. 水溶液における生体分子の機能とその発現機構に関する量子化学的研究

    高橋 英明

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 特定領域研究

    Institution: 大阪大学

    2006 - 2007

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    我々は、最近、実空間グリッドを基底とするハイブリッド型の第一原理分子法(QM/MM法)と新規な溶液論(エネルギー表示の理論)を組み合わせることによって、効率良く、正確に溶液内の化学過程の自由エネルギー変化を計算する方法を開発した(QM/MM-ER法)。本研究課題の主たる目的は、酵素内の様々な化学過程の自由エネルギー変化を計算するためにQM/MM-ER法を拡張することである。本年度は、タンパク質1b4v中に埋め込まれた補酵素FADの還元反応に伴う自由エネルギー変化をQM/MM-ER法を拡張することによつて計算した。この方法の大きな特徴は、FADに付加する余剰電子1個を溶質と見なすことにある。水、アポタンパク、FADが混合溶媒を形成するとして、これらの溶媒について、エネルギー分布関数を構成し、各溶媒からの還元自由エネルギーに対する寄与を計算した。水分子、アポタンパク、FAD、ADPによる還元自由エネルギーへの寄与は、それぞれ、-57.5kcal/mol,-149.7 kcal/mol,-31.9 kcal/mol,55.1 kcal/molと計算された。また、バルクの水の寄与は、21.0 kcal/molである。FADの還元自由エネルギーは、これらの寄与の単純な和として、-163.1 kcal/molと計算される。このような大きな還元の自由エネルギー変化は、タンパク質全体が+3価に帯電している為である。この計算値は、報告されている実験値、-90.6kcal/molから大きくずれている。実験では、タンパク質の電荷を中和するようなカウンターイオンが含まれていることが、その差の原因と考えられる。 また、本年度の後半では、酵素活性サイトのプロトン化状態を決定するための方法論の定式化を行い、プログラム開発を行った。10個の残基からなる最小のタンパク質、シニョリン(iuao)をテスト系として、QM/MM-ERシミュレーションを行った。シニョリンのような小さなタンパク質でも気相中と溶液中の平均構造に大きな違いがあり、それ故に参照系と溶液系のエネルギー分布関数が十分にオーバーラップしないという結果がでた。

  8. ハイブリッド型第一原理分子動力学法による生体内酵素反応の研究

    高橋 英明

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 若手研究(B)

    Institution: 大阪大学

    2003 - 2004

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    本研究の実績は、次の2点に要約することが出来る。一つは、密度汎関数法にもとづく分子内QM/MM法を開発し、これを並列化したことである。もう一つは、ヒト免疫不全ウイルスのプロテアーゼ(HIV-1Pr)の反応の遷移状態を決定したことである。以下にそれぞれについて詳述する。 (1)遷移状態の決定 HIV1-Prのペプチド鎖解裂反応は2段階で進むとされている。我々は1、及び2段階目の反応の遷移状態をHF/3-21G^<**>レベルで構造最適化している。基質となるペプチド鎖のモデルとして、CH_3-CO-NH-CH_3を選択し、1対のAsp25の他に、Thr26とGly27のペプチド結合部を活性部位として扱った。現在のところ、1段階目の遷移状態の構造最適化が完了しており、この反応の活性部位のみのエネルギー障壁の高さは、24.8kcal/molであった。 (2)分子内QM/MM法の開発 QM/MM法のプログラム開発において、我々は、実空間の格子上で波動関数の値を計算する実空間グリッド法を導入した。この方法は、従来の原子基底や平面波基底に比べて計算精度が良い上に、並列計算も容易に行えるという利点がある。また、反応活性部位以外のMM領域は、Tinker Packageにより扱う。我々は、Link Atom法によりこれら二つの領域の力場を合成し、タンパク系のシミュレーションの実行が可能なプログラムを完成させた。また、QM系のほぼ全体、及びMM系の力の計算部分を並列化することに成功した。特にQM系の並列化においては、並列化効率を損なわないようにするために、HartreeポテンシャルをPoisson方程式を逐次的に解くことにより計算するなどの工夫をした。これにより、8CPUを使用した場合でも、量子化学計算において80%以上の並列化効率を実現することが可能になった。

  9. A quantum chemical approach to the study of a novel reaction path and its control in the supercritical water

    NITTA Tomoshige, TAKAHASHI Hideaki, FURUKAWA Shin-ichi

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: Osaka University

    2003 - 2004

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    The results obtained by present work can be summarized by the following two subjects. One is that a novel methodology (QM/MM-ER) has been developed to compute the free energy change associated with a chemical reaction in a condensed phase. The other is that a novel reaction pathway has been explored by means of the QM/MM-ER simulations. It has been suggested that the proton transfers along the hydrogen bonds of water molecules promote the dehyderation of butanediol in hot water. The details of the results have been itemized as follows. (1)Quantum chemical approach to the free energy calculation in condensed phase In order to compute the free energy change associated with a chemical reaction in aqueous solution, we have combined the quantum mechanical/molecular mechanical approach with the theory of energy representation. Within the theory of the energy representation, the solvation free energy of a solute is described in terms of the distribution functions of the solute-solvent interaction energy instead of the spatial distribution function used in the conventional theory of solution. Since the method of the energy representation does not need the concept of the interaction site, the combination with the quantum chemical treatment is straightforward. (2)Quantum chemical calculation for the dehydration reaction of alcohol Quantum chemical calculations have revealed that butanediol forms a biradical electronic structure at the transition state (TS) of the proton transferring reaction. The activation energy is extremely high (〜70 kcal/mol) in the gaseous phase, however, it reduces to 〜50 kcal/mol in hot water. The electronic state of the TS forms a zwitterionic structure in the polar solvent, which leads to the stabilization of the TS as compared to the reactant. Thus it has been suggested that the proton-transfer mechanism catalyzes the dehydration reaction of alcohol in hot water.

  10. 量子化学計算による材料表面の化学修飾

    高橋 英明

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 若手研究(B)

    Institution: 大阪大学

    2001 - 2002

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    本研究において、量子化学計算を基礎とする新しい表面化学修飾法を提案した。 その概要は、以下の様である。 (1)表面と吸着分子との相互作用を定性的に理解可能な種々の項に分解する。 (2)分解されたそれぞれのエネルギー項でどれが支配的であるかを見極め、吸着エネルギーを増大させるために支配的なエネルギー項をさらに増大させる。 (3)電荷移動相互作用が支配的なエネルギーである場合 ・表面から気体分子へ電荷移動が起こる→電気陰性度が小さい原子で化学修飾 ・気体分子から表面へ電荷移動が起こる→電気陰性度が大きい原子で化学修飾 分極相互作用が支配的なエネルギーである場合 ・原子の固さが小さい原子で化学修飾 二酸化チタン(110)面における二酸化炭素の吸着に着目し、上記の指針に基づいて化学修飾し、量子化学計算を用いて吸着エネルギーを計算した。化学修飾は、チタン原子よりも電気陰性度の大きなカルシウム原子の導入と、分極相互作用を増大させるためにチタン原子よりも柔らかいアルミニウム原子の導入を行った。いずれの場合も吸着エネルギーが増大し、化学修飾の指針の妥当性を確認した。 また、分解された吸着エネルギーの一つである静電相互作用において、定性的・定量的に理解する上で重要な原子の部分電荷を計算する方法を開発した。この方法は、対象分子を内包する空間をグリッドに区切り、それぞれのグリッドの電子密度を基に、最小二乗法を用いて部分電荷を求める。この方法を二酸化チタン(110)面における二酸化炭素の吸着に適用したところ、Mulliken-chargeによる計算よりもはるかに精度の良い結果を得た。従って、この方法を用いた表面ー気体分子間の静電相互作用エネルギー計算は、十分な指針となり得ることが解った。

  11. hybrid Quantum Chemical Studies for the Reaction Mechanism and the Control of Chemical Processes in the Supercritical Water

    NITTA Tomoshige, TAKAHASHI Hideaki

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: Osaka University

    2001 - 2002

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    (1) Ab initio density functional theory calculations have been performed to investigate the catalytic role of water molecules in the oxidation reaction of ethanol : CH_3CH_2OH + nH_2O -> CH_3CHO + H_2 + nH_2O (n = 0, 1, 2 ). The results show that the potential energy barrier for the reaction is 88.0 kcal/mol in case of n =0, while it is reduced by 〜 34 kcal/mol when two water molecules are involved (n = 2 ) in the reaction. As a result, the rate constant increases to 3.31x10^<-4>s^<-1>, which shows a significant catalytic role of water molecules in the ethanol oxidation reactions. (2) A real-space-grid quantum mechanical / molecular mechanical (QM/MM) simulations have been carried out to investigate the role of the water solvent on the novel ethanol oxidation reaction catalyzed by two water molecules through proton transfer mechanism. We have considered two thermodynamical conditions of solutions for the calculations; ambient(AW) and supercritical water(SCW). The QM/MM simulations have revealed that the solvation energy for the transition state(TS) is larger than that of the reactant state in the SCW resulting in the reduction of the activation energy by 3.7 kcal/mol. While, in the AW, the energy barrier is raised by 7.2 kcal/mol. Radial distribution functions show that hydrogen bonding between the solvent and the water molecules that participate in the reaction seriously collapses when the complex is changed from the reactant to the TS in the AW, suggesting that the closely packed hydrogen bond network attached to the reactant disturbs the proton migration to take place. A reaction mechanism by stepwise proton translocations has also been examined and found to be minor as compared with the concerted one.

  12. Studies on Membrane Permeation Mechanisms and Molecular Design of Inorganic Membranes by Using Molecular Simulations and Quantum Chemical Calculations

    NITTA Tomoshige, TAKAHASHI Hideaki

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B).

    Institution: Osaka University

    1999 - 2000

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    The objectives of the present work are twofold : molecular simulation studies on gas permeation mechanisms through inorganic membranes and studies on surface modification method by using ab initio quantum chemical calculations, toward molecular design of inorganic membranes. 1. In molecular simulations, three carbon membranes different in pore shape (diamond, zigzag, and smooth slit types) were proposed as model membranes and the permeation of methane/ethane mixtures were calculated. Followings are important results : (1) Molecular permeation and separation mechanisms of gases may be explained by three factors : selective adsorption, relative diffusion resistance in pores, and relative permeation resistance at the inlet and outlet of membranes.(2) For the diamond and zigzag shape membranes, the diffusion resistance and the outlet resistance are predominant while only the outlet resistance is predominant for the slit-shaped membrane.(3) The membrane structure that enhances the permeation rate of molecules strongly adsorbed may be the best. Furthermore, some programs for permeation of flexible molecules have been developed and simulations of permeation of butane isomers through a zeolite membrane have been carried out ; however, they are found to take a lot of computation time. Therefore, we have taken efforts to rewrite the programs for parallel processing, with expecting to have a new parallel computing system. 2. A strategy for modification of surface atoms has been proposed by means of ab initio quantum chemical calculations : i.e. selecting a candidate atom so as to enhance the factors of stabilization energy between a molecule and the surface (a cluster). The intermolecular interaction between NH_3-TiO_2 was found to be large and to be classified into chemical adsorption without modification. For the CO_2-MgO and CO_2-TiO_2 systems, the intermolecular potentials were found to be physical adsorption and the largest contribution for the stabilization was the charge transfer from the surface atoms to a CO_2 molecule. Therefore, Ca atoms, which have smaller electronegativity than Mg and Ti atoms, were selected to enhance the charge-transfer, which resulted in the increase in adsorption energy of CO_2 as the selection rule predicted. In the case when the molecular polarization is the major factor for the interaction, we can choose softer atoms than the original surface atoms, though the sensitivity of the polarization term on the intermolecular stabilization seems to be weak, suggested by our recent calculations.

  13. Molecular Simulation Studies on Membrane Permeation and Molecular Design of Membranes

    NITTA Tomoshige, TAKAHASHI Hideaki

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: Osaka University

    1997 - 1998

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    The objectives of the present work are twofold : molecular simulation studies of gas permeation mechanisms through inorganic membranes and an attempt of surface modification method by use of ab initio quantum chemical calculations. Followings are important results : (1) The gammaVT-NEMD method has been effectively used to simulate permeation of pure and mixed gases through carbon membranes ; it is found that the separation mechanism of mixed gases through a membrane composed of heterogeneous surfaces of belt-like potential barrier changes from adsorption-control to diffusion-control as the potential barrier increases. (2) One of interesting observations is a blocking phenomenon where ethane molecules, which are strongly adsorbed on carbon surfaces, cover outer mouths of slit pores, resulting in preventing small methane molecules to enter. (3) Simulations of permeation of helium, nitrogen, carbon dioxide, methane, ethane through the pure silica ZSM-5 membrane have been carried out and density profiles of gases are found to provide quantitative estimations of permeation-resistance through the entrance, inside and exit of the membrane. (4) A wavepacket analysis method was firstly. introduced to investigate the statistical behavior of molecules that penetrate a slit-shaped micropore ; the effect of kinetic energy vertical to the wall surface on gas permeation from inside to outside was investigated by the new method. A strategy has been suggested to modify surface atoms through ab initio quantum chemical calculations : the GAUSSIAN is used to optimize the geometry of a molecule and a cluster imitating a surface and the GAMESS is used to decompose the molecular interaction energy into various energy terms : electrostatic, exchange, polarization, charge-transfer and others. It is found that the charge-transfer term is the largest in the above interaction terms for molecular interactions between CO^2 and a cluster of MgO (electron charge is transferred from the surface to the CO^2 molecule) ; therefore, Ca atoms, which have smaller electronegativity than Mg atoms, are selected to enhance the charge-transfer effect from surface to the CO^2 atom. A partial exchange of Mg atoms with Ca atoms resulted in lower potential energy for adsorption of CO^2 on the modified surface as expected, which suggests that the proposed method will be a rational tool for the evaluation of atoms to be modified.

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  1. 第5回 分子シミュレーションスクール

    2014/10/14 - 2014/10/17

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    分子シミュレーション研究会が主催するウィンタースクールで講師を務める

  2. 研究セミナー

    2014/11/03 -

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    Institute of organic chemistry and biochemistry, Academy of Science (チェコ共和国) において研究に関するセミナーを実施

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  1. 水の気液界面に対するプロトンの親和性に対する量子化学的研究

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    水の気液界面に対するプロトンの親和性を量子化学計算と溶液論を結合した新規な方法によって研究し、プロトンの表面への吸着の自由エネルギーを解析した。

  2. 量子化学計算によるモノエタノールアミン水溶液の 二酸化炭素吸収反応の自由エネルギー解析

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    量子化学計算と統計力学を結合した新規な方法によって、モノエタノールアミン水溶液への二酸化炭素の吸蔵のメカニズムを明らかににするとともに、新規な二酸化炭素の吸蔵溶液の設計、開発をめざす。