KOBAYASHI, Masato

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KOBAYASHI, Masato
Associate Professor
Faculty of Science, Hokkaido University
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Contact

k-masato atmark sci.hokudai.ac.jp

TAKETSUGU, Tetsuya Group
Principal Investigator
Faculty Members
Postdoctoral Fellows
Research Collaborators
Staff

About the Research

Research Theme

Elucidating molecules and reactions with computational chemistry and data science

Keyword

Theoretical Chemistry, Quantum Chemistry, Electronic Structure Theory, Computational Chemistry, Data Science
Research Outline

Our goal is to predict structure, properties, and reactions of materials with computer.
Every material consists of electrons and nuclei. Very small substance such as electron behaves according to “quantum mechanics.” If we can solve the Schroedinger equation, which is the basic equation of the quantum mechanics, on computers, we can achieve our goal! But, it is not so easy. The number of electrons tructable in a calculation is limited because even the simplest method requires the computational time proportional to the 3rd power of the number of electrons. We are tackling to the prediction of the behavior of huge molecules (over 1 million atom in some cases) by using the divide-and-conquer (DC) method, which is an advanced computational technique, and massively parallel computers like K computer.
It is, however, still difficult to describe the real chemical world involving Avogadro number atoms. So, we are importing “informatics” and/or “artificial intelligence” and are trying to elucidate and predict the catalytic reaction mechanisms and efficiency.

Representative Research Achievements

  • A Combined Automated Reaction Pathway Searches and Sparse Modeling Analysis for Catalytic Properties of Lowest Energy Twins of Cu13
    T. Iwasa, T. Sato, M. Takagi, M. Gao, A. Lyalin, M. Kobayashi, K.-i. Shimizu, S. Maeda, and T. Taketsugu, J. Phys. Chem. A, 2019, 123, 210-217
    DOI: 10.1021/acs.jpca.8b08868
  • Automated Error Control in Divide-and-Conquer Self-Consistent Field Calculations
    M. Kobayashi, T. Fujimori, and T. Taketsugu, J. Comput. Chem., 2018, 38, 909-916. (Cover Article)
    DOI: 10.1002/jcc.25174
  • Divide-and-Conquer Hartree–Fock–Bogoliubov Method and Its Application to Conjugated Diradical Systems
    M. Kobayashi and T. Taketsugu, Chem. Lett., 2016, 45, 1268-1270
    DOI: 10.1246/cl.160699
  • Three Pillars for Realizing Quantum Mechanical Molecular Dynamics Simulations of Huge Systems: Divide-and-Conquer, Density Functional Tight-Binding, and Massively Parallel Computation
    H. Nishizawa, Y. Nishimura, M. Kobayashi, S. Irle, and H. Nakai, J. Comput. Chem., 2016, 37, 1983-1992
    DOI: 10.1002/jcc.24419
  • Alternative Linear-Scaling Methodology for the Second-Order Møller-Plesset Perturbation Calculation Based on the Divide-and-Conquer Method
    M. Kobayashi, Y. Imamura, and H. Nakai, J. Chem. Phys., 2007, 127, 074103
    DOI: 10.1063/1.2761878

Related Research

Publications

2024

  • Theoretical Design and Synthesis of Caged Compounds Using X-Ray-Triggered Azo Bond Cleavage
    K. Ogawara, O. Inanami, H. Takakura, K. Saita, K. Nakajima, S. Kumar, N. Ieda, M. Kobayashi, T. Taketsugu, M. Ogawa, Advanced Science, 2024, ,
    DOI: 10.1002/advs.202306586

2023

  • Reproducing the Reaction Route Map on the Shape Space from Its Quotient by the Complete Nuclear Permutation-Inversion Group
    H. Teramoto, T. Saito, M. Aoki, B. Murayama, M. Kobayashi, T. Nakamura, T. Taketsugu, J. Chem. Theory Comput., 2023, 19, 17, 5886–5896
    DOI: 10.1021/acs.jctc.3c00500
  • Computational Survey of Humin Formation from 5-(hydroxymethyl)furfural under Basic Conditions
    K. Tashiro, M. Kobayashi, K. Nakajima, T. Taketsugu, RSC Advances, 2023, 13, 16293-16299
    DOI: 10.1039/d3ra02870d
  • Time-Dependent Hartree-Fock-Bogoliubov Method for Molecular Systems: An Alternative Excited-State Methodology Including Static Electron Correlation
    M. Nishida, T. Akama, M. Kobayashi, T. Taketsugu, Chemical Physics Letters, 2023, 816, 140386
    DOI: 10.1016/j.cplett.2023.140386
  • Divide-and-Conquer Linear-Scaling Quantum Chemical Computations
    H. Nakai, M. Kobayashi, T. Yoshikawa, J. Seino, Y. Ikabata, Y. Nishimura, J. Phys. Chem. A, 2023, 127, 3, 589–618
    DOI: 10.1021/acs.jpca.2c06965

2022

  • Ligand Release from Silicon Phthalocyanine Dyes Triggered by X-Ray Irradiation
    H. Takakura, S. Matsuhiro, O. Inanami, M. Kobayashi, K. Saita, M. Yamashita, K. Nakajima, M. Suzuki, N. Miyamoto, T. Taketsugu, M. Ogawa, Org. Biomol. Chem., 2022, 20, 7270-7277
    DOI: 10.1039/d2ob00957a
  • Effective Photosensitization in Excited-State Equilibrium: Brilliant Luminescence of Tb-III Coordination Polymers Through Ancillary Ligand Modifications
    Y. Kitagawa, R. Moriake, T. Akama, K. Saito, K. Aikawa, S. Shoji, K. Fushimi, M. Kobayashi, T. Taketsugu, Y. Hasegawa, ChemPlusChem, 2022, ,
    DOI: 10.1002/cplu.202200151
  • Asymmetric Lumino-Transformer: Circularly Polarized Luminescence of Chiral Eu(III) Coordination Polymer with Phase-Transition Behavior
    M. Tsurui, Y. Kitagawa, S. Shoji, H. Ohmagari, M. Hasegawa, M. Gon, K. Tanaka, M. Kobayashi, T. Taketsugu, K. Fushimi, Y. Hasegawa, J. Phys. Chem. B, 2022, 126, 3799-3807
    DOI: 10.1021/acs.jpcb.2c01639
  • Practical Electronic Ground-and Excited-State Calculation Method for Lanthanide Complexes Based on Frozen Core Potential Approximation to 4f Electrons
    M. Kobayashi, Y. Oba, T. Akama, T. Taketsugu, Journal of Mathematical Chemistry, 2022, ,
    DOI: 10.1007/s10910-022-01356-5
  • Axial-Ligand-Cleavable Silicon Phthalocyanines Triggered by Near-Infrared Light Toward Design of Photosensitizers for Photoimmunotherapy
    H. Takakura, S. Matsuhiro, M. Kobayashi, Y. Goto, M. Harada, T. Taketsugu, M. Ogawa, Journal of Photochemistry and Photobiology a-Chemistry, 2022, 426,
    DOI: 10.1016/j.jphotochem.2021.113749

2021

  • Automatic Determination of Buffer Region in Divide-Anc-Conquer Quantum Chemical Calculations
    M. Kobayashi, T. Fujimori, T. Taketsugu, Journal of Computer Chemistry-Japan, 2021, 20, 48-59
    DOI: 10.2477/jccj.2021-0025
  • Energy-Based Automatic Determination of Buffer Region in the Divide-and-Conquer Second-Order Moller-Plesset Perturbation Theory
    T. Fujimori, M. Kobayashi, T. Taketsugu, Journal of Computational Chemistry, 2021, 42, 620-629
    DOI: 10.1002/jcc.26486
  • Coordination Geometrical Effect on Ligand-to-Metal Charge Transfer-Dependent Energy Transfer Processes of Luminescent Eu(III) Complexes
    P. P. F. da Rosa, S. Miyazaki, H. Sakamoto, Y. Kitagawa, K. Miyata, T. Akama, M. Kobayashi, K. Fushimi, K. Onda, T. Taketsugu, Y. Hasegawa, J. Phys. Chem. A, 2021, 125, 209-217
    DOI: 10.1021/acs.jpca.0c09337

2020

  • All-Electron Relativistic Spin-Orbit Multireference Computation to Elucidate the Ground State of CeH
    Y. Kondo, Y. Goto, M. Kobayashi, T. Akama, T. Noro, T. Taketsugu, Phys. Chem. Chem. Phys., 2020, 22, 27157-27162
    DOI: 10.1039/d0cp05070a
  • Theoretical and Experimental Studies on the Near-Infrared Photoreaction Mechanism of a Silicon Phthalocyanine Photoimmunotherapy Dye: Photoinduced Hydrolysis by Radical Anion Generation
    M. Kobayashi, M. Harada, H. Takakura, K. Ando, Y. Goto, T. Tsuneda, M. Ogawa, T. Taketsugu, ChemPlusChem, 2020, 85, 1959-1963
    DOI: 10.1002/cplu.202000338

2019

  • Combined Automated Reaction Pathway Searches and Sparse Modeling Analysis for Catalytic Properties of Lowest Energy Twins of Cu13
    T. Iwasa, T. Sato, M. Takagi, M. Gao, A. Lyalin, M. Kobayashi, K. Shimizu, S. Maeda, T. Taketsugu, J. Phys. Chem. A, 2019, 123, 210-217
    DOI: 10.1021/acs.jpca.8b08868