Researcher basic information

• PhD (Science), Waseda University, Mar. 2007

• https://researchmap.jp/masato.kobayashi?lang=en

• https://orcid.org/0000-0002-4001-3581
• https://jglobal.jst.go.jp/detail?JGLOBAL_ID=200901005800017432
• http://sites.google.com/site/chemistmasatokobayashi/

• https://orcid.org/0000-0002-4001-3581

• 200901005800017432

• electronic structure theory
• materials informatics
• catalyst informatics
• chemoinformatics
• Theoretical Chemistry
• Quantum Chemistry

• Nanotechnology/Materials, Fundamental physical chemistry, Theoretical Chemistry

• Bachelor's degree program, School of Science
• Master's degree program, Graduate School of Chemical Sciences and Engineering
• Doctoral (PhD) degree program, Graduate School of Chemical Sciences and Engineering

Research activity information

• 2012, 2nd CMSI Workshop, Excellent Poster Award
  Japan
• 2009, Society of Computer Chemistry, Japan, Yoshida Award (Excellent Paper Award)
  Japan
• 2008, WATOC2008, Poster Prize

• Constrained Møller–Plesset perturbation theory for charge transfer states
  Shohei Osaki; Masato Kobayashi; Toru Matsui; Kiyoshi Yagi
  The Journal of Chemical Physics, 164, 23, AIP Publishing, 15 Jun. 2026, [Peer-reviewed], [International Magazine]
  English, Scientific journal, We propose a constrained Møller–Plesset second-order perturbation theory (CMP2) that incorporates electron correlation into the constrained Hartree–Fock (CHF) framework. In CMP2, the CHF solution is employed as the reference state, and a common Lagrange multiplier is introduced for both the zeroth-order and constraint Hamiltonians, enabling the inclusion of correlation effects with minimal modification to existing MP2 implementations. Two schemes are developed for determining the Lagrange multiplier: (i) CMP2-i (iterative), which iteratively updates the multiplier until the MP2 electron density satisfies the constraint, and (ii) CMP2-s (single-shot), which performs a single MP2 calculation using a CHF reference that satisfies the constraint at the Hartree–Fock level. The methods are applied to an intramolecular charge-transfer reaction of the 1,3-dinitrobenzene anion radical. CMP2-s significantly reduces computational cost while reproducing relative energy profiles comparable with CMP2-i. In addition, adiabatic energy profiles obtained with configuration interaction calculations based on CMP2 (CMP2-CI) are in good agreement with those from extended multistate complete active space second-order perturbation theory (XMS-CASPT2), demonstrating that the present approach provides a practical and efficient extension of constrained electronic structure methods to the post-Hartree–Fock level.
• Antenna Tuning in Photoredox Nitric Oxide Releasers for Potent Photovasodilation
  Daisuke Saitoh; Sae Kitamura; Naoya Ieda; Kyoya Oyama; Yuhei Ohta; Yuji Hotta; Masato Kobayashi; Mei Harada; Mikako Ogawa; Mitsuyasu Kawaguchi; Kazunori Kimura; Tetsuya Taketsugu; Hidehiko Nakagawa
  Journal of Medicinal Chemistry, 69, 12, 14761, 14773, American Chemical Society (ACS), 11 Jun. 2026, [Peer-reviewed], [International Magazine]
  English, Scientific journal
• Rigor of Exact Lumping: Tailoring Multiscale Rate Equations to an Observation Timescale
  Yutaka NAGAHATA; Masato KOBAYASHI; Mikito TODA; Satoshi MAEDA; Tetsuya TAKETSUGU; Tamiki KOMATSUZAKI
  Journal of Computer Chemistry, Japan, 25, 1, 41, 44, Society of Computer Chemistry Japan, 2026, [Peer-reviewed], [Invited], [Domestic magazines]
  English, Scientific journal
• Doublet Charge Transfer Emission of Cerium(III) Complexes with Strong Electron-Accepting Ligands
  Toranosuke Tomikawa; Kenichiro Saita; Yuriko Ono; Tomoko Akama; Mengfei Wang; Sunao Shoji; Masato Kobayashi; Koji Fushimi; Takayuki Nakanishi; Tetsuya Taketsugu; Yasuchika Hasegawa; Yuichi Kitagawa
  The Journal of Physical Chemistry Letters, 16, 49, 12655, 12660, American Chemical Society (ACS), 04 Dec. 2025, [Peer-reviewed], [International Magazine]
  English, Scientific journal
• Divide-and-Conquer Extended Tight-Binding Molecular Dynamics: A General-Purpose, Very Large-Scale Quantum Molecular Dynamics Method
  Masatsugu Nishida; Kotaro Fujiwara; Tetsuya Taketsugu; Masato Kobayashi
  Journal of Computational Chemistry, 46, 28, e70255, Wiley, 24 Oct. 2025, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
  English, Scientific journal, ABSTRACT
  
  We have combined the linear‐scaling divide‐and‐conquer (DC) method with the semi‐empirical extended tight‐binding (xTB) method to develop a general‐purpose large‐scale quantum molecular dynamics simulation platform called DCxTBMD. Although the DC method is a fragmentation‐based acceleration scheme, it is possible to perform highly accurate calculations even when adopting formal grid‐based fragmentation, thanks to the mechanism called the buffer region. The program was developed by incorporating xTB Hamiltonian construction modules in the xTB program into the DCDFTBK package, a DC‐based density functional tight‐binding (DFTB) calculation suite. The accuracy and computational time, including the parallel scalability, of the present method were investigated on the Japanese supercomputer Fugaku, and it was found that the present method is suitable for the efficient calculation of large systems, including multiple heteroelements. We further implemented the energy gradient of the present method to enable the molecular dynamics simulation of such systems.
• Aggregation-induced emission mechanism of styrene derivative: a theoretical study
  Aarzoo; Kenichiro Saita; Masato Kobayashi; Takao Tsuneda; Tetsuya Taketsugu; Ram Kinkar Roy
  Physical Chemistry Chemical Physics, 27, 23, 12593, 12602, Royal Society of Chemistry (RSC), 21 Jun. 2025, [Peer-reviewed], ［Internationally co-authored］, [International Magazine]
  English, Scientific journal, The AIE mechanism of the styrene derivative 4-dimethylamino-2-benzylidene malonic acid dimethyl ester (BIM) in methanol solution is theoretically investigated using SF-LC-TDDFT.
• Fragmentation-Based Linear-Scaling Method for Strongly Correlated Systems: Divide-and-Conquer Hartree–Fock–Bogoliubov Method, Its Energy Gradient, and Applications to Graphene Nano-Ribbon Systems
  Masato Kobayashi; Ryosuke Kodama; Tomoko Akama; Tetsuya Taketsugu
  Chemistry, 18 Mar. 2025, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
  Scientific journal
• Charge transfer emission between π- and 4f-orbitals in a trivalent europium complex
  Yuichi Kitagawa; Toranosuke Tomikawa; Kota Aikawa; Shiori Miyazaki; Tomoko Akama; Masato Kobayashi; Mengfei Wang; Sunao Shoji; Koji Fushimi; Kiyoshi Miyata; Yuichi Hirai; Takayuki Nakanishi; Ken Onda; Tetsuya Taketsugu; Yasuchika Hasegawa
  Communications Chemistry, 28 Jan. 2025, [Peer-reviewed], [International Magazine]
  English, Scientific journal
• Piperazine based pH-responsive cyanine dyes for cancer cell photoacoustic imaging
  Koki Tsuchiya; Hideo Takakura; Kohei Nakajima; Naoya Ieda; Takashi Kaneko; Takeshi Hirasawa; Masato Kobayashi; Yoshihisa Yamaoka; Miya Ishihara; Tetsuya Taketsugu; Mikako Ogawa
  Journal of Photochemistry and Photobiology A: Chemistry, 453, 115634, 115634, Elsevier BV, Aug. 2024, [Peer-reviewed], [International Magazine]
  Scientific journal
• Molecular Dynamics‐Based Conformational Simulation Method for Analysis of Arrival Time Distributions in Ion Mobility Mass Spectrometry
  Keisuke Tashiro; Yuki Ide; Tetsuya Taketsugu; Kazuaki Ohara; Kentaro Yamaguchi; Masato Kobayashi; Yasuhide Inokuma
  Advanced Theory and Simulations, Wiley, 27 Jul. 2024, [Peer-reviewed], [Corresponding author], [International Magazine]
  English, Scientific journal, Abstract
  
  Ion mobility‐mass spectrometry (IM‐MS) has recently contributed to the structural analysis of molecules, including supramolecules and proteins, by determining the ion arrival time distributions correlated with the collision cross sections (CCSs), as well as the mass‐to‐charge ratios. However, its application range is still limited owing to the lack of general CCSs simulation methods based on possible molecular conformations. Here, a molecular dynamics‐based conformational search method for simulating CCS distributions using projection approximation is reported. As a case study, the gas‐phase conformations of the sodium adducts of conformationally flexible polyketones with 3,3‐dimethylpentane‐2,4‐dione as the monomer are analyzed. The sodium adduct of the hexamer (m/z 781.4 for [1 + Na]⁺) showed a monomodal arrival time distribution, but that of the octamer sodium adduct (m/z 1033.5 for [2 + Na]⁺) is multimodal. The conformational analysis indicated an unimodal CCS distribution of simulated [1 + Na]⁺ conformations in which the sodium cation is mainly bound at the chain terminal. Conversely, four clusters of conformations are obtained for [2 + Na]⁺ based on the Na⁺‐coordination sites, which qualitatively reproduced the observed CCS distribution. This approach will extend the utility of IM‐MS for the conformational analysis of flexible molecules in the gas phase.
• Chiral Tetrakis Eu(III) Complexes with Ammonium Cations for Improved Circularly Polarized Luminescence.
  Makoto Tsurui; Ryohei Takizawa; Yuichi Kitagawa; Mengfei Wang; Masato Kobayashi; Tetsuya Taketsugu; Yasuchika Hasegawa
  Angewandte Chemie (International ed. in English), e202405584, 26 May 2024, [Peer-reviewed], [International Magazine]
  English, Scientific journal, Large dissymmetry factor of the circularly polarized luminescence (gCPL) was observed in ligand and coordination tuned chiral tetrakis europium (Eu(III)) complexes with ammonium cations. The gCPL value was estimated to be -1.54, which is the largest among chiral luminescent molecules. Through photophysical measurements, single crystal X-ray structural analyses and quantum chemical calculations, changes in the geometric and electronic structures were observed for a series of chiral tetrakis Eu(III) complexes which enhanced the gCPL value. The emission quantum yield and photosensitized energy transfer efficiencies of chiral Eu(III) complexes with ammonium cations were also larger than that with previous Cs+. Based on the systematic modifications and analyses for chiral tetrakis Eu(III) complex, effect of the ammonium cation on enhanced CPL brightness is reported.
• Development of Complete Enumeration Program for Polymer Structural Isomers: A Case of Nylon-n (n = 3-10)
  Gikyo Usuki; Takuro Tsutsumi; Kohei Hasebe; Masato Kobayashi; Keitaro Matsuoka; Tetsuya Taketsugu; Kazuki Sada
  American Chemical Society (ACS), 24 May 2024
  The enumeration of structural isomers of organic molecules using programs capable of enumerating all structural isomers for a given molecular formula has been expanding the chemical library. Here, we report the development of the program (PolyENU) that completely enumerates polymer structural isomers. PolyENU program enumerates all isomers of the repeating unit defined by a molecular formula and a functional group constituting the polymer structure. From the repeating unit of nylon 6 (C6H11NO and an amide group), 387 polymer isomers were generated by PolyENU. The enumerated polymer library includes common organic polymers such as nylon 6, polyleucine, poly(2-isopropyl-oxazoline), and poly(N-propylacrylamide), as well as many unexplored polymers. The enumeration of nylon n (n = 3-10) yielded 36,505 polymers within 44 minutes. These results clearly indicate that PolyENU expands polymer chemical space and contributes to diversity in polymer science.
• Guest-Responsive Near-Infrared-Luminescent Metal–Organic Cage Organized by Porphyrin Dyes and Yb(III) Complexes
  Shota Hosoya; Sunao Shoji; Takayuki Nakanishi; Masato Kobayashi; Mengfei Wang; Koji Fushimi; Tetsuya Taketsugu; Yuichi Kitagawa; Yasuchika Hasegawa
  Inorganic Chemistry, American Chemical Society (ACS), 21 May 2024, [Peer-reviewed], [International Magazine]
  Scientific journal
• An encompassed representation of timescale hierarchies in first-order reaction network
  Yutaka Nagahata; Masato Kobayashi; Mikito Toda; Satoshi Maeda; Tetsuya Taketsugu; Tamiki Komatsuzaki
  Proceedings of the National Academy of Sciences, 121, 21, Proceedings of the National Academy of Sciences, 17 May 2024, [Peer-reviewed], [International Magazine]
  Scientific journal, Complex networks are pervasive in various fields such as chemistry, biology, and sociology. In chemistry, first-order reaction networks are represented by a set of first-order differential equations, which can be constructed from the underlying energy landscape. However, as the number of nodes increases, it becomes more challenging to understand complex kinetics across different timescales. Hence, how to construct an interpretable, coarse-graining scheme that preserves the underlying timescales of overall reactions is of crucial importance. Here, we develop a scheme to capture the underlying hierarchical subsets of nodes, and a series of coarse-grained (reduced-dimensional) rate equations between the subsets as a function of time resolution from the original reaction network. Each of the coarse-grained representations guarantees to preserve the underlying slow characteristic timescales in the original network. The crux is the construction of a lumping scheme incorporating a similarity measure in deciphering the underlying timescale hierarchy, which does not rely on the assumption of equilibrium. As an illustrative example, we apply the scheme to four-state Markovian models and Claisen rearrangement of allyl vinyl ether (AVE), and demonstrate that the reduced-dimensional representation accurately reproduces not only the slowest but also the faster timescales of overall reactions although other reduction schemes based on equilibrium assumption well reproduce the slowest timescale but fail to reproduce the second-to-fourth slowest timescales with the same accuracy. Our scheme can be applied not only to the reaction networks but also to networks in other fields, which helps us encompass their hierarchical structures of the complex kinetics over timescales.
• Development of a red-shifted photosensitizer for near-infrared photoimmunotherapy of cancer
  Yuto Goto; Kanta Ando; Hideo Takakura; Kohei Nakajima; Masato Kobayashi; Osamu Inanami; Tetsuya Taketsugu; Mikako Ogawa
  Journal of Photochemistry and Photobiology, 20, 100230, 100230, Elsevier BV, Apr. 2024, [Peer-reviewed], [International Magazine]
  English, Scientific journal
• Theoretical Design and Synthesis of Caged Compounds Using X‐Ray‐Triggered Azo Bond Cleavage
  Koki Ogawara; Osamu Inanami; Hideo Takakura; Kenichiro Saita; Kohei Nakajima; Sonu Kumar; Naoya Ieda; Masato Kobayashi; Tetsuya Taketsugu; Mikako Ogawa
  Advanced Science, Wiley, 15 Jan. 2024, [Peer-reviewed], [International Magazine]
  English, Scientific journal, Abstract
  
  Caged compounds are frequently used in life science research. However, the light used to activate them is commonly absorbed and scattered by biological materials, limiting their use to basic research in cells or small animals. In contrast, hard X‐rays exhibit high bio‐permeability due to the difficulty of interacting with biological molecules. With the main goal of developing X‐ray activatable caged compounds, azo compounds are designed and synthesized with a positive charge and long π‐conjugated system to increase the reaction efficiency with hydrated electrons. The azo bonds in the designed compounds are selectively cleaved by X‐ray, and the fluorescent substance Diethyl Rhodamine is released. Based on the results of experiments and quantum chemical calculations, azo bond cleavage is assumed to occur via a two‐step process: a two‐electron reduction of the azo bond followed by N─N bond cleavage. Cellular experiments also demonstrate that the azo bonds can be cleaved intracellularly. Thus, caged compounds that can be activated by an azo bond cleavage reaction promoted by X‐ray are successfully generated.
• Novel Descriptor of Potential Energy Surface: Persistent Homology of Reaction Route Map
  Burai MURAYAMA; Masato KOBAYASHI; Masamitsu AOKI; Suguru ISHIBASHI; Takuya SAITO; Takenobu NAKAMURA; Hiroshi TERAMOTO; Tetsuya TAKETSUGU
  Journal of Computer Chemistry, Japan, 23, 1, 33, 36, Society of Computer Chemistry Japan, 2024, [Peer-reviewed], [Domestic magazines]
  English, Scientific journal
• Reproducing the Reaction Route Map on the Shape Space from Its Quotient by the Complete Nuclear Permutation-Inversion Group
  Hiroshi Teramoto; Takuya Saito; Masamitsu Aoki; Burai Murayama; Masato Kobayashi; Takenobu Nakamura; Tetsuya Taketsugu
  Journal of Chemical Theory and Computation, 19, 17, 5886, 5896, American Chemical Society (ACS), 29 Aug. 2023
  Scientific journal
• Characterizing Reaction Route Map of Realistic Molecular Reactions Based on Weight Rank Clique Filtration of Persistent Homology
  Burai Murayama; Masato Kobayashi; Masamitsu Aoki; Suguru Ishibashi; Takuya Saito; Takenobu Nakamura; Hiroshi Teramoto; Tetsuya Taketsugu
  Journal of Chemical Theory and Computation, 19, 15, 5007, 5023, American Chemical Society (ACS), 03 Jul. 2023
  Scientific journal
• X線によるアゾ結合の開裂により活性化されるケージド化合物の開発
  小河原 浩輝; 高倉 栄男; 中島 孝平; 斉田 謙一郎; Kumar Sonu; 小林 正人; 武次 徹也; 稲波 修; 小川 美香子
  JSMI Report, 16, 2, 64, 64, 日本分子イメージング学会, May 2023
  Japanese
• Time-dependent Hartree–Fock–Bogoliubov method for molecular systems: An alternative excited-state methodology including static electron correlation
  Masatsugu Nishida; Tomoko Akama; Masato Kobayashi; Tetsuya Taketsugu
  Chemical Physics Letters, 816, 140386, 140386, Elsevier BV, Apr. 2023
  Scientific journal
• Divide-and-Conquer Linear-Scaling Quantum Chemical Computations
  Hiromi Nakai; Masato Kobayashi; Takeshi Yoshikawa; Junji Seino; Yasuhiro Ikabata; Yoshifumi Nishimura
  The Journal of Physical Chemistry A, 127, 3, 589, 618, American Chemical Society (ACS), 11 Jan. 2023, [Peer-reviewed]
  English, Scientific journal
• Computational survey of humin formation from 5-(hydroxymethyl)furfural under basic conditions
  Keisuke Tashiro; Masato Kobayashi; Kiyotaka Nakajima; Tetsuya Taketsugu
  RSC Advances, 13, 24, 16293, 16299, Royal Society of Chemistry (RSC), 2023
  Scientific journal
• Characterizing Reaction Route Map of Realistic Molecular Reactions based on Weight Rank Clique Filtration of Persistent Homology
  Burai Murayama; Masato Kobayashi; Masamitsu Aoki; Suguru Ishibashi; Takuya Saito; Takenobu Nakamura; Hiroshi Teramoto; Tetsuya Taketsugu
  Nov. 2022, [Corresponding author]
  English, Scientific journal
• Ligand release from silicon phthalocyanine dyes triggered by X-ray irradiation.
  Hideo Takakura; Shino Matsuhiro; Osamu Inanami; Masato Kobayashi; Kenichiro Saita; Masaki Yamashita; Kohei Nakajima; Motofumi Suzuki; Naoki Miyamoto; Tetsuya Taketsugu; Mikako Ogawa
  Organic & biomolecular chemistry, 20, 36, 16 Aug. 2022, [Peer-reviewed], [International Magazine]
  English, Scientific journal
• Effective Photosensitization in Excited‐State Equilibrium: Brilliant Luminescence of Tb ^III Coordination Polymers Through Ancillary Ligand Modifications
  Yuichi Kitagawa; Ryoma Moriake; Tomoko Akama; Koki Saito; Kota Aikawa; Sunao Shoji; Koji Fushimi; Masato Kobayashi; Tetsuya Taketsugu; Yasuchika Hasegawa
  ChemPlusChem, 87, 10, Wiley, 13 Jul. 2022, [Peer-reviewed]
  Scientific journal
• Axial-ligand-cleavable silicon phthalocyanines triggered by near-infrared light toward design of photosensitizers for photoimmunotherapy
  Hideo Takakura; Shino Matsuhiro; Masato Kobayashi; Yuto Goto; Mei Harada; Tetsuya Taketsugu; Mikako Ogawa
  Journal of Photochemistry and Photobiology A: Chemistry, 426, 113749, 113749, Apr. 2022, [Peer-reviewed]
  English, Scientific journal
• Development of Accurate Electron Correlation Calculation Method Using Annealing Machine and Machine Learning
  Masato KOBAYASHI; Ryo YONEYAMA; Sayoko NOJO; Keisuke TASHIRO; Tetsuya TAKETSUGU
  Journal of Computer Chemistry, Japan, 21, 4, 96, 98, Society of Computer Chemistry Japan, 2022
  English, Scientific journal
• Practical electronic ground- and excited-state calculation method for lanthanide complexes based on frozen core potential approximation to 4f electrons
  Masato Kobayashi; Yuta Oba; Tomoko Akama; Tetsuya Taketsugu
  J. Math. Chem., 61, 2, 322, 334, Springer Science and Business Media LLC, 2022, [Peer-reviewed], [Lead author, Corresponding author]
  English, Scientific journal
• Asymmetric Lumino-Transformer: Circularly Polarized Luminescence of Chiral Eu(III) Coordination Polymer with Phase-Transition Behavior
  Makoto Tsurui; Yuichi Kitagawa; Sunao Shoji; Hitomi Ohmagari; Miki Hasegawa; Masayuki Gon; Kazuo Tanaka; Masato Kobayashi; Tetsuya Taketsugu; Koji Fushimi; Yasuchika Hasegawa
  J. Phys. Chem. B, 126, 20, 3799, 3807, American Chemical Society (ACS), 2022, [Peer-reviewed]
  English, Scientific journal
• Predicting activity and activation factor of catalytic reactions using machine learning
  Masato Kobayashi
  Computational and Data-Driven Chemistry Using Artificial Intelligence, 217, 229, Elsevier, 2022, [Peer-reviewed], [Invited], [Lead author, Last author, Corresponding author], [International Magazine]
  English, In book
• Multi-objective Spatiotemporal Optimization of Transportation and Power Management by using Multiple Electric Vehicles in Nanogrid Networks
  Hiroshi Uchigaito; Mamoru Okamoto; Gleb Astashkin; Yuki Furubayashi; Norihiro Obata; Thantip Krasienapibal; Hiroshi Teramoto; Yuta Mizuno; Masato Kobayashi; Atsuyoshi Nakamura; Tamiki Komatsuzaki; Takashi Takemoto
  2021 IEEE Electrical Power and Energy Conference (EPEC), 365, 372, 22 Oct. 2021, [Peer-reviewed]
  English, International conference proceedings
• Automatic Determination of Buffer Region in Divide-anc-Conquer Quantum Chemical Calculations
  Masato KOBAYASHI; Toshikazu FUJIMORI; Tetsuya TAKETSUGU
  Journal of Computer Chemistry, Japan, 20, 2, 48, 59, Society of Computer Chemistry Japan, Sep. 2021, [Peer-reviewed], [Invited], [Lead author, Corresponding author], [Domestic magazines]
  Japanese, Scientific journal
• Application of Quantum Chemical Calculation and Informatics to Catalyst Development
  KOBAYASHI, Masato
  マテリアルズインフォマティクスのためのデータ作成とその解析、応用事例, 401, 408, Jul. 2021, [Peer-reviewed], [Invited], [Lead author, Last author, Corresponding author], [Domestic magazines]
  Japanese, In book
• Energy‐based automatic determination of buffer region in the divide‐and‐conquer second‐order Møller–Plesset perturbation theory
  Toshikazu Fujimori; Masato Kobayashi; Tetsuya Taketsugu
  Journal of Computational Chemistry, 42, 9, 620, 629, Wiley, 03 Feb. 2021, [Peer-reviewed], [Corresponding author], [International Magazine]
  English, Scientific journal

  
  Preprint
• Coordination Geometrical Effect on Ligand-to-Metal Charge Transfer-Dependent Energy Transfer Processes of Luminescent Eu(III) Complexes
  Pedro Paulo Ferreira da Rosa; Shiori Miyazaki; Haruna Sakamoto; Yuichi Kitagawa; Kiyoshi Miyata; Tomoko Akama; Masato Kobayashi; Koji Fushimi; Ken Onda; Tetsuya Taketsugu; Yasuchika Hasegawa
  The Journal of Physical Chemistry A, 125, 1, 209, 217, American Chemical Society (ACS), 14 Jan. 2021, [Peer-reviewed], [International Magazine]
  Scientific journal
• Front Cover: Theoretical and Experimental Studies on the Near‐Infrared Photoreaction Mechanism of a Silicon Phthalocyanine Photoimmunotherapy Dye: Photoinduced Hydrolysis by Radical Anion Generation (ChemPlusChem 9/2020)
  Masato Kobayashi; Mei Harada; Hideo Takakura; Kanta Ando; Yuto Goto; Takao Tsuneda; Mikako Ogawa; Tetsuya Taketsugu
  ChemPlusChem, 85, 9, 1949, 1949, Wiley, Sep. 2020
  Scientific journal
• Theoretical and Experimental Studies on the Near‐Infrared Photoreaction Mechanism of a Silicon Phthalocyanine Photoimmunotherapy Dye: Photoinduced Hydrolysis by Radical Anion Generation
  Masato Kobayashi; Mei Harada; Hideo Takakura; Kanta Ando; Yuto Goto; Takao Tsuneda; Mikako Ogawa; Tetsuya Taketsugu
  ChemPlusChem, 85, 9, 1959, 1963, Wiley, Sep. 2020, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
  English, Scientific journal

  
  Preprint
• データ科学を活用した触媒反応の活性予測、活性因子の特定
  小林正人
  マテリアルステージ, 20, 1, 42, 48, Apr. 2020, [Invited], [Lead author, Last author, Corresponding author]
  Japanese
• All-electron relativistic spin–orbit multireference computation to elucidate the ground state of CeH
  Yusuke Kondo; Yuri Goto; Masato Kobayashi; Tomoko Akama; Takeshi Noro; Tetsuya Taketsugu
  Physical Chemistry Chemical Physics, 22, 46, 27157, 27162, Royal Society of Chemistry (RSC), 2020
  Scientific journal,

  The all-electron relativistic spin–orbit multiconfiguration/multireference computations with the Sapporo basis sets were carried out to elucidate the characters of the low-lying quasi-degenerate electronic states for the CeH diatomic molecule.

• Machine Learning Applied to Yield or Activation Factor Prediction for Catalytic Reactions
  KOBAYASHI Masato
  Chemistry and Chemical Industry, 72, 5, 422, 422, May 2019, [Peer-reviewed]
  Japanese, Scientific journal
• Hartree-Fock(-Roothaan)法のエッセンス
  小林 正人
  フロンティア（理論化学会機関誌）, 1, 2, 5, 20, Apr. 2019, [Peer-reviewed], [Invited]
  Japanese, Scientific journal

  
  Preprint
• 量子化学計算を用いた光免疫療法における細胞障害メカニズムの検討
  原田 芽生; 小林 正人; 安藤 完太; 高倉 栄男; 武次 徹也; 小川 美香子
  日本薬学会年会要旨集, 139年会, 2, 80, 80, (公社)日本薬学会, Mar. 2019
  Japanese
• Dispersion Interaction and Crystal Packing Realize an Ultralong C–C Single Bond: A Theoretical Study on Dispirobis(10-methylacridan) Derivatives
  Yusuke Kuroda; Masato Kobayashi; Tetsuya Taketsugu
  Chemistry Letters, 48, 2, 137, 139, The Chemical Society of Japan, 05 Feb. 2019, [Peer-reviewed], [Corresponding author]
  English, Scientific journal
• Analysis and Prediction for Metal Nanocluster Catalyst Systems Using High-Throughput Quantum Chemical Calculation Techniques and Informatics
  KOBAYASHI Masato
  Ensemble, 21, 1, 22, 28, Jan. 2019, [Peer-reviewed], [Domestic magazines]
  Japanese, Scientific journal
• Large-scale quantum chemical calculation
  Ishimura, K.; Kobayashi, M.
  The Art of High Performance Computing for Computational Science, 2, 2019
  Scientific journal
• Surface Adsorption Model Calculation Database and Its Application to Activity Prediction of Heterogeneous Catalysts
  Masato KOBAYASHI; Haruka ONODA; Yusuke KURODA; Tetsuya TAKETSUGU
  Journal of Computer Chemistry, Japan, 18, 5, 251, 253, Society of Computer Chemistry Japan, 2019, [Peer-reviewed], [Lead author, Corresponding author], [Domestic magazines]
  Scientific journal
• Combined Automated Reaction Pathway Searches and Sparse Modeling Analysis for Catalytic Properties of Lowest Energy Twins of Cu₁₃
  Takeshi Iwasa; Takaaki Sato; Makito Takagi; Min Gao; Andrey Lyalin; Masato Kobayashi; Ken-ichi Shimizu; Satoshi Maeda; Tetsuya Taketsugu
  J. Phys. Chem. A, 123, 1, 210, 217, American Chemical Society ({ACS}), Jan. 2019, [Peer-reviewed], [International Magazine]
  English, Scientific journal, In nanocatalysis, growing attention has recently been given to investigation of energetically low-lying structural isomers of atomic clusters, because some isomers can demonstrate better catalytic activity than the most stable structures. In this study, we present a comparative investigation of catalytic activity for NO dissociation of a pair of the energetically degenerated isomers of Cu13 cluster having C2 and C s symmetries. It is shown that although these isomers have similar structural, electronic, and optical properties, they can possess very different catalytic activities. The effect of isomerization between cluster isomers is considered using state-of-the-art automated reaction pathway search techniques such as an artificial force induced reaction (AFIR) method as a part of a global reaction route mapping (GRRM) strategy. This method allows effectively to locate a large number of possible reaction pathways and transition states (TSs). In total, 12 TSs for NO dissociation were obtained for Cu13, of C2, C s, as well as I h isomers. Sparse modeling analysis shows that LUMO is strongly negatively correlated with total energy of TSs. For most TSs, LUMO has the antibonding character of NO, consisting of the interaction between π* of NO and SOMO of Cu13. Therefore, an increase in the strength of interaction between NO molecule and Cu13 cluster causes the rise in energy of the LUMO, resulting in lowering of the TS energy for NO dissociation. The combination of the automated reaction pathway search technique and sparse modeling represents a powerful tool for analysis and prediction of the physicochemical properties of atomic clusters, especially in the regime of structural fluxionality, where traditional methods based on random geometry search analyses are difficult.

  
  Preprint
• All-electron relativistic computations on the low-lying electronic states, bond length, and vibrational frequency of CeF diatomic molecule with spin–orbit coupling effects
  Yusuke Kondo; Masato Kobayashi; Tomoko Akama; Takeshi Noro; Tetsuya Taketsugu
  Journal of Computational Chemistry, 39, 16, 964, 972, John Wiley and Sons Inc., 15 Jun. 2018, [Peer-reviewed], [International Magazine]
  English, Scientific journal
• Automated error control in divide-and-conquer self-consistent field calculations
  Masato Kobayashi; Toshikazu Fujimori; Tetsuya Taketsugu
  Journal of Computational Chemistry, 39, 15, 909, 916, John Wiley and Sons Inc., 05 Jun. 2018, [Peer-reviewed], [International Magazine]
  English, Scientific journal
• Application of Informatics Techniques to Quantum Chemical Calculations of Catalyst and Surface Adsorption Systems
  KOBAYASHI Masato
  Chemical Industry, 69, 1, 27, 32, Jan. 2018, [Peer-reviewed], [Invited], [Domestic magazines]
  Japanese, Scientific journal
• Enhanced Luminescence of Asymmetrical Seven-Coordinate Eu-III Complexes Including LMCT Perturbation
  Kei Yanagisawa; Yuichi Kitagawa; Takayuki Nakanishi; Tomoko Akama; Masato Kobayashi; Tomohiro Seki; Koji Fushimi; Hajime Ito; Tetsuya Taketsugu; Yasuchika Hasegawa
  EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, 2017, 32, 3843, 3848, Sep. 2017, [Peer-reviewed]
  English, Scientific journal
• Divide-and-Conquer Hartree-Fock-Bogoliubov Method and Its Application to Conjugated Diradical Systems
  Masato Kobayashi; Tetsuya Taketsugu
  CHEMISTRY LETTERS, 45, 11, 1268, 1270, Nov. 2016, [Peer-reviewed]
  English, Scientific journal
• Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation
  Hiroaki Nishizawa; Yoshifumi Nishimura; Masato Kobayashi; Stephan Irle; Hiromi Nakai
  JOURNAL OF COMPUTATIONAL CHEMISTRY, 37, 21, 1983, 1992, Aug. 2016, [Peer-reviewed]
  English, Scientific journal
• Spin-Orbit Coupling Effects on Low-lying Electronic States of PtCN/PtNC and PdCN/PdNC
  Yuriko Ono; Yusuke Kondo; Masato Kobayashi; Tetsuya Taketsugu
  CHEMISTRY LETTERS, 45, 4, 478, 480, Apr. 2016, [Peer-reviewed]
  English, Scientific journal
• Coordination phenomena of alkali metal, alkaline earth metal, and indium ions with the 1,3,6-naphthalenetrisulfonate ion in protic and aprotic solvents
  Xiaohui Chen; Masashi Hojo; Zhidong Chen; Masato Kobayashi
  JOURNAL OF MOLECULAR LIQUIDS, 214, 369, 377, Feb. 2016, [Peer-reviewed]
  English, Scientific journal
• Mechanisms of Ligand Exchange and Ligand Coupling Reactions of Sb and Te Compounds
  Masato Kobayashi; Yusuke Kuroda; Kin-ya Akiba; Tetsuya Taketsugu
  J. Comput. Chem. Jpn., 14, 6, 199, 200, Society of Computer Chemistry, Japan, Dec. 2015, [Peer-reviewed]
  Japanese, Theoretical and computational studies on the mechanisms of ligand exchange reaction (LER) and ligand coupling reaction (LCR) of hypervalent pentacoordinate Sb and tetracoordinate Te compounds were carried out. Contrary to the previous suggestion from experimentalists, the lone pair electrons of Te do not participate in LER. Also, LER of R₅Sb proceeds via a similar mechanism to that of R₄Te. As for the LCR of R₅Sb, the apical-equatorial coupling mechanism was suggested.
• Theoretical Study on the Mechanism of the Ligand Coupling Reaction of Hypervalent Pentacoordinate Antimony Compounds
  Masato Kobayashi; Yusuke Kuroda; Kin-ya Akiba; Tetsuya Taketsugu
  BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN, 88, 11, 1584, 1590, Nov. 2015, [Peer-reviewed]
  English, Scientific journal
• Seven-Coordinate Luminophores: Brilliant Luminescence of Lanthanide Complexes with C-3v Geometrical Structures
  Kei Yanagisawa; Takayuki Nakanishi; Yuichi Kitagawa; Tomohiro Seki; Tomoko Akama; Masato Kobayashi; Tetsuya Taketsugu; Hajime Ito; Koji Fushimi; Yasuchika Hasegawa
  EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, 28, 4769, 4774, Oct. 2015, [Peer-reviewed]
  English, Scientific journal
• Second-order Moller-Plesset perturbation (MP2) theory at finite temperature: relation with Surjan's density matrix MP2 and its application to linear-scaling divide-and-conquer method
  Masato Kobayashi; Tetsuya Taketsugu
  THEORETICAL CHEMISTRY ACCOUNTS, 134, 9, Aug. 2015, [Peer-reviewed]
  English, Scientific journal
• Specific coordination phenomena of alkaline earth metal ions with aromatic sulfonate ions in alcohols and binary solvents of acetonitrile-alcohols
  Xiaohui Chen; Keita Ayabe; Masashi Hojo; Zhidong Chen; Masato Kobayashi
  JOURNAL OF MOLECULAR LIQUIDS, 199, 445, 453, Nov. 2014, [Peer-reviewed]
  English, Scientific journal
• Theoretical Study on the Ligand Exchange Reactions of Hypervalent Antimony and Tellurium Compounds
  Masato Kobayashi; Kin-ya Akiba
  ORGANOMETALLICS, 33, 5, 1218, 1226, Mar. 2014, [Peer-reviewed]
  English, Scientific journal
• Gradient of molecular Hartree-Fock-Bogoliubov energy with a linear combination of atomic orbital quasiparticle wave functions
  Masato Kobayashi
  JOURNAL OF CHEMICAL PHYSICS, 140, 8, 084115, Feb. 2014, [Peer-reviewed]
  English, Scientific journal
• Conductometric and UV-visible Spectroscopic Studies on the Strong Association between Polysulfonic or Dicarboxylic Acids and Their Conjugate Anions in Acetonitrile
  Masashi Hojo; Yusuke Kondo; Kosuke Zei; Kei Okamura; Zhidong Chen; Masato Kobayashi
  BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN, 87, 1, 98, 109, Jan. 2014, [Peer-reviewed]
  English, Scientific journal
• Divide-and-conquer-based symmetry adapted cluster method: Synergistic effect of subsystem fragmentation and configuration selection
  Takeshi Yoshikawa; Masato Kobayashi; Hiromi Nakai
  INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 113, 3, 218, 223, Feb. 2013
  English, Scientific journal
• Novel Approach to Excited-State Calculations of Large Molecules Based on Divide-and-Conquer Method: Application to Photoactive Yellow Protein
  Yoshikawa, Takeshi; Kobayashi, Masato; Fujii, Atsuhiko; Nakai, Hiromi
  Journal of Physical Chemistry B, 117, 18, 5565, 5573, 2013, [Peer-reviewed]
  English, Scientific journal
• Novel Approach to Excited-State Calculations of Large Molecules Based on Divide-and-Conquer Method: Application to Photoactive Yellow Protein
  Yoshikawa, Takeshi; Kobayashi, Masato; Fujii, Atsuhiko; Nakai, Hiromi
  Journal of Physical Chemistry B, 117, 18, 5565, 5573, 2013
  Scientific journal
• Accelerating convergence in the antisymmetric product of strongly orthogonal geminals method
  Tarumi, Moto; Kobayashi, Masato; Nakai, Hiromi
  International Journal of Quantum Chemistry, 113, 3, 239, 244, 2013
  Scientific journal
• Divide-and-conquer-based quantum chemical study for interaction between HIV-1 reverse transcriptase and MK-4965 inhibitor
  Saparpakorn, Patchreenart; Kobayashi, Masato; Hannongbua, Supa; Nakai, Hiromi
  International Journal of Quantum Chemistry, 113, 4, 510, 517, 2013
  Scientific journal
• Divide-and-Conquer Electronic-Structure Study on the Mechanism of the West Nile Virus NS3 Protease Inhibitor
  Saparpakorn, Patchreenart; Kobayashi, Masato; Nakai, Hiromi
  Bulletin of the Chemical Society of Japan, 86, 1, 67, 74, 2013
  Scientific journal
• An effective energy gradient expression for divide-and-conquer second-order Moller-Plesset perturbation theory
  Kobayashi, Masato; Nakai, Hiromi
  Journal of Chemical Physics, 138, 4, 044102, 2013, [Peer-reviewed]
  English, Scientific journal
• Accelerating convergence in the antisymmetric product of strongly orthogonal geminals method
  Tarumi, Moto; Kobayashi, Masato; Nakai, Hiromi
  International Journal of Quantum Chemistry, 113, 3, 2013
  Scientific journal
• Divide-and-conquer-based symmetry adapted cluster method: Synergistic effect of subsystem fragmentation and configuration selection
  Yoshikawa, Takeshi; Kobayashi, Masato; Nakai, Hiromi
  International Journal of Quantum Chemistry, 113, 3, 2013
  Scientific journal
• Divide-and-conquer-based quantum chemical study for interaction between HIV-1 reverse transcriptase and MK-4965 inhibitor
  Saparpakorn, Patchreenart; Kobayashi, Masato; Hannongbua, Supa; Nakai, Hiromi
  International Journal of Quantum Chemistry, 113, 4, 2013
  Scientific journal
• Divide-and-Conquer Electronic-Structure Study on the Mechanism of the West Nile Virus NS3 Protease Inhibitor
  Saparpakorn, Patchreenart; Kobayashi, Masato; Nakai, Hiromi
  Bulletin of the Chemical Society of Japan, 86, 1, 2013
  Scientific journal
• Generalized Moller-Plesset Multiconfiguration Perturbation Theory Applied to an Open-Shell Antisymmetric Product of Strongly Orthogonal Geminals Reference Wave Function
  Moto Tarumi; Masato Kobayashi; Hiromi Nakai
  JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8, 11, 4330, 4335, Nov. 2012
  English, Scientific journal
• Dynamic hyperpolarizability calculations of large systems: The linear-scaling divide-and-conquer approach
  Masato Kobayashi; Tsuguki Touma; Hiromi Nakai
  JOURNAL OF CHEMICAL PHYSICS, 136, 8, 084108, Feb. 2012
  English, Scientific journal
• Development of Divide-and-Conquer Quantum Chemical Code for Biomolecules and Nano Materials
  M. Kobayashi; P. Saparpakorn; H. Nakai
  31st Annual Conference of Japan Society for Simulation Technology, 330, 333, 2012
• Development of Divide-and-Conquer Quantum Chemical Code for Biomolecules and Nano Materials
  M. Kobayashi; P. Saparpakorn; H. Nakai
  31st Annual Conference of Japan Society for Simulation Technology, 2012
• How Does It Become Possible to Treat Delocalized and/or Open-Shell Systems in Fragmentation-Based Linear-Scaling Electronic Structure Calculation? The Case of the Divide-and-Conquer Method
  M. Kobayashi; H. Nakai
  Phys. Chem. Chem. Phys., 14, 21, 7629, 7639, 2012
• Dynamic hyperpolarizability calculations of large systems: the linear-scaling divide-and-conquer approach.
  Kobayashi Masato; Touma Tsuguki; Nakai Hiromi
  Dynamic hyperpolarizability calculations of large systems: the linear-scaling divide-and-conquer approach., 136, 8, 2012, [Peer-reviewed]
  :We report a linear-scaling computation method for evaluating the dynamic first hyperpolarizability β based on the divide-and-conquer (DC) method. In the present scheme, we utilized the quasi-density-matrix expression derived from Wigner's (2n + 1) rule for β, where the quasi-density matrices are constructed from the solution obtained via the DC time-dependent self-consistent field (TD-SCF) method [T. Touma, M. Kobayashi, and H. Nakai, Chem. Phys. Lett. 485, 247 (2010)]. Numerical evaluation of π-conjugated and saturated organic chain systems verified that the present scheme considerably reduces the computational time for the β evaluation with a slight loss of accuracy, even around the singular frequency appearing at the electronic excitation energy. This evaluation indicates that the present linear-scaling TD-SCF scheme can also be used to estimate the molecular excitation energy. Furthermore, we succeeded in accurately evaluating the macroscopic second-harmonic generation coefficient of the polyvinylidene fluoride from the molecular (hyper)polarizabilities.
• Finite-field evaluation of static (hyper)polarizabilities based on the linear-scaling divide-and-conquer method
  Tsuguki Touma; Masato Kobayashi; Hiromi Nakai
  THEORETICAL CHEMISTRY ACCOUNTS, 130, 4-6, 701, 709, Dec. 2011
  English, Scientific journal
• Linear-scaling divide-and-conquer second-order Møller-Plesset perturbation calculation for open-shell systems: Implementation and application
  Takeshi Yoshikawa; Masato Kobayashi; Hiromi Nakai
  Theoretical Chemistry Accounts, 130, 2-3, 411, 417, Oct. 2011
  English, Scientific journal
• DIVIDE-AND-CONQUER APPROACHES TO QUANTUM CHEMISTRY: THEORY AND IMPLEMENTATION
  Kobayashi, Masato; Nakai, Hiromi
  Linear-Scaling Techniques in Computational Chemistry and Physics: Methods and Applications, 13, 97, 127, 2011
  Scientific journal
• ナノ化学のための分割統治量子化学計算法
  小林正人; 中井浩巳
  ナノ学会会報, 9, 2, 85, 89, 2011
• Linear-scaling electronic structure calculation program based on divide-and-conquer method
  Hiromi Nakai; Masato Kobayashi
  PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE (ICCS), 4, 1145, 1150, 2011
  English, International conference proceedings
• Reconsidering an analytical gradient expression within a divide-and-conquer self-consistent field approach: Exact formula and its approximate treatment
  Masato Kobayashi; Tomotaka Kunisada; Tomoko Akama; Daisuke Sakura; Hiromi Nakai
  JOURNAL OF CHEMICAL PHYSICS, 134, 3, 034105, Jan. 2011
  English, Scientific journal
• Two-Level Hierarchical Parallelization of Second-Order Moller-Plesset Perturbation Calculations in Divide-and-Conquer Method
  Katouda, Michio; Kobayashi, Masato; Nakai, Hiromi; Nagase, Shigeru
  Journal of Computational Chemistry, 32, 13, 2756, 2764, 2011
  Scientific journal
• Reconsidering an analytical gradient expression within a divide-and-conquer self-consistent field approach: exact formula and its approximate treatment.
  Kobayashi Masato; Kunisada Tomotaka; Akama Tomoko; Sakura Daisuke; Nakai Hiromi
  Reconsidering an analytical gradient expression within a divide-and-conquer self-consistent field approach: exact formula and its approximate treatment., 134, 3, 2011, [Peer-reviewed]
  :An analytical energy gradient formula for the density-matrix-based linear-scaling divide-and-conquer (DC) self-consistent field (SCF) method was proposed in a previous paper by Yang and Lee (YL) [J. Chem. Phys. 103, 5674 (1995)]. Since the formula by YL does not correspond to the exact gradient of the DC-SCF energy, we derive the exact formula by direct differentiation, which requires solving the coupled-perturbed equations while including the inter-subsystem coupling terms. Next, we present an alternative formula for approximately evaluating the DC-SCF energy gradient, assuming the variational condition for the subsystem density matrices. Numerical assessments confirmed that the DC-SCF energy gradient values obtained by the present formula are in reasonable agreement with the conventional SCF values when adopting a reliable buffer region. Furthermore, the performance of the present method was found to be better than that of the YL method.
• Divide-and-conquer self-consistent field calculation for open-shell systems: Implementation and application
  Masato Kobayashi; Takeshi Yoshikawa; Hiromi Nakai
  CHEMICAL PHYSICS LETTERS, 500, 1-3, 172, 177, Nov. 2010
  English, Scientific journal
• Observation by UV-Visible and NMR Spectroscopy and Theoretical Confirmation of 4-Isopropyltropolonate Ion, 4-Isopropyltropolone (Hinokitiol), and Protonated 4-Isopropyltropolone in Acetonitrile
  Hojo, Masashi; Ueda, Tadaharu; Ike, Michitaka; Okamura, Kei; Sugiyama, Taku; Kobayashi, Masato; Nakai, Hiromi
  Journal of Chemical and Engineering Data, 55, 5, 1986, 1989, 2010
  Scientific journal
• Time-dependent Hartree-Fock frequency-dependent polarizability calculation applied to divide-and-conquer electronic structure method
  Touma, Tsuguki; Kobayashi, Masato; Nakai, Hiromi
  Chemical Physics Letters, 485, 1-3, 247, 252, 2010
  Scientific journal
• Generalized Moller-Plesset Partitioning in Multiconfiguration Perturbation Theory
  Kobayashi, Masato; Szabados, Agnes; Nakai, Hiromi; Surjan, Peter R.
  Journal of Chemical Theory and Computation, 6, 7, 2024, 2033, 2010
  Scientific journal
• 化学の領域を広げる巨大分子の電子状態計算
  小林正人; 中井浩巳
  月刊「化学」, 64, 1, 12, 16, 2009
• UV-visible, H-1 and C-13 NMR spectroscopic studies on the interaction between protons or alkaline earth metal ions and the benzoate ion in acetonitrile
  Hojo, Masashi; Ueda, Tadaharu; Ike, Michitaka; Kobayashi, Masato; Nakai, Hiromi
  Journal of Molecular Liquids, 145, 3, 152, 157, 2009
  Scientific journal
• Implementation of Divide-and-Conquer (DC) Electronic Structure Code to GAMESS Program Package
  KOBAYASHI Masato; AKAMA Tomoko; NAKAI Hiromi
  Journal of Chemical Software, 8, 1, 1, 21, Society of Computer Chemistry, Japan, 2009
  Japanese, The divide-and-conquer (DC) linear-scaling electronic structure method has been applied mainly to pure density functional theory (DFT) or semi-empirical molecular orbital (MO) calculations. The authors have applied the DC method to the Hartree-Fock (HF) and hybrid DFT calculations and confirmed its reliability and efficiency. In addition, they have developed a linear-scaling post-HF algorithm using subsystem orbitals obtained from DC-HF calculation by virtue of the idea of energy density analysis (EDA) and have shown its efficiency by applying it to second-order perturbation (MP2) and coupled-cluster (CCSD) calculations. In our group, these methods are implemented in the GAMESS quantum chemistry program and can easily be executed by slightly modifying the standard input file. In this paper, we describe the implementation and capabilities of our DC program on GAMESS and report the method to execute and the results of the calculations.
• Dual-Level Hierarchical Scheme for Linear-Scaling Divide-and-Conquer Correlation Theory
  Kobayashi, Masato; Nakai, Hiromi
  International Journal of Quantum Chemistry, 109, 10, 2227, 2237, 2009
  Scientific journal
• Electronic Temperature in Divide-and-Conquer Electronic Structure Calculation Revisited: Assessment and Improvement of Self-Consistent Field Convergence
  Akama, Tomoko; Kobayashi, Masato; Nakai, Hiromi
  International Journal of Quantum Chemistry, 109, 12, 2706, 2713, 2009
  Scientific journal
• Divide-and-conquer-based linear-scaling approach for traditional and renormalized coupled cluster methods with single, double, and noniterative triple excitations
  Kobayashi, Masato; Nakai, Hiromi
  Journal of Chemical Physics, 131, 11, 114108, 2009
  Scientific journal
• 化学の領域を広げる巨大分子の電子状態計算
  小林正人; 中井浩巳
  化学, 64, 1, 38, 42, 2009, [Peer-reviewed]
  Japanese
• 分割統治法に基づく線形スケーリング手法の開発
  中井浩巳; 赤間知子; 小林正人
  Bull. Soc. Discrete Var. Xα, 21, 1,2, 47, 54, 2008
• Application of the Sakurai-Sugiura projection method to core-excited-state calculation by time-dependent density functional theory
  Tsuchimochi, Takashi; Kobayashi, Masato; Nakata, Ayako; Imamura, Yutaka; Nakai, Hiromi
  Journal of Computational Chemistry, 29, 14, 2311, 2316, 2008
  Scientific journal
• Extension of linear-scaling divide-and-conquer-based correlation method to coupled cluster theory with singles and doubles excitations
  Kobayashi, Masato; Nakai, Hiromi
  Journal of Chemical Physics, 129, 4, 044103, 2008
  Scientific journal
• Development of linear scaling techniques based on divide-and-conquer method
  H. Nakai; T. Akama; M. Kobayashi
  Bull. Soc. Discrete Variational Xα, 21, 1,2, 47, 54, 2008, [Peer-reviewed]
  English
• Implementation of divide-and-conquer method including hartree-fock exchange interaction
  Tomoko Akama; Masato Kobayashi; Hiromi Nakai
  Journal of Computational Chemistry, 28, 12, 2003, 2012, Sep. 2007
  English, Scientific journal
• Alternative linear-scaling methodology for the second-order Moller-Plesset perturbation calculation based on the divide-and-conquer method
  Masato Kobayashi; Yutaka Imamura; Hiromi Nakai
  JOURNAL OF CHEMICAL PHYSICS, 127, 7, 074103, Aug. 2007
  English, Scientific journal
• UV-visible and H-1 or C-13 NMR spectroscopic studies on the specific interaction between lithium ions and the anion from tropolone or 4-isopropyltropolone (Hinokitiol) and on the formation of protonated tropolones in acetonitrile or other solvents
  Masashi Hojo; Tadaharu Ueda; Tomonori Inoue; Michitaka Ike; Masato Kobayashi; Hiromi Nakai
  JOURNAL OF PHYSICAL CHEMISTRY B, 111, 7, 1759, 1768, Feb. 2007
  English, Scientific journal
• Hybrid treatment combining the translation- and rotation-free nuclear orbital plus molecular orbital theory with generator coordinate method: TRF-NOMO/GCM
  Keitaro Sodeyama; Hiroaki Nishizawa; Minoru Hoshino; Masato Kobayashi; Hiromi Nakai
  CHEMICAL PHYSICS LETTERS, 433, 4-6, 409, 415, Jan. 2007
  English, Scientific journal
• Is the divide-and-conquer Hartree-Fock method valid for calculations of delocalized systems?
  Tomoko Akama; Atsuhiko Fujii; Masato Kobayashi; Hiromi Nakai
  MOLECULAR PHYSICS, 105, 19-22, 2799, 2804, 2007
  English, Scientific journal
• Second-order Moller-Plesset perturbation energy obtained from divide-and-conquer Hartree-Fock density matrix
  Masato Kobayashi; Tomoko Akama; Hiromi Nakai
  JOURNAL OF CHEMICAL PHYSICS, 125, 20, 204106, Nov. 2006
  English, Scientific journal
• Implementation of Surjan's density matrix formulae for calculating second-order Moller-Plesset energy
  M Kobayashi; H Nakai
  CHEMICAL PHYSICS LETTERS, 420, 1-3, 250, 255, Mar. 2006
  English, Scientific journal
• Practical performance assessment of accompanying coordinate expansion recurrence relation algorithm for computation of electron repulsion integrals
  M Katouda; M Kobayashi; H Nakai; S Nagase
  JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 4, 1, 139, 149, Mar. 2005
  English, Scientific journal
• New recurrence relations for the rapid evaluation of electron repulsion integrals based on the accompanying coordinate expansion formula
  M Kobayashi; H Nakai
  JOURNAL OF CHEMICAL PHYSICS, 121, 9, 4050, 4058, Sep. 2004
  English, Scientific journal
• New algorithm for the rapid evaluation of electron repulsion integrals: elementary basis algorithm
  Nakai, H; Kobayashi, M
  Chemical Physics Letters, 388, 1-3, 50, 54, 2004
  Scientific journal
• New algorithm for the rapid computation of molecular integrals: Elementary basis algorithm.
  Kobayashi, M; Nakai, H
  Abstracts of Papers of the American Chemical Society, 226, 2003, [Peer-reviewed]
  Scientific journal

• Development of X-ray Activatable Caged Compounds Using Azo Bond Cleavage
  小河原浩輝; 家田直弥; 中島孝平; 高倉栄男; 斉田謙一郎; KUMAR Sonu; KUMAR Sonu; 小林正人; 武次徹也; 武次徹也; 稲波修; 小川美香子; 小川美香子, 日本薬学会年会要旨集(Web), 144th, 2024
• テトラキス型キラルEu(III)錯体のπ-4f電荷移動励起状態に基づくキラル光学特性
  滝沢諒平; 富川虎乃輔; 板谷康佑; 中井拓真; ワン メンフィ; ワン メンフィ; 小林正人; 小林正人; 武次徹也; 武次徹也; 長谷川靖哉; 長谷川靖哉; 北川裕一; 北川裕一, 配位化合物の光化学討論会講演要旨集, 35th, 2024
• ヘキサフルオロアセチルアセトナートを有するセリウム錯体の電荷移動発光
  富川虎乃輔; ワン メンフィ; 庄司淳; 赤間知子; 小林正人; 小林正人; 伏見公志; 中西貴之; 武次徹也; 武次徹也; 長谷川靖哉; 長谷川靖哉; 北川裕一; 北川裕一, 配位化合物の光化学討論会講演要旨集, 34th, 2023
• 量子アニーリング計算と機械学習を用いた高精度量子化学計算法の開発
  米山亮; 能條小夜子; 小林正人; 小林正人; 武次徹也; 武次徹也, 化学系学協会北海道支部冬季研究発表会(Web), 2023, 2023
• Development of X-ray activated caged compounds by using azo bond cleavage
  小河原浩輝; 高倉栄男; 中島孝平; 斉田謙一郎; KUMAR Sonu; 小林正人; 武次徹也; 稲浪修; 小川美香子, 日本癌学会学術総会抄録集(Web), 82nd, 2023
• Creation of descriptors for potential energy surface using reaction route map and persistent homology
  村山武来; 小林正人; 小林正人; 青木雅允; 石橋卓; 齋藤琢弥; 中村壮伸; 寺本央; 武次徹也; 武次徹也, 分子科学討論会講演プログラム&要旨(Web), 17th, 2023
• Charge transfer emission of Ce(III) complexes with β-diketonate ligands
  富川虎乃輔; 庄司淳; 庄司淳; 赤間知子; 小林正人; 小林正人; 伏見公志; 中西貴之; 武次徹也; 武次徹也; 長谷川靖哉; 長谷川靖哉; 北川裕一; 北川裕一, 希土類, 82, 2023
• Molecular Recognition and Luminescent Properties of Supramolecular Cage Organized by Porphyrin and Yb(III) Complex
  庄司淳; 細谷祥太; 中西貴之; 小林正人; 小林正人; 伏見公志; 北川裕一; 北川裕一; 武次徹也; 武次徹也; 長谷川靖哉; 長谷川靖哉, 基礎有機化学討論会要旨集, 33rd (CD-ROM), 2023
• イジング計算機とfactorization machineを用いた「望みのプロパティ」を持つ化合物の提案
  米山亮; 田代啓介; 小林正人; 小林正人; 武次徹也; 武次徹也, 化学系学協会北海道支部冬季研究発表会(Web), 2022, 2022
• 機械学習を利用した第一原理MDトラジェクトリの自動分類
  小林正人; 小林正人; 原渕祐; 原渕祐; 堤拓朗; 小野ゆり子; 瀧川一学; 瀧川一学; 武次徹也; 武次徹也, 日本コンピュータ化学会年会講演予稿集, 2018, 73, 03 Nov. 2018
  Japanese
• DSAP類縁体のC‐C単結合長に関する理論的研究:環境効果の検討
  黒田悠介; 小林正人; 武次徹也, 基礎有機化学討論会要旨集, 28th, 253, 07 Sep. 2017
  Japanese
• 量子化学計算とインフォマティクスを用いたメタン水蒸気改質触媒能の評価
  小林正人; 小林正人; 小林正人; 小野田遼; 武次徹也; 武次徹也, 触媒討論会講演予稿集, 119th, 234, 10 Mar. 2017
  Japanese
• 分割統治法とHartree‐Fock‐Bogoliubov法を組み合わせた大規模強相関系電子状態計算手法の開発とグラフェンナノリボンへの適用
  児玉良輔; 小林正人; 小林正人; 小林正人; 武次徹也; 武次徹也, 日本化学会春季年会講演予稿集(CD-ROM), 97th, ROMBUNNO.1A7‐12, 03 Mar. 2017
  Japanese
• 分割統治(DC)法に基づいた大規模量子化学計算における誤差の自動制御化
  藤森俊和; 小林正人; 小林正人; 小林正人; 武次徹也; 武次徹也, 日本化学会春季年会講演予稿集(CD-ROM), 97th, ROMBUNNO.1A7‐11, 03 Mar. 2017
  Japanese
• 表面モデル計算と統計手法によるメタン水蒸気改質触媒活性の評価
  小野田遼; 小林正人; 小林正人; 小林正人; 武次徹也; 武次徹也, 日本化学会春季年会講演予稿集(CD-ROM), 97th, ROMBUNNO.2PA‐202, 03 Mar. 2017
  Japanese
• Estimation of isomer energies by sparse modeling with local explanatory variables
  Onoda Haruka; Kobayashi Masato; Taketsugu Tetsuya, Proceedings of the Symposium on Chemoinformatics, 2016, 0, P15, 2016
  If the molecular energy obtained from the quantum chemical calculation can be modeled with local explanatory variables such as atomic charges, it is possible to drastically reduce the computational cost. We attempted to model the total energies of C₃H₆O₂ isomers by using Mulliken, Lowdin, natural, and ESP charges as the explanatory variables. By applying the MC+ regression, we could obtain a model showing good agreement with the calculated energy with a couple of explanatory variables. Applying this modeling scheme to the isomers of C₈H₁₀O₂, C₉H₁₀O₂, C₉H₁₀O₃, and C₁₀H₁₂O₂, however, resulted in failing to obtain good models. By adding the numbers of 3 to 8 membered rings as the explanatory variable, we could obtain good sparse models. In addition, it was found that all these sparse models contain the largest natural charge and the number of 6-membered rings as the explanatory variable., Division of Chemical Information and Computer Sciences The Chemical Society of Japan, Japanese
• Specifying primary factors in the catalytic activity of metal clusters based on quantum chemical calculations and machine learning
  Kobayashi Masato; Iwasa Takeshi; Gao Min; Takagi Makito; Maeda Satoshi; Taketsugu Tetsuya, Proceedings of the Symposium on Chemoinformatics, 2016, 0, O18, 2016
  Because catalytic activities of metal nano clusters depend on the composition, size, environment, and structural isomers of the cluster, it has been difficult to elucidate the primary factors in their catalytic activities. In this study, we attempted to extract the factors in the catalytic activity using the sparse modeling techniques and the systematic quantum chemical calculations assisted by the automatic search of reaction pathways. In particular, the transition state energies for NO dissociation on Cu13 clusters were modeled with the orbital energies and local indices by the LASSO, SCAD, and MC+ regressions. It was found that the transition state energy negatively correlates with the LUMO energy. The SCAD and MC+ regressions could generate more compact and better models with higher correlation factors than the LASSO regression., Division of Chemical Information and Computer Sciences The Chemical Society of Japan, Japanese
• Divide-and-conquer-based symmetry adapted cluster method: Synergistic effect of subsystem fragmentation and configuration selection
  Takeshi Yoshikawa; Masato Kobayashi; Hiromi Nakai, International Journal of Quantum Chemistry, 113, 3, 218, 223, 05 Feb. 2013
  English
• Accelerating convergence in the antisymmetric product of strongly orthogonal geminals method
  Moto Tarumi; Masato Kobayashi; Hiromi Nakai, INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 113, 3, 239, 244, Feb. 2013
  English
• An effective energy gradient expression for divide-and-conquer second-order Møller-Plesset perturbation theory
  Masato Kobayashi; Hiromi Nakai, Journal of Chemical Physics, 138, 4, 044102, 28 Jan. 2013
  English
• Novel Approach to Excited-State Calculations of Large Molecules Based on Divide-and-Conquer Method: Application to Photoactive Yellow Protein
  Yoshikawa, Takeshi; Kobayashi, Masato; Fujii, Atsuhiko; Nakai, Hiromi, Journal of Physical Chemistry B, 117, 18, 5565, 5573, 2013
• Divide-and-conquer-based symmetry adapted cluster method: Synergistic effect of subsystem fragmentation and configuration selection
  Yoshikawa, Takeshi; Kobayashi, Masato; Nakai, Hiromi, International Journal of Quantum Chemistry, 113, 3, 218, 223, 2013
• Divide-and-conquer-based quantum chemical study for interaction between HIV-1 reverse transcriptase and MK-4965 inhibitor
  Saparpakorn, Patchreenart; Kobayashi, Masato; Hannongbua, Supa; Nakai, Hiromi, International Journal of Quantum Chemistry, 113, 4, 510, 517, 2013
• Divide-and-Conquer Electronic-Structure Study on the Mechanism of the West Nile Virus NS3 Protease Inhibitor
  Saparpakorn, Patchreenart; Kobayashi, Masato; Nakai, Hiromi, Bulletin of the Chemical Society of Japan, 86, 1, 67, 74, 2013
• Accelerating convergence in the antisymmetric product of strongly orthogonal geminals method
  Tarumi, Moto; Kobayashi, Masato; Nakai, Hiromi, International Journal of Quantum Chemistry, 113, 3, 2013
• Divide-and-conquer-based quantum chemical study for interaction between HIV-1 reverse transcriptase and MK-4965 inhibitor
  Saparpakorn, Patchreenart; Kobayashi, Masato; Hannongbua, Supa; Nakai, Hiromi, International Journal of Quantum Chemistry, 113, 4, 2013
• Generalized Moller-Plesset Multiconfiguration Perturbation Theory Applied to an Open-Shell Antisymmetric Product of Strongly Orthogonal Geminals Reference Wave Function
  Moto Tarumi; Masato Kobayashi; Hiromi Nakai, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8, 11, 4330, 4335, Nov. 2012
  English
• How does it become possible to treat delocalized and/or open-shell systems in fragmentation-based linear-scaling electronic structure calculations? the case of the divide-and-conquer method
  Masato Kobayashi; Hiromi Nakai, Physical Chemistry Chemical Physics, 14, 21, 7629, 7639, 07 Jun. 2012
  English
• Dynamic hyperpolarizability calculations of large systems: The linear-scaling divide-and-conquer approach
  Masato Kobayashi; Tsuguki Touma; Hiromi Nakai, Journal of Chemical Physics, 136, 8, 084108, 28 Feb. 2012
  English
• Development of Divide-and-Conquer Quantum Chemical Code for Biomolecules and Nano Materials
  M. Kobayashi; P. Saparpakorn; H. Nakai, 31st Annual Conference of Japan Society for Simulation Technology, 330, 333, 2012
• Development of Divide-and-Conquer Quantum Chemical Code for Biomolecules and Nano Materials
  M. Kobayashi; P. Saparpakorn; H. Nakai, 31st Annual Conference of Japan Society for Simulation Technology, 2012
• Two-Level Hierarchical Parallelization of Second-Order Moller-Plesset Perturbation Calculations in Divide-and-Conquer Method
  Michio Katouda; Masato Kobayashi; Hiromi Nakai; Shigeru Nagase, JOURNAL OF COMPUTATIONAL CHEMISTRY, 32, 13, 2756, 2764, Oct. 2011
  English
• Linear-scaling divide-and-conquer second-order Moller-Plesset perturbation calculation for open-shell systems: implementation and application
  Takeshi Yoshikawa; Masato Kobayashi; Hiromi Nakai, THEORETICAL CHEMISTRY ACCOUNTS, 130, 2-3, 411, 417, Oct. 2011
  English
• DIVIDE-AND-CONQUER APPROACHES TO QUANTUM CHEMISTRY: THEORY AND IMPLEMENTATION
  Kobayashi, Masato; Nakai, Hiromi, Linear-Scaling Techniques in Computational Chemistry and Physics: Methods and Applications, 13, 97, 127, 2011
• Linear-scaling electronic structure calculation program based on divide-and-conquer method
  Nakai, Hiromi; Kobayashi, Masato, Proceedings of the International Conference on Computational Science (Iccs), 4, 1145, 1150, 2011
• Reconsidering an analytical gradient expression within a divide-and-conquer self-consistent field approach: Exact formula and its approximate treatment
  Masato Kobayashi; Tomotaka Kunisada; Tomoko Akama; Daisuke Sakura; Hiromi Nakai, JOURNAL OF CHEMICAL PHYSICS, 134, 3, 034105, Jan. 2011
  English
• Finite-field evaluation of static (hyper)polarizabilities based on the linear-scaling divide-and-conquer method
  Touma, Tsuguki; Kobayashi, Masato; Nakai, Hiromi, Theoretical Chemistry Accounts, 130, 4-6, 701, 709, 2011
• Observation by UV-Visible and NMR Spectroscopy and Theoretical Confirmation of 4-Isopropyltropolonate Ion, 4-Isopropyltropolone (Hinokitiol), and Protonated 4-Isopropyltropolone in Acetonitrile
  Hojo, Masashi; Ueda, Tadaharu; Ike, Michitaka; Okamura, Kei; Sugiyama, Taku; Kobayashi, Masato; Nakai, Hiromi, Journal of Chemical and Engineering Data, 55, 5, 1986, 1989, 2010
• Time-dependent Hartree-Fock frequency-dependent polarizability calculation applied to divide-and-conquer electronic structure method
  Touma, Tsuguki; Kobayashi, Masato; Nakai, Hiromi, Chemical Physics Letters, 485, 1-3, 247, 252, 2010
• Generalized Moller-Plesset Partitioning in Multiconfiguration Perturbation Theory
  Kobayashi, Masato; Szabados, Agnes; Nakai, Hiromi; Surjan, Peter R., Journal of Chemical Theory and Computation, 6, 7, 2024, 2033, 2010
• Divide-and-conquer self-consistent field calculation for open-shell systems: Implementation and application
  Kobayashi, Masato; Yoshikawa, Takeshi; Nakai, Hiromi, Chemical Physics Letters, 500, 1-3, 172, 177, 2010
• UV-visible, H-1 and C-13 NMR spectroscopic studies on the interaction between protons or alkaline earth metal ions and the benzoate ion in acetonitrile
  Hojo, Masashi; Ueda, Tadaharu; Ike, Michitaka; Kobayashi, Masato; Nakai, Hiromi, Journal of Molecular Liquids, 145, 3, 152, 157, 2009
• Dual-Level Hierarchical Scheme for Linear-Scaling Divide-and-Conquer Correlation Theory
  Kobayashi, Masato; Nakai, Hiromi, International Journal of Quantum Chemistry, 109, 10, 2227, 2237, 2009
• Electronic Temperature in Divide-and-Conquer Electronic Structure Calculation Revisited: Assessment and Improvement of Self-Consistent Field Convergence
  Akama, Tomoko; Kobayashi, Masato; Nakai, Hiromi, International Journal of Quantum Chemistry, 109, 12, 2706, 2713, 2009
• Divide-and-Conquer-Based Linear-Scaling Approach for Traditional and Renormalized Coupled Cluster Methods with Single, Double, and Noniterative Triple Excitations
  M. Kobayashi; H. Nakai, J. Chem. Phys., 131, 11, 114108, 114108, 2009
• Application of the Sakurai-Sugiura projection method to core-excited-state calculation by time-dependent density functional theory
  Tsuchimochi, Takashi; Kobayashi, Masato; Nakata, Ayako; Imamura, Yutaka; Nakai, Hiromi, Journal of Computational Chemistry, 29, 14, 2311, 2316, 2008
• Extension of Linear-Scaling Divide-and-Conquer-Based Correlation Method to Coupled Cluster Theory with Singles and Doubles Exciations
  M. Kobayashi; H. Nakai, J. Chem. Phys., 129, 4, 044103, 44103, 2008
• Implementation of divide-and-conquer method including Hartree-Fock exchange interaction
  Tomoko Akama; Masato Kobayashi; Hiromi Nakai, JOURNAL OF COMPUTATIONAL CHEMISTRY, 28, 12, 2003, 2012, Sep. 2007
  English
• UV-visible and H-1 or C-13 NMR spectroscopic studies on the specific interaction between lithium ions and the anion from tropolone or 4-isopropyltropolone (Hinokitiol) and on the formation of protonated tropolones in acetonitrile or other solvents
  Masashi Hojo; Tadaharu Ueda; Tomonori Inoue; Michitaka Ike; Masato Kobayashi; Hiromi Nakai, JOURNAL OF PHYSICAL CHEMISTRY B, 111, 7, 1759, 1768, Feb. 2007
  English
• Hybrid treatment combining the translation- and rotation-free nuclear orbital plus molecular orbital theory with generator coordinate method: TRF-NOMO/GCM
  Keitaro Sodeyama; Hiroaki Nishizawa; Minoru Hoshino; Masato Kobayashi; Hiromi Nakai, CHEMICAL PHYSICS LETTERS, 433, 4-6, 409, 415, Jan. 2007
  English
• Alternative linear-scaling methodology for the second-order Moller-Plesset perturbation calculation based on the divide-and-conquer method
  Kobayashi, Masato; Imamura, Yutaka; Nakai, Hiromi, Journal of Chemical Physics, 127, 7, 074103, 2007
• Is the divide-and-conquer Hartree-Fock method valid for calculations of delocalized systems?
  Tomoko Akama; Atsuhiko Fujii; Masato Kobayashi; Hiromi Nakai, MOLECULAR PHYSICS, 105, 19-22, 2799, 2804, 2007
  English
• Implementation of Surján's density matrix formulae for calculating second-order Møller-Plesset energy
  Masato Kobayashi; Hiromi Nakai, Chemical Physics Letters, 420, 1-3, 250, 255, 10 Mar. 2006
  English
• Second-order Moller-Plesset perturbation energy obtained from divide-and-conquer Hartree-Fock density matrix
  Kobayashi, Masato; Akama, Tomoko; Nakai, Hiromi, Journal of Chemical Physics, 125, 20, 204106, 2006
• Practical performance assessment of accompanying coordinate expansion recurrence relation algorithm for computation of electron repulsion integrals
  M Katouda; M Kobayashi; H Nakai; S Nagase, JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 4, 1, 139, 149, Mar. 2005
  English
• New algorithm for the rapid evaluation of electron repulsion integrals: elementary basis algorithm
  H Nakai; M Kobayashi, CHEMICAL PHYSICS LETTERS, 388, 1-3, 50, 54, Apr. 2004
  English
• New recurrence relations for the rapid evaluation of electron repulsion integrals based on the accompanying coordinate expansion formula
  Kobayashi, M; Nakai, H, Journal of Chemical Physics, 121, 9, 4050, 4058, 2004
• Divide-and-Conquer Electronic-Structure Study on the Mechanism of the West Nile Virus NS3 Protease Inhibitor
  P. Saparpakorn; M. Kobayashi; H. Nakai, Bull. Chem. Soc. Jpn.

• Fundamental Coordination Ability of s-Block Metal Ions
  Masashi Hojo
  Elsevier, Sep. 2025, 9780128219812, [Contributor]
• Quantum chemical calculations using density functional theory
  常田, 貴夫; 武次, 徹也
  講談社, May 2025, 9784065396780, vi, 242p, Japanese, [Contributor]
• 量子生命科学ハンドブック
  瀬藤, 光利; 荒牧, 修平, 第2編第1章第3節
  エヌ・ティー・エス, Mar. 2024, 9784860438821, iii, x, 346, viiip, Japanese, [Contributor]
• ケモインフォマティクスにおけるデータ収集の最適化と解析手法
  技術情報協会, 第３章第２節
  技術情報協会, Apr. 2023, 9784861049446, 657p, Japanese, [Contributor]
• 計算化学
  Jensen, Frank; 五十幡, 康弘; 内田, 希; 神谷, 宗明; 北, 幸海; 小林, 正人; 佐藤, 啓文; 重田, 育照; 砂賀, 彩光; 武次, 徹也; 常田, 貴夫; 長谷川, 淳也; 波田, 雅彦; 森, 聖治; 後藤, 仁志; 立川, 仁典; 長嶋, 雲兵
  森北出版, Mar. 2023, 9784627242333, xx, 882p, Japanese, [Joint translation]
• 触媒総合事典
  触媒学会; 山下, 弘巳; 福岡, 淳; 田中, 庸裕; 関根, 泰
  朝倉書店, 12 Jan. 2023, 4254252749, 530, Japanese, [Contributor]
• 量子技術の実用化と研究開発業務への導入方法
  技術情報協会, 第１章第３節
  技術情報協会, Jan. 2023, 9784861049156, 484p, Japanese, [Contributor]
• Computational and data-driven chemistry using artificial intelligence : fundamentals, methods and applications
  Akitsu, Takashiro, Chap. 7
  Elsevier, 2022, 9780128222492, xiii, 264 p., English, [Contributor]
• マテリアルズインフォマティクスのためのデータ作成とその解析、応用事例
  技術情報協会, 第８章１節
  技術情報協会, Jul. 2021, 9784861048548, 500p, Japanese, [Contributor]
• The Art of High Performance Computing for Computational Science, Vol. 2
  Masaaki Geshi, Chap. 6
  Springer, 2019, [Contributor]
• Keisan Kagaku no tameno HPC Gijutsu 2
  Masaaki Geshi, Chap. 7
  Osaka University Press, Mar. 2017, 9784872595871, 326, 205-238, Japanese, Scholarly book, [Contributor]
• すぐできる量子化学計算ビギナーズマニュアル
  武次, 徹也; 平尾, 公彦
  講談社, Mar. 2015, 9784061543881, viii, 212p, Japanese, [Joint work]
• Linear-scaling techniques in computational chemistry and physics : methods and applications
  Robert Zalesny; Manthos G. Papadopoulos; Paul G. Mezey; Jerzy Leszczynski, Chap. 5
  Springer, 2011, 9789048128525, xix, 513 p., English, [Contributor]

• Analyses for Catalytic and Surface Adsorption Systems by Quantum Chemical Calculations × Informatics
  KOBAYASHI, Masato
  Lecture in AI Advanced Research Center at Gifu Univ., 22 Jan. 2021, Japanese, Invited oral presentation
  22 Jan. 2021 - 22 Jan. 2021, [Invited]
• Analyses and Prediction for Catalytic and Surface Adsorption Systems by Combining Quantum Chemical Calculations and Data Science
  小林正人
  RCCS & Nanotechnology Platform Workshop 2021, 13 Jan. 2021, Japanese, Invited oral presentation
  12 Jan. 2021 - 13 Jan. 2021, [Invited]
• Data Scientific Analysis of Quantum Chemical Calculation Results for Surface Adsorption Systems and Its Application to Catalysis
  Masato Kobayashi
  36th Computational Materials Design Workshop, Feb. 2020, English, Invited oral presentation
  [Invited]
• Construction of quantum chemical calculation database of surface adsorption systems and its application to catalytic activity analysis
  KOBAYASHI Masato
  ESICB Electron Theory Meeting, Dec. 2019, Japanese, Invited oral presentation
  [Invited], [Domestic Conference]
• Data-Scientific Analysis of Quantum Chemical Calculation Results for Surface Adsorption Systems and Its Application to Catalysts
  KOBAYASHI Masato
  Rare Events Workshop 2019, Dec. 2019, Japanese, Invited oral presentation
  [Invited], [Domestic Conference]
• Surface model calculation database for predicting catalytic activity: An application to methane steam reforming
  KOBAYASHI Masato
  The ninth conference of the Asia-Pacific Association of Theoretical and Computational Chemists (APATCC2019), Oct. 2019, English, Invited oral presentation
  [Invited], [International presentation]
• Calculation, Analysis, and Prediction for Catalyst and Surface Adsorption Systems with Informatics Techniques and Automated Reaction Path Search
  KOBAYASHI Masato
  2nd International Workshop on Phase Interfaces Science for Highly Efficient Energy Utilization, Nov. 2018, English, Invited oral presentation
  [Invited], [International presentation]
• Recent Trends on Catalyst Informatics
  KOBAYASHI Masato
  CSE 1st Young Researcher Workshop, Aug. 2018, Japanese, Invited oral presentation
  [Invited], [Domestic Conference]
• Calculation, Analysis, and Prediction for Catalytic and Surface Adsorption Systems Using Informatics and Reaction Path Search Method
  KOBAYASHI Masato
  2nd PRESTO Symposium on Materials Informatics, Aug. 2018, Japanese, Invited oral presentation
  [Invited], [Domestic Conference]
• Tutorial for Informatics, Artificial Intelligence, and Machine Learning
  KOBAYASHI Masato
  ESICB Young Researcher Workshop on "Frontiers in Practical Theoretical Chemistry for Catalyst and Battery", Aug. 2018, Japanese, Invited oral presentation
  [Invited], [Domestic Conference]
• Analysis of Quantum Chemical Calculation Results and Applications to Catalysis Using Large-Scale Quantum Chemical Calculation and Data Science
  KOBAYASHI Masato
  Lecture at Institute for Molecular Science, May 2018, Japanese, Invited oral presentation
  [Invited], [Domestic Conference]
• Reaction Path Search Method and Informatics: Applications to Catalyst and Surface Adsorption System Calculations
  KOBAYASHI Masato
  NAIST Interdisciplinary Workshop "New Frontiers in Chemistry by Combination with Data Science, Mar. 2018, Japanese, Invited oral presentation
  [Invited], [Domestic Conference]
• Theoretical Studies on Catalysts Using Reaction Path Search Method and Informatics
  KOBAYASHI Masato
  5th RIST Workshop for Materials Science, Feb. 2018, Japanese, Invited oral presentation
  [Invited], [Domestic Conference]
• Theoretical Studies on Catalysts Using Reaction Path Search Method and Informatics
  KOBAYASHI Masato
  4th Open Symposium of Priority Issue 5 on Post-K Computer, Dec. 2017, Japanese, Invited oral presentation
  [Invited], [Domestic Conference]
• Analyzing Quantum Chemical Calculation Results with Informatics Techniques: Toward Application to Catalyst Development
  KOBAYASHI Masato
  International Symposium on Pure & Applied Chemistry (ISPAC) 2017, Jun. 2017, English, Invited oral presentation
  [Invited], [International presentation]
• Analysis of Quantum Chemical Calculation Results Using Data Science Techniques and Its Application to Catalysis
  KOBAYASHI Masato
  1st AICS Materials Informatics School, Mar. 2017, Japanese, Invited oral presentation
  [Invited], [Domestic Conference]
• Fundamentals of Large-Scale Quantum Chemical Calculation
  KOBAYASHI Masato
  6th Quantum Chemistry School, Dec. 2016, Japanese, Invited oral presentation
  [Invited], [Domestic Conference]
• Quantum chemical calculation meets informatics: Toward application to catalyst development
  KOBAYASHI Masato
  Thai-Japan Symposium in Chemistry, Nov. 2016, English, Invited oral presentation
  [Invited], [International presentation]
• Static and dynamical electron correlation calculations of large systems based on the divide-and-conquer method
  KOBAYASHI Masato
  EMN Meeting on Computation and Theory 2016, Oct. 2016, English, Invited oral presentation
  [Invited], [International presentation]
• Static Electron Correlations Described via Two-Electron Wave Functions
  KOBAYASHI Masato
  Collaborative Conference on Materials Research 2014 (CCMR2014), Jun. 2014, English, Invited oral presentation
  [Invited], [International presentation]
• アンチモンおよびテルルの超原子価化合物のリガンド交換反応に関する理論的研究
  第40回有機典型元素化学討論会, 2013, Poster presentation
• ペア行列を用いた平均場電子状態計算による静的電子相関の取り扱い
  第7回分子科学討論会, 2013, Poster presentation
• Geminal-based wavefunction theory and its perturbative improvement
  VIIIth Congress of the International Society for Theoretical Chemical Physics (ISTCP-VIII), 2013
• Hartree-Fock-Bogoliubov法による分子の電子状態計算とエネルギー勾配法
  日本コンピュータ化学会2013春季年会, 2013
• Hartree-Fock-Bogoliubov法を用いた量子化学計算の検討
  第16回理論化学討論会, 2013
• Excited-state calculations based on divide-and-conquer method for large systems
  17th International Annual Symposium on Computational Science and Engineering (ANSCSE17), 2013, Poster presentation
• Binding investigation of the West Nile Virus NS3 Protease Inhibitor using Divide-and-Conquer method
  17th International Annual Symposium on Computational Science and Engineering (ANSCSE17), 2013
• Divide-and-Conquer Program in GAMESS: 開発と最近の成果
  グランドチャレンジ・アプリケーションの研究開発 公開シンポジウム, 2013, Poster presentation
• 分割統治MP2法: エネルギー勾配法の開発と抗ウィルス薬への適用
  スーパーコンピューターワークショップ2013「理論と計算科学による新たな展開と可能性を探る」, 2013, Poster presentation
• Divide-and-conquer quantum chemistry program in GAMESS: Implementation and application
  International Workshop on Massively Parallel Programming Now in Molecular Science, 2013
• Quantum chemical calculations of large delocalized molecules with the divide-and-conquer method
  日本化学会第93春季年会 アジア国際シンポジウム, 2013
• Development of efficient quantum chemical calculation methods for nano material research
  Collaborative Conference on Materials Research (CCMR) 2013, 2013
• ナノ・生体系の化学反応ダイナミクス: 分割統治法を用いた検討
  第4回TCCI研究会, 2013
• Divide-and-conquer method for linear-scaling electronic sturcture calculations
  5th JCS International Symposium on Theoretical Chemistry, 2013
• Theoretical study on the ligand exchange reaction of hypervalent Sb and Te compounds
  The 40th Symposium on Main Group Element Chemistry, 2013, Poster presentation
• Static electron correlation treated by mean-field electronic structure calculations with pairing matrix
  Annual Meeting of Japan Society for Molecular Science 2013, 2013, Poster presentation
• Geminal-based wavefunction theory and its perturbative improvement
  VIIIth Congress of the International Society for Theoretical Chemical Physics (ISTCP-VIII), 2013
• Electronic structure calculations of molecules with Hartree-Fock-Bogoliubov method and its energy gradient
  Spring Meeting 2013, Society of Computer Chemistry, Japan, 2013
• Quantum chemical calculations with Hartree-Fock-Bogoliubov method
  16th Annual Forum on Theoretical Chemistry, 2013
• Excited-state calculations based on divide-and-conquer method for large systems
  17th International Annual Symposium on Computational Science and Engineering (ANSCSE17), 2013, Poster presentation
• Binding investigation of the West Nile Virus NS3 Protease Inhibitor using Divide-and-Conquer method
  17th International Annual Symposium on Computational Science and Engineering (ANSCSE17), 2013
• Divide-and-Conquer Program in GAMESS: Development and recent results
  Public Symposium on Research and Development of Grand Challenge Applications, 2013, Poster presentation
• Divide-and-conquer MP2 method: Formulation of energy gradient and application to anti-virus drug
  Supercomputer Workshop 2013, 2013, Poster presentation
• Divide-and-conquer quantum chemistry program in GAMESS: Implementation and application
  International Workshop on Massively Parallel Programming Now in Molecular Science, 2013
• Quantum chemical calculations of large delocalized molecules with the divide-and-conquer method
  Asian International Symposium in the 93rd Annual Meeting of the Chemical Society of Japan, 2013
• Development of efficient quantum chemical calculation methods for nano material research
  Collaborative Conference on Materials Research (CCMR) 2013, 2013
• Chemical reaction dynamics of nano and biological systems: Divide-and-conquer approaches
  4th TCCI Symposium, 2013
• Divide-and-conquer method for linear-scaling electronic sturcture calculations
  5th JCS International Symposium on Theoretical Chemistry, 2013
• 分割統治MP2プログラムの最近の展開と性能評価
  第3回CMSI研究会, 2012
• Development of divide-and-conquer quantum chemical code for biomolecules and nano materials
  JSST 2012 International Conference on Simulation Technology, 2012
• GAMESSに実装された分割統治(DC)量子化学計算法のハイブリッド並列化
  第6回分子科学討論会, 2012, Poster presentation
• APSG and its perturbative correction: Application to open-shell systems
  Theory and Applications of Computational Chemistry 2012 (TACC2012), 2012, Poster presentation
• Excited-state calculation of photoactive yellow protein using divide-and-conquer SAC-CI theory
  XVIIth International Workshop on Quantum Systems in Chemistry and Physics (QSCP-XVII), 2012, Poster presentation
• DC-SAC-CI法による光活性タンパクの励起状態計算
  第15回理論化学討論会, 2012, Poster presentation
• 開殻APSG波動関数を参照とした多体摂動計算
  第15回理論化学討論会, 2012, Poster presentation
• DC-SAC-CI法～大規模励起状態理論の構築～
  日本コンピュータ化学会2012春季年会, 2012, Poster presentation
• 量子化学計算を用いた有機電子材料の電荷移動特性の解析
  日本コンピュータ化学会2012春季年会, 2012, Poster presentation
• 分割統治(DC)量子化学計算法: その高精度化と高速化，超並列化
  先駆的計算科学に関するフォーラム2012～京コンピュータ利用に向けた分子科学分野での取り組み～, 2012
• 分割統治(DC)量子化学計算プログラム: 開発と応用、そして展望
  次世代ナノ統合シミュレーションソフトウェアの研究開発・次世代生命体統合シミュレーションソフトウェアの研究開発 公開シンポジウム, 2012
• 分割統治(DC)法に基づく大規模量子化学計算プログラムの開発と『京』での実装
  第4回HPCI戦略プログラム合同研究交流会, 2012
• 大規模系の量子化学計算：化学理論と計算機の発展が開いた世界とその近未来
  第26期CAMMフォーラム例会, 2012
• Recent advances in the divide-and-conquer MP2 program and its performance assessment
  3rd CMSI Symposium, 2012
• Development of divide-and-conquer quantum chemical code for biomolecules and nano materials
  JSST 2012 International Conference on Simulation Technology, 2012
• Hybrid parallelization of divide-and-conquer (DC) quantum chemical method implemented in GAMESS
  Annual Meeting of Japan Society for Molecular Science 2012, 2012, Poster presentation
• APSG and its perturbative correction: Application to open-shell systems
  Theory and Applications of Computational Chemistry 2012 (TACC2012), 2012, Poster presentation
• Excited-state calculation of photoactive yellow protein using divide-and-conquer SAC-CI theory
  XVIIth International Workshop on Quantum Systems in Chemistry and Physics (QSCP-XVII), 2012, Poster presentation
• Excited-state calculation of photo-active protein by DC-SAC-CI method
  15th Annual Forum on Theoretical Chemistry, 2012, Poster presentation
• Many-body perturbation calculation based on open-shell APSG wavefunction
  15th Annual Forum on Theoretical Chemistry, 2012, Poster presentation
• DC-SAC-CI method - Construction of large-scale excited-state theory
  Spring Meeting 2012, Society of Computer Chemistry, Japan, 2012, Poster presentation
• Analysis of charge mobility of organic electronic device using quantum chemical calculation
  Spring Meeting 2012, Society of Computer Chemistry, Japan, 2012, Poster presentation
• Divide-and-Conquer (DC) Quantum Chemical Calculation Method: Its Improvements in Accuracy, Efficiency, and Parallelism
  Forum on Pioneering Computational Science 2012 (Kyushu Univ.), 2012
• Divide-and-Conquer (DC) Quantum Chemical Calculation Program: Developments, applications, and Perspectives
  Open Symposium on Grand Challenges in Next-Generation Integrated Nanoscience and Living Matter, 2012
• Development of Large-Scale Quantum Chemical Calculation Program Based on Divide-and-Conquer (DC) Method and Its Implementation into K Supercomputer
  4th Joint Symposium of the Strategic Program for Innovative Research (SPIRE), 2012
• Quantum Chemical Calculations of Large Systems: The World Pioneered by Recent Developments in Chemical Theory and Computer Science, and Its Future
  26th CAMM Forum, 2012
• Divide-and-Conquer量子化学計算プログラム
  次世代ナノ統合シミュレーションソフトウェア説明会, 2009
• 分割統治(DC)電子状態計算法のGAMESSへの実装と応用
  日本コンピュータ化学会2009春季年会, 2009
• Divide-and-Conquer quantum chemistry program
  Next-Generation Integrated Nanoscience Simulation Software Explanatory Meeting, 2009
• Implimentation of divide-and-conquer (DC) electronic structure code to GAMESS program package and its applications
  Spring Meeting 2009, Society of Computer Chemistry, Japan, 2009
• Divide-and-conquer electronic structure method: Extension to post-HF correlation theories
  The International Conference on the Theory and Applications of Computational Chemistry in 2008 (TACC2008), 2008
• Divide-and-conquer electronic structure method: Extension to post-HF correlation theories
  The International Conference on the Theory and Applications of Computational Chemistry in 2008 (TACC2008), 2008
• 大規模系の高精度量子化学計算法: Divide-and-Conquer法に基づくMP2計算
  科研費特定領域研究「次世代量子シミュレータ・量子デザイン手法の開発」 A02班ミニワークショップ「大規模・高精度電子状態計算手法に関する研究会II」, 2007
• Accurate quantum chemical methodology for large systems: MP2 calculation based on the divide-and-conquer method
  Mini workshop on large-scale accurate electronic structure calculation methods II, 2007

• 計算機実習, 2024年, 学士課程, 総合教育部
• 分子化学Ａ（分子理論化学）, 2024年, 修士課程, 総合化学院
• 一般教育演習(ﾌﾚｯｼｭﾏﾝｾﾐﾅｰ), 2024年, 学士課程, 全学教育
• 量子化学Ⅰ, 2024年, 学士課程, 理学部
• 教科教育法（理科Ⅱ）, 2024年, 学士課程, 教育学部

• Jun. 2019 - Present
  Japan Society of Theoretical Chemistry
• Nov. 2016 - Present
  CATALYSIS SOCIETY OF JAPAN
• Jan. 2007 - Present
  THE CHEMICAL SOCIETY OF JAPAN
• Sep. 2006 - Present
  JAPAN SOCIETY FOR MOLECULAR SCIENCE
• Mar. 2006 - Present
  SOCIETY OF COMPUTER CHEMISTRY, JAPAN

• 重水素学を進める総括班研究
  科学研究費助成事業
  Apr. 2026 - Mar. 2031
  中 寛史
  日本学術振興会, 学術変革領域研究(A), 京都大学, 26H00485
• 重水素学のための理論実験複合データベースと学理構築
  科学研究費助成事業
  Apr. 2026 - Mar. 2031
  小林 正人
  日本学術振興会, 学術変革領域研究(A), 北海道大学, 26H00486
• Feature extraction of reaction route map by topological data analysis and its application to reactivity comparison, classification, and prediction
  Grants-in-Aid for Scientific Research
  01 Apr. 2023 - 31 Mar. 2026
  小林 正人; 中村 壮伸; 寺本 央
  「反応経路地図(RRM)を表現する重み付きグラフに対するパーシステント・ホモロジー(PH)解析法の確立」の項目については、基盤となるadjusted weight rank clique filtrationを開発して貨幣金属ナノクラスターと有機化学反応に適用し、その有用性を報告した。また、GRRMプログラムの出力を用いてPH解析を行うプログラムを整備して公開した。一方、GRRMプログラムの出力は対称性と同種核置換反転に関して縮約されているため、元のポテンシャルエネルギー曲面(PES)全体を表すものにはなっていない。そこで、3N-6次元のPESの空間に対応するRRMをGRRMの出力から復元する手法を並行して開発し、公開した。この復元されたPESに対するPH解析についても、予備的な検討を行った。
  「グローバル反応経路地図の作成とデータベース化」の項目に関しては、遷移金属元素の少数原子クラスターの計算とデータベース化を進めている。
  「PH解析に基づく記述子を用いた系の分類と機能・性質解明」の項目に関しては、Wasserstein距離およびボトルネック距離を用いた金属ナノクラスターのRRMの類似度比較を開始したが、RRMの比較に最適のものであるとは言いがたい結果となった。今後は、RRMの特徴を活かした新たな「距離」の定義方法について検討を進める。
  PESや反応経路地図の解析、という観点では、様々な観測時間スケールでPESの速度論的な可視化を実現する手法を新たに共同で開発した。PESのエネルギー値の関係をそのまま表示する従来のdisconnectivity graphとは異なり、時間スケールに基づいた階層性を表現するものになっている。
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 23K26608
• 位相的データ解析による反応経路地図の特徴量抽出と反応性比較・分類・予測への応用
  科学研究費助成事業 基盤研究(B)
  01 Apr. 2023 - 31 Mar. 2026
  小林 正人
  日本学術振興会, 基盤研究(B), 北海道大学, 23H01915
• Computational Research on Materials with Better Functions and Durability Toward Sustainable Development
  Program for Promoting Researches on the Supercomputer Fugaku
  Apr. 2023 - Mar. 2026
  館山 佳尚; 三宅 隆; 松林 伸幸; 大谷 実; 泰岡 顕治; 藤本 和士; 福島 鉄也; 笠松 秀輔; 久保 百司; 新里 秀平; 赤木 和人; 小林 正人; 新屋 ひかり; 中田 彩子
  MEXT, NIMS, Coinvestigator, Competitive research funding, JPMXP1020230325
• 大規模量子分子動力学計算と準安定結晶構造探索に基づく超秩序構造の理論的研究
  科学研究費助成事業 学術変革領域研究(A)
  01 Apr. 2023 - 31 Mar. 2025
  小林 正人
  日本学術振興会, 学術変革領域研究(A), 北海道大学, 23H04093
• Acceleration of the Development of Organic Reactions Based on the Fusion of Automatic Synthesis Robots and Information Science
  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
  01 Apr. 2021 - 31 Mar. 2024
  長田 裕也; 水野 雄太; 田畑 公次; 辻 信弥; 小林 正人
  有機合成研究において反応条件の最適化は極めて重要であり、研究遂行のためには多大な労力と時間を費やし続けている。本研究は、自動合成ロボットと量子化学計算によって得られる分子記述子を用いた強化学習を用いることで、反応条件の最適化を飛躍的に加速させることを目的としている。
  ２０２１年度の研究においては、自動合成ロボットにおける予備的有機合成実験を実施し、さらに実験結果の自動測定に取り組んだ。初期検討として、熱的フィスゲン環化付加反応と縮合剤を用いたアミド化反応に関する検討に取り組んだ。遷移金属触媒を用いずにフィスゲン環化付加反応を行った場合、1,4-付加体と1,5-付加体の混合物が得られ、これらの生成比は基質の構造に依存する。あらかじめ量子化学計算によって生成比の予測を行い、続いて自動合成ロボットを用いた合成実験と生成比の決定を行うことで両者の比較を行い、反応モデルの改良を行うことで、良い精度で生成比の予測を行う方法の開発に成功した。
  また、縮合剤を用いたアミド化反応に関する検討では、種々のカルボン酸類とアミン類からアミド化合物を合成し、アミド類の構造と超臨界流体クロマトグラフィーでの保持時間の関係について検討を行った。超臨界流体クロマトグラフィーではポリブチレンテレフタレートがコーティングされたシリカゲルを固定相として用いたカラムを使用することで、迅速な分離分析を行うことができることを見出した。現在、アミド類の構造とその保持時間の相関について分子記述子を用いた解析を進めており、未知のアミド化合物の分析条件の推定が可能になるものと期待している。
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 21H01924
• Elucidation of synergistic effects and dynamic properties of hyper-ordered structures using large-scale quantum chemical calculations and crystal structure database
  Grants-in-Aid for Scientific Research
  10 Sep. 2021 - 31 Mar. 2023
  小林 正人
  本研究では、(1)多様な超秩序構造材料の大規模量子分子動力学計算を実現するプログラムの開発と、(2)準堰堤結晶構造データベースとパーシステント・ホモロジー解析を利用したアモルファス-結晶の構造相関解析手法の開発を推進することにより、超秩序構造材料の機能発現機構を原子レベルで解明する計算化学プラットフォームを構築し、領域内の融合研究に利用する。
  (1)に関して、我々は数千～数万原子系の量子化学計算法である分割統治密度汎関数強束縛（DC-DFTB）法を開発してきたが、元素ペアに対するパラメータが必要であり、既存のパラメータで多様な超秩序構造材料を広範に取り扱うことはできない。そこで本年度は、元素ごとのパラメータで計算可能なGFN-xTB法にDC法を導入したDC-xTB法の開発を行った。開発したDC-xTB法による計算時間は系の大きさに対してほぼ線形となっており、またDC法のバッファ領域の大きさを制御することにより通常のxTB法の計算結果が再現できることも確かめられた。
  (2)に関して、反応経路自動探索プログラムGRRMを使用して、ガラス化しないTiO2の準安定結晶構造データベースを作成し、すでに構築されていたSiO2の準安定結晶構造データベースとともにそのパーシステント・ホモロジー解析を行った。TiO2の方が低エネルギー準安定構造の数は多かったが、そのパーシステンス・ダイアグラムはスポット的に集中する傾向にあり、ガラス化しやすいSiO2とは大きく異なることが分かった。
  Japan Society for the Promotion of Science, Grant-in-Aid for Transformative Research Areas (A), Hokkaido University, 21H05544
• High-order many body correlation analysis of network forming glass based on comprehensive integration of experimental, theoretical and data sciences
  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
  Apr. 2020 - Mar. 2023
  志賀 元紀; 小原 真司; 小林 正人; 平田 秋彦; 小野寺 陽平
  非晶質材料に内在する秩序の記述および効率的な計算法の開発のために、理論計算による大規模な構造モデルの構築、量子ビームによる計測データから秩序を同定する方法の開発、また、実験データに適合する構造モデルから中距離秩序を抽出する試みを行った。
  大規模な構造モデル構築の課題において、構造エネルギーや原子にかかる力を高速に計算するために機械学習モデルの開発に取り組んだ。訓練データとして、DC-DFTB法を用いてシリカの様々な構造に対して計算した結果を用意した。DC-DFTB計算に対して、全エネルギーを構成原子に割り当てるエネルギー密度解析を用いて、学習データを高効率的に収集することが可能となった。こうして生成された訓練データに対して、原子配置に関する記述子を入力として、機械学習モデルを構築し、予測性能を検証した。
  計測データ解析の課題では、Åビーム電子回折実験を計算機において仮想的に行うヴァーチャルÅビーム電子回折法を開発し、計算ホモロジーおよび分子動力学法と組み合わせることで、代表的な金属ガラスであるPd-Siのトポロジー的な秩序領域から得られる電子回折の特徴を調べた。その結果、トポロジー的な秩序領域では1nm以上にわたり方向の揃った擬格子面が形成されており、これに対応して回折パターン中に強い強度のスポットが出現することがわかった。
  また、温度と圧力を精密に制御して合成した永久高密度化シリカガラスについて、その高密度化のメカニズムを量子ビーム実験と構造モデリング、トポロジカル解析を駆使することによって明らかにした。ガラスの3次元構造モデルをSPring-8、海外の原子炉・パルス中性子源を利用して測定した量子ビーム実験データを再現する構造モデルを構築し、化学結合によるネットワークが形成するリング、原子分布が形成する空隙を解析することで、永久高密度化ガラスの構造秩序の起源を明らかにした。
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Gifu University, 20H04241
• パーシステント・ホモロジーを用いたグローバル反応経路地図に対する記述子の開拓
  研究助成（一般）
  Oct. 2020 - Sep. 2022
  小林正人; 寺本央; 青木雅充; 石橋卓
  量子化学探索研究所, 北海道大学, Principal investigator
• 大規模複雑電子構造系の遷移状態・電子励起状態計算法の確立と生体反応への応用
  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)
  01 Apr. 2017 - 31 Mar. 2021
  小林 正人; 赤間 知子
  本研究では、大規模計算法の分割統治(DC)法と複雑系電子状態計算法のHartree-Fock-Bogoliubov (HFB)法を土台として、大規模で複雑な電子構造を持つ系の遷移状態探索や電子励起状態を取り扱うための量子化学理論の確立を目的としている。
  本年度は、昨年度着手したDC-MP2電子相関計算に対するバッファ領域の自動決定法の開発を行った。電子相関は、電子状態の高精度な記述に欠かせないものである。また、バッファ領域はDC法の精度を決める重要なパラメータであるが、これまでは精度が適切な範囲となるように経験的に決められていた。昨年度、電子相関を含まない一電子近似の範囲で、これを自動的に決定する方法を確立したが、一電子近似計算は反復的な計算であり、徐々にバッファ領域を調節することが可能であった。しかし、MP2計算は一回で終わる計算であるため、計算中の調整ができないという難点がある。本研究では、Laplace変換MP2法というDC法とは異なるMP2計算の効率的計算法の表式にヒントを得て、一電子近似計算で決めたバッファ領域の各原子からのエネルギー寄与を概算し、適切なバッファ領域を決めるスキームを開発した。これについては、現在論文を執筆中である。本手法のエネルギー勾配（遷移状態構造最適化などに必要）は、以前代表者が開発したDC-MP2エネルギー勾配を直接用いることが可能であり、これを利用して昨年度達成した反応経路自動探索法との接続も可能である。また、現在、エネルギー勾配計算に対して適切なバッファ領域を自動決定する方法も検討している。
  一方、分担研究者の産休のため遅れていた電子励起状態を取り扱うための時間依存HFB (TD-HFB)法の検討を開始した。現在、理論の精査を進めており、プログラム開発にも着手する予定である。
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Hokkaido University, 17K05738
• Evaluation of synergistic effects in chemical reactions of multinary systems and its application to catalyst development
  PRESTO
  Dec. 2015 - Mar. 2019
  Japan Science and Technology Agency, Advanced Materials Informatics through Comprehensive Integration among Theoretical, Experimental, Computational and Data-Centric Sciences, Hokkaido University, Principal investigator
• 感応性化学種が持つ中間的な電子構造とその反応に関する理論的研究
  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
  01 Apr. 2015 - 31 Mar. 2017
  小林 正人
  本課題では、分散力・強い電子相関・環境効果などを介した「中間的な電子構造」が感応性化学種を支配する重要なキーワードであると捉え、精緻な量子化学計算により感応性化学種の構造と反応、物性を理解することを目的として研究を行った。
  本年度はまず、異常に長い結合長を持つ化合物DSAPの構造起源に関する研究を行った。DSAPはX線構造解析により177.1 pmのC-C結合長を持つ化合物である。この異常な結合長は単分子の性質だけから現れるものではなく、結晶のパッキング効果や、分子内および分子間に働く分散力のバランスによって実現されていることを理論・計算化学的観点から示した。具体的には、Grimmeの補正法により分散力を、ONIOM法や周期境界条件計算により環境効果を取り込んだ精緻な量子化学計算により、DSAPのユニットセル中に含まれる4種類の分子の構造を全て精度よく再現することに成功した。
  また、強い電子相関を記述するのに有効なHartree-Fock-Bogoliubov (HFB)法を大規模系に適用するため、DC法と組み合わせたDC-HFB法の開発と感応性化学種への応用を行った。代表的な感応性化学種に中間ジラジカル性を持つ分子があるが、これらの適切な構造計算には強い電子相関を考慮することが欠かせない。また強い電子相関を考慮できる大規模系計算法は、これまで確立されていない。本年度は、ポリフェノキノジメタンに対するDC-HFB計算により、本手法が系の大きさに対して線形の計算時間で強い電子相関の効果を有効的に記述できるものであることを示した。今後は、バッファ領域というDC法のパラメータを自動的に決定できるアダプティブDC-HFB法や、大規模強相関系の構造計算を可能とするDC-HFBエネルギー勾配法へと展開し、感応性化学種を中心に応用展開する予定である。
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Hokkaido University, 15H00908
• Development and application of black-box quantum chemical theory for large strongly correlated systems
  Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)
  01 Apr. 2013 - 31 Mar. 2016
  Kobayashi Masato
  The black-box computational method that enables us to perform quantum chemical calculations of large strongly correlated electronic systems was developed. The divide-and-conquer (DC) method was used to treat large systems, while the Hartree-Fock-Bogoliubov (HFB) method based on the electron-pair wave functions (geminals) was used to consider the strong electron correlation. In particular, we developed the adaptive DC method that controls the energy error introduced by the DC method, the HFB energy gradient method, and the DC-HFB method that combines the DC method and HFB method.
  Japan Society for the Promotion of Science, Grant-in-Aid for Young Scientists (B), Hokkaido University, 25810011
• 分割統治(DC)大規模高精度計算法を活用した有機分子集合系の超構造と電子状態論
  Research Grant 2011
  Apr. 2011 - Mar. 2012
  Association for the Progress of New Chemistry, 有機電子材料の集合体構造と電子特性の関係の計算科学的研究, Waseda University
• Development of the geminal-based quantum chemical theory and its application to nanomagnetic devices
  Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)
  2010 - 2012
  KOBAYASHI Masato
  Beyond the current quantum chemical framework that is based on the one-electron wavefunction (orbital), a novel quantum chemical theory that is based on the two-electron wavefunction (geminal) and its computer program have been established. It enabled highly accurate quantum chemical calculations of strongly-correlated systems with few parameters. Furthermore, the divide-and-conquer method, which is a large-scale calculation theory, has been developed to enable highly accurate quantum chemical calculations of real systems.
  Japan Society for the Promotion of Science, Grant-in-Aid for Young Scientists (B), Waseda University, 22750016
• Development of accelerated quantum dynamics theory
  Grants-in-Aid for Scientific Research
  2006 - 2009
  NAKAI Hiromi; IMAMURA Yutaka; KOBAYASHI Masato; SATO Takeshi; KIKUCHI Yasuaki; ATSUMI Teruo
  The present study presented the theoretical development of electronicstructure calculations for large systems. The theoretical treatment for quantum dynamics of nuclei was developed based on the nuclear orbital plus molecular orbital (NOMO) theory. The energy density analysis (EDA) techniques were improved for effective analysis of the electronic-structure calculations of real systems.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Priority Areas, Waseda University, 18066016
• 大規模電子状態計算を用いた光合成アンテナ複合体に関する研究
  Grants-in-Aid for Scientific Research Grant-in-Aid for JSPS Fellows
  2006 - 2007
  小林 正人
  光合成アンテナ系のようなタンパク質複合体の電子状態を精度良く表すためには、現在広く用いられている密度汎関数理論(DFT)では十分でないため、波動関数理論に基づいた電子相関を含む高精度な電子状態計算の高速化が必要不可欠である。報告者はこのニーズに応えるため、全系を部分系に分割して計算を行う分割統治(DC)法に注目し、これに基づく高速な2次Moller-Plesset摂動(MP2)計算法、DC-MP2法を開発してきた(J. Chem. Phys. 127, 074103)。これにより計算コストを系の大きさNに対してほぼ線形と、従来法のN^5に対して劇的に改善することに成功した。しかし、そのプレファクターは大きく、実際の計算のためにはこの改善が求められていた。そこで、Hartree-Fockと電子相関計算の両者で同程度の精度を保つために要求される部分系の環境(バッファ領域)の大きさが異なることを用い、このプレファクターを削減するdual-level DC-MP2法を開発した。さらに、DC法をMP2よりもさらに精度の高い結合クラスター(CC)法に適用したDC-CCSD法の理論およびプログラムを開発し、線形の計算時間を保ったまま高精度の計算手法に拡張することに成功した。
  MP2法やCCSD法によって、動的電子相関を定量的に取り扱うことはできるが、静的電子相関はほとんど取り入れることができない。これを効率よく取り入れることができ、大規模系への適用も期待される手法にAPSG法があるが、この手法は動的電子相関を取り入れることができなかった。申請者は、APSG波動関数に対して摂動的に動的相関を取り入れる手法を開発した。これにより、結合の解離などを伴う化学反応のエネルギー局面を定量的に再現することに成功した。
  Japan Society for the Promotion of Science, Grant-in-Aid for JSPS Fellows, Waseda University, 06J00448

• エリアデザイン提案システム、及びエリアデザイン提案方法
  Patent right, 岡本 守; 竹本 享史; 内垣内; 洋; クラシエンアピバーン; タンティップ; シリナピグ; 中村 篤祥; 小林 正人; 水野 雄太; 寺本 央
  特願2023-555979, 28 Oct. 2021
  特許7670276
  30 Apr. 2025
• セリウム（ＩＩＩ）イオンと、該セリウム（ＩＩＩ）イオンと配位結合を形成する配位子と、を含む希土類錯体
  Patent right, 北川 裕一; 富川 虎乃輔; 庄司 淳; 長谷川 靖哉; 伏見 公志; 赤間 知子; 小林 正人; 武次 徹也
  特願2022-35630, 08 Mar. 2022
  特開2023-130997, 21 Sep. 2023
• エネルギー取引支援装置及びエネルギー取引支援方法
  Patent right, 岡本 守; 竹本 享史; 内垣内 洋; 古林 優希; 寺田 圭佑; 中村 篤祥; 寺本 央; 長山 雅晴; 水野 雄太; 小松▲崎▼ 民樹; 小林 正人, 国立大学法人北海道大学, 株式会社日立製作所
  特願2021-082895, 17 May 2021
  特開2022-176451, 30 Nov. 2022
  202203013856597361