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研究者情報

マスター

アカウント（マスター）

  • 氏名

    小林　正人(コバヤシ　マサト), コバヤシ　マサト

所属（マスター）

  • 理学研究院　化学部門　物理化学分野

所属（マスター）

  • 理学研究院　化学部門　物理化学分野

独自項目

syllabus

  • 2021, 分子化学Ａ（分子理論化学）, Molecular Chemistry A (Theoretical Chemistry), 修士課程, 総合化学院, シュレディンガー方程式，分子軌道法，ハートリー・フォック方程式，密度汎関数理論，ボルン・オッペンハイマー近似，ポテンシャルエネルギー曲面，振動回転状態，遷移状態，反応経路，ダイナミクス，凝縮系，分子シミュレーション
  • 2021, 大学院共通授業科目（一般科目）：自然科学・応用科学, Inter-Graduate School Classes(General Subject):Natural and Applied Sciences, 修士課程, 大学院共通科目, Photofunctional molecules, Semiconductor, Quantum chemical calculation, Nanomaterial, Catalyst, Energy source, Diffusion, Reaction
  • 2021, 総合化学特論Ⅰ(Modern Trends in Physical and Material Chemistry), Modern Trends in Physical and Material Chemistry, 修士課程, 総合化学院, Photofunctional molecules, Semiconductor, Quantum chemical calculation, Nanomaterial, Catalyst, Energy source, Diffusion, Reaction
  • 2021, 先端総合化学特論Ⅰ, Modern Trends in Chemical Sciences and Engineering I, 博士後期課程, 総合化学院, Photofunctional molecules, Semiconductor, Quantum chemical calculation, Nanomaterial, Catalyst, Energy source, Diffusion, Reaction
  • 2021, 一般教育演習(ﾌﾚｯｼｭﾏﾝｾﾐﾅｰ), Freshman Seminar, 学士課程, 全学教育, 化学　機能性物質　環境　健康　ものづくり　化学産業　高分子科学　生物物理学　科学倫理　
  • 2021, 量子化学Ⅰ, Quantum Chemistry I, 学士課程, 理学部, 量子化学、電子状態理論、分子軌道法、群論
  • 2021, 教科教育法（理科II）, Teaching Method of School Subjects(Science Ⅱ), 学士課程, 教育学部, 教員養成、理科教育法、指導法

researchmap

プロフィール情報

所属

  • 北海道大学, WPI-ICReDD, 兼務教員
  • 北海道大学, 電子科学研究所附属社会創造数学研究センター, 兼務教員

学位

  • 博士（理学）（2007年03月 早稲田大学）

プロフィール情報

  • 姓

    小林, コバヤシ

  • 名

    正人, マサト

  • ID各種

    200901005800017432

対象リソース

所属

  • 北海道大学, WPI-ICReDD, 兼務教員
  • 北海道大学, 電子科学研究所附属社会創造数学研究センター, 兼務教員

業績リスト

研究キーワード

  • 電子状態理論   マテリアルズ・インフォマティクス   触媒インフォマティクス   ケモインフォマティクス   理論化学   量子化学   

研究分野

  • ナノテク・材料 / 基礎物理化学 / 理論化学

経歴

  • 2021年10月 - 現在 北海道大学 電子科学研究所 附属社会創造数学研究センター 兼務教員
  • 2020年11月 - 現在 北海道大学 大学院理学研究院 化学部門 准教授
  • 2019年04月 - 現在 北海道大学 化学反応創成研究拠点 兼務教員
  • 2014年04月 - 2022年03月 京都大学 触媒・電池元素戦略研究拠点ユニット 拠点教員
  • 2017年07月 - 2020年10月 北海道大学 大学院理学研究院 講師
  • 2015年12月 - 2019年03月 科学技術振興機構 さきがけ研究員
  • 2014年03月 - 2017年06月 北海道大学 大学院理学研究院 助教
  • 2012年04月 - 2014年02月 早稲田大学 高等研究所 助教
  • 2008年04月 - 2012年03月 早稲田大学 理工学術院 客員講師
  • 2008年04月 - 2012年03月 自然科学研究機構 分子科学研究所 専門研究職員
  • 2007年04月 - 2008年03月 日本学術振興会 特別研究員(PD)
  • 2007年10月 - 2007年12月 エトヴェシュ・ロラーンド大学(ブダペスト) 訪問研究員
  • 2006年04月 - 2007年03月 日本学術振興会 特別研究員(DC2)

学歴

  • 2004年04月 - 2007年03月   早稲田大学   大学院理工学研究科   化学専攻
  • 1999年04月 - 2003年03月   早稲田大学   理工学部   化学科

委員歴

  • 2023年04月 - 現在   日本化学会   理論化学・情報化学・計算化学ディビジョン 幹事
  • 2016年04月 - 現在   科学技術・学術政策研究所   科学技術専門家ネットワーク・専門調査員
  • - 現在   Theory and Applications of Computational Chemistry 2020 (TACC2020)   事務局員
  • 2021年10月 - 2025年09月   理論化学会   幹事
  • - 2021年09月   第15回分子科学討論会   実行委員
  • - 2019年05月   第22回理論化学討論会   実行委員
  • - 2017年05月   ナノ学会第15回大会   実行委員
  • - 2015年06月   第31回化学反応討論会   実行委員
  • 2012年04月 - 2014年03月   早稲田大学高等研究所   編集委員
  • - 2011年07月   第7回理論化学物理国際会議(ISTCP-VII)   事務局員（広報）

受賞

  • 2012年 第2回CMSI研究会 優秀ポスター賞
  • 2009年 日本コンピュータ化学会 吉田賞(論文賞)
  • 2008年 WATOC2008 ポスター発表賞

論文

  • 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 2024年08月
  • Makoto Tsurui, Ryohei Takizawa, Yuichi Kitagawa, Mengfei Wang, Masato Kobayashi, Tetsuya Taketsugu, Yasuchika Hasegawa
    Angewandte Chemie (International ed. in English) e202405584  2024年05月26日 
    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.
  • Shota Hosoya, Sunao Shoji, Takayuki Nakanishi, Masato Kobayashi, Mengfei Wang, Koji Fushimi, Tetsuya Taketsugu, Yuichi Kitagawa, Yasuchika Hasegawa
    Inorganic Chemistry 2024年05月21日
  • Yutaka Nagahata, Masato Kobayashi, Mikito Toda, Satoshi Maeda, Tetsuya Taketsugu, Tamiki Komatsuzaki
    Proceedings of the National Academy of Sciences 121 21 2024年05月17日 
    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.
  • Yuto Goto, Kanta Ando, Hideo Takakura, Kohei Nakajima, Masato Kobayashi, Osamu Inanami, Tetsuya Taketsugu, Mikako Ogawa
    Journal of Photochemistry and Photobiology 20 100230 - 100230 2024年04月
  • Koki Ogawara, Osamu Inanami, Hideo Takakura, Kenichiro Saita, Kohei Nakajima, Sonu Kumar, Naoya Ieda, Masato Kobayashi, Tetsuya Taketsugu, Mikako Ogawa
    Advanced Science 2024年01月15日 
    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.
  • 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 2024年
  • Hiroshi Teramoto, Takuya Saito, Masamitsu Aoki, Burai Murayama, Masato Kobayashi, Takenobu Nakamura, Tetsuya Taketsugu
    Journal of Chemical Theory and Computation 19 17 5886 - 5896 2023年08月29日
  • 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 2023年07月03日
  • 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 2023年05月
  • Masatsugu Nishida, Tomoko Akama, Masato Kobayashi, Tetsuya Taketsugu
    Chemical Physics Letters 816 140386 - 140386 2023年04月
  • Hiromi Nakai, Masato Kobayashi, Takeshi Yoshikawa, Junji Seino, Yasuhiro Ikabata, Yoshifumi Nishimura
    The Journal of Physical Chemistry A 127 3 589 - 618 2023年01月11日 [査読有り][通常論文]
  • Keisuke Tashiro, Masato Kobayashi, Kiyotaka Nakajima, Tetsuya Taketsugu
    RSC Advances 13 24 16293 - 16299 2023年 
    By repeatedly utilizing the MC-AFIR method, a comprehensive reaction-path search for the oligomerization of HMF was conducted to clarify the mechanism of humin formation in the oxidation of HMF to FDCA.
  • Burai Murayama, Masato Kobayashi, Masamitsu Aoki, Suguru Ishibashi, Takuya Saito, Takenobu Nakamura, Hiroshi Teramoto, Tetsuya Taketsugu
    2022年11月 [査読無し][通常論文]
  • 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 2022年08月16日 [査読有り][通常論文]
     
    Ligand release from silicon phthalocyanine (SiPc) dyes triggered by near-infrared (NIR) light is a key photochemical reaction involving caged compounds based on SiPc. Although NIR light is relatively permeable compared with visible light, this light can be attenuated by tissue absorption and scattering; therefore, using light to induce photochemical reactions deep inside the body is difficult. Herein, because X-rays are highly permeable and can produce radicals through the radiolysis of water, we investigated whether the axial ligands of SiPcs can be cleaved using X-ray irradiation. SiPcs with different axial ligands (alkoxy, siloxy, oxycarbonyl, and phenoxy groups) were irradiated with X-rays under hypoxic conditions. We found that the axial ligands were cleaved via reactions with hydrated electrons (e-aq), not OH radicals, generated from water in response to X-ray irradiation, and SiPc with alkoxy groups exhibited the highest cleavage efficiency. A quantitative investigation revealed that X-ray-induced axial ligand cleavage proceeds via a radical chain reaction. The reaction is expected to be applicable to the molecular design of X-ray-activatable functional molecules in the future.
  • Yuichi Kitagawa, Ryoma Moriake, Tomoko Akama, Koki Saito, Kota Aikawa, Sunao Shoji, Koji Fushimi, Masato Kobayashi, Tetsuya Taketsugu, Yasuchika Hasegawa
    ChemPlusChem 2022年07月13日 [査読有り][通常論文]
  • Hideo Takakura, Shino Matsuhiro, Masato Kobayashi, Yuto Goto, Mei Harada, Tetsuya Taketsugu, Mikako Ogawa
    Journal of Photochemistry and Photobiology A: Chemistry 426 113749 - 113749 2022年04月 [査読有り][通常論文]
     
    Near-infrared photoimmunotherapy (NIR-PIT) is a novel phototherapy for the treatment of cancer that uses NIR light and conjugates of antibody-IR700, a silicon phthalocyanine photosensitizer. A key feature of NIR-PIT is light-induced axial ligand cleavage of IR700, which finally causes cytotoxicity. Here, we focused on protonation of the axial ligand on the IR700 anion radical during the photochemical process. The Gibbs energy in the protonation reaction of IR700 derivatives with different axial ligands was calculated. These calculations suggested the order of the cleavage efficiency corresponds to the basicity of the axial ligand (i.e. alkoxy > siloxy (IR700) > phenoxy > oxycarbonyl), which was confirmed by the photoirradiation experiments with synthesized compounds. Thus, axial ligand cleavage is significantly dependent on the basicity of the axial ligand. Our findings suggest that PIT reagent with an IR700 derivative bearing alkoxy group would show better efficacy than IR700.
  • Masato KOBAYASHI, Ryo YONEYAMA, Sayoko NOJO, Keisuke TASHIRO, Tetsuya TAKETSUGU
    Journal of Computer Chemistry, Japan 21 4 96 - 98 2022年
  • Masato Kobayashi, Yuta Oba, Tomoko Akama, Tetsuya Taketsugu
    J. Math. Chem. 61 2 322 - 334 2022年 [査読有り][通常論文]
  • 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 2022年 [査読有り][通常論文]
  • Masato Kobayashi
    Computational and Data-Driven Chemistry Using Artificial Intelligence 217 - 229 2022年 [査読有り][招待有り]
  • 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 2021年10月22日 [査読有り][通常論文]
     
    For achieving a low-carbon society and providing stable energy supply to local areas, we propose a distributed energy system in which multiple small grids are installed in a distributed manner in an area. Multiple electric vehicles located in the area are used as mobile batteries for power leveling between grids and used as regional transportation. To construct this system, it is necessary to provide practical solutions in accordance with the needs in various areas by adjusting the balance between optimization of power management and transportation, which are in a trade-off relationship, while dealing with uncertainties such as climate change and time-varying transportation demand in a short time. In this paper, we propose a multi-objective spatiotemporal optimization algorithm for solving the above problem. We compared the performance of the proposed algorithm with a vehicle-routing-problem solver of Google OR-Tools, demonstrating that the transportation rate increased by 13% and sum of power excess and shortage in grids decreased by 87%. The proposed algorithm can also adjust the balance between optimizations of transportation and electricity-management, suggesting that it can be applied in various areas.
  • 小林正人, 藤森俊和, 武次徹也
    Journal of Computer Chemistry, Japan 20 2 48 - 59 2021年09月 [査読有り][招待有り]
  • 量子化学計算とインフォマティクスによる触媒開発への応用
    小林正人
    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 2021年07月 [査読有り][招待有り]
  • Toshikazu Fujimori, Masato Kobayashi, Tetsuya Taketsugu
    Journal of Computational Chemistry 42 9 620 - 629 2021年02月03日 [査読有り][通常論文]
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  • 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 2021年01月14日 [査読有り][通常論文]
  • Masato Kobayashi, Mei Harada, Hideo Takakura, Kanta Ando, Yuto Goto, Takao Tsuneda, Mikako Ogawa, Tetsuya Taketsugu
    ChemPlusChem 85 9 1959 - 1963 2020年09月 [査読有り][通常論文]
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  • 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 2020年04月 [査読無し][招待有り]
  • Yusuke Kondo, Yuri Goto, Masato Kobayashi, Tomoko Akama, Takeshi Noro, Tetsuya Taketsugu
    Physical Chemistry Chemical Physics 22 46 27157 - 27162 2020年 

    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.

  • 触媒反応の収率予測や活性因子の特定に機械学習を利用
    小林 正人
    化学と工業 72 5 422 - 422 2019年05月 [査読有り][通常論文]
  • 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 2019年04月 [査読有り][招待有り]
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  • 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 2019年03月
  • Yusuke Kuroda, Masato Kobayashi, Tetsuya Taketsugu
    Chemistry Letters 48 2 137 - 139 2019年02月05日 [査読有り]
  • ハイスループット量子化学計算技術とインフォマティクスを活用した金属ナノクラスター触媒系の解析と予測
    小林 正人
    アンサンブル 21 1 22 - 28 2019年01月 [査読有り][通常論文]
  • Masato KOBAYASHI, Haruka ONODA, Yusuke KURODA, Tetsuya TAKETSUGU
    Journal of Computer Chemistry, Japan 18 5 251 - 253 2019年 [査読有り][通常論文]
  • 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 2019年01月 [査読有り][通常論文]
     
    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.
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  • Yusuke Kondo, Masato Kobayashi, Tomoko Akama, Takeshi Noro, Tetsuya Taketsugu
    Journal of Computational Chemistry 39 16 964 - 972 2018年06月15日 [査読有り][通常論文]
     
    Ab initio all-electron computations have been carried out for Ce+ and CeF, including the electron correlation, scalar relativistic, and spin–orbit coupling effects in a quantitative manner. First, the n-electron valence state second-order multireference perturbation theory (NEVPT2) and spin–orbit configuration interaction (SOCI) based on the state-averaged restricted active space multiconfigurational self-consistent field (SA-RASSCF) and state-averaged complete active space multiconfigurational self-consistent field (SA-CASSCF) wavefunctions have been applied to evaluations of the low-lying energy levels of Ce+ with [Xe]4f15d16s1 and [Xe]4f15d2 configurations, to test the accuracy of several all-electron relativistic basis sets. It is shown that the mixing of quartet and doublet states is essential to reproduce the excitation energies. Then, SA-RASSCF(CASSCF)/NEVPT2 + SOCI computations with the Sapporo(-DKH3)-2012-QZP basis set were carried out to determine the energy levels of the low-lying electronic states of CeF. The calculated excitation energies, bond length, and vibrational frequency are shown to be in good agreement with the available experimental data. © 2018 Wiley Periodicals, Inc.
  • Masato Kobayashi, Toshikazu Fujimori, Tetsuya Taketsugu
    Journal of Computational Chemistry 39 15 909 - 916 2018年06月05日 [査読有り][通常論文]
     
    In linear-scaling divide-and-conquer (DC) electronic structure calculations, a buffer region is used to control the error introduced by the DC approximation. In this study, an energy-based error estimation scheme is proposed for the DC self-consistent field method with a two-layer buffer region scheme. Based on this scheme, a procedure to automatically determine the appropriate buffer region in the DC method is proposed. It was confirmed that the present method works satisfactorily in calculations of water clusters and proteins, although its performance was insufficient for the calculation of a delocalized graphene system. © 2018 Wiley Periodicals, Inc.
  • 触媒・表面吸着系計算へのインフォマティクス応用事例
    小林 正人
    化学工業 69 1 27 - 32 2018年01月 [査読有り][招待有り]
  • 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 2017年09月 [査読有り][通常論文]
     
    Luminescent mononuclear seven-coordinate Eu-III complexes, with monocapped-octahedral (point group: C-3v), monocapped-trigonal-prismatic (C-2v), and pentagonal-bipyramidal (D-5h) coordination structures, are reported. The complexes each consist of a Eu-III ion, three tetramethylheptanedionates, and a phosphine oxide derivative. Controlling steric hindrance by means of introducing methyl groups into the phosphine oxide ligands resulted in the formation of three types of coordination polyhedral structures. The coordination geometrical structures of the Eu-III complexes were evaluated by single-crystal X-ray diffraction analysis and shape-factor calculations. The radiative rate constant of the Eu-III complex with a monocapped-octahedral structure was larger than those with monocapped-trigonal-prismatic and pentagonal-bipyramidal structures. Characteristic photophysical properties of the seven-coordinate Eu-III complexes are discussed with TD-DFT calculations and Arrhenius analysis of the ligand-to-metal charge transfer.
  • Masato Kobayashi, Tetsuya Taketsugu
    Chem. Lett. 45 11 1268 - 1270 2016年11月 [査読有り][通常論文]
     
    The Hartree-Fock-Bogoliubov (HFB) theory has recently attracted considerable attention in quantum chemistry as a novel strategy to account for the static electron correlation, which plays an essential role when breaking chemical bonds and treating diradical systems. The linear-scaling divide-and-conquer (DC) method is applied to the HFB method to treat large-scale bond-breaking and/or diradical systems with reasonable computational effort.
  • Hiroaki Nishizawa, Yoshifumi Nishimura, Masato Kobayashi, Stephan Irle, Hiromi Nakai
    JOURNAL OF COMPUTATIONAL CHEMISTRY 37 21 1983 - 1992 2016年08月 [査読有り][通常論文]
     
    The linear-scaling divide-and-conquer (DC) quantum chemical methodology is applied to the density-functional tight-binding (DFTB) theory to develop a massively parallel program that achieves on-the-fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC-DFTB potential energy surface are implemented to the program called DC-DFTB-K. A novel interpolation-based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC-DFTB-K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC-DFTB-K program, a single-point energy gradient calculation of a one-million-atom system is completed within 60 s using 7290 nodes of the K computer. (c) 2016 Wiley Periodicals, Inc.
  • Yuriko Ono, Yusuke Kondo, Masato Kobayashi, Tetsuya Taketsugu
    CHEMISTRY LETTERS 45 4 478 - 480 2016年04月 [査読有り][通常論文]
     
    It was demonstrated that spin-orbit coupling changed the lowest-lying electronic states of PtCN and PtNC from (2)Sigma to (2)Delta(5/2)d by highly correlated electronic structure theory, considering relativistic effects. On the other hand, the electronic ground states of PdCN and PdNC remained (2)Sigma(1/2), even after considering spin-orbit coupling effects.
  • Xiaohui Chen, Masashi Hojo, Zhidong Chen, Masato Kobayashi
    JOURNAL OF MOLECULAR LIQUIDS 214 369 - 377 2016年02月 [査読有り][通常論文]
     
    Not only in acetonitrile (MeCN) but also in primary alcohols (from methanol to 1-hexanol), the coordination ability of alkali metal (Li+, Na+), alkaline earth metal (Mg2+, Ca2+, or Ba2+), and indium (In3+) ions with the 1,3,6-naphthalenetrisulfonate ion (L3-, 1.0 x 10(-4) mol dm(-3)) has been examined by means of UV-visible spectroscopy. In MeCN, the precipitation takes place completely between alkali metal or alkaline earth metal ions and L3-. In the presence of excess amounts of the metal ions, the precipitates of Li3L and Mg2L3 tend to re-dissolve partially to form the "reverse" coordinated species of Li4L+ and Mg2L+. However, those precipitates of Na3L, Ca3L2, and Ba3L2 would not re-dissolve even in the presence of large excess amounts of the metal ions in MeCN. Between In3+ and L3-, both precipitation and successive re-dissolution reactions can occur in all the primary alcohols. The solubility products (pK(sp)) and "reverse" coordination constants with L3- (log K4(1+), log K2(2+), and log K2(3+) for alkali metal, alkaline earth metal, and indium ions, respectively) have been evaluated in MeCN, the primary alcohols, and binary solvents of MeCN-H2O and MeCN-MeOH. Where, for instance, K4(1+) = [M4L+]/([M+](4)[L3-]) for the reaction: 4M(+) + L3- reversible arrow M4L+. DFT calculations have been performed to predict the coordinating structures of the Li4L+ species in MeCN. (C) 2016 Elsevier B.V. All rights reserved.
  • 小林 正人, 黒田 悠介, 秋葉 欣哉, 武次 徹也
    J. Comput. Chem. Jpn. 14 6 199 - 200 日本コンピュータ化学会 2015年12月 [査読有り][通常論文]
     
    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.
  • Masato Kobayashi, Yusuke Kuroda, Kin-ya Akiba, Tetsuya Taketsugu
    BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 88 11 1584 - 1590 2015年11月 [査読有り][通常論文]
     
    The ligand coupling reaction (LCR) of hypervalent pentacoordinate antimony compounds (Ar(n)Tol(5-n)Sb; Ar = p-tri-fluoromethylphenyl, Tol = p-methylphenyl; n = 0-5) was analyzed via the long-range-corrected density functional theory. Although previous experimental or computational investigations have suggested apical apical or equatorial equatorial coupling of Ar(n)Tol(5-n)Sb compounds, the present results lead to apical equatorial coupling. The biased experimental ratios of the coupling products, which were grounds for apical apical coupling, can be explained by the stability of the transition-state (TS) structure for the apical equatorial coupling, where n-pi* interaction plays an important role to the stabilization. We further investigated the potential energy surface of H5Sb, for which the intrinsic reaction coordinate (IRC) from the TS structure for LCR indicates the equatorial equatorial coupling. It is found that the valley-ridge transition occurs along the IRC near the TS structure and the transverse vibrational mode with imaginary frequency, orthogonal to the IRC, directs to the reactant structure corresponding to the apical equatorial coupling.
  • 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 2015年10月 [査読有り][通常論文]
     
    Enhanced luminescence properties of mononuclear lanthanide complexes with asymmetric seven-coordination structures are reported for the first time. The lanthanide complexes are composed of a lanthanide ion (Eu-III or Tb-III), three tetramethyl heptanedionato ligands, and one triphenylphosphine oxide ligand. The coordination geometries of the lanthanide complexes have been evaluated by using single-crystal X-ray analyses and shape-measurement calculations. The complexes are categorized to be seven-coordinate monocapped octahedral structures (point group C-3v). The seven-coordinate lanthanide complexes show high intrinsic emission quantum yields, extra-large radiative rate constants, and unexpected small nonradiative rate constants. The brilliant luminescence properties have been elucidated in terms of the asymmetric coordination geometry and small vibrational quanta related to thermal relaxation.
  • Masato Kobayashi, Tetsuya Taketsugu
    THEORETICAL CHEMISTRY ACCOUNTS 134 9 2015年08月 [査読有り][通常論文]
     
    In 2005, Surjan showed two explicit formulas for evaluating the second-order Moller-Plesset perturbation (MP2) energy as a functional of the Hartree-Fock density matrix D (Chem Phys Lett 406: 318, 2005), which are referred to as the Delta E-MP2[D] functionals. In this paper, we present the finite-temperature (FT) MP2 energy functionals of the FT Hartree-Fock density matrix. There are also two formulas for the FT-MP2, namely the conventional and renormalized ones; the latter of which has recently been formulated by Hirata and He (J Chem Phys 138: 204112, 2013). We proved that there exists one-to-one correspondence between the formulas of two FT-MP2 and the Delta E-MP2[D] functionals. This fact can explain the different behavior of two Delta E-MP2[D] functionals when an approximate Hartree-Fock density matrix is applied, which was previously investigated by Kobayashi and Nakai (Chem Phys Lett 420: 250, 2006). We also applied the FT-MP2 formalisms to the linear-scaling divide-and-conquer method for improving the accuracy with tiny addition of the computational efforts.
  • Xiaohui Chen, Keita Ayabe, Masashi Hojo, Zhidong Chen, Masato Kobayashi
    JOURNAL OF MOLECULAR LIQUIDS 199 445 - 453 2014年11月 [査読有り][通常論文]
     
    The specific interactions between alkaline earth metal (Mg2+, Ca2+, or Ba2+) and p-toluenesulfonate (L-), 1,5-naphthalenedisulfonate (L2-), or 1,3,6-naphthalenetrisulfonate (L3-) ions (from the tetraethylammonium salt of L-, L2-, or L3-) have been examined by means of UV-visible spectroscopy in primary alcohols (from methanol to hexanol) as well as in the binary acetonitrile-alcohols (MeCN-MeOH, MeCN-EtOH), ethanol-methanol (EtOH-MeOH) and methanol-water (MeOH-H2O) solvents. The precipitation of non-charged species (e.g. ML0) and the successive re-dissolution of the precipitates, with increasing concentration of M(ClO4)(2), have revealed the formation of cationic charged species or "reverse coordinated" species, M2L2+, even in the protic media as well as in the aprotic solvent MeCN. The solubility products (K-sp) and the "reverse coordination" constants (2M(2+) + L2- reversible arrow M2L2+, K2(-2) = [M2L2+] / [M2+](2)[L2-] have been evaluated. In ethanol, both phenomena of the precipitation of ML and the successive re-dissolution to produce M2L2+ are observed for Ca2+ or Ba2+, but not for Mg2+. In butanol, the interaction between Mg2+ and the L2- causes the complete precipitation of MgL0 (pK(sp) = 1039) and also the successive re-dissolution of Mg2L2+ (log K2(-2) = 8.08). Even in methanol, the interaction between Ba2+ and L2- results in precipitation (log K-sp = 8.28) and the "reverse coordinated" species, Ba2L2+ (log K2(-2) = 5.58). The interaction of Ba2+ with L- or L3- causes no precipitation in methanol; however, in all the other alcohols, it results both in precipitation (BaL2 or Ba3L2) and the "reverse coordinated" species, BaL+ or Ba2L+. The formulation for the formation constants (K2(-3)) for M2+ and L3- is newly presented and the constants (2Ba(2+) + L3- reversible arrow Ba2L+, K2(-3) = [Ba2L+] / [Ba2+](2) [L3-]) are evaluated in ethanol and propanol as well as in the binary EtOH-MeOH solvents, up to 70% (v/v) MeOH. The donicities toward M2+ of the media have been related to the pKsp and "reverse coordination" constants for L-, L2- and L3-. (C) 2014 Elsevier B.V. All rights reserved.
  • Masato Kobayashi, Kin-ya Akiba
    ORGANOMETALLICS 33 5 1218 - 1226 2014年03月 [査読有り][通常論文]
     
    The ligand exchange reactions (LERs) of hypervalent compounds of antimony (R5Sb: R = Me, Ph) and tellurium (R4Te: R = Me, Ph) were analyzed via dispersion corrected density functional theory (DFT) and coupled cluster calculations. The dispersion force plays a key role in forming reactant/product complexes. For the phenyl ligand compounds, the pathway of the LER was predicted as being stepwise, while that for the methyl ligand compounds was predicted to be concerted. From the natural localized molecular orbital analysis for the reaction of Me4Te, it was found that the lone pair electrons of tellurium do not participate in LER. The LER of antimony compounds was elucidated to proceed along the mechanism similar to that of Me4Te. LER of a mixture of Me4Te and Me5Sb was shown to proceed more easily than that of each component.
  • M. Kobayashi
    J. Chem. Phys. 140 8 084115  2014年02月 [査読有り][通常論文]
     
    The analytical gradient for the atomic-orbital-based Hartree-Fock-Bogoliubov (HFB) energy functional, the modified form of which was proposed by Staroverov and Scuseria to account for the static electron correlation [J. Chem. Phys. 117, 11107 (2002)], is derived. Interestingly, the Pulay force for the HFB energy is expressed with the same formula as that for the Hartree-Fock method. The efficiency of the present HFB energy gradient is demonstrated in the geometry optimizations of conjugated and biradical systems. The geometries optimized by using the HFB method with the appropriate factor zeta, which controls the degree of static correlation included, are found to show good agreement with those obtained by using a complete active-space self-consistent field method, although they are significantly dependent on zeta. (C) 2014 AIP Publishing LLC.
  • Masashi Hojo, Yusuke Kondo, Kosuke Zei, Kei Okamura, Zhidong Chen, Masato Kobayashi
    BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 87 1 98 - 109 2014年01月 [査読有り][通常論文]
     
    Conductometric titrations with triethylamine (Et3N) of mono-, di-, and trisulfonic acids have been performed in acetonitrile, and strong homoconjugation (homoassociation) for di- and trisulfonic acids have been revealed. The appearance of a maximum in the conductometric titration curve enables us to predict the stable homoconjugation species in the solution. The homoconjugation reaction of monosulfonic acids, such as methanesulfonic and p-toluenesulfonic acids, are not large enough to give a maximum. However, disulfoiaic acids, 1,5, 2,6-, and 2,7-naphthalenedisulfonic acids, give maxima at the first equivalence point, which indicates that the conjugate ions (HA(-)) cause homoconjugation reactions. By means of UV-visible spectroscopy, the stability constant (K-D) of dimerization or homoconjugation reaction between two anions [2 HA(-) reversible arrow; (HA-)2] of the hydrogen 1,5-naphthalenedisulfonate (HA(-)) has been given to be logK(D) = 4.11 in acetonitrile. In the same solvent, 1,3,6-naphthalenetrisulfonic acid forms more stable species of not only (H(2)A(-))2 but also (H2A-)(HA(2-)). Double hydrogen-bonds can operate between two H(2)A(-) anions in the (H2A(-))2 species, while even triple hydrogen-bonds in the (H2A(-))(HA(2-)) species. Effects of second solvents, including H2O, have been examined in detail on the homoconjugation reactions. In order to differentiate the role of acidities of acids on homoconjugation, the conductometric titrations of nitrobenzenedicarboxylic acids have been also performed. The geometries of homoconjugated sulfonic acids have been justified by DFT calculations.
  • Takeshi Yoshikawa, Masato Kobayashi, Hiromi Nakai
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 113 3 218 - 223 2013年02月 [査読無し][通常論文]
     
    In this article, we develop the symmetry adopted cluster (SAC) theory based on the divide-and-conquer (DC) method, which accomplishes the linear-scaling computational time with respect to the system size, as well as the DC-based coupled cluster (CC) method does. Although the perturbative configuration selection adopted in the SAC program significantly reduces its computational cost compared with the CC calculations, the reduction of the configurations leads to less inclusion of the total correlation energy. However, the numerical assessments confirmed that the use of the local orbitals constructed in each subsystem in DC-SAC calculations reduces the loss in total correlation energy, which provides more reliable total and relative energies than the standard SAC method. (c) 2012 Wiley Periodicals, Inc.
  • Yoshikawa, Takeshi, Kobayashi, Masato, Fujii, Atsuhiko, Nakai, Hiromi
    Journal of Physical Chemistry B 117 18 5565 - 5573 2013年 [査読有り][通常論文]
  • Yoshikawa, Takeshi, Kobayashi, Masato, Fujii, Atsuhiko, Nakai, Hiromi
    Journal of Physical Chemistry B 117 18 5565 - 5573 2013年 [査読無し][通常論文]
  • Tarumi, Moto, Kobayashi, Masato, Nakai, Hiromi
    International Journal of Quantum Chemistry 113 3 239 - 244 2013年 [査読無し][通常論文]
  • Saparpakorn, Patchreenart, Kobayashi, Masato, Hannongbua, Supa, Nakai, Hiromi
    International Journal of Quantum Chemistry 113 4 510 - 517 2013年 [査読無し][通常論文]
  • Saparpakorn, Patchreenart, Kobayashi, Masato, Nakai, Hiromi
    Bulletin of the Chemical Society of Japan 86 1 67 - 74 2013年 [査読無し][通常論文]
  • M. Kobayashi, H. Nakai
    J. Chem. Phys. 138 4 044102  2013年 [査読有り][通常論文]
  • Tarumi, Moto, Kobayashi, Masato, Nakai, Hiromi
    International Journal of Quantum Chemistry 113 3 2013年 [査読無し][通常論文]
  • Yoshikawa, Takeshi, Kobayashi, Masato, Nakai, Hiromi
    International Journal of Quantum Chemistry 113 3 2013年 [査読無し][通常論文]
  • Saparpakorn, Patchreenart, Kobayashi, Masato, Hannongbua, Supa, Nakai, Hiromi
    International Journal of Quantum Chemistry 113 4 2013年 [査読無し][通常論文]
  • Saparpakorn, Patchreenart, Kobayashi, Masato, Nakai, Hiromi
    Bulletin of the Chemical Society of Japan 86 1 2013年 [査読無し][通常論文]
  • M. Tarumi, M. Kobayashi, H. Nakai
    J. Chem. Theory Comput. 8 11 4330 - 4335 2012年11月 [査読無し][通常論文]
     
    The antisymmetric product of strongly orthogonal geminals (APSG) method is a wave function theory that can effectively treat the static electron correlation. Recently, we proposed the open shell APSG method using one electron orbitals for open shell parts. In this paper, we have extended the perturbation correction to the open shell APSG calculations through Moller-Plesset-type multiconfiguration perturbation theory (MP-MCPT). Numerical applications demonstrate that the present open shell MP-MCPT can reasonably reproduce the dissociation energies or equilibrium distances for open shell systems.
  • Masato Kobayashi, Tsuguki Touma, Hiromi Nakai
    JOURNAL OF CHEMICAL PHYSICS 136 8 084108  2012年02月 [査読無し][通常論文]
     
    We report a linear-scaling computation method for evaluating the dynamic first hyperpolarizability beta 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 beta, 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 pi-conjugated and saturated organic chain systems verified that the present scheme considerably reduces the computational time for the beta 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. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3687341]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • M. Kobayashi, H. Nakai
    Phys. Chem. Chem. Phys. 14 21 7629 - 7639 2012年 [査読無し][通常論文]
  • Kobayashi Masato, Touma Tsuguki, Nakai Hiromi
    Dynamic hyperpolarizability calculations of large systems: the linear-scaling divide-and-conquer approach. 136 8 2012年 [査読有り][通常論文]
     
    :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.
  • Tsuguki Touma, Masato Kobayashi, Hiromi Nakai
    THEORETICAL CHEMISTRY ACCOUNTS 130 4-6 701 - 709 2011年12月 [査読無し][通常論文]
     
    This article describes the finite-field (FF) approach for calculating static (hyper)polarizabilities based on the divide-and-conquer (DC) method. The method is assessed by the Hartree-Fock (HF) and post-HF calculations of pi-conjugated model systems: a terminal donor or acceptor substituent on polyene chains. The DC-FF approach enables the evaluation of molecular polarizabilities with highly accurate coupled-cluster theory. Numerical assessments demonstrate that the (hyper)polarizabilities calculated by the present DC-FF method agree with the conventional FF results to within a few percent by employing an appropriate buffer size.
  • Takeshi Yoshikawa, Masato Kobayashi, Hiromi Nakai
    Theoretical Chemistry Accounts 130 2-3 411 - 417 2011年10月 [査読無し][通常論文]
     
    We have developed the spin-unrestricted divide-and-conquer (DC)-based linear-scaling self-consistent field method for treating open-shell systems (Kobayashi et al. in Chem Phys Lett 500:172, 2010). Because the method does not require the position of excess spins or charges, it made the treatment of large spin-delocalized systems tractable. The present study extends the DC-based unrestricted open-shell scheme to the correlated second-order Møller-Plesset perturbation (MP2) theory. Numerical applications to polyene cations demonstrate that the present method gives highly accurate results with less computational costs even for spin-delocalized systems. © 2011 Springer-Verlag.
  • Kobayashi, Masato, Nakai, Hiromi
    Linear-Scaling Techniques in Computational Chemistry and Physics: Methods and Applications 13 97 - 127 2011年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • Hiromi Nakai, Masato Kobayashi
    PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE (ICCS) 4 1145 - 1150 2011年 [査読無し][通常論文]
     
    In 2009, the authors implemented the linear-scaling divide-and-conquer (DC) methods into the GAMESS quantum chemistry package. This program enabled fast energy calculations of closed-shell large molecules with high accuracy in Hartree-Fock (HF), density functional theory, and post-HF levels of theory. After the first implementation, we extended the applicability of the DC scheme into several directions. In this Paper, we summarized recent and future developments in the DC code in GAMESS, namely, the energy gradient methods and open-shell treatments.
  • Masato Kobayashi, Tomotaka Kunisada, Tomoko Akama, Daisuke Sakura, Hiromi Nakai
    JOURNAL OF CHEMICAL PHYSICS 134 3 034105  2011年01月 [査読無し][通常論文]
     
    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. (C) 2011 American Institute of Physics. [doi:10.1063/1.3524337]
  • M. Katouda, M. Kobayashi, H. Nakai, S. Nagase
    J. Comput. Chem. 32 13 2756 - 2764 2011年 [査読無し][通常論文]
  • 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年 [査読有り][通常論文]
     
    :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.
  • Masato Kobayashi, Takeshi Yoshikawa, Hiromi Nakai
    CHEMICAL PHYSICS LETTERS 500 1-3 172 - 177 2010年11月 [査読無し][通常論文]
     
    In this Letter, the divide-and-conquer (DC) linear-scaling self-consistent field method is extended to the spin-unrestricted Hartree-Fock (UHF) method or Kohn-Sham density functional theory (UDFT) for treating large open-shell systems. Although the DC method is one of the fragmentation-based linear-scaling schemes, the present DC-UHF/UDFT framework can avoid specifying the number of up-and down-spin electrons in each fragment by introducing up-and down-spin Fermi levels. Test calculations for oligoth-iophenes demonstrate the high efficiency and accuracy of the DC-UHF/UDFT method even for spin-delocalized systems. (C) 2010 Elsevier B.V. All rights reserved.
  • 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年 [査読無し][通常論文]
  • Touma, Tsuguki, Kobayashi, Masato, Nakai, Hiromi
    Chemical Physics Letters 485 1-3 247 - 252 2010年 [査読無し][通常論文]
  • M. Kobayashi, Á. Szabados, H. Nakai, P. R. Surján
    J. Chem. Theory Comput. 6 7 2024 - 2033 2010年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • Hojo, Masashi, Ueda, Tadaharu, Ike, Michitaka, Kobayashi, Masato, Nakai, Hiromi
    Journal of Molecular Liquids 145 3 152 - 157 2009年 [査読無し][通常論文]
  • 小林正人, 赤間知子, 中井浩巳
    J. Comput. Chem. Jpn. 8 1 1 - 21 Society of Computer Chemistry, Japan 2009年 [査読無し][通常論文]
     
    線形コストスケーリング電子状態計算法のひとつである分割統治(DC)法は，これまで主にHartree-Fock (HF)交換項を含まない密度汎関数理論(DFT)や半経験的な分子軌道計算に適用されてきた．著者らは，このDC法をHF計算やハイブリッドDFT計算に適用し，効率的で有用な方法であることを確認してきた．さらに，エネルギー密度解析(EDA)の考え方を利用して，DC-HF計算で得られる部分系の軌道を用いた線形スケーリングポストHF計算法を独自に開発し，2次摂動(MP2)および結合クラスター(CCSD)計算でこの方法が有用であることを示した．著者らの研究室では，これらの手法は量子化学計算プログラムGAMESSに実装されており，通常の入力ファイルに多少の変更を施すだけで簡単に利用できるようになっている．本論文では，これまでにGAMESS上で開発を行ってきたDC計算プログラムの実装と計算可能なプロパティについて述べ，DC計算の実行方法および計算結果について報告する．
  • Kobayashi, Masato, Nakai, Hiromi
    International Journal of Quantum Chemistry 109 10 2227 - 2237 2009年 [査読無し][通常論文]
  • Akama, Tomoko, Kobayashi, Masato, Nakai, Hiromi
    International Journal of Quantum Chemistry 109 12 2706 - 2713 2009年 [査読無し][通常論文]
  • Kobayashi, Masato, Nakai, Hiromi
    Journal of Chemical Physics 131 11 114108  2009年 [査読無し][通常論文]
  • 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年 [査読有り][通常論文]
  • 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年 [査読無し][通常論文]
  • Tsuchimochi, Takashi, Kobayashi, Masato, Nakata, Ayako, Imamura, Yutaka, Nakai, Hiromi
    Journal of Computational Chemistry 29 14 2311 - 2316 2008年 [査読無し][通常論文]
  • Kobayashi, Masato, Nakai, Hiromi
    Journal of Chemical Physics 129 4 044103  2008年 [査読無し][通常論文]
  • 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年 [査読有り][通常論文]
  • Tomoko Akama, Masato Kobayashi, Hiromi Nakai
    Journal of Computational Chemistry 28 12 2003 - 2012 2007年09月 [査読無し][通常論文]
     
    The divide-and-conquer (DC) method, which is one of the linear-scaling methods avoiding explicit diagonalization of the Fock matrix, has been applied mainly to pure density functional theory (DFT) or semiempirical molecular orbital calculations so far. The present study applies the DC method to such calculations including the Hartree-Fock (HF) exchange terms as the HF and hybrid HF/DFT. Reliability of the DC-HF and DC-hybrid HF/DFT is found to be strongly dependent on the cut-off radius, which defines the localization region in the DC formalism. This dependence on the cut-off radius is assessed from various points of view: that is, total energy, energy components, local energies, and density of states. Additionally, to accelerate the self-consistent field convergence in DC calculations, a new convergence technique is proposed. © 2007 Wiley Periodicals, Inc.
  • M. Kobayashi, Y. Imamura, H. Nakai
    J. Chem. Phys. 127 7 074103  2007年08月 [査読無し][通常論文]
     
    A new scheme for obtaining the approximate correlation energy in the divide-and-conquer (DC) method of Yang [Phys. Rev. Lett. 66, 1438 (1991)] is presented. In this method, the correlation energy of the total system is evaluated by summing up subsystem contributions, which are calculated from subsystem orbitals based on a scheme for partitioning the correlation energy. We applied this method to the second-order Moller-Plesset perturbation theory (MP2), which we call DC-MP2. Numerical assessment revealed that this scheme provides a reliable correlation energy with significantly less computational cost than the conventional MP2 calculation. (c) 2007 American Institute of Physics.
  • M. Hojo, T. Ueda, T. Inoue, M. Ike, M. Kobayashi, H. Nakai
    J. Phys. Chem. B 111 7 1759 - 1768 2007年02月 [査読無し][通常論文]
     
    UV-Visible and <sup>1</sup>H or <sup>13</sup>C 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
  • Keitaro Sodeyama, Hiroaki Nishizawa, Minoru Hoshino, Masato Kobayashi, Hiromi Nakai
    CHEMICAL PHYSICS LETTERS 433 4-6 409 - 415 2007年01月 [査読無し][通常論文]
     
    The translation- and rotation-free nuclear orbital plus molecular orbital (TRF-NOMO) theory was developed in order to accurately determine the nonadiabatic nuclear and electronic wave functions without Born-Oppenheimer approximation. This study presents a hybrid method combining the TRF-NOMO theory with the generator coordinate method (GCM). The TRF-NOMO/GCM treatment is capable of giving the vibrational excited states with high accuracy, as well as improving the ground-state description by inclusion of the many-body effect. Numerical applications of the TRF-NOMO/GCM calculations to an HF molecule confirm its reliability and usefulness. (c) 2006 Elsevier B.V. All rights reserved.
  • Tomoko Akama, Atsuhiko Fujii, Masato Kobayashi, Hiromi Nakai
    MOLECULAR PHYSICS 105 19-22 2799 - 2804 2007年 [査読無し][通常論文]
     
    Recently, we applied Yang's divide-and-conquer (DC) method to the Hartree-Fock (HF) and hybrid density functional theories and assessed its reliability in calculations of bond-alternating polyene chains. In this paper, we investigate the cut-off behaviour of the HF exchange interaction in the DC-HF method by comparing the results of bond-alternating polyene chains with those of more delocalized uniform polyene chains. The cut-off error of the uniform chain is much larger than that of the bond-alternating chain because of the delocalized electronic structure of the uniform polyene chain. We also estimate the exponential decay coefficient of the cut-off error in the DC scheme and compare it with that of the real-space one-particle density matrix, which can be represented by the band gap in the insulator limit. It can be concluded that the cut-off derived from the DC-HF method can be reduced to an arbitrary magnitude of error by adopting an appropriate buffer radius corresponding to the band gap.
  • M. Kobayashi, T. Akama, H. Nakai
    J. Chem. Phys. 125 20 204106  2006年11月 [査読無し][通常論文]
     
    The density matrix (DM) obtained from Yang's [Phys. Rev. Lett. 66, 1438 (1991)] divide-and-conquer (DC) Hartree-Fock (HF) calculation is applied to the explicit second-order Moller-Plesset perturbation (MP2) energy functional of the HF DM, which was firstly mentioned by Ayala and Scuseria [J. Chem. Phys. 110, 3660 (1999)] and was improved by Surjan [Chem. Phys. Lett. 406, 318 (2005)] as DM-Laplace MP2. This procedure, termed DC-DM MP2, requires the HF DM of holes, for which we propose two evaluation schemes in DC manner. Numerical studies reveal that the DC-DM MP2 energy deviation from canonical MP2 is the same order of magnitude as DC-HF energy deviation from conventional HF whichever type of hole DM is adopted. It is also confirmed that the central processing unit time of DC-DM MP2 is less than that of DM-Laplace MP2 because the DC-HF DM is sparser than conventional DM. (c) 2006 American Institute of Physics.
  • M. Kobayashi, H. Nakai
    Chem. Phys. Lett. 420 1-3 250 - 255 2006年03月 [査読無し][通常論文]
     
    We numerically assess the method for obtaining second-order Moller-Plesset (MP2) energy from the Hartree-Fock density matrix (DM) recently proposed by Surjan [Surjan, Chem. Phys. Lett. 406 (2005) 318]. It is confirmed that Surjan's method, referred to as DM-Laplace MP2, can obtain MP2 energy accurately by means of appropriate integral quadrature and a matrix exponential evaluation scheme. Numerical tests reveal that the Euler-Maclaurin and the Romberg numerical integration schemes can achieve milli-hartree accuracy with small quadrature points. This Letter also indicates the possibility of the application of DM-Laplace MP2 to linear-scaling self-consistent field techniques, which give approximate DM. (c) 2006 Elsevier B.V. All rights reserved.
  • M Katouda, M Kobayashi, H Nakai, S Nagase
    JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 4 1 139 - 149 2005年03月 [査読無し][通常論文]
     
    We have developed a computer program for evaluation of electron repulsion integrals (ERIs) based on the accompanying coordinate expansion recurrence relation (ACE-RR) algorithm, which has been recently developed as an efficient algorithm for computation of ERIs using Pople-type basis sets (STO-3G and 6-31G, for example) and derivatives of ERIs [Kobayashi and Nakai, J Chem Phys 21:4050, 2004]. The computer program can be linked to GAMESS ab initio quantum chemistry program. The practical performance of the ACE-RR method is assessed by means of the central processing unit (CPU) time for the first direct self-consistent field cycle on a model system (4 x 4 x 4 cubic hydrogen lattice), taxol (C47H51NO14), and valinomycin (C54H90N6O18) using Pople-type basis sets. The considerable efficiency of the present ACE-RR method is demonstrated by measuring the CPU time. The present ACF-RR method is comparable to or at most 30% faster than the Pople-Hehre method which is also designed for efficient computation of ERIs using Pople-type basis sets. Furthermore, the ACE-RR method is drastically faster than the Dupuis-Rys-King method in the case where the degree of contraction of Pople-type basis sets is high: 7.5 times faster in the case of valinomycin using STO-6G basis set, for example.
  • M Kobayashi, H Nakai
    JOURNAL OF CHEMICAL PHYSICS 121 9 4050 - 4058 2004年09月 [査読無し][通常論文]
     
    We present an algorithm for the rapid computation of electron repulsion integrals (ERIs) over Gaussian basis functions based on the accompanying coordinate expansion (ACE) formula. The present algorithm uses equations termed angular momentum reduced expressions and introduces two types of recurrence relations to ACE formulas. Numerical efficiencies are assessed for (p p\p p) and (sp sp\sp sp) ERIs by using the floating-point operation count. The algorithm is suitable for calculating ERIs for the same exponents but different angular momentum functions, such as L shells and derivatives of ERIs. The present algorithm is also capable of calculating ERIs with highly contracted Gaussian basis functions. (C) 2004 American Institute of Physics.
  • Nakai, H, Kobayashi, M
    Chemical Physics Letters 388 1-3 50 - 54 2004年 [査読無し][通常論文]
  • Kobayashi, M, Nakai, H
    Abstracts of Papers of the American Chemical Society 226 2003年 [査読有り][通常論文]

MISC

  • 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年
  • 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年
  • 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年
  • 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年
  • 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年
  • 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年
  • 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年
  • 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 2018年11月03日 [査読無し][通常論文]
  • 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 2017年09月07日 [査読無し][通常論文]
  • 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 2017年03月10日 [査読無し][通常論文]
  • 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 2017年03月03日 [査読無し][通常論文]
  • 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 2017年03月03日 [査読無し][通常論文]
  • 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 2017年03月03日 [査読無し][通常論文]
  • 小野田 遼, 小林 正人, 武次 徹也 ケモインフォマティクス討論会予稿集 2016 (0) P15 2016年 [査読無し][通常論文]
     
    原子電荷のような局所的な説明変数でエネルギーを簡便にモデル化することができれば、量子化学計算の計算量の大幅削減が可能である。我々は、C<sub>3</sub>H<sub>6</sub>O<sub>2</sub>の異性体40種に対してMulliken、Lowdin、Natural、ESP電荷を説明変数としたMC+推定によるエネルギーのモデル化を試みた。その結果、少ない変数で当てはまりの良いモデルを作ることができた。次に対象をC<sub>8</sub>H<sub>10</sub>O<sub>2</sub>、C<sub>9</sub>H<sub>10</sub>O<sub>2</sub>、C<sub>9</sub>H<sub>10</sub>O<sub>3</sub>、C<sub>10</sub>H<sub>12</sub>O<sub>2</sub>異性体群に拡張した。しかし、良いモデルを作ることはできなかった。そのため環の数を加えて説明変数の改良を行うと、ある程度の共通性を持った良いモデルを作成することができた。そして、良いモデルには必ず炭素中で最も大きなNatural電荷および6員環の数が含まれていることが分かった。
  • 小林 正人, 岩佐 豪, 高 敏, 高木 牧人, 前田 理, 武次 徹也 ケモインフォマティクス討論会予稿集 2016 (0) O18 2016年 [査読無し][通常論文]
     
    金属ナノクラスター触媒の反応性は、構成元素だけでなく、サイズや環境、構造など様々なファクターに依存するため、触媒活性の決定的因子の解明は困難であった。本研究では、銅クラスター触媒によるNO解離反応を例に、反応経路自動探索法を用いた系統的量子化学計算とスパースモデリングの手法を併用した触媒活性因子の抽出を試みた。具体的には、LASSO推定、SCAD推定、MC+推定の3つの手法を使い、軌道エネルギーや局所的な指標などの説明変数を用いて、Cu13クラスター上でのNO解離の遷移状態エネルギーを回帰した。その結果、遷移状態のエネルギーはLUMOの軌道エネルギーと負の相関があること、SCAD推定やMC+推定ではLASSO推定よりもコンパクトで相関係数の高いモデルが得られることがわかった。
  • Takeshi Yoshikawa, Masato Kobayashi, Hiromi Nakai International Journal of Quantum Chemistry 113 (3) 218 -223 2013年02月05日 [査読無し][通常論文]
     
    In this article, we develop the symmetry adopted cluster (SAC) theory based on the divide-and-conquer (DC) method, which accomplishes the linear-scaling computational time with respect to the system size, as well as the DC-based coupled cluster (CC) method does. Although the perturbative configuration selection adopted in the SAC program significantly reduces its computational cost compared with the CC calculations, the reduction of the configurations leads to less inclusion of the total correlation energy. However, the numerical assessments confirmed that the use of the local orbitals constructed in each subsystem in DC-SAC calculations reduces the loss in total correlation energy, which provides more reliable total and relative energies than the standard SAC method. © 2012 Wiley Periodicals, Inc.
  • Moto Tarumi, Masato Kobayashi, Hiromi Nakai INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 113 (3) 239 -244 2013年02月 [査読無し][通常論文]
     
    Antisymmetric product of strongly orthogonal geminals (APSG) method is a wavefunction theory that can effectively treat the static electron correlation using two-electron wavefunctions, called geminals. However, the APSG method has the problem of slow convergence in the optimization of the geminal function. In this study, we introduced the direct inversion in the iterative subspace (DIIS) method, for both closed- and open-shell systems, for accelerating its convergence. Two types of error vectors, that is, unitary transformation and orbital gradient, were examined for the DIIS procedure. Numerical assessments revealed that the orbital-gradient error vector shows better performance than the unitary-transformation one. (c) 2012 Wiley Periodicals, Inc.
  • Masato Kobayashi, Hiromi Nakai Journal of Chemical Physics 138 (4) 044102 2013年01月28日 [査読無し][通常論文]
     
    We recently proposed a linear-scaling evaluation scheme for the second-order Møller-Plesset perturbation (MP2) energy based on the divide-and-conquer (DC) method [M. Kobayashi, Y. Imamura, and H. Nakai, J. Chem. Phys. 127, 074103 (2007)10.1063/1.2761878]. In this paper, we propose an approximate but effective expression for the first derivative of the DC-MP2 energy. The present scheme evaluates the one- and two-body density matrices, which appear in the MP2 gradient formula, in the DC manner that is, the entire matrix is obtained as the sum of subsystem matrices masked by the partition matrix. Therefore, the method requires solving only the local Z-vector equations. Illustrative applications to three types of systems, peptides, Si surface model, and delocalized polyenes, reveal the effectiveness of the present method. © 2013 American Institute of Physics.
  • Yoshikawa, Takeshi, Kobayashi, Masato, Fujii, Atsuhiko, Nakai, Hiromi Journal of Physical Chemistry B 117 (18) 5565 -5573 2013年 [査読無し][通常論文]
  • Yoshikawa, Takeshi, Kobayashi, Masato, Nakai, Hiromi International Journal of Quantum Chemistry 113 (3) 218 -223 2013年 [査読無し][通常論文]
  • Saparpakorn, Patchreenart, Kobayashi, Masato, Hannongbua, Supa, Nakai, Hiromi International Journal of Quantum Chemistry 113 (4) 510 -517 2013年 [査読無し][通常論文]
  • Saparpakorn, Patchreenart, Kobayashi, Masato, Nakai, Hiromi Bulletin of the Chemical Society of Japan 86 (1) 67 -74 2013年 [査読無し][通常論文]
  • Tarumi, Moto, Kobayashi, Masato, Nakai, Hiromi International Journal of Quantum Chemistry 113 (3) 2013年 [査読無し][通常論文]
  • Saparpakorn, Patchreenart, Kobayashi, Masato, Hannongbua, Supa, Nakai, Hiromi International Journal of Quantum Chemistry 113 (4) 2013年 [査読無し][通常論文]
  • Moto Tarumi, Masato Kobayashi, Hiromi Nakai JOURNAL OF CHEMICAL THEORY AND COMPUTATION 8 (11) 4330 -4335 2012年11月 [査読無し][通常論文]
     
    The antisymmetric product of strongly orthogonal geminals (APSG) method is a wave function theory that can effectively treat the static electron correlation. Recently, we proposed the open shell APSG method using one electron orbitals for open shell parts. In this paper, we have extended the perturbation correction to the open shell APSG calculations through Moller-Plesset-type multiconfiguration perturbation theory (MP-MCPT). Numerical applications demonstrate that the present open shell MP-MCPT can reasonably reproduce the dissociation energies or equilibrium distances for open shell systems.
  • Masato Kobayashi, Hiromi Nakai Physical Chemistry Chemical Physics 14 (21) 7629 -7639 2012年06月07日 [査読無し][通常論文]
     
    The authors have developed a fragmentation-based linear-scaling electronic structure calculation strategy named the divide-and-conquer (DC) method, which has been implemented into the Gamess program package. Although there are many sorts of fragmentation-based linear-scaling schemes, most of them require the charge and spin multiplicity of each fragment a priori. Therefore, their applications to delocalized and/or open-shell systems have been limited. However, the DC method is a notable exception because the distribution of electrons in the entire system is automatically determined by the universal Fermi level. In this perspective, the authors have summarized the performance of the linear-scaling self-consistent field (SCF) and post-SCF calculations of delocalized and/or open-shell systems based on the DC method. Furthermore, some future prospects of the method have been discussed. © 2012 the Owner Societies.
  • Masato Kobayashi, Tsuguki Touma, Hiromi Nakai Journal of Chemical Physics 136 (8) 084108 2012年02月28日 [査読無し][通常論文]
     
    We report a linear-scaling computation method for evaluating the dynamic first hyperpolarizability based on the divide-and-conquer (DC) method. In the present scheme, we utilized the quasi-density-matrix expression derived from Wigners (2n 1) rule for , 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)10.1016/j.cplett.2009.12.043]. Numerical evaluation of -conjugated and saturated organic chain systems verified that the present scheme considerably reduces the computational time for the 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. © 2012 American Institute of Physics.
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • Michio Katouda, Masato Kobayashi, Hiromi Nakai, Shigeru Nagase JOURNAL OF COMPUTATIONAL CHEMISTRY 32 (13) 2756 -2764 2011年10月 [査読無し][通常論文]
     
    A two-level hierarchical parallelization scheme including the second-order Moller-Plesset perturbation (MP2) theory in the divide-and-conquer method is presented. The scheme is a combination of coarse-grain parallelization assigning each subsystem to a group of processors, with fine-grain parallelization, where the computational tasks for evaluating MP2 correlation energy of the assigned subsystem are distributed among processors in the group. Test calculations demonstrate that the present scheme shows high parallel efficiency and makes MP2 calculations practical for very large molecules. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 2756-2764, 2011
  • Takeshi Yoshikawa, Masato Kobayashi, Hiromi Nakai THEORETICAL CHEMISTRY ACCOUNTS 130 (2-3) 411 -417 2011年10月 [査読無し][通常論文]
     
    We have developed the spin-unrestricted divide-and-conquer (DC)-based linear-scaling self-consistent field method for treating open-shell systems (Kobayashi et al. in Chem Phys Lett 500:172, 2010). Because the method does not require the position of excess spins or charges, it made the treatment of large spin-delocalized systems tractable. The present study extends the DC-based unrestricted open-shell scheme to the correlated second-order Moller-Plesset perturbation (MP2) theory. Numerical applications to polyene cations demonstrate that the present method gives highly accurate results with less computational costs even for spin-delocalized systems.
  • Kobayashi, Masato, Nakai, Hiromi Linear-Scaling Techniques in Computational Chemistry and Physics: Methods and Applications 13 97 -127 2011年 [査読無し][通常論文]
  • Nakai, Hiromi, Kobayashi, Masato Proceedings of the International Conference on Computational Science (Iccs) 4 1145 -1150 2011年 [査読無し][通常論文]
  • Masato Kobayashi, Tomotaka Kunisada, Tomoko Akama, Daisuke Sakura, Hiromi Nakai JOURNAL OF CHEMICAL PHYSICS 134 (3) 034105 2011年01月 [査読無し][通常論文]
     
    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. (C) 2011 American Institute of Physics. [doi:10.1063/1.3524337]
  • Touma, Tsuguki, Kobayashi, Masato, Nakai, Hiromi Theoretical Chemistry Accounts 130 (4-6) 701 -709 2011年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • Touma, Tsuguki, Kobayashi, Masato, Nakai, Hiromi Chemical Physics Letters 485 (1-3) 247 -252 2010年 [査読無し][通常論文]
  • Kobayashi, Masato, Szabados, Agnes, Nakai, Hiromi, Surjan, Peter R. Journal of Chemical Theory and Computation 6 (7) 2024 -2033 2010年 [査読無し][通常論文]
  • Kobayashi, Masato, Yoshikawa, Takeshi, Nakai, Hiromi Chemical Physics Letters 500 (1-3) 172 -177 2010年 [査読無し][通常論文]
  • Hojo, Masashi, Ueda, Tadaharu, Ike, Michitaka, Kobayashi, Masato, Nakai, Hiromi Journal of Molecular Liquids 145 (3) 152 -157 2009年 [査読無し][通常論文]
  • Kobayashi, Masato, Nakai, Hiromi International Journal of Quantum Chemistry 109 (10) 2227 -2237 2009年 [査読無し][通常論文]
  • Akama, Tomoko, Kobayashi, Masato, Nakai, Hiromi International Journal of Quantum Chemistry 109 (12) 2706 -2713 2009年 [査読無し][通常論文]
  • KOBAYASHI M. The Journal of Chemical Physics 131 (11) 114108 -114108 2009年 [査読無し][通常論文]
  • Tsuchimochi, Takashi, Kobayashi, Masato, Nakata, Ayako, Imamura, Yutaka, Nakai, Hiromi Journal of Computational Chemistry 29 (14) 2311 -2316 2008年 [査読無し][通常論文]
  • KOBAYASHI M. The Journal of Chemical Physics 129 (4) 044103 -44103 2008年 [査読無し][通常論文]
  • Tomoko Akama, Masato Kobayashi, Hiromi Nakai JOURNAL OF COMPUTATIONAL CHEMISTRY 28 (12) 2003 -2012 2007年09月 [査読無し][通常論文]
     
    The divide-and-conquer (DC) method, which is one of the linear-scaling methods avoiding explicit diagonalization of the Fock matrix. has been applied mainly to pure density functional theory (DFT) or semiempirical molecular orbital calculations so far. The present study applies the DC method to such calculations including the Hartree-Fock (HF) exchange terms as the HF and hybrid HF/DFT. Reliability of the DC-HF and DC-hybrid HF/DFT is found to be strongly dependent oil the cut-off radius, which defines the localization region in the DC formalism. This dependence on the cut-off radius is assessed from various points of view: that is, total energy, energy components, local energies, and density of states. Additionally, to accelerate the self-consistent field convergence in DC calculations, a new convergence technique is proposed. (c) 2007 Wiley, Periodicals, Inc.
  • Masashi Hojo, Tadaharu Ueda, Tomonori Inoue, Michitaka Ike, Masato Kobayashi, Hiromi Nakai JOURNAL OF PHYSICAL CHEMISTRY B 111 (7) 1759 -1768 2007年02月 [査読無し][通常論文]
     
    The specific interaction between lithium ions and the tropolonate ion (C7H5O2-: L-) was examined by means of UV-visible and H-1 or C-13 NMR spectroscopy in acetonitrile and other solvents. On the basis of the electronic spectra, we can propose the formation of not only coordination-type species (Li+(L-)(2)) and the ion pair (Li+L-) but also a "triple cation" ((Li+)(2)L-) in acetonitrile and acetone; however, no "triple cation" was found in N,N-dimethylformamide (DMF) and in dimethylsulfoxide (DMSO), solvents of higher donicities and only ion pair formation between Li+ and L- in methanol of much higher donicity and acceptivity. The H-1 NMR chemical shifts of the tropolonate ion with increasing Li+ concentration verified the formation of (Li+)(2)L- species in CD3CN and acetone-d(6), but not in DMF-d(6) or CD3OD. With increasing concentration of LiClO4 in CD3CN, the H-1 NMR signals of 4-isopropyltropolone (HL') in coexistence with an equivalent amount of Et3N shifted first toward higher and then toward lower magnetic-fields, which were explained by the formation of (Li+)(Et3NH+)L'(-) and by successive replacement of Et3NH+ with a second Li+ to give (Li+)(2)L'(-). In CD3CN, the 1,2-C signal in the C-13 NMR spectrum of tetrabutylammnium tropolonate (n-Bu4NC7H5O) appeared at an unexpectedly lower magnetic-field (184.4 ppm vs TMS) than that of tropolone (172.7 ppm), while other signals of the tropolonate showed normal shifts toward higher magnetic-fields upon deprotonation from tropolone. Nevertheless, with addition of LiClO4 at higher concentrations, the higher and lower shifts of magnetic-fields for 1,2-C and other signals, respectively, supported the formation of the (Li+)(2)L- species, which can cause redissolution of LiL precipitates. All of the data with UV-visible and H-1 and C-13 NMR spectroscopy demonstrated that the protonated tropolone (or the dihydroxytropylium ion), H2L+, was produced by addition of trifluoromethanesulfonic or methanesulfonic acid to tropolone in acetonitrile. The order of the 5-C and 3,7-C signals in C-13 NMR spectra of the tropolonate ions was altered by addition of less than an equivalent amount of H+ to the tropolonate ion in CD3CN. Theoretical calculations satisfied the experimental C-13 NMR chemical shift values of L-, HL, and H2L+ in acetonitrile and were in accordance with the proposed reaction schemes.
  • Keitaro Sodeyama, Hiroaki Nishizawa, Minoru Hoshino, Masato Kobayashi, Hiromi Nakai CHEMICAL PHYSICS LETTERS 433 (4-6) 409 -415 2007年01月 [査読無し][通常論文]
     
    The translation- and rotation-free nuclear orbital plus molecular orbital (TRF-NOMO) theory was developed in order to accurately determine the nonadiabatic nuclear and electronic wave functions without Born-Oppenheimer approximation. This study presents a hybrid method combining the TRF-NOMO theory with the generator coordinate method (GCM). The TRF-NOMO/GCM treatment is capable of giving the vibrational excited states with high accuracy, as well as improving the ground-state description by inclusion of the many-body effect. Numerical applications of the TRF-NOMO/GCM calculations to an HF molecule confirm its reliability and usefulness. (c) 2006 Elsevier B.V. All rights reserved.
  • Kobayashi, Masato, Imamura, Yutaka, Nakai, Hiromi Journal of Chemical Physics 127 (7) 074103 2007年 [査読無し][通常論文]
  • Tomoko Akama, Atsuhiko Fujii, Masato Kobayashi, Hiromi Nakai MOLECULAR PHYSICS 105 (19-22) 2799 -2804 2007年 [査読無し][通常論文]
     
    Recently, we applied Yang's divide-and-conquer (DC) method to the Hartree-Fock (HF) and hybrid density functional theories and assessed its reliability in calculations of bond-alternating polyene chains. In this paper, we investigate the cut-off behaviour of the HF exchange interaction in the DC-HF method by comparing the results of bond-alternating polyene chains with those of more delocalized uniform polyene chains. The cut-off error of the uniform chain is much larger than that of the bond-alternating chain because of the delocalized electronic structure of the uniform polyene chain. We also estimate the exponential decay coefficient of the cut-off error in the DC scheme and compare it with that of the real-space one-particle density matrix, which can be represented by the band gap in the insulator limit. It can be concluded that the cut-off derived from the DC-HF method can be reduced to an arbitrary magnitude of error by adopting an appropriate buffer radius corresponding to the band gap.
  • Masato Kobayashi, Hiromi Nakai Chemical Physics Letters 420 (1-3) 250 -255 2006年03月10日 [査読無し][通常論文]
     
    We numerically assess the method for obtaining second-order Møller-Plesset (MP2) energy from the Hartree-Fock density matrix (DM) recently proposed by Surján [Surján, Chem. Phys. Lett. 406 (2005) 318]. It is confirmed that Surján's method, referred to as DM-Laplace MP2, can obtain MP2 energy accurately by means of appropriate integral quadrature and a matrix exponential evaluation scheme. Numerical tests reveal that the Euler-Maclaurin and the Romberg numerical integration schemes can achieve milli-hartree accuracy with small quadrature points. This Letter also indicates the possibility of the application of DM-Laplace MP2 to linear-scaling self-consistent field techniques, which give approximate DM. © 2006 Elsevier B.V. All rights reserved.
  • Kobayashi, Masato, Akama, Tomoko, Nakai, Hiromi Journal of Chemical Physics 125 (20) 204106 2006年 [査読無し][通常論文]
  • M Katouda, M Kobayashi, H Nakai, S Nagase JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 4 (1) 139 -149 2005年03月 [査読無し][通常論文]
     
    We have developed a computer program for evaluation of electron repulsion integrals (ERIs) based on the accompanying coordinate expansion recurrence relation (ACE-RR) algorithm, which has been recently developed as an efficient algorithm for computation of ERIs using Pople-type basis sets (STO-3G and 6-31G, for example) and derivatives of ERIs [Kobayashi and Nakai, J Chem Phys 21:4050, 2004]. The computer program can be linked to GAMESS ab initio quantum chemistry program. The practical performance of the ACE-RR method is assessed by means of the central processing unit (CPU) time for the first direct self-consistent field cycle on a model system (4 x 4 x 4 cubic hydrogen lattice), taxol (C47H51NO14), and valinomycin (C54H90N6O18) using Pople-type basis sets. The considerable efficiency of the present ACE-RR method is demonstrated by measuring the CPU time. The present ACF-RR method is comparable to or at most 30% faster than the Pople-Hehre method which is also designed for efficient computation of ERIs using Pople-type basis sets. Furthermore, the ACE-RR method is drastically faster than the Dupuis-Rys-King method in the case where the degree of contraction of Pople-type basis sets is high: 7.5 times faster in the case of valinomycin using STO-6G basis set, for example.
  • H Nakai, M Kobayashi CHEMICAL PHYSICS LETTERS 388 (1-3) 50 -54 2004年04月 [査読無し][通常論文]
     
    We propose a new algorithm for the rapid evaluation of electron repulsion integrals over Gaussian type orbitals, termed elementary basis algorithm (EBA). In the EBA, the information of the atomic basis functions is divided into two parts: an elementary and an atomic basis part. In the conventional algorithm, all information is assigned to atoms, which requires that all computations must be performed in the atomic loops. In the EBA, computations can be partly carried out in the elementary loops. We apply the EBA to the accompanying coordinate expansion method of Ishida. (C) 2004 Elsevier B.V. All rights reserved.
  • Kobayashi, M, Nakai, H Journal of Chemical Physics 121 (9) 4050 -4058 2004年 [査読無し][通常論文]
  • P. Saparpakorn, M. Kobayashi, H. Nakai Bull. Chem. Soc. Jpn. [査読無し][通常論文]

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    XVIIth International Workshop on Quantum Systems in Chemistry and Physics (QSCP-XVII) 2012年 ポスター発表
  • DC-SAC-CI法による光活性タンパクの励起状態計算  [通常講演]
    第15回理論化学討論会 2012年 ポスター発表
  • 開殻APSG波動関数を参照とした多体摂動計算  [通常講演]
    第15回理論化学討論会 2012年 ポスター発表
  • DC-SAC-CI法～大規模励起状態理論の構築～  [通常講演]
    日本コンピュータ化学会2012春季年会 2012年 ポスター発表
  • 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  [通常講演]
    日本コンピュータ化学会2012春季年会 2012年 ポスター発表
  • 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  [通常講演]
    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年
  • 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  [通常講演]
    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年
  • 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  [通常講演]
    第4回HPCI戦略プログラム合同研究交流会 2012年
  • 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  [通常講演]
    第26期CAMMフォーラム例会 2012年
  • Recent advances in the divide-and-conquer MP2 program and its performance assessment  [通常講演]
    3rd CMSI Symposium 2012年
  • Development of divide-and-conquer quantum chemical code for biomolecules and nano materials  [通常講演]
    JSST 2012 International Conference on Simulation Technology 2012年
  • Hybrid parallelization of divide-and-conquer (DC) quantum chemical method implemented in GAMESS  [通常講演]
    Annual Meeting of Japan Society for Molecular Science 2012 2012年 ポスター発表
  • APSG and its perturbative correction: Application to open-shell systems  [通常講演]
    Theory and Applications of Computational Chemistry 2012 (TACC2012) 2012年 ポスター発表
  • Excited-state calculation of photoactive yellow protein using divide-and-conquer SAC-CI theory  [通常講演]
    XVIIth International Workshop on Quantum Systems in Chemistry and Physics (QSCP-XVII) 2012年 ポスター発表
  • Excited-state calculation of photo-active protein by DC-SAC-CI method  [通常講演]
    15th Annual Forum on Theoretical Chemistry 2012年 ポスター発表
  • Many-body perturbation calculation based on open-shell APSG wavefunction  [通常講演]
    15th Annual Forum on Theoretical Chemistry 2012年 ポスター発表
  • DC-SAC-CI method - Construction of large-scale excited-state theory  [通常講演]
    Spring Meeting 2012, Society of Computer Chemistry, Japan 2012年 ポスター発表
  • Analysis of charge mobility of organic electronic device using quantum chemical calculation  [通常講演]
    Spring Meeting 2012, Society of Computer Chemistry, Japan 2012年 ポスター発表
  • Divide-and-Conquer (DC) Quantum Chemical Calculation Method: Its Improvements in Accuracy, Efficiency, and Parallelism  [通常講演]
    Forum on Pioneering Computational Science 2012 (Kyushu Univ.) 2012年
  • Divide-and-Conquer (DC) Quantum Chemical Calculation Program: Developments, applications, and Perspectives  [通常講演]
    Open Symposium on Grand Challenges in Next-Generation Integrated Nanoscience and Living Matter 2012年
  • Development of Large-Scale Quantum Chemical Calculation Program Based on Divide-and-Conquer (DC) Method and Its Implementation into K Supercomputer  [通常講演]
    4th Joint Symposium of the Strategic Program for Innovative Research (SPIRE) 2012年
  • Quantum Chemical Calculations of Large Systems: The World Pioneered by Recent Developments in Chemical Theory and Computer Science, and Its Future  [通常講演]
    26th CAMM Forum 2012年
  • Divide-and-Conquer量子化学計算プログラム  [通常講演]
    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年
  • 分割統治(DC)電子状態計算法のGAMESSへの実装と応用  [通常講演]
    日本コンピュータ化学会2009春季年会 2009年
  • Divide-and-Conquer quantum chemistry program  [通常講演]
    Next-Generation Integrated Nanoscience Simulation Software Explanatory Meeting 2009年
  • Implimentation of divide-and-conquer (DC) electronic structure code to GAMESS program package and its applications  [通常講演]
    Spring Meeting 2009, Society of Computer Chemistry, Japan 2009年
  • Divide-and-conquer electronic structure method: Extension to post-HF correlation theories  [通常講演]
    The International Conference on the Theory and Applications of Computational Chemistry in 2008 (TACC2008) 2008年
  • Divide-and-conquer electronic structure method: Extension to post-HF correlation theories  [通常講演]
    The International Conference on the Theory and Applications of Computational Chemistry in 2008 (TACC2008) 2008年
  • 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  [通常講演]
    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年
  • Accurate quantum chemical methodology for large systems: MP2 calculation based on the divide-and-conquer method  [通常講演]
    Mini workshop on large-scale accurate electronic structure calculation methods II 2007年

担当経験のある科目（授業）

  • 教科教育法（理科）北海道大学
  • 量子化学I北海道大学
  • 一般教育演習「化学・タイムトラベル」北海道大学
  • 計算機実習北海道大学
  • 分子化学A（分子理論化学）【分担】北海道大学
  • 化学I (基礎物理化学)北海道大学
  • 物理学通論 (解析力学入門)北海道大学
  • 計算科学技術特論B【分担】大阪大学
  • 一般教育演習「化学の奥深さを体験しよう」【分担】北海道大学
  • 自然科学実験（化学）北海道大学
  • 計算科学が開く新しい科学【分担】北海道大学
  • 量子化学II【分担】北海道大学
  • 物理化学演習早稲田大学
  • 基礎化学演習早稲田大学

所属学協会

  • 理論化学会   触媒学会   日本化学会   分子科学会   日本コンピュータ化学会   

共同研究・競争的資金等の研究課題

  • 日本学術振興会：科学研究費助成事業 基盤研究(B)
    研究期間 : 2023年04月 -2026年03月 
    代表者 : 小林 正人
  • 物理-化学連携による持続的成長に向けた高機能・長寿命材料の探索・制御
    文部科学省：スーパーコンピュータ｢富岳｣成果創出加速プログラム
    研究期間 : 2023年04月 -2026年03月 
    代表者 : 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
  • 日本学術振興会：科学研究費助成事業 学術変革領域研究(A)
    研究期間 : 2023年04月 -2025年03月 
    代表者 : 小林 正人
  • 日本学術振興会：科学研究費助成事業 基盤研究(B)
    研究期間 : 2021年04月 -2024年03月 
    代表者 : 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。
  • 日本学術振興会：科学研究費助成事業 学術変革領域研究(A)
    研究期間 : 2021年09月 -2023年03月 
    代表者 : 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。
  • 日本学術振興会：科学研究費助成事業 基盤研究(B)
    研究期間 : 2020年04月 -2023年03月 
    代表者 : 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。
  • 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
    量子化学探索研究所：研究助成（一般）
    研究期間 : 2020年10月 -2022年09月 
    代表者 : 小林正人, 寺本央, 青木雅充, 石橋卓
  • 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
    日本学術振興会：科学研究費助成事業 基盤研究(C)
    研究期間 : 2017年04月 -2021年03月 
    代表者 : 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。
  • 化学反応における多元系のシナジー効果の評価と触媒反応への応用
    科学技術振興機構：戦略的創造研究推進事業さきがけ
    研究期間 : 2015年12月 -2019年03月
  • 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
    日本学術振興会：科学研究費助成事業 新学術領域研究(研究領域提案型)
    研究期間 : 2015年04月 -2017年03月 
    代表者 : 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。
  • 日本学術振興会：科学研究費助成事業 若手研究(B)
    研究期間 : 2013年04月 -2016年03月 
    代表者 : 小林 正人
     
    本研究では，大規模系計算理論である分割統治(DC)法と電子対波動関数（ジェミナル）に基づく強相関系計算法のHartree-Fock-Bogoliubov (HFB)法を用いることにより，ブラックボックス，すなわち手法の名前だけで計算が可能な大規模系および強相関電子系の計算手法を開発した．具体的には，エネルギー誤差を一定以内に抑えることができるアダプティブなDC法の開発，HFB法に基づくエネルギー勾配法の開発，DC法とHFB法を融合したDC-HFB法の開発を行った．
  • 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
    新化学発展協会：平成23年度研究奨励金
    研究期間 : 2011年04月 -2012年03月
  • 日本学術振興会：科学研究費助成事業 若手研究(B)
    研究期間 : 2010年 -2012年 
    代表者 : 小林 正人
     
    本研究では,現在広く用いられている一電子波動関数(オービタル)に基づく量子化学の枠組みを超え,二電子波動関数(ジェミナル)に基づく量子化学理論とプログラムの構築を行った.これにより,静的電子相関と呼ばれる効果が強くはたらく系の高精度量子化学計算を,ほぼパラメータなしで実行することを可能とした.さらに,大規模系計算理論のひとつである分割統治法を整備し,実在系の高精度量子化学計算が可能となった.
  • 日本学術振興会：科学研究費助成事業
    研究期間 : 2006年 -2009年 
    代表者 : 中井 浩巳, 今村 穣, 小林 正人, 佐藤 健, 菊地 那明, 渥美 照夫, 菊池 那明, 今村 穣, 星野 稔, 山内 佑介
     
    本研究では,AIMD計算のボトルネックである電子状態理論計算の高速化,大規模化を目指した理論開発を行った。また,原子核の量子効果を考慮したダイナミックスについては,核・電子軌道(NOMO)法を発展させることにより研究を進めた。さらに実在系に対する様々な応用計算のため,エネルギー密度解析(EDA)を発展させ,計算結果の効果的な解析を行った。
  • 日本学術振興会：科学研究費助成事業 特別研究員奨励費
    研究期間 : 2006年 -2007年 
    代表者 : 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。

産業財産権

  • 特開2023-130997: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  2023年09月21日
    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
  • 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  202203013856597361

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