2024/02/01 更新

写真b

モチヅキ ユウジ
望月 祐志
MOCHIZUKI Yuji
*大学が定期的に情報更新している項目(その他は、researchmapの登録情報を転載)
所属*
理学部 化学科
理学研究科 化学専攻 博士課程後期課程
理学研究科 化学専攻 博士課程前期課程
職名*
教授
学位
理学博士 ( 北海道大学 )
研究テーマ*
  • 量子化学を主軸とする計算分子科学。特に、大規模分子の扱いが可能なフラグメント分子軌道法を援用する電子状態計算の応用とプログラムの開発(ABINIT-MP)。最近では、粗視化シミュレーション、機械学習・深層学習(化学分野に限らない)も活動領域に。

  • 研究キーワード
  • 計算化学

  • 量子化学

  • Fragment Molecular Orbital (FMO)

  • フラグメント分子軌道法

  • ABINIT-MP プログラム

  • スーパーコンピュータ

  • 並列処理

  • 生体分子

  • マルチスケールシミュレーション

  • 散逸粒子動力学

  • 機械学習

  • 量子コンピュータ

  • 化学情報教育

  • 学内職務経歴*
    • 2010年4月 - 現在 
      理学部   化学科   教授
    • 2010年4月 - 現在 
      理学研究科   化学専攻 博士課程前期課程   教授
    • 2010年4月 - 現在 
      理学研究科   化学専攻 博士課程後期課程   教授
    • 2007年4月 - 2010年3月 
      理学部   化学科   准教授
    • 2007年4月 - 2010年3月 
      理学研究科   化学専攻 博士課程前期課程   准教授
    • 2007年4月 - 2010年3月 
      理学研究科   化学専攻 博士課程後期課程   准教授
    • 2006年4月 - 2007年3月 
      理学部   化学科   助教授
    • 2006年4月 - 2007年3月 
      理学研究科   化学専攻 博士課程前期課程   助教授
    • 2006年4月 - 2007年3月 
      理学研究科   化学専攻 博士課程後期課程   助教授

    ▼全件表示

    プロフィール

    フラグメント分子軌道(FMO)法プログラムABINIT-MPの取り纏め役(電子相関、励起状態系モジュールの開発者、高速化と超大規模系対応の推進責任者)。 URL:<http://www.cenav.org/abinit-mp-open_ver-2-rev-8/>
    FMO応用計算の他、粗視化シミュレーションとの連携によるナノ-メゾのマルチスケールシミュレーション手法、機械学習の応用、ならびに量子コンピュータの基礎的利用(シミュレータ含む)も手がける。また、化学情報教育にも関心を持っている。

     

    研究分野

    • ナノテク・材料 / 基礎物理化学  / 量子化学、理論化学

    経歴

    • 2017年4月 - 現在 
      東京大学   生産技術研究所   リサーチフェロー

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    • 2010年4月 - 現在 
      立教大学   理学研究科 化学専攻博士課程後期課程   教授

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    • 2010年4月 - 現在 
      立教大学   理学研究科 化学専攻博士課程前期課程   教授

      詳細を見る

    • 2010年4月 - 現在 
      立教大学   理学部 化学科   教授

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    • 2006年4月 - 2017年3月 
      東京大学   生産技術研究所   非常勤研究員

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    • 2007年4月 - 2010年3月 
      立教大学   理学部 化学科   准教授

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    • 2006年4月 - 2007年3月 
      立教大学   理学部 化学科   助教授

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    • 2003年2月 - 2006年3月 
      アドバンスソフト(株) 研究開発センター   主任研究員

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    • 2000年7月 - 2003年1月 
      (財)高度情報科学技術研究機構   研究員

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    • 1997年10月 - 2000年6月 
      (科学技術振興事業団) 日本原子力研究所計算科学技術推進センター   特別研究員

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    • 1990年4月 - 1997年9月 
      NEC(株)基礎研究所   研究員

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    ▼全件表示

    学歴

    • - 1990年3月 
      北海道大学   理学研究科   化学第二専攻

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      国名: 日本国

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    • - 1987年3月 
      北海道大学   理学研究科   化学第二専攻

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      国名: 日本国

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    • - 1985年3月 
      北海道大学   理学部   化学第二学科

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      国名: 日本国

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    受賞

    • 2020年3月  
      日本コンピュータ化学会  2019年度学会賞 
       
      望月祐志

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    • 2004年7月  
      CBI学会  ポスター賞  FMO法の発展: MP2法による電子相関の導入
       
      望月祐志

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    論文

    • Enhancement of energy decomposition analysis in fragment molecular orbital calculations 査読有り 国際誌

      Sota Matsuoka, Kota Sakakura, Yoshinobu Akinaga, Kazuki Akisawa, Koji Okuwaki, Hideo Doi, Yuji Mochizuki

      J. Comp. Chem.   2023年12月

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      担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

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    • Development of reverse mapping system bridging dissipative particle dynamics and fragment molecular orbital calculation 査読有り

      Koji Okuwaki, Hideo Doi, Taku Ozawa, Yuji Mochizuki

      Japanese Journal of Applied Physics62 ( 11 ) 110902   2023年10月23日

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      担当区分:最終著者, 責任著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:IOP Publishing  

      Abstract

      We have developed a reverse mapping system to convert mesoscale structures generated by dissipative particle dynamics (DPD) simulations into nanoscale structures. This system is called DSRMS (DPD-based Structure Reverse Mapping System) and is controlled by Python3 scripts using OCTA's COGNAC program for DPD and molecular dynamics (MD). The restored structures can be subjected to fragment molecular orbital (FMO) calculations using the ABINIT-MP program for detailed nanoscale interaction analysis. Polyelectrolyte and lipid membranes have been used as illustrative example.

      DOI: 10.35848/1347-4065/ad0601

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      その他リンク: https://iopscience.iop.org/article/10.35848/1347-4065/ad0601/pdf

    • Bayesian phase difference estimation algorithm for direct calculation of fine structure splitting: accelerated simulation of relativistic and quantum many-body effects 査読有り

      Kenji Sugisaki, Srinivasa Prasannaa, Satoshi Ohshima, Takahiro Katagiri, Yuji Mochizuki, Bijaya Kumar Sahoo, Bhanu Pratap Das

      Electronic Structure5 ( 3 ) 035006   2023年9月12日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:IOP Publishing  

      Abstract

      Despite rapid progress in the development of quantum algorithms in quantum computing as well as numerical simulation methods in classical computing for atomic and molecular applications, no systematic and comprehensive electronic structure study of atomic systems that covers almost all of the elements in the periodic table using a single quantum algorithm has been reported. In this work, we address this gap by implementing the recently-proposed quantum algorithm, the Bayesian Phase Difference Estimation (BPDE) approach, to determine fine structure splittings of a wide range of boron-like atomic systems. Since accurate estimate of fine structure splittings strongly depend on the relativistic as well as quantum many-body effects, our study can test the potential of the BPDE approach to produce results close to the experimental values. Our numerical simulations reveal that the BPDE algorithm, in the Dirac–Coulomb–Breit framework, can predict fine structure splittings of ground states of the considered systems quite precisely. We performed our simulations of relativistic and electron correlation effects on Graphics Processing Unit by utilizing NVIDIA’s cuQuantum, and observe a ×42.7 speedup as compared to the Central Processing Unit-only simulations in an 18-qubit active space.

      DOI: 10.1088/2516-1075/acf909

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      その他リンク: https://iopscience.iop.org/article/10.1088/2516-1075/acf909/pdf

    • Dissipative particle dynamics simulation for peptoid nanosheet with non-empirical parameter set 査読有り

      Yusuke Tachino, Koji Okuwaki, Hideo Doi, Kazuki Akisawa, Yuji Mochizuki

      Japanese Journal of Applied Physics62 ( 9 ) 090902   2023年8月23日

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      担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:IOP Publishing  

      Abstract

      Peptoids are biomimetic materials in which the substituent groups are located on the nitrogen atom of the peptide bond, facilitating the formation of nanosheet structures as reported by Mannige et al. (Nature, 526 (2015) 415). Dissipative particle dynamics (DPD) simulations were performed to investigate the aggregation stability of peptoids with different unit lengths. The crucial effective interaction parameters were determined by fragment molecular orbital (FMO) calculations, which allowed to evaluate different molecular interactions (electrostatic and dispersion) in a balanced way. The experimental observation of the unit length dependence was finally reproduced by this FMO-DPD method.

      DOI: 10.35848/1347-4065/acf356

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      その他リンク: https://iopscience.iop.org/article/10.35848/1347-4065/acf356/pdf

    • Prediction of Binding Pose and Affinity of SARS-CoV-2 Main Protease and Repositioned Drugs by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations

      Yuma Handa, Koji Okuwaki, Yusuke Kawashima, Ryo Hatada, Yuji Mochizuki, Yuto Komeiji, Shigenori Tanaka, Takayuki Furuishi, Etsuo Yonemochi, Teruki Honma, Kaori Fukuzawa

          2023年7月25日

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      出版者・発行元:American Chemical Society (ACS)  

      COVID-19 remains a global pandemic, necessitating the urgent development of more effective therapeutics. By combining molecular docking, molecular dynamics (MD), and fragment molecular orbital (FMO) calculations, the binding structure and properties with Mpro were predicted for Nelfinavir (NLF), which was identified as a candidate compound through drug repositioning targeting the Main Protease (Mpro) produced by the causative virus, SARS-CoV-2. For the four docking poses selected by scoring using FMO energy, 100 structures each from the MD trajectory were sampled, and FMO calculations were performed and ranked based on binding energy. Besides the interaction between NLF and each Mpro residue, the desolvation effect of the pocket affected the ranking order. Furthermore, we identified several residues important in ligand recognition, including Glu47, Asp48, Glu166, Asp187, and Gln189, all of which interacted strongly with NLF. Asn142 was mentioned as a residue with hydrogen bonds or CH/π interaction with NLF; however, it was considered a transient interacting residue because of its unstable structure. Moreover, the tert-butyl group of NLF had no interaction with Mpro. Identifying weak interactions provides candidates for substituting ligand functional groups and important suggestions for drug discovery using drug repositioning. Our approach provides a new guideline for structure-based drug design starting from a candidate compound whose complex crystal structure has not been obtained.

      DOI: 10.26434/chemrxiv-2023-hrsvj

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    • Machine learning to improve efficiency of non-empirical interaction parameter for dissipative particle dynamics (DPD) simulation 査読有り

      Hideo Doi, Sota Matsuoka, Koji Okuwaki, Ryo Hatada, Soujiro Minami, Ryosuke Suhara, Yuji Mochizuki

      Japanese Journal of Applied Physics62 ( 7 ) 070901   2023年7月7日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:IOP Publishing  

      Abstract

      We have attempted to use machine learning to streamline the calculation of non-empirical &amp;#xD;parameters for use in dissipative particle dynamics (DPD) simulations. We replaced the &amp;#xD;calculation of molecular interaction energies by the non-empirical molecular orbital method, &amp;#xD;which requires a lot of computational resources, with predictions by machine learning. We &amp;#xD;developed two methods for prediction replacement, which are a 1-step method and a 2-step &amp;#xD;method. The prediction accuracy of the results obtained with these methods was investigated. &amp;#xD;A reduction of about half of the computational cost was expected.

      DOI: 10.35848/1347-4065/ace575

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      その他リンク: https://iopscience.iop.org/article/10.35848/1347-4065/ace575/pdf

    • Bifurcated Hydrogen Bonds in a Peptide Crystal Unveiled by X-ray Diffraction and Polarized Raman Spectroscopy 査読有り

      Kazunori Motai, Nao Koishihara, Takuma Narimatsu, Hiroyoshi Ohtsu, Masaki Kawano, Yuki Wada, Kazuki Akisawa, Koji Okuwaki, Takehiko Mori, Ji-Seon Kim, Yuji Mochizuki, Yuhei Hayamizu

      Crystal Growth & Design23 ( 6 ) 4556 - 4561   2023年5月10日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

      DOI: 10.1021/acs.cgd.3c00302

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    • Practical Computational Chemistry Course for a Comprehensive Understanding of Organic, Inorganic, and Physical Chemistry: From Molecular Interactions to Chemical Reactions 査読有り 国際誌

      Nahoko Kuroki, Yuji Mochizuki, Hirotoshi Mori

      J. Chem. Educ.100 ( 2 ) 647 - 654   2023年1月4日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ACS  

      DOI: 10.1021/acs.jchemed.2c00837

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    • Lattice Folding Simulation of Peptide by Quantum Computation 査読有り

      Rui SAITO, Koji OKUWAKI, Yuji MOCHIZUKI, Ryutaro NAGAI, Takumi KATO, Kenji SUGISAKI, Yuichiro MINATO

      Journal of Computer Chemistry, Japan -International Edition9 ( 2022 ) 2036   2023年

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      担当区分:責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Society of Computer Chemistry Japan  

      DOI: 10.2477/jccjie.2022-0036

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    • Variational quantum eigensolver simulations with the multireference unitary coupled cluster ansatz: a case study of the C2v quasi-reaction pathway of beryllium insertion into a H2 molecule 査読有り 国際誌

      Kenji Sugisaki, Takumi Kato, Yuichiro Minato, Koji Okuwaki, Yuji Mochizuki

      Phys. Chem. Chem. Phys.24   8439 - 8452   2022年3月15日

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      担当区分:最終著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:RSC  

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      その他リンク: https://chemrxiv.org/engage/chemrxiv/article-details/60d448e8926ad00c6e02e5c3

    • Collective residue interactions in trimer complexes of SARS-CoV-2 spike proteins analyzed by fragment molecular orbital method 査読有り

      Koji Okuwaki, Kazuki Akisawa, Ryo Hatada, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji, Shigenori Tanaka

      Applied Physics Express15   017001   2021年12月24日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:応用物理学会  

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    • Interaction Analysis on the SARS-CoV-2 Spike Protein Receptor Binding Domain Using Visualization of the Interfacial Electrostatic Complementarity 査読有り

      Takeshi Ishikawa, Hiroki Ozono, Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Yuji Mochizuki

      J. Phys. Chem. Lett.12   11267 - 11272   2021年11月12日

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      担当区分:最終著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

      DOI: 10.1021/acs.jpclett.1c02788

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    • Fragment Molecular Orbital Based Interaction Analyses on Complexes Between SARS-CoV-2 RBD Variants and ACE2 査読有り

      Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Shun Kitahara, Yusuke Tachino, Yuji Mochizuki, Yuto Komeiji, Shigenori Tanaka

      Jpn. J. Appl. Phys.60 ( 9 ) 090901   2021年8月13日

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      担当区分:責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

      DOI: 10.35848/1347-4065/ac1857.

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      その他リンク: https://doi.org/10.26434/chemrxiv.14318459.v1

    • Dynamical Cooperativity of Ligand-Residue Interactions Evaluated with the Fragment Molecular Orbital Method 査読有り

      Shigenori Tanaka, Shusuke Tokutomi, Ryo Hatada,, Koji Okuwaki, Kazuki Akisawa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Yuji Mochizuki

      J. Phys. Chem. B125 ( 24 ) 6501 - 6512   2021年6月14日

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      担当区分:最終著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

      By the splendid advance in computation power realized with Fugaku supercomputer, it has become
      possible to perform ab initio fragment molecular orbital (FMO) calculations for thousands of
      dynamical structures of a protein-ligand complex in a parallelized way. We have thus carried out the
      electron-correlated FMO calculations for a complex of the 3C-like (3CL) main protease (Mpro) of the
      new coronavirus (SARS-CoV-2) and its inhibitor N3 incorporating the structural fluctuations sampled
      by classical molecular dynamics (MD) simulation in hydrated condition. Along with a statistical
      evaluation of inter-fragment interaction energies (IFIEs) between the N3 ligand and surrounding
      amino-acid residues for a thousand of dynamical structure samples, we have applied in this study a
      novel approach based on the principal component analysis (PCA) and the singular value
      decomposition (SVD) to the analysis of IFIE data in order to extract the dynamically cooperative
      interactions between the ligand and residues. We have found that the relative importance of each
      residue is modified via the structural fluctuations and that the ligand is bound in the pharmacophore
      in a dynamical manner through collective interactions formed by multiple residues, thus providing a
      new insight into structure-based drug discovery

      DOI: 10.1021/acs.jpcb.1c03043

      DOI: 10.26434/chemrxiv.13775182.v1

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    • Density-Matrix Based Scheme of Basis Selection for Linear Combination of Fragment Molecular Orbitals 査読有り 国際誌

      Yoshio Okiyama, Yuji Mochizuki, Masanori Yamanaka, Shigenori Tanaka

      J. Phys. Soc. Jpn.90 ( 6 ) 064301 - 064301   2021年5月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:日本物理学会  

      DOI: 10.7566/JPSJ.90.064301

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    • 分子動力学計算とFMO計算を用いたSARS-CoV-2メインプロテアーゼと既存薬との結合性予測

      半田 佑磨, 川嶋 裕介, 畑田 崚, 奥脇 弘次, 望月 祐志, 古明地 勇人, 田中 成典, 本間 光貴, 古石 誉之, 福澤 薫, 米持 悦生

      日本薬学会年会要旨集141年会   27V04 - am12S   2021年3月

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      記述言語:日本語   出版者・発行元:(公社)日本薬学会  

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    • Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations 査読有り 国際誌

      Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji, Shigenori Tanaka

      RSC Advances11 ( 6 ) 3272 - 3279   2021年1月14日

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      担当区分:責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:RSC  

      At the stage of SARS-CoV-2 infection in human cells, the spike protein consisting of three chains, A, B, and C, with a total of 3300 residues plays a key role, and thus its structural properties and the binding nature of receptor proteins to host human cells or neutralizing antibodies has attracted considerable interest. Here, we report on interaction analyses of the spike protein in both closed (PDB-ID: 6VXX) and open (6VYB) structures, based on large-scale fragment molecular orbital (FMO) calculations at the level of up to the fourth-order Møller–Plesset perturbation with singles, doubles, and quadruples (MP4(SDQ)). Inter-chain interaction energies were evaluated for both structures, and a mutual comparison indicated considerable losses of stabilization energies in the open structure, especially in the receptor binding domain (RBD) of chain-B. The role of charged residues in inter-chain interactions was illuminated as well. By two separate calculations for the RBD complexes with angiotensin-converting enzyme 2 (ACE2) (6M0J) and B38 Fab antibody (7BZ5), it was found that the binding with ACE2 or antibody partially compensated for this stabilization loss of RBD.

      DOI: 10.1039/D0RA09555A

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      その他リンク: https://chemrxiv.org/articles/preprint/Interaction_Analyses_on_SARS-CoV-2_Spike_Protein_Based_on_Large-Scale_Correlated_Fragment_Molecular_Orbital_Calculations/12941606

    • Statistical interaction analyses between SARS-CoV-2 main protease and inhibitor N3 by combining molecular dynamics simulation and fragment molecular orbital calculation 査読有り

      Ryo Hatada, Koji Okuwaki, Kazuki Akisawa, Yuji Mochizuki, Yuma Handa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Shigenori Tanaka

      Applied Physics Express14   027003   2021年1月

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      担当区分:責任著者   記述言語:英語  

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    • Extension to Multiscale Simulations 招待有り

      Koji Okuwaki, Taku Ozawa, Yuji Mochizuki

      Recent Advances of the Fragment Molecular Orbital Method   529 - 546   2021年1月

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      担当区分:最終著者  

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    • Modeling of Solid and Surface

      Koichiro Kato, Aya Hashimoto, Eiichi Tamiya, Kaori Fukuzawa, Yuichiro Ishikawa, Yuji Mochizuki

      Recent Advances of the Fragment Molecular Orbital Method   407 - 424   2021年1月

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      担当区分:最終著者  

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    • The ABINIT-MP Program 招待有り

      Yuji Mochizuki, Tatsuya Nakano, Kota Sakakura, Yoshio Okiyama, Hiromasa Watanabe, Koichiro Kato, Yoshinobu Akinaga, Shinya Sato, Jun-inchi Yamamoto, Katsumi Yamashita, Tadashi Murase, Takeshi Ishikawa, Yuto Komeiji, Yuji Kato, Naoki Watanabe, Takashi Tsukamoto, Hirotoshi Mori, Koji Okuwaki, Shigenori Tanaka, Akifumi Kato, Chiduru Watanabe, Kaori Fukuzawa

      Recent Advances of the Fragment Molecular Orbital Method   53 - 67   2021年1月

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      担当区分:筆頭著者, 責任著者   掲載種別:論文集(書籍)内論文   出版者・発行元:Springer Singapore  

      DOI: 10.1007/978-981-15-9235-5_4

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    • Acceleration of Environmental Electrostatic Potential Using Cholesky Decomposition with Adaptive Metric (CDAM) for Fragment Molecular Orbital (FMO) Method 査読有り

      Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Yuto Komeiji, Katsunori Segawa, Yuji Mochizuki

      Bull. Chem. Soc. Jpn.94 ( 1 ) 91 - 96   2021年1月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:The Chemical Society of Japan  

      DOI: 10.1246/bcsj.20200227

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    • Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease - Inhibitor N3 Complex (PDB ID: 6LU7). 査読有り 国際誌

      Ryo Hatada, Koji Okuwaki, Yuji Mochizuki, Yuma Handa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Shigenori Tanaka

      Journal of chemical information and modeling60 ( 7 ) 3593 - 3602   2020年6月25日

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      担当区分:責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

      The worldwide spread of COVID-19 (new coronavirus found in 2019) is an emergent issue to be tackled. In fact, a great amount of works in various fields have been made in a rather short period. Here, we report a fragment molecular orbital (FMO) based interaction analysis on a complex between the SARS-CoV-2 main protease (Mpro) and its peptide-like inhibitor N3 (PDB ID: 6LU7). The target inhibitor molecule was segmented into five fragments in order to capture site specific interactions with amino acid residues of the protease. The interaction energies were decomposed into several contributions, and then the characteristics of hydrogen bonding and dispersion stabilization were made clear. Furthermore, the hydration effect was incorporated by the Poisson-Boltzmann (PB) scheme. From the present FMO study, His41, His163, His164, and Glu166 were found to be the most important amino acid residues of Mpro in interacting with the inhibitor, mainly due to hydrogen bonding. A guideline for optimizations of the inhibitor molecule was suggested as well based on the FMO analysis.

      DOI: 10.1021/acs.jcim.0c00283

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    • Self-Degradable Lipid-Like Materials Based on "Hydrolysis accelerated by the intra-Particle Enrichment of Reactant (HyPER)" for Messenger RNA Delivery 査読有り

      Hiroki Tanaka, Tatsunari Takahashi, Manami Konishi, Nae Takata, Masaki Gomi, Daiki Shirane, Ryo Miyama, Shinya Hagiwara, Yuki Yamasaki, Yu Sakurai, Keisuke Ueda, Kenjirou Higashi, Kunikazu Moribe, Eiji Shinsho, Ruka Nishida, Kaori Fukuzawa, Etsuo Yonemochi, Koji Okuwaki, Yuji Mochizuki, Yuta Nakai, Kota Tange, Hiroki Yoshioka, Shinya Tamagawa, Hidetaka Akita

      ADVANCED FUNCTIONAL MATERIALS30 ( 34 ) 1910575-1 - 1910575-17   2020年6月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

      RNA-based therapeutics is a promising approach for curing intractable diseases by manipulating various cellular functions. For eliciting RNA (i.e., mRNA and siRNA) functions successfully, the RNA in the extracellular space must be protected and it must be delivered to the cytoplasm. In this study, the development of a self-degradable lipid-like material that functions to accelerate the collapse of lipid nanoparticles (LNPs) and the release of RNA into cytoplasm is reported. The self-degradability is based on a unique reaction "Hydrolysis accelerated by intra-Particle Enrichment of Reactant (HyPER)." In this reaction, a disulfide bond and a phenyl ester are essential structural components: concentrated hydrophobic thiols that are produced by the cleavage of the disulfide bonds in the LNPs drive an intraparticle nucleophilic attack to the phenyl ester linker, which results in further degradation. An oleic acid-scaffold lipid-like material that mounts all of these units (ssPalmO-Phe) shows superior transfection efficiency to nondegradable or conventional materials. The insertion of the aromatic ring is unexpectedly revealed to contribute to the enhancement of endosomal escape. Since the intracellular trafficking is a sequential process that includes cellular uptake, endosomal escape, the release of mRNA, and translation, the improvement in each process synergistically enhances the gene expression.

      DOI: 10.1002/adfm.201910575

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    • 小角X線散乱と分子シミュレーションを融合したDOPC/Cholesterol二重膜の物性解析

      新庄 永治, 西田 瑠花, 奥脇 弘次, 望月 祐志, 古石 誉之, 福澤 薫, 米持 悦生

      日本薬学会年会要旨集140年会   27Y - pm04S   2020年3月

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      記述言語:日本語   出版者・発行元:(公社)日本薬学会  

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    • Fragmentation at sp2 carbon in fragment molecular orbital (FMO) method 査読有り

      Yoshinobu Akinaga, Kouichiro Kato, Tatsuya Nakano, Kaori Fukuzawa, Yuji Mochizuki

      J. Comp. Chem.41   1416 - 1420   2020年3月

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      担当区分:最終著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

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    • Ab initio fragment molecular orbital-based molecular dynamics (FMO-MD) simulations of (NH3)32 cluster: effects of electron correlation 査読有り

      Moeko Ninomiya, Hideo Doi, Yoshiteru Matsumoto, Yuji Mochizuki, Yuto Komeiji

      Bulletin of the Chemical Society of Japan93 ( 4 ) 553 - 560   2020年2月

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      記述言語:英語  

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    • Interaction Analyses between Calcite/Apatite and Peptides by Fragment Molecular Orbital Method 査読有り

      Ryo HATADA, Kouichiro KATO, Koji OKUWAKI, Kaori FUKUZAWA, Yuji MOCHIZUKI

      Journal of Computer Chemistry, Japan19 ( 1 ) 1 - 7   2020年

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      担当区分:責任著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Society of Computer Chemistry Japan  

      DOI: 10.2477/jccj.2019-0030

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    • Stabilization Mechanism for a Nonfibrillar Amyloid β Oligomer Based on Formation of a Hydrophobic Core Determined by Dissipative Particle Dynamics 査読有り

      Ryoko Kawai, Shuntaro Chiba, Koji Okuwaki, Ryo Kanada, Hideo Doi, Masahiro Ono, Yuji Mochizuki, Yasushi Okuno

      ACS Chemical Neuroscience20 ( 11 ) 385 - 394   2020年1月

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    • Folding simulation of small proteins by dissipative particle dynamics (DPD) with non-empirical interaction parameters based on fragment molecular orbital calculations 査読有り

      Koji Okuwaki, Hideo Doi, Kaori Fukuzawa, Yuji Mochizuki

      Applied Physics Express13   017002   2020年1月

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      担当区分:責任著者   出版者・発行元:Japan Society of Applied Physics  

      DOI: 10.7567/1882-0786/ab5e0a

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    • Interaction between calcite and adsorptive peptide analyzed by fragment molecular orbital method 査読有り

      Koichiro Kato, Kaori Fukuzawa, Yuji Mochizuki

      Japanese Journal of Applied Physics58 ( 12 ) 120906 - 120906   2019年12月1日

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:IOP Publishing  

      DOI: 10.7567/1347-4065/ab5335

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      その他リンク: http://iopscience.iop.org/article/10.7567/1347-4065/ab5335/pdf

    • Reduction of Orbital Space for Molecular Orbital Calculations with Quantum Computation Simulator for Educations

      Yuji Mochizuki Koji Okuwaki Takumi Kato Yuichiro Minato

      ChemRxiv   2019年9月

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      担当区分:筆頭著者   記述言語:英語  

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    • Cm3+/Eu3+ induced structural, mechanistic and functional implications for calmodulin 査読有り

      Björn Drobot, Moritz Schmidt, Yuji Mochizuki, Takaya Abe, Koji Okuwaki, Florian Brulfert, Sven Falke, Sergey A. Samsonov, Yuto Komeiji, Christian Betzel, Thorsten Stumpf, Johannes Raff, Satoru Tsushima

      Phys. Chem. Chem. Phys.21 ( 38 ) 21213 - 21222   2019年8月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)  

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    • 物性測定とFMO-DPD法による脂質微粒子の構造解析 査読有り

      新庄 永治, 奥脇 弘次, 土居 英男, 望月 祐志, 古石 誉之, 福澤 薫, 米持 悦生

      日本DDS学会学術集会プログラム予稿集35回   135 - 135   2019年6月

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      記述言語:日本語   出版者・発行元:日本DDS学会  

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    • 小角X線散乱測定とFMO-DPDシミュレーションによる脂質/Cholesterol混合二重膜における物性の解析 査読有り

      新庄 永治, 奥脇 弘次, 土居 英男, 望月 祐志, 古石 誉之, 福澤 薫, 米持 悦生

      日本薬学会年会要旨集139年会 ( 4 ) 80 - 80   2019年3月

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      記述言語:日本語   出版者・発行元:(公社)日本薬学会  

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    • Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies 査読有り

      Yoshio Okiyama, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

      The Journal of Physical Chemistry B123 ( 5 ) 957 - 973   2019年2月7日

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society ({ACS})  

      DOI: 10.1021/acs.jpcb.8b09326

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    • Destabilization of DNA through interstrand crosslinking by UO22+ 査読有り

      Andr{\'{e } } Rossberg, Takaya Abe, Koji Okuwaki, Astrid Barkleit, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Satoru Tsushima

      Chemical Communications55 ( 14 ) 2015 - 2018   2019年2月

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      出版者・発行元:Royal Society of Chemistry ({RSC})  

      DOI: 10.1039/C8CC09329F

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    • X線小角散乱と散逸粒子動力学法を用いた脂質膜およびベシクル形成メカニズムの解明 査読有り

      新庄永治, 奥脇弘次, 土居英男, 望月祐志, 古石誉之, 福澤薫, 米持悦生

      J. Comp. Chem. Jpn.17 ( 4 ) 172 - 179   2019年1月

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      記述言語:日本語  

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    • Bond detached atom (BDA)を共有しているフラグメント間の相互作用エネルギーの補正に関する試みII:ラジカル開裂補正 査読有り

      中野 達也, 望月 祐志, 福澤 薫, 沖山 佳生, 渡邉 千鶴

      Journal of Computer Aided Chemistry20 ( 0 ) 1 - 6   2019年

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      記述言語:日本語   掲載種別:研究論文(学術雑誌)  

      DOI: 10.2751/jcac.20.1

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    • Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations 査読有り

      Takaki Tokiwa, Shogo Nakano, Yuta Yamamoto, Takeshi Ishikawa, Sohei Ito, Vladimir Sladek, Kaori Fukuzawa, Yuji Mochizuki, Hiroaki Tokiwa, Fuminori Misaizu, Yasuteru Shigeta

      Journal of Chemical Information and Modeling59 ( 1 ) 25 - 30   2019年1月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society ({ACS})  

      DOI: 10.1021/acs.jcim.8b00649

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    • FMOプログラムABINIT-MPのOakForest-PACS上での多層並列化と性能評価 招待有り 査読有り

      渡邊啓正, 佐藤伸哉, 坂倉耕太, 齊藤天菜, 望月祐志

      J. Comp. Chem. Jpn.17   147 - 149   2018年11月

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      記述言語:日本語  

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    • Interaction between a Single-Stranded DNA and a Binding Protein Viewed by the Fragment Molecular Orbital Method 査読有り

      Yuto Komeiji, Yoshio Okiyama, Yuji Mochizuki, Kaori Fukuzawa

      Bulletin of the Chemical Society of Japan91 ( 11 ) 1596 - 1605   2018年11月

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:The Chemical Society of Japan  

      DOI: 10.1246/bcsj.20180150

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    • <b>Accuracy of Dimer-ES Approximation on Fragment Molecular Orbital (FMO) Method</b><b> </b> 査読有り

      Tatsuya Nakano, Kaori Fukuzawa, Yoshio Okiyama, Chiduru Watanabe, Yuto Komeiji, Yuji Mochizuki

      Chem-Bio Informatics Journal18 ( 0 ) 119 - 122   2018年10月5日

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      担当区分:最終著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Chem-Bio Informatics Society  

      DOI: 10.1273/cbij.18.119

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    • Theoretical Analyses on Water Cluster Structures in Polymer Electrolyte Membrane by Using Dissipative Particle Dynamics Simulations with Fragment Molecular Orbital Based Effective Parameters 査読有り

      Okuwaki Koji, Mochizuki Yuji, Doi Hideo, Kawada Shutaro, Ozawa Taku, Yasuoka Kenji

      RSC Advances8 ( 60 ) 34582 - 34595   2018年10月

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      担当区分:責任著者   出版者・発行元:Royal Society of Chemistry  

      DOI: 10.1039/C8RA07428C

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    • RI-MP3 calculations of biomolecules based on the fragment molecular orbital method 査読有り

      Journal of Computer Chemistry39   1970 - 1978   2018年9月

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    • AIを活用した流体解析シミュレーション技術の開発

      小杉範仁, 近藤修司, 秋永宜伸, 望月祐志

      機械設計62   42 - 46   2018年7月

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      記述言語:日本語  

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    • A portable code for dissipative particle dynamics (DPD) simulations with additional specific interactions 査読有り

      Okuwaki Koji, Naito Takamitsu, Saitou Sona, Mochizuki Yuji, other

      Chem-Bio Informatics Journal   2018年6月

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      担当区分:責任著者  

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      その他リンク: http://orcid.org/0000-0002-7310-5183

    • Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: Implementation and DNA Study 査読有り

      Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka

      The Journal of Physical Chemistry B122 ( 16 ) 4457 - 4471   2018年4月26日

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society ({ACS})  

      DOI: 10.1021/acs.jpcb.8b01172

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    • Development of the Fragment Molecular Orbital Method for Calculating Nonlocal Excitations in Large Molecular Systems 査読有り

      Takatoshi Fujita, Yuji Mochizuki

      Journal of Physical Chemistry A122 ( 15 ) 3886 - 3898   2018年4月19日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society  

      We developed the fragment-based method for calculating nonlocal excitations in large molecular systems. This method is based on the multilayer fragment molecular orbital method and the configuration interaction single (CIS) wave function using localized molecular orbitals. The excited-state wave function for the whole system is described as a superposition of configuration state functions (CSFs) for intrafragment excitations and for interfragment charge-transfer excitations. The formulation and calculations of singlet excited-state Hamiltonian matrix elements in the fragment CSFs are presented in detail. The efficient approximation schemes for calculating the matrix elements are also presented. The computational efficiency and the accuracy were evaluated using the molecular dimers and molecular aggregates. We confirmed that absolute errors of 50 meV (relative to the conventional calculations) are achievable for the molecular systems in their equilibrium geometries. The perturbative electron correlation correction to the CIS excitation energies is also demonstrated. The present theory can compute a large number of excited states in large molecular systems
      in addition, it allows for the systematic derivation of a model exciton Hamiltonian. These features are useful for studying excited-state dynamics in condensed molecular systems based on the ab initio electronic structure theory.

      DOI: 10.1021/acs.jpca.8b00446

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    • Development and Performance Evaluation of a Simulation Code for Dissipative Particle Dynamics (DPD) CAMUS 査読有り

      Doi Hideo, Saitou Sona, Okuwaki Koji, Naito Takamitsu, Mochizuki Yuji

      Journal of Computer Chemistry, Japan16 ( 5 ) 126   2018年2月

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      出版者・発行元:SOC COMPUTER CHEMISTRY, JAPAN 2-1-13 HIGASHIUENO, TAITO-KU, TOWA HIGH TOWN UENO 607, TOKYO, 110-0015, JAPAN  

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    • An automated framework to evaluate effective interactionparameters for dissipative particle dynamics simulations basedon the fragment molecular orbital (FMO) method 査読有り

      Okuwaki Koji, Doi Hideo, Mochizuki Yuji

      Journal of Computer Chemistry, Japan17 ( 2 ) 102   2018年2月

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      出版者・発行元:SOC COMPUTER CHEMISTRY, JAPAN 2-1-13 HIGASHIUENO, TAITO-KU, TOWA HIGH TOWN UENO 607, TOKYO, 110-0015, JAPAN  

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    • Fragment Molecular Orbital Based Parametrization Procedure for Mesoscopic Structure Prediction of Polymeric Materials 査読有り

      Koji Okuwaki, Yuji Mochizuki, Hideo Doi, Taku Ozawa

      Journal of Physical Chemistry B122 ( 1 ) 338 - 347   2018年1月11日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society  

      In the analyses of miscibility behaviors of macromolecules and polymers, dissipative particle dynamics (DPD) simulations are generally performed. In these simulations, the so-called χ parameters describing the effective interactions among particles are crucial. It has been known that such parameters can be obtained within the classical or empirical force field frameworks. However, there is a potential problem that charge transfer and polarization occasionally occur. Additionally, satisfactory reference parameters are not available for some cases. Therefore, we developed a new procedure to evaluate the set of parameters by using the ab initio fragment molecular orbital (FMO) method which can provide the set of interaction energies among segments as polymer units. Moreover, we evaluated the anisotropy of molecules by using the FMO-based effective interaction parameters for three standard binary mixture systems (hexane-nitrobenzene, polyisobutylene-diisobutyl ketone, and polyisoprene-polystyrene). The calculated values showed good agreement with the experimental values with about 10% errors.

      DOI: 10.1021/acs.jpcb.7b08461

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      その他リンク: http://orcid.org/0000-0002-7310-5183

    • FMO計算-粗視化シミュレーション連携手法の開発と応用 査読有り

      奥脇弘次, 土居英男, 望月祐志, 小沢拓, 泰岡顕治, 福澤薫

      J. Comp. Chem. Jpn.17   144 - 146   2018年

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      記述言語:日本語  

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    • 大学初年度向け化学教育のためのScratchプログラムの開発 査読有り

      満野仁美, 中川知樹, 土居英男, 望月祐志

      J. Comp. Chem. Jpn.17   111 - 112   2018年

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      担当区分:責任著者   記述言語:日本語  

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    • フラグメント分子軌道(FMO)法を用いた散逸粒子動力学シミュレーションのための有効相互作用パラメータ算出の自動化フレームワーク 査読有り

      奥脇弘次, 土居英男, 望月祐志

      J. Comp. Chem. Jpn.17   102 - 109   2018年

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      記述言語:日本語  

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    • Application of tensorflow to recognition of visualized results of fragment molecular orbital (FMO) calculations 査読有り

      Sona Saitou, Jun Iijima, Mayu Fujimoto, Yuji Mochizuki, Koji Okuwaki, Hideo Doi, Yuto Komeiji

      Chem-Bio Informatics Journal18   58 - 69   2018年1月1日

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      担当区分:責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Chem-Bio Informatics Society  

      We have applied Google’s TensorFlow deep learning toolkit to recognize the visualized results of the fragment molecular orbital (FMO) calculations. Typical protein structures of α-helix and β-sheet provide some characteristic patterns in the two-dimensional map of inter-fragment interaction energy termed as IFIE-map (Kurisaki et al., Biophys. Chem. 130 (2007) 1). A thousand of IFIE-map images with labels depending on the existences of α-helix and β-sheet were prepared by employing 18 proteins and 3 non-protein systems and were subjected to training by TensorFlow. Finally, TensorFlow was fed with new data to test its ability to recognize the structural patterns. We found that the characteristic structures in test IFIE-map images were judged successfully. Thus the ability of pattern recognition of IFIE-map by TensorFlow was proven.

      DOI: 10.1273/cbij.18.58

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    • Development and Application of FMO Calculation − DPD Simulation Conbination Scheme 査読有り

      Okuwaki Koji, Doi Hideo, Mochizuki Yuji, Ozawa Taku, Yasuoka Kenji, Fukuzawa Kaori

      Journal of Computer Chemistry, Japan17 ( 3 ) 144   2018年

    • Formation Mechanism of Lipid Membrane and Vesicle Using Small Angle X-ray Scattering and Dissipative Particle Dynamics (DPD) Method 査読有り

      Eiji Shinsho, Koji Okuwaki, Hideo Doi, Yuji Mochizuki, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi

      JOURNAL OF COMPUTER CHEMISTRY-JAPAN17 ( 4 ) 172 - 179   2018年

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      記述言語:中国語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SOC COMPUTER CHEMISTRY, JAPAN  

      In order to perform efficient nanoparticle design in drug delivery systems, prediction of physical properties and elucidation of the molecular mechanism are expected by using molecular simulation. In this study, we investigated the molecular mechanism of lipid bilayer formation and mixed lipid vesicle formation using the dissipative particle dynamics (DPD) method and small angle X-ray scattering measurement. Parameters of inter-molecular interaction used for the DPD simulation were estimated in quantum mechanical level by the fragment molecular orbital method (FMO-DPD method). In lipid bilayer formation, it was found that the phospholipid having an unsaturated bond (DOPC) has higher membrane fluidity than the phospholipid (DPPC) having only saturated bonds. In the vesicle formation mixed with phospholipid and positively charged lipid, it was also found that as the proportion of positively charged lipid increases, the fluidity of the membrane increases and the shape changes from a sphere to a flat sphere.

      DOI: 10.2477/jccj.2018-0012

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    • Dissipative particle dynamics (DPD) simulations with fragment molecular orbital (FMO) based effective parameters for 1-Palmitoyl-2-oleoyl phosphatidyl choline (POPC) membrane 査読有り

      Hideo Doi, Koji Okuwaki, Yuji Mochizuki, Taku Ozawa, Kenji Yasuoka

      CHEMICAL PHYSICS LETTERS684   427 - 432   2017年9月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      In dissipative particle dynamics (DPD) simulations, it is necessary to use the so-called chi parameter set that express the effective interactions between particles. Recently, we have developed a new scheme to evaluate the chi parameters in a non-empirical way through a series of fragment molecular orbital (FMO) calculations. As a challenging test, we have performed the DPD simulations using the FMO-based chi parameters for a mixture of 1-Palmitoyl-2-oleoyl phosphatidyl choline (POPC) and water. The structures of both membrane and vesicle were formed successfully. The calculated structural parameters of membrane were in good agreement with experimental results. (C) 2017 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2017.07.032

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    • Theoretical Calculations on Cation-capturing ofMacrocyclic Peptoid with Phenyl Rings in Main Chain 査読有り

      Kawada Shutaro, Hakamata Mayu, Mochizuki Yuji

      Journal of Computer Chemistry, Japan16 ( 3 ) 77   2017年8月

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      記述言語:日本語   出版者・発行元:SOC COMPUTER CHEMISTRY, JAPAN 2-1-13 HIGASHIUENO, TAITO-KU, TOWA HIGH TOWN UENO 607, TOKYO, 110-0015, JAPAN  

      <p>ペプトイドは,側鎖がα-炭素原子上ではなく窒素原子上に位置するペプチド模倣物である.近年,主鎖にフェニル環を含む大環状のペプトイドが開発され,カチオン捕捉の興味深い能力が示された.この論文では,この新しいペプトイドのフェニル環部によるカチオンの対捕捉に関する理論計算を報告する.この結果,カチオンに対するπ電子供与の重要性が示された.</p>

      DOI: 10.2477/jccj.2017-0014

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    • A New Treatment for Water near the Interface between Lipid Membrane and Silica in Dissipative Particle Dynamics Simulation 査読有り

      Doi Hideo, Okuwaki Koji, Mochizuki Yuji, Ozawa Taku

      Journal of Computer Chemistry, Japan16 ( 1 ) 28   2017年4月

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      記述言語:日本語   出版者・発行元:SOC COMPUTER CHEMISTRY, JAPAN 2-1-13 HIGASHIUENO, TAITO-KU, TOWA HIGH TOWN UENO 607, TOKYO, 110-0015, JAPAN  

      <p>散逸粒子動力学(DPD: Dissipative Particle Dynamics)法を用いたシミュレーションは生体膜などの幅広い分野で用いられている.従来,このようなDPD シミュレーションでは,バルクの水と界面付近の水を同じように扱う場合がほとんどであった.しかし,こうしたやり方では系の性質を必ずしも忠実に再現しているとはいえない.界面付近の水分子の性質とバルクの水分子の性質がかなり異なったものであるという実験的,あるいは理論的な研究がなされているからである.そこで,我々はこの問題を解決すべく,バルク水と界面水を区別して取り扱うアプローチを提案する.このアプローチを,脂質膜-シリカ-水の系のDPDシミュレーションに対して適用したところ,シリカに脂質膜が吸着する現象をうまくモデル化することができた.</p>

      DOI: 10.2477/jccj.2017-0003

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    • Fragment molecular orbital (FMO) calculations on DNA by a scaled third-order Møller-Plesset perturbation (MP2. 5) scheme 査読有り

      Yamada Haruka, Mochizuki Yuji, Fukuzawa Kaori, Okiyama Yoshio, Komeiji Yuto

      Computational and Theoretical Chemistry1101   46 - 54   2017年2月

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      担当区分:責任著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier  

      DOI: 10.1016/j.comptc.2016.12.008

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    • FMOプログラムABINIT-MPの開発状況と機械学習との連携 査読有り

      望月祐志, 坂倉耕太, 秋永宜伸, 加藤幸一郎, 渡邊啓正, 沖山佳生, 中野達也, 古明地勇人, 奥沢明, 福澤薫, 田中成典

      J. Comp. Chem. Jpn.16 ( 5 ) 119 - 122   2017年

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      担当区分:筆頭著者, 責任著者   記述言語:日本語   掲載種別:研究論文(学術雑誌)  

      DOI: 10.2477/jccj.2017-0051

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    • Bond detached atom (BDA)を共有しているフラグメント間の相互作用エネルギーの補正に関する試み 査読有り

      中野達也, 望月祐志, 福澤薫, 沖山佳生, 渡邉千鶴

      J. Comp. Aided Chem18 ( 0 ) 143 - 148   2017年

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      記述言語:日本語   掲載種別:研究論文(学術雑誌)  

      DOI: 10.2751/jcac.18.143

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    • ベンゼンを基本骨格に持つ正イオン内包ペプトイドの理論的計算 査読有り

      川田修太郎, 袴田真由, 望月祐志

      J. Comp. Chem. Jpn.16   77 - 79   2017年

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      記述言語:日本語   出版者・発行元:日本コンピュータ化学会  

      <p>ペプトイドは,側鎖がα-炭素原子上ではなく窒素原子上に位置するペプチド模倣物である.近年,主鎖にフェニル環を含む大環状のペプトイドが開発され,カチオン捕捉の興味深い能力が示された.この論文では,この新しいペプトイドのフェニル環部によるカチオンの対捕捉に関する理論計算を報告する.この結果,カチオンに対するπ電子供与の重要性が示された.</p>

      DOI: 10.2477/jccj.2017-0014

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    • フラグメント分子軌道(FMO)計算の結果の自動解析の試み

      望月祐志, 奥沢明

      計算工学22   3539 - 3542   2017年

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      記述言語:日本語  

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    • 散逸粒子動力学におけるシリカ-脂質膜界面付近の水の取扱い 査読有り

      土居英男, 奥脇弘次, 望月祐志, 小沢拓

      J. Comp. Chem. Jpn.16   28 - 31   2017年

      詳細を見る

      記述言語:日本語   出版者・発行元:日本コンピュータ化学会  

      <p>散逸粒子動力学(DPD: Dissipative Particle Dynamics)法を用いたシミュレーションは生体膜などの幅広い分野で用いられている.従来,このようなDPD シミュレーションでは,バルクの水と界面付近の水を同じように扱う場合がほとんどであった.しかし,こうしたやり方では系の性質を必ずしも忠実に再現しているとはいえない.界面付近の水分子の性質とバルクの水分子の性質がかなり異なったものであるという実験的,あるいは理論的な研究がなされているからである.そこで,我々はこの問題を解決すべく,バルク水と界面水を区別して取り扱うアプローチを提案する.このアプローチを,脂質膜-シリカ-水の系のDPDシミュレーションに対して適用したところ,シリカに脂質膜が吸着する現象をうまくモデル化することができた.</p>

      DOI: 10.2477/jccj.2017-0003

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    • Explicit solvation of a single-stranded DNA, a binding protein, and their complex: a suitable protocol for fragment molecular orbital calculation 査読有り

      Yuto Komeij, Yoshio Okiyama, Yuji Mochizuki, Kaori Fukuzawa

      Chem-Bio Informatics Journal17 ( 0 ) 72 - 84   2017年

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Chem-Bio Informatics Society  

      DOI: 10.1273/cbij.17.72

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    • Performance Evaluations of Parallelized DFT Calculations with SMASH on Intel Xeon Phi Processor 査読有り

        15 ( 4 ) 92 - 96   2016年11月

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      掲載種別:研究論文(学術雑誌)  

      DOI: 10.2477/jccj.2016-0047

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    • Evaluations of Molecular Structure and Aromaticity of C5Ch5 and C6Ch6 (Ch=S, Se, Te) 査読有り

      川田 修太郎, 望月 祐志, 中野 克洋

      Journal of Computer Chemistry, Japan15 ( 4 ) 87 - 91   2016年11月

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      記述言語:日本語   出版者・発行元:日本コンピュータ化学会  

      <p> (CO)<sub>n</sub>で記されるCO単位の環状重合体であるオキソカーボンは長年関心を集めてきた.しかし,Oをカルコゲン原子Ch = (S, Se, Te)で置換した擬オキソカーボン類については,これまで系統的に理論計算による検討はなされてはいない.そこで今回,(CCh)<sub>n</sub> (n = 5,6)についてDFT計算による分子構造の最適化とNICS値の算定を試みた.最適化計算からは,カルコゲンが高周期になるにつれて構造の平面性が増すことが分かった.NICS値からは,(CTe)<sub>6</sub>でベンゼンに匹敵する芳香族性が示唆された.</p>

      DOI: 10.2477/jccj.2016-0042

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    • Practical Usages Of 3D-printer for Scientific Education of Chemistry and Biology 査読有り

          2016年10月

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    • Fragment Molecular Orbital (FMO) Calculations of Peptoids 査読有り

      川田 修太郎, 坂口 正貴, 米倉 伊吹, 奥脇 弘次, 望月 祐志, 福澤 薫

      Journal of Computer Chemistry, Japan15 ( 3 ) 51 - 52   2016年10月

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      記述言語:日本語   出版者・発行元:日本コンピュータ化学会  

      <p>Peptoids are a class of peptide mimetics whose side chains contain nitrogen atoms rather than α-carbon atoms. This structural feature restricts the intrinsic capacity to form hydrogen bond networks of α-helix, therefore peptoid oligomers are attracting attention due to the ability to design chemical properties such as self-assembling by selecting proper side chains. This paper shows some illustrative peptoid calculations, based on the fragment molecular orbital (FMO) method.</p>

      DOI: 10.2477/jccj.2016-0032

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    • Hydration of ligands of influenza virus neuraminidase studied by the fragment molecular orbital method 査読有り

      Kana Tokuda, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji

      Journal of Molecular Graphics and Modelling69   144 - 153   2016年9月

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier {BV}  

      DOI: 10.1016/j.jmgm.2016.08.004

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    • Intel Xeon Phi上でのSMASHによる並列化DFT計算の性能評価 査読有り

      齊藤天菜, 望月祐志, 山崎大, 石村和也

      J. Comp. Chem. Jpn.15 ( 4 ) 92 - 96   2016年

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      記述言語:日本語   掲載種別:研究論文(学術雑誌)  

      DOI: 10.2477/jccj.2016-0047

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    • C5Ch5およびC6Ch6 (Ch=S, Se, Te)の分子構造と芳香族性の評価 査読有り

      川田修太郎, 望月祐志, 中野克洋

      J. Comp. Chem. Jpn.15 ( 4 ) 87 - 91   2016年

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      記述言語:日本語   出版者・発行元:日本コンピュータ化学会  

      <p> (CO)<sub>n</sub>で記されるCO単位の環状重合体であるオキソカーボンは長年関心を集めてきた.しかし,Oをカルコゲン原子Ch = (S, Se, Te)で置換した擬オキソカーボン類については,これまで系統的に理論計算による検討はなされてはいない.そこで今回,(CCh)<sub>n</sub> (n = 5,6)についてDFT計算による分子構造の最適化とNICS値の算定を試みた.最適化計算からは,カルコゲンが高周期になるにつれて構造の平面性が増すことが分かった.NICS値からは,(CTe)<sub>6</sub>でベンゼンに匹敵する芳香族性が示唆された.</p>

      DOI: 10.2477/jccj.2016-0042

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    • 化学・生命科学系の理学教育における3Dプリンタの活用事例 査読有り

      望月祐志, 中村昇太, 山中正浩, 山田康之, 工藤光子, 常盤広明, 川上勝, 北本俊二

      J. Comp. Chem. Jpn.15   65 - 67   2016年

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      記述言語:日本語  

      DOI: 10.2477/jccj.2016-0034

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    • ペプトイド類のフラグメント分子軌道計算 査読有り

      川田修太郎, 坂口正貴, 米倉伊吹, 奥脇弘次, 望月祐志, 福澤薫

      J. Comp. Chem. Jpn.15 ( 3 ) 51 - 52   2016年

      詳細を見る

      記述言語:日本語   出版者・発行元:日本コンピュータ化学会  

      <p>Peptoids are a class of peptide mimetics whose side chains contain nitrogen atoms rather than α-carbon atoms. This structural feature restricts the intrinsic capacity to form hydrogen bond networks of α-helix, therefore peptoid oligomers are attracting attention due to the ability to design chemical properties such as self-assembling by selecting proper side chains. This paper shows some illustrative peptoid calculations, based on the fragment molecular orbital (FMO) method.</p>

      DOI: 10.2477/jccj.2016-0032

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    • Effects of Water Molecules and Configurations of Neighboring Amino Acid Residues Surrounding DsRed Chromophore on Its Excitation Energy 査読有り

      坂口正貴, 望月祐志, 望月祐志, 渡邉千鶴, 福澤薫, 福澤薫

      Journal of Computer Chemistry, Japan (Web)14 ( 5 )   2015年12月

    • Reversible Structural Changes Accompanying the Two-Electron Redox Reaction of Pt(tacn) (tacn: 1,4,7-triazacyclononane) Complexes 査読有り

      Tohru Wada, Koki Enami, Ryohei Kojima, Tomoki Okada, Yuki Ishikawa, Yuji Miyazato, Ernst Horn, Yuji Mochizuki

      BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN88 ( 9 ) 1230 - 1237   2015年9月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:CHEMICAL SOC JAPAN  

      Platinum complexes with 1,4,7-triazacyclononane (tacn) as facial ligands, [(PtCl3)-Cl-Iv(tacn)](ClO4), [(PtCl)-Cl-Iv(bpy)-(tacn)](ClO4)(3) ([1](ClO4), and [2](ClO4)(3), bpy: 2,2'-bipyridine) were prepared, and their hexa-coordinated octahedral structures were determined via single-crystal X-ray analysis. In aqueous solutions containing NaCl as the electrolyte, [2](3+) exhibited a quasi-reversible two-electron redox wave at +0.22 V (vs. SCE) with a large peak separation Delta E = E-pc - E-pa = 0.28 V). In addition, controlled-potential reduction of [2](3+) at -0.30 V in aqueous solutions containing NaCl afforded [Pt-II(bpy)(tacn)](2+) ([3](2+)), which was then re-oxidized to regenerate [2](3+). X-ray analysis of [3](2+) revealed a tetra-coordinated square-planar structure in which both tacn and bpy were bound to the central Pt as bidentate ligands. The redox potential of this reaction is coupled with dissociation/association of Cl- from/to Pt in the solution. MO/DFT calculations indicate that structural changes in tacn promote the reversible two-electron redox reaction between the octahedral Pt(IV) and square planar Pt(II) complexes.

      DOI: 10.1246/bcsj.20150097

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    • Modeling of hydroxyapatite-peptide interaction based on fragment molecular orbital method 査読有り

      Koichiro Kato, Kaori Fukuzawa, Yuji Mochizuki

      CHEMICAL PHYSICS LETTERS629   58 - 64   2015年6月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We have applied the four-body corrected fragment molecular orbital (FMO4) calculations to analyze the interaction between a designed peptide motif (Glu1-Ser2-Gln3-Glu4-Ser5) and the hydroxyapatite (HA) solid mimicked by a cluster model consisting of 1408 atoms. To incorporate statistical fluctuations, a total of 30 configurations were generated through classical molecular dynamics simulation with water molecules and were subjected to FMO4 calculations at the MP2 level. It was found that Ser5 plays a leading role in interacting with the phosphate moieties of HA via charge transfer and also that negatively charged Glu1 and Glu4 provide electrostatic stabilizations with the calcium ions. (C) 2015 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2015.03.057

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    • ペプチド結合における新規フラグメント分割方法の検証および精度評価

      坂口正貴, 福澤薫, 渡邉千鶴, 望月祐志

      日本化学会講演予稿集95th ( 2 ) 231   2015年3月11日

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      記述言語:日本語  

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    • Explicit solvation modulates intra- and inter-molecular interactions within DNA: Electronic aspects revealed by the ab initio fragment molecular orbital (FMO) method 査読有り

      Kaori Fukuzawa, Ikuo Kurisaki, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Shigenori Tanaka, Yuto Komeiji

      Computational and Theoretical Chemistry1054   29 - 37   2015年2月

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier {BV}  

      DOI: 10.1016/j.comptc.2014.11.020

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    • 赤色蛍光タンパク質 DsRed の色素部周辺における水分子ならびに隣接アミノ酸残基の構造の励起エネルギーへの影響評価 査読有り

      坂口正貴, 望月祐志, 渡邉千鶴, 福澤薫

      J. Comp. Chem. Jpn.14 ( 5 ) 155 - 163   2015年

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      記述言語:日本語  

      DOI: 10.2477/jccj.2015-0033

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    • 相互作用エネルギー成分分割解析機能PIEDAの実装とタンパク質-リガンド間の相互作用解析 査読有り

      塚本貴志, 加藤幸一郎, 加藤昭史, 中野達也, 望月祐志, 福澤薫

      J. Comp. Chem. Jpn.14 ( 1 ) 1 - 9   2015年

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      記述言語:日本語   掲載種別:研究論文(学術雑誌)  

      DOI: 10.2477/jccj.2014-0039

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    • Fragment Molecular Orbital-Based Molecular Dynamics Study on Hydrated Ln (III) Ions 査読有り

      Fujiwara Takayuki, Mori Hirotoshi, Komeiji Yuto, Mochizuki Yuji

      Proceedings of Computational Science Workshop 2014 (CSW2014)   011001   2015年

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    • 相互作用エネルギー成分分割解析機能PIEDAの実装とタンパク質-リガンド間の相互作用解析 査読有り

      Journal of Computer Chemistry, Japan14 ( 1 ) 1 - 9   2015年

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      掲載種別:研究論文(学術雑誌)  

      DOI: 10.2477/jccj.2014-0039

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    • Optimal damping algorithm for unrestricted Hartree-Fock calculations 査読有り

      Jun-Ichi Yamamoto, Yuji Mochizuki

      Chem-Bio Informatics Journal14   14 - 33   2014年9月13日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Chem-Bio Informatics Society  

      We have developed a couple of optimal damping algorithms (ODAs) for unrestricted Hartree-Fock (UHF) calculations of open-shell molecular systems. A series of equations were derived for both concurrent and alternate constructions of α and β Fock matrices in the integral-direct self-consistent-field (SCF) procedure. Several test calculations were performed to check the convergence behaviors. It was shown that the concurrent algorithm provides better performance than does the alternate one.

      DOI: 10.1273/cbij.14.14

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    • Interaction energy analysis on specific binding of influenza virus hemagglutinin to avian and human sialosaccharide receptors: Importance of mutation-induced structural change 査読有り

      Satoshi Anzaki, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka

      JOURNAL OF MOLECULAR GRAPHICS & MODELLING53   48 - 58   2014年9月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE INC  

      On the basis of available molecular structures registered in Protein Data Bank, we have theoretically carried out the interaction energy analysis for the complexes of influenza virus hemagglutinin (HA) proteins and sialosaccharide receptor analogs of host cells. Employing the fragment molecular orbital method for quantum-chemical calculations, the differences in magnitude and pattern of the interactions between the amino acid residues of avian-type (H7N3) or human-type (H7N9) HA and each saccharide part of avian or human receptor were studied in order to elucidate the molecular mechanism of avian-to-human infectious transmission of influenza virus. We have thus confirmed quantitatively that the mutations from the avian HA to the human HA significantly strengthened the binding affinity of human HA to human receptor, while retaining the affinity to avian receptor. In addition to direct effects regarding the changes of interactions between the altered residues and the receptors, we have also found the importance of indirect effects in which structural changes caused by the mutations play vital roles to modify the intermolecular interactions. (C) 2014 Elsevier Inc. All rights reserved.

      DOI: 10.1016/j.jmgm.2014.07.004

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    • Hydration effects on enzyme–substrate complex of nylon oligomer hydrolase: inter-fragment interaction energy study by the fragment molecular orbital method 査読有り

      Hiroyuki Ando, Yasuteru Shigeta, Takeshi Baba, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Masayoshi Nakano

      Molecular Physics113 ( 3-4 ) 319 - 326   2014年8月

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Informa {UK} Limited  

      DOI: 10.1080/00268976.2014.941311

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    • Improved Description of the Orbital Relaxation Effect by Practical Use of the Self-Energy 査読有り

      Masaaki Saitow, Tomonori Ida, Yuji Mochizuki

      INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY114 ( 9 ) 577 - 586   2014年5月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-BLACKWELL  

      The self-energy shift in the orbital relaxation (OR) term of the polarization propagator complete through the second-order is presented. In combination with the optimal damping parameter in the OR term, the modified propagator produces the excitation energy of the coupled-cluster with singles and doubles (CCSD) accuracy. The self-energy shift requires the floating-point operation of O(N4), where N refers to the magnitude of the molecular size. Because the second-order polarization propagator requires the floating-point operation of O(N5), the additional O(N4) computational effort to construct the self-energy is negligibly small. Numerical results are shown for several molecules including glycine, 2,3,5,6-tetrafluorobenzene, and naphthalene, and promising agreements with those of CCSD are confirmed within less than 0.2 eV. The basis set dependence is also tested for the water molecule using aug-cc-pV NZ (N=D-7), where this newly developed approach mimics the behavior of the CCSD values. The self-energy shifting for the second-order response matrix in combination with the use of a dumping parameter is efficiently implemented for calculations of medium-sized molecular systems, including glycine and naphthalene. The developed approach provides CCSD-like accuracy at a more affordable computational expense. (c) 2014 Wiley Periodicals, Inc.

      DOI: 10.1002/qua.24625

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    • Accuracy of the fragment molecular orbital (FMO) calculations for DNA: Total energy, molecular orbital, and inter-fragment interaction energy 査読有り

      Kaori Fukuzawa, Chiduru Watanabe, Ikuo Kurisaki, Naoki Taguchi, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka, Yuto Komeiji

      COMPUTATIONAL AND THEORETICAL CHEMISTRY1034   7 - 16   2014年4月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      The fragment molecular orbital (FMO) method can calculate the electronic structure of macromolecules such as DNA by dividing them into several fragments and introducing suitable approximations. To establish guiding principles for FMO calculation of DNA, benchmark tests were performed for several small DNA models consisting of one or two bases or two base pairs. The effects of several factors on the accuracy of FMO calculations were investigated, including the methods used to fragment the nucleotide units, approximations for the electrostatic potential, charge neutralization, and electron correlation. It was found that charge neutralization is indispensable for the reliable calculation of energies and spatial distribution of molecular orbitals, but not necessarily so for inter-fragment interaction energy analyses, such as calculation of the base-base interaction. The electrostatic approximations were shown to have only an insignificant effect on the qualitative nature of the calculations. It was also confirmed that the base-base stacking energy can be reproduced semi-quantitatively by the Moller-Plesset second-order perturbation (MP2) method though with some overestimation, and that the overestimation can be alleviated by the spin-component-scaled MP2 method. (C) 2014 Elsevier B.V. All rights

      DOI: 10.1016/j.comptc.2014.02.002

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    • フラグメント分子軌道法を用いたspin-component-scaled MP2法に基づくタンパク-リガンド相互作用クラスター解析

      甘利真司, 望月祐志, 加藤昭史, 福澤薫, 渡邉千鶴, 沖山佳生, 田中成典, 中野達也

      CBI学会誌2 ( 4 ) 17 - 25   2014年

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      記述言語:日本語  

      J-GLOBAL

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    • Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems 査読有り

      Shigenori Tanaka, Yuji Mochizuki, Yuto Komeiji, Yoshio Okiyama, Kaori Fukuzawa

      Phys. Chem. Chem. Phys.16 ( 22 ) 10310 - 10344   2014年

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Royal Society of Chemistry ({RSC})  

      DOI: 10.1039/c4cp00316k

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    • Fragment molecular orbital−based molecular dynamics (FMO-MD) simulations on hydrated Cu(II) ion 査読有り

      Yuji Kato, Takayuki Fujiwara, Yuto Komeiji, Tatsuya Nakano, Hirotoshi Mori, Yoshio Okiyama, Yuji Mochizuki

      Chem-Bio Informatics Journal14 ( 0 ) 1 - 13   2014年

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Chem-Bio Informatics Society  

      DOI: 10.1273/cbij.14.1

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    • Modeling of peptide–silica interaction based on four-body corrected fragment molecular orbital (FMO4) calculations 査読有り

      Yoshio Okiyama, Takayuki Tsukamoto, Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka, Yuji Mochizuki

      Chemical Physics Letters566   25 - 31   2013年4月

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier {BV}  

      DOI: 10.1016/j.cplett.2013.02.020

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    • Three- and four-body corrected fragment molecular orbital calculations with a novel subdividing fragmentation method applicable to structure-based drug design 査読有り

      Chiduru Watanabe, Kaori Fukuzawa, Yoshio Okiyama, Takayuki Tsukamoto, Akifumi Kato, Shigenori Tanaka, Yuji Mochizuki, Tatsuya Nakano

      Journal of Molecular Graphics and Modelling41   31 - 42   2013年4月

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier {BV}  

      DOI: 10.1016/j.jmgm.2013.01.006

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    • Importance of spin-orbit coupling effect and solvent effect in electronic transition assignments of Pt-II complexes: In the case of cis/trans-[(PtCl2)-Cl-II(NH3)(2)] 査読有り

      Hirotoshi Mori, Ryohei Kojima, Yuji Mochizuki, Waka Uenohara, Izumi Umezawa, Nobuyuki Matsushita

      JOURNAL OF MOLECULAR STRUCTURE1035   218 - 223   2013年3月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      Electronic excitation spectra of cis-platin (cis-[(PtCl2)-Cl-II(NH3)(2)]), which is a well-known antitumor drug, and trans-platin (trans-[(PtCl2)-Cl-II(NH3)(2)]) were experimentally observed and theoretically analyzed using ab initio spin-orbit CASPT2 (SO-CASPT2) calculations. Cis-platin showed two series of absorption bands in the wavelength regions of 250-350 nm and 350-450 nm. On the other hand, trans-platin showed three series of absorption bands in the wavelength regions of 260-280 nm, 300-340 nm and 360-400 nm. Comparing SO-CASPT2 calculations at the optimum structures in gas-phase conditions with those in DMF solvent, which were obtained by PCM implicit solvation model, it was clarified that both spin-orbit effect and solvent effect cannot be negligible even for quantitative assignments of electronic excitation spectra of cis/trans-platin. (c) 2012 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.molstruc.2012.11.027

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    • Device, system, method and program for producing fragment model 査読有り

      Mochizuki Yuji, Tsukamoto Takayuki, Fukuzawa Kaori

          2013年3月

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      出版者・発行元:Google Patents  

      US Patent App. 14/442,321

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    • Cartesian Gaussianの積分の初期積分の計算

      中野達也, 山下勝美, 瀬川勝智, 沖山佳生, 望月祐志

      CBI学会誌1   42 - 46   2013年

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      記述言語:日本語  

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    • フラグメント分子軌道法によるインフルエンザウイルス表面タンパク質の大規模量子化学計算

      福澤薫, 望月祐志, 中野達也, 田中成典

      CBI学会誌1   25 - 31   2013年

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      記述言語:日本語  

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    • FMO法における電子相関計算

      望月祐志

      日本化学会・情報部会31   64 - 72   2013年

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      記述言語:日本語  

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    • Analysis of Global Ecosystem Ecology by Fragment Molecular Orbital (FMO) Method--Analyses of the interactions between virus hemagglutinins and their receptors-- 査読有り

      Maruyama Tadashi, Shimane Yasuhiro, Ohishi Kazue, Iwasawa Misako, Hatada Yuji, Usui Keiko, Takaki Yoshihiro, Yoshida Takao, Tanaka Shigenori, Anzaki Satoshi, other

      Annual Report of the Earth Simulator Center April2014   2013年

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    • Dynamic fragmentation with static fragments (DF/SF) algorithm designed for ab initio fragment molecular orbital-based molecular dynamics (FMO-MD) simulations of polypeptides 査読有り

      Yuto Komeiji, Takayuki Fujiwara, Yoshio Okiyama, Yuji Mochizuki

      Chem-Bio Informatics Journal13 ( 0 ) 45 - 57   2013年

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Chem-Bio Informatics Society  

      DOI: 10.1273/cbij.13.45

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    • Ab initio path integral Monte Carlo simulations for water trimer with electron correlation effects 査読有り

      Takatoshi Fujita, Shigenori Tanaka, Takayuki Fujiwara, Masa-Aki Kusa, Yuji Mochizuki, Motoyuki Shiga

      COMPUTATIONAL AND THEORETICAL CHEMISTRY997   7 - 13   2012年10月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We have performed ab initio path integral Monte Carlo simulations for water trimer (H2O)(3) system. The electron correlation effects have been taken into account up to the level of third-order Moller-Plesset (MP3) perturbation theory. Through comparisons of calculated geometrical properties of water trimer such as O-O distance, O-H-O angle, and torsional angle between O-H and O-O-O plane, the interplays among the nuclear quantum, thermal and electron correlation effects are analyzed quantitatively. (c) 2012 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.comptc.2012.07.029

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    • Interaction energy calculation system, method and program 査読有り

      Nakano Tatsuya, Mochizuki Yuji, Fukuzawa Kaori

          2012年8月

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      出版者・発行元:Google Patents  

      US Patent App. 14/356,744

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    • FMO-MD Simulations on the Hydration of Formaldehyde in Water Solution with Constraint Dynamics 査読有り

      Makoto Sato, Hiroshi Yamataka, Yuto Komeiji, Yuji Mochizuki

      CHEMISTRY-A EUROPEAN JOURNAL18 ( 31 ) 9714 - 9721   2012年7月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

      Full-quantum mechanical fragment molecular orbital-based molecular dynamics (FMO-MD) simulations were applied to the hydration reaction of formaldehyde in water solution under neutral conditions. Two mechanisms, a concerted and a stepwise one, were considered with respect to the nucleophilic addition and the proton transfer. Preliminary molecular orbital calculations by means of polarized continuum model reaction field predicted that the hydration prefers a concerted mechanism. Because the calculated activation barriers were too high for free FMO-MD simulations to give reactive trajectories spontaneously, a More OFerrallJencks-type diagram was constructed from the statistical analysis of the FMO-MD simulations with constraint dynamics. The diagram showed that the hydration proceeds through a zwitterionic-like (ZW-like) structure. The free energy changes along the reaction coordinate calculated by means of the blue moon ensemble for the hydration and the amination of formaldehyde indicated that the hydration proceeds through a concerted process through the ZW-like structure, whereas the amination goes through a stepwise mechanism with a ZW intermediate. In inspection of the FMO-MD trajectories, water-mediated cyclic proton transfers were observed in both reactions on the way from the ZW-like structure to the product. These proton transfers also have an asynchronous character, in which deprotonation from the nucleophilic oxygen atom (or nitrogen atom for amination) precedes the protonation of the carbonyl oxygen atom. The results showed the strong advantage of the FMO-MD simulations to obtain detailed information at a molecular level for solution reactions.

      DOI: 10.1002/chem.201200874

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    • Partial geometry optimization with FMO-MP2 gradient: Application to TrpCage 査読有り

      Takayuki Tsukamoto, Yuji Mochizuki, Naoki Watanabe, Kaori Fukuzawa, Tatsuya Nakano

      CHEMICAL PHYSICS LETTERS535   157 - 162   2012年5月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      The reliability of protein structure is a critical concern to grasp the insights with respect to residue-residue and residue-ligand interactions by computational methods. In such calculations, the molecular geometries are usually prepared by the optimization of experimental structure with empirical molecular mechanics (MM) parameters. As an alternative to MM methods, we have developed a partial geometry optimization with the fragment molecular orbital (FMO) scheme at the second-order Moller-Plesset perturbation (MP2) level. The TrpCage miniprotein was used as a demonstrative example. The geometries of the central region were partially optimized at the FMO-MP2 and Hartree-Fock (FMO-HF) levels, and the former with the correlation correction showed reasonable agreement with the experimental structure. (C) 2012 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2012.03.046

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    • Differences in hydration between cis- and trans-platin: Quantum insights by ab initio fragment molecular orbital-based molecular dynamics (FMO-MD) 査読有り

      Hirotoshi Mori, Natsumi Hirayama, Yuto Komeiji, Yuji Mochizuki

      COMPUTATIONAL AND THEORETICAL CHEMISTRY986   30 - 34   2012年4月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      Differences in hydration between cis- and trans-platin were investigated using ab initio fragment molecular orbital-based molecular dynamics (FMO-MD) simulations. Analyzing quantum charge fluctuation in water, we found that the Pt-Cl bond fluctuation of cis/trans-platin, which is important for activating their anticancer functions, was induced by charge transfer interaction between an anti-bonding pi(Pt-Cl) orbital of platin complex and unoccupied orbital of solvent water molecules. The hydration number of Cl ligand in the first hydration shell was found to be larger for cis-platin than for trans-platin due to their difference in charge distribution. Our FMO-MD simulations showed that the amplitude of the Pt-Cl bond fluctuation is larger in hydrated cis-platin than in hydrated trans-platin. (C) 2012 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.comptc.2012.02.008

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    • Excited state calculation for free-base and metalloporphyrins with the partially renormalized polarization propagator approach 査読有り

      Masaaki Saitow, Yuji Mochizuki

      CHEMICAL PHYSICS LETTERS525-26   144 - 149   2012年2月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      Free-base porphyrin and its derivatives have been attracting chemical interests with regard to their characteristic spectral behavior, showing two specific peaks called B- and Q-bands. In this Letter, a modification on the second order polarization propagator scheme is developed and the performance for porphyrin derivatives is examined. The modification is based on Dykstra and Davidson's partial renormalization technique in terms of the coupled-pair functional aspect and has significant resistance to the quasi-degeneracy. As a consequence, the improved scheme shows encouraging results compared with the other theoretical values as well as the experimental data. (C) 2011 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2011.12.063

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    • Continuous multipole methodによるfragment molecular orbital法の高速化

      中野達也, 山下勝美, 瀬川勝智, 沖山佳生, 渡邊千鶴, 福澤薫, 田中成典, 望月祐志

        13 ( 0 ) 44 - 50   2012年

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      記述言語:日本語   掲載種別:研究論文(学術雑誌)  

      DOI: 10.2751/jcac.13.44

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    • New fragmentation of fragment molecular orbital method applicable to fragment based drug design 査読有り

      Watanabe Chiduru, Fukuzawa Kaori, Okiyama Yoshio, Tsukamoto Takayuki, Kato Akifumi, Tanaka Shigenori, Nakano Tatsuya, Mochizuki Yuji

          2012年

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    • Development of the four-body corrected fragment molecular orbital (FMO4) method 査読有り

      Tatsuya Nakano, Yuji Mochizuki, Katsumi Yamashita, Chiduru Watanabe, Kaori Fukuzawa, Katsunori Segawa, Yoshio Okiyama, Takayuki Tsukamoto, Shigenori Tanaka

      Chemical Physics Letters523   128 - 133   2012年1月

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier {BV}  

      DOI: 10.1016/j.cplett.2011.12.004

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    • Ab Initio Path Integral Molecular Dynamics and Monte Carlo Simulations for Water Trimer and Oligopeptide 査読有り

      Takatoshi Fujita, Masa-Aki Kusa, Takayuki Fujiwara, Yuji Mochizuki, Shigenori Tanaka

      ADVANCES IN QUANTUM MONTE CARLO1094   187 - +   2012年

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      記述言語:英語   掲載種別:研究論文(国際会議プロシーディングス)   出版者・発行元:AMER CHEMICAL SOC  

      We have performed ab initio path integral molecular dynamics and Monte Carlo simulations for water trimer and oligopeptide. In the first part, we illustrate the path integral molecular dynamics method based on fragment molecular orbital (FMO-PIMD) method. The FMO-PIMD method is applied to water trimer and glycine pentamer to investigate nuclear quantum effects on the structure and molecular interactions. In the second part, we employ the Moller-Plesset perturbation theory and discuss interplay of nuclear quantum effects and electron correlations. (C) 2012 American Chemical Society

      DOI: 10.1021/bk-2012-1094.ch015

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    • Antigen-antibody interactions of influenza virus hemagglutinin revealed by the fragment molecular orbital calculation 査読有り

      Akio Yoshioka, Kazutomo Takematsu, Ikuo Kurisaki, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Eri Nobusawa, Katsuhisa Nakajima, Shigenori Tanaka

      THEORETICAL CHEMISTRY ACCOUNTS130 ( 4-6 ) 1197 - 1202   2011年12月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

      Effective interactions between amino acid residues in antigen-antibody complex of influenza virus hemagglutinin (HA) protein can be evaluated in terms of the inter-fragment interaction energy (IFIE) analysis with the fragment molecular orbital (FMO) method, in which each fragment contains the side chain of corresponding amino acid residue. We have carried out the FMO-MP2 (second-order Moeller-Plesset) calculation for the complex of HA antigen and Fab antibody of influenza virus H3N2 A/Aichi/2/68 and obtained the IFIE values between each amino acid residue in HA and the whole antibody as the sums over the residues contained in the latter. Combining this IFIE data with experimental data for hemadsorption activity of HA mutants, we succeeded in theoretically explaining the mutations in HA observed after the emergence of influenza virus H3N2 A/Aichi/2/68 in an earlier study, except for those of THR83. In the present study, we employ an alternative way of fragment division in the FMO calculation at the carbonyl C site of the peptide bond instead of the C(alpha) site used in the previous work, which provides revised IFIE values consistent with all the historical mutation data in the antigenic region E of HA including the case of THR83 in the present prediction scheme for probable mutations in HA.

      DOI: 10.1007/s00214-011-1048-z

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    • Higher-order correlated calculations based on fragment molecular orbital scheme 査読有り

      Yuji Mochizuki, Katsumi Yamashita, Tatsuya Nakano, Yoshio Okiyama, Kaori Fukuzawa, Naoki Taguchi, Shigenori Tanaka

      THEORETICAL CHEMISTRY ACCOUNTS130 ( 2-3 ) 515 - 530   2011年10月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

      We have developed a new module for higher-order correlated methods up to coupled-cluster singles and doubles with perturbative triples (CCSD(T)). The matrix-matrix operations through the DGEMM routine were pursued for a number of contractions. This code was then incorporated into the ABINIT-MPX program for the fragment molecular orbital (FMO) calculations. Intra-fragment processings were parallelized with OpenMP in a node-wise fashion, whereas the message passing interface (MPI) was used for the fragment-wise parallelization over nodes. Our new implementation made the FMO-based higher-order calculations applicable to realistic proteins. We have performed several benchmark tests on the Earth Simulator (ES2), a massively parallel computer. For example, the FMO-CCSD(T)/6-31G job for the HIV-1 protease (198 amino acid residues)-lopinavir complex was completed in 9.8 h with 512 processors (or 64 nodes). Another example was the influenza neuraminidase (386 residues) with oseltamivir calculated at the full fourth-order Moller-Plesset perturbation level (MP4), of which job timing was 10.3 h with 1024 processors. The applicability of the methods to commodity cluster computers was tested as well.

      DOI: 10.1007/s00214-011-1036-3

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    • Prediction of probable mutations in influenza virus hemagglutinin protein based on large-scale ab initio fragment molecular orbital calculations 査読有り

      Akio Yoshioka, Kaori Fukuzawa, Yuji Mochizuki, Katsumi Yamashita, Tatsuya Nakano, Yoshio Okiyama, Eri Nobusawa, Katsuhisa Nakajima, Shigenori Tanaka

      Journal of Molecular Graphics and Modelling30   110 - 119   2011年9月

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier {BV}  

      DOI: 10.1016/j.jmgm.2011.06.011

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    • 4f-in-core model core potentials for trivalent lanthanides 査読有り

      Takayuki Fujiwara, Hirotoshi Mori, Yuji Mochizuki, You Osanai, Eisaku Miyoshi

      CHEMICAL PHYSICS LETTERS510 ( 4-6 ) 261 - 266   2011年7月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      4f-in-core large-core model core potentials (LC-MCP), in which the effects of open shell 4f electrons as well as those of other electrons up to 4d were replaced with MCPs, were developed for the lanthanide trivalent ions. In order to achieve desired accuracy, the LC-MCPs were calibrated using static quantum-chemical calculations for LnF(3), and tested by ab initio molecular dynamics simulation on the hydration dynamics of La(3+). Comparing calculated results using the 4f-in-core LC-MCPs with those employing 4f-in-valence MCPs, we found that the 4f-in-core LC-MCPs require less computational costs than the 4f-in-valence MCPs with keeping enough accuracy for describing chemical properties of trivalent lanthanide systems. (C) 2011 Elsevier B. V. All rights reserved.

      DOI: 10.1016/j.cplett.2011.05.028

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    • Counterpoise-corrected interaction energy analysis based on the fragment molecular orbital scheme 査読有り

      Yoshio Okiyama, Kaori Fukuzawa, Haruka Yamada, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

      Chemical Physics Letters509 ( 1-3 ) 67 - 71   2011年6月

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier {BV}  

      DOI: 10.1016/j.cplett.2011.04.070

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    • Fragment molecular orbital-based molecular dynamics (FMO-MD) method with MP2 gradient 査読有り

      Yuji Mochizuki, Tatsuya Nakano, Yuto Komeiji, Katsumi Yamashita, Yoshio Okiyama, Hikaru Yoshikawa, Hiroshi Yamataka

      Chemical Physics Letters504 ( 1-3 ) 95 - 99   2011年2月

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier {BV}  

      DOI: 10.1016/j.cplett.2011.01.039

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    • Fragment molecular orbital calculations for excitation energies of blue- and yellow-fluorescent proteins 査読有り

      Naoki Taguchi, Yuji Mochizuki, Tatsuya Nakano

      CHEMICAL PHYSICS LETTERS504 ( 1-3 ) 76 - 82   2011年2月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      The excitation energies of blue- and yellow-fluorescent proteins (BFP and YFP) were evaluated by the method of configuration interaction singles and perturbative doubles CIS(D) in conjunction with the fragment molecular orbital (FMO) scheme. Three amino acid residues were identified to be contributive to the excitation energy by the so-called pairwise procedure. Under the multilayer treatment (MFMO) with these selected residues, the best estimates for BFP and YFP were obtained as 3.36 and 2.53 eV, respectively, where the second-order self-energy shift was utilized to modify the CIS(D) expression [Mochizuki, Chem. Phys. Lett. 472 (2009) 143]. These values were comparable to the respective experimental values of 3.21/3.25 and 2.41 eV. (C) 2011 Elsevier B. V. All rights reserved.

      DOI: 10.1016/j.cplett.2011.01.054

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    • Development of QC2AS- A computer algebra system for symbolic quantum chemical computations 査読有り

      Takeshi Osoekawa, Yuji Mochizuki, Kazuhiro Kyokoyama

      Proceedings - 2011 International Conference on Computational Science and Its Applications, ICCSA 2011   102 - 109   2011年

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      記述言語:英語   掲載種別:研究論文(国際会議プロシーディングス)  

      This paper introduces QC2AS which is a newly designed and developed computer algebra system for symbolic quantum chemical computations. With the rapid advancement of computer, the concern with high-level model chemistry has been growing. To handle such models, it is necessary to manipulate huge algebraic formulas. QC2AS has been designed to handle algebraic formulas appeared in quantum chemistry and it provides an access to our computer algebraic techniques without knowing the background theories. In this paper, we introduce its features and the architecture with some illustrative examples. This is the first report about the development of QC2AS. © 2011 IEEE.

      DOI: 10.1109/ICCSA.2011.39

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    • Fragment molecular orbital (FMO) study on stabilization mechanism of neuro-oncological ventral antigen (NOVA)-RNA complex system 査読有り

      Ikuo Kurisaki, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Hirofumi Watanabe, Shigenori Tanaka

      JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM962 ( 1-3 ) 45 - 55   2010年12月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We report the molecular mechanism of protein-RNA complex stabilization based on the electronic state calculation Fragment molecular orbital (FMO) method based quantum mechanical calculations were performed for neuro-oncological ventral antigen (NOVA)-RNA complex system The inter-molecular interactions and their effects on the electronic state of NOVA were examined in the framework of ab initio quantum calculation The strength of inter molecular interactions was evaluated using inter-fragment interaction energies (IFIEs) associated with residue-RNA base and residue-RNA backbone interactions Under the influence of Inter-molecular interactions the change of electronic state of NOVA upon the complex formation was examined based on IFIE values associated with ultra-NOVA residue-residue interactions and the change of atomic charges by each residue The results indicated that non-specifically recognized bases contributed to the stability of the complex as well as specifically recognized bases and that the secondary structure of NOVA was remarkably associated with the change of electronic state upon the complex formation (C) 2010 Elsevier B V All rights reserved

      DOI: 10.1016/j.theochem.2010.09.013

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    • Theoretical study of hydration models of trivalent rare-earth ions using model core potentials 査読有り

      Takayuki Fujiwara, Hirotoshi Mori, Yuji Mochizuki, Hiroshi Tatewaki, Eisaku Miyoshi

      JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM949 ( 1-3 ) 28 - 35   2010年6月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We performed geometry optimization calculations and ab initio molecular dynamics calculations for hydration models of trivalent ions, Y(3+), La(3+), Gd(3+), and Lu(3+), by using molecular orbital calculations to examine the so-called gadolinium break. The geometry optimization calculations revealed that the M-O distances of Y(H(2)O)(8)(3+), Lu(H(2)O)(8)(3+), and La(H(2)O)(9)(3+) calculated at the MP2 level were 2.39 angstrom, 2.36 angstrom, and 2.63 angstrom, respectively, which agreed well with observed values. The calculated Gd-O distance (2.44 angstrom) of Gd(H(2)O)(8)(3+) also agrees reasonably well with the existing observed values. The differences in the M-O distances arise from the differences in the ionic radii. When the coordination number increased, the degree of decrease in the M-O binding energies per bond (B.E.) occurred in the following order: La(3+) &lt; Gd(3+) &lt; Y(3+) &lt; Lu(3+). This order is consistent with the order of the ionic radii&apos;s inverse. In ab initio molecular dynamics calculations, by using the Y(H(2)O)(24)(3+) model we could realize the hydration structure where eight water molecules are located around the Y(3+) ion. By using the bigger model of La(H(2)O)(64)(3+), the experimentally suggested structure coordinated by nine water molecules was reproduced. (C) 2010 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.theochem.2010.02.032

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    • Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA) 査読有り

      Yuji Mochizuki, Katsumi Yamashita, Kaori Fukuzawa, Kazutomo Takematsu, Hirofumi Watanabe, Naoki Taguchi, Yoshio Okiyama, Misako Tsuboi, Tatsuya Nakano, Shigenori Tanaka

      Chemical Physics Letters493 ( 4-6 ) 346 - 352   2010年6月

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier {BV}  

      DOI: 10.1016/j.cplett.2010.05.034

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    • Flexible ligand recognition of peroxisome proliferator-activated receptor-$γ$ (PPAR$γ$) 査読有り

      Yamagishi Kenji, Yamamoto Keiko, Mochizuki Yuji, Nakano Tatsuya, Yamada Sachiko, Tokiwa Hiroaki

      Bioorganic & medicinal chemistry letters20 ( 11 ) 3344 - 3347   2010年6月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier  

      DOI: 10.1016/j.bmcl.2010.04.031

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    • Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations on hydrated Zn(II) ion 査読有り

      Takayuki Fujiwara, Yuji Mochizuki, Yuto Komeiji, Yoshio Okiyama, Hirotoshi Mori, Tatsuya Nakano, Eisaku Miyoshi

      Chemical Physics Letters490 ( 1-3 ) 41 - 45   2010年4月

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier {BV}  

      DOI: 10.1016/j.cplett.2010.03.020

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    • Acceleration of fragment molecular orbital calculations with Cholesky decomposition approach 査読有り

      Yoshio Okiyama, Tatsuya Nakano, Katsumi Yamashita, Yuji Mochizuki, Naoki Taguchi, Shigenori Tanaka

      Chemical Physics Letters490 ( 1-3 ) 84 - 89   2010年4月

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier {BV}  

      DOI: 10.1016/j.cplett.2010.03.001

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    • Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations on hydrated Zn(II) ion 査読有り

      Takayuki Fujiwara, Yuji Mochizuki, Yuto Komeiji, Yoshio Okiyama, Hirotoshi Mori, Tatsuya Nakano, Eisaku Miyoshi

      Chemical Physics Letters490 ( 1-3 ) 41 - 45   2010年4月

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier {BV}  

      DOI: 10.1016/j.cplett.2010.03.020

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    • Three-body expansion and generalized dynamic fragmentation improve the fragment molecular orbital-based molecular dynamics (FMO-MD) 査読有り

      Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano

      CHEMICAL PHYSICS LETTERS484 ( 4-6 ) 380 - 386   2010年1月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      The fragment molecular orbital-based molecular dynamics (FMO-MD) was improved by the introduction of the three-body extension (FMO3) and the generalized dynamic fragmentation. An analytical energy gradient was derived for FMO3 to realize FMO3-MD. An algorithm of generalized dynamic fragmentation was devised to treat each covalent-bonded and, optionally, hydrogen-bonded atom cluster as a fragment in the course of FMO-MD. The new algorithms were tested by performing conventional MO-MD, FMO2-MD, based on two-body extension, and FMO3-MD simulations of (H(2)O)(32) and H(+)(H(2)O)(32). FMO2-MD resulted in lower precision, especially in H(+)(H(2)O)(32), while FMO3-MD gave a precision comparable to that of MO-MD. (C) 2009 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2009.11.045

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    • Theoretical Analysis of the Molecular Mechanism of Stabilization of Nova-RNA Complex System: Fragment Molecular Orbital Method Based Quantum Chemical Calculation For the Effect of the Complex Formation on the Electronic State of Biomacromolecular System 査読有り

      Ikuo Kurisaki, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Hirofumi Watanabe, Shigenori Tanaka

      BIOPHYSICAL JOURNAL98 ( 3 ) 74A - 74A   2010年1月

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      記述言語:英語   出版者・発行元:CELL PRESS  

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    • Gröbner Basis Technique for Algebraic Formulas in Electron Correlation Theories 査読有り

      Osoekawa Takeshi, Shinohara Naoyuki, Mochizuki Yuji, Yokoyama Kazuhiro

      Computational Science and Its Applications (ICCSA), 2010 International Conference on   17   2010年

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    • Does Amination of Formaldehyde Proceed Through a Zwitterionic Intermediate in Water? Fragment Molecular Orbital Molecular Dynamics Simulations by Using Constraint Dynamics 査読有り

      Makoto Sato, Hiroshi Yamataka, Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano

      CHEMISTRY-A EUROPEAN JOURNAL16 ( 22 ) 6430 - 6433   2010年

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-V C H VERLAG GMBH  

      DOI: 10.1002/chem.201000442

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    • 1P260 Fragment molecular orbital calculation of the absorption maxima of bacteriorhodopsin and pharaonis phoborhodopsin (Photobiology: Vision & Photoreception, The 48th Annual Meeting of the Biophysical Society of Japan) 査読有り

      Hayashi Tomohiko, Taguchi Naoki, Mochizuki Yuji, Sakurai Minoru

      Seibutsu Butsuri50 ( supplement2 ) S65   2010年

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      記述言語:英語   出版者・発行元:The Biophysical Society of Japan General Incorporated Association  

      DOI: 10.2142/biophys.50.S65_4

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    • Accuracy of fragmentation in ab initio calculations of hydrated sodium cation 査読有り

      Takatoshi Fujita, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

      CHEMICAL PHYSICS LETTERS478 ( 4-6 ) 295 - 300   2009年8月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We discuss the accuracy of fragmentation in fragment molecular orbital (FMO) calculations for the hydrated sodium ion. Two-body expansion shows a considerable error in total energy even if water molecules in the second hydration shell are included in the same fragment as the sodium ion. Inclusion of the three-body term significantly improves both the total energy and the charge distributions. We also illustrate the dependence of the net charge of sodium ion on solvent size and the interfacial property of water molecules. The present study will thus provide fundamental information about hydrated ion to facilitate further theoretical and experimental studies. (C) 2009 Elsevier B. V. All rights reserved.

      DOI: 10.1016/j.cplett.2009.07.060

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    • Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding 査読有り

      Kazutomo Takematsu, Kaori Fukuzawa, Katsumi Omagari, Setsuko Nakajima, Katsuhisa Nakajima, Yuji Mochizuki, Tatsuya Nakano, Hirofumi Watanabe, Shigenori Tanaka

      JOURNAL OF PHYSICAL CHEMISTRY B113 ( 15 ) 4991 - 4994   2009年4月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

      We have performed a quantum-chemical MP2/6-31G* calculation for the hemagglutinin (HA) antigen-antibody system of the H3N2 influenza virus with the fragment molecular orbital method, which provides one of the world&apos;s largest ab initio electron-correlated calculations for biomolecular systems. On the basis of the calculated interfragment interaction energies (IFIEs) representing the molecular interactions between the amino acid residues in the antigen-antibody complex, we have identified those residues in the antigenic region E of HA protein that are significantly recognized by the Fab fragment of antibody with strongly attractive interactions. Combining these IFIE results with those of hemadsorption experiments by which the mutation-prohibited sites are specified has enabled us to explain most of the historical mutation data (five of six residues), which would thus provide a promising method for predicting the HA residues that have a high probability of forthcoming mutation.

      DOI: 10.1021/jp810997c

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    • Application of Dyson-corrected second-order perturbation theories 査読有り

      Yuji Mochizuki

      CHEMICAL PHYSICS LETTERS472 ( 1-3 ) 143 - 148   2009年4月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      Previously [Y. Mochizuki, Chem. Phys. Lett. 453 (2008) 109], the self-energy shift obtained from the Dyson equation was introduced to modify the energy denominator of the second-order perturbational estimate for orbital relaxations in the method of configuration interaction singles with perturbative doubles, CIS(D). This Dyson correction technique is then applied also to the differential second-order correlation energy in CIS(D) calculations, in conjunction with the partial renormalization (PR) of amplitudes by using the topological factor. The potential of Dyson/PR-corrected second-order perturbation itself is separately examined with a couple of small systems having elongated bonds at the ground state. (C) 2009 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2009.02.075

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    • Ab initio quantum-chemical study on emission spectra of bioluminescent luciferases by fragment molecular orbital method 査読有り

      Ayumu Tagami, Nobuhiro Ishibashi, Dai-ichiro Kato, Naoki Taguchi, Yuji Mochizuki, Hirofumi Watanabe, Mika Ito, Shigenori Tanaka

      CHEMICAL PHYSICS LETTERS472 ( 1-3 ) 118 - 123   2009年4月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      Bioluminescence spectra of firefly Luciola cruciata were theoretically analyzed on the basis of the fragment molecular orbital (FMO) method. The CIS(D) and PR-CIS(Ds) methods were employed for the calculations of emission energies of wild-type and mutant luciferase-oxyluciferin systems, and various multilayer FMO calculations were performed changing the sizes of the luciferase protein and of the chromophore to which the excited-state calculations were applied. We have thus reproduced the experimental emission energies of wild-type and mutant luciferase systems with good accuracy, which provides useful information concerning the roles of protein environment for the color tuning of the bioluminescence spectra of firefly. (C) 2009 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2009.02.076

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    • Fragment molecular orbital-based molecular dynamics (FMO-MD), a quantum simulation tool for large molecular systems 査読有り

      Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano, Dmitri G. Fedorov

      JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM898 ( 1-3 ) 2 - 7   2009年3月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      Fragment Molecular Orbital-based Molecular Dynamics (FMO-MD) is an ab initio molecular dynamics method based on the Fragment Molecular Orbital method. FMO-MD is a general tool for quantum-mechanical MD simulations of large molecular systems that works because of the high parallel efficiency and accuracy of FMO. We review the methodology of FMO-MD and its applications to the conformation sampling of formaldehyde in a solvent, the direct simulation of hydrolysis of methyl diazonium cation, and the comparison of free energy profiles of the Menschutkin reaction in the presence and absence of the solvent. Based on these studies, we compare FMO-MD with other MD methods and discuss the future prospects of the FMO-MD method. (C) 2008 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.theochem.2008.07.001

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    • Fragment Molecular Orbital Calculations on Red Fluorescent Proteins (DsRed and mFruits) 査読有り

      Naoki Taguchi, Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Kaori Fukuzawa, Takeshi Ishikawa, Minoru Sakurai, Shigenori Tanaka

      JOURNAL OF PHYSICAL CHEMISTRY B113 ( 4 ) 1153 - 1161   2009年1月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

      We have performed a series of fragment molecular orbital (FMO) calculations for a family of red fluorescent proteins, DsRed and mFruits. The electronic transition energies were evaluated by the method of configuration interaction singles with perturbative doubles [CIS(D)] including higher-order corrections. The calculated values were in good agreement with the corresponding experimental peak values of spectra. Additionally, the chromophore environment was systematically analyzed in terms of the interaction energies between the pigment moiety and neighboring residues. It was&apos; theoretically revealed that the electrostatic interactions play a dominant role in the DsRed chromophore, whereas the color tunings in mFruits are controlled in a more delicate fashion.

      DOI: 10.1021/jp808151c

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    • Fragment Molecular Orbital Method-Based Molecular Dynamics (FMO-MD) as a Simulator for Chemical Reactions in Explicit Solvation 査読有り

      Yuto Komeiji, Takeshi Ishikawa, Yuji Mochizuki, Hiroshi Yamataka, Tatsuya Nakano

      JOURNAL OF COMPUTATIONAL CHEMISTRY30 ( 1 ) 40 - 50   2009年1月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:JOHN WILEY & SONS INC  

      Fragment Molecular Orbital based-Molecular Dynamics (FMO-MD, Komeiji et al., Chem Phys Lett 2003, 372, 342) is an ab initio MD method suitable for large molecular systems. Here, FMO-MD was implemented to conduct full quantum simulations of chemical reactions in explicit solvation. Several FMO-MD simulations were performed for a sphere of water to find a suitable simulation protocol. It was found that annealing of the initial configuration by a classical MD brought the subsequent FMO-MD trajectory to faster stabilization, and also that use of bond constraint in the FMO-MD heating stage effectively reduced the computation time. Then, the blue moon ensemble method (Sprik and Ciccotti, J Chem Phys 1998, 109, 7737) was implemented and was tested by calculating free energy profiles of the Menschutkin reaction (H(3)N + CH(3)Cl -&gt; (+)H(3)NCH(3) + Cl(-)) in the presence and absence of the solvent water via FMO-MD. The obtained free energy profiles were consistent with the Hammond postulate in that stabilization of the product by the solvent, namely hydration of Cl(-), shifted the transition state to the reactant-side. Based on these FMO-MD results, plans for further improvement of the method are discussed. (C) 2008 Wiley Periodicals, Inc. J Comput Chem 30: 40-50, 2009

      DOI: 10.1002/jcc.21025

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    • Developments of FMO methodology and graphical user interface in ABINIT-MP 査読有り

      Nakano Tatsuya, Mochizuki Yuji, Kato Akifumi, Fukuzawa Kaori, Ishikawa Takeshi, Amari Shinji, Kurisaki Ikuo, Tanaka Shigenori

          37 - 62   2009年

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      掲載種別:論文集(書籍)内論文   出版者・発行元:CRC Press: Boca Raton, FL  

      DOI: 10.1201/9781420078497-6

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    • Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Towards an improvement of force fields used for classical molecular dynamics simulations 査読有り

      Yoshio Okiyama, Hirofumi Watanabe, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Takeshi Ishikawa, Kuniyoshi Ebina, Shigenori Tanaka

      Chemical Physics Letters467 ( 4-6 ) 417 - 423   2009年1月

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier {BV}  

      DOI: 10.1016/j.cplett.2008.11.044

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    • Analysis of Mutation Mechanisms of Influenza Virus Based on the Fragment Molecular Orbital Method 査読有り

      Tanaka Shigenori, Mochizuki Yuji, Fukuzawa Kaori, Yamashita Katsumi, Nakano Tatsuya

      Annual Report of the Earth Simulator Center April2010   2009年

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    • 7 Application of the FMO Method to Specific Molecular Recognition of Biomacromolecules 査読有り

      Fukuzawa Kaori, Mochizuki Yuji, Nakano Tatsuya, Tanaka Shigenori

      The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems   133 - 169   2009年

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      掲載種別:論文集(書籍)内論文   出版者・発行元:CRC Press  

      DOI: 10.1201/9781420078497-10

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    • 4 Excited States of Photoactive Proteins by Configuration Interaction Studies 査読有り

      Mochizuki Yuji, Nakano Tatsuya, Taguchi Naoki, Tanaka Shigenori

      The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems   63 - 89   2009年

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      掲載種別:論文集(書籍)内論文   出版者・発行元:CRC Press  

      DOI: 10.1201/9781420078497-7

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    • 3P-063 Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding (Protein: Function, 2SP6 Towards Supercomputiong for Electronic Structures of Biological 査読有り

      Takematsu Kazutomo, Fukuzawa Kaori, Omagari Katsumi, Nakajima Katsuhisa, Nakajima Setsuko, Mochizuki Yuji, Nakano Tatsuya, Watanabe Hirofumi, Tanaka Shigenori

      Seibutsu Butsuri49 ( supplement ) S161   2009年

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      出版者・発行元:The Biophysical Society of Japan General Incorporated Association  

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    • 2SP6-07 Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding (2SP6 Towards Supercomputing for Electronic Structures of Biological Macromolecules, The 査読有り

      Takematsu Kazutomo, Fukuzawa Kaori, Omagari Katsumi, Nakajima Katsuhisa, Nakajima Setsuko, Mochizuki Yuji, Nakano Tatsuya, Watanabe Hirofumi, Tanaka Shigenori

      Seibutsu Butsuri49 ( supplement ) S15   2009年

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      出版者・発行元:The Biophysical Society of Japan General Incorporated Association  

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    • 3P-063 赤血球凝集反応実験とフラグメント分子軌道法計算に基づくインフルエンザヘマグルチニンの変異予測(蛋白質-機能(反応機構,生物活性など),2SP6生体高分子の電子構造解析スーパーコンピューティングへ向けて,シンポジウム,第47回日本生物物理学会年会)

      竹松 和友, 福澤 薫, 尾曲 克己, 中島 捷久, 中島 節子, 望月 祐志, 中野 達也, 渡邉 博文, 田中 成典

      生物物理49   S161   2009年

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      記述言語:英語   出版者・発行元:一般社団法人 日本生物物理学会  

      DOI: 10.2142/biophys.49.S161_5

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    • An application of fragment interaction analysis based on local MP2 査読有り

      Takeshi Ishikawa, Yuji Mochizuki, Shinji Amari, Tatsuya Nakano, Shigenori Tanaka, Kiyoshi Tanaka

      CHEMICAL PHYSICS LETTERS463 ( 1-3 ) 189 - 194   2008年9月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We have developed a method named &apos;fragment interaction analysis based on local MP2&apos; (abbreviated as FILM). This method enables us to decompose the interaction energy associated with dispersion interactions into contributions of localized occupied orbitals. In this study, the basis set dependence of the results derived from FILM was examined. The results suggested that the individual ratio of pair correlation energies of selected orbital pairs to the total dispersion interaction was almost independent of the basis set size. As an illustrative example, detailed analysis was performed on the human immunodeficiency virus type 1 protease complexed with lopinavir molecule. (c) 2008 Elsevier B. V. All rights reserved.

      DOI: 10.1016/j.cplett.2008.08.022

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    • Ab initio fragment molecular orbital study of molecular interactions in liganded retinoid X receptor: Specification of residues associated with ligand inducible information transmission 査読有り

      Mika Ito, Kaori Fukuzawa, Takeshi Ishikawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

      JOURNAL OF PHYSICAL CHEMISTRY B112 ( 38 ) 12081 - 12094   2008年9月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

      The ab initio fragment molecular orbital calculations were performed for the (x-subtype of the human retinoid X receptor (hRXR alpha) complex with its natural ligand 9-cis retinoic acid (9cRA) to quantitatively specify the key residues with important roles for the ligand inducible information transmission of RXR. In the RXR-9cRA complex, the transactivation helix 12 (H12) adopts a canonical agonist conformation, which just corresponds to the transcriptional activation function 2 activating domain core (AF2C). Through the analyses of molecular interactions by the second-order Moller-Plesset perturbation (MP2) method, it was proved that Trp305 and Leu436 of the AF2C binding pocket would be important for the stabilization of the H12 canonical agonist conformation, and, at the same time, for the recognition of the 9cRA molecule. Besides, through the analyses of orbital interactions by the local MP2 (LMP2) method, it was found that Trp305 and Leu436 would recognize the 9cRA molecule especially at its C 19 methyl group, which has been most notably targeted to modify for agonist and antagonist design. Moreover, on the basis of the relationships of molecular interactions, it was suggested that the interactions of Trp305 and Leu436 with AF2C residues would be significantly influenced by the interactions of Trp305 and Leu436 with 9cRA. Taken together, our findings quantitatively demonstrated that Trp305 and Leu436 would be the possible key residues for the information transmission in liganded RXR, accounting for their importance suggested by experiments. Altogether, these results substantiated that our approach is useful for the understanding of the detailed molecular mechanism underlying the transcriptional regulation of RXR and related nuclear receptors at the quantum mechanical level.

      DOI: 10.1021/jp803369x

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    • COMP 246-Simulation study of RNA-binding protein by fragment molecular orbital (FMO) method 査読有り

      Ikuo Kurisaki, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Stuart M. Rothstein, Hirofumi Watanabe, Shigenori Tanaka

      ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY236   2008年8月

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      記述言語:英語   出版者・発行元:AMER CHEMICAL SOC  

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    • Theoretical analysis of binding specificity of influenza viral hemagglutinin to avian and human receptors based on the fragment molecular orbital method 査読有り

      Tatsunori Iwata, Kaori Fukuzawa, Katsuhisa Nakajima, Sachiko Aida-Hyugaji, Yuji Mochizuki, Hirofumi Watanabe, Shigenori Tanaka

      COMPUTATIONAL BIOLOGY AND CHEMISTRY32 ( 3 ) 198 - 211   2008年6月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCI LTD  

      The hemagglutinin (HA) protein of the influenza virus binds to the host cell receptor in the early stage of viral infection. A change in binding specificity from avian alpha 2-3 to human alpha 2-6 receptor is essential for optimal human-to-human transmission and pandemics. Therefore, it is important to reveal the key factors governing the binding affinity of HA-receptor complex at the molecular level for the understanding and prediction of influenza pandemics. In this work, on the basis of ab initio fragment molecular orbital (FMO) method, we have carried out the interaction energy analysis of HA-receptor complexes to quantitatively elucidate the binding specificity of HAs to avian and human receptors. To discuss the binding property of influenza HA comprehensively, a number of HAs from human H1, swine H1, avian H3 and avian H5 viruses were analyzed. We performed detailed investigations about the interaction patterns of complexes of various HAs and receptor analogues, and revealed that intra-molecular interactions between conserved residues in HA play an important role for HA-receptor binding. These results may provide a hint to understand the role of conserved acidic residues at the receptor binding site which are destabilized by the electrostatic repulsion with sialic acid. The calculated binding energies and interaction patterns between receptor and HAs are consistent with the binding specificities of each HA and thus explain the receptor binding mechanism. The calculated results in the present analysis have provided a number of viewpoints regarding the models for the HA-receptor binding specificity associated with mutated residues. Examples include the role of Glu190 and Gln226 for the binding specificity of H5 HA. Since H5 HA has not yet been adapted to human receptor and the mechanism of the specificity change is unknown, this result is helpful for the prediction of the change in receptor specificity associated with forthcoming possible pandemics. (C) 2008 Elsevier Ltd. All rights reserved.

      DOI: 10.1016/j.compbiolchem.2008.03.006

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    • Large scale FMO-MP2 calculations on a massively parallel-vector computer 査読有り

      Yuji Mochizuki, Katsumi Yamashita, Tadashi Murase, Tatsuya Nakano, Kaori Fukuzawa, Kazutomo Takematsu, Hirofumi Watanabe, Shigenori Tanaka

      CHEMICAL PHYSICS LETTERS457 ( 4-6 ) 396 - 403   2008年5月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      The fragment molecular orbital (FMO) calculations have been successfully applied to a variety of realistic biochemical problems, by using our original ABINIT-MP program. In these applications, the inclusion of electron correlation through the second-order Moller-Plesset perturbation (MP2) was demonstrated to be essential to obtain qualitatively correct descriptions. Recently, the FMO calculations in ABINIT-MP were tuned for a massively parallel-vector processing. A series of FMO-MP2/6-31G calculations were performed on the Earth Simulator by which up to 4096 vector processors are available. The largest FMO-MP2 computation was carried out for an influenza hemagglutinin antigen-antibody system consisting of 921 residues, which was completed within one hour with 4096 processors. (c) 2008 Elsevier B. V. All rights reserved.

      DOI: 10.1016/j.cplett.2008.03.090

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    • Ab initio fragment molecular orbital study of molecular interactions between liganded retinoid X receptor and its coactivator; Part II: Influence of mutations in transcriptional activation function 2 activating domain core on the molecular interactions 査読有り

      Mika Ito, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

      JOURNAL OF PHYSICAL CHEMISTRY A112 ( 10 ) 1986 - 1998   2008年3月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

      The ab initio fragment molecular orbital (FMO) calculations were performed for retinoid X receptor (RXR) complexes with its ligand 9-cis retinoic acid (9cRA) and steroid receptor coactivator-1 (SRC1) to examine the influence of mutations in transcriptional activation function 2 activating domain core (AF2C) of RXR on molecular interactions between 9cRA liganded RXR and SRC1 coactivator. The RXR-SRC1 interactions in three types of RXR-9cRA-SRC1 complexes, namely, a wild type (WT), a mutant whose Glu453 of AF2C was substituted by Lys (E453K), and another mutant whose Glu456 of AF2C was substituted by Lys (E456K), were compared. Through the comparison of WT, E453K, and E456K, possible causes for a marked decrease in the transcriptional activity of RXR by the mutation of Glu453, which is known as a highly conserved charged residue of AF2C, were discussed. It was quantitatively demonstrated that the strength of the RXR-SRC1 interaction correlates with the degree of the transcriptional activation (WT &gt; E456K &gt; E453K). In E453K, the RXR-SRC1 interaction was substantially reduced by the AF2C-SRC1 repulsive interaction, and the charge transfer (CT) from RXR to SRC1 was also inhibited by the decreased electron donation from AF2C to SRC1. Our findings suggest that the inhibitions of the local RXR-SRC1 interaction via AF2C and of the local CT from RXR to SRC1 via AF2C would be the possible causes for the marked decrease in the transcriptional activity of RXR.

      DOI: 10.1021/jp075430r

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    • Ab initio fragment molecular orbital study of molecular interactions between liganded retinoid X receptor and its coactivator; Part II: Influence of mutations in transcriptional activation function 2 activating domain core on the molecular interactions

      Mika Ito, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

      JOURNAL OF PHYSICAL CHEMISTRY A112 ( 10 ) 1986 - 1998   2008年3月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

      The ab initio fragment molecular orbital (FMO) calculations were performed for retinoid X receptor (RXR) complexes with its ligand 9-cis retinoic acid (9cRA) and steroid receptor coactivator-1 (SRC1) to examine the influence of mutations in transcriptional activation function 2 activating domain core (AF2C) of RXR on molecular interactions between 9cRA liganded RXR and SRC1 coactivator. The RXR-SRC1 interactions in three types of RXR-9cRA-SRC1 complexes, namely, a wild type (WT), a mutant whose Glu453 of AF2C was substituted by Lys (E453K), and another mutant whose Glu456 of AF2C was substituted by Lys (E456K), were compared. Through the comparison of WT, E453K, and E456K, possible causes for a marked decrease in the transcriptional activity of RXR by the mutation of Glu453, which is known as a highly conserved charged residue of AF2C, were discussed. It was quantitatively demonstrated that the strength of the RXR-SRC1 interaction correlates with the degree of the transcriptional activation (WT &gt; E456K &gt; E453K). In E453K, the RXR-SRC1 interaction was substantially reduced by the AF2C-SRC1 repulsive interaction, and the charge transfer (CT) from RXR to SRC1 was also inhibited by the decreased electron donation from AF2C to SRC1. Our findings suggest that the inhibitions of the local RXR-SRC1 interaction via AF2C and of the local CT from RXR to SRC1 via AF2C would be the possible causes for the marked decrease in the transcriptional activity of RXR.

      DOI: 10.1021/jp075430r

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    • How does an S(N)2 reaction take place in solution? Full ab initio MD simulations for the hydrolysis of the methyl diazonium ion 査読有り

      Makoto Sato, Hiroshi Yamataka, Yuto Komeiji, Yuji Mochizuki, Takeshi Ishikawa, Tatsuya Nakano

      JOURNAL OF THE AMERICAN CHEMICAL SOCIETY130 ( 8 ) 2396 - 2397   2008年2月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

      An important goal of mechanistic studies of chemical reactions is to understand how atoms in reacting molecules behave at the molecular level. Toward this goal, full quantum mechanical molecular dynamics (MD) simulations, which employed the recently developed fragment molecular orbital (FMO)-MD method, were carded out for the hydrolysis of the methyl diazonium ion in water. The simulations illustrated for the first time how the solvent water molecules participate in the reaction and how the C-N bond cleavage and O-C bond formation take place during the reaction. It was revealed that this typical S(N)2 reaction does not always proceed through the energetically favorable synchronous pathway, but that it shows mechanistic diversity.

      DOI: 10.1021/ja710038c

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    • A practical use of self-energy shift for the description of orbital relaxation 査読有り

      Yuji Mochizuki

      CHEMICAL PHYSICS LETTERS453 ( 1-3 ) 109 - 116   2008年2月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      A practical use of self-energy is proposed for the description of orbital relaxation involving excited states. The proposal is first applied to modify the energy contribution from orbital relaxation in the method of configuration interaction singles with perturbative doubles, originated by Head-Gordon et al. as CIS(D). Namely, the self-energy shift is introduced for outer valence orbital energies in the denominator of contraction formula. This modification is found to be effective for Rydberg states with keeping a balance of correction for valence states. The second application of self-energy shift concerns the polarizability which is evaluated as a linear response (LR) property. The modified polarizability values become closer to those obtained by correlated calculations. (C) 2008 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2008.01.014

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    • フラグメント分子軌道法によるホタルルシフェラーゼの発光特性に関する理論的研究

      田上歩, 石橋延裕, 加藤太一郎, 田口尚貴, 望月祐志, 渡邉博文, 伊藤三香, 田中成典

      J. Comp. Aided Chem9   47 - 54   2008年

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      記述言語:日本語  

      DOI: 10.2751/jcac.9.47

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    • Research on Innovative Simulation Software 査読有り

      Kato Chisachi, Tsubokura Makoto, Yamade Yoshinobu, Mochizuki Yuji, Yamashita Katsumi, Nakano Tatsuya, Yamamoto Takenori, Yamasaki Takahiro, Ohno Takahisa

      Annual Report of the Earth Simulator Center April2008   2008年

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    • Infantosi, AFC, 5, 273 Ioannidis, JPA, 39 Iwata, T., 198 Ji, Z., 243 査読有り

      Josic K, Kandemir-Cavas C, Kanwar JR, Karabencheva TG, Khaladkar M, Khoshmanesh K, Kim H, Kim JR, Kiran K, Komeiji Y

      Computational Biology and Chemistry32   470   2008年

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    • Multi-reference calculations of nitric oxide dimer 査読有り

      Naoki Taguchi, Yuji Mochizuki, Takeshi Ishikawa, Kiyoshi Tanaka

      CHEMICAL PHYSICS LETTERS451 ( 1-3 ) 31 - 36   2008年1月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      The nitric oxide dimer, (NO)2, has been known as an archetype with severe near-degeneracy because of the weak N-N bonding. We thus performed a series of multi-reference calculations of fourth-order coupled pair approximation (MRCPA4) and configuration interaction (MRCI). For the ground state, the molecular structure of cis form was optimized by these calculations. The MRCPA4 geometry was favorably compared with the recent experimental data, indicating the importance of higher excitations. Low-lying singlet excited states were also addressed. Through these calculations, the intrinsic MR character of this system was illustrated. (C) 2007 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2007.11.084

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    • Fragment interaction analysis based on local MP2 査読有り

      Takeshi Ishikawa, Yuji Mochizuki, Shinji Amari, Tatsuya Nakano, Hiroaki Tokiwa, Shigenori Tanaka, Kiyoshi Tanaka

      THEORETICAL CHEMISTRY ACCOUNTS118 ( 5-6 ) 937 - 945   2007年12月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

      We have developed a fragment interaction analysis based on local MP2 (FILM) in the context of the fragment molecular orbital (FMO) scheme. The primary purpose of this work is to provide a tool for analyzing inter-fragment interaction associated with dispersion interactions in a large molecule such as protein and DNA. Our implementation of local MP2 (LMP2) is based on the algorithm developed by Pulay and Werner. A potential of FILM was demonstrated using the human immunodeficiency virus type 1 protease (HIV-1 PR) complexed with lopinavir (LPV). The total energy, binding affinity, and inter-fragment interaction energy (IFIE) by the FMO method using LMP2 were compared with those obtained by canonical MP2 and the site-specific information in dispersion interaction was obtained. It turned out that the FILM is a useful tool for analyzing the dispersion interaction between an amino acid residue and a specific site of a ligand.

      DOI: 10.1007/s00214-007-0374-7

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    • Fragment interaction analysis based on local MP2

      Takeshi Ishikawa, Yuji Mochizuki, Shinji Amari, Tatsuya Nakano, Hiroaki Tokiwa, Shigenori Tanaka, Kiyoshi Tanaka

      THEORETICAL CHEMISTRY ACCOUNTS118 ( 5-6 ) 937 - 945   2007年12月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

      We have developed a fragment interaction analysis based on local MP2 (FILM) in the context of the fragment molecular orbital (FMO) scheme. The primary purpose of this work is to provide a tool for analyzing inter-fragment interaction associated with dispersion interactions in a large molecule such as protein and DNA. Our implementation of local MP2 (LMP2) is based on the algorithm developed by Pulay and Werner. A potential of FILM was demonstrated using the human immunodeficiency virus type 1 protease (HIV-1 PR) complexed with lopinavir (LPV). The total energy, binding affinity, and inter-fragment interaction energy (IFIE) by the FMO method using LMP2 were compared with those obtained by canonical MP2 and the site-specific information in dispersion interaction was obtained. It turned out that the FILM is a useful tool for analyzing the dispersion interaction between an amino acid residue and a specific site of a ligand.

      DOI: 10.1007/s00214-007-0374-7

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    • Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method 査読有り

      Ikuo Kurisaki, Kaori Fukuzawa, Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano, Janine Imada, Arleta Chmielewski, Stuart M. Rothstein, Hirofumi Watanabe, Shigenori Tanaka

      BIOPHYSICAL CHEMISTRY130 ( 1-2 ) 1 - 9   2007年10月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      A visualization method for inter-fragment interaction energies (IFIEs) of biopolymers is presented on the basis of the fragment molecular orbital (FMO) method. The IFIEs appropriately illustrate the information about the interaction energies between the fragments consisting of amino acids, nucleotides and other molecules. The IFTEs are usually analyzed in a matrix form called an IFTE matrix. Analyzing the IFIE matrix, we detect important fragments for the function of biomolecular systems and quantify the strength of interaction energies based on quantum chemistry, including the effects of charge transfer, electronic polarization and dispersion force. In this study, by analyzing a protein-DNA complex, we report a visual representation of the IFTE matrix, a so-called IFTE map. We comprehensively examine what information the THE map contains concerning structures and stabilities of the protein-DNA complex. (c) 2007 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.bpc.2007.06.011

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    • Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method

      Ikuo Kurisaki, Kaori Fukuzawa, Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano, Janine Imada, Arleta Chmielewski, Stuart M. Rothstein, Hirofumi Watanabe, Shigenori Tanaka

      BIOPHYSICAL CHEMISTRY130 ( 1-2 ) 1 - 9   2007年10月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      A visualization method for inter-fragment interaction energies (IFIEs) of biopolymers is presented on the basis of the fragment molecular orbital (FMO) method. The IFIEs appropriately illustrate the information about the interaction energies between the fragments consisting of amino acids, nucleotides and other molecules. The IFTEs are usually analyzed in a matrix form called an IFTE matrix. Analyzing the IFIE matrix, we detect important fragments for the function of biomolecular systems and quantify the strength of interaction energies based on quantum chemistry, including the effects of charge transfer, electronic polarization and dispersion force. In this study, by analyzing a protein-DNA complex, we report a visual representation of the IFTE matrix, a so-called IFTE map. We comprehensively examine what information the THE map contains concerning structures and stabilities of the protein-DNA complex. (c) 2007 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.bpc.2007.06.011

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    • Modification for spin-adapted version of configuration interaction singles with perturbative doubles 査読有り

      Yuji Mochizuki, Kiyoshi Tanaka

      Chemical Physics Letters443 ( 4-6 ) 389 - 397   2007年8月6日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier  

      We propose a couple of modifications for the spin-adapted version of configuration interaction singles with perturbative doubles, originated by Head-Gordon et al. as CIS(D). A partial renormalization technique is first introduced for the T2 doubles operator of second-order Møller-Plesset perturbation (MP2) theory. Second, an extra correction from the T1 singles operator is taken into account. The combined modifications can be abbreviated as PR-CIS(Ds) (partially renormalized variant of configuration interaction singles with perturbative doubles and extra singles). A series of calculations with a benchmark set of molecules are performed for both singlet and triplet excited states. Through these tests, it is observed that favorable improvements are obtainable by the proposed modifications for low-lying valence states. © 2007 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2007.06.059

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    • Modification for spin-adapted version of configuration interaction singles with perturbative doubles

      Yuji Mochizuki, Kiyoshi Tanaka

      CHEMICAL PHYSICS LETTERS443 ( 4-6 ) 389 - 397   2007年8月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We propose a couple of modifications for the spin-adapted version of configuration interaction singles with perturbative doubles, originated by Head-Gordon et at. as CIS(D). A partial renormalization technique is first introduced for the T(2) doubles operator of second-order Moller-Plesset perturbation (MP2) theory. Second, an extra correction from the T, singles operator is taken into account. The combined modifications can be abbreviated as PR-CIS(Ds) (partially renormalized variant of configuration interaction singles with perturbative doubles and extra singles). A series of calculations with a benchmark set of molecules are performed for both singlet and triplet excited states. Through these tests, it is observed that favorable improvements are obtainable by the proposed modifications for low-lying valence states. (c) 2007 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2007.06.059

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    • Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital scheme 査読有り

      Yuji Mochizuki, Kiyoshi Tanaka, Katsumi Yamashita, Takeshi Ishikawa, Tatsuya Nakano, Shinji Amari, Katsunori Segawa, Tadashi Murase, Hiroaki Tokiwa, Minoru Sakurai

      THEORETICAL CHEMISTRY ACCOUNTS117 ( 4 ) 541 - 553   2007年4月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

      We have developed a parallelized integral-direct code of the perturbative doubles correction for configuration interaction with singles, proposed as CIS(D) by Head-Gordon et al. (Chem Phys Lett 219:21, 1994). The CIS(D) method provides the energy corrections both of the relaxation and differential correlation for the respective CIS excited states. The implementation of CIS(D) is based on our original algorithm for the second-order Moller-Plesset perturbation (MP2) calculations (Mochizuki et al. in Theor Chem Acc 112:442, 2004). There is no need to communicate bulky intermediate data among worker processes of the parallelized execution. This CIS(D) code is then incorporated into a developer version of ABINIT-MP program, in order to improve the overestimation in excitation energies calculated by the CIS method in conjunction with the multilayer fragment molecular orbital scheme (MLFMO-CIS) (Mochizuki et al. in Chem Phys Lett 406:283, 2005). The MLFMO-CIS(D) method is first used in evaluating the lowest n pi* excitation energy of the hydrated formaldehyde. The photoactive yellow protein (PYP) is the second target of MLFMO-CIS(D) calculation. Through these applications, it is shown that the CIS(D) correction improves the CIS results favorably.

      DOI: 10.1007/s00214-006-0181-6

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    • Ab initio fragment molecular orbital study of molecular interactions between liganded retinoid x receptor and its coactivator: Roles of helix 12 in the coactivator binding mechanism 査読有り

      Mika Ito, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

      JOURNAL OF PHYSICAL CHEMISTRY B111 ( 13 ) 3525 - 3533   2007年4月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

      On the basis of the fragment molecular orbital method we addressed molecular interactions of liganded retinoid X receptor (RXR) with steroid receptor co-activating factor-1 (SRC1) coactivator to examine the contribution of helix 12 (H12), which contains the core of the transcriptional activation function 2 activating domain, to the coactivator binding of RXR. The interaction between H12 and SRC1 was proved to be the main cause for the stabilization of the coactivator binding. In particular, highly conserved charged (Glu453) and hydrophobic (Phe450) residues in H12 were found to have stronger electrostatic and dispersion interactions with SRC1 than the other charged and hydrophobic residues in H12, respectively. In addition, the charge transfer (CT) from RXR to SRC1 was found to occur mainly by the changes in charges of H12 residues. Large positive and negative charge changes were observed especially for Glu453 and for Lys631 and Ile632 in SRC1, respectively, indicating that Glu453 is an electron donor for Lys631 and Ile632 in this CT. Taken together, our findings quantitatively demonstrated that H12 and its highly conserved residues significantly contribute to the coactivator binding not only by the Coulomb and dispersion interactions but also by the CT described with the quantum-mechanical framework.

      DOI: 10.1021/jp070054w

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    • Ab initio fragment molecular orbital study of molecular interactions between liganded retinoid x receptor and its coactivator: Roles of helix 12 in the coactivator binding mechanism

      Mika Ito, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

      JOURNAL OF PHYSICAL CHEMISTRY B111 ( 13 ) 3525 - 3533   2007年4月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

      On the basis of the fragment molecular orbital method we addressed molecular interactions of liganded retinoid X receptor (RXR) with steroid receptor co-activating factor-1 (SRC1) coactivator to examine the contribution of helix 12 (H12), which contains the core of the transcriptional activation function 2 activating domain, to the coactivator binding of RXR. The interaction between H12 and SRC1 was proved to be the main cause for the stabilization of the coactivator binding. In particular, highly conserved charged (Glu453) and hydrophobic (Phe450) residues in H12 were found to have stronger electrostatic and dispersion interactions with SRC1 than the other charged and hydrophobic residues in H12, respectively. In addition, the charge transfer (CT) from RXR to SRC1 was found to occur mainly by the changes in charges of H12 residues. Large positive and negative charge changes were observed especially for Glu453 and for Lys631 and Ile632 in SRC1, respectively, indicating that Glu453 is an electron donor for Lys631 and Ile632 in this CT. Taken together, our findings quantitatively demonstrated that H12 and its highly conserved residues significantly contribute to the coactivator binding not only by the Coulomb and dispersion interactions but also by the CT described with the quantum-mechanical framework.

      DOI: 10.1021/jp070054w

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    • Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital scheme

      Yuji Mochizuki, Kiyoshi Tanaka, Katsumi Yamashita, Takeshi Ishikawa, Tatsuya Nakano, Shinji Amari, Katsunori Segawa, Tadashi Murase, Hiroaki Tokiwa, Minoru Sakurai

      THEORETICAL CHEMISTRY ACCOUNTS117 ( 4 ) 541 - 553   2007年4月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

      We have developed a parallelized integral-direct code of the perturbative doubles correction for configuration interaction with singles, proposed as CIS(D) by Head-Gordon et al. (Chem Phys Lett 219:21, 1994). The CIS(D) method provides the energy corrections both of the relaxation and differential correlation for the respective CIS excited states. The implementation of CIS(D) is based on our original algorithm for the second-order Moller-Plesset perturbation (MP2) calculations (Mochizuki et al. in Theor Chem Acc 112:442, 2004). There is no need to communicate bulky intermediate data among worker processes of the parallelized execution. This CIS(D) code is then incorporated into a developer version of ABINIT-MP program, in order to improve the overestimation in excitation energies calculated by the CIS method in conjunction with the multilayer fragment molecular orbital scheme (MLFMO-CIS) (Mochizuki et al. in Chem Phys Lett 406:283, 2005). The MLFMO-CIS(D) method is first used in evaluating the lowest n pi* excitation energy of the hydrated formaldehyde. The photoactive yellow protein (PYP) is the second target of MLFMO-CIS(D) calculation. Through these applications, it is shown that the CIS(D) correction improves the CIS results favorably.

      DOI: 10.1007/s00214-006-0181-6

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    • A fully quantum mechanical simulation study on the lowest n-π* state of hydrated formaldehyde

      Yuji Mochizuki, Yuto Komeiji, Takeshi Ishikawa, Tatsuya Nakano, Hiroshi Yamataka

      Chemical Physics Letters437 ( 1-3 ) 66 - 72   2007年3月22日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)  

      We report a fully quantum mechanical simulation on the lowest n-π* excited state of the hydrated formaldehyde, by using the fragment molecular orbital (FMO) scheme. For a droplet cluster consisting of a formaldehyde molecule and 128 water molecules, the molecular dynamics (MD) simulation was directly carried out by the FMO-based Hartree-Fock/6-31G energy gradient. The FMO-MD run generated a series of configuration samples with geometrical fluctuation. These samples were then subjected to the excited state calculation of configuration interaction singles with perturbative doubles (CIS(D)) in the multilayer FMO (MLFMO) framework. The final estimation of the excitation energy was obtained to be 4.22 eV through averaging the MLFMO-CIS(D)/6-31G* energies. © 2007 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2007.02.016

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    • A graphical symmetric group approach for a spin adapted full configuration interaction: partitioning of a configuration graph into sets of closed-shell and open-shell graphs 査読有り

      Kiyoshi Tanaka, Yuji Mochizuki, Takeshi Ishikawa, Hidemi Terashima, Hiroaki Tokiwa

      THEORETICAL CHEMISTRY ACCOUNTS117 ( 3 ) 397 - 405   2007年3月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

      We developed a spin adapted full configuration interaction (FCI) method which was expected to be effective for parallel processing. The graphical symmetric group approach (GSGA) was employed, where a configuration graph was partitioned into several sets of closed-shell and open-shell graphs. The configuration state functions (CSFs) bearing the same number of closed-shells and open-shells were assembled in a configuration group. The graphical approach provided a number to identify each CSF in a sequential order within the group. Combination of this partitioning and an intermediate configuration-driven algorithm in calculating the so-called sigma vectors allowed us to use symbolic coupling constants. Furthermore, this combination made it easy to implement an efficient algorithm suitable to task-distributed parallel procedure for evaluating sigma vectors. A program was written and some test calculations were carried out with high parallel efficiency. The largest size of FCI used 10 million CSFs (20 million determinants).

      DOI: 10.1007/s00214-006-0171-8

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    • A fully quantum mechanical simulation study on the lowest n--$π$∗ state of hydrated formaldehyde 査読有り

      Mochizuki Yuji, Komeiji Yuto, Ishikawa Takeshi, Nakano Tatsuya, Yamataka Hiroshi

      Chemical physics letters437 ( 1-3 ) 66 - 72   2007年3月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier  

      DOI: 10.1016/j.cplett.2007.02.016

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    • Frontier Simulation Software for Industrial Science

      望月 祐志

      Annual Report of the Earth Simulator Center April 2005 - March 200656 ( 4 ) 299 - 304   2007年

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      記述言語:英語  

      J-GLOBAL

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    • On Mechanism of Enhanced Fluorescence in Green Fluorescent Protein 査読有り

      STARIKOV EVGENI B, Panas Itai, MOCHIZUKI YUJI, TANAKA SHIGENORI, Luo Yi, AA}gren Hans

      Biophysical Reviews and Letters2 ( 03n04 ) 221 - 227   2007年

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:World Scientific  

      DOI: 10.1142/s1793048007000568

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    • Fragment molecular orbital calculations on red fluorescent protein (DsRed) 査読有り

      Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Takeshi Ishikawa, Kiyoshi Tanaka, Minoru Sakurai, Shigenori Tanaka

      CHEMICAL PHYSICS LETTERS433 ( 4-6 ) 360 - 367   2007年1月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We have performed the calculations of configuration interaction singles with perturbative doubles correction (CIS(D)) in conjunction with the multilayer fragment molecular orbital (MLFMO) scheme for a red fluorescent protein isolated from Discosoma coral (known as DsRed). The pigment geometry of DsRed was first examined by employing several model molecules whose spectra in gas-phase were actually observed, and an adequacy was confirmed. The excitation energy was then calculated to be 2.28 eV at the MLFMO-CIS(D)/6-31G* level. The emission energy was also estimated to be 2.21 eV similarly. These theoretical values were in good agreement with the corresponding experimental values of 2.22 eV and 2.13 eV. (c) 2006 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2006.11.088

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    • Application of the fragment molecular orbital method for determination of atomic charges on polypeptides 査読有り

      Yoshio Okiyama, Hirofumi Watanabe, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Takeshi Ishikawa, Shigenori Tanaka, Kuniyoshi Ebina

      Chemical Physics Letters449 ( 4-6 ) 329 - 335   2007年

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier {BV}  

      DOI: 10.1016/j.cplett.2007.10.066

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    • Ab initio FMO-MD method reimplemented and applied to pure water 査読有り

      Yuto Komeiji, Takeshi Ishikawa, Yuji Mochizuki, Hiroshi Yamataka, Tatsuya Nakano

      COMPUTATION IN MODERN SCIENCE AND ENGINEERING VOL 2, PTS A AND B2 ( 2 ) 1261 - +   2007年

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      記述言語:英語   掲載種別:研究論文(国際会議プロシーディングス)   出版者・発行元:AMER INST PHYSICS  

      The: Fragment Molecular Orbital based Molecular Dynamics method (FMO-MD, Komeiji et al., Chem. Phys. Lett. 372, 342, 2003) was reimplemented by combining the latest versions of PEACH and ABINIT-MP programs. Several simulations were performed for a spherical cluster of 125 water molecules at HF/6-31G* level to examine methods in FMO-MD. It was found that use of a molecular configuration prepared by annealing with classical MD lead to a better stabilization of the subsequent FMO-MD simulation. It was also found that use RATTLE bond length constraint in the heating stage could save computational time. These data are expected to serve as a basis for future simulations of solvated molecules.

      DOI: 10.1063/1.2835978

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    • 2P058 Theoretical study on the sequence specific recognition mechanism of Pumilio RNA-binding domain by Fragment Molecular Orbital (FMO) method (Proteins-structure and structure-function relationship, Poster Presentations) 査読有り

      Kurisaki Ikuo, Fukuzawa Kaori, Nakano Tatsuya, Mochizuki Yuji, Watanabe Hirofumi, Tanaka Shigenori

      Seibutsu Butsuri47 ( supplement ) S127   2007年

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      記述言語:英語   出版者・発行元:The Biophysical Society of Japan General Incorporated Association  

      DOI: 10.2142/biophys.47.S127_3

      CiNii Article

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    • Fragment molecular orbital calculations on red fluorescent protein (DsRed)

      Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Takeshi Ishikawa, Kiyoshi Tanaka, Minoru Sakurai, Shigenori Tanaka

      CHEMICAL PHYSICS LETTERS433 ( 4-6 ) 360 - 367   2007年1月

      詳細を見る

      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We have performed the calculations of configuration interaction singles with perturbative doubles correction (CIS(D)) in conjunction with the multilayer fragment molecular orbital (MLFMO) scheme for a red fluorescent protein isolated from Discosoma coral (known as DsRed). The pigment geometry of DsRed was first examined by employing several model molecules whose spectra in gas-phase were actually observed, and an adequacy was confirmed. The excitation energy was then calculated to be 2.28 eV at the MLFMO-CIS(D)/6-31G* level. The emission energy was also estimated to be 2.21 eV similarly. These theoretical values were in good agreement with the corresponding experimental values of 2.22 eV and 2.13 eV. (c) 2006 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2006.11.088

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    • フラグメント分子軌道法に基づいた生体巨大分子の電子状態計算の現状と今後の展望

      望月 祐志

      中野達也, 望月祐志, 甘利真司, 小林将人, 福澤薫, 田中成典 J. Comp. Chem. Jpn.6 ( 3 ) 173 - 184   2007年1月1日

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      記述言語:日本語   掲載種別:研究論文(その他学術会議資料等)   出版者・発行元:日本コンピュータ化学会  

      1999年に北浦らにより提唱されたフラグメント分子軌道(FMO)法は、分子系をフラグメントに分割し、フラグメントのモノマー、ダイマー・・・の計算から系全体を計算する方法であり、タンパク質やDNAのような巨大分子系全体を量子論的に扱う計算方法として、近年注目を集めている。本稿では、FMO法の概要と、多層FMO(MLFMO)法に基づいたタンパク質の励起状態計算、及びFMO法に基づいたconfiguration analysis for fragment interaction (CAFI)やvisualized cluster analysis of protein-ligand interaction (VISCANA)といった解析方法について報告し、FMO法の今後について展望する。

      DOI: 10.2477/jccj.6.173

      CiNii Article

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    • フラグメント分子軌道法による生体高分子の応用計算

      望月 祐志

      福澤薫, 中野達也, 加藤昭史, 望月祐志, 田中成典 J. Comp. Chem. Jpn.6 ( 3 ) 185 - 198   2007年1月1日

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      記述言語:日本語   掲載種別:研究論文(その他学術会議資料等)   出版者・発行元:Society of Computer Chemistry, Japan  

      フラグメント分子軌道(FMO)法プログラムABINIT-MPを用いた生体高分子の応用計算の現状をGUIシステムBioSation Viewerの機能とともに紹介する。具体例として、核内受容体とリガンドの相互作用、DNAと転写因子タンパク質との結合などについて、主に転写に関わる分子認識機構を詳細に解析した。フラグメント間相互作用エネルギー、電荷分布、及び軌道相互作用の解析などを通じて、生体高分子の分子認識における各アミノ酸残基の役割や相互作用の様式を明らかにした。またこれらの分子認識には、静電的な相互作用ばかりでなく、分散力に基づくvan der Waals相互作用が重要であることを明らかにし、電子相関を適切に取り入れた量子化学計算が必要となることが具体例を通じて示された。その他にも、光励起特性の解析などの先駆的な研究も進めている。

      DOI: 10.2477/jccj.6.185

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      その他リンク: https://jlc.jst.go.jp/DN/JALC/00301036791?from=CiNii

    • A graphical symmetric group approach for a spin adapted full configuration interaction

      望月 祐志

      K. Tanaka, Y. Mochizuki, T. Ishikawa, H. Terashima, and H. Tokiwa, ( 117 ) 397 - 405   2007年1月1日

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      記述言語:英語   掲載種別:研究論文(その他学術会議資料等)  

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    • Erratum: Intra- and intermodular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study (Journal of Computational Chemistry (2006) 27 (948)) 査読有り

      Fukuzawa, K., Komeiji, Y., Mochizuki, Y., Kato, A., Nakano, T., Tanaka, S.

      Journal of Computational Chemistry28 ( 13 )   2007年

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      掲載種別:研究論文(学術雑誌)  

      DOI: 10.1002/jcc.20803

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    • Molecular interactions between estrogen receptor and its ligand studied by the ab initio fragment molecular orbital method (vol 110, pg 24276, 2006) 査読有り

      Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka, Kazuo Kitaura, Tatsuya Nakano

      JOURNAL OF PHYSICAL CHEMISTRY B110 ( 47 ) 24276 - 24276   2006年11月

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      記述言語:英語   出版者・発行元:AMER CHEMICAL SOC  

      DOI: 10.1021/jp065705n

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    • Application of fragment molecular orbital scheme to silicon-containing systems 査読有り

      Takeshi Ishikawa, Yuji Mochizuki, Kenji Imamura, Tatsuya Nakano, Hirotoshi Mori, Hiroaki Tokiwa, Kiyoshi Tanaka, Eisaku Miyoshi, Shigenori Tanaka

      CHEMICAL PHYSICS LETTERS430 ( 4-6 ) 361 - 366   2006年10月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      The fragment molecular orbital (FMO) scheme has been successfully used for a variety of large-scale molecules such as proteins and nucleic acids so far. We have applied the FMO calculations to the silicon-containing systems like polysilanes. The error caused by the fragmentation was examined by the Hartree-Fock method and the second-order Moller-Plesset (MP2) perturbation method for the ground state energy. The dynamic polarizability as a linear response property was also evaluated with and without the fragmentation. A series of numerical comparisons showed that the FMO scheme is applicable to silicon-based molecules with reasonable accuracy. This implied a potential availability of FMO calculations for the issues relevant to nanoscience and nanotechnology. (c) 2006 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2006.09.015

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    • Application of fragment molecular orbital scheme to silicon-containing systems

      Takeshi Ishikawa, Yuji Mochizuki, Kenji Imamura, Tatsuya Nakano, Hirotoshi Mori, Hiroaki Tokiwa, Kiyoshi Tanaka, Eisaku Miyoshi, Shigenori Tanaka

      CHEMICAL PHYSICS LETTERS430 ( 4-6 ) 361 - 366   2006年10月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      The fragment molecular orbital (FMO) scheme has been successfully used for a variety of large-scale molecules such as proteins and nucleic acids so far. We have applied the FMO calculations to the silicon-containing systems like polysilanes. The error caused by the fragmentation was examined by the Hartree-Fock method and the second-order Moller-Plesset (MP2) perturbation method for the ground state energy. The dynamic polarizability as a linear response property was also evaluated with and without the fragmentation. A series of numerical comparisons showed that the FMO scheme is applicable to silicon-based molecules with reasonable accuracy. This implied a potential availability of FMO calculations for the issues relevant to nanoscience and nanotechnology. (c) 2006 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2006.09.015

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    • Molecular interactions between estrogen receptor and its ligand studied by the ab initio fragment molecular orbital method 査読有り

      Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka, Kazuo Kitaura, Tatsuya Nakano

      JOURNAL OF PHYSICAL CHEMISTRY B110 ( 32 ) 16102 - 16110   2006年8月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

      The ab initio fragment molecular orbital calculations were performed for molecular interactions of the whole estrogen receptor (ER) ligand-binding domain with a natural ligand, 17 ss-estradiol (EST). The interaction energies of the ligand at the residue level were calculated using HF and MP2 methods with several basis sets. The charge-transfer (CT) interactions were also analyzed based on configuration analysis for fragment interaction. Strong electrostatic interactions were observed between the EST and surrounding charged/polarized residues, Glu353, Arg394, His524, and Thr347. Weak electrostatic and significant van der Waals dispersion interactions were observed between the EST and the many surrounding hydrophobic residues. Together with the experimental interpretations, both interactions equally contributed to the total binding energies, and it was found that the inclusion of electron correlation was essential to obtain an appropriate picture of the interaction. The strongest interaction energy was observed between Glu353 and the EST, and the CT interactions from the lone- pair orbital of the carbonyl oxygen of Glu353 to the alpha*(OH) orbital of the hydroxyl group of EST were found to be important. The CT interactions from the lone- pair orbital of EST to the alpha*(NH) of Arg394 and from the lone- pair orbital of EST to the alpha*(NH) of His524 were also observed. These CT interactions occurred through the hydrogen-bond networks between the ER and EST. Therefore, electron donations from the ER to the EST and electron back-donations from EST to the ER were characteristic of ER-ligand binding. Our approach provides a powerful tool to understanding detailed molecular interactions at the quantum mechanical level.

      DOI: 10.1021/jp060770i

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    • Fragment molecular orbital calculations on large scale systems containing heavy metal atom 査読有り

      Takeshi Ishikawa, Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Hirotoshi Mori, Hiroaki Honda, Takatoshi Fujita, Hiroaki Tokiwa, Shigenori Tanaka, Yuto Komeiji, Kaori Fukuzawa, Kiyoshi Tanaka, Eisaku Miyoshi

      CHEMICAL PHYSICS LETTERS427 ( 1-3 ) 159 - 165   2006年8月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We have realized a fully quantum mechanical treatment of large scale systems containing heavy metal atom, by introducing the model core potential (MCP) technique into the fragment molecular orbital (FMO) scheme. The scalar relativistic effects are incorporated by the use of MCP. This FMO/MCP method was applied to the divalent mercury ion hydrated, with 256 water molecules at the second-order Moller-Plesset (MP2) perturbation level. The complex between cisplatin and DNA was also calculated with MP2, where about a thousand of water molecules and dozens of sodium ions were employed for the explicit treatment of hydration. (c) 2006 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2006.06.103

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    • Fragment molecular orbital calculations on large scale systems containing heavy metal atom

      Takeshi Ishikawa, Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Hirotoshi Mori, Hiroaki Honda, Takatoshi Fujita, Hiroaki Tokiwa, Shigenori Tanaka, Yuto Komeiji, Kaori Fukuzawa, Kiyoshi Tanaka, Eisaku Miyoshi

      CHEMICAL PHYSICS LETTERS427 ( 1-3 ) 159 - 165   2006年8月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We have realized a fully quantum mechanical treatment of large scale systems containing heavy metal atom, by introducing the model core potential (MCP) technique into the fragment molecular orbital (FMO) scheme. The scalar relativistic effects are incorporated by the use of MCP. This FMO/MCP method was applied to the divalent mercury ion hydrated, with 256 water molecules at the second-order Moller-Plesset (MP2) perturbation level. The complex between cisplatin and DNA was also calculated with MP2, where about a thousand of water molecules and dozens of sodium ions were employed for the explicit treatment of hydration. (c) 2006 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2006.06.103

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    • Molecular interactions between estrogen receptor and its ligand studied by the ab initio fragment molecular orbital method

      Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka, Kazuo Kitaura, Tatsuya Nakano

      JOURNAL OF PHYSICAL CHEMISTRY B110 ( 32 ) 16102 - 16110   2006年8月

      詳細を見る

      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

      The ab initio fragment molecular orbital calculations were performed for molecular interactions of the whole estrogen receptor (ER) ligand-binding domain with a natural ligand, 17 ss-estradiol (EST). The interaction energies of the ligand at the residue level were calculated using HF and MP2 methods with several basis sets. The charge-transfer (CT) interactions were also analyzed based on configuration analysis for fragment interaction. Strong electrostatic interactions were observed between the EST and surrounding charged/polarized residues, Glu353, Arg394, His524, and Thr347. Weak electrostatic and significant van der Waals dispersion interactions were observed between the EST and the many surrounding hydrophobic residues. Together with the experimental interpretations, both interactions equally contributed to the total binding energies, and it was found that the inclusion of electron correlation was essential to obtain an appropriate picture of the interaction. The strongest interaction energy was observed between Glu353 and the EST, and the CT interactions from the lone- pair orbital of the carbonyl oxygen of Glu353 to the alpha*(OH) orbital of the hydroxyl group of EST were found to be important. The CT interactions from the lone- pair orbital of EST to the alpha*(NH) of Arg394 and from the lone- pair orbital of EST to the alpha*(NH) of His524 were also observed. These CT interactions occurred through the hydrogen-bond networks between the ER and EST. Therefore, electron donations from the ER to the EST and electron back-donations from EST to the ER were characteristic of ER-ligand binding. Our approach provides a powerful tool to understanding detailed molecular interactions at the quantum mechanical level.

      DOI: 10.1021/jp060770i

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    • Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study 査読有り

      K Fukuzawa, Y Komeiji, Y Mochizuki, A Kato, T Nakano, S Tanaka

      JOURNAL OF COMPUTATIONAL CHEMISTRY27 ( 8 ) 948 - 960   2006年6月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-BLACKWELL  

      The ab initio fragment molecular orbital (FMO) calculations were performed for the cAMP receptor protein (CRP) complexed with a cAMP and DNA duplex to elucidate their sequence-specific binding and the stability of the DNA duplex, as determined by analysis of their inter- and intramolecular interactions. Calculations were performed with the AMBER94 force field and at the HF and MP2 levels with several basis sets. The interfragment interaction energies (IFIEs) were analyzed for interactions of CRP-cAMP with each base pair, DNA duplex with each amino acid residue, and each base pair with each residue. In addition, base-base interactions were analyzed including hydrogen bonding and stacking of DNA. In the interaction between DNA and CRP-cAMP, there was a significant charge transfer (CT) from the DNA to CRP. and this CT interaction played an important role as well as the electrostatic interactions. It is necessary to apply a quantum mechanical approach beyond the "classical" force-field approach to describe the sequence specificity. In the DNA intramolecular interaction, the dispersion interactions dominated the stabilization of the base-pair stacking interactions. Strong, attractive 1,2-stacking interactions and weak, repulsive 1,3-stacking interactions were observed. Comparison of the intramolecular interactions of free and complexed DNA revealed that the base-pairing interactions were stronger, and the stacking interactions were weaker, in the complexed structure. Therefore, the DNA duplex stability appears to change due to both the electrostatic and the CT interactions that take place under conditions of DNA-CRP binding. (c) 2006 Wiley Periodicals, Inc.

      DOI: 10.1002/jcc.20399

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    • Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study

      K Fukuzawa, Y Komeiji, Y Mochizuki, A Kato, T Nakano, S Tanaka

      JOURNAL OF COMPUTATIONAL CHEMISTRY27 ( 8 ) 948 - 960   2006年6月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-BLACKWELL  

      The ab initio fragment molecular orbital (FMO) calculations were performed for the cAMP receptor protein (CRP) complexed with a cAMP and DNA duplex to elucidate their sequence-specific binding and the stability of the DNA duplex, as determined by analysis of their inter- and intramolecular interactions. Calculations were performed with the AMBER94 force field and at the HF and MP2 levels with several basis sets. The interfragment interaction energies (IFIEs) were analyzed for interactions of CRP-cAMP with each base pair, DNA duplex with each amino acid residue, and each base pair with each residue. In addition, base-base interactions were analyzed including hydrogen bonding and stacking of DNA. In the interaction between DNA and CRP-cAMP, there was a significant charge transfer (CT) from the DNA to CRP. and this CT interaction played an important role as well as the electrostatic interactions. It is necessary to apply a quantum mechanical approach beyond the "classical" force-field approach to describe the sequence specificity. In the DNA intramolecular interaction, the dispersion interactions dominated the stabilization of the base-pair stacking interactions. Strong, attractive 1,2-stacking interactions and weak, repulsive 1,3-stacking interactions were observed. Comparison of the intramolecular interactions of free and complexed DNA revealed that the base-pairing interactions were stronger, and the stacking interactions were weaker, in the complexed structure. Therefore, the DNA duplex stability appears to change due to both the electrostatic and the CT interactions that take place under conditions of DNA-CRP binding. (c) 2006 Wiley Periodicals, Inc.

      DOI: 10.1002/jcc.20399

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    • Dynamic polarizability calculation with fragment molecular orbital scheme 査読有り

      Y Mochizuki, T Ishikawa, K Tanaka, H Tokiwa, T Nakano, S Tanaka

      CHEMICAL PHYSICS LETTERS418 ( 4-6 ) 418 - 422   2006年2月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We have developed a linear response module to evaluate the dynamic polarizability, by accepting the fragment molecular orbital (FMO) scheme proposed by Kitaura. The module is parallelized in an integral-driven fashion with atomic-orbital indices in a local version Of ABINIT-MP program. The error caused by fragmentation was checked through test calculations on the water pentamer and the glycine pentamer. The error is shown to be small even under nonzero frequency, indicating the potential applicability of the FMO-based polarizability evaluation for large molecules. (c) 2005 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2005.11.014

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    • Dynamic polarizability calculation with fragment molecular orbital scheme

      Y Mochizuki, T Ishikawa, K Tanaka, H Tokiwa, T Nakano, S Tanaka

      CHEMICAL PHYSICS LETTERS418 ( 4-6 ) 418 - 422   2006年2月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We have developed a linear response module to evaluate the dynamic polarizability, by accepting the fragment molecular orbital (FMO) scheme proposed by Kitaura. The module is parallelized in an integral-driven fashion with atomic-orbital indices in a local version Of ABINIT-MP program. The error caused by fragmentation was checked through test calculations on the water pentamer and the glycine pentamer. The error is shown to be small even under nonzero frequency, indicating the potential applicability of the FMO-based polarizability evaluation for large molecules. (c) 2005 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2005.11.014

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    • VISCANA: Visualized cluster analysis of protein-ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening 査読有り

      S Amari, M Aizawa, JW Zhang, K Fukuzawa, Y Mochizuki, Y Iwasawa, K Nakata, H Chuman, T Nakano

      JOURNAL OF CHEMICAL INFORMATION AND MODELING46 ( 1 ) 221 - 230   2006年1月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

      We have developed a visualized cluster analysis of protein-ligand interaction (VISCANA) that analyzes the pattern of the interaction of the receptor and ligand on the basis of quantum theory for virtual ligand screening. Kitaura et al. (Chem. Phys. Lett. 1999, 312, 319-324.) have proposed an ab initio fragment molecular orbital (FMO) method by which large molecules such as proteins can be easily treated with chemical accuracy. In the FMO method, a total energy of the molecule is evaluated by summation of fragment energies and interfragment interaction energies (IFIEs). In this paper, we have proposed a cluster analysis using the dissimilarity that is defined as the squared Euclidean distance between IFIEs of two ligands. Although the result of an ordered table by clustering is still a massive collection of numbers, we combine a clustering method with a graphical representation of the IFIEs by representing each data point with colors that quantitatively and qualitatively reflect the IFIEs. We applied VISCANA to a docking study of pharmacophores of the human estrogen receptor alpha ligand-binding domain (57 amino acid residues). By using VISCANA, we could classify even structurally different ligands into functionally similar clusters according to the interaction pattern of a ligand and amino acid residues of the receptor protein. In addition, VISCANA could estimate the correct docking conformation by analyzing patterns of the receptor-ligand interactions of some conformations through the docking calculation.

      DOI: 10.1021/ci050262q

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    • Revolutionary Simulation Software for 21st Century 査読有り

      Kato Chisachi, Tsubokura Makoto, Yamade Yoshinobu, Arakawa Takamichi, Mochizuki Yuji, Yamashita Katsumi, Murase Tadashi, Nakano Tatsuya, Yamamoto Takenori, Ohno Takahisa, o, h

      Annual Report of the Earth Simulator Center April2007   2006年

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    • Developments and applications of ABINIT-MP software based on the fragment molecular orbital method 査読有り

      Tatsuya Nakano, Yuji Mochizuki, Kaori Fukuzawa, Shinji Amari, Shigenori Tanaka

      Modern Methods for Theoretical Physical Chemistry of Biopolymers   39 - 52   2006年

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      記述言語:英語   掲載種別:論文集(書籍)内論文   出版者・発行元:Elsevier  

      The fragment molecular orbit (FMO) method relies on the division of a large molecular system into a collection of small fragments and on the molecular orbital (MO) calculations for the fragments (monomers) and their pairs (dimers) performed to obtain the total energy and other molecular properties. The ABINIT-MP software is a program code freely available on the web to perform the FMO calculations for biopolymers, such as proteins and nucleic acids. The chapter focuses on the recent developments of the ABINIT-MP software and some examples of its application to the MO calculations for proteins. The FMO calculations in the Hartree-Fock , the second-order Møller-Plesset perturbation , and the configuration interaction with singles approximations are now available in an efficiently parallelized fashion. The application examples are demonstrated for the virtual screening of ligand molecules for estrogen receptor and the evaluation of the excitation energy of photoactive yellow protein. ABINIT-MP software is developed to make ab initio calculations for biomolecules more efficient. © 2006 Elsevier B.V. All rights reserved.

      DOI: 10.1016/B978-044452220-7/50066-6

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    • VISCANA: Visualized cluster analysis of protein-ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening

      S Amari, M Aizawa, JW Zhang, K Fukuzawa, Y Mochizuki, Y Iwasawa, K Nakata, H Chuman, T Nakano

      JOURNAL OF CHEMICAL INFORMATION AND MODELING46 ( 1 ) 221 - 230   2006年1月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

      We have developed a visualized cluster analysis of protein-ligand interaction (VISCANA) that analyzes the pattern of the interaction of the receptor and ligand on the basis of quantum theory for virtual ligand screening. Kitaura et al. (Chem. Phys. Lett. 1999, 312, 319-324.) have proposed an ab initio fragment molecular orbital (FMO) method by which large molecules such as proteins can be easily treated with chemical accuracy. In the FMO method, a total energy of the molecule is evaluated by summation of fragment energies and interfragment interaction energies (IFIEs). In this paper, we have proposed a cluster analysis using the dissimilarity that is defined as the squared Euclidean distance between IFIEs of two ligands. Although the result of an ordered table by clustering is still a massive collection of numbers, we combine a clustering method with a graphical representation of the IFIEs by representing each data point with colors that quantitatively and qualitatively reflect the IFIEs. We applied VISCANA to a docking study of pharmacophores of the human estrogen receptor alpha ligand-binding domain (57 amino acid residues). By using VISCANA, we could classify even structurally different ligands into functionally similar clusters according to the interaction pattern of a ligand and amino acid residues of the receptor protein. In addition, VISCANA could estimate the correct docking conformation by analyzing patterns of the receptor-ligand interactions of some conformations through the docking calculation.

      DOI: 10.1021/ci050262q

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    • A size-extensive modification of super-CI for orbital relaxation 査読有り

      Yuji Mochizuki

      Chemical Physics Letters410 ( 1-3 ) 165 - 171   2005年7月10日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier  

      A size-extensive modification is proposed for the configuration interaction with the Hartree-Fock (HF) reference plus single excitations (super-CI) for the orbital relaxation, where a partial renormalization is utilized. The way of renormalization owes to Ahlrichs's coupled pair functional. This proposal is named concurrent electron relaxation functional (CERF). The size-extensivity and performance of CERF are checked through test calculations. © 2005 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2005.05.066

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    • 1A configuration analysis for fragment interaction 査読有り

      Y Mochizuki, K Fukuzawa, A Kato, S Tanaka, K Kitaura, T Nakano

      CHEMICAL PHYSICS LETTERS410 ( 4-6 ) 247 - 253   2005年7月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We propose a modified version of configuration analysis (CA) for the fragment interaction in conjunction with Kitaura's fragment molecular orbital (FMO) scheme. The proposal is abbreviated as CAFI. The MO sets of fragments are merged and then orthonormalized by the use of a weighted Lowdin orthonormalization. The energy calculation is performed with the concurrent electron relaxation functional (CERF). The relaxation energy is obtained in an orbital-wise fashion and is distinguished as the charge-transfer and the polarization. The utility of CAM is demonstrated through test calculations on hydrogen-bonding systems. (c) 2005 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2005.05.079

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    • A size-extensive modification of super-Cl for orbital relaxation

      Y Mochizuki

      CHEMICAL PHYSICS LETTERS410 ( 1-3 ) 165 - 171   2005年7月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      A size-extensive modification is proposed for the configuration interaction with the Hartree-Fock (HF) reference plus single excitations (super-CI) for the orbital relaxation, where a partial renormalization is utilized. The way of renormalization owes to Ahlrichs's coupled pair functional. This proposal is named concurrent electron relaxation functional (CERF). The size-extensivity and performance of CERF are checked through test calculations. (c) 2005 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2005.05.066

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    • 1A configuration analysis for fragment interaction

      Y Mochizuki, K Fukuzawa, A Kato, S Tanaka, K Kitaura, T Nakano

      CHEMICAL PHYSICS LETTERS410 ( 4-6 ) 247 - 253   2005年7月

      詳細を見る

      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We propose a modified version of configuration analysis (CA) for the fragment interaction in conjunction with Kitaura's fragment molecular orbital (FMO) scheme. The proposal is abbreviated as CAFI. The MO sets of fragments are merged and then orthonormalized by the use of a weighted Lowdin orthonormalization. The energy calculation is performed with the concurrent electron relaxation functional (CERF). The relaxation energy is obtained in an orbital-wise fashion and is distinguished as the charge-transfer and the polarization. The utility of CAM is demonstrated through test calculations on hydrogen-bonding systems. (c) 2005 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2005.05.079

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    • Configuration interaction singles method with multilayer fragment molecular orbital scheme 査読有り

      Y Mochizuki, S Koikegami, S Amari, K Segawa, K Kitaura, T Nakano

      CHEMICAL PHYSICS LETTERS406 ( 4-6 ) 283 - 288   2005年5月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We have developed a parallelized integral-direct solver for configuration interaction singles (CIS) in the ABINIT-MP program, by accepting the recently proposed multilayer fragment molecular orbital (MLFMO) method. In the MLFMO-CIS scheme, the region of interest in photoactive issues can be treated with the environmental potential at the Hartree-Fock (HF) level. The parallel efficiency is observed to be reasonable for the formaldehyde hydration system. A realistic applicability of the method is demonstrated for the photoactive yellow protein (PYP) including 125 amino acid residues. (c) 2005 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2005.03.008

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    • Configuration interaction singles method with multilayer fragment molecular orbital scheme

      Y Mochizuki, S Koikegami, S Amari, K Segawa, K Kitaura, T Nakano

      CHEMICAL PHYSICS LETTERS406 ( 4-6 ) 283 - 288   2005年5月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We have developed a parallelized integral-direct solver for configuration interaction singles (CIS) in the ABINIT-MP program, by accepting the recently proposed multilayer fragment molecular orbital (MLFMO) method. In the MLFMO-CIS scheme, the region of interest in photoactive issues can be treated with the environmental potential at the Hartree-Fock (HF) level. The parallel efficiency is observed to be reasonable for the formaldehyde hydration system. A realistic applicability of the method is demonstrated for the photoactive yellow protein (PYP) including 125 amino acid residues. (c) 2005 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2005.03.008

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    • Frontier Simulation Software for Industrial Science 査読有り

      Kato Chisachi, Tsubokura Makoto, Mochizuki Yuji, Yamashita Katsumi, Murase Tadashi, Yamagishi Kenji, Tokiwa Hiroaki, Nakano Tatsuya, Yamamoto Takenori, Ohno Takahisa

      Annual Report of the Earth Simulator Center April2006 ( 4 )   2005年

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    • Fragment Molecular Orbital Study on Molecular Interaction between Estrogen Receptor and Their Ligands

      福澤 薫, 望月 祐志, 田中 成典, 甘利 真志, 北浦 和夫, 中野 達也

      Proceedings of 7th Congress of the World Association of Theoretically Oriented Chemists (WATOC) (Cape Town, South Africa)ES-P23,   2005年

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      掲載種別:研究論文(国際会議プロシーディングス)  

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    • A parallelized integral-direct second-order Møller--Plesset perturbation theory method with a fragment molecular orbital scheme 査読有り

      Mochizuki Yuji, Nakano Tatsuya, Koikegami Shigeru, Tanimori Souichirou, Abe Yukinobu, Nagashima Umpei, Kitaura Kazuo

      Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)112 ( 5-6 ) 442 - 452   2004年12月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Springer  

      DOI: 10.1007/s00214-004-0602-3

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    • A parallelized integral-direct second-order Moller-Plesset perturbation theory method with a fragment molecular orbital scheme

      Y Mochizuki, T Nakano, S Koikegami, S Tanimori, Y Abe, U Nagashima, K Kitaura

      THEORETICAL CHEMISTRY ACCOUNTS112 ( 5-6 ) 442 - 452   2004年12月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

      We propose a parallelized integral-direct algorithm of the second-order Moller-Plesset perturbation theory (MP2) as a size-consistent correlated method. The algorithm is a modification of the recipe by Mochizuki et al. [(1996) Theor Chim Acta 93:211]. There is no need to communicate the bulky data of integrals across worker processes, keeping the formal fifth-power dependence on the number of basis functions. A multiple integral screening procedure is incorporated to reduce the operation costs effectively. An approximate MP2 density matrix can also be directly calculated through the integral contraction with orbital energies. We implement the MP2 code by accepting Kitaura&apos;s fragment molecular orbital (FMO) scheme as in the program ABINIT-MP developed by Nakano et al. [(2002) Chem Phys Lett 351:475]. The error in the FMO-MP2 energies is found to be within the order of the chemical accuracy. Timing and parallel acceleration results are shown for test molecules.

      DOI: 10.1007/s00214-004-0602-3

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    • Large scale MP2 calculations with fragment molecular orbital scheme 査読有り

      Y Mochizuki, S Koikegami, T Nakano, S Amari, K Kitaura

      CHEMICAL PHYSICS LETTERS396 ( 4-6 ) 473 - 479   2004年10月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We have recently developed a parallelized integral-direct algorithm for the second-order Moller-Plesset perturbation theory (MP2) and implemented it into the ABINIT-MP program of the fragment molecular orbital (FMO) scheme. A flexible parallelization is possible by combining the fragment indices (upper level) and the two-electron integral indices (lower level) on distributed computational resources, leading to an enhancement of in-core processings. In this Letter, we carry out a series of benchmark FMO-MP2 calculations of realistic proteins consisting of the tens of thousands of basis functions. The performance is shown to be high, indicating that the ABINIT-MP program is easily applicable to the realistic systems. (C) 2004 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2004.08.082

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    • Large scale MP2 calculations with fragment molecular orbital scheme

      Y Mochizuki, S Koikegami, T Nakano, S Amari, K Kitaura

      CHEMICAL PHYSICS LETTERS396 ( 4-6 ) 473 - 479   2004年10月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      We have recently developed a parallelized integral-direct algorithm for the second-order Moller-Plesset perturbation theory (MP2) and implemented it into the ABINIT-MP program of the fragment molecular orbital (FMO) scheme. A flexible parallelization is possible by combining the fragment indices (upper level) and the two-electron integral indices (lower level) on distributed computational resources, leading to an enhancement of in-core processings. In this Letter, we carry out a series of benchmark FMO-MP2 calculations of realistic proteins consisting of the tens of thousands of basis functions. The performance is shown to be high, indicating that the ABINIT-MP program is easily applicable to the realistic systems. (C) 2004 Elsevier B.V. All rights reserved.

      DOI: 10.1016/j.cplett.2004.08.082

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    • Development of integral transformation modules for correlated calculations

      望月 祐志

      J. Comp. Chem. Jpn.3 ( 1 ) 1 - 12   2004年

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      記述言語:日本語   出版者・発行元:Society of Computer Chemistry, Japan  

      分子軌道計算において配置展開に基づいて電子相関を導入する場合、積分は基底関数の添字から分子軌道の添字に変換しておく必要がある。特に、基底関数の総数に対して4乗量である2電子積分の変換は計算コストが大きいために、演算数を可能な限り減らして効率的に処理することが重要となる。そこで、山本と長嶋によるアルゴリズム (<I>J. Comp. Chem.</I>, <B>9</B>, 627 (1988) ) に基づいて閾値以上の積分のみを扱い、さらに基本線形代数ルーチンDAXPYとDDOTを導入して高速化を図った2電子積分変換モジュールを開発した。

      DOI: 10.2477/jccj.3.1

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      その他リンク: https://jlc.jst.go.jp/DN/JALC/00237366801?from=CiNii

    • Comparative study of dehydrogenation at Pt(111)/water and Pt(111)/vacuum of methanol interfaces 査読有り

      Y Okamoto, O Sugino, Y Mochizuki, T Ikeshoji, Y Morikawa

      CHEMICAL PHYSICS LETTERS377 ( 1-2 ) 236 - 242   2003年8月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      The dehydrogenation of methanol on Pt(1 1 1)/water and Pt(1 1 1)/vacuum interfaces was investigated by using ab initio theoretical calculations. Possible reactive intermediate structures were optimized, and energetically favorable reaction pathways were traced at these two interfaces. When all products formed through the dehydrogenation remained on a Pt(1 1 1) surface, the reaction energy of a whole dehydrogenation was smaller at the Pt(1 1 1)/water interface than that at the Pt(1 1 1)/vacuum interface by about 0.7 eV. (C) 2003 Elsevier B.V. All rights reserved.

      DOI: 10.1016/S0009-2614(03)01144-8

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    • Comparative study of dehydrogenation at Pt(111)/water and Pt(111)/vacuum of methanol interfaces

      Y Okamoto, O Sugino, Y Mochizuki, T Ikeshoji, Y Morikawa

      CHEMICAL PHYSICS LETTERS377 ( 1-2 ) 236 - 242   2003年8月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      The dehydrogenation of methanol on Pt(1 1 1)/water and Pt(1 1 1)/vacuum interfaces was investigated by using ab initio theoretical calculations. Possible reactive intermediate structures were optimized, and energetically favorable reaction pathways were traced at these two interfaces. When all products formed through the dehydrogenation remained on a Pt(1 1 1) surface, the reaction energy of a whole dehydrogenation was smaller at the Pt(1 1 1)/water interface than that at the Pt(1 1 1)/vacuum interface by about 0.7 eV. (C) 2003 Elsevier B.V. All rights reserved.

      DOI: 10.1016/S0009-2614(03)01144-8

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    • Prolapses in four-component relativistic Gaussian basis sets 査読有り

      H Tatewaki, T Koga, Y Mochizuki

      CHEMICAL PHYSICS LETTERS375 ( 3-4 ) 399 - 405   2003年7月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      The prolapse problem in the four-component relativistic Gaussian basis sets, recently developed by Koga, Tatewaki, and Matsuoka for the atoms H-1 through Lr-103, is discussed. Deficiency in the number of s(+), basis functions is pointed out for the atoms in the fourth and higher periods. A small prolapse is detected in the p(-) symmetry of the sixth and seventh period atoms. However, no problem is found for the remaining five symmetries. (C) 2003 Published by Elsevier Science B.V.

      DOI: 10.1016/S0009-2614(03)00873-X

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    • Prolapses in four-component relativistic Gaussian basis sets

      H Tatewaki, T Koga, Y Mochizuki

      CHEMICAL PHYSICS LETTERS375 ( 3-4 ) 399 - 405   2003年7月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      The prolapse problem in the four-component relativistic Gaussian basis sets, recently developed by Koga, Tatewaki, and Matsuoka for the atoms H-1 through Lr-103, is discussed. Deficiency in the number of s(+), basis functions is pointed out for the atoms in the fourth and higher periods. A small prolapse is detected in the p(-) symmetry of the sixth and seventh period atoms. However, no problem is found for the remaining five symmetries. (C) 2003 Published by Elsevier Science B.V.

      DOI: 10.1016/S0009-2614(03)00873-X

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    • Ab initio study on the structures of Th(IV) hydrate and its hydrolysis products in aqueous solution 査読有り

      S Tsushima, TX Yang, Y Mochizuki, Y Okamoto

      CHEMICAL PHYSICS LETTERS375 ( 1-2 ) 204 - 212   2003年6月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      Ab initio calculations have been performed to study the structures of thorium(IV) hydrate and its hydrolysis products in aqueous solution. The conductor-like polarizable continuum model (CPCM) has been used to perform geometry optimization calculations in aqueous solution. The calculated results demonstrate that the molecule geometries obtained in solvent are generally consistent with the experiments. The coordination number of thorium(IV) hydrolysis products has been investigated. The effect of the relativistic effective core potential (RECP) on the structures is also discussed. (C) 2003 Elsevier Science B.V. All rights reserved.

      DOI: 10.1016/S0009-2614(03)00806-6

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    • Ab initio study on the structures of Th(IV) hydrate and its hydrolysis products in aqueous solution

      S Tsushima, TX Yang, Y Mochizuki, Y Okamoto

      CHEMICAL PHYSICS LETTERS375 ( 1-2 ) 204 - 212   2003年6月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      Ab initio calculations have been performed to study the structures of thorium(IV) hydrate and its hydrolysis products in aqueous solution. The conductor-like polarizable continuum model (CPCM) has been used to perform geometry optimization calculations in aqueous solution. The calculated results demonstrate that the molecule geometries obtained in solvent are generally consistent with the experiments. The coordination number of thorium(IV) hydrolysis products has been investigated. The effect of the relativistic effective core potential (RECP) on the structures is also discussed. (C) 2003 Elsevier Science B.V. All rights reserved.

      DOI: 10.1016/S0009-2614(03)00806-6

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    • Theoretical study of hydrolysis reactions of tetravalent thorium ion 査読有り

      Y Okamoto, Y Mochizuki, S Tsushima

      CHEMICAL PHYSICS LETTERS373 ( 1-2 ) 213 - 217   2003年5月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      The hydrolysis reaction of the tetravalent thorium (Th4+) ion was investigated by ab initio theoretical calculations on hydration complex models. The transition state structure was optimized, and the intrinsic reaction coordinate was traced. The results showed that the hydrolysis is highly exothermic and the transition state is close to the reactant. Reaction dependency upon the number of non-reactive water molecules was examined. (C) 2003 Elsevier Science B.V. All rights reserved.

      DOI: 10.1016/S0009-2614(03)00592-X

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    • On the electronic structure of CmFn (n=1-4) by all-electron Dirac-Hartree-Fock calculations 査読有り

      Y Mochizuki, H Tatewaki

      JOURNAL OF CHEMICAL PHYSICS118 ( 20 ) 9201 - 9207   2003年5月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

      All-electron Dirac-Hartree-Fock calculations were performed to investigate the electronic structure of curium fluoride molecules (CmFn, n = 1-4). The curium-fluorine distances, atomization energies, and Mulliken populations were all evaluated. The bonding was found to be of ionic type with the electron delocalization primarily from F 2p to Cm 6d, where the formal configurations of Cm were 7s(2)5f(7), 5f(7)7s(1), 5f(7), 5f(6) for n = 1, 2, 3, 4, respectively. The 2p-6d delocalization is significant in the tetrafluoride. For comparison, the isovalent gadolinium fluorides were also studied. CmF4 exists but GdF4 does not, reflecting the fact that 5f(7) in CmF3 is less stable than 4f(7) in GdF3. (C) 2003 American Institute of Physics.

      DOI: 10.1063/1.1568075

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    • Theoretical study of hydrolysis reactions of tetravalent thorium ion

      Y Okamoto, Y Mochizuki, S Tsushima

      CHEMICAL PHYSICS LETTERS373 ( 1-2 ) 213 - 217   2003年5月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      The hydrolysis reaction of the tetravalent thorium (Th4+) ion was investigated by ab initio theoretical calculations on hydration complex models. The transition state structure was optimized, and the intrinsic reaction coordinate was traced. The results showed that the hydrolysis is highly exothermic and the transition state is close to the reactant. Reaction dependency upon the number of non-reactive water molecules was examined. (C) 2003 Elsevier Science B.V. All rights reserved.

      DOI: 10.1016/S0009-2614(03)00592-X

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    • On the electronic structures of Th4+ and Ac3+ hydrate models 査読有り

      Yuji Mochizuki, Satoru Tsushima

      Chemical Physics Letters372 ( 1-2 ) 114 - 120   2003年4月22日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier  

      Electronic structures of hydrate complex models of Th4+ and Ac3+ ions (Th(H2O)n 4+ and Ac(H2O)n 3+ (n=1,2,4,6)) were investigated by all-electron four-component relativistic calculations based on the Dirac-Hartree-Fock (DHF) method. Picture of the coordinate bond in the complexes was observed, and the difference between Th4+ and Ac3+ cases was shown. Relativistic effective-core potential (RECP) calculations were also performed on the higher hydrate models to assess the bulk solvation effect by using the conductive polarizable continuum model (CPCM) reaction-field scheme. © 2003 Elsevier Science B.V. All rights reserved.

      DOI: 10.1016/S0009-2614(03)00373-7

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    • On the electronic structures of Th4+ and Ac3+ hydrate models

      Y Mochizuki, S Tsushima

      CHEMICAL PHYSICS LETTERS372 ( 1-2 ) 114 - 120   2003年4月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      Electronic structures of hydrate complex models of Th4+ and Ac3+ ions (Th(H2O)n(4)(+) and Ac(H-2)(n)(3+) (n = 1,2,4,6)) were investigated by all-electron four-component relativistic calculations based on the Dirac-Hartree-Fock (DHF) method. Picture of the coordinate bond in the complexes was observed, and the difference between Th4+ and Ac3+ cases was shown. Relativistic effective-core potential (RECP) calculations were also performed on the higher hydrate models to assess the bulk solvation effect by using the conductive polarizable continuum model (CPCM) reaction-field scheme. (C) 2003 Elsevier Science B.V. All rights reserved.

      DOI: 10.1016/S0009-2614(03)00373-7

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    • Comments on relativistic basis sets 査読有り

      H Tatewaki, Y Mochizuki

      THEORETICAL CHEMISTRY ACCOUNTS109 ( 1 ) 40 - 42   2003年2月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER-VERLAG  

      Adding the tight and diffuse Gaussian-type functions (GTFs), Faegri's variationally determined double-zeta-quality basis sets for molecular relativistic calculations are examined. An example atom is Cm. When the tight s-type GTF is added the total energy increases, whereas when diffuse GTFs are added the total energy decreases. The reasons for these findings are clarified. It is also pointed out that not only the Faegri's sets but also other variationally determined basis sets would show similar behavior so far as the expansion terms are not sufficient.

      DOI: 10.1007/s00214-002-0412-4

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    • Comments on relativistic basis sets

      Hiroshi Tatewaki, Yuji Mochizuki

      Theoretical Chemistry Accounts109 ( 1 ) 40 - 42   2003年2月1日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)  

      Adding the tight and diffuse Gaussian-type functions (GTFs), Faegri's variationally determined double-zeta-quality basis sets for molecular relativistic calculations are examined. An example atom is Cm. When the tight s-type GTF is added the total energy increases, whereas when diffuse GTFs are added the total energy decreases. The reasons for these findings are clarified. It is also pointed out that not only the Faegri's sets but also other variationally determined basis sets would show similar behavior so far as the expansion terms are not sufficient.

      DOI: 10.1007/s00214-002-0412-4

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    • Electric structure calculations on heavy element systems using the DIRAC code 査読有り

      Mochizuki Yuji

          2003年

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    • On the electronic of CmFn(n=1-4) by all-electron Dirac -Hartree-Fock calculations

      望月 祐志

      (不明) ( 118 ) 9201 - 9207   2003年1月1日

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      記述言語:英語   掲載種別:研究論文(その他学術会議資料等)  

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    • Four-component relativistic calculations on the mono-ammine complexes of trivalent f0, f7, and f14 ions

      Yuji Mochizuki, Yasuharu Okamoto

      Chemical Physics Letters359 ( 3-4 ) 331 - 336   2002年6月20日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)  

      Mono-ammine complexes of trivalent f0, f7, and f14 ions were investigated by using all-electron four-component relativistic calculations based on the Dirac-Hartree-Fock (DHF) method. Relativistic second-order Møller-Plesset perturbation (RMP2) calculations were also performed to incorporate electron correlation for the closed-shell systems. A comparison with the previous data of the aqua complexes showed that the ammine complex provides longer metal-ligand distance, larger stabilization energy, and larger amount of electron donation than the aqua complex does for a certain metal ion. © 2002 Elsevier Science B.V. All rights reserved.

      DOI: 10.1016/S0009-2614(02)00727-3

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    • Four-component relativistic calculations on the mono-ammine complexes of trivalent f(0), f(7), and f(14) ions 査読有り

      Y Mochizuki, Y Okamoto

      CHEMICAL PHYSICS LETTERS359 ( 3-4 ) 331 - 336   2002年6月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      Mono-ammine complexes of trivalent f(0), f(7), and f(14) ions were investigated by using all-electron four-component relativistic calculations based on the Dirac-Hartree-Fock (DHF) method. Relativistic second-order Mphiller-Plesset perturbation (RMP2) calculations were also performed to incorporate electron correlation for the closed-shell systems. A comparison with the previous data of the aqua complexes showed that the ammine complex provides longer metal-ligand distance, larger stabilization energy, and larger amount of electron donation than the aqua complex does for a certain metal ion. (C) 2002 Elsevier Science B.V. All rights reserved.

      DOI: 10.1016/S0009-2614(02)00727-3

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    • On the electronic structure of Cm(H2O)(n)(3+) (n=1,2,4,6) by all-electron Dirac-Hartree-Fock calculations 査読有り

      Y Mochizuki, H Tatewaki

      JOURNAL OF CHEMICAL PHYSICS116 ( 20 ) 8838 - 8842   2002年5月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

      Dirac-Hartree-Fock (DHF) calculations were performed to investigate the hydration of the trivalent Cm ion with a 5f(7) configuration on the models of Cm(H2O)(n)(3+) (n=1,2,4,6). The curium-oxygen distances and stabilization energies were evaluated. The DHF wave functions were analyzed by the Mulliken populations and spinor projections. Hydration was found to be characterized by the coordinate bond. An increase in the number of water molecules caused an increase in the curium-oxygen distance and a reduction of the stabilization energy per water molecule. The fluorescence transition energy was also estimated using the complete open-shell configuration interaction (COSCI) method. Redshifts due to hydration were obtained and were in accord with observations of the nephelauxetic effect. The isovalent gadolinium ion Gd3+ was also studied for comparison. (C) 2002 American Institute of Physics.

      DOI: 10.1063/1.1473803

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    • On the electronic structure of Cm(H2O)(n)(3+) (n=1,2,4,6) by all-electron Dirac-Hartree-Fock calculations

      Y Mochizuki, H Tatewaki

      JOURNAL OF CHEMICAL PHYSICS116 ( 20 ) 8838 - 8842   2002年5月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

      Dirac-Hartree-Fock (DHF) calculations were performed to investigate the hydration of the trivalent Cm ion with a 5f(7) configuration on the models of Cm(H2O)(n)(3+) (n=1,2,4,6). The curium-oxygen distances and stabilization energies were evaluated. The DHF wave functions were analyzed by the Mulliken populations and spinor projections. Hydration was found to be characterized by the coordinate bond. An increase in the number of water molecules caused an increase in the curium-oxygen distance and a reduction of the stabilization energy per water molecule. The fluorescence transition energy was also estimated using the complete open-shell configuration interaction (COSCI) method. Redshifts due to hydration were obtained and were in accord with observations of the nephelauxetic effect. The isovalent gadolinium ion Gd3+ was also studied for comparison. (C) 2002 American Institute of Physics.

      DOI: 10.1063/1.1473803

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    • Vectorization of direct Fock matrix construction in DIRAC-DHF calculations 査読有り

      Y Mochizuki, M Matsumura, T Yokura, Y Hirahara, T Imamura

      JOURNAL OF NUCLEAR SCIENCE AND TECHNOLOGY39 ( 2 ) 195 - 199   2002年2月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ATOMIC ENERGY SOC JAPAN  

      Iterations of the Fock matrix construction from two-electron integrals completely dominates the total cost of direct self-consistent-field (DSCF) calculations, especially for the four-component Dirac-Hartree-Fock (DHF) relativistic molecular-orbital method. We revive here the notion of vectorization as helpful to accelerate DSCF-DHF calculations. DIRAC is a representative state-of-the-art DHF code on which we consider the vectorized Fock matrix construction. While the integral generation is straightforwardly vectorizable, the contraction of generated integrals with associated densities into the Fock matrix elements is unable to vectorize simply due to frequent address conflicts. In this report, we present a vectorization of the direct Fock matrix construction by introducing a working-array technique. Total vectorization efficiency for DHF runs is improved from 50-60% by the original DIRAC to more than 90% by the modified version.

      DOI: 10.3327/jnst.39.195

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    • Size, order, and dimensional relations for silicon cluster polarizabilities 査読有り

      B Jansik, B Schimmelpfennig, P Norman, Y Mochizuki, Y Luo, H Agren

      JOURNAL OF PHYSICAL CHEMISTRY A106 ( 2 ) 395 - 399   2002年1月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

      Response theory calculations in the random phase approximation are applied to linear polarizabilities and second hyperpolarizabilities of 1-, 2-, and 3-dimensional hydrogen-terminated silicon clusters. Successive enlargement of the clusters to embody on the order of 50 silicon atoms plus bond-saturating hydrogen atoms allows for extrapolation to bulk values of individual silicon atom contributions in the 1D and 3D cases. Modern effective core potentials are shown to provide excellent approximations to the all-electron values in all cases; errors for both polarizabilities and hyperpolarizabilities are on the order of 1%. The findings indicate considerable time savings in predictions of the electric polarizability properties of elements beyond the first row atoms.

      DOI: 10.1021/jp012654f

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    • Ab initio MO studies on the hydration of trivalent curium ion 査読有り

      Yuji Mochizuki, Hiroshi Tatewaki, Yasuharu Okamoto

      Journal of Nuclear Science and Technology39 ( sup3 ) 418 - 421   2002年

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Taylor \& Francis  

      We have performed a series of ab initio relativistic molecular-orbital calculations to model the hydration of trivalent curium ion. Up to the hexa-hydrate model, Dirac-Hartree-Fock calculations as a four-component recipe were used to investigate the interaction between the ion and water molecules. The fluorescence transition energy was estimated by complete open-shell configuration interaction calculations. Hydrates having more than six water molecules were treated using the B3LYP hybrid density-functional theory with effective-core potential. © 2002 Atomic Energy Society of Japan.

      DOI: 10.1080/00223131.2002.10875496

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    • Size, order, and dimensional relations for silicon cluster polarizabilities

      B Jansik, B Schimmelpfennig, P Norman, Y Mochizuki, Y Luo, H Agren

      JOURNAL OF PHYSICAL CHEMISTRY A106 ( 2 ) 395 - 399   2002年1月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

      Response theory calculations in the random phase approximation are applied to linear polarizabilities and second hyperpolarizabilities of 1-, 2-, and 3-dimensional hydrogen-terminated silicon clusters. Successive enlargement of the clusters to embody on the order of 50 silicon atoms plus bond-saturating hydrogen atoms allows for extrapolation to bulk values of individual silicon atom contributions in the 1D and 3D cases. Modern effective core potentials are shown to provide excellent approximations to the all-electron values in all cases; errors for both polarizabilities and hyperpolarizabilities are on the order of 1%. The findings indicate considerable time savings in predictions of the electric polarizability properties of elements beyond the first row atoms.

      DOI: 10.1021/jp012654f

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    • Vectorization of direct fock matrix construction in DIRAC-DHF calculations

      Yuji Mochizuki, Masayuki Matsumura, Tetsui-Chi Yokura, Yukio Hirahara, Toshiyuki Imamura

      Journal of Nuclear Science and Technology39 ( 2 ) 195 - 199   2002年

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      記述言語:英語   掲載種別:研究論文(学術雑誌)  

      Iterations of the Fock matrix construction from two-electron integrals completely dominates the total cost of direct self-consistent-field (DSCF) calculations, especially for the four-component Dirac-Hartree-Fock (DHF) relativistic molecular-orbital method. We revive here the notion of vectorization as helpful to accelerate DSCF-DHF calculations. DIRAC is a representative state-of-the-art DHF code on which we consider the vectorized Fock matrix construction. While the integral generation is straightforwardly vectorizable, the contraction of generated integrals with associated densities into the Fock matrix elements is unable to vectorize simply due to frequent address conflicts. In this report, we present a vectorization of the direct Fock matrix construction by introducing a working-array technique. Total vectorization efficiency for DHF runs is improved from 50–60% by the original DIRAC to more than 90% by the modified version. © 2002 Taylor and Francis Group, LTD.

      DOI: 10.1080/18811248.2002.9715175

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    • Ab initio MO studies on the hydration of trivalent curium ion

      Yuji Mochizuki, Hiroshi Tatewaki, Yasuharu Okamoto

      Journal of Nuclear Science and Technology39 ( 3 ) 418 - 421   2002年

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      記述言語:英語   掲載種別:研究論文(学術雑誌)  

      We have performed a series of ab initio relativistic molecular-orbital calculations to model the hydration of trivalent curium ion. Up to the hexa-hydrate model, Dirac-Hartree-Fock calculations as a four-component recipe were used to investigate the interaction between the ion and water molecules. The fluorescence transition energy was estimated by complete open-shell configuration interaction calculations. Hydrates having more than six water molecules were treated using the B3LYP hybrid density-functional theory with effective-core potential. © 2002 Atomic Energy Society of Japan.

      DOI: 10.1080/00223131.2002.10875496

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    • Modification of nonrelativistic gaussian basis sets for relativistic calculations

      Hiroshi Tatewaki, Yuji Mochizuki, Toshikatsu Koga, Jacek Karwowski

      Journal of Chemical Physics115 ( 20 ) 9160 - 9164   2001年11月22日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)  

      A simple set of rules were formulated that allows to easily transform nonrelativistic basis sets of GTFs into their relativistic analogs. The relativistic basis sets were obtained by augmenting the nonrelativistic ones by auxiliary GTFs determined from relativistic DFR calculations for hydrogen ions. By properly modifying the nonrelativistic KTS basis sets, the Dirac-Fock energies of lanthanide and actinide atoms were predicted with the accuracy up to 4-9 mhartree and 21-42 mhartree, respectively.

      DOI: 10.1063/1.1415080

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    • Four-component relativistic calculations on the complexes between a water molecule and trivalent lanthanoid and actinoid ions

      Yuji Mochizuki, Hiroshi Tatewaki

      Chemical Physics273 ( 2-3 ) 135 - 148   2001年11月15日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)  

      Complexes between a water molecule and trivalent lanthanoid and actinoid ions were investigated by all-electron four-component relativistic calculations using the Dirac-Hartree -Fock (DHF) method. DHF-based relativistic second-order Møller-Plesset perturbation (RMP2) calculations were also performed to incorporate electron correlation for the closed-shell systems. Non-relativistic calculations using the HF and MP2 methods were carried out in parallel to compare with the DHF and RMP2 results. Metal-oxygen distances and stabilization energies were evaluated, and a separability between relativity and correlation was found. Mulliken population analysis and spinor projection were used to analyze the wave functions, and a nature of coordinate bond was revealed. © 2001 Elsevier Science B.V. All rights reserved.

      DOI: 10.1016/S0301-0104(01)00483-9

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    • Four-component relativistic calculations on the complexes between a water molecule and trivalent lanthanoid and actinoid ions 査読有り

      Y Mochizuki, H Tatewaki

      CHEMICAL PHYSICS273 ( 2-3 ) 135 - 148   2001年11月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      Complexes between a water molecule and trivalent lanthanoid and actinoid ions were investigated by all-electron four-component relativistic calculations using the Dirac-Hartree-Fock (DHF) method. DHF-based relativistic second-order Moller-Plesset perturbation (RMP2) calculations were also performed to incorporate electron correlation for the closed-shell systems. Non-relativistic calculations using the HF and MP2 methods were carried out in parallel to compare with the DHF and RMP2 results. Metal-oxygen distances and stabilization energies were evaluated, and a separability between relativity and correlation was found. Mulliken population analysis and spinor projection were used to analyze the wave functions, and a nature of coordinate bond was revealed. (C) 2001 Elsevier Science B.V. All rights reserved.

      DOI: 10.1016/S0301-0104(01)00483-9

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    • Modification of nonrelativistic Gaussian basis sets for relativistic calculations 査読有り

      H Tatewaki, Y Mochizuki, T Koga, J Karwowski

      JOURNAL OF CHEMICAL PHYSICS115 ( 20 ) 9160 - 9164   2001年11月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

      A simple method is proposed in which basis sets of Gaussian-type functions (GTFs), suitable for relativistic Dirac-Fock-Roothaan (DFR) calculations, are derived from their nonrelativistic analogs. The relativistic basis set is obtained through augmenting the nonrelativistic one by several GTFs determined from relativistic calculations for hydrogen-like atoms. The usefulness and reliability of the method is illustrated by DFR calculations of the ground-state energies of lanthanide and actinide atoms. (C) 2001 American Institute of Physics.

      DOI: 10.1063/1.1415080

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    • Vapor-liquid equilibrium data for the four binary systems containing fluorocarbon, hydrofluorocarbon, and fluorinated ethers at 101.3 kPa 査読有り

      K. Tochigi, T. Satou, K. Kurihara, K. Ochi, H. Yamamoto, Y. Mochizuki, T. Sako

      Journal of Chemical and Engineering Data46 ( 4 ) 913 - 917   2001年7月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society  

      Isobaric vapor-liquid equilibria were measured for the four binary systems of perfluoro-2-methylpentane (FC-5114mmyc2) + perfluorooctane (FC-7118mc6), 1,1,1,2,2,3,3,4,4-nonafluorohexane (HFC-569mccf) + octane, 2,2,2-trifluorodiethyl ether (HFE-356mf-f) + butyl ethyl ether, and methylperfluoroisopropyl ether (HFE-347 mmy) + heptane at atmospheric pressure. The HFE-356mf-f + butyl ethyl ether system formed a minimum boiling azeotrope. The experimental data except for those for the FC-5114mmyc2 + FC-7118mc6 system were correlated by the Wilson and NRTL activity coefficient models. The Wilson and NRTL equations gave similar results. The VLE for the FC-5114mmyc2 + FC-7118mc6 system was predicted to be an ideal solution.

      DOI: 10.1021/je000192d

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    • HF-STEX and RASSCF calculations on nitrogen K-shell X-ray absorption of purine base and its derivative 査読有り

      Y Mochizuki, H Koide, T Imamura, H Takemiya

      JOURNAL OF SYNCHROTRON RADIATION8 ( 2 ) 1003 - 1005   2001年3月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:MUNKSGAARD INT PUBL LTD  

      The nitrogen K-shell X-ray absorption spectra of the purine bases present in nucleic acids, adenine and guanine, were analyzed by using ab initio Hartree-Fock static exchange and restricted-active-space self-consistent-field calculations. A variety of derivative molecules were calculated to investigate the energetic shifts due to environmental effects on the nitrogen atoms. Shake-up excitations were also addressed.

      DOI: 10.1107/S0909049500017696

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    • Polarizability of silicon clusters 査読有り

      Y Mochizuki, H Agren

      CHEMICAL PHYSICS LETTERS336 ( 5-6 ) 451 - 456   2001年3月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      The polarizability of hydrogen-terminated silicon dusters derived from the silicon diamond-lattice structure was evaluated by linear response calculations. The dependences on cluster size and basis set were systematically investigated. A convergence in calculated polarizability per silicon atom toward the bulk value was found. Frequency-dependent polarizabilities were also addressed. (C) 2001 Elsevier Science B.V. All rights reserved.

      DOI: 10.1016/S0009-2614(01)00176-2

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    • HF-STEX and RASSCF calculations nitrogen K-shell X-ray absorption of purine base and its derivative

      望月 祐志

      (不明) ( 8 ) 1003 - 1005   2001年1月1日

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      記述言語:英語   掲載種別:研究論文(その他学術会議資料等)  

      DOI: 10.1107/S0909049500017696

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    • Polarizability of silicon clusters

      望月 祐志

      (不明) ( 273 ) 135 - 148   2001年1月1日

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      記述言語:英語   掲載種別:研究論文(その他学術会議資料等)  

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    • A theoretical investigation of sulphur K-shell X-ray absorption of cysteine 査読有り

      Y Mochizuki, H Agren, LGM Pettersson, Carravetta, V

      CHEMICAL PHYSICS LETTERS309 ( 3-4 ) 241 - 248   1999年8月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      The near-edge X-ray absorption fine structure (NEXAFS) spectrum at the sulphur K-edge of the cysteine amino acid is simulated by the ab initio Hartree-Fock static-exchange method. Several forms of cysteine are investigated, including neutral, zwitterionic and water-solvated forms. The simulations indicate that the presence of an environment induces a small lowering of the edge position in the spectrum of the neutral form. (C) 1999 Elsevier Science B.V. All rights reserved.

      DOI: 10.1016/S0009-2614(99)00684-3

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    • Multireference coupled-pair approximation study of the CuSi molecule 査読有り

      M Tomonari, Y Mochizuki, K Tanaka

      THEORETICAL CHEMISTRY ACCOUNTS101 ( 5 ) 332 - 335   1999年4月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

      The electronic structure of the CuSi molecule was examined using the multireference coupled pair-approximation (MRCPA) following multireference single and double excitation configuration interaction calculations. We found the ground state to be the (2)Pi state, and we evaluated the bond length, dissociation energy, vibrational frequency, and dipole moment for the (2)Pi ground state and for low-lying (4)Sigma(-) and (2)Delta excited states. The dissociation energy of the (2)Pi. ground state by MRCPA is 2.13 eV, which agrees well with the experimental value of 2.26 eV. The inclusion of higher excitations by MRCPA significantly improves the description of the bonding and the accuracy of the spectroscopic constants.

      DOI: 10.1007/s002140050449

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    • Theoretical investigation of the GaF molecule and its positive ion 査読有り

      Y Mochizuki, K Tanaka

      THEORETICAL CHEMISTRY ACCOUNTS101 ( 4 ) 257 - 261   1999年3月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

      Coupled pair approximation and configuration interaction calculations were carried out on the gallium fluoride molecule and its positive ion with flexible basis sets. Spectroscopic constants of these species were examined in detail through step-wise extensions of correlating space. The contribution from correlations of the semi-core 3d electrons in Ga was found to be sizable. The bonding character was revealed to be highly ionic even for the positive ion.

      DOI: 10.1007/s002140050438

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    • Theoretical spectroscopic constants of the GaN molecule 査読有り

      Y Mochizuki, K Tanaka

      THEORETICAL CHEMISTRY ACCOUNTS101 ( 4 ) 292 - 296   1999年3月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

      Fourth-order multi-reference coupled pair approximation (MRCPA-4) calculations were performed to predict spectroscopic constants of the gallium nitride (GaN) diatomic molecule. The calculations showed that the ground state is (3)Sigma(-) but that the (3)Pi state is low lying and separated from the former by 0.5 eV. The contribution of the correlations among the Ga 3d semi-core electrons was found to be crucial for a quantitative description of the molecule.

      DOI: 10.1007/s002140050443

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    • MULTI-REFERENCE COUPLED PAIR APPROXIMATION: a state-universal approach of a CEPA type variant of MRSDCI 査読有り

      Tanaka Kiyoshi, Sakai Takeo, Mochizuki Yuji

      Recent Advances in Multireference Methods4   95   1999年

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      出版者・発行元:World Scientific  

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    • Molecular Orbital Study on the Oxidative Decomposition of Hfc-32 査読有り

      Mochizuki Yuji

      Data/Code/Japan atomic energy research institute (Tokyo)99   015   1999年

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      出版者・発行元:Tokai  

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    • Theoretical study of the spectroscopic constants of low-lying states of Ga-2 査読有り

      TK Ghosh, K Tanaka, Y Mochizuki

      THEOCHEM-JOURNAL OF MOLECULAR STRUCTURE451 ( 1-2 ) 61 - 71   1998年9月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      Spectroscopic constants for the ground and low-lying excited electronic states of the Ga-2 molecule have been studied using MRSDCI and MRCPA methods with an extensive basis set of Gaussian-type functions. In this study, we are going to present spectroscopic constants and potential energy curves for the ground (3)Pi(u) and the excited (3)Sigma(g)(-), (1)Sigma(g)(+), (1)Pi(u), (1)Delta(g), (2) (1)Sigma(g)(+) and (3)Sigma(u)(-) states, in which electron correlation between semi-valence (3d) and valence (4s,(4) over bar p) and among valence electrons is taken into account. Our calculated vibrational frequency for the ground state, (3)Pi(u), is 175 cm(-1) by CISD with Davidson's correction and 170 cm(-1) by MRCPA, which are in good agreement with the experimental value of 180 cm(-1). The dissociation energy for the ground state, reported to be 1.28 eV, compares well with the experimental value of 1.4 eV. Avoided crossing between the two lowest (1)Sigma(g)(+) states was properly described by MRCPA. (C) 1998 Elsevier Science B.V. All rights reserved.

      DOI: 10.1016/S0166-1280(98)00160-2

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    • Precise control of pn-junction profiles for GaN-based LD structures using GaN substrates with low dislocation densities 査読有り

      N Kuroda, C Sasaoka, A Kimura, A Usui, Y Mochizuki

      JOURNAL OF CRYSTAL GROWTH189   551 - 555   1998年6月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      Doping profiles of pn-junctions for GaN-based laser diode structures were studied using SIMS and EBIC measurements. Mg impurity, a p-type dopant, was found to diffuse heavily into the n-type region of the order of 10(17) cm(-3) when a sample is grown on a sapphire substrate. This unwanted diffusion appears closely related to the presence of threading dislocations, and can be eliminated by using high-quality GaN substrates for epitaxial growth. (C) 1998 Elsevier Science B.V. All rights reserved.

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    • Theoretical investigation on the GaH molecule and its positive ion 査読有り

      Y Mochizuki, K Tanaka

      THEORETICAL CHEMISTRY ACCOUNTS99 ( 2 ) 88 - 94   1998年4月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER VERLAG  

      The gallium monohydride (GaH) molecule and its positive ion were theoretically investigated by abinitio molecular orbital calculations with a flexible basis set including g-type functions on the Ga atom. Electron correlations among not only the valence electrons of Ga 4s4p and H 1s but also the semi-core electrons of Ga 3d were incorporated by a size-consistent scheme of the coupled pair approximation. The contribution of the 3d electron correlation was found to be considerable on spectroscopic constants of both GaH and GaH+, especially on the bond length.

      DOI: 10.1007/s002140050308

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    • Determination of valence band splitting parameters in GaN 査読有り

      AA Yamaguchi, Y Mochizuki, H Sunakawa, A Usui

      JOURNAL OF APPLIED PHYSICS83 ( 8 ) 4542 - 4544   1998年4月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

      Valence band structures and their strain effects in GaN have been investigated by optical spectroscopy for thick GaN films with high optical quality grown by hydride vapor phase epitaxy. Excitons associated with the A, B, and C valence bands an clearly observed in reflectance measurements without modulation techniques. It is found that the exciton energies shift with the film thickness because of the relaxation of the residual, strain. From the quantitative analysis of this behavior, we have precisely determined the valence band splitting parameters in GaN as Delta(1)=10 meV, Delta(2)=5.5 meV, and Delta(3)=6.0 meV. (C) 1998 American Institute of Physics.

      DOI: 10.1063/1.367217

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    • Uniaxial stress effects on valence band structures of GaN 査読有り

      AA Yamaguchi, Y Mochizuki, C Sasaoka, A Kimura, M Nido, A Usui

      NITRIDE SEMICONDUCTORS482   893 - 898   1998年

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      記述言語:英語   掲載種別:研究論文(国際会議プロシーディングス)   出版者・発行元:MATERIALS RESEARCH SOCIETY  

      Valence band modification by uniaxial stress in GaN is investigated by reflectance spectroscopy. It is observed that the energy separation between the A and B valence bands increases with the applied uniaxial stress in the c-plane. Changes of the wavefunctions by the stress are also investigated by the polarization characteristics of the reflectance spectra. The experimental results are analyzed on the basis of k.p theory, and deformation potential D-5 is experimentally determined as -3.3 eV. It is indicated that the uniaxial strain effect could be utilized for improving GaN-based laser performance.

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    • A CSF-based multi-reference coupled pair approximation III. An application to F2, As2 and As+ 2 査読有り

      Tanaka Kiyoshi, Mochizuki Yuji

      Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)98 ( 4 ) 165   1998年

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      出版者・発行元:Springer  

      DOI: 10.1007/s002140050289

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    • Program linkage method for using dummy arguments to link program having hierarchical structure 査読有り

      Takada Toshikazu, Mochizuki Yuji

          1997年10月

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      出版者・発行元:Google Patents  

      US Patent 5,675,806

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    • Computational study of the spectroscopic constants of the ground state of the As-2 molecule 査読有り

      Y Mochizuki, K Tanaka

      CHEMICAL PHYSICS LETTERS274 ( 1-3 ) 264 - 268   1997年8月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      Spectroscopic constants of the ground state of the As, molecule have been evaluated using a series of complete active space self-consistent-field and second-order configuration interaction calculations with all-electron basis jets. Angular correlation is found to contribute significantly to the dissociation energy. The calculation with a set of [8s6p3d2flg] basis functions gives 3.58 eV for the dissociation energy. in contrast to the experimental value of 3.99 eV. (C) 1997 Elsevier Science B.V.

      DOI: 10.1016/S0009-2614(97)00655-6

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    • Reflectance spectroscopy on GaN films under uniaxial stress 査読有り

      AA Yamaguchi, Y Mochizuki, C Sasaoka, A Kimura, M Nido, A Usui

      APPLIED PHYSICS LETTERS71 ( 3 ) 374 - 376   1997年7月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

      The uniaxial stress effects on valence band structures in GaN are investigated by reflectance spectroscopy. It is observed that the energy separation between A and B valence bands increases with the application of uniaxial stress in the c plane. The experimental results are analyzed on the basis of the k.p theory, and deformation potential D-5 is determined as -3.3 eV. It is indicated that the uniaxial strain effect could be utilized for improving GaN-based laser performance. (C) 1997 American Institute of Physics.

      DOI: 10.1063/1.119541

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    • Theoretical study of the surface reaction mechanism of GaN with HCl 査読有り

      Y Okamoto, T Takada, Y Mochizuki

      JAPANESE JOURNAL OF APPLIED PHYSICS PART 2-LETTERS & EXPRESS LETTERS35 ( 12B ) L1641 - L1643   1996年12月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:JAPAN SOC APPLIED PHYSICS  

      Ab initio molecular orbital calculations are performed to investigate the three successive surface reactions of GaN with HCl. These reactions correspond to the simplest model which accounts for GaN chemical etching by HCl. We observed two characteristic points about these reactions. First, all of these reactions are exothermic and the reaction energies are about 20-29kcal/mol. Second, the activation energy of the reaction decreases as the number of Ga-Cl bonds increases. The calculation shows that the first reaction of the GaN surface with HCl is the rate-determining one and the calculated reaction barrier is less than 10kcal/mol.

      DOI: 10.1143/jjap.35.L1641

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    • Generalized doubly symbolic formulation for integral-driven direct configuration interaction method 査読有り

      Y Mochizuki, N Nishi, Y Hirahara, T Takada

      THEORETICA CHIMICA ACTA93 ( 4 ) 211 - 233   1996年4月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER VERLAG  

      A direct configuration interaction (CI) scheme using the generalized double symbolism both for the external space and for the internal space is proposed in an integral-driven context. The reason why the double symbolism is used in the present formulation is that the main target is in investigating large molecular systems. The integrals, configuration state functions, and energy expressions are systematically classified in terms of the orbital labels and their mutual relations. Various types of CI wavefunctions can be set up flexibly. The resulting structure of integral processings in the sigma vector construction is complicated. The number of unique loop types for two-electron integrals is 1325. Because the parallel architecture is gaining importance in the recent computational platforms, the parallelism is also addressed.

      DOI: 10.1007/s002140050148

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    • Epitaxial growth method of semiconductor crystal and molecular beam epitaxy apparatus for the same 査読有り

      Mochizuki Yuji, Usui Akira, Takada Toshikazu

          1996年4月

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      出版者・発行元:Google Patents  

      US Patent 5,505,159

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    • Method for epitaxial growth of semiconductor crystal by using halogenide 査読有り

      Mochizuki Yuji, Chiba Yoshie, Takada Toshikazu, Usui Akira

          1995年11月

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      出版者・発行元:Google Patents  

      US Patent 5,469,806

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    • ON THE REACTION SCHEME FOR TI/TIN CHEMICAL-VAPOR-DEPOSITION (CVD) PROCESS USING TICL4 査読有り

      Y MOCHIZUKI, Y OKAMOTO, A ISHITANI, K HIROSE, T TAKADA

      JAPANESE JOURNAL OF APPLIED PHYSICS PART 2-LETTERS34 ( 3A ) L326 - L329   1995年3月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:JAPAN J APPLIED PHYSICS  

      A schematic reaction mechanism is proposed to explain the Ti/TiN chemical vapor deposition (CVD) process using the TiCl4 molecule as the source species. The scheme can be considered as two successive steps: (I) TiCl4 molecules are adsorbed onto surface reactive sites through concerted electron delocalizations, (II) ambient reducing agents such as H-2 or NH3 reactively eliminate Cl atoms from Ti atoms in the form of HCl. Preliminary molecular orbital (MO) calculations indicate that step (I) is an energetically easy process. Conversely, step (II) is expected to be the rate-determining process with a considerable activation energy. As a whole, the characteristics of resultant CVD films (e.g., the conformality) are probably controlled not by the TiCl4-adsorption step (I) but by the Cl elimination step (II).

      DOI: 10.1143/JJAP.34.L326

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    • THEORETICAL-STUDY ON THE DIRECT REACTION BETWEEN ASH3 AND SURFACE-ADSORBED GACL 査読有り

      Y MOCHIZUKI, A USUI, S HANDA, T TAKADA

      JOURNAL OF CRYSTAL GROWTH148 ( 1-2 ) 96 - 105   1995年2月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      Ab initio molecular orbital calculations are performed to investigate the GaAs growth through a direct reaction between AsH3 and the adsorbed GaCl (symbolically written as GaClads). The formal reaction scheme is represented as GaClads + AsH3 --&gt; Ga(AsH2)(ads) + HCl, where the electron delocalization is the driving factor. The reason why the direct AsH3/GaClads reaction presents a very fast growth rate is attributed to the existence of a stable precursor state that occurs before the four-centered transtion state.

      DOI: 10.1016/0022-0248(94)00644-X

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    • THEORETICAL-STUDIES ON THE CHLORIDE ALE PROCESS 査読有り

      Y MOCHIZUKI, T TAKADA, A USUI

      APPLIED SURFACE SCIENCE82-3   200 - 207   1994年12月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      Ab initio molecular orbital calculations were performed to systematically investigate the chloride atomic layer epitaxy (ALE) process of GaAs. In the Ga layer formation, the GaCl molecular as a source is first adsorbed onto the As dangling-bond (DB) site through electronic ''configuration mixing''. Consequently, the ambient H2 reactively eliminates the Cl atom as HCl, where the ''electron delocalization'' is the driving factor of reaction. As layer formation via As2 adsorption onto the Ga-DB site was also investigated. The results show that the pi orbitals of As2 are used to form the As-Ga bonds through ''configuration mixing'', as in the case of GaCl/As-DB. The calculated energetics are consistent with the experimental data.

      DOI: 10.1016/0169-4332(94)90217-8

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    • THEORETICAL-STUDY OF AS2 DESORPTION FROM THE GA DANGLING-BOND SITE 査読有り

      Y MOCHIZUKI, T TAKADA, C SASAOKA, A USUI, E MIYOSHI, Y SAKAI

      PHYSICAL REVIEW B49 ( 7 ) 4658 - 4667   1994年2月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER PHYSICAL SOC  

      The cluster model As2-(GaH2)4 is used for ab initio complete active space self-consistent-field (CASSCF) molecular-orbital calculations, to investigate the electronic mechanism of As2 desorption from the fourfold-hollow Ga dangling-bond (DB) site. The electronic state of the adsorbed As2 is revealed to be the sigma(g)2pi(u)2pi(g)2 doubly excited configuration, where the free As2 Molecule is characterized by sigma(g)2pi(u)4 with the triple bond. Namely, the four pi orbitals of the As2 unit are used to form the four Ga-As covalent bonds with the Ga-DB site and a weak sigma bond remains between the two As atoms. The calculated CASSCF wave functions indicate that the desorption process could be just the chemical reaction of multiple bond conversions having strong electron correlations due to the near degeneracy. The single-configurational picture is completely invalid in understanding the As2 desorption. The transition state is found to be of the ''late-barrier'' type, and from this the ''cold'' vibrational distribution of the desorbed AS2 ig predicted.

      DOI: 10.1103/PhysRevB.49.4658

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    • THEORETICAL-STUDY OF THE CL DESORPTION REACTION INDUCED BY H-2 IN THE CHLORIDE ATOMIC LAYER EPITAXY 査読有り

      Y MOCHIZUKI, T TAKADA, T SAKUMA, S HANDA, C SASAOKA, A USUI

      JOURNAL OF CRYSTAL GROWTH135 ( 1-2 ) 259 - 268   1994年1月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      The chloride ALE (atomic layer epitaxy) technique is now common to grow GaAs crystals, where the GaCl molecule is used to supply Ga atoms for the As dangling bond site. The present ab initio molecular orbital calculations predict that Cl atoms are desorbed as HCI by the single-site reaction which is induced by H-2. The reaction scheme is represented as &gt; GaCl + H-2 --&gt; &gt; GaH + HCI, which is driven by the concerted electron delocalizations among those four atoms. It is shown that the reaction is endothermic by the amount of 30 kcal/mol and occurs through the four-centred transition state of ''late-barrier'' type. The activation energy is estimated to be 37-44 kcal/mol, which agrees well with the experimental value of 40-50 kcal/mol.

      DOI: 10.1016/0022-0248(94)90749-8

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    • The combination of computational techniques such as computer graphics (CG), molecular dynamics (MD) and quantum chemistry (QC) methods are demonstrated to be effective for investigating the dynamics and formation of ordered metal species in zeolite pores. 査読有り

      Mochizuki Y, Takada T, Usui A

      Applied Surface Science82 ( 83 ) 543   1994年

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    • Theoretical Studies on the Dielectric Breakdown of the SiO_2 Thin Films 査読有り

      YOKOZAWA Ayumi, OHTA Noriko, MOCHIZUKI Yuji, ISHITANI Akihiko, TAKADA Toshikazu

      Science reports of the Research Institutes, Tohoku University. Ser. A, Physics, chemistry and metallurgy39 ( 1 ) 81 - 84   1994年

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      記述言語:英語   出版者・発行元:東北大学  

      Electronic structures of oxygen deficiency in the SiO_2 thin film are theoretically studied by using the cluster models of Si_2O_7H_6 and Si_2O_6H_6 in order to reveal the mechanism of dielectric breakdown observed in the thin films. It is found that the oxygen deficiency induces electron traps rather than hole traps. Furthermore, F^- ions captured through the HF treatments are considered to be a key to introduce the oxygen deficiency in the SiO_2 thin films.

      CiNii Article

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    • THEORETICAL-STUDY OF THE GALLIUM CHLORIDE MOLECULE AND ITS INTERACTION WITH ARSENIC DANGLING BONDS 査読有り

      Y MOCHIZUKI, T TAKADA, A USUI

      PHYSICAL REVIEW B47 ( 20 ) 13420 - 13431   1993年5月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMERICAN PHYSICAL SOC  

      Ab initio molecular-orbital calculations have been carried out on the ground, excited, and ionized states of the gallium monochloride GaCl, which is used as a source molecule to generate Ga layers in GaAs epitaxial crystal growth. The calculated spectroscopic constants show good agreement with the experimental data. The calculated molecular properties of GaCl explain reasonably well the mechanism of its adsorption onto the As surface. The adsorption process is investigated by using a cluster model of GaCl-(AsH2)2. The adsorption is found to occur as the result of covalent-bond formation with the As atoms through electronic-configuration mixing.

      DOI: 10.1103/PhysRevB.47.13420

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    • NEW CONCERTED MECHANISM OF THE CL-REMOVAL REACTION INDUCED BY H-2 IN CHLORIDE ATOMIC LAYER EPITAXY 査読有り

      Y MOCHIZUKI, T TAKADA, A USUI

      JAPANESE JOURNAL OF APPLIED PHYSICS PART 2-LETTERS32 ( 2A ) L197 - L199   1993年2月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:JAPAN J APPLIED PHYSICS  

      A new concerted mechaniSM is proposed to explain the Cl removal from the adsorbed GaCl on the outermost As surface, by the ab initio configuration interaction (CI) calculations on the simple model system of H2GaCl + H-2. The proposed reaction scheme is written as &gt;GaCl + H-2 --&gt; &gt;GaH + HCl which occurs through the single-site collision of H-2 with the adsorbed GaCl on the surface. Concerted electron delocalizations induced by H-2 is the driving force to proceed the reaction. The present calculation predicts that the reaction is endothermic with an energy of 29 kcal/mol and has a four-centered transition state. The estimated activation energy is 83 kcal/mol, which will be reduced by improving the present cluster model.

      DOI: 10.1143/JJAP.32.L197

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    • THEORETICAL-STUDIES ON THE ALE PROCESS OF GAAS CRYSTALS 査読有り

      Y MOCHIZUKI, T TAKADA

      NEC RESEARCH & DEVELOPMENT33 ( 3 ) 518 - 531   1992年7月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:NEC CORPORATION  

      The chloride ALE (Atomic Layer Epitaxy) process of GaAs crystals is theoretically studied by the ab initio Molecular Orbital (MO) calculations. The electron correlations are carefully considered to obtain correct descriptions of the GaAs electronic states. For the growth of Ga layers, Ga atoms are supplied as a form of GaCl to the As surface, and then the GaCl is adsorbed onto the As DB (Dangling Bond) site. The computational results are summarized as follows; (1) the GaCl overrides the potential barrier during the adsorption, (2) the valence excitation of Ga 4s --&gt; 4p pi in GaCl is essential to form the covalent bonds with the As DB site, and (3) the "self-dissociation' of the Cl atom is unlikely. From the present simulations, a concerted reaction mechanism is also predicted for the Cl-removal by the collision with H2. As a whole, the nature of the epitaxial Ga layer growth is found to be analogous to the Si epitaxial growth in which the SiCl2 is used as the Si carrier.

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    • ELECTRONIC-STRUCTURE OF LOWER SINGLET-STATES OF BINUCLEAR COPPER-ACETATE MONOHYDRATE 査読有り

      K OGASAWARA, Y MOCHIZUKI, T NORO, K TANAKA

      CANADIAN JOURNAL OF CHEMISTRY-REVUE CANADIENNE DE CHIMIE70 ( 2 ) 393 - 398   1992年2月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:NATL RESEARCH COUNCIL CANADA  

      The electronic structures of the ground state and the excited states due to the 3d-3d transition of copper acetate monohydrate are investigated by ab initio calculations. No direct bond is obtained between the two Cu ions, but they are bonded by bridges of the four acetates. The excited states represented by the one-electron excitation of an occupied 3d electron to an unoccupied 3d orbital in either of the two Cu's are located around 1.6-1.8 eV, which corresponds to the energy region of band I. Those of the simultaneous one-electron 3d-3d excitation in both Cu's (i.e., two-electron excitation) are located around 3.2-3.4 eV. They correspond to the energy region of band II.

      DOI: 10.1139/v92-056

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    • A THEORETICAL-STUDY OF THE CUOH MOLECULE 査読有り

      Y MOCHIZUKI, T TAKADA, A MURAKAMI

      CHEMICAL PHYSICS LETTERS185 ( 5-6 ) 535 - 543   1991年10月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      Ab initio configuration-interaction calculations were carried out on the copper hydroxide (CuOH) molecule in its ground and excited states. The characteristics of these states are discussed in terms of the excitation energies and the one-electron properties. Electron correlation is found to be an important factor in the energetics of this molecule.

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    • ELECTRONIC-STRUCTURE OF THE LINEAR FORM OF OCUO 査読有り

      Y MOCHIZUKI, K TANAKA, H KASHIWAGI

      CHEMICAL PHYSICS151 ( 1 ) 11 - 20   1991年3月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      The low-lying doublet states of the linear form of the copper dioxide molecule, OCuO, are investigated by the use of ab initio CASSCF (complete active space self-consistent field) and POLCI (polarization configuration interaction) calculations. The emission bands experimentally observed are discussed in terms of the calculated excitation energies of the dipole-allowed transitions from the 2-PI-g ground state.

      DOI: 10.1016/0301-0104(91)80002-Y

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    • A THEORETICAL-STUDY OF THE BENT FORM OF CUO2 査読有り

      Y MOCHIZUKI, U NAGASHIMA, S YAMAMOTO, H KASHIWAGI

      CHEMICAL PHYSICS LETTERS164 ( 2-3 ) 225 - 230   1989年12月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      DOI: 10.1016/0009-2614(89)85019-5

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    • ELECTRONIC-STRUCTURE OF CO ADSORBED ON SMALL CU CLUSTERS - THEORETICAL-STUDY ON EXCITED-STATES 査読有り

      Y MOCHIZUKI, K TANAKA, K OHNO, H TATEWAKI

      PHYSICAL REVIEW B39 ( 16 ) 11907 - 11913   1989年6月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMERICAN PHYSICAL SOC  

      DOI: 10.1103/PhysRevB.39.11907

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    • ABINITIO CAS SCF/MRSDCI STUDY OF THE CUCH2 CLUSTER 査読有り

      Y MOCHIZUKI, K TANAKA, K OHNO, H TATEWAKI, S YAMAMOTO

      CHEMICAL PHYSICS LETTERS152 ( 6 ) 457 - 463   1988年11月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      DOI: 10.1016/0009-2614(88)80441-X

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    • Theoretical Study of the Electronic Structure of CO Adsorbed on Small Cu Clusters 査読有り

      Tanaka K, Mochizuki Y, Kawaguchi T, Ohno K, Tatewaki H

      Microclusters   82   1987年

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      出版者・発行元:Springer, Berlin, Heidelberg  

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    • 散逸粒子動力学(DPD)プログラムCAMUSの新規開発と性能評価 査読有り

      土居英男, 齊藤天菜, 奥脇弘次, 内藤貴充, 望月祐志

      J. Comp. Chem. Jpn.16   126 - 128  

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      記述言語:日本語  

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    • Structure-based drug designを指向した新規フラグメント分割法に基づく4体補正フラグメント分子軌道(FMO4)計算

      渡邉千鶴, 福澤薫, 沖山佳生, 望月祐志, 塚本貴志, 加藤昭史, 田中成典, 中野達也

      CBI学会誌1   42 - 46  

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      記述言語:日本語  

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    • AMOSSWEB: ab initio molecular orbital calculation service system in the world-wide web environment 査読有り

      Mochizukia Yuji, Yamamotob Akinori, Hiraharab Yukio, Okamotob Naoki, Nishizawab Kaori, Okamotoa Yasuharu, Handab Susumu, Sakumab Toshihiro, Nakadab Hiroshi, Sanoa Tohru, o

         

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    • Summary of this category 査読有り

      Dumitrache A, Frunzulica F, Ionescu TC, c{C } }ekinmez Abdulkerim, Karaosmano{\u{g } }lu Bari{\c{s } }can, Erg{\"u}l, O}zg{\"u}r, Komeiji Yuto, Mochizuki Yuji, Nakano Tatsuya, Mori Hirotoshi

         

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    MISC

    • タンパク質に関する FMO-DPD シミュレーション用パラメータ算定と試行 招待有り 査読有り

      太刀野 雄介, 土居 英男, 奥脇 弘次, 平野 秀典, 望月 祐志

      J. Comp. Chem. Jpn.22 ( 2 ) 15 - 17   2023年12月9日

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      担当区分:最終著者, 責任著者  

      DOI: 10.2477/jccj.2023-0019

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      その他リンク: https://www.jstage.jst.go.jp/article/jccj/22/2/22_2023-0019/_pdf

    • ABINIT-MP Openシリーズ (Ver.2 Rev.8)

      望月祐志

          2023年8月

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      担当区分:責任著者   記述言語:日本語  

      ABINIT-MPプログラムOpenシリーズのVer. 2 Rev. 8のリリースノート

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    • 「富岳」時代のフラグメント分子軌道計算 招待有り

      望月祐志

      化学78 ( 8 ) 12 - 15   2023年7月

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      担当区分:筆頭著者   記述言語:日本語  

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    • FMOプログラムABINIT-MPの整備状況2022 招待有り 査読有り

      望月 祐志, 中野 達也, 坂倉 耕太, 渡邊 啓正, 佐藤 伸哉, 奥脇 弘次, 秋澤 和輝, 土居 英男, 大島 聡史, 片桐 孝洋

      J. Comp. Chem. Jpn.21 ( 4 ) 106 - 110   2023年4月29日

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      担当区分:筆頭著者, 責任著者   記述言語:日本語   掲載種別:速報,短報,研究ノート等(学術雑誌)   出版者・発行元:日本コンピュータ化学会  

      We have been developing the ABINIT-MP program for fragment molecular orbital (FMO) calculations over 20 years. Several improvements for accelerated processing were made after the release of Open Version 2 Revision 4 at September 2021. Functionalities were enhanced as well. In this short report, we summarize such developments toward the next release of Revision 8.

      DOI: 10.2477/jccj.2022-0037

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    • 量子アプリケーション 招待有り

      杉﨑研司, 望月祐志

      映像情報メディア学会誌77   43 - 48   2023年2月

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      担当区分:最終著者   記述言語:日本語   掲載種別:書評論文,書評,文献紹介等  

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    • 量子コンピュータを利用したタンパク質の畳み込みモデル 招待有り 査読有り

      齊藤 瑠偉, 奥脇 弘次, 望月 祐志, 永井 隆太郎, 加藤 拓己, 杉﨑 研司, 湊 雄一郎

      J. Comp. Chem. Jpn.21 ( 2 ) 39 - 42   2022年11月

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      担当区分:責任著者   記述言語:日本語   掲載種別:速報,短報,研究ノート等(学術雑誌)   出版者・発行元:日本コンピュータ化学会  

      DOI: 10.2477/jccj.2022-0022

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    • FMOプログラムABINIT-MPの整備状況2021 招待有り 査読有り

      望月祐志, 中野達也, 佐藤伸哉, 坂倉耕太, 渡邊啓正, 奥脇弘次, 大島聡史, 片桐孝洋

      J. Comp. Chem. Jpn.20 ( 4 ) 132 - 136   2022年3月

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      担当区分:筆頭著者, 責任著者   記述言語:日本語   掲載種別:速報,短報,研究ノート等(学術雑誌)  

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    • A64FXを用いたフラグメント分子軌道計算プログラムの性能評価

      満田, 晴紀, 片桐, 孝洋, 坂倉, 耕太, 中野, 達也, 望月, 祐志, 大島, 聡史, 永井, 亨

      第84回全国大会講演論文集2022 ( 1 ) 63 - 64   2022年2月17日

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      記述言語:日本語  

      フラグメント分子軌道計算(FMO)を行うソフトウェアABINIT-MPについて、名古屋大学情報基盤センターが提供するスーパーコンピュータ「不老」TypeⅠサブシステム(CPU:ARMA64FX)を用いて性能評価した結果を示す。

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    • ABINIT-MP Openシリーズ (Ver.2 Rev.4)

      望月祐志

          2021年9月

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      担当区分:責任著者   記述言語:日本語  

      ABINIT-MPプログラムOpenシリーズのVer. 2 Rev. 4のリリースノート

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    • FMOプログラム「ABINIT-MP」のA64FXスーパーコンピュータ向け高速化と大規模化 招待有り

      望月 祐志, 中野 達也, 坂倉 耕太

      計算工学ナビ ( 21 ) 6 - 6   2021年9月

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      担当区分:筆頭著者, 責任著者   記述言語:日本語   掲載種別:機関テクニカルレポート,技術報告書,プレプリント等  

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      その他リンク: http://www.cenav.org/wp-content/uploads/2021/09/NL21_low.pdf

    • 種々の科学データにおける機械学習を用いた分析の試み 招待有り 査読有り

      奥脇 弘次, 増田 淳希, 柿沼 紗也果, 長谷川 貴一, 水野 寛哉, 満野 仁美, 伊藤 雅仁, 藤方 玲衣, 望月 祐志

      J. Comp. Chem. Jpn.19 ( 4 ) A21 - A24   2021年6月

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      担当区分:最終著者  

      DOI: 10.2477/jccj.2021-0018

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    • FMOプログラムABINIT-MPの整備状況2020 招待有り 査読有り

      望月 祐志, 坂倉 耕太, 渡邊 啓正, 奥脇 弘次, 加藤 幸一郎, 渡辺 尚貴, 沖山 佳生, 福澤 薫, 中野 達也

      J. Comp. Chem. Jpn.19 ( 4 ) 142 - 145   2021年4月

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      担当区分:筆頭著者, 責任著者   記述言語:日本語   掲載種別:速報,短報,研究ノート等(学術雑誌)  

      DOI: 10.2477/jccj.2021-0015

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    • SARS-CoV-2メインプロテアーゼと既存薬のFMO動的相互作用解析

      半田佑磨, 川嶋裕介, 畑田崚, 奥脇弘次, 望月祐志, 古石誉之, 米持悦生, 本間光貴, 古明地勇人, 田中成典, 福澤薫, 福澤薫

      構造活性相関シンポジウム講演要旨集49th (CD-ROM)   2021年

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    • 分子シミュレーションによるssPalm脂質ナノ粒子の構造と相互作用解析

      小浪なおこ, 西田瑠花, 氏家かれん, 佐々木香純, 奥脇弘次, 望月祐志, 田中浩揮, 秋田英万, 古石誉之, 福澤薫, 米持悦生

      日本薬学会関東支部大会講演要旨集65th (CD-ROM)   2021年

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    • 自己組織化写像によるフラグメント間相互作用解析手法の開発

      川嶋裕介, 田雨時, 半田佑磨, 奥脇弘次, 渡邉千鶴, 渡邉千鶴, 川下理日人, 古石誉之, 米持悦生, 本間光貴, 田中成典, 望月祐志, 高木達也, 福澤薫

      日本薬学会関東支部大会講演要旨集65th (CD-ROM)   2021年

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    • 分子シミュレーションによるssPalm/コレステロール混合系脂質ナノ粒子の構造解析

      氏家かれん, 西田瑠花, 奥脇弘次, 望月祐志, 田中浩揮, 秋田英万, 古石誉之, 福澤薫, 米持悦生

      日本薬学会年会要旨集(Web)141st   2021年

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    • FMO動的相互作用解析によるSARS-CoV-2メインプロテアーゼと既存薬のポーズ推定と結合性予測

      半田佑磨, 奥脇弘次, 畑田崚, 望月祐志, 望月祐志, 古明地勇人, 田中成典, 古石誉之, 米持悦生, 川嶋裕介, 本間光貴, 福澤薫, 福澤薫

      日本コンピュータ化学会年会講演予稿集2021   2021年

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    • 新型コロナウイルスのタンパク質に関するフラグメント分子軌道計算の事例 招待有り

      望月 祐志, 奥脇 弘次

      計算工学会誌26 ( 1 ) 4204 - 4209   2021年1月

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      掲載種別:記事・総説・解説・論説等(その他)  

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    • 新型コロナウイルスタンパク質のフラグメント分子軌道計算 招待有り

      望月祐志

      現代化学596 ( 2020年11月号 ) 34 - 35   2020年10月

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      担当区分:責任著者   記述言語:日本語   出版者・発行元:東京化学同人  

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    • フラグメント分子軌道(FMO)法、ならびに散逸粒子動力学(DPD)シミュレーションとの連携 招待有り 査読有り

      望月祐志, 奥脇弘次

      応用物理89 ( 10 ) 566 - 572   2020年10月

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      担当区分:筆頭著者, 責任著者   記述言語:日本語   掲載種別:記事・総説・解説・論説等(その他)   出版者・発行元:応用物理学会  

      DOI: 10.11470/oubutsu.89.10_566

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    • 「富岳」を使った新型コロナウイルスの関連タンパク質のFMO計算 招待有り

      望月 祐志

      計算工学ナビ ( 19 ) 6 - 6   2020年9月

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      担当区分:筆頭著者, 責任著者   記述言語:日本語   掲載種別:機関テクニカルレポート,技術報告書,プレプリント等  

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      その他リンク: http://www.cenav.org/wp-content/uploads/2020/08/NL19_low.pdf

    • 新型コロナウイルスのタンパク質に対するフラグメント分子軌道計算による解析事例 招待有り 査読有り

      望月 祐志

      応用物理学会 「特別WEBコラム 新型コロナウィルス禍に学ぶ応用物理」   2020年8月

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      担当区分:責任著者  

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      その他リンク: https://www.jsap.or.jp/columns-covid19/covid19_2-3-2

    • フラグメント分子軌道法によるSARS-CoV-2Mproと阻害剤の相互作用解析

      川嶋裕介, 半田佑磨, 奥脇弘次, 望月祐志, 古明地勇人, 田中成典, 渡邉千鶴, 本間光貴, 福澤薫

      構造活性相関シンポジウム講演要旨集48th (CD-ROM)   2020年

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    • FMO-DPDシミュレーションによる脂質二重膜,ナノ粒子の詳細解析

      奥脇弘次, 新庄永治, 西田瑠花, 氏家かれん, 望月祐志, 望月祐志, 福澤薫, 福澤薫, 福澤薫, 米持悦生, 田中浩揮, 秋田英万

      応用物理学会秋季学術講演会講演予稿集(CD-ROM)81st   2020年

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    • FMO-DPD連携による脂質ナノ粒子,ペプチドのマルチスケールシミュレーション

      奥脇弘次, 西田瑠花, 氏家かれん, 土屋裕大朗, 望月祐志, 望月祐志, 福澤薫, 福澤薫, 福澤薫, 米持悦生, 田中浩揮, 秋田英万

      分子シミュレーション討論会講演要旨集34th (CD-ROM)   2020年

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    • 分子動力学とフラグメント分子軌道計算を用いたSARS-CoV-2主要プロテアーゼへの既存薬物の結合の予測【JST・京大機械翻訳】

      HANDA Yuma, KAWASHIMA Yusuke, HATADA Ryo, OKUWAKI Koji, AKISAWA Kazuki, MOCHIZUKI Yuji, KOMEIJI Yuto, TANAKA Shigenori, FURUISHI Takayuki, FUKUZAWA Kaori, YONEMOCHI Etsuo

      CBI学会大会2020 (CD-ROM)   2020年

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    • FMO-DPDの連携による脂質二重膜,タンパク質の構造解析システムの整備と応用

      奥脇弘次, 新庄永治, 西田瑠花, 加藤幸一郎, 土屋裕大朗, 土居英男, 望月祐志, 望月祐志, 福澤薫, 福澤薫, 米持悦生

      応用物理学会春季学術講演会講演予稿集(CD-ROM)67th   2020年

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    • フラグメント分子軌道法による動的相互作用解析を用いたSARS-CoV-2メインプロテアーゼと既存薬との結合性予測

      半田佑磨, 川嶋裕介, 畑田崚, 奥脇弘次, 秋澤和輝, 望月祐志, 古明地勇人, 田中成典, 古石誉之, 福澤薫, 福澤薫, 米持悦生

      日本薬学会関東支部大会講演要旨集64th   2020年

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    • 深層学習とシミュレーションの連携事例 招待有り

      伊藤 雅仁, 遠藤 克浩, 望月 祐志, 泰岡 顕治

      計算工学会誌24 ( 4 ) 3983 - 3987   2019年10月

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      担当区分:責任著者   記述言語:日本語   掲載種別:記事・総説・解説・論説等(学術雑誌)  

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    • 転移学習と生成ネットワークの試行事例 招待有り 査読有り

      伊藤 雅仁, 篠嶋 友也, 望月 祐志, 秋永 宜伸, 小杉 範仁

      J. Comp. Chem. Jpn.18 ( 3 ) 132 - 135   2019年10月

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      担当区分:責任著者   記述言語:日本語   掲載種別:速報,短報,研究ノート等(学術雑誌)  

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    • Scratchを経由する機械学習教材の開発の試み 招待有り 査読有り

      満野 仁美, 奥脇 弘次, 伊藤 雅仁, 望月 祐志

      J. Comp. Chem. Jpn.18 ( 3 ) 126 - 128   2019年10月

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      担当区分:責任著者   記述言語:日本語   掲載種別:速報,短報,研究ノート等(学術雑誌)  

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    • 機械学習によるテキスト処理ツールの開発と応用 招待有り 査読有り

      亘理 結香, 奥脇 弘次, 望月 祐志

      J. Comp. Chem. Jpn.18 ( 3 ) 123 - 125   2019年10月

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      担当区分:責任著者   記述言語:日本語   掲載種別:速報,短報,研究ノート等(学術雑誌)  

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    • ペプトイド対応のフラグメント分割ツールの開発

      吉田杏平, 加藤幸一郎, 奥脇弘次, 阿部鷹也, 望月祐志, 望月祐志, 福澤薫, 福澤薫

      日本コンピュータ化学会年会講演予稿集2019   2019年

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    • 高分子電解質膜材料設計に向けた非経験的パラメータに基づく粗視化シミュレーション解析

      加藤幸一郎, 奥脇弘次, 土居英男, 米田雅一, 望月祐志, 望月祐志

      電池討論会PDF要旨集(CD-ROM)60th   2019年

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    • カルサイト/アパタイト結晶表面とペプチドのFMO相互作用解析

      畑田崚, 加藤幸一郎, 奥脇弘次, 福澤薫, 望月祐志, 望月祐志

      応用物理学会秋季学術講演会講演予稿集(CD-ROM)80th   2019年

      詳細を見る

    • 固体とタンパクの出会いを計算する

      加藤幸一郎, 畑田崚, 奥脇弘次, 福澤薫, 望月祐志, 望月祐志

      応用物理学会秋季学術講演会講演予稿集(CD-ROM)80th   2019年

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    • 小角X線散乱とCryo-TEMを用いた物性測定と非経験的粗視化シミュレーションによる脂質膜構成メカニズムの解明

      新庄永治, 奥脇弘次, 土居英男, 望月祐志, 望月祐志, 古石誉之, 福澤薫, 福澤薫, 米持悦生

      量子ビームサイエンスフェスタ(Web)2018   2019年

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    • 散逸動力学シミュレーションによるアミロイドβオリゴマーの自己組織化の検討

      河合良子, 千葉峻太朗, 金田亮, 奥脇弘次, 土居英男, 望月祐志, 望月祐志, 奥野恭史, 奥野恭史, 奥野恭史

      日本細胞生物学会大会(Web)71st   2019年

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    • 散逸動力学シミュレーションによるアミロイドβオリゴマーの自己組織化の検討

      河合良子, 千葉峻太朗, 金田亮, 奥脇弘次, 土居英男, 望月祐志, 望月祐志, 奥野恭史, 奥野恭史

      日本コンピュータ化学会年会講演予稿集2019   2019年

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    • FMO計算に基づく脂質二重膜,タンパク質の非経験的粗視化シミュレーションの展開

      奥脇弘次, 新庄英治, 土居英男, 望月祐志, 望月祐志, 福澤薫, 福澤薫, 米持悦生

      応用物理学会春季学術講演会講演予稿集(CD-ROM)66th   2019年

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    • ABINIT‐MP(X)による京でのFMO計算

      沖山佳生, 望月祐志, 望月祐志, 福澤薫, 福澤薫, 古明地勇人, 森寛敏, 渡邉千鶴, 田中成典

      分子科学討論会講演プログラム&amp;要旨(Web)6th   ROMBUNNO.4P105 (WEB ONLY)   2012年

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      記述言語:日本語  

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    • Grb2SH2ドメイン‐阻害剤間の結合親和性のFMO4法と新規フラグメント分割法に基づくCH/π相互作用解析

      渡邉千鶴, 福澤薫, 福澤薫, 中野達也, 中野達也, 望月祐志, 望月祐志, 梅沢洋二, 西尾元宏

      分子科学討論会講演プログラム&amp;要旨(Web)6th   ROMBUNNO.4P106 (WEB ONLY)   2012年

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      記述言語:日本語  

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    • QC2ASの設計について

      小副川 健, 望月 祐志, 横山 和弘

      数式処理18 ( 1 ) 16 - 19   2011年12月1日

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      記述言語:日本語   出版者・発行元:日本数式処理学会  

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    • Fragment molecular orbital study for interaction between influenza virus neuraminidase and antiviral drug

      FUKUZAWA Kaori, MOCHIZUKI Yuji, MIBE Hiroki, WATANABE Chiduru, TANAKA Shigenori, NAKANO Tatsuya

      情報計算化学生物学会大会予稿集2011 (CD-ROM)   ROMBUNNO.CBI-P1-13   2011年11月8日

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      記述言語:英語  

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    • 電子相関理論のための数式処理システムに向けて (数式処理研究の新たな発展)

      小副川 健, 望月 祐志, 横山 和弘

      数理解析研究所講究録1759   99 - 104   2011年9月

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      出版者・発行元:京都大学  

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      その他リンク: http://hdl.handle.net/2433/171330

    • Large-Scale Electronic-State Calculations of Influenza Viral Proteins with Fragment Molecular Orbital Method and Applications to Mutation Prediction

      田中 成典, A. Yoshioka, Y. Mochizuki, K. Fukuzawa, K. Yamashita, T. Nakano

      Annual Report of the Earth Simulator Center, April 2010 – March 2011   187 - 191   2011年

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      記述言語:英語   掲載種別:機関テクニカルレポート,技術報告書,プレプリント等  

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    • Fragment‐based drug design(FBDD)を指向した新規分割法に基づくFMO計算

      渡邉千鶴, 福澤薫, 福澤薫, 沖山佳生, 望月祐志, 望月祐志, 塚本貴志, 塚本貴志, 山下勝美, 守田伸明, 田中成典, 中野達也, 中野達也

      分子科学討論会講演プログラム&amp;要旨(Web)5th   ROMBUNNO.3P099 (WEB ONLY)   2011年

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      記述言語:日本語  

      J-GLOBAL

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    • Development of ABINIT-MP(X) program for processing fragment molecular orbital calculations 招待有り

      Yoshio Okiyama, Tatsuya Nakano, Yuji Mochizuki, Katsumi Yamashita, Kaori Fukuzawa, Takayuki Tsukamoto, Chiduru Watanabe, Shigenori Tanaka

      Proceedings of JSST 2011, International Conference on Modeling and Simulation Technology   101 - 104   2011年

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      掲載種別:記事・総説・解説・論説等(国際会議プロシーディングズ)  

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    • FMO-MD法 : フラグメント分子軌道法による分子のダイナミクスシミュレーション

      古明地 勇人, 中野 達也, 望月 祐志

      シミュレーション29 ( 1 ) 2 - 9   2010年3月15日

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      記述言語:日本語   出版者・発行元:日本シミュレーション学会  

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    • Three-Body Expansion and Generalized Dynamic Fragmentation Improve the Fragment Molecular Orbital-Based Molecular Dynamics (fMO-MD), An ab Initio MD Method

      Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano

      BIOPHYSICAL JOURNAL98 ( 3 ) 573A - 573A   2010年1月

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      記述言語:英語   掲載種別:研究発表ペーパー・要旨(国際会議)   出版者・発行元:CELL PRESS  

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    • フラグメント分子軌道法によるポリシラン類の物性に関する理論的研究

      田口尚貴, 望月祐志, 石川岳志, 中野達也, 森寛敏, 三好永作, 田中成典

      日本化学会講演予稿集89th ( 1 )   2009年

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    • FMO-MD法によるメチルジアゾニウムカチオンの加水分解反応シミュレーション

      佐藤真, 山高博, 古明地勇人, 古明地勇人, 望月祐志, 望月祐志, 望月祐志, 石川岳志, 石川岳志, 中野達也, 中野達也, 中野達也

      日本化学会講演予稿集88th ( 2 )   2008年

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    • フラグメント分子軌道法によるポリシラン類の物性に関する理論的研究

      田口尚貴, 望月祐志, 望月祐志, 石川岳志, 中野達也, 中野達也, 森寛敏, 森寛敏, 三好永作, 三好永作, 田中成典, 田中成典

      分子科学討論会講演プログラム&要旨(Web)2nd   2008年

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    • フラグメント分子軌道法によるDsRed類縁種の励起状態に関する理論的研究

      田口尚貴, 望月祐志, 中野達也, 甘利真司, 石川岳志, 福澤薫, 櫻井実, 田中成典

      日本化学会講演予稿集88th ( 1 )   2008年

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    • エストロゲン受容体のアミノ酸変異によるエストラジオール結合エネルギーの変化

      前田紘輔, Alexander Schug, 渡邉博文, 福澤薫, 望月祐志, 中野達也, 田中成典

      J. Comp. Chem. Jpn.6 ( 1 ) 33 - 46   2007年

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      記述言語:日本語   出版者・発行元:Society of Computer Chemistry, Japan  

      エストロゲン受容体とエストラジオールとの結合に関する分子メカニズムを解明することを目的とし、エストロゲン受容体にコンピュータ上でアミノ酸変異を導入して、エストラジオールとの結合能をフラグメント分子軌道法を用いて評価した。アミノ酸変異の導入方法の妥当性を検討するために、実験で用いられたのと同じアミノ酸変異を導入して、結合エネルギーを評価し、実験データと比較した。その結果、6種類のアミノ酸変異のうち、3つは定性的に一致し、残り3つは不一致となった。それらの結果の原因を検討した。

      DOI: 10.2477/jccj.6.33

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      その他リンク: https://jlc.jst.go.jp/DN/JALC/00291774567?from=CiNii

    • フラグメント分子軌道法を用いたポリペプチドのESP電荷の決定

      沖山佳生, 渡邉博文, 渡邉博文, 福澤薫, 中野達也, 中野達也, 望月祐志, 望月祐志, 石川岳志, 石川岳志, 田中成典, 田中成典, 蛯名邦禎

      分子科学討論会講演要旨集(CD-ROM)1st   2007年

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    • FMO-MD法の再実装と溶液計算への応用

      古明地勇人, 石川岳志, 望月祐志, 山高博, 中野達也

      分子科学討論会講演要旨集(CD-ROM)1st   2007年

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    • FMO-MD法によるジアゾニウムカチオンの加水分解反応シミュレーション

      佐藤真, 山高博, 古明地勇人, 古明地勇人, 望月祐志, 望月祐志, 望月祐志, 石川岳志, 石川岳志, 中野達也, 中野達也, 中野達也

      分子科学討論会講演要旨集(CD-ROM)1st   2007年

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    • FMO-MD/MLFMO-CIS(D)法による水和分子の励起状態シミュレーション

      望月祐志, 望月祐志, 望月祐志, 古明地勇人, 古明地勇人, 石川岳志, 石川岳志, 中野達也, 中野達也, 中野達也, 山高博, 山下勝美, 栗崎以久男, 田中成典, 田中成典

      分子科学討論会講演要旨集(CD-ROM)1st   2007年

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    • FMO-MD法の最近の進展

      古明地勇人, 中野達也, 佐藤真, 石川岳志, 望月祐志, 山高博

      分子シミュレーション討論会講演要旨集21st   2007年

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    • 二量化した一酸化窒素分子の高度相関計算による研究

      田口尚貴, 望月祐志, 望月祐志, 望月祐志, 石川岳志, 石川岳志, 田中皓, 田中皓

      分子科学討論会講演要旨集(CD-ROM)1st   2007年

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    • スピン適合並列化中間状態駆動CASCIプログラムと応用計算

      田中皓, 田中皓, 望月祐志, 望月祐志, 望月祐志, 石川岳志, 石川岳志, 山下勝美, 村瀬匡, 田口尚貴, 田中成典, 田中成典

      分子科学討論会講演要旨集(CD-ROM)1st   2007年

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    • FMO法における局在化MP2法を用いた相互作用解析:FILMの開発と応用

      石川岳志, 石川岳志, 望月祐志, 望月祐志, 甘利真司, 中野達也, 中野達也, 常盤広明, 田中成典, 田中成典, 田中皓, 田中皓, 田中皓

      分子科学討論会講演要旨集(CD-ROM)1st   2007年

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    • フラグメント分子軌道法における大規模Post-HF計算

      望月祐志, 望月祐志, 望月祐志, 中野達也, 中野達也, 田中皓, 田中皓, 石川岳志, 石川岳志, 三好永作, 三好永作, 古明地勇人, 古明地勇人, 山下勝美, 村瀬匡, 甘利真司, 福澤薫, 福澤薫, 櫻井実, 田中成典, 田中成典

      分子科学討論会講演要旨集(CD-ROM)1st   2007年

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    • BioStation Viewer:生体高分子の相互作用解析と可視化

      加藤昭史, 福澤薫, 望月祐志, 甘利真司, 中野達也

      可視化情報学会誌26 ( 101 ) 124 - 129   2006年

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      記述言語:日本語   出版者・発行元:The Visualization Society of Japan  

      DOI: 10.3154/jvs.26.124

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    • 量子化学計算(FMO法)

      中野達也, 望月祐志, 甘利真司, 福澤薫

      スーパーコンピューティングニュース8   63 - 74   2006年

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    • FMO法へのMCPの導入と生体分子系への適用

      石川岳志, 石川岳志, 望月祐志, 望月祐志, 中野達也, 中野達也, 甘利真司, 森寛敏, 本田宏明, 藤田貴敏, 常盤広明, 常盤広明, 田中成典, 田中成典, 古明地勇人, 福澤薫, 福澤薫, 田中皓, 田中皓, 田中皓, 三好永作, 三好永作

      分子構造総合討論会講演要旨集(CD-ROM)2006   2006年

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    • FMO法を基盤とした新規創薬手法の開発と応用

      山岸賢司, 山岸賢司, 山本恵子, 石川岳志, 石川岳志, 望月祐志, 望月祐志, 望月祐志, 中野達也, 中野達也, 山田幸子, 常盤広明, 常盤広明

      日本薬学会年会要旨集126th ( 3 )   2006年

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    • レチノイドXレセプターのヘリックス12に関する理論的研究

      伊藤三香, 伊藤三香, 福澤薫, 望月祐志, 望月祐志, 石川岳志, 石川岳志, 中野達也, 中野達也, 田中成典, 田中成典

      分子構造総合討論会講演要旨集(CD-ROM)2006   2006年

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    • グラフ表示の閉殻と開殻への分離によるCASCIの並列,ベクトル処理アルゴリズム

      田中あきら, 田中あきら, 田中あきら, 田中あきら, 石川岳志, 石川岳志, 常盤広明, 常盤広明, 望月祐志, 望月祐志, 望月祐志

      分子構造総合討論会講演要旨集(CD-ROM)2005   2005年

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    • 新型コロナウイルスのタンパク質に対するフラグメント分子軌道計算による解析事例

      望月祐志

      応用物理学会 「特別WEBコラム 新型コロナウィルス禍に学ぶ応用物理」   2000年8月

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      記述言語:日本語  

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      その他リンク: https://www.jsap.or.jp/columns-covid19/covid19_2-3-2

    • 非経験的分子軌道法プログラム(AMOSS)の並列化

      平原 幸男, 望月祐志, 高田 俊和, 中田 宏, 土谷 正人

      情報処理学会研究報告ハイパフォーマンスコンピューティング(HPC)1995 ( 28 ) 41 - 48   1995年3月9日

      詳細を見る

      記述言語:日本語   出版者・発行元:一般社団法人情報処理学会  

      非経験的分子軌道法は、分子系の電子状態、化学反応性を理論的に調べる為の有力な手段であるが、その基本近似であるハートリーフォック()法においてさえ、展開基底関数の4乗のオーダーの積分を扱う必要がある。従って、生体分子など軌道数が千以上に達するような大型の系をルーチン的に解くためには分散・並列化による高速処理が不可欠である。私たちは、こうしたことから自主開発のソフトAMOSSを軸にして分子軌道計算の並列化に取り組んでいる。この報告では、WSクラスター及びMPP(nju?)上での並列化HF計算の結果について述べるが、共に16台構成時に約15倍の加速を得ている。Ab initio molecular orbital (MO) methods are promising to investigate the variety of electronic structures and/or chemical reactivities for the molecular systems in the balanced fashion. However, their computational efforts are considerably demanding. Even the standard Hartree-Fock procedure requires the N^4 order processings related with two-electron integrals, where N is the number of basis functions. To solve the systems having more than thousand functions routinely, the acceleration through parallelizations is crucial. Thus we have been developing the parallelized MO calculations based on the AMOSS package. In this report, we discuss the HF parallelizations on the clustered WS's and the MPP(Cenju-3). In the case of 16 nodes, the acceleration is observed to be 15 for both types of parallel environment, indicating a satisfactory scalability of our coarse-grained algorithm.

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    • Theoretical study of As2 desorption from the Ga dangling-bond site

      Yuji Mochizuki, Toshikazu Takada, Chiaki Sasaoka, Akira Usui, Eisaku Miyoshi, Yoshiko Sakai

      Physical Review B49 ( 7 ) 4658 - 4667   1994年

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      記述言語:英語  

      The cluster model As2-(GaH2)4 is used for ab initio complete active space self-consistent-field (CASSCF) molecular-orbital calculations, to investigate the electronic mechanism of As2 desorption from the fourfold-hollow Ga dangling-bond (DB) site. The electronic state of the adsorbed As2 is revealed to be the σg2πu2πg2 doubly excited configuration, where the free As2 molecule is characterized by σg2πu4 with the triple bond. Namely, the four π orbitals of the As2 unit are used to form the four Ga-As covalent bonds with the Ga-DB site and a weak σ bond remains between the two As atoms. The calculated CASSCF wave functions indicate that the desorption process could be just the chemical reaction of multiple bond conversions having strong electron correlations due to the near degeneracy. The single-configurational picture is completely invalid in understanding the As2 desorption. The transition state is found to be of the ''late-barrier'' type, and from this the ''cold'' vibrational distribution of the desorbed As2 is predicted. © 1994 The American Physical Society.

      DOI: 10.1103/PhysRevB.49.4658

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    • III-V族化合物半導体気相成長プロセスの解明 - 実験とシミュレーション -

      笹岡 千秋, 望月 祐志, 碓井 彰

      應用物理62 ( 8 ) 786 - 791   1993年8月10日

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      記述言語:日本語   出版者・発行元:応用物理学会  

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    書籍等出版物

    • Recent Advances of the Fragment Molecular Orbital Method - Enhanced Performance and Applicability -

      Yuji Mochizuki, Shigenori Tanaka, Kaori Fukuzawa( 担当: 共編者(共編著者) ,  範囲: Main editor)

      Springer  2021年1月  ( ISBN:9789811592348

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    • 科学技術未来戦略ワークショップ報告書 みんなの量子コンピューター ~情報・数理・物理で拓く新しい量子アプリ~

      望月 祐志( 担当: 分担執筆 ,  範囲: 量子化学計算関係)

      2019年1月 

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    • FMO計算によるマルチスケール手法の開発と材料開発への応用

      望月祐志, 奥脇弘次, 土居英男, 小沢拓( 担当: 共著 ,  範囲: 「マテリアルズ・インフォマティクスによる材料開発と活用集」の担当節)

      (株)技術情報協会  2019年1月 

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    • レアメタル・希少金属リサイクル技術の最先端

      望月祐志, 古明地勇人( 範囲: フラグメント分子軌道法と分子動力学シミュレーション)

      フロンティア出版  2011年 

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    • The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems

      望月 祐志( 担当: 共著 ,  範囲: Excited states of photoactive proteins by configuration interaction studies)

      Boca Raton, CRC press  2009年 

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    • プログラムで実践する生体分子量子化学計算

      佐藤文俊, 中野達也, 望月祐志( 担当: 共著)

      2008年10月 

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    • Modern Methods for Theoretical Physical Chemistry of Biopolymers

      望月 祐志( 担当: 共著)

      Elsevier B.V., Amsterdam, The Netherlands  2006年 

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    • 米欧日の量子化学ソフトウェアの現状と今後の応用

      望月 祐志( 担当: 共著)

      アドバンスソフト  2005年1月 

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      記述言語:日本語 著書種別:その他

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    • Recent Advances in Multireference Methods

      K. Tanaka, T. Sakai, Y. Mochizuki( 担当: 共著 ,  範囲: Multireference Coupled Pair Approximation: A State-Universal Approach of a CEPA Type Variant of MRSDCI)

      1999年 

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    • 新しい量子化学 (上下)

      大野 公男, 阪井 健男, 望月 祐志( 担当: 共訳)

      東京大学出版会  1987年 

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    ▼全件表示

    所属学協会

    ▼全件表示

    共同研究・競争的資金等の研究

    • 生体膜へのイオン配位状態の分子レベルでの理解:水中X線吸収分光

      日本学術振興会  科学研究費助成事業 

      手老 龍吾, 長坂 将成, 望月 祐志

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      2020年7月 - 2022年3月

      課題番号:20K21125

      配分額:6500000円 ( 直接経費:5000000円 、 間接経費:1500000円 )

      生体膜の基本構造である脂質二重膜は、両親媒性の脂質分子が水中で形成する自己組織化構造であり、その物性や膜内ドメイン形成は水溶液中のイオンによって強く影響される。流動状態にある水溶液中の脂質二重膜内におけるイオンの配位部位と結合定数を明らかにすることを目的とする。水中X線吸収分光(XAS)法によってリン二重膜内のリン脂質へのNa+イオンの配位を実験的に計測し、第一原理計算に基づいて検証を行った。

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    • 脂質およびタンパク質に関するマルチスケールシミュレーション手法の開発整備と応用展開

      立教大学  立教SFR 

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      2019年6月 - 2021年3月

      担当区分:研究代表者 

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    • 重点課題6 「革新的クリーンエネルギーシステムの実用化」

      文部科学省  ポスト「京」 

      吉村忍

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      2015年4月 - 2020年3月

      資金種別:競争的資金

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    • アクチニド分子種と生体分子の相互作用に関する計算化学的研究

      文部科学省  科研費 基盤B 

      望月祐志

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      2016年4月 - 2019年3月

      担当区分:研究代表者  資金種別:競争的資金

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    • 有機反応ダイナミクス支配現象の微視的解析

      日本学術振興会  科学研究費助成事業 

      山高 博, 望月 祐志, 古明地 勇人, 佐藤 真

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      2010年4月 - 2014年3月

      課題番号:22350023

      配分額:18720000円 ( 直接経費:14400000円 、 間接経費:4320000円 )

      有機化学反応の機構や生成物が必ずしも遷移状態の性質や構造によって規定されることがないことを理論化学計算と物理有機化学実験によって明らかにした。理論計算法として、フラグメント分子軌道法を援用した量子分子動力学シミュレーション法(FMO-MD法)を開発し、水中の有機化学反応における水分子の動的役割についてシミュレーションによって検討した。また、種々の転位反応、脱離反応、付加反応や置換反応のシミュレーションを実施した。さらに、転位反応、付加/置換反応については有機化学実験によって検証した。これらの結果から、有機反応におけるダイナミクス効果が伝統的な反応理論の枠を超えて重要であることを示した。

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    • 実在系の分子理論

      文部科学省  科研費 新学術 

      榊 茂好

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      2008年4月 - 2010年3月

      資金種別:競争的資金

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    • 量子化学、理論化学

      JST戦略的創造研究推進制度(研究チーム型) (戦略的基礎研究推進事業:CREST) 

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      2005年10月 - 2010年3月

      資金種別:競争的資金

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    • フラグメント分子軌道法による生体分子計算システムの開発

      文部科学省  科学技術振興調整費 

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      2004年4月 - 2010年3月

      資金種別:競争的資金

      「シミュレーション技術の革新と実用化基盤の構築」領域 プロジェクト分担研究者
      代表研究者:田中成典

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    • FMO法に基づく計算手法とプログラムの発展的開発

      日本学術振興会  科学研究費助成事業 

      望月 祐志

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      2008年 - 2009年

      課題番号:20038044

      配分額:2900000円 ( 直接経費:2900000円 )

      本研究は、FMO法の発展的開発を電子相関計算と分子動力学シミュレーション(FMO-MD)の二つの軸線を取って展開している。各々の平成21年度の成果概要を以下にまとめる。
      電子相関計算では、golden standardといえるCCSD(T)まで計算可能なファイルレス並列化エンジンの独自開発に成功したことがハイライトと言える。多電子論では下位の近似は系統的に導出されるので、その特徴を活かしてQCISD(T)やMP4(SDQ)などもキーワード指定でそのまま実行出来る。実行速度的には世界水準をクリアしており、さらにFMO計算との連携も既に取れているために、実タンパク質への応用も出来ている。一例を挙げると、HIV-1プロテアーゼ(198残基)に阻害剤が結合した系のFMO-CCD/6-31G計算が64コアのPCクラスター上でも6日間で完走するレベルであり、かっては想像すら出来なかったタンパク質のCC計算が本研究によって実現されたインパクトは極めて大きい。励起状態の計算では、CIS(D)の繰込み修正を発展させた他、計算コストを低減しつつ精度を保持する新しいアプローチとして2体および3体の励起エネルギー補正法を実装し、蛍光タンパク質群についてテスト計算を行って良好な結果を得た。
      FMO-MD関係では、3体のエネルギーと力の補正を実装し、水和系のシミュレーションの信頼性を大幅に改善することに成功した。応用例を示すと、Zn(II)イオンに64個の水を水和させた液滴モデルをHF/6-31Gレベルでシミュレーションしたところ、コレまでの2体ではZn-0距離の平均値は2.09A、3体では2.05Aとなり、実験値の2.06±0.02Aとの対応において後者が勝ることは明らかである。また、懸案であったMP2のエネルギー微分計算の高速並列エンジンの開発にも成功しており、FMO-MDの信頼性が電子相関導入の点からも高められた。

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    • 新規な非経験的分子動力学計算手法の開発と生命化学と物質科学への応用

      海外  立教大学学術推進特別重点資金(立教SFR) 

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      2006年4月 - 2008年3月

      資金種別:競争的資金

      自由プロジェクト研究
      代表研究者

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    • 新規FMO計算手法の開発とその応用-FMOに基づく多配置SCF法ならびに分子物性値計算手法の実装、蛋白質ならびに凝集系へのFMO計算の応用-

      (独)科学技術振興機構  (独)科学技術振興機構 

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      2006年4月 - 2007年3月

      資金種別:競争的資金

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