大規模・高精度な第一原理計算による超秩序構造の機能解明とデザイン

• Project Area: Progressive condensed matter physics inspired by hyper-ordered structures
• Project/Area Number: 20H05883
• Research Category: Grant-in-Aid for Transformative Research Areas (A)
• Allocation Type: Single-year Grants
• Review Section: Transformative Research Areas, Section (II)
• Research Institution: National Institute for Materials Science
• Principal Investigator: 中田 彩子 国立研究開発法人物質・材料研究機構, ナノアーキテクトニクス材料研究センター, 主幹研究員 (20595152)
• Co-Investigator(Kenkyū-buntansha): 鷹野 優 広島市立大学, 情報科学研究科, 教授 (30403017) ; 森川 良忠 大阪大学, 大学院工学研究科, 教授 (80358184)
• Project Period (FY): 2020-11-19 – 2025-03-31
• Project Status: Granted (Fiscal Year 2024)
• Budget Amount: ¥137,540,000 (Direct Cost: ¥105,800,000、Indirect Cost: ¥31,740,000); Fiscal Year 2024: ¥26,910,000 (Direct Cost: ¥20,700,000、Indirect Cost: ¥6,210,000); Fiscal Year 2023: ¥35,490,000 (Direct Cost: ¥27,300,000、Indirect Cost: ¥8,190,000); Fiscal Year 2022: ¥26,780,000 (Direct Cost: ¥20,600,000、Indirect Cost: ¥6,180,000); Fiscal Year 2021: ¥26,130,000 (Direct Cost: ¥20,100,000、Indirect Cost: ¥6,030,000); Fiscal Year 2020: ¥22,230,000 (Direct Cost: ¥17,100,000、Indirect Cost: ¥5,130,000)
• Keywords: 第一原理計算 / 大規模第一原理計算 / 化学反応計算 / 分子動力学計算 / 超秩序構造 / 大域的構造探索 / 金属含有タンパク質 / 物性物理 / 理論化学 / 巨大誘電応答 / 酸化物 / 化学反応解析

Outline of Research at the Start

近年、ナノスケールでの中距離秩序構造である「超秩序構造」が非晶質や生体材料、複合欠陥等の中距離非周期構造を持つ材料の物性・機能に寄与することが指摘されつつある。
本研究では、超秩序構造を持つ物質の詳細な構造、物性や反応性を独自の大規模第一原理計算手法、分子動力学計算、遷移状態理論に基づく化学反応解析、高精度に解明、予測する。
得られる知見に基づき、実験研究や機械学習による研究と連携しながら新規超秩序構造物質のデザインを目指す。

Outline of Annual Research Achievements

本研究班の2023年度の研究実績を以下に示す。
物質・材料研究機構のグループではMORゼオライト骨格におけるN2O吸着について、CaカチオンのN2O分子吸着における優位性と電子状態、分子構造変化の関連性を示した。また、シリカ系のアモルファス構造作成過程における圧力効果に対して第一原理分子動力学による解析を行った。本課題で用いてきた独自の教師なし次元削減手法による局所構造解析を行うことにより、アモルファス構造に圧力印加して得られた構造と作成過程で圧力印加した構造は大きく異なることを示した。
阪大のグループでは、誘電材料における異種元素ドープによる巨大誘電応答に関して研究を進めた。TiO2中にドープされたNbはTiサイトに入り、5価のイオンとなり、電子を格子に一つ出してポーラロンを生じる。精密な計算結果から、室温ではNbから離れて自由に結晶中を動き回り低温ではNbの最近接サイトに束縛されることがわかった。しかしながらこのポーラロンは、極低温においても外部電場に応答して動くことが可能であり、誘電率の増強を見積もると、実験的に報告されている値とかなりよく合うことが判明した。これは極低温での新たな巨大誘電応答の機構である。
広島市大のグループでは、金属含有タンパク質内の「超秩序構造」が生み出す機能の解明に取り組んだ。植物型フェレドキシン内の[2Fe-2S]クラスターに関して、量子化学計算およびアンブレラサンプリングシミュレーションを使用することによって還元時に起こる立体構造変化過程のエネルギー変化について明らかにした。また、ヘムについては、データベースPyDISHの自動更新を可能にし、機械学習・深層学習を用いてヘムタンパク質の機能分類器の作成・評価を行った。さらには脱窒に関わるヘムタンパク質であるP450norの中間体構造から亜酸化窒素を生成する反応過程を量子化学計算により明らかにした。

Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

全てのメンバーが実験との共同研究について議論し、進捗が見られている。装置の導入や研究員の雇用も順調に行われた。

Strategy for Future Research Activity

物質・材料研究機構ではゼオライトの分子吸着に関して、領域内のトポロジー解析と連携しながら、格子の形状と吸着性能との相関の解析を行う。また、大規模第一原理計算と統計解析により、担持ナノ粒子における担体欠陥の電子状態への影響を解析する。反強誘電体を示す新規材料の探索にも取り組む。ガラス系の構造モデリングに対しては、以前から取り組んできたシリカ系に加えてアルミナ系の非周期構造に対する圧力効果を明らかにする。本研究課題で取り組んできた局所構造解析をこれらの複合系に対しても行い、これらの物質群における構造形成のメカニズム解明に取り組む。
大阪大学ではTiO2に異種元素をドープした系の巨大誘電応答について引き続き研究を進める。Nbを単原子でドープした際に誘電率の増強について、新たな機構を見出したが、エネルギー汎函数への依存性が大きい。そこで、エネルギー汎函数の精度についてさらに精密に検討を加える。さらに、極低温で起こる現象であるので、量子効果も大きいと考えられ、量子効果の影響について丹念に研究を行う。加えて、別の元素をドープした場合についても系統的に検討を行う。
広島市大では生体超秩序構造として考えられる金属タンパク質の活性サイトの電子状態や構造歪みによるタンパク質の構造や機能への影響を分子シミュレーションや機械学習を用い明らかにする。植物型フェレドキシンについてはA01班と連携し、これまで実験的に解明されていない還元型フェレドキシンと電子受容タンパク質との複合体構造や相互作用様式を分子シミュレーションによって解明し、電子伝達機構の解明を目指す。ヘムタンパク質に関しては、データベースPyDISHの拡張を進めるとともに、タンパク質のポケット構造およびヘムの構造とヘムタンパク質機能の構造機能相関の解明を進める。

Research Products

• [Int'l Joint Research] ロンドン大学(英国)
• [Int'l Joint Research] ボルドー大学(フランス)
• [Int'l Joint Research] マレーシア科學大学(マレーシア)
• [Int'l Joint Research] バンドン工科大学(インドネシア)
• [Int'l Joint Research] ロンドン大学(英国)
• [Int'l Joint Research] ボルドー大学(フランス)
• [Int'l Joint Research] マレーシア科學大学(マレーシア)
• [Int'l Joint Research] バンドン工科大学(インドネシア)
• [Int'l Joint Research] ロンドン大学(英国)
• [Int'l Joint Research] ボルドー大学(フランス)
• [Int'l Joint Research] マレーシア科學大学(マレーシア)
• [Int'l Joint Research] バンドン工科大学(インドネシア)
• [Int'l Joint Research] ロンドン大学(英国)
• [Int'l Joint Research] ボルドー大学(フランス)
• [Journal Article] C?H bond dissociation enthalpy prediction with machine learning reinforced semi-empirical quantum mechanical calculations (2024)
  • Author(s): Kaneko Miki、Takano Yu、Saito Toru
  • Journal Title: Chemistry Letters Volume: 53 Issue: 2
  • DOI: 10.1093/chemle/upae016
  • Peer Reviewed / Open Access
• [Journal Article] Stability of PdxOy Particles Supported on Strontium Titanate Perovskite under Three-Way Catalyst Operating Conditions: Implications for Sintering Resistance (2024)
  • Author(s): Thanh Ngoc Pham, Beatriz Andrea Choi Tan, Yuji Hamamoto, KoujiInagaki, Ikutaro Hamada,and Yoshitada Morikawa
  • Journal Title: ACS Catalysis Volume: 14 Issue: 3 Pages: 1443-1458
  • DOI: 10.1021/acscatal.3c05673
  • Peer Reviewed / Open Access
• [Journal Article] Large-scale DFT calculations of multi-component glass systems (SiO2)0.70(Al2O3)0.13(XO)0.17 (X = Mg, Ca, Sr, Ba) : Accuracy of classical force fields (2024)
  • Author(s): Tanaka Atsushi、Saito Atsuki、Murata Takashi、Nakata Ayako、Miyazaki Tsuyoshi
  • Journal Title: Journal of Non-Crystalline Solids Volume: 625 Pages: 122714-122714
  • DOI: 10.1016/j.jnoncrysol.2023.122714
  • Peer Reviewed / Open Access
• [Journal Article] Unveiling a medium-range structural commonality of amorphous alloys (2024)
  • Author(s): Nishio Kengo、Lu Anh Khoa Augustin
  • Journal Title: Journal of Non-Crystalline Solids Volume: 624 Pages: 122696-122696
  • DOI: 10.1016/j.jnoncrysol.2023.122696
  • Peer Reviewed / Open Access
• [Journal Article] On atomic segregation in metallic glasses induced by shear deformation: A computer simulation study (2024)
  • Author(s): Zanaeva E.N.、Lu A.K.A.、Louzguine-Luzgin D.V.
  • Journal Title: Computational Materials Science Volume: 238 Pages: 112923-112923
  • DOI: 10.1016/j.commatsci.2024.112923
  • Peer Reviewed
• [Journal Article] Origin of the Surface Facet Dependence in the Oxidative Etching of the Diamond (111) and (100) Surfaces from First-Principles Calculations (2024)
  • Author(s): Enriquez John Isaac G.、Yamasaki Takahiro、Michiuchi Masato、Inagaki Kouji、Geshi Masaaki、Hamada Ikutaro、Morikawa Yoshitada
  • Journal Title: The Journal of Physical Chemistry C Volume: 128 Issue: 15 Pages: 6294-6308
  • DOI: 10.1021/acs.jpcc.3c08378
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Extraction of local structure differences in silica based on unsupervised learning (2024)
  • Author(s): Lu Anh Khoa Augustin、Lin Jianbo、Futamura Yasunori、Sakurai Tetsuya、Tamura Ryo、Miyazaki Tsuyoshi
  • Journal Title: Physical Chemistry Chemical Physics Volume: 26 Issue: 15 Pages: 11657-11666
  • DOI: 10.1039/d3cp06298h
  • Peer Reviewed / Open Access
• [Journal Article] Random Forest Classifier of Heme Proteins Using Porphyrin Distortions and Axial Ligands of Heme (2023)
  • Author(s): Fujikawa Hinako、Kondo Hiroko X.、Kanematsu Yusuke、Takano Yu
  • Journal Title: Chemistry Letters Volume: 52 Issue: 6 Pages: 503-507
  • DOI: 10.1246/cl.230150
  • Peer Reviewed / Open Access
• [Journal Article] Origin of unexpected Ir3+ in superconducting candidate Sr2IrO4 analyzed by photoelectron holography (2023)
  • Author(s): R. Horie, T. Matsushita, S. Kawamura, T. Hase K. Horigane, H. Momono, S. Takeuchi, H. Tomita, Y. Hashimoto, K. Kobayashi, Y. Haruyama, H. Daimon, Y. Morikawa, M. Taguchi, J. Akimitsu
  • Journal Title: Inorganic Chemistry Volume: 62 Issue: 28 Pages: 10897-10904
  • DOI: 10.1021/acs.inorgchem.2c03788
  • Peer Reviewed
• [Journal Article] Polymorphs of Titanium Dioxide: An Assessment of the Variants of Projector Augmented Wave Potential of Titanium on Their Geometric and Dielectric Properties (2023)
  • Author(s): Varadwaj Pradeep R.、Dinh Van An、Morikawa Yoshitada、Asahi Ryoji
  • Journal Title: ACS Omega Volume: 8 Issue: 24 Pages: 22003-22017
  • DOI: 10.1021/acsomega.3c02038
  • Peer Reviewed / Open Access
• [Journal Article] Electronic and optical properties of the hydrogen boride sheet from the many-body perturbation theory (2023)
  • Author(s): Thi Ta Luong、Morikawa Yoshitada、Hamada Ikutaro
  • Journal Title: Journal of Physics: Condensed Matter Volume: 35 Issue: 43 Pages: 435002-435002
  • DOI: 10.1088/1361-648x/ace8e3
  • Peer Reviewed
• [Journal Article] Determination of hyper-parameters in the atomic descriptors for efficient and robust molecular dynamics simulations with machine learning forces (2023)
  • Author(s): Lin Jianbo、Tamura Ryo、Futamura Yasunori、Sakurai Tetsuya、Miyazaki Tsuyoshi
  • Journal Title: Physical Chemistry Chemical Physics Volume: 25 Issue: 27 Pages: 17978-17986
  • DOI: 10.1039/d3cp01922e
  • Peer Reviewed
• [Journal Article] Roadmap on electronic structure codes in the exascale era (2023)
  • Author(s): Gavini Vikram、Baroni Stefano、Blum Volker、et al.
  • Journal Title: Modelling and Simulation in Materials Science and Engineering Volume: 31 Issue: 6 Pages: 063301-063301
  • DOI: 10.1088/1361-651x/acdf06
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 超秩序構造の理論計算による解明に向けて-第一原理計算や分子動力学、機械学習による解析- (2023)
  • Author(s): 中田彩子、宮崎剛、鷹野優、森川良忠
  • Journal Title: CERAMICS JAPAN Volume: 58 Pages: 522-526
• [Journal Article] Machine learning molecular dynamics simulation of CO-driven formation of Cu clusters on the Cu(111) surface (2023)
  • Author(s): Halim Harry H、Ueda Ryo、Morikawa Yoshitada
  • Journal Title: Journal of Physics: Condensed Matter Volume: 35 Issue: 49 Pages: 495001-495001
  • DOI: 10.1088/1361-648x/acf2d8
  • Peer Reviewed
• [Journal Article] Computational Exploration of Minimum Energy Reaction Pathway of N2O Formation from Intermediate I of P450nor Using an Active Center Model (2023)
  • Author(s): Kanematsu Yusuke、Kondo Hiroko X.、Takano Yu
  • Journal Title: International Journal of Molecular Sciences Volume: 24 Issue: 24 Pages: 17172-17172
  • DOI: 10.3390/ijms242417172
  • Peer Reviewed / Open Access
• [Journal Article] Semi-empirical and machine learning-based prediction of site of metabolisms mediated by aldehyde oxidase (2023)
  • Author(s): Shiotake Yuto、Takano Yu、Saito Toru
  • Journal Title: Chemical Physics Letters Volume: 833 Pages: 140942-140942
  • DOI: 10.1016/j.cplett.2023.140942
  • Peer Reviewed / Open Access
• [Journal Article] First-Principles Microkinetic Study of NO Reduction on Cu Catalysts (2023)
  • Author(s): Al Fauzan Muhammad Rifqi、Pham Thanh Ngoc、Halim Harry Handoko、Hamamoto Yuji、Inagaki Kouji、Hamada Ikutaro、Morikawa Yoshitada
  • Journal Title: The Journal of Physical Chemistry C Volume: 127 Issue: 39 Pages: 19451-19467
  • DOI: 10.1021/acs.jpcc.3c02820
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] DFT investigation of the oxygen reduction reaction over nitrogen (N) doped graphdiyne as an electrocatalyst: the importance of pre-adsorbed OH* and the solvation effect (2023)
  • Author(s): Wang Yuelin、Pham Thanh Ngoc、Halim Harry H.、Yan Likai、Morikawa Yoshitada
  • Journal Title: Materials Advances Volume: 4 Issue: 24 Pages: 6542-6552
  • DOI: 10.1039/d3ma00502j
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Development of serial X-ray fluorescence holography for radiation-sensitive protein crystals (2023)
  • Author(s): Ang Artoni Kevin R.、Umena Yasufumi、Sato-Tomita Ayana、Shibayama Naoya、Happo Naohisa、Marumi Riho、Yamamoto Yuta、Kimura Koji、Kawamura Naomi、Takano Yu、Matsushita Tomohiro、Sasaki Yuji C.、Shen Jian-Ren、Hayashi Kouichi
  • Journal Title: Journal of Synchrotron Radiation Volume: 30 Issue: 2 Pages: 368-378
  • DOI: 10.1107/s1600577522011833
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Prediction of Protein Function from Tertiary Structure of the Active Site in Heme Proteins by Convolutional Neural Network (2023)
  • Author(s): Kondo Hiroko X.、Iizuka Hiroyuki、Masumoto Gen、Kabaya Yuichi、Kanematsu Yusuke、Takano Yu
  • Journal Title: Biomolecules Volume: 13 Issue: 1 Pages: 137-137
  • DOI: 10.3390/biom13010137
  • Peer Reviewed / Open Access
• [Journal Article] Negative fragmentation approach for investigating the depolarization effect of neighboring residues on hydrogen bonds in π-helix (2023)
  • Author(s): Kondo Hiroko X.、Nakamura Haruki、Takano Yu
  • Journal Title: Chemical Physics Letters Volume: 815 Pages: 140361-140361
  • DOI: 10.1016/j.cplett.2023.140361
  • Peer Reviewed / Open Access
• [Journal Article] Unraveling Binding Mechanism and Stability of Urease Inhibitors: A QM/MM MD Study (2023)
  • Author(s): Suenaga Shunya、Takano Yu、Saito Toru
  • Journal Title: Molecules Volume: 28 Issue: 6 Pages: 2697-2697
  • DOI: 10.3390/molecules28062697
  • Peer Reviewed / Open Access
• [Journal Article] Atomic Imaging of Interface Defects in an Insulating Film on Diamond (2023)
  • Author(s): Fujii Mami N.、Tanaka Masaki、Tsuno Takumi、Hashimoto Yusuke、Tomita Hiroto、Takeuchi Soichiro、Koga Shunjo、Sun Zexu、Enriquez John Isaac、Morikawa Yoshitada、Mizuno Jun、Uenuma Mutsunori、Uraoka Yukiharu、Matsushita Tomohiro
  • Journal Title: Nano Letters Volume: 23 Issue: 4 Pages: 1189-1194
  • DOI: 10.1021/acs.nanolett.2c04176
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] The quantitative study of methane adsorption on the Pt(997) step surface as the initial process for reforming reactions (2023)
  • Author(s): Choi Young Hyun、Putra Septia Eka Marsha、Shiozawa Yuichiro、Tanaka Shunsuke、Mukai Kozo、Hamada Ikutaro、Morikawa Yoshitada、Yoshinobu Jun
  • Journal Title: Surface Science Volume: 732 Pages: 122284-122284
  • DOI: 10.1016/j.susc.2023.122284
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Structures and mechanisms of actin ATP hydrolysis (2022)
  • Author(s): Kanematsu Yusuke、Narita Akihiro、Oda Toshiro、Koike Ryotaro、Ota Motonori、Takano Yu、Moritsugu Kei、Fujiwara Ikuko、Tanaka Kotaro、Komatsu Hideyuki、Nagae Takayuki、Watanabe Nobuhisa、Iwasa Mitsusada、Ma?da Yuichiro、Takeda Shuichi
  • Journal Title: Proceedings of the National Academy of Sciences Volume: 119 Issue: 43
  • DOI: 10.1073/pnas.2122641119
  • Peer Reviewed / Open Access
• [Journal Article] Predicting Reaction Mechanisms for the Threonine-Residue Stereoinversion Catalyzed by a Dihydrogen Phosphate Ion (2022)
  • Author(s): Nakayoshi Tomoki、Kato Koichi、Kurimoto Eiji、Takano Yu、Oda Akifumi
  • Journal Title: ACS Omega Volume: 7 Issue: 22 Pages: 18306-18314
  • DOI: 10.1021/acsomega.2c00372
  • Peer Reviewed / Open Access
• [Journal Article] Evaluation of an Appropriate Standard Hydrogen Electrode Potential for Computing Redox Potentials of Catechins with Density Functional Theory (2022)
  • Author(s): Duan Lian、Takano Yu、Shigeta Yasuteru
  • Journal Title: Chemistry Letters Volume: 51 Issue: 7 Pages: 673-677
  • DOI: 10.1246/cl.220165
  • Peer Reviewed / Open Access
• [Journal Article] Structure of Heme-binding Pocket in Heme Protein is Generally Rigid and can be Predicted by AlphaFold2 (2022)
  • Author(s): Kondo Hiroko X.、Kanematsu Yusuke、Takano Yu
  • Journal Title: Chemistry Letters Volume: 51 Issue: 7 Pages: 704-708
  • DOI: 10.1246/cl.220172
  • Peer Reviewed / Open Access
• [Journal Article] Large-Scale DFT Methods for Calculations of Materials with Complex Structures (2022)
  • Author(s): Nakata Ayako、Bowler David R.、Miyazaki Tsuyoshi
  • Journal Title: Journal of the Physical Society of Japan Volume: 91 Issue: 9 Pages: 91011-91011
  • DOI: 10.7566/jpsj.91.091011
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Depolarizing Effects in Hydrogen Bond Energy in 310-Helices Revealed by Quantum Chemical Analysis (2022)
  • Author(s): Kondo Hiroko X.、Nakamura Haruki、Takano Yu
  • Journal Title: International Journal of Molecular Sciences Volume: 23 Issue: 16 Pages: 9032-9032
  • DOI: 10.3390/ijms23169032
  • Peer Reviewed / Open Access
• [Journal Article] Elucidation of the Correlation between Heme Distortion and Tertiary Structure of the Heme-Binding Pocket Using a Convolutional Neural Network (2022)
  • Author(s): Kondo Hiroko X.、Iizuka Hiroyuki、Masumoto Gen、Kabaya Yuichi、Kanematsu Yusuke、Takano Yu
  • Journal Title: Biomolecules Volume: 12 Issue: 9 Pages: 1172-1172
  • DOI: 10.3390/biom12091172
  • Peer Reviewed / Open Access
• [Journal Article] Conformational Preference of Flavonols and Its Effect on the Chemical Properties Involved in Radical Scavenging Activity (2022)
  • Author(s): Kondo Hiroko X.、Takano Yu
  • Journal Title: Chemistry Volume: 4 Issue: 4 Pages: 1123-1135
  • DOI: 10.3390/chemistry4040076
  • Peer Reviewed / Open Access
• [Journal Article] Hydrogenation of Formate Species Using Atomic Hydrogen on a Cu(111) Model Catalyst (2022)
  • Author(s): Kotaro Takeyasu, Yasutaka Sawaki, Takumi Imabayashi, Septia Eka Marsha Putra, Harry Handoko Halim, Jiamei Quan, Yuji Hamamoto, Ikutaro Hamada, Yoshitada Morikawa, Takahiro Kondo, Tadahiro Fujitani, and Junji Nakamura
  • Journal Title: Journal of the American Chemical Society Volume: 144 Issue: 27 Pages: 12158-12166
  • DOI: 10.1021/jacs.2c02797
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Density functional theory study of NO-H2O coadsorption on Cu(111) (2022)
  • Author(s): Pham Thanh Ngoc、Hamamoto Yuji、Inagaki Kouji、Hamada Ikutaro、Morikawa Yoshitada
  • Journal Title: Physical Review Materials Volume: 6 Issue: 7 Pages: 75801-75801
  • DOI: 10.1103/physrevmaterials.6.075801
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Activity and selectivity of N2 fixation on B doped g-C9N10: a density functional theory study (2022)
  • Author(s): Wang Yuelin、Pham Thanh Ngoc、Yan Likai、Morikawa Yoshitada
  • Journal Title: Journal of Materials Chemistry C Volume: 10 Issue: 32 Pages: 11791-11800
  • DOI: 10.1039/d2tc02041f
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Elucidation of Cu-Zn Surface Alloying on Cu(997) by Machine-Learning Molecular Dynamics (2022)
  • Author(s): Halim Harry H.、Morikawa Yoshitada
  • Journal Title: ACS Physical Chemistry Au Volume: 2 Issue: 5 Pages: 430-447
  • DOI: 10.1021/acsphyschemau.2c00017
  • Peer Reviewed / Open Access
• [Journal Article] Effects of Active-Center Reduction of Plant-Type Ferredoxin on Its Structure and Dynamics: Computational Analysis Using Molecular Dynamics Simulations (2022)
  • Author(s): Nakayoshi Tomoki、Ohnishi Yusuke、Tanaka Hideaki、Kurisu Genji、Kondo Hiroko X.、Takano Yu
  • Journal Title: International Journal of Molecular Sciences Volume: 23 Issue: 24 Pages: 15913-15913
  • DOI: 10.3390/ijms232415913
  • Peer Reviewed / Open Access
• [Journal Article] Quantum chemical studies on hydrogen bonds in helical secondary structures (2022)
  • Author(s): Takano Yu、Kondo Hiroko X.、Nakamura Haruki
  • Journal Title: Biophysical Reviews Volume: 14 Issue: 6 Pages: 1369-1378
  • DOI: 10.1007/s12551-022-01034-5
  • Peer Reviewed / Open Access
• [Journal Article] Crystal nucleation and growth processes in Cu-rich glass-forming Cu-Zr alloys (2022)
  • Author(s): Lu A. K. A.、Louzguine-Luzgin D. V.
  • Journal Title: The Journal of Chemical Physics Volume: 157 Issue: 1 Pages: 014506-014506
  • DOI: 10.1063/5.0097023
  • Peer Reviewed / Open Access
• [Journal Article] Phosphorus-Alloying as a Powerful Method for Designing Highly Active and Durable Metal Nanoparticle Catalysts for the Deoxygenation of Sulfoxides: Ligand and Ensemble Effects of Phosphorus (2022)
  • Author(s): H. Ishikawa, S. Yamaguchi, A. Nakata, K. Nakajima, S. Yamazoe, J. Yamasaki, T. Mizugaki, T. Mitsudome
  • Journal Title: JACS Au Volume: 2 Issue: 2 Pages: 419-427
  • DOI: 10.1021/jacsau.1c00461
  • Peer Reviewed / Open Access
• [Journal Article] Analysis of Fluctuation in the Heme-Binding Pocket and Heme Distortion in Hemoglobin and Myoglobin (2022)
  • Author(s): Kondo Hiroko X.、Takano Yu
  • Journal Title: Life Volume: 12 Issue: 2 Pages: 210-210
  • DOI: 10.3390/life12020210
  • Peer Reviewed / Open Access
• [Journal Article] Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket (2022)
  • Author(s): Kondo Hiroko X.、Fujii Masanori、Tanioka Takuma、Kanematsu Yusuke、Yoshida Takashi、Takano Yu
  • Journal Title: Journal of Chemical Information and Modeling Volume: 62 Issue: 4 Pages: 775-784
  • DOI: 10.1021/acs.jcim.1c01315
  • Peer Reviewed
• [Journal Article] QM/MM Molecular Dynamics Simulations Revealed Catalytic Mechanism of Urease (2022)
  • Author(s): Saito Toru、Takano Yu
  • Journal Title: The Journal of Physical Chemistry B Volume: 126 Issue: 10 Pages: 2087-2097
  • DOI: 10.1021/acs.jpcb.1c10200
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Structural analysis based on unsupervised learning: Search for a characteristic low-dimensional space by local structures in atomistic simulations (2022)
  • Author(s): Tamura Ryo、Matsuda Momo、Lin Jianbo、Futamura Yasunori、Sakurai Tetsuya、Miyazaki Tsuyoshi
  • Journal Title: Physical Review B Volume: 105 Issue: 7 Pages: 1-18
  • DOI: 10.1103/physrevb.105.075107
  • Peer Reviewed
• [Journal Article] Theoretical Studies on the Effect of Isomerized Aspartic Acid Residues on the Three-Dimensional Structures of Bovine Pancreatic Ribonucleases A (2021)
  • Author(s): Nakayoshi Tomoki、Kato Koichi、Kurimoto Eiji、Oda Akifumi
  • Journal Title: Biological and Pharmaceutical Bulletin Volume: 44 Issue: 7 Pages: 967-975
  • DOI: 10.1248/bpb.b21-00083
  • NAID: 130008060364
  • ISSN: 0918-6158, 1347-5215
  • Year and Date: 2021-07-01
  • Peer Reviewed / Open Access
• [Journal Article] The Emergence of Multiple Coordination Numbers in Gold-Cyanoarene Complexes: A Study of the On-Surface Coordination Mechanism (2021)
  • Author(s): Nakanishi Waka、Nakata Ayako、Perez Paola、Takeuchi Masayuki、Joachim Christian、Sagisaka Keisuke
  • Journal Title: The Journal of Physical Chemistry C Volume: 125 Issue: 18 Pages: 9937-9946
  • DOI: 10.1021/acs.jpcc.1c02456
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Short-lived intermediate in N2O generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography (2021)
  • Author(s): Nomura, T., Kimura, T., Kanematsu, Y., Yamada, D., Yamashita, K., Hirata, K., Ueno, G., Murakami, H., Hisano, T., Yamagiwa, R., Takeda, H., Gopalasingam, C., Kousaka, R., Yanagisawa, S., Shoji, O., Kumasaka, T., Yamamoto, M., Takano, Y., Sugimoto, H., Tosha, T., Kubo, M., Shiro, Y
  • Journal Title: Proceedings of the National Academy of Sciences Volume: 118 Issue: 21
  • DOI: 10.1073/pnas.2101481118
  • Peer Reviewed / Open Access
• [Journal Article] Molecular dynamics simulations for the protein-ligand complex structures obtained by computational docking studies using implicit or explicit solvents (2021)
  • Author(s): Kato Koichi、Nakayoshi Tomoki、Kurimoto Eiji、Oda Akifumi
  • Journal Title: Chemical Physics Letters Volume: 781 Pages: 139022-139022
  • DOI: 10.1016/j.cplett.2021.139022
  • Peer Reviewed
• [Journal Article] Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2 (2021)
  • Author(s): Nakayoshi Tomoki、Kato Koichi、Kurimoto Eiji、Oda Akifumi
  • Journal Title: International Journal of Molecular Sciences Volume: 22 Issue: 18 Pages: 9837-9837
  • DOI: 10.3390/ijms22189837
  • Peer Reviewed / Open Access
• [Journal Article] Adsorption of toxic gases on borophene: surface deformation links to chemisorptions (2021)
  • Author(s): Ta Luong Thi、Hamada Ikutaro、Morikawa Yoshitada、Dinh Van An
  • Journal Title: RSC Advances Volume: 11 Issue: 30 Pages: 18279-18287
  • DOI: 10.1039/d1ra02738g
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Theoretical study on adsorption and reaction of polymeric formic acid on the Cu(111) surface (2021)
  • Author(s): Putra Septia Eka Marsha、Muttaqien Fahdzi、Hamamoto Yuji、Inagaki Kouji、Shiotari Akitoshi、Yoshinobu Jun、Morikawa Yoshitada、Hamada Ikutaro
  • Journal Title: Physical Review Materials Volume: 5 Issue: 7 Pages: 75801-75801
  • DOI: 10.1103/physrevmaterials.5.075801
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A flat-lying dimer as a key intermediate in NO reduction on Cu(100) (2021)
  • Author(s): Kuroishi Kenta、Al Fauzan Muhammad Rifqi、Pham Thanh Ngoc、Wang Yuelin、Hamamoto Yuji、Inagaki Kouji、Shiotari Akitoshi、Okuyama Hiroshi、Hatta Shinichiro、Aruga Tetsuya、Hamada Ikutaro、Morikawa Yoshitada
  • Journal Title: Physical Chemistry Chemical Physics Volume: 23 Issue: 31 Pages: 16880-16887
  • DOI: 10.1039/d1cp02746h
  • Peer Reviewed
• [Journal Article] Isotope effect of methane adsorbed on fcc metal (1 1 1) surfaces (2021)
  • Author(s): Putra Septia Eka Marsha、Morikawa Yoshitada、Hamada Ikutaro
  • Journal Title: Chemical Physics Letters Volume: 780 Pages: 138943-138943
  • DOI: 10.1016/j.cplett.2021.138943
  • Peer Reviewed
• [Journal Article] Hydrotalcite-Supported Cobalt Phosphide Nanorods as a Highly Active and Reusable Heterogeneous Catalyst for Ammonia-Free Selective Hydrogenation of Nitriles to Primary Amines (2021)
  • Author(s): M. Sheng, S. Yamaguchi, A. Nakata, S. Yamazoe, K. Nakajima, J. Yamasaki, T. Mizugaki, T. Mitsudome
  • Journal Title: ACS Sustainable Chemistry & Engineering Volume: 33 Issue: 33 Pages: 11238-11246
  • DOI: 10.1021/acssuschemeng.1c03667
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Dry Reforming of Methane on Cobalt Catalysts: DFT-Based Insights into Carbon Deposition Versus Removal (2021)
  • Author(s): Wong YeeJie、Halim Harry H.、Khairudin N. Fazila、Pham Thanh Ngoc、Putra Septia E. M.、Hamamoto Yuji、Inagaki Kouji、Hamada Ikutaro、Mohamed Abdul Rahman、Morikawa Yoshitada
  • Journal Title: The Journal of Physical Chemistry C Volume: 125 Issue: 40 Pages: 21902-21913
  • DOI: 10.1021/acs.jpcc.1c04819
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Deciphering Structural Alterations Associated with Activity Reductions of Genetic Polymorphisms in Cytochrome P450 2A6 Using Molecular Dynamics Simulations (2021)
  • Author(s): Kato Koichi、Nakayoshi Tomoki、Nokura Rika、Hosono Hiroki、Hiratsuka Masahiro、Ishikawa Yoshinobu、Kurimoto Eiji、Oda Akifumi
  • Journal Title: International Journal of Molecular Sciences Volume: 22 Issue: 18 Pages: 10119-10119
  • DOI: 10.3390/ijms221810119
  • Peer Reviewed / Open Access
• [Journal Article] Computational Analysis of the Mechanism of Nonenzymatic Peptide Bond Cleavage at the C-Terminal Side of an Asparagine Residue (2021)
  • Author(s): Kato Koichi、Nakayoshi Tomoki、Ishikawa Yoshinobu、Kurimoto Eiji、Oda Akifumi
  • Journal Title: ACS Omega Volume: 6 Issue: 44 Pages: 30078-30084
  • DOI: 10.1021/acsomega.1c04821
  • Peer Reviewed / Open Access
• [Journal Article] Adsorption of CO2 on Pt terrace surface, stepped, and defective sites: A combined TPD and DFT study (2021)
  • Author(s): Wong YeeJie、Choi Young Hyun、Tanaka Shunsuke、Yoshioka Haruka、Mukai Kozo、Halim Harry H.、Mohamed Abdul Rahman、Inagaki Kouji、Hamamoto Yuji、Hamada Ikutaro、Yoshinobu Jun、Morikawa Yoshitada
  • Journal Title: The Journal of Physical Chemistry C Volume: 125 Issue: 43 Pages: 23657-23668
  • DOI: 10.1021/acs.jpcc.1c05228
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Spin‐projected QM/MM Free Energy Simulations for Oxidation Reaction of Guanine in B?DNA by Singlet Oxygen (2021)
  • Author(s): Saito Toru、Takano Yu
  • Journal Title: ChemPhysChem Volume: 22 Issue: 6 Pages: 561-568
  • DOI: 10.1002/cphc.202000978
  • Peer Reviewed / Open Access
• [Presentation] Large-scale DFT calculations for nanoarchitectonics (2024)
  • Author(s): Ayako Nakata
  • Organizer: APS March Meeting 2024
  • Int'l Joint Research / Invited
• [Presentation] Large-scale DFT calculations using CONQUEST code for materials with complex structures (2024)
  • Author(s): Ayako Nakata
  • Organizer: International Workshop on Massively Parallel Programming for Quantum Chemistry and Physics (MPQCP2024)
  • Int'l Joint Research / Invited
• [Presentation] 大規模DFT計算手法の開発とナノ材料への応用 (2023)
  • Author(s): 中田彩子
  • Organizer: アトムハイブリッドシンポジウム
  • Invited
• [Presentation] Large-scale DFT calculations using multi-site support functions for materials with complex structures (2023)
  • Author(s): Ayako Nakata
  • Organizer: The 5th conference of Theory and Applications of Computational Chemistry (TACC 2023)
  • Int'l Joint Research / Invited
• [Presentation] Machine Learning Molecular Dynamics Simulation of CO-driven Formation of Cu Clusters on a Cu(111) Surface (2023)
  • Author(s): Yoshitada Morikawa
  • Organizer: 36th European Conference on Surface Science
  • Int'l Joint Research / Invited
• [Presentation] First-principles and machine-learning study of interface chemical reactions for energy and environmental problems (2023)
  • Author(s): Yoshitada Morikawa
  • Organizer: The 4th International Workshop in Advanced Materials and Devices -IWAMD 2023
  • Int'l Joint Research / Invited
• [Presentation] Hydrogenation process of CO2 on metal catalysts studied by combined first-principles and machine learning methods (2023)
  • Author(s): Yoshitada Morikawa
  • Organizer: The 48th Vietnam Conference on Theoretical Physics
  • Int'l Joint Research / Invited
• [Presentation] Large-scale DFT calculations for materials with complex structures (2023)
  • Author(s): Ayako Nakata
  • Organizer: The 6th China-Japan-Korea Workshop on Theoretical and Computational Chemistry
  • Int'l Joint Research / Invited
• [Presentation] Large-scale DFT calculations of materials with complex structures (2023)
  • Author(s): Ayako Nakata
  • Organizer: WE-Heraeus-Seminar: Beyond Imperfections: New Structure-Property Relationships in Ceramics and Glasses
  • Int'l Joint Research / Invited
• [Presentation] Theoretical Study of Hydrogenation Process of CO2 on Metal Catalysts (2023)
  • Author(s): Yoshitada Morikawa
  • Organizer: Surface Science Discussion 2023, Modern trends in surface science studies,
  • Int'l Joint Research / Invited
• [Presentation] Theoretical Study on the Dry Reforming of Methane (2022)
  • Author(s): Yoshitada Morikawa
  • Organizer: 6th International Conference on Catalysis and Chemical Engineering
  • Int'l Joint Research / Invited
• [Presentation] 実材料解析に向けた大規模DFT計算手法の開発と応用 (2022)
  • Author(s): 中田彩子
  • Organizer: 日本コンピュータ化学会20周年記念シンポジウム
  • Invited
• [Presentation] Theoretical Study of Hydrogenation Process of CO2 on Metal Catalysts (2022)
  • Author(s): Yoshitada Morikawa
  • Organizer: The 22nd International Vacuum Congress IVC-22
  • Int'l Joint Research / Invited
• [Presentation] Theoretical Study of Complex Nanostructures and Disordered Systems using a Large-Scale DFT code CONQUEST (2022)
  • Author(s): Tsuyoshi Miyazaki
  • Organizer: International Workshop on Exploration of Atomistic Disorder in Long-Range Ordered Systems and of Order in Disordered Materials
  • Int'l Joint Research / Invited
• [Presentation] Depolarizing effects in hydrogen bond energy in 310-helices revealed by quantum chemical analysis (2022)
  • Author(s): Yu Takano
  • Organizer: International Congress on Pure & Applied Chemistry Kota Kinabalu (ICPAC Kota Kinabalu 2022)
  • Int'l Joint Research / Invited
• [Presentation] Computational study of metal centers in proteins (2022)
  • Author(s): Yu Takano
  • Organizer: 10th Asian Biological Inorganic Chemistry Conference
  • Int'l Joint Research / Invited
• [Presentation] 大規模第一原理DFT計算による材料解析 (2022)
  • Author(s): 中田彩子
  • Organizer: 産研テクノサロン 第105回
  • Invited
• [Presentation] 計算科学による金属蛋白質活性中心の電子構造制御に関する研究－ヘムの構造歪みに関する構造機能相関－ (2021)
  • Author(s): 鷹野優
  • Organizer: CBI学会フォーカストセッション「金属タンパク質解析における構造生物学と量子化学計算の融合」
  • Invited
• [Presentation] Computational study of the structural-function relationship of heme proteins (2021)
  • Author(s): Yu Takano
  • Organizer: 第59回日本生物物理学会年会シンポジウム「実験と理論の共同による生命金属動態研究の最前線」
  • Invited
• [Presentation] Theoretical Study on Dry Reforming of Methane (2021)
  • Author(s): Yoshitada Morikawa
  • Organizer: Soedirman’s International Conference on Mathematics and Applied Sciences (SICoMAS 2021)
  • Int'l Joint Research / Invited
• [Presentation] 複雑、不規則材料のための大規模第一原理計算 (2021)
  • Author(s): 中田彩子
  • Organizer: 日本物理学会第76回年会
  • Invited
• [Presentation] Large-Scale DFT Calculations for Materials with ComplicatedStructures (2021)
  • Author(s): Ayako Nakata, Tsuyoshi Miyazaki, David R. Bowler
  • Organizer: MANA international symposium 2021 jointly with ICYS
  • Int'l Joint Research
• [Book] Density Functional Theory Calculations for Materials with Complex Structures (2023)
  • Author(s): Ayako Nakata, Yoshitada Morikawa
  • Total Pages: 30
  • Publisher: Springer
  • ISBN: 9789819952342
• [Book] Molecular dynamics (2023)
  • Author(s): Yu Takano, Takahiro Ohkubo, Satoshi Watanabe
  • Total Pages: 31
  • Publisher: Springer
  • ISBN: 9789819952342
• [Remarks] CONQUEST: Linear Scaling DFT
  • URL: http://www.order-n.org/