SHOJI Mitsuo
- Affiliation
- Center for Computational Sciences
- Official title
- Professor
- ORCID
- 0000-0001-7465-6326
- URL
- />D9@;:Tc_44D]EDF<F32]24];Aj
- Office
- Biophysics
- Phone
- 029-853-6259
- Research fields
Biological physics/Chemical physics/Soft matter physics Basic chemistry - Research keywords
Quantum Chemistry QM/MM 酵素反応 反応機構の理論解明 生物無機化学 多核金属錯体 Molecular Dynamics 分子磁性 - Research projects
生体内量子多体系における特異的化学反応の機構解明 2019-10 -- 2023-03 庄司光男 JST/JST-PRESTO 40,000,000Yen 自然・半導体・分子触媒で利用可能な多様な水分解反応機構の解明 2020-04 -- 2022-03 庄司光男 日本学術振興会/新学術領域研究(研究領域提案型) 3,900,000Yen 光化学系II酸素発生中心における再活性化機構についての理論的解明 2018-04 -- 2020-03 庄司 光男 Japan Society for the Promotion of Science/Grant-in-Aid for Scientific Research on Innovative Areas 5,200,000Yen 光化学系II酸素発生中心における水分解反応の全反応経路解明 2017-04 -- 2020-03 庄司 光男 Japan Society for the Promotion of Science/Grant-in-Aid for Young Scientists(A) 25,870,000Yen トレオニン合成酵素の全反応機構の理論的解明 2014-04 -- 2017-03 庄司 光男 Japan Society for the Promotion of Science/基盤研究(C) 5,070,000Yen 生体酵素における反応機構と反応制御機構解明のための理論的研究 2012-04 -- 2014-03 庄司光男 Japan Society of for the Promotion of Science/若手研究(B) 3,770,000Yen - Career history
2023-10 -- (current) 筑波大学計算科学研究センター教授 2019-10 -- 2023-03 JSTPRESTO研究員(兼任) 2016-04 -- 2023-09 筑波大学計算科学研究センター助教 2011-10 -- 2016-03 筑波大学数理物質系助教 2010-07 -- 2011-09 筑波大学数理物質科学研究科助教 2008-04 -- 2010-06 日本学術振興会特別研究員(PD) 2007-04 -- 2008-03 日本学術振興会特別研究員(PD) 2006-04 -- 2007-03 日本学術振興会特別研究員(DC2) - Academic background
-- 2007-03 大阪大学 理学研究科 博士課程 - Degree
2007-03 博士(理学) 大阪大学 - Academic societies
2021 -- (current) 量子生命科学会 2018 -- (current) The Molecular Simulation Society of Japan 2014 -- (current) 理論化学研究会 2012 -- 2021-03 PROTEIN SCIENCE SOCIETY OF JAPAN 2011 -- (current) THE BIOPHYSICAL SOCIETY OF JAPAN 2011 -- 2021-03 The Japanese Biochemical Society 2005 -- 2021-03 Society of Computer Chemistry, Japan 2002 -- (current) Chemical Society of Japan - Honors & Awards
2023-05 量子生命科学会 研究奨励賞 量子生命科学に関連する研究において顕著な業績を挙げた 2022-05 Best Presentation 優れた研究内容について講演を行なったため 2021-09 Best Presentation for a presentation of eminent research 2020-12 量子生命科学会 第二回大会 優秀発表賞 優れた学術研究発表を行ったため - Articles
- A machine learning potential construction based on radial distribution function sampling
Watanabe Natsuki; Hori Yuta; Sugisawa Hiroki; Ida Tom...
JOURNAL OF COMPUTATIONAL CHEMISTRY/45(32)/p.2949, 2024-09-03 - Specific Zinc Binding to Heliorhodopsin
Masanori Hashimoto; Koichi Miyagawa; Manish Singh; Kot...
Physical Chemistry Chemical Physics/25(4)/pp.3535-3543, 2023-01 - Calcium binding mechanism in TAT rhodopsin
Sugimoto Teppei; Miyagawa Koichi; SHOJI Mitsuo; Kataya...
The Journal of Physical Chemistry Part B/128(29)/pp.7102-7111, 2024-07 - Real-time observation of a metal complex-driven reaction intermediate using a porous protein crystal and serial femtosecond crystallography
Maity Basudev; SHOJI Mitsuo; Luo Fangjia; Nakane Taka...
Nature Communications/15(1)/p.5518, 2024-06 - Origin of Homochirality in Amino Acids Induced by Lyman-α Irradiation in the Early Stage of the Milky Way
Sato Akimasa; Shoji Mitsuo; Watanabe Natsuki; Boero M...
ASTROBIOLOGY/23(10)/pp.1019-1026, 2023-10-01 - Water oxidation utilizing a ruthenium complex featuring a phenolic moiety inspired by the oxygen-evolving centre (OEC) of photosystem II
Kumagai Yugo; Takabe Risa; Nakazono Takashi; Shoji Mi...
SUSTAINABLE ENERGY & FUELS/8(5)/pp.905-913, 2024-01 - A new small molecule DoNA binding to CAG repeat RNA
Chen Qingwen; Yamada Takeshi; Miyagawa Koichi; Murata ...
BIOORGANIC & MEDICINAL CHEMISTRY/98/p.117580, 2024-01-15 - Neutron Crystallography of a Semiquinone Radical Intermediate of Copper Amine Oxidase Reveals a Substrate-Assisted Conformational Change of the Peptidyl Quinone Cofactor
Murakawa Takeshi; Kurihara Kazuo; Shoji Mitsuo; Yano ...
ACS CATALYSIS/13(18)/pp.12403-12413, 2023-09-07 - Theoretical elucidation of the structure, bonding, and reactivity of the CaMn4Ox clusters in the whole Kok cycle for water oxidation embedded in the oxygen evolving center of photosystem II. New molecular and quantum insights into the mechanism of the O-O bond formation
Yamaguchi Kizashi; Miyagawa Koichi; Shoji Mitsuo; Kawa...
PHOTOSYNTHESIS RESEARCH/Epub, 2023-11-09 - The Nature of the Chemical Bonds of High-Valent Transition-Metal Oxo (M=O) and Peroxo (MOO) Compounds: A Historical Perspective of the Metal Oxyl-Radical Character by the Classical to Quantum Computations
Yamaguchi Kizashi; Isobe Hiroshi; Shoji Mitsuo; Kawaka...
MOLECULES/28(20), 2023-10 - Organocatalytic-racemization reaction elucidation of aspartic acid by density functional theory
Watanabe Natsuki; Hori Yuta; Shoji Mitsuo; Boero Maur...
CHIRALITY/35(9)/pp.645-651, 2023-04 - Geometric, electronic and spin structures of the CaMn4O5 catalyst for water oxidation in oxygen-evolving photosystem II. Interplay between experiments and theoretical computations
Yamaguchi Kizashi; Shoji Mitsuo; Isobe Hiroshi; Kawaka...
COORDINATION CHEMISTRY REVIEWS/471, 2022-11 - Enantioselective Amino Acid interactions in Solution
Watanabe Natsuki; Shoji Mitsuo; Miyagawa Koichi; Hori ...
PHYSICAL CHEMISTRY CHEMICAL PHYSICS/25(21)/pp.15023-15029, 2023-05 - Biological advantage of the arrangements of C-phycocyanin chromophores in phycobilisome from the electronic energy transfer viewpoint
Mishima Kenji; Shoji Mitsuo; Umena Yasufumi; Shigeta ...
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN/96(4)/pp.381-393, 2023-04 - Specific zinc binding to heliorhodopsin
Hashimoto Masanori; Miyagawa Koichi; Singh Manish; Kat...
PHYSICAL CHEMISTRY CHEMICAL PHYSICS/25(4)/pp.3535-3543, 2023-01 - Molecular mechanism of a large conformational change of the quinone cofactor in the semiquinone intermediate of bacterial copper amine oxidase
Shoji Mitsuo; Murakawa Takeshi; Nakanishi Shota; Boero...
CHEMICAL SCIENCE/13(36)/pp.10923-10938, 2022-09 - Elucidation of a multiple S-3 intermediates model for water oxidation in the oxygen evolving complex of photosystem II. Calcium-assisted concerted O-O bond formation
Yamaguchi Kizashi; Miyagawa Koichi; Shoji Mitsuo; Isobe ...
CHEMICAL PHYSICS LETTERS/806, 2022-11 - Roles of the Flexible Primary Coordination Sphere of the Mn4CaOx Cluster: What Are the Immediate Decay Products of the S-3 State?
Isobe Hiroshi; Shoji Mitsuo; Suzuki Takayoshi; Shen J...
JOURNAL OF PHYSICAL CHEMISTRY B/Epub, 2022-09 - 有機分子触媒を用いたアミノ酸ラセミ化反応の理論的研究
渡辺 七都稀; 堀 優太; 庄司 光男; 重田 育照
Journal of Computer Chemistry, Japan/21(4)/pp.80-81, 2023-03 - Relative energies among S3 intermediates in the photosystem II revealed by DLPNO coupled cluster and hybrid DFT calculations. Possible pathways of water insertion in the S-2 to S-3 transition
Miyagawa Koichi; Shoji Mitsuo; Isobe Hiroshi; Kawakami...
CHEMICAL PHYSICS LETTERS/793, 2022-04 - Theoretical Investigation into a Possibility of Formation of Propylene Oxide Homochirality in Space
Hori Yuta; Nakamura Honami; Sakawa Takahide; Natsuki Wat...
Astrobiology/22(11)/pp.1330-1336, 2022-09 - Comprehensive Search of Stable Isomers of Alanine and Alanine Precursors in Prebiotic Syntheses
Mitsuo Shoji; Natsuki Watanabe; Hori Yuta; Kenji Furuya; ...
Astrobiology/22(9)/pp.1129-1142, 2022-09 - Relative energies among proton-shifted S2 isomers in the photosystem II revealed by DLPNO coupled cluster and hybrid DFT calculations. Proton transfer coupled spin transitions of the CaMn4Ox cluster in OEC of PSII
Miyagawa Koichi; Shoji Mitsuo; Isobe Hiroshi; Kawakami T...
Chemical Physics Letters/790/p.139357, 2022-01 - Heme-bound tyrosine vibrations in hemoglobin M: Resonance Raman, crystallography, and DFT calculation
Nagatomo Shigenori; Shoji Mitsuo; Terada Takuto; Nakatani...
BIOPHYSICAL JOURNAL/121(14)/pp.2767-2780, 2022-06 - Estimation of the relative contributions to the electronic energy transfer rates based on Forster theory: The case of C-phycocyanin chromophores
Mishima Kenji; Shoji Mitsuo; Umena Yasufumi; Boero Ma...
Biophysics and physicobiology/18/pp.196-214, 2021 - more...
- A machine learning potential construction based on radial distribution function sampling
- Books
- Isolobal and isospin analogy between organic and inorganic open-shell molecules-Application to oxygenation reactions by active oxygen and oxy-radicals and water oxidation in the native and artificial photosynthesis
Yamaguchi Kizashi; Miyagawa Koichi; Isobe Hiroshi; Sho...
ADVANCES IN QUANTUM CHEMISTRY, VOL 84/ELSEVIER ACADEMIC PRESS INC/pp.425-564, 2021 - 量子化学計算ビギナーズガイド
庄司 光男
環境技術/pp.45-49, 2020-10 - フリーソフトで始める分子モデリング
庄司 光男
Amazon Kindle direct publishing, 2020-04 - A practical introduction to quantum chemical calculations with Gaussian16
庄司 光男
Amazon Kindle direct publishing, 2019-11
- Isolobal and isospin analogy between organic and inorganic open-shell molecules-Application to oxygenation reactions by active oxygen and oxy-radicals and water oxidation in the native and artificial photosynthesis
- Conference, etc.
- 機械学習ポテンシャルのための動径分布関数を用いた効率的データサンプリング法
渡辺 七都稀; 堀 優太; 杉澤 宏樹; 井田 朋智; 庄司 光男; 重田 育照
第26回理論化学討論会/2024-05-21--2024-05-23 - アミノ酸のホモキラリティはアミノニトリル前駆体の異性体過剰に起因する
Shoji Mitsuo
量子生命科学会第5回大会/2023-05-18--2023-05-18 - QM/MM Free energy simulation for the catalytic reaction of bacterial copper amine oxidase
Shoji Mitsuo
The 61st Annual Meeting of the Biophysical Society of Japan/2023-11-14--2023-11-14 - Overview of our research collaborations performed in the research area of “molecular movies”
庄司 光男
高速分子動画国際シンポジウム2023/2023-11-30--2023-12-01 - ”高速分子動画”領域で研究連携中の酵素反応の量子化学解析についての最近の進捗
Shoji Mitsuo
令和5年度シンポジウム・領域会議/2023-05-10--2023-05-11 - 量子化学計算を活用した複雑酵素反応および生体分子ホモキラリティ機構の解明
Shoji Mitsuo
量子生命科学会第5回大会/2023-05-19--2023-05-19 - Quantum chemistry study of the origin of homochirality of amino acids
Shoji Mitsuo
CJK-WTCC/2023-06-20--2023-06-23 - The reaction mechanism of bacterial copper amine oxidase: interplay of theoretical QM/MM calculations and experimental methods
Shoji Mitsuo
CJK-WTCC/2023-06-20--2023-06-23 - Origin of homochirality of amino acids
Shoji Mitsuo
ICPAC Bali 2023/2023-09-12--2023-09-17 - QM/MM study of the reaction mechanism of sesamin biosynthesis by cytochrome P450
Shoji Mitsuo
ICCP450-JSSS/2023-09-25--2023-09-29 - 星間空間におけるホモキラリティー発生の理論的研究
堀 優太; 渡辺 七都稀; 庄司 光男; 重田 育照
第17回分子科学討論会/2023-09-12--2023-09-15 - ヘモグロビンM IwateとM BostonのFe-O伸縮振動の理論計算の改良およびヘモグロビンAとの構造の比較
長友重紀; 寺田拓人; 庄司光男; 重田育照; 中谷清治; 廣田俊; 柳澤幸子; 久保稔; 北川禎三; 長井雅子; 大木規央; 朴三用; ...
第49回生体分子科学討論会/2023-06-01--2023-06-02 - 酵素反応のQM/MM解析
Shoji Mitsuo
スーパーコンピュータワークショップ2022「複雑電子状態の理論・計算科学」/2023-01-17--2023-01-17 - Unique reaction mechanism of copper amine oxidase revealed by theoretical QM/MM and experimental approaches
Shoji Mitsuo
CCS-KISTI workshop/2023-02-22--2023-02-22 - A Large Conformational Change of the Quinone Cofactor in Bacterial Copper Amine Oxidase
Shoji Mitsuo
ICPAC Kota Kinabalu 2022/2022-11-25--2022-11-25 - 酵素反応における構造変化の重要性
Shoji Mitsuo
令和4年度新学術領域研究「高速分子動画」シンポジウム/2022-11-21--2022-11-21 - アミノ酸ホモキラリティ起源についての電子状態探査
Shoji Mitsuo
計算アストロバイオロジー2022/2022-11-10--2022-11-10 - QM/MM-MD study of the role of valine 185 in the oxygen-evolving complex of photosystem II
Shoji Mitsuo
60th Annual Meeting of BSJ/2022-09-30--2022-09-30 - Natural selection of the Mn cluster in the photosynthetic water oxidation
Shoji Mitsuo
Satellite Meeting to 18th International Congress on Photosynthesis Research (WOX-ICPR2022)/2022-08-07--2022-08-07 - GLASアルゴリズムによる酵素反応機構の理論解明:新規反応経路探索手法の開発と適用
Shoji Mitsuo
物性研短期研究会「理論タンパク質物性科学の最前線:理論と実験との密な協働」/2022-07-27--2022-07-27 - 銅含有アミン酸化酵素におけるトパキノン補酵素の構造変化機構
Shoji Mitsuo
第22回日本蛋白質科学会年会/2022-06-08--2022-06-08 - 銅含有アミン酸化酵素におけるトパキノン補酵素の構造変化機構
Shoji Mitsuo
第22回日本蛋白質科学会年会/2022-06-08--2022-06-08 - 光合成水分解酸素発生におけるMnの自然選択の理由
Shoji Mitsuo
量子生命科学会第4回大会/2022-05-26--2022-05-26 - Theoretical insights into the molecular mechanisms of dynamical biochemical reactions
Shoji Mitsuo
Molecular Movies International Symposium 2022/2022-05-13--2022-05-13 - 有機分子触媒を用いたアミノ酸ラセミ化反応の理論的研究
渡辺 七都稀; 庄司 光男; 堀 優太; 重田 育照
日本コンピュータ化学会2022年秋季年会/2022-11-25--2022-11-27 - more...
- 機械学習ポテンシャルのための動径分布関数を用いた効率的データサンプリング法
- Teaching
2024-04 -- 2024-08 Seminar on Theoretical Condensed Matter Physics C University of Tsukuba. 2024-04 -- 2024-08 Special Seminar for Condensed Matter Theory VB University of Tsukuba. 2024-04 -- 2024-08 Special seminar for condensed matter theory IIIB University of Tsukuba. 2024-04 -- 2024-08 Special Seminar for Condensed Matter Theory IB University of Tsukuba. 2024-10 -- 2025-02 Seminar on Theoretical Condensed Matter Physics D University of Tsukuba. 2024-04 -- 2024-08 Special seminar for condensed matter theory IVA University of Tsukuba. 2024-04 -- 2024-08 Collaborative Research in Physics IV University of Tsukuba. 2024-10 -- 2025-02 Collaborative Research in Physics IV University of Tsukuba. 2024-10 -- 2025-02 Collaborative Research in Physics III University of Tsukuba. 2024-04 -- 2024-08 Collaborative Research in Physics III University of Tsukuba. more... - Talks
- 構造探索手法(GLAS)による酵素反応機構の解明
庄司 光男
SRPS2020/2020-9-13--2020-9-13 - サルコシンオキシダーゼにおけるシクロプロピルグリシンの反応機構についての理論的解明
庄司 光男
第93回日本生化学学会年会/2020-9-14--2020-9-14 - Recent Progress in the Reaction Mechanism of Water-Splitting in Photosystem II
Shoji Mitsuo
70th JSCC/2020-9-28--2020-9-28 - QM/MMで見えてきた酵素反応の特徴
庄司 光男
高速分子動画領域会議/2020-10-20--2020-10-20 - 銅含有アミン酸化酵素のプロトン化状態についてのQM/MM解析
庄司 光男
量子生命科学会第2回大会/2020-12-23--2020-12-23
- 構造探索手法(GLAS)による酵素反応機構の解明
- Professional activities
2024-04 -- 2026-03 Japan Society for Theoretical Chemistry フロンティア編集委員 2023-10 -- 2025-10 Japan Society for Theoretical Chemistry 幹事 2020-04 -- 2021-03 Japan Society for Theoretical Chemistry 将来構想委員 2019-04 -- 2022-03 The Molecular Simulation Society of Japan アンサンブル編集委員
(Last updated: 2024-09-02)