MORI TOSHIFUMI
Organization
Institute for Materials Chemistry and Engineering Department of Applied Molecular Chemistry Associate Professor
Interdisciplinary Graduate School of Engineering Sciences Department of Interdisciplinary Engineering Sciences（Joint Appointment）
Title
Associate Professor
Contact information
Profile
Conformational dynamics and fluctuations are essential for molecules to react and function in condensed phase. As molecular understanding of these motions are difficult to reach via experiments, our lab use computer simulations and theoretical analyses to study chemical reactions and conformational transitions of molecules in solution. The goal is to elucidate the molecular mechanisms that lead to functions of biomolecules and macromolecules. We also develop theoretical approaches to reveal the hierarchy of events that occur in condensed phase.
Homepage
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https://kyushu-u.pure.elsevier.com/en/persons/toshifumi-mori
Reseacher Profiling Tool (Kyushu University Pure)
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http://theoc.cm.kyushu-u.ac.jp
Mori Group, Institute for Materials Chemistry and Engineering (Interdisciplinary Graduate School of Engineering Sciences)
External link
ORCID
Degree
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Ph. D. (Science)
Research History
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2008年4月 - 2010年3月 日本学術振興会特別研究員 (DC2) 2010年4月 - 2012年9月 Stanford大学 博士研究員 2012年10月 - 2013年11月 Wisconsin大学Madison校 博士研究員 （2013年4月 - 2013年11月 日本学術振興会海外特別研究員） 2013年12月 - 2020年9月 分子科学研究所 助教 2014年4月 - 2020年9月 総合研究大学院大学 助教
Research Interests・Research Keywords
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Research theme：Molecular origin of conformational dynamics in condensed phase reactions and functions
Keyword：theoretical chemistry, molecular simulation, condensed phase reaction, conformational dynamics
Research period： 2021.5
Awards
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奨励賞
2018.9 分子科学会 気相および凝縮系における反応のダイナミクスの理論的解明
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若手招待講演賞
2017.9 日本生物物理学会 Pin1 の酵素反応におけるタンパク質ダイナミクスの重要性
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14th ICQC ポスター賞
2012.6 Beyond Minimum Energy Conical Intersections: Paths in Conical Intersection Seam Space and their Role in Nonadiabatic Dynamics
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第５回分子科学討論会優秀講演賞
2011.9 分子科学会 エチレンの光化学反応におけるRydberg状態の研究 ~第一原理計算によるダイナミクスと光イオン化スペクトルについて~
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WATOC 2008 ポスター賞
2008.9 The Reaction of a Grignard Reagent with Acetone in Solution: A Theoretical Study
Papers
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Molecular Insights into the Intrinsic Dynamics and Their Roles During Catalysis in Pin1 Peptidyl-prolyl Isomerase Reviewed International journal
Toshifumi Mori, Shinji Saito
The Journal of Physical Chemistry B 126 5185 - 5193 2022.7
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Conformational Excitation and Nonequilibrium Transition Facilitate Enzymatic Reactions: Application to Pin1 Peptidyl-Prolyl Isomerase Reviewed International journal
Toshifumi Mori, Shinji Saito
JOURNAL OF PHYSICAL CHEMISTRY LETTERS 10 ( 3 ) 474 - 480 2019.2
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Carbamoylarylation of Alkenes with N-Aryl Oxamic Acids Involving 1,4-Aryl Migration Via C(aryl)–N Bond Cleavage
2024.4
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Conformational Dynamics in Proteins: Entangled Slow Fluctuations and Nonequilibrium Reaction Events
Junichi Ono, Yoshihiro Matsumura, Toshifumi Mori, Shinji Saito
The Journal of Physical Chemistry B 2023.12
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Tuning the ATP–ATP and ATP–disordered protein interactions in high ATP concentration by altering water models Reviewed International journal
2023.7
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Structural and Dynamic Alteration of Glycated Human Serum Albumin in Schiff Base and Amadori Adducts: A Molecular Simulation Study
Sirin Sittiwanichai, Deanpen Japrung, Toshifumi Mori, Prapasiri Pongprayoon
The Journal of Physical Chemistry B 2023.6
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Bifunctional 1-Hydroxypyrene Photocatalyst for Hydrodesulfurization via Reductive C(Aryl)–S Bond Cleavage
25 ( 18 ) 3293 - 3297 2023.5
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Near‐Infrared and Dual Emissions of Diphenylamino Group‐Substituted Malachite Green Derivatives
2022.8
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Photoinduced Divergent Deaminative Borylation and Hydrodeamination of Primary Aromatic Amines
Akira Shiozuka, Kohei Sekine, Takumi Toki, Kyohei Kawashima, Toshifumi Mori, Yoichiro Kuninobu
Organic Letters 2022.6
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Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI) Reviewed International journal
Takuma Kikutsuji, Yusuke Mori, Kei-ichi Okazaki, Toshifumi Mori, Kang Kim, Nobuyuki Matubayasi
The Journal of Chemical Physics 156 ( 15 ) 154108 - 154108 2022.4
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Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide Reviewed
Yusuke Mori, Kei-ichi Okazaki, Toshifumi Mori, Kang Kim, Nobuyuki Matubayasi
JOURNAL OF CHEMICAL PHYSICS 153 ( 5 ) 2020.8
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Dissecting the Dynamics during Enzyme Catalysis: A Case Study of Pin1 Peptidyl-Prolyl Isomerase Reviewed
Toshifumi Mori, Shinji Saito
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 16 ( 5 ) 3396 - 3407 2020.5
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Excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene. II. Ab initio multiple spawning simulations Reviewed
Journal of Chemical Physics 148 ( 16 ) 164303 2018.4
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Excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene. I. Time-resolved photoelectron-photoion coincidence spectroscopy. Reviewed
The Journal of chemical physics 148 ( 16 ) 164302 2018.4
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Structure and dynamics of solvent molecules inside the polytheonamide B channel in different environments: A molecular dynamics study Reviewed
Mahroof Kalathingal, Takashi Sumikama, Toshifumi Mori, Shigetoshi Oiki, Shinji Saito
Physical Chemistry Chemical Physics 20 ( 5 ) 3334 - 3348 2018.2
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The critical role of dimer formation in monosaccharides binding to human serum albumin Reviewed
Prapasiri Pongprayoon, Toshifumi Mori
Physical Chemistry Chemical Physics 20 ( 5 ) 3249 - 3257 2018.2
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Molecular Mechanism Behind the Fast Folding/Unfolding Transitions of Villin Headpiece Subdomain: Hierarchy and Heterogeneity Reviewed
Toshifumi Mori, Shinji Saito
JOURNAL OF PHYSICAL CHEMISTRY B 120 ( 45 ) 11683 - 11691 2016.11
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3D-RISM-MP2 Approach to Hydration Structure of Pt(II) and Pd(II) Complexes: Unusual H-Ahead Mode vs Usual O-Ahead One Reviewed
Shinji Aono, Toshifumi Mori, Shigeyoshi Sakaki
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12 ( 3 ) 1189 - 1206 2016.3
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Atomic-scale origins of slowness in the cyanobacterial circadian clock Reviewed
Jun Abe, Takuya B. Hiyama, Atsushi Mukaiyama, Seyoung Son, Toshifumi Mori, Shinji Saito, Masato Osako, Julie Wolanin, Eiki Yamashita, Takao Kondo, Shuji Akiyama
SCIENCE 349 ( 6245 ) 312 - 316 2015.7
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Dynamic heterogeneity in the folding/unfolding transitions of FiP35 Reviewed
Toshifumi Mori, Shinji Saito
JOURNAL OF CHEMICAL PHYSICS 142 ( 13 ) 135101 2015.4
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Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models Reviewed
Puja Goyal, Hu-Jun Qian, Stephan Irle, Xiya Lu, Daniel Roston, Toshifumi Mori, Marcus Elstner, Qiang Cui
JOURNAL OF PHYSICAL CHEMISTRY B 118 ( 38 ) 11007 - 11027 2014.9
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Integrated Hamiltonian Sampling: A Simple and Versatile Method for Free Energy Simulations and Conformational Sampling Reviewed
Toshifumi Mori, Robert J. Hamers, Joel A. Pedersen, Qiang Cui
JOURNAL OF PHYSICAL CHEMISTRY B 118 ( 28 ) 8210 - 8220 2014.7
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Photochemical Dynamics of Ethylene Cation C2H4+ Reviewed
Baptiste Joalland, Toshifumi Mori, Todd J. Martinez, Arthur G. Suits
JOURNAL OF PHYSICAL CHEMISTRY LETTERS 5 ( 8 ) 1467 - 1471 2014.4
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An Explicit Consideration of Desolvation is Critical to Binding Free Energy Calculations of Charged Molecules at Ionic Surfaces Reviewed
Toshifumi Mori, Robert J. Hamers, Joel A. Pedersen, Qiang Cui
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 9 ( 11 ) 5059 - 5069 2013.11
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Exploring the Conical Intersection Seam: The Seam Space Nudged Elastic Band Method. Reviewed
Journal of chemical theory and computation 9 ( 2 ) 1155 - 1163 2013.2
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Between ethylene and polyenes - the non-adiabatic dynamics of cis-dienes Reviewed
Thomas S. Kuhlman, William J. Glover, Toshifumi Mori, Klaus B. Moller, Todd J. Martinez
FARADAY DISCUSSIONS 157 193 - 212 2012.4
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Role of Rydberg States in the Photochemical Dynamics of Ethylene Reviewed
Toshifumi Mori, William J. Glover, Michael S. Schuurman, Todd J. Martinez
JOURNAL OF PHYSICAL CHEMISTRY A 116 ( 11 ) 2808 - 2818 2012.3
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Conical intersections of free energy surfaces in solution: Effect of electron correlation on a protonated Schiff base in methanol solution Reviewed
Toshifumi Mori, Katsuhiro Nakano, Shigeki Kato
JOURNAL OF CHEMICAL PHYSICS 133 ( 6 ) 064107 2010.8
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Dynamic electron correlation effect on conical intersections in photochemical ring-opening reaction of cyclohexadiene: MS-CASPT2 study Reviewed
Toshifumi Mori, Shigeki Kato
CHEMICAL PHYSICS LETTERS 476 ( 1-3 ) 97 - 100 2009.7
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Grignard Reagents in Solution: Theoretical Study of the Equilibria and the Reaction with a Carbonyl Compound in Diethyl Ether Solvent Reviewed
Toshifumi Mori, Shigeki Kato
JOURNAL OF PHYSICAL CHEMISTRY A 113 ( 21 ) 6158 - 6165 2009.5
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Analytical RISM-MP2 free energy gradient method: Application to the Schlenk equilibrium of Grignard reagent Reviewed
Toshifumi Mori, Shigeki Kato
CHEMICAL PHYSICS LETTERS 437 ( 1-3 ) 159 - 163 2007.3
Presentations
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Dissecting the heterogeneous dynamics of proteins during folding and catalysis Invited International conference
Toshifumi Mori
Telluride Science Research Center Protein Dynamics Workshop 2023 2023.7
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Role of dynamics in conformational transitions and functions of biomolecules Invited
2022.3
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Theoretical study on the role of dynamics during enzyme catalysis Invited International conference
Toshifumi Mori
Pure and Applied Chemistry International Conference 2024 2024.1
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深層学習モデルのハイパーパラメータチューニングによる溶液内反応の反応座標探索
#佐藤拓海, 川島恭平, @岡崎 圭一, @金 鋼, @松林 伸幸, 森 俊文
第37回分子シミュレーション討論会 2023.4
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高濃度ATPの自己会合とATP-タンパク質相互作用に水モデルが与える影響の理論解析
森 俊文, @吉田 紀生
第17回分子科学討論会 2023.9
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Theoretical study on the role of protein conformational dynamics during enzyme catalysis Invited International conference
2023.9
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Bridging the gap between static and dynamic reaction mechanisms in enzyme catalysis Invited International conference
Toshifumi Mori
Multi-scale Molecular Dynamics Simulation and Machine Learning of Biomolecular Systems Workshop 2023.8
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タンパク質の変性状態に対する溶媒環境の影響の理論的解析 Invited
森 俊文
「凝縮系の理論化学」研究会 2023.3
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酵素反応における反応ダイナミクスと反応座標の解明
森 俊文
第36回分子シミュレーション討論会 2022.12
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Elucidating the Role of Dynamics During Enzyme Catalysis using Molecular Simulations Invited International conference
Toshifumi Mori
7th International Symposium of Quantum Beam Science at Ibaraki University 2022.12
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タンパク質の変性状態における構造ダイナミクスと溶媒環境依存性の理論的解析 Invited
森 俊文
第60回日本生物物理学会年会 2022.9
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凝縮系反応の動的機構と反応座標の理論的解明 Invited
森 俊文
「化学反応経路探索のニューフロンティア 2022」シンポジウム 2022.9
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生体分子の動的構造と機能発現機構の理論的解明 Invited
森 俊文
京都大学福井謙一記念研究センターオンラインシンポジウム 2022.1
MISC
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最近の研究から「酵素反応の静的・動的分子構造の解明に向けて」
@森 俊文
分子シミュレーション学会会誌「アンサンブル」 2021.4
Professional Memberships
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Japan Society of Molecular Science
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The Biophysical Society of Japan
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The Molecular Simulation Society of Japan
Committee Memberships
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分子科学会 顕彰委員会委員 Domestic
2023.10 - 2025.9
Academic Activities
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分子シミュレーション学会会誌「アンサンブル」
2023.1 - 2026.12
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ポスター賞代表選考委員（「液相および生体関連分子」分野）
第15回分子科学討論会 （ オンライン（札幌） ） 2021.9 - 2022.9
Research Projects
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酵素の構造ダイナミクスと活性制御の分子機構の理論的解明
Grant number：22H02035 2022 - 2025
日本学術振興会 科学研究費助成事業 基盤研究(B)
Authorship：Principal investigator Grant type：Scientific research funding
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令和４年度学術研究活動助成事業
2022
Grant type：Donation
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キラル分子を光学活性体として得る革新的手法DYASINの開発
Grant number：20H05677 2020 - 2025
日本学術振興会 科学研究費助成事業 基盤研究(S)
Authorship：Coinvestigator(s) Grant type：Scientific research funding
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酵素反応の動的機構の理論的解明
Grant number：18K05049 2018 - 2020
日本学術振興会 科学研究費助成事業 基盤研究(C)
Authorship：Principal investigator Grant type：Scientific research funding
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タンパク質の構造変化と化学反応が織り成す協働的な反応機構の解明
Grant number：16H00856 2016 - 2017
日本学術振興会・文部科学省 科学研究費助成事業 新学術領域研究（研究領域提案型）
Authorship：Principal investigator Grant type：Scientific research funding
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タンパク質の動的構造と機能発現ダイナミクスの分子論的解明
Grant number：15K17813 2015 - 2017
科学研究費助成事業 若手研究(A,B)
Authorship：Principal investigator Grant type：Scientific research funding
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天然変性タンパク質の動的構造と機能発現機構の分子論的解明
Grant number：26888019 2014
日本学術振興会 科学研究費助成事業 研究活動スタート支援
Authorship：Principal investigator Grant type：Scientific research funding
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溶液内における有機金属反応の理論的研究
Grant number：08J01112 2008 - 2009
日本学術振興会 科学研究費助成事業 特別研究員奨励費
Grant type：Scientific research funding
Class subject
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計算化学
2023.6 - 2023.8 Summer quarter
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総合理工学修士実験
2023.4 - 2024.3 Full year
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総合理工学修士演習
2023.4 - 2024.3 Full year
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総合理工学修士演習
2023.4 - 2024.3 Full year
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機能有機化学
2023.4 - 2023.6 Spring quarter
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計算化学
2022.6 - 2022.8 Summer quarter
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総合理工学修士演習
2022.4 - 2023.3 Full year
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総合理工学修士実験
2022.4 - 2023.3 Full year
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機能有機化学
2022.4 - 2022.6 Spring quarter
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有機機器分析
2022.4 - 2022.6 Spring quarter
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計算化学
2021.6 - 2021.8 Summer quarter
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機能有機化学
2021.4 - 2021.6 Spring quarter
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有機機器分析
2021.4 - 2021.6 Spring quarter
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機能有機化学
2020.10 - 2021.3 Second semester
FD Participation
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2022.1 Role：Participation Title：先導研FD
Organizer：[Undergraduate school/graduate school/graduate faculty]
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2021.1 Role：Speech Title：先導物質化学研究所 R2年度 第一回ファカルティディベロップメント
Organizer：[Undergraduate school/graduate school/graduate faculty]
Visiting, concurrent, or part-time lecturers at other universities, institutions, etc.
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2022 奈良先端科学技術大学院大学 Classification:Part-time lecturer Domestic/International Classification:Japan
Semester, Day Time or Duration：12月
Travel Abroad
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2012.10 - 2013.11
Staying countory name 1：United States Staying institution name 1：University of Wisconsin, Madison
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2010.4 - 2012.9
Staying countory name 1：United States Staying institution name 1：Stanford大学