Updated on 2024/12/12

Information

 

写真a

 
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(Concurrent)
Title
Associate Professor
Contact information
メールアドレス
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

Research Areas

  • Nanotechnology/Materials / Fundamental physical chemistry

  • Life Science / Biophysics

Degree

  • Ph. D. (Science)

Research History

  • Kyushu University Interdisciplinary Graduate School of Engineering Sciences Associate Professor

    2020.10 - Present

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  • Kyushu University Institute for Materials Chemistry and Engineering, Division of Applied Molecular Chemistry Associate Professor

    2020.10 - Present

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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

  • Research theme:Physical Chemistry

    Keyword:Physical Chemistry

    Research period: 2024

  • Research theme:conformational dynamics

    Keyword:conformational dynamics

    Research period: 2024

  • Research theme:reaction dynamics

    Keyword:reaction dynamics

    Research period: 2024

  • Research theme:Molecular Simulation

    Keyword:Molecular Simulation

    Research period: 2024

  • Research theme:Folding

    Keyword:Folding

    Research period: 2024

  • Research theme:Pin1

    Keyword:Pin1

    Research period: 2024

  • Research theme:KaiC

    Keyword:KaiC

    Research period: 2024

  • Research theme:Physical Biology

    Keyword:Physical Biology

    Research period: 2024

  • Research theme:Enzymatic Reaction

    Keyword:Enzymatic Reaction

    Research period: 2024

  • Research theme:Quantum Chemistry

    Keyword:Quantum Chemistry

    Research period: 2024

  • Research theme:Theoretical Chemistry

    Keyword:Theoretical Chemistry

    Research period: 2024

  • 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

  • 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

  • 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

  • 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

  • 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~

  • WATOC 2008 ポスター賞

    2008.9   The Reaction of a Grignard Reagent with Acetone in Solution: A Theoretical Study

Papers

  • 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 ( 28 )   5185 - 5193   2022.7   ISSN:15206106 eISSN:15205207

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    Proteins are intrinsically dynamic and change conformations over a wide range of time scales. While the conformational dynamics have been realized to be important for protein functions, e.g., in activity–stability trade-offs, how they play a role during enzyme catalysis has been of debate over decades. By studying Pin1 peptidyl-prolyl isomerase using extensive molecular dynamics simulations, here we discuss how the slow intrinsic dynamics of Pin1 observed in the NMR relaxation dispersion experiment occur and couple to isomerization reactions in molecular detail. In particular, we analyze the angular correlation functions of the backbone N–H bonds and find that slow conformational transitions occur at about the 3_10 helix in the apo state. These events at the helical region further affect the residues at about the ligand binding site. Unfolding of this helix leads to a tight hydrogen bond between the helical region and the ligand binding loop, thus forming a stable coiled structure. The helical and coiled structures are found to be characteristic of the Pin1–ligand complex with the ligand in the trans and cis states, respectively. These results indicate that the changes in the slow dynamics of Pin1 by the isomerization reaction occur via the shift in populations of the helical and coiled states, where the balance is dependent on the ligand isomerization states.

    DOI: 10.1021/acs.jpcb.2c02095

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    Repository Public URL: https://hdl.handle.net/2324/6789517

  • 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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    Conformational Excitation and Nonequilibrium Transition Facilitate Enzymatic Reactions: Application to Pin1 Peptidyl-Prolyl Isomerase

    DOI: 10.1021/acs.jpclett.8b03607

  • Mechanistic insights into the role of cyclodextrin in the regioselective radical CH trifluoromethylation of aromatic compounds Reviewed

    Kyohei Kawashima, Xu Lu, Yoichiro Kuninobu, Toshifumi Mori

    Journal of Computational Chemistry   45 ( 25 )   2112 - 2118   2024.9   ISSN:0192-8651 eISSN:1096-987X

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    DOI: 10.1002/jcc.27430

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  • Aggregation of Apo/Glycated Human Serum Albumins and Aptamer-Saturated Graphene Quantum Dot: A Simulation Study Reviewed

    Sirin Sittiwanichai, Chanya Archapraditkul, Deanpen Japrung, Yasuteru Shigeta, Toshifumi Mori, Prapasiri Pongprayoon

    Biochemistry   63 ( 13 )   1697 - 1707   2024.6   ISSN:0006-2960 eISSN:1520-4995

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    DOI: 10.1021/acs.biochem.4c00155

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  • Unveiling interatomic distances influencing the reaction coordinates in alanine dipeptide isomerization: An explainable deep learning approach Reviewed

    Kazushi Okada, Takuma Kikutsuji, Kei-ichi Okazaki, Toshifumi Mori, Kang Kim, Nobuyuki Matubayasi

    The Journal of Chemical Physics   160 ( 17 )   2024.5   ISSN:0021-9606 eISSN:1089-7690

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    DOI: 10.1063/5.0203346

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  • Carbamoylarylation of Alkenes with N-Aryl Oxamic Acids Involving 1,4-Aryl Migration Via C(aryl)–N Bond Cleavage Reviewed

    Akira Shiozuka, Di Wu, Kyohei Kawashima, Toshifumi Mori, Kohei Sekine, Yoichiro Kuninobu

    ACS Catalysis   14 ( 8 )   5972 - 5977   2024.4   ISSN:2155-5435

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    DOI: 10.1021/acscatal.4c00523

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  • The priming phosphorylation of KaiC is activated by the release of its autokinase autoinhibition

    Yoshihiko Furuike, Yasuhiro Onoue, Shinji Saito, Toshifumi Mori, Shuji Akiyama

    2024.3

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    DOI: 10.1101/2024.03.21.584037

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  • Conformational Dynamics in Proteins: Entangled Slow Fluctuations and Nonequilibrium Reaction Events Invited Reviewed

    Junichi Ono, Yoshihiro Matsumura, Toshifumi Mori, Shinji Saito

    The Journal of Physical Chemistry B   128 ( 1 )   20 - 32   2023.12   ISSN:1520-6106 eISSN:1520-5207

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    DOI: 10.1021/acs.jpcb.3c05307

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  • Tuning the ATP–ATP and ATP–disordered protein interactions in high ATP concentration by altering water models Reviewed International journal

    Toshifumi Mori, Norio Yoshida

    The Journal of Chemical Physics   159 ( 3 )   035102-1 - 035102-11   2023.7   ISSN:00219606 eISSN:10897690

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    The adenosine triphosphate (ATP)–protein interactions have been of great interest since the recent experimental finding of ATP’s role as a hydrotrope. The interaction between ATP and disordered proteins is fundamental to the dissolution of protein aggregates and the regulation of liquid–liquid phase separation by ATP. Molecular dynamics simulation is a powerful tool for analyzing these interactions in molecular detail but often suffers from inaccuracies in describing disordered proteins and ATPs in high concentrations. Recently, several water models have been proposed to improve the description of the protein-disordered states, yet how these models work with ATP has not been explored. To this end, here, we study how water models affect ATP and alter the ATP–ATP and ATP–protein interactions for the intrinsically disordered protein, α-Synuclein. Three water models, TIP4P-D, OPC, and TIP3P, are compared, while the protein force field is fixed to ff99SBildn. The results show that ATP over-aggregates into a single cluster in TIP3P water, but monomers and smaller clusters are found in TIP4P-D and OPC waters. ATP–protein interaction is also over-stabilized in TIP3P, whereas repeated binding/unbinding of ATP to α-Synuclein is observed in OPC and TIP4P-D waters, which is in line with the recent nuclear magnetic resonance experiment. The adenine ring-mediated interaction is found to play a major role in ATP–ATP and ATP–protein contacts. Interestingly, changing Mg^2^+ into Na^+ strengthened the electrostatic interaction and promoted ATP oligomerization and ATP–α-Synuclein binding. Overall, this study shows that changing the water model can be an effective approach to improve the properties of ATP in high concentration.

    DOI: 10.1063/5.0158046

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    Repository Public URL: https://hdl.handle.net/2324/7159646

  • Structural and Dynamic Alteration of Glycated Human Serum Albumin in Schiff Base and Amadori Adducts: A Molecular Simulation Study Reviewed

    Sirin Sittiwanichai, Deanpen Japrung, Toshifumi Mori, Prapasiri Pongprayoon

    The Journal of Physical Chemistry B   127 ( 23 )   5230 - 5240   2023.6   ISSN:15206106 eISSN:15205207

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    Human serum albumin (HSA) is a protein carrier in blood transporting metabolites and drugs. Glycated HSA (GHSA) acts as a potential biomarker for diabetes. Thus, many attempts have been made to detect GHSA. Glycation was reported to damage the structure and ligand binding capability, where no molecular detail is available. Recently, the crystal structure of GHSA has been solved, where two glucose isomers (pyranose/ GLC and open-chain/GLO) are located at Sudlow’s site I. GLO was found to covalently bind to K_195, while GLC is trapped by noncontact interactions. GHSA exists in two forms (Schiff base (SCH) and Amadori (AMA) adducts), but how both disrupt albumin activity microscopically remains unknown. To this end, molecular dynamics simulations were performed here to explore the nature of SCH and AMA. Both forms are found to alter the main protein dynamics, resulting in (i) the widening of Sudlow’s site I entrance, (ii) the size reduction of nine fatty acid-binding pockets, (iii) the enlargement of Sudlow’s site I and the shrinking of Sudlow’s site II, (iv) the enhancement of C_34 reactivity, and (v) the change in the W_214 microenvironment. These unique characteristics found here can be useful for understanding the effect of glycation on the albumin function in more detail and designing specific and selective GHSA detection strategies.

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    Repository Public URL: https://hdl.handle.net/2324/7159643

  • Bifunctional 1-Hydroxypyrene Photocatalyst for Hydrodesulfurization via Reductive C(Aryl)–S Bond Cleavage Reviewed

    Di Wu, Akira Shiozuka, Kyohei Kawashima, Toshifumi Mori, Kohei Sekine, Yoichiro Kuninobu

    Organic Letters   25 ( 18 )   3293 - 3297   2023.5   ISSN:1523-7060 eISSN:1523-7052

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    We developed the visible-light-induced hydrodesulfurization of alkyl aryl thioethers via the reductive cleavage of the C(aryl)-S bond using 1-hydroxypyrene as a Brønsted acid-reductant bifunctional photocatalyst. The hydrodesulfurization reaction proceeded under simple reaction conditions (1-hydroxypyrene and Et3N in THF under purple LED illumination); this reaction did not require chemicals commonly used for hydrodesulfurization, such as hydrosilanes, transition metal catalysts, and/or stoichiometric amounts of metal reagents. Detailed mechanistic studies based on control experiments, spectroscopic measurements, and computational studies revealed that the cleavage of the C(aryl)-S bond and the formation of the C(aryl)-H bond proceeded via the formation of the ion pair between the radical anion of alkyl aryl thioether and Et3N+H, resulting in the generation of a sulfur radical. In addition, the 1-hydroxypyrene catalyst was regenerated via hydrogen atom transfer (HAT) from Et3N.

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  • Near‐Infrared and Dual Emissions of Diphenylamino Group‐Substituted Malachite Green Derivatives Reviewed

    Toshiaki Mori, Kohei Sekine, Kyohei Kawashima, Toshifumi Mori, Yoichiro Kuninobu

    European Journal of Organic Chemistry   2022 ( 31 )   2022.8   ISSN:1434-193X eISSN:1099-0690

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    DOI: 10.1002/ejoc.202200873

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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   24 ( 23 )   4281 - 4285   2022.6   ISSN:15237060 eISSN:15237052

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    We have developed the divergent deaminative borylation and hydrodeamination of primary aromatic amines using bis(pinacolato)diboron. These transformations can be switched by the reaction conditions. Mechanistic and computational studies have suggested that the cleavage of the C–N bond and the formation of C–B bond are unlikely to involve free aryl radical intermediates. However, hydrodeamination is shown to proceed via hydrogen atom transfer between the corresponding aryl radical and an ethereal solvent.

    DOI: 10.1021/acs.orglett.2c01663

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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   ISSN:00219606 eISSN:10897690

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    A method for obtaining appropriate reaction coordinates is required to identify transition states distinguishing the product and reactant in complex molecular systems. Recently, abundant research has been devoted to obtaining reaction coordinates using artificial neural networks from deep learning literature, where many collective variables are typically utilized in the input layer. However, it is difficult to explain the details of which collective variables contribute to the predicted reaction coordinates owing to the complexity of the nonlinear functions in deep neural networks. To overcome this limitation, we used Explainable Artificial Intelligence (XAI) methods of the Local Interpretable Model-agnostic Explanation (LIME) and the game theory-based framework known as Shapley Additive exPlanations (SHAP). We demonstrated that XAI enables us to obtain the degree of contribution of each collective variable to reaction coordinates that is determined by nonlinear regressions with deep learning for the committor of the alanine dipeptide isomerization in vacuum. In particular, both LIME and SHAP provide important features to the predicted reaction coordinates, which are characterized by appropriate dihedral angles consistent with those previously reported from the committor test analysis. The present study offers an AI-aided framework to explain the appropriate reaction coordinates, which acquires considerable significance when the number of degrees of freedom increases.

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    Repository Public URL: http://hdl.handle.net/2324/4785205

  • 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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    DOI: 10.1063/5.0009066

  • 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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    DOI: 10.1021/acs.jctc.9b01279

  • 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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    DOI: 10.1063/1.5018130

  • 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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    Excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene. I. Time-resolved photoelectron-photoion coincidence spectroscopy.

    DOI: 10.1063/1.5016452

  • 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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    DOI: 10.1039/c7cp06299k

  • 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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    DOI: 10.1039/c7cp06324e

  • 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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    DOI: 10.1021/acs.jpcb.6b08066

  • 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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    DOI: 10.1021/acs.jctc.5b01137

  • 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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    DOI: 10.1126/science.1261040

  • 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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    DOI: 10.1063/1.4916641

  • 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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    DOI: 10.1021/jp503372v

  • 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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    DOI: 10.1021/jp501339t

  • 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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    DOI: 10.1021/jz500352x

  • 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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    DOI: 10.1021/ct400487e

  • 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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    Exploring the Conical Intersection Seam: The Seam Space Nudged Elastic Band Method.

    DOI: 10.1021/ct300892t

  • 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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    DOI: 10.1039/c2fd20055d

  • 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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    DOI: 10.1021/jp2097185

  • 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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    DOI: 10.1063/1.3472033

  • 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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    DOI: 10.1016/j.cplett.2009.05.067

  • 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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    DOI: 10.1021/jp9009788

  • 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

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    DOI: 10.1016/j.cplett.2007.02.018

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Presentations

  • 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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    Event date: 2023.7

    Language:English   Presentation type:Oral presentation (general)  

    Country:United States  

  • Role of dynamics in conformational transitions and functions of biomolecules Invited

    2022.3 

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    Event date: 2022.3

    Language:English   Presentation type:Oral presentation (general)  

    Country:Japan  

  • 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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    Event date: 2024.1

    Language:English   Presentation type:Oral presentation (general)  

    Country:Thailand  

  • Theoretical study on the role of dynamics during enzyme catalysis Invited

    Toshifumi Mori

    Pure and Applied Chemistry International Conference 2024  2024.1 

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    Event date: 2024.1

    Language:English   Presentation type:Oral presentation (invited, special)  

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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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    Event date: 2023.12

    Language:Japanese  

    Venue:福井県福井市   Country:Japan  

  • 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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    Event date: 2023.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:大阪府豊中市   Country:Japan  

  • Theoretical study on the role of protein conformational dynamics during enzyme catalysis Invited International conference

    2023.9 

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    Event date: 2023.9

    Language:English   Presentation type:Oral presentation (general)  

    Country:Japan  

  • Theoretical study on the role of protein conformational dynamics during enzyme catalysis Invited

    2023.9 

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    Event date: 2023.9

    Language:English   Presentation type:Oral presentation (invited, special)  

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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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    Event date: 2023.8

    Language:English   Presentation type:Oral presentation (general)  

    Country:Japan  

  • Bridging the gap between static and dynamic reaction mechanisms in enzyme catalysis Invited

    Toshifumi Mori

    Multi-scale Molecular Dynamics Simulation and Machine Learning of Biomolecular Systems Workshop  2023.8 

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    Event date: 2023.8

    Language:English   Presentation type:Oral presentation (invited, special)  

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  • Dissecting the heterogeneous dynamics of proteins during folding and catalysis Invited

    Toshifumi Mori

    Telluride Science Research Center Workshop on Protein Dynamics  2023.7 

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    Event date: 2023.7

    Language:English   Presentation type:Oral presentation (invited, special)  

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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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    Event date: 2023.3

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:沖縄   Country:Japan  

  • 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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    Event date: 2022.12

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:東京   Country:Japan  

  • 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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    Event date: 2022.12

    Language:English   Presentation type:Oral presentation (general)  

    Country:Japan  

    Elucidating the Role of Dynamics During Enzyme Catalysis using Molecular Simulations
    Toshifumi Mori
    7th International Symposium of Quantum Beam Science at Ibaraki University

  • Elucidating the Role of Dynamics During Enzyme Catalysis using Molecular Simulations Invited

    Toshifumi Mori

    7th International Symposium of Quantum Beam Science at Ibaraki University  2022.12 

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    Event date: 2022.12

    Language:English   Presentation type:Oral presentation (invited, special)  

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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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    Event date: 2022.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:北海道   Country:Japan  

  • Theoretical study on the conformational dynamics of proteins in disordered states under different solvent environments Invited

    Toshifumi Mori

    The 60th Annual Meeting of the Biophysical Society of Japan;Symposium on Protein aggregation driven by dynamic solution environments  2022.9 

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    Event date: 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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    Event date: 2022.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:神奈川   Country:Japan  

  • 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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    Event date: 2022.9

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

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  • Role of dynamics in conformational transitions and functions of biomolecules Invited

    Toshifumi Mori

    2022.3 

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    Event date: 2022.3

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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 

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    Event date: 2022.1

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:オンライン   Country:Japan  

  • 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 

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    Event date: 2022.1

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

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  • 哺乳類メラノプシンと特異的アンタゴニストとの相互作用の生化学的・理論的解析(Biochemical and computational analyses of interactions between mammalian melanopsins and a specific antagonist)

    Obayashi Kohei, Zou Ruisi, Mori Toshifumi, Tsukamoto Hisao

    生物物理  2023.10  (一社)日本生物物理学会

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    Language:English  

  • 動的溶液環境が駆動するタンパク質凝集 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(Theoretical study on the conformational dynamics of proteins in disordered states under different solvent environments)

    Mori Toshifumi

    生物物理  2022.8  (一社)日本生物物理学会

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    Language:English  

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MISC

  • 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

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    Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)  

    酵素の構造揺らぎは酵素反応の活性に重要であるが,実際に酵素の運動が化学反応にどのように関与するのかは明らかでない.我々は,プロリン異性化酵素Pin1が触媒する異性化反応の静的(自由エネルギー面上の反応経路)および動的(遷移経路)機構の解析を行い,2つの経路の違いと構造励起状態の重要性を見出してきた.今回,交差エントロピーの最小化法を用いて2つの反応経路を特徴づける反応座標を調べた.その結果,静的な反応経路では様々な基質−酵素相互作用が関与しているのに対して,遷移経路では局所的な座標が顕著な寄与を果たしていることが分かり,2つの経路の違いを特徴づける分子機構が見えた.

Professional Memberships

  • The Molecular Simulation Society of Japan

  • Japan Society of Molecular Science

  • The Biophysical Society of Japan

Committee Memberships

  • 分子科学会   顕彰委員会委員   Domestic

    2022.10 - 2024.9   

Academic Activities

  • 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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    Type:Academic society, research group, etc. 

  • 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

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    Type:Competition, symposium, etc. 

Research Projects

  • Elucidating the molecular mechanism of chiral chromatography from theoretical approaches

    Grant number:24K21756  2024.6 - 2027.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Challenging Research (Exploratory)

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    Grant type:Scientific research funding

    CiNii Research

  • Theoretical study of reaction dynamics of enzyme catalysis

    Grant number:23KK0254  2024 - 2026

    Grants-in-Aid for Scientific Research  Fund for the Promotion of Joint International Research (Fostering Joint International Research)

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    Grant type:Scientific research funding

    CiNii Research

  • Theoretical study on the molecular mechanism of conformational transitions and catalysis in enzymes

    Grant number:23K23303  2022.4 - 2026.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

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    Grant type:Scientific research funding

    CiNii Research

  • 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)

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    Authorship:Principal investigator  Grant type:Scientific research funding

  • 令和4年度学術研究活動助成事業

    2022

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    Grant type:Donation

  • Development of DYASIN: Novel Approach to Enantioenriched Chiral Molecules

    Grant number:20H05677  2020 - 2025

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (S)

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    Authorship:Coinvestigator(s)  Grant type:Scientific research funding

    CiNii Research

  • 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)

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    Authorship:Principal investigator  Grant type:Scientific research funding

  • 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)

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    Authorship:Principal investigator  Grant type:Scientific research funding

  • 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)

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    Authorship:Principal investigator  Grant type:Scientific research funding

  • 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

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    Authorship:Principal investigator  Grant type:Scientific research funding

  • 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

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    Grant type:Scientific research funding

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Class subject

  • 計算化学

    2023.6 - 2023.8   Summer quarter

  • 総合理工学修士実験

    2023.4 - 2024.3   Full year

  • 総合理工学修士演習

    2023.4 - 2024.3   Full year

  • 総合理工学修士演習

    2023.4 - 2024.3   Full year

  • 機能有機化学

    2023.4 - 2023.6   Spring quarter

  • 計算化学

    2022.6 - 2022.8   Summer quarter

  • 総合理工学修士演習

    2022.4 - 2023.3   Full year

  • 総合理工学修士実験

    2022.4 - 2023.3   Full year

  • 機能有機化学

    2022.4 - 2022.6   Spring quarter

  • 有機機器分析

    2022.4 - 2022.6   Spring quarter

  • 計算化学

    2021.6 - 2021.8   Summer quarter

  • 機能有機化学

    2021.4 - 2021.6   Spring quarter

  • 有機機器分析

    2021.4 - 2021.6   Spring quarter

  • 機能有機化学

    2020.10 - 2021.3   Second semester

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FD Participation

  • 2022.1   Role:Participation   Title:先導研FD

    Organizer:[Undergraduate school/graduate school/graduate faculty]

  • 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.

  • 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

Social Activities

  • 出前授業(甲山中学校・3年生)

    Role(s): Lecturer

    2015.11

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    Type:Visiting lecture

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Travel Abroad

  • 2012.10 - 2013.11

    Staying countory name 1:United States   Staying institution name 1:University of Wisconsin, Madison

  • 2010.4 - 2012.9

    Staying countory name 1:United States   Staying institution name 1:Stanford大学