• Toshifumi Mori

    Associate Professor

    Institute for Materials Science and Engineering, Kyushu University

  • News

    Looking for graduate students, external students and postdocs who are motivated and interested in the boundary of theoretical chemistry, organic chemistry and biophysics!

    If interested, please contact me!!

    Apr. 5, 2021

    Oct. 1, 2020

    Moved to Kyushu University, and started a new lab!

    Group web page is coming soon!

  • Research

    Chemical reaction plays an essential role in various complex systems, e.g. materials and proteins. Yet, how reaction occurs, and how it interacts with the environment, are often not clear. I am interested in the hierarchical events that occur around chemical reactions, and have been developing and applying theoretical tools to study these systems.

    My recent focus has been on the dynamics of protein itself, and how it affects the reaction in enzymes. I hope to pursue these research to understand the molecular mechanism of enzyme catalysis and protein function regulation by chemical reactions.

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    Conformational dynamics of enzyme and ligand during enzyme catalysis

    J. Phys. Chem. Lett. 10, 474-480 (2019) Suppl. Cover

    J. Chem. Theory Comput. 16, 3396-3407 (2020)

    We studied the transition dynamics during Pin1-catalyzed isomerization reaction using transition path sampling simulations. The results show that, in contrast to the coupled protein-ligand dynamics indicated by minimum free energy path, protein-ligand interactions necessary for catalysis are set up prior to the isomerization event, i.e. as a conformational excited state. Conformational flexibility of protein thus helps access the excited state during catalysis.

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    Molecular details behind protein's heterogeneous dynamics

    J. Phys. Chem. B 120, 11683-11691 (2016)

    J. Chem. Phys. 142, 135101 (2015)

    We proposed an approach to analyze the slow dynamics in MD trajectories. By studying the folding mechanisms of Pin1 WW domain and Villin headpiece, we found that folding/unfolding transitions happen in various time scales. Multiple transition pathways are found in both proteins, indicating that folding occurs in a heterogeneous manner, even in proteins as small as 35 residues.

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    Molecular origin of slow ATP hydrolysis in KaiC

    Science 349, 312-316 (2015)

    In collaboration with the experimental group lead by Prof. Akiyama at IMS, we have been studying the clock protein KaiC to understand the molecular mechanism of circadian rhythm in cyanobacteria. So far, we found that the slow ATP hydrolysis in the N-terminal domain of KaiC determines the circadian oscillation period, and revealed the molecular origin of this slowness.

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    Ligand binding at the water-material interface

    J. Phys. Chem. B 118, 8210-8220 (2014)

    J. Chem. Theory Comput. 9, 5059-5069 (2013)

    We studied the mechanism of peptide binding onto a titanium dioxide surface. The result shows that the water molecule on the surface needs to be accounted for to understand the binding mechanism. Furthermore, peptides on the surface were shown to sample conformations different from those in solution.

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    Simulating photochemical reaction dynamics

    J. Phys. Chem. A 116, 2808-2818 (2012)

    We developed a method to perform ab initio molecular dynamics simulations of photoreaction dynamics involving multiple electronic excited states. The method was applied to photoisomerizations of multiple molecules involving ethylene, and time-resolved photoelectron spectrum of ethylene was predicted.

  • Curriculum Vitae

    Professional Experience

    Associate Professor

    Institute for Materials Science and Engineering, Kyushu University, Oct. 2020 - present


    Assistant Professor

    Institute for Molecular Science, Dec. 2013 - Sep. 2020

    The Graduate University for Advanced Studies, Apr. 2014 - Sep. 2020


    Postdoctoral Researcher

    University of Wisconsin, Madison, Oct. 2012 - Nov. 2013

    (JSPS Postdoctoral fellow, Apr. 2013 - Nov. 2013)

    Supervisor: Qiang Cui


    Postdoctoral Researcher

    Stanford University, Apr. 2010 - Sep. 2012

    Supervisor: Todd J. Martínez



    Kyoto University

    Mar. 2010, Ph.D. in Chemistry, Graduate School of Science

    Ph.D. Advisor: Shigeki Kato


    Grants (from JSPS)

    • Apr. 2018 - Mar. 2021, Grant-in-Aid for Scientific Research (C)
    • Apr. 2016 - Mar. 2018, Grant-in-Aid for Scientific Research on Innovative Areas (Proposed Research)
    • Apr. 2015 - Mar. 2018, Grant-in-Aid for Young Scientists (B)
    • Aug. 2014 - Mar. 2015, Grant-in-Aid for Research Activity Startup
    • Apr. 2008 - Mar. 2010, Grant-in-Aid for JSPS Fellows



    • Apr. 2013 - Nov. 2013, JSPS Postdoctoral Fellow for Research Abroad
    • Apr. 2008 - Mar. 2010, JSPS Research Fellow (DC2)


    Honors & Awards

    • Sep. 2018, Young Scientist Award, Japan Society for Molecular Science
    • Sep. 2017, Early Carrier Presentation Award, The 55th Annual Meeting of The Biophysical Society of Japan
    • Jun. 2012, Postor Award, 14th International Congress of Quantum Chemistry
    • Sep. 2011, Presentation Award, Annual Meeting of Japan Society for Molecular Science
    • Sep. 2008, Poster Award, 2008 World Congress of World Association of Theoretical and Computational Chemists (WATOC2008)


    PDF version can be found here.

  • Publications

    (*: co-corresponding author, #: co-first author)

    1. Y. Mori, K. Okazaki*, T. Mori*, K. Kim*, N. Matsubayashi*, “Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide”, J. Chem. Phys. 153, 054115 (2020) [link]
    2. T. Mori*, S. Saito*, "Dissecting the dynamics during enzyme catalysis: A case study of Pin1 peptidyl-prolyl isomerase", J. Chem. Theory Comput. 16, 3396-3407 (2020) [link]
    3. T. Mori*, S. Saito*, "Conformational Excitation and Nonequilibrium Transition Facilitate Enzymatic Reactions: Application to Pin1 Peptidyl-Prolyl Isomerase", J. Phys. Chem. Lett. 10, 474-480 (2019) Suppl. Cover [link] [image]
    4. W. J. Glover, T. Mori, M. Schuurman, A. Boguslavskiy, O. Schalk, A. Stolow, T. J. Martínez, "Excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene. II. Ab initio multiple spawning simulations", J. Chem. Phys. 148, 164303 (2018) Featured Article [link]
    5. A. Boguslavskiy, O. Schalk, N. Gador, W. J. Glover, T. Mori, T. Schultz, M. Schuurman, T. J. Martínez, A. Stolow, "Excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene. I. Time-resolved photoelectron-photoion coincidence spectroscopy", J. Chem. Phys. 148, 164302 (2018) Featured Article [link]
    6. P. Pongprayoon*, T. Mori*, "Critical role of dimer formation in monosaccharide binding to human serum albumin", Phys. Chem. Chem. Phys. 20, 3249-3257 (2018) [link]
    7. K. Mahroof, T. Sumikama, T. Mori, S. Oiki, S. Saito, "Structure and dynamics of solvent molecules inside Polytheonamide B channel in different environments: A molecular dynamics study", Phys. Chem. Chem. Phys. 20, 3334-3348 (2018) [link]
    8. T. Mori*, S. Saito*, "Molecular Mechanism Behind the Fast Folding/Unfolding Transitions of Villin Headpiece Subdomain: Hierarchy and Heterogeneity", J. Phys. Chem. B 120, 11683-11691 (2016) [link]
    9. S. Aono, T. Mori, S. Sakaki, "3D-RISM-MP2 Approach to Hydration Structure of Pt(II) and Pd(II) Complexes: Unusual H-Ahead Mode vs Usual O-Ahead One", J. Chem. Theory Comput. 12, 1189-1206 (2016) [link]
    10. J. Abe#, T. Hiyama#, A. Mukaiyama#, S. Son#, T. Mori#, S. Saito, M. Osako, J. Wolanin, E. Yamashita, T. Kondo, S. Akiyama, "Atomic-Scale Origins of Slowness in the Cyanobacterial Circadian Clock", Science 349, 312-316 (2015) #contributed equally [link]
    11. T. Mori*, S. Saito*, "Dynamic Heterogeneity in the Folding/Unfolding Transitions of FiP35", J. Chem. Phys. 142, 135101 (2015) selected as one of the "2015's most read papers" in J. Chem. Phys. [link]
    12. P. Goyal, H.-J. Qian, S. Irle, X. Lu, D. Roston, T. Mori, M. Elstner, Q. Cui, "Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models", J. Phys. Chem. B Feature Article, 118, 11007-11027 (2014) [link]
    13. B. Joalland, T. Mori, T. J. Martínez, A. G. Suits, "Photochemical Dynamics of Ethylene Cation C2H4+", J. Phys. Chem. Lett. 5, 1467-1471 (2014) [link]
    14. T. Mori*, R. J. Hamers, J. A. Pedersen, Q. Cui*, "Integrated Hamiltonian Sampling: A Simple and Versatile Method for Free Energy Simulations and Conformational Sampling", J. Phys. Chem. B, 118, 8210-8220 (2014) [link]
    15. T. Mori, R. J. Hamers, J. A. Pedersen, Q. Cui, "An explicit consideration of desolvation is critical to binding free energy calculations of charged molecules at ionic surfaces", J. Chem. Theory Comput. 9, 5059-5069 (2013) [link]
    16. T. Mori, T. J. Martínez, "Exploring the Conical Intersection Seam: The Seam Space Nudged Elastic Band Method", J. Chem. Theory Comput. 9, 1155-1163 (2013) [link]
    17. T. Kuhlman, W. J. Glover, T. Mori, K. B. Møller, T. J. Martínez, "Between Ethylene and Polyenes - The Non-adiabatic Dynamics of cis-dienes", Faraday Discuss. 157, 193-212 (2012) [link]
    18. T. Mori, W. J. Glover, M. Schuurman, T. J. Martínez, "Role of Rydberg States in the Photochemical Dynamics of Ethylene", J. Phys. Chem. A 116, 2808-2818 (2012) [link]
    19. T. Mori*, K. Nakano, S. Kato, "Conical intersections of free energy surfaces: Effect of electron correlation on a protonated Schiff base in methanol solution", J. Chem. Phys. 113, 064107 (2010) [link]
    20.  T. Mori, S. Kato, "Dynamic electron correlation effect on conical intersections in photochemical ring-opening reaction of cyclohexadiene: MS-CASPT2 study", Chem. Phys. Lett. 476, 97-100 (2009) [link]
    21. T. Mori, S. Kato, "Grignard Reagents in Solution: Theoretical Study of the Equilibria and the Reaction with a Carbonyl Compound in Diethyl Ether Solvent", J. Phys. Chem. A 113, 6158-6165 (2009) [link]
    22. T. Mori, S. Kato, "Analytical RISM-MP2 free energy gradient method: Application to the Schlenk equilibrium of Grignard reagent", Chem. Phys. Lett. 437, 159-163 (2007) [link]
    Reviews in Japanese
    1. T. Mori*, “気相・凝縮系における反応ダイナミクスの理論研究 (Award Accounts)”, Molecular Science 13, A0106 (2019) [link]
    2. T. Mori*, “酵素のダイナミクスは酵素反応の理解に重要か?(Are Conformational Dynamics of Enzymes Important for Enzyme Catalysis?)”, 生物物理 (Seibutsu Butsuri) 59, 271-272 (2019) [link]
    3. T. Mori*, S. Saito*, "超長時間シミュレーションで見るタンパク質のフォールディング過程 (What We can Learn about Protein Folding from Ultra-long Molecular Dynamics Simulations) ", 生物物理 (Seibutsu Butsuri) , 57, 030-032 (2017) [link]
    4. T. Mori*, "分子の光化学反応における非断熱遷移と時間分解光電子スペクトル (Theory of nonadiabatic dynamics and time resolved photoelectron spectrum for photochemistry of molecules)", アンサンブル (Ensemble) 18, 240-243 (2016) [link]