Publications

Google Scholar / ORCID profiles
  1. K. Okada, T. Kikutsuji, K. Okazaki*, T. Mori*, K. Kim*, N. Matubayasi*, “Unveiling interatomic distances influencing the reaction coordinates in alanine dipeptide isomerization: An explainable deep learning approach”, arXiv:2402.08448
  2. Y. Furuike, Y. Onoue, S. Saito, T. Mori*, S. Akiyama*, “The priming phosphorylation of KaiC is activated by the release of its autokinase autoinhibition”, BioRxiv:2024.03.21.584037
  3. A. Shiozuka, D. Wu, K. Kawashima, T. Mori, K. Sekine*, Y. Kuninobu*, “Carbamoylarylation of Alkenes with N-Aryl Oxamic Acids Involving 1,4-Aryl Migration Via C(aryl)–N Bond Cleavage”, ACS Catal. 14, 5972–5977 (2024)
  4. J. Ono‡, Y. Matsumura‡, T. Mori‡, S. Saito*, “Conformational Dynamics in Proteins: Entangled Slow Fluctuations and Nonequilibrium Reaction Events”, J. Phys. Chem. B 128, 20-32 (2024) ‡contributed equally
  5. T. Mori*, N. Yoshida, “Tuning the ATP–ATP and ATP–disordered protein interactions in high ATP concentration by altering water models”, J. Chem. Phys. 159, 035102 (2023)
  6. S. Sittiwanichai, D. Japrung, T. Mori*, P. Pongprayoon*, “Structural and Dynamic Alteration of Glycated Human Serum Albumin in Schiff Base and Amadori Adducts: A Molecular Simulation Study”, J. Chem. Phys. B 127, 5230-5240 (2023)
  7. D. Wu, A. Shiozuka, K. Kawashima, T. Mori, K. Sekine*, Y. Kuninobu*, “Bifunctional 1-Hydroxypyrene Photocatalyst for Hydrodesulfurization via Reductive C(Aryl)–S Bond Cleavage”, Org. Lett. 25, 3293-3297 (2023)
  8. T. Mori, K. Sekine, K. Kawashima, T. Mori, Y. Kuninobu*, “Near-Infrared and Dual Emissions of Diphenylamino Group-Substituted Malachite Green Derivatives”, Eur. J. Org. Chem. 2022, e202200873 (2022)
  9. T. Mori*, S. Saito*, “Molecular Insights into the Intrinsic Dynamics and their Roles During Catalysis in Pin1 Peptidyl-prolyl Isomerase”, J. Phys. Chem. B 126, 5185-5193 (2022)
  10. A. Shiozuka, K. Sekine*, T. Toki, K. Kawashima, T. Mori*, Y. Kuninobu*, “Photoinduced Divergent Deaminative Borylation and Hydrodeamination of Primary Aromatic Amines”, Org. Lett. 24, 4281-4285 (2022)
  11. T. Kikutsuji, Y. Mori, K. Okazaki*, T. Mori*, K. Kim*, N. Matubayasi*, “Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI)”, J. Chem. Phys. 156, 154108 (2022)
  12. Y. Mori, K. Okazaki*, T. Mori*, K. Kim*, N. Matubayasi*, “Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide”, J. Chem. Phys. 153, 054115 (2020)
  13. 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)
  14. 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
  15. 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
  16. 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
  17. P. Pongprayoon*, T. Mori*, “Critical role of dimer formation in monosaccharide binding to human serum albumin”, Phys. Chem. Chem. Phys. 20, 3249-3257 (2018)
  18. M. Kalathingal, 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)
  19. 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)
  20. 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)
  21. 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
  22. T. Mori*, S. Saito*, “Dynamic heterogeneity in the folding/unfolding transitions of FiP35”, J. Chem. Phys. 142, 135101 (7 pages) (2015) Selected as one of the “2015’s most read papers” in J. Chem. Phys.
  23. 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)
  24. B. Holland, T. Mori, T. J. Martínez*, A. G. Suits*, “Photochemical dynamics of Ethylene Cation C2H4+”, J. Phys. Chem. Lett. 5, 1467-1471 (2014)
  25. 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)
  26. 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)
  27. T. Mori and T. J. Martínez*, “Exploring the Conical Intersection Seam: The Seam Space Nudged Elastic Band Method”, J. Chem. Theory Comput. 9, 1155-1163 (2013)
  28. 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)
  29. T. Mori, W. J. Glover, M. Schuurman, T. J. Martínez*, “The role of Rydberg states in the photochemical dynamics of ethylene”, J. Phys. Chem. A 116, 2808-2818 (2012)
  30. T. Mori*, K. Nakano and S. Kato, “Conical intersections of free energy surfaces: Effect of electron correlation on a protonated Schiff base in methanol solution”, J. Chem. Phys. 133, 064107 (11 pages) (2010)
  31. T. Mori and 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)
  32. T. Mori and 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)
  33. T. Mori and S. Kato*, “Analytical RISM-MP2 free energy gradient method: Application to the Schlenk equilibrium of Grignard reagent”, Chem. Phys. Lett. 437, 159-163 (2007)

Invited Reviews in Japanese:

  1. T. Mori*, “酵素反応の静的・動的分子機構の解明に向けて”, アンサンブル (Ensemble) 23, 121-126 (2021)
  2. 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)
  3. 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)
  4. 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)
  5. 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)