Shigehiko HAYASHI

Professor

Theoretical Chemistry Group

Department of Chemistry, Graduate School of Science

Kyoto University

Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto 606-8502

Tel: +81-75-753-4006,  Fax: +81-75-753-4000

E-Mail: hayashig(at)kuchem.kyoto-u.ac.jp

Class:

Basic Physical Chemistry (Quantum Mechanics) (05/29/2019) Problems #1 Solutions #1

Basic Physical Chemistry (Quantum Mechanics) (06/19/2019) Problems #2 Solutions #2

Basic Physical Chemistry (Quantum Mechanics) (07/17/2019) Problems #3 Solutions #3

Basic Physical Chemistry (Thermodynamics) (05/29/2019) Problems #1 Solutions #1

Basic Physical Chemistry (Thermodynamics) (07/17/2019) Problems #2 Solutions #2

Quantum Chemistry II (06/27/2019) Problems #1 Solutions #1

Publications:

Role of bulk water environment in regulation of functional hydrogen-bond network in photoactive yellow protein. Koichi Tamura and Shigehiko Hayashi*, Journal of Physical Chemistry B, 119:15537-15549, 2015.

Molecular mechanism of wide photoabsorption spectral shifts of color variants of human cellular retinol binding protein II. Cheng Cheng, Motoshi Kamiya, Yoshihiro Uchida, Shigehiko Hayashi*, Journal of the American Chemical Society, 137:13362-13370, 2015.

Molecular dynamics of channelrhodopsin at the early stages of channel opening. Mizuki Takemoto, Hideaki E. Kato, Michio Koyama, Jumpei Ito, Motoshi Kamiya, Shigehiko Hayashi, Andres D. Maturana, Karl Deisseroth, Ryuichiro Ishitani*, Osamu Nureki*, PLoS ONE, 10:e0131094, 2015.

Linear response path following: a molecular dynamics method to simulate global conformational changes of protein upon ligand binding. Koichi Tamura and Shigehiko Hayashi*, Journal of Chemical Theory and Computation, 11:2900-2917, 2015.

Atomistic design of microbial opsin-based blue-shifted optogenetics tools. Hideaki E. Kato, Motoshi Kamiya, Seiya Sugo, Jumpei Ito, Reiya Taniguchi, Ayaka Orito, Kunio Hirata, Ayumu Inutsuka, Akihiro Yamanaka, Andres D. Maturana, Ryuichiro Ishitani, Yuki Sudo, Shigehiko Hayashi*, and Osamu Nureki*, Nature Communications, 6:7177, 2015.

Converting a light-driven proton pump into a light-gated proton channel. Keiichi Inoue, Takashi Tsukamoto, Kazumi Shimono, Yuto Suzuki, Seiji Miyauchi, Shigehiko Hayashi, Hideki Kandori, and Yuki Sudo*, Journal of the American Chemical Society, 137:3291-3299, 2015.

Key chemical factors of arginine finger catalysis of F1-ATPase clarified by an unnatural amino acid mutation. Ayako Yukawa, Ryota Iino, Rikiya Watanabe, Shigehiko Hayashi, and Hiroyuki Noji*, Biochemistry, 54:472-480, 2015.

Quantum Biology of Retinal. Klaus Schulten and Shigehiko Hayashi, Quantum Effects in Biology, Cambridge University Press, Chapt. 11, 237-263, 2014.

Theoretical study on excited states of bacteriochlorophyll a in solutions with density functional assessment. Masahiro Higashi*, Takahiro Kosugi, Shigehiko Hayashi, and Shinji Saito*, Journal of Physical Chemistry B, 118:10906-10918, 2014.

Perspective: Silencing neurons with light. Shigehiko Hayashi*, Science, 344:369-370, 2014.

Facile catch and release of fullerenes using a photoresponsive molecular tube. Norifumi Kishi, Munetaka Akita, Motoshi Kamiya, Shigehiko Hayashi, Hsiu-Fu Hsu, and Michito Yoshizawa* Journal of the American Chemical Society, 135:12976-12979, 2013.

A blue-shifted light-driven proton pump for neural silencing. Yuki Sudo*, Ayako Okazaki, Hikaru Ono, Jin Yagasaki, Seiya Sugo, Motoshi Kamiya, Louisa Reissig, Keiichi Inoue, Kunio Ihara, Hideki Kandori, Shin Takagi and Shigehiko Hayashi, Journal of Biological Chemistry, 288:20624-20632, 2013.

Adenosine triphosphate hydrolysis mechanism in kinesin studied by combined quantum-mechanical/molecular-mechanical metadynamics simulations. Matthew J. McGrath*, I.-F. Will Kuo, Shigehiko Hayashi, and Shoji Takada*, Journal of the American Chemical Society, 135:8908-8919, 2013.

The reaction mechanism of Claisen rearrangement obtained by transition state spectroscopy and single direct-dynamics trajectory. Izumi Iwakura*, Yu Kaneko, Shigehiko Hayashi, Atsushi Yabushita, and Takayoshi Kobayashi*, Molecules, 18:1995-2004, 2013.

Structural and spectral characterizations of C1C2 channelrhodopsin and its mutants by molecular simulations. Motoshi Kamiya, Hideaki E. Kato, Ryuichiro Ishitani, Osamu Nureki, and Shigehiko Hayashi*, Chemical Physics Letters, 556:266-271, 2013.

Molecular mechanism of ATP hydrolysis in F1-ATPase revealed by molecular simulations and single molecule observations. Shigehiko Hayashi*, Hiroshi Ueno, Abdul Rajjak Shaikh, Myco Umemura, Motoshi Kamiya, Yuko Ito, Mitsunori Ikeguchi, Yoshihito Komoriya, Ryota Iino, and Hiroyuki Noji. Journal of the American Chemical Society, 134:8447-8454, 2012.

Crucial role of protein flexibility in formation of a stable reaction transition state in an a-amylase catalysis. Kosugi Takahiro and Shigehiko Hayashi*. Journal of the American Chemical Society, 134:7045-7055, 2012.

Crystal structure of the channelrhodopsin light-gated cation channel. Hideaki E. Kato, Feng Zhang, Ofer Yizhar, Charu Ramakrishnan, Tomohiro Nishizawa, Kunio Hirata, Jumpei Ito, Yusuke Aita, Tomoya Tsukazaki, Shigehiko Hayashi, Peter Hegemann, Andres D. Maturana, Ryuichiro Ishitani, Karl Deisseroth*, and Osamu Nureki*. Nature, 482:369-374, 2012.

QM/MM reweighting free energy SCF for geometry optimization on extensive free energy surface of enzymatic reaction. Takahiro Kosugi and Shigehiko Hayashi*. Journal of Chemical Theory and Computation, 8:322-334, 2012.

A theoretical study on excited state double proton transfer reaction of a 7-azaindole dimer: an ab initio potential energy surface and its empirical valence bond model. Kohei Ando*, Shigehiko Hayashi, and Shigeki Kato. Physical Chemistry Chemical Physics, 13:11118-11127, 2011.

Local entropy difference upon a substrate binding of a psychrophilic a-amylase and a mesophilic homologue. Takahiro Kosugi and Shigehiko Hayashi*. Chemical Physics Letters, 501:517-522, 2011.

Protein collective motions coupled to ligand migration in myoglobin. Yasutaka Nishihara, Shigeki Kato, and Shigehiko Hayashi*. Biophysical Journal, 98:1649-1657, 2010.

Electronic coulombic coupling of excitation-energy transfer in xanthorhodopsin. Kazuhiro Fujimoto and Shigehiko Hayashi*. Journal of the American Chemical Society (communication), 131:14152-14153, 2009.

Proton transfer reactions in reaction center of photosynthetic bacteria, Rhodobacter sphaeroides. Yu Kaneko, Shigehiko Hayashi, and Iwao Ohmine*. Journal of Physical Chemistry B, 113:8993-9003, 2009.

Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation. Shigehiko Hayashi*, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 96:403-416, 2009.

A search for ligand diffusion pathway in myoglobin using a metadynamics simulation. Yasutaka Nishihara, Shigehiko Hayashi, and Shigeki Kato*. Chmical Physics Letters, 464:220-225, 2008.

Mechanism of efficient firefly bioluminescence via adiabatic transition state and seam of sloped conical intersection. Lung Wa Chung, Shigehiko Hayashi, Marcus Lundberg, Toru Nakatsu, Hiroaki Kato, and Keiji Morokuma*. Journal of the American Chemical Society (communication), 130:12880-12881, 2008.

Geometry optimization based on linear response free energy with quantum mechanical/molecular mechanical method: Application to Menshutkin-type and Claisen rearrangement reactions in aqueous solution. Masahiro Higashi, Shigehiko Hayashi, and Shigeki Kato*. Journal of Chemical Physics, 126:Art. No. 144503, 2007.

Transition state determination of enzyme reaction on free energy surface: Application to chorismate mutase. Masahiro Higashi, Shigehiko Hayashi, and Shigeki Kato*. Chemical Physics Letters, 437:293-297, 2007.

Analysis of structure and function of F1-ATPase molecular motor protein studied by molecular simulations. Shigehiko Hayashi*. Protein, Nucleic Acid and Enzyme, 52:329-334, 2007 (a review in Japanese).

Theoretical studies on color tuning mechanism in retinal proteins. Kazuhiro Fujimoto, Shigehiko Hayashi, Jun-ya Hasegawa, and Hiroshi Nakatsuji*. Journal of Chemical Theory and Computation, 3:605-618, 2007.

On the color tuning mechanism of human-blue visual pigment: SAC-CI and QM/MM study. Kazuhiro Fujimoto, Jun-ya Hasegawa, Shigehiko Hayashi, and Hiroshi Nakatsuji*. Chemical Physics Letters, 432:252-256, 2006.

Chemical reactions and functions of biological systems studied by hybrid QM/MM molecular simulations. Shigehiko Hayashi*. Biophysics (Seibutsu Butsuri), 46:76-81, 2006 (a review in Japanese).

Critical role of a thiolate-quinone charge transfer complex and its adduct form in de novo disulfide bond generation by DsbB. Kenji Inaba, Yoh-hei Takahashi, Koreaki Ito*, and Shigehiko Hayashi*. Proceedings of the National Academy of Sciences, USA., 103:287-292, 2006.

Simulation of functions and dynamics of proteins. Shigehiko Hayashi*. In Protein Science, ed. Yuji Goto, Kunihiro Kuwajima, and Katsuyuki Tanizawa, published by Kagaku Dojin, Chapter 5-2:233-243, 2005 (a book chapter in Japanese).

Mechanism of color tuning in retinal proteins: SAC-CI and QM/MM study. Kazuhiro Fujimoto, Jun-ya Hasegawa, Shigehiko Hayashi, Shigeki Kato, and Hiroshi Nakatsuji*. Chemical Physics Letters, 414:239-242, 2005.

A theoretical study on mechanism of bacteriorhodopsin's proton pump. Shigehiko Hayashi*. Chemical Information and Computer Sciences The Chemical Society of Japan Bulletin, 22:86-91, 2004 (a review in Japanese).

Role of hydrogen-bond network in energy storage of bacteriorhodopsin's light driven proton pump revealed by ab initio normal mode analysis. Shigehiko Hayashi, Emad Tajkhorshid, Hideki Kandori, and Klaus Schulten*. Journal of the American Chemical Society (communication), 126:10516-10517, 2004.

ATP hydrolysis in the bTP and bDP catalytic sites of F1-ATPase. Markus Dittrich, Shigehiko Hayashi, and Klaus Schulten*. Biophysical Journal,  87:2954-2967, 2004.

Thermophilic ATP synthase has a decamer c-ring; indication of non-integer 10:3 H+/ATP ratio and permissive elastic coupling. Noriyo Mitome, Toshiharu Suzuki, Shigehiko Hayashi, and Masasuke Yoshida*. Proceedings of the National Academy of Sciences, USA., 101:12159-12164, 2004.

On the mechanism of ATP hydrolysis in F1-ATPase. Markus Dittrich, Shigehiko Hayashi, and Klaus Schulten*. Biophysical Journal, 85:2253-2266, 2003.

Molecular dynamics simulation of bacteriorhodopsin's photoisomerization using ab initio forces for the excited chromophore. Shigehiko Hayashi, Emad Tajkhorshid, and Klaus Schulten*. Biophysical Journal, 85:1440-1449, 2003.

Molecular dynamics investigation of primary photoinduced events in the activation ofrhodopsin.Jan Saam, Emad Tajkhorshid, Shigehiko Hayashi, and Klaus Schulten*. Biophysical. Journal, 83:3097-3112, 2002.

Structural changes during the formation of early intermediates in the bacteriorhodopsin photocycle. Shigehiko Hayashi, Emad Tajkhorshid, and Klaus Schulten*. Biophysical. Journal, 83:1281-1297, 2002.

Structure and spectral tuning mechanism of photo-sensory protein sRII (pR). Shigehiko Hayashi, Emad Tajkhorshid, and Klaus Schulten*. Biophysics (Seibutsu-Butsuri) 42:127-130, 2002 (a review in Japanese).

Structural determinants of spectral tuning in retinal proteins - bacteriorhodopsin vs sensory rhodopsin II. Shigehiko Hayashi, Emad Tajkhorshid, Eva Pebay-Peyroula, Antoine Royant, Ehud M. Landau, Javier Navarro, and Klaus Schulten*. Journal of Physical Chemistry B, 105:10124-10131, 2001, featuring the cover page of the journal.

Proton transfer in bacteriorhodopsin: structure, excitation, IR spectra, and potential energy surface analyses by an ab initio QM/MM Method. Shigehiko Hayashi and Iwao Ohmine*. Journal of Physical Chemistry B, 104:10678-10691, 2000.

Solvent effect on intramolecular long-range electron-transfer reactions between porphyrin and benzoquinone in an acetonitrile solution: molecular dynamics calculations of reaction rate constants. Shigehiko Hayashi and Shigeki Kato*. Journal of Physical Chemistry A, 102:3333-3342, 1998.

Theoretical study of intramolecular long-range electron transfer reactions between porphyrin and benzoquinone: ab initio calculations of electronic coupling element. Shigehiko Hayashi and Shigeki Kato. Journal of Physical Chemistry A, 102:2878-2887, 1998.

Reaction dynamics of charge-transfer state formation of 4-(N,N-dimethylamino)benzonitrile in a methanol solution: theoretical analyses. Shigehiko Hayashi, Koji Ando, and Shigeki Kato*. Journal of Physical Chemistry, 99:955-964, 1995.

Electronic structures of poly-cations and -anions of C60. Possible mechanisms of organic ferromagnetism. K. Yamaguchi*, S. Hayashi, M. Okumura, M. Nakano, and W. Mori. Chemical Physics Letters, 226:372-380, 1994.

Education:

1988-1992 Hokkaido University, Japan. Awarded B.S. in chemistry.

1992-1994 Kyoto University, Japan. Awarded M.S. in chemistry.

1994-1997 Kyoto University, Japan. Awarded Ph.D. in chemistry.

Research and professional experience:

1996-1998 Research fellow of the Japan society for the promotion of science at Kyoto University,  working with Professor S. Kato.

1998-2001 Research fellow of the Japan society for the promotion of science at Nagoya University,  working with Professor I. Ohmine.

2000-2001 Visiting postdoctoral research associate at University of Illinois at Urbana-Champaign, working with Professor K. Schulten.

2001-2003 Postdoctoral research associate at University of Illinois at Urbana-Champaign, working with Professor K. Schulten.

2003-2005 Postdoctoral research associate at Fukui Institute for fundamental chemistry, Kyoto University.

2003-2006 Researcher of PRESTO, Japan Science and Technology Agency.

2005-2013 Associate Professor at Graduate School of Science, Kyoto University.

2013-present Professor at Graduate School of Science, Kyoto University.