Shigehiko HAYASHI Associate 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 B Problems #1 (10/26/2009)

Basic Physical Chemistry B Problems #2 (11/16/2009)

Publications:

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 mioglobin 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 b_TP and b_DP 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-present Associate Professor at Graduate School of Science, Kyoto University.