Publications

Akihiro Kimura, Hirotaka Kitoh-Nishioka, Toru Kondo, Hirozo Oh-oka, Shigeru Itoh, Chihiro Azai (2024). Experimental and Theoretical Mutation of Exciton States on the Smallest Type-I Photosynthetic Reaction Center Complex of a Green Sulfur Bacterium Chlorobaclum tepidum. The Journal of Physical Chemistry B.

Tomoki Nishiyama, Hirotaka Kitoh-Nishioka, Senku Tanaka, Masahiko Maekawa, Takayoshi Kuroda-Sowa, Masaki Yoshida, Masako Kato, Takashi Okubo (2024). A copper(i) thiocyanate-based photoresponsive semiconducting 2D coordination polymer. Dalton Trans..

Hirofumi Yanagisawa, Markus Bohn, Hirotaka Kitoh-Nishioka, Florian Goschin, Matthias F. Kling (2023). Light-Induced Subnanometric Modulation of a Single-Molecule Electron Source. Phys. Rev. Lett..

Hiroya Nakata, Hirotaka Kitoh-Nishioka, Wakana Sakai, Cheol Ho Choi (2023). Toward Accurate Prediction of Ion Mobility in Organic Semiconductors by Atomistic Simulation. Journal of Chemical Theory and Computation.

Akihiro Kimura, Hirotaka Kitoh-Nishioka, Toshimichi Aota, Tasuku Hamaguchi, Koji Yonekura, Keisuke Kawakami, Kyoko Shinzawa-Itoh, Natsuko Inoue-Kashino, Kentaro Ifuku, Eiki Yamashita, Yasuhiro Kashino, Shigeru Itoh (2022). Theoretical Model of the Far-Red-Light-Adapted Photosystem I Reaction Center of Cyanobacterium Acaryochloris marina Using Chlorophyll d and the Effect of Chlorophyll Exchange. The Journal of Physical Chemistry B.

Yuhei Hosokawa, Pavel Müller, Hirotaka Kitoh-Nishioka, Shigenori Iwai, Junpei Yamamoto (2022). Limited solvation of an electron donating tryptophan stabilizes a photoinduced charge-separated state in plant (6--4) photolyase. Scientific Reports.

Shigenori Tanaka, Toshihito Umegaki, Akihiro Nishiyama, Hirotaka Kitoh-Nishioka (2022). Dynamical free energy based model for quantum decision making. Physica A: Statistical Mechanics and its Applications.

Hirotaka Kitoh-Nishioka, Hiroaki Umeda, Yasuteru Shigeta (2021). Open-Architecture Program of Fragment Molecular Orbital Method for Massive Parallel Computing (OpenFMO) with GPU Acceleration. Recent Advances of the Fragment Molecular Orbital Method.

Hirotaka Kitoh-Nishioka, Ryuma Sato, Yasuteru Shigeta, Koji Ando (2021). Linear Combination of Molecular Orbitals of Fragments (FMO-LCMO) Method: Its Application to Charge Transfer Studies. Recent Advances of the Fragment Molecular Orbital Method.

Akihiro Kimura, Hirotaka Kitoh-Nishioka, Yasuteru Shigeta, Shigeru Itoh (2021). Comparison between the Light-Harvesting Mechanisms of Type-I Photosynthetic Reaction Centers of Heliobacteria and Photosystem I: Pigment Site Energy Distribution and Exciton State. The Journal of Physical Chemistry B Vol. 125, num.15, pp. 3727-3738 (2021).

Hirotaka Kitoh-Nishioka, Yasuteru Shigeta, Koji Ando (2020). Tunneling matrix element and tunneling pathways of protein electron transfer calculated with a fragment molecular orbital method. The Journal of Chemical Physics Vol. 153, num.10, 104104 (2020).

Kenji Kamada, Ryuma Sato, Toshiko Mizokuro, Hirotaka Kito-Nishioka, Yasuteru Shigeta (2020). Photosynergetic Effects on Triplet--Triplet Annihilation Upconversion Processes in Solid Studied by Theory and Experiments. Photosynergetic Responses in Molecules and Molecular Aggregates.

Hirotaka Kitoh-Nishioka, Yasuteru Shigeta, Shigeru Itoh, Akihiro Kimura (2020). Excitonic Coupling on a Heliobacterial Symmetrical Type-I Reaction Center: Comparison with Photosystem I. The Journal of Physical Chemistry B Vol. 124, num.2, pp. 389–403 (2020).

Hirotaka Kitoh-Nishioka, Koji Ando (2019). Calculation of Charge-Transfer Electronic Coupling with Nonempirically Tuned Range-Separated Density Functional. The Journal of Physical Chemistry C Vol. 123, num.18, pp. 11351–11361 (2019).

Ryuma Sato, Hirotaka Kitoh-Nishioka, Kenji Kamada, Toshiko Mizokuro, Kenji Kobayashi, Yasuteru Shigeta (2018). Synergetic Effects of Triplet–Triplet Annihilation and Directional Triplet Exciton Migration in Organic Crystals for Photon Upconversion. The Journal of Physical Chemistry Letters Vol. 9, num.22, pp. 6638–6643 (2018).

Naoya Suzuki, Kayo Suda, Daisuke Yokogawa, Hirotaka Kitoh-Nishioka, Stephan Irle, Akihiro Ando, Luis M. G. Abegão, Kenji Kamada, Aiko Fukazawa, Shigehiro Yamaguchi (2018). Near infrared two-photon-excited and -emissive dyes based on a strapped excited-state intramolecular proton-transfer (ESIPT) scaffold. Chem. Sci. Vol. 9, issue 10, pp. 2666–2673 (2018).

Ryuma Sato, Hirotaka Kitoh-Nishioka, Koji Ando, Takahisa Yamato (2018). Electron Transfer Pathways of Cyclobutane Pyrimidine Dimer Photolyase Revisited. The Journal of Physical Chemistry B Vol. 122, num.27, pp. 6912–6921 (2018).

Ryuma Sato, Hirotaka Kitoh-Nishioka, Kenji Kamada, Toshiko Mizokuro, Kenji Kobayashi, Yasuteru Shigeta (2018). Does Inactive Alkyl Chain Enhance Triplet–Triplet Annihilation of 9,10-Diphenylanthracene Derivatives?. The Journal of Physical Chemistry C Vol. 122, num.10, pp. 5334–5340 (2018).

Ryuma Sato, Hirotaka Kitoh-Nishioka, Takeshi Yanai, Yasuteru Shigeta (2017). Theoretical Analyses of Triplet–Triplet Annihilation Process of 9,10-Diphenylanthracene in Solution. Chemistry Letters Vol. 46, num.6, pp. 873–875 (2017).

Hirotaka Kitoh-Nishioka, Kai Welke, Yoshio Nishimoto, Dmitri G. Fedorov, Stephan Irle (2017). Multiscale Simulations on Charge Transport in Covalent Organic Frameworks Including Dynamics of Transfer Integrals from the FMO-DFTB/LCMO Approach. The Journal of Physical Chemistry C Vol. 121, num.33, pp. 17712-17726 (2017).

Hirotaka Kitoh-Nishioka, Daisuke Yokogawa, Stephan Irle (2017). Förster Resonance Energy Transfer between Fluorescent Proteins: Efficient Transition Charge-Based Study. The Journal of Physical Chemistry C Vol. 121, num.8 pp.4220–4238 (2017).

Yasuteru Shigeta, Ryuhei Harada, Ryuma Sato, Hirotaka Kitoh-Nishioka, Thi Kieu My Bui, Akimasa Sato, Takaki Tokiwa, Akane Kyan, Yuki Ishii, Masato Kimatsuka, Sotaro Yamasaki, Megumi Kayanuma, Mitsuo Shoji (2017). Classical cumulant dynamics for statistical chemical physics. Molecular Simulation Vol. 43, num.13–16, pp. 1260–1268 (2017).

Hirotaka Kitoh-Nishioka, Koji Ando (2016). FMO3-LCMO study of electron transfer coupling matrix element and pathway: Application to hole transfer between two tryptophans through cis- and trans-polyproline-linker systems. The Journal of Chemical Physics Vol. 145, num. 11, 114103 (2016).

Hirotaka Kitoh-Nishioka, Koji Ando (2015). Electron transfer pathway analysis in bacterial photosynthetic reaction center. Chemical Science of $π$-Electron Systems.

Ryuma Sato, Hirotaka Kitoh-Nishioka, Koji Ando, Takahisa Yamato (2015). Computational study on the roles of amino acid residues in the active site formation mechanism of blue-light photoreceptors. Chemical Physics Letters Vol. 633, pp. 247–251 (2015).

Hirotaka Kitoh-Nishioka, Koji Ando (2015). Charge-transfer matrix elements by FMO-LCMO approach: Hole transfer in DNA with parameter tuned range-separated DFT. Chemical Physics Letters Vol. 621, pp.96–101 (2015).

Naoya Suzuki, Aiko Fukazawa, Kazuhiko Nagura, Shohei Saito, Hirotaka Kitoh-Nishioka, Daisuke Yokogawa, Stephan Irle, Shigehiro Yamaguchi (2014). A Strap Strategy for Construction of an Excited-State Intramolecular Proton Transfer (ESIPT) System with Dual Fluorescence. Angewandte Chemie International Edition Vol. 53, num.31, pp. 8231–8235 (2014).

Hirotaka Kitoh-Nishioka, Koji Ando (2012). Fragment Molecular Orbital Study on Electron Tunneling Mechanisms in Bacterial Photosynthetic Reaction Center. The Journal of Physical Chemistry B Vol. 116, num.43, pp. 12933–12945 (2012).

Hirotaka Nishioka, Koji Ando (2011). Pathway analysis of super-exchange electronic couplings in electron transfer reactions using a multi-configuration self-consistent field method. Phys. Chem. Chem. Phys. Vol. 13, issue 15, pp.7043–7059 (2011).

Hirotaka Nishioka, Koji Ando (2011). Electronic coupling calculation and pathway analysis of electron transfer reaction using ab initio fragment-based method. I. FMO–LCMO approach. The Journal of Chemical Physics Vol. 134, num. 20, 204109 (2011).

倭剛久, 西岡宏任, 由良敬 (2009). 理論計算＋生命情報学で初めて見いだされた機能性残基―DNA補修酵素の場合―. 生物物理 Vol. 49, num.4, pp. 196–197 (2009).

Yuji Miyazawa, Hirotaka Nishioka, Kei Yura, Takahisa Yamato (2008). Discrimination of Class I Cyclobutane Pyrimidine Dimer Photolyase from Blue Light Photoreceptors by Single Methionine Residue. Biophysical Journal Vol.94, Num. 6, pp.2194–2203 (2008).

Hirotaka Nishioka, Nobuharu Ueda, Toshiaki Kakitani (2008). Correlation between square of electron tunneling matrix element and donor-acceptor distance in fluctuating protein media. BIOPHYSICS Vol. 4 pp. 19–28 (2008).

Hirotaka Nishioka, Toshiaki Kakitani (2008). Average Electron Tunneling Route of the Electron Transfer in Protein Media. The Journal of Physical Chemistry B Vol. 112, num. 32, pp.9948-9958 (2008).

Hirotaka Nishioka, Akihiro Kimura, Takahisa Yamato, Toshiaki Kakitani (2007). Non-Condon Theory for the Energy Gap Dependence of Electron Transfer Rate. Frontiers of Computational Science.

H. Nishioka, T. Yamato, T. Kakitani (2006). Temperature dependence of the inelastic electron tunneling. Molecular Simulation Vol.32, Num. 9, pp.727–734 (2006).

Hirotaka Nishioka, Akihiro Kimura, Takahisa Yamato, Tsutomu Kawatsu, Toshiaki Kakitani (2005). Interference, Fluctuation, and Alternation of Electron Tunneling in Protein Media. 2. Non-Condon Theory for the Energy Gap Dependence of Electron Transfer Rate. The Journal of Physical Chemistry B Vol.109, Num. 32, pp.15621–15635 (2005).

Hirotaka Nishioka, Akihiro Kimura, Takahisa Yamato, Tsutomu Kawatsu, Toshiaki Kakitani (2005). Interference, Fluctuation, and Alternation of Electron Tunneling in Protein Media. 1. Two Tunneling Routes in Photosynthetic Reaction Center Alternate Due to Thermal Fluctuation of Protein Conformation. The Journal of Physical Chemistry B Vol.109, Num. 5, pp.1978–1987 (2005).