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Dynamics of nitric oxide controlled by protein complex in bacterial system.
E. Terasaka, K. Yamada, P.-H. Wang, K. Hosokawa, R. Yamagiwa, K. Matsumoto, S. Ishii, T. Mori, K. Yagi, H. Sawai, H. Arai, H. Sugimoto, Y. Sugita, Y. Shiro, and T. Tosha.
Proc. Natl. Acad. Sci., U.S.A., 114, 9888-9893 (2017).
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Quantum simulation for muoniated and deuterated methyl radicals in implicit water solvent: combined ab initio path integral molecular dynamics and the polarizable continuum model simulation study.
Yamada, K.; Kawashima, Y.; Tachikawa, M.*
Mol. Simul., DOI:10.1080/08927022.2014.938070
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Molecular dynamics simulation of self-assembled nanocubes in methanol.
Mashiko, T.; Yamada, K.; Hiraoka, S.; Nagashima, U.; Tachikawa, M.*
Mol. Simul., DOI:10.1080/08927022.2014.940523
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Accurate Prediction of Hyperfine Coupling Constants in Muoniated and Hydrogenated Ethyl Radicals: Ab Initio Path Integral Simulation Study with Density Functional Theory Method.
Yamada, K.; Kawashima, Y.; Tachikawa, M.*
J. Chem. Theory. Comput., 10, 2005-2015 (2014).
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Analysis of Photoexcitation Energy Dependence in the Photo Luminescence of Firefly Luciferin.
Hiyama, M.*; Akiyama, H.; Mochizuki, T.; Yamada, K.; Koga, N.
Photochem. Photobio., 90, 820-828 (2014).
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Molecular dynamics and principal component analysis for a self-assembled nanocube in aqueous solution.
Mashiko, T.; Yamada, K.; Kojima, T.; Hiraoka, S.; Nagashima, U.; Tachikawa, M.*
Chem. Lett., 43, 366-368 (2014).
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Theoretical Study of Fluorescence Spectra Utilizing the pKa Values of Acids in Their Excited States.
Hiyama, M.*; Akiyama, H.; Yamada, K.; Koga, N.
Photochem. Photobio., 90, 35-44 (2014).
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Muon-electron hyperfine coupling constants of muoniated ethyl radical: a path integral simulations study with semiempirical molecular orbital method.
Yamada, K.; Kawashima, Y.; Tachikawa, M.*
Chin. J. Phys., 52, 126-137 (2014).
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Theoretical Study of Firefly Luciferin pKa values —Relative Absorption Intensity in Aqueous Solutions.
Hiyama, M.*; Akiyama, H.; Yamada, K.; Koga, N.
Photochem. Photobio., 89, 571-578 (2012).
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Variationally Determined Electronic States for the Theoretical Analysis of Intramolecular Interaction. II. Qualitative Nature of the P–O Bond in Phosphine Oxides.
Yamada, K.; Koga, N.*
J. Comput. Chem., 34, 149-161 (2012).
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Theoretical Study of Absorption and Fluorescence Spectra of Firefly Luciferin in Aqueous Solutions.
Hiyama, M.*; Akiyama, H.; Yamada, K.; Koga, N.
Photochem. Photobio., 88, 889-898 (2012).
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Variationally determined electronic states for the theoretical analysis of intramolecular interaction: I. Resonance energy and rotational barrier of the C–N bond in formamide and its analogs.
Yamada, K.; Koga, N.*
Theor. Chem. Acc., 131, 1178-1195 (2012).
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Toward a New Approach for Determination of Solute's Charge Distribution to Analyze Interatomic Electrostatic Interactions in QM/MM Simulations.
Yamada, K.; Koyano, Y.; Okamoto, T.; Asada, T.; Koga, N.*; Nagaoka, M.*
J. Comput. Chem., 32, 3092-3104 (2011).
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A Minimal Implementation of the AMBER–GAUSSIAN Interface for Ab Initio QM/MM-MD Simulation.
Okamoto, T.; Yamada, K.; Koyano, Y.; Asada, T.; Koga, N.; Nagaoka, M.*
J. Comput. Chem., 32, 932-942 (2011).
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Theoretical Study on the Reaction Mechanism for the Formation of 2-Methylpyridine Cobalt(I) Complex from Cobaltacyclopentadiene and Acetonitrile.
Dahy, A. A.; Yamada, K.; Koga, N.*
Organometallics, 28, 3636-3649 (2009).
