論文 - 長岡 正隆
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The number-adaptive multiscale QM/MM molecular dynamics simulation: Application to liquid water 査読有り
N.Takenaka, Y.Kitamura, Y.Koyano, M.Nagaoka
Chemical Physics Letters 524 巻 ( 6 ) 頁: 56-61 2012年2月
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Spatio-Temporal Characteristics of the Transfer Free Energy of Apomyoglobin into the Molecular Crowding Condition with Trimethylamine N-oxide: A Study with Three Types of the Kirkwood-Buff Integral. 査読有り
I.Yu, K.Nakada, M.Nagaoka
The Journal of Physical Chemistry B 116 巻 ( 13 ) 頁: 4080-4088 2012年
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Toward a New Approach for Determination of Solute's Charge Distribution to Analyze Interatomic Electrostatic Interactions in QM/MM Simulations 査読有り
K.Yamada, Y.Koyano, T.Okamoto, T.Asada, N.Koga, M.Nagaoka
Journal of Computational Chemistry 32 巻 ( 14 ) 頁: 3082-3104 2011年11月
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On the Smoothing of Free Energy Landscape of Solute Molecules in Solution: A Demonstration of the Stability of Glycine Conformers via Ab Initio QM/MM Free Energy Calculation 査読有り
Y.Kitamura, N.Takenaka, Y.Koyano, M.Nagaoka
Chemical Physics Letters 514 巻 ( 4-6 ) 頁: 261-266 2011年10月
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A Minimal Implementation of the AMBER-GAUSSIAN Interface for Ab Initio QM/MM-MD Simulation 査読有り
T.Okamoto, K.Yamada, Y.Koyano, T.Asada, N.Koga, M.Nagaoka
Journal of computational Chemistry 32 巻 ( 5 ) 頁: 932-942 2011年4月
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Ab Initio Electron Correlated Studies on the Intracluster Reaction of NO+(H2O)n -> H3O+(H2O)n-2(HONO) (n=4 and 5) 査読有り
T.Asada, M.Nagaoka, S.Koseki
Physical Chemistry Chemical Physics 13 巻 ( 4 ) 頁: 1590-1596 2011年1月
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Incipient Structural and Vibrational Relaxation Process of Photolyzed Carbonmonoxy Myoglobin:Statistical Analysis by Perturbation Ensemble Molecular Dynamics Method 査読有り
M.Takayanagi, M.Nagaoka
Theoretical Chemistry Accounts 130 巻 ( 4-6 ) 頁: 1115-1129 2011年
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Reaction Path Optimization and Vibrational Frequency Analysis via Ab Initio QM/MM Free Energy Gradient (FEG) Method: Application to Isomerization Process of Glycine in Aqueous Solution 査読有り
N.Takenaka, Y.Kitamura, Y.Koyano, T.Asada, M.Nagaoka
Theoretical Chemistry Accounts 130 巻 ( 2-3 ) 頁: 215-226 2011年
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An Optimum Strategy for Solution Chemistry Using Semiempirical Molecular Orbital Method II: Primary Importance of Reproducing Electrostatic Interaction in the QM/MM Framework 査読有り
N.Takenaka, Y.Koyano, Y.Nakagawa, M.Nagaoka
Journal of Computational Chemistry 31 巻 ( 14 ) 頁: 2628-2641 2010年11月
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Unveiling Thermal Transitions of Polymers in Subnanometre Pores 査読有り
T.Uemura, N.Yanai, S.Watanabe, H.Tanaka, R.Numaguchi, M.T. Miyahara, Y.Ohta, M.Nagaoka, S.Kitagawa
Nature Communications 1 巻 頁: 83 2010年10月
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Influence of Hydrostatic Pressure on Dynamics and Spatial Distribution of Protein Partial Molar Volume: Time-Resolved Surficial Kirkwood-Buff Approach 査読有り
I.Yu, T.Tasaki, K.Nakada, M.Nagaoka
The Journal of Physical Chemistry B 114 巻 ( 38 ) 頁: 12392-12397 2010年9月
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Structural Dynamics of Clamshell Rotation during the Incipient Relaxation Process of Photodissociated Carbonmonoxy Myoglobin: Statistical Analysis by the Perturbation Ensemble Method 査読有り
M. Takayanagi, C. Iwahashi, M. Nagaoka
The Journal of Physical Chemistry B 114 巻 ( 38 ) 頁: 12340-12348 2010年9月
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On the Importance of Lennard-Jones Parameter Calibration in QM/MM Framework: Reaction Path Tracing via Free Energy Gradient Method for Ammonia Ionization Process in Aqueous Solution 査読有り
Y.Koyano, N.Takenaka, Y.Nakagawa, M.Nagaoka
Bulletin of the Chemical Society of Japan 83 巻 ( 5 ) 頁: 486-494 2010年5月
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An Optimum Strategy for Solution Chemistry Using Semiempirical Molecular Orbital Method: Importance of Description of Charge Distribution 査読有り
N.Takenaka, Y.Koyano, Y.Nakagawa, M.Nagaoka
Journal of Computational Chemistry 31 巻 ( 6 ) 頁: 1287-1296 2010年4月
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Microscopic Hydration Mechanism in the Ammonia Dissolution Process: Importance of the Solute QM Polarization 査読有り
N.Takenaka, Y.Koyano, M.Nagaoka
485 巻 ( 1-3 ) 頁: 119-123 2010年1月
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*Intrinsic Alteration in the Partial Molar Volume on the Protein Denaturation: Surficial Kirkwood-Buff Approach 査読有り
I.Yu, M.Takayanagi, M.Nagaoka
The Journal of Physical Chemistry B 113 巻 ( 11 ) 頁: 3543-3547 2009年2月
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Surficial Kirkwood-Buff Approach on the Preferential Interaction of Urea and Ectoine 査読有り
I.Yu, M.Nagaoka
Proceedings of International Symposium on Frontiers of Computational Science 2008 頁: 9-14 2008年11月
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Conformation and Molecular Dynamics of Single Polystyrene Chain Confined in Coordination Nanospace 査読有り
T.Uemura, S.Horike, K.Kitagawa, M.Mizuno, K.Endo, S.Bracco, A.Comotti, P.Sozzani, M.Nagaoka, S.Kitagawa
Journal of the American Chemical Society 130 巻 ( 21 ) 頁: 6781-6788 2008年5月
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Theoretical Characterization of Coordination Space: Adsorption State and Behavior of Small Molecules in Nanochanneled Metal-Organic Frameworks via Electronic State Theory, Molecular Mechanical and Monte Carlo Simulation 査読有り
M.Nagaoka, Y.Ohta, H.Hitomi
Coordination Chemistry Reviews 251 巻 ( 21-24 ) 頁: 2522-2536 2007年11月
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Microscopic Understanding of Preferential Exclusion of Compatible Solute Ectoine: Direct Interaction and Hydration Alteration 査読有り
I.Yu, Y.Jindo, M.Nagaoka
The Journal of Physical Chemistry B 111 巻 ( 34 ) 頁: 10231-10238 2007年8月