Publications

Title	Date published online	Journal, Vol.(No.), Pages (Year)	Author(s)
Atomistic Chemical Elucidation of the Higher-Rate Reaction Mechanism in Hf-Pyridyl Amido-Catalyzed Copolymerization of Ethene and 1-Octene: Application of Red Moon Simulation with Polymer Propagation Diagrams	Sep. 2023	The Journal of Physical Chemistry B, 127(36), 7735-7747 (2023)	S. Kanesato, K. Yasoshima, N. Misawa, K. Matsumoto, Y. Suzuki, N. Koga, M. Nagaoka
Microscopic Analysis of Mechanical Stability of SEI Layer Structure Depending on FEC Additive Concentration in Na-ion Batteries: Maximum Appearance in Vickers Hardness at the Lower FEC Concentration	May. 2023	ACS Omega, 8(19), 16570-16578 (2023)	A. Bouibes, N. Sakaki, M. Nagaoka
(Pyridylamido)Hf(IV)-catalyzed 1-octene polymerization reaction interwoven with the structural dynamics of the ion pair active species: Bridging from microscopic simulation to chemical kinetics with the Red Moon method	Feb. 2023	The Journal of Physical Chemistry B, 127(5), 1209-1218 (2023)	N. Misawa, K. Matsumoto, Y. Suzuki, S. Saha, N. Koga, M. Nagaoka
Verification for Temperature Dependence of Tacticity in Polystyrene Radical Polymerization with the Combination of Reaction Pathway Analysis and Red Moon Methodology	Jul. 2022	Journal of Physical Chemistry B, 126(28), 5343-5350 (2022)	Z. Rao, M. Takayanagi, M. Nagaoka
Theoretical prediction of pH-dependent electronic spectra in aqueous solution: A combinational application of QM/MM calculations and constant-pH simulations with configuration-selection scheme	Apr. 2022	Chemical Physics Letters, 798, 139624 (2022)	C. Bistafa, Y. Kitamura, M. Nagaoka
Development of Advanced Electrolytes in Na-ion Batteries: Application of Red Moon Method for Molecular Structure Design of SEI Layer	Jan. 2022	RSC Advances, 12, 971-984 (2022)	A. Bouibes, N. Takenaka, K. Kubota, S. Komaba, M. Nagaoka
Chloride Ions Stabilize Human Adult Hemoglobin in T-State, Competing with Allosteric Interaction of Oxygen Molecules	Nov. 2021	Journal of Physical Chemistry B, 125(46), 12670-12677 (2021)	I. Kurisaki, Y. Takahashi, Y. Kitamura, M. Nagaoka
Data Scientific Study on Allosteric Regulation of Hemoglobin -The Role of Chloride Ion in Quaternary Structual Change-	Nov. 2021	Journal of Computer Chemistry Japan, 20(3), 97-99 (2021)	M. Tanaka, Y. Takahashi, K. Takami, Y. Kitamura, M. Nagaoka
Frontiers in Theoretical Analysis of Solid Electrolyte Interphase Formation Mechanism	Aug. 2021	Advanced Materials, 2100574 (2021)	N. Takenaka, A. Bouibes, Y. Yamada, M. Nagaoka, A. Yamada
Performance Research of Clustering Methods for Detecting State Transition Trajectories in Hemoglobin	Apr. 2021	Journal of Computer Chemistry Japan, 19(4), 154-157 (2020)	K. Takami, Y. Kitamura, M. Nagaoka
Atomistic Simulation of Polymerization Reaction by (Pyridylamido)Hf(IV) Catalyst: Both Reaction Rate and Living Character of Catalytic System Influenced by Its Counteranions	Jan. 2021	The Journal of the Physical Chemistry B, 125(5), 1453-1467 (2021)	N. Misawa, Y. Suzuki, K. Matsumoto, S. Saha, N. Koga, M. Nagaoka
A Constant-pH Hybrid Monte Carlo Method with Configuration-Selection Scheme using Zero Energy Difference Condition: Elucidation of Molecular Diffusivity Correlated with pH-Dependent Solvation Shell	Jan. 2021	Journal of Chemical Theory and Computation, 17(2), 1030-1044 (2021)	Y. Kitamura, M. Nagaoka
Theoretical Elucidation of the Effect of Counteranions on the Olefin Polymerization Activity of (Pyridylamido)Hf(IV) Catalyst by QM and REMD Studies: MeB(C₆F₅)₃^- vs. B(C₆F₅)₄^-	Dec. 2020	Organometallics, 40(1), 48-62 (2021)	N. Misawa, Y. Suzuki, S. Saha, N. Koga, M. Nagaoka
Theoretically Predicting the Feasibility of Highly-Fluorinated Ethers as Promising Diluents for Non-flammable Concentrated Electrolytes	Dec. 2020	Scientific Reports, 10, 21966 (2020)	A. Bouibes, S. Saha, M. Nagaoka
Ab initio Quantitative Prediction of Tacticity in Radical Polymerization of Poly(methyl methacrylate) by Molecular Simulation Technique with the Conformation Indexing for Multiple Transition States	Jul. 2020	The Journal of the Physical Chemistry C, 124(31), 16895-16901 (2020)	Z. Rao, M. Takayanagi, M. Nagaoka
Theoretical Analysis of Electrode-dependent Interfacial Structurs on Hydrate-melt Electrolytes	Mar. 2020	The Journal of Chemical Physics, 152, 124706 (2020)	N. Takenaka, T. Inagaki, T. Shimada, M. Nagaoka, A. Yamada
Scalable and Precise Synthesis of Armchair-Edge Graphene Nanoribbon in Metal-Organic Framework	Mar. 2020	Journal of the American Chemical Society, 142, 5509-5514 (2020)	T. Kitao, M. MacLean, K. Nakata, M. Takayanagi, M. Nagaoka, T. Uemura
Microscopic Origin of the Solid Electrolyte Interphase Formation in Fire-Extinguishing Electrolyte: Formation of Pure Inorganic Layer in High Salt Concentration	Sep. 2019	The Journal of Physical Chemistry Letters, 10, 5949-5955 (2019)	A. Bouibes, N. Takenaka, S. Saha, M. Nagaoka
Vibrational Spectroscopy in Solution Through Perturbative Ab Initio Molecular Dynamics Simulations	Jun. 2019	Journal of Chemical Theory and Computaion, 15, 4615-4622 (2019)	C. Bistafa, Y. Kitamura, M. Martins-Costa, M. Nagaoka, M. Ruiz-Lopez,
Electrode Polarization Effects on Interfacial Kinetics of Ionic Liquid at Graphite Surface: An Extended Lagrangian-based Constant Potential Molecular Dynamics Simulation Study	May 2019	Journal of Computational Chemistry, 40(24), 2131-2145 (2019)	T. Inagaki, M. Nagaoka
Impact of Cis- versus Trans- Configuration of Butylene Carbonate Electrolyte on Microscopic Solid Electrolyte Interphase Formation Processes in Lithium-Ion Batteries	Apr. 2019	ACS Applied Matererials & Interfaces, 11(17), 15623-15629 (2019)	K. Miyazaki, N. Takenaka, T. Fujie, E. Watanabe, Y. Yamada, A. Yamada, M. Nagaoka
Microscopic Elucidation of Solid-Electrolyte Interphase (SEI) Film Formation via Atomistic Reaction Simulations: Importance of Functional Groups of Electrolyte and Intact Additive Molecules	Mar. 2019	The Chemistry Record, 19, 799-810 (2019)	N. Takenaka, M.Nagaoka
SEI Film Formation Simulation by Using Red Moon Method Combined with QM/MM Method	Jan. 2019	Journal of Computer Chemistry, Japan, 18(1), 29-37 (2019)	T. Fujie, N. Takenaka, M. Nagaoka
The Crucial Role of Electron Transfer from Interfacial Molecules in Negative Potential Shift of Au Electrode Immersed in Ionic Liquid	Oct. 2018	Physical Chemistry Chemical Physics, 20, 29362-29373 (2018)	T. Inagaki, N. Takenaka, M. Nagaoka
Atomistic Chemical Computation of Olefin Polymerization Reaction Catalyzed by (Pyridylamido)hafnium(IV) Complex: Application of Red Moon Simulation	Oct. 2018	Journal of Computational Chemistry, 40, 421-429 (2019)	K. Matsumoto, M. Takayanagi, Y.Suzuki, N. Koga, M. Nagaoka
Microscopic Origin of Different Hydration Pattern of Paranitrophenol and Its Anion: A Study Combining Multiconfigurational Calculations and the Free Energy Gradient Method	Aug. 2018	The Journal of Physical Chemistry B, 122(39), 9202-9209 (2018)	C. Bistafa, Y. Kitamura, M. Nagaoka, S. Canuto
Selective Sorting of Polymers with Different Terminal Groups Using Metal-Organic Frameworks	Aug. 2018	Nature Communications, 9, 3635 (2018)	B. Le Ouay, C. Watanabe, S. Mochizuki, M. Takayanagi, M. Nagaoka, T. Kitao, T. Uemura
Concentration Effect of the Fluoroethylene Carbonate on Formation of Solid Electrolyte Interphase Layer in Sodium-Ion Batteries	Aug. 2018	ACS Applied Materials & Interfaces, 10(34), 28525-28532 (2018)	A. Bouibes, N. Takenaka, T. Fujie, K. Kubota, S. Komaba, M. Nagaoka
Red Moon Methodology Compatible with Quantum Mechanics/Molecular Mechanics Framework: Application to Solid Electrolyte Interphase Film Formation in Lithium-ion Battery System	Jul. 2018	The Journal of Chemical Physics, 149(4), 044113 (2018)	T. Fujie, N.Takenaka, Y.Suzuki, M. Nagaoka
A Cost-Effective Method for Free-Energy Minimization in Complex Systems with Elaborated Ab Initio Potentials	May 2018	Journal of Chemical Theory and Computaion, 14(6), 3262-3271 (2018)	C. Bistafa, Y. Kitamura, M. T. C. Martins-Costa, M. Nagaoka, M. F. Ruiz-Lopez
Probing the Most Stable Isomer of Zirconium Bis(phenoxy-Imine) Cation : A Computational Investigation	Feb. 2018	The Journal of Physical Chemistry A, 122(8), 2198-2208 (2018)	S. Saha, M. Takayanagi, K. Matsumoto, S. K. Sankaran, Sandhya; Y. Tanaka, N. Koga, M. Nagaoka
Microscopic Formation Mechanism of Solid Electrolyte Interphase Film in Lithium-Ion Batteries with Highly Concentrated Electrolyte	Jan. 2018	The Journal of Physical Chemistry C, 122(5), 2564-2571 (2018)	N. Takenaka, T. Fujie, A. Bouibes, Y. Yamada, A. Yamada, M. Nagaoka
Role of the Counter Anion in the Reaction Mechanism of Propylene Polymerization Catalyzed by (Pyridylamido)hafnium(IV) Complex	Jan. 2018	Organometallics, 37(3), 343-349 (2018)	K. Matsumoto, M. Takayanagi, S. K. Sankaran, N. Koga, M. Nagaoka
Sequence-regulated Copolymerization Based on Periodic Covalent Positioning of Monomers along One-Dimensional Nanochannels	Jan. 2018	Nature Communications, 9, 329 (2018)	S. Mochizuki, N. Ogiwara, M. Takayanagi, M. Nagaoka, S. Kitagawa, T. Uemura
A Transformation Theory of Stochastic Evolution in Red Moon Methodology to Time Evolution of Chemical Reaction Process in the Full Atomistic System	May 2017	The Journal of Chemical Physics, 146 , 204102 (2017)	Y. Suzuki, M. Nagaoka
An Active Site Opening Mechanism in a (Pyridylamide)hafnium(IV) Ion Pair Catalyst: An Associative Mechanism	Dec. 2016	Organometallics, 35(24), 4099-4105 (2016)	K. Matsumoto, K. S. Sandhya, M. Takayanagi, N. Koga, M. Nagaoka
Na⁺ Binding is Ineffective in Forming a Primary Substrate Pocket of Thrombin	Oct. 2016	The Journal of Physical Chemistry B, 120(46), 11873-11879 (2016)	I. Kurisaki, M. Nagaoka
Formation of Reactant Complex Structure for Initiation Reaction of Lactone Ring-Opening Polymerization by Cooperation of Multiple Cyclodextrin	Jul. 2016	The Journal of Physical Chemistry B, 120(29), 7174-7181 (2016)	M. Takayanagi, S. Ito, K. Matsumoto, M. Nagaoka
Additive Effect of Fluoroethylene and Difluoroethylene Carbonates for the Solid Electrolyte Interphase Film Formation in Sodium-Ion Batteries: A Quantum Chemical Study	Jul. 2016	RSC Advances, 6 65232-65242 (2016)	U. Purushotham, N. Takenaka, M. Nagaoka
Revisiting the Stereochemistry of Propylene Isotactic Polymerization Reaction Mechanism on C₂ Symmetric [SiH₂(Ind)₂ZrCH₃]⁺ and [SiH₂(Ind)₂ZrCH₃]⁺[CH₃B(C₆F₅)₃]^-	Jun. 2016	Bulletin of the Chemical Society of Japan, 89 1093-1105 (2016)	K. S. Sandhya, N. Koga, M. Nagaoka
The Bound Na⁺ is Negative Effecter for Thrombin-Substrate Stereospecific Complex Formation	May 2016	The Journal of Physical Chemistry B, 120(20), 4540-4547 (2016)	I. Kurisaki, M. Takayanagi, M. Nagaoka
Efficient Computational Research Protocol to Survey Free Energy Surface for Solution Chemical Reaction in the QM/MM Framework: The FEG-ER Methodology and its Application to Isomerization Reaction of Glycine in Aqueous Solution	Jan. 2016	The Journal of Physical Chemistry B, 120(8), 2001-2011 (2016)	N. Takenaka, Y. Kitamura, M. Nagaoka
Diverse Rotational Flexibility of Substituted Dicarboxylate Ligands in Functional Porous Coordination Polymers	Dec. 2015	The Journal of Physical Chemistry C, 119(52), 28789-28799 (2015)	S. Pakhira, M. Takayanagi, M. Nagaoka
Dewetting of S1-Pocket via Water Channel Upon Thrombin-Substrate Association Reaction	Dec. 2015	The Journal of Physical Chemistry B, 119(52), 15807-15812 (2015)	I. Kurisaki, C. Barberot, M. Takayanagi, M. Nagaoka
Control of Diffusion and Conformation Behavior of Methyl Methacrylate Monomer by Phenylene Fin in Porous Coordination Polymers	Nov. 2015	The Journal of Physical Chemistry C, 119(49), 27291-27297 (2015)	M. Takayanagi, S. Pakhira, M.Nagaoka
Efficient Approach to Include Molecular Polarizations Using Charge and Atom Dipole Response Kernels to Calculate Free Energy Gradients in QM/MM Scheme	Sep. 2015	Physical Chemistry Chemical Physics, 17(40), 26955-26968 (2015)	T.Asada, K.Ando, K.Sakurai, S.Koseki, M.Nagaoka
Molecule-Level Studies on Dynamic Behavior of Oligomeric Chain Molecules in Porous Coordination Polymers	Aug. 2015	The Journal of Physical Chemistry C, 119(37), 21504-21514 (2015)	T.Uemura, G.Washino, S.Kitagawa, H.Takahashi, A.Yoshida, K.Takeyasu, M.Takayanagi, M.Nagaoka
A Computational Chemical Insight into Microscopic Additive Effect on Solid Electrolyte Interphase Film Formation in Sodium-Ion Batteries: Suppression of Unstable Film Growth by Intact Fluoroethylene Carbonate	Jul. 2015	The Journal of Physical Chemistry C, 119(32), 18046-18055 (2015)	N.Takenaka, H.Sakai, Y.Suzuki, P.Uppula, M.Nagaoka
Influence of Monomer Mixing Ratio on Membrane Nanostructure in Interfacial Polycondensation: Application of Hybrid MC/MD Reaction Method with Minimum Bond Convention	May 2015	The Journal of Physical Chemistry B, 119(22), 6776-6785 (2015)	Y.Suzuki, Y.Koyano, M.Nagaoka
Toward Understanding Allosteric Activation of Thrombin: A Conjecture for Important Roles of Unbound Na+ Molecules around Thrombin	Feb. 2015	The Journal of Physical Chemistry B, 119(9), 3635-3642 (2015)	I.Kurisaki, M.Takayanagi, M.Nagaoka
Dual Approach to Vibrational Spectra in Solution: Microscopic Influence of Hydrogen Bonding to the State of Motion of Glycine in Water	Jul. 2014	Journal of Chemical Theory and Computation, 10(8), 3369-3379 (2014)	Y.Kitamura, N.Takenaka, Y.Koyano, M.Nagaoka
Combined Mechanism of Conformational Selection and Induced Fit in U1A-RNA Molecular Recognition	May 2014	Biochemistry, 53(22), 3646-3657 (2014)	I.Kurisaki, M.Takayanagi, M.Nagaoka
On Electrolyte-Dependent Formation of Solid Electrolyte Interphase Film in Lithium-Ion Batteries: Strong Sensitivity to Small Structural Difference of Electrolyte Molecules	Apr. 2014	The Journal of Physical Chemistry C, 118(20), 10874-10882 (2014)	N.Takenaka, Y.Suzuki, H.Sakai, M.Nagaoka
Non-Site-Specific Allosteric Effect of Oxygen on Human Hemoglobin under High Oxygen Partial Pressure	Apr. 2014	Scientific Reports, 4, 4601 (2014)	M.Takayanagi, I.Kurisaki, M.Nagaoka
A Hybrid MC/MD Reaction Method with Rare Event-Driving Mechanism: Atomistic Realization of 2-Chlorobutane Racemization Process in DMF Solution	Sep. 2013	Chemical Physics Letters, 583, 80-86 (2013)	M.Nagaoka, Y.Suzuki, T.Okamoto, N.Takenaka
Oxygen Entry through Multiple Pathways in T-state Human Hemoglobin	Apr. 2013	The Journal of Physical Chemistry B, 117(20), 6082-6091 (2013)	M.Takayanagi, I.Kurisaki, M.Nagaoka
A Minimal Implementation of the AMBER-PAICS Interface for Ab Initio FMO-QM/MM-MD Simulation	Oct. 2012	Bulletin of the Chemical Society of Japan, 86(2), 210-222 (2013) (Selected Paper)	T.Okamoto, T.Ishikawa, Y.Koyano, N.Yamamoto, K.Kuwata, M.Nagaoka
Ferryl-Oxo Species Produced from Fenton's Reagent via a Two-Step Pathway: Minimum Free-Energy Path Analysis	Nov. 2012	The Journal of Physical Chemistry B, 116(48), 14178-14182 (2012)	N.Yamamoto, N.Koga, M.Nagaoka
An Improvement in Quantum Mechanical Description of Solute-Solvent Interactions in Condensed Systems via the Number-Adaptive Multiscale Quantum Mechanical/Molecular Mechanical-Molecular Dynamics Method: Application to Zwitterionic Glycine in Aqueous Solution	Jul. 2012	The Journal of Chemical Physics, 137(2), 024501(2012)	N.Takenaka, Y.Kitamura, Y.Koyano, M.Nagaoka
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	Feb. 2012	The Journal of Physical Chemistry B, 116(13), 4080-4088 (2012)	I.Yu, K.Nakada, M.Nagaoka
The Number-Adaptive Multiscale QM/MM Molecular Dynamics Simulation: Application to Liquid Water	Feb. 2012	Chemical Physics Letters, 524 56-61 (2012)	N.Takenaka, Y.Kitamura, Y.Koyano, M.Nagaoka
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	Sep. 2011	Chemical Physics Letters, 514(4-6), 261-266 (2011)	Y.Kitamura, N.Takenaka, Y.Koyano, M.Nagaoka
Incipient Structural and Vibrational Relaxation Process of Photolyzed Carbonmonoxy Myoglobin: Statistical Analysis by Perturbation Ensemble Molecular Dynamics Method	Sep. 2011	Theoretical Chemistry Accounts, 130(4-6), 1115-1129 (2011)	M.Takayanagi, M.Nagaoka
Toward a New Approach for Determination of Solute's Charge Distribution to Analyze Interatomic Electrostatic Interactions in QM/MM Simulations	Aug. 2011	Journal of Computational Chemistry, 32(14), 3092-3104 (2011)	K.Yamada, Y.Koyano, T.Okamoto, T.Asada, N.Koga, M.Nagaoka
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	May 2011	Theoretical Chemistry Accountss, 130(2-3), 215-226 (2011)	N.Takenaka, Y.Kitamura, Y.Koyano, T.Asada, M.Nagaoka
Ab Initio Electron Correlated Studies on the Intracluster Reaction of NO⁺(H₂O)_n -> H₃O⁺(H₂O)_n-2(HONO) (n=4 and 5)	Nov. 2010	Physical Chemistry Chemical Physics, 13(4), 1590-1596 (2011)	T.Asada, M.Nagaoka, S.Koseki
A Minimal Implementation of the AMBER-GAUSSIAN Interface for Ab Initio QM/MM-MD Simulation	Oct. 2010	Journal of Computational Chemistry, 32(5), 932-942 (2011)	T.Okamoto, K.Yamada, Y.Koyano, T.Asada, N.Koga, M.Nagaoka
Unveiling Thermal Transitions of Polymers in Subnanometre Pores	Oct. 2010	Nature Communications, 1, 83 (2010)	T.Uemura, N.Yanai, S.Watanabe, H.Tanaka, R.Numaguchi, M.T. Miyahara, Y.Ohta, M.Nagaoka, S.Kitagawa
Influence of Hydrostatic Pressure on Dynamics and Spatial Distribution of Protein Partial Molar Volume: Time-Resolved Surficial Kirkwood-Buff Approach	Sep. 2010	The Journal of Physical Chemistry B, 114(38), 12392-12397 (2010)	I.Yu, T.Tasaki, K.Nakada, M.Nagaoka
Structural Dynamics of Clamshell Rotation during the Incipient Relaxation Process of Photodissociated Carbonmonoxymyoglobin: Statistical Analysis by Perturbation Ensemble Method	Sep. 2010	The Journal of Physical Chemistry B, 114(38), 12340-12348 (2010)	M.Takayanagi, C. Iwahashi, M.Nagaoka
An Optimum Strategy for Solution Chemistry Using Semiempirical Molecular Orbital Method. II. Primary Importance of Reproducing Electrostatic Interaction in the QM/MM Framework	May 2010	Journal of Computational Chemistry, 31(14), 2628-2641 (2010)	Y.Koyano, N.Takenaka, Y.Nakagawa, M.Nagaoka
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	Apr. 2010	Bulletin of the Chemical Society of Japan, 83(5), 486-494 (2010)	Y.Koyano, N.Takenaka, Y.Nakagawa, M.Nagaoka
Microscopic Hydration Mechanism in the Ammonia Dissolution Process: Importance of the Solute QM Polarization	Dec. 2009	Chemical Physics Letters, 485(1-3), 119-123 (2010)	N.Takenaka, Y.Koyano, M.Nagaoka
An Optimum Strategy for Solution Chemistry Using Semiempirical Molecular Orbital Method: Importance of Description of Charge Distribution	Oct. 2009	Journal of Computational Chemistry, 31(6), 1287-1296 (2010)	N.Takenaka, Y.Koyano, Y.Nakagawa, M.Nagaoka
Intrinsic Alteration in the Partial Molar Volume on the Protein Denaturation: Surficial Kirkwood-Buff Approach	Feb. 2009	The Journal of Physical Chemistry B, 113(11), 3543-3547 (2009)	I.Yu, M.Takayanagi, M.Nagaoka
Surficial Kirkwood-Buff Approach on the Preferential Interaction of Urea and Ectoine with Protein	Nov. 2008	Proceedings of International Symposium on Frontiers of Computational Science 2008, 9-14 (2008)	I.Yu, M.Nagaoka
Conformation and Molecular Dynamics of Single Polystyrene Chain Confined in Coordination Nanospace	May 2008	Journal of the American Chemical Society, 130(21), 6781-6788 (2008)	T.Uemura, S.Horike, K.Kitagawa, M.Mizuno, K.Endo, S.Bracco, A.Comotti, P.Sozzani, M.Nagaoka, S.Kitagawa
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	Aug. 2007	Coordination Chemistry Reviews, 251(21-24), 2522-2536 (2007)	M.Nagaoka, Y.Ohta, H.Hitomi
Microscopic Understanding of Preferential Exclusion of Compatible Solute Ectoine: Direct Interaction and Hydration Alteration	Aug. 2007	The Journal of Physical Chemistry B, 111(34), 10231-10238 (2007)	I.Yu, Y.Jindo, M.Nagaoka
Elongation of Water Residence Time at the Protein Interior in Aqueous Solution with Ectoine	Mar. 2007	Proceedings of International Symposium on Frontiers of Computational Science, 269-273 (2007)	I.Yu, M.Nagaoka
Anisotropic Structural Relaxation and its Correlation with the Excess Energy Diffusion in the Incipient Process of Photo-Dissociated MbCO: High Resolution Analysis via Ensemble Perturbation Method	Jan. 2007	The Journal of Physical Chemistry B, 111(4), 864-869 (2007)	M.Takayanagi, H.Okumura, M.Nagaoka
The Body-Centered Cubic Structure of Methyllithium Tetramer Crystal: Staggered Methyl Conformation by Electrostatic Stabilization via Intra-Tetramer Multipolarization	Jun. 2006	The Journal of Physical Chemistry B, 110(25), 12640-12644 (2006)	Y.Ohta, A.Demura, T.Okamoto, H.Hitomi, M.Nagaoka
Nanochannel-Promoted Polymerization of Substituted Acetylenes in Porous Coordination Polymers	May 2006	Angewandte Chemie International Edition, 45(25), 4112-4116 (2006)	T.Uemura, R.Kitaura, Y.Ohta, M.Nagaoka, S.Kitagawa
Transition-State Characterization of Ammonia Ionization Process in Aqueous Solution via Free-Energy Gradient Method	Mar. 2006	The Journal of Physical Chemistry A, 110(13), 4555-4563 (2006)	M.Nagaoka, Y.Nagae, Y.Koyano, Y.Oishi
Theoretical Study on Stabilities of N-terminal Partial Chains from Apo-Myoglobin	Feb. 2006	Chemical Physics Letters, 421(1-3), 300-304 (2006)	M.Takayanagi, I.Yu, M.Nagaoka
Coarse-Grained Approach to Nonequilibrium Molecular Dynamics: Application to Relaxation Process of Vibrationally Excited Hydrogen Fluoride in Aqueous Solution	May 2005	Chemical Physics Letters, 407, 444-449 (2005)	T.Okamoto, M.Nagaoka
Slowdown of Water Diffusion around Protein in Aqueous Solution with Ectoine	Apr. 2004	Chemical Physics Letters, 388, 316-321 (2004)	I.Yu, M.Nagaoka
Ab Initio Study of Noncatalytic Beckmann Rearrangement and Hydrolysis of Cyclohexanone-Oxime in Subcritical and Supercritical Water Using the Polarizable Continuum Model	Aug. 2003	Journal of Molecular Structure (Theochem), 639, 137-150 (2003)	Y.Yamaguchi, N.Yasutake, M.Nagaoka
Hydrated Structure of Ammonia-Water Molecule Pair via the Free Energy Gradient Method: Realization of Zero Gradient and Force Balance on Free Energy Surfaces	Jul. 2003	The Journal of Chemical Physics, 119, 7972-7978 (2003)	Y.Nagae, Y.Oishi, N.Naruse, M.Nagaoka
Structure Optimization of Solute Molecules via Free Energy Gradient Method	Jun. 2003	Bulletin of The Korean Chemical Society, 24, 805-808 (2003)	M.Nagaoka
Kramers-Fokker-Planck Equation for Polyatomic Molecules	Sep. 2002	The Journal of Chemical Physics, 117, 5594-5606 (2002)	M.Nagaoka, T.Okamoto, Y.Maruyama
Toward Quantum Chemodynamics in Condensed Phase via Stochastic Quantization Method	Apr. 2002	Recent Advances in Quantum Monte Calro Methods II, 254-278 (2002)	M.Nagaoka, K.Suenobu
Ab Intio Study of Ammonia Adsorption States on an Ice Surface II: Theoretical Characterization of the Surface Bound State	Dec. 2001	Chemical Physics Letters, 350, 141-146 (2001)	N.Hashimoto, Y.Hara, M.Nagaoka
Ab Intio Study of Ammonia Adsorption States on an Ice Surface I : Structures, Adsorption Energies and Linear Dependences on Coverage Rate	Nov. 2001	Chemical Physics Letters, 348, 107-114 (2001)	Y.Hara, N.Hashimoto, M.Nagaoka
Transition-State Optimization by the Free Energy Gradient Method : Application to Aqueous phase Menshutkin Reaction between Ammonia and Methyl Chloride	Nov. 2001	Chemical Physics Letters, 348, 350-356 (2001)	H.Hirao, Y.Nagae, M.Nagaoka
On Vibrational Cooling upon Photodissociation of Carbonmonoxymyoglobin and its Microscopic Mechanism from the Viewpoint of Vibrational Modes of Heme	Nov. 2001	Chemical Physics Letters, 337, 151-157 (2001)	I.Okazaki, Y.Hara, M.Nagaoka
Ab Initio Study of Proton Chemical Shift in Supercritical Methanol using Gas-Phase Approximation	Oct. 2001	The Journal of Physical Chemistry A, 106, 404-410 (2001)	Y.Yamaguchi, N.Yasutake, M.Nagaoka
Theoretical Prediction of Proton Chemical Shift in Supercritical Water using Gas-Phase Approximation	May 2001	Chemical Physics Letters, 340, 129-136 (2001)	Y.Yamaguchi, N.Yasutake, M.Nagaoka
Ab Initio MO Study of the Structures of N₂ NO, and CO Molecules to the Pd_n (n=1,2,5,25) Clusters as a Model of Pd(110) Surface	Jan. 2001	The Journal of Physical Chemistry B, 105, 3235-3244 (2001)	T.Matsubara, T.Nagai, M.Nagaoka, T.Yamabe
Internal Heat Flux and Entropy Production Rate for Chemically Reacting System in Solution	Dec. 2000	Progress of Theoretical Physics supplement, 138, 588-589 (2000)	M.Nagaoka
Structure Optimization via Free Energy Grandient Method: Application to Glycine Zwitterion in Aqueous Solution	Sep. 2000	The Journal of Chemical Physics, 113, 3519-3524 (2000)	N.Okuyama-Yoshida, K.Kataoka, M.Nagaoka, T.Yamabe
Internal Temperature Concept for Fast Transient Dynamics of Chemical Species in Solution	Jan. 2000	International Journal of Quantum Chemistry, 80, 117-124 (2000)	T.Okamoto, Y.Maruyama, M.Nagaoka
Non-Markovian Stochastic Schrodinger Equation	Nov. 1999	The Journal of Chemical Physics, 111, 5676-5690 (1999)	P.Gaspard, M.Nagaoka
Slippage of Initial Conditions for the Redfield Master Equation	Oct. 1999	The Journal of Chemical Physics, 111, 5668-5675 (1999)	P.Gaspard, M.Nagaoka
Product Energy Distribution of Molecular Hydrogen Formed on Icy Mantles of Interstellar Dust	Aug. 1999	The Astrophysical Journal, 520, 724-731 (1999)	J.Takahashi, K.Masuda, M.Nagaoka
Inertia Ratchets:A Numerical Study versus Theory	Aug. 1999	Physical Review E, 59, 1417-1424 (1999)	B.Lindner, L.Schimansky-Geier, P.Reimann, P.Hanggi, M.Nagaoka
The Faster Conversion of Ethene Thiol than Vinyl Alcohol in Tautomerization Reactions in Aqueous Solution --- Theoretical Prediction ---	Aug. 1999	Journal of Molecular Structure (Theochem), 461-462, 581-588 (1999)	K.Suenobu, M.Nagaoka, T.Yamabe
Kinetic Lattice Model for Long-Time Chemical Phenomena: Introduction of Time-Scale into Monte Carlo Simulation	Jun. 1999	Molecular Simulation 21, 343-355 (1999)	M.Nagaoka, K.Suenobu, T.Yamabe
Characteristics of Numerical Realization via Stochastic Partial Differential Equation: An Application to Density Matrix Calculation	Apr. 1999	International Journal of Quantum Chemistry, 74, 653-660 (1999)	Y.Saito, M.Nagaoka
The Formation Mechanism of Molecular Hydrogen on Icy Mantles of Interstellar Dust	Dec. 1998	Monthly Notices of Royal Astronomical Society, 306, 20-30 (1998)	J.Takahashi, K.Masuda, M.Nagaoka
Quantum Mechanical Treatment for the Diffusion Process of a Hydrogen Atom on the Amorphous Water Ice Surface	Dec. 1998	International Journal of Quantum Chemistry,70, 379-385 (1998)	J.Takahashi, M.Nagaoka, K.Masuda
Kinetic Lattice Model for Long-Time Chemical Phenomena: Crystallization Dynamics of Optical Isomers in Solution	Nov. 1998	AIP Conference Proceedings (Slow Dynamics in Complex Systems) 469, 297-298 (1998)	M.Nagaoka, K.Suenobu, T.Yamabe
Ab Initio Molecular Orbital Study on Molecular and Hydration Structures of Ectoine	Aug. 1998	The Journal of Physical Chemistry A, 102, 7505-7511 (1998)	K.Suenobu, M.Nagaoka, T.Yamabe, S.Nagata
"Statistical-Mechanical" Understanding of Chemical-Reaction Mechanism in Solution: Energy Fluctuation and Heat Capacities for Isomerization of Formamidine in Aqueous Solution	Aug. 1998	International Journal of Quantum Chemistry, 70, 133-145 (1998)	M.Nagaoka, Y.Okuno, T.Yamabe
Origin of the Transition State on the Free Energy Surface: Intramolecular Proton Transfer Reaction of Glycine in Aqueous Solution	Jun. 1998	The Journal of Physical Chemistry A, 102, 8202-8208 (1998)	M.Nagaoka, N.Okuyama-Yoshida, T.Yamabe
Transition-State Optimization on Free Energy Surfaces: Toward Solution Chemical Reaction Ergodography	Apr. 1998	International Journal of Quantum Chemistry, 70, 95-103 (1998)	N.Okuyama-Yoshida, M.Nagaoka, T.Yamabe
Potential Energy Function for Intramolecular Proton Transfer Reaction of Glycine in Aqueous Solution	Jan. 1998	The Journal of Physical Chemistry A, 102, 285-292 (1998)	N.Okuyama-Yoshida, M.Nagaoka, T.Yamabe
Lithium Diffusion in Li_xCoO₂ Electrode Materials	Dec. 1997	Bulletin of Chemical Society of Japan, 71, 2259-2265 (1997)	G.Nuspl, M.Nagaoka, K.Yoshizawa, T.Yamabe
Experimental and Theoretical Study on Isomerization of Allyl Thiocyanate to Allyl Isothiocyanate	May. 1997	Jounral of Heteroatom Chemistry, 8, 35-43 (1997)	M.Kotani, Y.Shigetomi, M.Imada, M.Oki, M.Nagaoka
Study on "Regurality" of Barrier Recrossing Motion	Dec. 1996	The Journal of Chemical Physics, 105, 10838-1084 (1996)	T.Komatsuzaki, M.Nagaoka
A Dividing Surface Free from a Barrier Recrossing Motion in Many-Body Systems	Nov. 1996	Chemical Physics Letters, 265, 91-98 (1996)	T.Komatsuzaki, M.Nagaoka
On the Hydronium ion Catalyzed Mechanism in Vinyl Alcohol-Acetaldehyde Isomerization: Ab Initio Molecular Orbital Theory and Monte Carlo Simulation	Oct. 1996	Journal of American Chemical Society, 119, 8023-8030 (1996)	M.Nagaoka, K.Suenobu, T.Yamabe
A Microscopic Frictional Theory for Reactions in Condensed Phases: Influence of Nonlinear Couplings	Oct. 1996	The Journal of Chemical Physics, 105, 13, 5431-5445 (1996)	M.Nagaoka, N.Yoshida, T.Yamabe
On the Equivalence Between the Microscopic Frictional Theory and Transition-State Theory	Oct. 1996	International Journal of Quantum Chemistry, 60, 287-295 (1996)	M.Nagaoka, N.Yoshida, T.Yamabe
Stochastic Path-Integral Method for Chemical Reaction Dynamics: Application to the Full 3D H₃ System	Aug. 1996	International Journal of Quantum Chemistry, 30, 91-98 (1996)	M.Nagaoka
Deviation of the TST Rate Constant through the Nonlinear Couplings	Jul. 1995	Journal of Molecular Liquids, 65/66, 289-292 (1995)	M.Nagaoka, N.Yoshida, T.Yamabe
Chemical Reaction Molecular Dynamics Simulation and Energy Transfer of Formamidine in Aqueous Solution	Jul. 1994	The Journal of Physical Chemistry, 98, 12506-12515 (1994)	M.Nagaoka, Y.Okuno, T.Yamabe
A Microscopic Theory for Solution Chemical Reactions: Introduction of Reactant and Medium Structures into Generalized Langevin Equation Formalism	Sep. 1994	International Journal of Quantum Chemistry, 51, 519-527 (1994)	M.Nagaoka, Y.Okuno, N.Yoshida, T.Yamabe
Extended Transition State Theory and Constant Energy Chemical Reaction Molecular Dynamics Method for Liquid-Phase Chemical Recations	Aug. 1992	The Journal of Chemical Physics, 97, 8143-8155 (1992)	M.Nagaoka, Y.Okuno, T.Yamabe
Dynamic Transition State in the Constant Energy Scheme CRMD Simulation and the Relative Velocity Correlation Function	Aug. 1992	Chemical Physics Letters, 196, 197-201 (1992)	M.Nagaoka, Y.Okuno, T.Yamabe
Ab Initio Calculations and the Chemical Reaction Molecular Dynamics Simulation	Jul. 1992	Canadian Journal of Chemistry, 70, 377-387 (1992)	M.Nagaoka, Y.Okuno, T.Yamabe, K.Fukui
A Heuristic Potential Function for Intramolecular and Intrasupermolecular Chemical Reaction in Formamidine-Water System	Jul. 1992	International Journal of Quantum Chemistry, 42, 889-905 (1992)	M.Nagaoka, Y.Okuno, T.Yamabe, K.Fukui
The Chemical Reaction Molecular Dynamics Method and the Dynamic Transition State: Proton Transfer Reaction in Formamidine and Water Solvent System	Jul. 1990	Journal of American Chemical Society, 113, 769-778 (1990)	M.Nagaoka, Y.Okuno, T.Yamabe