67 Publications (Page 2 of 3)
2015
Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations.Ojeda-May, Pedro and Pu, JingzhiThe Journal of chemical physics, vol. 143, (no. 17), pp. 174111, November 7, 2015.
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2014
Assessing the accuracy of the isotropic periodic sum method through Madelung energy computationOjeda-May, Pedro and Pu, JingzhiThe Journal of chemical physics, vol. 140, (no. 16), pp. 164106, 2014-Apr-28.
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Isotropic Periodic Sum Treatment of Long-Range Electrostatic Interactions in Combined Quantum Mechanical and Molecular Mechanical CalculationsOjeda-May, Pedro and Pu, JingzhiJournal of Chemical Theory and Computation, vol. 10, (no. 1), pp. 145, 20140114.
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Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM SimulationsZhou, Yan and Pu, JingzhiJournal of Chemical Theory and Computation, vol. 10, (no. 8), pp. 3054, 20140812.
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Trapping the ATP binding state leads to a detailed understanding of the F-1-ATPase mechanismNam, Kwangho⋅Pu, Jingzhi and Karplus, MartinProceedings of the National Academy of Sciences of the United States of America, vol. 111, (no. 50), pp. 17851, 2014.
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Trapping the ATP binding state leads to a detailed understanding of the F1-ATPase mechanism.Nam, Kwangho⋅Pu, Jingzhi and Karplus, MartinProceedings of the National Academy of Sciences of the United States of America, vol. 111, (no. 50), pp. 17851-17856, December 16, 2014.
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2013
H-loop histidine catalyzes ATP hydrolysis in the E. coli ABC-transporter HlyB.Zhou, Yan⋅Ojeda-May, Pedro and Pu, JingzhiPhysical chemistry chemical physics : PCCP, vol. 15, (no. 38), pp. 15811-5, 2013/Oct/14.
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Replica exchange molecular dynamics simulations of an α/β-type small acid soluble protein (SASP).Ojeda-May, P and Pu, JingzhiBiophysical chemistry, vol. 184, pp. 17-21, 2013/Dec/31.
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2012
Expanding the horizon of the thymine isostere biochemistry: unique cyclobutane dimers formed by photoreaction between a thymine and a toluene residue in the dinucleotide framework.Liu, Degang⋅Zhou, Yan⋅Pu, Jingzhi and Li, LeiChemistry (Weinheim an der Bergstrasse, Germany), vol. 18, (no. 25), pp. 7823-7833, June 18, 2012.
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2011
Chemical synthesis, crystal structure and enzymatic evaluation of a dinucleotide spore photoproduct analogue containing a formacetal linker.Lin, Gengjie⋅Lin, Gengjie⋅Chen, Chun-Hsing⋅Chen, Chun-Hsing⋅Pink, Maren⋅Pink, Maren⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Li, Lei and Li, LeiChemistry (Weinheim an der Bergstrasse, Germany), vol. 17, (no. 35), pp. 9658-68, 2011/Aug/22.
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2009
A coupled polarization-matrix inversion and iteration approach for accelerating the dipole convergence in a polarizable potential function.Xie, Wangshen⋅Pu, Jingzhi and Gao, JialiThe journal of physical chemistry. A, vol. 113, (no. 10), pp. 2109-16, 2009/Mar/12.
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CHARMM: the biomolecular simulation program.Brooks, B R⋅Brooks III, C.L.⋅Brooks, C L⋅Mackerell, A D⋅Mackerell Jr., A.D.⋅Nilsson, L⋅Petrella, R J⋅Roux, B⋅Won, Y⋅Archontis, G⋅Bartels, C⋅Boresch, S⋅Caflisch, A⋅Caves, L⋅Cui, Q⋅Dinner, A R⋅Feig, M⋅Fischer, S⋅Gao, J⋅Hodoscek, M⋅Im, W⋅Kuczera, K⋅Lazaridis, T⋅Ma, J⋅Ovchinnikov, V⋅Paci, E⋅Pastor, R W⋅Post, C B⋅Pu, J Z⋅Schaefer, M⋅Tidor, B⋅Venable, R M⋅Woodcock, H L⋅Wu, X⋅Yang, W⋅York, D M and Karplus, MJournal of computational chemistry, vol. 30, (no. 10), pp. 1545-1614, July 30, 2009.
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2008
How subunit coupling produces the [gamma]-subunit rotary motion in [F.sub.1]-ATPasePu, Jingzhi and Karplus, MartinProceedings of the National Academy of Sciences of the United States, vol. 105, (no. 4), pp. 1192, 20080129.
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How subunit coupling produces the [gamma]-subunit rotary motion in F^sub 1^-ATPasePu, Jingzhi and Karplus, MartinProceedings of the National Academy of Sciences of the United States of America, vol. 105, (no. 4), pp. 1192, 20080129.
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How Subunit Coupling Produces the γ-Subunit Rotary Motion in F₁-ATPasePu, Jingzhi and Karplus, MartinProceedings of the National Academy of Sciences of the United States of America, vol. 105, (no. 4), pp. 1197, 20080129.
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2007
Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes.Xie, Wangshen⋅Pu, Jingzhi⋅Mackerell, Alexander D⋅Mac Kerell Jr., A.D. and Gao, JialiJournal of chemical theory and computation, vol. 3, (no. 6), pp. 1878-1889, 2007.
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Multicoefficient Gaussian-3 calculation of the rate constant for the OH + CH4 reaction and its 12C/13C kinetic isotope effect with emphasis on the effects of coordinate system and torsional treatment.Ellingson, Benjamin A⋅Pu, Jingzhi⋅Lin, Hai⋅Zhao, Yan and Truhlar, Donald GThe journal of physical chemistry. A, vol. 111, (no. 45), pp. 11706-17, 2007/Nov/15.
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Multicoefficient Gaussian-3 Calculation of the Rate Constant for the OH + CH4 Reaction and Its 12C/13C Kinetic Isotope Effect with Emphasis on the Effects of Coordinate System and Torsional TreatmentEllingson, Benjamin A⋅ELLINGSON, BA⋅Ellingson, Benjamin A.⋅PU, J⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Lin, Hai⋅Lin, H⋅Lin, Hai⋅Zhao, Yan⋅al.⋅Zhao, Yan⋅Truhlar, Donald G. and Truhlar, Donald GThe Journal of Physical Chemistry A, vol. 111, (no. 45), pp. 11717, 20071115.
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Multicoefficient Gaussian-3 calculation of the rate constant for the OH + [CH.sub.4] reaction and its [super 12]C/[super 13]C kinetic isotope effect with emphasis on the effects of coordinate system and torsional treatmentEllingson, Benjamin⋅Pu, Jingzhi⋅Lin, Hai⋅Zhao, Yan and Truhlar, DonaldJournal of Physical Chemistry A, vol. 111, (no. 45), pp. 11706, 20071115.
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2006
Hydride transfer reaction catalyzed by hyperthermophilic dihydrofolate reductase is dominated by quantum mechanical tunneling and is promoted by both inter- and intramonomeric correlated motions.Pang, Jiayun⋅Pu, Jingzhi⋅Gao, Jiali⋅Truhlar, Donald G and Allemann, Rudolf KJournal of the American Chemical Society, vol. 128, (no. 24), pp. 8015-23, 2006/Jun/21.
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Mechanisms and free energies of enzymatic reactions.Gao, Jiali⋅Ma, Shuhua⋅Major, Dan⋅Nam, Kwangho⋅Pu, Jingzhi and Truhlar, Donald GChemical reviews, vol. 106, (no. 8), pp. 3188-209, 2006/Aug.
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Mechanisms and Free Energies of Enzymatic ReactionsGao, Jiali⋅Ma, Shuhua⋅Major, Dan T⋅Nam, Kwangho⋅Pu, Jingzhi and Truhlar, Donald GChemInform, vol. 37, (no. 44), pp. no, October 31, 2006.
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Multidimensional Tunneling, Recrossing, and the Transmission Coefficient for Enzymatic ReactionPu, Jingzhi⋅Gao, Jiali and Truhlar, Donald GChemInform, vol. 37, (no. 44), pp. no, October 31, 2006.
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Multidimensional Tunneling, Recrossing, and the Transmission Coefficient for Enzymatic ReactionsPu, Jingzhi⋅Gao, Jiali and Truhlar, Donald GChemical Reviews, vol. 106, (no. 8), pp. 3140-3169, Aug 2006.
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Searching for Saddle Points by Using the Nudged Elastic Band Method: An Implementation for Gas-Phase SystemsGonzález-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅González-García, Núria⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅González-Lafont, Àngels⋅Lluch, José M and Truhlar, Donald GJournal of Chemical Theory and Computation, vol. 2, (no. 4), pp. 904, 20060711.
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