Difference between revisions of "Publications"
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− | "Treating Electrostatics with Wolf Summation in Combined Quantum Mechanical and Molecular Mechanical Simulations," Ojeda-May, P.; '''Pu, J.''' ''J. Chem. Phys.'' '''2015''', ''143'', 174111 ([http://dx.doi.org/10.1063/1.4934880 | + | "Treating Electrostatics with Wolf Summation in Combined Quantum Mechanical and Molecular Mechanical Simulations," Ojeda-May, P.; '''Pu, J.''' ''J. Chem. Phys.'' '''2015''', ''143'', 174111 ([http://dx.doi.org/10.1063/1.4934880 doi:10.1063/1.4934880]; PubMed [http://www.ncbi.nlm.nih.gov/pubmed/26547162 PMID:26547162]). |
</li> | </li> | ||
<li value="34"> | <li value="34"> | ||
− | "Trapping the ATP Binding State Leads to a Detailed Understanding of the F<sub>1</sub>-ATPase Mechanism," Nam, K.; '''Pu, J.'''; Karplus, M. ''Proc. Natl. Acad. Sci. USA'' '''2014''', ''111'', 17851-17856 ([http://dx.doi.org/10.1073/pnas.1419486111 | + | "Trapping the ATP Binding State Leads to a Detailed Understanding of the F<sub>1</sub>-ATPase Mechanism," Nam, K.; '''Pu, J.'''; Karplus, M. ''Proc. Natl. Acad. Sci. USA'' '''2014''', ''111'', 17851-17856 ([http://dx.doi.org/10.1073/pnas.1419486111 doi:10.1073/pnas.1419486111]; PubMed PMID: 27498639). |
</li> | </li> | ||
<li value="33"> | <li value="33"> | ||
− | "Assessing the Accuracy of the Isotropic Periodic Sum Method through Madelung Energy Computation," Ojeda-May, P.; '''Pu, J.''' ''J. Chem. Phys.'' '''2014''', ''140'', 164106 ([http://dx.doi.org/10.1063/1.4871871 | + | "Assessing the Accuracy of the Isotropic Periodic Sum Method through Madelung Energy Computation," Ojeda-May, P.; '''Pu, J.''' ''J. Chem. Phys.'' '''2014''', ''140'', 164106 ([http://dx.doi.org/10.1063/1.4871871 doi:10.1063/1.4871871]). |
</li> | </li> | ||
<li value="32"> | <li value="32"> | ||
"Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations," Zhou, Y.; '''Pu, J.''' ''J. Chem. Theory Comput.'' '''2014''', ''10'', 3038-3054 | "Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations," Zhou, Y.; '''Pu, J.''' ''J. Chem. Theory Comput.'' '''2014''', ''10'', 3038-3054 | ||
− | ([http://dx.doi.org/10.1021/ct4009624 | + | ([http://dx.doi.org/10.1021/ct4009624 doi:10.1021/ct4009624]). |
</li> | </li> | ||
<li value="31"> | <li value="31"> | ||
− | "Isotropic Periodic Sum Treatment of Long-Range Electrostatic Interactions in Combined Quantum Mechanical and Molecular Mechanical Calculations," Ojeda-May, P.; '''Pu, J.''' ''J. Chem. Theory Comput.'' '''2014''', ''10'', 134-145 ([http://dx.doi.org/10.1021/ct400724d | + | "Isotropic Periodic Sum Treatment of Long-Range Electrostatic Interactions in Combined Quantum Mechanical and Molecular Mechanical Calculations," Ojeda-May, P.; '''Pu, J.''' ''J. Chem. Theory Comput.'' '''2014''', ''10'', 134-145 ([http://dx.doi.org/10.1021/ct400724d doi:10.1021/ct400724d]). |
</li> | </li> | ||
<li value="30"> | <li value="30"> | ||
− | "Replica Exchange Molecular Dynamics Simulations of an α/β-type Small Acid Soluble Protein (SASP)," Ojeda-May, P.; '''Pu, J.''' ''Biophys. Chem.'' '''2013''', ''184'', 17-21 ([http://dx.doi.org/10.1016/j.bpc.2013.07.014 | + | "Replica Exchange Molecular Dynamics Simulations of an α/β-type Small Acid Soluble Protein (SASP)," Ojeda-May, P.; '''Pu, J.''' ''Biophys. Chem.'' '''2013''', ''184'', 17-21 ([http://dx.doi.org/10.1016/j.bpc.2013.07.014 doi:10.1016/j.bpc.2013.07.014]). |
</li> | </li> | ||
<li value="29"> | <li value="29"> | ||
− | "H-loop Histidine Catalyzes ATP Hydrolysis in the ''E. coli'' ABC-Transporter HlyB," Zhou, Y.; Ojeda-May, P.; '''Pu, J.''' ''Phys. Chem. Chem. Phys.'' '''2013''', ''15'', 15811-15815 ([http://dx.doi.org/10.1039/C3CP50965F | + | "H-loop Histidine Catalyzes ATP Hydrolysis in the ''E. coli'' ABC-Transporter HlyB," Zhou, Y.; Ojeda-May, P.; '''Pu, J.''' ''Phys. Chem. Chem. Phys.'' '''2013''', ''15'', 15811-15815 ([http://dx.doi.org/10.1039/C3CP50965F doi:10.1039/C3CP50965F]; SI: [[Media:QMMM_HlyB_GAC_Movie_S1_240x200.mpg|movie_S1]]& [[Media:QMMM_HlyB_SAC_Movie_S2_240x200.mpg|movie_S2]]; see also [http://arxiv.org/abs/1304.0052 arXiv:1304.0052] [q-bio.BM]). |
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<li value="28"> | <li value="28"> | ||
− | "Expanding the Horizon of the Thymine Isostere Biochemistry: Unique Dimers formed via Photoreaction between a Thymine and a Toluene residue in the Dinucleotide Framework," Liu, D.; Zhou, Y.; '''Pu, J.'''; Li, L. ''Chem. Eur. J.'' '''2012''', ''18'', 7823-7833 ([http://dx.doi.org/10.1002/chem.201200816 | + | "Expanding the Horizon of the Thymine Isostere Biochemistry: Unique Dimers formed via Photoreaction between a Thymine and a Toluene residue in the Dinucleotide Framework," Liu, D.; Zhou, Y.; '''Pu, J.'''; Li, L. ''Chem. Eur. J.'' '''2012''', ''18'', 7823-7833 ([http://dx.doi.org/10.1002/chem.201200816 doi:10.1002/chem.201200816]). |
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<li value="27"> | <li value="27"> | ||
"Chemical Synthesis, Crystal Structure and Enzymatic Evaluation of a Dinucleotide Spore Photoproduct Analogue Containing Formacetal Linker," Lin, G.; Chen, C.-H; Pink, M.; '''Pu, J.'''; Li, L. ''Chem. Eur. J.'' '''2011''', ''17'', 9658-9668 | "Chemical Synthesis, Crystal Structure and Enzymatic Evaluation of a Dinucleotide Spore Photoproduct Analogue Containing Formacetal Linker," Lin, G.; Chen, C.-H; Pink, M.; '''Pu, J.'''; Li, L. ''Chem. Eur. J.'' '''2011''', ''17'', 9658-9668 | ||
− | ([http://dx.doi.org/10.1002/chem.201101821 | + | ([http://dx.doi.org/10.1002/chem.201101821 doi:10.1002/chem.201101821]). |
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− | "A Coupled Polarization-Matrix Inversion and Iteration Approach for Accelerating the Dipole Convergence in a Polarizable Potential Function," Xie, W.; '''Pu, J.'''; Gao, J. ''J. Phys. Chem. A'' '''2009''', ''113'', 2109-2116 ([http://dx.doi.org/10.1021/jp808952m | + | "A Coupled Polarization-Matrix Inversion and Iteration Approach for Accelerating the Dipole Convergence in a Polarizable Potential Function," Xie, W.; '''Pu, J.'''; Gao, J. ''J. Phys. Chem. A'' '''2009''', ''113'', 2109-2116 ([http://dx.doi.org/10.1021/jp808952m doi:10.1021/jp808952m]). |
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<li value="24"> | <li value="24"> | ||
− | "CHARMM: The Biomolecular Simulation Program," Brooks, B. R.; Brooks III, C. L.; 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.'''; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. ''J. Comput. Chem.'' '''2009''', ''30'', 1545-1614 ([http://dx.doi.org/10.1002/jcc.21287 | + | "CHARMM: The Biomolecular Simulation Program," Brooks, B. R.; Brooks III, C. L.; 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.'''; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. ''J. Comput. Chem.'' '''2009''', ''30'', 1545-1614 ([http://dx.doi.org/10.1002/jcc.21287 doi:10.1002/jcc.21287]). |
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<li value="23"> | <li value="23"> | ||
− | "How Subunit Coupling Produces the Rotary Motion in F<sub>1</sub>-ATPase," '''Pu, J.'''; Karplus, M. ''Proc. Natl. Acad. Sci. USA'' '''2008''', ''105'', 1192-1197 (track II, direction submission) ([http://dx.doi.org/10.1073/pnas.0708746105 | + | "How Subunit Coupling Produces the Rotary Motion in F<sub>1</sub>-ATPase," '''Pu, J.'''; Karplus, M. ''Proc. Natl. Acad. Sci. USA'' '''2008''', ''105'', 1192-1197 (track II, direction submission) ([http://dx.doi.org/10.1073/pnas.0708746105 doi:10.1073/pnas.0708746105]); selected by [http://f1000.com/1102040 Faculty of 1000]. |
</li> | </li> | ||
<li value="22"> | <li value="22"> | ||
− | "Development of a Polarizable Intermolecular Potential Function (PIPF) for Liquid Amides and Alkanes," Xie, W.; '''Pu, J.'''; MacKerell, Jr. A. D.; Gao, J. ''J. Chem. Theory Comput.'' '''2007''', ''3'', 1878-1889 ([http://dx.doi.org/10.1021/ct700146x | + | "Development of a Polarizable Intermolecular Potential Function (PIPF) for Liquid Amides and Alkanes," Xie, W.; '''Pu, J.'''; MacKerell, Jr. A. D.; Gao, J. ''J. Chem. Theory Comput.'' '''2007''', ''3'', 1878-1889 ([http://dx.doi.org/10.1021/ct700146x doi:10.1021/ct700146x]). |
</li> | </li> | ||
<li value="21"> | <li value="21"> | ||
− | "Multicoefficient Gaussian-3 Calculation of the Rate Constant for the OH + CH<sub>4</sub> Reaction and its <sup>12</sup>C/<sup>13</sup>C Kinetic Isotope Effect with Emphasis on the Effects of Coordinate System and Torsional Treatment," Ellingson, B. A.; '''Pu, J.'''; Lin, H.; Zhao, Y.; Truhlar, D. G. ''J. Phys. Chem. A'' '''2007''', ''111'', 11706-11717 ([http://dx.doi.org/10.1021/jp072843j | + | "Multicoefficient Gaussian-3 Calculation of the Rate Constant for the OH + CH<sub>4</sub> Reaction and its <sup>12</sup>C/<sup>13</sup>C Kinetic Isotope Effect with Emphasis on the Effects of Coordinate System and Torsional Treatment," Ellingson, B. A.; '''Pu, J.'''; Lin, H.; Zhao, Y.; Truhlar, D. G. ''J. Phys. Chem. A'' '''2007''', ''111'', 11706-11717 ([http://dx.doi.org/10.1021/jp072843j doi:10.1021/jp072843j]). |
</li> | </li> | ||
<li value="20"> | <li value="20"> | ||
− | "Mechanisms and Free Energies of Enzymatic Reactions," Gao, J.; Ma, S.; Major, D. T.; Nam, K.; '''Pu, J.'''; Truhlar, D. G. ''Chem. Rev.'' '''2006''', ''106'', 3188-3209 ([http://dx.doi.org/10.1021/cr050293k | + | "Mechanisms and Free Energies of Enzymatic Reactions," Gao, J.; Ma, S.; Major, D. T.; Nam, K.; '''Pu, J.'''; Truhlar, D. G. ''Chem. Rev.'' '''2006''', ''106'', 3188-3209 ([http://dx.doi.org/10.1021/cr050293k doi:10.1021/cr050293k]). |
</li> | </li> | ||
<li value="19"> | <li value="19"> | ||
− | "Multidimensional Tunneling, Recrossing, and Transmission Coefficient for Enzymatic Reactions," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''Chem. Rev.'' '''2006''', ''106'', 3140-3169 ([http://dx.doi.org/10.1021/cr050308e | + | "Multidimensional Tunneling, Recrossing, and Transmission Coefficient for Enzymatic Reactions," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''Chem. Rev.'' '''2006''', ''106'', 3140-3169 ([http://dx.doi.org/10.1021/cr050308e doi:10.1021/cr050308e]). |
. | . | ||
</li> | </li> | ||
<li value="18"> | <li value="18"> | ||
− | "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, J.; '''Pu, J.'''; Gao, J.; Truhlar, D. G; Allemann, R. K. ''J. Am. Chem. Soc.'' '''2006''', ''128'', 8015-8023 ([http://dx.doi.org/10.1021/ja061585l | + | "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, J.; '''Pu, J.'''; Gao, J.; Truhlar, D. G; Allemann, R. K. ''J. Am. Chem. Soc.'' '''2006''', ''128'', 8015-8023 ([http://dx.doi.org/10.1021/ja061585l doi:10.1021/ja061585l]). |
</li> | </li> | ||
<li value="17"> | <li value="17"> | ||
− | "Searching for Saddle Points by Using the Nudged Elastic Band Method: An Implementation for Gas-Phase Systems," Gonzalez-Garcia, N.; '''Pu, J.'''; Gonzalez-Lafont, A.; Lluch, J. M.; Truhlar, D. G. ''J. Chem. Theory Comput.'' '''2006''', ''2'', 895-904 ([http://dx.doi.org/10.1021/ct060032y | + | "Searching for Saddle Points by Using the Nudged Elastic Band Method: An Implementation for Gas-Phase Systems," Gonzalez-Garcia, N.; '''Pu, J.'''; Gonzalez-Lafont, A.; Lluch, J. M.; Truhlar, D. G. ''J. Chem. Theory Comput.'' '''2006''', ''2'', 895-904 ([http://dx.doi.org/10.1021/ct060032y doi:10.1021/ct060032y]). |
</li> | </li> | ||
<li value="16"> | <li value="16"> | ||
− | "Nonperfect Synchronization of Reaction Center Rehybridization in the Transition State of the Hydride Transfer Catalyzed by Dihydrofolate Reductase," '''Pu, J.'''; Ma, S.; Garcia-Viloca, M.; Gao, J.; Truhlar, D. G.; Kohen, A. ''J. Am. Chem. Soc.'' '''2005''', ''127'', 14879-14886 ([http://dx.doi.org/10.1021/ja054170t | + | "Nonperfect Synchronization of Reaction Center Rehybridization in the Transition State of the Hydride Transfer Catalyzed by Dihydrofolate Reductase," '''Pu, J.'''; Ma, S.; Garcia-Viloca, M.; Gao, J.; Truhlar, D. G.; Kohen, A. ''J. Am. Chem. Soc.'' '''2005''', ''127'', 14879-14886 ([http://dx.doi.org/10.1021/ja054170t doi:10.1021/ja054170t]). |
</li> | </li> | ||
<li value="15"> | <li value="15"> | ||
− | "Generalized Hybrid-Orbital Method for Combined Density Functional Theory and Molecular Mechanics," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''ChemPhysChem'' '''2005''', ''6'', 1853-1865 ([http://dx.doi.org/10.1002/cphc.200400602 | + | "Generalized Hybrid-Orbital Method for Combined Density Functional Theory and Molecular Mechanics," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''ChemPhysChem'' '''2005''', ''6'', 1853-1865 ([http://dx.doi.org/10.1002/cphc.200400602 doi:10.1002/cphc.200400602]). |
</li> | </li> | ||
<li value="14"> | <li value="14"> | ||
− | "Small Temperature Dependence of the Kinetic Isotope Effect for the Hydride Transfer Reaction Catalyzed by Escherichia coli Dihydrofolate Reductase," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''J. Phys. Chem. B'' '''2005''', ''109'', 8551-8556 ([http://dx.doi.org/10.1021/jp051184c | + | "Small Temperature Dependence of the Kinetic Isotope Effect for the Hydride Transfer Reaction Catalyzed by Escherichia coli Dihydrofolate Reductase," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''J. Phys. Chem. B'' '''2005''', ''109'', 8551-8556 ([http://dx.doi.org/10.1021/jp051184c doi:10.1021/jp051184c]). |
</li> | </li> | ||
<li value="13"> | <li value="13"> | ||
− | "Temperature Dependence of Carbon-13 Kinetic Isotope Effects of Importance to Global Climate Change," Lin, H.; Zhao, Y.; Ellingson, B. A.; '''Pu, J.'''; Truhlar, D. G. ''J. Am. Chem. Soc.'' '''2005''', ''127'', 2830-2831 ([http://dx.doi.org/10.1021/ja0434026 | + | "Temperature Dependence of Carbon-13 Kinetic Isotope Effects of Importance to Global Climate Change," Lin, H.; Zhao, Y.; Ellingson, B. A.; '''Pu, J.'''; Truhlar, D. G. ''J. Am. Chem. Soc.'' '''2005''', ''127'', 2830-2831 ([http://dx.doi.org/10.1021/ja0434026 doi:10.1021/ja043402]). |
</li> | </li> | ||
<li value="12"> | <li value="12"> | ||
− | "Benchmark Calculations of Reaction Energies, Barrier Heights, and Transition State Geometries for Hydrogen Abstraction from Methanol by a Hydrogen Atom," '''Pu, J.'''; Truhlar, D. G. ''J. Phys. Chem. A'' '''2005''', ''109'', 773-778 ([http://dx.doi.org/10.1021/jp045574v | + | "Benchmark Calculations of Reaction Energies, Barrier Heights, and Transition State Geometries for Hydrogen Abstraction from Methanol by a Hydrogen Atom," '''Pu, J.'''; Truhlar, D. G. ''J. Phys. Chem. A'' '''2005''', ''109'', 773-778 ([http://dx.doi.org/10.1021/jp045574v doi:10.1021/jp045574v]). |
</li> | </li> | ||
<li value="11"> | <li value="11"> | ||
− | "Use of Block Hessians for the Optimization of Molecular Geometries," '''Pu, J.'''; Truhlar, D. G. ''J. Chem. Theory Comput.'' '''2005''', ''1'', 54-60 ([http://dx.doi.org/10.1021/ct0400020 | + | "Use of Block Hessians for the Optimization of Molecular Geometries," '''Pu, J.'''; Truhlar, D. G. ''J. Chem. Theory Comput.'' '''2005''', ''1'', 54-60 ([http://dx.doi.org/10.1021/ct0400020 doi:10.1021/ct0400020]). |
</li> | </li> | ||
<li value="10"> | <li value="10"> | ||
− | "Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''J. Phys. Chem. A'' '''2004''', ''108'', 5454-5463 ([http://dx.doi.org/10.1021/jp049529z | + | "Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''J. Phys. Chem. A'' '''2004''', ''108'', 5454-5463 ([http://dx.doi.org/10.1021/jp049529z doi:10.1021/jp049529z]). |
</li> | </li> | ||
<li value="9"> | <li value="9"> | ||
− | "Efficient Molecular Mechanics for Chemical Reactions: Multiconfiguration Molecular Mechanics using Partial Electronic Structure Hessians," Lin, H.; '''Pu, J.'''; Albu, T. V.; Truhlar, D. G. ''J. Phys. Chem. A'' '''2004''', ''108'', 4112-4124 ([http://dx.doi.org/10.1021/jp049972+ | + | "Efficient Molecular Mechanics for Chemical Reactions: Multiconfiguration Molecular Mechanics using Partial Electronic Structure Hessians," Lin, H.; '''Pu, J.'''; Albu, T. V.; Truhlar, D. G. ''J. Phys. Chem. A'' '''2004''', ''108'', 4112-4124 ([http://dx.doi.org/10.1021/jp049972+ doi:10.1021/jp049972+]). |
</li> | </li> | ||
<li value="8"> | <li value="8"> | ||
− | "Tests of Second-Generation and Third-Generation Density Functionals for Thermochemical Kinetics," Zhao, Y.; '''Pu, J.'''; Lynch, B. J. Truhlar, D. G. ''Phys. Chem. Chem. Phys.'' '''2004''', ''6'', 673-676 ([http://dx.doi.org/10.1039/B316260E | + | "Tests of Second-Generation and Third-Generation Density Functionals for Thermochemical Kinetics," Zhao, Y.; '''Pu, J.'''; Lynch, B. J. Truhlar, D. G. ''Phys. Chem. Chem. Phys.'' '''2004''', ''6'', 673-676 ([http://dx.doi.org/10.1039/B316260E doi:10.1039/B316260E]). |
</li> | </li> | ||
<li value="7"> | <li value="7"> | ||
− | "Benchmark Results for Hydrogen Atom Transfer between Carbon Centers and Validation of Electronic Structure Methods for Bond Energies and Barrier Heights," Dybala-Defratyka, A.; Paneth, P.; '''Pu, J.'''; Truhlar, D. G. ''J. Phys. Chem. A'' '''2004''', ''108'', 2475-2486 ([http://dx.doi.org/10.1021/jp037312j | + | "Benchmark Results for Hydrogen Atom Transfer between Carbon Centers and Validation of Electronic Structure Methods for Bond Energies and Barrier Heights," Dybala-Defratyka, A.; Paneth, P.; '''Pu, J.'''; Truhlar, D. G. ''J. Phys. Chem. A'' '''2004''', ''108'', 2475-2486 ([http://dx.doi.org/10.1021/jp037312j doi:10.1021/jp037312j]). |
</li> | </li> | ||
<li value="6"> | <li value="6"> | ||
− | "Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree-Fock Wave Functions with Molecular Mechanics," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''J. Phys. Chem. A'' '''2004''', ''108'', 632-650 ([http://dx.doi.org/10.1021/jp036755k | + | "Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree-Fock Wave Functions with Molecular Mechanics," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''J. Phys. Chem. A'' '''2004''', ''108'', 632-650 ([http://dx.doi.org/10.1021/jp036755k doi:10.1021/jp036755k]). |
</li> | </li> | ||
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<li value="4"> | <li value="4"> | ||
− | "Tests of Potential Energy Surfaces for H + CH<sub>4</sub> → CH<sub>3</sub> + H<sub>2</sub>: Deuterium and Muonium Kinetic Isotope Effects for the Forward and Reverse Reaction," '''Pu, J.'''; Truhlar, D. G. ''J. Chem. Phys.'' '''2002''', ''117'', 10675 ([http://dx.doi.org/10.1063/1.1518471 | + | "Tests of Potential Energy Surfaces for H + CH<sub>4</sub> → CH<sub>3</sub> + H<sub>2</sub>: Deuterium and Muonium Kinetic Isotope Effects for the Forward and Reverse Reaction," '''Pu, J.'''; Truhlar, D. G. ''J. Chem. Phys.'' '''2002''', ''117'', 10675 ([http://dx.doi.org/10.1063/1.1518471 doi:10.1063/1.1518471]). |
</li> | </li> | ||
<li value="3"> | <li value="3"> | ||
− | "Validation of Variational Transition State Theory with Multidimensional Tunneling Contributions against Accurate Quantum Mechanical Dynamics for H + CH<sub>4</sub> → CH<sub>3</sub> + H<sub>2</sub> in an Extended Temperature Interval," '''Pu, J.'''; Truhlar, D. G. ''J. Chem. Phys.'' '''2002''', ''117'', 1479 ([http://dx.doi.org/10.1063/1.1485063 | + | "Validation of Variational Transition State Theory with Multidimensional Tunneling Contributions against Accurate Quantum Mechanical Dynamics for H + CH<sub>4</sub> → CH<sub>3</sub> + H<sub>2</sub> in an Extended Temperature Interval," '''Pu, J.'''; Truhlar, D. G. ''J. Chem. Phys.'' '''2002''', ''117'', 1479 ([http://dx.doi.org/10.1063/1.1485063 doi:10.1063/1.1485063]). |
</li> | </li> | ||
<li value="2"> | <li value="2"> | ||
− | "Parametrized Direct Dynamics Study of Rate Constants of H with CH<sub>4</sub> from 250 to 2400 K," '''Pu, J.'''; Truhlar, D. G. ''J. Chem. Phys.'' '''2002''', ''116'', 1468 ([http://dx.doi.org/10.1063/1.1427917 | + | "Parametrized Direct Dynamics Study of Rate Constants of H with CH<sub>4</sub> from 250 to 2400 K," '''Pu, J.'''; Truhlar, D. G. ''J. Chem. Phys.'' '''2002''', ''116'', 1468 ([http://dx.doi.org/10.1063/1.1427917 doi:10.1063/1.1427917]). |
</li> | </li> | ||
<li value="1"> | <li value="1"> | ||
− | "Test of Variational Transition State Theory with Multidimensional Tunneling Contributions Against an Accurate Full-Dimensional Rate Constant Calculation for a Six-Atom system," '''Pu, J.'''; Corchado, J. C.; Truhlar, D. G. ''J. Chem. Phys.'' '''2001''', ''115'', 6266 ([http://dx.doi.org/10.1063/1.1398581 | + | "Test of Variational Transition State Theory with Multidimensional Tunneling Contributions Against an Accurate Full-Dimensional Rate Constant Calculation for a Six-Atom system," '''Pu, J.'''; Corchado, J. C.; Truhlar, D. G. ''J. Chem. Phys.'' '''2001''', ''115'', 6266 ([http://dx.doi.org/10.1063/1.1398581 doi:10.1063/1.1398581]). |
</li> | </li> | ||
</ol> | </ol> |
Revision as of 23:30, 9 August 2016
- "Mapping Free Energy Paths of ATP Hydrolysis in the E. coli ABC-Transporter HlyB by the Finite Temperature String Method," Zhou, Y.; Ojeda-May, P.; Nagaraju, M.; Pu, J., to be submitted.
- "All-atom Simulations of Torque Generation in F1-ATPase," Pu, J.; Nam, K.; Karplus, M., submitted.
- "Toward Determining ATPase Mechanism in ABC-Transporters: Development of the Reaction Path-Force Matching QM/MM Method," Zhou, Y.; Ojeda-May, P.; Nagaraju, M.; Pu, J., Methods Enzymol. 2016, 577, 185-212. (doi:10.1016/bs.mie.2016.05.054; PubMed PMID:27498639).
- "Treating Electrostatics with Wolf Summation in Combined Quantum Mechanical and Molecular Mechanical Simulations," Ojeda-May, P.; Pu, J. J. Chem. Phys. 2015, 143, 174111 (doi:10.1063/1.4934880; PubMed PMID:26547162).
- "Trapping the ATP Binding State Leads to a Detailed Understanding of the F1-ATPase Mechanism," Nam, K.; Pu, J.; Karplus, M. Proc. Natl. Acad. Sci. USA 2014, 111, 17851-17856 (doi:10.1073/pnas.1419486111; PubMed PMID: 27498639).
- "Assessing the Accuracy of the Isotropic Periodic Sum Method through Madelung Energy Computation," Ojeda-May, P.; Pu, J. J. Chem. Phys. 2014, 140, 164106 (doi:10.1063/1.4871871).
- "Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations," Zhou, Y.; Pu, J. J. Chem. Theory Comput. 2014, 10, 3038-3054 (doi:10.1021/ct4009624).
- "Isotropic Periodic Sum Treatment of Long-Range Electrostatic Interactions in Combined Quantum Mechanical and Molecular Mechanical Calculations," Ojeda-May, P.; Pu, J. J. Chem. Theory Comput. 2014, 10, 134-145 (doi:10.1021/ct400724d).
- "Replica Exchange Molecular Dynamics Simulations of an α/β-type Small Acid Soluble Protein (SASP)," Ojeda-May, P.; Pu, J. Biophys. Chem. 2013, 184, 17-21 (doi:10.1016/j.bpc.2013.07.014).
- "H-loop Histidine Catalyzes ATP Hydrolysis in the E. coli ABC-Transporter HlyB," Zhou, Y.; Ojeda-May, P.; Pu, J. Phys. Chem. Chem. Phys. 2013, 15, 15811-15815 (doi:10.1039/C3CP50965F; SI: movie_S1& movie_S2; see also arXiv:1304.0052 [q-bio.BM]).
- "Expanding the Horizon of the Thymine Isostere Biochemistry: Unique Dimers formed via Photoreaction between a Thymine and a Toluene residue in the Dinucleotide Framework," Liu, D.; Zhou, Y.; Pu, J.; Li, L. Chem. Eur. J. 2012, 18, 7823-7833 (doi:10.1002/chem.201200816).
- "Chemical Synthesis, Crystal Structure and Enzymatic Evaluation of a Dinucleotide Spore Photoproduct Analogue Containing Formacetal Linker," Lin, G.; Chen, C.-H; Pink, M.; Pu, J.; Li, L. Chem. Eur. J. 2011, 17, 9658-9668 (doi:10.1002/chem.201101821).
--- Before IUPUI ---
- "How Biomolecular Motors Work: Synergy between Single Molecule Experiments and Single Molecule Simulations," Karplus, M.; Pu, J., in Springer Series in Chemical Physics 2010, 96 (Single Molecule Spectroscopy in Chemistry, Physics, and Biology), pp. 271-285.
- "A Coupled Polarization-Matrix Inversion and Iteration Approach for Accelerating the Dipole Convergence in a Polarizable Potential Function," Xie, W.; Pu, J.; Gao, J. J. Phys. Chem. A 2009, 113, 2109-2116 (doi:10.1021/jp808952m).
- "CHARMM: The Biomolecular Simulation Program," Brooks, B. R.; Brooks III, C. L.; 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.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. J. Comput. Chem. 2009, 30, 1545-1614 (doi:10.1002/jcc.21287).
- "How Subunit Coupling Produces the Rotary Motion in F1-ATPase," Pu, J.; Karplus, M. Proc. Natl. Acad. Sci. USA 2008, 105, 1192-1197 (track II, direction submission) (doi:10.1073/pnas.0708746105); selected by Faculty of 1000.
- "Development of a Polarizable Intermolecular Potential Function (PIPF) for Liquid Amides and Alkanes," Xie, W.; Pu, J.; MacKerell, Jr. A. D.; Gao, J. J. Chem. Theory Comput. 2007, 3, 1878-1889 (doi:10.1021/ct700146x).
- "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, B. A.; Pu, J.; Lin, H.; Zhao, Y.; Truhlar, D. G. J. Phys. Chem. A 2007, 111, 11706-11717 (doi:10.1021/jp072843j).
- "Mechanisms and Free Energies of Enzymatic Reactions," Gao, J.; Ma, S.; Major, D. T.; Nam, K.; Pu, J.; Truhlar, D. G. Chem. Rev. 2006, 106, 3188-3209 (doi:10.1021/cr050293k).
- "Multidimensional Tunneling, Recrossing, and Transmission Coefficient for Enzymatic Reactions," Pu, J.; Gao, J.; Truhlar, D. G. Chem. Rev. 2006, 106, 3140-3169 (doi:10.1021/cr050308e). .
- "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, J.; Pu, J.; Gao, J.; Truhlar, D. G; Allemann, R. K. J. Am. Chem. Soc. 2006, 128, 8015-8023 (doi:10.1021/ja061585l).
- "Searching for Saddle Points by Using the Nudged Elastic Band Method: An Implementation for Gas-Phase Systems," Gonzalez-Garcia, N.; Pu, J.; Gonzalez-Lafont, A.; Lluch, J. M.; Truhlar, D. G. J. Chem. Theory Comput. 2006, 2, 895-904 (doi:10.1021/ct060032y).
- "Nonperfect Synchronization of Reaction Center Rehybridization in the Transition State of the Hydride Transfer Catalyzed by Dihydrofolate Reductase," Pu, J.; Ma, S.; Garcia-Viloca, M.; Gao, J.; Truhlar, D. G.; Kohen, A. J. Am. Chem. Soc. 2005, 127, 14879-14886 (doi:10.1021/ja054170t).
- "Generalized Hybrid-Orbital Method for Combined Density Functional Theory and Molecular Mechanics," Pu, J.; Gao, J.; Truhlar, D. G. ChemPhysChem 2005, 6, 1853-1865 (doi:10.1002/cphc.200400602).
- "Small Temperature Dependence of the Kinetic Isotope Effect for the Hydride Transfer Reaction Catalyzed by Escherichia coli Dihydrofolate Reductase," Pu, J.; Gao, J.; Truhlar, D. G. J. Phys. Chem. B 2005, 109, 8551-8556 (doi:10.1021/jp051184c).
- "Temperature Dependence of Carbon-13 Kinetic Isotope Effects of Importance to Global Climate Change," Lin, H.; Zhao, Y.; Ellingson, B. A.; Pu, J.; Truhlar, D. G. J. Am. Chem. Soc. 2005, 127, 2830-2831 (doi:10.1021/ja043402).
- "Benchmark Calculations of Reaction Energies, Barrier Heights, and Transition State Geometries for Hydrogen Abstraction from Methanol by a Hydrogen Atom," Pu, J.; Truhlar, D. G. J. Phys. Chem. A 2005, 109, 773-778 (doi:10.1021/jp045574v).
- "Use of Block Hessians for the Optimization of Molecular Geometries," Pu, J.; Truhlar, D. G. J. Chem. Theory Comput. 2005, 1, 54-60 (doi:10.1021/ct0400020).
- "Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method," Pu, J.; Gao, J.; Truhlar, D. G. J. Phys. Chem. A 2004, 108, 5454-5463 (doi:10.1021/jp049529z).
- "Efficient Molecular Mechanics for Chemical Reactions: Multiconfiguration Molecular Mechanics using Partial Electronic Structure Hessians," Lin, H.; Pu, J.; Albu, T. V.; Truhlar, D. G. J. Phys. Chem. A 2004, 108, 4112-4124 (doi:10.1021/jp049972+).
- "Tests of Second-Generation and Third-Generation Density Functionals for Thermochemical Kinetics," Zhao, Y.; Pu, J.; Lynch, B. J. Truhlar, D. G. Phys. Chem. Chem. Phys. 2004, 6, 673-676 (doi:10.1039/B316260E).
- "Benchmark Results for Hydrogen Atom Transfer between Carbon Centers and Validation of Electronic Structure Methods for Bond Energies and Barrier Heights," Dybala-Defratyka, A.; Paneth, P.; Pu, J.; Truhlar, D. G. J. Phys. Chem. A 2004, 108, 2475-2486 (doi:10.1021/jp037312j).
- "Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree-Fock Wave Functions with Molecular Mechanics," Pu, J.; Gao, J.; Truhlar, D. G. J. Phys. Chem. A 2004, 108, 632-650 (doi:10.1021/jp036755k).
- "Lateral Confinement of Image Electron Wave Function by an Interfacial Dipole Lattice," Dutton, G.; Pu, J.; Truhlar, D. G.; Zhu, X. -Y. J. Chem. Phys. 2003, 118, 4337 (DOI:10.1063/1.1556848).
- "Tests of Potential Energy Surfaces for H + CH4 → CH3 + H2: Deuterium and Muonium Kinetic Isotope Effects for the Forward and Reverse Reaction," Pu, J.; Truhlar, D. G. J. Chem. Phys. 2002, 117, 10675 (doi:10.1063/1.1518471).
- "Validation of Variational Transition State Theory with Multidimensional Tunneling Contributions against Accurate Quantum Mechanical Dynamics for H + CH4 → CH3 + H2 in an Extended Temperature Interval," Pu, J.; Truhlar, D. G. J. Chem. Phys. 2002, 117, 1479 (doi:10.1063/1.1485063).
- "Parametrized Direct Dynamics Study of Rate Constants of H with CH4 from 250 to 2400 K," Pu, J.; Truhlar, D. G. J. Chem. Phys. 2002, 116, 1468 (doi:10.1063/1.1427917).
- "Test of Variational Transition State Theory with Multidimensional Tunneling Contributions Against an Accurate Full-Dimensional Rate Constant Calculation for a Six-Atom system," Pu, J.; Corchado, J. C.; Truhlar, D. G. J. Chem. Phys. 2001, 115, 6266 (doi:10.1063/1.1398581).