☰

Jingzhi Pu, Ph.D. - Publications

Affiliations: 
1999-2005 University of Minnesota, Twin Cities, Minneapolis, MN 
 2005-2010 Harvard University, Cambridge, MA, United States 
 2010- Indiana University - Purdue University Indianapolis, Indianapolis, IN, United States 
Area:
Theoretical and Computational Chemistry
Tree Info Similar researchers PubMed Report error

55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Pan X, Van R, Pu J, Nam K, Mao Y, Shao Y. Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions. Journal of Chemical Theory and Computation. PMID 37943896 DOI: 10.1021/acs.jctc.3c00973  0.314
2023 Hati S, Yang X, Gupta P, Muhoberac BB, Pu J, Zhang J, Sardar R. Hybrid Metal-Ligand Interfacial Dipole Engineering of Functional Plasmonic Nanostructures for Extraordinary Responses of Optoelectronic Properties. Acs Nano. PMID 37579222 DOI: 10.1021/acsnano.3c06047  0.287
2023 Snyder R, Kim B, Pan X, Shao Y, Pu J. Bridging semiempirical and ab initio QM/MM potentials by Gaussian process regression and its sparse variants for free energy simulation. The Journal of Chemical Physics. 159. PMID 37530109 DOI: 10.1063/5.0156327  0.41
2023 Hege M, Li L, Pu J. Revealing intrinsic changes of DNA induced by spore photoproduct lesion through computer simulation. Biophysical Chemistry. 296: 106992. PMID 36933500 DOI: 10.1016/j.bpc.2023.106992  0.233
2023 Yao S, Van R, Pan X, Park JH, Mao Y, Pu J, Mei Y, Shao Y. Machine learning based implicit solvent model for aqueous-solution alanine dipeptide molecular dynamics simulations. Rsc Advances. 13: 4565-4577. PMID 36760282 DOI: 10.1039/d2ra08180f  0.361
2023 Hege M, Li L, Pu J. Revealing Intrinsic Changes of DNA Induced by Spore Photoproduct Lesion through Computer Simulation Biophysical Chemistry. 296: 106992. DOI: 10.1016/j.bpc.2023.106992  0.213
2022 Snyder R, Kim B, Pan X, Shao Y, Pu J. Facilitating QM/MM free energy simulations by Gaussian process regression with derivative observations. Physical Chemistry Chemical Physics : Pccp. PMID 36222412 DOI: 10.1039/d2cp02820d  0.41
2022 Pan X, Van R, Epifanovsky E, Liu J, Pu J, Nam K, Shao Y. Accelerating Quantum Mechanical and Molecular Mechanical (QM/MM) Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semiempirical QM/MM Hamiltonian. The Journal of Physical Chemistry. B. PMID 35653199 DOI: 10.1021/acs.jpcb.2c02262  0.391
2022 Pu J. Accelerating ab initio QM/MM Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semiempirical QM/MM Hamiltonian J. Phys. Chem. B. 126: 4226-4235. DOI: 10.1021/acs.jpcb.2c02262  0.319
2021 Kim B, Shao Y, Pu J. Doubly Polarized QM/MM with Machine Learning Chaperone Polarizability. Journal of Chemical Theory and Computation. 17: 7682-7695. PMID 34723536 DOI: 10.1021/acs.jctc.1c00567  0.44
2021 Pan X, Yang J, Van R, Epifanovsky E, Ho J, Huang J, Pu J, Mei Y, Nam K, Shao Y. Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions. Journal of Chemical Theory and Computation. PMID 34468138 DOI: 10.1021/acs.jctc.1c00565  0.414
2021 Dille SA, Colston KJ, Ratvasky SC, Pu J, Basu P. Interligand communication in a metal mediated LL'CT system - a case study. Rsc Advances. 11: 24381-24386. PMID 34354823 DOI: 10.1039/d1ra04716g  0.295
2021 Kim B, Snyder R, Nagaraju M, Zhou Y, Ojeda-May P, Keeton S, Hege M, Shao Y, Pu J. Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force. Journal of Chemical Theory and Computation. PMID 34283604 DOI: 10.1021/acs.jctc.1c00245  0.436
2020 Cruse C, Pu J, Goodpaster JV. EXPRESS: Identifying Thermal Decomposition Products of Nitrate Ester Explosives Using Gas Chromatography-Vacuum Ultraviolet Spectroscopy: An Experimental and Computational Study. Applied Spectroscopy. 3702820915506. PMID 32192365 DOI: 10.1177/0003702820915506  0.333
2019 Pan X, Li P, Ho J, Pu J, Mei Y, Shao Y. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching. Physical Chemistry Chemical Physics : Pccp. PMID 31508625 DOI: 10.1039/C9Cp02593F  0.529
2019 Huang D, Chen S, Pu J, Tan X, Zhou Y. Exploring Cycloreversion Reaction of Cyclobutane Pyrimidine Dimers Quantum Mechanically. The Journal of Physical Chemistry. A. PMID 30776239 DOI: 10.1021/Acs.Jpca.8B12345  0.462
2018 Zhou Y, Ojeda-May P, Nagaraju M, Kim B, Pu J. Mapping Free Energy Pathways for ATP Hydrolysis in the ABC Transporter HlyB by the String Method. Molecules (Basel, Switzerland). 23. PMID 30332773 DOI: 10.3390/Molecules23102652  0.484
2017 Teunis MB, Nagaraju M, Dutta P, Pu J, Muhoberac BB, Sardar R, Agarwal M. Elucidating the role of surface passivating ligand structural parameters in hole wave function delocalization in semiconductor cluster molecules. Nanoscale. PMID 28902194 DOI: 10.1039/C7Nr04874B  0.413
2016 Zhou Y, Ojeda-May P, Nagaraju M, Pu J. Toward Determining ATPase Mechanism in ABC Transporters: Development of the Reaction Path-Force Matching QM/MM Method. Methods in Enzymology. 577: 185-212. PMID 27498639 DOI: 10.1016/Bs.Mie.2016.05.054  0.49
2015 Ojeda-May P, Pu J. Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations. The Journal of Chemical Physics. 143: 174111. PMID 26547162 DOI: 10.1063/1.4934880  0.479
2015 Pu J. Multiscale QM/MM Simulations of ATP Hydrolysis Mechanism in ABC-Transporters Biophysical Journal. 108: 146a. DOI: 10.1016/j.bpj.2014.11.804  0.269
2014 Zhou Y, Pu J. Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations. Journal of Chemical Theory and Computation. 10: 3038-54. PMID 26588275 DOI: 10.1021/Ct4009624  0.503
2014 Ojeda-May P, Pu J. Isotropic Periodic Sum Treatment of Long-Range Electrostatic Interactions in Combined Quantum Mechanical and Molecular Mechanical Calculations. Journal of Chemical Theory and Computation. 10: 134-45. PMID 26579897 DOI: 10.1021/Ct400724D  0.468
2014 Nam K, Pu J, Karplus M. Trapping the ATP binding state leads to a detailed understanding of the F1-ATPase mechanism. Proceedings of the National Academy of Sciences of the United States of America. 111: 17851-6. PMID 25453082 DOI: 10.1073/Pnas.1419486111  0.608
2014 Ojeda-May P, Pu J. Assessing the accuracy of the isotropic periodic sum method through Madelung energy computation. The Journal of Chemical Physics. 140: 164106. PMID 24784252 DOI: 10.1063/1.4871871  0.453
2013 Ojeda-May P, Pu J. Replica exchange molecular dynamics simulations of an α/β-type small acid soluble protein (SASP). Biophysical Chemistry. 184: 17-21. PMID 24029407 DOI: 10.1016/J.Bpc.2013.07.014  0.362
2013 Zhou Y, Ojeda-May P, Pu J. H-loop histidine catalyzes ATP hydrolysis in the E. coli ABC-transporter HlyB. Physical Chemistry Chemical Physics : Pccp. 15: 15811-5. PMID 23955493 DOI: 10.1039/C3Cp50965F  0.401
2012 Liu D, Zhou Y, Pu J, Li L. 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. Chemistry (Weinheim An Der Bergstrasse, Germany). 18: 7823-33. PMID 22588824 DOI: 10.1002/Chem.201200816  0.312
2011 Lin G, Chen CH, Pink M, Pu J, Li L. Chemical synthesis, crystal structure and enzymatic evaluation of a dinucleotide spore photoproduct analogue containing a formacetal linker. Chemistry (Weinheim An Der Bergstrasse, Germany). 17: 9658-68. PMID 21780208 DOI: 10.1002/Chem.201101821  0.246
2010 Karplus M, Pu J. How biomolecular motors work: Synergy between single molecule experiments and single molecule simulations Springer Series in Chemical Physics. 96: 3-22. DOI: 10.1007/978-3-642-02597-6_1  0.523
2009 Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, ... ... Pu JZ, et al. CHARMM: the biomolecular simulation program. Journal of Computational Chemistry. 30: 1545-614. PMID 19444816 DOI: 10.1002/Jcc.21287  0.665
2009 Xie W, Pu J, Gao J. A coupled polarization-matrix inversion and iteration approach for accelerating the dipole convergence in a polarizable potential function. The Journal of Physical Chemistry. A. 113: 2109-16. PMID 19123850 DOI: 10.1021/Jp808952M  0.724
2008 Pu J, Karplus M. How subunit coupling produces the gamma-subunit rotary motion in F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America. 105: 1192-7. PMID 18216260 DOI: 10.1073/Pnas.0708746105  0.565
2007 Xie W, Pu J, Mackerell AD, Gao J. Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes. Journal of Chemical Theory and Computation. 3: 1878-1889. PMID 18958290 DOI: 10.1021/Ct700146X  0.734
2007 Ellingson BA, Pu J, Lin H, Zhao Y, Truhlar DG. 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. The Journal of Physical Chemistry. A. 111: 11706-17. PMID 17949061 DOI: 10.1021/Jp072843J  0.768
2006 González-García N, Pu J, González-Lafont À, Lluch JM, Truhlar DG. Searching for Saddle Points by Using the Nudged Elastic Band Method:  An Implementation for Gas-Phase Systems. Journal of Chemical Theory and Computation. 2: 895-904. PMID 26633048 DOI: 10.1021/Ct060032Y  0.52
2006 Gao J, Ma S, Major DT, Nam K, Pu J, Truhlar DG. Mechanisms and free energies of enzymatic reactions. Chemical Reviews. 106: 3188-209. PMID 16895324 DOI: 10.1021/Cr050293K  0.766
2006 Pu J, Gao J, Truhlar DG. Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions. Chemical Reviews. 106: 3140-69. PMID 16895322 DOI: 10.1021/Cr050308E  0.668
2006 Pang J, Pu J, Gao J, Truhlar DG, Allemann RK. Hydride transfer reaction catalyzed by hyperthermophilic dihydrofolate reductase is dominated by quantum mechanical tunneling and is promoted by both inter- and intramonomeric correlated motions. Journal of the American Chemical Society. 128: 8015-23. PMID 16771517 DOI: 10.1021/Ja061585L  0.718
2005 Pu J, Truhlar DG. Use of Block Hessians for the Optimization of Molecular Geometries. Journal of Chemical Theory and Computation. 1: 54-60. PMID 26641115 DOI: 10.1021/Ct0400020  0.512
2005 Pu J, Ma S, Gao J, Truhlar DG. Small temperature dependence of the kinetic isotope effect for the hydride transfer reaction catalyzed by Escherichia coli dihydrofolate reductase. The Journal of Physical Chemistry. B. 109: 8551-6. PMID 16852008 DOI: 10.1021/Jp051184C  0.711
2005 Pu J, Truhlar DG. Benchmark calculations of reaction energies, barrier heights, and transition-state geometries for hydrogen abstraction from methanol by a hydrogen atom. The Journal of Physical Chemistry. A. 109: 773-8. PMID 16838946 DOI: 10.1021/Jp045574V  0.607
2005 Pu J, Ma S, Garcia-Viloca M, Gao J, Truhlar DG, Kohen A. Nonperfect synchronization of reaction center rehybridization in the transition state of the hydride transfer catalyzed by dihydrofolate reductase. Journal of the American Chemical Society. 127: 14879-86. PMID 16231943 DOI: 10.1021/Ja054170T  0.68
2005 Pu J, Gao J, Truhlar DG. Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 6: 1853-65. PMID 16086343 DOI: 10.1002/Cphc.200400602  0.726
2005 Lin H, Zhao Y, Ellingson BA, Pu J, Truhlar DG. Temperature dependence of carbon-13 kinetic isotope effects of importance to global climate change. Journal of the American Chemical Society. 127: 2830-1. PMID 15740100 DOI: 10.1021/Ja0434026  0.769
2004 Zhao Y, Pu J, Lynch BJ, Truhlar DG. Tests of second-generation and third-generation density functionals for thermochemical kineticsElectronic supplementary information (ESI) available: Mean errors for pure and hybrid DFT methods. See http://www.rsc.org/suppdata/cp/b3/b316260e/ Physical Chemistry Chemical Physics. 6: 673. DOI: 10.1039/B316260E  0.705
2004 Lin H, Pu J, Albu TV, Truhlar DG. Efficient Molecular Mechanics for Chemical Reactions:  Multiconfiguration Molecular Mechanics Using Partial Electronic Structure Hessians The Journal of Physical Chemistry A. 108: 4112-4124. DOI: 10.1021/Jp049972+  0.655
2004 Pu J, Gao J, Truhlar DG. Combining self-consistent-charge density-functional tight-binding (SCC-DFTB) with molecular mechanics by the generalized hybrid orbital (GHO) method Journal of Physical Chemistry A. 108: 5454-5463. DOI: 10.1021/Jp049529Z  0.718
2004 Dybala-Defratyka A, Paneth P, Pu J, Truhlar DG. Benchmark Results for Hydrogen Atom Transfer between Carbon Centers and Validation of Electronic Structure Methods for Bond Energies and Barrier Heights The Journal of Physical Chemistry A. 108: 2475-2486. DOI: 10.1021/Jp037312J  0.551
2004 Pu J, Gao J, Truhlar DG. Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree−Fock Wave Functions with Molecular Mechanics The Journal of Physical Chemistry A. 108: 632-650. DOI: 10.1021/Jp036755K  0.709
2003 Dutton G, Pu J, Truhlar DG, Zhu X. Lateral confinement of image electron wave function by an interfacial dipole lattice The Journal of Chemical Physics. 118: 4337-4340. DOI: 10.1063/1.1556848  0.484
2002 Pu J, Truhlar DG. Tests of potential energy surfaces for H+CH4↔CH3+H2: Deuterium and muonium kinetic isotope effects for the forward and reverse reaction Journal of Chemical Physics. 117: 10675-10687. DOI: 10.1063/1.1518471  0.554
2002 Pu J, Truhlar DG. Validation of variational transition state theory with multidimensional tunneling contributions against accurate quantum mechanical dynamics for H+CH4→H2+CH3 in an extended temperature interval Journal of Chemical Physics. 117: 1479-1481. DOI: 10.1063/1.1485063  0.532
2002 Pu J, Truhlar DG. Parametrized direct dynamics study of rate constants of H with CH4 from 250 to 2400 K Journal of Chemical Physics. 116: 1468-1478. DOI: 10.1063/1.1427917  0.563
2001 Pu J, Corchado JC, Truhlar DG. Test of variational transition state theory with multidimensional tunneling contributions against an accurate full-dimensional rate constant calculation for a six-atom system The Journal of Chemical Physics. 115: 6266-6267. DOI: 10.1063/1.1398581  0.589
Show low-probability matches.