Publications

From Jingzhi Pu Lab
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  1. "CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed," Hwang, W. et al. J. Phys. Chem. B, submitted.
  2. "The Role of E283 in Cycloreversion Reaction of Cyclobutane Pyrimidine Dimer Catalyzed by DNA Photolyase Studied by Combined DFT/MM Method," Xue, P.; Huang, D.; Pu, J.; Zhou, Y. J. Phys. Chem. B 2024, under revision.
  3. "Design of Light-Induced Solid-State Plasmonic Rulers via Tethering Photoswitchable Molecular Machines to Gold Nanostructures Displaying Angstrom Length Resolution," Langlais, S.; Hati, S.; Simas, V.; Pu, J.; Muhoberac, B.; Sardar, R. Adv. Optical Mater. 2024, 2400801 (doi:10.1002/adom.202400801).
  4. "Training Machine Learning Potentials for Reactive Systems: A Colab Tutorial on Basic Models," Pan, X.; Snyder, R.; Wang, J.-N.; Lander, C.; Wickizer, C.; Van, R.; Chesney, A.; Xue, Y.; Mao, Y.; Mei, Y.; Pu, J.; Shao, Y. J. Comput. Chem. 2024, 45, 638-647 (doi:10.1002/jcc.27269; PMID: 38082539; preprint: doi:10.26434/chemrxiv-2023-545gw).
  5. "Polyrate 2023: A Computer Program for the Calculation of Chemical Reaction Rates for Polyatomics. New Version Announcement," Meana-Paneda, R.; Zheng, J.; Bao, J. L.; Zhang, S.; Lynch, B. J.; Corchado, J. C.; Chuang, Y.-Y.; Fast, P. L.; Hu, W.-P.; Liu, Y.-P.; Lynch, G. C.; Nguyen, K. A.; Jackels, C. F.; Fernandez-Ramos, A.; Ellingson, B. A.; Melissas, V. S.; Villa, J.; Rossi, I.; Coitino, E. L.; Pu, J.; Albu, T. V.; Zhang, R. M.; Xu, X.; Ratkiewicz, A.; Steckler, R.; Garrett, B. C.; Isaacson, A. D.; Truhlar, D. G. Comput. Phys. Commun. 2024, 294, 108933 (doi:10.1016/j.cpc.2023.108933).
  6. "Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions," Pan, X.; Van, R.; Pu, J.; Nam, K.; Mao, Y.; Shao, Y. J. Chem. Theory Comput. 2023, 19, 8234-8244 (doi:10.1021/acs.jctc.3c00973; PMID:37943896; preprint: doi:10.26434/chemrxiv-2023-mrm25) .
  7. "Hybrid Metal-Ligand Interfacial Dipole Engineering of Functional Plasmonic Nanostructures for Extraordinary Responses of Optoelectronic Properties," Hati, S.; Yang, X.; Gupta, P.; Muhoberac, B.; Pu, J.; Zhang, J.; Sardar, R. ACS Nano 2023, 17, 17499-17515 (doi:10.1021/acsnano.3c06047).
  8. "Bridging Semiempirical and Ab Initio QM/MM Potentials by Gaussian Process Regression and Its Sparse Variants for Free Energy Simulation," Snyder, R.; Kim, B.; Pan, X.; Shao, Y.; Pu, J. J. Chem. Phys. 2023, 159, 054107 (doi:10.1063/5.0156327 PMID:37530109).
  9. "Revealing Intrinsic Changes of DNA Induced by Spore Photoproduct Lesion through Computer Simulation," Hege, M.; Li, L.; Pu, J. Biophys. Chem. 2023, 296, 106992 (doi:10.1016/j.bpc.2023.106992 PMID: 36933500).
  10. "Photoactivities of Thiophene Monomer/Polymer Transition in Gel-Based Photoelectrochemical Assembly: A Theoretical/Experimental Approach." Kasem, K.; Pu, J.; Cox, L. Int. J. Electrochem. Sci. 2023, 18, 100077 (doi:10.1016/j.ijoes.2023.100077).
  11. "Machine Learning Based Implicit Solvent Model for Aqueous-Solution Alanine Dipeptide Molecular Dynamics Simulations," Yao, S.; Van, R.; Pan, X.; Park, J. H.; Mao, Y.; Pu, J.; Mei, Y.; Shao, Y. RSC Adv. 2023, 13, 4565-4577 (doi:10.1039/D2RA08180F PMID: 36760282).
  12. "Facilitating Ab Initio QM/MM Free Energy Simulations by Gaussian Process Regression with Derivative Observations," Snyder, R.; Kim, B.; Pan, X.; Shao, Y.; Pu, J. Phys. Chem. Chem. Phys. 2022, 24, 25134-25143 (doi:10.1039/d2cp02820d; PMID:36222412; selected as a 2022 PCCP HOT Article).
  13. "Photoinduced Site-Selective Functionalization of Aliphatic C-H Bonds by Pyridine N-oxide Based HAT Catalysts," Wang, B.; Ascenzi Pettenuzzo, C.; Singh, J.; Mccabe, G.; Clark, L.; Young, R.; Pu, J.; Deng, Y. ACS Catalysis 2022, 12, 10441-10448 (doi:10.1021/acscatal.2c02993; preprint: doi:10.26434/chemrxiv-2022-0rb4h).
  14. "Accelerating ab initio QM/MM Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semiempirical QM/MM Hamiltonian," Pan, X.; Van, R.; Epifanovsky, E.; Liu, J.; Pu, J.; Nam, K.; Shao, Y. J. Phys. Chem. B 2022, 126, 4226-4235 (doi:10.1021/acs.jpcb.2c02262; preprint: doi:10.26434/chemrxiv-2022-0zg7j).
  15. "Doubly Polarized QM/MM with Machine Learning Chaperone Polarizability," Kim, B.; Shao, Y.; Pu, J. J. Chem. Theory Comput. 2021, 17, 7682-7695 (doi:10.1021/acs.jctc.1c00567; PMID:34723536).
  16. "Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions," Pan, X.; Yang, J.; Van, R.; Epifanovsky, E.; Ho, J.; Huang, J.; Pu, J., Mei, Y.; Nam, K.; Shao, Y. J. Chem. Theory Comput. 2021, 17, 5745-5758 (doi:10.1021/acs.jctc.1c00565; PMID:34468138).
  17. "Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force," Kim, B.; Snyder, R.; Nagaraju, M.; Zhou, Y.; Ojeda-May, P.; Keeton, S.; Hege, M.; Shao, Y.; Pu, J. J. Chem. Theory Comput. 2021, 17, 4961-4980 (doi: 10.1021/acs.jctc.1c00245; PMID:34283604).
  18. "Interligand Communication in a Metal Mediated LL’CT System - A Case Study," Dille, S.; Colston, K.; Ratvasky, S. C.; Pu, J.; Basu, P. RSC Adv. 2021, 11, 24381–24386 (doi: 10.1039/d1ra04716g).
  19. "Identifying Thermal Decomposition Products of Nitrate Ester Explosives Using Gas Chromatography–Vacuum Ultraviolet Spectroscopy: An Experimental and Computational Study," Cruse, C.; Pu, J.; Goodpaster, J. V. Appl. Spectrosc. 2020, 74, 1486-1495 (doi: 10.1177/0003702820915506).
  20. "Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. II. Recalibrating Semi-Empirical Parameters with Force Matching," Pan, X.; Li, P.; Ho, J.; Pu, J.; Mei, Y.; Shao, Y. Phys. Chem. Chem. Phys. 2019, 21, 20595-20605 (doi: 10.1039/c9cp02593f; PMID:31508625).
  21. "Exploring Cycloreversion Reaction of Cyclobutane Pyrimidine Dimers Quantum Mechanically," Huang, D.; Chen, S.; Pu, J.; Tan, X.; Zhou, Y. J. Phys. Chem. A 2019, 123, 2025-2039 (doi:10.1021/acs.jpca.8b12345).
  22. "Mapping Free Energy Pathways for ATP Hydrolysis in the E. coli ABC Transporter HlyB by the String Method," Zhou, Y.; Ojeda-May, P.; Nagaraju, M.; Kim, B.; Pu, J. Molecules 2018, 23, 2652 (QM/MM Special Issue; doi:10.3390/molecules23102652; PMID:30332773).
  23. "All-atom Simulations of Torque Generation in F1-ATPase," Pu, J.; Nam, K.; Karplus, M., submitted.
  24. "Elucidating the Role of Surface Passivating Ligand Structural Parameters in Hole Wave Function Delocalization in Semiconductor Cluster Molecules," Teunis, M. B.; Mulpuri, N.; Dutta, P; Pu, J.; Muhoberac, B. B.; Sardar, R.; Agarwal, M. Nanoscale 2017, 9, 14127-14138 (doi:10.1039/C7NR04874B).
  25. "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; PMID:27498639).
  26. "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; PMID:26547162).
  27. "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).
  28. "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).
  29. "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).
  30. "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).
  31. "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).
  32. "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; preprint: arXiv:1304.0052 [q-bio.BM]).
  33. "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).
  34. "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 ---

  1. "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.
  2. "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).
  3. "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).
  4. "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.
  5. "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).
  6. "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).
  7. "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).
  8. "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). .
  9. "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).
  10. "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).
  11. "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).
  12. "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).
  13. "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).
  14. "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/ja0434026).
  15. "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).
  16. "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).
  17. "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).
  18. "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+).
  19. "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).
  20. "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).
  21. "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).
  22. "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).
  23. "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).
  24. "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).
  25. "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).
  26. "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).
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