Jiali Gao - Publications

Affiliations: 
Chemistry University of Minnesota, Twin Cities, Minneapolis, MN 
Area:
Chemical Biology; Chemical Physics; Computational Chemistry; Physical Chemistry; Organic Chemistry
Website:
http://www.chem.umn.edu/directory/faculty.lasso?serial=1189

141 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
2019 Walker C, Wang Y, Olivieri C, Karamafrooz A, Casby J, Bathon K, Calebiro D, Gao J, Bernlohr DA, Taylor SS, Veglia G. Cushing's syndrome driver mutation disrupts protein kinase A allosteric network, altering both regulation and substrate specificity. Science Advances. 5: eaaw9298. PMID 31489371 DOI: 10.1126/sciadv.aaw9298  1
2019 Asgari P, Hua Y, Bokka A, Thiamsiri C, Prasitwatcharakorn W, Karedath A, Chen X, Sardar S, Yum K, Leem G, Pierce BS, Nam K, Gao J, Jeon J. Catalytic hydrogen atom transfer from hydrosilanes to vinylarenes for hydrosilylation and polymerization. Nature Catalysis. 2: 164-173. PMID 31460492 DOI: 10.1038/s41929-018-0217-z  0.8
2019 Larsen EK, Weber DK, Wang S, Gopinath T, Blackwell DJ, Dalton MP, Robia SL, Gao J, Veglia G. Intrinsically disordered HAX-1 regulates Ca cycling by interacting with lipid membranes and the phospholamban cytoplasmic region. Biochimica Et Biophysica Acta. Biomembranes. 183034. PMID 31400305 DOI: 10.1016/j.bbamem.2019.183034  0.48
2019 Tang GY, Gao J. Low Free Sugar Diet in Adolescents With Nonalcoholic Fatty Liver Disease. Jama. 321: 2468-2469. PMID 31237631 DOI: 10.1001/jama.2019.5141  0.4
2019 Wang Y, Huang J, Xu X, Chen J, Wu Z, Gao J, Tang J, Hu M, Yu X. [Application of standardized venous thromboembolism prevention program in burn patients]. Zhongguo Xiu Fu Chong Jian Wai Ke Za Zhi = Zhongguo Xiufu Chongjian Waike Zazhi = Chinese Journal of Reparative and Reconstructive Surgery. 33: 726-729. PMID 31198001 DOI: 10.7507/1002-1892.201812061  1
2019 Yang L, Zhang Q, Gao J, Wang Y. Why Can Normal Palladium Catalysts Efficiently Mediate Aerobic C-H Hydroxylation of Arylpyridines by Intercepting Aldehyde Autoxidation? A Nascent Palladium(III)-Peracid Intermediate Makes a Difference. Inorganic Chemistry. PMID 30895779 DOI: 10.1021/acs.inorgchem.8b03515  1
2019 Li Q, Wu Y, Wang W, Deng S, Jiang C, Chen F, Zhao J, Li H, Bai X, Hou J, Da L, Zhao L, Gao J, Jin G. Effectiveness and safety of combined neurokinin-1 antagonist aprepitant treatment for multiple-day anthracycline-induced nausea and vomiting. Current Problems in Cancer. PMID 30709557 DOI: 10.1016/j.currproblcancer.2019.01.003  0.8
2019 Gao J, Liu Q, Song L, Shi B. Risk assessment of heavy metals in pipe scales and loose deposits formed in drinking water distribution systems. The Science of the Total Environment. 652: 1387-1395. PMID 30586823 DOI: 10.1016/j.scitotenv.2018.10.347  0.84
2018 Yang L, Wang F, Gao J, Wang Y. What factors tune the chemical equilibrium between metal-iodosylarene oxidants and high-valent metal-oxo ones? Physical Chemistry Chemical Physics : Pccp. PMID 30566123 DOI: 10.1039/c8cp06117c  1
2018 Liu M, Youmans KN, Gao J. Dual QM and MM Approach for Computing Equilibrium Isotope Fractionation Factor of Organic Species in Solution. Molecules (Basel, Switzerland). 23. PMID 30326599 DOI: 10.3390/molecules23102644  0.92
2018 Liu M, Chen X, Grofe A, Gao J. Diabatic States At Construction (DAC) Through Generalized Singular Value Decomposition. The Journal of Physical Chemistry Letters. PMID 30277783 DOI: 10.1021/acs.jpclett.8b02472  0.92
2018 Yang L, Chen X, Qu Z, Gao J. Combined Multistate and Kohn-Sham Density Functional Theory Studies of the Elusive Mechanism of -Dealkylation of -Dimethylanilines Mediated by the Biomimetic Nonheme Oxidant Fe(O)(N4Py)(ClO). Frontiers in Chemistry. 6: 406. PMID 30250841 DOI: 10.3389/fchem.2018.00406  0.8
2018 Larsen EK, Olivieri C, Walker C, V S M, Gao J, Bernlohr DA, Tonelli M, Markley JL, Veglia G. Probing Protein-Protein Interactions Using Asymmetric Labeling and Carbonyl-Carbon Selective Heteronuclear NMR Spectroscopy. Molecules (Basel, Switzerland). 23. PMID 30081441 DOI: 10.3390/molecules23081937  0.48
2018 Dixit M, Weitman M, Gao J, Major DT. Comment on "Substrate Folding Modes in Trichodiene Synthase: A Determinant of Chemo- and Stereoselectivity". Acs Catalysis. 8: 1371-1375. PMID 29805842 DOI: 10.1021/acscatal.7b02823  1
2018 Tomasini MD, Wang Y, Karamafrooz A, Li G, Beuming T, Gao J, Taylor SS, Veglia G, Simon SM. Conformational Landscape of the PRKACA-DNAJB1 Chimeric Kinase, the Driver for Fibrolamellar Hepatocellular Carcinoma. Scientific Reports. 8: 720. PMID 29335433 DOI: 10.1038/s41598-017-18956-w  1
2017 Dixit M, Weitman M, Gao J, Major DT. Chemical Control in the Battle against Fidelity in Promiscuous Natural Product Biosynthesis: The Case of Trichodiene Synthase. Acs Catalysis. 7: 812-818. PMID 29399379 DOI: 10.1021/acscatal.6b02584  1
2017 Olson CM, Grofe A, Huber CJ, Spector IC, Gao J, Massari AM. Enhanced vibrational solvatochromism and spectral diffusion by electron rich substituents on small molecule silanes. The Journal of Chemical Physics. 147: 124302. PMID 28964044 DOI: 10.1063/1.5003908  0.64
2017 Grofe A, Chen X, Liu W, Gao J. Spin-Multiplet Components and Energy Splittings by Multistate Density Functional Theory. The Journal of Physical Chemistry Letters. PMID 28914545 DOI: 10.1021/acs.jpclett.7b02202  0.8
2017 Grofe A, Qu Z, Truhlar DG, Li H, Gao J. Diabatic-At-Construction (DAC) Method for Diabatic and Adiabatic Ground and Excited States Based on Multistate Density Functional Theory. Journal of Chemical Theory and Computation. PMID 28135420 DOI: 10.1021/acs.jctc.6b01176  1
2017 Cote JM, Ramirez-Mondragon CA, Siegel ZS, Czyzyk DJ, Gao J, Sham YY, Mukerji I, Taylor EA. The Stories Tryptophans Tell: Exploring Protein Dynamics of Heptosyltransferase I from Escherichia coli. Biochemistry. PMID 28098447 DOI: 10.1021/acs.biochem.6b00850  0.6
2017 Xue RJ, Grofe A, Yin H, Qu Z, Gao J, Li H. Perturbation Approach for Computing Infrared Spectra of the Local Mode of Probe Molecules. Journal of Chemical Theory and Computation. 13: 191-201. PMID 28068771 DOI: 10.1021/acs.jctc.6b00733  0.8
2016 Gao J, Grofe A, Ren H, Bao P. Beyond Kohn-Sham Approximation: Hybrid Multistate Wave Function and Density Functional Theory. The Journal of Physical Chemistry Letters. 7: 5143-5149. PMID 27973892 DOI: 10.1021/acs.jpclett.6b02455  0.76
2016 Lewis AK, Dunleavy KM, Senkow TL, Her C, Horn BT, Jersett MA, Mahling R, McCarthy MR, Perell GT, Valley CC, Karim CB, Gao J, Pomerantz WC, Thomas DD, Cembran A, et al. Oxidation increases the strength of the methionine-aromatic interaction. Nature Chemical Biology. PMID 27547920 DOI: 10.1038/nchembio.2159  1
2016 Ren H, Provorse MR, Bao P, Qu Z, Gao J. Multistate Density Functional Theory for Effective Diabatic Electronic Coupling. The Journal of Physical Chemistry Letters. PMID 27248004 DOI: 10.1021/acs.jpclett.6b00915  0.8
2015 Sun W, Ren H, Tao Y, Xiao D, Qin X, Deng L, Shao M, Gao J, Chen X. Two Aromatic Rings Coupled a Sulfur-Containing Group to Favor Protein Electron Transfer by Instantaneous Formations of π∴S:π↔π:S∴π or π∴π:S↔π:π∴S Five-Electron Bindings. The Journal of Physical Chemistry. C, Nanomaterials and Interfaces. 119: 9149-9158. PMID 26120374 DOI: 10.1021/acs.jpcc.5b01740  0.8
2015 Sun W, Shao M, Ren H, Xiao D, Qin X, Deng L, Chen X, Gao J. A New Type of Electron Relay Station in Proteins: Three-Piece S:Π∴S↔S∴Π:S Resonance Structure. The Journal of Physical Chemistry. C, Nanomaterials and Interfaces. 119: 6998-7005. PMID 26113884 DOI: 10.1021/jp512628x  0.8
2015 Kim J, Masterson LR, Cembran A, Verardi R, Shi L, Gao J, Taylor SS, Veglia G. Dysfunctional conformational dynamics of protein kinase A induced by a lethal mutant of phospholamban hinder phosphorylation. Proceedings of the National Academy of Sciences of the United States of America. 112: 3716-21. PMID 25775607 DOI: 10.1073/pnas.1502299112  1
2015 Gao J, Orozco M, Peishoff CE. Tribute to William L. Jorgensen. The Journal of Physical Chemistry. B. 119: 621-3. PMID 25608798 DOI: 10.1021/jp511519w  0.68
2015 Wang Y, Gao J. Projected hybrid orbitals: a general QM/MM method. The Journal of Physical Chemistry. B. 119: 1213-24. PMID 25317748 DOI: 10.1021/jp507983u  1
2014 Liu M, Wang Y, Chen Y, Field MJ, Gao J. QM/MM through the 1990s: The First Twenty Years of Method Development and Applications. Israel Journal of Chemistry. 54: 1250-1263. PMID 29386687 DOI: 10.1002/ijch.201400036  1
2014 Govender K, Gao J, Naidoo KJ. AM1/d-CB1: A Semiempirical Model for QM/MM Simulations of Chemical Glycobiology Systems. Journal of Chemical Theory and Computation. 10: 4694-4707. PMID 26120288 DOI: 10.1021/ct500372s  0.6
2014 Desai BJ, Goto Y, Cembran A, Fedorov AA, Almo SC, Gao J, Suga H, Gerlt JA. Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution. Proceedings of the National Academy of Sciences of the United States of America. 111: 15066-71. PMID 25275007 DOI: 10.1073/pnas.1411772111  1
2014 Gao J, Zhang JZ, Houk KN. Beyond QM/MM: fragment quantum mechanical methods. Accounts of Chemical Research. 47: 2711. PMID 25223725 DOI: 10.1021/ar500293u  0.64
2014 Gao J, Truhlar DG, Wang Y, Mazack MJ, Löffler P, Provorse MR, Rehak P. Explicit polarization: a quantum mechanical framework for developing next generation force fields. Accounts of Chemical Research. 47: 2837-45. PMID 25098651 DOI: 10.1021/ar5002186  0.64
2014 Mazack MJ, Gao J. Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization. The Journal of Chemical Physics. 140: 204501. PMID 24880295 DOI: 10.1063/1.4875922  1
2014 Cembran A, Kim J, Gao J, Veglia G. NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding. Physical Chemistry Chemical Physics : Pccp. 16: 6508-18. PMID 24604024 DOI: 10.1039/c4cp00110a  1
2013 Han J, Mazack MJ, Zhang P, Truhlar DG, Gao J. Quantum mechanical force field for water with explicit electronic polarization. The Journal of Chemical Physics. 139: 054503. PMID 23927266 DOI: 10.1063/1.4816280  1
2013 Yu T, Higashi M, Cembran A, Gao J, Truhlar DG. Concerted hydrogen atom and electron transfer mechanism for catalysis by lysine-specific demethylase. The Journal of Physical Chemistry. B. 117: 8422-9. PMID 23725223 DOI: 10.1021/jp404292t  1
2013 Isegawa M, Fiedler L, Leverentz HR, Wang Y, Nachimuthu S, Gao J, Truhlar DG. Polarized Molecular Orbital Model Chemistry 3. The PMO Method Extended to Organic Chemistry. Journal of Chemical Theory and Computation. 9: 33-45. PMID 23704835 DOI: 10.1021/ct300509d  1
2013 Chan WL, Berkelbach TC, Provorse MR, Monahan NR, Tritsch JR, Hybertsen MS, Reichman DR, Gao J, Zhu XY. The quantum coherent mechanism for singlet fission: experiment and theory. Accounts of Chemical Research. 46: 1321-9. PMID 23581494 DOI: 10.1021/ar300286s  1
2013 Fan Y, Cembran A, Ma S, Gao J. Connecting protein conformational dynamics with catalytic function as illustrated in dihydrofolate reductase. Biochemistry. 52: 2036-49. PMID 23297871 DOI: 10.1021/bi301559q  0.92
2012 Zhang P, Fiedler L, Leverentz HR, Truhlar DG, Gao J. Erratum: Polarized Molecular Orbital Chemistry. 2. The PMO Method. Journal of Chemical Theory and Computation. 8: 2983. PMID 26592135 DOI: 10.1021/ct3005134  1
2012 Nachimuthu S, Gao J, Truhlar DG. A Benchmark Test Suite for Proton Transfer Energies and its Use to Test Electronic Structure Model Chemistries. Chemical Physics. 400: 8-12. PMID 23230346 DOI: 10.1016/j.chemphys.2012.01.014  1
2012 Cembran A, Provorse MR, Wang C, Wu W, Gao J. The Third Dimension of a More O'Ferrall-Jencks Diagram for Hydrogen Atom Transfer in the Isoelectronic Hydrogen Exchange Reactions of (PhX)(2)H(•) with X = O, NH, and CH(2). Journal of Chemical Theory and Computation. 8: 4347-4358. PMID 23226989 DOI: 10.1021/ct3004595  0.76
2012 Cembran A, Masterson LR, McClendon CL, Taylor SS, Gao J, Veglia G. Conformational equilibrium of N-myristoylated cAMP-dependent protein kinase A by molecular dynamics simulations. Biochemistry. 51: 10186-96. PMID 23205665 DOI: 10.1021/bi301279f  1
2012 Valley CC, Cembran A, Perlmutter JD, Lewis AK, Labello NP, Gao J, Sachs JN. The methionine-aromatic motif plays a unique role in stabilizing protein structure. The Journal of Biological Chemistry. 287: 34979-91. PMID 22859300 DOI: 10.1074/jbc.M112.374504  1
2012 Han J, Truhlar DG, Gao J. Optimization of the explicit polarization (X-Pol) potential using a hybrid density functional. Theoretical Chemistry Accounts. 131: 1161. PMID 22707915 DOI: 10.1007/s00214-012-1161-7  1
2012 Zhang P, Truhlar DG, Gao J. Fragment-based quantum mechanical methods for periodic systems with Ewald summation and mean image charge convention for long-range electrostatic interactions. Physical Chemistry Chemical Physics : Pccp. 14: 7821-9. PMID 22552612 DOI: 10.1039/c2cp23758j  1
2012 Wang Y, Sosa CP, Cembran A, Truhlar DG, Gao J. Multilevel X-Pol: a fragment-based method with mixed quantum mechanical representations of different fragments. The Journal of Physical Chemistry. B. 116: 6781-8. PMID 22428657 DOI: 10.1021/jp212399g  1
2012 Gao J, Wang Y. Communication: variational many-body expansion: accounting for exchange repulsion, charge delocalization, and dispersion in the fragment-based explicit polarization method. The Journal of Chemical Physics. 136: 071101. PMID 22360228 DOI: 10.1063/1.3688232  1
2011 Leverentz HR, Gao J, Truhlar DG. Using multipole point charge distributions to provide the electrostatic potential in the variational explicit polarization (X-Pol) potential. Theoretical Chemistry Accounts. 129: 3-13. PMID 23493545 DOI: 10.1007/s00214-011-0889-9  1
2011 Zhang P, Fiedler L, Leverentz HR, Truhlar DG, Gao J. Polarized Molecular Orbital Model Chemistry. II. The PMO Method. Journal of Chemical Theory and Computation. 7: 857-867. PMID 23378824 DOI: 10.1021/ct100638g  1
2011 Fiedler L, Gao J, Truhlar DG. Polarized Molecular Orbital Model Chemistry. I. Ab Initio Foundations. Journal of Chemical Theory and Computation. 7: 852-856. PMID 23236264 DOI: 10.1021/ct1006373  1
2011 Isegawa M, Gao J, Truhlar DG. Incorporation of charge transfer into the explicit polarization fragment method by grand canonical density functional theory. The Journal of Chemical Physics. 135: 084107. PMID 21895159 DOI: 10.1063/1.3624890  1
2011 Perlmutter JD, Drasler WJ, Xie W, Gao J, Popot JL, Sachs JN. All-atom and coarse-grained molecular dynamics simulations of a membrane protein stabilizing polymer. Langmuir : the Acs Journal of Surfaces and Colloids. 27: 10523-37. PMID 21806035 DOI: 10.1021/la202103v  1
2011 Lin YL, Gao J, Rubinstein A, Major DT. Molecular dynamics simulations of the intramolecular proton transfer and carbanion stabilization in the pyridoxal 5'-phosphate dependent enzymes L-dopa decarboxylase and alanine racemase. Biochimica Et Biophysica Acta. 1814: 1438-46. PMID 21600315 DOI: 10.1016/j.bbapap.2011.05.002  1
2011 Wong KY, Gao J. Insight into the phosphodiesterase mechanism from combined QM/MM free energy simulations. The Febs Journal. 278: 2579-95. PMID 21595828 DOI: 10.1111/j.1742-4658.2011.08187.x  1
2011 Grimes S, Ma S, Gao J, Atz R, Jardine PJ. Role of φ29 connector channel loops in late-stage DNA packaging. Journal of Molecular Biology. 410: 50-9. PMID 21570409 DOI: 10.1016/j.jmb.2011.04.070  0.92
2011 Zhang P, Bao P, Gao J. Dipole preserving and polarization consistent charges. Journal of Computational Chemistry. 32: 2127-39. PMID 21541954 DOI: 10.1002/jcc.21795  0.92
2011 Masterson LR, Shi L, Metcalfe E, Gao J, Taylor SS, Veglia G. Dynamically committed, uncommitted, and quenched states encoded in protein kinase A revealed by NMR spectroscopy. Proceedings of the National Academy of Sciences of the United States of America. 108: 6969-74. PMID 21471451 DOI: 10.1073/pnas.1102701108  1
2011 Fleisher AJ, Young JW, Pratt DW, Cembran A, Gao J. Flickering dipoles in the gas phase: structures, internal dynamics, and dipole moments of β-naphthol-H2O in its ground and excited electronic states. The Journal of Chemical Physics. 134: 114304. PMID 21428616 DOI: 10.1063/1.3562373  1
2011 Mo Y, Bao P, Gao J. Energy decomposition analysis based on a block-localized wavefunction and multistate density functional theory. Physical Chemistry Chemical Physics : Pccp. 13: 6760-75. PMID 21369567 DOI: 10.1039/c0cp02206c  0.76
2011 Lin YL, Gao J. Kinetic isotope effects of L-Dopa decarboxylase. Journal of the American Chemical Society. 133: 4398-403. PMID 21366322 DOI: 10.1021/ja108209w  1
2011 Shi L, Traaseth NJ, Verardi R, Gustavsson M, Gao J, Veglia G. Paramagnetic-based NMR restraints lift residual dipolar coupling degeneracy in multidomain detergent-solubilized membrane proteins. Journal of the American Chemical Society. 133: 2232-41. PMID 21287984 DOI: 10.1021/ja109080t  1
2011 Rajamani R, Lin YL, Gao J. The opsin shift and mechanism of spectral tuning in rhodopsin. Journal of Computational Chemistry. 32: 854-65. PMID 20941732 DOI: 10.1002/jcc.21663  1
2010 Gao J, Cembran A, Mo Y. Generalized X-Pol Theory and Charge Delocalization States. Journal of Chemical Theory and Computation. 6: 2402-10. PMID 26613495 DOI: 10.1021/ct100292g  0.76
2010 Mazack MJ, Cembran A, Gao J. Internal Dynamics of a Coarse-Grained Protein Using Analytical Harmonic Representation. Journal of Chemical Theory and Computation. 6: 3601-3612. PMID 21243085 DOI: 10.1021/ct100426m  1
2010 Cembran A, Bao P, Wang Y, Song L, Truhlar DG, Gao J. On the Interfragment Exchange in the X-Pol Method. Journal of Chemical Theory and Computation. 6: 2469-2476. PMID 20730021 DOI: 10.1021/ct100268p  1
2010 Cembran A, Payaka A, Lin YL, Xie W, Mo Y, Song L, Gao J. A Non-Orthogonal Block-Localized Effective Hamiltonian Approach for Chemical and Enzymatic Reactions. Journal of Chemical Theory and Computation. 6: 2242-2251. PMID 20694172 DOI: 10.1021/ct1001686  1
2010 Liu Y, Zhao C, Li H, Yu M, Gao J, Wang L, Zhai Y. Cytotoxicity and apoptosis induced by a new podophyllotoxin glucoside in human hepatoma (HepG2) cells. Canadian Journal of Physiology and Pharmacology. 88: 472-9. PMID 20555416 DOI: 10.1139/y10-008  0.8
2010 Lin YL, Gao J. Internal proton transfer in the external pyridoxal 5'-phosphate Schiff base in dopa decarboxylase. Biochemistry. 49: 84-94. PMID 19938875 DOI: 10.1021/bi901790e  1
2009 Valero R, Song L, Gao J, Truhlar DG. Perspective on Diabatic Models of Chemical Reactivity as Illustrated by the Gas-Phase SN2 Reaction of Acetate Ion with 1,2-Dichloroethane. Journal of Chemical Theory and Computation. 5: 2191. PMID 26613158 DOI: 10.1021/ct9002459  1
2009 Xie W, Orozco M, Truhlar DG, Gao J. X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water. Journal of Chemical Theory and Computation. 5: 459-467. PMID 20490369 DOI: 10.1021/ct800239q  1
2009 Cembran A, Song L, Mo Y, Gao J. Block-Localized Density Functional Theory (BLDFT), Diabatic Coupling, and Their Use in Valence Bond Theory for Representing Reactive Potential Energy Surfaces. Journal of Chemical Theory and Computation. 5: 2702-2716. PMID 20228960 DOI: 10.1021/ct9002898  0.84
2009 Song L, Mo Y, Gao J. An Effective Hamiltonian Molecular Orbital-Valence Bond (MOVB) Approach for Chemical Reactions Applied to the Nucleophilic Substitution Reaction of Hydrosulfide Ion and Chloromethane. Journal of Chemical Theory and Computation. 5: 174-185. PMID 20047006 DOI: 10.1021/ct800421y  0.84
2009 Valero R, Song L, Gao J, Truhlar DG. Perspective on Diabatic Models of Chemical Reactivity as Illustrated by the Gas-Phase S(N)2 Reaction of Acetate Ion with 1,2-Dichloroethane. Journal of Chemical Theory and Computation. 5: 1-22. PMID 20047005 DOI: 10.1021/ct800318h  1
2009 Major DT, Heroux A, Orville AM, Valley MP, Fitzpatrick PF, Gao J. Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction. Proceedings of the National Academy of Sciences of the United States of America. 106: 20734-9. PMID 19926855 DOI: 10.1073/pnas.0911416106  1
2009 Wong KY, Richard JP, Gao J. Theoretical analysis of kinetic isotope effects on proton transfer reactions between substituted alpha-methoxystyrenes and substituted acetic acids. Journal of the American Chemical Society. 131: 13963-71. PMID 19754046 DOI: 10.1021/ja905081x  0.4
2009 Song L, Han J, Lin YL, Xie W, Gao J. Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory. The Journal of Physical Chemistry. A. 113: 11656-64. PMID 19618944 DOI: 10.1021/jp902710a  1
2009 Shi L, Traaseth NJ, Verardi R, Cembran A, Gao J, Veglia G. A refinement protocol to determine structure, topology, and depth of insertion of membrane proteins using hybrid solution and solid-state NMR restraints. Journal of Biomolecular Nmr. 44: 195-205. PMID 19597943 DOI: 10.1007/s10858-009-9328-9  1
2009 Becucci L, Cembran A, Karim CB, Thomas DD, Guidelli R, Gao J, Veglia G. On the function of pentameric phospholamban: ion channel or storage form? Biophysical Journal. 96: L60-2. PMID 19450461 DOI: 10.1016/j.bpj.2009.03.013  1
2009 Shi L, Cembran A, Gao J, Veglia G. Tilt and azimuthal angles of a transmembrane peptide: a comparison between molecular dynamics calculations and solid-state NMR data of sarcolipin in lipid membranes. Biophysical Journal. 96: 3648-62. PMID 19413970 DOI: 10.1016/j.bpj.2009.02.025  1
2009 Ruiz-Pernía JJ, Garcia-Viloca M, Bhattacharyya S, Gao J, Truhlar DG, Tuñón I. Critical role of substrate conformational change in the proton transfer process catalyzed by 4-oxalocrotonate tautomerase. Journal of the American Chemical Society. 131: 2687-98. PMID 19199636 DOI: 10.1021/ja8087423  1
2009 Wu EL, Wong KY, Zhang X, Han K, Gao J. Determination of the structure form of the fourth ligand of zinc in Acutolysin A using combined quantum mechanical and molecular mechanical simulation. The Journal of Physical Chemistry. B. 113: 2477-85. PMID 19191509 DOI: 10.1021/jp808182y  1
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  1
2008 Wong KY, Gao J. A Systematic Approach for Computing Zero-Point Energy, Quantum Partition Function, and Tunneling Effect Based on Kleinert's Variational Perturbation Theory. Journal of Chemical Theory and Computation. 4: 1409-1422. PMID 19749977 DOI: 10.1021/ct800109s  1
2008 Xie W, Song L, Truhlar DG, Gao J. Incorporation of a QM/MM buffer zone in the variational double self-consistent field method. The Journal of Physical Chemistry. B. 112: 14124-31. PMID 18937511 DOI: 10.1021/jp804512f  1
2008 Song L, Gao J. On the construction of diabatic and adiabatic potential energy surfaces based on ab initio valence bond theory. The Journal of Physical Chemistry. A. 112: 12925-35. PMID 18828577 DOI: 10.1021/jp803050e  0.84
2008 Xie W, Song L, Truhlar DG, Gao J. The variational explicit polarization potential and analytical first derivative of energy: Towards a next generation force field. The Journal of Chemical Physics. 128: 234108. PMID 18570492 DOI: 10.1063/1.2936122  1
2008 Nam K, Gao J, York DM. Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases. Rna (New York, N.Y.). 14: 1501-7. PMID 18566190 DOI: 10.1261/rna.863108  1
2008 Miller DJ, Gao J, Truhlar DG, Young NJ, Gonzalez V, Allemann RK. Stereochemistry of eudesmane cation formation during catalysis by aristolochene synthase from Penicillium roqueforti. Organic & Biomolecular Chemistry. 6: 2346-54. PMID 18563268 DOI: 10.1039/b804198a  1
2008 Nesmelova IV, Sham Y, Gao J, Mayo KH. CXC and CC chemokines form mixed heterodimers: association free energies from molecular dynamics simulations and experimental correlations. The Journal of Biological Chemistry. 283: 24155-66. PMID 18550532 DOI: 10.1074/jbc.M803308200  1
2008 Gao J, Major DT, Fan Y, Lin YL, Ma S, Wong KY. Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymes. Methods in Molecular Biology (Clifton, N.J.). 443: 37-62. PMID 18446281 DOI: 10.1007/978-1-59745-177-2_3  1
2008 Nam K, Gao J, York DM. Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis. Journal of the American Chemical Society. 130: 4680-91. PMID 18345664 DOI: 10.1021/ja0759141  1
2008 Nilsson Lill SO, Gao J, Waldrop GL. Molecular dynamics simulations of biotin carboxylase. The Journal of Physical Chemistry. B. 112: 3149-56. PMID 18271571 DOI: 10.1021/jp076326c  1
2008 Gao J, Wong KY, Major DT. Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water. Journal of Computational Chemistry. 29: 514-22. PMID 17722009 DOI: 10.1002/jcc.20810  1
2007 Nam K, Cui Q, Gao J, York DM. Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions:  H, O, and P Atoms. Journal of Chemical Theory and Computation. 3: 486-504. PMID 26637030 DOI: 10.1021/ct6002466  1
2007 Major DT, Gao J. An Integrated Path Integral and Free-Energy Perturbation-Umbrella Sampling Method for Computing Kinetic Isotope Effects of Chemical Reactions in Solution and in Enzymes. Journal of Chemical Theory and Computation. 3: 949-60. PMID 26627415 DOI: 10.1021/ct600371k  1
2007 Xie W, Gao J. The Design of a Next Generation Force Field: The X-POL Potential. Journal of Chemical Theory and Computation. 3: 1890-1900. PMID 18985172 DOI: 10.1021/ct700167b  0.88
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  1
2007 Wong KY, Gao J. An automated integration-free path-integral method based on Kleinert's variational perturbation theory. The Journal of Chemical Physics. 127: 211103. PMID 18067342 DOI: 10.1063/1.2812648  1
2007 Wong KY, Gao J. The reaction mechanism of paraoxon hydrolysis by phosphotriesterase from combined QM/MM simulations. Biochemistry. 46: 13352-69. PMID 17966992 DOI: 10.1021/bi700460c  1
2007 Ma S, Devi-Kesavan LS, Gao J. Molecular dynamics simulations of the catalytic pathway of a cysteine protease: a combined QM/MM study of human cathepsin K. Journal of the American Chemical Society. 129: 13633-45. PMID 17935329 DOI: 10.1021/ja074222+  1
2007 Allemann RK, Young NJ, Ma S, Truhlar DG, Gao J. Synthetic efficiency in enzyme mechanisms involving carbocations: aristolochene synthase. Journal of the American Chemical Society. 129: 13008-13. PMID 17918834 DOI: 10.1021/ja0722067  1
2007 Bhattacharyya S, Stankovich MT, Truhlar DG, Gao J. Combined quantum mechanical and molecular mechanical simulations of one- and two-electron reduction potentials of flavin cofactor in water, medium-chain acyl-CoA dehydrogenase, and cholesterol oxidase. The Journal of Physical Chemistry. A. 111: 5729-42. PMID 17567113 DOI: 10.1021/jp071526+  1
2007 Atz R, Ma S, Gao J, Anderson DL, Grimes S. Alanine scanning and Fe-BABE probing of the bacteriophage ø29 prohead RNA-connector interaction. Journal of Molecular Biology. 369: 239-48. PMID 17433366 DOI: 10.1016/j.jmb.2007.03.033  1
2007 Mo Y, Gao J. Theoretical analysis of the rotational barrier of ethane. Accounts of Chemical Research. 40: 113-9. PMID 17309192 DOI: 10.1021/ar068073w  1
2006 Major DT, Garcia-Viloca M, Gao J. Path Integral Simulations of Proton Transfer Reactions in Aqueous Solution Using Combined QM/MM Potentials. Journal of Chemical Theory and Computation. 2: 236-45. PMID 26626510 DOI: 10.1021/ct050257t  1
2006 Major DT, Gao J. A combined quantum mechanical and molecular mechanical study of the reaction mechanism and alpha-amino acidity in alanine racemase. Journal of the American Chemical Society. 128: 16345-57. PMID 17165790 DOI: 10.1021/ja066334r  1
2006 Brauer CS, Craddock MB, Kilian J, Grumstrup EM, Orilall MC, Mo Y, Gao J, Leopold KR. Amine-hydrogen halide complexes: experimental electric dipole moments and a theoretical decomposition of dipole moments and binding energies. The Journal of Physical Chemistry. A. 110: 10025-34. PMID 16913676 DOI: 10.1021/jp062101a  1
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  1
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  1
2006 Major DT, Nam K, Gao J. Transition state stabilization and alpha-amino carbon acidity in alanine racemase. Journal of the American Chemical Society. 128: 8114-5. PMID 16787057 DOI: 10.1021/ja062272t  1
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  1
2006 Mo Y, Gao J. Polarization and charge-transfer effects in aqueous solution via ab initio QM/MM simulations. The Journal of Physical Chemistry. B. 110: 2976-80. PMID 16494296 DOI: 10.1021/jp057017u  1
2005 Nam K, Gao J, York DM. An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations. Journal of Chemical Theory and Computation. 1: 2-13. PMID 26641110 DOI: 10.1021/ct049941i  1
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  1
2005 Bhattacharyya S, Ma S, Stankovich MT, Truhlar DG, Gao J. Potential of mean force calculation for the proton and hydride transfer reactions catalyzed by medium-chain acyl-CoA dehydrogenase: effect of mutations on enzyme catalysis. Biochemistry. 44: 16549-62. PMID 16342946 DOI: 10.1021/bi051630m  1
2005 Major DT, York DM, Gao J. Solvent polarization and kinetic isotope effects in nitroethane deprotonation and implications to the nitroalkane oxidase reaction. Journal of the American Chemical Society. 127: 16374-5. PMID 16305206 DOI: 10.1021/ja055881u  1
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  1
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  1
2005 Major DT, Gao J. Implementation of the bisection sampling method in path integral simulations. Journal of Molecular Graphics & Modelling. 24: 121-7. PMID 15936231 DOI: 10.1016/j.jmgm.2005.04.002  1
2005 Zhang Y, Sham YY, Rajamani R, Gao J, Portoghese PS. Homology modeling and molecular dynamics simulations of the mu opioid receptor in a membrane-aqueous system. Chembiochem : a European Journal of Chemical Biology. 6: 853-9. PMID 15776407 DOI: 10.1002/cbic.200400207  1
2004 Hensen C, Hermann JC, Nam K, Ma S, Gao J, Höltje HD. A combined QM/MM approach to protein--ligand interactions: polarization effects of the HIV-1 protease on selected high affinity inhibitors. Journal of Medicinal Chemistry. 47: 6673-80. PMID 15615516 DOI: 10.1021/jm0497343  1
2004 Xu D, Wei Y, Wu J, Dunaway-Mariano D, Guo H, Cui Q, Gao J. QM/MM studies of the enzyme-catalyzed dechlorination of 4-chlorobenzoyl-CoA provide insight into reaction energetics. Journal of the American Chemical Society. 126: 13649-58. PMID 15493922 DOI: 10.1021/ja0460211  1
2004 Garcia-Viloca M, Poulsen TD, Truhlar DG, Gao J. Sensitivity of molecular dynamics simulations to the choice of the X-ray structure used to model an enzymatic reaction. Protein Science : a Publication of the Protein Society. 13: 2341-54. PMID 15322278 DOI: 10.1110/ps.03504104  1
2004 Mo Y, Wu W, Song L, Lin M, Zhang Q, Gao J. The magnitude of hyperconjugation in ethane: a perspective from ab initio valence bond theory. Angewandte Chemie (International Ed. in English). 43: 1986-90. PMID 15065281 DOI: 10.1002/anie.200352931  0.84
2004 Xu D, Guo H, Gao J, Cui Q. A QM/MM study of a nucleophilic aromatic substitution reaction catalyzed by 4-chlorobenzoyl-CoA dehalogenase. Chemical Communications (Cambridge, England). 892-3. PMID 15045116 DOI: 10.1039/b401159g  0.8
2004 Nam K, Prat-Resina X, Garcia-Viloca M, Devi-Kesavan LS, Gao J. Dynamics of an enzymatic substitution reaction in haloalkane dehalogenase. Journal of the American Chemical Society. 126: 1369-76. PMID 14759194 DOI: 10.1021/ja039093l  1
2004 Garcia-Viloca M, Gao J, Karplus M, Truhlar DG. How enzymes work: analysis by modern rate theory and computer simulations. Science (New York, N.Y.). 303: 186-95. PMID 14716003 DOI: 10.1126/science.1088172  1
2003 Garcia-Viloca M, Truhlar DG, Gao J. Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase. Biochemistry. 42: 13558-75. PMID 14622003 DOI: 10.1021/bi034824f  1
2003 Rajamani R, Gao J. Balancing kinetic and thermodynamic control: the mechanism of carbocation cyclization by squalene cyclase. Journal of the American Chemical Society. 125: 12768-81. PMID 14558824 DOI: 10.1021/ja0371799  1
2003 Rajamani R, Naidoo KJ, Gao J. Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution. Journal of Computational Chemistry. 24: 1775-81. PMID 12964196 DOI: 10.1002/jcc.10315  1
2003 Garcia-Viloca M, Truhlar DG, Gao J. Importance of substrate and cofactor polarization in the active site of dihydrofolate reductase. Journal of Molecular Biology. 327: 549-60. PMID 12628257  1
2003 Devi-Kesavan LS, Gao J. Combined QM/MM study of the mechanism and kinetic isotope effect of the nucleophilic substitution reaction in haloalkane dehalogenase. Journal of the American Chemical Society. 125: 1532-40. PMID 12568613 DOI: 10.1021/ja026955u  1
2003 Garcia-Viloca M, Alhambra C, Truhlar DG, Gao J. Hydride transfer catalyzed by xylose isomerase: mechanism and quantum effects. Journal of Computational Chemistry. 24: 177-90. PMID 12497598 DOI: 10.1002/jcc.10154  1
2002 Garcia-Viloca M, Alhambra C, Truhlar DG, Gao J. Quantum dynamics of hydride transfer catalyzed by bimetallic electrophilic catalysis: synchronous motion of Mg(2+) and H(-) in xylose isomerase. Journal of the American Chemical Society. 124: 7268-9. PMID 12071725  1
2002 Truhlar DG, Gao J, Alhambra C, Garcia-Viloca M, Corchado J, Sánchez ML, Villà J. The incorporation of quantum effects in enzyme kinetics modeling. Accounts of Chemical Research. 35: 341-9. PMID 12069618  1
2002 Gao J, Truhlar DG. Quantum mechanical methods for enzyme kinetics. Annual Review of Physical Chemistry. 53: 467-505. PMID 11972016 DOI: 10.1146/annurev.physchem.53.091301.150114  1
2002 Mo Y, Subramanian G, Gao J, Ferguson DM. Cation-pi interactions: an energy decomposition analysis and its implication in delta-opioid receptor-ligand binding. Journal of the American Chemical Society. 124: 4832-7. PMID 11971733 DOI: 10.1021/ja0174433  1
2002 Rajamani R, Gao J. Combined QM/MM study of the opsin shift in bacteriorhodopsin. Journal of Computational Chemistry. 23: 96-105. PMID 11913393 DOI: 10.1002/jcc.1159  1
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