Publications

2021

[281]
Minimal-active-space multistate density functional theory for excitation energy involving local and charge transfer states

Zhao, R.; Hettich, C.P.; Chen, X.; Gao, J..  npj Computational Material, 2021, 7, 148

 

DOI
[280]
Variational Energy Decomposition Analysis of Charge-Transfer Interactions between Metals and Ligands in Carbonyl Complexes

Han, J.; Grofe, A.; Gao, J..  Inorg. Chem., 2021, 60, 18, 14060–14071.

DOI
[279]
Dynamic-then-Static Approach for Core Excitations of Open-Shell Molecules

Zhao, R.; Grofe, A.; Wang, Z.; Bao, P.; Chen, X.; Liu, W.; Gao, J..  J. Phys. Chem. Lett., 2021, 12, 31, 7409–7417. 

DOI
[278]
Exact-two-component block-localized wave function: A simple scheme for the automatic computation of relativistic ΔSCF

Grofe, A.; Gao, J.; Li, X..  The Journal of Chemical Physics, 2021, 155, 014103. 

DOI
[277]
Is Disrupted Nucleotide-Substrate Cooperativity a Common Trait for Cushing's Syndrome Driving Mutations of Protein Kinase A?

Walker, C.; Wang, Y.; Olivieri, C.; Subrahmanian, M. V.; Gao, J.; Bernlohr, D. A.; Calebiro, D.; Taylor, S. S.; Veglia, G.. Journal of Molecular Biology, 2021, volume 433, Issue 18,167123. 

DOI
[276]
Activation mechanism of Drosophila cryptochrome through an allosteric switch

Wang, Y.; Veglia, G.; Zhong, D.; Gao, J.. Science Advances, 2021, Vol.7, no. 25, eabg3815

DOI
[275]
Conserved Conformational Hierarchy across Functionally Divergent Glycosyltransferases of the GT-B Structural Superfamily as Determined from Microsecond Molecular Dynamics

Ramirez-Mondragon, C. A.; Nguyen, M. E.; Milicaj, J.; Hassan, B. A.; Tucci, F. J.; Muthyala, R.; Gao, J.; Taylor, E. A.; Sham, Y. Y.. International Journal of Molecular Sciences, 2021,  22(9), 4619.

DOI
[274]
Solvation Induction of Free Energy Barriers of Decarboxylation Reactions in Aqueous Solution from Dual-Level QM/MM Simulations

Zhou, S.; Wang, Y.; Gao, J.. JACS Au, 2021, 1, 233-244

DOI
[273]
Origin of Free Energy Barriers of Decarboxylation and the Reverse Process of CO2 Capture in Dimethylformamide and in Water

Zhou, S.; Nguyen, B. T.; Richard, J. P.; Kluger, R.; Gao, J.. Journal of the American Chemical Society, 2021, 143, 137−141.

DOI
[272]
Block-Localized Excitation for Excimer Complex and Diabatic Coupling

Bao, P.; Hettich, C. P.; Shi, Q.; Gao J.. Journal of Chemical Theory and Computation,  2021, 17, 240−254.

DOI
[271]
Generalization of Block-Localized Wave Function for Constrained Optimization of Excited Determinants

Grofe, A.; Zhao, R.; Wildman, A.; Stetina, T. F.; Li, X.; Bao, P.; Gao, J.. Journal of Chemical Theory and Computation, 2021, 17, 277−289.

DOI

2020

[270]
Exploring the reaction mechanism of HIV reverse transcriptase with a nucleotide substrate

Wang, H.; Huang, N.; Dangerfield, T.; Johnson, K. A.; Gao, J.; Elber, R. Exploring the reaction mechanism of HIV reverse transcriptase with a nucleotide substrate. The Journal of Physical Chemistry B, 2020, 124 (21), 4270-4283.

DOI
[269]
Dynamics and mechanism of light harvesting in UV photoreceptor UVR8

Li, X.; Liu, Z.; Ren, H.; Kundu, M.; Wang, L.; Gao, J.; Zhong, D. Dynamics and mechanism of light harvesting in UV photoreceptor UVR8. Chemical Science, 2020, 11 (46), 12553-12569.

DOI
[268]
Selection of mutant µplasmin for amyloid-β cleavage in vivo

Yang, D.; Zhu, W.; Wang, Y.; Tan, F.; Ma, Z.; Gao, J.; Lin, X. Selection of mutant µplasmin for amyloid-β cleavage in vivo. Scientific reports, 2020, 10 (1), 1-12.

DOI
[267]
A leap in quantum efficiency through light harvesting in photoreceptor UVR8

Li, X.; Ren, H.; K, M.; Liu, Z.; Zhong, F. W.; Wang, L.; Gao, J.; Zhong, D. A leap in quantum efficiency through light harvesting in photoreceptor UVR8. Nature communications, 2020, 11 (1), 1-9.

DOI
[266]
Sunitinibinhibits RNase L by destabilizing its active dimer conformation

Tang, J.; Wang, Y.; Zhou, H.; Ye, Y.; Talukdar, M.; Fu, Z.; Liu, Z.; Li, J.; Neculai, D.; Gao, J.; Huang, H.. Biochemical Journal, 2020. 477 (17): 3387–3399.

DOI
[265]
Coupled electron and proton transfer in the piperidine drug metabolism pathway by the active species of cytochromes P450

Fu, Z.; Yang, L.; Sun, D.; Qu, Z.; Zhao, Y.; Gao, J.; Wang, Y.. Dalton Transactions, 2020, 49, 11099-11107

DOI
[264]
Enhanced receptor binding of SARS-CoV-2 through networks of hydrogen-bonding and hydrophobic interactions

Wang, Y.; Liu, M.; Gao, J.. Proceedings of the National Academy of Sciences, 2020, 117 (25) 13967-13974

DOI
[263]
A self-consistent coulomb bath model using density fitting

Chen, X.; Qu, Z.; Suo, B.; Gao, J.. Journal of Computational Chemistry, 2020, 41, 1698–1708.

DOI
[262]
Fragment Exchange Potential for Realizing Pauli Deformation of Interfragment Interactions

Chen, X.; Gao, J.. Journal of Physical Chemistry Letters, 2020, 11, 4008−4016.

DOI
[261]
Multi-state recognition pathway of the intrinsically disordered protein kinase inhibitor by protein kinase A

Olivieri, C.; Wang, Y.; Li, G. C.; Subrahmanian, M. V.; Kim, J.; Stultz, B. R.; Neibergall, M.; Porcelli, F.; Muretta, J. M.; Thomas, D. D.; Gao, J.; Blumenthal, D. K.; Taylor, S. S.; Veglia, G.. eLife, 2020, 9: e55607.

DOI
[260]
Dynamical and Allosteric regulation of photoprotection of light-harvesting complex II

Li, H.; Wang, Y.; Ye, M.; Li, S.; Li, D.; Ren, H.; Wang, M.; Du, L.; Veglia, G.; Gao, J.; Weng, Y.. Science China Chemistry, 2020, 63, 1121–1133.

DOI
[259]
Intrinsically disordered HAX-1 regulates Ca2+ cycling by interacting with lipid membranes and the phospholamban cytoplasmic region

Larsen, E. K.; Weber, D. K.; Wang, S.; Gopinath, T.; Blackwell, D. J.; Dalton, M. P.; Robia, S. L.; Gao, J.; Veglia, G.. BBA - Biomembranes, 2020, 1862, 183034

DOI

2019

[258]
Molecular-bond breaking induced by interatomic decay processes

Chiang, Y.; Engin, S.; Bao, P.; Otto, F.; Kolorenc, P.; Votavová, P.; Miteva, T.; Gao, J.; Sisourat, N.. Physical Review A, 2019, 100, 052701

DOI
[257]
Multistate density functional theory applied with 3 unpaired electrons in 3 orbitals: The singdoublet and tripdoublet states of the ethylene cation

Yang, L.; Grofe, A.; Reimers, J.; Gao, J.. Chemical Physics Letters, 2019, 736, 136803 (1-5).

DOI
[256]
Cushing’s syndrome driver mutation disrupts proteinkinase A allosteric network, altering both regulationand substrate specificity

Walker, C.; Wang, Y.; Olivieri, C.; Karamafrooz, A.; Casby, J.; Bathon, K.; Calebiro, D.; Gao, J.; Bernlohr, D. A.; Taylor, S. S.; Veglia, G.. Science Advances, 2019, 5, eaaw9298(1-11).

DOI
[255]
Active-site heterogeneity of lactate dehydrogenase

Yin, H.; Li, H.; Grofe, A.; Gao, J.. ACS Catalysis, 2019, 9, 4236-4246.

 

DOI
[254]
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

Yang, L.; Zhang, Q.; Gao, J.; Wang, Y.. Inorganic Chemistry, 2019, 58, 4376-4384

DOI
[253]
Catalytic hydrogen atom transfer from hydrosilanes to vinylarenes for hydrosilylation and polymerization

Asgari, P.; Hua, Y.; Bokka, A.; Thiamsiri, C.; Prasitwatcharakorn, W.; Karedath, A.; Chen, X.; Sardar, S.; Yum, K.; Leem, G.; Pierce, B. S.; Nam, K.; Gao, J.; Jeon, J..   Nature Catalysis, 2019, 2, 163-174.

DOI
[252]
What factors tune the chemical equilibrium between metal-iodosylarene oxidants and high-valent metal-oxo ones?

Yang, L.; Wang, F.; Gao,J.; Wang, Y. Phys. Chem. Chem. Phys., 2019, 21, 1271-1276.

DOI

2018

[251]
Diabatic States at Construction (DAC) through Generalized Singular Value Decomposition

Liu, M.; Chen, X.; Grofe, A. Gao, J.  Journal of Physical Chemistry Letters, 2018, 9, 6038–6046.

DOI
[250]
Dual QM and MM Approach for Computing Equilibrium Isotope Fractionation Factor of Organic Species in Solution

Liu, M.; Youmans K. N.; Gao, J. Molecules, 2018, 23, 2644.

DOI
[249]
Combined Multistate and Kohn-Sham Density Functional Theory Studies of the Elusive Mechanism of N-Dealkylation of N,N-Dimethylanilines Mediated by the Biomimetic Nonheme Oxidant FeIV(O)(N4Py)(ClO4)2

Yang, L.; Chen, X.; Qu, Z.; Gao, J.  Frontiers in Chemistry, 2018, 6, 406.

DOI
[248]
Probing Protein-Protein Interactions Using Asymmetric Labeling and Carbonyl-Carbon Selective Heteronuclear NMR Spectroscopy

Larsen, E.K.; Olivieri, C.; Walker, C.; V.S., M.; Gao, J.; Bernlohr, D.; Tonelli, M.; Markley, J.L.; Veglia, G. Molecules, 2018, 23(8), 1937.

 

DOI
[247]
Inactivation Mechanism of Protein Kinase a Revealed by Markov Model

Wang, Y.; Kim, J.; Olivieri, C.; Gao, J.; Veglia, G. Biophysical Journal, 2018, 114(3), 190a.

DOI
[246]
Comment on “Substrate Folding Modes in Trichodiene Synthase: A Determinant of Chemo- and Stereoselectivity”

Dixit, M.; Weitman, M.; Gao, J.; Major, D.T. ACS Catal., 2018, 8(2), 1371-1375.

DOI
[245]
Conformational Landscape of the PRKACA-DNAJB1 Chimeric Kinase, the Driver for Fibrolamellar Hepatocellular Carcinoma

Tomasini, M.D.; Wang, Y.; Karamafrooz, A.; Li, G.; Beuming, T.; Gao, J.; Taylor, S.S.; Veglia, G.; Simon, S.M. Scientific Reports, 2018, 8, 720.

DOI
[244]
The charge transfer electronic coupling in diabatic perspective: A multi-state density functional theory study

Guo, X.; Qu, Z.; Gao, J. Chem. Phys. Lett., 2018, 691, 91-97.

DOI

2017

[243]
Enhanced vibrational solvatochromism and spectral diffusion by electron rich substituents on small molecule silanes

Olson, C. M.; Grofe, A.; Huber, C. J.; Spector, I. C.; Gao, J.; Massari, A. M. J. Chem. Phys., 2017, 147(12), 124302.

DOI
[242]
Spin-Multiplet Components and Energy Splittings by Multistate Density Functional Theory

Grofe, A.; Chen, X.; Liu, W.; Gao, J.; J. Phys. Chem. Lett., 2017 (just accepted manuscript).

DOI
[241]
Diabatic-At-Construction (DAC) Method for Diabatic and Adiabatic Ground and Excited States Based on Multistate Density Functional Theory

Grofe, A.; Qu, Z.; Truhlar, D.G.; Li, H.; Gao, J. Journal of Chemical Theory and Computation, 2017, 13 (3), 1176-1187

DOI
[240]
The Stories Tryptophans Tell: Exploring Protein Dynamics of Heptosyltransferase I from Escherichia coli

Cote, J.M.; Ramirez-Mondragon, C.A.; Siegel, Z.S.; Czyzyk, D.J.; Gao, J.; Sham, Y.Y.; Mukerji, I.; Taylor, E.A. Biochemistry, 2017, 56 (6), 886-895.

DOI

2016

[239]
Chemical Control in the Battle against Fidelity in Promiscuous Natural Product Biosynthesis: The Case of Trichodiene Synthase

Dixit, M.; Weitman, M.; Gao, J.; Major, D.T. ACS Catalysis, 2016, 7(1), 812-818

DOI
[238]
Perturbation Approach for Computing Infrared Spectra of the Local Mode of Probe Molecules

Xue, R.J.; Grofe, A.; Yin, H.; Qu, Z.; Gao, J.; Li, H. J. Chem. Theory Comput., 2016, 13 (1), 191–201
 

DOI
[237]
Beyond Kohn–Sham Approximation: Hybrid Multistate Wave Function and Density Functional Theory

Gao, J.; Grofe, A.; Ren, H.; Bao, P. J. Phys. Chem. Lett., 2016, 7 (24), 5143–5149

DOI
[236]
Oxidation increases the strength of the methionine-aromatic interaction

Lewis, A. K.; Dunleavy, K.; Senkow, T. L.; Her, C.; Horn, B. T.; Jersett, M.A.; Mahling, R.; McCarthy, M.R.; Perell, G.T.; Valley, C.C.; Karim, C.B.; Gao, J.; Pomerantz, W.C.K.; Thomas, D.D.; Cembran, A.; Hinderliter, A.; Sachs, J. N. Nat. Chem. Biol., 2016, 12(10), 860–866

DOI
[235]
Multistate Density Functional Theory for Effective Diabatic Electronic Coupling

Ren, H.; Provorse, M.R.; Bao, P.; Qu, Z; Gao, J.; J. Phys. Chem. Lett., 2016, 7 (12), 2286–2293

DOI
[234]
Explicit Polarization Theory

Wang, Y.; Mazack, M.J.; Truhlar, D.G.; Gao, J. in Many-Body Effects and Electrostatics in Biomolecules, edited by Cui, Q.; Meuwly, M.; Ren, P. (CRC Press, Boca Raton, FL), 2016, 33-64.

DOI

2015

[233]
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

Sun, W.; Ren, H.; Tao, Y.; Xiao, D.; Qin, X.; Deng, L.; Shao, M.; Gao, J.; Chen, X. J. Phys. Chem. C, 2015, 119 (17), pp 9149–9158

DOI
[232]
Dysfunctional conformational dynamics of protein kinase A induced by a lethal mutant of phospholamban hinder phosphorylation

Kim, J.; Masterson, L.R.; Cembran, A.; Verardi, R.; Shi, L.; Gao, J.; Taylor, S.S.; Veglia, G. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112(12), 3716-3721.

DOI
[231]
A new type of electron relay station in proteins: three-piece S: π∴ S↔ S∴ π: S Resonance Structure

Sun, W.; Shao, M.; Ren, H.; Xiao, D.; Qin, X.; Deng, L.; Chen, X.; Gao, J. J. Phys. Chem. C, 2015, 119 (13), 6998–7005.

DOI
[230]
Oxidation Increases the Strength of the Methionine-Aromatic Interaction

Lewis, A.K.; Cembran, A.; Senkow, T.L.; Mahling, R.; Perell, G.T.; McCarthy, M.R.; Her, C.; Horn, B.T.; Valley, C.C.; Karim, C.B.; Gao, J. Biophysical Journal, 2015, 108(2), 17a.

DOI

2014

[229]
Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution

Desai, B.J.; Goto, Y.; Cembran, A.; Fedorov, A.A.; Almo, S.C.; Gao, J.; Suga, H.; Gerlt, J.A., Proceedings of the National Academy of Sciences, 2014, 111 (42), 15066-15071.

DOI
[228]
Projected Hybrid Orbitals: A General QM/MM Method

Wang, Y.; Gao, J.; J. Phys. Chem. B, 2014, 119 (3), 1213–1224.

DOI
[227]
AM1/d-CB1: A semiempirical model for QM/MM simulations of chemical glycobiology systems

Govender, K.; Gao, J.; Naidoo, K.J. J. Chem. Theory Comput., 2014, 10 (10), 4694–4707.

DOI
[226]
"Multistate density functional theory for simulation of enzymatic reactions"

Gao, J. Abstracts of Papers of the American Chemical Society, 2014, 248.

DOI
[225]
"Development of a quantum mechanical force field: The XP3P model for water and applications"

Gao, J. Abstracts of Papers of the American Chemical Society, 2014, 248.

DOI
[224]
"Explicit polarization: A quantum mechanical framework for developing next generation force fields"

Gao, J.; Truhlar, D.G.; Wang, Y.; Mazack, M.J.; Löffler, P.; Provorse, M.R.; Rehak, P. Accounts of Chemical Research, 2014, 47(9), 2837-2845.

DOI
[223]
"QM/MM through the 1990s: The First Twenty Years of Method Development and Applications"

Liu, M.; Wang, Y.; Chen, Y.; Field, M.J.; Gao, J. Israel Journal of Chemistry, 2014, 54(8‐9),1250-1263.

DOI
[222]
"Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization"

Mazack, M.J.; Gao, J. The Journal of Chemical Physics, 2014, 140(20), 204501.

DOI
[221]
"NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding"

Cembran A, Kim J, Gao J, Veglia G. Physical Chemistry Chemical Physics, 2014, 16(14), 6508-6518.

DOI

2013

[220]
"Quantum mechanical force field for water with explicit electronic polarization"

Han, J.; Mazack, M.J.; Zhang, P.; Truhlar, D.G.; Gao, J. The Journal of Chemical Physics, 2013, 139(5), 054503.

DOI
[219]
"Concerted Hydrogen Atom and Electron Transfer Mechanism for Catalysis by Lysine-Specific Demethylase"

Yu, T.; Higashi, M.; Cembran, A.; Gao, J.; Truhlar, D.G. The Journal of Physical Chemistry B, 2013, 117(28), 8422-8429.

DOI
[218]
"The quantum coherent mechanism for singlet fission: Experiment and theory"

Chan, W.L.; Berkelbach, T.C.; Provorse, M.R.; Monahan, N.R.; Tritsch, J.R.; Hybertsen, M.S.; Reichman, D.R.; Gao, J.; Zhu, X.Y. Accounts of Chemical Research, 2013, 46(6), 1321-1329.

DOI
[217]
"Connecting Protein Conformational Dynamics with Catalytic Function As Illustrated in Dihydrofolate Reductase"

Fan, Y.; Cembran; A., Ma; S.; Gao, J. Biochemistry, 2013, 52(12), 2036–2049

DOI

2012

[216]
"Conformational equilibrium of N-myristoylated cAMP-dependent protein kinase A by molecular dynamics simulations"

Cembran, A.; Masterson, L.R.; McClendon, C.L.; Taylor, S.S.; Gao, J.; Veglia, G. Biochemistry, 2012, 51(51), 10186-10196.

DOI
[215]
"Polarized Molecular Orbital Model Chemistry 3. The PMO Method Extended to Organic Chemistry"

Isegawa, M.; Fiedler, L.; Leverentz, H.R.; Wang, Y.; Nachimuthu, S.; Gao, J.; Truhlar, D.G. Journal of Chemical Theory and Computation, 2012, 9(1), 33-45.

DOI
[214]
"The methionine-aromatic motif plays a unique role in stabilizing protein structure"

Valley, C.C.; Cembran, A.; Perlmutter, J.D.; Lewis, A.K.; Labello, N.P.; Gao, J.; Sachs, J.N. Journal of Biological Chemistry, 2012, 287(42), 34979-34991.

DOI
[213]
"The Third Dimension of a More O’Ferrall–Jencks Diagram for Hydrogen Atom Transfer in the Isoelectronic Hydrogen Exchange Reactions of (PhX)2H• with X=O, NH, and CH2"

Cembran, A.; Provorse, M.R.; Wang, C.; Wu, W.; Gao, J. Journal of Chemical Theory and Computation, 2012, 8(11), 4347-4358.

DOI
[212]
"Variational many-body expansion theory as a practical tool for ab initio molecular dynamics simulations"

Gao, J. Abstracts of Papers of the American Chemical Society, 2012, 244.

DOI
[211]
Erratum:“Polarized Molecular Orbital Chemistry. 2. The PMO Method”.

Zhang, P.; Fiedler, L.; Leverentz, H.R.; Truhlar, D.G.; Gao, J. Journal of Chemical Theory and Computation, 2012, 8(8), 2983.

DOI
[210]
" A benchmark test suite for proton transfer energies and its use to test electronic structure model chemistries"

Nachimuthu, S.; Gao, J.; Truhlar, D.G. Chemical Physics, 2012, 400, 8-12.

DOI
[209]
"General implementation of the X-Pol method"

Wang, Y.; Sosa, C.; Truhlar, D.G.; Gao, J. Abstracts of Papers of the American Chemical Society, 2012, 243.

DOI
[208]
"Multistate density functional theory (MSDFT) with block-localized diabatic configurations"

Gao, J. Abstracts of Papers of the American Chemical Society, 2012, 243.

DOI
[207]
"Multilevel X-Pol: A fragment-based method with mixed quantum mechanical representations of different fragments."

Wang, Y.; Sosa, C.P.; Cembran, A.; Truhlar, D.G.; Gao, J. The Journal of Physical Chemistry B, 2012, 116(23), 6781-6788.

DOI
[206]
"Optimization of the explicit polarization (X-Pol) potential using a hybrid density functional"

Han, J.; Truhlar, D.G.; Gao, J. Theoretical Chemistry Accounts, 2012, 131(3), 1161.

DOI
[205]
"Communication: Variational many-body expansion: Accounting for exchange repulsion, charge delocalization, and dispersion in the fragment-based explicit polarization method"

Gao, J.; Wang, Y. The Journal of Chemical Physics, 2012,136(7), 071101.

DOI
[204]
"JBC Papers in Press. Published on August 1, 2012 as Manuscript M112. 374504"

Valley, C.C.; Cembran, A.; Perlmutter, J.D.; Lewis, A.K.; Labello, N.P.; Gao, J.; Sachs, J.N. JBC Papers in Press, 2012, Manuscript M112. 374504.

DOI
[203]
"Fragment-based quantum mechanical methods for periodic systems with Ewald summation and mean image charge convention for long-range electrostatic interactions"

Zhang, P.; Truhlar, D.G.; Gao, J. Physical Chemistry Chemical Physics, 2012, 14(21), 7821-7829.

DOI

Older Publications

[202]  Gao, J. "Computation of Kinetic Isotope Effects for Enzymatic Reactions," Science China - Chemistry (Special Issue on Year of Chemistry), 2011, 54, 1841-1850.
[201]  Lin, Y.; Gao, J.; Rubinstein, A.; Major, D.T. "Molecular Dynamics Simulations of the Intramolecular Proton Transfer and Carbanion Stabilization in the Pyridoxal 5'-Phosphate Dependent Enzymes L-Dopa Decarboxylase and Alanine Racemase." BBA - Proteins and Proteomics, 2011, 1814, 1438-1446.
[200]  Miho, I.; Gao, J.; Truhlar, D.G. "Incorporation of charge transfer into the explicit polarization fragment method by grand canonical density functional theory," Journal of Chemical Physics, 2011, 135(8), 084107.
[199]  Perlmutter, J.D.; Drasler, W.J.; Xie, W.; Gao, J.; Popot, J.; Sachs, J. "All-atom and coarse-grained molecular dynamics simulations of a membrane protein stabilizing polymer," Langmuir, 2011, 27, 10523-10537.
[198]  Wong, K.; Gao, J. " Insight into Phosphodiesterase Mechanism from Combined QM/MM Molecular Dynamics Simulations." FEBS J., 2011, 278, 2579-2595
[197]  Atz, R.; Ma, S.; Gao, J.; Jardine, P.J.; Grimes, S. "Role of φ29 connector channel loops in late stage DNA packaging," Journal of Molecular Biology, 2011, 410, 50-59.
[196]  Fleisher, A.J.; Young, J.W.; Pratt, D.W.; 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," Journal of Chemical Physics, 2011, 134, 114304. 
[195]  Zheng, P.; Fiedler, L.; Leverentz, H.; Truhlar, D.G.; Gao, J." Polarized Molecular Orbital Theory. II. The PMO Method," Journal of Chemical Theory and Computation, 2011, 857-867. 
[194]  Fiedler, L.; Gao, J.; Truhlar, D.G. "Polarized Molecular Orbital Theory. I. Ab Initio Foundations," Journal of Chemical Theory and Computation, 2011, 7, 852-856. 
[193]  Mo, Y.; Bao, P.; Gao, J. "Energy Decomposition Analysis Based on Block-Localized Wavefunction and Multistate Density Functional Theory," Physical Chemistry Chemical Physics, 2011, 13, 6760-6775.
[192]  Shi, L.; Traaseth, N.J.; Verardi, R.; Gustavsson, M.; Gao, J.; Veglia, G. "Paramagnetism-Based NMR Restraints Lift Residual Dipolar Coupling Degeneracy in Multidomain Detergent-Solubilized Membrane Proteins," Journal of the American Chemical Society, 2011, 113, 2232-2241.
[191]  Masterson, L.R.; Shi, L.; Metcalfe, E.E.; Gao, J.; Taylor, S.S.; Veglia, G. "Intrinsic Dynamics Encodes for Catalytically Committed, Uncommitted, and Quenched States in Protein Kinase A," Proceedings of the National Academy of Sciences, 2011, 108, 6969-6974.
[190]  Zhang, P.; Bao, P.; Gao, J. "Dipole Preserving and Polarization Consistent Charges," Journal of Computational Chemistry, 2011, 32, 2127-2139.
[189]  Lin, Y.; Gao, J. "Kinetic Isotope Effects of L-Dopa Decarboxylase," Journal of the American Chemical Society, 2011, 133, 4398-4403. 
[188]  Rajamani, R.; Lin, Y.; Gao, J. "The Opsin Shift and Mechanism of Spectral Tuning of Rhodopsin," Journal of Computational Chemistry, 2011, 32, 854-865. 
[187]  Leverentz, H.R.; Gao, J.; Truhlar, D.G. "Using Multipole Point Charge Distributions to Provide the Electrostatic Potential in the Variational Explicit Polarization (X-Pol) Potential," Theoretical Chemistry Accounts, 2011, 129, 3-13. 
[186]  Mazack, M.J.M.; Cembran, A.; Gao, J. "Internal Dynamics of an Analytically Coarse-Grained Protein," Journal of Chemical Theory and Computation, 2010, 6, 3601-3612. 
[185]  Cembran, A.; Bao, P.; Wang, Y.; Song, L.; Truhlar, D.G.; Gao, J. "On the Interfragment Exchange in the X-Pol Method." Journal of Chemical Theory and Computation, 2010, 6, 2469-2476. 


[184]  Jiali Gao, Alessandro Cembran and Yirong Mo;"Generalized X-Pol Theory and Charge Delocalization States." Journal of Chemical Theory and Computation, 2010, 6, 2402-2410. 
[183]  Alessandro Cembran, Apirak Payaka, Yen-lin Lin, Wangshen Xie, Yirong Mo, Lingchun Song and Jiali Gao; "A Non-Orthogonal Block-Localized Effective Hamiltonian Approach for Chemical and Enzymatic Reactions," Journal of Chemical Thoery and Computation, 2010, 6, 2242-2251.
[182]  Yen-lin Lin, Jiali Gao,; "Protonation State of the External Pyridoxal 5'-phosphate Schiff Base in Dopa Decarboxylase," Biochemistry, 2010, 49, 84-84.
[181]  Dan T. Major, Annie Heroux, Allen M. Orville, Michael P. Valley, Paul F. Fitzpatrick, Jiali Gao,; "Differential Quantum Tunneling Contributions in Nitroalkane Oxidase Catalyzed and the Uncatalyzed Proton Transfer Reaction," Proceedings of the National Academy of Sciences, 2009, 106, 20736-20739.
[180]  Kin-Yiu Wong, John P. Richard, Jiali Gao,; "Theoretical Analysis of Kinetic Isotope Effects on Proton Transfer Reactions between Substituted _-Methoxystyrenes and Substituted Acetic Acids," Journal of the American Chemical Society, 2009, 131, 13963-13971.
[179]  Alessandro Cembran, Lingchun Song, Yirong Mo, and Jiali Gao,; "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, 2009, 5, 2702-2716.
[178]  Lingchun Song, Jaebeom Han, Yen-lin Lin, Jiali Gao,; "Explicit Polarization (X-Pol) Potential Using ab initio Molecular Orbital Theory and Density Functional Theory," Journal of Physical Chemistry A, 2009, 113, 11656-11664. 
[177]  Tai-Sung Lee, George M. Giambasu, Adam Moser, Kwangho Nam, Carlos Silva-Lopez, Francesca Guerra, Olalla Nieto-Faza, Timothy J. Giese, Jiali Gao and Darrin M. York,; "Unraveling the mechanisms of ribozyme catalysis with multi-scale simulations," in Multi-scale Quantum Models for Biocatalysis, D. M. York and T.-S. Lee eds. 2009, Springer Science+Business Media B. V. pp. 377-408.
[176]  Kin-Yiu Wong, Lingchun Song, Wangshen Xie, Dan T. Major, Yen-lin Lin, Alessandro Cembran, Jiali Gao,; "Quantum Mechanical Methods for Biomolecular Simulations," in Multi-scale Quantum Models for Biocatalysis, D. M. York and T.-S. Lee eds. 2009, Springer Science+Business Media B. V. pp. 79-101. 
[175]  B. B. Brooks, C. L. Brooks III, A. D. MacKerell, Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. D. Wong, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Wang, D. M. York, M. Karplus,; "CHARMM: The Biomolecular Simulation Programm," Journal of Computational Chemistry, 2009, 30, 1545-1614.
[174]  J. Javier Ruiz-Pernia, Mireia Garcia-Viloca, Sudeep Bhattacharyya, Jiali Gao, Donald G. Truhlar, and Inaki Tunon,; "Critical Role of Substrate Conformational Change in the Proton Transfer Process Catalyzed by 4-Oxalocrotonate Tautomerase," Journal of the American Chemical Society, 2009, 131, 2687-2698.
[173]  Emilia L. Wu, Kin-Yiu Wong, Xin Zhang, Keli Ha, Jiali Gao,; "Determination of the Structure Form of the Fourth Ligand of Zinc in Acutolysin A using Combined Quantum Mechanical and Molecular Mechanical Simulation," Journal of Physical Chemistry B, 2009, 113, 2477-2485.
[172]  Lucia Becucci, Alessandro Cembran, Christine B. Karim, David D. Thomas, Rolando Guidelli, Jiali Gao, and Gianluigi Veglia,; "On the Function of Pentameric Phospholamban: Ion Channel or Storage Form?," Biophysical Journal (Letter), 2009, 96, L60-L62.
[171]  Xie, Wangshen; Orozco, Modesto; Truhlar, Donald G.; Gao, Jiali; "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, 2009, 5, 459-467.
[170]  Lingchun Song, Yirong Mo, and Jiali Gao,; "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, 2009, 5, 174-185.
[169]  Wangshen Xie, Jingzhi Pu and Jiali Gao; "A Coupled Polarization-Matrix Inversion and Iteration Approach for Accelerating the Dipole Convergence in a Polarizable Potential Function." Journal of Physical Chemistry A, 2009, 113, 2109-2116.
[168]  Valero, Rosendo; Song, Lingchun; Gao, Jiali; Truhlar, Donald G.; "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, 2009, 5, 1-22. Erratum: 5, 2191.
[167]  Shi, Lei; Cembran, Alessandro; Gao, Jiali; Veglia, Gianluigi; "Tilt and Azymuthal angles of a Transmembrane Peptide: A Comparison of Molecular Dynamics Calculations and Solid-State NMR Data of Sarcolipin in Lipid Membranes." Biophysical Journal, 2009, 96, 3648-3662.
[166]  Gao, Jiali; Wong, Kin-Yiu; Major, Dan T.; Cembran, Alessandro; Song, Lingchun ; Lin, Yen-lin; Fan, Yao; Ma, Shuhua; "Kinetic Isotope Effects from Hybrid Classical and Quantum Path Integral Computations." In Kinetic Isotoped Effects in Enzyme Catalysis, Eds. R. Alleman and M. Scruton, RSC Biomolecular Sciences, 2009, pp 105-131.
[165]  Xie, Wangshen; Song, Lingchun; Truhlar, Donald G.; Gao, Jiali; "Incorporation of a QM/MM Buffer Zone in the Variational Double Self-Consistent Field Method." Journal of Physical Chemistry B, 2008, 112, 14124-14131.
[164]  Song, Lingchun; Gao, Jiali; "On the Construction of Diabatic and Adiabatic Potential Energy Surfaces." Journal of Physical Chemistry A, 2008, 120, 12925-12935. The Sason Shaik Festschrift issue.
[163]  Xie, Wangshen; Song, Lingchun; Truhlar, Donald G.; Gao, Jiali; "The Variational X-POL Potential and Analytical First Derivative of Energy: Towards a Next Generation Force Field." Journal of Chemical Physics, 2008, 128, 234108.
[162]  Wong, Kin-Yiu; Gao, Jiali; "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, 2008, 4, 1409-1422.
[161]  Nam, Kwangho; Gao, Jiali; York, Darrin M.; "Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases." RNA, 2008, 14, 1501-1507.
[160]  Lill, Sten O. Nilsson; Gao, Jiali; Waldrop, Grover L.; "Molecular dynamics simulations of biotin carboxylase." Journal of Physical Chemistry B, 2008, 112, 3149-3156.
[159]  Nam, Kwangho; Gao, Jiali; York, Darrin M.; "New QM/MM models for multiscale simulation of phosphoryl transfer reactions in solution." In Multiscale Simulation Methods for Nanomaterials, Eds. R. B. Ross and S. Mohanty, John Wiley & Sons; Hoboken, New Jersey, 2008, pp. 201-218.
[158]  Nam, Kwangho; Gao, Jiali; York, Darrin M.; "Quantum Mechanical/Molecular Mechanical Simulation Study of the Mechanism of Hairpin Ribozyme Catalysis." Journal of the American Chemical Society, 2008, 130, 4680-4691.
[157]  Gao, Jiali; Major, Dan T.; Fan, Yao; Lin, Yen-Lin; Ma, Shuhua; Wong, Kin-Yiu; "Hybrid Quantum and Classical Methods for Computing Kinetic Isotope Effects of Chemical Reactions in Solution and in Enzymes." in Journal of Computational Chemistry, Andreas Kukol Ed., The Humana Press: Totowa, NJ, 2008, pp. 37-62. (Series: Methods in Molecular Biology, #443)
[156]  Gao, Jiali; Wong, Kin-Yiu; Major, Dan T.; "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, 2007, Volume Date 2008, 29, 514-522.
[155]  Wong, Kin-Yiu; Gao, Jiali.; "An automated integration-free path-integral method based on Kleinert's variational perturbation theory." Journal of Chemical Physics, 2007, 127, 211103/1-211103/4.
[154]  Ma, Shuhua; Devi-Kesavan, Lakshmi S.; Gao, Jiali.; "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, 2007, 129, 13633-13645.
[153]  Xie, Wangshen; Gao, Jiali.; "Design of a Next Generation Force Field: The X-POL Potential." Journal of Chemical Theory and Computation, 2007, 3, 1890-1900.
[152]  Xie, Wangshen; Pu, Jingzhi; MacKerell, Alexander D., Jr.; Gao, Jiali; "Development of a Polarizable Intermolecular Potential Function (PIPF) for Liquid Amides and Alkanes." Journal of Chemical Theory and Computation, 2007, 3, 1878-1889.
[151]  Wong, K. Gao, J.; "The Reaction Mechanism of Paraoxon Hydrolysis by Phosphotriesterase from Combined QM/MM Simulations." Biochemistry, 2007, 46, 13352-13369.
[150]  Gao, J.; Wong, K.-Y.; Major, D. T.; "Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water." Journal Computational Chemistry, 2007, 29, 514-522.
[149]  Allemann, Rudolf K.; Young, Neil J.; Ma, Shuhua; Truhlar, Donald G.; Gao, Jiali; "Synthetic Efficiency in Enzyme Mechanisms Involving Carbocations: Aristolochene Synthase." Journal of the American Chemical Society, 2007, 129, 13008-13013.
[148]  Bhattacharyya, S.; Stankovich, M. T.; Truhlar, D. G.; Gao, J.; "Combined QM/MM simulations of one and two-electron reduction potentials of flavin cofactor in water, medium-chain Acyl-CoA dehydrogenase and cholesterol oxidase." Journal Physical Chemistry A, 2007, 111, 5729-5742.
[147]  Atz, Rockney; Ma, Shuhua; Gao, Jiali; Anderson, Dwight L.; Grimes, Shelley; "Alanine Scanning and Fe-BABE Probing of the ¿29 Prohead RNA-Connector Interactions." Journal Molecular Biology, 2007, 369, 239-248.
[146]  Lin, Y.-L.; Gao, J.; "Solvatochromic Shifts of the n ( _* Transition of Acetone from Steam Vapor to Ambient Aqueous Solution: A Combined Configuration Interaction QM/MM Simulation Study Incorporating Solvent Polarization." Journal Chemical Theory and Computation 2007, 3, 1484-1493.
[145]  Cembran, A.; Gao, J.; "Potential energy functions for an intramolecular proton transfer reaction in the ground and excited state." Theoretical Chemistry Accounts, 2007,118, 211-218. 
[144]  Major, D. T. 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 Chemical Theory and Computation 2007, 3, 949-960.
[143]  Nam, Kwangho; Cui, Qiang; Gao, Jiali; York, Darrin M.; "Specific reaction parameterization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms." Journal Chemical Theory and Computation 2007, 3, 486-504.
[142]  Mo, Y. Gao, J.; "The Origin of the Internal Rotational Barrier of Ethane." Accounts of Chemical Research, 2007, 40, 113-119.
[141]  Naidoo, Kevin; Brady, John; Field, Martin J.; Gao, Jiali; Hann, Michael; Editors.; "Modelling Molecular Structure and Reactivity in Biological Systems." The Royal Society of Chemistry Publishing: Dorchester, Dorset, UK., 2006, 293 pp.
[140]  Major, D. T. 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, 2006, 128, 16345-16357.
[139]  Brauer, C. S.; Craddock, M. B.; Kilian, J.; Grumstrup, E. M.; Orilall, M. C.; Mo, Y.; Gao, J.; Leopold, K. R. .Amine-Hydrogen Halide Complexes: Experimental Electric Dipole Moments and a Theoretical Decomposition of Dipole Moments and Binding Energies.. Journal of Physical Chemistry A  2006,  110,  10025-10034.
[138]  Gao, J.; Ma, S.; Major, D. T.; Nam, K.; Pu, J.; Truhlar, D. G. .Mechanisms and free energies of enzymatic reactions.. Chemical Reviews 2006,  106,  3188-3209.
[137]  Pu, J.; Gao, J.; Truhlar, D. G. .Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions.. Chemical Reviews 2006,  106,  3140-3169.
[136]  Major, D. T.; Nam, K.; Gao, J. "Transition State Stabilization and  a-Amino Carbon Acidity in Alanine Racemase." Journal of the American Chemical Society  2006,  128,  8114-8115.
[135]  Pang, J.; Pu, J.; Gao, J.; Truhlar, D. G.; Allemann, R. K. "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  2006,  128,  8015-8023.
[134]  Major, D. T.; 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, 2006, 2, 236-245.
[133]  Mo, Y.; Gao, J. "Polarization and Charge-Transfer Effects in Aqueous Solution via Ab Initio QM/MM Simulations." Journal of Physical chemistry B, 2006, 110, 2976-2980.
[132]  Cembran, A.; Gao, J. .Excited State Intramolecular Proton Transfer in 1-(trifluoroacytylamino)quinone: A CASPT2/CASSCF Computational Study..Molecular Physics, 2006, 104, 943-955 (special issue in honor of Michael Robb).
[131]  Bhattacharyya, S.; Ma, S.; Stankovich, M. T.; Truhlar, D. G.; Gao, J. .Potential of Mean Force Calculation for the Proton and Hydride Transfer Reactions Catalyzed by Medium Chain Acyl-CoA Dehydrogenase: The Effect of Mutaions on Enzyme Catalysis.. Biochemistry, 2005, 44, 16549-16562.
[130]  Major, D. T.; York, D. M.; Gao, J. .Solvent Polarization and Kinetic Isotope Effects in Nitroethane Deprotonation and Implications to the Nitroalkane Oxidase Reaction.. Journal of the American Chemical Society, 2005, 127, 16374-16375.
[129]  Pu, J.; Ma, S.; Garcia-Viloca, M.; Gao, J.; Truhlar, D. G.; 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, 2005, 127, 14879-14886.
[128]  Major, D. T.; Gao, J. .Implementation of the Bisection Sampling Method in Path Integral Simulations.. Journal of Molecular Graphics and Modeling, 2005, 24, 121-127.
[127]  Pu, J.; Gao, J.; Truhlar, D. G. .Generalized Hybrid Orbital Method for Combined Quantum Mechanical and Molecular Mechanical Calculations Based on Density Functional Theory and Hybrid Density Functional Theory.. ChemPhysChem, 2005, 6, 1853-1865.
[126]  Pu, J.; Ma, S.; Gao, J.; Truhlar, D. G. .Small Temperature Dependence of the Kinetic Isotope Effect for the Hydride Transfer Reaction Catalyzed by Escherichia coli Dihydrofolate Reductase.. Journal of Physical Chemistry B, 2005, 109, 8551-8556 (communication).
[125]  Zhang, Yan; Sham, Yuk Y.; Rajamani, R.; Gao, J.; Portoghese, Philip S. .Mu Opioid Receptor Model in a Membrane-Aqueous System: Homology Modeling and Molecular Dynamic Simulation. ChemBioChem, 2005, 6, 853-859.
[124]  Nam, K.; Gao, J.; York, D. M. .An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations..Journal of Chemical Theory and Computation,  2005, 1, 2-13.
[123]  Xu, Dingguo; Wei, Yanseng; Wu, Jingbo; Dunaway-Mariano, Debra; Guo, Hua; Cui, Qiang; Gao, Jiali "QM/MM Studies of the Enzyme-Catalyzed De-chlorination of  4-Chlorobenzoyl-CoA Provide Insight into Reaction Energetics." Journal of the American Chemical Society, 2004, 126, 13649-13658.
[122]  Truhlar, D. G.; Gao, J.; Garcia-Viloca, M.; Alhambra, C.; Corchado, J.; Sanchez, M. L.; Poulsen, T. D. "Ensemble-averaged variational transition state theory with optimized multidimensional tunneling for enzyme kinetics and other condensed-phase reactions" International Journal of Quantum Chemistry, Quantum Chemistry Symposium, 2004, 100, 1136-1152.
[121]  Zhang, Yan; Sham, Yuk Y.; Rajamani, R.; Gao, J.; Portoghese, Philip S. "Mu Opioid Receptor Model in a Membrane-Aqueous System: Homology Modeling and Molecular Dynamic Simulation" ChemBioChem, 2004, in press.
[120]  Hensen, Christian; Hermann, Johannes C.; Nam, K.; Ma, S.; Gao, J.; Höe, Hans-Dieter "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, 2004, ASAP.
[119]  Garcia-Viloca, Mireia; Poulsen, Tina D.; Truhlar, Donald G.; Gao, Jiali "Sensitivity of Molecular Dynamics Simulations to the Choice of the X-ray Structure Used to Model an Enzymatic Reaction" Protein Science, 2004, 13, 2341-2354.
[118]  Xu, Dingguo; Guo, Hua; Gao, Jiali; Cui, Qiang "A QM/MM Study of a Nucleophilic Aromatic Substitution Reaction  Catalyzed by 4-Chlorobenzoyl-CoA Dehalogenase." Chemical Communication, 2004, 892-893.
[117]  Pu, Jingzhi; Gao, Jiali; Truhlar, Donald G. "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, 2004, 108, 5454-5463.
[116]  Garcia-Viloca, M.; Nam, K.; Alhambra, C.; Gao, J. "Solvent and Protein Effects on the Asymmetric Stretch Frequency of Azide Ligand in the Active Site of Carbonic Anhydrase: a Combined QM/MM  Study" Journal of Physical Chemistry A, 2004, 108, 13501-13512.
[115]  Mo, Y.; Wu, W.; Song, S.; Lin, M.; Zhang, Q.; Gao, J. "The magnitude of hyperconjugation in ethane: A perspective from ab initio valence bond theory" Angewandte Chemie International Edition, 2004, 43, 1986-1990.
[114]  Nam, K.; Prat-Resina, X.; Garcia-Viloca, M.; Devi-Kesavan, L. S.; Gao, J. "Dynamics of an Enzymatic Substitution Reaction in Haloalkane Dehalogenase" Journal of the American Chemical Society, 2004, 126, 1369-1376.
[113]  Gao, J.; Byun, K. L.; Kluger, R. "Catalysis by Protein Conformational Change." Topics in Current Chemistry, 2004, 238, 113-136.
[112]  Pu, J.; Truhlar, D. G.; Gao, J. "The Generalized Hybrid Orbital (GHO) Method for Ab Initio Combined QM/MM Calculations" Journal of Physical Chemistry A, 2004, 108, 632-650.
[111]  Garcia-Viloca, M.; Gao, J. "Generalized Hybrid Orbital for the Treatment of Boundary Atoms in Combined Quantum Mechanical and Molecular Mechanical Calculations using the Semiempirical Parameterized Model 3 Method." Theoretical Chemistry Accounts, 2004, 111, 280-286.
[110]  Garcia-Viloca, M.; Gao, J.; M. Karplus, Truhlar, D. G. "How enzymes work: Analysis by modern reaction rate theory and computer simulations" Science,2004, 303, 186-195.
[109]  Rajamani, R. ; Gao, J. "Balancing kinetic and thermodynamic control: The mechanism of  carbocation cyclization by squalene cyclase." Journal of the American Chemical Society, 2003, 115, 12768-12781.
[108]  Mo, Y.; Schleyer, P. v. R.; Wu, W.; Lin, M.; Zhang, Q..; Gao, J. "Importance of electronic delocalization on the C-N bond rotation in HCX(NH2) (X = O, NH, CH2, S, and Se)." Journal of Physical Chemistry A, 2003, 107, 10011-10018.
[107]  Wierzchowski, S. J.; Kofke, D. A.; Gao, J. "Hydrogen fluoride phase behavior and molecular structure from a combined QM/MM polarizable potential function" Journal of Chemical Physics, 2003, 119, 7365-7371.
[106]  Garcia-Viloca, M.; Truhlar, D. G.; Gao, J. "Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase" Biochemistry, 2003, 42, 13558-13575.
[105]  Gao, J.; Garcia-Viloca, M.; Poulsen, T. D.; Mo, Y. "Solvent Effects, Reaction Coordinates, and Reorganization Energies on Nucleophilic Substitution Reactions in Aqueous Solution" Advances in Physical Organic Chemistry, 2003, 38, 161-181.
[104]  Rajamani, R.; Naidoo, K. J.; Gao, J. "Implementation of an Adaptive Umbrella Sampling Method for the Calculation of Multidimensional Potential of Mean Force for Chemical Reaction in Solution" Journal of Computational Chemistry, 2003, 24, 1775-1781.
[103]  Poulsen, T. D.; Garcia-Viloca, M.; Gao, J.; Truhlar, D. G."Free Energy Surface, Reaction Path, and Kinetic Isotope Effect of Short-Chain Acyl-CoA Dehydrogenase." Journal of Physical Chemistry B, 2003, 107, 9567-9578.
[102]  Garcia-Viloca, M.; Truhlar, D. G.; Gao, J. "Importance of Substrate and Cofactor Polarization in the Active Site of Dihydrofolate Reductase" Journal of Molecular Biology, 2003, 327, 549-560.
[101]  Devi-Kesavan, L. S.; Gao, J. "Semiempirical QM/MM Potential with Simple Valence Bond (SVB) for Enzyme Reactions. Application to the Nucleophilic Addition Reaction in Haloalkane Dehalogenase." Theoretical Chemistry Accounts, 2003, 109, 133-139.
[100]  Gao, J. "Catalysis Involving Enzyme Conformational Change as Illustrated by Orotidine 5'-Monophosphate Decarboxylase." Current Opinion in Structural Biology, 2003, 13, 184-192.
[99]  Cubero, E.; Luque, F. J.; Orozco, M.; Gao, J. "Perturbation Approach to Combined QM/MM Simulaitons of Solute-Solvent Interactions in Solution" Journal of Physical Chemistry B, 2003, 107, 1464-1471.
[98]  Devi-Kesavan, L. S.; 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, 2003, 125, 1532-1540.
[97]  Garcia-Viloca, M.; Alhambra, C.; Truhlar, D. G.; Gao, J. "Hydride Transfer Catalyzed by Xylose Isomerase: Mechanism and Quantum Effects" Journal of Computational Chemistry, 2003, 24, 177-190.
[96]  Garcia-Viloca, M.; Alhambra, C.; Truhlar, D. G.; Gao, J. "Quantum Dynamics of Hydride Transfer Catalyzed by Bimetallic Electrophilic Catalysis: Synchronous Motion of Mg2+ and H- in Xylose Isomerase." Journal of the American Chemical Society, 2002, 124, 7268-7269.
[95]  J. Gao, D. G. Truhlar, "Quantum Mechanical Methods for Enzyme Kinetics.”  Annual Review in Physical Chemistry, 2002, 53, 467-505.
[94]  G. Subramanian,Y. Mo, J. Gao, D. M. Ferguson, "The Nature of Cation-p Interactions in Opioid Receptor-Ligand Binding.”  Journal of the American Chemical Society, 2002, in press.
[93]  D. G. Truhlar, J. Gao, C. Alhambra, M. Garcia-Viloca, J. Corchado, M. L. Sáhez, J. Villàspan>, "The Incorporation of Quantum Effects in Enzyme Kinetics Modeling.”  Accounts of Chemical Research, 2002, ASAP.
[92]  R. Rajamani, J. Gao, "Combined QM/MM Study of the Opsin Shift in Bacteriorhodopsin.”  Journal of Computational Chemistry, Special Issue on Computational Biology, 2002, 23, 96-105.
[91]  Alhambra, C.; Corchado, J.; Sanchez, M. L.; Garcia-Viloca, M.; Gao, J.; Truhlar, D. G., "Canonical Variational Theory for Enzyme Kinetics with the Protein Mean Force and Multidimensional Quantum Mechanical Tunneling Dynamics. Theory and Application to Liver Alcohol Dehydrogenase.”  Journal of Physical Chemistry B, 2001, 105, 11326-11340.
[90]  Alhambra, C.; Sanchez, M. L.; Corchado, J.; Gao, J.; Truhlar, D. G., "Quantum Mechanical Tunneling in Methylamine Dehydrogenase.”  Chemical Physics Letters, 2001, 347, 512-518.
[89]  Garcia-Viloca, M.; Alhambra, C.; Truhlar, D. G.; Gao, J., "Inclusion of Quantum Mechanical Vibrational Energy in Reactive Potentials of Mean Force.” Journal of Chemical Physics, 2001, 114, 9953-9958.
[88]  Y. Mo, J. Gao, "Polarization and Charge-Transfer Effects in Lewis Acid-Base Complexes.” Journal of Physical Chemistry, 2001, 105, 6530-6536.
[87]  Y. Mo, C. Alhambra, J. Gao, "Recent Development and Applications of Combined QM/MM Methods.”  Acta Chimica Sinica, 2000, 58, 1504-1510.
[86]  Y. Mo, J. Gao, "Simulation of Chemical Reactions in Solution Using Ab Initio Molecular Orbital-Valence Bond Model.” Theoretical Methods in Condensed Phase Chemistry, S. Schwartz, Ed., Klumar Academic Publishers: Dordrecht, 2000, pp. 247-268.
[85]  K. Byun, Y. Mo, J. Gao, "New Insight on the Origin of the Unusual Acidity of Meldrum's Acid from ab initio and Combined QM/MM Simulation Study.” Journal of the American Chemical Society, 2001, 123, 3974-3979.
[84]  Y. Mo, J. Gao, "Ab Initio QM/MM Simulations with a Molecular Orbital-Valence Bond (MOVB) Method : Application to an SN2 Reaction in Water.” Journal of Computational Chemistry, 2000, 21, 1458-1469..
[83]  C. Alhambra, J. Gao, "Hydrogen Bonding Interactions in the Active Site of a Low Molecular Weight Protein Tyrosine Phosphatase.” Journal of Computational Chemistry, 2000, 21, 1192-1203.
[82]  C. Alhambra, J. C. Corchado, M. L. Sanchez, J. Gao, D. G. Truhlar, "Quantum Dynamics of Hydride Transfer in Enzyme Catalysis.”  Journal of the American Chemical Society, 2000, 122, 8197-9203.
[81]  Y. Mo, J. Gao, S. D. Peyerimhoff, "Energy Decomposition Analysis of Intermolecular Interactions using a Block-localized Wavefunction Approach.”  Journal of Chemical Physics, 2000, 112, 5530-5538.
[80]  Y. Mo, J. Gao, "An Ab Initio Molecular Orbital-Valence Bond (MOVB) Method for Simulating Chemical Reactions in Solution.” Journal of Physical Chemistry A,  2000, 104, 3012-3020.
[79]  K. Byun, J. Gao, "A Combined QM/MM Study of the Nucleophilic Addition Reaction of Methanethiolate and N-methylacetamide.”  Journal of Molecular Graphics and Modeling, 2000, 18, 50-55.
[78]  A. Amara, M. J. Field, C. Alhambra, J. Gao, "The Generalized Hybrid Orbital (GHO) Method for Combined QM/MM Calculations: Formulation and Tests of the Analytical Derivatives.” Theoretical Chemistry Accounts, 2000, 104, 336-343.
[77]  N. Wu, Y. Mo, J. Gao, E. F. Pai, "Electrostatic Stress in Catalysis: Structure and Mechanism of the Enzyme Orotidine Monophosphate Decarboxylase." Proceedings of the National Academy of Sciences, 2000, 97, 2017-2022.
[76]  J. Gao, "Perspective on "Theoretical Studies of Enzymic Reactions: Dielectric, Electrostatic and Steric Stabilization of the Carbonium Ion in the Reaction of Lysozyme"." Theoretical Chemistry Accounts, 2000, 103, 328-329 (New Century Issue).
[75]  Y. Mo, Y. Zhang, J. Gao, "A Simple Electrostatic Model for Trisilylamine: Theoretical Examinations of the n→σ* Negative Hyperconjugation, pπ→dπ Bonding, and Stereoelectronic Interaction." Journal of the American Chemical Society, 1999, 121, 5737-5742.
[74]  C. Alhambra, J. Gao, J. C. Corchado, J. Villa, D. G. Truhlar, "Quantum Mechanical Dynamical Effects in an Enzyme-Catalyzed Proton Transfer Reaction." Journal of the American Chemical Society, 1999, 121, 2553-2558.
[73]  J. P. Richard, G. Williams, J. Gao, "Experimental and Computational Determination of the Effect of the Cyano Group on Carbon Acidity in Water." Journal of the American Chemical Society, 1999, 121, 715-726.
[72]  L. Shao, H.-A. Yu, J. Gao, "XSOL, a Combined Extended Integral Equation (XRISM) and Quantum Mechanical Solvation Model: Free Energies of Hydration and Applications to Solvent Effects on Organic Equilibria." Journal of Physical Chemistry A, 1998, 102,10366-10373.
[71]  J. Gao, P. Amara, C. Alhambra, M. J. Field, "A Generalized Hybrid Orbital (GHO) Approach for the Treatment of Link-Atoms using Combined QM/MM Potentials." Journal of Physical Chemistry A, 1998, 102, 4714-4721.
[70]  J. Gao, M. A. Thompson, Editors Combined Quantum Mechanical and Molecular Mechanical Methods, ACS Symposium Series 712, American Chemical Society: Washington, D.C., 1998.
[69]  C. Alhambra, K. Byun, J. Gao, "The Geometry of Water in Liquid Water from Hybrid Ab Initio-Monte Carlo and Density Functional-Molecular Dynamics Simulations." In Combined Quantum Mechanical and Molecular Mechanical Methods, J. Gao and M. A. Thompson, Eds., ACS Symposium Series 712, American Chemical Society: Washington, D.C., 1998, pp. 35-49.
[68]  A. D. MacKerell, Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus, "All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins." Journal of Physical Chemistry B, 1998, 102, 3586-3616.
[67]  J. Gao, "Simulation of Liquid Water using a Molecular Orbital-Derived Empirical Potential." Journal of Chemical Physics, 1998, 109, 2346-2354.
[66]  D. Gao, Y-K. Pan, K. Byun, J. Gao, "Theoretical Evidence for a Concerted Mechanism of the Oxirane Cleavage and A-Ring Formation in Oxidosqualene Cyclization." Journal of the American Chemical Society, 1998, 120, 4045-4046.
[65]  C. Alhambra, L. Wu, Z.-Y. Zhang, J. Gao, "Walden-Inversion Enforced Transition State Stabilization in a Protein Tyrosine Phosphatase." Journal of the American Chemical Society, 1998,120, 3858-3866.
[64]  J. Gao, "Theoretical Organic Chemistry." Annual Review B, Royal Chemical Society, 1997, 93, 3-26.
[63]  J. Gao, K. Byun, "Solvent Effects on the n * Transition of Pyrimidine in Aqueous Solution." Theoretical Chemistry Accounts, 1997, 96, 151-156.
[62]  J. Gao, C. Alhambra, "A Hybrid Semiempirical QM and Lattice-Sum Method for Electrostatic Interactions in Fluid Simulations." Journal of Chemical Physics, 1997, 107, 1212-1217.
[61]  J. Gao, M. Freindorf, "Hybrid ab Initio QM/MM simulation of N-Methylacetamide in Aqueous Solution." Journal of Physical Chemistry A, 1997, 101, 3182-3188.
[60]  J. Gao, C. Alhambra, "Solvent Effects on the Bond Length Alternation and Absorption Energy of Conjugated Compounds." Journal of the American Chemical Society, 1997, 119, 2962-2963.
[59]  J. Gao, "Toward a Molecular Orbital Derived Empirical Potential for Liquid Simulations." Journal of Physical Chemistry B, 1997, 101, 657-663.
[58]  J. Gao, "Energy Components of Aqueous Solution: Insight from Hybrid QM/MM Simulations using a Polarizable Solvent Potential." Journal of Computational Chemistry, 1997, 18, 1062-1071.
[57]  J. J. Pavelites, J. Gao, P. A. Bash, A. D. MacKerell, Jr., "A Molecular Mechanics Force Field for Simulations of NAD+, NADH, and Phosphate." Journal of Computational Chemistry, 1997, 18, 221-239.
[56]  J. Gao, N. Li, M. Freindorf, "Hybrid QM/MM Simulations Yield the Ground and Excited State pKa Difference: Phenol in Aqueous Solution." Journal of the American Chemical Society, 1996, 118, 4912-4913.
[55]  J. Gao, "A Theoretical Investigation of the Enol Content of Acetic Acid and Acetate Ion in Aqueous Solution." THEOCHEM, 1996, 370, 203-208.
[54]  M. Field, J. Gao, "Report for the Joint CECAM-NSF Planning Meeting on Hybrid Quantum and Classical Mechanical Methods for the Simulation of Biopolymers in Solution (May 9-11), 1995." International Journal of Quantum Chemistry, 1996, 60, 1093-1096.
[53]  J. Gao, "Hybrid QM/MM Simulations: An Alternative Avenue to Solvent Effects in Organic Chemistry." Accounts of Chemical Research, 1996, 29, 298-305..
[52]  T. R. Furlani, J. Gao, "Importance of Hydrophobic Effects in the Rate Acceleration of Diels-Alder Reactions in Aqueous Solution." Journal of Organic Chemistry, 1996, 61, 5492-5497.
[51]  F. J. Luque, Y. Zhang, C. Alemá M. Bachs, J. Gao, M. Orozco, "Solvent Effects in Chloroform Solution: Parameterization of the MST/SCRF Continuum Model." Journal of Physical Chemistry, 1996, 100, 4269-4276.
[50]  J. Gao, J. J. Pavelites, D. Habibollahzadeh, "Simulations of Liquid Amides using a Polarizable Intermolecular Potential Functions (PIPF)." Journal of Physical Chemical, 1996, 100, 2689-2697.
[49]  M. Freindorf, J. Gao, "Optimization of the Lennard-Jones Parameters for a Combined Ab Initio QM/MM Potential Using the 3-21G Basis Set." Journal of Computational Chemistry, 1996, 17, 386-395.
[48]  J. Gao, D. Habibollahzadeh, L. Shao, "A Polarizable Intermolecular Potential Functions for Simulations of Liquid Alcohols."Journal of Physical Chemical, 1995, 99, 16460-16467.
[47]  A. Sehgal, L. Shao, J. Gao, "Transition Structure and Substituent Effects on the Rate Acceleration of the Claisen Rearrangement." Journal of the American Chemical Society, 1995, 117, 11337-11340.
[46]  J. Gao, T. R. Furlani, "Combined Quantum Mechanical and Molecular Mechanical Monte Carlo Simulations of Solvent Effects in Organic Chemistry." IEEE Computational Science & Engineering, 1995, fall issue, 24. 
[45]  J. Gao, "Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials." In Reviews in Computational Chemistry, Vol. 7, Eds., K. B. Lipkowitz and D. B. Boyd, VCH Publishers, New York, 1995, pp. 119-185.
[44]  M. Orozco, F. J. Luque, D. Habibollahzadeh, J. Gao, "Polarization Contribution to the Free Energy of Hydration." Journal of Chemical Physics, 1995, 102, 6145-6152.
[43]  J. Gao, L. Shao, "Polarization Effects on the Tautomeric Equilibria of 2-, and 4-hydroxypyridine in Aqueous and Organic Solution." Journal of Physical Chemistry, 1994, 98, 13772-13779.
[42]  J. Gao, "An Automated Procedure for Simulating Chemical Reactions in Solution: Application to the Decarboxylation of 3-Carboxybenzisoxazole in Water." Journal of the American Chemical Society, 1995, 117, 8600-8607.
[41]  J. Gao, "Monte Carlo QM-CI/MM Simulation of Solvent Effects on the n * Blue Shifts of Acetone." Journal of the American Chemical Society, 1994, 116, 9324-9328.
[40]  J. Gao, "Simulation of the Na+Cl- Ion Pair in Supercritical Water." Journal of Physical Chemistry, 1994, 98, 6049-6053.
[39]  J. Gao, "Solvent Polarization Effects and the Hydration of Nucleotide Bases." Biophysical Chemistry, 1994, 51, 253-262. (a special issue on solvent effects).
[38]  J. Gao, "A Combined QM/MM Simulation Study of the Claisen Rearrangement of Allyl Vinyl Ether in Aqueous Solution." Journal of the American Chemical Society, 1994, 116, 1563-1564.
[37]  J. Gao, "Origin of the Solvent Effects on the Barrier to Amide Isomerization from Combined QM/MM Simulations." Proceedings of the Indian Academy of Sciences (A Special issue on Theoretical Chemistry), 1994, 106, 507-519.
[36]  J. Gao, X. Xia, "Simulating Solvent Effects on Reactivity and Interactions in Ambient and Supercritical Water." in Structure and Reactivity in Aqueous Solution: Characterization of Chemical and Biological Systems, Eds. Cramer, C. J. and Truhlar, D. G.; ACS Symposium Series #568, Chapter 15, pp. 212-228, 1994.
[35]  J. Gao, "Computation of Intermolecular Interactions with the Combined Quantum Mechanical and Classical Approach." in Modeling the Hydrogen Bond, Ed. Smith, D. A.; ACS Symposium Series #569, Chapter 2, pp. 8-21, 1994.
[34]  J. Gao and X. Xia, "A Two-dimensional Energy Surface for a Type II SN2 Reaction in Aqueous Solution." Journal of the American Chemical Society, 1993, 115, 9667-9675.
[33]  J. Gao, "Solvent Effect on the Potential Surface of the Proton Transfer in [H3N-H-NH3]+." International Journal of Quantum Chemistry: Quantum Chemical Symposium, 1993, 27, 491-499.
[32]  J. Gao, X. Xia and T. F. George, "Importance of Biomolecular Interactions in Developing Empirical Potential Functions for Liquid Ammonia." Journal of Physical Chemistry, 1993, 97, 9241-9247.
[31]  J. Gao, "Supercritical Hydration of Organic Compounds. The Potential of Mean Force for Benzene Dimer in Supercritical Water." Journal of the American Chemical Society, 1993, 115, 6893-6895.
[30]  J. Gao, L. W. Chou and A. Auerbach, "The Nature of Cation- Binding: Interactions between Tetramethylammonium Ion and Benzene in Aqueous Solution." Biophysical Journal, 1993, 65, 43-47.
[29]  D. A. Jelski, J. R. Bowser, X. Xia, J. Gao and T. F. George, "Structures and Relative Stabilities of Silicon-Containing Buckminsterfullerenes: An AM1 Computational Study." Journal of Cluster Science, 1993, 4, 173-183.
[28]  J. Gao, F. J. Luque and M. Orozco, "Induced Dipole Moment and Atomic Charges Based on Average Electrostatic Potentials in Aqueous Solution." Journal of Chemical Physics, 1993, 98, 2975-2982.
[27]  J. Gao, "Potential of Mean Force for the Isomerization of DMF in Aqueous Solution: A Monte Carlo QM/MM Simulation Study." Journal of the American Chemical Society, 1993, 115, 2930-2935.
[26]  J. Gao and X. Xia, "A Priori Evaluation of Aqueous Polarization Effects Through Monte Carlo QM/MM Simulations." Science, 1992, 258, 631-635.
[25]  J. Gao, "Comparison of the Hybrid AM1/TIP3P and the OPLS Functions through Monte Carlo Simulations of Acetic Acid in Water." Journal of Physical Chemistry, 1992, 96, 6432-6439.
[24]  J. Gao and J. J. Pavelites, "Aqueous Basicity of the Carboxylate Lone Pairs and the C-O Barrier in Acetic Acid: A Combined Quantum and Statistical Mechanical Study." Journal of the American Chemical Society, 1992, 114, 1912-1914.
[23]  J. Gao, "Absolute Free Energy of Solvation from Monte Carlo Simulations using Combined Quantum and Molecular Mechanical Potentials." Journal of Physical Chemistry, 1992, 96, 537-540.
[22]  J. Gao, "Polarization Contributions to Solute/Solvent Interactions: Partial Atomic Charges and Induced Dipole Moments." in Proceedings of the 2nd Conference on Solute/Solvent Interactions, G. R. Famini Ed., CRDEC, Aberdeen Proving Ground, MD. May 1992.
[21]  J. Gao, "A Priori Computation of a Solvent-Enhanced SN2 Reaction Profile in Water: the Menshutkin Reaction." Journal of the American Chemical Society,1991, 113, 7796-7797.
[20]  J. Gao, S. Boudon and G. Wipff, Ab Initio and Crystal Structural Analysis of Like-Charged Ion Pairs." Journal of the American Chemical Society, 1991, 113, 9610-9614.
[19]  S. Ha, J. Gao, B. Tidor, J. W. Brady and M. Karplus, "Solvent Effect on the Anomeric Equilibrium in D-glucose: A Free Energy Simulation Analysis." Journal of the American Chemical Society, 1991, 113, 1553-1557.
[18]  J. Gao and W. L. Jorgensen, Condensation and Commentary on "Enzyme-catalyzed entioconvergent lactonization of -hydroxy diesters in organic solvent" by Gutman ang Bravdo, J. Org. Chem. 1989, 54, 6864. ChemTracks-Organic Chemistry, 1990, 3, 244-246.
[17]  K. Kuzcera, J. Gao, B. Tidor and M. Karplus, "Free Energy of Sickling: A Simulation Analysis." Proceedings of the National Academy of Sciences, 1990, 87, 8481-8485.
[16]  J. Gao and M. Karplus, "Theoretical Investigation of the AlC2H4 Complex." Chemical Physics Letters,1990, 169, 410-415.
[15]  K. S. Ratliff, D. L. DeLaet, J. Gao, P. E. Fanwick and C. P. Kubiak, "Roles of Bridging Ligand -Acidity in Determining the Nature of the Lowest Excited States of Binuclear Complexes of Nickel (0). Ligand-Centered (M2 µ-LCT), Metal-Centered (µ-L M2CT), and Intraligand (IL) Lowest Excited States for the Series of Complexes Ni2 (µ-L)(CNMe)2(PPh2CH2PPh2)2 (L = CNR, CNMe(R)+, NO+)." Inorganic Chemistry, 1990, 29, 4022-4027.
[14]  M. Karplus, R. Elber, J. Gao, K. Kuzcera and B. Tidor, "Simulations of Proteins" In Highlights of Modern Biochemistry, Kotyk, A.; Skoda, J.; Paces, V. and Kostka, V. Eds.; VSP International Science Publishers: Zeist, Czechoslovakia, 1989; pp 3-10.
[13]  M. Karplus, R. Elber, J. Gao, K. Kuzcera and B. Tidor, "Simulations of Proteins" In Cytochrome P-450: Biochem. & Biophys. Proc. 6th Intnl. Conf. Taylor & Francis Inc., Philadelphia, 1989; pp 258-265.
[12]  J. Gao, K. Kuczera, B. Tidor and M. Karplus, "Hidden Thermodynamics of Mutant Proteins: A Molecular Dynamics Analysis" Science, 1989, 244, 1069-1072.
[11]  J. Gao and W. L. Jorgensen, Condensation and Commentary on "Structural Requirements for Catalysis by Chorismate Mutase" by Pawlak, J. L.; Padykula, R. E.; Kronis, J. D.; Aleksejczyk, R. A.; Berchtold, G. A. J. Am. Chem. Soc. 1989, 111, 3374. ChemTracks-Organic Chemistry, 1989, 2, 300-302.
[10]  J. Gao and W. L. Jorgensen, Condensation and Commentary on "Biomimetic Ion Transport: A Functional Model of a Unimolecular Ion Channel" by Carmichael, V. E.; Dutton, P. J.; Flyes, T. M.; James, T. D.; Swan, J. A.; Zojaju, M. J. Am. Chem. Soc. 1989, 111, 767. ChemTracks-Organic Chemistry, 1989, 2, 100-102.
[9]  W. L. Jorgensen, J. K. Buckner and J. Gao, "Modelling Molecular Transformations in Solution." In Chemical Reactivity in Liquids, Moreau, M. and Turq, P. Eds.; Plenum Press; New York, 1988; pp 253-263.
[8]  J. Gao and W. L. Jorgensen, "Theoretical Examination of Hexanol-Water Interfaces." Journal of Physical Chemistry, 1988, 92, 5813-5822.
[7]  F. R. Lemke, D. L. DeLaet, J. Gao and C. P. Kubiak, "Photochemical Activation of CO2. Transient Absorbance Kinetic Studies of the Addition of CO2 to a Metal-to-Bridging Ligand Charge-Transfer State of a Binuclear Ni(O) Complex." Journal of the American Chemical Society, 1988, 110, 6904-6906.
[6]  W. L. Jorgensen and J. Gao, "Cis-Trans Energy Difference for the Peptide Bond in the Gas Phase and in Aqueous Solution." Journal of the American Chemical Society, 1988, 110, 4212-4216.
[5]  W. L. Jorgensen, J. M. Briggs and J. Gao, "A Priori Calculations of pKa's for Organic Compounds in Water. The pKa of Ethane." Journal of the American Chemical Society, 1987, 109, 6857-6858.
[4]  J. Gao, D. S. Garner and W. L. Jorgensen, "Ab Initio Studies of Structures and Binding Energies for Anion-Water Complexes." Journal of the American Chemical Society, 1986, 108, 4784-4790.
[3]  W. L. Jorgensen and J. Gao, "Monte Carlo Simulations of Hydration of Ammonium and Carboxylate Ions." Journal of Physical Chemistry, 1986, 90, 2174-2182.
[2]  W. L. Jorgensen, J. Gao and C. Ravimohan, "Monte Carlo Simulations of Alkanes in Water: Hydration Number and the Hydrophobic Effect." Journal of Physical Chemistry, 1985, 89, 3470-3473.
[1]  J. Gao, "Calculations of Internal Rotational Barriers of Organic Molecules." Huaxue Tongbao, 1983, (12), 19-22. (Ch.)