Jiali Gao

发表

The opsin shift and mechanism of spectral tuning in rhodopsin

Ramkumar Rajamani, Yen-Lin Lin, Jiali Gao, 2011, J. Comput. Chem..

Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution

Kevin J. Naidoo, Ramkumar Rajamani, Jiali Gao, 2003, J. Comput. Chem..

Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water

Jiali Gao, Kin-Yiu Wong, Dan Thomas Major, 2008, J. Comput. Chem..

Hydride transfer catalyzed by xylose isomerase: Mechanism and quantum effects

Donald G. Truhlar, Jiali Gao, Mireia Garcia-Viloca, 2003, J. Comput. Chem..

Erratum: Polarized Molecular Orbital Chemistry. 2. The PMO Method.

Peng Zhang, Donald G Truhlar, Jiali Gao, 2012, Journal of chemical theory and computation.

CHARMM: The biomolecular simulation program

Jianpeng Ma, Charles L. Brooks, Themis Lazaridis, 2009, J. Comput. Chem..

Optimization of the Lennard-Jones parameters for a combined ab initio quantum mechanical and molecular mechanical potential using the 3-21G basis set

Jiali Gao, Marek Freindorf, M. Freindorf, 1996, J. Comput. Chem..

A molecular mechanics force field for NAD+ NADH, and the pyrophosphate groups of nucleotides

Alexander D. MacKerell, Jiali Gao, Joseph J. Pavelites, 1997, J. Comput. Chem..

Combined QM/MM study of the opsin shift in bacteriorhodopsin

Ramkumar Rajamani, Jiali Gao, Jiali Gao, 2002, J. Comput. Chem..

Energy components of aqueous solution: Insight from hybrid QM/MM simulations using a polarizable solvent model

Jiali Gao, 1997, J. Comput. Chem..

Ab initio QM/MM simulations with a molecular orbital-valence bond (MOVB) method: application to an SN2 reaction in water

Jiali Gao, Yirong Mo, 2000, J. Comput. Chem..

Internal Dynamics of a Coarse-Grained Protein Using Analytical Harmonic Representation.

Jiali Gao, Alessandro Cembran, Michael J M Mazack, 2010, Journal of chemical theory and computation.

Hydrogen-bonding interactions in the active site of a low molecular weight protein-tyrosine phosphatase

Jiali Gao, Cristóbal Alhambra, 2000, J. Comput. Chem..

Potential of mean force for the isomerization of DMF in aqueous solution: a Monte Carlo QM/MM simulation study

Jiali Gao, Jiali Gao, 1993 .

Homology Modeling and Molecular Dynamics Simulations of the Mu Opioid Receptor in a Membrane–Aqueous System

Jiali Gao, Yan Zhang, Ramkumar Rajamani, 2005, Chembiochem : a European journal of chemical biology.

Monte Carlo simulations of the hydration of ammonium and carboxylate ions

William L. Jorgensen, Jiali Gao, W. L. Jorgensen, 1986 .

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).

Jiali Gao, Alessandro Cembran, Wei Wu, 2012, Journal of chemical theory and computation.

The generalized hybrid orbital method for combined quantum mechanical/molecular mechanical calculations: formulation and tests of the analytical derivatives

Martin J. Field, Jiali Gao, Patricia Amara, 2000 .

Combined QM/MM Simulation Study of the Claisen Rearrangement of Allyl Vinyl Ether in Aqueous Solution

Jiali Gao, Jiali Gao, 1994 .

Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials

Jiali Gao, Jiali Gao, 2007 .

A molecular mechanics force field for NAD+ NADH, and the pyrophosphate groups of nucleotides

Alexander D. MacKerell, Jiali Gao, Joseph J. Pavelites, 1997, J. Comput. Chem..

Monte Carlo Quantum Mechanical-Configuration Interaction and Molecular Mechanics Simulation of Solvent Effects on the n .fwdarw. .pi.* Blue Shift of Acetone

Jiali Gao, 1994 .

The magnitude of hyperconjugation in ethane: a perspective from ab initio valence bond theory.

Jiali Gao, Yirong Mo, Lingchun Song, 2004, Angewandte Chemie.

A hybrid semiempirical quantum mechanical and lattice-sum method for electrostatic interactions in fluid simulations

Jiali Gao, Jiali Gao, C. Alhambra, 1997 .

Potential energy functions for an intramolecular proton transfer reaction in the ground and excited state

Jiali Gao, Alessandro Cembran, Jiali Gao, 2007 .

Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes.

Alexander D. MacKerell, Jiali Gao, Jingzhi Pu, 2007, Journal of chemical theory and computation.

Molecular dynamics simulations of the catalytic pathway of a cysteine protease: a combined QM/MM study of human cathepsin K.

Jiali Gao, Shuhua Ma, Jiali Gao, 2007, Journal of the American Chemical Society.

Computation of Intermolecular Interactions with a Combined Quantum Mechanical and Classical Approach

Jiali Gao, Jiali Gao, 1994 .

A Polarizable Intermolecular Potential Function for Simulation of Liquid Alcohols

Jiali Gao, Lei Shao, Jiali Gao, 1995 .

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.

Donald G Truhlar, Jiali Gao, D. Truhlar, 2007, The journal of physical chemistry. A.

Toward a Molecular Orbital Derived Empirical Potential for Liquid Simulations

Jiali Gao, Jiali Gao, 1997 .

Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions.

Donald G Truhlar, Jiali Gao, Jingzhi Pu, 2006, Chemical reviews.

A priori computation of a solvent-enhanced SN2 reaction profile in water : the Menshutkin reaction

Jiali Gao, Jiali Gao, 1991 .

Solvent effect on the potential surface of the proton transfer in [H3NHNH3]+

Jiali Gao, Jiali Gao, 1993 .

Cis-trans energy difference for the peptide bond in the gas phase and in aqueous solution

William L. Jorgensen, Jiali Gao, W. L. Jorgensen, 1988 .

Conformational equilibrium of N-myristoylated cAMP-dependent protein kinase A by molecular dynamics simulations.

Jiali Gao, Gianluigi Veglia, Christopher L. McClendon, 2012, Biochemistry.

A coupled polarization-matrix inversion and iteration approach for accelerating the dipole convergence in a polarizable potential function.

Jiali Gao, Jingzhi Pu, Wangshen Xie, 2009, The journal of physical chemistry. A.

The variational explicit polarization potential and analytical first derivative of energy: Towards a next generation force field.

Donald G Truhlar, Jiali Gao, Lingchun Song, 2008, The Journal of chemical physics.

Perspective on Diabatic Models of Chemical Reactivity as Illustrated by the Gas-Phase SN2 Reaction of Acetate Ion with 1,2-Dichloroethane.

Rosendo Valero, Donald G Truhlar, Jiali Gao, 2009, Journal of chemical theory and computation.

QM/MM through the 1990s: The First Twenty Years of Method Development and Applications.

Jiali Gao, Martin J Field, M. Field, 2014, Israel journal of chemistry.

A two-dimensional energy surface for a type II SN2 reaction in aqueous solution

Jiali Gao, Jiali Gao, X. Xia, 1993 .

A combined quantum mechanical and molecular mechanical study of the reaction mechanism and alpha-amino acidity in alanine racemase.

Jiali Gao, Dan Thomas Major, Jiali Gao, 2006, Journal of the American Chemical Society.

Explicit Polarization: A Quantum Mechanical Framework for Developing Next Generation Force Fields

Donald G. Truhlar, Jiali Gao, Pavel Rehak, 2014, Accounts of chemical research.

Enhanced receptor binding of SARS-CoV-2 through networks of hydrogen-bonding and hydrophobic interactions

Jiali Gao, Jiali Gao, Yingjie Wang, 2020, Proceedings of the National Academy of Sciences.

Importance of substrate and cofactor polarization in the active site of dihydrofolate reductase.

Donald G Truhlar, Jiali Gao, Mireia Garcia-Viloca, 2003, Journal of molecular biology.

The quantum coherent mechanism for singlet fission: experiment and theory.

Timothy C. Berkelbach, Jiali Gao, David R Reichman, 2013, Accounts of chemical research.

Energy components of aqueous solution: Insight from hybrid QM/MM simulations using a polarizable solvent model

Jiali Gao, Jiali Gao, 1997, J. Comput. Chem..

Hydride transfer reaction catalyzed by hyperthermophilic dihydrofolate reductase is dominated by quantum mechanical tunneling and is promoted by both inter- and intramonomeric correlated motions.

Donald G Truhlar, Jiali Gao, Jingzhi Pu, 2006, Journal of the American Chemical Society.

Polarization and Charge-Transfer Effects in Lewis Acid-Base Complexes

Jiali Gao, Yirong Mo, Y. Mo, 2001 .

Polarization and charge-transfer effects in aqueous solution via ab initio QM/MM simulations.

Jiali Gao, Yirong Mo, Y. Mo, 2006, The journal of physical chemistry. B.

Implementation of the bisection sampling method in path integral simulations.

Jiali Gao, Dan Thomas Major, Jiali Gao, 2005, Journal of molecular graphics & modelling.

Energy decomposition analysis based on a block-localized wavefunction and multistate density functional theory.

Jiali Gao, Yirong Mo, Peng Bao, 2011, Physical chemistry chemical physics : PCCP.

Dynamically committed, uncommitted, and quenched states encoded in protein kinase A revealed by NMR spectroscopy

Jiali Gao, Gianluigi Veglia, Susan S. Taylor, 2011, Proceedings of the National Academy of Sciences.

Ab initio and crystal structure analysis of like-charged ion pairs

Jiali Gao, Georges Wipff, Jiali Gao, 1991 .

Perturbation approach to combined QM/MM simulation of solute-solvent interactions in solution

F. Javier Luque, Modesto Orozco, Jiali Gao, 2003 .

Optimization of the Lennard‐Jones parameters for a combined ab initio quantum mechanical and molecular mechanical potential using the 3‐21G basis set

Jiali Gao, Marek Freindorf, M. Freindorf, 1996 .

Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases.

Darrin M York, Jiali Gao, Kwangho Nam, 2008, RNA.

Importance of Electronic Delocalization on the C−N Bond Rotation in HCX(NH2) (X = O, NH, CH2, S, and Se)

Paul von Ragué Schleyer, Jiali Gao, Yirong Mo, 2003 .

Walden-Inversion-Enforced Transition-State Stabilization in a Protein Tyrosine Phosphatase

Jiali Gao, Jiali Gao, C. Alhambra, 1998 .

X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water.

Donald G Truhlar, Modesto Orozco, Jiali Gao, 2009, Journal of chemical theory and computation.

Hybrid QM/MM Simulations Yield the Ground and Excited State pKa Difference: Phenol in Aqueous Solution

Jiali Gao, Marek Freindorf, Naiqi Li, 1996 .

Generalized X-Pol Theory and Charge Delocalization States.

Jiali Gao, Yirong Mo, Alessandro Cembran, 2010, Journal of chemical theory and computation.

Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals.

Donald G Truhlar, Jiali Gao, Jingzhi Pu, 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.

An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations.

Darrin M York, Jiali Gao, Kwangho Nam, 2005, Journal of chemical theory and computation.

THE POLARIZATION CONTRIBUTION TO THE FREE ENERGY OF HYDRATION

Modesto Orozco, Jiali Gao, Francisco Javier Luque, 1995 .

Solvent Effects on the Bond Length Alternation and Absorption Energy of Conjugated Compounds

Jiali Gao, Jiali Gao, C. Alhambra, 1997 .

HYBRID AB INITIO QM/MM SIMULATION OF N-METHYLACETAMIDE IN AQUEOUS SOLUTION

Jiali Gao, Marek Freindorf, M. Freindorf, 1997 .

Dynamics of an enzymatic substitution reaction in haloalkane dehalogenase.

Jiali Gao, Xavier Prat-Resina, Mireia Garcia-Viloca, 2004, Journal of the American Chemical Society.

Cation−π Interactions: An Energy Decomposition Analysis and Its Implication in δ-Opioid Receptor−Ligand Binding

Jiali Gao, David M. Ferguson, Yirong Mo, 2002 .

Solvent effects on the nπ* transition of pyrimidine in aqueous solution

Jiali Gao, Jiali Gao, Kyoungrim Byun, 1997 .

Quantum mechanical tunneling in methylamine dehydrogenase

Donald G. Truhlar, Jiali Gao, José C. Corchado, 2001 .

Absolute free energy of solvation from Monte Carlo simulations using combined quantum and molecular mechanical potentials

Jiali Gao, Jiali Gao, 1992 .

Solvent effect on the anomeric equilibrium in D-glucose: a free energy simulation analysis

Bruce Tidor, Jiali Gao, Martin Karplus, 1991 .

Incorporation of a QM/MM buffer zone in the variational double self-consistent field method.

Donald G Truhlar, Jiali Gao, Lingchun Song, 2008, The journal of physical chemistry. B.

A molecular-orbital derived polarization potential for liquid water

Jiali Gao, Jiali Gao, 1998 .

Theoretical analysis of the rotational barrier of ethane.

Jiali Gao, Yirong Mo, Y. Mo, 2007, Accounts of chemical research.

Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction

Jiali Gao, Annie Heroux, Jiali Gao, 2009, Proceedings of the National Academy of Sciences.

Balancing kinetic and thermodynamic control: the mechanism of carbocation cyclization by squalene cyclase.

Jiali Gao, Ramkumar Rajamani, Jiali Gao, 2003, Journal of the American Chemical Society.

Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method

Donald G. Truhlar, Jiali Gao, Jingzhi Pu, 2004 .

Simulation of Liquid Amides Using a Polarizable Intermolecular Potential Function

Jiali Gao, Joseph J. Pavelites, Jiali Gao, 1996 .

Hybrid Quantum and Molecular Mechanical Simulations: An Alternative Avenue to Solvent Effects in Organic Chemistry

Jiali Gao, Jiali Gao, 1996 .

Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree-Fock Wave Functions with Molecular Mechanics

Donald G. Truhlar, Jiali Gao, Jingzhi Pu, 2004 .

Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory.

Jiali Gao, Jaebeom Han, Lingchun Song, 2009, The journal of physical chemistry. A.

The Design of a Next Generation Force Field: The X-POL Potential.

Jiali Gao, Jiali Gao, W. Xie, 2007, Journal of chemical theory and computation.

Monte Carlo simulations of alkanes in water: hydration numbers and the hydrophobic effect

William L. Jorgensen, Jiali Gao, C. Ravimohan, 1985 .

Combined QM/MM study of the mechanism and kinetic isotope effect of the nucleophilic substitution reaction in haloalkane dehalogenase.

Jiali Gao, Lakshmi S Devi-Kesavan, 2003, Journal of the American Chemical Society.

Path Integral Simulations of Proton Transfer Reactions in Aqueous Solution Using Combined QM/MM Potentials.

Jiali Gao, Dan Thomas Major, Mireia Garcia-Viloca, 2006, Journal of chemical theory and computation.

Induced dipole moment and atomic charges based on average electrostatic potentials in aqueous solution

F. J. Luque, Modesto Orozco, Jiali Gao, 1993 .

Perspective on Diabatic Models of Chemical Reactivity as Illustrated by the Gas-Phase S(N)2 Reaction of Acetate Ion with 1,2-Dichloroethane.

Rosendo Valero, Donald G Truhlar, Jiali Gao, 2009, Journal of chemical theory and computation.

Combined Quantum Mechanical and Molecular Mechanical Methods

Jiali Gao, M. Thompson, Jiali Gao, 1999 .

Projected Hybrid Orbitals: A General QM/MM Method

Jiali Gao, Jiali Gao, Yingjie Wang, 2014, The journal of physical chemistry. B.

Determination of the structure form of the fourth ligand of zinc in Acutolysin A using combined quantum mechanical and molecular mechanical simulation.

Jiali Gao, Keli Han, Emilia L Wu, 2009, The journal of physical chemistry. B.

AM1/d-CB1: A Semiempirical Model for QM/MM Simulations of Chemical Glycobiology Systems.

Jiali Gao, Kevin J Naidoo, Jiali Gao, 2014, Journal of chemical theory and computation.