J. H. Zhang

发表

Calculation of hot spots for protein–protein interaction in p53/PMI‐MDM2/MDMX complexes

Jianing Song, John Z. H. Zhang, Yifei Qi, 2018, J. Comput. Chem..

Analysis of internal short-circuit in a lithium ion cell

P. Ramadass, S. Santhanagopalan, J. H. Zhang, 2009 .

Computational Alanine Scanning with Interaction Entropy for Protein-Ligand Binding Free Energies.

J. H. Zhang, Xiao Liu, Long Peng, 2018, Journal of chemical theory and computation.

Interaction entropy for computational alanine scanning in protein–protein binding

Jianing Song, Zhaoxi Sun, Yuna Yan, 2018 .

Interaction specific binding hotspots in Endonuclease colicin-immunity protein complex from MD simulations

Changge Ji, John Z. H. Zhang, J. H. Zhang, 2013, Science China Chemistry.

Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches.

Tingjun Hou, Peichen Pan, Huiyong Sun, 2018, Physical chemistry chemical physics : PCCP.

End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design.

Junmei Wang, J. H. Zhang, Huiyong Sun, 2019, Chemical reviews.

New Advance in Computational Chemistry: Full Quantum Mechanical ab Initio Computation of Streptavidin-Biotin Interaction Energy.

John Z H Zhang, J. H. Zhang, Yun Xiang, 2003, The journal of physical chemistry. B.

Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy

John Z. H. Zhang, J. H. Zhang, Da W. Zhang, 2003 .

Theoretical method for full ab initio calculation of DNA/RNA-ligand interaction energy.

John Z H Zhang, J. H. Zhang, X. H. Chen, 2004, The Journal of chemical physics.

An efficient linear scaling method for ab initio calculation of electron density of proteins

Yingkai Zhang, John Z. H. Zhang, J. H. Zhang, 2004 .

Quantum mechanical map for protein-ligand binding with application to beta-trypsin/benzamidine complex.

John Z H Zhang, J. H. Zhang, Yun Xiang, 2004, The Journal of chemical physics.

FULL AB INITIO COMPUTATION OF PROTEIN-WATER INTERACTION ENERGIES

John Z. H. Zhang, J. H. Zhang, Da W. Zhang, 2004 .

MFCC-DOWNHILL SIMPLEX METHOD FOR MOLECULAR STRUCTURE OPTIMIZATION

J. H. Zhang, X. Chen, 2004 .

An efficient approach for ab initio energy calculation of biopolymers.

John Z H Zhang, Yingkai Zhang, J. H. Zhang, 2005, The Journal of chemical physics.

Quantum computational analysis for drug resistance of HIV‐1 reverse transcriptase to nevirapine through point mutations

Xiao He, Ye Mei, J. H. Zhang, 2005, Proteins.

A new method for direct calculation of total energy of protein.

Xiao He, John Z H Zhang, J. H. Zhang, 2005, The Journal of chemical physics.

The generalized molecular fractionation with conjugate caps/molecular mechanics method for direct calculation of protein energy.

Xiao He, John Z H Zhang, J. H. Zhang, 2006, The Journal of chemical physics.

Treating hydrogen bonding in ab initio calculation of biopolymers

J. H. Zhang, Keli Han, E. Wu, 2006 .

A new quantum method for electrostatic solvation energy of protein.

Ye Mei, John Z H Zhang, Changge Ji, 2006, The Journal of chemical physics.

Quantum study of HIV-1 protease-bridge water interaction.

J. H. Zhang, Lili Duan, Y. Mei, 2007, The Journal of chemical physics.

QUANTUM CALCULATION OF PROTEIN SOLVATION AND PROTEIN–LIGAND BINDING FREE ENERGY FOR HIV-1 PROTEASE/WATER COMPLEX

Ye Mei, John Z. H. Zhang, J. H. Zhang, 2009 .

Simulation of NMR data reveals that proteins' local structures are stabilized by electronic polarization.

J. H. Zhang, C. Ji, Y. Mei, 2009, Journal of the American Chemical Society.

Electronic polarization is important in stabilizing the native structures of proteins.

John Z H Zhang, J. H. Zhang, C. Ji, 2009, The journal of physical chemistry. B.

NMR scalar coupling constant reveals that intraprotein hydrogen bonds are dynamically stabilized by electronic polarization.

John Z H Zhang, J. H. Zhang, C. Ji, 2009, The journal of physical chemistry. B.

Communications: Electron polarization critically stabilizes the Mg2+ complex in the catalytic core domain of HIV-1 integrase.

Ye Mei, John Z H Zhang, Yunpeng Lu, 2010, The Journal of chemical physics.

Electrostatic polarization makes a substantial contribution to the free energy of avidin-biotin binding.

Ye Mei, John Z H Zhang, J. H. Zhang, 2010, Journal of the American Chemical Society.

Folding of a helix at room temperature is critically aided by electrostatic polarization of intraprotein hydrogen bonds.

Ye Mei, John Z H Zhang, J. H. Zhang, 2010, Journal of the American Chemical Society.

Assessing the performance of popular QM methods for calculation of conformational energies of trialanine

J. H. Zhang, Xiao He, Yongxiu Li, 2016 .

Hybrid QM/MM study of FMO complex with polarized protein-specific charge

J. H. Zhang, Y. Mei, X. Jia, 2015, Scientific Reports.

Coupled two-dimensional main-chain torsional potential for protein dynamics II: performance and validation.

J. H. Zhang, Y. Mei, Yongxiu Li, 2015, The journal of physical chemistry. B.

Correct folding of an α-helix and a β-hairpin using a polarized 2D torsional potential

J. H. Zhang, Y. Mei, Yongxiu Li, 2015, Scientific Reports.

Acidic pH retards the fibrillization of human Islet Amyloid Polypeptide due to electrostatic repulsion of histidines.

J. H. Zhang, Y. Mu, Yang Li, 2013, The Journal of chemical physics.

ℒ2 Solution of the quantum mechanical reactive scattering problem. The threshold energy for D + H2(v = 1) → HD + H

D. Kouri, J. H. Zhang, D. Truhlar, 1986 .

New method for quantum reactive scattering, with applications to the 3-D H+H2 reaction

W. Miller, J. H. Zhang, 1987 .

Quantum reactive scattering via the S‐matrix version of the Kohn variational principle: Differential and integral cross sections for D+H2 →HD+H

W. Miller, J. H. Zhang, 1989 .

Reactant-product decoupling method for state-to-state reactive scattering: A case study for 3D H+H2 exchange reaction (J=0)

Wei Zhu, J. H. Zhang, Tong Peng, 1997 .

Reactant–product decoupling approach to state-to-state dynamics calculation for bimolecular reaction and unimolecular fragmentation

Wei Zhu, J. H. Zhang, Tong Peng, 1998 .

Accurate quantum-mechanical calculation for O(1D)+DCl reaction

J. H. Zhang, Keli Han, Shi Ying Lin, 2000 .

Time-dependent wavepacket study for O(1D)+HCl (v0=0; j0=0) reaction

J. H. Zhang, Keli Han, Shi Ying Lin, 2000 .

Dynamics of molecules and chemical reactions

R. Wyatt, J. H. Zhang, 1996 .

Full‐dimensional time‐dependent treatment for diatom–diatom reactions: The H2+OH reaction

Dong H. Zhang, J. H. Zhang, 1994 .

Erratum: “Generalized semirigid vibrating rotor target model for atom–poly reaction: Inclusion of umbrella mode for H+CH4 reaction” [J. Chem. Phys. 117, 3081 (2002)]

J. H. Zhang, Ming L. Wang, 2002 .

Time-dependent quantum wave packet calculation for nonadiabatic F(2P3/2,2P1/2)+H2 reaction

J. H. Zhang, Keli Han, Ting-xian Xie, 2003 .

Nonadiabatic reactant-product decoupling calculation for the F(2P(1/2)) + H2 reaction.

J. H. Zhang, Keli Han, Ting-xian Xie, 2006, The Journal of chemical physics.

Reactant–product decoupling approach to state-resolved reactive scattering Time-independent wavepacket formulation

D. Hoffman, D. Kouri, J. H. Zhang, 1997 .

Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water

J. H. Zhang, Y. Cong, Yuchen Li, 2019, Front. Chem..

Molecular basis of SMAC-XIAP binding and the effect of electrostatic polarization

J. H. Zhang, C. Ji, Shuaizhen Tian, 2020, Journal of biomolecular structure & dynamics.

Computational approaches to studying methylated H4K20 recognition by DNA repair factor 53BP1.

Yifei Qi, J. H. Zhang, Zhendong Li, 2020, Physical chemistry chemical physics : PCCP.

Developing an effective polarizable bond method for small molecules with application to optimized molecular docking

J. H. Zhang, C. Ji, Guanfu Duan, 2020, RSC advances.

A force consistent method for electrostatic energy calculation in fluctuating charge model.

J. H. Zhang, C. Ji, Guanfu Duan, 2019, The Journal of chemical physics.

Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase.

Xiao He, John Z H Zhang, J. H. Zhang, 2015, The Journal of chemical physics.

Folding of a helix is critically stabilized by polarization of backbone hydrogen bonds: study in explicit water.

Ye Mei, John Z H Zhang, Ya Gao, 2012, The journal of physical chemistry. B.

Folding and thermodynamic studies of Trp-cage based on polarized force field

Ye Mei, John Z. H. Zhang, J. H. Zhang, 2012, Theoretical Chemistry Accounts.

Entropic effect and residue specific entropic contribution to the cooperativity in streptavidin-biotin binding.

J. H. Zhang, Y. Cong, Yuchen Li, 2020, Nanoscale.

Alanine scanning combined with interaction entropy studying the differences of binding mechanism on HIV-1 and HIV-2 proteases with inhibitor

J. H. Zhang, Y. Cong, Lili Duan, 2020, Journal of biomolecular structure & dynamics.

Molecular Mechanism of Selective Binding of NMS-P118 to PARP-1 and PARP-2: A Computational Perspective

Yifei Qi, J. H. Zhang, Mengxin Li, 2020, Frontiers in Molecular Biosciences.

The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction

Huiyong Sun, John Z. H. Zhang, J. H. Zhang, 2018, Structural dynamics.

Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy.

John Z. H. Zhang, J. H. Zhang, Lili Duan, 2016, Journal of the American Chemical Society.

BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: the nonequilibrium stratification.

J. H. Zhang, Zhaoxi Sun, Xiaohui Wang, 2018, Physical chemistry chemical physics : PCCP.

BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation.

J. H. Zhang, Zhao-Xia Sun, X. H. Wang, 2017, Physical chemistry chemical physics : PCCP.

Automated Fragmentation QM/MM Calculation of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model.

Xiao He, John Z H Zhang, Tong Zhu, 2013, Journal of chemical theory and computation.

Residue-specific free energy analysis in ligand bindings to JAK2

J. H. Zhang, Xiao Liu, Long Peng, 2018 .

Theoretical understanding of the thermodynamics and interactions in transcriptional regulator TtgR-ligand binding.

J. H. Zhang, Zhaoxi Sun, Xiaohui Wang, 2019, Physical chemistry chemical physics : PCCP.

Theoretical understanding of the thermodynamics and interactions in transcriptional regulator TtgR-ligand binding.

J. H. Zhang, Zhaoxi Sun, Xiaohui Wang, 2019, Physical chemistry chemical physics : PCCP.

Thermodynamic Insights of Base Flipping in TNA Duplex: Force Fields, Salt Concentrations, and Free Energy Simulation Methods

J. H. Zhang, Zhaoxi Sun, 2020 .

Determination of binding affinities of 3-Hydroxy-3-Methylglutaryl Coenzyme A reductase inhibitors from free energy calculation

J. H. Zhang, Zhaoxi Sun, Xiaohui Wang, 2019, Chemical Physics Letters.

Sulfur-substitution-induced base flipping in the DNA duplex.

J. H. Zhang, Zhaoxi Sun, Xiaohui Wang, 2019, Physical chemistry chemical physics : PCCP.

Supporting Information: Theoretical understanding of the thermodynamics and interactions in transcriptional regulator TtgR-inhibitor binding from free energy simulation

J. H. Zhang, Zhaoxi Sun, Xiaohui Wang, 2019 .

The origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations

J. H. Zhang, Fengjiao Liu, Y. Mei, 2016, Scientific Reports.

Mechanistic Studies of CO2 Cycloaddition Reaction Catalyzed by Amine-Functionalized Ionic Liquids

J. H. Zhang, Jian Chen, F. Xia, 2019, Front. Chem..

Folding of EK peptide and its dependence on salt concentration and pH: A computational study

J. H. Zhang, Dawei Zhang, Lili Duan, 2011 .

Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation of CO in the Heme Distal Pocket of Myoglobin

J. H. Zhang, Xiao He, Xianwei Wang, 2017 .

Dissociation of heme from gaseous myoglobin ions studied by infrared multiphoton dissociation spectroscopy and Fourier-transform ion cyclotron resonance mass spectrometry.

Chau-Chung Han, Huan-Cheng Chang, J. H. Zhang, 2006, The Journal of chemical physics.

Exploring the Reasons for Decrease in Binding Affinity of HIV-2 Against HIV-1 Protease Complex Using Interaction Entropy Under Polarized Force Field

J. H. Zhang, Y. Cong, Yuchen Li, 2018, Front. Chem..

Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations

J. H. Zhang, Lili Duan, T. Zhu, 2017, Scientific Reports.

Accurate quantum calculation for the benchmark reaction H2+OH→H2O +H in five‐dimensional space: Reaction probabilities for J=0

Dong H. Zhang, J. H. Zhang, 1993 .

State‐to‐state time‐dependent quantum calculation for reaction H2+OH→H+H2O in six dimensions

Wei Zhu, Dong H. Zhang, J. H. Zhang, 1996 .

Time-dependent quantum wave packet studies of the F+HCl and F+DCl reactions

Ruiqin Q. Zhang, J. H. Zhang, Keli Han, 2000 .

Stereodynamics studies of the Sr+HF reaction using time-dependent quantum wave packet method

J. H. Zhang, Keli Han, Benhui Yang, 2000 .

Time-Dependent Quantum Dynamics Study of the C + CH Reaction on the 2A` Surface

J. H. Zhang, Keli Han, Mao-du Chen, 2001 .

Crius: A novel fragment‐based algorithm of de novo substrate prediction for enzymes

J. H. Zhang, Bei Gao, D. Wei, 2018, Protein science : a publication of the Protein Society.

Six-dimensional quantum calculations of vibration-rotation-tunneling levels of ν1 and ν2 HCl-stretching excited (HCl)2

J. H. Zhang, Z. Bačić, Yanhui Qiu, 1998 .

Exact full‐dimensional bound state calculations for (HF)2, (DF)2, and HFDF

Dong H. Zhang, J. H. Zhang, Z. Bačić, 1995 .

Quantum dynamics study of the reaction HD+OH --> H+DOH, D+HOH

Dong H. Zhang, J. H. Zhang, Dunyou Wang, 1995 .

Implementing electrostatic polarization cannot fill the gap between experimental and theoretical measurements for the ultrafast fluorescence decay of myoglobin

J. H. Zhang, Y. Mei, Yongxiu Li, 2014, Journal of Molecular Modeling.

Drug-resistance mechanisms of three mutations in anaplastic lymphoma kinase against two inhibitors based on MM/PBSA combined with interaction entropy.

J. H. Zhang, Y. Cong, Susu Zhong, 2019, Physical chemistry chemical physics : PCCP.

Electronic polarization stabilizes tertiary structure prediction of HP-36

J. H. Zhang, Lili Duan, T. Zhu, 2014, Journal of Molecular Modeling.

Protein's native structure is dynamically stabilized by electronic polarization

J. H. Zhang, Lili Duan, Y. Mei, 2014 .

Computational analysis for residue-specific CDK2-inhibitor bindings

J. H. Zhang, Jingxiao Bao, Yunpeng Yang, 2019, Chinese Journal of Chemical Physics.

MFCC‐Based Fragmentation Methods for Biomolecules

J. H. Zhang, Tong Zhu, Xiao He, 2017 .

An algebraic variational approach to dissociative adsorption of a diatomic molecule on a smooth metal surface

J. H. Zhang, J. Sheng, 1992 .

Two-bead polarizable water models combined with a two-bead multipole force field (TMFF) for coarse-grained simulation of proteins.

J. H. Zhang, Min Li, 2017, Physical chemistry chemical physics : PCCP.

NUMERICAL STABILITIES IN FITTING ATOMIC CHARGES TO ELECTRIC FIELD AND ELECTROSTATIC POTENTIAL

Ye Mei, John Z. H. Zhang, J. H. Zhang, 2009 .

QuantumMechanics–Based Polarizable Force Field for Proteins

J. H. Zhang, C. Ji, Y. Mei, 2016 .

Molecular dynamics simulation of protein crystal with polarized protein-specific force field.

J. H. Zhang, Y. Mei, Yongxiu Li, 2014, The journal of physical chemistry. B.

Optimization of Convergence Criteria for Fragmentation Methods

J. H. Zhang, Zhaoxi Sun, T. Zhu, 2017 .

Comparison of quantum and mixed quantum–classical semirigid vibrating rotor target studies for isotopic reactions H(D,T)+CH4→HH(D,T)+CH3

Q. Cui, J. H. Zhang, Xiao He, 2003 .

Mixed quantum-classical semi-rigid vibrating rotor target model for atom-polyatom reaction: O(3P) + CH4 → CH3 + OH

J. H. Zhang, Ming-Liang Wang, 2003 .

Effect and siting of Nafion in a Pt/C proton exchange membrane fuel cell catalyst

J. H. Zhang, J. Goodwin, Kitiya Hongsirikarn, 2011 .

Time‐dependent treatment of vibrational predissociation within the golden rule approximation

Dong H. Zhang, J. H. Zhang, 1991 .

Variational calculation of integral cross sections for the reaction F+H2→HF+H

J. H. Zhang, 1991 .

Quantum dynamics study of H2+CN → HCN+H reaction in full dimensions

Yi Zhang, Wei Zhu, John Z. H. Zhang, 1998 .

Reactant-product decoupling approach to state-to-state reactive scattering H+DH

J. H. Zhang, Yi-ci Zhang, Shao-long Zhang, 2000 .

Quantum Dynamics Study for D2 + OH Reaction

Dong H. Zhang, J. H. Zhang, Dunyou Wang, 1995 .

A method for efficient calculation of thermal stability of proteins upon point mutations.

Yifei Qi, J. H. Zhang, Ya Gao, 2020, Physical chemistry chemical physics : PCCP.

DMD048264 60..71

S. F. Yan, J. H. Zhang, Juan Zeng, 2012 .

An accurate free energy estimator: based on MM/PBSA combined with interaction entropy for protein-ligand binding affinity.

J. H. Zhang, Y. Cong, Susu Zhong, 2020, Nanoscale.

Assessing the accuracy of the general AMBER force field for 2,2,2-trifluoroethanol as solvent

J. H. Zhang, Y. Mei, X. Jia, 2013, Journal of Molecular Modeling.

Computational search for aflatoxin binding proteins

J. H. Zhang, Xiao He, Ying Wang, 2017 .

3D quantum scattering calculations of the reaction He + H+2 → HeH+ + H for total angular momentum J = 0

W. Miller, J. H. Zhang, D. Yeager, 1990 .

Computational Insights into the Binding Mechanism of OxyS sRNA with Chaperone Protein Hfq

Yifei Qi, J. H. Zhang, Mengxin Li, 2021, Biomolecules.

Accurate quantum mechanical calculation for the N+OH reaction

N. Lou, J. H. Zhang, Keli Han, 2003 .

Functional Loop Dynamics of the Streptavidin-Biotin Complex

Jianing Song, J. H. Zhang, C. Ji, 2015, Scientific Reports.

Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes

J. H. Zhang, Tong Zhu, Xiao He, 2018, Front. Chem..

Hydrogen-bond structure dynamics in bulk water: insights from ab initio simulations with coupled cluster theory† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc04205a

J. H. Zhang, Lian‐Wen Qi, Xiao He, 2017, Chemical science.

Computational analysis of hot spots and binding mechanism in the PD-1/PD-L1 interaction

Dading Huang, J. H. Zhang, Xiao Liu, 2019, RSC advances.

An efficient method for computing excess free energy of liquid

Jianing Song, J. H. Zhang, Linqiong Qiu, 2017, Science China Chemistry.

DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet

Yifei Qi, J. H. Zhang, 2020, J. Chem. Inf. Model..

A three-point coarse-grained model of five-water cluster with permanent dipoles and quadrupoles.

J. H. Zhang, Wencai Lu, Min Li, 2020, Physical chemistry chemical physics : PCCP.

Stereodynamics and rovibrational effect for H+CH4(v,j,K,n)→H2+CH3 reaction

J. H. Zhang, Ming-Liang Wang, 2002 .

Atomic-level reconstruction of biomolecules by a rigid-fragment- and local-frame-based (RF-LF) strategy

J. H. Zhang, Wencai Lu, Min Li, 2020, Journal of Molecular Modeling.

Binding Modes of Small-molecule Inhibitors to EED Pocket of PRC2.

Dading Huang, Yifei Qi, J. H. Zhang, 2019, Chemphyschem : a European journal of chemical physics and physical chemistry.

Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.

J. H. Zhang, T. Zhu, Xiao He, 2014, Physical chemistry chemical physics : PCCP.

REACTANT-PRODUCT DECOUPLING FOR STATE-TO-STATE REACTIVE SCATTERING : FURTHER PARTITIONING IN THE PRODUCT ARRANGEMENTS

D. Hoffman, D. Kouri, J. H. Zhang, 1996 .

Origins of Protons in C-H Bond Insertion Products of Phenols: Proton-Self-Sufficient Function via Water Molecules.

J. H. Zhang, Ya Gao, F. Xia, 2017, The journal of physical chemistry. A.

Folding simulation of Trp-cage utilizing a new AMBER compatible force field with coupled main chain torsions

J. H. Zhang, Y. Mei, Yongxiu Li, 2014 .

Progress of basis optimization techniques in variational calculation of quantum reactive scattering

J. H. Zhang, 1991 .

Identification of three new compounds that directly target human serine hydroxymethyltransferase 2

Yifei Qi, J. H. Zhang, Liping He, 2020, Chemical biology & drug design.

Phase transitions and thermotropic phase boundaries in MnO2-doped (K0.5Na0.5)NbO3-0.05LiNbO3 single crystals: Raman scattering evidence at elevated temperatures

J. H. Zhang, K. Jiang, Guangzhi Xu, 2015 .

Time-dependent quantum dynamics study of reactive scattering of the HD+CN system in the potential averaged 5D model

J. H. Zhang, Qinggang Zhang, Yi-ci Zhang, 2000 .

Accurate quantum mechanical reaction probabilities for the reaction O+H2→OH+H

D. Kouri, J. H. Zhang, D. Truhlar, 1987 .

Uniform J-shifting approach for calculating reaction rate constant

Dong H. Zhang, J. H. Zhang, 1999 .

Accurate time-dependent quantum scattering calculation for diatom-diatom reaction with branching: HD + OH → H + DOH, D + HOH

Dong H. Zhang, J. H. Zhang, 1995 .

Accurate quantum calculations for H2+OH→H2O+H: Reaction probabilities, cross sections, and rate constants

Dong H. Zhang, J. H. Zhang, 1994 .

APPLICATION OF REACTANT-PRODUCT DECOUPLING METHOD FOR STATE-TO-STATE CALCULATION OF D + H2 REACTION FOR J = 0 AND 1

J. H. Zhang, J. Dai, 1997 .

Dynamical binding of hydrogen-bond surrogate derived Bak helices to antiapoptotic protein Bcl-xL.

J. H. Zhang, P. Arora, Xiaoyan Dong, 2009, The journal of physical chemistry. B.

Theoretical Investigations of Photoionization Efficiency of Naphthalene

J. H. Zhang, T. Zhu, C. Chin, 2019 .

Thermodynamic Insights of Base Flipping in TNA Duplex: Force Fields, Salt Concentrations, and Free-Energy Simulation Methods

J. H. Zhang, Zhaoxi Sun, 2020, CCS Chemistry.

Mechanistic Investigation of Aromatic C(sp(2))-H and Alkyl C(sp(3))-H Bond Insertion by Gold Carbenes.

J. H. Zhang, F. Xia, Yuan Liu, 2016, The journal of physical chemistry. A.

Discovery and Characterization of Novel , Potent , and Selective Cytochrome P 450 2 J 2 Inhibitors

S. F. Yan, J. H. Zhang, Juan Zeng, 2012 .

A time‐dependent golden rule wave packet calculation for vibrational predissociation of D2HF

Dong H. Zhang, J. H. Zhang, Z. Bačić, 1992 .

Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations

Jianzhong Chen, J. H. Zhang, Laixue Pang, 2019, Nucleic acids research.

Local Linear Least Square Fitting of Potential Energy Surface

J. H. Zhang, Da W. Zhang, Yi M. Li, 2003 .

Ab initio SOFA quantum dynamics for chemical reaction

J. H. Zhang, Tong Peng, Dunyou Wang, 1999 .

Quantum dynamics from ab initio points

J. H. Zhang, C. Yu, Tong Peng, 1999 .

DFT Calculations on the Mechanism of Transition-Metal-Catalyzed Reaction of Diazo Compounds with Phenols: O-H Insertion versus C-H Insertion.

J. H. Zhang, F. Xia, Yuan Liu, 2016, The journal of physical chemistry. A.

SVRT calculation for bond-selective reaction H+HOD→H2+OD, HD+OH

J. H. Zhang, Keli Han, Xin Zhang, 2002 .

Semirigid vibrating rotor target calculation for reaction H+HOD→H2+OD, HD+OH

Dong H. Zhang, J. H. Zhang, Ming-Liang Wang, 2001 .

Quantum wavepacket approach to chemical reaction dynamics. Perspective on “Dynamics of the collinear H + H2 reaction. I. Probability density and flux”

J. H. Zhang, D. H. Zhang, 2000 .

Hybrid many-body-expansion/Shepard-interpolation method for constructing ab initio potential energy surfaces for quantum dynamics calculations

J. H. Zhang, Shi Ying Lin, Pei-Yu Zhang, 2013 .

Comparison of quantum scattering calculations for the H + H2 reaction using the LSTH and DMBE potentials

W. Miller, J. H. Zhang, S. Auerbach, 1990 .

Differential cross section (angular distribution) for the reaction H+H2(v=j=0)→H2(v′, ODD j′)+H in the energy range 0.90-1.35 eV

W. Miller, J. H. Zhang, 1989 .

An implementation of hydrophobic force in implicit solvent molecular dynamics simulation for packed proteins

J. H. Zhang, Lili Duan, T. Zhu, 2013, Journal of Molecular Modeling.

Combined theoretical and experimental study on high diastereoselective chirality transfer based on [2.2]paracyclophane derivative chiral reagent.

J. H. Zhang, D. Xie, B. Jiang, 2012, The Journal of organic chemistry.

ect of Site-Speci fi c Hydrophobicity and Polarization on Hydrogen Bond Energy of Protein Using a Polarizable Method

J. H. Zhang, C. Ji, X. Xiao, 2012 .

Energy and electron transfer in β-alkynyl-linked porphyrin-[60]fullerene dyads

D. Schuster, J. H. Zhang, D. Guldi, 2006 .

Product state distribution in time-dependent quantum wave packet calculation with an optical potential

Omar A. Sharafeddin, Dong H. Zhang, J. H. Zhang, 1992 .

Inverse perturbation via singular value decomposition: Application to correction of potential surface for HCN

J. H. Zhang, J. Bowman, Qian Wu, 1997 .

Picosecond, narrow‐band, widely tunable optical parametric oscillator using a temperature‐tuned lithium borate crystal

Tangsheng Chen, Yaochun Shen, J. H. Zhang, 1993 .

The investigation of spin-orbit effect for the F((2)P)+HD reaction.

J. H. Zhang, Keli Han, Ting-xian Xie, 2004, The Journal of chemical physics.

Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations

Jianzhong Chen, J. H. Zhang, Laixue Pang, 2020, Journal of biomolecular structure & dynamics.

Molecular mechanism of ligand bindings to Zika virus at SAM site

J. H. Zhang, Xiao Liu, Yang Zhao, 2019, Chemical Physics Letters.

Direct folding simulation of helical proteins using an effective polarizable bond force field.

J. H. Zhang, Lili Duan, C. Ji, 2017, Physical chemistry chemical physics : PCCP.

Unveiling the gating mechanism of ECF Transporter RibU

Jianing Song, J. H. Zhang, C. Ji, 2013, Scientific Reports.

Theoretical model for the dynamics of hydrogen recombination on the Si(100)‐(2×1) surface

J. H. Zhang, J. Sheng, 1992 .

Arrangement transformation approach to state-to-state quantum reactive scattering H + DH→DH + H, HH + D

J. H. Zhang, Qinggang Zhang, Yi-ci Zhang, 1999 .

Comment on: Resonance structure in the energy dependence of state-to-state differential scattering cross sections for the

W. Miller, J. H. Zhang, R. Continetti, 1990 .

Total and partial decay widths in vibrational predissociation of HF dimer

Dong H. Zhang, J. H. Zhang, 1993 .

Vibrational predissociation in HD—HF

Dong H. Zhang, J. H. Zhang, 1992 .

DESIGN OF HYBRID INHIBITORS TO HIV-1 PROTEASE

J. H. Zhang, S. Lee-Huang, Da W. Zhang, 2008 .

Dissociative chemisorption of H2 on Ni surface: Time‐dependent quantum dynamics calculation and comparison with experiment

J. H. Zhang, J. Sheng, 1992 .

Correction of repulsive potential energy surface for photodissociation of H2O in the Ã state

J. H. Zhang, Dunyou Wang, 1998 .

Perturbative approach to potential surface inversion for bound and half-scattering problems

J. H. Zhang, Qian Wu, 1997 .

6D quantum calculation of energy levels for HF stretching excited (HF) 2

Dong H. Zhang, J. H. Zhang, Qian Wu, 1995 .

Theoretical study of the absorption and emission spectrum and non‐adiabatic excited state dynamics of gas‐phase xanthone

J. H. Zhang, Tong Zhu, C. Chin, 2023, Journal of the Chinese Chemical Society.

Dramatic influence of Dy3+ doping on strain and domain structure in lead-free piezoelectric 0.935(Na1/2Bi1/2)TiO3−0.065BaTiO3 ceramics

J. H. Zhang, Zhigao Hu, W. Shi, 2015 .

PHOTODISSOCIATION OF OZONE IN THE HARTLEY BAND: FRAGMENT ROTATIONAL QUANTUM STATE DISTRIBUTIONS

J. H. Zhang, Keli Han, G. He, 2004 .

Selectivity of neutral/weakly basic P1 group inhibitors of thrombin and trypsin by a molecular dynamics study.

John Z H Zhang, J. H. Zhang, Keli Han, 2008, Chemistry.

Determining Optimal Coarse‐Grained Representation for Biomolecules Using Internal Cluster Validation Indexes

Fei Xia, Kelin Xia, Yuwei Zhang, 2020, J. Comput. Chem..

Protein-Ligand Empirical Interaction Components for Virtual Screening

Weijun Wang, Zhaoxi Sun, Changge Ji, 2017, J. Chem. Inf. Model..

How CuCl and CuCl2 Insert into C-N Bonds of Diazo Compounds: An Electronic Structure and Mechanistic Study.

J. H. Zhang, Fengyu Li, F. Xia, 2020, The journal of physical chemistry. A.

Double Twist in Helical Polymer "Soft" Crystals

Stephen Z. D. Cheng, J. H. Zhang, L. Chien, 1999 .

Molecular Orientations in Flat-Elongated and Helical Lamellar Crystals of a Main-Chain Nonracemic Chiral Polyester

Stephen Z. D. Cheng, J. H. Zhang, B. Lotz, 2000 .

Helical Twist Senses, Liquid Crystalline Behavior, Crystal Microtwins, and Rotation Twins in a Polyester Containing Main-Chain Molecular Asymmetry and Effects of the Number of Methylene Units in the Backbones on the Phase Structures and Morphologies of Its Homologues

Stephen Z. D. Cheng, J. H. Zhang, B. Lotz, 2002 .

Molecular Physics: An International Journal at the Interface Between Chemistry and Physics

J. H. Zhang, Y. Mei, Ya Gao, 2012 .

Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation.

Xiao He, John Z H Zhang, Tong Zhu, 2012, Physical chemistry chemical physics : PCCP.

Quantum dynamics studies of adsorption and desorption of hydrogen at a Cu(111) surface

J. H. Zhang, J. Sheng, 1993 .

Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.

J. H. Zhang, T. Zhu, Xiao He, 2015, Advances in experimental medicine and biology.

Time-dependent density functional theory study of absorption spectra of metallocenes

J. H. Zhang, Y. Mei, Yong L. Li, 2009 .

Fragment quantum chemical approach to geometry optimization and vibrational spectrum calculation of proteins.

Xiao He, John Z H Zhang, J. H. Zhang, 2016, Physical chemistry chemical physics : PCCP.

Time-dependent quantum wave packet study of the C+CH reaction

J. H. Zhang, Keli Han, Mao-du Chen, 2001 .

Investigation on the characteristics and mechanisms of ACE inhibitory peptides by a thorough analysis of all 8000 tripeptides via binding free energy calculation

J. H. Zhang, Bei Gao, Sha Li, 2021, Food science & nutrition.

The critical effect of polarization on the dynamical structure of guanine quadruplex DNA.

Jianing Song, J. H. Zhang, C. Ji, 2013, Physical chemistry chemical physics : PCCP.

Molecular mechanism related to the binding of fluorophores to Mango-II revealed by multiple-replica molecular dynamics simulations.

Jianzhong Chen, J. H. Zhang, T. Zhu, 2021, Physical chemistry chemical physics : PCCP.

Protonation-dependent base flipping in the catalytic triad of a small RNA

Zhaoxi Sun, John Z. H. Zhang, Xiaohui Wang, 2017 .

Full QM Calculation of RNA Energy Using Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method.

Xiao He, John Z H Zhang, Xinsheng Jin, 2017, The journal of physical chemistry. A.

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

Xiao He, John Z H Zhang, Tong Zhu, 2015, Journal of chemical theory and computation.

An Energy Optimization Strategy Based on the Perfect Conformation of Prolyl Endopeptidase for Improving Catalytic Efficiency.

J. H. Zhang, Y. Cong, Bei Gao, 2020, Journal of agricultural and food chemistry.

Quantum mechanical calculation for photodissociation of hydrogen peroxide

Dong H. Zhang, J. H. Zhang, 1993 .

Effect of strong electric field on the conformational integrity of insulin.

J. H. Zhang, Xiao He, Shude Chen, 2014, The journal of physical chemistry. A.

Molecular dynamics simulation and computational two-dimensional infrared spectroscopic study of model amyloid β-peptide oligomers.

J. H. Zhang, Yun Xiang, Jun Xu, 2013, The journal of physical chemistry. A.

Folding dynamics of a small protein at room temperature via simulated coherent two-dimensional infrared spectroscopy.

J. H. Zhang, Yun Xiang, Lili Duan, 2010, Physical chemistry chemical physics : PCCP.

Quantum dynamics study of isotope effect for H+CH4 reaction using the SVRT model

Guang-Hui Yang, John Z. H. Zhang, J. H. Zhang, 2003 .

Generalized semirigid vibrating rotor target model for atom–poly reaction: Inclusion of umbrella mode for H+CH4 reaction

John Z. H. Zhang, J. H. Zhang, Ming L. Wang, 2002 .

Application of semirigid vibrating rotor target model to reaction of H+CH4→CH3+H2

John Z. H. Zhang, Dong H. Zhang, J. H. Zhang, 2000 .

Discovery and Characterization of Novel, Potent, and Selective Cytochrome P450 2J2 Inhibitors

Ye Mei, John Z H Zhang, Jian Fei, 2013, Drug Metabolism and Disposition.

Effect of entrance channel topology on reaction dynamics: O(3P) + CH4 → CH3 + OH

John Z. H. Zhang, Q. Cui, J. H. Zhang, 2005 .

Quantum reactive scattering with a deep well: Time‐dependent calculation for H+O2 reaction and bound state characterization for HO2

John Z. H. Zhang, Dong H. Zhang, J. H. Zhang, 1994 .

High‐lying rovibrational states of floppy X3 triatomics by a new D3h symmetry adapted method: Application to the H+3 molecule

J. H. Zhang, Z. Bačić, 1992 .

A new D3h symmetry-adapted method for highly excited vibrational levels of floppy triatomics: the H+ 3 molecule

J. H. Zhang, Z. Bačić, 1991 .

Formation mechanism and spectroscopy of C6H radicals in extreme environments: a theoretical study.

J. H. Zhang, T. Zhu, C. Chin, 2019, Physical chemistry chemical physics : PCCP.

Reaction mechanism and product branching ratios of OH+C2H3F reaction: A theoretical study

J. H. Zhang, T. Zhu, C. Chin, 2020 .

Quasi-adiabatic basis functions for the S-matrix Kohn variational approach to quantum reactive scattering

W. Miller, J. H. Zhang, 1990 .

L2 amplitude density method for multichannel inelastic and rearrangement collisions

D. Kouri, J. H. Zhang, D. Truhlar, 1988 .

Variational basis-set calculations of accurate quantum mechanical reaction probabilities

D. Kouri, J. H. Zhang, D. Truhlar, 1987 .

Quantum mechanical algebraic variational methods for inelastic and reactive molecular collisions

D. Kouri, J. H. Zhang, D. Truhlar, 1988 .

Vibrational predissociation of HF dimer in νHF=1: Influence of initially excited intermolecular vibrations on the fragmentation dynamics

Dong H. Zhang, J. H. Zhang, Z. Bačić, 1995 .

A time‐dependent approach to flux calculation in molecular photofragmentation: Vibrational predissociation of HF–DF

Dong H. Zhang, J. H. Zhang, Qian Wu, 1995 .

Photofragmentation of HF dimer: Quantum dynamics studies on ab initio potential energy surfaces

Dong H. Zhang, J. H. Zhang, 1993 .

A time‐dependent calculation for vibrational predissociation of H2HF

Dong H. Zhang, J. H. Zhang, Z. Bačić, 1992 .

Mode-specific decay widths in vibrational predissociation of D2HF

Dong H. Zhang, J. H. Zhang, Z. Bačić, 1992 .

Quantum calculation of photodetachment spectrum of OH−(H2)

J. H. Zhang, C. Yu, Dunyou Wang, 1997 .

Quantum dynamical studies for photodissociation of H2O2 at 248 and 266 nm

Dong H. Zhang, J. H. Zhang, Zhengli Cai, 1994 .

Quantum scattering via the S‐matrix version of the Kohn variational principle

William H. Miller, John Z. H. Zhang, W. Miller, 1988 .

Time-Dependent Wave Packet Approach to State-to-State Reactive Scattering and Application to H + O2 Reaction

J. H. Zhang, J. Dai, 1996 .

Performance Comparison of Systematic Methods for Rigorous Definition of Coarse-Grained Sites of Large Biomolecules

Yuwei Zhang, Fei Xia, Zexing Cao, 2017, J. Chem. Inf. Model..

Improving the Scoring of Protein-Ligand Binding Affinity by Including the Effects of Structural Water and Electronic Polarization

Xiao He, John Z. H. Zhang, Jinfeng Liu, 2013, J. Chem. Inf. Model..

THEORY AND APPLICATION OF QUANTUM MOLECULAR DYNAMICS

John Z. H. Zhang, J. H. Zhang, 1999 .

Cyclopentadienyl radical formation from the reaction of excited nitrogen atoms with benzene: a theoretical study.

J. H. Zhang, Tong Zhu, C. Chin, 2021, Physical chemistry chemical physics : PCCP.

Efficient calculation of excess free energy of pure and mixed alcohol solutions

J. H. Zhang, Cuiyu Li, Bowen Wang, 2020 .

Global dynamics and transition state theories: Comparative study of reaction rate constants for gas‐phase chemical reactions

John Z. H. Zhang, Ke-Li Han, Li-Ping Ju, 2009, J. Comput. Chem..

Class I Phospho-inositide-3-kinases (PI3Ks) Isoform-Specific Inhibition Study by the Combination of Docking and Molecular Dynamics Simulation

Ming Han, John Z. H. Zhang, J. H. Zhang, 2010, J. Chem. Inf. Model..

Computational analysis of binding free energies, hotspots and the binding mechanism of Bcl-xL/Bcl-2 binding to Bad/Bax.

J. H. Zhang, Y. Cong, Lili Duan, 2021, Physical chemistry chemical physics : PCCP.

Computational Protein Design with Deep Learning Neural Networks

John Z. H. Zhang, Yifei Qi, Jingxue Wang, 2018, Scientific Reports.

Understanding the selectivity of inhibitors toward PI4KIIIα and PI4KIIIβ based molecular modeling.

Jianzhong Chen, J. H. Zhang, Tong Zhu, 2019, Physical chemistry chemical physics : PCCP.

Computational Alanine Scanning Reveals Common Features of TCR/pMHC Recognition in HLA-DQ8-Associated Celiac Disease.

Jianing Song, J. H. Zhang, Linqiong Qiu, 2021, Methods in molecular biology.

An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins.

Xiao He, Ye Mei, John Z H Zhang, 2013, The Journal of chemical physics.

Probing the Ion-Specific Effects at the Water/Air Interface and Water-Mediated Ion Pairing in Sodium Halide Solution with Ab Initio Molecular Dynamics.

J. H. Zhang, Xiao He, Jinfeng Liu, 2018, The journal of physical chemistry. B.

Structure of liquid water - a dynamical mixture of tetrahedral and 'ring-and-chain' like structures.

J. H. Zhang, Xiao He, Jinfeng Liu, 2017, Physical chemistry chemical physics : PCCP.

Fragment Quantum Mechanical Method for Large-Sized Ion-Water Clusters.

J. H. Zhang, Lian‐Wen Qi, Xiao He, 2017, Journal of chemical theory and computation.

Calculation of protein–ligand binding affinities based on a fragment quantum mechanical method

John Z. H. Zhang, J. H. Zhang, Xiao He, 2015 .

Fragment quantum mechanical calculation of proteins and its applications.

Xiao He, Tong Zhu, John Z H Zhang, 2014, Accounts of chemical research.

Electrostatically embedded generalized molecular fractionation with conjugate caps method for full quantum mechanical calculation of protein energy.

Xiao He, John Z H Zhang, J. H. Zhang, 2013, The journal of physical chemistry. A.

A Fragment Quantum Mechanical Method for Metalloproteins.

J. H. Zhang, Mingyuan Xu, T. Zhu, 2019, Journal of chemical theory and computation.

Development of an effective polarizable bond method for biomolecular simulation.

J. H. Zhang, Tong Zhu, C. Ji, 2013, The journal of physical chemistry. B.

A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation

Xiao He, Ye Mei, Ya Gao, 2013, Journal of Molecular Modeling.

A New Quantum Calibrated Force Field for Zinc-Protein Complex.

John Z H Zhang, Xudong Xiao, Changge Ji, 2013, Journal of chemical theory and computation.

Accurate and Efficient Calculation of Protein-Protein Binding Free Energy-Interaction Entropy with Residue Type-Specific Dielectric Constants.

Xiao Liu, John Z H Zhang, Long Peng, 2018, Journal of chemical information and modeling.

Insights into small molecule inhibitor bindings to PD-L1 with residue-specific binding free energy calculation

Yifei Qi, J. H. Zhang, Liping He, 2021, Journal of biomolecular structure & dynamics.

DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks

Liping He, Yifei Qi, Jingxue Wang, 2019, J. Chem. Inf. Model..

Understanding the molecular mechanism of enzyme dynamics of ribonuclease A through protonation/deprotonation of HIS48.

John Z H Zhang, J. H. Zhang, C. Ji, 2011, Journal of the American Chemical Society.

Full quantum mechanical study of binding of HIV‐1 protease drugs

J. H. Zhang, Da W. Zhang, 2005 .

A Double-Well Ultra-Coarse-Grained Model to Describe Protein Conformational Transitions.

J. H. Zhang, Z. Cao, Yuwei Zhang, 2020, Journal of chemical theory and computation.

Engineering the biomimetic cofactors of NMNH for cytochrome P450 BM3 based on binding conformation refinement

J. H. Zhang, Y. Cong, Qiangzi Li, 2021, RSC advances.

A stochastic golden-rule treatment for thermal desorption of gases from solid surfaces

J. H. Zhang, 1992 .

The effect of POPC acyl chains packing by aromatic amino acid methyl esters investigated by ATR-FTIR combined with QM calculations

J. H. Zhang, Bo Peng, Xiaoyan Ding, 2016 .

Use of negative complex potential as absorbing potential

John Z. H. Zhang, J. H. Zhang, † Jiu-Yuan Ge, 1998 .

Quantum reactive scattering via the S-matrix version of the Kohn variational principle: Integral cross sections For H+H2(ν1=j1=0)→H2(ν2=1, j2= 1, 3) + H in the energy range Etotal = 0.9–1.4 eV

W. Miller, J. H. Zhang, 1988 .

Quantum calculations of reaction probabilities for HO + CO→ H + CO2 and bound states of HOCO

John Z. H. Zhang, Dong H. Zhang, J. H. Zhang, 1995 .

Nonadiabatic effects in the H+D2 reaction.

John Z H Zhang, Yan Zhang, J. H. Zhang, 2006, The Journal of chemical physics.

DEVELOPMENT OF ACCURATE QUANTUM DYNAMICAL METHODS FOR TETRAATOMIC REACTIONS

John Z. H. Zhang, Wei Zhu, J. H. Zhang, 1997 .

Quantum mechanical studies of residue-specific hydrophobic interactions in p53-MDM2 binding.

Ye Mei, John Z H Zhang, J. H. Zhang, 2008, The journal of physical chemistry. B.

A numerically stable restrained electrostatic potential charge fitting method

Ye Mei, John Z. H. Zhang, Juan Zeng, 2013, J. Comput. Chem..

How to observe the elusive resonances in H or D + H2 → H2 or HD + H reactive scattering

W. Miller, J. H. Zhang, 1991 .

An Electrochemical Biosensor with Dual Signal Outputs: Toward Simultaneous Quantification of pH and O2 in the Brain upon Ischemia and in a Tumor during Cancer Starvation Therapy.

John Z H Zhang, Huisheng Peng, Zhihui Dai, 2017, Angewandte Chemie.

Single Biosensor for Simultaneous Quantification of Glucose and pH in a Rat Brain of Diabetic Model Using Both Current and Potential Outputs.

J. H. Zhang, T. Zhu, Yang Tian, 2017, Analytical chemistry.

Development of a polynomial scoring function P3-Score for improved scoring and ranking powers

J. H. Zhang, Aiwei Zhang, Lifei Wang, 2023, Chemical Physics Letters.

DeepBSP - a Machine Learning Method for Accurate Prediction of Protein-Ligand Docking Structures

Jingxiao Bao, John Z. H. Zhang, Xiao He, 2021, J. Chem. Inf. Model..

Development of a New Scoring Function for Virtual Screening: APBScore

Xiao He, Jingxiao Bao, John Z H Zhang, 2020, J. Chem. Inf. Model..

Anchor-Locker Binding Mechanism of the Coronavirus Spike Protein to Human ACE2: Insights from Computational Analysis

J. H. Zhang, Y. Cong, Yinghui Feng, 2021, J. Chem. Inf. Model..

Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation Maximization.

Fei Xia, Min Li, John Zenghui Zhang, 2016, Journal of chemical theory and computation.

Quantum reactive scattering calculations of Franck—Condon factors for the photodetachment of H2F− and D2F− and comparisons with experiment

W. Miller, J. H. Zhang, D. Neumark, 1991 .

Photodissociation and continuum resonance Raman cross sections and general Franck–Condon intensities from S‐matrix Kohn scattering calculations with application to the photoelectron spectrum of H2F−+hν→H2+F, HF+H + e−

W. Miller, J. H. Zhang, 1990 .

Accurate three‐dimensional quantum scattering calculations for F+H2→HF+H

William H. Miller, John Z. H. Zhang, W. Miller, 1988 .

Analysis of the binding modes of the first‐ and second‐generation antiandrogens with respect to F876L mutation

Yifei Qi, J. H. Zhang, Xiao He, 2021, Chemical biology & drug design.

Computational Analysis of Residue-Specific Binding Free Energies of Androgen Receptor to Ligands

Yifei Qi, J. H. Zhang, Xiao He, 2021, Frontiers in Molecular Biosciences.

MolGpka: A Web Server for Small Molecule pKa Prediction Using a Graph-Convolutional Neural Network

John Z. H. Zhang, Changge Ji, Xiaolin Pan, 2021, J. Chem. Inf. Model..

New method in time‐dependent quantum scattering theory: Integrating the wave function in the interaction picture

J. H. Zhang, 1990 .

The semirigid vibrating rotor target model for quantum polyatomic reaction dynamics

John Z. H. Zhang, J. H. Zhang, 1999 .

Quantum adsorption dynamics of a diatomic molecule on surface: Four‐dimensional fixed‐site model for H2 on Cu(111)

J. H. Zhang, J. Dai, 1995 .

Steric effect in dissociative chemisorption of hydrogen on Cu

J. H. Zhang, J. Dai, 1994 .

Symmetry and rotational orientation effects in dissociative adsorption of diatomic molecules on metals: H2 and HD on Cu(111)

J. H. Zhang, J. Dai, J. Sheng, 1994 .

Reaction of O(1D) + H2 → HO + H. A three-dimensional quantum dynamics study

Dong H. Zhang, J. H. Zhang, Tong Peng, 1996 .

Interaction entropy for protein-protein binding.

J. H. Zhang, Yuna Yan, Zhaoxi Sun, 2017, The Journal of chemical physics.

Accessing the applicability of polarized protein‐specific charge in linear interaction energy analysis

Ye Mei, John Z. H. Zhang, Juan Zeng, 2014, J. Comput. Chem..

COMPUTATIONAL STUDY FOR BINDING OF OSCILLARIN TO HUMAN α-THROMBIN

J. H. Zhang, Keli Han, E. Wu, 2009 .

Quantum and Molecular Dynamics Study for Binding of Macrocyclic Inhibitors to Human α-Thrombin

Ye Mei, Emilia L. Wu, John Z. H. Zhang, 2007 .

Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics.

Bernard R Brooks, Ye Mei, John Z H Zhang, 2016, Journal of chemical theory and computation.

Temperature dependent near infrared ultraviolet range dielectric functions of nanocrystalline (Na 0.5 Bi 0.5 ) 1- x Ce x (Ti 0.99 Fe 0.01 )O 3 films

Min Han, J. H. Zhang, Yifan Li, 2014 .

Quantum scattering calculation of the O(1D)+HBr reaction.

J. H. Zhang, Keli Han, Mao-du Chen, 2004, The Journal of chemical physics.

Novel theoretically designed HIV-1 non-nucleoside reverse transcriptase inhibitors derived from nevirapine

Xiao He, John Z. H. Zhang, J. H. Zhang, 2014, Journal of Molecular Modeling.

Predicting mutation-induced Stark shifts in the active site of a protein with a polarized force field.

Xiao He, John Z H Zhang, J. H. Zhang, 2013, The journal of physical chemistry. A.

Polarization of intraprotein hydrogen bond is critical to thermal stability of short helix.

Ye Mei, John Z H Zhang, Ya Gao, 2012, The journal of physical chemistry. B.

Structure, mechanism, and enantioselectivity shifting of lipase LipK107 with a simple way.

J. H. Zhang, Zuanning Yuan, Bei Gao, 2014, Biochimica et biophysica acta.

Quantum dynamics study of Li + HF reaction

Wei Zhu, J. H. Zhang, Dunyou Wang, 1997 .

Residue-specific binding mechanisms of PD-L1 to its monoclonal antibodies by computational alanine scanning.

Dading Huang, J. H. Zhang, Jingxiao Bao, 2021, Physical chemistry chemical physics : PCCP.

A DVR based time-dependent wave packet treatment for reactive scattering

Omar A. Sharafeddin, J. H. Zhang, 1993 .

Reply to comment on: Accurate three-dimensional quantum scattering calculations for F+H2→HF+H

W. Miller, J. H. Zhang, 1989 .

Time‐dependent spectral calculation of bound and resonance energies of HO2

J. H. Zhang, J. Dai, 1996 .

Time-dependent wave packet calculation for state-to-state reaction of Cl+H2 using the reactant-product decoupling approach

J. H. Zhang, Qinggang Zhang, Haiyan Zhang, 2001 .

Time-dependent quantum dynamics study of the Cl+H2 reaction

John Z. H. Zhang, J. H. Zhang, Keli Han, 2000 .

A reactant-product decoupling method for state-to-state reactive scattering

Tong Peng, John Z. H. Zhang, J. H. Zhang, 1996 .

A theoretical study of the substituent effect on reactions of amines, carbon dioxide and ethylene oxide catalyzed by binary ionic liquids

J. H. Zhang, Jian Chen, T. Zhu, 2017 .

Time-dependent quantum wave packet study of the H¿DCN\HD¿CN reaction

John Z. H. Zhang, J. H. Zhang, Keli Han, 2002 .

Time-dependent quantum wave packet study of H+HCN→H2+CN reaction

John Z. H. Zhang, J. H. Zhang, Keli Han, 2002 .

Application of Semirigid Vibrating Rotor Target Model to the Reaction of O(3P) + CH4 → CH3 + OH†

John Z. H. Zhang, J. H. Zhang, Ming-Liang Wang, 2001 .

Noise‐free spectrum for time‐dependent calculation of eigenenergies

J. H. Zhang, J. Dai, 1995 .

A theoretical study for H2 + CN ↔ HCN + H reaction and its kinetic isotope effects with variational transition state theory

John Z. H. Zhang, J. H. Zhang, Keli Han, 2006 .

Storage management strategies in large-scale quantum dynamics calculations

D. Kouri, R. Schweitzer, J. H. Zhang, 1987 .

2?* Calculations of Accurate Quantal-dynamical Reactive Scattering Transition Probabilities and their Use to test Semiclassical Applications

B. C. Garrett, D. Kouri, J. H. Zhang, 1987 .

New time-dependent and time-independent computational methods for molecular collisions

D. Kouri, J. H. Zhang, D. Truhlar, 1988 .

Quantitative analysis of ACE2 binding to coronavirus spike proteins: SARS-CoV-2 vs. SARS-CoV and RaTG13.

J. H. Zhang, Zhendong Li, 2021, Physical chemistry chemical physics : PCCP.

Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88

J. H. Zhang, Juan Zeng, Y. Mei, 2016, Journal of Molecular Modeling.

Quantum dynamics study of the Cl+D2 reaction: Time-dependent wave packet calculations

John Z. H. Zhang, J. H. Zhang, Keli Han, 2000 .

Glycosylation Modulates Human CD2-CD58 Adhesion via Conformational Adjustment.

J. H. Zhang, C. Ji, Xingyu Wang, 2015, The journal of physical chemistry. B.

Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologies

Jianzhong Chen, J. H. Zhang, Laixue Pang, 2020, Journal of biomolecular structure & dynamics.

A new algorithm for construction of coarse‐grained sites of large biomolecules

Fei Xia, Min Li, John Z. H. Zhang, 2016, J. Comput. Chem..

Multiscale polarizable coarse-graining water models on cluster-level electrostatic dipoles.

J. H. Zhang, Min Li, 2021, Physical chemistry chemical physics : PCCP.

Total and partial decay widths in vibrational predissociation of the HeI2 van der Waals complex for lower initial vibrational excitations

J. H. Zhang, Xian Zhao, C. Deng, 1997 .

An efficient time-dependent Golden Rule treatment for three-dimensional vibrational predissociation of helium diiodide

Dong H. Zhang, J. H. Zhang, 1992 .

Studying the Effect of Site-Specific Hydrophobicity and Polarization on Hydrogen Bond Energy of Protein Using a Polarizable Method.

J. H. Zhang, C. Ji, X. Xiao, 2012, Journal of chemical theory and computation.

Selective binding of antiinfluenza drugs and their analogues to 'open' and 'closed' conformations of H5N1 neuraminidase.

John Z H Zhang, J. H. Zhang, Pei Wang, 2010, The journal of physical chemistry. B.

BAR‐based optimum adaptive steered MD for configurational sampling

Xiaohui Wang, John Z. H. Zhang, Zhaoxi Sun, 2018, J. Comput. Chem..

Comment on: ‘‘Quantum scattering via the S‐matrix version of the Kohn variational principle’’

W. Miller, J. H. Zhang, 1988 .

Quantum mechanical tunneling through a time‐dependent barrier

J. H. Zhang, J. Ge, 1996 .

A Coupled Ionization-Conformational Equilibrium Is Required To Understand the Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease.

A. Roitberg, J. H. Zhang, Xiao He, 2018, Journal of the American Chemical Society.

Interaction Entropy for Computational Alanine Scanning

John Z. H. Zhang, Yuna Yan, Maoyou Yang, 2017, J. Chem. Inf. Model..

A Comparative Insight into Amprenavir Resistance of Mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 Protease Based on Thermodynamic Integration and MM-PBSA Methods

Xingyu Wang, Tong Zhu, John Z. H. Zhang, 2015, J. Chem. Inf. Model..

A mixed quantum-classical semirigid vibrating rotor target approach to methane dissociation on Ni surface

J. H. Zhang, Yun Xiang, 2003 .

HobPre: accurate prediction of human oral bioavailability for small molecules

Bo Wang, Xiaolin Pan, Min Wei, 2022, Journal of Cheminformatics.

Fully quantum mechanical energy optimization for protein–ligand structure

John Z. H. Zhang, Yun Xiang, Da W. Zhang, 2004, J. Comput. Chem..

Efficient bond function basis set for π‐π interaction energies

Ye Mei, John Z. H. Zhang, Yun Ding, 2008, J. Comput. Chem..

nhibition mechanism and hot-spot prediction of nine potential drugs for SARS-CoV-2 Mpro by large-scale molecular dynamic simulations combined with accurate binding free energy calculations.

J. H. Zhang, Y. Cong, Lili Duan, 2021, Nanoscale.

Effect of Self-Assembly of Fullerene Nano-Particles on Lipid Membrane

J. H. Zhang, Saiqun Zhang, Y. Mu, 2013, PloS one.

Exploring the molecular mechanism of stabilization of the adhesion domains of human CD2 by N-glycosylation.

J. H. Zhang, C. Ji, Xing-Yu Wang, 2012, The journal of physical chemistry. B.

Semirigid vibrating rotor target model for CH4 dissociation on a Ni(111) surface

J. H. Zhang, Yun Xiang, Dunyou Wang, 2002 .

Beyond QM/MM: fragment quantum mechanical methods.

K. Houk, J. H. Zhang, Jiali Gao, 2014, Accounts of chemical research.

Quantum dynamics study of H+NH3-->H2+NH2 reaction.

John Z H Zhang, Q. Cui, J. H. Zhang, 2007, The Journal of chemical physics.

PBSA_E: A PBSA-Based Free Energy Estimator for Protein-Ligand Binding Affinity

Xiao Liu, Xiao He, Tong Zhu, 2016, J. Chem. Inf. Model..

A systematic study on RNA NMR chemical shift calculation based on the automated fragmentation QM/MM approach

Xiao He, Tong Zhu, Xinsheng Jin, 2016 .

Full-dimensional quantum dynamics calculation for D2+CN reaction

John Z. H. Zhang, Wei Zhu, Dong H. Zhang, 1998 .

An electrostatic energy-based charge model for molecular dynamics simulation.

J. H. Zhang, Zhousu Xu, Xianwei Wang, 2021, The Journal of chemical physics.

An Approach to Computing Solvent Reorganization Energy.

J. H. Zhang, Tong Zhu, Cuiyu Li, 2020, Journal of chemical theory and computation.

Insights from MD Simulation on Na+ Binding and Loop Dynamics in Multidrug Resistance Transporter Norm

Jianing Song, J. H. Zhang, C. Ji, 2018 .

Predicted PAR1 inhibitors from multiple computational methods

J. H. Zhang, Tong Zhu, Xiao He, 2016 .

Effect of mismatch on binding of ADAR2/GluR-2 pre-mRNA complex

Jianing Song, J. H. Zhang, C. Ji, 2015, Journal of Molecular Modeling.

Energetics of protein backbone hydrogen bonds and their local electrostatic environment

J. H. Zhang, Lili Duan, C. Ji, 2014, Science China Chemistry.

The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect

Ye Mei, John Z. H. Zhang, Juan Zeng, 2013, J. Comput. Chem..

Comparison of the unfolding and oligomerization of human prion protein under acidic and neutral environments by molecular dynamics simulations

J. H. Zhang, T. Zhu, Chaomin Zhang, 2018, Chemical Physics Letters.

Investigating effects of bridging water on the binding of neuraminidase−ligands using computational alanine scanning combined with interaction entropy method

J. H. Zhang, Y. Cong, Lili Duan, 2021 .

The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions: a replica exchange molecular dynamics study

J. H. Zhang, Dawei Zhang, Juan Zeng, 2013, Journal of Molecular Modeling.

Mixed quantum-classical study of energy transfer between H2O and a dipeptide

J. H. Zhang, Ming-Liang Wang, 2003 .

Temperature dependent phonon evolutions and optical properties of highly c-axis oriented CuGaO2 semiconductor films grown by the sol-gel method

Min Han, J. H. Zhang, K. Jiang, 2011 .

Protein–water hydrogen bonds are stabilized by electrostatic polarization

Ye Mei, Ya Gao, John Z. H. Zhang, 2012 .

Phase Transformations in Chiral Non-racemic Main-chain Liquid Crystalline Polyesters Involving Doubletwist Helical Crystals

Stephen Z. D. Cheng, J. H. Zhang, L. Chien, 2003 .

Ab initio quantum dynamics study of rotationally inelastic scattering of glycine by hydrogen atom

J. H. Zhang, Da W. Zhang, M. Wang, 2003 .

Developing polarized protein-specific charges for protein dynamics: MD free energy calculation of pKa shifts for Asp26/Asp20 in thioredoxin.

Ye Mei, Changge Ji, John Z. H. Zhang, 2008, Biophysical journal.

Quantitative quantum dynamics calculation of H2 + CH3 -> H + CH4 reaction

J. H. Zhang, Yi M. Li, 2002 .

Computational Study of PCSK9-EGFA Complex with Effective Polarizable Bond Force Field

J. H. Zhang, Lili Duan, Jian Chen, 2018, Front. Mol. Biosci..

pH-dependent conformational ensemble and polymorphism of amyloid-β core fragment.

J. H. Zhang, Ce Zhang, Y. Mu, 2013, The journal of physical chemistry. B.

Direct folding simulation of a long helix in explicit water

J. H. Zhang, Dawei Zhang, Lili Duan, 2013 .

Effect of Substituents in Different Positions of Aminothiazole Hinge-Binding Scaffolds on Inhibitor–CDK2 Association Probed by Interaction Entropy Method

Jianzhong Chen, J. H. Zhang, T. Zhu, 2018, ACS Omega.

An Electrochemical Biosensor with Dual Signal Outputs: Toward Simultaneous Quantification of pH and O2 in the Brain upon Ischemia and in a Tumor during Cancer Starvation Therapy.

Huisheng Peng, J. H. Zhang, Z. Dai, 2017, Angewandte Chemie.

Understanding the molecular mechanism of enzyme dynamics of ribonuclease A through protonation/deprotonation of HIS48.

J. H. Zhang, Changge Ji, 2011, Journal of the American Chemical Society.

Electrostatic Polarization Effect on Cooperative Aggregation of Full Length Human Islet Amyloid

Fei Xia, Yang Li, Xianwei Wang, 2018, J. Chem. Inf. Model..

Evaluation of the Coupled Two-Dimensional Main Chain Torsional Potential in Modeling Intrinsically Disordered Proteins

Ye Mei, John Z. H. Zhang, Chaomin Zhang, 2017, J. Chem. Inf. Model..

Channel-dependent complex absorbing potential for multi-channel scattering

J. H. Zhang, J. Ge, 1998 .

REACTANT-PRODUCT DECOUPLING APPROACH TO HALF-SCATTERING PROBLEMS : PHOTODISSOCIATION OF H2O IN THREE DIMENSIONS

Wei Zhu, D. Kouri, J. H. Zhang, 1997 .

Rational Design of Pepsin for Enhanced Thermostability via Exploiting the Guide of Structural Weakness on Stability

J. H. Zhang, Jianguo Zhang, Lujia Zhang, 2021, Frontiers in Physics.

Simulation of the thermodynamics of folding and unfolding of the Trp-cage mini-protein TC5b using different combinations of force fields and solvation models

J. H. Zhang, Dawei Zhang, Lili Duan, 2010 .

Combined effect of confinement and affinity of crowded environment on conformation switching of adenylate kinase

John Z H Zhang, J. H. Zhang, Fei Xia, 2014, Journal of Molecular Modeling.

Theoretical understanding of the thermodynamics and interactions in transcriptional regulator TtgR-ligand binding.

J. H. Zhang, Zhaoxi Sun, Xiaohui Wang, 2019, Physical chemistry chemical physics : PCCP.

BAR‐based optimum adaptive steered MD for configurational sampling

J. H. Zhang, Zhaoxi Sun, Xiaohui Wang, 2018, J. Comput. Chem..

Structure of liquid water - a dynamical mixture of tetrahedral and 'ring-and-chain' like structures.

J. H. Zhang, Xiao He, Jinfeng Liu, 2017, Physical chemistry chemical physics : PCCP.

Molecular dynamics simulation of protein crystal with polarized protein-specific force field.

J. H. Zhang, Y. Mei, Yongxiu Li, 2014, The journal of physical chemistry. B.

A new algorithm for construction of coarse‐grained sites of large biomolecules

J. H. Zhang, Min Li, Fei Xia, 2016, J. Comput. Chem..

Molecular caps for full quantum mechanical computation of peptide–water interaction energy

X. H. Chen, John Z. H. Zhang, Da W. Zhang, 2003, J. Comput. Chem..

Energy and electron transfer in beta-alkynyl-linked porphyrin-[60]fullerene dyads.

D. Schuster, J. H. Zhang, D. Guldi, 2006, The journal of physical chemistry. B.

Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation of CO in the Heme Distal Pocket of Myoglobin

J. H. Zhang, Xiao He, Xianwei Wang, 2017 .

Structure and dynamics of a dizinc metalloprotein: effect of charge transfer and polarization.

Ye Mei, John Z H Zhang, J. H. Zhang, 2011, The journal of physical chemistry. B.

Functional loop dynamics of the S-component of ECF transporter FolT

Jianing Song, J. H. Zhang, Yingkai Zhang, 2018 .

Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches.

J. H. Zhang, Lili Duan, Huiyong Sun, 2018, Physical chemistry chemical physics : PCCP.

Mixed quantum-classical study of energy transfer in a Na+ collision with a peptide

J. H. Zhang, M. Wang, 2003 .

Molecular dynamic simulation of the Kv1.2 voltage-gated potassium channel in open and closed state conformations.

J. H. Zhang, Ming Han, 2008, The journal of physical chemistry. B.