Publications

1.

Dupuis, R., Benoit, M., Tuckerman, M. E., & Méheut, M. Importance of a Fully Anharmonic Treatment of Equilibrium Isotope Fractionation Properties of Dissolved Ionic Species As Evidenced by Li+ (aq)Acc. Chem. Res., 50 (7), pp 1597–1605 (2017)

2.

Shtukenberg, A. G., Zhu, Q., Carter, D. J., Vogt, L., Hoja, J., Schneider, E., ... Tuckerman, M. E. & Oganov, A. R. Powder diffraction and crystal structure prediction identify four new coumarin polymorphsChem. Sci., 8, 4926-4940 (2017)

3.

Sepehr, F., Liu, H., Luo, X., Bae, C., Tuckerman, M. E., Hickner, M. A., & Paddison, S. J. Mesoscale Simulations of Anion Exchange Membranes Based on Quaternary Ammonium Tethered Triblock CopolymersMacromolecules, 50 (11), pp 4397–4405 (2017)

4.

Bascom, G. D., Kim, T., & Schlick, T. Kilobase Pair Chromatin Fiber Contacts Promoted by Living-System-Like DNA Linker Length Distributions and Nucleosome DepletionJ. Phys. Chem. B, 121 (15), pp 3882–3894 (2017)

5.

Bascom, G., & Schlick, T.  Linking chromatin fibers to gene folding by hierarchical loopingBiophysical Journal, 112 (3), 434-445, (2017)

6.

Rooklin, D. W., Modell, A. E., Li, H., Berdan, V., Arora, P. S., & Zhang, Y.  Targeting Unoccupied Surfaces on Protein-Protein InterfacesJ. Am. Chem. Soc., DOI: 10.1021/jacs.7b05960 (2017)

7.

Mu, H., Geacintov, N. E., Min, J. H., Zhang, Y., & Broyde, S.  Nucleotide Excision Repair Lesion-Recognition Protein Rad4 Captures a Pre-Flipped Partner Base in a Benzo [a] pyrene-Derived DNA Lesion: How Structure Impacts the Binding Pathway. Chem. Res. Toxicol., 30 (6), pp 1344–1354 (2017)

8.

Zho, C. C., Farr, E. P., Glover, W. J., and Schwartz, B. J., Temperature dependence of the hydrated electron’s excited-state relaxation. I. Simulation predictions of resonance Raman and pump-probe transient absorption spectra of cavity and non-cavity models. J. Chem. Phys. 147, 074503 (2017)

9.

Felker, Peter M., and Zlatko Bačić. "Accurate quantum calculations of translation-rotation eigenstates in electric-dipole-coupled H2O@ C60 assemblies.Chem. Phys. L., 683, 172–178(2017)

10.

Xinsheng Jin, John Z. H. Zhang, and Xiao HeFull QM Calculation of RNA Energy Using Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps MethodJ. Phys. Chem. A, 121 (12),,pp 2503–2514 (2017)

11.

Yan Y, Yang M, Ji C, John Z. H. ZhangInteraction Entropy for Computational Alanine ScanningJ Chem Inf Model. 57(5), 1112-1122, (2017)

12.

Liu J, Qi LW, John Z. H. Zhang, He XFragment Quantum Mechanical Method for Large-Sized Ion-Water Clusters, J Chem Theory Comput., 13(5), 2021-2034 (2017)

13.

Sun Z, Yan YN, Yang M, John Z. H. ZhangInteraction Entropy for Protein-protein BindingJ Chem Phys. ,146(12), 124124 (2017)

14.

Gao Y, Zhang C, John Z. H. Zhang, Mei YEvaluation of the Coupled Two-Dimensional Main Chain Torsional Potential in Modeling Intrinsically Disordered Proteins, J Chem Inf Model., 57(2), 267-274 (2017)

15.

Li M, John Z. H. ZhangProtein Simulation Using Coarse-grained Two-bead Multipole Force Field with Polarizable Water ModelsJ Chem Phys., 146(6), 065101 (2017)

16.

Duan LL, Zhu T, Li YC, Zhang QG, John Z. H. ZhangEffect of polarization on HIV-1protease and fluoro-substituted inhibitorsbinding energies by large scale molecular dynamics simulationsSci Rep., 7:42223 (2017)

17.

I. Fu, Y. Cai, Y. Zhang, N. E. Geacintov, and S. Broyde, Nucleosome histone tail conformation and dynamics: impacts of lysine acetylation and a nearby minor groove benzo[a]pyrene-derived lesionBiochemistry, 56 ,1963-1973 (2017)

18.

Peter M. Felker and Zlatko BačićElectric-dipole-coupled H2O@C60 dimer: Translation-rotation eigenstates from twelve-dimensional quantum calculationsJ Chem Phys. 146, 084303 (2017)

19.

C. Wang and Y. ZhangImproving Scoring-Docking-Screening Powers of Protein-Ligand Scoring Functions using Random ForestJ. Comput. Chem. , 38 ,169 - 177 (2017)

20.

X. Hou, D. Rooklin, H. Fang and Y. ZhangResveratrol Serves as a Protein-Substrate Interaction Stabilizer in Human SIRT1 ActivationSci. Rep., 6, 38186 (2016)

21.

Y. Zhou, S. Wang, Y. Li and Y. Zhang. Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions Methods in Enzymology, 577,105-118 (2016)

22.

Glover, W. J., Schwartz, B. J. Short-range Electron Correlation Stabilizes Non-Cavity Solvation of the Hydrated ElectronJ. Chem. Theory Comput. 12 , 5117–5131 (2016)

23.

Casey, J. R., Schwartz, B. J., Glover W. J. Free Energies of Cavity and Noncavity Hydrated Electrons Near the Instantaneous Air/Water Interface. J. Phys. Chem. Lett.73192−3198 (2016)

24.

Cendagorta, J. R., Powers, A., Hele, T. J., Marsalek, O., Bačić, Z., & Tuckerman, M. E. Competing quantum effects in the free energy profiles and diffusion rates of hydrogen and deuterium molecules through clathrate hydratesPhys. Chem. Chem. Phys., 18, 32169-32177 (2016)

25.

Peter M. Felker and Zlatko BačićTranslation-rotation States of H2 in C60: New Insights from a Perturbation-theory Treatment, J. Chem. Phys. 145, 084310 (2016)

26.

Liu, Y., Yu, Z., John Z. H. Zhang, Liu, L., Xia, F., & Zhang, J., Origins of unique gold-catalysed chemo-and site-selective C–H functionalization of phenols with diazo compoundsChem. Sci., 7, 1988-1995, (2016)

27.

Liu, Y., Yu, Z., Luo, Z., John Z. H. Zhang, Liu, L., & Xia, F.Mechanistic Investigation of Aromatic C (sp2)–H and Alkyl C (sp3)–H Bond Insertion by Gold CarbenesJ. Phys. Chem. A, 120(11), 1925-1932, (2016)

28.

Li, M.,  John Z. H. Zhang, & Xia, F., Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation MaximizationJ. Chem. Theory Comput., 12(4), 2091-2100, (2016)

29.

L.L. Duan, X. Liu, John Z. H. Zhang, Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein–Ligand Binding Free EnergyJ. Am. Chem. Soc., 138, 5722–5728 (2016)

30.

X. Liu, J.F. Liu, T. Zhu, L.J. Zhang, X. He, and John Z. H. ZhangPBSA_E: A PBSA-Based Free Energy Estimator for Protein–Ligand Binding AffinityJ. Chem. Inf. Model., 56, 854-861 (2016)

31.

M. Li, John Z. H. ZhangF. Xia, A new algorithm for construction of coarse-grained sites of large biomoleculesJ. Comput. Chem., 37, 795–804, (2016)

32.

X.Y. Jia, M.T. Wang, Y.H. Shao, G. König, B.R. Brooks, John Z. H. ZhangY. Mei, Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum MechanicsJ. Chem. Theory Comput., 12, 499–511 (2016)

33.

Felker, Peter M. and Bačić Z.Communication: Quantum Six-dimensional Calculations of the Coupled Translation-rotation Eigenstates of H2O@C60J. Chem. Phys., 144, 201101 (2016)

34.

J.F. Liu, John Z. H. ZhangX. He, Fragment quantum chemical approach to geometry optimization and vibrational spectrum calculation of proteinsPhys. Chem. Chem. Phys., 18, 1864-1875 (2016)

35.

Y. Zhou, D. Xie and Y. Zhang, Amide Rotation Hindrance Predicts Proteolytic Resistance of Cystine-Knot PeptidesJ. Phys. Chem. Lett. , 7, 1138-1142 (2016)

36.

I. Fu, Y. Cai, Y. Zhang, N. E. Geacintov, and S. Broyde, Entrapment of a Histone Tail by a DNA Lesion in a Nucleosome Suggests the Lesion Impacts Epigenetic Marking: A Molecular Dynamics Study, Biochemistry, 55, 239 - 242 (2016)

37.

Powers, A., Marsalek, O., Xu, M., Ulivi, L., Colognesi, D., Tuckerman, M. E., & Bačić, Z.Impact of the Condensed-Phase Environment on the Translation-Rotation Eigenstates and Spectra of a Hydrogen Molecule in Clathrate HydratesJ. Phys. Chem. Lett., 7,  308–313 (2016) 

38.

J.F. Liu, X.W. Wang, John Z. H. Zhang and X. He, Calculation of protein–ligand binding affinities based on a fragment quantum mechanical methodRSC Adv., 5, 107020-107030 (2015)

39.

X.Y. Jia, Y. MeiJohn Z. H. Zhang, Y. Mo, Hybrid QM/MM study of FMO complex with polarized proteinspecific chargeSci. Rep., 5, 17096 (2015)

40.

J.F. Liu, T. Zhu, X.W. Wang, X. He and John Z. H. Zhang, Quantum Fragment Based ab Initio Molecular Dynamics for ProteinsJ. Chem. Theory Comput., 11, 5897−5905 (2015)

41.

Li, Yongxiu; John Z. H. Zhang; Mei, Ye, Molecular Dynamics Simulation of Protein Crystal with Polarized Protein-Specific Charge, Biophys. J., 108, 2: 160A-160A (2015)

42.

Gao, Ya; Li, Yongxiu; John Z. H. Zhang; Mei, Ye, A Coupled Two-Dimensional Main Chain Torsional Potential for Protein Dynamics, Biophys. J., 108, 2:159A-160A (2015)

43.

Gao, Ya; Li, Yongxiu; Mou, Lirong; Lin, BB; John Z. H. Zhang; Mei, Y, Correct folding of an alpha-helix and a beta-hairpin using a polarized 2D torsional potential, Sci. Rep.,5 ,10359 (2015)

44.

Wang, Xianwei; John Z. H. Zhang; He, Xiao, Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase, J. Chem. Phys., 143, 18: 184111 (2015)

45.

Gong, W., Wu, R., & Zhang, Y. Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An Ab initio QM/MM molecular dynamics study. Journal of computational chemistry, 36(30), 2228-2235 (2015)

46.

Swails, J., Zhu, T., He, X., & Case, D. A.  AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomoleculesJournal of biomolecular NMR, 63(2), 125-139 (2015)

47.

Chen, J., Wang, X., Zhu, T., Zhang, Q., & John Z. H. Zhang  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 MethodsJ. Chem. Inf. Model., 55 (9), pp 1903–1913 (2015)

48.

Xu M.Z., Ye S.F., Bačić Z.  General Selection Rule in the Inelastic Neutron Scattering Spectroscopy of a Diatomic Molecule Confined Inside a Near-Spherical NanocavityJ. Phys. Chem. Lett., 6, 3721–3725 (2015)

49.

Mu, H., Geacintov, N. E., Zhang, Y., & Broyde, S.  Recognition of Damaged DNA for Nucleotide Excision Repair: A Correlated Motion Mechanism with a Mismatched cis-syn Thymine Dimer LesionBiochemistry, 54(34), 5263-5267 (2015)

50.

Yang, J.Song, J.John Z. H. Zhang, & Ji, C.  Effect of mismatch on binding of ADAR2/GluR-2 pre-mRNA complexJ Mol Model,  21: 222 (2015)

51.

Rooklin, D., Wang, C., Katigbak, J., Arora, P. S., & Zhang, Y.  AlphaSpace: Fragment-Centric Topographical Mapping To Target Protein–Protein Interaction Interfaces. J. Chem. Inf. Model., 55 (8), pp 1585–1599 (2015)

52.

Mei, Y., Simmonett, A. C., Pickard, F. C., DiStasio, R., Brooks, B. R., & Shao, Y.  Numerical Study on the Partitioning of the Molecular Polarizability into Fluctuating Charge and Induced Atomic Dipole ContributionsJ. Phys. Chem. A, 119 (22), pp 5865–5882 (2015)

53.

Wang, X., Ji, C., & John Z. H. Zhang  Glycosylation Modulates Human CD2-CD58 Adhesion via Conformational AdjustmentJ. Phys. Chem. B, 119 (22), pp 6493–6501 (2015)

54.

Ozer, G., Luque, A., & Schlick, T.  The chromatin fiber: multiscale problems and approaches. Curr Opin Struct Biol , 31, 124-139 (2015)

55.

Zhou J., Li M., Chen N., Wang S., Luo H-B., Zhang Y., and Wu, R.  Computational design of a time-dependent histone deacetylase 2 selective inhibitorACS Chem. Biol., 10(3), 687-692 (2015)

56.

Gao, Y., Li, Y., Mou, L., Hu, W., Zheng, J., John Z. H. Zhang, & Mei, Y. Coupled Two-Dimensional Main-Chain Torsional Potential for Protein Dynamics II: Performance and ValidationJ. Phys. Chem. B, 119 (11), pp 4188–4193 (2015)

57.

Chen M., Yu T. Q., and Tuckerman M. E.,  Locating landmarks on high-dimensional free energy surfacesProc. Natl. Acad Sci., 112, 11, 3235-3240 (2015)

58.

Song, J., Li Y., Ji C., and John Z. H. ZhangFunctional loop dynamics of the streptavidin-biotin complexSci. Rep., 5, 7906 (2015)

59.

Lei J., Zhou Y., Xie D., and Zhang Y., Mechanistic insights into a classic wonder drug-Aspirin, J. Am. Chem. Soc., 137(1), 70-73 (2015)

60.

Ozer, G., Collepardo-Guevara, R., & Schlick, T.. Forced unraveling of chromatin fibers with nonuniform linker DNA lengthsJ. Phys. Condens. Matter, 27(6), 064113 (2015)

61.

Li M., John Z. H. Zhang, and Xia F., Heterogeneous Elastic Network Model Improves Description of Slow Motions of Proteins in Solution, Chem. Phys. Lett., 618, 102-107 (2015)

62.

Lei, J., Zhou, Y., Xie, D., & Zhang, Y.. Mechanistic Insights into a Classic Wonder Drug-AspirinJ. Am. Chem. Soc., 137 (1), pp 70–73 (2015)

63.

Sirin, G. S., & Zhang, Y. How is acetylcholinesterase phosphonylated by soman? An ab initio QM/MM molecular dynamics studyJ. Phys. Chem. A, 118 (39), pp 9132–9139 (2014)

64.

Yu, T. Q., Chen, P. Y., Chen, M., Samanta, A., Vanden-Eijnden, E., & Tuckerman, M. Order-parameter-aided temperature-accelerated sampling for the exploration of crystal polymorphism and solid-liquid phase transitions J. Chem. Phys., 140(21), 214109 (2014)

65.

Li, M., Xu, W., John Z. H. Zhang, & Xia, F.  Combined effect of confinement and affinity of crowded environment on conformation switching of adenylate kinase. J Mol Model, 20: 2530 (2014)

66.

Shimshovitz A., Bacic Z., and Tannor D. J.,  The Von Neumann Basis in Non-Cartesian Coordinates: Application to Floppy Triatomic Molecules, J. Chem. Phys., 141, 2341061 (2014)

67.

Freudenthal B. D., Beard W. A., Perera L., Shock D.D., Kim T., Schlick T., and Wilson S. H., Uncovering the Polymerase-induced Cytotoxicity of an Oxidized Nucleotide, Nature 517, 635–639 (2015)

68.

Samanta A., Tuckerman M. E., Yu T. Q., Weinan E., Microscopic Mechanisms of Equilibrium Melting of a Solid, Science, 346, 729-732  (2014)

69.

Samanta A., Chen M., Yu T. Q., Tucherman M. E., and Weinan E., Sampling saddle points on a free energy surface, J. Chem. Phys., 140, 164109 (2014)

70.

Sodt A. J., Mei Y., König G., Tao P., Steele, R. P., Brooks, B. R., and Shao Y. H., Multiple Environment Single System Quantum Mechanical/molecular Mechanical (MESS-QM/MM) Calculations. 1. Estimation of Polarization Energies, J. Phys. Chem. A, 119 (9), pp 1511–1523 (2015)

71.

Duan L. L., Gao Y., Ji C. G., Mei Y., Zhang Q. G., Tang B., and John Z. H. Zhang, Energetics of Protein Backbone Hydrogen Bonds and Their Local Electrostatic Environment,  Sci. China Chem. 57: 1708 (2014)

72.

Li Y. X., John Z. H. Zhang, and Mei Y., "Molecular Dynamics Simulation of Protein Crystal with Polarized Protein-specific Force Field, J. Phys. Chem. B, 118, 12326−12335  (2014)

73.

D. Colognesi, A. Powers, M. Celli, M. Xu, Z. Bačić, and L. Ulivi., The HD Molecule in Small and Medium Cages of Clathrate Hydrates: Quantum Dynamics Studied by Neutron Scattering Measurements and Computation, J. Chem. Phys. 141, 134501 (2014)

74.

Minzhong Xu, Mónica Jiménez-Ruiz, Mark R. Johnson, Stéphane Rols, Shufeng Ye, Marina Carravetta, Mark S. Denning, Xuegong Lei, Zlatko Bačić, and Anthony J. Horsewill., Confirming a Predicted Selection Rule in Inelastic Neutron Scattering Spectroscopy: The Quantum Translator-Rotator H2 Entrapped Inside C60, Phys. Rev. Lett. 113, 123001 (2014)

75.

N. J. Zhou,Z. Y. Lu, Q. Wu and Y. K. Zhang.Improved Parameterization of Interatomic Potentials for Rare Gas Dimers with Density-based Energy Decomposition Analysis, J. Chem. Phys. 140, 214117 (2014)

76.

X. Xiao, N. Kallenbach, Y.K. Zhang., Peptide Conformation Analysis Using an Integrated Bayesian Approach, J. Chem. Theory Comput., 10 (9), 4152-4159 (2014)

77.

Liu J. F., He X., and John Z. H. Zhang, Novel Theoretically Designed HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors Derived from Nevirapine, J Mol Model, 20, 2451 (2014)

78.

T. Zhu, John Z. H. Zhang and X. He.Correction of Erroneously Packed Protein’s Side Chains in the NMR Structure Based on Ab Initio Chemical Shift Calculations, Phys.Chem.Chem.Phys., 16, 18163-18169 (2014)

79.

Ji, C.; Mei, Y.,  Some Practical Approaches to Treating Electrostatic Polarization of ProteinsAcc. Chem. Res., 47.9, 2795-2803 (2014)

80.

Sirin, G. S.; Zhang, Y. K.,  How Is Acetylcholinesterase Phosphonylated by Soman An Ab Initio QMMM Molecular Dynamics StudyJ. Phys. Chem. A., 118(39), 9132-9139 (2014)

81.

He, X.; Zhu, T.; Wang, X. W.; Liu, J. F.; John Z. H. Zhang, Fragment Quantum Mechanical Calculation of Proteins and Its ApplicationsAcc. Chem. Res., 47(9), 2748-2757 (2014)

82.

Mou, L. R., X. Y. Jia, Y. Gao, Y.X. Li, John Z. H. Zhang and Y. Mei, Folding simulation of Trp-cage utilizing a new AMBER compatible force field with coupled main chain torsionsJ. Theor. Comput. Chem. 13, 1450026 (2014)

83.

Wang, X. W.; Li, Y. X.; He, X.; Chen, S. D.; John Z. H. ZhangEffect of Strong Electric Field on the Conformational Integrity of Insulin. J. Phys. Chem. A 2013, 117, 6015−6023 (2014)

84.

Duan, L.L.; Ye Mei; Zhang, Q.G.; Bo Tang; John Z. H. ZhangProtein's Native Structure is Dynamically Stabilized by Electronic Polarization. J Theor Comput Chem,13(3):1440005 (2014)

85.

Ji, C. G., Mei, Y., & John Z. H. Zhang (2014, August). Protein structure and dynamics-polarization in MD simulation. In ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY (Vol. 248). 1155 16TH ST, NW, WASHINGTON, DC 20036 USA: AMER CHEMICAL SOC.

86.

Lin B. B.; Gao Y.; Li Y. X; John Z. H. Zhang; Mei Y., Implementing Electrostatic Polarization Cannot Fill the Gap between Experimental and Theoretical Measurements for the Ultrafast Fluorescence Decay of Myoglobin, J Mol Model, 20, 2189 (2014)

87.

Duan LL, Zhu T, Zhang QG, Tang B, John Z. H. ZhangElectronic Polarization Stabilizes Tertiary Structure Prediction of HP-36, J Mol Model, 20(4):2195 (2014)

88.

Jia, Xingyu; Zeng, Juan; John Z. H. Zhang; Mei, YeAccessing the Applicability of Polarized Protein-specific Charge in Linear Interaction Energy AnalysisJ. Comput. Chem. 35(9):737–747 (2014)

 

89.

Ondrej Marsalek, Pei-Yang Chen, Romain Dupuis, Magali Benoit, Merlin Méheut, Zlatko Bačić, and Mark E. Tuckerman​, Efficient Calculation of Free Energy Differences Associated with Isotopic Substitution Using Path-Integral Molecular Dynamics,  J. Chem. Theory Comput., 10 (4), 1440–1453​ (2014)

90.

Xiao, Xudong; Zhu, Tong; Ji, Chang G; John Z. H. ZhangDevelopment of an Effective Polarizable Bond Method for Biomolecular SimulationJ. Phys. Chem. B 117(48): 14885-93 (2013)

91.

Jia, Xiangyu; Wang, Xianwei; Liu, Jinfeng; John Z. H. Zhang; Mei, Ye; He, XiaoAn Improved Fragment-based Quantum Mechanical Method for Calculation of Electrostatic Solvation Energy of ProteinsJ. Chem. Phys. 139: 214104 (2013)

92.

Song, Jianing; Changge Ji; John Z. H. ZhangUnveiling the Gating Mechanism of ECF Transporter RibUScientific reports 3: 3566 (2013)