Publications

1.

Schneider, E., Dai, L., Topper, R. Q., Drechsel-Grau, C., and Tuckerman, M. E. Stochastic neural network approach for learning high-dimensional free energy surfaces. Phys. Rev. Lett. 119, 150601 (2017)

2.

Wang, M., Li, P., Jia, X., Liu, W., Shao, Yi., Hu, W., Zheng, J., Brooks, B. R., and Mei, Y. Efficient strategy for the calculation of solvation free energies in water and chloroform at the quantum mechanical/molecular mechanical level. J. Chem. Inf. Model. 57, 2476-2489 (2017)

3.

Brockherde, F., Vogt, L., Li, L., Tuckerman, M. E., Burke, K., and Müller, K. R. Bypassing the Kohn-Sham equations with machine learning. Nat. Commun. 8, 872 (2017)

4.

Dupuis, R., Benoit, M., Tuckerman, M. E., and 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, 1597-1605 (2017)

5.

Shtukenberg, A. G., Zhu, Q., Carter, D. J., Vogt, L., Hoja, J., Schneider, E., Song, H., Pokroy, B., Polishchuk, I., Tkatchenko, A., Oganov, A. R., Rohl, A. L., Tuckerman, M. E., and Kahr, B. Powder diffraction and crystal structure prediction identify four new coumarin polymorphs.  Chem. Sci. 8, 4926-4940 (2017)

6.

Sepehr, F., Liu, H., Luo, X., Bae, C., Tuckerman, M. E., Hickner, M. A., and Paddison, S. J. Mesoscale simulations of anion exchange membranes based on quaternary ammonium tethered triblock copolymers. Macromolecules. 50, 4397-4405 (2017)

7.

Bascom, G. D., Kim, T., and Schlick, T. Kilobase pair chromatin fiber contacts promoted by living-system-like DNA linker length distributions and nucleosome depletion. J. Phys. Chem. B. 121, 3882-3894 (2017)

8.

Bascom, G. and Schlick, T. Linking chromatin fibers to gene folding by hierarchical looping. Biophys. J. 112, 434-445 (2017)

9.

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

10.

Mu, H., Geacintov, N. E., Min, J. H., Zhang, Y., and 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, 1344-1354 (2017)

11.

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)

12.

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

13.

Jin, X., Zhang, J. Z. H., and He, X. Full QM calculation of RNA energy using electrostatically embedded generalized molecular fractionation with conjugate caps method. J. Phys. Chem. A. 121, 2503–2514 (2017)

14.

Yan, Y., Yang, M., Ji, C., and Zhang, J. Z. H. Interaction entropy for computational alanine scanning. J. Chem. Inf. Model. 57, 1112-1122, (2017)

15.

Liu, J., Qi L., Zhang, J. Z. H., and He, X. Fragment quantum mechanical method for large-sized ion-water clusters. J. Chem. Theory Comput. 13, 2021-2034 (2017)

16.

Sun, Z., Yan, Y. N., Yang, M., and Zhang, J. Z. H. Interaction entropy for protein-protein binding. J. Chem. Phys. 146, 124124 (2017)

17.

Gao, Y., Zhang, C., Zhang, J. Z. H., and Mei, Y. Evaluation of the coupled two-dimensional main chain torsional potential in modeling intrinsically disordered proteins. J. Chem. Inf. Model. 57, 267-274 (2017)

18.

Li, M. and Zhang, J. Z. H. Protein simulation using coarse-grained two-bead multipole force field with polarizable water models. J. Chem. Phys. 146, 065101 (2017)

19.

Duan, L. L., Zhu, T., Li, Y. C., Zhang, Q. G., and Zhang, J. Z. H. Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations. Sci. Rep. 7, 42223 (2017)

20.

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

21.

Felker, P. M. and Bačić, Z. Electric-dipole-coupled H2O@C60 dimer: Translation-rotation eigenstates from twelve-dimensional quantum calculations. J. Chem. Phys. 146, 084303 (2017)

22.

Wang, C. and Zhang, Y. Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest. J. Comput. Chem. 38, 169 - 177 (2017)

23.

Hou, X., Rooklin, D., Fang, H., and Zhang, Y. Resveratrol serves as a protein-substrate interaction stabilizer in human SIRT1 activation. Sci. Rep. 6, 38186 (2016)

24.

Zhou, Y., Wang, S., Li, Y., and Zhang, Y. Born-Oppenheimer ab initio QM/MM molecular dynamics simulations of enzyme reactions. Methods Enzymol. 577, 105-118 (2016)

25.

Glover, W. J. and Schwartz, B. J. Short-range electron correlation stabilizes non-cavity solvation of the hydrated electron. J. Chem. Theory Comput. 12, 5117–5131 (2016)

26.

Casey, J. R., Schwartz, B. J., and Glover W. J. Free energies of cavity and noncavity hydrated electrons near the instantaneous air/water interface. J. Phys. Chem. Lett. 7, 3192−3198 (2016)

27.

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

28.

Felker, P. M. and Bačić, Z. Translation-rotation states of H2 in C60: New insights from a perturbation-theory treatment. J. Chem. Phys. 145, 084310 (2016)

29.

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

30.

Liu, Y., Yu, Z., Luo, Z., Zhang, J. Z. H., Liu, L., and Xia, F. Mechanistic investigation of aromatic C (sp2)–H and alkyl C (sp3)–H bond insertion by gold carbenes. J. Phys. Chem. A. 120, 1925-1932 (2016)

31.

Li, M., Zhang, J. Z. H., and Xia, F. Constructing optimal coarse-grained sites of huge biomolecules by fluctuation maximization. J. Chem. Theory Comput., 12, 2091-2100 (2016)

32.

Duan, L. L., Liu, X., and Zhang, J. Z. H. Interaction entropy: A new paradigm for highly efficient and reliable computation of protein–ligand binding free energy. J. Am. Chem. Soc. 138, 5722–5728 (2016)

33.

Liu, X., Liu, J. F., Zhu, T., Zhang, L. J., He, X., and Zhang, J. Z. H. PBSA_E: A PBSA-based free energy estimator for protein–ligand binding affinity. J. Chem. Inf. Model. 56, 854-861 (2016)

34.

Li, M., Zhang, J. Z. H., and Xia, F. A new algorithm for construction of coarse-grained sites of large biomolecules. J. Comput. Chem. 37, 795–804 (2016)

35.

Jia, X. Y., Wang, M. T., Shao, Y. H., König, G., Brooks, B. R., Zhang, J. Z. H., and Mei, Y. Calculations of solvation free energy through energy reweighting from molecular mechanics to quantum mechanics. J. Chem. Theory Comput. 12, 499–511 (2016)

36.

Felker, P. M. and Bačić, Z. Communication: Quantum six-dimensional calculations of the coupled translation-rotation eigenstates of H2O@C60. J. Chem. Phys. 144, 201101 (2016)

37.

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

38.

Zhou, Y., Xie, D., and Zhang, Y. Amide rotation hindrance predicts proteolytic resistance of cystine-knot peptides. J. Phys. Chem. Lett. 7, 1138-1142 (2016)

39.

Fu, I., Cai, Y., Zhang, Y., Geacintov, N. E., and Broyde, S. 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)

40.

Powers, A., Marsalek, O., Xu, M., Ulivi, L., Colognesi, D., Tuckerman, M. E., and Bačić, Z. Impact of the condensed-phase environment on the translation-rotation eigenstates and spectra of a hydrogen molecule in clathrate hydrates. J. Phys. Chem. Lett. 7, 308–313 (2016)

41.

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

42.

Jia, X. Y., Mei, Y., Zhang, J. Z. H., and Mo, Y. Hybrid QM/MM study of FMO complex with polarized proteinspecific charge. Sci. Rep. 5, 17096 (2015)

43.

Liu, J. F., Zhu, T., Wang, X. W., He, X., and Zhang, J. Z. H. Quantum fragment based ab initio molecular dynamics for proteins. J. Chem. Theory Comput. 11, 5897−5905 (2015)

44.

Li, Y., Zhang, J. Z. H., and Mei, Y. Molecular dynamics simulation of protein crystal with polarized protein-specific charge. Biophys. J. 108, 160a (2015)

45.

Gao, Y., Li, Y., Zhang, J. Z. H., and Mei, Y. A coupled two-dimensional main chain torsional potential for protein dynamics. Biophys. J. 108, 159a-160a (2015)

46.

Gao, Y., Li, Y., Mou, L., Lin, B., Zhang, J. Z. H., and Mei, Y. Correct folding of an alpha-helix and a beta-hairpin using a polarized 2D torsional potential. Sci. Rep. 5, 10359 (2015)

47.

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

48.

Gong, W., Wu, R., and Zhang, Y. Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An ab initio QM/MM molecular dynamics study. J. Comput. Chem. 36, 2228-2235 (2015)

49.

Swails, J., Zhu, T., He, X., and Case, D. A. AFNMR: Automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. J. Biomol. NMR. 63, 125-139 (2015)

50.

Chen, J., Wang, X., Zhu, T., Zhang, Q., and Zhang, J. Z. H. 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. J. Chem. Inf. Model. 55, 1903–1913 (2015)

51.

Xu, M., Ye, S., and Bačić, Z. General selection rule in the inelastic neutron scattering spectroscopy of a diatomic molecule confined inside a near-spherical nanocavity. J. Phys. Chem. Lett. 6, 3721–3725 (2015)

52.

Mu, H., Geacintov, N. E., Zhang, Y., and Broyde, S. Recognition of damaged DNA for nucleotide excision repair: A correlated motion mechanism with a mismatched cis-syn thymine dimer lesion. Biochemistry. 54, 5263-5267 (2015)

53.

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

54.

Rooklin, D., Wang, C., Katigbak, J., Arora, P. S., and Zhang, Y. AlphaSpace: Fragment-centric topographical mapping to target protein–protein interaction interfaces. J. Chem. Inf. Model. 55, 1585–1599 (2015)

55.

Mei, Y., Simmonett, A. C., Pickard, F. C., DiStasio, R., Brooks, B. R., and Shao, Y.  Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions. J. Phys. Chem. A. 119, 5865–5882 (2015)

56.

Wang, X., Ji, C., and Zhang, J. Z. H. Glycosylation modulates human CD2-CD58 adhesion via conformational adjustment. J. Phys. Chem. B. 119, 6493–6501 (2015)

57.

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

58.

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

59.

Gao, Y., Li, Y., Mou, L., Hu, W., Zheng, J., Zhang, J. Z. H., and Mei, Y. Coupled two-dimensional main-chain torsional potential for protein dynamics II: Performance and validation. J. Phys. Chem. B. 119, 4188–4193 (2015)

60.

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

61.

Song, J., Li Y., Ji, C., and Zhang, J. Z. H. Functional loop dynamics of the streptavidin-biotin complex. Sci. Rep. 5, 7906 (2015)

62.

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

63.

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

64.

Li, M., Zhang, J. Z. H., and Xia, F. Heterogeneous elastic network model improves description of slow motions of proteins in solution. Chem. Phys. Lett. 618, 102-107 (2015)

65.

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

66.

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

67.

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

68.

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

69.

Shimshovitz, A., Bačić, Z., and Tannor, D. J. The von Neumann basis in non-Cartesian coordinates: Application to floppy triatomic molecules. J. Chem. Phys. 141, 2341061 (2014)

70.

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)

71.

Samanta, A., Tuckerman, M. E., Yu, T. Q. Weinan, E. Microscopic mechanisms of equilibrium melting of a solid. Science. 346, 729-732 (2014)

72.

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

73.

Sodt, A. J., Mei, Y., König, G., Tao, P., Steele, R. P., Brooks, B. R., and Shao, Y. Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies. J. Phys. Chem. A. 119, 1511–1523 (2015)

74.

Duan, L. L., Gao, Y., Ji, C. G., Mei, Y., Zhang, Q. G., Tang, B., and Zhang, J. Z. H. Energetics of protein backbone hydrogen bonds and their local electrostatic environment. Sci. China Chem. 57, 1708 (2014)

75.

Li, Y., Zhang, J. Z. H., and Mei, Y. Molecular dynamics simulation of protein crystal with polarized protein-specific force field. J. Phys. Chem. B. 118, 12326−12335 (2014)

76.

Colognesi, D., Powers, A., Celli, M., Xu, M., Bačić, Z., and Ulivi, L. 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)

77.

Xu, M., Jiménez-Ruiz, M., Johnson, M. R., Rols, S., Ye, S., Carravetta, M., Denning, M. S., Lei, X., Bačić, Z., and Horsewill, A. J. Confirming a predicted selection rule in inelastic neutron scattering spectroscopy: The quantum translator-rotator H2 entrapped inside C60. Phys. Rev. Lett. 113, 123001 (2014)

78.

Zhou, N., Lu, Z., Wu, Q., and Zhang, Y. Improved parameterization of interatomic potentials for rare gas dimers with density-based energy decomposition analysis. J. Chem. Phys. 140, 214117 (2014)

79.

Xiao, X., Kallenbach, N., and Zhang, Y. Peptide conformation analysis using an integrated Bayesian approach. J. Chem. Theory Comput. 10, 4152-4159 (2014)

80.

Liu, J., He, X., and Zhang, J. Z. H. Novel theoretically designed HIV-1 non-nucleoside reverse transcriptase inhibitors derived from nevirapine. J. Mol. Model. 20, 2451 (2014)

81.

Zhu, T., Zhang, J. Z. H., and He, X. 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)

82.

Ji, C. and Mei, Y. Some practical approaches to treating electrostatic polarization of proteins. Acc. Chem. Res. 47, 2795-2803 (2014)

83.

Sirin, G. S. and Zhang, Y. How is acetylcholinesterase phosphonylated by soman? An ab initio QM/MM molecular dynamics study. J. Phys. Chem. A. 118, 9132-9139 (2014)

84.

He, X., Zhu, T., Wang, X., Liu, J., and Zhang, J. Z. H. Fragment quantum mechanical calculation of proteins and its applications. Acc. Chem. Res. 47, 2748-2757 (2014)

85.

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

86.

Wang, X., Li, Y., He, X., Chen, S., and Zhang, J. Z. H. Effect of strong electric field on the conformational integrity of insulin. J. Phys. Chem. A. 117, 6015−6023 (2014)

87.

Duan, L. L., Mei, Y., Zhang, Q. G., Tang, B., and Zhang, J. Z. H. Protein's native structure is dynamically stabilized by electronic polarization. J. Theor. Comput. Chem. 13, 1440005 (2014)

88.

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.

89.

Lin, B., Gao, Y., Li, Y., Zhang, J. Z. H., and 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)

90.

Duan, L. L., Zhu, T., Zhang, Q. G., Tang, B., Zhang, J. Z. H. Electronic polarization stabilizes tertiary structure prediction of HP-36. J. Mol. Model. 20, 2195 (2014)

91.

Jia, X., Zeng, J., Zhang, J. Z. H., and Mei, Y. Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis. J. Comput. Chem. 35, 737–747 (2014)

92.

Marsalek, O., Chen, P., Dupuis, R., Benoit, M., Méheut, M., Bačić, Z., and Tuckerman​, M. E. Efficient calculation of free energy differences associated with isotopic substitution using path-integral molecular dynamics. J. Chem. Theory Comput. 10, 1440–1453​ (2014)

93.

Xiao, X., Zhu, T., Ji, C. G., and Zhang, J. Z. H. Development of an effective polarizable bond method for biomolecular simulation. J. Phys. Chem. B. 117, 14885-93 (2013)

94.

Jia, X., Wang, X., Liu, J., Zhang, J. Z. H., Mei, Y., and He, X. An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins. J. Chem. Phys. 139, 214104 (2013)

95.

Song, J., Ji, C., and Zhang, J. Z. H. Unveiling the gating mechanism of ECF transporter RibU. Sci. rep. 3, 3566 (2013)