Publications

Huang, M., Luo, Z., Zhu, T., Chen, J., Zhang, J. Z., and Xia, F. A theoretical study of the substituent effect on reactions of amines, carbon dioxide and ethylene oxide catalyzed by binary ionic liquids. RSC Adv. 7, 51521-51527 (2017) 

Sun, Z., Wang, X., and Zhang, J. Z. H. Protonation-dependent base flipping in the catalytic triad of a small RNA. Chem. Phys. Lett. 684, 239-244 (2017)

Sun, Z., Zhu, T., Wang, X., Mei, Y., and Zhang, J. Z. H. Optimization of convergence criteria for fragmentation methods. Chem. Phys. Lett. 687, 163-170 (2017)

Liu, F., Yang, Z., Yu, Y., Mei, Y., and Houk, K. N. Bimodal Evans–Polanyi relationships in dioxirane oxidations of sp3 C–H: Non-perfect synchronization in generation of delocalized radical intermediates. J. Am. Chem. Soc. 139, 16650-16656 (2017)

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)

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

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)

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)

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)

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)

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)

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)

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)

Rao, S. S. P., Huang, S. C., Brian, G. S. H., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K. R., Sanborn, A. L., Johnstone, S. E., Bascom, G. D., Bochkov, I. D., Huang, X., Shamim, M. S., Shin, J., Turner, D., Ye, Z., Omer, A. D., Robinson, J. T., Schlick, T., Bernstein, B. E., Casellas, R., Lander, E. S., and Aiden, E. L. Cohesin loss eliminates all loop domains. Cell. 171, 305-320.e24 (2017)

Jain, S. and Schlick, T. F-RAG: Generating atomic coordinates from RNA graphs by fragment assembly. J. Mol. Biol. 429, 3587-3605 (2017)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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