Publications

 Jin, X., Glover, W. J., and He, X. Fragment quantum mechanical method for excited states of proteins: Development and application to the green fluorescent protein. J. Chem. Theory Comput. 16, 5174–5188 (2020)

Felker, P. M. and Bačić, Z. H₂O–CO and D₂O–CO complexes: Intra- and intermolecular rovibrational states from full-dimensional and fully coupled quantum calculations. J. Chem. Phys. 153, 074107 (2020)

Xu, M., Felker, P. M., and Bačić, Z. Light molecules inside the nanocavities of fullerenes and clathrate hydrates: Inelastic neutron scattering spectra and the unexpected selection rule from rigorous quantum simulations. Int. Rev. Phys. Chem. 39, 425-463 (2020)

Zhang, W., Liu, J., Jin, X., Gu, X., Zeng, X. C., He, X., and Li, H. Quantitative prediction of aggregation‐induced emission: A full quantum mechanical approach to the optical spectra. Angew. Chem. Int. Ed. 59, 2-8 (2020)

Liu, J. and He, X. Fragment-based quantum mechanical approach to biomolecules, molecular clusters, molecular crystals and liquids. Phys. Chem. Chem. Phys. 22, 12341-12367 (2020)

Huang, L., Han, Y., Liu, J., He, X., and Li, J. Ab initio prediction of the phase transition for solid ammonia at high pressures. Sci. Rep. 10, 7546 (2020)

Tinnin, J., Bhandari, S., Zhang, P., Aksu, H., Maiti, B., Geva, E., Dunietz, B. D., Sun, X., and Cheung, M. S. Molecular-level exploration of the structure-function relations underlying interfacial charge transfer in the subphthalocyanine/C₆₀ organic photovoltaic system. Phys. Rev. Appl. 13, 054075 (2020)

Duan, G., Ji, C., and Zhang, J. Z. H. Developing an effective polarizable bond method for small molecules with application to optimized molecular docking. RSC Adv. 10, 15530-15540 (2020)

Huang, K., Luo, S., Cong, Y., Zhong, S., Zhang, J. Z. H., and Duan, L. An accurate free energy estimator: based on MM/PBSA combined with interaction entropy for protein–ligand binding affinity. Nanoscale. 12, 10737-10750 (2020)

Shan, J., Pan, X., Wang, X., Xiao, X., and Ji, C. FragRep: A web server for structure-based drug design by fragment replacement. J. Chem. Inf. Model. 60, 5900–5906 (2020)

Zhang, B., Ma, Y., Jin, X., Wang, Y., Suo, B., He, X., and Jin, Z. GridMol2. 0: Implementation and application of linear‐scale quantum mechanics methods and molecular visualization. Int. J. Quantum Chem. 120, e26402 (2020)

Zha, J., Zhang, Y., Xia, K., Gräter, F., and Fei Xia. Coarse-grained simulation of mechanical properties of single microtubules with micrometer length. Front. Biosci. 7, 632122 (2020)

Cendagorta, J. R., Tolpin, J., Schneider, E., Topper, R. Q., and Tuckerman, M. E. Comparison of the performance of machine learning models in representing high-dimensional free energy surfaces and generating observables. J. Phys. Chem. B. 124, 3647–3660 (2020)

Guo, J., Yang, L., Gao, Z., Zhao, C., Mei, Y., and Song, Y.-Y. Insight of MOF environment-dependent enzyme activity via MOFs-in-nanochannels configuration. ACS Catal. 10, 5949–5958 (2020)

Tong, Z., Huai, Z., Mei, Y., and Mo, Y. Reproducing the low-temperature excitation energy transfer dynamics of phycoerythrin 545 light-harvesting complex with a structure-based model Hamiltonian. J. Chem. Phys. 152, 135101 (2020)

Li, X., Cong, Y., Ma, M., You, Z.-N., Gao, B., Zhang, J. Z. H., and Zhang, L. An energy optimization strategy based on the perfect conformation of prolyl endopeptidase for improving catalytic efficiency. J. Agric. Food Chem. 68, 5129–5137 (2020)

Liu, L., Gao, H., Yang, S.-Q., Chen, X.-C., Lu, Y., Liu, Y., and Xia, F. Ir-catalyzed tandem hydroformylation-transfer hydrogenation of olefins with (trans-/cis-)formic acid as hydrogen source in presence of 1,10-phenanthroline. J. Catal. 385, 183-193 (2020)

Huang, L., Han, Y., He, X., and Li, J. Ab initio-enabled phase transition prediction of solid carbon dioxide at ultra-high temperatures. RSC Adv. 10, 236-243 (2020)

Wang, Z., Han, Y., Li, J., He, X. Combining the fragmentation approach and neural network potential energy surfaces of fragments for accurate calculation of protein energy. J. Phys. Chem. B. 124, 3027-3035 (2020)

Hou, X., Sun, J., Ge, L., Liang, X., Li, K., Zhang, Y., and Fang, H. Inhibition of striatal-enriched protein tyrosine phosphatase by targeting computationally revealed cryptic pockets.  Eur. J. Med. Chem. 190, 112131 (2020)

Katigbak, J., Li, H., Rooklin, D., and Zhang, Y. AlphaSpace 2.0: Representing concave biomolecular surfaces using β-clusters. J. Chem. Inf. Model. 60, 1494-1508 (2020)

Sadek, J., Wuo, M. G., Rooklin, D., Hauenstein, A., Hong, S. H., Gautam, A., Wu, H., Zhang, Y., Cesarman, E., and Arora, P. S. Modulation of virus-induced NF-κB signaling by NEMO coiled coil mimics. Nat. Commun. 11, 1786 (2020)

Sridhara, A., Farra, S. E., Portellab, G., Schlick, T., Orozco, M., and Collepardo-Guevara, R. Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry. Proc. Natl. Acad. Sci. U.S.A. 117, 7216–7224 (2020)

Myers, C. G., Olins, D. E., Olins, A. L., and Schlick, T. Mesoscale modeling of nucleosome-binding antibody PL2-6: Mono- versus bivalent chromatin complexes. Biophys. J. 118, 2066-2076 (2020)

Huang, D., Tian, S., Qi, Y., and Zhang, J. Z. H. Binding modes of small-molecule inhibitors to the EED pocket of PRC2. ChemPhysChem. 21, 263-271 (2020)

Li, M., Teng, B., and Zhang, J. Z. H. Atomic-level reconstruction of biomolecules by a rigid-fragment- and local-frame-based (RF-LF) strategy. J. Mol. Model. 26, 31 (2020)

Wang, R., Cong, Y., Li, M., Bao, J., Qi, Y., and Zhang, J. Z. H. Molecular mechanism of selective binding of NMS-P118 to PARP-1 and PARP-2: A computational perspective. Front. Mol. Biosci. 7, 50 (2020)

Wang, B., Qi, Y., Gao, Y., and Zhang, J. Z. H. A method for efficient calculation of thermal stability of proteins upon point mutations.  Phys. Chem. Chem. Phys. 22, 8461-8466 (2020)

Cong, Y., Huang, K., Li, Y., Zhong, S., Zhang, J. Z. H., and Duan, L. Entropic effect and residue specific entropic contribution to the cooperativity in streptavidin–biotin binding. Nanoscale. 12, 7134-7145 (2020)

Li, C., Wang, B., Jia, X., and Zhang, J. Z. H. Efficient calculation of excess free energy of pure and mixed alcohol solutions. Chem. Phys. Lett. 749, 137397 (2020)

Fellah, N., Shtukenberg, A. G., Chan, E. J., Vogt-Maranto, L., Xu, W., Li, C., Tuckerman, M. E., Kahr, B., and Ward, M. D. Disorderly conduct of benzamide IV: Crystallographic and computational analysis of high entropy polymorphs of small molecules. Cryst. Growth Des. 20, 2670-2682 (2020)

Cong, Y., Duan, L., Huang, K., Bao, J., and Zhang, J. Z. H. Alanine scanning combined with interaction entropy studying the differences of binding mechanism on HIV-1 and HIV-2 proteases with inhibitor. J. Biomol. Struct. Dyn. 39, 1588-1599 (2020)

Li, Z., Bao, J., Qi, Y., and Zhang, J. Z. H. Computational approaches to studying methylated H4K20 recognition by DNA repair factor 53BP1. Phys. Chem. Chem. Phys. 22, 6136-6144 (2020)

Jain, S., Zhu, Q., Paz, A. S. P., and Schlick, T. Identification of novel RNA design candidates by clustering the extended RNA-As-Graphs library. BBA General Subjects. 1864, 129534 (2020)

Xu, R., Hu, Z., Wang, X., Liu, Y., Zhou, Z., Xu, J., Sun, Z., Sun, H., and Chen, J. Intramolecular charge transfer in 5-halogen cytidines revealed by femtosecond time-resolved spectroscopy. J. Phys. Chem. B. 124, 2560-2567 (2020)

Li, F., Zhang, J. Z., and Xia, F. How CuCl and CuCl₂ insert into C–N bonds of diazo compounds: An electronic structure and mechanistic study. J. Phys. Chem. A. 124, 2029-2035 (2020)

Qi, Y. and Zhang, J. Z. H. DenseCPD: Improving the accuracy of neural-network-based computational protein sequence design with DenseNet. J. Chem. Inf. Model. 60, 1245-1252 (2020)

Felker, P. M. and Bačić, Z. Benzene–H₂O and benzene–HDO: Fully coupled nine-dimensional quantum calculations of flexible H₂O/HDO intramolecular vibrational excitations and intermolecular states of the dimers, and their infrared and Raman spectra using compact bases. J. Chem. Phys. 152, 124103 (2020)

Jain, S., Tao, Y., and Schlick, T. Inverse folding with RNA-As-Graphs produces a large pool of candidate sequences with target topologies. J. Struct. Biol. 209, 107438 (2020)

Cendagorta, J. R., Shen, H., Bačić, Z., and Tuckerman, M. E. Enhanced sampling path integral methods using neural network potential energy surfaces with application to diffusion in hydrogen hydrates. Adv. Theory Simul. 4, 2000258 (2020)

Gao, Z., Bao, J., Shi, S., Zhang, X., Gao, Y., and Zhu, T. Effect of mutations on drug resistance of smoothened receptor toward inhibitors probed by molecular modeling. Chem. Phys. Lett. 741, 137126 (2020)

Liu J., He X. (2020) QM Implementation in Drug Design: Does It Really Help? In: Heifetz A. (eds) Quantum Mechanics in Drug Discovery. Methods in Molecular Biology, vol 2114. Humana, New York, NY

Xu, J., Liu, J., Liu, J., Hu, W., He, X., and Li, J. Phase transition of ice at high pressures and low temperatures. Molecules. 25, 486 (2020)

Wang, Y., Verma, P., Zhang, L., Li, Y., Liu, Z., Truhlar, D. G., and He, X. M06-SX screened-exchange density functional for chemistry and solid-state physics. Proc. Natl. Acad. Sci. U.S.A. 117, 2294-2301 (2020)

Glover, W. J. and Schwartz, B. J. The fluxional nature of the hydrated electron: Energy and entropy contributions to aqueous electron free energies. J. Chem. Theory Comput. 16, 1263-1270 (2020)

Zeng, J., Cao, L., Chin, C.-H., Ren, H., Zhang, J. Z. H., and Zhu, T. ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations. Phys. Chem. Chem. Phys. 22, 683-691 (2020)

Sun, Z., Wang, X., and Zhang, J. Z. H. Theoretical understanding of the thermodynamics and interactions in transcriptional regulator TtgR–ligand binding. Phys. Chem. Chem. Phys. 22, 1511-1524 (2020)

Meng, G., Tariq, M., Jain, S., Elmetwaly, S., and Schlick, T. RAG-Web: RNA structure prediction/design using RNA-As-Graphs. Bioinformatics. 36, 647–648 (2020)

Felker, P. M. and Bačić, Z. Flexible water molecule in C₆₀: Intramolecular vibrational frequencies and translation-rotation eigenstates from fully coupled nine-dimensional quantum calculations with small basis sets. J. Chem. Phys. 152, 014108 (2020)

Wang, T., Su, X., Zhang, X., Nie, X., Huang, L., Zhang, X., Sun, X., Luo, Y., and Zhang, G. Aggregation-induced dual-phosphorescence from organic molecules for non-doped light-emitting diodes. Adv. Mater. 31, 1904273 (2019)