Publications

251.	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)
252.	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)
253.	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)
254.	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)
255.	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)
256.	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)
257.	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)
258.	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)
259.	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)
260.	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)
261.	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)
262.	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)
263.	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)
264.	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)
265.	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)
266.	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)
267.	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)
268.	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)
269.	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)
270.	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)
271.	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)
272.	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)
273.	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)
274.	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)
275.	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)
276.	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)
277.	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)
278.	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)
279.	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)
280.	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)
281.	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)
282.	Curchod, B. F. E., Glover, W. J., and Martínez, T. J. SSAIMS—stochastic-selection ab initio multiple spawning for efficient nonadiabatic molecular dynamics. J. Phys. Chem. A. 124, 6133–6143 (2020)
283.	Tong, Z., Gao, X., Cheung, M. S., Dunietz, B. D., Geva, E., and Sun, X. Charge transfer rate constants for the carotenoid-porphyrin-C60 molecular triad dissolved in tetrahydrofuran: The spin-boson model vs the linearized semiclassical approximation. J. Chem. Phys. 153, 044105 (2020)
284.	Tong, Z., Videla, P. E., Jung, K. A., Batista, V. S., and Sun, X. Two-dimensional Raman spectroscopy of Lennard-Jones liquids via ring-polymer molecular dynamics. J. Chem. Phys. 153, 034117 (2020)
285.	Long, Z., Atsango, J. A., Napoli, J. A., Markland, T. E., and Tuckerman, M. E. Elucidating the proton transport pathways in liquid imidazole with first-principles molecular dynamics. J. Phys. Chem. Lett. 11, 6156–6163 (2020)
286.	Luo, X., Liu, H., Bae, C., Tuckerman, M. E., Hickner, M. A., and Paddison, S. J. Mesoscale simulations of quaternary ammonium-tethered triblock copolymers: Effects of the degree of functionalization and styrene content. J. Phys. Chem. C. 124, 16315–16323 (2020)
287.	Zelovich, T. and Tuckerman, M. E. Water layering affects hydroxide diffusion in functionalized nanoconfined environments. J. Phys. Chem. Lett. 11, 5087–5091 (2020)
288.	Zhang, Y., Poe, D., Heroux, L., Squire, H., Doherty, B. W., Long, Z., Dadmun, M., Gurkan, B., Tuckerman, M. E., and Maginn, E. J. Liquid structure and transport properties of the deep eutectic solvent ethaline. J. Phys. Chem. B. 124, 5251–5264 (2020)
289.	Li, C., Chin, C.-H., Zhu, T., Zhang, J. Z. H. An ab initio/RRKM study of the reaction mechanism and product branching ratios of CH₃OH⁺ and CH₃OH⁺⁺ dissociation. J. Mol. Struct. 1217, 128410 (2020)
290.	Bogojeski, M., Vogt-Maranto, L., Tuckerman, M. E., Müller, K.-R., and Burke, K. Quantum chemical accuracy from density functional approximations via machine learning. Nat. Commun. 11, 5223 (2020)
291.	Zha, J., Ding, T., Chen, J., Wang, R., Gao, G., and Xia, F. Reaction mechanism of CO₂ and styrene oxide catalyzed by ionic liquids: A combined DFT calculation and experimental study. J. Phys. Chem. A. 124, 7991–7998 (2020)
292.	Hu, Z., Tong, Z., Cheung, M. S., Dunietz, B. D., Geva, E., and Sun, X. Photoinduced charge transfer dynamics in the carotenoid–porphyrin–C₆₀ triad via the linearized semiclassical nonequilibrium Fermi’s golden rule. J. Phys. Chem. B. 124, 9579–9591 (2020)
293.	Han, J., Zhang, P., Aksu, H., Maiti, B., Sun, X., Geva, E., Dunietz, B. D., and Cheung, M. S. On the interplay between electronic structure and polarizable force fields when calculating solution-phase charge-transfer rates. J. Chem. Theory Comput. 16, 6481–6490 (2020)
294.	Wang, B., Li, C., Jia, X., Zhu, T., and Zhang, J. Z. H. An approach to computing solvent reorganization energy. J. Chem. Theory Comput. 16, 6513–6519 (2020)
295.	Shan, J. and Ji, C. MolOpt: A web server for drug design using bioisosteric transformation. Curr. Comput. Aided Drug Des. 16, 460 - 466 (2020)
296.	Zhang, Y., Cao, Z., Zhang, J. Z. H., and Xia, F. Double-well ultra-coarse-grained model to describe protein conformational transitions. J. Chem. Theory Comput. 16, 6678–6689 (2020)
297.	Du, J., Li, W., Liu, B., Zhang, Y., Yu, J., Hou, X., and Fang, H. An in silico mechanistic insight into HDAC8 activation facilitates the discovery of new small-molecule activators. Bioorg. Med. Chem. 28, 115607 (2020)
298.	Chin, C.-H., Zhu, T., and Zhang, J. Z. H. Reaction mechanism and product branching ratios of OH+C2H3F reaction: A theoretical study. Chin. J. Chem. Phys. 33, 203 (2020)
299.	Li, M., Lu, W.C., and Zhang, J. Z. H. A three-point coarse-grained model of five-water cluster with permanent dipoles and quadrupoles. Phys. Chem. Chem. Phys. 22, 26289-26298 (2020)
300.	Zeng, J., Cao, L., Xu, M., Zhu, T., and Zhang. J. Z. H. Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation. Nat. Commun. 11, 5713 (2020)

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