Publications

251.

Song, H., Vogt-Maranto, L., Wiscons, R., Matzger, A. J., and Tuckerman, M. E. Generating cocrystal polymorphs with information entropy driven by molecular dynamics-based enhanced sampling. J. Phys. Chem. Lett. 11, 9751–9758 (2020)

252.

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)

253.

Abreu, C. R. A. and Tuckerman, M. E. Molecular dynamics with very large time steps for the calculation of solvation free energiesJ. Chem. Theory Comput. 16, 7314–7327 (2020)

254.

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)

255.

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)

256.

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 contentJ. Phys. Chem. C. 124, 16315–16323 (2020)

257.

Zelovich, T. and Tuckerman, M. E. Water layering affects hydroxide diffusion in functionalized nanoconfined environmentsJ. Phys. Chem. Lett. 11, 5087–5091 (2020)

258.

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 ethalineJ. Phys. Chem. B. 124, 5251–5264 (2020)

259.

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++ dissociationJ. Mol. Struct. 1217, 128410 (2020)

260.

Bogojeski, M., Vogt-Maranto, L., Tuckerman, M. E., Müller, K.-R., and Burke, K. Quantum chemical accuracy from density functional approximations via machine learningNat. Commun. 11, 5223 (2020)

261.

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

262.

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)

263.

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)

264.

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)

265.

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

266.

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 setsJ. Chem. Phys. 152, 014108 (2020)

267.

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 simulationsInt. Rev. Phys. Chem. 39, 425-463 (2020)

268.

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)

269.

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)

270.

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 pocketsEur. J. Med. Chem. 190, 112131 (2020)

271.

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 affinityNanoscale. 12, 10737-10750 (2020)

272.

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)

273.

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)

274.

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 basesJ. Chem. Phys. 152, 124103 (2020)

275.

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

276.

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)

277.

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)

278.

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

279.

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 systemPhys. Rev. Appl. 13, 054075 (2020)

280.

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

281.

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)

282.

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)

283.

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

284.

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)

285.

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 spectroscopyJ. Phys. Chem. B. 124, 2560-2567 (2020)

286.

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

287.

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)

288.

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)

289.

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 spectraAngew. Chem. Int. Ed. 59, 2-8 (2020)

290.

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)

291.

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)

292.

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)

293.

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)

294.

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)

295.

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)

296.

Tian, S., Ji, C., and Zhang, J. Z. H. Molecular basis of SMAC-XIAP binding and the effect of electrostatic polarizationJ. Biomol. Struct. Dyn. 39, 1588-1599 (2021)

297.

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)

298.

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 configurationACS Catal. 10, 5949–5958 (2020)

299.

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)

300.

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)

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