Publications

101.

Xiong, D., Zhao, X., Luo, S., Cong, Y., Zhang, J. Z. H., and Duan, L. Immune escape mechanisms of SARS-CoV-2 delta and omicron variants against two monoclonal antibodies that received emergency use authorizationJ. Phys. Chem. Lett. 13, 6064–6073 (2022)

102.

Zhang, H., Saravanan, K. M., Yang, Y., Wei, Y., Yi, P., and Zhang, J. Z. H. Generating and screening de novo compounds against given targets using ultrafast deep learning models as core componentsBrief. Bioinform. 23, bbac226 (2022)

103.

Chen, S., Ding, X., Sun, C. Wang, F., He, X., Watts, A., and Zhao X. Archaeal Lipids Regulating the Trimeric Structure Dynamics of Bacteriorhodopsin for Efficient Proton Release and UptakeInt. J. Mol. Sci. 23, 6913 (2022)

104.

Zhang, C., Miao, Y., Feng, Y., Wang, J., Tian, Z., Dong, J., ... and Zhang, L. Umami polypeptide detection system targeting the human T1R1 receptor and its taste-presenting mechanismBiomaterials 287, 121660 (2022)

105.

Yang, C., Chen, E. A., and Zhang, Y. Protein–ligand docking in the machine-learning eraMolecules 27, 4568 (2022)

106.

Zelovich, T., Hensen, T., and Tuckerman, M. E. A Green’s function approach for determining surface induced broadening and shifting of molecular energy levelsNano Lett. 22, 9854–9860 (2022)

107.

Guo, X.-K. and Zhang, Y. CovBinderInPDB: A structure-based covalent binder databaseJ. Chem. Inf. Model. 62, 6057–6068 (2022)

108.

Xiong, L., He, X., and Yang, J. Origin of humidity influencing the excited state electronic properties of silicon quantum dot based light-emitting diodesPhys. Chem. Chem. Phys. 24, 28222-28231 (2022)

109.

Jiang, Y., Cai, Z., Yuan, Q., Cao, W., Hu, Z., Sun, H., Wang, X.-B., and Sun, Z. Highly structured water networks in microhydrated dodecaborate clustersJ. Phys. Chem. Lett. 13, 11787–11794 (2022)

110.

Felker, P. M. and Bačić, Z. Intermolecular vibrational states of HF trimer from rigorous nine-dimensional quantum calculations: Strong coupling between intermolecular bending and stretching vibrations and the importance of the three-body interactionsJ. Chem. Phys. 157, 194103 (2022)

111.

Liu, Z., Xu, W., Tuckerman, M. E., and Sun, X. Imaginary-time open-chain path-integral approach for two-state time correlation functions and applications in charge transferJ. Chem. Phys. 157, 114111 (2022)

112.

Hu, Z., Liu, Z., and Sun, X. Effects of heterogeneous protein environment on excitation energy transfer dynamics in the Fenna–Matthews–Olson complexJ. Phys. Chem. B 126, 9271–9287 (2022)

113.

Shakiba, M., Smith, B., Li, W., Dutra, M., Jain, A., Sun, X., Garashchuk, S., and Akimov, A. Libra: A modular software library for quantum nonadiabatic dynamicsSoftware Impacts 14, 100445 (2022)

114.

Bai, Y., Vogt-Maranto, L., Tuckerman, M. E., and Glover, W. J. Machine learning the Hohenberg-Kohn map for molecular excited statesNat. Commun. 13, 7044 (2022)

115.

Liu, X., Zheng, L., Qin, C., Zhang, J. Z. H., and Sun, Z. Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: I. Standard procedureJ. Comput. Aided Mol. Des. 36, 735–752 (2022)

116.

Liu, X., Zheng, L., Cong, Y., Gong, Z., Yin, Z., Zhang, J. Z. H., Liu, Z., and Sun, Z. Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constantJ. Comput. Aided Mol. Des. 36, 879–894 (2022).

117.

Liu, X., Humeniuk, A., and Glover, W. J. Conical intersections in solution with polarizable embedding: Integral-exact direct reaction fieldJ. Chem. Theory Comput. 18, 6826–6839 (2022)

118.

Cao, W., Hu, Z., Peng, X., Sun, H., Sun, Z., and Wang, X.-B. Annihilating actinic photochemistry of the pyruvate anion by one and two water moleculesJ. Am. Chem. Soc. 144, 19317–19325 (2022)

119.

Portillo-Ledesma, S., Wagley, M., and Schlick, T. Chromatin transitions triggered by LH density as epigenetic regulators of the genomeNucleic Acids Res. 50, 10328–10342 (2022)

120.

Luo, F., Zhao, J., Liu, S., Xue, Y., Tang, D., Yang, J., Mei, Y., ... and Xie, Y. Ursolic acid augments the chemosensitivity of drug-resistant breast cancer cells to doxorubicin by AMPK-mediated mitochondrial dysfunctionBiochem. Pharmacol. 205, 115278 (2022)

121.

Felker, P. M. and Bačić, Z. Noncovalently bound molecular complexes beyond diatom–diatom systems: full-dimensional, fully coupled quantum calculations of rovibrational statesPhys. Chem. Chem. Phys. 24, 24655-24676 (2022)

122.

Hong, R. S., Mattei, A., Sheikh, A. Y., and Tuckerman, M. E. A data-driven and topological mapping approach for the a priori prediction of stable molecular crystalline hydratesProc. Natl. Acad. Sci. U.S.A. 119, e2204414119 (2022)

123.

Li, X., Jia, X., Paz, A. S. P., Cao, Y., and Glover, W. J. Evidence for water antibonding orbital mixing in the hydrated electron from its oxygen 1s X-ray absorption spectrumJ. Am. Chem. Soc. 144, 19668–19672 (2022)

124.

Hu, Z. and Sun, X. All-atom nonadiabatic semiclassical mapping dynamics for photoinduced charge transfer of organic photovoltaic molecules in explicit solventsJ. Chem. Theory Comput. 18, 5819–5836 (2022)

125.

Zhang, F., Wei, M., Chen, H., Ji, L., Nie, Y., and Kang, J. The genomic stability regulator PTIP is required for proper chromosome segregation in mitosisCell Div. 17, 5 (2022)

126.

Xiong, D., Zhao, X., Luo, S., Zhang, J. Z. H., and Duan, L. Molecular mechanism of the non-covalent orally targeted SARS-CoV-2 Mpro inhibitor S-217622 and computational assessment of its effectiveness against nainstream variantsJ. Phys. Chem. Lett. 13, 38, 8893–8901 (2022)

127.

Zhang, Y., Wang, Y., Xia, F., Cao, Z., and Xu, X. Accurate and efficient estimation of Lennard–Jones interactions for coarse-grained particles via a potential matching methodJ. Chem. Theory Comput. 18, 4879–4890 (2022)

128.

Liu, L., Luo, C., Zhang, J., He, X., Shen, Y., Yan, B., ... and Jiang, L. Synergistic effect of bio‐inspired nanochannels: Hydrophilic DNA probes at inner wall and hydrophobic coating at outer surface for highly sensitive detectionSmall 18, 2201925 (2022)

129.

Zhao, Y., Miao, Y., Cong, Y., Wang, J., Zhi, F., Pan, Y., ... Zhang, J. Z. H. and Zhang, L. High-level expression and improved pepsin activity by enhancing the conserved domain stability based on a scissor-like modelLWT 167, 113877 (2022)

130.

Liu, D., Zhao, W., and Yuan, Q. Breaking the linear relation in the dissociation of nitrogen on iron surfacesChemPhysChem 23, e202200147 (2022)

131.

Yin, Y., Ding, F., and Yuan, Q. Stabilization of black phosphorene by edge-selective adsorption of C60 moleculesJ. Phys. Chem. C 126, 6874–6879 (2022)

132.

Gu, S., Chin, C.-H., Zhu, T., and Zhang, Z. H. Theoretical investigations on photodissociation dynamics of deuterated alkyl halides CD3CH2FChin. J. Chem. Phys. 35, 431 (2022)

133.

Pan, Y., Bao, J., Zhang, X., Ni, H., Zhao, Y., Zhi, F., Fang, B., He, X.Zhang, J. Z. H., and Zhang, L. Rational design of P450 aMOx for improving anti-Markovnikov selectivity based on the “butterfly” modelFront. Mol. Biosci. 9, 888721 (2022)

134.

Chen, Y. and Yuan, Q. Carbon induced segregation of Ni atoms in Cu-Ni alloyChem. Phys. Lett. 806, 139979 (2022)

135.

Ren, L., Jing, Z., Xia, F.Zhang, J. Z., and Li, Y. Toxic effect of fullerene and its derivatives upon the transmembrane β2-adrenergic receptorsMolecules 27, 4562 (2022)

136.

Humeniuk, A. and Glover, W. J. Efficient CPU and GPU implementations of multicenter integrals over long-range operators using Cartesian Gaussian functionsComput. Phys. Commun. 280, 108467 (2022)

137.

Zhu, Q., Petingi, L., and Schlick, T. RNA-as-graphs motif atlas—dual graph library of RNA modules and viral frameshifting-element applicationsInt. J. Mol. Sci. 23, 9249 (2022)

138.

Wang, B., Mao, J., Wei, M., Qi, Y., and Zhang, J. Z. H. SeBPPI: A sequence-based protein-protein binding predictorJ. Comput. Biophys. Chem. 21, 729-737 (2022)

139.

Yan, S., Zhu, Q., Jain, S., and Schlick, T. Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppressionNat. Commun. 13, 4284 (2022)

140.

Li, T., Yu, L., Sun, J., Liu, J., and He, X. Ionization of D571 is coupled with SARS-CoV-2 spike up/down equilibrium revealing the pH-dependent allosteric mechanism of receptor-binding domainsJ. Phys. Chem. B 126, 4828–4839 (2022)

141.

Wang, T., Hu, Z., Nie, X., Huang, L., Hui, M., Sun, X., and Zhang, G. Thermochromic aggregation-induced dual phosphorescence via temperature-dependent sp3 -linked donor-acceptor electronic coupling. Nat. Commun. 12, 1364 (2021)

142.

Zeng, J., Zhang, L., Wang, H., and Zhu, T. Exploring the chemical space of linear alkane pyrolysis via deep potential GENeratorEnergy Fuels. 35, 762–769 (2021)

143.

Zelovich, T. and Tuckerman, M. E. OH− and H3O+ Diffusion in model AEMs and PEMs at low hydration: Insights from ab initio molecular dynamicsMembranes. 11, 355 (2021)

144.

Chin, C.-H., Zhu, T., and Zhang, J. Z. H. Cyclopentadienyl radical formation from the reaction of excited nitrogen atoms with benzene: A theoretical study. Phys. Chem. Chem. Phys. 23, 12408-12420 (2021)

145.

Zhao, J., Blayney, A., Liu, X., Gandy, L., Jin, W., Yan, L., Ha, J.-H., Canning, A. J., Connelly, M., Yang, C., Liu, X., Xiao, Y., Cosgrove, M. S., Solmaz, S. R., Zhang, Y., Ban, D., Chen, J., Loh, S. N., and Wang, C. EGCG binds intrinsically disordered N-terminal domain of p53 and disrupts p53-MDM2 interactionNat. Commun. 12, 986 (2021)

146.

Wang, X, Yan, J., Zhang, H., Xu, Z., and Zhang, J. Z. H. An electrostatic energy-based charge model for molecular dynamics simulationJ. Chem. Phys. 154, 134107 (2021)

147.

Brian, D., Liu, Z., Dunietz, B. D., Geva, E., and Sun, X. Three-state harmonic models for photoinduced charge transfer. J. Chem. Phys. 154, 174105 (2021)

148.

Brian, D. and Sun, X. Linear-response and nonlinear-response formulations of the instantaneous Marcus theory for nonequilibrium photoinduced charge transferJ. Chem. Theory Comput. 17, 2065–2079 (2021)

149.

Chen, J., Li, N., Wang, X., Chen, J., Zhang, J. Z. H., and Zhu, T. Molecular mechanism related to the binding of fluorophores to Mango-II revealed by multiple-replica molecular dynamics simulationsPhys. Chem. Chem. Phys. 23, 10636-10649 (2021)

150.

Lu, J., Xia, S., Lu, J., and Zhang, Y. Dataset construction to explore chemical space with 3D geometry and deep learningJ. Chem. Inf. Model. 61,1095-1104 (2021)

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