Publications

101.

Tinnin, J., Bhandari, S., Zhang, P., Geva, E., Dunietz, B. D., Sun, X., and Cheung, M. S. Correlating interfacial charge transfer rates with interfacial molecular structure in the tetraphenyldibenzoperiflanthene/C70 organic photovoltaic systemJ. Phys. Chem. Lett. 13, 763–769 (2022)

102.

Wei, M., Zhang, X., Pan, X., Wang, B., Ji, C., Qi, Y., and Zhang, J. Z. H. HobPre: accurate prediction of human oral bioavailability for small moleculesJ. Cheminform. 14, 1 (2022)

103.

Qiu L., Song J., Zhang J.Z.H. (2022) Computational Alanine Scanning Reveals Common Features of TCR/pMHC Recognition in HLA-DQ8-Associated Celiac Disease. In: Vanhaelen Q. (eds) Computational Methods for Estimating the Kinetic Parameters of Biological Systems. Methods in Molecular Biology, vol 2385. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1767-0_13

104.

Jin, S., Wang, J.-N., Xue, Y., Li, P., and Mei, Y. Selectivity of parvalbumin B protein binding to Ca2+ and Mg2+ at an ab initio QM/MM level using the reference-potential methodChin. J. Chem. Phys. 34, 741 (2022)

105.

Zheng, L., Yang, Y., Bao, J., He, L., Qi, Y., and Zhang, J. Z. H. Discovery of novel inhibitors of CDK2 using docking and physics- based binding free energy calculationChem. Biol. Drug Des. 1– 12 (2022)

106.

Felker, P. M. and Bačić, Z. Intermolecular rovibrational states of the H2O–CO2 and D2O–CO2 van der Waals complexesJ. Chem. Phys. 156, 064301 (2022)

107.

Hu, A., Zhang, J.-Z., Wang, J., Li, C.-C., Yuan, M., Deng, G., … He, X., … and Song, B.-L. Cholesterylation of Smoothened is a calcium-accelerated autoreaction involving an intramolecular ester intermediateCell Res. 32, 288–301 (2022)

108.

Zelovich, T., Vogt-Maranto, L., Simari, C., Nicotera, E., Hickner, M. A., Paddison, S. J., Bae, C., Dekel, D. R., and Tuckerman, M. E. Non-monotonic temperature dependence of hydroxide ion diffusion in anion exchange membranes. Chem. Mater. 34, 2133–2145 (2022)

109.

Spittle, S., Poe, D., Doherty, B., Kolodziej, C., Heroux, L., Haque, M. A., … Tuckerman, M., … and Sangoro, J. Evolution of microscopic heterogeneity and dynamics in choline chloride-based deep eutectic solventsNat. Commun. 13, 219 (2022)

110.

Zelovich, T. and Tuckerman, M. E. Controlling hydronium diffusivity in model proton exchange membranesJ. Phys. Chem. Lett. 13, 2245–2253 (2022)

111.

Metz, M. P., Shahbaz, M., Song, H., Vogt-Maranto, L., Tuckerman, M. E., and Szalewicz, K. Crystal structure predictions for 4-amino-2,3,6-trinitrophenol using a tailor-made first-principles-based force fieldCryst. Growth Des. 22, 1182–1195 (2022)

112.

Xu, M., Felker, P. M., and Bačić, Z. H2O inside the fullerene C60: Inelastic neutron scattering spectrum from rigorous quantum calculationsJ. Chem. Phys. 156, 124101 (2022)

113.

Li, Z. and Zhang, J. Z. H. Mutational effect of some major COVID-19 variants on binding of the S protein to ACE2Biomolecules. 12, 572 (2022)

114.

Li, Y., Li, Y., Ning, C., Yue, J., Zhang, C., He, X., … & Liu, Z. Discovering inhibitors of TEAD palmitate binding pocket through virtual screening and molecular dynamics simulationComput. Biol. Chem. 98, 107648 (2022)

115.

Lu, J. and Zhang, Y. Unified deep learning model for multitask reaction predictions with explanationJ. Chem. Inf. Model. 62, 1376–1387 (2022)

116.

Zhang, X., Mao, J., Wei, M., Qi, Y., and Zhang, J. Z. H. HergSPred: Accurate classification of hERG blockers/nonblockers with machine-learning modelsJ. Chem. Inf. Model. 62, 1830–1839 (2022)

117.

Pan, X., Wang, H., Zhang, Y., Wang. X., Li, C., Ji, C., and Zhang, J. Z. H. AA-score: A new scoring function based on amino acid-specific interaction for molecular dockingJ. Chem. Inf. Model. 62, 2499–2509 (2022)

118.

Cao, L., Zeng, J., Wang, B., Zhu, T., and Zhang, J. Z. H. Ab initio neural network MD simulation of thermal decomposition of a high energy material CL-20/TNTPhys. Chem. Chem. Phys. 24, 11801-11811 (2022)

119.

Yang, L., Feng, J., Wang, J. N., Gao, Z., Xu, J., Mei, Y., and Song, Y. Y. Engineering large-scaled electrochromic semiconductor films as reproductive SERS substrates for operando investigation at the solid/liquid interfacesChin. Chem. Lett. (2022)

120.

Xu, J., Xue, Y., Jian, X., Zhao, Y., Dai, Z., Xu, J., … Mei, Y., and Song, Y. Y. Understanding of chiral site-dependent enantioselective identification on plasmon-free semiconductor based SERS substrateChem. Sci. (2022)

121.

Zelovich, T., Simari, C., Nicotera, I., Dekel, D. R., and Tuckerman, M. E. The impact of carbonation on hydroxide diffusion in nano-confined anion exchange membranesJ. Mater. Chem. A. 10, 11137-11149 (2022)

122.

Xiong, Y., Zeng, J., Xia, F., Cui, Q., Deng, X., and Xu, X. Conformations and binding pockets of HRas and its guanine nucleotide exchange factors complexes in the guanosine triphosphate exchange processJ. Comput. Chem. 43, 906-916 (2022)

123.

Yang, C. and Zhang, Y. Delta machine learning to improve scoring-ranking-screening performances of protein–ligand scoring functions. J. Chem. Inf. Model  62, 2696–2712 (2022)

124.

Zhang, D., Xia, S., and Zhang, Y. Accurate prediction of aqueous free solvation energies using 3D atomic feature-based graph neural network with transfer learningJ. Chem. Inf. Model. 62, 1840–1848 (2022)

125.

Karashima, S., Humeniuk, A., Glover, W. J., and Suzuki, T. Ultrafast photoisomerization of ethylene studied using time-resolved extreme ultraviolet photoelectron spectroscopy. J. Phys. Chem. A (2022)

126.

Liu, J., Lan, J., and He, X. Toward high-level machine learning potential for water based on quantum fragmentation and neural networksJ. Phys. Chem. A (2022)

127.

Wang, H., Pan, X., Zhang, Y., Wang, X., Xiao, X., and Ji, C. MolHyb: A web server for structure-based drug design by molecular hybridizationJ. Chem. Inf. Model. 62, 2916–2922 (2022)

128.

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)

129.

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)

130.

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)

131.

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)

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.

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)

134.

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)

135.

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)

136.

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)

137.

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)

138.

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)

139.

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)

140.

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)

141.

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).

142.

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)

143.

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)

144.

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)

145.

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

146.

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)

147.

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

148.

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)

149.

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)

150.

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)

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