Publications

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)

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

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)

Cong, Y., Li, M., Qi, Y., and Zhang, J. Z. H. A fast–slow method to treat solute dynamics in explicit solvent. Phys. Chem. Chem. Phys. 24, 14498-14510 (2022)

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 process. J. Comput. Chem. 43, 906-916 (2022)

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 membranes. J. Mater. Chem. A. 10, 11137-11149 (2022)

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 substrate. Chem. Sci. (2022)

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 interfaces. Chin. Chem. Lett. (2022)

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/TNT. Phys. Chem. Chem. Phys. 24, 11801-11811 (2022)

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 docking. J. Chem. Inf. Model. 62, 2499–2509 (2022)

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

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

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 simulation. Comput. Biol. Chem. 98, 107648 (2022)

Li, Z. and Zhang, J. Z. H. Mutational effect of some major COVID-19 variants on binding of the S protein to ACE2. Biomolecules. 12, 572 (2022)

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

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 field. Cryst. Growth Des. 22, 1182–1195 (2022)

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

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 solvents. Nat. Commun. 13, 219 (2022)

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)

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 intermediate. Cell Res. 32, 288–301 (2022)

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

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 calculation. Chem. Biol. Drug Des. 1– 12 (2022)

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 method. Chin. J. Chem. Phys. 34, 741 (2022)

Miao, Y., Ni, H., Zhang, X., Zhi, F., Long, X., Yang, X., He, X., and Zhang, L. Investigating mechanism of sweetness intensity differences through dynamic analysis of sweetener–T1R2–membrane systems. Food Chem. 374, 131807 (2022)

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

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 molecules. J. Cheminform. 14, 1 (2022)

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 system. J. Phys. Chem. Lett. 13, 763–769 (2022)

 Kleimeier, N. F., Liu, Y., Turner, A. M., Young, L. A., Chin, C.-H., Yang, T., He, X., Lo, J., Cheng, B. M., and Kaiser, R. I. Excited state photochemically driven surface formation of benzene from acetylene ices on Pluto and in the outer solar system. Phys. Chem. Chem. Phys. 24, 1424-1436 (2022)

Qu, K., Xu, J., Xue, Y., Guo, J., Gao, Z., Song, Y.-Y., and Mei, Y. Near infrared light-driven photothermal effect on homochiral Au/TiO2 nanotube arrays for enantioselective desorption. Anal. Chem. 94, 588–592 (2022)

Tuckerman, M. E. The curse of dimensionality loses its power. Nat. Comput. Sci. 2, 6–7 (2022)

Swygert, S. G., Lin, D., Portillo-Ledesma, S., Lin, P.-Y., Hunt, D. R., Kao, C.-F., Schlick, T., Noble, W. S., Tsukiyama, T. Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells. eLife. 10, e72062 (2021)

Brian, D. and Sun, X. Charge-transfer landscape manifesting the structure–rate relationship in the condensed phase via machine learning. J. Phys. Chem. B. 125, 13267–13278 (2021)

Hu, Z., Brian, D., and Sun, X. Multi-state harmonic models with globally shared bath for nonadiabatic dynamics in the condensed phase. J. Chem. Phys. 155, 124105 (2021)

Zhao, X., Luo, S., Huang, K., Xiong, D., Zhang, J. Z. H., and Duan, L. Targeting mechanism for SARS-CoV-2 in silico: interaction and key groups of TMPRSS2 toward four potential drugs. Nanoscale. 13, 19218-19237 (2021)

Li, M., Lu, W.C., and Zhang, J. Z.H. Introducing the effective polarizable bond (EPB) model in DNA simulations. Chem. Phys. Lett. 785, 139160 (2021)

Liu, J., Yang, J., Zeng, X. C., Xantheas, S. S., Yagi, K., and He, X. Towards complete assignment of the infrared spectrum of the protonated water cluster H+(H₂O)₂₁. Nat. Commun. 12, 6141 (2021)

Brian, D. and Sun, X. Generalized quantum master equation: A tutorial review and recent advances. Chin. J. Chem. Phys. 34, 497 (2021)

Dong, G., Hu, Z., Sun, X., and Dong, H. Structural reconstruction of optically invisible state in a single molecule via scanning tunneling microscope. J. Phys. Chem. Lett. 12, 10034–10039 (2021)

Zhu, X., Hu, C. T., Erriah, B., Vogt-Maranto, L., Yang, J., Yang, Y., Qiu, M., Fellah, N., Tuckerman, M. E., Ward, M. D., and Kahr, B. Imidacloprid crystal polymorphs for disease vector control and pollinator protection. J. Am. Chem. Soc. 143, 17144–17152 (2021)

Abreu, C. R. A. and Tuckerman, M. E. Multiple timescale molecular dynamics with very large time steps: avoidance of resonances. Eur. Phys. J. B. 94, 231 (2021)

Dai, D., Wang, X., Liu, Y., Yang, X.-L., Glaubitz, C., Denysenkov, V., He, X., Prisner, T., and Mao, J. Room-temperature dynamic nuclear polarization enhanced NMR spectroscopy of small biological molecules in water. Nat. Commun. 12, 6880 (2021)

Xu, M., Zhu, T., and Zhang, J. Z. H. Automated construction of neural network potential energy surface: The enhanced self-organizing incremental neural network deep potential method. J. Chem. Inf. Model. 61, 5425–5437 (2021)

 Li, M., Cong, Y., Qi, Y., and Zhang, J. Z. H. Computational insights into the binding mechanism of OxyS sRNA with chaperone protein Hfq. Biomolecules. 11, 1653 (2021)

Shen, Z., Peng, S., and Glover, W. J. Flexible boundary layer using exchange for embedding theories. II. QM/MM dynamics of the hydrated electron. J. Chem. Phys. 155, 224113 (2021)

Shen,  Z. and Glover, W. J. Flexible boundary layer using exchange for embedding theories. I. Theory and implementation. J. Chem. Phys. 155, 224112 (2021) 

Paz, A. S., Baleeva, N. S., and Glover, W. J. Active orbital preservation for multiconfigurational self-consistent field. J. Chem. Phys. 155, 071103 (2021)

Yang, C. and Zhang, Y. Lin_F9: A linear empirical scoring function for protein–ligand docking. J. Chem. Inf. Model. 61, 4630–4644 (2021)

Pan, X., Yang, J., Van, R., Epifanovsky, E., Ho, J., Huang, J., Pu, J., Mei, Y., Nam, K., and Shao, Y. Machine-learning-assisted free energy simulation of solution-phase and enzyme reactions. J. Chem. Theory Comput. 17, 5745–5758 (2021)

Atsango, A. O., Tuckerman, M. E., and Markland, T. E. Characterizing and contrasting structural proton transport mechanisms in azole hydrogen bond networks using ab initio molecular dynamics. J. Phys. Chem. Lett. 12, 8749–8756 (2021)

Chan, E. J., Shtukenberg, A. G., Tuckerman, M. E., and Kahr, B. Crystal structure prediction as a tool for identifying components of disordered structures from powder diffraction: A case study of benzamide II. Cryst. Growth Des. 21, 5544–5557 (2021)