Publications

Gong, J., Zhu, J., He, X., and Yang, J. Using a cyclocarbon additive as a cyclone separator to achieve fast lithiation and delithiation without dendrite growth in lithium-ion batteries. Nanoscale 16, 427-437 (2024)

Liu, X., Zheng, L., Qin, C., Li, Y., Zhang, J. Z. H., and Sun, Z. Screening power of end-point free-energy calculations in cucurbituril host–guest systems. J. Chem. Inf. Model. 63, 6938–6946 (2023)

Duan, L., Tang, B., Luo, S., Xiong, D., Wang, Q., Xu, X., and Zhang, J. Z. H. Entropy driven cooperativity effect in multi-site drug optimization targeting SARS-CoV-2 papain-like protease. Cell. Mol. Life Sci. 80, 313 (2023)

Yang, Y., Lyu, X., Cong, Y., Miao, T., Fang, B., Zhang, C., Shen, Q., Matthews, M., Fisher, A. J., Zhang, J. Z. H., Zhang, L., and Yang, R. A precise swaying map for how promiscuous cellobiose-2-epimerase operate bi-reaction. Int. J. Biol. Macromol. 253, 127093 (2023)

Liu, Z., Hu, H., and Sun, X. Multistate reaction coordinate model for charge and energy transfer dynamics in the condensed phase. J. Chem. Theory Comput. 19, 7151–7170 (2023)

Vindel-Zandbergen, P., Kȩdziera, D., Żółtowski, M., Kłos, J., Żuchowski, P., Felker, P. M., Lique, F., and Bačić, Z. H₂O–HCN complex: A new potential energy surface and intermolecular rovibrational states from rigorous quantum calculations. J. Chem. Phys. 159, 174302 (2023)

Yu, L., He, X., Fang, X., Liu, L., and Liu, J. Deep learning with geometry-enhanced molecular representation for augmentation of large-scale docking-based virtual screening. J. Chem. Inf. Model. 63, 6501–6514 (2023)

Zhang, J., Kriebel, C. N., Wan, Z., Shi, M., Glaubitz, C., and He, X. Automated fragmentation quantum mechanical calculation of 15N and 13C chemical shifts in a membrane protein. J. Chem. Theory Comput. 19, 7405–7422 (2023)

Jiang, Y., Wan, Z., He, X., and Yang, J. Fine-tuning electrolyte concentration and metal–organic framework surface toward actuating fast Zn2+ dehydration for aqueous Zn-ion batteries. Angew. Chem. 62, e202307274 (2023)

Li, Y., Yang, J., and He, X. Characterizing polyproline II conformational change of collagen superhelix unit on adsorption on gold surface. Nanoscale Adv. 5, 5322-5331 (2023)

Guo, J., Xue, Y., Zhao, C., Zhao, J., Gao, Z., Mei, Y., and Song, Y.-Y. Integrated separation-electrochemical detection device based on wood column for online identification of enantiomer. Nano Res. (2023)

Li, Z., Portillo-Ledesma, S., and Schlick, T. Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data. Curr. Opin. Cell Biol. 83, 102209 (2023)

Zha, J. and Xia, F. Developing hybrid all-atom and ultra-coarse-grained models to investigate taxol-binding and dynein interactions on microtubules. J. Chem. Theory Comput. 19, 5621–5632 (2023)

Tang, X., Wang, J., Zhang, J., Miao, Y., Zhao, Y., Gao, B., and Zhang, L. Rational design of lipase MAS1 for the long-chain substrate affinity. Journal of East China University of Science and Technology, 49, 529-535 (2023)

Xia, S., Chen, E., and Zhang, Y. Integrated molecular modeling and machine learning for drug design. J. Chem. Theory Comput. 19, 7478–7495 (2023)

Zeng, J., Cao, L., & Zhu, T. (2023). Neural network potentials. In Quantum Chemistry in the Age of Machine Learning (pp. 279-294). Elsevier.

Wang, X., Wang, Y., Guo, M., Wang, X., Li, Y., and Zhang, J. Z. H. Assessment of an electrostatic energy-based charge model for modeling the electrostatic interactions in water solvent. J. Chem. Theory Comput. (2023)

Bajpai, S., Petkov, B. K., Tong, M., Abreu, C. R. A., Nair, N. N., and Tuckerman, M. E. An interoperable implementation of collective-variable based enhanced sampling methods in extended phase space within the OpenMM package. J. Comput. Chem. 44, 2166-2183 (2023)

Naleem, N., Abreu, C. R. A., Warmuz, K., Tong, M., Kirmizialtin, S., and Tuckerman, M. E. An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions. J. Chem. Phys. 159, 034102 (2023)

Jiang, Y., Hu, Z., Yang, Y., and Peng, P., Zhong, C., Sun, H., Sun, Z., and Wang, X.-B. Beyond duality: Rationalizing repulsive coulomb barriers in host–guest cyclodextrin–dodecaborate complexes. J. Phys. Chem. Lett. 14, 6736–6742 (2023)

Jin, P., Wang, J.-N., Wang, X., Jia, M., Pan, H., Mei, Y., and Chen, J. Tracking the early stage of triplet-induced photodamage in a DNA dimer and oligomer containing 5-methylcytosine. J. Phys. Chem. B 127, 6878–6886 (2023)

Li, C., Zhang, A., Wang, L., Zuo, J., Zhu, C., Xu, J., Wang, M., and Zhang, J. Z. H. Development of a polynomial scoring function P3-Score for improved scoring and ranking powers. Chem. Phys. Lett. 824, 140547 (2023)

Zhang, J., Cong, Y., Duan, L., and Zhang, J. Z. H. Combined antibodies evusheld against the SARS-CoV-2 Omicron variants BA.1.1 and BA.5: Immune escape mechanism from molecular simulation. J. Chem. Inf. Model. 63, 5297–5308 (2023)

Felker, P. M. and Bačić, Z. HF trimer: 12D fully coupled quantum calculations of HF-stretch excited intramolecular and intermolecular vibrational states using contracted bases of intramolecular and intermolecular eigenstates. J. Chem. Phys. 158, 234109 (2023)

Zhang, Q. and Zhu, T. Interaction of divalent cations and amino acids in bulk water: Molecular simulations with neural network potentials. Chin. J. Chem. Phys. 36, 162 (2023)

Wang, J.-N., Xue, Y., Li, P., Pan, X., Wang, M., Shao, Y., Mo, Y., and Mei, Y. Perspective: Reference-potential methods for the study of thermodynamic properties in chemical processes: Theory, applications, and pitfalls. J. Phys. Chem. Lett. 14, 4866–4875 (2023)

Li, Y., Wang, Y., Zhang, R. M., He, X., and Xu, X. Comprehensive theoretical study on four typical intramolecular hydrogen shift reactions of peroxy radicals: Multireference character, recommended model chemistry, and kinetics. J. Chem. Theory Comput. 19, 3284–3302 (2023)

Paz, A. S. P. and Glover, W. J. Efficient analytical gradients of property-based diabatic states: Geometry optimizations for localized holes. J. Chem. Phys. 158, 204107 (2023)

Zhang, H., Saravanan, K. M., and Zhang, J. Z. H. DeepBindGCN: Integrating molecular vector representation with graph convolutional neural networks for protein–ligand interaction prediction. Molecules 28, 4691 (2023)

Ma, M., Cong, Y., Zhang, J. Z. H., and Zhang, L. Rational design of a highly specific prolyl endopeptidase to activate the antihypertensive effect of peptides. ChemBioChem 24, e202200691 (2023)

Liu, J. and He, X. Recent advances in quantum fragmentation approaches to complex molecular and condensed-phase systems. WIREs Comput Mol Sci. 13, e1650 (2023)

Chin, C.-H., Zhu, T., and Zhang, J. Z. H. Theoretical study of the absorption and emission spectrum and non-adiabatic excited state dynamics of gas-phase xanthone. J. Chin. Chem. Soc. 70, 372-385 (2023)

Ma, M., Feng, Y., Miao, Y., Shen, Q., Tang, S., Dong, J., Zhang, J. Z. H., and Zhang, L. Revealing the sequence characteristics and molecular mechanisms of ACE inhibitory peptides by comprehensive characterization of 160,000 tetrapeptides. Foods 12, 1573 (2023)

Li, M., Cong, Y., Qi, Y., and Zhang, J. Z. H. Binding of berberine derivates to G-quadruplex: insight from a computational study. Phys. Chem. Chem. Phys. 25, 10741-10748 (2023)

Pan, X., Zhao, F., Zhang, Y., Wang, X., Xiao, X., Zhang, J. Z. H., and Ji, C. MolTaut: A tool for the rapid generation of favorable tautomer in aqueous solution. J. Chem. Inf. Model. 63, 1833–1840 (2023)

Liu, X., Zheng, L., Qin, C., Cong, Y., Zhang, J. Z. H., and Sun, Z. Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: III. Force-field comparison, three-trajectory realization and further dielectric augmentation. Molecules 28, 2767 (2023)

Song, L., Xiong, L., Ni, D., Chen, W., Ji, J., Xue, J., Chen, X., Wu, X., He, X., and Liu, S. One-pot construction of β-selective quinolines with γ-quaternary carbon from vinylquinolines with active ylides via Pd/Sc/Brønsted acid co-catalysis. ACS Catal. 13, 6509–6517 (2023)

Yan, S., Zhu, Q., Hohl, J., Dong, A., and Schlick, T. Evolution of coronavirus frameshifting elements: Competing stem networks explain conservation and variability. Proc. Natl. Acad. Sci. U.S.A. 120, e2221324120 (2023)

Mao, A., Chen, C., Portillo-Ledesma, S., and Schlick, T. Effect of single-residue mutations on CTCF binding to DNA: Insights from molecular dynamics simulations. Int. J. Mol. Sci. 24, 6395 (2023)

Zelovich, T., Dekel, D. R., and Tuckerman, M. E. Functional groups in anion exchange membranes: Insights from Ab initio molecular dynamics. J. Membr. Sci. 678, 121638 (2023)

Kilgour, M., Rogal, J., and Tuckerman, M. Geometric deep learning for molecular crystal structure prediction. J. Chem. Theory Comput. (2023)

Zhu, X., Liu, X., Xia, F., and Liu, L. Theoretical study on the copper-catalyzed ortho-selective C-H functionalization of naphthols with α-phenyl-α-diazoesters. Molecules 28, 1767 (2023)

Li, F., Zhang, Y., Xia, F., and Xu, X. Development of multiscale ultra-coarse-grained models for the SARS-CoV-2 virion from cryo-electron microscopy data. Phys. Chem. Chem. Phys. 25, 12882-12890 (2023)

Jiang, G., Hu, Z., Bai, L., Zhong, C., Lu, S., Han, B., Sun, Z., Zhu, S., Liang, Y., and Sun, H. Origins of near-infrared-II emission tail and fluorescence enhancement of the albumin-chaperoned cyanine dyes from a multiscale computational study. J. Mater. Chem. C (2023)

Long, Z. and Tuckerman, M. E. Hydroxide diffusion in functionalized cylindrical nanopores as idealized models of anion exchange membrane environments: An ab initio molecular dynamics study. J. Phys. Chem. C 127, 2792–2804 (2023)

Liu, Y., Liu, J., and He, X. Different pKa shifts of internal GLU8 in human β-endorphin amyloid revealing a coupling of internal ionization and stepwise fibril disassembly. J. Phys. Chem. B 127, 1089–1096 (2023)

Zhang, H., Saravanan, K. M., Wei, Y., Jiao, Y., Yang, Y., Pan, Y., Wu, X., and Zhang, J. Z. H. Deep learning-based bioactive therapeutic peptide generation and screening. J. Chem. Inf. Model. 63, 835–845 (2023)

Huang, C.-J., Lyu, X., and Kang, J. The molecular characteristics and functional roles of microspherule protein 1 (MCRS1) in gene expression, cell proliferation, and organismic development. Cell Cycle 22, 619-632 (2023)

Zhang, C., Verma, P., Wang, J., Liu, Y., He, X., Wang, Y., Truhlar, D. G., and Liu, Z. Performance of screened-exchange functionals for band gaps and lattice constants of crystals. J. Chem. Theory Comput. 19, 311–323 (2023)

Liu, Y., Zhang, C., Liu, Z., Truhlar, D. G., Wang, Y., and He, X. Supervised learning of a chemistry functional with damped dispersion. Nat Comput Sci. 3, 48-58 (2023)