Publications

1.

Fu, H., Zhang, M., Leng, J., Hu, W., Zhu, T., and Zhang, Y. Predicting two-photon absorption spectra of octupolar molecules: A deep-learning approach based exclusively on molecular structuresJ. Phys. Chem. A 128, 431–438 (2024)

2.

Zelovich, T., Dekel, D. R., and Tuckerman, M. E. Electrostatic potential of functional cations as a predictor of hydroxide diffusion pathways in nanoconfined environments of anion exchange membranesJ. Phys. Chem. Lett. 15, 408–415 (2024)

3.

Portillo-Ledesma, S., Chung, S., Hoffman, J., and Schlick, T. Regulation of chromatin architecture by transcription factor bindingeLife 12, RP91320 (2024)

4.

Wang, S., Liu, F., Li, P., Wang, J.-N., Mo, Y., Lin, B., and Mei, Y. Potent inhibitors targeting cyclin-dependent kinase 9 discovered via virtual high-throughput screening and absolute binding free energy calculationsPhys. Chem. Chem. Phys. (2024)

5.

Wan, Z., Shi, M., Gong, Y., Lucci, M., Li, J., Zhou, J., Yang, X.-L., Lelli, M., He X., and Mao, J. Multitasking pharmacophores support cabotegravir-based long-acting HIV pre-exposure prophylaxis (PrEP)Molecules 29, 376 (2024)

6.

Mao, J., Jin, X., Shi, M., Heidenreich, D., Brown, L. J., Brown, R. C. D., Lelli, M., He, X., and Glaubitz, C. Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins. Sci. Adv. 10,  eadj0384 (2024)

7.

Sun, X., Zhang, X., and Liu, Z. Generalized nonequilibrium Fermi’s golden rule and its semiclassical approximations for electronic transitions between multiple statesJ. Chem. Phys. 160, 034108 (2024)

8.

Zhang, X., Feng, Y., Hua, Y., Zhang, C., Fang, B., Long, X., Pan, Y., Gao, B., Zhang, J. Z. H., Li, L., Ni, H., and Zhang, L. Biosynthesis of eriodictyol in citrus waster by endowing P450BM3 activity of naringenin hydroxylationAppl. Microbiol. Biotechnol. 108,  84 (2024)

9.

Xiao, J., Chen, Y., Zhang, L.F., Wang, H., and Zhu, T. A machine learning-based high-precision density functional method for drug-like moleculesArtificial Intelligence Chemistry 2, 100037 (2024)

10.

Liang, J. and Yuan, Q. Effects of graphitic- and pyridinic-N co-doping on structure regulation and ORR activity of N-doped grapheneAppl. Surf. Sci. 648, 159025 (2024)

11.

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 batteriesNanoscale 16, 427-437 (2024)

12.

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)

13.

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

14.

Yue, J., Li, Y., Li, F., Zhang, P., Li, Y., Xu, J., Zhang, Q., Zhang, C., He, X., Wang, Y., and Liu, Z. Discovery of Mcl-1 inhibitors through virtual screening, molecular dynamics simulations and in vitro experimentsComput. Biol. Med. 152, 106350 (2023)

15.

Xia, S., Zhang, D., and Zhang, Y. Multitask deep ensemble prediction of molecular energetics in solution: From quantum mechanics to experimental propertiesJ. Chem. Theory Comput. 19, 659–668 (2023)

16.

Yao, S., Van, R., Pan, X., Park, J. H., Mao, Y., Pu, J., Mei, Y., and Shao, Y. Machine learning based implicit solvent model for aqueous-solution alanine dipeptide molecular dynamics simulationsRSC Adv. 13, 4565-4577 (2023)

17.

Portillo-Ledesma, S., Li, Z., and Schlick, T. Genome modeling: From chromatin fibers to genesCurr. Opin. Struct. Biol. 78, 102506 (2023)

18.

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

19.

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 crystalsJ. Chem. Theory Comput. 19, 311–323 (2023)

20.

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 developmentCell Cycle 22, 619-632 (2023)

21.

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 screeningJ. Chem. Inf. Model. 63, 835–845 (2023)

22.

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)

23.

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 studyJ. Phys. Chem. C 127, 2792–2804 (2023)

24.

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)

25.

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)

26.

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)

27.

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

28.

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)

29.

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)

30.

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)

31.

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)

32.

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)

33.

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)

34.

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)

35.

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)

36.

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)

37.

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)

38.

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

39.

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

40.

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

41.

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

42.

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 enantiomerNano Res. (2023)

43.

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

44.

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 batteriesAngew. Chem. 62, e202307274 (2023)

45.

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 proteinJ. Chem. Theory Comput. 19, 7405–7422 (2023)

46.

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 screeningJ. Chem. Inf. Model. 63, 6501–6514 (2023)

47.

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 calculationsJ. Chem. Phys. 159, 174302 (2023)

48.

Pan, X., Snyder, R., Wang, J.-N., Lander, C., Wickizer, C., Van, R., Chesney, A., Xue, Y., Mao, Y., Mei, Y., Pu, J., and Shao, Y. Training machine learning potentials for reactive systems: A Colab tutorial on basic models.  J. Comput. Chem. (2023)

49.

Zhao, C., Yang, G., Zhang, S., He, X., Zhong, Y., and Gao, X. Enhanced breathing effect of nanoporous UIO-66-DABA metal–organic frameworks with coordination defects for high selectivity and rapid adsorption of Hg(II)ACS Appl. Nano Mater. 6, 18372–18380 (2023)

50.

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 systemsJ. Chem. Inf. Model. 63, 6938–6946 (2023)

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