Publications

Bao, T., Zhao, C., Tang, C., Wu, Y., Xi, Y., Zhang, C., Yuan, P., He, X., Yu, C., and Liu, C. A Janus conductive MOF-on-conductive-MOF heterostructure enables simultaneous production of H2O2 and active chlorine by seawater electrolysis. eScience 6, 100581 (2026)

Zeng, H. and Sun, X. Estimating memory time within the frameworks of generalized quantum master equation and transfer tensor methods. J. Chem. Phys. 164, 224117 (2026)

Infante, C., Lu, J., Pan, X., Xia, S., and Zhang, Y. Unifying pKa and Protonation Prediction with Sequence-Based Deep Learning. J. Chem. Inf. Model. 66, 6972-6982 (2026)

Han, C., Pan, X., and Zhang, Y. End-to-end molecular structure elucidation from multimodal NMR spectra images using vision transformers. Chem. Sci. 17, 13072-13082 (2026)

Portillo-Ledesma, S., Lee, S., Laederach, A., and Schlick, T. Open questions on viral frameshifting: Exploiting structural plasticity of the frameshifting element for therapeutic intervention. Biophys. J. (2026)

Li, Z. and Xia, F. Metadynamics simulation of the DFG conformational transition in calmodulin kinase II. Chem. Phys. Lett. 891, 142768 (2026)

Robledo, A. and Tuckerman, M. E. A staging Monte Carlo algorithm for sampling off-diagonal density matrix elements via open-chain path integrals. J. Chem. Phys. 164, 194105 (2026)

Fang, B., Zeng, D., Duan, Z., Gao, B., Zhu, T., He, X., Xu, L., Liu, X., He, Q., Huang, L., Shen, H., Yuan, Z., Li, S., Jiang, Y., Zhang, Y., Feng, Y., Zhang, C., Wei, H., Zhang, J. Z. H., Jensen, G. J., Fan, D., and Zhang, L. Real-time visualization of collagen assembly uncovers metastable properties in hierarchical organization. Nat. Commun. 17, 71205 (2026)

Liu, Y., Wei, L., Tao, S., Wu, Y., Wu, F., Wang, Y., and He, X. Insights Into Density Functional Performance From a Main‐Group and Transition‐Metal Molecular Benchmark. J. Comput. Chem. 47, e70388 (2026)

Ren, W., Xiao, J., Zhang, Y., Zhu, T., and Zhang, J. Z. H. GMFCC-UMA: A Fragment-Based Machine Learning Framework for Scalable Ab Initio-Quality Protein Energies. J. Chem. Theory Comput. 22, 4822-4834 (2026)

Zhou, W., D′ Oliviera, A., Dai, X., Mugridge, J. S., and Zhang, Y. A Novel Covalent Inhibitor Fragment for the SARS-CoV-2 Main Protease Identified by Target-Specific Deep Learning. ACS Chem. Biol. 21, 1112-1124 (2026)

Thongyod, W., Lu, T., Bai, Y., Punwong, C., and Glover, W. J. UV Response of the Green Fluorescent Protein Chromophore: Insights from Ab Initio Nonadiabatic Simulations. J. Phys. Chem. Lett. 17, 5005-5011 (2026)

Zhang, Y., Hao, H., Wang, S., Zhuang, J., Wang, H., Li, T., Zhang, Y., Qian, Y., Hu, L., Gao, S., He, X., and Zhou, A. MBERA: Multi-Branch Evolutionary Retrosynthesis Algorithm. Swarm Evol. Comput. 104, 102374 (2026)

Kilgour, M., Tuckerman, M. E., and Rogal, J. MXtalTools: A Toolkit for Machine Learning on Molecular Crystals. J. Chem. Inf. Model. 66, 3402-3408 (2026)

Sun, X. and Liu, Z. Molecular origin of correlated bath effects in photoinduced charge transfer dynamics in polar solvents. J. Phys. Chem. Lett. 17, 3406-3418 (2026)

Wang, H., Zhang, Y., Wang, Z., Zhuang, J., Cheng, Z., Qian, Y., Zhou, A., Peng, S., and He, X. Enhancing diversity of template-free retrosynthesis prediction via hierarchical latent variables. J. Chem. Inf. Model. 66, 3074-3090 (2026)

Liu, Y., Zhai, J., Cao, S., Guo, H., Zhang, H., Song, B., Guo, J., Men, D., He, X., and Li, D. Single-engineered-residue solvation perturbations regulate global protein architecture and function. Nat. Commun 17, 3754 (2026)

Sun, X. Instantaneous Marcus theory for photoinduced charge transfer in condensed phase. WIREs Comput. Mol. Sci. 16, e70069 (2026)

Feng, Z., Kim, M., Richards, A., Lupoli, T. J., and Zhang, Y. ProMol_Func: A Structure-Free Deep Learning Model for Virtual Screening. JACS Au 6, 1495-1502 (2026)

Liu, Z., Zeng, H., and Sun, X. Bridging atomistic accuracy and computational efficiency in condensed-phase spectroscopy via the multistate harmonic model. APL Comput. Phys. 2, 016107 (2026)

Ren, W., Xiao, J., Zhang, Y., Zhu, T., and Zhang, J. Z. H. A practical framework for rapid calculation of protein polarization energies with anisotropic atomic polarizabilities. J. Chem. Phys. 164, 055101 (2026)

Leng, J., Huang, Z., Zheng, L., Yang, Y., Huang, H., Gao, Y., Huo, L., Li, Y., Sun, Z., and Zhang, J. Z. H. Revealing the limits of covalent docking and advancing affinity prediction with covalent-aware multi-task learning. Phys. Chem. Chem. Phys. 28, 4822-4834 (2026)

Lee, S. and Schlick, T. Kinetic Traps in RNA Folding: Targeted Design of Frameshifting Element Mutants by Thermodynamic and Kinetic Analysis of the Chikungunya Virus. J. Phys. Chem. B 130, 1810-1831 (2026)

Li, Z., Portillo-Ledesma, S., Janani, M., and Schlick, T. The influence of 10n and 10n + 5 linker lengths on chromatin fiber topologies explored by mesoscale modeling. Biophys. J. 125, 530-545 (2026)

Lahouari, A., Rogal, J., and Tuckerman, M. E. Automated Machine Learning Pipeline: Large Language Models-Assisted Automated Data set Generation for Training Machine-Learned Interatomic Potentials. J. Chem. Theory Comput. 22, 305-317 (2026)

Zhou, W., Ke, D., Zhang, Z., Jin, C., Wu, Y., Pan, X., Wang, X., Xiao, X., Zhang, K., and Ji, C. qMol: A Web Server for Efficient Molecular Queries Using Fragment-Based Reduced Graphs. J. Chem. Inf. Model. 66, 7-15 (2026)

Allen, S. R., Schlick, T., and Laederach, A. RNA Structural Ensemble Determinants of-1 Programmed Ribosomal Frameshifting Efficiency Across Coronavirus Evolution. J. Mol. Biol. 437, 169512 (2025)

Liu, Z., Zeng, H., and Sun, X. Consistent and Generalizable Effective Model Hamiltonian Framework for Studying Nonadiabatic Dynamics in the Condensed Phase. J. Chem. Theory Comput. 21, 12393-12442 (2025)

Ma, Y., Wang, L., Kong, F., Yang, M., Su, T., Guo, J., Mei, Y., and Song, Y. Y. In Situ Reactive Oxygen Species‐Generating Semiconductor Nanopore for Real Time Peptide Oxidation Analysis. Adv. Funct. Mater. 36, e27203 (2025)

Li, F., Zhang, Y., Xia, F., and Xu, X. Development of Shell-Space Electrostatic Potential Fitting Charges in a United-Atom Model for Amino Acids Simulations. J. Chem. Theory Comput. 21, 12149-12161 (2025)

Wang, L., Wang, L., Wang, X., Shen, Z., Jia, M., Pan, H., Mei, Y., and Chen, J. Chirality Enhanced Triplet-State Generation in a DNA-Intercalated Natural Antibiotic. J. Am. Chem. Soc. 147, 45629-45638 (2025)

Ke, D., Zhou, W., Zhang, Z., Jin, C., Wu, Y., Pan, X., Wang, X., Xiao, X., and Ji, C. SiteMatcher: A Web Server for Structure-Based Drug Design Using Protein–Ligand Interaction Patterns. J. Chem. Inf. Model. 65, 13028-13036 (2025)

Portillo-Ledesma, S., Li, Z., and Schlick, T. Molecular dynamics simulations reveal subtle consequences of H3K9 and H3K27 tri-methylation on chromatin constituents. Biophys. J. 124, 4005-4017 (2025)

Wu, X., Zhang, X., Xia, W., Zhang, Y., Huang, K., Zhao, F., Ji, C., Wang, J., Zhou, B., and Zhang, J. Z. H. Discovery of novel Cytochrome bd oxidase inhibitors against Mycobacterium tuberculosis. Eur. J. Med. Chem. 298, 118010 (2025)

Zhai, J., Xiong, D., Zhang, Y., Shi, Y., Gu, Y., Chen, X., He, S., He, X., and Hu, L. SFMMoE: A Semi-Empirical Descriptor-Augmented Multi-Expert Graph Neural Network for Accurate Prediction of Singlet Fission Properties. J. Phys. Chem. Lett. 16, 12146-12154 (2025)

Simkó, I., Felker, P. M., and Bačić, Z. D₂O trimer: Intermolecular vibration-tunneling states, low-frequency spectrum, and the effects of the three-body interactions from rigorous 12D quantum calculations. J. Chem. Phys. 163, 184304 (2025)

Dai, X., Wang, R., and Zhang, Y. Topological deep learning for enhancing peptide-protein complex prediction. Commun. Chem. 8, 347 (2025)

Li, S., Xiong, D., Klochkov, V. V., Khodov, I. A., and He, X. Molecular dynamics reveals novel small-molecule inhibitors block PD-1/PD-L1 by promoting PD-L1 dimer stability. Phys. Chem. Chem. Phys. 27, 24932-24947 (2025)

Jing, A., Vindel-Zandbergen, P., Felker, P. M., Bačić, Z., and Szalewicz, K. HF dimer: a new full-dimensional potential energy surface validated by rigorous 6D quantum calculations of HF-stretch excited intra-and intermolecular vibrational states and tunneling splittings. Mol. Phys. 123, e2549516 (2025)

Chen, M. S., Robledo, A., Schäfer, C., Han, K. Y., Clementi, C., and Tuckerman, M. E. Machine learning-accelerated path integral molecular dynamics simulations of reactive organic electrolytes. J. Chem. Phys. 163, 144110 (2025)

Schlick, T. and Grigoryev, S. Nucleosome Linker Length and Distribution as Major Players in Epigenetic Regulation: Insights from Cryo-Electron Microscopy and Modeling of Retina Cell Maturation. DNA Cell Biol. 44, 581-638 (2025)

Li, Z., Portillo-Ledesma, S., and Schlick, T. Chromatin higher-order folding as influenced by preferred values of linker DNA. Curr. Opin. Struct. Biol. 95, 103154 (2025)

Shi, Y., Li, Y., Zhai, J., Zhang, Y., Hu, B., Gu, Y.-C., Chen, X., Hu, L., and He, X. AI-driven advances in the design of RTP and TADF luminescent material. Chem. Phys. Rev. 6, 031309 (2025)

Li, Z., Zheng, L., Yang, Y., Wang, X., Sun, Z., and Zhang, J. Z. H. dMSGB-IE: Computational mutational scanning for (de)methylation thermodynamics. J. Chem. Phys. 163, 115101 (2025)

Kilgour, M., Tuckerman, M. E., and Rogal, J. Multi-type point cloud autoencoder: a complete equivariant embedding for molecule conformation and pose. Mach. Learn.: Sci. Technol. 6, 035055 (2025)

Gu, Y., Xia, S., Ouyang, Q., and Zhang, Y. Bioactivity Deep Learning for Complex Structure-Free Compound-Protein Interaction Prediction. J. Chem. Inf. Model. 65, 9910–9926 (2025)

Zeng, H. and Sun, X. Data-Driven Versus Physics-Informed Neural Networks for Nonadiabatic Semiclassical Mapping Dynamics. Commun. Comp. Chem. 7, 217-225 (2025)

Zou, X., He, Y., Gao, Y., Wang, J., and Zhang, J. Z. H. Understanding the activation mechanism of GLP-1R/GIPR by dual agonist Tirzepatide via molecular dynamics and protein-peptide binding. Int. J. Bio. Macromol. 321, 146141 (2025)

Cao, J., Liu, C., Chen, Z., Li, H., Xu, L., Xiao, H., Wang, S., He, X., and Fang, G. Accelerated Discovery of Refractory High-Entropy Alloys via Interpretable Machine Learning. J. Phys. Chem. Lett. 16, 8806–8814 (2025)

Hong, R. S., Mattei, A., Tuckerman, M. E., and Sheikh, A. Y. 3D conformation and crystal interaction insights into drug development challenges for HCV drug analogues via molecular simulations. Comm. Chem. 8, 229 (2025)