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


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)


Hu, Z. and Sun, X. All-atom nonadiabatic semiclassical mapping dynamics for photoinduced charge transfer of organic photovoltaic molecules in explicit solventsJ. Chem. Theory Comput. 18, 5819–5836 (2022)


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)


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


Chen, Y. and Yuan, Q. Carbon induced segregation of Ni atoms in Cu-Ni alloyChem. Phys. Lett. 806, 139979 (2022)


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


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)


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.


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)


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)


Pan, Y., Bao, J., Zhang, X., Ni, H., Zhao, Y., Zhi, F., Fang, B., He, X.Zhang, J. Z. H., and Zhang, L. Rational design of P450 aMOx for improving anti-Markovnikov selectivity based on the “butterfly” modelFront. Mol. Biosci. 9, 888721 (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 membranesJ. Mater. Chem. A. 10, 11137-11149 (2022)


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)


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)


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)


Liang, J., Chen, Y., Bu, S., Song, S., Yang, J., Wang, M., and Yuan, Q. Computational study of the C2P4 monolayer as a stable two-dimensional material with high carrier mobility: Implications for nanoelectronic devicesACS Appl. Nano Mater. 5, 6972–6979 (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 desorptionAnal. Chem. 94, 588–592 (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 processJ. Comput. Chem. 43, 906-916 (2022)


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)


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)


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)


Yin, Y., Ding, F., and Yuan, Q. Stabilization of black phosphorene by edge-selective adsorption of C60 moleculesJ. Phys. Chem. C 126, 6874–6879 (2022)


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


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)


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)


Yang, C., Chen, E. A., and Zhang, Y. Protein–ligand docking in the machine-learning eraMolecules 27, 4568 (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 simulationComput. Biol. Chem. 98, 107648 (2022)


Liu, D., Zhao, W., and Yuan, Q. Breaking the linear relation in the dissociation of nitrogen on iron surfacesChemPhysChem 23, e202200147 (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)


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)


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)


Ren, L., Jing, Z., Xia, F.Zhang, J. Z., and Li, Y. Toxic effect of fullerene and its derivatives upon the transmembrane β2-adrenergic receptorsMolecules 27, 4562 (2022)


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


Zhao, Y., Miao, Y., Cong, Y., Wang, J., Zhi, F., Pan, Y., ... Zhang, J. Z. H. and Zhang, L. High-level expression and improved pepsin activity by enhancing the conserved domain stability based on a scissor-like modelLWT 167, 113877 (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 learningJ. Chem. Inf. Model. 62, 1840–1848 (2022)


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)


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)


Zhu, Q., Petingi, L., and Schlick, T. RNA-as-graphs motif atlas—dual graph library of RNA modules and viral frameshifting-element applicationsInt. J. Mol. Sci. 23, 9249 (2022)


Liu, L., Luo, C., Zhang, J., He, X., Shen, Y., Yan, B., ... and Jiang, L. Synergistic effect of bio‐inspired nanochannels: Hydrophilic DNA probes at inner wall and hydrophobic coating at outer surface for highly sensitive detectionSmall 18, 2201925 (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 systemPhys. Chem. Chem. Phys. 24, 1424-1436 (2022)


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)


Li, T., Yu, L., Sun, J., Liu, J., and He, X. Ionization of D571 is coupled with SARS-CoV-2 spike up/down equilibrium revealing the pH-dependent allosteric mechanism of receptor-binding domainsJ. Phys. Chem. B 126, 4828–4839 (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 systemsFood Chem. 374, 131807 (2022)


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)


Zhang, Y., Wang, Y., Xia, F., Cao, Z., and Xu, X. Accurate and efficient estimation of Lennard–Jones interactions for coarse-grained particles via a potential matching methodJ. Chem. Theory Comput. 18, 4879–4890 (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 systemJ. Phys. Chem. Lett. 13, 763–769 (2022)


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)


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)


Yan, S., Zhu, Q., Jain, S., and Schlick, T. Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppressionNat. Commun. 13, 4284 (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 dockingJ. Chem. Inf. Model. 62, 2499–2509 (2022)


Xiong, D., Zhao, X., Luo, S., Zhang, J. Z. H., and Duan, L. Molecular mechanism of the non-covalent orally targeted SARS-CoV-2 Mpro inhibitor S-217622 and computational assessment of its effectiveness against nainstream variantsJ. Phys. Chem. Lett. 13, 38, 8893–8901 (2022)


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)


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)


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)


Wang, B., Mao, J., Wei, M., Qi, Y., and Zhang, J. Z. H. SeBPPI: A sequence-based protein-protein binding predictorJ. Comput. Biophys. Chem. 21, 729-737 (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/TNTPhys. Chem. Chem. Phys. 24, 11801-11811 (2022)


Zhang, F., Wei, M., Chen, H., Ji, L., Nie, Y., and Kang, J. The genomic stability regulator PTIP is required for proper chromosome segregation in mitosisCell Div. 17, 5 (2022)


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)


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)


Humeniuk, A. and Glover, W. J. Efficient CPU and GPU implementations of multicenter integrals over long-range operators using Cartesian Gaussian functionsComput. Phys. Commun. 280, 108467 (2022)


Brian, D., Liu, Z., Dunietz, B. D., Geva, E., and Sun, X. Three-state harmonic models for photoinduced charge transfer. J. Chem. Phys. 154, 174105 (2021)


Wen, W., Huang, D., Bao, J., Zhang, J. Z. H. Residue-specific binding mechanisms of PD-L1 to its monoclonal antibodies by computational alanine scanningPhys. Chem. Chem. Phys. 23, 15591-15600 (2021)


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


Hong, R. S., Chan, E. J., Vogt-Maranto, L., Mattei, A., Sheikh, A. Y., and Tuckerman, M. E. Insights into the polymorphic structures and enantiotropic layer-slip transition in paracetamol form III from enhanced molecular dynamicsCryst. Growth Des. 21, 886-896 (2021)


Long, B., Wang, Y., Xia, Y., He, X., Bao, J. L., and Truhlar, D. G. Atmospheric kinetics: Bimolecular reactions of carbonyl oxide by a triple-level strategy. J. Am. Chem. Soc. 143, 8402–8413 (2021)


Li, N., Gao, Y., Qiu, F., and Zhu, T. Benchmark force fields for the molecular dynamic simulation of G-quadruplexesMolecules. 26, 5379 (2021)


Chen, S., Ding, X., Sun, C., Watts, A., He, X., and Zhao, X. Dynamic coupling of tyrosine 185 with the bacteriorhodopsin photocycle, as revealed by chemical shifts, assisted AF-QM/MM calculations and molecular dynamic simulationsInt. J. Mol. Sci. 22, 13587 (2021)


Ding, T., Zha, J., Zhang, D., Zhang, J., Yuan, H., Xia, F, and Gao, G. CO2 atmosphere enables efficient catalytic hydration of ethylene oxide by ionic liquids/organic bases at low water/epoxide ratiosGreen Chem. 23, 3386-3391 (2021)


Cao, L., Zeng, J., Xu, M., Chin, C.-H., Zhu, T., and Zhang, J. Z. H. Fragment-based ab initio molecular dynamics simulation for combustion. Molecules. 26, 3120 (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)


Brian, D. and Sun, X. Linear-response and nonlinear-response formulations of the instantaneous Marcus theory for nonequilibrium photoinduced charge transferJ. Chem. Theory Comput. 17, 2065–2079 (2021)


Cong, Y., Feng, Y., Ni, H., Zhi, F., Miao, Y., Fang, B., Zhang, L., and Zhang, J. Z. H. Anchor-Locker binding mechanism of the coronavirus spike protein to human ACE2: Insights from computational analysisJ. Chem. Inf. Model. 61, 3529–3542 (2021)


Sun, Z. and Zhang, J. Z. H. Thermodynamic insights of base flipping in TNA duplex: Force fields, salt concentrations, and free-energy simulation methodsCCS Chem. 3, 1026-1039 (2021)


Bao, J., He, X., and Zhang, J. Z. H. DeepBSP—a machine learning method for accurate prediction of protein–ligand docking structures. Chem. Inf. Model. 61, 2231–2240 (2021)


Hu, Z., Sun, Z., and Sun, H. Simulation of negative ion photoelectron spectroscopy using a nuclear ensemble approach: Implications from a nuclear vibration effectJ. Phys. Chem. A. 125, 6621–6628 (2021)


Jia, X., Ge, H., and Mei, Y. Free energy change estimation: The divide and conquer MBAR methodJ. Comput. Chem. 42, 1204-1211 (2021)


Luo, S., Huang, K., Zhao, X., Cong, Y., Zhang, J. Z. H., and Duan, L. Inhibition mechanism and hot-spot prediction of nine potential drugs for SARS-CoV-2 Mpro by large-scale molecular dynamic simulations combined with accurate binding free energy calculationsNanoscale. 13, 8313-8332 (2021)


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


Chen, J., Li, N., Wang, X., Chen, J., Zhang, J. Z. H., and Zhu, T. Molecular mechanism related to the binding of fluorophores to Mango-II revealed by multiple-replica molecular dynamics simulationsPhys. Chem. Chem. Phys. 23, 10636-10649 (2021)


Li, M., Lu, W.C., and Zhang, J. Z. H. Ultra-coarse-graining modeling of liquid waterJ. Chem. Phys. 154, 224506 (2021)


Schlick, T. From butterflies to bits: A sweeping vision for the code of lifeBiophys. Rep. 1, 100010 (2021)


Shao, G., Bao, J., Pan, X., He, X., Qi, Y., and Zhang, J. Z. Computational analysis of residue-specific binding free energies of androgen receptor to ligandsFront. Biosci. 8, 646524 (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 IICryst. Growth Des. 21, 5544–5557 (2021)


Xia, W., He, L., Bao, J., Qi, Y., and Zhang, J. Z. H. Insights into small molecule inhibitor bindings to PD-L1 with residue-specific binding free energy calculationJ. Biomol. Struct. Dyn. 1-9 (2021)


Liu, Y., Cong, Y., Zhang, C., Fang, B., Pan, Y., Li, Q., You, C., Gao, B., Zhang, J. Z. H., Zhu, T., and Zhang, LEngineering the biomimetic cofactors of NMNH for cytochrome P450 BM3 based on binding conformation refinementRSC Adv. 11, 12036-12042 (2021)


Lv, Y., Luo, S., Huang, K., Wang, H., Dong, S., Cong, Y., Zhang, J. Z. H., and Duan, L. Investigating effects of bridging water on the binding of neuraminidase−ligands using computational alanine scanning combined with interaction entropy methodJ. Mol. Liq. 336, 116214 (2021)


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


Wang, X, Yan, J., Zhang, H., Xu, Z., and Zhang, J. Z. H. An electrostatic energy-based charge model for molecular dynamics simulationJ. Chem. Phys. 154, 134107 (2021)


Kaplan, M., Wang, Y., Chreifi, G., Zhang, L., Chang, Y.-W., and Jensen, G. J. Programmed flagellar ejection in caulobacter crescentus leaves PL-subcomplexesJ. Mol. Biol. 433, 1670042 (2021)


Chen, R., Miao, Y., Hao, X., Gao, B., Ma, M., Zhang, J. Z. H., Wang, R., Li, S., He, X., and Zhang, L. Investigation on the characteristics and mechanisms of ACE inhibitory peptides by a thorough analysis of all 8000 tripeptides via binding free energy calculationFood Sci. Nutr. 9, 2943-2953 (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 dynamicsJ. Phys. Chem. Lett. 12, 8749–8756 (2021)


Zheng, L., Chen, Y., Bao, J., He, L., Dong, S., Qi, Y., and Zhang, J. Z. H. Discovery of novel inhibitors of SARS-CoV-2 main proteaseJ. Biomol. Struct. Dyn. 1-9 (2021)


Li, M. and Zhang, J. Z. H. Multiscale polarizable coarse-graining water models on cluster-level electrostatic dipolesPhys. Chem. Chem. Phys. 23, 8926-8935 (2021)


Zelovich, T. and Tuckerman, M. E. OH− and H3O+ Diffusion in model AEMs and PEMs at low hydration: Insights from ab initio molecular dynamicsMembranes. 11, 355 (2021)


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


Yin, Y., Chen, H., and Yuan, Q. Strain-induced bandgap engineering in C3N nanotubesChem. Phys. Lett. 768, 138390 (2021)


Pan, X., Wang, H., Li, C., Zhang, J. Z. H., and Ji, C. MolGpka: A web server for small molecule pKa prediction using a graph-convolutional neural networkJ. Chem. Inf. Model. 61, 3159–3165 (2021)


Xue, Y., Wang, J.-N., Hu, W., Zheng, J., Li, Y., Pan, X., Mo, Y., Shao, Y., Wang, L., and Mei, Y. Affordable ab initio path integral for thermodynamic properties via molecular dynamics simulations using semiempirical reference potentialJ. Phys. Chem. A 125, 10677–10685 (2021)


Zhang, L., Zheng, J., Ma, M., Zhao, Y., Song, J., Chen, X., Cao, W., He, X., Xue, C., and Tang, Q. Drug-guided screening for pancreatic lipase inhibitors in functional foods. Food Funct. 12, 4644-4653 (2021)


Schlick, T. and Portillo-Ledesma, S. Biomolecular modeling thrives in the age of technology. Nat. Comput. Sci. 1, 321-331 (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 reactionsJ. Chem. Theory Comput. 17, 5745–5758 (2021)


Schlick, T., Zhu, Q., Jain, S., and Yan, S. Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element. Biophys. J. 120, 1040-1053 (2021)


T. Schlick, “Isabella Karle: A Crystallography Pioneer”, DNA Cell Biol. June 14, 2021. doi: 10.1089/dna.2021.0372.


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 drugsNanoscale. 13, 19218-19237 (2021)


Portillo-Ledesma, S., Tsao, L. H., Wagley, M., Lakadamyali, M., Cosma, M. P., and Schlick, T. Nucleosome clutches are regulated by chromatin internal parametersJ. Mol. Biol. 433, 166701 (2021)


Huai, Z., Tong, Z., Mei, Y., and Mo, Y. Theoretical study of the spectral differences of the Fenna–Matthews–Olson protein from different species and their mutantsJ. Phys. Chem. B. 125, 8313–8324 (2021)


Shen, C., Wang, X., and He, X. Fragment-based quantum mechanical calculation of excited-state properties of fluorescent RNAsFront. Chem. 9, 801062 (2021)


Shi, M., Jin, X., Wan, Z., and He, XAutomated fragmentation quantum mechanical calculation of 13C and 1H chemical shifts in molecular crystalsJ. Chem. Phys. 154, 064502 (2021)


Schlick, T. and Bishop, T. C. MGO on the go: Multiscale genome symposium-annual biophysical society meeting 2021. Biophys. Rev. 13, 309–310 (2021)


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


Wang, J.-N., Liu, W., Li, P., Mo, Y., Hu, W., Zheng, J., Pan, X., Shao, Y., and Mei, Y. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanics accuracy via a semiempirical reference potential. 4. adaptive QM/MMJ. Chem. Theory Comput. 17, 1318-1325 (2021)


Tinnin, J., Aksu, H., Tong, Z., Zhang, P., Geva, E., Dunietz, B. D., Sun, X., and Cheung, M. S. CTRAMER: An open-source software package for correlating interfacial charge transfer rate constants with donor/acceptor geometries in organic photovoltaic materialsJ. Chem. Phys. 154, 214108 (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)


Zeng, J., Weng, J., Zhang, Y., Xia, F., Cui, Q., and Xu, X. Conformational features of Ras: Key hydrogen-bonding interactions of Gln61 in the intermediate state during GTP hydrolysisJ. Phys. Chem. B. 125, 8805–8813 (2021)


Liu, J. and He, X. Ab initio molecular dynamics simulation of liquid water with fragment- based quantum mechanical approach under periodic boundary conditionsChin. J. Chem. Phys. 34, 761-768 (2021)


Hao, X., Liu, J., Ali, I., Luo, H., Han, Y., Hu, W., Liu, J., He, X. and Li, J. Ab initio determination of crystal stability of di-p-tolyl disulfideSci. Rep. 11, 7076 (2021)


Schlick, T., Portillo-Ledesma, S., Myers, C. G., Beljak, L., Chen, J., Dakhel, S., Darling, D., Ghosh, S., Hall, J., Jan, M., Liang, E., Saju, S., Vohr, M., Wu, C., Xu, Y., Xue, E. Biomolecular modeling and simulation: A prospering multidisciplinary field. Annu. Rev. Biophys. 50, 267-301 (2021)


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


Paz, A. S. P. and Glover, W. J. Diabatic many-body expansion: Development and application to charge-transfer reactionsJ. Chem. Theory Comput. 17, 1497-1511 (2021)


Xu, M., Zhu, T., and Zhang, J. Z. H. Automatically constructed neural network potentials for molecular dynamics simulation of zinc proteinsFront. Chem. 9, 692200 (2021)


Brian, D. and Sun, X. Charge-transfer landscape manifesting the structure–rate relationship in the condensed phase via machine learningJ. Phys. Chem. B. 125, 13267–13278 (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)21Nat. Commun. 12, 6141 (2021)


Lu, J., Xia, S., Lu, J., and Zhang, Y. Dataset construction to explore chemical space with 3D geometry and deep learningJ. Chem. Inf. Model. 61,1095-1104 (2021)


Li, Z. and Zhang, J. Z. H. Quantitative analysis of ACE2 binding to coronavirus spike proteins: SARS-CoV-2 vs. SARS-CoV and RaTG13Phys. Chem. Chem. Phys. 23, 13926-13933 (2021)


Liu, J., Liu, Y., Yang, J., Zeng, X. C., and He, XDirectional proton transfer in the reaction of the simplest criegee intermediate with water involving the formation of transient H3O+J. Phys. Chem. Lett. 12, 3379-3386 (2021)


Gómez-García, P. A., Portillo-Ledesma, S., Neguembor, M. V., Pesaresi, M., Oweis, W., Rohrlich, T., Wieser, S., Meshorer, E., Schlick, T., Cosma, M. P., Lakadamyali, M. Mesoscale modeling and single-nucleosome tracking reveal remodeling of clutch folding and dynamics in stem cell differentiation. Cell Rep. 34, 108614 (2021)


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


Felker, P. M. and Bačić, Z. Intra- and intermolecular rovibrational states of HCl-H2O and DCl-H2O dimers from full-dimensional and fully coupled quantum calculationsChin. J. Chem. Phys. 34, 6 (2021)


Zhu, Q. and Schlick, T. A Fiedler vector scoring approach for novel RNA motif selectionJ. Phys. Chem. B. 125,1144-1155 (2021)


Shen, C., Jin, X., Glover, J. W., and He, X. Accurate prediction of absorption spectral shifts of proteorhodopsin using a fragment-based quantum mechanical methodMolecules. 26, 4486 (2021)


Zhao, J., Blayney, A., Liu, X., Gandy, L., Jin, W., Yan, L., Ha, J.-H., Canning, A. J., Connelly, M., Yang, C., Liu, X., Xiao, Y., Cosgrove, M. S., Solmaz, S. R., Zhang, Y., Ban, D., Chen, J., Loh, S. N., and Wang, C. EGCG binds intrinsically disordered N-terminal domain of p53 and disrupts p53-MDM2 interactionNat. Commun. 12, 986 (2021)


Wang, X., Li, X., He, X., and Zhang, J. Z. H. A fixed multi-site interaction charge model for an accurate prediction of the QM/MM interactionsPhys. Chem. Chem. Phys. 23, 21001-21012 (2021)


Shao, G., Bao, J., Pan, X., He, X.Qi, Y., and Zhang, J. Z. H. Analysis of the binding modes of the first- and second-generation antiandrogens with respect to F876L mutationChem. Biol. Drug Des. 98, 60-72 (2021)


Yusufova, N., Kloetgen, A., Teater, M., Osunsade, A., Camarillo, J. M., Chin, C. R., Doane, A. S., Venters, B. J., Portillo-Ledesma, S., Conway, J., Phillip, J. M., Elemento, O., Scott, D. W., Béguelin, W., Licht, J. D., Kelleher, N. L., Staudt, L. M., Skoultchi, A. I., Keogh, M.-C., Apostolou, E., Mason, C. E., Imielinski, M., Schlick, T., David, Y., Tsirigos, A., Allis, C. D., Soshnev, A. A., Cesarman, E., and Melnick, A. M. Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture. Nature. 589, 299-305 (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)


Duan, L., Dong, S., Huang, K., Cong, Y., Luo, S., and Zhang, J. Z. H. Computational analysis of binding free energies, hotspots and the binding mechanism of Bcl-xL/Bcl-2 binding to Bad/Bax. Phys. Chem. Chem. Phys. 23, 2025-2037 (2021)


Zhao, X., Zhang, P., Li, Y., Wu, S., Li, F., Wang, Y., Liang, S., He, X., Zeng, Y., and Liu, Z. Glucose–lipopeptide conjugates reveal the role of glucose modification position in complexation and the potential of malignant melanoma therapy. J. Med. Chem. 64, 11483–11495 (2021)


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 cellseLife. 10, e72062 (2021)


Liu, Y., Li, J., Felker, P. M., and Bačić, Z. HCl–H2O dimer: An accurate full-dimensional potential energy surface and fully coupled quantum calculations of intra- and intermolecular vibrational states and frequency shiftsPhys. Chem. Chem. Phys. 23, 7101–7114 (2021)


Chin, C.-H., Zhu, T., and Zhang, J. Z. H. Cyclopentadienyl radical formation from the reaction of excited nitrogen atoms with benzene: A theoretical study. Phys. Chem. Chem. Phys. 23, 12408-12420 (2021)


Zhao, Y., Miao, Y., Zhi, F., Pan, Y., Zhang, J., Yang, X., Zhang, J. Z. H., and Zhang, L. Rational design of pepsin for enhanced thermostability via exploiting the guide of structural weakness on stabilityFront. Phys. 9, 755253 (2021)


Sun, Z., Gong, Z., Xia, F., and He, X. Ion dynamics and selectivity of Nav channels from molecular dynamics simulationChem. Phys. 548, 111245 (2021)


Wang, F., Hu, Z., Wang, X. B., Sun, Z., and Sun, H. Assessment of DFT methods for the prediction of detachment energies and electronic structures of complex and multiply charged anions. Comput. Theor. Chem. 1202, 113295 (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 waterNat. Commun. 12, 6880 (2021)


Zeng, J., Zhang, L., Wang, H., and Zhu, T. Exploring the chemical space of linear alkane pyrolysis via deep potential GENeratorEnergy Fuels. 35, 762–769 (2021)


Felker, P. M., Liu, Y., Li, J., and Bačić, Z. DCl–H2O, HCl–D2O, and DCl–D2O dimers: Inter- and intramolecular vibrational states and frequency shifts from fully coupled quantum calculations on a full-dimensional neural network potential energy surfaceJ. Phys. Chem. A. 125, 6437–6449 (2021)


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


Zelovich, T., Winey, K. I., and Tuckerman, M. EHydronium ion diffusion in model proton exchange membranes at low hydration: Insights from ab initio molecular dynamicsJ. Mater. Chem. A. 9, 2448-2458 (2021)


Wang, T., Hu, Z., Nie, X., Huang, L., Hui, M., Sun, X., and Zhang, G. Thermochromic aggregation-induced dual phosphorescence via temperature-dependent sp3 -linked donor-acceptor electronic coupling. Nat. Commun. 12, 1364 (2021)


Rogal, J., & Tuckerman, M. E. (2021). Pathways in Classification Space: Machine Learning as a Route to Predicting Kinetics of Structural Transitions in Atomic Crystals. In Multiscale Dynamics Simulations (pp. 312-348).


Wu, D., Hu, Z., Li, J., and Sun, X. Forecasting nonadiabatic dynamics using hybrid convolutional neural network/long short-term memory networkJ. Chem. Phys. 155, 224104 (2021)


Abreu, C. R. A. and Tuckerman, M. E. Hamiltonian based resonance-free approach for enabling very large time steps in multiple time-scale molecular dynamicsMol. Phys. e1923848 (2021)


Han, Y., He, L., Qi, Y., Zhao, Y., Pan, Y., Fang, B., Li, S., Zhang, J. Z. H., and Zhang, L. Identification of three new compounds that directly target human serine hydroxymethyltransferase 2. Chem. Biol. Drug Des. 97, 221-230 (2021)


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


Zhang, B., Ma, Y., Jin, X., Wang, Y., Suo, B., He, X., and Jin, Z. GridMol2. 0: Implementation and application of linear‐scale quantum mechanics methods and molecular visualization. Int. J. Quantum Chem. 120, e26402 (2020)


Shan, J., Pan, X., Wang, X., Xiao, X., and Ji, C. FragRep: A web server for structure-based drug design by fragment replacement. J. Chem. Inf. Model. 60, 5900–5906 (2020)


Zha, J., Zhang, Y., Xia, K., Gräter, F., and Fei Xia. Coarse-grained simulation of mechanical properties of single microtubules with micrometer length. Front. Biosci. 7, 632122 (2020)


Felker, P. M. and Bačić, Z. HDO−CO complex: D‑bonded and H‑bonded isomers and intra- and intermolecular rovibrational states from full-dimensional and fully coupled quantum calculationsJ. Phys. Chem. A. 125, 980−989 (2021)


Cendagorta, J. R., Shen, H., Bačić, Z., and Tuckerman, M. E. Enhanced sampling path integral methods using neural network potential energy surfaces with application to diffusion in hydrogen hydratesAdv. Theory Simul. 4, 2000258 (2020)


Bao, J., He, X., and Zhang, J. Z. H. Development of a new scoring function for virtual screening: APBScoreJ. Chem. Inf. Model. 60, 6355–6365 (2020)


Shan, J. and Ji, C. MolOpt: A web server for drug design using bioisosteric transformationCurr. Comput. Aided Drug Des. 16, 460 - 466 (2020)


Zhang, Y., Cao, Z., Zhang, J. Z. H., and Xia, F. Double-well ultra-coarse-grained model to describe protein conformational transitions. J. Chem. Theory Comput. 16, 6678–6689 (2020)


Du, J., Li, W., Liu, B., Zhang, Y., Yu, J., Hou, X., and Fang, H. An in silico mechanistic insight into HDAC8 activation facilitates the discovery of new small-molecule activators.  Bioorg. Med. Chem. 28, 115607 (2020)


Chin, C.-H., Zhu, T., and Zhang, J. Z. H. Reaction mechanism and product branching ratios of OH+C2H3F reaction: A theoretical study. Chin. J. Chem. Phys. 33, 203 (2020)


Li, M., Lu, W.C., and Zhang, J. Z. H. A three-point coarse-grained model of five-water cluster with permanent dipoles and quadrupoles. Phys. Chem. Chem. Phys. 22, 26289-26298 (2020)


Zeng, J., Cao, L., Xu, M., Zhu, T., and Zhang. J. Z. H. Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation. Nat. Commun. 11, 5713 (2020)


Burnham, C. J., Futera, Z., Bačić, Z., and English, N. J. Hydrogen intramolecular stretch redshift in the electrostatic environment of type II clathrate hydrates from Schrödinger equation treatment. Appl. Sci. 10, 8504 (2020)


Hu, Z., Tong, Z., Cheung, M. S., Dunietz, B. D., Geva, E., and Sun, X. Photoinduced charge transfer dynamics in the carotenoid–porphyrin–C60 triad via the linearized semiclassical nonequilibrium Fermi’s golden rule. J. Phys. Chem. B. 124, 9579–9591 (2020)


Hu, W., Li, P., Wang, J.-N., Xue, Y., Mo, Y., Zheng, J., Pan, X., Shao, Y., Mei, Y. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanics accuracy via a semiempirical reference potential. 3. Gaussian smoothing on density-of-states. J. Chem. Theory Comput. 16, 6814–6822 (2020)


Han, J., Zhang, P., Aksu, H., Maiti, B., Sun, X., Geva, E., Dunietz, B. D., and Cheung, M. S. On the interplay between electronic structure and polarizable force fields when calculating solution-phase charge-transfer rates. J. Chem. Theory Comput. 16, 6481–6490 (2020)


Song, H., Vogt-Maranto, L., Wiscons, R., Matzger, A. J., and Tuckerman, M. E. Generating cocrystal polymorphs with information entropy driven by molecular dynamics-based enhanced sampling. J. Phys. Chem. Lett. 11, 9751–9758 (2020)


Wang, B., Li, C., Jia, X., Zhu, T., and Zhang, J. Z. H. An approach to computing solvent reorganization energy. J. Chem. Theory Comput. 16, 6513–6519 (2020)


Abreu, C. R. A. and Tuckerman, M. E. Molecular dynamics with very large time steps for the calculation of solvation free energiesJ. Chem. Theory Comput. 16, 7314–7327 (2020)


Zha, J., Ding, T., Chen, J., Wang, R., Gao, G., and Xia, F. Reaction mechanism of CO2 and styrene oxide catalyzed by ionic liquids: A combined DFT calculation and experimental study. J. Phys. Chem. A. 124, 7991–7998 (2020)


Long, Z., Atsango, J. A., Napoli, J. A., Markland, T. E., and Tuckerman, M. E. Elucidating the proton transport pathways in liquid imidazole with first-principles molecular dynamics. J. Phys. Chem. Lett. 11, 6156–6163 (2020)


Luo, X., Liu, H., Bae, C., Tuckerman, M. E., Hickner, M. A., and Paddison, S. J. Mesoscale simulations of quaternary ammonium-tethered triblock copolymers: Effects of the degree of functionalization and styrene contentJ. Phys. Chem. C. 124, 16315–16323 (2020)


Zelovich, T. and Tuckerman, M. E. Water layering affects hydroxide diffusion in functionalized nanoconfined environmentsJ. Phys. Chem. Lett. 11, 5087–5091 (2020)


Zhang, Y., Poe, D., Heroux, L., Squire, H., Doherty, B. W., Long, Z., Dadmun, M., Gurkan, B., Tuckerman, M. E., and Maginn, E. J. Liquid structure and transport properties of the deep eutectic solvent ethalineJ. Phys. Chem. B. 124, 5251–5264 (2020)


Li, C., Chin, C.-H., Zhu, T.Zhang, J. Z. H. An ab initio/RRKM study of the reaction mechanism and product branching ratios of CH3OH+ and CH3OH++ dissociationJ. Mol. Struct. 1217, 128410 (2020)


Bogojeski, M., Vogt-Maranto, L., Tuckerman, M. E., Müller, K.-R., and Burke, K. Quantum chemical accuracy from density functional approximations via machine learningNat. Commun. 11, 5223 (2020)


 Jin, X., Glover, W. J., and He, X. Fragment quantum mechanical method for excited states of proteins: Development and application to the green fluorescent proteinJ. Chem. Theory Comput. 16, 5174–5188 (2020)


Curchod, B. F. E., Glover, W. J., and Martínez, T. J. SSAIMS—stochastic-selection ab initio multiple spawning for efficient nonadiabatic molecular dynamics. J. Phys. Chem. A. 124, 6133–6143 (2020)


Tong, Z., Gao, X., Cheung, M. S., Dunietz, B. D., Geva, E., and Sun, X. Charge transfer rate constants for the carotenoid-porphyrin-C60 molecular triad dissolved in tetrahydrofuran: The spin-boson model vs the linearized semiclassical approximation. J. Chem. Phys. 153, 044105 (2020)


Tong, Z., Videla, P. E., Jung, K. A., Batista, V. S., and Sun, X. Two-dimensional Raman spectroscopy of Lennard-Jones liquids via ring-polymer molecular dynamics. J. Chem. Phys. 153, 034117 (2020)


Felker, P. M. and Bačić, Z. H2O–CO and D2O–CO complexes: Intra- and intermolecular rovibrational states from full-dimensional and fully coupled quantum calculationsJ. Chem. Phys. 153, 074107 (2020)


Felker, P. M. and Bačić, Z. Flexible water molecule in C60: Intramolecular vibrational frequencies and translation-rotation eigenstates from fully coupled nine-dimensional quantum calculations with small basis setsJ. Chem. Phys. 152, 014108 (2020)


Xu, M., Felker, P. M., and Bačić, Z. Light molecules inside the nanocavities of fullerenes and clathrate hydrates: Inelastic neutron scattering spectra and the unexpected selection rule from rigorous quantum simulationsInt. Rev. Phys. Chem. 39, 425-463 (2020)


Cendagorta, J. R., Tolpin, J., Schneider, E., Topper, R. Q., and Tuckerman, M. E. Comparison of the performance of machine learning models in representing high-dimensional free energy surfaces and generating observables. J. Phys. Chem. B. 124, 3647–3660 (2020)


Fellah, N., Shtukenberg, A. G., Chan, E. J., Vogt-Maranto, L., Xu, W., Li, C., Tuckerman, M. E., Kahr, B., and Ward, M. D. Disorderly conduct of benzamide IV: Crystallographic and computational analysis of high entropy polymorphs of small molecules. Cryst. Growth Des. 20, 2670-2682 (2020)


Hou, X., Sun, J., Ge, L., Liang, X., Li, K., Zhang, Y., and Fang, H. Inhibition of striatal-enriched protein tyrosine phosphatase by targeting computationally revealed cryptic pocketsEur. J. Med. Chem. 190, 112131 (2020)


Huang, K., Luo, S., Cong, Y., Zhong, S., Zhang, J. Z. H., and Duan, L. An accurate free energy estimator: based on MM/PBSA combined with interaction entropy for protein–ligand binding affinityNanoscale. 12, 10737-10750 (2020)


Li, C., Wang, B., Jia, X., and Zhang, J. Z. H. Efficient calculation of excess free energy of pure and mixed alcohol solutions. Chem. Phys. Lett. 749, 137397 (2020)


Wang, Z., Han, Y., Li, J., He, X. Combining the fragmentation approach and neural network potential energy surfaces of fragments for accurate calculation of protein energy. J. Phys. Chem. B. 124, 3027-3035 (2020)


Felker, P. M. and Bačić, Z. Benzene–H2O and benzene–HDO: Fully coupled nine-dimensional quantum calculations of flexible H2O/HDO intramolecular vibrational excitations and intermolecular states of the dimers, and their infrared and Raman spectra using compact basesJ. Chem. Phys. 152, 124103 (2020)


Duan, G., Ji, C., and Zhang, J. Z. H. Developing an effective polarizable bond method for small molecules with application to optimized molecular dockingRSC Adv. 10, 15530-15540 (2020)


Cong, Y., Huang, K., Li, Y., Zhong, S., Zhang, J. Z. H., and Duan, L. Entropic effect and residue specific entropic contribution to the cooperativity in streptavidin–biotin binding. Nanoscale. 12, 7134-7145 (2020)


Huang, L., Han, Y., He, X., and Li, J. Ab initio-enabled phase transition prediction of solid carbon dioxide at ultra-high temperatures. RSC Adv. 10, 236-243 (2020)


Qi, Y. and Zhang, J. Z. H. DenseCPD: Improving the accuracy of neural-network-based computational protein sequence design with DenseNetJ. Chem. Inf. Model. 60, 1245-1252 (2020)


Tinnin, J., Bhandari, S., Zhang, P., Aksu, H., Maiti, B., Geva, E., Dunietz, B. D., Sun, X., and Cheung, M. S. Molecular-level exploration of the structure-function relations underlying interfacial charge transfer in the subphthalocyanine/C60 organic photovoltaic systemPhys. Rev. Appl. 13, 054075 (2020)


Wang, B., Qi, Y., Gao, Y., and Zhang, J. Z. H. A method for efficient calculation of thermal stability of proteins upon point mutationsPhys. Chem. Chem. Phys. 22, 8461-8466 (2020)


Liu, L., Gao, H., Yang, S.-Q., Chen, X.-C., Lu, Y., Liu, Y., and Xia, F. Ir-catalyzed tandem hydroformylation-transfer hydrogenation of olefins with (trans-/cis-)formic acid as hydrogen source in presence of 1,10-phenanthroline. J. Catal. 385, 183-193 (2020)


Li, F., Zhang, J. Z., and Xia, F. How CuCl and CuCl2 insert into C–N bonds of diazo compounds: An electronic structure and mechanistic study. J. Phys. Chem. A. 124, 2029-2035 (2020)


Huang, L., Han, Y., Liu, J., He, X., and Li, J. Ab initio prediction of the phase transition for solid ammonia at high pressuresSci. Rep. 10, 7546 (2020)


Wang, R., Cong, Y., Li, M., Bao, J., Qi, Y., and Zhang, J. Z. H. Molecular mechanism of selective binding of NMS-P118 to PARP-1 and PARP-2: A computational perspective. Front. Mol. Biosci. 7, 50 (2020)


Xu, R., Hu, Z., Wang, X., Liu, Y., Zhou, Z., Xu, J., Sun, Z., Sun, H., and Chen, J. Intramolecular charge transfer in 5-halogen cytidines revealed by femtosecond time-resolved spectroscopyJ. Phys. Chem. B. 124, 2560-2567 (2020)


Liu, J. and He, X. Fragment-based quantum mechanical approach to biomolecules, molecular clusters, molecular crystals and liquidsPhys. Chem. Chem. Phys. 22, 12341-12367 (2020)


Li, M., Teng, B., and Zhang, J. Z. H. Atomic-level reconstruction of biomolecules by a rigid-fragment- and local-frame-based (RF-LF) strategy. J. Mol. Model. 26, 31 (2020)


Jain, S., Zhu, Q., Paz, A. S. P., and Schlick, T. Identification of novel RNA design candidates by clustering the extended RNA-As-Graphs library. BBA General Subjects. 1864, 129534 (2020)


Zhang, W., Liu, J., Jin, X., Gu, X., Zeng, X. C., He, X., and Li, H. Quantitative prediction of aggregation‐induced emission: A full quantum mechanical approach to the optical spectraAngew. Chem. Int. Ed. 59, 2-8 (2020)


Huang, D., Tian, S., Qi, Y., and Zhang, J. Z. H. Binding modes of small-molecule inhibitors to the EED pocket of PRC2. ChemPhysChem. 21, 263-271 (2020)


Myers, C. G., Olins, D. E., Olins, A. L., and Schlick, T. Mesoscale modeling of nucleosome-binding antibody PL2-6: Mono- versus bivalent chromatin complexes. Biophys. J. 118, 2066-2076 (2020)


Li, X., Cong, Y., Ma, M., You, Z.-N., Gao, B., Zhang, J. Z. H., and Zhang, L. An energy optimization strategy based on the perfect conformation of prolyl endopeptidase for improving catalytic efficiency. J. Agric. Food Chem. 68, 5129–5137 (2020)


Li, Z., Bao, J., Qi, Y., and Zhang, J. Z. H. Computational approaches to studying methylated H4K20 recognition by DNA repair factor 53BP1. Phys. Chem. Chem. Phys. 22, 6136-6144 (2020)


Sridhara, A., Farra, S. E., Portellab, G., Schlick, T., Orozco, M., and Collepardo-Guevara, R. Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry. Proc. Natl. Acad. Sci. U.S.A. 117, 7216–7224 (2020)


Tong, Z., Huai, Z., Mei, Y., and Mo, Y. Reproducing the low-temperature excitation energy transfer dynamics of phycoerythrin 545 light-harvesting complex with a structure-based model Hamiltonian. J. Chem. Phys. 152, 135101 (2020)


Tian, S., Ji, C., and Zhang, J. Z. H. Molecular basis of SMAC-XIAP binding and the effect of electrostatic polarizationJ. Biomol. Struct. Dyn. 39, 1588-1599 (2021)


Sadek, J., Wuo, M. G., Rooklin, D., Hauenstein, A., Hong, S. H., Gautam, A., Wu, H., Zhang, Y., Cesarman, E., and Arora, P. S. Modulation of virus-induced NF-κB signaling by NEMO coiled coil mimics. Nat. Commun. 11, 1786 (2020)


Guo, J., Yang, L., Gao, Z., Zhao, C., Mei, Y., and Song, Y.-Y. Insight of MOF environment-dependent enzyme activity via MOFs-in-nanochannels configurationACS Catal. 10, 5949–5958 (2020)


Cong, Y., Duan, L., Huang, K., Bao, J., and Zhang, J. Z. H. Alanine scanning combined with interaction entropy studying the differences of binding mechanism on HIV-1 and HIV-2 proteases with inhibitor. J. Biomol. Struct. Dyn. 39, 1588-1599 (2020)


Katigbak, J., Li, H., Rooklin, D., and Zhang, Y. AlphaSpace 2.0: Representing concave biomolecular surfaces using β-clusters. J. Chem. Inf. Model. 60, 1494-1508 (2020)


Chin, C.-H., Zhu, T., and Zhang, J. Z. H. Formation mechanism and spectroscopy of C6H radicals in extreme environments: a theoretical study. Phys. Chem. Chem. Phys. 21, 23044-23055 (2019)


Tian, S., Zeng, J., Liu, X., Chen, J., Zhang, J. Z. H., and Zhu, T. Understanding the selectivity of inhibitors toward PI4KIIIα and PI4KIIIβ based molecular modeling. Phys. Chem. Chem. Phys. 21, 22103-22112 (2019)


Luo, H., Liu, J., He, X., and Li, J. Low-temperature polymorphic transformation of β-lactam antibiotics. Crystals. 9, 460 (2019)


Yang, H., Zhang, F., Huang, C.-J., Liao, J., Han, Y., Hao, P., Chu, Y., Lu, X., Li, W., Yu, H., and Kang, J. Mps1 regulates spindle morphology through MCRS1 to promote chromosome alignment. Mol. Biol. Cell. 30, 1051-1128 (2019)


Jain, S., Tao, Y., and Schlick, T. Inverse folding with RNA-As-Graphs produces a large pool of candidate sequences with target topologiesJ. Struct. Biol. 209, 107438 (2020)


Petkov, B. K., Gellen, T. A., Farfan, C. A., Carbery, W. P., Hetzler, B. E., Trauner, D., Li, X., Glover, W. J., Ulness, D. J., and Turner, D. B. Two-dimensional electronic spectroscopy reveals the spectral dynamics of Förster resonance energy transferChem. 5, 1928-1929 (2019)


Wang, Y., Verma, P., Zhang, L., Li, Y., Liu, Z., Truhlar, D. G., and He, X. M06-SX screened-exchange density functional for chemistry and solid-state physics. Proc. Natl. Acad. Sci. U.S.A. 117, 2294-2301 (2020)


Xu, J., Liu, J., Liu, J., Hu, W., He, X., and Li, J. Phase transition of ice at high pressures and low temperatures. Molecules. 25, 486 (2020)


Rogal, J., Schneider, E., and Tuckerman, M. E. Neural-network-based path collective variables for enhanced sampling of phase transformationsPhys. Rev. Lett. 123, 245701 (2019)


Liu J., He X. (2020) QM Implementation in Drug Design: Does It Really Help? In: Heifetz A. (eds) Quantum Mechanics in Drug Discovery. Methods in Molecular Biology, vol 2114. Humana, New York, NY


Meng, G., Tariq, M., Jain, S., Elmetwaly, S., and Schlick, T. RAG-Web: RNA structure prediction/design using RNA-As-Graphs. Bioinformatics. 36, 647–648 (2020)


Mao, J., Aladin, V., Jin, X., Leeder, A. J., Brown, L. J., Brown, R. C. D., He, X., Corzilius, B., and Glaubitz, C. Exploring protein structures by DNP-enhanced methyl solid-state NMR spectroscopy. J. Am. Chem. Soc. 141, 19888-19901 (2019)


Gao, Z., Bao, J., Shi, S., Zhang, X., Gao, Y., and Zhu, T. Effect of mutations on drug resistance of smoothened receptor toward inhibitors probed by molecular modelingChem. Phys. Lett. 741, 137126 (2020)


Wu, Z., Zhang, Y., Zhang, J. Z., Xia, K., and Xia, F. Determining optimal coarse-grained representation for biomolecules using internal cluster validation indexesJ. Comput. Chem. 41, 14-20 (2019)


Sun, Z., Wang, X., and Zhang, J. Z. H. Theoretical understanding of the thermodynamics and interactions in transcriptional regulator TtgR–ligand binding. Phys. Chem. Chem. Phys. 22, 1511-1524 (2020)


Zeng, J., Cao, L., Chin, C.-H., Ren, H., Zhang, J. Z. H., and Zhu, T. ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations. Phys. Chem. Chem. Phys. 22, 683-691 (2020)


Shao, Y., Mei, Y., Sundholm, D., and Kaila, V. R. I. Benchmarking the performance of time-dependent density functional theory methods on biochromophoresJ. Chem. Theory Comput. 16, 587-600 (2019)


Glover, W. J. and Schwartz, B. J. The fluxional nature of the hydrated electron: Energy and entropy contributions to aqueous electron free energies. J. Chem. Theory Comput. 16, 1263-1270 (2020)


Marsiglia, W., Katigbak, J., Zheng, S., Mohammadi, M., Zhang, Y., and Traaseth N. A conserved allosteric pathway in tyrosine kinase regulation. Structure. 27, 1308-1315.e3 (2019)


Yang, Y., Lu, J., Yang, C., and Zhang, Y. Exploring fragment-based target specific ranking protocol with machine learning on cathepsin S. J. Comput. Aided Mol. Des. 33, 1095-1105 (2019)


Lu, J., Hou, X., Wang, C., and Zhang Y. Incorporating explicit water molecules and ligand conformation stability in machine-learning scoring functions. J. Chem. Inf. Model. 59, 4540-4549 (2019)


Glover, W. J., Paz, A. S. P., Thongyod, W., and Punwong, C. Analytical gradients and derivative couplings for dynamically weighted complete active space self-consistent fieldJ. Chem. Phys. 151, 201101 (2019)


Wang, T., Su, X., Zhang, X., Nie, X., Huang, L., Zhang, X., Sun, X., Luo, Y., and Zhang, G. Aggregation-induced dual-phosphorescence from organic molecules for non-doped light-emitting diodesAdv. Mater. 31, 1904273 (2019)


Sun, X. Hybrid equilibrium-nonequilibrium molecular dynamics approach for two-dimensional solute-pump/solvent-probe spectroscopyJ. Chem. Phys. 151, 194507 (2019)


Wang, M., Mei, Y., and Ryde, U. Host-guest relative binding affinities at density-functional theory level from semiempirical molecular dynamics simulations. J. Chem. Theory Comput. 15, 2659-2671 (2019)


Zhang, Y., Xia, K., Cao, Z., Gräter, F., and Xia, F. A new method for the construction of coarse-grained models of large biomolecules from low-resolution cryo-electron microscopy data. Phys. Chem. Chem. Phys. 21, 9720-9727 (2019)


Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J. Z. H., and Hou, T. End-point binding free energy calculation with MM/PBSA and MM/GBSA: Strategies and applications in drug design. Chem. Rev. 119, 9478-9508 (2019)


Han, Y., Liu, J., Huang, L., He, X., and Li, J. Predicting the phase diagram of solid carbon dioxide at high pressure from first principles. npj Quantum Materials. 4, 10 (2019)


Zhang, L., Mei, D., Wu, Y., Shen, C., Hu, W., Zhang, L., Li, J., Wu, Y., and He, X. Syntheses, structures, optical properties, and electronic structures of Ba6Cu2GSn4S16 (G= Fe, Ni) and Sr6D2FeSn4S16 (D= Cu, Ag). J. Solid State Chem. 272, 69-77 (2019)


Duan, L., Guo, X., Cong, Y., Feng, G., Li, Y., and Zhang, J. Z. H. Accelerated molecular dynamics simulation for helical proteins folding in explicit water. Front Chem. 7, 540 (2019)


Verma, P., Janesko, B. G., Wang, Y., He, X., Scalmani, G., Frisch, M. J., and Truhlar, D. G. M11plus: A range-separated hybrid meta functional with both local and rung-3.5 correlation terms and high across-the-board accuracy for chemical applications. J. Chem. Theory Comput. 15, 4804-4815 (2019)


He, L., Bao, J., Yang, Y., Dong, S., Zhang, L., Qi, Y., and Zhang, J. Z. H. Study of SHMT2 inhibitors and their binding mechanism by computational alanine scanning. J. Chem. Inf. Model. 59, 3871-3878 (2019)


Xu, M., Zhu, T., and Zhang, J. Z. H. Molecular dynamics simulation of zinc ion in water with an ab initio based neural network potential. J. Phys. Chem. A. 123, 6587-6595 (2019)


Liu, J., Sun, H., Glover, W. J., and He, X. Prediction of excited-state properties of oligoacene crystals using fragment-based quantum mechanical method. J. Phys. Chem. A. 123, 5407-5417 (2019)


Lu, J., Wang, C., and Zhang, Y. Predicting molecular energy using force-field optimized geometries and atomic vector representations learned from an improved deep tensor neural network. J. Chem. Theory Comput. 15, 4113-4121 (2019)


Chen, J., Wang, X., Pang, L., Zhang, J. Z. H., and Zhu, T. Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations. Nucleic Acids Res. 47, 6618-6631 (2019)


Lu, Q., He, X., Hu, W., Chen, X., and Liu, J. Stability, vibrations, and diffusion of hydrogen gas in clathrate hydrates: Insights from ab initio calculations on condensed-phase crystalline structures. J. Phys. Chem. C. 123, 12052-12061 (2019)


Li, K., Hou, X., Li, R., Bi, W., Yang, F., Chen, X., Xiao, P., Liu, T., Lu, T., Zhou, Y., Tian, Z., Shen, Y., Zhang, Y., Wang, J., Fang, H., Sun, J., and Yu, X. Identification and structure-function analyses of an allosteric inhibitor of the tyrosine phosphatase PTPN22. J. Biol. Chem. 294, 8653-8663 (2019)


Cao, H., Wang, J., He, L., Qi, Y., and Zhang, J. Z. H. DeepDDG: Predicting the stability change of protein point mutations using neural networks. J. Chem. Inf. Model. 59, 1508-1514 (2019)


Verma, P., Wang, Y., Ghosh, S., He, X., and Truhlar, D. G. Revised M11 exchange-correlation functional for electronic excitation energies and ground-state properties. J. Phys. Chem. A. 123, 2966-2990 (2019)


Luo, H., Hao, X., Gong, Y., Zhou, J., He, X., and Li, J. Rational crystal polymorph design of olanzapine. Cryst. Growth Des. 19, 2388-2395 (2019)


Sun, Z., Wang, X., Zhang, J. Z. H., and He, Q. Sulfur-substitution-induced base flipping in the DNA duplex. Phys. Chem. Chem. Phys. 21, 14923-14940 (2019)


Tuckerman, M. E. Machine learning transforms how microstates are sampled. Science. 365, 982-983 (2019)


Xiao, Z., Cong, Y., Huang, K., Zhong, S., Zhang, J. Z. H., and Duan, L. Drug-resistance mechanisms of three mutations in anaplastic lymphoma kinase against two inhibitors based on MM/PBSA combined with interaction entropy. Phys. Chem. Chem. Phys. 21, 20951-20964 (2019)


Zelovich, T., Vogt-Maranto, L., Hickner, M. A., Paddison, S. J., Bae, C., Dekel, D. R., and Tuckerman, M. E. Hydroxide ion diffusion in anion-exchange membranes at low hydration: Insights from ab initio molecular dynamics. Chem. Mater. 31, 5778-5787 (2019)


Chen, J., Yin, B., Pang, L., Wang, W., Zhang, J. Z. H., and Zhu, T. Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologiesJ. Biomol. Struct. Dyn. 1-15 (2019)


Shtukenberg, A. G., Tan, M., Vogt-Maranto, L., Chan, E. J., Xu, W., Yang, J., Tuckerman, M. E., Hu, C. T., and Kahr, B. Melt crystallization for paracetamol polymorphism. Cryst. Growth Des. 19, 4070-4080 (2019)


Li, P., Liu, F., Shao, Y., and Mei, Y. Computational insights into endo/exo selectivity of the Diels-Alder reaction in explicit solvent at ab initio quantum mechanical/molecular mechanical level. J. Phys. Chem. B. 123, 5131-5138 (2019)


Zhang, Z., Liu, X., Yan, K., Tuckerman, M. E., and Liu, J. Unified efficient thermostat scheme for the canonical ensemble with holonomic or isokinetic constraints via molecular dynamics. J. Phys. Chem. A. 123, 6056-6079 (2019)


Liu, X., Zhao, Y., and Zhang, J. Z. H. Molecular mechanism of ligand bindings to Zika virus at SAM site. Chem. Phys. Lett. 735, 136771 (2019)


Chen, J., Gao, H., Ding, T., Ji, L., Zhang, J. Z. H., Gao, G., and Xia, F. Mechanistic studies of CO2 cycloaddition reaction catalyzed by amine-functionalized ionic liquids. Front Chem. 7, 615 (2019)


Duan, G., Ji, C., and Zhang, J. Z. H. A force consistent method for electrostatic energy calculation in fluctuating charge model. J. Chem. Phys. 151, 094105 (2019)


Xu, M., Felker, P. M., Mamone, S., Horsewill, A. J., Rols, S., Whitby, R. J., and Bačić, Z. The endofullerene HF@C60: Inelastic neutron scattering spectra from quantum simulations and experiment, validity of the selection rule, and symmetry breakingJ. Phys. Chem. Lett. 10, 5365−5371 (2019)


Felker, P. M., Lauvergnat, D., Scribano, Y., Benoit, D. M., and Bačić, Z. Intramolecular stretching vibrational states and frequency shifts of (H2)2 confined inside the large cage of clathrate hydrate from an eight-dimensional quantum treatment using small basis setsThe Journal of Chemical Physics151, 124311 (2019)


Wang, T., Su, X., Zhang, X., Huang, W., Huang, L., Zhang, X., Sun, X., Luo, Y., and Zhang, G. A combinatory approach towards the design of organic polymer luminescent materials. J. Mater. Chem. C. 7, 9917-9925 (2019)


Mulvihill, E., Schubert, A., Sun, X., Dunietz, B. D., and Geva, E. A modified approach for simulating electronically nonadiabatic dynamics via the generalized quantum master equationJ. Chem. Phys. 150, 034101 (2019)


L. Petingi and T. Schlick, "Graph-Theoretic Partitioning of RNAs and Classification of Pseudoknots'', In: I. Holmes, C. Martín-Vide, M. Vega-Rodríguez, Editors, Algorithms for Computational Biology (AlCoB 2019), Lec. Notes in Comp. Sci. (LNCS) 11488: 68-79 (2019) 


Jung, J., Nishima, W., Daniels, M., Bascom, G., Kobayashi, C., Adedoyin, A., Wall. M., Lappala, A., Phillips, D., Fischer, W., Tung, C.-S., Schlick, T., Sugita, Y., and Sanbonmatsu,  K. Y. Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulationsJ. Comp. Chem. 40, 1919-1930 (2019)


Jain, S., Saju, S., Petingi, L., and Schlick, T. An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structuresMethods. 162-163, 74-84 (2019)


Portillo-Ledesma, S. and Schlick, T. Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modelingWIREs Comput. Mol. Sci. e1434 (2019)


Felker, P. M. and  Bačić, Z. Weakly bound molecular dimers: Intramolecular vibrational fundamentals, overtones, and tunneling splittings from full-dimensional quantum calculations using compact contracted bases of intramolecular and low-energy rigid-monomer intermolecular eigenstatesJ. Chem. Phys. 151, 024305 (2019)


Chen, J., Wang, X., Zhang, J. Z. H., and Zhu, T. Effect of Substituents in Different Positions of Aminothiazole Hinge-Binding Scaffolds on Inhibitor-CDK2 Association Probed by Interaction Entropy Method. ACS Omega. 3, 18052-18064 (2018)


Zhao, P., Cao, H., Chen, Y., and Zhu, T. Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations. Chem. Phys. Lett. 728, 94-101 (2019)


Perišić, O., Portillo-Ledesma, S, and Schlick, T. Sensitive effect of linker histone binding mode and subtype on chromatin condensation. Nucleic Acids Res. 47, 4948-4957 (2019)


Sun, Z., Wang, X., and Zhang, J. Z. H. Determination of binding affinities of 3-Hydroxy-3-Methylglutaryl Coenzyme A reductase inhibitors from free energy calculation. Chem. Phys. Lett. 723, 1-10 (2019)


Liu, W., Li, P., and Mei, Y. Discovery of SBF1 as an allosteric inhibitor targeting the PIF-pocket of 3-phosphoinositide-dependent protein kinase-1. J. Mol. Model. 25, 187 (2019)


Wang, X., Tu, X., Deng, B., Zhang, J. Z. H., and Sun, Z. BAR-based optimum adaptive steered MD for configurational sampling. J. Comput. Chem. 40, 1270-1289 (2019)


Huang, D., Qi, Y., Song, J., and Zhang, J. Z. H. Calculation of hot spots for protein-protein interaction in p53/PMI-MDM2/MDMX complexes. J. Comput. Chem. 40, 1045-1056 (2019)


Tong, Z., Huai, Z., Mei, Y., and Mo, Y. Influence of the protein environment on the electronic excitation of chromophores in the phycoerythrin 545 light-harvesting complex: A combined MD-QM/MM method with polarized protein-specific charge scheme. J. Phys. Chem. B. 123, 2040-2049 (2019)


Chen, J., Pang, L., Wang, W., Wang, L., Zhang, J. Z. H., and Zhu, T. Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculationsJ. Biomol. Struct. Dyn. 1-15 (2019)


Liu, W., Dai, X., Jih, J., Chan, K., Trang, P., Yu, X., Balogun, R., Mei, Y., Liu, F., Zhou, Z. H. Atomic structures and deletion mutant reveal different capsid-binding patterns and functional significance of tegument protein pp150 in murine and human cytomegaloviruses with implications for therapeutic development. PLOS Pathog. 15, e1007615 (2019)


Yang, Y., He, L., Bao, J., Qi, Y., and Zhang, J. Z. H. Computational analysis for residue-specific CDK2-inhibitor bindings. Chinese Journal of Chemical Physics. 32, 134-142 (2019)


Albaugh, A., Tuckerman, M. E., and Head-Gordon, T. Combining iteration-free polarization with large time step stochastic-isokinetic integration. J. Chem. Theory Comput. 15, 2195-2205 (2019)


Xu, M., He, X., Zhu, T., and Zhang, J. Z. H. A fragment quantum mechanical method for metalloproteins. J. Chem. Theory Comput. 15, 1430-1439 (2019)


Jeon, J. Y., Park, S. Han, J., Maurya, S., Mohanty, A. D. Tian, D. Saikia, N., Hickner, M. A., Ryu, C. Y., Tuckerman, M. E., Paddison, S. J., Kim, Y. S., and Bae, C. Synthesis of aromatic anion exchange membranes by Friedel–Crafts bromoalkylation and cross-linking of polystyrene block copolymers. Macromolecules. 52, 2139-2147 (2019)


Huang, D., Wen, W., Liu, X., Li, Y., and Zhang, J. Z. H. Computational analysis of hot spots and binding mechanism in the PD-1/PD-L1 interaction. RSC Adv. 9, 14944-14956 (2019)


Zelovich, T., Long, Z., Hickner, M., Paddison, S. J., Bae, C., and Tuckerman, M. E. Ab initio molecular dynamics study of hydroxide diffusion mechanisms in nanoconfined structural mimics of anion exchange membranes. J. Phys. Chem. C. 123, 4638-4653 (2019)


Liu, X., Peng, L., and Zhang, J. Z. H. Accurate and efficient calculation of protein-protein binding free energy-interaction entropy with residue type-specific dielectric constants. J. Chem. Inf. Model. 59, 272-281 (2019)


Lauvergnat, D., Felker, P., Scribano, Y., Benoit, D. M., and Bačić, Z. H2, HD, and D2 in the small cage of structure II clathrate hydrate: Vibrational frequency shifts from fully coupled quantum six-dimensional calculations of the vibration-translation-rotation eigenstatesJ. Chem. Phys. 150, 154303 (2019)


Bascom, G. D., Myers, C. G., and Schlick, T. Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hubProc. Natl. Acad. Sci., 116, 4955-4962 (2019)


Tse, C. K. M., Xu, J., Xu, L., Sheong, F. K., Wang, S., Chow, H. Y., Gao, X., Li, X., Cheung, P. P. H., Wang, D., Zhang, Y., and Huang, X. Intrinsic cleavage of RNA polymerase II adopts a nucleobase-independent mechanism assisted by transcript phosphateNature Catalysis, 2, 228-235 (2019)


Lei, J., Sheng, G., Cheung, P. P. H., Wang, S., Li, Y., Gao, X., Zhang, Y., Wang, Y., and Huang, X. Two symmetric arginine residues play distinct roles in Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavageProc. Natl. Acad. Sci., 116, 845-853 (2019)


Wang, Y., Verma, P., Jin, X., Truhlar, D. G., and He, X. Revised M06 density functional for main-group and transition-metal chemistry. Proc. Natl. Acad. Sci. U.S.A. 115, 10257–10262 (2018)


Li, Y., Cong, Y., Feng, G., Zhong, S., Zhang, J. Z. H., Sun, H., and Duan, L. The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction. Struct. Dyn. 5, 064101 (2018)


Yan, Y., Wang, W., Sun, Z., Zhang, J. Z. H., and Ji, C. Protein–ligand empirical interaction components for virtual screeningJ. Chem. Inf. Model. 57, 1793–1806 (2017)


Liu, J., Zhang, J. Z. H., and He, X. Probing the ion-specific effects at the water/air interface and water-mediated ion pairing in sodium halide solution with ab initio molecular dynamics. J. Phys. Chem. B. 122, 10202-10209 (2018)


Sun, Z. X., Wang, X. H., and Zhang, J. Z. H. BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformationPhys. Chem. Chem. Phys. 19, 15005 (2017)


Luo, Z., Gao, Y., Zhu, T., Zhang, J. Z. H., and Xia, F. Origins of protons in C−H bond insertion products of phenols: Proton-self-sufficient function via water molecules.  J. Phys. Chem. A. 121, 6523-6529 (2017)


Liu, J., He, X., and Zhang, J. Z. H. Structure of liquid water – a dynamical mixture of tetrahedral and ‘ring-and-chain’ like structuresPhys. Chem. Chem. Phys. 19, 11931-11936 (2017)


Jain, S., Laederach, A., Ramos, S. B. V., and Schlick, T. A pipeline for computational design of novel RNA-like topologies. Nucleic Acids Res. 46, 7040–7051 (2018)


Li, M. and Zhang, J. Z. H. Two-bead polarizable water models combined with a two-bead multipole force field (TMFF) for coarse-grained simulation of proteins. Phys. Chem. Chem. Phys. 19, 7410-7419 (2017)


Shiga, M. and Tuckerman, M. E. Finding free-energy landmarks of chemical reactions. J. Phys. Chem. Lett. 9, 6207−6214 (2018)


Wang, Y., Liu, J., Li, J., and He, X. Fragment-based quantum mechanical calculation of protein–protein binding affinities. J. Comput. Chem. 39, 1617-1628 (2018)


Bačić, Z., Vlček, V., Neuhauser, D., and Felker, P. M. Effects of symmetry breaking on the translation–rotation eigenstates of H2, HF, and H2O inside the fullerene C60Faraday Discuss. 212, 547-567 (2018)


Chen, J., Huang, M., and Xia, F. Conformer-related pathways in cycloaddition of vinylaziridines and alkynes catalyzed by rhodium(I)-complex. Chem. Phys. Lett. 713, 21-25 (2018)


Cai, Y., Fu, I., Geacintov, N. E., Zhang, Y., and Broyde, S. Synergistic effects of H3 and H4 nucleosome tails on structure and dynamics of a lesion-containing DNA: Binding of a displaced lesion partner base to the H3 tail for GG-NER recognitionDNA Repair. 65, 73-78 (2018)


Wang, Y., Jin, X., Yu, H. S., Truhlar, D. G., and He, X. Revised M06-L functional for improved accuracy on chemical reaction barrier heights, noncovalent interactions, and solid-state physics. Proc. Natl. Acad. Sci. U.S.A. 114, 8487-8492 (2017)


Mu, H., Zhang, Y., Geacintov, N. E., and Broyde, S. Lesion sensing during initial binding by yeast XPC/Rad4: Toward predicting resistance to nucleotide excision repairChem. Res. Toxicol. 31, 1260-1268 (2018)


Qiu, L., Shen, C., Song, J.Zhang, Y., and Zhang, J. Z. H. Functional loop dynamics of the S-component of ECF transporter FolTMol. Phys. 116, 2613-2621 (2018)


Wang, M., Mei, Y., and Ryde, U. Predicting relative binding affinity using nonequilibrium QM/MM simulationsJ. Chem. Theory Comput. 14, 6613-6622 (2018)


Hou, X., Rooklin, D., Yang, D., Liang, X., Li, K., Lu, J., Wang, C., Xiao, P., Zhang, Y., Sun, J., and Fang, H. Computational strategy for bound state structure prediction in structure-based virtual screening: A case study of protein tyrosine phosphatase receptor type O inhibitors. J. Chem. Inf. Model. 58, 2331-2342 (2018)


Zhu, T., Wu, C., Song, J., Reimers, J. R., and Li, Y. Polarization effect within a protein crystal: A molecular dynamics simulation studyChem. Phys. Lett. 706, 303-307 (2018)


Li, P., Jia, X., Pan, X., Shao, Y., and Mei, Y. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanics accuracy via a semi-empirical reference potential. I. weighted thermodynamics perturbation. J. Chem. Theory Comput. 14, 5583-5596 (2018)


Li, P., Liu, F., Jia, X., Shao, Y., Hu, W., Zheng, J., and Mei, Y. Efficient computation of free energy surfaces of Diels–Alder reactions in explicit solvent at ab initio QM/MM level. Molecules. 23, 2487 (2018)


Yao, Z., Jiang, S., Zhang, L., Gao, B., He, X.Zhang, J. Z. H., and Wei, D. Crius: A novel fragment‐based algorithm of de novo substrate prediction for enzymesProtein Sci. 27, 1526-1534 (2018)


Huang, J., Mei, Y., König, G., Simmonett, A. C., Pickard IV, F. C., Wu, Q., Wang, L.-P., MacKerell Jr., A. D., Brooks, B. R., and Shao, Y. An estimation of hybrid quantum mechanical molecular mechanical polarization energies for small molecules using polarizable force-field approaches. J. Chem. Theory Comput. 13, 679-695 (2017)


Duan, L., Zhu, T., Ji, C., Zhang, Q., and Zhang, J. Z. H. Direct folding simulation of helical proteins using an effective polarizable bond force fieldPhys. Chem. Chem. Phys. 19, 15273-15284 (2017)


Liu, W., Jia, X., Wang, M., Li, P., Wang, X., Hu, W., Zheng, J., and Mei, Y. Calculations of the absolute binding free energies for Ralstonia solanacearum lectins bound with methyl-α-L-fucoside at molecular mechanical and quantum mechanical/molecular mechanical levels. RSC Adv. 7, 38570 (2017)


Bačić, Z. Perspective: Accurate treatment of the quantum dynamics of light molecules inside fullerene cages: Translation-rotation states, spectroscopy, and symmetry breaking. J. Chem. Phys. 149, 100901 (2018)


Bascom, G. D. and Schlick, T. Chromatin fiber folding directed by cooperative histone tail acetylation and linker histone binding. Biophys. J. 114, 2376-2385 (2018)


Cuendet, M. A., Margul, D. T., Schneider, E., Vogt-Maranto, L., and Tuckerman, M. E. Endpoint-restricted adiabatic free energy dynamics approach for the exploration of biomolecular conformational equilibria. J. Chem. Phys. 149, 072316 (2018)


Gao, Y., Zhu T., Zhang, C. M., Zhang, J. Z. H., and Mei, Y. Comparison of the unfolding and oligomerization of human prion protein under acidic and neutral environments by molecular dynamics simulationsChem. Phys. Lett. 706, 594-600 (2018)


Silletta, E. V., Tuckerman, M. E., and Jerschow, A. Unusual protont transfer kinetics in water at the temperature of maximum density. Phys. Rev. Lett. 121, 076001 (2018)


Xu, M., Zhu, T., and Zhang, J. Z. H. A force balanced fragmentation method for ab initio molecular dynamic simulation of proteinFront. Chem. 6, 189 (2018)


Sun, X., Zhang, P., Lai, Y., Williams, K. L., Cheung, M. S., Dunietz, B. D., and Geva, E. Computational study of charge-transfer dynamics in the carotenoid–porphyrin–C60 molecular triad solvated in explicit tetrahydrofuran and its spectroscopic signature. J. Phys. Chem. C. 122, 11288-11299 (2018)


Cong, Y., Li, Y., Jin, K., Zhong, S., Zhang, J. Z. H., Li, H., and Duan, L. Exploring the reasons for decrease in binding affinity of HIV-2 against HIV-1 protease complex using interaction entropy under polarized force field. Front. Chem. 6, 380 (2018)


Chen, J., Duan, L., Ji, C., and Zhang, J. Z. H. Computational study of PCSK9-EGFA complex with effective polarizable bond force field. Front. Mol. Biosci. 4, 101 (2018)


Zhou, Y., Liu, X., Zhang, Y., Peng, L. and Zhang, J. Z. H. Residue-specific free energy analysis in ligand bindings to JAK2. Mol. Phys. 116, 2633-2641 (2018)


Li, Y., Wang, X., Ren, L., Cao, X., Ji, C., Xia, F., and Zhang, J. Z. H. Electrostatic polarization effect on cooperative aggregation of full length human islet amyloid. J. Chem. Inf. Model.  58, 1587-1595 (2018)


Sun, H., Duan, L., Chen, F., Liu, H., Wang, Z., Pan, P., Zhu, F., Zhang, J. Z. H., and Hou, T. Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches. Phys. Chem. Chem. Phys. 20, 14450-14460 (2018)


Jain, S., Bayrak, C. S., Petingi, L., and Schlick, T. Dual graph partitioning highlights a small group of pseudoknot-containing RNA submotifs. Genes. 9, 371 (2018)


Schlick, T. Adventures with RNA graphs. Methods. 143, 16-33, 2018


Wang, J., Cao, H., Zhang, J. Z. H., and Qi, Y. Computational protein design with deep learning neural networks. Sci. Rep. 8, 6349 (2018)


Li, Y., Zhang, Y., Großerüschkamp, F., Stephan, S., Cui, Q., Kötting, C., Xia, F., and Gerwert, K. Specific substates of Ras to interact with GAPs and effectors: Revealed by theoretical simulations and FTIR experiments. J. Phys. Chem. Lett. 9, 1312-1317 (2018)


Liu, X., Peng, L., Zhou, Y., Zhang, Y, and Zhang, J. Z. H. Computational alanine scanning with interaction entropy for protein–ligand binding free energies. J. Chem. Theory Comput. 14, 1772-1780 (2018)


Qiu, L., Yan, Y., Sun, Z., Song, J., and Zhang, J. Z. H. Interaction entropy for computational alanine scanning in protein–protein binding. Wiley Interdiscip. Rev. Comput. Mol. Sci. 8, e1342 (2018)


Liu, J., Swails, J., Zhang, J. Z. H., He, X., and Roitberg, A. E. A coupled ionization-conformational equilibrium is required to understand the properties of ionizable residues in the hydrophobic interior of staphylococcal nuclease. J. Am. Chem. Soc. 140, 1639–1648 (2018)


Ji, L., Luo, Z., Zhang, Y., Wang, R., Ji, Y., Xia, F., Gao, G. Imidazolium ionic liquids/organic bases: Efficient intermolecular synergistic catalysts for the cycloaddition of  CO and epoxides under atmospheric pressure. Molecular Catalysis. 446, 124-130 (2018)


Wang, P., Liu, L., Luo, Z., Zhou, Q., Lu, Y., Xia, F., and Liu, Y. Combination of transition metal Rh-catalysis and tautomeric catalysis through a bi-functional ligand for one-pot tandem methoxycarbonylation-aminolysis of olefins towards primary amides. J. Catal. 361, 230-237 (2018)


Bačić, Z., Xu, M., and Felker, P. M. Coupled translation-rotation dynamics of H2 and H2O inside C60: Rigorous quantum treatment. Adv. Chem. Phys. 163, 195-216 (2018)


Wang, X., Tu, X., Zhang, J. Z. H., and Sun, Z. BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: the nonequilibrium stratification. Phys. Chem. Chem. Phys. 20, 2009-2021 (2018)


Powers, A., Scribano, Y., Lauvergnat, D., Mebe, E., Benoit, D. M., and Bačić, Z. The effect of the condensed-phase environment on the vibrational frequency shift of a hydrogen molecule inside clathrate hydrates. J. Chem. Phys. 148, 144304 (2018)


Gao, B., Jiang, S., Wang, L., Zhang, L., Wei, D. Energy and conformation determine the enantioselectivity of enzyme. Biochem. Eng. J. 129, 106-112 (2018)


Jin, X., Zhu, T., Zhang, J. Z. H., and He, X. Automated fragmentation QM/MM calculation of NMR chemical shifts for protein-ligand complexes. Front. Chem. 6, 150 (2018)


Tuckerman M. and Ceperley, D. Preface: Special topic on nuclear quantum effectsJ. Chem. Phys. 148, 102001 (2018) 


Chen, P.-Y., and Tuckerman, M. E. Molecular dynamics based enhanced sampling of collective variables with very large time stepsJ. Chem. Phys. 148, 024106 (2018)


Cendagorta, J. R., Bačić, Z., and Tuckerman, M. E. An open-chain imaginary-time path-integral sampling approach to the calculation of approximate symmetrized quantum time correlation functionsJ. Chem. Phys. 148, 102340 (2018)


Liu, J., He, X., Zhang, J. Z. H., and Qi, L.-W. Hydrogen-bond structure dynamics in bulk water: Insights from ab initio simulations with coupled cluster theory. Chem. Sci. 9, 2065-2073 (2018)


Song, J., Qiu, L., and Zhang, J. Z. H. An efficient method for computing excess free energy of liquidScience China Chemistry, 61, 135-140 (2018)  


Glover, W. J., Mori, T., Schuurman, M. S., Boguslavskiy, A. E., Schalk, O., Stolow, A., and Martínez, T. J. Excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene. II. Ab initio multiple spawning simulations. J. Chem. Phys. 148, 164303 (2018)


Hagras, M. A. and Glover, W. J. Polarizable embedding for excited-state reactions: Dynamically weighted polarizable QM/MM. J. Chem. Theory Comput. 14, 2137-2144 (2018)


Felker, P. M. and Bačić, Z. Accurate quantum calculations of translation-rotation eigenstates in electric-dipole-coupled H 2 O@C 60 assemblies. Chem. Phys. Lett. 683, 172-178 (2017)


Jiang, M., Zhang, L., Wang, F., Zhang, J., Liu, G., Gao, B., and Wei, D. Novel application of magnetic protein: Convenient one-step purification and immobilization of proteins. Sci. Rep. 7, 13329 (2017)


Wang, Y., Wang, X., Truhlar, D. G., and He, X. How well can the M06 suite of functionals describe the electron densities of Ne, Ne6+, and Ne8+? J. Chem. Theory Comput. 13, 6068-6077 (2017)


Wang, X., Zhang, J. Z. H., and He, X. Ab initio quantum mechanics/molecular mechanics molecular dynamics simulation of CO in the heme distal pocket of myoglobinChin. J. Chem. Phys. 30, 705-716 (2017)


Zhang, Y. and He, X. Reaction mechanisms of CO oxidation on cationic, neutral, and anionic X-O-Cu (X = Au, Ag) clustersChem. Phys. Lett. 686, 116-123 (2017)


Wang, Y., Liu, J., Zhang, L., He, X., Zhang, J. Z. H. Computational search for aflatoxin binding proteins. Chem. Phys. Lett. 685, 1-8 (2017)


Li, P., Jia, X., Wang, M., and Mei, Y. Comparison of accuracy and convergence rate between equilibrium and nonequilibrium alchemical transformations for calculation of relative binding free energyChin. J. Chem. Phys. 30, 789−799 (2017)


Huang, M., Luo, Z., Zhu, T., Chen, J., Zhang, J. Z., and Xia, F. A theoretical study of the substituent effect on reactions of amines, carbon dioxide and ethylene oxide catalyzed by binary ionic liquidsRSC Adv. 7, 51521-51527 (2017) 


Sun, Z., Wang, X., and Zhang, J. Z. H. Protonation-dependent base flipping in the catalytic triad of a small RNAChem. Phys. Lett. 684, 239-244 (2017)


Sun, Z., Zhu, T., Wang, X., Mei, Y., and Zhang, J. Z. H. Optimization of convergence criteria for fragmentation methodsChem. Phys. Lett. 687, 163-170 (2017)


Liu, F., Yang, Z., Yu, Y., Mei, Y., and Houk, K. N. Bimodal Evans–Polanyi relationships in dioxirane oxidations of sp3 C–H: Non-perfect synchronization in generation of delocalized radical intermediatesJ. Am. Chem. Soc. 139, 16650-16656 (2017)


Jain, S. and Schlick, T. F-RAG: Generating atomic coordinates from RNA graphs by fragment assembly. J. Mol. Biol. 429, 3587-3605 (2017)


Rao, S. S. P., Huang, S. C., Brian, G. S. H., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K. R., Sanborn, A. L., Johnstone, S. E., Bascom, G. D., Bochkov, I. D., Huang, X., Shamim, M. S., Shin, J., Turner, D., Ye, Z., Omer, A. D., Robinson, J. T., Schlick, T., Bernstein, B. E., Casellas, R., Lander, E. S., and Aiden, E. L. Cohesin loss eliminates all loop domains. Cell. 171, 305-320.e24 (2017)


Felker, P.M., Vlček, V., Hietanen, I., Fitzgerald, S., Neuhauser, D. and Bačić, Z.Explaining the symmetry breaking observed in the endofullerenes H2@C60, HF@C60, and H2O@C60Phys. Chem. Chem. Phys., 19, 31274-31283 (2017)


Schneider, E., Dai, L., Topper, R. Q., Drechsel-Grau, C., and Tuckerman, M. E. Stochastic neural network approach for learning high-dimensional free energy surfaces. Phys. Rev. Lett. 119, 150601 (2017)


Wang, M., Li, P., Jia, X., Liu, W., Shao, Yi., Hu, W., Zheng, J., Brooks, B. R., and Mei, Y. Efficient strategy for the calculation of solvation free energies in water and chloroform at the quantum mechanical/molecular mechanical levelJ. Chem. Inf. Model. 57, 2476-2489 (2017)


Brockherde, F., Vogt, L., Li, L., Tuckerman, M. E., Burke, K., and Müller, K. R. Bypassing the Kohn-Sham equations with machine learning. Nat. Commun. 8, 872 (2017)


Dupuis, R., Benoit, M., Tuckerman, M. E., and Méheut, M. Importance of a fully anharmonic treatment of equilibrium isotope fractionation properties of dissolved ionic species as evidenced by Li+ (aq). Acc. Chem. Res. 50, 1597-1605 (2017)


Shtukenberg, A. G., Zhu, Q., Carter, D. J., Vogt, L., Hoja, J., Schneider, E., Song, H., Pokroy, B., Polishchuk, I., Tkatchenko, A., Oganov, A. R., Rohl, A. L., Tuckerman, M. E., and Kahr, B. Powder diffraction and crystal structure prediction identify four new coumarin polymorphs.  Chem. Sci. 8, 4926-4940 (2017)


Sepehr, F., Liu, H., Luo, X., Bae, C., Tuckerman, M. E., Hickner, M. A., and Paddison, S. J. Mesoscale simulations of anion exchange membranes based on quaternary ammonium tethered triblock copolymers. Macromolecules. 50, 4397-4405 (2017)


Bascom, G. D., Kim, T., and Schlick, T. Kilobase pair chromatin fiber contacts promoted by living-system-like DNA linker length distributions and nucleosome depletion. J. Phys. Chem. B. 121, 3882-3894 (2017)


Bascom, G. and Schlick, T. Linking chromatin fibers to gene folding by hierarchical looping. Biophys. J. 112, 434-445 (2017)


Rooklin, D. W., Modell, A. E., Li, H., Berdan, V., Arora, P. S., and Zhang, Y.  Targeting unoccupied surfaces on protein-protein interfacesJ. Am. Chem. Soc. 139, 15560-15563 (2017)


Mu, H., Geacintov, N. E., Min, J. H., Zhang, Y., and Broyde, S. Nucleotide excision repair lesion-recognition protein Rad4 captures a pre-flipped partner base in a benzo[a]pyrene-derived DNA lesion: How structure impacts the binding pathway. Chem. Res. Toxicol. 30, 1344-1354 (2017)


Zho, C. C., Farr, E. P., Glover, W. J., and Schwartz, B. J. Temperature dependence of the hydrated electron’s excited-state relaxation. I. Simulation predictions of resonance Raman and pump-probe transient absorption spectra of cavity and non-cavity models. J. Chem. Phys. 147, 074503 (2017)


Jin, X., Zhang, J. Z. H., and He, X. Full QM calculation of RNA energy using electrostatically embedded generalized molecular fractionation with conjugate caps method. J. Phys. Chem. A. 121, 2503–2514 (2017)


Yan, Y., Yang, M., Ji, C., and Zhang, J. Z. H. Interaction entropy for computational alanine scanning. J. Chem. Inf. Model. 57, 1112-1122, (2017)


Liu, J., Qi L., Zhang, J. Z. H., and He, X. Fragment quantum mechanical method for large-sized ion-water clusters. J. Chem. Theory Comput. 13, 2021-2034 (2017)


Sun, Z., Yan, Y. N., Yang, M., and Zhang, J. Z. H. Interaction entropy for protein-protein bindingJ. Chem. Phys. 146, 124124 (2017)


Gao, Y., Zhang, C., Zhang, J. Z. H., and Mei, Y. Evaluation of the coupled two-dimensional main chain torsional potential in modeling intrinsically disordered proteins. J. Chem. Inf. Model. 57, 267-274 (2017)


Li, M. and Zhang, J. Z. H. Protein simulation using coarse-grained two-bead multipole force field with polarizable water models. J. Chem. Phys. 146, 065101 (2017)


Duan, L. L., Zhu, T., Li, Y. C., Zhang, Q. G., and Zhang, J. Z. H. Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations. Sci. Rep. 7, 42223 (2017)


Fu, I., Cai, Y., Zhang, Y., Geacintov, N. E., and Broyde, S. Nucleosome histone tail conformation and dynamics: Impacts of lysine acetylation and a nearby minor groove benzo[a]pyrene-derived lesionBiochemistry. 56, 1963-1973 (2017)


Wang, C. and Zhang, Y. Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest. J. Comput. Chem. 38, 169 - 177 (2017)


Hou, X., Rooklin, D., Fang, H., and Zhang, Y. Resveratrol serves as a protein-substrate interaction stabilizer in human SIRT1 activation. Sci. Rep. 6, 38186 (2016)


Zhou, Y., Wang, S., Li, Y., and Zhang, Y. Born-Oppenheimer ab initio QM/MM molecular dynamics simulations of enzyme reactions. Methods Enzymol. 577, 105-118 (2016)


Glover, W. J. and Schwartz, B. J. Short-range electron correlation stabilizes non-cavity solvation of the hydrated electron. J. Chem. Theory Comput. 12, 5117–5131 (2016)


Casey, J. R., Schwartz, B. J., and Glover W. J. Free energies of cavity and noncavity hydrated electrons near the instantaneous air/water interface. J. Phys. Chem. Lett. 7, 3192−3198 (2016)


Cendagorta, J. R., Powers, A., Hele, T. J., Marsalek, O., Bačić, Z., and Tuckerman, M. E. Competing quantum effects in the free energy profiles and diffusion rates of hydrogen and deuterium molecules through clathrate hydrates. Phys. Chem. Chem. Phys. 18, 32169-32177 (2016)


Felker, P. M. and Bačić, Z. Translation-rotation states of H2 in C60: New insights from a perturbation-theory treatment. J. Chem. Phys. 145, 084310 (2016)


Liu, Y., Yu, Z., Zhang, J. Z. H., Liu, L., Xia, F., and Zhang, J., Origins of unique gold-catalysed chemo-and site-selective C–H functionalization of phenols with diazo compounds. Chem. Sci. 7, 1988-1995 (2016)


Liu, Y., Yu, Z., Luo, Z., Zhang, J. Z. H., Liu, L., and Xia, F. Mechanistic investigation of aromatic C (sp2)–H and alkyl C (sp3)–H bond insertion by gold carbenes. J. Phys. Chem. A. 120, 1925-1932 (2016)


Li, M., Zhang, J. Z. H., and Xia, F. Constructing optimal coarse-grained sites of huge biomolecules by fluctuation maximization. J. Chem. Theory Comput., 12, 2091-2100 (2016)


Duan, L. L., Liu, X., and Zhang, J. Z. H. Interaction entropy: A new paradigm for highly efficient and reliable computation of protein–ligand binding free energy. J. Am. Chem. Soc. 138, 5722–5728 (2016)


Liu, X., Liu, J. F., Zhu, T., Zhang, L. J., He, X., and Zhang, J. Z. H. PBSA_E: A PBSA-based free energy estimator for protein–ligand binding affinity. J. Chem. Inf. Model. 56, 854-861 (2016)


Li, M., Zhang, J. Z. H., and Xia, F. A new algorithm for construction of coarse-grained sites of large biomolecules. J. Comput. Chem. 37, 795–804 (2016)


Jia, X. Y., Wang, M. T., Shao, Y. H., König, G., Brooks, B. R., Zhang, J. Z. H., and Mei, Y. Calculations of solvation free energy through energy reweighting from molecular mechanics to quantum mechanics. J. Chem. Theory Comput. 12, 499–511 (2016)


Felker, P. M. and Bačić, Z. Communication: Quantum six-dimensional calculations of the coupled translation-rotation eigenstates of H2O@C60. J. Chem. Phys. 144, 201101 (2016)


Liu, J. F., Zhang, J. Z. H., and He, X. Fragment quantum chemical approach to geometry optimization and vibrational spectrum calculation of proteins. Phys. Chem. Chem. Phys. 18, 1864-1875 (2016)


Zhou, Y., Xie, D., and Zhang, Y. Amide rotation hindrance predicts proteolytic resistance of cystine-knot peptides. J. Phys. Chem. Lett. 7, 1138-1142 (2016)


Fu, I., Cai, Y., Zhang, Y., Geacintov, N. E., and Broyde, S. Entrapment of a histone tail by a DNA lesion in a nucleosome suggests the lesion impacts epigenetic marking: A molecular dynamics study. Biochemistry. 55, 239 - 242 (2016)


Powers, A., Marsalek, O., Xu, M., Ulivi, L., Colognesi, D., Tuckerman, M. E., and Bačić, Z. Impact of the condensed-phase environment on the translation-rotation eigenstates and spectra of a hydrogen molecule in clathrate hydrates. J. Phys. Chem. Lett. 7, 308–313 (2016)


Liu, J. F., Wang, X. W., Zhang, J. Z. H., and He, X. Calculation of protein–ligand binding affinities based on a fragment quantum mechanical method. RSC Adv. 5, 107020-107030 (2015)


Jia, X. Y., Mei, Y., Zhang, J. Z. H., and Mo, Y. Hybrid QM/MM study of FMO complex with polarized proteinspecific charge. Sci. Rep. 5, 17096 (2015)


Liu, J. F., Zhu, T., Wang, X. W., He, X., and Zhang, J. Z. H. Quantum fragment based ab initio molecular dynamics for proteins. J. Chem. Theory Comput. 11, 5897−5905 (2015)


Li, Y., Zhang, J. Z. H., and Mei, Y. Molecular dynamics simulation of protein crystal with polarized protein-specific charge. Biophys. J. 108, 160a (2015)


Gao, Y., Li, Y., Zhang, J. Z. H., and Mei, Y. A coupled two-dimensional main chain torsional potential for protein dynamics. Biophys. J. 108, 159a-160a (2015)


Gao, Y., Li, Y., Mou, L., Lin, B., Zhang, J. Z. H., and Mei, Y. Correct folding of an alpha-helix and a beta-hairpin using a polarized 2D torsional potential. Sci. Rep. 5, 10359 (2015)


Wang, X., Zhang, J. Z. H., and He, X. Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase. J. Chem. Phys. 143, 184111 (2015)


Gong, W., Wu, R., and Zhang, Y. Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An ab initio QM/MM molecular dynamics study. J. Comput. Chem. 36, 2228-2235 (2015)


Swails, J., Zhu, T., He, X., and Case, D. A. AFNMR: Automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. J. Biomol. NMR. 63, 125-139 (2015)


Chen, J., Wang, X., Zhu, T., Zhang, Q., and Zhang, J. Z. H. A comparative insight into amprenavir resistance of mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 protease based on thermodynamic integration and MM-PBSA methods. J. Chem. Inf. Model. 55, 1903–1913 (2015)


Xu, M., Ye, S., and Bačić, Z. General selection rule in the inelastic neutron scattering spectroscopy of a diatomic molecule confined inside a near-spherical nanocavity. J. Phys. Chem. Lett. 6, 3721–3725 (2015)


Mu, H., Geacintov, N. E., Zhang, Y., and Broyde, S. Recognition of damaged DNA for nucleotide excision repair: A correlated motion mechanism with a mismatched cis-syn thymine dimer lesion. Biochemistry. 54, 5263-5267 (2015)


Yang, J., Song, J., Zhang, J. Z. H., and Ji, C. Effect of mismatch on binding of ADAR2/GluR-2 pre-mRNA complex. J. Mol. Model. 21, 222 (2015)


Rooklin, D., Wang, C., Katigbak, J., Arora, P. S., and Zhang, Y. AlphaSpace: Fragment-centric topographical mapping to target protein–protein interaction interfaces. J. Chem. Inf. Model. 55, 1585–1599 (2015)


Mei, Y., Simmonett, A. C., Pickard, F. C., DiStasio, R., Brooks, B. R., and Shao, Y.  Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions. J. Phys. Chem. A. 119, 5865–5882 (2015)


Wang, X., Ji, C., and Zhang, J. Z. H. Glycosylation modulates human CD2-CD58 adhesion via conformational adjustment. J. Phys. Chem. B. 119, 6493–6501 (2015)


Ozer, G., Luque, A., and Schlick, T. The chromatin fiber: Multiscale problems and approaches. Curr. Opin. Struct. Biol. 31, 124-139 (2015)


Zhou J., Li M., Chen N., Wang S., Luo H., Zhang Y., and Wu, R. Computational design of a time-dependent histone deacetylase 2 selective inhibitor. ACS Chem. Biol. 10, 687-692 (2015)


Gao, Y., Li, Y., Mou, L., Hu, W., Zheng, J., Zhang, J. Z. H., and Mei, Y. Coupled two-dimensional main-chain torsional potential for protein dynamics II: Performance and validation. J. Phys. Chem. B. 119, 4188–4193 (2015)


Chen, M., Yu, T. Q., and Tuckerman, M. E. Locating landmarks on high-dimensional free energy surfaces. Proc. Natl. Acad. Sci. 112, 3235-3240 (2015)


Song, J., Li Y., Ji, C., and Zhang, J. Z. H. Functional loop dynamics of the streptavidin-biotin complex. Sci. Rep. 5, 7906 (2015)


Lei, J., Zhou, Y., Xie, D., and Zhang, Y. Mechanistic insights into a classic wonder drug-aspirin. J. Am. Chem. Soc. 137, 70-73 (2015)


Ozer, G., Collepardo-Guevara, R., and Schlick, T. Forced unraveling of chromatin fibers with nonuniform linker DNA lengths. J. Phys. Condens. Matter. 27, 064113 (2015)


Li, M., Zhang, J. Z. H., and Xia, F. Heterogeneous elastic network model improves description of slow motions of proteins in solution. Chem. Phys. Lett. 618, 102-107 (2015)


Yu, T. Q., Chen, P. Y., Chen, M., Samanta, A., Vanden-Eijnden, E., and Tuckerman, M. Order-parameter-aided temperature-accelerated sampling for the exploration of crystal polymorphism and solid-liquid phase transitions. J. Chem. Phys. 140, 214109 (2014)


Li, M., Xu, W., Zhang, J. Z. H., and Xia, F. Combined effect of confinement and affinity of crowded environment on conformation switching of adenylate kinase. J Mol. Model. 20, 2530 (2014)


Shimshovitz, A., Bačić, Z., and Tannor, D. J. The von Neumann basis in non-Cartesian coordinates: Application to floppy triatomic molecules. J. Chem. Phys. 141, 2341061 (2014)


Freudenthal, B. D., Beard, W. A., Perera, L., Shock, D. D., Kim, T., Schlick, T., and Wilson, S. H. Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature. 517, 635–639 (2015)


Samanta, A., Tuckerman, M. E., Yu, T. Q. Weinan, E. Microscopic mechanisms of equilibrium melting of a solid. Science. 346, 729-732 (2014)


Samanta, A., Chen, M., Yu, T. Q., Tuckerman, M. E., and Weinan, E. Sampling saddle points on a free energy surface. J. Chem. Phys. 140, 164109 (2014)


Sodt, A. J., Mei, Y., König, G., Tao, P., Steele, R. P., Brooks, B. R., and Shao, Y. Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies. J. Phys. Chem. A. 119, 1511–1523 (2015)


Duan, L. L., Gao, Y., Ji, C. G., Mei, Y., Zhang, Q. G., Tang, B., and Zhang, J. Z. H. Energetics of protein backbone hydrogen bonds and their local electrostatic environment. Sci. China Chem. 57, 1708 (2014)


Li, Y., Zhang, J. Z. H., and Mei, Y. Molecular dynamics simulation of protein crystal with polarized protein-specific force field. J. Phys. Chem. B. 118, 12326−12335 (2014)


Colognesi, D., Powers, A., Celli, M., Xu, M., Bačić, Z., and Ulivi, L. The HD molecule in small and medium cages of clathrate hydrates: Quantum dynamics studied by neutron scattering measurements and computation. J. Chem. Phys. 141, 134501 (2014)


Xu, M., Jiménez-Ruiz, M., Johnson, M. R., Rols, S., Ye, S., Carravetta, M., Denning, M. S., Lei, X., Bačić, Z., and Horsewill, A. J. Confirming a predicted selection rule in inelastic neutron scattering spectroscopy: The quantum translator-rotator H2 entrapped inside C60. Phys. Rev. Lett. 113, 123001 (2014)


Zhou, N., Lu, Z., Wu, Q., and Zhang, Y. Improved parameterization of interatomic potentials for rare gas dimers with density-based energy decomposition analysis. J. Chem. Phys. 140, 214117 (2014)


Xiao, X., Kallenbach, N., and Zhang, Y. Peptide conformation analysis using an integrated Bayesian approach. J. Chem. Theory Comput. 10, 4152-4159 (2014)


Liu, J., He, X., and Zhang, J. Z. H. Novel theoretically designed HIV-1 non-nucleoside reverse transcriptase inhibitors derived from nevirapine. J. Mol. Model. 20, 2451 (2014)


Zhu, T., Zhang, J. Z. H., and He, X. Correction of erroneously packed protein’s side chains in the NMR structure based on ab initio chemical shift calculations. Phys. Chem. Chem. Phys. 16, 18163-18169 (2014)


Ji, C. and Mei, Y. Some practical approaches to treating electrostatic polarization of proteins. Acc. Chem. Res. 47, 2795-2803 (2014)


Sirin, G. S. and Zhang, Y. How is acetylcholinesterase phosphonylated by soman? An ab initio QM/MM molecular dynamics study. J. Phys. Chem. A. 118, 9132-9139 (2014)


He, X., Zhu, T., Wang, X., Liu, J., and Zhang, J. Z. H. Fragment quantum mechanical calculation of proteins and its applications. Acc. Chem. Res. 47, 2748-2757 (2014)


Mou, L., Jia, X., Gao, Y., Li, Y., Zhang, J. Z. H., and Mei, Y. Folding simulation of Trp-cage utilizing a new AMBER compatible force field with coupled main chain torsions. J. Theor. Comput. Chem. 13, 1450026 (2014)


Wang, X., Li, Y., He, X., Chen, S., and Zhang, J. Z. H. Effect of strong electric field on the conformational integrity of insulin. J. Phys. Chem. A. 117, 6015−6023 (2014)


Duan, L. L., Mei, Y., Zhang, Q. G., Tang, B., and Zhang, J. Z. H. Protein's native structure is dynamically stabilized by electronic polarization. J. Theor. Comput. Chem. 13, 1440005 (2014)


Ji, C. G., Mei, Y., & John Z. H. Zhang (2014, August). Protein structure and dynamics-polarization in MD simulation. In ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY (Vol. 248). 1155 16TH ST, NW, WASHINGTON, DC 20036 USA: AMER CHEMICAL SOC.


Lin, B., Gao, Y., Li, Y., Zhang, J. Z. H., and Mei, Y. Implementing electrostatic polarization cannot fill the gap between experimental and theoretical measurements for the ultrafast fluorescence decay of myoglobin. J. Mol. Model. 20, 2189 (2014)


Duan, L. L., Zhu, T., Zhang, Q. G., Tang, B., Zhang, J. Z. H. Electronic polarization stabilizes tertiary structure prediction of HP-36. J. Mol. Model. 20, 2195 (2014)


Jia, X., Zeng, J., Zhang, J. Z. H., and Mei, Y. Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis. J. Comput. Chem. 35, 737–747 (2014)


Marsalek, O., Chen, P., Dupuis, R., Benoit, M., Méheut, M., Bačić, Z., and Tuckerman​, M. E. Efficient calculation of free energy differences associated with isotopic substitution using path-integral molecular dynamics. J. Chem. Theory Comput. 10, 1440–1453​ (2014)


Xiao, X., Zhu, T., Ji, C. G., and Zhang, J. Z. H. Development of an effective polarizable bond method for biomolecular simulation. J. Phys. Chem. B. 117, 14885-93 (2013)


Jia, X., Wang, X., Liu, J., Zhang, J. Z. H., Mei, Y., and He, X. An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins. J. Chem. Phys. 139, 214104 (2013)


Song, J., Ji, C., and Zhang, J. Z. H. Unveiling the gating mechanism of ECF transporter RibU. Sci. rep. 3, 3566 (2013)