Publications

201.

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)

202.

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)

203.

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)

204.

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)

205.

Schlick, T. and Portillo-Ledesma, S. Biomolecular modeling thrives in the age of technology. Nat. Comput. Sci. 1, 321-331 (2021)

206.

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

207.

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)

208.

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)

209.

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)

210.

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)

211.

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)

212.

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)

213.

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)

214.

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)

215.

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)

216.

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

217.

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)

218.

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)

219.

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)

220.

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)

221.

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)

222.

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)

223.

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)

224.

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)

225.

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

226.

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)

227.

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

228.

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)

229.

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

230.

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)

231.

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)

232.

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)

233.

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)

234.

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)

235.

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

236.

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)

237.

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)

238.

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)

239.

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)

240.

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)

241.

 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)

242.

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)

243.

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)

244.

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)

245.

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)

246.

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)

247.

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)

248.

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)

249.

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)

250.

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)

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