Publications

151.

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)

152.

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)

153.

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)

154.

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)

155.

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)

156.

Liu, X., Humeniuk, A., and Glover, W. J. Conical intersections in solution with polarizable embedding: Integral-exact direct reaction fieldJ. Chem. Theory Comput. 18, 6826–6839 (2022)

157.

Liu, X., Zheng, L., Cong, Y., Gong, Z., Yin, Z., Zhang, J. Z. H., Liu, Z., and Sun, Z. Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constantJ. Comput. Aided Mol. Des. 36, 879–894 (2022).

158.

Liu, X., Zheng, L., Qin, C., Zhang, J. Z. H., and Sun, Z. Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: I. Standard procedureJ. Comput. Aided Mol. Des. 36, 735–752 (2022)

159.

Bai, Y., Vogt-Maranto, L., Tuckerman, M. E., and Glover, W. J. Machine learning the Hohenberg-Kohn map for molecular excited statesNat. Commun. 13, 7044 (2022)

160.

Shakiba, M., Smith, B., Li, W., Dutra, M., Jain, A., Sun, X., Garashchuk, S., and Akimov, A. Libra: A modular software library for quantum nonadiabatic dynamicsSoftware Impacts 14, 100445 (2022)

161.

Hu, Z., Liu, Z., and Sun, X. Effects of heterogeneous protein environment on excitation energy transfer dynamics in the Fenna–Matthews–Olson complexJ. Phys. Chem. B 126, 9271–9287 (2022)

162.

Liu, Z., Xu, W., Tuckerman, M. E., and Sun, X. Imaginary-time open-chain path-integral approach for two-state time correlation functions and applications in charge transferJ. Chem. Phys. 157, 114111 (2022)

163.

Felker, P. M. and Bačić, Z. Intermolecular vibrational states of HF trimer from rigorous nine-dimensional quantum calculations: Strong coupling between intermolecular bending and stretching vibrations and the importance of the three-body interactionsJ. Chem. Phys. 157, 194103 (2022)

164.

Jiang, Y., Cai, Z., Yuan, Q., Cao, W., Hu, Z., Sun, H., Wang, X.-B., and Sun, Z. Highly structured water networks in microhydrated dodecaborate clustersJ. Phys. Chem. Lett. 13, 11787–11794 (2022)

165.

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

166.

Xiong, L., He, X., and Yang, J. Origin of humidity influencing the excited state electronic properties of silicon quantum dot based light-emitting diodesPhys. Chem. Chem. Phys. 24, 28222-28231 (2022)

167.

Guo, X.-K. and Zhang, Y. CovBinderInPDB: A structure-based covalent binder databaseJ. Chem. Inf. Model. 62, 6057–6068 (2022)

168.

Zelovich, T., Hensen, T., and Tuckerman, M. E. A Green’s function approach for determining surface induced broadening and shifting of molecular energy levelsNano Lett. 22, 9854–9860 (2022)

169.

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

170.

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

171.

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)

172.

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)

173.

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)

174.

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)

175.

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)

176.

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)

177.

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)

178.

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)

179.

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)

180.

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

181.

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

182.

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)

183.

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)

184.

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)

185.

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)

186.

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)

187.

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)

188.

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)

189.

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

190.

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)

191.

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)

192.

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)

193.

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)

194.

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)

195.

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)

196.

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)

197.

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)

198.

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)

199.

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)

200.

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)

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