Publications

351.

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)

352.

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)

353.

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)

354.

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)

355.

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)

356.

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)

357.

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) 

358.

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)

359.

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)

360.

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)

361.

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)

362.

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)

363.

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)

364.

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)

365.

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)

366.

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)

367.

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)

368.

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)

369.

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)

370.

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)

371.

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)

372.

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)

373.

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)

374.

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)

375.

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)

376.

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)

377.

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)

378.

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)

379.

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)

380.

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)

381.

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)

382.

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)

383.

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)

384.

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)

385.

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)

386.

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)

387.

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)

388.

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)

389.

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)

390.

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)

391.

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)

392.

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

393.

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)

394.

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)

395.

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)

396.

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)

397.

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)

398.

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)

399.

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)

400.

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

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