Publications

451.

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)

452.

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)

453.

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

454.

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)

455.

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)

456.

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)

457.

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)

458.

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)

459.

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)

460.

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)

461.

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)

462.

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)

463.

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

464.

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)

465.

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)

466.

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)

467.

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)

468.

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)

469.

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)

470.

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

471.

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)

472.

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)

473.

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)

474.

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)

475.

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)

476.

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)

477.

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)

478.

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)

479.

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)

480.

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)

481.

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)

482.

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)

483.

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)

484.

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)

485.

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)

486.

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)

487.

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)

488.

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)

489.

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)

490.

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)

491.

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)

492.

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)

493.

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)

494.

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)

495.

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)

496.

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)

497.

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)

498.

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)

499.

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)

500.

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)

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