向云 - 华东师范大学 - 物理与电子科学学院

研究领域

理论与计算生物物理化学酶催化反应的理论计算研究蛋白分子折叠和聚集的多维非线性光谱凝聚态化学体系的量子动力学

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Xiang Y, Zhang JZH*, Wang DY, J. Chem. Phys. 117, 7698-7704 (2002) Semi-rigid vibrating rotor target model for CH4 dissociation on a Ni (111) surface. Xiang Y, Zhang JZH*, J. Chem. Phys. 118,8954-8959 (2003) A mixed quantum-classical semi-rigid vibrating rotor target approach to methane dissociation on Ni surface. Zhang DW, Xiang Y, Zhang JZH*, J. Phys. Chem. B 107, 12039-12041 (2003) New advance in computational chemistry: full quantum mechanical ab initio computation of streptavidin-biotin interaction energy. Zhang DW, Xiang Y, Gao AM, Zhang JZH*, J. Chem. Phys. 120, 1145-1148 (2004) Quantum mechanical map for protein-ligand binding with application to β-trypsin/benzamidine complex. Zhang JZH*, Wang ML, Li YM, Xiang Y, Advanced Series in Physical Chemistry 14, 209-248 (2004) Theoretical dynamics treatment of chemical reactions. Xiang Y*, Zhang DW, Zhang JZH*, J. Comput. Chem. 25, 1431-1437 (2004) Fully quantum mechanical energy optimization for protein-ligand structure. Mei Y, He X, Xiang Y, Zhang DW, Zhang JZH*, Proteins 59, 489-495 (2005) Quantum study of mutational effect in binding of efavirenz to HIV-1 RT. He X, Mei Y, Xiang Y, Zhang DW, Zhang JZH*, Proteins 61, 423-432(2005) Quantum computational analysis for drug resistance of HIV-1 reverse transcriptase to nevirapine through point mutations. Sharma PK, Xiang Y, Kato M, Warshel A*, Biochemistry 44, 11307-11314 (2005) What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome? Xiang Y, Olesheger P, Florian J, Goodman MF, Warshel A*, Biochemistry 45, 7036-7048 (2006) Simulating the effect of mutations on the energetics of the transition state of the reaction of DNA polymerase β; Evaluating group contribution and allosteric coupling for ionized residues in pol-β. Warshel A*, Sharma PK, Kato M, Xiang Y, Liu HB, Olsson MH, Chem. Rev. 106, 3210-3235 (2006) Electrostatic basis for enzyme catalysis. Sucato CA, Upton TG, Kashemirov BA, Martínek V, Xiang Y, Beard WA, Batra VK, Pedersen LC, Wilson SH, McKenna CE, Florián J, Warshel A, Goodman MF*, Biochemistry 46, 461-471 (2007) Modifying the β-γ leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity and catalytic mechanism of DNA polymerase β. Xiang Y*, Goodman MF, Beard WM, Wilson SH, Warshel A*, Proteins 70, 231-247 (2008) Exploring the role of large conformational changes in the fidelity of DNA polymerase β. Xiang Y*, Warshel A*, J. Phys. Chem. B 11, 1007-1015 (2008) Quantifying free energy profiles of proton transfer reactions in solution and in proteins by using a FDFT diabatic mapping. Xiang Y*, Duan LL, Zhang JZH, Phys. Chem. Chem. Phys. 12, 15681-15688 (2010) Folding dynamics of a small protein at room temperature via simulated two-dimensional infrared spectroscopy. Xiang Y*, Duan LL, Zhang JZH, J. Chem. Phys. 134, 205101 (2011) Protein’s electronic polarization contributes significantly to its catalytic function. Xu J, Zhang JZH, Xiang Y*, J. Am. Chem. Soc. 134，16424-16429 (2012) Ab initio QM/MM free energy simulations of peptide bond formation in the ribosome support an eight-membered ring reaction mechanism. Xu J, Zhang JZH, Xiang Y*, J. Phys. Chem. A, 117, 6373-6379 (2013) Molecular dynamics simulation and computational two-dimensional infrared spectroscopic study of model amyloid β-peptide oligomers. (Invited article)