Book chapters

2020

  1. Chapter 6: Understanding Enzyme Catalysis Mechanism using QM/MM Simulation Methods T. Yu* and Hong Guo in ACS Book: Bridging Structure and Function in Mechanistic Enzymology.

Publications

    Tenure-track period

    2021

  1. M. A. Jabed, J. Zhao, D. Kilin, T. Yu*, "Understanding of Properties of the N-Doped Graphene Oxide Quantum Dot with TD-DFT", submitted to the Joural of Physical Chemistry C
  2. S. Zaharias, Z. Zhang, K. Davis, T. Fargason, D. Cashman, T. Yu, J. Zhang "Intrinsically Disordered Electronegative Clusters Improve Stability and Binding Specificity of RNA-Binding Proteins" submitted to Nucleic Acids Research
  3. T. Yu*, D. Lingerfelt*, J. Jakowski*, P. Ganesh, B. Sumpter Electron-Beam-Induced Molecular Plasmon Excitation and Energy Transfer in Silver Molecular Nanowires J. Phys. Chem. A 2021, 2021, 125, 74.
  4. D. Lingerfelt*, T. Yu*, A. Yoshimura, P. Ganesh, J. Jakowski, B. Sumpter “Nonadiabatic Effects on Defect Diffusion in Silicon-Doped Nanographenes” Nano. Lett. 2021, 21, 236.

    5. 2020

  5. Z.-Y. Zhang, Y. Su, L.-X. Shi, S.-F. Li, F. Fabunmi, S.-L. Li, T. Yu, Z.-N. Chen, Z. Su, H.-K. Liu, Coordination-Bond-Driven Dissolution–Recrystallization Structural Transformation with the Expansion of Cuprous Halide Aggregate. Ing. Chem. 2020, 59, 13326.
  6. B. He, X. Wang, L. Xia, Y. Guo, Y. Tang, Y. Zhao, Q. Hao, T. Yu*, H. Liu*, Z. Su* Metal‐organic framework‐derived Fe‐doped Co1.11Te2 embedded in nitrogen‐doped carbon nanotube for water splitting. ChemSusChem accepted
  7. W. Ren, K. Jiang, H. Deng, N. Lu, T. Yu*, H. Guo*, P. Qian* Catalytic mechanism and product specificity of protein arginine methyltransferase PRMT7: A study from QM/MM molecular dynamics and free energy simulations. J. Chem. Theory Comput. 2020, 16, 8, 5301.
  8. J. Chen, Q. Tao, J. Wu, M. Wang, Z. Su, Y. Qian, T. Yu, Y. Wang, X. Xue, H.-K. Liu A lysosome-targeted ruthenium(II) polypyridyl complex as photodynamic anticancer agent J. Inorg. Biochem. 2020, 210, 111132.

    9. 2019

  9. R. A. Bennett, A. Bele, C. M. Will, E. C. Small, B. Nabet, R. Ghosh, A. T. Grzybowski, T. Yu, Q. Zhang, A. Riva, T. Lele, G. C. Schatz, A. J. Ruthenburg, J. Liphardt, and J. D. Licht, A mutation in the core of histone H2B represents a new class of oncogenic drivers, Cancer Discov. 2019, 10, 1438
  10. T. Yu*, F. Fabunmi, J. Huang, B. Sumpter, and J. Jakowski*, A fast scheme to calculate electronic couplings in P3HT polymer units using diabatic orbitals for charge transfer dynamics. J. Comput. Chem., 2019, 40, 532.
  11. W. H. Morris, J. D. Conner, L. Ngo, J. T.Wilson, W. Medawala, A. R. Brown, M. T. Stephens, F. Fabunmi, D. Cashman, E. C. Lisic, T. Yu, J. E. Deweese, and X. Jiang, Structural and metal ion effects on human topoisomerase IIα inhibition by α-(N)-heterocyclic thiosemicarbazones. Chem. Res. Toxicol. 2019, 32, 90.

    12. 2018

  12. J. D. Marsee, A. Ridings, T. Yu*, J. M. Miller*, Mycobacterium tuberculosis ClpC1 N-terminal domain is dispensable for adaptor protein-dependent allosteric regulation. Int. J. Mol. Sci. 2018, 19, 3651.

    13. 2017

  13. J. Li, P. Zhang, Y. Xu, Z. Su, Y. Qian, S. Li, T. Yu*, P. J Sadler*, H.-K. Liu*, A novel strategy to construct Janus metallamacrocycles with both a Ru-carene face and an imidazolium face. Dalton Trans. 2017, 46, 16205.
  14. P. Wang, Y. Zhao, H. Zhang, T. Yu, Y. Zhang, Y. Tang, Effect of pyrazolium-derived compounds as templates in zeolite synthesis. RSC Adv., 2017, 7, 23272.
  15. M. Horitani, A. R. Offenbacher, C. A. M. Carr, T. Yu, V. Hoeke, G. E. Cutsail III, S. Hammes-Schiffer, J. P. Klinman, B. M. Hoffman, 13C ENDOR spectroscopy of lipoxygenase–substrate complexes reveals the structural basis for C–H activation by tunneling. J. Am. Chem. Soc. 2017, 139, 1984.

    16. Before tenure-track

    2016

  16. T. Yu, A.V. Soudackov, and S. Hammes-Schiffer, Computational insights into five-versus six-coordinate iron center in ferrous soybean lipoxygenase. J. Phys. Chem. Lett. 2016, 7, 3429.
  17. Z. Yu, F. Tantakitti, T. Yu, L. C. Palmer, G. C. Schatz, and S. I. Stupp, Simultaneous covalent and non-covalent polymerizations. Science 2016, 351, 497.
  18. F. Tantakitti, J. Boekhoven, J. Li, E. Zhuang, R. Zandi, J. H. Ortony, C. J. Newcomb, L. C. Palmer, T. Yu, G. C. Schatz, Samuel I. Stupp, The energy landscapes of supramolecular systems determine their function. Nat. Mater. 2016, 15, 694.

    19. 2015

  19. A. K. Harshan, T. Yu (co-first author), A. V. Soudackov, and S. Hammes-Schiffer, Dependence of vibronic coupling on molecular geometry and environment: bridging hydrogen atom transfer and electron-proton transfer. J. Am. Chem. Soc. 2015, 137, 13545.
  20. F. Li, E. S. Burgie, T.Yu*, A. Héroux, G. C. Schatz, R. D. Vierstra*, and A. M. Orville*, X-ray induced deprotonation of the Bilin chromophore in crystalline D. radiodurans phytochrome. J. Am. Chem. Soc. 2015, 137, 2792.

    21. 2014—2006

  21. T. Yu, OS. Lee, and G. C Schatz, Molecular dynamics simulations and electronic excited state properties of a self-assembled peptide amphiphile nanofiber with metalloporphyrin arrays. J. Phys. Chem. A 2014, 118, 8553.
  22. T. Yu, and G. C. Schatz, Free-Energy Landscape for peptide amphiphile self-assembly: stepwise versus continuous assembly mechanisms. J. Phys. Chem. B 2013, 117, 14059.
  23. T. Yu, and G. C. Schatz, Free energy profile and mechanism of self-assembly of peptide amphiphiles based on a collective assembly coordinate. J. Phys. Chem. B 2013, 117, 9004.
  24. T. Yu, OS. Lee, and G. C. Schatz, Steered molecular dynamics studies of the potential of mean force for peptide amphiphile self-assembly into cylindrical nanofibers. J. Phys. Chem. A 2013, 117, 7453.
  25. T. Yu, J. M. Higashi, A. Cembran, J. Gao, and D. G. Truhlar, Concerted hydrogen atom and electron transfer mechanism for catalysis by lysine-specific demethylase. J. Phys. Chem. B 2013, 117, 8422. (Cover Article)
  26. I. M. Alecu, J. Zheng, E. Papajak, T. Yu, and D. G. Truhlar, Biofuel combustion energetics and kinetics of hydrogen abstraction from carbon-1 in n-butanol by the hydroperoxyl radical calculated by coupled cluster and density functional theories and Multistructural variational transition-state theory with multidimensional tunneling. J. Phys. Chem. A 2012, 116, 12206.
  27. X. F. Xu, T. Yu, E. Papajak, and D. G. Truhlar, Multistructural variational transition state theory: kinetics of the hydrogen abstraction from carbon-2 of 2-methyl-1-propanol by hydroperoxyl radical including all structures and torsional anharmonicity. J. Phys, Chem. A 2012, 116, 10480.
  28. P. Seal, E. Papajak, T. Yu, and D. G. Truhlar, Statistical thermodynamics of 1-butanol, 2-methyl-1-propanol, and butanol. J. Chem. Phys. 2012, 136, 034306.
  29. T. Yu, J. Zheng, and D. G. Truhlar, Multipath variational transition state theory: rate constant of the 1, 4-hydrogen shift isomerization of the 2-cyclohexylethyl radical. J. Phys. Chem. A 2012, 116, 297.
  30. T. Yu, J. Zheng, and D. G. Truhlar, Statistical thermodynamics of the isomerization reaction between n-heptane and isoheptane. Phys. Chem. Chem. Phys. 2012, 14, 482.
  31. T. Yu, J. Zheng, and D. G. Truhlar, Multi-structural variational transition state theory. Kinetics of the 1, 4-hydrogen shift isomerization of the pentyl radical with torsional anharmonicity. Chem. Sci. 2011, 11, 2199.
  32. J. Zheng, T. Yu, and D. G. Truhlar, Multi-structural thermodynamics of C–H bond dissociation in hexane and isohexane yielding seven isomeric hexyl radicals. Phys. Chem. Chem. Phys. 2011, 13, 19318.
  33. J. Zheng, T. Yu, E. Papajak, I, M. Alecu, S. L. Mielke, and D. G. Truhlar, Practical methods for including torsional anharmonicity in thermochemical calculations on complex molecules: The internal-coordinate multi-structural approximation. Phys. Chem. Chem. Phys. 2011, 13, 10885.
  34. L. R. Masterson, T. Yu, L. Shi; Y. Wang, M. Gustavsson, M. M. Mueller, and G. Veglia, cAMP-dependent protein kinase A selects the excited state of the membrane substrate phospholamban. J. Mol. Biol. 2011, 412, 155.
  35. L. R. Masterson, C.Y. Cheng, T. Yu, M. Tonelli, A. Kornev, S. S. Taylor, and G. Veglia, Dynamics connect substrate recognition to catalysis in protein kinase A. Nat. Chem. Biol. 2010, 6, 821.
  36. L. R. Masterson, N. Bortone, T. Yu, K. N. Ha, E. C. Gaffarogullari, O. Nguyen, and G. Veglia, Expression and purification of isotopically labeled peptide inhibitors and substrates of cAMP-dependent protein kinase A for NMR analysis. Prot. Expr. Pur. 2009, 64, 231.
  37. X. Q. Zhou, T. Yu, Y. H. Zhang, J. Kong, Y. Tang, J.-L. Marty, and B. Liu, Nanozeolite-assembled interface towards sensitive biosensing. Electrochem. Commun. 2007, 9, 1525.
  38. T. Yu, Y. H. Zhang, J. H. Zhuang, B. Wang, B. H. Liu, Y. J. Kang, and Y. Tang, Controlled nanozeolite‐assembled electrode: remarkable enzyme‐immobilization ability and high sensitivity as biosensor. Chem.-A Eur. J. 2006, 12, 1137.
  39. W. Shan, T. Yu, B. Wang, J. K. Hu, Y. H. Zhang, X. Y. Wang, and Y. Tang, Magnetically separable nanozeolites: promising candidates for bio-applications. Chem. Mater. 2006, 18, 3169.