Publications

(To open PDF: 5 sig figs of π)

(** indicates the only corresponding author, * denotes one of the corresponding authors)

  1. Wong, K.-Y.;** Xu, Y.; Xu, L., “Pitfall in Free-Energy Simulations on Simplest Systems“, ChemistrySelect 2017, 2, (16), 4398 to 4418. [Free Clip of Video Abstract: (i) YouTube; (ii) Vimeo for “Download“; (iii) Brightcove] [Free Graphical Abstract] [DOI] [PDF]
  2. Wong, K.-Y.;** Xu, Y.; Xu, L., “Review of Computer Simulations of Isotope Effects on Biochemical Reactions: from the Bigeleisen Equation to Feynman’s Path Integral“, Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics 2015, 1854, (11), 1782 to 1794. [Highlighted in Atlas of Science] [DOI] [PDF]
  3. Chen, H.; Giese, T. J.; Huang, M.; Wong, K.-Y.; Harris, M. E.; York, D. M., Mechanistic Insights into RNA Transphosphorylation from Kinetic Isotope Effects and Linear Free Energy Relationships of Model Reactions“, Chemistry – A European Journal 2014, 20, (44), 14336 to 14343. [selected by the Editors as one of “Hot Papers“] [DOI] [PDF]
  4. Wong, K.-Y.;* Xu, Y.; York, D. M., “Ab Initio Path-Integral Calculations of Kinetic and Equilibrium Isotope Effects on Base-Catalyzed RNA Transphosphorylation Models“, Journal of Computational Chemistry 2014, 35, (17), 1302 to 1316. [DOI] [PDF]
  5. Wong, K.-Y.,** “Review of Feynman’s Path Integral in Quantum Statistics: from the Molecular Schrödinger Equation to Kleinert’s Variational Perturbation Theory“, Communications in Computational Physics 2014, 15, (4), 853 to 894. [DOI] [Free PDF]
  6. Lee, T.-S.; Radak, B. K.; Huang, M.; Wong, K.-Y.; York, D. M., “Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach“, Journal of Chemical Theory and Computation 2014, 10, (1), 24 to 34. [DOI] [PDF] [Free PDF (until the end of 2014)]
  7. Lee, T.-S.; Wong, K.-Y.; Giambasu, G. M.; York, D. M., “Bridging the Gap between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis“. In Progress in Molecular Biology and Translational Science: Catalytic RNA, Soukup, G. A., Ed. Elsevier (Academic Press): 2013, (120), p 25 to 91. [DOI] [PDF]
  8. Gu, H.; Zhang, S.; Wong, K.-Y.; Radak, B. K.; Dissanayake, T.; Kellerman, D. L.; Dai, Q.; Miyagi, M.; Anderson, V. E.; York, D. M.; Piccirilli, J. A.; Harris, M. E., “Experimental and computational analysis of the transition state for ribonuclease A catalyzed RNA 2′-O-transphosphorylation”, Proceedings of the National Academy of Sciences (USA) 2013, 110, (32), 13002 to 13007. [Recommended in F1000Prime] [DOI] [Free PDF]
  9. Wong, K.-Y.;* York, D. M., “Exact Relation between Potential of Mean Force and Free-Energy Profile”, Journal of Chemical Theory and Computation 2012, 8, (11), 3998 to 4003. [DOI] [PDF] [Free Full Access via Free ACS ID]
  10. Wong, K.-Y.,**Developing a systematic approach for ab initio path-integral simulations”. In Molecular Dynamics/Book 1 – Theoretical Developments and Applications in Nanotechnology and Energy, Wang, L., Ed. InTech (Open Access Publisher): 2012, p 107 to 132. [DOI] [Free PDF]
  11. [Cover Image] Wong, K.-Y.;* Gu, H.; Zhang, S.; Piccirilli, J. A.; Harris, M. E.; York, D. M., “Characterization of the reaction path and transition states for RNA transphosphorylation models from theory and experiment”, Angewandte Chemie International Edition 2012, 51, (3), 647 to 651 [DOI] [PDF]
  12. Wong, K.-Y.;* Gao, J., “Insight into the phosphodiesterase mechanism from combined QM/MM free energy simulations“, FEBS Journal 2011, 278, (14), 2579 to 2595. [DOI] [PDF] [Free PDF] [also selected in Virtual Issue on Molecular Enzymology May 2012]
  13. [Cover ImageWong, K.-Y.; Lee, T.-S.; York, D. M., “Active participation of Mg2+ ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme“, Journal of Chemical Theory and Computation 2011, 7, (1), 1 to 3. [DOI] [PDF] [Free Full Access via Free ACS ID]
  14. Wong, K.-Y.;* Richard, J. P.; Gao, J., “Theoretical analysis of kinetic isotope effects on proton transfer reactions between substituted α-methoxystyrenes and substituted acetic acids“, Journal of the American Chemical Society 2009, 131, (39), 13963 to 13971. [DOI] [PDF] [Free Full Access via Free ACS ID]
  15. Wong, K.-Y.; Song, L.; Xie, W.; Major, D. T.; Lin, Y.-l.; Cembran, A.; Gao, J., “Quantum mechanical methods for biomolecular simulations“. In Multi-Scale Quantum Models for Biocatalysis, York, D. M.; Lee, T.-S., Ed. Springer Netherlands: 2009; p 79 to 101. [DOI] [PDF]
  16. Wu, E.; Wong, K.-Y.; Zhang, X; Han, K. L.; Gao, J., “Determination of the structure form of the fourth ligand of zinc in acutolysin A using combined quantum mechanical and molecular mechanical simulation“, Journal of Physical Chemistry B 2009, 113, (8), 2477 to 2485. [DOI] [PDF] [Free Full Access via Free ACS ID]
  17. Gao. J; Wong, K.-Y.; Major, D. T.; Cembran, A.; Song, L.; Lin, Y-L.; Fan, Y.; Ma, S., “Kinetic isotope effects from hybrid classical and quantum path integral computations“. In Quantum Tunnelling in Enzyme-Catalysed Reactions, Scrutton, N. S.; Allemann, R. K., Ed. Royal Society of Chemistry: 2009; p 105 to 134. [DOI] [PDF]
  18. Wong, K.-Y.;** Gao, J., “Systematic approach for computing zero-point energy, quantum partition function, and tunneling Effect based on Kleinert’s variational perturbation theory“, Journal of Chemical Theory and Computation 2008, 4, (9), 1409 to 1422. [DOI] [PDF]
  19. Gao, J.; Wong, K.-Y.; Major, D. T., “Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water“, Journal of Computational Chemistry 2008, 29, (4), 514 to 522. [DOI] [PDF]
  20. Gao, J.; Major, D. T.; Fan, Y.; Lin, Y.-l.; Ma, S.; Wong, K.-Y., “Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymes“. In Molecular Modeling of Proteins, Kukol, A., Ed. Springer Verlag: 2008; p 37 to 62. [DOI] [PDF]
  21. Wong, K.-Y.;** Gao, J., “An automated integration-free path-integral method based on Kleinert’s variational perturbation theory“, Journal of Chemical Physics 2007, 127, (21), 211103. [DOI] [PDF] [Supp. Material]
  22. Wong, K.-Y.; Gao, J., “The reaction mechanism of paraoxon hydrolysis by phosphotriesterase from combined QM/MM simulations“, Biochemistry 2007, 46, (46), 13352 to 13369. [DOI] [PDF]
  23. Wong, K. Y.; Lo, C. F.; Sham, W. Y.; Fong, H. H.; So, S. K.; Leung, L. M., “Theoretical investigation of a blue hydroxyquinaldine-based aluminum(III) complex“, Physics Letters A 2004, 321, (3), 194 to 198. [DOI] [PDF]
  24. Wong, K. Y.; Smallfield, J. A. O.; Fahlman, M.; Epstein, A. J., “Electronic state of nitrogen containing polypyridine at the interfaces with model sulfonic acid containing polymer and molecule“, Synthetic Metals 2003, 137, (1-3), 1031 to 1032. [DOI] [PDF]