Published as a postdoc at Harvard (1998-2001)

39. Is "proton wire" concerted or step-wise? A model study of proton transfers in carbonic anhydrase, Q. Cui, M. Karplus, J. Phys. Chem. B 107, 1071-1078 (2003) PDF version

38. Understanding the role of active-site residues in chorimsmate mutase catalysis from molecular dynamics simulations, H. Guo, Q. Cui, W. N. Lipscomb, M. Karplus, Angew. Chim. Intl. Ed. 42, 1508-1511 (2003)

37. Does Chorismate Mutase catalyze a conformational change of the substrate prior to the chemical rearrangement? H. Guo, Q. Cui, W. N. Lipscomb, M. Karplus, NATO Sci. Ser. I 364, 63-74 (2005)

36. Modeling zinc in biomolecules with the Self-Consistent Charge Density Functional Tight-Binding (SCC-DFTB) method: application to structural and energetical analysis, M. Elstner, Q. Cui, P. Munih, E. Kaxiras, T. Frauenheim, and M. Karplus, J. Comput. Chem. 24, 565-581 (2003) PDF version

35. Combining ab initio and density functional theory with semi-empirical methods , Q. Cui, H. Guo, M. Karplus, J. Chem. Phys. 117, 5617-5631 (2002) PDF version

34. A dynamical analysis of the rotation mechanism for conformational change in F1-ATPase, J. Ma, T. C. Flynn, Q. Cui, A. Leslie, J. E. Walker, M. Karplus, Structure, 10, 921-930 (2002) PDF version

33. Promoting modes and demoting modes in enzyme catalyzed proton transfer reactions: A study of models and realistic systems, Q. Cui, M. Karplus, J. Phys. Chem. B 106, 7927-7947 (2002) PDF version

32. QM/MM Studies of the Triosephosphate Isomerase (TIM) Catalyzed Reactions: The effect of geometry and tunneling on proton transfer rate constants, Q. Cui, M. Karplus J. Am. Chem. Soc. 124, 3093 (2002) PDF version

31. QM/MM Studies of the Triosephosphate Isomerase (TIM) Catalyzed Reactions: Verification of Methodology and Analysis of the Reaction Mechanisms, Q. Cui, M. Karplus J. Phys. Chem. B 106, 1768 (2002) PDF version

30. A theoretical analysis of the proton and hydride transfer in liver alcohol dehydrogenase (LADH), Q. Cui, M. Elstner, M. Karplus, J. Phys. Chem. B 106, 2721 (2002) PDF version

29. Substrate conformational transitions in the active site of chorismate mutase: Their role in the catalytic mechanism, H. Guo, Q. Cui, W. N. Lipscomb and M. Karplus, Proc. Natl. Acad. Sci. USA 98, 9032 (2001) PDF version

28. Triosephosphate Isomerase: A Theoretical Comparison of Alternative Pathways, Q. Cui, M. Karplus, J. Am. Chem. Soc. 123, 2284 (2001) PDF version

27. A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method, Q. Cui, M. Elstner, E. Kaxiras, T. Frauenheim, M. Karplus, J. Phys. Chem. B 105, 569,(2001) PDF version

26. Molecular Properties from combined QM/MM methods. II. Chemical shifts in large molecules. Q. Cui, M. Karplus, J. Phys. Chem. B 104, 3721 (2000) PDF version

25. Molecular Properties from combined QM/MM methods. I. Analytical second derivative and vibrational calculations. Q. Cui, M. Karplus, J. Chem. Phys. 112, 1133 (2000) PDF version