All Department Publications

Found 179 results
Author Title Type [ Year(Asc)]
Filters: Author is Cui, Q.  [Clear All Filters]
2005
Casey CP, Johnson JB, Singer SW, Cui Q. Hydrogen elimination from a hydroxycyclopentadienyl ruthenium(II) hydride: study of hydrogen activation in a ligand-metal bifunctional hydrogenation catalyst. J Am Chem Soc. 2005;127(9):3100-9.
Casey CP, Johnson JB, Singer SW, Cui Q. Hydrogen elimination from a hydroxycyclopentadienyl ruthenium(II) hydride: Study of hydrogen activation in a ligand-metal bifunctional hydrogenation catalyst. Journal of the American Chemical Society. 2005;127:3100-3109.
Riccardi D, Schaefer P, Cui Q. pK(a) calculations in solution and proteins with QM/MM free energy perturbation simulations: A quantitative test of QM/MM protocols [Review]. Journal of Physical Chemistry BJournal of Physical Chemistry B. 2005;109:17715-17733.
Casey CP, Bikzhanova GA, Cui Q, Guzei IA. Reduction of imines by hydroxycyclopentadienyl ruthenium hydride: intramolecular trapping evidence for hydride and proton transfer outside the coordination sphere of the metal. J Am Chem Soc. 2005;127(40):14062-71.
Casey CP, Bikzhanova GA, Cui Q, Guzei IA. Reduction of Imines by hydroxycyclopentadienyl ruthenium hydride: Intramolecular trapping evidence for hydride and proton transfer outside the coordination sphere of the metal. Journal of the American Chemical Society. 2005;127:14062-14071.
Schaefer P, Riccardi D, Cui Q. Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules - art. no. 014905. Journal of Chemical Physics. 2005;123:14905.
Schaefer P, Riccardi D, Cui Q. Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules. J Chem Phys. 2005;123(1):014905.
2004
Li GH, Cui Q. Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: Myosin-II and Ca2+-ATPase [Review]. Biophysical Journal. 2004;86:743-763.
Li G, Cui Q. Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: myosin-II and Ca2+ -ATPase. Biophys J. 2004;86(2):743-63.
Riccardi D, Li G, Cui Q. Importance of van der Waals Interactions in QM/MM Simulations. J Phys Chem B. 2004;108(20):6467-78.
Riccardi D, Li GH, Cui Q. Importance of van der Waals interactions in QM/MM Simulations. Journal of Physical Chemistry BJournal of Physical Chemistry B. 2004;108:6467-6478.
Li GH, Cui Q. Mechanochemical coupling in myosin: A theoretical analysis with molecular dynamics and combined QM/MM reaction path calculations. Journal of Physical Chemistry BJournal of Physical Chemistry B. 2004;108:3342-3357.
Cui Q, Li G, Ma J, Karplus M. A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase. J Mol Biol. 2004;340(2):345-72.
Van Wynsberghe A, Li GH, Cui Q. Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle. BiochemistryBiochemistry. 2004;43:13083-13096.
Van Wynsberghe A, Li G, Cui Q. Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle. Biochemistry. 2004;43(41):13083-96.
Xu D, Wei Y, Wu J, Dunaway-Mariano D, Guo H, Cui Q, Gao J. QM/MM studies of the enzyme-catalyzed dechlorination of 4-chlorobenzoyl-CoA provide insight into reaction energetics. J Am Chem Soc. 2004;126(42):13649-58.
Xu DG, Guo H, Gao JL, Cui Q. A QM/MM study of a nucleophilic aromatic substitution reaction catalyzed by 4-chlorobenzoyl-CoA dehalogenase. Chemical CommunicationsChemical Communications. 2004:892-893.
2003
Formaneck MS, Li GH, Zhang XD, Cui Q. Calculating accurate redox potentials in enzymes with a combined QM/MM free energy perturbation approach. Journal of Theoretical and Computational Chemistry. 2003;1:53-67.
Cui Q, Karplus M. Catalysis and specificity in enzymes: A study of triosephosphate isomerase and comparison with methyl glyoxal synthase [Review]. Protein SimulationsProtein Simulations. 2003;66:315-+.
Li G, Zhang X, Cui Q. Free Energy Perturbation Calculations with Combined QM/MM Potentials Complications, Simplifications, and Applications to Redox Potential Calculations. The Journal of Physical Chemistry B. 2003;107:8643-8653.
Li GH, Zhang XD, Cui Q. Free energy perturbation calculations with combined QM/MM Potentials complications, simplifications, and applications to redox potential calculations. Journal of Physical Chemistry BJournal of Physical Chemistry B. 2003;107:8643-8653.
Smedarchina Z, Siebrand W, Fernández-Ramos A, Cui Q. Kinetic isotope effects for concerted multiple proton transfer: a direct dynamics study of an active-site model of carbonic anhydrase II. J Am Chem Soc. 2003;125(1):243-51.
Smedarchina Z, Siebrand W, Fernandez-Ramos A, Cui Q. Kinetic isotope effects for concerted multiple proton transfer: A direct dynamics study of an active-site model of carbonic anhydrase. Journal of the American Chemical Society. 2003;125:243-251.
Yang W, Gao YQ, Cui Q, Ma J, Karplus M. The missing link between thermodynamics and structure in F1-ATPase. Proceedings of the National Academy of Sciences. 2003;100:874-879.
Yang W, Gao YQ, Cui Q, Ma J, Karplus M. The missing link between thermodynamics and structure in F-1-ATPase. Proceedings of the National Academy of Sciences of the United States of America. 2003;100:874-879.
Elstner M, Cui Q, Munih P, Kaxiras E, Frauenheim T, Karplus M. Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: Applications to structural and energetic analysis [Review]. Journal of Computational Chemistry. 2003;24:565-581.
Elstner M, Cui Q, Munih P, Kaxiras E, Frauenheim T, Karplus M. Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis. J Comput Chem. 2003;24:565-81.
Li GH, Cui Q. pK(a) calculations with QM/MM free energy perturbations. Journal of Physical Chemistry BJournal of Physical Chemistry B. 2003;107:14521-14528.
Cui Q, Karplus M. Is a "proton wire" concerted or stepwise? A model study of proton transfer in carbonic anhydrase. Journal of Physical Chemistry BJournal of Physical Chemistry B. 2003;107:1071-1078.
Guo H, Cui Q, Lipscomb WN, Karplus M. Understanding the role of active-site residues in chorismate mutase catalysis from molecular-dynamics simulations. Angew Chem Int Ed Engl. 2003;42(13):1508-11.
Guo H, Cui Q, Lipscomb WN, Karplus M. Understanding the role of active-site residues in chorismate mutase catalysis from molecular-dynamics simulations. Angewandte Chemie-International EditionAngewandte Chemie-International Edition. 2003;42:1508-1511.
Li G, Cui Q. What is so special about Arg 55 in the catalysis of cyclophilin A? insights from hybrid QM/MM simulations. J Am Chem Soc. 2003;125(49):15028-38.
Li GH, Cui Q. What is so special about Arg 55 in the catalysis of cyclophilin A? Insights from hybrid QM/MM simulations. Journal of the American Chemical Society. 2003;125:15028-15038.
2002
Li GH, Cui Q. A coarse-grained normal mode approach for macromolecules: An efficient implementation and application to Ca2+-ATPase. Biophysical Journal. 2002;83:2457-2474.
Li G, Cui Q. A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase. Biophys J. 2002;83(5):2457-74.
Cui Q, Guo H, Karplus M. Combining ab initio and density functional theories with semiempirical methods. Journal of Chemical Physics. 2002;117:5617-5631.
Cui Q, Guo H, Karplus M. Combining ab initio and density functional theories with semiempirical methods. The Journal of Chemical Physics. 2002;117:5617-5631.
Cui Q. Combining implicit solvation models with hybrid quantum mechanical/molecular mechanical methods: A critical test with glycine. Journal of Chemical Physics. 2002;117:4720-4728.
Ma JP, Flynn TC, Cui Q, Leslie AGW, Walker JE, Karplus M. A dynamic analysis of the rotation mechanism for conformational change in F-1-ATPase. StructureStructure. 2002;10:921-931.
Ma J, Flynn TC, Cui Q, Leslie AGW, Walker JE, Karplus M. A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase. Structure. 2002;10(7):921-31.
Zhang XD, Harrison DHT, Cui Q. Functional Specificities of methylglyoxal synthase and triosephosphate isomerase: A combined QM/MM analysis. Journal of the American Chemical Society. 2002;124:14871-14878.
Zhang X, Harrison DHT, Cui Q. Functional specificities of methylglyoxal synthase and triosephosphate isomerase: a combined QM/MM analysis. J Am Chem Soc. 2002;124(50):14871-8.
Cui Q, Karplus M. {Promoting modes and demoting modes in enzyme-catalyzed proton transfer reactions: a study of models and realistic systems}. J. Phys. Chem. B. 2002;106:7927–7947.
Cui Q, Karplus M. Quantum mechanical/molecular mechanical studies of the triosephosphate isomerase-catalyzed reaction: verification of methodology and analysis of reaction mechanisms. J. Phys. Chem. B. 2002;106:1768–1798.
Cui Q, Karplus M. Quantum mechanical/molecular mechanical studies of the triosephosphate isomerase-catalyzed reaction: Verification of methodology and analysis of reaction mechanisms. Journal of Physical Chemistry BJournal of Physical Chemistry B. 2002;106:1768-1798.
Cui Q, Karplus M. Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: Effect of geometry and tunneling on proton-transfer rate constants. Journal of the American Chemical Society. 2002;124:3093-3124.
Cui Q, Karplus M. Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton-transfer rate constants. J Am Chem Soc. 2002;124:3093-124.
Cui Q, Elstner M, Karplus M. A theoretical analysis of the proton and hydride transfer in liver alcohol dehydrogenase (LADH). Journal of Physical Chemistry BJournal of Physical Chemistry B. 2002;106:2721-2740.
Cui Q, Elstner M, Karplus M. {A theoretical analysis of the proton and hydride transfer in liver alcohol dehydrogenase (ladh)}. J. Phys. Chem. B. 2002;106:2721–2740.
2001
Cui Q, Elstner M, Kaxiras E, Frauenheim T, Karplus M. A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method. Journal of Physical Chemistry B. 2001;105:569-585.

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