All Faculty and Research Staff Publications

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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 Simulations. 2003 ;66:315-+.
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 B. 2003 ;107:8643-8653.
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 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.
Li GH, Cui Q. pK(a) calculations with QM/MM free energy perturbations. Journal 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 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. Angewandte Chemie-International Edition. 2003 ;42:1508-1511.
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.
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. 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. Structure. 2002 ;10:921-931.
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.
Cui Q, Karplus M. Promoting modes and demoting modes in enzyme-catalyzed proton transfer reactions: A study of models and realistic systems [Review]. Journal of Physical Chemistry 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. Journal 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, Elstner M, Karplus M. A theoretical analysis of the proton and hydride transfer in liver alcohol dehydrogenase (LADH). Journal of Physical Chemistry B. 2002 ;106:2721-2740.
1998
Stevens JE, Cui Q, Morokuma K. An ab initio investigation of spin-allowed and spin-forbidden pathways of the gas phase reactions of O(P-3)+C2H5I. Journal of Chemical Physics. 1998 ;108:1544-1551.
Cui Q, Morokuma K. Ab initio molecular orbital studies on the structure, energies, and photodissociation of the electronic excited states of C2H. Journal of Chemical Physics. 1998 ;108:626-636.
Kaledin AL, Heaven MC, Lawrence WG, Cui Q, Stevens JE, Morokuma K. Ab initio molecular-orbital study of the trichlorine radical, Cl-3. Journal of Chemical Physics. 1998 ;108:2771-2783.
Cui Q, Morokuma K. Ab initio studies on the electronic excited states and photodissociation of O-3 anion. Journal of Chemical Physics. 1998 ;108:7684-7694.
Stevens JE, Cui Q, Morokuma K. An ab initio study of the dissociation of HNCO in the S-1 electronic state. Journal of Chemical Physics. 1998 ;108:1452-1458.
Cui Q, Morokuma K. Ab initio study on the mechanism of C2H2+NH3 reaction: Efficient charge transfer and proton transfer processes competing with stable complex formation. Journal of Chemical Physics. 1998 ;108:4021-4030.
Cui Q, Musaev DG, Morokuma K. Density functional study on the mechanism of palladium(0)-catalyzed thioboration reaction of alkynes. Differences between Pd(0) and Pt(0) catalysts and between thioboration and diboration. Organometallics. 1998 ;17:1383-1392.
Cui Q, Musaev DG, Morokuma K. Molecular orbital study of H-2 and CH4 activation on small metal clusters. I. Pt, Pd, Pt-2, and Pd-2. Journal of Chemical Physics. 1998 ;108:8418-8428.
Cui Q, Musaev DG, Morokuma K. Molecular orbital study of H-2 and CH4 activation on small metal clusters. 2. Pd-3 and Pt-3. Journal of Physical Chemistry A. 1998 ;102:6373-6384.
Morokuma K, Cui Q, Liu ZW. Potential-energy surfaces and their dynamic implications. Faraday Discussions. 1998 ;110:71-89.
Cui Q, Liu ZW, Morokuma K. Theoretical study on the mechanism CH4+C2H2+ reaction: Mode-enhancement effect. Journal of Chemical Physics. 1998 ;109:56-62.
Cui Q, Musaev DG, Morokuma K. Why do Pt(PR3)(2) complexes catalyze the alkyne diboration reaction, but their palladium analogues do not? A density functional study. Organometallics. 1998 ;17:742-751.

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