All Department Publications

Found 179 results
Author Title [ Type(Desc)] Year
Filters: Author is Cui, Q.  [Clear All Filters]
Book Chapter
Yang W, Cui Q, Min D, Li H. Chapter 4 - QM/MM Alchemical Free Energy Simulations: Challenges and Recent Developments. In: Wheeler RA Annual Reports in Computational Chemistry. Vol. 6. Annual Reports in Computational Chemistry. Elsevier; 2010. pp. 51 - 62.
Schwede T, Peitsch MC, Cui Q. Functional Motions in Biomolecules: Insights from Computational Studies at Multiple Scales. In: World Scientific; 2008.
G. MD, Cui Q, Mats S, Keiji M. Theoretical Studies of the N2 Cleavage by Three-Coordinate Group 6 Complexes ML3. In: Transition State Modeling for Catalysis. Transition State Modeling for Catalysis. ; 1998. pp. 198-207.
Journal Article
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, Stanton JF. Ab initio MO studies on the photodissociation of C2H2 from the S-1((1)A(u)) state. Non-adiabatic effects and S-T interaction. Chemical Physics Letters. 1996;263:46-53.
Cui Q, Morokuma K. Ab initio MO studies on the photodissociation of C2H2 from the S-1((1)A(u)) state .2. Mechanism involving triplet states. Chemical Physics Letters. 1997;272:319-327.
Cui Q, Morokuma K. Ab initio MO studies on the photodissociation of the methoxy family CX(3)Y (X=H,F; Y=O,S) from the (A)over-tilda(2)A(1) state. Chemical Physics Letters. 1996;263:54-62.
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.
Liu RF, Cui Q, Dunn KM, Morokuma K. Ab initio molecular orbital study of the mechanism of photodissociation of trans-azomethane. Journal of Chemical Physics. 1996;105:2333-2345.
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.
Cui Q, Morokuma K. Ab initio study of nonadiabatic interactions in the photodissociation of ketene. Journal of Chemical Physics. 1997;107:4951-4959.
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.
Kaledin AL, Cui Q, Heaven MC, Morokuma K. Ab initio theoretical studies on photodissociation of HNCO upon S-1((1)A '')<- S-0((1)A(')) excitation: The role of internal conversion and intersystem crossing. Journal of Chemical Physics. 1999;111:5004-5016.
Ma L, Cui Q. Activation mechanism of a signaling protein at atomic resolution from advanced computations. Journal of the American Chemical Society. 2007;129:10261-10268.
Cui Q, Karplus M. Allostery and cooperativity revisited. Protein Science. 2008;17:1295-1307.
Phatak P, Ghosh N, Yu HB, Cui Q, Elstner M. Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin. Proceedings of the National Academy of Sciences of the United States of America. 2008;105:19672-19677.
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.
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.
Cui Q, Musaev DG, Svensson M, Morokuma K. Analytical second derivatives for effective core potential. Application to transition structures of Cp(2)Ru(2)(mu-H)(4) and to the mechanism of reaction Cu+Ch(2)N(2). Journal of Physical Chemistry. 1996;100:10936-10944.
Xu D, Guo H, Cui Q. Antibiotic binding to dizinc beta-lactamase L1 from Stenotrophomonas maltophilia: SCC-DFTB/CHARMM and DFT Studies. Journal of Physical Chemistry A. 2007;111:5630-5636.
Xu D, Guo H, Cui Q. Antibiotic deactivation by a dizinc beta-lactamase: mechanistic insights from QM/MM and DFT studies. J Am Chem Soc. 2007;129(35):10814-22.
Riccardi D, Cui Q, Phillips GN. Application of Elastic Network Models to Proteins in the Crystalline State. Biophysical Journal. 2009;96:464-475.
Cai Z-L, Lopez P, Reimers JR, Cui Q, Elstner M. Application of the computationally efficient self-consistent-charge density-functional tight-binding method to magnesium-containing molecules. Journal of Physical Chemistry A. 2007;111:5743-5750.
Goyal P, Elstner M, Cui Q. Application of the SCC-DFTB Method to Neutral and Protonated Water Clusters and Bulk Water. Journal of Physical Chemistry B. 2011;115:6790-6805.
Range K, Riccardi D, Cui Q, Elstner M, York DM. Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer. Phys Chem Chem Phys. 2005;7(16):3070-9.
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-+.
Lu XY, Cui Q. Charging Free Energy Calculations Using the Generalized Solvent Boundary Potential (GSBP) and Periodic Boundary Condition: A Comparative Analysis Using Ion Solvation and Oxidation Free Energy in Proteins. Journal of Physical Chemistry B. 2013;117:2005-2018.
Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, et al. CHARMM: the biomolecular simulation program. J Comput Chem. 2009;30(10):1545-614.
Yoo J, Cui Q. Chemical versus mechanical perturbations on the protonation state of arginine in complex lipid membranes: insights from microscopic pKa calculations. Biophys J. 2010;99(5):1529-38.
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.
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, 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.
Yoo J, Jackson MB, Cui Q. A Comparison of Coarse-Grained and Continuum Models for Membrane Bending in Lipid Bilayer Fusion Pores. Biophysical Journal. 2013;104:841-852.
Van Wynsberghe AW, Cui Q. Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophysical Journal. 2005;89:2939-2949.
Van Wynsberghe AW, Cui Q. Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophys J. 2005;89(5):2939-49.
Ma L, Yethiraj A, Chen X, Cui Q. A Computational Framework for Mechanical Response of Macromolecules: Application to the Salt Concentration Dependence of DNA Bendability. Biophysical Journal. 2009;96:3543-3554.
Van Wynsberghe AW, Cui Q. Conservation and Variation of Structural Flexibility in Protein Families. Structure. 2010;18:281-283.
Konig PH, Hoffmann M, Frauenheim T, Cui Q. A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method [Review]. Journal of Physical Chemistry BJournal of Physical Chemistry B. 2005;109:9082-9095.
König PH, Hoffmann M, Frauenheim T, Cui Q. A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method. J Phys Chem B. 2005;109(18):9082-95.
Yoo J, Cui Q. Curvature Generation and Pressure Profile Modulation in Membrane by Lysolipids: Insights from Coarse-Grained Simulations. Biophysical Journal. 2009;97:2267-2276.
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.
Yang Y, Yu HB, York D, Elstner M, Cui Q. Description of Phosphate Hydrolysis Reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) Theory. 1. Parameterization. Journal of Chemical Theory and Computation. 2008;4:2067-2084.
Xia F, Rudack T, Cui Q, Kotting C, Gerwert K. Detailed Structure of the H2PO4--Guanosine Diphosphate Intermediate in Ras-GAP Decoded from FTIR Experiments by Biomolecular Simulations. Journal of the American Chemical Society. 2012;134:20041-20044.
Riccardi D, Schaefer P, Yang Y, Yu H, Ghosh N, Prat-Resina X, König P, Li G, Xu D, Guo H, et al. Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. J Phys Chem B. 2006;110(13):6458-69.
Li G, Cui Q. Direct determination of reaction paths and stationary points on potential of mean force surfaces. J Mol Graph Model. 2005;24(2):82-93.

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