All Faculty and Research Staff Publications

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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, Zhang LL, Wu Z, Yethiraj A. Generation and sensing of membrane curvature: Where materials science and biophysics meet. Current Opinion in Solid State & Materials Science. 2013 ;17:164-174.
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, Morokuma K. The spin-forbidden reaction CH((2)Pi)+N-2 -> HCN+N(S-4) revisited I. Ab initio study of the potential energy surfaces. Theoretical Chemistry Accounts. 1999 ;102:127-133.
Cui Q, Musaev DG, Morokuma K. Molecular orbital study of the mechanism of platinum(0)-catalyzed alkene and alkyne diboration reactions. Organometallics. 1997 ;16:1355-1364.
Cui Q, Li GH, Ma JP, Karplus M. A normal mode analysis of structural plasticity in the biomolecular motor F-1-ATPase. Journal of Molecular Biology. 2004 ;340:345-372.
Cui Q. Theoretical and computational studies of vectorial processes in biomolecular systems. Theoretical Chemistry Accounts. 2006 ;116:51.
Cui Q, Karplus M. Triosephosphate isomerase: A theoretical comparison of alternative pathways. Journal of the American Chemical Society. 2001 ;123:2284-2290.
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.
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, 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, Morokuma K, Bowman JM, Klippenstein SJ. The spin-forbidden reaction CH((2)Pi)+N-2 -> HCN+N(S-4) revisited. II. Nonadiabatic transition state theory and application. Journal of Chemical Physics. 1999 ;110:9469-9482.
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, Nussinov R. Making Biomolecular Simulations Accessible in the Post-Nobel Prize Era. Plos Computational Biology. 2014 ;10.
Cui Q. Theoretical analysis of mechanochemical coupling in the biomolecular motor myosin. Modelling Molecular Structure and Reactivity in Biological Systems. 2006 :66-75.
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.
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, 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.
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. Molecular properties from combined QM/MM methods. I. Analytical second derivative and vibrational calculations. Journal of Chemical Physics. 2000 ;112:1133-1149.
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.
Cui Q, Elstner M. Density functional tight binding: values of semi-empirical methods in an ab initio era. Physical Chemistry Chemical Physics. 2014 ;16:14368-14377.
Cui Q, Thorgersen MP, Westler WM, Markley JL, Downs DM. Solution structure of YggX: A prokaryotic protein involved in Fe(II) trafficking. Proteins Structure Function & Bioinformatics. 2006 ;62:578-586.
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.
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, 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. Perspective: Quantum mechanical methods in biochemistry and biophysics. Journal of Chemical Physics. 2016 ;145.
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.
Cui Q, Karplus M. Molecular properties from combined QM/MM methods. 2. Chemical shifts in large molecules. Journal of Physical Chemistry B. 2000 ;104:3721-3743.
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, Svensson M, Sieber S, Morokuma K. N-2 CLEAVAGE BY 3-COORDINATE GROUP-6 COMPLEXES - W(III) COMPLEXES WOULD-BE BETTER THAN MO(III) COMPLEXES. Journal of the American Chemical Society. 1995 ;117:12366-12367.
Cui Q, Karplus M. Allostery and cooperativity revisited. Protein Science. 2008 ;17:1295-1307.
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, 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.
Cui Q, Morokuma K. Ab initio study of nonadiabatic interactions in the photodissociation of ketene. Journal of Chemical Physics. 1997 ;107:4951-4959.
Cui Q, Hernandez R, Mason SE, Frauenheim T, Pedersen JA, Geiger F. Sustainable Nanotechnology: Opportunities and Challenges for Theoretical/Computational Studies. Journal of Physical Chemistry B. 2016 ;120:7297-7306.
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-+.
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.
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.