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  1. 1.   Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer
  2. Saneyoshi, H.; Mazzini, S.; Avino, A.; Portella, G.; Gonzalez, C.; Orozco, M.; Marquez, V. E.; Eritja, R.
  3. Nucleic Acids Research. 2009 37(17): 5589-5601.
  1. 2.   Mechanism of the myosin catalyzed hydrolysis of ATP as rationalized by molecular modeling
  2. Grigorenko, B. L.; Rogov, A. V.; Topol, I. A.; Burt, S. K.; Martinez, H. M.; Nemukhin, A. V.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2007, Apr; 104(17): 7057-7061.
  1. 3.   Comparison of large basis set DFT and MP2 calculations in the study of the barrier for internal rotation of 2,3,5,6-tetrafluoroanisole
  2. Kieninger, M.; Cachau, R. E.; Oberhammer, H.; Ventura, O. N.
  3. International Journal of Quantum Chemistry. 2007, Feb; 107(2): 403-417.
  1. 4.   A new perspective in the Lewis acid catalyzed ring opening of epoxides. Theoretical study of some complexes of methanol, acetic acid, dimethyl ether, diethyl ether, and ethylene oxide with boron trifluoride
  2. Saenz, P.; Cachau, R. E.; Seoane, G.; Kieninger, M.; Ventura, O. N.
  3. Journal of Physical Chemistry A. 2006, Oct; 110(41): 11734-11751.
  1. 5.   Molecular modeling the reaction mechanism of serine-carboxyl peptidases
  2. Bravaya, K.; Bochenkova, A.; Grigorenko, B.; Topol, I.; Burt, S.; Nemukhin, A.
  3. Journal of Chemical Theory and Computation. 2006, Jul; 2(4): 1168-1175.
  1. 6.   Chemistry of the diazeniumdiolates: Z reversible arrow E isomerism
  2. Wang, Y. N.; Bohle, D. S.; Bonifant, C. L.; Chmurny, G. N.; Collins, J. R.; Davies, K. M.; Deschamps, J.; Flippen-Anderson, J. L.; Keefer, L. K.; Klose, J. R.; Saavedra, J. E.; Waterhouse, D. J.; Ivanic, J.
  3. Journal of the American Chemical Society. 2005, APR 20; 127(15): 5388-5395.
  1. 7.   Long-range ordering in water-halide ion interactions: A database study
  2. Prabakaran, P.; Singarayan, M. G.
  3. Chemistry Letters. 2004, DEC 5; 33(12): 1640-1641.
  1. 8.   Multiple proton translocation in biomolecular systems: concerted to stepwise transition in a simple model
  2. Kohanoff, J. J.; Cachau, R. E.
  3. Molecular Physics. 2004, MAY 10; 102(9-10): 1007-1014.
  1. 9.   The application of the effective fragment potential method to molecular anion solvation: A study of ten oxyanion-water clusters, A(-)(H2O)(1-4)
  2. Merrill, G. N.; Webb, S. P.
  3. Journal of Physical Chemistry A. 2004 108(5): 833-839.
  1. 10.   Modeling of serine protease prototype reactions with the flexible effective fragment potential quantum mechanical/molecular mechanical method
  2. Nemukhin, A. V.; Grigorenko, B. L.; Rogov, A. V.; Topol, I. A.; Burt, S. K.
  3. Theoretical Chemistry Accounts. 2004 111(1): 36-48.
  1. 11.   QM/MM modeling of the glutathione-hydroxymethyl radical reaction in watery
  2. Nemukhin, A. V.; Grigorenko, B. L.; Topol, I. A.; Burt, S. K.
  3. Physical Chemistry Chemical Physics. 2004 6(5): 1031-1038.
  1. 12.   Theoretical studies on the hydrolysis of mono-phosphate and tri-phosphate in gas phase and aqueous solution
  2. Wang, Y. N.; Topol, I. A.; Collins, J. R.; Burt, S. K.
  3. Journal of the American Chemical Society. 2003 125(43): 13265-13273.
  1. 13.   Direct configuration interaction and multiconfigurational self- consistent-field method for multiple active spaces with variable occupations. II. Application to oxoMn(salen) and N2O4
  2. Ivanic, J.
  3. Journal of Chemical Physics. 2003 119(18): 9377-9385.
  1. 14.   Peptide models. XXXIII. Extrapolation of low-level Hartree-Fock data of peptide conformation to large basis set SCF, MP2, DFT, and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory
  2. Perczel, A.; Farkas, O.; Jakli, I.; Topol, I. A.; Csizmadia, I. G.
  3. Journal of Computational Chemistry. 2003 24(9): 1026-1042.
  1. 15.   Flexible effective fragment QM/MM method: Validation through the challenging tests
  2. Nemukhin, A. V.; Grigorenko, B. L.; Topol, I. A.; Burt, S. K.
  3. Journal of Computational Chemistry. 2003 24(12): 1410-1420.
  1. 16.   A quantum mechanical study on the electrostratic interactions of poly(L-lysine)center dot alkyl sulfate complexes
  2. Aleman, C.; Zanuy, D.; Casanovas, J.
  3. Journal of Physical Chemistry A. 2003 107(20): 4151-4156.
  1. 17.   Complete basis set and density functional determination of the enthalpy of formation of the controversial HO3 radical: a discrepancy between theory and experiment
  2. Denis, P. A.; Kieninger, M.; Ventura, O. N.; Cachau, R. E.; Diercksen, G. H. F.
  3. Chemical Physics Letters. 2002 365(5-6): 440-449.
  1. 18.   Modeling of biomolecular systems with the quantum mechanical and molecular mechanical method based on the effective fragment potential technique: Proposal of flexible fragments
  2. Grigorenko, B. L.; Nemukhin, A. V.; Topol, I. A.; Burt, S. K.
  3. Journal of Physical Chemistry A. 2002 106(44): 10663-10672.
  1. 19.   Chemistry of the diazeniumdiolates - 1. Structural and spectral characteristics of the N(O)NO (-) functional group
  2. Keefer, L. K.; Flippen-Anderson, J. L.; George, C.; Shanklin, A. P.; Dunams, T. A.; Christodoulou, D.; Saavedra, J. E.; Sagan, E. S.; Bohle, D. S.
  3. Nitric Oxide-Biology and Chemistry. 2001 5(4): 377-394.
  1. 20.   Acidity of organic molecules in the gas phase and in aqueous solvent
  2. Topol, I. A.; Tawa, G. J.; Caldwell, R. A.; Eissenstat, M. A.; Burt, S. K.
  3. Journal of Physical Chemistry A. 2000 104(42): 9619-9624.
  1. 21.   Quantum chemical studies of reactions of the cyclic disulfides with the zinc finger domains in the HIV-1 nucleocapsid protein (NCp7)
  2. Topol, I. A.; Nemukhin, A. V.; Chao, M.; Iyer, L. K.; Tawa, G. J.; Burt, S. K.
  3. Journal of the American Chemical Society. 2000 122(29): 7087-7094.
  1. 22.   Hydrogen bonding at the diatomics-in-molecules level: Water clusters
  2. Grigorenko, B. L.; Nemukhin, A. V.; Topol, I. A.; Burt, S. K.
  3. Journal of Chemical Physics. 2000 113(7): 2638-2647.
  1. 23.   On the structure and thermodynamics of solvated monoatomic ions using a hybrid solvation model
  2. Topol, I. A.; Tawa, G. J.; Burt, S. K.; Rashin, A. A.
  3. Journal of Chemical Physics. 1999 111(24): 10998-11014.
  1. 24.   Calculation of the Aqueous Solvation Free Energy of the Proton
  2. Tawa, G. J.; Topol, I. A.; Burt, S. K.; Caldwell, R. A.; Rashin, A. A.
  3. Journal of Chemical Physics. 1998 109(12): 4852-4863.
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