STRUCTURE AND RELATIVE STABILITY OF DEOXYRIBOSE RADICALS IN A MODEL DNA BACKBONE - AB-INITIO MOLECULAR-ORBITAL CALCULATIONS

Ab initio molecular orbital calculations have been performed in this study to determine the stability of five deoxyribose centered radicals embedded in a short DNA segment. The effect of phosphate groups on the sugar radical conformation, energetics, and electronic properties are evaluated through a comparison of models with and without phosphate groups. Geometry optimization performed at the ROHF/3-21G level reveals the C1' centered radical is the most energetically favored in all the DNA fragments considered in this study, while the C2' radical is the least stable and maintains a near planar configuration (T-4(0)). All energy minima calculated correspond to deoxyribose radicals with a pseudorotation phase angle lying in the S quadrant of the pseudorotation cycle. The phosphate groups significantly affect the puckering mode of the C2' and C3' radicals and energetically destabilize C3' radical relative to the other sugar radicals. Isotropic hyperfine coupling constants significantly differ between models with and without phosphate groups, most particularly in the C3' and C4' radicals. Owing to the nonplanarity of the sugar ring in the C4' radical, the proton couplings are found to have a significant cos Theta dependence in the relation a = B-0 + B-1 cos Theta + B-2 cos(2) Theta. The trend in oxidizing power based on the calculated HOMO energies is predicted to follow the order . C1' < . C4' < . C2' < . C3' < . C5'. Cytosine attachment to the C1' and C4' deoxyribose radicals does not appear to affect the relative energies nor the isotropic hyperfine couplings of these two species. In both deoxycytidine radicals, the base maintains an anti conformation, which therefore does not disrupt the hydrogen bonding pattern in the base pair.