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 s tudy 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 g roups. 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 e nergy minima calculated correspond to deoxyribose radicals with a pseu dorotation phase angle lying in the S quadrant of the pseudorotation c ycle. The phosphate groups significantly affect the puckering mode of the C2' and C3' radicals and energetically destabilize C3' radical rel ative to the other sugar radicals. Isotropic hyperfine coupling consta nts significantly differ between models with and without phosphate gro ups, most particularly in the C3' and C4' radicals. Owing to the nonpl anarity 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 b ased 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 en ergies 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 b ase pair.