Theoretical study on the deoxyribose radicals formed by hydrogen abstraction

The structures of C₁, C₂, C₃, and C₄ centered deoxyribose radicals are optimized at the UHF/6-31G level. For each radical two puckered conformations are observed, which are significantly different from those of deoxyribose. In C₁ and C₂ radicals the pseudorotation angle, P, is shifted toward higher values compared to that of deoxyribose. In C₃ and C₄ radicals the shift of P is in the opposite direction. In addition, the puckering amplitude τ(m) is significantly decreased in the radicals, indicating a flattening of the five- membered ring. The C₂ centered radical has the sp²-type electronic structure, while C₁, C₃, and C₄ centered radicals are pyramidal. The enthalpies for H-atom abstraction from deoxyribose are calculated at the MP2/6-31G* level including ZPE and a scaling of correlation energy. The abstractions from C₁, C₃, and C₄ positions require similar energies, whereas the abstraction from the C₂ carbon of deoxyribose is less favorable by 3-4 kcal/mol. The susceptibility of different deoxyribose hydrogens for abstraction is estimated on the basis of their bond strength and their accessibility in nucleotides and in DNA.