Effects of electron attachment on C5′O5′ and C1′N1 bond cleavages of pyrimidine nucleotides: A theoretical study

Sugar‐base C1′N1 and phosphate‐sugar C5′O5′ bond breakings of 2′‐deoxycytidine‐5′‐monophosphates (dCMP) and 2′‐deoxythymidine‐5′‐ monophosphates (dTMP) and their radical anions have been explored theoretically at the B3LYP/DZP++ level of theory. Calculations show that the low‐energy electrons attachment to the pyrimidine nucleotides results in remarkable structural and chemical bonding changes. Predicted Gibbs free energies of reaction ΔG for the C5′O5′ bond dissociation process of the radical anions are −14.6 and −11.5 kcal mol−1, respectively, and such dissociation processes may be intrinsically spontaneous in the gas phase. Furthermore, the C5′O5′ bond cleavage processes of the anionic dCMP and dTMP were predicted to have activation energies of 6.9 and 8.0 kcal mol−1 in the gas phase, respectively, much lower than the barriers for the C1′N1 bond breaking process, showing that the CO bond dissociation in DNA single strand breaks is a dominant process as observed experimentally. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008