Publication Details (including relevant citation information):
S. Kim, T. Meehan, and H.F. Schaefer;
Journal of Physical Chemistry A, 2007, 111, 6806.
The hydrogen-abstracted radicals from the adenine-uracil (AU) base pair have been studied at the B3LYP/ DZP++ level of theory. The A(N9)-U and A-U(N1) radicals, which correspond to hydrogen-atom abstraction at the adenine N9 and uracil N1 atoms, respectively, were predicted to be the two lowest-lying among the nine (AU-H) radicals studied in this study. The removal of the amino hydrogen of the adenine moiety that forms a hydrogen bond with the uracil 04 atom in the AU pair resulted in radical A(N6a)-U, which has the smallest base-pair dissociation energy, 5.9 kcal mol-1. This radical is more likely to dissociate into the two isolated bases than to recover the hydrogen bond with the 04 atom through N6-H bond rotation along the C6-N6 bond. In general, the radicals generated by C-H bond breaking were higher in energy than those arising from N-H bond cleavage, because the unpaired electrons in the carbon-centered radicals were mainly localized on the carbon atom from which the hydrogen atom was removed. However, the highest-lying radical was found to arise from removal of the N3 hydrogen of uracil. The most remarkable structural feature of this radical is a very short C-H⋯O distance of 2.094 Å, consistent with a substantial hydrogen bond. Although this radical lost the N1⋯H-N3 hydrogen bond between the two bases, its dissociation energy was predicted to be 12.9 kcal mol-1, similar to that of the intact AU base pair. This is due to the transfer of electron density from the adenine N1 atom to the uracil N3 atom.
Address (URL): http://dx.doi.org/10.1021/jp070225x