Sunghwan Kim - Hydrogen-atom abstraction from the adenine-uracil base pair

Version 3

      Publication Details (including relevant citation   information):

      S. Kim, T.   Meehan, and H.F. Schaefer;

      Journal of Physical Chemistry A,   2007111, 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.


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