Pyrimidine and purine radiation products problematic cases

The difference between theory and experiment for the geometry of T(04H) arises due to the rapid rotation of the methyl group in the experimental environment, which is characterized by the presence of three equivalent methyl group protons in the ENDOR spectra. Allowing for the rotation of the methyl group, the 04-hydrogen and the in-plane methyl hydrogen positions are only 

Dihedral Angle Methyl group optimized Aijo(04H) Rel. Energies Methyl group rotated Aiso(04H) Rel. Energies  

The results obtained for the thymine 04-hydrogenated radical can be extended to 1-methylthymine and deoxythymidine since geometrical and electronic changes are expected to be small upon substitution at the N1 position. Comparison of calculated and experimental HFCCs indicates that the 04-hydrogen remains in the molecular plane and at an angle of approximately 60° out of the molecular plane in 1-methylthymine [25] and deoxythymidine [15,25] crystals, respectively. The differences in these systems relative to unsubstituted thymine arise due to the characteristic hydrogen bonding patterns in the crystals. 

The possibility that the observed radical is not protonated can be eliminated. In particular, the C8H HFCC for the planar 06-hydrogenated radical (Aiso = -3.9 G  

Radical Experiment Theory Radical Experiment Theory 

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