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We have performed electronic-structure calculations on the AM1 level for the two fragments (7:GC and 8:TA) within the matched DNA sequence used in the text. The geometry was optimized using the Amber99 force field in vacuum. The results of our calculations indicate that both HOMO and HOMO-1 levels have a strong weight onto the backbones while base-localized MOs appear at the HOMO-2 level. This is consistent with the results obtained from snapshots along the MD trajectory. Similar calculations were then carried out for deoxythymidine monophosphate anion (dTMP ⊃-) optimized in vacuum using again the Amber99 force field. In this case, the HOMO state is localized onto the backbone and a thymine-localized MO appears at the HOMO-4. It seems possible that force-field-optimized geometries and/or the electronic-structure calculation level (AM1) contributed to the discrepancy with the results by M. Rubio (Ref.), where it came out that the most easily oxidized part of the dTMP ⊃- is the thymine at the CASPT2 level of calculation.
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