DFT study of the fragmentation mechanism of uracil RNA base

Abstract

The fragmentation process of the uracil RNA base has been investigated via DFT calculations in order to assign fragments to the ionisation mass spectrum obtained after dissociation induced by collision experiments. The analysis of the electronic distribution and geometry parameters of the cation allows selection of several bonds that may be cleaved and lead to the formation of various fragments. Differences are observed in the electronic behaviour of the bond breaking as well as the energy required for the cleavage. It is reported that N₃–C₄ and N₁–C₂ bonds are more easily cleaved than the C₅–C₆ bond, since the corresponding energy barriers amount to ΔG = +1.627, +1.710, +5.459 eV, respectively, which makes the C₅–C₆ bond cleavage almost prohibited. Among all possible formed fragments, the formation of the OCN⁺ fragment for the peak at m/z = 42 Da is excluded because of an intermediate that was not observed experimentally and too a large free energy barrier. Based on the required free energy, it is observed that two fragment derivatives: C₂H₄N⁺ and C₂H₂O˙⁺ may be formed, with a small preference for C₂H₄N⁺. This latter product is not formed through a retro Diels Alder reaction in contrast to C₂H₂O˙⁺. The following sequence is proposed for the peak at 42 Da: C₂H₄N⁺ (from N₁–C₂, C₄–C₅ cleavages) > C₂H₂O˙⁺ (from N₃–C₄, N₁–C₂ and C₅–C₆ cleavages) > C₂H₄N⁺ (from N₁–C₂, N₃–C₄ and C₄–C₅) > C₂H₂O˙⁺ (from C₅–C₆, N₁–C₂ and N₃–C₄ cleavages) > NCO⁺ (from N₁–C₂, C₄–C₅ and N₃–C₄ cleavages). Finally the peak at 28 Da is assigned to CNH₂⁺ derivatives that can be formed through two different paths, the easiest one requiring 5.4 eV.