REACTIVITY OF URACIL IN THE GAS PHASE: STATISTICAL & NON-STATISTICAL STUDY
Résumé
DNA’s role in heritage and coding protein was described long time ago. The presence of Uracil in DNA gives rise to nucleic bases misparings which can be cytotoxic and mutagenic for the cell. It is therefore important to understand the chemical reactivity of nucleobases, including Uracil. Studying the reactivity in the gas phase allows to get rid of environmental effects, giving direct access to important intrinsic properties of the molecule of interest. In this context, we coupled Tandem Mass Spectrometry Experiments (MS/MS) to mixed Quantum-Classical (QM+MM) Molecular Dynamic Simulations of collisions between protonated Uracil and Argon.Experiments: MS/MS spectra of protonated Uracil, 2-13C-uracil; 3-15N-uracil and 1,3-15N2-213C-uracil generated by electrospray ionization from aqueous solutions, were recorded at different collision energies, ranging from 5 to 30 eV, using an Applied Biosystems/MDS Sciex API2000 triple-quadrupole instrument.Simulations : Chemical dynamic simulations were performed using VENUS coupled with MOPAC or with Gaussian09 for six Uracil’s protonated forms, at AM1, PM3 and B3LYP/6-31g levels of theory. Thousands of trajectories were performed to have statistically valid results.We chose 300K as initial temperature for the ions. Energies for the normal modes of vibration were selected from a 300 K Boltzmann distribution. Random orientations in Euler angles between Argon and protonated Uracil were sampled to account for random orientations of collisions.We achieved a deeper understanding of the fragmentation mechanisms occurring during Collision Induced Dissociation (CID) of protonated Uracil generated by electrospray (ESI). We successfully characterized the main fragmentation paths: ammonia loss (m/z 96), water loss (m/z 95) and cyanic acid loss (m/z 70) as well as other minor paths. The latter corresponds to a retro-Diels-Alder reaction, which has been proposed in the literature, but has recently been questioned. We obtained perfect agreement for fragmentation mechanisms obtained during simulations and those deduced from isotopic labeling.RRKM approach was used to stimate rate constants for different paths and understand the long time scale reactivity.We have already successfully applied this approach to the study of disaccharides, and our new good dynamic results open the door to the possibility of studying the reactivity of other systems, such as Uracil with metals and other DNA building blocks. Our research is moving forward this direction.
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