DFT study of the fragmentation mechanism of uracil RNA base

Physical Chemistry Chemical Physics : PCCP
Leila Sadr AraniHenry Chermette

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 N(3)-C(4) and N(1)-C(2) bonds are more easily cleaved than the C(5)-C(6) bond, since the corresponding energy barriers amount to ΔG = +1.627, +1.710, +5.459 eV, respectively, which makes the C(5)-C(6) 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: C(2)H(4)N(+) and C(2)H(2)O˙(+) may be formed, with a small preference for C(2)H(4)N(+). This latter product is not formed through a retro Diels Alder reaction in contrast to C...Continue Reading

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Citations

Apr 18, 2013·Physical Chemistry Chemical Physics : PCCP·Roberto Rodríguez-FernándezEmilio Martínez-Núñez
May 8, 2014·Journal of the American Society for Mass Spectrometry·Adrien NyakasStefan Schürch
May 4, 2016·The Journal of Physical Chemistry. a·Christoph Alexander Bauer, Stefan Grimme
Jul 7, 2017·The Journal of Physical Chemistry. B·Rodrigo SeraideAngel Rubio
Jun 9, 2016·Physical Chemistry Chemical Physics : PCCP·Pal MarkushLorenzo Avaldi
Apr 15, 2015·Physical Chemistry Chemical Physics : PCCP·Leila Sadr-AraniMichel Farizon
Feb 19, 2019·Physical Chemistry Chemical Physics : PCCP·Abderrahmane SemmeqMichael Badawi
Aug 3, 2019·Chemistry : a European Journal·Abderrahamane SemmeqSaid Ouaskit
Feb 28, 2020·Physical Chemistry Chemical Physics : PCCP·Julie RenoudJean-Philippe Champeaux
Aug 19, 2015·Journal of Computational Chemistry·Al Mokhtar LamsabhiManuel Yáñez
Aug 7, 2019·Chembiochem : a European Journal of Chemical Biology·Aleksandr B SahakyanShankar Balasubramanian
Jul 19, 2014·Physical Chemistry Chemical Physics : PCCP·Callie A ColeVeronica M Bierbaum
Aug 28, 2012·The Journal of Physical Chemistry. a·Congyi ZhouThomas C Weinacht
Oct 13, 2021·ChemPlusChem·Abderrahmane SemmeqAntonio Monari

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