Ionization and fragmentation of uracil upon microhydration

Abstract

Microhydration of the uracil cation stabilizes it with regard to fragmentation, which confirms recent experimental results.

Ab Initio Study of the Stepwise versus Concerted Fragmentation Pathways in Microhydrated Thymine Radical Cations

“…Relaxing TS0‐a leads to a proton transfer from N 3 to N 1 and the system is stabilised in MIN0‐a (N 1 −C 2 : 3.83 Å) at 0.36 eV above the thymine cation energy. Such a mechanism is reminiscent of the uracil fragmentation . We highlight that this is not in agreement with the B1LYP results of Improta et al., since they hypothesised that N 1 −C 2 bond breaking proceeds without proton transfer.…”

“…This is also owing to the fact that the sugar and phosphate backbone may be screened by the presence of water. In this context, while the fragmentation of uracil as well as pyrimidine nucleobases has been thoroughly examined, thymine is, to the best of our knowledge, less well addressed. However, Improta et al .…”

“…Although the stepwise and the concerted mechanisms are competitive in gas phase, the present study indicates that the presence of water can partially favour one mechanism over another. A similar effect has been proposed for uracil, in which it has been shown that the microhydration leads to a change of the fragmentation pathways. In addition, uracil was stabilised by water up to 0.5 eV, in good agreement with the present study of thymine reporting a global stabilising effect amounting to 0.47 eV.…”

“…In accordance with these results, the experimental work of Castrovilli and co‐workers reported the stabilising effect played by water when studying clusters of hydrated 5Br‐uracil. A recent theoretical study on microhydrated uracil demonstrated the stabilising role of water on the activation energies related to the different dissociation channels in the presence of one and two water molecules. Indeed, water molecules increased the activation energies up to 0.5 eV, while opening the possibility of different channels as compared to the gas‐phase situation.…”

“…Resorting to ag as-phase model,a lthoughd isregarding the effecto fc omplex biological environment, was further justified by Smith et al, [3] who showed that in aD NA strand, NBs are the mostr eactive components, since electrons show ap referentiali nteractionw ithN Bs. This is also owing to the fact that the sugar and phosphate backbonem ay be screened by the presence of water.I nt his context, while the fragmentation of uracila sw ell as pyrimidine nucleobases has been thoroughly examined, [9,10,15,16] thymine is, to the best of our knowledge, less well addressed. However,I mprota et al [17] examined the HNCOl oss for isolated thymine at the B1LYP/6-311G(d,p) level of theory and found as tepwise mechanism of the rDA reaction.…”