Collision-induced dissociation mechanisms of [Li(uracil)]+

Abstract

The collision-induced dissociation (CID) of the [Li(uracil)](+) complex with Xe is studied by means of quasi-classical trajectory calculations. The potential energy surface is obtained "on the fly" from AM1 semiempirical calculations, supplemented with two-body analytical potentials to model the intermolecular interactions. The simulations show that Li(+) production is the primary channel, in agreement with a previous experimental study [M. T. Rodgers and P. B. Armentrout, J. Am. Chem. Soc., 2000, 122, 8548]. Collision-induced isomerization of [Li(uracil)](+) was found to be very important as well in the 2.5-10 eV collision energy range. Three minor channels are also identified: complex formation between Xe and [Li(uracil)](+), ligand exchange to form LiXe(+), and fragmentations of the uracil ring, which are strongly nonstatistical. Additional quasi-classical trajectory calculations carried out to investigate in more detail the fragmentations of the uracil ring reveal the presence of bifurcations in the potential energy surface, as trajectories starting from a transition state give rise to four different product channels. The integral cross sections for Li(+) production calculated in this work agree well with those obtained in the experiments only for the lowest collision energies, being ∼20 times greater than the experimental values for a collision energy of 10 eV. Finally, the initial translational energy is transferred preferentially to the [Li(uracil)](+) vibrational degrees of freedom, with energy transfer to rotation being modest. The amount of energy transfer to the different degrees of freedom as a function of the collision energy follows quite nicely a model recently proposed by our group.

Elucidating collision induced dissociation products and reaction mechanisms of protonated uracil by coupling chemical dynamics simulations with tandem mass spectrometry experiments

“…[26][27][28] Direct dynamics is able to provide information on the structure of fragment ions obtained after collision of a gaseous precursor ion with an inert gas, and thus on the reaction pathways, without preimposing any reaction coordinate. Recently, Li + /uracil complexes CID was studied theoretically by the same approach by Martinez-Nuñez and co-workers, [29] and we presently applied this strategy to elucidate the dissociation mechanisms of protonated uracil.…”

Time-dependent density-functional-theory investigation of the collisions of protons and α particles with uracil and adenine

“…Additional studies have been performed on ion collisions with gas phase and aqueous uracil [18,20], though these studies were limited by treating ionization as an instantaneous loss of electrons. Other studies have modeled collisions with heavier ions [16,17]. Simulations have also been performed that include the electron dynamics in the collision using various theoretical treatments, but these calculations used atomic orbital (Gaussian based) basis sets on various small molecules [12][13][14][15].…”

On the gas phase fragmentation of protonated uracil: a statistical perspective

“…41,42 The model is an adaptation of two limiting models of energy transfer to atom-diatom collisions, and it was successfully applied to a number of systems. 12,41,42 In the model, the average energy 〈 〉 transferred to rotation or vibration of the ion is given by: Interestingly, for collision energies lower than 7.5 eV rotational activation dominates, but for higher collisional energies, transfer to vibration becomes increasingly more important. This is clearly seen in Table 1, where the percent energy transfer to rotation is 24% for 1.3 eV compared to a modest 8% transfer to vibration.…”

“…This means that only fast processes, often non-statistical, are observed. This approach was pioneered by Hase and co-workers 6,7 and it was successfully applied to a number of systems, from organic molecules [8][9][10][11][12] to peptides [13][14][15] and carbohydrates. 16 Such an approach furnishes detailed information of the internal energy content of the ion after collisional activation; simulations also provide the partitioning between vibrational and rotational energy.…”