Dissociative multi-photon ionization of isolated uracil and uracil-adenine complexes

Abstract

Recent multi-photon ionization (MPI) experiments on uracil revealed a fragment ion at m/z 84 that was proposed as a potential marker for ring opening in the electronically excited neutral molecule. The present MPI measurements on deuterated uracil identify the fragment as C 3 H 4 N 2 O + (uracil + less CO), a plausible dissociative ionization product from the theoretically predicted open-ring isomer. Equivalent measurements on thymine do not reveal an analogous CO loss channel, suggesting greater stability of the excited DNA base. MPI and electron impact ionization experiments have been carried out on uracil-adenine clusters in order to better understand the radiation response of uracil within RNA.Evidence for C 3 H 4 N 2 O + production from multi-photon-ionized uracil-adenine clusters is tentatively attributed to a significant population of π-stacked configurations in the neutral beam. Graphical AbstractHighlights UV multi-photon ionization measurements on deuterated uracil have identified a CO loss pathway that may indicate ring opening in the electronically excited neutral molecule. The first dissociative ionization experiments on uracil-adenine complexes have revealed that the CO loss channel is also accessible in these clusters.Keywords: Uracil; adenine-uracil clusters; fragmentation; multi-photon ionization; electron impact ionization; mass spectrometry Ryszka et al. Int. J. Mass. Spectrom. 396 (2016) 48 2 IntroductionThe dynamics and stabilities of nucleobases following excitation to their bright S 2 (ππ* of the ring-opening crossing seam [9] and the geometry of the predicted isomer indicates likely CO abstraction. Therefore MPI production of this fragment ion was proposed as a potential experimental marker for ring opening in neutral excited uracil, suggesting possibilities for diverse measurements exploring the process in depth (e.g. using coincidence and / or time-resolved methods). The first aim of the present work was to test if the new fragment ion is indeed due to CO loss by studying MPI of deuterated uracil (dominantly C 4 D 4 N 2 O 2 ). These results have the added value of identifying several previously debated fragments from the radical cation, while further evidence to assign specific peaks is provided by high-resolution MPI mass spectra. The paper also presents equivalent MPI measurements on thymine, for which no analogous ring-opening process has been predicted [9]. A distinctly higher pump energy (5.64 eV, 220 nm) was applied than in the previous MPI studies of thymine (4.34-4.77 eV, 285.7-260 nm) [6, 12, 13, 14, 15, 16, 17], increasing the likelihood of isomeric transitions during radiationless deactivation. Finally, MPI and electron impact ionization (EII) experiments were carried out on uracil-adenine clusters as a step towards better understanding the dissociative ionization pathways of uracil within RNA. Whereas several spectroscopic studies have been carried out on adenine-thymine complexes in supersonic beams [18,19,20], to our knowledge no previous experiments on isolated u...

Stabilities of nanohydrated thymine radical cations: insights from multiphoton ionization experiments and ab initio calculations

“…The experimental system has been described in previous publications [5,17,18]. Briefly, argon carrier gas (1.1 bar) seeded with sublimated thymine (Sigma-Aldrich with stated purity ≥99%) expanded continuously through a 50 μm diameter pinhole into a pumped chamber (1000 l s −1 ) to form a supersonic jet.…”

Threshold behavior in metastable dissociation of multi-photon ionized thymine and uracil

“…In particular, tautomeric transitions and ring opening conical intersections have been predicted theoretically [10,11]. Our recent studies of uracil indicate that the analysis of fragment ion production from multiphoton ionized molecules can provide evidence for structural changes in neutral excited states [12,13]. Matsika and co-workers [14][15][16] have also studied fragment ion production from multiphoton ionized nucleobases and argued that the detection of intact singly ionized uracil (uracil + ) in 260 nm pump -780 nm probe experiments could only be traced to ionization from S 2 , whereas the C 3 H 3 NO + yield (uracil + less HNCO) could provide information about the wavepacket evolution on both S 2 and S 1 .…”

“…The experimental system has been described in previous publications [12,13,17,18]. Briefly, helium carrier gas (0.6-0.8 bar) seeded with sublimated thymine or uracil (both from Sigma-Aldrich with stated purity ≥99%) flowed continuously through a 50 μm diameter pinhole into a pumped chamber (500 ls -1 ) to form a supersonic jet.…”

“…A convex lens on a slider was used to control the diameter of the laser beam when it crosses the molecular beam and the average laser pulse energy was adjusted using the delay between the pulses triggering the xenon flash lamps and the Qswitch of the Nd:YAG laser. This corresponds to the voltage at the point in space where the focused laser beam crossed the molecular beam (explained in detail by Ryszka et al [13]). Hence the KE of the radical cations in the field free region (FFR) was 1815±2 eV.…”

Effect of Laser Radiation on Biomolecules

“…Numerous works about this topic can be found in the literatures covering a large energy range. Different ions formation from Adenine (A) and Uracil (U) have been previously reported using electrons, synchrotron radiation or laser at different wavelengths and techniques [8][9][10][11].…”