Ultraviolet relaxation dynamics in uracil: Time-resolved photoion yield studies using a laser-based thermal desorption source

Abstract

Wavelength-dependent measurements of the RNA base uracil, undertaken with nanosecond ultraviolet laser pulses, have previously identified a fragment at m/z = 84 (corresponding to the CHNO ion) at excitation wavelengths ≤232 nm. This has been interpreted as a possible signature of a theoretically predicted ultrafast ring-opening occurring on a neutral excited state potential energy surface. To further investigate the dynamics of this mechanism, and also the non-adiabatic dynamics operating more generally in uracil, we have used a newly built ultra-high vacuum spectrometer incorporating a laser-based thermal desorption source to perform time-resolved ion-yield measurements at pump wavelengths of 267 nm, 220 nm, and 200 nm. We also report complementary data obtained for the related species 2-thiouracil following 267 nm excitation. Where direct comparisons can be made (267 nm), our findings are in good agreement with the previously reported measurements conducted on these systems using cold molecular beams, demonstrating that the role of initial internal energy on the excited state dynamics is negligible. Our 220 nm and 200 nm data also represent the first reported ultrafast study of uracil at pump wavelengths <250 nm, revealing extremely rapid (<200 fs) relaxation of the bright S(ππ) state. These measurements do not, however, provide any evidence for the appearance of the m/z = 84 fragment within the first few hundred picoseconds following excitation. This key finding indicates that the detection of this specific species in previous nanosecond work is not directly related to an ultrafast ring-opening process. An alternative excited state process, operating on a more extended time scale, remains an open possibility.

State-Dependent Fragmentation of Protonated Uracil and Uridine

“…Many groups have investigated in detail the relaxation dynamics of neutral uracil, e.g. [33,39,40,41,42,43,44], and related species (for a recent review, see [45]). These fragments indicates that the sugar group provides deexcitation mechanisms that compete with ring opening reactions and thus stabilize the nucleobase itself, a finding which appears very relevant for the field of radiobiology.…”

Dynamics of electronically excited states in the eumelanin building block 5,6-dihydroxyindole

“…These parameters were typically set to produce a laser power of ~150 mW and a spot on the foil ~1 mm in diameter, yielding a localized estimated foil temperature of ~370 ± 30 K, as detailed in earlier work using this instrument. 16 Calculations by Il'ichev and Simon have shown the 5,6-DHI tautomer depicted in Fig. 1 to be the lowest energy form both in the gas-phase and when solvated.…”

“…This instrument incorporates a laser desorption source based on the design of Greenwood and co-workers, 33,34 and has recently been described in detail elsewhere. 16 Briefly, the source consisted of a piece of 10 µm thick 316 stainless steel foil (Ø = 32 mm) onto which 5,6-DHI powder was deposited using application of methanol. This produced a uniform coating 300-500 µm thick.…”

“…This issue has been overcome, however, through the use of a laser-based thermal desorption approach that we have previously demonstrated for the uracil and 2-thiouracil systems. 16 This technique has the potential to facilitate vapour generation in a broad range of nonvolatile species and we anticipate it will find wider application beyond the work outlined here.…”

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].…”