Photofragmentation of 2-Deoxy-D-Ribose Molecules in the Gas Phase

Radiation-Induced Transfer of Charge, Atoms, and Energy within Isolated Biomolecular Systems

In biological tissues, ionizing radiation interacts with a variety of molecules and the consequences include cell killing and the modification of mechanical properties. Applications of biological radiation action are for instance radiotherapy, sterilization, or the tailoring of biomaterial properties. During the first femtoseconds to milliseconds after the initial radiation action, biomolecular systems typically respond by transfer of charge, atoms, or energy. In the condensed phase, it is usually very difficult to distinguish direct effects from indirect effects. A straightforward solution for this problem is the use of gas-phase techniques, for instance from the field of mass spectrometry. In this review, we survey mainly experimental but also theoretical work, focusing on radiation-induced intra- and inter-molecular transfer of charge, atoms, and energy within biomolecular systems in the gas phase. Building blocks of DNA, proteins, and saccharides, but also antibiotics are considered. The emergence of general processes as well as their timescales and mechanisms are highlighted.

Mass Spectral Signatures of Complex Post-Translational Modifications in Proteins: A Proof-of-Principle Based on X-ray Irradiated Vancomycin

Characterizing post-translational modifications (PTM) of proteins is of key relevance for the understanding of many biological processes, as these covalent modifications strongly influence or even determine protein function. Among the different analytical techniques available, mass spectrometry is attracting growing attention because recent instrumental and computational improvements have led to a massive rise of the number of PTM sites that can be identified and quantified. However, multiple PTM occurring at adjacent amino acid residues can lead to complex and dense chemical patterns that are a challenge to characterize. By means of X-ray synchrotron radiation coupled to mass spectrometry, and through the test-case of the glycopeptide antibiotic vancomycin, we show that such a pattern has a unique and robust signature in terms of photon energy and molecular environment. This highlights the potential of this technique in proteomics and its value as a tool to understand the biological roles of PTM.

Hole Migration in Telomere-Based Oligonucleotide Anions and G-Quadruplexes

Vacuum ultraviolet photoionization of a gas-phase oligonucleotide anion leads to the formation of a valence hole. This hole migrates towards an energetically favorable site where it can weaken bonds and ultimately lead to bond cleavage. We have studied Vacuum UV photoionization of deprotonated oligonucleotides containing the human telomere sequence dTTAGGG and G-quadruplex structures consisting of four dTGGGGT single strands, stabilized by NH4 + counter ions. The oligonucleotide and G-quadruplex anions were confined in a radiofrequency ion trap, interfaced with a synchrotron beamline and the photofragmentation was studied using time-of-flight mass spectrometry. Oligonucleotide 12-mers containing the 5'-TTAGGG sequence were found to predominantly break in the GGG region, whereas no selective bond cleavage region was observed for the reversed 5'-GGGATT sequence. For G-quadruplex structures, fragmentation was quenched and mostly non-dissociative single and double electron removal was observed.

Modelling charge transfer processes in C2+-tetrahydrofuran collision for ion-induced radiation damage in DNA building blocks

Investigations of collision-induced processes involving carbon ions and molecules of biological interest, in particular DNA building blocks, are crucial to model the effect of radiation on cells in order to improve medical treatments for cancer therapy. Using carbon ions appears to be one of the most efficient ways to increase biological effectiveness to damage cancerous cells by irradiating deep-seated tumors. Therefore, interest in accurate calculations to understand fundamental processes occurring in ion-molecule collision systems has been growing recently. In this context, the charge transfer process in the collision of C²⁺(1s²2s²) ions with the heterocyclic sugar moiety building block tetrahydrofuran (THF) was studied in order to interpret the mechanisms occurring at the molecular level. The molecular structure properties of THF were obtained by means of ab initio quantum chemistry methods. The role of the conformational structure and the orientation of the THF molecule in collision with C²⁺ ions are particularly discussed. Anisotropic effects of the process dynamics in the collision energy ranging from eV to keV by means of semiclassical treatment are also presented and compared to previous experimental and theoretical investigations. A detailed analysis of the obtained cross sections points out an increase in these values by three orders of magnitude by a change of the THF symmetry from C_2v to C_s in collision with C²⁺, which determines a more efficient charge transfer in this case.

Vacuum ultraviolet photoionization mass spectrometric study of cyclohexene

In this work, photoionization and dissociation of cyclohexene have been studied by means of coupling a reflectron time-of-flight mass spectrometer with the tunable vacuum ultraviolet (VUV) synchrotron radiation. The adiabatic ionization energy of cyclohexene as well as the appearance energies of its fragment ions C6 H9 (+) , C6 H7 (+) , C5 H7 (+) , C5 H5 (+) , C4 H6 (+) , C4 H5 (+) , C3 H5 (+) and C3 H3 (+) were derived from the onset of the photoionization efficiency (PIE) curves. The optimized structures for the transition states and intermediates on the ground state potential energy surfaces related to photodissociation of cyclohexene were characterized at the ωB97X-D/6-31+g(d,p) level. The coupled cluster method, CCSD(T)/cc-pVTZ, was employed to calculate the corresponding energies with the zero-point energy corrections by the ωB97X-D/6-31+g(d,p) approach. Combining experimental and theoretical results, possible formation pathways of the fragment ions were proposed and discussed in detail. The retro-Cope rearrangement was found to play a crucial role in the formation of C4 H6 (+) , C4 H5 (+) and C3 H5 (+) . Intramolecular hydrogen migrations were observed as dominant processes in most of the fragmentation pathways of cyclohexene. The present research provides a clear picture of the photoionization and dissociation processes of cyclohexene in the 8- to 15.5-eV photon energy region.

Vacuum ultraviolet photoionization of carbohydrates and nucleotides

Carbohydrates (2-deoxyribose, ribose, and xylose) and nucleotides (adenosine-, cytidine-, guanosine-, and uridine-5(')-monophosphate) are generated in the gas phase, and ionized with vacuum ultraviolet photons (VUV, 118.2 nm). The observed time of flight mass spectra of the carbohydrate fragmentation are similar to those observed [J.-W. Shin, F. Dong, M. Grisham, J. J. Rocca, and E. R. Bernstein, Chem. Phys. Lett. 506, 161 (2011)] for 46.9 nm photon ionization, but with more intensity in higher mass fragment ions. The tendency of carbohydrate ions to fragment extensively following ionization seemingly suggests that nucleic acids might undergo radiation damage as a result of carbohydrate, rather than nucleobase fragmentation. VUV photoionization of nucleotides (monophosphate-carbohydrate-nucleobase), however, shows that the carbohydrate-nucleobase bond is the primary fragmentation site for these species. Density functional theory (DFT) calculations indicate that the removed carbohydrate electrons by the 118.2 nm photons are associated with endocyclic C-C and C-O ring centered orbitals: loss of electron density in the ring bonds of the nascent ion can thus account for the observed fragmentation patterns following carbohydrate ionization. DFT calculations also indicate that electrons removed from nucleotides under these same conditions are associated with orbitals involved with the nucleobase-saccharide linkage electron density. The calculations give a general mechanism and explanation of the experimental results.

Breaking DNA strands by extreme-ultraviolet laser pulses in vacuum

Ionizing radiation induces a variety of DNA damages including single-strand breaks (SSBs), double-strand breaks (DSBs), abasic sites, modified sugars, and bases. Most theoretical and experimental studies have been focused on DNA strand scissions, in particular production of DNA double-strand breaks. DSBs have been proven to be a key damage at a molecular level responsible for the formation of chromosomal aberrations, leading often to cell death. We have studied the nature of DNA damage induced directly by the pulsed 46.9-nm (26.5 eV) radiation provided by an extreme ultraviolet (XUV) capillary-discharge Ne-like Ar laser (CDL). Doses up to 45 kGy were delivered with a repetition rate of 3 Hz. We studied the dependence of the yield of SSBs and DSBs of a simple model of DNA molecule (pBR322) on the CDL pulse fluence. Agarose gel electrophoresis method was used for determination of both SSB and DSB yields. The action cross sections of the single- and double-strand breaks of pBR322 plasmid DNA in solid state were determined. We observed an increase in the efficiency of strand-break induction in the supercoiled DNA as a function of laser pulse fluence. Results are compared to those acquired at synchrotron radiation facilities and other sources of extreme-ultraviolet and soft x-ray radiation.

Electronic states of tetrahydrofurfuryl alcohol (THFA) as studied by VUV spectroscopy and ab initio calculations

The electronic spectroscopy of isolated tetrahydrofurfuryl alcohol (THFA) in the gas phase has been investigated using high-resolution photoabsorption spectroscopy in the 5.0-10.8 eV energy-range, with absolute cross-section measurements derived. The He(I) photoelectron spectrum was also collected to quantify ionization energies in the 9-16 eV spectral region. These experiments are supported by the first high-level ab initio calculations performed on the excited states of the neutral molecule and on the ground and excited state of the positive ion. The good agreement between the theoretical results and the measurements allows us to quantify for the first time the electronic-state spectroscopy of THFA. The present work also considers the question of the lowest energy conformers of the molecule and its population distribution at room temperature.

Resistance of bacterial endospores to outer space for planetary protection purposes--experiment PROTECT of the EXPOSE-E mission

Spore-forming bacteria are of particular concern in the context of planetary protection because their tough endospores may withstand certain sterilization procedures as well as the harsh environments of outer space or planetary surfaces. To test their hardiness on a hypothetical mission to Mars, spores of Bacillus subtilis 168 and Bacillus pumilus SAFR-032 were exposed for 1.5 years to selected parameters of space in the experiment PROTECT during the EXPOSE-E mission on board the International Space Station. Mounted as dry layers on spacecraft-qualified aluminum coupons, the "trip to Mars" spores experienced space vacuum, cosmic and extraterrestrial solar radiation, and temperature fluctuations, whereas the "stay on Mars" spores were subjected to a simulated martian environment that included atmospheric pressure and composition, and UV and cosmic radiation. The survival of spores from both assays was determined after retrieval. It was clearly shown that solar extraterrestrial UV radiation (λ≥110 nm) as well as the martian UV spectrum (λ≥200 nm) was the most deleterious factor applied; in some samples only a few survivors were recovered from spores exposed in monolayers. Spores in multilayers survived better by several orders of magnitude. All other environmental parameters encountered by the "trip to Mars" or "stay on Mars" spores did little harm to the spores, which showed about 50% survival or more. The data demonstrate the high chance of survival of spores on a Mars mission, if protected against solar irradiation. These results will have implications for planetary protection considerations.

A VUV Photoionization and Ab Initio Determination of the Ionization Energy of a Gas-Phase Sugar (Deoxyribose)

The ionization energy of gas-phase deoxyribose was determined using tunable vacuum ultraviolet synchrotron radiation coupled to an effusive thermal source. Adiabatic and vertical ionization energies of the ground and first four excited states of α-pyranose, the structure that dominates in the gas phase, were calculated using high-level electronic structure methods. An appearance energy of 9.1(±0.05) eV was recorded, which agrees reasonably well with a theoretical value of 8.8 eV for the adiabatic ionization energy. A clear picture of the dissociative photoionization dynamics of deoxyribose emerges from the fragmentation pattern recorded using mass spectrometry and from ab initio molecular dynamics calculations. The experimental threshold 9.4 (±0.05) eV for neutral water elimination upon ionization is captured well in the calculations, and qualitative insights are provided by molecular orbital analysis and molecular dynamics snapshots along the reaction coordinate.