10–100 eV Ar+ ion induced damage to d-ribose and 2-deoxy-d-ribose molecules in condensed phase

Unveiling the electron-induced ionization cross sections and fragmentation mechanisms of 3,4-dihydro-2H-pyran

The interactions of electrons with molecular systems under various conditions are essential to interdisciplinary research fields extending over the fundamental and applied sciences. In particular, investigating electron-induced ionization and dissociation of molecules may shed light on the radiation damage to living cells, the physicochemical processes in interstellar environments, and reaction mechanisms occurring in combustion or plasma. We have, therefore, studied electron-induced ionization and dissociation of the gas phase 3,4-dihydro-2H-pyran (DHP), a cyclic ether appearing to be a viable moiety for developing efficient clinical pharmacokinetics and revealing the mechanisms of biofuel combustion. The mass spectra in the m/z = 10-90 mass range were measured at several different energies of the ionizing electron beam using mass spectrometry. The mass spectra of DHP at the same energies were simulated using on-the-fly semi-classical molecular dynamics (MD) within the framework of the QCxMS formalism. The MD settings were suitably adjusted until a good agreement with the experimental mass spectra intensities was achieved, thus enabling a reliable assignment of cations and unraveling the plausible fragmentation channels. Based on the measurement of the absolute total ionization cross section of DHP (18.1 ± 0.9) × 10-16 cm2 at 100 eV energy, the absolute total and partial ionization cross sections of DHP were determined in the 5-140 eV electron energy. Moreover, a machine learning algorithm that was trained with measured cross sections from 25 different molecules was used to predict the total ionization cross section for DHP. Comparison of the machine learning simulation with the measured data showed acceptable agreement, similar to that achieved in past predictions of the algorithm.

Innovations in nanosynthesis: emerging techniques for precision, scalability, and spatial control in reactions of organic molecules on solid surfaces

The surface science-based approach to synthesising new organic materials on surfaces has gained considerable attention in recent years, owing to its success in facilitating the formation of novel 0D, 1D and 2D architectures. The primary mechanism used to date has been the catalytic transformation of small organic molecules through substrate-enabled reactions. In this Topical Review, we provide an overview of alternate approaches to controlling molecular reactions on surfaces. These approaches include light, electron and ion-initiated reactions, electrospray ionisation deposition-based techniques, collisions of neutral atoms and molecules, and superhydrogenation. We focus on the opportunities afforded by these alternative approaches, in particular where they may offer advantages in terms of selectivity, spatial control or scalability.

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.

Fragmentation of tetrahydrofuran molecules by H(+), C(+), and O(+) collisions at the incident energy range of 25-1000 eV

We have studied fragmentation processes of the gas-phase tetrahydrofuran (THF) molecules in collisions with the H(+), C(+), and O(+) cations. The collision energies have been varied between 25 and 1000 eV and thus covered a velocity range from 10 to 440 km/s. The following excited neutral fragments of THF have been observed: the atomic hydrogen H(n), n = 4-9, carbon atoms in the 2p3s (1)P1, 2p4p (1)D2, and 2p4p (3)P states and vibrationally and rotationally excited diatomic CH fragments in the A(2)Δ and B(2)Σ(-) states. Fragmentation yields of these excited fragments have been measured as functions of the projectile energy (velocity). Our results show that the fragmentation mechanism depends on the projectile cations and is dominated by electron transfer from tetrahydrofuran molecules to cations. It has been additionally hypothesized that in the C(+)+THF collisions a [C-C4H8O](+) complex is formed prior to dissociation. The possible reaction channels involved in fragmentation of THF under the H(+), C(+), and O(+) cations impact are also discussed.

Novel apparatus to measure hyperthermal heavy ion damage to DNA: strand breaks, base loss, and fragmentation

We have developed a novel apparatus that allows us to irradiate nonvolatile organic films of high mass (1-100 microg range) spread out over a large surface area (42 cm(2)) with low energy (kT-100 eV) heavy ions and to quantitatively analyze the film substance via standard biochemical techniques afterwards. Here we discuss the details of the apparatus and method and show that it allows us to measure substantial damage to double stranded DNA molecules (plasmids) and its fundamental subunits induced by heavy ions with unprecedented low energies, i.e., 2.5 eV/amu; these energies correspond to track end energies of stopping ions or secondary ions created along primary ion tracks. We find that hyperthermal Ar(+) ions interacting with plasmid DNA will lead to the formation of single and double strand breaks, as well as fragmentation of nucleosides, which also involve chemical modifications and site specific rupture along the N1-C1 glycosidic bond, resulting in base release. In cells, such localized clustered damage will enhance the severity of DNA strand lesions, thus making them harder to repair.

Reactive scattering damage to DNA components by hyperthermal secondary ions

We have observed reactive scattering damage to fundamental DNA building blocks by the type of hyperthermal secondary ions that are produced along heavy ion tracks in biological media. Reactions include carbon abstraction by N+, and hydrogen abstraction by O- and N+, at collision energies down to 1 eV. Our results show that localized reactive scattering by hyperthermal secondary fragments can lead to important physicochemical damage to DNA in cells irradiated by heavy ions. This suggests a fundamentally different picture of nascent DNA damage induced by heavy ion tracks, compared to conventional (x or gamma) radiation tracks.