N-site de-methylation in pyrimidine bases as studied by low energy electrons and ab initio calculations

Sensing the ortho Positions in C6Cl6 and C6H4Cl2 from Cl2− Formation upon Molecular Reduction

The geometrical effect of chlorine atom positions in polyatomic molecules after capturing a low-energy electron is shown to be a prevalent mechanism yielding Cl₂⁻. In this work, we investigated hexachlorobenzene reduction in electron transfer experiments to determine the role of chlorine atom positions around the aromatic ring, and compared our results with those using ortho-, meta- and para-dichlorobenzene molecules. This was achieved by combining gas-phase experiments to determine the reaction threshold by means of mass spectrometry together with quantum chemical calculations. We also observed that Cl₂⁻ formation can only occur in 1,2-C₆H₄Cl₂, where the two closest C–Cl bonds are cleaved while the chlorine atoms are brought together within the ring framework due to excess energy dissipation. These results show that a strong coupling between electronic and C–Cl bending motion is responsible for a positional isomeric effect, where molecular recognition is a determining factor in chlorine anion formation.

Bound Electron Enhanced Radiosensitisation of Nimorazole upon Charge Transfer

This novel work reports nimorazole (NIMO) radiosensitizer reduction upon electron transfer in collisions with neutral potassium (K) atoms in the lab frame energy range of 10–400 eV. The negative ions formed in this energy range were time-of-flight mass analyzed and branching ratios were obtained. Assignment of different anions showed that more than 80% was due to the formation of the non-dissociated parent anion NIMO•− at 226 u and nitrogen dioxide anion NO2− at 46 u. The rich fragmentation pattern revealed that significant collision induced the decomposition of the 4-nitroimidazole ring, as well as other complex internal reactions within the temporary negative ion formed after electron transfer to neutral NIMO. Other fragment anions were only responsible for less than 20% of the total ion yield. Additional information on the electronic state spectroscopy of nimorazole was obtained by recording a K+ energy loss spectrum in the forward scattering direction (θ ≈ 0°), allowing us to determine the most accessible electronic states within the temporary negative ion. Quantum chemical calculations on the electronic structure of NIMO in the presence of a potassium atom were performed to help assign the most significant lowest unoccupied molecular orbitals participating in the collision process. Electron transfer was shown to be a relevant process for nimorazole radiosensitisation through efficient and prevalent non-dissociated parent anion formation.

Ion-Pair Formation in Neutral Potassium-Neutral Pyrimidine Collisions: Electron Transfer Experiments

We report novel data on ion-pair formation in hyperthermal (30–800 eV) neutral potassium collisions with neutral pyrimidine (Pyr, C₄H₄N₂) molecules. In this collision regime, negative ions formed by electron transfer from the alkali atom to the target molecule were time-of-flight mass analyzed and the fragmentation patterns and branching ratios have been obtained. The most abundant product anions have been assigned to CN⁻ and C₂H⁻ and the electron transfer mechanisms are comprehensively discussed. Particular importance is also given to the efficient loss of integrity of the pyrimidine ring in the presence of an extra electron, which is in contrast to dissociative electron attachment experiments yielding the dehydrogenated parent anion. Theoretical calculations were performed for pyrimidine in the presence of a potassium atom and provided a strong basis for the assignment of the lowest unoccupied molecular orbitals accessed in the collision process. In order to further our knowledge about the collision dynamics, potassium cation (K⁺) energy loss spectrum has been obtained and within this context, we also discuss the role of the accessible electronic states. A vertical electron affinity of (−5.69 ± 0.20) eV was obtained and may be assigned to a π3*(b₁) state that leads to CN⁻ formation.

Electron transfer driven decomposition of adenine and selected analogs as probed by experimental and theoretical methods

We report on a combined experimental and theoretical study of electron-transfer-induced decomposition of adenine (Ad) and a selection of analog molecules in collisions with potassium (K) atoms. Time-of-flight negative ion mass spectra have been obtained in a wide collision energy range (6-68 eV in the centre-of-mass frame), providing a comprehensive investigation of the fragmentation patterns of purine (Pu), adenine (Ad), 9-methyl adenine (9-mAd), 6-dimethyl adenine (6-dimAd), and 2-D adenine (2-DAd). Following our recent communication about selective hydrogen loss from the transient negative ions (TNIs) produced in these collisions [T. Cunha et al., J. Chem. Phys. 148, 021101 (2018)], this work focuses on the production of smaller fragment anions. In the low-energy part of the present range, several dissociation channels that are accessible in free electron attachment experiments are absent from the present mass spectra, notably NH₂ loss from adenine and 9-methyl adenine. This can be understood in terms of a relatively long transit time of the K⁺ cation in the vicinity of the TNI tending to enhance the likelihood of intramolecular electron transfer. In this case, the excess energy can be redistributed through the available degrees of freedom inhibiting fragmentation pathways. Ab initio theoretical calculations were performed for 9-methyl adenine (9-mAd) and adenine (Ad) in the presence of a potassium atom and provided a strong basis for the assignment of the lowest unoccupied molecular orbitals accessed in the collision process.

Stripping off hydrogens in imidazole triggered by the attachment of a single electron

Imidazole [C₃H₄N₂] is ubiquitous in nature as an important biological building block of amino acids, purine nucleobases or antibiotics. In the present study, dissociative electron attachment to imidazole shows low energy shape resonances at 1.52 and 2.29 eV leading to the most abundant dehydrogenated anion [imidazole - H]^- through dehydrogenation at the N1 position. All the other anions formed exhibit core excited resonances observed dominantly at similar electron energies of ∼7 and 11 eV, suggesting an initial formation through two temporary negative ion states. Among these anions, multiple dehydrogenation reactions are observed resulting in the loss of 2 up to 4 hydrogens, thus, leading to a complete dehydrogenation of the imidazole molecule, an interesting prototype of complex unimolecular decay induced by the attachment of a single electron. Additionally, the quantum chemical calculations reveal that these multiple dehydrogenation reactions are responsible for the remarkable one electron-induced gas-phase chemistry leading to the opening of the ring. The formation of the observed anions is likely driven by the high positive electron affinity of cyanocarbon molecules supported by quantum chemical calculations. The formation of H^- showed additional resonance at about 5 eV and dipolar dissociation above ∼14 eV.

Study of Electron Ionization and Fragmentation of Non-hydrated and Hydrated Tetrahydrofuran Clusters

Mass spectroscopic investigations on tetrahydrofuran (THF, C₄H₈O), a common model molecule of the DNA-backbone, have been carried out. We irradiated isolated THF and (hydrated) THF clusters with low energy electrons (electron energy ~70 eV) in order to study electron ionization and ionic fragmentation. For elucidation of fragmentation pathways, deuterated TDF (C₄D₈O) was investigated as well. One major observation is that the cluster environment shows overall a protective behavior on THF. However, also new fragmentation channels open in the cluster. In this context, we were able to solve a discrepancy in the literature about the fragment ion peak at mass 55 u in the electron ionization mass spectrum of THF. We ascribe this ion yield to the fragmentation of ionized THF clusters. Graphical Abstract ᅟ.

Fragmentation pathways of tungsten hexacarbonyl clusters upon electron ionization

Electron ionization of neat tungsten hexacarbonyl (W(CO)6) clusters has been investigated in a crossed electron-molecular beam experiment coupled with a mass spectrometer system. The molecule is used for nanofabrication processes through electron beam induced deposition and ion beam induced deposition techniques. Positive ion mass spectra of W(CO)6 clusters formed by electron ionization at 70 eV contain the ion series of the type W(CO)n (+) (0 ≤ n ≤ 6) and W2(CO)n (+) (0 ≤ n ≤ 12). In addition, a series of peaks are observed and have been assigned to WC(CO)n (+) (0 ≤ n ≤ 3) and W2C(CO)n (+) (0 ≤ n ≤ 10). A distinct change of relative fragment ion intensity can be observed for clusters compared to the single molecule. The characteristic fragmentation pattern obtained in the mass spectra can be explained by a sequential decay of the ionized organometallic, which is also supported by the study of the clusters when embedded in helium nanodroplets. In addition, appearance energies for the dissociative ionization channels for singly charged ions have been estimated from experimental ion efficiency curves.

Electron interactions with the focused electron beam induced processing (FEBID) precursor tungsten hexachloride

RATIONALE

Secondary electrons with an energy distribution below 100 eV are formed when high-energy particles interact with matter. In the focused electron beam induced deposition, high-energy beams are used to decompose organometallic compounds on surfaces. We investigated the electron ionisation of WCl6 and dissociative electron attachment to WCl6 in the gas phase in order to better understand the decomposition mechanism driven by secondary electrons.

METHODS

A double-focusing mass spectrometer coupled with a Nier-type ion source was used to perform the present studies. The electron ionisation studies were performed with an electron energy of 70 eV and dissociative electron attachment studies in the energy range of ~0-14 eV.

RESULTS

Tungsten hexachloride rapidly oxidises, leading to the formation of a mixture of pure WCl6 and WCl4 O together with WCl2 O2 species. The fragmentation of the three chlorinated compounds is effective, although electron ionisation to WCl6 leads to W(+) in contrast with WCl2 O2 and WCl4 O leading to WO2 (+) and WO(+) , respectively, as lighter fragments. With regard to electron attachment, decomposition of the precursor molecules is observed; however, W(-) was not detected within the detection limit of the instrument.

CONCLUSIONS

Electron ionisation and dissociative electron attachment (DEA) to WCl6 , WCl4 O and WCl2 O2 lead to strong fragmentation. In electron ionisation, the fragmentation by loss of chlorine atoms was observed for both WCl6 and the oxidised species. Additionally, the loss of all chlorine ligands is observable for WCl6 as well as the oxidised species. The DEA results have shown dissociation by the scission of chlorine atoms as well as by the scission of an oxygen atom. The formation of chlorine and oxygen anions was observed, indicating the formation of a neutral counterpart containing the metal atom, free to be attacked by the next electron.

Complete ligand loss in electron ionization of the weakly bound organometallic tungsten hexacarbonyl dimer

We observed the bare W2(+) metal cation upon electron ionization of the weakly bound W(CO)6 dimer. This metal cation can be only observed due to the fast conversion of the weak cluster bond into a strong covalent bond between the metal moieties.

The Effect of Solvation on Electron Attachment to Pure and Hydrated Pyrimidine Clusters

The interaction of low‐energy electrons with biomolecules plays an important role in the radiation‐induced alteration of biological tissue at the molecular level. At electron energies below 15 eV, dissociative electron attachment is one of the most important processes in terms of the chemical transformation of molecules. So far, a common approach to study processes at the molecular level has been to carry out investigations with single biomolecular building blocks like pyrimidine as model molecules. Electron attachment to single pyrimidine, as well as to pure clusters and hydrated clusters, was investigated in this study. In striking contrast to the situation with isolated molecules and hydrated clusters, where no anionic monomer is detectable, we were able to observe the molecular anion for the pure clusters. Furthermore, there is evidence that solvation effectively prevents the ring fragmentation of pyrimidine after electron capture.

Potassium-uracil/thymine ring cleavage enhancement as studied in electron transfer experiments and theoretical calculations

We report experimental and theoretical studies on ring cleavage enhancement in collisions of potassium atoms with uracil/thymine to further increase the understanding of the complex mechanisms yielding such fragmentation pathways. In these electron transfer processes time-of-flight (TOF) negative ion mass spectra were obtained in the collision energy range 13.5-23.0 eV. We note that CNO(-) is the major ring breaking anion formed and its threshold formation is discussed within the collision energy range studied. Such a decomposition process is supported by the first theoretical calculations to clarify how DNA/RNA pyrimidine base fragmentation is enhanced in electron transfer processes yielding ion-pair formation.

NCO(-), a key fragment upon dissociative electron attachment and electron transfer to pyrimidine bases: site selectivity for a slow decay process

We report gas phase studies on NCO(-) fragment formation from the nucleobases thymine and uracil and their N-site methylated derivatives upon dissociative electron attachment (DEA) and through electron transfer in potassium collisions. For comparison, the NCO(-) production in metastable decay of the nucleobases after deprotonation in matrix assisted laser desorption/ionization (MALDI) is also reported. We show that the delayed fragmentation of the dehydrogenated closed-shell anion into NCO(-) upon DEA proceeds few microseconds after the electron attachment process, indicating a rather slow unimolecular decomposition. Utilizing partially methylated thymine, we demonstrate that the remarkable site selectivity of the initial hydrogen loss as a function of the electron energy is preserved in the prompt as well as the metastable NCO(-) formation in DEA. Site selectivity in the NCO(-) yield is also pronounced after deprotonation in MALDI, though distinctly different from that observed in DEA. This is discussed in terms of the different electronic states subjected to metastable decay in these experiments. In potassium collisions with 1- and 3-methylthymine and 1- and 3-methyluracil, the dominant fragment is the NCO(-) ion and the branching ratios as a function of the collision energy show evidence of extraordinary site-selectivity in the reactions yielding its formation.