Dissociative photoionization of adenine following valence excitation

Electron Impact Ionization of Adenine: Partial Cross Sections

Electron ionization of a genetically important nucleobase, adenine, was investigated from threshold to 500 eV using crossed electron beam–effusive molecular beam geometry and time-of-flight mass spectrometry. We measured the complete set of absolute partial cross sections for adenine using the relative flow technique (RFT) up to an electron energy of 500 eV. Normalization to absolute values was performed using electron ionization cross sections for argon and the vapor pressure data of adenine. The total cross sections obtained by summing the partial cross sections were compared with the existing theoretical and experimental data. The appearance energies of various fragment ions were also measured and compared with the reported data. The prominence of ions with mass (HCN)n+ (n = 1 to 5) indicated a possible pathway to form adenine in the interstellar medium through aggregation of HCN units. Analysis of the partial cross sections for various groups of fragment ions as a function of electron energy was found to give insights into their composition.

Real-time observation of a correlation-driven sub 3 fs charge migration in ionised adenine

Sudden ionisation of a relatively large molecule can initiate a correlation-driven process dubbed charge migration, where the electron density distribution is expected to rapidly move along the molecular backbone. Capturing this few-femtosecond or attosecond charge redistribution would represent the real-time observation of electron correlation in a molecule with the enticing prospect of following the energy flow from a single excited electron to the other coupled electrons in the system. Here, we report a time-resolved study of the correlation-driven charge migration process occurring in the nucleic-acid base adenine after ionisation with a 15-35 eV attosecond pulse. We find that the production of intact doubly charged adenine - via a shortly-delayed laser-induced second ionisation event - represents the signature of a charge inflation mechanism resulting from many-body excitation. This conclusion is supported by first-principles time-dependent simulations. These findings may contribute to the control of molecular reactivity at the electronic, few-femtosecond time scale.

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.

Photoionization and ionic dissociation of the C3 H3 NS molecule induced by soft X-ray near the C1s edge

Time of flight mass spectrometry, electron-ion coincidence, and ion yield spectroscopy were employed to investigate for the first time the thiazole (C₃ H₃ NS) molecule in the gas phase excited by synchrotron radiation in the soft X-ray domain. Total ion yield (TIY) and photoelectron-photoion coincidence (PEPICO) spectra were recorded as a function of the photon energy in the vicinity of the carbon K edge (C1s). The C1s resonant transitions as well as the core ionization thresholds have been determined from the profile of TIY spectrum, and the features were discussed. The corresponding partial ion yields were determined from the PEPICO spectra for the cation species produced upon the molecular photodissociation. Additional ab initio calculations have also been performed from where relevant structural and electronic configuration parameters were obtained for this molecule.

Ultrafast dynamics in the DNA building blocks thymidine and thymine initiated by ionizing radiation

Ultrafast dynamics and fragmentation of thymidine and thymine after ionization by attosecond extreme ultraviolet radiation studied in the time-domain.

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.

VUV photodissociation of thiazole molecule investigated by TOF-MS and photoelectron photoion coincidence spectroscopy

Photoelectron photoion coincidence measurements have been performed for the thiazole (C3H3NS) molecule in gas phase, using time-of-flight mass spectrometry in the electron-ion coincidence mode and vacuum ultraviolet synchrotron radiation. photoelectron photoion coincidence spectra have been recorded as a function of the photon energy covering the valence range from 10 to 21 eV. The resulting photoionization products as well as the dissociation pathways leading to the ionic species were proposed and discussed. We have also performed density functional theory and ab initio calculations for the neutral molecule, its cation and the ion fragments produced in order to determine their electronic and structural parameters.

Electronic properties of FC(O)SCH2CH3. a combined helium(I) photoelectron spectroscopy and synchrotron radiation study

The valence electronic properties of S-ethyl flouromethanethioate (S-ethyl fluoromethsanethioate), FC(O)SCH2CH3, were investigated by means of He(I) photoelectron spectroscopy in conjunction with the analysis of the photofragmentation products determined by PEPICO (phtoelectron-photoion-coincidence) by using synchrotron radiation in the 11.1-21.6 eV photon energy range. The first band observed at 10.28 eV in the HeI photoelectron spectrum can be assigned with confidence to the ionization process from the HOMO [nπ(S) orbital], which is described as a lone pair formally localized on the sulfur atom, in agreement with quantum chemical calculations using the outer valence Green function method [OVGF/6-311++G (d,p)]. One of the most important fragmentation channels also observed in the valence region corresponds to the decarbonylation process yielding the [M-CO](·+) ion, which is clearly observed at m/z = 80. Moreover, S 2p and S 2s absorption edges have been examined by measuring the total ion yield spectra in the 160-240 eV region using variable synchrotron radiation. The dynamic of ionic fragmentation following the Auger electronic decay has been evaluated with the help of the PEPIPICO (photoion-photoion-photoelectron-coincidence spectra) technique.

Outermost and inner-shell electronic properties of ClC(O)SCH2CH3 studied using HeI photoelectron spectroscopy and synchrotron radiation

A study of valence electronic properties of S-ethyl chlorothioformate (S-ethyl chloromethanethioate), ClC(O)SCH(2)CH(3), using HeI photoelectron spectra (PES) and synchrotron radiation is presented. Moreover, the photon impact excitation and dissociation dynamics of ClC(O)SCH(2)CH(3) excited at the S 2p and Cl 2p levels are elucidated by analyzing the total ion yield (TIY) spectra and time-of-flight mass spectra acquired in multicoincidence mode [photoelectron-photoion coincidence (PEPICO) and photoelectron-photoion-photoion coincidence (PEPIPICO)]. The HeI photoelectron spectrum is dominated by features associated with lone-pair electrons from the ClC(O)S- group, the HOMO at 9.84 eV being assigned to the n(π)(S) sulfur lone-pair orbital. Whereas the formation of C(2)H(5)(+) ion dominates the fragmentation in the valence energy region, the most abundant ion formed in both the S and Cl 2p energy ranges is C(2)H(3)(+). Comparison with related XC(O)SR (X = H, F, Cl and R = -CH(3), -C(2)H(5)) species reveals the impact of the alkyl chain on the photodissociation behavior of S-alkyl (halo)thioformates.

Survival of gas phase amino acids and nucleobases in space radiation conditions

We present experimental studies on the photoionization and photodissociation processes (photodestruction) of gaseous amino acids and nucleobases in interstellar and interpla-netary radiation analogs conditions. The measurements have been undertaken at the Brazilian Synchrotron Light Laboratory (LNLS), employing vacuum ultraviolet (VUV) and soft X-ray photons. The experimental set up basically consists of a time-of-flight mass spectrometer kept under high vacuum conditions. Mass spectra were obtained using a photoelectron photoion coincidence technique. We have shown that the amino acids are effectively more destroyed (up to 70–80%) by the stellar radiation than the nucleobases, mainly in the VUV. Since polycyclic aromatic hydrocarbons have the same survival capability and seem to be ubiquitous in the ISM, it is not unreasonable to predict that nucleobases could survive in the interstellar medium and/or in comets, even as a stable cation.