D. T. Ha

Fragmentation patterns of core-ionized thymine and 5-bromouracil

Photofragmentation of thymine and 5-bromouracil into cation and neutral fragments following the core ionization by soft x-rays using photoelectron-photoion-photoion coincidence technique has been studied. The fragment ion mass spectra were recorded in coincidence with the C 1s photoelectron spectra. In the case of thymine, deuterated samples were used to identify fragments. Deuteration or bromination allowed us to study not only the main fragmentation channels of these pyrimidine bases, but also to investigate if replacement of an exocyclic functional group affects molecular fragmentation. We found that the dominant fragmentation channels involve only one starting geometry, and the base ring and other bond cleavages, leading to the detected fragments, are essentially identical between thymine and 5-bromouracil. In addition, the relative intensities of the strongest fragmentation channels were determined and compared with calculated appearance energies using ab initio unrestricted Hartree-Fock theory.

Size selective spectroscopy of Se microclusters

The electronic structure and photofragmentation in outer and inner valence regions of Se(n) (n ≤ 8) clusters produced by direct vacuum evaporation have been studied with size-selective photoelectron-photoion coincidence technique by using vacuum-ultraviolet synchrotron radiation. The experimental ionization potentials of these clusters were extracted from the partial ion yield measurements. The calculations for the possible geometrical structures of the Se(n) microclusters have been executed. The ionization energies of the clusters have been calculated and compared with the experimental results. In addition, theoretical fragment ion appearance energies were estimated. The dissociation energies of Se(n) clusters were derived from the recurrent relation between the gas phase enthalpies of the formation of corresponding cationic clusters and experimental ionization energies.

Fragmentation patterns of doubly charged acrylonitrile molecule following carbon core ionization

Dissociation of acrylonitrile into pairs of cations and neutral fragments following molecular core ionization was investigated using the photoelectron-photoion-photoion coincidence (PEPIPICO) technique. The fragment ion mass spectra were recorded in coincidence with the carbon 1s photoelectrons. Deuterated and (13)C-substituted samples were used for resolving fragment mass ambiguities. Slope analysis of the PEPIPICO patterns was used in determining the fragment separation sequences in case of multiparticle processes. The results show that there are several fragmentation channels producing a wide range of charged coincident fragments. The dynamics of the dominant fragmentation processes is investigated in detail.

Dissociation Pathways in the Cysteine Dication after Site-Selective Core Ionization

A photoelectron-ion-ion coincidence experiment has been carried out on the amino acid molecule cysteine after core-ionization of the O 1s, N 1s, C 1s, and S 2p orbitals. A number of different dissociation channels have been identified. Some of them show strong site-selective dependence that can be attributed to a combination of nuclear motion in the core-ionized state and Auger processes that populate different final electronic states in the dication.

VUV-induced dissociation of methylchlorosilanes, studied by electron–ion coincidence spectroscopy

Fragmentation patterns of gas-phase trimethylchlorosilane and methyltrichlorosilane molecules were investigated using the electron-energy-resolved photoelectron–photoion coincidence technique. The production of parent ions and the dominant fragments by 30 eV synchrotron radiation was followed as a function of the photoelectron binding energy. Ion appearance energies were determined from these coincident ion yield curves. The fragmentation patterns and their development are discussed in terms of available internal excess energy as well as the molecular orbital character of the parent molecules. A common dissociation scenario is proposed for both molecules, producing methyl- and chlorine-loss fragments at lower excess energies and smaller fragments through second-step processes at sufficiently high energies.

Gas-phase study on uridine: Conformation and X-ray photofragmentation

Fragmentation of RNA nucleoside uridine, induced by carbon 1s core ionization, has been studied. The measurements by combined electron and ion spectroscopy have been performed in gas phase utilizing synchrotron radiation. As uridine is a combination of d-ribose and uracil, which have been studied earlier with the same method, this study also considers the effect of chemical environment and the relevant functional groups. Furthermore, since in core ionization the initial core hole is always highly localized, charge migration prior to fragmentation has been studied here. This study also demonstrates the destructive nature of core ionization as in most cases the C 1s ionization of uridine leads to concerted explosions producing only small fragments with masses ≤43 amu. In addition to fragmentation patterns, we found out that upon evaporation the sugar part of the uridine molecule attains hexagonal form.

Resonant Auger electron-photoion coincidence study of the fragmentation dynamics of an acrylonitrile molecule

Monochromatic synchrotron radiation was used to promote K-shell electrons of nitrogen and carbon from the cyano group (C ≡ N) of gaseous acrylonitrile (C2H3–CN) to the unoccupied antibonding π*C ≡ N orbital. Photofragmentation of acrylonitrile molecules following selective resonant core excitations of carbon and nitrogen core electrons to the π*C ≡ N orbital was investigated using the electron-energy-resolved photoelecton–photoion coincidence technique. The fragment ion mass spectra were recorded in coincidence with the resonant Auger electrons, emitted in the decay process of the core-excited states. Singly and triply deuterated samples were used for fragment identification. The results showed the initial core-hole localization to be of minor importance in determining the dissociation pattern of the molecular cation. The participator and spectator Auger transitions produce entirely different fragmentation patterns and the latter indicates that complex nuclear rearrangements take place. It is suggested that the calculated kinetic energy releases are caused by the existence of metastable states, which appear with the opening of the spectator Auger channels.

Photofragmentation of Serine Following C 1s Core Ionization-Comparison with Cysteine.

Photofragmentation pathways of doubly ionized serine molecules are investigated and compared with those of cysteine. The main motivation for the study is to investigate if an atomic substitution within the same group of elements, namely, replacing sulfur (in cysteine) with oxygen (in serine), causes a major change in the C 1s core ionization induced dissociation pattern in the molecules of an otherwise identical structure. The results show that in serine there is a single completely dominant fragmentation channel producing the (CNH2–4+, COH1–3+) pairs, whereas in cysteine there are also many other fragmentation channels. The employed experimental method was the photoelectron–photoion–photoion coincidence (PEPIPICO) technique combined with synchrotron radiation tuned to ionize desired core levels. Molecular dynamics calculations were also carried out in order to extract information on the fragmentation and the neutral final fragments.

Fragmentation network of doubly charged methionine: Interpretation using graph theory

The fragmentation of doubly charged gas-phase methionine (HO2CCH(NH2)CH2CH2SCH3) is systematically studied using the self-consistent charge density functional tight-binding molecular dynamics (MD) simulation method. We applied graph theory to analyze the large number of the calculated MD trajectories, which appears to be a highly effective and convenient means of extracting versatile information from the large data. The present theoretical results strongly concur with the earlier studied experimental ones. Essentially, the dication dissociates into acidic group CO2H and basic group C4NSH10. The former may carry a single or no charge and stays intact in most cases, whereas the latter may hold either a single or a double charge and tends to dissociate into smaller fragments. The decay of the basic group is observed to follow the Arrhenius law. The dissociation pathways to CO2H and C4NSH10 and subsequent fragmentations are also supported by ab initio calculations.

Theoretical and experimental study of VUV ionization and fragmentation of size-selected selenium microclusters

Ab initio and mass-resolved fragmentation study of thermally evaporated selenium clusters Sen induced by VUV synchrotron radiation.