Photoelectron spectroscopic studies of 5-halouracil anions

The parent negative ions of 5-chlorouracil, UCl(-) and 5-fluorouracil, UF(-) have been studied using anion photoelectron spectroscopy in order to investigate the electrophilic properties of their corresponding neutral halouracils. The vertical detachment energies (VDE) of these anions and the adiabatic electron affinities (EA) of their neutral molecular counterparts are reported. These results are in good agreement with the results of previously published theoretical calculations. The VDE values for both UCl(-) and UF(-) and the EA values for their neutral molecular counterparts are much greater than the corresponding values for both anionic and neutral forms of canonical uracil and thymine. These results are consistent with the observation that DNA is more sensitive to radiation damage when thymine is replaced by halouracil. While we also attempted to prepare the parent anion of 5-bromouracil, UBr(-), we did not observe it, the mass spectrum exhibiting only Br(-) fragments, i.e., 5-bromouracil apparently underwent dissociative electron attachment. This observation is consistent with a previous assessment, suggesting that 5-bromouracil is the best radio-sensitizer among these three halo-nucleobases.     

Electronic structure of adenine and thymine base pairs studied by femtosecond electron-ion coincidence spectroscopy

Femtosecond pump-probe spectroscopy was combined with photoelectron-photoion coincidence detection to investigate the electronic structure and dynamics of isolated adenine (A) and thymine (T) dimers and the adenine-thymine (AT) base pair. The photoelectron spectra show that pipi* and npi* states are only weakly perturbed in the hydrogen-bound dimers as compared to the monomers. For cationic base pairs with internal energies greater than 1 eV, we observed considerable cluster fragmentation into protonated monomers. This process selectively removed signals from the npi* --> n-1 ionization channel in all dimers. The photoelectron spectra are compared to time-resolved mass spectra and confirm the assignment of short-lived pipi* and npi* populations in the adenine, thymine, and mixed AT dimers.     

Characterization of neutral fragments issued from the photodissociation of protonated tryptophane

New information on the photo-fragmentation of biomolecules is obtained from the detection of neutral and ionic fragments using a time and position resolved coincidence technique that reveals whether an ionic photofragment is associated with one or more neutral fragments. In the case of a sequential dissociation, both fragmentation channels are identified as well as their time ordering.     

Electronic properties and dissociative photoionization of thiocyanates. Part II. Valence and shallow-core (sulfur and chlorine 2p) regions of chloromethyl thiocyanate, CH2ClSCN

A combination of photoelectron spectroscopy and synchrotron based photoelectron photoion coincidence (PEPICO) spectra has been applied to investigate the electronic structure and the dissociative ionization of the CH(2)ClSCN molecule in the valence region. The PES is assigned with the electronic structure calculations at the outer-valence Green's function and symmetry adapted cluster/configuration interaction (SAC-CI) levels offer an explanation of our experimental results. Upon vacuum ultraviolet irradiation the low-lying radical cation, located at 10.39 eV is formed. The molecular ion is observed in the time-of-flight mass spectra, together with the CH(2)SCN(+) and CH(2)Cl(+) daughter ions. The total ion yield spectra have been measured in the S 2p and Cl 2p regions and several channels have been determined in dissociative photoionization events for the core-excited species. Thus, by using time-of-flight mass spectrometry and synchrotron radiation the relative abundances of the ionic fragments and their kinetic energy release values were obtained from both PEPICO and photoelectron photoion photoion coincidence spectra. Possible fragmentation processes are discussed and compared with that found for the related CH(3)SCN species.     

Ionization and fragmentation of OCS and CS2 after photoexcitation around the sulfur 2p edge

Photo-ion time-of-flight mass spectra have been taken of OCS and CS₂ molecules and of argon after excitation with tunable monochromatized synchrotron radiation that was scanned through the entire resonance region of the sulfur (or argon) 2p absorotion. Flight times of up to three charged fragments were measured in coincidence. By means of a careful data reduction branching ratios of the molecules for numerous fragmentation channels, including those comprising ionic and neutral fragments, have been determined. Implicitly we obtain also spectra of the total charge which are found to closely resemble each other and the photo-ion spectrum of atomic argon, thus reflecting analogous electronic processes in this atom and both molecules. Such processes are simultaneous or sequential double Auger ejection and photoelectron recapture via post-collision interaction. Branching among dissociation channels of equal total charge is similar for both molecules and generally varies little with photon energy, with a few notable exceptions at the π^* resonances and the ionization limits. Maximum kinetic energies of fragments are determined for purely ionic channels and compare well, as do the momentum correlations, with results of simulations based on a simple kinematical model.     

Interstellar H3+ and HCS+ ions produced in the dissociative photoionization process of CH3C(O)SCH3 in the proximity of the sulfur 2p, carbon 1s, and oxygen 1s edges

In this work we present a study of the dissociative photoionization of S-methyl thioacetate [CH(3)C(O)SCH(3)] by using multicoincidence time-of-flight mass spectrometry and synchrotron radiation in the S 2p, C 1s, and O 1s edges. Total and partial ion yield spectra together with photoelectron-photoion coincidence (PEPICO) and photoelectron-photoion-photoion coincidence (PEPIPICO) spectra were measured. Fragmentation patterns deduced from PEPICO and PEPIPICO spectra at the various excitation energies show a moderate site-specific fragmentation. The dissociation dynamic for the main ion-pair production is discussed. Two-, three-, and four-body dissociation channels have been observed in the PEPIPICO spectra, and the dissociation mechanisms are proposed. The interstellar HCS(+) and H(3)(+) ions can be observed during the synchrotron experiments reported in the present work.     

Chemische synthese von nonadesoxyribonucleotiden mit den abgewandelten basen uracil, 5-bromuracil und 5-methylcytosin nach dem triester-verfahren

In order to investigate the interaction of Eco RII restriction and modification enzymes with synthetic DNA fragments three nonadeoxyribonucleotides containing the modified bases uracil, 5-bromouracil and 5-methylcytosine were synthesized according to the phosphate tri-ester approach using TPS/l-methylimidazole as the condensation agent. The patterns of these modified DNA fragments obtained by Maxam/Gilbert sequence technique are presented.     

Mass spectrometric characterization of 3'-imino[60]fulleryl-3'-deoxythymidine by collision-induced dissociation

The primary structure of 3'-imino[60]fulleryl-3'-deoxythymidine ions is studied using mass spectrometry both in the positive and negative modes. Interaction between the subunits is discussed using collision-induced dissociation (CID) spectra. Collisional activation with argon of the sodiated cations leads to the cleavage of the glycosidic bond and the transfer of a radical hydrogen from the deoxyribose to the thymine. The sodiated thymine is the only fragment observed for low collision energies in the positive mode. In the negative mode, two different ionization mechanisms take place, reduction and deprotonation in the presence of triethylamine. The 2.7 eV electron affinity of C60 and its huge cross section compared to the small cross section and predicted 0.44 eV electron affinity of the thymidine subunit most likely localize the radical electron on the fullerene. On the other hand, deprotonation of the 3'-azido-3'-deoxythymidine (AZT) is known to occur in N-3, the most acidic site of the nucleobase. Consequently, deprotonation causes the negative charge to be initially localized on the thymine. Both types of parent anions give the radical anion C60*- as fragment. The other fragments detected are the dehydrogenated 3'-imino[60]fulleryl-3'-deoxyribose anion, C60NH2-, C60N- and C60H-. Since in negative ion mass spectrometry all fragments include the [60]fullerene unit, this suggests that the fragmentation is driven by the electron affinity of the [60]fullerene, likely responsible for a charge transfer between the deprotonated thymine and the C60.     

Cationic and anionic fragmentation of dichloromethane following inner-shell (Cl 1s) photoexcitation

The cationic and anionic fragmentation of dichloromethane (CH2Cl2) molecule have been investigated in the energy range of the Cl K shell by using synchrotron radiation, ion yield spectroscopy, and electron-ion coincidence spectroscopy. Total and partial ion-yield and mass spectra have been recorded as a function of the photon energy. We were able to identify several singly and multiply charged cationic fragments and the following anionic species: H-; C-; Cl-. The present results provide the first experimental report of negative ion formation from a molecule excited at the Cl 1s edge. In addition, our electron-ion coincidence data provide strong evidence of the preservation of molecular alignment for the photodissociation of CH2Cl2 after deep core-electron resonant excitation.     

Evidence of site-specific fragmentation on thioacetic acid, CH3C(O)SH, irradiated with synchrotron radiation around the S 2p and O 1s regions

Site-specific fragmentations following S 2p and O 1s photoexcitation of thioacetic acid, CH3C(O)SH, have been studied by means of synchrotron radiation. Total ion yield (TIY) spectra were measured and multicoincidence techniques, which include photoelectron-photoion coincidence (PEPICO) and photoelectron-photoion-photoion coincidence (PEPIPICO) time-of-flight mass spectrometry, were applied. The equivalent-core approximation was employed in order to estimate ionization transition values, and the observed peaks were tentatively assigned. A site-specific fragmentation is moderately observed by comparing the mass spectra collected at resonant energies around the inner and shallow inner shell S 2p and O 1s ionization edges. Beside H+ ion, the most abundant ions observed at the S 2p edge excitation were CH3CO+, SH+, S+, and CH3+. At the O 1s region the large CH3CO+ fragment was depressed, and small CHx+ (x = 0, 1, 2, 3), S+, and SH+ fragments were dominant. The dissociation dynamic for the main ion-pair production has been discussed. Two- and three-body dissociation channels have been observed in the PEPIPICO spectra, and the dissociation mechanisms were proposed.     

Dissociative photoionization of methyl thiochloroformate, ClC(O)SCH3, following sulfur 2p, chlorine 2p, carbon 1s, and oxygen 1s excitations

The electronic transitions and the dissociative ionic photoionization mechanisms of gaseous ClC(O)SCH(3) have been investigated at the VUV and soft X-ray energy regions of S 2p, Cl 2p, C 1s, and O 1s core edges using tunable synchrotron radiation and time-of-flight mass spectrometry. The relative abundances of the ionic fragments were obtained from both PEPICO (photoelectron photoion coincidence) and PEPIPICO (photoelectron photoion photoion coincidence) spectra. The presence of a moderate site- and element-specific fragmentation effects and its implication regarding chemical reactions were analyzed. The relationship of the current results with the interstellar chemistry is also a goal of this piece of work.     

Statistical versus non-statistical photo-fragmentation of protonated GWG tri-peptide induced by UV excitation

A new experimental method is described in which photo-induced fragmentation of protonated molecules in an electric field is investigated by the detection in coincidence of the ion and neutral fragments. This technique allows measuring fragmentation times, in the tens of nanosecond range, for each fragmentation channel independently. As an example, the method has been used to study the photo-fragmentation of the protonated tri-peptide GWG. It is shown that the various fragmentation channels have different fragmentation times. This is a clear signature of non-ergodic mechanisms occurring during fragmentation of such a large molecule.     

Evidence for the formation of an interstellar species, HCS+, during the ionic fragmentation of methyl thiofluoroformate, FC(O)SCH3, in the 100-1000 eV region

Total ion yield spectra and photoinduced fragmentations following S 2p, C 1s, O 1s, and F 1s inner shell excitations of methyl thiofluoroformate, FC(O)SCH(3), have been studied in the gaseous phase by using synchrotron radiation and multicoincidence techniques, which include photoelectron-photoion coincidence (PEPICO) and photoelectron-photoion-photoion coincidence (PEPIPICO) time-of-flight mass spectrometry. Fragmentation patterns deduced from PEPICO spectra at the various excitation energies show a moderate site-specific fragmentation. The dissociation dynamic for the main ion-pair production has been discussed. Two-, three-, and four-body dissociation channels have been observed in the PEPIPICO spectra, and the dissociation mechanisms were proposed. The high stability of the interstellar HCS(+) ion can be observed over the whole range of photon energies analyzed.     

Etude de la fragmentation de derives de L'uracile et de la thymine par Spectrometrie de masse

Original mass spectra of uracil and thymine derivatives are presented with the corresponding fragmentation schemes. In the first series of spectra, the fragmentations of thymine derivatives, including ¹⁴C-2-thymine, dimers, and bromo thymines, confirm the basic retro Diels-Alder mechanism. The second series includes dihydro 5,6-derivatives of uracil (hydroxy and bromo substituents). The behaviour of these molecules is quite different; they are more sensitive to the substituents and a part of the fragmentation is often explained by protonated molecular ions.     

Fragmentation of alpha- and beta-alanine molecules by ions at Bragg-peak energies

The interaction of keV He(+), He(2+), and O(5+) ions with isolated alpha and beta isomers of the amino acid alanine was studied by means of high resolution coincidence time-of-flight mass spectrometry. We observed a strong isomer dependence of characteristic fragmentation channels which manifests in strongly altered branching ratios. Despite the ultrashort initial perturbation by the incoming ion, evidence for molecular rearrangement leading to the formation of H(3)(+) was found. The measured kinetic energies of ionic alanine fragments can be sufficient to induce secondary damage to DNA in a biological environment.     

Simultaneous determination of thymine and 5-bromouracil in DNA hydrolysates using gas chromatography-mass spectrometry with selected-ion monitoring

The gas chromatographic-mass spectrometric method using selected-ion monitoring (GC-MS-SIM) described here quantitatively determines the amount of DNA thymine replacement by 5-bromouracil (BU) after exposure to 5-bromo-2'-deoxyuridine (BUDR) in as few as 10(5) cells. DNA is extracted, enzymatically hydrolyzed, the nucleic acid bases (with added internal standards, 5-iodouracil and 5-chlorouracil) are extracted into ethyl acetate, concentrated and derivatized with bis(trimethylsilyl)trifluoroacetamide. Thymine and BU are then quantitated by GC-MS-SIM. Response is linear to thymine over the range of 100-2000 ng per sample and BU of 1.3-52 ng per sample with a coefficient of variation of less than 10% and an accuracy for seeded samples within 8% of theoretical value. With V79 cells in culture, exposure to increasing BUDR concentrations (0.03-1.0 microM) results in increasing thymine substitution by BU over a range of 1-28%. Other important applications of this technique are mentioned.     

Particle beam glow discharge mass spectrometry: spectral characteristics of nucleobases

Use of a particle beam glow discharge (PB-GD) source for mass spectrometric determinations of deoxy- and ribonucleosides and nucleotides is described. Use of this combination of sample introduction and ion source decouples the vaporization and ionization steps, leading to very simple spectral structure. The mass spectra of these compounds are EI-like in nature, with clearly identified molecular ions and fragmentation patterns that are easily rationalized. The PB-GDMS combination can be operated in a flow injection mode wherein the analyte is injected directly into the solvent flow, or can also be coupled to a high-performance liquid chromatography (HPLC) system allowing LC/MS analysis of mixtures. Mass spectra obtained for nucleic acid bases, nucleosides, and nucleotides are readily obtained with injections of low-nanomole quantities. Representative PB-GDMS spectra for deoxy- and ribonucleosides, nucleotides, and mixed-base oligonucleotides are presented to demonstrate the capabilities of the GD source. Characteristic fragmentation peaks from the spectra of adenine, cytosine, guanine, and thymine were identified in 22-base sequences of single-stranded DNA. The PB-GD source is capable of producing spectra that may be used to identify the individual bases present in mixed-base DNA and RNA fragments.     

Ionic fragmentation on ClC(O)SCl. Evidence of a highly charged molecular ion and confirmation of unusual dissociation mechanisms for halocarbonylsulfenyl chlorides

Total and partial ion yield spectra of chlorocarbonylsulfenyl chloride, ClC(O)SCl, are studied using tunable synchrotron radiation. Multicoincidence techniques, which include photoelectron-photoion coincidence (PEPICO) and photoelectron-photoion-photoion coincidence (PEPIPICO) time-of-flight mass spectrometry, were applied to study the fragmentation dynamics around the S 2p, Cl 2p, C 1s, and O 1s ionization edges. The search for site-specific fragmentation effects showed a definite enhancement of the Cl+ signal at the Cl 2p resonance. However, fragmentation patterns of the PEPICO spectra at the various excitation energies are essentially identical. Evidence for the occurrence of the previously reported charge separation after an ion rearrangement dissociation mechanism was found. Highly charged species were observed in the multicoincidence spectra at K shell transitions, revealing the formation of a highly charged molecular ion.     

High-resolution mass-selective UV spectroscopy of pseudoephedrine: evidence for conformer-specific fragmentation

Using resonance-enhanced two-photon ionization spectroscopy with mass resolution of jet-cooled molecules, a low-resolution S(1) ← S(0) vibronic spectrum of pseudoephedrine was recorded at the mass channels of three distinct fragments with m/z = 58, 71, and 85. Two of the fragments, with m/z = 71 and 85, are observed for the first time for this molecule. The vibronic spectra recorded at different mass channels feature different patterns, implying that they originate from different conformers in the cold molecular beam, following conformer-specific fragmentation pathways. Highly resolved spectra of all prominent vibronic features were measured, and from their analysis based on genetic algorithms, the molecular parameters of the conformers giving rise to the respective bands have been determined. Comparing the experimental results with those obtained from high-level ab initio quantum chemistry calculations, the observed prominent vibronic bands have been assigned to originate from four distinct conformers. The conformers are separated into two groups that have different fragmentation pathways determined by the different intramolecular interactions.     

Ionic Fragmentation Mechanisms of 2,2,2‐Trifluoroethanol Following Excitation with Synchrotron Radiation

Gaseous 2,2,2‐trifluoroethanol (TFE) is excited with synchrotron radiation between 10 and 1000 eV and the ejected electrons and positive ions are detected in coincidence. In the valence‐electron energy region, the most abundant species is CH₂OH⁺. Other fragments, including ions produced by atomic rearrangements, are also detected; the most abundant are COH⁺, CFH₂⁺ and CF₂H₂⁺. The energies of electronic transitions from C 1 s, O 1 s and F 1 s orbitals to vacant molecular orbitals are determined. A site‐specific C 1 s excitation is observed. The photofragmentation mechanisms after the excitation of core‐shell electrons are inferred from analysis of the shape and slope of the coincidence between two charged fragments in the bi‐dimensional coincidence spectra. The spectra are dominated by islands that correspond to the coincidence of H⁺ with several charged fragments. One of the most important channels leads to the formation of CH₂OH⁺ and CF₃⁺ in a concerted mechanism.