IR laser desorption of oligonucleotides A novel gas phase target for radiation damage studies

The desorption of oligonucleotides by 3 mu m laser irradiation has been studied by laser induced fluorescence imaging of the resulting gas phase plumes. Fitting of the plume data has been achieved by using a modified Maxwell Boltzmann distribution which incorporates a range of stream velocities. Spatial density profiles, velocities and temperature variation have been determined from these fits indicating that the oligonucleotide plume only achieves a partial thermal relaxation. This laser desorption technique may provide a means of overcoming the limited mass range of gas phase biomolecules available from thermal evaporation techniques.

THE ROLE OF GAS-PHASE OXIDATION AND COMBINATION DURING LASER DEPOSITION OF YBA2CU3O7-X IN AMBIENT OXYGEN

Spectroscopic absorption and emission measurements have been used to study laser deposition of YBCO films. They show that >95% of the monatomic Y and Ba initially ablated from the target undergo gas-phase chemical combination before film deposition. In contrast, considerable monatomic Cu persists into the deposition region. in this region, equilibrated gas temperatures are of the order of 2700 K. It is suggested that this high temperature facilitates film crystallization and epitaxial growth. The survival of monatomic Cu in the plume to the site of deposition is a manifestation of its endothermic reaction with O-2.

LIAD-fs scheme for studies of ultrafast laser interactions with gas phase biomolecules

Laser induced acoustic desorption (LIAD) has been used for the first time to study the parent ion production and fragmentation mechanisms of a biological molecule in an intense femtosecond (fs) laser field. The photoacoustic shock wave generated in the analyte substrate (thin Ta foil) has been simulated using the hydrodynamic HYADES code, and the full LIAD process has been experimentally characterised as a function of the desorption UV-laser pulse parameters. Observed neutral plumes of densities > 10(9) cm(-3) which are free from solvent or matrix contamination demonstrate the suitability and potential of the source for studying ultrafast dynamics in the gas phase using fs laser pulses. Results obtained with phenylalanine show that through manipulation of fundamental femtosecond laser parameters (such as pulse length, intensity and wavelength), energy deposition within the molecule can be controlled to allow enhancement of parent ion production or generation of characteristic fragmentation patterns. In particular by reducing the pulse length to a timescale equivalent to the fastest vibrational periods in the molecule, we demonstrate how fragmentation of the molecule can be minimised whilst maintaining a high ionisation efficiency.

An in situ spatially resolved analytical technique to simultaneously probe gas phase reactions and temperature within the packed bed of a plug flow reactor

This paper reports the detailed description and validation of a fully automated, computer controlled analytical method to spatially probe the gas composition and thermal characteristics in packed bed systems. As an exemplar, we have examined a heterogeneously catalysed gas phase reaction within the bed of a powdered oxide supported metal catalyst. The design of the gas sampling and the temperature recording systems are disclosed. A stationary capillary with holes drilled in its wall and a moveable reactor coupled with a mass spectrometer are used to enable sampling and analysis. This method has been designed to limit the invasiveness of the probe on the reactor by using the smallest combination of thermocouple and capillary which can be employed practically. An 80 mu m (O.D.) thermocouple has been inserted in a 250 mu m (O.D.) capillary. The thermocouple is aligned with the sampling holes to enable both the gas composition and temperature profiles to be simultaneously measured at equivalent spatially resolved positions. This analysis technique has been validated by studying CO oxidation over a 1% Pt/Al2O3 catalyst and the spatial resolution profiles of chemical species concentrations and temperature as a function of the axial position within the catalyst bed are reported.

Electrochemical versus gas-phase oxidation of ru single-crystal surfaces

The electrochemical uptake of oxygen on a Ru(0001) electrode was investigated by electron diffraction, Auger spectroscopy, and cyclic voltammetry. An ordered (2 × 2)-O overlayer forms at a potential close to the hydrogen region. At +0.42 and +1.12 V vs Ag/AgCl, a (3 × 1) phase and a (1 × 1)-O phase, respectively, emerge. When the Ru electrode potential is maintained at +1.12 V for 2 min, RuO2 grows epitaxially with its (100) plane parallel to the Ru(0001) surface. In contrast to the RuO domains, the non-oxidized regions of the Ru electrode surface are flat. If, however, the electrode potential is increased to +1.98 V for 2 min, the remaining non-oxidized Ru area also becomes rough. These findings are compared with O overlayers and oxides on the Ru(0001) and Ru(101¯1) surfaces created by exposure to gaseous O under UHV conditions. On the other hand, gas-phase oxidation of the Ru(101¯0) surface leads to the formation of RuO with a (100) orientation. It is concluded that the difference in surface energy between RuO(110) and RuO(100) is quite small. RuO again grows epitaxially on Ru(0001), but with the (110) face oriented parallel to the Ru(0001) surface. The electrochemical oxidation of the Ru(0001) electrode surface proceeds via a 3-dimensional growth mechanism with a mean cluster size of 1.6 nm, whereas under UHV conditions, a 2-dimensional oxide film (1-2 nm thick) is epitaxially formed with an average domain size of 20 µm. © 2000 American Chemical Society.

Molecular rearrangement reactions in the gas phase triggered by electron attachment

Bond formation and rearrangement reactions in gas phase electron attachment were studied through dissociative electron attachment (DEA) to pentafluorotoluene (PFT), pentafluoroaniline (PFA) and pentafluorophenol (PFP) in the energy range 0-14 eV. In the case of PFA and PFP, the dominant processes involve formation of [M - HF](-) through the loss of neutral HF. This fragmentation channel is most efficient at low incident electron energy and for PFP it is accompanied by a substantial conformational change of the anionic fragment. At higher energy, HF loss is also observed as well as a number of other fragmentation processes. Thermochemical threshold energies have been computed for all the observed fragments and classical trajectories of the electron attachment process were calculated to elucidate the fragmentation mechanisms. For the dominant reaction channel leading to the loss of HF from PFP, the minimum energy path was calculated using the nudged elastic band method.

Proton irradiation of DNA nucleosides in the gas phase

The four DNA nucleosides guanosine, adenosine, cytidine and thymidine have been produced in the gas phase by a laser thermal desorption source, and irradiated by a beam of protons with 5 keV kinetic energy. The molecular ions as well as energetic neutrals formed have been analyzed by mass spectrometry in order to shed light on the ionization and fragmentation processes triggered by proton collision. A range of 8-20 eV has been estimated for the binding energy of the electron captured by the proton. Glycosidic bond cleavage between the base and sugar has been observed with a high probability for all nucleosides, resulting in predominantly intact base ions for guanosine, adenosine, and cytidine but not for thymidine where intact sugar ions are dominant. This behavior is influenced by the ionization energies of the nucleobases (G < A < C < T), which seems to determine the localization of the charge following the initial ionization. This charge transfer process can also be inferred from the production of protonated base ions, which have a similar dependence on the base ionization potential. Other dissociation pathways have also been identified, including further fragmentation of the base and sugar moieties for thymidine and guanosine, respectively, and partial breakup of the sugar ring without glycosidic bond cleavage mainly for adenosine and cytidine. These results show that charge localization following ionization by proton irradiation is important in determining dissociation pathways of isolated nucleosides, which could in turn influence direct radiation damage in DNA.

Ultrafast Non-Radiative Decay of Gas-Phase Nucleosides

The ultrafast photo-physical properties of DNA are crucial in providing a stable basis for life. Although the DNA bases efficiently absorb ultraviolet (UV) radiation, this energy can be dissipated to the surrounding environment by the rapid conversion of electronic energy to vibrational energy within about a picosecond. The intrinsic nature of this internal conversion process has previously been demonstrated through gas phase experiments on the bases, supported by theoretical calculations. De-excitation rates appear to be accelerated when individual bases are hydrogen bonded to solvent molecules or their complementary Watson-Crick pair. In this paper, the first gas-phase measurements of electronic relaxation in DNA nucleosides following UV excitation are reported. Using a pump-probe ionization scheme, the lifetimes for internal conversion to the ground state following excitation at 267 nm are found to be reduced by around a factor of two for adenosine, cytidine and thymidine compared with the isolated bases. These results are discussed in terms of a recent proposition that a charge transfer state provides an additional internal conversion pathway mediated by proton transfer through a sugar to base hydrogen bond.

LIAD-fs: A novel method for studies of ultrafast processes in gas phase neutral biomolecules

A new experimental technique for femtosecond (fs) pulse studies of gas phase biomolecules is reported. Using Laser-Induced Acoustic Desorption (LIAD) to produce a plume of neutral molecules, a time-delayed fs pulse is employed for ionisation/fragmentation, with subsequent products extracted and mass analysed electrostatically. By varying critical laser pulse parameters, this technique can be used to implement control over molecular fragmentation for a range of small biomolecules, with specific studies of amino acids demonstrated.

First Detection of Gas-phase Methanol in a Protoplanetary Disk

The first detection of gas-phase methanol in a protoplanetary disk (TW Hya) is presented. In addition to being one of the largest molecules detected in disks to date, methanol is also the first disk organic molecule with an unambiguous ice chemistry origin. The stacked methanol emission, as observed with the Atacama Large Millimeter/submillimeter Array, is spectrally resolved and detected across six velocity channels (>3σ), reaching a peak signal-to-noise of 5.5σ, with the kinematic pattern expected for TW Hya. Using an appropriate disk model, a fractional abundance of 3 x 10^-12 – 4 x 10^-11 (with respect to H₂) reproduces the stacked line profile and channel maps, with the favored abundance dependent upon the assumed vertical location (midplane versus molecular layer). The peak emission is offset from the source position, suggesting that the methanol emission has a ring-like morphology: the analysis here suggests it peaks at ≈30 au, reaching a column density ≈3–6 x 10¹² cm⁻². In the case of TW Hya, the larger (up to millimeter-sized) grains, residing in the inner 50 au, may thus host the bulk of the disk ice reservoir. The successful detection of cold gas-phase methanol in a protoplanetary disk implies that the products of ice chemistry can be explored in disks, opening a window into studying complex organic chemistry during planetary system formation.

Continuous flow gas phase photoreforming of methanol at elevated reaction temperatures sensitised by Pt/TiO2

Gas phase photoreforming of methanol using a Pt/TiO2 photocatalyst has been performed under flow conditions at elevated temperatures. Comparing the activity of the reforming process as a function of temperature under dark and irradiated conditions shows a significant enhancement in the rate of H2 production using the photo-assisted conditions at temperatures between 100-140 °C. At higher temperatures, the effect of irradiation is small with the process dominated by the thermal process. Deactivation of the catalyst was observed under irradiation but the catalyst was easily regenerated using an oxygen treatment at 120 °C. Diffuse Reflectance Infra-red Fourier Transform Spectroscopy (DRIFTS) showed that the activity of the catalyst could be correlated with the presence of the photogenerated trapped electrons. In addition, lower amounts of CO adsorbed on Pt, compared to those observed in the dark reaction, were found for the UV-irradiated systems. It is proposed that CO and adsorbed intermediates, such as formate, can act as inhibitors in the photoreforming process and this is further supported by the observation that, before and after the regeneration process in O2, the CO and surface adsorbed organic intermediate products are removed and the activity is recovered.

Evaluation of Pt and Re oxidation state in a pressurized reactor: difference in reduction between gas and liquid phase

Determination of metal oxidation state under relevant working conditions is crucial to understand catalytic behaviour. The reduction behaviour of Pt and Re was evaluated simultaneously as a function of support and solvent in a pressurized reactor (autoclave). The bimetallic catalysts are used in selective hydrogenation of carboxylic acids and amides. Gas phase reduction reduced the metals more efficiently, in particular Pt.

Bimetallic effects in the liquid phase hydrogenation of 2-butanone

A series of bimetallic Ru-containing monometallic and bimetallic catalysts were prepared and tested for their activity for the hydrogenation of 2-butanone to 2-butanol at 30 °C and 3 bar H2. RuPt bimetallic catalysts were the most active for the reaction, with a ratio of 5 wt% Ru:1 wt% Pt on activated carbon (AC) found to be optimum. The activity of this bimetallic catalyst was more than double that of the sum of the activities of the monometallic Ru and Pt catalysts, providing evidence of a “bimetallic” effect. Structural analysis of the bimetallic catalysts revealed that they consisted of clusters of particles of the order of 1–2 nm. Extended X-ray absorption fine structure analysis showed that there were two types of particle on the surface of the bimetallic RuPt catalyst, specifically monometallic Ru and bimetallic RuPt particles. For the bimetallic particles, it was possible to fit the data with a model in which a Ru core of 1.1 nm is enclosed by two Pt-rich layers, the outer layer containing only 13 at% Ru. Pretreatment of the monometallic and bimetallic catalysts in hydrogen had a significant effect on the activity. Both the bimetallic and monometallic Ru-based catalysts showed a trend of decreasing activity with increasing temperature of prereduction in hydrogen. This loss of activity was almost fully reversible by exposure of the catalysts to air after reduction. The changing activity with exposure to different gas phase environments could not be attributed to changes in particle size or surface composition. It is proposed that the introduction of hydrogen results in a gradual smoothing of the surface and loss of defect sites; this process being reversible on introduction of air. These defect sites are particularly important for the dissociative adsorption of hydrogen, potentially the rate-determining step in this reaction.