Low molecular weight halocarbons in the Humber and Rhine estuaries determined using a new purge-and-trap gas chromatographic method

A number of chlorinated and brominated low molecular weight hydrocarbons (halocarbons) have been measured in and adjacent to the North Sea estuaries of the Humber and the Rhine. The measurements have been carried out using a newly constructed purge-and-trap sample work-up system coupled to megabore gas chromatography with electron capture detection. The results show that whereas the Humber is a pronounced source of the anthropogenic halocarbons carbon tetrachloride and perchloroethylene, the input from the Rhine into the North Sea of these compounds is more modest. Some halocarbons normally considered as mainly or even exclusively of natural origin are released from the two investigated estuaries into the North Sea. A distinct patch of high concentrations of the naturally produced compound bromoform was observed in the southwestern North Sea. The results have also been used to examine some of the halocarbons for common sources.

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.

Improving a gas ion source for C-14 AMS

For more than 4 years, gaseous samples of 1-50 mu g carbon have been routinely measured with the gas ion source of the small AMS (Accelerator Mass Spectrometer) facility MICADAS (Mini CArbon DAting System) at ETH Zurich. The applied measurement technique offers a simple and fast way of C-14 measurements without the need of sample graphitization. A major drawback of gaseous C-14 measurements, however, is the relatively low negative ion current, which results in longer measurement times and lower precision compared to graphitized samples. In December 2009, a new, improved Cs sputter ion source was installed at MICADAS and we began to optimize conditions for the measurement of gaseous samples. C-12(-) currents from the new ion source were improved from initially 3 to 12-15 mu A for routine measurements and the negative ion yield was increased by a factor of 2, reaching 8 on average during routine operation. Moreover, the new measurement settings enable a doubled CO2 flow, thus substantially reducing measurement times. The achieved performance allows closing the sample size gap between gaseous and solid samples and makes the gas ion source a promising tool for dating with a measurement precision of 5 parts per thousand on samples as small as 50 mu g carbon. (C) 2012 Elsevier B.V. All rights reserved.

A versatile gas interface for routine radiocarbon analysis with a gas ion source

In 2010 more than 600 radiocarbon samples were measured with the gas ion source at the MIni CArbon DAting System (MICADAS) at ETH Zurich and the number of measurements is rising quickly. While most samples contain less than 50 mu g C at present, the gas ion source is attractive as well for larger samples because the time-consuming graphitization is omitted. Additionally, modern samples are now measured down to 5 per-mill counting statistics in less than 30 min with the recently improved gas ion source. In the versatile gas handling system, a stepping-motor-driven syringe presses a mixture of helium and sample CO2 into the gas ion source, allowing continuous and stable measurements of different kinds of samples. CO2 can be provided in four different ways to the versatile gas interface. As a primary method. CO2 is delivered in glass or quartz ampoules. In this case, the CO2 is released in an automated ampoule cracker with 8 positions for individual samples. Secondly, OX-1 and blank gas in helium can be provided to the syringe by directly connecting gas bottles to the gas interface at the stage of the cracker. Thirdly, solid samples can be combusted in an elemental analyzer or in a thermo-optical OC/EC aerosol analyzer where the produced CO2 is transferred to the syringe via a zeolite trap for gas concentration. As a fourth method, CO2 is released from carbonates with phosphoric acid in septum-sealed vials and loaded onto the same trap used for the elemental analyzer. All four methods allow complete automation of the measurement, even though minor user input is presently still required. Details on the setup, versatility and applications of the gas handling system are given. (C) 2012 Elsevier B.V. All rights reserved.

Microstructural characterization of electron beam evaporated tungsten oxide films for gas sensing applications

Tungsten trioxide is one of the potential semiconducting materials used for sensing NH3, CO, CH4 and acetaldehyde gases. The current research aims at development, microstructural characterization and gas sensing properties of thin films of Tungsten trioxide (WO3). In this paper, we intend to present the microstructural characterization of these films as a function of post annealing heat treatment. Microstructural and elemental analysis of electron beam evaporated WO3 thin films and iron doped WO3 films (WO3:Fe) have been carried out using analytical techniques such as Transmission electron microscopy, Rutherford Backscattered Spectroscopy and XPS analysis. TEM analysis revealed that annealing at 300oC for 1 hour improves cyrstallinity of WO3 film. Both WO3 and WO3:Fe films had uniform thickness and the values corresponded to those measured during deposition. RBS results show a fairly high concentration of oxygen at the film surface as well as in the bulk for both films, which might be due to adsorption of oxygen from atmosphere or lattice oxygen vacancy inherent in WO3 structure. XPS results indicate that tungsten exists in 4d electronic state on the surface but at a depth of 10 nm, both 4d and 4f electronic states were observed. Atomic force microscopy reveals nanosize particles and porous structure of the film. This study shows e-beam evaporation technique produces nanoaparticles and porous WO3 films suitable for gas sensing applications and doping with iron decreases the porosity and particle size which can help improve the gas selectivity.

Electron beam evaporation of tungsten oxide films for gas sensors

Pure and Iron incorporated nanostructured Tungsten Oxide (WO3) thin films were investigated for gas sensing applications using noise spectroscopy. The WO3 sensor was able to detect lower concentrations (1 ppm-10 ppm) of NH3, CO, CH4 and Acetaldehyde gases at higher operating temperatures between 100oC to 250oC. The response of the WO3 sensor to NH3, CH4 and Acetaldehyde at lower temperatures (50oC-100oC) was significant when the sensor was photo-activated using blue-light emitting diode (Blue-LED). The WO3 with Fe (WO3:Fe) was found to show some response to Acetaldehyde gas only at relatively higher operating temperature (250oC) and gas concentration of 10 ppm.

Thin film deposition and characterization of pure and iron-doped electron-beam evaporated tungsten oxide for gas sensors

Pure Tungsten Oxide (WO3) and Iron-doped (10 at%) Tungsten Oxide (WO3:Fe) nanostructured thin films were prepared using a dual crucible Electron Beam Evaporation techniques. The films were deposited at room temperature in high vacuum condition on glass substrate and post-heat treated at 300 oC for 1 hour. From the study of X-ray diffraction and Raman the characteristics of the as-deposited WO3 and WO3:Fe films indicated non-crystalline nature. The surface roughness of all the films showed in the order of 2.5 nm as observed using Atomic Force Microscopy (AFM). X-Ray Photoelectron Spectroscopy (XPS) analysis revealed tungsten oxide films with stoichiometry close to WO3. The addition of Fe to WO3 produced a smaller particle size and lower porosity as observed using Transmission Electron Microscopy (TEM). A slight difference in optical band gap energies of 3.22 eV and 3.12 eV were found between the as-deposited WO3 and WO3:Fe films, respectively. However, the difference in the band gap energies of the annealed films were significantly higher having values of 3.12 eV and 2.61 eV for the WO3 and WO3:Fe films, respectively. The heat treated samples were investigated for gas sensing applications using noise spectroscopy and doping of Fe to WO3 reduced the sensitivity to certain gasses. Detailed study of the WO3 and WO3:Fe films gas sensing properties is the subject of another paper.

Electron beam evaporation of tungsten oxide films for gas sensors

Pure and Iron incorporated nanostructured Tungsten Oxide (WO3) thin films were investigated for gas sensing applications using noise spectroscopy. The WO3 sensor was able to detect lower concentrations (1 ppm-10 ppm) of NH3, CO, CH4 and Acetaldehyde gases at operating temperatures between 100 degrees celcius to 250 degrees celcius. The iron doped Tungsten Oxide sensor (WO3:Fe) showed some response to Acetaldehyde gas at relatively higher operating temperature (250 degrees celcius) and gas concentration of 10 ppm. The sensitivity of the WO3 sensor towards NH3, CH4 and Acetaldehyde at lower operating temperatures (50 degrees celcius - 100 degrees celcius) was significant when the sensor was photo-activated using blue-light emitting diode (Blue-LED). From the results, photo-activated WO3 thin film that operates at room temperature appeared to be a promising gas sensor. The overall results indicated that the WO3 sensor exhibited reproducibility for the detection of various gases and the WO3:Fe indicated some response towards Acetaldehyde gas.

Iron biogeochemistry and associated greenhouse gas evolution in a forested subtropical Australian coastal catchment : Poona Creek, Southeast Queensland

Iron (Fe) is the fourth most abundant element in the Earth’s crust. Excess Fe mobilization from terrestrial into aquatic systems is of concern for deterioration of water quality via biofouling and nuisance algal blooms in coastal and marine systems. Substantial Fe dissolution and transport involve alternate Fe(II) oxidation followed by Fe(III) reduction, with a diversity of Bacteria and Archaea acting as the key catalyst. Microbially-mediated Fe cycling is of global significance with regard to cycles of carbon (C), sulfur (S) and manganese (Mn). However, knowledge regarding microbial Fe cycling in circumneutral-pH habitats that prevail on Earth has been lacking until recently. In particular, little is known regarding microbial function in Fe cycling and associated Fe mobilization and greenhouse (CO2 and CH4, GHG) evolution in subtropical Australian coastal systems where microbial response to ambient variations such as seasonal flooding and land use changes is of concern. Using the plantation-forested Poona Creek catchment on the Fraser Coast of Southeast Queensland (SEQ), this research aimed to 1) study Fe cycling-associated bacterial populations in diverse terrestrial and aquatic habitats of a representative subtropical coastal circumneutral-pH (4–7) ecosystem; and 2) assess potential impacts of Pinus plantation forestry practices on microbially-mediated Fe mobilization, organic C mineralization and associated GHG evolution in coastal SEQ. A combination of wet-chemical extraction, undisturbed core microcosm, laboratory bacterial cultivation, microscopy and 16S rRNA-based molecular phylogenetic techniques were employed. The study area consisted primarily of loamy sands, with low organic C and dissolved nutrients. Total reactive Fe was abundant and evenly distributed within soil 0–30 cm profiles. Organic complexation primarily controlled Fe bioavailability and forms in well-drained plantation soils and water-logged, native riparian soils, whereas tidal flushing exerted a strong “seawater effect” in estuarine locations and formed a large proportion of inorganic Fe(III) complexes. There was a lack of Fe(II) sources across the catchment terrestrial system. Mature, first-rotation plantation clear-felling and second-rotation replanting significantly decreased organic matter and poorly crystalline Fe in well-drained soils, although variations in labile soil organic C fractions (dissolved organic C, DOC; and microbial biomass C, MBC) were minor. Both well-drained plantation soils and water-logged, native-vegetation soils were inhabited by a variety of cultivable, chemotrophic bacterial populations capable of C, Fe, S and Mn metabolism via lithotrophic or heterotrophic, (micro)aerobic or anaerobic pathways. Neutrophilic Fe(III)-reducing bacteria (FeRB) were most abundant, followed by aerobic, heterotrophic bacteria (heterotrophic plate count, HPC). Despite an abundance of FeRB, cultivable Fe(II)-oxidizing bacteria (FeOB) were absent in associated soils. A lack of links between cultivable Fe, S or Mn bacterial densities and relevant chemical measurements (except for HPC correlated with DOC) was likely due to complex biogeochemical interactions. Neither did variations in cultivable bacterial densities correlate with plantation forestry practices, despite total cultivable bacterial densities being significantly lower in estuarine soils when compared with well-drained plantation soils and water-logged, riparian native-vegetation soils. Given that bacterial Fe(III) reduction is the primary mechanism of Fe oxide dissolution in soils upon saturation, associated Fe mobilization involved several abiotic and biological processes. Abiotic oxidation of dissolved Fe(II) by Mn appeared to control Fe transport and inhibit Fe dissolution from mature, first-rotation plantation soils post-saturation. Such an effect was not observed in clear-felled and replanted soils associated with low SOM and potentially low Mn reactivity. Associated GHG evolution post-saturation mainly involved variable CO2 emissions, with low, but consistently increasing CH4 effluxes in mature, first-rotation plantation soil only. In comparison, water-logged soils in the riparian native-vegetation buffer zone functioned as an important GHG source, with high potentials for Fe mobilization and GHG, particularly CH4 emissions in riparian loam soils associated with high clay and crystalline Fe fractions. Active Fe–C cycling was unlikely to occur in lower-catchment estuarine soils associated with low cultivable bacterial densities and GHG effluxes. As a key component of bacterial Fe cycling, neutrophilic FeOB widely occurred in diverse aquatic, but not terrestrial, habitats of the catchment study area. Stalked and sheathed FeOB resembling Gallionella and Leptothrix were limited to microbial mat material deposited in surface fresh waters associated with a circumneutral-pH seep, and clay-rich soil within riparian buffer zones. Unicellular, Sideroxydans-related FeOB (96% sequence identity) were ubiquitous in surface and subsurface freshwater environments, with highest abundance in estuary-adjacent shallow coastal groundwater water associated with redox transition. The abundance of dissolved C and Fe in the groundwater-dependent system was associated with high numbers of cultivable anaerobic, heterotrophic FeRB, microaerophilic, putatively lithotrophic FeOB and aerobic, heterotrophic bacteria. This research represents the first study of microbial Fe cycling in diverse circumneutral-pH environments (terrestrial–aquatic, freshwater–estuarine, surface–subsurface) of a subtropical coastal ecosystem. It also represents the first study of its kind in the southern hemisphere. This work highlights the significance of bacterial Fe(III) reduction in terrestrial, and bacterial Fe(II) oxidation in aquatic catchment Fe cycling. Results indicate the risk of promotion of Fe mobilization due to plantation clear-felling and replanting, and GHG emissions associated with seasonal water-logging. Additional significant outcomes were also achieved. The first direct evidence for multiple biomineralization patterns of neutrophilic, microaerophilic, unicellular FeOB was presented. A putatively pure culture, which represents the first cultivable neutrophilic FeOB from the southern hemisphere, was obtained as representative FeOB ubiquitous in diverse catchment aquatic habitats.

Molecular dynamics study of ‘contact epitaxy’ in Ag clusters supported on a copper (001) surface

In this paper, the formation of heteroepitaxial interfacial layers was investigated by molecular dynamics simulation of soft silver particles landing on the (001) surface of single-crystal copper. In our simulations, the clusters Ag13, Ag55, Ag147 and Ag688 were chosen as projectiles. A small cluster will rearrange into an f.c.c. structure when it is supported on the substrate, due to the large value of its surface/volume ratio. Contact epitaxy appeared in large clusters. The characteristic structure of an epitaxial layer in large silver cluster shows the 〈111〉 direction to be the preferential orientation of heteroepitaxial layers on the surface because of the lattice mismatch between the cluster and the substrate. This was confirmed by studying soft landing events in other systems (Au/Cu and Al/Ni).

Hydroxyl radical formation in the gas phase oxidation of distonic 2-methylphenyl radical cations

The reactions of distonic 4-(N, N, N-trimethylammonium)-2-methylphenyl and 5-(N, N, N-trimethylammonium)-2-methylphenyl radical cations (m/z 149) with O-2 are studied in the gas phase using ion-trap mass spectrometry. Photodissociation (PD) of halogenated precursors gives rise to the target distonic charge-tagged methylphenyl radical whereas collision-induced dissociation (CID) is found to produce unreactive radical ions. The PD generated distonic radicals, however, react rapidly with O-2 to form \[M + O2](center dot+) and \[M + O-2 - OH](center dot+) ions, detected at m/z 181 and m/z 164, respectively. Quantum chemical calculations using G3SX(MP3) and M06-2X theories are deployed to examine key decomposition pathways of the 5-(N, N, N-trimethylammonium)-2-methylphenylperoxyl radical and rationalise the observed product ions. The prevailing product mechanism involves a 1,5- H shift in the peroxyl radical forming a QOOH-type intermediate that subsequently eliminates (OH)-O-center dot to yield charge-tagged 2-quinone methide. Our study suggests that the analogous process should occur for the neutral methylphenyl + O-2 reaction, thus serving as a plausible source of (OH)-O-center dot radicals in combustion environments. Grants: ARC/DP0986738, ARC/DP130100862

Formation of neutral C7H2 isomers from pour isomeric C7H2 radical anion precursors in the gas phase

Consideration of theoretical calculations \[E3LYP/aug-cc-pVDZ//B3LYP/6-31G(d)\] of the structures of ten C7H2 neutral isomers and the nine corresponding C7H2 radical anions have led us to synthesize four stable C7H2 radical anions in the ion source of our ZAB 2HF mass spectrometer, and to convert these to C7H2 neutrals. The four radical anion isomers prepared were (i) \[(HC equivalent to C)(2)C=C=C\](-.) \[from the reaction between (HC equivalent to C)(3)COCH3 and HO- \], (ii) \[HC=C=C=C=C=C=CH\](-.) \[from the reaction between HC equivalent to C-C equivalent to C-CD(OH)-C equivalent to CH and HO-\], (iii) \[C=C=C=C=C=C=CH2\](-.) \[from the reaction between DC equivalent to C-C equivalent to C-C equivalent to C-CH2OCH2CH3 and HO-\], and (iv) \[C equivalent to C-CH2-C equivalent to C-C equivalent to C\](-.) \[from the bis desilylation reaction of (CH3)(3)Si-C equivalent to C-CH2-C equivalent to C-C equivalent to C-Si (CH3)(3)With SF6-.\]. The four anions were further characterized by their collisional activation (negative ion) and charge reversal (CR, positive ion) mass spectra. The anions were converted into their corresponding neutrals by charge stripping, and the correspondence between the charge reversal (CR) and neutralization reionization (-NR+) mass spectra of each anion is taken as evidence that within the time frame of the -NR+ experiment (some 10(-6) s), each neutral is stable and undergoes no major rearrangement or interconversion to a more stable isomer. Theory and experiment are in accord for these systems.

Detection of the protein dimers, multiple monomeric states and hydrated forms of Plasmodium falciparum triosephosphate isomerase in the gas phase

Dimeric and monomeric forms of the enzyme triosephosphate isomerase (TIM) from Plasmodium falciparum (Pf) have been detected under conditions of nanoflow by electrospray mass spectrometry. The dimer (M = 55 663 Da) exhibits a narrow charge state distribution with intense peaks limited to values of 18(+) to 21(+), maximal intensity being observed for charge states 19(+) and 20(+). A monomeric species with a charge state distribution ranging from 11(+) to 16(+) is also observed, which may be assigned to folded dissociated subunits. Complete dimer dissociation results under normal electrospray condition. The effects of solution pH and source temperature have been investigated. The observation of four distinct charge state distributions which may be assigned to a dimer, folded monomer, partially folded monomer and unfolded monomer is reported. Circular dichromism and fluorescence studies of Pf TIM at low pH support the retention of substantial secondary and tertiary structures. Satellite peaks in mass spectra corresponding to hydrated species are also observed and isotope shift upon deuteration is demonstrated. The analysis of all available independent crystal structures of Pf TIM and TIMs from other organisms permits identification of structurally conserved water molecules. Hydration observed in the dimer and folded monomeric forms in the gas phase may correspond to these conserved sites.

Monte carlo simulation for molecular gas dynamics

The dynamics of low-density flows is governed by the Boltzmann equation of the kinetic theory of gases. This is a nonlinear integro-differential equation and, in general, numerical methods must be used to obtain its solution. The present paper, after a brief review of Direct Simulation Monte Carlo (DSMC) methods due to Bird, and Belotserkovskii and Yanitskii, studies the details of theDSMC method of Deshpande for mono as well as multicomponent gases. The present method is a statistical particle-in-cell method and is based upon the Kac-Prigogine master equation which reduces to the Boltzmann equation under the hypothesis of molecular chaos. The proposed Markoff model simulating the collisions uses a Poisson distribution for the number of collisions allowed in cells into which the physical space is divided. The model is then extended to a binary mixture of gases and it is shown that it is necessary to perform the collisions in a certain sequence to obtain unbiased simulation.