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1.
Selenium affects mercury ligand environment in terrestrial food chain – a XAS study
Katarina Vogel Mikuš, Alojz Kodre, Iztok Arčon, Anja Kavčič, 2022, published scientific conference contribution abstract

Abstract: Selenium (Se) supplied in inorganic form (as selenate or selenite) was shown to decrease mercury (Hg) toxicity by forming HgSe in soils as well as in animal and human tissues, while for plants there is no evidence of Hg-Se complexation. Although Se in not an essential element for plants it was shown to counteract various abiotic stresses when applied at trace amounts. The aim of this work was therefore to study physiological responses and Hg speciation in plant/ fungi-animal food chain. Lettuce (Lactuca sativa) and porcini mushrooms (Boletus edulis) were taken as model plant/ fungal species and Spanish slug (Arion vulgaris) as a model animal species. The plants, fed to the slugs, were grown in HgCl2 contaminated soil or soil from the vicinity of Hg mine in Idrija with traces of HgS and methyl Hg). Physiological parameters of plants and slugs were monitored during the experiment. At the end the biological material was frozen in LN2 and freeze dried. Hg L3-edge (12284 eV) XANES and EXAFS spectra of the biological samples and standards were measured at liquid helium temperature in fluorescence detection mode at the BM30B beamline of the ESRF synchrotron in Grenoble, using the 30-segment germanium solid state detector [1]. The results showed that addition of Se alleviated Hg toxic effects in the food chain started at HgCl2-contaminated soil, while for the soil from Idrija, containing low amounts of highly toxic methyl-Hg, the beneficial effect was less prominent [2]. No Hg-Se complexes were detected in plants, while in mushrooms and slugs the complexation was confirmed. Addition of Se to the plants, however, changed Hg ligand environment in plant tissues from sulphur to nitrogen ligands. Hg and Se both target the -SH functional groups in the plant tissues, so toxic effects of Hg are rather enhanced than alleviated by addition of Se. Nevertheless, the addition of Se to the plants is beneficial for higher trophic levels and lowers Hg toxicity for the primary consumers, the slugs.
Keywords: mercury, toxicity, ligand environment, XANES, EXAFS, food chain, plant, slug, fungi
Published in RUNG: 05.12.2022; Views: 1186; Downloads: 0
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2.
Photoexcitation processes in atoms
Alojz Kodre, Iztok Arčon, Jana Padežnik Gomilšek, 2021, independent scientific component part or a chapter in a monograph

Abstract: Photoelectric absorption is characterized by a smooth power-law decrease of the cross section with photon energy. Absorption edges reveal rich structure, which continues into the high-energy side. The quasiperiodic signal, superposed onto the smooth basis, due to scattering of the photoelectron on the neighbours of the target atom provides the basis for the structural (XAFS) analysis of the material. Irregular tiny resonances and edges that appear over the same general range as XAFS are recognized as intra-atomic effects: multielectron excitations (MEE) owing to correlated motion in the electronic cloud. The systematic study of MEE began on noble gases and metallic vapours, both of which are gases of free atoms. With some extremely strong MEE, mostly coexcitations of the subvalence d and f electrons, the structural XAFS analysis may be compromised; hence, there is a need to independently determine the MEE signal, the atomic absorption background (AAB) for the analyzed element, and remove it prior to analysis. In view of the scarcity of elements which can practically be prepared in a free-atom gas state, several approaches to approximate the AAB have been developed: analysis of disordered compounds, where the weak and simple XAFS signal can be modelled and removed, and correlation analysis of the absorption spectra of several independent samples, where the AAB is extracted in an iterative procedure.
Keywords: photoexcitation, XAFS, multielectron excitations, atomic absorption background
Published in RUNG: 15.12.2021; Views: 1529; Downloads: 0
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3.
X-ray absorption spectroscopy set-up for unstable gases: A study of 5p Hydrides
Robert Hauko, Jana Padežnik Gomilšek, Alojz Kodre, Iztok Arčon, 2020, original scientific article

Abstract: An absorption cell is constructed for x-ray absorption spectroscopy of reactive, unstable or hazardous gases at room temperature. In conjunction with in-situ micro-synthesis technique relying on handling the gas in syringes it enabled a first measurement of x-ray absorption spectra in the region of K and L edges for the series of hydrides of 5p elements (SnH4, SbH3, TeH2, HI). The signal-to-noise ratio above 103 was achieved, whereby fine detail is discerned in the spectra, in particular the small sharp features above each absorption edge, testifying of coexcitations of outer electrons in the core photoeffect.
Keywords: X-ray absorption spectroscopy Micro-synthesis absorption cell Gaseous hydrides Multielectron photoexcitations
Published in RUNG: 10.02.2020; Views: 3292; Downloads: 0
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4.
Localization, ligand environment, bioavailability and toxicity of mercury in Boletus spp. and Scutiger pes-caprae mushrooms
Anja Kavčič, Klemen Mikuš, Marta Debeljak, Johannes Teun van Elteren, Iztok Arčon, Alojz Kodre, Peter Kump, Andreas-Germanos Karydas, Alessandro Migliori, Mateusz Czyzycki, Katarina Vogel-Mikuš, 2019, original scientific article

Abstract: This study provides information on mercury (Hg) localization, speciation and ligand environment in edible mushrooms: Boletus edulis, B. aereus and Scutiger pes-caprae collected at non-polluted and Hg polluted sites, by LA-ICP-MS, SR-μ-XRF and Hg L3-edge XANES and EXAFS. Mushrooms (especially young ones) collected at Hg polluted sites can contain more than 100 μg Hg g−1 of dry mass. Imaging of the element distribution shows that Hg accumulates mainly in the spore-forming part (hymenium) of the cap. Removal of hymenium before consumption can eliminate more than 50% of accumulated Hg. Mercury is mainly coordinated to di-thiols (43–82%), followed by di-selenols (13–35%) and tetra-thiols (12–20%). Mercury bioavailability, as determined by feeding the mushrooms to Spanish slugs (known metal bioindicators owing to accumulation of metals in their digestive gland), ranged from 4% (S. pes-caprae) to 30% (B. aereus), and decreased with increasing selenium (Se) levels in the mushrooms. Elevated Hg levels in mushrooms fed to the slugs induced toxic effects, but these effects were counteracted with increasing Se concentrations in the mushrooms, pointing to a protective role of Se against Hg toxicity through HgSe complexation. Nevertheless, consumption of the studied mushroom species from Hg polluted sites should be avoided.
Keywords: edible mushrooms, HgSe complex, imaging of elemental distribution, LA-ICP-MS, alpha-XRF, XAS
Published in RUNG: 24.10.2019; Views: 3164; Downloads: 0
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5.
Effects of the molecular potential on coexcitations of valence electrons in the K-shell photoeffect of 3p and 4p elements
Robert Hauko, Jana Padežnik Gomilšek, Alojz Kodre, Iztok Arčon, Giuliana Aquilanti, 2019, original scientific article

Abstract: Photoabsorption spectra of gaseous hydrides of 3p (PH3, H2S, HCl) and 4p elements (GeH4, AsH3 , H2Se, HBr) are measured in the energy region within 50 eV above the K edge, to study coexcitations of valence electrons by photoeffect in the K shell. The analysis of the valence coexcitations is extended to Ar, Kr, and SiH4. Relative probabilities and energies of states in the individual coexcitation channels are recovered by modeling the spectral features with a minimal ansatz based on the features in the contiguous noble gas. The extracted parameters are compared to the results of theoretical calculations for molecules (ORCA code) and free atoms (Hartree-Fock code). The experimental results confirm that the valence coexcitations in the 3p and 4p hydride molecules can be satisfactorily described by a two-step process, with the shake of the outer electron following the excitation of the core electron. The total probability—relative to the K-edge jump—of the shake-up processes shows a steady decrease from 19% in Si to 14% in Cl, and from 15% in Ge to 12% in Br. The experimental values for Ar (12%) and Kr (10%) are in accord with the trend. The dominant contribution is the transition to quasiatomic orbitals, in contrast with the deeper coexcitation channels in hydride molecules where transition to molecular orbitals prevails.
Keywords: X-ray absorption spectra, gaseous hydrides, 3p K-edge spectra, DFT
Published in RUNG: 05.09.2019; Views: 2776; Downloads: 0
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6.
7.
K-edge absorption spectra of isoelectronic gaseous hydrides: a combination of atomic and molecular channels
Robert Hauko, Jana Padežnik Gomilšek, Alojz Kodre, Iztok Arčon, Giuliana Aquilanti, 2018, published scientific conference contribution abstract

Abstract: The fine detail in the x-ray absorption spectra in the energy region of absorption edges provides the insight into the mechanism of inner-shell photoexcitation: in particular in spectra of free atoms or simple molecules, the simplest being gaseous hydrides [1-2]. Measured K edge absorption spectra of hydrides of 3p (PH3, H2S in HCl) and 4p (GeH4, AsH3, H2Se, HBr) elements, and published data of 2p hydrides (CH4, NH3, H2O, HF) as well as SiH4 [3-6] and the noble gases at the end of the isoelectronic series (Ne, Ar, Kr) are compared to the respective calculated spectra, obtained by atomic HF86, GRASP codes [7] and molecular DFT (Density functional theory) ORCA code [8]. For a clearer view of intraatomic processes, the weak and simple structural (XAFS) signal of the molecule is removed from the spectra. Among the spectral features below the continuum limit, those with the lowest energy belong to the transition of the core electron to the lowermost free orbitals with the molecular character. They are, as a rule, wider than the transitions to the higher orbitals with prevailing atomic character. The theoretical description with DFT code without specific adaptations is sufficient for a qualitative picture of the pre-edge structure. The fine structure immediately above the K edge stems from the coexcitation of valence electrons. We have proved that the coexcitations can be explained as a two-step process: the inner-shell photoeffect followed by the shake-up of a valence electron predominantly to a free atomic orbital. This process is markedly different from coexcitations of more tightly bound electrons [9]. In the collection of consecutive and homologous data, analyzed by a common procedure, the reaction channels can be identified with better precision and reliability than in analysis of individual spectra. Our analysis showed that the energies and probabilities of single-electron transitions into the molecular orbitals are strongly affected by the symmetry of the molecule, essentially in the same way in 3p and 4p homologues, but not in 2p homologues with a stronger influence of the core charge. In transitions to atomic orbitals the influence of the molecular field is negligible.
Keywords: hidridi, rentgenska spektroskopija, XAFS
Published in RUNG: 12.09.2018; Views: 3707; Downloads: 0
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8.
K-edge absorption spectra of gaseous hydrides
Alojz Kodre, Robert Hauko, Jana Padežnik Gomilšek, Iztok Arčon, Giuliana Aquilanti, 2018, published scientific conference contribution abstract

Abstract: X-ray absorption spectra in the energy region of absorption edges reveal fine details of the mechanism of inner-shell photoexcitation: in particular in spectra of free atoms or simple molecules, the simplest being gaseous hydrides [1-2]. In a collection of data from consecutive and homologous elements, analyzed by a common procedure, the reaction channels can be identified with better precision and reliability than in analysis of individual spectra. Absorption spectra of the hydrides of 3p elements (PH3, H2S in HCl) were measured at the XAFS beamline of the Elettra synchrotron in Trieste: a new type of adjustable absorption cell for measurement of noxious gases at room temperature and at low photon energies was developed for the purpose. For the analysis, data from an earlier experiment on 4p hydrides (GeH4, AsH3, H2Se, HBr), and published data of 2p hydrides (CH4, NH3, H2O, HF) [3-4] as well as SiH4 and the noble gases concluding the isoelectronic series (Ne, Ar, Kr) were adopted. The spectra are compared to respective calculated spectra, obtained by atomic HF86, GRASP codes and molecular DFT (Density functional theory) ORCA code [5]. Our analysis of the pre-edge structures showed that the energies and probabilities of singleelectron transitions into the lowermost orbitals with the molecular character were strongly affected by the symmetry of the molecule, essentially in the same way in 3p and 4p homologues, but not in 2p homologues with a stronger influence of the core charge. In transitions to higher orbitals with prevailing atomic character the influence of the molecular field is negligible. The fine structure immediately above the K edge stems from the coexcitation of valence electrons. These coexcitations can be explained as a two-step process: the inner-shell photoeffect followed by the shake-up of a valence electron predominantly to a free atomic orbital. The process is markedly different from coexcitations of more tightly bound electrons [3]. The results of relative shake-up probabilities can be compared to results of emission spectroscopies, the probabilities of double excitation to bound states show a correlation with the dissociation probability of the molecule.
Keywords: večelektronske vzbuditve, hidridi, rentgenska absorpcijska spektroskopija
Published in RUNG: 12.09.2018; Views: 3977; Downloads: 0
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9.
Nickel coordination in hyperaccumulator plants studied by XANES and EXAFS
Jana Padežnik Gomilšek, Katarina Vogel-Mikuš, Alojz Kodre, Iztok Arčon, 2018, published scientific conference contribution abstract

Keywords: nickel, hyperaccumulator plants
Published in RUNG: 12.09.2018; Views: 2952; Downloads: 0
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10.
X-ray spectrometry in plant biology
Katarina Vogel-Mikuš, Iztok Arčon, Alojz Kodre, Anja Kavčič, Peter Kump, Primož Pelicon, 2018, published scientific conference contribution abstract (invited lecture)

Abstract: Trace elements are essential components of living systems, but at the same time they can be toxic at concentrations beyond those necessary for their biological functions. In addition, the toxicity can be extended to other non-essential elements of very similar atomic characteristics that can mimic the properties of a trace element. Trace element malnutrition affects more than half of the world’s population, while on the other hand industrialization, traffic and extensive use of fertilizers have resulted in exceedingly high concentrations of non-essential elements in food crops, posing risks to human health. In order to be able to develop and improve phyto-technologies that enable production of safe and quality food, knowledge on the basic mechanisms involved in trace and non-essential element uptake, transport, accumulation and ligand environment in plants is needed. Such studies are nowadays supported by highly sophisticated X-ray based techniques, such as synchrotron based X-ray fluorescence spectrometry, proton induced X-ray emission and X-ray absorption spectroscopy, enabling imaging of element distribution and determination of speciation and ligand environment of trace elements in biological tissues and cells with high spatial resolution and sensitivity. Selected case studies of metal distribution and speciation in selected model and crop plants, achieved by interdisciplinary work, will be presented.
Keywords: X-ray spectrometry, plants, XANES, EXAFS
Published in RUNG: 12.09.2018; Views: 3356; Downloads: 0
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