1. GasesAlojz Kodre, Iztok Arčon, Jana Padežnik Gomilšek, 2024, scientific entry in dictionary, encyclopaedia or lexicon Abstract: X-ray absorption spectroscopy of gases is seldom used for structural analysis,
except in as much as the extended X-ray absorption fine-structure (EXAFS)
signal is used to monitor some specific molecular process. Gas spectroscopy,
however, has been the main tool in the systematic study of higher-order
photoabsorption processes, multielectron photoexcitations (MEEs), which were
introduced with an experiment at the K edge of argon. Along with noble gases,
where MEEs are studied in the pure form, free of the structural signal,
measurements have been extended to monatomic metal vapours, although at the
cost of considerable experimental difficulties. Several types of absorption cells
have been devised, among them the ceramic double cell and the heat-pipe cell
for experiments in the low-energy region. In a high-temperature oven with
considerable technical refinement, edge profiles of nonvolatile metals were
measured up to 2500 K. Edge profiles and MEEs, which are strongly dependent
on electron correlation, provide sensitive tests of the theory of atomic and
molecular structure. Keywords: X-ray absorption spectroscopy, absorption cells, gas and vapour samples, multielectron photoexcitation, effects of electron
correlation Published in RUNG: 05.09.2024; Views: 616; Downloads: 4 Link to file This document has many files! More... |
2. Selenium affects mercury ligand environment in terrestrial food chain – a XAS studyKatarina 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: 2257; Downloads: 0 This document has many files! More... |
3. Photoexcitation processes in atomsAlojz 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: 2428; Downloads: 0 This document has many files! More... |
4. X-ray absorption spectroscopy set-up for unstable gases: A study of 5p HydridesRobert 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: 4476; Downloads: 0 This document has many files! More... |
5. Localization, ligand environment, bioavailability and toxicity of mercury in Boletus spp. and Scutiger pes-caprae mushroomsAnja 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: 5454; Downloads: 0 This document has many files! More... |
6. Effects of the molecular potential on coexcitations of valence electrons in the K-shell photoeffect of 3p and 4p elementsRobert 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: 3702; Downloads: 0 This document has many files! More... |
7. Recent advances in 2D imaging of element distribution in Plants by focused beam techniquesKatarina Vogel-Mikuš, Johannes Teun van Elteren, Marjana Regvar, Jitrin Chaiprapa, Boštjan Jenčič, Iztok Arčon, Alojz Kodre, Peter Kump, Anja Kavčič, Mitja Kelemen, Dino Metarapi, Marijan Nečemer, Primož Vavpetič, Primož Pelicon, Paula Pongrac, 2019, independent scientific component part or a chapter in a monograph Keywords: 2D Imiging, XRF, XANES, synchrotron light Published in RUNG: 05.09.2019; Views: 4115; Downloads: 0 This document has many files! More... |
8. K-edge absorption spectra of isoelectronic gaseous hydrides: a combination of atomic and molecular channelsRobert 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: 4792; Downloads: 0 This document has many files! More... |
9. K-edge absorption spectra of gaseous hydridesAlojz 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: 5159; Downloads: 0 This document has many files! More... |
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