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11.
An extracellular polymeric substance quickly chelates mercury(II) with N-heterocyclic groups
Claudia Faleri, Dario Battistel, Salvatore Daniale, Michele Gallo, Franco Baldi, Alojz Kodre, Iztok Arčon, 2017, izvirni znanstveni članek

Opis: A strain of Klebsiella oxytoca DSM 29614 is grown on sodium citrate in the presence of 50 mg l−1 of Hg as Hg(NO3)2. During growth, the strain produces an extracellular polymeric substance (EPS), constituted by a mixture of proteins and a specific exopolysaccharide. The protein components, derived from the outer membrane of cells, are co-extracted with the extracellular exopolysaccharide using ethanol. The extracted EPS contains 7.5% of Hg (total amount). This indicates that EPS is an excellent material for the biosorption of Hg2+, through chemical complexation with the EPS components. The binding capacity of these species towards Hg2+ is studied by cyclic voltammetry, and Hg L3-edge XANES and EXAFS spectroscopy. The results found indicate that Hg2+ is mainly bound to the nitrogen of the imidazole ring or other N-heterocycle compounds. The hydroxyl moities of sugars and/or the carboxyl groups of two glucuronic acids in the polysaccharide can also play an important role in sequestring Hg2+ ions. However, N-heterocyclic groups of proteins bind Hg2+ faster than hydroxyl and carboxyl groups of the polysaccharide.
Najdeno v: osebi
Ključne besede: Klebsiella oxytoca, Biosorption, Proteins, Polysaccharide, Cyclic voltammetry, EXAFS analysis
Objavljeno: 03.03.2017; Ogledov: 2787; Prenosov: 0
.pdf Polno besedilo (1,66 MB)

12.
Edge profiles in K shell photoabsorption spectra of gaseous hydrides of 3p elements and homologues
Giuliana Aquilanti, Alojz Kodre, Iztok Arčon, Robert Hauko, Jana Padežnik Gomilšek, izvirni znanstveni članek

Opis: Photoabsorption spectra of gaseous hydrides of 3p elements (PH3, H2S, HCl) are measured in the energy region of photoexcitations pertaining to K edge. The analysis of the edge profile is extended to hydrides of 4p series (GeH4, AsH3, H2Se, HBr) from an earlier experiment, and to published spectra of 2p hydrides (CH4, NH3, H2O, HF) and noble gases Ar, Kr and Ne and SiH4. The edge profiles are modelled with a linear combination of lorentzian components, describing excitations to individual bound states and to continuum. Transition energies and probabilities are also calculated in the non-relativistic molecular model of the ORCA code, in good agreement with the experiment. Edge profiles in the heavier homologues are closely similar, the symmetry of the molecule governs the transitions to the lowest unoccupied orbitals. In 2p series the effect of the strong nuclear potential prevails. Transitions to higher, atomic-like levels remain very much the same as in free atoms.
Najdeno v: osebi
Ključne besede: X-ray absorption spectra, gaseous hydrides, 3p K-edge spectra, DFT
Objavljeno: 23.08.2017; Ogledov: 1978; Prenosov: 0
.pdf Polno besedilo (703,57 KB)

13.
X-ray spectrometry in plant biology
Primož Pelicon, Peter Kump, Anja Kavčič, Alojz Kodre, Iztok Arčon, Katarina Vogel-Mikuš, 2018, objavljeni povzetek znanstvenega prispevka na konferenci (vabljeno predavanje)

Opis: 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.
Najdeno v: osebi
Ključne besede: X-ray spectrometry, plants, XANES, EXAFS
Objavljeno: 12.09.2018; Ogledov: 1787; Prenosov: 0
.pdf Polno besedilo (62,44 KB)

14.
Nickel coordination in hyperaccumulator plants studied by XANES and EXAFS
Jana Padežnik Gomilšek, Katarina Vogel-Mikuš, Alojz Kodre, Iztok Arčon, 2018, objavljeni povzetek znanstvenega prispevka na konferenci

Najdeno v: osebi
Ključne besede: nickel, hyperaccumulator plants
Objavljeno: 12.09.2018; Ogledov: 1417; Prenosov: 0
.pdf Polno besedilo (64,89 KB)

15.
K-edge absorption spectra of gaseous hydrides
Iztok Arčon, Jana Padežnik Gomilšek, Robert Hauko, Alojz Kodre, Giuliana Aquilanti, 2018, objavljeni povzetek znanstvenega prispevka na konferenci

Opis: 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.
Najdeno v: osebi
Ključne besede: večelektronske vzbuditve, hidridi, rentgenska absorpcijska spektroskopija
Objavljeno: 12.09.2018; Ogledov: 1957; Prenosov: 0
.pdf Polno besedilo (88,18 KB)

16.
K-edge absorption spectra of isoelectronic gaseous hydrides: a combination of atomic and molecular channels
Alojz Kodre, Jana Padežnik Gomilšek, Robert Hauko, Iztok Arčon, Giuliana Aquilanti, 2018, objavljeni povzetek znanstvenega prispevka na konferenci

Opis: 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.
Najdeno v: osebi
Ključne besede: hidridi, rentgenska spektroskopija, XAFS
Objavljeno: 12.09.2018; Ogledov: 1840; Prenosov: 0
.pdf Polno besedilo (63,16 KB)

17.
18.
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, izvirni znanstveni članek

Opis: 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.
Najdeno v: osebi
Ključne besede: X-ray absorption spectra, gaseous hydrides, 3p K-edge spectra, DFT
Objavljeno: 05.09.2019; Ogledov: 1256; Prenosov: 0
.pdf Polno besedilo (926,96 KB)

19.
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, izvirni znanstveni članek

Opis: 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.
Najdeno v: osebi
Ključne besede: edible mushrooms, HgSe complex, imaging of elemental distribution, LA-ICP-MS, alpha-XRF, XAS
Objavljeno: 24.10.2019; Ogledov: 1562; Prenosov: 0
.pdf Polno besedilo (1,79 MB)

20.
X-ray absorption spectroscopy set-up for unstable gases: A study of 5p Hydrides
Robert Hauko, Jana Padežnik Gomilšek, Alojz Kodre, Iztok Arčon, 2020, izvirni znanstveni članek

Opis: 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.
Najdeno v: osebi
Ključne besede: X-ray absorption spectroscopy Micro-synthesis absorption cell Gaseous hydrides Multielectron photoexcitations
Objavljeno: 10.02.2020; Ogledov: 1325; Prenosov: 0
.pdf Polno besedilo (756,39 KB)

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