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1.
Infrared spectra in amorphous alumina
Luigi Giacomazzi, Nikita S Shcheblanov, Mikhail E Povarnitsyn, Yanbo Li, Andraž Mavrič, Barbara Zupančič, Jože Grdadolnik, Alfredo Pasquarello, zaključena znanstvena zbirka raziskovalnih podatkov

Opis: We present a combined study based on experimental measurements of infrared (IR) dielectric function and first-principles calculations of IR spectra and vibrational density of states (VDOS) of amorphous alumina (am-Al₂O₃). In particular, we show that the main features of the imaginary part of the dielectric function ε₂(ω) at ~380 and 630 cm-¹ are related to the motions of threefold coordinated oxygen atoms, which are the vast majority of oxygen atoms in am-Al₂O₃. Our analysis (involving three model structures) provides an alternative point of view with respect to an earlier suggested assignment of the vibrational modes, which relates them to the stretching and bending vibrational modes of AlOₙ (n = 4, 5, and 6) polyhedra. Our assignment is based on the additive decomposition of the VDOS and ε₂(ω) spectra, which shows that: (i) the band at ~380 cm-¹ features oxygen motions occurring in a direction normal to the plane defined by the three nearest-neighbor aluminum atoms, i.e. out-of-plane motions of oxygen atoms; (ii) Al-O stretching vibrations (i.e. in-plane motions of oxygen atoms) appear at frequencies above ~500 cm-¹, which characterize the vibrational modes underlying the band at ~630 cm-¹.
Ključne besede: amorphous alumina, infrared spectra, first-principles calculations
Objavljeno v RUNG: 15.09.2023; Ogledov: 1140; Prenosov: 7
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2.
Infrared spectra in amorphous alumina : a combined ab initio and experimental study
Luigi Giacomazzi, Nikita S. Shcheblanov, Mikhail E. Povarnitsyn, Yanbo Li, Andraž Mavrič, Barbara Zupančič, Jože Grdadolnik, Alfredo Pasquarello, 2023, izvirni znanstveni članek

Opis: We present a combined study based on the experimental measurements of an infrared (IR) dielectric function and first-principles calculations of IR spectra and the vibrational density of states (VDOS) of amorphous alumina (am−Al2O3). In particular, we show that the main features of the imaginary part of the dielectric function ε2(ω) at ∼380 and 630 cm−1 are related to the motions of threefold-coordinated oxygen atoms, which are the vast majority of oxygen atoms in am-Al2O3. Our analysis provides an alternative point of view with respect to an earlier suggested assignment of the vibrational modes, which relates them to the stretching and bending vibrational modes of AlOn (n=4, 5, and 6) polyhedra. Our assignment is based on the additive decomposition of the VDOS and ε2(ω) spectra, which shows that (i) the band at ∼380cm−1 features oxygen motions occurring in a direction normal to the plane defined by the three nearest-neighbor aluminum atoms, i.e., out-of-plane motions of oxygen atoms; (ii) Al-O stretching vibrations (i.e., in-plane motions of oxygen atoms) appear at frequencies above ∼500cm−1, which characterize the vibrational modes underlying the band at ∼630cm−1. Aluminum and fourfold-coordinated oxygen atoms contribute uniformly to the VDOS and ε2(ω) spectra in the frequency region ∼350–650 cm−1 without causing specific features. Our numerical results are in good agreement with the previous and presently obtained experimental data on the IR dielectric function of am−Al2O3 films. Finally, we show that the IR spectrum can be modeled successfully by assuming isotropic Born charges for aluminum atoms and fourfold-coordinated oxygen atoms, while requiring the use of three parameters, defined in a local reference frame, for the anisotropic Born charges of threefold-coordinated oxygen atoms.
Ključne besede: dielectric properties, microstructure, amorphous materials, density functional calculations, infrared techniques, aluminium oxide
Objavljeno v RUNG: 10.05.2023; Ogledov: 1575; Prenosov: 7
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3.
Finite size effects at protein folding from the two-state perspective
Artem Badasyan, Matjaž Valant, Jože Grdadolnik, Vladimir N. Uversky, 2021, objavljeni povzetek znanstvenega prispevka na konferenci

Ključne besede: protein folding, two-state model, finite size effects
Objavljeno v RUNG: 27.09.2021; Ogledov: 2001; Prenosov: 0
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4.
1,8-dihydroxy naphthalene (DHN) - melanin confers tolerance to cadmium in isolates of melanised dark septate endophytes
Mateja Potisek, Matevž Likar, Katarina Vogel-Mikuš, Iztok Arčon, Jože Grdadolnik, Marjana Regvar, 2021, izvirni znanstveni članek

Opis: The contribution of 1,8-dihydroxy naphthalene (DHN) melanin to cadmium (Cd) tolerance in two dark septate endophytes (DSE) of the genus Cadophora with different melanin content was investigated in vitro. The DSE isolate Cad#148 with higher melanin content showed higher tolerance to Cd than the less melanised Cad#149. Melanin synthesis was significantly reduced by Cd in both isolates with uninhibited melanin synthesis, in a dosedependent manner. Inhibition of melanin synthesis by tricyclazole reduced the relative growth of Cad#148 exposed to Cd and did not affect Cad#149. Cd accumulation was not altered by tricyclazole in the two isolates, but it increased catalase and reduced glutathione reductase activity in more melanised Cad#148, indicating higher stress levels. In contrast, in Cad#149 the enzyme activity was less affected by tricyclazole, indicating a more pronounced role of melanin-independent Cd tolerance mechanisms. Cd ligand environment in fungal mycelia was analysed by extended EXAFS (X-ray absorption fine structure). It revealed that Cd was mainly bound to O- and S-ligands, including hydroxyl, carboxyl, phosphate and thiol groups. A similar proportion of S- and Oligands (~35% and ~65%) were found in both isolates with uninhibited melanin synthesis. Among O-ligands two types with Cd-O-C- and Cd-O-P- coordination were identified. Tricyclazole altered Cd-O- ligand environment in both fungal isolates by reducing the proportion of Cd-O-C- and increasing the proportion of Cd-O-P coordination. DHN-melanin, among other tolerance mechanisms, significantly contributes to Cd tolerance in more melanised DSE fungi by immobilising Cd to hydroxyl groups and maintaining the integrity of the fungal cell wall.
Ključne besede: DSE, melanin, Cd tolerance, inhibitor tricyclazole, antioxidant enzymes, EXAFS
Objavljeno v RUNG: 13.07.2021; Ogledov: 2369; Prenosov: 0
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5.
Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins
Artem Badasyan, Sh. A. Tonoyan, Matjaž Valant, Jože Grdadolnik, 2021, izvirni znanstveni članek

Opis: Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. While modern experiments allow study of single molecules in vivo, corresponding theories date back to the early 1950s and require an essential update to include the recent significant progress in the description of water. The Hamiltonian formulation of the Zimm-Bragg model we propose includes a simplified, yet explicit model of water-polypeptide interactions that transforms into the equivalent implicit description after performing the summation of solvent degrees of freedom in the partition function. Here we show that our model fits very well to the circular dichroism experimental data for both heat and cold denaturation and provides the energies of inter- and intra- molecular H-bonds, unavailable with other processing methods. The revealed delicate balance between these energies determines the conditions for the existence of cold dena- turation and thus clarifies its absence in some proteins.
Ključne besede: protein folding, cold denaturation, water, Zimm-Bragg model
Objavljeno v RUNG: 06.05.2021; Ogledov: 2428; Prenosov: 15
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6.
The finite size effects and two-state paradigm of protein folding
Artem Badasyan, Matjaž Valant, Jože Grdadolnik, Vladimir N. Uversky, 2021, izvirni znanstveni članek

Opis: The coil to globule transition of the polypeptide chain is the physical phenomenon behind the folding of globular proteins. Globular proteins with a single domain usually consist of about 30 to 100 amino acid residues, and this finite size extends the transition interval of the coil-globule phase transition. Based on the pedantic derivation of the two-state model, we introduce the number of amino acid residues of a polypeptide chain as a parameter in the expressions for two cooperativity measures and reveal their physical significance. We conclude that the k2 measure, defined as the ratio of van ’t Hoff and calorimetric enthalpy is related to the degeneracy of the denatured state and describes the number of cooperative units involved in the transition; additionally, it is found that the widely discussed k2=1 is just the necessary condition to classify the protein as the two-state folder. We also find that Ωc, a quantity not limited from above and growing with system size, is simply proportional to the square of the transition interval. This fact allows us to perform the classical size scaling analysis of the coil-globule phase transition. Moreover, these two measures are shown to describe different characteristics of protein folding
Ključne besede: protein folding, two-state model, size scaling, thermodynamic cooperativity
Objavljeno v RUNG: 24.02.2021; Ogledov: 2439; Prenosov: 69
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7.
Ionomic and metabolomic changes in mercury and selenium exposed plants and animals by X - ray and FTIR spectrometry
Anja Kavčič, Petra Gregorič, Jože Grdadolnik, Iztok Arčon, Katarina Vogel-Mikuš, 2018, objavljeni povzetek znanstvenega prispevka na konferenci

Ključne besede: mercury, selenium, plants, animals
Objavljeno v RUNG: 12.09.2018; Ogledov: 4210; Prenosov: 0
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