CuO atomic thin monolayer (mlCuO) was synthesized recently. Interest in the mlCuO is based on its close relation to CuO2 layers in typical high temperature cuprate superconductors. Here, we present ...the calculation of the band structure, the density of states and the Fermi surface of the flat mlCuO as well as the corrugated mlCuO within the density functional theory (DFT) in the generalized gradient approximation (GGA). In the flat mlCuO, the Cu-3dx2-y2 band crosses the Fermi level, while the Cu-3dxz,yz hybridized band is located just below it. The corrugation leads to a significant shift of the Cu-3dxz,yz hybridized band down in energy and a degeneracy lifting for the Cu-3dx2-y2 bands. Corrugated mlCuO is more energetically favorable than the flat one. In addition, we compared the electronic structure of the considered CuO monolayers with bulk CuO systems. We also investigated the influence of a crystal lattice strain (which might occur on some interfaces) on the electronic structure of both mlCuO and determined the critical strains of topological Lifshitz transitions. Finally, we proposed a number of different minimal models for the flat and the corrugated mlCuO using projections onto different Wannier functions basis sets and obtained the corresponding Hamiltonian matrix elements in a real space.
The magnetic properties of M2AX (M = Mn, Fe; A = Al, Ga, Si, Ge; X = C, N) phases were studied within DFT-GGA. The magnetic electronic ground state is determined. The investigation of the phase ...stability of M2AX phases is performed by comparing the total energy of MAX phases to that of the set of competitive phases for calculation of the phase formation enthalpy. As the result of such an approach, we have found one stable compound (Mn2GaC), and seven metastable ones. It is shown that several metastable MAX phases (Mn2AlC, Fe2GaC, Mn2GeC, and Mn2GeN) become stable at a small applied pressure (1.5–7 GPa). The mechanical, electronic and elastic properties of metastable MAX phases are studied.
Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been ...published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes.
We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do not encode cloverleaf-shaped tRNA structures. Indeed, in one genome, all 22 tRNA genes lack sequence to encode canonical cloverleaf structures. We also find that the large ribosomal RNA genes are substantially shorter than those of most arthropods. We inferred secondary structures of the LSU rRNAs from both pseudoscorpions, and find that they have lost multiple helices. Based on comparisons with the crystal structure of the bacterial ribosome, two of these helices were likely contact points with tRNA T-arms or D-arms as they pass through the ribosome during protein synthesis.The mitochondrial gene arrangements of both pseudoscorpions differ from the ancestral chelicerate gene arrangement. One genome is rearranged with respect to the location of protein-coding genes, the small rRNA gene, and at least 8 tRNA genes. The other genome contains 6 tRNA genes in novel locations. Most chelicerates with rearranged mitochondrial genes show a genome-wide reversal of the CA nucleotide bias typical for arthropods on their major coding strand, and instead possess a GT bias. Yet despite their extensive rearrangement, these pseudoscorpion mitochondrial genomes possess a CA bias on the major coding strand. Phylogenetic analyses of all 13 mitochondrial protein-coding gene sequences consistently yield trees that place pseudoscorpions as sister to acariform mites.
The well-supported phylogenetic placement of pseudoscorpions as sister to Acariformes differs from some previous analyses based on morphology. However, these two lineages share multiple molecular evolutionary traits, including substantial mitochondrial genome rearrangements, extensive nucleotide substitution, and loss of helices in their inferred tRNA and rRNA structures.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Abstract
Improving an enzyme's initially low catalytic efficiency with a new target substrate by an order of magnitude or two may require only a few rounds of mutagenesis and screening or selection. ...However, subsequent rounds of optimization tend to yield decreasing degrees of improvement (diminishing returns) eventually leading to an optimization plateau. We aimed to optimize the catalytic efficiency of bacterial phosphotriesterase (PTE) toward V-type nerve agents. Previously, we improved the catalytic efficiency of wild-type PTE toward the nerve agent VX by 500-fold, to a catalytic efficiency (kcat/KM) of 5 × 106 M−1 min−1. However, effective in vivo detoxification demands an enzyme with a catalytic efficiency of >107 M−1 min−1. Here, following eight additional rounds of directed evolution and the computational design of a stabilized variant, we evolved PTE variants that detoxify VX with a kcat/KM ≥ 5 × 107 M−1 min−1 and Russian VX (RVX) with a kcat/KM ≥ 107 M−1 min−1. These final 10-fold improvements were the most time consuming and laborious, as most libraries yielded either minor or no improvements. Stabilizing the evolving enzyme, and avoiding tradeoffs in activity with different substrates, enabled us to obtain further improvements beyond the optimization plateau and evolve PTE variants that were overall improved by >5000-fold with VX and by >17 000-fold with RVX. The resulting variants also hydrolyze G-type nerve agents with high efficiency (GA, GB at kcat/KM > 5 × 107 M−1 min−1) and can thus serve as candidates for broad-spectrum nerve-agent prophylaxis and post-exposure therapy using low enzyme doses.
Nucleic acid (NA) aptamers bind to their targets with high affinity and selectivity. The three-dimensional (3D) structures of aptamers play a major role in these non-covalent interactions. Here, we ...use a four-step approach to determine a true 3D structure of aptamers in solution using small-angle X-ray scattering (SAXS) and molecular structure restoration (MSR). The approach consists of (i) acquiring SAXS experimental data of an aptamer in solution, (ii) building a spatial distribution of the molecule’s electron density using SAXS results, (iii) constructing a 3D model of the aptamer from its nucleotide primary sequence and secondary structure, and (iv) comparing and refining the modeled 3D structures with the experimental SAXS model. In the proof-of-principle we analyzed the 3D structure of RE31 aptamer to thrombin in a native free state at different temperatures and validated it by circular dichroism (CD). The resulting 3D structure of RE31 has the most energetically favorable conformation and the same elements such as a B-form duplex, non-complementary region, and two G-quartets which were previously reported by X-ray diffraction (XRD) from a single crystal. More broadly, this study demonstrates the complementary approach for constructing and adjusting the 3D structures of aptamers, DNAzymes, and ribozymes in solution, and could supply new opportunities for developing functional nucleic acids.
Graphical abstract
Electronic and magnetic states of Fe ions in Co2FeBO5 Knyazev, Yurii V; Kazak, Natalia V; Zhandun, Vyacheslav S ...
Dalton transactions : an international journal of inorganic chemistry,
07/2021, Letnik:
50, Številka:
28
Journal Article
Recenzirano
Odprti dostop
The ludwigite Co2FeBO5 has been studied experimentally using 57Fe Mössbauer spectroscopy and theoretically using DFT + GGA calculations. The room-temperature Mössbauer spectra are composed of four ...quadrupole doublets corresponding to the high-spin Fe3+ ions in octahedral oxygen coordination. All components undergo splitting below 117 K due to the magnetic hyperfine fields. The DFT + GGA calculations performed for three models of Fe ion distributions have revealed that the ground state corresponds to the “Fe4(HS)” model with the high-spin Fe3+ ions located at the M4 site and the high-spin Co2+ ions located at the M1, M2, and M3 sites. A ferrimagnetic ground state, with the Co and Fe magnetic moments being nearly parallel to the b-axis and a total magnetic moment of circa 1.1μB f.u.−1, was found. The other Fe distributions cause an increase in the local octahedral distortions and transformation of the spin state. The calculated quadrupole splitting values are in good agreement with the experimental values obtained by Mössbauer spectroscopy.
Electronic structure and spin‐related properties of CoI2/NiI2 heterostructure were studied by means of density functional theory. It was shown that the electronic structure at the Fermi level can be ...characterized by a band gap. The effect of the external electric field on charge transfer and electronic properties of the CoI2/NiI2 interface was investigated, and it was found that band gap width depends on the strength of the applied electric field, switching its nature from semiconducting to a half‐metallic one. An easy control of the electronic properties and promising spin‐polarized nature of the CoI2/NiI2 spinterface allows the heterostructure to be used in spin‐related applications.
The CoI2/NiI2 spinterface is a heterostructure consisting of CoI2 and NiI2 monolayers stacked pairwise. This structure demonstrates special electronic properties under applied external electric field. Varying the strength of the electric field, it is possible to change the band gap. Therefore, it creates great opportunities to use such material in application of spintronics in the near future.
The growth of α-FeSi
2
nanocrystal ensembles on gold-activated and gold-free Si(001) surfaces at different Si/Fe flux ratios
via
molecular beam epitaxy is reported. The study reveals that the ...utilisation of gold as a catalyst regulates the preferable orientation relationship (OR) of the nanocrystals to silicon and their morphology at a given Si/Fe flux ratio. α-FeSi
2
free-standing crystals with continuously tuned sizes from 30 nm up to several micrometres can be grown with an α(001)//Si(001) basic OR under gold-assisted conditions and an α(111)//Si(001) OR under gold-free growth conditions on a Si(001) surface. The preferred morphology of nanocrystals with a particular OR can be altered through changes to the Si/Fe flux ratio. Herein, the microstructure and basic OR between the silicide nanocrystals and the silicon substrate, and the formation of nanocrystal facets were analysed in detail with the help of microscopic techniques and simulation methods based on the analysis of near coincidence site (NCS) distributions at silicide/silicon interfaces. On the basis of the simulations used, we managed to reveal the nature of the interfaces observed for the main types of α-FeSi
2
nanocrystals grown. Three types of interfaces typical for nanoplates with an α(001)//Si(001) basic OR, which are (i) stepped, (ii) stressed, and (iii) flat, are explained based on the tendency for the NCS density to increase at the interface. The results presented reveal the potential for the bottom-up fabrication of α-FeSi
2
nanocrystals with tuned physical properties as potentially important contact materials and as building blocks for future nanoelectronic devices.
An approach for tuning the preferable orientation relationships and shapes of free-standing α-FeSi
2
nanocrystals was demonstrated on a Si(001) surface.
The behavior of the resistivity and thermopower of the Gd0.2Sr0.8FeO3−δ ferrite samples with a perovskite structure and the sample stability in an inert gas atmosphere in the temperature range of ...300–800 K have been examined. It has been established that, in the investigated temperature range, the thermoelectric properties in the heating‒cooling mode are stabilized at δ ≥ 0.21. It is shown that the temperature dependencies of the resistivity obtained at different δ values obey the activation law up to the temperatures corresponding to the intense oxygen removal from a sample. The semiconductor‒semiconductor electronic transitions accompanied by a decrease in the activation energy have been observed with increasing temperature. It is demonstrated that the maximum thermoelectric power factor of 0.1 µW/(cm·K2) corresponds to a temperature of T = 800 K.
We derived simple rules for the sign of 180∘ superexchange interaction based on the multielectron calculations of the superexchange interaction in the transition metal oxides that are valid both ...below and above spin crossover under high pressure. The superexchange interaction between two cations in dn configurations is given by a sum of partial contributions related to the electron-hole virtual excitations to the different states of the dn+1 and dn−1 configurations. Using these rules, we have analyzed the sign of the 180∘ superexchange interaction of a number of oxides with magnetic cations in electron configurations from d2 until d8: the iron, cobalt, chromium, nickel, copper, and manganese oxides with increasing pressure. The most interesting result concerns the magnetic state of cobalt and nickel oxides CoO, Ni2O3 and also La2CoO4, LaNiO3 isostructural to well-known high-TC and colossal magnetoresistance materials. These oxides have a spin 12 at the high pressure. Change of the interaction from antiferromagnetic below spin crossover to ferromagnetic above spin crossover is predicted for oxide materials with cations in d5(FeBO3) and d7(CoO) configurations, while for materials with the other dn configurations spin crossover under high pressure does not change the sign of the 180∘ superexchange interaction.
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