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Structure, electronic and magnetic characterization, and calculated electronic structures of two oxyhalide hexagonal perovskites
Herein we report the crystal structures, initial magnetic and charge transport characterization, and calculated electronic structures of the hexagonal oxyhalide perovskites, Ba 7 Ru 4 O 15 Cl 2 and Ba 7 Ru 4 O 15 Br 2 . The experimental information is obtained through the study of single crystals. Face-sharing Ru O 6 octahedra form Ru 2 O 9 dimers in a layered triangular geometry in these materials; minor amounts of off-magnetic-site structural disorder are present in our crystals. Both are magnetically isotropic, with 2.5 μB/mol-Ru, Curie-Weiss theta –185 K, and 2.9 μB/mol-Ru, Curie-Weiss theta –168 K, respectively. Broad features in the magnetic susceptibility and heat capacity associated with magnetic ordering (at 35 and 37 K, respectively) are observed. The charge transport band gaps are 0.03 eV for the oxychloride and 0.006 eV for the oxybromide. There is no gap at the Fermi level for either of these compounds in density-functional theory electronic structure calculations.
Defect Structure in Quantum-Cutting Yb3+-Doped CsPbCl3 Perovskites Probed by X-Ray Absorption and Atomic Pair Distribution Function Analysis
Ytterbium-doping in all-inorganic lead-halide perovskites (CsPb(Cl1-xBrx)3) generates novel properties including quantum cutting and narrow line emission, making these materials attractive spectral down-converters for solar photovoltaics. The relationship between this optical efficiency and the defect structure(s) associated with Yb3+ dopants within perovskites is not well understood. Various charge-neutral doping motifs have previously been proposed and studied computationally, including clusters involving two substitutional Yb3+ ions charge-compensated by a single local Pb2+ vacancy. Near-band-edge defect states associated with such motifs are believed to play an important mechanistic role in quantum cutting itself. Here, we report the results of X-ray absorption and X-ray total-scattering measurements on ytterbium-doped CsPbCl3. XANES shows that the dopant oxidation state is exclusively Yb3+, and a combination of Yb L3 and Pb L3 EXAFS shows that this Yb3+ substitutes exclusively at Pb2+ sites, where it adopts a pseudo-octahedral [YbCl6]3- coordination environment. Shell-by-shell fits to the data show a short Yb-Cl bond distance of 2.58 Å compared to the Pb-Cl bond distance of 2.83 Å. We confirm this finding by X-ray pair distribution function analysis, which also shows evidence of additional Pb2+ vacancy formation induced by Yb3+ doping. We evaluate whether this is the primary mechanism of charge compensation using simulated EXAFS and pair distribution function data for several computed defect structures. Together, these results resolve the local dopant structures and charge-compensation mechanisms in lanthanide-doped all-inorganic lead-halide perovskites, and, as such, significantly advance the understanding of structure-function relationships in this important class of materials.
Structural plasticity of the selectivity filter in a nonselective ion channel
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The seventh blind test of crystal structure prediction: structure ranking methods
A seventh blind test of crystal structure prediction has been organized by the Cambridge Crystallographic Data Centre. The results are presented in two parts, with this second part focusing on methods for ranking crystal structures in order of stability. The exercise involved standardized sets of structures seeded from a range of structure generation methods. Participants from 22 groups applied several periodic DFT-D methods, machine learned potentials, force fields derived from empirical data or quantum chemical calculations, and various combinations of the above. In addition, one non-energy-based scoring function was used. Results showed that periodic DFT-D methods overall agreed with experimental data within expected error margins, while one machine learned model, applying system-specific AIMnet potentials, agreed with experiment in many cases demonstrating promise as an efficient alternative to DFT-based methods. For target XXXII, a consensus was reached across periodic DFT methods, with consistently high predicted energies of experimental forms relative to the global minimum (above 4 kJ mol −1 at both low and ambient temperatures) suggesting a more stable polymorph is likely not yet observed. The calculation of free energies at ambient temperatures offered improvement of predictions only in some cases (for targets XXVII and XXXI). Several avenues for future research have been suggested, highlighting the need for greater efficiency considering the vast amounts of resources utilized in many cases.
1.15 Å resolution structure of the proteasome-assembly chaperone Nas2 PDZ domain
Abstract not provided
Crystal structure of the toxin Msmeg_6760, the structural homolog of Mycobacterium tuberculosis Rv2035, a novel type II toxin involved in the hypoxic response
The structure of Msmeg_6760, a protein of unknown function, has been determined. Biochemical and bioinformatics analyses determined that Msmeg_6760 interacts with a protein encoded in the same operon, Msmeg_6762, and predicted that the operon is a toxin–antitoxin (TA) system. Structural comparison of Msmeg_6760 with proteins of known function suggests that Msmeg_6760 binds a hydrophobic ligand in a buried cavity lined by large hydrophobic residues. Access to this cavity could be controlled by a gate–latch mechanism. The function of the Msmeg_6760 toxin is unknown, but structure-based predictions revealed that Msmeg_6760 and Msmeg_6762 are homologous to Rv2034 and Rv2035, a predicted novel TA system involved in Mycobacterium tuberculosis latency during macrophage infection. The Msmeg_6760 toxin fold has not been previously described for bacterial toxins and its unique structural features suggest that toxin activation is likely to be mediated by a novel mechanism.
Structures of the substrate-binding protein YfeA in apo and zinc-reconstituted holo forms
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Structure Prediction from Neutron Scattering Profiles: A Data Sciences Approach
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Ab initio GGA+U investigations of the structural, electronic, and magnetic properties of Cd 1-x Mn x Te alloy
The structural, electronic and magnetic properties of Cd 1-x Mn x Te alloy in the zinc-blende (ZB) phase within the framework of spin-polarized density functional theory using the generalized gradient approximation (GGA) are studied. In particular, we employ GGA+U SIC method that gives a better description of systems with strong Coulomb correlations of the d-electrons. First, we discuss implementation of GGA+U method to the ground state calculations of pure CdTe and ferromagnetic MnTe. The alloy is modelled at some selected compositions by ordered structures described in terms of periodically repeated supercells for the compositions x = 0.25, 0.5, and 0.75. The compositional dependence of the lattice constant, electronic band structure and partial densities of states of ferromagnetic Cd 1-x Mn x Te alloy are studied. We estimate the spin-exchange splitting energies produced by the Mn 3d-states and determine the exchange constants for the conduction and valence bands of the alloy. The energy positions of the occupied and unoccupied Mn 3d-bands in the electronic structure of ferromagnetic Cd 1-x Mn x Te alloy are also presented. Our calculations using GGA+U SIC approach agree well with the available experimental data and other calculations.
Crystal Structure of a CRISPR RNA-guided Surveillance Complex Bound to a ssDNA Target
In prokaryotes, RNA derived from type I and type III CRISPR loci direct large ribonucleoprotein complexes to destroy invading bacteriophage and plasmids. In Escherichia coli, this 405-kilodalton complex is called Cascade. We report the crystal structure of Cascade bound to a single-stranded DNA (ssDNA) target at a resolution of 3.03 angstroms. The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. This noncanonical structure is facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid and is stabilized by the highly interlocked organization of protein subunits. These studies provide insight into both the assembly and the activity of this complex and suggest a mechanism to enforce fidelity of target binding.
Structural evidence for a dynamic metallocofactor during N 2 reduction by Mo-nitrogenase
The enzyme nitrogenase uses a suite of complex metallocofactors to reduce dinitrogen (N 2 ) to ammonia. Mechanistic details of this reaction remain sparse. We report a 1.83-angstrom crystal structure of the nitrogenase molybdenum-iron (MoFe) protein captured under physiological N 2 turnover conditions. This structure reveals asymmetric displacements of the cofactor belt sulfurs (S2B or S3A and S5A) with distinct dinitrogen species in the two αβ dimers of the protein. The sulfur-displaced sites are distinct in the ability of protein ligands to donate protons to the bound dinitrogen species, as well as the elongation of either the Mo–O5 (carboxyl) or Mo–O7 (hydroxyl) distance that switches the Mo-homocitrate ligation from bidentate to monodentate. These results highlight the dynamic nature of the cofactor during catalysis and provide evidence for participation of all belt-sulfur sites in this process.
Electron momentum density, band structure, and structural properties of SrS
The electron momentum density, the electronic band structure, and the structural properties of SrS are presented in this paper. The isotropic Compton profile, anisotropies in the directional Compton profiles, the electronic band structure and density of states are calculated using the ab initio periodic linear combination of atomic orbitals method with the CRYSTAL06 code. Structural parameters of SrS-lattice constants and bulk moduli in the B1 and B2 phases-are computed together with the transition pressure. The computed parameters are well in agreement with earlier investigations. To compare the calculated isotropic Compton profile, measurement on polycrystalline SrS is performed using 5Ci-{sup 241}Am Compton spectrometer. Additionally, charge transfer is studied by means of the Compton profiles computed from the ionic model. The nature of bonding in the isovalent SrS and SrO compounds is compared on the basis of equal-valenceelectron-density profiles and the bonding in SrS is found to be more covalent than in SrO.
Effect of Cr Spacer on Structural and Magnetic Properties of Fe/Gd Multilayers
Here, we analyze the role of a thin Cr spacer between Fe and Gd layers on the structure and magnetic properties of a [Fe(35 Å)/Cr(t Cr )/Gd(50 Å)/Cr(t Cr )] 12 superlattice. Samples without the Cr spacer (t Cr = 0) and with a thin spacer (t Cr = 4 Å) are investigated using X-ray diffraction, polarized neutron and resonance X-ray magnetic reflectometry, static magnetometry, magneto-optical Kerr effect, and ferromagnetic resonance techniques. Magnetic properties are studied experimentally in a wide temperature range 4–300 K and analyzed theoretically using numerical simulation on the basis of the mean-field model. We show that a reasonable agreement with the experimental data can be obtained considering temperature dependence of the effective field parameter in gadolinium layers. In conclusion, the analysis of the experimental data shows that besides a strong reduction of the antiferromagnetic coupling between Fe and Gd, the introduction of Cr spacers into Fe/Gd superlattice leads to modification of both structural and magnetic characteristics of the ferromagnetic layers.
Synthesis, structure, electronic characterization, and halogenation of gold(III) phlorin complexes
The metalation chemistry of the phlorin, which is a non-aromatic tetrapyrrole macrocycle containing a single sp 3 -hybridized meso-carbon has remained underdeveloped, as compared to that of more traditional tetrapyrroles such as porphyrins, corroles and phthalocyanines. There have been few prior efforts to prepare metallophlorins, and those that have been reported have relied on either reduction or nucleophilic attack of parent metalloporphyrins, rather than direct metalation of freebase phlorin constructs. In this work, an alternate synthetic approach for preparation of gold(III) phlorin complexes that involves the first direct metalation of two different freebase phlorin derivatives (3H(Phl tBu ) and 3H(Phl F )) with AuBr 3 to produce the stable and fully isolable gold(III) phlorin complexes Au(Phl tBu ) and Au(Phl F ) is reported. The first structural characterization of a metallophlorin bearing geminal dimethyl substituents at the sp 3 -hybridized meso-carbon via X-ray crystallography is also reported. In addition to the preparation of Au(Phl tBu ) and Au(Phl F ), the UV-vis absorption and redox properties of these two gold(III) phlorins in comparison to those of their freebase homologues is also detailed. Notably, the metallophlorins are characterized by panchromatic absorbance profiles and intense and broad bands that span the long-visible and into the near-IR regions, as well as two fully reversible oxidation and reduction waves as probed by cyclic voltammetry. Lastly, the chlorination of Au(Phl tBu ) using PhI(Cl 2 ) was probed and it was found that this regioslective reaction generates monochlorinated (Au(Phl tBu Cl)) and dichlorinated (Au(Phl tBu Cl 2 )) products, which were both structurally characterized by X-ray crystallography.
Vertical Structure of Radiative Heating Rates of the MJO during DYNAMO
The vertical structure of radiative heating rates over the region of the tropi-cal Indian Ocean associated with the MJO during the DYNAMO/ARM MJO Investigation Experiment is presented. The mean and variability of heating rates during active, suppressed, and disturbed phases are determined from the Paci?c Northwest National Laboratory combined remote sensing retrieval (CombRet) from Gan Island, Maldives (0.69? S, 73.15? E). TOA and surface ?uxes from the CombRet product are compared with collocated three-hourly CERES SYN1deg Ed4A satellite retrievals. The ?uxes are correlated in time with correlation coef?cients around 0.9, yet CombRet time-mean OLR is 15 W m-2 larger. Previous work has suggested that CombRet under-samples high clouds, due to attenuation by low-level clouds and reduced instrument sensitivity with altitude. However, mean OLR differs between CombRet and CERES for all values of OLR, not just the lowest values corresponding to widespread high clouds. The discrepancy peaks for mid-range OLR, sugges-tive of precipitating, towering cumulus convective clouds, rather than strati-form cirrus clouds. Biases in the cloud-top height of thick clouds substantially contribute to the overestimate of OLR by CombRet. CombRet data is used to generate composite shortwave and longwave atmospheric heating rate pro-?les as a function of the local OLR. Though there is considerable variability in CombRet not directly related to OLR, the time-height structure of mean heating rate composites generated using OLR as the interpolant is broadly representative of tropical convective variability on intraseasonal time scales.
Coupling of regional geophysics and local soil-structure models in the EQSIM fault-to-structure earthquake simulation framework
Accurate understanding and quantification of the risk to critical infrastructure posed by future large earthquakes continues to be a very challenging problem. Earthquake phenomena are quite complex and traditional approaches to predicting ground motions for future earthquake events have historically been empirically based whereby measured ground motion data from historical earthquakes are homogenized into a common data set and the ground motions for future postulated earthquakes are probabilistically derived based on the historical observations. This procedure has recognized significant limitations, principally due to the fact that earthquake ground motions tend to be dictated by the particular earthquake fault rupture and geologic conditions at a given site and are thus very site-specific. Historical earthquakes recorded at different locations are often only marginally representative. There has been strong and increasing interest in utilizing large-scale, physics-based regional simulations to advance the ability to accurately predict ground motions and associated infrastructure response. However, the computational requirements for simulations at frequencies of engineering interest have proven a major barrier to employing regional scale simulations. In a U.S. Department of Energy Exascale Computing Initiative project, the EQSIM application development is underway to create a framework for fault-to-structure simulations. This framework is being prepared to exploit emerging exascale platforms in order to overcome computational limitations. This article presents the essential methodology and computational workflow employed in EQSIM to couple regional-scale geophysics models with local soil-structure models to achieve a fully integrated, complete fault-to-structure simulation framework. Here, the computational workflow, accuracy and performance of the coupling methodology are illustrated through example fault-to-structure simulations.
Nop9 recognizes structured and single-stranded RNA elements of preribosomal RNA
Nop9 is an essential factor in the processing of preribosomal RNA. Its absence in yeast is lethal, and defects in the human ortholog are associated with breast cancer, autoimmunity, and learning/language impairment. PUF family RNA-binding proteins are best known for sequence-specific RNA recognition, and most contain eight α-helical repeats that bind to the RNA bases of single-stranded RNA. Nop9 is an unusual member of this family in that it contains eleven repeats and recognizes both RNA structure and sequence. Here we report a crystal structure of Saccharomyces cerevisiae Nop9 in complex with its target RNA within the 20S preribosomal RNA. This structure reveals that Nop9 brings together a carboxy-terminal module recognizing the 5' single-stranded region of the RNA and a bifunctional amino-terminal module recognizing the central double-stranded stem region. We further show that the 3' single-stranded region of the 20S target RNA adds sequence-independent binding energy to the RNA–Nop9 interaction. Both the amino- and carboxy-terminal modules retain the characteristic sequence-specific recognition of PUF proteins, but the amino-terminal module has also evolved a distinct interface, which allows Nop9 to recognize either single-stranded RNA sequences or RNAs with a combination of single-stranded and structured elements.