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  • Blackwell Publishing Ltd
  • International Union of Crystallography
  • 2020-2022  (393)
  • 2000-2004
  • 1980-1984
  • 1925-1929
  • 2021  (393)
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  • 1
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    Evaluating learning spaces in flood risk management in Germany: Lessons for governance research (2021)
    Blackwell Publishing Ltd | Oxford, UK
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    Publikationsdatum: 2021-06-28
    Beschreibung: Efforts to collaboratively manage the risk of flooding are ultimately based on individuals learning about risks, the decision process, and the effectiveness of decisions made in prior situations. This article argues that much can be learned about a governance setting by explicitly evaluating the relationships through which influential individuals and their immediate contacts receive and send information to one another. We define these individuals as “brokers,” and the networks that emerge from their interactions as “learning spaces.” The aim of this article is to develop strategies to identify and evaluate the properties of a broker's learning space that are indicative of a collaborative flood risk management arrangement. The first part of this article introduces a set of indicators, and presents strategies to employ this list so as to systematically identify brokers, and compare their learning spaces. The second part outlines the lessons from an evaluation that explored cases in two distinct flood risk management settings in Germany. The results show differences in the observed brokers' learning spaces. The contacts and interactions of the broker in Baden‐Württemberg imply a collaborative setting. In contrast, learning space of the broker in North Rhine‐Westphalia lacks the same level of diversity and polycentricity.
    Beschreibung: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Beschreibung: MWK Baden‐Württemberg
    Schlagwort(e): 333.91 ; brokerage ; collaborative water governance ; comanagement ; comparative analysis ; social networks
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  • 2
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    Facilitated crystal handling using a simple device for evaporation reduction in microtiter plates (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-03-30
    Beschreibung: In the past two decades, most of the steps in a macromolecular crystallography experiment have undergone tremendous development with respect to speed, feasibility and increase of throughput. The part of the experimental workflow that is still a bottleneck, despite significant efforts, involves the manipulation and harvesting of the crystals for the diffraction experiment. Here, a novel low‐cost device is presented that functions as a cover for 96‐well crystallization plates. This device enables access to the individual experiments one at a time by its movable parts, while minimizing evaporation of all other experiments of the plate. In initial tests, drops of many typically used crystallization cocktails could be successfully protected for up to 6 h. Therefore, the manipulation and harvesting of crystals is straightforward for the experimenter, enabling significantly higher throughput. This is useful for many macromolecular crystallography experiments, especially multi‐crystal screening campaigns.
    Beschreibung: A simple and low‐cost device has been developed to minimize evaporation in microtiter plates for easy crystal handling and harvesting. image
    Schlagwort(e): 548 ; evaporation reduction ; crystal handling ; crystal harvesting ; crystallographic fragment screening
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  • 3
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    Cation distribution in Cu2ZnSnSe4, Cu2FeSnS4 and Cu2ZnSiSe4 by multiple‐edge anomalous diffraction (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publikationsdatum: 2021-03-30
    Beschreibung: Multiple‐Edge Anomalous Diffraction (MEAD) has been applied to various quaternary sulfosalts belonging to the adamantine compound family in order to validate the distribution of copper, zinc and iron cations in the structure. Semiconductors from this group of materials are promising candidates for photovoltaic applications. Their properties strongly depend on point defects, in particular related to cation order–disorder. However, Cu+, Zn2+ and Fe2+ have very similar scattering factors and are all but indistinguishable in usual X‐ray diffraction experiments. Anomalous diffraction utilizes the dependency of the atomic scattering factors f′ and f′′ of the energy of the radiation, especially close to the element‐specific absorption edges. In the MEAD technique, individual Bragg peaks are tracked over an absorption edge. The intensity changes depending on the structure factor can be highly characteristic for Miller indices selected for a specific structural problem, but require very exact measurements. Beamline KMC‐2 at synchrotron BESSY II, Berlin, has been recently upgraded for this technique. Anomalous X‐ray powder diffraction and XAFS compliment the data. Application of this technique confirmed established cation distribution in Cu2ZnSnSe4 (CZTSe) and Cu2FeSnS4 (CFTS). In contrast to the literature, cation distribution in Cu2ZnSiSe4 (CZSiSe) is shown to adopt a highly ordered wurtz‐kesterite structure type.
    Beschreibung: Multiple‐Edge Anomalous Diffraction (MEAD) has been applied to various quaternary sulfosalts belonging to the adamantine compound family in order to validate the distribution of copper, zinc and iron cations in the structure. Application of this technique confirms established cation distribution in Cu2ZnSnSe4 (CZTSe) and Cu2FeSnS4 (CFTS), but in Cu2ZnSiSe4 (CZSiSe) the cation distribution is shown to adopt a highly ordered wurtz‐kesterite structure type in contrast to the literature. image
    Schlagwort(e): 548 ; synchrotron ; anomalous diffraction ; semiconductor ; MEAD
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  • 4
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    The copper(II)‐binding tripeptide GHK, a valuable crystallization and phasing tag for macromolecular crystallography (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publikationsdatum: 2021-03-27
    Beschreibung: The growth of diffraction‐quality crystals and experimental phasing remain two of the main bottlenecks in protein crystallography. Here, the high‐affinity copper(II)‐binding tripeptide GHK was fused to the N‐terminus of a GFP variant and an MBP‐FG peptide fusion. The GHK tag promoted crystallization, with various residues (His, Asp, His/Pro) from symmetry molecules completing the copper(II) square‐pyramidal coordination sphere. Rapid structure determination by copper SAD phasing could be achieved, even at a very low Bijvoet ratio or after significant radiation damage. When collecting highly redundant data at a wavelength close to the copper absorption edge, residual S‐atom positions could also be located in log‐likelihood‐gradient maps and used to improve the phases. The GHK copper SAD method provides a convenient way of both crystallizing and phasing macromolecular structures, and will complement the current trend towards native sulfur SAD and MR‐SAD phasing.
    Beschreibung: A novel three‐residue tag containing the residues GHK that can be used to promote crystallization and in SAD phasing experiments using its tightly bound copper ion is described. image
    Schlagwort(e): 548 ; phasing ; crystallization ; GHK ; SAD
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  • 5
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    Determining paracrystallinity in mixed‐tacticity polyhydroxybutyrates (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-03-30
    Beschreibung: Recently, the authors reported on the development of crystallinity in mixed‐tacticity polyhydroxybutyrates. Comparable values reported in the literature vary depending on the manner of determination, the discrepancies being partially attributable to scattering from paracrystalline portions of the material. These portions can be qualified by peak profile fitting or quantified by allocation of scattered X‐ray intensities. However, the latter requires a good quality of the former, which in turn must additionally account for peak broadening inherent in the measurement setup, and due to limited crystallite sizes and the possible presence of microstrain. Since broadening due to microstrain and paracrystalline order both scale with scattering vector, they are easily confounded. In this work, a method to directionally discern these two influences on the peak shape in a Rietveld refinement is presented. Allocating intensities to amorphous, bulk and paracrystalline portions with changing tactic disturbance provided internal validations of the obtained directional numbers. In addition, the correlation between obtained thermal factors and Young's moduli, determined in earlier work, is discussed.
    Beschreibung: A method to robustly determine paracrystalline contents from Rietveld‐refined powder X‐ray data is presented and discussed for the example of mixed‐tacticity polyhydroxybutyrates. image
    Schlagwort(e): 548 ; polyhydroxybutyrates ; mixed tacticity ; paracrystallinity ; Rietveld refinement ; thermal factors
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  • 6
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    Concepts for nondestructive and depth‐resolved X‐ray residual stress analysis in the near‐surface region of nearly single crystalline materials with mosaic structure (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-03-27
    Beschreibung: Two evaluation concepts for nondestructive depth‐resolved X‐ray residual stress analysis in the near‐surface region of materials with cubic symmetry and nearly single crystalline structure are introduced by simulated examples. Both concepts are based on the same data acquisition strategy, which consists in the determination of lattice‐spacing depth profiles along the ⟨hkl⟩ poles by stepwise sample rotation around the scattering vector. Segmentation of these profiles parallel to the sample surface provides the lattice strain state as a function of depth. The first evaluation concept extends the crystallite group method developed for materials with pronounced crystallographic texture by the feature of depth resolution and can be applied to samples with arbitrary orientation. The second evaluation concept, which adapts the linear regression approach of the sin2ψ method for the case of single crystalline materials, is restricted to samples with (001) orientation. The influence of the strain‐free lattice parameter a0 on residual stress analysis using both evaluation concepts is discussed on the basis of explicitly derived relations.
    Beschreibung: Two data evaluation concepts are proposed for nondestructive and depth‐resolved X‐ray residual stress analysis by means of energy‐dispersive diffraction on materials featuring cubic symmetry and a nearly single crystalline structure. image
    Schlagwort(e): 548 ; residual stress ; X‐ray diffraction ; depth‐resolved analysis ; mosaic crystals
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  • 7
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    X‐ray dichroism in polyimide caused by non‐resonant scattering (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-03-30
    Beschreibung: Dichroism is one of the most important optical effects in both the visible and the X‐ray range. Besides absorption, scattering can also contribute to dichroism. This paper demonstrates that, based on the example of polyimide, materials can show tiny dichroism even far from electronic resonances due to scattering. Although the effect is small, it can lead to a measurable polarization change and might have influence on highly sensitive polarimetric experiments.
    Beschreibung: Aligned molecules, for example in polyimide foils, lead to small dichroism even far from resonances, which can be revealed by high‐precision X‐ray polarimetry. image
    Schlagwort(e): 548 ; polyimide ; polarization ; X‐ray polarimetry ; wide‐angle scattering ; X‐ray dichroism
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  • 8
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    Elastic stiffness coefficients of thiourea from thermal diffuse scattering (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-03-27
    Beschreibung: The complete elastic stiffness tensor of thiourea has been determined from thermal diffuse scattering (TDS) using high‐energy photons (100 keV). Comparison with earlier data confirms a very good agreement of the tensor coefficients. In contrast with established methods to obtain elastic stiffness coefficients (e.g. Brillouin spectroscopy, inelastic X‐ray or neutron scattering, ultrasound spectroscopy), their determination from TDS is faster, does not require large samples or intricate sample preparation, and is applicable to opaque crystals. Using high‐energy photons extends the applicability of the TDS‐based approach to organic compounds which would suffer from radiation damage at lower photon energies.
    Beschreibung: The elastic stiffness coefficients of thiourea are determined from thermal diffuse scattering. image
    Schlagwort(e): 548 ; thermal diffuse scattering ; elastic stiffness ; thiourea
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  • 9
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    Fast fitting of reflectivity data of growing thin films using neural networks (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-07-03
    Beschreibung: X‐ray reflectivity (XRR) is a powerful and popular scattering technique that can give valuable insight into the growth behavior of thin films. This study shows how a simple artificial neural network model can be used to determine the thickness, roughness and density of thin films of different organic semiconductors [diindenoperylene, copper(II) phthalocyanine and α‐sexithiophene] on silica from their XRR data with millisecond computation time and with minimal user input or a priori knowledge. For a large experimental data set of 372 XRR curves, it is shown that a simple fully connected model can provide good results with a mean absolute percentage error of 8–18% when compared with the results obtained by a genetic least mean squares fit using the classical Parratt formalism. Furthermore, current drawbacks and prospects for improvement are discussed.
    Beschreibung: Artificial neural networks trained with simulated data are shown to correctly and quickly determine film parameters from experimental X‐ray reflectivity curves.
    Schlagwort(e): 548 ; X‐ray reflectivity ; machine learning ; organic semi‐conductors ; neural networks
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  • 10
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    Numerically stable form factor of any polygon and polyhedron (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-06-05
    Beschreibung: Coordinate‐free expressions for the form factors of arbitrary polygons and polyhedra are derived using the divergence theorem and Stokes's theorem. Apparent singularities, all removable, are discussed in detail. Cancellation near the singularities causes a loss of precision that can be avoided by using series expansions. An important application domain is small‐angle scattering by nanocrystals.
    Beschreibung: Coordinate‐free expressions for the form factors of arbitrary polygons and polyhedra are derived using the divergence theorem and Stokes's theorem. Series expansions are used to ensure numeric precision close to apparent singularities. image
    Schlagwort(e): 548 ; form factors ; polyhedra ; Fourier shape transform
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  • 11
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    ROBL‐II at ESRF: a synchrotron toolbox for actinide research (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-06-30
    Beschreibung: ROBL‐II provides four different experimental stations to investigate actinide and other alpha‐ and beta‐emitting radionuclides at the new EBS storage ring of ESRF within an energy range of 3 to 35 keV. The XAFS station consists of a highly automatized, high sample throughput installation in a glovebox, to measure EXAFS and conventional XANES of samples routinely at temperatures down to 10 K, and with a detection limit in the sub‐p.p.m. range. The XES station with its five bent‐crystal analyzer, Johann‐type setup with Rowland circles of 1.0 and 0.5 m radii provides high‐energy resolution fluorescence detection (HERFD) for XANES, XES, and RIXS measurements, covering both actinide L and M edges together with other elements accessible in the 3 to 20 keV energy range. The six‐circle heavy duty goniometer of XRD‐1 is equipped for both high‐resolution powder diffraction as well as surface‐sensitive CTR and RAXR techniques. Single crystal diffraction, powder diffraction with high temporal resolution, as well as X‐ray tomography experiments can be performed at a Pilatus 2M detector stage (XRD‐2). Elaborate radioprotection features enable a safe and easy exchange of samples between the four different stations to allow the combination of several methods for an unprecedented level of information on radioactive samples for both fundamental and applied actinide and environmental research.
    Beschreibung: ROBL‐II at ESRF provides four experimental stations to investigate actinides with X‐ray absorption and emission spectroscopy, and with surface, high‐resolution powder, and single‐crystal X‐ray diffractometry.
    Schlagwort(e): 549 ; actinides ; EXAFS ; XANES ; HERFD‐XANES ; XAS ; XES ; RIXS ; XRD ; CTR ; RAXR ; surface diffraction
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  • 12
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    ATSAS 3.0: expanded functionality and new tools for small‐angle scattering data analysis (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-03-30
    Beschreibung: The ATSAS software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small‐angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the ATSAS 3.0 package are described. They include IMSIM, for simulating isotropic 2D scattering patterns; IMOP, to perform operations on 2D images and masks; DATRESAMPLE, a method for variance estimation of structural invariants through parametric resampling; DATFT, which computes the pair distance distribution function by a direct Fourier transform of the scattering data; PDDFFIT, to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in DATMW for Bayesian consensus‐based concentration‐independent molecular weight estimation; DATMIF, an ab initio shape analysis method that optimizes the search model directly against the scattering data; DAMEMB, an application to set up the initial search volume for multiphase modelling of membrane proteins; ELLLIP, to perform quasi‐atomistic modelling of liposomes with elliptical shapes; NMATOR, which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; DAMMIX, which reconstructs the shape of an unknown intermediate in an evolving system; and LIPMIX and BILMIX, for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the PRIMUS graphical interface to Qt5, updating SASpy – a PyMOL plugin to run a subset of ATSAS tools – to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future ATSAS releases. All these features are implemented in ATSAS 3.0, freely available for academic users at https://www.embl‐hamburg.de/biosaxs/software.html.
    Beschreibung: ATSAS is a comprehensive software suite for the processing, visualization, analysis and modelling of small‐angle scattering data. This article describes developments in the ATSAS 3.0 release, including new programs for data simulation and for the structural modelling of lipids, nucleic acids and polydisperse systems. image
    Schlagwort(e): 548 ; small‐angle scattering ; data analysis ; biological macromolecules ; structural modelling ; ATSAS
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  • 13
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    Synthetic resampling strategies and machine learning for digital soil mapping in Iran (2021)
    Blackwell Publishing Ltd | Oxford, UK
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    Publikationsdatum: 2021-07-04
    Beschreibung: Most common machine learning (ML) algorithms usually work well on balanced training sets, that is, datasets in which all classes are approximately represented equally. Otherwise, the accuracy estimates may be unreliable and classes with only a few values are often misclassified or neglected. This is known as a class imbalance problem in machine learning and datasets that do not meet this criterion are referred to as imbalanced data. Most datasets of soil classes are, therefore, imbalanced data. One of our main objectives is to compare eight resampling strategies that have been developed to counteract the imbalanced data problem. We compared the performance of five of the most common ML algorithms with the resampling approaches. The highest increase in prediction accuracy was achieved with SMOTE (the synthetic minority oversampling technique). In comparison to the baseline prediction on the original dataset, we achieved an increase of about 10, 20 and 10% in the overall accuracy, kappa index and F‐score, respectively. Regarding the ML approaches, random forest (RF) showed the best performance with an overall accuracy, kappa index and F‐score of 66, 60 and 57%, respectively. Moreover, the combination of RF and SMOTE improved the accuracy of the individual soil classes, compared to RF trained on the original dataset and allowed better prediction of soil classes with a low number of samples in the corresponding soil profile database, in our case for Chernozems. Our results show that balancing existing soil legacy data using synthetic sampling strategies can significantly improve the prediction accuracy in digital soil mapping (DSM). Highlights Spatial distribution of soil classes in Iran can be predicted using machine learning (ML) algorithms. The synthetic minority oversampling technique overcomes the drawback of imbalanced and highly biased soil legacy data. When combining a random forest model with synthetic sampling strategies the prediction accuracy of the soil model improves significantly. The resulting new soil map of Iran has a much higher spatial resolution compared to existing maps and displays new soil classes that have not yet been mapped in Iran.
    Beschreibung: Alexander von Humboldt‐Stiftung http://dx.doi.org/10.13039/100005156
    Beschreibung: German Research Foundation http://dx.doi.org/10.13039/501100001659
    Beschreibung: Soil and Water Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
    Schlagwort(e): 631.4 ; covariates ; imbalanced data ; machine learning ; random forest ; soil legacy data
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  • 14
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    XGANDALF – extended gradient descent algorithm for lattice finding (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-03-27
    Beschreibung: Serial crystallography records still diffraction patterns from single, randomly oriented crystals, then merges data from hundreds or thousands of them to form a complete data set. To process the data, the diffraction patterns must first be indexed, equivalent to determining the orientation of each crystal. A novel automatic indexing algorithm is presented, which in tests usually gives significantly higher indexing rates than alternative programs currently available for this task. The algorithm does not require prior knowledge of the lattice parameters but can make use of that information if provided, and also allows indexing of diffraction patterns generated by several crystals in the beam. Cases with a small number of Bragg spots per pattern appear to particularly benefit from the new approach. The algorithm has been implemented and optimized for fast execution, making it suitable for real‐time feedback during serial crystallography experiments. It is implemented in an open‐source C++ library and distributed under the LGPLv3 licence. An interface to it has been added to the CrystFEL software suite.
    Beschreibung: A description and evaluation are given of XGANDALF, extended gradient descent algorithm for lattice finding, an algorithm developed for fast and accurate indexing of snapshot diffraction patterns. image
    Schlagwort(e): 548 ; indexing ; XGANDALF ; CrystFEL ; multiple lattices ; serial crystallography
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  • 15
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    pinkIndexer – a universal indexer for pink‐beam X‐ray and electron diffraction snapshots (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-03-27
    Beschreibung: A crystallographic indexing algorithm, pinkIndexer, is presented for the analysis of snapshot diffraction patterns. It can be used in a variety of contexts including measurements made with a monochromatic radiation source, a polychromatic source or with radiation of very short wavelength. As such, the algorithm is particularly suited to automated data processing for two emerging measurement techniques for macromolecular structure determination: serial pink‐beam X‐ray crystallography and serial electron crystallography, which until now lacked reliable programs for analyzing many individual diffraction patterns from crystals of uncorrelated orientation. The algorithm requires approximate knowledge of the unit‐cell parameters of the crystal, but not the wavelengths associated with each Bragg spot. The use of pinkIndexer is demonstrated by obtaining 1005 lattices from a published pink‐beam serial crystallography data set that had previously yielded 140 indexed lattices. Additionally, in tests on experimental serial crystallography diffraction data recorded with quasi‐monochromatic X‐rays and with electrons the algorithm indexed more patterns than other programs tested.
    Beschreibung: pinkIndexer, an algorithm developed for indexing of snapshot diffraction patterns recorded with pink‐beam X‐rays, monochromatic X‐rays and electrons, is described and its use evaluated. image
    Schlagwort(e): 548 ; indexing ; pinkIndexer ; CrystFEL ; pink X‐ray beam ; serial electron diffraction
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  • 16
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    Crystal structure of human CRM1, covalently modified by 2‐mercaptoethanol on Cys528, in complex with RanGTP (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-06-17
    Beschreibung: CRM1 is a nuclear export receptor that has been intensively targeted over the last decade for the development of antitumor and antiviral drugs. Structural analysis of several inhibitor compounds bound to CRM1 revealed that their mechanism of action relies on the covalent modification of a critical cysteine residue (Cys528 in the human receptor) located in the nuclear export signal‐binding cleft. This study presents the crystal structure of human CRM1, covalently modified by 2‐mercaptoethanol on Cys528, in complex with RanGTP at 2.58 Å resolution. The results demonstrate that buffer components can interfere with the characterization of cysteine‐dependent inhibitor compounds.
    Beschreibung: The covalent modification of human CRM1 by 2‐mercaptoethanol interferes with the characterization of cysteine‐dependent inhibitor compounds. image
    Schlagwort(e): 548 ; nuclear export ; cancer ; exportin 1 ; cysteine modification
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  • 17
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    Impact of biochar on nutrient supply, crop yield and microbial respiration on sandy soils of northern Germany (2021)
    Blackwell Publishing Ltd | Oxford, UK
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    Publikationsdatum: 2021-06-16
    Beschreibung: The application of biochar to agricultural soils to increase nutrient availability, crop production and carbon sequestration has gained increasing interest but data from field experiments on temperate, marginal soils are still under‐represented. In the current study, biochar, produced from organic residues (digestates) from a biogas plant, was applied with and without digestates at low (3.4 t ha−1) and intermediate (17.1 t ha−1) rates to two acidic and sandy soils in northern Germany that are used for corn (Zea mays L.) production. Soil nutrient availability, crop yields, microbial biomass and carbon dioxide (CO2) emissions from heterotrophic respiration were measured over two consecutive years. The effects of biochar application depended on the intrinsic properties of the two tested soils and the biochar application rates. Although the soils at the fallow site, with initially low nutrient concentrations, showed a significant increase in pH, soil nutrients and crop yield after low biochar application rates, a similar response was found at the cornfield site only after application of substantially larger amounts of biochar. The effect of a single dose of biochar at the beginning of the experiment diminished over time but was still detectable after 2 years. Whereas plant available nutrient concentrations increased after biochar application, the availability of potentially phytotoxic trace elements (Zn, Pb, Cd, Cr) decreased significantly, and although slight increases in microbial biomass carbon and heterotrophic CO2 fluxes were observed after biochar application, they were mostly not significant. The results indicate that the application of relatively small amounts of biochar could have positive effects on plant available nutrients and crop yields of marginal arable soils and may decrease the need for mineral fertilizers while simultaneously increasing the sequestration of soil organic carbon. Highlights A low rate of biochar increased plant available nutrients and crop yield on marginal soils. Biochar application reduced the availability of potentially harmful trace elements. Heterotrophic respiration showed no clear response to biochar application. Biochar application may reduce fertilizer need and increase carbon sequestration on marginal soils.
    Beschreibung: German Academic Exchange Service http://dx.doi.org/10.13039/501100001655
    Beschreibung: Institute Strategic Programme grants, “Soils to Nutrition”
    Schlagwort(e): 631.4 ; black carbon ; carbon sequestration ; corn ; digestate ; heterotrophic respiration ; marginal soils ; microbial biomass
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  • 18
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    Staircase array of inclined refractive multi‐lenses for large field of view pixel super‐resolution scanning transmission hard X‐ray microscopy (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-06-26
    Beschreibung: Owing to the development of X‐ray focusing optics during the past decades, synchrotron‐based X‐ray microscopy techniques allow the study of specimens with unprecedented spatial resolution, down to 10 nm, using soft and medium X‐ray photon energies, though at the expense of the field of view (FOV). One of the approaches to increase the FOV to square millimetres is raster‐scanning of the specimen using a single nanoprobe; however, this results in a long data acquisition time. This work employs an array of inclined biconcave parabolic refractive multi‐lenses (RMLs), fabricated by deep X‐ray lithography and electroplating to generate a large number of long X‐ray foci. Since the FOV is limited by the pattern height if a single RML is used by impinging X‐rays parallel to the substrate, many RMLs at regular intervals in the orthogonal direction were fabricated by tilted exposure. By inclining the substrate correspondingly to the tilted exposure, 378000 X‐ray line foci were generated with a length in the centimetre range and constant intervals in the sub‐micrometre range. The capability of this new X‐ray focusing device was first confirmed using ray‐tracing simulations and then using synchrotron radiation at BL20B2 of SPring‐8, Japan. Taking account of the fact that the refractive lens is effective for focusing high‐energy X‐rays, the experiment was performed with 35 keV X‐rays. Next, by scanning a specimen through the line foci, this device was used to perform large FOV pixel super‐resolution scanning transmission hard X‐ray microscopy (PSR‐STHXM) with a 780 ± 40 nm spatial resolution within an FOV of 1.64 cm × 1.64 cm (limited by the detector area) and a total scanning time of 4 min. Biomedical implant abutments fabricated via selective laser melting using Ti–6Al–4V medical alloy were measured by PSR‐STHXM, suggesting its unique potential for studying extended and thick specimens. Although the super‐resolution function was realized in one dimension in this study, it can be expanded to two dimensions by aligning a pair of presented devices orthogonally.
    Beschreibung: A new X‐ray focusing device generates hundreds of thousands of line foci, periodically spaced in the sub‐micrometre range, with centimetre length. It enables to achieve large FOV pixel super‐resolution scanning transmission hard X‐ray microscopy. image
    Schlagwort(e): 502.82 ; inclined refractive X‐ray multi‐lens array ; pixel super‐resolution ; scanning transmission hard X‐ray microscopy ; deep X‐ray lithography and electroplating
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  • 19
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    A new concept for temporal gating of synchrotron X‐ray pulses (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-07-02
    Beschreibung: A new concept for temporal gating of synchrotron X‐ray pulses based on laser‐induced thermal transient gratings is presented. First experimental tests of the concept yield a diffraction efficiency of 0.18%; however, the calculations indicate a theoretical efficiency and contrast of 〉30% and 10−5, respectively. The full efficiency of the pulse picker has not been reached yet due to a long‐range thermal deformation of the sample after absorption of the excitation laser. This method can be implemented in a broad spectral range (100 eV to 20 keV) and is only minimally invasive to an existing setup.
    Beschreibung: A new concept for temporal gating of synchrotron X‐ray pulses based on laser‐induced thermal transient gratings is presented.
    Schlagwort(e): 548 ; synchrotron ; time‐resolved ; thermal deformation ; transient grating ; pulse picking
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  • 20
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    The time‐resolved hard X‐ray diffraction endstation KMC‐3 XPP at BESSY II (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-06-06
    Beschreibung: The time‐resolved hard X‐ray diffraction endstation KMC‐3 XPP for optical pump/X‐ray probe experiments at the electron storage ring BESSY II is dedicated to investigating the structural response of thin film samples and heterostructures after their excitation with ultrashort laser pulses and/or electric field pulses. It enables experiments with access to symmetric and asymmetric Bragg reflections via a four‐circle diffractometer and it is possible to keep the sample in high vacuum and vary the sample temperature between ∼15 K and 350 K. The femtosecond laser system permanently installed at the beamline allows for optical excitation of the sample at 1028 nm. A non‐linear optical setup enables the sample excitation also at 514 nm and 343 nm. A time‐resolution of 17 ps is achieved with the `low‐α' operation mode of the storage ring and an electronic variation of the delay between optical pump and hard X‐ray probe pulse conveniently accesses picosecond to microsecond timescales. Direct time‐resolved detection of the diffracted hard X‐ray synchrotron pulses use a gated area pixel detector or a fast point detector in single photon counting mode. The range of experiments that are reliably conducted at the endstation and that detect structural dynamics of samples excited by laser pulses or electric fields are presented.
    Beschreibung: The KMC‐3 XPP endstation of the synchrotron BESSY II is dedicated to time‐resolved studies of structural dynamics of matter upon optical and/or electrical excitation using hard X‐ray diffraction with an accessible time range from 17 ps to several microseconds. image
    Schlagwort(e): 548 ; beamline instrumentation ; time‐resolved X‐ray diffraction ; optical excitation ; thermal transport ; ferroelectric switching
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  • 21
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    Self‐stated recovery from flooding: Empirical results from a survey in Central Vietnam (2021)
    Blackwell Publishing Ltd | Oxford, UK
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    Publikationsdatum: 2021-06-27
    Beschreibung: Social inequalities lead to flood resilience inequalities across social groups, a topic that requires improved documentation and understanding. The objective of this paper is to attend to these differences by investigating self‐stated flood recovery across genders in Vietnam as a conceptual replication of earlier results from Germany. This study employs a regression‐based analysis of 1,010 respondents divided between a rural coastal and an urban community in Thua Thien‐Hue province. The results highlight an important set of recovery process‐related variables. The set of relevant variables is similar across genders in terms of inclusion and influence, and includes age, social capital, internal and external support after a flood, perceived severity of previous flood impacts, and the perception of stress‐resilience. However, women were affected more heavily by flooding in terms of longer recovery times, which should be accounted for in risk management. Overall, the studied variables perform similarly in Vietnam and Germany. This study, therefore, conceptually replicates previous results suggesting that women display slightly slower recovery levels as well as that psychological variables influence recovery rates more than adverse flood impacts. This provides an indication of the results' potentially robust nature due to the different socio‐environmental contexts in Germany and Vietnam.
    Schlagwort(e): 333.7 ; flood recovery ; resilience ; societal equity ; vulnerability
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  • 22
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    Disordered sodium alkoxides from powder data: crystal structures of sodium ethoxide, propoxide, butoxide and pentoxide, and some of their solvates (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-03-27
    Beschreibung: The crystal structures of sodium ethoxide (sodium ethanolate, NaOEt), sodium n‐propoxide (sodium n‐propanolate, NaOnPr), sodium n‐butoxide (sodium n‐butanolate, NaOnBu) and sodium n‐pentoxide (sodium n‐amylate, NaOnAm) were determined from powder X‐ray diffraction data. NaOEt crystallizes in space group P421m, with Z = 2, and the other alkoxides crystallize in P4/nmm, with Z = 2. To resolve space‐group ambiguities, a Bärnighausen tree was set up, and Rietveld refinements were performed with different models. In all structures, the Na and O atoms form a quadratic net, with the alkyl groups pointing outwards on both sides (anti‐PbO type). The alkyl groups are disordered. The disorder becomes even more pronounced with increasing chain length. Recrystallization from the corresponding alcohols yielded four sodium alkoxide solvates: sodium ethoxide ethanol disolvate (NaOEt·2EtOH), sodium n‐propoxide n‐propanol disolvate (NaOnPr·2nPrOH), sodium isopropoxide isopropanol pentasolvate (NaOiPr·5iPrOH) and sodium tert‐amylate tert‐amyl alcohol monosolvate (NaOtAm·tAmOH, tAm = 2‐methyl‐2‐butyl). Their crystal structures were determined by single‐crystal X‐ray diffraction. All these solvates form chain structures consisting of Na+, –O− and –OH groups, encased by alkyl groups. The hydrogen‐bond networks diverge widely among the solvate structures. The hydrogen‐bond topology of the iPrOH network in NaOiPr·5iPrOH shows branched hydrogen bonds and differs considerably from the networks in pure crystalline iPrOH.
    Beschreibung: The crystal structures of NaOEt, NaOPr, NaOBu and NaOAm (Am = amyl = pentyl) were determined from powder data. These compounds crystallize in an anti‐PbO structure in the space groups P21m and P4/nmm. Additionally, solvates with the composition NaOEt·2EtOH, NaOPr·2PrOH, NaOiPr·5iPrOH and NaOtAm·tAmOH were synthesized, and their structures were determined from single crystals. They form interesting chain structures of different compositions and topologies. image
    Schlagwort(e): 548 ; sodium alkoxide ; powder data ; solvate ; isopropanol ; Bärnighausen tree ; PXRD
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  • 23
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    The potential of ryegrass as cover crop to reduce soil N2O emissions and increase the population size of denitrifying bacteria (2021)
    Blackwell Publishing Ltd | Oxford, UK
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    Publikationsdatum: 2021-07-05
    Beschreibung: Nitrogen (N) fertilization is the major contributor to nitrous oxide (N2O) emissions from agricultural soil, especially in post‐harvest seasons. This study was carried out to investigate whether ryegrass serving as cover crop affects soil N2O emissions and denitrifier community size. A microcosm experiment was conducted with soil planted with perennial ryegrass (Lolium perenne L.) and bare soil, each with four levels of N fertilizer (0, 5, 10 and 20 g N m−2; applied as calcium ammonium nitrate). The closed‐chamber approach was used to measure soil N2O fluxes. Real‐time PCR was used to estimate the biomass of bacteria and fungi and the abundance of genes involved in denitrification in soil. The results showed that the presence of ryegrass decreased the nitrate content in soil. Cumulative N2O emissions of soil with grass were lower than in bare soil at 5 and 10 g N m−2. Fertilization levels did not affect the abundance of soil bacteria and fungi. Soil with grass showed greater abundances of bacteria and fungi, as well as microorganisms carrying narG, napA, nirK, nirS and nosZ clade I genes. It is concluded that ryegrass serving as a cover crop holds the potential to mitigate soil N2O emissions in soils with moderate or high NO3− concentrations. This highlights the importance of cover crops for the reduction of N2O emissions from soil, particularly following N fertilization. Future research should explore the full potential of ryegrass to reduce soil N2O emissions under field conditions as well as in different soils. Highlights This study was to investigate whether ryegrass serving as cover crop affects soil N2O emissions and denitrifier community size; Plant reduced soil N substrates on one side, but their root exudates stimulated denitrification on the other side; N2O emissions were lower in soil with grass than bare soil at medium fertilizer levels, and growing grass stimulated the proliferation of almost all the denitrifying bacteria except nosZ clade II; Ryegrass serving as a cover crop holds the potential to mitigate soil N2O emissions.
    Beschreibung: China Scholarship Council http://dx.doi.org/10.13039/501100004543
    Beschreibung: The National Science Project for University of Anhui Province
    Schlagwort(e): 551.9 ; 631.4 ; denitrification ; perennial ryegrass (Lolium perenne L.) ; soil bacteria ; soil CO2 emissions ; soil N2O emissions
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  • 24
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    Small‐angle X‐ray scattering from GaN nanowires on Si(111): facet truncation rods, facet roughness and Porod's law (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-03-27
    Beschreibung: Small‐angle X‐ray scattering from GaN nanowires grown on Si(111) is measured in the grazing‐incidence geometry and modelled by means of a Monte Carlo simulation that takes into account the orientational distribution of the faceted nanowires and the roughness of their side facets. It is found that the scattering intensity at large wavevectors does not follow Porod's law I(q) ∝ q−4. The intensity depends on the orientation of the side facets with respect to the incident X‐ray beam. It is maximum when the scattering vector is directed along a facet normal, reminiscent of surface truncation rod scattering. At large wavevectors q, the scattering intensity is reduced by surface roughness. A root‐mean‐square roughness of 0.9 nm, which is the height of just 3–4 atomic steps per micrometre‐long facet, already gives rise to a strong intensity reduction.
    Beschreibung: The intensity of small‐angle X‐ray scattering from GaN nanowires on Si(111) depends on the orientation of the side facets with respect to the incident beam. This reminiscence of truncation rod scattering gives rise to a deviation from Porod's law. A roughness of just 3–4 atomic steps per micrometre‐long side facet notably changes the intensity curves. image
    Schlagwort(e): 548 ; nanowires ; Porod's law ; facet truncation rods ; small‐angle X‐ray scattering ; SAXS ; grazing‐incidence small‐angle X‐ray scattering ; GISAXS
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  • 25
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    The accuracy of protein models automatically built into cryo‐EM maps with ARP/wARP (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-06-28
    Beschreibung: Recent developments in cryogenic electron microscopy (cryo‐EM) have enabled structural studies of large macromolecular complexes at resolutions previously only attainable using macromolecular crystallography. Although a number of methods can already assist in de novo building of models into high‐resolution cryo‐EM maps, automated and reliable map interpretation remains a challenge. Presented here is a systematic study of the accuracy of models built into cryo‐EM maps using ARP/wARP. It is demonstrated that the local resolution is a good indicator of map interpretability, and for the majority of the test cases ARP/wARP correctly builds 90% of main‐chain fragments in regions where the local resolution is 4.0 Å or better. It is also demonstrated that the coordinate accuracy for models built into cryo‐EM maps is comparable to that of X‐ray crystallographic models at similar local cryo‐EM and crystallographic resolutions. The model accuracy also correlates with the refined atomic displacement parameters.
    Schlagwort(e): 548 ; ARP/wARP ; model building ; cryo‐EM ; model accuracy ; sequence assignment
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  • 26
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    Synthesis, crystal structure and structure–property relations of strontium orthocarbonate, Sr2CO4 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-06-05
    Beschreibung: Carbonates containing CO4 groups as building blocks have recently been discovered. A new orthocarbonate, Sr2CO4 is synthesized at 92 GPa and at a temperature of 2500 K. Its crystal structure was determined by in situ synchrotron single‐crystal X‐ray diffraction, selecting a grain from a polycrystalline sample. Strontium orthocarbonate crystallizes in the orthorhombic crystal system (space group Pnma) with CO4, SrO9 and SrO11 polyhedra as the main building blocks. It is isostructural to Ca2CO4. DFT calculations reproduce the experimental findings very well and have, therefore, been used to predict the equation of state, Raman and IR spectra, and to assist in the discussion of bonding in this compound.
    Beschreibung: A new orthocarbonate, Sr2CO4, was synthesized under extreme pressure and temperature conditions of 92 GPa and 2500 K, respectively. The crystal structure of the compound s fully characterized in situ by synchrotron single‐crystal X‐ray diffraction and DFT calculations were employed to provide insight into its equation of state, Raman and IR spectra, and bonding. image
    Schlagwort(e): 548 ; orthocarbonates ; crystal structure ; single‐crystal X‐ray diffraction ; high pressure ; Sr2CO4
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  • 27
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    Anomalous SAXS at P12 beamline EMBL Hamburg: instrumentation and applications (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-06-28
    Beschreibung: Small‐angle X‐ray scattering (SAXS) is an established method for studying nanostructured systems and in particular biological macromolecules in solution. To obtain element‐specific information about the sample, anomalous SAXS (ASAXS) exploits changes of the scattering properties of selected atoms when the energy of the incident X‐rays is close to the binding energy of their electrons. While ASAXS is widely applied to condensed matter and inorganic systems, its use for biological macromolecules is challenging because of the weak anomalous effect. Biological objects are often only available in small quantities and are prone to radiation damage, which makes biological ASAXS measurements very challenging. The BioSAXS beamline P12 operated by the European Molecular Biology Laboratory (EMBL) at the PETRA III storage ring (DESY, Hamburg) is dedicated to studies of weakly scattering objects. Here, recent developments at P12 allowing for ASAXS measurements are presented. The beamline control, data acquisition and data reduction pipeline of the beamline were adapted to conduct ASAXS experiments. Modelling tools were developed to compute ASAXS patterns from atomic models, which can be used to analyze the data and to help designing appropriate data collection strategies. These developments are illustrated with ASAXS experiments on different model systems performed at the P12 beamline.
    Schlagwort(e): 548 ; ASAXS ; biological SAXS ; metalloproteins ; gold nanoparticles ; anomalous scattering ; beamline development
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  • 28
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    Symmetry relations in wurtzite nitrides and oxide nitrides and the curious case of Pmc21 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-06-27
    Beschreibung: Binary III–V nitrides such as AlN, GaN and InN in the wurtzite‐type structure have long been considered as potent semiconducting materials because of their optoelectronic properties, amongst others. With rising concerns over the utilization of scarce elements, a replacement of the trivalent cations by others in ternary and multinary nitrides has led to the development of different variants of nitrides and oxide nitrides crystallizing in lower‐symmetry variants of wurtzite. This work presents the symmetry relationships between these structural types specific to nitrides and oxide nitrides and updates some prior work on this matter. The non‐existence of compounds crystallizing in Pmc21, formally the highest subgroup of the wurtzite type fulfilling Pauling's rules for 1:1:2 stoichiometries, has been puzzling scientists for a while; a rationalization is given, from a crystallographic basis, of why this space group is unlikely to be adopted.
    Schlagwort(e): 548 ; group–subgroup relationships ; nitride materials ; wurtzite type
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  • 29
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    Comparison and evaluation of pair distribution functions, using a similarity measure based on cross‐correlation functions (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-06-20
    Beschreibung: An approach for the comparison of pair distribution functions (PDFs) has been developed using a similarity measure based on cross‐correlation functions. The PDF is very sensitive to changes in the local structure, i.e. small deviations in the structure can cause large signal shifts and significant discrepancies between the PDFs. Therefore, a comparison based on pointwise differences (e.g. R values and difference curves) may lead to the assumption that the investigated PDFs as well as the corresponding structural models are not in agreement at all, whereas a careful visual inspection of the investigated structural models and corresponding PDFs may reveal a relatively good match. To quantify the agreement of different PDFs for those cases an alternative approach is introduced: the similarity measure based on cross‐correlation functions. In this paper, the power of this application of the similarity measure to the analysis of PDFs is highlighted. The similarity measure is compared with the classical Rwp values as representative of the comparison based on pointwise differences as well as with the Pearson product‐moment correlation coefficient, using polymorph IV of barbituric acid as an example.
    Beschreibung: A novel approach to the quantification of the agreement between pair distribution functions by a similarity measure based on cross‐correlation functions is introduced and evaluated. image
    Schlagwort(e): 548 ; pair distribution functions ; similarity measures ; total scattering techniques ; cross‐correlation functions ; R values
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  • 30
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    Novel experimental setup for megahertz X‐ray diffraction in a diamond anvil cell at the High Energy Density (HED) instrument of the European X‐ray Free‐Electron Laser (EuXFEL) (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-06-26
    Beschreibung: The high‐precision X‐ray diffraction setup for work with diamond anvil cells (DACs) in interaction chamber 2 (IC2) of the High Energy Density instrument of the European X‐ray Free‐Electron Laser is described. This includes beamline optics, sample positioning and detector systems located in the multipurpose vacuum chamber. Concepts for pump–probe X‐ray diffraction experiments in the DAC are described and their implementation demonstrated during the First User Community Assisted Commissioning experiment. X‐ray heating and diffraction of Bi under pressure, obtained using 20 fs X‐ray pulses at 17.8 keV and 2.2 MHz repetition, is illustrated through splitting of diffraction peaks, and interpreted employing finite element modeling of the sample chamber in the DAC.
    Beschreibung: The high‐precision X‐ray diffraction (XRD) setup for work with diamond anvil cells (DACs) in Interaction Chamber 2 of the High Energy Density (HED) instrument of the European X‐ray Free‐Electron Laser is described. image
    Schlagwort(e): 548 ; diamond anvil cells ; X‐ray free‐electron lasers ; high‐precision X‐ray diffraction ; finite element modeling
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  • 31
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    The anisotropy in the optical constants of quartz crystals for soft X‐rays (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-06-26
    Beschreibung: The refractive index of a y‐cut SiO2 crystal surface is reconstructed from orientation‐dependent soft X‐ray reflectometry measurements in the energy range from 45 to 620 eV. Owing to the anisotropy of the crystal structure in the (100) and (001) directions, a significant deviation of the measured reflectance at the Si L2,3 and O K absorption edges is observed. The anisotropy in the optical constants reconstructed from these data is also confirmed by ab initio Bethe–Salpeter equation calculations for the O K edge. This new experimental data set expands the existing literature data for quartz crystal optical constants significantly, particularly in the near‐edge regions.
    Beschreibung: The refractive index of a y‐cut SiO2 crystal surface is reconstructed from polarization‐dependent soft X‐ray reflectometry measurements in the energy range from 45 to 620 eV. The reconstructed anisotropy in the optical constants is also confirmed by ab initio Bethe–Salpeter equation calculations of the O K edge. image
    Schlagwort(e): 548 ; optical constants ; quartz ; anisotropy ; soft X‐ray reflectometry
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  • 32
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    Unravelling the crystal structure of Nd5.8WO12−δ and Nd5.7W0.75Mo0.25O12−δ mixed ionic electronic conductors (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-07-05
    Beschreibung: Mixed ionic electronic conducting ceramics Nd6−yWO12−δ (δ is the oxygen deficiency) provide excellent stability in harsh environments containing strongly reactive gases such as CO2, CO, H2, H2O or H2S. Due to this chemical stability, they are promising and cost‐efficient candidate materials for gas separation, catalytic membrane reactors and protonic ceramic fuel cell technologies. As in La6−yWO12−δ, the ionic/electronic transport mechanism in Nd6−yWO12−δ is expected to be largely controlled by the crystal structure, the conclusive determination of which is still lacking. This work presents a crystallographic study of Nd5.8WO12−δ and molybdenum‐substituted Nd5.7W0.75Mo0.25O12−δ prepared by the citrate complexation route. High‐resolution synchrotron and neutron powder diffraction data were used in combined Rietveld refinements to unravel the crystal structure of Nd5.8WO12−δ and Nd5.7W0.75Mo0.25O12−δ. Both investigated samples crystallize in a defect fluorite crystal structure with space group Fm3m and doubled unit‐cell parameter due to cation ordering. Mo replaces W at both Wyckoff sites 4a and 48h and is evenly distributed, in contrast with La6−yWO12−δ. X‐ray absorption spectroscopy as a function of partial pressure pO2 in the near‐edge regions excludes oxidation state changes of Nd (Nd3+) and W (W6+) in reducing conditions: the enhanced hydrogen permeation, i.e. ambipolar conduction, observed in Mo‐substituted Nd6−yWO12−δ is therefore explained by the higher Mo reducibility and the creation of additional – disordered – oxygen vacancies.
    Beschreibung: The crystal structures of non‐substituted and Mo‐substituted neodymium tungstates are described in detail through neutron diffraction and high‐resolution X‐ray diffraction. Combined X‐ray and neutron diffraction refinements and electron probe micro‐analysis were employed to locate Mo atoms in the crystal structure of Nd6−yW1−zMozO12−δ (z = 0, 0.25), while X‐ray absorption spectroscopy in the near‐edge regions confirmed no changes in the oxidation states of Nd and W.
    Schlagwort(e): 548 ; powder diffraction ; mixed conductors ; X‐ray absorption spectroscopy (XAS) ; Nd6−yWO12−δ
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  • 33
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    ogs5py: A Python‐API for the OpenGeoSys 5 Scientific Modeling Package (2021)
    Blackwell Publishing Ltd | Malden, US
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    Publikationsdatum: 2021-07-04
    Beschreibung: High‐performance numerical codes are an indispensable tool for hydrogeologists when modeling subsurface flow and transport systems. But as they are written in compiled languages, like C/C++ or Fortran, established software packages are rarely user‐friendly, limiting a wider adoption of such tools. OpenGeoSys (OGS), an open‐source, finite‐element solver for thermo‐hydro‐mechanical–chemical processes in porous and fractured media, is no exception. Graphical user interfaces may increase usability, but do so at a dramatic reduction of flexibility and are difficult or impossible to integrate into a larger workflow. Python offers an optimal trade‐off between these goals by providing a highly flexible, yet comparatively user‐friendly environment for software applications. Hence, we introduce ogs5py, a Python‐API for the OpenGeoSys 5 scientific modeling package. It provides a fully Python‐based representation of an OGS project, a large array of convenience functions for users to interact with OGS and connects OGS to the scientific and computational environment of Python.
    Beschreibung: German Federal Environmental Foundation http://dx.doi.org/10.13039/100007636
    Beschreibung: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Schlagwort(e): 551.49 ; hydrogeology ; subsurface flow ; modeling ; software
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  • 34
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    High‐temperature treatments of niobium under high vacuum, dilute air‐ and nitrogen‐atmospheres as investigated by in situ X‐ray absorption spectroscopy (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publikationsdatum: 2021-06-30
    Beschreibung: Niobium metal foils were heat‐treated at 900°C under different conditions and in situ investigated with time‐resolved X‐ray absorption fine‐structure (EXAFS and XANES) measurements. The present study aims to mimic the conditions usually applied for heat treatments of Nb materials used for superconducting radiofrequency cavities, in order to better understand the evolving processes during vacuum annealing as well as for heat treatments in controlled dilute gases. Annealing in vacuum in a commercially available cell showed a substantial amount of oxidation, so that a designated new cell was designed and realized, allowing treatments under clean high‐vacuum conditions as well as under well controllable gas atmospheres. The experiments performed under vacuum demonstrated that the original structure of the Nb foils is preserved, while a detailed evaluation of the X‐ray absorption fine‐structure data acquired during treatments in dilute air atmospheres (10−5 mbar to 10−3 mbar) revealed a linear oxidation with the time of the treatment, and an oxidation rate proportional to the oxygen (air) pressure. The structure of the oxide appears to be very similar to that of polycrystalline NbO. The cell also permits controlled exposures to other reactive gases at elevated temperatures; here the Nb foils were exposed to dilute nitrogen atmospheres after a pre‐conditioning of the studied Nb material for one hour under high‐vacuum conditions, in order to imitate typical conditions used for nitrogen doping of cavity materials. Clear structural changes induced by the N2 exposure were found; however, no evidence for the formation of niobium nitride could be derived from the EXAFS and XANES experiments. The presented results establish the feasibility to study the structural changes of the Nb materials in situ during heat treatments in reactive gases with temporal resolution, which are important to better understand the underlaying mechanisms and the dynamics of phase formation during those heat treatments in more detail.
    Schlagwort(e): 548 ; in situ EXAFS ; high temperature ; time‐resolved EXAFS ; niobium
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  • 35
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    High‐Resolution Integrated Transport Model for Studying Surface Water–Groundwater Interaction (2021)
    Blackwell Publishing Ltd | Malden, US
    Details
    Publikationsdatum: 2021-06-27
    Beschreibung: Transport processes that lead to exchange of mass between surface water and groundwater play a significant role for the ecological functioning of aquatic systems, for hydrological processes and for biogeochemical transformations. In this study, we present a novel integral modeling approach for flow and transport at the sediment–water interface. The model allows us to simultaneously simulate turbulent surface and subsurface flow and transport with the same conceptual approach. For this purpose, a conservative transport equation was implemented to an existing approach that uses an extended version of the Navier–Stokes equations. Based on previous flume studies which investigated the spreading of a dye tracer under neutral, losing and gaining flow conditions the new solver is validated. Tracer distributions of the experiments are in close agreement with the simulations. The simulated flow paths are significantly affected by in‐ and outflowing groundwater flow. The highest velocities within the sediment are found for losing condition, which leads to shorter residence times compared to neutral and gaining conditions. The largest extent of the hyporheic exchange flow is observed under neutral condition. The new solver can be used for further examinations of cases that are not suitable for the conventional coupled models, for example, if Reynolds numbers are larger than 10. Moreover, results gained with the integral solver provide high‐resolution information on pressure and velocity distributions at the rippled streambed, which can be used to improve flow predictions. This includes the extent of hyporheic exchange under varying ambient groundwater flow conditions.
    Beschreibung: Technische Universität Berlin, Germany
    Beschreibung: German Research Foundation http://dx.doi.org/10.13039/501100001659
    Schlagwort(e): 551.4 ; aquatic systems ; sediment-water interface ; transport model
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  • 36
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    Pressure‐induced Pb–Pb bonding and phase transition in Pb2SnO4 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-03-27
    Beschreibung: High‐pressure single‐crystal to 20 GPa and powder diffraction measurements to 50 GPa, show that the structure of Pb2SnO4 strongly distorts on compression with an elongation of one axis. A structural phase transition occurs between 10 GPa and 12 GPa, with a change of space group from Pbam to Pnam. The resistivity decreases by more than six orders of magnitude when pressure is increased from ambient conditions to 50 GPa. This insulator‐to‐semiconductor transition is accompanied by a reversible appearance change from transparent to opaque. Density functional theory‐based calculations show that at ambient conditions the channels in the structure host the stereochemically‐active Pb 6s2 lone electron pairs. On compression the lone electron pairs form bonds between Pb2+ ions. Also provided is an assignment of irreducible representations to the experimentally observed Raman bands.
    Beschreibung: The structure of Pb2SnO4 is found to strongly distort on compression and a structural phase transition with a change of space group from Pbam to Pnam occurs at ∼11 GPa. Our complementary DFT‐based calculations show that at ambient conditions, the channels in the structure host the stereochemically active Pb 6s2 lone electron pairs which form bonds between the Pb2+ ions with increasing pressure. image
    Schlagwort(e): 548 ; lead stannate (Pb2SnO4) ; density functional theory ; high‐pressure X‐ray diffraction ; pressure‐induced phase transition ; insulator–semiconductor transition
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  • 37
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    Iron isotope fractionation in soil and graminaceous crops after 100 years of liming in the long‐term agricultural experimental site at Berlin‐Dahlem, Germany (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publikationsdatum: 2021-07-05
    Beschreibung: Sustainable arable cropping relies on repeated liming. Yet, the associated increase in soil pH can reduce the availability of iron (Fe) to plants. We hypothesized that repeated liming, but not pedogenic processes such as lessivage (i.e., translocation of clay particles), alters the Fe cycle in Luvisol soil, thereby affecting Fe isotope composition in soils and crops. Hence, we analysed Fe concentrations and isotope compositions in soil profiles and winter rye from the long‐term agricultural experimental site in Berlin‐Dahlem, Germany, where a controlled liming trial with three field replicates per treatment has been conducted on Albic Luvisols since 1923. Heterogeneity in subsoil was observed at this site for Fe concentration but not for Fe isotope composition. Lessivage had not affected Fe isotope composition in the soil profiles. The results also showed that almost 100 years of liming lowered the concentration of the HCl‐extractable Fe that was potentially available for plant uptake in the surface soil (0–15 cm) from 1.03 (standard error (SE) 0.03) to 0.94 (SE 0.01) g kg−1. This HCl‐extractable Fe pool contained isotopically lighter Fe (δ56Fe = −0.05 to −0.29‰) than the bulk soil (δ56Fe = −0.08 to 0.08‰). However, its Fe isotope composition was not altered by the long‐term lime application. Liming resulted in relatively lower Fe concentrations in the roots of winter rye. In addition, liming led to a heavier Fe isotope composition of the whole plants compared with those grown in the non‐limed plots (δ56FeWholePlant_ + Lime = −0.12‰, SE 0.03 vs. δ56FeWholePlant_‐Lime = −0.21‰, SE 0.01). This suggests that the elevated soil pH (increased by one unit due to liming) promoted the Fe uptake strategy through complexation of Fe(III) from the rhizosphere, which favoured heavier Fe isotopes. Overall, the present study showed that liming and a related increase in pH did not affect the Fe isotope compositions of the soil, but may influence the Fe isotope composition of plants grown in the soil if they alter their Fe uptake strategy upon the change of Fe availability. Highlights Fe concentrations and stocks, but not Fe isotope compositions, were more heterogeneous in subsoil than in topsoil. Translocation of clay minerals did not result in Fe isotope fractionation in the soil profile of a Luvisol. Liming decreased Fe availability in topsoil, but did not affect its δ56Fe values. Uptake of heavier Fe isotopes by graminaceous crops was more pronounced at elevated pH.
    Beschreibung: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Schlagwort(e): 551.9 ; liming ; plant‐available Fe pool in soil ; winter rye ; δ56Fe
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  • 38
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    A discussion on `Domain formation and phase transitions in the wurtzite‐based heterovalent ternaries: a Landau theory analysis' (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publikationsdatum: 2021-06-05
    Beschreibung: Heterovalent ternary nitrides are considered one of the promising classes of materials for photovoltaics, combining attractive physical properties with low toxicity and element abundance. One of the front‐runner systems under consideration is ZnSnN2. Although it is nominally a ternary compound, no clear crystallographic evidence for cation ordering has been observed so far. An attempt to elucidate this discrepancy [Quayle (2020). Acta Cryst. A76, 410–420] was the trigger for an intensive discussion between the authors, and an agreement was reached to elaborate on some points in order to set things in perspective. Rather than using a conventional comment–answer scheme, this is published in the form of a joint discussion to celebrate constructive criticism and collegiality.
    Beschreibung: A scientific exchange on an earlier paper [Quayle (2020). Acta Cryst. A76, 410–420] has led to the clarification of some of the points. image
    Schlagwort(e): 548 ; group–subgroup relationships ; nitride materials ; wurtzite type
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  • 39
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    X‐SPEC: a 70 eV to 15 keV undulator beamline for X‐ray and electron spectroscopies (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-06-26
    Beschreibung: X‐SPEC is a high‐flux spectroscopy beamline at the KIT (Karlsruhe Institute of Technology) Synchrotron for electron and X‐ray spectroscopy featuring a wide photon energy range. The beamline is equipped with a permanent magnet undulator with two magnetic structures of different period lengths, a focusing variable‐line‐space plane‐grating monochromator, a double‐crystal monochromator and three Kirkpatrick–Baez mirror pairs. By selectively moving these elements in or out of the beam, X‐SPEC is capable of covering an energy range from 70 eV up to 15 keV. The flux of the beamline is maximized by optimizing the magnetic design of the undulator, minimizing the number of optical elements and optimizing their parameters. The beam can be focused into two experimental stations while maintaining the same spot position throughout the entire energy range. The first experimental station is optimized for measuring solid samples under ultra‐high‐vacuum conditions, while the second experimental station allows in situ and operando studies under ambient conditions. Measurement techniques include X‐ray absorption spectroscopy (XAS), extended X‐ray absorption fine structure (EXAFS), photoelectron spectroscopy (PES) and hard X‐ray PES (HAXPES), as well as X‐ray emission spectroscopy (XES) and resonant inelastic X‐ray scattering (RIXS).
    Beschreibung: X‐SPEC is a high‐flux undulator beamline for electron and X‐ray spectroscopy with an energy range from 70 eV to 15 keV. It offers X‐ray absorption spectroscopy (XAS), extended X‐ray absorption fine structure (EXAFS), photoelectron spectroscopy (PES) and hard X‐ray PES (HAXPES), as well as X‐ray emission spectroscopy (XES) and resonant inelastic X‐ray scattering (RIXS) for in vacuo, in situ and operando sample environments. image
    Schlagwort(e): 548 ; undulator beamline ; soft X‐ray ; tender X‐ray ; hard X‐ray ; in situ ; operando ; HAXPES ; RIXS ; XAS ; XES
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  • 40
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    Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-06-26
    Beschreibung: A method for the ab initio crystal structure determination of organic compounds by a fit to the pair distribution function (PDF), without prior knowledge of lattice parameters and space group, has been developed. The method is called `PDF‐Global‐Fit' and is implemented by extension of the program FIDEL (fit with deviating lattice parameters). The structure solution is based on a global optimization approach starting from random structural models in selected space groups. No prior indexing of the powder data is needed. The new method requires only the molecular geometry and a carefully determined PDF. The generated random structures are compared with the experimental PDF and ranked by a similarity measure based on cross‐correlation functions. The most promising structure candidates are fitted to the experimental PDF data using a restricted simulated annealing structure solution approach within the program TOPAS, followed by a structure refinement against the PDF to identify the correct crystal structure. With the PDF‐Global‐Fit it is possible to determine the local structure of crystalline and disordered organic materials, as well as to determine the local structure of unindexable powder patterns, such as nanocrystalline samples, by a fit to the PDF. The success of the method is demonstrated using barbituric acid as an example. The crystal structure of barbituric acid form IV solved and refined by the PDF‐Global‐Fit is in excellent agreement with the published crystal structure data.
    Schlagwort(e): 548 ; pair distribution function analysis ; structure determination ; total scattering technique ; similarity measures ; PDF‐Global‐Fit
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  • 41
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    Structural basis of chitin utilization by a GH20 β‐N‐acetylglucosaminidase from Vibrio campbellii strain ATCC BAA‐1116 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-07-01
    Beschreibung: Vibrio species play a crucial role in maintaining the carbon and nitrogen balance between the oceans and the land through their ability to employ chitin as a sole source of energy. This study describes the structural basis for the action of the GH20 β‐N‐acetylglucosaminidase (VhGlcNAcase) in chitin metabolism by Vibrio campbellii (formerly V. harveyi) strain ATCC BAA‐1116. Crystal structures of wild‐type VhGlcNAcase in the absence and presence of the sugar ligand, and of the unliganded D437A mutant, were determined. VhGlcNAcase contains three distinct domains: an N‐terminal carbohydrate‐binding domain linked to a small α+β domain and a C‐terminal (β/α)8 catalytic domain. The active site of VhGlcNAcase has a narrow, shallow pocket that is suitable for accommodating a small chitooligosaccharide. VhGlcNAcase is a monomeric enzyme of 74 kDa, but its crystal structures show two molecules of enzyme per asymmetric unit, in which Gln16 at the dimeric interface of the first molecule partially blocks the entrance to the active site of the neighboring molecule. The GlcNAc unit observed in subsite −1 makes exclusive hydrogen bonds to the conserved residues Arg274, Tyr530, Asp532 and Glu584, while Trp487, Trp546, Trp582 and Trp505 form a hydrophobic wall around the −1 GlcNAc. The catalytic mutants D437A/N and E438A/Q exhibited a drastic loss of GlcNAcase activity, confirming the catalytic role of the acidic pair (Asp437–Glu438).
    Beschreibung: Crystal structures of a GH20 β‐N‐acetylglucosaminidase from V. campbellii reveal substrate specificity in chitin utilization.
    Schlagwort(e): 577.14 ; GH20 β‐N‐acetylglucosaminidase ; chitin recycling ; Vibrio spp ; marine bacteria
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  • 42
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    Resolution of a bent‐crystal spectrometer for X‐ray free‐electron laser pulses: diamond versus silicon (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-09-29
    Beschreibung: The resolution function of a spectrometer based on a strongly bent single crystal (bending radius of 10 cm or less) is evaluated. It is shown that the resolution is controlled by two parameters: (i) the ratio of the lattice spacing of the chosen reflection to the crystal thickness and (ii) a single parameter comprising crystal thickness, its bending radius, distance to a detector, and anisotropic elastic constants of the chosen crystal. The results allow the optimization of the parameters of bent‐crystal spectrometers for the hard X‐ray free‐electron laser sources.
    Beschreibung: The resolution function of a bent‐crystal spectrometer for pulses of an X‐ray free‐electron laser is evaluated. Under appropriate conditions, the energy resolution reaches the ratio of the lattice spacing to the crystal thickness. image
    Schlagwort(e): 548 ; X‐ray free‐electron lasers ; X‐ray spectroscopy ; bent crystals ; diamond crystal optics ; femtosecond X‐ray diffraction
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  • 43
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    Separation of the inelastic and elastic scattering in time‐of‐flight mode on the pinhole small‐angle neutron scattering diffractometer KWS‐2 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-09-29
    Beschreibung: To study and control the incoherent inelastic background in small‐angle neutron scattering, which makes a significant contribution to the detected scattering from hydrocarbon systems, the KWS‐2 small‐angle neutron scattering diffractometer operated by the Jülich Centre for Neutron Science (JCNS) at Heinz‐Maier Leibnitz Zentrum (MLZ), Garching, Germany, was equipped with a secondary single‐disc chopper that is placed in front of the sample stage. This makes it possible to record in time‐of‐flight mode the scattered neutrons in the high‐Q regime of the instrument (i.e. short incoming wavelengths and detection distances) and to discard the inelastic component from the measured data. Examples of measurements on different materials routinely used as standard samples, sample containers and solvents in the experiments at KWS‐2 are presented. When only the elastic region of the spectrum is used in the data‐reduction procedure, a decrease of up to two times in the incoherent background of the experimentally measured scattering cross section may be obtained. The proof of principle is demonstrated on a solution of bovine serum albumin in D2O.
    Beschreibung: A new chopper has been installed at the sample position in front of the sample stage at the KWS‐2 small‐angle neutron‐scattering diffractometer of the Jülich Centre for Neutron Science. The pulsed beam and the time‐of‐flight data acquisition enable the separation of elastic and inelastic scattering from hydrogenous samples.
    Schlagwort(e): 548 ; TOF‐SANS ; incoherent neutron scattering ; inelastic neutron scattering ; hydrocarbon systems
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  • 44
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    The ‘Flood Resilience Rose’: A management tool to promote transformation towards flood resilience (2021)
    Blackwell Publishing Ltd | Oxford, UK
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    Publikationsdatum: 2021-09-29
    Beschreibung: Coping with the growing impacts of flooding in EU countries, a paradigm shift in flood management can be observed, moving from safety‐based towards risk‐based approaches and holistic perspectives. Flood resilience is a common denominator of most of the approaches. In this article, we present the ‘Flood Resilience Rose’ (FRR), a management tool to promote harmonised action towards flood resilience in European regions and beyond. The FRR is a result of a two‐step process. First, based on scientific concepts as well as analysis of relevant policy documents, we identified three ‘levels of operation’. The first level refers to the EU Floods Directive and an extended multi‐layer safety approach, comprising the four different layers of protection, prevention, preparedness and recovery, and related measures to be taken. This level is not independent but depends both on the institutional (second level) and the wider (third level) context. Second, we used surveys, semi‐structured interviews and group discussions during workshops with experts from Belgium, Denmark, Germany, the Netherlands and the United Kingdom to validate the definitions and the FRR's practical relevance. The presented FRR is thus the result of rigorous theoretical and practical consideration and provides a tool capable to strengthen flood risk management practice.
    Beschreibung: European Regional Development Fund http://dx.doi.org/10.13039/501100008530
    Schlagwort(e): 551.48 ; flood defence measures ; governance and institutions ; integrated flood risk management ; resilience
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  • 45
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    Czochralski growth of mixed cubic sesquioxide crystals in the ternary system Lu2O3–Sc2O3–Y2O3 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publikationsdatum: 2021-09-29
    Beschreibung: Cubic rare‐earth sesquioxide crystals are strongly demanded host materials for high power lasers, but due to their high melting points investigations on their thermodynamics and the growth of large‐size crystals of high optical quality remain a challenge. Detailed thermal investigations of the ternary system Lu2O3–Sc2O3–Y2O3 revealing a large range of compositions with melting temperatures below 2200°C and a minimum of 2053°C for the composition (Sc0.45Y0.55)2O3 are presented. These reduced temperatures enable for the first time the growth of high optical quality mixed sesquioxide crystals with disordered structure by the conventional Czochralski method from iridium crucibles. An (Er0.07Sc0.50Y0.43)2O3 crystal is successfully grown and characterized with respect to its crystallographic properties as well as its composition, thermal conductivity and optical absorption in the 1 µm range.
    Beschreibung: The phase diagram of the ternary system Lu2O3–Sc2O3–Y2O3 is investigated and compositions with melting points below 2200°C are found. This allows for the first successful growth of the mixed cubic sesquioxide crystal (Er0.07Sc0.50Y0.43)2O3 by the Czochralski method from an iridium crucible. image
    Schlagwort(e): 548 ; crystal growth ; optical materials ; phase diagrams ; melting points ; rare earth sesquioxides
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  • 46
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    Mathematics for Physicists. Introductory Concepts and Methods. By Alexander Altland and Jan von Delft. Cambridge University Press, 2019. Hardback, Pp. 720. Price GBP 39.99. ISBN 9781108471220. (2021)
    International Union of Crystallography
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    Publikationsdatum: 2021-01-01
    Digitale ISSN: 2053-2733
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 47
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    A cloud platform for atomic pair distribution function analysis: PDFitc (2021)
    International Union of Crystallography
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    Publikationsdatum: 2021-01-01
    Beschreibung: A cloud web platform for analysis and interpretation of atomic pair distribution function (PDF) data (PDFitc) is described. The platform is able to host applications for PDF analysis to help researchers study the local and nanoscale structure of nanostructured materials. The applications are designed to be powerful and easy to use and can, and will, be extended over time through community adoption and development. The currently available PDF analysis applications, structureMining, spacegroupMining and similarityMapping, are described. In the first and second the user uploads a single PDF and the application returns a list of best-fit candidate structures, and the most likely space group of the underlying structure, respectively. In the third, the user can upload a set of measured or calculated PDFs and the application returns a matrix of Pearson correlations, allowing assessment of the similarity between different data sets. structureMining is presented here as an example to show the easy-to-use workflow on PDFitc. In the future, as well as using the PDFitc applications for data analysis, it is hoped that the community will contribute their own codes and software to the platform.
    Digitale ISSN: 2053-2733
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 48
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    Spiral tetrahedral packing in the β-Mn crystal as symmetry realization of the 8D E 8 lattice (2021)
    International Union of Crystallography
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    Publikationsdatum: 2021-01-01
    Beschreibung: Experimental values of atomic positions in the β-Mn crystal permit one to distinguish among them a fragment of the helix containing 15 interpenetrating distorted icosahedra, 90 vertices and 225 tetrahedra. This fragment corresponds to the closed helix of 15 icosahedra in the 4D {3, 3, 5} polytope. The primitive cubic lattice of these icosahedral helices envelopes not only all atoms of β-Mn, but also all tetrahedra belonging to the tiling of the β-Mn structure. The 2D projection of all atomic positions in the β-Mn unit cells shows that they are situated (by neglecting small differences) on three circumferences containing 2D projections of 90 vertices of the {3, 3, 5} polytope on the same plane. Non-crystallographic symmetry of the β-Mn crystal is defined by mapping the closed icosahedral helix of the {3, 3, 5} polytope into 3D Euclidean space E 3. This interpretation must be correlated also with the known previous determination of non-crystallographic symmetry of the β-Mn crystal by mapping into the 3D E 3 space system of icosahedra from the 6D cubic B 6 lattice. The recently proposed determination of non-crystallographic symmetry of the β-Mn crystal actually uses the symmetries of the 8D E 8 lattice, in which both the 4D {3, 3, 5} polytope and cubic 6D B 6 lattice can be inserted.
    Digitale ISSN: 2053-2733
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 49
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    Crystal structure, Hirshfeld surface analysis, DFT and molecular docking investigation of 2-(2-oxo-1,3-oxazolidin-3-yl)ethyl 2-[2-(2-oxo-1,3-oxazolidin-3-yl)ethoxy]quinoline-4-carboxylate (2021)
    International Union of Crystallography
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    Publikationsdatum: 2021-01-01
    Beschreibung: In the molecular structure of the title compound, C20H21N3O7, the quinoline ring system is slightly bent, with a dihedral angle between the phenyl and the pyridine rings of 3.47 (7)°. In the crystal, corrugated layers of molecules extending along the ab plane are generated by C—H...O hydrogen bonds. The intermolecular interactions were quantified by Hirshfeld surface analysis and two-dimensional fingerprint plots. The most significant contributions to the crystal packing are from H...H (42.3%), H...O/O...H (34.5%) and H...C/ C...H (17.6%) contacts. Molecular orbital calculations providing electron-density plots of the HOMO and LUMO as well as molecular electrostatic potentials (MEP) were computed, both with the DFT/B3LYP/6–311 G++(d,p) basis set. A molecular docking study between the title molecule and the COVID-19 main protease (PDB ID: 6LU7) was performed, showing that it is a good agent because of its affinity and ability to adhere to the active sites of the protein.
    Digitale ISSN: 2056-9890
    Thema: Chemie und Pharmazie , Geologie und Paläontologie
    Publiziert von International Union of Crystallography
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  • 50
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    Synthesis and structural characterization of hexa-μ2-chlorido-μ4-oxido-tetrakis{[4-(phenylethynyl)pyridine-κN]copper(II)} dichloromethane monosolvate (2021)
    International Union of Crystallography
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    Publikationsdatum: 2021-01-01
    Beschreibung: In the crystal structure of the title compound, [Cu4Cl6O(C13H9N)4]·CH2Cl2, the core molecular structure consists of a Cu4 tetrahedron with a central interstitial O atom. Each edge of the Cu4 tetrahedron is bridged by a chlorido ligand. Each copper(II) cation is coordinated to the central O atom, two chlorido ligands and one N atom of the 4-phenylethynylpyridine ligand. In the crystal, the molecules are linked by intermolecular C—H...Cl interactions. Furthermore, C—H...π and π–π interactions also connect the molecules, forming a three-dimensional network. Hirshfeld surface analysis indicates that the most important contributions for the packing arrangement are from H...H and C...H/H...C interactions.
    Digitale ISSN: 2056-9890
    Thema: Chemie und Pharmazie , Geologie und Paläontologie
    Publiziert von International Union of Crystallography
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  • 51
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    Crystal structure, Hirshfeld surface analysis and energy framework study of 6-formyl-7,8,9,11-tetrahydro-5H-pyrido[2,1-b]quinazolin-11-one (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-01-01
    Beschreibung: At 100 K, the title compound, C13H12N2O2, crystallizes in the orthorhombic space group Pna21 with two very similar molecules in the asymmetric unit. An intramolecular N—H...O hydrogen bond leads to an S(6) graph-set motif in each of the molecules. Intermolecular π–π stacking and C=O...π interactions involving the aldehyde O atoms link molecules into stacks parallel to [100]. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing stem from H...H (49.4%) and H...O/O...H (21.5%) interactions. Energy framework calculations reveal a significant contribution of dispersion energy. The crystal studied was refined as a two-component inversion twin.
    Digitale ISSN: 2056-9890
    Thema: Chemie und Pharmazie , Geologie und Paläontologie
    Publiziert von International Union of Crystallography
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  • 52
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    Two 3-amino-1H-pyrazol-2-ium salts containing organic anions, and an orthorhombic polymorph of 3-amino-1H-pyrazol-2-ium nitrate (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-01-01
    Beschreibung: Co-crystallization from methanol of 3-amino-1H-pyrazole with 3,5-dinitrobenzoic acid produces 3-amino-1H-pyrazol-2-ium 3,5-dinitrobenzoate monohydrate, C3H6N3 +·C7H3N2O6 −·H2O, (I), while similar co-crystallization of this pyrazole with an equimolar quantity of fumaric acid produces bis(3-amino-1H-pyrazol-2-ium) fumarate–fumaric acid (1/1), 2C3H6N3 +·C4H2O4 2−·C4H4O4, (II). The reaction of 3-amino-1H-pyrazole with a dilute solution of nitric acid in methanol yields a second, orthorhombic polymorph of 3-amino-1H-pyrazol-2-ium nitrate, C3H6N3 +·NO3 −, (III). In each of (I)–(III), the bond distances in the cation provide evidence for extensive delocalization of the positive charge. In each of (I) and (II), an extensive series of O—H...O and N—H...O hydrogen bonds links the components into complex sheets, while in the structure of (III), the ions are linked by multiple N—H...O hydrogen bonds into a three-dimensional arrangement. Comparisons are made with the structures of some related compounds.
    Digitale ISSN: 2056-9890
    Thema: Chemie und Pharmazie , Geologie und Paläontologie
    Publiziert von International Union of Crystallography
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  • 53
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    Evaluation of the data-collection strategy for room-temperature micro-crystallography studied by serial synchrotron rotation crystallography combined with the humid air and glue-coating method (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-02-25
    Beschreibung: Synchrotron serial crystallography (SSX) is an emerging data-collection method for micro-crystallography on synchrotron macromolecular (MX) crystallography beamlines. At SPring-8, the feasibility of the fixed-target approach was examined by collecting data using a 2D raster scan combined with goniometer rotation. Results at cryogenic temperatures demonstrated that rotation is effective for efficient data collection in SSX and the method was named serial synchrotron rotation crystallography (SS-ROX). To use this method for room-temperature (RT) data collection, a humid air and glue-coating (HAG) method was developed in which data were collected from polyvinyl alcohol-coated microcrystals fixed on a loop under humidity-controlled air. The performance and the RT data-collection strategy for micro-crystallography were evaluated using microcrystals of lysozyme. Although a change in unit-cell dimensions of up to 1% was observed during data collection, the impact on data quality was marginal. A comparison of data obtained at various absorbed doses revealed that absorbed doses of up to 210 kGy were tolerable in both global and local damage. Although this limits the number of photons deposited on each crystal, increasing the number of merged images improved the resolution. On the basis of these results, an equation was proposed that relates the achievable resolution to the total photon flux used to obtain a data set.
    Digitale ISSN: 2059-7983
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 54
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    Diffraction structural biology – an introductory overview (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-02-25
    Digitale ISSN: 2059-7983
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 55
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    Crystal structure of the GTP-binding protein-like domain of AGAP1 (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-31
    Beschreibung: AGAP1 is often considered to regulate membrane trafficking, protein transport and actin cytoskeleton dynamics. Recent studies have shown that aberrant expression of AGAP1 is associated with many diseases, including neurodevelopmental disorders and acute lymphoblastic leukemia. It has been proposed that the GTP-binding protein-like domain (GLD) is involved in the binding of cofactors and thus regulates the catalytic activity of AGAP1. To obtain a better understanding of the pathogenic mechanism underpinning AGAP1-related diseases, it is essential to obtain structural information. Here, the GLD (residues 70–235) of AGAP1 was overexpressed in Escherichia coli BL21 (DE3) cells. Affinity and gel-filtration chromatography were used to obtain AGAP1GLD with high purity for crystallization. Using the hanging-drop vapor-diffusion method with the protein at a final concentration of 20 mg ml−1, AGAP1GLD protein crystals of suitable size were obtained. The crystals were found to diffract to 3.0 Å resolution and belonged to space group I4, with unit-cell parameters a = 100.39, b = 100.39, c = 48.08 Å. The structure of AGAP1GLD exhibits the highly conserved functional G1–G5 loops and is generally similar to other characterized ADP-ribosylation factor (Arf) GTPase-activating proteins (GAPs), implying an analogous function to Arf GAPs. Additionally, this study indicates that AGAP1 could be classified as a type of NTPase, the activity of which might be regulated by protein partners or by its other domains. Taken together, these results provide insight into the regulatory mechanisms of AGAP1 in cell signaling.
    Digitale ISSN: 2053-230X
    Thema: Biologie , Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 56
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    Novel clostridial cell-surface hemicellulose-binding CBM3 proteins (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-31
    Beschreibung: A novel member of the family 3 carbohydrate-binding modules (CBM3s) is encoded by a gene (Cthe_0271) in Clostridium thermocellum which is the most highly expressed gene in the bacterium during its growth on several types of biomass substrates. Surprisingly, CtCBM3-0271 binds to at least two different types of xylan, instead of the common binding of CBM3s to cellulosic substrates. CtCBM3-0271 was crystallized and its three-dimensional structure was solved and refined to a resolution of 1.8 Å. In order to learn more about the role of this type of CBM3, a comparative study with its orthologue from Clostridium clariflavum (encoded by the Clocl_1192 gene) was performed, and the three-dimensional structure of CcCBM3-1192 was determined to 1.6 Å resolution. Carbohydrate binding by CcCBM3-1192 was found to be similar to that by CtCBM3-0271; both exhibited binding to xylan rather than to cellulose. Comparative structural analysis of the two CBM3s provided a clear functional correlation of structure and binding, in which the two CBM3s lack the required number of binding residues in their cellulose-binding strips and thus lack cellulose-binding capabilities. This is an enigma, as CtCBM3-0271 was reported to be a highly expressed protein when the bacterium was grown on cellulose. An additional unexpected finding was that CcCBM3-1192 does not contain the calcium ion that was considered to play a structural stabilizing role in the CBM3 family. Despite the lack of calcium, the five residues that form the calcium-binding site are conserved. The absence of calcium results in conformational changes in two loops of the CcCBM3-1192 structure. In this context, superposition of the non-calcium-binding CcCBM3-1192 with CtCBM3-0271 and other calcium-binding CBM3s reveals a much broader two-loop region in the former compared with CtCBM3-0271.
    Digitale ISSN: 2053-230X
    Thema: Biologie , Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 57
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    Structural differences/similarities of diastereotopic groups in three new chiral phosphoramides (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-29
    Beschreibung: The crystal structures of two single-enantiomer amidophosphoesters with an (O)2P(O)(N) skeleton and one single-enantiomer phosphoric triamide with an (N)2P(O)(N) skeleton were studied. The compounds are diphenyl [(R)-(+)-α-4-dimethylbenzylamido]phosphate, (I), and diphenyl [(S)-(−)-α-4-dimethylbenzylamido]phosphate, (II), both C21H22NO3P, and N-(2,6-difluorobenzoyl)-N′,N′′-bis[(R)-(+)-α-ethylbenzyl]phosphoric triamide, C25H28F2N3O2P, (III). The asymmetric units contain two amidophosphoester molecules for (I) and (II), and one phosphoric triamide molecule for (III). In the crystal structures of (I) and (II), molecules are assembled in a similar one-dimensional chiral ribbon architecture, but with almost a mirror-image relationship with respect to each other through N—H...O(P) and C—H...O(P) hydrogen bonds along [010]. In the crystal structure of (III), the chiral tape architecture along [100] is mediated by N—H...O(P) and N—H...O(C) hydrogen bonds, and the tapes are connected into slabs by C—H...O interactions (along the ab plane). The differences/similarities of the two diastereotopic phenoxy groups in (I)/(II) and the two chiral amine fragments in (III) were studied on the grounds of geometry, conformation and contribution to the crystal packing, as well as 1H and 13C signals in a solution NMR study.
    Digitale ISSN: 2053-2296
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 58
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    Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-31
    Beschreibung: Lytic polysaccharide monooxygenases (LPMOs) are copper-center enzymes that are involved in the oxidative cleavage of the glycosidic bond in crystalline cellulose and other polysaccharides. The LPMO reaction is initiated by the addition of a reductant and oxygen to ultimately form an unknown activated copper–oxygen species that is responsible for polysaccharide-substrate H-atom abstraction. Given the sensitivity of metalloproteins to radiation damage, neutron protein crystallography provides a nondestructive technique for structural characterization while also informing on the positions of H atoms. Neutron cryo-crystallography permits the trapping of catalytic intermediates, thereby providing insight into the protonation states and chemical nature of otherwise short-lived species in the reaction mechanism. To characterize the reaction-mechanism intermediates of LPMO9D from Neurospora crassa, a cryo-neutron diffraction data set was collected from an ascorbate-reduced crystal. A second neutron diffraction data set was collected at room temperature from an LPMO9D crystal exposed to low-pH conditions to probe the protonation states of ionizable groups involved in catalysis under acidic conditions.
    Digitale ISSN: 2053-230X
    Thema: Biologie , Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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    Chloridotetrakis(imidazole)copper(II) chloride. Corrigendum (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-31
    Beschreibung: In the article by Li et al. [Acta Cryst. (2007), E63, m2536], four imidazole H atoms are missing in the refinement.
    Digitale ISSN: 2056-9890
    Thema: Chemie und Pharmazie , Geologie und Paläontologie
    Publiziert von International Union of Crystallography
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  • 60
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    Structure of Λ(δλλ)-[Co(en)3]I3(I)2 (2021)
    International Union of Crystallography
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    Publikationsdatum: 2021-03-31
    Beschreibung: The structure of tris(ethane-1,2-diamine-κ2 N,N')cobalt(III) bis(iodide) triiodide, [Co(C2H8N2)3]I3(I)2, at 120 K has orthorhombic (P212121) symmetry. The diamine nitrogen atoms form N—H...I hydrogen bonds throughout the lattice, resulting in a three-dimensional network, which involves the iodide and all atoms in the triiodide anions.
    Digitale ISSN: 2056-9890
    Thema: Chemie und Pharmazie , Geologie und Paläontologie
    Publiziert von International Union of Crystallography
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    Symmetry relations in wurtzite nitrides and oxide nitrides and the curious case of Pmc21 (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-23
    Beschreibung: Binary III–V nitrides such as AlN, GaN and InN in the wurtzite-type structure have long been considered as potent semiconducting materials because of their optoelectronic properties, amongst others. With rising concerns over the utilization of scarce elements, a replacement of the trivalent cations by others in ternary and multinary nitrides has led to the development of different variants of nitrides and oxide nitrides crystallizing in lower-symmetry variants of wurtzite. This work presents the symmetry relationships between these structural types specific to nitrides and oxide nitrides and updates some prior work on this matter. The non-existence of compounds crystallizing in Pmc21, formally the highest subgroup of the wurtzite type fulfilling Pauling's rules for 1:1:2 stoichiometries, has been puzzling scientists for a while; a rationalization is given, from a crystallographic basis, of why this space group is unlikely to be adopted.
    Digitale ISSN: 2053-2733
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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    A discussion on `Domain formation and phase transitions in the wurtzite-based heterovalent ternaries: a Landau theory analysis' (2021)
    International Union of Crystallography
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    Publikationsdatum: 2021-03-23
    Beschreibung: Heterovalent ternary nitrides are considered one of the promising classes of materials for photovoltaics, combining attractive physical properties with low toxicity and element abundance. One of the front-runner systems under consideration is ZnSnN2. Although it is nominally a ternary compound, no clear crystallographic evidence for cation ordering has been observed so far. An attempt to elucidate this discrepancy [Quayle (2020). Acta Cryst. A76, 410–420] was the trigger for an intensive discussion between the authors, and an agreement was reached to elaborate on some points in order to set things in perspective. Rather than using a conventional comment–answer scheme, this is published in the form of a joint discussion to celebrate constructive criticism and collegiality.
    Digitale ISSN: 2053-2733
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 63
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    Crystal structure of cis-(1,4,8,11-tetraazacyclotetradecane-κ4 N)bis(thiocyanato-κN)chromium(III) bromide from synchrotron X-ray diffraction data (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-02-02
    Beschreibung: The crystal structure of the title complex, cis-[Cr(NCS)2(cyclam)]Br (cyclam = 1,4,8,11-tetraazacyclotetradecane, C10H24N4), has been determined from synchrotron X-ray data. The asymmetric unit contains one [Cr(NCS)2(cyclam)]+ cation and one bromide anion. The CrIII ion of the complex cation is coordinated by the four N atoms of the cyclam ligand and by two N-coordinating NCS groups in a cis arrangement, displaying a distorted octahedral coordination sphere. The Cr—N(cyclam) bond lengths are in the range 2.075 (3) to 2.081 (3) Å while the average Cr—N(NCS) bond length is 1.996 (16) Å. The macrocyclic cyclam moiety adopts the most stable cis-V conformation. The crystal structure is stabilized by intermolecular hydrogen bonds involving the cyclam N—H groups as donor groups, and the bromide anion and the S atom of one of the NCS ligands as acceptor groups.
    Digitale ISSN: 2056-9890
    Thema: Chemie und Pharmazie , Geologie und Paläontologie
    Publiziert von International Union of Crystallography
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  • 64
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    Synthesis, crystal structure and Hirshfeld surface analysis of [bis(diphenylphosphanyl)methane-κP]chloridobis[2-(pyridin-2-yl)phenyl-κ2 N,C 1]iridium(III) (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-02-02
    Beschreibung: The title IrIII complex, [Ir(C11H8N)2Cl(C25H22P2)], was synthesized from the substitution reaction between the (ppy)2Ir(μ-Cl)2Ir(ppy)2 (ppy = deprotonated 2-phenylpyridine, C11H8N−) dimer and 1,1-bis(diphenylphosphanyl)methane (dppm, C25H22P2) under an argon gas atmosphere for 20 h. The IrIII atom is coordinated by two C,N-bidentate ppy anions, a unidentate dppm ligand and a chloride anion in a distorted octahedral IrC2N2PCl arrangement. The N donor atoms of the ppy ligands are mutually trans while the C atoms are cis. Intramolecular aromatic π–π stacking between the phenyl rings of ppy and dppm, and C—H...Cl interactions are observed. In the crystal, C—H...Cl and C—H...π contacts link the molecules into a three-dimensional network. A Hirshfeld surface analysis was carried out to further quantify the intermolecular interactions, and indicated that H...H contacts (63.9%) dominate the packing.
    Digitale ISSN: 2056-9890
    Thema: Chemie und Pharmazie , Geologie und Paläontologie
    Publiziert von International Union of Crystallography
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  • 65
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    Crystal structure of (E)-1-(3-benzyl-5-phenyl-1,3-thiazol-2-ylidene)-2-[(E)-1,2,3,4-tetrahydronaphthalen-1-ylidene]hydrazin-1-ium bromide (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-23
    Beschreibung: In the title molecular salt, C26H24N3S+·Br−, the dihedral angles between the thiazole ring and its attached phenyl and benzoyl rings are 54.81 (7) and 85.51 (7)°, respectively. In the crystal, ion pairs are linked by C—H...Br and N—H...Br hydrogen bonds and are connected into helical chains extending along the c-axis direction by weak, electrostatic S...Br− interactions. A Hirshfeld surface analysis was performed, which showed the dominant role of H...H contacts (51.3%).
    Digitale ISSN: 2056-9890
    Thema: Chemie und Pharmazie , Geologie und Paläontologie
    Publiziert von International Union of Crystallography
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  • 66
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    The structure of Prp2 bound to RNA and ADP-BeF3 − reveals structural features important for RNA unwinding by DEAH-box ATPases (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-30
    Beschreibung: Noncoding intron sequences present in precursor mRNAs need to be removed prior to translation, and they are excised via the spliceosome, a multimegadalton molecular machine composed of numerous protein and RNA components. The DEAH-box ATPase Prp2 plays a crucial role during pre-mRNA splicing as it ensures the catalytic activation of the spliceosome. Despite high structural similarity to other spliceosomal DEAH-box helicases, Prp2 does not seem to function as an RNA helicase, but rather as an RNA-dependent ribonucleoprotein particle-modifying ATPase. Recent crystal structures of the spliceosomal DEAH-box ATPases Prp43 and Prp22, as well as of the related RNA helicase MLE, in complex with RNA have contributed to a better understanding of how RNA binding and processivity might be achieved in this helicase family. In order to shed light onto the divergent manner of function of Prp2, an N-terminally truncated construct of Chaetomium thermophilum Prp2 was crystallized in the presence of ADP-BeF3 − and a poly-U12 RNA. The refined structure revealed a virtually identical conformation of the helicase core compared with the ADP-BeF3 −- and RNA-bound structure of Prp43, and only a minor shift of the C-terminal domains. However, Prp2 and Prp43 differ in the hook-loop and a loop of the helix-bundle domain, which interacts with the hook-loop and evokes a different RNA conformation immediately after the 3′ stack. On replacing these loop residues in Prp43 by the Prp2 sequence, the unwinding activity of Prp43 was abolished. Furthermore, a putative exit tunnel for the γ-phosphate after ATP hydrolysis could be identified in one of the Prp2 structures.
    Digitale ISSN: 2059-7983
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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    Cryo-EM of kinesin-binding protein: challenges and opportunities from protein-surface interactions (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-30
    Beschreibung: Kinesin-binding protein (KBP) is an important selective inhibitor of specific kinesin family members and its genetic disruption causes Goldberg–Shprintzen syndrome. Cryo-electron microscopy (cryo-EM) has recently been used to reveal the structure of KBP alone (72 kDa) and in complex with the motor domain of the mitotic kinesin-12 KIF15 (110 kDa). KBP is an α-solenoid, tetratricopeptide-repeat protein that interacts with the microtubule-binding region of the kinesin motor domain and blocks microtubule attachment. Numerous challenges arose relating to the behavior of KBP and KBP–kinesin complexes during cryo-EM sample preparation. These included the partial denaturation of KBP by air–water interfaces, protein aggregation resulting from carbon interaction and preferential orientation. Sample preparation with a graphene oxide substrate enabled the eventual structure determination. Here, experiences with preparing these samples are detailed, bringing attention to some of the challenges and opportunities that are likely to arise from protein-surface interactions.
    Digitale ISSN: 2059-7983
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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    Identification of Mg2+ ions next to nucleotides in cryo-EM maps using electrostatic potential maps (2021)
    International Union of Crystallography
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    Publikationsdatum: 2021-03-30
    Beschreibung: Cryo electron microscopy (cryo-EM) can produce maps of macromolecules that have resolutions that are sufficiently high that structural details such as chemical modifications, water molecules and bound metal ions can be discerned. However, those accustomed to interpreting the electron-density maps of macromolecules produced by X-ray crystallography need to be careful when assigning features such as these in cryo-EM maps because cations, for example, interact far more strongly with electrons than they do with X-rays. Using simulated electrostatic potential (ESP) maps as a tool led us to re-examine a recent cryo-EM map of the human ribosome, and we realized that some of the ESP peaks originally identified as novel groups covalently bonded to the N7, O6 or O4 atoms of several guanines, adenines or uridines, respectively, in this structure are likely to instead represent Mg2+ ions coordinated to these atoms, which provide only partial charge compensation compared with Mg2+ ions located next to phosphate groups. In addition, direct evidence is provided for a variation in the level of 2′-O ribose methylation of nucleotides in the human ribosome. ESP maps can thus help in identifying ions next to nucleotide bases, i.e. at positions that can be difficult to address in cryo-EM maps due to charge effects, which are specifically encountered in cryo-EM. This work is particularly relevant to nucleoprotein complexes and shows that it is important to consider charge effects when interpreting cryo-EM maps, thus opening possibilities for localizing charges in structures that may be relevant for enzymatic mechanisms and drug interactions.
    Digitale ISSN: 2059-7983
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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    Crystal structures of β-1,4-N-acetylglucosaminyltransferase 2: structural basis for inherited muscular dystrophies (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-30
    Beschreibung: The canonical O-mannosylation pathway in humans is essential for the functional glycosylation of α-dystroglycan. Disruption of this post-translational modification pathway leads to congenital muscular dystrophies. The first committed step in the construction of a functional matriglycan structure involves the post-translational modification of α-dystroglycan. This is essential for binding extracellular matrix proteins and arenaviruses, and is catalyzed by β-1,4-N-acetylglucosaminyltransferase 2 (POMGNT2). While another glycosyl transferase, β-1,4-N-acetylglucosaminyltransferase 1 (POMGNT1), has been shown to be promiscuous in extending O-mannosylated sites, POMGNT2 has been shown to display significant primary amino-acid selectivity near the site of O-mannosylation. Moreover, several single point mutations in POMGNT2 have been identified in patients with assorted dystroglycanopathies such as Walker–Warburg syndrome and limb girdle muscular dystrophy. To gain insight into POMGNT2 function in humans, the enzyme was expressed as a soluble, secreted fusion protein by transient infection of HEK293 suspension cultures. Here, crystal structures of POMGNT2 (amino-acid residues 25–580) with and without UDP bound are reported. Consistent with a novel fold and a unique domain organization, no molecular-replacement model was available and phases were obtained through crystallization of a selenomethionine variant of the enzyme in the same space group. Tetragonal (space group P4212; unit-cell parameters a = b = 129.8, c = 81.6 Å, α = γ = β = 90°) crystals with UDP bound diffracted to 1.98 Å resolution and contained a single monomer in the asymmetric unit. Orthorhombic (space group P212121; unit-cell parameters a = 142.3, b = 153.9, c = 187.4 Å, α = γ = β = 90°) crystals were also obtained; they diffracted to 2.57 Å resolution and contained four monomers with differential glycosylation patterns and conformations. These structures provide the first rational basis for an explanation of the loss-of-function mutations and offer significant insights into the mechanics of this important human enzyme.
    Digitale ISSN: 2059-7983
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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    Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching (2021)
    International Union of Crystallography
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    Publikationsdatum: 2021-03-30
    Beschreibung: Using single-particle electron cryo-microscopy (cryo-EM), it is possible to obtain multiple reconstructions showing the 3D structures of proteins imaged as a mixture. Here, it is shown that automatic map interpretation based on such reconstructions can be used to create atomic models of proteins as well as to match the proteins to the correct sequences and thereby to identify them. This procedure was tested using two proteins previously identified from a mixture at resolutions of 3.2 Å, as well as using 91 deposited maps with resolutions between 2 and 4.5 Å. The approach is found to be highly effective for maps obtained at resolutions of 3.5 Å and better, and to have some utility at resolutions as low as 4 Å.
    Digitale ISSN: 2059-7983
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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    Polymorphs of phenazine hexacyanoferrate(II) hydrate: supramolecular isomerism in a 2D hydrogen-bonded network (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-10
    Beschreibung: The crystal structures of two polymorphs of a phenazine hexacyanoferrate(II) salt/cocrystal, with the formula (Hphen)3[H2Fe(CN)6][H3Fe(CN)6]·2(phen)·2H2O, are reported. The polymorphs are comprised of (Hphen)2[H2Fe(CN)6] trimers and (Hphen)[(phen)2(H2O)2][H3Fe(CN)6] hexamers connected into two-dimensional (2D) hydrogen-bonded networks through strong hydrogen bonds between the [H2Fe(CN)6]2− and [H3Fe(CN)6]− anions. The layers are further connected by hydrogen bonds, as well as through π–π stacking of phenazine moieties. Aside from the identical 2D hydrogen-bonded networks, the two polymorphs share phenazine stacks comprising both protonated and neutral phenazine molecules. On the other hand, the polymorphs differ in the conformation, placement and orientation of the hydrogen-bonded trimers and hexamers within the hydrogen-bonded networks, which leads to different packing of the hydrogen-bonded layers, as well as to different hydrogen bonding between the layers. Thus, aside from an exceptional number of symmetry-independent units (nine in total), these two polymorphs show how robust structural motifs, such as charge-assisted hydrogen bonding or π-stacking, allow for different arrangements of the supramolecular units, resulting in polymorphism.
    Print ISSN: 2052-5192
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    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
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    Structural and theoretical analysis of 2-chloro-4-nitroaniline and 2-methyl-6-nitroaniline salts (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-02-18
    Beschreibung: The crystal structures of five new salts of 2-chloro-4-nitroaniline (2Cl4na) and 2-methyl-6-nitroaniline (2m6na) with inorganic acids, namely, 2-chloro-4-nitroanilinium bromide, C6H6ClN2O2 +·Br− (1), 2-chloro-4-nitroanilinium hydrogen sulfate, C6H6ClN2O2 +·HSO4 − (2), 2-methyl-6-nitroanilinium bromide, C7H9N2O2 +·Br− (3), 2-methyl-6-nitroanilinium triiodide, C7H9N2O2 +·I3 − (4), and 2-methyl-6-nitroanilinium hydrogen sulfate, C7H9N2O2 +·HSO4 − (5), were determined by single-crystal X-ray diffraction. Theoretical calculations of the relaxed potential energy surface (rPES) revealed that the energy barriers for the rotation of the nitro group for isolated H2Cl4na+ and H2m6na+ cations are 4.6 and 11.6 kcal mol−1, respectively. The ammonium group and respective anions form hydrogen bonds which are the most important interactions and are arranged in zero- (in 3), one- (in 1 and 4) or two-dimensional (in 2 and 5) networks. Hydrogen-bonding patterns were analyzed by means of mathematical relationships between graph-set descriptors and compared with previously reported nitroaniline salts. Hirshfeld surface analysis indicates that the nitro group plays a dominant role among the weak interactions, i.e. C—H...O(NO2), NO2...π(Ar) and O(NO2)...π(NO2). The frequency of the νsNO2 vibration is correlated with the type of interaction in which the NO2 group is involved. Analysis of the νsNO2 band observed in the IR and Raman spectra allowed an assessment of its shift in the sequence (H2m6na)I3 (4) 〈 (H2m6na)HSO4 (5) 〈 (H2m6na)Br (3) 〈 (H2Cl4na)Br (1) 〈 (H2Cl4na)HSO4 (2).
    Digitale ISSN: 2053-2296
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 73
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    Crystallographic characterization of (C5H4SiMe3)3U(BH4) (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-12
    Beschreibung: New syntheses have been developed for the synthesis of (borohydrido-κ3 H)tris[η5-(trimethylsilyl)cyclopentadienyl]uranium(IV), [U(BH4)(C8H13Si)3] or Cp′3U(BH4) (Cp′ = C5H4SiMe3) and its structure has been determined by single-crystal X-ray crystallography. This compound crystallized in the space group Poverline{1} and the structure features three η 5-coordinated Cp′ rings and a κ 3-coordinated (BH4)− ligand.
    Digitale ISSN: 2056-9890
    Thema: Chemie und Pharmazie , Geologie und Paläontologie
    Publiziert von International Union of Crystallography
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  • 74
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    Crystal structures of zinc(II) complexes with β-hydroxypyridinecarboxylate ligands: examples of structure-directing effects used in inorganic crystal engineering (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-02-27
    Beschreibung: The coordination properties of four hydroxypyridinecarboxylates, designed for the treatment of iron-overloading conditions as bidentate O,O′-donor ligands, have been studied with ZnII in the solid state. The coordination compounds [Zn(A1)2(H2O)2] (1), [Zn(A2)2(H2O)] (2), [Zn(A3)2(H2O)]·2H2O (3) and [Zn2(B1)4(H2O)2]·4H2O (4), where the ligands are 1-methyl-4-oxidopyridinium-3-carboxylate (A1, C7H6NO3), 1,6-dimethyl-4-oxidopyridinium-3-carboxylate (A2, C8H8NO3), 1,5-dimethyl-4-oxido-pyridinium-3-carboxylate (A3, C8H8NO3) and 1-methyl-3-oxidopyridinium-4-carboxylate (B1, C7H6NO3), have been synthesized and analysed by single-crystal X-ray diffraction. The ligands were chosen to probe (i) the electronic effects of inverting the positions of the O-atom donor groups (i.e. A1 versus B1) and (ii) the electronic and steric effects of the addition of a second methyl group in different positions on the pyridine ring. Two axially coordinated water molecules resulting in a six-coordinated symmetrical octahedron complement the bis-ligand complex of A1. Ligands A2 and A3 form five-coordinated trigonal bipyramidal complexes with one additional water molecule in the coordination sphere, which is a rarely reported geometry for ZnII complexes. Ligand B1 shows a dimeric structure, where the two Zn2+ dications have slightly distorted octahedral geometry and the pyridinolate O atom of the neighbouring complex bridges them. The coordination spheres of the Zn2+ dications and the supramolecular structures are discussed in detail. The packing arrangements of 1–3 are similar, having alternating hydrophilic and hydrophobic layers, however the similarity is broken in 4. The obtained coordination geometries are compared with their previously determined CuII analogues. The study of the individual complexes is complemented with a comprehensive analysis of ZnII complexes with oxygen donor ligands with data from the Cambridge Structural Database.
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    Novel aluminophosphate Na6[Al3P5O20] with the original microporous crystal structure established in the study of a pseudomerohedric microtwin (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-12
    Beschreibung: The synthesis and characterization of a new aluminophosphate, Na6[Al3P5O20], obtained as single crystals in the same experiment together with Cl-sodalite, Na8[Al6Si6O24]Cl2, is reported. Na6[Al3P5O20], with a strongly pseudo-orthorhombic lattice, is described by the monoclinic crystal structure established in the study of a pseudomerohedric microtwin. The design of Na6[Al3P5O20] can be interpreted as an alternative to sodalite, with a monoclinic (pseudo-orthorhombic) 2×4×1 super-structure and unit-cell parameters multiples of those of sodalite: a ≃ 2a s, b ≃ 4b s and c ≃ c s. The triperiodic framework is built by AlO6, AlO4 and PO4 polyhedra having vertex-bridging contacts. While all the oxygen vertices of the Al-centred octahedra and tetrahedra are shared with phosphate groups, some of the PO4 tetrahedra remain `pendant', e.g. containing vertices not shared with other polyhedra of the aluminophosphate construction. Na atoms occupy framework channels and cavities surrounded by eight-, six- and four-membered windows with maximal effective pore widths of 4.86 × 3.24 and 4.31 × 3.18 Å. The generalized framework density is equal to 19.8, which means that the compound may be classified as a microporous zeolite. The Na6[Al3P5O20] crystal structure is discussed as being formed from octahedral rods arranged in two perpendicular directions, similar to the rods elongated in one direction in the NASICON-type compounds, which have been intensively investigated as promising materials for batteries. Analogous properties can be expected for phases with a modified composition of the Na6Al3P5O20 topology, where the Al atoms at the centres of octahedra are replaced by Fe, V or Cr.
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    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
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    Symmetry analysis of complex magnetic structure in monoclinically distorted Er3Cu4Sn4 (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-11
    Beschreibung: The magnetic structure in Er3Cu4Sn4 has been determined using high-resolution powder neutron diffraction, supported by symmetry analysis. At low temperatures, Er3Cu4Sn4 assumes a crystal structure of the Tm3Cu4Sn4 type (in the monoclinic space group C2/m). The Er atoms occupy two distinct Wyckoff sites: 2c and 4i. It has been found that the Er magnetic moments on the 2c site form a commensurate antiferromagnetic structure (k 1 = [0, 0, ½]) below 6 K. The magnetic moments reach 8.91 (8) μB at 1.4 K and are parallel to the b axis. The Er magnetic moments on the 4i site order below 2 K and form an incommensurate antiferromagnetic sine-modulated structure (k 2 = [1, 0.4667 (1), ½]), with magnetic moments lying in the ac plane and perpendicular to the a axis. The amplitude of modulation equals 8.7 (1) μB at 1.4 K.
    Print ISSN: 2052-5192
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    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
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    Using RELION software within the Scipion framework (2021)
    International Union of Crystallography
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    Publikationsdatum: 2021-03-30
    Beschreibung: Scipion is a modular image-processing framework that integrates several software packages under a unified interface while taking care of file formats and conversions. Here, new developments and capabilities of the Scipion plugin for the widely used RELION software package are presented and illustrated with an image-processing pipeline for published data. The user interfaces of Scipion and RELION are compared and the key differences are highlighted, allowing this manuscript to be used as a guide for both new and experienced users of this software. Different on-the-fly image-processing options are also discussed, demonstrating the flexibility of the Scipion framework.
    Digitale ISSN: 2059-7983
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 78
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    Guest-protein incorporation into solvent channels of a protein host crystal (hostal) (2021)
    International Union of Crystallography
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    Publikationsdatum: 2021-03-30
    Beschreibung: Soaking small molecules into the solvent channels of protein crystals is the most common method of obtaining crystalline complexes with ligands such as substrates or inhibitors. The solvent channels of some protein crystals are large enough to allow the incorporation of macromolecules, but soaking of protein guests into protein crystals has not been reported. Such protein host crystals (here given the name hostals) incorporating guest proteins may be useful for a wide range of applications in biotechnology, for example as cargo systems or for diffraction studies analogous to the crystal sponge method. The present study takes advantage of crystals of the Escherichia coli tryptophan repressor protein (ds-TrpR) that are extensively domain-swapped and suitable for incorporating guest proteins by diffusion, as they are robust and have large solvent channels. Confocal fluorescence microscopy is used to follow the migration of cytochrome c and fluorophore-labeled calmodulin into the solvent channels of ds-TrpR crystals. The guest proteins become uniformly distributed in the crystal within weeks and enriched within the solvent channels. X-ray diffraction studies on host crystals with high concentrations of incorporated guests demonstrate that diffraction limits of ∼2.5 Å can still be achieved. Weak electron density is observed in the solvent channels, but the guest-protein structures could not be determined by conventional crystallographic methods. Additional approaches that increase the ordering of guests in the host crystal are discussed that may support protein structure determination using the hostal system in the future. This host system may also be useful for biotechnological applications where crystallographic order of the guest is not required.
    Digitale ISSN: 2059-7983
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 79
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    Ice in biomolecular cryocrystallography (2021)
    International Union of Crystallography
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    Publikationsdatum: 2021-03-30
    Beschreibung: Diffraction data acquired from cryocooled protein crystals often include diffraction from ice. Analysis of ice diffraction from crystals of three proteins shows that the ice formed within solvent cavities during rapid cooling is comprised of a stacking-disordered mixture of hexagonal and cubic planes, with the cubic plane fraction increasing with increasing cryoprotectant concentration and increasing cooling rate. Building on the work of Thorn and coworkers [Thorn et al. (2017), Acta Cryst. D73, 729–727], a revised metric is defined for detecting ice from deposited protein structure-factor data, and this metric is validated using full-frame diffraction data from the Integrated Resource for Reproducibility in Macromolecular Crystallography. Using this revised metric and improved algorithms, an analysis of structure-factor data from a random sample of 89 827 PDB entries collected at cryogenic temperatures indicates that roughly 16% show evidence of ice contamination, and that this fraction increases with increasing solvent content and maximum solvent-cavity size. By examining the ice diffraction-peak positions at which structure-factor perturbations are observed, it is found that roughly 25% of crystals exhibit ice with primarily hexagonal character, indicating that inadequate cooling rates and/or cryoprotectant concentrations were used, while the remaining 75% show ice with a stacking-disordered or cubic character.
    Digitale ISSN: 2059-7983
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 80
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    Theoretical and practical approaches to improve the performance of local correlation algorithms for volume data analysis and shape recognition (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-30
    Beschreibung: In this paper, several approaches to be used to accelerate algorithms for fitting an atomic structure into a given 3D density map determined by cryo-EM are discussed. Rotation and translation of the atomic structure to find similarity scores are used and implemented with discrete Fourier transforms. Several rotations can be combined into groups to accelerate processing. The finite resolution of experimental and simulated maps allows a reduction in the number of rotations and translations needed in order to estimate similarity-score values.
    Digitale ISSN: 2059-7983
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 81
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    Synthesis, crystal structure and thermal properties of poly[bis[μ2-3-(aminomethyl)pyridine]bis(thiocyanato)cobalt(II)] (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-26
    Beschreibung: The reaction of Co(NCS)2 with 3-(aminomethyl)pyridine as coligand leads to the formation of crystals of the title compound, [Co(NCS)2(C6H8N2)2] n , that were characterized by single-crystal X-ray analysis. In the crystal structure, the CoII cations are octahedrally coordinated by two terminal N-bonded thiocyanate anions as well as two pyridine and two amino N atoms of four symmetry-equivalent 3-(aminomethyl)pyridine coligands with all pairs of equivalent atoms in a trans position. The CoII cations are linked by the 3-(aminomethyl)pyridine coligands into layers parallel to the ac plane. These layers are further linked by intermolecular N—H...S hydrogen bonding into a three-dimensional network. The purity of the title compound was determined by X-ray powder diffraction and its thermal behavior was investigated by differential scanning calorimetry and thermogravimetry.
    Digitale ISSN: 2056-9890
    Thema: Chemie und Pharmazie , Geologie und Paläontologie
    Publiziert von International Union of Crystallography
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  • 82
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    Crystal structure of acetoacetyl-CoA reductase from Rickettsia felis (2021)
    International Union of Crystallography
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    Publikationsdatum: 2021-02-01
    Beschreibung: Rickettsia felis, a Gram-negative bacterium that causes spotted fever, is of increasing interest as an emerging human pathogen. R. felis and several other Rickettsia strains are classed as National Institute of Allergy and Infectious Diseases priority pathogens. In recent years, R. felis has been shown to be adaptable to a wide range of hosts, and many fevers of unknown origin are now being attributed to this infectious agent. Here, the structure of acetoacetyl-CoA reductase from R. felis is reported at a resolution of 2.0 Å. While R. felis acetoacetyl-CoA reductase shares less than 50% sequence identity with its closest homologs, it adopts a fold common to other short-chain dehydrogenase/reductase (SDR) family members, such as the fatty-acid synthesis II enzyme FabG from the prominent pathogens Staphylococcus aureus and Bacillus anthracis. Continued characterization of the Rickettsia proteome may prove to be an effective means of finding new avenues of treatment through comparative structural studies.
    Digitale ISSN: 2053-230X
    Thema: Biologie , Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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    Vagabond: bond-based parametrization reduces overfitting for refinement of proteins (2021)
    International Union of Crystallography
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    Publikationsdatum: 2021-03-30
    Beschreibung: Structural biology methods have delivered over 150 000 high-resolution structures of macromolecules, which have fundamentally altered our understanding of biology and our approach to developing new medicines. However, the description of molecular flexibility is instrinsically flawed and in almost all cases, regardless of the experimental method used for structure determination, there remains a strong overfitting bias during molecular model building and refinement. In the worst case this can lead to wholly incorrect structures and thus incorrect biological interpretations. Here, by reparametrizing the description of these complex structures in terms of bonds rather than atomic positions, and by modelling flexibility using a deterministic ensemble of structures, it is demonstrated that structures can be described using fewer parameters than in conventional refinement. The current implementation, applied to X-ray diffraction data, significantly reduces the extent of overfitting, allowing the experimental data to reveal more biological information in electron-density maps.
    Digitale ISSN: 2059-7983
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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    Leishmania major biotin protein ligase forms a unique cross-handshake dimer (2021)
    International Union of Crystallography
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    Publikationsdatum: 2021-03-30
    Beschreibung: Biotin protein ligase catalyses the post-translational modification of biotin carboxyl carrier protein (BCCP) domains, a modification that is crucial for the function of several carboxylases. It is a two-step process that results in the covalent attachment of biotin to the ɛ-amino group of a conserved lysine of the BCCP domain of a carboxylase in an ATP-dependent manner. In Leishmania, three mitochondrial enzymes, acetyl-CoA carboxylase, methylcrotonyl-CoA carboxylase and propionyl-CoA carboxylase, depend on biotinylation for activity. In view of the indispensable role of the biotinylating enzyme in the activation of these carboxylases, crystal structures of L. major biotin protein ligase complexed with biotin and with biotinyl-5′-AMP have been solved. L. major biotin protein ligase crystallizes as a unique dimer formed by cross-handshake interactions of the hinge region of the two monomers formed by partial unfolding of the C-terminal domain. Interestingly, the substrate (BCCP domain)-binding site of each monomer is occupied by its own C-terminal domain in the dimer structure. This was observed in all of the crystals that were obtained, suggesting a closed/inactive conformation of the enzyme. Size-exclusion chromatography studies carried out using high protein concentrations (0.5 mM) suggest the formation of a concentration-dependent dimer that exists in equilibrium with the monomer.
    Digitale ISSN: 2059-7983
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
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    Structure of the class XI myosin globular tail reveals evolutionary hallmarks for cargo recognition in plants (2021)
    International Union of Crystallography
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    Publikationsdatum: 2021-03-30
    Beschreibung: The plant-specific class XI myosins (MyoXIs) play key roles at the molecular, cellular and tissue levels, engaging diverse adaptor proteins to transport cargoes along actin filaments. To recognize their cargoes, MyoXIs have a C-terminal globular tail domain (GTD) that is evolutionarily related to those of class V myosins (MyoVs) from animals and fungi. Despite recent advances in understanding the functional roles played by MyoXI in plants, the structure of its GTD, and therefore the molecular determinants for cargo selectivity and recognition, remain elusive. In this study, the first crystal structure of a MyoXI GTD, that of MyoXI-K from Arabidopsis thaliana, was elucidated at 2.35 Å resolution using a low-identity and fragment-based phasing approach in ARCIMBOLDO_SHREDDER. The results reveal that both the composition and the length of the α5–α6 loop are distinctive features of MyoXI-K, providing evidence for a structural stabilizing role for this loop, which is otherwise carried out by a molecular zipper in MyoV GTDs. The crystal structure also shows that most of the characterized cargo-binding sites in MyoVs are not conserved in plant MyoXIs, pointing to plant-specific cargo-recognition mechanisms. Notably, the main elements involved in the self-regulation mechanism of MyoVs are conserved in plant MyoXIs, indicating this to be an ancient ancestral trait.
    Digitale ISSN: 2059-7983
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 86
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    Crystal chemistry of lamprophyllite-group minerals from the Murun alkaline complex (Russia) and pegmatites of Rocky Boy and Gordon Butte (USA): single crystal X-ray diffraction and Raman spectroscopy study (2021)
    International Union of Crystallography
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    Publikationsdatum: 2021-03-24
    Beschreibung: Specific features of the crystal chemistry of lamprophyllite-group minerals (LGMs) are discussed using the available literature data and the results of the single-crystal X-ray diffraction and a Raman spectroscopic studies of several samples taken from the Murun alkaline complex (Russia), and Rocky Boy and Gordon Butte pegmatites (USA) presented here. The studied samples are unique in their chemical features and the distribution of cations over structural sites. In particular, the sample from the Gordon Butte pegmatite is a member of the barytolamprophyllite–emmerichite solid solution series, whereas the samples from the Murun alkaline complex and from the Rocky Boy pegmatite are intermediate members of the solid solution series formed by lamprophyllite and a hypothetical Sr analogue of emmerichite. The predominance of O2− over OH− and F− at the X site is a specific feature of sample Cha-192 from the Murun alkaline complex. New data on the Raman spectra of LGMs obtained in this work show that the wavenumbers of the O—H stretching vibrations depend on the occupancies of the M2 and M3 sites coordinating with (OH)− groups. Cations other than Na+ and Ti4+ (mainly, Mg and Fe3+) can play a significant role in the coordination of the X site occupied by (OH)−. Data on polarized Raman spectra of an oriented sample indicate that the OH groups having different local coordinations have similar orientations with respect to the crystal. The calculated measures of similarity (Δ) for lamprophyllite and ericssonite are identical (0.157 and 0.077 for the 2M- and 2O-polytypes, respectively), which indicates that these minerals are crystal-chemically isotypic and probably should be considered within the same mineral group by analogy to the other mineralogical groups which combine isotypic minerals.
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    Depth-of-field extension in optical imaging for rapid crystal screening (2021)
    International Union of Crystallography
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    Publikationsdatum: 2021-03-30
    Beschreibung: The depth of field (DoF) was extended 2.8-fold to achieve rapid crystal screening by retrofitting a custom-designed micro-retarder array (µRA) in the optical beam path of a nonlinear optical microscope. The merits of the proposed strategy for DoF enhancement were assessed in applications of second-harmonic generation imaging of protein crystals. It was found that DoF extension increased the number of crystals detected while simultaneously reducing the number of `z-slices' required for screening. Experimental measurements of the wavelength-dependence of the extended DoF were in excellent agreement with theoretical predictions. These results provide a simple and broadly applicable approach to increase the throughput of existing nonlinear optical imaging methods for protein crystal screening.
    Digitale ISSN: 2059-7983
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 88
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    Crystal structure and Hirshfeld surface analysis of trans-2,5-dimethylpiperazine-1,4-diium tetrachloridocobaltate(II) (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-26
    Beschreibung: In the title molecular salt, (C6H16N2)[CoCl4], the complete dication is generated by crystallographic inversion symmetry and the piperazine ring adopts a chair conformation with the pendant methyl groups in equatorial orientations. The complete dianion is generated by crystallographic twofold symmetry. In the crystal, the (C6H16N2)2+ and [CoCl4]2− ions are linked by N—H...Cl and C—H...Cl hydrogen bonds, thereby forming a two-dimensional supramolecular network. The Hirshfeld surface analysis and fingerprint plots reveal that the largest contributions to the crystal stability come from H...Cl/Cl...H (68.4%) and H...H (27.4%) contacts.
    Digitale ISSN: 2056-9890
    Thema: Chemie und Pharmazie , Geologie und Paläontologie
    Publiziert von International Union of Crystallography
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  • 89
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    AB-stacked nanosheet-based hexagonal boron nitride (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-17
    Beschreibung: Hexagonal boron nitride (h-BN) has been generally interpreted as having an AA stacking sequence. Evidence is presented in this article indicating that typical commercial h-BN platelets (∼10–500 nm in thickness) exhibit stacks of parallel nanosheets (∼10 nm in thickness) predominantly in the AB sequence. The AB-stacked nanosheet occurs as a metastable phase of h-BN resulting from the preferred texture and lateral growth of armchair (110) planes. It appears as an independent nanosheet or unit for h-BN platelets. The analysis is supported by simulation of thin AB films (2–20 layers), which explains the unique X-ray diffraction pattern of h-BN. With this analysis and the role of pressure in commercial high-pressure high-temperature sintering (driving nucleation and parallelizing the in-plane crystalline growth of the nuclei), a growth mechanism is proposed for 2D h-BN (on a substrate) as `substrate-induced 2D growth', where the substrate plays the role of pressure.
    Print ISSN: 2052-5192
    Digitale ISSN: 2052-5206
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 90
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    Crystal structure and enantiomeric layer disorder of a copper(I) nitrate π-coordination compound (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-13
    Beschreibung: The novel π-coordination compound [CuI(m-dmphast)NO3], where m-dmphast = 5-(allylthio)-1-(3,5-dimethylphenyl)-1H-tetrazole, is characterized using single-crystal X-ray diffraction and crystallizes in a noncentrosymmetric space group. Additionally, for the first time in this group of materials, the streaks of X-ray diffuse scattering in the reciprocal space sections were observed and described. This gave the possibility for a deeper insight into the local structure of the title compound. The conjecture about the origin of diffuse scattering was derived from average structure solution. It was then confirmed using the local structure modelling. The extended [Cu(m-dmphast)NO3]∞ chains, connected by weak interactions, produce layers which can exist in two enantiomeric forms, one of which predominates.
    Print ISSN: 2052-5192
    Digitale ISSN: 2052-5206
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 91
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    Synthesis, crystal growth, characterization and DFT investigation of a nonlinear optically active cuminaldehyde derivative hydrazone (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-17
    Beschreibung: Single crystals of (E)-N′-(4-isopropylbenzylidene)isonicotinohydrazide monohydrate (IBIHM) were grown from ethanol by the slow evaporation from solution growth technique at room temperature. The structure was elucidated by single-crystal X-ray diffraction analysis and crystallized in the orthorhombic system with noncentrosymmetric space group P212121. Optical studies reveal that the absorption was minimum in the visible region and the band-gap energy was estimated using the Kubelka–Munk algorithm. The functional groups were identified by Fourier transform infrared spectral analysis. A scanning electron microscopy study revealed the surface morphology of the grown crystal. Investigation of the intermolecular interactions, crystal packing using Hirshfeld surface analysis and single-crystal X-ray diffraction confirm that the close contacts were associated with molecular interactions. Fingerprint plots of Hirshfeld surfaces are used to locate and analyze the percentage of hydrogen-bonding interactions. The second-harmonic generation efficiency of the grown specimen was superior to that of the reference material, potassium dihydrogen phosphate. The grown crystals were further characterized by mass spectrometry and elemental analysis. Theoretical studies using density functional theory (DFT) greatly substantiated the experimental observations. Large first-order molecular hyperpolarizability (β) of about ∼70× was observed for IBIHM. The efficiency of IBIHM in terms of nonlinear optical response was verified and the molecule displayed greater chemical stability and reactivity.
    Print ISSN: 2052-5192
    Digitale ISSN: 2052-5206
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 92
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    Crystal structure and Hirshfeld surface analysis of 3-cyano-4-hydroxy-2-(4-methylphenyl)-6-oxo-N-phenyl-4-(thiophen-2-yl)cyclohexane-1-carboxamide 0.04-hydrate (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-09
    Beschreibung: In the title compound, C25H22N2O3S·0.04H2O, the central cyclohexane ring adopts a chair conformation. In the crystal, molecules are linked by N—H...O, C—H...O, and C—H...N hydrogen bonds, forming the molecular layers parallel to the bc plane, which interact by the van der Waals forces between them. A Hirshfeld surface analysis indicates that the contributions from the most prevalent interactions are H...H (41.2%), C...H/H...C (20.3%), O...H/H...O (17.8%) and N...H/H...N (10.6%).
    Digitale ISSN: 2056-9890
    Thema: Chemie und Pharmazie , Geologie und Paläontologie
    Publiziert von International Union of Crystallography
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  • 93
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    A new electron diffraction approach for structure refinement applied to Ca3Mn2O7 (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-17
    Beschreibung: The digital large-angle convergent-beam electron diffraction (D-LACBED) technique is applied to Ca3Mn2O7 for a range of temperatures. Bloch-wave simulations are used to examine the effects that changes in different parameters have on the intensity in D-LACBED patterns, and atomic coordinates, thermal atomic displacement parameters and apparent occupancy are refined to achieve a good fit between simulation and experiment. The sensitivity of the technique to subtle changes in structure is demonstrated. Refined structures are in good agreement with previous determinations of Ca3Mn2O7 and show the decay of anti-phase oxygen octahedral tilts perpendicular to the c axis of the A21 am unit cell with increasing temperature, as well as the robustness of oxygen octahedral tilts about the c axis up to ∼400°C. The technique samples only the zero-order Laue zone and is therefore insensitive to atom displacements along the electron-beam direction. For this reason it is not possible to distinguish between in-phase and anti-phase oxygen octahedral tilting about the c axis using the [110] data collected in this study.
    Digitale ISSN: 2053-2733
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 94
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    Diffraction line profiles from polydisperse crystalline systems. Corrigenda (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-17
    Beschreibung: Equation (16) and some entries in Table 1 in the article by Scardi & Leoni [(2001), Acta Cryst. A57, 604–613] are corrected.
    Digitale ISSN: 2053-2733
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 95
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    Crystal structure of the nonclassical cadherin-17 N-terminus and implications for its adhesive binding mechanism (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-01
    Beschreibung: The cadherin superfamily of calcium-dependent cell-adhesion proteins has over 100 members in the human genome. All members of the superfamily feature at least a pair of extracellular cadherin (EC) repeats with calcium-binding sites in the EC linker region. The EC repeats across family members form distinct complexes that mediate cellular adhesion. For instance, classical cadherins (five EC repeats) strand-swap their N-termini and exchange tryptophan residues in EC1, while the clustered protocadherins (six EC repeats) use an extended antiparallel `forearm handshake' involving repeats EC1–EC4. The 7D-cadherins, cadherin-16 (CDH16) and cadherin-17 (CDH17), are the most similar to classical cadherins and have seven EC repeats, two of which are likely to have arisen from gene duplication of EC1–2 from a classical ancestor. However, CDH16 and CDH17 lack the EC1 tryptophan residue used by classical cadherins to mediate adhesion. The structure of human CDH17 EC1–2 presented here reveals features that are not seen in classical cadherins and that are incompatible with the EC1 strand-swap mechanism for adhesion. Analyses of crystal contacts, predicted glycosylation and disease-related mutations are presented along with sequence alignments suggesting that the novel features in the CDH17 EC1–2 structure are well conserved. These results hint at distinct adhesive properties for 7D-cadherins.
    Digitale ISSN: 2053-230X
    Thema: Biologie , Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 96
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    Crystal structure of human CRM1, covalently modified by 2-mercaptoethanol on Cys528, in complex with RanGTP (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-01
    Beschreibung: CRM1 is a nuclear export receptor that has been intensively targeted over the last decade for the development of antitumor and antiviral drugs. Structural analysis of several inhibitor compounds bound to CRM1 revealed that their mechanism of action relies on the covalent modification of a critical cysteine residue (Cys528 in the human receptor) located in the nuclear export signal-binding cleft. This study presents the crystal structure of human CRM1, covalently modified by 2-mercaptoethanol on Cys528, in complex with RanGTP at 2.58 Å resolution. The results demonstrate that buffer components can interfere with the characterization of cysteine-dependent inhibitor compounds.
    Digitale ISSN: 2053-230X
    Thema: Biologie , Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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  • 97
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    Crystal structures of 1-(4-chlorophenyl)-4-(4-methylphenyl)-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxylic acid and 4-(4-methoxyphenyl)-1-(4-methylphenyl)-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carbonitrile (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-05
    Beschreibung: In the title compounds C23H21ClN2O3 [I, namely 1-(4-chlorophenyl)-4-(4-methylphenyl)-3,8-dioxo-1,2,5,6,7,8-hexahydroquine-3-carboxylic acid] and C24H22N2O3 [II, namely 4-(4-methoxyphenyl)-1-(4-methylphenyl)-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carbonitrile], each of the cyclohexene and dihydropyridine rings of the 1,2,5,6,7,8-hexahydroquinoline moieties adopts a twisted-boat conformation. The asymmetric units of both compounds I and II consist of two independent molecules (A and B). In II A, three carbon atoms of the cyclohexene ring are disordered over two sets of sites in a 0.670 (11):0.330 (11) occupancy ratio. In the crystal of I, molecules are linked through classical N—H...O hydrogen bonds, forming inversion dimers with an R 2 2(8) ring motif and with their molecular planes parallel to the crystallographic (020) plane. Non-classical C—H...O hydrogen-bonding interactions connect the dimers, resulting in a three-dimensional network. In the crystal of II, molecules are linked by C—H...N, C—H...O and C—H...π interactions, forming a three-dimensional network.
    Digitale ISSN: 2056-9890
    Thema: Chemie und Pharmazie , Geologie und Paläontologie
    Publiziert von International Union of Crystallography
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  • 98
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    Crystal structure and Hirshfeld surface analysis of (3S,3aR,6aS)-3-(1,3-diphenyl-1H-pyrazol-4-yl)-5-(4-methoxyphenyl)-2-phenyl-3,3a,4,5,6,6a-hexahydro-2H-pyrrolo[3,4-d][1,2]oxazole-4,6-dione (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-05
    Beschreibung: In the title compound, C33H26N4O4, the two fused five-membered rings and their N-bound aromatic substituents form a pincer-like motif. The relative conformations about the three chiral carbon atoms are established. In the crystal, a combination of C—H...O and C—H...N hydrogen bonds and C—H...π(ring) interactions leads to the formation of layers parallel to the bc plane. A Hirshfeld surface analysis indicates that the most significant contributions to the crystal packing are from H...H (44.3%), C...H/H...C (29.8%) and O...H/H...O (15.0%) contacts.
    Digitale ISSN: 2056-9890
    Thema: Chemie und Pharmazie , Geologie und Paläontologie
    Publiziert von International Union of Crystallography
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  • 99
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    Crystal structure refinements of stoichiometric Ni3Se2 and NiSe (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-09
    Beschreibung: Single crystals of Ni3Se2 (trinickel diselenide) and NiSe (nickel selenide) with stoichiometric chemical compositions were grown in evacuated silica-glass tubes. The chemical compositions of the single crystals of Ni3Se2 and NiSe were determined by scanning electron microscopy and energy-dispersive X-ray spectroscopy (SEM/EDS). The crystal structures of Ni3Se2 [rhombohedral, space group R32, a = 6.02813 (13), c = 7.24883 (16) Å, Z = 3] and NiSe [hexagonal, space group P63/mmc, a = 3.66147 (10), c = 5.35766 (16) Å, Z = 2] were analyzed by single-crystal X-ray diffraction and refined to yield R values of 0.020 and 0.018 for 117 and 85 unique reflections, respectively, with F o 〉 4σ(F o). R32 is a Sohncke type of space group where enantiomeric structures can exist; the single-domain structure obtained by the refinement was confirmed to be correct by a Flack parameter of −0.05 (2). The existence of Ni—Ni bonds was confirmed in both compounds, in addition to the Ni—Se bonds. The value of the atomic displacement parameter (mean-square displacement) of each atom in NiSe was larger than that in Ni3Se2. The larger amplitude of the atoms in NiSe corresponds to longer Ni—Se and Ni—Ni bond lengths in NiSe than in Ni3Se2. The Debye temperatures, θD, estimated from observed mean-square displacements for Ni and Se in Ni3Se2, were 322 and 298 K, respectively, while those for Ni and Se in NiSe were 246 and 241 K, respectively. The existence of large cavities in the structure and the weak bonding force are likely responsible for the brittle and soft nature of the NiSe crystal.
    Digitale ISSN: 2053-2296
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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    Structural analysis of the Sulfolobus solfataricus TF55β chaperonin by cryo-electron microscopy (2021)
    International Union of Crystallography
    Details
    Publikationsdatum: 2021-03-01
    Beschreibung: Chaperonins are biomolecular complexes that assist in protein folding. Thermophilic factor 55 (TF55) is a group II chaperonin found in the archaeal genus Sulfolobus that has α, β and γ subunits. Using cryo-electron microscopy, structures of the β-only complex of S. solfataricus TF55 (TF55β) were determined to 3.6–4.2 Å resolution. The structures of the TF55β complexes formed in the presence of ADP or ATP highlighted an open state in which nucleotide exchange can occur before progressing in the refolding cycle.
    Digitale ISSN: 2053-230X
    Thema: Biologie , Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Publiziert von International Union of Crystallography
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