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  • Other Sources  (73)
  • International Union of Crystallography  (36)
  • Schweizerbart  (34)
  • American Meteorological Society
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  • 2020-2022  (50)
  • 1995-1999  (23)
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  • 1
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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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    Publication Date: 2021-03-30
    Description: 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.
    Description: A simple and low‐cost device has been developed to minimize evaporation in microtiter plates for easy crystal handling and harvesting. image
    Keywords: 548 ; evaporation reduction ; crystal handling ; crystal harvesting ; crystallographic fragment screening
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  • 2
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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
    Publication Date: 2021-03-30
    Description: 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.
    Description: 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
    Keywords: 548 ; synchrotron ; anomalous diffraction ; semiconductor ; MEAD
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  • 3
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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
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    Publication Date: 2021-03-27
    Description: 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.
    Description: 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
    Keywords: 548 ; phasing ; crystallization ; GHK ; SAD
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  • 4
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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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    Publication Date: 2021-03-30
    Description: 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.
    Description: 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
    Keywords: 548 ; polyhydroxybutyrates ; mixed tacticity ; paracrystallinity ; Rietveld refinement ; thermal factors
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  • 5
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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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    Publication Date: 2021-03-27
    Description: 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.
    Description: 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
    Keywords: 548 ; residual stress ; X‐ray diffraction ; depth‐resolved analysis ; mosaic crystals
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  • 6
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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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    Publication Date: 2021-03-30
    Description: 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.
    Description: 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
    Keywords: 548 ; polyimide ; polarization ; X‐ray polarimetry ; wide‐angle scattering ; X‐ray dichroism
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  • 7
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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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    Publication Date: 2021-03-27
    Description: 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.
    Description: The elastic stiffness coefficients of thiourea are determined from thermal diffuse scattering. image
    Keywords: 548 ; thermal diffuse scattering ; elastic stiffness ; thiourea
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  • 8
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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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    Publication Date: 2021-07-03
    Description: 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.
    Description: Artificial neural networks trained with simulated data are shown to correctly and quickly determine film parameters from experimental X‐ray reflectivity curves.
    Keywords: 548 ; X‐ray reflectivity ; machine learning ; organic semi‐conductors ; neural networks
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  • 9
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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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    Publication Date: 2021-06-05
    Description: 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.
    Description: 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
    Keywords: 548 ; form factors ; polyhedra ; Fourier shape transform
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  • 10
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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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    Publication Date: 2021-06-30
    Description: 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.
    Description: 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.
    Keywords: 549 ; actinides ; EXAFS ; XANES ; HERFD‐XANES ; XAS ; XES ; RIXS ; XRD ; CTR ; RAXR ; surface diffraction
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  • 11
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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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    Publication Date: 2021-03-30
    Description: 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.
    Description: 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
    Keywords: 548 ; small‐angle scattering ; data analysis ; biological macromolecules ; structural modelling ; ATSAS
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  • 12
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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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    Publication Date: 2021-03-27
    Description: 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.
    Description: 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
    Keywords: 548 ; indexing ; XGANDALF ; CrystFEL ; multiple lattices ; serial crystallography
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  • 13
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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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    Publication Date: 2021-03-27
    Description: 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.
    Description: 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
    Keywords: 548 ; indexing ; pinkIndexer ; CrystFEL ; pink X‐ray beam ; serial electron diffraction
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  • 14
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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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    Publication Date: 2021-06-17
    Description: 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.
    Description: The covalent modification of human CRM1 by 2‐mercaptoethanol interferes with the characterization of cysteine‐dependent inhibitor compounds. image
    Keywords: 548 ; nuclear export ; cancer ; exportin 1 ; cysteine modification
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  • 15
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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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    Publication Date: 2021-06-26
    Description: 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.
    Description: 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
    Keywords: 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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  • 16
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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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    Publication Date: 2021-07-02
    Description: 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.
    Description: A new concept for temporal gating of synchrotron X‐ray pulses based on laser‐induced thermal transient gratings is presented.
    Keywords: 548 ; synchrotron ; time‐resolved ; thermal deformation ; transient grating ; pulse picking
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  • 17
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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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    Publication Date: 2021-06-06
    Description: 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.
    Description: 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
    Keywords: 548 ; beamline instrumentation ; time‐resolved X‐ray diffraction ; optical excitation ; thermal transport ; ferroelectric switching
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  • 18
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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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    Publication Date: 2021-03-27
    Description: 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.
    Description: 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
    Keywords: 548 ; sodium alkoxide ; powder data ; solvate ; isopropanol ; Bärnighausen tree ; PXRD
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  • 19
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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
    Details
    Publication Date: 2021-03-27
    Description: 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.
    Description: 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
    Keywords: 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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  • 20
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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
    Details
    Publication Date: 2021-06-28
    Description: 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.
    Keywords: 548 ; ARP/wARP ; model building ; cryo‐EM ; model accuracy ; sequence assignment
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  • 21
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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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    Publication Date: 2021-06-05
    Description: 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.
    Description: 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
    Keywords: 548 ; orthocarbonates ; crystal structure ; single‐crystal X‐ray diffraction ; high pressure ; Sr2CO4
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  • 22
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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
    Details
    Publication Date: 2021-06-28
    Description: 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.
    Keywords: 548 ; ASAXS ; biological SAXS ; metalloproteins ; gold nanoparticles ; anomalous scattering ; beamline development
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  • 23
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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
    Details
    Publication Date: 2021-06-27
    Description: 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.
    Keywords: 548 ; group–subgroup relationships ; nitride materials ; wurtzite type
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  • 24
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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
    Details
    Publication Date: 2021-06-20
    Description: 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.
    Description: 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
    Keywords: 548 ; pair distribution functions ; similarity measures ; total scattering techniques ; cross‐correlation functions ; R values
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  • 25
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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
    Details
    Publication Date: 2021-06-26
    Description: 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.
    Description: 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
    Keywords: 548 ; diamond anvil cells ; X‐ray free‐electron lasers ; high‐precision X‐ray diffraction ; finite element modeling
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  • 26
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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
    Details
    Publication Date: 2021-06-26
    Description: 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.
    Description: 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
    Keywords: 548 ; optical constants ; quartz ; anisotropy ; soft X‐ray reflectometry
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  • 27
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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
    Details
    Publication Date: 2021-07-05
    Description: 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.
    Description: 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.
    Keywords: 548 ; powder diffraction ; mixed conductors ; X‐ray absorption spectroscopy (XAS) ; Nd6−yWO12−δ
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  • 28
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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
    Publication Date: 2021-06-30
    Description: 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.
    Keywords: 548 ; in situ EXAFS ; high temperature ; time‐resolved EXAFS ; niobium
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  • 29
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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
    Details
    Publication Date: 2021-03-27
    Description: 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.
    Description: 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
    Keywords: 548 ; lead stannate (Pb2SnO4) ; density functional theory ; high‐pressure X‐ray diffraction ; pressure‐induced phase transition ; insulator–semiconductor transition
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  • 30
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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
    Publication Date: 2021-06-05
    Description: 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.
    Description: 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
    Keywords: 548 ; group–subgroup relationships ; nitride materials ; wurtzite type
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  • 31
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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
    Details
    Publication Date: 2021-06-26
    Description: 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).
    Description: 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
    Keywords: 548 ; undulator beamline ; soft X‐ray ; tender X‐ray ; hard X‐ray ; in situ ; operando ; HAXPES ; RIXS ; XAS ; XES
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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
    Details
    Publication Date: 2021-06-26
    Description: 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.
    Keywords: 548 ; pair distribution function analysis ; structure determination ; total scattering technique ; similarity measures ; PDF‐Global‐Fit
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  • 33
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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
    Details
    Publication Date: 2021-07-01
    Description: 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).
    Description: Crystal structures of a GH20 β‐N‐acetylglucosaminidase from V. campbellii reveal substrate specificity in chitin utilization.
    Keywords: 577.14 ; GH20 β‐N‐acetylglucosaminidase ; chitin recycling ; Vibrio spp ; marine bacteria
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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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    Publication Date: 2021-09-29
    Description: 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.
    Description: 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
    Keywords: 548 ; X‐ray free‐electron lasers ; X‐ray spectroscopy ; bent crystals ; diamond crystal optics ; femtosecond X‐ray diffraction
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  • 35
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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
    Details
    Publication Date: 2021-09-29
    Description: 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.
    Description: 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.
    Keywords: 548 ; TOF‐SANS ; incoherent neutron scattering ; inelastic neutron scattering ; hydrocarbon systems
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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
    Details
    Publication Date: 2021-09-29
    Description: 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.
    Description: 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
    Keywords: 548 ; crystal growth ; optical materials ; phase diagrams ; melting points ; rare earth sesquioxides
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  • 37
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    Geologie der Tiefsee (2020)
    Schweizerbart
    In:  In: Tiefsee - Vielfalt in der Dunkelheit. , ed. by Müller, T. and Hoffmann-Wieck, G. Senckenberg-Buch, 83 . Schweizerbart, Stuttgart, pp. 46-50. ISBN 978-3-510-61415-8
    Details
    Publication Date: 2020-05-28
    Description: Die Geowissenschaft betrachtet die Erde und damit auch die Entstehung von Tiefsee-Ebenen und untermeerischen Hochgebirgen aus einem anderen Blickwinkel. Um diese Herangehensweise nachzuvollziehen, hilft es, sich die Erde ohne Wasser vorzustellen. Wie die übrigen inneren Planeten unseres Sonnensystems, Merkur, Venus und Mars, ist auch die Erde von einer festen äußeren Schale, der sogenannten Erdkruste, umgeben. Dabei ist unsere Erde jedoch einzigartig darin, dass hier nicht nur eine, sondern zwei unterschiedliche Krustentypen auftreten, die kontinentale Kruste auf der einen und die ozeanische Kruste auf der anderen Seite.
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  • 38
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    Hotspots des Lebens - die geologischen Voraussetzungen (2020)
    Schweizerbart
    In:  In: Tiefsee - Vielfalt in der Dunkelheit. , ed. by Müller, T. and Hoffmann-Wieck, G. Senckenberg-Buch, 83 . Schweizerbart, Stuttgart, pp. 51-55. ISBN 978-3-510-61415-8
    Details
    Publication Date: 2020-07-01
    Description: Geologische Prozesse und dabei entweichende wässrige Lösungen sind in vielen Bereichen der Ozeane für die Entstehung von Oasen in der Tiefsee verantwortlich. Das Leben dort ist an die spezifischen Eigenschaften der auftretenden Gesteine und chemischen Lösungen angepasst und unterscheidet sich daher erheblich von dem der normalen Tiefsee-Ebenen oder Seeberge. Zu den außergewöhnlichen Lebensräumen gehören die sogenannten Schwarzen Raucher, die sich in der Umgebung vulkanisch aktiver Bereiche bilden und an denen heiße (hydrothermale) Lösungen austreten. Dazu gehören aber auch Austrittsstellen von Gasen und Lösungen mit geringerer Temperatur, die sich häufig in den Sehelfgebieten der Kontinente oder in sehr stark sedimentierten Bereichen der Tiefsee finden. Diese werden unter dem Begriff „Cold Seeps" (,.kalte Sickerstellen") zusammengefasst, obwohl diese Stellen sehr unterschiedlich sein können.
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  • 39
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    Methanhydrate (2020)
    Schweizerbart
    In:  In: Tiefsee - Vielfalt ind der Dunkelheit. , ed. by Müller, T. and Hoffmann-Wieck, G. Senckenberg-Buch, 83 . Schweizerbart, Stuttgart, pp. 156-158. ISBN 978-3-510-61415-8
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    Publication Date: 2020-06-03
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  • 40
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    Massivsulfide (2020)
    Schweizerbart
    In:  In: Tiefsee - Vielfalt in der Dunkelheit. , ed. by Müller, T. and Hoffmann-Wieck, G. Senckenberg-Buch, 83 . Schweizerbart, Stuttgart, pp. 153-155. ISBN 978-3-510-61415-8
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    Publication Date: 2020-06-03
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  • 41
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    Manganknollen (2020)
    Schweizerbart
    In:  In: Tiefsee - Vielfalt in der Dunkelheit. , ed. by Müller, T. and Hoffmann-Wieck, G. Senckenberg-Buch, 83 . Schweizerbart, Stuttgart, pp. 149-152. ISBN 978-3-510-61415-8
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    Publication Date: 2020-06-03
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  • 42
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    Mineralische Rohstoffe der Tiefsee (2020)
    Schweizerbart
    In:  In: Tiefsee - Vielfalt in der Dunkelheit. , ed. by Müller, T. and Hoffmann-Wieck, G. Senckenberg-Buch, 83 . Schweizerbart, Stuttgart, pp. 147-149. ISBN 978-3-510-61415-8
    Details
    Publication Date: 2020-06-03
    Description: Die Erde hält eine Vielzahl natürlicher mineralischer Rohstoffe bereit, die wir in unserer hochtechnisierten Gesellschaft benötigen. Zurzeit werden fast alle diese Rohstoffe auf einer Fläche abgebaut, die weniger als ein Drittel unseres Planeten ausmacht -der Landfläche. Hier wird es jedoch immer schwieriger, reiche Vorkommen zu finden. Dies zwingt die Bergbauindustrie dazu, Lagerstätten mit geringeren Konzentrationen abzubauen bzw. nach Lagerstätten in abgelegenen Regionen der Erde oder in großer Tiefe zu suchen. Dies ist jedoch mit einem erheblichen Anstieg des Flächenverbrauchs und mit zusätzlichen Umweltbeeinträchtigungen verbunden.
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  • 43
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    Vom Telegraphenkabel zum Internet-Glasfaserkabel in der Tiefsee (2020)
    Schweizerbart
    In:  In: Tiefsee - Vielfalt ind der Dunkelheit. , ed. by Müller, T. and Hoffmann-Wieck, G. Senckenberg-Buch, 83 . Schweizerbart, Stuttgart, pp. 165-167. ISBN 978-3-510-61415-8
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    Publication Date: 2020-07-01
    Description: Bereits 1811 schickte Samuel Thomas von Sömmering elektrische Signale durch einen von Kautschuk isolierten Draht, welcher bei München durch die Isar verlegt wurde. Diese frühen Versuche scheiterten an der ungeeigneten Isolierung. Erst die Erfindung der Gutapercha-Presse 1847 durch Werner von Siemens ermöglichte die Unterwasserverlegung gut isolierter Kabel.
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  • 44
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    Die Lebenswelt der Tiefsee (2020)
    Schweizerbart
    In:  In: Tiefsee - Vielfalt in dder Dunkelheit. , ed. by Müller, T. and Hoffmann-Wieck, G. Senckenberg-Buch, 83 . Schweizerbart, Stuttgart, pp. 74-79. ISBN 978-3-510-61415-8
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    Publication Date: 2020-07-01
    Description: Die Tiefsee beginnt in einer Tiefe von 200 m. Der darüberliegende Bereich lichtdurchfluteter Wasserschichten wird „photische Zone" genannt, da hier genügend Licht zur Verfügung steht, um die Fotosynthese zu unterstützen, die für das Wachstum von Pflanzen und Algen erforderlich ist. Unterhalb von 200 m kommt nur wenig Licht an, nicht genug für die Fotosynthese. Dieser Bereich heißt Dämmerungszone oder auch „mesopelagische Zone".
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  • 45
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    Cold-Seep-Ökosysteme - Oasen oder Leben am Limit (2020)
    Schweizerbart
    In:  In: Tiefsee - Vielfalt in der Dunkelheit. , ed. by Müller, T. and Hoffmann-Wieck, G. Senckenberg-Buch, 83 . Schweizerbart, Stuttgart, pp. 62-68. ISBN 978-3-510-61415-8
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    Publication Date: 2020-07-01
    Description: Die uns vertraute Grundlage des Lebens ist die Fotosynthese, die Erzeugung organischer Kohlenstoffverbindungen mithilfe des Sonnenlichts durch Pflanzen, Algen und Cyanobakterien (Primärproduktion). Diese Organismen werden als „autotroph" ("sich selbst ernährend") bezeichnet und dienen uns Menschen und anderen heterotroph ("sich von anderen ernährend") lebenden Tieren als Nahrung. In den lichtlosen Tiefen der Ozeane wurden allerdings Ökosysteme entdeckt, die gänzlich anders funktionieren.
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  • 46
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    Zur Geschichte der Meeres- und Tiefseeforschung in Westeuropa und den USA (2020)
    Schweizerbart
    In:  In: Tiefsee - Vielfalt in der Dunkelheit. , ed. by Müller, T. and Hoffmann-Wieck, G. Senckenberg-Buch, 83 . Schweizerbart, Stuttgart, pp. 14-22. ISBN 978-3-510-61415-8
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    Publication Date: 2020-07-03
    Description: Lange galt das Meer als unendlicher Ressourcenraum, den wir Menschen nicht nachhaltig beeinflussen könnten. Heute wissen wir, dass auch das Meer endlich ist. Es wird diskutiert, ob der Mensch das gigantisch große „Ökosystem Meer" kollabieren lassen könnte. Gleichzeitig wird die Bedeutung der Meere für das Leben auf der Erde nicht mehr bestritten und die Relevanz der Meeresforschung für nachhaltiges gesellschaftliches, politisches und wirtschaftliches Handeln deutlich.
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  • 47
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    Bedingungen der Tiefsee (2020)
    Schweizerbart
    In:  In: Tiefsee - Vielfalt in der Dunkelheit. , ed. by Müller, T. and Hoffmann-Wieck, G. Senckenberg-Buch, 83 . Schweizerbart, Stuttgart, pp. 42-45. ISBN 978-3-510-61415-8
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    Publication Date: 2020-07-01
    Description: Je nach Definition beginnt die Tiefsee bei 200, 500 oder 1.000 m unter der Wasseroberfläche. Die Tiefsee ist dunkel, kalt, nährstoffarm, spärlich besiedelt und steht unter dem enormen Druck der auf ihr lastenden Wassersäule. Sämtliche Tiefseeorganismen müssen diesen z. T. lebensfeindlichen Bedingungen standhalten bzw. an diese angepasst sein. An einigen Stellen, den sogenannten Hotspots, ist die Artenvielfalt jedoch trotz dieser Extrembedingungen sehr hoch.
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  • 48
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    Lebensraum Tiefsee (2020)
    Schweizerbart
    In:  In: Tiefsee - Vielfalt in der Dunkelheit. , ed. by Müller, T. and Hoffmann-Wieck, G. Senckenberg-Buch, 83 . Schweizerbart, Stuttgart, pp. 40-41. ISBN 978-3-510-61415-8
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    Publication Date: 2020-07-03
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  • 49
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    Die menschengemachte Klimaerwärmung und die Tiefsee (2020)
    Schweizerbart
    In:  In: Tiefsee - Vielfalt in der Dunkelheit. , ed. by Müller, T. and Hoffmann-Wieck, G. Senckenberg-Buch, 83 . Schweizerbart, Stuttgart, pp. 184-185. ISBN 978-3-510-61415-8
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    Publication Date: 2020-07-01
    Description: Durch das Verbrennen von Kohle, Gas und Öl hat der Mensch die Erde seit Beginn der Industrialisierung um ca. 1 °C erwärmt, mit bereits deutlich spürbaren Auswirkungen -auch für uns Menschen.
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  • 50
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    Meerestechnik für die Tiefseeforschung (2020)
    Schweizerbart
    In:  In: Tiefsee - Vielfalt in der Dunkelheit. , ed. by Müller, T. and Hoffmann-Wieck, G. Senckenberg-Buch, 83 . Schweizerbart, Stuttgart, pp. 31-37. ISBN 978-3-510-61415-8
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    Publication Date: 2020-07-03
    Description: Die Tiefsee wird als eines der letzten Grenzgebiete in der Erforschung unseres blauen Planeten angesehen. Zu den großen Herausforderungen, die uns den Zugang zu diesem Lebensraum erschweren, zählen neben der Dunkelheit tiefe Temperaturen (im Mittel um 2 °C), hohe Korrosion im salzigen Meerwasser, hoher Umgebungsdruck, biologischer Bewuchs (..biofouling"), stürmische See mit hohem Wellengang sowie die schwierige Datenübertragung ohne Kabel, die nur auf die Akustik beschränkt ist. Dies macht die Tiefseetechnik zu einer Spitzentechnologie, die sehr viele Analogien zur Weltraumforschung aufweist.
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  • 51
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    Carbonate sedimentation through the late Precambrian and Phanerozoic (1999)
    Schweizerbart
    In:  Zentralblatt für Geologie und Paläontologie / Teil 1, 1998 (5-6). pp. 435-445.
    Details
    Publication Date: 2018-02-06
    Description: The global sediment mass-age distribution indicates large variations in the rates of carbonate sedimentation through time. The largest mass of carbonate deposited during the entire history of the earth was produced during the Cambrian, possibly following on an episode of phosphogenesis in the Late Precambrian. A second major episode occurred during the Late Devonian, probably reflecting the invasion of land by plants that altered the rock-weathering and soil-forming regimes. Other lesser pulses of carbonate deposition occurred in the Late Permian, Triassic, and Cretaceous. A shift in the locus of carbonate deposition from shallow waters to the deep sea occurred during the Cretaceous.
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  • 52
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    Verteilung und Artenzusammensetzung benthischer Ostracoden der Islandsee im Spätquartär [Distribution and abundance of benthic ostracods in the Iceland Sea during the Late Quaternary] (1999)
    Schweizerbart
    In:  Zentralblatt für Geologie und Paläontologie / Teil 1, 1998 (5-6). pp. 353-365.
    Details
    Publication Date: 2017-06-22
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  • 53
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    Indium geology, mineralogy, and economics - a review (1999)
    Schweizerbart
    In:  Zeitschrift für Angewandte Geologie, 45 . pp. 164-169.
    Details
    Publication Date: 2016-06-16
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  • 54
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    Increased seasonality in the gulf of Aquaba, Red Sea, recorded in the Oxygen Isotope Record of a Porites lutea coral (1999)
    Schweizerbart
    In:  Senckenbergiana Maritima, 30 . pp. 17-26.
    Details
    Publication Date: 2019-08-08
    Description: At Aqaba in the Northern Gulf of Aqaba, Red Sea, the stable oxygen isotope record of a Por#es lutea coral colony was studied. From a vertical and a horizontal core two parts from the base of the colony (10 years of coral growth), and two parts from the living surface (12 years of coral growth) were analysed with a monthly sampling resolution. The results show that seasonality of sea surface temperatures (SST) in the northem GulfofAqaba has increased since the early 19th century, mainly due to higher summer temper- atures. 8~80-ratios indicate that SST increased by at least 1.3~ Horizontal and vertical cores display dif- ferent variations in the modern parts, probably caused by the very shallow water depth of the youngest part of the vertical core.
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  • 55
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    A comment on the proper use of nutrient ratios in microalgal ecology (1999)
    Schweizerbart
    In:  Archiv für Hydrobiologie, 146 . pp. 55-64.
    Details
    Publication Date: 2019-03-05
    Description: Repeatable species dominance patterns across nutrient ratio gradients are found both in culture competition experiments and in natural waters. However, the mechanisms behind these similar patterns need not to be identical. In chemostat experiments, such patterns are caused by the two-way competitive interactions between contemporaneously occurring organisms. Nutrient competition may be important in situ too, but there is an additional effect of early successional species influencing the nutrient environment for later successional species, without being influenced themselves by their successors.
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  • 56
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    Factors determining cyanobacterial success in aquatic systems: A literature review (1998)
    Schweizerbart
    In:  Archiv für Hydrobiologie Spec. Iss. Advances in Limnology, 51 . pp. 41-62.
    Details
    Publication Date: 2017-12-01
    Description: Cyanobacteria are important constituents of most aquatic ecosystems on earth, and planktonic forms frequently show mass development in lakes and estuaries. Despite extensive scientific efforts directed towards research on cyanobacteria, a comprehensive theory explaining their success is lacking. Because cyanobacteria comprise a diverse group of organisms, it is concluded that any analysis of the conditions leading to cyanobacterial dominance in pelagic ecosystems should consider at least three different subgroups, classified based on presence or absence of (i) buoyancy regulation and (ii) the ability to fix molecular nitrogen. In this review, nine single-factor hypotheses regarding regulation of cyanobacterial development are examined against the background of physiological and ecological characteristics of these organisms. Special emphasis has been put on understanding differences in nitrogen metabolism between cyanobacteria and algae which directly relate to a hypothesis conceming inorganic nitrogen forms and cyanobacterial success previously presented by our research group. The review lends support to the theory that cyanobacteria have a low competitive ability for nitrate compared with algae and a high ability to compete for ammonium, particularly under nitrogen-limiting conditions. Finally it is concluded that to understand cyanobacterial devlopment and how high Standing Stocks in pelagic ecosystems are maintained requires parts o f all the single-factor hypotheses initially presented.
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  • 57
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    The role of salinity in circulation of the Cretaceous ocean (1998)
    Schweizerbart
    In:  Zentralblatt für Geologie und Paläontologie / Teil 1, 1996 (11/12). pp. 1445-1454.
    Details
    Publication Date: 2018-02-06
    Description: The density of seawater is a complex function of temperature, salinity, and pressure. Because of the non-linearity of the equation of state of seawater, the densities of sea waters having the same temperature and the same salinity differences (with respect to the mean salinity of the ocean) will vary with the mean salinity of the ocean. Although this strange property of seawater is evident in a plot of the equation of state, it has never been considered in trying to reconstruct ancient ocean circulation. These differences in the density field may have caused the ocean to respond differently to atmospheric forcing in the past. The different response may hold the key to understanding "ocean anoxic events" and episodes of large-scale burial of organic carbon and production of petroleum source rocks.
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  • 58
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    Modeling Late Cretaceous climate and vegetation (1998)
    Schweizerbart
    In:  Zentralblatt für Geologie und Paläontologie / Teil 1, 1996 (11/12). pp. 1433-1444.
    Details
    Publication Date: 2018-02-06
    Description: The Late Cretaceous was much warmer than today. There was no significant ice at high latitudes, meridional thermal gradients were low, and continental interiors remained warm during winter. Late Cretaceous atmospheric C02 concentrations were about four times greater than today and an enhanced "greenhouse" effect contributed to the overall warmth of the Late Cretaceous. However , increases in atmospheric C02 tend to increase temperatures at all latitudes and do not explain the very low thermal gradients recognized in the geologic record. Increased poleward ocean heat transport has been cited as a mechanism for maintaining low meridional thermal gradients during the Cretaceous. However , ocean heat transport values larger than the present day are difficult to reconcile. In addition, low meridional thermal gradients suggest sluggish atmospheric circulation, implying that the advection of heat from the warm oceans into the continental interiors was limited. In general, paleoclimate simulations using Atmospheric General Circulations Models (AGCMs) have not been successful in simulating the low meridional thermal gradients and warm winter continental interiors of the Cretaceous, forcing the concept of "equability" to be questioned. Until recently, the physical effects of vegetation on pre-Quaternary climates have largely been ignored. Terrestrial ecosystems influence global climate by affecting the exchange of energy, water, and momentum between the land surface and the atmosphere. In a new approach to pre-Quaternary paleoclimate modeling, Campanian (80 Ma) climate and vegetation have been simulated using a global climate model (GENESIS Version 2.0), coupled to a predictive vegetation model (EVE), resulting in a realistic simulation of Late Cretaceous climate. The predicted distribution of Late Cretaceous vegetation played an important role in the maintenance of low meridional thermal gradients, polar warmth, and equable continental interiors. High latitude forests reduced albedo, especially during snowcovered months, and increased net surface radiation and latent heat flux.
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  • 59
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    The Impact of Data Assimilation on ENSO Simulations and Predictions (1997)
    American Meteorological Society
    In:  Monthly Weather Review, 125 (5). pp. 819-830.
    Details
    Publication Date: 2020-06-30
    Description: In this study, the impact of oceanic data assimilation on ENSO simulations and predictions is investigated. The authors’ main objective is to compare the impact of the assimilation of sea level observations and three-dimensional temperature measurements relative to each other. Three experiments were performed. In a control run the ocean model was forced with observed winds only, and in two assimilation runs three-dimensional temperatures and sea levels were assimilated one by one. The root-mean-square differences between the model solution and observations were computed and heat content anomalies of the upper 275 m compared to each other. Three ensembles of ENSO forecasts were performed additionally to investigate the impact of data assimilation on ENSO predictions. In a control ensemble a hybrid coupled ocean–atmosphere model was initialized with observed winds only, while either three-dimensional temperatures or sea level data were assimilated during the initialization phase in two additional forecast ensembles. The predicted sea surface temperature anomalies were averaged over the eastern equatorial Pacific and compared to observations. Two different objective skill measures were computed to evaluate the impact of data assimilation on ENSO forecasts. The authors’ experiments indicate that sea level observations contain useful information and that this information can be inserted successfully into an oceanic general circulation model. It is inferred from the forecast ensembles that the benefit of sea level and temperature assimilation is comparable. However, the positive impact of sea level assimilation could be shown more clearly when the forecasted temperature differences rather than the temperature anomalies themselves were compared with observations.
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  • 60
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    Geochemical and Sm-Nd Characteristics of a polymetamorphic S-type granitoid: The Mönchalpgneiss - Silvretta nappe/Switzerland (1997)
    Schweizerbart
    In:  European Journal of Mineralogy, 9 (2). pp. 411-422.
    Details
    Publication Date: 2017-01-04
    Description: This paper presents trace element and Sm-Nd isotope data on the Mönchalpgneiss in order to compare the geochemistry of the two polymetamorphic igneous suites that comprise over 30% of the Austroalpine Silvretta nappe. The first are the so-called "Younger Orthogneisses" of the "Fliielagranitic Association" and the second are the "Older Orthogneisses" including the Mönchalpgneisswhich are associated with metagabbros, metadiorites, metatonalites and metagranitoids. U-Pb zircon results from the Mönchalpgneiss are indicative of anatectic processes in late Cambrian to Ordovician times. A volcanic-arc (VA) tectonic environment during intrusion explains the direct association of gabbroic and metagranitoid rocks in the Engadine area. This model is in line with the distribution of major, trace and rare earth elements in these anatectic rocks. However, the significance of the geochemical results remains ambiguous, since the average continental crust and paragneisses of the Silvretta also show VA-type signatures in the respective diagrams. Nd model ages on four Mönchalpgneiss whole-rock samples from the type locality are closely grouped around 1.70 Ga, which is a commonly obtained value for European continental crust. This age is interpreted to be the result of a homogeneous mixture of different crustal components
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  • 61
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    The Coupled GCM ECHO-2. Part I: The Tropical Pacific (1997)
    American Meteorological Society
    In:  Monthly Weather Review, 125 . pp. 703-720.
    Details
    Publication Date: 2020-06-30
    Description: In this paper the performance of the global coupled general circulation model (CGCM) ECHO-2, which was integrated for 10 years without the application of flux correction, is described. Although the integration is rather short, strong and weak points of this CGCM can be clearly identified, especially in view of the model's performance of the annual cycle in the tropical Pacific. The latter is simulated with more success relative to the earlier version, ECHO-I. A better representation of the low-level stratus clouds in the atmosphere model associated with a reduction in the shortwave radiative flux at the air-sea interface improved the coupled model's performance in the southeastern tropical oceans, with a strongly reduced warm bias in these regions. Modifications in the atmospheric convection scheme also eliminated the AGCM's tendency to simulate a double ITCZ, and this behavior is maintained in the CGCM simulation. Finally, a new numerical scheme for active tracer advection in the ocean model strongly reduced the numerical mixing, which seems to enhance considerably the level of interannual variability in the equatorial Pacific. One weak point is an overall cold bias in the Tropics and midlatitudes, which typically amounts to 1°C in open ocean regions. Another weak point is the still too strong equatorial cold tongue, which penetrates too far into the western equatorial Pacific. Although this model deficiency is not as pronounced as in ECHO-1, the too strong cold tongue reduces the level of interannual rainfall variability in the western and central equatorial Pacific. Finally, the interannual fluctuations in equatorial Pacific sea surface temperatures (SSTs) are too equatorially trapped, a problem that is also found in ocean-only simulations. Overall, however, the authors believe that the ECHO-2 CGCM has been considerably improved relative to ECHO-1.
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  • 62
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    Geochemistry of a meta-ophiolite suite: An association of metagabbros, eclogites and glaucophanites on the island of Syros, Greece (1996)
    Schweizerbart
    In:  European Journal of Mineralogy, 8 (3). pp. 607-624.
    Details
    Publication Date: 2020-07-31
    Description: Abstract The famous association of metagabbros, eclogites, glaucophanites, jadeite rocks and ultramafics from the island of Syros forms a distinct lithostratigraphic or tectonic unit. It is interpreted as a high-pressure metamorphic ophiolite suite. This paper provides geochemical and Sr-isotope constraints on the geotectonic setting in which the magmatic protoliths of the Syros metabasites were formed. A compositional gap exists between the metagabbros with Mg-numbers [Mg# = Mg/(0.85Fetot + Mg) atomic ratio] of 0.75-0.88 on the one hand and eclogites and garnet-glaucophanites on the other hand with Mg# of 0.35-0.62, and maximum total iron contents of up to 18 wt.% FeOtot. Metagabbros from various localities and glaucophanites collected around Manna form geochemically coherent groups with smooth correlations between compatible as well as immobile incompatible elements and Mg#. By contrast, the behaviour of immobile incompatible elements, and to some extent also of compatible elements, is highly unsystematic in the eclogites and garnet-glaucophanites. Also, the more mobile elements display a wide scatter in all rocks. This, in conjunction with the unsystematic variation of Sr-isotopes, is thought to be due to secondary alteration. From the strong correlation of Ni and Cr with Mg# and the flat REE patterns lacking Eu-anomalies, a cumulus nature is inferred for olivine, clinopyroxene, and spinel, associated with intercumulus formation of plagioclase in the magmatic protoliths of the metagabbros. There is no direct genetic link between these rocks and the precursors of the Manna-type glaucophanites with REE characteristics typical of N- to T-type MORB. The extremely high geochemical diversity of the eclogites and garnet-glaucophanites from Syros favours individual evolution of their protoliths in small magma bodies as suggested for superferric eclogites from the Western and Ligurian Alps, as well as the ferrogabbros from the ophiolites of the Northern Apennines. From the geochemistry of the Syros metabasites along with the initial 87Sr/86Sr ratios of the metagabbros between 0.7031 and 0.7033, as well as an eNd value of 7.7 from a garnet glaucophanite, the magmatic protoliths are inferred to have formed in a back-arc setting. By analogy to the association of gabbros and ferrogabbros adjacent to the Atlantis II fracture zone of the SW Indian Ridge, we further suggest an origin at a spreading ridge in proximity to a transform fault.
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    Geochemistry of the Yali volcano rhyolites and their relationship to the volcanic products of Nisyros, Aegean Volcanic Arc (1996)
    Schweizerbart
    In:  Neues Jahrbuch Für Mineralogie - Monatshefte, 1996 (2). pp. 57-72.
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    Publication Date: 2017-03-20
    Type: Article , PeerReviewed
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    Dinoflagellate cyst evidence of Holocene environmental conditions off East Greenland (1996)
    Schweizerbart
    In:  Zentralblatt für Geologie und Paläontologie / Teil 1, 1995 (1/2). pp. 271-286.
    Details
    Publication Date: 2017-06-23
    Type: Article , PeerReviewed
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    Chlorococcalalgen und Dinoflagellaten-Zysten in rezenten Sedimenten des Greifswalder Boddens (südliche Ostsee) (1996)
    Schweizerbart
    In:  Senckenbergiana Maritima, 27 (1/2). pp. 33-48.
    Details
    Publication Date: 2019-08-08
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    A simpler plate-tectonic history for the Caribbean (1996)
    Schweizerbart
    In:  Zentralblatt für Geologie und Paläontologie / Teil 1, 1994 (7/8). pp. 917-934.
    Details
    Publication Date: 2018-02-06
    Description: Evolution of the Caribbean Plate can be modeled by motions about six successive rotation poles. Opening of Cayman Trough has occurred since 49.5 Ma through westward motion of the Caribbean Plate, eastern Greater Antilles and Chortis Block. Before 49.5 Ma, the eastern Greater-Antilles were west of Cuba, and the southeastern margins of Yucatan and the Nicaragua Rise (Chortis) were aligned. From 67.5 to 49.5 Ma the Caribbean Plate rotated clockwise, opening the Yucatan Basin. From 100 Ma to 67.5 Ma, the Caribbean Plate, with Cuba attached, moved along the southeastern margin of Yucatan-Chortis. At 130 Ma it was attached to northwestern South America.
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    Mikro-Abdorptionsphotometrie: Neue Möglichkeiten der Faziesanalyse mit fossilen und rezenten Pollen (1996)
    Schweizerbart
    In:  Neues Jahrbuch für Geologie und Paläontologie - Monatshefte, 1996 (5). pp. 257-278.
    Details
    Publication Date: 2017-02-16
    Description: Microspectralphotometric examinations of various recent pollen point to a different sporopollenin chemistry of the different taxa which is distinguishable by the UV-VIS absorptionspectra. The measurement areas have a diameter of 6 micron, by which several measurements for the spectra control in one pollen grain are possible. Labaratory experiments with chemical treatments as used by palynological preparation, show a clear change in the sporopollenin chemistry whichcould be identified by the absorption spectra. Therefore a new preparation technique for fossil and recent palynomorphs has to be developed to avoid chemical changes. First investigations of recent and fossil Pinus pollen have been clone on material from various facies types and a sediment core. The variations in the absorption spectra of the pollen indicate the different chemical influence of different facies types which could be used for facies analyses. Furthermore, significant changes in the absorption spectra are useful to identify reworked pollen or pollen with a different burial history. Zusammenfassung: Vergleichende mikrospektralphotometrische Untersuchungen der UV-VIS Absorptionsspektren verschiedener rezenter Pollen-Taxa zeigen, daß die Zusammensetzung bzw. Struktur des Sporopollenins bei verschiedenen Taxa variiert und daß diese anhand der Absorptionsspektren klar unterschieden werden kann. Die gemessene Fläche auf den jeweiligen Pollen hat einen Durchmesser von 6 j.lm, so daß mehrere Kontrollmessungen an einem Pollen möglich sind. Laborversuche an rezenten Pollen zeigen, daß chemische Einflüsse (z. B. HN03, Acetolyse) deutlich meßbare Veränderungen in der Struktur des Sporopollenins verursachen. Um Veränderungen des Sporepollenins durch die chemische Probenaufbereitung auszuschließen, wurde eine neue Präparationsmethode für fossile und rezente Palynomorphen entwickelt.
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    Can ecosystem properties be optimized by natural selection? (1996)
    Schweizerbart
    In:  Senckenbergiana Maritima, 27 . pp. 145-150.
    Details
    Publication Date: 2019-08-08
    Description: ana marit., 27 (3/6): 145-150, 2 figs.; Frankfurt a. M.] According to the (neo-)Darwinian theory of evolution the appearance of "design" and optimization of biological properties are the results of natural selection and not of teleology. An opti· mization by selection is only possible for entities which are able to reproduce ("units of selection"). The "unit-of-selection"-problem will be discussed in relation to the atomism-holism-continuum of ecological and evolutionary concepts which range from Dawkins' "selfish gene" to LoveJock's "Gaia". Special emphasis will be given to the discussion of the group-selection problem which seems to be the critical breakpoint along this continuum. It will be shown that optimization through natural selection is only possible for units which can multiply and preserve their identity to a sufficient degree through multiplications. Such units are called replicators. Associations, communities, ecosystems and the biosphere do not qualify as replicators.
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    Stabile Isotope sorbierter Kohlenwasserstoffe aus flachen Nordseebohrungen [Stable isotope analysis of hydrocarbons in drill cores from shallow boreholes in the North Sea] (1996)
    Schweizerbart
    In:  Geologisches Jahrbuch: Reihe A, 146 (1). pp. 203-215.
    Details
    Publication Date: 2020-07-30
    Description: In Sedimenten aus flachen Bohrungen in der Nordsee wurden gasförmige Kohlenwasserstoffe gefunden. Kohlenstoff- (Methan bis Propan) und Wasserstoff-Isotopanwerte lassen auf eine Mischung von Gasen bakterieller und thermischer Entstehung schließen. Die thermischen Gase sind in größerer Tiefe aus überwiegend mariner organischer Substanz entstanden und in die oberflächennahen Sedimente migriert. [Methane through pentane have been found in sediments from shallow North Sea boreholes. Carbon (methane through propane) and hydrogen (methane) isotope ratlos indicate both bacterial and thermal origins. The gases of thermal origin are interpreted as having been generated at considerable depth from predominantly marine source rocks and then to have migrated into the overlying sediments.]
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    Studies on element bonding forms in sediments from the Reykjanes Ridge (59°N-60°N) (1995)
    Schweizerbart
    In:  Zentralblatt für Geologie und Paläontologie / Teil 1, 1994 (1/2). pp. 83-95.
    Details
    Publication Date: 2016-04-22
    Description: The chemical composition of sediments from the Reykjanes Ridge is controlled by allochthonous and autochthonous processes. The surface sediments are characterized by relatively high contents of calciumoxide and strontium. Calcium and strontium dominate in the carbonate phase due to the high content of biogenic carbonate. A high percentage of iron and manganese are bound to oxides and hydroxides. An indication of hydrothermal activity was not observed. A considerable portion of adsorbed barium is transported in clay minerals. The higher amounts of aluminium in glacial sequences indicate an enhanced input of terrigenous material; the increase of stable bonding elemen~s points toward the large influence of detrital minerals. The distinct differences in the bonding characteristics of elements in these marine sediments in comparison to fluvial and coastal - deposits could be due to the different environmental conditions.
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    The Seasonal Cycle over the Tropical Pacific in Coupled Ocean–Atmosphere General Circulation Models (1995)
    American Meteorological Society
    In:  Monthly Weather Review, 123 (9). pp. 2825-2838.
    Details
    Publication Date: 2020-06-30
    Description: The seasonal cycle over the tropical Pacific simulated by 11 coupled ocean–atmosphere general circulation models (GCMs) is examined. Each model consists of a high-resolution ocean GCM of either the tropical Pacific or near-global means coupled to a moderate- or high-resolution atmospheric GCM, without the use of flux correction. The seasonal behavior of sea surface temperature (SST) and eastern Pacific rainfall is presented for each model. The results show that current state-of-the-art coupled GCMs share important successes and troublesome systematic errors. All 11 models are able to simulate the mean zonal gradient in SST at the equator over the central Pacific. The simulated equatorial cold tongue generally tends to be too strong, too narrow, and extend too far west. SSTs are generally too warm in a broad region west of Peru and in a band near 10°S. This is accompanied in some models by a double intertropical convergence zone (ITCZ) straddling the equator over the eastern Pacific, and in others by an ITCZ that migrates across the equator with the seasons; neither behavior is realistic. There is considerable spread in the simulated seasonal cycles of equatorial SST in the eastern Pacific. Some simulations do capture the annual harmonic quite realistically, although the seasonal cold tongue tends to appear prematurely. Others overestimate the amplitude of the semiannual harmonic. Nonetheless, the results constitute a marked improvement over the simulations of only a few years ago when serious climate drift was still widespread and simulated zonal gradients of SST along the equator were often very weak.
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    Crystal structure of tricalcium silicate from a Portland cement clinker and its application to quantitative XRD analysis (1995)
    Schweizerbart
    In:  Neues Jahrbuch Für Mineralogie - Monatshefte, 1995 (4). pp. 146-160.
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    Publication Date: 2020-09-28
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    Organic-walled microfossils in Holocene sediments from Neustadt Bay, western Baltic Sea (1995)
    Schweizerbart
    In:  Zentralblatt für Geologie und Paläontologie / Teil 1, 1994 (1/2). pp. 67-81.
    Details
    Publication Date: 2017-06-23
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