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  • Periodicals Archive Online (PAO)  (12,766)
  • American Meteorological Society (AMS)
  • International Union of Crystallography
  • University of Chicago Press
  • 2020-2024  (109)
  • 1950-1954  (9,902)
  • 1945-1949  (6,724)
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  • 1
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    INSIGHT: in situ heuristic tool for the efficient reduction of grazing‐incidence X‐ray scattering data (2024)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-04-25
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉〈italic〉INSIGHT〈/italic〉 is a Python‐based software tool for processing and reducing 2D grazing‐incidence wide‐ and small‐angle X‐ray scattering (GIWAXS/GISAXS) data. It offers the geometric transformation of the 2D GIWAXS/GISAXS detector image to reciprocal space, including vectorized and parallelized pixel‐wise intensity correction calculations. An explicit focus on efficient data management and batch processing enables full control of large time‐resolved synchrotron and laboratory data sets for a detailed analysis of kinetic GIWAXS/GISAXS studies of thin films. It processes data acquired with arbitrarily rotated detectors and performs vertical, horizontal, azimuthal and radial cuts in reciprocal space. It further allows crystallographic indexing and GIWAXS pattern simulation, and provides various plotting and export functionalities. Customized scripting offers a one‐step solution to reduce, process, analyze and export findings of large 〈italic〉in situ〈/italic〉 and 〈italic〉operando〈/italic〉 data sets.〈/p〉
    Keywords: ddc:548 ; grazing‐incidence X‐ray scattering ; time‐resolved studies ; in situ studies ; operando studies ; computer programs
    Language: English
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  • 2
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    How Does Germline Regenerate? (2024)
    University of Chicago Press
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    Publication Date: 2024-04-04
    Description: A concise primer that complicates a convenient truth in biology—the divide between germ and somatic cells—with far-reaching ethical and public policy ramifications. Scientists have long held that we have two kinds of cells—germ and soma. Make a change to germ cells—say using genome editing—and that change will appear in the cells of future generations. Somatic cells are “safe” after such tampering; modify your skin cells, and your future children’s skin cells will never know. And, while germ cells can give rise to new generations (including all of the somatic cells in a body), somatic cells can never become germ cells. How did scientists discover this relationship and distinction between somatic and germ cells—the so-called Weismann Barrier—and does it actually exist? Can somatic cells become germ cells in the way germ cells become somatic cells? That is, can germ cells regenerate from somatic cells even though conventional wisdom denies this possibility? Covering research from the late nineteenth century to the 2020s, historian and philosopher of science Kate MacCord explores how scientists came to understand and accept the dubious concept of the Weismann Barrier and what profound implications this convenient assumption has for research and policy, from genome editing to stem cell research, and much more.
    Keywords: germline, germ cell, regeneration, genome editing, cell lineage, Weismann Barrier, August Weismann, germ plasm theory ; thema EDItEUR::P Mathematics and Science::PD Science: general issues ; thema EDItEUR::P Mathematics and Science::PD Science: general issues::PDA Philosophy of science ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSF Cellular biology (cytology)
    Language: English
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  • 3
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    Crystal diffraction prediction and partiality estimation using Gaussian basis functions (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-07-04
    Description: The recent diversification of macromolecular crystallographic experiments including the use of pink beams, convergent electron diffraction and serial snapshot crystallography has shown the limitations of using the Laue equations for diffraction prediction. This article gives a computationally efficient way of calculating approximate crystal diffraction patterns given varying distributions of the incoming beam, crystal shapes and other potentially hidden parameters. This approach models each pixel of a diffraction pattern and improves data processing of integrated peak intensities by enabling the correction of partially recorded reflections. The fundamental idea is to express the distributions as weighted sums of Gaussian functions. The approach is demonstrated on serial femtosecond crystallography data sets, showing a significant decrease in the required number of patterns to refine a structure to a given error.
    Description: Reflection position, size and shape prediction and partiality estimation of crystal diffraction by integrating using a Gaussian basis are described.
    Keywords: ddc:548 ; partiality estimation ; diffraction prediction ; merging ; serial snapshot crystallography
    Language: English
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  • 4
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    In situ neutron diffraction for analysing complex coarse‐grained functional materials (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-10-24
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Complex functional materials play a crucial role in a broad range of energy‐related applications and in general for materials science. Revealing the structural mechanisms is challenging due to highly correlated coexisting phases and microstructures, especially for 〈italic〉in situ〈/italic〉 or 〈italic〉operando〈/italic〉 investigations. Since the grain sizes influence the properties, these microstructural features further complicate investigations at synchrotrons due to the limitations of illuminated sample volumes. In this study, it is demonstrated that such complex functional materials with highly correlated coexisting phases can be investigated under 〈italic〉in situ〈/italic〉 conditions with neutron diffraction. For large grain sizes, these experiments are valuable methods to reveal the structural mechanisms. For an example of 〈italic〉in situ〈/italic〉 experiments on barium titanate with an applied electric field, details of the electric‐field‐induced phase transformation depending on grain size and frequency are revealed. The results uncover the strain mechanisms in barium titanate and elucidate the complex interplay of stresses in relation to grain sizes as well as domain‐wall densities and mobilities.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉This work reports 〈italic〉in situ〈/italic〉 neutron diffraction experiments on a broad range of grain sizes of barium titanate. The study reveals the grain‐size‐dependent strain mechanisms and shows the competitiveness of neutron diffraction with high‐resolution synchrotron diffraction.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005767:jcr2vb5054:jcr2vb5054-fig-0001"〉 〈alt-text〉image〈/alt-text〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:550.724 ; ddc:548 ; neutron diffraction ; in situ ; applied electric fields ; barium titanate ; strain mechanisms ; grain sizes ; complex functional materials ; microstructures ; coexisting phases
    Language: English
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  • 5
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    Energy‐dispersive X‐ray stress analysis under geometric constraints: exploiting the material's inherent anisotropy (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-09-12
    Description: Two data evaluation concepts for X‐ray stress analysis based on energy‐dispersive diffraction on polycrystalline materials with cubic crystal structure, almost random crystallographic texture and strong single‐crystal elastic anisotropy are subjected to comparative assessment. The aim is the study of the residual stress state in hard‐to‐reach measurement points, for which the sin2ψ method is not applicable due to beam shadowing at larger sample tilting. This makes the approaches attractive for stress analysis in engineering parts with complex shapes, for example. Both approaches are based on the assumption of a biaxial stress state within the irradiated sample volume. They exploit in different ways the elastic anisotropy of individual crystallites acting at the microscopic scale and the anisotropy imposed on the material by the near‐surface stress state at the macroscopic scale. They therefore complement each other, in terms of both their preconditions and their results. The first approach is based on the evaluation of strain differences, which makes it less sensitive to variations in the strain‐free lattice parameter a0. Since it assumes a homogeneous stress state within the irradiated sample volume, it provides an average value of the in‐plane stresses. The second approach exploits the sensitivity of the lattice strain to changes in a0. Consequently, it assumes a homogeneous chemical composition but provides a stress profile within the information depth. Experimental examples from different fields in materials science, namely shot peening of austenitic steel and in situ stress analysis during welding, are presented to demonstrate the suitability of the proposed methods.
    Description: The single‐crystal elastic anisotropy and the anisotropy of the near‐surface (residual) stress state of polycrystalline materials with random texture are exploited in energy‐dispersive X‐ray stress analysis to study samples under constrained measurement conditions.
    Keywords: ddc:548 ; X‐ray stress analysis ; energy‐dispersive diffraction ; polycrystalline materials ; single‐crystal elastic anisotropy
    Language: English
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  • 6
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    Use of electron backscatter diffraction patterns to determine the crystal lattice. Part 3. Pseudosymmetry (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-07-20
    Description: A pseudosymmetric description of the crystal lattice derived from a single wide‐angle Kikuchi pattern can have several causes. The small size (〈15%) of the sector covered by an electron backscatter diffraction pattern, the limited precision of the projection centre position and the Kikuchi band definition are crucial. Inherent pseudosymmetries of the crystal lattice and/or structure also pose a challenge in the analysis of Kikuchi patterns. To eliminate experimental errors as much as possible, simulated Kikuchi patterns of 350 phases have been analysed using the software CALM [Nolze et al. (2021). J. Appl. Cryst.54, 1012–1022] in order to estimate the frequency of and reasons for pseudosymmetric crystal lattice descriptions. Misinterpretations occur in particular when the atomic scattering factors of non‐equivalent positions are too similar and reciprocal‐lattice points are systematically missing. As an example, a pseudosymmetry prediction depending on the elements involved is discussed for binary AB compounds with B1 and B2 structure types. However, since this is impossible for more complicated phases, this approach cannot be directly applied to compounds of arbitrary composition and structure.
    Description: Distinguishing between actual and apparent pseudosymmetry in electron backscatter diffraction patterns is nearly impossible, even for simulated patterns. However, the resulting lattice is always a superlattice as long as the signal is not a superposition of multiple patterns.
    Keywords: ddc:548 ; Bravais lattices ; pseudosymmetry ; lattice point density ; ordered/disordered structures ; lattice distortion ; electron backscatter diffraction ; backscattered Kikuchi diffraction patterns ; lattice parameters ; Funk transform
    Language: English
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  • 7
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    Use of electron backscatter diffraction patterns to determine the crystal lattice. Part 2. Offset corrections (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-07-21
    Description: A band width determination using the first derivative of the band profile systematically underestimates the true Bragg angle. Corrections are proposed to compensate for the resulting offset Δa/a of the mean lattice parameters derived from as many Kikuchi band widths as possible. For dynamically simulated Kikuchi patterns, Δa/a can reach up to 8% for phases with a high mean atomic number Z, whereas for much more common low‐Z materials the offset decreases linearly. A predicted offset Δa/a = f(Z) is therefore proposed, which also includes the unit‐cell volume and thus takes into account the packing density of the scatterers in the material. Since Z is not always available for unknown phases, its substitution by Zmax, i.e. the atomic number of the heaviest element in the compound, is still acceptable for an approximate correction. For simulated Kikuchi patterns the offset‐corrected lattice parameter deviation is Δa/a 〈 1.5%. The lattice parameter ratios, and the angles α, β and γ between the basis vectors, are not affected at all.
    Description: Automatically determined band widths in simulated backscatter Kikuchi patterns exhibit differences from the double Bragg angles that correlate with the scatterer density. Corrections are proposed to compensate for this.
    Keywords: ddc:548 ; mean atomic number ; Kikuchi patterns ; lattice parameters ; automated Bragg angle determination ; lattice parameter determination ; dynamical theory of electron diffraction ; electron backscatter diffraction ; Funk transform
    Language: English
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  • 8
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    POWTEX visits POWGEN (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2023-07-21
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉The high‐intensity time‐of‐flight (TOF) neutron diffractometer POWTEX for powder and texture analysis is currently being built prior to operation in the eastern guide hall of the research reactor FRM II at Garching close to Munich, Germany. Because of the world‐wide 〈sup〉3〈/sup〉He crisis in 2009, the authors promptly initiated the development of 〈sup〉3〈/sup〉He‐free detector alternatives that are tailor‐made for the requirements of large‐area diffractometers. Herein is reported the 2017 enterprise to operate one mounting unit of the final POWTEX detector on the neutron powder diffractometer POWGEN at the Spallation Neutron Source located at Oak Ridge National Laboratory, USA. As a result, presented here are the first angular‐ and wavelength‐dependent data from the POWTEX detector, unfortunately damaged by a 50〈italic〉g〈/italic〉 shock but still operating, as well as the efforts made both to characterize the transport damage and to successfully recalibrate the voxel positions in order to yield nonetheless reliable measurements. Also described is the current data reduction process using the 〈italic〉PowderReduceP2D〈/italic〉 algorithm implemented in 〈italic〉Mantid〈/italic〉 [Arnold 〈italic〉et al.〈/italic〉 (2014). 〈italic〉Nucl. Instrum. Methods Phys. Res. A〈/italic〉, 〈bold〉764〈/bold〉, 156–166]. The final part of the data treatment chain, namely a novel multi‐dimensional refinement using a modified version of the 〈italic〉GSAS‐II〈/italic〉 software suite [〈ext-link ext-link-type="uri" xlink:href="http://scripts.iucr.org/cgi-bin/paper?aj5212"〉Toby & Von Dreele (2013). 〈italic〉J. Appl. Cryst.〈/italic〉〈bold〉46〈/bold〉, 544–549〈/ext-link〉], is compared with a standard data treatment of the same event data conventionally reduced as TOF diffraction patterns and refined with the unmodified version of 〈italic〉GSAS‐II〈/italic〉. This involves both determining the instrumental resolution parameters using POWGEN's powdered diamond standard sample and the refinement of a friendly‐user sample, BaZn(NCN)〈sub〉2〈/sub〉. Although each structural parameter on its own looks similar upon comparing the conventional (1D) and multi‐dimensional (2D) treatments, also in terms of precision, a closer view shows small but possibly significant differences. For example, the somewhat suspicious proximity of the 〈italic〉a〈/italic〉 and 〈italic〉b〈/italic〉 lattice parameters of BaZn(NCN)〈sub〉2〈/sub〉 crystallizing in 〈italic〉Pbca〈/italic〉 as resulting from the 1D refinement (0.008 Å) is five times less pronounced in the 2D refinement (0.038 Å). Similar features are found when comparing bond lengths and bond angles, 〈italic〉e.g.〈/italic〉 the two N—C—N units are less differently bent in the 1D results (173 and 175°) than in the 2D results (167 and 173°). The results are of importance not only for POWTEX but also for other neutron TOF diffractometers with large‐area detectors, like POWGEN at the SNS or the future DREAM beamline at the European Spallation Source.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉The first real‐world neutron diffraction data have been collected with one of the POWTEX detectors (FRM II, Garching, Germany) mounted for testing at the Spallation Neutron Source (Oak Ridge National Laboratory, USA). They allow for angular‐ and wavelength‐dispersive Rietveld refinement using a modified version of 〈italic〉GSAS‐II〈/italic〉.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005767:jcr2tu5033:jcr2tu5033-fig-0001"〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:548 ; neutron detectors ; POWGEN beamline ; POWTEX detector ; DREAM beamline ; time‐of‐flight diffraction ; angular‐dispersive refinement ; wavelength‐dispersive refinement ; powder diffraction ; Rietveld refinement ; multi‐dimensional refinement
    Language: English
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  • 9
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    A note on the wedge reversion antisymmetry operation and 51 types of physical quantities in arbitrary dimensions (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2023-07-21
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉The paper by Gopalan [〈ext-link ext-link-type="uri" xlink:href="http://scripts.iucr.org/cgi-bin/paper?ib5086"〉(2020). 〈italic〉Acta Cryst.〈/italic〉 A〈bold〉76〈/bold〉, 318–327〈/ext-link〉] presented an enumeration of the 41 physical quantity types in non‐relativistic physics, in arbitrary dimensions, based on the formalism of Clifford algebra. Gopalan considered three antisymmetries: spatial inversion, 〈overline〉1〈/overline〉, time reversal, 1′, and wedge reversion, 1〈sup〉†〈/sup〉. A consideration of the set of all seven antisymmetries (〈overline〉1〈/overline〉, 1′, 1〈sup〉†〈/sup〉, 1′〈sup〉†〈/sup〉, 〈overline〉1〈/overline〉〈sup〉†〈/sup〉, 〈overline〉1〈/overline〉′, 〈overline〉1〈/overline〉′〈sup〉†〈/sup〉) leads to an extension of the results obtained by Gopalan. It is shown that there are 51 types of physical quantities with distinct symmetry properties in total.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉It is shown that there are 51 types of physical quantities in arbitrary dimensions with distinct transformations by wedge reversion symmetry. In the paper by 〈ext-link ext-link-type="uri" xlink:href="http://scripts.iucr.org/cgi-bin/paper?ib5086"〉Gopalan [(2020). 〈italic〉Acta Cryst.〈/italic〉 A〈bold〉76〈/bold〉, 318–327]〈/ext-link〉 only 41 types were enumerated.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:20532733:aya2ib5117:aya2ib5117-fig-0001"〉 〈alt-text〉image〈/alt-text〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:548 ; multivectors ; wedge reversion ; antisymmetry ; Clifford algebra
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  • 10
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    Use of electron backscatter diffraction patterns to determine the crystal lattice. Part 1. Where is the Bragg angle? (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-07-19
    Description: The derivation of a crystal structure and its phase‐specific parameters from a single wide‐angle backscattered Kikuchi diffraction pattern requires reliable extraction of the Bragg angles. By means of the first derivative of the lattice profile, an attempt is made to determine fully automatically and reproducibly the band widths in simulated Kikuchi patterns. Even under such ideal conditions (projection centre, wavelength and lattice plane traces are perfectly known), this leads to a lattice parameter distribution whose mean shows a linear offset that correlates with the mean atomic number Z of the pattern‐forming phase. The consideration of as many Kikuchi bands as possible reduces the errors that typically occur if only a single band is analysed. On the other hand, the width of the resulting distribution is such that higher image resolution of diffraction patterns, employing longer wavelengths to produce wider bands or the use of higher interference orders is less advantageous than commonly assumed.
    Description: The lattice parameters of more than 350 phases have been determined from simulated backscatter Kikuchi patterns. The deviations correlating with the mean atomic number correspond to those observed previously for experimental electron backscatter diffraction patterns.
    Keywords: ddc:548 ; Bragg angles ; Kikuchi bands ; Kikuchi patterns ; first derivative ; lattice parameters ; lattice parameter determination ; Bravais lattice type ; electron backscatter diffraction ; Radon transform
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  • 11
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    Data reduction for X‐ray serial crystallography using machine learning (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2023-07-19
    Description: Serial crystallography experiments produce massive amounts of experimental data. Yet in spite of these large‐scale data sets, only a small percentage of the data are useful for downstream analysis. Thus, it is essential to differentiate reliably between acceptable data (hits) and unacceptable data (misses). To this end, a novel pipeline is proposed to categorize the data, which extracts features from the images, summarizes these features with the `bag of visual words' method and then classifies the images using machine learning. In addition, a novel study of various feature extractors and machine learning classifiers is presented, with the aim of finding the best feature extractor and machine learning classifier for serial crystallography data. The study reveals that the oriented FAST and rotated BRIEF (ORB) feature extractor with a multilayer perceptron classifier gives the best results. Finally, the ORB feature extractor with multilayer perceptron is evaluated on various data sets including both synthetic and experimental data, demonstrating superior performance compared with other feature extractors and classifiers.
    Description: A machine learning method for distinguishing good and bad images in serial crystallography is presented. To reduce the computational cost, this uses the oriented FAST and rotated BRIEF feature extraction method from computer vision to detect image features, followed by a multilayer perceptron (neural network) to classify the images.
    Keywords: ddc:548 ; serial crystallography ; data reduction ; machine learning ; feature extraction
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  • 12
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    Towards joint in situ determination of pressure and temperature in the large volume press exclusively from X‐ray diffraction (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2023-07-19
    Description: Since high‐pressure devices have been used at synchrotron facilities, accurate determination of pressure and temperature in the sample has been a crucial objective, particularly for experiments that simulate the Earth's interior. However, in some cases using a thermocouple may have a high likelihood of failure or is incompatible with a high‐pressure assembly. To address these challenges and similar issues, we aim to expand a previously proposed solution: to jointly estimate pressure and temperature (〈italic〉PT〈/italic〉) through 〈italic〉in situ〈/italic〉 X‐ray diffraction, to cover a wider range of internal 〈italic〉PT〈/italic〉 calibrants tested over larger 〈italic〉PT〈/italic〉 ranges. A modifiable Python‐based software is offered to quickly obtain results. To achieve these aims, 〈italic〉in situ〈/italic〉 large volume press experiments are performed on pellets of intimately mixed powders of a halide (NaCl, KCl, KBr, CsCl) or MgO and a metal (Pt, Re, Mo, W, Ni) in the pressure range 3–11 GPa and temperature range 300–1800 K. Although the pressure range was chosen for practical reasons, it also covers an equally important depth range in the Earth (down to 350 km) for geoscience studies. A thermocouple was used to validate the 〈italic〉PT〈/italic〉 conditions in the cell assemblies. The key results show that choosing the appropriate calibrant materials and using a joint 〈italic〉PT〈/italic〉 estimation can yield surprisingly small uncertainties (〈italic〉i.e.〈/italic〉 〈±0.1 GPa and 〈±50 K). This development is expected to benefit current and future research at extreme conditions, as other materials with high compressibility or high thermal pressure, stable over large 〈italic〉PT〈/italic〉 ranges, may be discovered and used as 〈italic〉PT〈/italic〉 calibrants.〈/p〉
    Description: Research in high‐pressure devices, such as the diamond anvil cell and the large volume press, requires knowledge of the pressure and temperature in the sample. Here, a large volume press and an internal resistive heater were used to generate high load and heat to various combinations of intimately mixed powders of materials. X‐ray diffraction and custom software were used to jointly estimate the pressures and temperatures in the samples and establish calibrants for 〈italic〉in situ〈/italic〉 experiments at extreme conditions.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005775:jsy2vl5008:jsy2vl5008-fig-0001"〉
    Description: https://gitlab.desy.de/robert.farla/eoscross
    Keywords: ddc:548 ; equations of state ; X‐ray diffraction ; large volume press ; high pressure ; resistive heating
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  • 13
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    Hard X‐ray full‐field nanoimaging using a direct photon‐counting detector (2023)
    Flenner, Silja ; Hagemann, Johannes ; Wittwer, Felix ; [et al.]
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-03-05
    Description: Full‐field X‐ray nanoimaging is a widely used tool in a broad range of scientific areas. In particular, for low‐absorbing biological or medical samples, phase contrast methods have to be considered. Three well established phase contrast methods at the nanoscale are transmission X‐ray microscopy with Zernike phase contrast, near‐field holography and near‐field ptychography. The high spatial resolution, however, often comes with the drawback of a lower signal‐to‐noise ratio and significantly longer scan times, compared with microimaging. In order to tackle these challenges a single‐photon‐counting detector has been implemented at the nanoimaging endstation of the beamline P05 at PETRA III (DESY, Hamburg) operated by Helmholtz‐Zentrum Hereon. Thanks to the long sample‐to‐detector distance available, spatial resolutions of below 100 nm were reached in all three presented nanoimaging techniques. This work shows that a single‐photon‐counting detector in combination with a long sample‐to‐detector distance allows one to increase the time resolution for in situ nanoimaging, while keeping a high signal‐to‐noise level.
    Description: A direct photon‐counting detector was used for different nanoimaging phase contrast techniques, increasing the temporal resolution.
    Keywords: ddc:548 ; nanotomography ; full‐field X‐ray microscopy ; near‐field holography ; near‐field ptychography ; Zernike phase contrast ; single‐photon‐counting detector ; phase contrast
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  • 14
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    Machine learning for scattering data: strategies, perspectives and applications to surface scattering (2023)
    Hinderhofer, Alexander ; Greco, Alessandro ; Starostin, Vladimir ; [et al.]
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-02-14
    Description: Machine learning (ML) has received enormous attention in science and beyond. Discussed here are the status, opportunities, challenges and limitations of ML as applied to X‐ray and neutron scattering techniques, with an emphasis on surface scattering. Typical strategies are outlined, as well as possible pitfalls. Applications to reflectometry and grazing‐incidence scattering are critically discussed. Comment is also given on the availability of training and test data for ML applications, such as neural networks, and a large reflectivity data set is provided as reference data for the community.
    Description: The status, opportunities, challenges and limitations of machine learning are discussed as applied to X‐ray and neutron scattering techniques, with an emphasis on surface scattering.
    Keywords: ddc:548 ; surface scattering ; X‐ray diffraction ; neutron scattering ; machine learning ; data analysis
    Language: English
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    Beam‐induced redox chemistry in iron oxide nanoparticle dispersions at ESRF–EBS (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-02-21
    Description: The storage ring upgrade of the European Synchrotron Radiation Facility makes ESRF–EBS the most brilliant high‐energy fourth‐generation light source, enabling in situ studies with unprecedented time resolution. While radiation damage is commonly associated with degradation of organic matter such as ionic liquids or polymers in the synchrotron beam, this study clearly shows that highly brilliant X‐ray beams readily induce structural changes and beam damage in inorganic matter, too. Here, the reduction of Fe3+ to Fe2+ in iron oxide nanoparticles by radicals in the brilliant ESRF–EBS beam, not observed before the upgrade, is reported. Radicals are created due to radiolysis of an EtOH–H2O mixture with low EtOH concentration (∼6 vol%). In light of extended irradiation times during insitu experiments in, for example, battery and catalysis research, beam‐induced redox chemistry needs to be understood for proper interpretation of insitu data.
    Description: With the increased brilliance at the European Research Facility–Extremely Brilliant Source (ESRF–EBS), a beam‐induced reduction of non‐stochiometric iron oxide nanoparticles (almost maghemite composition) to magnetite was observed in a mixture of ethanol and water with low ethanol concentration.
    Keywords: ddc:548 ; beam‐induced radiolysis ; radiation damage on inorganic materials ; ESRF–EBS
    Language: English
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    Mapping the 3D position of battery cathode particles in Bragg coherent diffractive imaging (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-12-14
    Description: In Bragg coherent diffractive imaging, the precise location of the measured crystals in the interior of the sample is usually missing. Obtaining this information would help the study of the spatially dependent behavior of particles in the bulk of inhomogeneous samples, such as extra‐thick battery cathodes. This work presents an approach to determine the 3D position of particles by precisely aligning them at the instrument axis of rotation. In the test experiment reported here, with a 60 µm‐thick LiNi0.5Mn1.5O4 battery cathode, the particles were located with a precision of 20 µm in the out‐of‐plane direction, and the in‐plane coordinates were determined with a precision of 1 µm.
    Description: A method to determine the 3D position of particles in Bragg coherent diffractive imaging experiments is proposed. Test measurements demonstrate depth‐resolution with a precision of 20 µm along the beam. image
    Keywords: ddc:548 ; extra‐thick battery cathodes ; Bragg coherent X‐ray diffractive imaging ; battery cathodes ; Bragg diffraction ; sphere of confusion ; 3D mapping
    Language: English
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    The soft X‐ray and XUV split‐and‐delay unit at beamlines FL23/24 at FLASH2 (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-01-12
    Description: A split‐and‐delay unit for the extreme ultraviolet and soft X‐ray spectral regions has been built which enables time‐resolved experiments at beamlines FL23 and FL24 at the Free‐electron LASer in Hamburg (FLASH). Geometric wavefront splitting at a sharp edge of a beam splitting mirror is applied to split the incoming soft X‐ray pulse into two beams. Ni and Pt coatings at grazing incidence angles have been chosen in order to cover the whole spectral range of FLASH2 and beyond, up to hν = 1800 eV. In the variable beam path with a grazing incidence angle of ϑd = 1.8°, the total transmission (T) ranges are of the order of 0.48 〈 T 〈 0.84 for hν 〈 100 eV and T 〉 0.50 for 100 eV 〈 hν 〈 650 eV with the Ni coating, and T 〉 0.06 for hν 〈 1800 eV for the Pt coating. For a fixed beam path with a grazing incidence angle of ϑf = 1.3°, a transmission of T 〉 0.61 with the Ni coating and T 〉 0.23 with a Pt coating is achieved. Soft X‐ray pump/soft X‐ray probe experiments are possible within a delay range of −5 ps 〈 Δt 〈 +18 ps with a nominal time resolution of tr = 66 as and a measured timing jitter of tj = 121 ± 2 as. First experiments with the split‐and‐delay unit determined the averaged coherence time of FLASH2 to be τc = 1.75 fs at λ = 8 nm, measured at a purposely reduced coherence of the free‐electron laser.
    Description: The properties of the recently installed split‐and‐delay unit at beamlines FL23 and FL24 at FLASH2 are presented. Its operational range, performance parameters and results of a first experiment are described. image
    Keywords: ddc:550.724 ; time‐resolved pump–probe ; XUV ; soft X‐rays ; free‐electron laser
    Language: English
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    XDSGUI: a graphical user interface for XDS, SHELX and ARCIMBOLDO (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-01-12
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉〈italic〉XDSGUI〈/italic〉 is a lightweight graphical user interface (GUI) for the 〈italic〉XDS〈/italic〉, 〈italic〉SHELX〈/italic〉 and 〈italic〉ARCIMBOLDO〈/italic〉 program packages that serves both novice and experienced users in obtaining optimal processing and phasing results for X‐ray, neutron and electron diffraction data. The design of the program enables data processing and phasing without command line usage, and supports advanced command flows in a simple user‐modifiable and user‐extensible way. The GUI supplies graphical information based on the tabular log output of the programs, which is more intuitive, comprehensible and efficient than text output can be.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉A customizable stateless graphical user interface simplifies the processing, analysis and phasing of diffraction data.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005767:jcr2yr5110:jcr2yr5110-fig-0001"〉 〈alt-text〉image〈/alt-text〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:548 ; X‐ray diffraction ; neutron diffraction ; electron diffraction ; data processing ; graphical user interfaces ; phasing ; XDS ; ARCIMBOLDO ; SHELX
    Language: English
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    Automatic Religion (2023)
    University of Chicago Press | University of Chicago Press
    Details
    Publication Date: 2024-04-08
    Description: What distinguishes humans from nonhumans? Two common answers—free will and religion—are in some ways fundamentally opposed. Whereas free will enjoys a central place in our ideas of spontaneity, authorship, and deliberation, religious practices seem to involve a suspension of or relief from the exercise of our will. What, then, is agency, and why has it occupied such a central place in theories of the human? Automatic Religion explores an unlikely series of episodes from the end of the nineteenth century, when crucial ideas related to automatism and, in a different realm, the study of religion were both being born. Paul Christopher Johnson draws on years of archival and ethnographic research in Brazil and France to explore the crucial boundaries being drawn at the time between humans, “nearhumans,” and automata. As agency came to take on a more central place in the philosophical, moral, and legal traditions of the West, certain classes of people were excluded as less-than-human. Tracking the circulation of ideas across the Atlantic, Johnson tests those boundaries, revealing how they were constructed on largely gendered and racial foundations. In the process, he reanimates one of the most mysterious and yet foundational questions in trans-Atlantic thought: what is agency?
    Keywords: brazil ; brazilian ; france ; french ; religion ; religious studies ; history ; historical ; humanity ; humans ; nonhumans ; free will ; freedom ; 19th century ; automatism ; ethnography ; archival research ; philosophy ; morality ; ethics ; morals ; ethical ; legalism ; legal ; gender ; race ; anthropology ; determinism ; case study ; culture ; agency ; action ; ability ; understanding ; thema EDItEUR::Q Philosophy and Religion::QR Religion and beliefs ; thema EDItEUR::Q Philosophy and Religion::QR Religion and beliefs::QRM Christianity ; thema EDItEUR::J Society and Social Sciences::JH Sociology and anthropology::JHM Anthropology::JHMC Social and cultural anthropology ; thema EDItEUR::N History and Archaeology::NH History::NHD European history ; thema EDItEUR::N History and Archaeology::NH History::NHK History of the Americas ; thema EDItEUR::Q Philosophy and Religion::QR Religion and beliefs ; thema EDItEUR::Q Philosophy and Religion::QR Religion and beliefs::QRM Christianity ; thema EDItEUR::J Society and Social Sciences::JH Sociology and anthropology::JHM Anthropology::JHMC Social and cultural anthropology ; thema EDItEUR::N History and Archaeology::NH History::NHD European history ; thema EDItEUR::N History and Archaeology::NH History::NHK History of the Americas
    Language: English
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    Intimate Disconnections (2023)
    University of Chicago Press | University of Chicago Press
    Details
    Publication Date: 2024-03-28
    Description: In many ways, divorce is a quintessentially personal decision—the choice to leave a marriage that causes harm or feels unfulfilling to the two people involved. But anyone who has gone through a divorce knows the additional public dimensions of breaking up, from intense shame and societal criticism to friends’ and relatives’ unsolicited advice. In Intimate Disconnections, Allison Alexy tells the fascinating story of the changing norms surrounding divorce in Japan in the early 2000s, when sudden demographic and social changes made it a newly visible and viable option. Not only will one of three Japanese marriages today end in divorce, but divorces are suddenly much more likely to be initiated by women who cite new standards for intimacy as their motivation. As people across Japan now consider divorcing their spouses, or work to avoid separation, they face complicated questions about the risks and possibilities marriage brings: How can couples be intimate without becoming suffocatingly close? How should they build loving relationships when older models are no longer feasible? What do you do, both legally and socially, when you just can’t take it anymore? Relating the intensely personal stories from people experiencing different stages of divorce, Alexy provides a rich ethnography of Japan while also speaking more broadly to contemporary visions of love and marriage during an era in which neoliberal values are prompting wide-ranging transformations in homes across the globe.
    Keywords: divorce ; romance ; marriage ; love ; intimacy ; japan ; trust ; relationships ; commitment ; shame ; social norms ; separation ; women ; gender ; feminism ; asia ; nonfiction ; reference ; freedom ; anxiety ; family ; relationality ; empowerment ; late life ; aging ; anthropology ; sociology ; jukunen rikon ; labor market ; dependence ; self interest ; solitude ; happiness ; thema EDItEUR::J Society and Social Sciences::JB Society and culture: general ; thema EDItEUR::J Society and Social Sciences::JH Sociology and anthropology::JHM Anthropology::JHMC Social and cultural anthropology ; thema EDItEUR::J Society and Social Sciences::JH Sociology and anthropology::JHB Sociology::JHBK Sociology: family and relationships
    Language: English
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    Building the American Republic, Volume 2 (2023)
    University of Chicago Press | University of Chicago Press
    Details
    Publication Date: 2024-04-06
    Description: Building the American Republic combines centuries of perspectives and voices into a fluid narrative of the United States. Throughout their respective volumes, Harry L. Watson and Jane Dailey take care to integrate varied scholarly perspectives and work to engage a diverse readership by addressing what we all share: membership in a democratic republic, with joint claims on its self-governing tradition. It will be one of the first peer-reviewed American history textbooks to be offered completely free in digital form. Visit buildingtheamericanrepublic.org for more information. The American nation came apart in a violent civil war less than a century after ratification of the Constitution. When it was reborn five years later, both the republic and its Constitution were transformed. Volume 2 opens as America struggles to regain its footing, reeling from a presidential assassination and facing massive economic growth, rapid demographic change, and combustive politics. The next century and a half saw the United States enter and then dominate the world stage, even as the country struggled to live up to its own principles of liberty, justice, and equality. Volume 2 of Building the American Republic takes the reader from the Gilded Age to the present, as the nation becomes an imperial power, rethinks the Constitution, witnesses the rise of powerful new technologies, and navigates an always-shifting cultural landscape shaped by an increasingly diverse population. Ending with the 2016 election, this volume provides a needed reminder that the future of the American republic depends on a citizenry that understands—and can learn from—its history.
    Keywords: democracy ; immigration ; manifest destiny ; urbanization ; transcontinental railroad ; labor ; slavery ; unions ; working conditions ; farmers alliance ; pullman ; 14th amendment ; jim crow ; reconstruction ; civil war ; patronage ; spanish american ; protest ; social change ; roosevelt ; progressive era ; dollar diplomacy ; revolution 1913 ; suffrage ; empire ; neutrality ; interventionism ; roaring 20s ; sexuality ; feminism ; great depression ; new deal ; south ; race ; ethnicity ; racism ; discrimination ; political movements ; nonfiction ; history ; vietnam ; thema EDItEUR::N History and Archaeology::NH History ; thema EDItEUR::N History and Archaeology::NH History::NHK History of the Americas ; thema EDItEUR::J Society and Social Sciences::JP Politics and government::JPA Political science and theory
    Language: English
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    The Contested Crown (2023)
    University of Chicago Press | University of Chicago Press
    Details
    Publication Date: 2024-04-04
    Description: Following conflicting desires for an Aztec crown, this book explores the possibilities of repatriation. In The Contested Crown, Khadija von Zinnenburg Carroll meditates on the case of a spectacular feather headdress believed to have belonged to Montezuma, the last emperor of the Aztecs. This crown has long been the center of political and cultural power struggles, and it is one of the most contested museum claims between Europe and the Americas. Taken to Europe during the conquest of Mexico, it was placed at Ambras Castle, the Habsburg residence of the author’s ancestors, and is now in Vienna’s Welt Museum. Mexico has long requested to have it back, but the Welt Museum uses science to insist it is too fragile to travel. Both the biography of a cultural object and a history of collecting and colonizing, this book offers an artist’s perspective on the creative potentials of repatriation. Carroll compares Holocaust and colonial ethical claims, and she considers relationships between indigenous people, international law and the museums that amass global treasures, the significance of copies, and how conservation science shapes collections. Illustrated with diagrams and rare archival material, this book brings together global history, European history, and material culture around this fascinating object and the debates about repatriation.
    Keywords: repatriation ; feather headdress ; mexico ; europe ; colonialism ; history ; aztec ; montezuma ; emperor ; exhibition ; ownership ; possession ; ambras castle ; welt museum ; conquest ; seizure ; dispossession ; holocaust ; looting ; ethics ; reparation ; nonfiction ; indigenous ; international law ; collection ; material culture ; crown ; anthropology ; el penacho ; replica ; thema EDItEUR::N History and Archaeology::NH History ; thema EDItEUR::N History and Archaeology::NH History::NHK History of the Americas ; thema EDItEUR::A The Arts::AG The Arts: treatments and subjects::AGA History of art ; thema EDItEUR::G Reference, Information and Interdisciplinary subjects::GL Library and information sciences / Museology::GLZ Museology and heritage studies ; thema EDItEUR::J Society and Social Sciences::JB Society and culture: general::JBS Social groups, communities and identities::JBSL Ethnic studies::JBSL1 Ethnic groups and multicultural studies::JBSL11 Indigenous peoples ; thema EDItEUR::5 Interest qualifiers::5P Relating to specific groups and cultures or social and cultural interests::5PB Relating to peoples: ethnic groups, indigenous peoples, cultures and other groupings of people::5PBA Relating to Indigenous peoples
    Language: English
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    American Girls in Red Russia (2023)
    University of Chicago Press | University of Chicago Press
    Details
    Publication Date: 2024-04-05
    Description: If you were an independent, adventurous, liberated American woman in the 1920s or 1930s where might you have sought escape from the constraints and compromises of bourgeois living? Paris and the Left Bank quickly come to mind. But would you have ever thought of Russia and the wilds of Siberia? This choice was not as unusual as it seems now. As Julia L. Mickenberg uncovers in American Girls in Red Russia, there is a forgotten counterpoint to the story of the Lost Generation: beginning in the late nineteenth century, Russian revolutionary ideology attracted many women, including suffragists, reformers, educators, journalists, and artists, as well as curious travelers. Some were famous, like Isadora Duncan or Lillian Hellman; some were committed radicals, though more were just intrigued by the “Soviet experiment.” But all came to Russia in search of social arrangements that would be more equitable, just, and satisfying. And most in the end were disillusioned, some by the mundane realities, others by horrifying truths. Mickenberg reveals the complex motives that drew American women to Russia as they sought models for a revolutionary new era in which women would be not merely independent of men, but also equal builders of a new society. Soviet women, after all, earned the right to vote in 1917, and they also had abortion rights, property rights, the right to divorce, maternity benefits, and state-supported childcare. Even women from Soviet national minorities—many recently unveiled—became public figures, as African American and Jewish women noted. Yet as Mickenberg’s collective biography shows, Russia turned out to be as much a grim commune as a utopia of freedom, replete with economic, social, and sexual inequities. American Girls in Red Russia recounts the experiences of women who saved starving children from the Russian famine, worked on rural communes in Siberia, wrote for Moscow or New York newspapers, or performed on Soviet stages. Mickenberg finally tells these forgotten stories, full of hope and grave disappointments.
    Keywords: america ; united states ; russian ; soviet union ; 1920s ; 1930s ; travel ; immigration ; escape ; siberia ; lost generation ; 20th century ; contemporary ; modern ; women ; feminism ; girls ; isadora duncan ; lillian hellman ; radical ; experiment ; equality ; revolutionary ; history ; historical ; men ; patriarchy ; divorce ; rights ; property ; benefits ; maternity ; childcare ; sexual ; economic ; social ; thema EDItEUR::N History and Archaeology::NH History ; thema EDItEUR::N History and Archaeology::NH History::NHK History of the Americas ; thema EDItEUR::N History and Archaeology::NH History::NHQ History of other geographical groupings and regions ; thema EDItEUR::D Biography, Literature and Literary studies::DN Biography and non-fiction prose::DNB Biography: general::DNBH Biography: historical, political and military ; thema EDItEUR::D Biography, Literature and Literary studies::DN Biography and non-fiction prose::DNB Biography: general
    Language: English
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    Make It Rain (2023)
    University of Chicago Press | University of Chicago Press
    Details
    Publication Date: 2024-04-02
    Description: Weather control. Juxtaposing those two words is enough to raise eyebrows in a world where even the best weather models still fail to nail every forecast, and when the effects of climate change on sea level height, seasonal averages of weather phenomena, and biological behavior are being watched with interest by all, regardless of political or scientific persuasion. But between the late nineteenth century—when the United States first funded an attempt to “shock” rain out of clouds—and the late 1940s, rainmaking (as it had been known) became weather control. And then things got out of control. In Make It Rain, Kristine C. Harper tells the long and somewhat ludicrous history of state-funded attempts to manage, manipulate, and deploy the weather in America. Harper shows that governments from the federal to the local became helplessly captivated by the idea that weather control could promote agriculture, health, industrial output, and economic growth at home, or even be used as a military weapon and diplomatic tool abroad. Clear fog for landing aircraft? There’s a project for that. Gentle rain for strawberries? Let’s do it! Enhanced snowpacks for hydroelectric utilities? Check. The heyday of these weather control programs came during the Cold War, as the atmosphere came to be seen as something to be defended, weaponized, and manipulated. Yet Harper demonstrates that today there are clear implications for our attempts to solve the problems of climate change.
    Keywords: contemporary ; modern ; weather ; control ; models ; forecast ; climate ; sea level ; seasons ; seasonal ; average ; rainfall ; snow ; wind ; behavior ; history ; historical ; 1940s ; funding ; government ; federal ; local ; agriculture ; health ; industry ; economy ; economic ; project ; snowpack ; cold war ; atmosphere ; research ; academic ; scholarly ; diplomacy ; international ; thema EDItEUR::N History and Archaeology::NH History ; thema EDItEUR::N History and Archaeology::NH History::NHK History of the Americas ; thema EDItEUR::R Earth Sciences, Geography, Environment, Planning::RB Earth sciences::RBP Meteorology and climatology ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TB Technology: general issues::TBX History of engineering and technology ; thema EDItEUR::J Society and Social Sciences::JP Politics and government::JPQ Central / national / federal government::JPQB Central / national / federal government policies
    Language: English
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    Stories of Capitalism (2023)
    University of Chicago Press | University of Chicago Press
    Details
    Publication Date: 2024-03-28
    Description: The financial crisis and the recession that followed caught many people off guard, including experts in the financial sector whose jobs involve predicting market fluctuations. Financial analysis offices in most international banks are supposed to forecast the rise or fall of stock prices, the success or failure of investment products, and even the growth or decline of entire national economies. And yet their predictions are heavily disputed. How do they make their forecasts—and do those forecasts have any actual value? Building on recent developments in the social studies of finance, Stories of Capitalism provides the first ethnography of financial analysis. Drawing on two years of fieldwork in a Swiss bank, Stefan Leins argues that financial analysts construct stories of possible economic futures, presenting them as coherent and grounded in expert research and analysis. In so doing, they establish a role for themselves—not necessarily by laying bare empirically verifiable trends but rather by presenting the market as something that makes sense and is worth investing in. Stories of Capitalism is a nuanced look at how banks continue to boost investment—even in unstable markets—and a rare insider’s look into the often opaque financial practices that shape the global economy.
    Keywords: capitalist ; money ; monetary ; wealth ; finances ; finance ; analysis ; crisis ; recession ; history ; historical ; academic ; scholarly ; research ; market ; job ; career ; sector ; international ; banks ; banking ; stocks ; prices ; success ; failure ; forecast ; prediction ; trends ; data ; global ; value ; information ; investment ; economy ; narrative ; story ; construction ; thema EDItEUR::J Society and Social Sciences::JB Society and culture: general ; thema EDItEUR::J Society and Social Sciences::JH Sociology and anthropology::JHM Anthropology::JHMC Social and cultural anthropology ; thema EDItEUR::K Economics, Finance, Business and Management::KF Finance and accounting::KFF Finance and the finance industry
    Language: English
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    Nuclear Minds (2023)
    University of Chicago Press | University of Chicago Press
    Details
    Publication Date: 2024-03-28
    Description: How researchers understood the atomic bomb’s effects on the human psyche before the recognition of Post-Traumatic Stress Disorder. In 1945, researchers on a mission to Hiroshima with the United States Strategic Bombing Survey canvassed survivors of the nuclear attack. This marked the beginning of global efforts—by psychiatrists, psychologists, and other social scientists—to tackle the complex ways in which human minds were affected by the advent of the nuclear age. A trans-Pacific research network emerged that produced massive amounts of data about the dropping of the bomb and subsequent nuclear tests in and around the Pacific rim. Ran Zwigenberg traces these efforts and the ways they were interpreted differently across communities of researchers and victims. He explores how the bomb’s psychological impact on survivors was understood before we had the concept of post-traumatic stress disorder. In fact, psychological and psychiatric research on Hiroshima and Nagasaki rarely referred to trauma or similar categories. Instead, institutional and political constraints—most notably the psychological sciences’ entanglement with Cold War science—led researchers to concentrate on short-term damage and somatic reactions or even, in some cases, on denial of victims’ suffering. As a result, very few doctors tried to ameliorate suffering. But, Zwigenberg argues, it was not only that doctors “failed” to issue the right diagnosis; the victims’ experiences also did not necessarily conform to our contemporary expectations. As he shows, the category of trauma should not be used uncritically in a non-Western context. Consequently, this book sets out, first, to understand the historical, cultural, and scientific constraints in which researchers and victims were acting and, second, to explore how suffering was understood in different cultural contexts before PTSD was a category of analysis
    Keywords: Hiroshima; nuclear trauma; Cold War; psychology; psychiatry; Post-Traumatic Stress Disorder ; thema EDItEUR::J Society and Social Sciences::JB Society and culture: general ; thema EDItEUR::J Society and Social Sciences::JM Psychology::JMP Abnormal psychology ; thema EDItEUR::J Society and Social Sciences::JW Warfare and defence::JWM Weapons and equipment::JWMN Nuclear weapons
    Language: English
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    Jane Addams's Evolutionary Theorizing (2023)
    University of Chicago Press
    Details
    Publication Date: 2024-05-12
    Description: In Jane Addams’s Evolutionary Theorizing, Marilyn Fischer advances the bold and original claim that Addams’s reasoning in her first book, Democracy and Social Ethics, is thoroughly evolutionary. While Democracy and Social Ethics, a foundational text of classical American pragmatism, is praised for advancing a sensitive and sophisticated method of ethical deliberation, Fischer is the first to explore its intellectual roots. Examining essays Addams wrote in the 1890s and showing how they were revised for Democracy and Social Ethics, Fischer draws from philosophy, history, literature, rhetoric, and more to uncover the array of social evolutionary thought Addams engaged with in her texts—from British socialist writings on the evolution of democracy to British and German anthropological accounts of the evolution of morality. By excavating Addams’s evolutionary reasoning and rhetorical strategies, Fischer reveals the depth, subtlety, and richness of Addams’s thought.
    Keywords: jane addams, socialism, socialist, united states of america, american history, usa, settlement activist, activism, reformer, social worker, sociology, public administrator, suffrage, womens rights, world peace, hull house, civil liberties union, philosophy, ethics, morality, pragmatism, deliberation, democracy, 19th century, evolution, immigration, science, morals, ethical considerations
    Language: English
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    Matatu (2023)
    University of Chicago Press | University of Chicago Press
    Details
    Publication Date: 2024-04-07
    Description: Drive the streets of Nairobi, and you are sure to see many matatus—colorful minibuses that transport huge numbers of people around the city. Once ramshackle affairs held together with duct tape and wire, matatus today are name-brand vehicles maxed out with aftermarket detailing. They can be stately black or extravagantly colored, sporting names, slogans, or entire tableaus, with airbrushed portraits of everyone from Kanye West to Barack Obama. In this richly interdisciplinary book, Kenda Mutongi explores the history of the matatu from the 1960s to the present. As Mutongi shows, matatus offer a window onto the socioeconomic and political conditions of late-twentieth-century Africa. In their diversity of idiosyncratic designs, they reflect multiple and divergent aspects of Kenyan life—including, for example, rapid urbanization, organized crime, entrepreneurship, social insecurity, the transition to democracy, and popular culture—at once embodying Kenya’s staggering social problems as well as the bright promises of its future. Offering a shining model of interdisciplinary analysis, Mutongi mixes historical, ethnographic, literary, linguistic, and economic approaches to tell the story of the matatu and explore the entrepreneurial aesthetics of the postcolonial world.
    Keywords: east african history ; mass transit ; kenya ; africa ; public transportation ; ethnic studies ; nairobi ; matatu ; matatus ; colorful minibus ; ramshackle ; vehicles ; aftermarket detailing ; taxis ; kanye west ; barack obama ; interdisciplinary research ; 1960s ; 20th century ; socioeconomic ; political conditions ; diversity ; idiosyncratic designs ; kenyan life ; rapid urbanization ; organized crime ; entrepreneurship ; social insecurity ; transition to democracy ; society ; popular culture ; thema EDItEUR::N History and Archaeology::NH History ; thema EDItEUR::N History and Archaeology::NH History::NHH African history ; thema EDItEUR::J Society and Social Sciences::JH Sociology and anthropology::JHM Anthropology ; thema EDItEUR::W Lifestyle, Hobbies and Leisure::WG Transport: general interest::WGC Road and motor vehicles: general interest::WGCF Buses, trams and commercial vehicles: general interest ; thema EDItEUR::J Society and Social Sciences::JB Society and culture: general::JBS Social groups, communities and identities::JBSD Urban communities
    Language: English
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  • 29
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    Building the American Republic, Volume 1 (2023)
    University of Chicago Press | University of Chicago Press
    Details
    Publication Date: 2024-04-02
    Description: Building the American Republic combines centuries of perspectives and voices into a fluid narrative of the United States. Throughout their respective volumes, Harry L. Watson and Jane Dailey take care to integrate varied scholarly perspectives and work to engage a diverse readership by addressing what we all share: membership in a democratic republic, with joint claims on its self-governing tradition. It will be one of the first peer-reviewed American history textbooks to be offered completely free in digital form. Visit buildingtheamericanrepublic.org for more information. Volume 1 starts at sea and ends on the battlefield. Beginning with the earliest Americans and the arrival of strangers on the eastern shore, it then moves through colonial society to the fight for independence and the construction of a federalist republic. From there, it explains the renegotiations and refinements that took place as a new nation found its footing, and it traces the actions that eventually rippled into the Civil War. This volume goes beyond famous names and battles to incorporate politics, economics, science, arts, and culture. And it shows that issues that resonate today—immigration, race, labor, gender roles, and the power of technology—have been part of the American fabric since the very beginning.
    Keywords: history ; historical ; southern culture ; united states of america ; american ; usa ; cultural ; democratic republic ; government ; governing ; digital textbook ; americans ; colonies ; colonization ; independence ; revolution ; federalist ; civil war ; slavery ; politics ; economics ; science ; arts ; society ; immigration ; race ; racism ; labor ; gender roles ; technology ; agriculture ; native peoples ; slave trade ; columbus ; conquest ; puritans ; religion ; jamestown ; salem ; kkk ; reconstruction ; george washington ; abraham lincoln ; manifest destiny ; democracy ; thema EDItEUR::N History and Archaeology::NH History ; thema EDItEUR::N History and Archaeology::NH History::NHK History of the Americas ; thema EDItEUR::J Society and Social Sciences::JP Politics and government::JPA Political science and theory
    Language: English
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  • 30
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    Whole-Genome Sequencing Reveals That Regulatory and Low Pleiotropy Variants Underlie Local Adaptation to Environmental Variability in Purple Sea Urchins (2023)
    University of Chicago Press
    Details
    Publication Date: 2024-02-07
    Description: Organisms experience environments that vary across both space and time. Such environmental heterogeneity shapes standing genetic variation and may influence species’ capacity to adapt to rapid environmental change. However, we know little about the kindof genetic variation that is involved in local adaptation to environmental variability. To address this gap, we sequenced the whole genomes of 140 purple sea urchins (Strongylocentrotus purpuratus) from seven populations that vary in their degree of pH variability. Despite no evidence of global population structure, we found a suite of single-nucleotide polymorphisms (SNPs) tightly correlated with local pH variability (outlier SNPs), which were overrepresented in regions putatively involved in gene regulation (long noncoding RNA and enhancers), supporting the idea that variation in regulatory regions is important for local adaptation to variability. In addition, outliers in genes were found to be (i) enriched for biomineralization and ion homeostasis functions related to low pH response, (ii) less central to the protein-protein interaction network, and (iii) underrepresented among genes highly expressed during early development. Taken together, these results suggest that loci that underlie local adaptation to pH variability in purple sea urchins fall in regions with potentially low pleiotropic effects (based on analyses involving regulatory regions, network centrality, and expression time) involved in low pH response (based on functional enrichment).
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  • 31
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    Uncovering the effects of symbiosis and temperature on coral calcification (2022)
    University of Chicago Press
    Details
    Publication Date: 2023-01-10
    Description: Author Posting. © University of Chicago, 2022. This article is posted here by permission of University of Chicago for personal use, not for redistribution. The definitive version was published in Biological Bulletin 242(1), (2022): 62-73, https://doi.org/10.1086/716711.
    Description: We tested the impact of temperature and symbiont state on calcification in corals, using the facultatively symbiotic coral Astrangia poculata as a model system. Symbiotic and aposymbiotic colonies of A. poculata were reared in 15, 20, and 27 °C conditions. We used scanning electron microscopy to quantify how these physiological and environmental conditions impact skeletal structure. Buoyant weight data over time revealed that temperature significantly affects calcification rates. Scanning electron microscopy of A. poculata skeletons showed that aposymbiotic colonies appear to have a lower density of calcium carbonate in actively growing septal spines. We describe a novel approach to analyze the roughness and texture of scanning electron microscopy images. Quantitative analysis of the roughness of septal spines revealed that aposymbiotic colonies have a rougher surface than symbiotic colonies in tropical conditions (27 °C). This trend reversed at 15 °C, a temperature at which the symbionts of A. poculata may exhibit parasitic properties. Analysis of surface texture patterns showed that temperature impacts the spatial variance of crystals on the spine surface. Few published studies have examined the skeleton of A. poculata by using scanning electron microscopy. Our approach provides a way to study detailed changes in skeletal microstructure in response to environmental parameters and can serve as a proxy for more expensive and time-consuming analyses. Utilizing a facultatively symbiotic coral that is native to both temperate and tropical regions provides new insights into the impact of both symbiosis and temperature on calcification in corals.
    Description: This work was supported by the Marine Biological Laboratory and the University of Chicago Metcalf program and by a National Institutes of Health Research Project Grant (grant R01EB26300 to PJLR).
    Description: 2023-01-10
    Repository Name: Woods Hole Open Access Server
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  • 32
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    Digitization of imaging plates from Guinier powder X‐ray diffraction cameras (2022)
    Nasir, Jamal ; Steinbrück, Nils ; Xu, Ke ; [et al.]
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-01-15
    Description: A Guinier camera equipped with an imaging plate is used to investigate and eliminate the sources of instrumental errors affecting the quality of the obtained scanned Guinier data. A program with a graphical user interface is presented which converts the data of the scanned images into different standard file formats for powder X‐ray patterns containing intensities, their standard deviations and the diffraction angles. The program also allows for manual and automatic correction of the 2gθ scale against a known reference material. It is shown using LaB6 that the exported X‐ray diffraction patterns provide a 2gθ scale reproducible enough to allow for averaging diffractograms obtained from different exposures of the imaging plate for the same sample. As shown on a mixture of NaCl and sodalite, the quality of the produced data is sufficient for Rietveld refinement. The software including source code is made available under a free software license.
    Description: A program for the digitization of Guinier powder diffraction images is described, which works with images from both optical and laser scanners. Thus, processing of data from storage‐phosphor‐based imaging plates and Ag‐based photographic films is possible.
    Keywords: ddc:548 ; IPreader software ; Guinier cameras ; imaging plates (IPs) ; diffraction pattern conversion into data columns ; powder X‐ray diffraction ; data processing ; Guinier method
    Language: English
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  • 33
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    Small‐angle neutron scattering of long‐wavelength magnetic modulations in reduced sample dimensions (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-07-04
    Description: Magnetic small‐angle neutron scattering (SANS) is ideally suited to providing direct reciprocal‐space information on long‐wavelength magnetic modulations, such as helicoids, solitons, merons or skyrmions. SANS of such structures in thin films or micro‐structured bulk materials is strongly limited by the tiny scattering volume vis a vis the prohibitively high background scattering by the substrate and support structures. Considering near‐surface scattering just above the critical angle of reflection, where unwanted signal contributions due to substrate or support structures become very small, it is established that the scattering patterns of the helical, conical, skyrmion lattice and fluctuation‐disordered phases in a polished bulk sample of MnSi are equivalent for conventional transmission and near‐surface SANS geometries. This motivates the prediction of a complete repository of scattering patterns expected for thin films in the near‐surface SANS geometry for each orientation of the magnetic order with respect to the scattering plane.
    Description: Near‐surface SANS is discussed for its potential as a probe of long‐wavelength magnetic modulations in specimens with reduced sample dimensions.
    Keywords: ddc:548 ; small‐angle neutron scattering ; near‐surface SANS ; magnetism ; non‐collinear magnetism ; thin films ; skyrmions ; MnSi
    Language: English
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  • 34
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    Using diffraction losses of X‐rays in a single crystal for determination of its lattice parameters as well as for monochromator calibration (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-12-04
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉A way has been developed to measure the unit‐cell parameters of a single crystal just from an energy scan with X‐rays, even when the exact energy of the X‐rays is not well defined due to an error in the pitch angle of the monochromator. The precision of this measurement reaches 〈italic〉da〈/italic〉/〈italic〉a〈/italic〉 ∼ 1 × 10〈sup〉−5〈/sup〉. The method is based on the analysis of diffraction losses of the beam, transmitted through a single crystal (the so‐called `glitch effect'). This method can be easily applied to any transmissive X‐ray optical element made of single crystals (for example, X‐ray lenses). The only requirements are the possibility to change the energy of the generated X‐ray beam and some intensity monitor to measure the transmitted intensity. The method is agnostic to the error in the monochromator tuning and it can even be used for determination of the absolute pitch (or 2gθ) angle of the monochromator. Applying the same method to a crystal with well known lattice parameters allows determination of the exact cell parameters of the monochromator at any energy.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Diffraction losses (glitches) at certain energies of the X‐ray beam, transmitted through a single crystal, can be used for lattice parameters determination as well as for calibrating the monochromator (absolute pitch angle and the unit‐cell parameter).〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005775:jsy2ay5590:jsy2ay5590-fig-0001"〉 〈alt-text〉image〈/alt-text〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:548 ; X‐ray glitches ; diffraction losses ; unit‐cell parameter ; single‐crystal X‐ray optics ; monochromator calibration
    Language: English
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  • 35
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    Combining reverse Monte Carlo analysis of X‐ray scattering and extended X‐ray absorption fine structure spectra of very small nanoparticles (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-07-21
    Description: Finite size effects in partial pair distribution functions generate artefacts in the scattering structure factor and scattering intensity. It is shown how they can be overcome using a binned version of the Debye scattering equation. Accordingly, reverse Monte Carlo simulations are used for very small nanoparticles of LaFeO3 with diameters below 10 nm to simultaneously analyse X‐ray scattering data and extended X‐ray absorption fine structure spectra at the La K and Fe K edges. The structural information obtained is consistent regarding local structure and long‐range order.
    Description: Computing scattering intensity using the Debye scattering equation after binning interatomic distances avoids finite size artefacts and is efficient enough for simultaneous refinement of scattering data and extended X‐ray absorption spectra by reverse Monte Carlo simulations.
    Keywords: ddc:548 ; extended X‐ray absorption fine structure ; EXAFS ; wide‐angle X‐ray scattering ; WAXS ; reverse Monte Carlo ; RMC ; nanocrystals ; LaFeO3
    Language: English
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  • 36
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    X‐ray diffraction with micrometre spatial resolution for highly absorbing samples (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-01-21
    Description: X‐ray diffraction with high spatial resolution is commonly used to characterize (poly)crystalline samples with, for example, respect to local strain, residual stress, grain boundaries and texture. However, the investigation of highly absorbing samples or the simultaneous assessment of high‐Z materials by X‐ray fluorescence have been limited due to the utilization of low photon energies. Here, a goniometer‐based setup implemented at the P06 beamline of PETRA III that allows for micrometre spatial resolution with a photon energy of 35 keV and above is reported. A highly focused beam was achieved by using compound refractive lenses, and high‐precision sample manipulation was enabled by a goniometer that allows up to 5D scans (three rotations and two translations). As experimental examples, the determination of local strain variations in martensitic steel samples with micrometre spatial resolution, as well as the simultaneous elemental distribution for high‐Z materials in a thin‐film solar cell, are demonstrated. The proposed approach allows users from the materials‐science community to determine micro‐structural properties even in highly absorbing samples.
    Description: A demonstration of high‐resolution micro X‐ray diffraction at high photon energies for highly absorbing samples.
    Keywords: ddc:548 ; X‐ray diffraction ; high spatial resolution ; high photon energy ; X‐ray fluorescence ; goniometers
    Language: English
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  • 37
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    Domain Auto Finder (DAFi) program: the analysis of single‐crystal X‐ray diffraction data from polycrystalline samples (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-01-21
    Description: This paper presents the Domain Auto Finder (DAFi) program and its application to the analysis of single‐crystal X‐ray diffraction (SC‐XRD) data from multiphase mixtures of microcrystalline solids and powders. Superposition of numerous reflections originating from a large number of single‐crystal domains of the same and/or different (especially unknown) phases usually precludes the sorting of reflections coming from individual domains, making their automatic indexing impossible. The DAFi algorithm is designed to quickly find subsets of reflections from individual domains in a whole set of SC‐XRD data. Further indexing of all found subsets can be easily performed using widely accessible crystallographic packages. As the algorithm neither requires a priori crystallographic information nor is limited by the number of phases or individual domains, DAFi is powerful software to be used for studies of multiphase polycrystalline and microcrystalline (powder) materials. The algorithm is validated by testing on X‐ray diffraction data sets obtained from real samples: a multi‐mineral basalt rock at ambient conditions and products of the chemical reaction of yttrium and nitrogen in a laser‐heated diamond anvil cell at 50 GPa. The high performance of the DAFi algorithm means it can be used for processing SC‐XRD data online during experiments at synchrotron facilities.
    Description: This paper presents the Domain Auto Finder (DAFi) program and its application to the analysis of single‐crystal X‐ray diffraction (SC‐XRD) data from multiphase mixtures of microcrystalline solids and powders. The DAFi algorithm is designed to quickly find subsets of reflections from individual domains in a whole set of SC‐XRD data and neither requires a priori crystallographic information nor is limited by the number of phases or individual domains.
    Keywords: ddc:548 ; single‐crystal domain auto finder ; DAFi ; single‐crystal X‐ray diffraction ; polycrystalline samples ; multiphase mixtures
    Language: English
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  • 38
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    High‐resolution XEOL spectroscopy setup at the X‐ray absorption spectroscopy beamline P65 of PETRA III (2022)
    Levcenko, S. ; Biller, R. ; Pfeiffelmann, T. ; [et al.]
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-01-25
    Description: A newly designed setup to perform steady‐state X‐ray excited optical luminescence (XEOL) spectroscopy and simultaneous XEOL and X‐ray absorption spectroscopy characterization at beamline P65 of PETRA III is described. The XEOL setup is equipped with a He‐flow cryostat and state‐of‐the‐art optical detection system, which covers a wide wavelength range of 300–1700 nm with a high spectral resolution of 0.4 nm. To demonstrate the setup functioning, low‐temperature XEOL studies on polycrystalline CuInSe2 thin film, single‐crystalline GaN thin film and single‐crystalline ZnO bulk semiconductor samples are performed.
    Description: X‐ray excited optical luminescence (XEOL) spectroscopy is increasingly important to understand the interplay between the optical properties, structure and chemical composition, providing insights into the mechanism of radiative recombination for a wide range of materials. This study demonstrates a newly implemented setup to perform steady‐state XEOL and simultaneous XEOL and XAFS characterizations at beamline P65 of PETRA III.
    Keywords: ddc:550.2 ; XEOL ; XAS ; CuInSe2 ; ZnO ; GaN
    Language: English
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  • 39
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    Automatic bad‐pixel mask maker for X‐ray pixel detectors with application to serial crystallography (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-02-14
    Description: X‐ray crystallography has witnessed a massive development over the past decade, driven by large increases in the intensity and brightness of X‐ray sources and enabled by employing high‐frame‐rate X‐ray detectors. The analysis of large data sets is done via automatic algorithms that are vulnerable to imperfections in the detector and noise inherent with the detection process. By improving the model of the behaviour of the detector, data can be analysed more reliably and data storage costs can be significantly reduced. One major requirement is a software mask that identifies defective pixels in diffraction frames. This paper introduces a methodology and program based upon concepts of machine learning, called robust mask maker (RMM), for the generation of bad‐pixel masks for large‐area X‐ray pixel detectors based on modern robust statistics. It is proposed to discriminate normally behaving pixels from abnormal pixels by analysing routine measurements made with and without X‐ray illumination. Analysis software typically uses a Bragg peak finder to detect Bragg peaks and an indexing method to detect crystal lattices among those peaks. Without proper masking of the bad pixels, peak finding methods often confuse the abnormal values of bad pixels in a pattern with true Bragg peaks and flag such patterns as useful regardless, leading to storage of enormous uninformative data sets. Also, it is computationally very expensive for indexing methods to search for crystal lattices among false peaks and the solution may be biased. This paper shows how RMM vastly improves peak finders and prevents them from labelling bad pixels as Bragg peaks, by demonstrating its effectiveness on several serial crystallography data sets.
    Description: Attention is focused on perhaps the biggest bottleneck in data analysis for serial crystallography at X‐ray free‐electron lasers, which has not received serious enough examination to date. An effective and reliable way is presented to identify anomalies in detectors, using machine learning and recently developed mathematical methods in the field referred to as `robust statistics'. image
    Keywords: ddc:548 ; bad‐pixel masks ; robust mask maker ; machine learning ; robust statistics ; serial crystallography
    Language: English
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  • 40
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    Updates in SASfit for fitting analytical expressions and numerical models to small‐angle scattering patterns (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-02-22
    Description: Small‐angle scattering is an increasingly common method for characterizing particle ensembles in a wide variety of sample types and for diverse areas of application. SASfit has been one of the most comprehensive and flexible curve‐fitting programs for decades, with many specialized tools for various fields. Here, a selection of enhancements and additions to the SASfit program are presented that may be of great benefit to interested and advanced users alike: (a) further development of the technical basis of the program, such as new numerical algorithms currently in use, a continuous integration practice for automated building and packaging of the software, and upgrades on the plug‐in system for easier adoption by third‐party developers; (b) a selection of new form factors for anisotropic scattering patterns and updates to existing form factors to account for multiple scattering effects; (c) a new type of a very flexible distribution called metalog [Keelin (2016). Decis. Anal.13, 243–277], and regularization techniques such as the expectation‐maximization method [Dempster et al. (1977). J. R. Stat. Soc. Ser. B (Methodological), 39, 1–22; Richardson (1972) J. Opt. Soc. Am.62, 55; Lucy (1974). Astron. J.79, 745; Lucy (1994). Astron. Astrophys.289, 983–994], which is compared with fits of analytical size distributions via the non‐linear least‐squares method; and (d) new structure factors, especially for ordered nano‐ and meso‐scaled material systems, as well as the Ornstein–Zernike solver for numerical determination of particle interactions and the resulting structure factor when no analytical solution is available, with the aim of incorporating its effects into the small‐angle scattering intensity model used for fitting with SASfit.
    Description: Recent enhancements and additions to the SASfit program are discussed, including anisotropic scattering models, flexible distributions, regularization techniques such as the expectation‐maximization method, and new structure factors, especially for ordered nano‐ and meso‐scaled material. The Ornstein–Zernike solver for numerical structure factors is also introduced. image
    Keywords: ddc:548 ; small‐angle scattering ; SASfit ; numerical models ; structure factors ; form factors ; regularization techniques
    Language: English
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  • 41
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    Extending MIEZE spectroscopy towards thermal wavelengths (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-02-05
    Description: A modulation of intensity with zero effort (MIEZE) setup is proposed for high‐resolution neutron spectroscopy at momentum transfers up to 3 Å〈sup〉−1〈/sup〉, energy transfers up to 20 meV and an energy resolution in the microelectronvolt range using both thermal and cold neutrons. MIEZE has two prominent advantages compared with classical neutron spin echo. The first is the possibility to investigate spin‐depolarizing samples or samples in strong magnetic fields without loss of signal amplitude and intensity. This allows for the study of spin fluctuations in ferromagnets, and facilitates the study of samples with strong spin‐incoherent scattering. The second advantage is that multi‐analyzer setups can be implemented with comparatively little effort. The use of thermal neutrons increases the range of validity of the spin‐echo approximation towards shorter spin‐echo times. In turn, the thermal MIEZE option for greater ranges (TIGER) closes the gap between classical neutron spin‐echo spectroscopy and conventional high‐resolution neutron spectroscopy techniques such as triple‐axis, time‐of‐flight and back‐scattering. To illustrate the feasibility of TIGER, this paper presents the details of its implementation at the RESEDA beamline at FRM II by means of an additional velocity selector, polarizer and analyzer.
    Description: A modulation of intensity with zero effort (MIEZE) setup is proposed for high‐resolution neutron spectroscopy at momentum transfers up to 3 Å〈sup〉−1〈/sup〉, energy transfers up to 20 meV and an energy resolution in the microelectronvolt range using both thermal and cold neutrons.
    Keywords: ddc:548 ; neutron resonant spin echo ; MIEZE ; quasielastic scattering ; thermal neutrons
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  • 42
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    Extreme conditions research using the large‐volume press at the P61B endstation, PETRA III (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-02-05
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Penetrating, high‐energy synchrotron X‐rays are in strong demand, particularly for high‐pressure research in physics, chemistry and geosciences, and for materials engineering research under less extreme conditions. A new high‐energy wiggler beamline P61 has been constructed to meet this need at PETRA III in Hamburg, Germany. The first part of the paper offers an overview of the beamline front‐end components and beam characteristics. The second part describes the performance of the instrumentation and the latest developments at the P61B endstation. Particular attention is given to the unprecedented high‐energy photon flux delivered by the ten wigglers of the PETRA III storage ring and the challenges faced in harnessing this amount of flux and heat load in the beam. Furthermore, the distinctiveness of the world's first six‐ram Hall‐type large‐volume press, Aster‐15, at a synchrotron facility is described for research with synchrotron X‐rays. Additionally, detection schemes, experimental strategies and preliminary data acquired using energy‐dispersive X‐ray diffraction and radiography techniques are presented.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉The operation of the P61B endstation large‐volume press and optics of P61 are reviewed. The instrumentation at P61B, including the large‐volume press, detection systems and data acquisition for 〈italic〉in situ〈/italic〉 high‐pressure experiments are described.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005775:jsy2ju5040:jsy2ju5040-fig-0001"〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:550.724 ; extreme conditions ; high‐pressure ; large‐volume press ; energy‐dispersive X‐ray diffraction ; radiography ; resistive heating ; ultrasonic interferometry ; acoustic emissions detection
    Language: English
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  • 43
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    Quantifying electron cascade size in various irradiated materials for free‐electron laser applications (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-12-12
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Studying electron‐ and X‐ray‐induced electron cascades in solids is essential for various research areas at free‐electron laser facilities, such as X‐ray imaging, crystallography, pulse diagnostics or X‐ray‐induced damage. To better understand the fundamental factors that define the duration and spatial size of such cascades, this work investigates the electron propagation in ten solids relevant for the applications of X‐ray lasers: Au, B〈sub〉4〈/sub〉C, diamond, Ni, polystyrene, Ru, Si, SiC, Si〈sub〉3〈/sub〉N〈sub〉4〈/sub〉 and W. Using classical Monte Carlo simulation in the atomic approximation, we study the dependence of the cascade size on the incident electron or photon energy and on the target parameters. The results show that an electron‐induced cascade is systematically larger than a photon‐induced cascade. Moreover, in contrast with the common assumption, the maximal cascade size does not necessarily coincide with the electron range. It was found that the cascade size can be controlled by careful selection of the photon energy for a particular material. Photon energy, just above an ionization potential, can essentially split the absorbed energy between two electrons (photo‐ and Auger), reducing their initial energy and thus shrinking the cascade size. This analysis suggests a way of tailoring the electron cascades for applications requiring either small cascades with a high density of excited electrons or large‐spread cascades with lower electron densities.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Studying electron‐ and X‐ray‐induced electron cascades in solids is essential for various research areas at free‐electron laser facilities, such as X‐ray imaging, crystallography, pulse diagnostics or X‐ray‐induced damage. To better understand the fundamental factors that define the duration and spatial size of such cascades, this work investigates the electron propagation in ten solids relevant for the applications of X‐ray lasers. Using classical Monte Carlo simulation in the atomic approximation, the dependence of the cascade size on the incident electron or photon energy and on the target parameters is studied.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005775:jsy2gb5123:jsy2gb5123-fig-0001"〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:548 ; electron cascades ; X‐ray free‐electron lasers ; Monte Carlo ; photon‐induced cascade ; electron transport
    Language: English
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  • 44
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    The PERCIVAL detector: first user experiments (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-03-13
    Description: The PERCIVAL detector is a CMOS imager designed for the soft X‐ray regime at photon sources. Although still in its final development phase, it has recently seen its first user experiments: ptychography at a free‐electron laser, holographic imaging at a storage ring and preliminary tests on X‐ray photon correlation spectroscopy. The detector performed remarkably well in terms of spatial resolution achievable in the sample plane, owing to its small pixel size, large active area and very large dynamic range; but also in terms of its frame rate, which is significantly faster than traditional CCDs. In particular, it is the combination of these features which makes PERCIVAL an attractive option for soft X‐ray science.
    Keywords: ddc:548 ; X‐ray detectors ; soft X‐rays ; ptychography ; holographic imaging ; XPCS ; detectors
    Language: English
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  • 45
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    On the Spread of Microbes That Manipulate Reproduction in Marine Invertebrates (2022)
    University of Chicago Press
    Details
    Publication Date: 2024-02-07
    Description: Bacterial symbionts are functionally integral to animal reproduction and development, some of which have evolved additional mechanisms to override these host programs. One habitat that is increasingly recognized to contain phylogenetically related lineages of reproductive manipulators is the ocean. The reproduction of marine invertebrates often occurs by free spawning instead of by the physical contact of copulation in terrestrial systems. We developed an integrated model to understand whether and when microbes that manipulate host reproduction by cytoplasmic incompatibility, feminization, and male killing spread within populations of free-spawning marine invertebrates. Our model supports three primary findings. First, sex ratio distortion leads to suboptimal fertilization and zygote production in planktotrophs (feeding larvae) but enhance these processes in lecithotrophs (nonfeeding larvae). Second, feminization and a combination of male killing plus enhanced growth are effective at spreading reproductive manipulators while also inducing a female-biased sex ratio. Third, the majority of free-spawning marine invertebrates could be infected across a range of life history combinations, with infections harming species with smaller eggs and longer pelagic durations while benefiting species with larger eggs and shorter pelagic durations. Together, this supports the general premise that microbes may manipulate the reproduction of free-spawning marine invertebrates (e.g., by inducing changes in developmental life history) and that these types of manipulations overlap considerably with terrestrial systems.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 46
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    Larvae of deep-sea invertebrates harbor low-diversity bacterial communities (2021)
    University of Chicago Press
    Details
    Publication Date: 2023-01-13
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Carrier, T. J., Beaulieu, S. E., Mills, S. W., Mullineaux, L. S., & Reitzel, A. M. Larvae of deep-sea invertebrates harbor low-diversity bacterial communities. Biological Bulletin, 241(1), (2021): 65–76, https://doi.org/10.1086/715669.
    Description: Microbial symbionts are a common life-history character of marine invertebrates and their developmental stages. Communities of bacteria that associate with the eggs, embryos, and larvae of coastal marine invertebrates tend to be species specific and correlate with aspects of host biology and ecology. The richness of bacteria associated with the developmental stages of coastal marine invertebrates spans four orders of magnitude, from single mutualists to thousands of unique taxa. This understanding stems predominately from the developmental stages of coastal species. If they are broadly representative of marine invertebrates, then we may expect deep-sea species to associate with bacterial communities that are similar in diversity. To test this, we used amplicon sequencing to profile the bacterial communities of invertebrate larvae from multiple taxonomic groups (annelids, molluscs, crustaceans) collected from 2500 to 3670 m in depth in near-bottom waters near hydrothermal vents in 3 different regions of the Pacific Ocean (the East Pacific Rise, the Mariana Back-Arc, and the Pescadero Basin). We find that larvae of deep-sea invertebrates associate with low-diversity bacterial communities (~30 bacterial taxa) that lack specificity between taxonomic groups. The diversity of these communities is estimated to be ~7.9 times lower than that of coastal invertebrate larvae, but this result depends on the taxonomic group. Associating with a low-diversity community may imply that deep-sea invertebrate larvae do not have a strong reliance on a microbiome and that the hypothesized lack of symbiotic contributions would differ from expectations for larvae of coastal marine invertebrates.
    Description: TJC was supported by a National Science Foundation (NSF) Graduate Research Fellowship; SEB, SWM, and LSM were supported by NSF (OCE-0424953, OCE-1028862, and OCE-1829773) and the Dalio Explore Fund; and AMR was supported by the Human Frontier Science Program Award RGY0079/2016.
    Repository Name: Woods Hole Open Access Server
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  • 47
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    Larvae of Deep-Sea Invertebrates Harbor Low-Diversity Bacterial Communities (2021)
    University of Chicago Press
    Details
    Publication Date: 2024-02-07
    Description: Microbial symbionts are a common life-history character of marine invertebrates and their developmental stages. Communities of bacteria that associate with the eggs, embryos, and larvae of coastal marine invertebrates tend to be species specific and correlate with aspects of host biology and ecology. The richness of bacteria associated with the developmental stages of coastal marine invertebrates spans four orders of magnitude, from single mutualists to thousands of unique taxa. This understanding stems predominately from the developmental stages of coastal species. If they are broadly representative of marine invertebrates, then we may expect deep-sea species to associate with bacterial communities that are similar in diversity. To test this, we used amplicon sequencing to profile the bacterial communities of invertebrate larvae from multiple taxonomic groups (annelids, molluscs, crustaceans) collected from 2500 to 3670 m in depth in near-bottom waters near hydrothermal vents in 3 different regions of the Pacific Ocean (the East Pacific Rise, the Mariana Back-Arc, and the Pescadero Basin). We find that larvae of deep-sea invertebrates associate with low-diversity bacterial communities (similar to 30 bacterial taxa) that lack specificity between taxonomic groups. The diversity of these communities is estimated to be similar to 7.9 times lower than that of coastal invertebrate larvae, but this result depends on the taxonomic group. Associating with a low-diversity community may imply that deep-sea invertebrate larvae do not have a strong reliance on a microbiome and that the hypothesized lack of symbiotic contributions would differ from expectations for larvae of coastal marine invertebrates.
    Type: Article , PeerReviewed
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  • 48
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    Synthesis and crystal structure of a solvated CoIII complex with 2-hydroxy-3-methoxybenzaldehyde thiosemicarbazone ligands (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-21
    Description: The title CoIII complex, bis[bis(2-hydroxy-3-methoxybenzaldehyde thiosemicarbazonato)cobalt(III)] dithionate–dimethylformamide–methanol (1/4/3), [Co(C9H10N3O2S)2]2(S2O6)·4C3H7NO·3CH3OH, with monodeprotonated 2-hydroxy-3-methoxybenzaldehyde thiosemicarbazone as ligands crystallizes in the space group Poverline{1}. The asymmetric unit consists of two mononuclear [CoL 2]+ cations, one dithionate anion (S2O6)2− as counter-anion and seven solvate molecules (four dimethylmethanamide and three methanol). Each CoIII ion has a moderately distorted octahedral S2N2O2 geometry. In the crystal, the components are linked by numerous N—H...O and O—H...O contacts.
    Electronic ISSN: 2056-9890
    Topics: Chemistry and Pharmacology , Geosciences
    Published by International Union of Crystallography
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  • 49
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    Comparison of the crystal structures of the low- and high-temperature forms of bis[4-(dimethylamino)pyridine]dithiocyanatocobalt(II) (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-19
    Description: Single crystals of the high-temperature form I of [Co(NCS)2(DMAP)2] (DMAP = 4-dimethylaminopyridine, C7H10N2) were obtained accidentally by the reaction of Co(NCS)2 with DMAP at slightly elevated temperatures under kinetic control. This modification crystallizes in the monoclinic space group P21/m and is isotypic with the corresponding Zn compound. The asymmetric unit consists of one crystallographically independent Co cation and two crystallographically independent thiocyanate anions that are located on a crystallographic mirror plane and one DMAP ligand (general position). In its crystal structure the discrete complexes are linked by C—H...S hydrogen bonds into a three-dimensional network. For comparison, the crystal structure of the known low-temperature form II, which is already thermodynamically stable at room temperature, was redetermined at the same temperature. In this polymorph the complexes are connected by C—H...S and C—H...N hydrogen bonds into a three-dimensional network. At 100 K the density of the high-temperature form I (ρ = 1.462 g cm−3) is lower than that of the low-temperature form II (ρ = 1.457 g cm−3), which is in contrast to the values determined by XRPD at room temperature. Therefore, these two forms represent an exception to the Kitaigorodskii density rule, for which extensive intermolecular hydrogen bonding in form II might be responsible.
    Electronic ISSN: 2056-9890
    Topics: Chemistry and Pharmacology , Geosciences
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  • 50
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    Synthesis and absolute structure of (R)-2-(benzylselanyl)-1-phenylethanaminium hydrogen sulfate monohydrate: crystal structure and Hirshfeld surface analyses (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-19
    Description: A hydrogen sulfate salt, C15H18NSe+·HSO4 −·H2O or [BnSeCH2CH(Ph)NH3 +](HSO4 −), of a chiral selenated amine (R)-2-(benzylselanyl)-1-phenylethanamine (BnSeCH2CH(Ph)NH2) has been synthesized and characterized by elemental analysis,1H and 13C{1H} NMR, FT–IR analysis, and single-crystal X-ray diffraction studies. The title salt crystallizes in the monohydrate form in the non-centrosymmetric monoclinic P21 space group. The cation is somewhat W shaped with the dihedral angle between the two aromatic rings being 60.9 (4)°. The carbon atom attached to the amine nitrogen atom is chiral and in the R configuration, and, the –C—C– bond of the –CH2—CH– fragment has a staggered conformation. In the crystal structure, two HSO4 − anions and two water molecules form an R 4 4(12) tetrameric type of assembly comprised of alternating HSO4 − anions and water molecules via discrete D(2) O—H...O hydrogen bonds. This tetrameric assembly aggregates along the b-axis direction as an infinite one-dimensional tape. Adjacent tapes are interconnected via discrete D(2) N—H...O hydrogen bonds between the three amino hydrogen atoms of the cation sandwiched between the two tapes and the three HSO4 − anions of the nearest asymmetric units, resulting in a complex two-dimensional sheet along the ab plane. The pendant arrangement of the cations is stabilized by C—H...π interactions between adjacent cations running as chains down the [010] axis. Secondary Se...O [3.1474 (4) Å] interactions are also observed in the crystal structure. A Hirshfeld surface analysis, including d norm, shape-index and fingerprint plots of the cation, anion and solvent molecule, was carried out to confirm the presence of various interactions in the crystal structure.
    Electronic ISSN: 2056-9890
    Topics: Chemistry and Pharmacology , Geosciences
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  • 51
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    A cadmium(II) coordination polymer with a fivefold interpenetrating diamondoid three-dimensional framework: synthesis, crystal structure, luminescence and photocatalytic properties (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-27
    Description: A novel three-dimensional (3D) CdII coordination polymer, namely, poly[[μ2-4,4′-bis(2-methylimidazol-1-yl)-[1,1′-biphenyl]](μ2-5-methylisophthalato)cadmium(II)], [Cd(C9H6O4)(C20H18N4)] n or [Cd(MIP)(4,4′-BMIBP)] n , (I), was synthesized by the hydrothermal method using 5-methylisophthalic acid (H2MIP), 4,4′-bis(2-methylimidazol-1-yl)-[1,1′-biphenyl] (4,4′-BMIBP) and Cd(NO3)2·6H2O, and characterized by single-crystal X-ray diffraction, elemental analysis, IR spectroscopy and thermogravimetric analysis. Compound (I) exhibits a novel fivefold interpenetrating 3D diamondoid framework. Additionally, it shows fluorescence emission in the solid state and promising photocatalytic activities for the degradation of methylene blue (MB) in water at room temperature.
    Electronic ISSN: 2053-2296
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 52
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    Parameterization of magnetic vector potentials and fields for efficient multislice calculations of elastic electron scattering (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-29
    Description: The multislice method, which simulates the propagation of the incident electron wavefunction through a crystal, is a well established method for analysing the multiple scattering effects that an electron beam may undergo. The inclusion of magnetic effects into this method proves crucial towards simulating enhanced magnetic interaction of vortex beams with magnetic materials, calculating magnetic Bragg spots or searching for magnon signatures, to name a few examples. Inclusion of magnetism poses novel challenges to the efficiency of the multislice method for larger systems, especially regarding the consistent computation of magnetic vector potentials A and magnetic fields B over large supercells. This work presents a tabulation of parameterized magnetic (PM) values for the first three rows of transition metal elements computed from atomic density functional theory (DFT) calculations, allowing for the efficient computation of approximate A and B across large crystals using only structural and magnetic moment size and direction information. Ferromagnetic b.c.c. (body-centred cubic) Fe and tetragonal FePt are chosen to showcase the performance of PM values versus directly obtaining A and B from the unit-cell spin density by DFT. The magnetic fields of b.c.c. Fe are well described by the PM approach while for FePt the PM approach is less accurate due to deformations in the spin density. Calculations of the magnetic signal, namely the change due to A and B of the intensity of diffraction patterns, show that the PM approach for both b.c.c. Fe and FePt is able to describe the effects of magnetism in these systems to a good degree of accuracy.
    Electronic ISSN: 2053-2733
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by International Union of Crystallography
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  • 53
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    The future of biomolecular simulation in the pharmaceutical industry: what we can learn from aerodynamics modelling and weather prediction. Part 1. understanding the physical and computational complexity of in silico drug design (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-27
    Description: The predictive power of simulation has become embedded in the infrastructure of modern economies. Computer-aided design is ubiquitous throughout industry. In aeronautical engineering, built infrastructure and materials manufacturing, simulations are routinely used to compute the performance of potential designs before construction. The ability to predict the behaviour of products is a driver of innovation by reducing the cost barrier to new designs, but also because radically novel ideas can be piloted with relatively little risk. Accurate weather forecasting is essential to guide domestic and military flight paths, and therefore the underpinning simulations are critical enough to have implications for national security. However, in the pharmaceutical and biotechnological industries, the application of computer simulations remains limited by the capabilities of the technology with respect to the complexity of molecular biology and human physiology. Over the last 30 years, molecular-modelling tools have gradually gained a degree of acceptance in the pharmaceutical industry. Drug discovery has begun to benefit from physics-based simulations. While such simulations have great potential for improved molecular design, much scepticism remains about their value. The motivations for such reservations in industry and areas where simulations show promise for efficiency gains in preclinical research are discussed. In this, the first of two complementary papers, the scientific and technical progress that needs to be made to improve the predictive power of biomolecular simulations, and how this might be achieved, is firstly discussed (Part 1). In Part 2, the status of computer simulations in pharma is contrasted with aerodynamics modelling and weather forecasting, and comments are made on the cultural changes needed for equivalent computational technologies to become integrated into life-science industries.
    Electronic ISSN: 2059-7983
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 54
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    Plate Tectonics and the Alpine Orogeny: Implications of Thermometric and Kinematic Analyses of the Upper and Lower Boundaries of the Pennine Zone in the Central Alps (2021)
    University of Chicago Press
    Details
    Publication Date: 2021-10-29
    Print ISSN: 0022-1376
    Electronic ISSN: 1537-5269
    Topics: Geosciences
    Published by University of Chicago Press
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  • 55
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    Crystal structure and Hirshfeld surface analysis of (E)-1-[2,2-dichloro-1-(4-fluorophenyl)ethenyl]-2-(2,4-dichlorophenyl)diazene (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-26
    Description: In the title compound, C14H7Cl4FN2, the dihedral angle between the 4-fluorophenyl ring and the 2,4-dichlorophenyl ring is 46.03 (19)°. In the crystal, the molecules are linked by C—H...N interactions along the a-axis direction, forming a C(6) chain. The molecules are further connected by C—Cl...π interactions and face-to-face π–π stacking interactions, forming ribbons along the a-axis direction. Hirshfeld surface analysis indicates that the greatest contributions to the crystal packing are from Cl...H/H...Cl (35.1%), H...H (10.6%), C...C (9.7%), Cl...Cl (9.4%) and C...H/H...C (9.2%) interactions.
    Electronic ISSN: 2056-9890
    Topics: Chemistry and Pharmacology , Geosciences
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  • 56
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    Monitoring reversion of hepatitis C virus-induced cellular alterations by direct-acting antivirals using cryo soft X-ray tomography and infrared microscopy (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-27
    Description: Hepatitis C virus (HCV) is an enveloped RNA virus. One of the hallmarks of HCV infection is a rearrangement of the host cell membranes, known as the `membranous web'. Full-field cryo soft X-ray tomography (cryo-SXT) in the water-window energy range (284–543 eV) was performed on the MISTRAL beamline to investigate, in whole unstained cells, the morphology of the membranous rearrangements induced in HCV replicon-harbouring cells in conditions close to the living physiological state. All morphological alterations could be reverted by a combination of sofosbuvir/daclatasvir, which are clinically approved antivirals (direct-acting antivirals; DAAs) for HCV infection. Correlatively combining cryo-SXT and 2D synchrotron-based infrared microscopy provides critical information on the chemical nature of specific infection-related structures, which allows specific patterns of the infection process or the DAA-mediated healing process to be distinguished.
    Electronic ISSN: 2059-7983
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 57
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    Crystal structure and Hirshfeld surface analysis of di-μ-chlorido-bis[(acetonitrile-κN)chlorido(ethyl 5-methyl-1H-pyrazole-3-carboxylate-κ2 N 2,O)copper(II)] (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-26
    Description: The title compound, [Cu2Cl4(C5H10N2O2)2(CH3CN)2] or [Cu2(μ2-Cl)2(CH3—Pz-COOCH2CH3)2Cl2(CH3CN)2], was synthesized using a one-pot reaction of copper powder, copper(II) chloride dihydrate and ethyl 5-methyl-1H-pyrazole-3-carboxylate (CH3—Pz-COOCH2CH3) in acetonitrile under ambient conditions. This complex consists of discrete binuclear molecules with a {Cu2(μ2-Cl)2} core, in which the Cu...Cu distance is 3.8002 (7) Å. The pyrazole-based ligands are bidentate coordinated, leading to the formation of two five-membered chelate rings. The coordination geometry of both copper atoms (ON2Cl3) can be described as distorted octahedral on account of the acetonitrile coordination. A Hirshfeld surface analysis suggests that the most important contributions to the surface contacts are from H...H (40%), H...Cl/Cl...H (24.3%), H...O/O...H (11.8%), H...C/C...H (9.2%) and H...N/N...H (8.3%) interactions.
    Electronic ISSN: 2056-9890
    Topics: Chemistry and Pharmacology , Geosciences
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  • 58
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    Structural basis for SdgB- and SdgA-mediated glycosylation of staphylococcal adhesive proteins (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-20
    Description: The initiation of infection of host tissues by Staphylococcus aureus requires a family of staphylococcal adhesive proteins containing serine–aspartate repeat (SDR) domains, such as ClfA. The O-linked glycosylation of the long-chain SDR domain mediated by SdgB and SdgA is a key virulence factor that protects the adhesive SDR proteins against host proteolytic attack in order to promote successful tissue colonization, and has also been implicated in staphylococcal agglutination, which leads to sepsis and an immunodominant epitope for a strong antibody response. Despite the biological significance of these two glycosyltransferases involved in pathogenicity and avoidance of the host innate immune response, their structures and the molecular basis of their activity have not been investigated. This study reports the crystal structures of SdgB and SdgA from S. aureus as well as multiple structures of SdgB in complex with its substrates (for example UDP, N-acetylglucosamine or SDR peptides), products (glycosylated SDR peptides) or phosphate ions. Together with biophysical and biochemical analyses, this structural work uncovered the novel mechanism by which SdgB and SdgA carry out the glycosyl-transfer process to the long SDR region in SDR proteins. SdgB undergoes dynamic changes in its structure such as a transition from an open to a closed conformation upon ligand binding and takes diverse forms, both as a homodimer and as a heterodimer with SdgA. Overall, these findings not only elucidate the putative role of the three domains of SdgB in recognizing donor and acceptor substrates, but also provide new mechanistic insights into glycosylation of the SDR domain, which can serve as a starting point for the development of antibacterial drugs against staphylococcal infections.
    Electronic ISSN: 2059-7983
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  • 59
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    Salts of purine alkaloids caffeine and theobromine with 2,6-dihydroxybenzoic acid as coformer: structural, theoretical, thermal and spectroscopic studies (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-27
    Description: The study of various forms of pharmaceutical substances with specific physicochemical properties suitable for putting them on the market is one of the elements of research in the pharmaceutical industry. A large proportion of active pharmaceutical ingredients (APIs) occur in the salt form. The use of an acidic coformer with a given structure and a suitable pK a value towards purine alkaloids containing a basic imidazole N atom can lead to salt formation. In this work, 2,6-dihydroxybenzoic acid (26DHBA) was used for cocrystallization of theobromine (TBR) and caffeine (CAF). Two novel salts, namely, theobrominium 2,6-dihydroxybenzoate, C7H9N4O2 +·C7H5O4 − (I), and caffeinium 2,6-dihydroxybenzoate, C8H11N4O2 +·C7H5O4 − (II), were synthesized. Both salts were obtained independently by slow evaporation from solution, by neat grinding and also by microwave-assisted slurry cocrystallization. Powder X-ray diffraction measurements proved the formation of the new substances. Single-crystal X-ray diffraction studies confirmed proton transfer between the given alkaloid and 26DHBA, and the formation of N—H...O hydrogen bonds in both I and II. Unlike the caffeine cations in II, the theobromine cations in I are paired by noncovalent N—H...O=C interactions and a cyclic array is observed. As expected, the two hydroxy groups in the 26DHBA anion in both salts are involved in two intramolecular O—H...O hydrogen bonds. C—H...O and π–π interactions further stabilize the crystal structures of both compounds. Steady-state UV–Vis spectroscopy showed changes in the water solubility of xanthines after ionizable complex formation. The obtained salts I and II were also characterized by theoretical calculations, Fourier-transform IR spectroscopy (FT–IR), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and elemental analysis.
    Electronic ISSN: 2053-2296
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 60
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    Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-20
    Description: In crystallography, the phase problem can often be addressed by the careful preparation of molecular-replacement search models. This has led to the development of pipelines such as MrBUMP that can automatically identify homologous proteins from an input sequence and edit them to focus on the areas that are most conserved. Many of these approaches can be applied directly to cryo-EM to help discover, prepare and correctly place models (here called cryo-EM search models) into electrostatic potential maps. This can significantly reduce the amount of manual model building that is required for structure determination. Here, MrBUMP is repurposed to fit automatically obtained PDB-derived chains and domains into cryo-EM maps. MrBUMP was successfully able to identify and place cryo-EM search models across a range of resolutions. Methods such as map segmentation are also explored as potential routes to improved performance. Map segmentation was also found to improve the effectiveness of the pipeline for higher resolution (
    Electronic ISSN: 2059-7983
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  • 61
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    Vanishing of the atomic form factor derivatives in non-spherical structural refinement – a key approximation scrutinized in the case of Hirshfeld atom refinement (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-29
    Description: When calculating derivatives of structure factors, there is one particular term (the derivatives of the atomic form factors) that will always be zero in the case of tabulated spherical atomic form factors. What happens if the form factors are non-spherical? The assumption that this particular term is very close to zero is generally made in non-spherical refinements (for example, implementations of Hirshfeld atom refinement or transferable aspherical atom models), unless the form factors are refinable parameters (for example multipole modelling). To evaluate this general approximation for one specific method, a numerical differentiation was implemented within the NoSpherA2 framework to calculate the derivatives of the structure factors in a Hirshfeld atom refinement directly as accurately as possible, thus bypassing the approximation altogether. Comparing wR 2 factors and atomic parameters, along with their uncertainties from the approximate and numerically differentiating refinements, it turns out that the impact of this approximation on the final crystallographic model is indeed negligible.
    Electronic ISSN: 2053-2733
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    Prices of IUCr journals (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-29
    Electronic ISSN: 2053-2733
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    On single-crystal total scattering data reduction and correction protocols for analysis in direct space (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-29
    Description: Data reduction and correction steps and processed data reproducibility in the emerging single-crystal total-scattering-based technique of three-dimensional differential atomic pair distribution function (3D-ΔPDF) analysis are explored. All steps from sample measurement to data processing are outlined using a crystal of CuIr2S4 as an example, studied in a setup equipped with a high-energy X-ray beam and a flat-panel area detector. Computational overhead as pertains to data sampling and the associated data-processing steps is also discussed. Various aspects of the final 3D-ΔPDF reproducibility are explicitly tested by varying the data-processing order and included steps, and by carrying out a crystal-to-crystal data comparison. Situations in which the 3D-ΔPDF is robust are identified, and caution against a few particular cases which can lead to inconsistent 3D-ΔPDFs is noted. Although not all the approaches applied herein will be valid across all systems, and a more in-depth analysis of some of the effects of the data-processing steps may still needed, the methods collected herein represent the start of a more systematic discussion about data processing and corrections in this field.
    Electronic ISSN: 2053-2733
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  • 64
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    Structure and metal-binding properties of PA4063, a novel player in periplasmic zinc trafficking by Pseudomonas aeruginosa (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-20
    Description: The capability to obtain essential nutrients in hostile environments is a critical skill for pathogens. Under zinc-deficient conditions, Pseudomonas aeruginosa expresses a pool of metal homeostasis control systems that is complex compared with other Gram-negative bacteria and has only been partially characterized. Here, the structure and zinc-binding properties of the protein PA4063, the first component of the PA4063–PA4066 operon, are described. PA4063 has no homologs in other organisms and is characterized by the presence of two histidine-rich sequences. ITC titration detected two zinc-binding sites with micromolar affinity. Crystallographic characterization, performed both with and without zinc, revealed an α/β-sandwich structure that can be classified as a noncanonical ferredoxin-like fold since it differs in size and topology. The histidine-rich stretches located at the N-terminus and between β3 and β4 are disordered in the apo structure, but a few residues become structured in the presence of zinc, contributing to coordination in one of the two sites. The ability to bind two zinc ions at relatively low affinity, the absence of catalytic cavities and the presence of two histidine-rich loops are properties and structural features which suggest that PA4063 might play a role as a periplasmic zinc chaperone or as a concentration sensor useful for optimizing the response of the pathogen to zinc deficiency.
    Electronic ISSN: 2059-7983
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  • 65
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    Crystal structure of N-terminal degron-truncated human glutamine synthetase (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-29
    Description: Glutamine synthetase (GS) is a decameric enzyme that plays a key role in nitrogen metabolism. Acetylation of the N-terminal degron (N-degron) of GS is essential for ubiquitylation and subsequent GS degradation. The full-length GS structure showed that the N-degron is buried inside the GS decamer and is inaccessible to the acetyltransferase. The structure of N-degron-truncated GS reported here reveals that the N-degron is not essential for GS decamer formation. It is also shown that the N-degron can be exposed to a solvent region through a series of conformational adjustments upon ligand binding. In summary, this study elucidated the dynamic movement of the N-degron and the possible effect of glutamine in enhancing the acetylation process.
    Electronic ISSN: 2053-230X
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Physics
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    Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-20
    Description: The SorC/DeoR family is a large family of bacterial transcription regulators that are involved in the control of carbohydrate metabolism and quorum sensing. To understand the structural basis of DNA recognition, structural studies of two functionally characterized SorC/DeoR family members from Bacillus subtilis were performed: the deoxyribonucleoside regulator bsDeoR and the central glycolytic genes regulator bsCggR. Each selected protein represents one of the subgroups that are recognized within the family. Crystal structures were determined of the N-terminal DNA-binding domains of bsDeoR and bsCggR in complex with DNA duplexes representing the minimal operator sequence at resolutions of 2.3 and 2.1 Å, respectively. While bsDeoRDBD contains a homeodomain-like HTH-type domain, bsCggRDBD contains a winged helix–turn–helix-type motif. Both proteins form C2-symmetric dimers that recognize two consecutive major grooves, and the protein–DNA interactions have been analyzed in detail. The crystal structures were used to model the interactions of the proteins with the full DNA operators, and a common mode of DNA recognition is proposed that is most likely to be shared by other members of the SorC/DeoR family.
    Electronic ISSN: 2059-7983
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    Improving sampling of crystallographic disorder in ensemble refinement (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-20
    Description: Ensemble refinement, the application of molecular dynamics to crystallographic refinement, explicitly models the disorder inherent in macromolecular structures. These ensemble models have been shown to produce more accurate structures than traditional single-model structures. However, suboptimal sampling of the molecular-dynamics simulation and modelling of crystallographic disorder has limited the utility of the method, and can lead to unphysical and strained models. Here, two improvements to the ensemble refinement method implemented within Phenix are presented: DEN restraints, which guide the local sampling of conformations and allow a more robust exploration of local conformational landscapes, and ECHT disorder models, which allow the selection of more physically meaningful and effective disorder models for parameterizing the continuous disorder components within a crystal. These improvements lead to more consistent and physically interpretable simulations of macromolecules in crystals, and allow structural heterogeneity and disorder to be systematically explored on different scales. The new approach is demonstrated on several case studies and the SARS-CoV-2 main protease, and demonstrates how the choice of disorder model affects the type of disorder that is sampled by the restrained molecular-dynamics simulation.
    Electronic ISSN: 2059-7983
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  • 68
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    Crystal structure of acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-19
    Description: The acetylxylan esterases (AXEs) classified into carbohydrate esterase family 4 (CE4) are metalloenzymes that catalyze the deacetylation of acetylated carbohydrates. AXE from Caldanaerobacter subterraneus subsp. tengcongensis (TTE0866), which belongs to CE4, is composed of three parts: a signal sequence (residues 1–22), an N-terminal region (NTR; residues 23–135) and a catalytic domain (residues 136–324). TTE0866 catalyzes the deacetylation of highly substituted cellulose acetate and is expected to be useful for industrial applications in the reuse of resources. In this study, the crystal structure of TTE0866 (residues 23–324) was successfully determined. The crystal diffracted to 1.9 Å resolution and belonged to space group I212121. The catalytic domain (residues 136–321) exhibited a (β/α)7-barrel topology. However, electron density was not observed for the NTR (residues 23–135). The crystal packing revealed the presence of an intermolecular space without observable electron density, indicating that the NTR occupies this space without a defined conformation or was truncated during the crystallization process. Although the active-site conformation of TTE0866 was found to be highly similar to those of other CE4 enzymes, the orientation of its Trp264 side chain near the active site was clearly distinct. The unique orientation of the Trp264 side chain formed a different-shaped cavity within TTE0866, which may contribute to its reactivity towards highly substituted cellulose acetate.
    Electronic ISSN: 2053-230X
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  • 69
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    The crystal structures of the enzyme hydroxymethylbilane synthase, also known as porphobilinogen deaminase (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-19
    Description: The enzyme hydroxymethylbilane synthase (HMBS; EC 4.3.1.8), also known as porphobilinogen deaminase, catalyses the stepwise addition of four molecules of porphobilinogen to form the linear tetrapyrrole 1-hydroxymethylbilane. Thirty years of crystal structures are surveyed in this topical review. These crystal structures aim at the elucidation of the structural basis of the complex reaction mechanism involving the formation of tetrapyrrole from individual porphobilinogen units. The consistency between the various structures is assessed. This includes an evaluation of the precision of each molecular model and what was not modelled. A survey is also made of the crystallization conditions used in the context of the operational pH of the enzyme. The combination of 3D structural techniques, seeking accuracy, has also been a feature of this research effort. Thus, SAXS, NMR and computational molecular dynamics have also been applied. The general framework is also a considerable chemistry research effort to understand the function of the enzyme and its medical pathologies in acute intermittent porphyria (AIP). Mutational studies and their impact on the catalytic reaction provide insight into the basis of AIP and are also invaluable for guiding the understanding of the crystal structure results. Future directions for research on HMBS are described, including the need to determine the protonation states of key amino-acid residues identified as being catalytically important. The question remains – what is the molecular engine for this complex reaction? Thermal fluctuations are the only suggestion thus far.
    Electronic ISSN: 2053-230X
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    Synthesis and crystal structure of a new chiral α-aminooxime nickel(II) complex (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-19
    Description: A dinuclear nickel complex with (S)-limonene based aminooxime ligand has been isolated and its crystal structure determined. The resolved structure of dichloridobis{(2S,5R)-2-methyl-5-(prop-1-en-2-yl)-2-[(pyridin-2-yl)methylamino]cyclohexan-1-one oxime}dinickel(II), [Ni2Cl2(C16H23ClN3O)2], at 100 K has monoclinic (P21) symmetry. The two NiII ions in the dinuclear complex are each coordinated in a distorted octahedral environment by three nitrogen atoms, a terminal chloride and two μ bridging chlorides. Each oxime ligand is coordinated to nickel(II) by the three nitrogen atoms, leading to two five-membered chelate rings, each displaying an envelope conformation. In the crystal, numerous intermolecular and intramolecular hydrogen bonds lead to the formation of a three-dimensional network structure.
    Electronic ISSN: 2056-9890
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  • 71
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    Crystal structure and Hirshfeld surface analysis of bis[(ethoxymethanethioyl)sulfanido](N,N,N′,N′-tetramethylethane-1,2-diamine)mercury(II) (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-19
    Description: The title four-coordinate mononuclear complex, [Hg(C3H5OS2)2(C6H16N2)] or [Hg(C3H5OS2)2(tmeda)] (tmeda: N,N,N′,N′-tetramethylethane-1,2-diamine), has a distorted tetrahedral geometry. The HgII ion is coordinated to two N atoms of the N,N,N′,N′-tetramethylethylenediamine ligand and two S atoms from two ethylxanthate xanthate ligands. In the crystal, molecules are linked by weak C—H...S hydrogen bonds, forming a two-dimensional supramolecular architecture in the ab plane. The most important contributions for the crystal packing are from H...H (59.3%), S...H (27.4%) and O...H (7.5%) interactions.
    Electronic ISSN: 2056-9890
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    Hydrogen-bonding landscape of the carbamoylcyanonitrosomethanide anion in the crystal structure of its ammonium salt (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-13
    Description: The structure of the title salt, ammonium carbamoylcyanonitrosomethanide, NH4 +·C3H2N3O2 −, features the co-existence of different hydrogen-bonding patterns, which are specific to each of the three functional groups (nitroso, carbamoyl and cyano) of the methanide anion. The nitroso O-atoms accept as many as three N—H...O bonds from the ammonium cations [N...O = 2.688 (3)–3.000 (3) Å] to form chains of fused rhombs [(NH4)(O)2]. The most prominent bonds of the carbamoyl groups are mutual and they yield 21 helices [N...O = 2.903 (2) Å], whereas the cyano N-atoms accept hydrogen bonds from sterically less accessible carbamoyl H-atoms [N...N = 3.004 (3) Å]. Two weaker NH4 +...O=C bonds [N...O = 3.021 (2), 3.017 (2) Å] complete the hydrogen-bonded environment of the carbamoyl groups. A Hirshfeld surface analysis indicates that the most important interactions are overwhelmingly O...H/H...O and N...H/H...N, in total accounting for 64.1% of the contacts for the individual anions. The relatively simple scheme of these interactions allows the delineation of the supramolecular synthons, which may be applicable to crystal engineering of hydrogen-bonded solids containing polyfunctional methanide anions.
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  • 73
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    Crystal structure of 2-oxo-1,2-diphenylethyl diisopropylcarbamate (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-13
    Description: The title compound, C21H25NO3, crystallized as a racemic twin in the Sohnke space group P21. In the molecular structure of the title compound, both enantiomers show a highly similar conformation with the urethane function and the benzoyl group showing an almost perpendicular arrangement [the dihedral angle is 72.46 (8)° in the S-enantiomer and 76.21 (8)° in the R-enantiomer]. In the crystal structure, molecules of both enantiomers show infinite helical arrangements parallel to the b axis formed by weak C—H...O hydrogen bonds between the phenyl ring of the benzoyl group and the carbamate carbonyl group. In case of the R-enantiomer, this helix is additionally stabilized by a bifurcated hydrogen bond between the carbonyl function of the benzoyl group towards both phenyl groups of the molecule.
    Electronic ISSN: 2056-9890
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  • 74
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    Crystal structures of two alanylpiperidine analogues (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-13
    Description: The structure of ethyl 1-[N-(4-methylphenyl)-N-(methylsulfonyl)alanyl]piperidine-4-carboxylate, C19H28N2O5S, I, a compound of interest as activator of Ubiquitin C-terminal Hydrolase-L1 (UCH-L1), was determined by single-crystal X-ray diffraction (SCXRD) analysis. In order to find new activators, a derivative of compound I, namely, 1-[N-(4-methylphenyl)-N-(methylsulfonyl)alanyl]piperidine-4-carboxylic acid, C17H24N2O5S, II, was studied. The synthesis and crystal structure are also reported. Despite being analogues, different crystal packings are observed. Compound II bears a carboxylic group, which favors a strong hydrogen bond. A polymorph risk assessment was carried out to study interactions in compound II.
    Electronic ISSN: 2056-9890
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  • 75
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    Formation of a macrocycle from dichlorodimethylsilane and a pyridoxalimine Schiff base ligand (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-13
    Description: The reaction of dichlorodimethylsilane with a polydentate Schiff base ligand derived from pyridoxal and 2-ethanolamine yielded the macrocyclic silicon compound (8E,22E)-4,4,12,18,18,26-hexamethyl-3,5,17,19-tetraoxa-8,13,22,27-tetraaza-4,18-disilatricyclo[22.4.0.010,15]octacosa-1(24),8,10,12,14,22,25,27-octaene-11,25-diol, C24H36N4O6Si2. The asymmetric unit contains the half macrocycle with an intramolecular O—H...N hydrogen bond between the imine nitrogen atom and a neighbouring oxygen atom. The crystal structure is dominated by C—H...O and C—H...π interactions, which form a high ordered molecular network.
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  • 76
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    Crystal structure and Hirshfeld surface analysis of (3aSR,6RS,6aSR,7RS,11bSR,11cRS)-2,2-dibenzyl-2,3,6a,11c-tetrahydro-1H,6H,7H-3a,6:7,11b-diepoxydibenzo[de,h]isoquinolin-2-ium trifluoromethanesulfonate (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-08
    Description: In the cation of the title salt, C30H28NO2 +·CF3O3S−, the four tetrahydrofuran rings adopt envelope conformations. In the crystal, pairs of cations are linked by dimeric C—H...O hydrogen bonds, forming two R 2 2(6) ring motifs parallel to the (001) plane. The cations and anions are connected by further C—H...O hydrogen bonds, forming a three-dimensional network structure. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H...H (47.6%), C...H/H...C (20.6%), O...H/H...O (18.0%) and F...H/H...F (9.9%) interactions.
    Electronic ISSN: 2056-9890
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    Synthesis and crystal structure of diaquabis(hexamethylenetramine-κN)bis(thiocyanato-κN)cobalt(II)–hexamethylenetetramine–acetonitrile (1/2/2) (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-08
    Description: The crystal structure of the title solvated coordination compound, [Co(NCS)2(C6H12N4)2(H2O)2]·2C6H12N4·2C2H3N, consists of discrete complexes in which the Co2+ cations (site symmetry overline{1}) are sixfold coordinated by two N-bonded thiocyanate anions, two water molecules and two hexamethylenetetramine (HMT) molecules to generate distorted trans-CoN4O2 octahedra. The discrete complexes are each connected by two HMT solvate molecules into chains via strong O—H...N hydrogen bonds. These chains are further linked by additional O—H...N and C—H...N and C—H...S hydrogen bonds into a three-dimensional network. Within this network, channels are formed that propagate along the c-axis direction and in which additional acetonitrile solvent molecules are embedded, which are hydrogen bonded to the network. The CN stretching vibration of the thiocyanate ion occurs at 2062 cm−1, which is in agreement with the presence of N-bonded anionic ligands. XRPD investigations prove the formation of the title compound as the major phase accompanied by a small amount of a second unknown phase.
    Electronic ISSN: 2056-9890
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  • 78
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    X-ray molecular orbital analysis. II. Application to diformohydrazide, (NHCHO)2 (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-04
    Description: The molecular orbitals (MOs) of diformohydrazide have been determined from the electron density measured by X-ray diffraction. The experimental and refinement procedures are explained in detail and the validity of the obtained MOs is assessed from the crystallographic point of view. The X-ray structure factors were measured at 100 K by a four-circle diffractometer avoiding multiple diffraction, the effect of which on the structure factors is comparable to two-centre structure factors. There remained no significant peaks on the residual density map and the R factors reduced significantly. Among the 788 MO coefficients, 731 converged, of which 694 were statistically significant. The C—H and N—H bond distances are 1.032 (2) and 1.033 (3) Å, respectively. The electron densities of theoretical and experimental MOs and the differences between them are illustrated. The overall features of the electron density obtained by X-ray molecular orbital (XMO) analysis are in good agreement with the canonical orbitals calculated by the restricted Hartree Fock (RHF) method. The bonding-electron distribution around the middle of each bond is well represented and the relative phase relationships of the π orbitals are reflected clearly in the electron densities on the plane perpendicular to the molecular plane. However, differences are noticeable around the O atom on the molecular plane. The orbital energies obtained by XMO analysis are about 0.3 a.u. higher than the corresponding canonical orbitals, except for MO10 to MO14 which are about 0.7 a.u. higher. These exceptions are attributed to the N—H...O′′ intermolecular hydrogen bond, which is neglected in the MO models of the present study. The hydrogen bond is supported by significant electron densities at the saddle points between the H(N) and O′′ atoms in MO7, 8, 14 and 17, and by that of O′′-p extended over H(N) in MO21 and 22, while no peaks were found in MO10, 11, 13 and 15. The electron density of each MO clearly exhibits its role in the molecule. Consequently, the MOs obtained by XMO analysis give a fundamental quantum mechanical insight into the real properties of molecules.
    Electronic ISSN: 2053-2733
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    Layer groups: Brillouin-zone and crystallographic databases on the Bilbao Crystallographic Server (2021)
    International Union of Crystallography
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    Publication Date: 2021-09-24
    Description: The section of the Bilbao Crystallographic Server (https://www.cryst.ehu.es/) dedicated to subperiodic groups contains crystallographic and Brillouin-zone databases for the layer groups. The crystallographic databases include the generators/general positions (GENPOS), Wyckoff positions (WYCKPOS) and maximal subgroups (MAXSUB). The Brillouin-zone database (LKVEC) offers k-vector tables and Brillouin-zone figures of all 80 layer groups which form the background of the classification of their irreducible representations. The symmetry properties of the wavevectors are described applying the so-called reciprocal-space-group approach and this classification scheme is compared with that of Litvin & Wike [(1991), Character Tables and Compatibility Relations of the Eighty Layer Groups and Seventeen Plane Groups. New York: Plenum Press]. The specification of independent parameter ranges of k vectors in the representation domains of the Brillouin zones provides a solution to the problems of uniqueness and completeness of layer-group representations. The Brillouin-zone figures and k-vector tables are described in detail and illustrated by several examples.
    Electronic ISSN: 2053-2733
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  • 80
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    A two-dimensional calcium (II) coordination polymer constructed from 2,2′-[terephthaloylbis(azanediyl)]diacetate: synthesis, structure and properties (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-18
    Description: A new two-dimensional (2D) coordination polymer, namely, poly[[diaqua-[μ4-2,2′-[terephthaloylbis(azanediyl)]diacetato]calcium(II)] monohydrate], {[Ca(C12H10N2O6)(H2O)2]·H2O} n , (I), has been synthesized by the reaction of CaCl2 with 2,2′-[terephthaloylbis(azanediyl)]diacetic acid (H2 L). The title compound was structurally characterized by single-crystal X-ray diffraction analysis, elemental analysis and IR spectroscopy. In the crystal structure of (I), each CaII cation binds to six carboxylate groups from four symmetry-related L 2− dianions. The hexadentate L 2− ligand links four symmetry-related calcium cations into a 2D layer-like structure, which can be simplified as a uninodal SP 2-periodic (3,6)III net with the point symbol (43·63). In the lattice, all layers pack in parallel arrays through weak interlayer hydrogen bonding and π–π interactions. The thermal stability and photoluminescence properties of (I) have been investigated. Thermogravimetric analysis reveals the different thermal stabilities of the two coordinated water molecules due to their different hydrogen-bonding interactions. The title coordination polymer exhibits an excitation-wavelength-dependent fluorescence in the solid state.
    Electronic ISSN: 2053-2296
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    Synthesis, crystal structure and magnetic properties of a one-dimensional Mn2+ complex constructed from (+)-dibenzoyltartaric acid and 2,2′-bipyridine (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-19
    Description: The self-assembly reaction of (+)-dibenzoyltartaric acid (D-H2DBTA) with 2,2′-bipyridine (bpy) and Mn(CH3CO2)2·4H2O yielded a new coordination polymer, namely, catena-poly[[[diaqua(2,2′-bipyridine-κ2 N,N′)manganese(II)]-μ-2,3-bis(benzoyloxy)butanedioato-κ2 O 2:O 3] dihydrate], {[Mn(C18H12O8)(C10H8N2)(H2O)2]·2H2O} n or {[Mn(DBTA)(bpy)(H2O)2]·2H2O} n , (I). Complex (I) has been characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis (TGA) and single-crystal and powder X-ray diffraction. It crystallizes in the orthorhombic space group P212121. In the complex, the Mn2+ cation displays a distorted octahedral {MnO4N2} geometry, formed from two carboxylate O atoms of two DBTA2− ligands, two cis-oriented N atoms from one chelating 2,2′-bipyridine ligand and two trans-oriented O atoms from coordinated water molecules. The polymer displays a 1D chain with an Mn...Mn distance of 9.428 (1) Å. Due to the presence of flexible polycarboxylate and rigid bipyridyl ligands in the molecular structure, a high thermal stability of the complex is attained. The magnetic properties of (I) were analyzed based on the mononuclear Mn2+ model due to the long intramolecular Mn...Mn distance. The zero field splitting (ZFS) contribution in the high-spin Mn2+ cation is almost negligible and there are weak antiferromagnetic couplings between 1D chains [zJ′ = −0.062 (5) cm−1], corresponding to an intermolecular Mn...Mn distance of 7.860 (2) Å.
    Electronic ISSN: 2053-2296
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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    Synthesis, structural, characterization and Hirshfeld analysis of a bisselenide and a zinc complex of a new hemilabile ferrocenylbisphosphane, [Fe{C5H4P(C6H4CH2NMe2-o)2}2] (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-27
    Description: The novel hemilabile ferrocenylbisphosphane 1,1′-bis(bis{2-[(dimethylamino)methyl]phenyl}phosphanyl)ferrocene, [Fe{C5H4P(C6H4CH2NMe2-o)2}2] (1), was synthesized by reacting bis(dichlorophosphanyl)ferrocene, [Fe{C5H4(PCl2)}2] with LiC6H4CH2NMe2-o. Treatment of 1 with gray selenium and anhydrous ZnCl2 yielded, respectively, the bisselenide (ferrocene-1,1′-diyl)bis(bis{2-[(dimethylamino)methyl]phenyl}phosphine selenide), [Fe(C23H28N2PSe)2] (2), and the dizinc complex [μ-1,1′-bis(bis{2-[(dimethylamino)methyl]phenyl}phosphanyl)ferrocene-κ2 N,P:κ2 N′,P′]bis[dichloridozinc(II)] dichloromethane monosolvate, [FeZn2Cl4(C23H28N2P)2]·CH2Cl2 (3), and both have been structurally characterized. Both compounds crystallized with the asymmetric unit containing half a molecule and with the Fe atom on an inversion centre. A Hirshfeld surface analysis indicated that the most significant contributions to the crystal packing of 2 are from H...H (76.7%), C...H/H...C (13.2%) and Se...H/H...Se (7.1%) contacts, while those for 3 are from H...H (62.3%), Cl...H/H...Cl (24.4%) and C...H/H...C (10.9%) contacts.
    Electronic ISSN: 2053-2296
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 83
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    Crystallization, structural characterization and kinetic analysis of a GH26 β-mannanase from Klebsiella oxytoca KUB-CW2-3 (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-20
    Description: β-Mannanase (EC 3.2.1.78) is an enzyme that cleaves within the backbone of mannan-based polysaccharides at β-1,4-linked D-mannose residues, resulting in the formation of mannooligosaccharides (MOS), which are potential prebiotics. The GH26 β-mannanase KMAN from Klebsiella oxytoca KUB-CW2-3 shares 49–72% amino-acid sequence similarity with β-mannanases from other sources. The crystal structure of KMAN at a resolution of 2.57 Å revealed an open cleft-shaped active site. The enzyme structure is based on a (β/α)8-barrel architecture, which is a typical characteristic of clan A glycoside hydrolase enzymes. The putative catalytic residues Glu183 and Glu282 are located on the loop connected to β-strand 4 and at the end of β-strand 7, respectively. KMAN digests linear MOS with a degree of polymerization (DP) of between 4 and 6, with high catalytic efficiency (k cat/K m) towards DP6 (2571.26 min−1 mM −1). The predominant end products from the hydrolysis of locust bean gum, konjac glucomannan and linear MOS are mannobiose and mannotriose. It was observed that KMAN requires at least four binding sites for the binding of substrate molecules and hydrolysis. Molecular docking of mannotriose and galactosyl-mannotetraose to KMAN confirmed its mode of action, which prefers linear substrates to branched substrates.
    Electronic ISSN: 2059-7983
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 84
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    Crystal structure, Hirshfeld surface analysis and DFT studies of tetrakis(μ-3-nitrobenzoato-κ2 O 1:O 1′)bis[(N,N-dimethylformamide-κO)copper(II)] dimethylformamide disolvate (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-26
    Description: The title compound, [Cu2(C7H4NO4)4(C3H7NO)2]·(C3H7NO)2, is a binuclear copper(II) complex located on an inversion center midway between the two copper(II) cations. The asymmetric unit consists of one CuII cation, two 3-nitrobenzoato ligands, and two dimethylformamide (DMF) molecules, one of which coordinates to the CuII cation and one is a solvate molecule. The carboxylate groups of the ligands bridge two CuII cations with a Cu—Cu distance of 2.6554 (6) Å, completing a distorted octahedral O5Cu coordination environment. The dihedral angles between the carboxylate and the aromatic ring planes of the two independent ligands are different from one another, viz. 5.2 (3) and 23.9 (3)°. The three-dimensional structure is consolidated by weak C—H...O interactions and stabilized by π–π stacking interactions between the aromatic rings. The complex and the free ligand were further characterized by Fourier-transform infrared spectroscopy (FT–IR), and the energies of the frontier molecular orbitals of the complex were determined by DFT calculations at the B3LYP/def2-TZVP level of theory.
    Electronic ISSN: 2056-9890
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  • 85
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    Role of pK a in establishing the crystal structures of six hydrogen-bonded compounds of 4-methylquinoline with different isomers of chloro- and nitro-substituted benzoic acids (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-26
    Description: The structures of the six hydrogen-bonded 1:1 compounds of 4-methylquinoline (C10H9N) with chloro- and nitro-substituted benzoic acids (C7H4ClNO4), namely, 4-methylquinolinium 2-chloro-4-nitrobenzoate, C10H10N+·C7H3ClNO4 −, (I), 4-methylquinoline–2-chloro-5-nitrobenzoic acid (1/1), C10H9N·C7H4ClNO4, (II), 4-methylquinolinium 2-chloro-6-nitrobenzoate, C10H9.63N0.63+·C7H3.37ClNO4 0.63−, (III), 4-methylquinolinium 3-chloro-2-nitrobenzoate, C10H9.54N0.54+·C7H3.46ClNO4 0.54−, (IV), 4-methylquinolinium 4-chloro-2-nitrobenzoate, C10H10N+·C7H3ClNO4 −, (V), and 4-methylquinolinium 5-chloro-2-nitrobenzoate, C10H10N+·C7H3ClNO4 −, have been determined at 185–190 K. In each compound, the acid and base molecules are linked by a short hydrogen bond between a carboxy (or carboxylate) O atom and an N atom of the base. The O...N distances are 2.5652 (14), 2.556 (3), 2.5485 (13), 2.5364 (13), 2.5568 (13) and 2.5252 (11) Å, respectively, for compounds (I)–(VI). In the hydrogen-bonded acid–base units of (III) and (IV), the H atoms are each disordered over two positions with O site:N site occupancies of 0.37 (3):0.63 (3) and 0.46 (3):0.54 (4), respectively, for (III) and (IV). The H atoms in the hydrogen-bonded units of (I), (V) and (VI) are located at the N-atom site, while the H atom in (II) is located at the O-atom site. In all the crystals of (I)–(VI), π–π stacking interactions between the quinoline ring systems and C—H...O hydrogen bonds are observed. Similar layer structures are constructed in (IV)–(VI) through these interactions together with π–π interactions between the benzene rings of the adjacent acid molecules. A short Cl...Cl contact and an N—O...π interaction are present in (I), while a C—H...Cl hydrogen bond and a π–π interaction between the benzene ring of the acid molecule and the quinoline ring system in (II), and a C—H...π interaction in (III) are observed. Hirshfeld surfaces for the title compounds mapped over d norm and shape index were generated to visualize the weak intermolecular interactions.
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  • 86
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    The structure of natively iodinated bovine thyroglobulin (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-29
    Description: Thyroglobulin is a homodimeric glycoprotein that is essential for the generation of thyroid hormones in vertebrates. Upon secretion into the lumen of follicles in the thyroid gland, tyrosine residues within the protein become iodinated to produce monoiodotyrosine (MIT) and diiodotyrosine (DIT). A subset of evolutionarily conserved pairs of DIT (and MIT) residues can then engage in oxidative coupling reactions that yield either thyroxine (T4; produced from coupling of a DIT `acceptor' with a DIT `donor') or triiodothyronine (T3; produced from coupling of a DIT acceptor with an MIT donor). Although multiple iodotyrosine residues have been identified as potential donors and acceptors, the specificity and structural context of the pairings (i.e. which donor is paired with which acceptor) have remained unclear. Here, single-particle cryogenic electron microscopy (cryoEM) was used to generate a high-resolution reconstruction of bovine thyroglobulin (2.3 Å resolution in the core region and 2.6 Å overall), allowing the structural characterization of two post-reaction acceptor–donor pairs as well as tyrosine residues modified as MIT and DIT. A substantial spatial separation between donor Tyr149 and acceptor Tyr24 was observed, suggesting that for thyroxine synthesis significant peptide motion is required for coupling at the evolutionarily conserved thyroglobulin amino-terminus.
    Electronic ISSN: 2059-7983
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  • 87
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    Thyroxine hormones visualized by the cryo-EM structure of bovine thyroglobulin (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-29
    Electronic ISSN: 2059-7983
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 88
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    Crystal structures of glycogen-debranching enzyme mutants in complex with oligosaccharides (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-29
    Description: Debranching is a critical step in the mobilization of the important energy store glycogen. In eukaryotes, including fungi and animals, the highly conserved glycogen-debranching enzyme (GDE) debranches glycogen by a glucanotransferase (GT) reaction followed by a glucosidase (GC) reaction. Previous work indicated that these reactions are catalyzed by two active sites located more than 50 Å apart and provided insights into their catalytic mechanisms and substrate recognition. Here, five crystal structures of GDE in complex with oligosaccharides with 4–9 glucose residues are presented. The data suggest that the glycogen main chain plays a critical role in binding to the GT and GC active sites of GDE and that a minimum of five main-chain residues are required for optimal binding.
    Electronic ISSN: 2053-230X
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Physics
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  • 89
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    Crystal structure, Hirshfeld surface and frontier molecular orbital analysis of 9-(3-bromo-4-hydroxy-5-methoxyphenyl)-3,3,6,6-tetramethyl-3,4,5,6,7,9-hexahydro-1H-xanthene-1,8(2H)-dione (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-29
    Description: In the fused ring system of the title compound, C24H27BrO5, the mean plane and maximum deviations of the central pyran ring are 0.0384 (2) and 0.0733 (2) Å, respectively. The cyclohexenone rings both adopt envelope conformations with the tetra-substituted C atoms as flap atoms, whereas the central pyran ring adopts a flattened boat conformation. The central pyran and phenyl substituent rings are almost perpendicular to each other, making a dihedral angle of 89.71 (2)°. In the crystal, pairs of molecules are linked via O—H...O hydrogen bonds, forming inversion dimers with an R 2 2(20) ring motif. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H...H (50.6%), O...H/H...O (22.9%) and C...H/H...C (11.1%) contacts. Quantum chemical calculations for the frontier molecular orbitals were undertaken to determine the chemical reactivity of the title compound.
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  • 90
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    The role of an objective function in the mathematical modelling of wide-angle X-ray diffraction curves of semi-crystalline polymers (2021)
    International Union of Crystallography
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    Publication Date: 2021-09-24
    Description: To decompose a wide-angle X-ray diffraction (WAXD) curve of a semi-crystalline polymer into crystalline peaks and amorphous halos, a theoretical best-fitted curve, i.e. a mathematical model, is constructed. In fitting the theoretical curve to the experimental one, various functions can be used to quantify and minimize the deviations between the curves. The analyses and calculations performed in this work have proved that the quality of the model, its parameters and consequently the information on the structure of the investigated polymer are considerably dependent on the shape of an objective function. It is shown that the best models are obtained employing the least-squares method in which the sum of squared absolute errors is minimized. On the other hand, the methods in which the objective functions are based on the relative errors do not give a good fit and should not be used. The comparison and evaluation were performed using WAXD curves of seven polymers: isotactic polypropylene, polyvinylidene fluoride, cellulose I, cellulose II, polyethylene, polyethylene terephthalate and polyamide 6. The methods were compared and evaluated using statistical tests and measures of the quality of fitting.
    Electronic ISSN: 2053-2733
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  • 91
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    Combinatorial aspects of the Löwenstein avoidance rule. Part I: the independence polynomial (2021)
    International Union of Crystallography
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    Publication Date: 2021-09-24
    Description: According to Löwenstein's rule, Al–O–Al bridges are forbidden in the aluminosilicate framework of zeolites. A graph-theoretical interpretation of the rule, based on the concept of independent sets, was proposed earlier. It was shown that one can apply the vector method to the associated periodic net and define a maximal Al/(Al+Si) ratio for any aluminosilicate framework following the rule; this ratio was called the independence ratio of the net. According to this method, the determination of the independence ratio of a periodic net requires finding a subgroup of the translation group of the net for which the quotient graph and a fundamental transversal have the same independence ratio. This article and a companion paper deal with practical issues regarding the calculation of the independence ratio of mainly 2-periodic nets and the determination of site distributions realizing this ratio. The first paper describes a calculation technique based on propositional calculus and introduces a multivariate polynomial, called the independence polynomial. This polynomial can be calculated in an automatic way and provides the list of all maximal independent sets of the graph, hence also the value of its independence ratio. Some properties of this polynomial are discussed; the independence polynomials of some simple graphs, such as short paths or cycles, are determined as examples of calculation techniques. The method is also applied to the determination of the independence ratio of the 2-periodic net dhc.
    Electronic ISSN: 2053-2733
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  • 92
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    Some New Concepts in the Plate Tectonics Paradigm Fifty Years after Its Inception (2021)
    University of Chicago Press
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    Publication Date: 2021-10-29
    Print ISSN: 0022-1376
    Electronic ISSN: 1537-5269
    Topics: Geosciences
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  • 93
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    Low-temperature phases of dicalcium barium hexakis(propanoate) (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-19
    Description: The structure determinations of phases (II) and (III) of barium dicalcium hexakis(propanoate) {or poly[hexa-μ4-propanoato-bariumdicalcium], [BaCa2(C3H5O2)6] n } are reported at 240 and 130 K, respectively [phase (I) was determined previously by Stadnicka & Glazer (1980). Acta Cryst. B36, 2977–2985; our structure determination of phase (I) at room temperature is included in the supporting information]. In the high-temperature phase, the Ba2+ cation is surrounded by six carboxylate groups in bidentate bridging modes. In the low-temperature phases, five carboxylate groups act in bidentate bridging modes and one acts in a monodentate bridging mode around Ba2+. The Ca2+ cations are surrounded by six carboxylate O atoms in a trigonal antiprism in all the structures. The Ba2+ and Ca2+ cations are underbonded and significantly overbonded, respectively, in all the phases. The bonding of the Ba2+ cation increases slightly at the cost of the bonding of Ca2+ cations during cooling to the low-temperature phases. The phase transitions during cooling are accompanied by ordering of the ethyl chains. In room-temperature phase (I), all six ethyl chains are positionally disordered over two positions in the crossed mode, with additional splitting of the ethyl α- and β-C atoms. In phase (II), on the other hand, there are three disordered ethyl chains, one with positionally disordered ethyl α- and β-C atoms, and the other two with positionally disordered ethyl β-C atoms only, and in the lowest-temperature phase (III) there are four ordered ethyl chains and two disordered ethyl chains with positionally disordered ethyl β-C atoms only.
    Electronic ISSN: 2053-2296
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  • 94
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    Crystal structure and Hirshfeld surface analysis of (Z)-2-{[(2,4-dimethylphenyl)imino]methyl}-4-methylphenol (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-13
    Description: The title compound, C16H17NO, is a Schiff base that exists in the enol–imine tautomeric form and adopts a Z configuration. The molecule is non-planar, with the twisted rings making a dihedral angle of 39.92 (4)°. The intramolecular O—H...N hydrogen bond forms an S(6) ring motif. In the crystal, molecules are linked by C—H...π interactions and very weak π-π stacking interactions also help to consolidate the crystal packing. A Hirshfeld surface analysis was performed to investigate the contributions of different intermolecular contacts within the supramolecular structure. The major contributions are from H...H (65%), C...H (19.2%) and O...H (6.6%) interactions.
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  • 95
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    Isostructural rubidium and caesium 4-(3,5-dinitropyrazol-4-yl)-3,5-dinitropyrazolates: crystal engineering with polynitro energetic species (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-13
    Description: In the structures of the title salts, poly[[μ4-4-(3,5-dinitropyrazol-4-yl)-3,5-dinitropyrazol-1-ido]rubidium], [Rb(C6HN8O8)] n , (1), and its isostructural caesium analogue [Cs(C6HN8O8) n , (2), two independent cations M1 and M2 (M = Rb, Cs) are situated on a crystallographic twofold axis and on a center of inversion, respectively. Mutual intermolecular hydrogen bonding between the conjugate 3,5-dinitopyrazole NH-donor and 3,5-dinitropyrazole N-acceptor sites of the anions [N...N = 2.785 (2) Å for (1) and 2.832 (3) Å for (2)] governs the self-assembly of the translation-related anions in a predictable fashion. Such one-component modular construction of the organic subtopology supports the utility of the crystal-engineering approach towards designing the structures of polynitro energetic materials. The anionic chains are further linked by multiple ion–dipole interactions involving the 12-coordinate cations bonded to two pyrazole N-atoms [Rb—N = 3.1285 (16), 3.2261 (16) Å; Cs—N = 3.369 (2), 3.401 (2) Å] and all of the eight nitro O-atoms [Rb—O = 2.8543 (15)–3.6985 (16) Å; Cs—O = 3.071 (2)–3.811 (2) Å]. The resulting ionic networks follow the CsCl topological archetype, with either metal or organic ions residing in an environment of eight counter-ions. Weak lone pair–π-hole interactions [pyrazole-N atoms to NO2 groups; N...N = 2.990 (3)–3.198 (3) Å] are also relevant to the packing. The Hirshfeld surfaces and percentage two-dimensional fingerprint plots for (1) and (2) are described.
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  • 96
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    Data- and diversity-driven development of a Shotgun crystallization screen using the Protein Data Bank (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-27
    Description: Protein crystallization has for decades been a critical and restrictive step in macromolecular structure determination via X-ray diffraction. Crystallization typically involves a multi-stage exploration of the available chemical space, beginning with an initial sampling (screening) followed by iterative refinement (optimization). Effective screening is important for reducing the number of optimization rounds required, reducing the cost and time required to determine a structure. Here, an initial screen (Shotgun II) derived from analysis of the up-to-date Protein Data Bank (PDB) is proposed and compared with the previously derived (2014) Shotgun I screen. In an update to that analysis, it is clarified that the Shotgun approach entails finding the crystallization conditions that cover the most diverse space of proteins by sequence found in the PDB, which can be mapped to the well known maximum coverage problem in computer science. With this realization, it was possible to apply a more effective algorithm for selecting conditions. In-house data demonstrate that compared with alternatives, the Shotgun I screen has been remarkably successful over the seven years that it has been in use, indicating that Shotgun II is also likely to be a highly effective screen.
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  • 97
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    Ambiguities in and completeness of SAS data analysis of membrane proteins: the case of the sensory rhodopsin II–transducer complex (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-20
    Description: Membrane proteins (MPs) play vital roles in the function of cells and are also major drug targets. Structural information on proteins is vital for understanding their mechanism of function and is critical for the development of drugs. However, obtaining high-resolution structures of membrane proteins, in particular, under native conditions is still a great challenge. In such cases, the low-resolution methods small-angle X-ray and neutron scattering (SAXS and SANS) might provide valuable structural information. However, in some cases small-angle scattering (SAS) provides ambiguous ab initio structural information if complementary measurements are not performed and/or a priori information on the protein is not taken into account. Understanding the nature of the limitations may help to overcome these problems. One of the main problems of SAS data analysis of solubilized membrane proteins is the contribution of the detergent belt surrounding the MP. Here, a comprehensive analysis of how the detergent belt contributes to the SAS data of a membrane-protein complex of sensory rhodopsin II with its cognate transducer from Natronomonas pharaonis (NpSRII–NpHtrII) was performed. The influence of the polydispersity of NpSRII–NpHtrII oligomerization is the second problem that is addressed here. It is shown that inhomogeneity in the scattering length density of the detergent belt surrounding a membrane part of the complex and oligomerization polydispersity significantly impacts on SAXS and SANS profiles, and therefore on 3D ab initio structures. It is described how both problems can be taken into account to improve the quality of SAS data treatment. Since SAS data for MPs are usually obtained from solubilized proteins, and their detergent belt and, to a certain extent, oligomerization polydispersity are sufficiently common phenomena, the approaches proposed in this work might be used in SAS studies of different MPs.
    Electronic ISSN: 2059-7983
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    Nanocrystalline protein domains via salting-out (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-19
    Description: Protein salting-out is a well established phenomenon that in many cases leads to amorphous structures and protein gels, which are usually not considered to be useful for protein structure determination. Here, microstructural measurements of several different salted-out protein dense phases are reported, including of lysozyme, ribonuclease A and an IgG1, showing that salted-out protein gels unexpectedly contain highly ordered protein nanostructures that assemble hierarchically to create the gel. The nanocrystalline domains are approximately 10–100 nm in size, are shown to have structures commensurate with those of bulk crystals and grow on time scales in the order of an hour to a day. Beyond revealing the rich, hierarchical nanoscale to mesoscale structure of protein gels, the nanocrystals that these phases contain are candidates for structural biology on next-generation X-ray free-electron lasers, which may enable the study of biological macromolecules that are difficult or impossible to crystallize in bulk.
    Electronic ISSN: 2053-230X
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Physics
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    New solvates and a salt of the anti-HIV compound etravirine (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-19
    Description: Four new solvates of the anti-HIV compound etravirine [systematic name: 4-({6-amino-5-bromo-2-[(4-cyanophenyl)amino]pyrimidin-4-yl}oxy)-3,5-dimethylbenzonitrile, C20H15BrN6O] with dimethyl sulfoxide (C2H6OS, two distinct monosolvates), 1,4-dioxane (C4H8O2, the 0.75-solvate) and N,N-dimethylacetamide (C4H9NO, the monosolvate), which exhibit conversion to the same anhydrous etravirine phase upon desolvation, and a stable etravirinium oxalate salt {6-amino-5-bromo-4-(4-cyano-2,6-dimethylphenoxy)-2-[(4-cyanophenyl)amino]pyrimidin-1-ium hemioxalate, C20H16BrN6O+·0.5C2O4 2−} were obtained. The crystal structures were solved by single-crystal X-ray diffraction and analyzed by powder X-ray diffraction, and the intermolecular interactions were explored by Hirshfeld surface analysis. Lattice energies were evaluated using the atom–atom force field Coulomb–London–Pauli (AA CLP) approximation, which distributes the total energy as four separate contributions: Coulombic, polarization, dispersion and repulsion. The formation of the solvates and the oxalate salt was further characterized by thermal analysis and IR spectroscopy.
    Electronic ISSN: 2053-2296
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by International Union of Crystallography
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    A new three-dimensional twofold interpenetrated cadmium(II) metal–organic framework: synthesis, structure and photoluminescence properties (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-19
    Description: The design and synthesis of metal–organic frameworks (MOFs) have attracted much interest due to the aesthetics of their crystalline architectures and their potential applications as new functional materials. A new twofold interpenetrated three-dimensional (3D) MOF, namely, poly[[triaqua(μ4-(2R,2′R)-2,2′-{[1,4-phenylenebis(carbonyl)]bis(azanediyl)}dipropionato-κ7 O 1:O 1,O 1′:O 4:O 4,O 4′,O 4′′)(μ3-(2R,2′R)-2,2′-{[1,4-phenylenebis(carbonyl)]bis(azanediyl)}dipropionato-κ3 O 1:O 4:O 4)dicadmium(II)] dihydrate], {[Cd2(C14H14N2O6)2(H2O)3]·2H2O} n , (I), has been synthesized by the reaction of Cd(CH3COO)2·2H2O with the synthesized ligand (2R,2′R)-2,2′-{[1,4-phenylenebis(carbonyl)]bis(azanediyl)}dipropionic acid (H2 L). Single-crystal X-ray diffraction analysis reveals that the carboxylate groups from two crystallographically independent L 2− dianions link the cadmium cations into a one-dimensional helical secondary building unit (SBU). The resulting SBUs are extended into a 3D metal–organic framework via the terephthalamide moiety of the ligand as a spacer. In the crystal, two independent MOFs interpenetrate each other, thus producing a twofold interpenetrated 3D architecture, which shows an unprecedented 2-nodal (7,9)-connected net with the point (Schläfli) symbol (37·46·58)(38·411·516·6). MOF (I) was further characterized by elemental analysis, IR spectroscopy, powder X-ray diffraction and thermogravimetric analysis. The photoluminescence properties and UV–Vis absorption spectrum of (I) have also been investigated. The MOF exhibits enhanced fluorescence emission with a high photoluminescence quantum yield of 31.55% and a longer lifetime compared with free H2 L.
    Electronic ISSN: 2053-2296
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by International Union of Crystallography
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