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  • International Union of Crystallography (IUCr)
  • 2015-2019  (98)
  • 2005-2009
  • 1975-1979
  • 1950-1954  (353)
  • 2018  (98)
  • 1954  (353)
Collection
Keywords
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  • 2015-2019  (98)
  • 2005-2009
  • 1975-1979
  • 1950-1954  (353)
Year
  • 1
    Publication Date: 2018-12-08
    Description: Metal–organic frameworks with highly ordered porosity have been studied extensively. In this paper, the effect of framework (pore) disorder on the gas sorption of azole-based isoreticular Cu(II) MOFs with rtl topology and characteristic 1D tubular pore channels is investigated for the first time. In contrast to other isoreticular rtl metal–organic frameworks, the Cu(II) metal–organic framework based on 5-(1H-imidazol-1-yl)isophthalate acid has a crystallographically identifiable disordered framework without open N-donor sites. The framework provides a unique example for investigating the effect of pore disorder on gas sorption that can be systematically evaluated. It exhibits remarkable temperature-dependent hysteretic CO2 sorption up to room temperature, and shows selectivity of CO2 over H2, CH4 and N2 at ambient temperature. The unique property of the framework is its disordered structure featuring distorted 1D tubular channels and DMF-guest-remediated defects. The results imply that structural disorder (defects) may play an important role in the modification of the performance of the material.
    Keywords: metal–organic frameworksT-shaped ligandsdisorderMOFssolid propertieschannel structuresgas separation
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 2
    Publication Date: 2018-12-08
    Description: SPIND (sparse-pattern indexing) is an auto-indexing algorithm for sparse snapshot diffraction patterns (`stills') that requires the positions of only five Bragg peaks in a single pattern, when provided with unit-cell parameters. The capability of SPIND is demonstrated for the orientation determination of sparse diffraction patterns using simulated data from microcrystals of a small inorganic molecule containing three iodines, 5-amino-2,4,6-triiodoisophthalic acid monohydrate (I3C) [Beck & Sheldrick (2008), Acta Cryst. E64, o1286], which is challenging for commonly used indexing algorithms. SPIND, integrated with CrystFEL [White et al. (2012), J. Appl. Cryst. 45, 335–341], is then shown to improve the indexing rate and quality of merged serial femtosecond crystallography data from two membrane proteins, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2 and the NTQ chloride-pumping rhodopsin (CIR). The study demonstrates the suitability of SPIND for indexing sparse inorganic crystal data with smaller unit cells, and for improving the quality of serial femtosecond protein crystallography data, significantly reducing the amount of sample and beam time required by making better use of limited data sets. SPIND is written in Python and is publicly available under the GNU General Public License from https://github.com/LiuLab-CSRC/SPIND.
    Keywords: serial crystallographyX-ray free-electron lasersXFELelectron diffractiondiffract-then-destroydynamical studiesauto-indexing algorithmsBragg peaks
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 3
    Publication Date: 2018-08-09
    Description: The natural sII-type clathrasil chibaite [chemical formula SiO2·(M12,M16), where Mx denotes a guest molecule] was investigated using single-crystal X-ray diffraction and Raman spectroscopy in the temperature range from 273 to 83 K. The O atoms of the structure at room temperature, which globally conforms to space group Fd{\overline 3}m [V = 7348.9 (17) Å3, a = 19.4420 (15) Å], have anomalous anisotropic displacement parameters indicating a static or dynamic disorder. With decreasing temperature, the crystal structure shows a continuous symmetry-lowering transformation accompanied by twinning. The intensities of weak superstructure reflections increase as temperature decreases. A monoclinic twinned superstructure was derived at 100 K [A2/n, V = 7251.0 (17) Å3, a′ = 23.7054 (2), b′ = 13.6861 (11), c′ = 23.7051 (2) Å, β′ = 109.47°]. The transformation matrix from the cubic to the monoclinic system is ai′ = (½ 1 ½ / ½ 0 −½ / ½ −1 ½). The A2/n host framework has Si—O bond lengths and Si—O—Si angles that are much closer to known values for stable silicate-framework structures compared with the averaged Fd{\overline 3}m model. As suggested from band splitting observed in the Raman spectra, the [512]-type cages (one crystallographically unique in Fd{\overline 3}m, four different in A2/n) entrap the hydrocarbon species (CH4, C2H6, C3H8, i-C4H10). The [51264]-type cage was found to be unique in both structure types. It contains the larger hydrocarbon molecules C2H6, C3H8 and i-C4H10.
    Keywords: chibaiteclathrasilshydrocarbonsRaman spectroscopyX-ray diffractionlow temperature
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 4
    Publication Date: 2018-08-09
    Description: Cyclobutane pyrimidine dimer (CPD) photolyases harness the energy of blue light to repair UV-induced DNA CPDs. Upon binding, CPD photolyases cause the photodamage to flip out of the duplex DNA and into the catalytic site of the enzyme. This process, called base-flipping, induces a kink in the DNA, as well as an unpaired bubble, which are stabilized by a network of protein–nucleic acid interactions. Previously, several co-crystal structures have been reported in which the binding mode of CPD photolyases has been studied in detail. However, in all cases the internucleoside linkage of the photodamage site was a chemically synthesized formacetal analogue and not the natural phosphodiester. Here, the first crystal structure and conformational analysis via molecular-dynamics simulations of a class II CPD photolyase in complex with photodamaged DNA that contains a natural cyclobutane pyrimidine dimer with an intra-lesion phosphodiester linkage are presented. It is concluded that a highly conserved bubble-intruding region (BIR) mediates stabilization of the open form of CPD DNA when complexed with class II CPD photolyases.
    Keywords: class II CPD photolyasesDNA repairDNA distortioncyclobutane pyrimidine dimercrystal structure
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 5
    Publication Date: 2018-08-09
    Description: During the past few years, serial crystallography methods have undergone continuous development and serial data collection has become well established at high-intensity synchrotron-radiation beamlines and XFEL radiation sources. However, the application of experimental phasing to serial crystallography data has remained a challenging task owing to the inherent inaccuracy of the diffraction data. Here, a particularly gentle method for incorporating heavy atoms into micrometre-sized crystals utilizing lipidic cubic phase (LCP) as a carrier medium is reported. Soaking in LCP prior to data collection offers a new, efficient and gentle approach for preparing heavy-atom-derivative crystals directly before diffraction data collection using serial crystallography methods. This approach supports effective phasing by utilizing a reasonably low number of diffraction patterns. Using synchrotron radiation and exploiting the anomalous scattering signal of mercury for single isomorphous replacement with anomalous scattering (SIRAS) phasing resulted in high-quality electron-density maps that were sufficient for building a complete structural model of proteinase K at 1.9 Å resolution using automatic model-building tools.
    Keywords: serial crystallographySIRAS phasinglipidic cubic phaseheavy-atom soakingde novo protein structure determination
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 6
    Publication Date: 2018-09-15
    Description: This paper reports on the polymorphism of 2-propyl-1H-benzimidazole (2PrBzIm) induced by temperature change. Upon heating, an irreversible reconstructive-type phase transition at T = 384 K from the ordered form I (P212121) to a new polymorph, form IIHT (Pcam), was observed. The structural transformation between forms I and II involves significant changes in the crystal packing, as well as a key conformational variation around the propyl chain of the molecule. After the first irreversible phase transition, the IIHT form undergoes two further (reversible) phase transitions upon cooling at 361 K (IIRT) and 181 K (IILT). All three phases (forms IIHT, IIRT and IILT) have almost identical crystal packing and, given the reversibility of the conversions as a function of temperature, they are referred to as form II temperature phases. They differ, however, with respect to conformational variations around the propyl chain of 2PrBzIm. Energy calculations of the gas-phase conformational energy landscape of this compound about its flexible bonds allowed us to classify the observed conformational variations of all forms into changes and adjustments of conformers. This reveals that forms I and II are related by conformational change, and that two of the form II phases (HT and RT) are related by conformational adjustment, whilst the other two (RT and LT) are related by conformational change. We introduce the term `conformational phases' for different crystal phases with almost identical packing but showing changes in conformation.
    Keywords: molecular crystalspolymorphismphase transitionsconformational changesenergy minimization
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 7
    Publication Date: 2018-09-15
    Description: It is shown that the average signal-to-noise ratio (SNR) in the three-dimensional electron-density distribution of a sample reconstructed by coherent diffractive imaging cannot exceed twice the square root of the ratio of the mean total number of scattered photons detected during the scan and the number of spatially resolved voxels in the reconstructed volume. This result leads to an upper bound on Shannon's information capacity of this imaging method by specifying the maximum number of distinguishable density distributions within the reconstructed volume when the radiation dose delivered to the sample and the spatial resolution are both fixed. If the spatially averaged SNR in the reconstructed electron density is fixed instead, the radiation dose is shown to be proportional to the third or fourth power of the spatial resolution, depending on the sampling of the three-dimensional diffraction space and the scattering power of the sample.
    Keywords: coherent diffractive imagingsignal-to-noise ratiospatial resolutioninformation capacity
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 8
    Publication Date: 2018-10-09
    Description: Under almost all circumstances, electron diffraction patterns contain information about the phases of structure factors, a consequence of the short wavelength of an electron and its strong Coulombic interaction with matter. However, extracting this information remains a challenge and no generic method exists. In this work, a set of simple analytical expressions is derived for the intensity distribution in convergent-beam electron diffraction (CBED) patterns recorded under three-beam conditions. It is shown that these expressions can be used to identify features in three-beam CBED patterns from which three-phase invariants can be extracted directly, without any iterative refinement processes. The octant, in which the three-phase invariant lies, can be determined simply by inspection of the indexed CBED patterns (i.e. the uncertainty of the phase measurement is ±22.5°). This approach is demonstrated with the experimental measurement of three-phase invariants in two simple test cases: centrosymmetric Si and non-centrosymmetric GaAs. This method may complement existing structure determination methods by providing direct measurements of three-phase invariants to replace `guessed' invariants in ab initio phasing methods and hence provide more stringent constraints to the structure solution.
    Keywords: crystallographic phase problemthree-phase invariantsconvergent-beam electron diffractionstructure determinationenantiomorph ambiguitynanocrystalsdynamical studiesmultiple scattering
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 9
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-10-09
    Description: Grazing-incidence small-angle X-ray scattering (GISAXS) is a powerful technique for measuring the nanostructure of coatings and thin films. However, GISAXS data are plagued by distortions that complicate data analysis. The detector image is a warped representation of reciprocal space because of refraction, and overlapping scattering patterns appear because of reflection. A method is presented to unwarp GISAXS data, recovering an estimate of the true undistorted scattering pattern. The method consists of first generating a guess for the structure of the reciprocal-space scattering by solving for a mutually consistent prediction from the transmission and reflection sub-components. This initial guess is then iteratively refined by fitting experimental GISAXS images at multiple incident angles, using the distorted-wave Born approximation (DWBA) to convert between reciprocal space and detector space. This method converges to a high-quality reconstruction for the undistorted scattering, as validated by comparing with grazing-transmission scattering data. This new method for unwarping GISAXS images will broaden the applicability of grazing-incidence techniques, allowing experimenters to inspect undistorted visualizations of their data and allowing a broader range of analysis methods to be applied to GI data.
    Keywords: X-ray scatteringGISAXSGTSAXSimage healingreconstructiondistorted-wave Born approximation
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 10
    Publication Date: 2018-12-19
    Description: The generation and motion of crystalline defects during plastic deformation are critical processes that determine the mechanical properties of a crystal. The types of defect generated are not only related to the symmetry of a crystal but also associated with the symmetry-breaking process during deformation. Proposed here is a new mathematical framework to capture the intrinsic coupling between crystal symmetry and deformation-induced symmetry breaking. Using a combination of group theory and graph theory, a general approach is demonstrated for the systematic determination of the types of crystalline defect induced by plastic deformation, through the construction of a crystal deformation group and a deformation pathway graph. The types of defect generated in the deformation of a face-centered cubic crystal are analyzed through the deformation pathway graph and compared with experimental observations.
    Keywords: crystal deformationcrystalline defectsgroup theoryCayley graph
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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