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Journal of Applied Crystallography
Journal Prestige (SJR): 1.635

Citation Impact (citeScore): 3
Number of Followers: 7

Hybrid journal (It can contain Open Access articles)
ISSN (Print) 0021-8898 - ISSN (Online) 1600-5767
Published by IUCr

[10 journals]

A multipurpose laboratory diffractometer for operando powder X-ray
diffraction investigations of energy materials
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  Authors: Geßwein; H., Stüble, P., Weber, D., Binder, J.R., Mönig, R.
  Abstract: Laboratory X-ray diffractometers are among the most widespread instruments in research laboratories around the world and are commercially available in different configurations and setups from various manufacturers. Advances in detector technology and X-ray sources push the data quality of in-house diffractometers and enable the collection of time-resolved scattering data during operando experiments. Here, the design and installation of a custom-built multipurpose laboratory diffractometer for the crystallographic characterization of battery materials are reported. The instrument is based on a Huber six-circle diffractometer equipped with a molybdenum microfocus rotating anode with 2D collimated parallel-beam X-ray optics and an optional two-bounce crystal monochromator. Scattered X-rays are detected with a hybrid single-photon-counting area detector (PILATUS 300K-W). An overview of the different diffraction setups together with the main features of the beam characteristics is given. Example case studies illustrate the flexibility of the research instrument for time-resolved operando powder X-ray diffraction experiments as well as the possibility to collect higher-resolution data suitable for diffraction line-profile analysis.
  Keywords: powder X-ray diffraction; instrumentation; operando; energy materials; diffractometers; area detectors
  Citation: urn:issn:1600-5767
  PubDate: 2022-05-16
  DOI: 10.1107/S1600576722003089
  Issue No: Vol. 55, No. 3 (2022)
Proving the correctness of the algorithm for building a crystallographic
space group
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  Authors: Petrauskas; K., Merkys, A., Vaitkus, A., Laibinis, L., Gražulis, S.
  Abstract: An application of formal verification (using the proof assistant Isabelle/HOL) for ensuring the correctness of scientific data processing software in the crystallographic domain is presented. The proposed process consists of writing a pseudocode that describes an algorithm in a succinct but mathematically unambiguous way, then formulating or reusing necessary Isabelle theories and proving algorithm properties within these theories, and finally implementing the algorithm in a practical programming language. Both the formal proof and the semi-formal algorithm analysis are demonstrated on an example of a simple but important algorithm (widely used in crystallographic computing) that reconstructs a space-group operator list from a subset of symmetry operators. The cod-tools software package that implements the verified algorithm is also presented. On the basis of the reported results, it is argued that broader application of formal methods (e.g. formal verification of algorithm correctness) allows developers to improve the reliability of scientific software. Moreover, the formalized (within the proof assistant) domain-specific theory can be reused and gradually extended, thus continuously increasing the automation level of formal algorithm verification.
  Keywords: space-group derivation; crystallographic algorithms; formal verification; theorem proving; Isabelle/HOL
  Citation: urn:issn:1600-5767
  PubDate: 2022-05-16
  DOI: 10.1107/S1600576722003107
  Issue No: Vol. 55, No. 3 (2022)
Bragg coherent diffraction imaging of single 20 nm Pt particles at the
ID01-EBS beamline of ESRF
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  Authors: Richard; M.-I., Labat, S., Dupraz, M., Li, N., Bellec, E., Boesecke, P., Djazouli, H., Eymery, J., Thomas, O., Schülli, T.U., Santala, M.K., Leake, S.J.
  Abstract: Electronic or catalytic properties can be modified at the nanoscale level. Engineering efficient and specific nanomaterials requires the ability to study their complex structure–property relationships. Here, Bragg coherent diffraction imaging was used to measure the three-dimensional shape and strain of platinum nanoparticles with a diameter smaller than 30 nm, i.e. significantly smaller than any previous study. This was made possible by the realization of the Extremely Brilliant Source of ESRF, The European Synchrotron. This work demonstrates the feasibility of imaging the complex structure of very small particles in three dimensions and paves the way towards the observation of realistic catalytic particles.
  Keywords: Bragg coherent diffraction imaging; Extremely Brilliant Source; structure; Pt particles; three-dimensional; nanoscale
  Citation: urn:issn:1600-5767
  PubDate: 2022-05-16
  DOI: 10.1107/S1600576722002886
  Issue No: Vol. 55, No. 3 (2022)
Robustness test of the spacegroupMining model for determining space groups
from atomic pair distribution function data
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  Authors: Lan; L., Liu, C.-H., Du, Q., Billinge, S. J. L.
  Abstract: Machine learning models based on convolutional neural networks have been used for predicting space groups of crystal structures from their atomic pair distribution function (PDF). However, the PDFs used to train the model are calculated using a fixed set of parameters that reflect specific experimental conditions, and the accuracy of the model when given PDFs generated with different choices of these parameters is unknown. In this work, the results of the top-1 accuracy and top-6 accuracy are robust when applied to PDFs of different choices of experimental parameters rmax, Qmax, Qdamp and atomic displacement parameters.
  Keywords: robustness testing; machine learning; data mining; space groups; pair distribution functions
  Citation: urn:issn:1600-5767
  PubDate: 2022-05-16
  DOI: 10.1107/S1600576722002990
  Issue No: Vol. 55, No. 3 (2022)
Towards kilohertz synchrotron coherent diffractive imaging
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  Authors: Hinsley; G.N., Kewish, C.M., van Riessen, G.A.
  Abstract: X-ray coherent diffractive imaging (CDI) techniques have been applied with widespread impact to study nanoscale material properties. New fast framing detectors may reveal dynamics that occur at millisecond timescales. This work demonstrates by simulation that kilohertz synchrotron CDI is possible, by making use of redundant information from static parts of the image field. Reconstruction ambiguities are strongly suppressed by applying a spatiotemporal constraint, obviating the need for slower methods of introducing diversity such as ptychography. The relationship between image fidelity and time resolution is investigated and shows that dynamics an order of magnitude faster can be reconstructed, compared with conventional CDI.
  Keywords: coherent diffractive imaging; coherent X-ray imaging; kHz X-ray imaging; nanoscale dynamics; phase retrieval
  Citation: urn:issn:1600-5767
  PubDate: 2022-05-08
  DOI: 10.1107/S1600576722003466
  Issue No: Vol. 55, No. 3 (2022)
Structure refinement, microstrains and crystallite sizes of
Mg-Ni-phyllosilicate nanoscroll powders
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  Authors: Levin; A., Khrapova, E., Kozlov, D., Krasilin, A., Gusarov, V.
  Abstract: The morphology and structure of (NixMg1−x)3Si2O5(OH)4 synthetic phyllosilicate nanoscrolls have been studied by means of electron microscopy and X-ray powder diffraction. Scrolling of phyllosilicate layers originates from size differences between octahedral and tetrahedral sheets. This strain-energy-driven process raises a number of questions, including the preferred direction of scrolling (along the a or b axis) and the presence of residual microstrain. In order to clarify these points, the structure of (NixMg1−x)3Si2O5(OH)4 phyllosilicates (x = 0, 0.33, 0.5, 0.67, 1) was first described by a monoclinic Cc (9) unit cell, whose parameters decrease with increasing Ni concentration. The Williamson–Hall plots constructed for x = 0 and 0.67 reveal the absence of microstrain, which suggests that scrolling is an effective means of stress relaxation. The sizes of the crystallites were determined by using Rietveld refinement with predefined needle-like models and fundamental parameter fitting with crystallites of arbitrary form. Both approaches show qualitative and quantitative correlation, in terms of aspect ratio, with electron microscopy data. At the same time, the phyllosilicates studied do not demonstrate one preferred direction of scrolling: instead, there might be a mixture of chirality vectors codirected with the a or b axis, with the proportion altering with Ni concentration.
  Keywords: chrysotile; Rietveld refinement; nanocrystallites; transmission electron microscopy (TEM); X-ray diffraction (XRD)
  Citation: urn:issn:1600-5767
  PubDate: 2022-05-08
  DOI: 10.1107/S1600576722003594
  Issue No: Vol. 55, No. 3 (2022)
DISEMM: a tool for the investigation of elasto-plastic behaviour on
polycrystalline samples using X-ray and neutron diffraction
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  Authors: Heldmann; A., Hofmann, M., Hoelzel, M.
  Abstract: The software DISEMM is designed to analyse diffraction data from in situ loading experiments on polycrystalline samples for the determination of single-crystal elastic constants (SECs) and elasto-plastic self-consistent (EPSC) modelling of lattice strains. The SECs can be obtained from powder-diffraction elastic constants using a variety of grain-to-grain interaction models, namely Voigt, Reuss, Hill, Kröner, de Wit and Matthies approaches. The texture of the polycrystalline sample can be taken into account using the orientation distribution function of the grains. For the analysis of two-phase materials, an approach was implemented to calculate the stress transfer between the phases and its impact on the apparent elastic properties. The calculated SECs can then be used as input into the EPSC model, which allows the user to predict the elasto-plastic behaviour for comparison with experimental lattice strain data and to investigate the activation of individual slip systems. For this purpose, critical resolved shear stresses and hardening parameters are adapted iteratively.
  Keywords: single-crystal elastic constants; elasto-plastic self-consistent (EPSC) modelling; DISEMM; mechanical modelling
  Citation: urn:issn:1600-5767
  PubDate: 2022-05-08
  DOI: 10.1107/S1600576722003314
  Issue No: Vol. 55, No. 3 (2022)
Model2SAS: software for small-angle scattering data calculation from
custom shapes
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  Authors: Li; M., Yin, P.
  Abstract: To meet the challenges in resolving the complex morphologies of emergent nanoparticles, a program with a user-friendly graphical user interface has been developed for calculating small-angle scattering curves from custom shapes. The software allows STL-format 3D models, models defined by mathematical functions or combinations of the two as initial input. As a transitional stage, lattice models are generated and the orientation-averaged small-angle scattering data can be calculated using typical spherical harmonics expansion. The validity of the protocol is verified by demonstration models with Protein Data Bank structures and known scattering functions. The software is applied to successfully calculate the scattering curves of a porous spherical shell model where traditional mathematical derivation fails.
  Keywords: small-angle scattering; custom shapes; three-dimensional models; computer programs
  Citation: urn:issn:1600-5767
  PubDate: 2022-05-08
  DOI: 10.1107/S1600576722003600
  Issue No: Vol. 55, No. 3 (2022)
Lower uncertainty bounds of diffraction-based nanoparticle sizes
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  Authors: Noyan; İ.C., Öztürk, H.
  Abstract: A self-consistent analysis is reported of traditional diffraction-based particle size determination techniques applied to synthetic diffraction profiles generated with the Patterson approach. The results show that dimensions obtained from traditional techniques utilizing peak fitting or Fourier analysis for single-crystal nanoparticles have best-case error bounds of around 5%. For arbitrarily shaped particles, lower error magnitudes are possible only if the zeroes of the thickness fringes are used. The errors for sizes obtained by integral-breadth- and Fourier-decomposition-based techniques depend on the shape of the diffracting domains. In the case of integral-breadth analysis, crystal shapes which scatter more intensity into the central peak of the rocking curve have lower size errors. For Fourier-decomposition analysis, crystals which have non-uniform distributions of chord lengths exhibit nonlinearities in the initial ranges of the normalized Fourier cosine coefficient versus column length ( AL versus L) plots, even when the entire rocking curve is used in the decomposition. It is recommended that, in routine analysis, all domain size determination techniques should be applied to all reflections in a diffraction pattern. If there is significant divergence among these results, the `average particle size(s)' obtained might not be reliable.
  Keywords: diffraction; particle size determination; Scherrer approach; integral breadth; Fourier analysis
  Citation: urn:issn:1600-5767
  PubDate: 2022-04-29
  DOI: 10.1107/S1600576722002564
  Issue No: Vol. 55, No. 3 (2022)
Experimental and simulation study on hydrogen-bond-induced crystallization
of spherical ammonium dinitramide
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  Authors: Li; J., Gong, L., Lan, Y., Zeng, T., Li, D., Li, J., Yang, R.
  Abstract: The effects of hydrogen bonding between solvents (ethanol, ethanol–acetone and ethanol–ethyl acetate) and ammonium dinitramide (ADN) crystal faces on the morphology of ADN are studied experimentally and by molecular dynamics (MD) simulation. Scanning electron microscopy shows that ADN recrystallized from ethanol, ethanol–acetone and ethanol–ethyl acetate takes the form of a slice, a sheet aggregate and a sphere, respectively. The MD results show that the order of the standard deviation (Edev) of the hydrogen-bonding energy (Eb) in the three solvent systems is as follows: ethanol > ethanol–acetone > ethanol–ethyl acetate. The larger the Edev, the larger the difference of each crystal plane size. The radial distribution function reveals that the carbonyl group of ethyl acetate promotes hydrogen-bond formation between O atoms in the nitro groups of ADN and H atoms in ethanol; meanwhile the O atom in the C—O bond of ethyl acetate forms a hydrogen bond with an H atom in ADN. Therefore, the Edev of each crystal face is further lowered, and finally a spherical ADN is obtained.
  Keywords: ammonium dinitramide; solvents; morphology; molecular dynamics
  Citation: urn:issn:1600-5767
  PubDate: 2022-04-29
  DOI: 10.1107/S1600576722003077
  Issue No: Vol. 55, No. 3 (2022)
CELLOPT: improved unit-cell parameters for electron diffraction data of
small-molecule crystals
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  Authors: Gruene; T., Clabbers, M.T.B., Luebben, J., Chin, J.M., Reithofer, M.R., Stowasser, F., Alker, A.M.
  Abstract: Electron diffraction enables structure determination of organic small molecules using crystals that are too small for conventional X-ray crystallography. However, because of uncertainties in the experimental parameters, notably the detector distance, the unit-cell parameters and the geometry of the structural models are typically less accurate and precise compared with results obtained by X-ray diffraction. Here, an iterative procedure to optimize the unit-cell parameters obtained from electron diffraction using idealized restraints is proposed. The cell optimization routine has been implemented as part of the structure refinement, and a gradual improvement in lattice parameters and data quality is demonstrated. It is shown that cell optimization, optionally combined with geometrical corrections for any apparent detector distortions, benefits refinement of electron diffraction data in small-molecule crystallography and leads to more accurate structural models.
  Keywords: electron diffraction; precision of unit-cell parameters; crystal structure determination; compensation for experimental and instrumental errors
  Citation: urn:issn:1600-5767
  PubDate: 2022-04-29
  DOI: 10.1107/S160057672200276X
  Issue No: Vol. 55, No. 3 (2022)
3D-printed equipment to decouple (powder) X-ray diffraction sample
preparation and measurement
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  Authors: Fuß; F., Rieckert, M., Steinhauer, S., Liesegang, M., Thiele, G.
  Abstract: An alternative storage method to separate sample preparation from single-crystal and powder X-ray diffraction measurements at home source diffractometers is described. For single crystals, a setup is presented which allows storage of preselected crystals under cryogenic and ambient temperatures. For powders, a disposable sample holder is introduced. The method is suitable for the storage of air- and moisture-sensitive samples. Equipment made of biodegradable polylactic acid is produced by 3D printing and can be adapted to individual needs. As 3D printers are widely available at research institutions nowadays, models of the presented equipment are provided for the reader to allow easy reproduction.
  Keywords: 3D printing; cryo-storage; single crystals; powders; diffraction; home sources
  Citation: urn:issn:1600-5767
  PubDate: 2022-04-29
  DOI: 10.1107/S160057672200293X
  Issue No: Vol. 55, No. 3 (2022)
Classification of diffraction patterns using a convolutional neural
network in single-particle-imaging experiments performed at X-ray
free-electron lasers
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  Authors: Assalauova; D., Ignatenko, A., Isensee, F., Trofimova, D., Vartanyants, I.A.
  Abstract: Single particle imaging (SPI) at X-ray free-electron lasers is particularly well suited to determining the 3D structure of particles at room temperature. For a successful reconstruction, diffraction patterns originating from a single hit must be isolated from a large number of acquired patterns. It is proposed that this task could be formulated as an image-classification problem and solved using convolutional neural network (CNN) architectures. Two CNN configurations are developed: one that maximizes the F1 score and one that emphasizes high recall. The CNNs are also combined with expectation-maximization (EM) selection as well as size filtering. It is observed that the CNN selections have lower contrast in power spectral density functions relative to the EM selection used in previous work. However, the reconstruction of the CNN-based selections gives similar results. Introducing CNNs into SPI experiments allows the reconstruction pipeline to be streamlined, enables researchers to classify patterns on the fly, and, as a consequence, enables them to tightly control the duration of their experiments. Incorporating non-standard artificial-intelligence-based solutions into an existing SPI analysis workflow may be beneficial for the future development of SPI experiments.
  Keywords: convolutional neural networks; single-particle imaging; classification of diffraction patterns; X-ray free-electron lasers
  Citation: urn:issn:1600-5767
  PubDate: 2022-04-22
  DOI: 10.1107/S1600576722002667
  Issue No: Vol. 55, No. 3 (2022)
Determination of the specific surface of a granular porous material by the
USAXS–SAXS intensity of a loosely packed powder sample
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  Authors: Ciccariello; S.
  Abstract: Developing an earlier suggestion by Spalla, Lyonnard & Testard [J. Appl. Cryst. (2003), 36, 338–347], it is shown that the porosity and the specific surface of a porous material can be determined by the small- and ultra-small-angle X-ray scattering (SAXS and USAXS, respectively) intensity of a sample made up of loosely packed and rather large grains of the material, provided the Porod plot of the intensity shows two plateaux within the range of the explored scattering vectors. To this end, it is necessary to consider the system geometrically as formed by three phases: the bulk matter, the macropores and the micropores.
  Keywords: small-angle X-ray scattering; ultra-small-angle X-ray scattering; SAXS and USAXS theory; three-phase systems; specific interphase surface area; porosity; amorphous materials; powder systems
  Citation: urn:issn:1600-5767
  PubDate: 2022-04-22
  DOI: 10.1107/S1600576722002710
  Issue No: Vol. 55, No. 3 (2022)
Efficiency enhancement in scintillation detectors by changing the
valence-band electron density and crystal structure of the scintillation
material
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  Authors: Couch; C., Halliwell, E., Begum, R., Ali, G., Khan, T., Maqbool, M.
  Abstract: Scintillation detectors are commonly used for detecting radiation in various situations. NaI:Tl, CsI:Tl, BaF2 and CaF2:Eu are a few compounds that act as scintillation crystals for these detectors. The efficiency of a scintillation detector is one of the most important factors in improving the detector's performance. The present work shows that the efficiency of a scintillation detector can be increased by increasing the valence-band electron density as a result of changing the crystal structure of the scintillating material. This will enhance the image quality of all imaging techniques based upon scintillation detectors. The results reveal that by changing the structure of the crystal from simple cubic to body-centered cubic or face-centered cubic the efficiency of the detector increases. The packing of more atoms into the crystal increases the number of atoms per unit cell and the density of the crystal. It is also observed that the increase in the number of atoms per unit cell and the density of the crystal will equally increase the efficiency of the detector. The additional atoms from changing the crystal structure contribute more valence-band electrons, which allows for a higher chance of interaction between the incoming radiation and the valence-band electrons to absorb more radiation energy.
  Keywords: scintillation detectors; image quality; crystal structure; valence bands; efficiency
  Citation: urn:issn:1600-5767
  PubDate: 2022-04-22
  DOI: 10.1107/S160057672200005X
  Issue No: Vol. 55, No. 3 (2022)
Scipion-ED: a graphical user interface for batch processing and analysis
of 3D ED/MicroED data
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  Authors: Bengtsson; V.E.G., Pacoste, L., Rosa-Trevin, J.M. de la, Hofer, G., Zou, X., Xu, H.
  Abstract: Three-dimensional electron diffraction (3D ED)/microcrystal electron diffraction (MicroED) techniques are gaining in popularity. However, the data processing often does not fit existing graphical user interface software, instead requiring the use of the terminal or scripting. Scipion-ED, described in this article, provides a graphical user interface and extendable framework for processing of 3D ED/MicroED data. An illustrative project is described, in which multiple 3D ED/MicroED data sets collected on tetragonal lysozyme were processed with DIALS through the Scipion-ED interface. The ability to resolve unmodelled features in the electrostatic potential map was compared between three strategies for merging data sets.
  Keywords: electron diffraction; 3D ED; MicroED; data processing; computer programs
  Citation: urn:issn:1600-5767
  PubDate: 2022-04-22
  DOI: 10.1107/S1600576722002758
  Issue No: Vol. 55, No. 3 (2022)