Authors of a paper that includes a new crystal-structure determination are expected to not only report the structural results of inter­est and their inter­pretation, but are also expected to archive in computer-readable CIF format the experimental data on which the crystal-structure analysis is based. Additionally, an IUCr/checkCIF validation report will be required for the review of a submitted paper. Such a validation report, automatically created from the deposited CIF file, lists as ALERTS not only potential errors or unusual findings, but also suggestions for improvement along with inter­esting information on the structure at hand. Major ALERTS for issues are expected to have been acted on already before the submission for publication or discussed in the associated paper and/or commented on in the CIF file. In addition, referees, readers and users of the data should be able to make their own judgment and inter­pretation of the underlying experimental data or perform their own calculations with the archived data. All the above is consistent with the FAIR (findable, accessible, inter­operable, and reusable) initiative [Helliwell (2019). Struct. Dyn. 6, 05430]. Validation can also be helpful for less experienced authors in pointing to and avoiding of crystal-structure determination and inter­pretation pitfalls. The IUCr web-based checkCIF server provides such a validation report, based on data uploaded in CIF format. Alternatively, a locally installable checkCIF version is available to be used iteratively during the structure-determination process. ALERTS come mostly as short single-line messages. There is also a short explanation of the ALERTS available through the IUCr web server or with the locally installed PLATON/checkCIF version. This paper provides additional background information on the checkCIF procedure and additional details for a number of ALERTS along with options for how to act on them.

https://journals.iucr.org/e/issues/2020/01/00/su5533/su5533.pdf

checkCIF validation ALERTS: what they mean and how to respond.

An X-ray scattering beamline for studying dynamics

X-ray computed tomography (CT) can reveal the internal details of objects in three dimensions non-destructively. In this Primer, we outline the basic principles of CT and describe the ways in which a CT scan can be acquired using X-ray tubes and synchrotron sources, including the different possible contrast modes that can be exploited. We explain the process of computationally reconstructing three-dimensional (3D) images from 2D radiographs and how to segment the 3D images for subsequent visualization and quantification. Whereas CT is widely used in medical and heavy industrial contexts at relatively low resolutions, here we focus on the application of higher resolution X-ray CT across science and engineering. We consider the application of X-ray CT to study subjects across the materials, metrology and manufacturing, engineering, food, biological, geological and palaeontological sciences. We examine how CT can be used to follow the structural evolution of materials in three dimensions in real time or in a time-lapse manner, for example to follow materials manufacturing or the in-service behaviour and degradation of manufactured components. Finally, we consider the potential for radiation damage and common sources of imaging artefacts, discuss reproducibility issues and consider future advances and opportunities. This Primer on X-ray computed tomography explores the different experimental configurations for three-dimensional data acquisition as well as the fundamentals of three-dimensional data reconstruction, segmentation and analysis with examples across the physical and life sciences.

/pdf/x-ray-computed-tomography-2vke1xkskf.pdf

X-ray computed tomography

Absorption-contrast x-ray imaging serves to visualize the variation in x-ray attenuation within the volume of a given sample, whereas phase contrast allows one to visualize variations in x-ray refractive index. The former imaging mechanism has been well known and widely utilized since the time of Rontgen’s Nobel prize winning work, whereas the latter mechanism—sought for, but not found, by Rontgen himself—has laid the foundation for a revolution in x-ray imaging which is the central topic of this review. We consider the physical imaging mechanisms underlying both absorption contrast and phase contrast, together with the associated inverse problem of how one may obtain quantitative two- or three-dimensional information regarding a sample, given one or more phase-contrast images of the same. Practical questions are considered, regarding optimized phase-contrast imaging geometries as a function of detector resolution, source size, x-ray spectrum, and dose. Experimental examples pertaining to biomedical appli...

Refracting Röntgen’s rays: Propagation-based x-ray phase contrast for biomedical imaging

Highly porous metal–organic frameworks (MOFs), which have undergone exciting developments over the past few decades, show promise for a wide range of applications. However, many studies indicate that they suffer from significant stability issues, especially with respect to their interactions with water, which severely limits their practical potential. Here we demonstrate how the presence of ‘sacrificial’ bonds in the coordination environment of its metal centres (referred to as hemilability) endows a dehydrated copper-based MOF with good hydrolytic stability. On exposure to water, in contrast to the indiscriminate breaking of coordination bonds that typically results in structure degradation, it is non-structural weak interactions between the MOF’s copper paddlewheel clusters that are broken and the framework recovers its as-synthesized, hydrated structure. This MOF retained its structural integrity even after contact with water for one year, whereas HKUST-1, a compositionally similar material that lacks these sacrificial bonds, loses its crystallinity in less than a day under the same conditions. The promise shown by metal–organic frameworks for various applications is somewhat dampened by their instability towards water. Now, an activated MOF has shown good hydrolytic stability owing to the presence of weak, sacrificial coordination bonds that act as a ‘crumple zone’. On hydration, these weak bonds are cleaved preferentially to stronger coordination bonds that hold the MOF together.

/pdf/hydrolytic-stability-in-hemilabile-metal-organic-frameworks-4b4kx2sb99.pdf

Hydrolytic stability in hemilabile metal–organic frameworks

One of the most useful characteristics of synchrotron radiation is the wide spectral distribution of the source. For applications involving tuned monochromatic beams it is often helpful to predict the x‐ray optical characteristics of a sample or the beam line optics at a particular wavelength. In contrast to this desire stands the fact that tabulated values for the optical parameters of interest are generally available only at wavelengths corresponding to typical x‐ray tube sources. We have developed a suite of fortran programs which calculate photoabsorption cross sections and atomic scattering factors for materials of arbitrary, uniform composition or for arbitrary layered materials. Further, the suite includes programs for calculation of x‐ray diffraction or reflection from such materials. These programs are of use for experimental planning, data analysis, and predictions of performance of beam line optical elements.

P. L. Cowan

Papers

A suite of programs for calculating x‐ray absorption, reflection, and diffraction performance for a variety of materials at arbitrary wavelengths