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ISSN: 2056-9890
Modern approaches and tools for teaching crystallography
Edited by Graciela Diaz de Delgado and Sean Parkin
This virtual issue of Acta Crystallographca Section E collects together articles that can be used as educational materials so that the younger generation may benefit from the knowledge and expertise of experienced crystallographers. Several article focus on teaching symmetry, including a multi-featured tutorial, a periodic-like table of space groups and a textbook example for the arrangement of small molecules and space-group symmetry. Instructional examples and case studies describe how to evaluate the quality of a model, the possible pitfalls of a structure determination and how to tackle whole-molecule disorder. Classroom experiments with artificial sweeteners can be used to introduce younger students to a number of different concepts, aided by freely available online tools. Electron crystallography and dedicated instrumentation in the increasingly important field of electron diffraction are reviewed. Other contributions offer practical advice on using crystallographic software to address different aspects of structure determination, refinement, graphics, analysis etc, including comprehensive examples. This virtual collection also includes articles with a strong teaching component previously published in the journal.
Cover illustration: The global health crisis caused by the COVID-19 pandemic has had a negative impact in our field as many laboratories had to close for long periods of time. However, scientists have continued working remotely, teaching online courses and tutoring students using different electronic meeting platforms.
A compilation of articles with a strong teaching element published since 2018 is presented alongside an overview of the articles in the special issue on this topic.
Knowledge of space groups and the implications of space group symmetry on the physical and chemical properties of solids are pivotal factors in all areas of structural science. The tutorial contains > 200 PowerPoint `slides', in five modules, arranged by crystal class; a sixth module covers special topics. A `credits' module gives the direct addresses of all embedded links. In the tutorial, lattice points build iteratively and interactively with keyclick, and the coordinates of points `pop up' as the unit cell is filled.
`Symmetry and Space Group Tutorial' (by Jerry P. Jasinski and Bruce M. Foxman) provides chemistry students an opportunity to learn space-group diagrams through the peer-tutoring approach.
An easily accessible experimental set-up to grow large single crystals of two sweeteners readily available in supermarkets, erythritol and xylitol, is described. The crystallization of these compounds illustrates the principles of crystallization by evaporation·The crystal-growing experiment is complemented with a simple calorimetric set-up to demonstrate the endothermic nature of the dissolution of the selected sweeteners in a more quantitative approach by measuring the heat of dissolution.
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The title compound represents a textbook example for the arrangement of small molecules and space-group symmetry: in space group Pnma the mirror planes should be occupied to ensure efficient space filling.
CCDC reference: 2203895
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The title amino-carborane {systematic name: closo-9-[4-(dibenzylamino)phenyl]-1,2-dicarbadodecaborane(12)}, C22H29B10N, crystallized with two molecules in the asymmetric unit which are closely related by pseudo-translation symmetry. With the correct unit-cell setting, the structure could be solved and refined without any problems and the final result is a non-disordered structure where all atoms could be localized successfully.
CCDC reference: 2216569
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The crystal structure of the phenylpyrazole insecticide ethiprole is presented along with a step-by-step overview of the model building and refinement process.
CCDC reference: 2235968
A periodic-like table of the 230 space groups, a sweeping overview in the spirit of the periodic table of the chemical elements, is presented. It organizes the 73 symmorphic space groups along two non-orthogonal axes of point group symmetry and general position multiplicity that separates the crystal systems in discrete color fields. The remaining non-symmorphic groups, for reasons of graphical economy, are enumerated as `isotopes' of their parent symmorphic groups.
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A sulfide/selenide solid-solution crystal structure is presented with an emphasis on model building and refinement. Some strategies and statistics for how to assess the accuracy of alternate models are described, including pitfalls, in the context of an instructional example that could be used as an activity in a classroom setting.
CCDC reference: 2231833
Recent years have seen a flurry of research activity in the field of electron diffraction. The introduction of the electron diffractometer, designed to be fully dedicated to its task of providing the best data from electron-diffraction experiments, will be a crucial factor for the continued growth and success of this technology.
We have selected a set of ten diverse crystallography articles to illustrate important moments in the development of our field of science. They are a mixture of `science pull and technology push'. Ten is an arbitrary number and our choice is personal, so many others might have been chosen.
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A large number of structural determinations of compounds containing 2-hydroxy-3,5-dinitrobenzoic acid and its various deprotonated forms, 2-hydroxy-3,5-dinitrobenzoate or 2-carboxy-4,6-dinitrophenolate, are biased. The reason for the bias follows from incorrectly applied constraints or restraints on the bridging hydrogen, which is involved in the intramolecular hydrogen bond between the neighbouring carboxylic/carboxylate and oxo/hydroxy groups. The present article examines the problem of the location and refinement of such a bridging hydrogen in a number of reported compounds. The analysis of the intramolecular hydrogen bonding is also discussed.
The analysis of atom-to-atom and/or residue-to-residue contacts remains a favoured mode of analysing the molecular packing in crystals. This contribution highlights tools for this analysis such as Crystal Explorer and NCIPLOT, which is used to evaluate the nature, i.e. attractive/weakly attractive/repulsive, of specific contacts. This is complemented by a discussion of the calculation of energy frameworks utilizing the latest version of Crystal Explorer. These programs are free of charge and straightforward to use. They complement each other to give a more complete picture of how molecules assemble in molecular crystals.
An outline is given of some basic concepts and applications of symmetry in crystallography. Three specific examples of structure determinations are discussed, for which an understanding of these aspects of symmetry avoids mistakes that can readily be made by reliance on automatic procedures. Topics addressed include pseudo-symmetry, twinning, real and apparent disorder, chirality, and structure validation.
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.
This article aims to encourage practitioners, young and seasoned, by enhancing their structure-determination toolboxes with a selection of tips and tricks on recognizing and handling aspects of data collection, structure modelling and refinement, and the interpretation of results.
Structure solution for pseudo-merohedric twins having roughly equal individual volume fractions are described in detail via worked examples of varying complexity.
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A distorted structure originally described as a monoclinic polymorph of meso-(E,E)-1,1′-[1,2-bis(4-chlorophenyl)ethane-1,2-diyl]bis(phenyldiazene) is better modeled as a threefold superposition of undistorted S,S and R,R enantiomers with a smaller fraction of the meso isomer. All reasoning behind the reassessment is explained in detail.
