Crystallographic education in the 21st century

Crystals in the community and the classroom

The growing pressure on school curricula has meant crystals and the science of crystallography have been cut from or made optional for many educational programs. This omission is a serious disservice to the history and understanding of modern sciences, given that crystallography underpins many of the greatest advancements in science over the past century, is a critical component of many modern research papers and patents, and has 29 Nobel Prizes awarded in the field. This contribution describes a simple activity to target classroom and public engagement with crystallography, using marshmallows or equivalent sweets/candy to represent atoms and cocktail sticks to represent bonds, together with examples of how crystals are studied and how they are useful. Though it has a simple basis, this activity can be extended in numerous ways to reflect the aims of the demonstrator, and a few of these are described.

From geology to biology: an interdisciplinary course in crystal growth

The authors share experience of teaching an interdisciplinary university course in crystal growth with examples ranging from geology to biology.

This contribution shares experience of teaching an interdisciplinary university course in crystal growth with examples ranging from geology to biology. This is an attempt to combine teaching the basics of the classical and non-classical theories of crystallization with impressive examples of crystals growing around us and in the human body, as well as demonstration of the common phenomena in the growth of minerals in nature, crystalline materials in industry and the laboratory, and biomimetic and stimulus-responsive crystals. Lectures are supported by laboratory exercises. Students can also perform an individual research project and present an oral contribution at a mini-conference. Examples of the topics considered in the course are given, and an extensive list of references to papers and web resources is provided, which may be useful to those who want to implement anything from the authors’ experience.

A new library of 3D models and problems for teaching crystallographic symmetry generated through Blender for use with 3D printers or Sketchfab

A new and growing library of 3D models that can be utilized to illustrate many important concepts in the field of crystallography is presented. These models are accessible in the classroom via computers and smartphones and offer significant advantages over 2D depictions found in crystallography textbooks. Through the use of Blender, a free 3D modeling and animation program, over 100 new models focusing on different aspects of crystallographic education have been created. To simplify distribution/access, all of these models have been uploaded to Sketchfab, a model hosting and viewing web site that works similarly to YouTube. The current set of models is also given as a list in the supporting information. All of these models are free to view in a web browser or through a smartphone application. Additionally, all of these models are freely downloadable through the supporting information and Sketchfab, and users are encouraged to download and modify these models to best suit their needs. This library of models is part of the authors' ongoing outreach program to provide 3D models for free for educational purposes, and the authors offer their services to create additional models and moderate this library as additional requests or critiques are provided.

CRISTAL-ITE: a single-crystal X-ray diffractometer scale model for scientific dissemination

This article presents the design and manufacture of an automated scale model of a four-circle single-crystal X-ray diffractometer that can be used for scientific dissemination. The purpose of this device is to reach out to the wider public and students to introduce them in an entertaining way to one of the laboratory apparatuses to which they do not usually have access, to talk to them about crystallography in the broadest sense, to develop concepts in various fields of science and technology, and to initiate interest and discussions. The main technical aspects of the project are described, with the expectation that such an approach could be useful to anyone involved in scientific dissemination and could be developed for other laboratory equipment and other disciplines. This kind of device can also be the subject of scientific and technological projects in close collaboration with educational institutions.

GESUS, an Interactive Computer Application for Teaching and Learning the Space Groups of Symmetry

This paper describes a digital application designed for learning Space Groups of Symmetry (SGS). It teaches how to recognize the operations performed by the symmetry elements, both point (or 2D) operators (proper and improper rotations, including mirroring, inversion, and other rotoinversions), and space (or 3D) operators (screw axes and glide planes), as well as their combinations with the translations of the lattice. The software applies a 3D space vision to identify the elements of symmetry compatible with the proposed structural models. The symbols of internationally accepted representation are used. The system, class, and space group of the crystal that agree with the proposed model are solved. Two settings are taken into account in the Monoclinic system. The application self-evaluates and assesses the knowledge acquired, allowing each exercise to be re-done until it is correctly completed with the appropriate recommendations. This application constitutes a useful and easy-to-use tool for SGS learning. It is aimed at beginner students of crystallography, with elementary knowledge about elements of symmetry, Bravais lattices, crystal classes, and wallpaper groups.

Stable magic angle spinning with Low-Cost 3D-Printed parts

A 3D-printed double-bearing magic angle spinning (MAS) system was developed with a home-built 4.0 mm MAS nuclear magnetic resonance (NMR) probe at 7 T. Various fused deposition modelling 3D printers were used to produce spinning modules of ignorable materials costs for rotors with a diameter of 7.0, 4.0, and 3.5 mm. High-performance MAS experiments on the 4.0 mm-diameter model using a pencil-type ceramic rotor and 3D-printed drive cap resulted in a high-resolution ¹H NMR signal of silicone grease. The 3.5 mm-diameter MAS system reached a spinning frequency of 23 kHz. Furthermore, 3D-printed inserts were designed for various rotor sizes which can isolate the sample from humidity for a duration of more than a week. Single crystal inserts for MAS rotors of commercial probes can readily be printed using two-color printers. Those developments enable customized low-cost MAS NMR for both adapting existing and manufacturing new probes, respectively.

Teaching periodicity and aperiodicity using 3D-printed tiles and polyhedra

Unit cell and periodicity are key concepts in crystallography and classically were thought to be inherent properties of ordered media like crystals. Aperiodic crystals (including quasicrystals) forced a change of paradigm, affecting the actual definition of a crystal. However, aperiodicity is usually not taught in crystallography undergraduate courses. The emergence of low-cost 3D-printing technologies makes it possible to tackle hands-on learning of the commonly taught crystallography concepts related to periodicity and to introduce in an uncomplicated manner aperiodic crystals and their related concepts that usually are skipped. In this paper, several examples of the use of 3D printing are shown, including 2D and 3D examples of periodic and aperiodic ordered media; these are particularly useful to understand both conventional periodic crystals and quasicrystals. The STL files of the presented models are made available with the paper.

From atoms to bonds, angles and torsions: molecular metrics from crystal space, and two Excel implementations

Values of molecular bond lengths, bond angles and (less frequently) bond torsion angles are readily available from databases, from crystallographic software, and/or from interactive molecular and crystal visualization programs such as Jmol. However, the methods used to calculate these values are less well known. In this paper, the computational methods are described in detail, and live Excel implementations, which permit readers to readily perform the calculations for their own molecular systems, are provided. The methods described apply to both fractional coordinates in crystal space and Cartesian coordinates in Euclidean space (space in which the geometric postulates of Euclid are valid) and are vector/matrix based. In their simplest computational form, they are applied as algebraic expansions which are summed. They are also available in matrix formulations, which are readily manipulated and calculated using the matrix functions of Excel. In particular, their general formulation as metric matrices is introduced. The methods in use are illustrated by a detailed example of the calculations. This contribution provides a significant practical application which can also act as motivation for the study of matrix mathematics with respect to its many uses in chemistry.

Piecewise 3D printing of crystallographic data for post-printing construction

A method of 3D printing complex or challenging structures by breaking them into parts with connectors, printing each part separately, and then assembling the structure post-printing has been developed.

Crystal growth, a research-driven laboratory course

The research-driven laboratory experiment described herein has at its core the individual development of students, combining core subject matter with the opportunity to explore, in a research environment, areas outside of traditional curricula; however, it maintains the pedagogical training for an undergraduate major degree in chemistry and sciences in general. The laboratory can feasibly be implemented in high schools to expose students to an engaging and intellectually fulfilling aspect of chemistry early in their career. This seven-week project is based on the growth and study of crystals and encourages students, from the outset, to conceive, propose, design, plan and carry out their own research on chemicals and conditions of their own choosing. The wide array of laboratory equipment, analytical instrumentation and techniques that the students are potentially exposed to, from micropipettes and optical microscopes to scanning electron microscopy and powder X-ray diffraction, puts these projects on a par with senior capstone research projects. The feedback from the students for the seven years this project has been in operation is almost unanimous in enthusiasm and praise.

Three-dimensional printing of ellipsoidal structures using Mercury

A simple method of 3D printing ellipsoidal crystal structure models from X-ray diffraction data using CCDC Mercury.

Synchrotron-based macromolecular crystallography module for an undergraduate biochemistry laboratory course

This paper describes the introduction of synchrotron-based macromolecular crystallography (MX) into an undergraduate laboratory class. An introductory 2 week experimental module on MX, consisting of four laboratory sessions and two classroom lectures, was incorporated into a senior-level biochemistry class focused on a survey of biochemical techniques, including the experimental characterization of proteins. Students purified recombinant protein samples, set up crystallization plates and flash-cooled crystals for shipping to a synchrotron. Students then collected X-ray diffraction data sets from their crystals via the remote interface of the Molecular Biology Consortium beamline (4.2.2) at the Advanced Light Source in Berkeley, CA, USA. Processed diffraction data sets were transferred back to the laboratory and used in conjunction with partial protein models provided to the students for refinement and model building. The laboratory component was supplemented by up to 2 h of lectures by faculty with expertise in MX. This module can be easily adapted for implementation into other similar undergraduate classes, assuming the availability of local crystallographic expertise and access to remote data collection at a synchrotron source.

Programmatic conversion of crystal structures into 3D printable files using Jmol

Background

Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious. To overcome this limitation, we developed a programmatic method that allows for facile conversion of thousands of crystal structures directly into 3D printable files.

Results

A collection of over 30,000 crystal structures in crystallographic information file (CIF) format from the Crystallography Open Database (COD) were programmatically converted into 3D printable files (VRML format) using Jmol scripting. The resulting data file conversion of the 30,000 CIFs proceeded as expected, however some inconsistencies and unintended results were observed with co-crystallized structures, racemic mixtures, and structures with large counterions that led to 3D printable files not containing the desired chemical structure. Potential solutions to these challenges are considered and discussed. Further, a searchable Jmol 3D Print website was created that allows users to both discover the 3D file dataset created in this work and create custom 3D printable files for any structure in the COD.

Conclusions

Over 30,000 crystal structures were programmatically converted into 3D printable files, allowing users to have quick access to a sizable collection of 3D printable crystal structures. Further, any crystal structure (>350,000) in the COD can now be conveniently converted into 3D printable file formats using the Jmol 3D Print website created in this work. The 3D Print website also allows users to convert their own CIFs into 3D printable files. 3D file data, scripts, and the Jmol 3D Print website are provided openly to the community in an effort to promote discovery and use of 3D printable crystal structures. The 3D file dataset and Jmol 3D Print website will find wide use with researchers and educators seeking to 3D print chemical structures, while the scripts will be useful for programmatically converting large database collections of crystal structures into 3D printable files.