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

Abstract

BackgroundThree-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.ResultsA 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.ConclusionsOver 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.

A systematic review of 3D printing in chemistry education – analysis of earlier research and educational use through technological pedagogical content knowledge framework

“…From a TPACK point of view, 3D printing was used as a method for manufacturing parts for instrument customisation, or the design was focused on developing 3D printing processes that are more suitable for educational purposes. (Scalfani et al, 2016) High cost of laboratory instrument parts "This paper proposes an in-house manufactured Ag/AgCl reference electrode that uses some 3Dprinted components in the fabrication process. This electrode is cheap to manufacture ($5 vs. $60−100 CAD for the commercial reference electrode), and the design can be quickly altered due to the 3D printer's capabilities in rapidly printing new electrode shapes to suit different analysts' needs."…”

“…Some articles describe new software that have been developed for supporting 3D printing. Scalfani et al (2016) introduced a Jmol script that enables conversion of crystal structures into 3D printable files. Paukstelis (2018) developed MolPrint3D add on for the Blender software that allows splitting molecules into smaller fragments.…”

Web Apps Come of Age for Molecular Sciences

“…Also, JSmol is often used for building molecules and submitting them to servers for calculations through third-party programs, as in the MolCalc [49] web app for fast quantum mechanics-based estimation of molecular properties using GAMESS [50], whose results are displayed back through JSmol-a very interesting tool for education, outreach, and simple research questions. Further interesting resources built from JSmol are a Crystal Symmetry Explorer, including a tool to create files for 3D printing directly from JSmol [51], web interfaces that connect structures to spectral data display with JSpecView described above, and a powerful molecular editor dubbed "Hack-a-mol", described next.…”

Crystallography and Databases

“…Teaching (Gražulis et al 2015), powder identification (Lutterotti et al 2015), and source of data for computational material science (First & Floudas 2013, Pizzi et al 2016 are among the latest areas where the COD has proved useful as a source of data. Structures from the COD were used to produce 3D-printed models that find use in educational work , Scalfani et al 2016. Moreover, the open nature of the COD allows structure descriptions to be matched against material properties (Pepponi et al 2012), yielding the first open collection of material properties and property-structure relations.…”