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Three-Dimensional Printing of Ellipsoidal Structures Using Mercury
Received 00th January 20xx, ,a b a c d Accepted 00th January 20xx Matthew L. Brown* , Ken Van Wieren , Hamel N. Tailor , David Hartling , Anthony Jean and Nabyl Merbouha DOI:
The ability to export structures from Mercury to 3D printing file the same position that is strongly ellipsoidal, in that the formats allows 3D ellipsodal models to be printed quickly and ellipsoidal oxygen is either strongly vibrating or disordered. easily. Since these physical models are similar to the output of Additionally, when teaching vibrational spectroscopy it would Oak Ridge Thermal Ellipsoid Plots (ORTEP), this will allow be useful to be able to show the deformation of electron students, instructors and crystallographers ready access to a density due to the vibrations of the atoms. For example the physical model of X-ray diffraction data normally only found on rotation of a CF3 group can often be seen in the ellipsoids of the computer screen or printed page. the fluorine atoms, as they stretch tangent to the path of rotation. The three-dimensional printing of crystallographic data has been demonstrated to have use in pedagogy, research, and scientific communication.1 A number of crystallography programs now include the ability to convert crystallographic data into printable models. The literature has seen the publication of a number of guides on how to generate printable files using these programs.2 However most of these programs, and to our knowledge, all of these guides, focus on Figure 1 Printed (left, a) Uranyl Peroxo Dicyanoaurate Coordination polymer4 and either space-filling or ball-and-stick crystallographic its Ellipsoidal plot in Mercury (right, b). (Structure printed on a ZPrinter 650 from representations. These models certainly have pedagogical and ZCorporation, approx. 20 cm × 18 cm x 6 cm) communicative uses:1 the ball and stick model excels at conveying connectivity and relative spatial position, and the Recent advances in 3D printing and the ubiquity of 3D printers, space-filling model is excellent for showing steric effects. as well as software support, make it possible to quickly and However, the ellipsoidal model (Figure 1) is often a more easily print ellipsoidal models from crystallographic data. appropriate choice, as in addition to all the information in the Additionally, The Cambridge Crystallographic Data Centre ball and stick model, it also conveys the anisotropic (CCDC) has announced that starting in 2018 the data to print displacement factors. These depict a representation of the ellipsoidal structures will be available in the Cambridge electron density around each atom, which can help expose Structural Database, allowing accesses to numerous structures 3 flaws in the model, show vibrational information and can ready for 3D printing. While there are challenges with printing convey contextual information on the reliability of the atomic ellipsoidal models, namely the fragility of the bonds supporting positions. the atoms, these challenges are not significantly worse than in printing a ball and stick model. Using the common A model that depicts an alcoholic oxygen that is nearly crystallography program Mercury (available gratis from CCDC), spherical conveys very different information from an oxygen in files suitable for importation into 3D printer specific software can be created from a crystallographic information file in very short order and produce a useful and aesthetically pleasing a. Department of Chemistry, Simon Fraser University, 8888 University Drive, physical model. As seen in Figure 2, the ellipsoid offers an Burnaby, BC, V5A 1S6, Canada additional set of information that greatly complements the ball b. Science Technical Center, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada and stick structure as well as the space filling model of any c. Document Solutions, Simon Fraser University, 8888 University Drive, Burnaby, BC, structure. V5A 1S6, Canada d. Hawk Ridge Systems, 318 Martin Avenue, Santa Clara, CA, 95050, USA * Corresponding Author. Electronic Supplementary Information (ESI) available: includes step by step instruction, including illustrations, and further details on the printing process. See DOI:
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File Preparation to be printed must be completely connected: if two halves of a non-coordinated salt are to be printed, for example, it is The first step to printing an ellipsoidal model is to prepare the recommended that they be saved as two separate files and relevant structure or structural fragment in Mercury. A printed separately. The easiest way to do this is to either crystallographic information file (CIF) that includes anisotropic delete or hide the unwanted atoms in Mercury. The colours of displacement parameters is needed. Currently the abbreviated the atoms to be printed should be set and any unwanted files deposited with the Cambridge Structural Database (CSD) bonds caused by close contact should be removed. or the Inorganic Crystal Structure Database (ICSD) lacked the Additionally, any hydrogen or coordination bond that is not anisotropic displacement parameters. However, the CCDC has automatically present in the structure should be added at this announced that starting in 2018 the CSD will include time. anisotropic displacement parameters with select structures.3 The Manage Styles menu has the 3D Print option that will set many of the default options to be closer to what a 3D printer is actually capable of constructing. It is recommended (but not required) to copy the 3D print style into a new entry such as “3D Print Ellipsoid” as to always have the default Mercury 3D printing settings backed up. This can be done in the Style Manager, opened by pressing Manage Styles… beside the style dropdown menu.
In the style manager features of the style can be altered, for example non-hydrogen atoms can be changed from ball and stick to ellipsoid. This is done by selecting the style to edit and pressing the edit button.
Once these operations performed (structure clean-up, settings changed, ellipsoids vs. ball and stick…), the ellipsoid probability level needs to be altered until the atoms are of the sufficient size to distinguish them clearly from the connecting bonds. (We have found the optimal setting to be between 90 and 99%). It is also common to have to alter the radius of the hydrogen atoms to aesthetically match the size of the non- hydrogen atoms. In the structures shown within this paper a value of 0.30–0.35 Å was used. As hydrogens are spherical, they were used to determine the scale of the rest of the model in the 3D printer’s proprietary software, as the printer software was able to easily measure the post-printing size of the spheres. This was used to estimate if the bonds were thick enough to support the weight of the structure. Based on these measurements, the thickness of the bonds may to be increased. A value 0.15–0.35 Å was used in the preparation of the models for this paper, though the exact thickness used will depend on the material used for printing, the size of the ellipsoids that need to be supported as well as the number and length of the supporting bonds. The results of these settings can be seen and compared to the output of the previously detailed2b ball and stick and space filling print methods.
Once the bond thickness is set the size of the ellipse may have to be adjusted so that the atoms are not hidden inside the connecting bonds. This is a balancing act and some Figure 2 Printed structure of 2-Dimethylsulfuranylidene-1,3-indanedione5 as experimentation will be required to see what the optimal mass ellipsoidal (top), ball and stick (middle), and space filling (bottom) forms on a ZPrinter 450 from ZCorporation and on Formlabs 2 SLA printer (inset). of spheres versus thickness of bond ratio, since a thicker bond can support a heavier mass, but that in turn requires a larger Once the selected file is verified to contain anisotropic atom to be seen around the connecting bond. The results can displacement parameters it must be made suitable for three- be previewed at any time by clicking close at the bottom of the dimensional printing. To start with this means that the object
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ellipsoid settings window and pressing apply at the bottom of Conclusions the style settings window.
Once the structure was deemed satisfactory for a trial export, We have demonstrated the ability to produce robust 3D the operation print in 3D was selected in the File menu. Two printed molecular models depicting the anisotropic file formats are available: VRML (Virtual Reality Modeling displacement factors from their respective crystallographic Language, which uses the file extension WRL for historical data. The method has been demonstrated to work across reasons) which will allow color printing and STL various 3D printing systems using several types of media for (STereoLithography) for monochrome printing. In all cases in printing. The models are scalable to produce models of this paper VRML files were used, even when monochrome varying colour and different sizes from palm sized to very structures were printed. There is an option to generate a large to so as to allow one to customize the representation support framework. This was not used in the generation of any to the audience being presented to. Furthermore, these files in this paper rather the support framework generated by ellipsoidal models offer an efficient way of providing a visual the printer specific software was used. The millimeters per representation of the electron density of a molecule in a angstrom scale setting was found to be inconsequential, since more intuitive way than on a computer screen. the printed object was rescaled to the specific printer in the manufacturer’s software. The resulting file can then be imported into any printer specific software and examined for Conflicts of interest 7 flaws. A comparison of different print materials is shown in There are no conflicts to declare. Figure 3.
Acknowledgements This work was supported by the Simon Fraser University Dean Of Science INSPIRE grant. Special thanks to the SFU Science Technical Centre, the SFU Document Solutions & Hawk Ridge Systems for the help printing all the structures shown in this paper.
Figure 3 Thermal ellipsoid structures of (2,2'-Bipyridyl)-dioxo-bis(nitrato-O,O')- uranium6 printed on SLS Printer (Left, white ABS 100% size), and SLA printer in white (middle, 98% size) and black (right, 96% size) . Notes and references
The VRML or STL files are examined for flaws (i.e. bad edges, 1 (a) S. Gražulis, A. A. Sarjeant, P. Moeck, J. Stone-Sundberg, T. J. planar holes, or overlapping triangles) and made watertight Snyder, W. Kaminsky, A. G. Oliver, C. L. Stern, L. N. Dawe, D. A. using software such as Materialize Magics (which is ideal for Rychkov, E. A. Losev, E. V. Boldyreva, J. M. Tanski, J. Bernstein, W. colored VRML files), Formlabs Preform or Fortus Insight used M. Rabeh and K. A. Kantardjieff, J. Appl. Crystallogr., 2015, 48, for the monochrome STL files. 1964–1975. b) P. P. Rodenbough, W. B. Vanti and S.-W. Chan, J.
When the VRML or STL file is imported into Magics all Chem. Educ., 2015, 92, 1960–1962. c) V. F. Scalfani and T. P. Vaid, J. operations revolve around solidifying the model into a single Chem. Educ., 2014, 91, 1174–1180 shell part. This is achieved by using the operations present in 2 (a) P. A. Wood, A. A. Sarjeant, I. J. Bruno, C. F. Macrae, H. E. the Fixing drop down menu repeatedly. The Unify Function is often used first to combine the parts and/or shells into one Maynard-Casely and M. Towler, CrystEngComm, 2017, 19, 690–698. unit. The Fix Wizard is used subsequently with the Follow (b) K. Van Wieren, H. N. Tailor, V. F. Scalfani and N. Merbouh, J. Advice operation. This Follow advice command is selected Chem. Educ., 2017, 94, 964–969. several times until there is only one shell is detected. Once a single shell is detected the part is saved as a VRML or STL file 3 Amy Sarjeant: We have a #CSD3DPrint contest winner!; The depending on the printer.8 Cambridge Crystallographic Data Centre Blog; https://www.ccdc.cam.ac.uk/Community/blog/2017-10-17-we- The STL files were “sliced” and repaired using Preform the have-a-csd3dprint-contest-winner/ 2017-10-17 (Accessed: 2017-10- software included with the Formlabs 2 SLA printer, and Insight 24) the software included with the Fortus 250mc ABS Printer. When the files are uploaded to Preform or Insight the software 4 M. L. Brown, J. S. Ovens and D. B. Leznoff, Dalton Trans., 2017, finds damaged points and auto corrects the file before adding 46, 7169–7180. the support for print. Once the file repaired it is sent to the printer. 5 (a) A. T. Christensen and E. Thom, Acta Cryst. 1971, B27, 581- 586; (b) I. A. Guzei, G. A. Bikzhanova, L. C. Spencer, T. V. Timofeeva,
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T. L. Kinnibrugh and C. F. Campana, Cryst. Growth Des., 2008, 8, 2411–2418.
6 N. W. Alcock, D. J. Flanders and D. Brown, J. Chem. Soc., Dalton Trans., 1985, 1001–1007; (b) N. W. Alcock, D. J. Flanders and D. Brown, Inorg. Chim. Acta, 1984, 94, 279–282.
7 Note: There is a small downside to printing ellipsoidal structures using Mercury. Imperfections in the ellipsoids will be visible at larger print sizes, as seen in Figure 1, particularly on the highly ellipsoidal nitrate oxygen. While the ellipsoids are shown to be smooth on screen, when converted to a printable file these shapes are formed from multiple parts, giving them a ribbed or paneled look. This is present in the generated file, and is not a result of the printer in use. This downside is considered to be minor compared to the advantages of printing in this manner, and it is hoped that future versions of Mercury will correct this. As can be seen when comparing Figures 1 and 3, this effect is less visible when printing at smaller sizes.
8 Note: In some cases the Follow Advice does not complete the unification of the part and the unifying operation may require other steps, the use of the Automatic Fixing command may be required before reselecting the Follow Advice command again to achieve the unification/single shell task.
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