Rapid Access to Multicolor Three-Dimensional Printed Chemistry and

Communication pubs.acs.org/jchemeduc

Rapid Access to Multicolor Three-Dimensional Printed Chemistry and Biochemistry Models Using Visualization and Three-Dimensional Printing Software Programs Ken Van Wieren,† Hamel N. Tailor,‡ Vincent F. Scalfani,§ and Nabyl Merbouh*,‡ †

Science Technical Center and ‡Department of Chemistry, Simon Fraser University 8888 University Drive Burnaby, British Columbia V5A 1S6, Canada § University Libraries, Rodgers Library for Science and Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States S Supporting Information *

ABSTRACT: Use of color 3D printers as a visualization tool is described in this paper. Starting from any file depicting a chemical structure, multicolor 3D printed chemical structures can be produced. Most structures were printed in hours, making the entire process from file preparation to tangible model quickly achievable. Chemical structure examples are showcased from organic chemistry, organometallic chemistry, and biochemistry. This paper presents a method of producing multicolor chemistry and biochemistry tangible models using Chimera and Magics molecular visualization and 3D printing software.

KEYWORDS: First-Year Undergraduate/General, Second-Year Undergraduate, Upper-Division Undergraduate, Biochemistry, Inorganic Chemistry, Organic Chemistry, Hands-On Learning/Manipulatives, Stereochemistry, X-ray Crystallography

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INTRODUCTION While chirality and stereochemistry are essential in organic chemistry and biochemistry,1,2 these are often challenging topics to teach in the early years of the chemistry curriculum. The inherent and infinite complexity of the chemical world coupled with the limited size of chemistry model kits available makes it difficult for most instructors to teach the realm of chirality beyond simple molecules.3−6 The use of ball and stick type © XXXX American Chemical Society and Division of Chemical Education, Inc.

chemistry models as visual tools has been indispensable in teaching the concepts of stereochemistry such as R and S, cis and trans, eclipsed and staggered;4 however, as soon as students are confronted with structures in excess of 15 carbon atoms, Received: August 9, 2016 Revised: January 22, 2017

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DOI: 10.1021/acs.jchemed.6b00602 J. Chem. Educ. XXXX, XXX, XXX−XXX

Journal of Chemical Education

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(.cdx) or Chem3D (.mol2) or available as a PDB or CIF format is manipulated to the desired visual representation in Chimera first (e.g., addition and deletion of bonds, atoms sizes, or colors). The chemical structure visualization is then saved as a VRML file (maintains all color) and further processed in Magics software to correct any inconsistencies in the 3D surface such as overlaps or holes. The digital 3D files are then loaded on the 3D printer toolpath software, and fabricated either with or without a support structure depending on the fragility and complexity of the structure.

such models become quickly cumbersome, too large in size, expensive, and, more importantly, subject to mistakes and breaking. The representations of supramolecular threedimensional structures, such as DNA, RNA, and proteins, to name a few, are almost impossible to visualize without advanced software and even harder to model physically. Add to those species the realm of inorganic molecules, extended structures such as unit cells and lattices, and metal complexes in organometallic chemistry, and one can see the vast field of structures that 3D printing can produce to bridge the gap needed to visualize these structures in tangible form. Several excellent reports and reliable methods to fabricate complex chemical structures via 3D printing are available in the literature;7−16 however, the increasing ubiquity of color 3D printers and the need for atom or fragment discrimination within structures has created the necessity for additional protocols to create multicolored 3D printed chemical structures. Additional protocols are important to highlight and document as each method has its own unique benefits. To our knowledge, there has not yet been a detailed article describing and producing 3D printed multicolor molecular structures using a combination of UCSF Chimera17 and Materialise Magics18 software. There has been a recent presentation on of the use of Magics coupled with CCDC Mercury at the 251st ACS National Meeting in San Diego.16 This communication presents one method for generating multicolor 3D printed molecular structures from either chemical structure drawings or crystallographic information files using a combination of Chimera, Magics, and color 3D printers.

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RESULTS

Organic Chemistry Models

When dealing with chemistry models, most students have access to chemistry drawing software packages such as Chemdraw that enable them to draw 2D chemical structures and save them as various chemical structure file formats such as the Chemdraw native file format (.cdx), chemical markup language (.cml), or MDL molfile (.mol). We have found that saving the chemical structures within Chem3D to a SYBLY2 (.mol2) file is a suitable workflow for importing chemical structures into Chimera. Chimera proved to be an easy-to-use tool to modify the structure visualization (e.g., atom radii, bonds, color). Moreover, Chimera allows for the rendering of the structure either as a ball and stick or space filling model, allowing two modes of visualization and structure representation (Figure 2). If the structures were too fragile to print, a quick change in the atom and bond sizes generally fixed the problem without drastically changing the molecular features and geometry. The 3D visualization within Chimera is then saved as a VRML format and subsequently processed in Magics before 3D printing. Other file formats are also available for export within Magics depending upon the 3D file needed for the printer used such as ZPR, ZPD, STL, or VRML. Most 3D printers accept either the STL or VRML format. The Magics software unifies, merges parts, and corrects any defects in the VRML file. An example of this process, also referred to as “water tightening”, is ensuring that all atoms and bonds within the molecules are bound together as one single structure to be 3D printed (Figure 3). In our experience, processing Chimera or CCDC Mercury produced VRML/STL chemical 3D files with software such as Magics is necessary before 3D printing the chemical structures. However, during the revision of this communication, a new version of Jmol (v14.6.4), an open source molecular visualization program, was released that can create 3D printable chemical structure files (VRML and STL) without the need for any postprocessing software before 3D printing.22,23

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METHODS A general workflow used to 3D print the models described in this paper is depicted in Figure 1. ChemDraw is commonly

Inorganic Chemistry Models

One of the challenges with printing metal complexes or lattices resides primarily in the presence of ionic bonds in the structures that represent extended structures with multiple bonds on a single atom. The presence of these bonds and their usual representation as a “dashed” line within the Chimera software make them impossible to 3D print the chemical structure as one unified structure. This problem was successfully addressed by Scalfani et al.13 where the ionic “dashed” bonds were replaced with covalent “solid” bonds in Chimera. Using this method, the usual concept of cis and trans ligands around metals can easily be rendered following this method (Figure 4). The use of Magics is also essential in this case to preserve the watertight properties of the structure and allow it to 3D print.

Figure 1. Flowchart describing the file manipulation leading to the final model print.

available in academic chemistry laboratories, and Chimera is freely available.18 Magics (19.01, 64 bit) is a commercial piece of software; however, it is becoming more widely available in academic 3D fabrication laboratories.19−21 All structures were 3D printed on a ZPrinter 450 or 660 from ZCorporation. Typically, any digital file generated with either Chemdraw B



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Figure 2. Space filling and ball and stick 3D prints of 8,8 armchair nanotube (ChemDraw file used as starting point, print size 8/8.5 cm and 7.3/7.5 cm).

Figure 3. Materialize Magics representation showing all the defects to be fixed for testosterone in a ball and stick model image. The defects are the inverted normals, the bad edges (yellow circles), and the numerous shells detected within the structure.

is straightforward in all cases and is required to be done with proper personal protective equipment and a well-vented area, preferably a fumehood. The integrity of the final products is generally excellent, and the mechanical properties are adequate to be repeatedly handled by students of all ages (Figure 5).

When it comes to organic and inorganic structures, this method is able to generate robust colored models with great visual appeal and applicability to teaching. The use of the powder printers (ZPrinter) allowed for rapid, reliable, repeatable, and scalable (size and number) 3D prints. The only step that proved to be slightly difficult was the extraction of the structures from the printer using the vacuum suction of the unbound powder. This minor difficulty was remediated by either supporting the structure (see Supporting Information) or simply scaling the size of the structures’ bonds. The curing step

Biochemistry Models

For large structures such as proteins, polymers, complex carbohydrates, or nucleic acids, the availability of 3D printable models is limited despite the existence of a large amount of available 3D information in the form of crystal structures.8 C



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Figure 4. Three-dimensional prints and Chimera rendering of cis-dichloro-bis(2-picolylamine)-iron(II) (left) and trans-dichloro-bis(2-picolylamine)iron(II) (right) (CIF file used as starting point, print size 12.2/6.1/5.7 cm).24

Figure 5. Three-dimensional prints of finished products of several metal complexes printed directly from their CIF files. From left to right, ferrocene, hexanitratothorate(IV) ion, and bis-terpyridine ruthenium(II) ion.25

Figure 6. Three-dimensional print of a purine.purine.pyrimidine DNA triplex containing G.GC and T.AT triples (right structure, PDB file used as starting point: 134D, print size 15/11 cm)26 and 3D print of an RNA double helix including uracil−uracil base pairs in an internal loop (left structure, PDB file used as starting point: 205D, print size 15/8 cm).27 D



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Figure 7. Printed 10 base pairs deoxyribose nucleic acid (AGAACCCTGT), with atom differentiation and strand differentiation, and as a single strand (PDB file used as starting point: DNA10, print size 11.6/9 cm).28

Using the large library of PDB (Protein Data Bank) files combined with Chimera, it is possible to print biochemistry models (Figure 6). Chimera combined with Magics allowed for the direct printing of colored structures with either the original atoms differentiated or with specific fragments isolated and differentiated for teaching purposes (Figure 7). When using Magics in dealing with structures exceeding 1000 parts (atoms and bonds), a large loss of data occurred at times. A way to avoid the problem was by opening the VRML file in the Zprinter software (3D print) first and saving the file in the ZPR format before using Magics to produce a “watertight” and ready to go model for 3D printing.

well as Professor Williams (SFU) for his valuable advise on the use of Chimera.

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(1) Eliel, E. L. Teaching organic stereochemistry. J. Chem. Educ. 1964, 41 (2), 73−76. (2) Eliel, E. L.; Wilen, S. H. Stereochemistry of Organic Compounds; Wiley & Sons: New York, 1994. (3) Boukhechem, M.-S.; Dumon, A. To what degree does handling concrete molecular models promote the ability to translate and coordinate between 2D and 3D molecular structure representations? A case study with Algerian students. Chem. Educ. Res. Pract. 2016, 17, 862−877. (4) Stull, A. T.; Gainer, M.; Padalkar, S.; Hegarty, M. Promoting Representational Competence with Molecular Models in Organic Chemistry. J. Chem. Educ. 2016, 93 (6), 994−1001. (5) Siodłak, D. Building Molecular Models Using Screw-On Bottle Caps. J. Chem. Educ. 2013, 90 (9), 1247−1249. (6) Flint, E. B. Teaching Point-Group Symmetry with ThreeDimensional Models. J. Chem. Educ. 2011, 88 (7), 907−909. (7) Griffith, K. M.; de Cataldo, R.; Fogarty, K. H. Do-It-Yourself: 3D Models of Hydrogenic Orbitals through 3D Printing. J. Chem. Educ. 2016, 93 (9), 1586−1590. (8) Meyer, S. C. 3D Printing of Protein Models in an Undergraduate Laboratory: Leucine Zippers. J. Chem. Educ. 2015, 92 (12), 2120− 2125. (9) Grazulis, S.; Sarjeant, A. A.; Moeck, P.; Stone-Sundberg, J.; Snyder, T. J.; Kaminsky, W.; Oliver, A. G.; Stern, C. L.; Dawe, L. N.; Rychkov, D. A.; Losev, E. A.; Boldyreva, E. V.; Tanski, J. M.; Bernstein, J.; Rabeh, W. M.; Kantardjieff, K. A. Crystallographic education in the 21st century. J. Appl. Crystallogr. 2015, 48, 1964−1975. (10) Smiar, K.; Mendez, J. D. Creating and Using Interactive, 3DPrinted Models to Improve Student Comprehension of the Bohr Model of the Atom, Bond Polarity, and Hybridization. J. Chem. Educ. 2016, 93 (9), 1591−1594. (11) Robertson, M. J.; Jorgensen, W. L. Illustrating Concepts in Physical Organic Chemistry with 3D Printed Orbitals. J. Chem. Educ. 2015, 92 (12), 2113−2116. (12) Chen, T.-H.; Lee, S.; Flood, A. H.; Miljanić, O. Š. How to print a crystal structure model in 3D. CrystEngComm 2014, 16 (25), 5488− 5493. (13) Scalfani, V. F.; Vaid, T. P. 3D printed molecules and extended solid models for teaching symmetry and point groups. J. Chem. Educ. 2014, 91 (8), 1174−1180. (14) Scalfani, V. F.; Turner, C. H.; Rupar, P. A.; Jenkins, A. H.; Bara, J. E. 3D Printed Block Copolymer Nanostructures. J. Chem. Educ. 2015, 92 (11), 1866−1870. (15) Rodenbough, P. P.; Vanti, W. B.; Chan, S.-W. 3D-Printing Crystallographic Unit Cells for Learning Materials Science and Engineering. J. Chem. Educ. 2015, 92 (11), 1960−1962. (16) Sarjeant, A.; Wood, P.; Bruno, I.; Li, Y.; Scalfani, V.; O’Grady, S. Enhanced chemical understanding through 3D-printed models.

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CONCLUSION By using a combination of Chimera and Magics software, we were able to demonstrate a method to fabricate complex and robust multicolor 3D printed chemical structure models. The structures created can be handled and displayed allowing for students to gain a better visual understanding of the chemicals they are studying.

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ASSOCIATED CONTENT

* Supporting Information S

The Supporting Information is available on the ACS Publications website at DOI: 10.1021/acs.jchemed.6b00602. All procedures and steps for the file manipulations (PDF, DOCX) Ready to print files (ZIP) Ready to print files (ZIP) Ready to print files (ZIP)

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REFERENCES

AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. ORCID

Nabyl Merbouh: 0000-0002-7835-0989 Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS This work was supported by the Simon Fraser University Dean of Science INSPIRE grant. The authors would like to thank Hawk Ridge Systems for the checking and printing of the parts shown in Figure 6, on a ZPrinter 660 from ZCorporation, as E



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Abstracts of Papers; 251st ACS National Meeting & Exposition, San Diego, CA, United States, March 13−17, 2016; CINF-139. (17) Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. UCSF ChimeraA visualization system for exploratory research and analysis. J. Comput. Chem. 2004, 25, 1605−1612. (18) Materialise Magics: 3D Printing Software; http://software. materialise.com/magics (accessed Dec 2016). (19) University of Michigan. UM3D Digital Media Commons: http:// um3d.dc.umich.edu/learning/ (accessed Dec 2016). (20) California College of The Arts. 3D Printing: https://www.cca. edu/about/administration/studio-resources/eden333 (accessed Dec 2016). (21) Iowa State University College of Engineering Rapid Manufacturing and Prototyping Laboratory: http://www.imse.iastate. edu/rmpl/facilities-and-equipment/ (accessed Dec 2016). (22) Jmol: An Open-Source Java Viewer for Chemical Structures in 3D: http://jmol.sourceforge.net/ (accessed Dec 2016). (23) Scalfani, V. F.; Williams, A. J.; Tkachenko, V.; Karapetyan, K.; Pshenichnov, A.; Hanson, R. M.; Liddie, J. M.; Bara, J. E. Programmatic Conversion of Crystal Structures into 3D Printable Files Using Jmol. J. Cheminf. 2016, 8 (1), 66−73. (24) Törnroos, K. W.; Chernyshov, D.; Hostettler, M.; Bürgi, H. B.Co-crystallized cis and trans isomers of dichlorobis(2-picolylamine)iron(II). Acta Crystallogr., Sect. C: Cryst. Struct. Commun. 2005, C61 (10), m450−m452. (25) Symmetry Resources at Otterbein University: http://symmetry. otterbein.edu/index.html (accessed Dec 2016). (26) Radhakrishnan, I.; Patel, D. J. Solution structure of a purine.purine.pyrimidine DNA triplex containing G.GC and T.AT triples. Structure 1993, 1 (2), 135−152. (27) Baeyens, K. J.; De Bondt, H. L.; Holbrook, S. R. Structure of an RNA double helix including uracil-uracil base pairs in an internal loop. Nat. Struct. Biol. 1995, 2 (1), 56−62. (28) University of Cambridge. The Goodman group webpage: http:// www-jmg.ch.cam.ac.uk/data/molecules/misc/dna10.html (accessed Dec 2016).

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Rapid Access to Multicolor Three-Dimensional Printed Chemistry and

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