Accessing 3D Printable Structures Online
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Accessing 3D Printable Chemical Structures Online ...

Accessing 3D Printable Chemical Structures Online
We have been exploring routes to create 3D printable chemical structure files (.WRL and .STL). These digital 3D files can be generated directly from crystallographic information files (.CIF) using a variety of software packages such as Jmol. After proper conversion to the .STL (or .WRL) file format, the chemical structures can be fabricated into tangible plastic models using 3D printers. This technique can theoretically be used for any molecular or solid structure. Researchers and educators are no longer limited to building models via traditional piecewise plastic model kits. As such, 3D printed molecular models have tremendous value for teaching and research. As the number of available 3D printable structures continues to grow, there is a need for a robust chemical database to store these files. This presentation will discuss our efforts to incorporate 3D printable chemical structures within the Royal Society of Chemistry’s online compound database.

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Accessing 3D Printable Structures Online Presentation Transcript

  • 1. 1 Accessing 3D Printable Structures Online Vincent F. Scalfani, Antony J. Williams, Robert M. Hanson, Jason E. Bara, Aileen Day, and Valery Tkachenko Science and Engineering Librarian, The University of Alabama vfscalfani@ua.edu 248th ACS National Meeting San Francisco, CA August 13, 2014
  • 2. 2 ...so Chemists build tangible models to overcome this challenge. We have used commercial and/or do-it-yourself techniques for many decades. Visualizing Molecules/Solids in 3D Has Always Been Challenging... Chuang, C. et al. J. Chem. Educ. 2012, 89, 414.; Siodłak, D. J. Chem. Educ. 2013, 90, 1247. Molymod kits Beads Bottle caps!
  • 3. 3 More Recently, Researchers have used 3D Printing Scalfani, V. F. and Vaid, T. P., J. Chem. Educ. 2014, ASAP. DOI: 10.1021/ed400887t 3D printing is an additive manufacturing process capable of producing objects with very high complexity! It is well suited to create any molecular structure. Manufacture object layer by layerconvert to slices (tool path)computer 3D model many different techniques and wide variety of materials available (e.g. thermoplastics (ABS/PLA), UV resins, glued powders, metals, and more)
  • 4. 4 How to Create 3D Printable Molecular Structure Files? 3D printers only understand specific 3D file formats. Two common formats are STL (triangulated mesh surface) and WRL (modeling language text file). STL = single color WRL = full color Scalfani, V. F. and Vaid, T. P., J. Chem. Educ. 2014, ASAP. DOI: 10.1021/ed400887t
  • 5. 5 Many Different Workflows Possible...Here is One Repaired STL file Netfabb Crystallographic information file (.cif) VRML file (.wrl) STL file (.stl) VRML 2.0 file (.wrl) MicroMouse AccuTrans 3D We have also used many variations of this workflow with UCSF Chimera, Python Molecular Viewer and Crystal Impact Diamond with great success... Scalfani, V. F. and Vaid, T. P., J. Chem. Educ. 2014, ASAP. DOI: 10.1021/ed400887t
  • 6. 6 We have used 3D Prints for Teaching Inorganic Chemistry 3D printing has allowed us to create many unique molecular models for teaching inorganic chemistry. Pb3 C6 S6 P6/mmm alkene porphyrin (R = p-tolyl) C1 Scalfani, V. F. and Vaid, T. P., J. Chem. Educ. 2014, ASAP. DOI: 10.1021/ed400887t
  • 7. 7 We have used 3D Prints for Teaching Inorganic Chemistry Cd N N N N N N 2 Cd N N N N N N 2 Fe H2N Cl NH2 Cl Fe Cl H2N NH2 Cl Λ-[Cd(en)3 ]2+ D3 Δ-[Cd(en)3 ]2+ D3 [FeCl2 (C6 H8 N2 )2 ] trans C2h cis C2 Scalfani, V. F. and Vaid, T. P., J. Chem. Educ. 2014, ASAP. DOI: 10.1021/ed400887t
  • 8. 8 Many Others Have Also Been Preparing 3D Printable Files Tim Herman and staff at the MSOE have been creating biomolecular 3D printed models for many years. www.cbm.msoe.edu
  • 9. 9 Many Others Have also been Preparing 3D Printable Files Kitson, P. J. et al. Crystal Growth & Design 2014, 14 (6), 2720.; Chen, T.-H. et al. CrystEngComm 2014, 16 (25), 5488. Amar Flood (Indiana University Bloomington) Ognjen Miljanic (University of Houston) Leroy Cronin (University of Glasgow) Peter Moeck (Portland State University) Marvin Hackert (UT Austin) Henry Rzepa (Imperial College London) ...and many other researchers, teachers, and hobbyists!
  • 10. 10 3D Printing Crystallography Community We started a Listserv [3DP-XTAL] and wiki hosted at UA Libraries for those interested in 3D printing Crystal Structures, http://apps.lib.ua.edu/ blogs/3dp-xtal/
  • 11. 11 3DP-XTAL Community Works Together at IUCr 2014 and last week in Montreal... 3DP-XTAL community for puts together a great display of 3D prints at the IUCr 2014, 23rd Congress on Crystallography Meeting, Montreal, Canada.
  • 12. 12 Where do we Store Files? How to Access Online? • The 3D printing crystallography community is growing rapidly. Many are now starting to generate 3D structure files from crystal structures, where do we store these files? How can we access this information? • There is a learning curve with software used to generate 3D printable files. Repositories overcome this limitation. • Current popular 3D model repositories such as Thingiverse and Trimble 3D Warehouse are not designed for chemical structures — can not search for chemicals via structure, formula, SMILES, and InChI key, etc.
  • 13. 13 Current 3D Model Repositories – NIH 3D Print Exchange New NIH 3D Print Exchange is great — target audience and data is for biomedical applications (e.g., anatomy, labware, protein and macromolecular structures, bacteria, cells). http://3dprint.nih.gov/ Searchable by names and phrases. This seems to work well for the target data.
  • 14. 14 We Need an Online Repository for Molecules and Solids We need a 3D printable structure database for molecules and extended solids that has robust chemical search tools. (e.g., searchable by structure, formula, SMILES, and InChI. Solution? Host 3D printable files on The Royal Society of Chemistry’s (RSC) Crystal Data Repository.
  • 15. 15 RSC Crystal Data Repository RSC Crystal Data Repository (http://api.beta.rsc-us.org/Crystals/v1/cod/) 1 One of four planned new RSC repositories (crystals, compounds, reactions, and spectra) 2 Currently contains: the entire Crystallography Open Database (COD) of 289,395 .cif and 48,022 .hkl files of molecules and extended solids; 3D Printable Files – 31,239 .wrl files (color printing) and 11,732 .stl files. 3 Still in beta mode, can manually browse through files. Repository will soon have user interface that is fully searchable (name, structure, formula, SMILES, InChI, and others) with deposition and crowd-source curation/ annotation platform.
  • 16. 16 RSC Crystal Data Repository – A Closer Look at the Beta
  • 17. 17 How to Create > 30,000 3D Printable Structures...A bit Tricky We used Jmol Scripting to batch convert COD .cif files into .wrl files. Let’s start with molecules, we need to remove unwanted counter ions and solvent molecules first. CHCl3 Cyclic Oligo(p- phenylene oxide) + chloroform Usually not interested in 3D printing any solvent or counter ions. COD ID: 4022031
  • 18. 18 Jmol Script Can Auto Delete Solvent and Counter Ions Counter ions and solvent molecules can be deleted with Jmol scripting: load “G:4022031.cif” info = getProperty(“moleculeInfo”) nmax = getProperty(info,”nAtoms”).max m = getProperty(info,”[select number where nAtoms = nmax]”)[1] print {molecule=m} select on molecule=m delete molecule !=m Selects largest molecule, deletes everything else, then you can export as a WRL file. Cool!
  • 19. 19 Quality of Current Data is“Pretty Good” Selecting only the molecule with greatest # of atoms works in majority of cases. One scenario it will fail is if counter ions/solvent molecules are larger than the compound of interest. Will need to manually curate these: COD ID: 2011077 NBu4 + (53 atoms) acetyl butyrolactonate (16 atoms)
  • 20. 20 How to Create > 30,000 3D Printable Structures...A bit Tricky What about the extended solids? Well, only the asymmetric unit loads by default (unique atom positions). Need to tell software to pack the unit cell. load “G:1010311.cif” {1 1 1} PACKED Bi2 O3 Bismuth Oxide COD ID: 1010311
  • 21. 21 Once We had the WRLs, the STLs are Easy to Prepare Repaired STL file Netfabb Crystallographic information file (.cif) VRML file (.wrl) STL file (.stl) VRML 2.0 file (.wrl) MicroMouse AccuTrans 3D Has excellent batch conversion tools built in.
  • 22. 22 Results–Examples From the RSC Crystal Data Respository (3-Methoxyphenyl) (2,4,6-triisopropylphenyl) methanone Printed on MakerBot 5th Generation COD ID: 2003038
  • 23. 23 Results–Examples From the RSC Crystal Data Respository COD ID: 2007214 natural product, ryanoid derivative.
  • 24. 24 Results–Examples From the RSC Crystal Data Respository Chloro Borazinediamine COD ID: 2237358 Shapeways.com Color Sandstone, $7 dollars Manganese complex COD ID: 2205559 MakerBot 5th Generation PLA Clear
  • 25. 25 Take Home Messages 1 The 3D printing crystallography community is growing rapidly. Scientists are using models for teaching and research. General population has a hobbyist interest in 3D molecules too (Great!). 2 In response to growing community, RSC has started to host 3D files on the RSC Crystal Data Repository – currently contains over 30,000 STL and WRL 3D printable molecules and extended solids. 3 Go 3D print some chemical structures! You can create your own or simply download one from the RSC repository (soon...). No 3D printer? Find a 3D printing service website such as shapeways.com.
  • 26. 26 Acknowledgements Collaborators Antony J. Williams (RSC) Valery Tkachenko (RSC) Aileen Day (RSC) Robert M. Hanson (St. Olaf College) Jason E. Bara (University of Alabama) Funding and Support Royal Society of Chemistry UA Libraries UA Department of Chemistry UA Engineering 3D Lab Slides Will be posted on 3DP-XTAL Wiki http://apps.lib.ua.edu/blogs/3dp-xtal/ How to Contact Me Vincent F. Scalfani Science and Engineering Librarian The University of Alabama vfscalfani@ua.edu