3D Printing: Chemistry and Crystal Structures

Transcription

1 3D Printing: Chemistry and Crystal Structures Ian Bruno - Director, Strategic Partnerships The Cambridge Crystallographic Science of 3D Printing SLA 2015 Annual Conference, June 14-16, Boston MA 1

2 The Cambridge Crystallographic Data Centre International Data Repository Archive of crystal structure data High quality scientific database Scientific Software Provider Search/analysis/visualisation tools Scientific applications Collaborative Research Organisation New methodologies Fundamental research Employer of over 60 staff Scientific editors Software developers Applications scientists Cambridge UK Piscataway NJ Established in 1965 UK Registered Charity Financially self-supporting, not-for-profit University Partner Institute 2

3 The Cambridge Structural Database Over 770,000 small-molecule crystal structures Organic and metal-organic compounds Experimentally-determined atom positions Arrangement of molecules in a crystal Links to associated journal articles All structures scientifically enriched by experts Used by around 2,000 institutions worldwide Fifty years of sustainability 3

4 CSD Community Services Deposition, dissemination and preservation of the structure of record no charge to deposit or retrieve no charge for referee and publisher services Free software tools Targeted teaching subsets Mercury - structure visualisation encifer - CIF syntax validation CellCheckCSD - reduced cell searching 4

5 The CSD System and Associated Software Desktop software for advanced search, analysis and visualisation Software applications for applying knowledge to realworld problems Web-based interfaces for wider accessibility Programming interfaces for interoperability and innovation 5

6 Mercury: Crystal Structure Visualisation High impact graphics of molecules and crystal structures interactions and networks crystallographic surfaces display of voids simulation of particle shapes Structure and statistical analysis Over 3,000 citations of primary Mercury references in last 5 years Mercury CSD New Features for the Visualization and Investigation of Crystal Structures Macrae et al. (2008) J. Appl. Cryst., 41, doi: /s

7 Physical Models in Chemistry 7

8 Physical Models in Biology 8

9 Physical Models in Biology PDB 1BNA PDB 41NS 9

10 3D Printing: Selected Bibliography Structural Biology and Computational Chemistry Tactile teaching: Exploring protein structure/function using physical models. Herman et al. (2006) Biochem Mol Biol Educ., 34(4), doi: /bmb Applied Computational Chemistry for the Blind and Visually Impaired. Wedler el al. (2012) J. Chem. Educ., 89 (11), doi: /ed Coarse-grained, foldable, physical model of the polypeptide chain. Chakraborty and Zuckermann (2013) PNAS, 110(33), , doi: /pnas Small-molecule Crystallography: How to print a crystal structure model in 3D. Chen et al. (2014) CrystEngComm, 16, doi: /c4ce00371c Bringing Crystal Structures to Reality by Three-Dimensional Printing. Kitson et al. (2014) Cryst. Growth Des., 14(6), doi: /cg D Printed Molecules and Extended Solid Models for Teaching Symmetry and Point Groups. Scalfani et al. (2014) J. Chem. Educ., 91(8), doi: /ed400887t One-click preparation of 3D print files (*.stl, *.wrl) from *.cif (crystallographic information framework) data using Cif2VRML. Kaminsky et al. (2014) Powder Diffraction, 29(S2), S42-S47. doi: /s

11 Physical vs Virtual Models Educational benefits success in STEM related to skill in visualising 3D spatial relationships no substitute for being able to touch and manipulate models directly Physical models help make concepts more accessible particularly advantageous for the blind and visually impaired 3D printing technology now widely accessible more efficient than building custom models from kits 11

12 NIH 3D Print Exchange 12

13 Chemistry Models Search Engine for 3D printable Models: > 340,000 models indexed 275 printable models tagged as molecule. 13

14 CCDC 3D Printing Aims Harness Mercury s ability to customise models for all crystal structures in the CSD for structures from other sources Simple workflow minimise the number of steps required avoid the need to master multiple packages Exploit both crystallography and chemistry models based on experimental data chemical representation to convey concepts BOTMAA 14

15 Technical Considerations Disconnected entities File formats Over 12 to choose from Many different ways to specify the same object Polygon limits imposed by some services Competing factors Desire for fine detail Need for robust models Characteristics of techniques and materials Access to a 3D printer Network of local 3D printer owners (3D Hubs) Online 3D printing services (Shapeways, Sculpteo) 15

16 User Interface File Formats: STL (monochrome), VRML (colour) 16

17 Learning the Limitations Supporting material required by additive techniques Full colour supported by a more limited range of materials Some materials more brittle than others - plastic better for fine detail, plaster for space-fill Model might print OK but can break during the finishing process Mercury s 3D Print style aims to minimise chances of failure 17

18 Successful Attempts Flexible Plastic, Shapeways, 8cm 19 Sandstone, Sculpteo, 13cm x 9cm x 9cm 71 Sandstone, Sculpteo, 6cm 65 BOSQAB: doi: /cc55fnd LALNIN49: doi: /cctlldc SAHYIK01: doi: /cc8md6g Prices include delivery and tax 18

19 Successful Attempts: Close Up 19

20 Community Feedback Kevin Messner: Miami University All in all, I'd say a round success! Stratasys Dimension 1200es printer using ABS plastic BASF My colleague successfully printed a first molecule without any problems. The machine may not offer the best resolution but it is still a lot of fun! MakerBot Replicator Dual Extruder with Open Source software Example files provided to those running 3D printing facilities Photos Courtesy of Kevin Messner, Miami University Early release of Mercury made available to researchers with access to 3D printers 20

21 Acknowledgements Kevin Messner and fellow speakers CCDC Materials Science Development Team Pete Wood Matthew Towler Clare Macrae Mercury 3.6 due for release Summer D Print functionality Ray tracing enhancements Animation and movie features Available free for anyone to download 21