CoolMolecules: Teaching Molecular Structure with the Cambridge Structural Database

1. CoolMolecules: Teaching Molecular Structure with the Cambridge Structural Database Robert M. Hanson, Melanie Casavant, and Michael McGuan St. Olaf College, Northfield, MN http://www.stolaf.edu/people/hansonr Scot Wherland Washington State University http://www.chem.wsu.edu/Faculty/wherland.html 20th Biennial Conference on Chemical Education Indiana University July 30, 2008

2. Goals of This Presentation • Background: “Data-Driven” Chemistry • Origin of the CoolMolecules Project • Goals of the Project • Project Outcomes • Future Directions

3. Background: “Data-Driven” Chemistry generate data analyze data extrapolate hypotheses generate hypotheses

4. Background: “Data-Driven Chemistry” • Start with raw data • Transform the data into meaningful information • Create actual paper 3D model R. M. Hanson, S. A. Bergman, "Data-Driven Chemistry: Making Molecular Models (Literally) from Electron Diffraction Data”, J. Chem. Educ.1994, 150

5. Background: “Molecular Origami” • St. Olaf College Chemistry 123 • Start with hand-held models • Develop concepts as needed http://www.stolaf.edu/people/hansonr/mo/acs2001

6. Background: “Molecular Origami” normal quartz http://www.stolaf.edu/people/hansonr/mo/acs2001/models.htm

7. Background: “Molecular Origami” http://www.stolaf.edu/people/hansonr/mo/acs2001/models.htm

8. Background: “Molecular Origami” http://www.stolaf.edu/people/hansonr/mo/acs2001/models.htm

9. Background: “Molecular Origami” http://www.stolaf.edu/depts/chemistry/mo/struc/data/f-xef8a.mol

10. Background: “Molecular Origami” http://www.stolaf.edu/depts/chemistry/mo/struc/data/f-xef8a.pdf

11. Background: “Molecular Origami” 150,000,000:1 hydrodroxyapatite model (New Museum of Contemporary Art, New York, NY) http://www.stolaf.edu/people/hansonr/mo

12. Background: focus on analysis analyze data (identify trends) generate data (experimental) generate hypothesis (explain shapes and trends) extrapolate hypothesis (predict shapes)

13. Origin of the Project: BCCE17 Molecular Origami + Crystal Structure Database (Bob Hanson) (Scot Wherland) = CoolMolecules: A Molecular Structure Explorer http://www.stolaf.edu/depts/chemistry/mo/struc

14. Goals of the CoolMolecules Project • Expand Scot’s database using CSD • Include foldable “Molecular Origami” models • Create a widely available, easy interface for searching the experimental data • Provide strategies for making the database useful in a classroom setting

15. CoolMolecules Project Outcomes: the site http://www.stolaf.edu/depts/chemistry/mo/struc

16. CoolMolecules Project Outcomes: methods 92 electron diffraction (includes all known structures < 1950) 11 infrared spectroscopy 39 microwave spectroscopy 29 neutron diffraction 3 raman spectroscopy 18 ultraviolet spectroscopy 774 x-ray diffraction (733 from CSD) ----- ----------------------- 962 total structures http://www.stolaf.edu/depts/chemistry/mo/struc

17. CoolMolecules Project Outcomes: interface http://www.stolaf.edu/depts/chemistry/mo/struc

18. CoolMolecules Project Outcomes: results http://www.stolaf.edu/depts/chemistry/mo/struc

19. CoolMolecules Project Outcomes: options http://www.stolaf.edu/depts/chemistry/mo/struc

20. CoolMolecules Project Outcomes: selection http://www.stolaf.edu/depts/chemistry/mo/struc

21. CoolMolecules Search Results: tabulation http://www.stolaf.edu/depts/chemistry/mo/struc

22. CoolMolecules Search Results: visualization http://www.stolaf.edu/depts/chemistry/mo/struc

23. CoolMolecules Search Results: all to scale http://www.stolaf.edu/depts/chemistry/mo/struc

24. CoolMolecules Search Results: all H atoms are present http://www.stolaf.edu/depts/chemistry/mo/struc

25. CoolMolecules Search Results: Jmol allows easy exploration http://www.stolaf.edu/depts/chemistry/mo/struc

26. CoolMolecules Search Results: just double-click for distances http://www.stolaf.edu/depts/chemistry/mo/struc

27. CoolMolecules Search Results: …or angles http://www.stolaf.edu/depts/chemistry/mo/struc

28. Just a few of the “cool” structures: http://www.stolaf.edu/depts/chemistry/mo/struc

29. Just a few of the “cool” structures: http://www.stolaf.edu/depts/chemistry/mo/struc

30. Just a few of the “cool” structures: http://www.stolaf.edu/depts/chemistry/mo/struc

31. Just a few of the “cool” structures: http://www.stolaf.edu/depts/chemistry/mo/struc

32. Just a few of the “cool” structures: http://www.stolaf.edu/depts/chemistry/mo/struc

33. Just a few of the “cool” structures: http://www.stolaf.edu/depts/chemistry/mo/struc

34. Just a few of the “cool” structures: http://www.stolaf.edu/depts/chemistry/mo/struc

35. Just a few of the “cool” structures: http://www.stolaf.edu/depts/chemistry/mo/struc

36. Just a few of the “cool” structures: http://www.stolaf.edu/depts/chemistry/mo/struc

37. Just a few of the “cool” structures: http://www.stolaf.edu/depts/chemistry/mo/struc

38. Just a few of the “cool” structures: http://www.stolaf.edu/depts/chemistry/mo/struc

39. Just a few of the “cool” structures: http://www.stolaf.edu/depts/chemistry/mo/struc

40. CoolMolecules Project Outcomes: Activities http://www.stolaf.edu/depts/chemistry/mo/struc

41. intro explore help Topic 1 Topic 10 Topic 2 Page Activity, 2007/2008 http://www.stolaf.edu/depts/chemistry/mo/struc

42. Topic 1 – Uncertainty -- 949 hits http://www.stolaf.edu/depts/chemistry/mo/struc

43. Topic 2 – SHAPES -- 576 hits http://www.stolaf.edu/depts/chemistry/mo/struc

44. Topic 10 – VSEPR -- 290 hits http://www.stolaf.edu/depts/chemistry/mo/struc

45. Month-By-Month http://www.stolaf.edu/depts/chemistry/mo/struc

46. Summary: • Close to 1000 “cool” molecules • Over 700 from the CSD • Moderate activity • Fun interface – about 33% of sessions involve Jmol http://www.stolaf.edu/depts/chemistry/mo/struc

47. Acknowledgments: Funding for this project was provided by the Howard Hughes Medical Institute and St. Olaf College Many thanks to CCDC for the permission to use CSD data in this public context http://www.stolaf.edu/depts/chemistry/mo/struc