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 http://www.stolaf.edu/depts/chemistry/mo/struc