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CoolMolecules: Teaching Molecular Structure with the Cambridge Structural Database

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

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CoolMolecules: Teaching Molecular Structure with the Cambridge Structural Database

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  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

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