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CoolMolecules: a web-accessible database of experimentally determined molecular structures

CoolMolecules: a web-accessible database of experimentally determined molecular structures . 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: a web-accessible database of experimentally determined molecular structures

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  1. CoolMolecules: a web-accessible database of experimentally determined molecular structures 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 228th ACS National Meeting , August 24, 2004

  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/people/hansonr/mo/acs2001/models.htm

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

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

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

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

  14. 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

  15. Goals of the CoolMolecules Project • Expand Scot’s database • 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

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

  17. 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 ----- ----------------------- 962 total structures http://www.stolaf.edu/depts/chemistry/mo/struc

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

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

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

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

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

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

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

  25. CoolMolecules Search Results: trends http://www.stolaf.edu/depts/chemistry/mo/struc

  26. CoolMolecules Search Results: trends http://www.stolaf.edu/depts/chemistry/mo/struc

  27. CoolMolecules Search Results: trends http://www.stolaf.edu/depts/chemistry/mo/struc

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

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

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

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

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

  33. CoolMolecules Search Results: …bonded or not http://www.stolaf.edu/depts/chemistry/mo/struc

  34. CoolMolecules Search Results: Jmol visualizes vibrations http://www.stolaf.edu/depts/chemistry/mo/struc

  35. CoolMolecules Search Results: Jmol “load-in-line” capability http://www.stolaf.edu/depts/chemistry/mo/struc

  36. An Unexpected Outcome: The “Vibration Generator” http://www.stolaf.edu/depts/chemistry/mo/struc/vibrate.htm

  37. Generating structures “on the fly” – look, Ma, no MOL file! http://www.stolaf.edu/depts/chemistry/mo/struc/vibrate.htm

  38. Test Platform: The “Vibration Generator” http://www.stolaf.edu/depts/chemistry/mo/struc/vibrate.htm

  39. Test Platform: The “Vibration Generator” http://www.stolaf.edu/depts/chemistry/mo/struc/vibrate.htm

  40. Test Platform: The “Vibration Generator” http://www.stolaf.edu/depts/chemistry/mo/struc/vibrate.htm

  41. Wide-Ranging Flexibility http://www.stolaf.edu/depts/chemistry/mo/struc/vibrate.htm

  42. Unusual Geometries http://www.stolaf.edu/depts/chemistry/mo/struc/vibrate.htm

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

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

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

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

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

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

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

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

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