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CoolMolecules: a web-accessible database of experimentally determined molecular structures Robert M. Hanson, Melanie Casavant, and Michael McGuan St. Olaf.

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Presentation on theme: "CoolMolecules: a web-accessible database of experimentally determined molecular structures Robert M. Hanson, Melanie Casavant, and Michael McGuan St. Olaf."— Presentation transcript:

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 228 th 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 generate dataanalyze data generate hypothesesextrapolate hypotheses Background: “Data-Driven” Chemistry

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

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

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

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

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

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

15 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 Goals of the CoolMolecules Project

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

17 92electron diffraction (includes all known structures < 1950) 11infrared spectroscopy 39 microwave spectroscopy 29 neutron diffraction 3raman spectroscopy 18ultraviolet spectroscopy 774x-ray diffraction ---------------------------- 962total structures CoolMolecules Project Outcomes: methods

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

59 Future Directions: complete the online set of PDF folding patterns develop a companion site focusing on metalloenzymes expand on the periodic table “JavaScript Application Object” idea further explore “on-the-fly” Jmol capabilities open-source chemistry web project chemwebdev-L (Google: chemwebdev)

60 Acknowledgments: Funding for this project was provided by the Howard Hughes Medical Institute and St. Olaf College http://www.stolaf.edu/depts/chemistry/mo/coolmolecules.ppt

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