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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 l.jpg

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


Goals of this presentation l.jpg
Goals of This Presentation determined molecular structures

  • Background: “Data-Driven” Chemistry

  • Origin of the CoolMolecules Project

  • Goals of the Project

  • Project Outcomes

  • Future Directions


Slide3 l.jpg

Background: “Data-Driven” Chemistry determined molecular structures

generate data

analyze data

extrapolate hypotheses

generate hypotheses


Slide4 l.jpg

Background: “Data-Driven Chemistry” determined molecular structures

  • 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


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Background: “Molecular Origami” determined molecular structures

  • St. Olaf College Chemistry 123

  • Start with hand-held models

  • Develop concepts as needed

http://www.stolaf.edu/people/hansonr/mo/acs2001


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Background: “Molecular Origami” determined molecular structures

normal quartz

http://www.stolaf.edu/people/hansonr/mo/acs2001/models.htm


Slide7 l.jpg

Background: “Molecular Origami” determined molecular structures

http://www.stolaf.edu/people/hansonr/mo/acs2001/models.htm


Slide8 l.jpg

Background: “Molecular Origami” determined molecular structures

http://www.stolaf.edu/people/hansonr/mo/acs2001/models.htm


Slide9 l.jpg

Background: “Molecular Origami” determined molecular structures

http://www.stolaf.edu/people/hansonr/mo/acs2001/models.htm


Slide10 l.jpg

Background: “Molecular Origami” determined molecular structures

http://www.stolaf.edu/depts/chemistry/mo/struc/data/f-xef8a.mol


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Background: “Molecular Origami” determined molecular structures

http://www.stolaf.edu/depts/chemistry/mo/struc/data/f-xef8a.pdf


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Background: “Molecular Origami” determined molecular structures

150,000,000:1 hydrodroxyapatite model

(New Museum of Contemporary Art, New York, NY)

http://www.stolaf.edu/people/hansonr/mo


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Background: focus on analysis determined molecular structures

analyze data

(identify trends)

generate data

(experimental)

generate hypothesis

(explain shapes

and trends)

extrapolate hypothesis

(predict shapes)


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Origin of the Project: BCCE17 determined molecular structures

Molecular Origami + Crystal Structure Database

(Bob Hanson) (Scot Wherland)

= CoolMolecules: A Molecular Structure Explorer

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


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Goals of the CoolMolecules Project determined molecular structures

  • 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


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CoolMolecules Project Outcomes: the site determined molecular structures

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


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CoolMolecules Project Outcomes: methods determined molecular structures

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


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CoolMolecules Project Outcomes: interface determined molecular structures

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


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CoolMolecules Project Outcomes: results determined molecular structures

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


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CoolMolecules Project Outcomes: options determined molecular structures

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


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CoolMolecules Project Outcomes: selection determined molecular structures

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


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CoolMolecules Search Results: tabulation determined molecular structures

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


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CoolMolecules Search Results: visualization determined molecular structures

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


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CoolMolecules Search Results: all to scale determined molecular structures

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


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CoolMolecules Search Results: trends determined molecular structures

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


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CoolMolecules Search Results: trends determined molecular structures

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


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CoolMolecules Search Results: trends determined molecular structures

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


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CoolMolecules Search Results determined molecular structures

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


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CoolMolecules Search Results: all H atoms are present determined molecular structures

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


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CoolMolecules Search Results: Jmol allows easy exploration determined molecular structures

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


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CoolMolecules Search Results: just double-click for distances

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


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CoolMolecules Search Results: …or angles distances

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


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CoolMolecules Search Results: …bonded or not distances

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


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CoolMolecules Search Results: Jmol visualizes vibrations distances

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


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CoolMolecules Search Results: Jmol “load-in-line” capability

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


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An Unexpected Outcome: The “Vibration Generator” capability

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


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Generating structures “on the fly” – look, Ma, no MOL file!

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


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Test Platform: The “Vibration Generator” file!

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


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Test Platform: The “Vibration Generator” file!

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


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Test Platform: The “Vibration Generator” file!

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


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Wide-Ranging Flexibility file!

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


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Unusual Geometries file!

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


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CoolMolecules Project Outcomes: Activities file!

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


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Just a few of the “cool” structures: file!

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


Slide45 l.jpg

Just a few of the “cool” structures: file!

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


Slide46 l.jpg

Just a few of the “cool” structures: file!

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


Slide47 l.jpg

Just a few of the “cool” structures: file!

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


Slide48 l.jpg

Just a few of the “cool” structures: file!

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


Slide49 l.jpg

Just a few of the “cool” structures: file!

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


Slide50 l.jpg

Just a few of the “cool” structures: file!

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


Slide51 l.jpg

Just a few of the “cool” structures: file!

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


Slide52 l.jpg

Just a few of the “cool” structures: file!

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


Slide53 l.jpg

Just a few of the “cool” structures: file!

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


Slide54 l.jpg

Just a few of the “cool” structures: file!

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


Slide55 l.jpg

Just a few of the “cool” structures: file!

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


Slide56 l.jpg

Just a few of the “cool” structures: file!

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


Slide57 l.jpg

Just a few of the “cool” structures: file!

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


Slide58 l.jpg

Just a few of the “cool” structures: file!

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


Future directions l.jpg
Future Directions: file!

  • 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)


Acknowledgments l.jpg
Acknowledgments: file!

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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