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

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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
• http//www.chem.wsu.edu/Faculty/wherland.html
• 228th ACS National Meeting , August 24, 2004

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Goals of This Presentation

• Background Data-Driven Chemistry
• Origin of the CoolMolecules Project
• Goals of the Project
• Project Outcomes
• Future Directions

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Background Data-Driven Chemistry
generate data
analyze data
generate hypotheses
extrapolate hypotheses
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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
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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
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Background Molecular Origami
normal quartz
http//www.stolaf.edu/people/hansonr/mo/acs2001/mo
dels.htm
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Background Molecular Origami
http//www.stolaf.edu/people/hansonr/mo/acs2001/mo
dels.htm
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Background Molecular Origami
http//www.stolaf.edu/people/hansonr/mo/acs2001/mo
dels.htm
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Background Molecular Origami
http//www.stolaf.edu/people/hansonr/mo/acs2001/mo
dels.htm
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Background Molecular Origami
http//www.stolaf.edu/depts/chemistry/mo/struc/dat
a/f-xef8a.mol
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Background Molecular Origami
http//www.stolaf.edu/depts/chemistry/mo/struc/dat
a/f-xef8a.pdf
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Background Molecular Origami
150,000,0001 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
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

• Molecular Origami Crystal Structure
  Database
• (Bob Hanson) (Scot
  Wherland)

• CoolMolecules A Molecular Structure
  Explorer
• http//www.stolaf.edu/depts/chemistry/mo/stru
  c

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Goals of the CoolMolecules Project

• Expand Scots 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
http//www.stolaf.edu/depts/chemistry/mo/struc
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CoolMolecules Project Outcomes methods
92 electron diffraction (includes all known
structures lt 1950) 11 infrared spectroscopy
39 microwave spectroscopy 29 neutron
diffraction 3 raman spectroscopy
18 ultraviolet spectroscopy 774 x-ray
diffraction ----- ----------------------- 962 tota
l structures
http//www.stolaf.edu/depts/chemistry/mo/struc
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CoolMolecules Project Outcomes interface
http//www.stolaf.edu/depts/chemistry/mo/struc
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CoolMolecules Project Outcomes results
http//www.stolaf.edu/depts/chemistry/mo/struc
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CoolMolecules Project Outcomes options
http//www.stolaf.edu/depts/chemistry/mo/struc
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CoolMolecules Project Outcomes selection
http//www.stolaf.edu/depts/chemistry/mo/struc
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CoolMolecules Search Results tabulation
http//www.stolaf.edu/depts/chemistry/mo/struc
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CoolMolecules Search Results visualization
http//www.stolaf.edu/depts/chemistry/mo/struc
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CoolMolecules Search Results all to scale
http//www.stolaf.edu/depts/chemistry/mo/struc
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CoolMolecules Search Results trends
http//www.stolaf.edu/depts/chemistry/mo/struc
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CoolMolecules Search Results trends
http//www.stolaf.edu/depts/chemistry/mo/struc
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CoolMolecules Search Results trends
http//www.stolaf.edu/depts/chemistry/mo/struc
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CoolMolecules Search Results
http//www.stolaf.edu/depts/chemistry/mo/struc
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CoolMolecules Search Results all H atoms are
present
http//www.stolaf.edu/depts/chemistry/mo/struc
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CoolMolecules Search Results Jmol allows easy
exploration
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
http//www.stolaf.edu/depts/chemistry/mo/struc
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CoolMolecules Search Results bonded or not
http//www.stolaf.edu/depts/chemistry/mo/struc
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CoolMolecules Search Results Jmol visualizes
vibrations
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
http//www.stolaf.edu/depts/chemistry/mo/struc/vib
rate.htm
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Generating structures on the fly look, Ma, no
MOL file!
http//www.stolaf.edu/depts/chemistry/mo/struc/vib
rate.htm
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Test Platform The Vibration Generator
http//www.stolaf.edu/depts/chemistry/mo/struc/vib
rate.htm
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Test Platform The Vibration Generator
http//www.stolaf.edu/depts/chemistry/mo/struc/vib
rate.htm
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Test Platform The Vibration Generator
http//www.stolaf.edu/depts/chemistry/mo/struc/vib
rate.htm
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Wide-Ranging Flexibility
http//www.stolaf.edu/depts/chemistry/mo/struc/vib
rate.htm
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Unusual Geometries
http//www.stolaf.edu/depts/chemistry/mo/struc/vib
rate.htm
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CoolMolecules Project Outcomes Activities
http//www.stolaf.edu/depts/chemistry/mo/struc
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Just a few of the cool structures
http//www.stolaf.edu/depts/chemistry/mo/struc
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Just a few of the cool structures
http//www.stolaf.edu/depts/chemistry/mo/struc
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Just a few of the cool structures
http//www.stolaf.edu/depts/chemistry/mo/struc
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Just a few of the cool structures
http//www.stolaf.edu/depts/chemistry/mo/struc
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Just a few of the cool structures
http//www.stolaf.edu/depts/chemistry/mo/struc
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Just a few of the cool structures
http//www.stolaf.edu/depts/chemistry/mo/struc
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Just a few of the cool structures
http//www.stolaf.edu/depts/chemistry/mo/struc
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Just a few of the cool structures
http//www.stolaf.edu/depts/chemistry/mo/struc
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Just a few of the cool structures
http//www.stolaf.edu/depts/chemistry/mo/struc
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Just a few of the cool structures
http//www.stolaf.edu/depts/chemistry/mo/struc
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Just a few of the cool structures
http//www.stolaf.edu/depts/chemistry/mo/struc
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Just a few of the cool structures
http//www.stolaf.edu/depts/chemistry/mo/struc
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Just a few of the cool structures
http//www.stolaf.edu/depts/chemistry/mo/struc
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Just a few of the cool structures
http//www.stolaf.edu/depts/chemistry/mo/struc
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Just a few of the cool structures
http//www.stolaf.edu/depts/chemistry/mo/struc
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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)

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