CoolMolecules: Teaching Molecular Structure with the Cambridge
Structural Database
Robert M. Hanson, Melanie Casavant, and Michael McGuanSt. Olaf College, Northfield, MN
http://www.stolaf.edu/people/hansonr
Scot WherlandWashington State University
http://www.chem.wsu.edu/Faculty/wherland.html
20th Biennial Conference on Chemical EducationIndiana University
July 30, 2008
Goals of This Presentation
• Background: “Data-Driven” Chemistry
• Origin of the CoolMolecules Project
• Goals of the Project
• Project Outcomes
• Future Directions
generate data analyze data
generate hypothesesextrapolate hypotheses
Background: “Data-Driven” Chemistry
• 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
• 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
Background: “Molecular Origami”
http://www.stolaf.edu/people/hansonr/mo/acs2001/models.htm
normal quartz
Background: “Molecular Origami”
http://www.stolaf.edu/people/hansonr/mo/acs2001/models.htm
Background: “Molecular Origami”
http://www.stolaf.edu/people/hansonr/mo/acs2001/models.htm
Background: “Molecular Origami”
http://www.stolaf.edu/depts/chemistry/mo/struc/data/f-xef8a.mol
Background: “Molecular Origami”
http://www.stolaf.edu/depts/chemistry/mo/struc/data/f-xef8a.pdf
Background: “Molecular Origami”
http://www.stolaf.edu/people/hansonr/mo
150,000,000:1 hydrodroxyapatite model (New Museum of Contemporary Art, New York, NY)
generate data(experimental)
analyze data(identify trends)
generate hypothesis(explain shapes
and trends)
extrapolate hypothesis(predict shapes)
Background: focus on analysis
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
• 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
Goals of the CoolMolecules Project
CoolMolecules Project Outcomes: the site
http://www.stolaf.edu/depts/chemistry/mo/struc
http://www.stolaf.edu/depts/chemistry/mo/struc
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
CoolMolecules Project Outcomes: methods
CoolMolecules Project Outcomes: interface
http://www.stolaf.edu/depts/chemistry/mo/struc
CoolMolecules Project Outcomes: results
http://www.stolaf.edu/depts/chemistry/mo/struc
CoolMolecules Project Outcomes: options
http://www.stolaf.edu/depts/chemistry/mo/struc
CoolMolecules Project Outcomes: selection
http://www.stolaf.edu/depts/chemistry/mo/struc
http://www.stolaf.edu/depts/chemistry/mo/struc
CoolMolecules Search Results: tabulation
http://www.stolaf.edu/depts/chemistry/mo/struc
CoolMolecules Search Results: visualization
http://www.stolaf.edu/depts/chemistry/mo/struc
CoolMolecules Search Results: all to scale
http://www.stolaf.edu/depts/chemistry/mo/struc
CoolMolecules Search Results: all H atoms are present
http://www.stolaf.edu/depts/chemistry/mo/struc
CoolMolecules Search Results: Jmol allows easy exploration
http://www.stolaf.edu/depts/chemistry/mo/struc
CoolMolecules Search Results: just double-click for distances
http://www.stolaf.edu/depts/chemistry/mo/struc
CoolMolecules Search Results: …or angles
Just a few of the “cool” structures:
http://www.stolaf.edu/depts/chemistry/mo/struc
Just a few of the “cool” structures:
http://www.stolaf.edu/depts/chemistry/mo/struc
Just a few of the “cool” structures:
http://www.stolaf.edu/depts/chemistry/mo/struc
Just a few of the “cool” structures:
http://www.stolaf.edu/depts/chemistry/mo/struc
Just a few of the “cool” structures:
http://www.stolaf.edu/depts/chemistry/mo/struc
Just a few of the “cool” structures:
http://www.stolaf.edu/depts/chemistry/mo/struc
Just a few of the “cool” structures:
http://www.stolaf.edu/depts/chemistry/mo/struc
Just a few of the “cool” structures:
http://www.stolaf.edu/depts/chemistry/mo/struc
Just a few of the “cool” structures:
http://www.stolaf.edu/depts/chemistry/mo/struc
Just a few of the “cool” structures:
http://www.stolaf.edu/depts/chemistry/mo/struc
Just a few of the “cool” structures:
http://www.stolaf.edu/depts/chemistry/mo/struc
Just a few of the “cool” structures:
http://www.stolaf.edu/depts/chemistry/mo/struc
CoolMolecules Project Outcomes: Activities
http://www.stolaf.edu/depts/chemistry/mo/struc
Page Activity, 2007/2008
intro
explore
help
Topic 1Topic 2
Topic 10
http://www.stolaf.edu/depts/chemistry/mo/struc
Topic 1 – Uncertainty -- 949 hits
http://www.stolaf.edu/depts/chemistry/mo/struc
Topic 2 – SHAPES -- 576 hits
http://www.stolaf.edu/depts/chemistry/mo/struc
Topic 10 – VSEPR -- 290 hits
http://www.stolaf.edu/depts/chemistry/mo/struc
Month-By-Month
http://www.stolaf.edu/depts/chemistry/mo/struc
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
Acknowledgments:
Funding for this project was provided by the Howard Hughes Medical Institute and St. Olaf College
Many thanks to CCDC for the permission to use CSD data in this public context
http://www.stolaf.edu/depts/chemistry/mo/struc