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CoolMolecules: Teaching Molecular Structure with the Cambridge Structural Database 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 teaching molecular structure with the cambridge structural database l.jpg

CoolMolecules: Teaching Molecular Structure with the Cambridge Structural Database

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

20th Biennial Conference on Chemical Education

Indiana University

July 30, 2008


Goals of this presentation l.jpg
Goals of This Presentation Cambridge Structural Database

  • 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 Cambridge Structural Database

generate data

analyze data

extrapolate hypotheses

generate hypotheses


Slide4 l.jpg

Background: “Data-Driven Chemistry” Cambridge Structural Database

  • 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” Cambridge Structural Database

  • 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” Cambridge Structural Database

normal quartz

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


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Background: “Molecular Origami” Cambridge Structural Database

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


Slide8 l.jpg

Background: “Molecular Origami” Cambridge Structural Database

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


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Background: “Molecular Origami” Cambridge Structural Database

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


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Background: “Molecular Origami” Cambridge Structural Database

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


Slide11 l.jpg

Background: “Molecular Origami” Cambridge Structural Database

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 Cambridge Structural Database

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 Cambridge Structural Database

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 Cambridge Structural Database

  • 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


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CoolMolecules Project Outcomes: the site Cambridge Structural Database

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


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CoolMolecules Project Outcomes: methods Cambridge Structural Database

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

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


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CoolMolecules Project Outcomes: interface Cambridge Structural Database

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


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CoolMolecules Project Outcomes: results Cambridge Structural Database

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


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CoolMolecules Project Outcomes: options Cambridge Structural Database

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


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CoolMolecules Project Outcomes: selection Cambridge Structural Database

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


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CoolMolecules Search Results: tabulation Cambridge Structural Database

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


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CoolMolecules Search Results: visualization Cambridge Structural Database

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


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CoolMolecules Search Results: all to scale Cambridge Structural Database

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


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CoolMolecules Search Results: all H atoms are present Cambridge Structural Database

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


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CoolMolecules Search Results: Jmol allows easy exploration Cambridge Structural Database

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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Just a few of the “cool” structures: distances

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


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Just a few of the “cool” structures: distances

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


Slide30 l.jpg

Just a few of the “cool” structures: distances

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


Slide31 l.jpg

Just a few of the “cool” structures: distances

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


Slide32 l.jpg

Just a few of the “cool” structures: distances

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


Slide33 l.jpg

Just a few of the “cool” structures: distances

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


Slide34 l.jpg

Just a few of the “cool” structures: distances

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


Slide35 l.jpg

Just a few of the “cool” structures: distances

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


Slide36 l.jpg

Just a few of the “cool” structures: distances

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


Slide37 l.jpg

Just a few of the “cool” structures: distances

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


Slide38 l.jpg

Just a few of the “cool” structures: distances

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


Slide39 l.jpg

Just a few of the “cool” structures: distances

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


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CoolMolecules Project Outcomes: Activities distances

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


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intro distances

explore

help

Topic 1

Topic 10

Topic 2

Page Activity, 2007/2008

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


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Topic 1 – Uncertainty -- 949 hits distances

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


Topic 2 shapes 576 hits l.jpg
Topic 2 – SHAPES -- 576 hits distances

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


Topic 10 vsepr 290 hits l.jpg
Topic 10 – VSEPR -- 290 hits distances

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


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Month-By-Month distances

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


Summary l.jpg
Summary: distances

  • 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 l.jpg
Acknowledgments: distances

Funding for this project was provided by the Howard Hughes Medical Institute and St. Olaf College

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