CoolMolecules: Teaching Molecular Structure with the Cambridge Structural Database

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


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

normal quartz


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


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


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


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

150,000,000:1 hydrodroxyapatite model (New Museum of Contemporary Art, New York, NY)

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

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



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


CoolMolecules Project Outcomes: results


CoolMolecules Project Outcomes: options


CoolMolecules Project Outcomes: selection



CoolMolecules Search Results: tabulation


CoolMolecules Search Results: visualization


CoolMolecules Search Results: all to scale


CoolMolecules Search Results: all H atoms are present


CoolMolecules Search Results: Jmol allows easy exploration


CoolMolecules Search Results: just double-click for distances


CoolMolecules Search Results: …or angles

Just a few of the “cool” structures:


CoolMolecules Project Outcomes: Activities


Page Activity, 2007/2008

introexplore

helpTopic 1

Topic 2Topic 10


Topic 1 – Uncertainty -- 949 hits


Topic 2 – SHAPES -- 576 hits


Topic 10 – VSEPR -- 290 hits


Month-By-Month


Summary:• Close to 1000 “cool” molecules

• Over 700 from the CSD

• Moderate activity

• Fun interface – about 33% of sessions involve Jmol


Acknowledgments:

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


CoolMolecules: Teaching Molecular Structure with the Cambridge Structural Database

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