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