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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

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
Goals of This Presentation
  • Background: “Data-Driven” Chemistry
  • Origin of the CoolMolecules Project
  • Goals of the Project
  • Project Outcomes
  • Future Directions
slide3

Background: “Data-Driven” Chemistry

generate data

analyze data

extrapolate hypotheses

generate hypotheses

slide4

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

slide5

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

slide6

Background: “Molecular Origami”

normal quartz

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

slide7

Background: “Molecular Origami”

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

slide8

Background: “Molecular Origami”

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

slide9

Background: “Molecular Origami”

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

slide10

Background: “Molecular Origami”

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

slide11

Background: “Molecular Origami”

150,000,000:1 hydrodroxyapatite model

(New Museum of Contemporary Art, New York, NY)

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

slide12

Background: focus on analysis

analyze data

(identify trends)

generate data

(experimental)

generate hypothesis

(explain shapes

and trends)

extrapolate hypothesis

(predict shapes)

slide13

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/struc

slide14

Goals of the CoolMolecules Project

  • 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
slide15

CoolMolecules Project Outcomes: the site

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

slide16

CoolMolecules Project Outcomes: methods

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

slide17

CoolMolecules Project Outcomes: interface

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

slide18

CoolMolecules Project Outcomes: results

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

slide19

CoolMolecules Project Outcomes: options

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

slide20

CoolMolecules Project Outcomes: selection

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

slide21

CoolMolecules Search Results: tabulation

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

slide22

CoolMolecules Search Results: visualization

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

slide23

CoolMolecules Search Results: all to scale

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

slide24

CoolMolecules Search Results: all H atoms are present

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

slide25

CoolMolecules Search Results: Jmol allows easy exploration

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

slide26

CoolMolecules Search Results: just double-click for distances

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

slide27

CoolMolecules Search Results: …or angles

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

slide28

Just a few of the “cool” structures:

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

slide29

Just a few of the “cool” structures:

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

slide30

Just a few of the “cool” structures:

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

slide31

Just a few of the “cool” structures:

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

slide32

Just a few of the “cool” structures:

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

slide33

Just a few of the “cool” structures:

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

slide34

Just a few of the “cool” structures:

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

slide35

Just a few of the “cool” structures:

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

slide36

Just a few of the “cool” structures:

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

slide37

Just a few of the “cool” structures:

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

slide38

Just a few of the “cool” structures:

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

slide39

Just a few of the “cool” structures:

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

slide40

CoolMolecules Project Outcomes: Activities

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

page activity 2007 2008

intro

explore

help

Topic 1

Topic 10

Topic 2

Page Activity, 2007/2008

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

topic 1 uncertainty 949 hits
Topic 1 – Uncertainty -- 949 hits

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

topic 2 shapes 576 hits
Topic 2 – SHAPES -- 576 hits

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

topic 10 vsepr 290 hits
Topic 10 – VSEPR -- 290 hits

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

month by month
Month-By-Month

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

summary
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
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