CoolMolecules: a web-accessible database of experimentally

determined molecular structures

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

228th ACS National Meeting , August 24, 2004

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/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

• 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

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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: trends

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

CoolMolecules Search Results: trends

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

CoolMolecules Search Results: trends

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

CoolMolecules Search Results

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

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

CoolMolecules Search Results: …bonded or not

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

CoolMolecules Search Results: Jmol visualizes vibrations

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

CoolMolecules Search Results: Jmol “load-in-line” capability

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

An Unexpected Outcome: The “Vibration Generator”

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

Generating structures “on the fly” – look, Ma, no MOL file!

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

Test Platform: The “Vibration Generator”

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

Test Platform: The “Vibration Generator”

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

Test Platform: The “Vibration Generator”

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

Wide-Ranging Flexibility

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

Unusual Geometries

CoolMolecules Project Outcomes: Activities

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

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

Future Directions:• complete the online set of PDF folding patterns

• develop a companion site focusing on metalloenzymes

• expand on the periodic table “JavaScript Application Object” idea

• further explore “on-the-fly” Jmol capabilities

• open-source chemistry web project

• chemwebdev-L (Google: chemwebdev)

Acknowledgments:

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

http://www.stolaf.edu/depts/chemistry/mo/coolmolecules.ppt