CoolMolecules: a web-accessible database of experimentally determined molecular structures Robert M. Hanson, Melanie Casavant, and Michael McGuan St. Olaf.

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Presentation transcript:

CoolMolecules: a web-accessible database of experimentally determined molecular structures Robert M. Hanson, Melanie Casavant, and Michael McGuan St. Olaf College, Northfield, MN Scot Wherland Washington State University th 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 dataanalyze 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”

Background: “Molecular Origami” normal quartz

Background: “Molecular Origami”

Background: “Molecular Origami”

Background: “Molecular Origami”

Background: “Molecular Origami”

Background: “Molecular Origami”

Background: “Molecular Origami” 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

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

92electron diffraction (includes all known structures < 1950) 11infrared spectroscopy 39 microwave spectroscopy 29 neutron diffraction 3raman spectroscopy 18ultraviolet spectroscopy 774x-ray diffraction 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: trends

CoolMolecules Search Results: trends

CoolMolecules Search Results: trends

CoolMolecules Search Results

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

CoolMolecules Search Results: …bonded or not

CoolMolecules Search Results: Jmol visualizes vibrations

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

An Unexpected Outcome: The “Vibration Generator”

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

Test Platform: The “Vibration Generator”

Test Platform: The “Vibration Generator”

Test Platform: The “Vibration Generator”

Wide-Ranging Flexibility

Unusual Geometries

CoolMolecules Project Outcomes: Activities

Just a few of the “cool” structures:

Just a few of the “cool” structures:

Just a few of the “cool” structures:

Just a few of the “cool” structures:

Just a few of the “cool” structures:

Just a few of the “cool” structures:

Just a few of the “cool” structures:

Just a few of the “cool” structures:

Just a few of the “cool” structures:

Just a few of the “cool” structures:

Just a few of the “cool” structures:

Just a few of the “cool” structures:

Just a few of the “cool” structures:

Just a few of the “cool” structures:

Just a few of the “cool” structures:

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