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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

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coolmolecules a web accessible database of experimentally determined molecular structures

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
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/people/hansonr/mo/acs2001/models.htm

slide10

Background: “Molecular Origami”

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

slide11

Background: “Molecular Origami”

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

slide12

Background: “Molecular Origami”

150,000,000:1 hydrodroxyapatite model

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

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

slide13

Background: focus on analysis

analyze data

(identify trends)

generate data

(experimental)

generate hypothesis

(explain shapes

and trends)

extrapolate hypothesis

(predict shapes)

slide14

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

slide15

Goals of the CoolMolecules Project

  • 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
slide16

CoolMolecules Project Outcomes: the site

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

slide17

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

----- -----------------------

962 total structures

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

slide18

CoolMolecules Project Outcomes: interface

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

slide19

CoolMolecules Project Outcomes: results

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

slide20

CoolMolecules Project Outcomes: options

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

slide21

CoolMolecules Project Outcomes: selection

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

slide22

CoolMolecules Search Results: tabulation

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

slide23

CoolMolecules Search Results: visualization

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

slide24

CoolMolecules Search Results: all to scale

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

slide25

CoolMolecules Search Results: trends

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

slide26

CoolMolecules Search Results: trends

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

slide27

CoolMolecules Search Results: trends

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

slide28

CoolMolecules Search Results

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

slide29

CoolMolecules Search Results: all H atoms are present

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

slide30

CoolMolecules Search Results: Jmol allows easy exploration

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

slide31

CoolMolecules Search Results: just double-click for distances

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

slide32

CoolMolecules Search Results: …or angles

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

slide33

CoolMolecules Search Results: …bonded or not

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

slide34

CoolMolecules Search Results: Jmol visualizes vibrations

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

slide35

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

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

slide36

An Unexpected Outcome: The “Vibration Generator”

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

slide37

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

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

slide38

Test Platform: The “Vibration Generator”

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

slide39

Test Platform: The “Vibration Generator”

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

slide40

Test Platform: The “Vibration Generator”

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

slide41

Wide-Ranging Flexibility

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

slide42

Unusual Geometries

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

slide43

CoolMolecules Project Outcomes: Activities

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

slide44

Just a few of the “cool” structures:

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

slide45

Just a few of the “cool” structures:

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

slide46

Just a few of the “cool” structures:

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

slide47

Just a few of the “cool” structures:

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

slide48

Just a few of the “cool” structures:

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

slide49

Just a few of the “cool” structures:

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

slide50

Just a few of the “cool” structures:

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

slide51

Just a few of the “cool” structures:

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

slide52

Just a few of the “cool” structures:

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

slide53

Just a few of the “cool” structures:

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

slide54

Just a few of the “cool” structures:

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

slide55

Just a few of the “cool” structures:

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

slide56

Just a few of the “cool” structures:

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

slide57

Just a few of the “cool” structures:

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

slide58

Just a few of the “cool” structures:

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

future directions
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
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

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