Cool Molecules a webaccessible database of experimentally determined

Cool. Molecules: a web-accessible database of experimentally determined molecular structures Robert M. Hanson, Melanie Casavant, and Michael Mc. Guan St. Olaf College, Northfield, MN http: //www. stolaf. edu/people/hansonr Scot Wherland Washington State University http: //www. chem. wsu. edu/Faculty/wherland. html 228 th ACS National Meeting , August 24, 2004

Goals of This Presentation • Background: “Data-Driven” Chemistry • Origin of the Cool. Molecules Project • Goals of the Project • Project Outcomes • Future Directions

Background: “Data-Driven” Chemistry generate data extrapolate hypotheses analyze data generate hypotheses

Background: “Data-Driven Chemistry” • Start with raw data • Transform the data into meaningful information • Create actual paper 3 D model R. M. Hanson, S. A. Bergman, "Data-Driven Chemistry: Making Molecular Models (Literally) from Electron Diffraction Data”, J. Chem. Educ. 1994, 150

Background: “Molecular Origami” • St. Olaf College Chemistry 123 • Start with handheld models • Develop concepts as needed http: //www. stolaf. edu/people/hansonr/mo/acs 2001

Background: “Molecular Origami” normal quartz http: //www. stolaf. edu/people/hansonr/mo/acs 2001/models. htm

Background: “Molecular Origami” http: //www. stolaf. edu/people/hansonr/mo/acs 2001/models. htm

Background: “Molecular Origami” http: //www. stolaf. edu/depts/chemistry/mo/struc/data/f-xef 8 a. mol

Background: “Molecular Origami” http: //www. stolaf. edu/depts/chemistry/mo/struc/data/f-xef 8 a. pdf

Background: “Molecular Origami” 150, 000: 1 hydrodroxyapatite model (New Museum of Contemporary Art, New York, NY) http: //www. stolaf. edu/people/hansonr/mo

Background: focus on analysis generate data (experimental) analyze data (identify trends) extrapolate hypothesis (predict shapes) generate hypothesis (explain shapes and trends)

Origin of the Project: BCCE 17 Molecular Origami (Bob Hanson) + Crystal Structure Database (Scot Wherland) = Cool. Molecules: A Molecular Structure Explorer http: //www. stolaf. edu/depts/chemistry/mo/struc

Goals of the Cool. Molecules 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

Cool. Molecules Project Outcomes: the site http: //www. stolaf. edu/depts/chemistry/mo/struc

$Cool. Molecules Project Outcomes: methods 1. 92 electron diffraction (includes all known structures <$

Cool. Molecules Project Outcomes: methods 1. 92 electron diffraction (includes all known structures < 1950) 2. 11 infrared spectroscopy 3. 39 microwave spectroscopy 4. 29 neutron diffraction 5. 6. 3 raman spectroscopy 18 ultraviolet spectroscopy 7. 774 x-ray diffraction 8. --------------9. 962 total structures http: //www. stolaf. edu/depts/chemistry/mo/struc

Cool. Molecules Project Outcomes: interface http: //www. stolaf. edu/depts/chemistry/mo/struc

Cool. Molecules Project Outcomes: results http: //www. stolaf. edu/depts/chemistry/mo/struc

Cool. Molecules Project Outcomes: options http: //www. stolaf. edu/depts/chemistry/mo/struc

Cool. Molecules Project Outcomes: selection http: //www. stolaf. edu/depts/chemistry/mo/struc

Cool. Molecules Search Results: tabulation http: //www. stolaf. edu/depts/chemistry/mo/struc

Cool. Molecules Search Results: visualization http: //www. stolaf. edu/depts/chemistry/mo/struc

Cool. Molecules Search Results: all to scale http: //www. stolaf. edu/depts/chemistry/mo/struc

Cool. Molecules Search Results: trends http: //www. stolaf. edu/depts/chemistry/mo/struc

Cool. Molecules Search Results http: //www. stolaf. edu/depts/chemistry/mo/struc

Cool. Molecules Search Results: all H atoms are present http: //www. stolaf. edu/depts/chemistry/mo/struc

Cool. Molecules Search Results: Jmol allows easy exploration http: //www. stolaf. edu/depts/chemistry/mo/struc

Cool. Molecules Search Results: just double-click for distances http: //www. stolaf. edu/depts/chemistry/mo/struc

Cool. Molecules Search Results: …or angles http: //www. stolaf. edu/depts/chemistry/mo/struc

Cool. Molecules Search Results: …bonded or not http: //www. stolaf. edu/depts/chemistry/mo/struc

Cool. Molecules Search Results: Jmol visualizes vibrations http: //www. stolaf. edu/depts/chemistry/mo/struc

Cool. Molecules Search Results: Jmol “load-in-line” capability http: //www. stolaf. edu/depts/chemistry/mo/struc

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

Wide-Ranging Flexibility http: //www. stolaf. edu/depts/chemistry/mo/struc/vibrate. htm

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

Cool. Molecules 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

Future Directions: • complete the online set of PDF folding patterns • develop a companion site focusing on metalloenzymes • expand on the periodic table “Java. Script 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