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Discovering the Real World of Molecular Structures: Interactive Computer Visualization Tools and Learner-centered Activi

Discovering the Real World of Molecular Structures: Interactive Computer Visualization Tools and Learner-centered Activities Scott A. Sinex Department of Physical Sciences and Engineering Prince George’s Community College

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Discovering the Real World of Molecular Structures: Interactive Computer Visualization Tools and Learner-centered Activi

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  1. Discovering the Real World of Molecular Structures:Interactive Computer Visualization Tools and Learner-centered Activities Scott A. Sinex Department of Physical Sciences and Engineering Prince George’s Community College Presented as part of REACTS/ACS High School Teachers Day at the 230th National Meeting of the American Chemical Society in Washington, DC on 28 August 2005.

  2. How do I represent thee, let me count the ways... benzene C6H6

  3. and count the ways... So what is a poor chemistry student suppose to do?

  4. Are students still in flatland? Where are our students?

  5. Objectives... • Two very useful computer visualization tools to complement model kits • Support documentation for technology • Classroom activities following national science education standards

  6. ...and what is it going to cost? ! 0 $ So what is the technology...

  7. Molecular Visualization Tools • ChemSketch (from ACD Labs) • chemical structure and general drawing • copy and paste into documents, export as gif, 3D optimize and export as Chime file • Chime (from MDL) • molecular structure rendering – 3D structures • installs as browser plug-in • works freestanding or incorporated into web pages

  8. The uses in the classroom… • Multiple representations • 2D to 3D in various modes • Interactive viewing of molecules • Measurements on molecules – • Bond lengths • Bond angles • Torsion angles • Molecular geometry and discover distortions due to lone pairs of electrons and bulky groups

  9. …and more uses • Molecular geometry and polarity using electrostatic potential maps • Molecular structure and reactivity • Attack points • Cartoons for proteins, nucleotides • Animations • Reaction mechanisms • Molecular vibrations • ChemSketch can build molecules for Chime

  10. Support documentation • ChemSketch: A Guide to Drawing Chemical Structures • Student Guide to the Use of Chime (interactive html tutorial by menu steps) • Creating Chime Web Pages in FrontPage (includes hot links to molecule sources)

  11. Examples from ChemSketch Chemical structures and drawing plus many templates

  12. Free standing use of Chime: O O - C O H C O H C H C 3 3 acetic acid acetate Carbon – oxygen bond lengths Drawn in ChemSketch Measure and compare C-O bonds in each. Compare two proteins hemoglobin concanavalin Changes to the cartoons display and then color, chains to see structure

  13. Chime in web pages: Online Activities... • The World of Molecules – introduction to molecular geometry from Styrofoam balls to physical model kits to virtual exploration (scroll down page) • Structure and Bonding (wealth of short activities) • Discovering Intramolecular Interactions • Molecules in Motion • Studying Vibrations in Molecules

  14. Why? • Interactive and discovery-based (just have to ask the right questions!) • Explore multiple modalities used by chemists • Explore more complicated molecules especially biological molecules

  15. Caution!!! • Many incorrect structures are available on the Internet • Keep the ball-&-stick model kits handy Good plastic, snap together models (MolyMod) are available from Indigo.

  16. Really can’t get enough... • Empowering Student Learning with Molecular Visualization Tools in Discovery-based General Chemistry • Interactive Visualization of Chemical Structures in Biology, Chemistry, and Geology • Instructional Technology Tools

  17. More information... • Webpage http://academic.pgcc.edu/~ssinex • E-mail ssinex@pgcc.edu • ChemSketch (from ACD Labs) http://www.acdlabs.com/download/chemsk.html • Chime (from MDL) http://www.mdli.com/downloads/index.jsp

  18. To Jack Dibler, PGCPS, and Elena Pisciotta, MCPS for the invitation to REACTS 2005. • To Barb Gage for being a constant collaborator. • To MDL and ACD Labs for the freeware!

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