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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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slide1

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.

slide3

and count the ways...

So what is a poor chemistry student suppose to do?

slide4

Are students still in flatland?

Where are our students?

objectives
Objectives...
  • Two very useful computer visualization tools to complement model kits
  • Support documentation for technology
  • Classroom activities following national science education standards
and what is it going to cost
...and what is it going to cost?

!

0

$

So what is the technology...

molecular visualization tools
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
the uses in the classroom
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
and more uses
…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
support documentation
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)
examples from chemsketch
Examples from ChemSketch

Chemical structures and drawing plus many templates

slide12

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

online activities

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
slide14
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
caution
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.

really can t get enough
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
more information
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

slide18
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!