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.
How do I represent thee,
let me count the ways...
benzene
C6H6
and count the ways...
So what is a poor chemistry student suppose to do?
Where are our students?
H H H H H
H C C C C C H
H H H H H
CH2
H3C
Are students still in flatland?
CH2
CH2
CH3
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?
$
0
!
So what is the technology...
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…
• 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
• 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
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
Chemical structures and drawing
plus many templates
O
H
C
0
1
0
2
0
H
3
0
4
0
5
0
Free standing use of Chime:
Carbon – oxygen bond lengths
Drawn in
ChemSketch
O
O
-
C
H
3
O H
C
C
H
3
acetic acid
O
C
acetate
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
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
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!!!
• 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...
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...
• 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
• 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!