Molecular Visualization in

Chemistry Workshop
Scott A. Sinex
Prince George’s Community College
22-25 June 2004
Sponsored by the Maryland Virtual High School
 What we want to accomplish…
The objectives of this workshop are three fold:
 Introduction to a student-based project
of using a template for producing a webpage (
http://academic.pgcc.edu/psc/eMol);
 Introduction to the use of FrontPage,
Chime, and ChemSketch to design web-based
activities, and;
 Develop a collection of web-based activity
for classroom use.
See activities from last summer – http://academic.pgcc.edu/~ssinex/MVCW
C C C C C

WHY?
Enhance student learning in
• General Chemistry
• Organic Chemistry
• Molecular Biology

Dynamic and Interactive

Technology too!
 The tools we have…
O • ChemSketch – chemical
C structure drawing program
H H plus other drawing
capabilities
• Chime/RasMol – molecular
structure rendering software
• FrontPage – build webpages
with Chime images
incorporated
• plus some other tricks!
A journey into molecular geometry…

Styrofoam balls and toothpicks

Construct and discover

Ball & stick models

Ideal geometries

Chime molecules
Ideal geometries
Lone pair distortion
Molecular polarity
 The uses in the classroom…
• Multiple representations
– 2D to 3D in various modes
– Cartoons for proteins, nucleotides

• Interactive viewing of
molecules
 …and more uses
• Measurements on molecules –
– Bond lengths
– Bond angles
– Torsion angles
• Molecular geometry and polarity using
electrostatic potential maps

CO2 H 2O
 Advantages to students…
• Compliments the good old
ball-and-stick molecular models
• Enriched active learning
environment
• Compare virtual and tactual
models
• More complicated
structures
 H3C

CH CH3

H3C C
ChemSketch - classical 2D
chemical structure
H3C CH3
3D energy
Save as gif for incorporation into optimization
Word or PowerPoint documents
(can copy and paste too) Save as MDL
molefile (.mol)

Can display in
Chime or RasMol

Chime images can be

embedded into web
pages using FrontPage
 Classroom Activities
• The World of Molecules (scroll down page)

• Structure and Bonding

• Discovering Intramolecular Interactions

• Molecules in Motion

• Studying Vibrations in Molecules

Online Instructor Resources
Interactive Visualization of Chemical Structures in Biology
Teaching the Structural Nature of Biological Molecules: M
Molecular Visualization: A Microcosm of the E-Revolution
Molecular simulation: What does my molecule look like?
Duane Sear’s biochemistry website
Some other useful instructional technology tools
 The game plan…
Tuesday – 22nd Wednesday - 23th Thursday - 24th Friday - 25th

Introduction ChemSketch – 2D Advanced Web- Webpage

eMolecules chemical structure pages and Chime Development
Project drawing plus more
Using Chime and
RasMol in the
Classroom
Web-based Webpage Webpage Showcase
Chime activities Development Development activities
Webpage Design developed
in FrontPage