discovering the real world of molecular structures: interactive computer visualization tools and...

Discovering the Real World of Molecular Structures:

Interactive Computer Visualization Tools and Learner-centered

Activities

Scott A. SinexDepartment of Physical Sciences and

EngineeringPrince 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?

Are students still in flatland?

CH2CH2CH3

CH2CH3

Where are our students?H

H

H C

H

H

H

C

H

H

C

H

H

C

H

H

C

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...

• 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

Molecular Visualization Tools

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

O

HHC

50

40

30

20

10

0Chemical structures and drawing plus many templates

O

O HC

CH3

O

O-

C

CH3

acetic acid acetate

Compare two proteins

hemoglobin concanavalin

Carbon – oxygen bond lengths

Free standing use of Chime:

Drawn inChemSketch

Measure and compare C-O bonds in each.

Changes to the cartoons display and then color, chains to see structure

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

Chime in web pages:

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!