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Molecular Visualization inChemistry Workshop

Scott A. Sinex

Prince Georges Community College

22-25 June 2004

Sponsored by the Maryland Virtual High School

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What we want to accomplish

The objectives of this workshop are three fold:

Introduction to a student-based projectof 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

http://academic.pgcc.edu/psc/eMolhttp://academic.pgcc.edu/psc/eMolhttp://academic.pgcc.edu/~ssinex/MVCWhttp://academic.pgcc.edu/~ssinex/MVCWhttp://academic.pgcc.edu/~ssinex/MVCWhttp://academic.pgcc.edu/psc/eMolhttp://academic.pgcc.edu/psc/eMol

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Enhance student learning in

General Chemistry Organic Chemistry

Molecular Biology

WHY?

Dynamic and InteractiveTechnology too!

C C C C C

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The tools we have

ChemSketch chemicalstructure drawing programplus other drawing

capabilities Chime/RasMol molecularstructure rendering software

FrontPage build webpageswith Chime imagesincorporated

plus some other tricks!

O

HHC

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A journey into molecular geometry

Styrofoam balls and toothpicks

Ball & stick models

Chime molecules

Lone pair distortion

Molecular polarity

Ideal geometries

Construct and discover

Ideal geometries

http://academic.pgcc.edu/~ssinex/geometry/geometry_LP.htmhttp://academic.pgcc.edu/~ssinex/polarity/polarity.htmhttp://academic.pgcc.edu/~bgage/vsepr/Molecular_Geometry.htmlhttp://academic.pgcc.edu/psc/chm101/Molec_Geom_2.pdfhttp://academic.pgcc.edu/psc/chm101/Molec_Geom_2.pdfhttp://academic.pgcc.edu/~bgage/vsepr/Molecular_Geometry.htmlhttp://academic.pgcc.edu/~ssinex/polarity/polarity.htmhttp://academic.pgcc.edu/~ssinex/geometry/geometry_LP.htm

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The uses in the classroom

Multiple representations

2D to 3D in various modes

Cartoons for proteins, nucleotides

Interactive viewing ofmolecules

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and more uses

Measurements on molecules Bond lengths

Bond angles

Torsion angles Molecular geometry and polarity using

electrostatic potential maps

CO2 H2O

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Advantages to students

Compliments the good old

ball-and-stick molecular models

Enriched active learningenvironment

Compare virtual and tactual

models More complicated

structures

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ChemSketch - classical 2Dchemical structure

Save as gif for incorporation intoWord or PowerPoint documents

(can copy and paste too) Save as MDLmolefile (.mol)

3D energyoptimization

Can display in

Chime or RasMolChime images can beembedded into webpages using FrontPage

CH3 C

CH3

CH

CH3

CH3

CH3

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Classroom Activities

The World of Molecules(scroll down page)

Structure and Bonding

DiscoveringIntramolecularInteractions

Molecules in Motion

Studying Vibrations in Molecules

http://academic.pgcc.edu/~ssinex/chm101.htmlhttp://academic.pgcc.edu/~ssinex/struc_bond/structure_and_bonding.htmhttp://academic.pgcc.edu/~ssinex/DII_103/intramol.htmhttp://academic.pgcc.edu/~ssinex/DII_103/intramol.htmhttp://academic.pgcc.edu/~ssinex/DII_103/intramol.htmhttp://academic.pgcc.edu/~ssinex/molecules_in_motion.htmhttp://academic.pgcc.edu/~ssinex/VibMol/vibrations_in_molecules.htmhttp://academic.pgcc.edu/~ssinex/VibMol/vibrations_in_molecules.htmhttp://academic.pgcc.edu/~ssinex/molecules_in_motion.htmhttp://academic.pgcc.edu/~ssinex/DII_103/intramol.htmhttp://academic.pgcc.edu/~ssinex/DII_103/intramol.htmhttp://academic.pgcc.edu/~ssinex/DII_103/intramol.htmhttp://academic.pgcc.edu/~ssinex/struc_bond/structure_and_bonding.htmhttp://academic.pgcc.edu/~ssinex/chm101.html

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Online Instructor Resources

Interactive Visualization of Chemical Structures in Biolog

Teaching the Structural Nature of Biological Molecules:

Molecular Visualization: A Microcosm of the E-Revolution

Molecular simulation: What does my molecule look like?Duane Sears biochemistry website

Some other useful instructional technology tools

http://academic.pgcc.edu/~ssinex/PUT/http://www.uoi.gr/cerp/2001_May/pdf/08Canning_Cox.pdfhttp://home.earthlink.net/~shalpine/gallery/CGA/halpine.pdfhttp://www.sciencebase.com/SCW.htmlhttp://tutor.lscf.ucsb.edu/instdev/sears/biochemistry/http://academic.pgcc.edu/~ssinex/ITToolshttp://academic.pgcc.edu/~ssinex/ITToolshttp://tutor.lscf.ucsb.edu/instdev/sears/biochemistry/http://www.sciencebase.com/SCW.htmlhttp://home.earthlink.net/~shalpine/gallery/CGA/halpine.pdfhttp://www.uoi.gr/cerp/2001_May/pdf/08Canning_Cox.pdfhttp://academic.pgcc.edu/~ssinex/PUT/

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The game plan

Tuesday 22nd Wednesday - 23th Thursday - 24th Friday - 25th

Introduction

eMoleculesProject

Using Chime and

RasMol in the

Classroom

ChemSketch 2D

chemical structuredrawing plus more

Advanced Web-

pages and Chime

Webpage

Development

Web-based

Chime activities

Webpage Design

in FrontPage

Webpage

Development

Webpage

Development

Showcase

activities

developed