Molecular Visualization in Chemistry Workshop Scott A. Sinex Prince George’s Community College 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 (  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 –

Enhance student learning in General Chemistry Organic Chemistry Molecular Biology WHY? Dynamic and Interactive Technology too! CCCCC

The tools we have… ChemSketch – chemical structure drawing program 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 Ball & stick models Chime molecules Lone pair distortion Molecular polarity Ideal geometries Construct and discover Ideal geometries

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 CO 2 H2OH2O

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

ChemSketch - classical 2D chemical structure Save as gif for incorporation into Word or PowerPoint documents (can copy and paste too) Save as MDL molefile (.mol) 3D energy optimization 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)The World of Molecules Structure and Bonding Discovering Intramolecular Interactions Molecules in Motion Studying Vibrations in Molecules

Online Instructor Resources Interactive Visualization of Chemical Structures in Biology, Chemistry, and Geology: Empowering Your Students with a Discovery Learning Tool Teaching the Structural Nature of Biological Molecules: Molecular Visualization in the Classroom and in the Hands of Students Molecular Visualization: A Microcosm of the E- Revolution Molecular simulation: What does my molecule look like? Duane Sear’s biochemistry websitebiochemistry website Some other useful instructional technology toolsinstructional technology tools

The game plan… Tuesday – 22nd Wednesday - 23th Thursday - 24thFriday - 25th Introduction eMolecules Project Using Chime and RasMol in the Classroom ChemSketch – 2D chemical structure drawing plus more Advanced Web- pages and Chime Webpage Development Web-based Chime activities Webpage Design in FrontPage Webpage Development Showcase activities developed