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JCE WebWare: Web-Based Learning Aids
William F. Coleman Wellesley College Wellesley, MA 02481
Visualization Tools for Organic Chemistry
Edward W. Fedosky University of Wisconsin–Madison Madison, WI 53715
Visualization Tools for Organic Chemistry by Jennifer L. Muzyka, Department of Chemistry, Centre College, Danville, KY 40422;
[email protected] Keywords: Domain: Organic Chemistry. Audience: SecondYear Undergraduate. Pedagogy: Internet/Web-Based Learning, Multimedia-Based Learning. Topics: Alkanes/Cycloalkanes, Conformational Analysis, Elimination Reactions, Mechanisms of Reactions, Nucleophilic Substitution, Stereochemistry. Requires Web Browser
One of the reasons that organic chemistry is often difficult for students is that they are not accustomed to thinking in a visual manner (1, 2). Understanding the shapes of molecules and changes in them is facilitated when students can “see” the molecules (Figure 1). Computer generated “models” can help bridge between the hand-held models and the two-dimensional representations we draw on paper. Making computer generated images available on the Web without requiring students to learn molecular modeling software is more student-friendly as well as being cost effective. There are various approaches used to that make interactive molecules available to students via a Web browser. These include RasMol (3), a helper application, the Chemscape Chime browser plug-in (4), and the Jmol java applet (5). The ability to display explanations and buttons to highlight structural features within
a Web page make Chime and Jmol more useful than RasMol for teaching purposes. (As a helper application, RasMol functions in its own window; users need to know scripts and commands to highlight structural features of molecules within RasMol.) The difficulties associated with the use of plug-ins have led many Web site authors to convert their Chime tutorials to use Jmol. Unlike normal animations, animated molecules displayed with Chime or Jmol may be manipulated in three dimensions, allowing a student to get a better perspective on how the chemical structures are changing as a particular reaction proceeds. These visualization tools focus on improving students’ ability to visualize by the interactive display of molecules, along with text and buttons that activate scripts to highlight structural features or start-and-stop appropriate animations. These tools target a series of topics that students have difficulty visualizing, rather than making the whole course Web-based. The tutorials cover conformations of alkanes and cycloalkanes, stereochemistry, and several reactions (SN1, SN2, E1, and E2). The site is being translated into Italian by Giuseppe Striccoli (6). These pages are used in first-semester organic chemistry classes. Using a computer equipped with an LCD projector, the Web page is opened in a browser to demonstrate how the molecules interact with the user’s action. The students are then told how to access the site, which is available by link to the class Web site. The site makes extensive use of both Java and JavaScript. Refer to the online material for more detailed information describing the content of the different tutorials. Literature Cited 1. Fleming, S. A.; Hart, G. R.; Savage, P. B. J. Chem. Educ. 2000, 77, 790–793. 2. Stueker, O.; Brunberg, I.; Fels, G.; Borkent, H.; van Rooij, J. J. Chem. Educ. 2003, 80, 583. 3. RasMol Home Page. http://www.umass.edu/microbio/rasmol/ (accessed Nov 2008). 4. MDL Chime. http://www.mdl.com/products/framework/chime/ (accessed Nov 2008). 5. Jmol Home Page. http://jmol.sourceforge.net/ (accessed Nov 2008). 6. Striccoli’s Italian translation (Molecole in Movimento) is available at http://digilander.libero.it/industrialegalilei/organica/ (accessed Nov 2008).
Supporting JCE Online Material Staggered Conformer Show some H-H interactions Original structure Figure 1. Computer generated model to help students understand steric interactions.
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http://www.jce.divched.org/Journal/Issues/2009/Feb/abs254.html Full text (HTML and PDF) Links to cited URLs and JCE articles Supplement Find “Visualization Tools for Organic Chemistry” in the JCE Digital Library at http://www.jce.divched.org/JCEDLib/WebWare/collection/reviewed/JCE2009p0254WW/index.html.
Journal of Chemical Education • Vol. 86 No. 2 February 2009 • www.JCE.DivCHED.org • © Division of Chemical Education
