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JCE WebWare: Web-Based Learning Aids
William F. Coleman Wellesley College Wellesley, MA 02481
Using Jmol To Help Students Better Understand Fluxional Processes This new WebWare neatly combines instructional text and Jmol interactive, animated illustrations to teach mechanisms that need to be clearly visualized in order to be well understood. The text is interspersed with six sets of interactive Jmol illustrations that students can manipulate and modify to help them visualize the mechanisms being described. A click opens each illustration in a separate browser window so that the text and animation can be used side-byside. Each illustration is actually a set of three Jmol images that illustrate beginning, transition, and end states parallel on one page. Individual images can be manipulated with buttons that guide the interaction, though students can also choose to manipulate the images freely using other viewing options built into Jmol. Take a look at this latest example of unique, Web-based instruction! Perhaps you can use this with your students or to create your own instructional tool using this as a model! View and download this and other Web-based instructional tools in the peer-reviewed and open-review collections of JCE WebWare at http://www.JCE.DivCHED.org/JCEDLib/ WebWare/. Mechanisms That Interchange Axial and Equatorial Atoms in Fluxional Processes: Illustration of the Berry Pseudorotation, the Turnstile, and the Lever Mechanisms via Animation of Transition State Normal Vibrational Modes by Marion E. Cass, Department of Chemistry, Carleton College, Northfield, MN 55057; King Kuok (Mimi) Hiib and Henry S. Rzepa, Department of Chemistry, Imperial College London, London SW7 A2Z UK Keywords: First-Year Undergraduate / General, Second-Year Undergraduate, Upper-Division Undergraduate; Inorganic Chemistry, Physical Chemistry; Internet/Web-Based Learning; Computational Chemistry, Enantiomers, Mechanisms of Reactions, Molecular Mechanics/Dynamics, Molecular Properties/Structure, NMR Spectroscopy, Nonmetals Requires: Web browser with Java enabled
The Berry pseudorotation is a classical mechanism for interchanging axial and equatorial ligands in molecules with trigonal bipyramidal geometry. Teaching this mechanism presents particular pedagogic problems due to both its dynamic
336
Journal of Chemical Education
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Edward W. Fedosky University of Wisconsin–Madison Madison, WI 53715
Screenshot illustrating the interchange of axial and equatorial atoms in a trigonal bipyramidal molecules from Mechanisms That Interchange Axial and Equatorial Atoms in Fluxional Processes.
and three dimensional character. Our approach illustrates these processes using interactive animations embedded in a Web page and overcomes many limitations of a printed page. The animated illustrations were created using the open-source Jmol applet in a scripted Web page, and are based on density functional (B3LYP/6-31G[3d] or B3LYP/TZVP) molecular orbital calculations applied to six molecules; PF5, IF5, SF4, SF4Cl2, IF7 and Sn(amidinate)2. Our visual/dynamic treatment yields some surprises. IF5 shows fluxional behavior with characteristics of Berry plus two other modes: one a turnstile rotation, and the other a lever mechanism. In recognition of the mixed character of this exchange mechanism, we have christened this a “chimeric pseudorotation”. The pure forms of the three mechanisms are illustrated with PF5 for the Berry pseudorotation, with SF4, which has a known lever mechanism as one of the pathways for terminal atom exchange, and with SF4Cl2, which has been shown to undergo a cis/trans isomerization via a turnstile rotation. Apical/equatorial exchange in IF7, first analyzed by Bartell, shows fluxional behavior of mixed character, similar to that observed for IF5. We conclude by animating the fluxional behavior of a simple model for a chiral metal catalyst Sn(amidinate)2, in which axial/equatorial exchange within the amidinate rings occurs via a Berry pseudorotation resulting in interconversion of the enantiomers. We argue that for students learning about fluxional behavior such as that observed in intramolecular axial/equatorial atom exchange processes in systems like these, it is important that they be able to view the dynamic process, and to be able to move the vibrating molecule into alternative views which correspond to their own ideal perception of the process. This can yield new insight into how molecules undergo such dynamic exchange.
Vol. 83 No. 2 February 2006
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