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  Home > JCE Print > Journal of Chemical Education > Issues > 2006  > February  >
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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
Marion E. Cass
Department of Chemistry, Carleton College, Northfield, MN 55057

King Kuok Hii and Henry S. Rzepa
Department of Chemistry, Imperial College London, London SW7 A2Z, UK

Cover
February 2006
Vol. 83 No. 2
p. 336

Full Text
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 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.

Figure 1. 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.

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.

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You can find Mechanisms That Interchange Axial and Equatorial Atoms in Fluxional Processes in the peer-reviewed collection of JCE WebWare.
More Information
*  Citation
Cass, Marion E.; Hii, King Kuok; Rzepa, Henry S. J. Chem. Educ. 2006 83 336.
*  Keywords
Computational Chemistry; Enantiomers; First-Year Undergraduate / General; Inorganic Chemistry; Internet / Web-Based Learning; Mechanisms of Reactions; Molecular Mechanics / Dynamics; Molecular Properties / Structure; NMR Spectroscopy; Nonmetals; Physical Chemistry; Second-Year Undergraduate; Upper-Division Undergraduate
*  History
Created:
Last Updated:
1/5/2006
1/10/2006
  Home > JCE Print > Journal of Chemical Education > Issues > 2006  > February  > Page 336


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