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 Cass,a King Kuok (Mimi) Hiib and Henry S. Rzepa*,b

aDepartment of Chemistry, Carleton College, Northfield, MN 55057 USA;
bDepartment of Chemistry, Imperial College London, UK.


The Berry pseudorotation is a classical mechanism for interchanging axial and equatorial ligands in molecules with trigonal bipyramidal geometry. It presents particular pedagogic problems due to both its dynamic and its three dimensional character. We present here an approach to illustrating such processes, which overcomes limitations of the printed page by using interactive animations. These were created using the opensource Jmol Java applet as a component of 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 calculations hold some surprises which uniquely emerge from this visual/dynamic treatment. IF5 shows fluxional behavior with characteristics of Berry and two other modes; one termed termed turnstile rotation and the other, a lever mechanism. In recognition of the mixed character of this exchange mechanism, we christen this a "chimeric pseudorotation". The "pure" forms of the three mechanisms are illustrated with PF5 for the Berry pseudorotation, SF4 that has a known lever mechanism as one of the pathways for terminal atom exchange, and with SF4Cl2 that has been shown calculationally to undergo a cis/trans isomerization via a turnstile rotation. Apical/equatorial exchange in IF7, first analysed 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 an important aspect of teaching about fluxional behavior such as that observed in intramolecular axial/equatorial ligand exchange processes in systems like these, is for students to be able to view the actual dynamic process, and to be able to move the vibrating molecule into alternative views which corresponds to their own ideal perception of the process. These techniques have led to new insight into how several relatively unstudied molecules undergo such dynamic exchange

Corresponding Author: Henry S. Rzepa Department of Chemistry Imperial College London, SW7 A2Z UK 020-7594-5774, 0870-132-3747 (efax) Keywords: Audience: First-Year, Second-Year and Upper-Division Undergraduate Domain: Inorganic Chemistry, Physical Chemistry Pedagogy: Internet/Web-Based Learning Topic: Mechanisms of Reactions, Molecular Properties/Structure, Computational Chemistry, Nonmetals Molecular Mechanics/Dynamics, Enantiomers, NMR Spectroscopy