Posts Tagged ‘CIP’

The perception of stereochemistry. A challenging case.

Tuesday, October 18th, 2011
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Most representational chemistry generated on a computer requires the viewer to achieve a remarkably subtle transformation in their mind from two to three dimensions (we are not quite yet in the era of the 3D iPad!). The Cahn-Ingold-Prelog convention was a masterwork (which won the Nobel prize). It is shown in action for the molecule on the left below. The CIP notation was actually generated by Chemdraw, and required a fair sprinkling of wedged and hashed bonds to (try to) remove stereoambiguity and generate the labels (try it for yourself). As part of a lecture course on pericyclic reactions, I tell the students that the reaction involves a [1,3] sigmatropic migration of the red carbon and that this migration proceeds with inversion of configuration at this migrating carbon (as the selection rules require). Perceiving what the correct CIP product label should be (with inferred stereochemical labels, resolving ? into either R or S) is IMHO one of the most difficult conceptual experiences in all of organic chemistry. I have over the years struggled to find a way of revealing this in lecture notes (these struggles with the “lecture notes” will be the topic of a future post here). However, I think I may have finally cracked it; my solution is set out below!