s-cis and s-trans. What does those terms mean?
Recall cis and trans. The reason Aldrich Chemical Co. can sell 99% cis-2-butene and 99% trans-2-butene in separate bottles is because of restricted rotation about the C-C pi bond. Rotation would destroy the overlap of the adjacent p-orbitals, and hence is energetically disfavoured.
We use the terms “cis” and “trans” to distinguish the different configurations of hydrogens across the C-C pi bond.
In contrast to pi bonds, rotation about single (sigma) bonds happens all the time – thousands of times per second, in fact.
You might recall that we refer to the different shapes of a molecule that arise through these rotations, “conformations“.
For reasons that will soon become clear, it’s sometimes helpful to borrow the “cis” and “trans” terminology for naming particularly important conformations.
A particularly important case comes up with dienes. In butadiene, the two individual pi bonds may be either on the opposite side of the single bond or on the same side of the single bond. It would be incorrect to refer to these as strictly trans and cis since these are conformations (dynamic!), not configurations (static). But we can get the best of both worlds if we cheat a bit and use the prefix “s” (for “sigma” , or “single” if you prefer).
Voila: s-cis and s-trans conformations!
A video says a thousand words. Pay attention to the two blue hydrogens of the diene below (butadiene) and their orientation about the central C-C single (“sigma”) bond. In one conformation, they’re oriented “trans” across the C-C single bond, and in the other conformation, they’re oriented “cis” across the C-C single bond.
That’s really all there is to it.
More On s-cis and s-trans
But while we’re on the topic of s-cis and s-trans for dienes, let’s look at a few more details.
Which conformation is lower energy?
Note that in the s-cis conformation, the “inside” hydrogens on C-1 and C-4 are in close proximity to each other. This leads to some Van Der Waals repulsion, and the result is that the s-cis conformation is about 2.3 kcal/mol less stable. At any one time, about 96% of butadiene is in the s-trans conformation.
There are situations where dienes are locked in a particular orientation. For example, in 1,3-cyclohexadiene and cyclopentadiene, the two pi bonds are locked in a s-cis orientation, while the diene bottom right is locked in the s-trans orientation.
This will become more relevant in the next post, when we introduce the Diels Alder reaction.
One final note. It’s also useful to borrow the terms for amides, which have free (if somewhat restricted) rotation about the C-N bond.
Here, we can refer to s-E or s-Z conformations of the amide (see below).
That’s really it for this topic. Did I forget anything? Feel free to leave a comment!