s-cis and s-trans

“s-cis and s-trans conformations of dienes.” What does those terms mean?

As we’ll soon see, in the Diels-Alder reaction, it’s important that the diene be in the “s–cis” conformation, otherwise the two reacting ends are too far apart. The “s–cis” is a conformation where both double bonds are on the same side of a sigma bond. Recall that there is free rotation about sigma bonds, so we say, “s-cis” and “s-trans” to distinguish it from “cis” and “trans” configurations which are locked.

Table of Contents

1. Recall That Cis- And Trans– Isomers (“Geometric Isomers” Cannot Interconvert Without Breaking Bonds
2. s-cis and s-trans Conformations In Butadiene
3. The s-trans Conformation Is Lower In Energy
4. Some Dienes Are “Locked” In The s-cis or s-trans Orientation
5. Conformations In Amides: (Z) and (E)
6. (Advanced) References and Further Reading

1. Recall That Cis- And Trans– Isomers (“Geometric Isomers” Cannot Interconvert Without Breaking Bonds

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 is energetically disfavored since it  would destroy the overlap of the adjacent p-orbitals.

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.

2. s-cis and s-trans Conformations In Butadiene

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.

via GIPHY

That’s really all there is to it.

3. The s-trans Conformation Is Of Lower Energy

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.

4. Some Dienes Are “Locked” In The s-cis or s-trans Orientation

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.

5. Conformations In Amides: (Z) and (E)

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!

(Advanced) References and Further Reading

1. Conformational studies on small molecules
   E. B. Wilson
   Chem. Soc. Rev. 1972, 1, 293-318
   DOI: 10.1039/CS9720100293
   This review mentions that dienes such as butadiene can exist in s-cis and s-trans forms. E. B. Wilson was a prominent spectroscopist in the 20^th century, and even though he never received a Nobel Prize, his son (K. G. Wilson) and PhD student (Dudley Herschbach) both did.
2. Diene Structure and Diels-Alder Reactivity
   Clare A. Stewart
   The Journal of Organic Chemistry 1963, 28 (12), 3320-3323
   DOI: 10.1021/jo01047a010
   This studies the Diels-Alder reactivity of various dienes. Most important here is that cis-1-methylbutadiene is relatively unreactive in the Diels-Alder, since in the s-cis conformation the methyl group “bumps” into the C-H bond of the terminal alkene.
3. Conformational analysis. 120. Small polyenes
   Julia C. Tai and Norman L. Allinger
   Journal of the American Chemical Society 1976, 98 (25), 7928-7932
   DOI: 10.1021/ja00441a007
   It is possible to investigate the structure of molecules in detail through computational methods, and Table 1 in this paper contains the energy differences between the s-cis and s-trans forms of various dienes.
4. Rotational barriers and stable rotamers in 1,3-butadiene, acrolein and glyoxal
   George R. De Maré
   Mol. Struc. THEOCHEM 1984, 107, 127-132
   DOI: 10.1016/0166-1280(84)80047-0
   Another paper studying the rotational barriers of butadiene through computational methods. While these calculations may have required supercomputers back then, nowadays a modern laptop will be able to carry these out in minutes (or less)!
5. Planar s-cis-1,3-butadiene
   E. Squillacote, R. S. Sheridan, O. L. Chapman, and F. A. L. Anet
   Journal of the American Chemical Society 1979, 101 (13), 3657-3659
   DOI: 10.1021/ja00507a042
   This paper reports the characterization (FT-IR) of s-cis butadiene through an unusual method – cooling the hot (400 – 900 °C) vapors on a very cold (30 K) surface. By measuring the rate of disappearance of a specific band attributed to s-cis butadiene (1430 cm^-1), the authors were able to determine the activation enthalpy for converting s-cis to s-trans butadiene to be 3.9 kcal/mol.
6. Thermodynamics of conformational change in 1,3-butadiene studied by high-temperature ultraviolet absorption spectroscopy
   Philip W. Mui and Ernest Grunwald
   Journal of the American Chemical Society 1982, 104 (24), 6562-6566
   DOI: 10.1021/ja00388a014
   In this paper, the authors do a more rigorous experimental study of the energy difference between the s-cis and s-trans forms of butadiene and determine it to be 2.9 kcal/mol. Prof. Grunwald did his undergraduate studies and PhD at UCLA under  Prof. Saul Winstein, and contributed to the development of the ‘Grunwald-Winstein equation’ in solvolysis.
7. Le 2,3‐Ditertiobutylbutadiène
   J. Backer
   Rec. Trav. Chim. Pays-Bas 1939, 58 (7), 643-661
   DOI: 10.1002/recl.19390580712
   Diels-Alder reactions of 2,3-di-t-butyl-1,3-butadiene have not been observed – the s-cis form is far too disfavored, since it brings together two t-butyl groups in close proximity!