[google470]

hi guys,

I am reading a paper published in Chem. Eur. J. 2014, 20, 14575 – 14578, and found one strange question about the configuration of 1,3-diene in the transformation 25-->26 using Lindlar/H2 condition.  After this reaction, the 1,3-diene of product rotate to form cis!...(see the photo attached)
Could anyone tell me why??
Thanks!

[google470]

I think the rotation barrier is very high, and the rotation cannot happen in this reaction. Do you think so?

[AWK]

This is not a reduction center. Rotation around a single bond shows a rather low barrier.

[google470]

This is not a reduction center. Rotation around a single bond shows a rather low barrier.

yeah I know it is NOT the reduction center, and I am asking the 1,3-diene.
Even the barrier is low, the trans one should be much more thermodynamically stable, so it is strange to see that the molecule is cis rather than trans.

[AWK]

I think this is effect of automatic drawing program, eg from SMILES.
Look at the Fig. 1 how different drowings are for very close structures.

[Borek]

Somehow I fail to see the rotation around the double bond. There is a rotation around a single bond, the one the arrows point at, but as far I can tell both involved double bonds stay trans.

[Dan]

Even the barrier is low, the trans one should be much more thermodynamically stable, so it is strange to see that the molecule is cis rather than trans.

There is no strict convention regarding the conformation in which molecules are depicted in papers if there is a low energy difference between them (unless you are specifically illustrating a point related to conformation).

This is not cis/trans isomerism, they are s-cis/s-trans conformers which will interconvert rapidly. Usually you pick the one that is more aesthetically pleasing, or the one that most efficiently fills the available space, which is not necessarily the lowest energy conformation. In some cases it might be clearer for the reader if you depict the molecule in a higher energy conformation - for example, if you are showing a Diels-Alder reaction, it is easier to follow if the diene is drawn in the s-cis reactive conformation (whether or not it is the lowest energy conformation).

[hairygorillaz]

Somehow I fail to see the rotation around the double bond. There is a rotation around a single bond, the one the arrows point at, but as far I can tell both involved double bonds stay trans.

I think the OP is referring to s-cis vs s-trans around the single bond (Something like when talking about diene conformation in a Diels-Alder)

[google470]

Even the barrier is low, the trans one should be much more thermodynamically stable, so it is strange to see that the molecule is cis rather than trans.

There is no strict convention regarding the conformation in which molecules are depicted in papers if there is a low energy difference between them (unless you are specifically illustrating a point related to conformation).

This is not cis/trans isomerism, they are s-cis/s-trans conformers which will interconvert rapidly. Usually you pick the one that is more aesthetically pleasing, or the one that most efficiently fills the available space, which is not necessarily the lowest energy conformation. In some cases it might be clearer for the reader if you depict the molecule in a higher energy conformation - for example, if you are showing a Diels-Alder reaction, it is easier to follow if the diene is drawn in the s-cis reactive conformation (whether or not it is the lowest energy conformation).

Thank you so much! I totally agree with you, and thank all the people replied above.