Field of Science

Weird scis-strans observation

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Not something I expected...the C1-C2 cis form is more stable than the C1-C2 trans form. Both ab initio methods and MMFF say this, and also indicate the geometry to be perfectly planar. The problem with the perfectly planar geometry is that the C4 hydrogen-carbonyl oxygen distance is short in the cis form (2.35 A) and the C4 hydrogen- sp3 ester oxygen distance is almost the same (2.39 A) in the trans. Both these distances are short. A little non planarity could preserve the conjugation, but get rid of the distances. However, both methods don't seem to be doing this. Electronics seems to overwhelm sterics.

Interestingly, a look through the Cambridge Structural Database also indicates several similar C1-C2 cis esters, with short distances (although longer than the ones above by perhaps 0.1 A or so). So this is not a purely theoretical observation.

The simple things that defy us...I am trying to figure the reasons for this one out. Maybe it's the electrostatic attraction/HB between the C4 hydrogen and carbonyl oxygen.


  1. Perhaps there is some orbital overlap going on between the C-O pi bond and the p orbital on C4? The cis form has vague hints of a six-membered conjugated ring going on, it seems.

  2. maybe, good point...although i don't know if that could contribute to a difference as large as 2 kcal/mol

  3. the right substance has a larger dipole moment. maybe that's a problem because electrons are less delocalised?

    btw: DFT like B3LYP is typically not considered ab initio because of the functionals used

  4. Could be...higher dipole moments would lead to better delocalisation in the strans I guess.
    About DFT, that's strange because, as you know, it is an exact in principle it should be called ab initio. But as you said, it's the form of the functionals that makes it approximate.


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