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Conformation search cis and trans bond

I noticed that the conformer search cannot search for conformer of a CH2CH=CHCH2, cis and trans
same if that double bond is attached to a cycle
see image

Are you asking for a conformer search to break cis / trans isomerization? I don’t know of any conformer search technique that will break stereochemistry.

To be honest, that seems like a really bad idea.

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Speculation: One of the checks the systematic search for conformation engaged prior to the rotation of groups around sigma-bonds is to count the molecules in the file. For me, the illustration posted suggests the simultaneous presence of the pentadiene and the diol in the same file (see e.g., the number of atoms); but if so, the sanity check fails because there are more than one molecules counted. This disables a subsequent conformer search.

I anticipate the presence of such a safe guard in Avogadro to discern

  • the search for conformations (of a single molecule) from
  • probing a system intentionally set up with multiple molecules in respect to energy as seen in molecular dynamics

regardless if one wants to see some similarities (in the outcome) the two share with each other, or not.

This does not prevent you to explicitly define (E) and (Z) isomer of your compounds, and to perform for both the search for conformers independently of each other. This is tangentially related to a recent post about the (P) and (M) isomer of e.g., BINAP posted on chemistry.se.

I guess for the diene but for the other compound the search does not let rotate that cc bond between the cycle and the double dond.
Pretty sure that Crest works fine for that type of rotation

Will look into that post thanks.
But indeed i just copy both molecules to show them. I did not do a search with them all.
In my hand like say above that cc bond between tje cycle and the double bond does not rotate with search.

Most conformer search methods include a set of “rotatable bonds” to keep the number of possibilities to a reasonable limit.

You can certainly drive that bond manually using either the bond-centric manipulation tool or by going into the Properties => Dihedral list and setting it.

Yes, Crest runs meta dynamics - it does a much more extensive search for conformers - at the cost of much more computational time. My group uses it a lot - but it definitely takes more time.

One other word of wisdom is that Crest can also substantially change chemistry. We’ve seen plenty of bond breaking, etc. that can be hard to constrain. It’s not simply a conformer search.

Yes i did just that. Thank you and thanks for thid great tools that is Avogadro.
Jean-Marie Galano

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