Structures with aromatics show inaccurate rotatable bonds


I’ve made some structures and the number of rotatable bonds seem to be inaccurate, limiting the usefulness of conformation search.

n-butyllbenzene is labelled as having 2 rotatable bonds (should be 3?)
1-hexene = 2 rotatable bond (should be 3?)
hexane = 3 rotatable bonds (should be 3)
N-benzylacetamide = 0 rotatable bonds (should be 3?)

I’ve found that sometimes this isn’t an issue and it shows the correct # of RBs, but more often than not structures with alkylgroups attached to aromatics show zero RBs.

Any help would be appreciated.

Mac using OS 10.14.6 Mojave
Avogadro 1.2.0

YMMV. The cheminformatics definition of ‘rotatable bond’ has a few different definitions, but may not always line up with your particular idea.

  • Carbons attached to an sp2 center are not rotatable (e.g., the =\ carbon in 1-hexene or the first carbon off the ring in n-butylbenzene)
  • Terminal CH3 groups are ignored

Now that’s part of the automated conformer search. You can, of course, use the auto-optimize and/or manipulate tools and push atoms around to see if you can find lower energy conformers, although particularly for sp3 carbons attached to an sp2 center, I’m not sure how much that helps.