# Flexibility of long-chain aliphatic compounds

PubChem is unable to generate the conformers of Z-6-Heneicosen-11-one? The website says that the molecule is too flexible

What does flexibility of a molecule mean in this context? I understand that it is a long chain compound, but I assumed that the bonds are rigid and do not flex? In layman’s terms, how does one quantify flexibility? Is it flexible like a skipping rope or like something else?

• The bonds are rigid, but the torsion angles aren't. – Ivan Neretin Jan 14 at 5:20
• – Geoff Hutchison Jan 14 at 5:32
• Rather than to flexible it want to say too much atoms /bonds – Alchimista Jan 14 at 7:58
• @Alchimista - it's not that it has too many atoms or bonds. A rigid molecule with the same number of atoms will appear (e.g, cholesterol is okay). – Geoff Hutchison Jan 14 at 14:19

PubChem 3D has limits on the number of 'rotatable bonds'

I recently answered a related question about PubChem 3D:

Beyond the limits of MMFF94 and MMFF94s themselves, PubChem3D had several limits indicated in the accompanying manuscript: Bolton et. al. "PubChem3D: a new resource for scientists" J Cheminf. (2011) v. 3, art. 32)

• Not too large (with ≤ 50 non-hydrogen atoms).
• Not too flexible (with ≤ 15 rotatable bonds).
• Consists of only supported elements (H, C, N, O, F, Si, P, S, Cl, Br, and I).
• Has only a single covalent unit (i.e., not a salt or a mixture).
• Contains only atom types recognized by the MMFF94s force field.
• Has fewer than six undefined atom or bond stereo centers.

Your molecule falls into the "more than 15 rotatable bonds" category. I count about 18 $$\ce{sp^3}-\ce{sp^3}$$ single bonds.

Basically, the problem is that the search space for conformers with that many rotatable bonds is too big. In principal, it's $$\approx3^n$$ where $$n$$ is the number of rotatable bonds.