Freeware that converts structure in a conformational model?
Short answer: yes, the dioxane has a minimum when it's in a twist-boat form.

I use Avogadro which offers a "auto-optimize" tool. You can grab atoms and throw them around to force rings into different conformations while the force field is minimizing.

So here's what I did.


File -> Import -> Fetch by chemical name: (2R,4R)-2-isobutyl-4-methyl-1,5-dioxaspiro[5.5]undecane. This grabs the 3D geometry from the NIH Resolver (i.e., PubChem)
Auto-Optimize Tool: Force Field MMFF94


Then I started minimizing and looking at the energies. I pulled various atoms around to try to minimize steric clashes and flip rings from chair to boat, etc.

For the figures that follow, I've removed the hydrogens for clarity, but they exist as far as the energies and minimization. I just removed them to save the graphic.

Chair/Chair: 24 kJ/mol



Twist-boat/Chair: 14 kJ/mol



So yes, there's a decent stabilization in the twisted form of the twist-boat. You have to get the hydrogens right, or you'll end up with a bunch of eclipsed interactions between the dioxane oxygens and hydrogens on the cyclohexane.