Freeware that converts structure in a conformational model? In order to draw chemical structures I use ChemBioDraw Ultra.

As an exercise I've to draw the most stable conformation.



I expect a twist-boat like structure (instead of usual chair conformation for substituted dioxanes)

Is there a freeware or an easy computer online tool to check if my propose (right side picture) is correct?

When I go to >Edit > Get 3D Model the program gives me a small picture with a 3D-Model:


By double-clicking this small image it opens ChemBio3DUltra and I can rotate this molecule:


@Martin: Is this correct (I've expected a twisted cyclic ring)?

@Martin I draw the structure at right with i-Bu and H exchanged in Chemdraw and do >Edit > Get 3D Model



The reason why I first thought it should be twist boat like was that one C-O is pointing up and the other pointing down. May be someone knows why people gives this stereoinformation inside the cyclic ring?



As I've drawn it as a twist boat I get exactly the same with ChemBioDraw. Is there a way to calculate by how many kcal/mol the first one is more stable then the second one with ChemBioDraw?

What's interesting: I searched for a structure in which the twist-boat conformation is the most favorable one and found one:


  However, when there are two large substituents in the cis-1,4 arrangement on 
  a cyclohexane ring, neither of which will go easily into an axial position, then 
  it appears that the twist-boat conformation (Section 12-3A) is most favorable 
  [http://authors.library.caltech.edu/25034/13/BPOCchapter12.pdf, page 458]


(The A-value of a tert-Butyl is in the range of 5 kcal/mol which is around the value of the energy difference between cyclohexane in twist-boat and chair conformation.
I've drawn cis-1,4-di-tert-butyl-cyclohexane with ChemDraw and used >Edit>Get 3D Model and ChemBioDraw gave me the structure which is NOT the energetical most suitable one! Why?
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.