Fwd: Building polymer structure

General Discussion
1

Thanks Geoff. does that mean we can not create polymers with aromatic rings
as repeat units in Avogadro?
I was trying to make polycarbonate structure and all the double bonds in
aromatic rind gets converted to single bonds so the structure doesn’t
remain the same.
Can you suggest some other toll to do that?
Jyotsna

I’m trying to make polymer structure using Avogadro. After creating unit
cell for the monomer unit when I try to create super cell, all the double
bonds become single bonds. Please let me know what could go wrong. Is this
the right way to create a polymer structure?

At the moment, the code does not attempt to detect multiple bonds across
unit cell boundaries. (In fact, I’d be curious to know what polymer you’re
building that has a double bond across the repeat boundary.)

Hope that helps,
-Geoff

2

Thanks Geoff. does that mean we can not create polymers with aromatic rings
as repeat units in Avogadro?

No. I’d suggest using copy/paste as a workaround. (This is what I do.)

I just coded a new version of the supercell builder for Avogadro 1.1, and I’ll see if I can add a heuristic to allow bond order perception. I’m also working on a general polymer builder tool, which will make this much easier.

-Geoff