The optimization is being done with the UFF force field. It's not a very exacting field, and I'm not terribly surprised by this. Nothing really that can be done from Jmol, I'm afraid.

On Sat, Feb 18, 2012 at 6:53 PM, <> wrote:

dear All

For aromatic C-C bonds (eg in benzene) I would expect the bond lengths
to be 140pm.  Jmol seems to think they should be 129pm.  This is what
I am doing:

1. Create 6C membered ring with alternate single/double bonds using
the model kit;
2. Choose 'Computation/Optimise structure' from right-click context menu;

At this point the single bonds are 148pm and double bonds 134pm.

2. Select the C atoms 'select _C;
3. Execute command 'connect aromatic 1.5';
4. Execute command 'calculate aromatic'
5. Choose 'Computation/Optimise structure' from right-click context menu.

This gives a six-membered ring with bond lengths all = 129pm.  This
means the ring is smaller than it ought to be.  Are there some
settings somewhere that I can change to get the correct bond lengths?


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If nature does not answer first what we want,
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900