> To be clear, are you asking why MMFF94 is so poor at predicting dipole 
> moments?

No, he's commenting on a bug. O=C=O clearly should have approximately 0.0D 
dipole moment. Regardless of the charges on the individual atoms, the charges 
should cancel in a symmetric molecule.

I have no idea the source of the bug, although I can reproduce it. I suspect 
it's some sort of "race condition" when the molecule is being modified, the 
dipole moment is not properly updated.

I'll take a look later this week. But if you can give me a list of examples for 
"the dipole moment is totally crazy," I'd appreciate it.

As for the accuracy of MMFF94 charges vs. other things, both MMFF94 and 
Gasteiger give fairly reasonable dipole moments for most organic molecules in 
my testing. It'd be great to have a more universal charge model, but I don't 
think one exists at present. It's on my "wish list" in the next year or two to 
get a charge model which is halfway decent across most elements.

-Geoff
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