Re: [Avogadro-Discuss] Inability to calculate carbon dioxide dipole moment?

[Marcus D. H. <mar...@ki...>]

On Sat, Jan 19, 2013 at 12:31 PM, Steven Petrovic <pet...@so...> wrote:
> Hello,
> Despite how wonderful I think Avogadro is for molecular modeling and its
> potential for educational purposes, I hesitate to use Avogadro in the
> chemistry laboratory when there seems to be such glaring issues as
> predicting the dipole moment for simple inorganic molecules such as carbon
> dioxide. When I build carbon dioxide using either 1.0.3 (in Ubuntu) or 1.1.0
> (on a PC) and optimize the geometry using MMFF94, the bond lengths are the
> same (1.197 angstroms for each C=O bond) and the bond angle is 180 degrees,
> just as you would predict with VSEPR theory. Yet, the dipole moment is a
> robust 9.72 Debye, not 0 Debye as would be predicted by VSEPR theory. In
> addition, if you build carbon dioxide in 1.0.3 by selecting double bonds and
> turning off adjust hydrogens, the partial charge on the carbon and oxygen
> atoms remains zero, and not 0.37 for C and -0.19 for each O. Unfortunately,
> Ubuntu has not put the latest version of Avogadro in its repository.
> I cannot explain why such discrepancies exist in the software and so I'm
> calling on the users and developers of Avogadro for some help on explaining
> or overcoming such discrepancies.
> Thank you for your assistance,

I think all of these numbers come from Open Babel, and the force
fields we use that were implemented by the Open Babel team. Perhaps
posing this question on the Open Babel list, or looking at other open
source implementations we could integrate would make sense.

I think Geoff and Tim would be more qualified to comment on how much
work it would be to correct some of these issues in Open Babel, we
also integrate with many third party quantum codes and using third
party MD packages might be another viable route to more accurate
numbers.

Marcus