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,
Steve
--
Dr. Steven Petrovic
Professor of Chemistry
Southern Oregon University
1250 Siskiyou Blvd.
Ashland, OR 97520
(541) 552-6803
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