Double bonds in avogadro

Dear all,

I wonder how Avogadro recognizes double bonds. The concrete problem is
as follows: I loaded gaussian log files (results from DFT geometry
opt.) of molecules with conjugated bonds into avogadro for
visualization, and some of the double bonds did not show up or were
misplaced leading to obscure depictions such as 3-valence C or 2-valence
N. The structure is fine and corresponds to the presence of double
bonds. Of course I am aware that gaussian does not ‘think’ in terms of
bond orders, but from the total nr. of electrons and the valences, it
should have been obvious where to place double bonds. Of course manual
redrawing is possible…

Many thanks in advance Peter

Hi Peter,

On Wed, Jul 6, 2011 at 7:35 PM, Peter Schellenberg
peter.schellenberg@fisica.uminho.pt wrote:

I wonder how Avogadro recognizes double bonds. The concrete problem is
as follows: I loaded gaussian log files (results from DFT geometry
opt.) of molecules with conjugated bonds into avogadro for
visualization, and some of the double bonds did not show up or were
misplaced leading to obscure depictions such as 3-valence C or 2-valence
N. The structure is fine and corresponds to the presence of double
bonds. Of course I am aware that gaussian does not ‘think’ in terms of
bond orders, but from the total nr. of electrons and the valences, it
should have been obvious where to place double bonds. Of course manual
redrawing is possible…

I’m sure one of the others who know the bond perception code will
chime in soon, but in the meantime, could you provide a sample
geometry file that shows this behavior? Avogadro should display these
bonds correctly, and having an example to reproduce the behavior will
make it easier to track down the bug.

I’m cc’ing this to the openbabel developers list, as the actual bond
perception takes place in their library, they may know more.

Thanks,

Dave

Many thanks in advance Peter


All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2


Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss

as follows: I loaded gaussian log files (results from DFT geometry
opt.) of molecules with conjugated bonds into avogadro for
visualization, and some of the double bonds did not show up or were
misplaced leading to obscure depictions such as 3-valence C or 2-valence
N.

I wrote the bond perception code, and I do lots of DFT calculations on conjugated molecules. So I’d be interested in an example or two to test. Certainly, I can modify the Open Babel code for the 2.3.1 release.

Best regards,
-Geoff