Re: A very strange molecule

As we teach our students that oxygen has a valence of 2, it is annoying
that they can make a molecule where it has four chemical bonds ;o((

Is it not possible to provide an option to compel compliance with the
rules of valence ?

Maybe I should post this message on the list of development ?

Thanks in advance,
best regards,

Le 2011-12-19 18:39, Geoffrey Hutchison a écrit :

Where the problem arises is if I click a second time, we
obtained a CO triple bond as you can see in attached file.

While I’m surprised at the hydrogen on the oxygen Avogadro does allow you to build “strange” molecules. Chemistry is vast and unusual, and people often want to do calculations or studies on unusual compounds. So yes, you can make a triple bond between carbon and oxygen, if you wish.

Thanks and best regards,
-Geoff


Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/


Physique et Chimie dans le secondaire et pour la préparation au CAPES
http://gwenaelm.free.fr/Physique
Du nouveau dans le Guppy
http://gwenaelm.free.fr/2008-9

As we teach our students that oxygen has a valence of 2, it is annoying
that they can make a molecule where it has four chemical bonds ;o((

Let me be clear that the hydrogen on the oxygen is a bug.

Is it not possible to provide an option to compel compliance with the
rules of valence ?

Using the “auto-adjust hydrogens” is the most effective way to do this. It’s very hard to truly “compel” compliance in a free-form draw tool like Avogadro uses. Spartan, for example, compels compliance because atoms and bonds only fit together in certain ways (e.g., an sp2-carbon can only make one double bond).

But a perfectly legitimate description of carbon monoxide has a triple bond between C#O.

-Geoff

Maybe a “Highlight dodgy valences using halos” would be a useful engine…

On 21 December 2011 18:50, Geoff Hutchison geoff.hutchison@gmail.com wrote:

As we teach our students that oxygen has a valence of 2, it is annoying
that they can make a molecule where it has four chemical bonds ;o((

Let me be clear that the hydrogen on the oxygen is a bug.

Is it not possible to provide an option to compel compliance with the
rules of valence ?

Using the “auto-adjust hydrogens” is the most effective way to do this. It’s very hard to truly “compel” compliance in a free-form draw tool like Avogadro uses. Spartan, for example, compels compliance because atoms and bonds only fit together in certain ways (e.g., an sp2-carbon can only make one double bond).

But a perfectly legitimate description of carbon monoxide has a triple bond between C#O.

-Geoff

Write once. Port to many.
Get the SDK and tools to simplify cross-platform app development. Create
new or port existing apps to sell to consumers worldwide. Explore the
Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join
http://p.sf.net/sfu/intel-appdev


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