[Avogadro-Discuss] A very strange molecule

[Gwenael Moreau]

Hi,
I've just discovered Avogadro and I tried to make a methanoic acid molecule.
I put an oxygen atom on a carbon and double-click
the CO bond then it becomes a C = O double bond.
Perfect.

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

How is it possible for Avogadro to do such a molecule ? Is it a bug or
is there somewhere some option I have to select ?

Thanks in advance for reply,
best regards,

[Geoffrey Hutchison]

Post by Gwenael Moreau
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: [phone]
email: ***@pitt.edu
web: http://hutchison.chem.pitt.edu/

[Gwenael Moreau]

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,

Post by Geoffrey Hutchison

Post by Gwenael Moreau
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: [phone]
web: http://hutchison.chem.pitt.edu/

[Geoff Hutchison]

Post by Gwenael Moreau
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.

Post by Gwenael Moreau
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

[Noel O'Boyle]

Maybe a "Highlight dodgy valences using halos" would be a useful engine...

Post by Geoff Hutchison

Post by Gwenael Moreau
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.

Post by Gwenael Moreau
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
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