Ionic Liquid in Avogadro

Hi - I’m having trouble finding out how to make ions in Avogadro so that I
can model ionic liquid systems. Does anyone know how to do this in Avogadro?
A brief “how-to” for me would be very appreciated.

As far as I can tell, the force field atom typer will determine this from
the connectivity. For example, if you draw NH4 or Cl (as opposed to HCl)
the molecules will be assigned a +1 and 1 charge, respectively.

The atomic charges can be displayed using Display settings > labels, but
there is a bug for ions. The displayed charges do not correspond to what
is shown on the screen

Hope this helps.

Best regards, Jan

“Patrick Yee” skrev:

Hi - I’m having trouble finding out how to make ions in Avogadro so that
I
can model ionic liquid systems. Does anyone know how to do this in
Avogadro?
A brief “how-to” for me would be very appreciated.



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The atomic charges can be displayed using Display settings > labels,
but
there is a bug for ions. The displayed charges do not correspond to
what
is shown on the screen

I think what you mean is that the partial charges do not add up to the
total for the ion. Unfortunately, since these are derived from an
empirical model (Gasteiger charges), there’s not much we can do.

That’s not to say that I don’t have a research project for a better
charge model.

It’s also probably a good idea to add labels for formal charges.

-Geoff

On Oct 9, 2009, at 1:36 PM, Geoffrey Hutchison wrote:

The atomic charges can be displayed using Display settings >
labels, but
there is a bug for ions. The displayed charges do not correspond
to what
is shown on the screen

I think what you mean is that the partial charges do not add up to
the total for the ion. Unfortunately, since these are derived from
an empirical model (Gasteiger charges), there’s not much we can do.

I didn’t write that very clearly, did I? What I mean is that the
force field calculations clearly are using charges different from
those shown by the labels when ions are used.

If you draw Cl and Na (not bonded) and compute the energy, the energy
calculations clearly uses -1 and +1 charges for the atoms (it says so
explicitly under “messages”) but the labels show the partial charges
as 0 and 0.

This looks like a bug to me.

Jan

That’s not to say that I don’t have a research project for a better
charge model.

It’s also probably a good idea to add labels for formal charges.

-Geoff