Re: [Jmol-users] Jmol's use of ionic radii

[Phillip B. <pw...@wi...>]

----- Original Message -----
From: Alan Hewat <he...@il...>
> 
> Angel, that is a beautiful illustration in 10.00.36. In particular it
> shows Mn+++ smaller than O-- and N--- But when I draw Hollandite
> (NH4)Mn8O16 with ionic radii in 10.9.65
> http://icsd.ill.fr/icsd/cifdraw.php?&id[]=38457
> the Mn+++ are more than twice the size of the other ions. I assume 
> thatthis is because Mn+++ is not listed in radii.xls so I suppose 
> that jmol
> defaults to van de Waals (or neutral atoms?).

Alan, the code for Mn+++ is in JmolConstants.java, as Angel says:

  919     (25 << 4) + (2 + 4),  // 25,2,0.8,"Mn"
  920     (25 << 4) + (3 + 4),  // 25,3,0.66,"Mn"
  921     (25 << 4) + (4 + 4),  // 25,4,0.6,"Mn"
  922     (25 << 4) + (7 + 4),  // 25,7,0.46,"Mn"

> Phillip, if you used Shannon's ionic radii that should be fine, but 
> in the
> table radii.xls I only saw one valence state listed for each ion.

I'm looking at a file, crystal_ionic-radii.xls, that was distributed
with the src code, at least in previous versions of Jmol, and it has
multiple oxidation states for ions...that was the purpose of adding
ionic radii, of course, to improve autobonding of inorganic substances
and to make spacefill ionic possible.

> In fact it would be possible to calculate the Brown-Shannon valence 
> sumfrom the interatomic distances and adjust the ionic radius 
> appropriatelyfor each ion for a given structure, but maybe this can 
> be left to jmol
> 12.00 :-) Jmol 11.00 is pretty complete as it is.

We too left the calculation of the coordination number--and the use of
the Shannon radii--until a later date :-)

--Phillip Barak


>