These are ionic radii in the sense that Linus Pauling used them for multiple
oxidation states, extended a number of times in the literature, and probably
reaching their pinnacle in the work of Shannon et al, who calculated ionic
radii as a functional of coordination number. See
http://en.wikipedia.org/wiki/Ionic_radius for a bit more.
They work tolerably well for help in calculating bonding in Jmol, particularly
for the inorganic components...values for carbon, for example, vary
considerably depending on whether it is +4 (as in carbonate) or -4 (organic
carbon). They are of course just another way of visualizing atoms, so they are
not 'right'.
On 04/18/14, Robert Hanson <hans...@stolaf.edu> wrote:
> "ionic" in Jmol is a bit of a misnomer. I have never liked it. It refers to a
> mix of covalent bonding radii and ionic radii, and really there is no
> "turning it off". The spreadsheet detailing this is online. See
> http://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/_documents/
>
>
>
> perhaps ionicradia11.xls
>
>
> Note that for these ionic values to apply, you need formal charges:
>
> load http://chemapps.stolaf.edu/jmol/docs/examples-12/data/nacl.cif packed
>
> {_Na}.formalCharge = 1
> {_Cl}.formalCharge = -1
> spacefill ionic
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> On Fri, Apr 18, 2014 at 9:19 AM, Pshemak Maslak <n...@psu.edu> wrote:
>
>
> > On 4/18/2014 5:47 AM, Angel Herráez wrote:
> >
> >
> > >
> > > Hi Pshemak try this: spacefill ionic;
> > > print {*}.radius.all; If you want the full list of original values used,
> > > you probably need to check the source code. The Scripting Doc page has a
> > > link to an Excel table (it may be not up to date, I know there was a
> > > recent change in something related to bonding radii) at
> > > http://chemapps.stolaf.edu/jmol/docs/misc/radii.xls
> > >
> >
> >
> >
> > Thanks! That helps.. It looks like there are some unusual discrepancies.
> > For example:
> >
> > Br(-1) 1.96 A on the xls list and 1.21 A in Jmol when read from KBr,cif
> > file
> > Cl(-1) 1.81 A on the xls list and 0.99 A in Jmol when read from CsCl.cif
> > file (it shows correctly at 1.81 A from NaCl.cif file)
> >
> > Any idea of what is happening?
> >
> > PM
> >
> > PS. (Can I enclose the cif files with the email?).
> >
> > ------------------------------------------------------------------------------
> >
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> >
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> >
>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
>
>
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