Just for the sake of clarification, ionic radii were introduced 'back when' by Miguel (at my prodding) so that inorganic compounds could be properly drawn and we made use of oxidation numbers for the elements, when specified, to select the proper Pauling-type crystal radius. This allowed the use of Jmol for both biological/organic compds (which tend to have chemically reduced C, N, and S) and mineral/inorganics, which tend to have elements in their oxidized forms, tho not exclusively of course.
I was aware of Shannon's values for oxides and halides but their use presented a more complicated problem, at least at the time: Shannon's values require not only an oxidation number but a coordination number. This is not trivial since some minerals have, say, Fe in both octahedral and tetrahedral coordination, both with the same oxidation number. This can be addressed easily in the CIF file by specifying the desired radius for each Fe-type, but Jmol will have to figure out coordination number on the fly to make use of Shannon's tables. This said, I think that Alan is quite right and it is desirable to bring the ionic radius feature up to the same high mark of Jmol's many other current features. --Phil Barak ----- Original Message ----- From: Alan Hewat <[email protected]> Date: Thursday, February 4, 2010 9:19 am Subject: [Jmol-users] Request to input custom table of ionic radii To: [email protected] Cc: Bob Hanson <[email protected]> > Alan Hewat wrote Sept 2006: > > > Can we eventually use our own table of radii ? > >... > > David Brown tells me that the best values for ionic radii are still > > those of Shannon and Prewitt 1969, Acta Cryst. B25, 925-946 (for oxides) > > and Shannon 1976 Acta Cryst. A32, 751-767 (for halides) > > Bob and others tidied up Jmol's ionic radii since I wrote that, and the > radii for different ionic states are included as tables in the Jmol source > code. I understand these values are taken from the CRC Handbook of > Chemistry and Physics (1996-97) with some mods to make them work for > organic compounds. > > But I would still like to be able to input my own table of ionic radii > :-) > > The reason is that to my mind ionic radii have been determined by > Brown-Shannon-Prewitt from bond lengths and strengths in simple inorganic > compounds, and are really only valid for that class of material. For the > Inorganic Crystal Structure Database (ICSD) we would prefer therefore > to > use ionic radii based only on simple inorganic materials. > > It would be great if we could load our own table of radii when Jmol is > launched. Bob? :-) > > Alan (now retired and working on other things as well) > ______________________________________________ > Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE > <[email protected]> +33.476.98.41.68 > http://www.NeutronOptics.com/hewat > ______________________________________________ > > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the business > Choose flexible plans and management services without long-term contracts > Personal 24x7 support from experience hosting pros just a phone call away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
