Miguel and I worked on that in 2004, at a time when Jmol was exclusively using covalent atomic radii for binding criteria. In the case of mineral oxides, like kaolinite, it was binding aluminum to oxygen alright, but also binding Al to Al _thru_ the oxygen as well, as an example of many, many superfluous bonds. We worked out a compromise that when the oxidation state of an element was supplied, Jmol would use that ionic radius instead of the covalent atomic radius. This appears to work fine to address the inorganic compounds for which it was designed.
I supplied 'handbook' values for ionic radii, using the handbook at hand, correctly referenced in Bob's quotation. I will add that the table header says: "CRYSTAL IONIC RADII OF THE ELEMENTS Numerical values of the radii of the ions may vary depending on how they were measured.They may have been calculated from wavefunctions and determined from the lattice spacings or crystal structure of various salts.Different values are obtained depending on the kind of salt used or the method of calcu- lating. Data for many of the rare-earth ions were furnished by F. H. Spedding and K.Gschneidner." I never scrutinized the unusual oxidation states that Bob has picked out of that table, nor had occasion to use them in my work. Over the years, we have occasionally discussed on the Jmol list the use of the more sophisticated ionic radii put forward by Shannon (1976, citation below) that requires a coordination number as well, but that seems relatively burdensome calculations for little additional power. You won't find O(-1) there, just O(-2) since that's one of the foundation values for the Shannon's calculations. No Si(-1), Se(-1), Sn(-1), or Te(-1) in Shannon's 1976 table either. REVISED EFFECTIVE IONIC-RADII AND SYSTEMATIC STUDIES OF INTERATOMIC DISTANCES IN HALIDES AND CHALCOGENIDES Source: Acta crystallographica. Section A, Foundations of crystallography [0108-7673] SHANNON yr:1976 vol:32 iss:SEP1 pg:751 -767 Hope this helps, --Phil Barak ----- Original Message ----- From: Robert Hanson <[EMAIL PROTECTED]> Date: Tuesday, September 16, 2008 10:58 pm Subject: [Jmol-users] help needed -- bonding radii of anions To: jmol-users@lists.sourceforge.net > Jmol has some very odd bonding radii for unusual anions. Note the numbers: > > (8 << 4) + (-2 + 4), 1320, // "O-2" > (8 << 4) + (-1 + 4), 1760, // "O-1" // WAY too large? > > (14 << 4) + (-4 + 4), 2710, // "Si-4" > (14 << 4) + (-1 + 4), 3840, // "Si-1" // same problem here? > > (34 << 4) + (-2 + 4), 1910, // "Se-2" > (34 << 4) + (-1 + 4), 2320, // "Se-1" // same problem here? > > (50 << 4) + (-4 + 4), 2940, // "Sn-4" > (50 << 4) + (-1 + 4), 3700, // "Sn-1" // same problem here? > > (52 << 4) + (-2 + 4), 2110, // "Te-2" > (52 << 4) + (-1 + 4), 2500, // "Te-1" // same problem here? > > My question is, why would it be that the X(1-) numbers are way larger > than > the X(2-) numbers? > > I'm guessing "O(1-)" is for something like Na2O2, sodium peroxide. But > still, that makes no sense whatsoever. The reference reads: > > * This data is from > * Handbook of Chemistry and Physics. 48th Ed, 1967-8, p. F143 > * (scanned for Jmol by Phillip Barak, Jan 2004) > > Can someone look that up, please? Where are these numbers really from? > The problem is that carboxylic acid salts are given a way too large maximum > bonding radius for their oxygen atoms. > > I've temporarily set the O- bonding radius to 1000, but still.... > > Bob > > -- > Robert M. Hanson > 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 > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the > world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users