At 15:10 11/01/2004 -0500, Eric Martz wrote: [and subsequent discussion...]
Are you talking about "used" for determining the presence of a covalent bond, or "used" in the spacefill rendering?
If the latter, do you really mean covalent radii?
As stated in
http://www.umass.edu/microbio/rasmol/rasbonds.htm
RasMol uses van der Waals radii or "united atom radii" by default for spacefill.
I think Jmol should do the same for backward compatibility.
I've never been clear about the rationale for using vdW radii in spacefill rendering instead of covalent radii.
Most of the principles will be found in "The Nature of the Chemical Bond" by Pauling (pub. Cornell)
The covalent radius is used to estimate whether elements are bonded. It works on the plausible but untheoretical idea that the distance between two bonded atoms is a linear function of the atoms.
The single bond distance is: covA + covB.
The values can be determined from the lengths of X-X bonds and Y-Y bonds and perhaps regressing against X
Many bonds deviate from this as the bonds order deviates from 1.0 Pauling developed a relationship (see also Dunitz "The structure of organic molecules" (Cornell) as:
r(A-B) = covA + covB - 0.7 log10(bondOrder)
If a molecule has only single bonds and the atoms are plotted with covalent radii then the spheres should just touch.
In ionic solids the coordination geometry can be simply modelled by the size of the holes in the lattice. In critical cases the ions are assumed to be in contact so that in (say) NaX the Na...X distance is half the cell edge. This does not lead unambiguously to individual values, but reasonable separations are possible and tabulated as ionic radii. If you draw the alkali halides with ionic radii then the M+ and X- should be in contact
In covalent crystals there is a minimum observed distance between non-bonded molecules, dependent on the atoms. This similarly gives rise to a set of covalent radii. Thus in graphite or benzene the non-bonded atoms are never less than 3.4 A distance giving a vdw radius of ca 1.7 for carbon. If you draw these with vdw radii then there should be places where the molecules just touch.
It's a matter of personal taste as to what radii are used and for what purpose. In a molecular crystal the VDW radii will capture "most" of the volume and "most" of the valence electrons. For that reason some people regard it as the shape of the molecule. Another approach is the Connolly surface, determined by rolling a probe (normally solvent) round the molecule and denoting every point of contact by a dot. This hat the serendipitous result that it gave a pseudo-transparent surface which could be clipped in a useful manner.
In very simple terms I'd suggest vdw radii for space filling in covalent molecules and ionic radii for single ionic species but it is a matter of taste in the end.
P.
Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069
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