Re: [Jmol-developers] Covalent bonding radius + autobonding

[Bob H. <ha...@st...>]

XeF8(2-)
XeF6(2-)
XeF2
XeF4

that enough reasons?

Miguel wrote:

> This problem pertains to autobonding and the 'covalent radius' of the
> noble gases.
> 
> --
> 
> Jmol must perform 'autobonding' when no bond connectivity data is present
> in the file ... .xyz for example.
> 
> The algorithm that is currently used is derived from open babel.
> 
>  distance <= covalentRadius(atom1) + covalentRadius(atom2) + 0.45 // bond
> tolerance
> AND
>  distance >= 0.4 // minimum bonding distance
> 
> I know that open babel makes other checks to determine whether or not a
> bond is appropriate. But Jmol does not currently do any other checks ...
> if two atoms are close enough (but not too close) then they will bond.
> 
> The table of covalent radii is taken directly from open babel.
> 
> I observe that the noble gases all have non-zero bonding radii. This means
> that Jmol will bond these things together if they are close enough. That
> seems like a problem to me.
> 
> Q: Why are there non-zero values for the covalent radii of the noble gases
> in openbabel?
> 
> Q: Is there any reason why we should not set them to zero in Jmol?
> 
> 
> I am reluctant to set them to zero in Jmol unless that is also done in
> open babel. But, I am also somewhat reluctant to add more complexity to
> the bonding algorithms in Jmol. Its job is rendering, not calculating.
> 
> 
> Thoughts/suggestions?
> 
> 
> Miguel
> 
> 
> 
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-- 

Robert M. Hanson, ha...@st..., 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:ha...@st...
http://www.stolaf.edu/people/hansonr

"Imagination is more important than knowledge."  - Albert Einstein