Re: [Open Babel] Covalent radii and bond order radii

[Geoff H. <ghu...@ws...>]

I should note that careful checking of the elements.txt revealed that 
it was basically unchanged from the equivalent file in the original 
Babel 1.6. So I've been wondering many of the same questions -- but I 
do have answers.

On Jul 26, 2004, at 8:29 AM, Peter Murray-Rust wrote:
> The "RCov" differs significantly from the values of covalent radii 
> that are found elsewhere (e.g. http://www.webelements.com )
> and the RBO appear to be closer to these other values.

...

> What is "RBO" - I am not familiar with the concept.
> How does "bond order radii" (usd in B.O. calc) work? Could covalent 
> radii be used instead?

The "bond order radii" were used in the original Babel code. The 
algorithm used for determining bond orders operated by comparing the 
distance between two atoms (e.g., a possible C=C bond) and scaled 
"covalent-like" radii. Certain bonds were flagged as possible multiple 
bonds based on this criteria. The rBO were used instead of the covalent 
radii -- for reasons I don't completely understand.

> Where did these values come from? (of course this may be ancient 
> history!)

I'm not particularly sure -- as you say, the rBO seem pretty close to 
the standard set of covalent radii. I don't know why the difference 
arose -- and I don't think any of the original Babel authors are 
reading this list anymore.

> Are there any definitive sources of radii that we should use (I would 
> suggest web elements if there are no other ideas).

As far as I'm concerned, any authoritative source is fine. There are 
obviously some nebulous copyright issues as far as compilation of data. 
Personally, I'm all in favor of merging the rBO and the covalent radii 
and establishing as complete and authoritative a compilation of much of 
this data as possible.

Somewhere around here, I have a paper establishing covalent radii 
systematically for many of the heavier elements... I'll see if I can 
dig it up again when it's not so late.

> Can the tabs in the table be replaced by spaces (or does it break the 
> reader)

In this particular table, any whitespace is fine.

> Obviously the values in the table are primarily for OB's purposes but 
> they are among the most complete compilation I have come across and 
> could be useful as a reference. As I've said before it could be useful 
> if the OpenSource chemistry community standardise on such things. (I 
> am sure that Jmol, CDK and JOELib will read this list and comment).

Both Open Babel and JOELib use the same data files -- with some minor 
formatting differences.

-Geoff