Subject: Conformational Isomers

From: "CBAS25 ::P_BLADON ::CBAS25" <[email-masked]>
Date: Thu, 23 Feb 1995 01:47:29 EST

Dear Dongchul Lim,

With regard to the conparisons of conformers.

There are several points to consider.

(1) If the problem involves small molecules like butane where the number 
of stable conformers is known, then simply superimposing the "unknown" 
structure on each of the "known" conformers in turn will give an answer.
The rms deviation of atom positions or some other figure of merit will afford
an answer even when an exact match is not achieved.

(2) If the structures are more complex, perhaps involving large membered rings,
then the number of conformers could be large.  But suppose that you have a set
of such structures, and wish to test which of them your "unknown" most 
resembles. You would still get an answer. 
If the "unknown" were a crystal structure and the "knowns" derived 
>from a conformer generating program, you would not expect a good match
necessarily.  What you could do then is to take the pair of best matched 
structures and refine them with your favourite MM or MO package, and see if 
they both decend into the same energy well.  

(3) To do the matching you could use atom to atom matching, or alternatively
use the icosahedral matching algorithm in programs like COMPARISONS or
CORRELATE.  The first of these programs will match an "unknown" against a
series of "unknowns", while the second would allow the correlation of a whole 
series of conformers. The matching of mirror-image forms is taken care of.   
Both programs are available from QCPE as part of the INTERCHEM package.  

Yours sincerely

Peter Bladon
[email-masked]
Phone/Fax +44-141-776-1718