Subject: COMPARING ISOMERS

From: "E. Lewars" <[email-masked]>
Date: Wed, 22 Feb 1995 17:10:28 -0500

When I suggested using the internuclear repulsion E to check if two isomers
are identical, I should have pointed out that enantiomers have precisely
the same energies--internuclear, electronic, etc (in the absence of a 
chiral perturbation; physicists may quibbl, too, that the negation of
parity by the weak nuclear force causes a miniscule difference in enantiomer
E's).  
Joel Polowin of HyperChem pointed out that as a practical matter identity
isn't an all-or-nothing phenomenon: how similar do two species have to be 
for a chemist to call them the same thing?  As several people said, there
are sophisticated algorithms for matching up two molecules and looking
at, e.g., RMS differences in geometric parameters.  I think the widely-
used MM program PCModel can do something like this; one or two other
programs were mentioned.  Joel's idea about a small tweak in one part
of a molecule causing a ratcheting effect that's amplified elsewhere
(cf. allosteric effects in enzymes?) is interesting.
Errol Lewars
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Regarding  internucl rep.--one could calc it for some test cases, alter
these geometries slightly, and see if it might be useful for the problem
at hand.
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