Subject: cartesians to z-mat and back

From: Jan Labanowski <[email-masked]>
Date: Mon, 28 Apr 2003 09:36:23 -0400 (EDT)

I love MOLDEN and use it often for my geometry conversions. It comes
with the Z-matrix editor:

http://www.cmbi.kun.nl/~schaft/molden/molden.html

It should be stressed that conversion of cartesians to Z-matrix can only
be a trivial task for molecules that are trees (i.e., do not contain cycles).
When rings (or more complicated arrangements, like cages, say, cubane) are
present, the well behaved Z-matrix should contain dummy atoms. You can try
to understand the problem by build the Z-matrix in such a way
that changing one parameter does not affect any other parameters.

For example, the z-matrix for benzene ring has to involve a centroid (a dummy
atom in the center of the ring) or otherwise, changing one torsion angles
within the ring will change other torsion angles. With the centroid, and
the rays going from it to the real atoms, you can build a Z-matrix which
does not involve dependencies between parameters.

Now... Can the software detect such situations automatically and deal with
them. Sure... However, quite frankly, I did not see much of such 
packages around. It is not a trivial problem, and even for simple molecules
with cycles, there are many ways to represent their geometry as a Z-matrix.
And deciding which Z-matrix is better, is again not a trivial thing. While
there are obviously objective measures, this is still an art, and the
beauty of the Z-matrix is in the eye of the beholder. And while there are
methods which make Z-matrix less important for unconstrained optimization
of the whole molecule (e.g., redundant internal coordinates in Gaussian),
there is nothing better than a well behaved Z-matrix when doing partial
optimizations of chosen geometrical features of the molecule(s), e.g.,
when studying transition states and reaction paths.

Jan

Jan K. Labanowski         |  phone: 614-292-9279,  FAX: 614-292-7168
Ohio Supercomputer Center |  E-mail: [email-masked] 
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