Re: CCL:cartesians to z-mat and back

2003 May 11
 I might just add that
 As Jan Labanowski implies, writing an algorithm to convert a general set of
 molecular Cartesians to a good Z-matrix is a problem in artificial intelligence
 (the converse is trivial).
 The dying (?) art of writing a Z-matrix is treated nicely and compactly, with
 useful caveats, in _A Handbook of Computational Chemistry_, Tim Clark, Wiley,
 New
 York, 1985; pp 102-119.
 E. Lewars
 ======
 Jan Labanowski wrote:
 > 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: jkl "at@at" ccl.net
 > 1224 Kinnear Rd,          |  http://www.ccl.net/~jkl
 > Columbus, OH 43212-1163   |  http://www.ccl.net/    http://asdn.net/
 >
 > -= This is automatically added to each message by mailing script =-
 > CHEMISTRY "at@at" ccl.net -- To Everybody  | CHEMISTRY-REQUEST "at@at"
 ccl.net -- To Admins
 > Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: jkl "at@at" ccl.net