From chemistry-request@server.ccl.net Sun May 11 18:41:02 2003 Received: from mx3.trentu.ca ([192.75.12.4]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h4BMf2t14858 for ; Sun, 11 May 2003 18:41:02 -0400 Received: (qmail 5723 invoked by uid 504); 11 May 2003 22:41:02 -0000 Received: from elewars@trentu.ca by mx3.trentu.ca by uid 501 with qmail-scanner-1.14 (fsecure: 4.15/4370/2003-05-09/2003-05-08. 2003-05-07/ Clear:. Processed in 16.289036 secs); 11 May 2003 22:41:02 -0000 X-Qmail-Scanner-Mail-From: elewars@trentu.ca via mx3.trentu.ca X-Qmail-Scanner: 1.14 (Clear:. Processed in 16.289036 secs) Received: from unknown (HELO trentu.ca) (209.42.101.30) by mx3.trentu.ca with SMTP; 11 May 2003 22:40:45 -0000 Message-ID: <3EBED228.3A272946@trentu.ca> Date: Sun, 11 May 2003 18:43:52 -0400 From: elewars X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: Jan Labanowski , chemistry@ccl.net Subject: Re: CCL:cartesians to z-mat and back References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit 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@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@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net