Dear Per-Ola Norrby:

I understand your point. But I really = don't want to=20 compare wit X-rays, but to do a comparison
between calculated = structures. Suppose, for=20 example, that  I optimize the geometry of a molecule =
with increasing basis set levels. Thus I have an STO-3G, 3-21G, 6-31G, = 6-311G=20 optimized structures.
Then I calculate the=20 RMSD between each of the structures and that coming from the 6-311G=20
optimization (the=20 highest level in this example). I guess that the RMSD is going to = decrease=20  from
a maximum value for=20 the STO-3G down to 0 corresponding to the 6-311G with = itself.

Of course, the best match will be 0. = But beside=20 this, can we take a RMSD value (what I call the
threshold value in my previous message) = and=20 consider it closely enough to the best match ?
In order words, that the structure = optimized with,=20 say 6-31G, will be almost as good as 6-311G ?

I know that the example I has given is = a very=20 simple and moreover abstract one. That is why I
asked my question in the CCL hoping = that the=20 experience of the members with different
molecular geometry optimizations will = help me. Of=20 course, I understand the problem in terms
of listings of bonds and = angles.

&nbs= p;            = ;            =             &= nbsp;          =20 Daniel

********************************************************************= **
Dr.=20 Daniel Glossman-Mitnik
Centro de Investigaci=F3n en Materiales = Avanzados=20 (CIMAV)
LAQUICOM - Laboratorio de Qu=EDmica Computacional
Miguel = de=20 Cervantes 120 - Comp. Ind. Chihuahua
Chihuahua, Chih. 31109 - = MEXICO
Tel.:=20 (52) 614 4391151
FAX: (52) 614 4391112
E-mail: daniel.glossman{at}cimav.edu.mx=
= ;=20 glossman{at}hotmail.com
&n= bsp;         =20 dglossman{at}yahoo.com
**********= ************************************************************
----- Original Message -----
From:=20 Per-Ola = Norrby=20
Sent: Friday, August 08, 2003 = 5:41=20 AM
Subject: Re: CCL:summary for = program for=20 superimposing (small) molecules and new question

Dear=20 Daniel,

Before I present=20 the summary, I was to ask the (neccessary)
follow-up=20 question:  In your experience, when a = comparison
of an = experimental=20 molecular structure (i.e. X-rays) and its
calculated=20 (Gaussian) counterpart is done, which will be = the
treshold RMSD value=20 which can be considered acceptable ?

The = RMSD value=20 is NOT a good measure of quality.  One reason is that soft modes = (mainly=20 torsions) are easily distorted by crystal packing, leading to huge=20 discrepancies if you only look at RMSD.  A case in point is = biphenyl,=20 where the crystal adopts a planar structure becuase it packs better, = whereas=20 the gas phase global minimum has a torsion angle around 41 = degrees.

You can = either=20 use a comparison that is insensitive to these discrepancies, or do the = calculation in the crystal (requiring QM with periodic boundaries, not = in=20 Gaussian).  I'd recommend comparison of lists of bond lengths and = angles.  Alternatively, you can use the energy of the crystal = structure=20 calculated by Gaussian and compare it to the global minimum in = Gaussian, but=20 that requires constrained relaxation of the crystal structure to allow = for=20 differences in paradigm between X-ray and QM.

Best=20 regards,

Per-Ola = Norrby
```--=20
```
Per-Ola Norrby, Assoc. Professor,=20 http://compchem.dfh.dk/PeO/
Technical University of Denmark, = Department of=20 Chemistry
Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, = Denmark
Email:=20 pon{at}kemi.dtu.dk  tel +45-45252123,  fax=20 +45-45933968
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