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.

Thanks in advance

&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

**********= ************************************************************

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

**********= ************************************************************

------=_NextPart_000_00B5_01C35D9B.C9197A30------- Original Message -----From:=20 Per-Ola = Norrby=20To:Dr. Daniel = Glossman-Mitnik=20Sent:Friday, August 08, 2003 = 5:41=20 AMSubject:Re: CCL:summary for = program for=20 superimposing (small) molecules and new questionDear=20 Daniel, Before I present=20 the summary, I was to ask the (neccessary)follow-up=20 question: In your experience, when a = comparisonof an = experimental=20 molecular structure (i.e. X-rays) and itscalculated=20 (Gaussian) counterpart is done, which will be = thetreshold 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 --=20Per-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