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From: Valentine Ananikov <val@cacr.ioc.ac.ru>
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To: CCL_post <CHEMISTRY@server.ccl.net>
Subject: Re-REPLY: CCL:1,3,5-cyclohexatriene
References: <39285C3B.2D92209C@trentu.ca>
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    Hello,

Not all of the possible 1,3,5-cyclohexatriene isomers could be
assumed as a resonance structures, neither the vibrational
extremes.

For example, cis,cis,trans-1,3,5-cyclohexatriene, so called
"Mobius benzene", does not seem to fit into the resonance
structures active space. It may be converted to classical
planar forms through the trans/cis isomerization, however
this implies some activation barrier.

The comments below concerning the resonance hybrid and real 
existence of a compound are qualitatively correct. Perhaps,
somebody may formulate the quantitative rules also?

best regards, Valentin.


> 
> 2000 mAY 21
> 
> Hello,
> 
> The answer to your question (below), phrased as a general problem, is
> not as quite simple as one may think. The conventional response would be
> that cyclohexatrine structures are resonance structures (canonical
> structures) contributing to the actual structure, a resonance hybrid,
> and so can't have any real existence: they are just bond-stretching
> vibrational extremes with benzene vibrating about a geometry of mean
> (average) hexagonal symmetry (think of a Morse curve). the energy of the
> purely hypothetical 1,3,5-cyclohexatriene has been evaluted in
> connection with its use as areference molecule in assigning a resonance
> energy to benzene (e.g. work by M. J. S. Dewar--treated in some org chem
> textbooks).
> 
>  So much for benzene, but for cyclobutadiene the alternating C-C/C=C
> structures are real: the potential energy surface has two minima
> separated by a transition state. Predicting the results for simple
> polyene cases requires, usually, only knowing about aromaticity and
> antiaromaticity and the Hueckel rule, but _generally_ distinguishing
> between resonance (as in benzene) and valence tautomerism (as in
> cyclobutadiene) requires actual calculation. The problem of "the thin
> line" (quoting Paquette) between the two was discussedby L. Paquette in
> J Am Chem Soc in a paper on homoaromaticity about 10-15 years ago.
> 
> E. Lewars
> ====
> 
> -------- Original Message --------
> Subject: CCL:1,3,5-cyclohexatriene
> Date: Thu, 11 May 2000 09:21:17 +0400
> From: Valentine Ananikov <val@cacr.ioc.ac.ru>
> Organization: IOC
> To: CCL_post <CHEMISTRY@server.ccl.net>
> 
>    Dear List Members,
> 
> Does anybody have an information about predicted structure and
> stability for 1,3,5-cyclohexatriene?
> 
> I mean a six-membered ring with alternating single and double
> C-C bonds, but without aromatic pi-electrons delocalization due
> to non-planar conformation (i.e. non-planar benzene isomer).
> Would such structure exist in principle?
> 
> Thanks!  Valentin.
> 
> ====================================================================
>                                              ,         ,      ,   ,
> Valentine P. Ananikov                        |\\\\ ////|     /////|
> NMR Group                                    | \\\|/// |    ///// |
> ND Zelinsky Institute of Organic Chemistry   |  |~~~|  |   |~~~|  |
> Leninsky Prospect 47                         |  |===|  |   |===|  |
> Moscow  117913                               |  |   |  |   |   |  |
> Russia                                       |  | A |  |   | Z |  |
>                                               \ |   | /    |   | /
> e-mail: val@cacr.ioc.ac.ru                     \|===|/     |===|/
> http://nmr.ioc.ac.ru/Staff/AnanikovVP/          '---'      '---'
>   Fax +7 (095)1355328   Phone +7 (095)9383536
> ====================================================================

====================================================================
                                             ,         ,      ,   ,
Valentine P. Ananikov                        |\\\\ ////|     /////|
NMR Group                                    | \\\|/// |    ///// |
ND Zelinsky Institute of Organic Chemistry   |  |~~~|  |   |~~~|  |
Leninsky Prospect 47                         |  |===|  |   |===|  |
Moscow  117913                               |  |   |  |   |   |  |
Russia                                       |  | A |  |   | Z |  |
                                              \ |   | /    |   | /
e-mail: val@cacr.ioc.ac.ru                     \|===|/     |===|/
http://nmr.ioc.ac.ru/Staff/AnanikovVP/          '---'      '---'
  Fax +7 (095)1355328   Phone +7 (095)9383536
====================================================================

From chemistry-request@server.ccl.net  Mon May 22 03:01:43 2000
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Hello, 

I've got a problem with analyzing data gathered during a MD simulation
with Discover and InsightII (a protein solvated in Water, about 16000
atoms). The .his file, where the trajectory data is stored, is huge
(more then 1 Gb) because the coordinates of water molecules are stored
also. When I try to load the trajectory into InsightII, the program
chrashes because of insufficient memory. As I'm only interested in the
coordinates of the protein itself I wondered wether there is a
possibility to tell Discover not to save the water molecule coordinates
in the trajectory file. 
I'd be happy if someone could help me.

Ute



------------------------------------
Ute Platzer
Molecular Biophysics Department
DKFZ (German Cancer Research Center) Heidelberg, Germany
mailto:uplatze@gwdg.de

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Subject:       SUMMARY: ab initio hyperfine constants
Priority: normal
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22 May 2000
SUMMARY of the answers to 
AB INITIO HYPERFINE CONSTANTS question

Dear CCL'ers,

I asked a question about the hyperfine constants from 
ab initio methods (listed at the end of this message)
two weeks ago. Thanks a lot to Dr. David Feller. You 
are the only person who has replied. I appreciate 
your efforts highly. 

Many people asked me to summarize the replies in return.
Hence I present this summary compiled from two
letters  from AUTHOR of the paper cited in my  question.  

Good luck with your calculations.
Adrian

------------------------EXCERPTS:--------------------------

I think there may be a misunderstanding here.  In our JCP 
paper on NO we used a finite field approach to computing 
the isotropic hyperfine properties with methods like UMP2, 
UMP3, UMP4 and UQCISD(T). The spin denisty matrix wasn't 
involved.  As far as I know, it isn't possible to obtain 
a UQCISD(T) density matrix from Gaussian. But maybe that 
has changed.

The Gaussian options that we used are as follows:
# UQCISD(T)=FULL/GEN SCF=(DIRECT,NOSINGLEPOINT) 
# UNITS=AU FIELD=F(2)-4

I don't have access to that paper from home (where I'm 
writing this), but I believe we did 2 point differencing 
to predict the isotropic hyperfine property at each nucleus.  
In our procedure, the isotropic hyperfine property is given 
as the derivative of the energy with respect to the applied 
field, evaluated at zero field.  For example, we ran 
calculations at +/- 0.0001 or +/-0.0004 andused a 2-point 
formula to obtain the derivative at zero field.
(f+) - (f-)/2*delta, where f+ is the energy with the positive 
field and f- is the energy at negative field.  Delta is 
the field strength. That just gives you the raw value of 
the property in atomic units.  You then need to convert that 
raw value into something useful, like MHz or G.

This has to be done for each nucleus of interest.

You should be sure to correlate *ALL* electrons, 
as the property is very sensistive to core correlation.  
The other methods require nothing more than changing 
the method indicated in the options.

David Feller                                | d3e102@emsl.pnl.gov 
Environmental Molecular Sciences Lab., K8-91| Box 999
Pacific Northwest National Laboratory       | Richland, WA 99352 
                                            | Fax: 509-375-6631


----------------------MY QUESTION---------------------------
I have read some papers of Chipman, Feller and Carmichael
about evaluation of the isotropic hyperfine coupling
constants (HFCC's) from ab initio methods. Unfortunately,
I have got some problems in the application (Gaussian94/98)
of the procedures described there, that are mainly of 
technical nature. 
Let me use the computations of the isotropic splittings for
NO radical (2 PI) as an example [D.Feller et al. J.Chem.Phys.
99 (1993) 2829].

Determination of the isotropic hyperfine constants using 
a given method (QCISD for instance), that are listed as 
a part of the population analysis output, requires inclusion
of the keyword Density=Current in the job's route section 
i.e.:  
%chk=filename
# UQCISD=(Conver=8,Full)/Gen SCF=(Tight,NoDIIS,MaxCyc=256)
# Density=Current Prop=EPR

Title section

0   2
o    0.000000    0.000000    0.000000
n    1.150431    0.000000    0.000000

basis set description

Of course, SCF and Prop=EPR keywords denote single point 
(but with tight convergence criteria) calculations and 
evaluation of the anisotropic hyperfine couplings, respectively.
The main problem is that the generalized densities are 
available only for HF, MP2, MP3, MP4(SDQ), QCISD, CCD and CISD
methods.
My question are:
1. How to calculate HFCC's using CCSD method that are included 
in Table II of the originally paper?
2. How to calculate HFCC's using QCISD(T) method? One can do this
from spin densities derived by finite-field perturbation theory 
in the presence of small Fermi contact field at each nucleus 
in turn but what changes in the input file should be made (in
comparison with this listed above). Should I use 
the Field=F(AtomNumber)FileSize command?
3. How to calculate HFCC's using CCSD(T) method?
4. How to calculate HFCC's using QCISD(TQ) method? Perturbation 
theory approach allows the inclusion of the effect of quadruple 
replacement through fifth order but how to avoid Density keyword
restrictions and what commands should be added to the route 
section of the input file?



From chemistry-request@server.ccl.net  Mon May 22 08:08:21 2000
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Dear CCL Users,

I've got a question about TD DFT method (in Gaussian 98). 

Is it possible to calculate excitations energies to the excited states
different from the ground state by 1 excitation within alpha framework and
1 excitation within beta? (using unrestricted formalism).


Tomek Borowski.


From chemistry-request@server.ccl.net  Mon May 22 05:41:07 2000
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Date: Mon, 22 May 2000 17:39:07 +0800
From: Yubo Fan <yubofan@guomai.sh.cn>
Subject: CheckPoint file converting
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Hi, everyone,

Are there some ways to convert G98 formatted checkpoint files into G94
ones? The OSs I am using are AIX 6.2, Redhat Linux 6.1 and Windows 98.

Thanks in advance.

--
=============================================================
Yubo Fan                         Email: yubofan@guomai.sh.cn
Organic Synthesis Lab
The Department of Chemistry
Fudan University                 Phone: 8621-65648139
No. 220 Handan Road              Fax:   8621-65641740
Shanghai, 200433
P. R. China
=============================================================





From chemistry-request@server.ccl.net  Mon May 22 11:59:01 2000
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Date: Mon, 22 May 2000 10:55:05 -0500
From: Monica Concha <mconcha@uno.edu>
Subject: Summary
To: "chemistry@ccl.net" <chemistry@ccl.net>
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Dear CCl'ers,

A few wanted me to summarize the replies to the CCL list.  Here it
comes,
and thanks to the six people who took time to respond.

Monica C. Concha
Research Associate
Dept. Of Chemistry
University of New Orleans
New Orleans LA 70148
E-mail mconcha@uno.edu


*********************************************************************
Q:

   I have been trying to optimize the vanadium dimer with multiplicity
of 3, using various dft methods. The problem is that depending on the
initial bond length, the dimer optimizes to different bond lengths with
different energies, and differ s**2 values.  The bond lengths only
differ
by about 0.01 Angstroms but the energies differ by 35 kcal.  The odd
thing is that the lowest energy corresponds to an s**2 value of 2.55
rather than the expected value of 2.0. Any suggestions?
**********************************************************************
A:

Hi Monica,

    If you haven't done much work with metal clusters before, you're
quickly going
to find out they are much tougher than simple organics.  The problem is
there are
lots of low-lying excited states arising from low overlap of the
incomplete d
shells.  In the case of V2, you have two dominantly s1d4 atoms bonded to
one
another, with the other atomic states, d5 and s2d3, probably mixing in.
This gives
you a large number of possible spin and orbital combinations to work
with.
    As for your DFT calculations, it's a given that you have to specify
spin.  But
in these cases, you may also have to play with the orbital occupations
in the
initial guess.  It's very easy for most codes to converge to excited
states of
these molecules.  The only solid solution is to be very thorough.
You've found two
different triplet states already, but it might not be guaranteed that
either is
actually the lowest energy triplet (or the ground state for that
matter!).  Be
aware of what states (d orbital occupations) are being converged.  Try
switching
around the orbital occupations and converging some other states.  Most
codes offer
some way of doing this either with the default initial guess or with a
restart
file.
    If you're worried about spin contamination, you might want to try a
restricted
open-shell approach.  I'd suggest sticking with unrestricted, though.
In this
case, I'd probably turn off any symmetry restrictions to allow the spins
to
localize.  I haven't reviewed the literature on V2, but I'd guess the
ground state
is singlet with one V alpha-spin s1d4 and the other beta-spin s1d4.  The
strong
exchange interaction between the d orbitals should be enough to localize
the spin.
But low-lying spin states could extend up to nonet states.
    Good Luck,

    Jason Perry

****************************************************************

Hi Mónica:

You should look at works of Casalot (Marsielle) on V-V bond in V2O4.

<Andre.Casalot@newsup.univ-mrs.fr>


Felicidades!!!

Julio César Llópiz Yurell
IMRE, UH
Zapata y G, Habana 10400, CUBA
Tel (537) 781182  Fax (537) 334247

******************************************************************
Hi Monika,

>from your non-integer value for <S^2> I conclude that
you used an unrestricted DFT method. Since V2 has
10 valence electrons but 9 bonding and 9 antibonding
combinations of atomic valence orbitals, I assume that
you converged to two different electronic states.

Although the p-functions of transition metals are not
occupied in the free atoms, they DO participate in bond
formation (e.g. 18 valence electron rule for TM complexes).
You can check that by printing out the MO vectors (i.e.
info on what basis functions/atomic orbitals participate in
a given MO) and compare them for your two optimized
structures.

If you have two different states, you need a multireference
method like CASSCF or MR-CI (maybe a powerful single
reference correlation method like CCSDT works too, but
that can only be decided after seeing the output from that
calculation). Anyhow, putting enough ligands around your
vanadiums to give them 18 valence electrons,
each, makes the molecule well-behaved again.

Stefan
______________________________________________________________________
Dr. Stefan Fau                    |      fau@qtp.ufl.edu
Quantum Theory Project     |     (352) 392-6714
University of Florida
Gainesville, FL 32611-8435
*******************************************************************
Hi,

  Before optimizing the V-V bond length, you need to sort out
the electronic structure.  That is, look at the initial guess
for starters, try and get a converged single point SCF and look
at the S**2 and occupation.  Is it reasonable?  Then you can
optimize the V-V bond length for whatever state you have found.
If you have spin contamination problems, you might try an rohf
calulation first to insure a reasonable spin function.
  It sounds like you have one triplet V-V state that is fully
optimized without spin contamination problems.  Compare the
electronic occupation with the 'bad' state.  Perhaps you can
switch around some orbitals in your higher energy but well
behaved case to find a lower energy triplet.  Perhaps a triplet
is a very high energy/unreasonable multiplicity for V2?  Atomic
spectral tables show the lowest doublet V neutral atom to be
10,900 cm-1 above ground state V.  The lowest V doublet without
an s2 population is 18,800 above the ground state.  So you're
paying a 4.7eV promotion simply to form reasonable doublets to
form the V2 triplet.  I don't have much experience with metal
cluster calculations though.  Hope this helps!

    - John
***********************************************************
Dear Monica,

I've recently come across a similar problem with VO (4 sigma ground
state). The problem was, that initial guess of occupied MO was totally
wrong (the distribution of electrons between different irreps). As I'm
using G98, the solution was quite easy: Guess=Alter (+ appropriate
labes of MO to exchange), and that was enough to get the proper
electronic
state.


Tomek Borowski
Chemistry Department
Jagiellonian Univ.
Krakow

*********************************************************
Dear Monica,

did you check the stability of your wavefunction? You mix in higher spin

states as
can be seen from the S2 value of 2.55

If you need help, please email directly to

thomas.strassner@ch.tum.de


Yours sincerely

Thomas Strassner

*********************************************************


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Content-type: text/html; charset=us-ascii
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<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
Dear CCl'ers,
<p>A few wanted me to summarize the replies to the CCL list.&nbsp; Here
it comes,
<br>and thanks to the six people who took time to respond.
<p><b><i><font face="Times">Monica C. Concha</font></i></b>
<br><b><i>Research Associate</i></b>
<br><b><i>Dept. Of Chemistry</i></b>
<br><b><i>University of New Orleans</i></b>
<br><b><i>New Orleans LA 70148</i></b>
<br><b><i>E-mail mconcha@uno.edu</i></b>
<br>&nbsp;
<p>*********************************************************************
<br><b>Q:</b>
<p>&nbsp;&nbsp; I have been trying to optimize the vanadium dimer with
multiplicity
<br>of 3, using various dft methods. The problem is that depending on the
<br>initial bond length, the dimer optimizes to different bond lengths
with
<br>different energies, and differ s**2 values.&nbsp; The bond lengths
only
<br>differ
<br>by about 0.01 Angstroms but the energies differ by 35 kcal.&nbsp; The
odd
<br>thing is that the lowest energy corresponds to an s**2 value of 2.55
<br>rather than the expected value of 2.0. Any suggestions?
<br>**********************************************************************
<br><b>A:</b>
<p>Hi Monica,
<p>&nbsp;&nbsp;&nbsp; If you haven't done much work with metal clusters
before, you're quickly going
<br>to find out they are much tougher than simple organics.&nbsp; The problem
is there are
<br>lots of low-lying excited states arising from low overlap of the incomplete
d
<br>shells.&nbsp; In the case of V2, you have two dominantly s1d4 atoms
bonded to one
<br>another, with the other atomic states, d5 and s2d3, probably mixing
in.&nbsp; This gives
<br>you a large number of possible spin and orbital combinations to work
with.
<br>&nbsp;&nbsp;&nbsp; As for your DFT calculations, it's a given that
you have to specify spin.&nbsp; But
<br>in these cases, you may also have to play with the orbital occupations
in the
<br>initial guess.&nbsp; It's very easy for most codes to converge to excited
states of
<br>these molecules.&nbsp; The only solid solution is to be very thorough.&nbsp;
You've found two
<br>different triplet states already, but it might not be guaranteed that
either is
<br>actually the lowest energy triplet (or the ground state for that matter!).&nbsp;
Be
<br>aware of what states (d orbital occupations) are being converged.&nbsp;
Try switching
<br>around the orbital occupations and converging some other states.&nbsp;
Most codes offer
<br>some way of doing this either with the default initial guess or with
a restart
<br>file.
<br>&nbsp;&nbsp;&nbsp; If you're worried about spin contamination, you
might want to try a restricted
<br>open-shell approach.&nbsp; I'd suggest sticking with unrestricted,
though.&nbsp; In this
<br>case, I'd probably turn off any symmetry restrictions to allow the
spins to
<br>localize.&nbsp; I haven't reviewed the literature on V2, but I'd guess
the ground state
<br>is singlet with one V alpha-spin s1d4 and the other beta-spin s1d4.&nbsp;
The strong
<br>exchange interaction between the d orbitals should be enough to localize
the spin.
<br>But low-lying spin states could extend up to nonet states.
<br>&nbsp;&nbsp;&nbsp; Good Luck,
<p>&nbsp;&nbsp;&nbsp; Jason Perry
<p>****************************************************************
<p>Hi M&oacute;nica:
<p>You should look at works of Casalot (Marsielle) on V-V bond in V2O4.
<p>&lt;Andre.Casalot@newsup.univ-mrs.fr>
<br>&nbsp;
<p>Felicidades!!!
<p>Julio C&eacute;sar Ll&oacute;piz Yurell
<br>IMRE, UH
<br>Zapata y G, Habana 10400, CUBA
<br>Tel (537) 781182&nbsp; Fax (537) 334247
<p>******************************************************************
<br>Hi Monika,
<p>from your non-integer value for &lt;S^2> I conclude that
<br>you used an unrestricted DFT method. Since V2 has
<br>10 valence electrons but 9 bonding and 9 antibonding
<br>combinations of atomic valence orbitals, I assume that
<br>you converged to two different electronic states.
<p>Although the p-functions of transition metals are not
<br>occupied in the free atoms, they DO participate in bond
<br>formation (e.g. 18 valence electron rule for TM complexes).
<br>You can check that by printing out the MO vectors (i.e.
<br>info on what basis functions/atomic orbitals participate in
<br>a given MO) and compare them for your two optimized
<br>structures.
<p>If you have two different states, you need a multireference
<br>method like CASSCF or MR-CI (maybe a powerful single
<br>reference correlation method like CCSDT works too, but
<br>that can only be decided after seeing the output from that
<br>calculation). Anyhow, putting enough ligands around your
<br>vanadiums to give them 18 valence electrons,
<br>each, makes the molecule well-behaved again.
<p>Stefan
<br>______________________________________________________________________
<br>Dr. Stefan Fau&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
|&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; fau@qtp.ufl.edu
<br>Quantum Theory Project&nbsp;&nbsp;&nbsp;&nbsp; |&nbsp;&nbsp;&nbsp;&nbsp;
(352) 392-6714
<br>University of Florida
<br>Gainesville, FL 32611-8435
<br>*******************************************************************
<br>Hi,
<p>&nbsp; Before optimizing the V-V bond length, you need to sort out
<br>the electronic structure.&nbsp; That is, look at the initial guess
<br>for starters, try and get a converged single point SCF and look
<br>at the S**2 and occupation.&nbsp; Is it reasonable?&nbsp; Then you
can
<br>optimize the V-V bond length for whatever state you have found.
<br>If you have spin contamination problems, you might try an rohf
<br>calulation first to insure a reasonable spin function.
<br>&nbsp; It sounds like you have one triplet V-V state that is fully
<br>optimized without spin contamination problems.&nbsp; Compare the
<br>electronic occupation with the 'bad' state.&nbsp; Perhaps you can
<br>switch around some orbitals in your higher energy but well
<br>behaved case to find a lower energy triplet.&nbsp; Perhaps a triplet
<br>is a very high energy/unreasonable multiplicity for V2?&nbsp; Atomic
<br>spectral tables show the lowest doublet V neutral atom to be
<br>10,900 cm-1 above ground state V.&nbsp; The lowest V doublet without
<br>an s2 population is 18,800 above the ground state.&nbsp; So you're
<br>paying a 4.7eV promotion simply to form reasonable doublets to
<br>form the V2 triplet.&nbsp; I don't have much experience with metal
<br>cluster calculations though.&nbsp; Hope this helps!
<p>&nbsp;&nbsp;&nbsp; - John
<br>***********************************************************
<br>Dear Monica,
<p>I've recently come across a similar problem with VO (4 sigma ground
<br>state). The problem was, that initial guess of occupied MO was totally
<br>wrong (the distribution of electrons between different irreps). As
I'm
<br>using G98, the solution was quite easy: Guess=Alter (+ appropriate
<br>labes of MO to exchange), and that was enough to get the proper electronic
<br>state.
<br>&nbsp;
<p>Tomek Borowski
<br>Chemistry Department
<br>Jagiellonian Univ.
<br>Krakow
<p>*********************************************************
<br>Dear Monica,
<p>did you check the stability of your wavefunction? You mix in higher
spin
<br>states as
<br>can be seen from the S2 value of 2.55
<p>If you need help, please email directly to
<p>thomas.strassner@ch.tum.de
<br>&nbsp;
<p>Yours sincerely
<p>Thomas Strassner
<p>*********************************************************
<br>&nbsp;</html>

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From chemistry-request@server.ccl.net  Mon May 22 21:01:13 2000
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From: Roy Jensen <royj@uvic.ca>
To: chemistry@ccl.net
Subject: metal halogen/sulfur clusters
Date: Mon, 22 May 2000 18:01:09 -0700
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I am looking for a method that reasonable predicts the structure of
transition metal--halogen or metal--sulfur clusters,
Metal(x)Halo/Sulfur(y) where 1<=x<=6 and 1<=y<=10. 

We have Gaussian and Hyperchem available; both running on PC's. Our
goal is to compliment our expt data with reasonable predictions on
structure and stability and explain some of the trends we observe.

I will summarize responses.

Roy Jensen

