From chemistry-request@server.ccl.net  Mon Jul 24 02:12:10 2000
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Date: Mon, 24 Jul 2000 08:12:00 +0200 (MDT)
From: Kim Bolton <kim@phc.chalmers.se>
To: chemistry@server.ccl.net
Subject: Semiempirical codes for metal clusters
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Dear CCLers,

Can anyone suggest (free) *semiempirical* codes that can be used to
study metal clusters, especially sodium, aluminium and transition
metal (Vanadium) clusters.  I would like to couple this code to our
existing dynamics program so that we can run direct dynamics
simulations of these clusters.  Our previous studies (of molecular
systems) have been based on AM1 and PM3 methods, but I am experiencing
problems with these methods when applying them to the above metal
clusters (V parameters are not available, Na is a 'sparkle' and
converging even the Al dimer to the lowest energy surface is difficult
- using both Gaussian and MOPAC).

I have heard of the PM3(tm) and MNDO/d options but have no experience
with them.  Are they available as free (cheap), small (no too many
other peripherals), userfriendly packages?

Many thanks,
Kim

========================================================================
=  Kim Bolton                  E-mail - kim.bolton@hb.se               =
=  School of Engineering       Home page -                             =
=  University of Boraas           www.ing.hb.se/users/adm/kib/homepage =
=  SE-50190, Boraas            Phone - 46-31-7722271 / 46-33-174602 (W)=
=  Sweden                      Fax   - 46-31-167194  (W)               =
========================================================================


From chemistry-request@server.ccl.net  Mon Jul 24 09:12:54 2000
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Hi all...

 I want to view the structure for Gaussian98  IRC output with Review.
 So I tried to convert gaussian IRC output file to xyz(multi structure).

 But  "no bond length information for atom .........." message is out.
 I use babel16 and babelwin.  I dont know why.
 Please tell me why or show me a new idea for view structure.

Thanks.

--
*****************************************
  Jee-Young  Lee
  The Catholic University of  Korea
  Department of Chemistry
  Ph.D candidate
  Tel. +82-32-3403-674
*****************************************




From chemistry-request@server.ccl.net  Mon Jul 24 09:14:03 2000
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To: Steven Feldgus <sfeldgus@students.wisc.edu>
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Subject: Re: CCL:G98 ONIOM and TM
References: <v04011704b59f99d611d0@[128.104.71.134]>
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Dear Steve:

In reply to your message, I repeat my firm conviction that, in general, there are
no force fields for transitiom metal systems (see my latest book by Wiley, NY,
1996, p. 439, and in Combined QM and MM Methods, Ed. J. Gao, M. A. Thompson, ACS
Series 712, Washington 1998, pp. 66-91).

Regards
Isaac


Steven Feldgus wrote:

> We've been doing a lot of ONIOM(B3LYP:HF:UFF) jobs on a transition metal
> complex, and from our experience, we've found that the Gaussian UFF
> routines are not tremendously robust. I sent Gaussian several emails in
> late 1998 telling them of what we found, but never got any response. We
> needed to add several UFF atom types into the UFF code (in the utilam.f and
> utilnz.f files) in order for UFF to handle square planar rhodium complexes
> and coordinated olefins. The potential for linear bonds, like -CN, was also
> wrong (there was a maximum at 180). More recently, we've found that the
> ordering of the first few atoms can make a HUGE difference in whether UFF
> has a prayer of handling the molecule. Virtually everything in our molecule
> is within three bonds of rhodium, but we zeroed out what torsions we could.
> Having proper connectivity was critical for getting our systems to work.
>
> Steve Feldgus
> Dept. of Chemistry
> University of Wisconsin-Madison
>
> -= This is automatically added to each message by mailing script =-
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--
Isaac B. Bersuker
Institute for Theoretical Chemistry
Department of Chemistry & Biochemistry
The University of Texas at Austin
Austin, TX 78712, USA
Ph: (512) 471-4671
Fax: (512) 471-8696
Email: bersuker@eeyore.cm.utexas.edu




From chemistry-request@server.ccl.net  Mon Jul 24 00:34:42 2000
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From: "David  Hakala" <hakalad@ameritech.net>
To: "Henry Pang" <hpangaus@hotmail.com>, <CHEMISTRY@ccl.net>
Cc: <vinutha.ramakrishna@ntu.edu.au>, <Ted.Lloyd@vcp.monash.edu.au>,
        <marg@freon.chem.swin.edu.au>, <Brian.Yates@chem.utas.edu.au>,
        <b_duke@lacebark.ntu.edu.au>
References: <20000721000557.33833.qmail@hotmail.com>
Subject: Re: CCL:Seeing molecular orbitals?
Date: Sun, 23 Jul 2000 23:35:27 -0500
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Henry are you familiar with the following link:
http://alphanla.chem.uga.edu/~buyong/philo/philo.html
This is a summary of a thesis on the Philosophy of Computational Quantum
Chemistry by Dr. Buyong Ma done at the University of Georgia, which may be
of some interest to you, although from your comments I sense that you are
taking a significantly different approach than Ma.
                    Dave Hakala
----- Original Message -----
From: "Henry Pang" <hpangaus@hotmail.com>
To: <CHEMISTRY@ccl.net>
Cc: <vinutha.ramakrishna@ntu.edu.au>; <Ted.Lloyd@vcp.monash.edu.au>;
<marg@freon.chem.swin.edu.au>; <Brian.Yates@chem.utas.edu.au>;
<b_duke@lacebark.ntu.edu.au>
Sent: Thursday, July 20, 2000 7:05 PM
Subject: CCL:Seeing molecular orbitals?


> Hi Jens (Denmark)
>
> You said <But strictly speaking, this does not turn MOs into
> >observable quantities; MOs have no physical existence>
>
> I am new to computational chemistry. My background is medicine and human
> ecology in Australia. Your post is the first indicator I have seen over a
> wide range of CCL and books which signals caution. I am overwhelmed by the
> volume and intensity of work on the methodology and mensuration of
> molecules, as if that were the end in itself. No where do I see any
concern
> for a Philosophy of Computational Chemistry, which addresses just what is
> computational chemistry and what its purpose might be in our Universe. I
> cannot believe the objective is merely to measure everything and simply
> document these data?
>
> Even at my early stage, I am seriously pondering writing material jointly
> with my academic supervisor who is a computational chemist, which sets out
> the link (as I see it) between cosmology, quantum theory, relativity and
> higher dimensions theory on the one hand and computational chemistry on
the
> other. I think molecules are the beautiful building blocks of our Universe
> and created for a purpose. I decline the view molecules are just chance
> particles. I suspect from my reading of CCL, my intention may be seen as
> revolutionary if not outrageous and could well cause an uproar?
>
> Best wishes from Australia
>
> Dr Henry Pang
> Postgraduate Student, Computational Chemistry
> Faculty of Science, Information Technology and Education
> Northern Territory University
> PO Box U273 NT University 0815 Australia
> Mobile 61 419 682121 Fax 61 8 8946 6847 hpangaus@hotmail.com
>
> ----------------------------------------------------------------------
>
> >From: "Jens Spanget-Larsen" <jsl@virgil.ruc.dk>
> >To: CHEMISTRY@ccl.net
> >Subject: CCL:Seeing molecular orbitals?
> >Date: Thu, 20 Jul 2000 10:43:01 +0100
> >
> >Dear CCL:
> >
> >In a recent, most interesting publication ('Seeing molecular orbitals',
> >Chem.Phys.Letters 321, 78-82 [2000]) scanning tunneling microscopy is
used
> >to
> >observe the shapes of single molecular orbitals of the fullerene C60:
> >
> >   "..the scanning tunneling microscope (STM) is probing a single
molecular
> >   orbital (MO)."
> >
> >However, this reminds me of previous statements in the literature some
time
> >ago, associated with the advent of molecular photoelectron spectroscopy,
> >f.i.
> >
> >   "Chemists can see the orbital structure of even fairly large molecules
> >and no
> >   longer have to rely on the predictions of theoreticians"
> >
> >   "Photoelectron spectroscopy has demonstrated experimentally to
chemists,
> >   physicists and other sceptics that molecular orbitals really do exist"
> >
> >I wonder whether this is acceptable terminology, considering the fact
> >that molecular orbitals are model constructs; they are not physical
> >observables. By using approximations, such as Koopmans' approximation,
many
> >experimental observations can be conveniently interpreted in terms of
> >theoretical MO data. But strictly speaking, this does not turn MOs into
> >observable quantities; MOs have no physical existence.
> >
> >Any comments?
> >
> >Yours, Jens >--<
> >
> >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> >JENS SPANGET-LARSEN         Phone:  +45 4674 2000  (RUC)
> >Department of Chemistry             +45 4674 2710  (direct)
> >Roskilde University (RUC)   Fax:    +45 4674 3011
> >P.O.Box 260                 E-Mail: JSL@virgil.ruc.dk
> >DK-4000 Roskilde, Denmark   http://www.rub.ruc.dk/dis/chem/psos/
> >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> >
> >
> >CHEMISTRY@ccl.net -- To Everybody    |   CHEMISTRY-REQUEST@ccl.net -- To
> >Admins
> >CHEMISTRY-SEARCH@ccl.net -- archive search    |    Gopher: gopher.ccl.net
> >70
> >Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan:
> >jkl@ccl.net
> >
> >
> >
> >
> >
>
> ________________________________________________________________________
> Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com
>
>
>
> -= This is automatically added to each message by mailing script =-
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70
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jkl@ccl.net
>
>
>
>
>



From chemistry-request@server.ccl.net  Mon Jul 24 13:47:32 2000
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From: Gerry Tanoury <gtanoury@sepracor.com>
To: "'chemistry@ccl.net'" <chemistry@ccl.net>
Subject: Having problems restarting a transition state search at a specifi
	c step using Gaussian 98W
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I am involved in a transition state geometry optimization using Gaussian
98W.  The optimization was proceeding well, but took a wrong step after step
10.
I killed the job and wanted to restart the job at step 10 with an initial
force calculation.  The checkpoint file was saved as: Mg synchairTS
321G.chk.
I used the following in the route section to restart the calculation from
the checkpoint file.:

# opt(calcfc,ts,noeigentest) rhf/3-21g* geom(connectivity,check,step=10)

However, I obtained an error message and the following message in the output
file:
 
Redundant internal coordinates taken from checkpoint file:
 Mg synchairTS 321G.chk
 Z-Matrix unexpectedly found in input stream.
 Error termination via Lnk1e in d:\G98W\l101.exe.

I have not been able to get past this. I would appreciate your help.  I
assume this is just a simple syntax error that I cannot seem to correct.

Thank you for your help,

Gerald J. Tanoury
gtanoury@sepracor.com


From chemistry-request@server.ccl.net  Mon Jul 24 15:21:36 2000
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Date: Mon, 24 Jul 2000 16:24:27 -0300
To: chemistry@ccl.net
From: "Ajit J. Thakkar" <ajit@unb.ca>
Subject: CCL: Announcing CSTC 2001
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"

CSTC 2001: First E-mail Announcement

14th Canadian Symposium on Theoretical Chemistry  (CSTC 2001)
	August 5-9, 2001

Dear Colleague,

We are pleased to announce that the 14th Canadian Symposium on
Theoretical Chemistry (CSTC2001) will be held in Ottawa, Canada on Aug.
5-9, 2001.  Please mark this date on your calendar and plan to attend
this important milestone:  As the first Canadian Theoretical meeting of
the new millenium, we plan to look at new developments in theory, and to
have a number of experimental talks as well.  

Ottawa is the capital city of Canada.  With the Parliament Buildings,
the National Gallery, the proximity to Quebec (just across the Ottawa
River) and the Gatineau Park, Ottawa is a popular tourist destination
and a great place to bring your family for the week.  Ottawa has an
international airport with direct flights to many international cities
as well as connections through Montreal and Toronto airports.

The Conference will be held on the campus of Carleton University, with
inexpensive rooms available in the University Residence. For those who
prefer it, hotel and motel accomodation will be available near the
University. The Conference Web site is located at:
http://chemistry.carleton.ca/theory/cstc2001
<http://chemistry.carleton.ca/theory/cstc2001> 

At this time (July, 2000) the list of invited speakers is essentially
complete, and is shown below.  The Web Site already contains links to
Ottawa and to the University, for those who want a preview of coming
attractions.  Hope to see you in 2001!

	Conference Co-Chairs:  

	Jim Wright (Carleton) jim_wright@carleton.ca 
	Fred McCourt (Waterloo) mccourt@theochem.uwaterloo.ca

	Organizing Committee:

	Bob Leroy (Waterloo) <leroy@uwaterloo.ca> 
	Dennis Salahub (NRC, Ottawa) <dennis.salahub@nrc.ca> 
	P. Sundararajan (Xerox, Toronto)
	Ajit Thakkar (New Brunswick) <ajit@unb.ca> 

Invited Speakers:
W. Andreoni* (IBM, Zurich)                  P. Kollmann (San Francisco) 
R. Bader (McMaster)                         P. Kusalik (Dalhousie)
A. Becke (Queen's)                          W.-Ki Liu (Waterloo)
D. Bishop (Ottawa)                          R. Marcus (CalTech)
A. Boldyrev (Utah State)                    W. Meath (Western Ontario)
R. Boyd (Dalhousie)                         R. Miller (North Carolina)
R. Buenker (Wuppertal)                      G. Patey (British Columbia)
N. Cann (Queen's)                           J. Polanyi (Toronto)
D. Clary (London)                           L. Radom* (Canberra)
C. Cramer (Minnesota)                       T. Seideman (NRC, Ottawa)
M. Cybulski (Miami)                         A. Stone (Cambridge)
A. Dalgarno (Harvard)                       P. Sundararajan (Xerox, Toronto))
J. Delos (William & Mary)                   J. Tennyson (London)
T. Dunning (Pacific Northwest Labs)         A. Thakkar (New Brunswick)
B. Eu (McGill)                              A. van der Avoird (Njimegen)
N. Halberstadt (Toulouse)                   J. Watson (NRC, Ottawa)
J. Hutson (Durham)                          T. Ziegler (Calgary)
P. Jorgensen* (Aarhus)                      R. Zare (Stanford)
R. Kapral (Toronto)

*acceptance is still tentative as of July 21, 2000



From chemistry-request@server.ccl.net  Mon Jul 24 15:02:43 2000
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Date: Mon, 24 Jul 2000 15:05:16 -0400
From: "Michael K. Gilson" <gilson@carb.nist.gov>
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Dear Colleagues,
<p>I've just posted an introduction to continuum electrostatics with application
<br>to molecular modeling to my web-site as a pdf file.&nbsp; If you are
interested, go to:
<br><a href="http://gilsonlab.umbi.umd">gilsonlab.umbi.umd.edu/</a>
<br>and select "Intro Electrostatics" at the bottom of the right-hand panel.
<p>Please let me know of any errors or important omissions.&nbsp; More
generally,
<br>I would be interested in knowing whether you found it helpful!
<p>Mike Gilson</html>

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Subject: RE: Having problems restarting a transition state search at a spe	cifi
 c step using Gaussian 98W
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Is there, in fact, a Z-matrix in the input?  I get the same error when I use
geom=check and forget to delete the lines containing the (original
input)z-matrix.

--David Shobe
Süd-Chemie Inc.
phone (502) 634-7409
fax     (502) 634-7724
email  dshobe@sud-chemieinc.com

Any opinions herein are not necessarily representative of Süd-Chemie.


-----Original Message-----
From: Gerry Tanoury [mailto:gtanoury@sepracor.com]
Sent: Monday, July 24, 2000 1:45 PM
To: 'chemistry@ccl.net'
Subject: CCL:Having problems restarting a transition state search at a
specifi c step using Gaussian 98W


I am involved in a transition state geometry optimization using Gaussian
98W.  The optimization was proceeding well, but took a wrong step after step
10.
I killed the job and wanted to restart the job at step 10 with an initial
force calculation.  The checkpoint file was saved as: Mg synchairTS
321G.chk.
I used the following in the route section to restart the calculation from
the checkpoint file.:

# opt(calcfc,ts,noeigentest) rhf/3-21g* geom(connectivity,check,step=10)

However, I obtained an error message and the following message in the output
file:
 
Redundant internal coordinates taken from checkpoint file:
 Mg synchairTS 321G.chk
 Z-Matrix unexpectedly found in input stream.
 Error termination via Lnk1e in d:\G98W\l101.exe.

I have not been able to get past this. I would appreciate your help.  I
assume this is just a simple syntax error that I cannot seem to correct.

Thank you for your help,

Gerald J. Tanoury
gtanoury@sepracor.com


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Date: Mon, 24 Jul 2000 18:19:21 -0400
From: "Michael K. Gilson" <gilson@carb.nist.gov>
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Hi,
<p>Sorry about the hyperlink problem; hopefully this will
<br>work:
<p><a href="http://gilsonlab.umbi.umd.edu">gilsonlab.umbi.umd.edu</a>
<p>Mike Gilson</html>

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