From XIENING@MEENA.CC.UREGINA.CA  Thu Jun  5 00:46:53 1997
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 4 Jun 1997 22:10:52 CST
Date: Wed, 04 Jun 1997 22:10:49 -0600 (CST)
From: "XIE, NING" <XIENING@MEENA.CC.UREGINA.CA>
Subject: summary
To: chemistry@www.ccl.net
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Hi, there,
Thanks to those who replied to my question as cited below. Here is the
summary of the discussion.


My question:
> 
> Hi, there,
> I need to calculate the energies of HOMO for some para-substituted phenyl
> methyl sulfides such as p-MeOPhSCH3, p-MePhSCH3, p-FPhSCH3, p-ClPhSCH3,
> p-NO2PhSCH3, PhSCH3 and their corresponding sulfoxides, and probably
> CH3SCH3 or (n-butyl)2S too. I have software like Gaussian 94 and Hyperchem
> at hand. I am wondering if someone can give me some suggestions that what
> kind of method (semi-empiracal or ab initio) and force field/basis set
> will work well with these compounds, I mean, give decent results? We tried
> HF/6-31G*  and becke3LYP/6-31G* on two compounds and got quite different
> results (on Gaussian94).
> Any infomation is appreciated.
> Thank you for your time. I'll summerize the discussion.
------------------------------------------------------------------------------
From sc18@truman.edu Wed Jun  4 09:20:51 1997
Date: Tue, 03 Jun 1997 18:40:15 -0500
From: sc18 <sc18@truman.edu>
To: "XIE, NING" <XIENING@MEENA.CC.UREGINA.CA>
Subject: Re: CCL:G:sulfur containing compounds

Hi,

I've been working with these kinds of compounds for a couple of years. 
See K.R.Fountain, et al. J.Org. Chem., 1997,2738, vol. 62, for
computations on the dimethylsulfonium salts.  We also have an article
earlier this year (same journal) on the leaving group behavior of these
compounds.

Sincerely,

Ken Fountain
========================================================================
From Alan.Shusterman@directory.Reed.EDU Wed Jun  4 09:21:02 1997
Date: Tue, 03 Jun 1997 16:53:20 -0700 (PDT)
From: Alan Shusterman <Alan.Shusterman@directory.Reed.EDU>
To: XIENING@MEENA.CC.UREGINA.CA
Subject: Re: CCL:G:sulfur containing compounds

Hi 
	Its not surprising that HF and becke3LYP gave very different results
for orbital energies. Theoretically, the HF and DFT orbital energies need not
(should not) agree.
	You don't say what you want the HOMO values for, but if you are trying
to estimate the ionization potential then any of the following methods should
prove useful:

AM1
PM3
HF/3-21G(*)
HF/6-31G*

Alan Shusterman
Department of Chemistry
Reed College
Portland, OR
============================================================================
From FAU@ps1515.chemie.uni-marburg.de Wed Jun  4 09:21:10 1997
Date: Wed, 04 Jun 1997 10:22:29 -0600 (MDT)
From: Stefan Fau <FAU@ps1515.chemie.uni-marburg.de>
To: XIENING@MEENA.CC.UREGINA.CA
Subject: Re: CCL:G:sulfur containing compounds

Hi ,

the different results for HF and DFT(B3LYP) are not surprising, since DFT 
includes a part of the correlation energy, which is important for (distorted) 
aromatic systems. Therefore either a well parametrized semiempirical method or 
DFT should be appropriate. It would be a good idea to check the results of the 
calculations against good literature values of Delta(H) for an isodesmic 
reaction like Me2S + PhS(O)Me --> Me2SO + PhSMe if you are interested in energy 
differences.

Maybe somebody else can tell you more specifically about methods that give good 
results with your molecules.
                                 Stefan
__________________________________________________________
 | Stefan Fau                fau@mailer.uni-marburg.de |
 |                                                     |
 | FB Chemie der Philipps-Universitaet Marburg         |
 | Hans-Meerwein-Str.                                  |
 | D-35032 Marburg                                     |
 -------------------------------------------------------
================================================================================

From cachau@fcindy5.ncifcrf.gov  Thu Jun  5 02:46:58 1997
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From: "Raul E. Cachau" <cachau@fcindy5.ncifcrf.gov>
Message-Id: <9706050244.ZM14662@fcindy5.ncifcrf.gov>
Date: Thu, 5 Jun 1997 02:44:46 -0700
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To: cachau@ncifcrf.gov
Subject: Symposium on Open Shell Calcs. FINAL
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                         **************
                       FINAL ANNOUNCEMENT
                         **************


          Quantum Chemistry Symposium on Current Aspects of    
                     Open-Shell Calculations                 
 
                           June 17, 1997
 
                     National Cancer Institute
             Frederick Biomedical Supercomputer Center
                     Frederick, Maryland, USA

  The schedule for the symposium is now available at the WWW address


                   ---------------------------               


  To access the symposium WWW page in USA enter:

                 http://129.43.50.12/tmmec/

  and look for the symposium icon (a shell) on the top-left  corner
  of the page. From outside USA find the mirror of TMMeC closest to
  your place in any of these locations:

       USA:      http://129.43.50.11/tmmec/mirrors.html
       Uruguay:  http://164.73.160.8/tmmec/mirrors.html
       Spain:    http://130.206.125.40/tmmec/mirrors.html
       Germany:  http://192.54.49.75/tmmec/mirrors.html

  When you have  access TMMeC, look for the symposium icon (a shell)
  on the top-left corner of the page.
  
                 ---------------------------               

  Address of the Symposium

       Dr. Raul E. Cachau
       NCI-FCRDC
       Frederick Biomedical Supercomputer Center
       Building 430
       Frederick, MD 21702-1201
     
       e-Mail: cachau@ncifcrf.gov
       Fax:    USA-(301)-846-5762
       Phone:  USA-(301)-846-6062

                 ---------------------------               


From mzim@mvax.cc.conncoll.edu  Thu Jun  5 08:46:56 1997
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Date: Thu, 5 Jun 1997 08:24:32 -0400 (EDT)
From: Marc Zimmer <mzim@mvax.cc.conncoll.edu>
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To: chemistry@www.ccl.net
Subject: A protein database question
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Hi

	Does anyone know of any software that will go through the Protein
Database and tabulate all the distances from the carbonyl carbon of
residue i to the amide nitrogen of residue I+2 (as can be done for small
molecules in the Cambridge Structural Database). If this doesnt exist is
there some program that will find all these distance within a protein? 

Thanks

Marc Zimmer
Chemistry Department
Connecticut College
New London
http://camel.conncoll.edu/ccacad/zimmer/MZ-8/MZ-8



From rconnors@WPI.EDU  Thu Jun  5 10:47:02 1997
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Date: Thu, 5 Jun 1997 09:53:41 -0400 (EDT)
From: Robert E Connors <rconnors@WPI.EDU>
To: chemistry@www.ccl.net
Subject: CCL: Sulfuric acid dielectric Constant
Message-ID: <Pine.OSF.3.95q.970605094832.7270A-100000@camd.WPI.EDU>
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I have not been able to locate a value for the dielectric
constant of 98% sulfuric acid.  Does anyone know where to
find or how to estimate this property?

Thanks,
Bob Connors

------------------------------------------------------------------------
Robert E. Connors
Professor of Chemistry
Worcester Polytechnic Institute
Worcester,MA  01609
email:rconnors@wpi.edu
fax:(508) 831-5933



From genghis@darkwing.uoregon.edu  Thu Jun  5 11:46:59 1997
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Date: Thu, 5 Jun 1997 07:57:44 -0700 (PDT)
From: Dale Andrew Braden <genghis@darkwing.uoregon.edu>
To: cclpost <chemistry@www.ccl.net>
Subject: open shell CIS code
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Dear CCL,

Does anyone know of any code (commercial or otherwise) that can do
configuration interaction singles (CIS) calculations on open-shell
systems?

I'll summarize.

Dale Braden
Department of Chemistry
University of Oregon
Eugene, OR 97403-1253
genghis@darkwing.uoregon.edu


From s.hogg@ic.ac.uk  Thu Jun  5 11:53:33 1997
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Subject: Contraceptive / Endocrine Modelling?
To: chemistry@www.ccl.net
Date: Thu, 5 Jun 1997 16:34:48 +0100 (BST)
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I'd just like to ask if there are any groups out there who are interested
(or are doing,) modelling of contraceptive interactions of hormones (things
like RU486, oestrogen, progesterone, oestradiols, etc.)  This is just out of
curiosity.

--	Simon Hogg
	Imperial College, London, UK

From malisa@nirvana.uncor.edu  Thu Jun  5 12:46:59 1997
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From: Malisa Chiappero <malisa@nirvana.uncor.edu>
Message-Id: <199706051337.NAA21624@nirvana.uncor.edu>
To: chemistry@www.ccl.net
Subject: dissociative reaction cooordinate


Dear CCL helpers:
                  I  need  to describe a reaction coordinate of a system that has neither a real minimum nor a transition state, that is, a dissociative surface. I am not sure whether I could use RHF and/or CI . The IRC strategy generally used for this purpose, needs a transition state (something that I do not have) to implement the steep-descent algorithm. For these reasons I am asking for help.
Please, if you have an answer and are willing to share your knowledge, I will appreciate your help.




From malisa@nirvana.uncor.edu  Thu Jun  5 12:59:27 1997
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Date: Thu, 5 Jun 1997 13:39:33 GMT
From: Malisa Chiappero <malisa@nirvana.uncor.edu>
Message-Id: <199706051339.NAA21633@nirvana.uncor.edu>
To: chemistry@www.ccl.net
Subject: dissociative reaction cooordinate


Dear CCL helpers:
                  I  need  to describe a reaction coordinate of a system that has neither a real minimum nor a transition state, that is, a dissociative surface. I am not sure whether I could use RHF and/or CI . The IRC strategy generally used for this purpose, needs a transition state (something that I do not have) to implement the steep-descent algorithm. For these reasons I am asking for help.
Please, if you have an answer and are willing to share your knowledge, I will appreciate your help.



                         Malisa

From berriz@chasma.harvard.edu  Thu Jun  5 13:05:35 1997
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From: berriz@chasma.harvard.edu (Gabriel Berriz)
Message-Id: <9706051614.AA17972@chasma.harvard.edu>
To: chemistry@www.ccl.net
Subject: Quaternion formula needed




Dear netters:

Is there a formula that will take as argument a set of two orthonormal
vectors X, Y in R^3, and yield a unit quaternion Q such that

                                  -1
                        Q*(0, X)*Q  = (0,1,0,0)

                                  -1
                        Q*(0, Y)*Q  = (0,0,1,0)

(It would then be automatically true that:
                                      -1
                        Q*(0, X x Y)*Q  = (0,0,0,1) .)

I wrote a simple two-stage algorithm to perform the required
computation, but it is rather inelegant, with several if-then
statements to handle "pathological" situations.  I'd prefer an
analytical expression, if it exists, that would allow general
mathematical manipulation.  Any information on this problem would be
greatly apreciated.

Thank you very much,

Gabriel Berriz
berriz@chasma.harvard.edu

From hinsen@lmspc1.ibs.fr  Thu Jun  5 15:47:06 1997
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Date: Thu, 5 Jun 1997 20:56:06 +0200
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From: Konrad Hinsen <hinsen@ibs.ibs.fr>
To: berriz@chasma.harvard.edu
CC: chemistry@www.ccl.net
In-reply-to: <9706051614.AA17972@chasma.harvard.edu>
	(berriz@chasma.harvard.edu)
Subject: Re: CCL:Quaternion formula needed


> Is there a formula that will take as argument a set of two orthonormal
> vectors X, Y in R^3, and yield a unit quaternion Q such that
> 
>                                   -1
>                         Q*(0, X)*Q  = (0,1,0,0)
> 
>                                   -1
>                         Q*(0, Y)*Q  = (0,0,1,0)
> 
> (It would then be automatically true that:
>                                       -1
>                         Q*(0, X x Y)*Q  = (0,0,0,1) .)

That depends on what you call "a formula". I doubt there is a formula
in terms of sines, cosines, and basic arithmetic; you always run into
singularities when doing the conversion in this direction. But there
is no singularity in the final result, i.e. Q as a function of X and Y
is well-behaved. So if you are willing to use a "nonstandard"
function, which would nevertheless have nice and easy to determine
analytical properties, you can probably come up with an analytic form.
The special function could numerically be calculated just like any of
the standard ones (i.e. by polynomial approximation).

Entering "speculation mode", I'd attempt to construct the full
transformation as two steps (first X->(1,0,0), then Q*Y->(0, 1, 0)).
For the first one do X x (1,0,0) = axis*sin(phi), and multiply it by
sin(phi/2)/sin(phi), expressed as a function of cos(phi) which you get
>from the dot product. If I didn't overlook anything that function
should be singularity-free. The second step would be easier since the
rotation axis is known to be (1, 0, 0). Once you have the quaternions
for the two parts, just take the product. The resulting formula won't
be simple, of course...
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                          | E-Mail: hinsen@ibs.ibs.fr
Laboratoire de Dynamique Moleculaire   | Tel.: +33-4.76.88.99.28
Institut de Biologie Structurale       | Fax:  +33-4.76.88.54.94
41, av. des Martyrs                    | Deutsch/Esperanto/English/
38027 Grenoble Cedex 1, France         | Nederlands/Francais
-------------------------------------------------------------------------------

From boufer@cennas.nhmfl.gov  Thu Jun  5 19:47:01 1997
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Date: Thu, 5 Jun 1997 19:00:16 -0400 (EDT)
From: Ahmed Bouferguene <boufer@CeNNAs.nhmfl.gov>
X-Sender: boufer@cennas
To: chemistry@www.ccl.net
Subject: Software to draw curves...
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Content-Type: TEXT/PLAIN; charset=US-ASCII



Hi netters, 

	I wonder if somebody knows a site from which one can dowload (for
free) a software drawing curves, functions (given by their explicit
forms), etc... 

						Thanks a lot. 




From churca@opium.q1.fcen.uba.ar  Thu Jun  5 19:55:06 1997
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Date: Thu, 5 Jun 1997 19:55:27 -0300 (ARST)
From: Ojitos <churca@opium.q1.fcen.uba.ar>
To: chemistry@www.ccl.net
Subject: Amsol Solvent in QSAR
In-Reply-To: <23626.9706051534@mtcsh.mt.ic.ac.uk>
Message-ID: <Pine.LNX.3.95.970605193632.3143B-100000@opium.q1.fcen.uba.ar>
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Hi

       Does anyone work with the program Amsol and uses the solvent model
(Aqueos or hidrocarbons) to calculate QSAR with a  molecule. I'm
interesting in shear information becouse I do not know anybody who work
with it.
                Thanks

Adrian Turjanski
churca@q1.fcen.uba.ar



From sra@bernal.anu.edu.au  Thu Jun  5 19:59:16 1997
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From: "Shoba Ranganathan" <sra@bernal.anu.edu.au>
Message-Id: <9706060909.ZM7782@bernal.anu.edu.au>
Date: Fri, 6 Jun 1997 09:09:14 -0500
In-Reply-To: Marc Zimmer <mzim@mvax.cc.conncoll.edu>
        "CCL:A protein database question" (Jun  5,  8:24am)
References: <Pine.OSF.3.95.970605082357.6816A-100000@oak.cc.conncoll.edu>
X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail)
To: Marc Zimmer <mzim@mvax.cc.conncoll.edu>
Subject: Re: CCL:A protein database question
Cc: CHEMISTRY@www.ccl.net
Mime-Version: 1.0
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Marc,

The IDITIS software (and the associated database) does exactly this.  It can
also address any other complex query that you can pose.

More information from the software company Oxford Molecular Group Inc :
http://www.oxmol.com/

Shoba


On Jun 5,  8:24am, Marc Zimmer wrote:
> Subject: CCL:A protein database question
>
> Hi
>
> 	Does anyone know of any software that will go through the Protein
> Database and tabulate all the distances from the carbonyl carbon of
> residue i to the amide nitrogen of residue I+2 (as can be done for small
> molecules in the Cambridge Structural Database). If this doesnt exist is
> there some program that will find all these distance within a protein?
>
> Thanks
>
> Marc Zimmer
> Chemistry Department
> Connecticut College
> New London
> http://camel.conncoll.edu/ccacad/zimmer/MZ-8/MZ-8

-- 
===========================================================
Dr. Shoba RANGANATHAN                     
Computational Mol Biology & Drug Design Group
Div. of Biochemistry & Mol. Biology 
John Curtin School of Medical Research                 
Australian National University          Tel: +616-279-8301                           
Canberra ACT 0200                       Fax: +616-249-0415
Australia.              email:Shoba.Ranganathan@anu.edu.au
                                 sra@bernal.anu.edu.au 
===========(http://biocomp.anu.edu.au/~sra/)==============

From rvenable@deimos.cber.nih.gov  Thu Jun  5 20:47:04 1997
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From: Rick Venable <rvenable@deimos.cber.nih.gov>
To: Ahmed Bouferguene <boufer@CeNNAs.nhmfl.gov>
Cc: chemistry@www.ccl.net
Subject: Re: CCL:Software to draw curves...
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On Thu, 5 Jun 1997, Ahmed Bouferguene wrote:
> 	I wonder if somebody knows a site from which one can dowload (for
> free) a software drawing curves, functions (given by their explicit
> forms), etc... 

Try the   gnuplot   program; for details, see

http://www.cs.dartmouth.edu/gnuplot_info.html

--
Rick Venable                  =====\     |=|    "Eschew Obfuscation"
FDA/CBER Biophysics Lab       |____/     |=|
Bethesda, MD  U.S.A.          |   \    / |=|  ( Not an official statement or
rvenable@deimos.cber.nih.gov  |    \  /  |=|    position of the FDA; for that,
http://nmr1.cber.nih.gov/           \/   |=|    see   http://www.fda.gov  )


From chmjs@pippin.cc.flinders.edu.au  Thu Jun  5 22:47:03 1997
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Date: Fri, 06 Jun 1997 11:37:34 +0900
To: chemistry@www.ccl.net
From: Matthew James Sykes <chmjs@flinders.edu.au>
Subject: Curve plotting 


In answer to the previous question on plotting:


The best programme is:

Sigmaplot:

Demo available from http://www.spss.com/software/science/sigmaplot/index.html

Excellent plotting programme designed specifically for science+engineering.

There is also a programme called Curve expert that can plot most graphs as
well as do regression analyses and spline fits etc..

I can't remember the web site, but use Infoseek and you'll get a match.

                        Cheers,
 
_____________________________________
Matthew Sykes
Phd student
Room 200A
Department of Chemistry
Flinders University
Adelaide


