From owner-chemistry@ccl.net  Thu Nov 30 06:54:18 1995
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Date:     Thu, 30 Nov 95 6:41:22 EST
From: George R Famini   <grfamini@cbdcom.apgea.army.mil>
To: chemistry@ccl.net
Subject:  Preliminary COMP Program for New Orleans
Organization:  International Programs Office
Priority:  Normal
Message-ID:  <9511300641.aa06383@cbdcom.apgea.army.mil>


Well folks,

I have pretty much finished putting together the symposia for the Division
of Computers in Chemistry (COMP) program for the New Orleans
American Chemical Sociey meeting (end of March 1996).  Below is
the preliminary agenda, representing only the listing of when the
symposia will happen.  As always, I reserve the right to change the
times of the symposia (or cancel one or more) without notice.  But, this
is the schedule we will attempt to adhere to.  

All of the symposia look to be very interesting, I will post a complete
program (with paper titles) in a few weeks.  Of special note is the
Computers in Chemistry award symposium, honoring Norman Allinger. 

If you have any questions concerning the schedule for New Orleans,
please do not hesitate to contact me.


					George R. Famini
					COMP Program Chair




 211th ACS National Meeting, New Orleans, LA                 DUE DATE:
                                                             December 18,1995

DIVISION OR COMMIDivision of Computers In Chemistry
PROGRAM CHAIRPERSG. R. Famini,  US Army Edgewood RD&E Center,  Aberdeen Prvg Gd, MD

                                                Poster   Estimated seating 
 Session Title                      Cosponsor  Session:     Key
                                    ing        Time & #     Speakers

 SUNDAY, MARCH 24 - AM
 A.Computational Chemistry Assisted                     250
   Drug Discovery
 B.Monte Carlo Methods in                               200
   Chemistry

 SUNDAY, MARCH 24 - PM
 A.Computational Chemistry Assisted                     250
   Drug Discovery
 B.Monte Carlo Methods in                               200
   Chemistry
 C.Physical/Chemical Property                           200
   Prediction

 MONDAY, MARCH 25 - AM
 A.Computational Chemistry Assisted                     250
   Drug Discovery
 B.Monte Carlo Methods in                               200
   Chemistry
 C.Physical/Chemical Property                           200
   Prediction

 MONDAY, MARCH 25 - PM
 A.Computational Chemistry Assisted                     250
   Drug Discovery
 B.Experimental Methods for         Division of         150
   CHemical Models                  Analytical
                                    Chemistry
 C.Physical/Chemical Property                           200
   Prediction

 MONDAY, MARCH 25 - EVE
   Sci-Mix                                     8:00 PM
                                                   11


 TUESDAY, MARCH 26 - AM
 A.Computers in Chemistry Award                         250
   Symposium Honoring Norman L.
   Allinger
 B.Experimental Methods for                             150
   Chemical Models

 TUESDAY, MARCH 26 - PM
 A.Computational Chemistry Assisted                     250
   Drug Discovery
 B.Molecular Modeling Applications  Division of         200
   to Environmental Problems        Environmental
                                    Chemistry
                                    Inc
 C.Frugal Chemist's Software        Division of         200
                                    Chemical
                                    Information

 TUESDAY, MARCH 26 - EVE
 A.General Poster Session                      7:00 PM
                                                   33


 WEDNESDAY, MARCH 27 - AM
 A.Semi-Empirical Methods:  Is      Division of         200
   There a Future?                  Physical
                                    Chemistry
 B.Molecular Modeling Applications                      200
   to Environmental Problems

 WEDNESDAY, MARCH 27 - PM
 A.Semi-Empirical Methods:  Is                          200
   There a Future?
 B.Molecular Modeling Applications                      200
   to Environmental Problems

 THURSDAY, MARCH 28 - AM
 A.Semi-Empirical Methods:  Is                          200
   There a Future?
 B.General Oral                                         100


 THURSDAY, MARCH 28 - PM
 A.Semi-Empirical Methods:  Is                          150
   There a Future?
 B.General Oral                                         100

From owner-chemistry@ccl.net  Thu Nov 30 09:24:20 1995
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Date: Wed, 29 Nov 1995 08:16:17 -0600
To: chemistry@ccl.net
From: ljs@interaccess.com (Louis J. Sharp IV)
Subject: Hyperchem


Is anyone out there using Hyperchem for modelling of polymer systems?  I
would be interested in knowing about it and would like to discuss some of my
ideas on this.

Lou Sharp

==========================================================================
Dr. Louis J. Sharp IV
Director Scientific Affairs
Dexter Packaging Products
Phone  (708)623-4200 ext 4418
email  ljs@interaccess.com
==========================================================================


From cwm@proteus.co.uk  Thu Nov 30 10:24:21 1995
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Date: Thu, 30 Nov 1995 15:03:56 +0000
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Hi all,

When designing new molecules in drug discovery projects, an important
consideration is the synthetic feasibility of the molecules. This is a somewhat
different question than programs like LHASA address since they seem to
concentrate on suggesting synthesis routes. Does anybody have information or
experience of synthetic feasibility programs? References to papers describing
the programs appear to be few and far between.

I will summarise to the net if there is any interest.

chris

-- 

Chris Murray                     | 
Proteus Molecular Design Ltd.,   |  Tel: 01625-500555
Lyme Green Business Park,        |  Fax: 01625-500666
Macclesfield, Cheshire,          |  Email: C.W.Murray@proteus.co.uk
SK11 0JL, UK                     |

From owner-chemistry@ccl.net  Thu Nov 30 10:54:21 1995
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From: "Michael Probst" <Michael.Probst@uibk.ac.at>
To: chemistry@ccl.net
Date:          Thu, 30 Nov 1995 16:53:01 +0000
Subject:       g94 compound freq+opt
Reply-To: michael.probst@uibk.ac.at
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Priority: normal
X-Mailer: Pegasus Mail for Windows (v2.01)


Dear Gaussian - experts:
The following input:




-----------------------------------------------
 #P BLYP/aug-cc-pVTZ SCF=DIRECT OPT=Z-MATRIX FREQ MAXDISK=13000000

 NITRAT:aug-cc-pVTZ

-1 1
 N1
 O2    1     RONN
 O3    1     RONN      2     AOON
 O4    1     RONN      2     AOON      3     TORS      0
Variables:
 RONN=1.271
Constants:
 AOON=120.
 TORS=180.
------------------------------------

seems to work well but upon cloeser looking there is a large energy 
difference between the energy at the end of the optimization 
(-280.470491943) and the energy calculated in the frequency step 
(-280.446822509). 
I would not expect the NO3- ion to behave that way and further, if I 
make a independent frequency calculation with the optimized N-O 
distance (1.280612 Angstroem) I get the same energy as in the 
optimization job (and, of course, different frequencies as in the 
compound job) 
Can somebody tell me the reason for the differences in the job with 
freq and opt together ?

Thanks a lot !
Michael


---------------------------------------------------------------------------
Michael Probst                          Internet: michael.probst@uibk.ac.at
Department of Inorganic Chemistry       Fax:      ++43(512)507 2934
Innsbruck University                    Tel:      ++43(512)507 5153
Innrain 52a
Austria

From rochus@felix.anorg.chemie.tu-muenchen.de Tue Nov 28 08:00:00 1995
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From: "Rochus Schmid" <rochus@felix.anorg.chemie.tu-muenchen.de>
Message-Id: <9511281351.ZM23908@felix>
Date: Tue, 28 Nov 1995 13:51:26 +0100
To: chemistry@www.ccl.net
Subject: Free energy calculation
Cc: rochus@felix.anorg.chemie.tu-muenchen.de



Dear Netters:

I'm new in that field and I have some questions concerning the calculation of
free energies of sissociation.

I have a molecule like this:

                       A2         B3
                         \       /
                          A1---B1---B2
                         /       \
                        A3        B4


I want to get the free energy of dissociation of bond A1-B1. My potential
energy function is a classical forcefield and the bond A1--B1 is parametrized
via QM-calculations (also the change in the forcefield of the fragments A and B
upon dissociation is parametrized analytically).

David A. Pearlman (J. Chem. Phys. 1993, 98, 8946) suggest thermodynamic
integration to be the method of coice. If I understood it correctly, I have to
sum up the components of the cartesian forces on all atoms along the vector
>from A1 to B1 (with oposite signs for the fragments A and B) and integrate the
over the distance between A1 and B1.

My problem are the internal degrees of freedom, which will be "converted" to
rotational and translational degrees of freedom if the coupling parameter
lambda reaches 1 (complete dissociation). I guess, it will take more and more
sampling for increasing lambda. And there must be a point, where it is not
longer reasonable.

What to do then?
Are there any tricks to make life easier?
Any hints?

I would appreciate every comment on this.
Thank you very much in advance.
I will summarize to the net.

Greetings,

Rochus




-- 

********************************************************************************
Rochus Schmid
Technische Universitaet Muenchen	Tel. 	++49 89 3209 3140
Anorganisch Chemisches Institut 1	Fax. 	++49 89 3209 3473
Prof. W. A. Herrmann			E-mail:	
Lichtenbergstrasse 4			rochus@felix.anorg.chemie.tu-muenchen.de
85747 Garching
********************************************************************************


From owner-chemistry@ccl.net Tue Nov 28 13:03:59 1995
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Date: Tue, 28 Nov 1995 10:03:11 -0800
From: mjf@biosym.com (Mark J Forster )
Subject: Chemical Shift and Shielding Calculations
Message-Id: <199511281803.KAA01618@iris120.biosym.com>
To: chemistry@ccl.net




Subject: Chemical Shift and Shielding Calculations. 

Seiji Mori asked the following question:

>   Dear Sirs,
> 
>  I posted to CCL about the methods of NMR calculation a fey days ago , and
> had an other question.
> In G94, I tried to calculate the chemical shifts , there are magnetic
> shieldings
snip... 
> Would you please tell me the physical meaning of isotropic  and anitrosopy, 
> and which is an equivalent of the experimental chemical shift? It is better
> that 
> you show the references. 
> 
>     Sincerely yours,
>     Seiji Mori email:smori@chem.s.u-tokyo.ac.jp

The property calculated by an ab initio shielding scheme is typically a
nuclear magnetic shielding tensor in the form of a 3x3 matrix. In 
physical terms the elements of the tensor represent the shielding along
x,y and z when the applied magnetic field is along x,y and z in turn.
This matrix may then be separated into symmetric and antisymmetric 
components, when the former is diagonalised then one obtains the three
principal components of the shielding tensor denoted 

	sigma(1,1) sigma(2,2) and sigma(3,3) 

with the convention 

	sigma(3,3) >= sigma(2,2) >= sigma(1,1)

the isotropic part of the shielding tensor is the trace or average of
these three components and represents the value expected for an atom
in a molecule that tumbles rapidly and isotropically. 
	trace = ( sigma(1,1) + sigma(2,2) + sigma(3,3)) /3

In non isotropic
systems such as single crystals or oriented liquid crystals the shielding
takes on an orientational dependence. The shielding anisotropy is defined
as 
	anisotropy = sigma(3,3) - ( sigma(1,1)+sigma(2,2) )/2

and is a measure of the deviation of the shielding from spherical symmetry.
For heavier nuclei the shielding anisotropy can be large (eg  > 5000 ppm 
in 199Hg and 205Tl compounds) and this can often be a significant 
mechanism for nuclear spin relaxation.

In addition the shielding asymmetry may be defined as

	asymmetry = (sigma(2,2)-sigma(1,1) ) / (sigma(3,3) -trace)

An axially symmetric shielding tensor has a non zero anisotropy but a
zero value for the asymmetry.

The chemical shift measured by NMR is the difference between 
the shielding tensors for a nucleus in the compound under study and in the 
reference compound (typically TMS for 1H, 13C and 29Si). So to compare
ab initio computed shielding with experimental chemical shifts two 
calculations will need to be performed one for the molecule under study
and one for the reference compound. In addition experimental shifts are
often found to be sensitive to environmental conditions such as solvent
used, temperature, salt concentration etc. These are usually not taken 
into consideration in an ab initio calculation and so the comparison may
only be valid if the intrinsic shift variations across a range of compounds
far outweigh the environmental effects. 


No references to hand at the moment but I hope this helps.




	


Best Wishes       __________________________________________________________
Mark             /
         ___    /                     
        /  /|  /                     Mark J Forster
       /  / | /                     Biosym / Molecular Simulations. 
      /__/__|/     \__O_/          9685 Scranton Rd, 
     /__/             |           San Diego, CA 92121, USA.
    /   |            /|          Tel: (619) 458 9990
   /  o |<--------  / |         FAX: (619) 458 0136
  /__ __|                      e-mail: mjf@biosym.com
       /                      Follower of Manchester United FC.   
      /                      FA cup winners 1990,  
     /     European cup winners cup winners 1991, League cup winners 1992, 
    /     FA Premier League champions 1993, FA charity shield winners 1993/4.
   /     FA Premier League champions AND FA cup winners 1994.   
  /_________________________________________________________

*******************************************************************************
* DISCLAIMER: Unless indicated otherwise, everything in this note is          *
* personal opinion, not an official statement of Biosym / MSI                 *
*******************************************************************************


From peon@medchem.dfh.dk Wed Nov 29 05:10:01 1995
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Date: Wed, 29 Nov 1995 11:10:00 +0100
To: "Moshe Olshansky" <moshe_o@VNET.IBM.COM>
From: peon@medchem.dfh.dk (Per-Ola Norrby)
Subject: Re: CCL:combining different basis sets - an addition
Cc: chemistry@www.ccl.net



Moshe Olshansky wrote <<first part deleted>>:
>
>P.S. and now I have an additional question:
>     I am a mathematician,  not a chemist,  so let me look at the
>     basis sets purely mathematically.  If one has a complete (and
>     hence necessarily infinite) basis set,  he/she gets a limit
>     of Hartree-Fock model.  Otherwise (with limited basis set) one
>     gets some approximation to this limit and the more complete the
>     basis set is the better is the approximation.  Now assume one
>     uses a certain "standard" basis set and gets some result (from
>     Hartree-Fock model).  And now we add ANY additional function to
>     this basis set.  This does not make the basis set less complete
>     and so it should lead to at least as good (or even better) an
>     approximation as the original basis did (it is also possible
>     to get the original solution by taking that additional function
>     with zero coefficient for every electron).
>     Is there anything wrong with this statement?

        It of course depends on what you mean with "better".  The SCF will
minimize the energy, adding any new function should give an energy closer
to the HF limit.  However, most of the time this is not really interesting.
When you want energies, you usually want relative energies, and then it's
quite important that you make the same approximations, that is, calculate
at a constant level of theory, so that systematic errors cancel.  Also, as
you said in the part of the message I deleted, adding functions in an
unbalanced way will definitely affect the charge distribution, probably not
making it "better" :-)  Specific questions can sometimes be answered by
including functions that are not atom-centered, but then you get the
problem of findning a completely reproducable way of doing that for any
system.

        Per-Ola Norrby


^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  ---  Bureaucracy is a challenge to be conquered with a
       righteous attitude, a tolerance for stupidity, and
       a bulldozer when necessary
                                    --  Peter's Law 15.
 *  Per-Ola Norrby
 *  The Royal Danish School of Pharmacy, Dept. of Med. Chem.
 *  Universitetsparken 2, DK 2100 Copenhagen, Denmark
 *  tel. +45-35376777-506, +45-35370850    fax +45-35372209
 *  Internet: peon@medchem.dfh.dk, peo@compchem.dfh.dk




From owner-chemistry@ccl.net Wed Nov 29 12:10:45 1995
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Date: Wed, 29 Nov 1995 18:10:20 +0100 (MET)
From: Jean-Luc Verschelde <JeanLuc.Verschelde@rug.ac.be>
To: OHIO SUPER <CHEMISTRY@ccl.net>
Subject: solvent continuum
Message-Id: <Pine.SOL.3.91.951129180403.28849A-100000@allserv.rug.ac.be>



Hi all,


	I want to extend the ECEPP/2 force field with a solvation
	energy term. 
	
	Is there a stand-alone package that calculates the energy of 
        solvation and that I can use with the ECEPP/2 f.f.  .


	Thanks,

				Jean-Luc
  
===================================================================================

                                  Verschelde Jean-Luc


                                  University of Ghent

                              Lab. of Physiological Chemistry
                                                                          
                                  K.L. Ledeganckstraat 35
                                  9000 Ghent
                                  Belgium.

    Tel.:09/264 53 06    Fax:09/264 53 37  Email:Jeanluc.Verschelde@rug.ac.be

46q===================================================================================


From owner-chemistry@ccl.net Thu Nov 30 10:35:37 1995
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          Thu, 30 Nov 95 15:52:56 GMT
Date: Thu, 30 Nov 1995 15:52:56 +0000 (GMT)
From: Darryl Ellson <darryl@om3.ch.umist.ac.uk>
Subject: DZP' Basis Sets.
To: chemistry@ccl.net
Message-Id: <Pine.3.89.9511301549.G3795-0100000@trigger.ch.umist.ac.uk>




Dear All,

Recently I have been using the DZP' basis set of Barone et al in the 
study of phenoxyl radicals.
In the future I would like to extend this study to the histidine and
tryptophanyl radicals.
What I would like to know is whether anyone out there has used this basis 
set (also designated Chip1 by Chipman) for any systems containing 
Nitrogen, and whether they have access to the numerical values and the 
contraction coefficients for nitrogen, and would be willing to share these.


		Many Thanks.


			Darryl A. Ellson.


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   Darryl A. Ellson - Dept. Chemistry, UMIST, Manchester. M60 1QD
              Molecular Simulation & Design Laboratory
	    Tel: 061-236-3311 x4476    Fax: 061-236-7677
                E-mail: darryl@trigger.ch.umist.ac.uk

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~





From owner-chemistry@ccl.net  Thu Nov 30 22:09:30 1995
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From: Jeremy R Greenwood <jeremy@med.su.oz.au>
Message-Id: <199512010303.OAA28138@blackburn.med.su.oz.au>
Subject: Small +ve freqs in HF
To: chemistry@ccl.net
Date: Fri, 1 Dec 1995 14:03:26 +1100 (EST)
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Greetings all,

Some simple questions for those more familiar with ab initio than I:

As I understand it, the presence of a small real frequency in a
Hartree-Fock calculation is regarded as evidence that on increasing
basis size, the constrained structure may turn out to be a saddle point, 
with the mode in question becomming imaginary.

My question is: How small is small?

I am performing calculations on semi-aromatic heterocycles, and at
HF|6-31g* in Cs symmetry, I find a frequency of 8 /cm. Others around 
30-50 /cm. The ring is somewhat prone to puckering, and indeed some 
similar calculations have produced C1 structures.

My other question is: Does inclusion of electron correlation (e.g. MP2) 
with analytic second derivatives tend to produce similar results in terms 
of symmetry breaking as increasing basis set? (I understand that answers 
to these questions may depend very much on the nature of the systems 
being studied.)

Jeremy
--
Jeremy Greenwood
Department of Pharmacology
University of Sydney

From parcom.ernet.in!gadre@parcom.ernet.in  Thu Nov 30 23:09:31 1995
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Date: Fri Dec  1 09:00:40 1995 (GMT + 0530)
From: gadre@parcom.ernet.in
Message-Id: <9512010330.AA17688@parcom.parcom.ernet.in>
To: CHEMISTRY@www.ccl.net
Subject: Buckingham-Fowler and Legon-Millen Models


Dear Colleagues :
Could you send me a list of successes/failures of Buckingham-Fowler
as well as Legon-Millen models for studying weak intermolecular complexes?
One success, for instance is the reasonable geometry for the HCHO-HF complex
using the former.
Needless to say that I am more interested in failures! Thanks a lot.
 .........................................Shridhar R. Gadre
November 30, 1995.

