From peeter@tera.chem.ut.ee  Mon Oct 16 05:11:16 1995
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From: Peeter Burk <peeter@tera.chem.ut.ee>
Message-Id: <199510161008.MAA05210@tera.chem.ut.ee>
Subject: Complex-formation reactions
To: CHEMISTRY@www.ccl.net
Date: Mon, 16 Oct 1995 12:08:29 +0200 (EET)
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Dear Colleagues,

     Recently I was asked about the possibility of modeling 
complex formation reaction between metal cations (Mg2++, Zn2++,
etc.) and different complexing agents (EDTA, citric acid, etc.
anions) using semiempirical (or ab initio or DFT) calculations.
It seemed to me an interesting problem and so I looked for
literature references on this topic. So far I have not found
anything. Can some kind sound point me to  relevant references?
And what is your opinion on such modeling - suggestions, tips,
criticisms?
     I will summarize for the list if there will be something to
summarize.

Best regards
          Peeter

-- 
Peeter Burk, Ph.D.                      Jakobi 2, EE2400 Tartu, Estonia
Institute of Chemical Physics           Phone (372-7) 441-453   	
Tartu University                        Fax   (372-7) 441-453   	
Estonia                                 E-mail peeter@chem.ut.ee


From Vincent@averell.umh.ac.be  Mon Oct 16 06:26:17 1995
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Subject: IR and Raman Intensities?
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Hi everybody,
Could anybody explain me how are calculated
the IR and Raman intensities in the G92 programm?
Those intensities are expressed in km/mol and A**4/amu,
respectively, from expression including variation of
dipolar moment or polarisability. However I can not
find the exact expression leading to those units.
Could anybody help me?

Thanks in advance.
Vincent

****************************************************************
*                       Vincent  Parente                       * 
*           Service de Chimie des Materiaux Nouveaux           *
*  Center for Research in Molecular Electronics and Photonics  *
*                  University of Mons-Hainaut                  *
*           20, Place du Parc,  B-7000 Mons, BELGIUM           *
*    e-mail : svincent@vm1.umh.ac.be                           *
*             Vincent@averell.umh.ac.be                        *
*    fax    : +32 65 37 3366                                   *
*             +32 65 37 3054                                   *
*    tel    : +32 65 37 3361                                   *
****************************************************************

From tomura@crystal.ims.ac.jp  Mon Oct 16 07:26:18 1995
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Date: Mon, 16 Oct 1995 20:20:27 +0900
To: CHEMISTRY@www.ccl.net
From: Masaaki TOMURA <tomura@crystal.ims.ac.jp>
Subject: Band Structure Calculation of Organic Conductor
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Dear all,

        I've studied synthesis and structure of organic conductors such as 
TTF-TCNQ or BEDT-TTF salts etc...  I am looking for a program for calculating
a crystal orbital and a band structure of my compound with a semi-empirical MO
method.  Of course, the molecular structure of my compound was already solved by
X-ray crystallographic analysis.

What program is better?  And how can I get the program?

        Thanks in advance,




-------------------------------------------
Masaaki TOMURA  <tomura@crystal.ims.ac.jp>

Chemical Materials Center
Institute for Molecular Science

Myodaiji, Okazaki 444, Japan
Phone:     +81(Japan)-564-55-7486
Facsimile: +81(Japan)-564-54-2254
-------------------------------------------


From doublet@cth.u-psud.fr  Mon Oct 16 10:41:21 1995
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Date: Mon, 16 Oct 1995 15:29:05 +0100
From: Marie-Liesse Doublet <Marie-Liesse.Doublet@cth.u-psud.fr>
Message-Id: <199510161429.PAA19264@cth.cth.u-psud.fr>
To: CHEMISTRY@www.ccl.net, tomura@crystal.ims.ac.jp
Subject: Re:  CCL:Band Structure Calculation of Organic Conductor








        Hi,
        
        For this kind of huge compounds, Extended Huckel method
is one of the best. Of course it depends of what you want to
calculate. If you are interested in the electrical properties,
this method has already given the proof of its usefulness.
Canadell and coworkers have shown for a large variety of these 
salts (as well as for the M(dmit)2, BET-TTF, EDT-TTF salts)
that the electrical properties are govern by the intermolecular
interactions. These intermolecular interactions are quite
well described by the Huckel method.                    
                                    
        The programm called EHMACC has been initially written
by Whangbo and coworkers. (whangbo@chvzmw.chem.ncsu.edu).    
If you are interested in this programm you can contact 
Prof. M.-H. Whangbo in north Carolina.

	For a review of the validity of EHT on the calculation
of the physical properties of organic conductors, you can find
few examples in J. Phys. France I (1993, 1994, 1995).

	Good luck,

		Marie-Liesse DOUBLET


***************************************
Laboratoire de Structure et Dynamique
des Systemes Moleculaires et Solides
	Universite de Montpellier II
	Bat. 15  -  Boite Courrier 14
	
	34 095 Montpellier Cedex
		FRANCE
tel : (33) 67 14 38 83 
fax : (33) 67 14 33 04
e-mail : doublet@cth.u-psud.fr
***************************************


From owner-chemistry@ccl.net  Mon Oct 16 11:41:21 1995
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 16 Oct 1995 10:36:50 -0500 (CDT)
Date: Mon, 16 Oct 1995 10:36:21 -0500 (CDT)
Subject: Gaussian92 question
To: chemistry@ccl.net
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Dear netters,

recently we had a problem when running Gaussian92 on a large system.
We were modelling dna segments running STO-3G single shot calculations
on an RS6000.
Everything was fine until we tried to run a case with 1177 basis functions
(790 occupied). Using the same input as for the smaller members of the series

$ RunGauss
%Mem=12000000
#p hf/sto-3g geom=coord scf=direct pop=mk scfcon=7 test

   pentamer

0  1
 coordinates for a bunch of atoms

we got the following error message:

Leave Link  401 at Fri Oct 13 00:10:38 1995, MaxMem=   12000000 cpu:   10810.0
 (Enter /ibmtmp/dennis/g92/g92/l502.exe)
 A Direct SCF calculation will be performed.
 Using DIIS extrapolation.
 IExCor= 0 DFT=F Ex=HF Corr=None ScaHFX= 1.0000 IRadAn=      0
 ScaDFX=   .0000   .0000   .0000   .0000
 Closed shell SCF:
 Requested convergence on RMS density matrix=1.00D-07 within  64 cycles.
 Requested convergence on MAX density matrix=1.00D-05.
 Integral symmetry usage will be decided dynamically.
 IEnd=   4526890 IEndB=   4526890 NGot=  12000000 MDV=   8863841
 LenX=   8863841
 Fock matrices will be formed incrementally for  20 cycles.
 Integral accuracy reduced to 1.0D-05 until final iterations.

 Cycle   1  Pass 0:
 MinBra= 0 MaxBra= 3 MinLOS=-1 MaxLOS=-1 MinRaf= 0 MaxRaf= 3 MinLRy= 4.
 IRaf=       0 NMat=   1 IRICut=       1 DoRegI=T DoRafI=F ISym2E= 1 JSym2E=1.
 Fock matrices symmetrized in FoFDir.
E= -.933531580916218D+05
Erroneous write. write -1 instead of 4096

Could you tell me what should we do to run this job? (and perhaps larger ones as well?)

Your help is greatly appreciated.


Agnes Derecskei

Department of Chemistry and Biochemistry
The University of Texas at Arlington
Arlington, Texas


From owner-chemistry@ccl.net  Mon Oct 16 13:26:22 1995
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From: S Parthiban <parthi@aero.iisc.ernet.in>
To: B314U09@UTARLG.UTA.EDU
cc: chemistry@ccl.net
Subject: Re: CCL:G:Gaussian92 question
In-Reply-To: <01HWI6WEEOLU9OHEQS@UTARLG.UTA.EDU>
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Dear Agnes Derecskei
A while ago, another CCl member also posted similar question. 
But no one had responded. So I would like to share my views,
although i am a novice in this area.
Please do the following:
1) check your scratch file size.
2)type "limit" in the prompt; it will display the machine
configuration values. Find the value of "filesize" (in Kbytes)

If your scratch file size is higher than the filesize showed in
step 2, then you will have this problem. This is one possible answer
for your question.
Best wishes
S. Parthiban 

On Mon, 16 Oct 1995 B314U09@UTARLG.UTA.EDU wrote:

> 
> Dear netters,
> 
> recently we had a problem when running Gaussian92 on a large system.
> We were modelling dna segments running STO-3G single shot calculations
> on an RS6000.
> Everything was fine until we tried to run a case with 1177 basis functions
> (790 occupied). Using the same input as for the smaller members of the series
> 
> $ RunGauss
> %Mem=12000000
> #p hf/sto-3g geom=coord scf=direct pop=mk scfcon=7 test
> 
>    pentamer
> 
> 0  1
>  coordinates for a bunch of atoms
> 
> we got the following error message:
> 
> Leave Link  401 at Fri Oct 13 00:10:38 1995, MaxMem=   12000000 cpu:   10810.0
>  (Enter /ibmtmp/dennis/g92/g92/l502.exe)
>  A Direct SCF calculation will be performed.
>  Using DIIS extrapolation.
>  IExCor= 0 DFT=F Ex=HF Corr=None ScaHFX= 1.0000 IRadAn=      0
>  ScaDFX=   .0000   .0000   .0000   .0000
>  Closed shell SCF:
>  Requested convergence on RMS density matrix=1.00D-07 within  64 cycles.
>  Requested convergence on MAX density matrix=1.00D-05.
>  Integral symmetry usage will be decided dynamically.
>  IEnd=   4526890 IEndB=   4526890 NGot=  12000000 MDV=   8863841
>  LenX=   8863841
>  Fock matrices will be formed incrementally for  20 cycles.
>  Integral accuracy reduced to 1.0D-05 until final iterations.
> 
>  Cycle   1  Pass 0:
>  MinBra= 0 MaxBra= 3 MinLOS=-1 MaxLOS=-1 MinRaf= 0 MaxRaf= 3 MinLRy= 4.
>  IRaf=       0 NMat=   1 IRICut=       1 DoRegI=T DoRafI=F ISym2E= 1 JSym2E=1.
>  Fock matrices symmetrized in FoFDir.
> E= -.933531580916218D+05
> Erroneous write. write -1 instead of 4096
> 
> Could you tell me what should we do to run this job? (and perhaps larger ones as well?)
> 
> Your help is greatly appreciated.
> 
> 
> Agnes Derecskei
> 
> Department of Chemistry and Biochemistry
> The University of Texas at Arlington
> Arlington, Texas
> 
> 
> -------This is added Automatically by the Software--------
> -- Original Sender Envelope Address: owner-chemistry@ccl.net
> -- Original Sender From: Address: B314U09@UTARLG.UTA.EDU
> CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator
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> Anon. ftp: www.ccl.net   | CHEMISTRY-SEARCH@www.ccl.net -- archive search
>              Web: http://www.ccl.net/chemistry.html 
> 

From qocruces@usc.es  Mon Oct 16 14:56:23 1995
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	id AA06886; Mon, 16 Oct 1995 19:43:07 +0100
Date: Mon, 16 Oct 1995 19:43:07 +0100
From: qocruces@usc.es (Jacobo Cruces Colado)
Message-Id: <199510161843.AA06886@uscmail.usc.es>
To: chemistry@www.ccl.net
Subject: SwaN-MR again on line


Dear netters:

The last week, a small problem took out of line the server where the SwaN-MR program of Dr. Balacco can be found. Incidentally, Dr. Ballaco is also changing hise-mail address, so he could not be contacted.

The sfdzuma.usc.es (193.144.75.69) is on line again, so the program is availablefor all of you. Dr. Balacco will get a new address very soon.

Sorry by all problems & useless time...

Jacobo Cruces


From whitbeck1@llnl.gov  Mon Oct 16 19:11:27 1995
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Message-Id: <199510162306.QAA14222@pierce.llnl.gov>
Date: Mon, 16 Oct 1995 16:05:02 -0700
From: whitbeck1@llnl.gov (Mike Whitbeck)
To: chemistry@www.ccl.net
Subject: React 3.21
Organization: LLNL


Hello all,

This note is to inform those interested in the availability of a new 
release of my reaction kinetics software. The program is available in
compiled form for the Macintosh, DOS, and OS/2 platforms. I compiled and
tested it on a Mac PPC using system 7.5; the DOS and OS/2 compiles are
courtesy of George McBane (OSU).

Look for React 3.21 in the CCL archives.
(****** this program is not supported, no affialiation with the 
University of California, LLNL or the US Gov't. **************)


A brief reminder. This program takes reaction mechanisms in the form:

      Mechanism from Edelson, J Chem Ed 52, 642 (1975)
      5e-8     O2- + Cs+ --> Cs + O2
      1e-12    Cs+ + e- --> Cs
      3.24e-3     Cs --> Cs+ + e-
      .4       O2-   --> O2 + e-
      this is a comment
      1.76e-16    O2 + Cs --> CsO2
      1.24e-30 O2 + O2 + e- --> O2 + O2-
      1.4e-16     O2  + e- --> O2- 

builds the differential equation set and finds a numerical solution. It
borrows heavily from programs available from netlib@ornl.gov

As a bonus specific reactions can be flagged to have their rate constants
adjusted using a least-squares criterion and experimental measurements of
time-concentration profiles.

Sample files and a brief manual are included. Plain text (ascii), and MS 
Word versions.

No promises, warranties not even decent error messages so use at your own risk.

If you use it in published research cite the program please.

Copy and share freely but don't sell, remarket or charge for the program!

Enjoy,

Dr. Michael Whitbeck (whitbeck1@popcorn.llnl.gov)
Chemistry & Material Science Division
Lawrence Livermore National Laboratory

****** this program is not supported, no affialiation with the 
University of California, LLNL or the US Gov't. **************

From info@molecules.com  Mon Oct 16 19:41:27 1995
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Date: Mon, 16 Oct 95 16:24:04 PDT
From: David Segrist <info@molecules.com>
Subject: Molecules-3D Test Drive now available
To: chemistry@www.ccl.net
X-Mailer: Chameleon - TCP/IP for Windows by NetManage, Inc.
Message-ID: <Chameleon.4.00.951016162831.info@>
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The Molecules-3D Test Drive (for both Windows and Macintosh
is available by anonymous FTP.  The files (M3DTDWIN.ZIP and 
M3DTDMAC.BIN) and information about them are located at 
ftp.cerf.net in the directory /pub/vendor/molecules/test_drive.

This is a "test drive" of simple-to-use package that enables you to: 
(A) build, optimize, edit and export 3D molecular models, as well as, 
(B) construct 2D Lewis diagrams and convert them to 3D models.

David Segrist
Molecular Arts Technical Support

---------------------------------------------------------
Molecular Arts Corporation       | <info@molecules.com>
Hanover Corporate Centre         | CompuServe: 71644,3626
1532 E. Katella Ave., Suite 1000 | Voice: (714) 634-8100
Anaheim, California 92805, USA   | FAX: (714) 634-1999
---------------------------------------------------------
           ftp.cerf.net /pub/vendor/molecules


From owner-chemistry@ccl.net Mon Oct 16 16:14:03 1995
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Date: Mon, 16 Oct 1995 15:17:32 -0500 (CDT)
From: BILL WELSH <C1790@SLVAXA.UMSL.EDU>
Subject: Calculating polymer moduli via ampac/mopac
To: chemistry@ccl.net
Message-id: <01HWIGQG1Y1GAC2WD0@SLVAXA.UMSL.EDU>



Dear Netters,

Can someone direct me to a version of ampac and/or mopac that enables 
calculations of the tensile modulus of polymers.  I know that some of 
the commercial packages contain such modules, but I was looking for something 
cheaper.

Thanks ...

Bill Welsh
Dept. of Chemistry
Univ. of MO-St. Louis



From owner-chemistry@ccl.net Mon Oct 16 15:07:54 1995
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To: chemistry@ccl.net
From: marty@ionchannel.med.harvard.edu (Marty Gallagher)
Subject: bioavailability/summary of antivirals
Cc: JayHTI5151@aol.com



-----BEGIN PGP SIGNED MESSAGE-----


Hello,

       I am interested in obtaining a list of pharmaceuticals that have an
especially low oral bioavailability.  Does anyone know where such a list
has been published?

        On an unrelated note, last week I asked the CCL subscribers for
pointers to good review articles that outline current questions concerning
the development of antivirals.  Since then, I received many excellent
responses.  Thanks to all those who replied!  I've summarized the responses
below for those who are interested.

                                        Thanks again,


                                        Marty Gallagher


==============================================================================
SUMMARY OF REVIEWS ON ANTIVIRAL DEVELOPMENT  --- Thanks to all those who
responded!


cpatterson@watson.princeton.edu (Catherine Patterson):

There is a three volume set of books by Fields on _Virology_.  One of the
chapters is specifically titled "Antivirals".  I think it references
clincally used as well as drugs used in research.

From: STEWARTK@randb.pprd.abbott.com Kent Stewart
Marty:  Every year the American Chemistry Society Division
of Medicinal Chemistry publishes a volume of  Annual Reports
in Medicinal Chemistry.  I would expect that any research library
would have the set of volumes.  The nice thing about the indexing
is that it is cummulative.  Thus you can easily pull off the
latest volume and search antiviral, antiinfective, antibacterial,
etc. and within minutes get a "cutting edge" review from
experts in the field.  This is always a good place to start
when starting a new field within medicinal chemistry.  In
your case, there are several nice reviews of anti-viral agents
in the last few years.


Saul Wolfe <swolfe@sfu.ca>

Please take a look at Can. J. Chem. 66, 2687-2762 (1988) (5 papers),
Can. J. Chem. 72, 1014-1075 (1994) (5 papers) and JACS 117, 4240 (1995).
The JACS paper is the tip of an iceberg.


Ronald D Ferguson <rferguso@U.Arizona.EDU>

Have you ever considered using a combinatorial chemical approach. You
could either use synthetic techniques or Phage CombiChem approaches.
Another news group which I review discusses these topics and
I'm sure that you would find some insight into your research topic. The
address is given below. If you want, in a few days I could scan my
literature articles for a viral application and return the results.
Unfortunately, I won't have time until the weekend.
Combinatorial Chemical News Group:  bionet.molecules.repertoires


amt@ftn.net (Adi Treasurywala)

        Some time ago I was involved with a project to do some structure based
 drug design on agents against the common cold virus (Rhinoviruses). I found
that to be an EXCELLENT challenge. Many questions remain unanswered about the
details of the reproductive cycle of these viruses although an ENORMOUS amount
(including several good X-ray structures of the intact virions) is known.
Behind each one of these unknowns IMHO lies a potential drug design target
and a potential for the greater understanding about these fascinating entities.
        I have published some papers in this area but the principles are Guy
Diana, and Michael Rossmann.

 Walter Hoeksma <YD03@MUSIC.FERRIS.EDU>

Although somewhat dated you might try looking at the review
ANTIVIRAL THERAPY:CURRENT CONCEPTS AND PRACTICES by Bonnie Bean
This review is in CLINICAL MICROBIOLOGY REVIEWS April 1992 vol 5 no 2
pages146-182


Wayne Steinmetz <WSTEINMETZ@POMONA.EDU>

1) The following review article outlines the development of inhibitors to HIV
protease.  Leads from that project are in Phase II clinical trials.

J. Greer, J. W. Erickson, J. J. Baldwin, and M. D. Varney, "Application of the
Three-Dimensional Structures of Protein Target Molecules in Structure-Based
Drug Design", J. Med. Chem., Vol. 37, 1035-1054 (1994).

2) Vol. 203 in Methods of Enzymology is dedicated to molecular design and
modeling and has a number of useful articles.

Have you considered spending a postdoc in industry?  I spent my third
sabbatical leave at Abbott Labs and greatly benefited from the year there.

 Marja_van_Zeijl_at_USPRMG42@internetmail.pr.cyanamid.com

A supplement of the journal Antiviral Chemistry and Chemotherapy covered
most of
the current issues in antiviral chemotherapy. The issue is: #6, Supplement 1.
One of the papers was: In search of the perfect antiiral, by G. Darby (p54-63).
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=========================================================================
Martin J. Gallagher             phone:  (617) 432-1729
Dept. of Neurobiology           fax:    (617) 734-7557
Harvard Medical School          E-mail: marty@ionchannel.med.harvard.edu
220 Longwood Ave                http://ionchannel.med.harvard.edu/~marty
Boston, MA  02115

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