From toukie@zui.unizh.ch  Thu Aug  8 03:16:11 1996
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From: toukie@zui.unizh.ch (Hr Dr. S. Shapiro)
Message-Id: <9608080643.AA22884@rzurs3.unizh.ch>
Subject: Deconvoluting a spectrum
To: chemistry@www.ccl.net
Date: Thu, 8 Aug 1996 08:43:56 +0200 (MEST)
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Dear Colleages;

     I have digital data (X/Y) for a spectrum that displays a principal peak and
a prominent shoulder.  I would like to deconvolute this spectrum into two Gauss-
ian spectral bands so that I can separately examine the two peaks constituting
the principal peak and the shoulder.  Therefore, I would like to hear from any-
one who knows of software (preferably for DOS/Windows, preferably shareware or
freeware, though other possibilites are welcome) that can be used to accomplish
the desired deconvolution.

     Thanks in advance to all responders.


Sincerely,

S. Shapiro
Zuerich
toukie@zui.unizh.ch

From qftjesus@usc.es  Thu Aug  8 04:16:17 1996
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Date: Thu, 8 Aug 1996 10:17:52 +0200 (MET DST)
From: Jesus Otero Rodriguez <qftjesus@usc.es>
To: CCL <chemistry@www.ccl.net>
Subject: Request: Huckel for PC
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Dear CCLrs:

Anybody has (or knows) a program for Huckel calculations on a personal 
computer (PC or Macintosh) ? 
It is for student practices.

Thanks

-----------------------------
Jesus Rodriguez Otero
Departamento de Quimica Fisica
Facultad de Quimica
Univ. de Santiago
15706 Santiago de Compostela, SPAIN

qftjesus@usc.es

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

From David.DeCorte@unifr.ch  Thu Aug  8 06:16:09 1996
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From: DE CORTE DAVID <David.DeCorte@unifr.ch>
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Cc: David.DeCorte@unifr.ch
Subject: CCL: Polymer Volume Calculations
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Hi there,
does anybody know a program able to calculate (or say estimate) the volume of
any kind of polymer in solution, using as parameters the concentration, the
primair structure and if necessary the degree of protonation of the polymer.
Thanks in advance,

				David

From qftjesus@usc.es  Thu Aug  8 07:16:11 1996
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From: Jesus Otero Rodriguez <qftjesus@usc.es>
To: CCL <chemistry@www.ccl.net>
Subject: Huckel: I have already got the program
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Thanks to everybody !!

In less than 2 hours, the problem was solved

That is efficacy !!!!

Best wishes to everybody

From owner-chemistry@ccl.net  Thu Aug  8 08:16:13 1996
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Date: Thu, 8 Aug 1996 13:20:05 +0200 (MET DST)
From: Xose Manuel Valladares Pernas <famava@usc.es>
To: chemistry@ccl.net
Subject: CCL:Restarting Gaussian
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Hello,
maybe it is a stupid question but I don't know how to restart Gaussian. I 
am doing the same that it is written in the manual but it doesn't work.
After running the initial job that works properly, I sent this one

%chk=Co3b
#BP86 / LANL2DZ SCF(NoDIIS,Vshift=300) OPT(Restart)

But instead of getting the result the output was

Restoring state from the checkpoint file "Co3b.chk,-1".
 FILEIO OPERATION ON NON-EXISTANT FILE.
 FILEIO: IOPER= 2 IFILNO(1)=  -997 LEN=    4504 IPOS=       0 Q=          
5887232

Do you know what is my error?
		Thank you very much
				Manuel


*****************************************************
Manuel Valladares Pernas  (famava@uscmail.usc.es)
Dpto. Fisica Aplicada
Universidade de Santiago de Compostela
SPAIN
*****************************************************


From robert@europa.chem.uga.edu  Thu Aug  8 10:16:14 1996
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From: Jenn-Huei Lii <robert@europa.chem.uga.edu>
Organization: Computational Center for Molecular Structure and Design (CCMSD)
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Dear Matthew:

You may compare AM1 results with experimental value directly, since AM1
reports Heat of Formation values.  But you can not compare MM+ values
with experimental values.   MM+ reports steric energy NOT Heat of
Formation.   Allinger's MM2 or MM3 will give you a reasonable answer.


>     In the Handbook of Chem and Physics, it reports
>     
>     octane:               -49.82
>     2,2,3,3,TMB:          -53.99
>     
>     
>     My results for AM1 and MM+ show (Hyperchem 3.0 calculations)
     
                 MM3        am1                mm+               exp
     
 octane        -49.92     -58.628            (6.448 s.e.)       -49.82
     
 2,2,3,3,TMB   -53.82     -40.155            (12.36 s.e.)       -53.99
     

MM3 values are form the following ref.

N. L. Allinger, Young H. Yuh and Jenn-Huei Lii, J. Amer. Chem. Soc.,
111, 8551 (1989). 

-Robert

From bbendik@telerama.lm.com  Thu Aug  8 10:24:07 1996
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Subject: QSAR and Gov. approval
Date: Thu, 8 Aug 96 10:03:27 -0000
From: Beverly Bendiksen <bbendik@telerama.lm.com>
To: "CCL" <CHEMISTRY@www.ccl.net>
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I'm in search of experiences, both published and unpublished, successes 
or failures, of the use of QSAR to model data for new compounds that are 
being proposed for FDA approval.  For example, in my company we are 
seeking to reduce the time it takes to run extraction studies for paper 
processing chemicals for food-contact paper.  The FDA requires estimates 
of how much of the chemicals used to make paper might wind up in human 
tissue.  The extraction studies can take several weeks, yet alternative 
of mathematical estimates of worst case (all the compound leaches from 
paper to food to humans) are usually much too high, and overestimate 
potential toxic effects.  The use of FDA databases and QSAR molecular 
modeling poses a unique possibility, providing that the US government 
would be willing to accept a modeled result of this type.  Certainly, the 
model would need some verification, but this would still reduce 
experimental time.  

Replies will be summarized to the list.

bev

Beverly Bendiksen
bbendik@telerama.lm.com
Pittsburgh, PA


From owner-chemistry@ccl.net  Thu Aug  8 10:26:50 1996
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Date: Thu, 8 Aug 1996 15:01:16 +0100 (BST)
From: Wu J H <wujih@solb1.essex.ac.uk>
To: chemistry%ccl.net@mailhost.essex.ac.uk
Subject: SCIPCM model in g94 
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Dear CCL netter,

I am using SCIPCM solvation model. It work for small molecules
such as Ethanol ..., but for molecule [Co^III(NH3)6]^3+, I always get the
error message like  'Out of space in DoRhGr'. I have tried
 
 (1) Just solvating the cation Co^3+, the job is fine.
 (2) Cobalt complex larger than [Co^III(NH3)6]^3+ in gas phase 
     (blyp/DZVP), the job is fine as well.
 (3) For SCIPCM solvation model, I increase the memory allocation using 
     '#BSUB -M 1000 mb', I still got the error message 'Out of space in DoRhGr'.
     for the molecule  [Co^III(NH3)6]^3+.

It seems the SCIPCM solvation model need much more memory than the 
calculation in gas phase(HF and DFT). In g94 SCIPCM model, it just work for 
small molecule such as ethanol, pyridine...., is it true? Or I have made 
mistakes somewhere?

Thank for your help,


WU J 
University of Essex
Colchester CO4 3SQ
UK

email wujih@essex.ac.uk


PS: (1) my input look like 

     #BSUB -q e5 
     #BSUB -c 6:00 
     #BSUB -M 1000 mb
      rung94_new << EOF
      %chk=D1bms.chk 
     #P blyp/gen SCF=direct VSHIFT Guess=CheckPoint 
      SCFCyc=100 SCRF=SCIPCM

      Co 6NH3 3+ solvate  blyp/DZVP Co N H 

      3 1
      Co 0 x1 y1 z1
      N 0 x2 y2 z2
      N 0 x3 y3 z3
      ........
      
      78.3
      

   (2) The error look like

 Dielectric constant of solvent = 78.300000
 Solute cavity defined by isodensity surface of value= 0.000400 au
 Using Becke method to do surface integrals. 
 Intersections with cavity surface found from nucleus 1
 Out of space in DoRhGr. 
 Error termination via Lnk1e in /usr/local/g94_new/l502.exe. 
 Job cpu time:  0 days 0 hours 1 minutes 47.1 seconds. 
  File lengths (MBytes):  RWF= 11 Int= 0 D2E= 0 Chk= 2 Scr= 1 sh: 3026
 Memory fault: A memory image file is created as "core". 



From jpcannady@dcrn.e-mail.com  Thu Aug  8 10:28:52 1996
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Subject: CCL:G:Restarting Gaussian



And if anyone can help Xose with his question, I have the same one, but
it is for G90 running under IBM mainframe (MVS) in batch mode.  Any help with
combinations of JCL and keywords (from those of you who are familiar) would
be appreciated.  I have made a couple of stabs but have not cracked the nut
yet.  I am especially interested in using the Hessian calculated at RHF in
a FREQ job for a transition state as the starting point for the TS search
at MP2.

Pat
*** Forwarding note from I1511326--IBMMAIL  08/08/96 08:22 ***
Date: Thu, 8 Aug 1996 13:20:05 +0200 (MET DST)
From: Xose Manuel Valladares Pernas <famava@usc.es>
To: chemistry@ccl.net
Subject: CCL:G:Restarting Gaussian

Hello,
maybe it is a stupid question but I don't know how to restart Gaussian. I
am doing the same that it is written in the manual but it doesn't work.
After running the initial job that works properly, I sent this one

%chk=Co3b
#BP86 / LANL2DZ SCF(NoDIIS,Vshift=300) OPT(Restart)

But instead of getting the result the output was

Restoring state from the checkpoint file "Co3b.chk,-1".
 FILEIO OPERATION ON NON-EXISTANT FILE.
 FILEIO: IOPER= 2 IFILNO(1)=  -997 LEN=    4504 IPOS=       0 Q=
5887232

Do you know what is my error?
      Thank you very much
            Manuel


*****************************************************
Manuel Valladares Pernas  (famava@uscmail.usc.es)
Dpto. Fisica Aplicada
Universidade de Santiago de Compostela
SPAIN
*****************************************************


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From saxena@physics.purdue.edu  Thu Aug  8 11:16:22 1996
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Date: Thu, 8 Aug 1996 09:24:00 -0500 (EST)
From: "Virendra K. Saxena" <saxena@physics.purdue.edu>
To: chemistry@www.ccl.net
Subject: short and long hydrogen bonds
Cc: saxena@physics.purdue.edu



       Does anyone have information on recent (may be last ten years)
    ab initio or any other calculations for hydrogen bonds of relatively
    shorter lenghs (as in case of RNA) and the hydrogen bonds of longer
    lengths (in case of proteins). The original Lippencot-Schroeder model
    (very emperical) is valid only for a very limited range of bond lengths.
    Besides, the potential form gives negative force constants for shorter
    bonds.

      We are interested in calculating the force constants (and the potential
    forms) for vareity of hydrogen bonds occuring in RNA and proteins and use
    them for dynamical calculations.

      Any help will be very much appreciated. Thanks

      V. K. Saxena
      Physics Dept.
      Purdue University
      West Lafayette, IN 47906
      saxena@physics.purdue.edu
      (317) 494-9575

From moto@ch.wani.osaka-u.ac.jp  Thu Aug  8 13:16:16 1996
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Date: Fri, 09 Aug 1996 01:12:12 +0900
From: Motohiro NAKANO <moto@ch.wani.osaka-u.ac.jp>
To: toukie@zui.unizh.ch (Hr Dr. S. Shapiro)
Cc: chemistry@www.ccl.net
Subject: Re: CCL:Deconvoluting a spectrum
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Hello, Dr.Shapiro !

> I would like to deconvolute this spectrum into two Gauss-
> ian spectral bands so that I can separately examine the two peaks constituting
> the principal peak and the shoulder.

If your environment allows you to compile a FORTRAN source code,
the program LGFIT2 will help you to solve your problem.

LGFIT2
A LEAST-SQUARES SPECTRAL CURVE FITTING ROUTINE FOR STRONGLY
OVERLAPPING LORENTZIANS OR GAUSSIANS.
  REF. VON MEERWALL, E., COMP. PHYS. COMMUN. 9 (1975) 117.

This program is available from
http://www.kfa-juelich.de:80/zam/CompServ/software/mathe/mathsrc/cpc/abmk.cpc

-- 
  Motohiro NAKANO  <moto@ch.wani.osaka-u.ac.jp>
  Dept. of Applied Chemistry, Osaka University
  Tel +81-6-850-5770  Fax +81-6-850-5785

From ryanmd@mms.sbphrd.com  Thu Aug  8 14:16:21 1996
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Date: Thu, 8 Aug 1996 13:27:05 -0400
From: ryanmd@mms.sbphrd.com (Dominic Ryan)
Message-Id: <199608081727.NAA22185@phu198.um.us.sbphrd.com>
To: chemistry@www.ccl.net
Subject: Hydrogen Bonds



Check out the work by Steve Sheiner and others.  Some of that is in 
Reviews in Computational Chemistry.  There was (and perhaps for some 
still is) a bit of a brouhaha about very short hydrogen bonds.  Some of
that came up in Science and Nature in the last year.  Those should 
point you to the relevant literature. 
__
M. Dominic Ryan   (610)-270-6529     SmithKline Beecham Pharmaceuticals 
Internet:  ryanmd@mms.sbphrd.com     King of Prussia, PA  

From owner-chemistry@ccl.net  Thu Aug  8 17:16:16 1996
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Date: Thu, 08 Aug 1996 12:41:18 -0400
To: chemistry@ccl.net, CHMINF-L@iubvm.ucs.indiana.edu
From: Tom Pierce <THPierce@rohmhaas.com>
Subject: NEW  URL -Request for "Best Chemistry Web Sites" votes


My apologies - the last message had the wrong URL..
a reprise...
Dear Folks,

The American Chemical Society National meeting is coming this month.
Henry Rzepa, Steven Bachrach, and I  are putting together the
1996 Best Chemistry Sites electronic poster on August 18th. Please assist
us by voing for your selection of Best Site  at:

http://www.ch.ic.ac.uk/vote.html

This poster will be electronically accessible during the ACS conference,
and with your help it could be useful to us all.
-----
Sincerely, Tom Pierce - THPierce@RohmHaas.Com - Computational Chemist
"These opinions are those of the writer and not the Rohm and Haas Company."


From LONGO@NPD.UFPE.BR  Thu Aug  8 18:16:16 1996
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 08 Aug 1996 19:17:51 -0300
Date: Thu, 08 Aug 1996 19:17:51 -0300
Subject: Epoxidation reaction
To: chemistry@www.ccl.net
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   Dear CCLers,

   I'd appreciate if anybody could send me references on epoxidation
   reactions calculated at semiempirical and/or ab initio levels.
   I went to CA down to 1984 and came out empty handed...
   So, any help will be very wellcome.
   Thanks a lot,

                      Ricardo Longo
                      longo@npd.ufpe.br


From owner-chemistry@ccl.net  Thu Aug  8 18:22:35 1996
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Date: Thu, 08 Aug 1996 12:39:16 -0400
To: chemistry@ccl.net, CHMINF-L@iubvm.ucs.indiana.edu
From: Tom Pierce <THPierce@rohmhaas.com>
Subject: Request for "Best Chemistry Web Sites" votes


Dear Folks,

The American Chemical Society National meeting is coming this month.
Henry Rzepa, Steven Bachrach, and I  are putting together the
1996 Best Chemistry Sites electronic poster on August 18th. Please assist
us by voing for your selection of Best Site  at:

http://www.ch.ic.ac.uk/infobahn/votes

This poster will be electronically accessible during the ACS conference,
and with your help it could be useful to us all.
-----
Sincerely, Tom Pierce - THPierce@RohmHaas.Com - Computational Chemist
"These opinions are those of the writer and not the Rohm and Haas Company."


