From jsl@virgil.ruc.dk  Thu Aug 15 04:17:40 1996
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From: "Jens Spanget-Larsen" <jsl@virgil.ruc.dk>
Organization: Roskilde Universitetscenter
To: chemistry@www.ccl.net
Date: Thu, 15 Aug 1996 10:06:59 +0100
Subject: Transition metals / semiempirical parametrizations
Priority: normal
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Fredrik Bokman sent:

>  I am interested in the recent developments
> in semiempirical parametrizations for 
> transition metal atoms. E.g., Spartan 
> (Wavefunction) has included Thiel's MNDO/d 
> and Ampac (Semichem) has Dewar's SAM1.
> 
>  The incorporation of these features is a strong 
> argument in selling the programs to organometallic 
> chemists (for example), but I find that there is 
> rather little documentation on the performance
> of the transition metal parametrizations.
> Do you know of any published evaluations? 
> 
>  By the way, do you know of any other recent (or old)
> parametrizations of the 3d-, 4d-, or 5d elements?

Michael J. Zerner and his coworkers in Florida have developed the 
programs ZINDO/1 and ZINDO/S.  Both treat transition metal complexes 
and are included in the HyperChem Package (HyperCube Inc., Canada).  
ZINDO/1 is parametrized for geometry calculations, ZINDO/S is for 
predictions of electronic transitions.  Some references:  

Theor.Chim.Acta 32, 111 (1973)
Theor.Chim.Acta 42, 223 (1976)
Theor.Chim.Acta 53, 21 (1979)
J.Am.Chem.Soc. 102, 589 (1980)
Inorg.Chem. 25, 2728 (1986)
Int.J.Quantum.Chem. 39, 31 (1991)

Yours, Jens >--< 

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
JENS SPANGET-LARSEN
Department of Chemistry              Phone:  +45 46757711
Roskilde University (RUC)            Fax:    +45 46757721 
POB 260, DK-4000 Roskilde, Denmark   E-Mail: JSL@virgil.ruc.dk
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-








From mckennam@curie.ml.wpafb.af.mil  Thu Aug 15 08:17:42 1996
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Date: Thu, 15 Aug 1996 07:25:29 -0400 (EDT)
From: "Alan M. McKenney" <mckennam@curie.ml.wpafb.af.mil>
Message-Id: <199608151125.HAA29912@curie.ml.wpafb.af.mil>
To: chemistry@www.ccl.net
Subject: Re: Szabo & Ostlund's book
Reply-To: mckennam@curie.ml.wpafb.af.mil



A while back, Sergei Vyboishchikov <SERGEI@ps1515.chemie.uni-marburg.de>
asked on the CCL list about the availability of "Modern
Quantum Chemistry, Introduction to Advanced Electronic Structure
Theory" by Attila Szabo and Neil S. Ostlund.

    I have in my hands a copy of the Dover edition, which came out this
summer.

(1) The ISBN number is 0-486-69186-1.  The price in the USA is $13.95.

(2) My nearest bookstore (Barnes & Noble) couldn't get it (consistent
    with my previous experiences with them.)

(3) The publisher, Dover Publications will accept mail orders, but not 
    telephoned-in credit card orders.  The address is

	Dover Publications, Inc.
	Department CRX
	31 East Second Street
	Mineola, NY 11501

    I don't remember the telephone number, but the area code is
    516 (the code for Long Island, New York.)  You send them a
    check for $13.95 plus $4 shipping and handling for shipments
    within the (continental?) USA.  Also add your local sales tax
    if you're in New York State.  I paid $7 shipping because I
    wanted 2-day delivery.

    If you want to mail order from outside the USA, you'd have to
    call them to find out how.  Get the telephone number from
    directory information for area code 516, and tell them you
    want to mail order a single copy.  I don't know whether they
    will ship outside the USA.


Alan McKenney			( telecommuting to:		   )
Tarrytown, NY			( Wright-Patterson AFB, Dayton, OH )
Off.: (914) 332-0760    	( <mckennam@curie.ml.wpafb.af.mil> )
Home: (914) 332-1019

From owner-chemistry@ccl.net  Thu Aug 15 09:17:40 1996
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From: "Magan Govender" <GOVENDEM@che.und.ac.za>
Organization:  University of Natal - Durban
To: chemistry@ccl.net
Date:          Thu, 15 Aug 1996 14:52:28 SAST
Subject:       RE: 13C-H stretching wavenumber
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Dear Netters

Does anyone know what the 13C-H stretching frequency is in
either the gas or matrix isolated state?....

Many thanks









______________________________________________________________________

M.G. Govender
Centre for Theoretical, Computational Chemistry and Vibrational
Spectrscopy.
Dept of Chemistry & Applied Chemistry
University of Natal
Private Bag x10
Dalbridge
Durban                              
South Africa                                                          
   
Phone: +27 - 31 - 2601102

email : govendem@che.und.ac.za
        govendem@lourie.und.ac.za
        govendem@hoopoe.und.ac.za
        
        
        oo^o0ooo             ooo0ooo             ooo0ooo
        
______________________________________________________________________

From tp@elptrs7.rug.ac.be  Thu Aug 15 09:24:50 1996
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Date: Thu, 15 Aug 1996 14:45:55 +0200 (DFT)
From: "Park, Tae-Yun" <tp@elptrs7.rug.ac.be>
To: Computational Chemistry List <chemistry@www.ccl.net>
Subject: HESSIAN in GAMESS
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Dear all,

I'm trying to do some vibrational analysis for some
carbenium ions using GAMESS.  At the end of the result
file, I always have the following message, which makes
me quite uncomfortable:

     *******************************************************
     * THIS IS NOT A STATIONARY POINT ON THE MOLECULAR PES *
     *     THE VIBRATIONAL ANALYSIS IS NOT VALID !!!       *
     *******************************************************

I've tried with different optimization method available in 
$STATPT group, but it was unsuccessful.  Is there any other
way to avoid this message?

One of my input file for C-C(+) carbenium ion is the 
following(I need 6-31G* basis set with MP2 level for
enough accuracy):

----------------------------------------------------------------
 $CONTRL SCFTYP=RHF RUNTYP=HESSIAN ICHARG=1 COORD=ZMTMPC 
  MPLEVL=2 NZVAR=15 $END
 $SYSTEM MEMORY=1000000 $END
 $BASIS GBASIS=N31 NGAUSS=6 $END
 $FORCE METHOD=ANALYTIC $END
 $STATPT METHOD=SCHLEGEL $END
!          <-- This has been tried with other methods
 $GUESS GUESS=HUCKEL $END
 $SCF DIRSCF=.TRUE. $END
 $DATA
  RHF/6-31G* AM1 GEOMETRY
  C1
  C     .000000 0     .000000 0     .000000 0       0    0    0
  C    1.414000 1     .000000 0     .000000 0       1    0    0
  H    1.122928 1  115.373840 1     .000000 0       1    2    0
  H    1.144622 1  109.014397 1  125.070099 1       1    3    2
  H    1.144376 1  101.224930 1 -114.885567 1       1    4    3
  H    1.110789 1  121.301445 1 -179.752487 1       2    1    3
  H    1.110784 1  121.852570 1     .261124 1       2    1    3
 $END
-----------------------------------------------------------------

Many thanks to all the responses in advance.


				Sincerely,

				     Park, TAE-YUN    
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
State University of Ghent
Laboratorium voor Petrochemische Techniek
Krijgslaan 281, Blok S5  
9000 Gent, Belgium	  
TEL:+(32)-0(9)-264-4527
FAX:+(32)-0(9)-264-4999
e-mail: tp@elptrs7.rug.ac.be
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=


From JERICKSON@elvax2.dowelanco.com  Thu Aug 15 10:17:40 1996
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Date: Thu, 15 Aug 1996 9:12:03 -0500 (EST)
To: CHEMISTRY@www.ccl.net
Subject: correlated SP calcs on HF geoms...


Alan Shusterman writes:

> ...
> Two examples drawn from Hehre's book (p 106-107), rearrangement of
> methylisocyanide to acetonitrile, and elimination of formic acid from ethyl
> formate, illustrate what may (?) be typical results.
> ...

Just to comment a bit further about my experience in this area. We looked
at the ethylformate --> ethylene + formic acid TS (See JACS, 1994, 116, 6271)
at both the MP2/6-31G*//MP2/6-31G* and RHF/6-31G*//RHF/6-31G* levels. Although there
were some differences in the TS geometries, the differences were not enough
to change any conclusions in the study.  In fact the Eact in the
MP2/6-31G*//MP2/6-31G* and in the MP2/6-31G*//RHF/6-31G* single point
calculation were almost identical. This work, however, does hilight the
influence electron correlation can have on TS geometries. So care should be
used in substituting single point calculations with correlated methods for
full optimization without examining at least one case optimized at both levels.

Jon Erickson
DowElanco CAMD
jerickson@dowelanco.com

From JERRY@chem1.chem.dal.ca  Thu Aug 15 11:17:51 1996
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From: "CHAN CHUN CHUNG (JERRY)" <JERRY@chem1.chem.dal.ca>
To: chemistry@www.ccl.net
Date:          Thu, 15 Aug 1996 11:16:55 AST
Subject:       Optimized Geometries for CH3COCH3, etc.
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Dear Netters,

    I am looking for the optimized gemetries of CH3COCH3 (acetone), 
CH3CSCH3 and CH3CSeCH3.  Could anyone please tell me how I could find 
them.  Thanks in advance for any suggestion.

Cheers,
Jerry 
Dalhousie University

From jhwang@bphp.sci.ccny.cuny.edu  Thu Aug 15 12:17:47 1996
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Date: Thu, 15 Aug 1996 12:12:32 -0400
From: jianghua wang <jhwang@bphp.sci.ccny.cuny.edu>
To: chemistry@www.ccl.net
Subject: Intensity


Hi, everyone:

I am struggling with calculating the Raman Intensity
and ask for your help now.

The problem is as following:

I use Gaussian94 to calculate the normal mode:
geometry, force field, frequency and intensity.
then I scale the force field in order to fit
my experimental Raman spectrum. But how the Raman
intensity should be changed due to the change of force
field? Any suggestion will be appreciated.

Sincerely,

Joshua Wang

************************************************************
*Joshua Wang		*Phone: 212-650-5502	           *
*Physics Department     *Fax:   212-650-5503	      	   *
*CCNY			*Email: 			   *
*New York, NY 10031     *  jhwang@cgraph.sci.ccny.cuny.edu *
************************************************************

From oscar@bilbo.edu.uy  Thu Aug 15 14:17:45 1996
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Date: Thu, 15 Aug 1996 15:07:20 -0700
From: "Oscar N. Ventura" <oscar@bilbo.edu.uy>
Organization: MTC-Lab
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Dear CCLers,

In performing a DFT analytical frequencies calculation (UB3LYP/ 
6-311+G(d,p), forces and displacements converged to less than 5E-05) I 
found the following usual data about low frequencies (it is a 
hydrogen-bonded complex)

>Low frequencies ---  -30.7468   -0.0030    0.0077    0.0087    6.7016   
>8.4499
>Low frequencies ---   21.8223  136.3306  308.7007

However, just inmediately follows:

>******    1 imaginary frequencies (negative signs) ******
>                    1                      2                      3
>                   A"                     A'                     A"
>Frequencies --   -14.8965               136.3300               308.7004

While the second and third frequencies are coincident, the first is not. 
Although not so extreme, the same difference occurred with the MP2 
frequency calculation (41.38 vs 40.51), and the UHF one (12.8456 vs 
12.8388 cm-1).

Questions: (a) has anyone suffered the same problem?
	   (b) which of the two sets of info is wrong? (I could not
		get useful info from the eigenvectors)
	   (c) is there some ground to consider it a numerical problem?

Thanks for all the help,

		Oscar


----------------------------------
Prof. Dr. Oscar N. Ventura
MTC-Lab, C.C. 1157, 11800 Montevideo, Uruguay - 
http://bilbo.edu.uy/MTC-Lab.html
Tel:+598-2-941860 Fax:+598-2-941906/948396 e-mail: oscar@bilbo.edu.uy

From bbendik@telerama.lm.com  Thu Aug 15 14:23:27 1996
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Subject: Summary:QSAR and Gov. approval
Date: Thu, 15 Aug 96 13:57:52 -0000
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This serves as a summary of replies that I received on this topic.

My original post:
_______________________________________________________________________
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.  

From:        William Welsh, wwelsh@jinx.umsl.edu

Predict the chromatographic retention of  a family of polycyclic aromatic 
hydrocarbons (PAHs) based on their chemical structures:
E. R. Collantes, W. Tong, W. J. Welsh, and W. L. Zielinski, Anal. Chem., 
68,
2038 (1996).

Predict the chemotherapeutic activity of anti-Alzheimer's Disease drugs 
based on their chemical structures:  
W. Tong, E. R. Collantes, Y. Chen, and W. J. Welsh, J. Medicinal Chem., 
39, 380
(1996).
___________________________________________________________________________


From:        Soaring Bear, bear@ellington.pharm.arizona.edu

	Your scenario of trying QSAR for paper toxins is interesting.
I applaud your interest in using new tools for old methods.  As 
a QSAR scientist, I would be the first to admit its limits.   It
should only be used as an indicator for directing further research
and it would never be accepted as a sole method.   
	Keep in mind that it is just a statistical method to make 
a linear regression based on certain physical properties of the 
compounds.   There are often outliers which are hard to explain
and the presence of those exceptions will keep governmental
agencies from accepting QSAR on its own.
	I do encourage you to use QSAR to help you concentrate
your research efforts, but don't expect it to replace experimental
verification.
__________________________________________________________________

From:        Phil Howard, howardp@syrres.com

        I am not aware of any uses of QSARs that have been accepted by 
FDA.
We have discussed with FDA a lot of estimation methods that we have
developed with EPA (see http://esc.syrres.com/~ESC/estsoft.htm) which have
been used for new chemicals under the Toxic Substances Control Act (TSCA).
The response I have gotten was that they don't rely on estimated values -
they test.  I will be interested to hear other peoples experience.
_____________________________________________________________________

From:        David Livingstone, davel@chmqst.demon.co.uk

There is quite a bit of literature on PBPK (Physiologically Based 
PharmacoKinetic) modelling.  This is (it seems to me) a better 
approach than the "traditional" method of mathematical modelling of 
chemical distribution in Man (and animals).  In your "worst case" 
modelling the amount that gets into Man is less important than what 
happens to it when it gets there.  There is a report of an EC funded 
workshop on the replacement of animals in experiments which contains 
quite a lot of references to QSAR studies of toxicity and PBPK models:

The Integrated Use of Alternative Approaches for Predicting Toxic
Hazard" M.D. Barratt, J.M. Castell, M. Chamberlain, R.D. Combes, J.C.
dearden, J.H. Fentem, I. Gerner, A. Giuliani, T.J.B. Gray, D.J.
Livingstone, W. McL. Provan, A.J.J.L. Rutten, H.J.M. Verhaar and P.
Zbinden. ATLA, 23, 410-29 (1995).

There are also stacks of papers on QSAR models of various kinds of 
toxicity - I expect someone will send you a reference to a recent 
review.

I believe that the FDA uses TopKat to draw up priority lists for 
testing - try speaking to the people at Health Design (now owned by 
Oxford Molecular).  There are also various other programs around 
which attempt to predict hazards and metabolic fate (you can't really 
have one without the other).  There is a chapter in my book which 
briefly discusses some of these systems if you are not very familiar 
with them:

"Data Analysis for Chemists: Application to QSAR and Chemical Product 
Design", D.J. Livingstone, Oxford University Press, 1995, ISBN 
0-19-855728-0.
__________________________________________________________________

Many thanks to all who replied!
bev


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


From boyd@chem.iupui.edu  Thu Aug 15 17:17:44 1996
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 15 Aug 1996 15:43:07 -0500
Date: Thu, 15 Aug 1996 15:33:11 -0500
From: Boyd <boyd@chem.iupui.edu>
Subject: Reviews in Computational Chemistry
To: OSC CCL <chemistry@www.ccl.net>
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CCLers,
We wish to announce the publication of Volume 9 of REVIEWS IN 
COMPUTATIONAL CHEMISTRY.  The emphasis of this volume is on 
molecular modeling, covering computer-aided ligand/drug design, 
thermodynamic perturbation and thermodynamic integration, 
oligosaccharides, molecular mechanics force fields, and molecular 
shape.

The authors and chapters are:
1.  James R. Damewood, Jr.,  Peptide Mimetic Design with the Aid of 
Computational Chemistry.
2.  T. P. Straatsma, Free Energy by Molecular Simulation.
3.  Robert J. Woods,  The Application of Molecular Modeling Techniques 
to the Determination of Oligosaccharide Solution Conformations.
4.  Ingrid Pettersson and Tommy Liljefors,  Molecular Mechanics 
Calculated Conformational Energies of Organic Molecules:  A Comparison 
of Force Fields.
5.  Gustavo A. Arteca,  Molecular Shape Descriptors.

The book will be available for your perusal at the VCH Publishers 
(Wiley) booth at the Orlando ACS meeting later this month.  Volume 9 
(xxxiii + 282 pp) has ISBN 1-56081-930-8.

We recently doubled our book give-away program.  If you are interested 
in winning a free copy of Volume 9 or other volumes, check out our 
home page at 
http://chem.iupui.edu/~boyd/rcc.html

Thanks,
Don
Donald B. Boyd, Ph.D.
Co-editor, REVIEWS IN COMPUTATIONAL CHEMISTRY
Department of Chemistry
Indiana University-Purdue University at Indianapolis
402 North Blackford Street
Indianapolis, Indiana 46202-3274, U.S.A.

From ademan@UDel.Edu  Thu Aug 15 18:17:46 1996
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Date: Thu, 15 Aug 1996 17:43:50 -0400
From: Andries de Man <ademan@UDel.Edu>
Organization: University of Delaware
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Subject: Meeting for PChem graduate students
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On Friday November 1st, 1996, the fifth Manhattan Poster Project
will take place at the the University of Delaware.

The Manhattan Poster Project is a poster session hosted by graduate
students to promote interaction between experimental and theoretical
physical chemistry graduate students and post-docs. This conference
began in 1991 at Columbia University, and has since been hosted by
Boston University, University of Pennsylvania, and Georgetown
University.
This year's event will include a Keynote Speaker, ACS Career Workshops
on Effective Job Searching, Employment Outlook and Job Security, and a
Job Fair in addition to the Poster Session.

The day-long meeting provides graduate students and post-docs the
opportunity to present posters on their current research, and to
establish contacts with chemists from other universities and from
industries in an informal atmosphere.

For more information, and on-line registration, see our Web site:
  http://www.udel.edu/mpp96/

           Andries de Man,  MPP96 Committee
           Department of Chemistry, University of Delaware
           Newark DE 19716
phone (302)8313522  fax (302)8316335 Email mpp96@smalldog.duch.udel.edu

