From CHAMH@INDSVAX1.INDSTATE.EDU  Thu May 13 18:32:00 1993
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Date: Thu, 13 May 1993 23:32 EST
From: CHAMH@INDSVAX1.INDSTATE.EDU
Subject: Info on Collision Diameters
To: CHEMISTRY@ccl.net
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	Does anyone know the whereabouts of experimental or
experimentally-based
(isotropic) collision diameters of radicals and other metastables, such as
CH2, CH3, C2H5, CHO, CH3CO, CN, ClO, C6H5, C6H5O ?  Does anyone care about
such information these days?
	Computational estimates would be of interest, too.

	I would be grateful for any suggestions or clues about good sources
of these data; the thought of slogging though Chemical Abstracts for such
info piecemeal is a bit too daunting.

	Many thanks.

Arthur M. Halpern
Department of CHemistry
Indiana State University
Terre Haute, IN  47809

voice (812) 237-2182
fax   (812) 237-2232

BITNET  CHAMH@INDAVAX1

From wolf@molout.tutkie.tut.ac.jp  Fri May 14 04:51:18 1993
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From: wolf@molout.tutkie.tut.ac.jp (Wolf-D. Ihlenfeldt)
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To: CHEMISTRY@ccl.net
Subject: Chemistry Tools





Chemistry Tools

Since a few days this newsgroup enjoys a lively discussion about
the usefulness of tools which can be combined to advanced systems.

A year ago I was thinking about the same problems, and I actually 
decided to tackle the problem and provide a complete algorithm
development, chaining, exchange and verification system to the scientific
community. The system under development is called CACTVS -
Chemistry Algorithm Construction, Threading and Verification
System. It will be public domain, but I will need some more months
to work on some problems. After that there will be an alpha test
phase before it becomes truely public. Volunteers welcome.

Lectures and posters on the system are scheduled for the
- 3rd International Conference on Chemical Structures
  June 6-10, Norrdwijkerhout, Netherlands
- 3rd World Congress of Theoretical Organic Chemists (WATOC'93),
  July 18-24, Toyohashi, Japan


What does CACTVS ?

- The basic aim of most chemical computations is to derived properties
  of ensembles of molecules (can be a single molecule ensemble, of course).
  Besides being subjected to computations, molecules are probably
  edited structurally or in property values (i.e. 3D-coordinates). And
  you want to see/vizualize the result and analyse them. We need
  to provide this basic functionality, but we must be as open as possible
  to incorporate new data structures, data and computation methods.
- Chemical properties come in a wide variety of formats. They can be ensemble-,
  molecule-, atom-, bond-, ring- etc. oriented. They can have different
  formats (a single boolean or a catalog number string or a raytracer 
  gif image file or a pair of variable length vectors of 3D coordinates
  attached only to bonds which pass a specific filter condition,
  where there are two independent sets of properties when the bond is
  viewed in different directions, and this data becomes invalid
  when another prop changes or the structure is edited).
  Cactvs allows properties to have a complex structure built from primitives.
  New primitives can be defined dynamically at runtime without
  recompilation by dynamic linking.
- You are allowed to have your own ideas on what a 'bond' or 'atom' is.
  New classes can be defined on the spot. Torsional angles are a
  property of a special 'bond' type with 4 atoms. All data structures
  are allocated dynamically, no size limitations.
- Properties typically rely on input data (values of other properties).
  These are simply requested in the computation module. No need to know
  anything about subroutine calling orders, parameters or the way the prop is
  actually computed - this is all looked up by the system. This process
  is recursive. All your routine gets are the values or an error code
  if some start values were not computable.
- The system maintain a validity status of the current props. I.e. after
  editing the structure or some property value, the system automatically
  knows which props are invalidated.
- New properties can be defined at runtime, and the definitions can be stored
  in files and databases privately for for public access. If a property
  is mentioned which is not yet known to the system, directories and 
  databases (networked, even worldwide) are searched automatically.
  Property definitions are interactively editable.
- Properties are computed by a limited set of built-in functions,
  dynamically loaded object files, a scripting language or servers. This
  process is transparent. The computation method is part of the property 
  definition. Property definitions in databases can contain objects
  for dynamic loading, independent server programs and/or source. The
  system tries to locate an object or server program compatible with the
  local architecture. If this fails, you still get the source (if it
  was deposited) and can try to compile it locally. A property definition
  without objects or source can be considered useful as a
  'we can do this, contact us for further information' advertisement.
  Databases can be searched for keywords in property descriptions and other
  criteria. Documentation of the module is part of the definition.
  Scripts and dynamically loaded modules can be edited/replaced at runtime
  for interactive algorithm development. Using scripts, classical external
  unadapted programs may be started and results reread. Or the user is asked 
  interactively for some data which is not computable.
- Molecules and all computed results can be stored,retrieved and searched
  in an object-oriented database including historic access (i.e.
  'what was the result with version 0.7 from feb93 ?' 'which are the
  molecules from the standard data set where the value changed
  from vers 0.7 to 0.8 by more than 0.1 units'?). New search and
  indexing methods can be added dynamically to the database. Search modules
  will be stored in databases like property compuation modules.
- Various popular file I/O formats are supported. New formats can be added
  by dynamically linking new I/O methods as objects or command language scripts.
  File I/O modules are again distributable by networked databases.
- The whole property computation/maintenance system is embedded
  into a X11/Xview/Slingshot graphical environment. The operation
  follows visual programming paradigmens. Property
  computation requests, structure editing methods or result analysis
  procedures are coded as tool objects. Tool objects are again
  archiveable in databases. Tools can present forms for user 
  interaction and numerical result output. Tools and other objects can
  be chained to pipes and trees. Pipelines are fed by dropping files
  or molecules onto them. Tools can manipulate the number of
  molecules passing through them, i.e. filter out unfit species or
  generate isomers. Other objects like archives, database portals,
  output files, molecule editors, display server objects and the undispensible
  trashbin can be integrated in those pipes or used as isolated utility objects.
  Display servers use the same mechanisms as computation servers,
  only that they typically do not report results back (but they may, i.e.
  change 3D-coordinates of rotated molecules). Displays may
  request arbitrary properties for vizualisation via the standard lookup
  service. Complete executable display servers, their manuals
  and their source can be stored in databases. 
- The sequence of instructions for script-based property computations
  and tool actions is defined by a general-purpose interpreted
  command language (Tcl/TclX). New commands (for example for
  the statistical analysis of results) can be added as script procedures
  or dynamically linked language extensions. The language has
  access to files, databases, property definitions, tool definitions etc.

More questions ? Send Email.

WDI

(System used for development: Sun SparcII, SunOS4.1.2. No ports yet,
but should not be too difficult, provided the various libraries are
available. The Postgres4.1 data base system, Xview3 X toolkit and GnuDLD3.2.3
dynamic loader are probably the most problematic. You find them all on the
net. This system uses LOTS of usenet software. The internal programming
language is C)

Caveats:

 Currently, the emphasis of the system is on empirical/topological/mm
 methods, not heavy duty quantum chemistry. But of course you are free
 to define a z-matrix basic data type, probably attached to ensembles.
 Then write a couple of functions transforming between z-matrix and
 coordinates and put them for world-wide access into your local
 CACTVS database. Maybe add input and output modules for the file format
 of your favorite numbercrunching program.
 And don't forget to tell the community about it.

 Furthermore, CACTVS is not an vizualisation system
 per se, although the display server concept makes it easy to use
 all kinds of displays once they are provided - hopefully people
 will put plenty of display servers for the vizualisation
 of the most obscure data into their databases for global access. Or
 somebody writes an interface (server?) to AVS or Chorus.

WDI

From C1790@slvaxa.umsl.edu  Tue May 14 04:32:07 1993
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Date: 14 May 1993 10:32:07 -0600 (CST)
From: C1790@slvaxa.umsl.edu
Subject: CALL FOR PAPERS
To: CHEMISTRY@ccl.net
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CALL FOR PAPERS

           
	


            THE 28TH MIDWEST REGIONAL ACS MEETING
                         
                         to be held in

                     COLUMBIA, MISSOURI

                            on

                    NOVEMBER 10-12, 1993

                 is sponsoring a symposium


     "FRONTIERS IN APPLICATIONS OF COMPUTATIONAL CHEMISTRY"


The Symposium will emphasize all aspects in applications of computational

chemistry, including on small molecules, on polymer systems, on biological

systems, and on materials, surfaces, interfaces, and in clusters.  

The Program will include a plenary session of invited speakers

(see below) as well as contributed oral and poster sessions.  Please

submit abstracts (on ACS abstract forms) to 

Dr. William J. Welsh, Symposium Chair 
Department of Chemistry
University of Missouri-St. Louis    
8001 Natural Bridge Rd.
St. Louis, MO 63121

LIST OF PLENARY SPEAKERS (Titles of Talks will follow later)

PROF. RICHARD BOYD, DEPT. OF CHEMICAL ENGINEERING, UNIV. OF UTAH

PROF. PETER A. KOLLMAN, SCHOOL OF PHARMACY, UNIV. OF CALIF.-SAN FRANCISCO

PROF. DONALD TRUHLAR, DEPT. OF CHEMISTRY, UNIV. OF MINNESOTA

PROF. KEN WIBERG, DEPT. OF CHEMISTRY, YALE UNIVERSITY

  

From ROY@nickel.laurentian.ca  Fri May 14 06:34:51 1993
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 14 May 1993 11:34:51 EST
Date: Fri, 14 May 1993 11:34:51 -0500 (EST)
From: Roy Kari <ROY@nickel.laurentian.ca>
Subject: Small tools!
To: chemistry@ccl.net
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Hi folks,

Most of the "tools" I have seen described seem more like systems to me.

For small tools, I would like to make a pitch for Microsoft Excel
and the Excel Software Development Kit. The SDK makes it quite
easy to interface a C/C++ program to Excel and Excel serves as
an ideal I/O interface with good graphics. To see an example
of what I am speaking about download the file 
PD1:<MSDOS.WINDOWS3>XLMATH.ZIP from WSMR-SIMTEL20.ARMY.MIL or
one of the mirror sites. The XLMATH add-in will let you do
a simple Huckel calculation in Excel but the prupose of XLMATH
is really to demo the SDK.

Roy

-------------------------------------------------------------------
Roy Kari                     INTERNET:   Roy@Nickel.Laurentian.CA
Department of Chemistry      COMPUSERVE: 70410,2372
 & Biochemistry
Laurentian University        VOICE: (705) 675-1151 ext 2111
Sudbury, ON                  FAX:   (705) 675-4844
Canada P3E2C6
-------------------------------------------------------------------



From fagerbur@Kodak.COM  Fri May 14 08:28:07 1993
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From: fagerbur@Kodak.COM
To: "chemistry@ccl.net"@Kodak.COM
Subject: Zeolite molecular modeling


Hi netters!
    I would like to find out who out there might be working in the area of 
getting good models of zeolites.  Our company has recently purchased MSI's 
Cerius software which claims to do zeolites.  I have, in looking into it 
just a bit, however, found that apparently the force field being used has 
not really been validated (MSI it turns out did not claim it was - I think 
we just misunderstood).  So, not wishing to reinvent the wheel, I am 
interested in what is going on out there.  In a cursory look, I find no 
activity in the area but perhaps I have not looked in the correct spots 
and/or the work is not in print yet.
    I will summarize the results for the net if there seems to be 
interest.  Until then, thanks in advance for your replies/help.

  Dave Fagerburg
  Eastman Chemical Co.
  Kingsport,  TN  37662

    fagerbur@kodak.com



From hou@agouron.agouron.com  Fri May 14 02:50:02 1993
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From: hou@tbone.agouron.com (Xinjun Hou)
Message-Id: <9305141650.AA20971@agouron>
To: chemistry@ccl.net
Subject: RE: C++ classes


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From:	IN%"lim@rani.chem.yale.edu"  "Dongchul Lim"
> It would be nice to put these tools (I mean source code) together as a library,
> for example, "chemlib", as compared to "netlib" or "statlib".
> We won't need QCPE soon, if we keep depositing our code to anon ftp sites
> such as www.ccl.net, preferably in a library form, so that the code can
> be reused without much modification.

In Message-Id: <01GY4L4L9DMU007C9J@UOFT02.UTOLEDO.EDU> DSOUTH@uoft02.utoledo.edu
wrote:
>
>Along the same lines, why not develop a set of C++ classes for computational
>chemistry?  Of course this only benifits the people that can program in
>C++, but the advantages would be an order of magnitude about the advantages
>gained by creating a chem.h.  Perhaps Mark T. (of Argus) has something
>to add...I know he was trying to move Argus into the OOP universe.
>

During March, 1993 NIH "High Performance Computing in Chemistry" workshop,
a group from Pacific Northwest Laboratory mentioned that they were using G++
(a GNU C++) for programming developing, and they would release the C++
classes as PD once the coding are completed. Anyone has more information on
this?


Xinjun (Jason)

Xinjun Jason Hou                                       010110000110100101101110
Agouron Pharmaceuticals, Inc                           011010100111010101101110
hou@agouron.com                                        010010000110111101110101




From DSMITH@uoft02.utoledo.edu  Fri May 14 07:59:51 1993
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Date: Fri, 14 May 1993 12:59:51 -0500 (EST)
From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" <DSMITH@uoft02.utoledo.edu>
Subject: modeling high spin, d5 Fe
To: chemistry@ccl.net
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For anyone who can help with transition metal calculations --

I have need of calculating an optimized geometry and atomic charges (MEP,
Mulliken, whatever) for iron(III) tris(catecholate) 3- ion.  The iron is
a high spin, d5 species.  I want to use the geometry and charges in subsequent
molecular dynamics and/or Monte Carlo studies.  What is the recommended 
method?  In particular, how do I treat the d5 system?

I have access to G90 and G92, GAMESS, MOPAC and Hyperchem.  I can therefore 
do ab initio with or without ECPs in the basis set, UHF or CI or MCSCF, GVB, 
or I can do any one of a number of semiempirical calculations including INDO,
ZINDO/1 or /2, MNDO, AM1, PM3.  I do not have access to DFT or Xalpha 
programs.

Also, can anyone point me in the direction of previous studies of high spin
d5 iron complexes, even such as Fe(OH)6 3-?


Thanks in advance for any advice.

Doug

Douglas A. Smith
Assistant Professor of Chemistry
The University of Toledo
Toledo, OH  43606-3390

voice    419-537-2116
fax      419-537-4033
email    dsmith@uoft02.utoledo.edu


From DSMITH@uoft02.utoledo.edu  Fri May 14 08:34:54 1993
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Date: Fri, 14 May 1993 13:34:54 -0500 (EST)
From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" <DSMITH@uoft02.utoledo.edu>
Subject: hydrogen bonding involving aromatic hydrogens
To: chemistry@ccl.net, hyperchem@autodesk.com, mmodinfo@uoft02.utoledo.edu
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Does anybody have any experience, references, or knowledge of systems in
which the hydrogen of an aromatic ring (preferably benzene but any aromatic
system is really of interest) is involved in a hydrogen bond?  I will 
summarize responses for the net.

Doug

Douglas A. Smith
Assistant Professor of Chemistry
The University of Toledo
Toledo, OH  43606-3390

voice    419-537-2116
fax      419-537-4033
email    dsmith@uoft02.utoledo.edu


From CHAMH@INDSVAX1.INDSTATE.EDU  Fri May 14 07:48:00 1993
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Date: Fri, 14 May 1993 12:48 EST
From: CHAMH@INDSVAX1.INDSTATE.EDU
Subject: Collision Diameters - Corrigendum
To: chemistry@ccl.net
Message-Id: <01GY5ZLRGILS004D3M@INDSVAX1.INDSTATE.EDU>
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	Relative to my recent query about collision diameters, I mistyped
my E-mail address.  For those of you who plan(ned) to provide me with some
information/leads, my BITNET address is:

CHAMH@INDSVAX1

Thanks,

Arthur M. Halpern
Indiana State University

From merkle@parc.xerox.com  Fri May 14 06:49:19 1993
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From: Ralph Merkle <merkle@parc.xerox.com>
To: chemistry@ccl.net
Subject: Putting QCPE on the net
Message-Id: <93May14.134923pdt.12171@manarken.parc.xerox.com>
Date: 	Fri, 14 May 1993 13:49:19 PDT


I realize that commercial advertising is usually frowned upon, but in this
case (given the recent discussion of how to make QCPE available on the
net) I thought people would be interested in Amix.  (I'm not affiliated
with Amix, though I do have friends there).

Amix lets people buy and sell data of any type (manuals, software, whatever).
Right now, you need an IBM PC and some way of connecting to Amix (dial
up their telephone number, connect to them through a packet switched
network, or whatever).  They'll have a Mac version out soon.  They aren't
connected to the Internet yet, but the're working on it.  Monthly
fees are reasonable ($8/month).  They let buyers and sellers of
information negotiate whatever price they want, and then Amix takes
a percentage of the selling price.  Their fees are listed at the end
of this message.

It looks like the ideal way to solve many of the problems people have been
talking about here.


Ralph C. Merkle
merkle@xerox.com


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*       Upload and sell your existing articles, tips, solutions, analyses,
and papers that might be of value to others.

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AMiX lets you evaluate a growing selection of goods and services the same
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REAL TALK
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"I was wondering when someone would do this." - Wendy Woods, Newsbytes

ABOUT AMiX
The American Information Exchange Corporation was incorporated in 1986.
After several years of product research and development, the AMiX Service
went online in January, 1992.

For additional product or company information, or to get your own AMiX
account, contact:
        American Information Exchange Corporation
        540 N. Santa Cruz Ave., #271
        Los Gatos, CA    95030-4347


AMiX, American Information Exchange Corporation
The Information Marketplace (R)

AMiX, AMiX Service, Information Marketplace, and Information Markets are
trademarks of the American Information Exchange Corporation. All other
product, brand, or company names are trademarks of their respective
holders. (c) 1992 American Information Exchange Corporation.

==============================================================================

We would also like to send you the AMiX PC software - free of charge.  With
it you can log on as a GUEST and browse the service.  You can also sign-up
through an online registration process. (Macintosh software is in
development, and will be released later this year.)

In order to receive the software, please forward the following information:     
        name
        mailing address
        telephone number
        preferred disk size (DOS 3.5" or 5.25")
        how you heard about AMiX

We look forward to seeing your services available online soon!  Please
contact us if you have any further questions.

==============================================================================
MARKETS

SOFTWARE AND CODE
Software for Sale or Evaluation
Smalltalk
C and C++

PRODUCTS AND TECHNICAL INFORMATION
Microsoft Windows
MS-DOS
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Databases & Templates
Engineering, Architecture & Manufacturing

BUSINESS & SERVICES
Business Information
Computing Trends & Analysis
Marketing & Management Services
Information Brokers
Writers & Editors


=============================================================

PRICES

Setting up Your Account:
$35 one-time account set-up fee for each person or company establishing an
AMIX account.

Monthly Account Charges:
$8/month per account.  Invoice billing available for most U.S. corporations
at an additional $5/month.

Connect Charges:
Nationwide packet-switch network:  Contiguous United States $5.50/hour;
Alaska, Hawaii and Canads: $9.50/hour.  Direct dial (San Francisco Bay area
only):  $3/hour. Direct dial (all other areas): $2/hour plus long-distance
charges.  For more information on international connect fees, contact AMIX.

Storage Fees:
Up to 2 megabytes of information may be stored on the AMIX host computers
at no charge. Storage fees will be charged at $0.75 per megabyte per month
for amount over 2 megabytes.

Mail Message Fees:
No fee for first 100 recipient-messages per month. (Examples: 1 message to
100 recipients or 100 messages to 1 recipient) Subsequent messages charged
to sender at $0.05 per recipient.

New Account Credit Limit:
New account credit limit is established at $500 unless arranged otherwise
with AMIX Customer Support.

Purchase of any item or consulting:
The price is determined by the seller, or by the buyer and seller during
negotiations.  Upon purchase, buyer's account is automatically charged and
seller's account is credited according to payment terms  (On Agreement, On
Delivery, On Acceptance, or On Evaluation).

Transaction Fees:
The minimum price for an item or consulting is $1 and maximum is $2,500.
The transaction fee is determined by the price and is charged to the
seller, as follows:
        
        40% of the first $50 +
        25% of second $50 +
        15% of next $400 +
        10% of the amount over $500
(Example:  Fee for a $10 transaction is:  $4;  Fee for a $600 transaction
is:  $20 + $12.50 + $60 + $10 = $112.50.)

Note:  This is a general summary of the fees. For a detailed pricing
summary, contact AMIX customer support or view the document "POLICIES &
PRICES" on AMIX. Fees are subject to change.


From bieron@SERVER.uwindsor.ca  Fri May 14 14:05:00 1993
Received: from server.uwindsor.ca  for bieron@SERVER.uwindsor.ca
	by oscsunb.ccl.net (5.65c+KVa/921206.2314) id AA03926; Fri, 14 May 1993 18:04:28 -0400
Received: by SERVER.uwindsor.ca (920330.SGI/920502.SGI.AUTO)
	for CHEMISTRY@ccl.net id AA12977; Fri, 14 May 93 18:05:04 -0400
From: bieron@SERVER.uwindsor.ca (JACEK BIERON)
Message-Id: <9305142205.AA12977@SERVER.uwindsor.ca>
Subject: MOPAC6
To: CHEMISTRY@ccl.net (COMPUTATIONAL CHEMISTRY LIST)
Date: Fri, 14 May 93 18:05:00 EDT
X-Mailer: ELM [version 2.3 PL11]



Hello All,

could someone tell me where can I find MOPAC6 ?

regards
jb


 ==========================================================================
 |                             |                                          |
 |   Dr. Jacek Bieron          |                                          |
 |   Department of Physics     |   Internet:  bieron@server.uwindsor.ca   |
 |   Essex Hall                |                                          |
 |   University of Windsor     |      Phone:  (519) 253 4232 ext 2670     |
 |   401, Sunset Avenue        |                                          |
 |   WINDSOR                   |        Fax:  (519) 973 7075              |
 |   Ontario N9B 3P4, Canada   |                                          |
 |                             |                                          |
 ==========================================================================



From soperpd@esvax.dnet.dupont.com  Fri May 14 14:39:04 1993
Received: from gatekeeper.es.dupont.com  for soperpd@esvax.dnet.dupont.com
	by oscsunb.ccl.net (5.65c+KVa/921206.2314) id AA04545; Fri, 14 May 1993 18:49:02 -0400
Received: by gatekeeper.es.dupont.com (5.65/ULTRIX-mjr-062991);
	id AA17732; Fri, 14 May 93 18:49:00 -0400
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	id AA17709; Fri, 14 May 93 18:39:04 -0400
Date: Fri, 14 May 93 18:39:04 -0400
Message-Id: <9305142239.AA17709@esds01.es.dupont.com>
From: soperpd@esvax.dnet.dupont.com
To: "CHEMISTRY@ccl.net"@esds01.dnet.dupont.com
Subject: Computational Chemistry on the Cheap


    Imagine you are an eager computational chemist who dreams
of doing semi-empirical, Hatree-Fock, many-body perturbation
theory, and coupled cluster calculations.  Now imagine that 
you are dirt poor and have no access to a unix workstation,
let alone a supercomputer.  You don't need a fancy front end,
but you would like to be able to visualize a molecular orbital
or electron density map now and then.

    What is the least expensive way to go?  A 486 PC clone?
Running what software for computation?  For visualization?

Paul Soper
DuPont
soperpd@esvax.dnet.dupont.com

