From owner-chemistry@ccl.net  Mon Jul 24 04:09:13 1995
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Message-Id: <ABB5r4m80U@qsar.chem.msu.su>
Organization: Lab. of Org.Synth., MSU
Date: Mon, 24 Jul 1995 11:52:43 +0400 (MSD)
From: "Igor Baskin" <baskin@qsar.chem.msu.su>
X-Mailer: dMail [Demos Mail for DOS v1.23]
Subject: Applicability range of QSAR models
Lines: 27


        Dear CCL'ers,

        Now we (three other authors and me) are finishing preparation
of an article dealing with rigorous mathematical study of the problem
of defining applicability range of QSAR/QSPR models. Most frequently
this problem arises when (i) developing QSAR models for noncongeneric
data sets, (ii) designing bioactive molecules based on QSAR models,
(iii) comparing advantages and disadvantages of "knowledge-based"
QSAR/SAR approaches (aimed at making predictions through understanding
molecular mechanisms) vs "correlative" approaches (aimed at making
predictions via applying formal statistical procedures without the
need to understand molecular mechanisms). In this connection I am
_very_ interested in collecting a whole spectrum of current opinions,
approaches and ideas on this topic. Any suggestion or reference will
be welcome and appreciated. All responses shall be summarized.




--
-------------------------------------------------------------------------
Dr. Igor I. Baskin               !  e-mail: baskin@qsar.chem.msu.su
Institute of Organic Chemistry & !  phone : 7-095-939-3557
Chemistry Department,            !  FAX   : 7-095-939-0290
Moscow State University,         !
Moscow, Russia                   !
--------------------------------------------------------------------------


From owner-chemistry@ccl.net  Mon Jul 24 09:24:18 1995
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Date: Mon, 24 Jul 95 15:12:26 +0200
Message-Id: <9507241312.AA13042@otto.mpimf-heidelberg.mpg.de>
To: toukie@zui.unizh.ch
From: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing)
Subject: Re: CCL:Question about charged micellar spheres
Cc: CHEMISTRY@ccl.net (Computational Chemistry List)


Dear Dr. Shapiro,

>     Suppose there are two sets of positively-charged spherical micelles
>one "big" and one "small", and these micelles are capable of binding to a
>surface.  It stands to reason that when two such positively-charged micelles
>bind to a surface they will not come right up against one another because
>they will be repulsed by their mutual positively-charged surfaces.  Now, if
>the _density_ of charges on the surface of the spheres is the same (i.e.,
>both the big micelles and the small micelles have the same number of positive
>charges per unit surface area), will two small micelles be able to sit closer
>to one another than two large micelles, i.e., will there be greater repulsive
>forces between two large micelles resulting in their sitting further away
>from one another than between the two smaller micelles?

The interaction of the micelles with the wall depends on the charge density
of the wall, the diameter d of the micelles compared to the Debye-length
lDH of the system, i.e., the ionic strength of the surounding electrolytes.

As long as the Debye length lDH is small compared to the diameter d of the
micelles, the concentration of the micelles at the wall (before contact)
will be close to the bulk solution concentration. Any charge at the wall
will be screened by the ions in solution. If, however, lDH >> d, the
micelles and the ions will compete with each other in screening the wall
charges. 

On has to bear in mind that the binding of micelles to the wall may change
the charge density in the wall.

> If you could explain the answer to this problem in a
>straightforward mathematical way, I would be most grateful.

You may have a look at:

David C. Grahame (1947). "The Electrical Double Layer and the Theory of
Electrocapillarity." Chemical Reviews 41 441-501.

Robert U. Muller and Alan Finkelstein (1972). "The effect of surface charge
on th voltage-dependent conductance induced in thin lipid membranes by
Monazomycin." The Journal of General Physiology 60 285-306.


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

Eberhard von Kitzing
Max-Planck-Institut fuer Medizinische Forschung
Jahnstr. 29, D69120 Heidelberg, FRG

Carl-Zuckmayer Str. 17, D69126 Heidelberg (privat)

FAX : +49-6221-486 459  (work)
Tel.: +49-6221-486 467  (work)
Tel.: +49-6221-385 129  (home)

internet: vkitzing@sunny.MPImF-Heidelberg.mpg.de


From owner-chemistry@ccl.net  Mon Jul 24 10:39:27 1995
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From: lin@chu.chem.nthu.edu.tw (Chiu-Ling Lin)
Message-Id: <9507241339.AA20150@chu.chem.nthu.edu.tw>
Subject: Parameter wanted ?
To: CHEMISTRY@ccl.net
Date: Mon, 24 Jul 95 22:39:21 TAIDT
X-Mailer: ELM [version 2.4dev PL17]



Does anybody have parameters of Li+,Na+,and K+
in Extend Huckel method ? 

    Thanks in advance to all responders.
 
 

From owner-chemistry@ccl.net  Mon Jul 24 11:09:24 1995
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Date: Mon, 24 Jul 1995 10:58:48 -0400 (EDT)
From: "Mark A. Zottola" <markz@chem.duke.edu>
To: CHEMISTRY@ccl.net
Subject: Jarvis-Patrick Clustering
Message-Id: <Pine.SUN.3.91.950724105528.9323A@dna.chem.duke.edu>
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Is there a public domain code for doing jarvis patrick clustering?
I already have written the code for creating the distance table, but
I wouldn't mind a pointer to where JP code might live. I have already
checked at GAMS and have not found it. I am open to any suggestions.
Thanks!

-Mark


******************************************************
*                                                    *
*                                                    *
* Mark A. Zottola                                    *
* markz@dna.chem.duke.edu                            *
* Department of Chemistry                            *
* Duke University                                    *
* Durham, NC 27704                                   *
*                                                    *
*                                                    *
* The fault, dear Brutus, lies not with ourselves,   *
* but rather within our CPUs.                        *  
* (with apologies to Shakespeare                     *
*                                                    *
*                                                    *
******************************************************



From owner-chemistry@ccl.net  Mon Jul 24 11:24:21 1995
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Date: Mon, 24 Jul 1995 10:07:25 -0500
Message-Id: <9507241507.AA21224@daffy.bnpi.com>
To: CHEMISTRY@ccl.net
Subject: Help for Molecular Design Software



Dear Netters,

Could someone please tell me the 
molecular design/molecular modeling
software available for PC's or MACs?
Is there anything in the public domain?


Thanks for your help
pavan

Please e.mail your replies to
pavan@bnpi.com

From owner-chemistry@ccl.net  Mon Jul 24 12:09:33 1995
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From: "Michael L Hall" <mlhall@garvey-lab.chem.buffalo.edu>
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Date: Mon, 24 Jul 1995 12:01:27 -0400
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Subject: pc computational software
Content-Type: text/plain; charset=us-ascii
Mime-Version: 1.0


Two programs available for a pc include Hyperchem and Alchemy.

Options include:


Hyperchem- vibrational frequency, molecular dynamics, semi-empirical
	   and molecular mechanics calculations.


Alchemy- raw molecular mechanics minimization



From owner-chemistry@ccl.net  Mon Jul 24 12:24:22 1995
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Date: Mon, 24 Jul 1995 11:04:48 -0500 (CDT)
From: David Chalmers <david@wucmd.wustl.edu>
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To: CHEMISTRY@ccl.net
Subject: Parameters for sulfonamides, 
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Hi all,

I am looking for molecular mechanics parameters for sulfonamides.  So far 
my literatures searches have had no success.  Does anybody have 
parameters that they would be prepared to give me or can anybondy direct 
me towards an appropriate reference?

I will post a summary to the group.

David

--------------------------------------------------------------------------------
David Chalmers				   		david@wucmd.wustl.edu
Department of Mol. Biol. and Pharmacol.
Washington University School of Medicine
Campus Box 8103, 660 S. Euclid Ave			Lab:  +1 314 362 2515
St Louis, MO 63110, USA					Fax:  +1 314 362 7058
-------------------------------------------------------------------------------



From owner-chemistry@ccl.net  Mon Jul 24 13:54:23 1995
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From: "Wayne Huang" <huang@mazda.wavefun.com>
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Date: Mon, 24 Jul 1995 10:47:33 -0700
Reply-To: huang@wavefun.com
X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail)
To: chemistry@ccl.net
Subject: Computational Chemistry Workshop
Cc: workshop@wavefun.com
Content-Type: text/plain; charset=us-ascii
Mime-Version: 1.0


Announcing the upcoming fall quarter schedule for ...

		------------------------------------
		| COMPUTATIONAL CHEMISTRY WORKSHOP |
		------------------------------------

	September 6-8, October 11-13 & November 8-10, 1995

Intensive 3-day workshops focus on application of modern electronic
structure methods to chemistry. Lectures will describe underlying
theory, assess performance of modern electronic structure methods,
outline practical strategies for doing calculations, and illustrate
results of applications to diverse chemical problems. Laboratories
provide molecular modeling demostration, hands-on experience using
a wide selection of experiments, as well as ample of time to explore
your own chemistry. Visualization and animation techniques will also
be presented for both educational and research presentation.

Here are the summary of workshop information:

_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
_/                                                                _/
_/                COMPUTATIONAL CHEMSITRY WORKSHOPS               _/
_/						                  _/
_/ Format:      3-day intensive workshop on electronic structure  _/
_/              methods and applications, and hands-on molecular  _/
_/              modeling laboratory on individual workstations.   _/
_/              It will provide:                                  _/
_/							          _/
_/		 o Concise summary of modern electronic structure _/
_/                 methods;                                       _/
_/		 o Assessment of range and performance of their   _/
_/		   applications;				  _/
_/		 o Hands-on experience in molecular modeling      _/
_/		 o Graphical Analysis of results;                 _/
_/		 o Visualization and animation of structures and  _/
_/		   reactions. 					  _/
_/							          _/
_/ Schedule:	September Workshop: Sept. 6-8, 1995               _/
_/              October Workshop:   Oct. 11-13, 1995              _/
_/              November Workshop:  Nov. 8-10, 1995               _/
_/								  _/
_/ Instructors: Lecture Section - Prof. Warren J. Hehre		  _/
_/              Lab Section     - Dr. Wayne Huang		  _/
_/								  _/
_/ Location:    Wavefunction, Inc. Irvine, California, USA	  _/
_/								  _/
_/ Textbooks:   o "Short Course in Modern Electronic Structure    _/
_/                 Theory", Warren Hehre, 1995.                   _/
_/              o "Chemistry with Computation", Warren Hehre and  _/
_/		   Wayne Huang, 1995.				  _/
_/		o "Experiments in Computational Organic Chemistry"_/
_/		   Lonnie Burke, Alan Shusterman, William Pietro  _/
_/		   Warren Hehre, 1993.				  _/
_/		o "Practical Strategies for Electronic Structure  _/
_/		   Calculations", Warren Hehre, 1995.		  _/
_/		o "CD-ROM: Visualization of Chemical Structures   _/
_/		   Reactions", Thomas Hehre, Lonnie Burke,        _/
_/		   Wayne Huang & Warren Hehre, 1995.		  _/
_/		   						  _/
_/ Fee:         $1000 (50% off for academics, $500), which        _/
_/		includes course registration, four computational  _/
_/		textbooks and animated CD-ROM, all breakfasts and _/
_/		lunches.  			                  _/
_/								  _/
_/ Information: Workshop Web Page:http://wavefun.com/workshop.html_/
_/		or contact Wayne Huang for further information    _/
_/		including detailed brochure and course curriculum._/
_/              Tel: (714)955-2120 Fax: (714)955-2118	          _/
_/              E-mail: workshop@wavefun.com		          _/
_/							          _/
_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/

This workshop is also available on site upon request, although the
format could be varied. Please contact us for more information. We
have been providing these monthly workshops in house and on-site
around the world for the past three years. Special thanks to
participants and people who have helped to organize and support
the workshops in the past.

"What I hear I forget; What I see I remember; What I do I know."

						-- Chinese Proverb


-- 

+---------------------------------------------------------------------+
|  Wayne Huang, Ph.D.    |  /--- ----\  /---/ ---\ ----- /---/ /|   / |
|  Computational Chemist |  \    /   / /   / /   /  /   /   / / |  /  |
|  Wavefunction, Inc.    |   \  /---/ /---/ /---/  /   /---/ /  | /   |
|  huang@wavefun.com     |---/ /     /   / /   \  /   /   / /   |/    |
+---------------------------------------------------------------------+
| Wavefunction, Inc., 18401 Von Karman, Suite 370,  Irvine,  Ca 92715 |
| Telephone: (714)955-2120     Fax: (714)955-2118  http://wavefun.com |
+---------------------------------------------------------------------+



From owner-chemistry@ccl.net  Mon Jul 24 15:24:25 1995
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Date: Mon, 24 Jul 1995 15:13:54 -0400
From: "E. Lewars" <elewars@alchemy.chem.utoronto.ca>
Message-Id: <199507241913.PAA09201@alchemy.chem.utoronto.ca>
To: chemistry@ccl.net
Subject: PROGRAMS FOR PC AND MAC


The subject of modelling programs for personal computers was considered
on the Net a few months ago; to learn how to check the archives try
	MAILSERV@ccl.net   and send a message:   help search

========

From owner-chemistry@ccl.net  Mon Jul 24 15:28:02 1995
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Date: Mon, 24 Jul 95 12:21:57 PDT
From: Masayuki Yuki <masayuki@hsc.usc.edu>
To: chemistry@ccl.net
Subject: ftp Out from HP Workstation
Message-ID: <CMM.0.90.2.806613717.masayuki@hsc.usc.edu>


Dear Netters:

I was trying to ftp a ca. 10 MB coordinate file generated by AMBER 4.0 from
the HP 9000/712 workstation with HP-UX 9.05 to SGI Indigo Elan, and it does
not work.  We can transfer a coordinate file from SGI to HP.  There seems to
be a major problem which prevent me from ftping a large file out of the HP
workstation.  

I am suspecting that there could be a bug in the ftp protocol in HP-UX
9.05.  

I would appreciate it if anyone can help me out of this
problem.  A software patch available through Internet might work.  
Thank you very much in advance.

Sincerely,



Masayuki Yuki
email:  masayuki@hsc.usc.edu
Dept. of Pharmaceutical Sciences
School of Pharmacy 
University of Southern California



From owner-chemistry@ccl.net  Mon Jul 24 15:39:29 1995
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 chemistry@ccl.net; Mon, 24 Jul 1995 14:24:30 -0500 (CDT)
Date: Mon, 24 Jul 1995 14:14:58 -0500
Subject: ISIS Draw FTP site
To: in@"chemistry@ccl.net"
Reply-to: macmillan@uni.edu
Message-id: <01HT92ENV83A8X0CXQ@uni.edu>
MIME-version: 1.0
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CCL;

A while back I saw a refernce to an FTP site for ISIS Draw.  I did not save the 
address and now I suddenly need it.  Can someone please send me the address to 

    macmillan@uni.edu

Thankyou in advance.

Jim Macmillan
Department of Chemistry
University of Northern Iowa

From owner-chemistry@ccl.net  Mon Jul 24 15:42:23 1995
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Date: Mon, 24 Jul 1995 14:24:40 -0600
To: chemistry@ccl.net
From: patterson@chem.wisc.edu (Eric V. Patterson)
Subject: SUMMARY:  G94 warning against LANL1DZ


        A short time ago, I posted a question about the warning in the G94
manual against using the LANL1DZ basis set.  I received several helpful
responses.  The responders all pretty much said the same thing.  The short
answer is:

        LANL1DZ only treats the valence shell electrons specifically. 
LANL2DZ also treats the (n-1)s and (n-1)p electrons specifically.  So,
LANL2DZ has a smaller ECP than LANL1DZ, and is more flexible ("better",
"reliable").  The note in the G94 manual has been included at the request
Jeff Hay.  References to check would be:  P. J. Hay and W. R. Wadt, J.
Chem. Phys. 82, 1985, p. 270, and the next two articles following that one.

        My thanks to all those who helped clear this up for me:
                Ole Swang               oles@kjemi.uio.no
                Andreas Ehlers          ehlers@iodine.chem.vu.nl
                Mike Frisch             frisch@lorentzian.com
                Jason Perry             jkp@anny.psgvb.com
                H. Tang                 tang@kitten.chem.uh.edu


                

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

From the desk of:
Eric Patterson                               voice:  (608) 262-0599
Department of Chemistry                      FAX:    (608) 262-0381
University of Wisconsin - Madison            email:  patterson@chem.wisc.edu
1101 University Ave.
Madison, WI  53706

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


From owner-chemistry@ccl.net  Mon Jul 24 16:09:22 1995
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From: TOPPER ROBERT <topper@cooper.edu>
Message-Id: <199507241455.AA05452@zeus.cooper.edu>
Subject: mass spec prediction: summary
To: CHEMISTRY@ccl.net, topper@cooper.edu
Date: Mon, 24 Jul 1995 10:55:50 -0400 (EDT)
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Hi all, here is a summary of responses I got from my inquiry 
about software to help interpret mass spectra. A summary
is given below. Many thanks to those who wrote in with
suggestions!

In the end, we contacted Trinity Software, who gave us
an upgrade from MassSpec 1.0 to MassSpec EXT 3.0.1 for the
Macintosh at a very reasonable price. It is a nice program,
it runs well under System 7.1 on a Quadra 660AV, 
and we are quite happy with it.
Note however that it lacks the ability to directly interface
with programs like ChemDraw and ChemIntosh, so that will probably
be a downside as far as some are concerned. However, it is easy
to draw structures and the mass-spec options are easily tunable
(C13 peaks can be suppressed, cleavage of rings can be suppressed,
etc.) 

Trinity Software can be contacted at 1-800-352-1282.

best wishes, robert

************************************************************************
 Prof. Robert Q. Topper                 email:   topper@cooper.edu
 Department of Chemistry                phone:   (212) 353-4378
 School of Engineering                  WWW:     watch this space, coming soon!
 The Cooper Union                       FAX:     (212) 353-4341 
 51 Astor Place                         subway:  take the 6 to Astor Place 
 New York, NY 10003 USA                          or the N/R to 8th St/NYU
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The original posting:

Hello all,
I'm writing on behalf of a colleague who does quite a bit
of mass spectroscopy. He would like to acquire a program
which, given a molecular formula, can "predict" the
mass spectrum. He'd prefer it if it ran on a Mac, but
we also have MS/DOS/Windows and UNIX machines available.

Does anyone have any recommendations?

We are aware of the existence of MassSpec 3.0 (Trinity Software)
for Macintosh, but would welcome any comments on the code's
usability, usefulness, etc.. we have a very old version
(1.0) of MassSpec, but it doesn't run under system 7 and it's
pretty clunky under system 6.

************************************************************************
Responses:

From Jim.Macmillan@uni.edu Wed Jul 12 18:43:40 1995

I bought ChemWindows at the ACS meeting last spring and at the time I got MS 
Palate.  It allows you to take a structure you have drawen with ChemWindows and 
see the fragments and masses as you bisect the molecule.  It is a simple 
package but useful, I think.  I don't do a lot of MS work but it seems to be 
useful.

Jim Macmillan
Department of Chemistry
University of Northern Iowa
macmillan@uni.edu

From MARTIN@cmda.abbott.com Wed Jul 12 18:44:41 1995

ChemIntosh does this I am told.

  @@@@@@@@@@@      Yvonne Martin, Senior Project Leader
             @     Computer Assisted Molecular Design Project
   @@@@@@@@  @     D-47E, AP10 2fl
  @          @     Abbott Laboratories
  @          @     100 Abbott Park Road
   @@@@@@@@@@      Abbott Park, IL 60064-3500
                   Phone: 708 937-5362 FAX: 708 937-2625
                   yvonne.martin@abbott.com

From cye@chem.QueensU.CA Wed Jul 12 19:41:59 1995

I haven't used it but MacSpec (Spire Software) is available 
through the American Chemican
Chemical Society, cat # 2325-4-154.
Good luck,
Ray Bowers.

From wallyr@netcom.netcom.com Wed Jul 12 20:05:17 1995

I don't do MS, but have heard about a couple of Mac (or Win) programs from
SoftShell that might do the trick.  They're at 970-242-7502.

Wally
========================================================================
Walter E. Reiher III, Ph.D.                            WallyR@netcom.com
Consultant in Computational Chemistry
P.O. Box 61056                                        voice 408-720-0240
Sunnyvale, CA 94088                                     fax 408-720-0378


From owner-chemistry@ccl.net  Mon Jul 24 16:24:36 1995
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Date: 	Mon, 24 Jul 1995 14:17:46 -0700
From: "Mark Hanning-Lee" <mark_hanning-lee@qmail2.aero.org>
Subject: URL for IsisDraw
To: "Compchem List" <chemistry@ccl.net>
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I have downloaded IsisDraw by accessing the following URL:

http://www.mdli.com

Mark

Mark A. Hanning-Lee		|  Tel:  (310) 336 2835
The Aerospace Corporation	|  FAX:  (310) 336 7680
PO Box 92957, M5-754		|
Los Angeles CA 90009, USA	|  Email: mark_hanning-lee@qmail2.aero.org



From owner-chemistry@ccl.net  Mon Jul 24 16:26:34 1995
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From owner-chemistry@ccl.net  Mon Jul 24 17:24:28 1995
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From: Pedro A M Vazquez <vazquez@iqm.unicamp.br>
Message-Id: <199507242058.RAA24195@kalypso.iqm.unicamp.br>
Subject: Re: CCL:ISIS Draw FTP site
To: chemistry@ccl.net
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Hello:
	Please try

http://www.ch.ic.ac.uk:80/mdl/isis
ftp://ftp.demon.co.uk/pub/ibmpc/windows/isis
http://www-dsed.llnl.gov/files/programs/PC

Pedro

Jim.Macmillan@uni.edu said:
> CCL;
> 
>A while back I saw a refernce to an FTP site for ISIS Draw. I did not save the 
>address and now I suddenly need it.  Can someone please send me the address to 
> 
>     macmillan@uni.edu
> 
> Thankyou in advance.
> 
> Jim Macmillan
> Department of Chemistry
> University of Northern Iowa

From owner-chemistry@ccl.net  Mon Jul 24 21:39:32 1995
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From: "Angelica Garcia Zacarias" <zacarias@PAPALOTL.PQUIM.UNAM.MX>
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Date: Mon, 24 Jul 1995 19:32:37 -0600
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Dear CCL's:

Does someone there have information on
experimental data of Pd2, Pd3, Pd4 clusters?

I have been looking extensively, but I only
found for Pd2
  S. S. Lin, B. Strauss and A. Kant, J. Chem.
   Phys. 51, 2282 (1969)

Thanks in advance.

Angelica Zacarias

-- 
_________________________________________________
Claudia Angelica Garcia Zacarias
Quimica Inorganica. Fisica y Quimica Teorica
DEPg., Facultad de Quimica, UNAM
Mexico, D.F. 04510
Tel/Fax: (525) 622 3724; Tel: (525) 622 3776
e-mail: zacarias@papalotl.pquim.unam.mx
        zac@servidor.unam.mx
_________________________________________________
Solo con nuestras flores nos alegramos
Solo con nuestros cantos florece nuestra tristeza
                            Nezahualcoyotl
_________________________________________________


From owner-chemistry@ccl.net  Mon Jul 24 22:09:27 1995
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From: "Angelica Garcia Zacarias" <zacarias@PAPALOTL.PQUIM.UNAM.MX>
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Date: Mon, 24 Jul 1995 19:51:44 -0600
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Subject: Pdn clusters information
Content-Type: text/plain; charset=us-ascii
Mime-Version: 1.0


Dear CCL's:

Does someone there have information on
experimental data of Pd2, Pd3, Pd4 clusters?

I have been looking extensively, but I only
found for Pd2
   S. S. Lin, B. Strauss and A. Kant, J. Chem.
    Phys. 51, 2282 (1969)

Thanks in advance.

Angelica Zacarias

-- 
_________________________________________________
Claudia Angelica Garcia Zacarias
Quimica Inorganica. Fisica y Quimica Teorica
DEPg., Facultad de Quimica, UNAM
Mexico, D.F. 04510
Tel/Fax: (525) 622 3724; Tel: (525) 622 3776
e-mail: zacarias@papalotl.pquim.unam.mx
        zac@servidor.unam.mx
_________________________________________________
Solo con nuestras flores nos alegramos
Solo con nuestros cantos florece nuestra tristeza
                            Nezahualcoyotl
_________________________________________________


