From sanja@indigo.irb.hr  Fri Jun  2 03:30:33 1995
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From: "sanja" <sanja@indigo.irb.hr>
Message-Id: <9506020931.ZM28577@indigo.irb.hr>
Date: Fri, 2 Jun 1995 09:31:03 -0700
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To: CHEMISTRY@ccl.net
Subject: smiles converter
Mime-Version: 1.0
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Hi, netters,

Does anyone know if there is a program available which converts smiles notation
in the picture format or any other format conventionally used in computational
chemistry, e.g. Z-matrix, cartesian coordinates, etc.

                             Zeljka Medven
                             Rugjer Boskovic Institute
                             Zagreb, Croatia
                             e-mail:medven@olimp.irb.hr

-- 
*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*
Sanja Sekusak                         e-mail: sanja@indigo.irb.hr
Rudjer Boskovic Institute             phone: (385-1) 46 10 89
HR-41001 Zagreb, CROATIA              fax: (385-1) 27 26 48           
*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*

From bouyer@ext.jussieu.fr  Fri Jun  2 03:33:54 1995
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Date: Fri, 2 Jun 1995 09:26:24 +0100
To: chemistry@ccl.net
From: bouyer@ext.jussieu.fr (Frederic BOUYER)
Subject: Thermochemistry and Point Group
Cc: hyperchem@hyper.com


Hello Netters,

Is anyone aware of thermochemistry based on structural and vibrational HF
or DFT calculations to determine thermochemical functions?

My problem is the following :

I have two molecules (of the same stoechiometry) of which structural and
energetic differences are very (around 5 10-5 Ha, DMol BLYP functional)
very small. Only the point group is different, one is C3v, the other Cs.

The rotational contribution on thermochemical functions is not the same,
because of the symmetry number (3 or 1, depending on the point group) and
the consequence is drastic on the free enthalpy of formation ! (about 12
kJ/mol, and around 3 for the order of magnitude on the reaction constant at
1300K) I don't know how to decide which symmetry I am to take into account
(5 10-5 Ha is too small) (-by vibrational calculations only ? If I can get
frequencies at this level of accuracy-). I have verified these
thermo-quantities with a simple run with Gamess, and I have the same
difference (12 kJ/mol) on the free enthalpie of reaction (with the same
structures).

Why is there a so big difference between these thermo-quantities for these
two symmetries? I expected that thermochemical functions would be
continuous vs. the structure.

Any comments, suggestions ?

Frederic Bouyer
Lab.Electrochimie-ENSCP-Paris-France
bouyer@ext.jussieu.fr
http://alcyone.enscp.jussieu.fr/
http://alcyone.enscp.jussieu.fr/Pages/LECA/GP/FB/



From mw@crystal.uwa.edu.au  Fri Jun  2 04:00:31 1995
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From: mw@crystal.uwa.edu.au (Magda Wajrak)
Message-Id: <9506020746.AA23444@pack.crystal.uwa.edu.au>
Subject: Singlet-Triplet Splittings?
To: CHEMISTRY@ccl.net
Date: Fri, 2 Jun 95 15:46:43 "WST
Mailer: Elm [revision: 70.85]


Dear Netters,

I would like to ask for some help in locating some articles or books
which give singlet-triplet energy splittings of some
simple sulfur and/or nitrogen containing compounds. I 
especially need experimental results, but theoretical
results would also be helpfull.

Thank you very much.

Magdalena Wajrak

(email:  mw@crystal.uwa.edu.au)

From tamasgunda@tigris.klte.hu  Fri Jun  2 04:07:14 1995
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Date: Fri, 2 Jun 1995 09:48:38 +1
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Subject: Re: CCL:Plotting Programs
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> > 	I am looking for a programs that will take 3D coordinates and 
> > plot them.  The input file is an ASCII text of a series of numbers.  Does 
> > anyone know of a good program and where I could find it?
> > 	Thanks,
> 
> If your data is molecular then a good program would be SCHAKAL from 
> Egbert Keller (kell@ruf.uni-freiburg.de).  It is very good at plotting 
> molecules using various ball-and-stick and space filling models.

If you need file format conversion prior to using SCHAKAL, you may 
need the conversion program MOL2MOL, available from

Cherwell Scientific Publishing  
The Magdalen Centre, Oxford Science Park
Oxford OX4 4GA, UK
Fax +44 (0)1865 784801
e-mail: csp@sable.ox.ac.uk

The program is capable of interconverting about 24 file formats, 
plus some utilities are also included.




*****************************************************************************
   Tamas E. Gunda, Ph.D.               phone: (+36-52) 316666 ext 2479
   Research Group of Antibiotics       fax  : (+36-52) 310936
   L. Kossuth University               e-mail: tamasgunda@tigris.klte.hu
   POBox 36                                   
   H-4010 Debrecen
   Hungary
*****************************************************************************

From hermann@handel.RZ-Berlin.MPG.DE  Fri Jun  2 05:30:36 1995
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From: hermann@handel.RZ-Berlin.MPG.DE (Klaus Hermann )
Message-Id: <9506020923.AA17900@handel.RZ-Berlin.MPG.DE>
Subject: Plotting Programs
To: chemistry@ccl.net
Date: Fri, 2 Jun 1995 11:23:42 +0200 (MSZ)
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To throw in another product:

BALSAC (Build and Analyze Lattices, Surfaces, and Clusters) is widely used
by surface scientists and crystallographers to visualize general atom 
positions and geometries in crystals and molecules. It is in its interactive 
features more modern and flexible than Schakal advertized previously.

BALSAC was developed at the Fritz-Haber-Institute, Berlin and comes in both
DOS(VGA) and Inix(X.11) versions. For more information consult 
Mrs. M. Pasecky, Garching Innovation GmbH, 
Koeniginstr. 19, D-80539 Muenchen, Germany
Tel. [+49] 89 288279, Fax. [+49] 89 21081593

===========================================================================
 Prof.Dr. K. Hermann                    Tel.: [+49]-30-8413-4812/3 (office)
 Abt. Theorie, Fritz-Haber-Institut           [+49]-30-8413-4702   (secrt.)
 Faradayweg 4-6                         Fax.: [+49]-30-8413-4701        
 D-14195 Berlin   
 Germany 

 e-mail:   hermann@FHI-Berlin.MPG.DE
    WWW:   http://www.fhi-berlin.mpg.de/th/member/hermann_k.html
===========================================================================

From SANTOS@VM1.UMH.AC.BE  Fri Jun  2 06:30:33 1995
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From: "D.A. dos Santos" <SANTOS@VM1.UMH.AC.BE>
Subject: PC M.O. plotting programs
To: chemistry@ccl.net
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Dear netters,
 
 
     I am looking for PC (windows) programs to plot the LCAO coefficients of
selected molecular orbitals; something simple which provides ball and stick (or
wire and frame) representation of a given molecule and in adition the values of
MO LCAO coefficients or their graphical representation would be perfect (even
more if it is public domain :-) ). Any suggestions?
      Thanks a lot in advance for your help,
 
 
 
 
+------------------------------------------+--------------------------------+
| Dr. Donizetti A. dos Santos              !                                |
| Service de Chimie des Materiaux Nouveaux ! e-mail: santos at vm1.umh.ac.be|
| et                                       !                                |
| Centre de Recherche en Electronique et   !                                |
| Photonique Moleculaires                  !    fax: +32 65 37 3366         |
| Universite Mons-Hainaut                  !         +32 65 37 3054         |
| 20, Place du Parc                        !                                |
| B7000 MONS, BELGIUM                      !    TEL: +32 65 37 3361         |
+------------------------------------------+--------------------------------+

From fdeprof@is1.vub.ac.be  Fri Jun  2 09:15:35 1995
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To: chemistry@ccl.net
From: fdeprof@is1.vub.ac.be
Subject: Book series info


Dear all,

On this list,  I frequently encounter references to the series "Reviews in
Computational Chemistry", edited by Boyd.  Can anyone give me some
information about this book series.

Sincerely

F. De Proft



From pis_diez@nahuel.biol.unlp.edu.ar  Fri Jun  2 10:30:41 1995
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To: chemistry@ccl.net
From: pis_diez@nahuel.biol.unlp.edu.ar (Reinaldo Pis Diez)
Subject: Program to analyze G92 vibrational outputs


        Dear netters

                I'm looking for a program to read and convert cartesians to
internal coordinates from G92 vibrational force constants outputs. I know
REDONG program from QCPE (#628) but I'm interested in something newer (if any).

                Please don't reply this mail. Send your replies to 

                                        varetti@biol.unlp.edu.ar 

                Thanks in advance.

                                                                            
            Dr. E.L. Varetti


From boyd@chem.iupui.edu  Fri Jun  2 15:25:43 1995
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Date: Fri, 02 Jun 1995 14:16:19 -0500
From: Boyd <boyd@chem.iupui.edu>
Subject: Reviews in Computational Chemistry
To: OSC CCL <chemistry@ccl.net>
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CCLers:
Dr. De Proft's question about "Reviews in Computational Chemistry" is
especially timely because Volume 6 just rolled off the presses.  I will try to
answer.  This new volume examines quantum chemistry of solvated molecules,
molecular mechanics of inorganics and organometallics, modeling of polymers,
technology of massively parallel computing, and comparative productivity of
molecular modeling software.  In the summary that follows, I explain the
mission of the series, and I list the table of contents of each volume
published to date.
Don
Donald B. Boyd, Ph.D.
Co-editor, REVIEWS IN COMPUTATIONAL CHEMISTRY
Department of Chemistry
Indiana University-Purdue University at Indianapolis
Indianapolis, Indiana 46202-3274 U.S.A.
Internet boyd@chem.iupui.edu
World Wide Web URL http://chem.iupui.edu/

Original posting-
>Dear all,
>On this list,  I frequently encounter references to the series "Reviews in
>Computational Chemistry", edited by Boyd.  Can anyone give me some
>information about this book series.
>Sincerely
>F. De Proft

Summary (this message is 3-typed pages long)-
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
REVIEWS IN COMPUTATIONAL CHEMISTRY

Kenny B. Lipkowitz & Donald B. Boyd, Editors

"Reviews in Computational Chemistry" brings together respected experts in the
field of computer-aided molecular research.  The book series has become a
standard reference source.  Unlike most review series, "Reviews in
Computational Chemistry" considers teaching the methodologies to newcomers an
important part of its mission.  Most chapters have both introductory and
advanced material.  Chapters written as tutorials make the volumes valuable
adjuncts to textbooks in more traditional disciplines.  At the same time, the
advanced material in each volume will be of interest to practicing
computational chemists.

Contained in each volume is the popular Compendium of Software for Molecular
Modeling, which has information on hundreds of programs, services, suppliers,
and other helpful information.

Authors of Volume 1 (1990):

David Feller and Ernest R. Davidson,  Basis Sets for Ab Initio Molecular
Orbital 	Calculations and Intermolecular Interactions.
James J. P. Stewart,  Semiempirical Molecular Orbital Methods.
Clifford E. Dykstra, Joseph D. Augspurger, Bernard Kirtman, and David J. Malik,
 	Properties of Molecules by Direct Calculation.
Ernest L. Plummer,  The Application of Quantitative Design Strategies in
Pesticide 	Design.
Peter C. Jurs,  Chemometrics and Multivariate Analysis in Analytical Chemistry.
Yvonne C. Martin, Mark G. Bures, and Peter Willett,  Searching Databases of
Three-	Dimensional Structures.
Paul G. Mezey,  Molecular Surfaces.
Terry P. Lybrand,  Computer Simulation of Biomolecular Systems Using Molecular 
Dynamics and Free Energy Perturbation Methods.
Donald B. Boyd,  Aspects of Molecular Modeling.
Donald B. Boyd,  Successes of Computer-Assisted Molecular Design.
Ernest R. Davidson,  Perspectives on Ab Initio Calculations.

Authors of Volume 2 (1991):

Andrew R. Leach,  A Survey of Methods for Searching the Conformational Space 
of Small and Medium-Sized Molecules.
John M. Troyer and Fred E. Cohen,  Simplified Models for Understanding and 
Predicting Protein Structure.
J. Phillip Bowen and Norman L. Allinger,  Molecular Mechanics: The Art and 
Science of Parameterization.
Uri Dinur and Arnold T. Hagler,  New Approaches to Empirical Force Fields.
Steve Scheiner,  Calculating the Properties of Hydrogen Bonds by Ab Initio 
Methods.
Donald E. Williams,  Net Atomic Charge and Multipole Models for the Ab Initio 
Molecular Electric Potential.
Peter Politzer and Jane S. Murray,  Molecular Electrostatic Potentials and
Chemical 	Reactivity.
Michael C. Zerner,  Semiempirical Molecular Orbital Methods.
Lowell H. Hall and Lemont B. Kier,  The Molecular Connectivity Chi Indexes and 
Kappa Shape Indexes in Structure-Property Modeling.
I. B. Bersuker and A. S. Dimoglo,  The Electron-Topological Approach to the
QSAR 	Problem.
Donald B. Boyd,  The Computational Chemistry Literature.

Authors of Volume 3 (1992):

Tamar Schlick,  Optimization Methods in Computational Chemistry.
Harold A. Scheraga,  Predicting Three-Dimensional Structures of Oligopeptides.
Andrew E. Torda and Wilfred F. van Gunsteren,  Molecular Modeling Using NMR 
Data.
David F. V. Lewis,  Computer-Assisted Methods in the Evaluation of Chemical 
Toxicity.

Authors of Volume 4 (1993):

Jerzy Cioslowski,  Ab Initio Calculations on Large Molecules: Methodology and 
Applications.
Michael L. McKee and Michael Page,  Computing Reaction Pathways on Molecular 
Potential Energy Surfaces.
Robert M. Whitnell and Kent R. Wilson,  Computational Molecular Dynamics of 
Chemical Reactions in Solution.
Roger L. DeKock, Jeffry D. Madura, Frank Rioux, and Joseph Casanova,  
Computational Chemistry in the Undergraduate Curriculum.

Authors of Volume 5 (1994):

John D. Bolcer and Robert B. Hermann,  The Development of Computational 
Chemistry in the United States.
Rodney J. Bartlett and John F. Stanton,  Applications of Post-Hartree-Fock 
Methods: A Tutorial.
Steven M. Bachrach,  Population Analysis and Electron Densities from Quantum 
Mechanics.
Jeffry D. Madura, Malcolm E. Davis, Michael K. Gilson, Rebecca C. Wade, Brock
A. 	Luty, and J. Andrew McCammon,  Biological Applications of Electrostatic 
Calculations and Brownian Dynamics Simulations.
K. V. Damodaran and Kenneth M. Merz Jr.,  Computer Simulation of Lipid Systems.
Jeffrey M. Blaney and J. Scott Dixon,  Distance Geometry in Molecular Modeling.
Lisa M. Balbes, S. Wayne Mascarella, and Donald B. Boyd,  A Perspective of
Modern 	Methods in Computer-Aided Drug Design.

Authors of Volume 6 (1995):

Christopher J. Cramer and Donald G. Truhlar,  Continuum Solvation Models: 
Classical and Quantum Mechanical Implementations.
Clark R. Landis, Daniel M. Root, and Thomas Cleveland,  Molecular Mechanics 
Force Fields for Modeling Inorganic and Organometallic Compounds.
Vassilios Galiatsatos,  Computational Methods for Modeling Polymers: An 
Introduction.
Rick A. Kendall, Robert J. Harrison, Rik J. Littlefield, and Martyn F. Guest, 
High 	Performance Computing in Computational Chemistry: Methods and 	Machines.
Donald B. Boyd,  Molecular Modeling Software in Use:  Publication Trends.
Eiji Osawa and Kenny B. Lipkowitz,  Appendix 1:  Published Force Field
Parameters.
Donald B. Boyd,  Appendix 2:  Compendium of Software for Molecular Modeling.

Ordering information-
Single copies may be purchased, of course.  In addition, individuals and
libraries can save money by placing a standing order for the whole series.  The
prices below are for single copy/standing order.  Volumes 7, 8, 9, and 10 are
in the works, each offering new and unique chapters.

"Reviews In Computational Chemistry", K. B. Lipkowitz and D. B. Boyd, Editors
Volume 1 (xix + 419 pp)  ISBN 0-89573-754-X,  $115/$95
Volume 2 (xvi + 527 pp)  ISBN 1-56081-515-9,  $125/$100
Volume 3 (xvi + 271 pp)  ISBN 1-56081-619-8,  $75/$60
Volume 4 (xix + 280 pp)  ISBN 1-56081-620-1,  $79/$65
Volume 5 (xxi + 458 pp)  ISBN 1-56081-658-9,  $110/$90
Volume 6 (xvii + 480 pp) ISBN 1-56081-667-8,  $110/$90

U.S.A. source-
VCH Publishers, 303 Northwest 12th Avenue, Deerfield Beach, FL 33442-1788.
Toll-free tel. (within US & Canada):  800-367-8249
Toll-free fax (within US & Canada):  800-367-8247
Tel.:  305-428-5566,  fax:  305-428-8201.
Europe source-
VCH Verlagsgesellschaft mbH, P.O. Box 10-11-61, 69451 Weinheim, Germany.
Tel.:  49-6201-6060,  fax:  49-6201-606328.

>From reviews of the series-
     "The book transfers a working knowledge of existing computational methods
and programs to an interested reader and potential user."  (Structural
Chemistry).
     "It can be recommended for everyone who wants to learn about the present
state of development in computational chemistry."  Angewandte Chemie
International Edition in English). 
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

From rtindall@pinegov.co.pinellas.fl.us  Fri Jun  2 15:31:47 1995
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Date: Fri, 2 Jun 1995 20:21:00 +0100 (EDT)
From: Reta Tindall <rtindall@pinegov.co.pinellas.fl.us>
To: chemistry@ccl.net
Subject: molar enthalpy change for adsorption
Message-Id: <Pine.SUN.3.91.950602201203.9731A-100000@pinegov>
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII
content-length: 0


My name is Reta Newman and I am a forensic chemist in Largo, Florida.  I 
am currently working on a research project studying the adsorption of 
accelerants on activated charcoal.  In a literature search, I found and 
equation which relates the time a molecule remains on an adsorption 
site to the temperature of the system .  The equation includes a 
value (Q) which is the molar enthalpy 
change for adsorption.  How is this value determined: does it have to be 
determined experimentally or is their a table of values which would make 
my study (and my life) much easier? 

From jfptak@access.digex.net  Fri Jun  2 16:25:44 1995
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Date: Fri, 2 Jun 1995 16:14:18 -0400 (EDT)
From: John Ptak <jfptak@access.digex.net>
To: chemistry@ccl.net
Subject: discovery of ET oxygen?
Message-ID: <Pine.SUN.3.91.950602160623.19530A-100000@access4.digex.net>
MIME-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII


Just a question here about the first confirmation of extra-terrestrial 
oxygen... Henry Draper (who was the first to 
photograph the spectrum of a star other than the sun) photographed the 
dark lines of oxygen in the sun in 1877 and seems to be the first to have 
done so.  
Before I start to research this I was just wondering if someone knew 
this fact off-hand.   
Thanks from a non-chemist.
Oh yes--I'm also posting this to an astrophys list.
John Ptak                 The Science Bookstore  - Alexandria, VA USA
jfptak@access.digex.net   Rare and Out-of-Print Science Texts (703)683-6837


