From hebant@ext.jussieu.fr  Mon Feb 12 04:42:37 1996
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Date: Mon, 12 Feb 1996 10:35:25 +0100
To: CHEMISTRY@www.ccl.net
From: hebant@ext.jussieu.fr (Pascal HEBANT)
Subject: Iglo basis summary


Some days ago, I posted a question about IGLO basis. Here are the answers I
got:

* Kutzelnigg et al, in: NMR, Basic Principles and Progress,
Vol. 23, Springer-Verlag, 1990, page 165

* Kutzelnigg et al, in: Nuclear Magnetic Shielding and Molecular Structure,
J.A.Tossell, Ed., NATO ASI C386, Kluwer Academic Publishers 1993, page 141

These references are of the IGLO basis people.

See also :
* J. Am. Chem. Soc. 1994, 116, 5298 and the cited references from
24-28

Thanks to all that have reply to me



From owner-chemistry@ccl.net  Mon Feb 12 05:12:39 1996
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                      Subject:                              Time:  2:59 AM
  OFFICE MEMO         SHELX File Format                     Date:  2/12/96

Is the file format description for SHELX on the Internet?  If you know where
this is documented, please send e-mail to craigs@softshell.com.


From hebant@ext.jussieu.fr  Mon Feb 12 07:57:40 1996
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Date: Mon, 12 Feb 1996 13:51:12 +0100
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From: hebant@ext.jussieu.fr (Pascal HEBANT)
Subject:  IGLO basis **ERRATUM**


There is a mistake in the summary I sent today...

>I would like to correct an erratum in your reference to our paper:
>
>> See also :
>> * J. Am. Chem. Soc. 1994, 116, 5298 and the cited references from
>                                  $
>The correct page number is 5898.
>Also, the only refernce 24 in our paper refers to Bochum's group
>basis sets (IGLO-II and IGLO-II).
>Last time (see Paul von Schleyer's papers for example) people refer to
>these basis sets as to "BII" and "BIII".
>In general , the reference wich your already included in your list:
>
>> * Kutzelnigg et al, in: NMR, Basic Principles and Progress,
>> Vol. 23, Springer-Verlag, 1990, page 165
>
>surely is the best one.
>With the best wishes,
>
>Vladimir Malkin
>
> ***************************************************************
> *   Dr. Vladimir G. Malkin                                    *
> *   Senior Research Scientist                                 *
> *   Institute of Inorganic Chemistry                          *
> *   Slovak Academy of Sciences                                *
> *   Dubravska cesta 9                malkin@savba.sk          *
> *   SK-84236 Bratislava              Fax    (42-7) 373-541    *
> *   Slovakia                         Phone  (42-7) 378-2923   *
> ***************************************************************
>


*****************************************************************************

Pascal HEBANT

Laboratoire d'Electrochimie et de Chimie Analytique
Ecole Nationale Superieure de Chimie de Paris
11 rue Pierre et Marie Curie
75005 Paris FRANCE

tel: 33 (1) 44 27 66 94                             fax: 33 (1) 44 27 67 50

http://alcyone.enscp.jussieu.fr/Pages/LECA/Electrochimie.html
*****************************************************************************





From jaouad@goliat.ugr.es  Mon Feb 12 08:57:41 1996
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Date: Mon, 12 Feb 1996 14:55:44 +0000 (WET)
From: Jauoad El Bahraoui <jaouad@goliat.ugr.es>
To: chemistry@www.ccl.net
Subject: logP
Message-ID: <Pine.SUN.3.91.960212145207.13884K-100000@goliat>
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Please tell me about programs does permit the calculation of the 
partition coefficients octanol-water (logP) ?
regards.

From sunger@a.crl.com  Mon Feb 12 11:42:44 1996
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To: Jauoad El Bahraoui <jaouad@goliat.ugr.es>
From: sunger@a.crl.com (Stefan Unger)
Subject: Re: CCL:logP
Cc: chemistry@www.ccl.net


Several programs are described in The Store in The Marketplace at the web site
www.bio.com
At the moment, you will need Netscape to enter the store.  I hope this
information helps.


>Please tell me about programs does permit the calculation of the
>partition coefficients octanol-water (logP) ?
>regards.
>
>-------This is added Automatically by the Software--------
>-- Original Sender Envelope Address: jaouad@goliat.ugr.es
>-- Original Sender From: Address: jaouad@goliat.ugr.es
>CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator
>MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73
>Anon. ftp: www.ccl.net   | CHEMISTRY-SEARCH@www.ccl.net -- archive search
>             Web: http://www.ccl.net/chemistry.html

@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@@#@@#@@#@@#@@#@@#@@#@@#
Stefan Unger, Ph.D.
President
BioSoftware Marketing
4151 Middlefield Rd., Ste 109
Palo Alto, CA 94303-4743
sunger@a.crl.com

BioSoftware Marketing specializes in a full range of marketing services
(market studies to collateral design and production) for start-up and small
technical software companies, especially biopharm related.  E-mail your
full mailing address to receive a full-color brochure describing these
services.  We also offer consulting on computer aided drug design and
biological/chemical databases.

Product Manager, Scientific Software, Bio Online Store (www.bio.com)
@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@@#@@#@@#@@#@@#@@#@@#



From rochus@felix.anorg.chemie.tu-muenchen.de  Mon Feb 12 12:27:45 1996
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From: "Rochus Schmid" <rochus@felix.anorg.chemie.tu-muenchen.de>
Message-Id: <9602121813.ZM18904@felix>
Date: Mon, 12 Feb 1996 18:13:16 +0100
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Dear netters,

I have a question concerning TS-search and confirmation of it by a vibrational
analysis:

I've located a TS (DGauss 3.0, LDA-level, DZVP Basis) by EF with the
convergence criterion of the max. component of the (cartesian) gradient vector
to be less than 0.0008 au (which is the default in Dgauss as suggested by
Andzelm for the DZVP-level).

The mass weigthed Hessian matrix (2nd derivs. calculated analytically) shows
three imag. frequencies. One is large (700 1/cm) and the other two are small
(less than 50 1/cm). These two and four other small, but real frequencies
should represent the six degrees of rotation and translation which are not zero
since I'm not exactly at the stationary point. Correct?

After projecting out these six degrees of freedom only one neg. frequency
remains (about 700 1/cm).

Can I trust in that?
Or is it necessery to tighten the convergence criterion?
What is your experience?

Every comment or advise is highly appreciated. Thanx in advance.
(I will summarize.)

Greetings from Munich to all of you,

Rochus


-- 

********************************************************************************
Rochus Schmid
Technische Universitaet Muenchen	Tel. 	++49 89 3209 3140
Anorganisch Chemisches Institut 1	Fax. 	++49 89 3209 3473
Prof. W. A. Herrmann			E-mail:	
Lichtenbergstrasse 4			rochus@felix.anorg.chemie.tu-muenchen.de
85747 Garching
********************************************************************************

From owner-chemistry@ccl.net  Mon Feb 12 13:12:44 1996
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Date: Mon, 12 Feb 1996 13:05:47 -0500 (EST)
From: Sergei Tretiak <serg@markov.chem.rochester.edu>
To: chemistry@ccl.net
Subject: Summary: Fock and other hamiltonian matrices in G94
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Dear Netters,

Here is the summary of the messages I got in response to my previous
message about printing of hamiltonian matrices from G94.  
Many thanks to everybody who kindly replied my query.
		
		Sincerely,
				Sergei Tretiak

*********************** my first message *************************
 
How to print: 

1.Fock matrix F (Probably the easiest way is to use NBO 
block: $NBO keywords FAO, FNAO, .....) 

2.Core-Hamiltonian h(1). (Can be printed by using IOP(3/33=1-5) to print 
one and two electron integrals) 

3.An effective one-electron potential-the Hartree-Fock potential v(1).
Presumably F=h(1)+v(1).  


************************* summary of replies************************
 
1.  IOp33(5=3) (equivalently, IOp(5/33=3) turns on print during the
    SCF, including Fock matrices among other things.  It's a bit
    verbose since these are printed every iteration, so if your case
    is big, you might want to converge the SCF first and then do
    Guess=Read with the print turned on so you only get print for 1
    cycle.  

2.  IOp33(3=1) should get you the core hamiltonian.  

3.  V = F- H isn't printed as such but you can get it by
    subtraction.  If you want to read back the printed matrices,
    routine LTRead in util.a reads in a lower triangular matrix in the
    format in which Gaussian prints it.  
 
					Mike Frisch

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

1.  You can use the NBO pacakge to print these. Use POP=NBOREAD and then
supply the NBO keywords at the end of the input. 

2.  The one electron integrals are printed this way IOP(3/33=1) To get the
two electron integrals you need IOP(3/33=6) and ExtraLinks=L316. You
should also add NoRaff so that the integrals are not summed into
Raffenetti contractions. 

3.  I am not sure what you want here. The formulas for producing the Fock
matrix are well known if you have the integrals and the indices as
produced by the above but is that what you are trying to produce? 

  Douglas J. Fox
  Director of Technical Support
  help@gaussian.com

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


***********************my second message ************************* 
1.I want to print two electon matrices from G94. I use following input: 

# GEOM=CHECKPOINT GUESS=CHECKPOINT TEST HF DIRECT STO-3G 
#p POP=NBORead iop(3/33=6) ExtraLinks=L316 NoRaff
 
but I get an error message: 
 ...   *** Dumping Two-Electron integrals *** 
ISMode= 0 Mode=1 IBase= 1 IBasD= 1 262145 
 DBase= 0 DBasD= 0 0 IReset= 2 262139 
IntCnt= 0 ITotal= 0 NWIIB= 262144 ISym2E=1 
 Illegal range for read: IUnit= 10 Address= 0 Length= 131072 File length= 
 \ 0.  
 Error termination in NtrErr:  
 NtrErr called from NtrIO.  
Segmentation fault - core dumped 
 What is wrong?
  
2.Can I print all (1,2) integrals to FORTRAN readable files? 

************************* reply ************************

1. The problem is that DIRECT says not to write out the integrals, so
   there aren't any on the disk for L316 to print out.  In G94, just
   leave out DIRECT.  In G94, where Direct is the default, you need to
   say SCF=Conventional to tell it to write the integrals. 

2. There's no built-in way to write out the integrals to a fortran
   unformatted file, so you have three choices, all of which are   
   relatively easy:

   a.  Follow the example in the manual (which is similar to link 317)
       which shows how to make your own link which processes
   b.  Modify link 316 to write the integrals out unformatted as it
       prints them. 
   c.  Make link (or modify an existing link) which can run in-core,
       using a call to FoFDir to load the integrals in canonical order. 
       You can find a sample call in routine UHFOpn in link 502. 

			
				Mike Frisch



From huang@mazda.wavefun.com  Mon Feb 12 14:57:47 1996
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From: "Wayne Huang" <huang@mazda.wavefun.com>
Message-Id: <9602121142.ZM7750@mazda.wavefun.com>
Date: Mon, 12 Feb 1996 11:42:39 -0800
In-Reply-To: Jauoad El Bahraoui <jaouad@goliat.ugr.es>
        "CCL:logP" (Feb 12,  2:55pm)
References: <Pine.SUN.3.91.960212145207.13884K-100000@goliat>
Reply-To: huang@wavefun.com
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To: Jauoad El Bahraoui <jaouad@goliat.ugr.es>, chemistry@www.ccl.net
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On Feb 12,  2:55pm, Jauoad El Bahraoui wrote:
> Subject: CCL:logP
>
>
> Please tell me about programs does permit the calculation of the
> partition coefficients octanol-water (logP) ?


Spartan's QSAR module has the molecular descriptor which allows calculation
of a wide range of molecular properties such as Electronegativity, Hardness,
Estimated Polarizability, Molecular Volume/Area, Ovality, logP etc. There are
three methods available within the program to obtain logP: Ghost-Crippen,
Villar-AM1 and Dixon/Leonard/Hehre (in-house). Check Spartan Web Page
http://www.wavefun.com for further info.

--Wayne



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



From gerardo@houston.cray.com  Mon Feb 12 15:12:46 1996
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Message-Id: <199602122009.OAA16881@houston.cray.com>
Subject: Deadline Extension: 3rd UNAM-Cray Supercomputing Conference
To: CHEMISTRY@www.ccl.net
Date: Mon, 12 Feb 1996 14:09:08 -0600 (CST)
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A brief update:

  +---------------------------------------------------------------+
  |       ----THIRD UNAM-CRAY SUPERCOMPUTING CONFERENCE----       |
  |           -----------------------------------------           |
  |        C O M P U T A T I O N A L    C H E M I S T R Y         |
  |                                                               |
  |            A symposium to be held in Mexico City              |
  |           from August 13th through the 16th, 1996             |
  +---------------------------------------------------------------+

    THE ABSTRACT DEADLINE HAS BEEN EXTENDED TO MARCH 3, 1996.

    Besides details on invited speakers, topics, etc., there
    is a registration form available via the WWW at

    http://www.super.unam.mx/super/symposium/simposio96.html

I will be happy to e-mail the announcement and registration form to
those for whom WWW access is awkward or nonexistent, or who just want
a plain ASCII copy.

Saludos,

Gerardo
-- 
Dr. Gerardo Cisneros	|Cray Research de M'exico, S.A. de C.V.
Technical Services Mgr.	|Tuxpan 10-403, Col. Roma Sur
gerardo@cray.com	|06760 M'exico, D.F.
(+52+5)622-8584 	|MEXICO

From haney@netcom.com  Mon Feb 12 15:24:25 1996
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From: haney@netcom.com (Dr. David N. Haney)
Message-Id: <199602122008.MAA18053@netcom14.netcom.com>
Subject: Re: CCL:logP
To: jaouad@goliat.ugr.es (Jauoad El Bahraoui)
Date: Mon, 12 Feb 1996 12:08:09 -0800 (PST)
Cc: chemistry@www.ccl.net
In-Reply-To: <Pine.SUN.3.91.960212145207.13884K-100000@goliat> from "Jauoad El Bahraoui" at Feb 12, 96 02:55:44 pm
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jaouad@goliat.ugr.es writes:

> Please tell me about programs does permit the calculation of the 
> partition coefficients octanol-water (logP) ?
> regards.

HINT is a third-party program that works in the molecular modeling
environment of Biosym's InsightII, Tripos's Sybyl or Chemical Design's
Chem-X.  HINT calculates logP using a library for proteins, nucleic acids
and certain other materials.  HINT can calculate logP of any molcule
in its "calculate mode" using rules based on the chemical fragment types,
and a translation of the fragment method of Leo and Abraham.

In addition to calculating logP, HINT calculates (1) 3-D visual maps that
aid in the 3-D understanding of hydrophobicity for small and large molecules, 
and (2) molecular interaction constants (including hydrophobic, electrostatic 
and VDW) useful for studying binding of drugs to proteins or proteins to 
proteins.

Information about HINT, publications and seminars can be found on the web at:

	http://www.i2020.net/edusoft/hint/hint.html

-- 

        **************  David N. Haney, Ph.D.    ****************
        *  Haney Associates               Phone - 619-566-1127  *
        *  12010 Medoc Ln.                                      *
        *  San Diego, CA 92131            Fax - 619-586-1481    *
	*  http://www.i2020.net/edusoft/haney/haney.html        *
        **************  Email - haney@netcom.com  ***************

From owner-chemistry@ccl.net  Mon Feb 12 16:27:47 1996
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We want to hire a theoretical chemist.  Check our ad in the archives or drop
me a line.

===============================================================================
                              David M. Schrader
                           Professor of Chemistry
Department of Chemistry		      |  Telephone numbers:
Marquette University                  |		(414) 288-3332 (office)
P.O. Box 1881                         |		(414) 288-7066 (FAX)
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From owner-chemistry@ccl.net  Mon Feb 12 17:57:51 1996
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Date:     Mon, 12 Feb 96 15:08:36 EST
From: George R Famini   <grfamini@cbdcom.apgea.army.mil>
To: chemistry@ccl.net
Subject:  Death of Bob Taft
Organization:  International Programs Office
Priority:  Normal
Message-ID:  <9602121508.aa21541@cbdcom.apgea.army.mil>


I know that this is not normally posted to this list, but  many
of you on the list no doubt knew, or knew of Bob Taft. 

For those of you that are interested:

Bob Taft, professor emeritus  from UC-Irvine, and one of the pioneers
of linear free energy relationships, passed away last Friday evening.
Bob was instrumental in extending the LFER technique developed
by Louis Hammett.  In later years, he, along with Mort Kamlet
and Mike Abraham, promulgated the linear solvation energy relationship.

No doubt the field of physical organic chemistry will sorely miss
Bob.


				George Famini
				COMP Program Chair
				(and a fried of Bob's)




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This press release is simultaneously submitted to CHMINF-L, CHEMIND-L, CCL, 
ISISforum-l, and Mol-Diversity lists.  If you have subscriptions to more 
than one of these lists, we apologize for the multiple posting.

-----------------------------------			
   MDL INFORMATION SYSTEMS, INC. AND TRIPOS, INC. TO PROVIDE SOLUTIONS
              FOR PHARMACEUTICAL AND CHEMICAL RESEARCHERS 

ST. LOUIS, Missouri February 12, 1996 MDL Information Systems, Inc. (Nasdaq
National Market System: MDLI), a leading supplier of chemical information
management systems, and Tripos, Inc. (Nasdaq: TRPS), a leading supplier of
molecular discovery, design, and analysis technologies, today announced a
collaboration to provide integrated software solutions. These solutions will
incorporate simulation, analysis, and database management capabilities for
customers in the pharmaceutical, agrochemical, and chemical industries.  The
two companies will accomplish this by separately offering products that in
combination provide comprehensive, integrated solutions addressing customer
needs in areas such as combinatorial chemistry and molecular design and
analysis.  Each company will continue to develop technologies independently
while working on integration of key products. 

The goal of this collaboration is to provide more comprehensive solutions that
help customers accelerate the compound discovery process and enhance research
productivity.  The two firms will collaborate initially in combinatorial
chemistry informatics, a new technology that is revolutionizing compound
research methods.  Tripos was the first company to deliver molecular diversity
technology tools for combinatorial library design, storage, and analysis and
has expertise in pharmacological activity prediction.  MDL was the first
company to deliver combinatorial chemistry data management tools and has
additional expertise in library management, workflow support, and databases of
reactions and reagent information. 

The other initial area of major collaboration will be in combined solutions for
molecular design and analysis.  Researchers will benefit from transparent
access to MDL s databases and ISIS, an open, client/server scientific
information management system, from Tripos products including SYBYL (advanced
molecular design and analysis), Alchemy (desktop molecular design) and Unity
(integrated 3D database system for bio-active molecular discovery). 

Tripos will rely on ISIS as the information pipeline for its design solution. 
Tripos will continue to aggressively develop and improve Unity for 3D searching
and analysis.  Tripos announced that it intends to cease further development of
Unison and will work with MDL to allow Unison customers to convert their
current systems to integrated solutions based on ISIS. 

Steven Goldby, MDL's chairman and CEO, said,  MDL and Tripos each have achieved
leadership in complementary technologies, and we are now combining these
strengths to better serve our customers. The beauty of this arrangement is that
each company can concentrate on the things it does best for new compound
discovery.  MDL's customers will benefit in many ways.  ISIS users will have
easier access to Tripos  integrated design and analysis applications.  We look
forward to a long relationship in which we continue to exploit opportunities
for innovative shared solutions. 

John McAlister, president and CEO of Tripos said, "Tripos' collaboration with
MDL will rpovide our customers with the unique opportunity to combine their
data management facilities with data analysis, modeling, and experimental
design in a seamless fashion.  As Tripos focuses more of its efforts on new
compound discovery and combinatorial library design, our customers will benefit
from rapid product innovation and deployment.  We are confident that this
alliance will significantly advance the use and application of high technology
and computational methods in pharmaceutical, agrochemical, and chemical
research." 

About the Companies 
===================
Tripos, Inc., with headquarters in St. Louis, Missouri and offices worldwide,
is a leader in the creation, development, and delivery of chemical libraries,
discovery software and related services to facilitate the discovery of new
therapeutic and bioactive compounds in the pharmaceutical, biotechnology,
chemical, and agrochemical industries. The customer base includes the world s
largest scientific research organizations. 

Established in 1978, MDL Information Systems, Inc. is a leading commercial
supplier of chemical information management software, chemical information
databases, and related services to the pharmaceutical, agrochemical, and
chemical industries.  The company's software and database products enable its
customers to discover and develop new products more rapidly by allowing
scientists to access and use scientific information more effectively.  MDL has
offices worldwide with headquarters in San Leandro, California. 

                                   ### 

MDL is a registered trademark of MDL Information Systems, Inc.  ISIS is a
trademark of MDL Information Systems, Inc.  Unity, SYBYL, and Alchemy are
registered trademarks of Tripos, Inc.  All other products are trademarks or
registered trademarks of their respective holders. 

The statements which are not historical facts contained in this release are
forward-looking statements that involve risks and uncertainties, including, but
not limited to, product demand and market acceptance risks, the effect of
economic conditions, the impact of competitive products and pricing, product
development, commercialization and technological difficulties, and other risks
detailed in both Companies  Securities and Exchange Commission filings. 

