From darryl@om3.ch.umist.ac.uk  Mon Nov 18 23:38:35 1996
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Date: Mon, 18 Nov 1996 13:40:38 +0000 (GMT)
From: Darryl Ellson <darryl@om3.ch.umist.ac.uk>
Subject: Computational studies of histidine radicals.
To: chemistry@www.ccl.net
Message-Id: <Pine.3.89.9611181325.E326-0100000@trigger.ch.umist.ac.uk>





Dear All,

I am looking for any computational studies (particularly, but not 
necesssarily, DFT )which have been carried out on histidine radicals (neutral,
cationic and +2 charged) or on related  truncated species, such as 
4Me-Imidazole.

I am particularly interested in calculated vibrational frequencies and/or 
mode assignments for these species.

If anyone could point me in a useful direction I would be most grateful.

Regards.

Darryl A. Ellson


Darryl A. Ellson - Molecular Design & Simulation Laboratory.
Dept. Chemistry, UMIST, Manchester. UK. M60 1QD
Tel: 0161-236-3311 x4476    Fax: 0161-236-7677
   |_o_|   "Unless I am very much mistaken... I AM very much mistaken !"
 []=(_)=[] (M.Walker)




From jaw@camsoft.com  Mon Nov 18 16:38:35 1996
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X-Sender: jaw@helium.camsoft.com
Date: Mon, 18 Nov 1996 15:43:50 -0500
To: janet.cicariello-cook@roche.com
From: Joel Wolff <jaw@camsoft.com>
Subject: Re: CCL:Getting structures from SYBYL to FMPro
Cc: CHEMISTRY@www.ccl.net



At 10:30 AM 11/18/96 -0500, you wrote:
>Hi All,
>
>I am trying to put together an automated (semi-automated?) procedure for our 
>chemists to get their structures from SYBYL (3D-structure, on the SGI) into 
>FileMaker Pro v3.0 (2D-structures, on their Macintoshes). They are currently 
>re-drawing their structures (you can imagine the problem this is, especially 
>with the CombiChem folks)
>

Janet,

The makers of ChemDraw can probably help you here. I can think of several
easier ways to deal with this problem:

1. Export from SYBYL and open in Chem3D. Then export from Chem3D to ChemDraw
format.

2. Contact us about our upcoming support of SMILES in ChemDraw 4.0. This
would remove several steps in your process.

3. Move the files through ChemFinder, which already has links between
Chem3D, ChemDraw and FileMaker.

Everything can be done via AppleScript once the files are moved to the
Macintosh.

Let me know how I can help.

Joel Wolff, Ph.D.
Director, Technical Services
CambridgeSoft Corporation
875 Massachusetts Avenue
Cambridge, MA 02139
jaw@camsoft.com



From comartin@wicc.weizmann.ac.il  Mon Nov 18 03:46:26 1996
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X-Wisdom: Language Can Kill
Date: Mon, 18 Nov 1996 09:28:54 +0200
To: chemistry@www.ccl.net
From: "Jan M.L. Martin" <comartin@wicc.weizmann.ac.il>
Subject: apologies




Dear subscribers,

a number of people complained about my posting an entire program to CCL,
and suggested that I give an ftp URL instead of wasting precious bandwidth.

Let me point out in my defense that I checked the list WWW pages for submission
instructions and that what I came up with was the following:
http://www.ccl.net/ccl/welcome.html
>
>
> Topics which may appear on the list include:
>
>[...]
> *Programs and utilities
> [...]
> If you are posting a long file (e.g. a program), please split it into
> chunks which are smaller than 50 KBytes. Always identify the part number
> and total number of parts in the Subject line (e.g. NiceDraw Part 2 of
> 5).
> [...]

So I just did what it *says* in these pages.

Nevertheless, I apologize for any long downloads and aggravation I may have
caused people who do not receive their mail on Unix boxes and had their
modems clogged up by my "garbage". The package is now up for download by
FTP at:

ftp://www.ccl.net/pub/chemistry/software/SOURCES/FORTRAN/gar2ped

Future updates and/or corrections will be made to the FTP file *only*, and
only announcements will sent out to the list.

As a final note, I would respectfully suggest that the moderator update the
above submission information.

Sincerely,
Jan Martin

----------------------------------------------------------------------------
dr. Jan M.L. Martin                 Senior Lecturer, Computational Chemistry
       Department of Organic Chemistry/Kimmelman Building, Room 262
            Weizmann Institute of Science/Rechovot 76100/ISRAEL
FAX +972(8)9344142  Phone +972(8)9342533  E-mail comartin@wicc.weizmann.ac.il
  *** temporary WWW home page       http://theochem.weizmann.ac.il/  ***
------ kol ha-olam kulo gesher tzar me'od, v'ha-ikar lo lefached k'lal -----




From psto@xs4all.nl  Mon Nov 18 06:42:47 1996
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Date: Mon, 18 Nov 1996 12:04:13 +0100 (MET)
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X-Sender: psto@xs4all.nl (Unverified)
To: chemistry@www.ccl.net
From: psto@xs4all.nl (Peter Stone)
Subject: Gene processing toolbox for the Mac




Hi, I'm not a chemist but a programmer, and I've written several
hundred general-purpose algorithms that might be useful for you.
The algorithms let you generate and process rna and turn the results
into amino acids. Let me know if such program is needed, and what 
other features it should have.

I'm not a regular on this list and would appreciate answers directly
to my email.

Peter
psto@xs4all.nl

---

Here is an example of how a recursive van kock gene can be constructed.
Implement it in an organism and we might get interesting new properties,
designed with mathematical perfection from the algorithm library of:

        - fractals       - chaos
        - lsystems       - fourier synthesis
        - autocatalysis  - neurons
        - energy fields  - fibonacci numbers
        - loops          - morphs
        - transforms     - interpolations
        - palindromes    - variations
        - divisions      - primes
        - solar systems  - rna
        - clusters       - proportions
        - permutations   - rotations
 
You can also process existing genes with the above. Morph eye to ear,
or permute hiv hxb2 env gene, experiment if a rotated fibonacci neuron
structure performs better than non-rotated, loop genes for better 
beef productivity, etc.

; define recursive kock-curve

(def-grammar 'koch-curve
   axiom (f + f + f + f)
   f (f + f - f - f f + f + f - f)
   - (-)
   + (+)
   < (<)
   > (>)
)

; define neuron to convert linear symbols to rna symbols

(def-neuron symbols-to-rna
   (in 1 'a) 
   'u 
   (in 1 'b) 
   'g 
   (in 1 'c) 
   't 
   (in 1 'd) 
   'a 
)

; generate master-rna from kock-curve in 3 recursion levels, and scale the
; symbols into rna symbols

(setq master-rna
      (run-neuron 'symbols-to-rna
          (symbol-scale '(a d) 
              (gen-lsystem axiom 3 '(f + - < >) 'koch-curve))))

; compile rna into aminoacids

(rna-compile master-rna)
--> (gly leu gly trp gly gly val gly cys phe val val leu trp val gly val gly 
trp gly trp gly gly val phe gly leu trp gly gly val gly gly leu gly trp gly val 
trp phe val gly cys leu val leu phe tyr phe gly leu trp gly gly gly val phe gly 
phe ile leu phe trp phe tyr phe ile asn stp ile phe tyr phe gly phe leu val 
leu phe tyr lys leu asn ile leu)





From usdccz73@ibmmail.com  Tue Nov 19 13:39:09 1996
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Date: Tue, 19 Nov 1996 13:29:28 EST
To: Chemistry@www.ccl.net
Subject: Looking for UNIFAC model





NOTE FROM: C. Peter Qian
  NITC EXPR CTR CO41B1
  Dow Corning Corp.
SUBJECT: Looking for UNIFAC model
I would like to get any current information (such as e-mail address or
phone number ) on the UNIFAC model for estimating activity coefficients of
organosilicon compounds.

Thanking you in advance

 C. Peter Qian
 NITC EXPR CTR, CO41B1, Dow Corning Corp.
 Midland, MI 48686-0994
 usdccz73@ibmmail.com, Tel. (517)496-6938, Fax (517)496-5121


From buehler@chclu.chemie.uni-konstanz.de  Wed Nov 20 03:38:53 1996
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          08:59:50 CET
Date: Wed, 20 Nov 1996 08:59:49 CET
From: JOCHEN BUEHLER <buehler@chclu.chemie.uni-konstanz.de>
To: chemistry@www.ccl.net
Message-ID: <009ABA49.A649E095.75@chclu.chemie.uni-konstanz.de>
Subject: RPAC 11.0



Dear CCL'ers,

has anybody successfully compiled RPAC 11.0 on a SGI running IRIX 6.2
or a Cray J916 ?
I'm getting a clean compile on the Cray but incorrect results and
failing compiles on the SGI...

     any help greatly appreciated

              Jochen

From Schiffer@MSMWIA.hoechst.hoechst-ag.d400.de  Wed Nov 20 04:38:54 1996
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From: "Schiffer, Heinz, Dr., WIA / SC" <Schiffer@MSMWIA.hoechst.hoechst-ag.d400.de>
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To: CCL <chemistry@www.ccl.net> (Receipt Notification Requested) (Non Receipt Notification Requested)
Cc: "Frank, Dierk, Dr., WIA/CAMD" <Frank@MSMWIA.hoechst.hoechst-ag.d400.de> (Receipt Notification Requested) (Non Receipt Notification Requested)
Subject:  minimum distance periodic systems



Dear netters,

I am looking for a formula for the minimum distance of to points in an 
arbitrary
three dimensional lattice, in particular if it is NOT rectangular. The 
formula
should be easy and fast to be evaluated.
Thank you,
                      Dierk

 -------------------------------------------------------
Dr. Heinz Schiffer              65926 Frankfurt am Main
Hoechst AG                        Phone ++49-69-305-2330
Scientific Computing        Fax   ++49-69-305-81162

Email :   schiffer@wia.hoechst-ag.d400.de
     schiffer@msmwia.hoechst.hoechst-ag.d400.de
 -------------------------------------------------------

From kessler@mpi-muelheim.mpg.de  Wed Nov 20 05:38:54 1996
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Date: Wed, 20 Nov 1996 11:05:25 +0100
From: Magnus Kessler <kessler@mpi-muelheim.mpg.de>
Organization: Max-Planck-Institut fuer Kohlenforschung
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To: Computational Chemistry List <chemistry@www.ccl.net>
Subject: CCL:Atoms In Molecules for transition metal complexes
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Dear CCLer's

I would like to do a bonding analysis with Bader's "atoms in molecules"
(AIM) concept on transition metal complexes. Two questions arise:

1. Which software is capable to do such an analysis. (According to the
   manual, AIM in G94 Rev. B3 cannot handle d-electrons; BTW the 
   AIM functionality seems not to be implemented in G94 Rev. B3)

2. Has anyone made any experience with AIM analysis on transition
   metals?

Any information will be greatly appreciated

Thanks a lot in advance


Magnus Kessler


========================================================================
Magnus Kessler                  kessler@mpi-muelheim.mpg.de
PhD Student
MPI fuer Kohlenforschung	Lembkestrasse 5
Strukturchemie                  D-45470 Muelheim / Germany
========================================================================

From jerry@Ramsey.chem.dal.ca  Wed Nov 20 08:38:56 1996
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Date: Wed, 20 Nov 1996 09:40:35 -0400 (AST)
From: "Jerry C.C. Chan" <jerry@Ramsey.chem.dal.ca>
To: chemistry@www.ccl.net
Subject: Transition metal Shielding Calculation 
Message-ID: <Pine.SGI.3.91.961120093543.7526C-100000@Ramsey.chem.dal.ca>
MIME-Version: 1.0
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Dear CCLers,

	I am interested in the chemical shielding calculation of 
transition metal nucleus by DFT method.  Could anyone please give me some 
references.

Many thanks,
Jerry

jerry@Ramsey.chem.dal.ca
Department of Chemistry
Dalhousie University

From info@molecules.com  Wed Nov 20 12:39:03 1996
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	by www.ccl.net (8.8.2/950822.1) id MAA29242; Wed, 20 Nov 1996 12:17:12 -0500 (EST)
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Date: Tue, 19 Nov 96 10:24:17 PST
From: David Segrist <info@molecules.com>
Subject: RE: CCL:Molecule Builder 
To: "William R. Smith" <WSMITH@msnet.mathstat.uoguelph.ca>,
        chemistry@www.ccl.net
X-Mailer: Chameleon - TCP/IP for Windows by NetManage, Inc.
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>    Does anyone know of a simple Windows 3.1/NT/95 product that can be used
>to build molecules?

My employer produces this product:

Molecules-3D (TM), Version 2.1
3D Molecular Model Builder for Apple Macintosh and Microsoft Windows

A simple-to-use package that enables you to: (A) build, optimize, 
edit and export 3D molecular models, as well as, (B) construct 2D 
Lewis diagrams and convert them to 3D models. $29.95.

Please send e-mail to info@molecules.com if you would like further
information.

David Segrist
Molecular Arts Technical Support

---------------------------------------------------------
Molecular Arts Corporation       | <info@molecules.com>
Hanover Corporate Centre         | CompuServe: 71644,3626
1532 E. Katella Ave., Suite 1000 | Voice: (714) 634-8100
Anaheim, California 92805, USA   | FAX: (714) 634-1999
---------------------------------------------------------
         ftp.cerfnet.com /pub/vendor/molecules


From dapprich@euch4g.chem.emory.edu  Wed Nov 20 12:48:06 1996
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	by www.ccl.net (8.8.2/950822.1) id MAA29087; Wed, 20 Nov 1996 12:02:19 -0500 (EST)
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          id AA14380; Wed, 20 Nov 1996 11:56:11 -0500
Message-Id: <32933B4C.12D@euch4g.chem.emory.edu>
Date: Wed, 20 Nov 1996 12:09:26 -0500
From: "Dr. Stefan Dapprich" <dapprich@euch4g.chem.emory.edu>
Reply-To: dapprich@euch4g.chem.emory.edu
Organization: Emory University
X-Mailer: Mozilla 3.0Gold (Macintosh; I; 68K)
Mime-Version: 1.0
To: Richard Wong <wong@chemistry.uq.edu.au>
Cc: chemistry@www.ccl.net
Subject: Re:electron donating ability
References: <199611200348.NAA16966@chem.chemistry.uq.oz.au>
Content-Type: text/plain; charset=us-ascii
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Richard Wong wrote:
> I am looking for papers which discuss the electron donating ability of
> simple molecules such as NH3, OH2, FH, PH3, SH2, Cl, CO and N2, etc.

If you are interested in the electron donor/acceptor properties of those
molecules as ligands in transition metal complexes, the following papers
might be helpful:

1. A. W. Ehlers, S. Dapprich, S. F. Vyboishchikov, G. Frenking,
"Structure and Bonding of Transition-Metal Carbonyl Complexes M(CO)5L (M
= Cr, Mo, W) and M(CO)3L (M = Ni, Pd, Pt; L = CO, SiO, CS, N2, NO+, CN-,
NC-, HCCH, CCH2, CH2, CF2, H2)", Organometallics 1996, 15, 105. 

2. S. Dapprich, G. Frenking, "Ligand Effects in Transition Metal
Dihydrogen Complexes: A Theoretical Study", Organometallics 1996, 15,
4547.

3. S. Dapprich, G. Frenking, "Investigation of Donor-Acceptor
Interactions: A Charge Decomposition Analysis Using Fragment Molecular
Orbitals", J. Phys. Chem. 1995, 99, 9352. 

Hope this helps,
Stefan

--------
Dr. Stefan Dapprich
Cherry L. Emerson Center for Scientific Computation
Chemistry Department, Emory University
Atwood Hall
1515 Pierce Drive
Atlanta GA 30322
Phone +1-404-727-2381
Fax +1-404-727-7412
Email dapprich@euch4g.chem.emory.edu
URL http://euch4m.chem.emory.edu/~dapprich
--------

From gmercier@mail.med.upenn.edu  Wed Nov 20 15:38:59 1996
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Received: (from gmercier@localhost) by mail.med.upenn.edu (8.6.12/8.6.12) id PAA10637 for CHEMISTRY@www.ccl.net; Wed, 20 Nov 1996 15:02:43 -0500
From: "Gustavo A. Mercier Jr" <gmercier@mail.med.upenn.edu>
Message-Id: <199611202002.PAA10637@mail.med.upenn.edu>
Subject: CC software/Linux/Motif?
To: CHEMISTRY@www.ccl.net
Date: Wed, 20 Nov 1996 15:02:42 -0500 (EST)
X-Mailer: ELM [version 2.4 PL23-upenn3.1]
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Hi!

I am interested in running CC applications in a P6 box running
Linux with XFree86. Many applications make use of OpenGL and Motif
which I understand are not available through the vanilla XFree86.

I need to find out in what ways to extend (or replace) XFree86
to support the widest range of CC applications, at a reasonable
added cost. For example, 3rd party Xserver software vendors that
include Motif and OpenGl, etc.

Comments in this area are welcomed, particularly updates to
previous discussions on this topic.

I will summarize if there is interest.

Thanks!

-- 
                                      ("`-/")_.-'"``-._
Gustavo A. Mercier,Jr.,MD,PhD         (. . `) -._    )-;-,_() 
Division of Nuclear Medicine          (v_,)'  _  )`-.\  ``-
Dept. of Radiology                    _;- _,-_/ / ((,'
University of Pennsylvania           ((,.-'  ((,/
3400 Spruce St.                  gmercier@mail.med.upenn.edu
Philadelphia, PA 19104         215-662-3069/3091 fax: 215-349-5843



From kneth@serf2.Colorado.EDU  Wed Nov 20 18:38:59 1996
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Date: Wed, 20 Nov 1996 16:28:49 -0700 (MST)
From: Kenneth Geisshirt <kneth@serf2.Colorado.EDU>
To: "Gustavo A. Mercier Jr" <gmercier@mail.med.upenn.edu>
Cc: CHEMISTRY@www.ccl.net
Subject: Re: CCL:CC software/Linux/Motif?
In-Reply-To: <199611202002.PAA10637@mail.med.upenn.edu>
Message-Id: <Pine.SGI.3.94.961120160746.11268A-100000@serf2.Colorado.EDU>
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII


Hello.

On Wed, 20 Nov 1996, Gustavo A. Mercier Jr wrote:
 
> I need to find out in what ways to extend (or replace) XFree86
> to support the widest range of CC applications, at a reasonable
> added cost. For example, 3rd party Xserver software vendors that
> include Motif and OpenGl, etc.

Well, you can buy Motif and OpenGL. I would guess that both of them cost
about $200 each but I might be wrong. Motif has been ported to Linux/Xfree
by Metrolink and there are at least two companies offering OpenGL. Check
e.g. www.li.org or www.linux.org - they might have links to those
companies.

OpenGL is - as far as I understand - VERY slow. The implementations on
Linux/Xfree are basically just emulators, i.e. they run on top of X11.

Someone is working on a freeware implementation of Motif, but since I have
strong feelings against Motif (looks too much like M$-Windows to me), I
don't know the status of that project.

> Comments in this area are welcomed, particularly updates to
> previous discussions on this topic.

I tried to compile GAMESS on a Linux box and that was easy - basically
it compiled out-of-the-box. I wasn't extremely excited about the speed
even though the study by Jorgensen et al. (in J. Comput. Chem. this
summer) showed that a Pentium based computer is fast. On the other hand, I
didn't dig into all the options of the compiler.

BTW, GAMESS doesn't require Motif - at least not the computational part
which is normally the primary interest. GAMESS supports parallel
processing, so if you have more than one Linux box, you can run in
parallel. The same is true for DLpoly (and Gromacs?).

My experience with Fortran on Linux is that it works. I have tried both
f2c and g77 but I haven't done any benchmarks (does someone have any info
on that?).

Linux is pretty much a 'standard' U**x, e.g. it follows the POSIX
guidelines and implements SysV and BSD. I have never had any problems
porting programs - well, maybe an old one written in K&R C, but even that
can be solved.


Best wishes
  Kenneth

+-----------------------------------------------------------------+
| Kenneth Geisshirt                                 Ph.D.-student |
| Department of Life Sciences and Chemistry,  Roskilde University |
| Currently at: University of Colorado at Boulder                 |
+-----------------------------------------------------------------+
| kneth@fatou.ruc.dk                 http://virgil.ruc.dk/~kneth/ |
+-----------------------------------------------------------------+
| Geek Code 2.1: d++h--s!gp2!aua-w+vc+U++p+L++3EN++K-W---M-       |
|               !V-po+Y+t!5jRG?!tvb++D+B?e---u+h--grn++y+         |
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