From lnl@novo.dk  Thu Nov  9 05:32:33 1995
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Date: Thu, 9 Nov 95 11:28:08 +0100
From: lnl@novo.dk (Leif Norskov)
Message-Id: <9511091028.AA15231@bisse.novo.dk>
To: chemistry@www.ccl.net
Subject: Re: structure of d4T



TJ O'Donnell asked about d4T (and I have no idea, what it could be).
He also mentioned 3TC:

 > The NY Times and Chicago Tribune reported today about the FDA
 > approval of 3TC.  They didn't even give the (equally obscure)
 > names lamivudine or epivir.  I guess its too much to ask
 > that they give a proper chemical name, much less a structure.
 > Well, I found 3TC=lamivudine=epivir easily enough.

Maybe it would be of general interest to know how you found it ?
[ I could not, and asked my chemistry friends, who informed me
  that it is (2'R-cis)-2'-deoxy-3'-thiacytidine ]

While we are at it, TJ O'Donnell wants "a real structure (2D or 3D) of d4T".
That made me wonder just how commonly used Smiles strings are.
Would most CCL'ers be able to decipher "N1C(=O)N(C=C[C]1N)C2OC(C3C2S3)CO"
as the equivalent of 2'R-cis)-2'-deoxy-3'-thiacytidine (minus chirality) ?
Commercial software like Catalyst, Daylight and Sybyl support it,
but is there anything for academic users ?

Regards,

Leif Norskov
Novo Nordisk A/S
Copenhagen
Denmark
lnl@novo.dk


From mcgsw@cotton.vislab.olemiss.edu  Thu Nov  9 08:17:35 1995
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From: Scott Weston <mcgsw@cotton.vislab.olemiss.edu>
To: "Dr. T. J. O'Donnell" <tj@eecs.uic.edu>
Cc: "osc comp. chem. list" <chemistry@www.ccl.net>
Subject: re: d4T/stavudine
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TJ,

d4T is a nucleoside HIV reverse transcriptase inhibitor also known
by its generic name of stavudine or trade name of Zerit(R).  Its 
chemical name is 2',3'-didehydro-2',3'-dideoxythymidine, and it is a 
Bristol-Myers Squibb product. A chemical structure may be found at
http://pharminfo.com./pubs/msb/stavud.html.


Hope this helps,

Scott

=================================================================
Scott Weston                   Lab Phone:  (601) 232-7187
Grad. Student                  Lab FAX:  (601) 232-5118
Dept. of Medicinal Chemistry   Home Phone:  (601) 234-0067
University of Mississippi      mcgsw@cotton.vislab.olemiss.edu
University, MS  38677								
=================================================================



From slayten@cas.org  Thu Nov  9 08:25:30 1995
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Date: Thu, 9 Nov 95 08:05:21 EST
From: slayten@cas.org (Steve Layten x3451)
Message-Id: <9511090805.AA26954@cas.org>
Subject: Re: CCL:structure of d4T
In-Reply-To: <9511091028.AA15231@bisse.novo.dk> of Thu, 9 Nov 95 11:28:08 +0100
To: lnl@novo.dk
Cc: chemistry@www.ccl.net


a search for d4t in the CAS Registry file on STN did not find any answers.
A search for that term in the CAPLUS file on STN found 111 answers. The
first reference cited indicated that d4t is 2',3'-Didehydro-3'-deoxythymidine.
(an anti-aids drug, alternate name stavudine.)

Going back to the Registry file, I found "D 4T" (note the space) had two
answers. This nucleoside and N-[3-(4-Methylphenoxy)-2-hydroxypropyl]-
tert-butylamine. I think the structure referred to in the original message
is the former nucleoside.

2-D structure diagrams can be obtained for both substances in the CAS Registry
file on STN. A CONCORD (Tripos, Inc.) generated 3D structure of the latter
substance can be downloaded from STN.

Regards,

Steve Layten

>Date: Thu, 9 Nov 95 11:28:08 +0100
>From: lnl@novo.dk (Leif Norskov)
>Subject: CCL:structure of d4T
>Sender: Computational Chemistry List <chemistry-request@www.ccl.net>
>
>TJ O'Donnell asked about d4T (and I have no idea, what it could be).
>He also mentioned 3TC:
>
> > The NY Times and Chicago Tribune reported today about the FDA
> > approval of 3TC.  They didn't even give the (equally obscure)
> > names lamivudine or epivir.  I guess its too much to ask
> > that they give a proper chemical name, much less a structure.
> > Well, I found 3TC=lamivudine=epivir easily enough.
>
>
>Maybe it would be of general interest to know how you found it ?
>[ I could not, and asked my chemistry friends, who informed me
>  that it is (2'R-cis)-2'-deoxy-3'-thiacytidine ]
>
>While we are at it, TJ O'Donnell wants "a real structure (2D or 3D) of d4T".
>That made me wonder just how commonly used Smiles strings are.
>Would most CCL'ers be able to decipher "N1C(=O)N(C=C[C]1N)C2OC(C3C2S3)CO"
>as the equivalent of 2'R-cis)-2'-deoxy-3'-thiacytidine (minus chirality) ?
>Commercial software like Catalyst, Daylight and Sybyl support it,
>but is there anything for academic users ?
>
>Regards,
>
>Leif Norskov
>Novo Nordisk A/S
>Copenhagen
>Denmark
>lnl@novo.dk
-- 
Steven W. Layten, Senior Research Scientist
Chemical Abstracts Service, PO Box 3012, Columbus, OH 43210    +1 614 447 3600
INET: slayten@cas.org                                     FAX: +1 614 447 3813
# # # Speaking only for myself, and NOT for Chemical Abstracts Service! # # #

From tj@eecs.uic.edu  Thu Nov  9 11:47:41 1995
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Subject: re: d4T/stavudine
To: chemistry@www.ccl.net (CCL)
Date: Thu, 9 Nov 1995 10:45:50 -0600 (CST)
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Forwarded message:
> From mcgsw@cotton.vislab.olemiss.edu Thu Nov  9 07:09:19 1995
> TJ,
> 
> d4T is a nucleoside HIV reverse transcriptase inhibitor also known
> by its generic name of stavudine or trade name of Zerit(R).  Its 
> chemical name is 2',3'-didehydro-2',3'-dideoxythymidine, and it is a 
> Bristol-Myers Squibb product. A chemical structure may be found at
> http://pharminfo.com./pubs/msb/stavud.html.
> 
> 
> Hope this helps,
> 
> Scott
> 
> =================================================================
> Scott Weston                   Lab Phone:  (601) 232-7187
> Grad. Student                  Lab FAX:  (601) 232-5118
> Dept. of Medicinal Chemistry   Home Phone:  (601) 234-0067
> University of Mississippi      mcgsw@cotton.vislab.olemiss.edu
> University, MS  38677								
> =================================================================
> 

Warning to people: http://pharminfo.com./pubs/msb/stavud.html
is wrong.  It does not show the pyrimidine ring of
3TC=stavudine=Zerit=2',3'-didehydro-2',3'-dideoxythymidine.

-- 
*---------------------------------------------------------------------*
*     If you need a quote: http://www.eecs.uic.edu/~tj/quotes.html    *
*---------------------------------------------------------------------*
| Dr. TJ O'Donnell  > tj@eecs.uic.edu <  http://www.eecs.uic.edu/~tj/ |
*---------------------------------------------------------------------*

From tj@eecs.uic.edu  Thu Nov  9 12:02:40 1995
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Subject: structure of 3TC/d4T
To: chemistry@www.ccl.net (CCL)
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> 
> TJ O'Donnell asked about d4T (and I have no idea, what it could be).
> He also mentioned 3TC:
> 
> Maybe it would be of general interest to know how you found it ?
> [ I could not, and asked my chemistry friends, who informed me
>   that it is (2'R-cis)-2'-deoxy-3'-thiacytidine ]

I found 3TC referred to in
http://health.nyam.org:8000/public_html/network/sf.html
after a NetSearch using http://home.mcom.com/home/internet-search.html
Info in sf.html connected 3TC to Epivir and lamivudine.
I usually rely on the Merck Index to decipher the plethora
of chemical synonyms, but the latest edition (1989) did not
have these relatively new drugs.  Is there a Merck Index on-line?
I thought I heard about this a while back.  Sure would be swell.

> 
> While we are at it, TJ O'Donnell wants "a real structure (2D or 3D) of d4T".
> That made me wonder just how commonly used Smiles strings are.
> Would most CCL'ers be able to decipher "N1C(=O)N(C=C[C]1N)C2OC(C3C2S3)CO"
> as the equivalent of 2'R-cis)-2'-deoxy-3'-thiacytidine (minus chirality) ?
> Commercial software like Catalyst, Daylight and Sybyl support it,
> but is there anything for academic users ?

> 
> Leif Norskov
> Novo Nordisk A/S
> Copenhagen
> Denmark
> lnl@novo.dk

I would like to see wider acceptance and use of Smiles strings
to name chemical structures.  There are extensions of Smiles to
handle chirality.  I know Concord supports Smiles.  Is that
"for academic users"?  Does Concord exists outside of Sybyl?
Steve Layten wrote in response to my inquiry about d4T and 3TC:

2-D structure diagrams can be obtained for both substances in the CAS Registry
file on STN. A CONCORD (Tripos, Inc.) generated 3D structure of the latter
substance can be downloaded from STN.

Can STN be used to generate 3D structures from 2D smiles that I input?


TJ
-- 
*---------------------------------------------------------------------*
*     If you need a quote: http://www.eecs.uic.edu/~tj/quotes.html    *
*---------------------------------------------------------------------*
| Dr. TJ O'Donnell  > tj@eecs.uic.edu <  http://www.eecs.uic.edu/~tj/ |
*---------------------------------------------------------------------*

From KARPATI@ch.bme.hu  Thu Nov  9 12:32:39 1995
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From: "Karpati Tamas" <KARPATI@ch.bme.hu>
To: chemistry@www.ccl.net
Date:          Thu, 9 Nov 1995 18:28:48 GMT+100
Subject:       CCL:polarization ftns for bulky atoms
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Hi netters,

I am interested in doing ab initio calculations for some Hg, As and Sb
compunds. Because of bulky atoms I have to use ECP basis set LANL1DZ 
of G94, but I would like to include polarization funtions. So my 
problem is that I do not know the standard polarization funtions for 
these atoms. Could anyone help me? Thanks in advance.

Tamas Karpati, student (TU of Budapest)
KARPATI@CH.BME.HU

From ui22204@sunmail.lrz-muenchen.de  Thu Nov  9 13:02:40 1995
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From: Eugene Leitl <ui22204@sunmail.lrz-muenchen.de>
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To: "Todd J. Raeker" <raeker@saturn.kent.edu>
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Subject: Re: CCL:pdb file generator
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On Wed, 8 Nov 1995, Todd J. Raeker wrote:

> 
> Hello CCLer's
> 
>   Does anyone know of a program, free or commercial that will create a 
> pdb file given the amino acid sequence. Either a MS Windows or UNIX 
> program would be great to have.  A graphical display is not required.  

This does not make sense, as pdb contains structure information
(3d atomic coordinates) which cannot be deduced from the primary 
sequence yet (protein folding problem). Of course one can compute 
the coordinates of a linear AA sequence and a syntactically correct 
pdb from that, but that's probably not what you wanted.

-- Eugene
 
> Thanks,
> 
> Todd.
> 
> 
> Dr. Todd J. Raeker         |  Department of Chemistry
> raeker@saturn.kent.edu     |  Kent State University
> Phone (216)-672-2986       |  Kent, OH 44242-0001
> 
> 
> 
> -------This is added Automatically by the Software--------
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>              Web: http://www.ccl.net/chemistry.html 
> 
> 

From xiaopeng@astro.ocis.temple.edu  Thu Nov  9 14:17:40 1995
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Date: Thu, 9 Nov 1995 14:10:23 -0500 (EST)
From: Peking <xiaopeng@astro.ocis.temple.edu>
To: chemistry@www.ccl.net
Subject: 3d graph and 2d contour
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Hello, Dear CCLs,
	I am looking for a PC or SGI software that can show a 3-dimension 
optential surface and its 2-d contour on the same graph.

	Anybody can kindly give me info?

	Thanks!

xiaopeng

			xiaopeng@astro.ocis.temple.edu


From heelisp@delta.newi.ac.uk  Thu Nov  9 14:32:40 1995
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Date: Thu, 9 Nov 1995 19:08:14 +0100
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CCLers,
As a new user of Gaussian 94 for windows I would appreciate advice on the best
basis set for the calculation of ground and excited state dipoles.
the molecule is a 20 none hydrogen atom nitrogen heterocycle, +1 charge.
It will be a single point calculation on a crystal structure. I have a Pentium 90 with 16MB ram.
Any help much appreciated

Paul Heelis
Heelisp@newi.ac.uk

From owner-chemistry@ccl.net  Thu Nov  9 14:41:26 1995
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In-Reply-To: "Todd J. Raeker" <raeker@saturn.kent.edu>
        "CCL:pdb file generator" (Nov  8, 12:22pm)
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On Nov 8, 12:22pm, Todd J. Raeker wrote:
> Subject: CCL:pdb file generator
>
> Hello CCLer's
>
>   Does anyone know of a program, free or commercial that will create a
> pdb file given the amino acid sequence. Either a MS Windows or UNIX
> program would be great to have.  A graphical display is not required.
>
> Thanks,
>
> Todd.

Hi, Todd:

Spartan can do what you described. Spartan peptide builder allows one
to specify amino acid sequence and secondary structure and generate it
automatically with the terminamtion you want. Spartan export feature
could create PDB file for the structure.

--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 owner-chemistry@ccl.net  Thu Nov  9 16:02:43 1995
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Date: 9 Nov 1995 13:48:42 -0700
From: "Craig Shelley" <craig@SoftShell.com>
Subject: Property Prediction Betas
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                      Subject:                              Time:  2:45 PM
  OFFICE MEMO         Property Prediction Betas             Date:  11/9/95

SoftShell will be publishing programs to predict various properties from
the chemical structure.  We are looking for several beta testers for each
property.  If you are interested in beta testing software to predict one of
these properties, please send e-mail to craigs@softshell.com (not to this
list) telling me how you currently use the property in your research or
why it might be useful to you.  Right now you must have Windows (3.1, 95
or NT is fine), and ChemWindow (preferred) or ChemWeb (free at
http://www.softshell.com) or another program that can copy an MDL molfile
to the clipboard (e.g., ChemDraw,ISIS/Draw).  Beta testers will receive a
complimentary copy of the finished property prediction program.

Property prediction programs being developed:

Molar Refractivity
logP
Henry's Constant
Boiling Point
Freezing Point
Critical Temperature, Pressure, & Volume
Heat of Formation
Gibbs Free Energy
Ideal Gas Thermal Heat Capacity

Thanks.  Craig Shelley (craigs@softshell.com)



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To: xiaopeng@astro.ocis.temple.edu
Cc: chemistry@www.ccl.net
In-Reply-To: <Pine.BSD.3.91.951109140723.29769A-100000@astro.ocis.temple.edu> (message from Peking on Thu, 9 Nov 1995 14:10:23 -0500 (EST))
Subject: Re: CCL:3d graph and 2d contour
Reply-To: hcj@wavefun.com


>>>>> "xiaopeng" == Peking  <xiaopeng@astro.ocis.temple.edu> writes:

    xiaopeng> Hello, Dear CCLs, I am looking for a PC or SGI software
    xiaopeng> that can show a 3-dimension optential surface and its
    xiaopeng> 2-d contour on the same graph.

If you have already generated the data you can use gnuplot, available
>from ftp://prep.ai.mit.edu/pub/gnu.

-Harry

+-----------------------+------------------+-------------------------+
|Harry C. Johnson IV    |  ______________  | E-Mail: hcj@wavefun.com |
|Computational Chemist  |  \  _________	/  | Phone:  (714)955-2120   |
|Wavefunction Inc.      |   \ \\\\\\\\/	   | Fax:    (714)955-2118   |
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From mam@atc.atccu.chula.ac.th  Thu Nov  9 23:02:47 1995
Received: from atc.atccu.chula.ac.th  for mam@atc.atccu.chula.ac.th
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Date: Fri, 10 Nov 95 10:46:15 GMT
From: mam@atc.atccu.chula.ac.th (Thammarat Aree)
Message-Id: <9511101046.AA25482@atc.atccu.chula.ac.th>
To: chemistry@www.ccl.net
Subject: Software of Molecular Dynamics Simulation


Dear CCls;
	I am looking for freeware for MD simulation in solid phase.
	Anybody can give me the information? Please tell me.
	Thank you very much for your kindness.

Thammarat

		mam@atc.atccu.chula.ac.th

