From chemistry-request@ccl.net Mon May  2 23:22:15 2005
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From: "Yubo Fan" <yubofan [a] mail.chem.tamu.edu>
Subject: Free energy barrier
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CCLers,

We are trying to calculate the free energy barriers for 
some dissociative reactions. As a model, we scan the B-N 
bondlength in H3B-NH3from the equilibrium distance to 
three times of that, then the frequency analyses were 
performed for each optimized points. Surprisingly, the 
free energies oscilate when the distance is longer than 
about twice of the equilibrium distance. So, we cannot 
find the free energy barrier by this way.

Is there any other way to calculate activation free energy 
for dissociative processes? Or some program available for 
this goal?

Thanks in advance,

Yubo Fan

Chemistry Department at TAMU


From chemistry-request@ccl.net Tue May  3 12:12:37 2005
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To: "David J Anick" <david.anick{at}rcn.com>
Subject: Re: CCL:eigenvalues & eigenvectors
Date: Tue, 3 May 2005 09:07:17 -0500
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On Monday 02 May 2005 01:21 pm, David J Anick wrote:
> Dear CCL,
> 
> Does anyone have or know of freeware that can
> compute the eigenvalues and eigenvectors of a
> real symmetric matrix (e.g a Hessian, but not
> necessarily a Hessian)?  I'd be content to run
> under either Windows or Linux.
> 
> Thank you,
> David Anick PhD MD
> david.anick{at}rcn.com
> 

Look on Fionn Murtagh's web page:
http://astro.u-strasbg.fr/~fmurtagh/mda-sw/

at pca.f (Fortran) and pca.c (C).  He also has other multivariate
analysis s/w available there.

Bud Dodson

-- 
M. L. Dodson                                bdodson{at}scms.utmb.edu
409-772-2178                                FAX: 409-747-8608


From chemistry-request@ccl.net Tue May  3 11:25:03 2005
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Date: Tue, 03 May 2005 10:15:55 -0400
From: "William T. Winter" <wtwinter #%# syr.edu>
Organization: Cellulose Research Foundation@SUNY-ESF
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Subject: CCL:eigenvalues & eigenvectors
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David,
Have a look at LABPACK http://www.netlib.org/lapack/ and its precursor 
EISPACK http://www.netlib.org/eispack/.  The latter  was developed at 
Argonne  while the former is an OAk Ridge NL product that  incorporates 
Eispack equivalent routines and much more.  It also has its own search  
engine to help identify suitable subroutines. The program are written in 
Fortran 77
Bill Winter

David J Anick wrote:

> Dear CCL,
>  
> Does anyone have or know of freeware that can
> compute the eigenvalues and eigenvectors of a
> real symmetric matrix (e.g a Hessian, but not
> necessarily a Hessian)?  I'd be content to run
> under either Windows or Linux.
>  
> Thank you,
> David Anick PhD MD
> david.anick #%# rcn.com <mailto:david.anick #%# rcn.com>
>  


-- 
==============================================================
Prof. W.T.Winter                                       
                               Tel: 315-470-6876
SUNY-ESF                                                                
              FAX: 315-470-6856
Cellulose Research Institute                                             
          E-Mail:  wtwinter #%# syr.edu
121 E.C. Jahn 
Laboratory                                                         
http://www.esf.edu/cellulose
Syracuse, NY 13210

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David,<br>
Have a look at LABPACK <a href="http://www.netlib.org/lapack/">http://www.netlib.org/lapack/</a>
and its precursor EISPACK <a href="http://www.netlib.org/eispack/">http://www.netlib.org/eispack/</a>.&nbsp;
The latter&nbsp; was developed at Argonne&nbsp; while the former is an OAk Ridge
NL product that&nbsp; incorporates Eispack equivalent routines and much
more.&nbsp; It also has its own search&nbsp; engine to help identify suitable
subroutines. The program are written in Fortran 77 <br>
Bill Winter<br>
<br>
David J Anick wrote:
<blockquote cite="mid001201c54f43$c696c560$25d806d1 #%# cable.rcn.com"
 type="cite">
  <meta http-equiv="Context-Type"
 content="text/html; charset=iso-8859-1">
  <div> Dear CCL, </div>
  <div> &nbsp;</div>
  <div> Does anyone have or know of freeware that can </div>
  <div> compute the eigenvalues and eigenvectors of a </div>
  <div> real symmetric matrix (e.g&nbsp;a Hessian, but not </div>
  <div> necessarily a Hessian)?&nbsp; I'd be content to run </div>
  <div> under either Windows or Linux. </div>
  <div> &nbsp;</div>
  <div> Thank you, </div>
  <div> David Anick PhD MD </div>
  <div> <a href="mailto:david.anick #%# rcn.com">david.anick #%# rcn.com</a> </div>
  <div> &nbsp;</div>
</blockquote>
<br>
<div class="moz-signature">-- <br>
<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
<title>signature</title>
==============================================================<br>
Prof. W.T.Winter&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;
&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;
&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Tel: 315-470-6876<br>
SUNY-ESF&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
&nbsp; &nbsp; &nbsp; &nbsp; FAX: 315-470-6856<br>
Cellulose Research Institute&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;
&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;
&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; E-Mail:&nbsp; <a class="moz-txt-link-abbreviated" href="mailto:wtwinter #%# syr.edu">wtwinter #%# syr.edu</a><br>
121 E.C. Jahn
Laboratory&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
<a class="moz-txt-link-freetext" href="http://www.esf.edu/cellulose">http://www.esf.edu/cellulose</a><br>
Syracuse, NY 13210<br>
</div>
</body>
</html>

--------------090406000308040205020701--


From chemistry-request@ccl.net Tue May  3 11:11:53 2005
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Date: Tue, 03 May 2005 17:11:48 +0200
From: Andreas Klamt <klamt #%# cosmologic.de>
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To: "Jan, , Pedersen" <me #%# torleif.org>
Cc: chemistry #%# ccl.net
Subject: Re: CCL:W:glycine template isosters
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Dear Jan,

your request met us during the ot phase of the writing a paper on our 
novel COSMOsim tool for bioisoster similarity screening. We felt tempted 
to use it as a test case.

We have performed a search for compounds similar to Glycine using our 
latest tool: COSMOsim. In short terms, COSMOsim calculates 
intermolecular similarity based the sigma profiles of the target and 
probe molecules. The sigma profile represents the sigma shielding 
potential distribution of the molecular surface based on DFT-COSMO 
calculations. We have shown previously that all kinds of physicochemical 
and biopharmacological properties can be computed directly from such 
sigma profiles. We are currently preparing an article that describes the 
COSMOsim method in detail and its general application to bioisosterism. 
The compounds presented in the list attached are the most similar 
isosters of glycine which have approximately the same size and 
electronic surface properties.
You will find that some of the known isosteres for the carboxylic acid 
(tetrazole, phosphinic and boronic acids) and primary amine moieties 
(secondary amine, hydroxyl). Small variations in the molecular size are 
also accepted. Moreover, there are very interesting combinations thereof 
and the cyclic variants that are worth trying. Please note that the 
search could have benefitted from using the protein-bound conformation 
which here was not available to us. We hope that these results stimulate 
your research and would be happy to get feedback on the experimental 
results.

Please find the detailed results under
http://www.cosmologic.de/glycine_ccl.zip

Best regards

Andreas Klamt
Marttin Hornig
Michael Thormann (Morphochem AG)

 USmiles  	SMS similarity
 NCC(O)=O  	1
 NC(C)C(O)=O  	0.862
 O=C1NN=CC1  	0.853
 NCCC(O)=O  	0.827
 OC(C1NC1)=O  	0.821
 O=Cc1[nH]cnc1  	0.817
 OCn1cncn1  	0.813
 O=Cc1[nH]ccn1  	0.811
 OCNC=O  	0.805
 NCP(O)O  	0.804
 O=C1NC(=N)NC1  	0.804
 Oc1nn(ccc1)=O  	0.803
 CC(=N)NC#N  	0.798
 NC1CCONC1=O  	0.797
 CNCC(O)=O  	0.792
 NOCC(O)=O  	0.79
 ON=C(C)N  	0.789
 Cc1[nH]nnn1  	0.786
 O=C1NN=CC=C1  	0.784
 N=C2NC(=O)N1CC21  	0.784
 COC(=O)NN  	0.784
 OCC(O)=O  	0.783
 NCCOB(O)O  	0.78
 NOC(C)C(O)=O  	0.776
 O=C1NC(=O)C=C1  	0.772
 OCS(O)=O  	0.77
 CCC(N)C(O)=O  	0.77
 OC1C=CC(O1)=O  	0.768
 COCC(O)=O  	0.768
 OC(C1C=CCN1)=O  	0.766
 O=Cc1c[nH]nc1  	0.766
 O=Cc1c[nH]cn1  	0.766
 NCCB(O)O  	0.765
 OC1CNCCC1=O  	0.763
 OC1=COC=CC1=O  	0.762
 OCC(O)C=O  	0.762
 O=Cc1n[nH]cc1  	0.761
 NCC(F)C(O)=O  	0.761
 NC(C)(C)C(O)=O  	0.76
 OC(C1CCCN1)=O  	0.759
 Nc1nccnn1  	0.758
 NOCC#N  	0.758
 OC(=O)c1cncn1C  	0.758
 Oc1cnncn1  	0.757
 OCCC#N  	0.757
 OC1NC(=O)C=C1  	0.757
 FCC(=O)N  	0.757
 OC(C1OC1)=O  	0.756
 OC1=CC=COC1=O  	0.754
 CC(=O)C(=O)N  	0.754
 OC(=O)c1cscn1  	0.753
 NCC=CC(O)=O  	0.752
 CC1NCC(=O)N1O  	0.75



Jan, , Pedersen wrote:

>Greetings CCLers,
>
>A question to all of you.
>
>I am trying to list possible isosters of the aminoacid motif H2N-C(R)-COOH or of glycine if you wish that formulation. I am not interested in this from a polymer point of view, I am just trying to list species that would have similar properties (in a QM sense) as glycine or as the aminoacid backbone.
>
>I am looking at a receptor that binds a single aminoacid, and the main interactions are with the "backbone" H2N- and -COOH groups. So I am thinking about which other small functional groups may serve this purpose...
>
>Does any of you have any pointers to reviews on this subject or a list of possible isosters please join in the discussion.
>
>Thanks -- Jan
>
>
>
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