From owner-chemistry@ccl.net Sun Jul 17 12:34:00 2005
From: "CCL" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL: W:SMILES AND MODELLING
Message-Id: <-28899-050715085834-19638-gJKokDZHWSap5rm98+rrIw{:}server.ccl.net>
X-Original-From: "Antonio  Starcevic" <astar{:}pbf.hr>


Sent to CCL by: "Antonio  Starcevic" <astar{:}pbf.hr>
Dear All;

We are a academic group working on a bioinformatics application written in Java, that involves certain chemistry solutions. That's the part we need some help solving. We are storing our molecules in SMILES format, and at the end our goal is to turn linear structures into cyclisized. 

FIRST QUESTION: are SMILES the best choice for database entries and computation   
of new structres???

SECOND QUESTION: if you model spontaneous cyclization from a linear compound, how can you determine which product out of all possible ones is most likely to be the real thing

THIRD QUESTION: is there a software that can help us solve "second question", and could you recomend us some(it should cooperate with SMILES "Daylight toolkit" if possible)

P.S. are there any Java libraries for this stuff???

Thanks for all suggestions!


From owner-chemistry@ccl.net Sun Jul 17 17:35:01 2005
From: "CCL" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL: W:Calculation of the electrost potential of a single surface in a crysta
Message-Id: <-28900-050717173059-26890-gJKokDZHWSap5rm98+rrIw]*[server.ccl.net>
X-Original-From: "Adrian  Villegas" <adriano]*[eps.mcgill.ca>


Sent to CCL by: "Adrian  Villegas" <adriano]*[eps.mcgill.ca>
Hey folks,
Has any of you calculated the electrostatic potential using (Gaussian 03)
for a particular face of a crystal?
I assume that I have to define a specific grid for that particular face
in order to distinguish it from the overall electrostatic potential estimated for the entire molecule.
How should I do this?

Thanks a lot

Adrian Villegas