From owner-chemistry@ccl.net Thu Apr 15 14:22:00 2010
From: "Michel Petitjean petitjean.chiral%%gmail.com" <owner-chemistry*o*server.ccl.net>
To: CCL
Subject: CCL: Smiles convention for stereoisomers ?
Message-Id: <-41667-100415133518-10151-l9dfurI4W3mgSAt2ug0olQ*o*server.ccl.net>
X-Original-From: Michel Petitjean <petitjean.chiral-*-gmail.com>
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Date: Thu, 15 Apr 2010 18:38:18 +0200
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Sent to CCL by: Michel Petitjean [petitjean.chiral_+_gmail.com]
Hi there,

Does anybody know about the exact convention to specify atoms
positions from a SMILES having stereocenters in rings ?
It seems there is a difference in treatment for ring closure and other atoms ?
For instance for C[C|,||,|H]1C[C|,||,|H](O)CC(=O)O1
For the second center, not a ring closure, we look from the CC bond,
and we have H,O,C clockwise.
For the first one how does one proceed ?
If one looks from first C to second C, then H, C, O should be
positioned clockwise, whereas actually it seems it is
countercloskwise.

Idem from the example on their site :
http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html

C[C|,|H]1CCCCO1
I could not understand the few sentences on SMILES theory related to
ring closure digit appearance.

Thanks by advance

Michel Petitjean.