|
A stereodescriptive annotation consisists of a one-character
stereodescriptor
(SD). Stereodescriptive
annotations are atom-anchored.
The stereodescriptors are:
-
R and S
to mark a stereogenic atom of a chiral molecule based on
absolute configuration,
-
D and L
to mark a stereogenic atom of a chiral molecule
based on relative configuration,
-
E and Z
to denote cis/trans isomerism in reference
to a double bond.
The following table provides a more detailed overview of
these descriptors with links to pages that demonstrate their
use in encoding stereoisomers.
| SD |
Use in CurlySMILES notations |
| D |
To mark a stereogenic atom of a chiral molecule in
reference to the configuration of the
D-(+)-glyceraldehyde enantiomer
(see examples: D/L-enantiomers)
Anchor atom:
stereogenic atom
|
| E |
To mark a stereoisomer with vicinal substituents at a
double bond when the two vicinal substituents with highest
seniority, according to the sequence rules by Cahn,
Ingold, and Prelog, exhibit trans arrangement
(see examples: cis/trans-isomers)
Anchor atom:
double-bond atom that comes second in notation
|
| L |
To mark a stereogenic atom of a chiral molecule in
reference to the configuration of the
L-(-)-glyceraldehyde enantiomer
(see examples: D/L-enantiomers)
Anchor atom:
stereogenic atom
|
| R |
To mark a stereogenic atom of a chiral molecule based on
on the sequence rules by Cahn, Ingold, and Prelog
(see examples: R/S-enantiomers)
Anchor atom:
stereogenic atom
|
| S |
To mark a stereogenic atom of a chiral molecule based on
on the sequence rules by Cahn, Ingold, and Prelog
(see examples: R/S-enantiomers)
Anchor atom:
stereogenic atom
|
| Z |
To mark a stereoisomer with vicinal substituents at a
double bond when the two vicinal substituents with highest
seniority, according to the sequence rules by Cahn,
Ingold, and Prelog, exhibit cis arrangement
(see examples: cis/trans-isomers)
Anchor atom:
double-bond atom that comes second in notation
|
|
Suggested Readings and References
| [1] |
B. Testa:
Principles of organic stereochemistry.
Marcel Dekker,
New York and Basel,
1979.
|
| [1a] |
The R and S Nomenclature. pp. 50-53 in [1].
|
| [1b] |
The D and L Nomenclature. pp. 49-50 in [1].
|
| [1c] |
π Diastereoisomerism About Carbon-Carbon
Double Bonds. pp. 73-76 in [1].
|
| [2] |
D. Hellwinkel:
Section 6.7.1: cis/trans Isomersim; the E/Z Convention
in
Systematic Nomenclature of Organic Chemistry.
Springer-Verlag,
Berlin und Heidelberg, Germany,
2001.
|
| [3] |
A. Drefahl:
CurlySMILES: a chemical language
to customize and annotate encodings of molecular and
nanodevice structures
.
J. Cheminf.
2011, 3:1;
doi:
10.1186/1758-2946-3-1
.
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