CurlySMILES encoding of R/S-enantiomers

Axel Drefahl •
The R and S stereodescriptors are IUPAC-approved designations of absolute configuration at four-coordinate (quadriligant) and six-coordinate (sexiligant) stereogenic centers [1]. In CurlySMILES an R/S enantiomer is encoded by anchoring the corresponding curly codes {R} and {S} at stereogenic centers of a chiral molecule. The following examples illustrates this for two chiral molecules (presented as Fischer projections) with one asymmetric C-atom:
load gif/R_CHBrClF.gif load gif/S_C4H8_35Cl_37Cl.gif
ClC{R}(Br)F CC{S}([35Cl])([37Cl])CC
(R)-bromochlorofluoromethane (S)-2,2-di(37Cl,35Cl)chlorobutane
A molecules with multiple asymmetric atoms is encoded in the same way by anchoring the respective stereodescriptors at the stereogenic-center atoms:
load gif/C6H9BrClNO2_aaa.gif
CC{S}(Cl)C{R}(N(=O)=O)C{S}(Br)OC(C)=O
(1S,2R,3S)-1-bromo-3-chloro-2-nitrobutyl acetate
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References

[1] G. P. Moss (prepared recommondations for publication): Basic Terminology of Stereochemistry. Pure & Appl. Chem. 1996, 68 (12), pp. 2193-2222. pdf: www.iupac.org/publications/pac/1996/pdf/6812x2193.pdf .
[2] B. Testa: Principles of organic stereochemistry.
Marcel Dekker, New York and Basel, 1979.
[3] D. Hellwinkel: Systematic Nomenclature of Organic Chemistry.
Springer-Verlag, Berlin und Heidelberg, Germany, 2001.
[4] 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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