E/Z isomers (cis/trans isomers) are encoded with CurlySMILES using the curly codes {E} and {Z}, which are applied to pairs of atoms that are connected by a double bond. The anchor atom for a curly code of this type is always that atom of the pair that comes second in the overall notation—reading from left to right. The following example illustrates this for the two 1,2-dichloroethene stereoisomers:
load gif/E_C2H2Cl2.gif load gif/Z_C2H2Cl2.gif
ClC=C{E}Cl ClC=C{Z}Cl
(E)-1,2-dichloroethene (Z)-1,2-dichloroethene
Notice that the stereodescriptors E and Z are assigned according to the IUPAC sequencing rules for substituents and not according to cis or trans position of substituents of the same kind (see, for example, page 74 in [1] or page 187 in [2]). For example, the 1,2-dibromo-1-chloro-2-iodoethene molecule with cis positioning of the two bromo atoms is the E isomer and the molecule with trans Br-atoms is the Z isomer:
load gif/E_C2Br2ClI.gif load gif/Z_C2Br2ClI.gif
BrC(I)=C{E}(Br)Cl BrC(I)=C{Z}(Br)Cl
(E)-1,2-dibromo-1-chloro-2-iodoethene (Z)-1,2-dibromo-1-chloro-2-iodoethene
Stereoisomers, in which one or both double-bond atoms are heteroatoms, are similarly designated via IUPAC rules and accordingly encoded with CurlySMILES, as shown for piperonal (E)-oxime (traditionally named piperonal syn-oxime) and 3,5,5-trimethylcyclohex-2-ene (Z)-oxime:
load gif/piperonalEoxime.gif load gif/triMeCycHexenoneZoxime.gif
ON=C{E}c1cc2OCOc2c1 C1=C(C)CC(C)(C)CC1=N{Z}O
piperonal (E)-oxime 3,5,5-trimethylcyclohex-2-enone (Z)-oxime
_ __ __ submit to reddit __

__ Share on Tumblr ___ bookmark this page


[1] B. Testa: Principles of organic stereochemistry.
Marcel Dekker, New York and Basel, 1979.
[2] D. Hellwinkel: 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 .

Custom Search