Tuesday, 14 April 2009

Are you on my side or not? It's E/Z

Handling cis/trans stereochemistry with SMILES should be easy, right? You have the canonical examples for trans:
A. I/C=C/Cl
(I is down, Cl is up)
B. I\C=C\Cl
(I is up, Cl is down)
and cis:
C. I/C=C\Cl (both are down)
D. I\C=C/Cl (both are up)
The "/" or "\" symbols should be chosen based on whether the substituent occurs before or after the atom attached to the double-bond. Bearing this in mind, the following represents the same trans structure as A:
E. C(=C/Cl)\I
Note that the effect of moving the "I" from one side of the "C" to the other (that is, A vs E) causes the bond symbol to change.

When ring closures occur on the double bond, a further complication arises as the stereobond appears twice, once at each end of the ring closure. The symbol indicating the stereochemistry should only appear at the end on the double bond:
F. I/C=C\1/CCCN1
Of course, where two substituents are shown explicitly at one end of a double bond, it's not necessary to show the stereochemisty for both of the bonds (although it makes things clearer). That is, the following two representations are identical to F:

Image credit: suttonhoo