Wednesday, 4 April 2012

Getting your double bonds in a twist - How to depict unspecified stereo

I've just been adding depiction support for double bonds with unspecified stereo, and thinking about how this should be done: a squiggly bond for a substituent on the double bond, or make the double bond itself twisted? Actually, I didn't have to think too much as Rich and others (also mcule) have already worked through these same issues. In short, the IUPAC recommendation (from 2006) is best avoided, and a twisted bond should be used instead.

So, here's the result after implementing the twisted bond:
obabel -:"Cl/C=C/Br" -:"Cl/C=C\Br" -:"ClC=CBr"
       -O tmp.svg -xr 1

...and with an asymmetric double bond for extra pizazz:
obabel -:"Cl/C=C/Br" -:"Cl/C=C\Br" -:"ClC=CBr"
       -O tmp.svg -xr 1 -xs

Credits: Twisted double bond by me. Everything else of depiction by Chris Morley and Tim Vandermeersch. Structure layout by Sergei Trepalin.

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