#187 Radical curly arrows

closed
5
2011-03-09
2011-03-08
No

We have had 3D curly arrows for "normal" two-electron reactions for some time and they work well.
http://chemapps.stolaf.edu/jmol/docs/examples-11/draw.htm

I notice that there has been almost no discussion on this list about radical reactions that involve unpaired electrons and are conventionally represented by curly arrows with half a head sometimes called fishhook arrows.
http://chemistry2.csudh.edu/rpendarvis/Radicals.html#homolyt

We are working on representing radical reactions and would like to be able to show the mechanisms in 3D with fishhook curly arrows. Could this be done in Jmol ?

Discussion

  • Bob Hanson

    Bob Hanson - 2011-03-08

    Try to think of a nifty way to do this in 3D. Remember that that head could be pointing straight at the user, or perpendicular to the screen, or straight away. What would work for that?

     
  • Nick Greeves

    Nick Greeves - 2011-03-09

    I don't think the view when the arrow is pointing directly at the viewer of directly away is critical. The current curly arrows don't look that clever from those directions. But that is OK as the user will simply rotate to see the full story.

    I think for the radical arrows having half a cone and always the "top" if the arrow is mainly horizontal at the end or the "right" if it is mainly vertical.

    Or maybe a translucent cone for single electrons and an opaque one for pairs. Or a differently coloured cone. Either might work well and be easy to implement. One might argue that the translucent idea is also in keeping with the lower weighting of the representation - fishhook v double headed

     
  • Nick Greeves

    Nick Greeves - 2011-03-09
    • status: open --> closed
     
  • Nick Greeves

    Nick Greeves - 2011-03-09

    Fantastic Bob, many thanks

     

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