I use Avogadro (the modified for ORCA version to be precise) a lot, both for computational chemistry and visualization. I really love it and in general it does everything that I need very well, but recently I have started working with big aromatic systems featuring very delocalized bonds ; while for the comp-chem side it does not change anything, I was wondering if there was a way/plugin to display delocalized bonds (dotted-lines or similar) for visualization.
In any case, thank you for the great work (and have a nice weekend)
So, it would probably be something like that indeed, but possible to expand outside a “traditional” five/six-atoms aromatic ring. I am working with porphyrins, which have this very characteristic massive aromatic ring, and since it’s at the core of why I am working with them, I would really like to be able to display it a bit more “properly”, if that makes sense.
For this reason, what would really be best would be a “1.5” bond option with a single bond coupled with a dashed one of around the same thickness, instead of the kind of (sometimes dashed) circle people sometimes draw inside simple aromatic cycles.
EDIT: of course I would not expect such bonds to be compatible with the Molecular Mechanics modules, it would be purely for visualization on an already optimized structure.
I’m not sure what you refer to with “this very characteristic massive aromatic ring”. If simply trim off the inner of ChemDraw’s template about porphyrin (no peripheral decoration; no Zn, Cu or other metal complexation), aromaticity is absent:
to obtain a conformer from NIH’ servers followed by the user defined highlight of pyrrole structures which looks a little bit like the custom of colored rings by KC Nicolau & co-authors in papers and classics in total synthesis
It could be that I forgot Avogadro has such a highlight option, but if not it might be an appealing thing after Avogadro 2.0.1 is shipped.
So, this is more or less off-topic anyway, but you missed the aromaticity because your trimming basically removed it entirely. For an overview of what’s going on in systems with a porphin core, this image is a good representation: