One of the recent features is the “template tool” which helps to assemble metal complexes and functional groups.
I’m building up a bigger library of ligands, but this also requires preview images. The auto-generation script (which uses RDKit) is … not great (to say the least) at handling multi-dentate ligands.
I could use some help re-drawing some of the following, (And if you have ideas for other common ligands, please add some comments below.)
The example of triphos appears very busy, leaning to too crowded to provide an iconic preview. I forgot if there is a way to let RDKit condense groups commonly seen as an abbreviation.
As an illustration, the open/unloaded chelate as depicted on Wikipedia:
though if it comes to a preview maybe an explicit Me on the methyl group, similar to the catalogue by STREM is safer:
CDK Depict shows an implementation. With the SMILES string of triphos as provided by said Wikipedia lemma’s property box
It exports the illustrations in either .svg, .png, or .pdf.
Does the preview need to depict a chelate with a cation enclosed and the dative bonds? Possibly easier to decide with a couple of examples with and without the red dot. A gentle highlight of the ligand’s atoms which eventually may engage in dative bonds (a bit like the fragment-based building of metal complexes elsewhere) might suffice.
Does the preview need to be a diagram of a somewhat geometry optimized structure? This is about example 4/cyclam, in comparison with the (unloaded) chelate shown on Wikipedia
or with its SMILES string N1CCNCCCNCCNCCC1 by CDK Depict (same parameters of generation as above):
Fine and sufficient if the 3D model eventually displayed on Avogadro’s canvas were a somewhat reasonable conformation to easily add, or modify the chelated cation. The crossing of cation nitrogen carbon in the Northeastern loop is not easy to scale to lower dimensions of a preview while retaining the desirable discern about how many atoms are there.
Yes. While I’m open to input, I showed a variety of examples to both colleagues and students here and showing the bonds to the metal site were clearly preferred. Ideally, I’d like to keep the depiction of the phenyl rings as well.
The unloaded triphos ligands, for example, dont’ show much in the way of “how does this ligand wrap a metal.”
Thanks for the cyclam. For whatever reason, I hadn’t tried the SMILES in ChemDraw and it’s generating a reasonable image:
Biased because being used to read “Ph” as “phenyl group”, a triphos formula like the one below were “iconic enough” for me (I attach the files in the archive attached) – both with Irfan View scaling to 20% on a non-retina display, as well as an icon in file browser Thunar, with about 60 by 60 pixels for the illustration it self (about 1.6 cm or approx 0.5").
It is not the red of red nose day… the first association I got with cyclam redrawn by you.
Because of the shortened US American version for the British original. But re the icons for Avogadro: if the drawing is easy discernible at distance/small dimension, then the icon is good.
