cdk
Drawing a carbene with a lone pair of electrons instead of putting 2.
Hi, I am interested to draw the following carbene with a lone pair of electrons on atom 3. Is that possible in SMILES? Any help is appreciated.
You can and CDK Depict supports this, for instance by input of C#CC#C[C]C#N:
At least some molecule editors (ChemDraw, ChemDoodle, BioViaDraw, ChemSketch, ...) allow to mark and define a specific atom explicitly as mono or diradical (singulet/triplet). This affects the subsequent export as a text string (e.g., SMILES, InChI), and files like .sdf and .mol. The example about a NHC ligand indeed is inspired by a recent discussion about InChI.
Note e.g., CN1CCN(C)[CH-]1 defines an explicit negative charge and thus CDK Depict displays this differently.
I would like to draw as a carbene by putting a lone pair on Carbon atom. Putting 2. (numeral two period) symbol is not a very common way to depict carbenes. Because, they could be either singlets or triplets as you had mentioned. I am dealing with singlet carbenes and therefore I want to be specific. In OPSIN, I could generate such an image. However, the clarity of figures in OPSIN isn't that great. But, the clarity of figures generated by CDK Depict is excellent. I thought that by inserting lp:3:1 at position 3 on the following C(#N)[C]C#CC#C I would be able to get the image that I wanted. But, looks like that didn't happen here.
So the lp:3:1 needs to be at the end in CXSMILES, it will be read in but it will not show up in the depiction. It would be too hard to add because the data model is mostly/already there.
If we put it on the other way around then it has to be changed from lp:3:1 to lp:5:1. In any case, the image is not getting generated and therefore I would take no as an answer at the moment.