Dear users,
while constructing a complex, would you prefer the addition of \ce{F^-}, \ce{Cl^-}, \ce{Br^-}, or \ce{I^-} anions to a complex via
Doesn’t @Thomas 's option of “the drawing tool” imply adding the ability to select the formal charge of the atom(/ion) to be added via the Draw Tool’s pane?
Otherwise it would be just adding a chlorine, surely?
But perhaps I misunderstood the question.
For now, drawing a complex with the complex tool allows to pick a central atom with an adjustable charge and coordination geometry. The subsequent addition of e.g., a chlorine by the drawing tool currently adds these ligands as neutral; i.e. the subsequent export as a SMILES then yields [Ni+4](Cl)(Cl)(Cl)Cl instead of a [Cl-][Ni+4]([Cl-])([Cl-])[Cl-] to retain chloride’s negative charge while building the tetrachloronickelate anion. An example I found on Wikipedia is tetraethylammonium tetrachloronickelate, which in the article’s property pox is described by the SMILES string CC[N+](CC)(CC)CC.CC[N+](CC)(CC)CC.Cl[Ni]([Cl-])([Cl-])Cl which is the same as the one “[c]omputed by OEChem 2.3.0” on PubChem.
Hence the addition of chloride as a chlorido ligand via a .json with an explicit charge on the atom (line 20, file below) and the ligand as such (line 38) appears to me as a suitable approach
{
"atoms": {
"coords": {
"3d": [
5.485189,
0.088312,
0.013203,
3.285018,
0.088312,
0.013203
]
},
"elements": {
"number": [
17,
0
]
},
"formalCharges": [
-1,
0
]
},
"bonds": {
"connections": {
"index": [
1,
0
]
},
"order": [
1
]
},
"chemicalJson": 1,
"properties": {
"name": "chlorido",
"totalCharge": -1,
"totalSpinMultiplicity": 1
}
}
Edit: By today, the simultaneous addition of (atom and charge) appears to me this much as the better approach to build a complex that I changed my previous vote. Instead of “sometimes so, sometimes the other”, I’m now in favor of the addition via the ligand tool. But I’m biased because of a PR which includes this approach.