importing H gives radical

If I import the SMILES fragment H or [H] into a Molecule object, the atom in the resulting molecule has its radical flag turned on. (This is relatively new behavior.) The same is not true if I import Br or C, for example. Is there any other fragment that, when imported, has a radical flag automatically tuned on?

Hi,

 

Importing a H as SMILES leads to a H atom for me.

Importing a [H] puts a radical on the atom, but so does [Br] too, because the number of implicit H atoms is restricted in this case.

 

BRs

Peter

Hi Bob,

The '[ ]' brackets in SMILES means that the number of attached Hydrogen atoms is exactly specified after the atom, in this case we add radicals to correct the valence of the atom (since we are not allowed to add implicit Hydrogen  atoms). In the case of H or Br atoms we have to add one radical to correct the valence. Or, for example, in case of [CH2] we add two radicals, in case of [CH3] we add one radical. In case of [C] the valence can not be corrected by adding four radicals, thus here we set the valence property of the atom to 0.

If the atom is not in  '[ ]' brackets then the correct valence is achieved by adding implicit H atoms (except the standalone H atom where no other H, or radical or any other property is added, instead valence error is indicated).

Please refer to https://docs.chemaxon.com/display/FF/SMILES for further details about other atom types.

Best regards,

Zsuzsa