The `.' (period or "dot") is used in SMILES to represent disconnections. In terms of the valence model being represented, the dot literally represents a bond of formal order zero: the atoms on either side of the dot are explicitly not bonded to each other.
In practice, one can just write individual structures separated by a dot. The order in which ions or ligands are listed is arbitrary. There is no implied pairing of one charge with another, nor is it neccessary to have a net zero charge.
The semantics of the SMILES "dot" notation are defined in terms of the
molecular graph of the valence model (like everything else in SMILES).
It is often a surpise to SMILES-parser implementers that
is a valid synonym for
Because bonds can be specified with "ring closures",
not all SMILES which contain dots are disconnected
nor are all SMILES which contain ring closures cyclic.
C1.O2.C12 is a valid SMILES for ethanol.
|[Na+].[Cl-]||sodium chloride||The "dot" typically specifies a disconnection.|
|sodium phenoxide||Note that the "dot" is a "non-bond". It's not as simple as just <smiles>.<smiles>.|
|ethanol||Perverse, but correct.|