SMILES Tutorial: Disconnections

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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.

Advanced issues

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 c1cc([O-].[Na+])ccc1 is a valid synonym for [Na+].[O-]c1ccccc1.

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. Although perverse, C1.O2.C12 is a valid SMILES for ethanol.


Table 7. Dot disconnections in SMILES.
Depiction SMILES Name Remark
[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.

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