Disconnected & Isomeric SMILES

Disconnected, Isomeric and Chiral SMILES

Disconnected Structures

Disconnected compounds are designated as individual structures or ions separated by a period (“.”).  A common example of a simple disconnected structure is tetramethyl ammonium bromide; the SMILE could be:   C[N+](C)(C)C.[Br-].   The EPI Suite programs can not evaluate a disconnected SMILES string.  However, they can evaluate the structure if the disconnected parts are “connected” by attaching charged atoms.  Tetramethyl ammonium bromide can be evaluated if it is entered as:  CN(Br)(C)(C)C.  

The current versions of the EPI Suite programs will automatically convert some disconnected SMILES to a “non-disconnected” SMILES to enable the programs to evaluate the structure.  At present, the automatic conversion is limited to single, charged species such as the bromide, chloride, iodide, sodium, and potassium ions.  More complex disconnected SMILES require manual “connection”.  Examples of entered disconnected SMILES that work properly in EPI include:

 C[N+](CCCCCC)(C)C.[Cl-]

 CCCC(=O)[O-].[Na+]

 [K+].CCCCCC(=O)[O-]

Isomeric and Chiral SMILES

Isomeric configuration is specified by the “slash” characters “\” and “/”.  These symbols indicate the relative directionality between connected atoms.  Example SMILES for trans- and cis-1,2-dibromoethene could be:  Br/C=C/Br   and   Br/C=C\Br .   The current MS-Windows versions of the EPI Suite programs remove all “slashes” from SMILES notations since they are not used in any evaluation.

SMILES chirality is specified by the “@” symbol.  The current versions of the EPI Suite programs remove all “@” from SMILES notations since they are not used in any evaluation.