The Functional SMILES Perspective

Simplified Molecular-Input Line-Entry System or SMILES is a notation scheme for representing chemical structures in a single line of text, encoding atom connectivity and stereochemistry, as well as charge and ring structures. There are a large number of possible SMILES notations for any one chemical structure, which has led to the development of the canonical SMILES notation. In contrast, I describe here a SMILES approach or “perspective” which encodes functional groups into valid SMILES strings. It is shown that this functional SMILES perspective further simplifies the human interpretation of SMILES strings, can be easily formed from reading IUPAC nomenclature, and has the ability to encode limited chemical reaction histories.