Selected Fragment Notations

Notations For Selected Fragments

Most users who are new to writing SMILES notations have trouble coding certain chemical fragments. The following list should be useful:

Nitro:    N(=O)(=O)  or  N(=O)=O  or T

     eg: nitroethane -->  CCN(=O)=O   or    CCT

Nitrate:  ON(=O)(=O)  or  ON(=O)=O

     eg: ethyl nitrate -->  CCON(=O)=O

Nitrite:  ON(=O)  or  ON=O

     eg: propyl nitrite -->  CCCON(=O)

Sulfonic acid:   S(=O)(=O)O

     eg: benzenesulfonic acid -->  c1ccccc1S(=O)(=O)O

Cyanide: C#N    eg: methyl cyanide -->  CC#N

Azide:  N=N#N   eg: methyl azide -->  CN=N#N

Azido as [N+]=[N-]   --->   N#N

**** The nitro function (NO2) is usually written as  N(=O)(=O)  or  N(=O)=O  in SMILES notation.  In this program version, the nitro function can also be designated (simply) by the capital letter  T ... this is an exclusive feature of the EPI Suite SMILES interpreter.