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SMILES

 

SMILES (Simplified Molecular Input Line Entry System) is a line notation (a typographical method using printable characters) for entering and representing molecules and reactions.

 

Here we present a brief introduction to the SMILES rules and some examples. If you like to know more about SMILES, please see Wikipedia and Daylight web site.

 

SMILES Specification Rules:

 

1. Atoms are represented by their atomic symbols.

2. Hydrogen atoms are omitted (are implicit).

3. Neighboring atoms are represented next to each other.

4. Double bonds are represented by ‘=‘, triple bonds by ‘#’.

5. Branches are represented by parentheses.

6. Rings are represented by allocating digits to the two connecting ring atoms.

7. Aromatic rings are indicated by lower-case letters.

 

Examples:

 

1.   Propan-1-ol (C3H8O), has the following unique SMILES representation: ‘CCCO‘, if you like to navigate the molecular structure please use the NavMol program and load the file ‘propan1ol.mol‘.

 

 

2.   3-Chloropent-1-ene (C5H9Cl), has the following unique SMILES representation: ‘CCC(Cl)C=C‘, if you like to navigate in the molecular structure please use the NavMol program and load the file ‘3chloropent1ene.mol‘.

 

3.   Cyclohexane (C6H12), has the following unique SMILES representation: ‘C1CCCCC1‘, if you like to navigate in the molecular structure please use the NavMol program and load the file ‘cyclohexane.mol‘.

 

4.   Aniline or phenylamine (C6H7N), has the following unique SMILES representation: ‘Nc1ccccc1‘, if you like to navigate in the molecular structure please use the NavMol program and load the file ‘aniline.mol‘.

 

 

SMILES strings can be imported by most molecular editors for conversion into two-dimensional drawings or three-dimensional models of the molecules. SMILES strings are easily converted into other chemical formats (e.g. MDL Molfile) with software such as molconvert (Marvin Beans from ChemAxon) or babel tool (OpenBabel).

 

 

 

 

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last update: 01.06.2010