Simplified molecular input line entry specification

The simplified molecular input line entry specification or SMILES is a line notation for the chemical structure of molecules. It uses short series ASCII characters to represent structures. Most molecule editor computer programs can draw a two-dimensional diagram or a three-dimensional model of a molecule based on its SMILES code.

Arthur Weininger and David Weininger wrote the original SMILES specification in the late 1980s. It has since been modified and extended by others, including by Daylight Chemical Information Systems Inc. In 2007, the Blue Obelisk open-source chemistry community developed an open standard called "OpenSMILES".

In July 2006, the International Union of Pure and Applied Chemistry introduced the InChI as a standard line notation for representing chemical structures.  People think that it is easier for humans to understand SMILES than InChI. Some chemists argue that SMILES is better than InChI because many different software programs support it. SMILES also has theoretical (for example, graph theory) backing.

Conversion
SMILES can be converted back to 2-dimensional representations using Structure Diagram Generation algorithms. This conversion can sometimes be ambiguous. Because SMILES just says which atoms are connected without any information about the angles between chemical bonds, computer programs use energy minimization to convert SMILES to 3-dimensional representations. There are many downloadable and web-based conversion utilities.
Examples
Here are some examples of the SMILES for molecules:

MoleculeStructureSMILES FormulaDinitrogenN≡NN#NMethyl isocyanate (MIC)CH3–N=C=OCN=C=OCopper(II) sulfateCu2+ SO42-[Cu+2].[O-]S(=O)(=O)[O-]Œnanthotoxin (C17H22O2)180px|Molecular structure of œnanthotoxinCCC[C@@H](O)CC\C=C\C=C\C#CC#C\C=C\COPyrethrin II (C22H28O5)180px|Molecular structure of pyrethrin IICOC(=O)C(\C)=C\C1C(C)(C)[C@H]1C(=O)O[C@@H]2C(C)=C(C(=O)C2)CC=CC=CAflatoxin B1 (C17H12O6)130px|Molecular structure of aflatoxin B1O1C=C[C@H]([C@H]1O2)c3c2cc(OC)c4c3OC(=O)C5=C4CCC(=O)5Glucose (glucopyranose) (C6H12O6)140px|Molecular structure of glucopyranoseOC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)1Bergenin (cuscutin) (a resin) (C14H16O9)130px|Molecular structure of cuscutine (bergenin)OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H]2[C@@H]1c3c(O)c(OC)c(O)cc3C(=O)O2A pheromone of the Californian scale insect180px|(3Z,6R)-3-methyl-6-(prop-1-en-2-yl)deca-3,9-dien-1-yl acetateCC(=O)OCCC(/C)=C\C[C@H](C(C)=C)CCC=C2S,5R-Chalcogran: a pheromone of the bark beetle Pityogenes chalcographusIsolation of Pheromone Synergists of Bark Bettle, Pityogenes chalcographus, From Complex Insect-Plant Odors by Fractionation and Subtractive-Combination Bioassay130px|(2S,5R)-2-ethyl-1,6-dioxaspiro[4.4]nonane CC[C@H](O1)CC[C@@]12CCCO2Vanillin70px|Molecular structure of vanillinO=Cc1ccc(O)c(OC)c1Melatonin (C13H16N2O2)160px|Molecular structure of melatoninCC(=O)NCCC1=CNc2c1cc(OC)cc2Flavopereirin (C17H15N2)160px|Molecular structure of flavopereirinCCc(c1)ccc2[n+]1ccc3c2Nc4c3cccc4Nicotine (C10H14N2)80px|Molecular structure of nicotineCN1CCC[C@H]1c2cccnc2Alpha-thujone (C10H16O)100px|Molecular structure of thujoneCC(C)[C@@]12C[C@@H]1[C@@H](C)C(=O)C2Thiamin (C12H17N4OS+)(vitamine B1)150px|SMolecular structure of thiaminOCCc1c(C)[n+](=cs1)Cc2cnc(C)nc(N)2

References






Other websites
Specifications
 "SMILES - A Simplified Chemical Language"
 The OpenSMILES home page
 "SMARTS - SMILES Extension"
 Daylight SMILES tutorial
 Parsing SMILES
SMILES related software utilities
 NCI/CADD Chemical Identifier Resolver – resolves or generates SMILES from chemical names, CAS Registry Numbers, InChI/InChIKey and many other chemical structure file formats
 NCI/CADD Online SMILES Translator and Structure File Generator  – Java online molecule editor
 PubChem server side structure editor – online molecule editor 
  smi23d  – 3D Coordinate Generation
 Daylight Depict  – Translate a SMILES formula into graphics
 GIF/PNG-Creator for 2D Plots of Chemical Structures 
 JME molecule editor  
 ACD/ChemSketch  
 Marvin  by ChemAxon – online chemical editor/viewer and SMILES generator/converter
 Instant JChem  by ChemAxon – desktop application for storing/generating/converting/visualizing/searching SMILES structures, particularly batch processing; personal edition free
 JChem for Excel  by ChemAxon – MS Excel add-in for storing/generating/converting/visualizing/searching SMILES structures
 Smormo-Ed – a molecule editor for Linux which can read and write SMILES
 InChI.info – an unofficial InChI website featuring on-line converter from InChI and SMILES to molecular drawings
 Balloon  – A free program for 3D coordinate generation and conformational analysis.
 Indigo  – an open-source cross-platform cheminformatics library with a plugin for IUPAC-compliant molecule and reaction 2D structural formula rendering.
 Open Babel – an open-source chemical toolbox allowing anyone to search, convert, analyze, or store biochemical data.
 Bioclipse  – a free and open source workbench for the life sciences
 MolEngine  – A .NET cheminformatics toolkit to read/write SMILES, generate 2D coordinate from SMILES, and convert SMILES from/into other Chemical file formats.
 JSDraw  – A cross-platform javascript chemical structure editor to generate SMILES and SMARTS.

Category:Chemical nomenclature
Category:Cheminformatics