Simplified molecular-input line-entry system(SMILES)
For further inquiry..
- is a specification in form of a line notation for describing the structure of chemical molecules using short ASCII strings
- SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules
Graph-based definition
The chemical graph is first trimmed to remove hydrogen atoms and cycles are broken to turn it into a spanning tree. Where cycles have been broken, numeric suffix labels are included to indicate the connected nodes
Atoms
An atom holding one or more electrical charges is enclosed in brackets, followed by the symbol H if it is bonded to one or more atoms of hydrogen, followed by the number of hydrogen atoms (as usual one is omitted example: NH4 for ammonium), then by the sign '+' for a positive charge or by '-' for a negative charge. The number of charges is specified after the sign (except if there is one only); however, it is also possible write the sign as many times as the ion has charges: instead of "Ti+4", one can also write "Ti++++" (Titanium IV, Ti4+). Thus, the hydroxide anion is represented by [OH-], the oxonium cation is [OH3+] and the cobalt III cation (Co3+) is either [Co+3] or [Co+++].
Bonds
Bonds between aliphatic atoms are assumed to be single unless specified otherwise and are implied by adjacency in the SMILES string. For example the SMILES for ethanol can be written as CCO. Ring closure labels are used to indicate connectivity between non-adjacent atoms in the SMILES string, which for cyclohexane and dioxane can be written as C1CCCCC1 and O1CCOCC1 respectively. For a second ring, the label will be 2 (naphthalene: c1cccc2c1cccc2 (note the lower case for aromatic compounds)), and so on. After reaching 9, the label must be preceded by a '%', in order to differentiate it from two different labels bonded to the same atom (~C12~ will mean the atom of carbon holds the ring closure labels 1 and 2, whereas ~C%12~ will indicate one label only, 12). Double, triple, and quadruple bonds are represented by the symbols '=', '#', and '$' respectively as illustrated by the SMILES O=C=O (carbon dioxide), C#N (hydrogen cyanide) and [Ga-]$[As+] (gallium arsenide).
Branching
Branches are described with parentheses, as in CCC(=O)O for propionic acid and C(F)(F)F for fluoroform. Substituted rings can be written with the branching point in the ring as illustrated by the SMILES COc(c1)cccc1C#N (see depiction) and COc(cc1)ccc1C#N (see depiction) which encode the 3 and 4-cyanoanisole isomers. Writing SMILES for substituted rings in this way can make them more human-readable.
Isotopes
Isotopes are specified with a number equal to the integer isotopic mass preceding the atomic symbol. Benzene in which one atom is carbon-14 is written as [14c]1ccccc1 and deuterochloroform is [2H]C(Cl)(Cl)Cl.
| Molecule | Structure | SMILES Formula |
|---|---|---|
| Dinitrogen | N≡N | N#N |
| Methyl isocyanate (MIC) | CH3–N=C=O | CN=C=O |
| Copper(II) sulfate | Cu2+ SO42- | [Cu+2].[O-]S(=O)(=O)[O-] |
| Œnanthotoxin (C17H22O2) |  | CCC[C@@H](O)CC\C=C\C=C\C#CC#C\C=C\CO |
| Pyrethrin II (C22H28O5) |  | COC(=O)C(\C)=C\C1C(C)(C)[C@H]1C(=O)O[C@@H]2C(C)=C(C(=O)C2)CC=CC=C |
| Aflatoxin B1 (C17H12O6) |  | O1C=C[C@H]([C@H]1O2)c3c2cc(OC)c4c3OC(=O)C5=C4CCC(=O)5 |
| Glucose (glucopyranose) (C6H12O6) |  | OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)1 |
| Bergenin (cuscutin) (a resin) (C14H16O9) |  | OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H]2[C@@H]1c3c(O)c(OC)c(O)cc3C(=O)O2 |
| A pheromone of the Californian scale insect |  | CC(=O)OCCC(/C)=C\C[C@H](C(C)=C)CCC=C |
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