Simplified Molecular Input Line Entry System: Difference between revisions

Revision as of 14:27, 25 April 2023

Revision as of 10:57, 29 April 2023

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The '''simplified molecular-input line-entry system''' ('''SMILES''') is a specification in the form of a [[line notation]] for describing the structure of [[chemical species]] using short [[ASCII]] [[string (computer science)|strings]]. SMILES strings can be imported by most [[molecule editor]]s for conversion back into [[two-dimensional]] drawings or [[dimension|three-dimensional]] models of the molecules.

The original SMILES specification was initiated in the 1980s. It has since been modified and extended. In 2007, an [[open standard]] called OpenSMILES was developed in the [[Open source|open source]] chemistry community.

==History==

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An additional type of bond is a "non-bond", indicated with <code>.</code>, to indicate that two parts are not bonded together. For example, aqueous [[sodium chloride]] may be written as <code>[Na+].[Cl-]</code> to show the dissociation.

An aromatic "one and a half" bond may be indicated with <code>:</code>; see {{slinksection link||Aromaticity}} below.

Single bonds adjacent to double bonds may be represented using <code>/</code> or <code>\</code> to indicate stereochemical configuration; see {{slinksection link||Stereochemistry}} below.

===Rings===

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Branches may be written in any order. For example, [[bromochlorodifluoromethane]] may be written as <code>FC(Br)(Cl)F</code>, <code>BrC(F)(F)Cl</code>, <code>C(F)(Cl)(F)Br</code>, or the like. Generally, a SMILES form is easiest to read if the simpler branch comes first, with the final, unparenthesized portion being the most complex. The only caveats to such rearrangements are:

* If ring numbers are reused, they are paired according to their order of appearance in the SMILES string. Some adjustments may be required to preserve the correct pairing.

* If stereochemistry is specified, adjustments must be made; see {{slinksection link|Stereochemistry}} below.

The one form of branch which does ''not'' require parentheses are ring-closing bonds. Choosing ring-closing bonds appropriately can reduce the number of parentheses required. For example, [[toluene]] is normally written as <code>Cc1ccccc1</code> or <code>c1ccccc1C</code>, avoiding the parentheses required if written as <code>c1cc(C)ccc1</code> or <code>c1cc(ccc1)C</code>.