Simplified Molecular Input Line Entry System: Difference between revisions

Revision as of 09:30, 13 January 2025

Revision as of 22:15, 16 May 2025

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| extended to =

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[[Image:SMILES.png|thumb|class=skin-invert-image|300px|SMILES generation algorithm for [[ciprofloxacin]]: break cycles, then write as branches off a main backbone]]

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.

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The Daylight and OpenEye algorithms for generating canonical SMILES differ in their treatment of aromaticity.

[[Image:3-cyanoanisole SMILES.svg|right|thumb|class=skin-invert-image|350px|Visualization of 3-cyanoanisole as <code>COc(c1)cccc1C#N</code>.]]

=== Branching ===

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=== Stereochemistry ===

{{See also|Skeletal formula}}[[File:Trans-1,2-difluoroethylene.svg|thumb|right|class=skin-invert-image|upright=0.5|''trans''-1,2-difluoroethylene]]

<!--[[File:Cis-1,2-difluoroethylene.svg|thumb|right|class=skin-invert-image|upright=0.5|''cis''-1,2-difluoroethylene]]-->

SMILES permits, but does not require, specification of [[stereoisomer]]s.

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Bond direction symbols always come in groups of at least two, of which the first is arbitrary. That is, <code>F\C=C\F</code> is the same as <code>F/C=C/F</code>. When alternating single-double bonds are present, the groups are larger than two, with the middle directional symbols being adjacent to two double bonds. For example, the common form of (2,4)-hexadiene is written <code>C/C=C/C=C/C</code>.

[[File:Beta-Carotene_conjugation.svg|thumb|right|class=skin-invert-image|upright=0.866|[[Beta-carotene]], with the eleven double bonds highlighted.]]

As a more complex example, [[beta-carotene]] has a very long backbone of alternating single and double bonds, which may be written <code>CC1CCC/C(C)=C1/C=C/C(C)=C/C=C/C(C)=C/C=C/C=C(C)/C=C/C=C(C)/C=C/C2=C(C)/CCCC2(C)C</code>.

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|-----

|[[Methyl isocyanate]] (MIC)

|[[File:Methyl isocyanate.svg|frameless|class=skin-invert-image]]

|<code>CN=C=O</code>

|-----

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|-----

|[[Vanillin]]

|[[Image:Vanillin.svg|class=skin-invert-image|70px|Molecular structure of vanillin]]

|<code>O=Cc1ccc(O)c(OC)c1</code><br/><code>COc1cc(C=O)ccc1O</code>

|-----

|[[Melatonin]] (C₁₃H₁₆N₂O₂)

|[[Image:Melatonin2.svg|class=skin-invert-image|160px|Molecular structure of melatonin]]

|<code>CC(=O)NCCC1=CNc2c1cc(OC)cc2</code><br/><code>CC(=O)NCCc1c[nH]c2ccc(OC)cc12</code>

|-----

|[[Flavopereirin]] (C₁₇H₁₅N₂)

|[[Image:Flavopereirine.svg|class=skin-invert-image|160px|Molecular structure of flavopereirin]]

|<code>CCc(c1)ccc2[n+]1ccc3c2[nH]c4c3cccc4</code><br/><code>CCc1c[n+]2ccc3c4ccccc4[nH]c3c2cc1</code>

|-----

|[[Nicotine]] (C₁₀H₁₄N₂)

|[[Image:Nicotine.svg|class=skin-invert-image|80px|Molecular structure of nicotine]]

|<code>CN1CCC[C@H]1c2cccnc2</code>

|-----

|[[Oenanthotoxin]] (C₁₇H₂₂O₂)

|[[Image:Oenanthotoxin-structure.png|class=skin-invert-image|180px|Molecular structure of oenanthotoxin]]

|<code>CCC[C@@H](O)CC\C=C\C=C\C#CC#C\C=C\CO</code><br/><code>CCC[C@@H](O)CC/C=C/C=C/C#CC#C/C=C/CO</code>

|-----

|[[Pyrethrin]] II (C₂₂H₂₈O₅)

|[[Image:Pyrethrin-II-2D-skeletal.svg|class=skin-invert-image|180px|Molecular structure of pyrethrin II]]

|<code>CC1=C(C(=O)C[C@@H]1OC(=O)[C@@H]2[C@H](C2(C)C)/C=C(\C)/C(=O)OC)C/C=C\C=C</code>

|-----

|[[Aflatoxin]] B₁ (C₁₇H₁₂O₆)

|[[Image:Aflatoxin B1.svg|class=skin-invert-image|130px|Molecular structure of aflatoxin B₁]]

|<code>O1C=C[C@H]([C@H]1O2)c3c2cc(OC)c4c3OC(=O)C5=C4CCC(=O)5</code>

|-----

|[[Glucose]] (β-<small>D</small>-glucopyranose) (C₆H₁₂O₆)

|[[Image:Beta-D-Glucose.svg|class=skin-invert-image|140px|Molecular structure of glucopyranose]]

|<code>OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)1</code>

|-----

|[[Bergenin]] (cuscutin, a [[resin]]) (C₁₄H₁₆O₉)

|[[Image:Cuscutine.svg|class=skin-invert-image|130px|Molecular structure of cuscutine (bergenin)]]

|<code>OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H]2[C@@H]1c3c(O)c(OC)c(O)cc3C(=O)O2</code>

|-----

|A [[pheromone]] of the Californian [[scale insect]]

|[[Image:Pheromone cochenille californienne.svg|class=skin-invert-image|180px|(3''Z'',6''R'')-3-methyl-6-(prop-1-en-2-yl)deca-3,9-dien-1-yl acetate]]

|<code>CC(=O)OCCC(/C)=C\C[C@H](C(C)=C)CCC=C</code>

|-----

|(2''S'',5''R'')-[[Chalcogran]]: a [[pheromone]] of the [[Scolytinae|bark beetle]] ''[[Pityogenes chalcographus]]''<ref>{{cite journal | vauthors = Byers JA, Birgersson G, Löfqvist J, Appelgren M, Bergström G | title = Isolation of pheromone synergists of bark beetle, Pityogenes chalcographus, from complex insect-plant odors by fractionation and subtractive-combination bioassay | journal = Journal of Chemical Ecology | volume = 16 | issue = 3 | pages = 861–876 | date = March 1990 | pmid = 24263601 | doi = 10.1007/BF01016496 | bibcode = 1990JCEco..16..861B | s2cid = 226090 }}</ref>

|[[Image:2S,5R-chalcogran-skeletal.svg|class=skin-invert-image|130px|(2''S'',5''R'')-2-ethyl-1,6-dioxaspiro[4.4]nonane]]

|<code>CC[C@H](O1)CC[C@@]12CCCO2</code>

|-----

|[[Thujone|α-Thujone]] (C₁₀H₁₆O)

|[[Image:Alpha-thujone.svg|class=skin-invert-image|100px|Molecular structure of thujone]]

|<code>CC(C)[C@@]12C[C@@H]1[C@@H](C)C(=O)C2</code>

|-----

|[[Thiamine]] (vitamin B₁, C₁₂H₁₇N₄OS⁺)

|[[Image:Thiamin.svg|class=skin-invert-image|150px|Molecular structure of thiamin]]

|<code>OCCc1c(C)[n+](cs1)Cc2cnc(C)nc2N</code>

|}

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To illustrate a molecule with more than 9 rings, consider [[cephalostatin]]-1,<ref name="PubChem-183413">{{cite web |title=CID 183413 |url=https://pubchem.ncbi.nlm.nih.gov/compound/183413 |website=[[PubChem]] |access-date=May 12, 2012 |language=en}}</ref> a steroidic 13-ringed [[pyrazine]] with the [[empirical formula]] C₅₄H₇₄N₂O₁₀ isolated from the [[Indian Ocean]] [[hemichordate]] ''[[Cephalodiscus gilchristi]]'':

{{Clear}}

:[[Image:Cephalostatine-1.svg|class=skin-invert-image|360px|Molecular structure of cephalostatin-1]]

Starting with the left-most methyl group in the figure: