SMILES notation

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Assalamualaikum, today I'm will introduce you about SMILES application

Simplified molecular input line entry specification (SMILES)

it is a software describing the structure of chemical molecular using short ASCII strings. Smile strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules.

the image is the example of SMILES application.

Canonical SMILES and Isomeric SMILES

The term Canonical SMILES refers to the version of the SMILES specification that includes rules for ensuring that each distinct chemical molecule has a single unique SMILES representation

- A common application of Canonical SMILES is for indexing and ensuring uniqueness of molecules in a database

The term Isomeric SMILES refers to the version of the SMILES specification that includes extensions to support the specification of isotopes, chirality, and configuration about double bonds

- A notable feature of these rules is that they allow rigorous partial specification of chirality.

SMILES Bonds

SINGLE	-
DOUBLE	=
TRIPLE	#
AROMATIC	:

SMILES Branches

- Represented by enclosure in parentheses

- Can be nested or stacked

- Examples:

CC(O)CC is 2-Butanol

OCC(C)C is iso-Butanol

OC(C)(C)C is tert-Butanol

SMILES BONDS

Ethene	C=C
Chloroethene	ClC=C
1,1-Dichloroethene	ClC(Cl)=C
cis-1,2-Dichloroethene	ClC=CCl
Trichloroethene	ClC(Cl)=CCl
Perchloroethene	ClC(Cl)=C(Cl)Cl

Table below show some of molecular structures and its SMILES formula.

Application on some molecules

Molecule	Structure	SMILES Formula
Dinitrogen	N≡N	N#N
Methyl isocyanate (MIC)	CH₃–N=C=O	CN=C=O
Copper(II) sulfate	Cu²⁺ SO4^2-	[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
2S,5R-Chalcogran: a pheromone of the bark beetle Pityogenes chalcographus^[8]		CC[C@H](O1)CC[C@@]12CCCO2
Vanillin		O=Cc1ccc(O)c(OC)c1
Melatonin (C₁₃H₁₆N₂O₂)		CC(=O)NCCC1=CNc2c1cc(OC)cc2
Flavopereirin (C₁₇H₁₅N₂)		CCc(c1)ccc2[n+]1ccc3c2Nc4c3cccc4
Nicotine (C₁₀H₁₄N₂)		CN1CCC[C@H]1c2cccnc2
Alpha-thujone (C₁₀H₁₆O)		CC(C)[C@@]12C[C@@H]1[C@@H](C)C(=O)C2
Thiamin (C₁₂H₁₇N₄OS⁺) (vitamin B1)		OCCc1c(C)[n+](=cs1)Cc2cnc(C)nc(N)2