View source for SMILES (Simplified Molecular Input Line Entry System)

== Introduction ==

The Simplified Molecular Input Line Entry System (SMILES) is a specification in the field of [[chemoinformatics]] used for describing the structure of chemical species using short ASCII strings. Developed in the 1980s, SMILES provides a way to encode molecular structures in a compact and human-readable form, facilitating the storage, retrieval, and manipulation of chemical information in databases and computational systems. It has become an essential tool in [[computational chemistry]], [[bioinformatics]], and [[pharmaceutical research]].

== History ==

SMILES was developed by Arthur Weininger and David Weininger in the late 1980s as part of their work at the company Daylight Chemical Information Systems. The system was designed to overcome the limitations of existing chemical notation systems, such as [[InChI]] and [[International Chemical Identifier|IUPAC]] names, which were often cumbersome and not easily machine-readable. The introduction of SMILES marked a significant advancement in the field of chemical informatics, providing a more efficient and versatile means of encoding molecular structures.

== SMILES Notation ==

SMILES notation is based on a series of rules that allow the representation of molecules as linear strings. These rules include:

=== Atoms ===

Atoms are represented by their chemical symbols. For example, carbon is denoted as 'C', oxygen as 'O', and nitrogen as 'N'. Hydrogen atoms are typically omitted unless they are explicitly needed to define the structure, such as in the case of charged species or isotopes.

=== Bonds ===

Bonds between atoms are indicated using specific characters: single bonds are usually implicit, double bonds are represented by '=', triple bonds by '#', and aromatic bonds by ':'.

=== Branches ===

Branches in the molecular structure are denoted using parentheses. This allows for the representation of complex branching structures in a linear format.

=== Rings ===

Rings are indicated by numbers that denote the start and end of the ring closure. For example, cyclohexane can be represented as 'C1CCCCC1'.

=== Chirality ===

Chirality is specified using the '@' symbol, which indicates the stereochemistry of chiral centers. This allows for the distinction between enantiomers in a concise manner.

== Applications ==

SMILES is widely used in various applications, including:

=== Chemical Databases ===

SMILES is a standard format for storing and retrieving molecular structures in chemical databases. Its compact nature allows for efficient storage and rapid searching of large datasets.

=== Drug Discovery ===

In [[drug discovery]], SMILES is used to encode and manipulate potential drug candidates. It facilitates the virtual screening of compounds and the prediction of their properties using [[quantitative structure-activity relationship|QSAR]] models.

=== Molecular Modeling ===

SMILES strings are often used as input for molecular modeling software, enabling the simulation of molecular interactions and the prediction of physical and chemical properties.

=== Bioinformatics ===

In [[bioinformatics]], SMILES is used to represent small molecules and ligands in protein-ligand interaction studies. It aids in the analysis of metabolic pathways and the identification of potential drug targets.

<div class='only_on_desktop image-preview'><div class='image-preview-loader'></div></div><div class='only_on_mobile image-preview'><div class='image-preview-loader'></div></div>

== Advantages and Limitations ==

=== Advantages ===

SMILES offers several advantages over other chemical notation systems:

* **Compactness**: SMILES strings are typically shorter and more concise than other representations, making them ideal for database storage.
* **Readability**: The linear format of SMILES is relatively easy to read and interpret, even for those with basic chemical knowledge.
* **Versatility**: SMILES can represent a wide range of chemical structures, including complex organic molecules, inorganic compounds, and polymers.

=== Limitations ===

Despite its advantages, SMILES has some limitations:

* **Ambiguity**: SMILES strings can sometimes be ambiguous, especially when representing complex stereochemistry or tautomers.
* **Lack of Standardization**: Different software tools may interpret SMILES strings differently, leading to inconsistencies in structure representation.
* **Complexity**: For very large or highly branched molecules, SMILES strings can become unwieldy and difficult to manage.

== Extensions and Variants ==

Several extensions and variants of SMILES have been developed to address its limitations and expand its capabilities:

=== SMARTS ===

SMARTS (SMILES Arbitrary Target Specification) is an extension of SMILES that allows for the specification of substructure patterns. It is widely used in [[chemical informatics]] for searching and matching molecular patterns within databases.

=== SMIRKS ===

SMIRKS is another extension that facilitates the representation of chemical reactions. It enables the encoding of reaction transformations in a format similar to SMILES, allowing for the automated processing of chemical reactions.

=== Isomeric SMILES ===

Isomeric SMILES is a variant that includes additional information about stereochemistry and isotopic composition. This allows for the unambiguous representation of stereoisomers and isotopologues.

== SMILES and Other Notation Systems ==

SMILES is one of several chemical notation systems used in chemoinformatics. Other notable systems include:

=== InChI ===

The [[International Chemical Identifier (InChI)]] is a non-proprietary identifier developed by IUPAC. It provides a standardized way to encode molecular structures and is widely used in scientific publications and databases.

=== CML ===

[[Chemical Markup Language (CML)]] is an XML-based format for representing chemical structures and data. It is designed to facilitate the exchange of chemical information between different software applications and databases.

=== MOLfile ===

The [[MOLfile]] format is a widely used file format for representing molecular structures in 2D or 3D. It is commonly used in cheminformatics software and databases.

== See Also ==

* [[Chemoinformatics]]
* [[Computational Chemistry]]
* [[Drug Discovery]]

== References ==

[References would be listed here if available.]

[[Category:Chemical Notation Systems]]
[[Category:Chemoinformatics]]
[[Category:Computational Chemistry]]