Simplified molecular-input line-entry system

Simplified Molecular-Input Line-Entry System (SMILES) is a notation that allows a user to represent a chemical structure in a way that can be used by the computer. It is a method of encoding molecular structures into a line of text. The SMILES notation is widely used in chemistry and bioinformatics for its simplicity and the ease with which it can be converted into other forms of representation or used for calculations.

Overview

SMILES strings can represent both organic and inorganic molecules, and they are composed of a series of characters including letters, numbers, and symbols that represent atoms, bonds, and other features of the molecule. The notation is designed to be readable by both humans and machines, making it a versatile tool in the field of computational chemistry.

Syntax and Features

The syntax of SMILES is designed to be compact and expressive. Atoms are represented by their chemical symbols, with hydrogen atoms usually omitted for simplicity. Bonds between atoms are represented by symbols such as '-' for a single bond, '=' for a double bond, '#' for a triple bond, and '.' for disconnected structures. Rings are denoted by using numbers to connect the opening and closing atoms of the ring.

Branching is handled by parentheses, and stereochemistry can be represented using the '@' symbol for chiral centers. The SMILES notation also supports the representation of isotopes, charged species, and radicals.

Applications

SMILES notation is used in various applications within chemical and pharmaceutical research. It is a standard format for the exchange of molecular information in databases and among different software tools. SMILES strings are used in cheminformatics for searching chemical databases, drug design, and the prediction of chemical properties and activities.

Advantages and Limitations

One of the main advantages of SMILES is its simplicity and ease of use, which allows for the efficient storage and sharing of molecular information. However, the notation has limitations, including the potential for ambiguity in the representation of certain molecular structures. There are also multiple ways to represent the same molecule, which can complicate database searches and comparisons.

Extensions and Alternatives

To address some of the limitations of SMILES, extensions and alternative notations have been developed. These include Extended SMILES (SMILES Arbitrary Target Specification, or SMARTS), which allows for more complex queries of chemical databases, and Simplified Chemical Language (SCL), which aims to provide a more human-readable alternative. Another notable alternative is the International Chemical Identifier (InChI), which provides a unique and non-ambiguous way to represent chemical substances.

Conclusion

SMILES notation is a powerful tool in the field of computational chemistry, offering a simple yet effective way to represent and manipulate molecular structures. Despite its limitations, it remains a widely used standard in chemical and pharmaceutical research, facilitating the exchange of information and the development of new computational methods and applications.