Simplified molecular-input line-entry specification (SMILES)

Basic characteristics and syntax

SMILES encodes molecules using letters for elements, symbols for bond types, and punctuation to indicate branching and ring closures. Atoms are written by their element symbols (for example, C, O, N). Single bonds are usually implicit, double bonds use "=", triple bonds use "#". Parentheses create branches off the main chain, and numeric labels indicate where a ring closes. Special notations represent charged atoms or isotopes, and stereochemistry can be indicated with markers such as "@". For an introduction to the idea of line notations used to represent molecular connectivity, see line notation. For basic chemical terminology, see chemical and for structure fundamentals, see structure.

Typical elements and examples

Simple examples show the notation's directness: ethanol can be written as CCO, benzene is c1ccccc1 (lowercase letters commonly denote aromatic atoms), and cyclohexane is C1CCCCC1. Branching appears in isopropanol as CC(O)C, while a charged molecule may include brackets like [NH4+]. Because many different linear sequences can represent the same molecule, various canonicalization algorithms exist to produce a unique SMILES for a given structure.

History and development

SMILES originated in the late 1980s, developed by Arthur and David Weininger and later extended by commercial and academic groups. The format evolved through implementations and became widely supported in cheminformatics software. One commercial steward, Daylight Chemical Information Systems, helped formalize conventions, and in the 2000s the open chemistry community produced the OpenSMILES specification to document an open standard. For community resources related to SMILES and open standards, see molecules and ASCII discussions.

Uses, importance and tools

SMILES is used in database indexing, similarity and substructure searching, virtual screening, QSAR modelling, and as input for programs that generate two- or three-dimensional depictions and coordinates. Many molecule editors and cheminformatics toolkits can parse SMILES into internal graph models and render images or compute properties. A typical workflow converts SMILES into 2D diagrams or 3D conformers with visualization libraries and modeling suites; see resources on 3D modeling at 3D model. SMILES is often preferred by practitioners because it is terse and relatively easy for humans to read and type compared with longer, layered identifiers.

Distinctions, limitations and related identifiers

SMILES should be distinguished from other textual structural identifiers such as InChI, an IUPAC-backed convention introduced in the 2000s. InChI aims for a standardized, normalized string, while SMILES emphasizes compactness and human readability; both have strengths and are used for different purposes. SMILES has several dialects and can be ambiguous without canonicalization: multiple valid SMILES can represent the same molecule, and different software may produce different canonical SMILES. Complex cases—mixtures, salts, polymers, or extended stereochemical detail—require careful handling. For the formal IUPAC perspective, see IUPAC, and for mathematical foundations and graph-theory concepts underlying molecular graphs, see graph theory.

Practical notes

• Many cheminformatics toolkits provide functions to convert SMILES to structural formats and back; check documentation for the toolkit you use.
• When exchanging SMILES between systems, note whether an isomeric or canonical SMILES is required to preserve stereochemistry and uniqueness.
• Open specifications such as OpenSMILES exist alongside proprietary implementations; choose formats and converters that match your interoperability needs.

Because of its balance of human readability and machine utility, SMILES remains a central element of digital chemical communication and computation. For more practical tutorials and conversion tools, consult cheminformatics resources and software libraries that demonstrate SMILES parsing, depiction and canonicalization.