SMILES to InChI

What is SMILES to InChI?

SMILES to InChI is a small-molecule identifier converter that turns a SMILES molecular graph into an IUPAC International Chemical Identifier, or InChI. SMILES is concise and convenient for storing or drawing a structure, but equivalent molecules can be written as different valid SMILES strings. An InChI applies a standardized structure-normalization procedure and writes the result as a layered identifier, making it useful for exchanging well-defined chemical structures across databases and software.

The conversion is performed with RDKit and its InChI support. Each submitted SMILES is parsed and chemically sanitized before the InChI is written. Invalid syntax, impossible valences, or structures RDKit cannot sanitize are reported as failed entries rather than being exported as uncertain identifiers.

An InChI carries structural information such as formula, connectivity, hydrogens, charge, and, when specified and retained, stereochemistry and isotopic composition. It is a structure identifier, not a 3D conformer or a prediction of the dominant protonation state at a particular pH. For a structure file with coordinates, SMILES to SDF is the appropriate next step.

How to use SMILES to InChI online

ProteinIQ converts one to ten SMILES entries into downloadable InChI identifiers. Paste one SMILES per line, upload a supported text file, or retrieve compounds from PubChem by name or CID. Each successfully parsed molecule receives an individual .inchi file, while multi-compound jobs also include a tab-separated batch file and a curated Run log that records failed inputs.

Inputs

A named input can be written as:

aspirin	CC(=O)Oc1ccccc1C(=O)O

SMILES should describe the intended chemical form before submission. In particular, charge, explicit stereochemistry, salts, isotopes, and tautomer choice can all affect the resulting InChI. A compound name is not accepted as plain SMILES text; use PubChem retrieval when a name or CID is the available starting point.

Results

One failed structure does not stop the remainder of the batch. Failed entries are omitted from the .inchi files and batch.inchi.tsv, while the Run log records the failed-entry count.

How the conversion works

The converter first reads the SMILES into an RDKit molecular graph. RDKit sanitization checks the graph for chemically consistent valence and assigns features such as aromaticity. The tool then removes hydrogens that can be represented implicitly and asks the InChI library to write the resulting structure as an InChI.

The identifier commonly begins with InChI=1S/, where 1S denotes a Standard InChI produced with the standard settings. Sections separated by / encode different layers of structural information. For example, the ethanol SMILES CCO produces InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3.

The tool does not generate an InChIKey. An InChIKey is a fixed-length hash derived from an InChI and is useful for indexing and web search, but it cannot be decoded back into a molecular structure. A full InChI can be converted back to a toolkit-specific canonical SMILES with InChI to SMILES.

Reading an InChI result

The InChI is a normalized identifier for the molecular structure RDKit and the InChI library obtained from the submitted SMILES. It should be treated as a chemistry-aware matching aid, not as a byte-for-byte preservation of the input notation.

• Different SMILES can yield the same InChI: Atom order and several textual choices can vary in SMILES without changing the represented molecule. This makes full InChI useful for standardizing library records before duplicate checking.
• Stereo must be present in the input: An achiral or stereo-unspecified SMILES cannot acquire a stereochemical InChI during conversion. Check the original input when enantiomers or alkene geometry matter.
• Salts and mixtures remain multi-component structures: A dot-disconnected SMILES can produce an InChI with multiple components. The converter does not select a parent fragment or remove counterions.
• Tautomer and protonation choices matter: InChI normalization may represent some forms differently from a source database's SMILES. Compare the molecular graph or original record before using the result for registration, synthesis planning, or a structure-sensitive assay analysis.

SMILES to InChI versus other format conversions

SMILES to InChI fits registry, deduplication, and data-exchange workflows where a standardized structure identifier is needed. InChI to SMILES is the reverse conversion for workflows that require a SMILES string. Neither direction should be used as a literal round-trip test because SMILES and InChI apply different representation and normalization rules.

For conversions involving coordinates, atom properties, or formats beyond a compact identifier, use Open Babel. It can translate between a wider range of chemical and structure file formats, whereas this tool focuses on producing a full InChI from SMILES.