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Search Chemical Compounds

chemistry.pubchem.search
Read-onlyIdempotent

Search 100M+ chemical compounds by name, formula, or SMILES string. Returns CID, molecular formula, weight, IUPAC name, SMILES, InChI, XLogP, H-bond donors/acceptors, exact mass, and complexity. The largest public chemical database (PubChem / NCBI)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
nameYesCompound name, formula, or SMILES string (e.g. "aspirin", "C9H8O4", "CC(=O)OC1=CC=CC=C1C(=O)O")
limitNoMaximum results to return (1-20, default 5)

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent only when the call failed. Includes error code, message, request_id, and any provider-specific extras.
resultNoTool response payload. Shape varies per tool — consult the tool description and inputSchema. May be an object, array, string, or number depending on the upstream provider response.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint=true, destructiveHint=false, idempotentHint=true. The description adds value by enumerating the exact fields returned (CID, molecular formula, etc.) and emphasizing the database scale (100M+ compounds), which helps the agent understand the tool's scope and output without contradicting annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is two sentences: the first succinctly states the action, input types, and output fields; the second establishes credibility. No filler words, front-loaded with key information.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the simple search tool with 2 parameters and an output schema, the description is complete: it covers input types, output fields, and database size. It lacks details on pagination or empty results, but these are standard and the output schema likely provides structure.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Input schema coverage is 100%, with both parameters well-described. The description does not add further detail beyond what the schema already provides for parameters; it reiterates the types of input (name, formula, SMILES) but not the limit parameter.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description is specific: searches chemical compounds by name, formula, or SMILES string, and lists return fields. It clearly distinguishes from sibling tools (e.g., bioassays, hazards) by focusing on compound search and retrieval of standard chemical identifiers.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description does not provide explicit when-to-use or when-not-to-use guidance relative to alternatives. The intended usage is implied by the tool name and description, but no exclusions or alternative suggestions are given.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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