mcp-molecules

Atoms and molecules for the artificial minds — trustworthy chemistry tools, computed for real and backed by authoritative data.

Atoms combine into molecules, and a language model asked about them should not have to recall facts from memory; it should compute answers it can trust. mcp-molecules is a growing toolbox for working with chemical elements and molecules — offline, deterministic, and backed by authoritative sources such as the NIST Atomic Weights and Isotopic Compositions database.

For example, it can already take a chemical formula and return its molecular weight: ask "what does C₆H₁₂O₆ weigh?" and it parses the formula, looks every element up in NIST data, and computes the molar mass rather than guessing it. More molecule-oriented tools are planned.

You can ask things like:

• "What does a mole of glucose weigh?" — resolves the name to C₆H₁₂O₆ and computes the molar mass.

• "How much of Fe₂(SO₄)₃'s mass is iron?" — per-element percent composition.

• "What's the molar mass of caffeine, with uncertainty?" — propagates the NIST standard uncertainties.

• "What does the mass spectrum of chloroform look like?" — the natural chlorine isotope pattern (the M, M+2, M+4 … peaks).

• "What's the [M+H]⁺ m/z for caffeine?" — the protonated-ion mass.

• "Which compound has the formula C₉H₈O₄?" — formula → name (aspirin, among its isomers).

• "What are the isomers of C₂H₆O?" — one formula, several names (ethanol and dimethyl ether).

What it gives you

• molecular_weight_calculator — (one example of what's here today) compute the molecular weight (molar mass) of a chemical formula. Parameters:

  • formula — element symbols, integer multipliers, arbitrarily nested parentheses, and the isotope labels D (deuterium) and T (tritium). Examples: H2O, C6H12O6, Ca(OH)2, Fe2(SO4)3, ((CH3)2CH)2, D2O, Tc.

  • unit — g/mol (default), kg/mol, Da, u, or kDa.

  • uncertainty — propagate the per-element NIST standard uncertainties in quadrature and report value ± sigma.

  • monoisotopic — use the most abundant isotope of each element (mass-spectrometry monoisotopic mass) instead of the standard atomic weight.

  • composition — return the per-element percent composition by mass.

• isotope_distribution — compute the natural isotopic pattern (the peaks a mass spectrometer would see) for a formula, with each peak's mass, m/z, and relative intensity, plus the monoisotopic and average masses. Parameters:

  • formula — same syntax as molecular_weight_calculator.

  • charge — 0 (default) reports neutral masses; a non-zero n reports m/z for the [M+nH]/[M-nH] ion.

  • threshold — drop peaks below this percent of the base peak (default 0.1).

  • limit — maximum peaks to return, most intense first (default 10).

  • grouping — unit (default) collapses to nominal integer masses; exact keeps every resolved isotopologue.

• find_chemical_compound — look up a compound by name or molecular formula. Searches a bundled offline database (a PubChem subset) and a writable user cache first, then — unless disabled — an online fallback (PubChem, Wikidata, and, when an API key is set, EPA CompTox), caching what it fetches. Parameters:

  • query — a name (aspirin, acetylsalicylic acid) or a formula (H2O, C9H8O4); formulae are matched in the Hill system.

  • by — auto (default) guesses name vs. formula and falls back to the other direction on a miss; name or formula pin the direction.

  • limit — maximum compounds to return for a formula lookup (isomers share a formula), preferred name first.

  The online fallback is on by default; set MCP_MOLECULES_ONLINE to a falsy value (0/false/no/off) to keep lookups fully offline. The EPA CompTox source additionally needs a free CCTE API key in MCP_MOLECULES_EPA_API_KEY; without it that source is skipped.

• info — server availability / version / environment health check.

Related MCP server: PubChem-MCP

Install

uv tool install mcp-molecules

Register with Claude Code

claude mcp add molecules -- mcp-molecules

Development

uv sync --all-extras
uv run mcp-molecules        # run the server over stdio
uv run pytest               # tests
uv run ruff format .        # format
uv run ruff check .         # lint
uv run mypy                 # type-check

A pre-commit hook in .githooks/ auto-formats and lints staged Python files so the CI format gate can't be missed. Enable it once per clone:

git config core.hooksPath .githooks

Data

Element masses come from the NIST Atomic Weights and Isotopic Compositions database (https://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl), which is in the public domain. The data is bundled in the package as mcp_molecules/data/nist_atomic_weights.json.

Sponsoring

Sponsoring this project will keep it alive. If it is useful to you, please consider sponsoring.

Credits

The idea and the inspiration came from Mátyás Mayer. The idea was excellent, the inspiration priceless.

License

GPL-3.0-or-later. See LICENSE. The bundled NIST data is public domain.