MurmurChem - Reaction Pathway Discovery

What is this?

MurmurChem discovers the hidden grammar of chemical reactions. It was fed 31,364 reaction mechanisms as pure token sequences — no chemistry textbook, no rules, no molecular simulation. The engine figured out which electron-flow steps belong together, which functional groups predict which reactions, and which reaction families share mechanistic DNA.

Everything you see here was learned from sequential timing alone.

How it works

1

Dataset. 31K organic reactions from mech-USPTO, each with a chemist-validated arrow-pushing mechanism: the step-by-step electron flow that makes the reaction happen.

2

Tokenization. Each mechanism becomes a sequence of tokens: electron-flow steps (e.g. bond_C-O → O), reaction class labels (e.g. SN2), and functional groups (e.g. carbonyl).

3

Learning. Tokens are fed in order. The engine learns which steps follow which, building a map of mechanistic grammar. Over 31K reactions, recurring patterns become strong connections. Rare co-occurrences fade away.

4

Query. Queries follow the strongest learned paths to find related chemistry. The graph reveals what the data says follows, connects, or clusters with your query.

Why it matters

Verification: The graph recovers known reaction families without being told they exist. Dense cores of triangle-connected concepts map onto textbook reaction classes — proof the engine learned real chemistry.

Discovery: Bridges between reaction classes reveal shared mechanistic subsequences that aren't in any label. Two reactions nobody grouped together might share an electron-flow fingerprint that the graph found.

Reading the visuals

Steps — electron-flow operations (e.g. bond_C-N → N)
Classes — named reaction types (e.g. SN2, Wittig)
Func. groups — molecular features (e.g. carbonyl, amine)
Mechanism types — broad categories (e.g. substitution, addition)

Colors match across the trail, routes, and fingerprints. Click any node to explore from it.

Try these

Explore: SN2

Classic nucleophilic substitution. Watch the trail trace through bond-breaking steps and halide leaving groups.

Bridge: SN2 ↔ Wittig

Very different chemistry. See the routes the graph finds to connect them through shared intermediates.

Complete: after C-O bond breaks

Starting from a C-O bond cleavage, what mechanistic steps typically follow?

Fingerprint: SN2

See the unique electron-flow signature that defines SN2 reactions.

Landscape: reaction map

All 63 reaction classes positioned by mechanistic similarity. Click to fingerprint, click two to compare.