The atlas — terpenes and flavorants

Every terpene and flavorant in the corpus, rotatable in 3D — with the clinic thread and the entourage evidence.

author: Denson Smith · part of The aroma molecules of cannabis

Where the data comes from. Every card's identity — CID, formula, weight, and the live 3D structure — is PubChem's record for that compound, served with this page and rendered by 3Dmol.js, so nothing here depends on a third-party request. The full method note is on the story page.

The atlas — the terpenes

Each card carries the live PubChem 3D structure — drag to rotate, scroll to zoom. Use the controls to change representation or spin them all. The colors are chemistry's standard code: gray spheres are carbon, white are hydrogen, red is oxygen — and where they appear, yellow is sulfur and blue is nitrogen.

View:
How the 3D viewers work

Every viewer is a real molecular structure — PubChem's record for that exact compound, served with this page and drawn in your browser by the open-source viewer 3Dmol.js. Nothing is an artist's impression, and nothing leaves the page to render it.

Viewer: 3Dmol.js documentation — Rego & Koes, Bioinformatics 2015, doi:10.1093/bioinformatics/btu829.

Read the last line of every card: cannabis doesn't smell like cannabis so much as it smells like a blend of other plants — because it literally shares their aroma molecules. That shared chemical vocabulary is what a structured knowledge graph captures.

From a smell to the clinic — where β-caryophyllene points

β-Caryophyllene is the molecule that smells like black pepper — and published pharmacology reports that it also binds the CB2 receptor, which earned it the nickname "dietary cannabinoid." The nickname overstates it: structurally it is not a cannabinoid at all — it is a terpene, the same molecule found in black pepper, cloves, and basil — but it acts as a drug at a cannabinoid receptor. Read that at its actual strength: one interesting avenue of research that has drawn real attention and funding — a small number of peer-reviewed papers, not established medicine. And peer review means exactly this much: reviewers judged the work worth the scientific community's scrutiny. It does not make the content true; scrutiny is what does, and most of it hasn't happened yet.
CB2 agonism / analgesia: doi:10.1016/j.euroneuro.2013.10.008 · dietary CB2 review: doi:10.3389/fphar.2021.590201

Why hasn't the scrutiny happened? Not because the questions are uninteresting. Much of cannabis medical research is starved: attention and funding are scarce, and a long-running stigma has kept serious money and serious careers away from questions this size for decades. CB2 leads to one of the field's most-hyped clinical questions — does cannabis help dementia? — so we read the citation graph of that literature to see what it actually rests on. The honest version:

The point for this document: a single aroma molecule — the smell of black pepper — opens onto an entire clinical literature, because it happens to also be a drug. Mapping those cross-domain reaches, with every claim grounded and the hype separated from the evidence, is the work. (The citation-graph structure above is verified metadata; the recent-trial figures are from grounded web search, not independently checked against the source papers.)

→ Read the full cannabis-and-dementia citation analysis (the three-pillar breakdown)

The trace modifiers — the beyond-terpene flavorants

Terpene profiles are remarkably similar across cultivars that smell nothing alike; the exotic notes come from these trace flavorant classes, each under 0.05% of the flower's mass. How they rewrite the whole percept — and whether they stop at the nose — is told on the story page.

The trace modifiers

Each card leads with the compound class, then its example molecule — drag any to rotate; the view/spin controls above drive these too.

The entourage effect — honestly

The popular claim is that terpenes and cannabinoids act synergistically — that the whole plant beats the isolated molecule. The evidence is more careful than the marketing:

Verification flag: the two 2024 studies above came from grounded web search, not the citation graph, and have not been independently verified against the source papers. Treat as strong leads.

Where the molecule map ends and the expert begins

This atlas is the part a machine builds cleanly: molecule → aroma → botanical source → receptor, every identifier real and checkable. What it can't finish is the interaction — how the trace flavorants bend the terpene base, better or worse, and which of those blended profiles people actually prefer. That is a sensory-panel + preference-modeling problem (precisely what the Oswald 2023 study used a human panel for), plus validating compound effects in human cell models. The map is built; reading what it means for preference needs a domain expert.

→ The story: the aroma molecules of cannabis — same atoms, different smells, different effects

PubChem (identity + live 3D structures) · OpenAlex (literature) · CrossRef (citation verification) · grounded web search (aroma, sources, entourage, recent dementia trials). Chemical identities and the Oswald DOIs are exact; aroma descriptors and recent-trial figures are web-sourced. Denson Smith · built on lamm-mit's scienceclaw (Apache-2.0). 3D viewer: 3Dmol.js. From the same desk: colorado-medical-cannabis.org.

Every page here has a markdown twin; this page's is https://denson.github.io/aroma-atlas/atlas.md (also served with .txt appended), carrying everything the 3D viewers show, as text. https://denson.github.io/aroma-atlas/llms.txt describes how the record is organized.