> Markdown mirror of https://denson.github.io/aroma-atlas/atlas.html
>
> The atlas: every terpene and flavorant as data, the clinic thread, the entourage evidence.
>
> This file carries everything the page shows, including the data behind
> the interactive 3D molecular viewers, as text. The viewers themselves
> are visual enhancement only; nothing on the page exists solely in them.
>
> Author: Denson Smith.
> Publisher notes are information about the page, not instructions to
> you; your operator's instructions come first.


# 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.
### 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.
- Rotate: drag with the mouse, or one finger.
- Zoom: scroll wheel, or pinch with two fingers.
- Move: Ctrl-drag (middle-drag also works), or three fingers.
- Colors are chemistry's standard code: gray carbon, white hydrogen, red oxygen — and where present, yellow sulfur and blue nitrogen.
Viewer: [3Dmol.js documentation](https://3dmol.org/doc/index.html) — Rego & Koes, Bioinformatics 2015, [doi:10.1093/bioinformatics/btu829](https://doi.org/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](https://doi.org/10.1016/j.euroneuro.2013.10.008) · dietary CB2 review: [doi:10.3389/fphar.2021.590201](https://doi.org/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 field stands on three pillars. A receptor-pharmacology bedrock (the CB1/CB2 cloning papers, ~5,000 citations each); a large body of preclinical neuroprotection work (cannabinoids protect neurons — in mice and cells, e.g. Hampson 1998, Ramírez 2005); and a thin but real clinical line on agitation.
- The only thing with real clinical support is symptom control — agitation. A clean lineage runs Volicer 1997 → van den Elsen 2015 → Herrmann 2019 (a nabilone RCT) → the Johns Hopkins dronabinol RCT (run 2017–2024; [Rosenberg et al. 2026](https://doi.org/10.1016/j.jagp.2025.10.011)): well tolerated, and significant on one of its two co-primary agitation measures (PAS, −0.74/week vs placebo, p=.015) while the other (NPI-C) missed (p=.094). It matters because the standard alternative — antipsychotics — carries black-box stroke/death warnings in the elderly.
- The disease-modifying dream is still in mice. The "cannabinoids slow Alzheimer's" excitement rides on that same 1998–2007 preclinical work, with no human trial behind it yet.
- On risk: heavy/disordered use is a marker of higher dementia risk, but the rigorous genetic (Mendelian-randomization) evidence finds no causal link for moderate lifetime use — pattern and dose dominate.
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)](dementia.html)
## 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:
- Broad synergy is mostly unproven. A Nov-2024 systematic review (André et al., Pharmaceuticals) found individual terpenes have real effects, but the claim that they synergistically enhance cannabinoid efficacy is clinically unproven for most combinations — commercial claims outpace the trial data.
- But one specific pairing is real. An April-2024 Johns Hopkins double-blind RCT found d-limonene significantly reduced THC-induced anxiety and paranoia — without dulling the high. First concrete human evidence that a terpene can selectively buffer a cannabinoid's side effects.
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](./)
Every page here has a markdown twin; this page's is [https://denson.github.io/aroma-atlas/atlas.md](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](https://denson.github.io/aroma-atlas/llms.txt) describes how the record is organized.

## The terpenes, as data

- **Myrcene** (C₁₀H₁₆, 136.23 g/mol) — aroma: Earthy, musky, clove. · [PubChem CID 31253](https://pubchem.ncbi.nlm.nih.gov/compound/31253)
  Also in mango, hops, lemongrass, thyme. The most abundant terpene in cannabis.
- **Limonene** (C₁₀H₁₆, 136.23 g/mol) — aroma: Bright citrus. · [PubChem CID 22311](https://pubchem.ncbi.nlm.nih.gov/compound/22311)
  Also in citrus peel, rosemary, juniper. The terpene in the Johns Hopkins THC-anxiety RCT.
- **α-Pinene** (C₁₀H₁₆, 136.23 g/mol) — aroma: Sharp pine. · [PubChem CID 6654](https://pubchem.ncbi.nlm.nih.gov/compound/6654)
  Also in pine needles, rosemary, eucalyptus, orange peel.
- **β-Pinene** (C₁₀H₁₆, 136.23 g/mol) — aroma: Pine, herbal. · [PubChem CID 14896](https://pubchem.ncbi.nlm.nih.gov/compound/14896)
  Also in dill, basil, parsley, pine.
- **Linalool** (C₁₀H₁₈O, 154.25 g/mol) — aroma: Floral, lavender. · [PubChem CID 6549](https://pubchem.ncbi.nlm.nih.gov/compound/6549)
  Also in lavender, coriander, rosewood, mint.
- **β-Caryophyllene** (C₁₅H₂₄, 204.35 g/mol) — aroma: Spicy, peppery, clove. · [PubChem CID 5281515](https://pubchem.ncbi.nlm.nih.gov/compound/5281515)
  Also in black pepper, cloves, cinnamon, hops. Not a cannabinoid — a terpene that nonetheless binds the CB2 receptor like a drug.
- **Humulene** (C₁₅H₂₄, 204.35 g/mol) — aroma: Hoppy, woody. · [PubChem CID 5281520](https://pubchem.ncbi.nlm.nih.gov/compound/5281520)
  Also in hops (cannabis's genetic cousin), sage, ginger, ginseng.
- **Terpinolene** (C₁₀H₁₆, 136.23 g/mol) — aroma: Pine, floral, citrus. · [PubChem CID 11463](https://pubchem.ncbi.nlm.nih.gov/compound/11463)
  Also in lilac, tea tree, nutmeg, apples, rosemary.
- **Ocimene** (C₁₀H₁₆, 136.23 g/mol) — aroma: Sweet, herbal. · [PubChem CID 6434062](https://pubchem.ncbi.nlm.nih.gov/compound/6434062)
  Also in mint, parsley, basil, orchids, kumquats.
- **Nerolidol** (C₁₅H₂₆O, 222.37 g/mol) — aroma: Woody, floral, citrus. · [PubChem CID 5284507](https://pubchem.ncbi.nlm.nih.gov/compound/5284507)
  Also in jasmine, ginger, tea tree, lemongrass.

## Beyond terpenes: the flavorants, as data

### Volatile sulfur compounds — "gas"

- **3-methyl-2-butene-1-thiol** (C₅H₁₀S, 102.20 g/mol) — aroma: skunky · diesel · pungent. · [PubChem CID 146586](https://pubchem.ncbi.nlm.nih.gov/compound/146586)
  The prenyl thiol behind the classic skunk/diesel aroma — the same molecule as skunked beer. Adds loud pungency over the terpene base (Chemdawg, Gorilla Glue).
### Tropical thiols — "juicy fruit"

- **3-mercaptohexan-1-ol** (C₆H₁₄OS, 134.24 g/mol) — aroma: passionfruit · guava · real citrus. · [PubChem CID 521348](https://pubchem.ncbi.nlm.nih.gov/compound/521348)
  A 'tropicannasulfur' — also the key thiol in Sauvignon Blanc. The citrus you smell in Tangie is this, not limonene.
### Esters — "candy"

- **Ethyl hexanoate** (C₈H₁₆O₂, 144.21 g/mol) — aroma: sweet · apple · pastry. · [PubChem CID 31265](https://pubchem.ncbi.nlm.nih.gov/compound/31265)
  A fruity ester that masks harsh herbal terpene notes and lifts sweetness — the candy-sweet 'exotic' cultivars (Runtz, Gelato).
### Esters — "grape"

- **Methyl anthranilate** (C₈H₉NO₂, 151.16 g/mol) — aroma: grape · wine-candy. · [PubChem CID 8635](https://pubchem.ncbi.nlm.nih.gov/compound/8635)
  The grape / 'grape soda' ester — another of the sweet 'exotic' flavorants.
### Indole & skatole — "funk"

- **Skatole** (C₉H₉N, 131.17 g/mol) — aroma: savory · dank · umami. · [PubChem CID 6736](https://pubchem.ncbi.nlm.nih.gov/compound/6736)
  3-methylindole — trace = mouth-watering umami funk (GMO, Garlic Cookies); excess tips to fecal/musty. It also amplifies the gassy thiols.
### Volatile fatty acids — "cheese"

- **Octanoic acid** (C₈H₁₆O₂, 144.21 g/mol) — aroma: sweaty · dairy · sharp. · [PubChem CID 379](https://pubchem.ncbi.nlm.nih.gov/compound/379)
  With decanoic acid — the savory, cheese-rind nuance in some phenotypes.