PubChem Names
Draw acetic acid, select it, and half a second later the status bar reads “acetic acid”. The name comes from PubChem, the public chemistry database run by the US National Library of Medicine. Molkit sends the structure’s SMILES string to PubChem’s PUG REST service and shows what comes back. The same service fills in the compound fields of SVG exports that embed chemistry metadata. Lookups need an internet connection.
Look up a name
- Draw a molecule, for example ethanol (
CCO, from Structure > Import SMILES…). - Select all of its atoms, or leave nothing selected if it is the only molecule on the canvas.
- The status bar shows “looking up name…” and then the name.
With nothing selected, Molkit names the whole canvas when it holds a single molecule or one salt such as sodium chloride; otherwise it names one molecule from the canvas. A partial selection is looked up as a fragment. Very large selections are not looked up at all.
Structures that contain a generic placeholder such as R are never looked up, because they do not stand for one compound.
What the status bar shows
The status bar shows PubChem’s common name first: the compound’s first listed synonym, in lower case, for example “ammonia” or “acetic acid”.
| Control | What it does |
|---|---|
| The name | Click to copy it. The name dims briefly to confirm. |
| Dropdown arrow | Appears when PubChem returns more than one name. It lists the systematic IUPAC name and other synonyms; click any entry to copy it. |
| External-link icon (“View on PubChem”) | Appears when PubChem matched a compound record. Opens that compound’s PubChem page in a new tab. |
Structure > Copy IUPAC Name (also in the command palette, Ctrl+K) copies the systematic IUPAC name, even though the status bar shows the common name first. If PubChem returned only a common name, or a stored name has no IUPAC form, it copies that name instead and the confirmation message says it is the common name.
A named selection or visual set that already stores a name shows that name without contacting PubChem.
Ions and radicals
Some species are stored in PubChem under a different structure from the one you drew. An ionic depiction may have no SMILES match at all, and a radical drawn with an open valence can come back as the hydrogen-completed compound: nitrogen dioxide (NO2) would be reported as nitrous acid. In both cases Molkit discards the SMILES result and searches PubChem by molecular formula instead, including the charge, so NO2 is named nitrogen dioxide. A formula result is accepted only when it matches exactly one compound.
PubChem data in SVG exports
When you export an SVG with the “Embed chemistry metadata” option on, Molkit also asks PubChem for the structure’s IUPAC name, compound ID (CID), common-name synonyms, InChI and InChIKey, and writes them into the file’s metadata. Because Molkit fetches these in the background while you select a molecule, the export usually does not have to wait. If PubChem cannot be reached, the export still completes without those fields.
Molkit does not import structures from PubChem by name or CID. To bring in a structure you found there, download its SDF and use MOL and SDF Import, or paste its SMILES into Import SMILES.
Network and privacy
Each lookup sends the SMILES string (or, for the fallback, the molecular formula) of the structure being named to pubchem.ncbi.nlm.nih.gov as part of the request URL. No other document content is sent. With nothing selected, the whole canvas or one molecule on it is looked up, so if you work with structures you cannot share, work offline.
When no name appears
Lookups fail without an error message. If you are offline, PubChem is unavailable, or the structure has no PubChem record, the status bar stays blank. Successful results are cached for the session and failures are not, so selecting the structure again retries.
To copy a plain-text summary that includes the name, see Copy Structure Description.