Tips and tricks: generating machine-readable structural data from a ChemDraw structure

Interested in making your article more discoverable and usable? As a reader, you have probably spent a lot of time re-drawing structures from an image in a PDF, or have struggled to find all relevant articles because your compound of interest is called by different names in different articles (IUPAC name, trivial name, registry number, drug development ID, generic name, brand name, revised trivial name etc etc etc…).

If you’re already drawing a structure in ChemDraw for an article you are preparing to submit, it only takes a few seconds to generate machine-readable mol files or structure identifiers like SMILES or InChI. Including these files or identifiers in your article or supplementary information helps make your article indexable and structure-searchable, and is a great way to make your article stand out.

Save as mol file

Save as MOL file

Choose File > Save As from the top menu

Select “MDL Molfile (*.mol)” in the Save as type dropdown.

Please note: There are two Molfile formats in this list. The first molfile option is the one with the widest support. The V3000 mol file is not supported by all cheminformatics software packages.

Copy as SMILES

Copy as SMILES

Start by selecting the structure you would like to copy as SMILES.

THEN

Press Alt+Ctrl+C

OR

From the top menu, choose Edit > Copy As > SMILES

OR

Right click, and choose Molecule > Copy As > SMILES

Finally, paste your SMILES string into your document.

Copy as InChI

Copy as InChI

Start by selecting the structure you would like to copy as InChI.

THEN

From the top menu, choose Edit > Copy As > InChI

OR

Right click, and choose Molecule > Copy As > InChI

Finally, paste your InChI into your document.

The less time we have to spend re-drawing structures from pdfs, the more time we can devote to doing science. Luckily, it really couldn’t be quicker or easier to improve the discoverability and reusability of your article by including machine-readable structure files or identifiers. Let’s work together to make chemistry articles easier to find and use.

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