MOL to InChI Converter
Turn a MOL file into the IUPAC standard InChI, so the structure can be compared and stored reliably.
Why convert MOL to InChI?
A MOL file describes one specific drawing of a structure — two drawings of the same compound can produce different files. InChI normalises the structure into a canonical string, so two different MOL files for aspirin produce the same InChI. That makes it the right form for compound registration and duplicate detection.
What gets preserved
Connectivity, tautomeric form, charge and stereochemistry are all encoded in separate InChI layers. If the MOL file carries wedge/hash bonds, they become the stereo layer of the InChI.
Common pitfalls
- A MOL file without explicit hydrogens may lose stereo information — check the chiral flags in your drawing tool before converting.
- Salts keep their counter-ions in the InChI unless you strip them first.
- To get a fixed-length key instead, convert to InChIKey.