A molecule was a collection of atoms.
The Sixth Doctor witnessed the death of a Time Lord who had exhausted his regenerations and commented that flesh broke down into degenerate matter, then into random molecules. (COMIC: The World Shapers)
To prevent the Divergence's future domination of the universe, Rassilon created a self-replicating, biogenic molecule which he sent back in time to seed all habitable planets in Gallifrey's galaxy. This ensured all intelligent life evolved in the form of the Gallifreyans. (AUDIO: Zagreus)
Single Molecule Transcription was developed by the Butler Corporation and replaced microprocessors by 2019. It indented the wall of a hydrogen molecule with code that responded to the physical excitation of surrounding space. (TV: The Long Game)
According to Adipose Industries, their diet pill was composed of a synthesised mobilising lipase, bound to a large protein molecule. The mobilising lipase supposedly broke up the triglycerides stored in the adipose cells. (TV: Partners in Crime)