Molecule
late 18th century: from French molécule, from modern Latin molecula, diminutive of Latin moles ‘mass’.
wiktionary
Summary: from French molécule, from New Latin molecula(“a molecule”), diminutive of Latin moles(“a mass”); see mole + -cule.
French molécule (1674, Pierre Le Gallois, Conversations tirées de l'Académie de M. l'abbé Bourdelot, contenant diverses recherches et observations physiques) cited in Quemada, Bernard (1965), Datations et documents lexicographiques (tome 3).
Medieval Latin molecula (early XVII cent., Pierre Gassendi), cited in Le Grand Robert de la Langue Française (2e édn) tome 6. →ISBN. pp. 522–23. Diminutive of moles
etymonline
molecule (n.)
1794, "extremely minute particle," from French molécule (1670s), from Modern Latin molecula, diminutive of Latin moles "mass, barrier" (see mole (n.3)). For ending see -cule. It has a vague meaning at first; the vogue for the word (used until late 18c. only in Latin form) can be traced to the philosophy of Descartes. First used of Modern Latin molecula in modern scientific sense ("smallest part into which a substance can be divided without destroying its chemical character") is by Amedeo Avogadro (1811).
