Illustrated Glossary of Organic Chemistry

Molecule: An electrically neutral collection of atoms held together by ionic bonds and/or covalent bonds.

Ammonium chloride (NH4+ Cl-) is a molecule. It's overall electrical charge is zero, and its atoms are held together by both covalent bonds and an ionic bond. The ammonium cation is not a molecule by itself because its net electrical charge is +1 (it is a cation). The chloride anion is not a molecule because it lacks both covalent bonds and ionic bonds, and its overall electrical charge is -1.

The CH3 portion of methylcyclohexane is a methyl group, not a methyl molecule.