The smallest particle of an element is an atom whereas the smallest particle of a compound is a molecule. The difference between an atom and a molecule is that the atom is the smallest unit of an element, which may or may not exist independently whereas a molecule is formed when two or more similar or different types of atoms are joined chemically. e.g. 'O', 'H', and 'C', etc are atoms but O2, H2, and CO2, etc are molecules.