The differences between molecules and compounds have been observed and carefully described. Molecules are a group of two or more atoms that are electrically neutral and which are bonded together with very strong chemical bonds that are also called covalent bonds.
A single molecule may have atoms of a single chemical element, such as oxygen (02). If there are complex connections of molecules that have covalent bonds, such as water, or H2O, then they can be included in the definition of molecule. If there are non covalent bonds, or ionic bonds, then the assembly is not considered to be a single molecule.
Gases can be considered molecules of gaseous particles and the classification includes noble gas atoms that are made of a single non-bonded atom.
Crystals are assemblies that are held together with ionic bonds rather than covalent bonds. They are unit cells that repeat in a well organized fashion on a single or three dimensional planes, and are not considered single molecules. These are referred to as repeating unit cells and they may have metallic bonds.
Where atoms are bonded by chemical bonds without any definable molecule or in repeating units, as with crystals, then these are not strictly defined as molecules, although looser classifications may include them. Salts, covalent crystals, network solids, diamonds or sodium chloride are examples.
There are polyatomic ions, charged organic molecules; organic molecules and bio molecules do not share all of these features. Biochemistry and Organic Chemistry, where there is not such a strict definition, will consider these as molecules.
Compounds are also called chemical compounds. These are chemical substances that have two or more chemical elements that can be separated into their simpler and independent form by using chemical reactions. Like molecules, they have atoms that hold together in a fixed ratio and in a well defined spatial arrangement by chemical bonding.
Compounds can be compound molecules that have covalent bonds to hold them together. They may also be salts that are held together by ionic bonds. Also metallic compounds are held together by metallic bonds. There are complexes of matter that have coordinate covalent bonds.
If the substance is a pure chemical element or made of multiple atoms of a single element, then it is not considered to be a chemical compound. Also, some non homogeneous compounds are regarded as chemical compounds. There can be varied amounts of heavy or light isotopes in compounds that are considered to be chemically identical. There might be a lack or a surplus of the main elements that are expected to constitute a compound. There might be foreign matter that is trapped inside of the crystal structure.