There are a limited number of the types of communities that fundamental particles can join in. Here on earth, we know of 109 kinds of fundamental particle communities that can form. These are represented on the periodic table of elements, which describes the organization of the fundamental particles that make up these communities. Each of these communities carries a particular frequency of energy. A good analogy for this is that of a city, which is a definable whole, yet it contains many smaller communities that may have their own physical boundaries, language, culture, etc.
Molecules can be either pure or compound.
When many atoms or communities of copper come together in a copper molecule, it forms as the metal copper. The energy or vibration of Cuprite is distinctly different than that of the metal copper. The combination of the copper communities vibration and the oxygen community's vibration creates a resonant field that is larger and quite different than the individual communities of the compound. So, we know that each of these atoms has its own vibration. These can then be classed according to the natural elemental forces of nature.