IMO only a pure chemical can have well-defined frequencies (electro-magnetic or acoustic). Chemically clean substances - one compound, one molecule - are rare in nature. Even the water molecule H-O-H or H2O has different forms, as we know, gaseous, liquid, icy. Can absorb and emit different frequencies.
You tossed a very complex subject.
No easy answer and probably no easy application of what you have in mind here.
Did you think of ultrasonic cleansing or of electromagnetic radiation?