A microwave oven heats water because the microwave radiation interacts with the dipole (separated positive and negative charge) of the water molecule. The microwaves turn the water molecules back and forth at approximately the frequency of the microwaves, imparting energy to them. Sometimes you may hear that the microwaves are interacting with a resonant frequency of the water molecule (like a radio gets tuned to a frequency), but that is actually not the case. Anything with a dipole moment will absorb microwave radiation, so microwave ovens will also heat fats and sugars, for example.
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