The frequency of radiation generated by a microwave is chosen to be equal to a vibrational resonance within the water molecule.
In short the size of the wave has been picked such that it excites only molecules that size – just like in order to swing on a swing you need to push it with the right frequency.
Microwaves can also be used to do all kinds of cool experiments as well 🙂 Check out how you can measure the speed of light with a microwave and some marshmallows!
Well… I don’t think it’s correct to say that microwaves only heat up water molecules. I’ve done poppadoms in the microwave (less greasy than deep frying them!) so that must be heating the oil not the water. I think it’s just that microwaves act on molecules that have an electric dipole moment (like little magnets with a north and south pole but just with electric charge, negative at one end and positive at the other) – the microwaves make the molecules rotate from one direction to the other (oscillate) as the electromagnetic field of the microwave alternates its direction. The energy from this molecular vibration gets converted to heat energy, and voi-la! perfect poppadoms.
As Peter says the microwaves have the right wavelength to excite vibration in water molecules – they are a resonance of the bonds within water molecules and so very effectively vibrate these bonds.
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