Does microwave cooking break molecular chains? Does any recombination of ions take place in the food and, if so, is there a possibility of eating some type of toxin formed during cooking?
The answers to all of these questions are no. Microwave cooking merely heats the water molecules, which in turn heat the food. The only molecular rearrangements that occur are those that are caused by warming the food toward the boiling temperature of water. In fact, there is less chemistry done during microwave cooking than is done in a normal oven. For example, one of the problems with microwave cooking is that food doesn’t brown because the high temperatures needed to chemically modify the food molecules (and cause browning) aren’t reached in microwave cooking. So you shouldn’t have any fear of food cooked in a microwave oven. The microwaves don’t damage it any more than heating it in boiling water would.