The only chemical and physical changes result from the heat generated. In fact, some of these changes are less obvious in foods heated in microwaves because the temperature rise is much faster than it is in regular ovens. Longer heating periods can lead to greater physical and chemical changes. For this reason, the nutritional quality of microwaved foods is often superior. That is also why it is possible to heat food more quickly in a microwave oven than in a conventional oven, where the food must be heated from outside in.
Microwaves do nothing more to food than heat it.
There is no evidence that microwaves alter the composition of food or have any other detrimental effects.