How does cooking with direct heat affect the nutritional value of food compared to using indirect heat?

Answer 1

Direct heat, say from an open flame, emits photons of EM radiation of various wavelengths, from weak to strong. http://en.wikipedia.org/wiki/Electromagnetic_radiation

While the vast majority will be in the IR spectrum (not particularly strong), there will be hundreds of millions in the UV spectrum. UV-spectrum photons have the power to damage or destroy complex organic molecules present in food, and this may affect the flavour, or even damage or destroy the molecules in food which are good for us. It is also the cause of charring.

Indirect heat, where a flame or other heat source boils water, does not do this because the water absorbs the photons and transmits the heat to food immersed in the water by conduction. In short, damaging UV photons do not strike the food in this manner, and so fewer chemical reactions happen.

It is not just water that does this. For example, bread will never toast in a microwave because the mircowaves (holding a very weak position on the EMR scale) do not have the power to cause the chemical reactions which occur in a toaster.

Answer 2

What a vague question with many possible answers!

Well, it usually breaks things down but sometimes heat causes things to combine. So it entirely depends on the thing you're cooking. Usually, it carbonizes things though, which is just breaking down but lots of foods have carbon so it's common.