This might qualify to be added to the stupidest posts ever hall of fame, but I've been wondering about this for a while. If you brew coffee in the morning and then decide to drink some more of it later in the day, is the caffeine still active? I have tried re heating it a few times I don't feel that stimulated. And why does it taste different? It is just beans and water and yet when you re heat it later in the day, it tastes completely different.
The caffein is still active.
The flavor part of your question is complicated. I'm sure a little Google research could tell you quite a bit, but in short, there are a lot of volatile flavor compounds in coffee.
The flavour and smell comes from aromatic and essential oils. For the same reason coffee grinds and beans tastes like ass if you leave it out for a while, the brewed coffee tastes different. Oils will oxidize with time, heat and exposure to light.
Microwaving coffee changes the chemical makeup somehow. I can't remember exactly how but I know it does.
Wow you guys know your shit. Thanks for the responses.
As mentioned, the caffeine is still completely active.
The volatile oils in coffee are extremely sensitive to heat and air. Coffee brewed at 198 degrees - 202 degrees is said to taste the best. I shelled out some serious cash for a top of the line coffee maker which brews at exactly 200 degrees, and I can honestly say that it makes any coffee beans taste 10x better.
Read the wikipedia entry on coffee. Essentially you continue to "roast" the coffee as long as it's heated. The coffee connoisseurs even say that after around 10 minutes on the burner the coffee is no longer good; it must be drank immediately after it's made.
I dont think it would make any difference to the caffeine though.