Nothing falls afoul of thermodynamics. This is not a closed system - you can inject as much energy into as you have available. Entropy and thermodynamics play no role here, but I would imagine that (a) the cost of the energy require (b) containment technology (c) what happens after you extract a given substance are/were all very involved in its failure.
This is already done with crude oil, and is called "cat cracking". You heat the crude oil until every component in it becomes gaseous (but still small-molecule) - the smaller the molecules they higher they rise up the "chimney", so you can siphon off particular components at particular heights.
