According to Star Trek Captain's Chair (a game that lets you tour the bridges of Star Trek's many ships) impulse engines are a secondary propulsion system for the vessel, employing nuclear fusion reactors to accelerate helium plasma products to near lightspeed, producing Newtonian thrust for space-normal velocities. I also remember a note on it saying: "Rocket Engines!" So I assume that impulse engines are a clean burning type of propulsion engines.