A instrument for performing synthesis of small molecules such as Oligos and Peptides when using solid phase synthesis techniques to synthesize small molecules. The system and methods include a mechanism for controlling the pressure differential across the reaction vessels that contain the solid support used in solid phase synthesis. Reaction vessels are held in a holder that provides a sealable chamber at the outlet ends of the reaction vessels. The rotor containing the reaction vessels is placed within a sealable chamber. The sealable chamber is fitted with a means for engaging the rotor and draining the reaction vessels to waste. The sealable chamber is also fitted with a means for engaging the rotor to drain the reaction vessels at a slower, variable rate.