A system for the multiple, simultaneous synthesis of compounds preferably uses a reaction apparatus comprising a reservoir rack having a plurality of reaction wells, a plurality of reaction tubes, usually gas dispersion tubes, having filters on their lower ends, a holder block, having a plurality of apertures, and a manifold, which has ports to allow introduction/maintenance of a controlled environment. The manifold top wall has a plurality of apertures in axial alignment with the reaction tubes and a gasket which allows penetration by a needle in order to dispense and aspirate materials from the reaction tubes. Sealing members, such as gaskets, are placed between the holder block, manifold and reservoir rack and the components are releasably fastened together. A robotic sample processor is used to automate the synthesis process using the reaction apparatus.