Building on the first-generation automated small molecule synthesizer designed by Burke and coworkers, we developed a second-generation small molecule synthesizer capable of parallel runs of deprotections, couplings, and purifications (Fig. ). Briefly, the synthesis strategy relies on the MIDA protecting group rendering boron unreactive until deprotected with mild aqueous base, analogous to the Fmoc group in iterative peptide synthesis (Fig. ). The new automated synthesis instrument leverages advances in hardware and software to enable up to 12 fully parallelized, simultaneous preparative-scale iterative Suzuki reactions. Importantly, the increased throughput allows for screening of large regions of chemical space in a single automated synthetic run. Using this approach, a library of symmetric terphenyl derivatives with different alkyl side chains (Rn) and an asymmetric target molecule (R6-H) were prepared using two automated procedures in conjunction with the standard building block set (Fig. ).