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Abstract: A hallmark of biological catalysts is their ability to achieve both high activity and high selectivity via precise nanoscale control over the catalytically active site. One of the most common motifs observed in these systems is the organization of an acid-base pair. Here, synthetic methods for the design and synthesis of nanostructured active sites in inorganic oxides are presented that specifically utilize this paradigm for application as advanced catalytic materials. Our approach uses the imprinting of bulk silica to synthesize isolated base catalysts within controlled nanostructured environments consisting of either acidic groups in close proximity (<1 nm) to the active base catalyst, or nonacidic functionality of either hydrophobic or hydrophilic character. These catalysts allow for a fundamental study of the mechanisms governing heterogeneous base catalyzed condensation reactions and have a significant impact on the rational design of catalysts.