The bacterial (Acinetobacter) flavoprotein monooxygenase cyclohexanone oxygenase was found by spectrophotometric NADPH consumption assays and product analysis studies to perform oxygenation reaction on ketones, aldehydes, sulfides,selenides, boronic acids, a phosphite ester, and an iodide ion, Kinetic parameters (Km Vmax) are reported for these substrates. The relevance of these results to possible active oxygen-transfer species in this enzyme is discussed. The potential utility of boronic acids as general probes for nucleophilic oxygen-transfer capability in oxygenases and in model chemistry is analyzed. The potential utility of cyclohexanone oxygenase as an enatioselective and/or chemoselective oxidant for organic molecules is assessed. Unsuccessful attempts at exploiting the 2,3-signatropic rearrangement of allyl sulfoxides and allyl selenoxides for mechanism-based inactivation of cyclohexanone oxygenase are reported. The use of the facile 2,3-sigmatropic rearrangement of allyl selenoxides to generate electrophilic allyl selenates for the design of mechanism-based inactivators for other enzymes is proposed.