We discovered anew type of molecular recognizing reaction of the interfacial aggregation of monocationic palladium(II)-2-(5-bromo-2-pyridylazo)-5-diethylaminophenol complex (PdL) with neutral diazine (Dz) or purine bases at the toluene-water system by use of centrifugal liquid membrane (CLM) spectrometry. The formation of the interfacial aggregates of PdL-Dz isomer complexes was investigated by CLM/UV-vis spectroscopy, CLM/resonance Raman spectroscopy and optical microscopic images. The high molar absorptivity of the PdLC1 complex (4.33 x 10(4) m(-1) cm(-1) at 564 nm) was drastically reduced by the formation of the interfacial aggregates with diazine. This suggested that the electric resonance structure (charged quinone structure) in Pd(II)-5-Br-PADAP was prevented by the interaction with ClO4-. The composition of the interfacial aggregates depended on the structure of Dz isomers; PdL-1,2-Dz formed fine domains with the molar ratio of 1,2-Dz/PdL = 1: 1, whereas PdL-1,4-Dz was as a very thin membrane with a molar ratio of l,4-Dz/PdL = 1:2. The ability for the formation of the interfacial aggregate of the PdL-Dz isomer complexes increased in the order 1,3-Dz < 1,2-Dz < 1,4-Dz. The formation of the interfacial aggregate of the PdL-Dz isomer was greatly dependent on the structure of Dz, not on the basicity of Dz. The interfacial aggregation was sensitively detected even in a diluted concentration lower than 10(-5) M for 1,4-Dz. Moreover, it was demonstrated that the molecular recognition by the aggregation of PdL was applicable for the bases of nucleic acids. PdL could form the interfacial aggregates preferentially with purine bases (adenine and guanine).