Molecular modeling simulating aqueous conditions is used to elucidate the formation of aggregates of sulfonated chromophores, including Congo Red and Trypan Blue. The relative energies involved in the aggregation process are calculated and geometric features of the molecules and their aggregates are discussed. Parallel stacking facing one another occurs with slight shifts along the long axes of the chromophores to accommodate the sterically demanding sulfonate groups. The Connolly surfaces and volumes of the indi vidual molecules as well as their aggregates are determined.
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