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The derivatives 5,7-dimethyl[1,3,4]thiadiazolo[3,2-<i>a</i>]pyrimidin-4-ium-2-thiolate (<b>1</b>) and 7-methyl-5-phenyl[1,3,4]thiadiazolo[3,2-<i>a</i>]pyrimidin-4-ium-2-thiolate (<b>2</b>) were fully characterized by single-crystal X-ray diffraction. Their supramolecular structure is built through both π–π stacking and C=S–π interactions for both compounds. The embedment of the tested compounds into Fe₃O₄@C₁₈ core-shell nanocoatings increased the protection degree against <i>Candida albicans</i> biofilms on the catheter surface, suggesting that these bioactive nanocoatings could be further developed as non-cytotoxic strategies for fighting biofilm-associated fungal infections.