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Other contaminants embody varied flavonoids and possibly cis-indigo and brown isoindigo. Because the composition of this cocktail varies from dye batch to dye batch, the colour of naturally derived indigo dye is rarely reproducible. One explanation is that leuco-indigo is strongly attracted to a material’s polar functional teams by a combination of hydrogen-bonding, ionic, polar and nonpolar interactions . As the dye is applied to the material, the molecules work together with the fabric and with one another. When the indigo is oxidized back into its insoluble form, the attraction between the dye molecules prevails over the attraction between the dye molecules and the substrate, creating dye aggregates. Textiles which seem bluer have a stronger dye molecule-material interplay, while supplies with violet hues have extra dye aggregates.

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It was found that smaller aggregates replicate blue mild, and bigger aggregates replicate pink. Monobromoindigo dye contained primarily small aggregates together with some larger aggregates that created a violet color. Heating broke down the larger aggregates into small aggregates, creating a bluer color. Conversely dibromoindigo dye has primarily larger aggregates alongside a number of smaller ones to provide a purple tone. Heating transformed the smaller aggregates into bigger ones, creating a redder color .

The implication is that the colour of indigo dyes depends simply as much upon how they type molecular aggregates as it does upon their fundamental molecular construction. The colors of indigo and Tyrian purple are each blue in an organic solvent, but are respectively blue and purple when used as dyes.

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Nylon has a stronger attraction to dye molecules than wool, thus nylon appears bluer. To study why the colour of bromoindigo adjustments with temperature carbon nanotubes have been used as surrogate fibres and the scale of the dye aggregates were measured using a transmission electron microscope.