Chemical reactions involved in staining I'm a geology student completing a project on chemical staining and was after some chemistry help on some of the reactions taking place. I am using various different stains to identify carbonate and feldspar minerals. 

One of the stains, in particular, is alizarin red S (1,2-dihydroxyanthraquinone) and is used to stain calcite ($\ce{CaCO3}$) red and Fe-calcite/Fe-dolomite blue. The stain powder is mixed with a weak (2%) HCl solution to react with the carbonate and produce the stain. However, I am just unsure about what reactions are taking place between the stain solution and the mineral that produce the precipitate on the surface of the grains. 

I'm not finding literature on this reaction - probably because it has been mainly used by geologists without a solid chemistry background. Any help would be much appreciated.
Alizarin red S can stain calcium deposits through interaction of its sulfonic acid and hydroxy groups with calcium ions.

I found a reference for you: http://jhc.sagepub.com/content/17/2/110.full.pdf+html

Interestingly, however, this research seems to suggest using a solution of pH $\approx$ 9, stating that solutions of acetic acid (pH 5) did not work that well.