[Tangential to your main question] If one separated beta-carotene (yellow-orange) and lycopene (orange-red) on silica, you don't need a dye to visualize them. These two compounds are chromophores by themselves, and I have separated them on alumina, as opposed to silica.
I don't have any direct experience with alkaloids. However, if you have protonate an alkaloid under acidic conditions, I expect that it will become much more polar and possibly more difficult to separate on silica. Do you know whether the compound of interest becomes water soluble upon protonation?
I believe it does based on what I've read. When I first posted, I think I misunderstood what was happening. I later realized that they are doing an acid/base extraction, I think.
Here is a list of the basic steps acquired from a study that already did it:
Plant material extracted into alcohol.
Alcohol is evaporated leaving crude extract with a bunch of junk + alkaloids.
That extract is dissolved in acetic acid/water mix.
Acidic mix is washed with pet ether
At this point, I'm assuming a separatory funnel is used and the pet ether layer is discarded.
Remaining acidic solution is then made alkaline to a specific PH.
solution is then extracted with chloroform (once again I think sep. funnel is used and only chloro layer is kept)
chloroform mix is washed with water
water is removed (via drying agent)
chloroform is evaporated leaving all alkaloid salts.
From here, a column chrom. would be used to further isolate/examine.
Thoughts?