[Bakterien]

So I'm reacting molecule A (UV-active) with (3-Aminopropyl)trimethoxysilane. When I check the reaction on TLC (silica) I can see my SM with a nice rf value. However I can't find my product. But on the baseline I can observe a dot that is visible under UV-light. Could this be my product ? I think that the silica has reacted with my molecule thus preventing it to move on the TLC plate. Could this be true ?

If that is the case: Then I can not flash it on silica? What else can I use , aluminumoxide ?

[discodermolide]

I think you may be correct in assuming that the silyl group falls off on silica-gel.
Try and get a NMR of the crude product to confirm the structure then advance it to the next step without any further purification.

You could try alumina to see if you can TLC this product but I may tend to go the route I suggested above.