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The chemistry of the experiment

The first stages of the uranium-238 series are involved in this experiment. 

Uranium-238 first stages
The aqueous solution (at the bottom of the bottle) contains the uranium-238, its daughter thorium-234 and the short-lived granddaughter protactinium-234. 
Uranium and protactinium both form anionic chloride complexes but thorium does not. At high hydrogen ion concentrations, these complexes will dissolve in the organic layer (which is floating on top of the aqueous solution). 
When you shake the bottle, about 95% of the short-lived granddaughter (protactinium) and some of the uranium will be dissolved in the organic layer. The thorium stays in the aqueous layer. 
Since radioactivity is a property of the innermost nucleus of the atom it is not affected by chemical combination. 
The granddaughter (in the organic layer) decays without any more being produced by its parent (thorium) all of which is still in the aqueous layer. It emits beta particles which travel through the plastic wall of the bottle. Isolating the protactinium in the top (organic) layer allows it to decay without any top-up from its parent (thorium). 
The radiation from the thorium and uranium should not interfere with the results, for two reasons: 

  • The counter does not detect the alpha particles from the uranium or the low energy beta particles from the thorium. It only records the high energy (2 MeV) beta particles from the granddaughter (protactinium). 
  • The uranium-238 decays with an extremely long half-life. It yields a meagre, almost constant, stream of low energy alpha particles. Its daughter, thorium-234, decays with a half-life of 24 days. During the length of this experiment the decay rate can be assumed to be constant. If these two isotopes contribute to the count at all, it will be accommodated in the background count. The stockpile of thorium is also constantly topped up in the aqueous layer as long as the protactinium is present with the thorium.