Calix[4]arene mono- and bis-crown6 in the 1,3 alternate conformation are highly selective extractants for cesium towards sodium in an acidic liquid waste. Extraction and selectivity are related to complexation properties which can be studied by Molecular Dynamics techniques. In this paper, we describe the results of Molecular Dynamics simulations in an explicit water phase for four complexes of 1,3-alternate mono- and bis-crown-calix[4]arenes. The structural features obtained are interpreted on the basis of cation/ligand complementarity and can explain the relative performances in Na+ and Cs+ extraction for the compounds simulated. The relative free energy of binding can be computed and is in a semi-quantitative agreement with complexation data in an homogeneous medium.