We used molecular dynamics (MD) techniques to examine the encapsulation of Bengal Rose (BR) molecules in the Meijer dendrimer box (DBox) formed by the addition of tert-butyloxycarbonyl-L-Phe (tBOC-L-Phe) cap molecules to the 64 terminal primary amines of a fifth generation poly(propyleneimine) (PPI-5) dendrimer. Using a large periodic box (including DBox, four to six BR, and CH2Cl2 solvent, totaling similar to 25 000 atoms), we examined the MD of these systems for similar to 0.5 ns. Without the cap we find that BR molecules establish a concentration dependent equilibrium between the interior and surface regions of PPI-5 and the solvent region outside the dendrimer. The number of BR molecules calculated to associate with the interior of the PPI-5 dendrimer agrees exactly with experiment (at the same BR/PPI concentration). MD simulations on the DBox in CH2Cl2 show that the tBOC-L-Phe surface is completely impermeable to encapsulated BR molecules, even when an excess is forced inside the box. The close correspondence of the theory with experiment suggests that these methods can be used to design such systems in advance of experiment.