A molecular dynamics model for tributyl phosphate (TBP) and diamyl amyl phosphonate (DAAP) is presented using the Generalized AMBER Force Field (GAFF) and the AM1-BCC method for calculated atomic charges with a modification to the phosphorus-containing dihedral parameters. The density and average molecular dipole in a neat liquid simulation, and dimerization in dodecane and octane diluents, compare favorably to experimental values. At low extractant concentration, investigation of the dimer structure reveals the offset "head-to-head" orientation as the predominant structure over a range of TBP and DAAP concentrations with a phosphoryl oxygen separation distance between dimerized extractants of 3-5.5 angstrom. At high extractant concentrations, a graph analysis of extractant aggregates was used to determine concentrations of each aggregate size and the average coordination number, which gives a measure of the linearity of the aggregates. For aggregates up to 7 extractant molecules, the mean free energy of association per molecule was found to be 0.55-0.59 and 0.72 kcal/mol for TBP and DAAP, respectively. In both diluents, TBP formed large aggregates more frequently than DAAP, and those aggregates were more nonlinear than their DAAP equivalents. This finding anticipates differences in aggregation chemistry between TBP and DAAP in PUREX extraction systems.