There is an ever-increasing body of evidence that metallic complexes involving amphiliphic ligands do not form normal solutions in organic solvents. Instead, they form complex fluids with intricate structures. For example, the metallic complexes may aggregate into clusters, and these clusters themselves may aggregate into superclusters. To gain a deeper insight into the mechanisms at play, we have used an improved force field to conduct extensive molecular dynamics simulations of a system composed of zirconium nitrate, water, nitric acid, tri-n-butyl phosphate, and n-octane. The important new finding is that a dynamic equilibrium between the cis and trans isomers of the metal complex is likely to play a key role in the aggregation behavior. The isolated cis and trans isomers have similar energies, but simulation indicates that the clusters consist predominantly of cis isomers. With increasing metal concentration, we hypothesize that more clustering occurs and the chemical equilibrium shifts toward the cis isomer. It is possible that such isomeric effects play a role in the liquid-liquid extraction of other species and the inclusion of such effects in flow sheet modeling may lead to a better description of the process.