The design of new supramolecular complexes often depends on reducing entropic contributions to improve binding. However, few studies provide reliable values for the cost of entropic contributions. Here, the binding affinities of a series of six alpha,omega-diamides to alpha,omega-dicarboxylates are calculated using a predominant states method and an implicit solvent model based upon finite difference solutions of the Poisson-Boltzmann equation. The calculations are able to reproduce the observed increase in binding free energy as the number of single bonds increases. However, calculations show that the increase in binding free energy is not due to an increase in entropy. Instead, the increase is due to the changing ability of the alpha,omega-diamides to form internal hydrogen bonds that must be disrupted to bind to the dicarboxylate receptors. This suggests that interpreting experimental free-energy trends to give rotational entropy contributions may be problematic.