A novel approach is presented for the application and interpretation of molecular mechanics calculations in ligand structural design. The methodology yields strain energies that (i) provide a yardstick for the measurement of ligand binding site organization for metal ion complexation and (ii) allow the comparison of any two ligands independent of either the number and type of donor atoms or the identity of the metal ion. Application of this methodology is demonstrated in a detailed examination of the influence of alkyl substitution on the structural organization of ethylene-bridged, bidentate, ether donor ligands for the alkali and alkaline earth cations. Nine cases are examined, including the unsubstituted ethylene bridge (dimethoxyethane), all possible arrangements of individual alkyl groups (monoalkylation, gem-dialkylation, meso-dialkylation, d,l-dialkylation, trialkylation, and tetraalkylation), and both cis and trans attachments of the cyclohexyl group. The calculated degree of binding site organization for metal ion complexation afforded by these connecting structures is shown to correlate with known changes in complex stability caused by alkyl substitution of crown ether macrocycles.