Structural control among hexagonal (trimer), rhomboidal (dimer), and infinite-chain supramolecular complexes with three different supporting ligands of ethylenediamine (en), N,N,N'N'-tetramethylethylenediamine (en*), and 1,2-bis(diphenyl)phosphinoethane (dppe) [(en)Pd(L)](3)(OTf)(6) 1t center dot OTf, [(en*)Pd(L))(2)(PF6)(4) 2d center dot PF6, and [(dppe)Pd(L)(OTf)(2)](infinity) 3 center dot OTf (OTf = trifluoromethane sulfonate; L = 1,3-bis(4-pyridylethynyl)benzene) in the solid and solution states was investigated. The encapsulation of a large Keggin-type polyoxometalate [alpha-PW12O40](3-) by these complexes was also examined. As the steric bulkiness of the supporting ligands increased in the order of en < en* < dppe, the hexagonal, rhomboidal, and infinite-chain structures were obtained, as confirmed by X-ray crystallography. In solution, equilibrium between the molecular hexagon (1t center dot OTf/2t center dot PF6) and the molecular rhomboid (1d center dot OTf/2d center dot PF6) was observed in the en/en* ligand systems, whereas 3 center dot OTf with the dppe ligand did not exhibit equilibrium and instead existed as a single species. These phenomena were established by cold-spray ionization mass spectroscopy (CSI-MS) and H-1 diffusion ordered NMR spectroscopy (DOSY). The addition of the highly negatively charged Keggin-type phosphododecatungstate [alpha-PW12O40](3-) to a solution of 2t/2d center dot PF6 resulted in the encapsulation of the tungstate species in the cavity of the molecular hexagon to form {[(en*)Pd(L)](3)[superset of alpha-PW12O40]}(PF6)(3) 2t center dot[alpha-PW12O40](3-), as confirmed by a combination of H-1 and P-31 DOSY and CSI-MS spectral data.