Bottom‐up chemical synthesis to construct intricate molecules has been a profound challenge. An effective approach is to utilize organic ligands and metal ions, but the formation of a single product among other possible candidates has proven difficult for dissymmetric structures. We now report the synthesis of single isomeric complexes with dissymmetric structures using the mismatch in the coordination valences of macrocyclic homooligomers and metal ions. A series of amide‐cyclodextrin derivatives possessing multiple 2,2′‐bipyridyl (bpy) groups forms mononuclear complexes whose specific three bpy groups are linked in the fac‐Λ configuration. The intermolecular coordination of the β‐cyclodextrin metal complex produces a dissymmetric cyclodextrin trimer as a single isomer, whose initially equivalent 21 (=7×3) bipyridylamide‐pyranose units are placed in different environments. Furthermore, we realize chiral recognition of amino acid anions utilizing the distinctive amide groups arranged on the unsymmetrically fixed scaffold.

An amide cyclodextrin with anion recognition ability exhibits unique binding mode in which unsymmetrically arranged functional groups play distinctive roles.

A cyclodextrin derivative 1 possessing multiple pnitrophenylamide groups, which is a strong hydrogen-bond donor, encapsulates phosphodiester anions in two recognition modes. One is the 'threading' mode, in which the phosphodiester passes through the cyclodextrin cavity. The other is the 'folding' mode, in which the included phosphodiester is bent inside the cyclodextrin cavity. The tendency between the two recognition modes depends on the substituents on the phosphodiesters.

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