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The title complex, [Cu(ClO4)2(C9H13N5O)(CH3OH)], was synthesized from a methanolysis reaction of N-(methyl­pyri­din-2-yl)cyano­guanidine (L3) and copper(II) perchlorate hexa­hydrate in a 1:1 molar ratio. The CuII ion is six-coordinated by an N3O3 donor set which confers a highly distorted and asymmetric octa­hedral geometry. Three N-donor atoms from the chelating 1-(meth­oxy­methanimido­yl)-2-(pyri­din-2-ylmeth­yl)guanidine (L3m) ligand and one O atom from the methanol mol­ecule define the equatorial plane, with two perchlorate O atoms in the apical sites, one of which has a long Cu—O bond of 2.9074 (19) Å. The dihedral angle between the five- and six-membered chelate rings is 8.21 (8)°. Two molecules are associated into a dimeric unit by inter­molecular N—H...O(perchlorate) hydrogen bonds. Additionally, the weakly coordinated perchlorate anions also link adjacent [Cu(ClO4)2(L3m)(CH3OH)] dimers by hydrogen-bonding inter­actions, resulting in a two-dimensional layer in the (100) plane. Further C—H...O hydrogen bonds link the two-dimensional layers along [100] to generate a three-dimensional network.
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