Synthesis, Crystal Structure, DFT Modeling and Biological Activity of a Trinuclear Copper(II) Azide Polymer Containing Imidazole and Bridging Imidazolate Ligands, [Cu3(Imz-H)4(Imz)2(N3)4

Abstract

The title compound, [Cu3(Imz-H)4(Imz)2(N3)4]n (1) (Imz-H = imidazole) was prepared by the reaction of CuCl2·2H2O with imidazole and sodium azide, and its structure was determined by X-ray crystallography. The crystal structure shows that the complex exists in the form of a two dimensional polymer consisting of dimeric [Cu(Imz-H)(Imz)0.5(N3)1.5]2 and monomeric [Cu(Imz-H)2(Imz)(N3)] units. In the dimeric part each Cu(II) ion is bound to two nitrogen atoms of Imz-H or Imz− and three nitrogen atoms of azide adopting a distorted square pyramidal geometry. In the monomeric part, the copper atom is disordered over two positions and is coordinated to two imidazole molecules (Imz-H), two bridging imidazolate (Imz-) groups, and two weakly bound azide ions. In order to validate the obtained structure, the structures of two complexes; [Cu3(Imz-H)5(Imz)(HN3)4(N3)2]3+ containing one monomer and one dimeric unit as a model of 1 and a hypothetical complex, [Cu4(Imz-H)6(Imz)(HN3)4(N3)4]3+ containing only dimeric units were fully optimized at the B3LYP-D3 level of theory. The interaction energy between the dimeric and monomeric units in the former complex was found to be almost twice larger that calculated between the dimeric units in the later complex. Therefore, the theoretical results support that the experimentally determined structure (1) is energetically more preferred than that containing only the dimeric units. The natural bond orbital (NBO) analysis of the model complexes of (1) was performed and the distribution of spin density at the atoms of [Cu3(Imz-H)5(Imz)(HN3)4(N3)2]3+ and [Cu5(Imz-H)8(Imz)2(HN3)6(N3)4]4+ was discussed. The NBO charge on copper cation in the dimeric unit is 0.90 e and is smaller than that on the Cu(II) ion in the monomeric unit by 0.09 e. Antimicrobial properties of the complex were evaluated by minimum inhibitory concentration and the results showed that the complex exhibited no significant activities against the selected microorganisms.