Molecular Orbital Study of Complexes of Zinc(II) with Sulphide, Thiomethanolate, Thiomethanol, Dimethylthioether, Thiophenolate, Formiate, Acetate, Carbonate, Hydrogen Carbonate, Iminomethane and Imidazole. Relationships with Structural and Catalytic Zinc in Some Metallo-Enzymes

Abstract

Geometry optimization and energy calculations have been performed at the density functional B3LYP/LANL2DZ level on hydrogen sulfide (HS-), dihydrogensulfide (H2S), thiomethanolate (CH3S-), thiomethanol (CH3SH), thiophenolate (C6H5S-), methoxyde (CH3O-), methanol (CH3OH), formiate (HCOO-), acetate (CH3COO-), carbonate (CO3 2-), hydrogen carbonate (HCO3−), iminomethane (NH=CH2), [ZnS], [ZnS2]2-, [Zn(HS)]+, [Zn(H2S)2+, [Zn(HS)4]2-, [Zn(CH3S)]+, [Zn(CH3S)2], [Zn(CH3S)3]−, [Zn(CH3S)4]2-, [Zn(CH3SH)]2+, [Zn(CH3SCH3)]2+, [Zn(C6H5S)]+, [Zn(C6H5S)2], [Zn(C6H5S)3]−, [Zn(HS)(NH=CH2)2]+ [Zn(HS)2(NH=CH2)2], [Zn(HS)(H2O)]+, [Zn(HS)(HCOO)], [Zn(HS)2(HCOO)]−, [Zn(CH3O)]+, [Zn(CH3O)2], [Zn(CH3O)3]−, [Zn(CH3O)4]2, [Zn(CH3OH)]2+, [Zn(HCOO)]+, [Zn(CH3COO)]+, [Zn(CH3COO)2], [Zn(CH3COO)3]−, [Zn(CO3)], [Zn(HCO3)]+, and [Zn(HCO3)(Imz)]+ (Imz, 1,3-imidazole). The computed Zn-S bond distances are 2.174Å for [ZnS], 2.274 for [Zn(HS)+ 2.283 for [Zn(CH3S)]+, and 2.271 for [Zn(C6H5S)]+, showing that sulfide anion forms stronger bonds than substituted sulfides. The nature of the substituents on sulfur influences only slightly the Zn-S distance. The optimized tetra-coordinate [Zn(HS)2(NH=CH2)2] molecules has computed Zn-S and Zn-N bond distances of 2.392 and 2.154Å which compare well with the experimental values at the solid state obtained via X-ray diffraction for a number of complex molecules. The computed Zn-O bond distances for chelating carboxylate derivatives like [Zn(HOCOO)]+ (1.998Å), [Zn(HCOO)]+ (2.021), and [Zn(CH3COO)]+ (2.001) shows that the strength of the bond is not much influenced by the substituent on carboxylic carbon atom and that CH3− and HO- groups have very similar effects. The DFT analysis shows also that the carboxylate ligand has a preference for the bidentate mode instead of the monodentate one, at least when the coordination number is small. The analysis of the bond formation energies for the species Zn(CH3S)n shows that the addition of a CH3S− ligand to the zinc(II) center is highly exothermic for Zn2+ (-415.26 kcal/mol), for [Zn(CH3S)]+ (-207.06) and for [Zn(CH3S)2] (-67.09). Interestingly, the formation of tetrahedral [Zn(CH3S)4]2- from tri-coordinate [Zn(CH3S)3]- is endothermic by 32.56 kcal/mol. This unfavorable enthalpy contribution for the stability of the tetra-coordinate species suggests a facile methylation of one of the sulfur atoms at the ZnS4 core.