Simulating the active sites of copper-trafficking proteins. Density functional structural and spectroscopy studies on copper(I) complexes with thiols, carboxylato, amide and phenol ligands

A series of mononuclear binary and ternary Cu(I) complexes with formato, formamide, methylphenol, and methanethiolato ligands were optimized at DFT-B3LYP/6-31G** (BS1) and DFT-B3LYP/6-311++G** (BS2) levels of theory. The solvent effect was taken into account via PCM method (BS1W and BS2W, respectively). The coordination arrangement for [Cu-I(SCH3/S(H)CH3)(OOCH)](-/0) and [Cu-I(SCH3/S(H)CH3)(O(H)(C6H4)CH3)](0/+) was pseudo-linear and for [Cu-I(SCH3/S(H)CH3)(OOCH)(OC(H)NH2)](-/0) was pseudo-trigonal. The [Cu-I(S-S(H)CH3/Cu-I(S-SCH3)](+/0) link even to amide carbonyl and to general O(H)R residues (R=C6H5CH3). [Cu-I(SCH3)(2)(O(H)(C6H4)CH3)](-) went towards dissociation of the O(H)(C6H4)CH3 ligand, whereas [Cu-I(S(H)CH3)(2)(O(H)(C6H4)CH3)](+) converged nicely, maintaining the hydroxy function linked to the metal. The trends of total electronic energies seemed to be significant, suggesting that linear (CuS2)-S-I coordination is more suitable than (CuS)-S-I, (CuS3)-S-I and (CuS4)-S-I arrangements. The formation energies of [Cu-I(S(H)CH3/SCH3)(OOCH)](0/-1) were higher than those of [Cu-I(S(H)CH3/SCH3)(2)](+/-) on starting from [Cu-I(S(H)CH3/Cu-I(SCH3)](+/0) by ca. 11-9kcalmol(-1) (BS2W). The structural arrangements, bond distances, and angles as well as computed spectroscopic parameters resulted in good agreement with experimental data for corresponding synthetic complexes and with metal site regions of several copper(I)-proteins. These data help in interpreting structural data of complex biological systems and in constructing reliable force fields for molecular mechanics computations. © 2016 Taylor and Francis.