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Interaction of Cu (II) ions with the matrix of soil and mineral phases of layered silicates was assessed by the Miller method of selective sequential fractionation and a set of synchrotron X-ray methods, including X-ray powder diffraction (XRD) and X-ray absorption spectroscopy (XANES). It was shown that the input of Cu into Calcic Chernozem in the form of monoxide (CuO) and salt (Cu(NO3)2) affected the transformation of Cu compounds and their affinity for metal-bearing phases. It was found that the contamination of soil with a soluble Cu(II) salt increased the bioavailability of the metal and the role of organic matter and Fe oxides in the fixation and retention of Cu. During the incubation of soil with Cu monoxide, the content of the metal in the residual fractions increased, which was related to the possible entry of Cu in the form of isomorphic impurities into silicates, as well as to the incomplete dissolution of exogenic compounds at the high level of their input into the soil. A mechanism for the structural transformation of minerals was revealed, which showed that ion exchange processes result in the sorption of Cu (II) ions from the saturated solution by active sites on the internal surface of the lattice of dioctahedral aluminosilicates. Surface hydroxyls at the octahedral aluminum atom play the main role. X-ray diagnostics revealed that excess Cu(II) ions are removed from the system due to the formation and precipitation of coarsely crystalline Cu(NO3)(OH)3. [ABSTRACT FROM AUTHOR]