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Here we present the study of the modification of structural properties and energy transfer to emission centers caused by partial substitution of Al and Ga cations by Sc in GAGG:Ce crystals. Unit cell parameters and space group were obtained using the XRD analysis. The chemical compositions of the crystals were determined using SEM-EDX and TEM-EDX techniques. Structures were refined by Rietveld method and the distribution of Al/Ga/Sc cations between octahedral and tetrahedral sites was obtained. The influence of Sc on the electronic band structure and the energy of the 4f and 5d Ce3+ levels is shown. The modification of the band structure induced by the Sc electronic states results in the suppression of Gd emission and enhancement of Ce3+ emission at low temperatures.