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Gas-phase synthesis of nanoparticles with different structural and chemical distribution is reported using a circular magnetron sputtering in an ion cluster source by applying high-power impulses. The influence of the pulse characteristics on the final deposit was evaluated on Au nanoparticles. The results have been compared with the more common direct current approach. In addition, it is shown for the first time that high-power impulses in magnetron based gas aggregation sources allows the growth of binary nanoparticles, CoAu in this case, with a variety of crystalline and chemical arrangements which are analyzed at the atomic level.