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Gold nanoclusters protected by organic ligands, [AunXm]q, have crucial interest in homogeneous and heterogeneous catalysis including CO oxidation [1,2]. The application of [AunXm]q as a catalysts has sufficient advantage, due to any property such as activity, selectivity or stability can correlate with particular composition and structure which are precisely defined. The mechanisms of catalytic reactions involving the [AunXm]q are still to be clarified, the quantum chemical study of their properties at the atomic level seems to have great prospects. Here we present the analysis of structure, electronic and chemical properties of Au20(SR)16 (R=CH3, Ph) and [Au4(dpmp)2X2]2+ (X= –C≡CH, –C≡CCH3, –СН3, –SCH3, –Cl; dpmp – bis(diphenylphosphinomethyl)phenylphosphine)); CO oxidation catalysed by the clusters and their fragments (Au2(SR)3–, (AuSR)4, Au(AuSR)4, PPh3AuCH3) is also simulated to predict the active site and the mechanism of catalytic reactions involving [AunXm]q. Spin–polarized DFT/PBE level in the scalar–relativistic approach were used. The method has been tested in details in respect to predict structure and electronic properties of [AunXm]q. According to calculation of [Au4(dpmp)2X2]2+ structure, it has flat Au4 fragment stabilized by two opposite located X groups and two staple-like dpmp. The calculated Au–Au, Au–X, and Au–P distances agree with X ray data. The X ligand affects on the electronic cluster’s stability, decomposition, and ligand exchange ability. The different pathways of CO oxidation on [Au4(dpmp)2(C≡CCH3)2]2+ including ligand shell conserving or ligand exchange through breaking of one Au–P contact have been simulated. The calculated activation energies of all steps are small and suggest that the reaction can occurs at room temperatures. The five isomers of Au20(SR)16 (R=CH3, Ph) have been calculated. The Au7 core consists of two tetrahedrons united by a common vertex; it is protected by an octameric ring, one triple and two monomeric staple motifs SR(AuSR)x. The cluster can catalyzed CO oxidation, but the activation energies of the corresponding steps calculated for the fragments: Au2(SR)3–, (AuSR)4, Au(AuSR)4, PPh3AuCH3 are less than for the clusters. This suggests that the atomic fragments of the ligand-protected gold clusters can be involved in catalysis.