The geometries and electronic structures of selenolate-protected Au nanoclusters, Au-24(SeR)(20) and Au-20(SeR)(16), and their thiolate analogues are theoretically investigated with DFT and SCS-MP2 methods, to elucidate the electronic structure of their unusual Au-8 core and the reason why they have the unusual entangled "staple-like" chain ligands. The Au-8 core is understood to be an [Au-4](2+) dimer in which the [Au-4](2+) species has a tetrahedral geometry with a closed-shell singlet ground state. The SCS-MP2 method successfully reproduced the distance between two [Au-4](2+) moieties, but the DFT with various functionals failed it, suggesting that the dispersion interaction is crucial between these two [Au-4](2+) moieties. The SCS-MP2-calculated formation energies of these nanocluster compounds indicate that the thiolate staple-like chain ligands are more stable than the selenolate ones, but the Au-8 core more strongly coordinates with the selenolate staple-like chain ligands than with the thiolate ones. Though Au-20(SeR)(16) has not been reported yet, its formation energy is calculated to be large, suggesting that this compound can be synthesized as a stable species if the concentration of Au(SeR) is well adjusted. The aurophilic interactions between the staple-like chain ligands and between the Au-8 core and the staple-like chain ligand play an important role for the stability of these compounds. Because of the presence of this autophilic interaction, Au-24(SeR)(20) is more stable than Au-20(SeR)(16) and the unusual entangled ligands are involved in these compounds.