Au8 Kernel Packing and Ring Shell Contact Redistribution in Thiolate and Selenolate Au24 Nanoclusters

The thiolate/selenolate pair [Au25(XR)18]− (X = S or Se) provides a useful reference for ligand substitution around a comparatively compact Au13-centered framework because the two derivatives retain closely related structures. Here, density functional theory calculations and reciprocal methyl models with S/Se exchange are used to examine how local geometry controlled by S or Se is accommodated by alternative Au24X20 kernel-shell topologies. The experimentally derived Au24(SR)20-A* framework contains a face-to-face Au4/Au4 Au8 kernel wrapped by four Au6(SR)5 rings, whereas the experimentally derived Au24(SeR)20-B* framework adopts a perpendicular-edge Au8 kernel and interlocked Au5(SeR)4/Au7(SeR)6 rings. Reciprocal ligand-exchange models separate the direct structural response to S/Se substitution within a fixed topology from that associated with A/B topology reorganization. Within either topology, S-to-Se replacement produces only modest changes in the kernel–motif d3 and inter-ring d5 Au···Au contacts. In contrast, A-to-B topology reorganization changes the Au8 kernel from face-to-face to perpendicular-edge Au4/Au4 packing and produces a substantially larger shortening of d5. This structural separation is retained across PBE-D3, PBE0-D3, and TPSS-D3 optimized structures, for which fixed-topology S-to-Se replacement changes d5 by only 0.01–0.05 Å whereas A-to-B topology reorganization shortens d5 by 0.24–0.32 Å. Complementary Au(I) dimer scans show that replacing S by Se shifts the local Au(I)···Au(I) potential toward a shorter minimum-energy separation and a deeper interaction well under a common coordination model. Together, these results support a structural picture in which S/Se identity shifts the local interaction landscape, while Au8 packing and the ring shell determine how this preference appears across the Au24X20 framework.