Atomic structure of a recently synthesized ligand-covered cluster Au-24(SR)(20) [J. Phys. Chem. Lett., 2010, 1, 1003] is resolved based on the developed classical force-field based divide-and-protect approach. The computed UV-vis absorption spectrum and powder X-ray diffraction (XRD) curve for the lowest-energy isomer are in good agreement with experimental measurements. Unique catenane-like staple motifs are predicted for the first time in core-stacked thiolate-group (RS-) covered gold nanoparticles (RS-AuNPs), suggesting the onset of structural transformation in RS-AuNPs at relatively low Au/SR ratio. Since the lowest-energy structure of Au-24(SR)(20) entails interlocked Au-5(SR)(4) and Au-7(SR)(6) oligomers, it supports a recently proposed growth model of RS-AuNPs [J. Phys. Chem. Lett., 2011, 2, 990], that is, Au-n(SR)(n-1) oligomers are formed during the initial growth of RS-AuNPs. By comparing the Au-core structure of Au-24(SR)(20) with other structurally resolved RS-AuNPs, we conclude that the tetrahedral Au-4 motif is a prevalent structural unit for small-sized RS-AuNPs with relatively low Au/SR ratio. The structural prediction of Au-24(SR)(20) offers additional insights into the structural evolution of thiolated gold clusters from homoleptic gold(I) thiolate to core-stacked RS-AuNPs. Specifically, with the increase of interfacial bond length of Au(core)-S in RS-AuNPs, increasingly larger "metallic" Au-core is formed, which results in smaller HOMO-LUMO (or optical) gap. Calculations of electronic structures and UV-vis absorption spectra of Au-24(SR)(20) and larger RS-AuNPs (up to similar to 2 nm in size) show that the ligand layer can strongly affect optical absorption behavior of RS-AuNPs.