Although the obtained crystalline structures do not share a common crystal system, we observed a quite similar cubic arrangement of Cu(I) atoms which is surrounded by protective ligands in both Cu58-I and Cu58-II NCs, similar to what was observed in the regular Cu58 NC (Figure ). Our detailed examination revealed that both Cu58-I and Cu58-II exhibit nested Keplerian architectures, featuring Cu8 cubic cores (Figure ) encircled by four concentric Cu(I) shells (Figure ). In both cases, the innermost Cu6 octahedron shell is positioned at the center, linking the Cu(I) atoms from each face of the Cu8 cubic core. The Cu24 rhombicuboctahedron shell shapes the facets of the overall cubic architecture by creating a middle plane with four Cu(I) atoms. Additionally, the Cu12 cuboctahedron shell contributes to the edge centers of the overall cubic architecture, while the outermost Cu8 cubic shell forms the vertices of the cube. These observations align with our previous findings on Cu58 NC. Furthermore, we detected three types of ligands (thiolate, PPh3 and hydride) arranged in specific geometries to protect these NCs by forming ligand shells. The hydride ligands are positioned interstitially in both cases, connecting the core and the inner shell by forming H8 cubic and an H12 icosahedron ligand shell geometries (Figure ). Despite the change in the carbon chain length, the thiolate ligands in both NCs are arranged similarly into two distinct geometries: an S12 icosahedron and an S24 truncated cubic ligand shell (Figure ). These thiolate ligand shells serve to protect the edges and facets of the cube, ensuring structural stability and integrity. However, a significant change is first visible in the attachment of the PPh3 ligands. In the regular Cu58 NC, eight PPh3 ligands form a complete cubic ligand shell (P8) around the NC, which is not observed in Cu58-I and Cu58-II NCs (Figures ). In Cu58-I NC, we observed one vacant site in the P8 ligand shell, where one vertex Cu atom of the Cu8 cubic shell is exposed due to this vacancy. In contrast, Cu58-II NC exhibited two vacant sites diagonally in the P8 ligand shell, exposing two Cu atoms from the Cu8 cubic shell. Since the construction of the P8 ligand shell relies on direct Cu-P bond formation involving the Cu(I) atoms from the Cu8 cubic shell, we anticipate irregularities in that cationic shell, which may prevent the PPh3 ligands from attaching at those specific positions. As we have already discussed the formation of the cationic shells is followed in a similar way however, we observed a notable geometric distortion in the outermost Cu8 cubic shells compared to Cu58 NC (Figure -e and Figure ). We identified that this outer Cu8 cubic shell was formed via thiolate bridging, lacking direct connections to the Cu(I) atoms of the inner shells. As a result, we noticed a distinct directional arrangement of the Cu-S3 moiety bridging, forming each vertex of the cube. However, here the distortions arise from the partial dislocation of vertex Cu(I) atoms, disrupting its typical outward directional bonding with the bridging thiolate ligands (Figure ). Due to this inward distortion of the Cu(I) atom alters the distance between Cu(I) atoms those forming the adjacent facets contributing from the Cu24 rhombicuboctahedron shell. In Cu58-I NC the average distance decreases to 2.665Å from 3.4108 ±0.0146Å (average from the other corners). Similarly, in Cu58-II NC, the average distance decreases to 2.6713 ±0.0065 Å from 3.4032 ±0.0173 Å (average from the other corners), indicating strong cuprophilic interactions at the defect sites (Figure ). These additional interactions help alleviate the strain from the distortion of the Cu(I) atom at the dislocation sites and stabilize the overall cluster structures. However, this inward orientation of the Cu(I) atom at the vertex sites presents challenges for the attachment of PPh3 ligands, likely due to steric crowding. This difficulty in ligand attachment constitutes the primary reason for the observed surface ligand vacancies. Therefore, this vacancy directly stems from the altered bonding environment induced by the distortion of the Cu(I) atoms in the outermost shell.