Ordered mesoporous silica nanocomposites, such as SBA-15 functionalized with metal-capturing propylphosphonic acid, offer precise control over physicochemical properties through appropriate functionalization of the pore interior. The configuration of functional groups is proving to be crucial to achieving the proper functionality of such materials. Our research focuses on rigorous analysis of the molecular structure of the resulting nanocomposites, using numerical calculations of X-ray absorption spectra to quantitatively assess the local structure and coordination environment of metal-containing molecules incorporated into the silica matrix, particularly copper-containing functionalities. These findings shed light on the relationship between the local environment of functional groups and the nonlinear optical (NLO) response observed in the material, which shows the possibility of tuning by changing the concentration of functional units to provide a comprehensive understanding of these nanocomposites.