I'm trying to understand the difference between these two mesoporous materials. They both have the same polys-siloxane backbone and surface silanol groups, the same hexagonal pores, and yet I don't understand why they are different materials.
The difference between your two materials is primarily in pore geometry: for MCM-41, the pores are hexagonal; for SBA-15, they are round. Further, there are apparently differences in wall thicknesses.
Using high-resolution transmission electronic micrograph (HR-TEM) observation, one can clearly see the pore geometry of the MCM-41 and SBA-15 mesoporous silicas to determine that their pore shapes are hexagonal and round, respectively. With the perpendicular orientations of the nanochannels to the electron beam, parallel line images of the (100) and (110) repeating spacings were observed. In the SBA-15 mesoporous silicas, there are byproducts of the granular silica and disordered mesostructures, attributed to the weak hydrogen interactions between Pluronic 123 blockcopolymer and the silica species. There are also many different and significant +π disclination defects in SBA-15 and MCM-41 surfactant-silica composites. The SBA-15 with a thicker silica wall is more stable under irradiation by high-energy electron beams compared to MCM-41, which has thinner wall thickness. Some carbon nanostructure impurities were found in some carbon films on the metal grids.
Reference: Lin, Tang, and Lin. Detailed Structural Characterizations of SBA-15 and MCM-41 Mesoporous Silicas on a High-Resolution Transmission Electron Microscope. Journal of the Chinese Chemical Society 49(6) 981-988 (2002). Abstract here.