Taking into account the measured interlayer spacing of HTO-PA and HTO-HDA, as well as the quantification of nanoconfined pillaring molecules, the energetically favorable pillar conformation within the interlayer space is calculated using density functional theory (DFT, Fig. ). For the HTO-PA system, we considered three configurations: fully perpendicular, fully parallel, and mixed models with respect to the HTO basal plane. The calculations show that in the fully perpendicular configuration, the d-spacing is only 1.38 nm, which is too short in comparison with the experimental value of 1.58 nm. As more PA molecules are aligned parallel to the basal plane, the d-spacing gradually increases. The PA bilayer structure allows the PA molecules to interact more effectively with the OH groups on both the upper and lower HTO layers via hydrogen bonds, achieving a d-spacing of 1.58 nm and the lowest energy (Fig. ). For the HTO-HDA system, we considered two scenarios: HDA aligned parallel or perpendicular to the HTO basal plane. DFT structural optimization revealed that in the perpendicular configuration, both NH₂ groups of HDA can interact with the OH groups of the top and bottom HTO layers, forming hydrogen bonds and having lower energy (Fig. ). In contrast, when HDA is aligned parallel to the basal plane, the energy is higher due to lack of strong hydrogen bonding and the d-spacing is shorter at 1.51 nm, in comparison with the experimental value. Analysis of the structural properties of HTOs with different nanoconfinement chemistries at a nanoscale is conducted using transmission electron microscopy (TEM, Fig. ). All samples (HTO, HTO-PA and HTO-HDA) demonstrate rod-like morphology (Fig. ), confirming prior SEM results. This allows to further analyze free-standing rods individually using selected area electron diffraction (SAED). The recorded patterns for single crystals are then compared to the DFT-optimized crystal structures to verify the proposed structural models. For the pristine HTO sample, the SAED pattern (Fig. ) aligns well with the simulated H2Ti4O9 structure (see supporting information for the coordinates). Specifically, the (002) reflection yields a d-spacing of 0.56 nm, which closely matches the 0.57 nm obtained from the calculated structure. Similarly, the (110) and (220) reflections, with d-spacings of 0.37 nm and 0.19 nm, respectively, correspond precisely to the values derived from the calculated pattern (0.37 nm and 0.19 nm).