<p>The encapsulation of small molecules such as formaldehyde (HCHO), formamide (HCONH2), and isocyanic acid (HNCO) inside fullerene cages (C₆₀ and C₈₀) has been investigated using density functional theory (DFT)-based calculations. The calculated interaction energy and energy decomposition analyses confirmed the thermodynamic stability of the endohedral complexes (Mol@C₈₀; here, Mol = HCHO, HCONH₂ and HNCO and HCHO@C₆₀). Furthermore, to assess the dynamic stability of the encapsulated complexes, <i>ab initio</i> molecular dynamics (AIMD) simulations were carried out at 213 K and 1 bar pressure. The results obtained from these simulations revealed that the encapsulated molecules remained stable inside the cage. The effect of confinement was further evaluated using vibrational frequency and frontier orbital analyses of the guest molecules. The findings show that confinement influences the vibrational modes and electronic properties. The results obtained from atoms in molecules (AIM) analysis reinforce the presence of non-covalent interactions between the guest and host cages. Energy decomposition analysis (EDA) quantifies and substantiates these results, indicating more effective charge transfer or polarization between the fullerene and the encapsulated molecule. Overall, this study demonstrates that HCHO, HCONH₂ and HNCO can be encapsulated within C₈₀, whereas only HCHO retains favorable encapsulation inside C₆₀, which is consistent with recent experimental observations.</p> Graphical abstract <p>The feasibility of encapsulating small polar molecules such as HCHO, HCONH₂, and HNCO was established through DFT calculations. This observation was further confirmed using topological (AIM) analysis, energy decomposition (EDA), ab initio molecular dynamics (AIMD), and frontier molecular orbital (FMO) studies.</p> <p></p>