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Using density functional theory (DFT) methods, we analyze the adsorption of acetylene and ethylene on the Si(001) surface in an unusual bond insertion mode. The insertion takes place at a saturated tetravalent silicon atom and the insight gained can thus be transferred to other saturated silicon compounds in molecular and surface chemistry. Molecular orbital analysis reveals that the distorted and symmetry-reduced coordination of the silicon atoms involved due to surface reconstruction raises the electrophilicity and, additionally, makes certain σ bond orbitals more accessible. The affinity towards bond insertion is, therefore, caused by the structural constraints of the surface. Additionally, periodic energy decomposition analysis (pEDA) is used to explain why the bond insertion structure is much more stable for acetylene than for ethylene. The increased acceptor abilities of acetylene due to the presence of two π*-orbitals (instead of one π*-orbital and a set of σ*(C–H) orbitals for ethylene), as well as the lower number of hydrogen atoms, which leads to reduced Pauli repulsion with the surface, are identified as the main causes. While our findings imply that this structure might be an intermediate in the adsorption of acetylene on Si(001), the predicted product distributions are in contradiction to the experimental findings. This is critically discussed and suggestions to resolve this issue are given.