The processes of etching and diffusion of atomic oxygen on the reconstructed Si(100)-2 × 1 surface are investigated using an embedded cluster QM/MM (Quantum Mechanics/Molecular Mechanics) method, called SIMOMM (Surface Integrated Molecular Orbital Molecular Mechanics). Hopping of an oxygen atom along the silicon dimer rows on a Si15H16 cluster embedded in an Si136H92 MM cluster model is studied using the SIMOMM/UB3LYP (unrestricted density functional theory (UDFT) with the Becke three-parameter Lee−Yang−Parr (B3LYP) hybrid functional) approach, the Hay−Wadt effective core potential, and its associated double-ζ plus polarization basis set. The relative energies at stationary points on the diffusion potential energy surface were also obtained with three coupled-cluster (CC) methods, including the canonical CC approach with singles, doubles, and noniterative quasi-perturbative triples (CCSD(T)), the canonical left-eigenstate completely renormalized (CR) analogue of CCSD(T), termed CR-CC(2,3), and the linear scaling variant of CR-CC(2,3) employing the cluster-in-molecule (CIM) local correlation ansatz, abbreviated as CIM-CR-CC(2,3). The pathway and energetics for the diffusion of oxygen from one dimer to another are presented, with the activation energy estimated to be 71.9 and 74.4 kcal/mol at the canonical CR-CC(2,3)/6-31G(d) and extrapolated, CIM-based, canonical CR-CC(2,3)/6-311G(d) levels of theory, respectively. The canonical and CIM CR-CC(2,3)/6-31G(d) barrier heights (excluding zero point vibrational energy contributions) for the etching process are both 87.3 kcal/mol.