The interaction of NF3-generated ion beam and plasma with a Si surface as studied by X-ray photoelectron spectroscopy was reported in Part I. Interpretation and rationalization of the peak positions were made initially based on the expected charge on each atom based on Pauling electronegativity values. Quantum chemical calculations based on density functional theory (DFT) were performed to test the validity of the qualitative electronegativity approach. Using Si10H16 clusters as a model, adsorption of F atoms on H-Si(111)-1 × 1 and H-Si(100)-1 × 1 surfaces, the stability of F atoms at two kinds of interstitial sites and their atomic charges, was determined. Mulliken atomic charge analysis indicated that the adsorbed F atoms on Si surfaces as well as at the interstitial sites possess large negative charges by forming Si-F bonds, whereas less negative charges were associated with F atoms bound to surface Si-N species. The DFT calculations confirmed the expected changes in atomic charge and the direction of binding energy shift for F-N-Si moieties.