We investigated link atom approaches for treating the polar C–O bond with particular reference to the glycosidic bond found in complex carbohydrates. We show that cutting this bond after the oxygen in the QM region and saturating the QM system with a hydrogen link atom leads to greater conformational and configurational accuracy at the boundary compared with cutting the bond before oxygen and saturating the QM system with a halogen link atom to represent the oxygen. Furthermore, we find that balancing the MM atom charges and redistributing the boundary atom charges at the QM/MM boundary minimizes the effect of the link atom, both energetically and structurally. This is illustrated via a series of calculations on a set of carbohydrate and carbohydrate-like model compounds. Finally, we confirm the validity of our model by performing molecular dynamics simulations for a typical disaccharide model compound in water. Our postsimulation conformational and configurational analyses show that the oxygen-to-water hydrogen pair distribution functions and the Φ,Ψ distributions at the glycosidic boundary between the quantum and classical regions compare favorably with results obtained from complete QM and complete MM treatments of the saccharide.