A shallow trench isolation structure is formed in a semiconductor substrate adjacent to an active semiconductor region. A selective self-assembling oxygen barrier layer is formed on the surface of the shallow trench isolation structure that includes a dielectric oxide material. The formation of the selective self-assembling oxygen barrier layer is selective in that it is not formed on the surface the active semiconductor region having a semiconductor surface. The selective self-assembling oxygen barrier layer is a self-assembled monomer layer of a chemical which is a derivative of alkylsilanes including at least one alkylene moiety. The silicon containing portion of the chemical forms polysiloxane, which is bonded to surface silanol groups via Si—O—Si bonds. The monolayer of the chemical is the selective self-assembling oxygen barrier layer that prevents diffusion of oxygen to a high dielectric constant material layer that is subsequently deposited as a gate dielectric.