A silicon on insulator (SOI) photonic device having a waveguide is provided that includes a mode overlap portion with a topology optimized structure situated below an electrode of the capacitance structure. The device can significantly change a refractive index in a volume of mode overlap depending upon the applied potential to the capacitor and allows for a π phase shift in a modest mode overlap volume. The topology optimized structure has a waveguide and substrate that are partitioned in three dimensions using an extruded projection design. The electrode is a transition metal di-chalcogenide monolayer sheet (2D TMD). The enhanced mode overlay from the topology optimized waveguide portion allows a large reduction in the length of the waveguide with the mode overlap to achieve the needed phase shift for a photonic device.