Polymer photonic waveguides on flexible substrates have been proposed as a solution for meeting the increased demand for rack-to-rack communication within data centers. These devices have clear advantages over copper electronics in terms of both power consumption and system density. To meet this need, we have been exploring the potential of photopatterned silicone-based optical interconnects consisting of clad and core layers on flexible substrates. When designing materials for polymeric waveguides, one critical metric is the optical crossing loss, which is related in part to the refractive index gradient. From a materials perspective, the refractive index gradient is caused by chemical gradients present across the core layer or at the core/clad interface. AFM-IR analysis has proven extremely fruitful for understanding how migration of small molecules from the clad layer into the 50 x 50-micron core impacts the crossing loss. In cross-sections of full waveguide builds, quantitative structure/function relationships have been demonstrated between crossing loss and the areas of peaks associated with O-H, aliphatic C-H, and aromatic C-H contributions in the core and clad layers. Additionally, AFM-IR spectra of model bilayer systems strongly demonstrate the impact of process variables such as temperature, order of layer deposition, and order of heating vs. UV cure on the extent of small molecule migration.