Collagen is the most abundant protein in mammals, constituting almost a third of the total protein content in the body. Its unique structure and versatility has attracted the attention of many researchers for the development of new types of materials. Here, the influence of the aza-amino acids α-azaproline, azaglycine, and -azaproline on the structure and stability of collagen is studied through incorporation into collagen model peptides (CMPs) and analyzed through a variety of computational methods including DFT and molecular dynamics calculations. Inspired by the success of generating multispectral imaging agents by using DNA as a scaffold for multichromophore assembly, the utilization of the distinctive self-assembly of collagen to template the arrangement of chromophores is also explored for the first time. Simple modifications regarding linker length, chromophore loading, chromophore spacing, and chromophore type are investigated and analyzed by computational methods to develop key insights in utilizing this novel scaffold for use in light harvesting applications. Separate projects regarding the development of novel photo-activatable probes based on the structure of xylopyridine, as well as chemical modifications to the pigment carbon black for the improvement of the jetness of coatings are also examined.