Perylene diimide phosphoramidite derivatives and methods for polymerization of perylene diimide phosphoramidite derivatives and applications thereof are provided. Compounds comprise at least an electronically active base surrogate and may also include a solubilizing functionality. The base surrogate may be comprised of an electrochemically active perylene diimide (PDI) molecule, the solubility chain may comprise a PEG functionality, and the PDI may further comprise a phosphoramidite functionality as an imide substituent. The phosphoramidite functionality may be used as a chemical coupling handle for use with established nucleic acid synthesis protocols and/or automated synthesis. One or more aromatic core functionalizations may be incorporated into the PDI molecules to allow for tuning the molecule's electronic and optical properties. One or more functional terminal groups may be incorporated into the PDI molecules, such as, for example terminal thiols for attachment to gold substrates and terminal ferrocenes for electrochemical measurements, among others.