This research presents a new approach to creating large, complex molecules to carry out molecular recognition and catalytic functions mimicking biological proteins. Development of new therapeutics that bind protein surfaces and disrupt protein-protein interactions was first addressed targeting the envelope transmembrane protein in HIV-1, gp41. In this work, spiroligomer inhibitors of gp41 were designed and synthesized, and then the biochemical activity was tested. Rationally designed inhibitors were developed using computational modeling with the Molecular Operating Environment software (MOE). To build the desired molecular shape according to the design, C-2 alkylation of a bis-amino acid monomer was investigated to synthesize the higher degree of bis-amino acids with various reaction conditions for access to all possible diastereomers. Based on this design and synthetic methodology, a spiroligomer targeting gp41 was built by synthesizing each monomer and then linking them together by diketopiperazine (DKP). For the biological evaluation, the gp41-5 gene was transformed into E. coli and the protein was expressed, purified, and refolded for an in vitro binding test. A direct binding, fluorescence polarization assay was used to evaluate the binding affinity of the functionalized spiroligomer to the gp41-5 protein. Its antiviral activity was assessed in collaboration with the Chaiken lab at Drexel University. In addition, investigation into how the unique structures provided by the spiroligomer backbone allow for various uses, such as functionalized struts in porous organic polymers (POPs). In the large internal space of a POP, a nucleophilic, catalytic spiroligomer was installed to increase the reaction rate for the hydrolysis of methyl paraoxon (a neurotoxin G agent stimulant). Spiroligomers were designed and synthesized with backbone DMAP moieties, and the activity of these catalysts was analyzed in collaboration with the Hupp lab at Northwestern University. / Chemistry