J-aggregates are comprised of conjugated organic molecules that, when given the correct solvation conditions, self-assemble into a slip-stacked arrangement. In this form, not only do their absorption and emission redshift due to dipolar coupling, but many exciting properties emerge from the coherent coupling of their excitations over long distances. Namely, they boast superradiant emission from their excitonic states, leading to extraordinarily fast energy transfer and amplified radiative rates. Yet, while the optical properties of J-aggregates are unparalleled, one of the greatest challenges preventing their widespread use remains controlling their self-assembly into highly ordered nanostructures. In this dissertation, I unpack how changes to a dye's molecular structure can affect its ability to undergo J-aggregation, with regard to the design and improvement of the resulting aggregate's optical properties. Chapter one contains a historical perspective on cyanine dyes and aggregates as colorants, as well as a short literature survey of how a dye's structure determines the optical properties of its resulting J-aggregates.In chapter two, I explore the design of superradiant J-aggregates in different spectral windows. By elongating the polymethine chain of a well-studied cyanine dye (colloquially known as C8S3), I demonstrate the formation of tubular aggregates in the near-infrared regime. This work begins with synthesis of penta- and heptamethine derivatives of C8S3, followed by a careful screening of their J-aggregation via absorbance and cryo-electron microscopy (cryo-EM), and lastly a thorough spectroscopic characterization of each aggregate's emissive properties. While the new aggregates were considerably redshifted, they displayed different kinetics of aggregation, ultimately leading to stabilization of a morphology with decreased superradiance. To better understand those changes in superradiance, we employed a computational screening that unraveled a correlation between tube radius and disorder. The above work opened many questions about why C8S3 organizes into highly-ordered superradiant J-aggregates while other cyanine dyes fall short. Around this time, our lab began a collaboration with Dr. Weili Zheng and Professor Edward Egelman (University of Virginia), who used cryo-EM to reconstruct the C8S3 nanotubes' structure with near-atomic resolution. Chapter three summarizes that work, which vastly expanded our knowledge of molecular packing in these systems. Prior to this work, the molecular structure of C8S3 J-aggregates had been posited from spectroscopic evidence and low-resolution cryo-electron micrographs. This result, however, unambiguously settled the long-standing dispute regarding C8S3 nanotube structure and represents an enormous advancement to our knowledge about how an individual dye organizes into a nanostructure. I contributed polarization-dependent spectroscopy and two molecules to this effort, which primarily demonstrated how chemical modifications to the C8S3 monomer can obfuscate its self-assembly. This result inspired the full-length follow-up work, covered in chapter 4. Chapter four investigates the role of electrostatics in the C8S3 nanotube self-assembly. This work begins from the revelation that C8S3 nanotubes feature a unique motif for self-assembly wherein the anionic sulfonate groups coordinate to the delocalized positive charge from the cyanine backbone. We tested this mechanism for self-assembly by synthesizing C8S3 derivatives with a variable number of methylene groups between the cationic cyanine and anionic sulfonate. Depending on the number of -CH2 units, we found the dyes formed aggregates with different absorption lineshapes, and confirmed their differing morphologies using cryo-EM. Lastly, we synthesized dyes that have differently charged functional groups, thereby turning off the cation/anion interactions, and found them to exhibit significantly reduced J-aggregation. Based on these experiments, we believe that the electrostatic interaction between the alkylsulfonate and cyanine core are a significant driving force in the C8S3 self-assembly. In chapter five, I examine the effect of a dye's steric bulk on its resulting J-aggregates. This work comprises a large-scale collaboration between many students in the Caram and Sletten labs, spanning the synthesis of new cyanines to computational screening of their self-assembly. We accomplished this goal by first synthesizing heptamethine benzothiazole dyes that differ in their 4' substitution (ranging from a phenyl ring to a 3,5-ditertbutylphenyl group). By modifying this position, we change neither the electronics nor the solubility of the dye, allowing a rational investigation of steric bulk on aggregation. Based on absorbance screening and cryo-EM, we found that these dyes form at least three J-aggregates each, all of which are extended 2D sheets (with one tubular anomaly). The addition of steric bulk was found to redshift the aggregate absorbance, while also changing the kinetics of self-assembly and therefore leading to stabilization of different nanoscale morphologies. In addition to these efforts, I have contributed to several other projects and conducted unpublished experiments that may inspire further investigation. Chapter six outlines these beginnings and gives direction for their future. Specifically, I discuss the potential for nuclear magnetic resonance (NMR) to offer structural knowledge on molecular aggregates and preliminary development of extremely redshifted J-aggregates in the shortwave infrared (SWIR). Taken together, these results inform the design of next-generation J-aggregated optical materials. By systematically exploring changes to the monomer chromophore, I have deduced clear structure-property relationships that serve as guidelines for making J-aggregates for applications in bioimaging, solar energy harvesting, or telecommunications. While many unsolved questions remain in J-aggregate self-assembly, this work breaks ground as a foundation for others to build upon our knowledge of cyanine dyes, their molecular aggregates, and, ultimately, their optical properties.