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The aggregation of plasmonic nanoparticles can lead to new and controllable properties useful for numerous applications. We recently showed the reversible aggregation of gold nanoparticles (AuNPs) via a small, cationic di-arginine peptide; however, the mechanism underlying this aggregation is not yet comprehensively understood. Here, we seek insights into the intermolecular interactions of cationic peptide-induced assembly of citrate-capped AuNPs by empirically measuring how peptide identity impacts AuNP aggregation. We examined the nanoscale interactions between the peptides and the AuNPs via UV-vis spectroscopy to determine the structure-function relationship of peptide length and charge on AuNP aggregation. Careful tuning of the sequence of the di-arginine peptide demonstrated that the mechanism of assembly is driven by a reduction in electrostatic repulsion. We show that acetylated N-terminals and carboxylic acid C-terminals decrease the effectiveness of the peptide in inducing AuNP aggregation. The increase in peptide size through the addition of glycine or proline units hinders aggregation and leads to less redshift. Arginine-based peptides were also found to be more effective in assembling the AuNPs than cysteine-based peptides of equivalent length. We also illustrate that aggregation is independent of peptide stereochemistry. Finally, we demonstrate the modulation of peptide-AuNP behavior through changes to the pH, salt concentration, and temperature. Notably, histidine-based and tyrosine-based peptides could reversibly aggregate the AuNPs in response to the pH.