Nanomaterials are widely used as pseudostationary and stationary phases in electrically driven separations. The advantages of using nanomaterials are numerous including tunable sizes, multiple core compositions, flexible injection schemes, and diverse surface chemistries. Nanomaterials, however, exhibit large surface energies which induce aggregation and may yield unpredictable function in separations. Because nanomaterials can modify buffer conductivity, viscosity, and pH; successful and systematic incorporation of nanomaterials into separations requires rigorous synthetic control and characterization of both the nanoparticle core and surface chemistry. This dissertation investigates the impact of gold nanoparticle surface chemistry and morphology to capillary electrophoresis separations. Gold nanoparticle core composition, shape, size, self assembled monolayer (SAM) formation, and SAM packing density are quantified for gold nanoparticles functionalized with thioctic acid, 6mercaptohexanoic acid, or 11-mercaptoundecanoic acid SAMs. TEM, 1 H NMR, extinction spectroscopy, zeta potential, X-ray photoelectron spectroscopy, and flocculation assess the morphology, surface chemistry, optical properties, surface charge, SAM packing density, and stability of the nanoparticles, respectively. Using well-characterized nanostructures, pseudostationary phases of gold nanoparticles in capillary electrophoresis are studied. Gold nanoparticles functionalized with thioctic acid and either 6-mercaptohexanoic acid or 6-aminohexanethiol impact the mobility of analytes in a concentration and surface chemistry-dependent manner. From these data, a novel parameter termed the critical nanoparticle concentration is developed and is used to estimate nanoparticle stability during capillary electrophoresis separations.