Carotenoids are lipophilic pigments that provide many of the colors found in nature, including the colors found in plants, flowers, and animals. The main interest in carotenoids concerns their participation in light harvesting in biological systems and prevention of light-induced oxidative damage. Another reason for the interest in the redox properties of carotenoids is related to their use as antioxidants in medicinal formulations as a result of radical-mediated processes that occur frequently in living systems. A specific group of carotenoids, known as xanthophylls, are active in photoprotection and radical scavenging. What makes xanthophylls differ from other carotenoids is that they contain oxygen. This dissertation focuses on the interaction of three xanthophylls, Zeaxanthin, Lutein, and Astaxanthin, with damaging energetic species. Chapter 3 is focused on the deprotonation of naturally-occurring zeaxanthin (Zea) radical cations (Zea*+) to form neutral radicals (#Zea*) and their involvement in the qE portion of non-photochemical quenching (NPQ) in the model organism Arabidopsis thaliana. An H/D exchange method was developed to test for the presence of #Zea* and was detected via liquid chromatography/mass spectrometry (LC/MS) methods and analyzed using analysis of variance (ANOVA) techniques. Chapter 4 examined the characteristics of xanthophyll carotenoids which self-assemble in aqueous solution to form J- and H-type aggregates. This aggregation significantly changes the photo-physical and optical properties of these xanthophylls, and has an impact on solar energy conversion and light induced oxidative damage. This study applied electron paramagnetic resonance (EPR) and optical absorption spectroscopy to investigate how complexation can affect the aggregation ability of the three xanthophylls mentioned above, their photostability, and antioxidant activity. Chapter 5 demonstrates the different chemistries of geometrical isomers of zeaxanthin isolated from various sources in mass spectrometry using electrospray ionization sources. Zeaxanthin exhibits antioxidant activity and also plays a role in photo-protection in the retina. These properties have led to it being marketed as a dietary supplement as it is not formed by the body and must be consumed as part of the diet. Understanding the different chemical properties of zeaxanthin isomers is important with regards to the nutraceutical and pharmaceutical industries.