Photoprotective nonphotochemical quenching (NPQ) in higher plants is the result of the formation of energy-quenching traps in the light-harvesting antenna of photosystem II (PSII). The primary driving forces behind NPQ are the protonation of the thylakoid lumen and the de-epoxidation of the xanthophyll violaxanthin to zeaxanthin in the antenna. There is currently some disagreement over whether de-epoxidation occurs only at the peripheral, VI, binding site of the major LHCII or also at the internal, L2, site of the minor antenna CP29 complex of PSII. We have used density functional theory (DFT) to study of hydrogen bonding between xanthophylls and the protein scaffold of LHCII and CP29. We argue that a lack of hydrogen bonding for violaxanthin in LHCII is consistent with it being weakly bound and accessible for de-epoxidation. Conversely, the strong violaxanthin-protein hydrogen bonding at the L2 site of CP29 is consistent with evidence that it is not readily accessible for de-epoxidation and therefore quenching by zeaxanthin at the L2 of CP29 is an unlikely candidate for in vivo NPQ