In this study, the theoretical and experimental results on the molecular structure and reactivity of the plant flavonoids naringenin chalcone and naringenin are reported. UV-vis and Raman spectra were recorded and their main bands have been assigned theoretically. Moreover, the analysis of the naringenin chalcone-naringenin cyclization-isomerization reaction and the formation of homodimers and heterodimers have been performed within a DFT framework. The presence of H-bonded water networks is mandatory to make the cyclization energetically suitable, suggesting that this equilibrium will occur in an aqueous intracellular environment rather than in the extracellular and hydrophobic plant cuticles. Additionally, the preferential formation of homodimers stabilized by π-π stacking that will interact with other dimers by H-bonding over the formation of naringenin chalcone-naringenin heterodimers is also proposed in a hydrophobic environment. These results give a plausible model to explain how flavonoids are located within the cuticle molecular arrangement.