A phylloquinone (PhQ) molecule, called A1, acts as the secondary electron accepter in the electron transfer chain in photosystem I of plants and bacteria. This PhQ molecule has a midpoint potential close to -800 mV making it one of the most reducing quinones in biology. This extreme redox potential is in part a result of the interaction of PhQ with the surrounding protein environment. To study some of the structural details of PhQ and its binding site we have been using time resolved FTIR difference spectroscopy. We have obtained A-1 / A1 difference spectra using labeled and unlabeled photosystem I particles and proposed the assignments for several bands in the spectra. To test these assignments we have studied photosystem I particles in which plastoquinone (PQ-9) replaces PhQ in the A1 binding site. To complement the experimental works we have used density functional theory (DFT) to calculate the vibrational properties of PQ-9 and PhQ.