Modeling the A1 binding site in photosystem: I. Density functional theory for the calculation of “anion − neutral” FTIR difference spectra of phylloquinone

A phylloquinone molecule occupies the A1 binding site in photosystem I. Previously we have obtained (A1− − A1) FTIR difference spectra using labeled and unlabeled photosystem I particles, and proposed assignments for several of the bands in the spectra [V. Sivakumar, R. Wang, G. Hastings, Biochemistry 44 (2005) 1880.]. Our aim here is to provide calculated infrared difference spectra that can be usefully compared to the experimental spectra, in order to test or verify the previously proposed band assignments.Here we use density functional theory, as implemented in Gaussian 03, to calculate the harmonic vibrational frequencies and intensities of 2,3-dimethyl,1,4-naphthoquinone (DMNQ) and phylloquinone (PhQ), in both the neutral and anionic forms. The harmonic vibrational frequencies and intensities of neutral and anionic DMNQ and PhQ molecules that have been 2H, 13C, 15N and 18O labeled are also calculated. In all calculations the B3LYP method and the 6-31+G(d) basis is used. Previous harmonic vibrational frequency calculations of quinone type molecular systems have been undertaken using the lower level 6-31G(d) basis. However, we show that vibrational frequency calculations for quinones are best undertaken using the 6-31+G(d) basis.From the calculated results infrared spectra and “anion minus neutral” infrared difference spectra are constructed that can be usefully compared to several types of experimental spectra. Calculated isotope-induced band-shifts closely agree with the experimentally observed band-shifts for quinones in vitro. In addition, differences in the magnitude of isotope-induced band-shifts observed for neutral and anionic quinones in vitro are also accurately predicted. The calculations therefore support the validity of previously reported quinone anion infrared spectra. Finally, the calculated spectra are used to critically assess the validity of several proposed band assignments in (A1− − A1) FTIR difference spectra.