PS II reaction center and photosynthetic pigments

Z.Vokáčová and J.V.Burda

Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic

Models based on the RC PS II¹ were studied. Photosystem II reaction center (RC PS II) is a central part of the PS II complex, in which primary charge separation occurs. It consists of small number of the pigment molecules – chlorophyll a and pheophytin a molecules.

For these molecules, model calculations using ZINDO/S and TDDFT methods were utilized.

Before spectral calculations, hydrogens were added and optimized with semiempirical PM3 method. The positions of all the atoms from the referenced structure¹ of RC PS II were fixed. In the TDDFT calculations, hydrogen atoms were re-optimized using B3PW91 method with 6-31G(d) basis set.

Spectra of all the monomers of chlorophyll a and pheophytin a were estimated. Red shift was found at the ZINDO level in comparison with experimental data. However, TDDFT spectra exhibit opposite slightly blue-shifted character.

Electron transitions of selected pigment oligomers, separated from RC PS II models, were also determined. These spectra show strong multi-particle character and exhibit complex additive character.

The ZINDO determined spectra of oligomers are also in good agreement with experimental results.

In second part of our study various pigment molecules were explored. They have an important role also in other biological processes, like oxygen absorption and transport, electron transfer in photosynthesis, etc.

The calculations of electronic spectra were performed on three large groups of pigments – carotenoids, phycobilins, and chlorophylls and bacteriochlorophylls.

At first, several conformers were chosen for all the pigments. Structural database was used as an important starting point.

Optimization calculations were performed at the Hartree-Fock level with 3-21 G basis set. For the global minima, the absorption spectra were determined with the density functional theory using B3PW91 functional and the 6-31G(d) basis set further extended with diffusion functions. Their effect was found important for correct calculations of the electron transitions.

[1] Svensson, B.; Etchebest, C.; Tuffery, P.; van Kan, P.; Smith, J.; Styring, S. Biochemistry 1996, 35, 14486