Marker Mode Structure in the Primary Donor State of Bacterial Reaction Centers

Abstract

Underlying structure for the primary donor absorption profiles of isolated reaction centers Rhodopseudomonas viridis and Rhodobacter sphaeroides (P960 and P870) has recently been uncovered by transient hole burning experiments [1]. A Franck-Condon progression of an intermolecular special pair marker mode (ωsp) was found to originate in the low energy shoulder of the absorption spectra and peak at the one quantum transition. The theory of Hayes and Small [2] for fitting hole burned spectra was extended to include the coupling of the marker mode. Briefly, the theory defines a single site absorption function as being made up of a sum of 0-,1-,… phonon lineshape functions composed of a gaussian distribution for the low energy side and a lorentzian for the high energy side. By constructing a gaussian distribution whose full-width at half maximum is equal to the inhomogeneous broadening and convolving with the single site absorption function, the absorption spectrum is obtained. By further convolving these functions with an exponential decay function of the single sites centered at the bum frequency the absorption spectra after burning a time T is obtained. Important parameters include the Huang-Rhys factor for the phonons and marker mode S,Ssp, the mean phonon frequency ωm, the marker mode frequency ωsp, the width of the one phonon profile Γ, the zero-phonon width γ, and the inhomogeneous broadening Γ1. Most of the parameter values required in the fit can be obtained from experiment. An important test for the theory is how well it can account for the bum wavelength dependence of the hole spectrum.