On the Shape of the Phonon Spectral Density in Photosynthetic Complexes

We provide a critical assessment of typical phonon spectral densities, <i>J</i>(ω), used to describe linear and nonlinear optical spectra in photosynthetic complexes. Evaluation is based on a more careful comparison to experiment than has been provided in the past. <i>J</i>(ω) describes the frequency-dependent coupling of the system to the bath and is an important component in calculations of excitation energy transfer times. On the basis of the shape of experimental <i>J</i>(ω) obtained for several photosynthetic complexes, we argue that the shape of <i>J</i>(ω) strongly depends on the pigment–protein complex. We show that many densities (especially the Drude–Lorentz/constant damping Brownian oscillator) display qualitatively wrong behavior when compared to experiment. Because of divergence of <i>J</i>(ω) at zero frequency, the Brownian oscillator cannot fit a single-site spectrum correctly. It is proposed that a log-normal distribution can be used to fit experimental data and exhibits desired attributes for a physically meaningful phonon <i>J</i>(ω), in contrast to several commonly used spectral densities which exhibit low-frequency behavior in qualitative disagreement with experiment. We anticipate that the log-normal <i>J</i>(ω) function proposed in this work will be further tested in theoretical modeling of both time- and frequency-domain data

Modeling of Optical Spectra of the Light-Harvesting CP29 Antenna Complex of Photosystem IIPart II

Until recently, it was believed that the CP29 protein from higher plant photosystem II (PSII) contains 8 chlorophylls (Chl’s) per complex (Ahn et al. <i>Science</i> <b>2008</b>, <i>320</i>, 794–797; Bassi et al. <i>Proc. Natl. Acad. Sci. U.S.A.</i> <b>1999</b>, <i>96</i>, 10056–10061) in contrast to the 13 Chl’s revealed by the recent X-ray structure (Pan et al. <i>Nat. Struct. Mol. Biol</i>. <b>2011</b>, <i>18</i>, 309–315). This disagreement presents a constraint on the interpretation of the underlying electronic structure of this complex. To shed more light on the interpretation of various experimental optical spectra discussed in the accompanying paper (part I, DOI 10.1021/jp4004328), we report here calculated low-temperature (5 K) absorption, fluorescence, hole-burned (HB), and 300 K circular dichroism (CD) spectra for CP29 complexes with a different number of pigments. We focus on excitonic structure and the nature of the low-energy state using modeling based on the X-ray structure of CP29 and Redfield theory. We show that the lowest energy state is mostly contributed to by <i>a</i>612, <i>a</i>611, and <i>a</i>615 Chl’s. We suggest that in the previously studied CP29 complexes from spinach (Pieper et al. <i>Photochem. Photobiol.</i> <b>2000</b>, <i>71</i>, 574–589) two Chl’s could have been lost during the preparation/purification procedure, but it is unlikely that the spinach CP29 protein contains only eight Chl’s, as suggested by the sequence homology-based study (Bassi et al. <i>Proc. Natl. Acad. Sci. U.S.A.</i> <b>1999</b>, <i>96</i>, 10056–10061). The likely Chl’s missing in wild-type (WT) CP29 complexes studied previously (Pieper et al. <i>Photochem. Photobiol.</i> <b>2000</b>, <i>71</i>, 574–589) include <i>a</i>615 and <i>b</i>607. This is why the nonresonant HB spectra shown in that reference were ∼1 nm blue-shifted with the low-energy state mostly localized on about one Chl <i>a</i> (i.e., <i>a</i>612) molecule. Pigment composition of CP29 is discussed in the context of light-harvesting and excitation energy transfer