Vibration-mediated energy transport in bacterial reaction center: Simulation study.

Exciton energy relaxation in a bacterial Reaction Center (bRC) pigment-protein aggregate presumably involves emission of high energy vibrational quanta to cover wide energy gaps between excitons. Here, we assess this hypothesis utilizing vibronic two-particle theory in modeling of the excitation relaxation process in bRC. Specific high frequency molecular vibrational modes are included explicitly one at a time in order to check which high frequency vibrations are involved in the excitation relaxation process. The low frequency bath modes are treated perturbatively within Redfield relaxation theory. The analysis of the population relaxation rate data indicates energy flow pathways in bRC and suggests that specific vibrations may be responsible for the excitation relaxation process.

Role of Bath Fluctuations in the Double-Excitation Manifold in Shaping the 2DES of Bacterial Reaction Centers at Low Temperature.

Spectroscopically relevant properties in photosynthetic reaction centers change during charge separation. In this paper, we focus on incorporation of the complete set of environmental fluctuations in the modeling of the nonlinear spectra of molecular aggregates. The model is applied in simulations of two-dimensional electronic spectra of a photosynthetic reaction center at low temperature (5 K), where spectral lines are narrow, such that more features can be resolved. We show that vertical cross sections of the simulated two-dimensional spectra (with all populations in the lowest excited state) reveal transient hole-burned spectra excited resonantly within the B band in agreement with experiment, thus providing new insight into environmental fluctuation parameters of Rhodobacter sphaeroides at low temperatures. Correlated fluctuations of molecular parameters are found to be necessary to describe charge separated configurations of molecular excited states.

Mutation-Induced Changes in the Protein Environment and Site Energies in the (M)L214G Mutant of the Rhodobacter sphaeroides Bacterial Reaction Center.

This work focuses on the low-temperature (5 K) photochemical (transient) hole-burned (HB) spectra within the P870 absorption band, and their theoretical analysis, for the (M)L214G mutant of the photosynthetic Rhodobacter sphaeroides bacterial reaction center (bRC). To provide insight into system-bath interactions of the bacteriochlorophyll a (BChl a) special pair, i.e., P870, in the mutated bRC, the optical line shape function for the P870 band is calculated numerically. On the basis of the modeling studies, we demonstrate that (M)L214G mutation leads to a heterogeneous population of bRCs with modified (increased) total electron-phonon coupling strength of the special pair BChl a and larger inhomogeneous broadening. Specifically, we show that after mutation in the (M)L214G bRC a large fraction (∼50%) of the bacteriopheophytin (HA) chromophores shifts red and the 800 nm absorption band broadens, while the remaining fraction of HA cofactors retains nearly the same site energy as HA in the wild-type bRC. Modeling using these two subpopulations allowed for fits of the absorption and nonresonant (transient) HB spectra of the mutant bRC in the charge neutral, oxidized, and charge-separated states using the Frenkel exciton Hamiltonian, providing new insight into the mutant's complex electronic structure. Although the average (M)L214G mutant quantum efficiency of P(+)QA(-) state formation seems to be altered in comparison with the wild-type bRC, the average electron transfer time (measured via resonant transient HB spectra within the P870 band) was not affected. Thus, mutation in the vicinity of the electron acceptor (HA) does not tune the charge separation dynamics. Finally, quenching of the (M)L214G mutant excited states by P(+) is addressed by persistent HB spectra burned within the B band in chemically oxidized samples.

Band Structure of the Rhodobacter sphaeroides Photosynthetic Reaction Center from Low-Temperature Absorption and Hole-Burned Spectra.

Persistent/transient spectral hole burning (HB) and computer simulations are used to provide new insight into the excitonic structure and excitation energy transfer of the widely studied bacterial reaction center (bRC) of Rhodobacter (Rb.) sphaeroides. We focus on site energies of its cofactors and electrochromic shifts induced in the chemically oxidized (P(+)) and charge-separated (P(+)QM(-)) states. Theoretical models lead to two alternative interpretations of the H-band. On the basis of our experimental and simulation data, we suggest that the bleach near 813-825 nm in transient HB spectra in the P(+)QM(-) state, often assigned to the upper exciton component of the special pair, is mostly due to different electrochromic shifts of the BL/M cofactors. From the exciton compositions in the charge-neutral (CN) bRC, the weak fourth excitonic band near 780 nm can be denoted PY+, that is, the upper excitonic band of the special pair, which in the CN bRC behaves as a delocalized state over PM and PL pigments that weakly mixes with accessory BChls. Thus, the shoulder in the absorption of Rb. sphaeroides near 813-815 nm does not contain the PY+ exciton band.

Polaronic effects at finite temperatures in the B850 ring of the LH2 complex.

Energy transfer and relaxation dynamics in the B850 ring of LH2 molecular aggregates are described, taking into account the polaronic effects, by a stochastic time-dependent variational approach. We explicitly include the finite temperature effects in the model by sampling the initial conditions of the vibrational states randomly. This is in contrast to previous applications of the variational approach, which consider only the zero-temperature case. The method allows us to obtain both the microscopic dynamics at the single-wavefunction level and the thermally averaged picture of excitation relaxation over a wide range of temperatures. Spectroscopic observables such as temperature dependent absorption and time-resolved fluorescence spectra are calculated. Microscopic wavefunction evolution is quantified by introducing the exciton participation (localization) length and the exciton coherence length. Their asymptotic temperature dependence demonstrates that the environmental polaronic effects range from exciton self-trapping and excitonic polaron formation at low temperatures to thermally induced state delocalization and decoherence at high temperatures. While the transition towards the polaronic state can be observed on the wavefunction level, it does not produce a discernible effect on the calculated spectroscopic observables.

Probing environment fluctuations by two-dimensional electronic spectroscopy of molecular systems at temperatures below 5 K.

Two-dimensional (2D) electronic spectroscopy at cryogenic and room temperatures reveals excitation energy relaxation and transport, as well as vibrational dynamics, in molecular systems. These phenomena are related to the spectral densities of nuclear degrees of freedom, which are directly accessible by means of hole burning and fluorescence line narrowing approaches at low temperatures (few K). The 2D spectroscopy, in principle, should reveal more details about the fluctuating environment than the 1D approaches due to peak extension into extra dimension. By studying the spectral line shapes of a dimeric aggregate at low temperature, we demonstrate that 2D spectra have the potential to reveal the fluctuation spectral densities for different electronic states, the interstate correlation of static disorder and, finally, the time scales of spectral diffusion with high resolution.

Static and Dynamic Disorder in Bacterial Light-Harvesting Complex LH2: A 2DES Simulation Study.

Two-dimensional coherent electronic spectroscopy (2DES) is a powerful technique in distinguishing homogeneous and inhomogeneous broadening contributions to the spectral line shapes of molecular transitions induced by environment fluctuations. Using an excitonic model of a double-ring LH2 aggregate, we perform simulations of its 2DES spectra and find that the model of a harmonic environment cannot provide a consistent set of parameters for two temperatures: 77 K and room temperature. This indicates the highly anharmonic nature of protein fluctuations for the pigments of the B850 ring. However, the fluctuations of B800 ring pigments can be assumed as harmonic in this temperature range.

Excitons in the LH3 complexes from purple bacteria.

The noncovalently bound and structurally identical bacteriochlorophyll a chromophores in the peripheral light-harvesting complexes LH2 (B800-850) and LH3 (B800-820) from photosynthetic purple bacteria ensure the variability of the exciton spectra in the near-infrared (820-850 nm) wavelength region. As a result, the spectroscopic properties of the antenna complexes, such as positions of the maxima in the exciton absorption spectra, give rise to very efficient excitation transfer toward the reaction center. In this work, we investigated the possible molecular origin of the excitonically coupled B820 bacteriochlorophylls in LH3 using femtosecond transient absorption spectroscopy, deconvolution of steady-state absorption spectra, and modeling of the electrostatic intermolecular interactions using a charge density coupling approach. Compared to LH2, the upper excitonic level is red-shifted from 755 to 790 nm and is associated with an approximate 2-fold decrease of B820 intrapigment coupling. The absorption properties of LH3 cannot be reproduced by only changing the B850 site energy but also require a different scaling factor to be used to calculate interpigment couplings and a change of histidine protonation state. Several protonation patterns for distinct amino acid groups are presented, giving values of 162-173 cm(-1) at 100 K for the intradimer resonance interaction in the B820 ring.

Insight into the structure of photosynthetic LH2 aggregate from spectroscopy simulations.

Using the electrostatic model of intermolecular interactions, we obtain the Frenkel exciton Hamiltonian parameters for the chlorophyll Qy band of a photosynthetic peripheral light harvesting complex LH2 of a purple bacteria Rhodopseudomonas acidophila from structural data. The intermolecular couplings are mostly determined by the chlorophyll relative positions, whereas the molecular transition energies are determined by the background charge distribution of the whole complex. The protonation pattern of titratable residues is used as a tunable parameter. By studying several protonation state scenarios for distinct protein groups and comparing the simulated absorption and circular dichroism spectra to experiment, we determine the most probable configuration of the protonation states of various side groups of the protein.