Comments on the optical lineshape function: Application to transient hole-burned spectra of bacterial reaction centers

Homogeneous Dephasing in Photosynthetic Bacterial Reaction Centers: Time Correlation Function Approach

A new tractable linear electronic transition dipole moment time correlation function (ETDMTCF) that accurately accounts for electronic dephasing, asymmetry, and width of 1-phonon profile, which the zero-phonon line (ZPL) contributes to it, in Rhodopseudomonas viridis bacterial reaction center is derived. This time correlation function proves to be superior to other frequency-domain expressions in case of strong electron-phonon coupling (which is often the case in bacterial RCs and pigment-protein complexes), many vibrational modes involved, and high temperature, whereby more vibronic and electronic (sequence) transitions would arise. The Fourier transform of this ETDMTCF leads to asymmetric multiphonon profiles composed of Lorentzian distribution and Gaussian distribution on the high- and low-energy sides, respectively, whereby the overtone widths fold themselves with that of the one-phonon profile. This ETDMTCF also features expedient computation in large systems using asymmetric phonon profiles to account correctly for dephasing and pigment-protein interaction (electron-phonon coupling). The derived ETDMTCF allows computing all nonlinear optical signals in both time and frequency domains, through the nonlinear dipole moment time correlation functions (as guided by nonlinear optical response theory) in line with the eight Liouville space pathways. The linear transition dipole moment time correlation function is of a central value as the nonlinear transition dipole moment time correlation function is expressed in terms of the linear transition dipole moment time correlation function, derived herein. One of the great advantages of presenting this ETDMTCF is its applicability to nonlinear transition dipole moment time correlation functions in line with the eight Liouville space pathways needed in computing nonlinear signals. As such, there is more to the utility and applicability of the presented ETDMTCF besides computational expediency and efficiency. Results show good agreement with the reported literature. The intimate connection between a one-phonon profile and the corresponding bath spectral density in photosynthetic complexes is discussed.

Exact simulation of pigment-protein complexes unveils vibronic renormalization of electronic parameters in ultrafast spectroscopy

The primary steps of photosynthesis rely on the generation, transport, and trapping of excitons in pigment-protein complexes (PPCs). Generically, PPCs possess highly structured vibrational spectra, combining many discrete intra-pigment modes and a quasi-continuous of protein modes, with vibrational and electronic couplings of comparable strength. The intricacy of the resulting vibronic dynamics poses significant challenges in establishing a quantitative connection between spectroscopic data and underlying microscopic models. Here we show how to address this challenge using numerically exact simulation methods by considering two model systems, namely the water-soluble chlorophyll-binding protein of cauliflower and the special pair of bacterial reaction centers. We demonstrate that the inclusion of the full multi-mode vibronic dynamics in numerical calculations of linear spectra leads to systematic and quantitatively significant corrections to electronic parameter estimation. These multi-mode vibronic effects are shown to be relevant in the longstanding discussion regarding the origin of long-lived oscillations in multidimensional nonlinear spectra.

Multimode vibronic mixing in model photosynthetic systems revealed by numerically exact simulations is shown to strongly modify linear and non-linear optical responses and facilitate the persistence of coherent dynamics.

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.

Mixed Upper Exciton State of the Special Pair in Bacterial Reaction Centers

Excitonic interactions between two closely separated bacteriochlorophyll a molecules (BChls) in the special pair of the reaction center (RC) of purple bacteria determine the positions and relative oscillator strengths of its two excitonic components. While the absorption of the lower excitonic band is well-defined, the position and the intensity of the upper excitonic band ( P_Y+) are still under debate. Recent 77 K two-dimensional electronic spectroscopy data on Rba. capsulatus suggested that the P_Y+ component absorbs at ∼840 nm, i.e., at a significantly lower energy than previously suggested. In the present work, we argue that the P_Y+ state is mixed with the excited states of the accessory BChls ( B*/ P _Y+) leading to excitons contributing to the 785-825 nm spectral region which is consistent with previously published data. This conclusion is based on hole-burning/linear dichroism data and modeling studies of the excitonic structure of the RC using a non-Markovian reduced density matrix approach.

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.