Modeling of fluorescence line-narrowed spectra in weakly coupled dimers in the presence of excitation energy transfer

This work describes simple analytical formulas to describe the fluorescence line-narrowed (FLN) spectra of weakly coupled chromophores in the presence of excitation energy transfer (EET). Modeling studies for dimer systems (assuming low fluence and weak coupling) show that the FLN spectra (including absorption and emission spectra) calculated for various dimers using our model are in good agreement with spectra calculated by: (i) the simple convolution method and (ii) the more rigorous treatment using the Redfield approach [T. Renger and R. A. Marcus, J. Chem. Phys.116, 9997 (2002)]. The calculated FLN spectra in the presence of EET of all three approaches are very similar. We argue that our approach provides a simplified and computationally more efficient description of FLN spectra in the presence of EET. This method also has been applied to FLN spectra obtained for the CP47 antenna complex of Photosystem II reported by Neupane et al. [J. Am. Chem. Soc.132, 4214 (2010)], which indicated the presence of uncorrelated EET between pigments contributing to the two lowest energy (overlapping) exciton states, each mostly localized on a single chromophore. Calculated and experimental FLN spectra for CP47 complex show very good qualitative agreement

The CP43 Proximal Antenna Complex of Higher Plant Photosystem II Revisited: Modeling and Hole Burning Study. I

The final version is available at: http://pubs.acs.org/journal/jpcbfkThe CP43 core antenna complex of photosystem II is known to possess two quasi-degenerate “red”-trap states (Jankowiak, R. et al. J. Phys. Chem. B 2000, 104, 11805). It has been suggested recently ( Zazubovich, V.; Jankowiak, R. J. Lumin. 2007, 127, 245) that the site distribution functions of the red states (A and B) are uncorrelated and that narrow holes are burned in the subpopulations of chlorophylls (Chls) from states A and B that are the lowest-energy Chl in their complex and previously thought not to transfer energy. This model of uncorrelated excitation energy transfer (EET) between the quasidegenerate bands is expanded by taking into account both electron−phonon and vibrational coupling. The model is applied to fit simultaneously absorption, emission, zero-phonon action, and transient hole burned (HB) spectra obtained for the CP43 complex with minimized contribution from aggregation. It is demonstrated that the above listed spectra can be well-fitted using the uncorrelated EET model, providing strong evidence for the existence of efficient energy transfer between the two lowest energy states, A and B (either from A to B or from B to A), in CP43. Possible candidate Chls for the low-energy A and B states are discussed, providing a link between CP43 structure and spectroscopy. Finally, we propose that persistent holes originate from regular NPHB accompanied by the redistribution of oscillator strength due to excitonic interactions, rather than photoconversion involving Chl−protein hydrogen bonding, as suggested before (Hughes J. L. et al. Biochemistry 2006, 45, 12345). In the accompanying paper ( Reppert, M.; Zazubovich, V.; Dang, N. C.; Seibert, M.; Jankowiak, R. J. Phys. Chem. B 2008, 9934), it is demonstrated that the model discussed in this manuscript is consistent with excitonic calculations, which also provide very good fits to both transient and persistent HB spectra obtained under non-line-narrowing conditions.This work was supported by the start-up funding at the Department of Chemistry, Kansas State University (RJ, NCD, MR and BN), and in part by the U.S. Department of Energy (DOE) EPSCoR grant (RJ), Energy Biosciences Program, Basic Energy Sciences, DOE (MS and NCD) and BFU2005-07422-CO2-01; Spain (RP). VZ acknowledges support by NSERC.Peer reviewe

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

© 2020 American Chemical Society. Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future

Modeling of Resonant Hole-Burning Spectra in Excitonically Coupled Systems: The Effects of Energy-Transfer Broadening

Resonant hole-burned (HB) spectra provide detailed insight into optical line shapes and single-site absorption spectra. In this work, a new method is presented for modeling low-fluence resonant HB spectra in excitonically coupled systems. Our calculations make use of the line shape theory of Renger and Marcus [J. Chem. Phys. 2002, 116, 9997−10019] to include explicitly the effects of excitonic interactions and energy transfer. We find that an accurate treatment of lifetime broadening is crucial for reproducing resonant hole shapes and zero-phonon action spectra. Representative spectra are calculated for a series of simple dimers, with a description and physical explanation of the main features of the calculated spectra. Qualitatively, the results are in excellent agreement with experimental literature data. It is anticipated that the new method will provide both more detailed insight into the excitonic information encoded in resonant HB spectra and a means of testing theoretical treatments of excitonic optical line shapes

Electron transfer in rhodobacter sphaeroides reaction centers containing Zn-bacteriochlorophylls : a hole-burning study

Nonresonant and resonant transient, photochemical hole-burned (HB) spectra are presented for primary electron donor states of a novel bacterial reaction center (Zn-RC) of Rhodobacter sphaeroides, containing six Zn-bacteriochlorophylls (Zn-BChls). A "Zn-β-RC" in which the Zn-BChl in the bacteriopheophytin (BPhe)-binding site on the A side (Hᴀ) has the Zn penta-coordinated, was also studied. The fifth ligand comes from a histidine introduced by site-directed mutagenesis. Formation of the P⁺Qᴀ⁻ state was observed in both types of RC, although under identical experimental conditions a significantly deeper P_ band band (corresponding to the lower-energy, special pair, excitonic component) was revealed in the Zn-RC. Assuming a similar lifetime of the P⁺Qᴀ⁻ state, the quantum yield of P⁺Qᴀ⁻ formation decreased by ~60% in the Zn-β-RC (compared to the Zn-RC), as was seen in a comparison of analogous (Mg) BChl-containing wild type and β-RCs of Rb. sphaeroides [Kirmaier et al. Science1991, 251, 922]. However, the average (weakly frequency-dependent) low-temperature electron transfer (ET) rates of the Zn-RC and Zn-β-RC (measured from zero phonon holes in resonant transient HB spectra) were both ~1 ps and similar to a rate previously measured in the Rb. sphaeroides native RC [Johnson et al. J. Phys. Chem. 1989, 93, 5953]. Electron transfer rates observed in this work on the Zn-RC yielded a P870* decay rate in good agreement with recent room-temperature, time-domain data [Lin et al. Proc. Natl. Acad. Sci.2009, 106, 8537]. A lack of correlation observed between the holes near 810 and 883 nm, accounting for electrochromically induced shifts of the Zn-BChl transitions in the Bᴀ,ʙ and Hᴀ,ʙ binding sites, produced by formation of the P⁺BHQᴀ⁻ state, indicates that the 810 nm bleach does not correspond to the P₊ (upper excitonic component of the dimer) band and is mostly contributed to by a shift of the Bʙ absorption band. ZPH-action spectra indicated inhomogeneous broadening (Γinh) of ~110 cm⁻¹ (Zn-RC) and ~130 cm⁻¹ (Zn-β-RC). Experimentally determined Γinh decreased the number of variables in theoretical fits of the absorption and frequency-dependent shapes of resonant HB spectra, leading to more reliable Huang—Rhys factors for both low-frequency phonons and a pseudolocalized phonon, ωSP, often referred to as the special pair marker mode.10 page(s

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