Gaussian Decomposition vs. Semiclassical Quantum Simulation: Obtaining the High-Order Derivatives of a Spectrum in the Case of Photosynthetic Pigment Optical Properties Studying.

In this paper, a procedure for obtaining undistorted high derivatives (up to the eighth order) of the optical absorption spectra of biomolecule pigments has been developed. To assess the effectiveness of the procedure, the theoretical spectra of bacteriochlorophyll a, chlorophyll a, spheroidene, and spheroidenone were simulated by fitting the experimental spectra using the differential evolution algorithm. The experimental spectra were also approximated using sets of Gaussians to calculate the model absorption spectra. Theoretical and model spectra can be differentiated without smoothing (high-frequency noise filtering) to obtain high derivatives. Superimposition of the noise track on the model spectra allows us to obtain test spectra similar to the experimental ones. Comparison of the high derivatives of the model spectra with those of the test spectra allows us to find the optimal parameters of the filter, the application of which leads to minimal differences between the high derivatives of the model and test spectra. For all four studied pigments, it was shown that smoothing the experimental spectra with optimal filters makes it possible to obtain the eighth derivatives of the experimental spectra, which were close to the eighth derivatives of their theoretical spectra.

The Relationship between the Spatial Arrangement of Pigments and Exciton Transition Moments in Photosynthetic Light-Harvesting Complexes.

Considering bacteriochlorophyll molecules embedded in the protein matrix of the light-harvesting complexes of purple bacteria (known as LH2 and LH1-RC) as examples of systems of interacting pigment molecules, we investigated the relationship between the spatial arrangement of the pigments and their exciton transition moments. Based on the recently reported crystal structures of LH2 and LH1-RC and the outcomes of previous theoretical studies, as well as adopting the Frenkel exciton Hamiltonian for two-level molecules, we performed visualizations of the LH2 and LH1 exciton transition moments. To make the electron transition moments in the exciton representation invariant with respect to the position of the system in space, a system of pigments must be translated to the center of mass before starting the calculations. As a result, the visualization of the transition moments for LH2 provided the following pattern: two strong transitions were outside of LH2 and the other two were perpendicular and at the center of LH2. The antenna of LH1-RC was characterized as having the same location of the strongest moments in the center of the complex, exactly as in the B850 ring, which actually coincides with the RC. Considering LH2 and LH1 as supermolecules, each of which has excitation energies and corresponding transition moments, we propose that the outer transitions of LH2 can be important for inter-complex energy exchange, while the inner transitions keep the energy in the complex; moreover, in the case of LH1, the inner transitions increased the rate of antenna-to-RC energy transfer.

Unique features of the 'photo-energetics' of purple bacteria: a critical survey by the late Aleksandr Yuryevich Borisov (1930-2019).

We provide here an edited version of the "Farewell discussion" by the late Aleksandr (Alex) Yuryevich (Yu) Borisov (1930-2019) on several aspects related to the excitation energy transfer in photosynthetic bacteria. It is preceded by a prolog giving the events that led to our decision to publish it. Further, we include here a few photographs to give a personal glimpse of this unique biophysicist of our time. In addition, we provide here a reminiscence, by Andrei B. Rubin, on the scientific beginnings of Borisov. This article follows a Tribute to Borisov by Semenov et al. (2019, Photosynthesis Research, this issue).

The role of vibronic modes in formation of red antenna states of cyanobacterial PSI.

Cyanobacterial photosystem I (PSI) constitutes monomeric and trimeric pigment-protein complexes whose optical properties are marked by the presence of long-wavelength absorption bands. In spite of numerous experimental studies, the nature of these bands is still under debate and requires intensive theoretical analysis. Collecting together the data of linear spectroscopy and single-molecule spectroscopy (SMS) of PSI from Arthrospira platensis, we performed quantum modeling of the optical response based on molecular exciton theory (ET) and the multimode Brownian oscillator model (MBOM). Applying MBOM, the spectra of the red antenna state were calculated considering a particular for each red state adjustment of the low-frequency vibronic modes. Within the framework of our PSI exciton model it was shown that the coupling energy between antenna chlorophylls cannot be a factor of the red states formation, thus the long-wavelength bands are calculated without attribution to so-called antenna red chlorophylls. By the fitting of Huang-Rhys factors and frequencies for the lowest vibronic modes, we were able to reproduce the effects of strong and weak electron-phonon coupling experimentally observed in SMS spectra of red antenna states. Based on our theoretical calculations and also analysis of existing crystal structures of cyanobacterial PSI, we assumed that long-wavelength Chls can be localized in the peripheral protein subunits containing one or two pigment molecules.

A Prototype Method for the Detection and Recognition of Pigments in the Environment Based on Optical Property Simulation.

The possibility of pigment detection and recognition in different environments such as solvents or proteins is a challenging, and at the same time demanding, task. It may be needed in very different situations: from the nondestructive in situ identification of pigments in paintings to the early detection of fungal infection in major agro-industrial crops and products. So, we propose a prototype method, the key feature of which is a procedure analyzing the lineshape of a spectrum. The shape of the absorption spectrum corresponding to this transition strongly depends on the immediate environment of a pigment and can serve as a marker to detect the presence of a particular pigment molecule in a sample. Considering carotenoids as an object of study, we demonstrate that the combined operation of the differential evolution algorithm and semiclassical quantum modeling of the optical response based on a generalized spectral density (the number of vibronic modes is arbitrary) allows us to distinguish quantum models of the pigment for different solvents. Moreover, it is determined that to predict the optical properties of monomeric pigments in protein, it is necessary to create a database containing, for each pigment, in addition to the absorption spectra measured in a predefined set of solvents, the parameters of the quantum model found using differential evolution.

Femtosecond spectroscopy of native and carotenoidless purple-bacterial LH2 clarifies functions of carotenoids.

EET between the two circular bacteriochlorophyll compartments B800 and B850 in native (containing the carotenoid rhodopin) and carotenoidless LH2 isolated from the photosynthetic purple sulfur bacterium Allochromatium minutissimum was investigated by femtosecond time-resolved transient absorption spectroscopy. Both samples were excited with 120-fs laser pulses at 800 nm, and spectral evolution was followed in the 720-955 nm range at different delay times. No dependence of transient absorption in the B800 band on the presence of the carotenoid rhodopin was found. Together with the likewise virtually unchanged absorption spectra in the bacteriochlorophyll Q(y) region, these observations suggest that absence of rhodopin does not significantly alter the structure of the pigment-protein complex including interactions between bacteriochlorophylls. Apparently, rhodopin does also not accelerate B800 to B850 EET in LH2, contrary to what has been suggested previously. Moreover, "carotenoid-catalyzed internal conversion" can also be excluded for the bacteriochlorophylls in LH2 of A. minutissimum. Together with previous results obtained with two-photon fluorescence excitation spectroscopy, it can also be concluded that there is neither EET from rhodopin to B800 nor (back-)EET from B800 to rhodopin.