Spectral shift mechanisms of chlorophylls in liquids and proteins

Chiral Supramolecular Nanofibers Regulated Tumor-Derived Exosomes Secretion for Constructing an Anti-Tumor Extracellular Microenvironment

Tumor-derived exosomes (TDEs) induced extracellular microenvironment has recently been validated to be critical for tumor progression and metastasis, however, remodeling it for oncotherapy still remains a major challenge due to difficulty in regulation of TDEs secretion. Herein, the supramolecular chiral nanofibers, composed of L/D -phenylalanine derivates (L/D-Phe) and linear hyaluronic acid (HA), are successfully employed to construct TDEs induced anti-tumor extracellular microenvironment. The left-handed L-Phe @HA nanofibers significantly inhibit TDEs secretion into extracellular microenvironment, which results in suppression of tumor proliferation and metastasis in vitro and vivo. Biological assays and theoretical modeling reveal that these results are mainly attributed to strong adsorption of the key exosomes transporters (Ras-related protein Rab-27A and synaptosome-associated protein 23) on left-handed L-Phe @HA nanofibers via enhanced stereoselective interaction, leading to degradation and phosphorylated dropping of exosomes transporters. Subsequently, transfer function of exosomes transporters is limited, which causes remarkable inhibition of TDEs secretion. These findings provide a promising novel insight of chiral functional materials to establish an anti-tumor extracellular microenvironment via regulation of TDEs secretion.

Enhancing solar spectrum utilization in photosynthesis: exploring exciton and site energy shifts as key mechanisms

Photosynthesis is a critical process that harnesses solar energy to sustain life across Earth's intricate ecosystems. Central to this phenomenon is nuanced adaptation to a spectrum spanning approximately from 300 nm to nearly 1100 nm of solar irradiation, a trait enabling plants, algae, and phototrophic bacteria to flourish in their respective ecological niches. While the Sun's thermal radiance and the Earth's atmospheric translucence naturally constrain the ultraviolet extent of this range, a comprehension of how to optimize the utilization of near-infrared light has remained an enduring pursuit. This study unveils the remarkable capacity of the bacteriochlorophyll b-containing purple photosynthetic bacterium Blastochloris viridis to harness solar energy at extreme long wavelengths, a property attributed to a synergistic interplay of exciton and site energy shift mechanisms. Understanding the unique native adaptation mechanisms offers promising prospects for advancing sustainable energy technologies of solar energy conversion.

Comment on "Applicability of perturbed matrix method for charge transfer studies at bio/metallic interfaces: a case of azurin" by O. Kontkanen, D. Biriukov and Z. Futera, Phys. Chem. Chem. Phys., 2023, , 12479

Polarizability is a fundamental property of all molecular systems describing the deformation of the molecular electronic density in response to an applied electric field. The question of whether polarizability of the active site needs to be included in theories of enzymatic activity remains open. Hybrid quantum mechanical/molecular mechanical calculations are hampered by difficulties faced by many quantum-chemistry algorithms to provide sufficiently accurate estimates of the anisotropic second-rank tensor of molecular polarizability. In this Comment, we provide general theoretical arguments for the values of polarizability of the quantum region or a molecule which have to be reproduced by electronic structure calculations.

Chlorophyll- and anthocyanin-rich cell organelles affect light scattering in apple skin

Apple skin contains several groups of strongly absorbing cell organelles with pigments that change dynamically in type and concentration during fruit maturation. Chlorophylls and carotenoids, both primarily involved in photosynthesis, are found in the grana of chloroplasts, while anthocyanin vacuolar inclusions (AVIs) accumulate for light protection in red-skinned cultivars. A Mie model describing light scattering by absorbing spherical particles in a non-absorbing medium allowed to theoretically investigate the explicit influence of grana and AVIs on the effective scattering coefficient [Formula: see text] and the absorption coefficient [Formula: see text]. The reconstruction of the complex refractive indices of the organelles predicted anomalous dispersion, i.e., a local increase in the real part of the refractive index in the spectral regions with high chlorophyll and anthocyanin absorption, in agreement with the Kramers-Kronig relations. As a result, peaks in [Formula: see text] were predicted to be shifted to longer wavelengths compared to the corresponding [Formula: see text] bands. This selective scattering effect was confirmed experimentally with integrating sphere measurements for red- or green-skinned apple samples of the cultivars 'Elstar', 'Gala' or 'Jonagold'. Comparison between simulations and measurements indicated that the Soret bands of chlorophyll a and chlorophyll b are at 435 nm and 469 nm, respectively, and overlap with the absorption of carotenoids, whose red-most edge is at 488 nm. For anthocyanin absorption, a pronounced blue shift from 550 to 520 nm was observed, indicating structural or chemical changes of AVIs.

Hydrostatic High-Pressure-Induced Denaturation of LH2 Membrane Proteins

The denaturation of globular proteins by high pressure is frequently associated with the release of internal voids and/or the exposure of the hydrophobic protein interior to a polar aqueous solvent. Similar evidence with respect to membrane proteins is not available. Here, we investigate the impact of hydrostatic pressures reaching 12 kbar on light-harvesting 2 integral membrane complexes of purple photosynthetic bacteria using two types of innate chromophores in separate strategic locations: bacteriochlorophyll-a in the hydrophobic interior and tryptophan at both protein-solvent interfacial gateways to internal voids. The complexes from mutant Rhodobacter sphaeroides with low resilience against pressure were considered in parallel with the naturally robust complexes of Thermochromatium tepidum. In the former case, a firm correlation was established between the abrupt blue shift of the bacteriochlorophyll-a exciton absorption, a known indicator of the breakage of tertiary structure pigment-protein hydrogen bonds, and the quenching of tryptophan fluorescence, a supposed result of further protein solvation. No such effects were observed in the reference complex. While these data may be naively taken as supporting evidence of the governing role of hydration, the analysis of atomistic model structures of the complexes confirmed the critical part of the structure in the pressure-induced denaturation of the membrane proteins studied.

Design of an efficient photocatalyst: a type II heterojunction for enhanced hydrogen production driven by visible light

Solar hydrogen production, which is an eco-friendly method to obtain energy, is still far away from wide commercialization due to the lack of an efficient catalyst. Effective calculations can reduce trial and error costs and provide mechanistic explanations while exploring efficient catalysts. Herein, a type II heterojunction Mg-containing-porphyrin/g-C3N4 is proven to be an efficient photocatalyst by using a combination of DFT and many-body Green's function theory. Our results show that the heterojunction can significantly enhance the absorption of visible light and realize the separation of photogenerated electrons and holes after excitation. Subsequently, water absorbing on the excited surface decomposes into H+ and OH- easily, and then produces H2 and O2 with reduced free energy. Our investigation and explanation can provide theoretical support for designing photonic devices based on porphyrin and g-C3N4, and deepen the understanding of how H2O splits into H2.

Identification of Metal Stresses in Arabidopsis thaliana Using Hyperspectral Reflectance Imaging

Industrial accidents, such as the Fukushima and Chernobyl disasters, release harmful chemicals into the environment, covering large geographical areas. Natural flora may serve as biological sensors for detecting metal contamination, such as cesium. Spectral detection of plant stresses typically employs a few select wavelengths and often cannot distinguish between different stress phenotypes. In this study, we apply hyperspectral reflectance imaging in the visible and near-infrared along with multivariate curve resolution (MCR) analysis to identify unique spectral signatures of three stresses in Arabidopsis thaliana: salt, copper, and cesium. While all stress conditions result in common stress physiology, hyperspectral reflectance imaging and MCR analysis produced unique spectral signatures that enabled classification of each stress. As the level of potassium was previously shown to affect cesium stress in plants, the response of A. thaliana to cesium stress under variable levels of potassium was also investigated. Increased levels of potassium reduced the spectral response of A. thaliana to cesium and prevented changes to chloroplast cellular organization. While metal stress mechanisms may vary under different environmental conditions, this study demonstrates that hyperspectral reflectance imaging with MCR analysis can distinguish metal stress phenotypes, providing the potential to detect metal contamination across large geographical areas.

Relaxation Dynamics of Chlorophyll b in the Sub-ps Ultrafast Timescale Measured by 2D Electronic Spectroscopy

A thorough characterization of the early time sub-100 fs relaxation dynamics of biologically relevant chromophores is of crucial importance for a complete understanding of the mechanisms regulating the ultrafast dynamics of the relaxation processes in more complex multichromophoric light-harvesting systems. While chlorophyll a has already been the object of several investigations, little has been reported on chlorophyll b, despite its pivotal role in many functionalities of photosynthetic proteins. Here the relaxation dynamics of chlorophyll b in the ultrafast regime have been characterized using 2D electronic spectroscopy. The comparison of experimental measurements performed at room temperature and 77 K allows the mechanisms and the dynamics of the sub-100 fs relaxation dynamics to be characterized, including spectral diffusion and fast internal conversion assisted by a specific set of vibrational modes.

Tuning antenna function through hydrogen bonds to chlorophyll a

We describe a molecular mechanism tuning the functional properties of chlorophyll a (Chl-a) molecules in photosynthetic antenna proteins. Light-harvesting complexes from photosystem II in higher plants - specifically LHCII purified with α- or β-dodecyl-maltoside, along with CP29 - were probed by low-temperature absorption and resonance Raman spectroscopies. We show that hydrogen bonding to the conjugated keto carbonyl group of protein-bound Chl-a tunes the energy of its Soret and Q_y absorption transitions, inducing red-shifts that are proportional to the strength of the hydrogen bond involved. Chls-a with non-H-bonded keto C13¹ groups exhibit the blue-most absorption bands, while both transitions are progressively red-shifted with increasing hydrogen-bonding strength - by up 382 & 605 cm^-1 in the Q_y and Soret band, respectively. These hydrogen bonds thus tune the site energy of Chl-a in light-harvesting proteins, determining (at least in part) the cascade of energy transfer events in these complexes.

Dimerization Behavior of Methyl Chlorophyllide a as the Model of Chlorophyll a in the Presence of Water Molecules-Theoretical Study

A dimerization of methyl chlorophyllide a molecules and a role of water in stabilization and properties of methyl chlorophyllide a dimers were studied by means of symmetry-adapted perturbation theory (SAPT), functional-group SAPT (F-SAPT), density-functional theory (DFT), and time-dependent DFT approaches. The quantification of various types of interactions, such as π-π stacking, coordinative, and hydrogen bonding by applying the F-SAPT energy decomposition scheme shows the major role of the magnesium atom and the pheophytin macrocycle in the stability of the complex. The examination of interaction energy components with respect to a mutual orientation of monomers and in the presence or absence of water molecules reveals that the dispersion energy is the main binding factor of the interaction, while water molecules tend to weaken the attraction between methyl chlorophyllide a species. The dimerization can be seen in computed UV-vis spectra, and results in a doubling of the lowest peaks, as compared to the monomer spectrum, and in an intensity rise of the lowest 1.8 and 2.4 eV peaks at a cost of the 3.5 eV peaks for the majority of dimer configurations. The complexation of water has little effect on the peaks' position; however, it affects the overall shape of simulated spectra through changes in peak intensities, which is strongly dependent on the structure of the complex. The VCD spectra for the dimers show several characteristic features attributed to the interaction of substituting groups and/or water ligand attached to macrocycle groups belonging to different monomers. VCD is sensitive to the type of the formed dimer, but not to the number of water molecules it contains. This and several other features, as well as the differential UV-vis spectra, may serve as the indicator of the presence of a given dimer structure in the experiment.

Structural Tuning of Quantum Decoherence and Coherent Energy Transfer in Photosynthetic Light Harvesting

Photosynthetic organisms capture energy from solar photons by constructing light-harvesting proteins containing arrays of electronic chromophores. Collective excitations (excitons) arise when energy transfer between chromophores is coherent, or wavelike, in character. Here we demonstrate experimentally that coherent energy transfer to the lowest-energy excitons is principally controlled in a light-harvesting protein by the temporal persistence of quantum coherence rather than by the strength of vibronic coupling. In the peridinin-chlorophyll protein from marine dinoflagellates, broad-band two-dimensional electronic spectroscopy reveals that replacing the native chlorophyll a acceptor chromophores with chlorophyll b slows energy transfer from the carotenoid peridinin to chlorophyll despite narrowing the donor-acceptor energy gap. The formyl substituent on the chlorophyll b macrocycle hastens decoherence by sensing the surrounding electrostatic noise. These findings demonstrate how quantum coherence enhances the efficiency of energy transfer despite being very short lived in light-harvesting proteins at physiological temperatures.

Exciton states and optical properties of the CP26 photosynthetic protein

The photosynthetic complex CP26, one of the minor antennae of the photosystem II, plays an important role in regulation of the excitation energy transfer in the PSII. Due to instability during isolation and purification, it remained poorly studied from the viewpoint of theoretical chemistry because of the absence of X-ray crystallography data. In this work, using the recently determined three-dimensional structure of the complex we apply the quantum chemical approach to study the properties of exciton states in it. Spectral properties, structure of exciton states and roles of the pigments in the complex and photosystem II are discussed.

Toward an Understanding of the Excitonic Structure of the CP47 Antenna Protein Complex of Photosystem II Revealed via Circularly Polarized Luminescence

Identification of the lowest energy pigments in the photosynthetic CP47 antenna protein complex of Photosystem II (PSII) is essential for understanding its excitonic structure, as well as excitation energy pathways in the PSII core complex. Unfortunately, there is no consensus concerning the nature of the low-energy state(s), nor chlorophyll (Chl) site energies in this important photosynthetic antenna. Although we raised concerns regarding the estimations of Chl site energies obtained from modeling studies of various types of CP47 optical spectra [Reinot, T; et al., Anal. Chem. Insights 2016, 11, 35-48] recent new assignments imposed by the shape of the circularly polarized luminescence (CPL) spectrum [Hall, J.; et al., Biochim. Biophys. Acta 2016, 1857, 1580-1593] necessitate our comments. We demonstrate that other combinations of low-energy Chls provide equally good or improved simultaneous fits of various optical spectra (absorption, emission, CPL, circular dichroism, and nonresonant hole-burned spectra), but more importantly, we expose the heterogeneous nature of the recently studied complexes and argue that the published composite nature of the CPL (contributed to by CPL₆₈₅, CPL₆₉₁, and CPL₆₉₅) does not represent an intact CP47 protein. A positive CPL₆₉₅ is extracted for the intact protein, which, when simultaneously fitted with multiple other optical spectra, provides new information on the excitonic structure of intact and destabilized CP47 complexes and their lowest energy state(s).

Fine Tuning of Chlorophyll Spectra by Protein-Induced Ring Deformation

The ability to tune the light-absorption properties of chlorophylls by their protein environment is the key to the robustness and high efficiency of photosynthetic light-harvesting proteins. Unfortunately, the intricacy of the natural complexes makes it very difficult to identify and isolate specific protein-pigment interactions that underlie the spectral-tuning mechanisms. Herein we identify and demonstrate the tuning mechanism of chlorophyll spectra in type II water-soluble chlorophyll binding proteins from Brassicaceae (WSCPs). By comparing the molecular structures of two natural WSCPs we correlate a shift in the chlorophyll red absorption band with deformation of its tetrapyrrole macrocycle that is induced by changing the position of a nearby tryptophan residue. We show by a set of reciprocal point mutations that this change accounts for up to 2/3 of the observed spectral shift between the two natural variants.

On the Conflicting Estimations of Pigment Site Energies in Photosynthetic Complexes: A Case Study of the CP47 Complex

We focus on problems with elucidation of site energies (E0n) for photosynthetic complexes (PSCs) in order to raise some genuine concern regarding the conflicting estimations propagating in the literature. As an example, we provide a stern assessment of the site energies extracted from fits to optical spectra of the widely studied CP47 antenna complex of photosystem II from spinach, though many general comments apply to other PSCs as well. Correct values of E0n for chlorophyll (Chl) a in CP47 are essential for understanding its excitonic structure, population dynamics, and excitation energy pathway(s). To demonstrate this, we present a case study where simultaneous fits of multiple spectra (absorption, emission, circular dichroism, and nonresonant hole-burned spectra) show that several sets of parameters can fit the spectra very well. Importantly, we show that variable emission maxima (690–695 nm) and sample-dependent bleaching in nonresonant hole-burning spectra reported in literature could be explained, assuming that many previously studied CP47 samples were a mixture of intact and destabilized proteins. It appears that the destabilized subpopulation of CP47 complexes could feature a weakened hydrogen bond between the 13¹-keto group of Chl29 and the PsbH protein subunit, though other possibilities cannot be entirely excluded, as discussed in this work. Possible implications of our findings are briefly discussed.

Towards an ab initio description of the optical spectra of light-harvesting antennae: application to the CP29 complex of photosystem II

Light-harvesting pigment-protein complexes (PPC) represent the fundamental units through which the photosynthetic organisms absorb sunlight and funnel the energy to the reaction centre for carrying out the primary energy conversion reactions of photosynthesis. Here we apply a multiscale computational strategy to a specific PPC present in the photosystem II of plants and algae (CP29) to investigate in what detail should the environment effects due to protein and membrane/solvent be included for an accurate description of optical spectra. We find that a refinement of the crystal structure is needed before any meaningful quantum chemical calculations of pigment transition energies can be performed. For this purpose we apply classical molecular dynamics simulations of the PPC within its natural environment and we perform ab initio computations of the exciton Hamiltonian of the complex, including the environment either implicitly by the polarizable continuum model (PCM) or explicitly using the polarizable QM/MM methodology (MMPol). However, PCM essentially leads to an unspecific redshift of all transition energies, and MMPol is able to reveal site-specific changes in the optical properties of the pigments. Based on the latter and the excitonic couplings obtained within a polarizable QM/MM methodology, optical spectra are calculated, which are in good qualitative agreement with experimental data. A weakness of the approach is however found in the overestimation of the fluctuations of the excitonic parameters of the pigments along the MD trajectory. An explanation for such a finding in terms of the limits of the force fields commonly used for protein cofactors is presented and discussed.

Solvent Induced Transformations of n-π* Absorption in Formaldehyde, Acetaldehyde, and Acetone

Absorption spectra of formaldehyde (FA), acetaldehyde (AA), and acetone are compared in the vapor phase, nonpolar, and polar solutions at 295 K. The vibronic n-π* transition of carbonyl chromophore is mainly composed of the overtones of >C═O stretching vibration. A new phenomenon is observed in liquid solutions, consisting of a relative increase of Franck-Condon factors for the second and third harmonics in FA, and the second to fourth replica in AA, with respect to the gas phase. In AA and acetone with poorly resolved vibronic structure, the redistribution of intensities produces a false "solvent shift" of the band maximum between the vapor and nonpolar liquid phase by -250 ± 50 cm(-1). Modification in vibronic coupling can also explain unusual narrowing of the band contour in the solution, reported earlier for acetone (Renge , I. J. Phys. Chem. A 2009, 113, 10678). No detectable shift occurs as a function of solvent polarizability (refractive index function (n(2) - 1)/(n(2) + 2)) in n-alkanes for FA, AA, and acetone, as well as for cyclopentanone and camphor. Incidentally, the bathochromic dispersive shift is almost exactly compensated by a hypsochromic induction shift. The latter is due to the diminishing dipole moment in the excited state of the carbonyl chromophore. Differences in polarizability α and dipole moments μ were estimated for FA (Δα = 0.33 ± 0.1 Å(3)), AA (Δμ = -1.05 ± 0.2 D, Δα = 0.5 ± 0.2 Å(3)), and acetone (Δμ = -1.3 ± 0.2 D, Δα = 0.65 ± 0.2 Å(3)). The increase of α by ∼10% upon excitation is plausible for a weak n-π* transition. By contrast, near doubling of α in the upper state has been reported recently for several ketones, with Δα reaching 10 Å(3) (Catalán, J.; Catalán, J. P. Phys. Chem. Chem. Phys. 2011, 13, 4072). Empirical partitioning of solvent shifts into repulsive-dispersive, induction, dipole-dipole, and hydrogen bonding contributions was proposed to serve as a benchmark in computer chemical calculations.

Protein dynamics tunes excited state positions in light-harvesting complex II

Light harvesting and excitation energy transfer in photosynthesis are relatively well understood at cryogenic temperatures up to ∼100 K, where crystal structures of several photosynthetic complexes including the major antenna complex of green plants (LHC II) are available at nearly atomic resolution. The situation is much more complex at higher or even physiological temperatures, because the spectroscopic properties of antenna complexes typically undergo drastic changes above ∼100 K. We have addressed this problem using a combination of quasielastic neutron scattering (QENS) and optical spectroscopy on native LHC II and mutant samples lacking the Chl 2/Chl a 612 pigment molecule. Absorption difference spectra of the Chl 2/Chl a 612 mutant of LHC II reveal pronounced changes of spectral position and their widths above temperatures as low as ∼80 K. The complementary QENS data indicate an onset of conformational protein motions at about the same temperature. This finding suggests that excited state positions in LHC II are affected by protein dynamics on the picosecond time scale. In more detail, this means that at cryogenic temperatures the antenna complex is trapped in certain protein conformations. At higher temperature, however, a variety of conformational substates with different spectral position may be thermally accessible. At the same time, an analysis of the widths of the absorption difference spectra of Chl 2/Chl a 612 reveals three different reorganization energies or Huang-Rhys factors in different temperature ranges, respectively. These findings imply that (dynamic) pigment-protein interactions fine-tune electronic energy levels and electron-phonon coupling of LHC II for efficient excitation energy transfer at physiological temperatures.

Theoretical study on excited states of bacteriochlorophyll a in solutions with density functional assessment

The excited-state properties of bacteriochlorophyll (BChl) a in triethylamine, 1-propanol, and methanol are investigated with the time-dependent density functional theory by using the quantum mechanical and molecular mechanical reweighting free energy self-consistant field method. It is found that no prevalent density functionals can reproduce the experimental excited-state properties, i.e., the absorption and reorganization energies, of BChl a in the solutions. The parameter μ in the range-separated hybrid functional is therefore optimized to reproduce the differences of the absorption energies in the solutions. We examine the origin of the differences of the absorption energies in the solutions and find that sensitive balance between contributions of structural changes and solute-solvent interactions determines the differences. The accurate description of the excitation with the density functional with the adjusted parameter is therefore essential to the understanding of the excited-state properties of BChl a in proteins and also the mechanism of the photosynthetic systems.