Vibrational techniques applied to photosynthesis: Resonance Raman and fluorescence line-narrowing

Raman analysis of lipids in cells: Current applications and future prospects

Lipids play an important role in the regulation of cell life processes. Although there are various lipid detection methods, Raman spectroscopy, a non-invasive technique, provides the detailed chemical composition of lipid profiles without a complex sample preparation procedure and possesses greater potential in basic biology, clinical diagnosis and disease therapy. In this review, we summarized the characteristics and advantages of Raman-based techniques and their primary contribution to illustrating cellular lipid metabolism.

Raman spectroscopy - a visit to the literature on plant, food, and agricultural studies

Raman spectroscopy, a fast, non-invasive, and label-free optical technique, has significantly advanced plant and food studies and precision agriculture by providing detailed molecular insights into biological tissues. Utilizing the Raman scattering effect generates unique spectral fingerprints that comprehensively analyze tissue composition, concentration, and molecular structure. These fingerprints are obtained without chemical additives or extensive sample preparation, making Raman spectroscopy particularly suitable for in-field applications. Technological enhancements such as surface-enhanced Raman scattering, Fourier-transform-Raman spectroscopy, and chemometrics have increased Raman spectroscopy sensitivity and precision. These and other advancements enable real-time monitoring of compound translocation within plants and improve the detection of chemical and biological contaminants, essential for food safety and crop optimization. Integrating Raman spectroscopy into agronomic practices is transformative and marks a shift toward more sustainable farming activities. It assesses crop quality - as well as the quality of the food that originated from crop production - early plant stress detection and supports targeted breeding programs. Advanced data processing techniques and machine learning integration efficiently handle complex spectral data, providing a dynamic and detailed view of food conditions and plant health under varying environmental and biological stresses. As global agriculture faces the dual challenges of increasing productivity and sustainability, Raman spectroscopy stands out as an indispensable tool, enhancing farming practices' precision, food safety, and environmental compatibility. This review is intended to select and briefly comment on outstanding literature to give researchers, students, and consultants a reference for works of literature in Raman spectroscopy mainly focused on plant, food, and agronomic sciences. © 2024 Society of Chemical Industry.

Raman Spectroscopic and Microbial Study of Biofilms Hosted Gypsum Deposits in the Hypersaline Wetlands: Astrobiological Perspective

Gypsum (CaSO4·2H2O) has been identified at the surface of Mars, by both orbiters and rovers. Because gypsum mostly forms in the presence of liquid water as an essential element for sustaining microbial life and has a low porosity, which is ideal for preserving organic material, it is a promising target to look for signs of past microbial life. In this article, we studied organic matter preservation within gypsum that precipitates in a salt flat or a so-called coastal sabkha located in Qatar. Sabkha's ecosystem is considered a modern analog to evaporitic environments that may have existed on early Mars. We collected the sediment cores in the areas where gypsum is formed and performed DNA analysis to characterize the community of extremophilic microorganisms that is present at the site of gypsum formation. Subsequently, we applied Raman spectroscopy, a technique available on several rovers that are currently exploring Mars, to evaluate which organic molecules can be detected through the translucent gypsum crystals. We showed that organic material can be encapsulated into evaporitic gypsum and detected via Raman microscopy with simple, straightforward sample preparation. The molecular biology data proved useful for assessing to what extent complex Raman spectra can be linked to the original microbial community, dominated by Halobacteria and methanogenic archaea, providing a reference for a signal that may be detected on Mars.

One drop only. Easy and rapid Raman evaluation of β-carotene in olive oil and its relevance as an index of olive fly attack

This paper presents, for the first time, a method for the rapid quantification of β-carotene in olive oil by Raman spectroscopy. Using a 532 nm Raman laser source, our procedure requires only one drop (100 µL) of oil, for β-carotene content to be determined. Results show that β-carotene content is associated with the lutein/β-carotene ratio, a parameter whose value describes how healthy the olives were before processing, specifically whether an olive fly attack occurred. Since olive fly attacks are not always visible to the oil producers, this method gives them the means to control the validity of the prevention strategies they adopted.

Electronic and Vibrational Properties of Allene Carotenoids

Carotenoids are conjugated linear molecules built from the repetition of terpene units, which display a large structural diversity in nature. They may, in particular, contain several types of side or end groups, which tune their functional properties, such as absorption position and photochemistry. We report here a detailed experimental study of the absorption and vibrational properties of allene-containing carotenoids, together with an extensive modeling of these experimental data. Our calculations can satisfactorily explain the electronic properties of vaucheriaxanthin, where the allene group introduces the equivalent of one C=C double bond into the conjugated C=C chain. The position of the electronic absorption of fucoxanthin and butanoyloxyfucoxanthin requires long-range corrections to be found correctly on the red side of that of vaucheriaxanthin; however, these corrections tend to overestimate the effect of the conjugated and nonconjugated C=O groups in these molecules. We show that the resonance Raman spectra of these carotenoids are largely perturbed by the presence of the allene group, with the two major Raman contributions split into two components. These perturbations are satisfactorily explained by modeling, through a gain in the Raman intensity of the C=C antisymmetric stretching mode, induced by the presence of the allene group in the carotenoid C=C chain.

Raman Scattering-Based Biosensing: New Prospects and Opportunities

The growing interest in the development of new platforms for the application of Raman spectroscopy techniques in biosensor technologies is driven by the potential of these techniques in identifying chemical compounds, as well as structural and functional features of biomolecules. The effect of Raman scattering is a result of inelastic light scattering processes, which lead to the emission of scattered light with a different frequency associated with molecular vibrations of the identified molecule. Spontaneous Raman scattering is usually weak, resulting in complexities with the separation of weak inelastically scattered light and intense Rayleigh scattering. These limitations have led to the development of various techniques for enhancing Raman scattering, including resonance Raman spectroscopy (RRS) and nonlinear Raman spectroscopy (coherent anti-Stokes Raman spectroscopy and stimulated Raman spectroscopy). Furthermore, the discovery of the phenomenon of enhanced Raman scattering near metallic nanostructures gave impetus to the development of the surface-enhanced Raman spectroscopy (SERS) as well as its combination with resonance Raman spectroscopy and nonlinear Raman spectroscopic techniques. The combination of nonlinear and resonant optical effects with metal substrates or nanoparticles can be used to increase speed, spatial resolution, and signal amplification in Raman spectroscopy, making these techniques promising for the analysis and characterization of biological samples. This review provides the main provisions of the listed Raman techniques and the advantages and limitations present when applied to life sciences research. The recent advances in SERS and SERS-combined techniques are summarized, such as SERRS, SE-CARS, and SE-SRS for bioimaging and the biosensing of molecules, which form the basis for potential future applications of these techniques in biosensor technology. In addition, an overview is given of the main tools for success in the development of biosensors based on Raman spectroscopy techniques, which can be achieved by choosing one or a combination of the following approaches: (i) fabrication of a reproducible SERS substrate, (ii) synthesis of the SERS nanotag, and (iii) implementation of new platforms for on-site testing.

A new, unquenched intermediate of LHCII

When plants are exposed to high-light conditions, the potentially harmful excess energy is dissipated as heat, a process called non-photochemical quenching. Efficient energy dissipation can also be induced in the major light-harvesting complex of photosystem II (LHCII) in vitro, by altering the structure and interactions of several bound cofactors. In both cases, the extent of quenching has been correlated with conformational changes (twisting) affecting two bound carotenoids, neoxanthin, and one of the two luteins (in site L1). This lutein is directly involved in the quenching process, whereas neoxanthin senses the overall change in state without playing a direct role in energy dissipation. Here we describe the isolation of an intermediate state of LHCII, using the detergent n-dodecyl-α-D-maltoside, which exhibits the twisting of neoxanthin (along with changes in chlorophyll–protein interactions), in the absence of the L1 change or corresponding quenching. We demonstrate that neoxanthin is actually a reporter of the LHCII environment—probably reflecting a large-scale conformational change in the protein—whereas the appearance of excitation energy quenching is concomitant with the configuration change of the L1 carotenoid only, reflecting changes on a smaller scale. This unquenched LHCII intermediate, described here for the first time, provides for a deeper understanding of the molecular mechanism of quenching.

Acute growth inhibition & toxicity analysis of nano-polystyrene spheres on Raphidocelis subcapitata

Micro/nano-plastics (MNPs) have been found within many environments and organisms including humans, making them a significant and growing concern. Initial research into the potential detrimental effects these MNPs both from acute and chronic exposure has been ongoing but still requires substantially more data to clarify. This research presents the response of nano-polystyrene (NPS) on Raphidocelis subcapitata, a freshwater alga, under an existing acute toxicity test along with additional analytical techniques to try identifying possible sources of toxicity. R. subcapitata cells were exposed for 72 h to a concentration range of 0-100 mg/l NPS. Growth Inhibition (GI) testing showed the R. subcapitata demonstrated statistically distinct reductions in growth over 72 h at all NPS exposure concentrations while not suffering culture collapse. By the 100 mg/l NPS exposure the R. subcapitata has suffered almost a 33.7% reduction in cell concentration after 72 h compared to control samples. Confocal imaging showed the NPS wasn't permeating into the algal plasma membrane or individual organelles but agglomerated onto the algal cell wall. The agglomeration was irregular but increased in total surface area covered as NPS concentration increases. UV-Vis fluorimetry testing produced a linear response of emission intensities to algae exposed to the 0-100 mg/l range of NPS. However, comparisons of emission intensity values of algae exposed to NPS to emission intensities of pure NPS at identical concentrations showed consistent intensity reduction. This response further indicated NPS agglomerating within the media and onto the alga cells seen from confocal imaging. Finally, Raman spectroscopy on R. subcapitata attempted to distinguish the key 1001 cm^-1 peak or other crucial identifier peaks of polystyrene from overall Raman spectra. This was not successful as emissions from algal component (e.g. phenylaniline) completely suppressed the signal region.

Fingerprinting molecular and isotopic biosignatures on different hydrothermal scenarios of Iceland, an acidic and sulfur-rich Mars analog

Detecting signs of potential extant/extinct life on Mars is challenging because the presence of organics on that planet is expected to be very low and most likely linked to radiation-protected refugia and/or preservative strategies (e.g., organo-mineral complexes). With scarcity of organics, accounting for biomineralization and potential relationships between biomarkers, mineralogy, and geochemistry is key in the search for extraterrestrial life. Here we explored microbial fingerprints and their associated mineralogy in Icelandic hydrothermal systems analog to Mars (i.e., high sulfur content, or amorphous silica), to identify potentially habitable locations on that planet. The mineralogical assemblage of four hydrothermal substrates (hot springs biofilms, mud pots, and steaming and inactive fumaroles) was analyzed concerning the distribution of biomarkers. Molecular and isotopic composition of lipids revealed quantitative and compositional differences apparently impacted by surface geothermal alteration and environmental factors. pH and water showed an influence (i.e., greatest biomass in circumneutral settings with highest supply and turnover of water), whereas temperature conditioned the mineralogy that supported specific microbial metabolisms related with sulfur. Raman spectra suggested the possible coexistence of abiotic and biomediated sources of minerals (i.e., sulfur or hematite). These findings may help to interpret future Raman or GC-MS signals in forthcoming Martian missions.

How water-mediated hydrogen bonds affect chlorophyll a/b selectivity in Water-Soluble Chlorophyll Protein

The Water-Soluble Chlorophyll Protein (WSCP) of Brassicaceae is a remarkably stable tetrapyrrole-binding protein that, by virtue of its simple design, is an exceptional model to investigate the interactions taking place between pigments and their protein scaffold and how they affect the photophysical properties and the functionality of the complexes. We investigated variants of WSCP from Lepidium virginicum (Lv) and Brassica oleracea (Bo), reconstituted with Chlorophyll (Chl) b, to determine the mechanisms by which the different Chl binding sites control their Chl a/b specificities. A combined Raman and crystallographic investigation has been employed, aimed to characterize in detail the hydrogen-bond network involving the formyl group of Chl b. The study revealed a variable degree of conformational freedom of the hydrogen bond networks among the WSCP variants, and an unexpected mixed presence of hydrogen-bonded and not hydrogen-bonded Chls b in the case of the L91P mutant of Lv WSCP. These findings helped to refine the description of the mechanisms underlying the different Chl a/b specificities of WSCP versions, highlighting the importance of the structural rigidity of the Chl binding site in the vicinity of the Chl b formyl group in granting a strong selectivity to binding sites.

Excited State Frequencies of Chlorophyll f and Chlorophyll a and Evaluation of Displacement through Franck-Condon Progression Calculations

We present ground and excited state frequency calculations of the recently discovered extremely red-shifted chlorophyll f. We discuss the experimentally available vibrational mode assignments of chlorophyll f and chlorophyll a which are characterised by particularly large downshifts of 13¹-keto mode in the excited state. The accuracy of excited state frequencies and their displacements are evaluated by the construction of Franck–Condon (FC) and Herzberg–Teller (HT) progressions at the CAM-B3LYP/6-31G(d) level. Results show that while CAM-B3LYP results are improved relative to B3LYP calculations, the displacements and downshifts of high-frequency modes are underestimated still, and that the progressions calculated for low temperature are dominated by low-frequency modes rather than fingerprint modes that are Resonant Raman active.

Distributions of Silica and Biopolymer Structural Components in the Spore Elater of Equisetum arvense, an Ancient Silicifying Plant

Equisetum species are primitive vascular plants that benefit from the biogenesis of silica bio-organic inclusions in their tissues and participate in the annual biosilica turnover in local eco-systems. As means of Equisetum reproduction and propagation, spores are expected to reflect the evolutionary adaptation of the plants to the climatic conditions at different times of the year. Combining methods of Raman and scanning electron microscopy and assisted with density functional theory, we conducted material spatial-spectral correlations to characterize the distribution of biopolymers and silica based structural elements that contribute to the bio-mineral content of the elater. The elater tip has underlying skeletal-like structural elements where cellulose fibers provide strength and flexibility, both of which are necessary for locomotion. The surface of the elater tips is rich with less ordered pectin like polysaccharide and shows a ridged, folded character. At the surface we observe silica of amorphous, colloidal form in nearly spherical structures where the silica is only a few layers thick. We propose the observed expansion of elater tips upon germination and the form of silica including encapsulated biopolymers are designed for ready dispersion, release of the polysaccharide-arginine rich content and to facilitate silica uptake to the developing plant. This behavior would help to condition local soil chemistry to facilitate competitive rooting potential and stem propagation.

Effects of carotenoids on the absorption and fluorescence spectral properties and fluorescence quenching of Chlorophyll a

Fluorescence and absorption characteristics of Chlorophyll a (Chl-a) were modulated by the carotenoids (Cars) with different numbers of conjugated carbon‑carbon double bonds in solutions. The Chl-a absorption appears the redshift phenomenon with the effective conjugated of Cars increasing. The absorption of Chl-a and Cars are linearly dependent on intrinsic factors, namely effective conjugate length and functional groups, and on environmental factors, such as the polarizability of the solvent. Cars can be able to quench the Chl-a fluorescence by producing the non-emitting exciplex intermediate. The effective conjugated length of Cars is one of the reasons that effect the fluorescence quenching of Chl-a. According to the Stern-Volmer plots, the Chl-a fluorescence quenching should be predominantly dynamic rather than static.

Pigment configuration in the light-harvesting protein of the xanthophyte alga Xanthonema debile

The soil chromophyte alga Xanthonema (X.) debile contains only non-carbonyl carotenoids and Chl-a. X. debile has an antenna system denoted Xanthophyte light-harvesting complex (XLH) that contains the carotenoids diadinoxanthin, heteroxanthin, and vaucheriaxanthin. The XLH pigment stoichiometry was calculated by chromatographic techniques and the pigment-binding structure studied by resonance Raman spectroscopy. The pigment ratio obtained by HPLC was found to be close to 8:1:2:1 Chl-a:heteroxanthin:diadinoxanthin:vaucheriaxanthin. The resonance Raman spectra suggest the presence of 8-10 Chl-a, all of which are 5-coordinated to the central Mg, with 1-3 Chl-a possessing a macrocycle distorted from the relaxed conformation. The three populations of carotenoids are in the all-trans configuration. Vaucheriaxanthin absorbs around 500-530 nm, diadinoxanthin at 494 nm and heteroxanthin at 487 nm at 4.5 K. The effective conjugation length of heteroxanthin and diadinoxanthin has been determined as 9.4 in both cases; the environment polarizability of the heteroxanthin and diadinoxanthin binding pockets is 0.270 and 0.305, respectively.

Photosynthetic Energy Transfer at the Quantum/Classical Border

Quantum mechanics diverges from the classical description of our world when very small scales or very fast processes are involved. Unlike classical mechanics, quantum effects cannot be easily related to our everyday experience and are often counterintuitive to us. Nevertheless, the dimensions and time scales of the photosynthetic energy transfer processes puts them close to the quantum/classical border, bringing them into the range of measurable quantum effects. Here we review recent advances in the field and suggest that photosynthetic processes can take advantage of the sensitivity of quantum effects to the environmental 'noise' as means of tuning exciton energy transfer efficiency. If true, this design principle could be a base for 'nontrivial' coherent wave property nano-devices.

Tracing feed-back driven exciton dynamics in molecular aggregates

Excitation, exciton transport, dephasing and energy relaxation, and finally detection processes shift molecular systems into a specific superposition of quantum states causing localization, local heating and finally excitonic polaronic effects.

Pigment structure in the violaxanthin-chlorophyll-a-binding protein VCP

Resonance Raman spectroscopy was used to evaluate pigment-binding site properties in the violaxanthin-chlorophyll-a-binding protein (VCP) from Nannochloropsis oceanica. The pigments bound to this antenna protein are chlorophyll-a, violaxanthin, and vaucheriaxanthin. The molecular structures of bound Chl-a molecules are discussed with respect to those of the plant antenna proteins LHCII and CP29, the crystal structures of which are known. We show that three populations of carotenoid molecules are bound by VCP, each of which is in an all-trans configuration. We assign the lower-energy absorption transition of each of these as follows. One violaxanthin population absorbs at 485 nm, while the second population is red-shifted and absorbs at 503 nm. The vaucheriaxanthin population absorbs at 525 nm, a position red-shifted by 2138 cm^-1 as compared to isolated vaucheriaxanthin in n-hexane. The red-shifted violaxanthin is slightly less planar than the blue-absorbing one, as observed for the two central luteins in LHCII, and we suggest that these violaxanthins occupy the two equivalent binding sites in VCP at the centre of the cross-brace. The presence of a highly red-shifted vaucheriaxanthin in VCP is reminiscent of the situation of FCP, in which (even more) highly red-shifted populations of fucoxanthin are present. Tuning carotenoids to absorb in the green-yellow region of the visible spectrum appears to be a common evolutionary response to competition with other photosynthetic species in the aquatic environment.

Concentration Effect on Quenching of Chlorophyll a Fluorescence by All-Trans-β-Carotene in Photosynthesis

Absorption, fluorescence spectra of chlorophyll a (Chl-a) and all-trans-β-carotene (β-Car) mixing solution are investigated in different polarity and polarizability solvents. The carotenoids regulate the energy flow in photosynthesis by interaction with chlorophyll, leading to an observable reduction of Chl-a fluorescence. The fluorescence red shifts with the increasing solvent polarizability. The energy transfer in the Chl-a and β-Car system is proposed. The electron transfer should be dominant in quenching Chl-a fluorescence rather than the energy transfer in this system. Polar solvent with large polarizability shows high quenching efficiency. When dissolved in carbon tetrachloride, Chl-a presents red shift of absorption and blue shift of fluorescence spectra with increasing β-Car concentration, which implies a Chl-a conformational change.

Dependence of the hydration status of bacterial light-harvesting complex 2 on polyol cosolvents

Tch. tepidumLH2 hydration correlates with water activity in water–polyol binary solvents as sensitively probed by near infrared electronic spectra and characteristic triplet carotenoid–bacteriochlorophyll interaction bands.

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.

Light-Induced Infrared Difference Spectroscopy in the Investigation of Light Harvesting Complexes

Light-induced infrared difference spectroscopy (IR-DS) has been used, especially in the last decade, to investigate early photophysics, energy transfer and photoprotection mechanisms in isolated and membrane-bound light harvesting complexes (LHCs). The technique has the definite advantage to give information on how the pigments and the other constituents of the biological system (proteins, membranes, etc.) evolve during a given photoreaction. Different static and time-resolved approaches have been used. Compared to the application of IR-DS to photosynthetic Reaction Centers (RCs), however, IR-DS applied to LHCs is still in an almost pioneering age: very often sophisticated techniques (step-scan FTIR, ultrafast IR) or data analysis strategies (global analysis, target analysis, multivariate curve resolution) are needed. In addition, band assignment is usually more complicated than in RCs. The results obtained on the studied systems (chromatophores and RC-LHC supercomplexes from purple bacteria; Peridinin-Chlorophyll-a-Proteins from dinoflagellates; isolated LHCII from plants; thylakoids; Orange Carotenoid Protein from cyanobacteria) are summarized. A description of the different IR-DS techniques used is also provided, and the most stimulating perspectives are also described. Especially if used synergically with other biophysical techniques, light-induced IR-DS represents an important tool in the investigation of photophysical/photochemical reactions in LHCs and LHC-containing systems.