Light Absorption and Energy Transfer in the Antenna Complexes of Photosynthetic Organisms

Size-Transferable Prediction of Excited State Properties for Molecular Assemblies with a Machine Learning Exciton Model

Computational modeling of the excited states of molecular aggregates faces significant computational challenges and size heterogeneity. Current machine learning (ML) models, typically trained on specific-sized aggregates, struggle with scalability. We found that the exciton model Hamiltonian of large aggregates can be decomposed into dimer pairs, allowing an ML model trained on dimers to reconstruct Hamiltonians for aggregates of any size. We also proposed a new method to address the phase-correction problem by introducing coupling terms' approximations. Our model accurately predicted the excitation energies of the trimer and tetramer of perylene and tetracene and estimated S1 oscillator strengths of perylene aggregates. Leveraging our ML model, the optical gaps of nanosized perylene aggregates with up to 50 monomers are analyzed, qualitatively revealing the role of different couplings on their size dependency. Future work will explore transferability across different monomers to predict optical properties in heterogeneous assemblies.

Cavity-enhanced energy transport in molecular systems

Molecules are the building blocks of all of nature's functional components, serving as the machinery that captures, stores and releases energy or converts it into useful work. However, molecules interact with each other over extremely short distances, which hinders the spread of energy across molecular systems. Conversely, photons are inert, but they are fast and can traverse large distances very efficiently. Using optical resonators, these distinct entities can be mixed with each other, opening a path to new architectures that benefit from both the active nature of molecules and the long-range transport obtained by the coupling with light. In this Review, we present the physics underlying the enhancement of energy transfer and energy transport in molecular systems, and highlight the experimental and theoretical advances in this field over the past decade. Finally, we identify several key questions and theoretical challenges that remain to be resolved via future research.

Pyrene-Based Light-Harvesting Antenna Molecules

Light-harvesting antenna systems (AS) with multiple light-absorbing chromophores play a vital role in absorbing sunlight and transferring the excitation energy to the reaction centers during the photosynthesis process. Learning from nature, a set of simple and artificial pyrene-based light-harvesting antenna systems have been designed and re-examined from the self-developing chemical intermediates, via combining the electron-donating 4,4-dimethoxy-triphenylamine moieties as the antenna for absorbing energy donors and transferring to the reaction center. These pyrene-based light-harvesting antenna systems exhibit a positive correlation between the molar absorption coefficient (ε), enhanced photoluminescence efficiency with unchanged emission peak, and two-photon absorption cross-section with an increasing number of antenna of TPA-OMe moieties in solution. Moreover, the excited-state dynamics of these AS indicated that the coexistence of the charge transfer (CT) state and charge separation (CS) state plays a significant role in affecting the emission behavior. The short-lived CS state was affected by the increased TPA-OMe moieties and low polar solvent, which can boost the CS decay to charge recombination (CR), resulting in enhanced emission. On the contrary, the long-lived CS state would overwhelm the CT state in high polar solvent or pyrene-based antenna molecules containing one or two TPA-OMe units.

Computational Approach to Phosphor-Sensitized Fluorescence Based on Monomer Transition Densities

We present here an extension of the monomer transition density approach to spin multiplicity-altering excitation energy transfer (EET) processes. It builds upon complex-valued wave functions of the density functional theory-based multireference spin-orbit coupling configuration interaction method for generating the one-particle transition density matrices of the donor and acceptor molecules, which are then contracted with two-electron Coulomb and exchange integrals of the dimer. Due to the extensive use of symmetry relations between tensor components, the computation of triplet-singlet coupling remains technically feasible. As a proof-of-principle application, we have chosen an EET system, consisting of the phosphorescent platinum complex AG97 as the donor and the fluorescein derivative FITC as the acceptor. Taking experimental conditions into account, we estimate a Förster radius of about 35 Å. For intermolecular donor-acceptor separations close to the Förster radius and beyond, the error introduced by the ideal dipole approximation is rather small.

Chiral Rotaxane-Branched Dendrimers as Relays in Artificial Light-Harvesting Systems with Boosted Circularly Polarized Luminescence

Starting from AIEgen-functionalized chiral [2]rotaxane building block, we have successfully synthesized a new class of chiral rotaxane-branched dendrimers through controllable divergent strategy for the first time, based on which novel chiral artificial light-harvesting systems (LHSs) were successfully constructed in aqueous phase by sequentially introducing achiral donor and acceptor. More importantly, accompanied by the two-step Förster resonance energy transfer (FRET) process in the resultant artificial LHSs, the sequentially amplified circularly polarized luminescence (CPL) performances were achieved, highlighting that the chiral rotaxane-branched dendrimers could serve as excellent relay for both energy transfer and chirality transmission. Impressively, compared with the sole chiral rotaxane-branched dendrimers, the dissymmetry factors (glum) values of the resultant artificial LHSs were amplified by one order of magnitude up to 0.038, enabling their further applications in information storage and encryption. The proof-of concept study provides not only a feasible approach for the efficient amplification of CPL performances but also a novel platform for the construction of novel chiral luminescent materials.

Electronic-vibrational resonance damping time-dependent photosynthetic energy transfer acceleration revealed by 2D electronic spectroscopy

The effects of damping time of electronic-vibrational resonance modes on energy transfer in photosynthetic light-harvesting systems are examined. Using the hierarchical equations of motion (HEOM) method, we simulate the linear absorption and two-dimensional electronic spectra (2DES) for a dimer model based on bottleneck sites in the light-harvesting complex of photosystem II. A site-dependent spectral density is incorporated, with only the low-energy site being coupled to the resonance mode. Similar patterns are observed in linear absorption spectra and early time 2DES for various damping times, owing to the weak coupling strength. However, notable differences emerge in the dynamics of the high-energy diagonal and cross-peaks in the 2DES. It is found that the coupling of electronic-vibrational resonance modes accelerates the energy transfer process, with rates being increased as the damping time is extended, but the impact becomes negligible when the damping time exceeds a certain threshold. To evaluate the reliability of the perturbation method, the modified Redfield (MR) method is employed to simulate 2DES under the same conditions. The results from the MR method are aligned with those obtained from the HEOM method, but the MR method predicts faster dynamics.

Solvent-Free Artificial Light-Harvesting System in a Fluid Donor with Highly Efficient Förster Resonance Energy Transfer

Multi-step Förster resonance energy transfer (FRET) plays a vital role in photosynthesis. While the energy transfer efficiency (ΦET) of a naturally occurring system can reach 95%, that of most artificial light-harvesting systems (ALHSs) is still limited. Herein, we propose a strategy to construct highly efficient ALHSs using a blue-emitting, supercooled ionic compound of naphthalimide (NPI) as the donor, a green-emitting BODIPY derivate as a relay acceptor, and a commercially available, red-emitting dye [rhodamine B (RhB)] as the final acceptor. The broad emission of the fluid donor can overlap simultaneously with the absorption of BODIPY and RhB, enabling the occurrence of a sequential FRET from NPI to BODIPY to RhB as well as a parallel FRET directly from NPI to RhB. These two complementary energy transfer routes lead to an overall ΦET up to 97.4%, which is the champion among all of the reported ALHSs and is also higher than that found in plants and photosynthetic bacteria. This strategy is universal, and ΦET of the system could be further improved by optimizing the structures of the fluid donor and relay acceptor.

Synthesis of Porphyrin Derivatives Bearing Six Carboxylic Acids for the Formation of Three-Dimensional Hydrogen-Bonded Network Structures

we synthesized a series of porphyrin derivatives with six carboxylic acid groups to explore their potential in forming hydrogen-bonded networks (YSHs). By systematically varying the position and structure of these carboxylic acid groups, we observed distinct types of hydrogen-bonded frameworks, including two- and three-dimensional networks. Using single-crystal X-ray crystallography, we confirmed that these derivatives form YSHs with unique structural properties influenced by carboxylic acid positioning and π-π interactions. The 1Zn derivative forms a robust 3D hydrogen-bonded network stabilized by π-π stacking interactions, while the 2Ni derivative, with no such stacking, exhibits reduced stability and collapses upon solvent removal. Structural variations like the terphenylene and biphenyl linkers in 3Zn and 4Zn lead to flexible frameworks, while the 5Zn dimer forms two distinct structures depending on the solvent environment. Our findings reveal that careful control over carboxylic acid orientation and linker structure enables the design of diverse hydrogen-bonded networks with tunable stability and dimensionality. These insights advance our understanding of supramolecular assembly principles in porphyrin-based materials and offer new pathways for developing high-performance frameworks for applications in catalysis, sensing, and materials science.

Quantum life science: biological nano quantum sensors, quantum technology-based hyperpolarized MRI/NMR, quantum biology, and quantum biotechnology

The emerging field of quantum life science combines principles from quantum physics and biology to study fundamental life processes at the molecular level. Quantum mechanics, which describes the properties of small particles, can help explain how quantum phenomena such as tunnelling, superposition, and entanglement may play a role in biological systems. However, capturing these effects in living systems is a formidable challenge, as it involves dealing with dissipation and decoherence caused by the surrounding environment. We overview the current status of the quantum life sciences from technologies and topics in quantum biology. Technologies such as biological nano quantum sensors, quantum technology-based hyperpolarized MRI/NMR, high-speed 2D electronic spectrometers, and computer simulations are being developed to address these challenges. These interdisciplinary fields have the potential to revolutionize our understanding of living organisms and lead to advancements in genetics, molecular biology, medicine, and bioengineering.

Smartphone-Assisted Fluorescence Determination of Inorganic Phosphorus Using a Samarium Metal-Organic Framework

Inorganic phosphori are widely used in food, whose quantitative detection method is of significance. This work presents a Sm-DDB (H4DDB = 1,3-di(3',5'-dicarboxylphenyl)benzene), which acts as a ratiometric fluorescence sensor to monitor PO43-, H2PO4-, and (PO3)66- with high sensitivity. The determination factors of pH, MOF dosage, and fluorescence response time are optimized as 7.35, 1 mg, and 2 min, respectively. The sensitivity tests show the linear fitting equations of I465/I598 = 0.00363·CP + 1.49183 (I465 and I598: the emission intensities at 465 and 598 nm; Cp = inorganic phosphorus concentration) for PO43-, I465/I598 = 0.00272·CP + 1.55944 for H2PO4-, and I465/I598 = 0.00957·CP + 1.55122 for (PO3)66- with LODs being 1.00 μM for PO43-, 1.33 μM for H2PO4-, and 0.38 μM for (PO3)66-. The detection method was applied in frozen shrimp, marine fish, and bacon, whose fluorescence recoveries of around 100% demonstrate its reliability. The analytical results are close to those determined by the phosphomolybdenum blue method. The Sm-DDB test paper shows an obvious emission color change, whose blue/red (B/R) values can be recognized by a smartphone APP. This work provides a smartphone-assisted visualization detection method for PO43-, H2PO4-, and (PO3)66-.

Proximal Oblique-Packing of Heptamethine Cyanines through Spiro-Connection Boosts Triplet State Generation in Near-Infrared

Near-infrared (NIR) triplet dyes are the cornerstones of cutting-edge biomedical and material applications. The difficulty in rational development of triplet dyes increases exponentially as the absorption wavelength shifts deeper into the NIR range. Although classical H-/J-typed packing of NIR dyes has the potential to enhance intersystem crossing (ISC) compared with that in single-chromophore dyes, the triplet state quantum yields remain limited in such strategy. Herein, proximal oblique-packed (V-shaped) heptamethine cyanines (SZ780) through spiro-connection were achieved. Multi-channel ultrafast ISC were direct observed in SZ780 and a record high ISC rate constant (up to ~1011 s-1) is registered among all the reported NIR triplet dyes. SZ780 exhibits a triplet state quantum yield of 18.9 % upon excitation at 750 nm, which is almost an order of magnitude higher than that of the monomer (IR780, 2.1 %) and nearly threefold increase compared to that of the H-packed dimer (SC780) (6.7 %). Moreover, SZ780 efficiently generates singlet oxygen under 808 nm light irradiation, inducing cancer cell apoptosis in vivo. These findings demonstrate that constructing V-aggregated dyes system by spiro-connection offers a powerful approach for the design of high-performance NIR triplet sensitizers.

Computational Design of (B)Chl Models: Structural and Chemical Modifications toward Enriched Properties

The functional units of natural photosynthetic systems control the process of converting sunlight into chemical energy. In this article, we explore a series of chemically and structurally modified bacteriochlorophyll and chlorophyll pigments through computational chemistry to evaluate their electronic spectroscopy properties. More specifically, we use multiconfigurational and time-dependent density functional theory methods, along with molecular dynamics simulations, to compute the models' energetics both in an implicit and explicit solvent environment. Structural modifications aimed at reducing the planarity of the macrocycle through alkyl-bridge anchoring reveal the significant role of the curvature in fine-tuning spectral properties, which mimics protein scaffold effects on naturally occurring pigments. Furthermore, chemical substitutions with a carbonyl group show potential for expanding absorption spectra toward the blue region, while incorporating an additional double bond decreases absorption efficiency. These insights lay the groundwork to design novel synthetic pigments, with potential applications in artificial light-harvesting systems and more efficient photovoltaic devices.

Four-Dimensional Data-Independent Acquisition-Based Proteomic Profiling Combined with Transcriptomic Analysis Reveals the Involvement of the Slym1-SlFHY3-CAB3C Module in Regulating Tomato Leaf Color

In green plants, the chloroplast is responsible for light energy transition and organic assimilation. However, the molecular mechanisms underlying chloroplast development in horticultural crops remain unclear. Here, four-dimensional data-independent acquisition-based proteomic profiling identified 1,727 differentially expressed proteins between "Zhongshu 4" (ZS4) and yellowing mutant (ym) leaves, a considerable proportion of which were down-regulated chloroplast proteins. Functional analysis revealed that light harvesting and chlorophyll biosynthesis were correlated with ym leaf yellowing, validated by RNA sequencing. Quantitative PCR confirmed that chlorophyll a/b-binding protein 3C (CAB3C) related to light harvesting and NADPH:protochlorophyllide oxidoreductase 3 (POR3) involved in chlorophyll biosynthesis were repressed in ym leaves. Virus-induced gene silencing showed that suppressing CAB3C and POR3 decreased the net photosynthetic rate and chlorophyll content. Additionally, the F-box protein Slym1 negatively regulated the expression of CAB3C by depressing transcription factor SlFHY3 levels. Our findings offer insights into the regulatory mechanisms of chloroplast development in tomato.

Revealing Single-Molecule Photocurrent Generation Mechanisms under On- and Off-Resonance Excitation

We investigate photocurrent generation mechanisms in a pentacene single-molecule junction using subnanometer resolved photocurrent imaging under both on- and off-resonance laser excitation. By employing a wavelength-tunable laser combined with a lock-in technique, net photocurrent signals are extracted to elucidate photoinduced electron tunneling processes. Under off-resonance excitation, photocurrents are found to arise from photon-assisted tunneling, with contributions from three distinct frontier molecular orbitals at different bias voltages. In contrast, under resonance excitation, photocurrents are found to be significantly enhanced at negative bias voltages, exhibiting a spatial distribution linked to molecular electronic transitions and associated transition dipoles. This study reveals the contributions of different frontier molecular orbitals in the photon-assisted tunneling processes under off-resonance excitation, while molecular optical transitions are also found to be important at negative bias under resonance excitation. These findings could be instructive to the design and optimization of advanced optoelectronic devices.

A new-to-nature photosynthesis system enhances utilization of one-carbon substrates in Escherichia coli

Photosynthesis harvests solar energy to convert CO2 into chemicals, offering a potential solution to reduce atmospheric CO2. However, integrating photosynthesis into non-photosynthetic microbes to utilize one-carbon substrates is challenging. Here, a photosynthesis system is reconstructed in E. coli, by integrating light and dark reaction to synthesize bioproducts from one-carbon substrates. A light reaction is reconstructed using the photosystem of photosynthetic bacteria, increasing ATP and NADH contents by 337.9% and 383.7%, respectively. A dark reaction is constructed by designing CO2 fixation pathway to synthesize pyruvate. By assembling the light and dark reaction, a photosynthesis system is established and further programmed by installing an energy adapter, enabling the production of acetone, malate, and α-ketoglutarate, with a negative carbon footprint of -0.84 ~ -0.23 kgCO2e/kg product. Furthermore, light-driven one-carbon trophic growth of E. coli is achieved with a doubling time of 19.86 h. This photosynthesis system provides a green and sustainable approach to enhance one-carbon substrates utilization in the future.

Light intensity moderates photosynthesis by optimizing photosystem mechanisms under high VPD stress

In recent decades, the global increase in vapor pressure deficit (VPD) has significantly inhibited plant growth and photosynthesis. Light intensity, a crucial environmental regulator, plays a vital role in stress response and photosynthetic adjustment. This study investigated whether increasing light intensity under high VPD conditions could optimise the photosystem and thereby enhance photosynthesis. We designed experiments using factorial combinations of two VPD levels (HVPD; high VPD, AVPD; appropriate VPD) and two irradiance gradients (L300; 300 μmol photons m-2 s-1, L600; 600 μmol photons m-2 s-1). Under high VPD, plants protect their photosystems by reducing light energy absorption and limiting photosynthetic electron flow, which results in reduced photosynthesis. However, when exposed to HVPD + L600, plants exhibited increased light energy absorption, as evidenced by elevated chlorophyll b and carotenoid levels, enhanced response to irradiance, and decreased NPQ and Y(NO). This regimen also enhanced photosynthetic electron transport by increasing the total driving force and plastoquinone pool, consequently improving the photochemical efficiency of the photosystem and ultimately boosting the net photosynthetic rate by 46.9%. This study confirmed that modulating light intensity under high VPD stress can improve photosynthesis by optimizing the photosystem. This novel approach can be utilized to enhance tomato production in arid regions.

Applied photosynthesis: An idea whose time has come

Advancements in materials science, synthetic biology, and nanomaterial engineering are revolutionizing renewable energy technologies, creating new pathways for sustainable energy production. Biohybrid devices-systems combining biological components with engineered synthetic materials-are emerging as powerful platforms for harnessing solar energy to drive hydrogen production, photovoltaics, catalysis, and biosensing. This collection of articles presents leading-edge research in biohybrid energy systems, where photosynthetic mechanisms are redeployed to develop eco-friendly, high-efficiency alternatives to conventional solar technologies. Central to these biohybrid designs are diverse organisms, from cyanobacteria and algae to purple bacteria and archaea, enabling researchers to employ a broad range of bioengineered proteins and photosynthetic complexes. By integrating advances in synthetic biology with precision nanomaterial fabrication, scientists can improve protein functionality and device stability at the nanoscale, optimizing these systems for light absorption, energy conversion, and resilience. This convergence allows exploring unique photoactive pigments, including type I and type II reaction centers, specialized light-harvesting and retinal-binding proteins. Through protein engineering and careful selection of photoactive components, biohybrid devices offer promising solutions for sustainable energy applications, positioning photosynthetic organisms as critical contributors to innovative energy technology.

Sequential Energy and Electron Transfer in Metal-Organic Frameworks

This study presents the design and characterization of a triad metal-organic framework (MOF) system composed of pyrene, porphyrin, and phenyl-C61-butyric acid (PCBA) for efficient energy and electron transfer processes mimicking natural photosynthesis. The triad MOF, synthesized through a mixed-ligand approach followed by postsynthetic modification, demonstrates sequential energy transfer from pyrene to porphyrin, followed by electron transfer to the PCBA acceptor. Time-resolved photoluminescence (TRPL) spectroscopy was employed to investigate the dynamics of energy and charge transfer, revealing fast interligand energy transfer and subsequent charge separation in the MOF structure. The PCBA-functionalized MOF (PCBA@nMLM) exhibited a significantly enhanced photocatalytic performance compared to the nonfunctionalized counterpart, particularly in the selective aerobic oxidation of sulfides to sulfoxides under visible light irradiation. The enhanced photocatalytic activity is attributed to the prolonged charge separation facilitated by the PCBA moieties, as confirmed by electrochemical impedance spectroscopy (EIS) and transient photocurrent measurements. This work highlights the potential of MOF-based systems in artificial photosynthesis and other photocatalytic applications by effectively harnessing solar energy through optimized energy and charge transfer mechanisms.

Absorption changes in Photosystem II in the Soret band region upon the formation of the chlorophyll cation radical [PD1PD2]. PHOTOSYNTHESIS RESEARCH 2024;162:211-223. [PMID: 37751034 DOI: 10.1007/s11120-023-01049-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Flash-induced absorption changes in the Soret region arising from the [PD1PD2]+ state, the chlorophyll cation radical formed upon light excitation of Photosystem II (PSII), were measured in Mn-depleted PSII cores at pH 8.6. Under these conditions, TyrD is i) reduced before the first flash, and ii) oxidized before subsequent flashes. In wild-type PSII, when TyrD● is present, an additional signal in the [PD1PD2]+-minus-[PD1PD2] difference spectrum was observed when compared to the first flash when TyrD is not oxidized. The additional feature was "W-shaped" with troughs at 434 nm and 446 nm. This feature was absent when TyrD was reduced, but was present (i) when TyrD was physically absent (and replaced by phenylalanine) or (ii) when its H-bonding histidine (D2-His189) was physically absent (replaced by a Leucine). Thus, the simple difference spectrum without the double trough feature at 434 nm and 446 nm, seemed to require the native structural environment around the reduced TyrD and its H bonding partners to be present. We found no evidence of involvement of PD1, ChlD1, PheD1, PheD2, TyrZ, and the Cytb559 heme in the W-shaped difference spectrum. However, the use of a mutant of the PD2 axial His ligand, the D2-His197Ala, shows that the PD2 environment seems involved in the formation of "W-shaped" signal.

Intramolecular charge transfer and the function of vibronic excitons in photosynthetic light harvesting

A widely discussed explanation for the prevalence of pairs or clusters of closely spaced electronic chromophores in photosynthetic light-harvesting proteins is the presence of ultrafast and highly directional excitation energy transfer pathways mediated by vibronic excitons, the delocalized optical excitations derived from mixing of the electronic and vibrational states of the chromophores. We discuss herein the hypothesis that internal conversion processes between exciton states on the <100 fs timescale are possible when the excitonic potential energy surfaces are controlled by the vibrational modes that induce charge transfer character in a strongly coupled system of chromophores. We discuss two examples, the peridinin-chlorophyll protein from marine dinoflagellates and the intact phycobilisome from cyanobacteria, in which the intramolecular charge-transfer (ICT) character arising from out-of-plane distortion of the conjugation of carotenoid or bilin chromophores also results in localization of the initially delocalized optical excitation on the vibrational timescale. Tuning of the ground state conformations of the chromophores to manipulate their ICT character provides a natural photoregulatory mechanism, which would control the overall quantum yield of excitation energy transfer by turning on and off the delocalized character of the optical excitations.

Vibrational Relaxation Completes the Excitation Energy Transfer and Localization of Vibronic Excitons in Allophycocyanin α84-β84

Phycobilisomes are light-harvesting complexes that play a key role in photosynthesis in cyanobacteria, which generate more than 40% of the world's oxygen. The near-unity excitation energy transfer efficiency from phycobilisomes to photosystems highlights its importance in understanding efficient energy transfer processes. Spectroscopic studies have shown that the 280 fs rapid excitonic downhill energy transfer within the α84-β84 chromophore dimer in allophycocyanin (APC), a subunit of phycobilisomes, is crucial to this efficiency. However, the role of strong chromophore-protein interactions and vibrational relaxation requires further exploration to fully explain this efficient downhill energy transfer. A theory is required that adequately describes exciton dynamics in an intermediate region while also incorporating vibrational relaxation mediated by protein bath modes. In this work, we incorporate vibrational relaxation into modified Redfield theory by introducing coupling fluctuation. We holistically simulate the rapid excitation energy transfer process of the α84-β84 chromophore dimer in APC and successfully model the recently observed rapid energy capture. We find that vibrational relaxation dictates capture of excitons by the localized state of the β84 chromophore. The calculated rate shows excellent agreement with previous ultrafast spectroscopic experiments. Our results show that the inclusion of vibrational relaxation is essential for systems that utilize vibronic coupling to enhance energy transfer and capture. Consequently, incorporating vibrational relaxation into Modified Redfield theory shows promise for accurately describing the excitation energy transfer process in other photosynthetic systems.

Hierarchical Equations of Motion for Quantum Chemical Dynamics: Recent Methodology Developments and Applications

ConspectusQuantum effects are critical to understanding many chemical dynamical processes in condensed phases, where interactions between molecules and their environment are usually strong and non-Markovian. In this Account, we review recent progress from our group in development and application of the hierarchical equations of motion (HEOM) method, highlighting its ability to address some challenging problems in quantum chemical dynamics.In the HEOM method, the bath degrees of freedom are represented using effective modes from exponential decomposition of the bath correlation function. Complex spectral densities and low temperature simulations often require a larger number of modes, making the simulations very expensive. Recent advances, such as the barycentric spectral decomposition (BSD) technique, can significantly reduce the number of effective modes, allowing to handle complex spectral densities and enabling simulations at very low temperatures, including near-zero temperature dynamics.Another key improvement in the computational efficiency is the use of tensor network methods like matrix product states and hierarchical tensor networks. These techniques allow for efficient HEOM propagation with thousands of effective modes, crucial for simulating large molecular systems interacting with multiple baths. This combination enables simulations of excitation energy transfer (EET) in systems like the Fenna-Matthews-Olson (FMO) complex and even larger systems with experimentally determined spectral densities.The versatility of the HEOM method is demonstrated through applications to a wide range of chemical dynamics problems. Simulations of EET and related ultrafast spectroscopy are first briefly covered. Applications of the HEOM to quantum tunneling effects in proton transfer reactions are then presented. Early works have studied the non-Kramers dependence of the rate constant as a function of bath friction due to deep tunneling and revealed vibrationally nonadiabatic dynamics within the so-called nontraditional view of proton transfer reactions. A recent work on the large kinetic isotope effects in soybean lipoxygenase also indicated that many quantum correction approximations to classical transition-state theory may fall short in describing deep tunneling effects.Charge transport and separation dynamics in organic semiconductors are another area where the HEOM method has been instrumental. We first demonstrate that the HEOM provides a unified description of both band-like and thermally assisted charge carrier transport in organic materials. The effect of non-nearest neighbor transitions is then investigated by combining generalized master equations with exact memory kernels. The HEOM method also enables simulation of charge separation in organic photovoltaics (OPVs) and reveals how factors such as external electric fields, entropy, and charge delocalization influence the charge separation barrier and dynamics.Moreover, HEOM has been applied to investigate hydrogen atom scattering on the Au(111) surface and vibrational energy relaxation at molecule-metal interfaces. These studies provide deeper insights into how electron-hole pair excitations and temporary charge transfer states influence the nuclear motion, offering a new framework for simulating nonadiabatic dynamics on metal surfaces.In summary, the HEOM method has developed into a robust tool for simulating quantum effects in condensed phases. Future developments in algorithm efficiency and computational power will likely expand its applicability to even more complex systems.

Spectral modulation of B850 bacteriochlorophyll a in light-harvesting complex 2 from purple photosynthetic bacterium Thermochromatium tepidum by detergents and calcium ions

Spectral variations of light-harvesting (LH) proteins of purple photosynthetic bacteria provide insight into the molecular mechanisms underlying spectral tuning of circular bacteriochlorophyll (BChl) arrays, which play crucial roles in photoenergy conversion in these organisms. Here we investigate spectral changes of the Qy band of B850 BChl a in LH2 protein from purple sulfur bacterium Thermochromatium tepidum (tepidum-LH2) by detergents and Ca2+. The tepidum-LH2 solubilized with lauryl dimethylamine N-oxide and n-octyl-β-D-glucoside (LH2LDAO and LH2OG, respectively) exhibited blue-shift of the B850 Qy band with hypochromism compared with the tepidum-LH2 solubilized with n-dodecyl-β-D-maltoside (LH2DDM), resulting in the LH3-like spectral features. Resonance Raman spectroscopy indicated that this blue-shift was ascribable to the loss of hydrogen-bonding between the C3-acetyl group in B850 BChl a and the LH2 polypeptides. Ca2+ produced red-shift of the B850 Qy band in LH2LDAO by forming hydrogen-bond for the C3-acetyl group in B850 BChl a, probably due to a change in the microenvironmental structure around B850. Ca2+-induced red-shift was also observed in LH2OG although the B850 acetyl group is still free from hydrogen-bonding. Therefore, the Ca2+-induced B850 red-shift in LH2OG would originate from an electrostatic effect of Ca2+. The current results suggest that the B850 Qy band in tepidum-LH2 is primarily tuned by two mechanisms, namely the hydrogen-bonding of the B850 acetyl group and the electrostatic effect.

Contribution of Protonation to the Dielectric Relaxation Arising from Bacteriopheophytin Reductions in the Photosynthetic Reaction Centers of Rhodobacter sphaeroides

The pH dependence of the free energy level of the flash-induced primary charge pair P+IA- was determined by a combination of the results from the indirect charge recombination of P+QA- and from the delayed fluorescence of the excited dimer (P*) in the reaction center of the photosynthetic bacterium Rhodobacter sphaeroides, where the native ubiquinone at the primary quinone binding site QA was replaced by low-potential anthraquinone (AQ) derivatives. The following observations were made: (1) The free energy state of P+IA- was pH independent below pH 10 (-370 ± 10 meV relative to that of the excited dimer P*) and showed a remarkable decrease (about 20 meV/pH unit) above pH 10. A part of the dielectric relaxation of the P+IA- charge pair that is not insignificant (about 120 meV) should come from protonation-related changes. (2) The single exponential decay character of the kinetics proves that the protonated/unprotonated P+IA- and P+QA- states are in equilibria and the rate constants of protonation konH +koffH are much larger than those of the charge back reaction kback ~103 s-1. (3) Highly similar pH profiles were measured to determine the free energy states of P+QA- and P+IA-, indicating that the same acidic cluster at around QB should respond to both anionic species. This was supported by model calculations based on anticooperative proton distribution in the cluster with key residues of GluL212, AspL213, AspM17, and GluH173, and the effect of the polarization of the aqueous phase on electrostatic interactions. The larger distance of IA- from the cluster (25.2 Å) compared to that of QA- (14.5 Å) is compensated by a smaller effective dielectric constant (6.5 ± 0.5 and 10.0 ± 0.5, respectively). (4) The P* → P+QA- and IA-QA → IAQA- electron transfers are enthalpy-driven reactions with the exemption of very large (>60%) or negligible entropic contributions in cases of substitution by 2,3-dimethyl-AQ or 1-chloro-AQ, respectively. The possible structural consequences are discussed.

Ultrafast Charge Separation Driven by Solvation-Coupled Intramolecular Torsion

Photoinduced intramolecular charge separation in a pyrene- and triarylamine-based donor-acceptor dyad was studied by polarization-dependent femtosecond time-resolved transient absorption (TA) spectroscopy in polar solvents. Photoexcitation forms an excited state with charge transfer (CT) character due to the intrinsic electronic coupling between the triarylamine and pyrene groups, resulting in ultrafast charge separation (CS) in polar solvents. TA measurements reveal a correlation between the rate of CS and solvation dynamics, which implies that solvation is involved in the CS reaction. In addition, polarization-dependent TA spectroscopy was devoted to tracking the ultrafast anisotropy evolution of the cationic absorption band, which is attributed to intramolecular torsional motion and is proposed to be coupled to diffusive orientational solvent modes. The results therefore reveal that the evolution of the CT state in the condensed phase is driven by solvation-coupled excited-state structural relaxation. In other words, intramolecular torsional motion is directly confirmed to be involved in the reaction coordinate of the CS reaction in a strongly coupled donor-acceptor dyad.

Biomimetic light-harvesting antennas via the self-assembly of chemically programmed chlorophylls

The photosynthetic pigment "chlorophyll" possesses attractive photophysical properties, including efficient sunlight absorption, photoexcited energy transfer, and charge separation, which are advantageous for applications for photo- and electro-functional materials such as artificial photosynthesis and solar cells. However, these functions cannot be realized by individual chlorophyll molecules alone; rather, they are achieved by the formation of sophisticated supramolecules through the self-assembly of the pigments. Here, we present strategies for constructing and developing artificial light-harvesting systems by mimicking photosynthetic antenna complexes through the highly ordered supramolecular self-assembly of synthetic dyes, particularly chlorophyll derivatives.

The development and applications of multidimensional biomolecular spectroscopy illustrated by photosynthetic light harvesting

The parallel and synergistic developments of atomic resolution structural information, new spectroscopic methods, their underpinning formalism, and the application of sophisticated theoretical methods have led to a step function change in our understanding of photosynthetic light harvesting, the process by which photosynthetic organisms collect solar energy and supply it to their reaction centers to initiate the chemistry of photosynthesis. The new spectroscopic methods, in particular multidimensional spectroscopies, have enabled a transition from recording rates of processes to focusing on mechanism. We discuss two ultrafast spectroscopies - two-dimensional electronic spectroscopy and two-dimensional electronic-vibrational spectroscopy - and illustrate their development through the lens of photosynthetic light harvesting. Both spectroscopies provide enhanced spectral resolution and, in different ways, reveal pathways of energy flow and coherent oscillations which relate to the quantum mechanical mixing of, for example, electronic excitations (excitons) and nuclear motions. The new types of information present in these spectra provoked the application of sophisticated quantum dynamical theories to describe the temporal evolution of the spectra and provide new questions for experimental investigation. While multidimensional spectroscopies have applications in many other areas of science, we feel that the investigation of photosynthetic light harvesting has had the largest influence on the development of spectroscopic and theoretical methods for the study of quantum dynamics in biology, hence the focus of this review. We conclude with key questions for the next decade of this review.

Fluorescence Visualization Quantitative Detection of Tetracycline and Nitrofurantoin in Food and Natural Water by Zn2+@Eu-bpdc Composite

Quantitative detection of tetracycline (TC) and nitrofurantoin (NFT) in food and water is of importance for food safety and environmental protection. Herein, Zn2+ was introduced into a europium metal-organic framework Eu-bpdc (H2bpdc = 2,2'-bipyridyl-5,5'-dicarboxylic acid) to prepare a composite of Zn2+@Eu-bpdc, which was developed as a fluorescence sensor for TC and NFT. The fluorescence mechanism concerns with bpdc2- ligand-to-Eu(III) charge transfer, and the detection mechanism is the inner filter effect. Zn2+@Eu-bpdc is a ratiometric fluorescence sensor for TC with the linear fitting equation of I520/I618 = 1.94 × 104 M-1CTC, whose limit of detection (LOD) is 0.148 μmol·L-1 (μM); it is also a fluorescence "turn-off" sensor for NFT with the fitting equation of (I0-I)/I = 3.62 × 104 M-1CNFT and LOD = 0.0792 μM. Zn2+@Eu-bpdc can detect TC or NFT in lake water, honey, and milk with high accuracy. The emission color changes of paper-based Zn2+@Eu-bpdc depending on CTC or CNFT reveal the visualization detections of TC and NFT. With the red and green values as input signals, smartphone-assisted on-site detection is utilized to recognize the antibiotic residuals of TC and NFT by a self-programmed APP. Zn2+@Eu-bpdc is promising in a smartphone-assisted intelligent platform for on-site detection of TC and NFT.

Discovery of Multiple Light-Harvesting States of the Photosynthetic Protein PE545

Cryptophytes are photosynthetic microalga that flourish in a remarkable diversity of natural environments by using pigment-containing proteins with absorption maxima tuned to each ecological niche. While this diversity in the absorption has been well established, the subsequent photophysics is highly sensitive to the local protein environment and so may exhibit similar variation. Thermal fluctuations of the protein conformation are expected to introduce photophysical heterogeneity of the pigments that may have evolved important functional properties in a manner similar to that of the absorption. However, such heterogeneity is averaged out in ensemble measurements and, therefore, has not yet been probed. Here, we report single-molecule measurements of phycoerythrin 545 (PE545), the prototypical cryptophyte antenna protein, in its native dimeric form. A conformational ensemble was resolved consisting of distinct photophysical states with different light-harvesting properties. Proteins that did not quench, partially quenched, or fully quenched absorbed light were observed. Light intensity increased the quenched-state population of the dimer, potentially as a mechanism to deal with the extreme light intensities found in aqueous environments. Cross-linking, which mimics local interactions, introduces this light-dependent functionality while also suppressing other conformational dynamics. The cellular organization can, therefore, actively modulate the protein conformation and dynamics, selecting for distinct levels of light harvesting. Thus, the complex conformational equilibrium provides an additional mechanism for cryptophytes and likely other photosynthetic organisms to optimize solar energy capture and conversion.

Excitonic Approach for Nonadiabatic Dynamics: Extending Beyond the Frenkel Exciton Model

We report the formulation and implementation of an extended Frenkel exciton model (EFEM) designed for simulating the dynamics of multichromophoric systems, taking into account the possible presence of interchromophore charge transfer states, as well as other states in which two chromophores are simultaneously excited. Our approach involves constructing a Hamiltonian based on calculations performed on monomers and selected dimers within the multichromophoric aggregate. Nonadiabatic molecular dynamics is addressed using a surface hopping approach, while the electronic wave functions and energies required for constructing the EFEM are computed utilizing the semiempirical floating occupation molecular orbitals-configuration interaction (FOMO-CI) electronic structure method. To validate our approach, we simulate the singlet fission process in a trimer of 2,5-bis(fluorene-9-ylidene)-2,5-dihydrothiophene (ThBF) molecules, embedded in their crystal environment, comparing the results of the EFEM to the standard "supermolecule" approach.

Perspectives on improving photosynthesis to increase crop yield

Improving photosynthesis, the fundamental process by which plants convert light energy into chemical energy, is a key area of research with great potential for enhancing sustainable agricultural productivity and addressing global food security challenges. This perspective delves into the latest advancements and approaches aimed at optimizing photosynthetic efficiency. Our discussion encompasses the entire process, beginning with light harvesting and its regulation and progressing through the bottleneck of electron transfer. We then delve into the carbon reactions of photosynthesis, focusing on strategies targeting the enzymes of the Calvin-Benson-Bassham (CBB) cycle. Additionally, we explore methods to increase carbon dioxide (CO2) concentration near the Rubisco, the enzyme responsible for the first step of CBB cycle, drawing inspiration from various photosynthetic organisms, and conclude this section by examining ways to enhance CO2 delivery into leaves. Moving beyond individual processes, we discuss two approaches to identifying key targets for photosynthesis improvement: systems modeling and the study of natural variation. Finally, we revisit some of the strategies mentioned above to provide a holistic view of the improvements, analyzing their impact on nitrogen use efficiency and on canopy photosynthesis.

Lighting the way: Compelling open questions in photosynthesis research

Photosynthesis-the conversion of energy from sunlight into chemical energy-is essential for life on Earth. Yet there is much we do not understand about photosynthetic energy conversion on a fundamental level: how it evolved and the extent of its diversity, its dynamics, and all the components and connections involved in its regulation. In this commentary, researchers working on fundamental aspects of photosynthesis including the light-dependent reactions, photorespiration, and C4 photosynthetic metabolism pose and discuss what they view as the most compelling open questions in their areas of research.

Photo- and Electrocatalytic Hydrogen Evolution by Heteroleptic Dirhodium(II,II) Complexes: Role of the Bridging and Diimine Ligands

A series of heteroleptic Rh2(II,II) complexes, cis-[Rh2(μ-DPhF)2(μ-bncn)2]2+ (1; bncn = benzo[c]cinnoline), cis-[Rh2(μ-DPhF)(μ-OAc)(μ-bncn)2]2+ (2), and cis-[Rh2(μ-OAc)2(μ-bncn)2]2+ (3), is presented, and the excited state and redox properties of each complex was characterized for the photo- and electrocatalytic production of H2. The oxidation potentials shift anodically from 1 to 3, consistent with a highest occupied molecular orbital (HOMO) with significant metal-ligand mixing, Rh2(δ*)/DPhF(π/nb). In contrast, modest differences in the first two bncn-localized reversible reduction potentials were observed in 1 - 3. The lowest energy metal/ligand-to-ligand charge transfer (1ML-LCT) transition, Rh2(δ*)/DPhF(π/nb) → bncn(π*), shifts from 633 nm in 1 to 553 nm in 2, and the metal-to-ligand charge transfer (1MLCT) Rh2(π*) → bncn(π*) absorption in 3 appears at 462 nm in CH3CN. Although the 3ML-LCT excited state of 2 is shorter lived than that of 1, 2.7 ns as compared to 19 ns, respectively, photocatalytic hydrogen generation is observed for the former upon 595 nm irradiation in the presence of 0.1 M TsOH (p-tolylsulfonic acid) and 0.1 M BNAH (1-benzyl-1,4-dihydronicotinamide). The temperature dependence of the 3ML-LCT lifetimes of 1 and 2 shows the presence of a thermally accessible deactivating state. In addition, the singly reduced intermediate, [2]-, is photoactive and able to generate hydrogen in the presence of TsOH. Importantly, the electrocatalytic currents generated by equimolar concentrations of 1 - 3 in CH3CN are nearly identical, consistent with a mechanism of catalysis that is localized on the bncn ligand and does not require a Rh-H hydride intermediate. This finding can be used to develop earth-abundant first-row transition metal complexes for photo- and electrocatalytic H2 production.

Effect of phytohormone on proliferation and accumulation of cellular metabolites of microalgae Isochrysis zhanjiangensis

Phytohormones play a role in regulating microalgae cells tolerance to adversity. This paper examines the effects of different temperatures (20 °C, 25 °C, 30 °C and 35 °C) on the physiological characteristics and endogenous phytohormones of the Isochrysis Zhanjiangensis (IZ) and its mutagenic strain (3005). The results showed that the endogenous phytohormones indole acetic acid (IAA) and jasmonic acid (JA) exhibited significant differences (P<0.05) between the two strains. The addition of 0.5 mg·L-1 exogenous JA inhibitor ibuprofen (IBU) improved cell growth of IZ, and was extremely effective in the accumulation of polysaccharides, which accounted for 33.25 %. Transcriptomic analyses revealed that genes involved in photosynthesis, such as PetC and PsbO, exhibited significantly elevated expression of the strain IZ, while the pathways related to JA synthesis may be the factor affecting microalgae temperature tolerance. This study provides a theoretical foundation for elucidating the underlying mechanisms and potential applications for high temperature tolerance in IZ.

Integrated physio-biochemistry and RNA-seq revealed the mechanism underlying biochar-mediated alleviation of compound heavy metals (Cd, Pb, As) toxicity in cotton

Biochar has been recognised as an efficacious amendment for the remediation of compound heavy metal contamination in soil. However, the molecular mechanism of biochar-mediated tolerance to compound heavy metal toxicity in cotton is unknown. The objective of this research was to investigate the positive impact of biochar (10 g·kg-1) on reducing damage caused by compound heavy metals (Cd, Pb, and As) in cotton (Gossypium hirsutum L.). The results revealed that biochar reduced Cd concentrations by 24.9 % (roots), and decreased Pb concentrations by 37.1 % (roots) and 59.53 % (stems). Biochar maintained ionic homoeostasis by regulating the expression of metal transporter proteins such as ABC, HIPP, NRAMP3, PCR, and ZIP, and genes related to the carbon skeleton and plasma membrane. Biochar also downregulated genes related to photosynthesis, thereby increasing photosynthesis. Biochar re-established redox homoeostasis in cotton by activating signal transduction, which regulated the activity of the enzymes POD, SOD, and CAT activity; and the expression of related genes. This research revealed the molecular mechanism by which biochar confers resistance to the harmful effects of compound heavy metal toxicity in cotton. The application of biochar as a soil amendment to neutralise the toxicity of compound heavy metals is recommended for cash crop production.

Light curve parametrization of three rice (Oryza sativa L.) cultivars based on mechanistic models

This study aimed to assess variations in leaf gas-exchange characteristics, leaf pigment contents, and some intrinsic traits of photosynthetic pigment molecules in three rice cultivars (cv. JR3015, Wufengyou3015, and Jifengyou3015) using mechanistic models. The findings revealed that chlorophyll content varied significantly among the three cultivars, but not maximum electron transport rate. JR3015 had lower chlorophyll content but the highest eigen-absorption cross-section (σik) and the lowest minimum average life-time of photosynthetic pigment molecules in the excited state (τmin). Our results suggested that the highest σik and the lowest τmin in JR3015 facilitated its electron transport rate despite its lower leaf chlorophyll content. Furthermore, compared to Jifengyou3015 and Wufengyou3015, JR3015 had the lowest photosynthetic electron-use efficiency via PSII, which contributed to its lowest maximum net photosynthetic rate. These findings are important in selecting rice cultivars based on their differences in photosynthetic capacity.

Polymorphism and flexibility of six-porphyrin nanorings in the solid state

Butadiyne-linked porphyrin nanorings are fascinating nanometer-sized platforms for exploring electronic delocalization and aromaticity, and they mimic ultra-fast photosynthetic energy-transfer phenomena in plants and purple bacteria. However, little is known about how they interact in the solid state. Here, we compare the crystal structures of several pseudopolymorphs of a six-porphyrin nanoring template complex, and report the structure of the free-base nanoring co-crystallized with C60. The structures differ not only in the molecular packing; they also feature different molecular conformations. The template is slightly too small for the cavity of the nanoring, and this size mismatch can be accommodated by two types of distortion: either the zinc atoms are pulled away from the planes of the porphyrins, or the nanorings contract by adopting a ruffled conformation, with butadiyne links alternatingly above and below the plane of the six zinc centers. The template-bound ring forms sheets and tubular stacks with interdigitated aryl groups. Upon demetallation, the nanoring becomes more flexible, adopting a highly elliptical conformation on co-crystallization with C60. The structure of this free-base nanoring features infinite solvent filled channels with a channel diameter of 13.5 Å. The high porosity of these materials points towards possible applications as porous light-harvesting frameworks.

From Coherence to Function: Exploring the Connection in Chemical Systems

ConspectusThe role of quantum mechanical coherences or coherent superposition states in excited state processes has received considerable attention in the last two decades largely due to advancements in ultrafast laser spectroscopy. These coherence effects hold promise for enhancing the efficiency and robustness of functionally relevant processes, even when confronted with energy disorder and environmental fluctuations. Understanding coherence deeply drives us to unravel mechanisms and dynamics controlled by order and synchronization at a quantum mechanical level, envisioning optical control of coherence to enhance functions or create new ones in molecular and material systems. In this frontier, the interplay between electronic and vibrational dynamics, specifically the influence of vibrations in directing electronic dynamics, has emerged as the leading principle. Here, two energetically disparate quantum degrees of freedom work in-sync to dictate the trajectory of an excited state reaction. Moreover, with the vibrational degree being directly related to the structural composition of molecular or material systems, new molecular designs could be inspired by tailoring certain structural elements.In the realm of chemical kinetics, our understanding of the dynamics of chemical transformations is underpinned by fundamental theories, such as transition state theory, activated rate theory, and Marcus theory. These theories elucidate reaction rates by considering the energy barriers that must be overcome for reactants to transform into products. Those barriers are surmounted by the stochastic nature of energy gap fluctuations within reacting systems, emphasizing that the reaction coordinate, the pathway from reactants to products, is not rigidly defined by a specific vibrational motion but encompasses a diverse array of molecular motions. While less is known about the involvement of specific intramolecular vibrational modes, their significance in certain cases cannot be overlooked.In this Account, we summarize key experimental findings that offer deeper insights into the complex electronic-vibrational trajectories encompassing excited states afforded from state-of-the-art ultrafast laser spectroscopy in three exemplary processes: photoinduced electron transfer, singlet-triplet intersystem crossing, and intramolecular vibrational energy flow in molecular systems. We delve into the rapid decoherence, or loss of phase and amplitude correlations, of vibrational coherences along promoter vibrations during subpicosecond intersystem crossing dynamics in a series of binuclear platinum complexes. This rapid decoherence illustrates the vibration-driven reactive pathways from the Franck-Condon state to the curve crossing region. We also explore the generation of new vibrational coherences induced by impulsive reaction dynamics rather than by the laser pulse in these systems, which sheds light on specific energy dissipation pathways and thereby on the progression of the reaction trajectory in the vicinity of the curve crossing on the product side. Another property of vibrational coherences, amplitude, reveals how energy can flow from one vibration to another in the electronic excited state of a terpyridine-molybdenum complex hosting a nonreactive dinitrogen substrate. A slight change in vibrational energy triggers a quasi-resonant interaction, leading to constructive wavepacket interference and ultimately intramolecular vibrational redistribution from a Franck-Condon active terpyridine vibration to a dinitrogen stretching vibration, energizing the dinitrogen bond.

Influence of Substituents on the Vectorial Difference Static Dipole Upon Excitation in Synthetic Bacteriochlorins

Organic dye aggregates have been shown to exhibit exciton delocalization in natural and synthetic systems. Such dye aggregates show promise in the emerging area of quantum information science (QIS). We believe that the difference in static dipole (Δd) is an essential dye parameter in the development of molecular QIS systems. However, a foundational understanding of the structural factors influencing Δd remains elusive. Bacteriochlorins play a vital role in photosynthesis due to their exceptional photophysical properties. Therefore, bacteriochlorins are particularly suitable dyes for the construction of aggregate systems for QIS. Synthetic bacteriochlorins further offer stability and tunability via chemical modifications. Here, the influence of substituents on the Δd of monomeric (nonaggregated) dyes was investigated via density functional theory (DFT) and time-dependent (TD)DFT in a set of 5-methoxybacteriochlorins progressively substituted with ethynyl, phenyl, and phenylethynyl substituents at the 3,13 and 3,13,15 positions of the macrocycle. Symmetrically substituted 5-methoxybacteriochlorins were shown to have the largest Δd. The increase in Δd in the series of dyes was largely due to changes in the orientation of the static dipole upon excitation rather than large changes in magnitude. In addition, the transition dipole (μ) and the angle between Δd and μ (ζ) were calculated. Three 5-methoxybacteriochlorins with large predicted Δd and μ values were synthesized and characterized spectroscopically. The trend in Δd values empirically determined using the solvatochromic Stokes shift method was comparable to the DFT calculations.

Leaves to Measure Light Intensity

Quantitative measurement of light intensity is a key step in ensuring the reliability and the reproducibility of scientific results in many fields of physics, biology, and chemistry. The protocols presented so far use various photoactive properties of manufactured materials. Here, leaves are introduced as an easily accessible green material to calibrate light intensity. The measurement protocol consists in monitoring the chlorophyll fluorescence of a leaf while it is exposed to a jump of constant light. The inverse of the characteristic time of the initial chlorophyll fluorescence rise is shown to be proportional to the light intensity received by the leaf over a wide range of wavelengths and intensities. Moreover, the proportionality factor is stable across a wide collection of plant species, which makes the measurement protocol accessible to users without prior calibration. This favorable feature is finally harnessed to calibrate a source of white light from exploiting simple leaves collected from a garden.

Phytoplankton cell-states: multiparameter fluorescence lifetime flow-based monitoring reveals cellular heterogeneity

Phytoplankton are a major source of primary productivity. Their photosynthetic fluorescence are unique measures of their type, physiological state, and response to environmental conditions. Changes in phytoplankton photophysiology are commonly monitored by bulk fluorescence spectroscopy, where gradual changes are reported in response to different perturbations, such as light intensity changes. What is the meaning of such trends in bulk parameters if their values report ensemble averages of multiple unsynchronized cells? To answer this, we developed an experimental scheme that enables tracking fluorescence intensities, brightnesses, and their ratios, as well as mean photon nanotimes equivalent to mean fluorescence lifetimes, one cell at a time. We monitored three different phytoplankton species during diurnal cycles and in response to an abrupt increase in light intensity. Our results show that we can define specific subpopulations of cells by their fluorescence parameters for each of the phytoplankton species, and in response to varying light conditions. Importantly, we identify the cells undergo well-defined transitions between these subpopulations. The approach shown in this work will be useful in the exact characterization of phytoplankton cell states and parameter signatures in response to different changes these cells experience in marine environments, which will be applicable for monitoring marine-related environmental effects.

Raman Vibrational Signatures of Excited States of Echinenone in the Orange Carotenoid Protein (OCP) and Implications for its Photoactivation Mechanism

In this study, the vibrational characteristics of optically excited echinenone in various solvents and the Orange Carotenoid Protein (OCP) in red and orange states are systematically investigated through steady-state and time-resolved spectroscopy techniques. Time-resolved experiments, employing both Transient Absorption (TA) and Femtosecond Stimulated Raman Spectroscopy (FSRS), reveal different states in the OCP photoactivation process. The time-resolved studies indicate vibrational signatures of exited states positioned above the S1 state during the initial 140 fs of carotenoid evolution in OCP, an absence of a vibrational signature for the relaxed S1 state of echinenone in OCP, and more robust signatures of a highly excited ground state (GS) in OCP. Differences in S1 state vibration population signatures between OCP and solvents are attributed to distinct conformations of echinenone in OCP and hydrogen bonds at the keto group forming a short-lived intramolecular charge transfer (ICT) state. The vibrational dynamics of the hot GS in OCP show a more pronounced red shift of ground state CC vibration compared to echinenone in solvents, thus suggesting an unusually hot form of GS. The study proposes a hypothesis for the photoactivation mechanism of OCP, emphasizing the high level of vibrational excitation in longitudinal stretching modes as a driving force. In conclusion, the comparison of vibrational signatures reveals unique dynamics of energy dissipation in OCP, providing insights into the photoactivation mechanism and highlighting the impact of the protein environment on carotenoid behavior. The study underscores the importance of vibrational analysis in understanding the intricate processes involved in early phase OCP photoactivation.

Theoretical model of donor-donor and donor-acceptor energy transfer on a nanosphere

In this study, we introduce a novel advancement in the field of theoretical exploration. Specifically, we investigate the transfer and trapping of electronic excitations within a two-component disordered system confined to a finite volume. The implications of our research extend to energy transfer phenomena on spherical nanoparticles, characterized by randomly distributed donors and acceptors on their surface. Utilizing the three-body Padé approximant technique, previously employed in single-component systems, we apply it to address the challenge of trapping within our system. To validate the robustness of our model, we conduct Monte Carlo simulations on a donor-acceptor system positioned on a spherical nanoparticle. In particular, very good agreement between the model and Monte Carlo simulations has been found for donor fluorescence intensity decay.

Probing photoinduced electron transfer events in phenylferrocene-corrole dyad

Herein, we investigated PhFC (10-phenylferrocenyl-5,15-diphenyl corrole), a corrole-based donor-acceptor (D-A) dyad, to understand the energy/electron transfer reaction dynamics. Phenylferrocene acts as the donor moiety when attached to the meso position of the corrole ring in the PhFC D-A system. The photophysical properties of the PhFC dyad and its parent molecule, TPC (5,10,15-triphenyl corrole), were studied by UV-vis spectroscopy, steady state fluorescence spectroscopy, TCSPC and optical microscopy techniques. A slight red shift and broadening of both the Q-band and Soret bands are observed in the absorption spectra of the PhFC dyad in comparison to TPC, representing the weak electronic interaction between the phenylferrocene moiety and corrole ring. The fluorescence emission spectrum of the PhFC dyad is significantly quenched (>80%) in comparison to TPC, attributed to the photoinduced electron transfer (PET) from phenylferrocene to the corrole ring. We observed that the electron transfer rate in the PhFC system is solvent dependent. Our theoretical investigation supported the experimental findings on the electron transfer mechanism. The HOMO and LUMO arrangements of these PhFC dyads demonstrate the electron density distribution and the ability of the donor moieties to transfer electrons to the corrole moiety. Fluorescence lifetime imaging microscopy (FLIM) was used to image the homogeneous lifetime distribution of the PhFC dyad and TPC.

Microbe-material hybrids for therapeutic applications

As natural living substances, microorganisms have emerged as useful resources in medicine for creating microbe-material hybrids ranging from nano to macro dimensions. The engineering of microbe-involved nanomedicine capitalizes on the distinctive physiological attributes of microbes, particularly their intrinsic "living" properties such as hypoxia tendency and oxygen production capabilities. Exploiting these remarkable characteristics in combination with other functional materials or molecules enables synergistic enhancements that hold tremendous promise for improved drug delivery, site-specific therapy, and enhanced monitoring of treatment outcomes, presenting substantial opportunities for amplifying the efficacy of disease treatments. This comprehensive review outlines the microorganisms and microbial derivatives used in biomedicine and their specific advantages for therapeutic application. In addition, we delineate the fundamental strategies and mechanisms employed for constructing microbe-material hybrids. The diverse biomedical applications of the constructed microbe-material hybrids, encompassing bioimaging, anti-tumor, anti-bacteria, anti-inflammation and other diseases therapy are exhaustively illustrated. We also discuss the current challenges and prospects associated with the clinical translation of microbe-material hybrid platforms. Therefore, the unique versatility and potential exhibited by microbe-material hybrids position them as promising candidates for the development of next-generation nanomedicine and biomaterials with unique theranostic properties and functionalities.

From leaf to multiscale models of photosynthesis: applications and challenges for crop improvement

To keep up with the growth of human population and to circumvent deleterious effects of global climate change, it is essential to enhance crop yield to achieve higher production. Here we review mathematical models of oxygenic photosynthesis that are extensively used, and discuss in depth a subset that accounts for diverse approaches providing solutions to our objective. These include models (1) to study different ways to enhance photosynthesis, such as fine-tuning antenna size, photoprotection and electron transport; (2) to bioengineer carbon metabolism; and (3) to evaluate the interactions between the process of photosynthesis and the seasonal crop dynamics, or those that have included statistical whole-genome prediction methods to quantify the impact of photosynthesis traits on the improvement of crop yield. We conclude by emphasizing that the results obtained in these studies clearly demonstrate that mathematical modelling is a key tool to examine different approaches to improve photosynthesis for better productivity, while effective multiscale crop models, especially those that also include remote sensing data, are indispensable to verify different strategies to obtain maximized crop yields.

Evaluating Pigments as a Biosignature: Abiotic/Prebiotic Synthesis of Pigments and Pigment Mimics in Planetary Environments

Pigments serve a multitude of functions in biology including light harvesting for photosynthesis, radiation protection, membrane support, and defense. The ubiquity of pigments-especially within extremophiles found in high-radiation, high-salinity, and dry environments-and their detectability via mission-ready techniques have elevated these molecules as promising targets in the search for evidence of life elsewhere. Moreover, the detection of pigments has been proposed as a "smoking gun" for extraterrestrial life as it has been suggested that these molecules cannot be generated abiotically. However, while pigments may hold promise as a biosignature, current understanding of their possible prebiotic origins remains understudied and uncertain. Better understanding of the abiotic synthesis of pigments is critical for evaluating the biogenicity of any pigment detected during missions, including by the Mars Perseverance rover or from returned samples. Compounding this uncertainty is the broad definition of pigment as it includes any compound capable of absorbing visible light and by itself does not specify a particular chemical motif. While not experimentally verified, there are promising prebiotic routes for generating pigments including hemes, chlorophylls, and carotenoids. Herein, we review the biochemistry of pigments, the inherent assumptions made when searching for these molecules in the field, their abiotic synthesis in industry and prebiotic reactions, prebiotically relevant molecules that can mimic their spectral signatures, and implications/recommendations for future work.

Probing ligands to reaction centers to limit the photocycle in photosynthetic bacterium Rubrivivax gelatinosus

Light-induced electron flow between reaction center and cytochrome bc1 complexes is mediated by quinones and electron donors in purple photosynthetic bacteria. Upon high-intensity excitation, the contribution of the cytochrome bc1 complex is limited kinetically and the electron supply should be provided by the pool of reduced electron donors. The kinetic limitation of electron shuttle between reaction center and cytochrome bc1 complex and its consequences on the photocycle were studied by tracking the redox changes of the primary electron donor (BChl dimer) via absorption change and the opening of the closed reaction center via relaxation of the bacteriochlorophyll fluorescence in intact cells of wild type and pufC mutant strains of Rubrivivax gelatinosus. The results were simulated by a minimum model of reversible binding of different ligands (internal and external electron donors and inhibitors) to donor and acceptor sides of the reaction center. The calculated binding and kinetic parameters revealed that control of the rate of the photocycle is primarily due to 1) the light intensity, 2) the size and redox state of the donor pool, and 3) the unbinding rates of the oxidized donor and inhibitor from the reaction center. The similar kinetics of strains WT and pufC lacking the tetraheme cytochrome subunit attached to the reaction center raise the issue of the physiological importance of this subunit discussed from different points of view. SIGNIFICANCE: A crucial factor for the efficacy of electron donors in photosynthetic photocycle is not just the substantial size of the pool and large binding affinity (small dissociation constant KD = koff/kon) to the RC, but also the mean residence time (koff)-1 in the binding pocket. This is an important parameter that regulates the time of re-activation of the RC during multiple turnovers. The determination of koff has proven challenging and was performed by simulation of widespread experimental data on the kinetics of P+ and relaxation of fluorescence. This work is a step towards better understanding the complex pathways of electron transfer in proteins and simulation-based design of more effective electron transfer components in natural and artificial systems.

Femtosecond Stimulated Raman Spectroscopy of Linear Carotenoids

Femtosecond stimulated Raman spectroscopy (FSRS) and transient absorption data measured in a single experiment are used to determine the vibronic properties of the S1 state of linear carotenoids with different conjugation lengths. The Raman band corresponding to the C═C stretching mode in the S1 state peaks at 1799 cm-1 (neurosporene), 1802 cm-1 (spheroidene), and 1791 cm-1 (lycopene). Contrary to the ground state C═C mode, variation of the C═C stretching mode in the S1 state is small and does not follow a linear dependence on N. The lifetime of the Raman band matches the S1 decays obtained from transient absorption, confirming its S1 state origin. Direct comparison of transient absorption and FSRS signals allowed us to assign Raman signatures of nonrelaxed S1 and S0 states. For lycopene, FSRS data identified a component associated with a downshifted ground state C═C mode, which matches the dynamics of the S* signal observed in transient absorption data.

Generalized quantum master equations can improve the accuracy of semiclassical predictions of multitime correlation functions

Multitime quantum correlation functions are central objects in physical science, offering a direct link between the experimental observables and the dynamics of an underlying model. While experiments such as 2D spectroscopy and quantum control can now measure such quantities, the accurate simulation of such responses remains computationally expensive and sometimes impossible, depending on the system's complexity. A natural tool to employ is the generalized quantum master equation (GQME), which can offer computational savings by extending reference dynamics at a comparatively trivial cost. However, dynamical methods that can tackle chemical systems with atomistic resolution, such as those in the semiclassical hierarchy, often suffer from poor accuracy, limiting the credence one might lend to their results. By combining work on the accuracy-boosting formulation of semiclassical memory kernels with recent work on the multitime GQME, here we show for the first time that one can exploit a multitime semiclassical GQME to dramatically improve both the accuracy of coarse mean-field Ehrenfest dynamics and obtain orders of magnitude efficiency gains.