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Photosynthesis is generally assumed to be initiated by a single photon1-3 from the Sun, which, as a weak light source, delivers at most a few tens of photons per nanometre squared per second within a chlorophyll absorption band1. Yet much experimental and theoretical work over the past 40 years has explored the events during photosynthesis subsequent to absorption of light from intense, ultrashort laser pulses2-15. Here, we use single photons to excite under ambient conditions the light-harvesting 2 (LH2) complex of the purple bacterium Rhodobacter sphaeroides, comprising B800 and B850 rings that contain 9 and 18 bacteriochlorophyll molecules, respectively. Excitation of the B800 ring leads to electronic energy transfer to the B850 ring in approximately 0.7 ps, followed by rapid B850-to-B850 energy transfer on an approximately 100-fs timescale and light emission at 850-875 nm (refs. 16-19). Using a heralded single-photon source20,21 along with coincidence counting, we establish time correlation functions for B800 excitation and B850 fluorescence emission and demonstrate that both events involve single photons. We also find that the probability distribution of the number of heralds per detected fluorescence photon supports the view that a single photon can upon absorption drive the subsequent energy transfer and fluorescence emission and hence, by extension, the primary charge separation of photosynthesis. An analytical stochastic model and a Monte Carlo numerical model capture the data, further confirming that absorption of single photons is correlated with emission of single photons in a natural light-harvesting complex.

Photosynthetic light-harvesting (LH) systems consist of photosynthetic pigments, which are non-covalently self-assembled with protein scaffolds in many phototrophs and attain highly efficient excitation energy transfer via ultrafast dynamics. In this study, we constructed a biohybrid LH system composed of an LH complex (LH2) from Rhodoblastus acidophilus strain 10050 and a hydrophobic fluorophore ATTO647N (ATTO) as an extrinsic antenna in the lipid bilayer. Through the addition of ATTOs into a solution of LH2-reconstituted lipid vesicles, ATTOs were incorporated into the hydrophobic interior of the lipid bilayer to configure the non-covalently self-assembled biohybrid LH. Steady-state fluorescence spectroscopy clearly showed efficient energy transfer from ATTO to B850 bacteriochlorophylls in LH2. Femtosecond transient absorption spectroscopy revealed that the energy transfer took place in the time range of 3–13 ps, comparable to that of the covalently linked LH2-ATTO that we previously reported. In addition, the biohybrid LH system exhibited a much higher antenna effect than the LH2-ATTO system because of the higher loading level of ATTO in the membrane. These findings suggest that the facile self-assembled biohybrid LH system is a promising system for constructing LH for solar-energy conversion. [ABSTRACT FROM AUTHOR]

To gain a deeper understanding of the highly efficient mechanisms within the photosynthetic bacterial reaction center (BRC), we have employed femtosecond broadband fluorescence spectroscopy to investigate the dynamics of initial photo-induced energy transfer and charge separation in BRC at room temperature. Benefiting from the broadband spectral coverage inherent of this technique, two distinct transient emission species associated with bacteriochlorophylls B and P are directly identified, with Stokes shifts determined to be ~197 and 450 cm−1, respectively. The ultrafast energy transfers from bacteriopheophytin H to B (98 fs) and from B to P (170 fs) are unveiled through fitting the emission dynamics. Notably, the anticipated sub-200 fs lifetime of B emission significantly extends to ~400 fs, suggesting a plausible coupling between the electronic excited state of Band the vibronic states of P, potentially influencing the acceleration of the energy transfer process. These findings should pave the way for understanding the impact of vibronic dynamics on the photo-induced primary processes in the photosynthetic reaction center. [ABSTRACT FROM AUTHOR]

The reaction centre light-harvesting 1 (RC-LH1) complex is the core functional component of bacterial photosynthesis. We determined the cryo-electron microscopy (cryo-EM) structure of the RC-LH1 complex from Rhodospirillum rubrum at 2.5 Å resolution, which reveals a unique monomeric bacteriochlorophyll with a phospholipid ligand in the gap between the RC and LH1 complexes. The LH1 complex comprises a circular array of 16 αβ-polypeptide subunits that completely surrounds the RC, with a preferential binding site for a quinone, designated QP, on the inner face of the encircling LH1 complex. Quinols, initially generated at the RC QB site, are proposed to transiently occupy the QP site prior to traversing the LH1 barrier and diffusing to the cytochrome bc1 complex. Thus, the QP site, which is analogous to other such sites in recent cryo-EM structures of RC-LH1 complexes, likely reflects a general mechanism for exporting quinols from the RC-LH1 complex.

Along the shoreline of the White Sea, due to the post-glacial uplift of the coast, some water bodies with stable stratification have been formed. They have been classified as meromictic as they are at different stages of isolation from the Sea. As separation progresses, significant changes occur in the water column, including the composition of chromophoric dissolved organic matter (CDOM) and the structure of the aquatic microbial community. In this work, we searched for optical proxies of euxinia (anoxic conditions with accumulated hydrogen sulfide) in the water column of the meromictic lagoon on Zeleny Cape. The lagoon is separated from the White Sea basin by a shallow threshold that completely isolates the lagoon during low tide, but marine water enters the lagoon during high tide. The ecosystem in the lagoon is characterized by the marine salinity of water and a high organic matter content in the bottom water and sediments. In this study, spectral methods were used to obtain the depth distribution of CDOM, chlorophyll, and bacteriochlorophyll in the lagoon with strong water stratification and euxinic conditions in the bottom water. The measured optical CDOM characteristics were compared with hydrochemical data (water salinity, Eh, pH, dissolved oxygen), phytoplankton (oxygenic phototrophs), and green sulfur bacteria (anoxygenic phototrophs) distribution along the water column. The spectroscopic methods showed to have the advantages of not requiring water sample pre-treatment and allowing rapid sensing of CDOM and photosynthetic pigments at each horizon. [ABSTRACT FROM AUTHOR]

We use real-time density functional theory on a real-space grid to calculate electronic excitations of bacteriochlorophyll chromophores of the light-harvesting complex 2 (LH2). Comparison with Gaussian basis set calculations allows us to assess the numerical trust range for computing electron dynamics in coupled chromophores with both types of techniques. Tuned range-separated hybrid calculations for one bacteriochlorophyll as well as two coupled ones are used as a reference against which we compare results from the adiabatic time-dependent local density approximation (TDLDA). The tuned range-separated hybrid calculations lead to a qualitatively correct description of the electronic excitations and couplings. They allow us to identify spurious charge-transfer excitations that are obtained with the TDLDA. When we take into account the environment that the LH2 protein complex forms for the bacteriochlorophylls, we find that it substantially shifts the energy of the spurious charge-transfer excitations, restoring a qualitatively correct electronic coupling of the dominant excitations also for TDLDA. [ABSTRACT FROM AUTHOR]

Most of our current understanding of mechanisms of photosynthesis comes from spectroscopy. However, the classical definition of a radio antenna can be extended to the optical regime to discuss the function of light-harvesting antennae. Further to our previously proposed model of a loop antenna, we provide several more physical explanations in considering the nonreciprocal properties of light harvesters of bacteria. We explain the function of the nonheme iron at the reaction center and present reasons for each module of the light harvester being composed of one carotenoid, two short α -helical polypeptides, and three bacteriochlorophylls; we also explained the toroidal shape of the light harvester, the upper bound of the characteristic length of the light harvester, the functional role played by the observed long-lasting spectrometric signal, and the observed photon antibunching. Based on these analyses, two mechanisms that might be used by radiation-durable bacteria, Deinococcus radiodurans; and the nonreciprocity of an archaeon, Haloquadratum walsbyi, are analyzed. The physical lessons involved are useful for designing artificial light harvesters, optical sensors, wireless power chargers, passive superPlanckian heat radiators, photocatalytic hydrogen generators, and radiation protective cloaks. In particular, it can predict what kind of particles should be used to separate sunlight into a photovoltaically and thermally useful range to enhance the efficiency of solar cells. [ABSTRACT FROM AUTHOR]

Light absorbed by light-harvesting antennae is transferred to the reaction center (RC). The excitation energy transfer (EET) to the RC is known to proceed with nearly perfect quantum yield. However, understanding of EET is still limited at the molecular level. Here, we examine the dynamics in the Fenna-Matthews-Olson (FMO) protein by developing an efficient molecular dynamics simulation that can properly describe the electronic properties of bacteriochlorophylls. We find that the FMO protein consists of sites with heterogeneous fluctuations extending from fast to slow modulation. We also find that efficient EETs are facilitated by site-dependent fluctuations that enhance the resonance condition between neighboring sites with large site energy differences and circumvent exciton trapping on the pathway to the RC. Knowledge of site-dependent fluctuations is an important component of understanding optimization of EET in photosynthetic systems.

The photosynthetic tetrapyrroles share a common structural feature comprised of a β-ketoester motif embedded in an exocyclic ring (ring E). As part of a total synthesis program aimed at preparing native structures and analogues, 3-(3-methoxy-1,3-dioxopropyl)pyrrole was sought. The pyrrole is a precursor to analogues of ring C and the external framework of ring E. Four routes were developed. Routes 1–3 entail a Pd-mediated coupling process of a 3-iodopyrrole with potassium methyl malonate, whereas route 4 relies on electrophilic substitution of TIPS-pyrrole with methyl malonyl chloride. Together, the four routes afford considerable latitude. A long-term objective is to gain the capacity to create chlorophylls and bacteriochlorophylls and analogues thereof by facile de novo means for diverse studies across the photosynthetic sciences. [ABSTRACT FROM AUTHOR]

Light-harvesting complexes in natural photosynthetic systems, such as those in purple bacteria, consist of photo-reactive chromophores embedded in densely packed "antenna" systems organized in well-defined nanostructures. In the case of purple bacteria, the chromophore antennas are composed of natural J-aggregates such as bacteriochlorophylls and carotenoids. Inspired by the molecular composition of such biological systems, we create a library of organic materials composed of densely packed J-aggregates in a polymeric matrix, in which the matrix mimics the optical role of a protein scaffold. This library of organic materials shows polaritonic properties which can be tuned from the visible to the infrared by choice of the model molecule. Inspired by the molecular architecture of the light-harvesting complexes of Rhodospirillum molischianum bacteria, we study the light–matter interactions of J-aggregate-based nanorings with similar dimensions to the analogous natural nanoscale architectures. Electromagnetic simulations show that these nanorings of J-aggregates can act as resonators, with subwavelength confinement of light while concentrating the electric field in specific regions. These results open the door to bio-inspired building blocks for metamaterials from visible to infrared in an all-organic platform, while offering a new perspective on light–matter interactions at the nanoscale in densely packed organic matter in biological organisms including photosynthetic organelles. [ABSTRACT FROM AUTHOR]

Photosynthesis converts light energy to chemical energy to fuel life on earth. Light energy is harvested by antenna pigments and transferred to reaction centers (RCs) to drive the electron transfer (ET) reactions. Here, we present cryo-electron microscopy (cryo-EM) structures of two forms of the RC from the microaerophilic Chloracidobacterium thermophilum (CabRC): one containing 10 subunits, including two different cytochromes; and the other possessing two additional subunits, PscB and PscZ. The larger form contained 2 Zn-bacteriochlorophylls, 16 bacteriochlorophylls, 10 chlorophylls, 2 lycopenes, 2 hemes, 3 Fe4S4 clusters, 12 lipids, 2 Ca2+ ions and 6 water molecules, revealing a type I RC with an ET chain involving two hemes and a hybrid antenna containing bacteriochlorophylls and chlorophylls. Our results provide a structural basis for understanding the excitation energy and ET within the CabRC and offer evolutionary insights into the origin and adaptation of photosynthetic RCs. During photosynthesis, light energy is harvested by an antenna systems and delivered to the reaction centers (RCs) for charge separation and electron transfer (ET). The authors report cryo-EM structures of two forms of RC from the microaerophilic Chloracidobacterium thermophilum (CabRC), providing a structural basis for ET within the CabRC. [ABSTRACT FROM AUTHOR]

The genomes of some purple photosynthetic bacteria contain a multigene puc family encoding a series of a- and ß-polypeptides that together form a heterogeneous antenna of light-harvesting 2 (LH2) complexes. To unravel this complexity, we generated four sets of puc deletion mutants in Rhodopseudomonas palustris, each encoding a single type of pucBA gene pair and enabling the purification of complexes designated as PucA-LH2, PucB-LH2, PucD-LH2, and PucE-LH2. The structures of all four purified LH2 complexes were determined by cryogenic electron microscopy (cryo-EM) at resolutions ranging from 2.7 to 3.6 Å. Uniquely, each of these complexes contains a hitherto unknown polypeptide, γ, that forms an extended undulating ribbon that lies in the plane of the membrane and that encloses six of the nine LH2 αβ-subunits. The γ-subunit, which is located near to the cytoplasmic side of the complex, breaks the C9 symmetry of the LH2 complex and binds six extra bacteriochlorophylls (BChls) that enhance the 800-nm absorption of each complex. The structures show that all four complexes have two complete rings of BChls, conferring absorption bands centered at 800 and 850 nm on the PucA-LH2, PucB-LH2, and PucE-LH2 complexes, but, unusually, the PucD-LH2 antenna has only a single strong near-infared (NIR) absorption peak at 803 nm. Comparison of the cryo-EM structures of these LH2 complexes reveals altered patterns of hydrogen bonds between LH2 aß-side chains and the bacteriochlorin rings, further emphasizing the major role that H bonds play in spectral tuning of bacterial antenna complexes. [ABSTRACT FROM AUTHOR]

In the structure of photosynthetic reaction center (RC) of the purple bacterium Cereibacter sphaeroides the highly conserved amino acid residue Ile-M206 is located near the bacteriochlorophyll dimer P, which is the primary electron donor, and the monomeric bacteriochlorophyll BA, which is the nearest electron acceptor. Since Ile-M206 is close to the C2-acetyl group of bacteriochlorophyll PB, the hydroxyl group of Tyr-M210, and to the C9-keto group of bacteriochlorophyll BA, as well as to the water molecule near the latter group, this site can be used for introducing mutations in order to study mechanisms of primary photochemical processes in the RC. Previously it was shown that the Ile→Glu substitution at the M204 position (analog of M206 in the RC of C. sphaeroides) in the RC of the closely related purple non-sulfur bacterium Rhodobacter capsulatus significantly affected kinetics of the P+HA– state formation, whereas the M204 Ile→Gln substitution led to the loss of BChl BA molecule from the complex structure. In the present work, it is shown that the single I(M206)Q or double I(M206)Q + F(M208)A amino acid substitutions in the RC of C. sphaeroides do not change the pigment composition and do not markedly influence redox potential of the primary electron donor. However, substitution of Ile M206 by Gln affected positions and amplitudes of the absorption bands of bacteriochlorophylls, increased lifetime of the primary electron donor P* excited state from 3.1 ps to 22 ps, and decreased quantum yield of the P+QA– state formation to 60%. These data suggest significant changes in the pigment–protein interactions in the vicinity of the primary electron donor P and the nearest electron acceptor BA. A considerable decrease was also noticed in the resistance of the mutant RC to thermal denaturation, which was more pronounced in the RC with the double substitution I(M206)Q + F(M208)A. This was likely associated with the disruption of the dense packing of the protein near bacteriochlorophylls PB and BA. Possible reasons for different effects of identical mutations on the properties of two highly homologous RCs from closely related purple non-sulfur bacteria are discussed. [ABSTRACT FROM AUTHOR]

The mechanism of bacteriochlorophyll photooxidation in light-harvesting complexes of a number of purple photosynthetic bacteria when the complexes are excited into the carotenoid absorption bands remains unclear for many years. Here, using narrow-band laser illumination we measured action spectrum of this process for the spectral ranges of carotenoid and bacteriochlorophyll. It is shown that bacteriochlorophyll excitation results in almost no photooxidation of these molecules, while carotenoid excitation leads to oxidation with quantum yield of about 0,0003. Low value of the yield enabled an assumption that the studied process is initiated by the triplet states of the main carotenoids of the complexes with the number of conjugated double-bond chain length of N = 11. Interaction of these states with oxygen facilitates formation, though with low efficiency, of the excited singlet oxygen, which oxidizes bacteriochlorophylls. The carotenoid triplet states are formed in the process of the earlier studied singlet-triplet fission. The obtained results point at the necessity of reconsidering the functions of carotenoids in the light-harvesting complexes of purple bacteria. [ABSTRACT FROM AUTHOR]

Roseiflexus castenholzii is an ancient green non-sulfur bacteria that absorbs the solar energy through bacteriochlorophylls (BChls) bound in the only light harvesting (LH) complex, and transfers to the reaction center (RC), wherein primary charge separation occurs and transforms the energy into electrochemical potentials. In contrast to purple bacteria, R. castenholzii RC-LH (rc RC-LH) does not contain an H subunit. Instead, a tightly bound tetraheme cytochrome c subunit is exposed on the P-side of the RC, which contains three BChls, three bacteriopheophytins (BPheos), two menaquinones, and one iron for electron transfer. These novel structural features of the rc RC-LH are advantageous for enhancing the electron transfer efficiency and subsequent photo-oxidation of the c -type hemes. However, the photochemical properties of rc RC-LH and its applications in developing the photo-bioelectrochemical cells (PBECs) have not been characterized. Here, we prepared a PBEC using overlapped fluorine-doped tin oxide (FTO) glass and Pt-coated glass as electrodes, and rc RC-LH mixed with varying mediators as the electrolyte. Absence of the H subunit allows rc RC-LH to be selectively adhered onto the hydrophilic surface of the front electrode with its Q-side. Upon illumination, the photogenerated electrons directly enter the front electrode and transfer to the counter electrode, wherein the accepted electrons pass through the exposed c -type hemes to reduce the excited P+, generating a steady-state current of up to 320 nA/cm2 when using 1-Methoxy-5-methylphenazinium methyl sulfate (PMS) as mediator. This study demonstrated the novel photoelectric properties of rc RC-LH and its advantages in preparing effective PBECs, showcasing a potential of this complex in developing new type PBECs. [ABSTRACT FROM AUTHOR]

The ability to prepare and tailor synthetic analogues of native bacteriochlorophylls enables diverse applications. A de novo route entails dimerization of a dihydrodipyrrin-acetal to afford the corresponding 5-methoxy and/or 5-unsubstituted bacteriochlorin, wherein each pyrroline ring contains a gem-dimethyl group to ensure stability toward adventitious dehydrogenation. The presence of a 5-methoxy group facilitates bromination at the distal meso-(15-)position. While bromination of 5-unsubstituted bacteriochlorins typically affords a mixture of brominated products, here the presence of two substitution patterns (2,12-dicarboethoxy, 2,12-diacetyl) has been found to facilitate selective meso-bromination in the absence of the methoxy substituent. The introduction of a single meso-bromine atom in a bacteriochlorin opens opportunities for Pd-mediated derivatization, which include (1) preparation of four ethynylphenyl building blocks (and two benchmark bacteriochlorins) with long-wavelength absorption bands tuned across 725–757 nm, for use in preparation of multichromophore arrays; (2) installation of a bioconjugatable group to free base bacteriochlorins or a copper bacteriochlorin, the latter for possible use in photoacoustic imaging; and (3) installation of an S-acetylthio group for surface attachment. Altogether, 25 new bacteriochlorins are described including 5 meso-bromobacteriochlorin intermediates and 12 target bacteriochlorins. [ABSTRACT FROM AUTHOR]

Synthetic bacteriochlorins, analogues of native bacteriochlorophylls, provide absorption in the near-infrared spectral region and hence are valuable for fundamental studies in photochemistry and applications ranging from solar energy conversion to photomedicine. The full realization of such opportunities hinges on access to synthetically malleable bacteriochlorins. Here, two established routes that rely on self-condensation of a dihydrodipyrrin-acetal or dihydrodipyrrin-carboxaldehyde have been exploited to prepare 6 bacteriochlorins (2 new, 4 known in improved fashion). Each bacteriochlorin contains a gem-dimethyl group in the reduced, pyrroline ring to ensure stability toward adventitious dehydrogenation. These and related synthetic bacteriochlorins have been derivatized to tailor the perimeter of the macrocycle with diverse groups, affording 9 additional new bacteriochlorins and 4 known bacteriochlorins. By direct installation and/or derivatization, the scope of attached entities in this collection includes alkyl, amino, aryl, bromo, carboethoxy, oxo, phenylethynyl, and pyridyl. The bacteriochlorins are suited for surface attachment, bioconjugation, water-solubilization, vibrational studies, and elaboration into multichromophore arrays. Altogether the synthesis of 25 new compounds (11 bacteriochlorins, 14 precursors) is described. [ABSTRACT FROM AUTHOR]

The dimeric reaction centre light-harvesting 1 (RC-LH1) core complex of Rhodobacter sphaeroides converts absorbed light energy to a charge separation, and then it reduces a quinone electron and proton acceptor to a quinol. The angle between the two monomers imposes a bent configuration on the dimer complex, which exerts a major influence on the curvature of the membrane vesicles, known as chromatophores, where the lightdriven photosynthetic reactions take place. To investigate the dimerisation interface between two RC-LH1 monomers, we determined the cryogenic electron microscopy structure of the dimeric complex at 2.9 Å resolution. The structure shows that each monomer consists of a central RC partly enclosed by a 14-subunit LH1 ring held in an open state by PufX and protein-Y polypeptides, thus enabling quinones to enter and leave the complex. Two monomers are brought together through N-terminal interactions between PufX polypeptides on the cytoplasmic side of the complex, augmented by two novel transmembrane polypeptides, designated protein-Z, that bind to the outer faces of the two central LH1 ß polypeptides. The precise fit at the dimer interface, enabled by PufX and protein-Z, by C-terminal interactions between opposing LH1 aß subunits, and by a series of interactions with a bound sulfoquinovosyl diacylglycerol lipid, bring together each monomer creating an S-shaped array of 28 bacteriochlorophylls. The seamless join between the two sets of LH1 bacteriochlorophylls provides a path for excitation energy absorbed by one half of the complex to migrate across the dimer interface to the other half. [ABSTRACT FROM AUTHOR]

Nitrogenase catalyzes biological nitrogen fixation, a key step in the global nitrogen cycle. Three homologous nitrogenases have been identified to date, along with several structural and/or functional homologs of this enzyme that are involved in nitrogenase assembly, bacteriochlorophyll biosynthesis and methanogenic process, respectively. In this article, we provide an overview of the structures and functions of nitrogenase and its homologs, which highlights the similarity and disparity of this uniquely versatile group of enzymes.

The initial energy transfer steps in photosynthesis occur on ultrafast timescales. We analyze the carotenoid to bacteriochlorophyll energy transfer in LH2 Marichromatium purpuratum as well as in an artificial light-harvesting dyad system by using transient grating and two-dimensional electronic spectroscopy with 10 fs time resolution. We find that Förster-type models reproduce the experimentally observed 60 fs transfer times, but overestimate coupling constants, which lead to a disagreement with both linear absorption and electronic 2D-spectra. We show that a vibronic model, which treats carotenoid vibrations on both electronic ground and excited states as part of the system's Hamiltonian, reproduces all measured quantities. Importantly, the vibronic model presented here can explain the fast energy transfer rates with only moderate coupling constants, which are in agreement with structure based calculations. Counterintuitively, the vibrational levels on the carotenoid electronic ground state play the central role in the excited state population transfer to bacteriochlorophyll; resonance between the donor-acceptor energy gap and the vibrational ground state energies is the physical basis of the ultrafast energy transfer rates in these systems. [ABSTRACT FROM AUTHOR]

We investigate the excitation energy transfer (EET) pathways in the photosynthetic light harvesting 1 (LH1) complex of purple bacterium Rhodospirillum rubrum with ultra-broadband two-dimensional electronic spectroscopy (2DES). We employ a 2DES apparatus in the partially collinear geometry, using a passive birefringent interferometer to generate the phase-locked pump pulse pair. This scheme easily lends itself to two-color operation, by coupling a sub-10 fs visible pulse with a sub-15-fs near-infrared pulse. This unique pulse combination allows us to simultaneously track with extremely high temporal resolution both the dynamics of the photoexcited carotenoid spirilloxanthin (Spx) in the visible range and the EET between the Spx and the B890 bacterio-chlorophyll (BChl), whose Qx and Qy transitions peak at 585 and 881 nm, respectively, in the near-infrared. Global analysis of the one-color and two-color 2DES maps unravels different relaxation mechanisms in the LH1 complex: (i) the initial events of the internal conversion process within the Spx, (ii) the parallel EET from the first bright state S2 of the Spx towards the Qx state of the B890, and (iii) the internal conversion from Qx to Qy within the B890. [ABSTRACT FROM AUTHOR]

The Fenna-Matthews-Olson (FMO) protein-pigment complex acts as a molecular wire conducting energy between the outer antenna system and the reaction center; it is an important photosynthetic system to study the transfer of excitonic energy. Recent crystallographic studies report the existence of an additional (eighth) bacteriochlorophyll α (BChl α) in some of the FMO monomers. To understand the functionality of this eighth BChl, we simulated the two-dimensional electronic spectra of both the 7-site (apo form) and the 8-site (holo form) variant of the FMO complex from green sulfur bacteria, Prosthecochloris aestuarii. By comparing the spectrum, it was found that the eighth BChl can affect two different excitonic energy transfer pathways: (1) it is directly involved in the first apo form pathway (6 → 3 → 1) by passing the excitonic energy to exciton 6; and (2) it facilitates an increase in the excitonic wave function overlap between excitons 4 and 5 in the second pathway (7 → 4,5 → 2 → 1) and thus increases the possible downward sampling routes across the BChls. [ABSTRACT FROM AUTHOR]

A route under development for the synthesis of bacteriochlorophyll a and analogues relies on joining an AD-dihydrodipyrrin (bearing a D-ring carboxaldehyde) and a BC-dihydrodipyrrin (bearing a C-ring β-ketoester group and a B-ring dimethoxymethyl group) via Knoevenagel condensation followed by double-ring closure (Nazarov cyclization, electrophilic aromatic substitution, and elimination of methanol). Prior synthetic studies afforded the bacteriochlorophyll skeleton containing a gem-dimethyl group in ring B, a trans-dialkyl group in ring D, and a carboethoxy group at the 3-position of ring A. To explore the incorporation of native substituents, the synthesis of two bacteriochlorophyll analogues thereof was pursued, one with 12-methyl and 3-carboethoxy groups and the other with 2,12-dimethyl and 3-acetyl groups. The 12-methyl group resulted in half the yield (versus the unsubstituted analogue) in the Knoevenagel reaction, but insignificant effects in all other steps including the rate and yield of double-ring closure despite the known effects of alkyl groups to facilitate electrophilic substitution of pyrroles. The 2-methyl-3-acetyl group, however, resulted in diminished yields in several steps, including the Knoevenagel reaction, but not the double-ring closure. The results point to obstacles and openings on the path to total syntheses of the native pigments. [ABSTRACT FROM AUTHOR]

Gemmatimonas phototrophica AP64 is the first phototrophic representative of the bacterial phylum Gemmatimonadetes. The cells contain photosynthetic complexes with bacteriochlorophyll a as the main light-harvesting pigment and an unknown carotenoid with a single broad absorption band at 490 nm in methanol. The carotenoid was extracted from isolated photosynthetic complexes, and purified by liquid chromatography. A combination of nuclear magnetic resonance (1H NMR, COSY, 1H-13C HSQC, 1H-13C HMBC, J-resolved, and ROESY), high-resolution mass spectroscopy, Fourier-transformed infra-red, and Raman spectroscopy was used to determine its chemical structure. The novel linear carotenoid, that we have named gemmatoxanthin, contains 11 conjugated double bonds and is further substituted by methoxy, carboxyl and aldehyde groups. Its IUPAC-IUBMB semi-systematic name is 1′-Methoxy-19′-oxo-3′,4′-didehydro-7,8,1′,2′-tetrahydro- Ψ, Ψ carotene-16-oic acid. To our best knowledge, the presence of the carboxyl, methoxy and aldehyde groups on a linear C40 carotenoid backbone is reported here for the first time. [ABSTRACT FROM AUTHOR]

The type-I, homodimeric photosynthetic reaction center (RC) of Heliobacteria (HbRC) is the only known RC in which bacteriochlorophyll g (BChl g) is found. It is also simpler than other RCs, having the smallest number of protein subunits and bound chromophores of any type-I RC. In the presence of oxygen, BChl g isomerizes to 81-hydroxychlorophyll aF (Chl aF). This naturally occurring process provides a way of altering the chlorophylls and studying the effect of these changes on energy and electron transfer. Transient absorbance difference spectroscopy reveals that triplet-state formation occurs in the antenna chlorophylls of HbRCs but does not provide site-specific information. Here, we report on an extended optically detected magnetic resonance (ODMR) study of the antenna triplet states in HbRCs with differing levels of conversion of BChl g to Chl aF. The data reveal pools of BChl g molecules with different triplet zero-field splitting parameters and different susceptibilities to chemical oxidation. By relating the detailed spectroscopic characteristics derived from the ODMR data to the recently solved crystallographic structure, we have tentatively identified BChl g molecules in which the probability of triplet formation is high and sites at which BChl g conversion is more likely, providing useful information about the fate of the excitation in the complex. [ABSTRACT FROM AUTHOR]

We describe polarization controlled two-color coherence photon echo studies of the reaction center complex from a purple bacterium Rhodobacter sphaeroides. Long-lived oscillatory signals that persist up to 2 ps are observed in neutral, oxidized, and mutant (lacking the special pair) reaction centers, for both (0°,0°,0°,0°) and (45°,-45°,90°,0°) polarization sequences. We show that the long-lived signals arise via vibronic coupling of the bacteriopheophytin (H) and accessory bacteriochlorophyll (B) pigments that leads to vibrational wavepackets in the B ground electronic state. Fourier analysis of the data suggests that the 685 cm(-1) mode of B may play a key role in the H to B energy transfer.

Chlorosomes are the main light-harvesting complexes of green photosynthetic bacteria that are adapted to a phototrophic life at low-light conditions. They contain a large number of bacteriochlorophyll c, d, or e molecules organized in self-assembling aggregates. Tight packing of the pigments results in strong excitonic interactions between the monomers, which leads to a redshift of the absorption spectra and excitation delocalization. Due to the large amount of disorder present in chlorosomes, the extent of delocalization is limited and further decreases in time after excitation. In this work we address the question whether the excitonic interactions between the bacteriochlorophyll c molecules are strong enough to maintain some extent of delocalization even after exciton relaxation. That would manifest itself by collective spontaneous emission, so-called superradiance. We show that despite a very low fluorescence quantum yield and short excited state lifetime, both caused by the aggregation, chlorosomes indeed exhibit superradiance. The emission occurs from states delocalized over at least two molecules. In other words, the dipole strength of the emissive states is larger than for a bacteriochlorophyll c monomer. This represents an important functional mechanism increasing the probability of excitation energy transfer that is vital at low-light conditions. Similar behaviour was observed also in one type of artificial aggregates, and this may be beneficial for their potential use in artificial photosynthesis. [ABSTRACT FROM AUTHOR]

Light-dependent protochlorophyllide oxidoreductase (LPOR) and dark-operative protochlorophyllide oxidoreductase are evolutionary and structurally distinct enzymes that are essential for the synthesis of (bacterio)chlorophyll, the primary pigment needed for both anoxygenic and oxygenic photosynthesis. In contrast to the long-held hypothesis that LPORs are only present in oxygenic phototrophs, we recently identified a functional LPOR in the aerobic anoxygenic phototrophic bacterium (AAPB) Dinoroseobacter shibae and attributed its presence to a single horizontal gene transfer event from cyanobacteria. Here, we provide evidence for the more widespread presence of genuine LPOR enzymes in AAPBs. An exhaustive bioinformatics search identified 36 putative LPORs outside of oxygenic phototrophic bacteria (cyanobacteria) with the majority being AAPBs. Using in vitro and in vivo assays, we show that the large majority of the tested AAPB enzymes are genuine LPORs. Solution structural analyses, performed for two of the AAPB LPORs, revealed a globally conserved structure when compared with a well-characterized cyanobacterial LPOR. Phylogenetic analyses suggest that LPORs were transferred not only from cyanobacteria but also subsequently between proteobacteria and from proteobacteria to Gemmatimonadetes. Our study thus provides another interesting example for the complex evolutionary processes that govern the evolution of bacteria, involving multiple horizontal gene transfer events that likely occurred at different time points and involved different donors. [ABSTRACT FROM AUTHOR]

We have observed that an assembly of the bacteriochloropyll a molecules into B850 and B875 groups of cyclic bacterial light-harvesting complexes LH2 and LH1, respectively, results an almost total loss of the intra-molecular vibronic structure in the fluorescence spectrum, and simultaneously, an essential enhancement of its phonon sideband due to electron-phonon coupling. While the sup-pression of the vibronic coupling in delocalized (excitonic) molecular systems is predictable, as also confirmed by our model calculations, a boost of the electron-phonon coupling is rather un-expected. The latter phenomenon is explained by exciton self-trapping, promoted by mixing the molecular exciton states with charge transfer states between the adjacent chromophores in the tightly packed B850 and B875 arrangements. Similar, although less dramatic trends were noted for the light-harvesting complexes containing chlorophyll pigments. [ABSTRACT FROM AUTHOR]

In the ferruginous and anoxic early Earth oceans, photoferrotrophy drove most of the biological production before the advent of oxygenic photosynthesis, but its association with ferric iron (Fe3+) dependent anaerobic methane (CH4) oxidation (AOM) has been poorly investigated. We studied AOM in Kabuno Bay, a modern analogue to the Archean Ocean (anoxic bottom waters and dissolved Fe concentrations > 600 µmol L−1). Aerobic and anaerobic CH4 oxidation rates up to 0.12 ± 0.03 and 51 ± 1 µmol L−1 d−1, respectively, were put in evidence. In the Fe oxidation–reduction zone, we observed high concentration of Bacteriochlorophyll e (biomarker of the anoxygenic photoautotrophs), which co-occurred with the maximum CH4 oxidation peaks, and a high abundance of Candidatus Methanoperedens, which can couple AOM to Fe3+ reduction. In addition, comparison of measured CH4 oxidation rates with electron acceptor fluxes suggest that AOM could mainly rely on Fe3+ produced by photoferrotrophs. Further experiments specifically targeted to investigate the interactions between photoferrotrophs and AOM would be of considerable interest. Indeed, ferric Fe3+-driven AOM has been poorly envisaged as a possible metabolic process in the Archean ocean, but this can potentially change the conceptualization and modelling of metabolic and geochemical processes controlling climate conditions in the Early Earth. [ABSTRACT FROM AUTHOR]

A long-term goal is to gain synthetic access to native photosynthetic bacteriochlorophylls. A recently developed route entails Knoevenagel condensation of an AD dihydrodipyrrin (I, bearing a carboxaldehyde attached to pyrroline ring D) and a BC dihydrodipyrrin (II, bearing a β-ketoester attached to pyrrole ring C) to form the Z/E-enone. Acid-mediated double-ring closure of the E-enone III-E (Nazarov cyclization, electrophilic aromatic substitution, and elimination of methanol) affords the bacteriochlorophyll skeleton BC-1 containing the isocyclic ring (ring E), a trans-dialkyl group in ring D, and a gem-dimethyl group in ring B. Prior work established the synthesis and the integrity of the resulting trans-dialkyl groups and bacteriochlorin chromophore. The counterpart report here concerns an in-depth study of conditions for the double-ring closure: catalyst/solvent surveys; grid search including time courses of [ III-E ] versus [acid] concentrations emphasizing equimolar, inverse molar, and variable acid lines of inquiry; and chlorin byproduct quantitation. Key findings are that (1) the double-ring closure can be carried out in 4 h (t1/2 ∼ 40 min) instead of 20 h, affording ∼1/5th the chlorin byproduct (0.16%) while maintaining the yield of BC-1 (up to 77%); (2) the separate Z/E-enones of III have comparable reactivity; (3) sub-stoichiometric quantities of acid are ineffective; (4) the Knoevenagel condensation (40 mM, room temperature, piperidine/acetic acid in acetonitrile) and the acid-mediated double-ring closure (0.20 mM, 80 °C, Yb(OTf)3 in acetonitrile) can be carried out in a two-step process; and (5) zinc insertion to form ZnBC-1 is straightforward. Together, the results enable streamlined conversion of dihydrodipyrrin reactants to the bacteriochlorophyll model compounds. [ABSTRACT FROM AUTHOR]

During bacteriochlorophyll a biosynthesis, the oxygen-independent conversion of Mg-protoporphyrin IX monomethyl ester (Mg-PME) to protochlorophyllide (Pchlide) is catalyzed by the anaerobic Mg-PME cyclase termed BchE. Bioinformatics analyses in combination with pigment studies of cobalamin-requiring Rhodobacter capsulatus mutants indicated an unusual radical S-adenosylmethionine (SAM) and cobalamindependent BchE catalysis. However, in vitro biosynthesis of the isocyclic ring moiety of bacteriochlorophyll using purified recombinant BchE has never been demonstrated. We established a spectroscopic in vitro activity assay which was subsequently validated by HPLC analyses and H218O isotope label transfer onto the carbonyl-group (C-131-oxo) of the isocyclic ring of Pchlide. The reaction product was further converted to chlorophyllide in the presence of light-dependent Pchlide reductase. BchE activity was stimulated by increasing concentrations of NADPH or SAM, and inhibited by S-adenosylhomocysteine. Subcellular fractionation experiments revealed that membrane-localized BchE requires an additional, heat-sensitive cytosolic component for activity. BchE catalysis was not sustained in chimeric experiments when a cytosolic extract from E. coli was used as a substitute. Size-fractionation of the soluble R. capsulatus fraction indicated that enzymatic activity relies on a specific component with an estimated molecular mass between 3 and 10 kDa. A structure guided site-directed mutagenesis approach was performed on the basis of a three-dimensional homology model of BchE. A newly established in vivo complementation assay was used to investigate 24 BchE mutant proteins. Potential ligands of the [4Fe-4S] cluster (Cys204, Cys208, Cys211), of SAM (Phe210, Glu308 and Lys320) and of the proposed cobalamin cofactor (Asp248, Glu249, Leu29, Thr71, Val97) were identified. [ABSTRACT FROM AUTHOR]

Developments in ultrafast-spectroscopy techniques have revealed notably long-lived quantum coherence between electronic states in Fenna–Matthews–Olson complex bacteriochlorophylls, a group of molecules setting a nanoscale structure responsible of the coherent energy transfer in the photosynthetic process of green sulfur bacteria. Despite the experimental advances, such a task should normally be complemented with physical computer simulations to understand its complexity. Several methods have been explored to model this quantum phenomenon, mainly using the quantum open systems theory as a first approach. The traditional methods used in this approach do not take into account the memory effects of the surroundings, which is commonly approximated as a phonon bath on thermal equilibrium. To surpass such an approximation, this article applies the Hierarchical Equations of Motion method, a non-markovian approach also used to analyze the dynamic of such a complex, for the modeling of the system evolution. We perform a parametric analysis about some physical features in the quantum regime involved during the quantum excitation process in order to get a comprehension about its non-trivial dependence on operation parameters. Thus, the analysis is conducted in terms of some relevant physical parameters in the system to track the complex global behavior in aspects as coherence, entanglement, decoherence times, transference times, and efficiency of the main process of energy capturing. As a complementary analysis from the derived outcomes, we compare those features for two different species as a suggestive possible roadmap to track genetic differences in the photosynthetic performance of the complex through its biological nature. [ABSTRACT FROM AUTHOR]

In photosynthetic reaction centers from purple bacteria (PbRC) and the water-oxidizing enzyme, photosystem II (PSII), charge separation occurs along one of the two symmetrical electron-transfer branches. Here we report the microscopic origin of the unidirectional charge separation, fully considering electron-hole interaction, electronic coupling of the pigments, and electrostatic interaction with the polarizable entire protein environments. The electronic coupling between the pair of bacteriochlorophylls is large in PbRC, forming a delocalized excited state with the lowest excitation energy (i.e., the special pair). The charge-separated state in the active branch is stabilized by uncharged polar residues in the transmembrane region and charged residues on the cytochrome c2 binding surface. In contrast, the accessory chlorophyll in the D1 protein (ChlD1) has the lowest excitation energy in PSII. The charge-separated state involves ChlD1 •+ and is stabilized predominantly by charged residues near the Mn4CaO5 cluster and the proceeding proton-transfer pathway. It seems likely that the acquirement of water-splitting ability makes ChlD1 the initial electron donor in PSII. [ABSTRACT FROM AUTHOR]

A cross-linking technique involving application of Bacteriochlorophyll Derivative WST-11 mixed with dextran (WST-D) to the epithelium-debrided cornea and illumination with Near Infrared (NIR), has been identified as a promising therapy for stiffening pathologically weakened corneas. To investigate its effect on corneal collagen architecture, x-ray scattering and electron microscopy data were collected from paired WST-D/NIR treated and untreated rabbit corneas. The treated eye received 2.5 mg/mL WST-D and was illuminated by a NIR diode laser (755 nm, 10 mW/cm2). An increase in corneal thickness (caused by corneal oedema) occurred at 1-day post-treatment but resolved in the majority of cases within 4 days. The epithelium was fully healed after 6–8 days. X-ray scattering revealed no difference in average collagen interfibrillar spacing, fibril diameter, D-periodicity or intermolecular spacing between treated and untreated specimens. Similarly, electron microscopy images of the anterior and posterior stroma in healed WST-D/NIR corneas and untreated controls revealed no obvious differences in collagen organisation or fibril diameter. As the size and organisation of stromal collagen is closely associated with the optical properties of the cornea, the absence of any large-scale changes following treatment confirms the potential of WST-D/NIR therapy as a means of safely stiffening the cornea. [ABSTRACT FROM AUTHOR]

Following the observation of long-lived coherences in the two-dimensional (2D) electronic spectra of the Fenna-Matthews-Olson (FMO) complex, many theoretical works suggest that coherences between excitons may play a role in the efficient energy transfer that occurs in photosynthetic antennae. This interpretation of the dynamics depends on the assignment of quantum beating signals to superpositions of excitons, which is complicated by the possibility of observing both electronic and vibrational coherences in 2D spectra. Here, we explore 2D spectra of bacteriochlorophyll a (BChla) in solution in an attempt to isolate vibrational beating signals in the absence of excitonic signals to identify the origin of the quantum beats in 2D spectra of FMO. Even at high laser power, our BChla spectra show strong beating only from the nonresonant response of the solvent. The beating signals that we can conclusively assign to vibrational modes of BChla are only slightly above the noise and at higher frequencies than those previously observed in spectra of FMO. Our results suggest that the beating observed in spectra of FMO is of a radically different character than the signals observed here and can therefore be attributed to electronic coherences or intermolecular degrees of freedom. [ABSTRACT FROM AUTHOR]

Key to efficient harvesting of sunlight in photosynthesis is the first energy conversion process in which electronic excitation establishes a trans-membrane charge gradient. This conversion is accomplished by the photosynthetic reaction center (RC) that is, in case of the purple photosynthetic bacterium Rhodobacter sphaeroides studied here, surrounded by light harvesting complex 1 (LH1). The RC employs six pigment molecules to initiate the conversion: four bacteriochlorophylls and two bacteriopheophytins. The excited states of these pigments interact very strongly and are simultaneously influenced by the surrounding thermal protein environment. Likewise, LH1 employs 32 bacteriochlorophylls influenced in their excited state dynamics by strong interaction between the pigments and by interaction with the protein environment. Modeling the excited state dynamics in the RC as well as in LH1 requires theoretical methods, which account for both pigment-pigment interaction and pigment-environment interaction. In the present study we describe the excitation dynamics within a RC and excitation transfer between light harvesting complex 1 (LH1) and RC, employing the hierarchical equation of motion method. For this purpose a set of model parameters that reproduce RC as well as LH1 spectra and observed oscillatory excitation dynamics in the RC is suggested. We find that the environment has a significant effect on LH1-RC excitation transfer and that excitation transfers incoherently between LH1 and RC. [ABSTRACT FROM AUTHOR]

Ultrafast excited state dynamics of spirilloxanthin in solution and bound to the light-harvesting core antenna complexes from Rhodospirillum rubrum S1 were investigated by means of femtosecond pump-probe spectroscopic measurements. The previously proposed S* state of spirilloxanthin was clearly observed both in solution and bound to the light-harvesting core antenna complexes, while the lowest triplet excited state appeared only with spirilloxanthin bound to the protein complexes. Ultrafast formation of triplet spirilloxanthin bound to the protein complexes was observed upon excitation of either spirilloxanthin or bacteriochlorophyll-a. The anomalous reaction of the ultrafast triplet formation is discussed in terms of ultrafast energy transfer between spirilloxanthin and bacteriochlorophyll-a. [ABSTRACT FROM AUTHOR]

A procedure for the identification of ligands bound in crystal structures of macromolecules is described. Two characteristics of the density corresponding to a ligand are used in the identification procedure. One is the correlation of the ligand density with each of a set of test ligands after optimization of the fit of that ligand to the density. The other is the correlation of a fingerprint of the density with the fingerprint of model density for each possible ligand. The fingerprints consist of an ordered list of correlations of each the test ligands with the density. The two characteristics are scored using a Z-score approach in which the correlations are normalized to the mean and standard deviation of correlations found for a variety of mismatched ligand-density pairs, so that the Z scores are related to the probability of observing a particular value of the correlation by chance. The procedure was tested with a set of 200 of the most commonly found ligands in the Protein Data Bank, collectively representing 57% of all ligands in the Protein Data Bank. Using a combination of these two characteristics of ligand density, ranked lists of ligand identifications were made for representative (F(o) - F(c))exp(i(phi)c) difference density from entries in the Protein Data Bank. In 48% of the 200 cases, the correct ligand was at the top of the ranked list of ligands. This approach may be useful in identification of unknown ligands in new macromolecular structures as well as in the identification of which ligands in a mixture have bound to a macromolecule.

Chlorophylls and bacteriochlorophylls, together with carotenoids, serve, noncovalently bound to specific apoproteins, as principal light-harvesting and energy-transforming pigments in photosynthetic organisms. In recent years, enormous progress has been achieved in the elucidation of structures and functions of light-harvesting (antenna) complexes, photosynthetic reaction centers and even entire photosystems. It is becoming increasingly clear that light-harvesting complexes not only serve to enlarge the absorption cross sections of the respective reaction centers but are vitally important in short- and long-term adaptation of the photosynthetic apparatus and regulation of the energy-transforming processes in response to external and internal conditions. Thus, the wide variety of structural diversity in photosynthetic antenna “designs” becomes conceivable. It is, however, common for LHCs to form trimeric (or multiples thereof) structures. We propose a simple, tentative explanation of the trimer issue, based on the 2D world created by photosynthetic membrane systems.

Earlier, it was suggested that carotenoids in light-harvesting complexes 2 (LH2) can generate singlet oxygen, further oxidizing bacteriochlorophyll to 3-acetyl-chlorophyll. In the present work, it was found that illumination of isolated LH2 preparations of purple sulfur bacterium Ectothiorhodospira haloalkaliphila with light in the carotenoid absorption region leads to the photoconsumption of molecular oxygen, which is accompanied by the formation of hydroperoxides of organic molecules in the complexes. Photoformation of two types of organic hydroperoxides were revealed: highly lipophilic (12 molecules per one LH2) and relatively hydrophobic (68 per one LH2). It has been shown that illumination leads to damage to light-harvesting complexes. On the one hand, photobleaching of bacteriochlorophyll and a decrease in its fluorescence intensity are observed. On the other hand, the photoinduced increase in the hydrodynamic radius of the complexes, the reduction in their thermal stability, and the change in fluorescence intensity indicate conformational changes occurring in the protein molecules of the LH2 preparations. Inhibition of the processes described above upon the addition of singlet oxygen quenchers (L-histidine, Trolox, sodium L-ascorbate) may support the hypothesis that carotenoids in LH2 preparations are capable of generating singlet oxygen, which, in turn, damage to protein molecules., Competing Interests: The authors declare there are no competing interests., (©2024 Yanykin et al.)

In the present work, separation and quantitative assessment of bacteriochlorophylls d and e of green sulfur bacteria (GSB) in lake water was attempted. The method developed reveals the ratio of green- and brown-colored GSB in natural water by measurement of absorption spectra of the pigments in the extracts from environmental samples. [ABSTRACT FROM AUTHOR]

Abstract Epimerically and homologously pure farnesyl bacteriochlorophylls- f (BChls- f F) were isolated from the cultured cells of the bchU gene-deleted mutant of Chlorobaculum limnaeum , which is a green sulfur bacterium, by reverse-phase HPLC. Homologously pure 8-ethyl-, propyl-, and isobutyl-BChls- f F with the 12-ethyl group were fully characterized by their VIS, 1H NMR, and MS spectra. All the 31-epimerically pure samples of each homolog showed nearly the same visible absorption and fluorescence emission spectra in THF, and their emission quantum yields and lifetimes were independent of the 31-stereochemistry and 82-methylation. Graphical abstract Image 1 Highlights • Epimerically and homologously pure farnesyl bacteriochlorophylls- f were isolated. • Homologously pure samples were fully characterized by VIS, 1H NMR, and MS spectra. • All epimers showed almost same VIS absorption and fluorescence emission spectra. • Emission quantum yields and lifetimes were independent on their substituents. [ABSTRACT FROM AUTHOR]