Long-range organization of bacteriochlorophyll in chlorosomes of Chlorobium tepidum investigated by cryo-electron microscopy

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.

Large Scale Simulations of Photosynthetic Antenna Systems: Interplay of Cooperativity and Disorder

Large-scale simulations of light-matter interaction in natural photosynthetic antenna complexes containing more than one hundred thousands of chlorophyll molecules, comparable with natural size, have been performed. Photosynthetic antenna complexes present in Green sulfur bacteria and Purple bacteria have been analyzed using a radiative non-Hermitian Hamiltonian, well-known in the field of quantum optics, instead of the widely used dipole-dipole Frenkel Hamiltonian. This approach allows us to study ensembles of emitters beyond the small volume limit (system size much smaller than the absorbed wavelength), where the Frenkel Hamiltonian fails. When analyzed on a large scale, such structures display superradiant states much brighter than their single components. An analysis of the robustness to static disorder and dynamical (thermal) noise shows that exciton coherence in the whole photosynthetic complex is larger than the coherence found in its parts. This provides evidence that the photosynthetic complex as a whole plays a predominant role in sustaining coherences in the system even at room temperature. Our results allow a better understanding of natural photosynthetic antennae and could drive experiments to verify how the response to electromagnetic radiation depends on the size of the photosynthetic antenna.

An integrated approach towards extracting structural characteristics of chlorosomes from a bchQ mutant of Chlorobaculum tepidum

Chlorosomes, the photosynthetic antenna complexes of green sulfur bacteria, are paradigms for light-harvesting elements in artificial designs, owing to their efficient energy transfer without protein participation. We combined magic angle spinning (MAS) NMR, optical spectroscopy and cryogenic electron microscopy (cryo-EM) to characterize the structure of chlorosomes from a bchQ mutant of Chlorobaculum tepidum. The chlorosomes of this mutant have a more uniform composition of bacteriochlorophyll (BChl) with a predominant homolog, [8Ethyl, 12Ethyl] BChl c, compared to the wild type (WT). Nearly complete 13C chemical shift assignments were obtained from well-resolved homonuclear 13C-13C RFDR data. For proton assignments heteronuclear 13C-1H (hCH) data sets were collected at 1.2 GHz spinning at 60 kHz. The CHHC experiments revealed intermolecular correlations between 132/31, 132/32, and 121/31, with distance constraints of less than 5 Å. These constraints indicate the syn-anti parallel stacking motif for the aggregates. Fourier transform cryo-EM data reveal an axial repeat of 1.49 nm for the helical tubular aggregates, perpendicular to the inter-tube separation of 2.1 nm. This axial repeat is different from WT and is in line with BChl syn-anti stacks running essentially parallel to the tube axis. Such a packing mode is in agreement with the signature of the Qy band in circular dichroism (CD). Combining the experimental data with computational insight suggests that the packing for the light-harvesting function is similar between WT and bchQ, while the chirality within the chlorosomes is modestly but detectably affected by the reduced compositional heterogeneity in bchQ.

Observation of Dark States in Two-Dimensional Electronic Spectra of Chlorosomes

Observations of low-lying dark states in several photosynthetic complexes challenge our understanding of the mechanisms behind their efficient energy transfer processes. Computational models are necessary for providing novel insights into the nature and function of dark states, especially since these are not directly accessible in spectroscopy experiments. Here, we will focus on signatures of dark-type states in chlorosomes, a light-harvesting complex from green sulfur bacteria well-known for uniting a broad absorption band with very efficient energy transfer. In agreement with experiments, our simulations of two-dimensional electronic spectra capture the ultrafast exciton transfer occurring in 100s of femtoseconds within a single chlorosome cylinder. The sub-100 fs process corresponds to relaxation within the single-excitation manifold in a single chlorosome tube, where all initially created populations in the bright exciton states are quickly transferred to dark-type exciton states. Structural inhomogeneities on the local scale cause a redistribution of the oscillator strength, leading to the emergence of these dark-type exciton states, which dominate ultrafast energy transfer. The presence of the dark-type exciton states suppresses energy loss from an isolated chlorosome via fluorescence quenching, as observed experimentally. Our results further question whether relaxation to dark-exciton states is a leading process or merely competes with transfer to the baseplate within the photosynthetic apparatus of green sulfur bacteria.

Ultrafast Anisotropy Decay Reveals Structure and Energy Transfer in Supramolecular Aggregates

Chlorosomes from green bacteria perform the most efficient light capture and energy transfer, as observed among natural light-harvesting antennae. Hence, their unique functional properties inspire developments in artificial light-harvesting and molecular optoelectronics. We examine two distinct organizations of the molecular building blocks as proposed in the literature, demonstrating how these organizations alter light capture and energy transfer, which can serve as a mechanism that the bacteria utilize to adapt to changes in light conditions. Spectral simulations of polarization-resolved two-dimensional electronic spectra unravel how changes in the helicity of chlorosomal aggregates alter energy transfer. We show that ultrafast anisotropy decay presents a spectral signature that reveals contrasting energy pathways in different chlorosomes.

Probing size variations of molecular aggregates inside chlorosomes using single-object spectroscopy

We theoretically investigate the possibility to use single-object spectroscopy to probe size variations of the bacteriochlorophyll aggregates inside chlorosomes. Chlorosomes are the light-harvesting organelles of green sulfur and non-sulfur bacteria. They are known to be the most efficient light-harvesting systems in nature. Key to this efficiency is the organization of bacteriochlorophyll molecules in large self-assembled aggregates that define the secondary structure inside the chlorosomes. Many studies have been reported to elucidate the morphology of these aggregates and the molecular packing inside them. It is widely believed that tubular aggregates play an important role. Because the size (radius and length) of these aggregates affects the optical and excitation energy transport properties, it is of interest to be able to probe these quantities inside chlorosomes. We show that a combination of single-chlorosome linear polarization resolved spectroscopy and single-chlorosome circular dichroism spectroscopy may be used to access the typical size of the tubular aggregates within a chlorosome and, thus, probe possible variations between individual chlorosomes that may result, for instance, from different stages in growth or different growth conditions.

Quantum Chemical Simulation of the Qy Absorption Spectrum of Zn Chlorin Aggregates for Artificial Photosynthesis

Zn chlorin (Znchl) is easy to synthesize and has similar optical properties to those of bacteriochlorophyll c in the nature, which is expected to be used as a light-harvesting antenna system in artificial photosynthesis. In order to further explore the optical characteristics of Znchl, various sizes of a parallel layered Znchl-aggregate model and the THF-Znchl explicit solvent monomer model were constructed in this study, and their Qy excited state properties were simulated by using time-dependent density functional theory (TDDFT) and exciton theory. For the Znchl monomer, with a combination of the explicit solvent model and the implicit solvation model based on density (SMD), the calculated Qy excitation energy agreed very well with the experimental one. The Znchl aggregates may be simplified to a Zn36 model to reproduce the experimental Qy absorption spectrum by the Förster coupling theory. The proposed Znchl aggregate model provides a good foundation for the future exploration of other properties of Znchl and simulations of artificial light-harvesting antennas. The results also indicate that J-aggregrates along z-direction, due to intermolecular coordination bonds, are the dominant factor in extending the Qy band of Znchl into the near infrared region.

Limitations of Linear Dichroism Spectroscopy for Elucidating Structural Issues of Light-Harvesting Aggregates in Chlorosomes

Linear dichroism (LD) spectroscopy is a widely used technique for studying the mutual orientation of the transition-dipole moments of the electronically excited states of molecular aggregates. Often the method is applied to aggregates where detailed information about the geometrical arrangement of the monomers is lacking. However, for complex molecular assemblies where the monomers are assembled hierarchically in tiers of supramolecular structural elements, the method cannot extract well-founded information about the monomer arrangement. Here we discuss this difficulty on the example of chlorosomes, which are the light-harvesting aggregates of photosynthetic green-(non) sulfur bacteria. Chlorosomes consist of hundreds of thousands of bacteriochlorophyll molecules that self-assemble into secondary structural elements of curved lamellar or cylindrical morphology. We exploit data from polarization-resolved fluorescence-excitation spectroscopy performed on single chlorosomes for reconstructing the corresponding LD spectra. This reveals that LD spectroscopy is not suited for benchmarking structural models in particular for complex hierarchically organized molecular supramolecular assemblies.

Unravelling the Role of Water in Ultrafast Excited-State Relaxation Dynamics within Nano-Architectures of Chlorophyll a

Water plays a pivotal role in structural stability of supramolecular pigment assemblies designed for natural light harvesting (for example, chlorosome antenna complex) as well as their artificial analogs. However, the dynamic role of water in the context of excite-state relaxation has not been explored till date, which we report here. Using femtosecond transient absorption spectroscopy, we investigate the excited-state dynamics of two types of nano-scale assemblies of chlorophyll a with different structural motifs, rod-shaped and micellar assemblies, that depend on the water content. We show how water participates in excess energy dissipation by vibrational cooling of the non-thermally populated Q_y band at different rates in different types of clusters but exhibits no polar solvation dynamics. For the micelles, we observe a bifurcation of stimulated emission line shape, whereas a positive-to-negative switching of differential absorption is observed for the rods; both these observations are correlated with their specific structural aspects. Density functional theory calculations reveal two possible stable ground state geometries of dimers, accounting for the bifurcation of line shape in micelles. Thus, our study elucidates water-mediated structure-function relationship within these pigment assemblies.

Growth model of chlorosome antenna by the environment-dependent stepwise assembly of a zinc chlorophyll derivative

A zinc chlorophyll derivative possessing an oligoethylene glycol ester at the 17-propionate residue was prepared as a model of specific pigments in chlorosomes, such as bacteriochlorophylls-c, d, and e, by chemical modification of naturally occurring chlorophyll-a. The zinc chlorophyll derivative aggregated in aqueous or hexane solutions containing 1% (v/v) ethanol to give red-shifted and broadened Soret/Qy absorption bands with intense circular dichroism signals, indicating the formation of its chlorosome-like J-type self-aggregates. The atomic force microscope images of the self-aggregates prepared in aqueous or hexane solutions showed thin tube-like (ca. 3 nm diameter) or thick rod-like aggregates (> 20 nm diameter), respectively. After standing these solutions for several days, the nanotubes or nanorods further assembled to give ribbon- or bundle-like aggregates, respectively. The latter transformation (tube to ribbon) was triggered by hydrogen bonding between oligoethylene glycol esters located outside of the tubes via water or ethanol molecules. These dynamic supramolecular transformations may also be useful for revealing the growth process of bacteriochlorophyll self-aggregates in a chlorosome.

Cryo-Electron Tomography Reveals the Complex Ultrastructural Organization of Multicellular Filamentous Chloroflexota (Chloroflexi) Bacteria

The cell biology of Chloroflexota is poorly studied. We applied cryo-focused ion beam milling and cryo-electron tomography to study the ultrastructural organization of thermophilic Roseiflexus castenholzii and Chloroflexus aggregans, and mesophilic “Ca. Viridilinea mediisalina.” These species represent the three main lineages within a group of multicellular filamentous anoxygenic phototrophic Chloroflexota bacteria belonging to the Chloroflexales order. We found surprising structural complexity in the Chloroflexales. As with filamentous cyanobacteria, cells of C. aggregans and “Ca. Viridilinea mediisalina” share the outer membrane-like layers of their intricate multilayer cell envelope. Additionally, cells of R. castenholzii and “Ca. Viridilinea mediisalina” are connected by septal channels that resemble cyanobacterial septal junctions. All three strains possess long pili anchored close to cell-to-cell junctions, a morphological feature comparable to that observed in cyanobacteria. The cytoplasm of the Chloroflexales bacteria is crowded with intracellular organelles such as different types of storage granules, membrane vesicles, chlorosomes, gas vesicles, chemoreceptor-like arrays, and cytoplasmic filaments. We observed a higher level of complexity in the mesophilic strain compared to the thermophilic strains with regards to the composition of intracellular bodies and the organization of the cell envelope. The ultrastructural details that we describe in these Chloroflexales bacteria will motivate further cell biological studies, given that the function and evolution of the many discovered morphological traits remain enigmatic in this diverse and widespread bacterial group.

Supramolecular Energy Materials

Self-assembly is a bioinspired strategy to craft materials for renewable and clean energy technologies. In plants, the alignment and assembly of the light-harvesting protein machinery in the green leaf optimize the ability to efficiently convert light from the sun to form chemical bonds. In artificial systems, strategies based on self-assembly using noncovalent interactions offer the possibility to mimic this functional correlation among molecules to optimize photocatalysis, photovoltaics, and energy storage. One of the long-term objectives of the field described here as supramolecular energy materials is to learn how to design soft materials containing light-harvesting assemblies and catalysts to generate fuels and useful chemicals. Supramolecular energy materials also hold great potential in the design of systems for photovoltaics in which intermolecular interactions in self-assembled structures, for example, in electron donor and acceptor phases, maximize charge transport and avoid exciton recombination. Possible pathways to integrate organic and inorganic structures by templating strategies and electrodeposition to create materials relevant to energy challenges including photoconductors and supercapacitors are also described. The final topic discussed is the synthesis of hybrid perovskites in which organic molecules are used to modify both structure and functions, which may include chemical stability, photovoltaics, and light emission.

On Excitation Energy Transfer within the Baseplate BChl a-CsmA Complex of Chloroflexus aurantiacus

Recently, a hybrid approach combining solid-state NMR spectroscopy and cryo-electron microscopy showed that the baseplate in green sulfur bacterium Chlorobaculum tepidum is a 2D lattice of BChl a-CsmA dimers [Nielsen, J. T.; et al., Nat. Commun. 2016, 7, 12454-12465]. While the existence of the BChl a-CsmA subunit was previously known, the proposed orientations of the BChl a pigments had only been elucidated from spectral data up to this point. Regarding the electronic structure of the baseplate, two models have been proposed. 2D electronic spectroscopy data were interpreted as revealing that at least four excitonically coupled BChl a might be in close contact. Conversely, spectral hole burning data suggested that the lowest energy state was localized, yet additional states are sometimes observed because of the presence of the Fenna-Matthews-Olson (FMO) antenna protein. To solve this conundrum, this work studies the chlorosome-baseplate complex from Chloroflexus aurantiacus, which does not contain the FMO protein. The results confirm that in both C. tepidum and C. aurantiacus, excitation energy is transferred to a localized low-energy trap state near 818 nm with similar rates, most likely via exciton hopping.

Bioinspired supramolecular nanosheets of zinc chlorophyll assemblies

Two-dimensional sheet-like supramolecules have attracted much attention from the viewpoints of their potential application as functional (nano)materials due to unique physical and chemical properties. One of the supramolecular sheet-like nanostructures in nature is visible in the self-assemblies of bacteriochlorophyll-c–f pigments inside chlorosomes, which are major components in the antenna systems of photosynthetic green bacteria. Herein, we report artificial chlorosomal supramolecular nanosheets prepared by the self-assembly of a synthetic zinc 3¹-methoxy-chlorophyll derivative having amide and urea groups in the substituent at the 17-position. The semi-synthetic zinc chlorophyll derivative kinetically formed dimeric species and transformed into more thermodynamically stable chlorosomal J-aggregates in the solid state. The kinetically and thermodynamically formed self-assemblies had particle-like and sheet-like supramolecular nanostructures, respectively. The resulting nanosheets of biomimetic chlorosomal J-aggregates had flat surfaces and well-ordered supramolecular structures. The artificial sheet-like nanomaterial mimicking chlorosomal bacteriochlorophyll-c–f J-aggregates was first constructed by the model molecule, and is potentially useful for various applications including artificial light-harvesting antennas and photosyntheses.

Spectral and Structural Variations of Biomimetic Light-Harvesting Nanotubes

Bioinspired, self-assembled nanotubes have been investigated by low-temperature, polarization-resolved single-tube spectroscopy. These assemblies are based on zinc chlorin monomers and are considered as model systems that resemble the secondary structural elements in the natural light-harvesting systems of green (non)sulfur bacteria. Compared to the natural systems, the spectral parameters extracted from the single-nanotube spectra feature distributions with significantly smaller widths, which is ascribed to a tremendous reduction of structural heterogeneity in the artificial systems. Employing quantum chemical molecular modeling the spectra of individual nanotubes can be explained consistently only for a molecular packing model that is fundamentally different from those considered so far for the natural systems. Subsequent theoretical simulations reveal that the remaining spectral variations between single nanotubes can be traced back to small variations of the mutual orientations of the monomer transition dipole moments that are far beyond the resolving power of high-resolution electron microscopy imaging techniques.

Structural Variations in Chlorosomes from Wild-Type and a bchQR Mutant of Chlorobaculum tepidum Revealed by Single-Molecule Spectroscopy

Green sulfur bacteria can grow photosynthetically by absorbing only a few photons per bacteriochlorophyll molecule per day. They contain chlorosomes, perhaps the most efficient light-harvesting antenna system found in photosynthetic organisms. Chlorosomes contain supramolecular structures comprising hundreds of thousands of bacteriochlorophyll molecules, which are properly positioned with respect to one another solely by self-assembly and not by using a protein scaffold as a template for directing the mutual arrangement of the monomers. These two features-high efficiency and self-assembly-have attracted considerable attention for developing light-harvesting systems for artificial photosynthesis. However, reflecting the heterogeneity of the natural system, detailed structural information at atomic resolution of the molecular aggregates is not yet available. Here, we compare the results for chlorosomes from the wild type and two mutants of Chlorobaculum tepidum obtained by polarization-resolved, single-particle fluorescence-excitation spectroscopy and theoretical modeling with results previously obtained from nuclear-magnetic resonance spectroscopy and cryo-electron microscopy. Only the combination of information obtained from all of these techniques allows for an unambiguous description of the molecular packing of bacteriochlorophylls within chlorosomes. In contrast to some suggestions in the literature, we find that, for the chlorosomes from the wild type as well as for those from mutants, the dominant secondary structural element features tubular symmetry following a very similar construction principle. Moreover, the results suggest that the various options for methylation of the bacteriochlorophyll molecules, which are a primary source of the structural (and spectral) heterogeneity of wild-type chlorosome samples, are exploited by nature to achieve improved spectral coverage at the level of individual chlorosomes.

Synthesis and Self-Aggregation of π-Expanded Chlorophyll Derivatives to Construct Light-Harvesting Antenna Models

Chlorosomes are one of the elegant light-harvesting antenna systems in anoxygenic photosynthetic bacteria, whose core is constructed from J-type self-aggregation of bacteriochlorophyll- c, bacteriochlorophyll- d, bacteriochlorophyll- e, and bacteriochlorophyll- f molecules without the influence of polypeptides. Chlorosomal supramolecular models were built up using synthetic porphyrin-type bacteriochlorophyll- d analogues with a methoxycarbonylethenyl, formyl, vinyl, or ethyl group at the 8-position. Their chlorosomal self-aggregates in an aqueous micelle solution showed relatively intense absorption bands around 500-600 nm where antennas of natural oxygenic phototrophs, as well as green sulfur bacteria possessing bacteriochlorophylls- c/ d, absorb light less efficiently; this observation is called the "green gap". Furthermore, the functional chlorosomal models were constructed by simple addition of a small amount of an energy acceptor model bearing a bacteriochlorin moiety to the pigment self-assemblies in an aqueous micelle. The resulting excited energy donor-acceptor supramolecules played the roles of chlorosomal light-harvesting and energy-transfer antenna systems and were efficient at light absorption in the "green gap" region.

Self-Assemblies of Zinc Bacteriochlorophyll-d Analogues Having Amide, Ester, and Urea Groups as Substituents at 17-Position and Observation of Lamellar Supramolecular Nanostructures

Chlorosomes are unique light-harvesting apparatuses in photosynthetic green bacteria. Single chlorosomes contain a large number of bacteriochlorophyll (BChl)-c, -d, -e, and -f molecules, which self-assemble without protein assistance. These BChl self-assemblies involving specific intermolecular interactions (Mg⋅⋅⋅O3² -H⋅⋅⋅O=C13¹ and π-π stacks of chlorin skeletons) in a chlorosome have been reported to be round-shaped rods (or tubes) with diameters of 5 or 10 nm, or lamellae with a layer spacing of approximately 2 nm. Herein, the self-assembly of synthetic zinc BChl-d analogues having ester, amide, and urea groups in the 17-substituent is reported. Spectroscopic analyses indicate that the zinc BChl-d analogues self-assemble in a nonpolar organic solvent in a similar manner to natural chlorosomal BChls with additional assistance by hydrogen-bonding of secondary amide (or urea) groups (CON-H⋅⋅⋅O=CNH). Microscopic analyses of the supramolecules of a zinc BChl-d analogue bearing amide and urea groups show round- or square-shaped rods with widths of about 65 nm. Cryogenic TEM shows a lamellar arrangement of the zinc chlorin with a layer spacing of 1.5 nm inside the rod. Similar thick rods are also visible in the micrographs of self-assemblies of zinc BChl-d analogues with one or two secondary amide moieties in the 17-substituent.

Pathway complexity in the self-assembly of a zinc chlorin model system of natural bacteriochlorophyll J-aggregates

Self-assembly studies of a model compound of bacteriochlorophyll revealed the formation of nanoparticles as off-pathway and nanofibers as on-pathway products.

Whilst bacteriochlorophyll c, d, and e dyes self-assemble into the most efficient light harvesting J-aggregate systems found in nature, their supramolecular packing arrangements are still a matter of debate and a significant number of models have been suggested for their local and long-range ordering. Here we reveal for a synthetic model system based on a zinc chlorin (ZnChl) dye an intriguing interplay of two competing aggregation pathways by kinetic and thermodynamic studies in MeOH/water solvent mixtures: the formation of kinetically controlled off-pathway nanoparticles consisting of excitonically coupled J-dimers versus the formation of thermodynamically more stable one-dimensional helical fibers consisting of J-coupled extended aggregates. The higher order of the latter is evidenced by atomic force microscopy and a more narrow absorption spectrum of the J-aggregates. Based on a recently developed thermodynamic model that combines the cooperative K₂–K growth model with a competing dimerization model, an energy landscape could be derived that describes the pathway complexity of this biomimetic system. Our studies reveal that the kinetic stability of the off-pathway nanoparticles increases with increasing concentration of ZnChl or water content in a MeOH/water solvent mixture. For a water content >90% deeply trapped off-pathway nanoparticle products are formed that do not transform anymore to the more ordered thermodynamic product within reasonable time scales. Based on these observations, we hypothesize that out-of-equilibrium aggregate structures of natural BChl dyes may also exist in the natural chlorosomes of green bacteria.

Effects of exogenous isoprenoid diphosphates on in vivo attachment to bacteriochlorophyllide c in the green sulfur photosynthetic bacterium Chlorobaculum tepidum

Metabolic substitution of the esterifying chain in bacteriochlorophyll (BChl) c in green photosynthetic bacteria grown by supplementation of exogenous alcohols has attracted attentions to study supramolecular structures and biogenesis of major antenna complexes chlorosomes in these bacteria as well as BChl pigment biosynthesis. Actual substrates in the enzymatic attachment of the esterifying moieties to the precursor of BChl c, namely bacteriochlorophyllide (BChlide) c, in these bacteria are believed to be diphosphate esters of alcoholic substrates, although only intact alcohols have so far been supplemented in the bacterial cultures. We report herein BChl c compositions in the green sulfur photosynthetic bacterium Chlorobaculum tepidum by supplementation with geranyl and geranylgeranyl diphosphates. The supplementation of these diphosphates hardly produced BChl c derivatives esterified with geraniol and geranylgeraniol in Cba. tepidum, whereas these BChl c derivatives were accumulated by supplementation of intact geraniol and geranylgeraniol. The sharp contrast of the incorporation efficiency of the supplemental isoprenoid moieties in BChl c using the isoprenoid diphosphates to that by the isoprenoid alcohols was mainly ascribable to less penetration abilities of the diphosphate substrates into Cba. tepidum cells because of their anionic and polar diphosphate moiety.

In situ high-resolution structure of the baseplate antenna complex in Chlorobaculum tepidum

Photosynthetic antenna systems enable organisms harvesting light and transfer the energy to the photosynthetic reaction centre, where the conversion to chemical energy takes place. One of the most complex antenna systems, the chlorosome, found in the photosynthetic green sulfur bacterium Chlorobaculum (Cba.) tepidum contains a baseplate, which is a scaffolding super-structure, formed by the protein CsmA and bacteriochlorophyll a. Here we present the first high-resolution structure of the CsmA baseplate using intact fully functional, light-harvesting organelles from Cba. tepidum, following a hybrid approach combining five complementary methods: solid-state NMR spectroscopy, cryo-electron microscopy, isotropic and anisotropic circular dichroism and linear dichroism. The structure calculation was facilitated through development of new software, GASyCS for efficient geometry optimization of highly symmetric oligomeric structures. We show that the baseplate is composed of rods of repeated dimers of the strongly amphipathic CsmA with pigments sandwiched within the dimer at the hydrophobic side of the helix.

The chlorosome of the photosynthetic bacterium C. tepidum harvests light and transfers the energy to the photosynthetic reaction centre. Here the authors determine the structure of the baseplate, a scaffolding super-structure, to show that the baseplate consists of rods of repeated CsmA dimers containing pigment molecules.

Introduction of perfluoroalkyl chain into the esterifying moiety of bacteriochlorophyll c in the green sulfur photosynthetic bacterium Chlorobaculum tepidum by pigment biosynthesis

The green sulfur photosynthetic bacterium Chlorobaculum (Cba.) tepidum was grown in liquid cultures containing perfluoro-1-decanol, 1H,1H,2H,2H-heptadecafluoro-1-decanol [CF3(CF2)7(CH2)2OH] or 1H,1H-nonadecafluoro-1-decanol [CF3(CF2)8CH2OH], to introduce rigid and fluorophilic chains into the esterifying moiety of light-harvesting bacteriochlorophyll (BChl) c. Exogenous 1H,1H,2H,2H-heptadecafluoro-1-decanol was successfully attached to the 17(2)-carboxy group of bacteriochlorophyllide (BChlide) c in vivo: the relative ratio of the unnatural BChl c esterified with this perfluoroalcohol over the total BChl c was 10.3%. Heat treatment of the liquid medium containing 1H,1H,2H,2H-heptadecafluoro-1-decanol with β-cyclodextrin before inoculation increased the relative ratio of the BChl c derivative esterified with this alcohol in the total BChl c in Cba. tepidum. In a while, 1H,1H-nonadecafluoro-1-decanol was not attached to BChlide c in Cba. tepidum, which was grown by its supplementation. These results suggest that the rigidity close to the hydroxy group of the esterifying alcohol is not suitable for the recognition by the BChl c synthase called BchK in Cba. tepidum. The unnatural BChl c esterified with 1H,1H,2H,2H-heptadecafluoro-1-decanol participated in BChl c self-aggregates in chlorosomes.

Nanotubes of Biomimetic Supramolecules Constructed by Synthetic Metal Chlorophyll Derivatives

Various supramolecular nanotubes have recently been built up by lipids, peptides, and other organic molecules. Major light-harvesting (LH) antenna systems in a filamentous anoxygenic phototroph, Chloroflexus (Cfl.) aurantiacus, are called chlorosomes and contain photofunctional single-wall supramolecular nanotubes with approximately 5 nm in their diameter. Chlorosomal supramolecular nanotubes of Cfl. aurantiacus are constructed by a large amount of bacteriochlorophyll(BChl)-c molecules. Such a pigment self-assembles in a chlorosome without any assistance from the peptides, which is in sharp contrast to the other natural photosynthetic LH antennas. To mimic chlorosomal supramolecular nanotubes, synthetic models were prepared by the modification of naturally occurring chlorophyll(Chl)-a molecule. Metal complexes (magnesium, zinc, and cadmium) of the Chl derivative were synthesized as models of natural chlorosomal BChls. These metal Chl derivatives self-assembled in hydrophobic environments, and their supramolecules were analyzed by spectroscopic and microscopic techniques. Cryo-transmission electron microscopic images showed that the zinc and cadmium Chl derivatives could form single-wall supramolecular nanotubes and their outer and inner diameters were approximately 5 and 3 nm, respectively. Atomic force microscopic images suggested that the magnesium Chl derivative formed similar nanotubes to those of the corresponding zinc and cadmium complexes. Three chlorosomal single-wall supramolecular nanotubes of the metal Chl derivatives were prepared in the solid state and would be useful as photofunctional materials.

Energy transfer in aggregates of bacteriochlorophyll c self-assembled with azulene derivatives

Bacteriochlorophyll (BChl) c is the main light-harvesting pigment of certain photosynthetic bacteria. It is found in the form of self-assembled aggregates in the so-called chlorosomes. Here we report the results of co-aggregation experiments of BChl c with azulene and its tailored derivatives. We have performed spectroscopic and quantum chemical characterization of the azulenes, followed by self-assembly experiments. The results show that only azulenes with sufficient hydrophobicity are able to induce aggregation of BChl c. Interestingly, only azulene derivatives possessing a conjugated phenyl ring were capable of efficient (∼50%) excitation energy transfer to BChl molecules. These aggregates represent an artificial light-harvesting complex with enhanced absorption between 220 and 350 nm compared to aggregates of pure BChl c. The results provide insight into the principles of self-assembly of BChl aggregates and suggest an important role of the π-π interactions in efficient energy transfer.

Fast delocalization leads to robust long-range excitonic transfer in a large quantum chlorosome model

Chlorosomes are efficient light-harvesting antennas containing up to hundreds of thousands of bacteriochlorophyll molecules. With massively parallel computer hardware, we use a nonperturbative stochastic Schrödinger equation, while including an atomistically derived spectral density, to study excitonic energy transfer in a realistically sized chlorosome model. We find that fast short-range delocalization leads to robust long-range transfer due to the antennae's concentric-roll structure. Additionally, we discover anomalous behavior arising from different initial conditions, and outline general considerations for simulating excitonic systems on the nanometer to micrometer scale.

Role of thermal excitation in ultrafast energy transfer in chlorosomes revealed by two-dimensional electronic spectroscopy

Two-dimensional electronic spectroscopy reveals the role of thermal excitation in excitation energy transfer in chlorosomes.

Insights into the excitonic states of individual chlorosomes from Chlorobaculum tepidum

Green-sulfur bacteria have evolved a unique light-harvesting apparatus, the chlorosome, by which it is perfectly adapted to thrive photosynthetically under extremely low light conditions. We have used single-particle, optical spectroscopy to study the structure-function relationship of chlorosomes each of which incorporates hundreds of thousands of self-assembled bacteriochlorophyll (BChl) molecules. The electronically excited states of these molecular assemblies are described as Frenkel excitons whose photophysical properties depend crucially on the mutual arrangement of the pigments. The signature of these Frenkel excitons and its relation to the supramolecular organization of the chlorosome becomes accessible by optical spectroscopy. Because subtle spectral features get obscured by ensemble averaging, we have studied individual chlorosomes from wild-type Chlorobaculum tepidum by polarization-resolved fluorescence-excitation spectroscopy. This approach minimizes the inherent sample heterogeneity and allows us to reveal properties of the exciton states without ensemble averaging. The results are compared with predictions from computer simulations of various models of the supramolecular organization of the BChl monomers. We find that the photophysical properties of individual chlorosomes from wild-type Chlorobaculum tepidum are consistent with a (multiwall) helical arrangement of syn-anti stacked BChl molecules in cylinders and/or spirals of different size.

Direct Measurement of Energy Migration in Supramolecular Carbocyanine Dye Nanotubes

Exciton transport lengths in double-walled and bundled cylindrical 3,3'-bis- (2-sulfopropyl)-5,5',6,6'-tetrachloro-1,1'-dioctylbenzimida-carbocyanine (C8S3) J-aggregates were measured using direct imaging of fluorescence from individual aggregates deposited on solid substrates. Regions identified in confocal images were excited with a focused laser spot, and the resulting fluorescence emission was imaged onto an electron multiplying charged coupled device camera. A two-dimensional Gaussian fitting scheme was used to quantitatively compare the excitation beam profile to the broadened aggregate emission profiles. The double-walled tubes exhibit average exciton transport lengths of 140 nm, while exciton transport in the bundled nanotubes was found to be remarkably long, with distances reaching many hundreds of nanometers. A steady-state one-dimensional diffusion model for the broadening of the emission profiles yields diffusion coefficients of 120 nm(2) ps(-1) for the nanotubes and 7000 nm(2) ps(-1) for the aggregate bundles. The level of structural hierarchy dramatically affects the exciton transport capabilities in these artificial light-harvesting systems, and energy migration is not limited to a single dimension in J-aggregate bundles.

Progress in the direct structural characterization of fibrous amphiphilic supramolecular assemblies in solution by transmission electron microscopic techniques

The self-assembly of amphiphilic molecules into fibrous structures has been the subject of numerous studies over past decades due to various current and promising technical applications. Although very different in their head group chemistry many natural as well as synthetic amphiphilic compounds derived from carbohydrates, carbocyanine dyes, or amino acids tend to form fibrous structures by molecular self-assembly in water predominantly twisted ribbons or tubes. Often a transition between these assembly structures is observed, which is a phenomenon already theoretically approached by Wolfgang Helfrich and still focus point in current research. With the development of suitable sample preparation and electron optical imaging techniques, cryogenic transmission electron microscopy (cryo-TEM) in combination with three-dimensional (3D) reconstruction techniques has become a particular popular direct characterization technique for supramolecular assemblies in general. Here we review the recent progress in deriving precise structural information from cryo-TEM data of particularly fibrous structures preferably in three dimensions.

Theoretical characterization of excitation energy transfer in chlorosome light-harvesting antennae from green sulfur bacteria

We present a theoretical study of excitation dynamics in the chlorosome antenna complex of green photosynthetic bacteria based on a recently proposed model for the molecular assembly. Our model for the excitation energy transfer (EET) throughout the antenna combines a stochastic time propagation of the excitonic wave function with molecular dynamics simulations of the supramolecular structure and electronic structure calculations of the excited states. We characterized the optical properties of the chlorosome with absorption, circular dichroism and fluorescence polarization anisotropy decay spectra. The simulation results for the excitation dynamics reveal a detailed picture of the EET in the chlorosome. Coherent energy transfer is significant only for the first 50 fs after the initial excitation, and the wavelike motion of the exciton is completely damped at 100 fs. Characteristic time constants of incoherent energy transfer, subsequently, vary from 1 ps to several tens of ps. We assign the time scales of the EET to specific physical processes by comparing our results with the data obtained from time-resolved spectroscopy experiments.

Electromagnetic study of the chlorosome antenna complex of Chlorobium tepidum

Green sulfur bacteria are an iconic example of nature's adaptation: thriving in environments of extremely low photon density, the bacterium ranks itself among the most efficient natural light-harvesting organisms. The photosynthetic antenna complex of this bacterium is a self-assembled nanostructure, ≈60 × 150 nm, made of bacteriochlorophyll molecules. We study the system from a computational nanoscience perspective by using electrodynamic modeling with the goal of understanding its role as a nanoantenna. Three different nanostructures, built from two molecular packing moieties, are considered: a structure built of concentric cylinders of aggregated bacteriochlorophyll d monomers, a single cylinder of bacteriochlorophyll c monomers, and a model for the entire chlorosome. The theoretical model captures both coherent and incoherent components of exciton transfer. The model is employed to extract optical spectra, concentration and depolarization of electromagnetic fields within the chlorosome, and fluxes of energy transfer for the structures. The second model nanostructure shows the largest field enhancement. Further, field enhancement is found to be more sensitive to dynamic noise rather than structural disorder. Field depolarization, however, is similar for all structures. This indicates that the directionality of transfer is robust to structural variations, while on the other hand, the intensity of transfer can be tuned by structural variations.

Coherent Oscillations in Chlorosome Elucidated by Two-Dimensional Electronic Spectroscopy

Chlorosomes are the most efficient photosynthetic light-harvesting complexes found in nature and consist of many bacteriochlorophyll (BChl) molecules self-assembled into supramolecular aggregates. Here we elucidate the presence and the origin of coherent oscillations in chlorosome at cryogenic temperature using 2D electronic spectroscopy. We observe coherent oscillations of multiple frequencies superimposed on the ultrafast amplitude decay of 2D spectra. Comparison of oscillatory features in the rephasing and nonrephasing 2D spectra suggests that an oscillation of 620 cm(-1) frequency arises from electronic coherence. However, this coherent oscillation can be enhanced by vibronic coupling with intermolecular vibrations of BChl aggregate, and thus it might originate from vibronic coherence rather than pure electronic coherence. Although the 620 cm(-1) oscillation dephases rapidly, the electronic (or vibronic) coherence may still take part in the initial step of energy transfer in chlorosome, which is comparably fast.

Temperature and carbon assimilation regulate the chlorosome biogenesis in green sulfur bacteria

Green photosynthetic bacteria adjust the structure and functionality of the chlorosome-the light-absorbing antenna complex-in response to environmental stress factors. The chlorosome is a natural self-assembled aggregate of bacteriochlorophyll (BChl) molecules. In this study, we report the regulation of the biogenesis of the Chlorobaculum tepidum chlorosome by carbon assimilation in conjunction with temperature changes. Our studies indicate that the carbon source and thermal stress culture of C. tepidum grows slower and incorporates fewer BChl c in the chlorosome. Compared with the chlorosome from other cultural conditions we investigated, the chlorosome from the carbon source and thermal stress culture displays (a) smaller cross-sectional radius and overall size, (b) simplified BChl c homologs with smaller side chains, (c) blue-shifted Qy absorption maxima, and (d) a sigmoid-shaped circular dichroism spectra. Using a theoretical model, we analyze how the observed spectral modifications can be associated with structural changes of BChl aggregates inside the chlorosome. Our report suggests a mechanism of metabolic regulation for chlorosome biogenesis.

Bacteriochlorophyll aggregates self-assembled on functionalized gold nanorod cores as mimics of photosynthetic chlorosomal antennae: a single molecule study

We prepare artificial aggregates that mimic the structure and function of natural chlorosomal light harvesting complexes of green photosynthetic bacteria. Gold nanorods functionalized with hydroxyl groups and immobilized on a substrate serve as cores for the growth of bacteriochlorophyll (BChl) aggregates from a buffer solution. The BChl pigments form large self-assembled aggregate particles with sizes more than twice that of natural chlorosomes. The size is controllable by the aggregation time. The aggregates are characterized on a single-particle level by atomic force microscopy, electron microscopy, and single-molecule spectroscopy. The absorption and fluorescence spectral properties which reflect the molecular level arrangement of the BChl aggregates closely resemble those of the natural chlorosomes of the photosynthetic bacterium Chlorobaculum tepidum. On the other hand, the results of linear dichroism and circular dichroism are different from those of the chlorosomes and indicate a different mesoscopic structure for the artificial aggregates. These results emphasize the structural role played by the baseplate pigment-protein complex in natural chlorosomes.

Biosynthesis of bacteriochlorophyll c derivatives possessing chlorine and bromine atoms at the terminus of esterifying chains in the green sulfur bacterium Chlorobaculum tepidum

The green sulfur photosynthetic bacterium Chlorobaculum tepidum newly produced BChl c derivatives possessing a chlorine or bromine atom at the terminus of the esterifying chain in the 17-propionate residue by cultivation with exogenous ω-halo-1-alkanols. The relative ratios of BChl c derivatives esterified with 8-chloro-1-octanol and 10-chloro-1-decanol were estimated to be 26.5% and 33.3% by cultivation with these ω-chloro-1-alkanols at the final concentrations of 300 and 150 μM, respectively. In contrast, smaller amounts of unnatural BChls c esterified with ω-bromo-1-alkanols were biosynthesized than those esterified with ω-chloro-1-alkanols: the ratios of BChl c derivatives esterified with 8-bromo-1-octanol and 10-bromo-1-decanol were 11.3% and 12.2% at the concentrations of 300 and 150 μM, respectively. These indicate that ω-chloro-1-alkanols can be incorporated into bacteriochlorophyllide c more than ω-bromo-1-alkanols in the BChl c biosynthetic pathway. The homolog compositions of the novel BChl c derivatives possessing a halogen atom were analogous to those of coexisting natural BChl c esterified with farnesol. These results demonstrate unique properties of BChl c synthase, BchK, which can utilize unnatural substrates containing halogen in the BChl c biosynthesis of Cba. tepidum.

Computational determination of the pigment binding motif in the chlorosome protein a of green sulfur bacteria

We present a molecular-scale model of Bacteriochlorophyll a (BChl a) binding to the chlorosome protein A (CsmA) of Chlorobaculum tepidum, and the aggregated pigment–protein dimer, as determined from protein–ligand docking and quantum chemistry calculations. Our calculations provide strong evidence that the BChl a molecule is coordinated to the His25 residue of CsmA, with the magnesium center of the bacteriochlorin ring situated\3 A° from the imidazole nitrogen atom of the histidine sidechain, and the phytyl tail aligned along the nonpolar residues of the a-helix of CsmA. We also confirm that the Qy band in the absorption spectra of BChl a experiences a large (?16 to ?43 nm) redshift when aggregated with another BChl a molecule in the CsmA dimer, compared to the BChl a in solvent; this redshift has been previously established by experimental researchers. We propose that our model of the BChl a–CsmA binding motif, where the dimer contains parallel aligned N-terminal regions, serves as the smallest repeating unit in a larger model of the para-crystalline chlorosome baseplate protein.

Chlorophyll J-aggregates: from bioinspired dye stacks to nanotubes, liquid crystals, and biosupramolecular electronics

Among the natural light-harvesting (LH) systems, those of green sulfur and nonsulfur photosynthetic bacteria are exceptional because they lack the support of a protein matrix. Instead, these so-called chlorosomes are based solely on "pigments". These are self-assembled bacteriochlorophyll c, d, and e derivatives, which consist of a chlorophyll skeleton bearing a 3(1)-hydroxy functional group. Chemists consider the latter as an essential structural unit to direct the formation of light-harvesting self-assembled dye aggregates with J-type excitonic coupling. The intriguing properties of chlorosomal J-type aggregates, particularly narrow red-shifted absorption bands, compared with monomers and their ability to delocalize and migrate excitons, have inspired intense research activities toward synthetic analogues in this field. The ultimate goal of this research field is the development of (opto-)electronic devices based on the architectural principle of chlorosomal LH systems. In this regard, the challenge is to develop small, functional building blocks with appropriate substituents that are preprogrammed to self-assemble across different length scales and to emulate functions of natural LH systems or to realize entirely new functions beyond those found in nature. In this Account, we highlight our achievements in the past decade with semisynthetic zinc chlorins (ZnChls) as model compounds of bacteriochlorophylls obtained from the naturally most abundant chlorin precursor: chlorophyll a. To begin, we explore how supramolecular strategies involving π-stacking, hydrogen bonding, and metal-oxygen coordination can be used to design ZnChl-based molecular stack, tube, and liquid crystalline assemblies conducive to charge and energy transport. Our design principle is based on the bioinspired functionalization of the 3(1)-position of ZnChl with a hydroxy or methoxy group; the former gives rise to tubular assemblies, whereas the latter induces stack assemblies. Functionalization of the 17(2)-position with esterified hydrophilic or hydrophobic chains, dendron-wedge substituents, and chromophores having complementary optical properties such as naphthalene bisimides (NBIs) is used to modulate the self-assembly of ZnChl dyes. The resulting assemblies exhibit enhanced charge transport and energy transfer abilities. We have used UV/vis, circular dichroism (CD), fluorescence spectroscopy, and dynamic light scattering (DLS) for the characterization of these assemblies in solution. In addition, we have studied assembly morphologies by atomic force microscopy (AFM), scanning tunneling microscopy (STM), transmission electron microscopy (TEM), and cryogenic-TEM. Crystallographic techniques such as powder X-ray and solid-state NMR have been used to explain the precise long- and short-range packing of dyes in these assemblies. Finally, functional properties such as charge and energy transport have been explored by pulse radiolysis time-resolved microwave conductivity (PR-TRMC), conductive AFM, and time-resolved fluorescence spectroscopy. The design principles discussed in this Account are important steps toward the utilization of these materials in biosupramolecular electronics and photonics in the future.

Chlorosome antenna complexes from green photosynthetic bacteria

Chlorosomes are the distinguishing light-harvesting antenna complexes that are found in green photosynthetic bacteria. They contain bacteriochlorophyll (BChl) c, d, e in natural organisms, and recently through mutation, BChl f, as their principal light-harvesting pigments. In chlorosomes, these pigments self-assemble into large supramolecular structures that are enclosed inside a lipid monolayer to form an ellipsoid. The pigment assembly is dictated mostly by pigment-pigment interactions as opposed to protein-pigment interactions. On the bottom face of the chlorosome, the CsmA protein aggregates into a paracrystalline baseplate with BChl a, and serves as the interface to the next energy acceptor in the system. The exceptional light-harvesting ability at very low light conditions of chlorosomes has made them an attractive subject of study for both basic and applied science. This review, incorporating recent advancements, considers several important aspects of chlorosomes: pigment biosynthesis, organization of pigments and proteins, spectroscopic properties, and applications to bio-hybrid and bio-inspired devices.

Half a century of molecular bioenergetics

Molecular bioenergetics deals with the construction, function and regulation of the powerhouses of life. The present overview sketches scenes and actors, farsighted goals and daring hypotheses, meticulous tool-making, painstaking benchwork, lucky discovery, serious scepticism, emphatic believing and strong characters with weak and others with hard arguments, told from a personal, admittedly limited, perspective. Bioenergetics will blossom further with the search focused on both where there is bright light for ever-finer detail and the obvious dark spots for surprise and discovery.

Comparison of the physical characteristics of chlorosomes from three different phyla of green phototrophic bacteria

Chlorosomes, the major antenna complexes in green sulphur bacteria, filamentous anoxygenic phototrophs, and phototrophic acidobacteria, are attached to the cytoplasmic side of the inner cell membrane and contain thousands of bacteriochlorophyll (BChl) molecules that harvest light and channel the energy to membrane-bound reaction centres. Chlorosomes from phototrophs representing three different phyla, Chloroflexus (Cfx.) aurantiacus, Chlorobaculum (Cba.) tepidum and the newly discovered "Candidatus (Ca.) Chloracidobacterium (Cab.) thermophilum" were analysed using PeakForce Tapping atomic force microscopy (PFT-AFM). Gentle PFT-AFM imaging in buffered solutions that maintained the chlorosomes in a near-native state revealed ellipsoids of variable size, with surface bumps and undulations that differ between individual chlorosomes. Cba. tepidum chlorosomes were the largest (133×57×36nm; 141,000nm(3) volume), compared with chlorosomes from Cfx. aurantiacus (120×44×30nm; 84,000nm(3)) and Ca. Cab. thermophilum (99×40×31nm; 65,000nm(3)). Reflecting the contributions of thousands of pigment-pigment stacking interactions to the stability of these supramolecular assemblies, analysis by nanomechanical mapping shows that chlorosomes are highly stable and that their integrity is disrupted only by very strong forces of 1000-2000pN. AFM topographs of Ca. Cab. thermophilum chlorosomes that had retained their attachment to the cytoplasmic membrane showed that this membrane dynamically changes shape and is composed of protrusions of up to 30nm wide and 6nm above the mica support, possibly representing different protein domains. Spectral imaging revealed significant heterogeneity in the fluorescence emission of individual chlorosomes, likely reflecting the variations in BChl c homolog composition and internal arrangements of the stacked BChls within each chlorosome.