Understanding the electronic energy transfer pathways in the trimeric and hexameric aggregation state of cyanobacteria phycocyanin within the framework of Förster theory

In the present study, the electronic energy transfer pathways in trimeric and hexameric aggregation state of cyanobacteria C‐phycocyanin (C‐PC) were investigated in term of the Förster theory. The corresponding excited states and transition dipole moments of phycocyanobilins (PCBs) located into C‐PC were examined by model chemistry in gas phase at time‐dependent density functional theory (TDDFT), configuration interaction‐singles (CIS), and Zerner's intermediate neglect of differential overlap (ZINDO) levels, respectively. Then, the long‐range pigment‐protein interactions were approximately taken into account by using polarizable continuum model (PCM) at TDDFT level to estimate the influence of protein environment on the preceding calculated physical quantities. The influence of the short‐range interaction caused by aspartate residue nearby PCBs was examined as well. Only when the protonation of PCBs and its long‐ and short‐range interactions were properly taken into account, the calculated energy transfer rates (1/K) in the framework of Förster model at TDDFT/B3LYP/6‐31+G* level were in good agreement with the experimental results of C‐PC monomer and trimer. Furthermore, the present calculated results suggested that the energy transfer pathway in C‐PC monomer is predominant from β‐155 to β‐84 (1/K = 13.4 ps), however, from α‐84 of one monomer to β‐84 (1/K = 0.3–0.4 ps) in a neighbor monomer in C‐PC trimer. In C‐PC hexamer, an additional energy flow was predicted to be from β‐155 (or α‐84) in top trimer to adjacent β‐155 (or α‐84) (1/K = 0.5–2.7 ps) in bottom trimer. © 2013 Wiley Periodicals, Inc.     

Excitation energy-transfer processes between two trimers in C-phycocyanin hexamer from the cyanobacterium Anabaena variabilis. Investigation by group theory and time-resolved fluorescence spectroscopy

We have employed group theory and picosecond time-resolved fluorescence isotropy and anisotropy spectroscopy methods to explore the excitation transfers within an isolated C-phycocyanin (C-PC) hexamer (αβ)₆^PCL²⁷_RC, situated at the end of the rod proximal to the core of the pycobilisome (PBS) in the cyanobacterium Anabaena variabilis. The group-theory results imply that excitation energy transfer between two trimers occurs between the lowest exciton level of each trimer. The excitation energy-transfer process might occur at a rate of 10–20 ps, and it may be described by an exciton hopping-like Förster transfer mechanism. Dynamic components of 45–50 ps are assigned to the excitation transfer from β₁₅₅-PCB chromophores to the exciton states of dimers, which consist of two neighbouring monomers of the same trimer in an isolated C-PC hexamer.     

Studies of the Energy Transfer among Allophycocyanin from Phycobilisomes of Polysiphonia urceolata by Time-Resolved Fluorescence Isotropic and Anisotropic Spectroscopy

Abstract— The excitation energy transfer processes in the allophycocyanin (APC) monomer and trimer from phycobilisomes of Polysiphonia urceolata were studied using picosecond time-resolved fluorescence isotropic and anisotropic spectroscopy. Based on our experimental results, conclusions could be drawn as follows: (1) After the processes of exciton localization are finished, the localized excitation energy on any chromophore can be transferred to the other chromophores due to the weak couplings between them, and the processes among three p₈₄-phycocyaninbilin (PCB) chromophores in the center of the ring shape of the APC trimer are more important than those of between a₈₄- and p₈₄-PCB chromophores in the same monomer. (2) The decay time constants of 95 ± 5 ps and 40 ± 5 ps components, observed by us in this work, were assigned to the excitation energy transfer or redistribution between α₈₄- and β₈₄-PCB chromophores in the same monomer of the APC trimer and among three β₈₄-PCB chromophores in the center of the ring shape of the APC trimer, respectively. Specifically, the assignment of the decay constants for the 40 ± 5 ps component was different from those of previous results. (3) Based on the model of Debreczeny, and using the fluorescence residual anisotropy r(∞) with a probing wavelength of 650 nm, the angles between the C₃ symmetry axis and transition dipoles of α₈₄- and -PCB chromophores were found to be φ_a84= 67° and φ_β84= 148°, respectively, which are in agreement with the prediction of the X-ray crystal structure of APC. (4) The results show that anisotropy decays, observed with the APC trimer, did exhibit a strongly probing wavelength dependence that did not show up in the monomer.     

Excitation energy transfer mechanism in C-phycocyanin hexamer

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Computer simulation on the energy transfer processes in allophycocyanins

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Azobenzene‐Bridged Porphyrin Nanorings: Syntheses,Structures, and Photophysical Properties

Azobenzene‐bridged β‐to‐β and meso‐to‐meso porphyrin nanorings were successfully synthesized by a palladium‐catalyzed Suzuki–Miyaura coupling reaction in a logical synthesis. The dimeric structure was confirmed by XRD analysis. The azo linkages in di‐ and tetramers are in the all‐trans conformation, whereas in the trimers one azo linkage can be interconverted between cis and trans under external stimulation. When trimeric isomers are heated to 333 K or higher, the azo linkages will be in the all‐trans configurations: the pure all‐trans trimer can be kept in the dark for several months. Fluorescence anisotropy and pump‐power‐dependent decay results revealed excitation energy transfer for azobenzene‐bridged zinc–porphyrin nanorings. The distances between porphyrin units of these azobenzene‐bridged porphyrin arrays are almost the same, but the exciton energy hopping (EEH) times for each wheel are markedly different. The dimer and meso‐to‐meso tetramer possess relatively short excitation energy transfer (EET) times (1.28 and 2.48 ps, respectively) due to their good planarity and rigidity. In contrast, the EET time for the trimeric zinc(II)–porphyrin array (6.9 ps) is relatively long due to its nonradiative decay pathway (i.e., cis/trans isomerization of azobenzene). Both di‐ and tetramers exhibit relatively high fluorescence quantum yields, whereas the trimers show weak emission because of structural differences.     

FLUORESCENCE AND CIRCULAR DICHROISM STUDIES ON THE PHYCOERYTHROCYANINS FROM THE CYANOBACTERIUM

Two phycoerythrocyanin (PEC) fractions have been obtained from the phycobilisomes of the cyanobac-terium Westiellopsis prolifica ARM 365. They have been characterized by absorption, fluorescence and circular dichroism spectroscopy. One of them is spectroscopically similar to a PEC trimer known from other organisms. Whereas efficient energy transfer from its violin (α-84) to the cyanin (β-84, 155) chromophores is efficient in the trimer (αβ it is impeded after dissociation to the monomer (α,β). A second fraction of PEC which we earlier termed PEC(X) (Maruthi Sai et al., Photochem. Photobiol. 55 ,119–124, 1992), exhibited the spectral properties similar to that of the α-subunit of PEC from Mastigocladus laminosus. With this highly photoactive fraction, the circular dichroism spectra of the violobilin chromophore in both photoreversible states were obtained.     

Through‐Space Conjugated Molecular Wire Comprising Three π‐Electron Systems

A [2.2]paracyclophane‐based through‐space conjugated oligomer comprising three π‐electron systems was designed and synthesized. The arrangement of three π‐conjugated systems in an appropriate order according to the energy band gap resulted in efficient unidirectional photoexcited energy transfer by the Förster mechanism. The energy transfer efficiency and rate constants were estimated to be >0.999 and >10¹² s^?1, respectively. The key point for the efficient energy transfer is the orientation of the transition dipole moments. The time‐dependent density functional theory (TD‐DFT) studies revealed the transition dipole moments of each stacked π‐electron system; each dipole moment was located on the long axis of each stacked π‐electron system. This alignment of the dipole moments is favorable for fluorescence resonance energy transfer (FRET).     

Picosecond time resolved energy transfer between rhodamine 6G and malachite green

The process of singlet—singlet resonance energy transfer between rhodamine 6G (donor) and malachite green (acceptor) has been studied with a picosecond laser : streak camera system. Unlike previous investigations, the measurements were conducted in a low viscosity solvent (ethanol) at room temperature. The donor fluorescence decay function was found to be in agreement with that predicted by the Förster theory over a tenfold range of acceptor concentrations (10^?3 M to 10^?2 M) and up to a limiting time resolution of 10 ps. An average R₀ value of 52.5 A was obtained from the fluorescence decay curves, in reasonable agreement with the value of 48 A calculated from spectroscopic data.     

Förster resonance energy transfer in poly(methyl methacrylates) copolymers bearing donor–acceptor 1,3‐thiazole dyes

The Förster resonance energy transfer (FRET) properties in poly(methyl methacrylate) copolymers containing 2‐(pyridine‐2‐yl) thiazole dyes were studied upon systematic variation of the donor‐to‐acceptor ratio. To this end, 2‐(pyridine‐2‐yl) thiazole dyes specially designed for the usage as energy donor and acceptor molecules were incorporated within one polymer chain. Poly(methyl methacrylate) copolymers containing these donor and acceptor dyes were synthesized using the RAFT polymerization method. Copolymers with a molar mass (M_n) of nearly 10,000 g/mol were achieved with dispersity index values (?) under 1.3. The presented copolymers act as a model system for the FRET investigation. Förster resonance energy transfer properties of the copolymers are characterized by steady state as well as time resolved fluorescence spectroscopy. The results indicate that the energy transfer rates and the transfer efficiencies are tunable by variation of the donor‐acceptor‐ratio. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013 , 51, 4765–4773     

Conformational Relaxation of p‐Phenylenevinylene Trimers in Solution Studied by Picosecond Time‐Resolved Fluorescence

Two p‐phenylenevinylene (PV) trimers, containing 3′‐methylbutyloxyl (in MBOPV3) and 2′‐ethylhexyloxyl (in EHOPV3) side chains, are used as model compounds of PV‐based conjugated polymers (PPV) with the purpose of clarifying the origin of fast (picosecond time) components observed in the fluorescence decays of poly[2‐methoxy‐5‐(2′‐ethylhexyloxy)‐p‐phenylenevinylene] (MEH‐PPV). The fluorescence decays of MBOPV3 and EHOPV3 reveal the presence of similar fast components, which are assigned to excited‐state conformational relaxation of the initial population of non‐planar trimer conformers to lower‐energy, more planar conformers. The rate constant of conformational relaxation k_CR is dependent on solvent viscosity and temperature, according to the empirical relationship k_CR=aη_o^?α?exp(?αE_η/RT), where aη_o^?α is the frequency factor, η_o is the pre‐exponential coefficient of viscosity, E_η is the activation energy of viscous flow. The empirical parameter α, relating the solvent microscopic friction involved in the conformational change to the macroscopic solvent friction (α=1), depends on the side chain. The fast component in the fluorescence decays of MEH‐PPV polymers (PPVs), is assigned to resonance energy transfer from short to longer polymer segments. The present results call for revising this assignment/interpretation to account for the occurrence of conformational relaxation, concurrently with energy transfer, in PPVs.     

Conjugated Polyelectrolyte‐Induced Self‐Assembly of Alkynylplatinum(II) 2,6‐Bis(benzimidazol‐2′‐yl)pyridine Complexes

Water‐soluble cationic alkynylplatinum(II) 2,6‐bis(benzimidazol‐2′‐yl)pyridine (bzimpy) complexes have been demonstrated to undergo supramolecular assembly with anionic polyelectrolytes in aqueous buffer solution. Metal–metal‐to‐ligand charge transfer (MMLCT) absorptions and triplet MMLCT (³MMLCT) emissions have been found in UV/Vis absorption and emission spectra of the electrostatic assembly of the complexes with non‐conjugated polyelectrolytes, driven by Pt???Pt and π–π interactions among the complex molecules. Interestingly, the two‐component ensemble formed by [Pt(bzimpy‐Et){C?CC₆H₄(CH₂NMe₃‐4)}]Cl₂ ( 1 ) with para‐linked conjugated polyelectrolyte (CPE), PPE‐SO₃^?, shows significantly different photophysical properties from that of the ensemble formed by 1 with meta‐linked CPE, mPPE‐Ala. The helical conformation of mPPE‐Ala allows the formation of strong mPPE‐Ala– 1 aggregates with Pt???Pt, electrostatic, and π–π interactions, as revealed by the large Stern–Volmer constant at low concentrations of 1 . Together with the reasonably large Förster radius, large HOMO–LUMO gap and high triplet state energy of mPPE‐Ala to minimize both photo‐induced charge transfer (PCT) and Dexter triplet energy back‐transfer (TEBT) quenching of the emission of 1 , efficient Förster resonance energy transfer (FRET) from mPPE‐Ala to aggregated 1 molecules and strong ³MMLCT emission have been found, while the less strong PPE‐SO₃^?– 1 aggregates and probably more efficient PCT and Dexter TEBT quenching would account for the lack of ³MMLCT emission in the PPE‐SO₃^?– 1 ensemble.     

Simultaneous time resolution of the emission spectra of fluorescent proteins and zooxanthellar chlorophyll in reef-building corals

Light is absorbed by photosynthetic algal symbionts (i.e. zooxanthellae) and by chromophoric fluorescent proteins (FP) in reef‐building coral tissue. We used a streak‐camera spectrograph equipped with a pulsed, blue laser diode (50 ps, 405 nm) to simultaneously resolve the fluorescence spectra and kinetics for both the FP and the zooxanthellae. Shallow water (<9 m)–dwelling Acropora spp. and Plesiastrea versipora specimens were collected from Okinawa, Japan, and Sydney, Australia, respectively. The main FP emitted light in the blue, blue‐green and green emission regions with each species exhibiting distinct color morphs and spectra. All corals showed rapidly decaying species and reciprocal rises in greener emission components indicating Förster resonance energy transfer (FRET) between FP populations. The energy transfer modes were around 250 ps, and the main decay modes of the acceptor FP were typically 1900–2800 ps. All zooxanthellae emitted similar spectra and kinetics with peak emission (～683 nm) mainly from photosystem II (PSII) chlorophyll (chl) a. Compared with the FP, the PSII emission exhibited similar rise times but much faster decay times, typically around 640–760 ps. The fluorescence kinetics and excitation versus emission mapping indicated that the FP emission played only a minor role, if any, in chl excitation. We thus suggest the FP could only indirectly act to absorb, screen and scatter light to protect PSII and underlying and surrounding animal tissue from excess visible and UV light. We conclude that our time‐resolved spectral analysis and simulation revealed new FP emission components that would not be easily resolved at steady state because of their relatively rapid decays due to efficient FRET. We believe the methods show promise for future studies of coral bleaching and for potentially identifying FP species for use as genetic markers and FRET partners, like the related green FP from Aequorea spp.     

Polymersomes Prepared from Thermoresponsive Fluorescent Protein–Polymer Bioconjugates: Capture of and Report on Drug and Protein Payloads

Polymersomes provide a good platform for targeted drug delivery and the creation of complex (bio)catalytically active systems for research in synthetic biology. To realize these applications requires both spatial control over the encapsulation components in these polymersomes and a means to report where the components are in the polymersomes. To address these twin challenges, we synthesized the protein–polymer bioconjugate PNIPAM‐b‐amilFP497 composed of thermoresponsive poly(N‐isopropylacrylamide) (PNIPAM) and a green‐fluorescent protein variant (amilFP497). Above 37 °C, this bioconjugate forms polymersomes that can (co‐)encapsulate the fluorescent drug doxorubicin and the fluorescent light‐harvesting protein phycoerythrin 545 (PE545). Using fluorescence lifetime imaging microscopy and Förster resonance energy transfer (FLIM‐FRET), we can distinguish the co‐encapsulated PE545 protein inside the polymersome membrane while doxorubicin is found both in the polymersome core and membrane.     

A combined spectroscopic and theoretical study of a series of conformationally restricted hexapeptides carrying a rigid binaphthyl-nitroxide donor-acceptor pair

The structural features of a series of linear hexapeptides of general formula Boc‐B‐A_r‐T‐A_m‐OtBu, where A is L ‐Ala or Aib (α‐aminoisobutyric acid), B is (R)‐Bin, a binaphthyl‐based C^α,α‐disubstituted Gly residue, T is Toac, a nitroxide spin‐labeled C^α,α‐disubstituted Gly, and r+m=4, were investigated in methanol solution by fluorescence, transient absorption, IR and CD spectroscopic studies, and by molecular mechanics calculations. These peptides are denoted as B‐T/r‐m, to emphasize the different position of Toac with respect to that of the Bin fluorophore in the amino acid sequence. The rigidity of the B‐T donor–acceptor pair and of the Aib‐rich backbone allowed us to investigate the influence of the interchromophoric distance and orientation on the photophysics of the peptides examined. The excited state relaxation processes of binaphthyl were investigated by time‐resolved fluorescence and transient absorption experiments. Dynamic quenching of the excited singlet state of binaphthyl by Toac was successfully interpreted by the Förster energy transfer model, provided that the mutual orientation of the chromophores is taken into account. This implies that interconversion among conformational substates, which involves puckering of the Toac piperidine ring, is slow on the time scale of the transfer process, that is slower than 5 ns. By comparison of the experimental and theoretical data, the type of secondary structure (right‐handed 3₁₀ helix) from the B‐T/r‐m peptides in solution was determined; this would not have been achievable by using the CD and NMR data only, as the data are not diagnostic in this case. Static quenching was observed in all peptides examined but B‐T/1‐3, where the effect can be ascribed to a non‐fluorescent complex. Among the computed low‐energy conformers of these peptides, there is one structure exhibiting a NO ^. –naphthalene center‐to‐center distance <6 Å, which might be assigned to this complex. The overall results emphasize the versatility of fluorescence experiments in 3D‐structural studies in solution.     

Dual Esterase‐ and Steroid‐Responsive Energy Transfer Modulation of Ruthenium(II) and Rhenium(I) Complex Functionalized Gold Nanoparticles

A number of adamantane‐containing ruthenium(II) and rhenium(I) complexes have been synthesized, characterized, and noncovalently functionalized with β‐cyclodextrin‐capped gold nanoparticles (β‐CD–GNPs) through the host–guest interaction between cyclodextrin and adamantane. The resultant nanoconjugates have been characterized by transmission electron microscopy (TEM), energy‐dispersive X‐ray analysis (EDX), and 2D ROESY ¹H NMR experiments. The Förster resonance energy transfer (FRET) properties of the nanoconjugates can be modulated by both esterase‐accelerated hydrolysis and competitive displacement of steroid, by monitoring the emission intensity and luminescence lifetime. The FRET efficiencies are found to vary with the nature of the chromophores and the length of the spacer between the transition metal complexes and the GNPs. This work constitutes a “proof‐of‐principle” assay method for the dual‐functional detection of important classes of biomolecules, such as enzymes and steroids.     

Sequence, structure and energy transfer in DNA

Excitation energy transfer in DNA has similarities to charge transfer, but the transport is of an excited state, not of mass or charge. Use of the fluorescent, modified adenine base 2‐aminopurine (2AP) as an energy trap in short (3‐ to 20‐base) single‐ and double‐stranded DNA oligomers is reviewed. Variation of 2AP’s neighboring sequence shows (1) relatively efficient transfer from adenine compared to that from cytosine and thymine, (2) efficient transfer from guanine, but only when 2AP is at the 3′ end, (3) approximate equality of efficiencies for 3′ to 5′ and 5′ to 3′ directional transfer in adenine tracks. The overall, average transfer distance at room temperature is about four adenine bases or less before de‐excitation. The transfer fluorescence excitation spectral shape is similar to that of the absorption spectrum of the neighboring normal bases, confirming that initial excitation of the normal bases, followed by emission from 2AP (i.e. energy transfer), is occurring. Transfer apparently may take place both along one strand and cross‐strand, depending on the oligomer sequence. Efficiency increases when the temperature is decreased, rising above 50% (overall efficiency) in decamers of adenine below ?60°C (frozen media). Modeling of the efficiencies of transfer from the nearest several adenine neighbors of 2AP in these oligomers suggests that the nearest two neighbors transfer with near 100% efficiency. As bases in B DNA, as well as in single‐stranded DNA, are separated by less than 5 Å (less than the size of a base), standard Förster transfer theory should not apply. Indeed, while both theory and experiment show efficiency decreasing with donor–acceptor distance, the experimental dependence clearly disagrees with Förster 1/r⁶ dependence. It is not yet clear what the best theoretical approach is, but any calculation must deal accurately with the excited states of bases, including strong base–base interactions and structural fluctuations, and should reflect the increase of efficiency with temperature decrease and the relative insensitivity to strandedness (single, double). Attempts to use DNA as a molecular “fiber optic” face three primary challenges. First, reasonable efficiency over more than a base or two occurs only in adenine stretches at temperatures well below freezing. Second, transfer in these adenine tracks is efficient in both directions. Third, absorption of UV light occurs randomly, making excitation at a specific site on this “fiber optic” a challenge.     

Energy transfer kinetics of phycoerythrocyanins (PECs) from the cyanobacteriumAnabaena variabilis (I)

The exritation energy transfer processes in monomeric phycoerythrocyanins (PEC) have been studied in detail using steady-state and time-resolved fluorescence spectra techniques as well as the deconvolution tech-nique of spectra. The results indicate that the energy transfer processes should take place between α₈₄,-PVB and β₈₄- or β₁₅₅-PCB chromophores. the time constants of energy transfer are 34.7 and 130 ps individually; the component with lifetime of 1.57 ns originates from the fluorescence lifetime of the terminal emitter of β₈₄- and /or β₁₅₅ -PCB chro-mophores; and the component with lifetime of 515 ps might be assigned to the energy transfer between two PCB chro-mophores of β subunit. Project supported by the National Natural Science Foundation of China.     

Design and Synthesis of Coumarin–Imidazole Hybrid Chromophores: Solvatochromism,Acidochromism and Nonlinear Optical Properties

A set of linear and asymmetric coumarin–imidazole hybrid compounds having a N,N‐diethylamine at 7‐position and imidazole at 3‐position on the coumarin were synthesized. Insertion of thiophene π‐spacer between coumarin and imidazole moieties (5b, 5d) leads to redshifted absorption and emission compared to 5a and 5c. All the compounds show a noticeable response to trifluoroacetic acid with a redshifted absorption and an increase in emission intensity by twofold. The ratio of ground and excited state acidity constant was calculated using Förster energy cycle, and the ratios were found to be 0.25, 0.96, 0.52 and 1.87, respectively, for 5a‐5d. Due to the thiophene π‐spacer, elongation of π‐conjugation in 5b and 5d leads to high values of polarizability (α), first‐order hyperpolarizability (β) and second‐order hyperpolarizability (γ). Compound 5b exhibits a high value (895 GM) of two‐photon absorption cross section (σ2PA), measured using two‐level model.     

Excitation energy transfer pathways in light‐harvesting proteins: Modeling with PyFREC

Excitation energy transfer (EET) determines the fate of sunlight energy absorbed by light‐harvesting proteins in natural photosynthetic systems and photovoltaic cells. As previously reported (D. Kosenkov, J. Comput. Chem. 2016, 37(19), 1847), PyFREC software enables computation of electronic couplings between organic molecules with a molecular fragmentation approach. The present work reports implementation of direct fragmentation‐based computation of the electronic couplings and EET rates in pigment–protein complexes within the Förster theory in PyFREC. The new feature enables assessment of EET pathways in a wide range of photosynthetic complexes, as well as artificial molecular architectures that include light‐harvesting proteins or tagged fluorescent biomolecules. The developed methodology has been tested analyzing EET in the Fenna–Matthews–Olson (FMO) pigment–protein complex. The pathways of excitation energy transfer in FMO have been identified based on the kinetics studies. © 2017 Wiley Periodicals, Inc.