PyFREC: Software for Förster electronic coupling evaluation in molecular fragments

Electronic couplings are crucial for understanding exciton dynamics and associated energy transfer in artificial and natural chromophores. The proposed PyFREC (Python FRagment Electronic Coupling) software enables evaluation of electronic couplings based on the Förster model. PyFREC features the decomposition of electronic couplings, obtained through quantum chemical calculations, into the orientation and dipole strength components. Furthermore, the variation method to evaluate energies of coupled electronic excited states and delocalization of electronic excitations is implemented in the software. PyFREC has been tested on the S22 benchmark dataset of non‐covalent complexes and water clusters. © 2016 Wiley Periodicals, Inc.     

Verification and Biophysical Characterization of a New Three‐Color Förster Resonance‐Energy‐Transfer (FRET) System in DNA

We report on a new three‐color FRET system consisting of three fluorescent dyes, i.e., of a carbostyril (=quinolin‐2(1H)‐one)‐derived donor D, a (bathophenanthroline)ruthenium complex as a relay chromophore A₁, and a Cy dye as A₂ (FRET=Förster resonance‐energy‐transfer) (cf. Fig. 1). With their widely matching spectroscopic properties (cf. Fig. 2), the combination of these dyes yielded excellent FRET efficiencies. Furthermore, fluorescence lifetime measurements revealed that the long fluorescence lifetime of the Ru complex was transferred to the Cy dye offering the possibility to measure the whole system in a time‐resolved mode. The FRET system was established on double‐stranded DNA (cf. Fig. 3) but it should also be generally applicable to other biomolecules.     

In‐capillary probing of quantum dots and fluorescent protein self‐assembly and displacement using Förster resonance energy transfer

Herein, a Förster resonance energy transfer system was designed, which consisted of CdSe/ZnS quantum dots donor and mCherry fluorescent protein acceptor. The quantum dots and the mCherry proteins were conjugated to permit Förster resonance energy transfer. Capillary electrophoresis with fluorescence detection was used for the analyses for the described system. The quantum dots and mCherry were sequentially injected into the capillary, while the real‐time fluorescence signal of donor and acceptor was simultaneously monitored by two channels with fixed wavelength detectors. An effective separation of complexes from free donor and acceptor was achieved. Results showed quantum dots and hexahistidine tagged mCherry had high affinity and the assembly was affected by His₆‐mCherry/quantum dot molar ratio. The kinetics of the self‐assembly was calculated using the Hill equation. The microscopic dissociation constant values for out of‐ and in‐capillary assays were 10.49 and 23.39 μM, respectively. The capillary electrophoresis with fluorescence detection that monitored ligands competition assay further delineated the different binding capacities of histidine containing peptide ligands for binding sites on quantum dots. This work demonstrated a novel approach for the improvement of Förster resonance energy transfer for higher efficiency, increased sensitivity, intuitionistic observation, and low sample requirements of the in‐capillary probing system.     

Clarifying and illustrating the electronic energy transfer pathways in trimeric and hexameric aggregation state of cyanobacteria allophycocyanin within the framework of Förster theory

Within the framework of the Förster theory, the electronic excitation energy transfer pathways in the cyanobacteria allophycocyanin (APC) trimer and hexamer were studied. The associated physical quantities (i.e., excitation energy, oscillator strength, and transition dipole moments) of the phycocyanobilins (PCBs) located in APC were calculated at time‐dependent density functional theory (TDDFT) level of theory. To estimate the influence of protein environment on the preceding calculated physical quantities, the long‐range interactions were approximately considered with the polarizable continuum model at the TDDFT level of theory, and the short‐range interaction caused by surrounding aspartate residue of PCBs were taken into account as well. The shortest energy transfer time calculated in the framework of the Förster model at TDDFT/B3LYP/6–31+G* level of theory are about 0.10 ps in the APC trimer and about 170 ps in the APC monomer, which are in qualitative agreement with the experimental finding that a very fast lifetime of 0.43–0.44 ps in APC trimers, whereas its monomers lacked any corresponding lifetime. These results suggest that the lifetime of 0.43–0.44 ps in the APC trimers determined by Sharkov et al. was most likely attributed to the energy transfer of α¹‐84 ? β³‐84 (0.23 ps), β¹‐84 ? α²‐84 (0.11 ps) or β²‐84 ? α³‐84 (0.10 ps). So far, no experimental or theoretical energy transfer rates between two APC trimmers were reported, our calculations predict that the predominate energy transfer pathway between APC trimers is likely to occur from α³‐84 in one trimer to α⁵‐84 in an adjacent trimer with a rate of 32.51 ps. © 2014 Wiley Periodicals, Inc.     

Förster Resonance Energy Transfer Investigations Using Quantum‐Dot Fluorophores

F?rster resonance energy transfer (FRET), which involves the nonradiative transfer of excitation energy from an excited donor fluorophore to a proximal ground-state acceptor fluorophore, is a well-characterized photophysical tool. It is very sensitive to nanometer-scale changes in donor-acceptor separation distance and their relative dipole orientations. It has found a wide range of applications in analytical chemistry, protein conformation studies, and biological assays. Luminescent semiconductor nanocrystals (quantum dots, QDs) are inorganic fluorophores with unique optical and spectroscopic properties that could enhance FRET as an analytical tool, due to broad excitation spectra and tunable narrow and symmetric photoemission. Recently, there have been several FRET investigations using luminescent QDs that focused on addressing basic fundamental questions, as well as developing targeted applications with potential use in biology, including sensor design and protein conformation studies. Herein, we provide a critical review of those developments. We discuss some of the basic aspects of FRET applied to QDs as both donors and acceptors, and highlight some of the advantages offered (and limitations encountered) by QDs as energy donors and acceptors compared to conventional dyes. We also review the recent developments made in using QD bioreceptor conjugates to design FRET-based assays.     

Capillary electrophoresis,a method for the determination of nucleic acid ligands covalently attached to quantum dots representing a donor of Förster resonance energy transfer

The synthesis and determination of the structure of a Förster resonance energy transfer probe intended for the detection of specific nucleic acid sequences are described here. The probe is based on the hybridization of oligonucleotide modified quantum dots with a fluorescently labeled nucleic acid sample resulting in changes of the fluorescence emission due to the energy transfer effect. The stoichiometry distribution of oligonucleotides conjugated to quantum dots was determined by capillary electrophoresis separation. The results indicate that one to four molecules of oligonucleotide are conjugated to the surface of a single nanoparticle. This conclusion is confirmed by the course of the dependence of Förster resonance energy transfer efficiency on the concentration of fluorescently labeled complementary single‐stranded nucleic acid, showing saturation. While the energy transfer efficiency of the probe hybridized with complementary nucleic acid strands was 30%, negligible efficiency was observed with a noncomplementary strand.     

Two‐Photon Photochromism of a Diarylethene Enhanced by Förster Resonance Energy Transfer from Two‐Photon Absorbing Fluorenes

Resonance energy transfer from two-photon absorbing fluorene derivatives to the photochromic compound 3,4-bis-(2,4,5-trimethyl-thiophen-3-yl)furan-2,5-dione (PC 1) is investigated in hexane under one- and two-photon excitation. The quenching of the steady-state fluorescence of donor molecules in the presence of the diarylethene acceptor is used to study the nature of resonance energy transfer. The F?rster distances and critical acceptor concentrations are determined for nonbound donor-acceptor pairs in homogeneous molecular ensembles. Quite significantly, up to a two-fold enhancement in the velocity of the photochromic transformation of 1, in the presence of two-photon absorbing fluorene derivatives, is demonstrated.     

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.     

Enhancement of Förster Energy Transfer within a Microspherical Cavity

Energy transfer from pyrene to perylene molecules co-doped within a poly(methyl methacrylate) latex microsphere was drastically accelerated relative to free space. Fluorescence spectra of the microspheres showed that the relative emission intensities of pyrene and perylene changed with the sphere diameter. Analyses of emission decay profiles clarified that F?rster-type energy-transfer processes were induced and that the transfer rates increased within the microspherical cavity. This enhancement can be ascribed not only to the quantum electrodynamic effects on the pyrene emission rate, but also the cavity effect of increasing the overlapping factor between donor emission and acceptor absorption spectra.     

Metal Linkage Effects on Ultrafast Energy Transfer

We report the preparation of several new porphyrin homodimers bridged by a platinum(II) ion in which very intense electronic communication through the coordination link occurs. Moreover, the synthesis of a new porphyrin dyad and its photophysical properties are reported. This dyad exhibits the fastest singlet energy transfer ever reported for synthetic systems between a zinc(II) porphyrin and a porphyrin free base. This extremely fast transfer (～100 femtoseconds) is in the same range as the fastest one measured in natural systems. This feature is due to the platinum(II) linker, which allows for strong MO couplings between the two porphyrin units as experimentally supported by electrochemistry and corroborated by DFT computations.     

Synthesis of Site‐Specific Dye‐Labeled Polymer via Atom Transfer Radical Polymerization (ATRP) for Quantitative Characterization of the Well‐Defined Interchain Distance

Novel difunctional initiators that incorporate Förster/fluorescence resonance energy transfer (FRET) pairs are generated to carry out atom transfer radical polymerization of styrene, methyl methacrylate, and n‐butyl methacrylate monomers by an efficient manner. Based on the chemical structures of the initiators, the locations of the fluorophore moiety are dictated to be in the center of the chain with accurately quantified chain functionality (>90% labeling ratio). The site‐specific integration of FRET dyes into separate polymer chain centers allows for characterization of the well‐defined interchain distance quantitatively based on the response between these fluorescent probes. The reliability of this technique is verified in bulk state, which is in well agreement with the theoretical ones. This well‐defined FRET system is expected to be a promising candidate to provide a distinct physical image at a microscopic level regarding scaling chain dimension, chain interpenetration, and polymer compatibility.

     

Light‐Harvesting Nanoparticle Probes for FRET‐Based Detection of Oligonucleotides with Single‐Molecule Sensitivity

Controlling the emission of bright luminescent nanoparticles by a single molecular recognition event remains a challenge in the design of ultrasensitive probes for biomolecules. Herein, we developed 20‐nm light‐harvesting nanoantenna particles, built of a tailor‐made hydrophobic charged polymer poly(ethyl methacrylate‐co‐methacrylic acid), encapsulating circa 1000 strongly coupled and highly emissive rhodamine dyes with their bulky counterion. Being 87‐fold brighter than quantum dots QDots 605 in single‐particle microscopy (with 550‐nm excitation), these DNA‐functionalized nanoparticles exhibit over 50 % total FRET efficiency to a single hybridized FRET acceptor, a highly photostable dye (ATTO665), leading to circa 250‐fold signal amplification. The obtained FRET nanoprobes enable single‐molecule detection of short DNA and RNA sequences, encoding a cancer marker (survivin), and imaging single hybridization events by an epi‐fluorescence microscope with ultralow excitation irradiance close to that of ambient sunlight.     

Light‐Harvesting Hybrid Assemblies

Light‐harvesting hybrids have gained much importance as they are considered as potential mimics for photosynthetic systems. In this Concept article we introduce the design concepts involved in the building up of light‐harvesting hybrids; these resemble the well‐studied organic‐based assemblies for energy transfer. We have structured this article into three parts based on the strategies adopted in the synthesis of hybrid assemblies, as covalent, semicovalent, and noncovalent procedures. Furthermore, the properties and structural features of the hybrids and analogous organic assemblies are compared. We also emphasize the challenges involved in the processability of these hybrid materials for device applications and present our views and results to address this issue through the design of soft‐hybrids by a solution‐state, noncovalent, self‐assembly process.     

Rod‐Like Nano‐Light Harvester

Imitating the natural “energy cascade” architecture, we present a single‐molecular rod‐like nano‐light harvester (NLH) based on a cylindrical polymer brush. Block copolymer side chains carrying (9,9‐diethylfluoren‐2‐yl)methyl methacrylate units as light absorbing antennae (energy donors) are tethered to a linear polymer backbone containing 9‐anthracenemethyl methacrylate units as emitting groups (energy acceptors). These NLHs exhibit very efficient energy absorption and transfer. Moreover, we manipulate the energy transfer by tuning the donor–acceptor distance.

     

Selective Detection of Hg2+ Ions with Boron Dipyrromethene‐Based Fluorescent Probes Appended with a Bis(1,2,3‐triazole)amino Receptor

By using a copper‐promoted alkyne–azide cycloaddition reaction, two boron dipyrromethene (BODIPY) derivatives bearing a bis(1,2,3‐triazole)amino receptor at the meso position were prepared and characterized. For the analogue with two terminal triethylene glycol chains, the fluorescence emission at 509 nm responded selectively toward Hg²⁺ ions, which greatly increased the fluorescence quantum yield from 0.003 to 0.25 as a result of inhibition of the photoinduced electron transfer (PET) process. By introducing two additional rhodamine moieties at the termini, the resulting conjugate could also detect Hg²⁺ ions in a highly selective manner. Upon excitation at the BODIPY core, the fluorescence emission of rhodamine at 580 nm was observed and the intensity increased substantially upon addition of Hg²⁺ ions due to inhibition of the PET process followed by highly efficient fluorescence resonance energy transfer (FRET) from the BODIPY core to the rhodamine moieties. The Hg²⁺‐responsive fluorescence change of these two probes could be easily seen with the naked eye. The binding stoichiometry between the probes and Hg²⁺ ions in CH₃CN was determined to be 1:2 by Job′s plot analysis and ¹H NMR titration, and the binding constants were found to be (1.2±0.1)×10¹¹ m ^?2 and (1.3±0.3)×10¹⁰ m ^?2, respectively. The overall results suggest that these two BODIPY derivatives can serve as highly selective fluorescent probes for Hg²⁺ ions. The rhodamine derivative makes use of a combined PET‐FRET sensing mechanism which can greatly increase the sensitivity of detection.     

Cooperative Veratryle and Nitroindoline Cages for Two‐Photon Uncaging in the NIR

Tandem uncaging systems in which a two‐photon absorbing module and a cage moiety, linked via a phosphorous clip, that act together by Förster resonance energy transfer (FRET) have been developed. A library of these compounds, using different linkers and cages (7‐nitroindolinyl or nitroveratryl) has been synthesized. The investigation of their uncaging and two‐photon absorption properties demonstrates the scope and versatility of the engineering strategy towards efficient two‐photon cages and reveals surprising cooperative and topological effects. The interactions between the 2PA module and the caging moiety are found to promote cooperative effects on the 2PA response while additional processes that enhance the uncaging efficiency are operative in well‐oriented nitroindoline‐derived dyads. These synergic effects combine to lead to record two‐photon uncaging cross‐section values (i.e., up to 20 GM) for uncaging of carboxylic acids.