Near-Infrared Perylenecarboximide Fluorophores for Live-Cell Super-Resolution Imaging.

Organic near-infrared (NIR) photoblinking fluorophores are highly desirable for live-cell super-resolution imaging based on single-molecule localization microscopy (SMLM). Herein we introduce a novel small chromophore, PMIP, through the fusion of perylenecarboximide with 2,2-dimetheylpyrimidine. PMIP exhibits an emission maximum at 732 nm with a high fluorescence quantum yield of 60% in the wavelength range of 700-1000 nm and excellent photoblinking without any additives. With resorcinol-functionalized PMIP (PMIP-OH), NIR SMLM imaging of lysosomes is demonstrated for the first time in living mammalian cells under physiological conditions. Moreover, metabolically labeled nascent DNA is site-specifically detected using azido-functionalized PMIP (PMIP-N3) via click chemistry, thereby enabling the super-resolution imaging of nascent DNA in phosphate-buffered saline with a 9-fold improvement in spatial resolution. These results indicate the potential of PMIP-based NIR blinking fluorophores for biological applications of SMLM.

A Terrylene-Anthraquinone Dyad as a Chromophore for Photothermal Therapy in the NIR-II Window.

A terrylenedicarboximide-anthraquinone dyad, FTQ, with absorption in the second near-infrared region (NIR-II) is obtained as a high-performance chromophore for photothermal therapy (PTT). The synthetic route proceeds by C-N coupling of amino-substituted terrylenedicarboximide (TMI) and 1,4-dichloroanthraquinone followed by alkaline-promoted dehydrocyclization. FTQ with extended π-conjugation exhibits an optical absorption band peaking at 1140 nm and extending into the 1500 nm range. Moreover, as determined by dielectric spectroscopy in dilute solutions, FTQ achieves an ultrastrong dipole moment of 14.4 ± 0.4 Debye due to intense intramolecular charge transfer. After encapsulation in a biodegradable polyethylene glycol (DSPE-mPEG2000), FTQ nanoparticles (NPs) deliver a high photothermal conversion efficiency of 49% under 1064 nm laser irradiation combined with excellent biocompatibility, photostability, and photoacoustic imaging capability. In vitro and in vivo studies reveal the great potential of FTQ NPs in photoacoustic-imaging-guided photothermal therapy for orthotopic liver cancer treatment in the NIR-II window.

2,2'-Bithiophene as sensor tag for ligand-protein binding assays based on Förster resonance energy transfer.

Ligand-protein binding assays based on intrinsic protein fluorescence are straightforward, inexpensive methods to study ligand-protein interactions. However, their applicability is limited to ligands that can interfere with protein emission. In this Note, we describe the applicability of 2,2'-bithiophene as a FRET-based sensor tag, that can be incorporated into high-affinity ligands to generate target-specific compounds able to quench protein fluorescence upon binding. The generated ligands were assessed in different assay designs. Considerations to account for possible sources of interference with the assay readout are addressed, besides interpretation of the obtained results.

High-Performance Near-Infrared Chlorinated Rylenecarboximide Fluorophores via Consecutive C-N and C-C Bond Formation.

A new class of near-infrared (NIR) fluorophores, PAI, is obtained by consecutive C-N/C-C bond formation between diphenylamines and 9,10-dibromoperylenecarboximide. Owing to the rigid structure, extended π-conjugation and pronounced push-pull substitution, these fluorophores show emission maxima up to 804 nm and large Stokes shifts. The extraordinarily high fluorescence quantum yields from 47 % to 70 % are attributed to chloro substitution in the bay positions of the perylene core. These characteristics, together with high photostability, qualify them as useful NIR emitters for applications as biomarkers and security inks.

The Energy Gap Law at Work: Emission Yield and Rate Fluctuations of Single NIR Emitters.

Internal conversion (IC) often is the dominating relaxation pathway in NIR emitters, lowering their fluorescence quantum yield. Here, we investigate dibenzoterrylene (DBT) by bulk and single molecule spectroscopy. With increasing solvent polarity, the S1-S0 energy gap decreases leading to a decrease of the fluorescence quantum yield and an increase of the IC rate in full accordance with the energy gap law. Making use of the unexpectedly strong fluorescence solvatochromism of this aromatic hydrocarbon, the validity of the energy gap law could also be demonstrated at the single molecule level. The S1-S0 energy gap not only controls the fluorescence lifetime and quantum yield of single molecules but also dictates how these quantities develop during spectral fluctuations. Our results open new avenues into unexplored single molecule photophysics and appear as a promising tool for nanoscale probing of dynamic heterogeneities.

Photostable NIR-II Pigments from Extended Rylenecarboximides.

A series of near-infrared (NIR) organic absorbers, named FNs and FPs, have been obtained with absorption maxima from 870 nm to 1100 nm and thus falling into the attractive second near-infrared region (NIR-II). The synthesis of their extended aromatic cores utilized an initial aryl-amination between 4-aminonaphthalene-1,8-dicarboximide (NMI-NH2 ) or 9-aminoperylene-3,4-dicarboximide (PMI-NH2 ) with chloro-substituted 9,10-anthraquinones followed by a novel base-induced cyclodehydrogenation. A NIR-II pigment, compound FPP, was obtained through de-alkylation of a soluble precursor. The synthesis of this photostable pigment is high-yielding and avoids column chromatographic purification which is important for many applications.

Excitation localization in a trimeric perylenediimide macrocycle: Synthesis, theory, and single molecule spectroscopy.

A novel trimeric perylenediimide (PDI) macrocycle was synthesized, and its intramolecular electronic couplings were investigated by bulk and single-molecule optical spectroscopy and by various theoretical approaches. In polarization-resolved excitation spectroscopy at 1.2 K in a PMMA matrix, the appearance and disappearance of the three zero-phonon lines (ZPLs) of an individual trimer by changing the polarization in steps of 60° nicely reflect an approximate triangular geometry of the macrocycle and indicate localized excitations that are transferred by incoherent hopping processes at time scales of around 1 ps as inferred from the ZPL linewidths. The electronic coupling strength deduced from the low temperature data is found to be in good agreement with theoretical estimates. Bulk spectroscopy in toluene at room temperature indicates that the excitations are also localized under these conditions. Theory reveals that the reasons for the localized nature of the excitations at room and low temperatures are different. For a rigid macrocycle, the excitations are predicted to be delocalized, but molecular dynamics simulations point to considerable structural flexibility at ambient temperatures, which counteracts excitation delocalization. At 1.2 K in a PMMA matrix, this effect is too small to lead to localization. Yet, supported by simple model calculations, the disorder in the PMMA host induces sufficient differences between the PDI chromophores, which again result in localized excitations. By addressing crucial aspects of excitation energy transfer, our combined approach provides a detailed and quantitative account of the interchromophore communication in a trimeric macrocycle.

Accidental Contamination of Substrates and Polymer Films by Organic Quantum Emitters.

We report the observation of ubiquitous contamination of dielectric substrates and poly(methyl methacrylate) matrices by organic molecules with optical transitions in the visible spectral range. Contamination sites of individual solvent-related fluorophores in thin films of poly(methyl methacrylate) constitute fluorescence hotspots with quantum emission statistics and quantum yields approaching 30% at cryogenic temperatures. Our findings not only resolve prevalent puzzles in the assignment of spectral features to various nanoemitters on bare dielectric substrates or in polymer matrices but also identify the means for the simple and cost-efficient realization of single-photon sources in the visible spectral range.

Dibenzo[hi,st]ovalene as Highly Luminescent Nanographene: Efficient Synthesis via Photochemical Cyclodehydroiodination, Optoelectronic Properties, and Single-Molecule Spectroscopy.

Dibenzo[hi,st]ovalene (DBOV), as a new nanographene, has demonstrated promising optical properties, such as red emission with a high fluorescence quantum yield of 79% and stimulated emission, as well as high thermal stability and photostability, which indicated its promise as a light-emitting and optical gain material. However, the previous synthetic routes required at least 12 steps. This obstructed access to different derivatives, e.g., to obtain crystals suitable for X-ray diffraction analysis and to tune the optoelectronic properties. Here, we report an efficient synthetic pathway to DBOV based on a sequential iodination-benzannulation of bi(naphthylphenyl)diyne, followed by photochemical cyclodehydroiodination (PCDHI). This protocol included a fused bischrysene as a key intermediate and furnished scalable amounts of meso-substituted DBOV derivatives with different substituents. DBOV with 2,6-dimethylphenyl groups could be used for single-crystal X-ray analysis, revealing the precise structure of the DBOV core. The optoelectronic properties of the DBOV derivatives were investigated by UV-vis absorption and fluorescence spectroscopy, cyclic voltammetry, and density functional theory calculations. Single-molecule spectroscopy at room and low temperatures provided novel insights into the photophysics of DBOV embedded in a polymer film. As a result of weak coupling of the optical transitions to the matrix, single-molecule emission spectra at 4.5 K showed narrow vibronic lines. The fluorescence autocorrelation function covering 9 orders of magnitude in time displayed high contrast photon antibunching and bunching, from which the fluorescence decay rate and the triplet population and depopulation rates could be retrieved. Remarkably, the intersystem crossing rate into the triplet state decreased by more than an order of magnitude at low temperature, demonstrating that temperature can be a crucial parameter to boost single photon emission of an aromatic hydrocarbon.

Alkali Blues: Blue-Emissive Alkali Metal Pyrrolates.

2-Iminopyrroles [HtBu L, 4-tert-butyl phenyl(pyrrol-2-ylmethylene)amine] are non-fluorescent π systems. However, they display blue fluorescence after deprotonation with alkali metal bases in the solid state and in solution at room temperature. In the solid state, the alkali metal 2-imino pyrrolates, M(tBu L), aggregate to dimers, [M(tBu L)(NCR)]2 (M=Li, R=CH3 , CH(CH3 )CNH2 ), or polymers, [M(tBu L)]n (M=Na, K). In solution (solv=CH3 CN, DMSO, THF, and toluene), solvated, uncharged monomeric species M(tBu L)(solv)m with N,N'-chelated alkali metal ions are present. Due to the electron-rich pyrrolate and the electron-poor arylimino moiety, the M(tBu L) chromophore possesses a low-energy intraligand charge-transfer (ILCT) excited state. The chelated alkali cations rigidify the chromophore, restricting intramolecular motions (RIM) by the chelation-enhanced fluorescence (CHEF) effect in solution and, consequently, switch-on a blue fluorescence emission.

Light-harvesting chlorophyll protein (LHCII) drives electron transfer in semiconductor nanocrystals.

Type-II quantum dots (QDs) are capable of light-driven charge separation between their core and the shell structures; however, their light absorption is limited in the longer-wavelength range. Biological light-harvesting complex II (LHCII) efficiently absorbs in the blue and red spectral domains. Therefore, hybrid complexes of these two structures may be promising candidates for photovoltaic applications. Previous measurements had shown that LHCII bound to QD can transfer its excitation energy to the latter, as indicated by the fluorescence emissions of LHCII and QD being quenched and sensitized, respectively. In the presence of methyl viologen (MV), both fluorescence emissions are quenched, indicating an additional electron transfer process from QDs to MV. Transient absorption spectroscopy confirmed this notion and showed that electron transfer from QDs to MV is much faster than fluorescence energy transfer between LHCII and QD. The action spectrum of MV reduction by LHCII-QD complexes reflected the LHCII absorption spectrum, showing that light absorbed by LHCII and transferred to QDs increased the efficiency of MV reduction by QDs. Under continuous illumination, at least 28 turnovers were observed for the MV reduction. Presumably, the holes in QD cores were filled by a reducing agent in the reaction solution or by the dihydrolipoic-acid coating of the QDs. The LHCII-QD construct can be viewed as a simple model of a photosystem with the QD component acting as reaction center.

State transition identification in multivariate time series (STIMTS) applied to rotational jump trajectories from single molecules.

Time resolved data from single molecule experiments often suffer from contamination with noise due to a low signal level. Identifying a proper model to describe the data thus requires an approach with sufficient model parameters without misinterpreting the noise as relevant data. Here, we report on a generalized data evaluation process to extract states with piecewise constant signal level from simultaneously recorded multivariate data, typical for multichannel single molecule experiments. The method employs the minimum description length principle to avoid overfitting the data by using an objective function, which is based on a tradeoff between fitting accuracy and model complexity. We validate our method with synthetic data from Monte Carlo simulations modeling fluorescence resonance energy transfer and rotational jumps, respectively. The method is applied to quantify rotational jump dynamics of single terrylene diimide (TDI) molecules deposited on a solid substrate. Depending on the substitution pattern of the TDI molecules and the chosen substrate materials, we find significant differences in time scale and geometry of molecular reorientation. From an additional application of our state transition identification in multivariate time series approach, a significant correlation between shifts of emission spectra and the occurrence of rotational jumps was found.

Single Semiconductor Nanocrystals under Compressive Stress: Reversible Tuning of the Emission Energy.

The photoluminescence of individual CdSe/CdS/ZnS core/shell nanocrystals has been investigated under external forces. After mutual alignment of a correlative atomic force and confocal microscope, individual particles were colocalized and exposed to a series of force cycles by using the tip of the AFM cantilever as a nanoscale piston. Thus, force-dependent changes of photophysical properties could be tracked on a single particle level. Remarkably, individual nanocrystals either shifted to higher or to lower emission energies with no indications of multiple emission lines under applied force. The direction and magnitude of these reversible spectral shifts depend on the orientation of nanocrystal axes relative to the external anisotropic force. Maximum pressures derived from the applied forces within a simple contact-mechanical model lie in the GPa range, comparable to values typically emerging in diamond anvil cells. Average spectral shift parameters of -3.5 meV/GPa and 3.0 meV/GPa are found for red- and blue-shifting species, respectively. Our results clearly demonstrate that the emission energy of single nanocrystals can be reversibly tuned over an appreciable wavelength range without degradation of their performance which appears as a promising feature with respect to tunable single photon sources or the creation of coherently coupled particle dimers.

Probing the self-assembly and stability of oligohistidine based rod-like micelles by aggregation induced luminescence.

The synthesis and self-assembly of a new C2-symmetric oligohistidine amphiphile equipped with an aggregation induced emission luminophore is reported. We observe the formation of highly stable and ordered rod-like micelles in phosphate buffered saline, with a critical aggregation concentration below 200 nM. Aggregation induced emission of the luminophore confirms the high stability of the anisotropic assemblies in serum.

Dye label interference with RNA modification reveals 5-fluorouridine as non-covalent inhibitor.

The interest in RNA modification enzymes surges due to their involvement in epigenetic phenomena. Here we present a particularly informative approach to investigate the interaction of dye-labeled RNA with modification enzymes. We investigated pseudouridine (Ψ) synthase TruB interacting with an alleged suicide substrate RNA containing 5-fluorouridine (5FU). A longstanding dogma, stipulating formation of a stable covalent complex was challenged by discrepancies between the time scale of complex formation and enzymatic turnover. Instead of classic mutagenesis, we used differentially positioned fluorescent labels to modulate substrate properties in a range of enzymatic conversion between 6% and 99%. Despite this variegation, formation of SDS-stable complexes occurred instantaneously for all 5FU-substrates. Protein binding was investigated by advanced fluorescence spectroscopy allowing unprecedented simultaneous detection of change in fluorescence lifetime, anisotropy decay, as well as emission and excitation maxima. Determination of Kd values showed that introduction of 5FU into the RNA substrate increased protein affinity by 14× at most. Finally, competition experiments demonstrated reversibility of complex formation for 5FU-RNA. Our results lead us to conclude that the hitherto postulated long-term covalent interaction of TruB with 5FU tRNA is based on the interpretation of artifacts. This is likely true for the entire class of pseudouridine synthases.

Comparison of quantum dot-binding protein tags: affinity determination by ultracentrifugation and FRET.

BACKGROUND: Hybrid complexes of proteins and colloidal semiconductor nanocrystals (quantum dots, QDs) are of increasing interest in various fields of biochemistry and biomedicine, for instance for biolabeling or drug transport. The usefulness of protein-QD complexes for such applications is dependent on the binding specificity and strength of the components. Often the binding properties of these components are difficult and time consuming to assess. METHODS: In this work we characterized the interaction between recombinant light harvesting chlorophyll a/b complex (LHCII) and CdTe/CdSe/ZnS QDs by using ultracentrifugation and fluorescence resonance energy transfer (FRET) assay experiments. Ultracentrifugation was employed as a fast method to compare the binding strength between different protein tags and the QDs. Furthermore the LHCII:QD stoichiometry was determined by separating the protein-QD hybrid complexes from unbound LHCII via ultracentrifugation through a sucrose cushion. RESULTS: One trimeric LHCII was found to be bound per QD. Binding constants were evaluated by FRET assays of protein derivatives carrying different affinity tags. A new tetra-cysteine motif interacted more strongly (Ka=4.9±1.9nM(-1)) with the nanoparticles as compared to a hexahistidine tag (His6 tag) (Ka~1nM(-1)). CONCLUSION: Relative binding affinities and binding stoichiometries of hybrid complexes from LHCII and quantum dots were identified via fast ultracentrifugation, and binding constants were determined via FRET assays. GENERAL SIGNIFICANCE: The combination of rapid centrifugation and fluorescence-based titration will be useful to assess the binding strength between different types of nanoparticles and a broad range of proteins.

Single molecule studies of a ladder type conjugated polymer: vibronic spectra, line widths, and energy transfer.

Confocal fluorescence microscopy and spectroscopy are employed to investigate single poly(ladder-type pentaphenylene) (LPPentP) molecules dispersed in thin poly(methyl methacrylate) (PMMA) films at 1.2 K. Emission spectra of single chains show single as well as multi-chromophore emission indicating variegated communication along the chains. The vibronic structure in the emission spectra resembles the one found for other ladder-type polymers. Purely electronic zero-phonon lines in emission are substantially broadened, most probably due to fast spectral diffusion. By surmounting the limitations of emission spectroscopy, nonemitting donor chromophores, which transfer their excitation energy in a radiationless manner to emitting chromophores, are accessed by excitation spectroscopy. Remarkably, by comparing the data of emitting and nonemitting chromophores a contribution to the zero-phonon excitation line width has to be considered which places a lower limit on the estimated energy transfer time of several picoseconds between adjacent chromophores. Finally, the data indicate qualitatively a restricted flexibility of LPPentP compared to poly[2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV).

Energy and charge transfer in nanoscale hybrid materials.

Hybrid materials composed of colloidal semiconductor quantum dots and π-conjugated organic molecules and polymers have attracted continuous interest in recent years, because they may find applications in bio-sensing, photodetection, and photovoltaics. Fundamental processes occurring in these nanohybrids are light absorption and emission as well as energy and/or charge transfer between the components. For future applications it is mandatory to understand, control, and optimize the wide parameter space with respect to chemical assembly and the desired photophysical properties. Accordingly, different approaches to tackle this issue are described here. Simple organic dye molecules (Dye)/quantum dot (QD) conjugates are studied with stationary and time-resolved spectroscopy to address the dynamics of energy and ultra-fast charge transfer. Micellar as well as lamellar nanostructures derived from diblock copolymers are employed to fine-tune the energy transfer efficiency of QD donor/dye acceptor couples. Finally, the transport of charges through organic components coupled to the quantum dot surface is discussed with an emphasis on functional devices.

Energy transfer at the single-molecule level: synthesis of a donor-acceptor dyad from perylene and terrylene diimides.

In 2004, we reported single-pair fluorescence resonance energy transfer (spFRET), based on a perylene diimide (PDI) and terrylene diimide (TDI) dyad (1) that was bridged by a rigid substituted para-terphenyl spacer. Since then, several further single-molecule-level investigations on this specific compound have been performed. Herein, we focus on the synthesis of this dyad and the different approaches that can be employed. An optimized reaction pathway was chosen, considering the solubilities, reactivities, and accessibilities of the building blocks for each individual reaction whilst still using established synthetic techniques, including imidization, Suzuki coupling, and cyclization reactions. The key differentiating consideration in this approach to the synthesis of dyad 1 is the introduction of functional groups in a nonsymmetrical manner onto either the perylene diimide or the terrylene diimide by using imidization reactions. Combined with well-defined purification conditions, this modified approach allows dyad 1 to be obtained in reasonable quantities in good yield.