Dye Aggregation Research Articles

A versatile vessel casting method for fine mapping of vascular networks using a hydrogel-based lipophilic dye solution

Efficient labeling of the vasculature is important for understanding the organization of vascular networks. Here, we propose VALID, a vessel-labeling method that enables visualization of vascular networks with tissue clearing and light-sheet microscopy. VALID transforms traditional lipophilic dye solution into hydrogel by introducing gelatin and restrains the dye aggregation, resulting in complete and uniform vessel-labeling patterns with high signal-to-background ratios. VALID also enhances the compatibility of lipophilic dyes with solvent-based tissue-clearing protocols, which was hard to achieve previously. Using VALID, we combined lipophilic dyes with solvent-based tissue-clearing techniques to perform 3D reconstructions of vasculature within mouse brain and spinal cord. We also employed VALID for 3D visualization and quantification of microvascular damage in a middle cerebral artery occlusion mouse model. VALID should provide a simple, cost-effective vessel-labeling protocol that would significantly widen the applications of lipophilic dyes in research on cerebrovascular complications.

Intramolecular Charge Transfer and Ultrafast Nonradiative Decay in DNA-Tethered Asymmetric Nitro- and Dimethylamino-Substituted Squaraines.

Molecular (dye) aggregates are a materials platform of interest in light harvesting, organic optoelectronics, and nanoscale computing, including quantum information science (QIS). Strong excitonic interactions between dyes are key to their use in QIS; critically, properties of the individual dyes govern the extent of these interactions. In this work, the electronic structure and excited-state dynamics of a series of indolenine-based squaraine dyes incorporating dimethylamino (electron donating) and/or nitro (electron withdrawing) substituents, so-called asymmetric dyes, were characterized. The dyes were covalently tethered to DNA Holliday junctions to suppress aggregation and permit characterization of their monomer photophysics. A combination of density functional theory and steady-state absorption spectroscopy shows that the difference static dipole moment (Δd) successively increases with the addition of these substituents while simultaneously maintaining a large transition dipole moment (μ). Steady-state fluorescence and time-resolved absorption and fluorescence spectroscopies uncover a significant nonradiative decay pathway in the asymmetrically substituted dyes that drastically reduces their excited-state lifetime (τ). This work indicates that Δd can indeed be increased by functionalizing dyes with electron donating and withdrawing substituents and that, in certain classes of dyes such as these asymmetric squaraines, strategies may be needed to ensure long τ, e.g., by rigidifying the π-conjugated network.

Energy Transfer between CdZnS Quantum Dots and Perylene Diimide Dyes

QD–dye systems are promising models for artificial photosynthesis and down-converter systems for LEDs and displays. To better understand the factors controlling energy transfer from the QDs to the dyes, we fabricated a series of CdxZn1–xS/ZnS quantum dot (QD)-perylene diimide (PDI) composite nanocrystals. The core–shell CdxZn1–xS/ZnS QDs were chosen for better control of surface chemistry and for the control of photophysical properties through core composition. The PDIs were designed with bulky substituents to reduce dye–dye aggregation effects. Energy transfer efficiency was found to depend upon both the length of the anchoring alkyl chain and the type of the terminal anchoring group. The maximum energy transfer efficiency of 91% from QDs to PDIs was achieved with composites containing PDIs with carboxylic acid anchoring groups and longer alkyl chains. It was found that composites with carboxylic acid anchors exhibited greater photostability than composites with amine anchors. Longer alkyl chains also led to greater photostability. Conversely, shorter chain alkanes promoted faster aggregation of the nanocrystal composites.

Mixing of Excitons in Nanostructures Based on a Perylene Dye with CdTe Quantum Dots.

Semiconductor quantum dots of the A2B6 group and organic semiconductors have been widely studied and applied in optoelectronics. This study aims to combine CdTe quantum dots and perylene-based dye molecules into advanced nanostructure system targeting to improve their functional properties. In such systems, new electronic states, a mixture of Wannier-Mott excitons with charge-transfer excitons, have appeared at the interface of CdTe quantum dots and the perylene dye. The nature of such new states has been analyzed by absorption and photoluminescence spectroscopy with picosecond time resolution. Furthermore, aggregation of perylene dye on the CdTe has been elucidated, and contribution of Förster resonant energy transfer has been observed between aggregated forms of the dye and CdTe quantum dots in the hybrid CdTe-perylene nanostructures. The studied nanostructures have strongly quenched emission of quantum dots enabling potential application of such systems in dissociative sensing.

New insights into the alkoxy effects on auxiliary adsorption and inhibiting charge recombination in dye-sensitized solar cells with high open circuit voltage: a theoretical investigation.

Although introducing an alkoxy group is one of the most popular methods to suppress the interfacial charge recombination process of dye-sensitized solar cells, understanding of its effects is still limited and a microscopic picture of the alkoxy effects is lacking. Two ullazine dyes with distinct alkoxy chains at the donor part are used to investigate the effects of the alkoxy group on the adsorption, dye aggregation and charge recombination process in our study. Different from the usual assumption, we find that alkoxy chains can not only play a shielding role, but can also assist dye adsorption and inhibit the charge recombination process more effectively by covering the TiO2 surface. We also find that the existence of alkyl chains can well inhibit the aggregation of dyes and reduce intermolecular electron transfer. Furthermore, an important structural feature at the interface, the Ti-O interaction between the oxygen atom of the alkoxy group and the Ti atom of the surface is also found to contribute substantially to the interface stability. New insights into the effects of the alkoxy group on auxiliary adsorption and inhibiting charge recombination through reducing the recombination sites pave the way for rational design of sensitizers with high performance.

Structural and optical variation of pseudoisocyanine aggregates nucleated on DNA substrates

Coherently coupled pseudoisocyanine (PIC) dye aggregates have demonstrated the ability to delocalize electronic excitations and ultimately migrate excitons with much higher efficiency than similar designs where excitations are isolated to individual chromophores. Here, we report initial evidence of a new type of PIC aggregate, formed through heterogeneous nucleation on DNA oligonucleotides, displaying photophysical properties that differ significantly from previously reported aggregates. This new aggregate, which we call the super aggregate (SA) due to the need for elevated dye excess to form it, is clearly differentiated from previously reported aggregates by spectroscopic and biophysical characterization. In emission spectra, the SA exhibits peak narrowing and, in some cases, significant quantum yield variation, indicative of stronger coupling in cyanine dyes. The SA was further characterized with circular dichroism and atomic force microscopy observing unique features depending on the DNA substrate. Then by integrating an AlexaFluorTM 647 (AF) dye as an energy transfer acceptor into the system, we observed mixed energy transfer characteristics using the different DNA. For example, SA formed with a rigid DNA double crossover tile (DX-tile) substrate resulted in AF emission sensitization. While SA formed with more flexible non-DX-tile DNA (i.e. duplex and single strand DNA) resulted in AF emission quenching. These combined characterizations strongly imply that DNA-based PIC aggregate properties can be controlled through simple modifications to the DNA substrate’s sequence and geometry. Ultimately, we aim to inform rational design principles for future device prototyping. For example, one key conclusion of the study is that the high absorbance cross-section and efficient energy transfer observed with rigid substrates made for better photonic antennae, compared to flexible DNA substrates.

Towards control of excitonic coupling in DNA-templated Cy5 aggregates: the principal role of chemical substituent hydrophobicity and steric interactions.

Understanding and controlling exciton coupling in dye aggregates has become a greater focus as potential applications such as coherent exciton devices, nanophotonics, and biosensing have been proposed. DNA nanostructure templates allow for a powerful modular approach. Using DNA Holliday junction (HJ) templates variations of dye combinations and precision dye positions can be rapidly assayed, as well as creating aggregates of dyes that could not be prepared (either due to excess or lack of solubility) through alternative means. Indodicarbocyanines (Cy5) have been studied in coupled systems due to their large transition dipole moment, which contributes to strong coupling. Cy5-R dyes were recently prepared by chemically modifying the 5,5'-substituents of indole rings, resulting in varying dye hydrophobicity/hydrophilicity, steric considerations, and electron-donating/withdrawing character. We utilized Cy5-R dyes to examine the formation and properties of 30 unique DNA templated homodimers. We find that in our system the sterics of Cy5-R dyes play the determining factor in orientation and coupling strength of dimers, with coupling strengths ranging from 50-138 meV. The hydrophobic properties of the Cy5-R modify the percentage of dimers formed, and have a secondary role in determining the packing characteristics of the dimers when sterics are equivalent. Similar to other reports, we find that positioning of the Cy5-R within the HJ template can favor particular dimer interactions, specifically oblique or H-type dimers.

One- and two-photon lasing from a TCF-based AIE dye

The aggregation of a TCF-based dye exhibiting AIE is used to enhance the random lasing emission intensity up to 170 times. The transition from small aggregates to crystals forms a second lasing band and is responsible for 2-photon pumped lasing.

Controlled packing of chiral assembly scaffolds to promote chiral J-aggregation of carbocyanine dyes.

Controlled aggregation of dyes is crucial to achieve their desired optical and electronic properties. Here, we report the induction of chiral J-aggregation of carbocyanine dyes by using lysine-derived amphiphile assemblies as scaffolds in water. The molecular structure of the amphiphiles affected the packing of the assembly. The tight packing with some flexibility promoted the formation of J-aggregates of the dyes with strong chiroptical properties.

Functional supramolecular aggregates based on BODIPY and aza-BODIPY dyes: control over the pathway complexity

The recent advances in the supramolecular assembly of BODIPY and aza-BODIPY dyes are reviewed, emphasizing the control over the kinetic pathway complexity of this class of dyes, and the prospects for future research are summarized.

Pursuing excitonic energy transfer with programmable DNA-based optical breadboards.

DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.

Keeping the chromophores crossed: evidence for null exciton splitting.

Fundamental understanding of the supramolecular assemblies of organic chromophores and the development of design strategies have seen endless ripples of interest owing to their exciting photophysical properties and optoelectronic applications. The independent discovery of dye aggregates by Jelley and Scheibe was the commencement of the remarkable advancement in the field of aggregate photophysics. Subsequent research warranted an exceptional model for defining the exciton interactions in aggregates, proposed by Davydov, Kasha and co-workers, independently, based on the long-range Coulombic coupling. Fascinatingly, the orthogonally cross-stacked molecular transition dipole arrangement was foretold by Kasha to possess null exciton interaction leading to spectroscopically uncoupled molecular assembly, which lacked an experimental signature for decades. There have been several attempts to identify and probe atypical molecular aggregates for decoding their optical behaviour. Herein, we discuss the recent efforts in experimentally verifying the unusual exciton interactions supported with quantum chemical computations, primarily focusing on the less explored null exciton splitting. Exciton engineering can be realized through synthetic modifications that can additionally offer control over the assorted non-covalent interactions for orchestrating precise supramolecular assembly, along with molecular editing. The task of attaining a minimal excitonic coupling through an orthogonally cross-stacked crystalline architecture envisaged to offer a monomer-like optical behaviour was first reported in 1,7-dibromoperylene-3,4,9,10-tetracarboxylic tetrabutylester (PTE-Br2). The attempt to stitch molecules covalently in an orthogonal fashion to possess null excitonic character culminated in a spiro-conjugated perylenediimide dimer exhibiting a monomer-like spectroscopic signature. The computational and experimental efforts to map the emergent properties of the cross-stacked architecture are also discussed here. Using the null aggregates formed by the interference effects between CT-mediated and Coulombic couplings in the molecular array is another strategy for achieving monomer-like spectroscopic properties in molecular assemblies. Moreover, identifying supramolecular assemblies with precise angle-dependent properties can have implications in functional material design, and this review can provide insights into the uncharted realm of null exciton splitting.

Multifaceted Excited State Dynamics of Coumarin Dyes Anchored on Al2O3 Film.

The co-facially stacked dyes on semiconductor films serve as an alternative model to elucidate the photo-driven exciton dynamics occurring in a molecular assembly. In this study, we report the unique emission properties of coumarin dye adsorbed on the surface of the semiconductor film, measured by ultrafast time-resolved fluorescence. When a rigid coumarin derivative, 7-hydroxycoumarin-3-carboxylic acid (OHCCA), is anchored on the Al2O3 film, the dye manifests dual emissions from the two lowest excited states. Various anchoring modes of a carboxylic acid group on the Al2O3 surface are invoked to account for the unusual emission process. Additionally, we identified characteristic transition dipole interactions in the well-stacked dye aggregates, which leads to discernible excitonic splitting in the electronic transitions. Femtosecond time-resolved fluorescence reveals that the excimer formation in the aggregate occurs with the time constant of 550 fs. Picosecond time-resolved emission spectra confirm the subsequent structural relaxations of the nascent excimer. The enhanced transition dipole via the electronic coupling between OHCCA and metal oxide can be responsible for the dual emission and the ultrafast excimer formation.

Emerging Trends of J‐Aggregate Formation within Polymeric Nanoassemblies

AbstractJ‐aggregation of dyes is a unique type of fluorescence aggregation phenomenon exhibiting bathochromic shift and higher absorption coefficient compared to the nonaggregated monomeric form. The incorporation of J‐aggregation dyes with polymeric nanoassemblies endows the former with enhanced microstructural stability and aqueous dispersity, as well as functional integration. Importantly, near‐infrared (NIR) polymeric J‐aggregates have been widely used for in vivo imaging and therapeutic functions. This perspective aims to discuss recent trends of J‐aggregate formation within polymeric nanoassemblies either covalently conjugating or physically encapsulating specific fluorescent dyes. Current challenges and future opportunities are also summarized for the subfield of polymeric J‐aggregates.

Detection of Lysozyme Amyloid Fibrils Using Trimethine Cyanine Dyes: Spectroscopic and Molecular Docking Studies

Due to their unique photophysical and photochemical properties and high sensitivity to the beta-pleated motifs, cyanine dyes have found numerical applications as molecular probes for the identification and characterization of amyloid fibrils in vitro and the visualization of amyloid inclusions in vivo. In the present study the spectroscopic and molecular docking techniques have been employed to evaluate the amyloid sensitivity and the mode of interaction between the trimethine cyanine dyes and native (LzN) and fibrillar (LzF) lysozyme. It was found that the trimethine association with non-fibrilar and fibrillar lysozyme is accompanied by the changes in dye aggregation extent. The molecular docking studies between trimethine dyes and lysozyme in the native and amyloid states indicate that: i) trimethines tend to form the most stable complexes with deep cleft of the native lysozyme; ii) the dye binding with non-fibrillar protein is governed by the hydrophobic interactions, π-stacking contacts between aromatic or cyclopentane ring of the cyanine and Trp in position 63 or 108 and hydrogen bonds between the OH-groups of the trimethines and acceptor atoms of Asp 101 (AK3-7) and Gln 57 (AK3-8) of LzN; iii) cyanine dyes form the energetically most favorable complexes with the groove Gly 2-Leu 4/Ser 8-Trp 10 of the lysozyme fibril core; iv) cyanines-LzF interaction is stabilised by hydrobhobic contacts, π-stacking interaction and hydrogen bonds. The dyes AK3-7, AK3-5 and AK3-11 were selected as the most prospective amyloid probes.

Guest Binding with Sulfated Cyclodextrins: Does the Size of Cavity Matter?

Sulfated cyclodextrins have recently emerged as potential candidates for producing host-induced guest aggregation with properties better than p-sulfonatocalixarenes that have previously shown numerous applications involving the phenomena of host-induced guest aggregation. In the class of sulfated cyclodextrins (SCD), sulfated β-cyclodextrin (β-SCD) remains the most extensively investigated host molecule. Although it is assumed that the host-induced guest aggregation is predominantly an outcome of interaction of the guest molecule with the charges on the exterior of SCD cavity, it has not been deciphered whether the variation in the cavity size will make a difference in the efficiency of host-induced guest-aggregation process. In this investigation, we present a systematic study of host-induced guest aggregation of a cationic molecular rotor dye, Thioflavin T (ThT) with three different sulfated cyclodextrin molecules, α-SCD, β-SCD and γ-SCD, which differ in their cavity size, using steady-state emission, ground-state absorption and time-resolved emission measurements. The obtained photophysical properties of ThT, upon interaction with different SCD molecules, indicate that the binding strength of ThT with different SCD molecules correlate with the cavity size of the host molecule, giving rise to the strongest complexation of ThT with the largest host molecule (γ-SCD). The binding affinity of ThT towards different host molecules has been supported by molecular docking calculations. The results obtained are further supported with the temperature and ionic strength dependent studies performed on the host-guest complex. Our results indicate that for host-induced guest aggregation, involving oppositely charged molecules, the size of the cavity also plays a crucial role beside the charge density on the exterior of host cavity.

Solvent-Dependent Functional Aggregates of Unsymmetrical Squaraine Dyes on TiO2 Surface for Dye-Sensitized Solar Cells.

Alkyl group wrapped donor-acceptor-donor (D-A-D) based unsymmetrical squaraine dyes SQ1, SQ5, and SQS4 were used to evaluate the effect of sensitizing solvents on dye-sensitized solar cell (DSSC) efficiency. A drastic change in DSSC efficiency was observed when the photo-anodes were sensitized in acetonitrile (bad solvent when considering dye solubility) and chloroform (good solvent) with an Iodolyte (I-/I3-) electrolyte. The DSSC device sensitized with squaraine dyes in acetonitrile showed better photovoltaic performance with enhanced photocurrent generation and photovoltage compared to the device sensitized in chloroform. In a good sensitizing solvent, dyes with long hydrophobic alkyl chains are deleterious forming aggregates on the TiO2 surface, which results in an incident photon-to-current conversion efficiency (IPCE) response mostly from monomeric and dimeric structures. Meanwhile, a bad sensitizing solvent facilitates the formation of well-packed self-assembled structures on the TiO2 surface, which are responsible for a broad IPCE response and high device efficiencies. The photoanode sensitized in the bad sensitizing solvent showed enhanced VOC values of 642, 675, and 699 mV; JSC values of 6.38, 11.1, and 11.69 mA/cm2; and DSSC device efficiencies of 3.0, 5.63, and 6.13% for the SQ1, SQ5, and SQS4 dyes in the absence of a coadsorbent (chenodeoxycholic acid (CDCA)), respectively, which were further enhanced by CDCA addition. Meanwhile, the photoanode sensitized in the good sensitizing solvent showed relatively low photovoltaic VOC values of 640, 652, and 650 mV; JSC values of 5.78, 6.79, and 6.24 mA/cm2; and device efficiencies of 2.73, 3.35, and 3.20% for SQ1, SQ5, and SQS4 in the absence of CDCA, respectively, which were further varied with equivalents of CDCA. The best DSSC device efficiencies of 6.13 and 3.20% were obtained for SQS4 without CDCA, where the dye was sensitized in acetonitrile (bad) and chloroform (good) sensitizing solvents, respectively.

Two‐Dimensional Excitonic Networks Directed by DNA Templates as an Efficient Model Light‐Harvesting and Energy Transfer System

AbstractPhotosynthetic organisms organize discrete light‐harvesting complexes into large‐scale networks to facilitate efficient light collection and utilization. Inspired by nature, herein, synthetic DNA templates were used to direct the formation of dye aggregates with a cyanine dye, K21, into discrete branched photonic complexes, and two‐dimensional (2D) excitonic networks. The DNA templates ranged from four‐arm DNA tiles, ≈10 nm in each arm, to 2D wireframe DNA origami nanostructures with different geometries and varying dimensions up to 100×100 nm. These DNA‐templated dye aggregates presented strongly coupled spectral features and delocalized exciton characteristics, enabling efficient photon collection and energy transfer. Compared to the discrete branched photonic systems templated on individual DNA tiles, the interconnected excitonic networks showed approximately a 2‐fold increase in energy transfer efficiency. This bottom‐up assembly strategy paves the way to create 2D excitonic systems with complex geometries and engineered energy pathways.

Two-Dimensional Excitonic Networks Directed by DNA Templates as an Efficient Model Light-Harvesting and Energy Transfer System.

Photosynthetic organisms organize discrete light-harvesting complexes into large-scale networks to facilitate efficient light collection and utilization. Inspired by nature, herein, synthetic DNA templates were used to direct the formation of dye aggregates with a cyanine dye, K21, into discrete branched photonic complexes, and two-dimensional (2D) excitonic networks. The DNA templates ranged from four-arm DNA tiles, ≈10 nm in each arm, to 2D wireframe DNA origami nanostructures with different geometries and varying dimensions up to 100×100 nm. These DNA-templated dye aggregates presented strongly coupled spectral features and delocalized exciton characteristics, enabling efficient photon collection and energy transfer. Compared to the discrete branched photonic systems templated on individual DNA tiles, the interconnected excitonic networks showed approximately a 2-fold increase in energy transfer efficiency. This bottom-up assembly strategy paves the way to create 2D excitonic systems with complex geometries and engineered energy pathways.

Intercalation of Mordant orange 1 into ZnAl-layered double hydroxide and its dual-color photoluminescence emission

This paper reports the preparation of dual-color emitting nanohybrid based on ZnAl-layered double hydroxide (LDH). Mordant orange 1(MO1) was intercalated into the interlayer space of LDH, using the microwave-assisted ion-exchange method. Dye/ZnAl-LDH-MA nanohybrid was characterized by X-ray diffraction pattern (XRD), Fourier transform-infrared spectroscopy (FT-IR), CHN elemental analysis, inductively coupled plasma spectrometry (ICP), thermogravimetric (TGA-DTG) analysis, and field-emission scanning electron microscopy (FE-SEM) method. Based on XRD results, the basal spacing of dye/ZnAl-LDH nanohybrid confirms the bilayer intercalation of MO1 into the interlayer gallery of ZnAl-LDH with good c-orientation. The photonic properties of dye/ZnAl-LDH-MA nanohybrid were investigated by photoluminescence (PL) curves. The PL emission of dye/ZnAl-LDH-MA displays a dual-color photoluminescence emission due to fluorescence resonance energy transfer (FRET). Also, the intensity of PL emission of dye/ZnAl-LDH is higher than that of ZnAl-LDH and MO1 due to a decrease in the dye aggregation after the intercalation process. Therefore, using the microwave-assisted ion-exchange method, an inorganic-organic matrix with two-color emission, and high stability can be designed which can be used in optoelectronic and dual-color optical devices.