Folding and fluorescence enhancement with strong odd-even effect for a series of merocyanine dye oligomers

pH-dependent complex formation with TAR RNA and DNA: application towards logic gates

Nucleic acid-based logic gates have shown great potential in biotechnology, medicine as well as diagnostics. Herein, we have constructed pH-responsive logic devices by utilizing HIV-1 TAR hairpins in combination with a thiazole peptide that exhibits turn-on fluorescence upon interacting with TAR RNA or DNA. Based on this, INHIBIT-AND and YES-INHIBIT-AND logic gates were constructed in parallel. The pH alteration leads to conformational changes of the hairpin structure, enabling the construction of a multi-reset reusable logic system which could be developed for in vitro sensing of the HIV-1 viral RNA.

Breaking Radial Dipole Symmetry in Planar Macrocycles Modulates Edge-to-Edge Packing and Disrupts Cofacial Stacking

Dipolar interactions are ever-present in supramolecular architectures, though their impact is typically revealed by making dipoles stronger. While it is also possible to assess the role of dipoles by altering their orientations by using synthetic design, doing so without altering the molecular shape is not straightforward. We have now done this by flipping one triazole unit in a rigid macrocycle, tricarb. The macrocycle is composed of three carbazoles (2 Debye) and three triazoles (5 Debye) defining an array of dipoles aligned radially but organized alternately in and out. These dipoles are believed to dictate edge-to-edge tiling and face-to-face stacking. We modified our synthesis to prepare isosteric macrocycles with the orientation of one triazole dipole rotated 40°. The new dipole orientation guides edge-to-edge contacts to reorder the stability of two surface-bound 2D polymorphs. The impact on dipole-enhanced π stacking, however, was unexpected. Our stacking model identified an unchanged set of short-range (3.4 Å) anti-parallel dipole contacts. Despite this situation, the reduction in self-association was attributed to long-range (~6.4 Å) dipolar repulsions between π-stacked macrocycles. This work highlights our ability to control the build-up and symmetry of macrocyclic skeletons by synthetic design, and the work needed to further our understanding of how dipoles control self-assembly.

Frustrated π-stacking

The properties of functional materials based on organic π-conjugated systems are governed extensively by intermolecular interactions between π-molecules. To establish clear relationships between supramolecular structures and functional properties, it is essential to attain structurally well-defined π-stacks, particularly in solution, as this enables the collection of valuable spectroscopic data. However, precise control and fine-tuning of π-stacks pose significant challenges due to the weak and bidirectional nature of π-π stacking interactions. This article introduces the concept of "frustrated π-stacking," strategically balancing attractive (π-π interaction) and repulsive (steric hindrance) forces in self-assembly to exert control over the sizes, sequences of π-stacks, and slip-stacked structures. These research efforts contribute to a deeper understanding of the correlation between π-stacks and their properties, thereby providing useful insights for the development of molecular materials with the desired performance.

Squaraine Appended with Benzodipyrrole for Fluorescent Sensing of Methanol: Exciton Coupling Controls Photophysical Properties

The photophysical properties of dyes composed of two squaraine chromophores fused with a benzodipyrrole central moiety (BS1 and BS2), were investigated using steady-state absorption, fluorescence, and transient absorption spectroscopy. The dyes exhibit solvent-independent split electronic absorption due to exciton-coupling. Interestingly significant solvent-dependent fluorescence properties were observed. In toluene, they emit from the lowest excited state, while in methanol, they show weak emission in the higher energy region. In the low-temperature glass matrix, emission from the lowest excited state dominates similarly to that in toluene. The transient absorption spectra exhibit similar ground-state bleaching in toluene and methanol, revealing the formation of delocalized excited states by exciton coupling independent of solvent. However, the excited state deactivates rapidly in ultrafast time scale in methanol, likely due to solvent interaction, leading to rapid non-radiative deactivation. The PEG film doped with the exciton-coupled bis-squaraine shows a distinct fluorescence response to methanol vapor.

Controlling aromatic helix dimerization in water by tuning charge repulsions

Several helically folded aromatic oligoamides were designed and synthesized. The sequences were all water-soluble thanks to the charged side chains borne by the monomers. Replacing a few, sometimes only two, charged side chains by neutral methoxy groups was shown to trigger the formation of various aggregates which could be tentatively assigned to head-to-head stacked dimers of single helices, double helical duplexes and a quadruplex, none of which would form in organic solvent with organic-soluble analogues. The nature of the aggregates was supported by concentration and solvent dependent NMR studies, 1H DOSY experiments, mass spectrometry, and X-ray crystallography or energy-minimized models, as well as analogies with earlier studies. The hydrophobic effect appears to be the main driving force for aggregation but it can be finely modulated by the presence or absence of a small number of charges to an extent that had no precedent in aromatic foldamer architectures. These results will serve as a benchmark for future foldamer design in water.

A Flexible Bivalent Approach to Comprehensively Improve the Performances of Stilbazolium Dyes as Amyloid-β Fluorescent Probes

Exploring new ways to reconstruct the structure and function of inappropriate organic fluorophores for improving amyloid-β (Aβ) fluorescent imaging performance is desired for precise detection and early diagnosis of Alzheimer's disease (AD). With stilbazolium dyes as examples, here, we present a multipronged approach to comprehensively improved the Aβ fluorescent imaging performance through a flexible bivalent method, where a flexible carbon chain was introduced to link two monomers to form a homodimer. Our results reveal a mechanism wherein the flexible linker creates a well-defined probe with specific orientations and distinct photophysical properties. Applying this approach in combination with theoretical simulation, the homodimers exhibited a comprehensive improvement of the Aβ fluorescent imaging performance of the dye monomers, including better photostability and higher signal-to-noise (S/N) ratio, higher "off-on" near-infrared fluorescence (NIRF) response sensitivity, higher specificity and affinity to Aβ deposits, and more reasonable lipophilicity for blood-brain barrier (BBB) penetrability. The results demonstrate that flexible homodimers offer a multipronged approach to obtaining high-performance NIRF imaging reagents for the detection of Aβ deposits both in vitro and in vivo.

Peptide Backbone Directed Self‐Assembly of Merocyanine Oligomers into Duplex Structures

The pseudopeptide backbone provided by N‐(2‐aminoethyl)‐glycine oligomers with attached nucleobases has been widely utilized in peptide nucleic acids (PNAs) as DNA mimics. Here we demonstrate the suitability of this backbone for the formation of structurally defined dye stacks. Toward this goal a series of peptide merocyanine (PMC) dye oligomers connected to a N‐(2‐aminoethyl)‐glycine backbone were prepared through peptide synthesis. Our concentration‐, temperature‐ and solvent‐dependent UV/Vis absorption studies show that under the control of dipole–dipole interactions, smaller‐sized oligomers consisting of one, two or three dyes self‐assemble into defined duplex structures containing two up to six chromophores. In contrast, upon further extension of the oligomer, the chosen peptide backbone cannot direct the formation of a defined duplex architecture anymore due to intramolecular aggregation between the dyes. For all aggregate species a moderate aggregation‐induced emission enhancement is observed.

Alkyl-Engineered Dual-State Luminogens with Pronounced Odd-Even Effects: Quantum Yields with up to 48% Difference and Crystallochromy with up to 22 nm Difference

Alkyl chain-resulted odd-even effects in fluorescence quantum yield (FLQY) have also been reported in organic luminescent materials (OLMs). However, the odd-even effects in FLQY caused by the alkyl substitutes in OLMs are generally very weak, with only single-digit differences. Here, we report a series of alkyl-substituted dual-state luminogens (DSEgens) showing extremely high solid-state FLQY in even-numbered analogues (>90% FLQY) and a dramatically pronounced odd-even effect in FLQY. The odd-even effect in FLQY is over 26% alternation, and a maximum of 48% difference in FLQY was observed between the compounds C1 and C2 with a methyl and ethyl substitution, respectively. C1 and C2 also displayed a crystallochromy with a 22 nm difference in emission wavelength. In addition, odd-even effects in the melting point and decomposition temperature were also observed. With these bright DSEgens, applications such as specific recognition of picric acid and ultrasensitive trace water detection have been demonstrated.

Crystallization-Driven Controlled Two-Dimensional (2D) Assemblies from Chromophore-Appended Poly(L-lactide)s: Highly Efficient Energy Transfer on a 2D Surface

A rational approach towards precision two-dimensional (2D) assemblies by crystallization-driven self-assembly (CDSA) of poly(L-lactides) (PLLAs), end-capped with dipolar dyes like merocyanine (MC) or naphthalene monoimide (NMI) and hydrophobic pyrene (PY) or benzene (Bn) is described. PLLA chains crystallize into diamond-shaped platelets in isopropanol, which forces the terminal dyes to assemble into a 2D array on the platelet surface by either dipolar interactions or π-stacking and exhibit tunable emission. Dipolar dyes play a critical role in imparting colloidal stability and structural uniformity to the 2D crystals, which is partly compromised for hydrophobic ones. Co-crystallization between NMI- and PY-labeled PLLAs yields similar diamond-shaped co-platelets with highly efficient (≈80 %) Förster Resonance Energy Transfer on the 2D surface. Further, the "living" CDSA method confers enlarged, segmented block co-platelets using one of the homopolymers as "seed" and the other as "unimer".

Fluorescent supramolecular polymers of barbiturate dyes with thiophene-cored twisted π-systems

Because supramolecular polymerization of emissive π-conjugated molecules depends strongly on π-π stacking interaction, the formation of well-defined one-dimensional nanostructures often results in a decrease or only a small increase of emission efficiency. This is also true for our barbiturate-based supramolecular polymers wherein hydrogen-bonded rosettes of barbiturates stack quasi-one-dimensionally through π-π stacking interaction. Herein we report supramolecular polymerization-induced emission of two regioisomeric 2,3-diphenylthiophene derivatives functionalized with barbituric acid and tri(dodecyloxy)benzyl wedge units. In CHCl3, both compounds are molecularly dissolved and accordingly poorly emissive due to a torsion-induced non-radiative decay. In methylcyclohexane-rich conditions, these barbiturates self-assemble to form crystalline nanofibers and exhibit strongly enhanced emission through supramolecular polymerization driven by hydrogen-bonding. Our structural analysis suggests that the barbiturates form a tape-like hydrogen-bonding motif, which is rationalized by considering that the twisted geometries of 2,3-diphenylthiophene cores prevend the competing rosettes from stacking into columnar supramolecular polymers. We also found that a small difference in the molecular polarity originating from the substitutional position of the thiophene core influences interchain association of the supramolecular polymers, affording different luminescent soft materials, gel and nanosheet.

Programmed Macromolecular Assembly by Dipole-Dipole Interactions with Aggregation-Induced Enhanced Emission in Aqueous Medium

Self-assembling polymers by bioinspired directional supramolecular interactions currently hold great scientific and technological interests. Herein, we report an unorthodox strategy based on a dipole-dipole interaction-mediated extended antiparallel dipolar assembly of a model merocyanine (MC) dye for maneuvering the self-assembly of a highly water-soluble MC-functionalized block copolymer (P2). Unlike traditional amphiphilic block copolymers featuring distinct hydrophobic segments (flexible aliphatic hydrocarbon chains or rigid nonpolar aromatic scaffolds), P2 comprises polyethylene glycol monomethyl ether (PEG) as a hydrophilic block and an unconventional structure-directing acrylate block functionalized with polar MC-dyes in the side chains of every repeat unit. In the absence of any additional hydrophobic assistance, P2 spontaneously self-assembles in water through the continuous opposite alignment of its pendant MCs by multiple dipole-dipole interactions to cancel out their ground state dipole moments, which initially generates an H-aggregated species with ill-defined morphology (Aggregate 1). Upon thermal annealing, Aggregate 1 reorganizes into higher-order core-shell nanodisc-like structures (Aggregate 2) driven by the orthogonal π-stacking interactions of the rigid aromatic framework derived from the extended cofacial MC-stacks. The aromatic interiors of the nanodiscs gain colloidal stability from the externally decorated hydrophilic PEG chains. While the initially formed Aggregate 1, predominantly by dipole-dipole interactions, showed remarkable thermal stability due to the cooperative effect of the polymer chain, the hierarchical assembly guided by relatively weaker dispersion forces of the MC-stacked π-surfaces could be tailored by dilution or thermal treatment. Such organized packing of pendant MCs by the dual effect of dipole-dipole interactions and π-stacking conferred several exciting properties to the P2 assembly in water. Long-range ordered antiparallel stacking of the pendant MCs rendered outstanding aggregation-induced enhanced emission (AIEE) properties to the resultant nanostructures in water with increased fluorescence lifetime, quantum yield, and Stokes shift compared to nonaggregating P2 in CHCl₃. The remarkable thermal and kinetic stability of the nanodiscs, their guest loading ability, and very low critical aggregation concentration (CAC) were demonstrated by Förster resonance energy transfer (FRET) studies with an encapsulated donor-acceptor dye pair.

Tuning exciton coupling of merocyanine nucleoside dimers by RNA, DNA and GNA double helix conformations

Exciton coupling between two or more chromophores in a specific environment is a key mechanism associated with color tuning and modulation of absorption energies. This concept is well exemplified by natural photosynthetic proteins, and can also be achieved in synthetic nucleic acid nanostructures. Here we report the coupling of barbituric acid merocyanine (BAM) nucleoside analogues and show that exciton coupling can be tuned by the double helix conformation. BAM is a nucleobase mimic that was incorporated in the phosphodiester backbone of RNA, DNA and GNA oligonucleotides. Duplexes with different backbone constitutions and geometries afforded different mutual dye arrangements, leading to distinct optical signatures due to competing modes of chromophore organization via electrostatic, dipolar, π–π‐stacking and hydrogen‐bonding interactions. The realized supramolecular motifs include hydrogen‐bonded BAM–adenine base pairs and antiparallel as well as rotationally stacked BAM dimer aggregates with distinct absorption, CD and fluorescence properties.

Folding-induced Fluorescence Enhancement in a Series of Merocyanine Hetero-Folda-Trimers

Many dyes suffer from fast non-radiative decay pathways, thereby showing only short-lived excited states and weak photoluminescence. Here we show a pronounced fluorescence enhancement for a weakly fluorescent merocyanine (MC) dye by being co-facially stacked to other dyes in hetero-folda-trimer architectures. By means of fluorescence spectroscopy (lifetime, quantum yield) the fluorescence enhancement was explained by the rigidification of the emitting chromophore in the defined foldamer architecture and the presence of a non-forbidden lowest exciton state in H-coupled hetero-aggregates. This folding-induced fluorescence enhancement (FIFE) for specific sequences of π-stacked dyes points at a viable strategy toward improved fluorophores that relates to the approach used by nature in the green fluorescent protein (GFP).