Sensing of Double-Stranded DNA/RNA Secondary Structures by Water Soluble Homochiral Perylene Bisimide Dyes

Supramolecular Engineering of Ti3C2Tx MXene -Perylene Diimide Hybrid Electrodes for the Pseudocapacitive Electrochemical Storage of Calcium Ions

The rare combination of metallic conductivity and surface redox activity enables 2D MXenes as versatile charge storage hosts for the design of high-rate electrochemical energy storage devices. However, high charge density metal ions including but not limited to Ca+2 and Mg+2 pose challenges such as sluggish solid-state diffusion and also inhibiting the charge transfer across electrode-electrolyte interfaces. In this work, free-standing hybrid electrode architectures based on 2D titanium carbide-cationic perylene diimide (Ti3C2Tx@cPDI) via supramolecular self-assembly are developed. Secondary bonding interactions such as dipole-dipole and hydrogen bonding between Ti3C2Tx and cPDI are investigated by zeta potential and Fourier-transformed infrared (FTIR) spectroscopy . Ti3C2Tx@cPDI free-standing electrodes show typical volumetric capacitance up to 260 F cm-3 in Mg2+ and Ca2+ aqueous electrolytes at charging times scales from 3 minutes to a few seconds. Three-dimensional (3D) Bode maps are constructed to understand the charge storage dynamics of Ti3C2Tx@cPDI hybrid electrode in an aqueous Ca-ion electrolyte. ,Pseudocapacitance is solely contributed by the nanoscale distribution of redox-active cPDI supramolecular polymers across 2D Ti3C2Tx. This study opens avenues for the design of a wide variety of MXene@redox active organic charge hosts for high-rate pseudocapacitive energy storage devices.

Concepts and principles of self-n-doping in perylene diimide chromophores for applications in biochemistry, energy harvesting, energy storage, and catalysis

Self-doping is an essential method of increasing carrier concentrations in organic electronics that eliminates the need to tailor host-dopant miscibility, a necessary step when employing molecular dopants. Self-n-doping can be accomplished using amines or ammonium counterions as an electron source, which are being incorporated into an ever-increasingly diverse range of organic materials spanning many applications. Self-n-doped materials have demonstrated exemplary and, in many cases, benchmark performances in a variety of applications. However, an in-depth review of the method is lacking. Perylene diimide (PDI) chromophores are an important mainstay in the semiconductor literature with well-known structure-function characteristics and are also one of the most widely utilized scaffolds for self-n-doping. In this review, we describe the unique properties of self-n-doped PDIs, delineate structure-function relationships, and discuss self-n-doped PDI performance in a range of applications. In particular, the impact of amine/ammonium incorporation into the PDI scaffold on doping efficiency is reviewed with regard to attachment mode, tether distance, counterion selection, and steric encumbrance. Self-n-doped PDIs are a unique set of PDI structural derivatives whose properties are amenable to a broad range of applications such as biochemistry, solar energy conversion, thermoelectric modules, batteries, and photocatalysis. Finally, we discuss challenges and the future outlook of self-n-doping principles.

Room temperature synthesis of perylene diimides facilitated by high amic acid solubility

A novel protocol for the synthesis of perylene diimides (PDIs), by reacting perylene dianhydride (PDA) with aliphatic amines is reported. Full conversions were obtained at temperatures between 20 and 60 °C, using DBU as the base in DMF or DMSO. A “green” synthesis of PDIs, that runs at higher temperatures, was developed using K₂CO₃ in DMSO. The reaction sequence for the imidization process, via perylene amic acid intermediates (PAAs), has been confirmed experimentally aided by the synthesis and full characterization of stable model amic acid salts and amic esters. Kinetic studies, using absorption spectroscopy, have established that PDI formation proceeds via fast amic acid formation, followed by a slow conversion to imides. Solubility of the intermediate PAA salts is found to be low and rate-limiting. Based on this finding, quantitative PDI synthesis at room temperature was achieved by diluting the reaction mixture with water, the solvent in which PAA salts have better solubility. Thus, the otherwise harsh synthesis of PDIs has been transformed into an extremely convenient functional group tolerant and highly efficient reaction that runs at room temperature.

Perylene diimides (PDIs) are synthesised at room temperature and obtained in quantitative yields after a single filtration. High solubility of the intermediate amic acid salts 5 and 9 is key to the success of this novel synthesis.

Terminal Groups Plays an Important Role in Enhancing the Performance of Organic Solar Cells Based on Non-Fused Electron Acceptors

Non-fused-ring electron acceptors (NFRAs) have made great progress resulting in their property of cheap and efficient in organic solar cells (OSCs). In order to solve the disadvantage of low device...

Combined spectroscopic and theoretical analysis of the binding of a water-soluble perylene diimide to DNA/RNA polynucleotides and G-quadruplexes

We present here a combined spectroscopic and theoretical analysis of the binding of N,N'-bis(2-(1-piperazino)ethyl)-3,4,9,10-perylenetetracarboxylic acid diimide dichloride (PZPERY) to different biosubstrates. Absorbance titrations and circular dichroism experiments, melting studies and isothermal calorimetry (ITC) titrations reveal a picture where the binding to natural double-stranded DNA is very different from that to double and triple-stranded RNAs (poly(A)∙poly(U) and poly(U)∙poly(A)⁎poly(U)). As confirmed also by the structural and energetic details clarified by density functional theory (DFT) calculations, intercalation occurs for DNA, with a process driven by the combination of aggregates disruption and monomers intercalation. Oppositely, for RNAs, no intercalation but groove binding with the formation of supramolecular aggregates is observed. Among all the tested biosubstrates, the affinity of PZPERY towards DNA G-quadruplexes (G4) is the greatest one with a preference for human telomeric G4s. Focusing on hybrid G4 forms, either sitting-atop ("tetrad-parallel") or lateral ("groove-parallel") binding modes were considered in the discussion of the experimental results and molecular dynamics (MD) simulations. Both turned out to be possible concurrently, in agreement also with the experimental binding stoichiometries higher than 2:1.

Solvent Effects in Supramolecular Chemistry: Linear Free Energy Relationships for Common Intermolecular Interactions

The proper choice of solvent is of major importance for all studies in supramolecular chemistry, including molecular recognition in host-guest systems, intramolecular folding, self-assembly, and supramolecular polymerization. In this Perspective, the usefulness of linear free energy relationships (LFERs) is highlighted to unravel the effect of solvents on coordinate bonding (e.g., cation-crown ether), hydrogen bonding, halogen bonding, dipolar aggregation, and π-π-stacking. For all of these intermolecular interactions widely applied in supramolecular systems, LFER relationships between the Gibbs binding energies and common solvent polarity scales including E_T(30), π*, α or β based on solvatochromic dyes, scales derived from binding processes such as Gutmann donor and acceptor numbers or hydrogen bond donor and acceptor scales, or physical functions like the Kirkwood-Onsager or the Liptay-Onsager functions could be demonstrated. These relationships can now be applied toward a better understanding of the prevailing intermolecular forces for supramolecular interactions. They further enable a rational selection of the most suitable solvent for the preparation of self-assembled materials and the estimation of binding constants without the need for time-consuming comprehensive investigations of solvents.

Bis(phenylethynyl)arene Linkers in Tetracationic Bis-triarylborane Chromophores Control Fluorimetric and Raman Sensing of Various DNAs and RNAs

We report four new luminescent tetracationic bis-triarylborane DNA and RNA sensors that show high binding affinities, in several cases even in the nanomolar range. Three of the compounds contain substituted, highly emissive and structurally flexible bis(2,6-dimethylphenyl-4-ethynyl)arene linkers (3: arene=5,5'-2,2'-bithiophene; 4: arene=1,4-benzene; 5: arene=9,10-anthracene) between the two boryl moieties and serve as efficient dual Raman and fluorescence chromophores. The shorter analogue 6 employs 9,10-anthracene as the linker and demonstrates the importance of an adequate linker length with a certain level of flexibility by exhibiting generally lower binding affinities than 3-5. Pronounced aggregation-deaggregation processes are observed in fluorimetric titration experiments with DNA for compounds 3 and 5. Molecular modelling of complexes of 5 with AT-DNA, suggest the minor groove as the dominant binding site for monomeric 5, but demonstrate that dimers of 5 can also be accommodated. Strong SERS responses for 3-5 versus a very weak response for 6, particularly the strong signals from anthracene itself observed for 5 but not for 6, demonstrate the importance of triple bonds for strong Raman activity in molecules of this compound class. The energy of the characteristic stretching vibration of the C≡C bonds is significantly dependent on the aromatic moiety between the triple bonds. The insertion of aromatic moieties between two C≡C bonds thus offers an alternative design for dual Raman and fluorescence chromophores, applicable in multiplex biological Raman imaging.

Perylene diimide-tagged N-heterocyclic carbene-stabilized gold nanoparticles: How much ligand desorbs from surface in presence of thiols?

N-Heterocyclic carbenes (NHCs) have recently emerged as viable alternatives to commonly used thiols to stabilize a variety of metal surfaces and nanoparticles. In this context, thanks to their biocompatibility and novel optical properties, NHC-stabilized gold nanoparticles (AuNPs) have been extensively studied. It has been shown that such materials exhibit improved stabilities in acidic and basic solutions, high temperatures, electrolyte solutions, cell culture media, and to some extent to nucleophilic thiols. Despite intense efforts, instability of NHC-functionalized AuNPs to thiols has been an ongoing challenge. In order to circumvent this problem, quantification of NHC desorption from nanoparticle surface by the invading thiols would constitute a necessary first step. To do this, we have first developed water-soluble azide decorated NHC-stabilized "clickable" AuNPs. Optically active perylene diimide (PDI)-tagged AuNP hybrids are then obtained by means of Cu-catalyzed alkyne-azide cycloaddition between these AuNPs and an alkyne-decorated PDI derivative. Investigation of photophysical properties of these AuNP/PDI hybrids revealed that the fluorescence of PDI molecules is effectively quenched by AuNPs in aqueous solution. The extent of NHC desorption from AuNP surface in presence of glutathione (4 mM), as a biologically relevant thiol, is then quantified by means of fluorescence emission restoration of PDI molecules upon detachment from AuNP surfaces. Our results demonstrate that while ∼20% of surface NHCs are displaced by glutathione within the first 24 h of their exposure to the thiol, ligand desorption reaches ∼45% after one week. We believe that these findings will provide more insight on true stability of NHC-stabilized materials.

Supramolecular Chiral Discrimination of D-Phenylalanine Amino Acid Based on a Perylene Bisimide Derivative

The interaction between homochiral substituted perylene bisimide (PBI) molecule and the D enantiomer of phenylalanine amino acid was monitored. Spectroscopic transitions of PBI derivative in aqueous solution in the visible range were used to evaluate the presence of D-phenylalanine. UV-visible, fluorescence, FT-IR, and AFM characterizations showed that D-phenylalanine induces significant variations in the chiral perylene derivative aggregation state and the mechanism is enantioselective as a consequence of the 3D analyte structure. The interaction mechanism was further investigated in presence of interfering amino acid (D-serine and D-histidine) confirming that both chemical structure and its 3D structure play a crucial role for the amino acid discrimination. A D-phenylalanine fluorescence sensor based on perylene was proposed. A limit of detection (LOD) of 64.2 ± 0.38 nM was calculated in the range 10-7-10-5 M and of 1.53 ± 0.89 μM was obtained in the range 10-5 and 10-3 M.

Efficient Capturing of Polycyclic Aromatic Micropollutants From Water Using Physically Crosslinked DNA Nanoparticles

Design and synthesis of physically (non-covalently) cross-linked nanoparticles through host-guest interaction between β-CD and adamantane is reported. Specific molecular recognition between β-CD functionalized branched DNA nanostructures (host) and a star-shaped adamantyl-terminated 8-arm poly(ethylene glycol) polymer (guest) is explored for the design of the nanoparticles. The most remarkable structural features of DNA nanoparticles include their excellent biocompatibility and the possibility of various non-covalent interactions with both hydrophobic and hydrophilic organic molecules. Potential of DNA nanoparticles for the rapid and efficient capture of various micropollutants typically present in water including carcinogens (hydrophobic micropollutants), organic dyes (hydrophilic), and pharmaceutical molecules (hydrophilic) is also demonstrated. The capture of micropollutants by DNA nanoparticles is attributed to the various non-covalent interactions between DNA nanoparticles and the micropollutants. Our results clearly suggest that DNA based nanomaterials would be an ideal candidate for the capturing and removal of both hydrophilic and hydrophobic micropollutants typically present in water.

Supramolecular Self-Assembly of Perylene Bisimide Derivatives Assisted by Various Groups

Anthra[2,1,9-def:6,5,10-d'e'f']diisoquinoline-1,3,8,10(2H,9H)-tetraone, namely, perylene bisimides (PBIs), belong to n-type organic semiconductors and possess potential applications in optoelectronic devices. The properties/performance of fabricated nanostructures/devices could be greatly influenced by both molecular structures of PBI building blocks and corresponding arrangement in assembled nanostructures. Many efforts have been made to modify the PBI core and then investigate the nanostructures and properties. However, it is still a great challenge to comprehensively understand the influence of molecular structures on the intermolecular interactions, the self-assembled structures, and the resulting performance. In the present contribution, we mainly summarize recent research aspects on supramolecular assembly behaviors of PBI derivatives assisted by various functional groups. First, a short introduction is given about basic molecular structure, properties, and self-assembly of PBI derivatives. Then, we mainly discuss the modulation of self-assembly of PBIs via introducing various functional groups (flexible or nonflexible chains, and biomolecules especially amino-acid-based groups). After that, the assembly of PBI derivatives from out-of-equilibrium states is described. Finally, a perspective is provided on the design of novel PBI derivatives and the fabrication of unique nanostructures with superior properties.

Pyrrolocytosine–pyrene conjugates as fluorescent and CD probes for the fine sensing of ds-polynucleotide secondary structure and specific recognition of poly G

Multipurpose dual method (fluorescence and CD) probes differentiate between various ds-RNA/RNA structures and specifically recognise Watson–Crick pairing complementary poly G.

Highly efficient one-step microwave-assisted synthesis of structurally diverse bis-substituted α-amino acid derived diimides

We report herein a facile and widely applicable microwave-assisted protocol for the synthesis of symmetrical diimides based on three structurally distinct aromatic dianhydrides: pyromellitic (PMA), biphenyl-tetracarboxylic acid (BPDA) and benzophenone-tetracarboxylic (BTDA) and five natural amino acids (Phe, Tyr, Ile, Lys, Cys). Fifteen symmetrical diimides with different structural characteristics containing a variety of functional groups can be produced with high yields and on a large scale.

Hydrogen-bonded perylene bisimide J-aggregate aqua material

A water-soluble perylene bisimide dye self-assembles in aqueous media into thermoresponsive aqua materials with photoluminescence within the biological transparency window.

A new twelvefold methoxy-triethyleneglycol-jacketed tetraphenoxy-perylene bisimide (MEG-PBI) amphiphile was synthesized that self-assembles into two types of supramolecular aggregates in water: red-coloured aggregates of low order and with weak exciton coupling among the PBIs and blue-coloured strongly coupled J-aggregates consisting of a highly ordered hydrogen-bonded triple helix of PBIs. At room temperature this PBI is miscible with water at any proportions which enables the development of robust dye aggregates in solution, in hydrogel states and in lyotropic liquid crystalline states. In the presence of 60–95 wt% water, self-standing coloured hydrogels exhibit colour changes from red to blue accompanied by a fluorescence light-up in the far-red region upon heating in the range of 30–50 °C. This phenomenon is triggered by an entropically driven temperature-induced hydrogen-bond-directed slipped stacking arrangement of the MEG-PBI chromophores within structurally well-defined J-aggregates. This versatile aqua material is the first example of a stable PBI J-aggregate in water. We anticipate that this study will open a new avenue for the development of biocompatible functional materials based on self-assembled dyes and inspire the construction of other hydrogen-bonded supramolecular materials in the highly competitive solvent water.

Synthesis and Self-Assembly of Bay-Substituted Perylene Diimide Gemini-Type Surfactants as Off-On Fluorescent Probes for Lipid Bilayers

Interest in bay-substituted perylene-3,4:9,10-tetracarboxylic diimides (PDIs) for solution-based applications is growing due to their improved solubility and altered optical and electronic properties compared to unsubstituted PDIs. Synthetic routes to 1,12-bay-substituted PDIs have been very demanding due to issues with steric hindrance and poor regioselectivity. Here we report a simple one-step regioselective and high yielding synthesis of a 1,12-dihydroxylated PDI derivative that can subsequently be alkylated in a straightforward fashion to produce nonplanar 1,12-dialkoxy PDIs. These PDIs show a large Stokes shift, which is specifically useful for bioimaging applications. A particular cationic PDI gemini-type surfactant has been developed that forms nonfluorescent self-assembled particles in water ("off state"), which exerts a high fluorescence upon incorporation into lipophilic bilayers ("on state"). Therefore, this probe is appealing as a highly sensitive fluorescent labelling marker with a low background signal for imaging artificial and cellular membranes.

Small molecule probes finely differentiate between various ds- and ss-DNA and RNA by fluorescence, CD and NMR response

Two small molecules showed intriguing properties of analytical multipurpose probes, whereby one chromophore gives different signal for many different DNA/RNA by application of several highly sensitive spectroscopic methods. Dyes revealed pronounced fluorescence ratiomeric differentiation between ds-AU-RNA, AT-DNA and GC-DNA in approximate order 10:8:1. Particularly interesting, dyes showed specific fluorimetric response for poly rA even at 10-fold excess of any other ss-RNA, and moreover such emission selectivity is preserved in multicomponent ss-RNA mixtures. The dyes also showed specific chiral recognition of poly rU in respect to the other ss-RNA by induced CD (ICD) pattern in visible range (400-500 nm), which was attributed to the dye-side-chain contribution to binding (confirmed by absence of any ICD band for reference compound lacking side-chain). Most intriguingly, minor difference in the side-chain attached to dye chromophore resulted in opposite sign of dye-ICD pattern, whereby differences in NMR NOESY contacts and proton chemical shifts between two dye/oligo rU complexes combined with MD simulations and CD calculations attributed observed bisignate ICD to the dimeric dye aggregate within oligo rU.

Anti-cooperative supramolecular polymerization: a new K2-K model applied to the self-assembly of perylene bisimide dye proceeding via well-defined hydrogen-bonded dimers

A new perylene bisimide dye self-assembles in an anti-cooperative process predominently into even numbered aggregates via dimers which could be interpreted by a newly developed K₂–K model.

A perylene bisimide dye bearing amide functionalities at the imide positions derived from amino acid l-alanine and a dialkoxy-substituted benzyl amine self-assembles into tightly bound dimers by π–π-stacking and hydrogen bonding in chloroform. In less polar or unpolar solvents like toluene and methylcyclohexane, and in their mixtures, these dimers further self-assemble into extended oligomeric aggregates in an anti-cooperative process in which even numbered aggregates are highly favoured. The stepwise transition from dimers into oligomers can not be properly described by conventional K₂–K model, and thus a new K₂–K aggregation model has been developed, which interpretes the present anti-cooperative supramolecular polymerization more appropriately. The newly developed K₂–K model will be useful to describe self-assembly processes of a plethora of other π-conjugated molecules that are characterized by a favored dimer species.