NDI and DAN DNA: nucleic acid-directed assembly of NDI and DAN

Sculpting photoproducts with DNA origami

Natural light-harvesting systems spatially organize densely packed dyes in different configurations to either transport excitons or convert them into charge photoproducts, with high efficiency. In contrast, artificial photosystems like organic solar cells and light-emitting diodes lack this fine structural control, limiting their efficiency. Thus, biomimetic multi-dye systems are needed to organize dyes with the sub-nanometer spatial control required to sculpt resulting photoproducts. Here, we synthesize 11 distinct perylene diimide (PDI) dimers integrated into DNA origami nanostructures and identify dimer architectures that offer discrete control over exciton transport versus charge separation. The large structural-space and site-tunability of origami uniquely provides controlled PDI dimer packing to form distinct excimer photoproducts, which are sensitive to interdye configurations. In the future, this platform enables large-scale programmed assembly of dyes mimicking natural systems to sculpt distinct photophysical products needed for a broad range of optoelectronic devices, including solar energy converters and quantum information processors.

Anion-π catalysis on carbon allotropes

Anion-π catalysis, introduced in 2013, stands for the stabilization of anionic transition states on π-acidic aromatic surfaces. Anion-π catalysis on carbon allotropes is particularly attractive because high polarizability promises access to really strong anion-π interactions. With these expectations, anion-π catalysis on fullerenes has been introduced in 2017, followed by carbon nanotubes in 2019. Consistent with expectations from theory, anion-π catalysis on carbon allotropes generally increases with polarizability. Realized examples reach from enolate addition chemistry to asymmetric Diels-Alder reactions and autocatalytic ether cyclizations. Currently, anion-π catalysis on carbon allotropes gains momentum because the combination with electric-field-assisted catalysis promises transformative impact on organic synthesis.

Anion-(π)n -π Catalytic Micelles

Anion-π catalysis operates by stabilizing anionic transition states on π-acidic aromatic surfaces. In anion-(π)n -π catalysis, π stacks add polarizability to strengthen interactions. In search of synthetic methods to extend π stacks beyond the limits of foldamers, the self-assembly of micelles from amphiphilic naphthalenediimides (NDIs) is introduced. To interface substrates and catalysts, charge-transfer complexes with dialkoxynaphthalenes (DANs), a classic in supramolecular chemistry, are installed. In π-stacked micelles, the rates of bioinspired ether cyclizations exceed rates on monomers in organic solvents by far. This is particularly impressive considering that anion-π catalysis in water has been elusive so far. Increasing rates with increasing π acidity of the micelles evince operational anion-(π)n -π catalysis. At maximal π acidity, autocatalytic behavior emerges. Dependence on position and order in confined micellar space promises access to emergent properties. Anion-(π)n -π catalytic micelles in water thus expand supramolecular systems catalysis accessible with anion-π interactions with an inspiring topic of general interest and great perspectives.

Stabilization of DNA Duplexes and Hairpins by Charge-Transfer Interactions Using DAN:NDI Pairs

Electron-rich 1,5-dialkoxynaphthalene (DAN) and electron-deficient 1,8,4,5-naphthalenetetracarboxylic diimide (NDI) are known to interact through the formation of charge-transfer complexes. The introduction of DAN and NDI into various DNA duplexes and hairpins was investigated by ultraviolet (UV) melting curve analysis. The positioning of the DAN:NDI pair was found to strongly influence the stability of DNA duplex and hairpins. In particular, while the introduction of one DAN/NDI pair in front of each other in the center of a DNA duplex led to a decrease of the thermal stability (ΔTm - 6 °C), the addition of a second pair restored or even increased the stability. In contrast, the introduction of DAN:NDI pairs at the end of a duplex always induced a strong stabilization (ΔTm up to +20 °C). Finally, a DAN:NDI pair positioned in the loop of a hairpin induced a stronger stabilization than a T4 loop (ΔTm + 10 °C). Based on charge-transfer interactions, the strong stabilizations observed allow the preparation of highly stabilized DNA nanostructures opening the way to numerous applications in nanotechnology.

Tailored Tolane-Perfluorotolane Assembly as Supramolecular Base Pair Replacement in DNA

Arene-fluoroarene interactions offer outstanding possibilities for engineering of supramolecular systems, including nucleic acids. Here, we implement the tolane-perfluorotolane interaction as base pair replacement in DNA. Tolane (THH) and perfluorotolane (TFF) moieties were connected to acyclic backbone units, comprising glycol nucleic acid (GNA) or butyl nucleic acid (BuNA) building blocks, that were incorporated via phosphoramidite chemistry at opposite positions in a DNA duplex. Thermodynamic analyses by UV thermal melting revealed a compelling stabilization by THH/TFF heteropairs only when connected to the BuNA backbone, but not with the shorter GNA linker. Detailed NMR studies confirmed the preference of the BuNA backbone for enhanced polar π-stacking. This work defines how orthogonal supramolecular interactions can be tailored by small constitutional changes in the DNA backbone, and it inspires future studies of arene-fluoroarene-programmed assembly of DNA.

Sequence-complementarity dependent co-assembly of phosphodiester-linked aromatic donor–acceptor trimers

Sequence-defined trimers of phosphodiester-linked aromatic donor–acceptors self-assemble according to monomer order, and co-assemble into new structures with their complementary sequence.

Radical anion formation exhibiting "turn-on" fluorescence sensing of hydrazine using a naphthalene diimide (NDI) derivative with a donor-acceptor-donor (D-A-D) molecular structure

In this paper, the synthesis of a naphthalene diimide (NDI) derivative with a donor-acceptor-donor (D-A-D) molecular structure substituted with a long alkyl chain (12 carbons) containing naphthalene hydrazide at the imide position is reported. The reduced emission quantum yield (φf = 0.01-0.03) of the NDI derivative in various solvents indicates the perturbation of the electronic state of π-electron deficient NDI (A) by the peripheral naphthalene (D) units. The investigation of the influence of the alkyl chain and naphthalene substituent on the self-assembling properties of the NDI derivative reveals an isodesmic mode of self-assembly in a chloroform/methylcyclohexane (CHCl3/MCH, 1 : 9, v/v) mixture. The self-assembling nature of the NDI derivative also results in the formation of an organogel in the CHCl3/MCH (1 : 9, v/v) mixture, and gel formation is well-comprehended by techniques such as P-XRD, rheological studies, and FT-IR measurements. Furthermore, radical anion (NDI˙-) formation of π-acidic NDI was used as a sensing tool for hydrazine by a fluorescence "turn-on" (φf = 0.12) method in the solution (DMSO), film, and gel state with a detection limit of 284.1 ppb in DMSO and 32 ppb in the gel state.

Naphthalenediimides with Cyclic Oligochalcogenides in Their Core

Naphthalenediimides (NDIs) are privileged scaffolds par excellence, of use in functional systems from catalysts to ion channels, photosystems, sensors, ordered matter in all forms, tubes, knots, stacks, sheets, vesicles, and colored over the full visible range. Despite this extensively explored chemical space, there is still room to discover core-substituted NDIs with fundamentally new properties: NDIs with cyclic trisulfides (i.e., trisulfanes) in their core absorb at 668 nm, emit at 801 nm, and contract into disulfides (i.e., dithietes) upon irradiation at <475 nm. Intramolecular 1,5-chalcogen bonds account for record redshifts with trisulfides, ring-tension mediated chalcogen-bond-mediated cleavage for blueshifts to 492 nm upon ring contraction. Cyclic oligochalcogenides (COCs) in the NDI core open faster than strained dithiolanes as in asparagusic acid and are much better retained on thiol exchange affinity columns. This makes COC-NDIs attractive not only within the existing multifunctionality, particularly artificial photosystems, but also for thiol-mediated cellular uptake.

Polyether Natural Product Inspired Cascade Cyclizations: Autocatalysis on π-Acidic Aromatic Surfaces

Anion-π catalysis functions by stabilizing anionic transition states on aromatic π surfaces, thus providing a new approach to molecular transformation. The delocalized nature of anion-π interactions suggests that they serve best in stabilizing long-distance charge displacements. Aiming therefore for an anionic cascade reaction that is as charismatic as the steroid cyclization is for conventional cation-π biocatalysis, reported here is the anion-π-catalyzed epoxide-opening ether cyclizations of oligomers. Only on π-acidic aromatic surfaces having a positive quadrupole moment, such as hexafluorobenzene to naphthalenediimides, do these polyether cascade cyclizations proceed with exceptionally high autocatalysis (rate enhancements k_auto /k_cat >10⁴  m^-1 ). This distinctive characteristic adds complexity to reaction mechanisms (Goldilocks-type substrate concentration dependence, entropy-centered substrate destabilization) and opens intriguing perspectives for future developments.

Peptide Stapling with Anion-π Catalysts

We report design, synthesis and evaluation of a series of naphthalenediimides (NDIs) that are bridged with short peptides. Reminiscent of peptide stapling technologies, the macrocycles are conveniently accessible by a chromogenic nucleophilic aromatic substitution of two bromides in the NDI core with two thiols from cysteine sidechains. The dimension of core-bridged NDIs matches that of one turn of an α helix. NDI-stapled peptides exist as two, often separable atropisomers. Introduction of tertiary amine bases in amino-acid sidechains above the π-acidic NDI surface affords operational anion-π catalysts. According to an enolate chemistry benchmark reaction, anion-π catalysis next to peptides occurs with record chemoselectivity but weak enantioselectivity. Catalytic activity drops with increasing distance of the amine base to the NDI surface, looser homocysteine bridges, mismatched, shortened and elongated α-helix turns, and acyclic peptide controls. Elongation of isolated turns into short α helices significantly increases activity. This increase is consistent with remote control of anion-π catalysis from the α-helix macrodipole.

Assembly of amino acid containing naphthalene diimide-based molecules: the role of intervening amide groups in self-assembly, gelation, optical and semiconducting properties

Two naphthalene diimide containing molecules, one with a covalently linked peptide (P1) and the other with a covalently attached amino acid residue and a diamine moiety (P2), have been chosen in such a way that the number of intervening amide groups and the centrally located imide moieties are the same, and their molecular formulae are also identical. However, the positions of the amide groups are different in these two molecules and this can dictate a different behaviour in molecular assembly and gelation processes for each of the individual NDI-appended peptide (P1) and pseudo-peptide (P2). The molecule P1 with an attached peptide moiety and the intervening -CO-NH groups forms an organogel in a mixture of chloroform-methylcyclohexane at a very rapid rate and the mechanical strength of the gel is quite high, whereas the molecule P2, containing the amino acid and diamide moieties, and with the intervening -NH-CO groups forms an organogel in a relatively much slower rate in chloroform-methylcyclohexane mixture. The mechanical strength of the P2 gel is significantly lower compared to that of the P1 gel at the same concentration and solvent system. The minimum gelation concentration of P1 is much smaller than that of P2 in the same solvent system. The thermal stability of the P1 gel is higher than that of the P2 gel at the same concentration and solvent system. However, both of these gels form J-type aggregates in a mixture of chloroform-methylcyclohexane with a red shift in the UV-vis spectrum. The gelator P1 exhibits enhanced fluorescence compared to that of P2 at a fixed concentration and in the same solvent system (mixture of chloroform-methylcyclohexane, 5 : 95 (v/v)). The lifetime and quantum yield of the P1 gel are also significantly higher than those of the P2 gel under similar gelation conditions. Moreover, both P1 and P2 are found to exhibit significant semiconducting behaviours in their dried/xerogel states. It is important to note that the stronger gel P1 exhibits relatively better semiconducting behaviour than the weak gel P2. Interestingly, the self-assembly, gelation, photoluminescence and electrical conductivity are different for the gels obtained from these two molecules. This indicates the role of the amide bond and its linkage (whether -CONH/-NHCO) in the self-assembly, gelation and optoelectronic behaviour of these molecules in their assembled states.

Intertwined gababutin-based supramolecular double helix

A dimer-assembly driven supramolecular double helix is observed for the gababutin-based short peptide sequence and this architecture exhibits electrochemical features.

Substituent effects in solid-state assembly of activated benzotriazoles

Aromatic donor–acceptor stacking involving electron-rich π-donors and electron-deficient π-acceptors has been utilized in a broad spectrum of diverse applications to great effect.

Exploiting the interactions of aromatic units for folding and assembly in aqueous environments

A variety of non-covalent interactions (including hydrogen bonding, ionic interactions, metal coordination and desolvation/solvation) have been utilized to organize oligomers into well-defined structures. Herein is described a survey of aromatic foldamers that capitalize on electrostatic complementarity of substituted aromatic units to drive folding and assembly in aqueous environments. A brief description of recent advances in the understanding of aromatic interactions is provided, followed by examples of foldamers that exploit interactions between aromatic units to drive their assembly in predictable fashion. The history of our aromatic foldamers is traced from the first structure designed to fold into a pleated structure in an aqueous environment to a heteroduplex system more related to nucleic acids. Taken together, the results demonstrate that electrostatic complementarity of aromatic units provides a versatile framework for driving predictable folding and assembly in aqueous environments.

Poly(norbornyl-NDIs) as a potential cathode-active material in rechargeable charge storage devices

Two pendant-type naphthalene diimide (NDI) polymers bearing a polynorbornene backbone were prepared and their electrochemical properties explored.

Donor/acceptor chromophores-decorated triazolyl unnatural nucleosides: synthesis, photophysical properties and study of interaction with BSA

We report the syntheses and photophysical properties of some triazolyl donor/acceptor unnatural nucleosides and studies on the interaction of one of the fluorescent nucleosides with BSA.

Hetero-Selective DNA-Like Duplex Stabilized by Donor-Acceptor Interactions

We report on the characterization of a novel hetero-selective DNA-like duplex of pyrene and anthraquinone pseudo base pairs. The pyrene/anthraquinone pairs showed excellent selectivity in hetero-recognition and even trimers were found to form a hetero-duplex. Pyrene and anthraquinone moieties were tethered on acyclic D-threoninol linkers and linked to adjacent residues by using standard phosphoramidite chemistry. When pyrene and anthraquinone were incorporated at pairing positions in complementary strands of natural DNA oligonucleotides, the duplex was stabilized significantly. Moreover, a pyrene hexamer and an anthraquinone hexamer formed a stable artificial hetero-duplex without the assistance of natural base pairs. The pyrene/anthraquinone pair was so stable that even trimers formed a hetero-duplex under conditions in which natural DNA strands of three residues do not.

Charge-transfer complexation between naphthalene diimides and aromatic solvents

Naphthalene diimides (NDIs) form emissive ground-state charge-transfer (CT) complexes with various electron rich aromatic solvents like benzene, o-xylene and mesitylene. TD-DFT calculation of the complexes suggests CT interaction and accounts for the observed ground-state changes.

Influence of perylenediimide-pyrene supramolecular interactions on the stability of DNA-based hybrids: Importance of electrostatic complementarity

Aromatic π-π stacking interactions are ubiquitous in nature, medicinal chemistry and materials sciences. They play a crucial role in the stacking of nucleobases, thus stabilising the DNA double helix. The following paper describes a series of chimeric DNA-polycyclic aromatic hydrocarbon (PAH) hybrids. The PAH building blocks are electron-rich pyrene and electron-poor perylenediimide (PDI), and were incorporated into complementary DNA strands. The hybrids contain different numbers of pyrene-PDI interactions that were found to directly influence duplex stability. As the pyrene-PDI ratio approaches 1:1, the stability of the duplexes increases with an average value of 7.5 °C per pyrene-PDI supramolecular interaction indicating the importance of electrostatic complementarity for aromatic π-π stacking interactions.

Direct core functionalisation of naphthalenediimides by iridium catalysed C–H borylation

We report the first boron-substituted naphthalenediimides (NDIs), prepared by iridium catalysed C–H activation. Both mono- and diborylated products are available, which have been further elaborated by Suzuki–Miyaura coupling.