Dissipative Synthetic DNA‐Based Receptors for the Transient Loading and Release of Molecular Cargo

Supramolecular chemistry is moving into a direction in which the composition of a chemical equilibrium is no longer determined by thermodynamics but by the efficiency with which kinetic states can be populated by energy consuming processes. Herein, we show that DNA is ideally suited for programming chemically fueled dissipative self‐assembly processes. Advantages of the DNA‐based systems presented in this study include a perfect control over the activation site for the chemical fuel in terms of selectivity and affinity, highly selective fuel consumption that occurs exclusively in the activated complex, and a high tolerance for the presence of waste products. Finally, it is shown that chemical fuels can be used to selectively activate different functions in a system of higher complexity embedded with multiple response pathways.     

Transient DNA-Based Nanostructures Controlled by Redox Inputs

Synthetic DNA has emerged as a powerful self-assembled material for the engineering of nanoscale supramolecular devices and materials. Recently dissipative self-assembly of DNA-based supramolecular structures has emerged as a novel approach providing access to a new class of kinetically controlled DNA materials with unprecedented life-like properties. So far, dissipative control has been achieved using DNA-recognizing enzymes as energy dissipating units. Although highly efficient, enzymes pose limits in terms of long-term stability and inhibition of enzyme activity by waste products. Herein, we provide the first example of kinetically controlled DNA nanostructures in which energy dissipation is achieved through a non-enzymatic chemical reaction. More specifically, inspired by redox signalling, we employ redox cycles of disulfide-bond formation/breakage to kinetically control the assembly and disassembly of tubular DNA nanostructures in a highly controllable and reversible fashion.     

Construction of a DNA-Based Supramolecular Nanosheet That Emits Bluish-White Light from Charge-Transfer Excited States of the Nucleobases

1,ω-Inosinic acid-bearing bolaamphiphiles dI(18), dI(19), and dI(20) with a 3′-phosphorylated inosine as a universal base connected to each end of an oligomethylene chain were synthesized for the first time. Single-component self-assemblies of these bolaamphiphiles and their binary self-assemblies with salmon sperm DNA were studied by AFM; temperature-dependent UV absorption, fluorescence, and circular dichroism spectroscopy; and gel electrophoresis. The binary self-assembly of dI(20) and salmon sperm DNA (dI(20)-DNA) had a nanosheet structure with a homogeneous thickness of about 6 nm and widths of several micrometers. Interestingly, an aqueous solution of the nanosheets showed a broad absorption band originating from the charge-transfer (CT) states of the nucleobase in the long-wavelength region (>300 nm), and the molar absorptivity per nucleobase was calculated to be approximately 150 times that of single-stranded (dT20 and dA20) and double-stranded (dT20-dA20) oligonucleotides. In addition, a continuous and broad emission band originating from CT excited states of the nucleobases was observed in the visible region. These observations indicate that CT states of the nucleobases were formed and stabilized in the supramolecular nanosheet and that bluish white light was emitted from CT excited states of the nucleobases.     

Positive Allosteric Control of Guests Encapsulation by Metal Binding to Covalent Porphyrin Cages

The allosteric control of the receptor properties of two flexible covalent cages is reported. These receptors consist of two zinc(II) porphyrins connected by four linkers of two different sizes, each incorporating two 1,2,3-triazolyl ligands. Silver(I) ions act as effectors, responsible for an on/off encapsulation mechanism of neutral guest molecules. Binding silver(I) ions to the triazoles opens the cages and triggers the coordination of pyrazine or the encapsulation of N,N′-dibutyl-1,4,5,8-naphthalene diimide. The X-ray structure of the silver(I)-complexed receptor with short connectors is reported, revealing the hollow structure with a cavity well-defined by two eclipsed porphyrins. Rather unexpectedly, the crystallographic structure of this receptor with pyrazine as a guest molecule showed that the cavity is occupied by two pyrazines, each binding to the zinc(II) porphyrin in a monotopic fashion.     

Self‐Assembly of DNA–Oligo(p‐phenylene‐ethynylene) Hybrid Amphiphiles into Surface‐Engineered Vesicles with Enhanced Emission

Surface‐addressable nanostructures of linearly π‐conjugated molecules play a crucial role in the emerging field of nanoelectronics. Herein, by using DNA as the hydrophilic segment, we demonstrate a solid‐phase “click” chemistry approach for the synthesis of a series of DNA–chromophore hybrid amphiphiles and report their reversible self‐assembly into surface‐engineered vesicles with enhanced emission. DNA‐directed surface addressability of the vesicles was demonstrated through the integration of gold nanoparticles onto the surface of the vesicles by sequence‐specific DNA hybridization. This system could be converted to a supramolecular light‐harvesting antenna by integrating suitable FRET acceptors onto the surface of the nanostructures. The general nature of the synthesis, surface addressability, and biocompatibility of the resulting nanostructures offer great promises for nanoelectronics, energy, and biomedical applications.     

Towards Dynamic Control of Wettability by Using Functionalized Altitudinal Molecular Motors on Solid Surfaces

We report the synthesis of altitudinal molecular motors that contain functional groups in their rotor part. In an approach to achieve dynamic control over the properties of solid surfaces, a hydrophobic perfluorobutyl chain and a relatively hydrophilic cyano group were introduced to the rotor part of the motors. Molecular motors were attached to quartz surfaces by using interfacial 1,3‐dipolar cycloadditions. To test the effect of the functional groups on the rotary motion, photochemical and thermal isomerization studies of the motors were performed both in solution and when attached to the surface. We found that the substituents have no significant effect on the thermal and photochemical processes, and the functionalized motors preserved their rotary function both in solution and on a quartz surface. Preliminary results on the influence of the functional groups on surface wettability are also described.     

Patterning Porous Networks through Self-Assembly of Programmed Biomacromolecules

Two-dimensional (2D) porous networks are of great interest for the fabrication of complex organized functional materials for potential applications in nanotechnologies and nanoelectronics. This review aims at providing an overview of bottom-up approaches towards the engineering of 2D porous networks by using biomacromolecules, with a particular focus on nucleic acids and proteins. The first part illustrates how the advancements in DNA nanotechnology allowed for the attainment of complex ordered porous two-dimensional DNA nanostructures, thanks to a biomimetic approach based on DNA molecules self-assembly through specific hydrogen-bond base pairing. The second part focuses the attention on how polypeptides and proteins structural properties could be used to engineer organized networks templating the formation of multifunctional materials. The structural organization of all examples is discussed as revealed by scanning probe microscopy or transmission electron microscopy imaging techniques.     

Formation and Dynamic Behavior of Mono‐ and Bimetallic Cadmium(II) Porphyrin Complexes: Allosteric Control of Coupled Intraligand Metal Migrations

The complexation behavior of a bis‐strapped porphyrin ligand ( 1 ) towards Cd^II has been investigated by ¹H and ¹¹³Cd NMR spectroscopy with the help of X‐ray diffraction structures. The presence of an overhanging carboxylic acid group on each side of the macrocycle is responsible for the instantaneous insertion of the metal ion(s) at room temperature, and allows the formation of bimetallic species with unusual coordination modes at the origin of unique dynamic behaviors. In the absence of base, a C₂‐symmetric bimetallic complex ( 1Cd₂ ) is readily formed, in which the porphyrin acts as a bridging ligand. Both Cd^II ions are bound to the N core and to a COO^? group of a strap. In contrast, the presence of a base induces a two‐step binding process with the successive formation of mono and bimetallic species ( 1^Cd and 1_Cd?CdOAc ). Formally, a Cd^II ion is first inserted into the N core and experiences a strong out‐of‐plane (OOP) displacement due to the binding of an overhanging carbonyl group in an apical position. A second Cd^II ion then binds exclusively to the strap on the opposite side, in a so‐called hanging‐atop (HAT) coordination mode. These two complexes display a fluxional behavior that relies on intraligand migration processes of the metal ion(s). In 1^Cd , the Cd^II ion exchanges between the two equivalent overhanging apical ligands by funneling through the porphyrin ring. In 1_Cd?CdOAc , the two Cd^II ions exchange their coordination mode (HAT?OOP) in a concerted way while staying on their respective side of the macrocycle, in a so‐called Newton’s cradle‐like motion. The intramolecular pathway was notably evidenced by variable temperature ¹¹³Cd heteronuclear NMR experiments. This coupled motion of the Cd^II cations is under allosteric control; the addition of an acetate anion (the allosteric effector) to the “resting” C₂‐symmetric complex 1Cd₂ affords the dissymmetric complex 1_Cd?CdOAc and triggers equilibrium between its two degenerate states. The rate of the swinging motion further depends on the concentration of AcO^?, with a higher concentration leading to a slower motion. As compared with the related Pb^II and Bi^III bimetallic complexes, the Newton’s cradle‐like motion proceeds faster with the smaller Cd^II ion. These results open the way to novel multistable devices and switches.     

Exploring the Limits of Bivalency by DNA‐Based Spatial Screening

Multivalency can facilitate complex formation when monovalent receptor–ligand interactions are weak. However, enhanced binding of two multivalent binding partners should be avoidable, for example when bivalent receptors ought to utilize multimolecular interactions to cross‐link binding partners. We herein report the first systematic study to assess the criteria deciding whether a bivalent system engages in bivalency‐enhanced interactions or cross‐linking. We used DNA‐instructed self‐assembly to arrange the cucurbit[7]uril–adamantane host–guest system in 70–360 Å distance. Measurements and statistical mechanics analyses revealed that the affinity gain is controlled by 1) the distance between recognition modules, 2) the scaffold flexibility, and, importantly, 3) the strength of the monovalent interaction. We show that the bivalency effect can extend beyond 150 Å and discuss how, on the contrary, weak monovalent interactions reduce the concentration threshold for cross‐linking. The findings are of interest for inhibitor design.     

Kinetic Control of the Supramolecular Chirality of Porphyrin J‐Aggregates

The aggregation of achiral sulfonatophenyl‐ and phenyl‐meso‐substituted diprotonated porphyrins to chiral J‐aggregates is a hierarchical noncovalent polymerization process preceded by a critical nucleation stage. This allows significant enantiomeric excesses by the formation of a few primary nuclei and the control of their growth by the effect that flows (imperfect mixing) have on the secondary nucleation of the J‐aggregate particles. In addition, the results strongly suggest that when only one species of aggregate predominates, the CD signals of the three excitonic bands in the visible region (around 420, 490, and 700 nm) show the same sign. Thus, differences on their relative sign would be due to the presence of different species.     

Kinetic versus Thermodynamic Control Over Multiple Conformations of Di-2,7-naphthihexaphyrin(1.1.1.1.1.1)

Di-2,7-naphthihexaphyrin(1.1.1.1.1.1), a non-aromatic carba-analogue of the hexaphyrin(1.1.1.1.1.1), incorporating two built-in 2,7-naphthylene moieties was synthesized as two separate, conformationally locked stereoisomers. Both conformers followed complex protonation pathways involving structurally different species, which can be targeted under kinetic and thermodynamic control. The neutralization of the ultimate dicationic product, accessible from both stereoisomers of the free base, allowed to realize the complex conformational switching cycle involving six structurally different species.     

Reversible Photoswitching of Rotaxane Character and Interplay of Thermodynamic Stability and Kinetic Lability in a Self‐Assembling Ring–Axle Molecular System

We have designed, synthesized, and investigated a self‐assembling system that can be reversibly interconverted between thermodynamically stable (pseudorotaxane) and kinetically inert (rotaxane) forms by light irradiation. The system is composed of a dibenzo[24]crown‐8 ring and an axle comprised of a dibenzylammonium recognition site and two azobenzene end groups. The isomeric form of the azobenzene units of the axle has a little influence on the stability constants of the respective pseudorotaxanes but greatly affects the threading–dethreading rate constants. In fact, equilibration of the ring and the axle in its EE isomeric form occurs within seconds in acetonitrile at room temperature, whereas the ZZ axle threads–dethreads the ring at least four orders of magnitude slower. Moreover, we show that a change in the stability of the complex, achieved by deprotonating the dibenzylammonium recognition site on the axle, affects its kinetic behavior. We compare the results of these experiments with those observed upon dethreading the (pseudo)rotaxane by using a competitive guest for the ring, an approach which does not inherently destabilize the ring–axle interaction. This study outlines a general strategy for the reversible photochemical control of motion kinetics in threaded and interlocked compounds and constitutes a starting point for the construction of multicomponent structures that can behave as photochemically driven nanomachines.     

Two‐Dimensional Assembly Based on Flow Supramolecular Chemistry: Kinetic Control of Molecular Interactions Under Solvent Diffusion

Self‐assembly of porphyrin molecules can be controlled kinetically to form structures with lengths extending from the nano‐ to the micrometer scale, through a programmed solvent‐diffusion process in designed microflow spaces. Temporal solvent structures generated in the microflow were successfully transcribed into molecular architectures.     

Supramolecular Chemistry in Microflow Fields: Toward a New Material World of Precise Kinetic Control

Constructing new and versatile self‐assembling systems in supramolecular chemistry is much like the development of new reactions or new catalysts in synthetic organic chemistry. As one such new technology, conventional supramolecular assembly systems have been combined with microflow techniques to control intermolecular or interpolymer interactions through precise regulation of a flowing self‐assembly field. The potential of the microflow system has been explored by using various simple model compounds. Uniform solvent diffusion in the microflow leads to rapid activation of molecules in a nonequilibrium state and, thereby, enhanced interactions. All of these self‐assembly processes begin from a temporally activated state and proceed in a uniform chemical environment, forming a synchronized cluster and resulting in effective conversion to supramolecules, with precise tuning of molecular (or polymer) interactions. This approach allows the synthesis of a variety of discrete microstructures (e.g., fibers, sheets) and unique supramolecules (e.g., hierarchical assemblies, capped fibers, polymer networks, supramolecules with time‐delayed action) that have previously been inaccessible.