Biomimetic temporal self-assembly via fuel-driven controlled supramolecular polymerization

Devising Synthetic Reaction Cycles for Dissipative Nonequilibrium Self-Assembly

Fuel-driven reaction cycles are found in biological systems to control the assembly and disassembly of supramolecular materials such as the cytoskeleton. Fuel molecules can bind noncovalently to a self-assembling building block or they can react with it, resulting in covalent modifications. Overall the fuel can either switch the self-assembly process on or off. Here, a closer look is taken at artificial systems that mimic biological systems by making and breaking covalent bonds in a self-assembling motif. The different chemistries used so far are highlighted in chronological order and the pros and cons of each system are discussed. Moreover, the desired traits of future reaction cycles, their fuels, and waste management are outlined, and two chemistries that have not been explored up to now in chemically fueled dissipative self-assembly are suggested.

Bioinspired, ATP-driven co-operative supramolecular polymerization and its pathway dependence

A bio-inspired, ATP-driven nucleation growth assembly is demonstrated using an amphiphilic naphthalene diimide (NDI) derivative appended with guanidinium receptors to promote specific salt-bridge type interaction with nucleotide phosphates. Detailed spectroscopic and microscopic probing revealed a pathway-dependent co-operative self-assembly to yield two-dimensional and scrolled nano-tubular bilayer assemblies under kinetic and thermodynamic conditions, respectively.

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.

Redox-Mediated, Transient Supramolecular Charge-Transfer Gel and Ink

Unprecedented spatiotemporal control exhibited by natural systems has aroused interest in the construction of its synthetic mimics. Cytoskeleton proteins utilize fuel-driven dissipative self-assembly to temporally regulate cell shape and motility. Until now, synthetic efforts have majorly contributed to fundamental strategies; however, temporally programmed functions are rarely explored. Herein, we work toward alleviating this scenario by using a charge-transfer (CT) based supramolecular polymer that undergoes structural changes under the effect of a redox fuel. The structural changes in supramolecular assembly amplify into observable macroscopic and material property changes. As a result, we achieve transient chemochromism,  a self-erasing ink and self-regenerating hydrogel, whose temporal profile can be regulated by varying the concentrations of the chemical cues (fuel and enzyme). The redox-mediated transient functions in the CT based supramolecular polymer pave way to create next-generation active, adaptive, and autonomous smart materials.

Supramolecular chiroptical switches

Recent progress in chiroptical switches including on/off, amplification, and inversion of the chiral signals such as ECD and CPL in supramolecular assemblies is shown.

The Power of Confocal Laser Scanning Microscopy in Supramolecular Chemistry: In situ Real-time Imaging of Stimuli-Responsive Multicomponent Supramolecular Hydrogels

Multicomponent supramolecular hydrogels are promising scaffolds for applications in biosensors and controlled drug release due to their designer stimulus responsiveness. To achieve rational construction of multicomponent supramolecular hydrogel systems, their in-depth structural analysis is essential but still challenging. Confocal laser scanning microscopy (CLSM) has emerged as a powerful tool for structural analysis of multicomponent supramolecular hydrogels. CLSM imaging enables real-time observation of the hydrogels without the need of drying and/or freezing to elucidate their static and dynamic properties. Through multiple, selective fluorescent staining of materials of interest, multiple domains formed in supramolecular hydrogels (e. g. inorganic materials and self-sorting nanofibers) can also be visualized. CLSM and the related microscopic techniques will be indispensable to investigate complex life-inspired supramolecular chemical systems.

Reversible hydrogen-bonded polymerization regulated by allosteric metal templation

A stable quadruple hydrogen bonded cyclic dimer assisted by metal templation was successfully self-assembled and its reversible transformation to supramolecular polymer was investigated.

Kinetically controlled Ag+-coordinated chiral supramolecular polymerization accompanying a helical inversion

We report kinetically controlled chiral supramolecular polymerization based on ligand-metal complex with a 3 : 2 (L : Ag+) stoichiometry accompanying a helical inversion in water. A new family of bipyridine-based ligands (d-L1, l-L1, d-L2, and d-L3) possessing hydrazine and d- or l-alanine moieties at the alkyl chain groups has been designed and synthesized. Interestingly, upon addition of AgNO3 (0.5-1.3 equiv.) to the d-L1 solution, it generated the aggregate I composed of the d-L1AgNO3 complex (d-L1 : Ag+ = 1 : 1) as the kinetic product with a spherical structure. Then, aggregate I (nanoparticle) was transformed into the aggregate II (supramolecular polymer) based on the (d-L1)3Ag2(NO3)2 complex as the thermodynamic product with a fiber structure, which led to the helical inversion from the left-handed (M-type) to the right-handed (P-type) helicity accompanying CD amplification. In contrast, the spherical aggregate I (nanoparticle) composed of the d-L1AgNO3 complex with the left-handed (M-type) helicity formed in the presence of 2.0 equiv. of AgNO3 and was not additionally changed, which indicated that it was the thermodynamic product. The chiral supramolecular polymer based on (d-L1)3Ag2(NO3)2 was produced via a nucleation-elongation mechanism with a cooperative pathway. In thermodynamic study, the standard ΔG° and ΔH e values for the aggregates I and II were calculated using the van't Hoff plot. The enhanced ΔG° value of the aggregate II compared to that of the formation of aggregate I confirms that aggregate II was thermodynamically more stable. In the kinetic study, the influence of concentration of AgNO3 confirmed the initial formation of the aggregate I (nanoparticle), which then evolved to the aggregate II (supramolecular polymer). Thus, the concentration of the (d-L1)3Ag2(NO3)2 complex in the initial state plays a critical role in generating aggregate II (supramolecular polymer). In particular, NO3 - acts as a critical linker and accelerator in the transformation from the aggregate I to the aggregate II. This is the first example of a system for a kinetically controlled chiral supramolecular polymer that is formed via multiple steps with coordination structural change.

Fuel-Driven Transient Crystallization of a Cucurbit[8]uril-Based Host-Guest Complex

Transient self-assembling systems often suffer from accumulation of chemical wastes that interfere with the formation of pristine self-assembled products in subsequent cycles. Herein, we report the transient crystallization of a cucurbit[8]uril-based host-guest complex, preventing the accumulation of chemical wastes. Base-catalyzed thermal decarboxylation of trichloroacetic acid that chemically fuels the crystallization process dissolves the crystals, and produces volatile chemical wastes that are spontaneously removed from the solution. With such self-clearance process, no significant damping in the formation of the crystals was observed. The morphology and structural integrity of the crystals was also maintained in subsequent cycles. The concept may be further extended to obtain other temporally functional materials, quasicrystals, etc., based on stimuli-responsive guest molecules.

Steering the Self-Assembly Outcome of a Single NDI Monomer into Three Morphologically Distinct Supramolecular Assemblies, with Concomitant Change in Supramolecular Polymerization Mechanism

Noncovalent self-assembly creates an effective route to highly sophisticated supramolecular polymers with tunable properties. However, the outcome of this assembly process is highly dependent on external conditions. In this work, a monomeric naphthalene diimide (NDI), designed to allow solubility in a wide range of solvents, can assemble into three distinct noncovalent supramolecular species depending on solvent composition and temperature. Namely, while the self-assembly in chlorinated solvents yields relatively short, hydrogen-bonded nanotubes, the reduction of solvent polarity changes the assembly outcome, yielding π-π stacking polymers, which can further bundle into a more complex aggregate. The obtained polymers differ not only in their global morphology but-more strikingly-also in the thermodynamics and kinetics of their supramolecular self-assembly, involving isodesmic or two-stage cooperative assembly with kinetic hysteresis, respectively. Ultimately, three distinct assembly states can be accessed in a single experiment.

Designer Peptide Amphiphiles: Self-Assembly to Applications

Peptide amphiphiles (PAs) are extremely attractive as molecular building blocks, especially in the bottom-up fabrication of supramolecular soft materials, and have potential in many important applications across various fields of science and technology. In recent years, we have designed and synthesized a large group of peptide amphiphiles. This library of PAs has the ability to self-assemble into a variety of aggregates such as fibers, nanosphere, vesicles, nanosheet, nanocups, nanorings, hydrogels, and so on. The mechanism behind the formation of such a wide range of structures is intriguing. Each system has its individual method of aggregation and results in assemblies with important applications in areas including chemistry, biology, and materials science. The aim of this feature article is to bring together our recent achievements with designer PAs with respect to their self-assembly processes and applications. Emphasis is placed on rational design, mechanistic aspects of the self-assembly processes, and the applications of these PAs. We hope that this article will provide a conceptual demonstration of the different approaches taken toward the construction of these task-specific PAs.

Tandem Interplay of the Host-Guest Interaction and Photoresponsive Supramolecular Polymerization to 1D and 2D Functional Peptide Materials

Peptide 1 with an Aβ42 amyloid nucleating core and a photodimerizable 4-methylcoumarin moiety at its N terminus demonstrates the step-wise self-assembly in water to form nanoparticles, with eventual transformation into 1D nanofibers. Addition of γ-cyclodextrin to 1 with subsequent irradiation with UV light at 320 nm resulted in morphological conversion to free-standing 2D nanosheets mediated by the host-guest interaction. Mechanical agitation of the 1D and 2D nanostructures led to seeds with narrow polydispersity indices, which by mediation of seeded supramolecular polymerization found seamless control over the dimensions of the nanostructures. Such structural and temporal control to differentiate the pathway was exploited to tune the mechanical strength of hierarchical hydrogel materials. Finally, the dimensional characteristics of the positively charged peptide fibers and sheets were envisaged as excellent exfoliating agents for inorganic hybrid materials, for example, MoS₂.

Adenosine Triphosphate Templated Self-Assembly of Cationic Porphyrin into Chiral Double Superhelices and Enzyme-Mediated Disassembly

Self-assembly of small molecules through noncovalent interactions into nanoscale architectures has been extensively studied in supramolecular chemistry. However, it is still challenging to develop a biologically inspired self-assembly system that functions in water with complex structure and dynamics by analogy with those found in nature. Here, we report a new water-soluble cationic porphyrin that undergoes adenosine triphosphate (ATP)-templated self-assembly into right-handed double-helical supramolecular structures. Direct observation of the porphyrin-ATP assembly by transmission electron microscopy has been accomplished. The assemblies consist of superhelical fibers with length greater than 1 μm and width ∼46 nm. The chiral superhelical fibers show reversible disassembly to monomers upon hydrolysis of ATP catalyzed by alkaline phosphatase (ALP), and the nanofibers can be re-formed with subsequent addition of ATP. Moreover, transient self-assembly of a chiral double helix is formed when ALP is present to consume ATP.

Living supramolecular polymerization based on reversible deactivation of a monomer by using a 'dummy' monomer

New method of living supramolecular polymerization is demonstrated. Spontaneous nucleation of a reactive monomer is suppressed by using a ‘dummy’ monomer. Addition of seeds can initiate supramolecular polymerization in a chain-growth manner.

Although living supramolecular polymerization (LSP) has recently been realized, the scope of the monomer structures applicable to the existing methods is still limited. For instance, a monomer that spontaneously nucleates itself cannot be processed in a manner consistent with LSP. Herein, we report a new method for such a “reactive” monomer. We use a ‘dummy’ monomer which has a similar structure to the reactive monomer but is incapable of one-dimensional supramolecular polymerization. We show that in the presence of the dummy monomer, the reactive monomer is kinetically trapped in the dormant state. In this way, spontaneous nucleation of the reactive monomer is retarded; yet, addition of seeds of a supramolecular polymer can initiate the supramolecular polymerization in a chain growth manner. As a result, we obtain the supramolecular polymer of the reactive monomer with a controlled length, which is otherwise thermodynamically inaccessible. We believe that this concept will expand the scope of LSP for the synthesis of other functional supramolecular polymers, and thus lead to a variety of applications.

Hydrogel Microellipsoids that Form Robust String-Like Assemblies at the Air/Water Interface

Soft colloidal particles such as hydrogel microspheres assemble at air/water or oil/water interfaces, where the soft colloids are highly deformed and their surface polymer chains are highly entangled with each other. Herein, we report the formation of robust one-dimensional, string-like colloidal assemblies through self-organization of hydrogel microspheres with shape anisotropy at the air/water interface of sessile droplets. Shape-anisotropic hydrogel microspheres were synthesized via two-step polymerization, whereby a hydrogel shell was formed onto preformed rigid microellipsoids. The shape anisotropy of the hydrogel microspheres was confirmed by transmission electron microscopy and high-speed atomic force microscopy as well as by light-scattering measurements. The present findings are crucial for the understanding of natural self-organization phenomena, where "softness" influences microscopic assembled structures such as those of Nostoc bacteria.

How Defects Control the Out-of-Equilibrium Dissipative Evolution of a Supramolecular Tubule

Supramolecular architectures that work out-of-equilibrium or that can change in specific ways when absorbing external energy are ubiquitous in nature. Gaining the ability to create via self-assembly artificial materials possessing such fascinating behaviors would have a major impact in many fields. However, the rational design of similar dynamic structures requires to understand and, even more challenging, to learn how to master the molecular mechanisms governing how the assembled systems evolve far from the equilibrium. Typically, this represents a daunting challenge due to the limited molecular insight that can be obtained by the experiments or by classical modeling approaches. Here we combine coarse-grained molecular models and advanced simulation approaches to study at submolecular (<5 Å) resolution a supramolecular tubule, which breaks and disassembles upon absorption of light energy triggering isomerization of its azobenzene-containing monomers. Our approach allows us to investigate the molecular mechanism of monomer transition in the assembly and to elucidate the kinetic process for the accumulation of the transitions in the system. Despite the stochastic nature of the excitation process, we demonstrate how these tubules preferentially dissipate the absorbed energy locally via the amplification of defects in their supramolecular structure. We find that this constitutes the best kinetic pathway for accumulating monomer transitions in the system, which determines the dynamic evolution out-of-equilibrium and the brittle behavior of the assembly under perturbed conditions. Thanks to the flexibility of our models, we finally come out with a general principle, where defects explain and control the brittle/soft behavior of such light-responsive assemblies.

Fuel-Responsive Allosteric DNA-Based Aptamers for the Transient Release of ATP and Cocaine

We show herein that allostery offers a key strategy for the design of out-of-equilibrium systems by engineering allosteric DNA-based nanodevices for the transient loading and release of small organic molecules. To demonstrate the generality of our approach, we used two model DNA-based aptamers that bind ATP and cocaine through a target-induced conformational change. We re-engineered these aptamers so that their affinity towards their specific target is controlled by a DNA sequence acting as an allosteric inhibitor. The use of an enzyme that specifically cleaves the inhibitor only when it is bound to the aptamer generates a transient allosteric control that leads to the release of ATP or cocaine from the aptamers. Our approach confirms that the programmability and predictability of nucleic acids make synthetic DNA/RNA the perfect candidate material to re-engineer synthetic receptors that can undergo chemical fuel-triggered release of small-molecule cargoes and to rationally design non-equilibrium systems.

Chemical fuel-driven living and transient supramolecular polymerization

Temporal control over self-assembly process is a desirable trait in the quest towards adaptable and controllable materials. The ability to devise synthetic ways to control the growth, as well as decay of materials has long been a property which only the biological systems could perform seamlessly. A common synthetic strategy which works on the biological principles such as chemical fuel-driven control over temporal self-assembly profile has not been completely realized synthetically. Here we show, we filled this dearth by showing that a chemical fuel driven self-assembling system can not only be grown in a controlled manner, but it can also result in precise control over the assembly and disassembly kinetics. Herein, we elaborate strategies which clearly show that once a chemical fuel driven self-assembly is established it can be made receptive to multiple molecular cues such that the inherent growth and decay characteristics are programmed into the ensemble.

Temperature-controlled helical inversion of asymmetric triphenylamine-based supramolecular polymers; difference of handedness at the micro- and macroscopic levels

The M-helicity of asymmetric N-triphenylamine-based supramolecular polymers was inverted to the P-helicity during heating.

Substrate-Induced Self-Assembly of Cooperative Catalysts

Dissipative self-assembly processes in nature rely on chemical fuels that activate proteins for assembly through the formation of a noncovalent complex. The catalytic activity of the assemblies causes fuel degradation, resulting in the formation of an assembly in a high-energy, out-of-equilibrium state. Herein, we apply this concept to a synthetic system and demonstrate that a substrate can induce the formation of vesicular assemblies, which act as cooperative catalysts for cleavage of the same substrate.

Substrate-Induced Self-Assembly of Cooperative Catalysts

Dissipative self-assembly processes in nature rely on chemical fuels that activate proteins for assembly through the formation of a noncovalent complex. The catalytic activity of the assemblies causes fuel degradation, resulting in the formation of an assembly in a high-energy, out-of-equilibrium state. Herein, we apply this concept to a synthetic system and demonstrate that a substrate can induce the formation of vesicular assemblies, which act as cooperative catalysts for cleavage of the same substrate.

Oscillations, travelling fronts and patterns in a supramolecular system

Supramolecular polymers, such as microtubules, operate under non-equilibrium conditions to drive crucial functions in cells, such as motility, division and organelle transport¹. In vivo and in vitro size oscillations of individual microtubules^2,3 (dynamic instabilities) and collective oscillations⁴ have been observed. In addition, dynamic spatial structures, like waves and polygons, can form in non-stirred systems⁵. Here we describe an artificial supramolecular polymer made of a perylene diimide derivative that displays oscillations, travelling fronts and centimetre-scale self-organized patterns when pushed far from equilibrium by chemical fuels. Oscillations arise from a positive feedback due to nucleation-elongation-fragmentation, and a negative feedback due to size-dependent depolymerization. Travelling fronts and patterns form due to self-assembly induced density differences that cause system-wide convection. In our system, the species responsible for the nonlinear dynamics and those that self-assemble are one and the same. In contrast, other reported oscillating assemblies formed by vesicles⁶, micelles⁷ or particles⁸ rely on the combination of a known chemical oscillator and a stimuli-responsive system, either by communication through the solvent (for example, by changing pH^7-9), or by anchoring one of the species covalently (for example, a Belousov-Zhabotinsky catalyst^6,10). The design of self-oscillating supramolecular polymers and large-scale dissipative structures brings us closer to the creation of more life-like materials¹¹ that respond to external stimuli similarly to living cells, or to creating artificial autonomous chemical robots¹².

Energy consumption in chemical fuel-driven self-assembly

Nature extensively exploits high-energy transient self-assembly structures that are able to perform work through a dissipative process. Often, self-assembly relies on the use of molecules as fuel that is consumed to drive thermodynamically unfavourable reactions away from equilibrium. Implementing this kind of non-equilibrium self-assembly process in synthetic systems is bound to profoundly impact the fields of chemistry, materials science and synthetic biology, leading to innovative dissipative structures able to convert and store chemical energy. Yet, despite increasing efforts, the basic principles underlying chemical fuel-driven dissipative self-assembly are often overlooked, generating confusion around the meaning and definition of scientific terms, which does not favour progress in the field. The scope of this Perspective is to bring closer together current experimental approaches and conceptual frameworks. From our analysis it also emerges that chemically fuelled dissipative processes may have played a crucial role in evolutionary processes.

ATP-Driven Temporal Control over Structure Switching of Polymeric Micelles

An adenosine triphosphate (ATP)-fueled micellar system in the out-of-equilibrium state was constructed based on 4,5-diamino-1,3,5-triazine (DAT)-containing block copolymer. The block copolymer self-assembled into spherical micelles in equilibrium steady state at pH higher than its p K_a. The pendant DAT residues in protonated form acted as ATP catchers via hydrogen bonding and electrostatic interactions. Activated by ATP fuel, the polymeric micelles spontaneously disrupted into small aggregates of ATP/polymer hybrid complexes. The consumption of ATP energy via the enzymatic hydrolysis led to dissociation of the complexes and reversible formation of polymeric micelles. A transient self-assembly cycle, in which the assembly underwent autonomous division-fusion motion, was created using ATP fuel and enzyme; the switching of assembly structure was sustained by continuous supply of ATP fuel. This DAT-containing block copolymer have good biocompatibility, and drug-loaded micelles display ATP-responsive release behavior. It is expected that this ATP-fueled supramolecular assembly system will provide a functional platform for biomimic chemistry and therapeutic applications.

Molecular modelling of supramolecular one dimensional polymers

Supramolecular polymers exemplify the need to employ several computational techniques to study processes and phenomena occuring at varied length and time scales. Electronic processes, conformational and configurational excitations of small aggregates of chromophoric molecules, solvent effects under realistic thermodynamic conditions and mesoscale morphologies are some of the challenges which demand hierarchical modelling approaches. This review focusses on one-dimensional supramolecular polymers, the mechanism of self-assembly of monomers in polar and non-polar solvents and properties they exhibit. Directions for future work are as well outlined.

Bioinspired temporal supramolecular polymerization

Thriving natural systems precisely regulate their complex chemical organizations in space and time by recruitment of a complex network of fuel-driven, kinetically controlled, out-of-equilibrium transformations. Indeed this provides an active, adaptive and autonomous smart actions & functions. In contrast, synthetic systems exhibit simpler behavior owing to thermodynamically driven supramolecular polymerization with no temporal modulation of spatial organization. Stimulated by an outstanding control that nature demonstrates, a drive towards artificial out-of-equilibrium systems with the ambition to program activation and duration of structural transformations has emerged. To realize this vision, overwhelming efforts across the globe have been initiated to design temporally programmed synthetic supramolecular polymers. In an attempt to contribute to this trending field, our supramolecular chemistry group has thoroughly investigated a structure–property relationship that determines the mechanism of supramolecular polymerization. Exploiting these mechanistic insights, along with a bio-inspired fuel-driven enzyme mediated approach, we further attempted to program supramolecular polymers in both structural and temporal regimes. We believe, nature is the inspiration to the current era challenges and it also provides with the solution, a fuel-driven approach to address these. In this account, we shall discuss the efforts made by our group to build generic concept to create temporally programmable supramolecular polymers.

Nature's fuel-driven approach as a generic concept for structural and temporal regulation over biomimetic synthetic supramolecular polymerization.

Pathway driven self-assembly and living supramolecular polymerization in an amyloid-inspired peptide amphiphile

Temperature dependent stepwise self-assembly and seeded supramolecular polymerization of a peptide amphiphile form metastable nanoparticles to single nanofibers or twisted bundles, to render a mechanically tunable hydrogel.