A dynamic supramolecular polymer with stimuli-responsive handedness for in situ probing of enzymatic ATP hydrolysis

In situ biocatalytic ATP regulated, transient supramolecular polymerization

Temporal control over self-assembly processes is a highly desirable attribute that is efficiently exhibited by biological systems, such as actin filaments. In nature, various proteins undergo enzymatically catalysed chemical reactions that kinetically govern their structural and functional properties. Consequently, any stimuli that can alter their reaction kinetics can lead to a change in their growth or decay profiles. This underscores the urgent need to investigate bioinspired, adaptable and controllable synthetic materials. Herein we intend to develop a general strategy for controlling the growth and decay of self-assembled systems via enzymatically coupled reactions. We achieve this by the coupling of enzymes phosphokinase/phosphatase with a bolaamphiphilic cationic chromophore (PDI) which selectively self-assembles with ATP and disassembles upon its enzymatic hydrolysis. The aggregation process is efficiently regulated by the controlled in situ generation of ATP, through enzymatic reactions. By carefully managing the ATP generating components, we realize precise control over the self-assembly process. Moreover, we also show self-assembled structures with programmed temporal decay profiles through coupled enzymatic reactions of ATP generation and hydrolysis, essentially rendering the process dissipative. This work introduces a novel strategy to generate a reaction-coupled one-dimensional nanostructure with controlled dimensions inspired by biological systems.

Multiple-State Control over Supramolecular Chirality through Dynamic Chemistry Mediated Molecular Engineering

Dynamic chemistry utilizing both covalent and noncovalent bonds provides valid protocols in manipulating properties of self-assemblies and functions. Here we employ dynamic chemistry to realize multiple-route control over supramolecular chirality up to five states. N-protected fluorinated phenylalanine in the carboxylate state self-assembled into achiral nanoparticles ascribed to the amphiphilicity. Protonation promoted one-dimensional growth into helices with shrunk hydrophilicity, which in the presence of disulfide pyridine undergo chirality inversion promoted by the hydrogen bonding-directed coassembly. Further interacting with the water-soluble reductant cleavages the disulfide bond to initiate the rearrangement of coassemblies with a chirality inversion as well. Finally, by tuning the pH environments, aromatic nucleophilic substitution reaction between reduced products and perfluorinated phenylalanine occurs, giving distinct chiral nanoarchitectures with emerged luminescence and circularly polarized luminescence. We thus realized a particular five-state control by combining dynamic chemistry at one chiral compound, which greatly enriches the toolbox in fabricating responsive chiroptical materials.

Heparin binding induced supramolecular chirality into the self-assembly of perylenediimide bolaamphiphile

Chirality is one of the hallmarks of biomolecules. Herein, we utilize heparin, a chiral biomolecule and potent drug, to induce chiral organization into the assembly of an achiral molecule. Polyanionic heparin binds with a dicationic perylenediimide derivative to induce supramolecular helical organization in aqueous medium as well as in a highly competitive cell culture medium.

ATP/azobenzene-guanidinium self-assembly into fluorescent and multi-stimuli-responsive supramolecular aggregates

Building stimuli-responsive supramolecular systems is a way for chemists to achieve spatio-temporal control over complex systems as well as a promising strategy for applications ranging from sensing to drug-delivery. For its large spectrum of biological and biomedical implications, adenosine 5'-triphosphate (ATP) is a particularly interesting target for such a purpose but photoresponsive ATP-based systems have mainly been relying on covalent modification of ATP. Here, we show that simply mixing ATP with AzoDiGua, an azobenzene-guanidium compound with photodependent nucleotide binding affinity, results in the spontaneous self-assembly of the two non-fluorescent compounds into photoreversible, micrometer-sized and fluorescent aggregates. Obtained in water at room temperature and physiological pH, these supramolecular structures are dynamic and respond to several chemical, physical and biological stimuli. The presence of azobenzene allows a fast and photoreversible control of their assembly. ATP chelating properties to metal dications enable ion-triggered disassembly and fluorescence control with valence-selectivity. Finally, the supramolecular aggregates are disassembled by alkaline phosphatase in a few minutes at room temperature, resulting in enzymatic control of fluorescence. These results highlight the interest of using a photoswitchable nucleotide binding partner as a self-assembly brick to build highly responsive supramolecular entities involving biological targets without the need to covalently modify them.

Multiple Chirality Switching of a Dye-Grafted Helical Polymer Film Driven by Acid & Base

A stimuli-responsive multiple chirality switching material, which can regulate opposed chiral absorption characteristics, has great application value in the fields of optical modulation, information storage and encryption, etc. However, due to the rareness of effective functional systems and the complexity of material structures, developing this type of material remains an insurmountable challenge. Herein, a smart polymer film with multiple chirality inversion properties was fabricated efficiently based on a newly-designed acid & base-sensitive dye-grafted helical polymer. Benefited from the cooperative effects of various weak interactions (hydrogen bonds, electrostatic interaction, etc.) under the aggregated state, this polymer film exhibited a promising acid & base-driven multiple chirality inversion property containing record switchable chiral states (up to five while the solution showed three-state switching) and good reversibility. The creative exploration of such a multiple chirality switching material can not only promote the application progress of current chiroptical regulation technology, but also provide a significant guidance for the design and synthesis of future smart chiroptical switching materials and devices.

Impact of Ring-Closing on the Photophysical Properties of One-Dimensional π-Conjugated Molecular Aggregate

The self-assembled state of molecules plays a pivotal role in determining how inherent molecular properties transform and give rise to supramolecular functionalities and has long attracted attention. However, understanding the influence of morphologies spanning the nano- to mesoscopic scales of supramolecular assemblies derived from identical intermolecular interactions has been notoriously challenging due to dynamic structural change and monomer exchange of assemblies in solution. In this study, we demonstrate that curved one-dimensional molecular assemblies (supramolecular polymers) of lengths of around 70-200 nm, originating from the same luminescent molecule, exhibit distinct photoluminescent properties when they form closed circular structures (toroids) versus when they possess chain termini in solution (random coils). By exploiting the difference in kinetic stability between the toroids and random coils, we developed a dialysis protocol to selectively purify the former. It was revealed that these terminus-free closed structures manifest higher energy and more efficient luminescence compared with their mixed state with random coils. Time-resolved fluorescence measurements unveiled that random coils, due to their dynamic structural fluctuation in solution, generate local defects throughout the main chain, leading to luminescence from lower energy levels. In mixtures of the two assemblies, luminescence was exclusively observed from such a lower energy level of random coils, a result attributed to energy transfer between the assemblies. This work emphasizes that for identical supramolecular assemblies, only averaged properties have traditionally been considered, but their structures at the nano- to mesoscopic scale are important especially if they have a certain degree of shape persistency even in solution.

Co-assembly-mediated biosupramolecular catalysis: thermodynamic insights into nucleobase specific (oligo)nucleotide attachment and cleavage

Gaining control over the stability and cleavage of phosphoester and phosphodiester remains a matter of interest for their application in biotechnology to oligonucleotide-based therapeutics. Herein, we report an efficient unactivated phosphoester hydrolysis (stable mono/di/tri/cyclic nucleotide to nucleoside conversion) via a biosupramolecular system comprising of a non-covalent complex of enzyme, alkaline phosphatase (ALP), and Zn(II)-metallosurfactant. We also demonstrate the nucleobase selective activation or inhibition of ALP-mediated oligonucleotide digestion process using that complex. The higher binding affinity of Zn(II)-containing headgroup with phosphate-containing substrate enhanced the effective substrate concentration surrounding the enzyme, which, in turn, results in a drastic decrease in the Michaelis constant (KM), along with an increase in the turnover (kcat). The catalytic activation or inhibition of nucleobase-specific oligonucleotide digestion depends on the hydration, localization of the substrates, and viscosity of the resultant co-assembly upon substrate binding with the enzyme-metallosurfactant complex. Additionally, through isothermal titration calorimetry experiment, we demonstrate enthalpy-entropy change during both the supramolecular binding of (oligo)nucleotides and simultaneous activation/inhibition in catalytic cleavage. Overall, it showed the possible modularity of Zn(II)-mediated biosupramolecular interaction, describing intrinsic thermodynamic aspects in developing complex biocatalytic circuits with nucleobase-specific oligonucleotides inputs, which are relevant in designing nucleic acid-based cargo for drug delivery and bioimaging.

Macroscopic handedness inversion of terbium coordination polymers achieved by doping homochiral ligand analogues

Inspired by natural biological systems, chiral or handedness inversion by altering external and internal conditions to influence intermolecular interactions is an attractive topic for regulating chiral self-assembled materials. For coordination polymers, the regulation of their helical handedness remains little reported compared to polymers and supramolecules. In this work, we choose the chiral ligands R-pempH2 (pempH2 = (1-phenylethylamino)methylphosphonic acid) and R-XpempH2 (X = F, Cl, Br) as the second ligand, which can introduce C-H⋯π and C-H⋯X interactions, doped into the reaction system of the Tb(R-cyampH)3·3H2O (cyampH2 = (1-cyclohexylethylamino)methylphosphonic acid) coordination polymer, which itself can form a right-handed superhelix by van der Waals forces, and a series of superhelices R-1H-x, R-2F-x, R-3Cl-x, and R-4Br-x with different doping ratios x were obtained, whose handedness is related to the second ligand and its doping ratio, indicating the decisive role of interchain interactions of different strengths in the helical handedness. This study could provide a new pathway for the design and self-assembly of chiral materials with controllable handedness and help the further understanding of the mechanism of self-assembly of coordination polymers forming macroscopic helical systems.

Nanoparticle Self-Assembly: From Design Principles to Complex Matter to Functional Materials

The creation of matter with varying degrees of complexities and desired functions is one of the ultimate targets of self-assembly. The ability to regulate the complex interactions between the individual components is essential in achieving this target. In this direction, the initial success of controlling the pathways and final thermodynamic states of a self-assembly process is promising. Despite the progress made in the field, there has been a growing interest in pushing the limits of self-assembly processes. The main inception of this interest is that the intended self-assembled state, with varying complexities, may not be "at equilibrium (or at global minimum)", rendering free energy minimization unsuitable to form the desired product. Thus, we believe that a thorough understanding of the design principles as well as the ability to predict the outcome of a self-assembly process is essential to form a collection of the next generation of complex matter. The present review highlights the potent role of finely tuned interparticle interactions in nanomaterials to achieve the preferred self-assembled structures with the desired properties. We believe that bringing the design and prediction to nanoparticle self-assembly processes will have a similar effect as retrosynthesis had on the logic of chemical synthesis. Along with the guiding principles, the review gives a summary of the different types of products created from nanoparticle assemblies and the functional properties emerging from them. Finally, we highlight the reasonable expectations from the field and the challenges lying ahead in the creation of complex and evolvable matter.

Phosphates Induced H-Type or J-Type Aggregation of Cationic Porphyrins with Varied Side Chains

Non-covalent interactions have been extensively used to fabricate nanoscale architectures in supramolecular chemistry. However, the biomimetic self-assembly of diverse nanostructures in aqueous solution with reversibility induced by different important biomolecules remains a challenge. Here, we report the synthesis and aqueous self-assembly of two chiral cationic porphyrins substituted with different types of side chains (branched or linear). Helical H-aggregates are induced by pyrophosphate (PPi) as indicated by circular dichroism (CD) measurement, while J-aggregates are formed with adenosine triphosphate (ATP) for the two porphyrins. By modifying the peripheral side chains from linear to a branched structure, more pronounced H- or J-type aggregation was promoted through the interactions between cationic porphyrins and the biological phosphate ions. Moreover, the phosphate-induced self-assembly of the cationic porphyrins is reversible in the presence of the enzyme alkaline phosphatase (ALP) and repeated addition of phosphates.

Chiral Supramolecular Polymers Assembled from Conformationally Flexible Amino-Acid-Substituted Biphenyldiimides

Hydrogen-bonded polymers are a class of highly dynamic supramolecular aggregates, whose self-assembly may be tuned by very mild external or internal stimuli. However, the rational design of chiral supramolecules remains challenging especially when flexible components are involved. The combination of the inherent weakness and dynamic nature of the intermolecular bonds that hold together such assemblies with unrestricted molecular motions introduces additional factors which may affect the self-assembly process. In this report, the self-assembly of four amino acid-derived chiral biphenyldiimides into open-chain 1D supramolecular polymers is presented. While the primary driving force, COOH···HOOC hydrogen bonding, is responsible for the polymer growth in all cases, the amino acid side chains play an important role in either stabilizing or destabilizing the assemblies obtained, as deduced from studies of the thermodynamics of the self-assembly process. Furthermore, substantial differences in the structural factors governing the polymerization process between dynamic liquid and static solid are found. This work demonstrates the potential of the rather unexplored class of diimide-based organic dyes in the formation of well-organized chiral supramolecular assemblies with tunable properties.

Modeling of minimal systems based on ATP-Zn coordination for chemically fueled self-assembly

Following nature's example, there is currently strong interest in using adenosine 5'-triphosphate (ATP) as a fuel for the self-assembly of functional materials with transient/non-equilibrium behaviours. These hold great promise for applications, e.g. in catalysis and drug delivery. In a recent seminal work [Maiti et al., Nat. Chem., 2016, 8, 725], binding of ATP to the metallosurfactant zinc hexadecyl-1,4,7-triazacyclononane ([ZnC₁₆ TACN]²⁺) was exploited to produce ATP-fueled transient vesicles. Crucial to the complex formation is the ability of ATP to bind to the metal ion. As a first step to unveil the key elements underlying this process, we investigate the interaction of ATP with Zn²⁺ and with methyl-1,4,7-triazacyclononane ([ZnCH₃ TACN]²⁺), using all-atom molecular dynamics simulations. The free energy landscape of the complex formation is sampled using well-tempered metadynamics with three collective variables, corresponding to the coordination numbers of Zn²⁺ with the oxygen atoms of the three phosphate groups. We find that the structure of the ternary complex is controlled by direct triphosphate coordination to zinc, with a minor role played by the interactions between ATP and CH₃ TACN which, however, may be important for the build-up of supramolecular assemblies.

Electrostatically Directed Long-Range Self-Assembly of Nucleotides with Cationic Nanoparticles To Form Multifunctional Bioplasmonic Networks

Precise control over interparticle interactions is essential to retain the functions of individual components in a self-assembled superstructure. Here, we report the design of a multifunctional bioplasmonic network via an electrostatically directed self-assembly process involving adenosine 5'-triphosphate (ATP). The present study unveils the ability of ATP to undergo a long-range self-assembly in the presence of cations and gold nanoparticles (AuNP). Modelling and NMR studies gave a qualitative insight into the major interactions driving the bioplasmonic network formation. ATP-Ca²⁺ coordination helps in regulating the electrostatic interaction, which is crucial in transforming an uncontrolled precipitation into a kinetically controlled aggregation process. Remarkably, ATP and AuNP retained their inherent properties in the multifunctional bioplasmonic network. The generality of electrostatically directed self-assembly process was extended to different nucleotide-nanoparticle systems.

ATP-Induced Emergent Circularly Polarized Luminescence and Encryption

Biomimetic ATP-driven supramolecular assembly is important to understand various biological processes and dissipative systems. Here, we report an ATP-driven chiral assembly exhibiting circularly polarized luminescence (CPL) via the interaction of an achiral terpyridine-based Zn^II complex with nucleotides. It was found that while the metal complexes could co-assemble with the nucleotides to form fluorescent assemblies, only a combination of furan-substituted terpyridine complex and ATP showed an intense CPL with a dissymmetry factor (g_lum ) as high as 0.20. This means that the complex could recognize ATP using CPL as a readout signal, thus providing an example of ATP encryption. Interestingly, when ATP was transferred into ADP or AMP under enzymatic hydrolysis, the CPL decreases or disappears. Addition of ATP generates CPL again, thus producing an ATP-induced CPL system. This work presents the first example of ATP-induced CPL and encryption.

Molecular communications in complex systems of dynamic supramolecular polymers

Supramolecular polymers are composed of monomers that self-assemble non-covalently, generating distributions of monodimensional fibres in continuous communication with each other and with the surrounding solution. Fibres, exchanging molecular species, and external environment constitute a sole complex system, which intrinsic dynamics is hard to elucidate. Here we report coarse-grained molecular simulations that allow studying supramolecular polymers at the thermodynamic equilibrium, explicitly showing the complex nature of these systems, which are composed of exquisitely dynamic molecular entities. Detailed studies of molecular exchange provide insights into key factors controlling how assemblies communicate with each other, defining the equilibrium dynamics of the system. Using minimalistic and finer chemically relevant molecular models, we observe that a rich concerted complexity is intrinsic in such self-assembling systems. This offers a new dynamic and probabilistic (rather than structural) picture of supramolecular polymer systems, where the travelling molecular species continuously shape the assemblies that statistically emerge at the equilibrium.

The dynamic structure of supramolecular polymers is challenging to determine both in experiments and in simulations. Here the authors use coarse-grained molecular models to provide a comprehensive analysis of the molecular communication in these complex molecular systems.

Arrow of Time, Entropy, and Protein Folding: Holistic View on Biochirality

Chirality is a universal phenomenon, embracing the space–time domains of non-organic and organic nature. The biological time arrow, evident in the aging of proteins and organisms, should be linked to the prevalent biomolecular chirality. This hypothesis drives our exploration of protein aging, in relation to the biological aging of an organism. Recent advances in the chirality discrimination methods and theoretical considerations of the non-equilibrium thermodynamics clarify the fundamental issues, concerning the biphasic, alternative, and stepwise changes in the conformational entropy associated with protein folding. Living cells represent open, non-equilibrium, self-organizing, and dissipative systems. The non-equilibrium thermodynamics of cell biology are determined by utilizing the energy stored, transferred, and released, via adenosine triphosphate (ATP). At the protein level, the synthesis of a homochiral polypeptide chain of L-amino acids (L-AAs) represents the first state in the evolution of the dynamic non-equilibrium state of the system. At the next step the non-equilibrium state of a protein-centric system is supported and amended by a broad set of posttranslational modifications (PTMs). The enzymatic phosphorylation, being the most abundant and ATP-driven form of PTMs, illustrates the principal significance of the energy-coupling, in maintaining and reshaping the system. However, the physiological functions of phosphorylation are under the permanent risk of being compromised by spontaneous racemization. Therefore, the major distinct steps in protein-centric aging include the biosynthesis of a polypeptide chain, protein folding assisted by the system of PTMs, and age-dependent spontaneous protein racemization and degradation. To the best of our knowledge, we are the first to pay attention to the biphasic, alternative, and stepwise changes in the conformational entropy of protein folding. The broader view on protein folding, including the impact of spontaneous racemization, will help in the goal-oriented experimental design in the field of chiral proteomics.

Thermotropic chirality enhancement of nanoparticles constructed from foldamer/bis(amino acid) complexes

Herein, chiral nanoparticles are constructed by mixing an artificial foldamer bearing aza-18-crown-6 pendants with l-homocystine perchlorate salt, showing a thermotropic chirality enhancement due to the binding mode changes in the heating process.

Chiral graphene-based supramolecular hydrogels toward tumor therapy

Drugs with chiral property are playing very important role on precise treatment of diseases (especially antitumor drugs), however, enantioselective delivery of chiral anticancer drugs is still challenge. Herein, a chiral...

Spatiotemporal dynamics of self-assembled structures in enzymatically induced agonistic and antagonistic conditions

Predicting and designing systems with dynamic self-assembly properties in a spatiotemporal fashion is an important research area across disciplines ranging from understanding the fundamental non-equilibrium features of life to the fabrication of next-generation materials with life-like properties. Herein, we demonstrate a spatiotemporal dynamics pattern in the self-assembly behavior of a surfactant from an unorganized assembly, induced by adenosine triphosphate (ATP) and enzymes responsible for the degradation or conversion of ATP. We report the different behavior of two enzymes, alkaline phosphatase (ALP) and hexokinase (HK), towards adenosine triphosphate (ATP)-driven surfactant assembly, which also results in contrasting spatiotemporal dynamic assembly behavior. Here, ALP acts antagonistically, resulting in transient self-assemblies, whereas HK shows agonistic action with the ability to sustain the assemblies. This dynamic assembly behavior was then used to program the time-dependent emergence of a self-assembled structure in a two-dimensional space by maintaining concentration gradients of the enzymes and surfactant at different locations, demonstrating a new route for obtaining 'spatial' organizational adaptability in a self-organized system of interacting components for the incorporation of programmed functionality.

Transpositional Circularly Polarized Luminescence from Transient Charge-Transfer Coassembly

Charge-transfer (CT) complexation between electron-rich and deficient aromatics has been widely applied in functional optical and photovoltaic materials. The selective complexation and spontaneous disassociation behavior of a dynamic charge-transfer coassembly possess potential in designing smart and dynamic luminescent materials, which however have not been addressed so far. In this work, the transient charge-transfer driven coassembly between π-conjugated amino acids and tetracyanobenzene, showing dynamic luminescent transition and circularly polarized luminescence (CPL) evolution property, is illustrated. Transient coassembly behaviors are independent to the diverse binding sites covering fluorene, naphthalene, and anthracene, attributed to the intramolecular CH…π interaction. Incorporation of fluorescent dyes enables a transient light harvesting process with hyperchromic CPL properties. Spontaneous green-to-red CPL transition hydrogels are also fabricated by embedding a competitive CT donor. Using a polymeric matrix treated by organic solvents, charge-transfer coassembly is immobilized with diverse circularly polarized luminescence. Such sensitive complexation shows applications in moisture-responsive luminescent materials and multiple luminescent color evolutions are realized.

Halogen Bonding Mediated Hierarchical Supramolecular Chirality

As a highly directional force, halogen bonds based on σ-holes have potential to manipulate supramolecular chirality and build functional chiral systems, which however are largely unexplored. In this work, we report the manipulation of supramolecular chirality in hierarchically self-assembled systems via intracomponent halogen bonds. Cholesteryl cyanostilbene conjugates and 1,3,5-trifluoro-2,4,6-triiodobenzene formed a C₃ symmetrical supramolecular complex with ultrahigh binding affinity and binding constants at 10¹¹ order of magnitude. The halogen bonded propeller geometries exhibited inversed chirality as well as chiroptical activity compared to the pristine helically orientated aggregates. Halogen bonds enabled the engineering of nanoarchitectures, affording supercoiled helical structures and highly aligned nanotubes. This work unveils the role of halogen bonds in controlling supramolecular chirality, establishing a protocol to build functional chiroptical materials from species containing σ-holes and halogenated domains.

The helical supramolecular assembly of oligopyridylamide foldamers in aqueous media can be guided by adenosine diphosphates

A metal-free and achiral tri-pyridylamide foldamer, DM 11, containing a critical naphthalimide side chain self-assembles in a left-handed helical manner in the presence of chiral adenosine phosphates, under physiological conditions. Surprisingly, a very high degree of helicity in the foldamer assemblies was observed with ADP compared to other nucleoside phosphates, including ATP.

Electrochemical Polymerization Induced Chirality Fixation of Crystalline Pillararene-Based Polymer and Its Application in Interfacial Chiral Sensing

A new strategy has been developed for the direct chirality fixation, which is induced by electrochemical polymerization, of macrocyclic hosts pillar[5]arene. Taking advantage of electrochemical polymerization, thiophene-modified pillar[5]arene monomers (Th-P[5]A) have been regularly arranged under the action of an electric field to form chiral nanofiber-like crystalline pillar[5]arene-based polymers (poly-Th-P[5]A), showing a significant circular dichroism (CD) signal. With the active photochemical properties, poly-Th-P[5]A is first used as a photoelectrochemical (PEC) chiral sensor for the identification and determination of l- and d-ascorbic acid (l-AA, d-AA) without adding any extra photoactive probes. Importantly, the chiral recognition between poly-Th-P[5]A and l-AA also triggers a polarity conversion for the photocurrent of the polymer, and it greatly results in a broad chiral detection range for l-AA, crossing 6 orders of magnitude. This work provides a promotional strategy for building a PEC chiral recognition platform based on pillararenes.

Dynamics in supramolecular nanomaterials

Self-assembly of amphiphilic small molecules in water leads to nanostructures with customizable structure-property relationships arising from their tunable chemistries. Characterization of these assemblies is generally limited to their static structures -e.g. their geometries and dimensions - but the implementation of tools that provide a deeper understanding of molecular motions has recently emerged. Here, we summarize recent reports showcasing dynamics characterization tools and their application to small molecule assemblies, and we go on to highlight supramolecular systems whose properties are substantially affected by their conformational, exchange, and water dynamics. This review illustrates the importance of considering dynamics in rational amphiphile design.

Water-Soluble Supramolecular Polymers of Paired and Stacked Heterocycles: Assembly, Structure, Properties, and a Possible Path to Pre-RNA

The hypothesis that RNA and DNA are products of chemical and biological evolution has motivated our search for alternative nucleic acids that may have come earlier in the emergence of life-polymers that possess a proclivity for covalent and non-covalent self-assembly not exhibited by RNA. Our investigations have revealed a small set of candidate ancestral nucleobases that self-assemble into hexameric rosettes that stack in water to form long, twisted, rigid supramolecular polymers. These structures exhibit properties that provide robust solutions to long-standing problems that have stymied the search for a prebiotic synthesis of nucleic acids. Moreover, their examination by experimental and computational methods provides insight into the chemical and physical principles that govern a particular class of water-soluble one-dimensional supramolecular polymers. In addition to efficient self-assembly, their lengths and polydispersity are modulated by a wide variety of positively charged, planar compounds; their assembly and disassembly are controlled over an exceedingly narrow pH range; they exhibit spontaneous breaking of symmetry; and homochirality emerges through non-covalent cross-linking during hydrogel formation. Some of these candidate ancestral nucleobases spontaneously form glycosidic bonds with ribose and other sugars, and, most significantly, functionalized forms of these heterocycles form supramolecular structures and covalent polymers under plausibly prebiotic conditions. This Perspective recounts a journey of discovery that continues to reveal attractive answers to questions concerning the origins of life and to uncover the principles that control the structure and properties of water-soluble supramolecular polymers.

Selective sensing of adenosine monophosphate (AMP) over adenosine diphosphate (ADP), adenosine triphosphate (ATP), and inorganic phosphates with zinc(II)-dipicolylamine-containing gold nanoparticles

Mixed monolayer-protected gold nanoparticles containing surface-bound triethylene glycol and dipicolylamine groups aggregated in water/methanol, 1 : 2 (v/v) in the presence of nucleotides, if the solution also contained zinc(ii) nitrate to convert the dipicolylamine units into the corresponding zinc complexes. Nanoparticle aggregation could be followed with the naked eye by the colour change of the solution from red to purple followed by nanoparticle precipitation. The sensitivity was highest for adenosine triphosphate (ATP), which could be detected at concentrations >10 μM, and decreased over adenosine diphosphate (ADP) to adenosine monophosphate (AMP), consistent with the typically higher affinity of zinc(ii)-dipicolylamine-derived receptors for higher charged nucleotides. Inorganic sodium diphosphate and triphosphate interfered in the assay by also inducing nanoparticle aggregation. However, while the nucleotide-induced aggregates persisted even at higher analyte concentrations, the nanoparticles that were precipitated with inorganic salts redissolved again when the salt concentration was increased. The thus resulting solutions retained their ability to respond to nucleotides, but they now preferentially responded to AMP. Accordingly, AMP could be sensed selectively at concentrations ≥50 μM in an aqueous environment, even in the presence of other nucleotides and inorganic anions. This work thus introduces a novel approach for the sensing of a nucleotide that is often the most difficult analyte to detect with other assays.

Strong Enantiomeric Preference on the Macroion-Counterion Interaction Induced by Weakly Associated Chiral Counterions

The role of chiral counterions on the attraction and self-assembly of chiral Pd₁₂L₂₄ metal organic cages (MOCs) with NO₃^- being the original counterion is studied by laser light scattering and isothermal titration calorimetry. Nitrates can trigger the self-assembly of macrocationic Pd₁₂L₂₄ into hollow spherical blackberry-type supramolecular structures via counterion-mediated attraction. Although chiral counteranions, such as N-(tert-butoxycarbonyl)-alanine (Boc-Ala), have weaker interaction with the MOCs compared to NO₃^-, they can induce different assembly behaviors between two enantiomeric MOCs by inhibiting the MOC-nitrate binding and weakening the interaction between them. The d-counterions are capable of selectively suppressing and slowing down the assembly of l-MOCs and also considerably decreasing their assembly size due to the much weaker MOC-nitrate interaction. The same scenario is observed for l-counterions when interacting with the d-MOCs. This study unveils the role of weakly associated chiral counterions on the central chiral macroions, especially their supramolecular structure formation, and provides additional evidence on the mechanism of the homochirality phenomenon.

ATP-Responsive and ATP-Fueled Self-Assembling Systems and Materials

Adenosine triphosphate (ATP) is a central metabolite that plays an indispensable role in various cellular processes, from energy supply to cell-to-cell signaling. Nature has developed sophisticated strategies to use the energy stored in ATP for many metabolic and non-equilibrium processes, and to sense and bind ATP for biological signaling. The variations in the ATP concentrations from one organelle to another, from extracellular to intracellular environments, and from normal cells to cancer cells are one motivation for designing ATP-triggered and ATP-fueled systems and materials, because they show great potential for applications in biological systems by using ATP as a trigger or chemical fuel. Over the last decade, ATP has been emerging as an attractive co-assembling component for man-made stimuli-responsive as well as for fuel-driven active systems and materials. Herein, current advances and emerging concepts for ATP-triggered and ATP-fueled self-assemblies and materials are discussed, shedding light on applications and highlighting future developments. By bringing together concepts of different domains, that is from supramolecular chemistry to DNA nanoscience, from equilibrium to non-equilibrium self-assembly, and from fundamental sciences to applications, the aim is to cross-fertilize current approaches with the ultimate aim to bring synthetic ATP-dependent systems closer to living systems.

Computationally Guided Tuning of Amino Acid Configuration Influences the Chiroptical Properties of Supramolecular Peptide-π-Peptide Nanostructures

Self-assembled supramolecular materials derived from peptidic macromolecules with π-conjugated building blocks are of enormous interest because of their aqueous solubility and biocompatibility. The design rules to achieve tailored optoelectronic properties from these types of materials can be guided by computation and virtual screening rather than intuition-based experimental trial-and-error. Using machine learning, we reported previously that the supramolecular chirality in self-assembled aggregates from VEVAG-π-GAVEV type peptidic materials was most strongly influenced by hydrogen bonding and hydrophobic packing of the alanine and valine residues. Herein, we build upon this idea to demonstrate through molecular-level experimental characterization and all-atom molecular modeling that varying the stereogenic centers of these residues has a profound impact on the optoelectronic properties of the supramolecular aggregates, whereas the variation of stereogenic centers of other residues has only nominal influence on these properties. This study highlights the synergy between computational and experimental insight relevant to the control of chiroptical or other electronic properties associated with supramolecular materials.

Self-Assembly Propensity Dictates Lifetimes in Transient Naphthalimide-Dipeptide Nanofibers

Transient self-assembly of dipeptide nanofibers with lifetimes that are predictably variable through dipeptide sequence design are presented. This was achieved using 1,8-naphthalimide (NI) amino acid methyl-esters (Phe, Tyr, Leu) that are biocatalytically coupled to amino acid-amides (Phe, Tyr, Leu, Val, Ala, Ser) to form self-assembling NI-dipeptides. However, competing hydrolysis of the dipeptides results in disassembly. It was demonstrated that the kinetic parameters like lifetimes of these nanofibers can be predictably regulated by the thermodynamic parameter, namely the self-assembly propensity of the constituent dipeptide sequence. These lifetimes could vary from minutes, to hours, to permanent gels that do not degrade. Moreover, the in-built NI fluorophore was utilized to image the transient nanostructures in solution with stimulated emission depletion (STED) based super-resolution fluorescence microscopy.

An Azobenzene-Based Single-Component Supramolecular Polymer Responsive to Multiple Stimuli in Water

One of the most appealing features of supramolecular assemblies is their ability to respond to external stimuli due to their noncovalent nature. This provides the opportunity to gain control over their size, morphology, and chemical properties and is key toward some of their applications. However, the design of supramolecular systems able to respond to multiple stimuli in a controlled fashion is still challenging. Here we report the synthesis and characterization of a novel discotic molecule, which self-assembles in water into a single-component supramolecular polymer that responds to multiple independent stimuli. The building block of such an assembly is a C₃-symmetric monomer, consisting of a benzene-1,3,5-tricarboxamide core conjugated to a series of natural and non-natural functional amino acids. This design allows the use of rapid and efficient solid-phase synthesis methods and the modular implementation of different functionalities. The discotic monomer incorporates a hydrophobic azobenzene moiety, an octaethylene glycol chain, and a C-terminal lysine. Each of these blocks was chosen for two reasons: to drive the self-assembly in water by a combination of H-bonding and hydrophobicity and to impart specific responsiveness. With a combination of microscopy and spectroscopy techniques, we demonstrate self-assembly in water and responsiveness to temperature, light, pH, and ionic strength. This work shows the potential to integrate independent mechanisms for controlling self-assembly in a single-component supramolecular polymer by the rational monomer design and paves the way toward the use of multiresponsive systems in water.

Helical supramolecular polymers with rationally designed binding sites for chiral guest recognition

Since various helical supramolecular polymers became available, their application to molecular chirality recognition have been anticipated but not extensively studied. So far, only a few examples of chiral reactions have been reported, but none for chiral separation. Here, we report the application of a helical supramolecular polymer to the enantio-separation of chiral guest molecules. The monomer of this supramolecular polymer is the salt-pair of a dendritic carboxylic acid with an enantiopure amino alcohol. In an apolar solvent, this salt-pair stacks via hydrogen bonds to form a helical polymer. In conjunction with this carboxylic acid, various amino alcohols afford supramolecular polymers, whose helical handedness is determined by the stereochemistry of the amino alcohols. When two salts with the same chirality are mixed, they undergo copolymerization, while those with opposite chirality do not. Owing to this stereoselective copolymerizability, the helical supramolecular polymer could bias the enantiomeric composition of chiral amino alcohols.

Since various helical supramolecular polymers became available, their application in molecular chirality recognition have been anticipated but not extensively studied. Here, the authors report the application of a helical supramolecular polymer for the enantio separation of chiral guest molecules.

Histidine Proton Shuttle-Initiated Switchable Inversion of Circularly Polarized Luminescence

Switchable inversion of the sign of circularly polarized luminescence (CPL) in chiral supramolecular systems has gained remarkable interest because of its role in understanding the chirality-switching phenomena in biological systems and developing smart chiral luminescent materials. Herein, inspired by the histidine proton shuttle in natural enzymes, we synthesized a histidine π-gel (PyC₃H) and realized reversible inversion of supramolecular chirality and CPL by receiving and then transferring a proton. It was found that in the course of histidine protonation by adding an external proton source, the transcription of intrinsic molecular chirality of PyC₃H to the supramolecular level biased, achieving dynamic control over the PyC₃H gel with left-handed CPL inversed into the right-handed one. The mechanism study revealed that the supramolecular chirality and CPL inversion are mainly affected by the cooperation adjustment of hydrogen bonds and π-π stacking upon histidine protonation and deprotonation, which causes the re-orientations of pyrene chromophores. This work sets up an alternative effective method to fabricate tunable CPL-active materials while using the same chiral small molecules, which provides a new insight into developing bio-inspired switchable supramolecular materials.

A Quinoline-Appended Cyclodextrin Derivative as a Highly Selective Receptor and Colorimetric Probe for Nucleotides

The design and development of specific recognition and sensing systems for biologically important anionic species has received growing attention in recent years, as they play significant roles in biology, pharmacy, and environmental sciences. Herein, a new supramolecular sensing probe L1 was developed for highly selective differentiation of nucleotides. L1 displayed extremely marked absorption and emission differentiation upon binding with nucleotide homologs of AMP, ADP, and ATP, due to the divergent spatial orientations of guests upon binding, which allowed for a naked-eye colorimetric differentiation for nucleotides. A differentiating mechanism was unambiguously rationalized by using various spectroscopic studies and theoretical calculations. Furthermore, we successfully demonstrated that L1 can be applied to the real-time monitoring of the enzyme-catalyzed phosphorylation/dephosphorylation processes and thus demonstrated an unprecedented visualizable strategy for selectively differentiating the structurally similar nucleotides and real-time monitoring of biological processes via fluorescent and colorimetric changes.

Programmed Recognition between Complementary Dinucleolipids To Control the Self-Assembly of Lipidic Amphiphiles

One of the major goals in systems chemistry is to create molecular assemblies with emergent properties that are characteristic of life. An interesting approach toward this goal is based on merging different biological building blocks into synthetic systems with properties arising from the combination of their molecular components. The covalent linkage of nucleic acids (or their constituents: nucleotides, nucleosides and nucleobases) with lipids in the same hybrid molecule leads, for example, to the so-called nucleolipids. Herein, we describe nucleolipids with a very short sequence of two nucleobases per lipid, which, in combination with hydrophobic effects promoted by the lipophilic chain, allow control of the self-assembly of lipidic amphiphiles to be achieved. The present work describes a spectroscopic and microscopy study of the structural features and dynamic self-assembly of dinucleolipids that contain adenine or thymine moieties, either pure or in mixtures. This approach leads to different self-assembled nanostructures, which include spherical, rectangular and fibrillar assemblies, as a function of the sequence of nucleobases and chiral effects of the nucleolipids involved. We also show evidence that the resulting architectures can encapsulate hydrophobic molecules, revealing their potential as drug delivery vehicles or as compartments to host interesting chemistries in their interior.

Controlling Supramolecular Chirality in Peptide-π-Peptide Networks by Variation of the Alkyl Spacer Length

Self-assembled supramolecular organic materials with π-functionalities are of great interest because of their applications as biocompatible nanoelectronics. A detailed understanding of molecular parameters to modulate the formation of hierarchical structures can inform design principles for materials with engineered optical and electronic properties. In this work, we combine molecular-level characterization techniques with all-atom molecular simulations to investigate the subtle relationship between the chemical structure of peptide-π-peptide molecules and the emergent supramolecular chirality of their spontaneously self-assembled nanoaggregates. We demonstrate through circular dichroism measurements that we can modulate the chirality by incorporating alkyl spacers of various lengths in between the peptides and thienylene-phenylene π-system chromophores: even numbers of alkyl carbons in the spacer units (0, 2) induce M-type helical character whereas odd numbers (1, 3) induce P-type. Corroborating molecular dynamics simulations and explicating machine learning analysis techniques identify hydrogen bonding and hydrophobic packing to be the principal discriminants of the observed chirality switches. Our results present a molecular-level design rule to engineer chirality into optically and electronically active nanoaggregates of these peptidic building blocks by exploiting systematic variations in the alkyl spacer length.

Stimulated transformation of soft helix among helicoidal, heliconical, and their inverse helices

Dynamic modulation of soft helix in terms of the molecular organization, handedness, and pitch length could result in a sophisticated control over its functions, opening numerous possibilities toward the exploration of previously unidentified applications. Here, we report a dynamic and reversible transformation of a soft helical superstructure among the helicoidal (molecules orthogonal to helical axis), heliconical (molecules oblique to the helical axis, i.e., oblique helicoidal), and their inverse helices, together with a tunability on the helical pitch, by combining electrical and optical manipulations. This multistate transformation depends on a matching of the temperature, the strength of external stimuli, and the bend and twist elastic effects of the system. A laser emission with tunable wavelength and polarization, and prescribed micropatterns formed by any aforementioned architectures were achieved.

Kinetic asymmetry allows macromolecular catalysts to drive an information ratchet

Molecular machines carry out their function by equilibrium mechanical motions in environments that are far from thermodynamic equilibrium. The mechanically equilibrated character of the trajectories of the macromolecule has allowed development of a powerful theoretical description, reminiscent of Onsager’s trajectory thermodynamics, that is based on the principle of microscopic reversibility. Unlike the situation at thermodynamic equilibrium, kinetic parameters play a dominant role in determining steady-state concentrations away from thermodynamic equilibrium, and kinetic asymmetry provides a mechanism by which chemical free-energy released by catalysis can drive directed motion, molecular adaptation, and self-assembly. Several examples drawn from the recent literature, including a catenane-based chemically driven molecular rotor and a synthetic molecular assembler or pump, are discussed.

The mechanism by which macromolecular catalysts use energy from exergonic reactions to move, adapt, and assemble has been unclear. In this Perspective article, R. Dean Astumian shows that in addition to disequilibrium of the catalyzed reaction, kinetic asymmetry is the essential feature required to drive non-equilibrium response by an information ratchet mechanism.

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.