Altering the structures of 3D supramolecular assemblies from melamine and cyanuric acid derivatives in water

Herein, we obtained two supramolecular assemblies with layered structures from melamine, N-methylmelamine, and hexynyl-cyanuric acid in water. By combination of X-ray diffraction, electron microscopy, and molecular dynamics studies, we found that introducing one methyl group in melamine alters the arrangement of the layers in these structures.

Visible-Light Driven Control Over Triply and Quadruply Hydrogen-Bonded Supramolecular Assemblies

Supramolecular polymers offer tremendous potential to produce new "smart" materials, however, there remains a need to develop systems that are responsive to external stimuli. In this work, visible-light responsive hydrogen-bonded supramolecular polymers comprising photoresponsive supramolecular synthons (I-III) consisting of two hydrogen bonding motifs (HBMs) connected by a central ortho-tetrafluorinated azobenzene have been characterized by DOSY NMR and viscometry. Comparison of different hydrogen-bonding motifs reveals that assembly in the low and high concentration regimes is strongly influenced by the strength of association between the HBMs. I, Incorporating a triply hydrogen-bonded heterodimer, was found to exhibit concentration dependent switching between a monomeric pseudo-cycle and supramolecular oligomer through intermolecular hydrogen bonding interactions between the HBMs. II, Based on the same photoresponsive scaffold, and incorporating a quadruply hydrogen-bonded homodimer was found to form a supramolecular polymer which was dependent upon the ring-chain equilibrium and thus dependent upon both concentration and photochemical stimulus. Finally, III, incorporating a quadruply hydrogen-bonded heterodimer represents the first photoswitchable AB type hydrogen-bonded supramolecular polymer. Depending on the concentration and photostationary state, four different assemblies dominate for both monomers II and III, demonstrating the ability to control supramolecular assembly and physical properties triggered by light.

Highly stretchable and self-healing photoswitchable supramolecular fluorescent polymers for underwater anti-counterfeiting

Thanks to the non-destructiveness and spatial-controllability of light, photoswitchable fluorescent polymers (PFPs) have been successfully applied in advanced anti-counterfeiting and information encryption. However, most of them are not suitable for use in harsh underwater environments, including high salinity seawater. In this study, by integrating photochromic molecules into a hydrophobic polymer matrix with the fluorine elastomer, including dipole-dipole interactions, we describe a class of novel photoswitchable supramolecular fluorescent polymers (PSFPs) that can adaptively change their fluorescence between none, green and red by the irradiation of different light. The PSFPs not only exhibited excellent photoswitchable properties, including fast photo-responsibility, prominent photo-reversibility, and photostability, but also exhibited some desired properties, including exceptional stretchability, hydrophobicity, antifouling, self-healing ability, simple preparation process, and processability. We thus demonstrated their applications in underwater data encryption and anti-counterfeiting labels.

Supernatural: Artificial Nucleobases and Backbones to Program Hybridization-Based Assemblies and Circuits

The specificity and predictability of hybridization make oligonucleotides a powerful platform to program assemblies and networks with logic-gated responses, an area of research which has grown into a field of its own. While the field has capitalized on the commercial availability of DNA oligomers with its four canonical nucleobases, there are opportunities to extend the capabilities of the hardware with unnatural nucleobases and other backbones. This Topical Review highlights nucleobases that favor hybridizations that are empowering for assemblies and networks as well as two chiral XNAs than enable orthogonal hybridization networks.

Structural and Thermodynamic Control of Supramolecular Polymers and DNA Assemblies with Cyanuric Acid: Influence of Substituents and Intermolecular Interactions

Understanding the interactions and thermodynamic parameters that govern the structure and stability of supramolecular polymers is challenging because of their flexible nature and high sensitivity to weak intermolecular interactions. The application of both experimental and computational analyses reveals the role that substituents on cyanuric acid (Cy), and other nitrogen-containing heterocycles, play in the formation of novel helical supramolecular structures. In this report, we focus on how noncovalent interactions, including steric and stacking interactions, modulate the structural and physical properties of these assemblies. In-depth analyses and several examples of critical steric and electrostatic effects provide insight into the relationship between intermolecular interactions of Cy with nucleic acids and the structure and thermodynamic stability of the supramolecular polymers they form.

Depsipeptide Nucleic Acids: Prebiotic Formation, Oligomerization, and Self-Assembly of a New Proto-Nucleic Acid Candidate

The mechanism by which informational polymers first formed on the early earth is currently unknown. The RNA world hypothesis implies that RNA oligomers were produced prebiotically, before the emergence of enzymes, but the demonstration of such a process remains challenging. Alternatively, RNA may have been preceded by an earlier ancestral polymer, or proto-RNA, that had a greater propensity for self-assembly than RNA, with the eventual transition to functionally superior RNA being the result of chemical or biological evolution. We report a new class of nucleic acid analog, depsipeptide nucleic acid (DepsiPNA), which displays several properties that are attractive as a candidate for proto-RNA. The monomers of depsipeptide nucleic acids can form under plausibly prebiotic conditions. These monomers oligomerize spontaneously when dried from aqueous solutions to form nucleobase-functionalized depsipeptides. Once formed, these DepsiPNA oligomers are capable of complementary self-assembly and are resistant to hydrolysis in the assembled state. These results suggest that the initial formation of primitive, self-assembling, informational polymers on the early earth may have been relatively facile if the constraints of an RNA-first scenario are relaxed.

Gelation Based on Host-Guest Interactions Induced by Multi-Functionalized Nanosheets

Host–guest interaction, being reversible and stimuli-responsive, is ideal to be applied to the design of hydrogels. We created a gelation system based on the host–guest interactions between the adamantyl groups and β-cyclodextrin (β-CD) polymer. N,N,N-trimethyl-1-adamantylammonium hydroxide (TriMAA) cations were attached to the pre-exfoliated α-zirconium phosphate (α-ZrP) nanosheets by ionic bonding through a displacement reaction with the exfoliating agents. The exfoliated α-ZrP nanosheets with adamantyl groups directly or indirectly attached to the surface act as reversible high-functionality crosslinkers within the β-CD polymer. The gelation occurred at a host-to-guest ratio of 1:10 or 1:5 at room temperature within minutes. The agents used to exfoliate α-ZrP can tailor the surface of the resultant α-ZrP nanosheets and the ionic strength of the system, which directly affects the further gelation results. Plus, the exfoliating agent cations may generate a host-and-guest interaction with the β-CD polymer as well. This gelation process without covalent bonding formation should help fellow researchers to better understand the gelation system and host–guest interactions.

Unveiling Polymerization Mechanism in pH-regulated Supramolecular Fibers in Aqueous Media

An amine functionalized C₃‐symmetric benzotrithiophene (BTT) monomer has been designed and synthetized in order to form pH responsive one‐dimensional supramolecular polymers in aqueous media. While most of the reported studies looked at the effect of pH on the size of the aggregates, herein, a detailed mechanistic study is reported, carried out upon modifying the pH to trigger the formation of positively charged ammonium groups. A dramatic and reversible change in the polymerization mechanism and size of the supramolecular fibers is observed and ascribed to the combination of Coulombic repulsive forces and higher monomer solubility. Furthermore, the induced frustrated growth of the fibers is further employed to finely control the one‐dimensional supramolecular polymerisation and copolymerization processes.

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.

Reversible Transformation of a Supramolecular Hydrogel by Redox Switching of Methylene Blue-A Noncovalent Chain Stopper

The simple and reversible control of the degree of polymerization, and thereby the bulk material properties, of a supramolecular polymer is reported. Noncovalent capping agents (chain stoppers) modulate the length of supramolecular polymers by stacking on the surfaces of the polymer's ends. Methylene blue (MB) is a positively charged, planar polycyclic dye that acts as a chain stopper. It can be reversibly switched between its colored, planar, cationic state and a colorless, nonplanar, neutral state (leucomethylene blue, LMB) by reduction with ascorbic acid and then reoxidized to MB by O₂. LMB does not act as a chain stopper. This behavior was utilized to reversibly trigger the gel to sol transformation of supramolecular polymers formed by the self-assembly of hexameric rosettes comprising 2,4,6-triaminopyrimidine and a hexanoic acid-substituted cyanuric acid (CyCo6) in aqueous media. The results of our experiments highlight the ability of this approach to reversibly switch between the gel and solution states of materials formed from supramolecular polymers and thereby control their bulk properties.

Triaminopyrimidine derivatives as transmembrane HCl transporters

A series of triaminopyrimidine-based anion transporters has been described, capable of diminishing proton gradients across lipid bilayers at physiologically relevant pH.

Metallacycle-Cored Supramolecular Polymers: Fluorescence Tuning by Variation of Substituents

Herein, we present a method for the preparation of supramolecular polymers with tunable fluorescence via the combination of metal-ligand coordination and phenanthrene-21-crown-7 (P21C7)-based host-guest interactions. A suite of rhomboidal metallacycles with different substituents were prepared via the coordination-driven self-assembly of a P21C7-based 60° diplatinum(II) acceptor and 120° dipyridyl donors. Upon variation of the substituents on the dipyridyl donors, the metallacycles exhibit emission wavelengths spanning the visible region (λmax = 427-593 nm). Metallacycle-cored supramolecular polymers were obtained via host-guest interactions between bis-ammonium salts and P21C7. The supramolecular polymers exhibit emission wavelengths similar to those of the individual metallacycles and higher fluorescent efficiency in solution and thin films. Utilizing a yellow-emitting supramolecular polymer thin film with high quantum yield (0.22), a white-light-emitting LED was fabricated by painting the thin film onto an ultraviolet LED. This study presents an efficient approach for tuning the properties of fluorescent supramolecular polymers and the potential of the metallacycle-cored supramolecular polymers as a platform for the fabrication of light-emitting materials with good processability and tunability.

Bifacial Nucleobases for Hexaplex Formation in Aqueous Solution

Although DNA can form triplex and quadruplex structures through hydrogen bonds, design and preparation of structures with more than five strands is difficult even when artificial nucleic acids are used. Herein we report a hexaplex formed by oligomers of artificial nucleic acids bearing bifacial molecules on d-threoninol. Aminopyrimidine and cyanuric acid derivatives were selected as bases because they have complementary hydrogen bonding patterns. The complex formed by aminopyrimidine and cyanuric acid decamers melted with large hysteresis. Hexaplex formation was indicated by gel electrophoresis, size exclusion chromatography and atomic force microscopy imaging, and proven directly through native mass spectrometry. CD measurements and molecular dynamics simulations indicated that the hexaplex adopts a helical structure. The hexaplex formation was highly dependent on pH and the presence of divalent cations. The hexaplex was stable in aqueous solution, and its unique structure and properties may lead to novel nanostructures, molecular assemblies, metal sensors, and ion channels.

Formation of supramolecular assemblies and liquid crystals by purine nucleobases and cyanuric acid in water: implications for the possible origins of RNA

The free nucleobases and mononucleotides of RNA do not form Watson-Crick base pairs in water, a fact that presents several challenges for the prebiotic synthesis of RNA. 2,6-Diaminopurine and adenosine-5'-monophosphate (AMP) are shown to form supramolecular assemblies with cyanuric acid in water. These assemblies and their propensity to form liquid crystals suggest a possible means by which non-covalent structures might have originally selected the shape of the Watson-Crick base pairs.

Exquisite regulation of supramolecular equilibrium polymers in water: chain stoppers control length, polydispersity and viscoelasticity

Positively charged molecules with planar surfaces control the length of supramolecular polymers formed by 2,4,6-triaminopyrimidine and a modified cyanuric acid.

Glycosylation of a model proto-RNA nucleobase with non-ribose sugars: implications for the prebiotic synthesis of nucleosides

The emergence of the earliest nucleosides is an important, but unresolved, element of the origins of life that may have been facilitated by heterocycle reactivity and self-assembly.

A 2,7-diamino-1,4,8-triazanaphthalene derivative selectively binds to cytosine bulge DNA only at a weakly acidic pH

The synthesis and properties of 2,7-diamino-1,4,8-triazanaphthalene (azaDANP) are described. AzaDANP is protonated only at a weakly acidic pH to bind to the cytosine bulge DNA duplex selectively. Upon binding of azaDANP to the cytosine bulge DNA, a new absorption band at 407 nm appears, and the absorption change of azaDANP on binding to the target is very sensitive to environmental pH with a bell-shaped pH-absorption profile.

Using a chitosan nanolayer as an efficient pH buffer to protect pH-sensitive supramolecular assemblies

We propose that chitosan can be used as an efficient pH-responsive protective layer for pH sensitive soft materials.

Visible-light responsive hydrogen-bonded supramolecular polymers based on ortho-tetrafluorinated azobenzene

Visible-light responsive hydrogen-bonded supramolecular polymers have been fabricated, whose properties could be regulated through the visible-light-triggered photoisomerization of the ortho-tetrafluorinated azobenzene.

Heterotypic Supramolecular Hydrogels

Supramolecular hydrogels, formed via intermolecular interactions in water, are emerging as a new type of versatile soft materials to be applied in many areas, such as biomedical applications, catalysis, food additives, and cosmetics. While most of the supramolecular hydrogels are homotypic (i.e., one type of building blocks), heterotypic supramolecular hydrogels are less explored, but may offer unique advantages. This review discribes supramolecular hydrogels that consist of more than one type building blocks (i.e., heterotypic) to illustrate the promises and challenges of heterotypic supramolecular hydrogels as soft biomaterials. First, we discuss the driving force for producing heterotypic supramolecular hydrogels. Second, we introduce the general methods for triggering heterotypic supramolecular hydrogels. Third, we summarize the examples of heterotypic supramolecular hydrogels made of hydrogelators with or without containing amino acid residues. Fourth, we describe the applications of heterotypic supramolecular hydrogels up-to-date. Finally, we give the outlook and propose a few future directions that likely worth to be explored.

Spontaneous formation and base pairing of plausible prebiotic nucleotides in water

The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. Even without purification, these nucleotides base pair in aqueous solution to create linear supramolecular assemblies containing thousands of ordered nucleotides. Nucleotide anomerization and supramolecular assemblies favour the biologically relevant β-anomer form of these ribonucleotides, revealing abiotic mechanisms by which nucleotide structure and configuration could have been originally favoured. These findings indicate that nucleotide formation and selection may have been robust processes on the prebiotic Earth, if other nucleobases preceded those of extant life.

One of the questions for prebiotic chemistry is the formation of complementary base pairing systems. Here, the authors show that plausible two prebiotic heterocycles can form glycosidic bonds with ribose in water and that these spontaneously base-pair in aqueous solution.

Thiosulfate-Hydrogen Peroxide Redox Oscillator as pH Driver for Ribozyme Activity in the RNA World

The RNA world of more than 3.7 billion years ago may have drawn on thermal and pH oscillations set up by the oxidation of thiosulfate by hydrogen peroxide (the THP oscillator) as a power source to drive replication. Since this primordial RNA also must have developed enzyme functionalities, in this work we examine the responses of two simple ribozymes to a THP periodic drive, using experimental rate and thermochemical data in a dynamical model for the coupled, self-consistent evolution of all reactants and intermediates. The resulting time traces show that ribozyme performance can be enhanced under pH cycling, and that thermal cycling may have been necessary to achieve large performance gains. We discuss three important ways in which the dynamic hydrogen peroxide medium may have acted as an agent for development of the RNA world towards a cellular world: proton gradients, resolution of the ribozyme versus replication paradox, and vesicle formation.

Supramolecular polyelectrolyte complex (SPEC): pH dependent phase transition and exploitation of its carrier properties

A supramolecular poly-electrolyte complex (SPEC) comprising poly-electrolyte acrylic acid with supramolecularly complexed guanidium is reported. This complex shows pH responsive phase transitions, which are described and characterized using microscopy, spectroscopy, density functional theory studies and Monte Carlo simulations. The phase behaviour of the SPEC is exploited by loading a dye like perylene and a drug, viz., doxorubicin, and their pH dependent controlled release is demonstrated, owing to the pH dependent phase change of the SPEC.

Supramolecular Hydrogelators and Hydrogels: From Soft Matter to Molecular Biomaterials

In this review we intend to provide a relatively comprehensive summary of the work of supramolecular hydrogelators after 2004 and to put emphasis particularly on the applications of supramolecular hydrogels/hydrogelators as molecular biomaterials. After a brief introduction of methods for generating supramolecular hydrogels, we discuss supramolecular hydrogelators on the basis of their categories, such as small organic molecules, coordination complexes, peptides, nucleobases, and saccharides. Following molecular design, we focus on various potential applications of supramolecular hydrogels as molecular biomaterials, classified by their applications in cell cultures, tissue engineering, cell behavior, imaging, and unique applications of hydrogelators. Particularly, we discuss the applications of supramolecular hydrogelators after they form supramolecular assemblies but prior to reaching the critical gelation concentration because this subject is less explored but may hold equally great promise for helping address fundamental questions about the mechanisms or the consequences of the self-assembly of molecules, including low molecular weight ones. Finally, we provide a perspective on supramolecular hydrogelators. We hope that this review will serve as an updated introduction and reference for researchers who are interested in exploring supramolecular hydrogelators as molecular biomaterials for addressing the societal needs at various frontiers.

The construction of supramolecular polymers through anion bridging: from frustrated hydrogen-bonding networks to well-ordered linear arrays

The construction of supramolecular polymers has been realized by converting random hydrogen-bonding networks into well-ordered linear hydrogen-bonding arrays through an anion-bridging strategy.

pH-switchable self-assembled materials

Self-assembled materials, which are able to respond to external stimuli, have been extensively studied over the last decades. A particularly exciting stimulus for a wide range of biomedical applications is the pH value of aqueous solutions, since deprotonation-protonation events are crucial for structural and functional properties of biopolymers. In living cells and tissues, intra- and extracellular pH values are stringently regulated, but can deviate from pH neutral as observed for example in tumorous, inflammatory sites, in endocytic pathways, and specific cellular compartments. By using a pH-switch as a stimulus, it is thereby possible to address specific targets in order to cause a programmed response of the supramolecular material. This strategy has not only been successfully applied in fundamental research but also in clinical studies. In this feature article, current strategies that have been used in order to design materials with pH-responsive properties are illustrated. This discussion only addresses selected examples from the last four years, the self-assembly of polymer-based building blocks, assemblies emerging from small molecules including surfactants or derived from biological macromolecules, and finally the controlled self-assembly of oligopeptides.

Abiotic synthesis of RNA in water: a common goal of prebiotic chemistry and bottom-up synthetic biology

For more than half a century chemists have searched for a plausible prebiotic synthesis of RNA. The initial advances of the 1960s and 1970s were followed by decades of measured progress and a growing pessimism about overcoming remaining challenges. Fortunately, the past few years have provided a number of important advances, including new abiotic routes for the synthesis of nucleobases, nucleosides, and nucleotides. Recent discoveries also provide additional support for the hypothesis that RNA is the product of evolution, being preceded by ancestral genetic polymers, or pre-RNAs, that are synthesized more easily than RNA. In some cases, parallel searches for plausible prebiotic routes to RNA and pre-RNAs have provided more than one experimentally verified synthesis of RNA substructures and possible predecessors. Just as the synthesis of a contemporary biological molecule cannot be understood without knowledge of cellular metabolism, it is likely that an integrated approach that takes into account both plausible prebiotic reactions and plausible prebiotic environments will ultimately provide the most satisfactory and unifying chemical scenarios for the origin of nucleic acids. In this context, recent advances towards the abiotic synthesis of RNA and candidates for pre-RNAs are beginning to suggest that some molecules (e.g., urea) were multi-faceted contributors to the origin of nucleic acids, and the origin of life.