A Portable Electrochemical Biosensor Based on an Amino-Modified Ionic Metal-Organic Framework for the One-Site Detection of Multiple Organophosphorus Pesticides

Constructing stable, portable sensors and revealing their mechanisms is challenging. Ion metal-organic frameworks (IMOFs) are poised to serve as highly effective electrochemical sensors for detecting organophosphorus pesticides (OPs), leveraging their unique charge properties. In this work, an amino-modified IMOF was constructed and combined with near-field communication (NFC) technology to develop a portable, touchless, and battery-free electrochemical biosensor NH2-IMOF@CS@AChE. -NH2 in NH2-IMOF gives the framework a higher electropositivity compared to IMOF, enhancing the electrostatic attraction with acetylcholinesterase (AChE), which is beneficial for immobilizing AChE. Furthermore, the uncoordinated O atoms and the (CH3)2NH2+ groups in NH2-IMOF help to form stronger bonds with AChE through hydrogen bonds. The results showed a wide linear response range of 1 × 10-15 to 1 × 10-9 M and a low detection limit of 1.24 × 10-13 M for glyphosate (Gly) in the practical detection of OPs. Additionally, electrochemical biosensor arrays were constructed to effectively identify and distinguish multiple OPs on the basis of their unique differential pulse voltammetry (DPV) electrochemical signals. This work provides a simple and effective solution for on-site OP analysis and can be widely applied in food safety and water quality monitoring.

A Modular and Convergent Synthetic Route to Supramolecular Cyclic Dimers Based on Amidinium-Carboxylate Interactions

We describe herein the optimized design and modular synthetic approach towards supramolecularly programmed monomers that can form discrete macrocyclic species of controllable size and shape through amidinium-carboxylate interactions in apolar and polar media.

Stacked or Folded? Impact of Chelate Cooperativity on the Self-Assembly Pathway to Helical Nanotubes from Dinucleobase Monomers

Self-assembled nanotubes exhibit impressive biological functions that have always inspired supramolecular scientists in their efforts to develop strategies to build such structures from small molecules through a bottom-up approach. One of these strategies employs molecules endowed with self-recognizing motifs at the edges, which can undergo either cyclization-stacking or folding-polymerization processes that lead to tubular architectures. Which of these self-assembly pathways is ultimately selected by these molecules is, however, often difficult to predict and even to evaluate experimentally. We show here a unique example of two structurally related molecules substituted with complementary nucleobases at the edges (i.e., G:C and A:U) for which the supramolecular pathway taken is determined by chelate cooperativity, that is, by their propensity to assemble in specific cyclic structures through Watson-Crick pairing. Because of chelate cooperativities that differ in several orders of magnitude, these molecules exhibit distinct supramolecular scenarios prior to their polymerization that generate self-assembled nanotubes with different internal monomer arrangements, either stacked or coiled, which lead at the same time to opposite helicities and chiroptical properties.

Self-Sorting Governed by Chelate Cooperativity

Self-sorting phenomena are the basis of manifold relevant (bio)chemical processes where a set of molecules is able to interact with no interference from other sets and are ruled by a number of codes that are programmed in molecular structures. In this work, we study, the relevance of chelate cooperativity as a code for achieving high self-sorting fidelities. In particular, we establish qualitative and quantitative relationships between the cooperativity of a cyclic system and the self-sorting fidelity when combined with other molecules that share identical geometry and/or binding interactions. We demonstrate that only systems displaying sufficiently strong chelate cooperativity can achieve quantitative narcissistic self-sorting fidelities either by dictating the distribution of cyclic species in complex mixtures or by ruling the competition between the intra- and intermolecular versions of a noncovalent interaction.

Chiral nanotubes self-assembled from discrete non-covalent macrocycles

Many strategies have been used to construct supramolecular hollow tubes, including helical folding of oligomers, bundling of rod-like structures, rolling-up of sheets and stacking of covalent cycles. On the other hand, controlling chirality at the supramolecular level continues attracting much interest because of its implications in future applications of porous systems. This review article covers the main examples in the literature that use simple molecular structures as chiral units for precise assembly into discrete non-covalent cyclic structures that are able to form chiral supramolecular tubular systems.

The Role of Peripheral Amide Groups as Hydrogen-Bonding Directors in the Tubular Self-Assembly of Dinucleobase Monomers

Nanotubes are a fascinating kind of self-assembled structure which have a wide interest and potential in supramolecular chemistry. We demonstrated that nanotubes of defined dimensions can be produced from dinucleobase monomers through two decoupled hierarchical cooperative processes: cyclotetramerization and supramolecular polymerization. Here we analyze the role of peripheral amide groups, which can form an array of hydrogen bonds along the tube axis, on this self-assembly process. A combination of 1 H NMR and CD spectroscopy techniques allowed us to analyze quantitatively the thermodynamics of each of these two processes separately. We found out that the presence of these amide directors is essential to guide the polymerization event and that their nature and number have a strong influence, not only on the stabilization of the stacks of macrocycles, but also on the supramolecular polymerization mechanism.

Stimuli-Responsive Self-Sorting Hybrid Hydrogen-Bonded/Metal-Coordinated Cage

The self-assembly of a unique molecular container is reported: a hybrid hydrogen-bonded/metal-coordinated cage where both hydrogen-bonding and metal-coordination form the crucial part of the topology. The hybrid cage was prepared combining hydrogen-bonded rosette motif and palladium(II)/platinum(II) coordination to a pyridine ligand. It was also shown that the hybrid cage could be prepared by integrative self-sorting from simple components. For the first time the genuine dual character of the hybrid cage was manifested as both self-assembling parts responded selectively to different stimuli (such as phosphine and cyanurate), which resulted in the disassembly of the cage.

Exploring the tubular self-assembly landscape of dinucleobase amphiphiles in water

The tubular aqueous assembly of dinucleobase amphiphilic monomers endowed with anionic, neutral or cationic groups is investigated under diverse conditions.

Quantification of cooperativity in the self-assembly of H-bonded rosettes

The self-assembly of triaminopyrimidines with barbiturates and with cyanates was investigated in chloroform solution. Equimolar mixtures of two complementary components form stable macrocyclic 3 : 3 complexes (rosettes). The thermodynamics of self-assembly were quantified by using 1H NMR titrations to measure the strength of pairwise H-bonding interactions between two rosette components (K), allosteric cooperativity associated with formation of a second H-bonding interaction with each component, and the effective molarity for cyclisation of the rosette motif (EM). Pyrimidine-cyanurate interactions are an order of magnitude more favourable than pyrimidine-barbiturate interactions, so the cyanurate rosettes are significantly more stable than barbiturate rosettes. There is no allosteric cooperativity associated with rosette formation, but the chelate cooperativity quantified by the product K EM is exceptionally high (102-104), indicating that there are no other species present that compete with rosette assembly. The values of EM for rosette formation are approximately 2 M for all four rosettes studied and are not affected by differences in peripheral substituents or intrinsic H-bond strength.

Elucidating Noncovalent Reaction Mechanisms: G-Quartet as an Intermediate in G-Quadruplex Assembly

In analogy to covalent reactions, the understanding of noncovalent association pathways is fundamental to influence and control any supramolecular process. Following an approach that is reminiscent of covalent methodologies, we study here, for the first time, the mechanism of G-quadruplex formation in organic solvents. Our results support a reaction pathway in which the cation shifts the equilibrium towards a G-quartet transient intermediate, which then acts as a template in the formation of the G-quadruplex product.

Functional Systems Derived from Nucleobase Self-assembly

Dynamic and reversible non-covalent interactions endow synthetic systems and materials with smart adaptive functions that allow them to response to diverse stimuli, interact with external agents, or repair structural defects. Inspired by the outstanding performance and selectivity of DNA in living systems, scientists are increasingly employing Watson-Crick nucleobase pairing to control the structure and properties of self-assembled materials. Two sets of complementary purine-pyrimidine pairs (guanine:cytosine and adenine:thymine(uracil)) are available that provide selective and directional H-bonding interactions, present multiple metal-coordination sites, and exhibit rich redox chemistry. In this review, we highlight several recent examples that profit from these features and employ nucleobase interactions in functional systems and materials, covering the fields of energy/electron transfer, charge transport, adaptive nanoparticles, porous materials, macromolecule self-assembly, or polymeric materials with adhesive or self-healing ability.

Synthesis of Phosphoramidite Monomers Equipped with Complementary Bases for Solid-Phase DNA Oligomerization

We describe the preparation of two monomers that bear complementary nucleobases at the edges (guanine-2'-deoxycytidine and 2-aminoadenine-2'-deoxyuridine) and that are conveniently protected and activated for solid-phase automated DNA synthesis. We report the optimized synthetic routes leading to the four nucleobase derivatives involved, their cross-coupling reactions into dinucleobase-containing monomers, and their oligomerization in the DNA synthesizer.

Fluorescence and Morphology of Self-Assembled Nucleobases and Their Diphenylalanine Hybrid Aggregates

Studies carried out in recent decades have revealed that the ability to self-assemble is a widespread property among biomolecules. Small nucleic acid moieties or very short peptides are able to generate intricate assemblies endowed with remarkable structural and spectroscopic properties. Herein, the structural/spectroscopic characterization of aggregates formed by nucleobases and peptide nucleic acid (PNA)-peptide conjugates are reported. At high concentration, all studied nucleobases form aggregates characterized by previously unreported fluorescence properties. The conjugation of these bases, as PNA derivatives, to the dipeptide Phe-Phe leads to the formation of novel hybrid assemblies, which are characterized by an amyloid-like association of the monomers. Although these compounds share the same basic cross-β motif, the nature and number of PNA units have an important impact on both the level of structural order and the intrinsic fluorescence of the self-assembled nanostructure.

Supramolecular Polymers Capable of Controlling Their Topology

One important class of supramolecular materials is one-dimensionally elongated supramolecular polymers, in which monomers are associated by reversible intermolecular interactions, yielding a fibrous morphology. Unlike frequently reported conventional supramolecular polymers based on, for instance, host-guest interactions, those composed of one-dimensionally stacked π-conjugated molecules can be encoded with high degrees of internal order by cooperative association of the rigid aromatic monomers, endowing such supramolecular polymers with extraordinary properties and functionality. However, their internal order has not yet been exploited to manipulate the complex landscape of well-defined states of the supramolecular polymer backbone, which may induce new functionalities beyond the intrinsic properties of the backbones. This Account will focus on the inceptive phase of our research on supramolecular polymers with high degrees of internal order able to impart intrinsic curvature to their backbones. Initially, we developed a naphthalene molecule functionalized with barbituric acid, which forms uniform toroidal short fibers with diameters of approximately 16 nm via the formation of hydrogen-bonded cyclic hexamers (rosettes). As we thought the uniformity of the toroid size to arise from the intrinsic curvature generated upon stacking of the rosettes, we exploited this intrinsic curvature to design continuously curved extended supramolecular polymers by extension of such molecular π-systems. The intrinsic curvature produced by the monomers with more expanded π-systems indeed gave us access to higher-order structures (topologies) ranging from randomly folded to helically folded coils in extended supramolecular polymers. We will discuss the kinetic aspects of the generation of intrinsic curvature for topology control, including the formation of toroidal structures resulting from ring-closing processes. For extended supramolecular polymers with well-defined topologies, we will discuss manipulation of a complex landscape of well-defined states by external stimuli. The incorporation of a photoresponsive azobenzene chromophore in the original naphthalene molecular scaffold allowed us to reversibly destroy or recover the curvature of the main chain through trans- cis photoisomerization. By means of this photocontrollable curvature, we have demonstrated light-induced unfolding of helically folded structures into entirely stretched structures. Furthermore, a direct extension of the π-conjugated core provided us with access to unprecedented supramolecular polymers with emergent time-dependent topology transitions. Molecules with a naphthalene core conjugated with two phenylene units kinetically afforded supramolecular polymers that consist of helically folded and misfolded domains. Upon aging the supramolecular polymer solution, we observed spontaneous folding of the misfolded domains in a time scale of days, eventually obtaining a supramolecular polymer topology analogous to the tertiary structure of proteins. These supramolecular polymers with unrivaled and active topologies provide new prospects for supramolecular polymers as one-dimensional nanomaterials.

Tuning the Circumference of Six-Porphyrin Nanorings

Most macrocycles are made from a simple repeat unit, resulting in high symmetry. Breaking this symmetry allows fine-tuning of the circumference, providing better control of the host–guest behavior and electronic structure. Here, we present the template-directed synthesis of two unsymmetrical cyclic porphyrin hexamers with both ethyne (C2) and butadiyne (C4) links, and we compare these nanorings with the symmetrical analogues with six ethyne or six butadiyne links. Inserting two extra carbon atoms into the smaller nanoring causes a spectacular change in binding behavior: the template affinity increases by a factor of 3 × 10⁹, to a value of ca. 10³⁸ M^–1, and the mean effective molarity is ca. 830 M. In contrast, removing two carbon atoms from the largest nanoring results in almost no change in its template-affinity. The strain in these nanorings is 90–130 kJ mol^–1, as estimated both from DFT calculation of homodesmotic reactions and from comparing template affinities of linear and cyclic oligomers. Breaking the symmetry has little effect on the absorption and fluorescence behavior of the nanorings: the low radiative rates that are characteristic of a circular delocalized S₁ excited state are preserved in the low-symmetry macrocycles.

The canonical behavior of the entropic component of thermodynamic effective molarity. An attempt at unifying covalent and noncovalent cyclizations

The statistically corrected entropic component of effective molarity (EM_S*) complies with the “canonical” values expressed by the log plot of EM_S* vs. the number n of single bonds in the ring product.

Guidelines for the assembly of hydrogen-bonded macrocycles

This article highlights selected examples on the synthesis of hydrogen-bonded macrocycles from ditopic molecules and analyze the main factors, often interrelated, that influence the equilibrium between ring and chain species.

Supramolecular crowns: a new class of cyclic hydrogen-bonded cavitands

A novel design of highly preorganized bicyclic monomers, based on quadruple hydrogen bonding motifs, is proposed to access noncovalent cavitands with large internal volumes and interesting shapes.

Understanding complex supramolecular landscapes: non-covalent macrocyclization equilibria examined by fluorescence resonance energy transfer

As molecular self-assembled systems increase in complexity, due to a large number of participating entities and/or the establishment of multiple competing equilibria, their full understanding becomes likewise more complicated, and the use of diverse analytical techniques that can afford complementary information is required. We demonstrate in this work that resonance excitation energy transfer phenomena, measured by fluorescence spectroscopy in combination with other optical spectroscopies, can be a valuable tool to obtain supplementary thermodynamic data about complex supramolecular landscapes that other methods fail to provide. In particular, noncovalent macrocyclization processes of lipophilic dinucleosides are studied here by setting up a competition between intra- and intermolecular association processes of Watson-Crick H-bonding pairs. Multiwavelength analysis of the monomer emission changes allowed us to determine cyclotetramerization constants and to quantify chelate cooperativity, which was confirmed to be substantially larger for the G-C than for the A-U pair. Furthermore, when bithiophene-BODIPY donor-acceptor energy transfer probes are employed in these competition experiments, fluorescence and circular dichroism spectroscopy measurements in different regions of the visible spectrum additionally reveal intermolecular interactions occurring simultaneously at both sides of the macrocyclization reaction: the cyclic product, acting as a host for the competitor, and the monomer reactant, ultimately leading to macrocycle denaturation.

Reversible dispersion and release of carbon nanotubes via cooperative clamping interactions with hydrogen-bonded nanorings

Due to their outstanding electronic and mechanical properties, single-walled carbon nanotubes (SWCNTs) are promising nanomaterials for the future generation of optoelectronic devices and composites. However, their scarce solubility limits their application in many technologies that demand solution-processing of high-purity SWCNT samples. Although some non-covalent functionalization approaches have demonstrated their utility in extracting SWCNTs into different media, many of them produce short-lived dispersions or ultimately suffer from contamination by the dispersing agent. Here, we introduce an unprecedented strategy that relies on a cooperative clamping process. When mixing (6,5)SWCNTs with a dinucleoside monomer that is able to self-assemble in nanorings via Watson-Crick base-pairing, a synergistic relationship is established. On one hand, the H-bonded rings are able to associate intimately with SWCNTs by embracing the tube sidewalls, which allows for an efficient SWCNT debundling and for the production of long-lasting SWCNT dispersions of high optical quality along a broad concentration range. On the other, nanoring stability is enhanced in the presence of SWCNTs, which are suitable guests for the ring cavity and contribute to the establishment of multiple cooperative noncovalent interactions. The inhibition of these reversible interactions, by just adding, for instance, a competing solvent for hydrogen-bonding, proved to be a simple and effective method to recover the pristine nanomaterial with no trace of the dispersing agent.

Self-Assembling of Fmoc-GC Peptide Nucleic Acid Dimers into Highly Fluorescent Aggregates

The study of molecules that self-assemble through noncovalent interactions is one of the most attractive topics in supramolecular chemistry. The use of short peptides or modified nucleotides as building blocks for the aggregates is particularly intriguing because these are very easy to synthesize; moreover, subtle changes in the chemical structure of such building blocks may drastically affect the properties of the aggregates. The ability of peptide nucleic acids (PNA) to aggregate has been very little explored, despite its practical applications. In this work we investigated the self-assembling properties of a PNA dimer, conjugated at the N-terminus to a fluorenylmethoxycarbonyl group. This PNA dimer forms nano-aggregates at low concentration in CHCl₃ /CH₃ OH mixtures. The aggregates retain very interesting fluorescent properties (high quantum yield in the visible region with lifetimes on the nanosecond scale), which make them promising materials for applications in optoelectronics.

Well-defined, persistent, chiral phthalocyanine nanoclusters via G-quadruplex assembly

Octameric near-IR dye nanoclusters are produced by complexation of potassium cations with a phthalocyanine-guanosine conjugate. The combination of hydrogen-bonding, K(+) coordination, π-π stacking and steric interactions between the chiral side groups is responsible for defining a specific helical chromophore arrangement in the clusters, which display high stability and maintain their supramolecular identity onto substrates.

High-fidelity self-assembly pathways for hydrogen-bonding molecular semiconductors

The design of molecular systems with high-fidelity self-assembly pathways that include several levels of hierarchy is of primary importance for the understanding of structure-function relationships, as well as for controlling the functionality of organic materials. Reported herein is a high-fidelity self-assembly system that comprises two hydrogen-bonding molecular semiconductors with regioisomerically attached short alkyl chains. Despite the availability of both discrete cyclic and polymeric linear hydrogen-bonding motifs, the two regioisomers select one of the two motifs in homogeneous solution as well as at the 2D-confined liquid-solid interface. This selectivity arises from the high directionality of the involved hydrogen-bonding interactions, which renders rerouting to other self-assembly pathways difficult. In thin films and in the bulk, the resulting hydrogen-bonded assemblies further organize into the expected columnar and lamellar higher-order architectures via solution processing. The contrasting organized structures of these regioisomers are reflected in their notably different miscibility with soluble fullerene derivatives in the solid state. Thus, electron donor-acceptor blend films deliver a distinctly different photovoltaic performance, despite their virtually identical intrinsic optoelectronic properties. Currently, we attribute this high-fidelity control via self-assembly pathways to the molecular design of these supramolecular semiconductors, which lacks structure-determining long aliphatic chains.

Thermodynamic and Kinetic Stabilities of G-Quadruplexes in Apolar Solvents

In contrast to more polar media, G-quadruplex assembly reveals remarkably high thermodynamic and kinetic stability in toluene solutions. Depending on the substituents installed at the lipophilic guanosine, either a dodecamer or an octamer complex is formed in the presence of K⁺ or Na⁺ salts that resist conditions of high dilution and elevated temperatures without exhibiting significant dissociation. Moreover, kinetic exchange between complexed and uncomplexed G is slow enough in NMR to monitor G-quadruplex formation along a day time scale.

Dye-conjugated complementary lipophilic nucleosides as useful probes to study association processes by fluorescence resonance energy transfer

Resonance energy transfer is used here to study the association and self-sorting events between lipophilic nucleosides in apolar aromatic solvents.

Applications of Palladium-Catalyzed C-N Cross-Coupling Reactions

Pd-catalyzed cross-coupling reactions that form C–N bonds have become useful methods to synthesize anilines and aniline derivatives, an important class of compounds throughout chemical research. A key factor in the widespread adoption of these methods has been the continued development of reliable and versatile catalysts that function under operationally simple, user-friendly conditions. This review provides an overview of Pd-catalyzed N-arylation reactions found in both basic and applied chemical research from 2008 to the present. Selected examples of C–N cross-coupling reactions between nine classes of nitrogen-based coupling partners and (pseudo)aryl halides are described for the synthesis of heterocycles, medicinally relevant compounds, natural products, organic materials, and catalysts.

Hydrogen-Bonded Macrocyclic Supramolecular Systems in Solution and on Surfaces

Cyclization into closed assemblies is the most recurrent approach to realize the noncovalent synthesis of discrete, well-defined nanostructures. This review article particularly focuses on the noncovalent synthesis of monocyclic hydrogen-bonded systems that are self-assembled from a single molecule with two binding-sites. Taking advantage of intramolecular binding events, which are favored with respect to intermolecular binding in solution, can afford quantitative amounts of a given supramolecular species under thermodynamic control. The size of the assembly depends on geometric issues such as the monomer structure and the directionality of the binding interaction, whereas the fidelity achieved relies largely on structural preorganization, low degrees of conformational flexibility, and templating effects. Here, we discuss several examples described in the literature in which cycles of different sizes, from dimers to hexamers, are studied by diverse solution or surface characterization techniques.

Flexible double-headed cytosine-linked 2'-deoxycytidine nucleotides. Synthesis, polymerase incorporation to DNA and interaction with DNA methyltransferases

New types of double-headed 2'-deoxycytidine 5'-O-triphosphates (dC(XC)TPs) bearing another cytosine or 5-fluorocytosine linked through a flexible propargyl, homopropargyl or pent-1-ynyl linker to position 5 were prepared by the aqueous Sonogashira cross-coupling reactions of 5-iodo-dCTP with the corresponding (fluoro)cytosine-alkynes. The modified dC(XC)TPs were good substrates for DNA polymerases and were used for enzymatic synthesis of cytosine-functionalized DNA by primer extension or PCR. The cytosine- or fluorocytosine-linked DNA probes did not significantly inhibit DNA methyltransferases and did not cross-link to these proteins.

From nucleobase to DNA templates for precision supramolecular assemblies and synthetic polymers

In this minireview, we report on the recent advances of utilization of nucleobases and DNA as templates to achieve well-defined supramolecular polymers, synthetic polymers, and sequence-controlled polymers.

Molecular and supramolecular chemistry of rosette nanotubes

Synthetic strategies used to tune the properties of a class of supramolecular 1D nanostructures, the rosette nanotubes, are reviewed herein.

Molecularly Defined Nanostructures Based on a Novel AAA-DDD Triple Hydrogen-Bonding Motif

A facile and flexible method for the synthesis of a new AAA-DDD triple hydrogen-bonding motif is described. Polytopic supramolecular building blocks with precisely oriented AAA and DDD groups are thus accessible in few steps. These building blocks were used for the assembly of large macrocycles featuring four AAA-DDD interactions and a macrobicyclic complex with a total of six AAA-DDD interactions.