Discrete Quadruple Stacks Formed in a Nanosized Metallorectangle

An iridium-cornered nanosized metallorectangle was obtained by combining a quinoxalinophenanthrophenazine-connected Janus-di-imidazolylidene ligand and 4,4'-bipyridine. This metallorectangle was used as host for a series of planar molecules, including pyrene, triphenylene, perylene, coronene, and N,N'-dimethyl-naphthalenetetracarboxy-diimide (NTCDI). The binding of coronene and NTCDI followed a strongly positive cooperative 1:2 stoichiometric binding model, as the inclusion of the first guest generates the geometrical requirements for the optimum encapsulation of the second planar molecule. The simultaneous encapsulation of coronene and NTCDI produces a heteroguest inclusion system, whose exchange dynamics was studied by means of variable temperature 1H NMR spectroscopy.

Cooperativity between metal centers in homobimetallic PdII-NHC complexes: catalytic potential towards hydrodefluorination

Among the several unsymmetrical bis-NHC derived distinct homo-bimetallic and mono-NHC supported PdII complexes studied here (1-5), the bimetallic complex 1 was noted to be the most effective catalyst for the challenging hydrodefluorination. The electron richness of the metal centers and the synergistic cooperation between the PdII centers (cooperativity index, ɑ = 8.67) have been recognized to be the deciding factor for its better activity.

Stimuli-Responsive Molecular Duplexes Displaying Duplex-to-Duplex Switching

Synthetic duplexes with high stabilities have promising potential for mimicking biomolecular functions and developing supramolecular smart materials. Herein, we describe the synthesis and stimuli-responsive properties of molecular duplexes derived from indolocarbazole-pyridine (I-P) oligomers. These duplexes adopt nonclassical helical structures, stabilized by I-P hydrogen-bonding pairs in anhydrous chlorinated solvents. Notably, the longest duplex 62 (11-mer)2 displays remarkable stability, forming twenty hydrogen bonds; its exchange energy barrier was determined to be ΔG≠=22.0 kcal ⋅ mol-1 at 75 °C in anhydrous (CDCl2)2. Upon the addition of water, a hydrated duplex 62 (11-mer)2⊃10H2O was formed, with one water molecule inserted between each I-P hydrogen-bonding pair. The Hill coefficient (n) for this process is 6.1, demonstrating extremely positive cooperativity. Conversely, the hydrated duplex 62 (11-mer)2⊃10H2O was completely converted into the original anhydrous duplex 62 (11-mer)2 when the temperature was increased. Interconversion between these two distinct duplexes can be repeatedly carried out by varying the temperature. Furthermore, reversible switching between hetero-duplexes and homo-duplexes was also demonstrated by controlling the temperature, with concomitant changes in the characteristic emission signals.

Understanding Cooperativity in Homo- and Heterometallic Complexes: From Basic Concepts to Design

Cooperative effects have attracted considerable attention in recent years. These effects are ubiquitous in chemistry and biology and can govern interactions of proteins with other biomolecules, mechanisms of supramolecular recognition and polymerization, catalysis, assembly of compounds on surfaces, and physical properties such as magnetic, electronic or optical properties, e. g. Consequently, the understanding of cooperative effects can lead to a structure-property relation that can pave the way to future applications in various research areas; however, with regard to cooperative effects in homo- and heterometallic complexes, we still are at the beginning of understanding. Nevertheless, concepts to describe cooperativity of metal centers as well as methodologies to investigate and model these effects have emerged over the last years. This concept article gives an overview of these existing concepts, approaches, and strategies to understand cooperative effects in homo- and heterometallic complexes. Special emphasis is put on concepts to define cooperative effects, their quantification, as well as methods to investigate cooperative effects.

Amplification sensing manipulated by a sumanene-based supramolecular polymer as a dynamic allosteric effector

The synthesis of signal-amplifying chemosensors induced by various triggers is a major challenge for multidisciplinary sciences. In this study, a signal-amplification system that was flexibly manipulated by a dynamic allosteric effector (trigger) was developed. Herein, the focus was on using the behavior of supramolecular polymerization to control the degree of polymerization by changing the concentration of a functional monomer. It was assumed that this control was facilitated by a gradually changing/dynamic allosteric effector. A curved-π buckybowl sumanene and a sumanene-based chemosensor (SC) were employed as the allosteric effector and the molecular binder, respectively. The hetero-supramolecular polymer, (SC·(sumanene)n), facilitated the manipulation of the degree of signal-amplification; this was accomplished by changing the sumanene monomer concentration, which resulted in up to a 62.5-fold amplification of a steroid. The current results and the concept proposed herein provide an alternate method to conventional chemosensors and signal-amplification systems.

Recognition of Amino Acid Salts by Temperature-Dependent Allosteric Binding with Stereodynamic Urea Receptors

Positive homotropic artificial allosteric systems are important for the regulation of cooperativity, selectivity and nonlinear amplification. Stereodynamic homotropic allosteric receptors can transmit and amplify induced chirality by the first ligand binding to axial chirality between two chromophores. We herein report stereodynamic allosteric urea receptors consisting of a rotational shaft as the axial chirality unit, terphenyl units as structural transmission sites and four urea units as binding sites. NMR titration experiments revealed that the receptor can bind two carboxylate guests in a positive homotropic allosteric manner attributed to the inactivation by intramolecular hydrogen-bonding between urea units within the receptor. In addition, the VT-CD spectra observed upon binding of the urea receptor with l- or D-amino acid salts in MeCN showed interesting temperature-dependent Cotton effects, based on the differences of the receptor shaft unit and the guest structure. The successful discrimination of hydrocarbon-based side chains of amino acid salts indicated that the input of chiral and steric information for the guest was amplified as outputs of the Cotton effect and the temperature-dependence of VT-CD spectra through cooperativity of positive allosteric binding.

Proximity Effects on the Reactivity of a Nonheme Iron (IV) Oxo Complex in C-H Oxidation

Precise control of substrate positioning and orientation (its proximity to the reactive unit) is often invoked to rationalize the superior enzymatic reaction rates and selectivities when compared to synthetic models. Artificial nonheme iron (IV) oxo (Fe(IV)=O) complexes react with C(sp3)-H bonds via a biomimetic Hydrogen Atom Transfer/Hydroxyl Rebound mechanism, but rates, site-selectivity and even hydroxyl rebound efficiency (ligand rebound versus substrate radical diffusion) are smaller than in oxygenases. Herein, we quantitatively analyze how substrate binding modulates nonheme Fe(IV)=O reactivity by comparing rates and outcomes of C-H oxidation by a pair of Fe(IV)=O complexes that share the same first coordination sphere but only one contains a crown ether receptor that recognizes the substrate. Substrate binding makes the reaction intramolecular, exhibiting Michaelis-Menten kinetics and increased reaction rates. In addition, C-H oxidation occurs with high site selectivity for remote sites. Analysis of Effective Molarity reveals that the system operates at its maximal theoretical capability for the oxidation of these remote sites. Remarkably, substrate positioning also affects Hydroxyl Rebound, whose efficiency only increases on the sites placed in proximity by recognition. Overall, these observations provide evidence that supramolecular control of substrate positioning can effectively modulate the reactivity of oxygenases and its models.

On the origin of cooperativity effects in the formation of self-assembled molecular networks at the liquid/solid interface

In this work we investigate the behaviour of molecules at the nanoscale using scanning tunnelling microscopy in order to explore the origin of the cooperativity in the formation of self-assembled molecular networks (SAMNs) at the liquid/solid interface. By studying concentration dependence of alkoxylated dimethylbenzene, a molecular analogue to 5-alkoxylated isophthalic derivatives, but without hydrogen bonding moieties, we show that the cooperativity effect can be experimentally evaluated even for low-interacting systems and that the cooperativity in SAMN formation is its fundamental trait. We conclude that cooperativity must be a local effect and use the nearest-neighbor Ising model to reproduce the coverage vs. concentration curves. The Ising model offers a direct link between statistical thermodynamics and experimental parameters, making it a valuable tool for assessing the thermodynamics of SAMN formation.

Patterns of Cross-Peaks in Two-Dimensional Correlation Spectra to Probe Intermolecular Interactions Described by Two Reversible Reactions

Two-dimensional correlation spectroscopy is used to investigate the intermolecular interaction between two substances dissolved in the same solutions, where the intermolecular interaction is described by two reversible reactions producing two supramolecular aggregates. The severe overlappings expected among the characteristic peaks of the original solute and aggregates make conventional one-dimensional spectra difficult to accurately reflect the physiochemical nature of the intermolecular interaction. The double asynchronous orthogonal sample design (DAOSD) approach is utilized to analyze the simulated data for proof-of-principle demonstration. The patterns of cross-peaks are much more complex compared with the intermolecular interaction described by only a single reaction. Four major groups of cross-peaks with characteristic patterns observed in the pair of DAOSD asynchronous spectra are systematically analyzed and classified. Further analysis of the spectral feature of the cross-peaks of the DAOSD asynchronous spectra is helpful to exact additional information concerning the variation of the peak position and peak width of the aggregates compared with those of the original solute. The result is important to reveal the physicochemical nature of intermolecular interaction between the solutes (e.g., changes in conformation, dynamical behavior, etc.). The pattern of cross-peaks in the corresponding 2D asynchronous spectra may become rather complex when the peak position, peak width, and peak intensity of two supramolecular aggregates change simultaneously. Further work using artificial intelligence techniques to interpret the complex cross-peaks is still being carried out.

Design and Thermodynamics Principles to Program the Cooperativity of Molecular Assemblies

Most functional nanosystems in living organisms are constructed using multimeric assemblies that provide multiple advantages over their monomeric counterparts such as cooperative or anti-cooperative responses, integration of multiple signals and self-regulation. Inspired by these natural nanosystems, chemists have been synthesizing self-assembled supramolecular systems over the last 50 years with increasing complexity with applications ranging from biosensing, drug delivery, synthetic biology, and system chemistry. Although many advances have been made concerning the design principles of novel molecular architectures and chemistries, little is still known, however, about how to program their dynamic of assembly so that they can assemble at the required concentration and with the right sensitivity. Here, we used synthetic DNA assemblies and double-mutant cycle analysis to explore the thermodynamic basis to program the cooperativity of molecular assemblies. The results presented here exemplify how programmable molecular assemblies can be efficiently built by fusing interacting domains and optimizing their compaction. They may also provide the rational basis for understanding the thermodynamic and mechanistic principles driving the evolution of multimeric biological complexes.

Supramolecular Self-Associating Amphiphiles Inhibit Biofilm Formation by the Critical Pathogens, Pseudomonas aeruginosa and Candida albicans

In 2019, 4.95 million deaths were directly attributed to antimicrobial-resistant bacterial infections globally. In addition, the mortality associated with fungal infections is estimated at 1.7 million annually, with many of these deaths attributed to species that are no longer susceptible to traditional therapeutic regimes. Herein, we demonstrate the use of a novel class of supramolecular self-associating amphiphilic (SSA) salts as antimicrobial agents against the critical pathogens Pseudomonas aeruginosa and Candida albicans. We also identify preliminary structure-activity relationships for this class of compound that will aid the development of next-generation SSAs demonstrating enhanced antibiofilm activity. To gain insight into the possible mode of action for these agents, a series of microscopy studies were performed, taking advantage of the intrinsic fluorescent nature of benzothiazole-substituted SSAs. Analysis of these data showed that the SSAs interact with the cell surface and that a benzothiazole-containing SSA inhibits hyphal formation by C. albicans.

Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1)

Herein, we conducted simulations of trimeric Spike from several SARS-CoV-2 variants of concern (Delta and Omicron sub-variants BA.2, BA.5, and BQ.1) and investigated the mechanisms by which specific mutations confer resistance to neutralizing antibodies. We observed that the mutations primarily affect the cooperation between protein domains within and between protomers. The substitutions K417N and L452R expand hydrogen bonding interactions, reducing their interaction with neutralizing antibodies. By interacting with nearby residues, the K444T and N460K mutations in the SpikeBQ.1 variant potentially reduces solvent exposure, thereby promoting resistance to antibodies. We also examined the impact of D614G, P681R, and P681H substitutions on Spike protein structure that may be related to infectivity. The D614G substitution influences communication between a glycine residue and neighboring domains, affecting the transition between up- and -down RBD states. The P681R mutation, found in the Delta variant, enhances correlations between protein subunits, while the P681H mutation in Omicron sub-variants weakens long-range interactions that may be associated with reduced fusogenicity. Using a multiple linear regression model, we established a connection between inter-protomer communication and loss of sensitivity to neutralizing antibodies. Our findings underscore the importance of structural communication between protein domains and provide insights into potential mechanisms of immune evasion by SARS-CoV-2. Overall, this study deepens our understanding of how specific mutations impact SARS-CoV-2 infectivity and shed light on how the virus evades the immune system.

An Insight into Anion Extraction by Amphiphiles: Hydrophobic Microenvironments as a Requirement for the Extractant Selectivity

Coupling of electron-deficient urea units with aliphatic chains gives rise to amphiphilic compounds that bind to phosphate and benzoate anions in the hydrogen bonding competitive solvent (DMSO) with KAss = 6 580 M-1 and KAss = 4 100 M-1, respectively. The anchoring of these receptor moieties to the dendritic support does not result in a loss of anion binding and enables new applications. Due to the formation of a microenvironment in the dendrimer, the high selectivity of the prepared compound toward benzoate is maintained even in the presence of aqueous media during extraction experiments. In the presence of binding sites at 5 mM concentration, the amount of benzoate corresponding to the full binding site occupancy is transferred into the chloroform phase from its 10 mM aqueous solution. A thorough investigation of the extraction behavior of the dendrimer reported here, supported by a series of molecular dynamics simulations, provides new insight into the fundamental principles of extraction of inorganic anions by amphiphiles.

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.

Tools to enable the study and translation of supramolecular amphiphiles

This tutorial review focuses on providing a summary of the key techniques used for the characterisation of supramolecular amphiphiles and their self-assembled aggregates; from the understanding of low-level molecular interactions, to materials analysis, use of data to support computer-aided molecular design and finally, the translation of this class of compounds for real world application, specifically within the clinical setting. We highlight the common methodologies used for the study of traditional amphiphiles and build to provide specific examples that enable the study of specialist supramolecular systems. This includes the use of nuclear magnetic resonance spectroscopy, mass spectrometry, X-ray scattering techniques (small- and wide-angle X-ray scattering and single crystal X-ray diffraction), critical aggregation (or micelle) concentration determination methodologies, machine learning, and various microscopy techniques. Furthermore, this review provides guidance for working with supramolecular amphiphiles in in vitro and in vivo settings, as well as the use of accessible software programs, to facilitate screening and selection of druggable molecules. Each section provides: a methodology overview - information that may be derived from the use of the methodology described; a case study - examples for the application of these methodologies; and a summary section - providing methodology specific benefits, limitations and future applications.

Theoretical investigation of tube-like supramolecular structures formed through bifurcated lithium bonds

The stability of three supramolecular naostructures, which are formed through the aggregation of identical belts of [12] arene containing p-nitrophenyllithium, 1,4-dilithiatedbenzene and 1,4-dinitrobenzene units, is investigated by density functional theory. The electrostatic potential calculations indicate the ability of these belts in forming bifurcated lithium bonds (BLBs) between the Li atoms of one belt and the oxygen atoms of the NO2 groups in the other belt, which is also confirmed by deformation density maps and quantum theory of atoms in molecules (QTAIM) analysis. Topological analysis and natural bond analysis (NBO) imply to ionic character for these BLBs with binding energies up to approximately - 60 kcal mol-1. The many-body interaction energy analysis shows the strong cooperativity belongs to the configuration with the highest symmetry (C4v) containing p-nitrophenyllithium fragments as the building unit. Therefore, it seems that this configuration could be a good candidate for designing a BLB-based supramolecular nanotube with infinite size in this study.

Allosteric control of olefin isomerization kinetics via remote metal binding and its mechanochemical analysis

Allosteric control of reaction thermodynamics is well understood, but the mechanisms by which changes in local geometries of receptor sites lower activation reaction barriers in electronically uncoupled, remote reaction moieties remain relatively unexplored. Here we report a molecular scaffold in which the rate of thermal E-to-Z isomerization of an alkene increases by a factor of as much as 104 in response to fast binding of a metal ion to a remote receptor site. A mechanochemical model of the olefin coupled to a compressive harmonic spring reproduces the observed acceleration quantitatively, adding the studied isomerization to the very few reactions demonstrated to be sensitive to extrinsic compressive force. The work validates experimentally the generalization of mechanochemical kinetics to compressive loads and demonstrates that the formalism of force-coupled reactivity offers a productive framework for the quantitative analysis of the molecular basis of allosteric control of reaction kinetics. Important differences in the effects of compressive vs. tensile force on the kinetic stabilities of molecules are discussed.

Functional DNA Superstructures Exhibit Positive Homotropic Allostery in Ligand Binding

Inspired by intrinsically disordered proteins in nature, DNA aptamers can be engineered to display strongly homotropic allosteric (or cooperative) ligand binding, representing a unique feature that could be of great utility in applications such as biosensing, imaging and drug delivery. The use of an intrinsic disorder mechanism, however, comes with an inherent drawback of significantly reduced overall binding affinity. We hypothesize that it could be addressed via the design of multivalent supramolecular aptamers. We built functional DNA superstructures (denoted as 3D DNA), made of long-chain DNA containing tandem repeating DNA aptamers (or concatemeric aptamers). The 3D DNA systems exhibit highly cooperative binding to both small molecules and proteins, without loss of binding affinities of their parent aptamers. We further produced a highly responsive sensor for fluorescence imaging of glutamate stimulation-evoked adenosine triphosphate (ATP) release in neurons, as well as force stimulus-triggered ATP release in astrocytes.

Cooperativity in Photofoldamer Chloride Double Helices Turned On with Sequences and Solvents, Around with Guests, and Off with Light

Photofoldamers are sequence-defined receptors capable of switching guest binding on and off. When two foldamer strands wrap around the guest into 2:1 double helical complexes, cooperativity emerges, and with it comes the possibility to switch cooperativity with light and other stimuli. We use lessons from nonswitchable sequence isomers of aryl-triazole foldamers to guide how to vary the sequence location of azobenzenes from the end (F_END) to the interior (F_IN) and report their impact on the cooperative formation of 2:1 complexes with Cl^-. This sequence change produces a 125-fold increase from anti-cooperative (α = 0.008) for F_END to non-cooperative with F_IN (α = 1.0). Density functional theory (DFT) studies show greater H-bonding and a more relaxed double helix for F_IN. The solvent and guest complement the synthetic designs. Use of acetonitrile to enhance solvophobicity further enhances cooperativity in F_IN (α = 126) but lowers the difference in cooperativity between sequences. Surprisingly, the impact of the sequence on cooperativity is inverted when the guest size is increased from Cl^- (3.4 Å) to BF₄^- (4.1 Å). While photoconversion of interior azobenzenes was poor, the cis-cis isomer forms 1:1 complexes around chloride consistent with switching cooperativity. The effect of the guest, solvent, and light on the double-helix cooperativity depends on the sequence.

One-Pot Cyclization to Large Peptidomimetic Macrocycles by In Situ-Generated β-Turn-Enforced Folding

Macrocycles have been targets of extensive synthetic efforts for decades because of their potent molecular recognition and self-assembly capabilities. Yet, efficient syntheses of macrocyclic molecules via irreversible covalent bonds remain challenging. Here, we report an efficient approach to large peptidomimetic macrocycles by using the in situ-generated β-turn structural motifs afforded in the amidothiourea moieties from the early steps of the reaction of 2 molecules of bilateral amino acid-based acylhydrazine with 2 molecules of diisothiocyanate. Four chiral and achiral peptidomimetic large macrocycles were successfully synthesized in high yields of 45-63% in a feasible one-pot reaction under sub-molar concentration conditions and were purified by simple filtration. X-ray crystallographic characterization of three macrocycles reveals an important feature that their four β-turn structures, each maintained by four 10-membered intramolecular hydrogen bonds, alternatively network the four aromatic arms. This affords an interesting conformation switching mode upon anion binding. Binding of SO₄^2- to 1L or 1D that contains 4 alanine residues (with the lowest steric hinderance among the macrocycles) leads to an inside-out structural change of the host macrocycle, as confirmed by the X-ray crystal structure of 1L-SO₄^2- and 1D-SO₄^2- complexes, accompanied by an inversion of the CD signals. On the basis of the strong sulfate affinity of the macrocycles, we succeeded in the removal of sulfate anions from water via a macrocycle-mediated liquid-liquid extraction method. Our synthetic protocol can be easily extended to other macrocycles of varying arms and/or chiral amino acid residues; thus, a variety of structurally and functionally diverse macrocycles are expected to be readily made.

Three-body interaction effects in heterolytic hydrogen splitting by frustrated Lewis pairs

The reaction of heterolytic dihydrogen splitting by frustrated Lewis pairs P(R)₃ and B(C₆F₅)₃ (where R = t-butyl and 1-adamantene) is driven by strong three-body contributions which originate from the induction and charge transfer effects. The three-body effect increases dramatically as a function of inter-hydrogen distance. As predicted by the symmetry adapted perturbation theory, the "frustration" of Lewis pairs originates from the dual role of the exchange effects. First, the exchange manifests itself in the first-order Pauli repulsion by keeping the pairs away. Second, and equally important, the second-order exchange-induction almost completely cancels the effects of the second-order induction. This suppression of induction effects eases up upon the interaction of the frustrated pairs with H₂. The activation of induction in this instance constitutes the three-body effect.

The "Nitrogen Effect": Complexation with Macrocycles Potentiates Fused Heterocycles to Form Halogen Bonds in Competitive Solvents

Weak intermolecular forces are typically very difficult to observe in highly competitive polar protic solvents as they are overwhelmed by the quantity of competing solvent. This is even more challenging for three-component ternary assemblies of pure organic compounds. In this work, we overcome these complications by leveraging the binding of fused aromatic N-heterocycles in an open resorcinarene cavity to template the formation of a three-component halogen-bonded ternary assembly in a protic polar solvent system.

Advanced supramolecular design for direct ink writing of soft materials

The exciting advancements in 3D-printing of soft materials are changing the landscape of materials development and fabrication. Among various 3D-printers that are designed for soft materials fabrication, the direct ink writing (DIW) system is particularly attractive for chemists and materials scientists due to the mild fabrication conditions, compatibility with a wide range of organic and inorganic materials, and the ease of multi-materials 3D-printing. Inks for DIW need to possess suitable viscoelastic properties to allow for smooth extrusion and be self-supportive after printing, but molecularly facilitating 3D printability to functional materials remains nontrivial. While supramolecular binding motifs have been increasingly used for 3D-printing, these inks are largely optimized empirically for DIW. Hence, this review aims to establish a clear connection between the molecular understanding of the supramolecularly bound motifs and their viscoelastic properties at bulk. Herein, extrudable (but not self-supportive) and 3D-printable (self-supportive) polymeric materials that utilize noncovalent interactions, including hydrogen bonding, host-guest inclusion, metal-ligand coordination, micro-crystallization, and van der Waals interaction, have been discussed in detail. In particular, the rheological distinctions between extrudable and 3D-printable inks have been discussed from a supramolecular design perspective. Examples shown in this review also highlight the exciting macroscale functions amplified from the molecular design. Challenges associated with the hierarchical control and characterization of supramolecularly designed DIW inks are also outlined. The perspective of utilizing supramolecular binding motifs in soft materials DIW printing has been discussed. This review serves to connect researchers across disciplines to develop innovative solutions that connect top-down 3D-printing and bottom-up supramolecular design to accelerate the development of 3D-print soft materials for a sustainable future.

Intra- and Intermolecular Cooperativity in the Catalytic Activity of Phosphodiester Cleavage by Self-Assembled Systems Based on Guanidinylated Calix[4]arenes

The calix[4]arene scaffold, blocked in the cone conformation through alkylation with long alkyl chains, and decorated at the upper rim with four guanidine or arginine units, effectively catalyzes the cleavage of the phosphodiester bond of DNA and RNA model compounds in water. An exhaustive kinetic investigation unequivocally points to the existence of spontaneous aggregation phenomena, driven by hydrophobic effect, occurring at different critical concentrations that depend on the identity of the compound. A pronounced superiority of the assembled structures compared with the monomers in solution was observed. Moreover, the catalytically active units, clustered on the macrocyclic tetrafunctional scaffold, were proved to efficiently cooperate in the catalytic mechanism and result in improved reaction rates compared to those of the monofunctional model compounds. The kinetic analysis is also integrated and corroborated with further experiments based on fluorescence spectroscopy and light scattering. The advantage of the supramolecular assemblies based on tetrafunctional calixarenes leads to believe that the active units can cooperate not only intramolecularly but also intermolecularly. The molecules in the aggregates can probably mold, flex and rearrange but, at the same time, keep an ordered structure that favors phosphodiester bond cleavage. This dynamic preorganization can allow the catalytic units to reach a better fitting with the substrates and perform a superior catalytic activity.

Parallel G-Quadruplex DNA Structures from Nuclear and Mitochondrial Genomes Trigger Emission Enhancement in a Nonfluorescent Nano-aggregated Fluorine-Boron-Based Dye

Molecular self-assembly is a powerful tool for the development of functional nanostructures with adaptive optical properties. However, in aqueous solution, the hydrophobic effects in the monomeric units often afford supramolecular architectures with typical side-by-side π-stacking arrangement with compromised emissive properties. Here, we report on the role of parallel DNA guanine quadruplexes (G4s) as supramolecular disaggregating-capture systems capable of coordinating a zwitterionic fluorine-boron-based dye and promoting activation of its fluorescence signal. The dye's high binding affinity for parallel G4s compared to nonparallel topologies leads to a selective disassembly of the dye's supramolecular state upon contact with parallel G4s. This results in a strong and selective disaggregation-induced emission that signals the presence of parallel G4s observable by the naked eye and inside cells. The molecular recognition strategy reported here will be useful for a multitude of affinity-based applications with potential in sensing and imaging systems.

Ultra-Tight Host-Guest Binding with Exceptionally Strong Positive Cooperativity

Cooperativity plays a critical role in self-assembly and molecular recognition. A rigid aromatic oligoamide macrocycle with a cyclodirectional backbone binds with DABCO-based cationic guests in a 2 : 1 ratio in high affinities (K_total ≈10¹³  M^-2 ) in the highly polar DMF. The host-guest binding also exhibits exceptionally strong positive cooperativity quantified by interaction factors α that are among the largest for synthetic host-guest systems. The unusually strong positive cooperativity, revealed by isothermal titration calorimetry (ITC) and fully corroborated by mass spectrometry, NMR and computational studies, is driven by guest-induced stacking of the macrocycles and stabilization from the alkyl end chains of the guests, interactions that appear upon binding the second macrocycle. With its tight binding driven by extraordinary positive cooperativity, this host-guest system provides a tunable platform for studying molecular interactions and for constructing stable supramolecular assemblies.

Analysing binding stoichiometries in NMR titration experiments using Monte Carlo simulation and resampling techniques

The application of Monte Carlo simulation and resampling techniques to analyse possible binding stoichiometries in NMR titration experiments is presented. Four simulated NMR titration experiments having complex species with 1:1, 2:1 and 1:2 stoichiometries were each analysed using a 1:1, 2:1/1:1, 1:1/1:2 and a 2:1/1:1/1:2 model as implemented in SupraFit. Each best-fit model was inspected using Monte Carlo simulation (MC), Cross Validation (CV) and a new protocol termed Reduction Analysis (RA). The results of the statistical post-processes were used to calculate characteristic descriptors that are the base of the judgment for both, the models and individual stability constants. The results indicate promising approaches to correctly identify 1:1, 2:1/1:1 and 1:1/1:2 models, however with some limitations in case of the 2:1/1:1/1:2 model. All simulations and post-processing protocols were performed with the newly presented SupraFit.

Parallel Allosteric Inhibition of Shuttling Motion and Catalysis in a Silver(I)-loaded [2]Rotaxane

A dynamic silver(I)-loaded [2]rotaxane shuttle (k₂₉₈ = 135 kHz) was converted allosterically into a conformationally restricted [2]rotaxane due to the creation of a bulky imine in the center of the axle component. Only the dynamic silver(I)-loaded [2]rotaxane was able to catalyze a 6-endo-cyclization reaction, whereas the static one was catalytically quiet. The mechanism of catalyst deactivation was elucidated.

Stereoelectronically-induced allosteric binding: shape complementarity promotes positive cooperativity in fullerene/buckybowl complexes

A novel 2 : 1 host-guest complex forms between 8-tert-butyl-6b²-azapenta-benzo[bc,ef,hi,kl,no]corannulene (1) and C₆₀ with positive cooperativity (α = 2.56) and high affinity (K₁ × K₂ = 2.8 × 10⁶ M^-2) at 25 °C. The C₆₀ undergoes increasing shape complementarity toward 1 throughout the binding process.

When Molecules Meet in Water-Recent Contributions of Supramolecular Chemistry to the Understanding of Molecular Recognition Processes in Water

Molecular recognition processes in water differ from those in organic solvents in that they are mediated to a much greater extent by solvent effects. The hydrophobic effect, for example, causes molecules that only weakly interact in organic solvents to stay together in water. Such water‐mediated interactions can be very efficient as demonstrated by many of the synthetic receptors discussed in this review, some of which have substrate affinities matching or even surpassing those of natural binders. However, in spite of considerable success in designing such receptors, not all factors determining their binding properties in water are fully understood. Existing concepts still provide plausible explanations why the reorganization of water molecules often causes receptor‐substrate interactions in water to be strongly exothermic rather than entropically favored as predicted by the classical view of the hydrophobic effect.

Encapsulation within a coordination cage modulates the reactivity of redox-active dyes

Confining molecules within well-defined nanosized spaces can profoundly alter their physicochemical characteristics. For example, the controlled aggregation of chromophores into discrete oligomers has been shown to tune their optical properties whereas encapsulation of reactive species within molecular hosts can increase their stability. The resazurin/resorufin pair has been widely used for detecting redox processes in biological settings; yet, how tight confinement affects the properties of these two dyes remains to be explored. Here, we show that a flexible Pd^II₆L₄ coordination cage can efficiently encapsulate both resorufin and resazurin in the form of dimers, dramatically modulating their optical properties. Furthermore, binding within the cage significantly decreases the reduction rate of resazurin to resorufin, and the rate of the subsequent reduction of resorufin to dihydroresorufin. During our studies, we also found that upon dilution, the Pd^II₆L₄ cage disassembles to afford Pd^II₂L₂ species, which lacks the ability to form inclusion complexes - a process that can be reversed upon the addition of the strongly binding resorufin/resazurin guests. We expect that the herein disclosed ability of a water-soluble cage to reversibly modulate the optical and chemical properties of a molecular redox probe will expand the versatility of synthetic fluorescent probes in biologically relevant environments.

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.

Activation of positive cooperativity by size-mismatch assembly via inclination of guests in a single-site receptor

A halogenated bowl-shaped guest, corannulene, was encapsulated in a cylindrical host, [4]cyclochrysenylene, to form a bowl-in-tube complex, which mimicked supramolecular complexes between bowl guests and carbon nanotubes. As was the case with carbon nanotubes, the cylindrical space of [4]cyclochrysenylene trapped multiple corannulene molecules in an array, and 1:2 complexes were commonly obtained with the corannulene guests with various halogen substituents (F, Cl, Br and I). Careful statistical analyses of isothermal titration calorimetry titration data succeeded in revealing the stoichiometry, and the molecular structures of the 1:2 complexes were further clarified by X-ray crystallographic analyses. Two fluorinated corannulene guests were stacked perpendicular to the cylinder axis, while two chlorinated guests were stacked with inclined orientations. The structural difference resulted in a large difference in the cooperativity of the two-stage association in solution: fluorinated corannulene guests showed negative cooperativity for the 1:2 complexation, and the other, larger halogenated corannulene guests showed positive cooperativity.

The Use of the Statistical Entropy in Some New Approaches for the Description of Biosystems

Some problems of describing biological systems with the use of entropy as a measure of the complexity of these systems are considered. Entropy is studied both for the organism as a whole and for its parts down to the molecular level. Correlation of actions of various parts of the whole organism, intercellular interactions and control, as well as cooperativity on the microlevel lead to a more complex structure and lower statistical entropy. For a multicellular organism, entropy is much lower than entropy for the same mass of a colony of unicellular organisms. Cooperativity always reduces the entropy of the system; a simple example of ligand binding to a macromolecule carrying two reaction centers shows how entropy is consistent with the ambiguity of the result in the Bernoulli test scheme. Particular attention is paid to the qualitative and quantitative relationship between the entropy of the system and the cooperativity of ligand binding to macromolecules. A kinetic model of metabolism. corresponding to Schrödinger's concept of the maintenance biosystems by "negentropy feeding", is proposed. This model allows calculating the nonequilibrium local entropy and comparing it with the local equilibrium entropy inherent in non-living matter.

Cooperativity as quantification and optimization paradigm for nuclear receptor modulators

A cooperativity framework describes the formation of nuclear receptor ternary complexes and deconvolutes ligand and cofactor binding into intrinsic affinities and a cooperativity factor, providing a conceptually new understanding of NR modulation.

Size-encoded hierarchical self-assembly of nanoparticles into chains and tubules

Hierarchical structures with sophisticated patterns allow the emergence of challenging properties. However, the highly cooperative and specific interactions needed for assembly spanning different length scales are typically lacking in inorganic nanoparticles (NPs). Here we show that size can be a common structural driving force for controlling hierarchical assembly of inorganic NPs into anisotropic superstructures. It involves first the self-limiting assembly of small CdS NPs into large supraparticles and their subsequent spontaneous organization into chains and tubules hundreds of nanometers long. Our quantitative calculations based on DLVO theory reveals an intrinsic size effect relating to the dimension change of assembly units in accordance with a negative cooperativity. It is shown that the size increase in building blocks creates an effective kinetic barrier contrast at different attachment sites due to the increase of interparticle electrostatic repulsion, switching the assembly from thermodynamically preferred 3D to kinetically favored 1D pathway. The size-encoded hierarchical assembly is accompanied by the ligand-controlled Oswald ripening process, which is responsible for the variation of hierarchical patterns from chains to tubules. The general principle in governing multistage inorganic NP ordering represents an important guideline toward the complex mesoscale structures that may surpass traditional materials in both design and functionality.

Avidity observed between a bivalent inhibitor and an enzyme monomer with a single active site

Although myriad protein–protein interactions in nature use polyvalent binding, in which multiple ligands on one entity bind to multiple receptors on another, to date an affinity advantage of polyvalent binding has been demonstrated experimentally only in cases where the target receptor molecules are clustered prior to complex formation. Here, we demonstrate cooperativity in binding affinity (i.e., avidity) for a protein complex in which an engineered dimer of the amyloid precursor protein inhibitor (APPI), possessing two fully functional inhibitory loops, interacts with mesotrypsin, a soluble monomeric protein that does not self-associate or cluster spontaneously. We found that each inhibitory loop of the purified APPI homodimer was over three-fold more potent than the corresponding loop in the monovalent APPI inhibitor. This observation is consistent with a suggested mechanism whereby the two APPI loops in the homodimer simultaneously and reversibly bind two corresponding mesotrypsin monomers to mediate mesotrypsin dimerization. We propose a simple model for such dimerization that quantitatively explains the observed cooperativity in binding affinity. Binding cooperativity in this system reveals that the valency of ligands may affect avidity in protein–protein interactions including those of targets that are not surface-anchored and do not self-associate spontaneously. In this scenario, avidity may be explained by the enhanced concentration of ligand binding sites in proximity to the monomeric target, which may favor rebinding of the multiple ligand binding sites with the receptor molecules upon dissociation of the protein complex.

Acridinone-based anion transporters

The arrangement of hydrogen bond donors around a central lipophilic scaffold has proven to be a successful strategy in the development of potent chloride transporters. In this work, we revisit an acridinone 1,9-bis(thio)urea motif which had previously shown promise as an anion sensor and expand the series of compounds by appending a variety of electron-withdrawing groups to the peripheral phenyl moieties. High levels of activity were achieved by the most effective compounds in the series, which facilitated strictly electroneutral transport.

Utilizing an Amino Acid Scaffold to Construct Heteroditopic Receptors Capable of Interacting with Salts under Interfacial Conditions

A 4-nitro-L-phenylalanine scaffold was used to construct effective ion pair receptors capable of binding anions in an enhanced manner with the assistance of alkali metal cations. A benzocrown ether was linked to a receptor platform via the amide function so as to support the squaramide function in anion binding and to allow all three NHs to act simultaneously. The binding properties of the receptors were determined using UV-vis, ¹H NMR, 2D NMR, and DOSY spectroscopy in MeCN and in the solid state by X-ray measurements. Ion pair receptor 2 was found to interact with the most strongly with salts, and the removal of its key structural elements was shown to hinder the receptor action. The amide proton was recognized to switch from having involvement in an intramolecular hydrogen bond to interacting with anions upon complexation. Apart from carboxylates, which promote deprotonation, and other monovalent salts creating 1:1 complexes with the receptor, more complex equilibria were established upon the complexation of 2 with sulfates. Receptor 2 was shown to be capable of the extraction of ion pairs from the aqueous to organic phase and of the cation-enhanced transport chloride and sulfate anions across a bulk chloroform membrane. These features may open the door for its use in regulating ion concertation under interfacial conditions and acting as a potential drug to treat channelopathies.

Spacer-Dependent Cooperativity of Helicity in Fluorescent Bishelical Foldamers Based on L-Shaped Dibenzopyrrolo[1,2-a][1,8]naphthyridine

For the construction of helical foldamers composed of π-frameworks, the choice of appropriate π-π stacking units and π-spacers connecting them is important. The transfer of helicity between the minimal helix structural units is also an essential factor in the construction of homochiral helical foldamers. Tetramers 4 a-4 d, which have four L-shaped dibenzopyrrolo[1,2-a]naphthyridine units, were synthesized to investigate the interplay and cooperativity of the helical structures. Tetramer 4 a bridged with a biphenyl unit formed a homochiral bishelical structure with π-π stacking between the L-shaped units (3.3 Å), consisting only of (P,P)- and (M,M)-enantiomers without the (P,M)-diastereomer, owing to interplay through the axial chirality of biphenyl unit in the solid state. Similarly, in solution, thermodynamic stabilization of the two helix formations worked cooperatively to favor the bishelical form of 4 a. Furthermore, bishelical foldamer 4 a emitted intense fluorescence (Φ=0.86).

Cooperative Effects in Switchable Catalysis: Enhancing Double-Click Reaction Yield of Symmetrical Rotaxanes

Reversible switching between the closed cyclic dimeric assembly [Cu2 (1)2 ]2+ (OFF state) and the extended dimeric homoleptic complex [FeCu2 (1)2 ]4+ (ON State) by addition/removal of Fe2+ triggered catalysis of a double-click reaction and high yield preparation of [2]rotaxanes. Mechanistic and computational studies provide valuable general insight for double-click strategies by revealing cooperative effects in the second cycloaddition step due to a distance-tolerant preorganization of the first-click product by the two copper(I)-loaded phenanthroline subunits of [FeCu2 (1)2 ]4+ .

Light-induced in situ chemical activation of a fluorescent probe for monitoring intracellular G-quadruplex structures

Light-activated functional materials capable of remote control over duplex and G-quadruplex (G4) nucleic acids formation at the cellular level are still very rare. Herein, we report on the photoinduced macrocyclisation of a helicenoid quinoline derivative of binaphthol that selectively provides easy access to an unprecedented class of extended heteroaromatic structures with remarkable photophysical and DNA/RNA binding properties. Thus, while the native bisquinoline precursor shows no DNA binding activity, the new in situ photochemically generated probe features high association constants to DNA and RNA G4s. The latter inhibits DNA synthesis by selectively stabilizing G4 structures associated with oncogenic promoters and telomere repeat units. Finally, the light sensitive compound is capable of in cellulo photoconversion, localizes primarily in the G4-rich sites of cancer cells, competes with a well-known G4 binder and shows a clear nuclear co-localization with the quadruplex specific antibody BG4. This work provides a benchmark for the future design and development of a brand-new generation of light-activated target-selective G4-binders.

A Minimalistic Coumarin Turn-On Probe for Selective Recognition of Parallel G-Quadruplex DNA Structures

G-quadruplex (G4) DNA structures are widespread in the human genome and are implicated in biologically important processes such as telomere maintenance, gene regulation, and DNA replication. Guanine-rich sequences with potential to form G4 structures are prevalent in the promoter regions of oncogenes, and G4 sites are now considered as attractive targets for anticancer therapies. However, there are very few reports of small “druglike” optical G4 reporters that are easily accessible through one-step synthesis and that are capable of discriminating between different G4 topologies. Here, we present a small water-soluble light-up fluorescent probe that features a minimalistic amidinocoumarin-based molecular scaffold that selectively targets parallel G4 structures over antiparallel and non-G4 structures. We showed that this biocompatible ligand is able to selectively stabilize the G4 template resulting in slower DNA synthesis. By tracking individual DNA molecules, we demonstrated that the G4-stabilizing ligand perturbs DNA replication in cancer cells, resulting in decreased cell viability. Moreover, the fast-cellular entry of the probe enabled detection of nucleolar G4 structures in living cells. Finally, insights gained from the structure–activity relationships of the probe suggest the basis for the recognition of parallel G4s, opening up new avenues for the design of new biocompatible G4-specific small molecules for G4-driven theranostic applications.