Allosteric, Chelate, and Interannular Cooperativity: A Mise au Point

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.

Crowding-Regulated Binding of Divalent Biomolecules

Macromolecular crowding affects biophysical processes as diverse as diffusion, gene expression, cell growth, and senescence. Yet, there is no comprehensive understanding of how crowding affects reactions, particularly multivalent binding. Herein, we use scaled particle theory and develop a molecular simulation method to investigate the binding of monovalent to divalent biomolecules. We find that crowding can increase or reduce cooperativity-the extent to which the binding of a second molecule is enhanced after binding a first molecule-by orders of magnitude, depending on the sizes of the involved molecular complexes. Cooperativity generally increases when a divalent molecule swells and then shrinks upon binding two ligands. Our calculations also reveal that, in some cases, crowding enables binding that does not occur otherwise. As an immunological example, we consider immunoglobulin G-antigen binding and show that crowding enhances its cooperativity in bulk but reduces it when an immunoglobulin G binds antigens on a surface.

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.

Functional advantages of building nanosystems using multiple molecular components

Over half of all the natural nanomachines in living organisms are multimeric and likely exploit the self-assembly of their components to provide functional benefits. However, the advantages and disadvantages of building nanosystems using multiple molecular components remain relatively unexplored at the thermodynamic, kinetic and functional levels. In this study we used theory and a simple DNA-based model that forms the same nanostructures with different numbers of components to advance our knowledge in this area. Despite its lower assembly rate, we found that a system built with three components may undergo a more cooperative assembly transition from less preorganized components, which facilitates the emergence of functionalities. Using simple variations of its components, we also found that trimeric nanosystems display a much higher level of programmability than their dimeric counterparts because they can assemble with various levels of cooperativity, self-inhibition and time-dependent properties. We show here how two simple strategies (for example, cutting and adding components) can be employed to efficiently programme the regulatory function of a more complex, artificially selected, RNA-cleaving catalytic nanosystem.

Preorganized Polyaromatic Soft Terdentate Hosts for the Capture of [Ln(β-diketonate)3 ] Guests in Solution

The concept of preorganization is famous in coordination chemistry for having transformed flexible bidentate 2,2'-bipyridine scaffolds into rigid 1,10-phenanthroline platforms. The resulting boosted affinities for d-block cations has successfully paved the way for the design of a wealth of functional complexes, devices and materials for analysis and optics. Its extension toward terdentate homologues adapted for the selective complexation of f-block cations with larger coordination numbers remains more overlooked. The resulting rigidification of 2,6-bis(1-methyl-1H-benzo[d]imidazol-2-yl)pyridine ligands (L1-L7) produces the highly preorganized and extended polyaromatic benzo[4',5']imidazo[1',2' : 1,2]pyrido[3,4-b]benzo[4,5]imidazo[1,2-h][1,7]naphthyridines (L8-L11) receptors, which offer some novel and rare opportunities for efficiently complexing trivalent lanthanides with polyaromatic soft terimine ligands. The crystal structures of the stable heteroleptic [LkLn(hfac)₃ ] adducts (Lk=L1, L8, L9; Ln=La, Eu, Gd, Er, Yb, Y; H-hfac=1,1,1,5,5,5-hexafluoropentane-2,4-dione) show a drastic decrease in the Ln-N bond valences upon replacement of the flexible ligand L1 with its preorganized counterparts L8 and L9. This points to a limited match between the preorganized cavity and the entering [Ln(hfac)₃ ] lanthanide containers. However, thermodynamic studies conducted in dichloromethane reach the opposite conclusion, with an improved affinity, by up to three orders of magnitude for catching Ln(hfac)₃ when L1 is replaced by the preorganized L8-L9 receptors. The key to the enigma lies in the removal of the energy penalty which accompanies the formation of flexible [L1Ln(hfac)₃ ] complexes in solution. This driving force overcomes the poor match between the preorganized terdentate N^∩ N^∩ N cavity in L8 and L9 and the size of trivalent lanthanides. As planned, the rigid, planar and extended π-conjugated system found in L8 and L9 shifts the ligand-centered absorption bands by about 5000 cm^-1 toward lower energies, a crucial point if these stable [L8Ln(hfac)₃ ] and [L9Ln(hfac)₃ ] platforms have to be considered for the visible sensitization of luminescent lanthanides in metallopolymers.

Controlling Superselectivity of Multivalent Interactions with Cofactors and Competitors

Moieties that compete with multivalent interactions or act as cofactors are common in living systems, but their effect on multivalent binding remains poorly understood. We derive a theoretical model that shows how the superselectivity of multivalent interactions is modulated by the presence of cofactors or competitors. We find that the role of these participating moieties can be fully captured by a simple rescaling of the affinity constant of the individual ligand–receptor bonds. Theoretical predictions are supported by experimental data of the membrane repair protein annexin A5 binding to anionic lipid membranes in the presence of Ca²⁺ cofactors and of the extracellular matrix polysaccharide hyaluronan (HA) binding to CD44 cell surface receptors in the presence of HA oligosaccharide competitors. The obtained findings should facilitate understanding of multivalent recognition in biological systems and open new routes for fine-tuning the selectivity of multivalent nanoprobes in medicinal chemistry.

Positive Cooperativity Induced by Interstrand Interactions in Silver(I) Complexes with α,α′‐Diimine Ligands

The allosteric positive cooperativity accompanying the formation of compact [Cu^I(α,α′‐diimine)₂]⁺ building blocks contributed to the historically efficient synthesis of metal‐containing catenates and knotted assemblies. However, its limited magnitude can easily be overcome by the negative chelate cooperativity that controls the overall formation of related polymetallic multistranded helicates and grids. Despite the more abundant use of analogous dioxygen‐resistant [Ag^I(α,α′‐diimine)₂]⁺ units in modern entangled metallo‐supramolecular assemblies, a related thermodynamic justification was absent. Solid‐state structural characterizations show the successive formation of [Ag^I(α,α′‐diimine)(CH₃CN)][X] and [Ag^I(α,α′‐diimine)₂][X] upon the stepwise reactions of α,α′‐diimine=2,2′‐bipyridine (bpy) or 1,10‐phenanthroline (phen) derivatives with AgX (X=BF₄⁻, ClO₄⁻, PF₆⁻). In room‐temperature, 5–10 mM acetonitrile solutions, these cationic complexes exist as mixtures in fast exchange on the NMR timescale. Spectrophotometric titrations using the unsubstituted bpy and phen ligands point to the statistical (=non‐cooperative) binding of two successive bidentate ligands around Ag^I, a mechanism probably driven by the formation of hydrophobic belts, that overcomes the unfavorable decrease in the positive charge borne by the metallic cation. Surprisingly, the addition of methyl groups adjacent to the nitrogen donors (6,6′ positions in dmbpy; 2,9 positions in dmphen) induces positive cooperativity for the formation of [Ag(dmbpy)₂]⁺ and [Ag(dmphen)₂]⁺, a trend assigned to additional stabilizing interligand interactions. Adding rigid and polarizable phenyl side arms in [Ag(Brdmbpy)₂]⁺ further reinforces the positively cooperative process, while limiting the overall decrease in metal–ligand affinity.

Transition Metal Catalysis Controlled by Hydrogen Bonding in the Second Coordination Sphere

Transition metal catalysis is of utmost importance for the development of sustainable processes in academia and industry. The activity and selectivity of metal complexes are typically the result of the interplay between ligand and metal properties. As the ligand can be chemically altered, a large research focus has been on ligand development. More recently, it has been recognized that further control over activity and selectivity can be achieved by using the "second coordination sphere", which can be seen as the region beyond the direct coordination sphere of the metal center. Hydrogen bonds appear to be very useful interactions in this context as they typically have sufficient strength and directionality to exert control of the second coordination sphere, yet hydrogen bonds are typically very dynamic, allowing fast turnover. In this review we have highlighted several key features of hydrogen bonding interactions and have summarized the use of hydrogen bonding to program the second coordination sphere. Such control can be achieved by bridging two ligands that are coordinated to a metal center to effectively lead to supramolecular bidentate ligands. In addition, hydrogen bonding can be used to preorganize a substrate that is coordinated to the metal center. Both strategies lead to catalysts with superior properties in a variety of metal catalyzed transformations, including (asymmetric) hydrogenation, hydroformylation, C-H activation, oxidation, radical-type transformations, and photochemical reactions.

A High Throughput Approach for Designing Polymers That Mimic the TRAIL Protein

We have leveraged a high throughput approach to design a fully synthetic polymer mimic of the chemotherapeutic protein "TRAIL". Our design enables the synthesis of libraries of star-shaped polymers presenting exactly one receptor binding peptide at the end of each arm with no purification steps. Clear structure-activity relationships in screening for receptor binding and the apoptotic activity on colon cancer lines (COLO205) led us to identify trivalent structures, ∼1.5 nm in hydrodynamic radius as the best mimics. These showed IC₅₀ values ∼2 μM and resulted in the elevated levels of caspase-8 expected from this mechanism of cell death. Our results demonstrate the potential for HTP screening methods to be used in the design of polymers that can mimic a whole range of complex therapeutic proteins.

Cryo-EM structures of staphylococcal IsdB bound to human hemoglobin reveal the process of heme extraction

Iron surface determinant B (IsdB) is a hemoglobin (Hb) receptor essential for hemic iron acquisition by Staphylococcus aureus. Heme transfer to IsdB is possible from oxidized Hb (metHb), but inefficient from Hb either bound to oxygen (oxyHb) or bound to carbon monoxide (HbCO), and encompasses a sequence of structural events that are currently poorly understood. By single-particle cryo-electron microscopy, we determined the structure of two IsdB:Hb complexes, representing key species along the heme extraction pathway. The IsdB:HbCO structure, at 2.9-Å resolution, provides a snapshot of the preextraction complex. In this early stage of IsdB:Hb interaction, the hemophore binds to the β-subunits of the Hb tetramer, exploiting a folding-upon-binding mechanism that is likely triggered by a cis/trans isomerization of Pro173. Binding of IsdB to α-subunits occurs upon dissociation of the Hb tetramer into α/β dimers. The structure of the IsdB:metHb complex reveals the final step of the extraction process, where heme transfer to IsdB is completed. The stability of the complex, both before and after heme transfer from Hb to IsdB, is influenced by isomerization of Pro173. These results greatly enhance current understanding of structural and dynamic aspects of the heme extraction mechanism by IsdB and provide insight into the interactions that stabilize the complex before the heme transfer event. This information will support future efforts to identify inhibitors of heme acquisition by S. aureus by interfering with IsdB:Hb complex formation.

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.

Supramolecular polymerization of thiobarbituric acid naphthalene dye

2-Thiobarbituric acid-functionalized naphthalene dye selectively self-assembles into crystalline fibers to show material properties that are different from those of a previously reported oxo-barbituric acid derivative affording curved supramolecular polymers via...

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.

A Molecular Replication Process Drives Supramolecular Polymerization

Supramolecular polymers are materials in which the connections between monomers in the polymer main chain are non-covalent bonds. This area has seen rapid expansion in the last two decades and has been exploited in several applications. However, suitable contiguous hydrogen-bond arrays can be difficult to synthesize, placing some limitations on the deployment of supramolecular polymers. We have designed a hydrogen-bonded polymer assembled from a bifunctional monomer composed of two replicating templates separated by a rigid spacer. This design allows the autocatalytic formation of the polymer main chain through the self-templating properties of the replicators and drives the synthesis of the bifunctional monomer from its constituent components in solution. The template-directed 1,3-dipolar cycloaddition reaction between nitrone and maleimide proceeds with high diastereoselectivity, affording the bifunctional monomer. The high binding affinity between the self-complementary replicating templates that allows the bifunctional monomer to polymerize in solution is derived from the positive cooperativity associated with this binding process. The assembly of the polymer in solution has been investigated by diffusion-ordered NMR spectroscopy. Both microcrystalline and thin films of the polymeric material can be prepared readily and have been characterized by powder X-ray diffraction and scanning electron microscopy. These results demonstrate that the approach described here is a valid one for the construction of supramolecular polymers and can be extended to systems where the rigid spacer between the replicating templates is replaced by one carrying additional function.

Divalent ligand-monovalent molecule binding

Simultaneous binding of a divalent ligand to two identical monovalent molecules is a widespread phenomenon in biology and chemistry. Here, we describe how two such monovalent molecules B bind to a divalent ligand AA to form the intermediate and final complexes AA·B and AA·B2. Cases wherein the total concentration [AA]T is either much larger or much smaller than the total concentration [B]T have been studied earlier, but a systematic description of comparable concentrations [AA]T and [B]T is missing. Here, we present numerical and analytical results for the concentrations [AA·B] and [AA·B2] for the entire range 0 < [B]T/[AA]T < ∞. Specifically, we theoretically study three types of experimental procedures: dilution of AA and B at fixed [B]T/[AA]T, addition of AA at fixed [B]T, and addition of B at fixed [AA]T. When [AA]T and [B]T are comparable, the concentrations of free ligands and molecules both decrease upon binding. Such depletion is expected to be important in cellular contexts, e.g., in antigen detection and in coincidence detection of proteins or lipids.

Conformational Regulation of Multivalent Terpyridine Ligands for Self-Assembly of Heteroleptic Metallo-Supramolecules

A two-ligand system composed of the predesigned multivalent and complementary terpyridine-based ligands was exploited to construct heteroleptic metallo-supramolecules and to investigate the self-assembly mechanism. Molecular stellation of the trimeric hexagon [Cd₆L²₃] gave rise to the exclusive self-assembly of the star hexagon [Cd₁₈L¹₆L³₃] through complementary ligand pairing between the ditopic and octatopic tectons. To understand how the intermolecular heteroleptic complexation influenced the self-assembly pathway, the star hexagon was truncated into two triangular fragments: [Cd₁₂L¹₃L⁴₃] and [Cd₁₂L¹₃L⁵₃]. In the self-assembly of [Cd₁₂L¹₃L⁴₃], the conformational movements of hexatopic ligand L⁴ could be regulated by L¹ to promote the subsequent coordination event, which was the key step to the successful multicomponent self-assembly. In contrast, the formation of [Cd₁₂L¹₃L⁵₃] was hampered by the geometrically mismatched intermediates.

Conformationally adaptable macrocyclic receptors for ditopic anions: analysis of chelate cooperativity in aqueous containing media

The effect of chelate cooperativity on the binding of several ditopic anions to two tetrathiourea macrocycles has been analysed in competitive solvent mixtures (H2O : DMSO 1 : 9 v/v). The semi-flexible receptors bind dicarboxylates with high affinity dependent on the length and flexibility of the guest. Chemical double mutant cycle (DMC) analysis allowed the chelate cooperativity effects to be measured in detail and revealed both positive and negative cooperativity effects which were dependent on guest size, flexibility and spacer interactions between guest and macrocycle. 1H NMR and crystallographic studies confirmed the macrocycle hosts are adaptable, changing conformation to match their pore size to a selected guest.

Cooperative Binding and Stepwise Encapsulation of Drug Molecules by Sulfonylcalixarene-Based Metal-Organic Supercontainers

The cooperative binding behavior of a face-directed octahedral metal-organic supercontainer featuring one endo cavity and six exo cavities was thoroughly examined in chloroform solution through ultraviolet-visible (UV-Vis) titration technique using two representative drug molecules as the guests. The titration curves and their nonlinear fit to Hill equation strongly suggest the efficient encapsulation of the guest molecules by the synthetic host, which exhibit interesting cooperative and stepwise binding behavior. Based on the control experiments using tetranuclear complex as a reference, it is clear that two equivalents of the guest molecules are initially encapsulated inside the endo cavity, followed by the trapping of six additional equivalents of the drug molecules through six exo cavities (1 eq. per exo cavity), and the remaining guests are entrapped by the external pockets. The results provide an in-depth understanding of the cooperative binding behavior of metal-organic supercontainers, which opens up new opportunities for designing synthetic receptors for truly biomimetic functional applications.

Hierarchical self-assembly of helical coordination polymers and formation of a lamellar structure via the cooperativity of two-step Ag(i) coordination and π-π interactions

Hierarchical self-assembly from a V-shaped ligand 2,9-di(pyridin-4-yl)-1,10-phenanthroline (DPP) to an initial interlocked dimer, further to a coordination polymer with an alternate linear and interlocked helical configuration and finally to a lamellar structure with an undulating surface was precisely achieved in sequence via the cooperativity of two-step Ag (i) coordination and π-π interactions for the first time.

Octapodal Corannulene Porphyrin-Based Assemblies: Allosteric Behavior in Fullerene Hosting

An octapodal corannulene-based supramolecular system has been prepared by introducing eight corannulene moieties in a porphyrin scaffold. Despite the potential of this double picket fence porphyrin for double-tweezer behavior, NMR titrations show exclusive formation of 1:1 adducts. The system exhibits very strong affinity for C₆₀ and C₇₀ (K₁ = (2.71 ± 0.08) × 10⁴ and (2.13 ± 0.1) × 10⁵ M^-1, respectively), presenting selectivity for the latter. Density functional theory (DFT) calculations indicate that, in addition to the four corannulene units, the relatively flexible porphyrin tether actively participates in the recognition process, resulting in a strong synergistic effect. This leads to a very strong interaction with C₆₀, which in turn also induces a large structural change on the other face (second potential binding site), leading to a negative allosteric effect. We also introduced Zn²⁺ in the porphyrin core in an attempt to modulate its flexibility. The resulting metalloporphyrin also displayed single-tweezer behavior, albeit with slightly smaller binding constants for C₆₀ and C₇₀, suggesting that the effect of the coordination of fullerene to one face of our supramolecular platform was still transmitted to the other face, leading to the deactivation of the second potential binding site.

The Tyranny of Arm-Wrestling Methyls on Iron(II) Spin State in Pseudo-Octahedral [Fe(didentate)3] Complexes

The connection of a sterically constrained 3-methyl-pyrazine ring to a N-methyl-benzimidazole unit to give the unsymmetrical α,α’-diimine ligand L5 has been programmed for the design of pseudo-octahedral spin-crossover [Fe(L5)3]2+ units, the transition temperature (T1/2) of which occurs in between those reported for related facial tris-didentate iron chromophores fitted with 3-methyl-pyridine-benzimidazole in a LaFe helicate (T1/2 ~ 50 K) and with 5-methyl-pyrazine-benzimidazole L2 ligands (T1/2 ~350 K). A thorough crystallographic analysis of [Fe(L5)3](ClO4)2 (I), [Ni(L5)3](ClO4)2 (II), [Ni(L5)3](BF4)2∙H2O (III), [Zn(L5)3](ClO4)2 (IV), [Ni(L5)3](BF4)2∙1.75CH3CN (V), and [Zn(L5)3](BF4)2∙1.5CH3CN (VI) shows the selective formation of pure facial [M(L5)3]2+ cations in the solvated crystals of the tetrafluoroborate salts and alternative meridional isomers in the perchlorate salts. Except for a slightly larger intra-strand interannular twist between the aromatic heterocycles in L5, the metric parameters measured in [Zn(L5)3]2+ are comparable to those reported for [Zn(L2)3]2+, where L2 is the related unconstrained ligand. This similitude is reinforced by comparable ligand-field strengths (∆oct) and nephelauxetic effects (as measured by the Racah parameters B and C) extracted from the electronic absorption spectra recorded for [Ni(L5)3]2+ and [Ni(L2)3]2+. In this context, the strictly high-spin behavior observed for [Fe(L5)3]2+ within the 5–300 K range contrasts with the close to room-temperature spin-crossover behavior of [Fe(L2)3]2+ (T1/2 = 349(5) K in acetonitrile). This can be unambiguously assigned to an intraligand arm wrestling match operating in bound L5, which prevents the contraction of the coordination sphere required for accommodating low-spin FeII. Since the analogous 3-methyl-pyridine ring in [Fe(L3)3]2+ derivatives are sometimes compatible with spin-crossover properties, the consequences of repulsive intra-strand methyl–methyl interactions are found to be amplified in [Fe(L5)3]2+ because of the much lower basicity of the 3-methyl-pyrazine ring and the resulting weaker thermodynamic compensation. The decrease of the stability constants by five orders of magnitude observed in going from [M(L2)3]2+ to [M(L5)3]2+ (M = NiII and ZnII) is diagnostic for the operation of this effect, which had been not foreseen by the authors.

Self-Assembly of Diacetylene-Bridged Phenylenevinylene Oligomers in Water and Organic Solvents

Rodlike π-conjugated molecules in which two OPV fragments are connected through a diacetylene bond self-assemble in aqueous and organic media. Optical spectroscopy and AFM measurements indicated that, in water, strong hydrophobic interactions between π-cores promote aggregation into robust, uniform micellar structures. In contrast, in apolar solvents, a fibrilar morphology is obtained by coiling of columnar stacks. These stacks are formed in a nucleation-elongation process with degrees of cooperativity of 0.006, that is influenced by the low rotation barriers around the σ-bonds in the diacetylene linker.

Photoinduced interruption of interannular cooperativity for delivery of cationic guests in water

Photoinduced decarboxylation of two hexaanionic baskets, surrounding a divalent cationic guest, reduced the interannular cooperativity (i.e. multivalency) holding the complex together to result in the release of guests.

A Dual Wavelength Polymerization and Bioconjugation Strategy for High Throughput Synthesis of Multivalent Ligands

Structure-function relationships for multivalent polymer scaffolds are highly complex due to the wide diversity of architectures offered by such macromolecules. Evaluation of this landscape has traditionally been accomplished case-by-case due to the experimental difficulty associated with making these complex conjugates. Here, we introduce a simple dual-wavelength, two-step polymerize and click approach for making combinatorial conjugate libraries. It proceeds by incorporation of a polymerization friendly cyclopropenone-masked dibenzocyclooctyne into the side chain of linear polymers or the α-chain end of star polymers. Polymerizations are performed under visible light using an oxygen tolerant porphyrin-catalyzed photoinduced electron/energy transfer-reversible addition-fragmentation chain-transfer (PET-RAFT) process, after which the deprotection and click reaction is triggered by UV light. Using this approach, we are able to precisely control the valency and position of ligands on a polymer scaffold in a manner conducive to high throughput synthesis.

A Tetra-Porphyrin Host Exhibiting Interannular Cooperativity

Recently identified as another form of cooperativity, interannular cooperativity is rarely observed in supramolecular chemistry. A tetra-porphyrin molecular tweezer with two bis-porphyrin binding sites is reported that exhibits archetypal interannular cooperativity when complexing 1,4-diazabicyclo[2.2.2]octane (DABCO). The UV/Vis titration data best supported a 1:2 plus 2:2 plus 1:4 complexation model (host:guest), giving K₁₂ =6.32×10¹³  m^-2 , K₂₂ =3.04×10²⁰  m^-3 , and K₁₄ =1.92×10¹⁶  m^-4 in CHCl₃ . The NMR titration data supported the formation of two sandwich species, including tetra-porphyrin⋅(DABCO)₂ as the major species, although there are speciation differences between UV/Vis and NMR concentrations. Using statistical analysis, interannular cooperativity (γ) for tetra-porphyrin⋅(DABCO)₂ was determined to be negative (γ=2.41×10^-3 ), which may be explained by DABCO being too small to be optimally bound simultaneously at both bis-porphyrin binding sites.

Modeling of Multivalent Ligand-Receptor Binding Measured by kinITC

In addition to the conventional Isothermal Titration Calorimetry (ITC), kinetic ITC (kinITC) not only gains thermodynamic information, but also kinetic data from a biochemical binding process. Moreover, kinITC gives insights into reactions consisting of two separate kinetic steps, such as protein folding or sequential binding processes. The ITC method alone cannot deliver kinetic parameters, especially not for multivalent bindings. This paper describes how to solve the problem using kinITC and an invariant subspace projection. The algorithm is tested for multivalent systems with different valencies.

Inverse Mixed-Mode Chromatography for the Evaluation of Multivalency and Cooperativity of Host-Guest Complexation in Porous Materials

A new separation-based analytical method was developed to evaluate the multivalency and cooperativity of supramolecular host-guest complexation in porous materials. The method is based on inverse mixed-mode chromatography in which a porous material with a multivalent functional group is packed into a column and bound with a complementary guest molecule to form a multivalent complex. The bound guest molecules are eluted in the mobile phase and detected by appropriate methods such as UV absorption. The retention factor of the guest molecule is determined and broken down into the contributions of noncovalent interactions between binding sites (e.g., hydrophobic and ionic components), thereby calculating the effective molarity and cooperativity factor of the complexation. Two model systems denoted as RP/SCX and RP/SAX were analyzed by the established method. On average, the RP/SCX system has an effective molarity (EM) of 0.14 M and a cooperativity factor (β) of 0.86, while the RP/SAX system has an EM value of 0.18 M and a β value of 2.3. Interestingly, experiments have shown that these values do not change with changes in the intrinsic binding strength of the constituent sites. In summary, the developed method allows for quantitative assessment of multivalency and cooperativity effects in porous materials, providing a valuable complement to the analytical toolbox for supramolecular chemists and materials scientists.

A stochastic view on surface inhomogeneity of nanoparticles

The interactions between and with nanostructures can only be fully understood when the functional group distribution on their surfaces can be quantified accurately. Here we apply a combination of direct stochastic optical reconstruction microscopy (dSTORM) imaging and probabilistic modelling to analyse molecular distributions on spherical nanoparticles. The properties of individual fluorophores are assessed and incorporated into a model for the dSTORM imaging process. Using this tailored model, overcounting artefacts are greatly reduced and the locations of dye labels can be accurately estimated, revealing their spatial distribution. We show that standard chemical protocols for dye attachment lead to inhomogeneous functionalization in the case of ubiquitous polystyrene nanoparticles. Moreover, we demonstrate that stochastic fluctuations result in large variability of the local group density between particles. These results cast doubt on the uniform surface coverage commonly assumed in the creation of amorphous functional nanoparticles and expose a striking difference between the average population and individual nanoparticle coverage.

Determining the spatial arrangement of molecules on a nanoparticle’s surface is key to understanding its interactions. Here, the authors use dSTORM imaging and probabilistic modelling to map the distribution of fluorophores on a nanoparticle, finding that ligand coverage is heterogeneous and highly variable between individual particles.

Strain effects determine the performance of artificial allosteric systems: calixarenes as models

It is shown that the performance of allosteric systems regarding the efficiency and the speed of response depends critically on the strain energy of the equilibrating conformers and of the corresponding interconversion transition state. The affinity of a substrate A can be large enough to overcome in the absence of an effector E by induced fit the strain involved in the formation of an optimal conformation for binding A. The efficiency as given by the ratio KAE/KA of binding constants in the presence or absence of an effector is, for many published synthetic allosteric systems, relatively low; in practice this means that these only function within rather limited concentration ranges. A small KAE/KA ratio means that the binding strength of A or the corresponding signal will increase only little by adding an effector, and may need higher concentration of E. Implementation of steric distortion in the minor conformer can lead to reduced binding of A in the absence of the effector E. Destabilization of conformers can also result from the inclusion of high energy water molecules within a cavity. Furthermore, until now it has been overlooked that strain in the transition state can lead to reaction times of up to days, and thus to the neglect of experimental observation. The role of conformational changes within an allosteric molecule is characterized with a variety of calixarenes and other compound classes, offering a clue for the design of more efficient synthetic systems with high cooperativity.

Cooperativity basis for small-molecule stabilization of protein-protein interactions

A cooperativity framework to describe and interpret small-molecule stabilization of protein–protein interactions (PPI) is presented, which allows elucidating structure–activity relationships regarding cooperativity and intrinsic affinity.

A cooperativity framework to describe and interpret small-molecule stabilization of protein–protein interactions (PPI) is presented. The stabilization of PPIs is a versatile and emerging therapeutic strategy to target specific combinations of protein partners within the protein interactome. Currently, the potency of PPI stabilizers is typically expressed by their apparent affinity or EC₅₀. Here, we propose that the effect of a PPI stabilizer be best described involving the cooperativity factor, α, between the stabilizer and binding partners in addition to the intrinsic affinity, K_D^II, of the stabilizer for one of the apo-proteins. By way of illustration, we combine fluorescence polarization measurements with thermodynamic modeling to determine the α and K_D^II for the PPI stabilization of 14-3-3 and TASK3 by fusicoccin-A (FC-A) and validate our approach by studying other PPI-partners of 14-3-3 proteins. Finally, we characterize a library of different stabilizer compounds, and perform structure–activity relationship studies in which molecular changes could be attributed to either changes in cooperativity or intrinsic affinity. Such insights should aid in the development of more effective protein–protein stabilizer drugs.

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.

Strong positive allosteric cooperativity in ternary complexes based on hydrogen-bonded aromatic amide macrocycles

Three new hydrogen-bonded aromatic amide macrocycles with eight residues were synthesized. The first single crystal structure of this class of larger macrocycles was obtained, which reveals a saddle-like conformation. Interestingly, in sharp contrast to previous negative cooperativity in binding paraquat with cyclo[6]aramide, strong positive allosteric cooperativity in ternary complexes was observed. This may open an avenue for the construction of mechanically interlocked molecules with these larger H-bonded macrocycles.

Sequential, Ultrafast Energy Transfer and Electron Transfer in a Fused Zinc Phthalocyanine-free-base Porphyrin-C60 Supramolecular Triad

A supramolecular triad composed of a fused zinc phthalocyanine-free-base porphyrin dyad (ZnPc-H₂ P) coordinated to phenylimidazole functionalized C₆₀ via metal-ligand axial coordination was assembled, as a photosynthetic antenna-reaction centre mimic. The process of self-assembly resulting into the formation of C₆₀ Im:ZnPc-H₂ P supramolecular triad was probed by proton NMR, UV-Visible and fluorescence experiments at ambient temperature. The geometry and electronic structures were deduced from DFT calculations performed at the B3LYP/6-31G(dp) level. Electrochemical studies revealed ZnPc to be a better electron donor compared to H₂ P, and C₆₀ to be the terminal electron acceptor. Fluorescence studies of the ZnPc-H₂ P dyad revealed excitation energy transfer from ¹ H₂ P* to ZnPc within the fused dyad and was confirmed by femtosecond transient absorption studies. Similar to that reported earlier for the fused ZnPc-ZnP dyad, the energy transfer rate constant, k_ENT was in the order of 10¹²  s^-1 in the ZnPc-H₂ P dyad indicating an efficient process as a consequence of direct fusion of the two π-systems. In the presence of C₆₀ Im bound to ZnPc, photoinduced electron transfer leading to H₂ P-ZnPc^.+ :ImC₆₀ ^.- charge separated state was observed either by selective excitation of ZnPc or H₂ P. The latter excitation involved an energy transfer followed by electron transfer mechanism. Nanosecond transient absorption studies revealed that the lifetime of charge separated state persists for about 120 ns indicating charge stabilization in the triad.

Molecular bionics - engineering biomaterials at the molecular level using biological principles

Life and biological units are the result of the supramolecular arrangement of many different types of molecules, all of them combined with exquisite precision to achieve specific functions. Taking inspiration from the design principles of nature allows engineering more efficient and compatible biomaterials. Indeed, bionic (from bion-, unit of life and -ic, like) materials have gained increasing attention in the last decades due to their ability to mimic some of the characteristics of nature systems, such as dynamism, selectivity, or signalling. However, there are still many challenges when it comes to their interaction with the human body, which hinder their further clinical development. Here we review some of the recent progress in the field of molecular bionics with the final aim of providing with design rules to ensure their stability in biological media as well as to engineer novel functionalities which enable navigating the human body.

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.

The effect of the linker size in C2-symmetrical chiral ligands on the self-assembly formation of luminescent triple-stranded di-metallic Eu(iii) helicates in solution

Chiral lanthanide-based supramolecular structures have gained significant importance in view of their application in imaging, sensing and other functional purposes. We have designed chiral C2-symmetrical ligands (L) based on the use of two 2,6-pyridine-dicarboxylic-amide moieties (pda), that differ from one another by the nature of the diamine spacer groups (from 1,3-phenylenedimethanamine (1(S,S), 2(R,R)) and benzene-1,3-diamine (3(S,S), 4(R,R)) to much bulkier 4,4'-(cyclohexane-1,1-diyl)bis(2,6-dimethylaniline) (5(S,S), 6(R,R))) between these two pda units. The self-assembly between L and Eu(iii) ions were investigated in CH3CN solution at low concentration whereby the changes in the absorbance, fluorescence and Eu(iii)-centred emission spectra allowed us to model the binding equilibria occurring in the solution to the presence of [Eu:L2], [Eu2:L2], [Eu2:L3] assemblies and reveal their high binding constant values. The self-assembly in solution were also studied at higher concentration by following the changes in the 1H NMR spectra of the ligands upon Eu(iii) addition, as well as by using MALDI-MS of the isolated solid state complexes. The chiroptical properties of the ligands were used in order to study the structural changes upon self-assembly between the ligands and Eu(iii) ions using circular dichroism (CD) and circularly polarised luminescence (CPL) spectroscopies. The photophysical properties of [Eu2:L3] complexes were evaluated in solution and showed a decrease of luminescence quantum yield when going from the ligand with smaller (1(S,S)) to bulkier (5(S,S)) linker from ∼5.8% to ∼2.6%. While mass-spectrometry revealed the possible formation of trinucler assemblies such as [Eu3:L3] and [Eu3:L2].

Molecular tweezers with a rotationally restricted linker and freely rotating porphyrin moieties

The effect of the degree of conformational rigidity and/or flexibility on preorganisation in artificial molecular receptors continues to be actively explored by supramolecular chemists. This work describes a bis-porphyrin architecture, linked via a rigid polycyclic backbone, in which a sterically bulky 2,3,5,6-tetramethylphenyl diimide core restricts rotation to afford two non-interconvertible tweezer conformations; syn- and anti-. After separation, the host-guest chemistry of each conformation was studied independently. The difference in host geometry allows only the syn-conformation to form a strong 1 : 1 bis-porphyrin complex with the diamino ligand 1,4-diazabicyclo[2.2.2]octane (DABCO) (K11 = 1.25 × 108 M-1), with the anti-conformation adopting a 2 : 2 sandwich complex with DABCO (K22 = 5.57 × 1017 M-3).

Thermodynamic Programming of Erbium(III) Coordination Complexes for Dual Visible/Near-Infrared Luminescence

Intrigued by the unexpected room-temperature dual visible/near-infrared (NIR) luminescence observed for fast-relaxing erbium complexes embedded in triple-stranded helicates, in this contribution, we explore a series of six tridentate N-donor receptors L4-L9 with variable aromaticities and alkyl substituents to extricate the stereoelectronic features responsible for such scarce optical signatures. Detailed solid-state (X-ray diffraction, differential scanning calorimetry, optical spectroscopy) and solution (speciations and thermodynamic stabilities, spectrophotometry, NMR and optical spectroscopy) studies of mononuclear unsaturated [Er(Lk)₂ ]³⁺ and saturated triple-helical [Er(Lk)₃ ]³⁺ model complexes reveal that the stereoelectronic changes induced by the organic ligands affect inter- and intramolecular interactions to such an extent that 1) melting temperatures in solids, 2) the affinity for trivalent erbium in solution, and 3) optical properties in luminescent complexes can be rationally varied and controlled. With this toolkit in hand, mononuclear erbium complexes with low stabilities displaying only NIR emission can be transformed into molecular-based dual Er-centered visible/NIR emitters operating at room temperature in both solid and solution states.