Salt-Induced Adaptation of a Dynamic Combinatorial Library of Pseudopeptidic Macrocycles: Unraveling the Electrostatic Effects in Mixed Aqueous Media

Further Dimensions for Sensing in Biofluids: Distinguishing Bioorganic Analytes by the Salt-Induced Adaptation of a Cucurbit[7]uril-Based Chemosensor

Insufficient binding selectivity of chemosensors often renders biorelevant metabolites indistinguishable by the widely used indicator displacement assay. Array-based chemosensing methods are a common workaround but require additional effort for synthesizing a chemosensor library and setting up a sensing array. Moreover, it can be very challenging to tune the inherent binding preference of macrocyclic systems such as cucurbit[n]urils (CBn) by synthetic means. Using a novel cucurbit[7]uril-dye conjugate that undergoes salt-induced adaptation, we now succeeded in distinguishing 14 bioorganic analytes from each other through the facile stepwise addition of salts. The salt-specific concentration-resolved emission provides additional information about the system at a low synthetic effort. We present a data-driven approach to translate the human-visible curve differences into intuitive pairwise difference measures. Ion mobility experiments combined with density functional theory calculations gave further insights into the binding mechanism and uncovered an unprecedented ternary complex geometry for CB7. TThis work introduces the non-selectively binding, salt-adaptive cucurbit[n]uril system for sensing applications in biofluids such as urine, saliva, and blood serum.

Sulfur in Dynamic Covalent Chemistry

Sulfur has been important in dynamic covalent chemistry (DCC) since the beginning of the field. Mainly as part of disulfides and thioesters, dynamic sulfur-based bonds (DSBs) have a leading role in several remarkable reactions. Part of this success is due to the almost ideal properties of DSBs for the preparation of dynamic covalent systems, including high reactivity and good reversibility under mild aqueous conditions, the possibility of exploiting supramolecular interactions, access to isolable structures, and easy experimental control to turn the reaction on/off. DCC is currently witnessing an increase in the importance of DSBs. The chemical flexibility offered by DSBs opens the door to multiple applications. This Review presents an overview of all the DSBs used in DCC, their applications, and remarks on the interesting properties that they confer on dynamic chemical systems, especially those containing several DSBs.

Tuning the Outcome of Enzyme-Mediated Dynamic Cyclodextrin Libraries to Enhance Template Effects

Enzyme-mediated dynamic combinatorial chemistry combines the concept of thermodynamically controlled covalent self-assembly with the inherent biological relevance of enzymatic transformations. A system of interconverting cyclodextrins has been explored, in which the glycosidic linkage is rendered dynamic by the action of cyclodextrin glucanotransferase (CGTase). External factors, such as pH, temperature, solvent, and salinity are reported to modulate the composition of the dynamic cyclodextrin library. Dynamic libraries of cyclodextrins (CDs) could be obtained in wide ranges of pH (5.0-9.0), temperature (5-37 °C), and salinity (up to 7.5 m NaNO₃ ), and with high organic solvent content (50 % by volume of ethanol), showing that enzyme-mediated dynamic systems can be robust and not limited to physiological conditions. Furthermore, it is demonstrated how strategic choice of reaction conditions can enhance template effects, in this case, to achieve highly selective production of α-CD, an otherwise challenging target due to competition from the structurally similar β-CD.

Template effects of vesicles in dynamic covalent chemistry

Vesicle lipid bilayers have been employed as templates to modulate the product distribution in a dynamic covalent library of Michael adducts formed by mixing a Michael acceptor with thiols. In methanol solution, all possible Michael adducts were obtained in similar amounts. Addition of vesicles to the dynamic covalent library led to the formation of a single major product. The equilibrium constants for formation of the Michael adducts are similar for all of the thiols used in this experiment, and the effect of the vesicles on the composition of the library is attributed to the differential partitioning of the library members between the lipid bilayer and the aqueous solution. The results provide a quantitative approach for exploiting dynamic covalent chemistry within lipid bilayers.

Guest Binding Drives Host Redistribution in Libraries of CoII 4 L4 Cages

Two CoII 4 L4 tetrahedral cages prepared from similar building blocks showed contrasting host-guest properties. One cage did not bind guests, whereas the second encapsulated a series of anions, due to electronic and geometric effects. When the building blocks of both cages were present during self-assembly, a library of five CoII LA x LB 4-x cages was formed in a statistical ratio in the absence of guests. Upon incorporation of anions able to interact preferentially with some library members, the products obtained were redistributed in favor of the best anion binders. To quantify the magnitudes of these templation effects, ESI-MS was used to gauge the effect of each template upon library redistribution.

Exploiting complexity to implement function in chemical systems

This feature article reflects a personal overview of the importance of complexity as an additional parameter to be considered in chemical research, being illustrated with selected examples in molecular recognition and catalysis.

An efficient dynamic asymmetric catalytic system within a zinc-templated network

Enhanced cooperativity leading to high catalytic activity and stereoselectivity has been achieved through a complex network of simple species interacting reversibly. This novel dynamic catalytic system relies on bipyridine-based organocatalytic ligands and zinc(ii) as the template. It demonstrates the effectiveness of dealing with mixtures rather than single species in asymmetric catalysis.

A Candidate for Multitopic Probes for Ligand Discovery in Dynamic Combinatorial Chemistry

Multifunctionalized materials are expected to be versatile probes to find specific interactions between a ligand and a target biomaterial. Thus, efficient methods to prepare possible combinations of the functionalities is desired. The concept of dynamic combinatorial chemistry (DCC) is ideal for the generation of any possible combination, as well as screening for target biomaterials. Here, we propose a new molecular design of multitopic probes for ligand discovery in DCC. We synthesized a new Gable Porphyrin, GP1, having prop-2-yne groups as a scaffold to introduce various functional groups. GP1 is a bis(imidazolylporphyrinatozinc) compound connected through a 1,3-phenylene moiety, and it gives macrocycles spontaneously and quantitatively by strong imidazole-to-zinc complementary coordination. Some different types of functional groups were introduced into GP1 in high yields. Formation of heterogeneous macrocycles composed of GP1 derivatives having different types of substituents was accomplished under equilibrium conditions. These results promise that enormous numbers of macrocycles having various functional groups can be provided when the kinds of GP components increase. These features are desirable for DCC, and the present system using GP1 is a potential candidate to provide a dynamic combinatorial library of multitopic probes to discover specific interactions between a ligand and a biomaterial.

Supramolecular cages as differential sensors for dicarboxylate anions: guest length sensing using principal component analysis of ESI-MS and 1H-NMR raw data

Dynamic covalent libraries (DCLs) have been widely used in the development of differential sensors. Inspired by recent studies which use supramolecular recognition systems for sensing, we report the use of a tris(-pyridylmethyl)amine (TPMA)-based supramolecular cage as a differential sensor for dicarboxylate anions. In particular, a library of molecular cages constituted by linkers differing in size and flexibility was allowed to equilibrate toward a series of guests differing in molecular size. The differential system was able to discriminate a series of dicarboxylates depending on their chain length. This differentiation was evaluated through the application of the Principal Component Analysis (PCA) method using interpolated and raw data obtained from ESI-MS. Interestingly, while the 1H NMR spectra of the differential system did not allow for the discrimination of the analytes by the naked eye, PCA of the raw data from the spectra revealed information on the chain length of the guest and also on the odd-even character of the carbon chain.

Diasteroselective multi-component assemblies from dynamic covalent imine condensation and metal-coordination chemistry: mechanism and narcissistic stereochemistry self-sorting

Self-assembly of a modified tris(2-pyridylmethyl)amine TPMA ligand, zinc(ii) or cobalt(ii) ions, and amino acids have been used effectively as stereo dynamic optical probes for the determination of the enantiomeric excess of free amino acids either using Electronic or Vibrational Circular Dichroism (CD and VCD). Herein, we report the mechanistic and stereochemical study of the self-assembly process which reveals a complex equilibrium in solution where even small variations in the experimental conditions can profoundly affect the final products of the reaction. In particular, variation on the metal stoichiometry switch give rises to an entirely enantio narcissistic self-assembly of the structure.

Enantio narcissistic self-assembly is observed in a multi-metallic structure used as stereodynamic probe for CD measurements.

Pseudopeptidic compounds for the generation of dynamic combinatorial libraries of chemically diverse macrocycles in aqueous media

The combination of pseudopeptidic dithiol building blocks leads to the generation of highly diverse dynamic libraries of macrocycles in aqueous media.

Entropy-driven homochiral self-sorting of a dynamic library

The efficient homochiral self-sorting of pseudopeptidic macrocycles, observed from a simple dynamic library, is driven by entropy.

Experimental Binding Energies in Supramolecular Complexes

On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.

From simplicity to complex systems with bioinspired pseudopeptides

This feature article highlights some of the recent advances in creating complexity from simple pseudopeptidic molecules. The bioinspired approaches discussed here allowed an increase in the structural, chemical and interactional complexity (see figure).

Dynamic assembly of a zinc-templated bifunctional organocatalyst in the presence of water for the asymmetric aldol reaction

A bifunctional organocatalytic system consisting of simple pyridine ligands containing separate catalytic functionalities was assembled using ZnCl2. This novel metal-templated catalyst furnished high yields and stereoselectivities towards the aldol reaction. The addition of controlled amounts of water turned out to be crucial to dissolve the system and achieve optimal results.

Intramolecular hydrogen bonding guides a cationic amphiphilic organocatalyst to highly stereoselective aldol reactions in water

A novel amphiphilic acylguanidine organocatalyst using intramolecular hydrogen bonding as a key structural motif is efficient for asymmetric aldol reactions of ketones in water at neutral pH.