Supramolecular Control for the Modular Synthesis of Pseudopeptidic Macrocycles through an Anion-Templated Reaction

Anion-Binding Properties of Short Linear Homopeptides

A comprehensive thermodynamic and structural study of the complexation affinities of tetra (L1), penta (L2), and hexaphenylalanine (L3) linear peptides towards several inorganic anions in acetonitrile (MeCN) and N,N-dimethylformamide (DMF) was carried out. The influence of the chain length on the complexation thermodynamics and structural changes upon anion binding are particularly addressed here. The complexation processes were characterized by means of spectrofluorimetric, 1H NMR, microcalorimetric, and circular dichroism spectroscopy titrations. The results indicate that all three peptides formed complexes of 1:1 stoichiometry with chloride, bromide, hydrogen sulfate, dihydrogen phosphate (DHP), and nitrate anions in acetonitrile and DMF. In the case of hydrogen sulfate and DHP, anion complexes of higher stoichiometries were observed as well, namely those with 1:2 and 2:1 (peptide:anion) complexes. Anion-induced peptide backbone structural changes were studied by molecular dynamic simulations. The anions interacted with backbone amide protons and one of the N-terminal amine protons through hydrogen bonding. Due to the anion binding, the main chain of the studied peptides changed its conformation from elongated to quasi-cyclic in all 1:1 complexes. The accomplishment of such a conformation is especially important for cyclopeptide synthesis in the head-to-tail macrocyclization step, since it is most suitable for ring closure. In addition, the studied peptides can act as versatile ionophores, facilitating transmembrane anion transport.

Synthetic Receptors Based on Abiotic Cyclo(pseudo)peptides

Work on the use of cyclic peptides or pseudopeptides as synthetic receptors started even before the field of supramolecular chemistry was firmly established. Research initially focused on the development of synthetic ionophores and involved the use of macrocycles with a repeating sequence of subunits along the ring to facilitate the correlation between structure, conformation, and binding properties. Later, nonnatural amino acids as building blocks were also considered. With growing research in this area, cyclopeptides and related macrocycles developed into an important and structurally diverse receptor family. This review provides an overview of these developments, starting from the early years. The presented systems are classified according to characteristic structural elements present along the ring. Wherever possible, structural aspects are correlated with binding properties to illustrate how natural or nonnatural amino acids affect binding properties.

Thermodynamic-dominated stereoselective meshing of molecular nano-links based on fluorenes

The path-selectivity and stereoselectivity of gridization pathways into fluorene-based Drawing Hand Grids (DHGs-F) are precisely modulated through tuning acid conditions and side-chain effects. BF3•OEt2 supports the realization of the gridization path (rac-DHG1-F, yield: 82%, meso-DHG1-F, yield: 11%). On the contrary, CF3SO3H will lead to the enhancements in polymerization pathways (about 85% yield). When the side chain is a methoxy group, rac-DHG1-F and meso-DHG1-F will be obtained. However, when the side chain is a group without an oxygen atom, only rac-DHG1-F can be obtained (de = 100%). Moreover, through excitonic physical proper-ties, rac-DHGs-F exhibits a more π-electronic delocalization, potentially serving as the intriguing tactic strategy to modulate the optoelectronic properties.

Spontaneous macrocyclization through multiple dynamic cyclic aminal formation

The use of aminals in dynamic covalent chemistry is slightly underexplored, probably due to their inherent instability. Here we report the spontaneous [2+2] macrocyclization of tetrakis(aminals). Their unexpected stability and structural modularity, the dynamic nature of the connections and their water tolerance make them appealing systems for future applications as stimulus-responsive materials.

Chloride-Assisted Peptide Macrocyclization

The role of the Cl^- anion as a templating agent for the synthesis of cyclopeptides was assessed through the preparation of three new homocyclolysines and other six cyclic peptides by head-to-tail lactamization. Isolated yields of products obtained by chloride-templating approach were considerably higher than those gained by a cation-promoted procedure, whereby, in some cases, only the anion-assisted synthesis yielded the desired cyclopeptides.

Selective Carboxylate Recognition Using Urea-Functionalized Unclosed Cryptands: Mild Synthesis and Complexation Studies

Herein we present the synthesis and evaluation of anion-binding properties of 12 new receptors from the unclosed cryptand family. Their core is built on the stable 26-membered tetraamidic macrocyclic scaffold, whereas various alkyl and aryl urea substituents were introduced after a yield-limiting macrocyclization step (65–98%). The receptors strongly bind anions, in particular carboxylates, even in a highly competitive solvent mixture (DMSO-d₆ + H₂O 95:5 v/v).

Highly Selective Anion Template Effect in the Synthesis of Constrained Pseudopeptidic Macrocyclic Cyclophanes

Herein, we report the synthesis of a novel family of constrained pseudopeptidic macrocyclic compounds containing the hexahydropyrrolo[3,4-f]isoindolocyclophane scaffold and involving four coupled substitution reactions in the macrocyclization process. Although the increase in the number of steps involved in the macrocyclization could lead to a larger number of possible side products, the optimization of the methodology and the study of the driving forces have made it possible to obtain the desired macrocycles in excellent yields. A thorough computational study has been carried out to understand the macrocyclization process, and the results obtained nicely agree with experimental data. Moreover, the bromide anion had a clear catalytic template effect in the macrocyclization reaction, and surprisingly, the chloride anion had a negative template effect in opposition to the results obtained for analogous macrocycles. The parameters responsible for the specific kinetic template effect observed have been studied in detail.

An excellent colorimetric and “turn off” fluorescent probe for tetrahydrofuran based on a luminescent macrocyclic samarium(iii) complex

We designed and prepared a macrocyclic samarium(iii) complex which served as an excellent colorimetric and “turn-off” fluorescent probe for sensing tetrahydrofuran.

Supramolecularly assisted synthesis of chiral tripodal imidazolium compounds

Supramolecular interactions based on amide groups direct the preferential formation of tritopic instead of monotopic or ditopic imidazolium compounds.

Anion-coordination-directed self-assemblies

This review introduces the interplay of anion coordination and supramolecular self-assembly, presenting recent progress in anion-induced and anion-coordination-based self-assemblies.

Oligocarboxylates as useful templates in dynamic combinatorial chemistry

Dynamic combinatorial chemistry deals with systems (libraries) of multiple compounds formed by reversible reactions. Interactions of all library components with introduced template molecule are reflected in modification of library composition and are analysed simultaneously. In our studies we investigated a single-substrate dynamic combinatorial library of macrocycles, based on dipicolinic acid diamide, with disulphide bond exchange as the reversible reaction. The library components equipped with hydrogen bond donors interact with anionic guests – carboxylates which act as templates inducing amplification of selected library members. We proved that quantitative analysis of interactions with templates is possible, which led us to a novel method of analysis of association constants of static receptors introduced to the system. With a large set of carboxylates differing in number of anionic groups, size, shape, and flexibility of the linker, we proved that the library is very sensitive to structural parameters of the template. We also showed that with mediation of a photoswitchable azobenzene-based template it is possible to change the library composition by light stimulus. Similarly, with mediation of EDTA the library is sensitive to introduction of metal cations.

8-Propyldithieno[3,2-b:2',3'-e]pyridine-3,5-diamine (DITIPIRAM) Derivatives as Neutral Receptors Tailored for Binding of Carboxylates

The DITIPIRAM (8-propyldithieno[3,2-b:2',3'-e]pyridine-3,5-diamine)-based receptors 11 and 12 were readily synthesized, and their anion-binding properties were studied both in solution and in the solid-state. ¹H NMR titrations revealed that receptor 12 equipped with two phenyl-urea groups preferentially binds carboxylates, even in the highly competitive DMSO-d₆/CD₃OH solvent mixture. X-ray analysis showed that receptor 12 exhibited great complementarity for benzoate, which is cooperatively bound by the means of four highly directional hydrogen bonds from the two urea groups. Comparison with the most effective acyclic receptors based on a structurally related rigid carbazole platform demonstrates that the DITIPIRAM motif provides a better suited geometry in the binding pocket, and consequently stronger anion binding.

Cu2+ recognition by N,N'-benzylated bis(amino amides)

Two new C₂-symmetric N,N'-benzylated bis(amino amides) have been synthesised and their interaction with different transition metals studied using a variety of techniques including UV-Vis and CD spectroscopy or ESI-MS. The determination of the corresponding stability constants with Cu²⁺ has been possible, in H₂O/CH₃CN 7/3 v/v, for one of these ligands (4) using potentiometric titrations. The results obtained reveal that N-benzylation affords significant changes to their properties and is accompanied by an appreciable decrease in the corresponding complexation stability constants. However, this, along with the low kinetics associated to Ni²⁺, facilitates the recognition of Cu²⁺ by 4 that can be followed by the naked-eye up to the submillimolar range. Very interestingly, the chiral nature of this ligand provides an intense and well defined CD curve for the corresponding Cu²⁺ complex, very sensitive to the coordination geometry, facilitating the analysis of this interaction even at the μM range. The formation by both ligands (3 and 4) of square planar complexes with Cu²⁺ and Ni²⁺ displaying a 1 : 1 stoichiometry was confirmed by their X-ray crystal structures.

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).

Bisferrocenyl-functionalized pseudopeptides: access to separated ionic and electronic contributions for electrochemical anion sensing

Pseudopeptidic receptors containing ferrocene fragments have been prepared and their response to a series of anions was measured by a voltammetry of microparticles methodology.

A General Method for Synthesis of Unclosed Cryptands via H-Bond Templated Macrocyclization and Subsequent Mild Postfunctionalization

A practical four-step synthesis of a model 26-membered N-Boc-protected macrocycle, starting from commercially available and inexpensive materials, is reported. The crucial macrocyclization step does not require high-dilution conditions and is completed in a short time (8 h). The high yield of macrocyclization (61%) is achieved owing to templation by intramolecular H-bonds and a chloride anion, which both help to adopt a favorable folded conformation of the open-chain intermediate. Finally, mild, selective, and efficient incorporation of intraannular amide function leading to five diversely functionalized unclosed cryptands (UCs) is described.

Synthesis, characterization and crystal structures of mono and dinuclear macrocyclic cobalt(ii) complexes with a new tetraaza m-xylyl-based macrocyclic ligand

Synthesis, characterization, cyclic voltammetry, magnetic susceptibility and crystal structures of mono and dinuclear macrocyclic cobalt(ii) complexes have been investigated.

Introducing a static receptor to compete with a dynamic combinatorial library in template binding

Association constants can be obtained from HPLC analysis of a system comprising a dynamic combinatorial library and a static host.

Copper(ii) complexes of macrocyclic and open-chain pseudopeptidic ligands: synthesis, characterization and interaction with dicarboxylates

Cu(ii) complexes of pseudopeptides interact with very similar dicarboxylates of biological interest (malate and aspartate) affording strikingly different outcomes.

Anion recognition by cyclic peptides

Cyclic peptides provide excellent scaffolds for anion recognition and improved binding affinity and selectivity has been achieved through peptide backbone rigidification and the introduction of side chains bearing anion recognition groups.

"Choose-a-size" approach in dynamic combinatorial chemistry: a single substrate dynamic combinatorial library of oligomacrocycles that adapts to the size and shape of carboxylates

A neutral anion binding receptor based on dipicolinic acid diamide was equipped with thiol groups in the amidic side arms. After the thiol was oxidized to disulfide groups with I2, a mixture of cyclic oligomers (a library) was obtained. The distribution of macrocycles can be controlled kinetically during the oxidation process or thermodynamically at basic conditions via disulfide bond exchange. The library proved to be very sensitive to templation with various carboxylates in DMSO. The amplification pattern reflects the structural features of the anionic template and is sensitive to changes in the template's geometry. The application of carboxylates with multiple functional groups resulted in very strong amplification of the large penta- and hexameric macrocycles. The thermodynamic parameters of some templation effects were rationalized using a simple model and confirmed using competitive NMR titration.

Advances in anion supramolecular chemistry: from recognition to chemical applications

Since the start of this millennium, remarkable progress in the binding and sensing of anions has been taking place, driven in part by discoveries in the use of hydrogen bonding, as well as the previously under-exploited anion-π interactions and halogen bonding. However, anion supramolecular chemistry has developed substantially beyond anion recognition, and now encompasses a diverse range of disciplines. Dramatic advance has been made in the anion-templated synthesis of macrocycles and interlocked molecular architectures, while the study of transmembrane anion transporters has flourished from almost nothing into a rapidly maturing field of research. The supramolecular chemistry of anions has also found real practical use in a variety of applications such as catalysis, ion extraction, and the use of anions as stimuli for responsive chemical systems.

Bioinspired chemistry based on minimalistic pseudopeptides

For years researchers have tried to understand the molecular behavior of complex biomolecules through the development of small molecules that can partially mimic their function. Now researchers are implementing the reverse approach: using the structural and mechanistic knowledge obtained from those complex systems to design small molecules with defined properties and for specific applications. One successful strategy for constructing bioinspired, minimalistic molecules is to combine natural building blocks that provide functional elements with abiotic fragments that serve as structural scaffolds. Therefore pseudopeptidic compounds, most of them based on C2 symmetric structures, represent a unique opportunity to explore and evaluate this approach. Some of these molecules are as simple as two amino acids connected by a diamino spacer. The results in this Account show how bioinspired minimalistic pseudopeptides can form ordered structures, participate in the recognition and transcription of information events in molecular devices, and catalyze reactions. This strategy allows researchers to design and prepare a variety of open-chain and macrocyclic compounds leading to systems that can self-aggregate to form hierarchically ordered micro- and nanostructures. In addition, small changes in the molecule or external stimuli can regulate the self-aggregation pattern. In the same way, researchers can also tune the molecular movements of simple pseudopeptides through environmental factors, providing a means to control new molecular devices. In addition, some of the prepared model compounds have shown interesting properties in molecular recognition and even as sensors for several targets of interest. Finally we have observed remarkable catalytic activities from these types of molecules, although those results are still far from the efficiency shown by natural peptides. This family of pseudopeptidic compounds offers the opportunity for the more elaborate design of relatively simple abiotic but bioinspired systems that display specific properties. In addition, the results can provide additional information that will increase the molecular understanding of the basic principles that underlie the extraordinary behavior of natural systems.

Pseudopeptidic ligands: exploring the self-assembly of isophthaloylbisglycine (H2IBG) and divalent metal ions

We present a systematic study of the complexation of the new pseudopeptidic ligand isophthaloylbisglycine (H(2)IBG) with divalent metal ions of varying ionic radius. This work represents the initial employment of H(2)IBG in the coordination chemistry of alkaline earth, 3d transition, Zn(II) and Cd(II) metal elements. Infrared, NMR, thermal, magnetic, adsorption and theoretical studies of these compounds are also discussed.

Synthesis and anion recognition properties of shape-persistent binaphthyl-containing chiral macrocyclic amides

We report on the synthesis and characterization of novel shape-persistent, optically active arylamide macrocycles, which can be obtained using a one-pot methodology. Resolved, axially chiral binol scaffolds, which incorporate either methoxy or acetoxy functionalities in the 2,2' positions and carboxylic functionalities in the external 3,3' positions, were used as the source of chirality. Two of these binaphthyls are joined through amidation reactions using rigid diaryl amines of differing shapes, to give homochiral tetraamidic macrocycles. The recognition properties of these supramolecular receptors have been analyzed, and the results indicate a modulation of binding affinities towards dicarboxylate anions, with a drastic change of binding mode depending on the steric and electronic features of the functional groups in the 2,2' positions.

Kinetic analysis for macrocyclizations involving anionic template at the transition state

Several kinetic models for the macrocyclization of a C₂ pseudopeptide with a dihalide through a S_N2 reaction have been developed. These models not only focus on the kinetic analysis of the main macrocyclization reaction, but also consider the competitive oligomerization/polymerization processes yielding undesired oligomeric/polymeric byproducts. The effect of anions has also been included in the kinetic models, as they can act as catalytic templates in the transition state reducing and stabilizing the transition state. The corresponding differential equation systems for each kinetic model can be solved numerically. Through a comprehensive analysis of these results, it is possible to obtain a better understanding of the different parameters that are involved in the macrocyclization reaction mechanism and to develop strategies for the optimization of the desired processes.