Design and Synthesis of Foldamers Based on an Anthracene Diels-Alder Adduct

Trends in the Diels-Alder reaction in polymer chemistry

The Diels-Alder (DA) reaction is regarded as quite a useful strategy in organic and macromolecular syntheses. The reversibility of this reaction and the advent of self-repair technology, as well as other applications in controlled macromolecular architectures and crosslinking, have strongly boosted the research activity, which is still attracting a huge interest in both academic and industrial research. The DA reaction is a simple and scalable toolbox. Though it is well-established that furan/maleimide is the most studied diene/dienophile couple, this perspective article reports strategies using other reversible systems with deeper features on other types of diene/dienophile pairs being either petro-sourced (cyclopentadiene, anthracene) or bio-sourced (muconic and sorbic acids, myrcene and farnesene derivatives, eugenol, cardanol). This review is composed of four sections. The first one briefly recalls the background on the DA reactions involving cyclodimerizations, dienes, and dienophiles, parameters affecting the reaction, while the second part deals with the furan/maleimide reaction. The third one deals with petro-sourced and bio-sourced (or products becoming bio-sourced) reactants involved in DA reactions are also listed and discussed. Finally, the authors' opinion is given on the potential future of the crosslinking-decrosslinking reaction, especially regarding the process (e.g., key temperatures of decrosslinking) or possibly monocomponents. It presents both fundamental and applied research on the DA reaction and its applications.

Local versus Global Control of Helical Folding in β-Peptide Segments Using Hydrazino Turns

Rational control of the self-organization of β-peptides sequences to adopt regular secondary structures is an important challenge in peptidomimetic foldamer science. By replacing the N- and C-terminal residues of homooligomers of trans-2-aminocyclobutanecarboxylic acid (tACBC)_n with N-aminoazetidine-2-carboxylic acid, an 8-helical topology is shown to dominate for sequences up to n = 7. This constitutes an atomic-level tool to override locally the preferred global 12-helix secondary structure of the corresponding tACBC homooligomers of the same length.

Exploration of Diverse Reactive Diad Geometries for Bifunctional Catalysis via Foldamer Backbone Variation

What is the best spatial arrangement of a pair of reactive groups for bifunctional catalysis of a chemical transformation? The conformational versatility of proteins allows reactive group geometry to be explored and optimized via evolutionary selection, but it has been difficult for chemists to identify synthetic scaffolds that allow broad comparative evaluation among alternative reactive group geometries. Here we show that a family of helices, adopted predictably by oligomers composed partially or exclusively of β-amino acid residues, enables us to explore a range of orientations for a pair of pyrrolidine units that must work in tandem to catalyze a crossed aldol reaction. Thus, the crossed aldol reaction serves as an assay of reactive diad efficacy. We have chosen a test reaction free of stereochemical complexity in order to streamline our study of reactivity. The best geometry enhances the initial rate of product formation by two orders of magnitude. Our findings raise the possibility that rudimentary catalysts involving an isolated secondary structure might have facilitated the development of prebiotic reaction networks.

Understanding the conformational analysis of gababutin based hybrid peptides

A new class of gababutin-based tetrapeptide shows a C₁₂/C₁₀ hydrogen-bonded hybrid turn.

Crystallographic characterization of 12-helical secondary structure in β-peptides containing side chain groups

Helices are the most extensively studied secondary structures formed by β-peptide foldamers. Among the five known β-peptide helices, the 12-helix is particularly interesting because the internal hydrogen bond orientation and macrodipole are analogous to those of α-peptide helices (α-helix and 3(10)-helix). The β-peptide 12-helix is defined by i, i+3 C═O···H-N backbone hydrogen bonds and promoted by β-residues with a five-membered ring constraint. The 12-helical scaffold has been used to generate β-peptides with specific biological functions, for which diverse side chains must be properly placed along the backbone and, upon folding, properly arranged in space. Only two crystal structures of 12-helical β-peptides have previously been reported, both for homooligomers of trans-2-aminocyclopentanecarboxylic acid (ACPC). Here we report five additional crystal structures of 12-helical β-peptides, all containing residues that bear side chains. Four of the crystallized β-peptides include trans-4,4-dimethyl-2-aminocyclopentanecarboxylic acid (dm-ACPC) residues, and the fifth contains a β(3)-hPhe residue. These five β-peptides adopt fully folded 12-helical conformations in the solid state. The new crystal structures, along with previously reported data, allow a detailed characterization of the 12-helical conformation; average backbone torsion angles of β-residues and helical parameters are derived. These structural parameters are found to be similar to those for i, i+3 C═O···H-N hydrogen-bonded helices formed by other peptide backbones generated from α- and/or β-amino acids. The similarity between the conformational behavior of dm-ACPC and ACPC is consistent with previous NMR-based conclusions that 4,4-disubstituted ACPC derivatives are compatible with 12-helical folding. In addition, our data show how a β(3)-residue is accommodated in the 12-helix, thus enhancing understanding of the diverse conformational behavior of this flexible class of β-amino acids.

Prevalence of eight-membered hydrogen-bonded rings in some bis(cyclobutane) beta-dipeptides including residues with trans stereochemistry

Three new bis(cyclobutane) beta-dipeptides have been synthesized from appropriate derivatives of cis- and trans-2-aminocyclobutane-1-carboxylic acid, respectively. The predominance of eight-membered hydrogen-bonded rings has been manifested for (trans,trans)- and (trans,cis)-beta-dipeptides while the formation of six-membered rings is preferred for the (cis,trans)- beta-dipeptide similarly to the previously described (cis,cis)-diastereomer.

Sculpting the beta-peptide foldamer H12 helix via a designed side-chain shape

The long-range side-chain repulsion between the (1R,2R,3R,5R)-2-amino-6,6-dimethyl-bicyclo[3.1.1]-heptane-3-carboxylic acid (trans-ABHC) residues stabilize the H12 helix in beta-peptide oligomers.

Synthesis of crescent aromatic oligoamides

[structures: see text] This article describes the synthetic procedures for the preparation of crescent (and helical) aromatic oligoamides developed in recent years in our laboratory. The large-scale preparation of a variety of monomers derived from various tetrasubstituted benzenes is presented. Three different strategies for constructing various oligomers consisting of meta- and meta/para-linked benzene residues are discussed. Factors affecting coupling efficiency and yields are analyzed. The developed synthetic methods have provided the basis for the preparation of longer oligomers and for the development of solid-phase synthesis.

Helical aromatic oligoamides: reliable, readily predictable folding from the combination of rigidified structural motifs

Factors responsible for the folding of aromatic oligoamides with backbones rigidified by local three-center H-bonds were investigated. The stability of the three-center H-bonds was quantified by the half-lives of amide proton-deuterium exchange reactions, which show that the three-center H-bonds were largely intact at room temperature in the oligomer examined. This result is consistent with our current and previous 2D NMR studies. The overall helical conformation of nonamer 1 was found by variable-temperature NOESY studies to be dynamic. As temperature rose, the end-to-end NOEs rapidly disappeared, while the amide side chain NOEs were still readily detectable, corresponding to the "breath" and stretching of the helix by slightly twisting the local H-bonded rings. Based on the simple repetition of the same structural motif and local conformational preference, undecamer 2 was found to fold into well-defined helical conformation. The predictability of the folding of these backbone-rigidified aromatic oligoamides was demonstrated by a simple modeling method using structural parameters from oligomers with known crystal structures. The reliability and generality of the modeling methods were shown by the excellent agreement between the modeled structures corresponding to 1 and 2 and data from NOESY studies.

Aromatic Foldamers with Iminodicarbonyl Linkers: Their Structures and Optical Properties

[structure: see text] Carboxamides possessing naphthalene rings connected by multiple iminodicarbonyl linkers were synthesized. These molecules forced the naphthalene rings to be placed in the positions facing each other, and they form helical foldamers both in solution and in the crystalline state. Their folding structures were investigated by single-crystal X-ray analysis and (1)H NMR spectroscopy. Their absorption and fluorescence spectra showed a red shift as the number of naphthalene moieties increased. This remarkable change is based on the intramolecular interaction between naphthalene moieties. Helicity of the foldamer can be controlled by the introduction of chiral auxiliaries at imide nitrogen atoms, which results in an observation of induced circular dichroism.

Hydrogen Bonded Oligohydrazide Foldamers and Their Recognition for Saccharides

This paper describes the synthesis and characterization of the first series of hydrogen bonding-driven hydrazide foldamers and their recognition for alkyl saccharides in chloroform. Oligomers 1, 2-4, 5, 6, and 7, which contain one, two, four, six, or twelve repeated dibenzoyl hydrazide residues, respectively, have been prepared. The rigid and planar conformations of 1 and 2 or 4 have been established with X-ray analysis and (1)H NMR spectroscopy, whereas the folding and helical conformations of 5-7 have been evidenced by the 1D and 2D (1)H NMR and IR spectroscopy and molecular mechanics calculations. Molecular mechanics calculations also revealed that 5, 6, and 7 possess a rigid cavity with size of ca. 10.6 to 11.1 A, and half of the carbonyl groups in the folding conformations are orientated inwardly inside the cavity. (1)H NMR and CD experiments revealed that 5-7 efficiently complex alkylated mono- and disaccharides 32-35 in chloroform. The association constants (K(assoc)) of the complexes have been determined with the (1)H NMR and fluorescent titration methods. The energy-minimized conformation of 6.34 has been obtained with molecular mechanics calculation. The hydrazide-based folding structures described here represent novel examples of hydrogen bonding-driven foldamers that act as artificial receptors for selective molecular recognition.

Backbone-rigidified oligo(m-phenylene ethynylenes)

Oligo(m-phenylene ethynylenes) (oligo(m-PE)) with backbones rigidified by intramolecular hydrogen bonds were found to fold into well-defined conformations. The localized intramolecular hydrogen bond involves a donor and an acceptor from two adjacent benzene rings, respectively, which enforces globally folded conformations on these oligomers. Oligomers with two to seven residues have been synthesized and characterized. The persistence of the intramolecular hydrogen bonds and the corresponding curved conformations were established by ab initio and molecular mechanics calculations, 1D and 2D (1)H NMR spectroscopy, and UV spectroscopy. Pentamer 5, hexamer 6, and heptamer 7 adopt well-defined helical conformations. Such a backbone-based conformational programming should lead to molecules whose conformations are resilient toward structural variation of the side groups. These m-PE oligomers have provided a new approach for achieving folded unnatural oligomers under conditions that are otherwise unfavorable for previously described, solvent-driven folding of m-PE foldamers. Stably folded structures based on the design principle described here can be developed and may find important applications.

Evaluation of two pairs of chiral stationary phases: Effects from the length of the achiral spacers

Two pairs of chiral stationary phases (CSPs) with different C(2)-symmetric central parts were prepared and evaluated by chromatography of a series of structurally different racemates. Within each pair, the selectors on which the CSPs are based had different lengths of their achiral spacers. The CSPs based on selectors with short spacers showed higher enantioselectivity than the phases incorporating long spacers. On one pair of the phases, a study of the influence from different retention modifiers was performed for a series of benzodiazepinones. This demonstrated the importance of the polymer structure formed from the selectors with different spacer lengths for the enantiodiscriminating ability of the CSPs.

Accommodation of alpha-substituted residues in the beta-peptide 12-helix: expanding the range of substitution patterns available to a foldamer scaffold

Beta-amino acid oligomers composed exclusively of homochiral trans-2-aminocyclopentanecarboxylic acid (ACPC) residues and/or related pyrrolidine-based residues are known to favor a specific helical secondary structure that is defined by 12-membered ring C=O(i)- -H-N(i+3) hydrogen bonds ("12-helix"). The 12-helix is structurally similar to the familiar alpha-helix and therefore represents a source of potential alpha-helix-mimics. The 12-helix will be most useful in this regard if this conformational scaffold can be employed to arrange specific sets of protein-like side chains in space. Here we examine whether the 12-helix tolerates insertion of acyclic beta-amino acid residues bearing a substituent in the alpha-position ("beta(2)-residues"). Seventeen homologous beta-peptide heptamers have been prepared in which one to four beta(2)-residues reside among ACPC and/or pyrrolidine residues. Circular dichroism comparisons suggest that beta(2)-residues have a lower 12-helical propensity than do residues preorganized by a five-membered ring, as expected, but that beta-peptides containing beta(2)-residues at one or two of the seven positions retain a significant preference for 12-helix formation. These results indicate that a limited number of beta(2)-residues can be used to introduce side chains at specific positions along the surface of a 12-helix.

Novel conformationally-constrained β-peptides characterized by1H NMR chemical shifts

For a novel family of oxanorbornene beta-peptides, density functional theory computations of the three-dimensional structure and 1H NMR chemical shifts predict that the dimer and trimer form consecutive 8-membered hydrogen-bonded ring helices, which is supported by excellent agreement with experimental solution NMR data.

Peptide tic-tac-toe: heterotrimeric coiled-coil specificity from steric matching of multiple hydrophobic side chains

Specific coiled-coil heterotrimers result from steric matching of hydrophobic core side chains. A 2:1 heterotrimer is formed by peptides containing alanine or cyclohexylalanine, respectively, at a central core residue. Detailed thermodynamic analysis reveals that the designed complex is considerably more stable than the corresponding alanine homotrimer (deltaT(m) = 25 degrees C, deltadeltaG(unf) = 4.5 kcal/mol), while control complexes with naphthylalanine or cyclopropylalanine peptides are much less stable. However, the cyclohexylalanine homotrimer is of comparable stability to the 2:1 complex, prompting an investigation of multiply substituted peptides. A specific 1:1:1 heterotrimer is formed from three independent peptide strands, each bearing one large (cyclohexylalanine) and two small (alanine) side chains at the same three core positions but in different order. The combined impact of three substitutions improves specificity to the point where each pure peptide and all pairwise equimolar mixtures form significantly less stable complexes (deltaTm = 22-24 degrees C). The capacity for specific complex formation governed by multiple unnatural core side chains should facilitate design of numerous new peptide assemblies.

Tolerance of acyclic residues in the beta-peptide 12-helix: access to diverse side-chain arrays for biological applications

Oligomeric backbones with well-defined conformational propensities can serve as scaffolds for displaying sets of functional groups in specific three-dimensional arrangements. beta-Peptides are particularly interesting in this regard because several distinct secondary structures can be induced by appropriate choice of beta-amino acid substitution pattern.3 The beta-peptide 12-helix (defined by 12-membered ring C=O(i)- -H-N(i + 3) hydrogen bonds) is of particular interest because this helix resembles the alpha-helix. To date 12-helices have been observed in beta-peptides comprised exclusively of residues containing a five-membered ring constraint. Here we show that 12-helical propensity is maintained when some cyclic beta-amino acid residues are replaced with more flexible acyclic residues. This result is important because use of acyclic residues greatly facilitates introduction of diverse side chains at specific sites along the 12-helix. We demonstrate the utility of this advance in the context of antibiotic design.

Models of higher-order structure: foldamers and beyond

Folding, an attribute common to biological macromolecules such as proteins and nucleic acids, enables the formation of complex three-dimensional structure and thus enables the function of these exquisite molecular machines. Chemists are exploring the folding of natural and artificial systems with increasing enthusiasm and boldness of molecular design. The most recent achievements in the area of artificial folding molecules are described in this review.