Isosteric Substitutions of Urea to Thiourea and Selenourea in Aliphatic Oligourea Foldamers: Site‐Specific Perturbation of the Helix Geometry

Nearly isosteric oxo to thioxo substitution was employed to interrogate the structure of foldamers with a urea backbone and explore the relationship between helical folding and hydrogen‐bonding interactions. A series of oligomers with urea bonds substituted by thiourea bonds at discrete or all positions in the sequence have been prepared and their folding propensity was studied by using a combination of spectroscopic methods and X‐ray diffraction. The outcome of oxo to thioxo replacements on the helical folding was found to depend on whether central or terminal ureas were modified. The canonical helix geometry was not affected upon insertion of thioureas close to the negative end of the helix dipole, whereas thioureas close to the positive pole were found to increase the terminal flexibility and cause helix fraying. Perturbation was amplified when a selenourea was incorporated instead, leading to a structure that is only partly folded.     

Increasing the Size of an Aromatic Helical Foldamer Cavity by Strand Intercalation

The postsynthetic modulation of capsules based on helical aromatic oligoamide foldamers would be a powerful approach for controlling their receptor properties without altering the initial monomer sequences. With the goal of developing a method to increase the size of a cavity within a helix, a single‐helical foldamer capsule was synthesized with a wide‐diameter central segment that was designed to intercalate with a second shorter helical strand. Despite the formation of stable double‐helical homodimers (K_dim>10⁷ M ^?1) by the shorter strand, when it was mixed with the single‐helical capsule sequence, a cross‐hybridized double helix was formed with K_a>10⁵ M ^?1. This strategy makes it possible to direct the formation of double‐helical heterodimers. On the basis of solution‐ and solid‐state structural data, this intercalation resulted in an increase in the central‐cavity size to give a new interior volume of approximately 150 ų.     

Helical Folding Competing with Unfolded Aggregation in Phenylene Ethynylene Foldamers

The folding and aggregation behavior of a pair of oligo(phenylene ethynylene) (OPE) foldamers are investigated by means of UV/Vis absorption and circular dichroism spectroscopy. With identical OPE backbones, two foldamers, 1 with alkyl side groups and 2 with triethylene glycol side chains, manifest similar helical conformations in solutions in n‐hexane and methanol, respectively. However, disparate and competing folding and aggregation processes are observed in alternative solvents. In cyclohexane, oligomer 1 initially adopts the helical conformation, but the self‐aggregation of unfolded chains, as a minor component, gradually drives the folding–unfolding transition eventually to the unfolded aggregate state completely. In contrast, in aqueous solution (CH₃OH/H₂O) both folded and unfolded oligomer 2 appear to undergo self‐association; aggregates of the folded chains are thermodynamically more stable. In solutions with a high H₂O content, self‐aggregation among unfolded oligomers is kinetically favored; these oligomers very slowly transform into aggregates of helical structures with greater thermodynamic stability. The folded–unfolded conformational switch thus takes place with the free (nonaggregated) molecules, and the very slow folding transition is due to the low concentration of molecularly dispersed oligomers.     

De Novo Left‐Handed Synthetic Peptidomimetic Foldamers

The development of peptidomimetic helical foldamers with a wide repertoire of functions is of significant interest. Herein, we report the X‐ray crystal structures of a series of homogeneous l ‐sulfono‐γ‐AA foldamers and elucidate their folding conformation at the atomic level. Single‐crystal X‐ray crystallography revealed that this class of oligomers fold into unprecedented dragon‐boat‐shaped and unexpected left‐handed helices, which are stabilized by the 14‐hydrogen‐bonding pattern present in all sequences. These l ‐sulfono‐γ‐AApeptides have a helical pitch of 5.1 Å and exactly four side chains per turn, and the side chains lie perfectly on top of each other along the helical axis. 2D NMR spectroscopy, computational simulations, and CD studies support the folding conformation in solution. Our results provide a structural basis at the atomic level for the design of novel biomimetics with a precise arrangement of functional groups in three dimensions.     

Folding and Anion‐Binding Properties of Fluorescent Oligoindole Foldamers

A series of oligoindole foldamers 1 a – d that are highly fluorescent were prepared by using a biindole derivative as the repeating unit, and their folding and anion‐binding properties were revealed by ¹H NMR and fluorescence spectroscopy. The oligoindoles exist in an extended conformation, but adopt a compact helical structure in the presence of an anion. The anion is entrapped inside the tubular cavity of the helical strand, comprising four aryl units per turn, by multiple hydrogen bonds with the indole NHs. These structural features were confirmed by ¹H NMR and fluorescence spectroscopy. When folded by anion binding, 1 b – d show characteristic downfield shifts of the NH signals and upfield shifts of the aromatic CH signals by Δδ=0.1–1.0 ppm. The average chemical shift for all the aromatic signals of 1 a – d is more upfield shifted as the chain lengthens, as anticipated from the degree of overlapped aromatic surfaces in the helical strand. Moreover, 1 a – d are strongly fluorescent in the absence of an anion. Upon binding an anion such as a chloride, the shorter oligoindoles 1 a and b lead to negligible change in the emission spectra, whereas the longer ones 1 c and d result in dramatic changes, that is, large hypochromic and bathochromic shifts (Δλ=65 and 70 nm) of the emission band, confirming the helical folding. The association constants (K_a) between oligoindoles and tetrabutylammonium chloride strongly depend on the chain length; <1 M ^?1 for 1 a , 630 M ^?1 for 1 b , 1.1×10⁵ M ^?1 for 1 c , and 2.9×10⁵ M ^?1 for 1 d in 20 % (v/v) MeOH/CH₂Cl₂ at 24±1 °C. In addition, the association constants of 1 c and 1 d with other anions such as fluoride, bromide, iodide, azide, cyanide, acetate, and nitrate are determined to be in the order of 10³–10⁶ M ^?1 under the same conditions.     

Helical Folding of Conjugated Oligo(phenyleneethynylene): Chain‐Length Dependence,Solvent Effects,and Intermolecular Assembly

As a representative folding system that features a conjugated backbone, a series of monodispersed (o‐phenyleneethynylene)‐alt‐(p‐phenyleneethynylene) (PE) oligomers of varied chain length and different side chains were studied. Molecules with the same backbone but different side‐chain structures were shown to exhibit similar helical conformations in respectively suitable solvents. Specifically, oligomers with dodecyloxy side chains folded into the helical structure in apolar aliphatic solvents, whereas an analogous oligomer with tri(ethylene glycol) (Tg) side chains adopted the same conformation in polar solvents. The fact that the oligomers with the same backbone manifested a similar folded conformation independent of side chains and the nature of the solvent confirmed the concept that the driving force for folding was the intramolecular aromatic stacking and solvophobic interactions. Although all were capable of inducing folding, different solvents were shown to bestow slightly varied folding stability. The chain‐length dependence study revealed a nonlinear correlation between the folding stability with backbone chain length. A critical size of approximately 10 PE units was identified for the system, beyond which folding occurred. This observation corroborated the helical nature of the folded structure. Remarkably, based on the absorption and emission spectra, the effective conjugation length of the system extended more effectively under the folded state than under random conformations. Moreover, as evidenced by the optical spectra and dynamic light‐scattering studies, intermolecular association took place among the helical oligomers with Tg side chains in aqueous solution. The demonstrated ability of such a conjugated foldamer in self‐assembling into hierarchical supramolecular structures promises application potential for the system.     

Selective Encapsulation of Disaccharide Xylobiose by an Aromatic Foldamer Helical Capsule

Xylobiose sequestration in a helical aromatic oligoamide capsule was evidenced by circular dichroism, NMR spectroscopy, and crystallography. The preparation of the 5 kDa oligoamide sequence was made possible by the transient use of acid‐labile dimethoxybenzyl tertiary amide substituents that disrupt helical folding and prevent double helix formation. Binding of other disaccharides was not detected. Crystallographic data revealed a complex composed of a d ‐xylobiose α anomer and two water molecules accommodated in the right‐handed helix. The disaccharide was found to adopt an unusual all‐axial compact conformation. A dense network of 18 hydrogen bonds forms between the guest, the cavity wall, and the two water molecules.     

α‐Peptide–Oligourea Chimeras: Stabilization of Short α‐Helices by Non‐Peptide Helical Foldamers

Short α‐peptides with less than 10 residues generally display a low propensity to nucleate stable helical conformations. While various strategies to stabilize peptide helices have been previously reported, the ability of non‐peptide helical foldamers to stabilize α‐helices when fused to short α‐peptide segments has not been investigated. Towards this end, structural investigations into a series of chimeric oligomers obtained by joining aliphatic oligoureas to the C‐ or N‐termini of α‐peptides are described. All chimeras were found to be fully helical, with as few as 2 (or 3) urea units sufficient to propagate an α‐helical conformation in the fused peptide segment. The remarkable compatibility of α‐peptides with oligoureas described here, along with the simplicity of the approach, highlights the potential of interfacing natural and non‐peptide backbones as a means to further control the behavior of α‐peptides.     

Allosteric Recognition of Homomeric and Heteromeric Pairs of Monosaccharides by a Foldamer Capsule

The recognition of either homomeric or heteromeric pairs of pentoses in an aromatic oligoamide double helical foldamer capsule was evidenced by circular dichroism (CD), NMR spectroscopy, and X‐ray crystallography. The cavity of the host was predicted to be large enough to accommodate simultaneously two xylose molecules and to form a 1:2 complex (one container, two saccharides). Solution and solid‐state data revealed the selective recognition of the α‐⁴C₁‐d ‐xylopyranose tautomer, which is bound at two identical sites in the foldamer cavity. A step further was achieved by sequestering a heteromeric pair of pentoses, that is, one molecule of α‐⁴C₁‐d ‐xylopyranose and one molecule of β‐¹C₄‐d ‐arabinopyranose despite the symmetrical nature of the host and despite the similarity of the guests. Subtle induced‐fit and allosteric effects are responsible for the outstanding selectivities observed.     

Mixed Oligoureas Based on Constrained Bicyclic and Acyclic β‐Amino Acids Derivatives: On the Significance of the Subunit Configuration for Folding

The combination of a non‐functionalized constrained bicyclo[2.2.2]octane motif along with urea linkages allowed the formation of a highly rigid 2.5_12/14 helical system both in solution and the solid state. In this work, we aimed at developing stable and functionalized systems as promising materials for biological applications in investigating the impact of this constrained motif and its configuration on homo and heterochiral mixed‐oligourea helix formation. Di‐, tetra‐, hexa‐, and octa‐oligoureas alternating the highly constrained bicyclic motif of (R) or (S) configuration with acyclic (S)‐β³‐amino acid derivatives were constructed. Circular dichroism (CD), NMR experiments, and the X‐ray crystal structure of the octamer unequivocally proved that the alternating heterochiral R/S sequences form a stable left‐handed 2.5‐helix in contrast to the mixed (S/S)‐oligoureas, which did not adopt any defined secondary structure. We observed that the (?)‐synclinal conformation around the C_α? C_β bond of the acyclic residues, although sterically less favorable than the (+)‐synclinal conformation, was imposed by the (R)‐bicyclic amino carbamoyl (BAC) residue. This highlighted the strong ability of the BAC residue to drive helical folding in heterochiral compounds. The role of the stereochemistry of the BAC unit was assessed and a model was proposed to explain the misfolding of the S/S sequences.