Oligoamide Foldamers Research Articles

Controlling Helix Sense at N- and C-Termini in Quinoline Oligoamide Foldamers by β-Pinene-Derived Pyridyl Moieties.

A series of quinoline oligoamide foldamers bearing a β-pinene-derived pyridyl group at the N-terminus or the C-terminus were synthesized, and the efficiencies of chiral inductions have been evaluated by 1H NMR and CD spectra. The chiral inductions were quantitative when chiral pyridyl acid was appended at the N-terminus, but were inferior when chiral pyridyl amine was appended at the C-terminus. Unexpectedly, N-oxidation on the pyridine ring at the C-terminus does not notably enhance the chiral induction efficiency in spite of the presence of three-center hydrogen bonds.

Computational Prediction and Rationalization, and Experimental Validation of Handedness Induction in Helical Aromatic Oligoamide Foldamers.

Metadynamics simulations were used to describe the conformational energy landscapes of several helically folded aromatic quinoline carboxamide oligomers bearing a single chiral group at either the C or N terminus. The calculations allowed the prediction of whether a helix handedness bias occurs under the influence of the chiral group and gave insight into the interactions (sterics, electrostatics, hydrogen bonds) responsible for a particular helix sense preference. In the case of camphanyl-based and morpholine-based chiral groups, experimental data confirming the validity of the calculations were already available. New chiral groups with a proline residue were also investigated and were predicted to induce handedness. This prediction was verified experimentally through the synthesis of proline-containing monomers, their incorporation into an oligoamide sequence by solid phase synthesis and the investigation of handedness induction by NMR spectroscopy and circular dichroism.

Inside Cover: Computational Prediction and Rationalization, and Experimental Validation of Handedness Induction in Helical Aromatic Oligoamide Foldamers (Chem. Eur. J. 15/2017)

Inside Cover: Computational Prediction and Rationalization, and Experimental Validation of Handedness Induction in Helical Aromatic Oligoamide Foldamers (Chem. Eur. J. 15/2017)

Signal transduction in oligoamide foldamers by selective non-covalent binding of chiral phosphates at a urea binding site

The transduction of biological signals depends on the spatial communication of conformational change. We report a synthetic mimic of this signal transduction process in which non-covalent binding induces a change in the position of equilibrium between two rapidly interconverting screw-sense conformers of a synthetic helical polyamide. Selectivity was achieved by incorporating at the N-terminus of the polyamide a urea-based anion recognition site capable of binding chiral phosphate anions. As a result of solvent-dependent binding, an induced conformational change propagates from the binding site through the amide chain, leading to a screw-sense preference detectable in the form of a chemical shift separation between two NMR active 13C labels. The remote induction of screw sense preference indicates successful communication of a signal originating solely from non-covalent binding.

Supramolecular chirality and symmetry breaking of fluoride complexes of achiral foldamers

Fluoride binding of achiral oligoamide foldamers produces polar and chiral crystal structures and induces exceptional symmetry breaking of the bulk sample.

Photoinduced Electron Transfer and Hole Migration in Nanosized Helical Aromatic Oligoamide Foldamers.

A series of photoactive triads have been synthesized and investigated in order to elucidate photoinduced electron transfer and hole migration mechanism across nanosized, rigid helical foldamers. The triads are comprised of a central helical oligoamide foldamer bridge with 9, 14, 18, 19, or 34 8-amino-2-quinolinecarboxylic acid repeat units, and of two chromophores, an N-terminal oligo(para-phenylenevinylene) electron donor and a C-terminal perylene bis-imide electron acceptor. Time-resolved fluorescence and transient absorption spectroscopic studies showed that, following photoexcitation of the electron acceptor, fast electron transfer occurs initially from the oligoquinoline bridge to the acceptor chromophore on the picosecond time scale. The oligo(para-phenylenevinylene) electron donor is oxidized after a time delay during which the hole migrates across the foldamer from the acceptor to the donor. The charge separated state that is finally generated was found to be remarkably long-lived (>80 μs). While the initial charge injection rate is largely invariant for all foldamer lengths (ca. 60 ps), the subsequent hole transfer to the donor varies from 1 × 109 s-1 for the longest sequence to 17 × 109 s-1 for the shortest. In all cases, charge transfer is very fast considering the foldamer length. Detailed analysis of the process in different media and at varying temperatures is consistent with a hopping mechanism of hole transport through the foldamer helix, with individual hops occurring on the subpicosecond time scale (kET = 2.5 × 1012 s-1 in CH2Cl2). This work demonstrates the possibility of fast long-range hole transfer over 300 Å (through bonds) across a synthetic modular bridge, an achievement that had been previously observed principally with DNA structures.

Multivalent Interactions between an Aromatic Helical Foldamer and a DNA G-Quadruplex in the Solid State.

Quinoline-based oligoamide foldamers have been identified as a potent class of ligands for G-quadruplex DNA. Their helical structure is thought to target G-quadruplex loops or grooves and not G-tetrads. We report a co-crystal structure of the antiparallel hairpin dimeric DNA G-quadruplex (G4 T4 G4 )2 with tetramer 1-a helically folded oligo-quinolinecarboxamide bearing cationic side chains-that is consistent with this hypothesis. Multivalent foldamer-DNA interactions that modify the packing of (G4 T4 G4 )2 in the solid state are observed.

Iterative Evolution of an Abiotic Foldamer Sequence for the Recognition of Guest Molecules with Atomic Precision

A synthetic helical aromatic oligoamide foldamer receptor with high affinity and selectivity for tartaric acid was subjected to a structure-based evolution of its sequence via mutations, additions, and deletions of monomers to produce a new receptor having high affinity and selectivity for malic acid, a guest that differs from tartaric acid by a single oxygen atom. Seven iteratively modified sequences were synthesized. Detailed structural investigations of host-guest complexes were carried out systematically to guide the design of the next generation. A first outcome was a reversal of selectivity of the receptors, with a starting preference for tartaric acid over malic acid of over 10(2) and an ending sequence showing a preference for malic acid over tartaric acid of over 10(2). Another outcome was a very strong enhancement of the affinity for malic acid, despite the fact that it has fewer recognition features for binding through polar interactions such as hydrogen bonds. Such a level of discrimination between resembling guests exemplifies the amenability of foldamers to outstanding achievements in molecular recognition. Altogether, our results demonstrate the viability of a rational receptor design approach that exploits the modularity of foldamer sequences and, in the case of aromatic amide foldamers, their amenability to structural elucidation, their relative ease of synthesis, and the predictability of their structure.

Selective Dynamic Assembly of Disulfide Macrocyclic Helical Foldamers with Remote Communication of Handedness

AbstractDisulfide bridge formation was investigated in helical aromatic oligoamide foldamers. Depending on the position of thiol‐bearing side chains, exclusive intramolecular or intermolecular disulfide bridging may occur. The two processes are capable of self‐sorting, presumably by dynamic exchange. Quantitative assessment of helix handedness inversion rates showed that bridging stabilizes the folded structures. Intermolecular disulfide bridging serendipitously yielded a well‐defined, C2‐symmetrical, two‐helix bundle‐like macrocyclic structure in which complete control over relative handedness, that is, helix–helix handedness communication, is mediated remotely by the disulfide bridged side chains in the absence of contacts between helices. MM calculations suggest that this phenomenon is specific to a given side chain length and requires disulfide functions

Selective Dynamic Assembly of Disulfide Macrocyclic Helical Foldamers with Remote Communication of Handedness.

Disulfide bridge formation was investigated in helical aromatic oligoamide foldamers. Depending on the position of thiol-bearing side chains, exclusive intramolecular or intermolecular disulfide bridging may occur. The two processes are capable of self-sorting, presumably by dynamic exchange. Quantitative assessment of helix handedness inversion rates showed that bridging stabilizes the folded structures. Intermolecular disulfide bridging serendipitously yielded a well-defined, C2 -symmetrical, two-helix bundle-like macrocyclic structure in which complete control over relative handedness, that is, helix-helix handedness communication, is mediated remotely by the disulfide bridged side chains in the absence of contacts between helices. MM calculations suggest that this phenomenon is specific to a given side chain length and requires disulfide functions.

Chiral separation by a terminal chirality triggered P-helical quinoline oligoamide foldamer

A P-helical quinoline oligoamide foldamer was grafted on silica and applied as an HPLC stationary phase for chiral separation. The P-handedness of the quinoline oligoamide foldamer was induced by a (1S)-camphanyl group, which was introduced at the N-terminus of a tetrameric quinoline oligoamide foldamer (Cmp-Q4). To immobilize the foldamer on porous silica particles, a trimethoxysilyl group was introduced at the opposing end of the foldamer. Elemental analysis indicated that the amount of foldamer on the silica surface was 0.57μmol/m2. Circular dichroism and vibrational CD spectra of Cmp-Q4 and Cmp-Q4-immobilized silica (Sil-Q4-Cmp) suggested that the helical structure of Cmp-Q4 was altered on the silica surface whilst retaining a chiral structure. The chiral recognition ability of Sil-Q4-Cmp was evaluated with various aromatic enantiomers. Sil-Q4-Cmp showed enantio-selectivity for axially chiral molecules (e.g., αTrigger’s base=1.26 and αBinaphthol=1.07). Sil-Q4-Cmp showed remarkable recognition of helical octameric quinoline oligoamides with isobutoxy and triethylene glycol side chains (α=10.35 and 14.98, respectively). In contrast, an (1S)-camphanyl group-immobilized porous silica showed no chiral recognition for any enantiomers tested in this study. To elucidate the chiral separation mechanism of Sil-Q4-Cmp, thermodynamic parameters were calculated using van’t Hoff plots. HPLC results and thermodynamic parameters suggested that the chiral recognition of Sil-Q4-Cmp is based on the helical structure of Cmp-Q4 and other thermally dependent interactions such as hydrophobic effects associated with aromatic stacking. This work represents the first known application of aromatic foldamers in chiral separation.

Solid-Phase Synthesis of Water-Soluble Helically Folded Hybrid α-Amino Acid/Quinoline Oligoamides

We report here a solid phase synthesis methodology that allows the incorporation of α-amino acids (X) into quinoline (Q) oligoamide foldamer sequences. Water-soluble hybrid oligoamides based on the XQ2 trimer repeat motif were shown to adopt helical conformations presenting α-amino acid side chains in a predictable linear array on one face of the helix. In contrast, sequences based on the XQ dimer motif expressed less well-defined behavior, most likely due to local conformational variability precluding long-range order. Also presented is a full structural investigation by NMR of a dodecameric XQ2-type foldamer containing four different amino acid residues (Lys, Ala, Asp, and Ser).

Conformational properties and folding analysis of a series of seven oligoamide foldamers

33 crystal structures (11 unsolvated and 22 solvates) of a series of seven oligoamide foldamers were analysed. The crystal structures revealed that despite the structural and environmental differences the series of foldamers prefer only two general conformations, a protohelical @-conformation and a sigmoidal S-conformation. Both conformations also have preferred crystal packing motifs and solvate forming tendencies. Hydrogen bonding was found to be the most decisive factor in conformational preference, but steric properties, the type of the peripheral substituents, as well as solvent and aromatic interactions were also found to have an effect on the conformational details and crystal form.

Polar solvent effects on tartaric acid binding by aromatic oligoamide foldamer capsules.

Aromatic oligoamide sequences able to fold into single helical capsules were functionalized with two types of side chains to make them soluble in various solvents such as chloroform, methanol or water and their propensity to recognize tartaric acid was evaluated. The binding affinities to tartaric acid and binding thermodynamics in different media were investigated by variable temperature (1)H NMR and ITC experiments, the two methods giving consistent results. We show that tartaric acid binding mainly rests on enthalpically favourable polar interactions that were found to be sufficiently strong to be effective in the presence of a polar aprotic solvent (DMSO) and even in pure methanol. Binding in water was very weak. The stronger binding interactions were found to be more susceptible to the effect of competitive solvents and compensated by unfavourable entropic effects. Thus, the best host in a less polar medium eventually was found to be the worst host in protic solvents. An interesting case of entropically driven binding was evidenced in methanol.

Solid phase synthesis of oligoethylene glycol-functionalized quinolinecarboxamide foldamers with enhanced solubility properties

Abstract A series of octameric quinoline oligoamide foldamers has been synthesized consisting exclusively of monomers which display mono-, di-, tri- or tetra-ethylene glycol side-chains. These oligomers adopt stable helical conformations. New Fmoc-acid monomer precursors were first developed. The microwave assisted solid-phase synthesis (SPS) methodology for oligomer preparation is described, and it is demonstrated that small adjustments in side-chain length translate into large differences in the solubility profile of the oligomers. The impact of such modifications on foldamer preparation, handedness inversion kinetics and potential applications is also discussed.

Electronic Energy Transfer Modulation in a Dynamic Foldaxane: Proof‐of‐Principle of a Lifetime‐Based Conformation Probe

AbstractAbiotic aromatic oligoamide foldamers are shown to self‐assemble in solution to form a double helix, which can accommodate a bichromophoric thread in its central void. While in solution reversible electronic energy transfer is instilled between chromophoric termini of the free, flexible thread as evidenced through delayed luminescence, upon rigidification of the rod the chromophores are mutually distanced and effectively decoupled. Consequently, the chromophores display their individual photophysical characteristics. The observed conformation‐dependent changes of dynamic luminescence properties, which are particularly sensitive to distance, offers a new strategy for lifetime‐based detection of geometry on the molecular scale as demonstrated through real‐time luminescence detection of molecular complexation leading to foldaxane formation.

Electronic Energy Transfer Modulation in a Dynamic Foldaxane: Proof-of-Principle of a Lifetime-Based Conformation Probe.

Abiotic aromatic oligoamide foldamers are shown to self-assemble in solution to form a double helix, which can accommodate a bichromophoric thread in its central void. While in solution reversible electronic energy transfer is instilled between chromophoric termini of the free, flexible thread as evidenced through delayed luminescence, upon rigidification of the rod the chromophores are mutually distanced and effectively decoupled. Consequently, the chromophores display their individual photophysical characteristics. The observed conformation-dependent changes of dynamic luminescence properties, which are particularly sensitive to distance, offers a new strategy for lifetime-based detection of geometry on the molecular scale as demonstrated through real-time luminescence detection of molecular complexation leading to foldaxane formation.

Inter- and intramolecular interactions of a series of oligoamide foldamers

Inter- and intramolecular interactions of a series of oligoamide foldamers

Folding Patterns in a Family of Oligoamide Foldamers.

A series of small, unsymmetrical pyridine-2,6-dicarboxylamide oligoamide foldamers with varying lengths and substituents at the end groups were synthetized to study their conformational properties and folding patterns. The @-type folding pattern resembled the oxyanion-hole motifs of enzymes, but several alternative folding patterns could also be characterized. Computational studies revealed several alternative conformers of nearly equal stability. These folding patterns differed from each other in their intramolecular hydrogen-bonding patterns and aryl-aryl interactions. In the solid state, the foldamers adopted either the globular @-type fold or the more extended S-type conformers, which were very similar to those foldamers obtained computationally. In some cases, the same foldamer molecule could even crystallize into two different folding patterns, thus confirming that the different folding patterns are very close in energy in spite of their completely different shapes. Finally, the best match for the observed NOE interactions in the liquid state was a conformation that matched the computationally characterized helix-type fold.

Iterative design of a helically folded aromatic oligoamide sequence for the selective encapsulation of fructose.

The ab initio design of synthetic molecular receptors for a specific biomolecular guest remains an elusive objective, particularly for targets such as monosaccharides, which have very close structural analogues. Here we report a powerful approach to produce receptors with very high selectivity for specific monosaccharides and, as a demonstration, we develop a foldamer that selectively encapsulates fructose. The approach uses an iterative design process that exploits the modular structure of folded synthetic oligomer sequences in conjunction with molecular modelling and structural characterization to inform subsequent refinements. Starting from a first-principles design taking size, shape and hydrogen-bonding ability into account and using the high predictability of aromatic oligoamide foldamer conformations and their propensity to crystallize, a sequence that binds to β-D-fructopyranose in organic solvents with atomic-scale complementarity was obtained in just a few iterative modifications. This scheme, which mimics the adaptable construction of biopolymers from a limited number of monomer units, provides a general protocol for the development of selective receptors.