Flaws in foldamers: conformational uniformity and signal decay in achiral helical peptide oligomers

Solvatomorphism of a 2,6-pyridyldicarboxamide-based foldamer

A detailed solvatomorphism study conducted on a diamine-terminated 2,6-pyridyldicarboxamide-based foldamer 1 is reported. This investigation establishes the influence of a diverse range of polar and non-polar solvents including chloroform (1A), a trifluorotoluene/dichloromethane mixture (1A), dimethylformamide/diethyl ether (1B), tetrahydrofuran (1·THF), butanone (1·butanone), dichloromethane (1·DCM), a methanol/dichloromethane mixture (1·MeOH) and dimethylsulfoxide (1·DMSO) on the solid-state conformation and crystal packing behaviour of this supramolecular scaffold. Single-crystal X-ray diffraction analysis of the seven solvatomorphs of the studied foldamer (1A, 1B, 1·DCM, 1·THF, 1·butanone, 1·MeOH and 1·DMSO) identified that 1·DCM, 1·THF, 1·butanone, 1·MeOH and 1·DMSO form supramolecular aggregates (e.g., channels/cavities) which incorporate solvent molecules within the voids of the system, leading them to adopt channels of differing dimensions between 3.5 and 9.0 Å. Solid-state analysis identified that a diverse array of intermolecular non-covalent interactions form between the foldamer and the solvent molecule, including N-H⋯O, N-H⋯Cl, O-H⋯O, N-H⋯Cl and C-H⋯O hydrogen-bonding interactions, stabilising the formation of these solvent-mediated channel aggregates within the different solvatomorphs of the studied foldamer. We envisage that these solvatomorphism studies will facilitate the future design of foldamers, particularly given the emerging solid-state applications of foldamers which could hold relevance in the field of crystal engineering or for the uptake of small molecules for long-term use in energy storage and materials chemistry.

How Rigid Are Anthranilamide Molecular Electrets?

As important as molecular electrets are for electronic materials and devices, conformational fluctuations strongly impact their macrodipoles and intrinsic properties. Herein, we employ molecular dynamics (MD) simulations with the polarizable charge equilibrium (PQEq) method to investigate the persistence length (LP) of molecular electrets composed of anthranilamide (Aa) residues. The PQEq-MD dissipates the accepted static notions about Aa macromolecules, and LP represents the shortest Aa rigid segments. The classical model with a single LP value does not describe these oligomers. Introducing multiple LP values for the same macromolecule follows the observed trends and discerns the enhanced rigidity in their middle sections from the reduced stiffness at their terminal regions. Furthermore, LP distinctly depends on solvent polarity. The Aa oligomers maintain extended conformations in nonpolar solvents with LP exceeding 4 nm, while in polar media, increased conformational fluctuations reduce LP to about 2 nm. These characteristics set key guidelines about the utility of Aa conjugates for charge-transfer systems within organic electronics and energy engineering.

Reaction, Recognition, Relay: Anhydride Hydrolysis Reported by Conformationally Responsive Fluorinated Foldamers in Micelles

Natural membrane receptors are proteins that can report on changes in the concentration of external chemical messengers. Messenger binding to a receptor produces conformational changes that are relayed through the membrane into the cell; this information allows cells to adapt to changes in their environment. Artificial membrane receptors (R)-1 and (S)-1 are helical α-aminoisobutyric acid (Aib) foldamers that replicate key parts of this information relay. Solution-phase 19F NMR spectroscopy of zinc(II)-capped receptor 1, either in organic solvent or in membrane-mimetic micelles, showed messenger binding produced an enrichment of either left- or right-handed screw-sense; the chirality of the bound messenger was relayed to the other receptor terminus. Furthermore, in situ production of a chemical messenger in the external aqueous environment could be detected in real-time by a racemic mixture of receptor 1 in micelles. The hydrolysis of insoluble anhydrides produced carboxylate in the aqueous phase, which bound to the receptors and gave a distinct 19F NMR output from inside the hydrophobic region of the micelles.

Enantioselective conjugate addition to nitroolefins catalysed by helical peptides with a single remote stereogenic centre

Two short pentapeptides rich in α-aminoisobutyric acid (Aib) residues have been shown to act as enantioselective organocatalysts for the conjugate addition of nucleophiles to nitroolefins. An L-alanine terminated peptide, (Aib)4(L-Ala)NHtBu, which has neither functionalised sidechains nor a highly designed reactive site, used an exposed N-terminal primary amine and the amide bonds of the backbone to mediate catalysis. Folding of this peptide into a 310 helical structure was observed by crystallography. Folding into a helix relays the conformational preference of the chiral alanine residue at the C-terminus to the primary amine at the N-terminus, 0.9 nm distant. The chiral environment and defined shape produced by the 310 helix brings the amine site into proximity to two exposed amide NHs. Reaction scope studies implied that the amine acts as a Brønsted base and the solvent-exposed NH groups of the helix, shown to weakly bind β-nitrostyrene, are needed to obtain an enantiomeric excess. Replacement of L-alanine with D-phenylalanine gave (Aib)4(D-Phe)NHtBu, a peptide that now catalysed the benchmark reaction with the opposite enantioselectivity. These studies show how achiral residues can play a key role in enantioselective catalysis by peptides through the promotion of folding.

α-Amino-iso-butyric acid foldamers terminated with rhodium(I) N-heterocyclic carbene catalysts

To investigate how remotely induced changes in ligand folding might affect catalysis by organometallic complexes, dynamic α‐amino‐iso‐butyric acid (Aib) peptide foldamers bearing rhodium(I) N‐heterocyclic carbene (NHC) complexes have been synthesized and studied. X‐ray crystallography of a foldamer with an N‐terminal azide and a C‐terminal Rh(NHC)(Cl)(diene) complex showed a racemate with a chiral axis in the Rh(NHC) complex and a distorted 3₁₀ helical body. Replacing the azide with either one or two chiral L‐α‐methylvaline (L‐αMeVal) residues gave diastereoisomeric foldamers that each possessed point, helical and axial chirality. NMR spectroscopy revealed an unequal ratio of diastereoisomers for some foldamers, indicating that the chiral conformational preference of the N‐terminal residue(s) was relayed down the 1 nm helical body to the axially chiral Rh(NHC) complex. Although the remote chiral residue(s) did not affect the stereoselectivity of hydrosilylation reactions catalysed by these foldamers, these studies suggest a potential pathway towards remote conformational control of organometallic catalysts.

Scalable synthesis and coupling of quaternary α-arylated amino acids: α-aryl substituents are tolerated in α-helical peptides

Quaternary amino acids are important tools for the modification and stabilisation of peptide secondary structures. Here we describe a practical and scalable synthesis applicable to quaternary alpha-arylated amino acids (Q4As), and the development of solid-phase synthesis conditions for their incorporation into peptides. Monomeric and dimeric α-helical peptides are synthesised with varying degrees of Q4A substitution and their structures examined using biophysical methods. Both enantiomers of the Q4As are tolerated in folded monomeric and oligomeric α-helical peptides, with the (R)-enantiomer slightly more so than the (S).

Chiral amines as initiators for ROP and their chiral induction on poly(2-aminoisobutyric acid) chains

Chirality induction by chiral amines in poly(amino acid)s by ring opening polymerization.

Automated solid-phase concatenation of Aib residues to form long, water-soluble, helical peptides

Iterative coupling of 2-aminoisobutyric acid (Aib) has been achieved rapidly and efficiently using automated solid-phase peptide synthesis, employing diisopropylcarbodiimide (DIC) in the presence of ethyl cyanohydroxyiminoacetate (Oxyma). This method has allowed the first total synthesis of the fungal antibiotic Cephaibol D, and enabled the synthesis of water-soluble oligomers of Aib containing up to an unprecedented sequence of 17 consecutive Aib residues. Conformational analysis of the Aib oligomers in aqueous solution shows a length dependence in their CD spectra, with oligomers of more than 14 Aib residues apparently adopting structured helical conformations.

Chirality Control of Screw-Sense in Aib-Polymers: Synthesis and Helicity of Amino Acid Functionalized Polymers

2-Aminoisobutyric acid (Aib) is an essential amino acid, leading to the formation of peptAibols as microbiologically active peptides and proteins. We here report on the ring-opening polymerization (ROP) of Aib-NCA (N-carboxy-anhydrides), enabling to prepare distinct Aib-polymers up to molecular weights of 1400 g/mol with precise end-group control. ROP of Aib-NCA was accomplished via various amine initiators in frozen and liquid solvent systems, in all cases revealing the desired structures as detected by MALDI-TOF-MS and ¹H NMR. We can prove living polymerization behavior until the limit of solubility via inline-IR spectroscopy in both solution and solid state polymerization, characterizing the final polymers via MALDI-TOF-analysis. The attachment of chiral (d or l)-amino acids onto the polymer' headgroup allows to systematically investigate the helical screw-sense of poly(Aib)_n, resulting in chiral induction to form either left (M)- or right (P)-handed screw-senses, depending on the chirality of the attached amino acid. The approach is extended toward a switchable, chiral azo-headgroup, able to change chirality of the attached poly(Aib)_n via a light-induced trigger, revealing a thermally stable cis-isomer when polymer units are attached. In contrast to many other amino acids easily polymerized into poly(amino-acids) via ring-opening polymerization (ROP) of their respective N-carboxyanhydrides (NCAs), the ROP of Aib-NCA (N-carboxy-anhydrides) here is novel and opens a general approach toward chiral, end group-modified helices with a defined screw-sense.

Extended Diethylglycine Homopeptides Formed by Desulfurization of Their Tetrahydrothiopyran Analogues

Diethylglycine (Deg) homopeptides adopt the rare 2.0₅-helical conformation, the longest three-dimensional structure that a peptide of a given sequence can adopt. Despite this unique conformational feature, Deg is rarely used in peptide design because of its poor reactivity. In this paper, we show that reductive desulfurization of oligomers formed from more reactive tetrahydrothiopyran-containing precursors provides a practical way to build the longest Deg homopeptides so far made, and we detail some conformational studies of the Deg oligomers and their heterocyclic precursors.

α-Methyl phenylglycines by asymmetric α-arylation of alanine and their effect on the conformational preference of helical Aib foldamers

α-Arylated alanine derivatives were made enantioselectively by migratory rearrangement of a urea derivative using (R,R)-pseudoephedrine as a chiral auxiliary. Incorporation of a single residue of the product α-methyl phenylglycine into an otherwise achiral oligomer of aminoisobutyric acid oligomer induced a preferred screw sense, detectable by a NMR reporter located at the remote terminus of the oligomer. The magnitude of the screw sense induction was greater when the chiral residue was located at the N-terminus of the foldamer, and in some cases the sense of induction was opposite to that of related α-methylated amino acids with α-substituents other than aryl.

Bis-pyrene probes of foldamer conformation in solution and in phospholipid bilayers

Exploring the detailed structural features of synthetic molecules in the membrane phase requires sensitive probes of conformation. Here we describe the design, synthesis and characterization of bis(pyrene) probes that report conformational changes in membrane-active dynamic foldamers. The probes were designed to distinguish between left-handed (M) and right-handed (P) screw-sense conformers of 3₁₀-helical α-aminoisobutyric acid (Aib) peptide foldamers, both in solution and in bilayer membranes. Several different bis(pyrene) probes were synthesized and ligated to the C-terminus of Aib tetramers that had different chiral residues at the N-terminus, residues that favored either an M or a P screw-sense in the 3₁₀-helix. The readily synthesized and conveniently incorporated N-acetyl-1,2-bis(pyren-1'-yl)ethylenediamine probe proved to have the best properties. In solution, changes in foldamer screw-sense induced substantial changes in the ratio of excimer/monomer fluorescence emission (E/M) for this reporter of conformation, with X-ray crystallography revealing that opposite screw-senses produce very different interpyrene distances in the reporter. In bilayers, this convenient and sensitive fluorescent reporter allowed, for the first time, an investigation of how the chirality of natural phospholipids affects foldamer conformation.

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.

A tendril perversion in a helical oligomer: trapping and characterizing a mobile screw-sense reversal

Helical oligomers of achiral monomers adopt domains of uniform screw sense, which are occasionally interrupted by screw-sense reversals. These rare, elusive, and fast-moving features have eluded detailed characterization. We now describe the structure and habits of a screw-sense reversal trapped within a fragment of a helical oligoamide foldamer of the achiral quaternary amino acid 2-aminoisobutyric acid (Aib). The reversal was enforced by compelling the amide oligomer to adopt a right-handed screw sense at one end and a left-handed screw sense at the other. The trapped reversal was characterized by X-ray crystallography, and its dynamic properties were monitored by NMR and circular dichroism, and modelled computationally. Raman spectroscopy indicated that a predominantly helical architecture was maintained despite the reversal. NMR and computational results indicated a stepwise shift from one screw sense to another on moving along the helical chain, indicating that in solution the reversal is not localised at a specific location, but is free to migrate across a number of residues. Analogous unconstrained screw-sense reversals that are free to move within a helical structure are likely to provide the mechanism by which comparable helical polymers and foldamers undergo screw-sense inversion.

Dibenzazepinyl ureas as dual NMR and CD probes of helical screw-sense preference in conformationally equilibrating dynamic foldamers

Dibenzazepinyl ureas act as probes to allow conformational analysis of screw-sense preference in dynamic foldamers by both NMR and CD spectroscopy.

Conformational photoswitching of a synthetic peptide foldamer bound within a phospholipid bilayer

The dynamic properties of foldamers, synthetic molecules that mimic folded biomolecules, have mainly been explored in free solution. We report on the design, synthesis, and conformational behavior of photoresponsive foldamers bound in a phospholipid bilayer akin to a biological membrane phase. These molecules contain a chromophore, which can be switched between two configurations by different wavelengths of light, attached to a helical synthetic peptide that both promotes membrane insertion and communicates conformational change along its length. Light-induced structural changes in the chromophore are translated into global conformational changes, which are detected by monitoring the solid-state (19)F nuclear magnetic resonance signals of a remote fluorine-containing residue located 1 to 2 nanometers away. The behavior of the foldamers in the membrane phase is similar to that of analogous compounds in organic solvents.

Dynamic foldamer chemistry

Foldamers can be made more than pieces of static, conformationally uniform molecular architecture by designing into their structure the conformational dynamism characteristic of functional molecular machines. We show that these dynamic foldamers display biomimetic properties reminiscent of allosteric proteins and receptor molecules. They can translate chemical signals into conformational changes, and hence into chemical outputs such as control of reactivity and selectivity. Future developments could see dynamic foldamers operating in the membrane phase providing artificial mechanisms for communication and control that integrate synthetic chemistry into synthetic biology.

Controlled Folding, Motional, and Constitutional Dynamic Processes of Polyheterocyclic Molecular Strands

General design principles have been developed for the control of the structural features of polyheterocyclic strands and their effector-modulated shape changes. Induced defined molecular motions permit designed enforcement of helical as well as linear molecular shapes. The ability of such molecular strands to bind metal cations allows the generation of coiling/uncoiling processes between helically folded and extended linear states. Large molecular motions are produced on coordination of metal ions, which may be made reversible by competition with an ancillary complexing agent and fueled by sequential acid/base neutralization energy. The introduction of hydrazone units into the strands confers upon them constitutional dynamics, whereby interconversion between different strand compositions is achieved through component exchange. These features have relevance for nanomechanical devices. We present a morphological and functional analysis of such systems developed in our laboratories.

Refoldable Foldamers: Global Conformational Switching by Deletion or Insertion of a Single Hydrogen Bond

Small changes in the structure of a foldamer may lead to gross changes in conformational preference. We show that the simple insertion or deletion of a single hydrogen bond by changes in pH or by photochemical deprotection is sufficient to refold a helical oligomer, interconverting M and P screw-sense preference. As a consequence of the switch, information may be transmitted to a remote catalytic site, selectively directing the formation of either of two enantiomeric products by a reaction involving 1,22-remote intermolecular asymmetric induction.

Achieving high resolution and optimizing sensitivity in spatial frequency encoding NMR spectroscopy: from theory to practice

A detailed analysis of NMR spectra based on spatial frequency encoding is presented.

Controllability of dynamic double helices: quantitative analysis of the inversion of a screw-sense preference upon complexation

We describe a quantitative analysis of the complexation-induced inversion of a screw-sense preference based on a conformationally dynamic double-helix structure in a macrocycle. The macrocycle is composed of two twisting units (terephthalamide), which are spaced by two strands (1,3-bis(phenylethynyl)benzene), and is designed to generate a double-helix structure through twisting about a C2 axis in a conrotatory manner. The attachment of chiral auxiliaries to the twisting units induces a helical preference for a particular sense of (M)- or (P)-helicity through the intramolecular transmission of chirality to dynamic double helices. The twisting unit can also act as a binding site for capturing a guest molecule, and, in a complexed state, the preferred screw sense of the dynamic double-helix structure is reversed to exhibit the contrary preference. We quantitatively monitored the complexation-induced inversion of the screw-sense preference using 1H NMR spectroscopy, which enabled us to observe independently two species with (M)- or (P)-helicity in both the absence and presence of a guest molecule. Inversion of the screw-sense preference was induced upon complexation with an achiral guest as well as a chiral guest.

Conformational Switching of a Foldamer in a Multicomponent System by pH-Filtered Selection between Competing Noncovalent Interactions

Biomolecular systems are able to respond to their chemical environment through reversible, selective, noncovalent intermolecular interactions. Typically, these interactions induce conformational changes that initiate a signaling cascade, allowing the regulation of biochemical pathways. In this work, we describe an artificial molecular system that mimics this ability to translate selective noncovalent interactions into reversible conformational changes. An achiral but helical foldamer carrying a basic binding site interacts selectively with the most acidic member of a suite of chiral ligands. As a consequence of this noncovalent interaction, a global absolute screw sense preference, detectable by (13)C NMR, is induced in the foldamer. Addition of base, or acid, to the mixture of ligands competitively modulates their interaction with the binding site, and reversibly switches the foldamer chain between its left and right-handed conformations. As a result, the foldamer-ligand mixture behaves as a biomimetic chemical system with emergent properties, functioning as a "proton-counting" molecular device capable of providing a tunable, pH-dependent conformational response to its environment.

Conformational cooperativity between helical domains of differing geometry in oligoamide–oligourea foldamer chimeras

Two foldamer domains of different classes (urea and amide) remain in conformational communication, and adopt a well-defined global structure in solution, provided the interdomain hydrogen-bonds are suitably orientated.

Screw sense alone can govern enantioselective extension of a helical peptide by kinetic resolution of a racemic amino acid

Helical secondary structure alone, even in the absence of local chiral residues, can direct the enantioselectivity of peptide coupling.