The conformational properties of Alanine (Ala) residue have been investigated to understand protein folding and develop force fields. In this work, we examined the neighbor effect on the conformational spaces of Ala residue using model azapeptides, Ac-Ala-azaGly-NHMe (3, AaG), and Ac-azaGly-Ala-NHMe (4, aGA1). Ramachandran energy maps were generated by scanning (φ, ψ) dihedral angles of the Ala residues in models with the fixed dihedral angles (φ = ±90°, ψ = ±0° or ±180°) of azaGly residue using LCgau-BOP and LCgau-BOP + LRD functionals in the gas and water phases. The integral-equation-formalism polarizable continuum model (IEF-PCM) and a solvation model density (SMD) were employed to mimic the solvation effect. The most favorable conformation of Ala residue in azapeptide models is found as the polyproline II (βP), inverse γ-turn (γ\'), β-sheet (βS), right-handed helix (αR), or left-handed helix (αL) depending on the conformation of neighbor azaGly residue in isolated form. Solvation methods exhibit that the Ala residue favors the βP, δR, and αR conformations regardless of its position in azapeptides 3 and 4 in water. Azapeptide 5, Ac-azaGly-Ala-NH2 (aGA2), was synthesized to evaluate the theoretical results. The X-ray structure showed that azaGly residue adopts the polyproline II (βP) and Ala residue adopts the right-handed helical (αR) structure in aGA2. The conformational preferences of aGA2 and the dimer structure of aGA2 based on the X-ray structure were examined to assess the performance of DFT functionals. In addition, the local minima of azapeptide 6, Ac-Phe-azaGly-NH2 (FaG), were compared with the previous experimental results. SMD/LCgau-BOP + LRD methods agreed well with the reported experimental results. The results suggest the importance of weak dispersion interactions, neighbor effect, and solvent influence in the conformational preferences of Ala residue in model azapeptides.

The modulation of biology utilizing foldamers has flourished over the last few decades thanks to their overwhelming promise in their applications in molecular design, catalysis, supramolecular, and rational design. However, the application of peptidomimetics is still restricted due to the limited availability of molecular frameworks and folding propensities. To broaden the scope of foldameric peptidomimetics we proposed the development of sulfonyl-γ-AApeptides-the oligomers of sulfonyl-γ-N-acylated-N-aminoethyl (AA) amino acids, a unique unnatural scaffold that possesses promising potential to modulate protein-protein interactions. In this chapter, the overall process of design, synthesis, and function of sulfonyl-γ-AApeptides is briefly reviewed for the use of unnatural foldamers to modulate PPIs.

We have designed and synthesized a helical cysteamine-terminated oligourea foldamer composed of ten urea residues featuring side carboxyl and amine groups. The carboxyl group is located in proximity to the C-terminus of the oligourea and hence at the negative pole of the helix dipole. The amine group is located close to the N-terminus and hence at the positive pole of the helix dipole. Beyond the already remarkable dipole moment inherent in oligourea 2.5 helices, the incorporation of additional charges originating from the carboxylic and amine groups is supposed to impact the overall charge distribution along the molecule. These molecules were self-assembled into monolayers on a gold substrate, allowing us to investigate the influence of an electric field on these polar helices. By applying surface-enhanced infrared reflection-absorption spectroscopy, we proved that molecules within the monolayers tend to reorient themselves more vertically when a negative bias is applied to the surface. It was also found that surface-confined oligourea molecules affected by the external electric field tend to rearrange the electron density at urea groups, leading to the stabilization of the resonance structure with charge transfer character. The presence of the external electric field also affected the nanomechanical properties of the oligourea films, suggesting that molecules also tend to reorient in the ambient environment without an electrolyte solution. Under the same conditions, the helical oligourea displayed a robust piezoresponse, particularly noteworthy given the slender thickness of the monolayer, which measured approximately 1.2 nm. This observation demonstrates that thin molecular films composed of oligoureas may exhibit stimulus-responsive properties. This, in turn, may be used in nanotechnology systems as actuators or functional films, enabling precise control of their thickness in the range of even fractions of nanometers.

Widespread outbreaks of threatening infections caused by unknown pathogens and water transmission have spawned the development of adsorption methods for pathogen elimination. We proposed a biochar functionalization strategy involving ε-polylysine (PLL), a bio-macromolecular poly(amino acid)s with variable folding conformations, as a \"pathogen gripper\" on biochar. PLL was successfully bridged onto biochar via polydopamine (PDA) crosslinking. The extension of electropositive side chains within PLL enables the capture of both nanoscale viruses and micrometer-scale bacteria in water, achieving excellent removal performances. This functionalized biochar was tentatively incorporated into ultrafiltration (UF) system, to achieve effective and controllable adsorption and retention of pathogens, and to realize the transfer of pathogens from membrane surface/pore to biochar surface as well as flushing water. The biochar-amended UF systems presents complete retention (∼7 LRV) and hydraulic elution of pathogens into membrane flushing water. Improvements in removal of organics and anti-fouling capability were observed, indicating the broken trade-off in UF pathogen removal dependent on irreversible fouling. Chemical characterizations revealed adsorption mechanisms encompassing electrostatic/hydrophobic interactions, pore filling, electron transfer, chemical bonding and secondary structure transitions. Microscopic and mechanical analyses validated the mechanisms for rapid adsorption and pathogen lysis. Low-concentration alkaline solution for used biochar regeneration, facilitated the deprotonation and transformation of PLL side chain to folded structures (α-helix/β-sheet). Biochar regeneration process also promoted the effective detachment/inactivation of pathogens and protection of functional groups on biochar, corroborated by physicochemical inspection and molecular dynamics simulation. The foldability of poly(amino acid)s acting like dynamic arms, significantly contributed to pathogen capture/desorption/inactivation and biochar regeneration. This study also inspires future investigation for performances of UF systems amended by poly(amino acid)s-functionalized biochar under diverse pressure, temperature, reactive oxygen species of feeds and chemical cleaning solutions, with far-reaching implications for public health, environmental applications of biochar, and UF process improvement.

UNASSIGNED: Peptide foldamers play a critical role in pharmaceutical research and biomedical applications. This review highlights recent (post-2020) advancements in novel foldamers, synthetic techniques, and their applications in pharmaceutical research.
UNASSIGNED: The authors summarize the structures and applications of peptide foldamers such as α, β, γ-peptides, hydrocarbon-stapled peptides, urea-type foldamers, sulfonic-γ-amino acid foldamers, aromatic foldamers, and peptoids, which tackle the challenges of traditional peptide drugs. Regarding antimicrobial use, foldamers have shown progress in their potential against drug-resistant bacteria. In drug development, peptide foldamers have been used as drug delivery systems (DDS) and protein-protein interaction (PPI) inhibitors.
UNASSIGNED: These structures exhibit resistance to enzymatic degradation, are promising for therapeutic delivery, and disrupt crucial PPIs associated with diseases such as cancer with specificity, versatility, and stability, which are useful therapeutic properties. However, the complexity and cost of their synthesis, along with the necessity for thorough safety and efficacy assessments, necessitate extensive research and cross-sector collaboration. Advances in synthesis methods, computational modeling, and targeted delivery systems are essential for fully realizing the therapeutic potential of foldamers and integrating them into mainstream medical treatments.

Organic materials with switchable dual circularly polarized luminescence (CPL) are highly desired because they can not only directly radiate tunable circularly polarized light themselves but also induce CPL for guests by providing a chiral environment in self-assembled structures or serving as the hosts for energy transfer systems. However, most organic molecules only exhibit single CPL and it remains challenging to develop organic molecules with dual CPL. Herein, novel through-space conjugated chiral foldamers are constructed by attaching two biphenyl arms to the 9,10-positions of phenanthrene, and switchable dual CPL with opposite signs at different emission wavelengths are successfully realized in the foldamers containing high-polarizability substitutes (cyano, methylthiol and methylsulfonyl). The combined experimental and computational results demonstrate that the intramolecular through-space conjugation has significant contributions to stabilizing the folded conformations. Upon photoexcitation in high-polar solvents, strong interactions between the biphenyl arms substituted with cyano, methylthio or methylsulfonyl and the polar environment induce conformation transformation for the foldamers, resulting in two transformable secondary structures of opposite chirality, accounting for the dual CPL with opposite signs. These findings highlight the important influence of the secondary structures on the chiroptical property of the foldamers and pave a new avenue towards efficient and tunable dual CPL materials.

This concept article explores the emerging role of atropisomerism in foldamer chemistry, a field focussed on oligomers that adopt well-defined conformations through non-covalent interactions. Atropisomerism introduces a novel dimension to foldamer design by restricting rotational freedom around single bonds to dictate molecular shape with precision. Despite the prevalence of atropisomeric bonds in organic synthesis, their application within foldamers remains underexplored. Here, we discuss key developments in both backbone and sidechain atropisomerism, and suggest future directions for atropisomeric foldamers in the context of a recent surge in atropselective synthetic methods. We propose that judicious use of atropisomerism may serve as a transformative tool in the construction of shape-defined macromolecules.

Foldamer is a scaled-down version of coil spring, which can absorb and release energy by conformational change. Here, polymer networks with high density of molecular springs were developed by employing anion-coordination-based foldamers as the monomer. The coiling of the foldamer is controlled by oligo(urea) ligands coordinating to chloride ions; subsequently, the folding and unfolding of foldamer conformations endow the polymer network with excellent energy dissipation and toughness. The mechanical performance of the corresponding polymer networks shows a dramatic increase from P-L2UCl (non-folding), to P-L4UCl (a full turn), and then to P-L6UCl (1.5 turns), in terms of strength (2.62 MPa; 14.26 MPa; 22.93 MPa), elongation at break (70 %; 325 %; 352 %), Young\'s modulus (2.69 MPa; 63.61 MPa; 141.50 MPa), and toughness (1.12 MJ/m3; 21.39 MJ/m3; 49.62 MJ/m3), respectively, which is also better than those without anion centers and the non-foldamer based counterparts. Moreover, P-L6UCl shows enhanced strength and toughness than most of the molecular-spring based polymer networks. Thus, an effective strategy for designing high-performance anion-coordination-based materials is presented.

Novel fluorinated foldamers based on aminomethyl-1,4-triazolyl-difluoroacetic acid (1,4-Tz-CF2) units were synthesized and their conformational behaviour was studied by NMR and molecular dynamics. Their activity on the aggregation of the human islet amyloid polypeptide (hIAPP) amyloid protein was evaluated by fluorescence spectroscopy and mass spectrometry. The fluorine labelling of these foldamers allowed the analysis of their interaction with the target protein. We demonstrated that the preferred extended conformation of homotriazolamers of 1,4-Tz-CF2 unit increases the aggregation of hIAPP, while the hairpin-like conformation of more flexible heterotriazolamers containing two 1,4-Tz-CF2 units mixed with natural amino acids from the hIAPP sequence reduces it, and more efficiently than the parent natural peptide. The longer heterotriazolamers having three 1,4-Tz-CF2 units adopting more folded hairpin-like and ladder-like structures similar to short multi-stranded β-sheets have no effect. This work demonstrates that a good balance between the structuring and flexibility of these foldamers is necessary to allow efficient interaction with the target protein.

π-π stacking interaction is an attractive interaction that involves aromatic groups containing π-conjugated domains. It is a promising strategy for stabilizing folded structures with interesting chiroptical properties and manipulating the supramolecular chiral self-assembly process. In this study, we report the engineering of π-conjugated amino acids that utilize π-π stacking interactions to manipulate chiral folding as well as self-assembly evolution. Stepwise conjugation of phenyl, naphthyl, and pyrenyl to N-terminal phenylalanine derivatives witnessed the folding through intramolecular π-interactions in solution phase, which facilitated the formation of chiral geometry and the emergence of chiral optics. Introduction of aromatic domains efficiently lowers the critical aggregation concentration in the aqueous media. Molecular folding enables a special concentration-dependent self-assembly, whereby the supramolecular chirality accomplished inversion with the evolution of helical nanoarchitectures. This work develops a strategy to engineer π-conjugated amino acids with controllable folding behaviors, which also offers implications for the rational design of functional chiral materials.