Oligoanthranilamides. Non-Peptide Subunits That Show Formation of Specific Secondary Structure

Supramolecular and molecular capsules, cages and containers

Stemming from early seminal notions of molecular recognition and encapsulation, three-dimensional, cavity-containing capsular compounds and assemblies have attracted intense interest due to the ability to modulate chemical and physical properties of species encapsulated within these confined spaces compared to bulk environments. With such a diverse range of covalent motifs and non-covalent (supramolecular) interactions available to assemble building blocks, an incredibly wide-range of capsular-type architectures have been developed. Furthermore, synthetic tunability of the internal environments gives chemists the opportunity to engineer systems for uses in sensing, sequestration, catalysis and transport of molecules, just to name a few. In this tutorial review, an overview is provided into the design principles, synthesis, characterisation, structural facets and properties of coordination cages, porous organic cages, supramolecular capsules, foldamers and mechanically interlocked molecules. Using seminal and recent examples, the advantages and limitations of each system are explored, highlighting their application in various tasks and functions.

Ultra-Fast-Healing Glassy Hyperbranched Plastics Capable of Restoring 26.4 MPa Tensile Strength within One Minute at Room Temperature

The growing concern regarding widespread plastic pollution has propelled the development of sustainable self-healing plastics. Although considerable efforts have been dedicated to fabricating self-healing plastics, achieving rapid healing at room temperature is extremely challenging. Herein, we have developed an ultra-fast-healing glassy polyurethane (UGPU) by designing a hyperbranched molecular structure with a high density of multiple hydrogen bonds (H-bonds) on compliant acyclic heterochains and introducing trace water to form water bridge across the fractured surfaces. The compliant acyclic heterochains allow the dense multiple hydrogen bonds to form a frozen network, enabling tensile strength of up to 70 MPa and storage modulus of 2.5 GPa. The hyperbranched structure can drive the reorganization of the H-bonding network through the high mobility of the branched chains and terminals, thereby leading to self-healing ability at room temperature. Intriguingly, the presence of trace water vapor facilitates the formation of activated layers and the rearrangement of networks across the fractured UGPU sections, thereby enabling ultra-fast self-healing at room temperature. Consequently, the restored tensile strength after healing for 1 minute achieves a historic-record of 26.4 MPa. Furthermore, the high transparency (>90 %) and ultra-fast healing property of UGPU make it an excellent candidate for advanced optical and structural materials.

How Permanent Are the Permanent Macrodipoles of Anthranilamide Bioinspired Molecular Electrets?

Dipoles are ubiquitous, and their impacts on materials and interfaces affect many aspects of daily life. Despite their importance, dipoles remain underutilized, often because of insufficient knowledge about the structures producing them. As electrostatic analogues of magnets, electrets possess ordered electric dipoles. Here, we characterize the structural dynamics of bioinspired electret oligomers based on anthranilamide motifs. We report dynamics simulations, employing a force field that allows dynamic polarization, in a variety of solvents. The results show a linear increase in macrodipoles with oligomer length that strongly depends on solvent polarity and hydrogen-bonding (HB) propensity, as well as on the anthranilamide side chains. An increase in solvent polarity increases the dipole moments of the electret structures while decreasing the dipole effects on the moieties outside the solvation cavities. The former is due to enhancement of the Onsager reaction field and the latter to screening of the dipole-generated fields. Solvent dynamics hugely contributes to the fluctuations and magnitude of the electret dipoles. HB with the solvent weakens electret macrodipoles without breaking the intramolecular HB that maintains their extended conformation. This study provides design principles for developing a new class of organic materials with controllable electronic properties. An animated version of the TOC graphic showing a sequence of the MD trajectories of short and long molecular electrets in three solvents with different polarities is available in the HTML version of this paper.

Construction of metallo-helicoids with high antimicrobial activity via intermolecular coordination

Metallo-helicoids are constructed by intermolecular coordination interactions between covalent linear polymer and tritopic/hexatopic molecular templates. These metallo-polymers with helicoidal conformation exhibit high antimicrobial activities against both Gram-positive and Gram-negative pathogens.

Unnatural helical peptidic foldamers as protein segment mimics

Unnatural helical peptidic foldamers have attracted considerable attention owing to their unique folding behaviours, diverse artificial protein binding mechanisms, and promising applications in chemical, biological, medical, and material fields. Unlike the conventional α-helix consisting of molecular entities of native α-amino acids, unnatural helical peptidic foldamers are generally comprised of well-defined backbone conformers with unique and unnatural structural parameters. Their folded structures usually arise from unnatural amino acids such as N-substituted glycine, N-substituted-β-alanine, β-amino acid, urea, thiourea, α-aminoxy acid, α-aminoisobutyric acid, aza-amino acid, aromatic amide, γ-amino acid, as well as sulfono-γ-AA amino acid. They can exhibit intriguing and predictable three-dimensional helical structures, generally featuring superior resistance to proteolytic degradation, enhanced bioavailability, and improved chemodiversity, and are promising in mimicking helical segments of various proteins. Although it is impossible to include every piece of research work, we attempt to highlight the research progress in the past 10 years in exploring unnatural peptidic foldamers as protein helical segment mimics, by giving some representative examples and discussing the current challenges and future perspectives. We expect that this review will help elucidate the principles of structural design and applications of existing unnatural helical peptidic foldamers in protein segment mimicry, thereby attracting more researchers to explore and generate novel unnatural peptidic foldamers with unique structural and functional properties, leading to more unprecedented and practical applications.

Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome

The Escherichia coli (E. coli) ribosome can incorporate a variety of non-l-α-amino acid monomers into polypeptide chains in vitro but with poor efficiency. Although these monomers span a diverse set of compounds, there exists no high-resolution structural information regarding their positioning within the catalytic center of the ribosome, the peptidyl transferase center (PTC). Thus, details regarding the mechanism of amide bond formation and the structural basis for differences and defects in incorporation efficiency remain unknown. Within a set of three aminobenzoic acid derivatives-3-aminopyridine-4-carboxylic acid (Apy), ortho-aminobenzoic acid (oABZ), and meta-aminobenzoic acid (mABZ)-the ribosome incorporates Apy into polypeptide chains with the highest efficiency, followed by oABZ and then mABZ, a trend that does not track with the nucleophilicity of the reactive amines. Here, we report high-resolution cryo-EM structures of the ribosome with each of these three aminobenzoic acid derivatives charged on tRNA bound in the aminoacyl-tRNA site (A-site). The structures reveal how the aromatic ring of each monomer sterically blocks the positioning of nucleotide U2506, thereby preventing rearrangement of nucleotide U2585 and the resulting induced fit in the PTC required for efficient amide bond formation. They also reveal disruptions to the bound water network that is believed to facilitate formation and breakdown of the tetrahedral intermediate. Together, the cryo-EM structures reported here provide a mechanistic rationale for differences in reactivity of aminobenzoic acid derivatives relative to l-α-amino acids and each other and identify stereochemical constraints on the size and geometry of non-monomers that can be accepted efficiently by wild-type ribosomes.

Molecular torsion springs: alteration of helix curvature in frustrated tertiary folds

The first abiotic foldamer tertiary structures have been recently reported in the form of aromatic helix-turn-helix motifs based on oligo-quinolinecarboxamides held together by intramolecular hydrogen bonds. Tertiary folds were predicted by computational modelling of the hydrogen-bonding interfaces between helices and later verified by X-ray crystallography. However, the prognosis of how the conformational preference inherent to each helix influences the tertiary structure warranted further investigation. Several new helix-turn-helix sequences were synthesised in which some hydrogen bonds have been removed. Contrary to expectations, this change did not strongly destabilise the tertiary folds. On closer inspection, a new crystal structure revealed that helices adopt their natural curvature when some hydrogen bonds are missing and undergo some spring torsion upon forming the said hydrogen bonds, thus potentially giving rise to a conformational frustration. This phenomenon sheds light on the aggregation behaviour of the helices when they are not linked by a turn unit.

Impact of Peptide Sequences on Their Structure and Function: Mimicking of Virus-Like Nanoparticles for Nucleic Acid Delivery

We rationally designed a series of amphiphilic hepta-peptides enriched with a chemically conjugated guanidiniocarbonylpyrrole (GCP) unit at the lysine side chain. All peptides are composed of polar (GCP) and non-polar (cyclohexyl alanine) residues but differ in their sequence periodicity, resulting in different secondary as well as supramolecular structures. CD spectra revealed the assembly of β-sheet-, α-helical and random structures for peptides 1, 2 and 3, respectively. Consequently, this enabled the formation of distinct supramolecular assemblies such as fibres, nanorod-like or spherical aggregates. Notably, all three cationic peptides are equipped with the anion-binding GCP unit and thus possess a nucleic acid-binding centre. However, only the helical (2) and the unstructured (3) peptide were able to assemble into small virus-like DNA-polyplexes and effectively deliver DNA into cells. Notably, as both peptides (2 and 3) were also capable of siRNA-delivery, they could be utilized to downregulate expression of the caner-relevant protein Survivin.

Precise Synthesis of Concentric Ring, Helicoid, and Ladder Metallo-Polymers with Chevron-Shaped Monomers

Molecular geometry represents one of the most important structural features and governs physical properties and functions of materials. Nature creates a wide array of substances with distinct geometries but similar chemical composition with superior efficiency and precision. However, it remains a formidable challenge to construct abiological macromolecules with various geometries based on identical repeating units, owing to the lack of corresponding synthetic approaches for precisely manipulating the connectivity between monomers and feasible techniques for characterizing macromolecules at the single-molecule level. Herein, we design and synthesize a series of tetratopic monomers with chevron stripe shape which serve as the key precursors to produce four distinct types of metallo-macromolecules with well-defined geometries, viz., the concentric hexagon, helicoid polymer, ladder polymer, and cross-linked polymer, via platinum-acetylide couplings. Concentric hexagon, helicoid, and ladder metallo-polymers are directly visualized by transmission electron microscopy, atomic force microscopy, and ultra-high-vacuum low-temperature scanning tunneling microscopy at the single-molecule level. Finally, single-walled carbon nanotubes (SWCNTs) are selected as the guest to investigate the structure-property relationship based on such macromolecules, among which the helicoid metallo-polymer shows high efficiency in wrapping SWCNTs with geometry-dependent selectivity.

Polyurethane-Based Stretchable Semiconductor Nanofilms with High Intrinsic Recovery Similar to Conventional Elastomers

Polymer semiconductors with large elastic recovery (ER) under high strain in thin film state are highly desirable for stretchable electronics. Here we report a type of stretchable semiconductor PU(DPP)x, by copolymerization of oligodiketopyrrolopyrrole-based conjugated block and hydrogenated polybutadiene flexible block via urethane linkage for intermolecular hydrogen bonding. By regulating block ratio, PU(DPP)35 with 35 wt % conjugated block exhibits high intrinsic ER > 80% under 175% strain (ε) in pseudo free-standing thin film state, comparable with commercial elastomers, and crack onset strain (COS) > 300% along with maximum hole mobility of 0.19 cm2 V-1 s-1 in organic thin film transistors to bring it to the best performing block copolymer-type stretchable semiconductors. Enhanced mobility is achieved using PU(DPP)35 as the binder for conjugated polymer PDPPT3. The 25 wt %-PDPPT3 blend displays mobility up to 1.28 cm2 V-1 s-1 along with COS ∼120%, and 10 wt %-PDPPT3 blend exhibits ER of 78% at ε = 150%, COS of ∼230%, modulus of 36.5 MPa, maximum mobility of 0.62 cm2 V-1 s-1 and no obvious degradation of mobility at ε = 150% after 100 cycles of strain. Moreover, the structural similarity enables the blend film uniform and stable microstructure against mechanical and thermal deformation. Notably, PU(DPP)35 and the blend are characterized by high mechanical performance similar to that of commercial elastomers in thin film state, and demonstrate their potential for high performance stretchable electronics.

Generalizing the Aromatic δ‐Amino Acid Foldamer Helix

A series of aromatic oligoamide foldamer sequences containing different proportions of three δ‐amino acids derived from quinoline, pyridine, and benzene and possessing varying flexibility, for example due to methylene bridges, were synthesized. Crystallographic structures of two key sequences and ¹H NMR data in water concur to show that a canonical aromatic helix fold prevails in almost all cases and that helix stability critically depends on the ratio between rigid and flexible units. Notwithstanding subtle variations of curvature, i. e. the numbers of units per turn, the aromatic δ‐peptide helix is therefore shown to be general and tolerant of a great number of sp³ centers. We also demonstrate canonical helical folding upon alternating two monomers that do not promote folding when taken separately: folding occurs with two methylenes between every other unit, not with one methylene between every unit. These findings highlight that a fine‐tuning of helix handedness inversion kinetics, curvature, and side chain positioning in aromatic δ‐peptidic foldamers can be realized by systematically combining different yet compatible δ‐amino acids.

Helical Foldamers and Stapled Peptides as New Modalities in Drug Discovery: Modulators of Protein-Protein Interactions

A “foldamer” is an artificial oligomeric molecule with a regular secondary or tertiary structure consisting of various building blocks. A “stapled peptide” is a peptide with stabilized secondary structures, in particular, helical structures by intramolecular covalent side-chain cross-linking. Helical foldamers and stapled peptides are potential drug candidates that can target protein-protein interactions because they enable multipoint molecular recognition, which is difficult to achieve with low-molecular-weight compounds. This mini-review describes a variety of peptide-based foldamers and stapled peptides with a view to their applications in drug discovery, including our recent progress.

In Vitro Selection of Foldamer-Like Macrocyclic Peptides Containing 2-Aminobenzoic Acid and 3-Aminothiophene-2-Carboxylic Acid

Aromatic cyclic β^2,3-amino acids (cβAAs), such as 2-aminobenzoic acid and 3-aminothiophene-2-carboxylic acid, are building blocks that can induce unique folding propensities of peptides. Although their ribosomal elongation had been a formidable task due to the low nucleophilicity of their amino groups, we have recently overcome this issue by means of an engineered tRNA^Pro1E2 that enhances their incorporation efficiency into nascent peptide chains. Here we report ribosomal synthesis of a random macrocyclic peptide library containing aromatic and aliphatic cβAAs, and its application to de novo discovery of binders against human IFNGR1 and FXIIa as model targets. The potent binding peptides showed not only high inhibitory activity but also high protease resistance in human serum. Moreover, these cβAAs play a critical role in exhibiting their properties, establishing a discovery platform for de novo foldamer-like macrocycles containing such unique building blocks.

Linear Dichroism Activity of Chiral Poly(p-Aryltriazole) Foldamers

Controllable higher-order assembly is a central aim of macromolecular chemistry. An essential challenge to developing these molecules is improving our understanding of the structures they adopt under different conditions. Here, we demonstrate how flow linear dichroism (LD) spectroscopy is used to provide insights into the solution structure of a chiral, self-assembled fibrillar foldamer. Poly(para-aryltriazole)s fold into different structures depending on the monomer geometry and variables such as solvent and ionic strength. LD spectroscopy provides a simple route to determine chromophore alignment in solution and is generally used on natural molecules or molecular assemblies such as DNA and M13 bacteriophage. In this contribution, we show that LD spectroscopy is a powerful tool in the observation of self-assembly processes of synthetic foldamers when complemented by circular dichroism, absorbance spectroscopy, and microscopy. To that end, poly(para-aryltriazole)s were aligned in a flow field under different solvent conditions. The extended aromatic structures in the foldamer give rise to a strong LD signal that changes in sign and in intensity with varying solvent conditions. A key advantage of LD is that it only detects the large assemblies, thus removing background due to monomers and small oligomers.

The helical supramolecular assembly of oligopyridylamide foldamers in aqueous media can be guided by adenosine diphosphates

A metal-free and achiral tri-pyridylamide foldamer, DM 11, containing a critical naphthalimide side chain self-assembles in a left-handed helical manner in the presence of chiral adenosine phosphates, under physiological conditions. Surprisingly, a very high degree of helicity in the foldamer assemblies was observed with ADP compared to other nucleoside phosphates, including ATP.

Influence of Terminal Functionality on the Crystal Packing Behaviour and Cytotoxicity of Aromatic Oligoamides

The synthesis and characterization of three aromatic oligoamides, constructed from the same pyridyl carboxamide core but incorporating distinct end groups of acetyl (Ac) 1, tert-butyloxycarbonyl (Boc) 2 and amine 3 is reported. Single crystal X-ray diffraction analysis of 1-3 and a dimethylsulfoxide (DMSO) solvate of 2 (2-DMSO), has identified the presence of a range of intra- and intermolecular interactions including N-H⋯N, N-H⋯O=C and N-H⋯O=S(CH3)2 hydrogen-bonding interactions, C-H⋯π interactions and off-set, face-to-face stacking π-π interactions that support the variety of slipped stack, herringbone and cofacial crystal packing arrangements observed in 1-3. Additionally, the cytotoxicity of this series of aromatic oligoamides was assessed against two human ovarian (A2780 and A2780cisR), two human breast (MCF-7 and MDA-MB-231) cancerous cell lines and one non-malignant human epithelial cell line (PNT-2), to investigate the influence of the terminal functionality of these aromatic oligoamides on their biological activity. The chemosensitivity results highlight that modification of the terminal group from Ac to Boc in 1 and 2 leads to a 3-fold increase in antiproliferative activity against the cisplatin-sensitive ovarian carcinoma cell line, A2780. The presence of the amine termini in 3 gave the only member of the series to display activity against the cisplatin-resistance ovarian carcinoma cell line, A2780cisR. Compound 2 is the lead candidate of this series, displaying high selectivity towards A2780 cancer cells when compared to non-malignant PNT-2 cells, with a selectivity index value >4.2. Importantly, this compound is more selective towards A2780 (cf. PNT-2) than the clinical platinum drugs oxaliplatin by > 2.6-fold and carboplatin by > 1.6-fold.

N-Alkylated Aromatic Poly- and Oligoamides

N-alkylated aromatic poly- and oligoamides are a particular class of abiotic foldamers that is deprived of the capability of forming intramolecular hydrogen-bonding networks to stabilize their tri-dimensional structure. The alkylation of the backbone amide nitrogen atoms greatly increases the chemical diversity accessible for aromatic poly- and oligoamides. However, the nature and the conformational preferences of the N,N-disubstituted amides profoundly modify the folding properties of these aromatic poly- and oligoamides. In this Review, representative members of this class of aromatic poly- and oligoamides will be highlighted, among them N-alkylated phenylene terephthalamides, benzanilides, pyridylamides, and aminomethyl benzamide oligomers. The principal synthetic pathways to the main classes of N-alkylated aromatic polyamides with narrow to broad molecular-weight distribution, or oligoamides with specific sequences, will be detailed and their foldameric properties will be discussed. The Review will end by describing the few applications reported to date and future prospects for the field.

A new method for detecting intramolecular H-bonds of aromatic amides based on the de-shielding effect of carbonyl groups on β-protons

Aromatic amide foldamers with highly predictable conformations possess potential for application in the fields of stereoselective recognition, charge transport and catalysis, whose conformations are commonly limited by the intramolecular hydrogen bonding between amide groups and hydrogen-bonding receptors. Herein, on the basis of the de-shielding effect of carbonyl groups on β-protons, we develop a new method for detecting intramolecular hydrogen bonds of aromatic amide compounds. The solvent-related changes in the βH chemical shifts (Δ(δβH)) and NH chemical shifts (Δ(δNH)) of three kinds of amide compounds, which are frequently used as building blocks of aromatic amide foldamers, were recorded in chloroform, nitromethane, acetonitrile and DMSO. The Δ(δβH) method is found to be highly suitable for studying methoxy-benzamides and fluoro-benzamides in chloroform and DMSO. It is worth noting that a reference compound is not required for applying the Δ(δβH) method, which is an advantage over the Δ(δNH) method. In addition, we extend the Δ(δNH) method from methoxy-benzamides to pyridine-carboxamides and fluoro-benzamides in chloroform and DMSO, and propose that nitromethane and acetonitrile will be possible alternatives for the Δ(δNH) method if a test compound is not soluble in chloroform.

Natural and Synthetic Oligoarylamides: Privileged Structures for Medical Applications

The term "privileged structure" refers to a single molecular substructure or scaffold that can serve as a starting point for high-affinity ligands for more than one receptor type. In this report, a hitherto overlooked group of privileged substructures is addressed, namely aromatic oligoamides, for which there are natural models in the form of cystobactamids, albicidin, distamycin A, netropsin, and others. The aromatic and heteroaromatic core, together with a flexible selection of substituents, form conformationally well-defined scaffolds capable of specifically binding to conformationally well-defined regions of biomacromolecules such as helices in proteins or DNA often by acting as helices mimics themselves. As such, these aromatic oligoamides have already been employed to inhibit protein-protein and nucleic acid-protein interactions. This article is the first to bring together the scattered knowledge about aromatic oligoamides in connection with biomedical applications.

Site-specific single point mutation by anthranilic acid in hIAPP8-37 enhances anti-amyloidogenic activity

Amylin or hIAPP, together with insulin, plays a significant role in glucose metabolism. However, it undergoes β-sheet rich amyloid formation associated with pancreatic β-cell dysfunction leading to type-2 diabetes (T2D). Recent studies suggest that restricting β-sheet formation in it may halt amyloid formation, which may limit the risk for the disease. Several peptide-based inhibitors have been reported to prevent aggregation. However, most of them have limitations, including low binding efficiency, active only at higher doses, poor solubility, and proteolytic degradation. Insertion of non-coded amino acids renders proteolytically stable peptides. We incorporated a structurally rigid β-amino acid, Anthranilic acid (Ant), at different sites within the central hydrophobic region of hIAPP and developed two singly mutated hIAPP_8–37 peptidomimetics. These peptidomimetics inhibited the amyloid formation of hIAPP substantially even at low concentration, as evident from in vitro ThT, CD, FT-IR, TEM, and Congo red staining birefringence results. These peptidomimetics also disrupted the preformed aggregates formed by hIAPP into non-toxic species. These β-amino acid-based peptidomimetics can be an attractive scaffold for therapeutic design towards T2D or other protein misfolding diseases.

β-Amino acid based peptidomimetics are attractive scaffolds for therapeutics design towards T2D. They prevent amyloid formation of hIAPP by forming non-fibrillar non-toxic aggregates.

Synthesis and properties of helically-folded poly(arylenediethynylene)s

Three arylenediethnylene-based helical foldamers having pyridine, naphthaleneimide and pyrene cores show unique conformational changes and photophysical properties in various organic solvents.

Beyond Size Complementary Factors in Anion-Tetralactam Macrocycle Complexes: From Intrinsic Gas-Phase to Solvent-Predicted Stabilities

The gas-phase affinities of different types of anions X- (halogen anions, oxoanions, and hydrogenated anions) toward a model tetralactam-based macrocycle receptor (1), defined in terms of stability of an anion-receptor complex (1 + X-) against its disintegration, were evaluated by dissociation studies using a mass spectrometry-based methodology and supported by theoretical calculations (density functional theory-PBE0). The gas-phase complex with Cl- was found to be tailor-made for the macrocycle 1, while 1 + SA- (SA- = salicylate anion) and 1 + HSO4- were the weakest ones. Other complexes displayed a relatively low-stability dispersion (<1.2 kcal·mol-1). The 1/εr approach of the electrostatic contribution scaling method was used to predict the stability trends in a dimethyl sulfoxide solvent from the gas-phase binding energy partition using the symmetry-adapted perturbation theory. High deformation energy and differences in solvation energies were suggested to be the main sources of inconsistency in the predicted and experimental stabilities of 1 + F- and 1 + H2PO4- complexes.

Biomimetic and bioinspired molecular electrets. How to make them and why does the established peptide chemistry not always work?

“Biomimetic” and “bioinspired” define different aspects of the impacts that biology exerts on science and engineering. Biomimicking improves the understanding of how living systems work, and builds tools for bioinspired endeavors. Biological inspiration takes ideas from biology and implements them in unorthodox manners, exceeding what nature offers. Molecular electrets, i.e. systems with ordered electric dipoles, are key for advancing charge-transfer (CT) science and engineering. Protein helices and their biomimetic analogues, based on synthetic polypeptides, are the best-known molecular electrets. The inability of native polypeptide backbones to efficiently mediate long-range CT, however, limits their utility. Bioinspired molecular electrets based on anthranilamides can overcome the limitations of their biological and biomimetic counterparts. Polypeptide helices are easy to synthesize using established automated protocols. These protocols, however, fail to produce even short anthranilamide oligomers. For making anthranilamides, the residues are introduced as their nitrobenzoic-acid derivatives, and the oligomers are built from their C- to their N-termini via amide-coupling and nitro-reduction steps. The stringent requirements for these reduction and coupling steps pose non-trivial challenges, such as high selectivity, quantitative yields, and fast completion under mild conditions. Addressing these challenges will provide access to bioinspired molecular electrets essential for organic electronics and energy conversion.

Solvent-induced selectivity of Williamson etherification in the pursuit of amides resistant against oxidative degradation

This article reports two discoveries. (1) 2-Methoxyethanol induces unprecedented selectivity for etherification of 5-hydroxy-2-nitrobenzic acids without forming undesired esters. (2) Such compounds are precursors for amides showing unusual robustness against oxidative degradation, essential for molecular electrets that transfer strongly oxidizing holes at about −6.4 eV vs. vacuum.

Selective etherification produces precursors for amides resistant to oxidative degradation, i.e., showing reversible oxidation at 1.5 to 1.7 V vs. SCE.

Receptors for sulfate that function across a wide pH range in mixed aqueous-DMSO media

Water soluble squaramide macrocycles (MSQs) display high sulfate binding affinities in aqueous DMSO mixtures. The introduction of pyridine spacers into the macrocycles resulted in increased sulfate binding affinity in comparison to compounds with benzene spacers. [3]MSQ 6 was found to be a selective ligand for SO42- in highly competitive conditions and over a wide pH range (3.2-14).

Enantiocomplementary Chiral Polyhydroxyenoate: Chemoenzymatic Synthesis and Helical Structure Control

Here, we present the chemoenzymatic synthesis of two pairs of configuration-customized unsaturated chiral polyesters and discover that they are able to self-assemble into a helical superstructure. The chiral (R)- or (S)-polyesters with a polar unsaturated main-chain and an apolar side chain were designed to be stereoregular and amphiphilic-like. The solvent polarity, stereoregularity, unsaturated bond in the backbone and the structure of side chains were found to be the key factors to affect the self-assembly performance of the chiral polyesters. As the solvent polarity increased, the nanostructures of stereoregular unsaturated polyesters transformed from spheres to helical fibers, while there was no such transformation for the racemic or saturated polyesters.

Modification-Free Fabricating Ratiometric Nanoprobe Based on Dual-Emissive Carbon Dots for Nitrite Determination in Food Samples

Great challenges still exist for facilely fabricating ratiometric fluorescent nanoprobes. Fortunately, the appearance of dual-emissive carbon dots (CDs) offers a glimmer of hope for the fabrication of modification-free ratiometric nanoprobe. The chemical and electronic structure characteristics of the dual-emissive CDs might be modulated by conjugated structures of carbon sources and the doped nitrogen and sulfur atoms, and the surface state also contributed to the fluorescence properties via surface functional groups. Herein, we report a one-pot strategy for simultaneous preparation of two kinds of CDs named RYDE CDs and RODE CDs, showing dual-emissive fluorescent peaks with long wavelength by 2,3-diaminobenzoic acid hydrochloride for the first time. Notably, trace nitrite determination with high sensitivity and selectivity was realized for the first time based on the modification-free ratiometric fluorescent nanoprobe fabricated rapidly and directly by the as-prepared RYDE CDs at constant room temperature (20 °C). Under the optimal conditions, the limit of detection for nitrite was 31.61 nM, with a wide concentration linear range of 0.1-100 μM. Furthermore, this ratiometric nanoprobe was successfully applied for nitrite analysis in bacon, sausage, pickle, and milk samples. Additionally, the nanoprobe was also capable of visually monitoring temperature fluctuations and cell imaging.

Complex Molecules That Fold Like Proteins Can Emerge Spontaneously

Folding can bestow macromolecules with various properties, as evident from nature's proteins. Until now complex folded molecules are the product either of evolution or of an elaborate process of design and synthesis. We now show that molecules that fold in a well-defined architecture of substantial complexity can emerge autonomously and selectively from a simple precursor. Specifically, we have identified a self-synthesizing macrocyclic foldamer with a complex and unprecedented secondary and tertiary structure that constructs itself highly selectively from 15 identical peptide-nucleobase subunits, using a dynamic combinatorial chemistry approach. Folding of the structure drives its synthesis in 95% yield from a mixture of interconverting molecules of different ring sizes in a one-step process. Single-crystal X-ray crystallography and NMR reveal a folding pattern based on an intricate network of noncovalent interactions involving residues spaced apart widely in the linear sequence. These results establish dynamic combinatorial chemistry as a powerful approach to developing synthetic molecules with folding motifs of a complexity that goes well beyond that accessible with current design approaches. The fact that such molecules can form autonomously implies that they may have played a role in the origin of life at earlier stages than previously thought possible.

How Do Amides Affect the Electronic Properties of Pyrene?

The electronic properties of amide linkers, which are intricate components of biomolecules, offer a wealth of unexplored possibilities. Herein, we demonstrate how the different modes of attaching an amide to a pyrene chromophore affect the electrochemical and optical properties of the chromophore. Thus, although they cause minimal spectral shifts, amide substituents can improve either the electron-accepting or electron-donating capabilities of pyrene. Specifically, inversion of the amide orientation shifts the reduction potentials by 200 mV. These trends indicate that, although amides affect to a similar extent the energies of the ground and singlet excited states of pyrene, the effects on the doublet states of its radical ions are distinctly different. This behavior reflects the unusually strong orientation dependence of the resonance effects of amide substituents, which should extend to amide substituents on other types of chromophores in general. These results represent an example where the Hammett sigma constants fail to predict substituent effects on electrochemical properties. On the other hand, Swain-Lupton parameters are found to be in good agreement with the observed trends. Examination of the frontier orbitals of the pyrene derivatives and their components reveals the underlying reason for the observed amide effects on the electronic properties of this polycyclic aromatic hydrocarbon and points to key molecular-design strategies for electronic and energy-conversion systems.

Dipole-induced effects on charge transfer and charge transport. Why do molecular electrets matter?

Charge transfer (CT) and charge transport (CTr) are at the core of life-sustaining biological processes and of processes that govern the performance of electronic and energy-conversion devices. Electric fields are invaluable for guiding charge movement. Therefore, as electrostatic analogues of magnets, electrets have unexplored potential for generating local electric fields for accelerating desired CT processes and suppressing undesired ones. The notion about dipole-generated local fields affecting CT has evolved since the middle of the 20th century. In the 1990s, the first reports demonstrating the dipole effects on the kinetics of long-range electron transfer appeared. Concurrently, the development of molecular-level designs of electric junctions has led the exploration of dipole effects on CTr. Biomimetic molecular electrets such as polypeptide helices are often the dipole sources in CT systems. Conversely, surface-charge electrets and self-assembled monolayers of small polar conjugates are the preferred sources for modifying interfacial electric fields for controlling CTr. The multifaceted complexity of such effects on CT and CTr testifies for the challenges and the wealth of this field that still remains largely unexplored. This review outlines the basic concepts about dipole effects on CT and CTr, discusses their evolution, and provides accounts for their future developments and impacts.

Development of Self-Healing d-Gluconic Acetal-Based Supramolecular Ionogels for Potential Use as Smart Quasisolid Electrochemical Materials

Formation of supramolecular ionic liquid (IL) gels (ionogels) induced by low-molecular-mass gelators (LMMGs) is an efficient strategy to confine ILs, and the negligible influence of LMMGs on the electrochemical properties of ILs makes ionogels ideal quasisolid electrochemical materials. Furthermore, the stimuli-responsive and self-healing characters of the supramolecular gel can be utilized for the potential development of smart electrochemical materials. However, the poor mechanical properties of supramolecular ionogels reported so far limit their practical applications. Herein, we investigated a series of efficient d-gluconic acetal-based gelators (Gn, PG16, and B8) that can harden a wide variety of ILs at low concentrations. It was shown that both alkyl chain length and the number of hydrogen bonding sites of a certain gelator, as well as the nature of the IL anion, significantly influenced the gelation abilities. The resulting ionogels were thermally reversible, and most of them were stable at room temperature. Interestingly, a PG16-based supramolecular ionogel showed rapid self-healing properties upon mechanical damage. Furthermore, the PG16-based ionogel demonstrated unprecedented performances including the favorable ionic conductivity, excellent mechanical strength, and enhanced viscoelasticity, which make it a great self-healing electrochemical material. The ionogel formation mechanism was proposed based on the analysis of Fourier transform infrared, ¹HNMR, and X-ray diffraction, indicating that a combination of hydrogen bonding, π-π stacking, and interactions between alkyl chains was responsible for the self-assembly of gelators in ILs. Overall, our present studies on exploring the structure-property relationship of gelators for the formation of practically useful supramolecular ionogels shed light for future development of more functionalized ionogels.

Structural Tuning and Conformational Stability of Aromatic Oligoamide Foldamers

A series of aromatic oligoamide foldamers with two or three pyridine-2,6-dicarboxamide units as their main folding motifs and varying aromatic building blocks as linkers have been synthetized to study the effects of the structural variation on the folding properties and conformational stability. Crystallographic studies showed that in the solid state the central linker unit either elongates the helices and more open S-shaped conformations, compresses the helices to more compact conformations, or acts as a rigid spacer separating the pyridine-2,6-dicarboxamide units, which for their part add the predictability of the conformational properties. Multidimensional NMR studies showed that, even in solution, foldamers show conformational stability and folded conformations comparable to the solid-state structures.

Optimizing side chains for crystal growth from water: a case study of aromatic amide foldamers

The growth of crystals of aromatic compounds from water much depends on the nature of the water solubilizing functions that they carry. Rationalizing crystallization from water, and structure elucidation, of aromatic molecular and supramolecular systems is of general value across various fields of chemistry. Taking helical aromatic foldamers as a test case, we have validated several short polar side chains as efficient substituents to provide both solubility in, and crystal growth ability from, water. New 8-amino-2-quinolinecarboxylic acids bearing charged or neutral aminomethyl, carboxymethyl, sulfonic acid, or bis(hydroxymethyl)-methoxy side chains in position 4 or 5, were prepared on a multi gram scale. Fmoc protection of the main chain amine and suitable protections of the side chains ensured compatibility with solid phase synthesis. One tetrameric and five octameric oligoamides displaying these side chains were synthesized and shown to be soluble in water. In all cases but one, crystals were obtained using the hanging drop method, thus validating the initial design principle to combine polarity and rigidity. The only case that resisted crystallization appeared to be due to exceedingly high water solubility endowed by eight sulfonic acid functions. The neutral side chain did provide crystal growth ability from water but contributed poorly to solubility.

Spectroscopic, DFT, and XRD Studies of Hydrogen Bonds in N-Unsubstituted 2-Aminobenzamides

The structures of the mono- and the dihalogenated N-unsubstituted 2-aminobenzamides were characterized by means of the spectroscopic (¹H-NMR, UV-Vis, FT-IR, and FT-Raman) and X-ray crystallographic techniques complemented with a density functional theory (DFT) method. The hindered rotation of the C(O)-NH₂ single bond resulted in non-equivalence of the amide protons and therefore two distinct resonances of different chemical shift values in the ¹H-NMR spectra of these compounds were observed. 2-Amino-5-bromobenzamide (ABB) as a model confirmed the presence of strong intramolecular hydrogen bonds between oxygen and the amine hydrogen. However, intramolecular hydrogen bonding between the carbonyl oxygen and the amine protons was not observed in the solution phase due to a rapid exchange of these two protons with the solvent and fast rotation of the Ar-NH₂ single bond. XRD also revealed the ability of the amide unit of these compounds to function as a hydrogen bond donor and acceptor simultaneously to form strong intermolecular hydrogen bonding between oxygen of one molecule and the NH moiety of the amine or amide group of the other molecule and between the amine nitrogen and the amide hydrogen of different molecules. DFT calculations using the B3LYP/6-311++G(d,p) basis set revealed that the conformer (A) with oxygen and 2-amine on the same side predominates possibly due to the formation of a six-membered intramolecular ring, which is assisted by hydrogen bonding as observed in the single crystal XRD structure.

Foldamers in Medicinal Chemistry

Bio-inspired synthetic backbones leading to foldamers can provide effective biopolymer mimics with new and improved properties in a physiological environment, and in turn could serve as useful tools to study biology and lead to practical applications in the areas of diagnostics or therapeutics. Remarkable progress has been accomplished over the past 20 years with the discovery of many potent bioactive foldamers originating from diverse backbones and targeting a whole spectrum of bio(macro)molecules such as membranes, protein surfaces, and nucleic acids. These current achievements, future opportunities, and key challenges that remain are discussed in this article.

Supramolecular Helical Systems: Helical Assemblies of Small Molecules, Foldamers, and Polymers with Chiral Amplification and Their Functions

In this review, we describe the recent advances in supramolecular helical assemblies formed from chiral and achiral small molecules, oligomers (foldamers), and helical and nonhelical polymers from the viewpoints of their formations with unique chiral phenomena, such as amplification of chirality during the dynamic helically assembled processes, properties, and specific functionalities, some of which have not been observed in or achieved by biological systems. In addition, a brief historical overview of the helical assemblies of small molecules and remarkable progress in the synthesis of single-stranded and multistranded helical foldamers and polymers, their properties, structures, and functions, mainly since 2009, will also be described.

Polymeric Tubular Structures

Nature makes use of tubular structures for the spatial separation of matter on many different length scales, ranging from the nanometer scale (selective channels based on folded proteins) up to the centimeter scale (blood vessels). Today, polymer chemists and engineers can prepare polymeric tubular structures via a variety of different methods also covering many lengthscales, from nanometers to meters. The synthetic approaches described in this chapter vary significantly from the folding of single polymer chains via the self-assembly of DNA fragments to coordinative metal-organic nanotubes to tubes engineerd from bulk polymers using a range of porous or fibrous templates. While all examples reported in this chapter form tubular structures and thereby mimic their naturally occuring counterparts, it is mainly the engineered tubes that are more straightforward to prepare that also show some bio-inspired function.

Therapeutic Potential of Foldamers: From Chemical Biology Tools To Drug Candidates?

Over the past decade, foldamers have progressively emerged as useful architectures to mimic secondary structures of proteins. Peptidic foldamers, consisting of various amino acid based backbones, have been the most studied from a therapeutic perspective, while polyaromatic foldamers have barely evolved from their nascency and remain perplexing for medicinal chemists due to their poor drug-like nature. Despite these limitations, this compound class may still offer opportunities to study challenging targets or provide chemical biology tools. The potential of foldamer drug candidates reaching the clinic is still a stretch. Nevertheless, advances in the field have demonstrated their potential for the discovery of next generation therapeutics. In this perspective, the current knowledge of foldamers is reviewed in a drug discovery context. Recent advances in the early phases of drug discovery including hit finding, target validation, and optimization and molecular modeling are discussed. In addition, challenges and focus areas are debated and gaps highlighted.

Solid Phase Synthesis of Helically Folded Aromatic Oligoamides

Aromatic amide foldamers constitute a growing class of oligomers that adopt remarkably stable folded conformations. The folded structures possess largely predictable shapes and open the way toward the design of synthetic mimics of proteins. Important examples of aromatic amide foldamers include oligomers of 7- or 8-amino-2-quinoline carboxylic acid that have been shown to exist predominantly as well-defined helices, including when they are combined with α-amino acids to which they may impose their folding behavior. To rapidly iterate their synthesis, solid phase synthesis (SPS) protocols have been developed and optimized for overcoming synthetic difficulties inherent to these backbones such as low nucleophilicity of amine groups on electron poor aromatic rings and a strong propensity of even short sequences to fold on the solid phase during synthesis. For example, acid chloride activation and the use of microwaves are required to bring coupling at aromatic amines to completion. Here, we report detailed SPS protocols for the rapid production of: (1) oligomers of 8-amino-2-quinolinecarboxylic acid; (2) oligomers containing 7-amino-8-fluoro-2-quinolinecarboxylic acid; and (3) heteromeric oligomers of 8-amino-2-quinolinecarboxylic acid and α-amino acids. SPS brings the advantage to quickly produce sequences having varied main chain or side chain components without having to purify multiple intermediates as in solution phase synthesis. With these protocols, an octamer could easily be synthesized and purified within one to two weeks from Fmoc protected amino acid monomer precursors.

Structural and morphological diversity of self-assembled synthetic γ-amino acid containing peptides

We report the synthesis of constrained amino acid building block gabapentin (Gpn) based hybrid peptides and their structural and morphological diversity in different conditions.

Synthesis and complexing properties of cyclic benzylopeptoids – a new family of extended macrocyclic peptoids

Members of a new class of cyclic “extended” peptoids (the “benzylopeptoids”) efficiently capture sodium ions with different stoichiometries depending on the ring morphology.