Interconversion of single and double helices formed from synthetic molecular strands

Selective Duplex Formation in Mixed Sequence Libraries of Synthetic Polymers

Recognition-encoded melamine oligomers (REMO) are synthetic polymers that feature an alternating 1,3,5-triazine-piperazine backbone and side-chains equipped with either a phenol or phosphine oxide recognition unit. An automated method for the solid-phase synthesis (SPS) of REMO of any specified sequence has been developed starting from dichlorotriazine monomer building blocks. Complementary homo-oligomers with either six phenols or six phosphine oxides were synthesized and shown to form a stable duplex in nonpolar solvents by NMR denaturation experiments. The duplex was covalently trapped by equipping the ends of the oligomers with an azide and an alkyne group and using a copper-catalyzed alkyne-azide cycloaddition (CuAAC) reaction. The SPS methodology was adapted to synthesize mixed sequence libraries by using a mixture of two different dichlorotriazine building blocks in each coupling cycle of an oligomer synthesis. The resulting libraries contain statistical mixtures of all possible sequences. The self-assembly properties of these libraries were screened by using the CuAAC reaction to trap any duplexes present. In mixed sequence libraries of 6-mers, the trapping experiments showed that only sequence-complementary oligomers formed duplexes at micromolar concentrations in dichloromethane. The automated synthesis approach developed here provides access to large libraries of mixed sequence synthetic polymers, and the covalent trapping experiment provides a convenient tool for screening functional properties of mixtures. The results suggest high-fidelity sequence-selective duplex formation in mixtures of 6-mer sequences of the REMO architecture.

Encoding ordered structural complexity to covalent organic frameworks

Installing different chemical entities onto crystalline frameworks with well-defined spatial distributions represents a viable approach to achieve ordered and complex synthetic materials. Herein, a covalent organic framework (COF-305) is constructed from tetrakis(4-aminophenyl)methane and 2,3-dimethoxyterephthalaldehyde, which has the largest unit cell and asymmetric unit among known COFs. The ordered complexity of COF-305 is embodied by nine different stereoisomers of its constituents showing specific sequences on topologically equivalent sites, which can be attributed to its building blocks deviating from their intrinsically preferred simple packing geometries in their molecular crystals to adapt to the framework formation. The insight provided by COF-305 supplements the principle of covalent reticular design from the perspective of non-covalent interactions and opens opportunities for pursuing complex chemical sequences in molecular frameworks.

Highly Luminescent Chiral Double π-Helical Nanoribbons

Unveiling the mechanism behind chirality propagation and dissymmetry amplification at the molecular level is of significance for the development of chiral systems with comprehensively outstanding chiroptical performances. Herein, we have presented a straightforward Cu-mediated Ullmann homocoupling approach to synthesize perylene diimide-entwined double π-helical nanoribbons encompassing dimer, trimer, and tetramer while producing homochiral or heterochiral linking of chiral centers. A significant dissymmetry amplification was achieved, with absorption dissymmetry factors (|gabs|) increasing from 0.009 to 0.017 and further to 0.019, and luminescence dissymmetry factors (|glum|) rising from 0.007 to 0.013 and eventually to 0.015 for homochiral double π-helical oligomers. The disparity of magnetic transition dipole moment (m) densities in homochiral and heterochiral tetramers by time-dependent density functional theory calculations confirmed that homochiral oligomerization can maximize the total m, which is favorable for achieving ever-increasing g factors. Notably, these double π-helices exhibited exceptional photoluminescence quantum yields (ΦPL) ranging from 83 to 95%. The circularly polarized luminescence brightness (BCPL) eventually reached a remarkable 575 M-1 cm-1 for the homochiral tetramer, which is among the highest values reported for chiral small molecules. This kind of linearly extended double π-helices offers a platform for a comprehensive understanding of the mechanism behind chirality propagation and dissymmetry amplification.

Preparative and Catalytic Properties of MoVI Mononuclear and Metallosupramolecular Coordination Assemblies Bearing Hydrazonato Ligands

A series of polynuclear, dinuclear, and mononuclear Mo(VI) complexes were synthesized with the hydrazonato ligands derived from 5-methoxysalicylaldehyde and the corresponding hydrazides (isonicotinic hydrazide (H2L1), nicotinic hydrazide (H2L2), 2-aminobenzhydrazide (H2L3), or 4-aminobenzhydrazide (H2L4)). The metallosupramolecular compounds obtained from non-coordinating solvents, [MoO2(L1,2)]n (1 and 2) and [MoO2(L3,4)]2 (3 and 4), formed infinite structures and metallacycles, respectively. By blocking two coordination sites with cis-dioxo ligands, the molybdenum centers have three coordination sites occupied by the ONO donor atoms from the rigid hydrazone ligands and one by the N atom of pyridyl or amine-functionalized ligand subcomponents from the neighboring Mo building units. The reaction in methanol afforded the mononuclear analogs [MoO2(L1-4)(MeOH)] (1a-4a) with additional monodentate MeOH ligands. All isolated complexes were tested as catalysts for cyclooctene epoxidation using tert-butyl hydroperoxide (TBHP) as an oxidant in water. The impact of the structure and ligand lability on the catalytic efficiency in homogeneous cyclooctene epoxidation was elucidated based on theoretical considerations. Thus, dinuclear assemblies exhibited better catalytic activity than mononuclear or polynuclear complexes.

Design of Chiral β-Double Helices from γ-Peptide Foldamers

Chirality is ubiquitous in nature, and homochirality is manifested in many biomolecules. Although β-double helices are rare in peptides and proteins, they consist of alternating L- and D-amino acids. No peptide double helices with homochiral amino acids have been observed. Here, we report chiral β-double helices constructed from γ-peptides consisting of alternating achiral (E)-α,β-unsaturated 4,4-dimethyl γ-amino acids and chiral (E)-α,β-unsaturated γ-amino acids in both single crystals and in solution. The two independent strands of the same peptide intertwine to form a β-double helix structure, and it is stabilized by inter-strand hydrogen bonds. The peptides with chiral (E)-α,β-unsaturated γ-amino acids derived from α-L-amino acids adopt a (P)-β-double helix, whereas peptides consisting of (E)-α,β-unsaturated γ-amino acids derived from α-D-amino acids adopt an (M)-β-double helix conformation. The circular dichroism (CD) signature of the (P) and (M)-β-double helices and the stability of these peptides at higher temperatures were examined. Furthermore, ion transport studies suggested that these peptides transport ions across membranes. Even though the structural analogy suggests that these new β-double helices are structurally different from those of the α-peptide β-double helices, they retain ion transport activity. The results reported here may open new avenues in the design of functional foldamers.

Selective chiral dimerization and folding driven by arene-perfluoroarene force

Oligomerization and folding of chiral compounds afford diversified chiral molecular architectures with interesting chiroptical properties, but their rational and precise control remain poorly understood. In this work, we employed arene-perfluoroarene (AP) interaction to manipulate the folding and dimerization of alanine derivatives bearing pyrene and a perfluoronaphthalene derivative. Based on X-ray crystallography and nuclear magnetic resonance, the compound with a smaller tether and high skeleton rigidity self-assembled into double helical dimers by duplex hydrogen bonding and AP forces in a less polar solvent. Reversible disassociation occurred upon switching to a dipolar solvent or applying heating-cooling cycles. In comparison, the compound with increased skeleton flexibility folds into chiral molecular clamps in a less polar solvent, and is transformed into planar dimers upon switching to a polar solvent. The dynamic geometrical transformation between dimerization and folding was accompanied by chiroptical switching. Beyond the molecular and supramolecular level, we showed hierarchy control in the self-assembled nanoarchitectures and columnar and lamellar arrangements of their molecular packing. This work utilized AP forces to prepare and manipulate the chiral architectures at different hierarchical levels, enriching methodologies in precise chiral synthetic chemistry.

High-Affinity Hybridization of Complementary Aromatic Oligoamide Strands in Water

We prepared a series of water-soluble aromatic oligoamide sequences all composed of a segment prone to form a single helix and a segment prone to dimerize into a double helix. These sequences exclusively assemble as antiparallel duplexes. The modification of the duplex inner rim by varying the nature of the substituents borne by the aromatic monomers allowed us to identify sequences that can hybridize by combining two chemically different strands, with high affinity and complete selectivity in water. X-ray crystallography confirmed the expected antiparallel configuration of the duplexes whereas NMR spectroscopy and mass spectrometry allowed us to assess precisely the extent of the hybridization. The hybridization kinetics of the aromatic strands was shown to depend on both the nature of the substituents responsible for strand complementarity and the length of the aromatic strand. These results highlight the great potential of aromatic hetero-duplex as a tool to construct non-symmetrical dynamic supramolecular assemblies.

Herringbone Helical Foldamers from Aromatic Ether Derived ϵ-Amino Acid Peptides

Oligomers based on an aromatic ether derived ϵ-amino acid peptides folded into herringbone helical structures, induced by successive NH-O-NH & O-NH-O bifurcated hydrogen bonding interactions and reinforced by π-π stacking between aryls from adjacent layers. The diaryl ether bonds -O- worked both as structural units to provide turn motifs for changing the amplitude of the slope along the axis of helix for herringbone formation, and also as acceptors for hydrogen bonding. Attachment of a single chiral carbon to the C-termini of the peptides induced excess of single-handed screw sense and amplification through the chain propagation as exemplified by chain length dependent circular dichroism (CD) investigations.

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.

Sulfur-Containing Foldamer-Based Artificial Lithium Channels

Unlike many other biologically relevant ions (Na+ , K+ , Ca2+ , Cl- , etc) and protons, whose cellular concentrations are closely regulated by highly selective channel proteins, Li+ ion is unusual in that its concentration is well tolerated over many orders of magnitude and that no lithium-specific channel proteins have so far been identified. While one naturally evolved primary pathway for Li+ ions to traverse across the cell membrane is through sodium channels by competing with Na+ ions, highly sought-after artificial lithium-transporting channels remain a major challenge to develop. Here we show that sulfur-containing organic nanotubes derived from intramolecularly H-bonded helically folded aromatic foldamers of 3.6 Å in hollow cavity diameter could facilitate highly selective and efficient transmembrane transport of Li+ ions, with high transport selectivity factors of 15.3 and 19.9 over Na+ and K+ ions, respectively.

Fractal Design of Hierarchical PtPd with Enhanced Exposed Surface Atoms for Highly Catalytic Activity and Stability

Hierarchical assembly of arc-like fractal nanostructures not only has its unique self-similarity feature for stability enhancement but also possesses the structural advantages of highly exposed surface-active sites for activity enhancement, remaining a great challenge for high-performance metallic nanocatalyst design. Herein, we report a facile strategy to synthesize a novel arc-like hierarchical fractal structure of PtPd bimetallic nanoparticles (h-PtPd) by using pyridinium-type ionic liquids as the structure-directing agent. Growth mechanisms of the arc-like nanostructured PtPd nanoparticles have been fully studied, and precise control of the particle sizes and pore sizes has been achieved. Due to the structural features, such as size control by self-similarity growth of subunits, structural stability by nanofusion of subunits, and increased numbers of exposed active atoms by the curved homoepitaxial growth, h-PtPd displays outstanding electrocatalytic activity toward oxygen reduction reaction and excellent stability during hydrothermal treatment and catalytic process.

One-Pot Cyclization to Large Peptidomimetic Macrocycles by In Situ-Generated β-Turn-Enforced Folding

Macrocycles have been targets of extensive synthetic efforts for decades because of their potent molecular recognition and self-assembly capabilities. Yet, efficient syntheses of macrocyclic molecules via irreversible covalent bonds remain challenging. Here, we report an efficient approach to large peptidomimetic macrocycles by using the in situ-generated β-turn structural motifs afforded in the amidothiourea moieties from the early steps of the reaction of 2 molecules of bilateral amino acid-based acylhydrazine with 2 molecules of diisothiocyanate. Four chiral and achiral peptidomimetic large macrocycles were successfully synthesized in high yields of 45-63% in a feasible one-pot reaction under sub-molar concentration conditions and were purified by simple filtration. X-ray crystallographic characterization of three macrocycles reveals an important feature that their four β-turn structures, each maintained by four 10-membered intramolecular hydrogen bonds, alternatively network the four aromatic arms. This affords an interesting conformation switching mode upon anion binding. Binding of SO₄^2- to 1L or 1D that contains 4 alanine residues (with the lowest steric hinderance among the macrocycles) leads to an inside-out structural change of the host macrocycle, as confirmed by the X-ray crystal structure of 1L-SO₄^2- and 1D-SO₄^2- complexes, accompanied by an inversion of the CD signals. On the basis of the strong sulfate affinity of the macrocycles, we succeeded in the removal of sulfate anions from water via a macrocycle-mediated liquid-liquid extraction method. Our synthetic protocol can be easily extended to other macrocycles of varying arms and/or chiral amino acid residues; thus, a variety of structurally and functionally diverse macrocycles are expected to be readily made.

Recognition-Encoded Synthetic Information Molecules

ConspectusNucleic acids represent a unique class of highly programmable molecules, where the sequence of monomer units incorporated into the polymer chain can be read through duplex formation with a complementary oligomer. It should be possible to encode information in synthetic oligomers as a sequence of different monomer units in the same way that the four different bases program information into DNA and RNA. In this Account, we describe our efforts to develop synthetic duplex-forming oligomers composed of sequences of two complementary recognition units that can base-pair in organic solvents through formation of a single H-bond, and we outline some general guidelines for the design of new sequence-selective recognition systems.The design strategy has focused on three interchangeable modules that control recognition, synthesis, and backbone geometry. For a single H-bond to be effective as a base-pairing interaction, very polar recognition units, such as phosphine oxide and phenol, are required. Reliable base-pairing in organic solvents requires a nonpolar backbone, so that the only polar functional groups present are the donor and acceptor sites on the two recognition units. This criterion limits the range of functional groups that can be produced in the synthesis of oligomers. In addition, the chemistry used for polymerization should be orthogonal to the recognition units. Several compatible high yielding coupling chemistries that are suitable for the synthesis of recognition-encoded polymers are explored. Finally, the conformational properties of the backbone module play an important role in determining the supramolecular assembly pathways that are accessible to mixed sequence oligomers.Almost all complementary homo-oligomers will form duplexes provided the product of the association constant for formation of a base-pair and the effective molarity for the intramolecular base-pairing interactions that zip up the duplex is significantly greater than one. For these systems, the structure of the backbone does not play a major role, and the effective molarities for duplex formation tend to fall in the range 10-100 mM for both rigid and flexible backbones. For mixed sequences, intramolecular H-bonding interactions lead to folding. The competition between folding and duplex formation depends critically on the conformational properties of the backbone, and high-fidelity sequence-selective duplex formation is only observed for backbones that are sufficiently rigid to prevent short-range folding between bases that are close in sequence. The final section of the Account highlights the prospects for functional properties, other than duplex formation, that might be encoded with sequence.

Early-Stage Oligomerization of Prion-like Polypeptides Reveals the Molecular Mechanism of Amyloid-Disrupting Capacity by Proline Residues

Proline cis/trans isomerization governs protein local conformational changes via its local mechanical rigidity. The amyloid-disrupting capacity of proline is widely acknowledged; however, the molecular mechanism is still not clear. To understand how proline residues in polypeptide chains influence amyloid propensity, we study several truncated sequences of the TDP-43 C-terminal region (287-322) and their triple proline variants (308PPP310). We use coarse-grained molecular simulation to study the time evolution of the process of aggregation in the early stages in an effective high-concentration condition (∼25 mM). This ensures the long time scales for protein association at laboratory concentrations. We use several experimentally determined structure templates as initial structures of monomer conformations. We carry out oligomer size analysis and cluster analysis, along with several structural measures, to characterize the size distributions of oligomers and their morphological/structural properties. We show that average oligomer size is not a good indicator of amyloid propensity. Structural order and/or morphological properties are better alternatives. We show that proline variants can efficiently maintain the formation of large "ordered" oligomers of shorter truncated sequences, i.e., 307-322. This "order" maintenance is weakened when using longer truncated sequences (i.e., 287-322), leading to the formation of "disordered" oligomers. From an energy trade-off perspective, if the entropic effect is weak (short sequence length), the shape-complementarity of proline variants effectively guides the oligomerization process to form "ordered" oligomer intermediates. This leads to a distinct aggregation pathway that promotes amyloid formation (on-pathway). Strong entropic effects (long sequence length), however, would cause the formation of "disordered" oligomers. This in turn will suppress amyloid formation (off-pathway). The proline shape-complementary effects provide a guided morphological restraint to facilitate the pathways of amyloid formation. Our study supports the importance of structure-based kinetic heterogeneity of prion-like sequence fragments in driving different aggregation pathways. This work sheds light on the role of morphological and structural order of early-stage oligomeric species in regulating amyloid-disrupting capacity by prolines.

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.

Double helices of dissymmetrical α,α'-disubstituted tripyrrins

Dissymmetrical α,α'-disubstituted tripyrrins have been prepared using a modified synthetic protocol. Tripyrrin 2a bearing 3,5-bis(trifluoromethyl)phenyl and 4-methoxyphenyl moieties showed an anti-type dimer arrangement in the solid state. In contrast, syn-type dimers were observed for tripyrrin 2b bearing 3,5-bis(trifluoromethyl)phenyl and 3,5-di-t-butylphenyl moieties. In addition, proton-exchange NH tautomerization was observed in 2b.

Synthesis of Synthetic Musks: A Theoretical Study Based on the Relationships between Structure and Properties at Molecular Scale

Synthetic musks (SMs), as an indispensable odor additive, are widely used in various personal care products. However, due to their physico-chemical properties, SMs were detected in various environmental media, even in samples from arctic regions, leading to severe threats to human health (e.g., abortion risk). Environmentally friendly and functionally improved SMs have been theoretically designed in previous studies. However, the synthesizability of these derivatives has barely been proven. Thus, this study developed a method to verify the synthesizability of previously designed SM derivatives using machine learning, 2D-QSAR, 3D-QSAR, and high-throughput density functional theory in order to screen for synthesizable, high-performance (odor sensitivity), and environmentally friendly SM derivatives. In this study, three SM derivatives (i.e., D52, D37, and D25) were screened and recommended due to their good performances (i.e., high synthesizability and odor sensitivity; low abortion risk; and bioaccumulation ability in skin keratin). In addition, the synthesizability mechanism of SM derivatives was also analyzed. Results revealed that high intramolecular hydrogen bond strength, electrostatic interaction, qH⁺ value, energy gap, and low E_HOMO would lead to a higher synthesizability of SMs and their derivatives. This study broke the synthesizability bottleneck of theoretically designed environment-friendly SM derivatives and advanced the mechanism of screening functional derivatives.

Macromolecular Information Transfer

Macromolecular information transfer can be defined as the process by which a coded monomer sequence is communicated from one macromolecule to another. In such a transfer process, the information sequence can be kept identical, transformed into a complementary sequence or even translated into a different molecular language. Such mechanisms are crucial in biology and take place in DNA→DNA replication, DNA→RNA transcription and RNA→protein translation. In fact, there would be no life on Earth without macromolecular information transfer. Mimicking such processes with synthetic macromolecules would also be of major scientific relevance because it would open up new avenues for technological applications (e.g. data storage and processing) but also for the creation of artificial life. In this important context, this minireview summarizes recent research about information transfer in synthetic oligomers and polymers. Medium- and long-term perspectives are also discussed.

Polymer-like Inorganic Double Helical van der Waals Semiconductor

In high-performance flexible and stretchable electronic devices, conventional inorganic semiconductors made of rigid and brittle materials typically need to be configured into geometrically deformable formats and integrated with elastomeric substrates, which leads to challenges in scaling down device dimensions and complexities in device fabrication and integration. Here we report the extraordinary mechanical properties of the newly discovered inorganic double helical semiconductor tin indium phosphate. This spiral-shape double helical crystal shows the lowest Young's modulus (13.6 GPa) among all known stable inorganic materials. The large elastic (>27%) and plastic (>60%) bending strains are also observed and attributed to the easy slippage between neighboring double helices that are coupled through van der Waals interactions, leading to the high flexibility and deformability among known semiconducting materials. The results advance the fundamental understanding of the unique polymer-like mechanical properties and lay the foundation for their potential applications in flexible electronics and nanomechanics disciplines.

Formation of supramolecular channels by reversible unwinding-rewinding of bis(indole) double helix via ion coordination

Stimulus-responsive reversible transformation between two structural conformers is an essential process in many biological systems. An example of such a process is the conversion of amyloid-β peptide into β-sheet-rich oligomers, which leads to the accumulation of insoluble amyloid in the brain, in Alzheimer's disease. To reverse this unique structural shift and prevent amyloid accumulation, β-sheet breakers are used. Herein, we report a series of bis(indole)-based biofunctional molecules, which form a stable double helix structure in the solid and solution state. In presence of chloride anion, the double helical structure unwinds to form an anion-coordinated supramolecular polymeric channel, which in turn rewinds upon the addition of Ag⁺ salts. Moreover, the formation of the anion-induced supramolecular ion channel results in efficient ion transport across lipid bilayer membranes with excellent chloride selectivity. This work demonstrates anion-cation-assisted stimulus-responsive unwinding and rewinding of artificial double-helix systems, paving way for smart materials with better biomedical applications.

Hydrogen-bonded aromatic amide macrocycles: synthesis, properties and functions

As a classic example of nearly planar cyclic compounds, hydrogen-bonded aromatic amide (H-bonded aramide) macrocycles, consisting of consecutive intramolecular hydrogen bonds and aromatic residues, receive considerable research attention due to their rich host-guest chemistry. This review provides a detailed summary of the synthesis, properties and functions of H-bonded aramide macrocycles and their derivatives. Herein, the constitutional patterns of these macrocycles are divided into two subcategories: interior hydrogen bonding motifs and exterior hydrogen bonding motifs. Based on these two motifs, we summarize the facile synthesis, self-assembly, host-guest interaction complexation of H-bonded aramide macrocycles and the resulting applications such as molecular recognition, artificial ion channels, soft materials, supramolecular catalysis, and artificial molecular machines. The development of H-bonded aramide macrocycles is still in its infancy, although a considerable number of examples have been reported. We hope that this review will provide useful information and unlock new opportunities in this field.

Cavity-containing aromatic oligoamide foldamers and macrocycles: progress and future perspectives

As a major class of foldamers, aromatic oligoamide foldamers have attracted intense interest. The rigidity of aromatic residues and amide linkages allows the development of foldamers with readily predictable, stable conformations. Aromatic oligoamide foldamers having backbones fully constrained by intramolecular hydrogen bonds have attracted wide attention. Depending on their lengths, such foldamers adopt crescent or helical conformations with highly negative inner cavities. Cyclizing the backbone of the aromatic oligoamides affords the corresponding macrocycles which are characterised by persistent shapes and non-deformable inner cavities. With their defined, inner cavities, such aromatic oligoamide foldamers and macrocycles have served as hosts for cationic and polar guests, and as transmembrane channels for transporting ions and molecules. Recent synthetic progress resulted in the construction of multi-turn hollow helices that offer three-dimensional inner pores with adjustable depth. Reducing the number of backbone-constraining hydrogen bonds leads to oligoamides which, with their partially constrained backbones, undergo either solvent- or guest-dependent folding. One class of such aromatic olgioamide foldamders, which offer multiple backbone amide NH groups as hydrogen-bond donors, are designed to bind anions with adjustable affinities.

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.

Residue-based program of a β-peptoid twisted strand shape via a cyclopentane constraint

N-Substituted peptides, such as peptoids and β-peptoids, have been reported to have unique structures with diverse functions, like catalysis and manipulation of biomolecular functions. Recently, the preorganization of monomer shape by restricting bond rotations about all backbone dihedral angles has been demonstrated to be useful for de novo design of peptoid structures. Such design strategies are hitherto unexplored for β-peptoids; to date, no preorganized β-peptoid monomers have been reported. Here, we report the first design strategy for β-peptoids, in which all four backbone dihedral angles (ω, ϕ, θ, ψ) are rotationally restricted on a per-residue basis. The introduction of a cyclopentane constraint realized the preorganized monomer structure and led to a β-peptoid with a stable twisted strand shape.

Boosting Circularly Polarized Luminescence Performance by a Double π-Helix and Heteroannulation

Design challenges in the development of circularly polarized luminescence (CPL) materials are focused on balancing the luminescence dissymmetry factor (g_lum) and photoluminescence quantum yield (Φ_PL) by regulating the electric (μ) and magnetic (m) transition dipole moment vectors. Aiming at designing efficient CPL emitters and clarifying the chiroptical variation mechanism, herein, we present a double π-helix based on a cyclooctatetraene-embedded perylene diimide dimer that combines chirality with molecular entanglement and very high barriers for racemization. Through finely regulating the magnitudes of μ and m, the maximal dissymmetry factors |g_abs| and |g_lum| can be boosted to 0.035 and 0.030, respectively, as revealed by circular dichroism (CD) and CPL spectra. The results indicate a 3-fold improvement of g values and a modulated Φ_PL from 1a, 4, to 5 by nitrogen heteroannulation at the bay region. The CPL brightness (B_CPL) of 5 reaches a recorded value of up to 573.4 M^-1 cm^-1, among the highest values of chiral small molecules reported so far. This work has provided a comprehensive insight into a new class of chiral materials with high CPL activities, further laying molecular fundamentals for chiral optoelectronics.

Substituent Effects at the 5,10-Positions of Dianilinotripyrrins on Their Dimerization Themodynamics

Control of the association behavior by the molecular design is one of the most essential benefits in artificial supramolecular systems. 1,14-Dianilinotripyrrin has recently emerged as a novel conjugated molecule which forms a double helix in non-polar solvents with the aid of multiple interstrand hydrogen bonding interactions. In this work, we investigated the substituent effects at the 5,10-positions of tripyrrin on their association thermodynamics. This study illuminated two key findings; 1) electronic tuning by the para-substituents reduce the entropic costs thereby slightly improve the association constants, and 2) ortho-substituents force the tripyrrin core to be relatively planar, which significantly decrease the association constant due to less feasible π-stacking.

Structural Basis of Pyridostatin and Its Derivatives Specifically Binding to G-Quadruplexes

The nucleic acid G-quadruplex (G4) has emerged as a promising therapeutic target for a variety of diseases such as cancer and neurodegenerative disease. Among small-molecule G4-binders, pyridostatin (PDS) and its derivatives (e.g., PyPDS) exhibit high specificity to G4s, but the structural basis for their specific recognition of G4s remains unknown. Here, we presented two solution structures of PyPDS and PDS with a quadruplex-duplex hybrid. The structures indicate that the rigid aromatic rings of PyPDS/PDS linked by flexible amide bonds match adaptively with G-tetrad planes, enhancing π-π stacking and achieving specific recognition of G4s. The aliphatic amine side chains of PyPDS/PDS adjust conformation to interact with the phosphate backbone via hydrogen bonding and electrostatic interactions, increasing affinity for G4s. Moreover, the N-H of PyPDS/PDS amide bonds interacts with two O₆s of G-tetrad guanines via hydrogen bonding, achieving a further increase in affinity for G4s, which is different from most G4 ligands. Our findings reveal from structural perspectives that the rational assembly of rigid and flexible structural units in a ligand can synergistically improve the selectivity and affinity for G4s through spatial selective and adaptive matching.

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.

Forming a Double-Helix Phase of Single Polymer Chains by the Cooperation between Local Structure and Nonlocal Attraction

Double-helix structures, such as DNA, are formed in nature to realize many unique functions. Inspired by this, researchers are pursuing strategies to design such structures from polymers. A key question is whether the double helix can be formed from the self-folding of a single polymer chain without specific interactions. Here, using Langevin dynamics simulation and theoretical analysis, we find that a stable double-helix phase can be achieved by the self-folding of single semiflexible polymers as a result of the cooperation between local structure and nonlocal attraction. The critical temperature of double-helix formation approximately follows T^{cri}∼ln(k_{θ}) and T^{cri}∼ln(k_{τ}), where k_{θ} and k_{τ} are the polymer bending and torsion stiffness, respectively. Furthermore, the double helix can exhibit major and minor grooves due to symmetric break for better packing. Our results provide a novel guide to the experimental design of the double helix.

Anion-coordination-driven single-double helix switching and chiroptical molecular switching based on oligoureas

Synthetic foldamers with helical conformation are widely seen, but controllable interconversion amongst different geometries (helical structure and sense) is challenging. Here, a family of oligourea (tetra-, penta-, and hexa-) ligands bearing stereocenters at both ends are designed and shown to switch between single and double helices with concomitant inversion of helical senses upon anion coordination. The tetraurea ligand forms a right-handed single helix upon chloride anion (Cl-) binding and is converted into a left-handed double helix when phosphate anion (PO4 3-) is coordinated. The helical senses of the single and double helices are opposite, and the conversion is further found to be dependent on the stoichiometry of the ligand and phosphate anion. In contrast, only a single helix is formed for the hexaurea ligand with the phosphate anion. This distinction is attributed to the fact that the characteristic phosphate anion coordination geometry is satisfied by six urea moieties with twelve H-bonds. Our study revealed unusual single-double helix interconversion accompanied by unexpected chiroptical switching of helical senses.

Mesogenic discrete metallofoldamer for columnar liquid crystal

A mesogenic metallofoldamer [(1_R,R-Ni)₂Pd] exhibits thermotropic columnar liquid crystalline properties. The metallofoldamer was prepared from two homochiral crescent-shaped precursors having β-diketonate ligands (1_R,R-Ni) through bridging by metal complexation; it exhibited a single helicity owing to the overlapping of both ends. The precursor and metallofoldamer formed similar hexagonal columnar phases. The helical metallofoldamer exhibited the hexagonal columnar phase at the higher temperature range owing to its rigid helical mesogenic structure.

Molecular Co-assembly of Two Building Blocks Harnesses Both Their Attributes into a Functional Supramolecular Hydrogel

Engineering ordered nanostructures through molecular self-assembly of simple building blocks constitutes the essence of modern nanotechnology to develop functional supramolecular biomaterials. However, the lack of adequate chemical and functional diversity often hinders the utilization of unimolecular self-assemblies for practical applications. Co-assembly of two different building blocks could essentially harness both of their attributes and produce nanostructured macro-scale objects with improved physical properties and desired functional complexity. Herein, we report the co-operative co-assembly of a modified amino acid, fluorenylmethoxycarbonyl-pentafluoro-Phenylalanine (Fmoc-F₅ -Phe), and a peptide, Fmoc-Lys(Fmoc)-Arg-Gly-Asp [Fmoc-K(Fmoc)-RGD] into a functional supramolecular hydrogel. A change in the morphology and fluorescence emission, as well as improvement of the mechanical properties in the mixed hydrogels compared to the pristine hydrogels, demonstrate the signature of co-operative co-assembly mechanism. Intriguingly, this approach harnesses the advantages of both components in a synergistic way, resulting in a single homogeneous biomaterial possessing the antimicrobial property of Fmoc-F₅ -Phe and the biocompatibility and cell adhesive characteristics of Fmoc-K(Fmoc)-RGD. This work exemplifies the importance of the co-assembly process in nanotechnology and lays the foundation for future developments in supramolecular chemistry by harnessing the advantages of diverse functional building blocks into a mechanically stable functional biomaterial. This article is protected by copyright. All rights reserved.

Significant photodegradation of carcinogenic organic dyes by a 1D supramolecular heteroleptic Cu(ii) complex under sunlight irradiation

The crucial role of supramolecular interactions in the self-assembly and architecture of the heteroleptic Cu(II) coordination polymer has been investigated and its ability to degrade organic molecules using sunlight.

Folding of aromatic polyamides into a rare intrachain β-sheet type structure and further reinforcement of the secondary structure through host–guest interactions

We report the design, synthesis, and folding of aromatic polyamides into an intrachain β-sheet-like structure. Additionally, the effect of a guest molecule in stabilizing the β-sheet structure has also been demonstrated here.

Spiers Memorial Lecture: Analysis and de novo design of membrane-interactive peptides

Membrane-peptide interactions play critical roles in many cellular and organismic functions, including protection from infection, remodeling of membranes, signaling, and ion transport. Peptides interact with membranes in a variety of ways: some associate with membrane surfaces in either intrinsically disordered conformations or well-defined secondary structures. Peptides with sufficient hydrophobicity can also insert vertically as transmembrane monomers, and many associate further into membrane-spanning helical bundles. Indeed, some peptides progress through each of these stages in the process of forming oligomeric bundles. In each case, the structure of the peptide and the membrane represent a delicate balance between peptide-membrane and peptide-peptide interactions. We will review this literature from the perspective of several biologically important systems, including antimicrobial peptides and their mimics, α-synuclein, receptor tyrosine kinases, and ion channels. We also discuss the use of de novo design to construct models to test our understanding of the underlying principles and to provide useful leads for pharmaceutical intervention of diseases.

Duplex vs. folding: tuning the self-assembly of synthetic recognition-encoded aniline oligomers

One of the challenges in the realization of synthetic oligomers capable of sequence-selective duplex formation is intramolecular folding interaction between complementary recognition units. To assess whether complementary hetero-oligomers can assemble into high fidelity duplex structures, the competing folding equilibria must be carefully considered. A family of recognition-encoded aniline oligomers were assembled via reductive amination of dianiline linkers and dialdehyde monomers, which were equipped with either a 2-trifluoromethylphenol or a phosphine oxide H-bond recognition unit. To test the possibility of 1,2-folding in mixed sequence oligomers, the self-assembly properties of the homo- and hetero-dimers were characterised by ¹⁹F and ¹H NMR titration and dilution experiments in toluene and in chloroform. Three different systems were investigated with variations in the steric bulk around the H-bond acceptor unit and the length of the dianiline linker. For two systems, the hetero-dimers folded with intramolecular H-bonding in the monomeric state, reducing stability of the intermolecular duplex by two to three orders of magnitude compared with the corresponding homo-oligomers. However, the use of a long rigid linker as the backbone connecting two monomer units successfully prevents 1,2-folding and leads to the formation of a stable mixed sequence duplex in toluene.

Crystal structures capture multiple stoichiometric states of an aqueous self-assembling oligourea foldamer

We report here an oligourea foldamer able to self-assemble in aqueous conditions into helix bundles of multiple stoichiometries. Importantly, we report crystal structures of several of these stoichiometries, providing a series of high-resolution snap-shots of the structural polymorphism of this foldamer and uncovering a novel self-assembly.

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.

Symmetry breaking-induced double-strand helices in H-bonded coassembly

Double-strand helical structures are important in information storage of biomacromolecules, while the artificial synthesis depends on chirality transfer from the molecular to supramolecular scale, and the synthesis through symmetry breaking has yet been accomplished. In this work, we present the multiple-constituent coassembly of a melamine derivative and an N-terminal aromatic amino acid into double helical nanoarchitectures via symmetry breaking. Multiple intramolecular H-bond formation between constituents played key roles in directing the formation of helical structures. Intertwining of single helices with identical helical parameters afforded double helical structures, benefiting from the uniformity and monodispersity of nanoarchitectures. With introduction of coded chiral amino acid derivatives as chiral sources, the handedness could be readily manipulated with exclusive correlation to the absolute chirality of amino acids. Molecular flexibility of the melamine derivative facilitates the propeller-shaped complex formation to afford helical columnar coassemblies and double helical structures. This work presents a rational control over the emergence and properties of double helical structures in multiple-constituent coassemblies through symmetry breaking, which provides an alternative method towards the synthesis of topological chiral composites and chiroptical materials.

Synthesis, Characterization and Evaluation of Peptide Nanostructures for Biomedical Applications

There is a challenging need for the development of new alternative nanostructures that can allow the coupling and/or encapsulation of therapeutic/diagnostic molecules while reducing their toxicity and improving their circulation and in-vivo targeting. Among the new materials using natural building blocks, peptides have attracted significant interest because of their simple structure, relative chemical and physical stability, diversity of sequences and forms, their easy functionalization with (bio)molecules and the possibility of synthesizing them in large quantities. A number of them have the ability to self-assemble into nanotubes, -spheres, -vesicles or -rods under mild conditions, which opens up new applications in biology and nanomedicine due to their intrinsic biocompatibility and biodegradability as well as their surface chemical reactivity via amino- and carboxyl groups. In order to obtain nanostructures suitable for biomedical applications, the structure, size, shape and surface chemistry of these nanoplatforms must be optimized. These properties depend directly on the nature and sequence of the amino acids that constitute them. It is therefore essential to control the order in which the amino acids are introduced during the synthesis of short peptide chains and to evaluate their in-vitro and in-vivo physico-chemical properties before testing them for biomedical applications. This review therefore focuses on the synthesis, functionalization and characterization of peptide sequences that can self-assemble to form nanostructures. The synthesis in batch or with new continuous flow and microflow techniques will be described and compared in terms of amino acids sequence, purification processes, functionalization or encapsulation of targeting ligands, imaging probes as well as therapeutic molecules. Their chemical and biological characterization will be presented to evaluate their purity, toxicity, biocompatibility and biodistribution, and some therapeutic properties in vitro and in vivo. Finally, their main applications in the biomedical field will be presented so as to highlight their importance and advantages over classical nanostructures.

Catalyst-free synthesis of substituted pyridin-2-yl, quinolin-2-yl, and isoquinolin-1-yl carbamates from the corresponding hetaryl ureas and alcohols

A novel catalyst-free synthesis of N-pyridin-2-yl, N-quinolin-2-yl, and N-isoquinolin-1-yl carbamates utilizes easily accessible N-hetaryl ureas and alcohols. The proposed environmentally friendly technique is suitable for the good-to-high yielding synthesis of a wide range of N-pyridin-2-yl or N-quinolin-2-yl substituted carbamates featuring electron-donating and electron-withdrawing groups in the azine rings and containing various primary, secondary, and even tertiary alkyl substituents at the oxygen atom (48-94%; 31 examples). The DFT calculation and experimental study showed that the reaction proceeds through the intermediate formation of hetaryl isocyanates. The method can be applied to obtain N-isoquinolin-1-yl carbamates, although in lower yields, and ethyl benzo[h]quinolin-2-yl carbamate has also been successfully synthesized (68%).

Potential Foldamers Based on an ortho-Terphenyl Amino Acid

We describe the synthesis and characterization of a new class of oligomers built from a terphenyl-based amino acid. These oligomeric amides are of interest because the adoption of specific conformations could potentially be driven by the coordinated formation of inter-residue hydrogen bonds and aromatic interactions. Although high-resolution structural data have proven inaccessible, circular dichroism and nuclear magnetic resonance studies suggest that the new oligomers fold concomitantly with discrete self-association in chloroform.

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.

Double-helical assembly of heterodimeric nanoclusters into supercrystals

DNA has long been used as a template for the construction of helical assemblies of inorganic nanoparticles^1-5. For example, gold nanoparticles decorated with DNA (or with peptides) can create helical assemblies^6-9. But without such biological ligands, helices are difficult to achieve and their mechanism of formation is challenging to understand^10,11. Atomically precise nanoclusters that are protected by ligands such as thiolate^12,13 have demonstrated hierarchical structural complexity in their assembly at the interparticle and intraparticle levels, similar to biomolecules and their assemblies¹⁴. Furthermore, carrier dynamics can be controlled by engineering the structure of the nanoclusters¹⁵. But these nanoclusters usually have isotropic structures^16,17 and often assemble into commonly found supercrystals¹⁸. Here we report the synthesis of homodimeric and heterodimeric gold nanoclusters and their self-assembly into superstructures. While the homodimeric nanoclusters form layer-by-layer superstructures, the heterodimeric nanoclusters self-assemble into double- and quadruple-helical superstructures. These complex arrangements are the result of two different motif pairs, one pair per monomer, where each motif bonds with its paired motif on a neighbouring heterodimer. This motif pairing is reminiscent of the paired interactions of nucleobases in DNA helices. Meanwhile, the surrounding ligands on the clusters show doubly or triply paired steric interactions. The helical assembly is driven by van der Waals interactions through particle rotation and conformational matching. Furthermore, the heterodimeric clusters have a carrier lifetime that is roughly 65 times longer than that of the homodimeric clusters. Our findings suggest new approaches for increasing complexity in the structural design and engineering of precision in supercrystals.

Macrocyclic Aromatic Amide Foldamer: Synthesis, Twisted-to-Boxlike Conformational Switching, and Molecular Recognition

In this study, a twisted macrocycle was synthesized via ring closure of a double-helical aromatic oligoamide foldamer with two disulfide bridges. Single-crystal X-ray structure and NMR spectroscopy demonstrate the twisted conformation of macrocycle both in the solid state and in solution. As a result of the rearrangement of hydrogen bonding preference, the twisted conformation could be transformed to boxlike through protonation of the pyridine segments of macrocycle. In addition, the NMR titration experiments revealed that flat aromatic guests (e. g., coronene and perylene) could bind to the boxlike macrocycle with a 1 : 1 binding stoichiometry. The addition of base to the host-guest complexes resulted in conformational reversal of the macrocycle from boxlike to twisted as well as the release of guest.