Double helix formation of oligoresorcinols in water: thermodynamic and kinetic aspects

From Double-Stranded Helicates to Abiotic Double Helical Supramolecular Assemblies

The folding of oligomeric strands is the method that nature has selected to generate ordered assemblies presenting spectacular functions. In the purpose to mimic these biomacromolecules and extend their properties and functions, chemists make important efforts to prepare artificial secondary, tertiary, and even quarternary structures based on folded abiotic backbones. A large variety of oligomers and polymers, encoded with chemical informations, were designed, synthesized and characterized, and the establishment of non-covalent interactions lead to complex and functional supramolecular architectures resulting from a spontaneous self-assembly process. The association of complementary molecular strands into double helical structures is a common structural pattern of nucleic acids and proteins, so the synthesis of bio-inspired double helices has emerged as an important subject. In recent years, a number of synthetic oligomers have been reported to form stable double helices and it was shown that the equilibrium between single and double helices can be controlled via different stimuli like the modification of the solvent or the temperature. This kind of structure presents highly interesting functions, such as molecular recognition within the cavity of double helices, and some other potential applications will emerge in the future.

Controlling aromatic helix dimerization in water by tuning charge repulsions

Several helically folded aromatic oligoamides were designed and synthesized. The sequences were all water-soluble thanks to the charged side chains borne by the monomers. Replacing a few, sometimes only two, charged side chains by neutral methoxy groups was shown to trigger the formation of various aggregates which could be tentatively assigned to head-to-head stacked dimers of single helices, double helical duplexes and a quadruplex, none of which would form in organic solvent with organic-soluble analogues. The nature of the aggregates was supported by concentration and solvent dependent NMR studies, 1H DOSY experiments, mass spectrometry, and X-ray crystallography or energy-minimized models, as well as analogies with earlier studies. The hydrophobic effect appears to be the main driving force for aggregation but it can be finely modulated by the presence or absence of a small number of charges to an extent that had no precedent in aromatic foldamer architectures. These results will serve as a benchmark for future foldamer design in water.

Functional Chirality: From Small Molecules to Supramolecular Assemblies

Many structures in nature look symmetric, but this is not completely accurate, because absolute symmetry is close to death. Chirality (handedness) is one form of living asymmetry. Chirality has been extensively investigated at different levels. Many rules were coined in attempts made for many decades to have control over the selection of handedness that seems to easily occur in nature. It is certain that if good control is realized on chirality, the roads will be ultimately open towards numerous developments in pharmaceutical, technological, and industrial applications. This tutorial review presents a report on chirality from single molecules to supramolecular assemblies. The realized functions are still in their infancy and have been scarcely converted into actual applications. This review provides an overview for starters in the chirality field of research on concepts, common methodologies, and outstanding accomplishments. It starts with an introductory section on the definitions and classifications of chirality at the different levels of molecular complexity, followed by highlighting the importance of chirality in biological systems and the different means of realizing chirality and its inversion in solid and solution-based systems at molecular and supramolecular levels. Chirality-relevant important findings and (bio-)technological applications are also reported accordingly.

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.

Water binding stabilizes stacked conformations of ferrocene containing sheet-like aromatic oligoamides

While water clusters play an essential role in the stability of biological structures, their ability to stabilize synthetic oligomers is less understood. We have synthesized a heptameric sheet-like aromatic oligoamide foldamer with ferrocene as turn unit. It shows strong interactions with water in the solid state and in solution. The water binding limits the fluxional processes resulting from the flexible ferrocene unit, highlighting the importance of such interactions for conformational studies on this class of molecule.

Metallo-Helicoid with Double Rims: Polymerization Followed by Folding by Intramolecular Coordination

In this study, we established a feasible strategy to construct a new type of metallo-polymer with helicoidal structure through the combination of covalent polymerization and intramolecular coordination-driven self-assembly. In the design, a tetratopic monomer (M) was prepared with two terminal alkynes in the outer rim for polymerization, and two terpyridines (TPYs) in the inner rim for subsequent folding by selective intramolecular coordination. Then, the linear covalent polymer (P) was synthesized by polymerization of M via Glaser-Hay homocoupling reaction. Finally, intramolecular coordination interactions between TPYs and Zn(II) folded the backbone of P into a right- or left-handed metallo-helicoid (H) with double rims. Owing to multiple positive charges on the inner rim of helicoid, double-stranded DNA molecules (dsDNA) could interact with H through electrostatic interactions. Remarkably, dsDNA allowed exclusive formation of H with right handedness by means of chiral induction.

Substitution Effects Regulate the Formation of Butterfly-Shaped Tetranuclear Dy(III) Cluster and Dy-Based Hydrogen-Bonded Helix Frameworks: Structure and Magnetic Properties

The generation of two types of complexes with different topological connections and completely different structural types merely via the substitution effect is extremely rare, especially for -CH₃ and -C₂H₅ substituents with similar physical and chemical properties. Herein, we used 3-methoxysalicylaldehyde, 1,2-cyclohexanediamine, and Dy(NO₃)₃·6H₂O to react under solvothermal conditions (CH₃OH:CH₃CN = 1:1) at 80 °C to obtain the butterfly-shaped tetranuclear Dy^III cluster [Dy₄(L¹)₄(μ₃-O)₂(NO₃)₂] (Dy₄, H₂L¹ = 6,6'-((1E,1'E)-(cyclohexane-1,3-diylbis(azanylylidene))bis(methanylylidene))bis(2-methoxyphenol)). The ligand H₂L¹ was obtained by the Schiff base in situ reaction of 3-methoxysalicylaldehyde and 1,2-cyclohexanediamine. In the Dy₄ structure, (L¹)^2- has two different coordination modes: μ₂-η¹:η²:η¹:η¹ and μ₄-η¹:η²:η¹:η¹:η²:η¹. The four Dy^III ions are in two coordination environments: N₂O₆ (Dy1) and O₉ (Dy2). The magnetic testing of cluster Dy₄ without the addition of an external field revealed that it exhibited a clear frequency-dependent behavior. We changed 3-methoxysalicylaldehyde to 3-ethoxysalicylaldehyde and obtained one case of a hydrogen-bonded helix framework, [DyL²(NO₃)₃]_n·2CH₃CN (Dy-HHFs, H₂L² = 6,6'-((1E,1'E)-(cyclohexane-1,3-diylbis(azanylylidene))bis(methanylylidene))bis(2-ethoxyphenol)), under the same reaction conditions. The ligand H₂L² was formed by the Schiff base in situ reaction of 3-ethoxysalicylaldehyde and 1,2-cyclohexanediamine. All Dy^III ions in the Dy-HHFs structure are in the same coordination environment (O₉). The twisted S-shaped (L²)^2- ligand is linked by a Dy(III) ion to form a spiral chain. The spiral chain is one of the independent units that is interconnected to form Dy-HHFs through three strong hydrogen-bonding interactions. Magnetic studies show that Dy-HHFs exhibits single-ion-magnet behavior (U_eff = 68.59 K and τ₀ = 1.10 × 10^-7 s, 0 Oe DC field; U_eff = 131.5 K and τ₀ = 1.22 × 10^-7 s, 800 Oe DC field). Ab initio calculations were performed to interpret the dynamic magnetic performance of Dy-HHFs, and a satisfactory consistency between theory and experiment exists.

Self-Assembly of N-Terminal Aryl Amino Acids into Adaptive Single- and Double-Strand Helices

Helical structures are important features of many important biomacromolecules such as double helices and single α-helices in DNA and protein, respectively, yet the self-organization of short oligopeptides (<3) or independent amino acids into artificial helical structures on the atomic level remains mysterious. Here we present the direct construction of artificial double and single helices from N-terminated aryl amino acids (ferrocene phenylalanine (Phe) conjugates) despite both Phe and Phe-Phe dipeptide self-aggregations adopting supramolecular β-sheet structures, which also demonstrated chirality evolution exposed to small molecular binders. In the solid state, the box-shaped building unit stacks into a double helix with enantiomer-resolved handedness driven orthogonally by H-bonds and the CH-π interaction. The entire double helix is noncovalently linked except for the hybridization regions. Asymmetric H-bonds between carboxylic acids and amides facilitates the one-dimensional helical packing of amino acid residues. The ditopic building unit adopts intramolecular H-bonds, facilitating single-strand helix formation. In aqueous self-assemblies, the superhelical structures were retained, which underwent chirality transfer and handedness inversion upon complexation orthogonally by H-bonds and charge-transfer interaction, showing adaptivity to environmental factors.

Nanoparticle induced limitless spiral of polyacetylene isomers

Helical nanomaterials represent an emerging group of nanostructures because of their multiple functionalities enabled by unique spiral geometry and nanoscale dimensions. This study demonstrates that several trans-transoid polyacetylene (Tt-PA) chains can self-spiral limitlessly over the whole length of polymers to form regular multiple helices under the inducement of water cluster, fullerene ball and metallic nanoparticles (NPs). Multi-helices possess random chirality selection which have equal probability of left-handedness and right-handedness. Energy components, geometric parameters and differences of helices induced by different NPs are analyzed to deeply probe the possible mechanism and the nature of the limitless spiral of the PA polymer. Furthermore, the helical self-assembly of cis-formed cis-transoid (Ct-PA) and trans-cisoid (Tc-PA) isomers is further studied. The spiral ability of Ct-PA is much higher, but Tc-PA is much lower than that of Tt-PA. Remarkably, Tc-PAs are always form five-helix at room temperature.

Single-handed supramolecular double helix of homochiral bis(N-amidothiourea) supported by double crossed C-I···S halogen bonds

The natural DNA double helix consists of two strands of nucleotides that are held together by multiple hydrogen bonds. Here we propose to build an artificial double helix from fragments of two strands connected by covalent linkages therein, but with halogen bonding as the driving force for self-assembling the fragments to the double helix. We succeed in building such a double helix in both solution and solid state, by using a bilateral N-(p-iodobenzoyl)alanine based amidothiourea which in its folded cis-form allows double and crossed C−I···S halogen bonds that lead to right- or left-handed double helix when the two alanine residues are of the same L,L- or D,D-configuration. The double helix forms in dilute CH₃CN solution of the micromolar concentration level, e.g., 5.6 μM from 2D NOESY experiments and exhibits a high thermal stability in solution up to 75 °C, suggesting cooperative and thereby strong intermolecular double crossed halogen bonding that makes the double helix stable. This is supported by the observed homochiral self-sorting in solution.

Building an artificial double helix is a compelling challenge, and most strategies rely on the intertwining of two helical strands. Here, in a very different approach, the authors construct a supramolecular double helix from multiple synthetic small molecules chained together by double crossed halogen bonds.

Quadruple hybridization of quinoline–triazole oligomers

A series of quinoline–triazole oligomers self-assembled into quadruple helical structures is presented.

Three-Component Synthesis of a Library of m-Terphenyl Derivatives with Embedded β-Aminoester Moieties

The three-component reaction between alkyl- or arylamines, β-ketoesters and chalcones in refluxing ethanol containing a catalytic amount of Ce(IV) ammonium nitrate allowed the construction of a large library of highly substituted dihydro- m-terphenyl derivatives containing β-alkylamino- or β-arylamino ester moieties. This process generates three new bonds and one ring and proceeds in high atom economy, having two molecules of water as the only side product. Another domino process, in which the original MCR was telescoped with a subsequent aza Michael/retro-aza Michael sequence, allowed the one-pot preparation of a library of compounds with a N-unsubstituted β-aminoester fragment. Finally, to extend the structural diversity of these libraries, we also examined the aromatization of the central ring of our compounds in the presence of dichlorodicyanoquinone. This reaction sequence did not affect the integrity of a stereogenic center belonging to the amino component.

A Long-Lived Halogen-Bonding Anion Triple Helicate Accommodates Rapid Guest Exchange

Anion-templated helical structures are emerging as a dynamic and tractable class of supramolecules that exhibit anion-switchable self-assembly. We present the first kinetic studies of an anion helicate by utilizing halogen-bonding m-arylene-ethynylene oligomers. These ligands formed high-fidelity triple helicates in solution with surprisingly long lifetimes on the order of seconds even at elevated temperatures. We propose an associative ligand-exchange mechanism that proceeded slowly on the same timescale. In contrast, intrachannel anion exchange occurred rapidly within milliseconds or faster as determined by stopped-flow visible spectroscopy. Additionally, the helicate accommodated bromide in solution and the solid state, while the thermodynamic stability of the triplex favored larger halide ions (bromide≈iodide≫chloride). Taken together, we elucidate a new class of kinetically stable helicates. These anion-switchable triplexes maintain their architectures while accommodating fast intrachannel guest exchange.

Halogen Bonding Directed Supramolecular Quadruple and Double Helices from Hydrogen-Bonded Arylamide Foldamers

Halogen bonding has been used to glue together hydrogen-bonded short arylamide foldamers to achieve new supramolecular double and quadruple helices in the solid state. Three compounds, which bear a pyridine at one end and either a CF₂ I or fluorinated iodobenzene group at the other end, engage in head-to-tail N⋅⋅⋅I halogen bonds to form one-component supramolecular P and M helices, which stack to afford supramolecular double-stranded helices. One of the double helices can dimerize to form a G-quadruplex-like supramolecular quadruple helix. Another symmetric compound, which bears a pyridine at each end, binds to ICF₂ CF₂ I through N⋅⋅⋅I halogen bonds to form two-component supramolecular P and M helices, with one turn consisting of four (2+2) molecules. Half of the pyridine-bearing molecules in two P helices and two M helices stack alternatingly to form another supramolecular quadruple helix. Another half of the pyridine-bearing molecules in such quadruple helices stack alternatingly with counterparts from neighboring quadruple helices, leading to unique quadruple helical arrays in two-dimensional space.

Helically twining polymerization for constructing polymeric double helices

Double helical substituted polyacetylenes (DHSPs) were successfully prepared by a novel chiral induction–helically twining polymerization strategy.

Supramolecular Double-Helix Formation by Diastereoisomeric Conformations of Configurationally Enantiomeric Macrocycles

Solid-state superstructures, resulting from assemblies programmed by homochirality, are attracting considerable attention. In addition, artificial double-helical architectures are being investigated, especially in relation to the ways in which homochiral small molecules can be induced to yield helical forms as a result of chiral induction. Herein, we report the highly specific self-assembly upon crystallization of a double-helical superstructure from an enantiopure macrocyclic dimer which adopts two diastereoisomeric conformations in a molar ratio of 1.5:1 in dimethyl sulfoxide. These two conformational diastereoisomers self-organize-and self-sort-in the crystalline phase in equimolar proportions to form two single-handed helices which are complementary to each other, giving rise to the assembly of a double helix that is stabilized by intermolecular [C-H···O] and π-π stacking interactions. The observed self-sorting phenomenon occurs on going from a mixed-solvent system containing two equilibrating conformational diastereoisomers, presumably present in unequal molar proportions, into the solid state. The diastereoisomeric conformations are captured upon crystallization in a 1:1 molar ratio in the double-helical superstructure, whose handedness is dictated by the choice of the enantiomeric macrocyclic dimer. The interconversion of the two conformational diastereoisomers derived from each configurationally enantiomeric macrocycle was investigated in CD₃SOCD₃ solution by variable-temperature ¹H NMR spectroscopy (VT NMR) and circular dichroism (VT CD). The merging of the resonances for the protons corresponding to the two diastereoisomers at a range of coalescence temperatures in the VT NMR spectra and occurrence of the isosbestic points in the VT CD spectra indicate that the two diastereoisomers are interconverting slowly in solution on the ¹H NMR time scale but rapidly on the laboratory time scale. To the best of our knowledge, the self-assembly of such solid-state superstructures from two conformational diastereoisomers of a homochiral macrocycle is a rare, if not unique, occurrence.

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.

"Inverse" thermoresponse: heat-induced double-helix formation of an ethynylhelicene oligomer with tri(ethylene glycol) termini

Ethynylhelicene oligomers with TEG terminal groups showed a unique thermoresponse in aqueous solvents: double-helix formation upon heating and disaggregation upon cooling.

An ethynylhelicene oligomer [(M)-d-4]-C₁₂-TEG with six tri(ethylene glycol) (TEG) groups at the termini was synthesized, and double-helix formation was studied using CD, UV-Vis, vapor pressure osmometry, dynamic light scattering, and ¹H NMR. [(M)-d-4]-C₁₂-TEG reversibly changed its structure between a double helix and a random coil in response to heating and cooling in aromatic solvents, non-aromatic polar organic solvents, and aqueous solvent mixtures of acetone/water/triethylamine. Notably, [(M)-d-4]-C₁₂-TEG in acetone/water/triethylamine (1/2/1) formed a double helix upon heating and disaggregated into random coils upon cooling. The double helix/random coil ratio sharply changed in response to temperature changes. This is an unprecedented “inverse” thermoresponse, which is opposite to the “ordinary” thermoresponse in molecular dimeric aggregate formation. This phenomenon was explained by the dehydration of the terminal TEG groups and the formation of condensed triethylamine domains upon heating.

Self-complementary double-stranded porphyrin arrays assembled from an alternating pyridyl-porphyrin sequence

Oligomeric porphyrin arrays with an alternating pyridyl-porphyrin sequence were synthesized to explore double-strand formation through self-complementary pyridyl-to-zinc axial coordination bonds. Competitive titration experiments revealed the thermodynamic aspects involved in the zipper effect within double-strand formation. Multiple axial coordination bonds defined the stacked conformation, despite a marginal contribution to the stability of the double-strands. Thus, the zipper cooperativity was the dominant factor for the remarkable stability. Moreover, the dimeric and trimeric porphyrin arrays were independently assembled into double-strands by self-sorting from a binary mixture. Double-strand formation engineered discretely stacked π-systems. Successive slipped-cofacial stacks of the porphyrin rings progressively extended the π-system via exciton coupling over the double-strand while keeping a relatively high fluorescence quantum yield.

Highly efficient stabilisation of meta-ethynylpyridine polymers with amide side chains in water by coordination of rare-earth metals

An amphiphilic meta-ethynylpyridine polymer with chiral amide side chains coordinated with rare-earth metal salts, especially strongly with Sc(iii), to stabilise its helical structure with CD enhancement.

Chiral tether-mediated stabilization and helix-sense control of complementary metallo-double helices

A series of novel PtII-linked double helices were prepared by inter- or intrastrand ligand-exchange reactions of the complementary duplexes composed of chiral or achiral amidine dimer and achiral carboxylic acid dimer strands joined by trans-PtII-acetylide complexes with PPh3 ligands using chiral and achiral chelating diphosphines. The structure and stability of the PtII-linked double helices were highly dependent on the diphosphine structures. An interstrand ligand exchange took place with chiral and achiral 1,3-diphosphine-based ligands, resulting in trans-PtII-bridged double helices, whose helical structures were quite stable even in dimethyl sulfoxide (DMSO) due to the interstrand cross-link, whereas a 1,2-diphosphine-based ligand produced non-cross-linked cis-PtII-linked duplexes, resulting from an intrastrand ligand-exchange that readily dissociated into single strands in DMSO. When enantiopure 1,3-diphosphine-based ligands were used, the resulting trans-PtII-bridged double helices adopted a preferred-handed helical sense biased by the chirality of the bridged diphosphines. Interestingly, the interstrand ligand exchange with racemic 1,3-diphosphine toward an optically-active PtII-linked duplex, composed of chiral amidine and achiral carboxylic acid strands, was found to proceed in a diastereoselective manner, thus forming complete homochiral trans-PtII-bridged double helices via a unique chiral self-sorting.

Triple helix formation in amphiphilic discotics: demystifying solvent effects in supramolecular self-assembly

A set of chiral, amphiphilic, self-assembling discotic molecules based on the 3,3'-bis(acylamino)-2,2'-bipyridine-substituted benzene-1,3,5-tricarboxamide motif (BiPy-BTA) was prepared. Amphiphilicity was induced into the discotic molecules by an asymmetrical distribution of alkyl and oligo(ethylene oxide) groups in the periphery of the molecules. Small-angle X-ray scattering, cryogenic transmission electron microscopy, and circular dichroism spectroscopy measurements were performed on the discotic amphiphiles in mixtures of water and alcohol at temperatures between 0 °C an 90 °C. The combined results show that these amphiphilic discotic molecules self-assemble into supramolecular fibers consisting of either one or three discotic molecules in the fiber cross-section and that the presence of water induces the bundling of the supramolecular fibers. The rich phase behavior observed for these molecules proves to be intimately connected to the mixing thermodynamics of the water-alcohol mixtures.

Synthesis and self-association of double-helical AADD arrays

The design and syntheses of four self-complementary oligomers that contain an underlying AADD hydrogen bond sequence are presented, and their self-association was examined in the solution and solid state. The molecular recognition between the two strands is highly sensitive to substitutions of their component heterocycles. Substitution with electron-donating and -withdrawing groups and the influence of preorganization has a large effect on the overall stabilities of the complexes studied. In particular, a wide range (>10(5) M(-1)) of stabilities with respect to substitutions at various positions in the AADD oligomers was demonstrated. In the most extreme case, the dimerization constant measured (K(dimer) ≥4.5×10(7) M(-1)) is comparable to the most stable homodimers of neutral AADD arrays reported to date.