Metal‐Coordination‐Assisted Folding and Guest Binding in Helical Aromatic Oligoamide Molecular Capsules

The development of foldamer‐based receptors is driven by the design of monomers with specific properties. Herein, we introduce a pyridazine‐pyridine‐pyridazine diacid monomer and its incorporation into helical aromatic oligoamide foldamer containers. This monomer codes for a wide helix diameter and can sequester metal ions on the inner wall of the helix cavity. Crystallographic studies and NMR titrations show that part of the metal coordination sphere remains available and may then promote the binding of a guest within the cavity. In addition to metal coordination, binding of the guest is assisted by cooperative interactions with the helix host, thereby resulting in significant enhancements depending on the foldamer sequence, and in slow guest capture and release on the NMR time scale. In the absence of metal ions, the pyridazine‐pyridine‐pyridazine monomer promotes an extended conformation of the foldamer that results in aggregation, including the formation of an intertwined duplex.     

Diversity of interstrand π—π stacking motifs in the double helices of pyridinedicarboxamide oligomers

Winding of oligoamide strands of 2,6-diaminopyridine and 2,6-pyridinedicarboxylic acid into molecular duplexes is illustrated by two new crystal structures of double helical dimers. The relative positions of the two strands within the double helices in these two structures are different; they also differ from the structures reported previously. Unlike the single helical structure of the monomeric strands, the double helical motif is not highly stable in the solid state. This implies that the interactions that lead to duplex formation are not directional. It suggests that the two strands have a significant motional freedom in the duplex.     

Designed Synthesis of a Highly Conjugated Hexaethynylbenzene‐Based Host for Supramolecular Architectures

The construction of efficient synthetic functional receptors with tunable cavities, and the self‐organization of guest molecules within these cavities through noncovalent interactions can be challenging. Here we have prepared a double‐cavity molecular cup based on hexaethynylbenzene that possesses a highly π‐conjugated interior for the binding of electron‐rich guests. X‐ray crystallography, NMR spectroscopy, UV/Vis spectroscopy, fluorescent spectroscopy, cyclic voltammetry, and SEM were used to investigate the structures and the binding behaviors. The results indicated that the binding of a guest in one cavity would affect the binding of the same or another guest in the other cavity. The effect of electron transfer in this system suggests ample opportunities for tuning the optical and electronic properties of the molecular cup and the encapsulated guest. The encapsulation of different guests would also lead to different aggregate nanostructures, which is a new way to tune their supramolecular architectures.     

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

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

Aza‐Bambusurils En Route to Anion Transporters

Previous calculations of anion binding with various bambusuril analogs predicted that the replacement of oxygen by nitrogen atoms to produce semiaza‐bambus[6]urils would award these new cavitands with multiple anion binding properties. This study validates the hypothesis by efficient synthesis, crystallography, thermogravimetric analysis and calorimetry. These unique host molecules are easily accessible from the corresponding semithio‐bambusurils in a one‐pot reaction, which converts a single anion receptor into a potential anion channel. Solid‐state structures exhibit simultaneous accommodation of three anions, linearly positioned within the cavity along the main symmetry axis. The ability to hold anions at a short distance of about 4 Å is reminiscent of natural chloride channels in E. coli, which exhibit similar distances between their adjacent anion binding sites. The calculated transition‐state energy for double‐anion movement through the channel suggests that although these host–guest complexes are thermodynamically stable they enjoy high kinetic flexibility to render them efficient anion channels.     

Increasing the Size of an Aromatic Helical Foldamer Cavity by Strand Intercalation

The postsynthetic modulation of capsules based on helical aromatic oligoamide foldamers would be a powerful approach for controlling their receptor properties without altering the initial monomer sequences. With the goal of developing a method to increase the size of a cavity within a helix, a single‐helical foldamer capsule was synthesized with a wide‐diameter central segment that was designed to intercalate with a second shorter helical strand. Despite the formation of stable double‐helical homodimers (K_dim>10⁷ M ^?1) by the shorter strand, when it was mixed with the single‐helical capsule sequence, a cross‐hybridized double helix was formed with K_a>10⁵ M ^?1. This strategy makes it possible to direct the formation of double‐helical heterodimers. On the basis of solution‐ and solid‐state structural data, this intercalation resulted in an increase in the central‐cavity size to give a new interior volume of approximately 150 ų.     

DNA double helices recognize mutual sequence homology in a protein free environment

The structure and biological function of the DNA double helix are based on interactions recognizing sequence complementarity between two single strands of DNA. A single DNA strand can also recognize the double helix sequence by binding in its groove and forming a triplex. We now find that sequence recognition occurs between intact DNA duplexes without any single-stranded elements as well. We have imaged a mixture of two fluorescently tagged, double helical DNA molecules that have identical nucleotide composition and length (50% GC; 294 base pairs) but different sequences. In electrolytic solution at minor osmotic stress, these DNAs form discrete liquid-crystalline aggregates (spherulites). We have observed spontaneous segregation of the two kinds of DNA within each spherulite, which reveals that nucleotide sequence recognition occurs between double helices separated by water in the absence of proteins, consistent with our earlier theoretical hypothesis. We thus report experimental evidence and discuss possible mechanisms for the recognition of homologous DNAs from a distance.     

Selective Encapsulation of Disaccharide Xylobiose by an Aromatic Foldamer Helical Capsule

Xylobiose sequestration in a helical aromatic oligoamide capsule was evidenced by circular dichroism, NMR spectroscopy, and crystallography. The preparation of the 5 kDa oligoamide sequence was made possible by the transient use of acid‐labile dimethoxybenzyl tertiary amide substituents that disrupt helical folding and prevent double helix formation. Binding of other disaccharides was not detected. Crystallographic data revealed a complex composed of a d ‐xylobiose α anomer and two water molecules accommodated in the right‐handed helix. The disaccharide was found to adopt an unusual all‐axial compact conformation. A dense network of 18 hydrogen bonds forms between the guest, the cavity wall, and the two water molecules.     

Molecular arrangement and assembly guided by hydrophobic cavities inside DNA

DNA is a unique yet useful material to organize nanoscale molecular arrays along the helix axis. In this study, we demonstrate a useful approach for creating molecular arrays inside a double helical DNA. Our approach is based on a host-guest system. Introducing abasic sites into DNA afforded a hydrophobic cavity that serves as a host. A planar aromatic molecule (cationic perylenediimide, PDI) was used as the guest molecule. In an aqueous solution, the PDI molecules tend to aggregate with themselves due to the strong hydrophobicity. In the presence of DNA with the cavity, the binding of the PDI was found to site-specifically occur in the hydrophobic cavity. The unique assembly and arrangement for more than two PDI molecules was achieved by controlling the sizes and positions of the cavities. Our approach would provide a simple and convenient way to construct one-dimensional aromatic arrays in DNA.     

Molecular design and synthesis of artificial double helices

This account describes novel artificial double helices recently developed by our group. We have designed and synthesized the double helices consisting of two complementary, m-terphenyl-based strands that are intertwined through chiral amidinium-carboxylate salt bridges. Due to the chiral substituents on the amidine groups, the double helices adopted an excess one-handed helical conformation in solution as well as in the solid state. By extending the modular strategy, we have synthesized double helices bearing Pt(II) linkers, which underwent the double helix-to-double helix transformations through the chemical reactions of the Pt(II) complex moieties. In addition, artificial double-stranded metallosupramolecular helical polymers were constructed by combining the salt bridges and metal coordination. In contrast to the design-oriented double helices based on salt bridges, we have serendipitously developed a spiroborate-based double helicate bearing oligophenol strands. The optical resolution of the helicate was successfully attained by a diastereomeric salt formation. We have also unexpectedly found that oligoresorcinols consisting of a very simple repeating unit self-assemble into double helices with the aid of aromatic interactions in water. Furthermore, a bias in the twist sense of the double helices can be achieved by incorporating chiral substituents at both ends of the strands.     

Metal-Coordination-Assisted Folding and Guest Binding in Helical Aromatic Oligoamide Molecular Capsules

The development of foldamer-based receptors is driven by the design of monomers with specific properties. Herein, we introduce a pyridazine-pyridine-pyridazine diacid monomer and its incorporation into helical aromatic oligoamide foldamer containers. This monomer codes for a wide helix diameter and can sequester metal ions on the inner wall of the helix cavity. Crystallographic studies and NMR titrations show that part of the metal coordination sphere remains available and may then promote the binding of a guest within the cavity. In addition to metal coordination, binding of the guest is assisted by cooperative interactions with the helix host, thereby resulting in significant enhancements depending on the foldamer sequence, and in slow guest capture and release on the NMR time scale. In the absence of metal ions, the pyridazine-pyridine-pyridazine monomer promotes an extended conformation of the foldamer that results in aggregation, including the formation of an intertwined duplex.     

Homo‐Helical Rod Packing as a Path Toward the Highest Density of Guest‐Binding Metal Sites in Metal–Organic Frameworks

In porous materials, metal sites with coordinate solvents offer opportunities for many applications, especially those promoted by host–guest chemistry, but such sites are especially hard to create for Li‐based materials, because unlike transition metals, lithium does not usually possess a high‐enough coordination number for both framework construction and guest binding. This challenge is addressed by mimicking the functional group ratio and metal‐to‐ligand charge ratio in MOF‐74. A family of rod‐packing lithium–organic frameworks (CPM‐47, CPM‐48, and CPM‐49) were obtained. These materials exhibit an extremely high density of guest‐binding lithium sites. Also unusual is the homo‐helical rod‐packing in the CPM series, as compared to the hetero‐helical rod packing by helices of opposite handedness in MOF‐74. This work demonstrates new chemical and structural possibilities in developing a record‐setting high density of guest‐binding metal sites in inorganic–organic porous materials.     

Ni2+ Ion Effect of Conformations on Single‐, Double‐ and Three‐Stranded Homopolynucleotides Containing Adenine and Uracil

Differential UV and visible spectroscopy and thermal denaturation were used to study the interaction of Ni²⁺ ions with adenosine 5′‐monophosphate (AMP), uridine 5′‐monophosphate (UMP), single‐stranded polyadenylic acid (polyA) and polyuridylic (polyU), double‐stranded polyA/polyU (AU) and three‐stranded polyA/2 polyU (A2U). The coil → helix transition observed in polyA, AU and A2U at room temperature is induced by Ni²⁺ binding to the oxygen atoms of the phosphate groups which belong to the disordered single‐stranded parts of the polynucleotides. Ni²⁺ ions coordinate with bases only in individual AMP and single‐stranded polyA. This coordination causes disordering of the helical parts of the strands. The disordered single strands form thermally stable compact particles with effective radii of ˜100 Å. Diagrams of the phase equilibrium between single‐, double‐ and three‐stranded conformations as a function of temperature and Ni²⁺ concentration have been obtained. The melting ranges of A2U and AU differ considerably, mainly due to different enthalpies of their helix–coil transitions. The behaviour of the transition parameters in the presence of Ni²⁺ ions agrees with the data obtained from the theory of equilibrium binding. The constants of the Ni²⁺ binding to AU and A2U are found. The effect of Ni²⁺ ions upon the thermal stability of AU and A2U is connected mainly with their different binding to multi‐stranded helices and polyU. The end of melting of the double‐stranded AU formed due to the A2U → AU + U transition has the character of a second‐order phase transition.     

Assessing the mechanical properties of a molecular spring

We report on the dramatic effect of increasing helix diameter on the hybridization of oligopyridine-dicarboxamide strands into double helices. Upon replacing a single pyridine by a 1,8-diazaanthracene unit within an oligomeric strand, a 4.7 A enlargement of the helix diameter occurs parallel to the long anthracene axis. This structure change results in a spectacular stabilization of the double helical hybrids derived from these strands (factors of over 10(7)). Detailed investigations of the hybridization process using X-ray crystallography, NMR, fluorescence measurements and molecular mechanics calculations allowed us to assign the duplex stabilization to two enthalpic effects. First, the increase in diameter results in an augmented surface, involved in intermolecular pi-pi stacking. Second, the enlarged diameter leads to a lower tilt angle of the helical strand, with respect to the helix axis, which in turn results in smaller dihedral angles at the aryl-amide linkages and thus a considerably lowered enthalpic cost of the spring-like extension of the strands during the hybridization process. These results provide novel insights into how subtle tuning of molecular components may result in considerable and rationalizable changes in double helical supramolecular architectures.     

Structural Characterization of l-proline and Morpholine Appended Chiral Calix[4]resorcinarene Molecules

Calix[4]resorcinarenes serve as host molecules for small guest molecules. Recently calixarenes have been appended to chiral molecules in an attempt to promote chiral recognition. To take advantage of both cavity host and chiral substituent properties the position of the chiral moiety is important. We report the synthesis and structural characterization of two calix[4]resorcinarene based molecules that have helical chirality in the solid state. The calix[4]resorcinarene 1 has chiral l-proline ethyl ester substituents positioned perpendicular to the cavity whereas the calix[4]resorcinarene 2 has morpholines positioned parallel to the cavity which extend the depth of the cavity. Compound 1 is one of the first compounds to show the position of chiral centers with respect to the calixarene cavity. 1H and 13C NMR spectroscopy indicate that the helical chirality of 2 is retained at low temperature in nonpolar solvents.     

Chalcogen-Bond-Induced Double Helix Based on Self-Assembly of a Small Planar Building Block

As a rule, helical structures at the molecular level are formed by non-planar units. This makes the design of helices, starting from planar building blocks via self-assembly, even more fascinating. Until now, however, this has only been achieved in rare cases, where hydrogen and halogen bonds were involved. Here, we show that the carbonyl-tellurium interaction motif is suitable to assemble even small planar units into helical structures in solid phase. We found two different types of helices: both single and double helices, depending on the substitution pattern. In the double helix, the strands are connected by additional Te⋅⋅⋅Te chalcogen bonds. In the case of the single helix, a spontaneous enantiomeric resolution occurs in the crystal. This underlines the potential of the carbonyl-tellurium chalcogen bond to generate complex three-dimensional patterns.     

Pressure effects on the structural,electronic, and optical properties of Sin@SWCNTs

Well‐ordered single, double/four parallel, three/four‐strands helical chains, and five‐strand helical chain with a single atom chain at the center of Si nanowires (NWs) inside single‐walled carbon nanotubes (Si_n@SWCNTs) are obtained by means of molecular dynamics. On the basis of these optimized structures, the structural evolution of Si_n@SWCNTs subjected to axial stress at low temperature is also investigated. Interestingly, the double parallel chains depart at the center and transform into two perpendicular parts, the helical shell transformed into chain, and the strand number of Si NWs increases during the stress load. Through analyzis of pair correlation function (PCF), the density of states (DOS), and the z‐axis polarized absorption spectra of Si_n@SWCNTs, we find that the behavior of Si_n@SWCNTs under stress strongly depends on SWCNTs' symmetry, diameter, as well as the shape of NWs, which provide valuable information for potential application in high pressure cases such as seabed cable. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Controlling the Host–Guest Interaction Mode through a Redox Stimulus

A proof‐of‐concept related to the redox‐control of the binding/releasing process in a host–guest system is achieved by designing a neutral and robust Pt‐based redox‐active metallacage involving two extended‐tetrathiafulvalene (exTTF) ligands. When neutral, the cage is able to bind a planar polyaromatic guest (coronene). Remarkably, the chemical or electrochemical oxidation of the host–guest complex leads to the reversible expulsion of the guest outside the cavity, which is assigned to a drastic change of the host–guest interaction mode, illustrating the key role of counteranions along the exchange process. The reversible process is supported by various experimental data (¹H NMR spectroscopy, ESI‐FTICR, and spectroelectrochemistry) as well as by in‐depth theoretical calculations performed at the density functional theory (DFT) level.     

Self‐Assembly of Conjugated Metallopolymers with Tunable Length and Controlled Regiochemistry

Self‐assembled materials can be designed to express useful optoelectronic properties; however, achieving structural control is a necessary precondition for the optimization of desired properties. Here we report a simple, metal‐templated polymerization process that generates helical metallopolymer strands over 75 repeat units long (28 kDa) from a single bifunctional monomer and Cu^I. The resulting polymer consists of a double helix of two identical conjugated organic strands enclosing a central column of metal ions. The length of this metallopolymer can be controlled by adding monofunctional subcomponents to end‐cap the conjugated ligands. The use of ditopic and bulky monotopic subcomponents, respectively, allows a head‐to‐head or head‐to‐tail double helix to be generated. Spectroscopic measurements of different polymer lengths demonstrate how control over polymer length leads to control over the electronic and luminescent properties of the resulting material, thereby enabling tunable white‐light emission.     

Helical molecular programming: supramolecular double helices by dimerization of helical oligopyridine-dicarboxamide strands

Helically preorganized oligopyridine-dicarboxamide strands are found to undergo dimerization into double helical supramolecular architectures. Dimerization of single helical strands with five or seven pyridine rings has been characterized by NMR and mass spectrometry in various solvent/ temperature conditions. Solution studies and stochastic dynamic simulations consistently show an increasing duplex stability with increasing strand length. The double helical structures of three different dimers was characterized in the solid phase by X-ray diffraction analysis. Both aromatic stacking and hydrogen bonding contribute the double helical arrangement of the oligopyridinedicarboxamide strand. Inter-strand interactions involve extensive face-to-face overlap between aromatic rings, which is not possible in the single helical monomers. Most hydrogen bonds occur within each strand of the duplex and stabilize its helical shape. Some inter-strand hydrogen bonds are found in the crystal structures. Dynamic studies by NMR as well as by molecular modeling computations yield structural and kinetic information on the double helices and on monomer-dimer interconversion. In addition, they reveal the presence of a spring-like extension/compression as well as rotational displacement motions.