Folding Of Oligomers Research Articles

Conformational Control of ortho-Phenylenes by Terminal Amides.

Control over the folding of oligomers, be it broad induction of a preferred helical handedness or subtle changes in the orientations of individual functional groups, is important for applications ranging from molecular recognition to long-range conformational communication. Here, we report a series of ortho-phenylene hexamers functionalized with achiral and chiral amides at their termini. NMR spectroscopy, taking advantage of 19F labeling, allows multiple conformers to be detected for each compound. In combination with CD spectroscopy and DFT calculations, specific geometries corresponding to each conformer have been identified and quantified. General conclusions about the effect of sterics and the amide linker on conformational behavior have been drawn, revealing some similarities to and key differences from previously reported imines. A model for twist sense control has been developed that is supported by computational models.

High-Fidelity Sequence-Selective Duplex Formation by Recognition-Encoded Melamine Oligomers.

Melamine oligomers composed of repeating triazine-piperidine units and equipped with phenol and phosphine oxide side-chains form H-bonded duplexes. The melamine backbone provides sufficient rigidity to prevent intramolecular folding of oligomers up to three recognition units in length, leading to reliable duplex formation between sequence complementary oligomers. NMR spectroscopy and isothermal titration calorimetry (ITC) were used to characterize the self-assembly properties of the oligomers. For length-complementary homo-oligomers, duplex formation in toluene is characterized by an increase in stability of an order of magnitude for every base-pair added to the chain. NMR spectra of dilute solutions of the AD 2-mer show that intramolecular H-bonding between neighboring recognition units on the chain (1,2-folding) does not occur. NMR spectra of dilute solutions of both the AAD and the ADD 3-mer show that 1,3-folding does not take place either. ITC was used to characterize interactions between all pairwise combinations of the six different 3-mer sequences, and the sequence complementary duplexes are approximately an order of magnitude more stable than duplexes with a single base mismatch. High-fidelity duplex formation combined with the synthetic accessibility of the monomer building blocks makes these systems attractive targets for further investigation.

Chiral nanotubes self-assembled from discrete non-covalent macrocycles.

Many strategies have been used to construct supramolecular hollow tubes, including helical folding of oligomers, bundling of rod-like structures, rolling-up of sheets and stacking of covalent cycles. On the other hand, controlling chirality at the supramolecular level continues attracting much interest because of its implications in future applications of porous systems. This review article covers the main examples in the literature that use simple molecular structures as chiral units for precise assembly into discrete non-covalent cyclic structures that are able to form chiral supramolecular tubular systems.

Folding of ortho-Phenylenes.

In nature, the folding of oligomers and polymers is used to generate complex three-dimensional structures, yielding macromolecules with diverse functions in catalysis, recognition, transport, and charge- and energy-transfer. Over the past 20-30 years, chemists have sought to replicate this strategy by developing new foldamers: oligomers that fold into well-defined secondary structures in solution. A wide array of abiotic foldamers have been developed, ranging from non-natural peptides to aromatics. The ortho-phenylenes represent a recent addition to the family of aromatic foldamers. Despite their structural simplicity (chains of benzenes connected at the ortho positions), it was not until 2010 that systematic studies of o-phenylenes showed that they reliably fold into helices in solution (and in the solid state). This conformational behavior is of fundamental interest: o-Arylene and o-heteroarylene structures are found embedded within many other systems, part of an emerging interest in sterically congested polyphenylenes. Further, o-phenylenes are increasingly straightforward to synthesize because of continuing developments in arene-arene coupling, the Asao-Yamamoto benzannulation, and benzyne polymerization. In this Account, we discuss the folding of o-phenylenes with emphasis on features that make them unique among aromatic foldamers. Interconversion between their different backbone conformers is slow on the NMR time scale around room temperature. The (1)H NMR spectra of oligomers can therefore be deconvoluted to give sets of chemical shifts for different folding states. The chemical shifts are both highly sensitive to conformation and readily predicted using ab initio methods, affording critical information about the conformational distribution. The picture that emerges is that o-phenylenes fold into helices with offset stacking between every third repeat unit. In general, misfolding occurs primarily at the oligomer termini (i.e., "frayed ends"). Because of their structural simplicity, the folding can be described by straightforward models. The overall population can be divided into two enantiomeric pools, with racemization and misfolding as two distinct processes. Examination of substituent effects on folding reveals that the determinant of the relative stability of different conformers is (offset) aromatic stacking interactions parallel to the helical axis. That is, the folding of o-phenylenes is analogous to that of α-helices, with aromatic stacking in place of hydrogen bonding. The folding propensity can be tuned using well-known substituent effects on aromatic stacking, with moderate electron-withdrawing substituents giving nearly perfect folding. The combination of a simple folding mechanism and readily characterized conformational populations makes o-phenylenes attractive structural motifs for incorporation into more-complex architectures, an important part of the next phase of foldamer research.

Hollow Crescents, Helices, and Macrocycles from Enforced Folding and Folding-Assisted Macrocyclization

This Account reviews the progress made by us on creating porous molecular crescents, helices, and macrocycles based on aromatic oligoamides. Inspired by natural pore- or cavity-containing secondary structures, work described in this Account stemmed from the development of foldamers consisting of benzene rings linked by secondary amide groups. Highly stable, three-center intramolecular hydrogen bonds involving the amide linkages are incorporated into these aromatic oligoamides, which, along with meta-linked benzene units that introduce curvatures into the corresponding backbones, leads to tape-like, curved backbones. Depending on their chain lengths, aromatic oligoamides that fold into crescent and helical conformations have been obtained. Combining results from modeling and experimentally measured data indicates that the folding of these oligomers is readily predictable, determined by the localized intramolecular three-center H-bonds and is independent of side-chain substitution. As a result, a variety of reliably folded, modifiable scaffolds can now be constructed. The well-defined crescent or helical conformations contain noncollapsible internal cavities having multiple introverted amide oxygen atoms. Changing the backbone curvature by tuning the ratio of meta- to para-linked benzene units leads to crescents or helices with cavities of tunable sizes. For example, oligoamides consisting of meta-linked units contain cavities of approximately 9 A across, while those with alternating meta- and para-linked units have cavities of over 30 A across. The generality of such a folding and cavity-creating strategy has also been demonstrated by the enforced folding of other types of aromatic oligomers such as oligo(phenylene ethynylene)s, aromatic oligoureas, and aromatic oligosulfonamides. More recently, the folding of aromatic oligoamides was found to assist efficient macrocyclization reactions, which has provided a convenient method for preparing a new class of large shape-persistent macrocycles in high yields. The folded and cyclic structures were extensively characterized based on multiple techniques such as one- and two-dimensional NMR, mass spectrometry, and X-ray crystallography, as well as theoretical calculations. The enforced folding and folding-assisted cyclization of oligomers have provided a predictable strategy for developing crescent, helical, and cyclic structures containing nanosized voids that are mostly associated with the tertiary and quaternary structures of proteins. The availability of these porous molecules has supplied a new class of nanosized building blocks that provide both opportunities and challenges for creating the next-generation nanostructures capable of presenting multiple introverted functional groups, forming various pores and channels, and finally, developing protein-like pockets.

高分子のらせん構造制御の新展開：一次元らせん分子のホスト‐ゲスト化学

The helical structure is one of the most significant motifs in macromolecules. In nature, helical structures are often found in biomacromolecules, and they appear to play a critical role in biological phenomena such as molecular recognition and information storage, as exemplified by the double helices of DNA and the α-helix of proteins. Some synthetic polymers and oligomers also adopt a helical conformation. Recently, the design and synthesis of macromolecules with a helical structure has attracted a great deal of interest, in view of their relationship to life science, as well as of their potential applications in materials science. This review deals mainly with 1) foldamers, 2) foldamer as receptors, and 3) helical folding in the cavity of helical polymers. The foldamer is any oligomer that folds into a conformationally ordered state in solution, the structure of which is stabilized by a collection of noncovalent interactions between nonadjacent monomer units. Recently, a number of examples of foldamers such as oligo (aromatic amide) and oligo (m-pheny-lene-ethynylene) have been reported. The foldamers can be employed as receptors for small molecules and metal ions confined within the helical cavity. The helical folding of oligomers in the cavity of helical polymers is also described.

Synthesis of molecular objects: Two‐dimensional polymers

AbstractThroughout this century polymer science has studied the linear chain and its architectural derivatives which include familiar forms such as the branched chain and the three dimensional network. Other derivatives with unique properties have been investigated more recently and include macromolecular rings, dendrimers, stars, combs and ladders. The objective of this work is to depart from the focus on linear chains and explore the “bulk” synthesis and properties of polymer molecules that can be considered molecular objects. Ideal molecular objects should be macromolecules with well defined shapes that persist as systems transform reversibly from solids to melts or solutions. The limited access to conformational space which is required in order to define and maintain shape in liquid and solid states of the system is an unusual molecular characteristic in common polymers. Our ability to create such objects through bulk reactions of reasonable scale will undoubtedly extend the current boundaries of polymer science and technology. Shapes that are particularly interesting are those not common in the conformational space of linear chains, for example, two‐dimensional polymers shaped as plates and macromolecular bundles shaped as cylinders or parallelepipeds. The molecular object to be discussed in this lecture is a rigid and anisotropic two‐dimensional polymer with planar dimensions greater than its thickness and a shape‐granting skeleton built by covalent bonds. We have so far developed three different strategies for their synthesis, all involving systems in which reactive oligomers organize spontaneously into the necessary planar assemblies to form the object. In one strategy molecular recognition driven by homochiral interactions plays a key role in the formation of two‐dimensional polymers.1 A different methodology relies on entropy‐driven nanophase separation in rodcoil block molecules in which a rigid segment is covalently bonded to a flexible one sharing the same backbone. The third strategy involves the folding of oligomers into hairpin structures which self assemble into two‐dimensional liquids. The lecture will also describe examples of unique properties that could be achieved in materials containing these rigid two‐dimensional objects. These examples will include bulk materials with self‐organized surfaces and also remarkably stable nonlinear optical properties.

Synthesis and ordering of two‐dimensional polymers

AbstractThe work to be discussed in this lecture departs from the usual focus of polymer science on linear chains and explores the “bulk” synthesis and properties of polymer molecules that can be considered shape‐persistent molecular objects. Shapes that are particularly interesting are those not common in the conformational space of linear chains, for example, two‐dimensional polymers shaped as plates or discs and macromolecules shaped as cylinders or parallelepipeds. The lecture focuses on a molecular object which is a rigid and internally anisotropic two‐dimensional polymer with planar dimensions greater than its thickness. The shape‐granting skeleton of this two‐dimensional polymer is built by covalent bonds. We have so far developed three different strategies for their bulk synthesis, all involving systems in which reactive oligomers organize spontaneously into the necessary planar assemblies to form the object. In one strategy molecular recognition events such as homochiral interactions play a key role in the formation of the two‐dimensional flat polymers /1/. A different methodology relies on nanophase separation in rodcoil block molecules in which a rigid segment is covalently bonded to a flexible one sharing the same backbone. The third strategy involves the folding of oligomers into hairpin structures which self assemble into two‐dimensional liquids. In these two last strategies the layered rodcoils or hairpins react to form the covalent backbones necessary to grant shape to the object. A computer simulation relevant to the experimental system suggests that large two‐dimensional polymers can be formed by extremely short backbones. The lecture will also describe examples of unique properties in advanced materials that could emerge from these rigid two‐dimensional objects. These examples include. materials with self‐organized surfaces of high chemical definition and temporal stability, self assembling membranes, molecular reinforcement, and films with remarkably stable electrical or optical properties.