Design of an inversion center between two helical segments

A new strategy is proposed to control the relative orientation of two folded helical oligomers in such a way that they diverge from an aromatic linker and have opposite helical handedness. Mutual steric exclusion between the two helices results from the fact that they cannot be at the same time folded and on the same side of the linker. The concept is validated using the helical conformations of oligoamides of 8-amino-2-quinolinecarboxylic acid, but it should be applicable to many families of oligomers and leads to the first designed meso-helices.     

Altering the folding patterns of naphthyl trimers

Proteins can adopt helical and sheet-type secondary structures that depend on their primary sequence of amino acids. Nonnatural foldamers have been developed to emulate these protein structures as well as investigate various types of noncovalent interactions. Here we report a strategy to access two distinct folding topologies in aqueous solutions using the inherent recognition properties of aromatic donor/acceptor interactions. These oligomers are constructed of electron-rich 1,5-dialkoxynaphthalene (Dan) and electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (Ndi) units. A trimer of the sequence Dan-Ndi-Dan was shown to adopt a pleated fold in solution, while its constitutional isomer, Dan-Dan-Ndi, adopted an intercalative or turn-type fold. UV-vis and NOESY spectroscopy analyses were consistent with the two different conformations. This study illustrates the designability of folding naphthyl oligomers and encourages the use of directed aromatic interactions to construct larger and more complex assemblies in water.     

Synthesis,characterization, and application of helical polymers

This review mainly describes the asymmetric synthesis of optically active polymers with helical conformation. Bulky methacrylates such as triphenylmethyl methacrylate and 1-phenyldibenzosuberyl methacrylate give one-handed helical and optically active polymers with almost perfectly isotactic main chain conformation by polymerization with chiral anionic initiators. The radical polymerization and copolymerization of these monomers under chiral conditions also afford optically active polymers with prevailing one-handed helicity. N, N-Disubstituted acrylamides also give optically active, helical polymers in the asymmetric anionic polymerization. Optically active polyisocyanates with a prevailing one-handed helical structure have been prepared in the copolymerization of an achiral isocyanate with a small amount of an optically active isocyanate and also in the polymerization of alkyl and aromatic isocyanates with optically active lithium alkoxide or amide compounds. The existence of a stable helical structure for polychloral has been successfully proved with the helical oligomers of chloral. One-handed helical polyisocyanides have been prepared by helix-sense-selective polymerization of bulky isocyanides and also by the cyclopolymerization of a 1, 2-diisocyanobenzene derivative with the Pd complex of a one-handed helical oligomer.     

Solution structure of quinoline- and pyridine-derived oligoamide foldamers

The unambiguous elucidation of a new folded structure in solution may prove to be a very challenging task. The NMR protocols developed for solving the solution structures of alpha-peptides have been applied to aliphatic beta- and gamma-peptides but are not directly applicable to aromatic oligomers. In particular, the string of spin systems in an aromatic sequence cannot be reconstituted solely from correlations between protons. For aromatic oligomers, it is shown that the assignment of a large part of the 13C NMR spectrum through HMBC and HSQC experiments allows to unambiguously assign proton NMR spectra and in turn to interpret NOE correlations. This has been implemented both with quinoline- and pyridine-derived oligoamide foldamers, and should be applicable to a wide range of oligomers including various combinations of monomers. The NOE correlations allow the unambiguous solution structure elucidation of helical conformations of oligoamides derived from pyridine and quinoline monomers showing that, in these series, the solution structures correspond very well to the structures observed in the solid state.     

Pyrene aromatic arrays on RNA duplexes as helical templates

RNA oligomers having multiple (2 to 4) pyrenylmethyl substituents at the 2'-O-sugar residues were synthesized. UV-melting studies showed that the pyrene-modified RNAs could form duplexes with complementary RNA sequences without loss of thermal stability. Absorption, fluorescence, and circular dichroism (CD) spectra revealed that the incorporated pyrenes projected toward the outside of A-form RNA duplexes and assembled in helical aromatic arrays along the minor grooves of the RNA duplexes. Results of computer simulations agreed with the assembled structures of the pyrenes. The helical pyrene arrays exhibited remarkably strong excimer fluorescence, which was dependent on the sequence contexts of RNA duplexes.     

Remarkable effects of terminal groups and solvents on helical folding of o-phenylene oligomers

Although o-phenylene oligomers (OP(n)R) made of dimethoxyphenylene units are thought to be intrinsically dynamic due to π-electronic repulsion, we show that they fold into a regular helical geometry in CH(3)CN when they carry terminal groups such as CH(3), CH(2)OH, Br, CO(2)Bn, and NO(2). We evaluated their helical inversion kinetics via optical resolution of long-chain oligomers (e.g. 16- and 24-mers) by chiral HPLC. OP(24)Br at 298 K shows a half-life for the optical activity of 5.5 h in CH(3)OH/water (7/3 v/v) and requires 34 h for complete racemization. The perfectly folded helical conformers of OP(n)R, unlike their imperfectly folded ones, are devoid of extended π-conjugation and show a cyclic voltammogram featuring reversible multistep oxidation waves.     

Marked effect of aromatic solvent on unfolding rate of helical ethynylhelicene oligomer

Optically active acyclic ethynylhelicene oligomers were synthesized in high yields by a two-directional method involving Sonogashira coupling and deprotection. Their CD spectra in chloroform exhibited large differences between the oligomers with less than seven helicenes and their higher homologues, which indicated the formation of helical structures for the latter and random coil structures for the former. The helical heptamer gradually unfolded to a random coil structure in chloroform at room temperature. The unfolding rate was examined by CD in several aromatic solvents as well, and the rate constant k was found to be highly dependent on the type of aromatic substituent: k differed by seven orders of magnitude between iodobenzene and trifluoromethylbenzene. Several features of the rates are notable: The reaction rates in halobenzenes were in the order of iodobenzene > bromobenzene > chlorobenzene > benzene > fluorobenzene > m-difluorobenzene, those in alkylbenzenes were styrene > phenylacetylene > ethylbenzene > toluene > benzene, and those in heteroatom-substituted arenes were thioanisole > benzonitrile > anisole > ethyl benzoate > benzene > trifluoromethylbenzene. The log k values exhibited good correlation with the absolute hardness, eta, of the arenes, and higher unfolding rates were observed in the soft arenes. Vapor pressure osmometry studies indicated that the helical structure of the heptamer is dimeric in benzene, fluorobenzene, and trifluoromethylbenzene, while the random coil structure of the heptamer is monomeric in chloroform and toluene. When a chloroform solution of the random coil structure was concentrated to a small volume, the helical structure could be regenerated.     

Helical aromatic oligoamides: reliable, readily predictable folding from the combination of rigidified structural motifs

Factors responsible for the folding of aromatic oligoamides with backbones rigidified by local three-center H-bonds were investigated. The stability of the three-center H-bonds was quantified by the half-lives of amide proton-deuterium exchange reactions, which show that the three-center H-bonds were largely intact at room temperature in the oligomer examined. This result is consistent with our current and previous 2D NMR studies. The overall helical conformation of nonamer 1 was found by variable-temperature NOESY studies to be dynamic. As temperature rose, the end-to-end NOEs rapidly disappeared, while the amide side chain NOEs were still readily detectable, corresponding to the "breath" and stretching of the helix by slightly twisting the local H-bonded rings. Based on the simple repetition of the same structural motif and local conformational preference, undecamer 2 was found to fold into well-defined helical conformation. The predictability of the folding of these backbone-rigidified aromatic oligoamides was demonstrated by a simple modeling method using structural parameters from oligomers with known crystal structures. The reliability and generality of the modeling methods were shown by the excellent agreement between the modeled structures corresponding to 1 and 2 and data from NOESY studies.     

Conformational analysis of o-phenylenes: helical oligomers with frayed ends

The o-phenylenes represent a fundamental class of conjugated polymers that, unlike the isomeric p-phenylenes, should exhibit rich conformational behavior. Recently, we reported the synthesis and characterization of a series of o-phenylene oligomers featuring unusual electronic properties, including surprisingly long-range delocalization as measured by UV-vis spectroscopy and hypsochromic shifts in fluorescence maxima with increasing length. To rationalize these properties, we hypothesized that the oligomers predominantly assume a stacked helical conformation in solution. This assertion, however, was supported by only indirect evidence. Here we present a thorough investigation of the conformational behavior of this series of o-phenylenes by dynamic NMR spectroscopy and computational chemistry. EXSY experiments, in combination with other two-dimensional NMR techniques, provided full (1)H chemical shift assignments for at least the two most prevalent conformers for each member of the series (hexamer to dodecamer). GIAO density functional theory calculations were then used to relate the NMR data to specific molecular geometries. We have found that the o-phenylenes do indeed assume stacked helical conformations with disorder occurring at the ends. Thus, the o-phenylene motif appears to have great potential as a means to organize arenes into predictable three-dimensional arrangements. Our results also illustrate the power of (1)H NMR GIAO predictions in the solution-phase conformational analysis of oligomers, particularly those with a high density of aromatic subunits.     

An approach to helical tubular self-aggregation using C2-symmetric self-complementary hydrogen-bonding cavity molecules

In an approach to helical self-aggregation, C2-symmetric cavity compounds based on the fusion of the bicyclo[3.3.1]nonane and indole framework and incorporating two 2-pyridone hydrogen-bonding motifs, compounds (-)-4 (pyrrole N-butyl) and (-)-5 (pyrrole N-decyl), have been synthesized. The 2-pyridone AD-DA hydrogen-bonding motif failed to operate in the solid state as demonstrated by X-ray diffraction analysis of (-)-4. Instead, the hydrogen-bonded (D-A) chains ...O=C-N-H...O=C-N-H...O=C-N-H..., interconnecting columnar stacks, comprise helices of the right-handed (P) chirality motif. In solution, the aggregation of (-)-5 was studied by NMR, electronic, and CD spectroscopies, and VPO measurements. These investigations strongly suggest that (-)-5 associates to oligomers in CHCl3 and CH2Cl2 using the 2-pyridone motif, fitting the equal K model, and that pi-stacking can be ruled out as a mode of aggregation. We conclude that the so formed aggregates of (-)-5 have a helical structure, based on the fact that only helical tubular structures can result when enantiomerically pure 5 uses its 2-pyridone AD-DA hydrogen-bonding motifs for aggregation.     

Recent advances in acetylene-based helical oligomers and polymers: Synthesis,structures, and properties

In this review, we describe the recent advances in the chemistry of helical polymers and oligomers containing acetylene units in the main chain. Owing to their great benefits such as high availability and handleability, good reactivity, rigidity, linearity, and low bulkiness, acetylene units have been utilized and incorporated in helical folding oligomers and polymers such as oligo- and poly(m-phenylene ethynylene)s. General synthetic methods as well as the structures, functions, and properties of acetylene-based helical oligomers and polymers are discussed by focusing on recent examples from 2009 to 2017.     

Backbone-rigidified oligo(m-phenylene ethynylenes)

Oligo(m-phenylene ethynylenes) (oligo(m-PE)) with backbones rigidified by intramolecular hydrogen bonds were found to fold into well-defined conformations. The localized intramolecular hydrogen bond involves a donor and an acceptor from two adjacent benzene rings, respectively, which enforces globally folded conformations on these oligomers. Oligomers with two to seven residues have been synthesized and characterized. The persistence of the intramolecular hydrogen bonds and the corresponding curved conformations were established by ab initio and molecular mechanics calculations, 1D and 2D (1)H NMR spectroscopy, and UV spectroscopy. Pentamer 5, hexamer 6, and heptamer 7 adopt well-defined helical conformations. Such a backbone-based conformational programming should lead to molecules whose conformations are resilient toward structural variation of the side groups. These m-PE oligomers have provided a new approach for achieving folded unnatural oligomers under conditions that are otherwise unfavorable for previously described, solvent-driven folding of m-PE foldamers. Stably folded structures based on the design principle described here can be developed and may find important applications.     

Development of synthetic double helical polymers and oligomers

There is growing interest in the design and synthesis of artificial helical polymers and oligomers, in connection with biological importance as well as development of novel chiral materials. Since the discovery of the helical structure of isotactic polypropylene, a significant advancement has been achieved for synthetic polymers and oligomers with a single helical conformation for about half a century. In contrast, the chemistry of double helical counterparts is still premature. This short review highlights the recent advances in the synthesis, structures, and functions of double helical polymers and oligomers, featuring an important role of supramolecular chemistry in the design and synthesis of double helices. Although the artificial double helices reported to date are still limited in number, recent advancement of supramolecular chemistry provides plenty of structural motifs for new designs. Therefore, artificial double helices hold great promise as a new class of compounds. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 5195–5207, 2009     

Folding a nonbiological polymer into a compact multihelical structure

The only molecules that are currently known to fold into unique three-dimensional conformations and perform sophisticated functions are biological polymers - proteins and some RNA molecules. Our aim is to create a nonbiological sequence-specific polymer that folds in aqueous solution. Toward that end, we synthesized sequence-specific 30mer, 45mer, and 60mer peptoid oligomers (N-substituted glycine polymers) consisting of 15mer units we chained together by disulfide and oxime linkages to mimic the helical bundle structures commonly found in proteins. Because these 15mer sequences were previously shown to form defined helical structures that aggregate together at submillimolar concentrations, we expected that by covalently linking multiple 15mers together, they might fold as helical bundles. To probe whether they folded, we used fluorescence resonance energy transfer (FRET) reporter groups. We found that certain constructs fold up with a hydrophobic core and have cooperative folding transitions. Such molecules may ultimately provide a platform for designing specific functions resembling those of proteins.     

Double versus single helical structures of oligopyridine-dicarboxamide strands. Part 1: Effect of oligomer length

Oligoamides of 2,6-diaminopyridine and 2,6-pyridinedicarboxylic acid were previously shown to fold into single helical monomers and to hybridize into double helical dimers. A new series of these oligomers comprising 5 to 15 pyridine units, 4-decyloxy residues, and benzylcarbamate end groups were synthesized using a new convergent scheme that involves an early disymmetrization of the diamine and of the diacid. The hybridization of these compounds into double helices was studied by ¹H NMR spectroscopy in chloroform solutions at various temperatures. Somewhat unexpectedly, these studies revealed that dimerization increases with oligomer length up to a certain point, and then decreases down to undetectable levels for the longest strands. NMR studies show that both double helices and single helices become more stable when strand length increases. The measured values of enthalpy and entropy of hybridization for oligomers of various length show that the enthalpic gain constantly decreases with strand length. This can be interpreted as being the result of an increasing enthalpic price of the spring-like extension that the strand undergoes upon hybridization as its length increases. On the other hand, the entropic loss of hybridization also constantly decreases with strand length. Presumably, the helical preorganization of the monomers increases with strand length, which allows the longer strands to hybridize with a minimal loss of motional freedom, that is to say at a low entropic price. The competiton between these two factors results in a maximum of hybridization for the strands having an intermediate length.     

Enforced helicity: efficient access to self-organized helical molecular strands by the imine route

The condensation of the two oligoheterocyclic aldehydes 8 and 16 with the bis-hydrazine 17 gives the bis-hydrazones 1 and 2. These molecular strands are shown to adopt helical conformations of 1.5 and 2.5 turns, respectively. The helical shape of 1 has been confirmed and structurally characterized by X-ray crystallography. The results indicate that the pyrimidine-hydrazone unit is a satisfatory helicity codon, so that the facile hydrazone formation provides an efficient procedure for generating helical structures. This greatly widens the scope of the methodology based on designed heterocyclic sequences for enforcing helicity in molecular strands, and opens interesting routes towards a variety of derived structures.     

Mimicking helical antibacterial peptides with nonpeptidic folding oligomers

Unnatural oligomeric scaffolds designed to adopt defined secondary structures (e.g., helices), while retaining the chemical diversity of amino acid side chains, are of practical value to elaborate functional mimetics of bioactive alpha-polypeptides. Enantiopure N,N'-linked oligoureas as short as seven residues long have been previously shown to fold into a stable helical structure, stabilized by 12- and 14-membered H-bonded rings. We now report that eight-residue oligoureas designed to mimic globally amphiphilic alpha-helical host-defense peptides are effective against both gram-negative and gram-positive bacteria (including methicillin-resistant Staphylococcus aureus [MRSA]) and exhibit selectivity for bacterial versus mammalian cells. Circular dichroism (CD) spectroscopy studies suggest enhanced helical propensity of oligoureas in the presence of phospholipid vesicles. The utility of this new class of nonpeptidic foldamers for biological applications is highlighted by high resistance to proteolytic degradation.     

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.     

m-Phenylene ethynylene sequences joined by imine linkages: dynamic covalent oligomers

Imine metathesis between m-phenylene ethynylene oligomers of various lengths was performed in acetonitrile, a solvent in which oligomers containing eight or more repeat units adopt a compact helical conformation. The equilibrium constants and corresponding free energy change for the imine metathesis reactions were estimated. The results showed that the magnitude of equilibrium shifting measured by the free energy change for the formation of imine-containing oligomers increases linearly below a critical product chain length and grows asymptotically above it. The linear region is ascribed to the constant increase in contact area between monomer units of adjacent helical turns as the product chain grows to the 12-mer. Once the ligation product is 12 units in length, full contact is made between adjacent helical turns. On the other hand, for imine metathesis between oligomers leading to products having more than 12 units, the driving force is the difference between the folding energy of products and that of reactants. The additional stabilizing energy is roughly constant, regardless of the chain length, since the contact area between adjacent helical turns is unchanged. Consistent with the notion that the imine bond only minimally destabilizes the helical conformation, the position of the imine bond in the ligation product has been observed to have no significant effect on the folding stability. The magnitudes of equilibrium shifting are similar for ligation products of the same length but having the imine at various positions along the sequence. This suggests that the imine bond is compatible with the m-phenylene ethynylene backbone, regardless of the position in the sequence. Imine metathesis of m-phenylene ethynylene oligomers could allow a quick access to an unbiased, dynamic library of oligomer sequences joined by imine linkages.     

Solvophobically-driven oligo(ethylene glycol) helical foldamers. Synthesis, characterization, and complexation with ethane-1,2-diaminium

Oligo(ethylene glycols) 1a-h, which are incorporated with one to eight 2,3-naphthylene units, respectively, have been synthesized and characterized. The conformational changes of the new oligomers have been investigated in chloroform-acetonitrile binary solvents by the UV-vis, (1)H NMR, and fluorescent spectroscopy. It has been revealed that the naphthalene units in hexamer 1f, heptamer 1g, and octamer 1h are driven by solvophobic interaction to stack in polar solvents. As a result, compact helical conformations are formed that give rise to a cavity similar to that of 18-crown-6. Shorter oligomers 1b-e exhibit weaker folding tendency. (1)H NMR studies reveal that 1f-h are able to complex ammonium or ethane-1,2-diaminium 19, but not secondary ammonium compounds. The association constants of complexes 1f.19, 1g.19, and 1h.19 in acetonitrile are determined to be 3.5(+/-0.4) x 10(3), 1.0(+/-0.12) x 10(4), and 2.5(+/-0.4) x 10(4) M(-1), respectively, with the (1)H NMR titration method. For comparison, hexamer 22, which incorporates six 1,5-naphthylene units, is also prepared. The UV-vis and fluorescent investigations show that 22 is also able to fold in polar solvents, but no helical structure can be produced due to mismatch of the stacking naphthalene units and consequently there is no obvious complexation between 22 with ethane-1,2-diaminium ion. The structures of the longest foldamer 1h and its complex with 19 have been studied with molecular mechanics calculations. This work represents a new approach to building folding conformations from flexible linear molecules.