Helical Folding Competing with Unfolded Aggregation in Phenylene Ethynylene Foldamers

The folding and aggregation behavior of a pair of oligo(phenylene ethynylene) (OPE) foldamers are investigated by means of UV/Vis absorption and circular dichroism spectroscopy. With identical OPE backbones, two foldamers, 1 with alkyl side groups and 2 with triethylene glycol side chains, manifest similar helical conformations in solutions in n‐hexane and methanol, respectively. However, disparate and competing folding and aggregation processes are observed in alternative solvents. In cyclohexane, oligomer 1 initially adopts the helical conformation, but the self‐aggregation of unfolded chains, as a minor component, gradually drives the folding–unfolding transition eventually to the unfolded aggregate state completely. In contrast, in aqueous solution (CH₃OH/H₂O) both folded and unfolded oligomer 2 appear to undergo self‐association; aggregates of the folded chains are thermodynamically more stable. In solutions with a high H₂O content, self‐aggregation among unfolded oligomers is kinetically favored; these oligomers very slowly transform into aggregates of helical structures with greater thermodynamic stability. The folded–unfolded conformational switch thus takes place with the free (nonaggregated) molecules, and the very slow folding transition is due to the low concentration of molecularly dispersed oligomers.     

Self-assembly of folded m-phenylene ethynylene oligomers into helical columns

Circular dichroism spectroscopy has been used to study the self-assembly of two series of m-phenylene ethynylene oligomers in highly polar solvents. The helical conformation of shorter oligomer lengths was found to be stabilized in aqueous acetonitrile solutions, while longer oligomers began to interact intermolecularly. The intermolecular aggregation of the oligomers in aqueous solutions revealed a chain length dependent association that required the presence of a stable helical conformation. Evidence for intermolecular interactions is provided by Sergeants and Soldiers experiments in which the twist sense bias of a chiral oligomer is transferred to an achiral oligomer.     

Conformational ordering of apolar, chiral m-phenylene ethynylene oligomers

A series of m-phenylene ethynylene oligomers containing nonpolar, (S)-3,7-dimethyl-1-octanoxy side chains have been synthesized and studied. In apolar alkane solvents, oligomers of sufficient length (n > 10) were found to adopt a helical conformation with a large twist sense bias. In contrast, in chloroform the oligomers adopt a random coil conformation. Surprisingly, the strong twist sense bias was determined to be highly time dependent and is partially attributed to intermolecular aggregation.     

Cationic and Neutral Rotaxanes Having Different Functional Groups in the Axle Molecule and Their Coordination to PtII

Dibenzo[24]crown‐8 (DB24C8) forms rotaxanes with a linear molecule having a dialkylammonium group and a triazole group as well as with the acetylation product of a cationic axle molecule. The former cationic rotaxane is stabilized by multiple intermolecular hydrogen bonds between the NH₂⁺ and oxyethylene groups. The neutral rotaxane contains the macrocycle in the vicinity of the terminal aryl group. The co‐conformation of both the cationic and neutral rotaxanes can be fixed by coordination of the triazole group of the axle molecule to PtCl₂(dmso)₂. A ¹H NMR spectroscopic study on the thermodynamics of the Pt coordination revealed a larger association constant for the rotaxanes than for the corresponding axle molecules and a larger value for the neutral rotaxane than for the cationic rotaxane.     

Nonpeptidic foldamers from amino acids: synthesis and characterization of 1,3-substituted triazole oligomers

Nonpeptidic foldamers capable of displaying protein-like functionality were prepared by swapping amide bonds with 1,2,3-triazole rings. The overall conformation of these triazole oligomers is largely dictated by dipole-dipole interactions between adjacent rings. Solution NMR studies suggest that a zigzag conformation, which closely mimics the beta-strand structure, predominates in two different tetramers.     

Acid/Base‐Mediated Uptake and Release of Halide Anions with a Preorganized Aryl‐Triazole Foldamer

A new approach for the construction of artificial receptors capable of selectively uptake and release of halides to mimic the biological halide ions pumps is developed, in which the preorganized aryl‐triazole foldamer was designed to bear a resorcinolic group in the central strand as a switch regulator. By using 1,8‐diazabicyclo[5.4.0]undec‐7‐ene/picric acid as the trigger, the foldamer can be switched between “w”‐shape and helical conformation. Due to the large, half‐open cavity as well as the additional electrostatic repulsion between oxyanions and guest halide, the foldamer in “w”‐shape possesses a much weaker affinity for chloride, bromide, and iodide anions than those in the helical conformation in 6:94 (v/v) [D₆]DMSO/CDCl₃. When the foldamer and chloride ions have the same initial concentrations of 1 mM , 70 % chloride ions in the solution could be reversibly bound or released upon switching.     

From helix to macrocycle: anion-driven conformation control of π-conjugated acyclic oligopyrroles

Anion-responsive pyrrole-based linear receptor oligomers were newly synthesized and their anion-driven dynamic conformation changes were investigated. Phenylene-bridged dimers and a tetramer of dipyrrolyldiketone boron complexes as π-conjugated acyclic anion receptors formed anion-driven helical structures in the solid and solution states. In fact, single-crystal X-ray analyses of the receptor-anion complexes exhibited various helical structures, such as [1+1]- and [1+2]-type single helices and a [2+2]-type double helix according to the lengths of oligomers and the existence of terminal aryl substituents. Anion-binding modes and behaviors of the oligomers in solution state were also examined by (1)H NMR and UV/Vis spectra along with ESI-TOF MS. Differences in the binding modes were observed in the solid and solution states. The oligomers showed augmented anion-binding constants and anion-tunable electronic and optical properties in comparison with the monomer receptor. A negative cooperative effect in the tetramer was observed in the second anion binding of the [1+2]-type single helix due to electrostatic repulsion between two anions captured in the helix. Further, an anion-template coupling reaction from the linear dimer provided a receptor macrocycle, which was obtained as a Cl(-) complex with distinct electronic and optical properties. The macrocycle exhibited extremely high anion-binding constants (>10(10) m(-1) in CH(2)Cl(2)) through multiple hydrogen bonding.     

Homo-N-oligonucleotides (N1/N9-C1' methylene bridge oligonucleotides): nucleic acids with left-handed helicity

Oligonucleotides containing a methylene bridge between N1 or N9 of the heterocyclic base and C1' of the pentofuranosyl ring (homo-N-oligonucleotides) were synthesized. Melting curves revealed that such homo-type oligomers could cross-pair with complementary homo-type or natural oligomers. Circular-dichroic studies provide evidence that the homo-type dimers have a left-handed stacked conformation and further suggest that single-stranded and double-stranded homo-type oligomers adopt a left-handed conformation, while duplexes with natural oligomers or nucleic acids form RNA-like right-handed helices. NMR spectroscopy (NOESY) provides supporting evidence for a left-handed stacked conformation of the homo-type dimer, while atomic force microscopy indicates a left-handed helical conformation of homo-type dsDNA. Homo-type dimers and oligomers showed high resistance to digestion by snake-venom and calf-spleen phosphodiesterases and nuclease S1.     

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.     

Tuned triazolatesilver(I) luminescent complexes from zero- to three-dimensionality based on bi- to tetratopic bridged ligands

The self-assembly of silver(I) salts with bitopic triazole ligands 4-(salicylideneamino)-1,2,4-triazole (L1) and 4-(2-pyridinyl)-1,2,4-triazole (L2) produced dinuclear complexes and a 1D molecular-ladder coordination polymer, while the reaction of tritopic ligand 4-(3-pyridinyl)-1,2,4-triazole (L3) with AgClO4 afforded a right-handed helical 2D network with (4,4) topology, a meso layer constructed via left- and right-handed helical chains with AgBF4, and a 2D 4.8(2) net containing no helical chain with AgNO3. Using a tetratopic triazole ligand 2,6-bis(4-triazolyl)pyridine (L4), a 3D coordination polymer was isolated. This complex contains a cationic 4.63 network with rhombic channels, accepting two columns of uncoordinated ClO4(-) anions filling into every central cavity. Our results show that (i) the increase of coordination sites of the ligands is an effective route to obtaining higher-dimensional structures and (ii) anions could influence the configuration of the ligand to tune the coordination network topology from those with helical chains to those without. In the solid state, all of the complexes exhibit strong fluorescent emission bands, which may be assigned to intraligand fluorescent emission. The luminescent properties of these complexes in a water solution varied from blue light to green light at ambient temperature.     

Ter(9,9-diarylfluorene)s: highly efficient blue emitter with promising electrochemical and thermal stability

Novel ter(9,9-diarylfluorene)s were synthesized by a Suzuki-coupling reaction of 2-bromofluorene (1) and 2,7-fluorenediboronic ester derivatives (3) with high isolated yields (63-86%). The X-ray structure analysis of ter(9,9'-spirobifluorene) (4aa) revealed that the conjugated chromophore adopts a helical conformation. This conformation effectively releases the steric interaction between the fluorene moieties and prevents inter-chromophore interactions. The introduction of aryl groups at the C9 position of fluorene was highly beneficial to the thermal and morphological stability of these oligomers. These terfluorenes exhibit intense blue fluorescence with excellent quantum yields both in solution ( approximately 100%) and in solid state (66-90%), and possess interesting reversible redox properties. Highly efficient blue light-emitting OLED devices were fabricated using 4aa and 4cc as emitters as well as hole transporters. The devices exhibit low turn-on voltage ( approximately 3 V) and high EL external quantum efficiency (2.5-3%).     

Aggregation-induced amplified quenching in conjugated polyelectrolytes with interrupted conjugation

A pair of anionic conjugated polyelectrolytes that contain three-ring (phenylene ethynylene) units linked by a single -CH(2)- or -O- tether (P1 and P2, respectively) are studied. The linkers serve to interrupt the π conjugation along the polymer backbone. Fluorescence spectroscopy reveals that P2 forms a fluorescent aggregate in methanol and water; however, the fluorescence of P1 is much weaker in water, and P1 exhibits only weak aggregate fluorescence. Fluorescence quenching of the polymers was examined using methyl viologen (MV(2+)) as a cationic quencher. P1 shows only a weak amplified quenching effect, with a Stern-Volmer quenching constant of K(SV) ≈ 6 × 10(5) M(-1) in methanol. Interestingly, for P2 in methanol, the aggregate emission is strongly quenched with K(SV) ≈ 5 × 10(6) M(-1), which is comparable to the highest quenching efficiency observed for fully π-conjugated polyelectrolytes. By contrast, the monomer emission is quenched much less efficiently, with K(SV) ≈ 2 × 10(5) M(-1). The results are explained by a model in which -O- linked polymer P2 is able to fold into a helical conformation in solution, which facilitates the formation of extended π-stacked aggregates allowing long-distance exciton transport.     

Helical pitch of m-phenylene ethynylene foldamers by double spin labeling

To investigate the helical conformation of oligo(m-phenylene ethynylene)s, a pair of TEMPO spin labels were appended to the backbone. The two TEMPO radicals were separated by the four, five, and six repeating units. ESR spectra of the labeled oligomers were measured in chloroform and in ethyl acetate solvents in which the oligomers are disordered and folded, respectively. The measurement and analysis of ESR spectra revealed that six repeating units make one helical turn.     

Synthetic Studies on Selectin Ligands/Inhibitors: One-Pot Synthesis of the Mono- and Oligo-Sulfated 2-(Tetradecyl)Hexadecyl β-D-Galacto- and Lactopyranosides as the Sulfatide Mimetics 1

Abstract

The ¹³C NMR spectra of inulin oligomers in D₂O with degree of polymerization (DP) of 3 through 9, along with two other inulin oligomer mixtures of average DP = 17 and DP = 31 were recorded. Significant variations in the chemical shift of some fructofuranose carbon signals indicates that unlike glucans, simple helical structures are not the predominant conformation for inulin oligomers—at least up to DP = 9. Models of the DP = 5 oligomer show that it should prefer a single helical conformation which however, would not be accessible to longer DP oligomers due to severe steric interactions.     

Photoinitiated cationic oligomerization of aryl 1-propenyl ethers

A series of aryl 1-propenyl ethers (ArPE) were prepared by the isomerization of the corresponding allyl aryl ethers (AArE) and used for photoinduced cationic polymerization studies. Attempted polymerization reactions using diaryliodonium salts as photoinitiators generally resulted in low yields of oligomers. Further studies revealed that these compounds have much lower reactivity in cationic vinyl polymerization as compared to their alkyl analogues. Moreover, side reactions resulting from chain transfer due to Friedel–Crafts alkylations take place and compete with vinyl polymerization. These side reactions are responsible for the low molecular weights observed in the cationic photopolymerization of aryl 1-propenyl ether monomers. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 3017–3025, 1999     

Exploring Helical Folding in Oligomers of Cyclopentane-Based ϵ-Amino Acids: A Computational Study

The conformational preferences of oligopeptides of an ϵ-amino acid (2-((1R,3S)-3-(aminomethyl)cyclopentyl)acetic acid, Amc₅a) with a cyclopentane substituent in the C^β−C^γ−C^δ sequence of the backbone were investigated using DFT methods in chloroform and water. The most preferred conformation of Amc₅a oligomers (dimer to hexamer) was the H₁₆ helical structure both in chloroform and water. Four residues were found to be sufficient to induce a substantial H₁₆ helix population in solution. The Amc₅a hexamer adopted a stable left-handed (M)-2.3₁₆ helical conformation with a rise of 4.8 Å per turn. The hexamer of Ampa (an analogue of Amc₅a with replacing cyclopentane by pyrrolidine) adopted the right-handed mixed (P)-2.9_18/16 helical conformation in chloroform and the (M)-2.4₁₆ helical conformation in water. Therefore, hexamers of ϵ-amino acid residues exhibited different preferences of helical structures depending on the substituents in peptide backbone and the solvent polarity as well as the chain length.     

Interplay among folding, sequence, and lipophilicity in the antibacterial and hemolytic activities of alpha/beta-peptides

Host-defense peptides inhibit bacterial growth but manifest relatively little toxicity toward eukaryotic cells. Many host-defense peptides adopt alpha-helical conformations in which cationic side chains and lipophilic side chains are segregated to distinct regions of the molecular surface ("globally amphiphilic helices"). Several efforts have been made to develop unnatural oligomers that mimic the selective antibacterial activity of host-defense peptides; these efforts have focused on the creation of molecules that are globally amphiphilic in the preferred conformation. One such endeavor, from our laboratories, focused on helix-forming alpha/beta-peptides, i.e., oligomers containing a 1:1 pattern of alpha- and beta-amino acid residues in the backbone [Schmitt, M. A.; Weisblum, B.; Gellman, S. H. J. Am. Chem. Soc. 2004, 126, 6848-6849]. We found, unexpectedly, that the most favorable biological activity profile was displayed by a "scrambled" sequence, which was designed not to be able to form a globally amphiphilic helix. Here we report new data, involving an expanded set of alpha/beta-peptides, from experiments designed to elucidate the origins of this surprising result. In addition, we evaluate the susceptibility of alpha/beta-peptides to proteolytic degradation. Our results support the hypothesis that the ability to adopt a globally amphiphilic helical conformation is not a prerequisite for selective antibacterial activity. This conclusion represents a significant advance in our understanding of the relationship among molecular composition, conformation, and biological activity. Our results should therefore influence the design of other unnatural oligomers intended to function as antibacterial agents.     

Novel self-assembled molecular aggregates formed by fluoroalkyl end-capped oligomers and their application

A variety of fluoroalkyl end-capped oligomers were prepared under mild conditions by the use of fluoroalkanoyl peroxide as a key intermediate. These oligomers can form the self-assembled molecular aggregates with the aggregations of end-capped fluoroalkyl groups in aqueous and organic media. Fluorinated self-assembled molecular aggregates containing carboxyl and sulfo groups were suggested to interact with positively charged HIV-1 to exhibit a potent anti-HIV-1 activity in vitro. In contrast, fluoroalkyl end-capped oligomers containing cationic segments exhibited not only the unique surface active properties imparted by fluorine as well as the usual low-molecular fluorinated surfactants, but also high surface antibacterial activity. Fluoroalkyl end-capped oligomers containing betaine-type segments were found to cause a gelation where the strong aggregation of the end-capped fluoroalkyl groups is involved in establishing the physical gel network in water and polar organic solvents under non-crosslinked conditions. Similarly, fluoroalkyl end-capped oligomers containing hydroxyl groups could cause a gelation, where the aggregation of fluoroalkyl groups and hydrogen-bonding interaction is involved in establishing a physical gel network in water and polar organic solvents under non-crosslinked conditions. Fluoroalkanoyl peroxide is also a convenient tool for the preparation of new fluoroalkyl end-capped oligomers containing recognition moieties such as diacetone segments. These fluorinated oligomers containing recognition moieties could form the self-assembled molecular aggregates to recognize selectively the hydrophilic amino and N,N-dimethylamino compounds as guest molecules.     

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     

Meta-linked poly(phenylene ethynylene) conjugated polyelectrolyte featuring a chiral side group: helical folding and guest binding

A water soluble, meta-linked poly(phenylene ethynylene) featuring chiral and optically active side groups based on L-alanine (mPPE-Ala) has been studied by using absorption, fluorescence, and circular dichroism spectroscopy. Studies of mPPE-Ala in methanol/water solvent mixtures show that the polymer folds into a helical conformation, and the extent of helical folding increases with the volume % water in the solvent. The presence of the helical conformation is signaled by the appearance of a broad, excimer-like visible fluorescence band, combined with a strong bisignate circular dichroism signal in the region of the pi,pi absorption of the polymer backbone. The circular dichroism signal exhibits negative chirality, suggesting that the left-handed (M-form) of the helix is in enantiomeric excess. Binding of the metallointercalator [Ru(bpy)2(dppz)]2+ (where bpy = 2,2-bipyridine and dppz = dipyrido[3,2-a:2',3'-c]phenazine) with the helical polymer is accompanied by the appearance of the orange-red photoluminescence from the metal complex. This effect is directly analogous to that observed when [Ru(bpy)2(dppz)]2+ binds to DNA via intercalation, suggesting that the metal complex binds to mPPE-Ala by intercalating between the pi-stacked phenylene ethynylene residues. Cationic cyanine dyes also bind to the periphery of the helical polymer in a manner that is interpreted as "groove binding". A circular dichroism signal is observed that is believed to arise from exciton coupling within the chiral cyanine dye chromophore aggregate that is formed as the dye molecules are oriented by the helical mPPE-Ala "template".