Sequence-specific binding of m-phenylene ethynylene foldamers to a piperazinium dihydrochloride salt

[reaction: see text] Binding properties of a series of isomeric m-phenylene ethynylene oligomers containing short amide sequences to a piperazinium dihydrochloride salt were investigated by using circular dichroism (CD) measurements. Although these isomeric oligomers exhibited similar helical conformations, high affinity was observed only for one oligomer. This behavior is presumably controlled by the orientation of amino groups of the amide sequence and the folded conformation of the oligomer.     

Molecular packing and morphology of oligo(m-phenylene ethynylene) foldamers

Understanding and controlling solid-state morphologies and molecular conformations is the key to optimizing the properties of materials. As an example for the influence of small chemical changes on solid-state structures, we studied oligo(m-phenylene ethynylene) foldamers, where the introduction of an endo-methyl group induces a transition from an extended all-transoid to a helical all-cisoid conformation. The resulting structural changes were analyzed by X-ray diffraction (XRD), polarized optical microscopy (POM), and low-dose high-resolution electron microscopy (LD-HREM) over several length scales from the molecular to the mesoscopic level. The strong tendency of the endo-methyl oligomer 1 to form stable compact helices in solution resulted in round droplets with an ordered hexagonal columnar (Col(ho)) liquid crystalline structure, where shrinkage during the crystallization resulted in the formation of a banded texture. On the other hand, the endo-hydrogen oligomer 2 exhibited a very different morphology; its extended linear shape was maintained during crystallization and resulted in an extended lamellar structure, which was determined by a compromise between crystalline packing and minimization of the surface area. Another pronounced difference between both molecular structures was the ability of the extended lamellar "crystals" to bend, whereas the helices form either straight or disordered domains. In addition, both materials exhibit strong surface effects, which extend considerably inside the droplet and induce uniform bending of the supramolecular structures.     

Solid-phase synthesis of m-phenylene ethynylene heterosequence oligomers

Both homo- and heterosequence m-phenylene ethynylene oligomers are synthesized using a conceptually simple iterative solid-phase strategy. Oligomers are attached to Merrifield's resin through a known triazene-type linkage. The phenylene ethynylene molecular backbone is constructed through a series of palladium-mediated cross-coupling reactions. The strategy employs two types of monomers that bear orthogonal reactivity, one being a monoprotected bisethynyl arene and the other being a 3-bromo-5-iodo arene. The catalyst conditions are tailored to the requirements of each monomer type. The monoprotected bisethynyl arene is coupled to the growing chain in 2 h at room temperature using a Pd(I) dimer precatalyst ((t)Bu3P(Pd(mu-Cl)(mu-2-methyl allyl)Pd)P(t)Bu3) in conjunction with ZnBr2 and diisopropylamine. In alternate steps, the resin is deprotected in situ with TBAF and coupled to the 3-bromo-5-iodo arene using the iodo selective Pd(tri-2-furylphosphine)4 catalyst in conjunction with CuI and piperidine; this reaction is also completed in 2 h at room temperature. These cross-coupling events are alternated until an oligomer of the desired length is achieved. The oligomer is then cleaved from the resin using CH(2)I(2)/I(2) at 110 degrees C and purified using preparatory GPC. Using this method, a series of homo- and heterosequence oligomers up to 12 units in length in excellent yield and purity were synthesized on the 100 mg scale. Longer oligomers were attempted; however, deletion sequences were found in oligomers longer than 12 units.     

Synthesis and self-association of an imine-containing m-phenylene ethynylene macrocycle

The purpose of this study was to test the suitability of the imine bond as a structural unit within the backbone of phenylene ethynylene macrocycles and oligomers by determining the ability of m-phenylene ethynylene macrocycle 1 to form pi-stacked aggregates in both solution and the solid state. Macrocycle 1, with two imine bonds, was synthesized in high yield from diamine 4 and dialdehyde 5. The imine-forming macrocyclization step was carried out under a variety of conditions, with the best yield obtained simply by refluxing the reactants in methanol. The self-association behavior of 1 in various solvents was probed by (1)H NMR. The association constants (K(E)) in acetone-d(6) and tetrahydrofuran-d(8) were determined by fitting the concentration-dependent chemical shifts with indefinite self-association models. The results showed that solvophobically driven intermolecular pi-pi stacking could be preserved in the imine-containing m-phenylene ethynylene macrocycles. Interestingly, in acetone macrocycle 1 exhibited a stronger tendency to form a dimer rather than higher aggregates. We postulate that this behavior may be due to electrostatic attraction between dipolar imine groups. The solid-state packing of 1 was studied by wide- and small-angle X-ray powder diffraction (WAXD and SAXD). Bragg reflections of 1 were consistent with a hexagonal packing motif similar to our previous studies on m-phenylene ethynylene macrocycles that formed columnar liquid crystal phases.     

Hydrogen bond-stabilized helix formation of a m-phenylene ethynylene oligomer

[reaction: see text] Incorporation of a single hydrogen bonded beta-turn mimic in the backbone of a m-phenylene ethynylene oligomer is shown to affect the thermodynamic properties of the folding reaction. Oligomers 1 and 2 both undergo solvophobic helix formation, but hydrogen bonded oligomer 1 was found to form a more stable helix with a higher tolerance to solvent denaturation than isomeric, non-hydrogen bonded oligomer 2.     

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.     

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.     

Vibronic structures in the electronic spectra of oligo(phenylene ethynylene): effect of m-phenylene to the optical properties of poly(m-phenylene ethynylene)

At the low temperature, hidden vibronic structures are successfully resolved in the absorption and emission spectra of oligo(phenylene ethynylene)s 3-5. Identification of the hidden bands allows estimation of the vibrational energy gaps in these molecules, which appears to increase with the oligomer conjugation length. The remarkable similarity between the absorption profiles of diphenylacetylene (3) and 1,3-bis(phenylethynyl)benzene (5), especially at -198 degrees C, confirms the effectiveness of conjugation interruption at m-phenylene. The function of precise conjugation length control via m-phenylene is further demonstrated from poly(m-phenylene ethynylene) (PmPE) (6). Even though the number of recurring unit (phenylene ethynylene) increases from 2 (for 5) to 12 (for 6), the absorption and emission spectra of the latter are nearly identical to that of the former.     

Single-site modifications and their effect on the folding stability of m-phenylene ethynylene oligomers

[reaction: see text] The folded structure of a m-phenylene ethynylene oligomer is tolerant to single-site modifications to both the backbone sequence and end groups. The helical structure is reinforced by multiple noncovalent interactions, allowing the oligomer sequence to be customized without a significant change in stability in most cases. The small changes that are observed are consistent with the expected behavior of pi-stacked systems and demonstrate subtle control over folding through single-site modifications.     

Helical pitch of ferroelectric liquid-crystalline polymers and copolymers

Ferroelectric liquid-crystalline polymers and copolymers were synthesized from acrylate polymers with side chains consisting of a flexible spacer unit, a mesogenic unit and an optically active substituent. In the chiral smectic C (S*_c) phases typical fan-shaped textures with equidistant lines (caused by the helical structures) were observed. It was found that the helical pitch increased with increasing polymer molecular weight. The helical pitch also increased in copolymers containing mixtures of right- and left-handed chiral side chains.     

Formation of weak polyelectrolyte multilayers studied by spin labeling

Multilayers of alternately adsorbing poly(allylamine) (PAH) and poly(acrylic acid) (PAA) of opposite charges on silica have been studied by the spin labeling technique, as a function of pH. The two polyelectrolytes have been labeled independently by a nitroxide free radical. Its electron paramagnetic resonance spectrum is mainly sensitive to the local Brownian motion and shows lines typical of two different environments, namely, loops protruding in solution with a fast motion and trains adsorbed on the solid with a hindered motion. These two parts have been evaluated for each of the polymer layers separately, and the thickness of the coatings has been described more precisely by characterizing the four contributions existing, for example, for a bilayer. Complexation is demonstrated by the loss of loops and tails belonging to the first polyelectrolyte. The overall picture emerging from the data is explained in terms of compensation of charges and entropy of confinement.     

Metal-assisted assembly of pyridine-containing arylene ethynylene strands to enantiopure double helicates

Pyridine-containing arylene ethynylene strands were connected to the 2- and 2'-positions of (R)- and (S)-1,1'-binaphthyl templates. The arylene ethynylene moieties underwent intramolecular coordination with Ag(I) or Cu(I) ion to afford enantiopure double helicates. The double-helical structure was elucidated on the basis of circular dichroic (CD) spectra. The importance of intramolecular complexation of the double strands for the helicate formation was confirmed by comparison with a ligand bearing a single strand. Connection of the strands through an ether linkage enabled a sorting out of the Cotton effect induced by double-helical arylene ethynylene moieties. The CD exciton chirality method unambiguously proved that the termini of the strands approach each other upon complexation and that the sense of the induced helicity is the same as predicted by molecular modeling.     

Helical twist sense bias in oligo(phenylene ethynylene)s induced by an optically active flexible tether

[graph and structure: see text] A series of tethered phenylene ethynylene oligomers, which undergo a solvent-dependent conformational transition from a random coil to a helix, has been synthesized. The use of trimethylsilyl ether protecting groups on the (+)-tartaric acid-derived tether results in the formation of helices with a large twist sense bias. In contrast, an isopropylidene ketal protecting group or no protecting group is not only ineffective at helical discrimination but may even inhibit helix formation.     

A spin labeling study of pig cardiac tropomyosin

Tropomyosin (TM) extracted from pig cardiac muscle was spin-labeled with 2,2,6,6-tetramethyl-4-(dichlorotriazin)-aminopiperidine-1-oxyl. The ESR spectra of the product (SL-TM) were of a type of weak immobilization. Effects of three means for the denaturation were observed on the above spectra. The ESR spectrum obtained for SL-TM after enzymatic degradation was found to be analogous to that for the label itself in a dilute solution and thereby the quantity of labels bound in SL-TM estimated. The Arrhenius plots attained through variable temperature measurement for SL-TM's exhibited two inflexion points (the conformational transition temperatures for TM) around 45 degrees C and 74-75 degrees C, the latter temperature having not been reported in literature so far. However, the enzymatic degradation product from SL-TM behaved quite differently from it in the response to microwave power saturation and temperature variation.     

Towards photocontrol over the helix-coil transition in foldamers: synthesis and photoresponsive behavior of azobenzene-core amphiphilic oligo(meta-phenylene ethynylene)s

Introduction of photochromic azobenzene units into amphiphilic oligo(meta-phenylene ethynylene)s allowed photocontrol over the helix-coil transition in this important class of foldamers. Two design principles were followed in efforts to accommodate cis- and trans-azobenzene moieties within the helical structure to selectively turn the helical state on and off, respectively. Several oligomer series with varying connectivities to the central azobenzene chromophore were synthesized and these photochromic oligomers were investigated with regard to their folding behavior in both dark and irradiated states. Both the foldamers' chain lengths and the electronic structures of the azobenzene moieties had to be optimized to ensure folding differences and selective excitation of the photochrome. The design of such stimuli-responsive macromolecules, displaying large structural changes upon irradiation, should guide the design of future materials in, for example, "smart" delivery applications.     

Monitoring structural transitions in icosahedral virus protein cages by site-directed spin labeling

This work describes an approach for calculating and measuring dipolar interactions in multispin systems to monitor conformational changes in icosahedral protein cages using site-directed spin labeling. Cowpea chlorotic mottle virus (CCMV) is used as a template that undergoes a pH-dependent reversible capsid expansion wherein the protein cage swells by 10%. The sequence-position-dependent geometric presentation of attached spin-label groups provides a strategy for targeting amino acid residues most probative of structural change. The labeled protein cage residues and structural transition were found to affect the local mobility and dipolar interactions of the spin label, respectively. Line-shape changes provided a spectral signature that could be used to follow the conformational change in CCMV coat dynamics. The results provide evidence for a concerted swelling process in which the cages exist in only two structural forms, with essentially no intermediates. This methodology can be generalized for all symmetry types of icosahedral protein architectures to monitor protein cage dynamics.     

Allosteric pitch length tuning of a dinuclear double helicate

Self assembly of the ditopic ligand L1 with Cu2+ gives the dinuclear double helicate [Cu2(L1)2]4+, which can further coordinate s-block cations. This coordination alters the helicate pitch to a variety of different lengths depending on the size and charge of the guest cation.     

Exploring the local conformational space of a membrane protein by site-directed spin labeling

Molecular modeling based on a hybrid evolutionary optimization and an information condensation algorithm, called GHOST, of spin label ESR spectra was applied to study the structure and dynamics of membrane proteins. The new method is capable of providing detailed molecular information about the conformational space of the spin-labeled segment of the protein in a membrane system. The method is applied to spin-labeled bacteriophage M13 major coat protein, which is used as a model membrane protein. Single cysteine mutants of the coat protein were labeled with nitroxide spin labels and incorporated in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers. The new computational method allows us to monitor distributions of local spatial constraints and molecular mobility, in addition to information about the location of the protein in a membrane. Furthermore, the results suggest that different local conformations may coexist in the membrane protein. The knowledge of different local conformations may help us to better understand the function-structure relationship of membrane proteins.     

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.     

Thickness of a silica-tethered poly(ethylene oxide) layer measured by spin labeling

EPR spectroscopy of labeled poly(ethylene oxide) (PEO) grafted on silica has been used to characterize the conformation and local dynamics of the chains. Grafted molecules of MW 2000 with grafting ratios of 0.045, 0.057, 0.126, and 0.42 molecules/nm² were in contact with benzene. The mobility of the label was compared with that observed for solution of PEO from very diluted to highly concentrated and even bulk PEO. Thus, the concentration inside the grafted layer could be evaluated and also the thickness, which evolves rather linearly with the grafting ratio. © 1995 John Wiley & Sons, Inc.