Synthesis of an elongated linear oligo(phenylene ethynylene)-based building block for application in DNA-programmed assembly

The synthesis of an elongated linear oligonucleotide-functionalised module (ELOM) is described. The ELOM structure is based on an oligo(phenylene ethynylene) backbone substituted with two decyloxy groups. The two termini constitute two salicylaldehyde moieties acting as chemical cross-linkers. Before incorporation into an oligonucleotide sequence the organic part of the module, the elongated linear module (ELM), is functionalised with a dimethoxytrityl group and a phosphoramidite group. This enables incorporation into the middle of 30-mer oligonucleotide sequences by automated DNA synthesis. The obtained ELOMs were characterised by polyacrylamide gel electrophoresis and MALDI-TOF mass spectrometry. In analogy with previously reported LOM and TOM structures the coupling reactions of the ELOM modules were tested.     

Synthesis of linear and V-shaped oligo(phenylene ethynylene) derivatives: geometric effects on photophysical properties

<正>A series of linear and V-shaped oligo(phenylene ethynylene) derivatives 1-3 were synthesized through sequent Sonogashira coupling and propargyl alcohol deprotection reaction in high yields.The alkoxy chains(i.e.,n-hexyloxy groups) were introduced to assure good solubility of compounds 1-3 in common solvents.The photophysical properties of 1-3 in solution depend strongly on the geometries of these compounds.     

Combinatorial synthesis of oligo(phenylene ethynylene)s

The combinatorial synthesis of oligo(phenylene ethynylene) tetramers, both in solution and on solid support, is described. These products are of interest for molecular electronics applications. An iterative sequence, coupling of aryl halides to alkynes under Sonogashira conditions, was used. Five monomers functionalized with electron-donating or electron-withdrawing groups were synthesized, and used to generate a library of 25 trimers in a solution-phase based process. A library of 24 tetramers was prepared by subsequent protodesilylation and coupling with the alligator clip 4-iodo-1-thioacetylbenzene. The solution-phase based sequence was successfully adapted to a higher yielding directed split-and-pool solid-phase process, with average yields of 78–86% for each step over seven steps. A triazene linker group was used to attach the starting monomer to the polymer beads. At the completion of the solid-phase-based process, traceless cleavage of trimers from the resin was achieved by sonication of the resin in 10% HCl/THF solution. The released products were then poised for the final step in the sequence, attachment of the alligator clip.     

Synthesis of oligo(phenylene ethynylene)s with dendrimer "shells" for molecular electronics

Two series of oligo(phenylene ethynylene)s (OPEs) with different dendrimer side groups have been designed and synthesized. The molecules contain thiol groups at both ends to enable interconnection between nanoscale gapped metallic electrodes. The different dendrimer groups act as "shells", allowing tailoring to the nanoscopic environment surrounding the OPE "core". Meanwhile, the dendrimer shells also act as spacers for the precise control of the packing density and intermolecular interaction between the OPE cores. [structure: see text].     

Diamine anchored molecular junctions of oligo(phenylene ethynylene) cruciform

Using diamine as anchoring group, the self-assembled monolayers (SAMs) based on oligo(phenylene ethynylene)s (OPEs) and cruciform OPEs with an extended tetrathiafulvalene (TTF) (OPE3 and OPE3-TTF) were successfully formed on the Au substrate and then utilized in molecular junctions by conductingprobe atomic force microscopy (CP-AFM).     

Electrochemical gate-controlled conductance of single oligo(phenylene ethynylene)s

We have studied electron transport properties of unsubstituted oligo(phenylene ethynylene) (OPE) (1) and nitro-substituted OPE (2) covalently bound to two gold electrodes. The conductance values of single 1 and 2 are approximately 13 and approximately 6 nS, respectively. In addition to a decrease in the conductance, the presence of the nitro moiety leads to asymmetric I-V characteristics and a negative differential resistance-like (NDR-like) behavior. We have altered the nitro-substituted OPE by electrochemically reducing the nitro group and by varying the pH of the electrolyte. The conductance decreases linearly with the electron-withdrawing capability (i.e., Hammett substituent values) of the corresponding reduced species. In contrast, the conductance of 1 is independent of the pH and the electrode potential.     

Synthesis and characterization of polymethacrylates containing conjugated oligo(phenylene ethynylene)s as side chains

In order to form suitable systems designed for resonance energy transfer, a series of monodisperse methacrylate‐based monomers containing rigid π‐conjugated oligo(phenylene ethynylenes) with different sizes of the conjugated systems ( M1 – M3 ), and therefore different optoelectronic properties, were synthesized and subsequently polymerized using the reversible addition–fragmentation chain transfer polymerization technique ( P1 – P3 ). In addition, these oligomers were also copolymerized with methyl methacrylate. The obtained polymers were characterized by ¹H NMR spectroscopy, size exclusion chromatography, and analytical ultracentrifugation. The photophysical properties of the polymers were studied by UV–vis absorption and emission spectroscopy in diluted solutions as well as in thin films and compared to the photophysics of the corresponding monomers. Thereby, changes going from monomeric to polymeric systems could be detected in fluorescence quantum yields and lifetimes pointing to energy trapping, e.g., energy transfer. Donor–acceptor copolymers containing different numbers of monomeric units within the side chain exhibit differences in the emission spectra, indicating that energy trapping in polymers is very sensitive to structural properties such as the chain length. UV–vis absorption spectroscopy as well as time‐resolved lifetime studies indicate intrapolymer and interpolymer energy transfer. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Synthesis of iduronic acid building blocks for the modular assembly of glycosaminoglycans

The modular synthesis of glycosaminoglycans requires straightforward methods for the production of large quantities of protected uronic acid building blocks. In particular, the preparation of fully differentiated iduronic acids has proven particularly challenging. An efficient route to methyl 3-O-benzyl-1,2-O-isopropylidene-alpha-l-idopyranosiduronate 6 from diacetone glucose in nine steps and 36% overall yield is described. Idopyranosiduronate 6 is useful as a glycosyl acceptor and as an intermediate that may be further elaborated into iduronic acid trichloroacetimidate glycosyl donors for the assembly of glycosaminoglycan structures as illustrated here.     

Molecular junctions based on SAMs of cruciform oligo(phenylene ethynylene)s

Cruciform oligo(phenylene ethynylene)s (OPEs) with an extended tetrathiafulvalene (TTF) donor moiety (OPE5-TTF and OPE3-TTF) and their simple analogues (OPE5-S and OPE3) without conjugated substituents were used to form high-quality self-assembled monolayers (SAMs) on ultraflat gold substrates. Molecular junctions based on these SAMs were investigated using conducting-probe atomic force microscopy (CP-AFM). The TTF substituent changes the molecular orbital energy levels and decreases the HOMO-LUMO energy gap, resulting in a 9-fold increase in conductance for both TTF cruciform OPEs compared to the unsubstituted analogues. The difference in electrical transport properties of the SAMs was reproduced by the theoretical transport calculations for the single molecules.     

DNA-programmed modular assembly of cyclic and linear nanoarrays for the synthesis of two-dimensional conducting polymers

Nanometer-scale arrays of conducting polymers were prepared on scaffolds of self-assembling DNA modules. A series of DNA oligomers was prepared, each containing six 2,5-bis(2-thienyl)pyrrole (SNS) monomer units linked covalently to N4 atoms of alternating cytosines placed between leading and trailing 12-nucleobase recognition sequences. These DNA modules were encoded so the recognition sequences would uniquely associate through Watson-Crick assembly to form closed-cycle or linear arrays of aligned SNS monomers. The melting behavior and electrophoretic migration of these assemblies showed cooperative formation of multicomponent arrays containing two to five DNA modules (i.e., 12-30 SNS monomers). The treatment of these arrays with horseradish peroxidase and H(2)O(2) resulted in oxidative polymerization of the SNS monomers with concomitant ligation of the DNA modules. The resulting cyclic and linear arrays exhibited chemical and optical properties typical of conducting thiophene-like polymers, with a red-end absorption beyond 1250 nm. AFM images of the cyclic array containing 18 SNS units revealed highly regular 10 nm diameter objects.     

Enantioselective sensing of carboxylic acids with a bis(urea)oligo(phenylene)ethynylene foldamer

The development of molecular probes for optical sensing of chiral compounds has received increasing attention in recent years, in particular because of the potential to accelerate asymmetric reaction analysis. In this study, we prepared conformationally flexible oligo(phenylene)ethynylene foldamers carrying peripheral bis(trifluoromethyl)phenylurea units that undergo hydrogen bonding with chiral carboxylic acids. This interaction results in a chiral amplification process across the stereodynamic sensor scaffold which coincides with characteristic circular dichroism signals at high wavelengths. The induced chiroptical signals allow quantitative determination of the enantiomeric excess of the substrate which was demonstrated with nonracemic samples of tartaric acid. The chirality sensing assay is fast, sufficiently accurate for high-throughput screening purposes and adaptable to parallel analysis with multiwell plate readers.     

Comparative study of electrochemically directed assembly versus conventional self-assembly of thioacetyl-terminated oligo(phenylene ethynylene)s on gold and platinum surfaces

The assembly of thioacetyl-terminated oligo(phenylene ethynylene)s (OPEs) on Au and Pt surfaces under an electric potential (electrochemical assembly, EA) was compared to assembly at an open circuit (conventional self-assembly, CSA). Cyclic voltammetry and ellipsometry were used to characterize the adsorption kinetics of self-assembled monolayers formed by these two techniques. The adsorption rate of the EA was remarkably faster at positive potentials but slower at negative potentials than that of the CSA, The EA at 400 mV proceeded about 800 times faster than the CSA when exposed to the same solution concentrations. The adsorption rates of both EA and CSA were found to be dependent on the molecular structures of OPEs. OPEs containing electron-donating groups assemble faster than those with electron-withdrawing groups. The amount of time that the thioacetyl-terminated OPE is in the presence of the base, for removal of the acetyl group to generate the thiolate, is called the deprotection time. Deprotection times play a critical role in achieving the maximum difference in adsorption rates between the EA and the CSA. The assembly must be initiated no later than 5 min after the basic deprotection is commenced so that the thiolate concentration remains low. The difference in the adsorption rates between EA and CSA might enable selective deposition of certain OPEs onto specific electrodes.     

Self-assembled oligo(phenylene ethynylene)s/graphene nanocomposite with improved electrochemical performances for dopamine determination

In this work, a novel 1,4-bis (4- aminophenylethynyl)benzene (OPE-NH₂, a symmetric linear conjugated oligo(phenylene ethynylene)s derive) and chemically-reduced graphene oxide (rGO) nanocomposite (OPE-NH₂/rGO) was synthesized by a simple self-assembly method. The OPE-NH₂/rGO nanocomposite was stable and water soluble. The formation of OPE-NH₂/rGO nanocomposite was ascribed to the π–π stacking interaction between the conjugated structure of OPE-NH₂ and rGO as well as the electrostatic force between the amino group of OPE-NH₂ and the carboxyl group on rGO, which was characterized by FT-IR, UV–vis spectra and fluorescence spectra. The OPE-NH₂/rGO nanocomposite exhibited significantly improved electrocatalytic activity to the oxidization of dopamine (DA) than that of rGO or OPE-NH₂. The electrochemical performances of OPE-NH₂/rGO were dependent on the OPE-NH₂ contents, and OPE-NH₂ content of 5 wt% exhibited the highest activity. Compared with that of rGO, the nanocomposite presented superior high sensitivity with detection limit of 5 nM, excellent selectivity, wide linear range (0.01–60 μM) and good stability on the determination of DA. The practical application of the developed OPE-NH₂/rGO nanocomposite modified electrode was successfully demonstrated for DA determination in human serum samples.     

Synthesis and self-assembly of an amphiphilic poly(phenylene ethynylene) ionomer

We have synthesized a conjugated amphiphilic polyelectrolyte, a poly(phenylene ethynylene) (PPE), and the structurally analogous neutral polymer. The solution-phase aggregation of the uncharged PPE can be reversibly controlled by varying the solvent polarity and concentration, while the charged polymer appears to self-assemble at any concentration in compatible solvents. These conclusions are based on a combination of absorption and photoluminescence spectroscopy and dynamic light scattering. Photoinduced absorption spectroscopy was also employed to investigate interchain electronic communication and the photoinduced production of free charge carriers. The uncharged PPE had a relatively high polaron yield, indicating pi-stacking of adjacent PPE chains and efficient exciton splitting, while the charged polymer did not produce polarons, indicating that the polymers are not pi-stacked despite their tendency to form aggregates. This is most likely due to the presence of the cationic trimethylammonium side chains which force neighboring polymer chains too far apart to achieve effective pi-orbital overlap. Polarons were observed in both polymers after chemical doping with iodine. The ability to control aggregation and interchain electronic communication could be a useful tool in designing nanostructured electronic materials.     

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.     

Synthesis and application of poly(phenylene ethynylene)s for bioconjugation: a conjugated polymer-based fluorogenic probe for proteases

A set of carboxylate-functionalized poly(phenylene ethynylene)s (PPEs) has been synthesized in which the carboxylic acid groups are separated from the polymer backbone by oligo(ethylene glycol) spacer units. These polymers are soluble in water and organic solvents and have photophysical properties that are sensitive to solvent conditions, with high salt content and the absence of surfactant promoting the formation of aggregates of relatively low quantum yield and long fluorescence lifetime. Quenching of these materials by the dinitrophenyl (DNP) chromophore (K(SV) approximately 10(4)) is also highly solvent-dependent. The presence of carboxylate groups far from the polymer backbone appended to each repeating unit allows for the postpolymerization modification of these PPEs with peptides by methods analogous to those described for carboxylate-functionalized small-molecule dyes. Covalent attachment of the fluorescence-quenching 14-mer Lys(DNP)-GPLGMRGLGGGGK to the PPE results in a nonemissive substrate whose fluorescence is restored upon treatment with trypsin. The rate of fluorescence turn-on in this case is increased 3-fold by the presence of surfactant, though the actual rate of peptide hydrolysis remains the same. A small-molecule mimic of the polymer-peptide system shows a smaller fluorescence enhancement upon treatment with trypsin, illustrating the value of polymer-based amplification in this sensory scheme.     

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.