Chain Folding Controlled by an Isomeric Repeat Unit: Helix Formation versus Random Aggregation in Acetylene‐Bridged Carbazole–Bipyridine Co‐Oligomers

An unprecedented, positional effect of the isomeric repeat unit on chain folding in donor–acceptor‐linked oligomers, which contain alternating bipyridine and carbazole moieties that are connected through an acetylinic linkage, is reported. 4,4′‐Linked oligomer 1 adopts an intrachain helical conformation (CD‐active) in CHCl₃/MeCN (20:80 v/v), whereas oligomer 2 , which contains an isomeric 6,6′‐linkage, forms interchain randomly coiled aggregates (CD‐inactive). The substitution position plays a significant role in controlling the variations in electronic effects and dipole moments around the bipyridyl moiety, which are responsible for this observed phenomenon. Two model compounds of oligomers 1 and 2 ( 3 and 4 , respectively) were prepared and their properties were compared. A systematic investigation of the photophysical and CD properties of these structures, as well as theoretical studies, support our conclusions.     

Synthesis of a bis-amino acid that creates a sharp turn

[reaction: see text] The synthesis of a new bis-amino acid 1 is presented. This monomer is designed to create a tightly curved structure when assembled into oligomers. The monomer is demonstrated to couple to the previously developed monomer 2 through pairs of amide bonds to create a strongly bent spiro-ladder oligomer. The structure of oligomer 3 was determined in aqueous solution using two-dimensional NMR.     

Nylon/DNA: Single-stranded DNA with a covalently stitched nylon lining

The synthesis of DNA/nylon ladder oligomers is described. Three stages of the development are addressed: the synthesis of 2'-beta-substituted phosphoramidites, the deprotection/purification protocols of ODNs modified with both amino and carboxyl groups, and amide bond-forming reactions on the ODNs. The established technology and the novel DNA-based ladder oligomer structure opens a pathway to the synthesis of topological molecular objects and networks templated by DNA through versatile DNA nanotechnology. The DNA-based ladder oligomers may find application in the antisense area.     

Oligo-Quinolylene–Vinylene Foldamers

Quinoline based aromatic amide foldamers are known to adopt stable folded conformations. We have developed a synthetic approach to produce similar oligomers where all amide bonds, or part of them, have been replaced by an isosteric vinylene group. The results of solution and solid state structural studies show that oligomers exclusively containing vinylene linkages are not well folded, and adopt predominantly flat conformations. In contrast, a vinylene segment flanked by helical oligoamides also folds in a helix, albeit with a slightly lower curvature. The presence of vinylene functions also result in an extension of π-conjugation across the oligomer that may change charge transport properties. Altogether, these results pave the way to foldamers in which both structural control and specific electronic properties may be engineered.     

Synthesis of novel fluoroalkyl end‐capped oligomers/silica gel polymer hybrids possessing antibacterial activity

New fluoroalkyl end‐capped oligomers/silica gel polymer hybrids‐low‐molecular weight biocide (hibitane) composites were prepared by the reactions of tetraethoxysilane (TEOS) with fluoroalkyl end‐capped N‐(1,1‐dimethyl‐3‐oxobutyl)acrylamide oligomer, N,N‐dimethylacrylamide oligomers, and acrylic acid oligomers in methanol under acidic conditions at room temperature. The presence of hibitane in the composites was clarified by the use of elementary analyses of nitrogen in fluorinated acrylic acid oligomer composite and thermogravimetric analysis (TGA) of these fluorinated composites. Thermal stability of fluorinated composites thus obtained were found to increase significantly compared to those of the parent fluorinated oligomers. Thermal stability of fluorinated N,N‐dimethylacrylamide oligomer, acrylic acid oligomer/silica gel polymers hybrid‐hibitane composites decreased compared to those of the corresponding fluorinated oligomers/silica gel polymer hybrids; however, the thermal stability of fluorinated N‐(1,1‐dimethyl‐3‐oxobutylacryl)amide oligomer/silica gel polymer hybrid‐hibitane composite increased significantly compared to that of the corresponding fluorinated oligomer hybrid. The sol methanol solutions of these fluorinated composites were applied to the surface modification of glass to exhibit not only a strong oleophobicity imparted by end‐capped fluoroalkyl groups in oligomers but also a good hydrophilicity on the glass surface. Fluorinated oligomers/silica gel polymer hybrids‐hibitane composites were found to exhibit high anti‐bacterial activity against Pseudomonas aeruginosa and Staphylococcus aureus. Therefore, these fluorinated hibitane composites are suggested to have high potential for new attractive functional materials through not only their excellent surface active property imparted by fluorine and their thermal stability but also through their anti‐bacterial activity. Copyright © 2005 John Wiley & Sons, Ltd.     

酰胺二醇与DTPA和EDTA双酸酐共聚形成寡聚物配体的合成

报道了5个酰胺二醇及其与DTPA双酸酐和EDTA双酸酐共聚得到寡聚物配体的合成方法。这类新型寡聚物同时含有酰胺基及酯基官能团，可望在形成顺磁性配合物后用作MRI造影剂时赋予造影剂组织特异性。     

Preparation and applications of a variety of fluoroalkyl end-capped oligomer/hydroxyapatite composites

A variety of fluoroalkyl end-capped oligomers were applied to the preparation of fluorinated oligomer/hydroxyapatite (HAp) composites (particle size: 38-356 nm), which exhibit a good dispersibility in water and traditional organic solvents. These fluoroalkyl end-capped oligomer/HAp composites were easily prepared by the reactions of disodium hydrogen phosphate and calcium chloride in the presence of self-assembled molecular aggregates formed by fluoroalkyl end-capped oligomers in aqueous solutions. In these fluorinated HAp composites thus obtained, fluoroalkyl end-capped acrylic acid oligomers and 2-methacryloyloxyethanesulfonic acid oligomer/HAp nanocomposites afforded transparent colorless solutions toward water; however, fluoroalkyl end-capped N,N-dimethylacrylamide oligomer and acryloylmorpholine oligomer were found to afford transparent colorless solutions with trace amounts of white-colored HAp precipitants under similar conditions. HAp could be encapsulated more effectively into fluorinated 2-methacryloyloxyethanesulfonic acid oligomeric aggregate cores to afford colloidal stable fluorinated oligomer/HAp composites, compared to that of fluorinated acrylic acid oligomers. These fluorinated oligomer/HAp composites were applied to the surface modification of glass and PVA to exhibit a good oleophobicity imparted by fluorine. HAp formation was newly observed on the modified polyethylene terephthalate film surface treated with fluorinated 2-methacryloyloxyethanesulfonic acid oligomers and acrylic acid oligomer/HAp composites by soaking these films into the simulated body fluid.     

Isomer separation of hyperbranched polyesteramides with gas-phase H/D exchange and a novel MS(n) approach: DoDIP

Two approaches are introduced that provide information about the isomeric composition of hyperbranched polyesteramides. The first approach is based on a novel tandem mass spectrometric (MS(n)) approach that allows the study of different types of isomeric structures by a separation based on their difference in appearance energy. The method is called DoDIP: dissociation of depleted ion populations. A first MS/MS step is used to fragment isomers with relatively low appearance energy. The isomers with higher appearance energy are fragmented in a second MS/MS step of higher energy. The second approach is based on gas-phase H/D exchange experiments that result in a bimodal isotopic distribution for oligomers X(n)D(n+1) of which one distribution corresponds to a type of isomeric structure that exhibits H/D exchange behaviour and the other to an isomeric structure that does not exhibit H/D exchange behaviour. X is a difunctional anhydride of phthalic acid (P), 1,2-cyclohexanedicarboxylic acid (C), succinic acid (S) or glutaric acid (G). D in X(n)D(n+1) is a trifunctional diisopropanolamine and n the degree of polymerization. The type of isomeric structure that does not exhibit H/D exchange behaviour has a non-alternating monomer sequence that contains an amine bond with a relatively high proton affinity. The other isomeric structure that does exhibit H/D exchange behaviour has an alternating monomer sequence containing only amide and ester bonds with relatively low proton affinity. Oligomer structures were confirmed with additional MS(2) experiments after H/D exchange. H/D exchange experiments on the fragments obtained after MS(2) of the parent ion show that next to previously postulated mechanisms for the cleavage of the ester and amide bond another reaction pathway must be operational. A new mechanism is introduced to explain the H/D exchange behaviour of the fragments that requires a cleavage of the amide bonds only. Two types of fragments are formed by this mechanism. One type is protonated due to the cleavage of the amide bond whereas the other type has an oxazolonium ion structure due to the loss of an additional H(2)O.     

Synthesis of orthogonally protected cyclic homooligomers from sugar amino acids

Two new families of orthogonally protected cyclic homooligomers with two to four sugar units were synthesized from pyranoid sugar amino acids. Cyclic oligomers composed of amide-linked sugar amino acids (1-3) were prepared by cyclization of linear oligomers of the novel orthogonally protected pyranoid sugar amino acid 12 using a solution-phase coupling method. These orthogonally protected cyclic molecules can be selectively or fully deprotected, affording the macrocycles ready to further functionalization. The straightforward reduction of the amide bonds in the cyclic oligomers 1-3 gave the corresponding amine-linked macrocycles 4-6. This kind of amine-linked carbohydrate-based cyclic oligomer has never been reported before. These flexible molecular receptors could be studied as molecular hosts for molecular, cationic, and anionic recognition. Conformational analysis by molecular modeling (AM1) showed that all of the deprotected cyclic trimers and tetramers preferred a (4)C(1) chair conformation with oxygen atoms of the sugar ring located on the interior of the cavity and the secondary hydroxyl groups outward. In the amide-linked macrocycles, all of the amide bonds are in s-trans conformation. The estimated size of the internal cavity is about 4.5 A for the cyclic trimer and 6.9 A for the cyclic tetramer. The amine-linked macrocycles displayed similar conformational behavior with a slight decrease in internal cavity.     

Surface modified microarray chip and laser induced fluorescence microscopy to detect DNA cleavage

This work describes a quantitative method to detect DNA damage in the presence of Pb and Cd ions using a surface modified microarray chip and a laser induced fluorescence microscopy (LIFM). The detection was carried out by the immobilization of a single-stranded DNA oligomer, tagged with a Cy5 fluorophore on a polydimethylsiloxane (PDMS) microarray chip followed by LIFM. Sulfosuccinimidyl-4-(N-maleimidomethyl) cyclohexane-1-carboxylate (Sulfo-SMCC) was attached as a cross-linker via the formation of covalent amide bonds. Then, the single-stranded DNA oligomer containing Cy5 as a fluorophore and thiol functional groups at both terminals, was bonded to the linker by reaction with sulfhydryl group. As the DNA oligomers were reacted with metal ions of Pb and Cd, the un-cleaved DNA oligomers were quantitatively identified by monitoring Cy5 fluorescence. Cadmium showed a quenching constant of 0.84 in the Stern–Volmer plot, whereas lead gave 0.22, indicating that cadmium ions suppress fluorescence more than lead ions. When optimized, fluorescence reductions of 23% (± 2.1) for Pb and 25% (± 1.4) for Cd were observed in air and decreased to almost < 5.0% in a radical scavenger of 5 mM. The cleaved DNA was also confirmed by MALDI-TOF-MS. In result, this experimental method using a microarray chip with surface modification provided quantitative determination of DNA oligomer damage with reproducible results, significantly reduced sample volumes and analysis times.     

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.     

Effect of the nature and associate structure of an epoxy oligomer on the rate of its curing with diamine

The supramolecular structure of a number of epoxy oligomers, monofunctional epoxy compounds, their mixtures, an oligoamine curing agent, and curing systems on their basis is studied by dynamic light scattering. In all of the starting oligomers and their mixtures, light scattering centers are detected that may be considered as the associates (aggregates) of oligomer molecules. The structure of associates that is determined by the flexibility of the oligomer chain, its branching degree, and the presence of proton-donor groups capable of hydrogen bonding is suggested. The relationship between the rate of curing of epoxy oligomers and their mixtures with oligoamine and the associate structure of oligomers and the nature of the substituent at the glycidyl group of the oligomer is ascertained.     

Kinetics of curing of diane and aliphatic epoxy oligomer blends: IR-spectroscopy study

The curing of diane and aliphatic epoxy oligomers and their blends is studied by IR spectroscopy. Methods for the quantitative determination of epoxy groups in diane and aliphatic oligomers and their blends during curing are developed. It is shown that, during the joint curing of epoxy oligomers, the reactivity of a more active (diane) oligomer remains practically the same, whereas the reactivity of a less active (aliphatic) epoxy oligomer increases. The rate constants for the consumption of epoxy groups of oligomers and primary amine groups of the curing agent are determined.     

Supramolecular substitution reactions between hydrazide-based molecular duplex strands: complexation induced nonsymmetry and dynamic behavior

Supramolecular substitution reactions between hydrazide-based oligomers 1a- c and 2a- c were systematically investigated. Each oligomer existed as hydrogen-bonding mediated molecular duplex strands or a polymeric zipper structure in apolar solvents. But when another oligomer with complementary hydrogen bonding sites was added, a heterodimer structure formed due to supramolecular substitution reaction driven by the formation of more hydrogen bonds, which was evidenced by NMR experiments, sometimes gel-sol transition. When a nonsymmetric oligomer and a symmetric oligomer were involved, complexation-induced nonsymmetry was observed. When two nonsymmetric oligomers were involved, two hydrogen-bonded isomers were observed in solution. Variable-temperature (1)H NMR experiments further revealed unique dynamic behavior for the individual oligomer and the complexes. When diacetyl-terminated oligomer 1c was involved, slides perpendicular to hydrogen bonds between two constituent molecules were observed, which led to complicated (1)H NMR spectra at lower temperature; otherwise, high selectivity was obtained. Combined with the results we reported previously, a detailed picture of the structure-property relationship for our hydrazide-based oligomers was depicted, which would provide guidelines for the design of hydrazide-based fine-tuning functional materials.     

Synthesis, structure, and nonlinear optical properties of cross-conjugated perphenylated iso-polydiacetylenes

Monodisperse, cross-conjugated perphenylated iso-polydiacetylene (iso-PDA) oligomers, ranging from monomer 15 to pentadecamer 25, have been synthesized by using a palladium-catalyzed cross-coupling protocol. Structural characteristics elucidated by X-ray crystallographic analysis demonstrate a non-planar backbone conformation for the oligomers due to the steric interactions between alkylidene phenyl groups. The electronic absorption spectra of the oligomers show a slight red-shift of the maximum absorption wavelength as the chain length increases from dimer 17 b to pentadecamer 25, a trend that has saturated by the stage of nonamer 22. Fluorescence spectroscopy confirms that the pendent phenyl groups present on the oligomer framework enhance emission, and the relative emission intensity consistently increases as a function of chain length n. The molecular third-order nonlinearities, gamma, for this oligomer series have been measured via differential optical Kerr effect (DOKE) detection and show a superlinear increase as a function of the oligomer chain length n. Molecular modeling and spectroscopic studies suggest that iso-PDA oligomers (n>7) adopt a coiled, helical conformation in solution.     

Co‐existence of Two Different α‐Synuclein Oligomers with Different Core Structures Determined by Hydrogen/Deuterium Exchange Mass Spectrometry

Neurodegenerative disorders are characterized by the formation of protein oligomers and amyloid fibrils, which in the case of Parkinson’s disease involves the protein α‐synuclein (αSN). Cytotoxicity is mainly associated with the oligomeric species, but we still know little about their assembly and structure. Hydrogen/deuterium exchange (HDX) monitored by mass spectrometry is used to analyze oligomers formed by wild‐type (wt) αSN and also three familial αSN mutants (A30P, E46K, and A53T). All four variants show co‐existence of two different oligomers. The backbone amides of oligomer type I are protected from exchange with D₂O until they dissociate into monomeric αSN by EX1 exchange kinetics. Fewer residues are protected against exchange in oligomer type II, but this type does not revert to αSN monomers. Both oligomers are protected in the core sequence Y39–A89. Based on incubation studies, oligomer type I appears to form straight fibrils, while oligomer type II forms amorphous clusters that do not directly contribute to the fibrillation process.     

Structural Characterization of Normal and Modified Oligonucleotides by Matrix-assisted Laser Desorption Fourier Transform Mass Spectrometry

Matrix-assisted UV laser desorption Fourier transform mass spectrometry (266 nm, nicotinic acid matrix) can be used for the detailed structural characterization of normal and modified oligonucleotides. The negative ion spectra for these compounds revealed abundant (M ? H) ^- ions as well as fragment ions that provided the information necessary to determine oligomer sequence and to differentiate isomers. The nicotinic acid matrix was required for the production of (M ? H) ^- ions for the oligonucleotide dimers, trimers, tetramers, and hexamers examined in this study. Elimination of the nicotinic acid matrix resulted in complete loss of the (M ?H) ^- ions as well as most of the larger fragment ions for the oligomers. The primary fragmentation pathway was observed to be phosphate ester bond cleavage with the resulting charge retained on the 3’ end of the oligomer and enabled isomeric differentiation of compounds such as d(S’-CGCG-3’) and d(S’-CCGG-3’). Collisioninduced dissociation experiments of the (M ? H) ^- ions for these compounds confirmed the preferential loss of nucleotides from the 5’ end of the oligomers. The presence and location of modifications such as methyl and ethyl alkyl groups to the oligonucleotides could also be identified.     

Solid-Phase Synthesis of Phenylacetylene Oligomers Utilizing a Novel 3-Propyl-3-(benzyl-supported) Triazene Linkage

Sequence-specific phenylacetylene oligomers consisting of functionalized monomers (hexyl benzoate, hexyl phenyl ether, benzonitrile, and tert-butylphenyl) are synthesized in gram quantities using solid-phase methods. Growing oligomers are attached to a divinylbenzene cross-linked polystyrene support by the 1-aryl-3-propyl-3-(benzyl-supported) triazene moiety. This linkage is obtained by reaction of arenediazonium tetrafluoroborate salts with a n-propylamino-modified Merrifield resin. Condensation strategies are described, producing oligomers with higher yields and simplified procedures compared to solution-phase methods. Terminal acetylene is protected with a trimethylsilyl group. After deprotection of the resin-bound terminal acetylene, an aryl iodide monomer or an aryl iodide-terminated oligomer is coupled to the supported oligomer using a palladium(0) catalyst. The cycle can be repeated to produce sequence-specific oligomers of varying length and functionality. The resulting oligomers are liberated from the polymer support by cleavage of the 1-aryl-3-propyl-3-(benzyl-supported) triazene group by reaction with iodomethane producing an aryl iodide.     

Biophysical and cellular-uptake properties of mixed-sequence pyrrolidine-amide oligonucleotide mimics

Previously we introduced the positively charged pyrrolidine-amide oligonucleotide mimics (POM), which possess a pyrrolidine ring and amide linkage in place of the sugar-phosphodiester backbone of natural nucleic acids. Short POM homo-oligomers have shown promising DNA and RNA recognition properties. However, to better understand the properties of POM and to assess their potential for use as modulators of gene expression and bioanalytical or diagnostic tools, more biologically relevant, longer, mixed-sequence oligomers need to be studied. In light of this, several mixed-sequence POM oligomers were synthesised, along with fluorescently labelled POM oligomers and a POM-peptide conjugate. UV thermal denaturation showed that mixed-sequence POMs hybridise to DNA and RNA with high affinity but slow rates of association and dissociation. The sequence specificity, influence of terminal amino acids, and the effect of pH and ionic strength on the DNA and RNA hybridisation properties of POM were extensively investigated. In addition, isothermal titration calorimetry (ITC) was used to investigate the thermodynamic parameters of the binding of a POM-peptide conjugate to DNA. Cellular uptake experiments have also shown that a fluorescently labelled POM oligomer is taken up into HeLa cells. These findings demonstrate that POM has the potential for use in a variety of applications, alongside other modified nucleic acids developed to date, such as peptide nucleic acids (PNA) and phosphoramidate morpholino oligomers (PMO).     

Electrospray and matrix-assisted laser desorption/ionization mass spectral characterization of linear single nylon-6 oligomers

Synthetic nylon-6 single molecular mass oligomers were studied by matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) mass spectrometry. These oligomers, considered as model compounds for the study of nylon-6 polymers, gave good mass spectrometric results using both MALDI and ESI. In spite of the gentle nature of both techniques, the MALDI and ESI spectra showed evidence of end-group cleavage from the oligomer chains. MALDI-MS was found to give similar fragmentation patterns for all of the oligomer samples. An increase in doubly charged ion signals with increasing oligomer mass was observed in the ESI mass spectra, as was end-group fragmentation. Signals from oligomer clusters were observed in ESI-MS for the dimer, tetramer and hexamer, most likely due to non-covalent bonding among the low-mass oligomer molecules.