Effects of oligoDNA template length and sequence on binary self-assembly of a nucleotide bolaamphiphile

Templated self-assembly of nucleotide bolaamphiphile 1 (in which a 3'-phosphorylated thymidine moiety is connected to each end of a long oligomethylene chain) with a 10-, 20-, 30-, or 40-meric single-stranded oligoadenylic acid (2, 3, 4, or 5) led to the formation of right-handed helical nanofibers in 0.1x Tris/EDTA (TE) buffer solutions. The helical pitch increased as the length of the oligoadenylic acid template increased. DNA composed of oligoadenylic and oligocytidylic acid sequences (6, 7, and 8) also acted as templates to induce the formation of helical nanofiber structures. The diameter of the nanofibers remained constant (6-6.6 nm) irrespective of the template used. The binary self-assembly of 1 with 4 also produced higher-order, double-stranded nanofibers.     

Oligo(p-phenylenevinylene)-peptide conjugates: synthesis and self-assembly in solution and at the solid-liquid interface

Two oligo(p-phenylenevinylene)-peptide hybrid amphiphiles have been synthesized using solid- and liquid-phase strategies. The amphiliphiles are composed of a pi-conjugated oligo(p-phenylenevinylene) trimer (OPV) which is coupled at either a glycinyl-alanyl-glycinyl-alanyl-glycine (GAGAG) silk-inspired beta-sheet or a glycinyl-alanyl-asparagyl-prolyl-asparagy-alanyl-alanyl-glycine (GANPNAAG) beta-turn forming oligopeptide sequence. The solid-phase strategy enables one to use longer peptides if strong acidic conditions are avoided, whereas the solution-phase coupling gives better yields. The study of the two-dimensional (2D) self-assembly of OPV-GAGAG by scanning tunneling microscopy (STM) at the submolecular level demonstrated the formation of bilayers in which the molecules are lying antiparallel in a beta-sheet conformation. In the case of OPV-GANPNAAG self-assembled monolayers could not be observed. Absorption, fluorescence, and circular dichroism studies showed that OPV-GAGAG and OPV-GANPNAAG are aggregated in a variety of organic solvents. In water cryogenic temperature transmission electron microscopy (cryo-TEM), atomic force microscopy (AFM), light scattering, and optical studies reveal that self-assembled nanofibers are formed in which the helical organization of the OPV segments is dictated by the peptide sequence.     

The influence of hydrogen bonding and pi-pi stacking interactions on the self-assembly properties of C3-symmetrical oligo(p-phenylenevinylene) discs

Three C3-symmetrical discotics containing a 1,3,5-benzenetricarboxamide unit functionalized with pi-conjugated oligo(p-phenylenevinylene)s (OPV)s have been synthesized and fully characterized. For the two amide OPV discs a two-step transition from helical stacks to molecularly dissolved species was observed and surprisingly, the topology of the amide determines the stability and helicity of the fibers in solution and the length of the fibrils at a surface. In case of the bipyridine disc, aggregates were formed that show little chiral ordering while the stacks remain present over a large temperature range. At a surface, completely disordered structures exist probably as a result of competing types of pi-pi stacking interactions that differ in strength and orientation. The results show that the design of functional self-assembled architectures based on hydrogen bonding and pi-pi stacking interactions is an extremely delicate matter and reveal that special demands have to be taken into account to balance the topology, directionality and strength of multiple secondary interactions.     

Hierarchical self-assembly of a biomimetic diblock copolypeptoid into homochiral superhelices

The aqueous self-assembly of a sequence-specific bioinspired peptoid diblock copolymer into monodisperse superhelices is demonstrated to be the result of a hierarchical process, strongly dependent on the charging level of the molecule. The partially charged amphiphilic diblock copolypeptoid 30-mer, [N-(2-phenethyl)glycine](15)-[N-(2-carboxyethyl)glycine](15), forms superhelices in high yields, with diameters of 624 ± 69 nm and lengths ranging from 2 to 20 μm. Chemical analogs coupled with X-ray scattering and crystallography of a model compound have been used to develop a hierarchical model of self-assembly. Lamellar stacks roll up to form a supramolecular double helical structure with the internal ordering of the stacks being mediated by crystalline aromatic side chain-side chain interactions within the hydrophobic block. The role of electrostatic and hydrogen bonding interactions in the hydrophilic block is also investigated and found to be important in the self-assembly process.     

Probing a conjugated polymer's transfer of organization-dependent properties from solutions to films

The dynamic transfer of a conjugated polymer's organization-dependent properties from the solution state to the solid film state was probed by circularly polarized luminescence (CPL) and circular dichroism (CD) spectroscopy. Different supramolecular organizations within films and aggregate solutions of a chiral poly(p-phenylenevinylene) derivative led to opposite CPL and CD spectra. These dramatic property differences were controlled by regulating the polymer's self-assembly through solvent selection and film annealing. Therefore, different processing conditions can greatly affect the functional properties of conjugated polymer films employed in various optoelectronic applications.     

Bridged bis(beta-cyclodextrin)s possessing coordinated metal center(s) and their inclusion complexation behavior with model substrates: enhanced molecular binding ability by multiple recognition.

To investigate quantitatively the cooperative binding ability of several beta-cyclodextrin oligomers bearing single or multiligated metal center(s), the inclusion complexation behavior of four bis(beta-cyclodextrin)s (2-5) linked by 2,2'-bipyridine-4,4'-dicarboxy tethers and their copper(II) complexes (6-9) with representative dye guests, i.e., methyl orange (MO), acridine red (AR), rhodamine B (RhB), ammonium 8-anilino-1-naphthalenesulfonic acid (ANS), and sodium 6-(p-toludino)-2-naphthalenesulfonate (TNS), have been examined in aqueous solution at 25 degrees C by means of UV-vis, circular dichroism, fluorescence, and 2D NMR spectroscopy. The results obtained indicate that bis(beta-cyclodextrin)s 2-5 can associate with one or three copper(II) ion(s) producing 2:1 or 2:3 bis(beta-cyclodextrin)-copper(II) complexes. These metal-ligated oligo(beta-cyclodextrin)s can bind two model substrates to form intramolecular 2:2 host-guest inclusion complexes and thus significantly enhance the original binding abilities of parent beta-cyclodextrin and bis(beta-cyclodextrin) toward model substrates through the cooperative binding of two guest molecules by four tethered cyclodextrin moieties, as well as the additional binding effect supplied by ligated metal center(s). Host 6 showed the highest enhancement of the stability constant, up to 38.3 times for ANS as compared with parent beta-cyclodextrin. The molecular binding mode and stability constant of substrates by bridged bis- and oligo(beta-cyclodextrin)s 2-9 are discussed from the viewpoint of the size/shape-fit interaction and molecular multiple recognition between host and guest.     

Helical arrangement of a hydrogen‐bonded columnar liquid crystal induced by a centered triphenylene derivative bearing chiral side‐chains

A hydrogen‐bonded helical columnar liquid crystal was synthesized, in which the helical structure is induced by a centered triphenylene derivative bearing chiral side‐chains. The triphenylene derivative, 2,6,10‐tris(carboxymethoxy)‐3,7,11‐tris((S)‐(‐)‐2‐methyl‐1‐butanoxy)triphenylene ( TPC4(S) ), and a dendric amphiphile, 3,5‐bis‐(3,4‐bis‐dodecyloxy‐benzyloxy)‐N‐pyridine‐4‐yl‐benzamide ( DenC12 ), were mixed in a 1:3 ratio to obtain a complex, TPC4(S)‐DenC12 . Analyses by ¹H‐NMR spectroscopy, diffusion ordered spectroscopy (DOSY), CD spectroscopy, infrared (IR) spectroscopy, polarized optical microscopy (POM), differential scanning calorimetry (DSC), and X‐ray diffractometry revealed that TPC4(S)‐DenC12 self‐assembles to form helical columnar stacks in solution and a helical columnar liquid crystal in bulk. The hydrogen bonding between TPC4(S) and DenC12 is essential for the helical columnar organization, and the preference for a one‐handed helical conformation is likely derived from the steric interaction between the chiral side‐chains and the dendric amphiphiles in the packing of the hydrogen‐bonded columnar assemblies. Copyright © 2008 John Wiley & Sons, Ltd.     

Oligomer-to-polymer transition in short ethylene glycol chains connected to mobile hydrophobic anchors.

We studied the structure of short ethylene glycol (EG) chains with N repeating units (EGN, N = 3, 6, 9, 12, and 15) connected to hydrophobic dihexadecyl chains by means of a combination of differential scanning calorimetry (DSC) and small- and wide-angle X-ray scattering (SAXS/WAXS). These synthetic amphiphiles dispersed in water form planar lamellar stacks and hexagonal cylinders confining the EG chains to restricted geometries. Owing to the self-assembly of the anchoring points, the lateral density of EG chains in planar lamella can be quantitatively controlled. Furthermore, the chain-melting phase transition of the anchors enables us to "switch" the intermolecular distance reversibly. SAXS/WAXS results suggest that the shorter EG chains (N = 3, 6, and 9) assume a helical conformation in stacks of planar lamella. When the EG chains are further elongated (N = 12 and 15), the lamellar periodicities cannot be explained by a linear extrapolation of shorter oligomers, but can be interpreted well as polymer brushes following the scaling theorem. Such rich phase behaviors of EGN molecules can be used as a simple model of oligo/poly-saccharide chains on cell surfaces, which act not only as flexible repellers between neighboring cells but also as stable spacers for functional ligands.     

Evaluation of NMR diffusion measurements for the conformational analysis of flexible peptides

The use of diffusion coefficients measured with pulsed-field gradient NMR spectroscopy for the determination of the relative population of conformers in solutions of the human Growth Hormone peptide fragment, hGH(9–19), has been studied in aqueous and in trifluoroethanol (TFE)/ water solutions. The peptide is a good model compound for this study because it adopts a predominantly random coil conformation in aqueous solution and is helical in TFE. The results of the diffusion measurements suggest that the peptide exhibits predominantly random coil structures in aqueous solution and adopts a more helical conformation in solutions containing increasing mole fractions of TFE, consistent with the qualitative findings of the standard CD and NMR experiments to probe peptide conformation. These results indicate that diffusion coefficients measured with NMR can provide additional information about temperature- and solvent-induced changes in the extent of the helical conformer for hGH(9–19) in aqueous solution and in solutions containing various mole fraction of TFE, respectively.     

Evaluation of NMR diffusion measurements for the conformational analysis of flexible peptides

The use of diffusion coefficients measured with pulsed-field gradient NMR spectroscopy for the determination of the relative population of conformers in solutions of the human Growth Hormone peptide fragment, hGH(9-19), has been studied in aqueous and in trifluoroethanol (TFE)/ water solutions. The peptide is a good model compound for this study because it adopts a predominantly random coil conformation in aqueous solution and is helical in TFE. The results of the diffusion measurements suggest that the peptide exhibits predominantly random coil structures in aqueous solution and adopts a more helical conformation in solutions containing increasing mole fractions of TFE, consistent with the qualitative findings of the standard CD and NMR experiments to probe peptide conformation. These results indicate that diffusion coefficients measured with NMR can provide additional information about temperature- and solvent-induced changes in the extent of the helical conformer for hGH(9-19) in aqueous solution and in solutions containing various mole fraction of TFE, respectively.     

Unexpected chain length dependence on a chiral memory effect of ‘meta-ethynylpyridine’ oligomers

The chain length dependence involving a chiral memory effect of 2,6-pyridylene ethynylene oligomers ‘meta-ethynylpyridines’ was investigated. The meta-ethynylpyridine oligomers associated with octyl β-d-glucopyranoside form a helical complex giving induced CD; the induced chirality could be memorized with the help of Cu(OTf)₂ as an additive. Contrary to our expectations, the study of the length dependence revealed that the 12-meric oligomer showed a more sustainable chiral memory effect than those observed in both of the shorter 6-meric and longer 18-meric oligomers.     

PHOTO-OXIDATION OF THYMINE SENSITIZED BY 2-METHYL-1,4-NAPHTHOQUINONE: ANALYSIS OF PRODUCTS INCLUDING THREE NOVEL PHOTO-DIMERS

Abstract —The near-UV photosensitization of thymine by 2-methyl-1,4-naphthoquinone in oxygenated aqueous solution leads to the formation of nine major thymine-derived products. Six of the photoproducts, representing 70% of the initial thymine loss, are also known to be formed by γ-ray or X-ray irradiation of oxygenated water solutions of thymine. They include the cis and trans isomers of 5-hydroperoxy-6-hydroxy-5,6-dihydrothymine, the cis and trans thymine glycols, 5-hydroxy-5-methylhydantoin, and N-formyl-N'-pyruvylurea. The three remaining major products, accounting for a further 25% of the initial thymine loss, are thymine di-adducts of a type not previously reported. Preliminary characterization of these novel photoproducts, based on their UV absorption, mass spectra, and proton and carbon-13 nuclear magnetic resonance spectra, suggests that in each of the three, the thymine moieties are linked by an N(1)-C(5) or N(1)-C(6) bond. A thymine cation radical is implicated as the common precursor of all 9 products. Accordingly. pyrimidine photosensitization by 2-methyl-1,4-naphthoquinone serves as a model system for studying the chemical consequences of radiation-induced ionization of the DNA bases.     

Right-handed helical structure of expanded oligo(L-leucine) containing [Ru(terpyridine)2]2+ moieties

Expanded oligo(l-leucine)s, containing an alternate arrangement of a bis(terpyridine)ruthenium(II) moiety and a l-leucine residue, were synthesized and characterized by 1H NMR, UV, CD, and electrochemical properties. The intensity of CD spectra per ruthenium unit increased with the elongation of the peptide chain. 1H NMR analysis of a tetramer indicated the right-handed helical structure in acetonitrile.     

Analogs of pyrimidine nucleosides. 20. Aminomethylation of 5-fluorouracil and thymine

Reactions were studied of 5-fluorouracil and thymine with formaldehyde and secondary amines (piperidine, morpholine) and also of their 2,4-bis(trimethylsilyl) derivatives with N-methoxymethylmorpholine and bis(amino)methanes. The N-aminomethylation products are slightly stable and in aqueous solutions decompose readily to the starting components; their structure was confirmed by PMR spectra.For Communication 19, see [1].Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 1, pp. 90–93, January, 1987.     

A series of chiral coordination polymers containing helicals assembled from a new chiral (R)-2-(4'-(4'-carboxybenzyloxy)phenoxy)propanoic acid: syntheses, structures and photoluminescent properties

Ten new chiral coordination polymers, namely, [Ni(L)(H(2)O)(2)] (1), [Co(L)(H(2)O)(2)] (2), [Cd(L)(H(2)O)] (3), [Cd(L)(phen)] (4), [Mn(2)(L)(2) (phen)(2)]·H(2)O (5), [Cd(2)(L)(2)(biim-4)(2)] (6), [Zn(2)(L)(2)(biim-4)(2)] (7), [Cd(L)(pbib)] (8), [Cd(L)(bbtz)] (9) and [Cd(L)(biim-6)] (10), where phen = 1,10-phenathroline, biim-4 = 1,1'-(1,4-butanediyl)bis(imidazole), pbib = 1,4-bis(imidazole-1-ylmethyl)benzene, bbtz = 1,4-bis(1,2,4-triazol-1-ylmethyl)benzene, biim-6 = 1,1'-(1,6-hexanedidyl)bis(imidazole), and H(2)L = (R)-2-(4'-(4'-carboxybenzyloxy)phenoxy)propanoic acid, have been synthesized under hydrothermal conditions. Their structures have been determined by single-crystal X-ray diffraction analyses and further characterized by infrared spectra (IR), powder X-ray diffraction (PXRD), elemental analyses and thermogravimetric (TG) analyses. Compounds 1 and 2 exhibit similar 1D left-handed helical chains, which are further extended into 3D supramolecular structures through O-H···O hydrogen-bonding interactions, respectively. Compound 3 shows a 2D double-layer architecture containing helical chains. Compound 4 features two types of 2D undulated sheets with helical chains, which are stacked in an ABAB fashion along the c direction. Compound 5 possesses a 1D double chain ribbon structure containing unusual meso-helical chains, which is linked by π-π interactions into a 2D supramolecular layer. These layers are further extended by hydrogen-bonding interactions to form a 3D supramolecular assembly. Compounds 6 and 7 are isostructural and exhibit 2D (4(4))-sql networks with helical chains. Neighboring sheets are further linked by C-H···O hydrogen-bonding interactions to generate 3D supramolecular architectures. Compounds 8-10 are isostructural and display 3D 3-fold interpenetrating diamond frameworks with helical chains. The effects of coordination modes of L anions, metal ions and N-donor ligands on the structures of the coordination polymers have been discussed. The luminescent properties of 3, 4 and 6-10 have also been investigated in detail.     

Mg-mediated self-assembly of an amphiphilic pyrene derivative with single-stranded DNA

An amphiphilic ethynyl-pyrene derivative modified with phosphonic acid groups (PyTOH) was synthesized and characterized. Single-stranded DNA (ssDNA), which carries negative charges, was found to induce the self-assembly of PyTOH through electrostatic interactions with Mg²⁺ as co-complexation ion in aqueous solution. UV-vis, fluorescence, and circular dichroism (CD) spectra revealed that left-handed helical architecture of PyTOH/Mg²⁺/DNA was formed. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) showed that nanoscale structures could be fabricated by self-assembly.     

Synthesis and micropatterning properties of a novel base‐soluble,positive‐working,photosensitive polyimide having an o‐nitrobenzyl ether group

A novel positive‐working, photosensitive polyimide, poly[1,4‐phenyleneoxy‐1,4‐phenylene‐2,2′‐di(2‐nitrobenzyloxy)benzophenone‐3,3′,4,4′‐tetracarboxdiimide] (OPI‐Nb), developable with an aqueous base was prepared by the o‐nitrobenzylation of a polyimide, poly(1,4‐phenyleneoxy‐1,4‐phenylene‐2,2′‐dihydroxybenzophenone‐3,3′,4,4′‐tetracarboxdiimide) (OPI), derived from 2,2′‐dihydroxy‐3,3′,4,4′‐benzophenonetetracarboxylic dianhydride (DHBA) and 4,4′‐oxydianiline, and it micropatterning properties were investigated. The o‐nitrobenzylation of OPI to OPI‐Nb was conducted with o‐nitrobenzyl bromide in N‐methyl‐2‐pyrrolidinone containing Et₃N. The DHBA monomer was synthesized by exhaustive KMnO₄ oxidation of bis(2‐dimethoxy‐3,4‐dimethylphenyl)methane obtained by etherification of bis(2‐hydroxy‐3,4‐dimethylphenyl)methane with iodomethane, followed by deprotection of the methoxy groups and cyclodehydration of the obtained 2,2′‐dihydroxy‐3,3′4,4′‐benzophenonetetracarboxylic acid. The intermediate bis(2‐hydroxy‐3,4‐dimethylphenyl)methane was prepared by the condensation of 2,3‐dimethylphenol with paraformaldehyde. The degree of o‐nitrobenzylation was determined to be over 94 mol % from ¹H NMR absorption of benzylic CH₂ protons. The aromatic OPI was perfectly soluble in a dilute aqueous NaOH solution and tetramethylammonium hydroxide (TMAH), whereas OPI‐Nb was not even swellable in them. In the micropatterning process, OPI‐Nb showed a line‐width resolution of 0.4‐μm and a sensitivity of 5.4 J/cm² when its thin films were irradiated with 365‐nm light and developed with a 2.38% aqueous TMAH solution at room temperature for 90 s. The thickness loss of OPI‐Nb films measured after postbaking at 350 °C was in the 8–9% range. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 776–788, 2007     

Study of aggregation induced emission of cyano-substituted oligo (p-phenylenevinylene) by femtosecond time resolved fluorescence

The aggregation induced emission (AIE) mechanism of the cyano-substituted oligo (p-phenylenevinylene)1,4-bis [1-cyano-2-(4-(diphenylamino) phenyl) vinyl] benzene (TPCNDSB) is investigated by time resolved fluorescence technique. By reconstructing the time resolved emission spectra (TRES), it is found that in solvent of low polarity, the emission is mainly from the local emission (LE) state with high quantum yield, but in high polarity solvent, the emission is mainly from the intramolecular charge transfer (ICT) state, which is a relatively dark state, with low quantum yield. In crystal form, the restriction of transfer from LE state to ICT state results in efficient AIE.     

Spectrophotometric study on the controlling factor of molecular selective binding of dyes by bridged bis(beta-cyclodextrin)s with diselenobis(benzoyl) linkers

A series of beta-cyclodextrin (beta-CD) dimers with 4,4'-diselenobis(benzoyl) linkers, that is, 6,6'-[4,4'-diselenobis(benzoyloxyl)]-bridged bis(beta-CD) (1a), 6,6'-[4,4'-diselenobis[2-(benzoylamino)ethyleneamino]]-bridged bis(beta-CD) (2a), and 6,6'-[4,4'-diselenobis[2-(benzoylamino)-3,6-diazaoctylamino]]-bridged bis(beta-CD) (3a), were synthesized in moderate yields by the reaction of 4,4'-diselenobis(benzoic acid) with beta-CD or oligo(ethylenediamino)-6-deoxy-beta-CD. Their binding behaviors with some structure-related substrates, such as acridine red (AR), neutral red (NR), rhodamine B (RhB), ammonium 8-anilino-1-naphthalenesulfonate (ANS), and 6-p-toluidino-2-naphthalenesulfonic acid (TNS), were investigated in aqueous phosphate buffer solution (pH 7.20) at 298.15 K by means of fluorescence, NMR, as well as circular dichroism spectroscopy and compared with those of their 2,2'-diselenobis(benzoyl)-linked analogues, that is, 6,6'-[2,2'-diselenobis(benzoyloxyl)]-bridged bis(beta-CD) (1b), 6,6'-[2,3'-diselenobis[2-(benzoylamino)ethyleneamino]]-bridged bis(beta-CD) (2b), and 6,6'-[2,2'-diselenobis[2-(benzoylamino)-3,6-diazaoctylamino]]-bridged bis(beta-CD) (3b). The results showed that bis(beta-CD)s 1a-3a, whose Se-Se bonds were located at the para position of the carboxyl group, gave stronger binding abilities toward nonlinear guests (RhB and ANS) than their analogues 1b-3b, whose Se-Se bonds were located at the ortho position relative to the carboxyl group. The molecular binding ability and selectivity of model substrates by these ditopic hosts were sufficiently discussed to reveal not only the cooperative contributions of the linker group and CD cavities upon inclusion complexation with dye guest molecules but also the controlling factors for the molecular selective binding.     

Helical supramolecular self-assembly by prolamide thymidine/uridine analogues

This report describes the syntheses of rationally designed non-sugar nucleoside as prolamide nucleosides which contain prolyl ring and pyrimidine nucleobases (uracil/thymine) via acetamide bonds. These nucleosides have propensity to form distinctive self-assembly supramolecular helical structures ubiquitously through Watson-Crick/reverse type of hydrogen bonding with nucleobases. Moreover, the prolyl acetamide backbone groups- carbonyl (-C = O) and hydroxyl (-OH) group, are also involved in strengthening of self-assembled helical structures. Importantly, both prolamide thymidine and prolamide uridine have shown two distinctive helical structural patterns, in spite of containing the same backbone. Hence thymine and uracil moieties of prolamide nucleosides are responsible for unique supramolecular helical structural architectures.