Oligomers In Solution Research Articles

Self-Assembly of Coordination Polymers: Evidence for Dynamic Exchange between Oligomers in Solution and the Isolation of a Homochiral Decagold(I) Oligomer

Reactions of the precursor molecules [Au2(mu-BINAP)(O2CCF3)2], 1a, racemic BINAP, 1b, S-BINAP (BINAP = 2,2'-bis(diphenylphosphino)-1,1'-binaphthyl) with the easily exchanged linear bis(pyridine) ligand 1,2-trans-bis(4-pyridyl)ethylene (bipyen) gave the polymeric complex [{Au2(mu-R-BINAP)0.5(mu-S-BINAP)0.5(mu-bipyen)}n](CF3CO2)2n, 2a, but either the polymer [{Au2(mu-S-BINAP)(mu-bipyen)}n](CF3CO2)2n, 2b, or the remarkable oligomeric [Au10(mu-S-BINAP)5(mu-bipyen)4(kappa1-bipyen)2](CF3CO2)10, 3, respectively. The type of oligomer 3 is a missing link in the ring-opening polymerization of macrocyclic coordination compounds.

Long-Lived Conformational Isomerism of Protein Dimers: The Role of the Free Energy of Subunit Association

The association of protein subunits to form N-mers (N≥3) does not follow the dependence on the law of mass action predicted by the classical thermodynamic description used for the equilibrium of association of small molecules. For those anomalous cases, a so-called deterministic model has been previously proposed. The latter model was based on the empirical observation that the dynamics of subunit exchange between protein oligomers can be very slow, leading to the existence of long-lived conformational isomers and to a persistently heterogeneous ensemble of oligomers in solution. Contrary to the expectation for a protein dimer, we have recently shown that the subunit association of triosephosphate isomerase (TIM) could also be described as a deterministic process and that long-lived conformational isomers of TIM could be isolated in solution. Here we show that a), observation of hysteresis in pressure dissociation curves is an additional indicator of deterministic behavior; b), the extent of deviation from the classical thermodynamic behavior correlates with the free-energy change of subunit association; and c), experimental manipulation of the free energy of subunit association through the addition of a subdenaturing concentration of a chaotropic agent restores the concentration dependence of subunit association of TIM. A model that explains these features and its biological relevance is discussed.

Development of Highly Soluble Addition-type Imide Oligomers for Matrix of Carbon Fiber Composite (I): Imide Oligomers Based on Asymmetric Biphenyltetracarboxylic Dianhydride and 9,9-Bis(4-aminophenyl) fluorene

Novel highly soluble addition-type imide oligomers were synthesized from 2,3,3′,4′-biphenyltetracarboxylic dianhydride (a-BPDA), 9,9-bis(4-aminophenyl)fluorene (BAFL), 4,4′-diaminodiphenyl ether (4,4′-ODA), and 4-phenylethynylphthalic anhydride (PEPA) to fabricate carbon fiber-reinforced plastics (CFRP) by routing imide solution prepreg. The imide oligomers were soluble in aprotic polar solvents of more than 35 wt.%. Imide oligomers consisting of less than 50mol% BAFL per total diamine had good processability when using a hot press. The glass transition temperature ( Tg)values of the cured resins were higher than 340°C. The Tg values increased when the BAFL component increased. The 5% weight loss temperatures ( Td5) were higher than 550°C. The elongations-at-break of the BAFL copolymers were less than that of the polymer without BAFL. An imide solution prepreg was prepared from the imide oligomer solution and carbon fibers. Polyimide/carbon fiber composite without voids was fabricated from the imide solution prepreg.

Cooperative Self-Assembly of Oligo(m-phenyleneethynylenes) into Supramolecular Coordination Polymers

Here we report the supramolecular coordination polymerization of four bis-functionalized phenyleneethynylene oligomers. Each oligomer was terminated with pyridyl end groups; three of them had meta backbone linkages and varied in the number of phenyleneethynylene units from four to eight. The fourth oligomer served as a geometric control with para connectivity and three phenyleneethynylene units. Upon the addition of trans-dichlorobis(acetonitrile)palladium to a solution of oligomer, supramolecular assembly by metal coordination was observed by UV spectroscopy, NMR, and isothermal titration calorimetry. For the tetramer and octamer, the experimental evidence is consistent with a cooperative polymerization mechanism involving pyridine−palladium coordination and π-stacking leading to a helical supramolecular polymer. For the hexamer, macrocyclization followed by columnar aggregation was indicated by the data. In contrast, the para-linked control oligomer exhibited noncooperative, isodesmic step-growth polyme...

Electronic spectral and photophysical properties of some p-phenylenevinylene oligomers in solution and thin films

A comprehensive photophysical and spectroscopic study of a new class of p-phenylenevinylene oligomers (PPV-trimers) possessing different alkyl and alkyloxy sidechain substituents and different end groups (aldehyde, C C, phenylene and anthracene units) was undertaken in solution at room temperature (293 K), low temperature (77 K) and in thin films. The study comprises absorption, emission and triplet–triplet absorption spectra, together with quantitative measurements of quantum yields (fluorescence, intersystem crossing, internal conversion and singlet oxygen formation) and lifetimes. The data allow the determination of rate constants for all decay processes. From these, several conclusions could be drawn. Changing from alkyl to alkyloxy substituents does not change fluorescence and internal conversion yields but decreases the (already small) intersystem crossing yield. The introduction of anthracene at the terminal ends of the PPV-trimers leads to the lowest fluorescence yield reported in this study. Of particular importance is the fact that the fluorescence quantum yields in films are of the same order of magnitude as those in solution, which suggests the potential for use of these oligomers for light-emitting device applications. With one of the alkyloxy derivatives, a more detailed study of the early part of the fluorescence decay was made, and it was found that upon excitation a fast conformational relaxation process of the initially excited oligomer occurs, leading to a more planar conjugation segment.

Near-Field Optical Microscopy of Defects in Cholesteric Oligomeric Liquid Crystal Films

This paper describes formation of 2-D-hexagonal structures with a periodicity ∼0.5–0.8 μm in the defects of thin films of cholesteric oligomeric liquid crystals prepared by the evaporation of the solvent from the oligomer solution on the substrate. These regular arrays were observed by scanning near-field optical and concurrent atomic force microscopy. The mechanisms considered are both Bénard-Marangoni and buoyancy convections induced by solvent evaporation and air-bubble creation around the condensed water droplets from the air during evaporative cooling. Hexagonal structures prepared by this method can be used in photonic devices for emission enhancement, for instance, in liquid crystal lasers and single photon sources with oligomeric liquid crystal hosts.

Crystal Structures of Human Tissue Kallikrein 4: Activity Modulation by a Specific Zinc Binding Site

Human tissue kallikrein 4 (hK4) belongs to a 15-member family of closely related serine proteinases. hK4 is predominantly expressed in prostate, activates hK3/PSA, and is up-regulated in prostate and ovarian cancer. We have identified active monomers of recombinant hK4 besides inactive oligomers in solution. hK4 crystallised in the presence of zinc, nickel, and cobalt ions in three crystal forms containing cyclic tetramers and octamers. These structures display a novel metal site between His25 and Glu77 that links the 70–80 loop with the N-terminal segment. Micromolar zinc as present in prostatic fluid inhibits the enzymatic activity of hK4 against fluorogenic substrates. In our measurements, wild-type hK4 exhibited a zinc inhibition constant (IC 50) of 16 μM including a permanent residual activity, in contrast to the zinc-independent mutants H25A and E77A. Since the Ile16 N terminus of wild-type hK4 becomes more accessible for acetylating agents in the presence of zinc, we propose that zinc affects the hK4 active site via the salt-bridge formed between the N terminus and Asp194 required for a functional active site. hK4 possesses an unusual 99-loop that creates a groove-like acidic S2 subsite. These findings explain the observed specificity of hK4 for the P1 to P4 substrate residues. Moreover, hK4 shows a negatively charged surface patch, which may represent an exosite for prime-side substrate recognition.

Environmentally stable organic thin-films transistors: Terminal styryl vs central divinyl benzene building blocks for p-type oligothiophene semiconductors

Abstract A series of linear oligomers combining thiophene, phenyl and vinyl units were designed and synthesized to investigate the influence of the number and sequence of the π-conjugating groups on the stability and performance of organic thin-film transistors. The optical and electrochemical properties of oligomers in solution were investigated by UV–vis absorption and photoluminescence spectroscopies, and cyclic voltammetry. High vacuum evaporated thin films were investigated by optical absorption, X-ray diffraction and AFM, and implemented as p-type semiconducting layers into organic thin-film transistors (OTFTs). Furthermore, shelf-live tests (under ambient conditions) of the OTFTs based on the distyryl-substituted oligomer, DS-2T , show that the mobility was almost unchanged for 100 days, indicating a high environmental stability and the great importance of end-substitution to provide stability against air-oxidation.

Otrzymywanie czastek sferycznych z oligomeru kwasu 3-hydroksymasłowego

Aqueous dispersions of 3-hydroxybutyric acid oligomer (molecular weight 890) were prepared using two physical methods: by solvent evaporation or by solvent diffusion from the emulsion of oligomer solution. Organic solvents were selected from these what would be applied in the future for the production of non-steroid antiphlogistic drugs (CHCl3 or CH2Cl2 for evaporation method and acetone for diffusion method). Due to the projected applications of the aqueous dispersion obtained in medicine we strove for decrease in concentrations of additives used in the system i.e. dispersion stabilizer [poly(vinyl alcohol) - PVAL] and a solvent as well as for the preparation of the particles of diameter Ł 1 mm. The effects of several basic parameters of the process on the dimensions and monodispersity of prepared particles were investigated (Table 1-3, Fig. 1-4). These parameters were as follows: concentration of an oligomer in organic phase (symbol in the Tables [10HB/D]org), concentration of a stabilizer in a continuous phase ([PVAL]woda), ratio of dispersion and continuous phases (O/W) and agitation speed.

Pressure−Volume−Temperature Properties for Binary Oligomeric Solutions of Poly(ethylene glycol) and Poly(ethylene glycol methyl ether) with Acetophenone up to 50 MPa

Pressure−volume−temperature (PVT) properties were measured with a high-pressure densitometer for the oligomeric solutions of acetophenone + poly(ethylene glycol)-200 (PEG-200) and acetophenone + poly(ethylene glycol methyl ether)-350 (PEGME-350) at temperatures from 298.15 K to 348.15 K and pressures up to 50 MPa. While the excess volumes are positive in acetophenone + PEG-200 over the entire composition range, those are found to change from positive to negative with increasing the mole fraction of the solvent in acetophenone + PEGME-350. The pressure effect on the liquid densities can be represented accurately by the Tait equation. Moreover, an empirical equation with two characteristic parameters correlates well the PVT data over the entire experimental conditions for each binary system. The experimental specific volumes were also correlated with the Flory−Orwoll−Vrij (FOV) and the Schotte equations of state to within the experimental uncertainty.

Coordination Chemistry of Tetradentate N-Donor Ligands Containing Two Pyrazolyl−Pyridine Units Separated by a 1,8-Naphthyl Spacer: Dodecanuclear and Tetranuclear Coordination Cages and Cyclic Helicates

The tetradentate ligand L(naph) contains two N-donor bidentate pyrazolyl-pyridine units connected to a 1,8-naphthyl core via methylene spacers; L45 and L56 are chiral ligands with a structure similar to that of L(naph) but bearing pinene groups fused to either C4 and C5 or C5 and C6 of the terminal pyridyl rings. The complexes [Cu(L(naph))](OTf) and [Ag(L(naph))](BF4) have unremarkable mononuclear structures, with Cu(I) being four-coordinate and Ag(I) being two-coordinate with two additional weak interactions (i.e., "2 + 2" coordinate). In contrast, [Cu4(L(naph))4][BF4]4 is a cyclic tetranuclear helicate with a tetrafluoroborate anion in the central cavity, formed by an anion-templating effect; electrospray mass spectrometry (ESMS) spectra show the presence of other cyclic oligomers in solution. The chiral ligands show comparable behavior, with [Cu(L45)](BF4) and [Ag(L45)](ClO4) having similar mononuclear crystal structures and with the ligands being tetradentate chelates. In contrast, [Ag4(L56)4](BF4)4 is a cyclic tetranuclear helicate in which both diastereomers of the complex are present in the crystal; the two diastereomers have similar gross geometries but are significantly different in detail. Despite their different crystal structures, [Ag(L45)](ClO4) and [Ag4(L56)4](BF4)4 behave similarly in solution according to ESMS studies, with a range of cyclic oligomers (up to Ag9L9) forming. With transition-metal dications Co(II), Cu(II), and Cd(II), L(naph) generates a series of unusual dodecanuclear coordination cages [M12(L(naph))18]X24 (X- = ClO4- or BF4-) in which the 12 metal ions occupy the vertices of a truncated tetrahedron and a bridging ligand spans each of the 18 edges. The central cavity of each cage can accommodate four counterions, and each cage molecule is chiral, with all 12 metal trischelates being homochiral; the crystals are racemic. Extensive aromatic stacking between ligands around the periphery of the cages appears to be a significant factor in their assembly. The chiral analogue L45 forms the simpler tetranuclear, tetrahedral coordination cage [Zn4(L45)6](ClO4)(8), with one anion in the central cavity; the steric bulk of the pinene chiral auxiliaries prevents the formation of a dodecanuclear cage, although trace amounts of [Zn12(L45)18](ClO4)24 can be detected in solution by ESMS. Formation of [Zn4(L45)6](ClO4)8 is diastereoselective, with the chirality of the pinene groups controlling the chirality of the tetranuclear cage.

Dynamics of P450 3A4 Oligomers in Solution

In previous studies we have found that P450 3A4 oligomers in solution as well as in the membrane consist of two stable conformers (Davydov at al., 2005, Biochemistry 44:13902; Davydov at al, 2003, BBRC 312:121). These conformers exhibit different accessibility and degree of hydration of the heme pocket, which is thought to be modulated by the interactions of the enzyme with substrates, including allosteric ligands. We suggested that the conformational heterogeneity of P450 3A4 plays an important role in the mechanisms of cooperativity. In our attempts to further investigate conformational heterogeneity and dynamics of P450 3A4 oligomers in solution, we incorporated an SH-reactive fluorescent probe BODIPY C1-IA (N-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-yl)methyl)iodoacetamide) into the protein. The changes in the fluorescence of the probe upon exchange of subunits between the oligomers of labeled and unlabeled preparations of the enzyme were used to assess the kinetic parameters of the formation of the oligomers. We demonstrate that in solution in the absence of detergents P450 3A4 forms very tight oligomers with no detectable subunit exchange in the time frame of our experiments. Addition of a low concentration of the non-ionic detergent Emulgen 913 (0.0025 %–0.015 %) results in a considerable increase in the rate of subunit exchange, which is further facilitated upon substrate 1-PB (1-pyrenebutanol) binding. Our results suggest that the interactions of P4503A4 with1-PB modulate the formation of enzyme oligomers and influences cooperativity. (Supported by NIH grant GM54995 and Center Grant ES06676).

Processing robustness for a phenylethynyl‐terminated polyimide composite

AbstractThe processability of a phenylethynyl‐terminated imide resin matrix (PETI‐5) composite was investigated. Unidirectional prepregs were made through the coating of an N‐methylpyrrolidone solution of an amide acid oligomer (PETAA‐5/NMP) onto unsized IM7 fibers. Two batches of prepregs were used: one was made by the National Aeronautics and Space Administration in house, and the other was from an industrial source. The composite processing robustness was investigated with respect to the prepreg shelf life, the effect of B‐staging conditions, and the optimal processing window. The prepreg rheology and open hole compression (OHC) strengths were not to affected by prolonged ambient storage (i.e., up to 60 days). Rheological measurements indicated that the PETAA‐5/NMP processability was only slightly affected over a wide range of B‐stage temperatures (from 250 to 300°C). The OHC strength values were statistically indistinguishable among laminates consolidated under various B‐staging conditions. An optimal processing window was established with response surface methodology. The IM7/PETAA‐5/NMP prepreg was more sensitive to the consolidation temperature than to the pressure. A good consolidation was achievable at 371°C (700°F)/100 psi, which yielded a room‐temperature OHC strength of 62 ksi. However, the processability declined dramatically at temperatures below 350°C (662°F), as evidenced by the OHC strength values. The processability of the IM7/PETI‐5 prepreg was robust. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 100: 3212–3221, 2006

A Critical Coiled Coil Motif in the Small Terminase, gp16, from Bacteriophage T4: Insights into DNA Packaging Initiation and Assembly of Packaging Motor

Double-stranded DNA packaging in bacteriophages is driven by one of the most powerful force-generating molecular motors reported to date. The phage T4 motor is composed of the small terminase protein, gpl6 (18kDa), the large terminase protein, gp17 (70kDa), and the dodecameric portal protein gp20 (61kDa). gp16, which exists as an oligomer in solution, is involved in the recognition of the viral DNA substrate, the very first step in the DNA packaging pathway, and stimulates the ATPase and packaging activities associated with gp17. Sequence analyses using COILS2 revealed the presence of coiled coil motifs (CCMs) in gp16. Sixteen T4-family and numerous phage small terminases show CCMs in the corresponding region of the protein, suggesting a common structural and functional theme. Biochemical properties such as reversible thermal denaturation and analytical gel filtration data suggest that the central CCM-1 is critical for oligomerization of gp16. Mutations in CCM-1 that change the hydrophobicity of key residues, or pH 6.0, destabilized coiled coil interactions, resulting in a loss of gp16 oligomerization. The gp16 oligomers are in a dynamic equilibrium with lower M(r) intermediate species and monomer. Monomeric gp16 is unable to stimulate gp17-ATPase, an activity essential for DNA packaging, while conversion back into oligomeric form restored the activity. These data for the first time defined a CCM that is critical for structure and function of the small terminase. We postulate a packaging model in which the gp16 CCM is implicated in the regulation of packaging initiation and assembly of a supramolecular DNA packaging machine on the viral concatemer.

Rhombohedral Structure of Highly Ordered and Oriented Self-Assembled Nanoporous Silica Thin Films

Nanoporous silica films have been synthesized by self-assembly on substrates by dip-coating from a combined solution of aged silica oligomers and poly(ethylene oxide)20−poly(propylene oxide)70−poly(ethylene oxides)20 triblock copolymer (Pluronic P123) in ethanol and water. The films are indexed with the rhombohedral space group R3̄m and are oriented through the thickness of the film with the (111) axis perpendicular to the substrate. Sixfold symmetry perpendicular to the substrate is directly observed by high-resolution top-view field emission scanning electron microscopy over the entire substrate. The films have domains that sample many orientations in the plane of the substrate resulting in a reciprocal space composed of rings. These rings are directly observed by collecting small-angle X-ray scattering data at many angles of incidence from transmission (beam perpendicular to the substrate) all the way down to the grazing angle of incidence. At each rotation, the Bragg spot location in the two-dimensional pattern is quantitatively predicted by an R3̄m unit cell with lattice constants a = 112 Å and α = 86°. On the basis of these lattice constants, it is conjectured that the rhombohedral structure results from a uniaxial contraction of a (111) oriented film of self-assembled aggregates ordered on a face-centered cubic lattice. The film structure and orientation reported here differ from previous reports of cubic, or distorted cubic, nanoporous films synthesized with P123 and F127 and are expected to be important steps in controlling structure and accessibility in nanoporous films.

Formation of a solubilized cobalt block oligomer from a M2L-type double helicate

The multi-dentate ligand, 2,3,5,6-tetrakis(2,2'-bipyridyl)pyrazine (L) and divalent cobalt self-assemble to a block co-polymer-like oligomer in solution, which contains at least the L(7)Co(8) fragment. The extent of oligomerization is sensitive to the water content in acetonitrile solution. In the solid state, the simple monomer [LCo(2)(CH(3)CN)(4)][ClO(4)](4) is isolated. The X-ray structure of the crystallized material (containing four CH(3)CN solvate molecules) reveals a double-helical complex with two heptadentate Co(II) sites, and a helical pitch of approximately 28.1 A. Coupled Co(I/II) redox processes are observed between the two metal centres.

Synthesis of linear and cyclic homo-β-peptides based on a binaphthylic β-amino acid with only axial chirality

The terminally protected, linear, homo-β-peptides Boc-[(R)-β2,2-HBin]n-OMe (n=2–6) as well as the cyclic homo-β-peptides c[(R)-β2,2-HBin]3 and c[(S)-β2,2-HBin]4, all derived from the 2′,1′:1,2;1″,2″:3,4-dinaphthcyclohepta-1,3-diene-6-aminomethyl-6-carboxylic acid residue β2,2-HBin possessing only axial chirality, have been synthesized in solution by the EDC/AtOH coupling method for chain elongation, and by cyclization of pentafluorophenyl esters. A conformational analysis suggested the concomitant occurrence of different intramolecularly H-bonded forms for the linear oligomers in solution.

Polaronic semiconductor behavior of long-range charge transfer in DNA oligomers in solution: controlling barriers to long-distance radical cation migration in DNA with thymine analogs

A series of anthraquinone-linked DNA oligonucleotides was prepared and the efficiency of long-distance radical cation migration was measured. In one set of oligonucleotides, two GG steps are separated by either a TATA or an ATAT bridge. In these two compounds, the efficiency of radical cation migration from GG to GG differs by more than an order of magnitude. Replacement of the thymines in the TATA or ATAT bridges with 3-methyl-2-pyridone (t, a thymine analog) results in the much more efficient radical cation migration across the bridge in both cases. This is attributed to a decrease in the oxidation potential of t to a value below that of A. In contrast, replacement of the thymines in the TATA or ATAT bridges with difluorotoluene (f, a thymine analog with high oxidation potential) does not measurably affect radical cation migration. These findings are readily accommodated by the phonon-assisted polaron-hopping mechanism for long-distance charge transfer in duplex DNA and indicate that DNA in solution behaves as a polaronic semiconductor.

Host–guest assembly of pyridinium-conjugated calix[4]arene via cation–π interaction

25-(4-Pyridiniumbutoxy)-26,27,28-trihydroxycalix[4]arene bromide 1 was designed to have both host and guest units in one molecule, and was assembled to become an oligomer via a cation–π interaction. X-ray diffraction (XRD) crystallographic study of 1 revealed that it oriented in a one-dimensional structure. Titrimetric 1H NMR analysis and electrospray ionization mass spectrometry (ESI-MS) analysis indicated that 1 formed an oligomer in solution, and the restraint of the segmental motion would lead to the stabilization of the cation–π interaction compared with a bi-molecular complex composed of 25,26,27,28-tetrahydroxycalix[4]arene and N-butylpyridinium bromide.

The polymerization of actin: Structural changes from small-angle neutron scattering

We present a new analysis of small-angle neutron-scattering data from rabbit muscle actin in the course of the polymerization from G-actin to F-actin as a function of temperature. The data, from Ivkov et al. [J. Chem. Phys. 108, 5599 (1998)], were taken in D2O buffer with Ca2+ as the divalent cation on the G-actin in the presence of ATP and with KCl as the initiating salt. The new analysis of the data using modeling and the method of generalized indirect fourier transform (O. Glatter, GIFT, University of Graz, Austria, http://physchem.kfunigraz.ac.at/sm/) provide shapes and dimensions of the G-actin monomer and of the growing actin oligomer in solution as a function of temperature and salt concentration. This analysis indicates that the G-actin monomer, under the conditions given above, is a sphere 50-54 A in diameter as opposed to the oblate ellipsoid seen by x-ray crystallography. The F-actin dimensions are consistent with x-ray crystal structure determinations.