Growth Of Oligomers Research Articles

Formation of Amyloid Fibrils via Longitudinal Growth of Oligomers

Mature amyloid fibrils are believed to be formed by the lateral association of discrete structural units designated as protofibrils, but this lateral association of protofibrils has never been directly observed. We have recently characterized a thioesterase from Alcaligenes faecalis, which was shown to exist as homomeric oligomers with an average diameter of 21.6 nm consisting of 22 kDa subunits in predominantly beta-sheet structure. In this study, we have shown that upon incubation in a 75% ethanol solution, the oligomeric particles of protein were transformed into amyloid-like fibrils. TEM pictures obtained at various stages during fibril growth helped us to understand to a certain extent the early events in the fibrillization process. When incubated in 75% ethanol, oligomeric particles of protein grew to approximately 35-40 nm in diameter before fusion. Fusion of two oligomers of 35-40 nm resulted in the formation of a fibril. Fibril formation was accompanied by a reduction in the diameter of the particle to approximately 20-25 nm along with concomitant elongation to approximately 110 nm, indicating reorganization and strengthening of the structure. The elongation process continued by sequential addition of oligomeric units to give fibers 500-1000 nm in length with a further reduction in diameter to 17-20 nm. Further elongation resulted in the formation of fibers that were more than 4000 nm in length; the diameter, however, remained constant at 17-20 nm. These data clearly show that the mature fibrils have assembled via longitudinal growth of oligomers and not via lateral association of protofibrils.

Monomer adds to preformed structured oligomers of Abeta-peptides by a two-stage dock-lock mechanism.

Nonfibrillar soluble oligomers, which are intermediates in the transition from monomers to amyloid fibrils, may be the toxic species in Alzheimer's disease. To monitor the early events that direct assembly of amyloidogenic peptides we probe the dynamics of formation of (Abeta(16-22))(n) by adding a monomer to a preformed (Abeta(16-22))(n-1) (n = 4-6) oligomer in which the peptides are arranged in an antiparallel beta-sheet conformation. All atom molecular dynamics simulations in water and multiple long trajectories, for a cumulative time of 6.9 mus, show that the oligomer grows by a two-stage dock-lock mechanism. The largest conformational change in the added disordered monomer occurs during the rapid ( approximately 50 ns) first dock stage in which the beta-strand content of the monomer increases substantially from a low initial value. In the second slow-lock phase, the monomer rearranges to form in register antiparallel structures. Surprisingly, the mobile structured oligomers undergo large conformational changes in order to accommodate the added monomer. The time needed to incorporate the monomer into the fluid-like oligomer grows even when n = 6, which suggests that the critical nucleus size must exceed six. Stable antiparallel structure formation exceeds hundreds of nanoseconds even though frequent interpeptide collisions occur at elevated monomer concentrations used in the simulations. The dock-lock mechanism should be a generic mechanism for growth of oligomers of amyloidogenic peptides.

Photochemical oligomerization pathways in 2,5-diiodothiophene film

The photochemical oligomerization mechanisms of 2,5-diiodothiopene in a multilayer film was studied with matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). The photo-dissociation of 2,5-diiodothiophene and subsequent reactions of the dissociated radical with surrounding molecules and other radicals can lead to the growth of oligothiophene species. The molecular weight distribution of the oligothiophene products indicated that the average number of iodine atoms in the oligothiophene molecule increases with the number of thiophenyl units in the molecule. All possible oligomerization mechanisms could be categorized in two pathways—the oligomer growth by insertion of a thiophenyl unit versus the growth by insertion of an iodothiophenyl unit. Using a modified Flory's model for a linear step polymerization process, we found that the probability of thiophenyl and iodothiophenyl insertion in each C C bond formation is ∼0.63 and ∼0.37, respectively. The model also predicted the most probable oligomer length to be about 3–4, which was consistent with the photoluminescence and FTIR analysis.

Critical Effect of Surfactant Concentration on the Structure of Mesoporous Silica Films Prepared on a Substrate Coated with Rubbing-Treated Polyimide

The change of nonionic surfactant C16(EO)10 (Brij56) concentration has a critical effect on the structure of mesoporous silica films grown hydrothermally on a substrate coated with a rubbing-treated polyimide film. The uniaxially aligned two-dimensional (2D) hexagonal mesoporous structure changes into a “single-crystalline” three-dimensional (3D) hexagonal structure, which means that the in-plane arrangement of spherical pores of the 3D-hexagonal structure is fully controlled, by simply decreasing the surfactant concentration. The investigation of the early stages of the film formation suggests that the initial formation of the uniaxially aligned tubular micelles and the subsequent transformation to the spherical ones are included in the formation mechanism. It is considered that such a transformation is caused by the increase in the size of headgroups of the building units, consisting of the surfactants and silica oligomers, due to the progress of silica condensation. The small association number of surfactant molecules in the building units would allow the growth of silica oligomers in the headgroups to the level that induces the total restructuring.

Cross-condensation and particle growth in aqueous silane mixtures at low concentration

We have observed the condensation of a mixture of γ-glycidoxypropylmethyldiethoxysilane and 3-aminopropyltriethoxysilane in dilute aqueous solutions. NMR and IR spectroscopy have allowed to follow the condensation process in the mixture, which is noticeably enhanced and proceeds faster than for each silane on its own. Cross-condensation between the two silanes was evidenced. When the hydrophilic aminosilane is in excess, the condensation, as evidenced by dynamic light scattering, proceeds toward gel formation because the oligomers formed are essentially hydrophilic. When the more hydrophobic epoxysilane is in excess, oligomer growth proceeds slowly and results in a destabilization of the solution: due to their hydrophobic character, the oligomers formed coalesce suddenly into 200-nm-diameter aggregates. Coatings deposited from such solutions with high epoxysilane content can be used to strengthen glass. We show that the progress of condensation in solution results in a wetting transition during deposition of the silane film on glass by dip coating. The production of increasingly hydrophobic oligomers as the reaction time increases results in adsorption of more hydrophobic aggregates at the surface, which eventually leads to dewetting of the film: in the absence of film, glass strengthening disappears.

Ultrathin film growth of p-phenylene oligomers on alkali halide substrates

Controlled growth of the aromatic p-phenylene oligomer molecules ( p-quaterphenyl, p-quinquephenyl, and p-sexiphenyl) adsorbed onto individual KBr(0 0 1), KCl(0 0 1), NaCl(0 0 1), and NaF(0 0 1) substrates has been investigated by X-ray diffraction (XRD). XRD analysis provides evidence that the temperature of the alkali halide substrate during deposition, substrate lattice constant, and molecular length affect the molecular orientations within these adsorbed ultrathin films. From this work, oriented films of the above-mentioned p-phenylene oligomer molecules can therefore be grown with varying molecular orientations by careful selection of an appropriate combination of the above deposition parameters.

Spontaneous Gas‐Phase Generation of Needle‐Shaped Clusters which Violate the Isolated Square Rule: A Facile Road to GaN Nanorods?

AbstractFor Abstract see ChemInform Abstract in Full Text.

Spontaneous gas-phase generation of needle-shaped clusters which violate the isolated square rule: a facile road to GaN nanorods?

Structures and thermodynamic properties of the imidogallanes [HGaNH](n) with high oligomerization degrees n = 7-16 and related amido-imido compounds have been investigated theoretically at the B3LYP level of theory with all-electron pVDZ and effective core potential LANL2DZ(d,p) basis sets. Needle-shaped oligomers which violate the "isolated square rule" were found to be more stable than cage isomers. The needle-shape oligomer with n = 16 is predicted to be exceptionally stable at low temperatures. Octamer and hexamer clusters dominate the gas phase at higher temperatures. The highest oligomerization degree of the spontaneous cluster formation has been estimated. It is concluded that generation of the gas-phase [HGaNH](n) clusters with oligomerization degree n >or= 60 is viable. This makes these species possible intermediates involved in the gas-phase generation of GaN nanoparticles. A case study of methyl-substituted analogues suggests that formation of the gaseous [MeGaNH](n) oligomers is even more favorable compared to that of [HGaNH](n). We predict that spontaneous growth of GaN oligomers is favorable thermodynamically. Laser-assisted generation of GaN nanorods at low-temperature conditions appears to be feasible.

Supramolecular Structures of Zinc (II) (8-Quinolinolato) Chelates

We investigate the oligomeric purity and stability of zinc (8-quinolinolato) (Znq2) and its methylated derivatives (nMeq2Zn, n = 2, 4, 5) through a combination of theoretical modeling of oligomerization energetics leading to supramolecular structures and experimental size-exclusion chromatography studies. Gas- and solution-phase (CHCl3) formation energies for dimeric, trimeric, and tetrameric species are reported. Favorable gas-phase thermodynamics were calculated and found to favor tetrameric structures for all Znq2 chelates (∼−50 kcal/mol for monomer dimerization to ∼−35 kcal/mol for dimer dimerization), with the exception of 2Meq2Zn, which gave lower formation energies by 30−45% due to steric hindrance. Solvation model computations indicate that these energies are reduced by ∼10−25% with the introduction of a dielectric medium. Computed structural parameters for the basic Zn−O core structure formed via bridging of phenolato oxygens do not change significantly as oligomer growth progresses. Size-exclusion chromatography experiments of crystalline and amorphous films (vapor deposited) dissolved in CHCl3 or CHCl3/DMSO mixtures showed that the dominant species for Znq2, 4Meq2Zn, and 5Meq2Zn is tetrameric, but partial disassociation to monomers can occur in the presence of nucleophilic solvent. The sterically hindered 2Meq2Zn was monomeric in all solvent systems. Implications for organic light-emitting devices using these materials are discussed.

Human Amylin Oligomer Growth and Fibril Elongation Define Two Distinct Phases in Amyloid Formation

Human amylin (hA), a 37-amino-acid polypeptide, is one of a number of peptides with the ability to form amyloid fibrils and cause disease. It is the main constituent of the pancreatic amyloid deposits associated with type 2 diabetes. Increasing interest in early assembly intermediates rather than the mature fibrils as the cytotoxic agent has led to this study in which the smallest hA oligomers have been captured by atomic force microscopy. These are 2.3 +/- 1.9 nm in height, 23 +/- 14 nm in length, and consist of an estimated 16 hA molecules. Oligomers first grow to a height of about 6 nm before they begin to significantly elongate into fibrils. Congo red inhibits elongation but not the growth in height of hA oligomers. Two distinct phases have thus been identified in hA fibrillogenesis: lateral growth of oligomers followed by longitudinal growth into mature fibrils. These observations suggest that mature fibrils are assembled directly via longitudinal growth of full-width oligomers, making assembly by lateral association of protofibrils appear less likely.

Molecular dynamics simulations of alanine rich beta-sheet oligomers: Insight into amyloid formation.

The aggregation observed in protein conformational diseases is the outcome of significant new beta-sheet structure not present in the native state. Peptide model systems have been useful in studies of fibril aggregate formation. Experimentally, it was found that a short peptide AGAAAAGA is one of the most highly amyloidogenic peptides. This peptide corresponds to the Syrian hamster prion protein (ShPrP) residues 113-120. The peptide was observed to be conserved in all species for which the PrP sequence has been determined. We have simulated the stabilities of oligomeric AGAAAAGA and AAAAAAAA (A8) by molecular dynamic simulations. Oligomers of both AGAAAAGA and AAAAAAAA were found to be stable when the size is 6 to 8 (hexamer to octamer). Subsequent simulation of an additional alpha-helical AAAAAAAA placed on the A8-octamer surface has revealed molecular events related to conformational change and oligomer growth. Our study addresses both the minimal oligomeric size of an aggregate seed and the mechanism of seed growth. Our simulations of the prion-derived 8-residue amyloidogenic peptide and its variant have indicated that an octamer is stable enough to be a seed and that the driving force for stabilization is the hydrophobic effect.

Linking mechanical properties of silanes to their chemical structure: an analytical study of γ-GPS solutions and films

The effects of hydrolysis and condensation processes on the molecular structure of γ-glycidoxypropyltrimethoxysilane (γ-GPS) in aqueous solutions were investigated using Fourier-transform nuclear magnetic resonance (FT-NMR) spectroscopy. Hydrolysis was characterized by monitoring the production of methanol and the decrease in concentration of SiOCH 3 groups in 1% solutions of deuterium oxide using proton NMR. Hydrolysis was found to be a very rapid process, whose rate could be increased or decreased by altering the pH of the solution. NMR spectroscopy showed that hydrolysis was completed in a 1% γ-GPS solution in deuterium oxide after 34 minutes. Condensation, on the other hand, took a relatively long time to occur. In the NMR spectra, condensation was observed by the broadening of peaks due to the protons on the carbon atom adjacent to the silicon atom. In addition to proton NMR, Si-29 NMR was used to characterize the siliane in 10% solutions of γ-GPS in water. The Si-29 NMR showed oligomer growth with respect to time . The oligomer growth was correlated to mechanical test results. Infrared spectroscopy was used to characterized the structure of the γ-GPS as a deposited film on aluminium during drying cycles at elevated temperature. The drying cycles caused increased oligomerization in the silane network and oxidation of the epoxide groups in the film.

Control of mesostructured silica particle morphology

The formation of mesostructured silica was investigated using acidic conditions with tetraethoxysilane (TEOS) as the silica precursor and cetyltrimethylammonium bromide (CTAB) as the structure directing agent. A synthesis mixture of composition 2.2TEOS ∶ 1.1CTAB ∶ 75HCl ∶ 1000H2O gave a well ordered material exhibiting a range of particle shapes from extended rope-like structures of hexagonal cross-section to gyroid structures. Addition of monomethyltriethoxysilane (MTES) or tetrahydrofuran (THF) to the synthesis mixture gave rise to spherical particles. Studies of particle development showed initial growth of gel-like particles within which the mesostructure developed. A new model is proposed for the formation of mesostructured precipitates in which (1) growth of inorganic oligomers gives rise to a thermodynamically unstable mixture, (2) phase separation occurs giving droplets of a second liquid (or liquid crystal) phase rich in oligomer and surfactant, (3) the droplets are colloidally stabilized, (4) microphase separation occurs within the droplets, giving rise to a mesostructure and (5) further polymerization fixes the mesostructure.

The Influence of β-Diketones on the Hydrolysis and Growth of Particles from Zirconium(IV) n-Propoxide

The influence of low ligand/Zr mole ratios (ρ = 0–0.1) on the hydrolysis and growth of oligomers from Zr(O n Pr)4 modified with a series of β-diketones (trifluoroacetylacetone, hexafluoroacetylacetone, benzoylacetone, dibenzoylmethane and dipivaloylmethane), and their subsequent aggregation to form uniform, dense spheres, has been investigated by light scattering and turbidometry. The addition of β-diketones results in a large increase in the induction time, t i (reduction in hydrolysis/condensation rates). A remarkable feature of the data is the dramatic reductions in rate observed even when a maximum of one in forty Zr–OR bonds have been replaced by the β-diketone and are no longer available for hydrolysis or further condensation. The largest effect is observed with dibenzoylmethane, which increases t i by a factor of 26 relative to acetylacetone. A mechanism rationalising the origin of the effect is discussed, which involves segregation of the β-diketone ligands on the surface of the growing particle, with subsequent particle growth restricted to those sites not occupied by the chelating ligands.

Effect of Processing Variables on the Solution Characteristics of γ-Glycidoxypropyltrimethoxysilane (γ-GPS)

The effects of the hydrolysis and condensation processes on the molecular structure of γ-glycidoxypropyltrimethoxysilane (γ-GPS) in aqueous solutions were investigated using Fourier-transform nuclear magnetic resonance (FT-NMR) spectroscopy and FT-Raman spectroscopy. Hydrolysis was characterized by monitoring the production of methanol and the decrease in concentration of SiOCH3 groups in 1% solutions of deuterium oxide using proton NMR. The production of methanol and loss of methoxy groups in 25% solutions of γ-GPS in water was characterized using Raman spectroscopy. Hydrolysis was found to be a very rapid process, whose rate could be increased or decreased by altering the pH of the solution. NMR spectroscopy showed that hydrolysis was complete in a 1% γ-GPS solution in deuterium oxide after 34 minutes. Raman spectroscopy also showed hydrolysis to be rapid and complete in a 25% solution of γ-GPS in water after 1 hour. Condensation, on the other hand, took a relatively long time to occur. In the NMR spectra, condensation was observed by the broadening of peaks due to the protons on the carbon atom adjacent to the silicon atom. In the Raman spectra, condensation was characterized by the disappearance of the SiOH band near 725 cm−1 and the development of an SiOSi band near 600 cm−1. In addition to the proton NMR, Si-29 NMR was used to characterize the silane in 10% solutions of γ-GPS in water. The Si-29 NMR showed oligomer growth with respect to time. The oligomer growth was correlated with mechanical test results.

Rapid bi-directional synthesis of oligo(1, 4-phenylene ethynylene)s

A new method for the preparation of oligo(1, 4-phenylene ethynylene)s is described. Only two sets of reaction conditions are needed for the entire iterative synthetic sequence: (1) Pd-catalyzed cross-coupling of trimethylsilylacetylene with an aryl halide and (2) in situ desilylation/Pd-catalyzed coupling with an aryl iodide. This method provides a fast synthetic route to short length oligo(1, 4-phenylene ethynylene)s by oligomer growth at both ends. Only two sets of iterative reaction conditions are needed for the synthesis of oligo(1, 4-phenylene ethynylene)s by oligomer growth at both ends. [Display omitted]

A reaction-transport model for AlGaN MOVPE growth

We present a systematic study of the complex chemistry and transport phenomena underlying metalorganic vapor phase epitaxy (MOVPE) of AlGaN; in particular, the mechanism underlying growth rate reduction at high temperatures and pressures. Thermodynamics and kinetics of formation of Lewis acid–base adducts of the organometallic precursors [TMGa–NH 3 and TMAl–NH 3] and the subsequent elimination of methane are investigated using hybrid density functional theory and transition state theory. The adduct pathway leads to the formation of stable dimer and trimer ring species containing Ga, Al, and N which strongly influence growth behavior in the reactor. Results from these studies, combined with reported data for gas-phase decomposition of TMGa and TMAl, are used in macroscopic, finite element reactor modeling studies to develop a reaction-transport model for AlGaN MOVPE growth. The model predicts growth rates in excellent agreement with experimental data for growth of AlGaN in different reactor configurations, including horizontal and `close-spaced-injector' reactors. Formation of dimers and trimers is identified as the major pathway for decreased growth efficiency with increasing pressure. A pathway involving nucleation and growth of oligomers from dimers and trimers, and ultimately particle formation, is consistent with decreased growth efficiency for increasing temperature.

Redox Reactivity as the Controlling Element in Coordination Polymer Stereochemistry: Redox-Switched Growth Mechanism in the [Fe(II)-CN-Pt(IV)](n)() System.

Coordination oligomers and polymers composed of [(CN)(5)Fe(II)-CN-Pt(IV)(NH(3))(4)] units have been synthesized. The oligomer growth mechanism is based on the oxidation state of the iron centers which can be specified either chemically or electrochemically to allow control over oligomer structure. Cyclic voltammetry is found to be a sensitive probe of oligomer and polymer structure. (13)C NMR is also shown to be a useful technique for characterizing the different geometric isomers. Thin films composed of [-(NC)(5)Fe(II)-CN-Pt(IV)(NH(3))(4)-](n)() were electropolymerized onto transparent indium tin oxide (ITO) electrode surfaces and characterized with regard to polymer morphology.

New approach to the mechanism of oligomer crystallization

A new mechanism for crystal growth of oligomers has been proposed. In order to grow, the crystals must have well ordered facets. This has been taken into account by assuming that their thickness is larger than C/(T*–Tc), where C is an appropriate constant, T* a reference temperature and Tc the temperature of crystallization. Application of this relation to crystals which have thermodynamic size is justified. These crystals grow by crystallographic attachment of sufficiently long molecules in a process exactly comparable to the growth of a crystal of an alk-1-ene (known from the measurement of the absolute entropy of the crystals). From these premises, the growth rate of poly(ethylene oxide) lamellae is predicted with surprising success. The segregation of the molecules according to their molecular weight and the very sensitive effect of seeding is also predicted. Application of the model to the crystallization of polyethylene fractions is discussed.

Probing the early stages of polymerization of ethylene on a model chromium/silica catalyst by Fourier transform infrared spectroscopy

The nature of the interaction of monomer, and the early stages of growth of oligomers of ethylene on a rather more uniform surface of Cr/SiO2 catalyst than hitherto studied has been investigated by differenceFTIR spectroscopy using C2D4 and C2H4 as reactants both with and without subsequent treatment of the catalyst with CO andTHF. The active catalyst was prepared by reaction of vapour phase CrO2Cl2 with the vicinal hydroxyls of the silica surface. Three distinct kinds of methylene groups were detected. Arguments are given for assigning the peaks at 2935 and 2860 cm−1 to CH2 groups directly bound to the active site and those at 2920 and 2850 to CH2s in the growing chain well removed from the Cr. The peaks at 2160 and 2165 cm−1 are attributed to CD2 groups hydrogen bonded to surface hydroxyls.