Well-defined Oligomers Research Articles

Rational protein design of Bacillus sp. MN chitosanase for altered substrate binding and production of specific chitosan oligomers

BackgroundPartially acetylated chito-oligosaccharides (paCOS) have a variety of potential applications in different fields, but to harness their benefits, pure paCOS or well-defined paCOS mixtures are essential. For example, if one could produce fully acetylated (A4) and fully deacetylated (D4) tetramers in abundance, all possible variants of tetrameric paCOS could be generated reliably from them. A promising approach for generating defined paCOS is by enzymatic depolymerization of chitosan polymers using chitosanases, since these enzymes’ subsite specificities directly influence the composition of the paCOS produced; however, enzymatic production of e.g. D4 is challenging because the substrate is generally hydrolyzed further by most chitosanases. To overcome this, chitosanases could potentially be engineered so that upon hydrolyzing chitosan, they are unable to hydrolyze certain substrates, leaving well-defined oligomers intact in the hydrolysate.ResultsFor this purpose, we performed rational protein engineering on the extensively studied GH 8 chitosanase CSN from Bacillus sp. MN. By specifically targeting residues with a predicted function in substrate binding, we created new muteins incapable of efficiently hydrolyzing the fully deacetylated tetramer D4, and we were able to demonstrate efficient large-scale production of D4 with an altered version of CSN. Furthermore, we were able to uncover differences in the substrate positioning and subsite specificities of the muteins, which result in altered paCOS mixtures produced from partially acetylated chitosan polymers, with possibly altered bioactivities.ConclusionThe value of protein engineering as a tool for the more efficient production of pure oligomers and potentially bioactive paCOS mixtures was demonstrated by the results and the suitability of specific muteins for the large-scale production of strictly defined, pure paCOS in a batch process was shown using the example of D4.

Synthesis and Self-Assembly of Xylan-Based Amphiphiles: From Bio-Based Vesicles to Antifungal Properties

This work aims at designing functional biomaterials through selective chemical modification of xylan from beechwood. Acidic hydrolysis of xylan led to well-defined oligomers with an average of six xylose units per chain and with an aldehyde group at the reductive end. Reductive amination was performed on this aldehyde end group to introduce an azide reactive group. "Click chemistry" was then applied to couple these hydrophilic xylans moieties with different hydrophobic fatty acid methyl esters that were previously functionalized with complementary alkyne functions. The resulting amphiphilic bio-based conjugates were then self-assembled using three different methods, namely, direct solubilization, thin-film rehydration/extrusion, and microfluidics. Well-defined micelles and vesicles were obtained, and their high loading capacity with propiconazole as an antifungal active molecule was shown. The resulting vesicles loaded with propiconazole in a microfluidic process proved to significantly improve the antifungal activity of propiconazole, demonstrating the high potential of such xylan-based amphiphiles.

Metathetic Degradation of Styrene-Butadiene Rubber via Ru-Alkylidene Complex Catalyzed Reaction

Metathetic degradation and functionalization of styrene-butadiene rubber (SBR) were performed with allyl hexanoate, allyl chloroacetate, 5-hexenyl acetate and trifluoroethyl methacrylate as chain transfer agents (CTAs) using Grubbs 2 nd generation catalyst. It has been demonstrated that the catalyst concentration, CTA concentration and reaction time were major factors influencing the molecular weights and polydispersity indices of targeted telechelic SBR oligomers. Well-defined oligomers with molecular weights ranging from 700 to 36600 g mol -1 and polydispersity indices ranging from 1.17 to 4.79 were realized. The structures of the SBR oligomers were determined by FTIR and 1 H NMR analyses, which indicated that the functional groups of the CTAs were successfully attached onto the end of the polymer chains. To further investigate the performance of SBR oligomers, differential scanning calorimetry (DSC) analysis was performed, which indicated that the glass transition temperature (T g ) of the metathesis products decreased with longer reaction time.

Singlet Fission in Polypentacene

Summary A recent surge of interest in singlet-fission (SF) dimers is inspired by their utility as model systems as well as by the inherent advantages of an intramolecular SF process. Here, we extend the scope of these materials to polypentacene, a model one-dimensional system designed to bridge studies of SF in constrained SF dimers and extended condensed phase systems. Using transient absorption spectroscopy, we studied a soluble polypentacene derivative and well-defined oligomers with 2–5 repeat units to elaborate the trend in triplet-pair dynamics with increasing lengths. We found that the SF rate constant increased monotonically with the number of repeat units. However, recombination in all cases was rapid (

Oligomerization Reactions of Bis(ethynyl)tetraphenylporphyrin Derivatives by Glaser–Hay Coupling Reaction: Isolation and Characterization of Dimer, Trimer, and Tetramer

The Glaser–Hay coupling reaction of a tetraphenylporphyrin derivative having two acetylenes in the quasi-trans positions was carried out. Although this oxidative coupling reaction has high reactivity and produces various butadiynylene oligomers, the degree of oligo­merization was low. A large substrate and/or product might decrease the frequency factor of the Arrhenius equation and the resultant rate constant. This finding is in agreement with that of the one-pot synthesis of structurally well-defined porphyrin oligomers, such as trimers and tetramers, which are used frequently in the field of advanced materials.

End Groups of Functionalized Siloxane Oligomers Direct Block-Copolymeric or Liquid-Crystalline Self-Assembly Behavior.

Monodisperse oligodimethylsiloxanes end-functionalized with the hydrogen-bonding ureidopyrimidinone (UPy) motif undergo phase separation between their aromatic end groups and dimethylsiloxane midblocks to form ordered nanostructures with domain spacings of <5 nm. The self-assembly behavior of these well-defined oligomers resembles that of high degree of polymerization (N)–high block interaction parameter (χ) linear diblock copolymers despite their small size. Specifically, the phase morphology varies from lamellar to hexagonal to body-centered cubic with increasing asymmetry in molecular volume fraction. Mixing molecules with different molecular weights to give dispersity >1.13 results in disorder, showing importance of molecular monodispersity for ultrasmall ordered phase separation. In contrast, oligodimethylsiloxanes end-functionalized with an O-benzylated UPy derivative self-assemble into lamellar nanostructures regardless of volume fraction because of the strong preference of the end groups to aggregate in a planar geometry. Thus, these molecules display more classically liquid-crystalline self-assembly behavior where the lamellar bilayer thickness is determined by the siloxane midblock. Here the lamellar nanostructure is tolerant to molecular polydispersity. We show the importance of end groups in high χ–low N block molecules, where block-copolymer-like self-assembly in our UPy-functionalized oligodimethylsiloxanes relies upon the dominance of phase separation effects over directional end group aggregation.

Stereoselective Arene‐Forming Aldol Condensation: Synthesis of Configurationally Stable Oligo‐1,2‐naphthylenes

Structurally well-defined oligomers are fundamental for the functionality of natural molecular systems and key for the design of synthetic counterparts. Herein, we describe a strategy for the efficient synthesis of individual stereoisomers of 1,2-naphthylene oligomers by iterative building block additions and consecutive stereoselective arene-forming aldol condensation reactions. The catalyst-controlled atropoenantioselective and the substrate-controlled atropodiastereoselective aldol condensation reaction provide structurally distinct ter- and quaternaphthalene stereoisomers, which represent configurationally stable analogues of otherwise stereodynamic, helically shaped ortho-phenylenes.

Soluble Prion Protein Binds Isolated Low Molecular Weight Amyloid-β Oligomers Causing Cytotoxicity Inhibition.

A growing number of observations indicate that soluble amyloid-β (Aβ) oligomers play a major role in Alzheimer's disease. Recent studies strongly suggest that at least some of the neurotoxic effects of these oligomers are mediated by cellular, membrane-anchored prion protein and that Aβ neurotoxicity can be inhibited by soluble recombinant prion protein (rPrP) and its fragments. However, the mechanism by which rPrP interacts with Aβ oligomers and prevents their toxicity is largely unknown, and studies in this regard are hindered by the large structural heterogeneity of Aβ oligomers. To overcome this difficulty, here we used photoinduced cross-linking of unmodified proteins (PICUP) to isolate well-defined oligomers of Aβ42 and characterize these species with regard to their cytotoxicity and interaction with rPrP, as well the mechanism by which rPrP inhibits Aβ42 cytotoxicity. Our data shows that the addition of rPrP to the assembling Aβ42 results in a shift in oligomer size distribution, decreasing the population of toxic tetramers and higher order oligomers and increasing the population of nontoxic (and possibly neuroprotective) monomers. Isolated oligomeric species of Aβ42 are cytotoxic to primary neurons and cause permeation of model lipid bilayers. These toxic effects, which are oligomer size-dependent, can be inhibited by the addition of rPrP, and our data suggest potential mechanisms of this inhibitory action. This insight should help in current efforts to develop PrP-based therapeutics for Alzheimer's disease.

Nucleation and Growth of Brushite in the Presence of Alginate

Biomineral formation in vivo is a complex process regulated by functional molecules. Highlighting the mechanisms underlying biomineralization is necessary for a better understanding of in vivo processes and for enhanced in vitro model systems. Here, the effect of alginate and its well-defined oligomers with M- or G-block structure on brushite nucleation and growth is investigated by seeded and unseeded experiments. Growth kinetics were studied by seeded experiments, and it was shown that molecular weight and functionality of alginate additives affect the crystal growth rates and the growth mechanisms. Growth retardation was most prominent when G-block additives were present. Growth proceeded by surface nucleation when alginate and G-block oligomers were added in the crystallization medium, whereas in the presence of M-block oligomers parabolic rate laws were obtained. By decoupling the seeded and unseeded experiments, information was deduced on the effects of additives on brushite nucleation. In the presence of alginate and G-block oligomers, nucleation was inhibited; however, M-blocks did not show a similar effect. Possible modes of interactions between the mineral and polymer additives are discussed by the evaluation of final crystal morphologies.

Why synthesize protein–polymer conjugates? The stability and activity of chymotrypsin-polymer bioconjugates synthesized by RAFT

α-Chymotrypsin, a commonly used protease, was modified with well-defined oligomers synthesized by RAFT. The well defined polymers were synthesized based on the monomers N,N-dimethylacrylamide (DMAm) or oligo(ethylene oxide) methyl ether acrylate (OEOA). The polymers were conjugated to free amine groups on chymotrypsin through an in-situ 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide/N-hydroxysuccinimide (EDC/NHS) coupling approach. The protein–polymer conjugates retained enzymatic activity, and the higher molecular weight DMAm and OEOA polymer, created protein–polymer conjugates with significantly enhanced stability, presumably due to the high molecular weight polymer preventing autolysis of the α-chymotrypsin.

Selective carboxylate induced thermal degradation of bacterial poly(3-hydroxybutyrate-co-4-hydroxybutyrate) – Source of linear uniform 3HB4HB oligomers

Study on bacterial poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (P(3HB4HB)) thermal degradation employing mild reaction conditions and carboxylate salt is described. The chemical structure of the obtained oligomers was determined with the aid of 1H NMR and ESI-mass spectrometry techniques. The comparison of a non-volatile degradation products obtained via carboxylate-induced thermal degradation of the P(3HB4HB) with products of the model polymer pyrolysis revealed significant differences in structure of the resulting oligomers. Exclusive formation of linear oligomers terminated with unsaturated, on one end, and carboxyl, on the other end, groups was noticed in case of base-catalyzed degradation contrary to oligomers produced via pyrolysis which contained also macrocyclic structures and γ-butyrolactone. Moreover, the elaborated method demonstrates the ability to produce well-defined oligomers with controlled molar mass. The resulting oligomers have huge potential as macroinitiators or macromonomers and can be useful for further synthesis of more sophisticated polymeric materials.

The Influence of Alkoxy Substitutions on the Properties of Diketopyrrolopyrrole-Phenyl Copolymers for Solar Cells.

A previously reported diketopyrrolopyrrole (DPP)-phenyl copolymer is modified by adding methoxy or octyloxy side chains on the phenyl spacer. The influence of these alkoxy substitutions on the physical, opto-electronic properties, and photovoltaic performance were investigated. It was found that the altered physical properties correlated with an increase in chain flexibility. Well-defined oligomers were synthesized to verify the observed structure-property relationship. Surprisingly, methoxy substitution on the benzene spacer resulted in higher melting and crystallization temperatures in the synthesized oligomers. This trend is not observed in the polymers, where the improved interactions are most likely counteracted by the larger conformational possibilities in the polymer chain upon alkoxy substitution. The best photovoltaic performance was obtained for the parent polymer: fullerene blends whereas the modifications on the other two polymers result in reduced open-circuit voltage and varying current densities under similar processing conditions. The current densities could be related to different polymer: fullerene blend morphologies. These results show that supposed small structural alterations such as methoxy substitution already significantly altered the physical properties of the parent polymer and also that oligomers and polymers respond divergent to structural alterations made on a parent structure.

Remarkable Photophysics and Amplified Quenching of Conjugated Polyelectrolyte Oligomers.

We report the photophysics and fluorescence quenching of a series of monodisperse, anionic π-conjugated oligomers that are molecularly dissolved in aqueous solution. These structurally well-defined oligomers feature oligo(phenylene ethynylene) backbones with two -CH2COO(-) units on each repeat unit, with overall lengths of 5, 7, and 9 repeats. The ionic oligomers display a structured fluorescence band with high quantum efficiency in water, in contrast to the low fluorescence quantum efficiency and pronounced aggregation displayed by structurally similar oligomeric and polymeric (phenylene ethynylene) conjugated polyelectrolytes studied previously. Stern-Volmer (SV) fluorescence quenching studies using cationic charge- and energy-transfer quenchers reveal that all of the oligomers give rise to SV quenching constants (KSV) in excess of 10(6) M(-1), with values increasing with oligomer length, consistent with the amplified quenching effect. The amplified quenching effect is proposed to occur due to the formation of comparatively small oligomer aggregates.

ChemInform Abstract: Efficient Synthesis of Oxygenated Terphenyls and Other Oligomers. Sequential Arylation Reactions Through Phenol Oxidation—Rearomatization.

One by one: starting from simple phenols, a diverse series of oxygenated terphenyl compounds can be prepared in a concise and practical manner using sequential arylation reactions involving phenol oxidation/rearomatization and quinone monoacetal intermediates. Many of the terphenyl products can be used for preparing well-defined oligomers and, furthermore, contain valuable functional groups that can be transformed for further diversification.

Effects of Electronics, Aromaticity, and Solvent Polarity on the Rate of Azaquinone–Methide-Mediated Depolymerization of Aromatic Carbamate Oligomers

This paper uses physical-organic studies on well-defined oligomers to establish design principles for creating aromatic poly(carbamates) that depolymerize from head-to-tail in low dielectric constant environments when exposed to specific applied signals. We show that either increasing electron density or decreasing the aromaticity of aromatic repeating units in poly(carbamates) increase the overall depolymerization rate. For example, a methoxybenzene-based repeating unit provides depolymerization rates that are 143× faster than oligomers that contain a benzene-based repeating unit. Furthermore, the rate of depolymerization in the methoxybenzene-based system is tolerant to low dielectric environments, whereas the benzene-based oligomers are not.

Efficient Synthesis of Oxygenated Terphenyls and Other Oligomers: Sequential Arylation Reactions Through Phenol Oxidation–Rearomatization

One by one: starting from simple phenols, a diverse series of oxygenated terphenyl compounds can be prepared in a concise and practical manner using sequential arylation reactions involving phenol oxidation/rearomatization and quinone monoacetal intermediates. Many of the terphenyl products can be used for preparing well-defined oligomers and, furthermore, contain valuable functional groups that can be transformed for further diversification.

Bivalent and co-operative binding of complement Factor H to heparan sulfate and heparin

FH (Factor H) with 20 SCR (short complement regulator) domains is a major serum regulator of complement, and genetic defects in this are associated with inflammatory diseases. Heparan sulfate is a cell-surface glycosaminoglycan composed of sulfated S-domains and unsulfated NA-domains. To elucidate the molecular mechanism of binding of FH to glycosaminoglycans, we performed ultracentrifugation, X-ray scattering and surface plasmon resonance with FH and glycosaminoglycan fragments. Ultracentrifugation showed that FH formed up to 63% of well-defined oligomers with purified heparin fragments (equivalent to S-domains), and indicated a dissociation constant K(d) of approximately 0.5 μM. Unchanged FH structures that are bivalently cross-linked at SCR-7 and SCR-20 with heparin explained the sedimentation coefficients of the FH-heparin oligomers. The X-ray radius of gyration, R(G), of FH in the presence of heparin fragments 18-36 monosaccharide units long increased significantly from 10.4 to 11.7 nm, and the maximum lengths of FH increased from 35 to 40 nm, confirming that large compact oligomers had formed. Surface plasmon resonance of immobilized heparin with full-length FH gave K(d) values of 1-3 μM, and similar but weaker K(d) values of 4-20 μM for the SCR-6/8 and SCR-16/20 fragments, confirming co-operativity between the two binding sites. The use of minimally-sulfated heparan sulfate fragments that correspond largely to NA-domains showed much weaker binding, proving the importance of S-domains for this interaction. This bivalent and co-operative model of FH binding to heparan sulfate provides novel insights on the immune function of FH at host cell surfaces.

The Emerging Bio-Refinery Industry Needs to Refine Lignin Prior to Use

In a manner similar to crude oil, technical lignins need refining if their potential as reactive polyphenols of well-defined molecular weight polymers and oligomers is to be actualized. Our recent work has demonstrated that a continuum of narrow fractions can be isolated by the incremental addition of a non-polar solvent (hexanes) in a polar (acetone) solution of softwood wood kraft lignin

Synthesis and Optoelectronic Properties of Blue-Emitting Star-Burst Oligomers Based on Triphenylamine and Spiro(fluorene-9,9'-xanthene)

Three star-burst conjugated oligomers based on triphenylamine (TPA), fluorene and spiro (fluorene-9,9'-xanthene) (SEX) have been synthesized via the Sonogashira cross-coupling reaction. These well-defined oligomers possess high decomposition temperatures (T-d) at 417, 439, and 425 degrees C, respectively. Differential scanning calorimetry (DSC) demonstrates two oligomers which incorporate the SFX unit, TPA-SFX and TPA-SFXCz, possess higher glass transition temperatures (T-g) at 141 and 127 degrees C, respectively, compared with 101 degrees C for TPA-F. The investigation of their optical properties shows TPA-SFX and TPA-SFXCz exhibit a single blue emission in film with emission peaks at 434 and 442 nm, respectively, whereas TPA-F shows a broad double-peak emission located at 424 and 455 nm, which implies the nonplanar TPA and spiro SFX moieties can effectively restrict the formation of aggregates or excimers. Electrochemical investigations show that these oligomers have relatively high HOMO levels at around -5.4 eV due to incorporation of the electron-rich TPA core. Electroluminescence (EL) devices with a configuration of ITO (indium tin oxide)/PEDOT:PSS (poly(3,4-ethylenedioxythiophene): poly (styrenesulfonate))/oligomer/TPBI (1,3,5-tris(1-phenyl-1H -benzimidazol-2-yl)benzene)/LiF/Al were constructed using these oligomers as the emitter by spin-coating, with TPBI as the electron-transporting and hole-blocking layer. The device using TPA-SFX as the emitting layer exhibits bright blue emission with the maximum brightness and maximum current efficiency of 2680 cd . A(-2) and 0.35 cd . A(-1), and CIE. color coordination of (0.17, 0.13).

Mechanism Studies of LCP Synthesis

The LCP (Liquid Crystal Polymer) known as Vectra is synthesized by acidolysis of 4-hydroxybenzoic acid with 6-hydroxy-2-naphthoic acid. The apparently simple acidolysis mechanism for LCP polycondensation is in fact a complex blend of mechanisms. Kinetics of model reactions and of actual polycondensations followed second-order kinetics and their rate constants were comparable. In the latter stages, ketene loss leads to phenolic ends, while decarboxylation provides phenyl ester ends. Accordingly, the mechanism changes to phenolysis. A quinone methide intermediate may also intervene, as revealed by kinetics studies and MALDI-TOF spectroscopy. Tailor-made matrices and synthesis of alternating well-defined oligomers assisted our studies. Nucleophilic aromatic substitutions may play a role, and we speculate on possible chain polycondensation. Esterolysis may be a useful alternative to LCP synthesis. Complications caused by ketene loss can be averted by the use of methoxycarbonyloxy monomers.