Influence of substrate type and orientation on the morphology and optical properties of selective area growth of GaN and InGaN nanocolumns

A relevant issue concerning optoelectronic devices based on III-nitrides is the presence of strong polarization fields that may reduce efficiency.

(4-Aminomethyl)phenylguanidine derivatives as nonpeptidic highly selective inhibitors of human urokinase

Increased expression of the serine protease urokinase-type plasminogen activator (uPA) in tumor tissues is highly correlated with tumor cell migration, invasion, proliferation, progression, and metastasis. Thus inhibition of uPA activity represents a promising target for antimetastatic therapy. So far, only the x-ray crystal structure of uPA inactivated by H-Glu-Gly-Arg-chloromethylketone has been reported, thus limited data are available for a rational structure-based design of uPA inhibitors. Taking into account the trypsin-like arginine specificity of uPA, (4-aminomethyl)phenylguanidine was selected as a potential P1 residue and iterative derivatization of its amino group with various hydrophobic residues, and structure–activity relationship-based optimization of the spacer in terms of hydrogen bond acceptor/donor properties led to N-(1-adamantyl)-N′-(4-guanidinobenzyl)urea as a highly selective nonpeptidic uPA inhibitor. The x-ray crystal structure of the uPA B-chain complexed with this inhibitor revealed a surprising binding mode consisting of the expected insertion of the phenylguanidine moiety into the S1 pocket, but with the adamantyl residue protruding toward the hydrophobic S1′ enzyme subsite, thus exposing the ureido group to hydrogen-bonding interactions. Although in this enzyme-bound state the inhibitor is crossing the active site, interactions with the catalytic residues Ser-195 and His-57 are not observed, but their side chains are spatially displaced for steric reasons. Compared with other trypsin-like serine proteases, the S2 and S3/S4 pockets of uPA are reduced in size because of the 99-insertion loop. Therefore, the peculiar binding mode of the new type of uPA inhibitors offers the possibility of exploiting optimized interactions at the S1′/S2′ subsites to further enhance selectivity and potency. Because crystals of the uPA/benzamidine complex allow inhibitor exchange by soaking procedures, the structure-based design of new generations of uPA inhibitors can rely on the assistance of x-ray analysis.

The nitrite reductase from Pseudomonas aeruginosa: Essential role of two active-site histidines in the catalytic and structural properties

Cd1 nitrite reductase catalyzes the conversion of nitrite to NO in denitrifying bacteria. Reduction of the substrate occurs at the d1-heme site, which faces on the distal side some residues thought to be essential for substrate binding and catalysis. We report the results obtained by mutating to Ala the two invariant active site histidines, His-327 and His-369, of the enzyme from Pseudomonas aeruginosa. Both mutants have lost nitrite reductase activity but maintain the ability to reduce O2 to water. Nitrite reductase activity is impaired because of the accumulation of a catalytically inactive form, possibly because the productive displacement of NO from the ferric d1-heme iron is impaired. Moreover, the two distal His play different roles in catalysis; His-369 is absolutely essential for the stability of the Michaelis complex. The structures of both mutants show (i) the new side chain in the active site, (ii) a loss of density of Tyr-10, which slipped away with the N-terminal arm, and (iii) a large topological change in the whole c-heme domain, which is displaced 20 Å from the position occupied in the wild-type enzyme. We conclude that the two invariant His play a crucial role in the activity and the structural organization of cd1 nitrite reductase from P. aeruginosa.

In vivo activity in a catalytic antibody-prodrug system: Antibody catalyzed etoposide prodrug activation for selective chemotherapy

Effective chemotherapy remains a key issue for successful cancer treatment in general and neuroblastoma in particular. Here we report a chemotherapeutic strategy based on catalytic antibody-mediated prodrug activation. To study this approach in an animal model of neuroblastoma, we have synthesized prodrugs of etoposide, a drug widely used to treat this cancer in humans. The prodrug incorporates a trigger portion designed to be released by sequential retro-aldol/retro-Michael reactions catalyzed by aldolase antibody 38C2. This unique prodrug was greater than 102-fold less toxic than etoposide itself in in vitro assays against the NXS2 neuroblastoma cell line. Drug activity was restored after activation by antibody 38C2. Proof of principle for local antibody-catalyzed prodrug activation in vivo was established in a syngeneic model of murine neuroblastoma. Mice with established 100-mm3 s.c. tumors who received one intratumoral injection of antibody 38C2 followed by systemic i.p. injections with the etoposide prodrug showed a 75% reduction in s.c. tumor growth. In contrast, injection of either antibody or prodrug alone had no antitumor effect. Systemic injections of etoposide at the maximum tolerated dose were significantly less effective than the intratumoral antibody 38C2 and systemic etoposide prodrug combination. Significantly, mice treated with the prodrug at 30-fold the maximum tolerated dose of etoposide showed no signs of prodrug toxicity, indicating that the prodrug is not activated by endogenous enzymes. These results suggest that this strategy may provide a new and potentially nonimmunogenic approach for targeted cancer chemotherapy.

Duplication and functional divergence in the chalcone synthase gene family of Asteraceae: evolution with substrate change and catalytic simplification.

Plant-specific polyketide synthase genes constitute a gene superfamily, including universal chalcone synthase [CHS; malonyl-CoA:4-coumaroyl-CoA malonyltransferase (cyclizing) (EC 2.3.1.74)] genes, sporadically distributed stilbene synthase (SS) genes, and atypical, as-yet-uncharacterized CHS-like genes. We have recently isolated from Gerbera hybrida (Asteraceae) an unusual CHS-like gene, GCHS2, which codes for an enzyme with structural and enzymatic properties as well as ontogenetic distribution distinct from both CHS and SS. Here, we show that the GCHS2-like function is encoded in the Gerbera genome by a family of at least three transcriptionally active genes. Conservation within the GCHS2 family was exploited with selective PCR to study the occurrence of GCHS2-like genes in other Asteraceae. Parsimony analysis of the amplified sequences together with CHS-like genes isolated from other taxa of angiosperm subclass Asteridae suggests that GCHS2 has evolved from CHS via a gene duplication event that occurred before the diversification of the Asteraceae. Enzyme activity analysis of proteins produced in vitro indicates that the GCHS2 reaction is a non-SS variant of the CHS reaction, with both different substrate specificity (to benzoyl-CoA) and a truncated catalytic profile. Together with the recent results of Durbin et al. [Durbin, M. L., Learn, G. H., Jr., Huttley, G. A. & Clegg, M. T. (1995) Proc. Natl. Acad. Sci. USA 92, 3338-3342], our study confirms a gene duplication-based model that explains how various related functions have arisen from CHS during plant evolution.

Catalytic editing properties of DNA polymerases.

Enzymatic incorporation of 2',3'-dideoxynucleotides into DNA results in chain termination. We report that 3'-esterified 2'-deoxynucleoside 5'-triphosphates (dNTPs) are false chain-terminator substrates since DNA polymerases, including human immunodeficiency virus reverse transcriptase, can incorporate them into DNA and, subsequently, use this new 3' end to insert the next correctly paired dNTP. Likewise, a DNA substrate with a primer chemically esterified at the 3' position can be extended efficiently upon incubation with dNTPs and T7 DNA polymerase lacking 3'-to-5' exonuclease activity. This enzyme is also able to use dTTP-bearing reporter groups in the 3' position conjugated through amide or thiourea bonds and cleave them to restore a DNA chain terminated by an amino group at the 3' end. Hence, a number of DNA polymerases exhibit wide catalytic versatility at the 3' end of the nascent DNA strand. As part of the polymerization mechanism, these capabilities extend the number of enzymatic activities associated with these enzymes and also the study of interactions between DNA polymerases and nucleotide analogues.

Evaluation of catalytic pyrolysis of cassava rhizome by principal component analysis

Rhizome of cassava plants (Manihot esculenta Crantz) was catalytically pyrolysed at 500 °C using analytical pyrolysis–gas chromatography/mass spectrometry (Py–GC/MS) method in order to investigate the relative effect of various catalysts on pyrolysis products. Selected catalysts expected to affect bio-oil properties were used in this study. These include zeolites and related materials (ZSM-5, Al-MCM-41 and Al-MSU-F type), metal oxides (zinc oxide, zirconium (IV) oxide, cerium (IV) oxide and copper chromite) catalysts, proprietary commercial catalysts (Criterion-534 and alumina-stabilised ceria-MI-575) and natural catalysts (slate, char and ashes derived from char and biomass). The pyrolysis product distributions were monitored using models in principal components analysis (PCA) technique. The results showed that the zeolites, proprietary commercial catalysts, copper chromite and biomass-derived ash were selective to the reduction of most oxygenated lignin derivatives. The use of ZSM-5, Criterion-534 and Al-MSU-F catalysts enhanced the formation of aromatic hydrocarbons and phenols. No single catalyst was found to selectively reduce all carbonyl products. Instead, most of the carbonyl compounds containing hydroxyl group were reduced by zeolite and related materials, proprietary catalysts and copper chromite. The PCA model for carboxylic acids showed that zeolite ZSM-5 and Al-MSU-F tend to produce significant amounts of acetic and formic acids.

Selective localization of organoclay and effects on the morphology and mechanical properties of LDPE/PA11 blends with distributed and co-continuous morphology

A study was made on the effect of small amounts of organically modified clay on the morphology and mechanical properties of blends of low-density polyethylene and polyamide 11 at different compositions. The influence of the filler on the blend morphology was investigated using wide angle X-ray diffractometry, scanning and transmission electron microscopy and selective extraction experiments. The filler was found to locate predominantly in the more hydrophilic polyamide phase. Although such uneven distribution does not have a significant effect on the onset of phase co-continuity of the polymer components, it brings about a drastic refinement of the microstructure for the blends both with droplets/matrix and co-continuous morphologies. In addition to the expected reinforcing action of the filler, the resulting fine microstructure plays an important role in enhancing the mechanical properties of the blends. This is essentially because of a good quality of stress transfer across the interface between the constituents, which also seems to benefit for a good interfacial adhesion promoted by the filler. Our results provide the experimental evidence for the capabilities of nanoparticles added to multiphase polymer systems to act selectively as a reinforcing agent for specific domains of the material and as a medium able to assist the refinement of the polymer phases during mixing.

Dynamic restructuring of Pd nanoparticles and single crystals during catalytic selective alcohol oxidation

The aerobic selective oxidation (selox) of alcohols represents an environmentally benign and atom efficient chemical valorisation route to commercially important allylic aldehydes, such as crotonaldehyde and cinnamaldehyde, which find application in pesticides, fragrances and food additives. Palladium nanoparticles are highly active and selective heterogeneous catalysts for such oxidative dehydrogenations, permitting the use of air (or dioxygen) as a green oxidant in place of stoichiometric chromate permanganate saltsor H2O2. Here we discuss how time-resolved, in-situ X-ray spectroscopies (XAS and XPS) reveal dynamic restructuring of dispersed Pd nanoparticles and Pd single-crystals in response to changing reaction environments, and thereby identify surface PdO as the active species responsible for palladium catalysed crotyl alcohol selox (Figure 1); on-stream reduction to palladium metal under oxygen-poor regimes thus appears the primary cause of catalyst deactivation. This insight has guided the subsequent application of surfactant-templating and inorganic nanocrystal methodologies to optimize the density of desired active PdO sites for the selective oxidation of natural products such as sesquiterpenoids.

Redox-controlled crotyl alcohol selective oxidation:in situ oxidation and reduction dynamics of catalytic Pd nanoparticles via synchronous XANES/MS

In-situ, synchronous MS/XANES reveals the Pd catalyzed selective aerobic oxidation of crotyl alcohol is regulated by the balance between the oxidation state and reducibility. Dynamic XANES measurements provide a new, rapid method to determine redox kinetics of nanoparticles and identify important parameters to optimize catalyst design. © 2012 American Chemical Society.

An investigation of support effects on the Pt-catalysed selective transformation of α,β-unsaturated substrates

Pt catalyst series were prepared on mesoporous SBA-15, SBA-16, KIT-6, true liquidcrystal-templated meso-macroporous SBA-15 and a commercial, low surface area silicasupport. Support structure can be easily fabricated using surfactant templating as a mode ofstringent control on porosity, surface area and internal structure. The impact of varying Pt-support physicochemical properties was systematically studied for the selective transformation of allylic substrates under chemoselective oxidation and hydrogenation regimes, a class of reactions highly applicable to industry. Pt-based heterogeneous catalysts are well-known for their utilisation in the hydrogenation of α,β-unsaturated aldehydes,although the mode of action and lack of systematic studies in the literature fuels continuing debate into the role of Pt nanoparticles and support choice for this area. This project attempts to shed some light on several frequently asked questions in this field. Successful support synthesis and stability after Pt impregnation is confirmed through HRTEM, XRD and N2 porosimetry. Decreasing metal loading promoted dispersion values,regardless of support choice, with surface PtO2 content also showing visible enhancement.Increasing support surface area and mesoporosity exhibited the following trend on Pt dispersion augmentation; low surface area commercial silica < true liquid crystal-templated SBA-15 < SBA-15 < SBA-16 ~ KIT-6. For the selective oxidation of cinnamyl alcohol,increasing PtO2 surface population confers substantial rate enhancements, with turnover frequencies evidencing PtO2 to be the active species .In the Pt-catalysed hydrogenation of cinnamaldehyde, strong support insensitivity was observed towards catalytic activity; as turnover frequencies normalised to Pt metal reveal constant values. However, structure sensitivity to the desired unsaturated alcohol arose,evidencing the requirement of flat, extended Pt (111) facets for C=O hydrogenation. Pt/SBA-15 proved the most selective, reflecting suppressed cinnamyl alcohol hydrogenation, with DRIFTS and in-situ ATR-IR evidencing the key role of support polarity in re-orientation of cinnamaldehyde to favour di-σCO adsorption and C=O versus C=C hydrogenation. High pressures increased activity, whilst a dramatic shift in selectivity from dominant C=C (1 bar)to C=O hydrogenation (10 bar) was also observed, attributed to surface crowding and suppression of di-σCC and η4 di-σCO+πC=C cinnamaldehyde binding modes.

Development of advanced catalytic systems for the selective hydrogenolysis of biomass-derived polyols

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Hybrid materials based on polyethylene and MCM-41 microparticles functionalized with silanes: catalytic aspects of in situ polymerization, crystalline features and mechanical properties

New nanocomposites based on polyethylene have been prepared by in situ polymerization of ethylene in presence of mesoporous MCM-41. The polymerization reactions were performed using a zirconocene catalyst either under homogenous conditions or supported onto mesoporous MCM-41 particles, which are synthesized and decorated post-synthesis with two silanes before polymerization in order to promote an enhanced interfacial adhesion. The existence of polyethylene chains able to crystallize within the mesoporous channels in the resulting nanocomposites is figured out from the small endothermic process, located at around 80 C, on heating calorimetric experiments, in addition to the main melting endotherm. These results indicate that polyethylene macrochains can grow up during polymerization either outside or inside the MCM-41 channels, these keeping their regular hexagonal arrangements. Mechanical response is observed to be dependent on the content in mesoporous MCM-41 and on the crystalline features of polyethylene. Accordingly, stiffness increases and deformability decreases in the nanocomposites as much as MCM-41 content is enlarged and polyethylene amount within channels is raised. Ultimate mechanical performance improves with MCM-41 incorporation without varying the final processing temperature.

Hafnocene catalyst for polyethylene and its nanocomposites with SBA-15 by in situ polymerization: immobilization approaches, catalytic behavior and properties evaluation

A hafnocene catalyst combined with methylaluminoxane (MAO) has been used as catalytic complex for the preparation of a set of polyethylene homopolymers by in situ polymerization under homogenous conditions and of different nanocomposites with mesoporous SBA- 15 particles, the latter playing the dual role of catalyst support and nanofiller. Distinct immobilization approaches have been explored for obtainment of these nanocomposites. Moreover, catalytic features, thermal stability, melting and crystallization transitions and mechanical behavior have been evaluated for those materials.

Ticks produce highly selective chemokine binding proteins with antiinflammatory activity

Bloodsucking parasites such as ticks have evolved a wide variety of immunomodulatory proteins that are secreted in their saliva, allowing them to feed for long periods of time without being detected by the host immune system. One possible strategy used by ticks to evade the host immune response is to produce proteins that selectively bind and neutralize the chemokines that normally recruit cells of the innate immune system that protect the host from parasites. We have identified distinct cDNAs encoding novel chemokine binding proteins (CHPBs), which we have termed Evasins, using an expression cloning approach. These CHBPs have unusually stringent chemokine selectivity, differentiating them from broader spectrum viral CHBPs. Evasin-1 binds to CCL3, CCL4, and CCL18; Evasin-3 binds to CXCL8 and CXCL1; and Evasin-4 binds to CCL5 and CCL11. We report the characterization of Evasin-1 and -3, which are unrelated in primary sequence and tertiary structure, and reveal novel folds. Administration of recombinant Evasin-1 and - 3 in animal models of disease demonstrates that they have potent antiinflammatory properties. These novel CHBPs designed by nature are even smaller than the recently described single-domain antibodies (Hollinger, P., and P. J. Hudson. 2005. Nat. Biotechnol. 23: 1126-1136), and may be therapeutically useful as novel antiinflammatory agents in the future.