Oligonucleotide cyclization: The thiol-maleimide reaction revisited

A novel method to synthesize cyclic oligonucleotides (5- to 26-mer) using the thiol-maleimide reaction is described. The target molecules were obtained after subsequent removal of thiol and maleimide protecting groups from 5′-maleimido-3′-thiol-derivatized linear precursors. Retro-Diels-Alder conditions deprotecting the maleimide simultaneously promoted cyclization cleanly and in high yield.

Diffantom: Whole-Brain Diffusion MRI Phantoms Derived from Real Datasets of the Human Connectome Project.

Food allergies are believed to be on the rise and currently management relies on the avoidance of the food. Hen's egg allergy is after cow's milk allergy the most common food allergy; eggs are used in many food products and thus difficult to avoid. A technological process using a combination of enzymatic hydrolysis and heat treatment was designed to produce modified hen's egg with reduced allergenic potential. Biochemical (SDS-PAGE, Size exclusion chromatography and LC-MS/MS) and immunological (ELISA, immunoblot, RBL-assays, animal model) analysis showed a clear decrease in intact proteins as well as a strong decrease of allergenicity. In a clinical study, 22 of the 24 patients with a confirmed egg allergy who underwent a double blind food challenge with the hydrolysed egg remained completely free of symptoms. Hydrolysed egg products may be beneficial as low allergenic foods for egg allergic patients to extent their diet. This article is protected by copyright. All rights reserved.

O6-Methylguanine-DNA methyltransferase protein expression by immunohistochemistry in brain and non-brain systemic tumours: systematic review and meta-analysis of correlation with methylation-specific polymerase chain reaction

Background: The DNA repair protein O6-Methylguanine-DNA methyltransferase (MGMT) confers resistance to alkylating agents. Several methods have been applied to its analysis, with methylation-specific polymerase chain reaction (MSP) the most commonly used for promoter methylation study, while immunohistochemistry (IHC) has become the most frequently used for the detection of MGMT protein expression. Agreement on the best and most reliable technique for evaluating MGMT status remains unsettled. The aim of this study was to perform a systematic review and meta-analysis of the correlation between IHC and MSP. Methods A computer-aided search of MEDLINE (1950-October 2009), EBSCO (1966-October 2009) and EMBASE (1974-October 2009) was performed for relevant publications. Studies meeting inclusion criteria were those comparing MGMT protein expression by IHC with MGMT promoter methylation by MSP in the same cohort of patients. Methodological quality was assessed by using the QUADAS and STARD instruments. Previously published guidelines were followed for meta-analysis performance. Results Of 254 studies identified as eligible for full-text review, 52 (20.5%) met the inclusion criteria. The review showed that results of MGMT protein expression by IHC are not in close agreement with those obtained with MSP. Moreover, type of tumour (primary brain tumour vs others) was an independent covariate of accuracy estimates in the meta-regression analysis beyond the cut-off value. Conclusions Protein expression assessed by IHC alone fails to reflect the promoter methylation status of MGMT. Thus, in attempts at clinical diagnosis the two methods seem to select different groups of patients and should not be used interchangeably.

Caracterização e propriedades catalíticas da zeolita HZSM5 modificada com nióbio

HZSM5 zeolite was modified by exchanging proton by niobium (V). Several samples were obtained with various degrees of exchange. Pore volumes and acidity were measured to characterize these exchanged zeolites. Catalytic properties were evaluated with two reaction tests: m-xylene transformation and n-heptane cracking. The introduction of niobium on HZSM5 zeolite decreases the diffusion coefficient of 2-methyl-pentane and increases the zeolite acidity. The sample containing niobium are initially more active in cracking of n-heptane and m-xylene isomerization than HZSM5 alone.

Ultramicroeletrodos. Parte II: construção e aplicações

This work describes the techniques of construction and several applications of ultramicroelectrodes in electrochemistry and electroanalytical chemistry. Disc shaped UME are produced by embedding metal wires on insulating materials such as glass or epoxy resin. In the field of electrochemistry, UME have been applied in studies of the hydrogen evolution reaction and the electrocrystallization of metals. The negligible values of sensibility for ohmic drop and the enhanced mass transport rate by spherical diffusion are the main advantages of UME in these applications. New important conclusions regarding the phenomena under study were drawn from the experimental results. The applications in electroanalytical chemistry involved the determination of contaminants such as heavy metals and nitrites in natural waters and food products. The use of UME requires little sample manipulation and, in general, no need for oxygen removal or the addition of supporting electrolytes.

Filmes de óxidos anódicos de nióbio: efeito eletrocrômico e cinética da reação de eletro-intercalação

The aim of this work is to study the electrochromism and the reaction kinetics of lithium electrointercalation in anodic niobium oxide films. The oxide grown in an acid environment by application of an alternating potential shows interference colour (iridescence) and when reduced in lithium perclorate/PC solution, the intercalation of Li+ ions and electrons causes a reversible colour change (electrochromism), characterized here by electrochemical and optical measurements. A model where the reaction kinetics is dominated by diffusion of ionic pairs (Li+, e-) in the oxide film permitted the reproduction of current and absorbance temporal dependence, confirming the relationship between the electrochromic and electrochemical reactions. From the results obtained, a relation was established where the colour change is associated to the reduction of Nb+5 to Nb+4 ions with simultaneous cations injection.

Stereoselective sodium borohydride reductions of cyclopentanones: influence of ceric chloride on the stereochemistry of reaction

In this paper we describe the reduction by NaBH4 of some cyclopentanones containing an oxygenated function at the side chain position beta to the carbonyl group, both in the presence and in the absence of CeCl3. Some suggestions for the rationalization of the results are discussed, considering the stereochemical course of the reactions.

Modeling of Gold Cyanidation

The chemistry of gold dissolution in alkaline cyanide solution has continually received attention and new rate equations expressing the gold leaching are still developed. The effect of leaching parameters on gold gold cyanidation is studied in this work in order to optimize the leaching process. A gold leaching model, based on the well-known shrinking-core model, is presented in this work. It is proposed that the reaction takes place at the reacting particle surface which is continuously reduced as the reaction proceeds. The model parameters are estimated by comparing experimental data and simulations. The experimental data used in this work was obtained from Ling et al. (1996) and de Andrade Lima and Hodouin (2005). Two different rate equations, where the unreacted amount of gold is considered in one equation, are investigated. In this work, it is presented that the reaction at the surface is the rate controlling step since there is no internal diffusion limitation. The model considering the effect of non-reacting gold shows that the reaction orders are consistent with the experimental observations reported by Ling et al. (1996) and de Andrade Lima and Hodouin (2005). However, it should be noted that the model obtained in this work is based on assumptions of no side reactions, no solid-liquid mass transfer resistances and no effect from temperature.

Accounting for adsorption and desorption in Lattice Boltzmann simulations

We report a Lattice-Boltzmann scheme that accounts for adsorption and desorption in the calculation of mesoscale dynamical properties of tracers in media of arbitrary complexity. Lattice Boltzmann simulations made it possible to solve numerically the coupled Navier-Stokes equations of fluid dynamics and Nernst-Planck equations of electrokinetics in complex, heterogeneous media. With the moment propagation scheme, it became possible to extract the effective diffusion and dispersion coefficients of tracers, or solutes, of any charge, e.g., in porous media. Nevertheless, the dynamical properties of tracers depend on the tracer-surface affinity, which is not purely electrostatic and also includes a species-specific contribution. In order to capture this important feature, we introduce specific adsorption and desorption processes in a lattice Boltzmann scheme through a modified moment propagation algorithm, in which tracers may adsorb and desorb from surfaces through kinetic reaction rates. The method is validated on exact results for pure diffusion and diffusion-advection in Poiseuille flows in a simple geometry. We finally illustrate the importance of taking such processes into account in the time-dependent diffusion coefficient in a more complex porous medium.

Sinkkirikasteen liukenemisnopeuteen vaikuttavat tekijät ja sinkkirikasteen suoraliuotuksen mallintaminen

Työn kirjallisuusosassa selvitettiin eri tekijöiden (lämpötila, paine, mineralogia, partikkelikoko, sekoitus, kiintoainepitoisuus, liuoksen happo-, rauta- ja happipitoisuus) vaikutusta sinkkirikasteen suoraliuotusprosessin tärkeimpiin ilmiöihin (diffuusio, aineensiirto, reaktiokinetiikka). Kirjallisuusosassa kartoitettiin myös tämän hetkistä tietämystä niistä tekijöistä, jotka ovat oleellisia, kun sinkkirikasteen suoraliuotusprosessia mallinnetaan. Näitä tekijöitä ovat: sinkkirikasteiden liuotuksen kemia, sinkkirikasteiden liuotuksen kinetiikka ja mekanismit, kaasuneste aineensiirto ja kiinteäneste aineensiirto. Lisäksi selvitettiin millä tavoin aikaisemmissa tutkimuksissa sinkkirikasteiden suoraliuotusta on mallinnettu. Mallinnusosassa käsiteltiin atmosfääristä sinkkirikasteen suoraliuotusta, jossa hapettimena toimi ferri(III)rauta. Mallintamisessa käytettiin kirjallisuudessa esitettyjä mittaustuloksia ja mallintaminen tehtiin Modest tietokoneohjelmistolla. Työssä tehty atmosfäärisen suoraliuotuksen mallintaminen labo-ratoriomittakaavassa (laimeat liuokset ja pienet kiintoainepitoisuudet) antoi lupaavia tuloksia. Ongelmia mallin ennustuksen kanssa esiintyi pienissä happopitoisuuksissa, alhaisissa lämpötiloissa sekä pienillä ja suurilla partikkeleilla. Työn kirjallisuusosassa tunnistettiin ne ongelmakohdat, jotka vaativat lisätutkimuksia, jotta sinkkirikasteen atmosfääriselle suoraliuotukselle pystytään kehittämään simulointimalli. Näitä ovat: 1. Hapen liukoisuus ja aineensiirto teollisuuden käyttämissä sinkkirikastelietteissä, 2. Sopivien mittaustulosten puuttuminen, jotta atmosfääristä suoraliuotusta, jossa O2 ja Fe3+ toimivat hapettimena voitaisiin mallintaa, 3. Kiinteäneste aineensiirron merkitys sinkkirikasteen suoraliuotuksessa. Mallinnusosassa osoitettiin, että mekanistisella mallintamisella voidaan simuloida sinkkirikasteen atmosfääristä suoraliuotusta ainakin laboratoriomittakaavassa. Työn perusteella voidaan todeta, että sinkkirikasteen atmosfääriselle suoraliuotukselle voidaan työssä ehdotettujen jatkotutkimusten avulla kehittää numeerinen mekanistinen malli, jolla atmosfääristä sinkkirikasteiden suoraliuotusprosessia voidaan simuloida eri olosuhteissa.

Modeling reaction kinetics and mass transfer in ozonation in water solutions

This dissertation is based on four articles dealing with modeling of ozonation. The literature part of this considers some models for hydrodynamics in bubble column simulation. A literature review of methods for obtaining mass transfer coefficients is presented. The methods presented to obtain mass transfer are general models and can be applied to any gas-liquid system. Ozonation reaction models and methods for obtaining stoichiometric coefficients and reaction rate coefficients for ozonation reactions are discussed in the final section of the literature part. In the first article, ozone gas-liquid mass transfer into water in a bubble column was investigated for different pH values. A more general method for estimation of mass transfer and Henry’s coefficient was developed from the Beltrán method. The ozone volumetric mass transfer coefficient and the Henry’s coefficient were determined simultaneously by parameter estimation using a nonlinear optimization method. A minor dependence of the Henry’s law constant on pH was detected at the pH range 4 - 9. In the second article, a new method using the axial dispersion model for estimation of ozone self-decomposition kinetics in a semi-batch bubble column reactor was developed. The reaction rate coefficients for literature equations of ozone decomposition and the gas phase dispersion coefficient were estimated and compared with the literature data. The reaction order in the pH range 7-10 with respect to ozone 1.12 and 0.51 the hydroxyl ion were obtained, which is in good agreement with literature. The model parameters were determined by parameter estimation using a nonlinear optimization method. Sensitivity analysis was conducted using object function method to obtain information about the reliability and identifiability of the estimated parameters. In the third article, the reaction rate coefficients and the stoichiometric coefficients in the reaction of ozone with the model component p-nitrophenol were estimated at low pH of water using nonlinear optimization. A novel method for estimation of multireaction model parameters in ozonation was developed. In this method the concentration of unknown intermediate compounds is presented as a residual COD (chemical oxygen demand) calculated from the measured COD and the theoretical COD for the known species. The decomposition rate of p-nitrophenol on the pathway producing hydroquinone was found to be about two times faster than the p-nitrophenol decomposition rate on the pathway producing 4- nitrocatechol. In the fourth article, the reaction kinetics of p-nitrophenol ozonation was studied in a bubble column at pH 2. Using the new reaction kinetic model presented in the previous article, the reaction kinetic parameters, rate coefficients, and stoichiometric coefficients as well as the mass transfer coefficient were estimated with nonlinear estimation. The decomposition rate of pnitrophenol was found to be equal both on the pathway producing hydroquinone and on the path way producing 4-nitrocathecol. Comparison of the rate coefficients with the case at initial pH 5 indicates that the p-nitrophenol degradation producing 4- nitrocathecol is more selective towards molecular ozone than the reaction producing hydroquinone. The identifiability and reliability of the estimated parameters were analyzed with the Marcov chain Monte Carlo (MCMC) method. @All rights reserved. No part of the publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior permission of the author.

Unambiguous assessments of reaction paths for selected pericyclic reactions

Four commonplace concerted reactions are examined using (i) correlation diagrams, (ii) frontier molecular orbital analyses for transition states, (iii) Zimmerman-Dewar analyses for transition states and (iv) modified Zimmerman-Dewar analyses for transition states. Only the latter approach is consistently satisfactory.

Reaction Kinetics and Viscosity Modelling in the Fusion Syntheses of Ca- and Ca/Mg-resinates

Rosin is a natural product from pine forests and it is used as a raw material in resinate syntheses. Resinates are polyvalent metal salts of rosin acids and especially Ca- and Ca/Mg- resinates find wide application in the printing ink industry. In this thesis, analytical methods were applied to increase general knowledge of resinate chemistry and the reaction kinetics was studied in order to model the non linear solution viscosity increase during resinate syntheses by the fusion method. Solution viscosity in toluene is an important quality factor for resinates to be used in printing inks. The concept of critical resinate concentration, c crit, was introduced to define an abrupt change in viscosity dependence on resinate concentration in the solution. The concept was then used to explain the non-inear solution viscosity increase during resinate syntheses. A semi empirical model with two estimated parameters was derived for the viscosity increase on the basis of apparent reaction kinetics. The model was used to control the viscosity and to predict the total reaction time of the resinate process. The kinetic data from the complex reaction media was obtained by acid value titration and by FTIR spectroscopic analyses using a conventional calibration method to measure the resinate concentration and the concentration of free rosin acids. A multivariate calibration method was successfully applied to make partial least square (PLS) models for monitoring acid value and solution viscosity in both mid-infrared (MIR) and near infrared (NIR) regions during the syntheses. The calibration models can be used for on line resinate process monitoring. In kinetic studies, two main reaction steps were observed during the syntheses. First a fast irreversible resination reaction occurs at 235 °C and then a slow thermal decarboxylation of rosin acids starts to take place at 265 °C. Rosin oil is formed during the decarboxylation reaction step causing significant mass loss as the rosin oil evaporates from the system while the viscosity increases to the target level. The mass balance of the syntheses was determined based on the resinate concentration increase during the decarboxylation reaction step. A mechanistic study of the decarboxylation reaction was based on the observation that resinate molecules are partly solvated by rosin acids during the syntheses. Different decarboxylation mechanisms were proposed for the free and solvating rosin acids. The deduced kinetic model supported the analytical data of the syntheses in a wide resinate concentration region, over a wide range of viscosity values and at different reaction temperatures. In addition, the application of the kinetic model to the modified resinate syntheses gave a good fit. A novel synthesis method with the addition of decarboxylated rosin (i.e. rosin oil) to the reaction mixture was introduced. The conversion of rosin acid to resinate was increased to the level necessary to obtain the target viscosity for the product at 235 °C. Due to a lower reaction temperature than in traditional fusion synthesis at 265 °C, thermal decarboxylation is avoided. As a consequence, the mass yield of the resinate syntheses can be increased from ca. 70% to almost 100% by recycling the added rosin oil.

Novos materiais à base de nanofibras de carbono como suporte de catalisador na decomposição da hidrazina

Today satellites propulsion is based on the use of monopropellant and/or bipropellant chemical systems. The maneuvering of satellite is based on the hydrazine decomposition micropropulsors catalyzed by metallic iridium supported on g-alumina. This reaction is a surface reaction and is strongly exothermic and implies that the operation of the micropropulsor is controlled by the mass and heat diffusions. For this reason and for the fact that the propulsor operation is frequently in pulsed regime, the catalyst should support high pressure and temperature variations within a short time period. The performance and the durability of the commercial catalyst are jeopardized by the low thermal conductivity of the alumina. The low thermal conductivity of the alumina support restricts the heat diffusion and leads to the formation of hot spots on the catalyst surface causing the metal sintering and/or fractures of the support, resulting in loss of the activity and catalyst destruction. This work presents the synthesis and characterization of new carbon composite support for the active element iridium, in substitution of the commercial catalysts alumina based support. These supports are constituted of carbon nanofibers (30 to 40 nm diameter) supported on a macroscopic carbon felt. These materials present high thermal conductivity and mechanical resistance, as well as the easiness to be shaped with different macroscopic shapes. The mechanical stability and the performance of the iridium supported on the carbon composite support, evaluated in a laboratory scale test in hydrazine decomposition reaction, are superior compared to the commercial catalyst.

Synthesis and NMR characterization of aliphatic-aromatic copolyesters by reaction of poly(ethylene terephthalate) post-consumer and poly(ethylene adipate)

An aliphatic-aromatic copolyester of poly(ethylene terephthalate), PET, and poly(ethylene adipate), PEA, PET-co-PEA, was synthesized by the high temperature melt reaction of post-consumer PET and PEA. As observed by NMR spectroscopy, the reaction yielded random copolyesters in a few minutes through ester-interchange reactions, even without added catalyst. The copolyesters obtained in the presence of a catalyst presented higher intrinsic viscosity than that obtained without the addition of catalyst, due to simultaneous polycondensation and ester-interchange reactions. The structure of the aliphatic-aromatic copolyesters obtained in different PET/PEA ratio is random as observed by NMR analysis.