Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications.

Small, single-module proteins that fold in a single cooperative step may be paradigms for understanding early events in protein-folding pathways generally. Recent experimental studies of the 64-residue chymotrypsin inhibitor 2 (CI2) support a nucleation mechanism for folding, as do some computer stimulations. CI2 has a nucleation site that develops only in the transition state for folding. The nucleus is composed of a set of adjacent residues (an alpha-helix), stabilized by long-range interactions that are formed as the rest of the protein collapses around it. A simple analysis of the optimization of the rate of protein folding predicts that rates are highest when the denatured state has little residual structure under physiological conditions and no intermediates accumulate. This implies that any potential nucleation site that is composed mainly of adjacent residues should be just weakly populated in the denatured state and become structured only in a high-energy intermediate or transition state when it is stabilized by interactions elsewhere in the protein. Hierarchical mechanisms of folding in which stable elements of structure accrete are unfavorable. The nucleation-condensation mechanism of CI2 fulfills the criteria for fast folding. On the other hand, stable intermediates do form in the folding of more complex proteins, and this may be an unavoidable consequence of increasing size and nucleation at more than one site.

I.~Synthesis, isolation, and characterization of 1-(2-anthryl)-2-cyclopropylethylene and 1-(2-naphthyl)-2-cyclopropylethylene. II.~Titanium dioxide photocatalysis of haloethers: A mechanistic study

I. The target molecules are classified as 1-aryl 2-cyclopropyl substituted ethylene. In the ground state, these molecules have a number of conformers, which are in equilibrium through rotation about single bonds. Once excited, the conformers have fixed conformation and are no longer in equilibrium and can be distinguished by their UV-vis as well as fluorescence spectra. The synthetic strategy involves standard steps. Both 2-methylanthracene and 2-methylnaphthalene were brominated using N-bromosuccinimide to give the bromomethyl adduct, which then was reacted with triphenylphosphine to form the phosphonium salt. This was followed by the formation of the phosphorus ylide, which upon treatment with cyclopropanecarboxaldehyde gave the product.^ II. The degradation of three aliphatic haloethers: bis-(2-chloroethyl) ether, bis-(2-chloroisopropyl) ether, and bis-(2-chloroethoxy)methane and two aromatic haloethers: 4-chlorodiphenyl ether and 4-bromodiphenyl ether was studied. Product studies have been conducted on the titanium dioxide photocatalysis of these compounds including mass balance, monitoring and identifying intermediates to establish the reaction pathways to deduce a mechanism for their degradation. The extent of mineralization was determined from the measurement of halogen anion (Cl$\sp-$/Br$\sp-$) as well as total organic carbon. The relative rates of disappearance of the individual haloethers appear to be related to the hydrophobic character of the given compound. Reaction mechanisms involving hydroxyl radical are proposed to explain the observed results. ^

Automatic text block separation in document images

Separation of printed text blocks from the non-text areas, containing signatures, handwritten text, logos and other such symbols, is a necessary first step for an OCR involving printed text recognition. In the present work, we compare the efficacy of some feature-classifier combinations to carry out this separation task. We have selected length-nomalized horizontal projection profile (HPP) as the starting point of such a separation task. This is with the assumption that the printed text blocks contain lines of text which generate HPP's with some regularity. Such an assumption is demonstrated to be valid. Our features are the HPP and its two transformed versions, namely, eigen and Fisher profiles. Four well known classifiers, namely, Nearest neighbor, Linear discriminant function, SVM's and artificial neural networks have been considered and efficiency of the combination of these classifiers with the above features is compared. A sequential floating feature selection technique has been adopted to enhance the efficiency of this separation task. The results give an average accuracy of about 96.

Rare-earth chromium citrates as precursors for rare-earth chromites: lanthanum biscitrato chromium(III) dihydrate, La[Cr(C6H5O7)2]·2H

The thermal decomposition of lanthanum biscitrato chromium(III) dihydrate has been studied in static air and dynamic argon atmospheres. The complex decomposes in four steps: dehydration, decomposition of the citrate to an intermediate oxycarbonate, formation of LaCrO4(V) from oxycarbonate, and finally decomposition of LaCrO4(V) to LaCrO3. Formation of LaCrCrO4(V) requires the presence of oxygen The decomposition behaviour of a mechanical mixture of lanthanum citrate hydrate and chromium citrate hydrate was compared with that of the citrato complex. Both the starting material and the intermediates were characterized by X-ray diffraction, IR electronic and ESR spectroscopy, surface area and magnetic susceptibility measurements, as well as by chemical analysis. A scheme is proposed for the decomposition of lanthanum biscitrato chromium(III) dihydrate in air. LaCrO3 can be obtained at temperatures as low as 875 K by isothermal decomposition of the complex.

Photocatalytic degradation of phenol by base metal-substituted orthovanadates

Base metal (Cr, Mn, Fe, Ni, Cu) substituted CeVO4 compounds were synthesized by the solution combustion technique. These compounds were characterized by X-ray diffraction, X-ray photoelectron spectroscopy, UV-vis spectroscopy, transmission electron microscopy and BET surface area analyzer. The characterization indicated that the base metals were substituted in the ionic state in all the compounds. These compounds were used for the photocatalytic degradation of phenol and the degradation rates obtained in the presence of these compounds werecompared against that obtained with the commercial Degussa P-25 TiO2 catalyst. Fe and Cr substituted CeVO4 showed photocatalytic activity that was comparable with that of Degussa P-25 TiO2. The concentration of toxic intermediates was high when the reaction was carried out in presence of Degussa P-25 TiO2 but it was found to be insignificant when the reaction was carried out in presence of base metal-substituted CeVO4. The effect of % Fe-substitution (varied from 1 to 5 at%) in CeVO4 on the photocatalytic activity was also investigated and it was observed that 1 at% Fe-substituted compound showed the highest activity. A mathematical model describing the kinetics of the photocatalytic degradation of phenol was developed on the basis of the catalyst structure and taking into account the formation of all the possible intermediates. The variation of the concentration of phenol and the intermediates was described by the model and the reaction rateconstants were determined. (C) 2010 Elsevier B.V. All rights reserved.

Thermoanalytical studies of hydrazidocarbonic acid derivatives

Preparation, thermal analysis and IR spectra of a number of transition metal hydrazidocarbonates have been described. Metal hydrazido carbonates decompose exothermically through oxalate and carbonate intermediates to the respective metal oxides. Reaction of ammonium carbonate with hydrazine hydrate yields hydrazinium derivative of hydrazidocarbonic acid; N2H3COON2H5

Dye sensitized visible light degradation of phenolic compounds

The present research work reports the eosin Y (EY) and fluorescein (FL) sensitized visible light degradation of phenol, 4-chlorophenol (CP), 2,4-dichlorophenol (DCP) and 2,4,6-trichlorophenol (TCP) using combustion synthesized nano-TiO2 (CS TiO2). The rate of degradation of the phenolic compounds was higher in the presence of EY/CS TiO2 compared to FL/CS TiO2 system. A detailed mechanism of sensitized degradation was proposed and a mechanistic model for the rate of degradation of the phenolic compound was derived using the pyramidal network reduction technique. It was found that at low initial dye concentrations, the rate of degradation of the phenolic compound is first order in the concentration of the dye, while at high initial dye concentrations, the rate is first order in the concentration of the phenolic compound. The order of degradation of the different phenolic compounds follows: CP > TCP > DCP > phenol. The different phenolic and dye intermediates that were formed during the degradation were identified by liquid chromatography-mass spectrometry (LC-MS) and the most probable pathway of degradation is proposed. (C) 2010 Elsevier B.V. All rights reserved.

Chemistry of secondary organic aerosol

The photooxidation of volatile organic compounds (VOCs) in the atmosphere can lead to the formation of secondary organic aerosol (SOA), a major component of fine particulate matter. Improvements to air quality require insight into the many reactive intermediates that lead to SOA formation, of which only a small fraction have been measured at the molecular level. This thesis describes the chemistry of secondary organic aerosol (SOA) formation from several atmospherically relevant hydrocarbon precursors. Photooxidation experiments of methoxyphenol and phenolic compounds and C₁₂ alkanes were conducted in the Caltech Environmental Chamber. These experiments include the first photooxidation studies of these precursors run under sufficiently low NO_x levels, such that RO₂ + HO₂ chemistry dominates, an important chemical regime in the atmosphere. Using online Chemical Ionization Mass Spectrometery (CIMS), key gas-phase intermediates that lead to SOA formation in these systems were identified. With complementary particle-phase analyses, chemical mechanisms elucidating the SOA formation from these compounds are proposed.

Three methoxyphenol species (phenol, guaiacol, and syringol) were studied to model potential photooxidation schemes of biomass burning intermediates. SOA yields (ratio of mass of SOA formed to mass of primary organic reacted) exceeding 25% are observed. Aerosol growth is rapid and linear with the organic conversion, consistent with the formation of essentially non-volatile products. Gas and aerosol-phase oxidation products from the guaiacol system show that the chemical mechanism consists of highly oxidized aromatic species in the particle phase. Syringol SOA yields are lower than that of phenol and guaiacol, likely due to unique chemistry dependent on methoxy group position.

The photooxidation of several C₁₂ alkanes of varying structure n-dodecane, 2-methylundecane, cyclododecane, and hexylcyclohexane) were run under extended OH exposure to investigate the effect of molecular structure on SOA yields and photochemical aging. Peroxyhemiacetal formation from the reactions of several multifunctional hydroperoxides and aldehyde intermediates was found to be central to organic growth in all systems, and SOA yields increased with cyclic character of the starting hydrocarbon. All of these studies provide direction for future experiments and modeling in order to lessen outstanding discrepancies between predicted and measured SOA.

Selective hydrogenation of nitrobenzene to aniline in dense phase carbon dioxide over Ni/gamma-Al2O3: Significance of molecular interactions

The selective hydrogenation of nitrobenzene (NB) over Ni/gamma-Al2O3 Catalysts Was investigated using different media of dense phase CO2, ethanol, and n-hexane. In dense phase CO2, the total rate of NB hydrogenation was larger than that in organic solvents under similar reaction conditions; the selectivity to the desired product, aniline, was almost 100% over the whole conversion range of 0-100%. The phase behavior of the reactant mixture in/under dense phase CO2 was examined at reaction conditions. In situ high-pressure Fourier transform infrared measurements were made to study the molecular interactions Of CO2 with the following reactant and reaction intermediates: NB, nitrosobenzene (NSB), and N-phenylhydroxylamine (PHA). Dense phase CO2 strongly interacts with NB, NSB, and PHA, modifying the reactivity of each species and contributing to positive effects on the reaction rate and the selectivity to aniline. A possible reaction pathway for the hydrogenation of NB in/under dense phase CO2 over Ni/gamma-Al2O3 is also proposed.

Synthesis of aromatic diaminospirodilactone

A new kind of aromatic diaminospirodilactone, i.e. 6,6'-diamino-3, 3'-spirobiphthalide, was synthesized through multistep reactions from p-nitrotoulene and paraformaldehyde, It was: found that dinitrospirolactone could be synthesized directly in the acid system through oxidation reaction with a high yield, The increase of solvent polarity leads to an increase of reduction yield of dinitrolactone. The resulting intermediates 6, 6'-dihydroxylamino-3, 3'-spirobiphthalide and 6-amino-6'-hydroxylanimo-3, 3'-spirobiphthalide were steady aromatic hydroxylamine. The structures of 6, 6'-diamino-3, 3'-spirobiphthalide and its intermediates were confirmed by H-1 NMR, C-13 NMR, MS, IR and elemental analyses.

THEORETICAL-STUDIES ON THE CYCLIZATION PROCESS OF A NEW ORGANOSULFUR REACTION

The cyclization process of a new organosulfur reaction was studied by the MNDO (UHF) method. The first reaction path was assumed to be via the organosulfur radical intermediate, the second via the ionic (cationic and anionic) intermediates. The dehydroxylation process was assumed to occur with the synergistic cyclization. The results obtained indicate that the potential energy barrier of the first reaction path was about 102 kcal mol(-1), and although the formation of the ionic intermediate is comparatively difficult, the potential energy barrier of the second path is comparable to the first. The sequential reaction path via the radical intermediate, i.e. first cyclization, then dehydroxylation, was investigated for comparison. The cyclization reaction was found to be the thermodynamically favored process, while the ensuing dehydroxylation process was found to have a potential energy barrier of about 62 kcal mol(-1).

Reductive ligation mediated one-step disulfide formation of S-nitrosothiols.

A one-step reductive ligation mediated disulfide formation of S-nitrosothiols was developed. This reaction involves the reaction of the S-nitroso group with phosphine-thioesters to form sulfenamide and thiolate intermediates, which then undergo a fast intermolecular disulfide formation to form stable conjugates. This reaction can be used to design new biosensors of S-nitrosated proteins.

Chemoenzymatic synthesis of the trans-dihydrodiol isomers of monosubstituted benzenes via anti-benzene dioxides

Enantiopure cis-2,3-dihydrodiols, available from dioxygenase-catalysed cis-dihydroxylation of monosubstituted benzene substrates, have been used as synthetic precursors of the corresponding trans-3,4-dihydrodiols. The six-step chemoenzymatic route from cis-dihydrodiol precursors, involving acetonide, tetraol, dibromodiacetate and diepoxide intermediates, and substitution of vinyl bromide and iodide atoms, has been used in the synthesis of ten trans-dihydrododiol derivatives of substituted benzenes. The general applicability of the method has been demonstrated by its use in the synthesis of both enantiomers of the trans-1,2- and 3,4-dihydrodiol derivatives of toluene.

Implementação de uma marca de produção e distribuição de citrinos biológicos: Orange made in Algarve

Trabalho de projeto apresentado à Escola Superior de Comunicação Social como parte dos requisitos para obtenção de grau de mestre em Publicidade e Marketing.

Functional Characterization of Monoterpenoid Indole Alkaloid (MIA) Biosynthetic Genes in Catharanthus roseus

The monoterpenoid indole alkaloids (MIAs) of Madagascar periwinkle (Catharanthus roseus) are known to be among the most important source of natural drugs used in various cancer chemotherapies. MIAs are derived by combining the iridoid secologanin with tryptamine to form the central precursor strictosidine that is then converted to most known MIAs, such as catharanthine and vindoline that dimerize to form anticancer vinblastine and vincristine. While their assembly is still poorly understood, the complex multistep pathways involved occur in several specialized cell types within leaves that are regulated by developmental and environmental cues. The organization of MIA pathways is also coupled to secretory mechanisms that allow the accumulation of catharanthine in the waxy leaf surface, separated from vindoline found within leaf cells. While the spatial separation of catharanthine and vindoline provides an explanation for the low levels of dimeric MIAs found in the plants, the secretion of catharanthine to the leaf surface is shown to be part of plant defense mechanisms against fungal infection and insect herbivores. The transcriptomic databases of Catharanthus roseus and various MIA producing plants are facilitating bioinformatic approaches to identify novel MIA biosynthetic genes. Virus-induced gene silencing (VIGS) is being used to screen these candidate genes for their involvement in iridoid biosynthesis pathway, especially in the identification of 7-deoxyloganic acid 7-hydroxylase (CrDL7H) shown by the accumulation of its substrate, 7-deoxyloganic acid and decreased level of secologanin along with catharanthine and vindoline. VIGS can also confirm the biochemical function of genes being identified, such as in the glucosylation of 7-deoxyloganetic acid by CrUGT8 shown by decreased level of secologanin and MIAs within silenced plants. Silencing of other iridoid biosynthetic genes, loganic acid O-methyltransferase (LAMT) and secologanin synthase (SLS) also confirm the metabolic route for iridoid biosynthesis in planta through 7-deoxyloganic acid, loganic acid, and loganin intermediates. This route is validated by high substrate specificity of CrUGT8 for 7-deoxyloganetic acid and CrDL7H for 7-deoxyloganic acid. Further localization studies of CrUGT8 and CrDL7H also show that these genes are preferentially expressed within Catharanthus leaves rather than in epidermal cells where the last two steps of secologanin biosynthesis occur.