Elucidação estrutural de substâncias orgânicas com auxílio de computador: evoluções recentes

The development of new tools for chemoinformatics, allied to the use of different algorithms and computer programmes for structure elucidation of organic compounds, is growing fast worldwide. Massive efforts in research and development are currently being pursued both by academia and the so-called chemistry software development companies. The demystification of this environment provoked by the availability of software packages and a vast array of publications exert a positive impact on chemistry. In this work, an overview concerning the more classical approaches as well as new strategies on computer-based tools for structure elucidation of organic compounds is presented. Historical background is also taken into account since these techniques began to develop around four decades ago. Attention will be paid to companies which develop, distribute or commercialize software as well as web-based and open access tools which are currently available to chemists.

STAPHYLOCOCCUS AUREUS BIOFILM FORMATION ON POLYPYRROLE: AN ELECTRICAL OVERVIEW

The development of organic devices based on conducting polymers for biofilm detection requires the combination of superior electrical response and high surface area for biofilm incorporation. Polypyrrole is a potential candidate for application in biofilm detection and control due to its characteristic superior electrical response and strong interaction with bacteria, which enables the use of the bioelectric effect in resulting devices. In this study, chemically synthesized polypyrrole was applied as a support for biofilm growth of S. aureus. Modifications in the electrical response of the polymeric template were explored to identify general mechanisms established during the deposition of the biofilm.

Determination of sugars and organic acids in pulp samples by capillary electrophoresis with UV detection

This MSc work was done in the project of BIOMECON financed by Tekes. The prime target of the research was, to develop methods for separation and determination of carbohydrates (sugars), sugar acids and alcohols, and some other organic acids in hydrolyzed pulp samples by capillary electrophoresis (CE) using UV detection. Aspen, spruce, and birch pulps are commonly used for production of papers in Finland. Feedstock components in pulp predominantly consist of carbohydrates, organic acids, lignin, extractives, and proteins. Here in this study, pulps have been hydrolyzed in analytical chemistry laboratories of UPM Company and Lappeenranta University in order to convert them into sugars, acids, alcohols, and organic acids. Foremost objective of this study was to quantify and identify the main and by-products in the pulp samples. For the method development and optimization, increased precision in capillary electrophoresis was accomplished by calculating calibration data of 16 analytes such as D-(-)-fructose, D(+)-xylose, D(+)-mannose, D(+)-cellobiose, D-(+)-glucose, D-(+)-raffinose, D(-)-mannitol, sorbitol, rhamnose, sucrose, xylitol, galactose, maltose, arabinose, ribose, and, α-lactose monohydratesugars and 16 organic acids such as D-glucuronic, oxalic, acetic, propionic, formic, glycolic, malonic, maleic, citric, L-glutamic, tartaric, succinic, adipic, ascorbic, galacturonic, and glyoxylic acid. In carbohydrate and polyalcohol analyses, the experiments with CE coupled to direct UV detection and positive separation polarity was performed in 36 mM disodium hydrogen phosphate electrolyte solution. For acid analyses, CE coupled indirect UV detection, using negative polarity, and electrolyte solution made of 2,3 pyridinedicarboxylic acid, Ca2+ salt, Mg2+ salts, and myristyltrimethylammonium hydroxide in water was used. Under optimized conditions, limits of detection, relative standard deviations and correlation coefficients of each compound were measured. The optimized conditions were used for the identification and quantification of carbohydrates and acids produced by hydrolyses of pulp. The concentrations of the analytes varied between 1 mg – 0.138 g in liter hydrolysate.

Recycling of nutrients with application of organic waste in degraded pasture

The utilization of organic wastes represents an alternative to recover degraded pasture. The experiment aimed to assess the changes caused by the provision of different organic waste (poultry litter, turkey litter and pig manure) in a medium-textured Oxisol in Brazilian Savanna under degraded pasture. It was applied different doses of waste compared to the use of mineral fertilizers and organic mineral and evaluated the effect on soil parameters (pH, organic matter, phosphorus and potassium) and leaf of Brachiariadecumbens (crude protein, phosphorus and dry mass production). It was observed that application of organic waste did not increase the level of soil organic matter and pH in the surface layer, and the application of turkey litter caused acidification at depths of 0.20-0.40 m and 0.40-0.60 m. There was an increase in P and K in the soil with the application of poultry litter and swine manure. All organic wastes increased the productivity of dry matter and crude protein and phosphorus. The recycling of nutrients via the application of organic waste allows efficiency of most parameters similar to those observed with the use of mineral sources, contributing to improving the nutritional status of soil-plantsystem.

Pulsed corona discharge as an advanced oxidation process for degradation of organic

Advanced oxidation processes (AOPs) have been studied and developed to suffice the effective removal of refractory and toxic compounds in polluted water. The quality and cost of wastewater treatment need improvements, and electric discharge technology has a potential to make a significant difference compared to other established AOPs based on energy efficiency. The generation of active oxidant species such as ozone and hydroxyl radicals by high voltage discharge is a relatively new technology for water treatment. Gas-phase pulsed corona discharge (PCD), where a treated aqueous solution is dispersed between corona-producing electrodes free of the dielectric barriers, was developed as an alternative approach to the problem. The short living radicals and ozone formed in the gas phase and at the gas-liquid interface react with dissolved impurities. PCD equipment has a relatively simple configuration, and with the reactor in an enclosed compartment, it is insensitive towards gas humidity and does not need the gas transport. In this thesis, PCD was used to study and evaluate the energy efficiency for degrading various organic compounds, as well as the chemistry of the oxidation products formed. The experiments investigate the aqueous oxidation of phenol, humic substances, pharmaceutical compounds (paracetamol, ibuprofen, indomethacin, salicylic acids, -estradiol), as well as lignin degradation and transformation to aldehydes. The study aims to establish the influence of initial concentration of the target pollutant, the pulsed discharge parameters, gas phase composition and the pH on the oxidation kinetics and the efficiency. Analytical methods to measure the concentrations of the target compounds and their by-products include HPLC, spectrophotometry, TOC and capillary electrophoresis. The results of the research included in this summary are presented in the attached publications and manuscripts accepted for publication. Pulsed corona discharge proved to be highly effective in oxidizing each of the target compounds, surpassing the closest competitor, conventional ozonation. The increase in oxidation efficiencies for some compounds in oxygen media and at lower pulse repetition frequencies shows a significant role of ozone. The role of the ·OH radicals was established in the surface reactions. The main oxidation products, formation of nitrates, and the lignin transformation were quantified. A compound specific approach is suggested for optimization of the PCD parameters that have the most significant impact on the oxidation energy efficiency because of the different characteristics and responses of the target compound to the oxidants, as well as different admixtures that are present in the wastewater. Further studies in the method’s safety (nitration and nitrosation of organic compounds, nitrite and nitrate formation enhancement) are needed for promoting the method.

An overview of lignin metabolism and its effect on biomass recalcitrance

Lignin, after cellulose, is the second most abundant biopolymer on Earth, accounting for 30% of the organic carbon in the biosphere. It is considered an important evolutionary adaptation of plants during their transition from the aquatic environment to land, since it bestowed the early tracheophytes with physical support to stand upright and enabled long-distance transport of water and solutes by waterproofing the vascular tissue. Although essential for plant growth and development, lignin is the major plant cell wall component responsible for biomass recalcitrance to industrial processing. The fact that lignin is a non-linear aromatic polymer built with chemically diverse and poorly reactive linkages and a variety of monomer units precludes the ability of any single enzyme to properly recognize and degrade it. Consequently, the use of lignocellulosic feedstock as a renewable and sustainable resource for the production of biofuels and bio-based materials will depend on the identification and characterization of the factors that determine plant biomass recalcitrance, especially the highly complex phenolic polymer lignin. Here, we summarize the current knowledge regarding lignin metabolism in plants, its effect on biomass recalcitrance and the emergent strategies to modify biomass recalcitrance through metabolic engineering of the lignin pathway. In addition, the potential use of sugarcane as a second-generation biofuel crop and the advances in lignin-related studies in sugarcane are discussed.

Volatile compounds from organic and conventional passion fruit (Passiflora edulis F. Flavicarpa) pulp

The volatile compositions from organic and conventional passion fruit pulps produced in Brazil were investigated. The pulps were also physicochemically characterized. The volatile compounds from the headspace of the passion fruit pulp were stripped to a Porapak Q trap for 2 hours; they were eluted with 300 µL of dichloromethane, separated by gas chromatography/flame ionisation detection and identified through gas chromatography/mass spectrometry. Both pulps conformed to the requirements of the Brazilian legislation, indicating they were suitable to be industrialized and consumed. A total of 77 compounds were detected in the headspace of the passion fruit pulps - 60 of which were identified, comprising 91% of the total chromatogram area. The major compounds were the following: ethyl butanoate, 52% and 57% of the total relative area of the chromatogram for the organic and conventional passion fruit pulps, respectively; ethyl hexanoate, 22% and 9%, respectively; and hexyl butanoate, 2% and 5%, respectively. The aroma of the organic passion fruit pulp is mainly related to the following volatile compounds: ethyl hexanoate, methyl hexanoate, β-myrcene and D-limonene. The conventional passion fruit pulp presented methyl butanoate, butyl acetate, hexanal, 1-butanol, butyl butanoate, trans-3-hexenyl acetate, cis-3-hexen-1-ol, butyl hexanoate, hexyl butanoate, 3-hexenyl butanoate and 3-hexenyl hexanoate as the main volatile compounds for aroma.

Kinetic studies of the effect of organic sulphides on the oxidation of other sulphides /

The rates of oxidation of three Organic sulphides viz. methyl phenyl sulphide, (P), p -me thoxyphenyl methyl sulphide (M) and methyl p-nitrophenyl sulphide (N). have been obtained in ethanol using MoO-(acac)- as catalyst and Bu OOH as the oxidizing agent. A Hammett plot gave a rho value of -2.1 and the activation energies for the oxidation of P, M and N were estimated to be 63.60, 40.12 and 197.46 Kj mol respectively. The effect of organic sulphide on the oxidation of another sulphide was also ascertained. Positive and negative deviations were observed from the expected slope.

An investigation into the oxidation of organic sulphides, organic selenides and simple hydrocarbons by Mortierella isabellina NRRL 1757

The work presented in this thesis is divided into three separate sections 4!> Each' 'section is involved wi th a different problem, however all three are involved with a microbial oxidation of a substrate~ A series of 'aryl substituted phenyl a.nd be,nzyl methyl sulphides were oxidized to the corre~pondi~g sulphoxides by 'Mo:rtierellai's'a'b'e'llina NRR.L17'S7 @ For this enzymic Qxidation, based on 180 labeled experiments, the oxygen atom is derived fr'orn the atmosphere and not from water. By way of an u~.traviolet analysis, the rates of oxidation, in terms of sulphox~ de appearance, were obtained and correlated with the Hatnmett p s~grna constants for the phenyl methyl sulphide series. A value of -0.67 was obtained and, is interpreted in terms of a mechanism of oxidation that involves an electrophilic attack on the sulphide sulphur by an enzymic ironoxygen activated complex and the conversion of the resulti!lg sulphur cation to sulphoxide. A series of alkyl phenyl selen~des have been incubated with the fu~gi, Aspergillus niger ATCC9l42, Aspergillus fO'etidus NRRL 337, MIIJisabellina NF.RLl757 and'He'lminth'osparium sp'ecies NRRL 4671 @l These fu?gi have been reported to be capable of carrying out the efficient oxidation of sulphide to sulphoxide, but in no case was there any evidence to supp'ort the occurrence of a microbialox,idation. A more extensive inves·t~gation was carried out with'M,e 'i's'a'b'e'l'l'i'na, this fu~gus was capable of oxidizing the correspondi~g sulphides to sulphoxi.de·s·$ Usi:ng a 1abel.edsubstra.te, [Methyl-l4c]-methyl phenyl selenide, the fate of this compound was invest~gated followi!lg an i'ncubation wi th Me isabellina .. BeSUldes th. e l4C-ana1YS1Q S-,'. a quant"ltta"lve selen'lum ana1Y"S1S was carried out with phenyl methyl selenide. These techniques indicate that thesel'enium was capable of enteri!1g thefu!1gal cell ef'ficiently but that s'ome metabolic cleav~ge of the seleni'um-carbon bond' may take plac'e Ie The l3c NMR shifts were assigned to the synthesized alkyl phenyl sulphides and selenides@ The final section involved the incubation ofethylben~ zene and p-e:rtr.hyltoluene wi th'M ~ 'isab'e'llina NRRL 17574b Followi~ g this incubation an hydroxylated product was isolated from the medium. The lH NMR and mass spectral data identify the products as I-phenylethanol and p-methyl-l-phenylethanol. Employi!lg a ch'iral shift re~gent,tri~ (3-heptafluorobutyl-dcamphorato)'- europium III, the enantiomeric puri ty of these products was invest~gated. An optical rotation measurement of I-phenylethanol was in ~greement with the results obtained with the chiral shift re~gen,te 'M.isabe'l'lina is capable of carryi~g out an hydroxylation of ethylbenzene and p-ethyltoluene at the ~ position.

Exchange reactions of organic halides and organo-silicon compounds with boron tribromide and boron triiodide

Reactions of the boron halides with organic halides and organo-silicon compounds have been investigated. The results show exchange of halogens between the BX3 (X = Br# 1) and the organic halidef exchange of the halogen of the C-X bond being proved. The rates of halogen exchange vary. Reaction of the heavier halides with organo-silicon compounds indicated that the silicon-carbon bonds ruptured in the absence of electronegative atom attached to the silicon. The presence of an electronegative atom (halogen or oxygen) attached to the silicon causes the bond between the silicon and the electronegative atom to be preferentially broken. Products of exchange reactions of the boron halides and the organic halides or the organo-silicon compounds were studied by use of 1H NMR and GC/MS. From these results some possible mechanisms for the exchange reactions are postulated, but further work is indicated to prove the real courses of the reactions

Kinetic and mechanistic studies for the molybdenum- catalyzed oxidation of organic sulfides and olefins by t- DuO2H

This research was focussed on the effects of light, solvent and substituents in the molybdenum-catalyzed oxidation of phenylmethyl sulfides with t-Bu02H and on the effect of light in the molybdenum-catalyzed epoxidation of l-octene with t-Bu02H. It was shown that the Mo(CO)6-catalyzed oxidation of phenylmethyl sulfide with t-Bu02H~ at 35°C, proceeds 278 times faster underUV light than under laboratory lighting, whereas the Mo02(acac)2-catalyzed oxidation proceeds only 1.7 times faster under UV light than under normal laboratory lighting. The difference between the activities of both catalysts was explained by the formation of the catalytically active species, Mo(VI). The formation of the Mo(VI) species, from Mo(CO)6 was observed from the IR spectrum of Mo(CO)6 in the carbonyl region. The Mo(CO)6-catalyzed epoxidation of l-octene with t-Bu02H showed that the reaction proceeded 4.6 times faster under UV light than in the dark or under normal laboratory lighting; the rates of epoxidations were found to be the same in the dark and under normal laboratory lighting. The kinetics of the epoxidations of l-octene with t-Bu02H, catalyzed by Mo02(acac)2 were found to be complicated; after fast initial rates, the epoxidation rates decreased with time. The effect of phenylmethyl sulfide on the Mo(CO)6-catalyzed epoxidation of l-octene waS studied. It was shown that instead of phenylmethyl sulfide, phenylmethyl sulfone, which formed rapidly at 85°C, lowered the reaction rate. The epoxidation of l-octene was found to be 2.5 times faster in benzene than in ethanol. The substituent effect on the Mo02(acac)2-catalyzed oxidations of p-OH, p-CHgO, P-CH3' p-H, p-Cl, p-Br, p-CHgCO, p-HCO and P-N02 substituted phenylmethyl sulfides were studied. The oxidations followed second order kinetics for each case; first order dependency on catalyst concentration was also observed in the oxidation of p-CHgOPhSMeand PhSMe. It was found that electron-donating groups on the para position of phenylmethyl sulfide increased the rate of reaction, while electronwithdrawing groups caused the reaction rate to decrease. The reaction constants 0 were determined by using 0, 0- and 0* constants. The rate effects were paralleled by the activation energies for oxidation. The decomposition of t-Bu02H in the presence of M.o (CO)6, Mo02 (acac)2 and VO(acac)2 was studied. The rates of decomposition were found to be very small compared to the oxidation rates at high concentration of catalysis. The relative rates of the Mo02(acac)2-catalyzed oxidation of p-N02PhSMe by t-Bu02H in the presence of either p-CH30PhSMe or PhSMe clearly show that PhSMe and p-CHgOPhSMe act as co-catalysts in the oxidation of p-N02PhSMe. Benzene, mesity1ene and cyclohexane were used to determine the effect of solvent in the Mo02 (acac)2 and Mo(CO)6-catalyzed oxidation of phenylmethyl sulfide. The results showed that in the absence of hydroxylic solvent, a second molecule of t-Bu02H was involved in the transition state. The complexation of the solvent with the catalyst could not be explained.The oxidations of diphenyl sulfoxide catalyzed by VO(acac)2, Mo(CO)6 and Mo02(acac)2 showed that VO(acac)2 catalyzed the oxidation faster than Mo(CO)6 and Mo02 (acac)2_ Moreover, the Mo(CO)6-catalyzed oxidation of diphenyl sulfoxide proceeded under UV light at 35°C.

Molecular mechanics calculations on some phosphine oxide metal complexes in aqueous and organic solvents

Molecular mechanics calculations were done on tetrahedral phosphine oxide zinc complexes in simulated water, benzene and hexane phases using the DREIDING II force field in the BIOGRAF molecular modeling program. The SUN workstation computer (SUN_ 4c, with SPARK station 1 processor) was used for the calculations. Experimental structural information used in the parameterization was obtained from the September 1989 version of the Cambridge Structural Database. 2 Steric and solvation energies were calculated for complexes of the type ZnCl2 (RlO)2' The calculations were done with and without inclusion of electrostatic interactions. More reliable simulation results were obtained without inclusion of charges. In the simulated gas phase, the steric energies increase regularly with number of carbons in the alkyl group, whereas they go through a maximum when solvent shells are included in the calculation. Simulated distribution ratios vary with chain length and type of chain branching and the complexes are found to be more favourable for extraction by benzene than by hexane, in accord with experimental data. Also, in line with what would be expected for a favorable extraction, calculations without electrostatics predict that the complexes are better solvated by the organic solvents than by water.

Strong hydrogen bonding in organic synthesis

The preparation of phenacyl and para-phenylphenacyl esters, the reactions of carboxylic acids, phenols, 2-nitropropane and alcohols with alkyl halides in the presence of fluoride anion are described. The reactions are thought to be accelerated by the formation of hydrogen bonds between the fluoride anion and the organic electron acceptor. The fluoride ,carboxylic acids, fluoride-phenols and fluoride-2-nitropropane are better reaction systems than the fluoride-alcohol. The source of the fluoride anion and the choice of solvents are also discussed.

Studies of some cocondensations of nickel atoms with unsaturated organic ligands and with mixed ligand systems

The cocondensation of nickel with a number of unsaturated ligands was studied, as was the cocondensation with a number of mixed ligand systems. Enamines were found not to react with nickel while acrylonitrile was polymerized. In the mixed ligand syst.ems different products were obtained than when the ligands were cocondensed individually. Cocondensations of benzyl halide/allyl halide mixtures gave unstable products that were not observed when the halides were cocondensed individually. The effect of Kao-Wool insulation on nickel/benzyl halide cocondensations was found to be significant. Kao-Wool caused the bulk of the benzyl halide to be polymeri zed to a number of poly-benzylic species. An alkali metal reactor was designed for the evaporation of sodium and potassium atoms into cold solutions of metal halide and an or ganic substrate. This apparatus was used to synthesize Ni(P¢3 )3' but proved unsuccessful for synthesizing a nickel-enamine compound.

Biotransformation of aromatic hydrocarbons and organic sulphides by fungi

Toluene is converted to benzyl alcohol by the fungi Mortierella isabellina and Helminthosporium species; in the latter case, the product is further metabolized. Toluene-a -d 1 , toluene-a,a-d2, and toluene-a,a,a-d 3 have been used with Mortierellaisabellina in a series of experiments to determine both primary and secondary deuterium kinetic isotope effects for the enzymic benzylic hydroxylation reaction. The values obtained, intermolecular primary kH/kD = intramolecular p rim a r y kH r kD = 1. 0 2 + O. 0 5, and sec 0 n dar y k H I kD = 1. 37 .:!. 0.05, suggest a mechanism for the reaction involving benzylic proton removal from a radical intermediate in a non-symmetrical transition state. 2H NMR (30.7 MHz) studies using ethylbenzene-l,1-d 2 , 3 -fluoroethylbenzene-l,1-d 2 , 4 -fluoroethylbenzene-l,1-d 2 , and toluene-dB as substrates with Mortierella isabellina suggest, based on the observable differences in rates of conversion between the substrates, that the hydroxylation of hydrocarbons at the benzylic position proceeds via a one electron abstraction from the aromatic ring, giving a radical cation. A series of 1,3-oxathiolanes (eight) were incubated with Mortierella isabellina , Helminthosporium , Rhizopus arrhizus , and Aspergillus niger . Sulphoxides were obtained from Mortierella isabellina and Rhizopus arrhizus using the substrates 2-phenyl-, 2-methyl-2-phenyl-, and 2-phenyl-2-tert. butyl-l,3-oxathiolane. The relative stereochemistry of 2-methyl-2-phenyl-l,3-oxathiolan-l-oxide was assigned based on lH decoupling, n.O.e, 1 and H NMR experiments. The lH NMR (200 MHz) of the methylene protons of 2-methyl-2-phenyl-l,3-oxathiolan-l-oxide was used as a diagnostic standard in assigning the relative stereochemistry of 2-phenyl-l,3-oxathiolan-l-oxide and 2-phenyl-2-tert. butyl-l,3-oxathiolan-l-oxide. The sulphoxides obtained were consistent with an oxidation occurring from the opposite side of the molecule to the phenyl substituent.