Propriedades relacionadas à acidez e basicidade a partir da abordagem em química computacional

Analytical Chemistry books lack a clear link between thermodynamic and equilibrium approaches involving acids and bases. In this work, theoretical calculations were performed to search for these relations. An excellent relationship was found between difference in Gibbs free energy, ∆G of acid dissociation reaction and ∆G of hydrolysis reaction of the corresponding conjugate base. A relationship between ∆G of hydrolysis reaction of conjugate acids and their corresponding atomic radius was also identified, showing that stability plays an important role in hydrolysis reactions. Finally, the importance of solvation in acid/base behavior was demonstrated when comparing the corresponding theoretical and experimental ∆G´s.

Imobilização de lipase por encapsulação em sílica aerogel

Lipase from Burkholderia cepacia was immobilized in a silica matrix and dried in high pressure carbon dioxide media (aerogel). The protic ionic liquid (PIL) was used in the immobilization process by encapsulation. The objective of this work was to evaluate the influence of the drying technique using supercritical carbon dioxide in biocatalysts obtained through the sol-gel technique by evaluating temperature and pressure and, after selecting the best drying conditions, to investigate the application of the technique for the biocatalyst using ionic liquid as an additive in the immobilization process. The results for immobilized biocatalysts showed that the best conditions of pressure and temperature were 100 bar and 25 ºC, respectively, giving a total activity recovery yield of 37.27% without PIL (EN) and 44.23% with PIL (ENLI). The operational stability of the biocatalysts showed a half-life of 11.4 h for ENLI and 6 h for EN. Therefore, solvent extraction using supercritical CO2, besides shortening drying time, offers little resistance to the immobilization of lipases, since their macropores provide ample room for their molecules. The use of the ionic liquid as an additive in the process studied for the immobilization of enzymes produced attractive yields for immobilization and therefore has potential for industrial applications in the hydrolysis of vegetable oils.

In vitro effect of isoschaftoside isolated from Syngonium podophyllum on pig kidney Na+, K+-ATPase

The present study aimed to investigate the in vitro effects of isoschaftoside isolated from Syngonium podophyllum on pig kidney Na+,K+-ATPase. The Na+, K+-ATPase activity was determined by colorimetric measurement of inorganic phosphate (Pi), resulting from ATP hydrolysis. Isoschaftoside significantly decreased the renal Na+, K+-ATPase activity at the highest concentration as well as at a lower concentration. Our work suggests that isoschaftoside is a promising compound for the treatment of hypertension.

ENZYMATIC RESOLUTION OF ANTIDEPRESSANT DRUG PRECURSORS IN AN UNDERGRADUATE LABORATORY

The use of biocatalysts in synthetic chemistry is a conventional methodology for preparing enantiomerically enriched compounds. Despite this fact, the number of experiments in chemical teaching laboratories that demonstrate the potential of enzymes in synthetic organic chemistry is limited. We describe a laboratory experiment in which students synthesized a chiral secondary alcohol that can be used in the preparation of antidepressant drugs. This experiment was conducted by individual students as part of a Drug Synthesis course held at the Pharmacy Faculty, Lisbon University. This laboratory experiment requires six laboratory periods, each lasting four hours. During the first four laboratory periods, students synthesized and characterized a racemic ester using nuclear magnetic resonance spectroscopy and gas chromatography. During the last two laboratory periods, they performed enzymatic hydrolysis resolution of the racemic ester using Candida antarctica lipase B to yield enantiomerically enriched secondary alcohol. Students successfully prepared the racemic ester with a 70%-81% overall yield in three steps. The enzymatic hydrolysis afforded (R)- secondary alcohol with good enantioselectivity (90%-95%) and reasonable yields (10%-19%). In these experiments, students were exposed to theoretical and practical concepts of aromatic acylation, ketone reduction, esterification, and enzymatic hydrolysis.

ISOLATION AND CHARACTERIZATION OF NANOFIBRILLATED CELLULOSE FROM OAT HULLS

The objectives of this work were to investigate the microstructure, crystallinity and thermal stability of nanofibrillated cellulose obtained from oat hulls using bleaching and acid hydrolysis at a mild temperature (45 ºC) followed by ultrasonication. The oat hulls were bleached with peracetic acid, and after bleaching, the compact structure around the cellulosic fibers was removed, and the bundles became individualized. The extraction time (30 or 60 min) did not affect the properties of the nanofibrillated cellulose, which presented a higher crystallinity index and thermal stability than the raw material (oat hulls). The nanocellulose formed interconnected webs of tiny fibers with diameters of 70-100 nm and lengths of several micrometers, producing nanofibers with a relatively high aspect ratio, thus indicating that these materials are suitable for polymer reinforcement.

HYDROLYTIC DEGRADATION BEHAVIOR OF PLLA NANOCOMPOSITES REINFORCED WITH MODIFIED CELLULOSE NANOCRYSTALS

Bionanocomposites derived from poly(L-Lactide) (PLLA) were reinforced with chemically modified cellulose nanocrystals (m-CNCs). The effects of these modified cellulose nanoparticles on the mechanical and hydrolytic degradation behavior of polylactide were studied. The m-CNCs were prepared by a method in which hydrolysis of cellulose chains is performed simultaneously with the esterification of hydroxyl groups to produce modified nanocrystals with ester groups. FTIR, elemental analysis, TEM, XRD and contact angle measurements were used to confirm and characterize the chemical modifications of the m-CNCs. These bionanocomposites gave considerably better mechanical properties than neat PLLA based on an approximately 100% increase in tensile strength. Due to the hydrophobic properties of the esterified nanocrystals incorporated into a polymer matrix, it was also demonstrated that a small amount of m-CNCs could lead to a remarkable decrease in the hydrolytic degradation rate of the biopolymer. In addition, the m-CNCs considerably delay the degradation of the nanocomposite by providing a physical barrier that prevents the permeation of water, which thus hinders the overall absorption of water into the matrix. The results obtained in this study show the nanocrystals can be used to reinforce polylactides and fine-tune their degradation rates in moist or physiological environments.

NANOCRISTAIS DE CELULOSE A PARTIR DE CELULOSE BACTERIANA

Bacterial cellulose produced from Gluconacetobacter xilinus was used to produce cellulose nanocrystals by sulfuric acid hydrolysis. Hydrolysis was performed with 64% sulfuric acid at 50 ºC with the hydrolysis time ranging between 5 and 90 min. The production of nanocrystals was observed to have size distributions that were dependent on hydrolysis times up to 10 min, after which time the suspensions showed distributions closer in size. Results from thermal analysis and X-ray diffraction showed that the amorphous cellulose was removed, leaving only the crystalline portion. Self-supported films were formed from the suspension of nanocrystals and had iridescence characteristics. The films were characterized by microscopy measures and specular reflectance.

The use of fluorescent probes to assess viability of the plant pathogenic bacterium Clavibacter michiganensis subsp. michiganensis by flow cytometry

Determination of the viability of bacteria by the conventional plating technique is a time-consuming process. Methods based on enzyme activity or membrane integrity are much faster and may be good alternatives. Assessment of the viability of suspensions of the plant pathogenic bacterium Clavibacter michiganensis subsp. michiganensis (Cmm) using the fluorescent probes Calcein acetoxy methyl ester (Calcein AM), carboxyfluorescein diacetate (cFDA), and propidium iodide (PI) in combination with flow cytometry was evaluated. Heat-treated and viable (non-treated) Cmm cells labeled with Calcein AM, cFDA, PI, or combinations of Calcein AM and cFDA with PI, could be distinguished based on their fluorescence intensity in flow cytometry analysis. Non-treated cells showed relatively high green fluorescence levels due to staining with either Calcein AM or cFDA, whereas damaged cells (heat-treated) showed high red fluorescence levels due to staining with PI. Flow cytometry also allowed a rapid quantification of viable Cmm cells labeled with Calcein AM or cFDA and heat-treated cells labeled with PI. Therefore, the application of flow cytometry in combination with fluorescent probes appears to be a promising technique for assessing viability of Cmm cells when cells are labeled with Calcein AM or the combination of Calcein AM with PI.

A simple method for the spectrophotometric determination of cephalosporins in pharmaceuticals using variamine blue

A simple spectrophotometric method for the determination of cefotaxime, ceftriaxone, cefadroxil and cephalexin with variamine blue is presented. The determination is based on the hydrolysis of β-lactam ring of cephalosporins with sodium hydroxide which subsequently reacts with iodate to liberate iodine in acidic medium. The liberated iodine oxidizes variamine blue to violet colored species of maximum absorption at 556 nm. The absorbance is measured within the pH range of 4.0-4.2. Beer's law is obeyed in the range of 0.5-5.8 µg mL-1, 0.2-7.0 µg mL-1, 0.2-5.0 µg mL-1 and 0.5-8.5 µg mL-1 for cefotaxime, ceftriaxone, cefadroxil and cephalexin respectively. The analytical parameters were optimized and the method is successfully applied for the determination of cefotaxime, ceftriaxone, cefadroxil and cephalexin in pharmaceuticals.

Cuticular and Suberin Polymers of Edible Plants. Analysis by Gas Chromatographic-Mass Spectrometric and Solid State Spectroscopic Methods

Cutin and suberin are structural and protective polymers of plant surfaces. The epidermal cells of the aerial parts of plants are covered with an extracellular cuticular layer, which consists of polyester cutin, highly resistant cutan, cuticular waxes and polysaccharides which link the layer to the epidermal cells. A similar protective layer is formed by a polyaromatic-polyaliphatic biopolymer suberin, which is present particularly in the cell walls of the phellem layer of periderm of the underground parts of plants (e.g. roots and tubers) and the bark of trees. In addition, suberization is also a major factor in wound healing and wound periderm formation regardless of the plants’ tissue. Knowledge of the composition and functions of cuticular and suberin polymers is important for understanding the physiological properties for the plants and for nutritional quality when these plants are consumed as foods. The aims of the practical work were to assess the chemical composition of cuticular polymers of several northern berries and seeds and suberin of two varieties of potatoes. Cutin and suberin were studied as isolated polymers and further after depolymerization as soluble monomers and solid residues. Chemical and enzymatic depolymerization techniques were compared and a new chemical depolymerization method was developed. Gas chromatographic analysis with mass spectrometric detection (GC-MS) was used to assess the monomer compositions. Polymer investigations were conducted with solid state carbon-13 cross polarization magic angle spinning nuclear magnetic resonance spectroscopy (13C CP-MAS NMR), Fourier transform infrared spectroscopy (FTIR) and microscopic analysis. Furthermore, the development of suberin over one year of post-harvest storage was investigated and the cuticular layers from berries grown in the North and South of Finland were compared. The results show that the amounts of isolated cuticular layers and cutin monomers, as well as monomeric compositions vary greatly between the berries. The monomer composition of seeds was found to differ from the corresponding berry peel monomers. The berry cutin monomers were composed mostly of long-chain aliphatic ω-hydroxy acids, with various mid-chain functionalities (double-bonds, epoxy, hydroxy and keto groups). Substituted α,ω-diacids predominated over ω-hydroxy acids in potato suberin monomers and slight differences were found between the varieties. The newly-developed closed tube chemical method was found to be suitable for cutin and suberin analysis and preferred over the solvent-consuming and laborious reflux method. Enzymatic hydrolysis with cutinase was less effective than chemical methanolysis and showed specificity towards α,ω-diacid bonds. According to ₁₃C CP-MAS NMR and FTIR, the depolymerization residues contained significant amounts of aromatic structures, polysaccharides and possible cutan-type aliphatic moieties. Cultivation location seems to have effect on cuticular composition. The materials studied contained significant amounts of different types of biopolymers that could be utilized for several purposes with or without further processing. The importance of the so-called waste material from industrial processes of berries and potatoes as a source of either dietary fiber or specialty chemicals should be further investigated in detail. The evident impact of cuticular and suberin polymers, among other fiber components, on human health should be investigated in clinical trials. These by-product materials may be used as value-added fiber fractions in the food industry and as raw materials for specialty chemicals such as lubricants and emulsifiers, or as building blocks for novel polymers.

The Significance of Hydrogen Bonding Interactions in the Cleavage of RNA

RNA is essential for all living organisms. It has important roles in protein synthesis, controlling gene expression as well as catalyzing biological reactions. Chemically RNA is a very stable molecule, although in biological systems many agents catalyze the cleavage of RNA, such as naturally occurring enzymes and ribozymes. Much effort has been put in the last decades in developing highly active artificial ribonucleases since such molecules could have potential in the therapeutic field and provide tools for molecular biology. Several potential catalysts have emerged, but usually detailed cleavage mechanism remains unresolved. This thesis is aimed at clarifying mechanistic details of the cleavage and isomerization of RNA by using simpler nucleoside models of RNA. The topics in the experimental part cover three different studies, one concerning the mechanism of catalysis by large ribozymes, one dealing with the reactivity of modified and unmodified RNA oligonucleotides and one showing an efficient catalysis of the cleavage and isomerization of an RNA phosphodiester bond by a dinuclear metal ion complex. A review of the literature concerning stabilization of the phosphorane intermediate of the hydrolysis and isomerization of RNA phosphodiester bond is first presented. The results obtained in the experimental work followed by mechanistic interpretations are introduced in the second part of the thesis. Especially the significance of hydrogen bonding interactions is discussed.

Functional studies on bacterial nucleotide-regulated inorganic pyrophosphatases

CBS domains are ~60 amino acid tandemly repeated regulatory modules forming a widely distributed domain superfamily. Found in thousands of proteins from all kingdoms of life, CBS domains have adopted a variety of functions during evolution, one of which is regulation of enzyme activity through binding of adenylate-containing compounds in a hydrophobic cavity. Mutations in human CBS domain-containing proteins cause hereditary diseases. Inorganic pyrophosphatases (PPases) are ubiquitous enzymes, which pull pyrophosphate (PPi) producing reactions forward by hydrolyzing PPi into phosphate. Of the two nonhomologous soluble PPases, dimeric family II PPases, belonging to the DHH family of phosphoesterases, require a transition metal and magnesium for maximal activity. A quarter of the almost 500 family II PPases, found in bacteria and archaea, contain a 120-250 amino acid N-terminal insertion, comprised of two CBS domains separated in sequence by a DRTGG domain. These enzymes are thus named CBS-PPases. The function of the DRTGG domain in proteins is unknown. The aim of this PhD thesis was to elucidate the structural and functional differences of CBS-PPases in comparison to family II PPases lacking the regulatory insert. To this end, we expressed, purified and characterized the CBS-PPases from Clostridium perfringens (cpCBS-PPase) and Moorella thermoacetica (mtCBS-PPase), the latter lacking a DRTGG domain. Both enzymes are homodimers in solution and display maximal activity against PPi in the presence of Co2+ and Mg2+. Uniquely, the DRTGG domain was found to enable tripolyphosphate hydrolysis at rates similar to that of PPi. Additionally, we found that AMP and ADP inhibit, while ATP and AP4A activate CBSPPases, thus enabling regulation in response to changes in cellular energy status. We then observed substrate- and nucleotide-induced conformational transitions in mtCBS-PPase and found that the enzyme exists in two differentially active conformations, interconverted through substrate binding and resulting in a 2.5-fold enzyme activation. AMP binding was shown to produce an alternate conformation, which is reached through a different pathway than the substrate-induced conformation. We solved the structure of the regulatory insert from cpCBS-PPase in complex with AMP and AP4A and proposed that conformational changes in the loops connecting the catalytic and regulatory domains enable activity regulation. We examined the effects of mutations in the CBS domains of mtCBS-PPase on catalytic activity, as well as, nucleotide binding and inhibition.

Immobilization of Burkholderia cepacia Lipase: Kinetic Resolution in Organic Solvents, Ionic Liquids and in Their Mixtures

Immobilization of Burkholderia cepacia Lipase: Kinetic Resolution in Organic Solvents, Ionic Liquids and in Their Mixtures Biocatalysis opens the door to green and sustainable processes in synthetic chemistry allowing the preparation of single enantiomers, since the enzymes are chiral and accordingly able to catalyze chemical reactions under mild conditions. Immobilization of enzymes enhances process robustness, often stabilizes and activates the enzyme, and enables reuse of the same enzyme preparation in multiple cycles. Although hundreds of variations of immobilization methods exist, there is no universal method to yield the highly active, selective and stable enzyme catalysts. Therefore, new methods need to be developed to obtain suitable catalysts for different substrates and reaction environments. Lipases are the most widely used enzymes in synthetic organic chemistry. The literature part together with the experimental part of this thesis discusses of the effects of immobilization methods mostly used to enhance lipase activity, stability and enantioselectivity. Moreover, the use of lipases in the kinetic resolution of secondary alcohols in organic solvents and in ionic liquids is discussed. The experimental work consists of the studies of immobilization of Burkholderia cepacia lipase (lipase PS) using three different methods: encapsulation in sol-gels, cross-linked enzyme aggregates (CLEAs) and supported ionic liquids enzyme catalysts (SILEs). In addition, adsorption of lipase PS on celite was studied to compare the results obtained with sol-gels, CLEAs and SILEs. The effects of immobilization on enzyme activity, enantioselectivity and hydrolysis side reactions were studied in kinetic resolution of three secondary alcohols in organic solvents, in ionic liquids (ILs), and in their mixtures. Lipase PS sol-gels were shown to be active and stable catalysts in organic solvents and solvent:IL mixtures. CLEAs and SILEs were highly active and enantioselective in organic solvents. Sol-gels and SILEs were reusable in several cycles. Hydrolysis side reaction was suppressed in the presence of sol-gels and CLEAs.

Kalvosuodatuksen ja adsorption yhdistäminen biojalostamon erotusprosesseissa

Tässä diplomityössä tutkittiin kalvosuodatuksen ja adsorption yhdistämistä biojalostamon erotusprosesseissa. Työn kirjallisuusosassa käsitellään hemiselluloosien erottamista puusta, kalvosuodatusta hemiselluloosien käsittelyssä sekä hemiselluloosien pilkkomista sokereiksi ja sokereiden kromatografista erotusta. Kokeellisessa osassa tutkittiin hemiselluloosahydrolysaatin fraktioimista kalvosuodatuksella ja adsorbenttikäsittelyn vaikutusta hydrolysaatin suodatettavuuteen. Kokeellisessa osassa tutkittiin myös fraktioinnin vaikutusta hartsien likaantumiseen happohydrolyysin jälkeisessä kromatografisessa erotuksessa. Työssä kokeiltiin useita erilaisia kalvoja, mutta suurin osa suodatuksista tehtiin regeneroidusta selluloosasta valmistetulla kalvolla UC030 ja polyeetterisulfoni kalvolla UFX5. Esikäsittelyyn käytettiin XAD16 adsorbenttia ja hartsien likaantumista tutkittiin CS12GC Na+ hartsilla. Suodatuskokeet tehtiin sekä laboratoriomittakaavan Amicon-suodattimella että pilot-mittakaavan CR- suodattimella. Työn tulokset osoittivat, että konsentroituneen hemiselluloosafraktion tuottaminen tehokkaasti ei onnistu kalvosuodatuksella ilman esikäsittelyä. Kalvon likaantumisen vuoksi permeaattivuo laski hyvin nopeasti niin alhaiseksi, ettei suodatuksen jatkaminen olisi taloudellisesti kannattavaa. Hydrolysaatin esikäsittely XAD16 adsorbentillä poisti tehokkaasti kalvoja likaavia uuteaineita ja ligniiniä. Adsorbenttikäsittelyn jälkeen hydrolysaatin suodattaminen onnistui ilman permeaattivuon huomattavaa alenemista toisessa suodatusvaiheessa ja saatiin aikaiseksi hyvin konsentroitunut hemiselluloosafraktio.

Purified lignin for demanding applications

Diplomityön tarkoituksena oli puhdistaa kraft ligniiniä. Raaka-aineena käytettiin pääasiassa Lignoboost -menetelmän kaltaisella menetelmällä havupuu- mustalipeästä saostettua ligniiniä. Diplomityön ensimmäisenä tavoitteena oli löytää menetelmä, jolla voidaan poistaa kraft ligniinistä tuhkaa. Työssä raaka-aineena käytetyn saostetun ligniinin tuhkapitoisuus oli noin 3 %. Tarkoituksena oli saada laskettua tuhkapitoisuutta uudelleenlieton, suodatuksen ja pesun avulla. Työn toisena tavoitteena oli hiilihydraattien poisto kraft ligniinistä. Hiilihydraatit, pääosin hemiselluloosaa, ovat kiinnittyneet ligniiniin vahvoin kovalenttisin sidoksin. Aiempien kokemusten perusteella hemiselluloosat eivät irtoa ligniinistä vesipesun yhteydessä, vaan niiden irrottaminen vaatii onnistuakseen happo-, entsyymi- tai mikrobikäsittelyn, mikäli halutaan säilyttää ligniinin rakenne muuttumattomana. Tässä työssä käytetyt kraft ligniinin puhdistusmenetelmät olivat lietto, happohydrolyysi ja entsymaattinen hydrolyysi, joista kumpikin sisälsi ligniinin uudelleenlieton, suodatuksen ja muodostuneen kakun pesun vedellä.