Zeolite Encapsulated Complexes Of Fe,Co,Ni,Cu And Pd:Synthesis , Characterization And Catalysis-2003

This thesis deals with the synthesis, characterization and catalysis activity studies of some zeolite encapsulated complexes. Encapsulation inside the zeolite cages makes the catalysts more stable. Further, the framework prevents the complexes from dimerising. Catalysis by metal complexes encapsulated in the cavities of zeolites and other molecular sieves has many features of homogeneous, heterogenous and enzymatic catalysis. Serious attempts has been made to gain product selectivity in catalysis .The catalytic activity shown by the encapsulated complexes can be correlated to the structure of the active site inside the zeolite pore. It deals with the studies on the partial oxidation of benzyl alcohol to benzaldehyde. The oxidatio was carried out using hydrogen peroxide as oxidant in presence of PdYDMG and CuYSPP as catalysts. The product (benzaldehyde) was detected using TLC and confirmed using GC.The catalytic activity of the complexes was tested for oxidation under various conditions. The operating conditions like the amount of the catalyst, reaction time, oxidant to substrate ratio, reaction temprature, and solvents have been optimized. No further oxidation products were obtained on continuing the reaction for four hours beyond the optimum time. Maximum conversion was obtained at room temperature and the percentage conversion decreased with increase in temperature. Activity was found to be dependent on the solvent used. With increasing awareness about the dangers of environmental degradation, research in chemistry is getting increasing geared to the development of ���green chemistry,��� by designing environmentally friendly products and processes that bring down the generation and use of hazardous substances.

Role of Water in the Enzymatic Catalysis: Study of ATP plus AMP -> 2ADP Conversion by Adenylate Kinase

The catalytic conversion ATP + AMP -> 2ADP by the enzyme adenylate kinase (ADK) involves the binding of one ATP. molecule to the LID domain and one AMP molecule to the NMP domain. The latter is followed by a. phosphate transfer and then the release of two ADP molecules. We have computed a novel two-dimensional configurational free energy surface (2DCFES), with one reaction coordinate each for the LID and the NMP domain motions, while considering explicit water interactions. Our computed 2DCFES clearly reveals the existence of a stable half-open half-closed (HOHC) intermediate stale of the enzyme. Cycling of the enzyme through the HOHC state reduces the conformational free energy barrier for. the reaction by about 20 kJ/mol. We find that the stability of the HOHC state (missed in all earlier studies with implicit solvent model) is largely because of the increase of specific interactions of the polar amino acid side chains with water, particularly with the arginine and the histidine residues. Free energy surface of the LID domain is rather rugged, which can conveniently slow down LID's conformational motion, thus facilitating a new substrate capture after the product release in the catalytic cycle.

Lipase-Mediated Enzymatic Catalysis For The Synthesis of New Chiral Polymers

Immobilized lipase B from Candida antarctica (N435) was investigated as a potential biocatalyst to generate silicone-based chiral polymers from monomers derived from the enzymatic dihydroxylation of bromobenzene. Several conditions and parameters have been investigated for this purpose and lipase transesterification preference to each of the free secondary alcohols in the chiral monomers was documented. The N435 was challenged with a series of substrates where the free alcohol moieties were systematically protected in order to study the substrate preference(s) for the transesterification reactions.

Isosorbide Polyesters from Enzymatic Catalysis

The synthesis of isosorbide aliphatic polyesters is demonstrated by the use of Novozym 435, a catalyst consisting of Candida antarctica lipase B immobilized on a macroporous support Several experimental procedures were tested and azeotropic distillation was most effective in removing low mass byproduct Furthermore, the use of diethyl ester derivatives of diacid comonomers gave isosorbide copolyesters with highest Isolated yield and molecular weights The length of the diacid aliphatic chain was less restrictive, but with a clear preference for longer aliphatic chains The molecular mass values of the obtained products were equivalent or higher than those obtained by nonenzymatic polymerizations, a clear illustration of the potential of enzymatic over conventional catalysis The ability of Novozym 435 to catalyze the synthesis of isosorbide polyester with weight-average molecular weights in excess of 40000 Da was unexpected given that isosorbide has two chemically distinct secondary hydroxyl groups This is the first example in which isosorbide polyesters were synthesized by enzyme catalysis, opening a large array of possibilities for this important class of biomass-derived building blocks Because these polymers are potential biomaterials the total absence of conventional Lewis acid catalyst residues represents a major Improvement in the toxicity of the material

The change in hydrogen bond strength accompanying charge rearrangement: Implications for enzymatic���catalysis

The equilibrium for formation of the intramolecular hydrogen bond (KHB) in a series of substituted salicylate monoanions was investigated as a function of ��pKa, the difference between the pKa values of the hydrogen bond donor and acceptor, in both water and dimethyl sulfoxide. The dependence of log KHB upon ��pKa is linear in both solvents, but is steeper in dimethyl sulfoxide (slope = 0.73) than in water (slope = 0.05). Thus, hydrogen bond strength can undergo substantially larger increases in nonaqueous media than aqueous solutions as the charge density on the donor or acceptor atom increases. These results support a general mechanism for enzymatic catalysis, in which hydrogen bonding to a substrate is strengthened as charge rearranges in going from the ground state to the transition state; the strengthening of the hydrogen bond would be greater in a nonaqueous enzymatic active site than in water, thus providing a rate enhancement for an enzymatic reaction relative to the solution reaction. We suggest that binding energy of an enzyme is used to fix the substrate in the low-dielectric active site, where the strengthening of the hydrogen bond in the course of a reaction is increased.

The hard-soft acid-base principle in enzymatic catalysis: dual reactivity of phosphoenolpyruvate.

In this paper, the chemical reactivity of C3 of phosphoenolpyruvate (PEP) has been analyzed in terms of density functional theory quantified through quantum chemistry calculations. PEP is involved in a number of important enzymatic reactions, in which its C3 atom behaves like a base. In three different enzymatic reactions analyzed here, C3 sometimes behaves like a soft base and sometimes behaves like a hard base in terms of the hard-soft acid-base principle. This dual nature of C3 of PEP was found to be related to the conformational change of the molecule. This leads to a testable hypothesis: that PEP adopts particular conformations in the enzyme-substrate complexes of different PEP-using enzymes, and that the enzymes control the reactivity through controlling the dihedral angle between the carboxylate and the C==C double bond of PEP.

A heterogeneous catalytic kinetics for enzymatic biodegradation of poly(epsilon-caprolactone) nanoparticles in aqueous solution

Water insoluble poly(epsilon-caprolactone) (PCL) was micronized into narrowly distributed stable nanoparticles. The biodegradation of such PCL nanoparticles in the presence of the enzyme, Lipase PS, was monitored by using laser light scattering because the scattering intensity is directly related to the particle concentration. The PCL and enzyme concentration dependence of the biodegradation rate supports a heterogeneous catalytic kinetics in which we have introduced an additional equilibrium between the inactive and active enzyme/substrate complexes. The initial rate equation derived on the basis of this mechanism was used to successfully explain the influence of surfactant, pH and temperature on the enzymatic biodegradation. Our results confirmed that both the adsorption and the enzymatic catalysis were important for the biodegradation of the PCL nanoparticles. (C) 2000 Elsevier Science Ltd. All rights reserved.

Modification of chitin properties for enzymatic deacetylation

Chitins produced via a conventional chemical route as well as from a new biological process were modified to increase the efficiency of enzymatic deacetylation reactions for the production of novel biological chitosan. These modified chitins were reacted for 24h with extracellular fungal enzymes from Colletotrichum lindemuthianum. The chemical and physical properties of the various substrates were analysed and their properties related to the effectiveness in the deacetylation reaction. Modifications of the chitins affected the degree of deacetylation with varied effects. Without further modification to reduce crystallinity and to open up the solid substrate structure, the chitins were found to be poor substrates for the heterogeneous solid-liquid enzymatic catalysis. It was found that the solvent and drying method used in modifying the chitins had significant impact on the final efficiency of the enzymatic deacetylation reaction. The most successful modifications through freeze drying of a colloidal chitin suspension increased the degree of enzymatic deacetylation by 20 fold. These processes reduce the crystallinity of the chitin making it easier for the enzymes to access their internal structure. X-ray diffraction, scanning electron microscopy, thermogravimetric analysis, and BET isotherm analysis are employed to characterise the modified chitins to ascertain the degree of crystallinity, porous structure, surface area, and morphology.

Combining Bio- and Chemo-catalysis for the Sustainable Production of Chemicals

The combination of bio- and chemo-catalysis to form a single synthetic route is a powerful methodology for the improvement of chemical synthesis. The extreme methods of biocatalysis (whole cell and isolated enzyme) fulfill very different roles. Biocatalysis by isolated enzymes enables highly efficient chemical transformations of extremely high selectivity and low contamination; however, conditions and substrates are limited to a narrow range. Whole cell biocatalysis enables the conversion of crude substrates, such as those derived from biomass; however, the products tend to be impure and delivered in dilute aqueous solution. Chemocatalysis is a well-established technique, and the addition of chemical catalysis and chemocatalytic methods to biocatalysis enables synthetic chemists to avoid the shortcomings of a biocatalytic step. For example, in enzymatic catalysis the addition of a chemical catalyst can allow the conversion of a racemic alcohol to an enantiopure, instead of racemic, product. In whole cell biocatalysis chemical reagents can assist the separation, transformation, and further isolation of the functionality of interest. The cooperation of bio- and chemocatalysts enables sustainable production of chemicals that would be impossible using biocatalysis alone, while achieving selectivities and using substrates not currently possible with chemocatalysis alone.

Oxygen isotope ratios of PO4: An inorganic indicator of enzymatic activity and P metabolism and a new biomarker in the search for life

The distinctive relations between biological activity and isotopic effect recorded in biomarkers (e.g., carbon and sulfur isotope ratios) have allowed scientists to suggest that life originated on this planet nearly 3.8 billion years ago. The existence of life on other planets may be similarly identified by geochemical biomarkers, including the oxygen isotope ratio of phosphate (��18Op) presented here. At low near-surface temperatures, the exchange of oxygen isotopes between phosphate and water requires enzymatic catalysis. Because enzymes are indicative of cellular activity, the demonstration of enzyme-catalyzed PO4���H2O exchange is indicative of the presence of life. Results of laboratory experiments are presented that clearly show that ��18OP values of inorganic phosphate can be used to detect enzymatic activity and microbial metabolism of phosphate. Applications of ��18Op as a biomarker are presented for two Earth environments relevant to the search for extraterrestrial life: a shallow groundwater reservoir and a marine hydrothermal vent system. With the development of in situ analytical techniques and future planned sample return strategies, ��18Op may provide an important biosignature of the presence of life in extraterrestrial systems such as that on Mars.

Allostery and conformational free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and structure networks

The interdependence of the concept of allostery and enzymatic catalysis, and they being guided by conformational mobility is gaining increased prominence. However, to gain a molecular level understanding of llostery and hence of enzymatic catalysis, it is of utter importance that the networks of amino acids participating in allostery be deciphered. Our lab has been exploring the methods of network analysis combined with molecular dynamics simulations to understand allostery at molecular level. Earlier we had outlined methods to obtain communication paths and then to map the rigid/flexible regions of proteins through network parameters like the shortest correlated paths, cliques, and communities. In this article, we advance the methodology to estimate the conformational populations in terms of cliques/communities formed by interactions including the side-chains and then to compute the ligand-induced population shift. Finally, we obtain the free-energy landscape of the protein in equilibrium, characterizing the free-energy minima accessed by the protein complexes. We have chosen human tryptophanyl-tRNA synthetase (hTrpRS), a protein esponsible for charging tryptophan to its cognate tRNA during protein biosynthesis for this investigation. This is a multidomain protein exhibiting excellent allosteric communication. Our approach has provided valuable structural as well as functional insights into the protein. The methodology adopted here is highly generalized to illuminate the linkage between protein structure networks and conformational mobility involved in the allosteric mechanism in any protein with known structure.

Proton transfers at the air-water interface

<p>Proton transfer reactions at the interface of water with hydrophobic media, such as air or lipids, are ubiquitous on our planet. These reactions orchestrate a host of vital phenomena in the environment including, for example, acidification of clouds, enzymatic catalysis, chemistries of aerosol and atmospheric gases, and bioenergetic transduction. Despite their importance, however, quantitative details underlying these interactions have remained unclear. Deeper insight into these interfacial reactions is also required in addressing challenges in green chemistry, improved water quality, self-assembly of materials, the next generation of micro-nanofluidics, adhesives, coatings, catalysts, and electrodes. This thesis describes experimental and theoretical investigation of proton transfer reactions at the air-water interface as a function of hydration gradients, electrochemical potential, and electrostatics. Since emerging insights hold at the lipid-water interface as well, this work is also expected to aid understanding of complex biological phenomena associated with proton migration across membranes.</p> <p>Based on our current understanding, it is known that the physicochemical properties of the gas-phase water are drastically different from those of bulk water. For example, the gas-phase hydronium ion, H₃O⁺(g), can protonate most (non-alkane) organic species, whereas H₃O⁺(aq) can neutralize only relatively strong bases. Thus, to be able to understand and engineer water-hydrophobe interfaces, it is imperative to investigate this fluctuating region of molecular thickness wherein the ���function��� of chemical species transitions from one phase to another via steep gradients in hydration, dielectric constant, and density. Aqueous interfaces are difficult to approach by current experimental techniques because designing experiments to specifically sample interfacial layers (&#60; 1 nm thick) is an arduous task. While recent advances in surface-specific spectroscopies have provided valuable information regarding the structure of aqueous interfaces, but structure alone is inadequate to decipher the function. By similar analogy, theoretical predictions based on classical molecular dynamics have remained limited in their scope.</p> <p>Recently, we have adapted an analytical electrospray ionization mass spectrometer (ESIMS) for probing reactions at the gas-liquid interface in real time. This technique is direct, surface-specific,and provides unambiguous mass-to-charge ratios of interfacial species. With this innovation, we have been able to investigate the following:</p> <p>1. How do anions mediate proton transfers at the air-water interface?</p> <p>2. What is the basis for the negative surface potential at the air-water interface?</p> <p>3. What is the mechanism for catalysis ���on-water���?</p> <p>In addition to our experiments with the ESIMS, we applied quantum mechanics and molecular dynamics to simulate our experiments toward gaining insight at the molecular scale. Our results unambiguously demonstrated the role of electrostatic-reorganization of interfacial water during proton transfer events. With our experimental and theoretical results on the ���superacidity��� of the surface of mildly acidic water, we also explored implications on atmospheric chemistry and green chemistry. Our most recent results explained the basis for the negative charge of the air-water interface and showed that the water-hydrophobe interface could serve as a site for enhanced autodissociation of water compared to the condensed phase.</p>

S��ntese de ��steres derivados do ��cido ol��ico empregando lipases produzidas por Yarrowia lipolytica

Biodiesel �� um biocombust��vel que consiste na mistura de ��steres monoalqu��licos de ��cidos graxos de cadeia longa. O processo usual de produ����o deste combust��vel �� a transesterifica����o de ��leos vegetais com ��lcoois de cadeia curta. Nesse processo, a mat��ria prima deve conter baixo conte��do de ��cido graxos livres ( &#8804; 1%) e ��gua (&#8804; 0,5%). Como alternativa ao processo de transesterifica����o, destaca-se o emprego de mat��rias-primas de baixo custo, com elevado teor de ��cidos graxos livres, para a s��ntese de ��steres alqu��licos atrav��s de rea����es de esterifica����o. As rea����es de produ����o do biodiesel podem ser catalisadas por via qu��mica (��cida e b��sica) ou enzim��tica. Na cat��lise enzim��tica, os biocatalisadores empregados s��o as lipases, que catalisam a hidr��lise e s��ntese de ��steres e podem ser obtidas a partir de microrganismos, plantas ou tecido animal, sendo as de origem microbiana as mais utilizadas. O objetivo principal deste trabalho foi avaliar o potencial da lipase de Yarrowia lipolytica, uma levedura n��o convencional, na s��ntese de ��steres do ��cido oleico visando �� obten����o de ��steres alqu��licos (biodiesel). Foram estudados os efeitos da temperatura (25, 30, 35, 40, 50 e 60oC), do teor enzim��tico (5, 10, 20, 30 e 40% v/v) e do tipo de ��lcool (metanol, etanol, n-propanol e n-butanol ) nas rea����es de esterifica����o do ��cido oleico empregando o extrato enzim��tico l��quido produzido por Yarrowia lipolytica. Os resultados obtidos mostraram que as rea����es conduzidas a 30oC e com 10% v/v do extrato enzim��tico apresentaram maior taxa inicial de rea����o. Tamb��m foi avaliada a utiliza����o do extrato enzim��tico liofilizado (5% m/v) e do PES (produto enzim��tico s��lido) (5% m/v) de Yarrowia lipolytica na rea����o de esterifica����o do ��cido oleico com n-butanol a 30oC. O maior consumo de ��cido oleico ocorreu na rea����o conduzida com o PES. O efeito da temperatura (25, 30, 35, 40 e 50oC) na s��ntese de oleato de butila foi, ent��o, investigado nas rea����es empregando PES como biocatalisador e a maior convers��o de ��cido oleico foi verificada na temperatura de 40oC

Study on the structure of hemoglobin in organic solvents by in situ STM

In situ STM has been used to study the structure of hemoglobin(Hb) in two kinds of organic media. In hydrophobic organic solvent such as carbon tetrachloride, the structure of Hb is almost the same as in aqueous solution, similar to its native structure. However, when in hydrophilic organic solvent such as dimethylformamide, the two dimers of Hb molecule become separate and unfold to a certain extent.