Extração de ácido trans-trans mucônico urinário com polímeros de impressão molecular e análise por cromatografia gasosa: espectrometria de massas

This paper describes selective molecularly imprinted solid-phase extraction of ttMA from urine samples followed by derivatization and analysis by gas chromatography/mass spectrometry (GC/MS). The analytical calibration curve ranged from 0.3 to 7.0 mg L-1 (r = 0.999) and the limit of quantitation (LOQ) was 0.3 mg L-1. The method was applied for the determination of ttMA in urine samples from smokers and concentrations detected ranged from < LOQ to 1.64 mg L-1. Thus, the proposed method proved adequate for the determination of urinary ttMA in the biomonitoring of occupational exposure to low levels of benzene.

Combined experimental powder X-ray diffraction and DFT data to obtain the lowest energy molecular conformation of friedelin

Friedelin molecular conformers were obtained by Density Functional Theory (DFT) and by ab initio structure determination from powder X-ray diffraction. Their conformers with the five rings in chair-chair-chair-boat-boat, and with all rings in chair, are energy degenerated in gas-phase according to DFT results. The powder diffraction data reveals that rings A, B and C of friedelin are in chair, and rings D and E in boat-boat, conformation. The high correlation values among powder diffraction data, DFT and reported single-crystal data indicate that the use of conventional X-ray diffractometer can be applied in routine laboratory analysis in the absence of a single-crystal diffractometer.

Molecular modeling of asymmetric induction in heterogeneously catalyzed hydrogenation of the C=O bond

Modifiering av metallytor med starkt adsorberade kirala organiska molekyler är eventuellt den mest relevanta teknik man vet i dag för att skapa kirala ytor. Den kan utnyttjas i katalytisk produktion av enantiomeriskt rena kirala föreningar som behövs t.ex. som läkemedel och aromkemikalier. Trots många fördelar av asymmetrisk heterogen katalys jämfört med andra sätt för att få kirala föreningar, har den ändå inte blivit ett allmänt verktyg för storskaliga tillämpningar. Detta beror t.ex. på brist på djupare kunskaper i katalytiska reaktionsmekanismer och ursprunget för asymmetrisk induktion. I denna studie användes molekylmodelleringstekniker för att studera asymmetriska, heterogena katalytiska system, speciellt hydrering av prokirala karbonylföreningar till motsvarande kirala alkoholer på cinchona-alkaloidmodifierade Pt-katalysatorer. 1-Fenyl-1,2-propandion (PPD) och några andra föreningar, som innehåller en prokiral C=O-grupp, användes som reaktanter. Konformationer av reaktanter och cinchona-alkaloider (som kallas modifierare) samt vätebundna 1:1-komplex mellan dem studerades i gas- och lösningsfas med metoder som baserar sig på vågfunktionsteori och täthetsfunktionalteori (DFT). För beräkningen av protonaffiniteter användes också högst noggranna kombinationsmetoder såsom G2(MP2). Den relativa populationen av modifierarnas konformationer varierade som funktion av modifieraren, dess protonering och lösningsmedlet. Flera reaktant–modifierareinteraktionsgeometrier beaktades. Slutsatserna på riktning av stereoselektivitet baserade sig på den relativa termodynamiska stabiliteten av de diastereomeriska reaktant–modifierare-komplexen samt energierna hos π- och π*-orbitalerna i den reaktiva karbonylgruppen. Adsorption och reaktioner på Pt(111)-ytan betraktades med DFT. Regioselektivitet i hydreringen av PPD och 2,3-hexandion kunde förklaras med molekyl–yta-interaktioner. Storleken och formen av klustret använt för att beskriva Pt-ytan inverkade inte bara på adsorptionsenergierna utan också på de relativa stabiliteterna av olika adsorptionsstrukturer av en molekyl. Populationerna av modifierarnas konformationer i gas- och lösningsfas korrelerade inte med populationerna på Pt-ytan eller med enantioselektiviteten i hydreringen av PPD på Pt–cinchona-katalysatorer. Vissa modifierares konformationer och reaktant–modifierare-interaktionsgeometrier var stabila bara på metallytan. Teoretiskt beräknade potentialenergiprofiler för hydrering av kirala α-hydroxiketoner på Pt implicerade preferens för parvis additionsmekanism för väte och selektiviteter i harmoni med experimenten. De uppnådda resultaten ökar uppfattningen om kirala heterogena katalytiska system och kunde därför utnyttjas i utvecklingen av nya, mera aktiva och selektiva kirala katalysatorer.

Thermal reactions of the major hydrocarbon components of biomass gasification gas

Gasification of biomass is an efficient method process to produce liquid fuels, heat and electricity. It is interesting especially for the Nordic countries, where raw material for the processes is readily available. The thermal reactions of light hydrocarbons are a major challenge for industrial applications. At elevated temperatures, light hydrocarbons react spontaneously to form higher molecular weight compounds. In this thesis, this phenomenon was studied by literature survey, experimental work and modeling effort. The literature survey revealed that the change in tar composition is likely caused by the kinetic entropy. The role of the surface material is deemed to be an important factor in the reactivity of the system. The experimental results were in accordance with previous publications on the subject. The novelty of the experimental work lies in the used time interval for measurements combined with an industrially relevant temperature interval. The aspects which are covered in the modeling include screening of possible numerical approaches, testing of optimization methods and kinetic modelling. No significant numerical issues were observed, so the used calculation routines are adequate for the task. Evolutionary algorithms gave a better performance combined with better fit than the conventional iterative methods such as Simplex and Levenberg-Marquardt methods. Three models were fitted on experimental data. The LLNL model was used as a reference model to which two other models were compared. A compact model which included all the observed species was developed. The parameter estimation performed on that model gave slightly impaired fit to experimental data than LLNL model, but the difference was barely significant. The third tested model concentrated on the decomposition of hydrocarbons and included a theoretical description of the formation of carbon layer on the reactor walls. The fit to experimental data was extremely good. Based on the simulation results and literature findings, it is likely that the surface coverage of carbonaceous deposits is a major factor in thermal reactions.

Molecular battles between plant and pathogenic bacteria in the phyllosphere

The phyllosphere, i.e., the aerial parts of the plant, provides one of the most important niches for microbial colonization. This niche supports the survival and, often, proliferation of microbes such as fungi and bacteria with diverse lifestyles including epiphytes, saprophytes, and pathogens. Although most microbes may complete the life cycle on the leaf surface, pathogens must enter the leaf and multiply aggressively in the leaf interior. Natural surface openings, such as stomata, are important entry sites for bacteria. Stomata are known for their vital role in water transpiration and gas exchange between the plant and the environment that is essential for plant growth. Recent studies have shown that stomata can also play an active role in limiting bacterial invasion of both human and plant pathogenic bacteria as part of the plant innate immune system. As counter-defense, plant pathogens such as Pseudomonas syringae pv tomato (Pst) DC3000 use the virulence factor coronatine to suppress stomate-based defense. A novel and crucial early battleground in host-pathogen interaction in the phyllosphere has been discovered with broad implications in the study of bacterial pathogenesis, host immunity, and molecular ecology of bacterial diseases.

Molecular and cellular pathogenesis of autosomal dominant polycystic kidney disease

Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common human life-threatening monogenic disorders. The disease is characterized by bilateral, progressive renal cystogenesis and cyst and kidney enlargement, often leading to end-stage renal disease, and may include extrarenal manifestations. ADPKD is caused by mutation in one of two genes, PKD1 and PKD2, which encode polycystin-1 (PC1) and polycystin-2 (PC2), respectively. PC2 is a non-selective cation channel permeable to Ca2+, while PC1 is thought to function as a membrane receptor. The cyst cell phenotype includes increased proliferation and apoptosis, dedifferentiation, defective planar polarity, and a secretory pattern associated with extracellular matrix remodeling. The two-hit model for cyst formation has been recently extended by the demonstration that early gene inactivation leads to rapid and diffuse development of renal cysts, while inactivation in adult life is followed by focal and late cyst formation. Renal ischemia/reperfusion, however, can function as a third hit, triggering rapid cyst development in kidneys with Pkd1 inactivation induced in adult life. The PC1-PC2 complex behaves as a sensor in the primary cilium, mediating signal transduction via Ca2+ signaling. The intracellular Ca2+ homeostasis is impaired in ADPKD, being apparently responsible for the cAMP accumulation and abnormal cell proliferative response to cAMP. Activated mammalian target for rapamycin (mTOR) and cell cycle dysregulation are also significant features of PKD. Based on the identification of pathways altered in PKD, a large number of preclinical studies have been performed and are underway, providing a basis for clinical trials in ADPKD and helping the design of future trials.

Serum metabolic profiling of human gastric cancer based on gas chromatography/mass spectrometry

Research on molecular mechanisms of carcinogenesis plays an important role in diagnosing and treating gastric cancer. Metabolic profiling may offer the opportunity to understand the molecular mechanism of carcinogenesis and help to non-invasively identify the potential biomarkers for the early diagnosis of human gastric cancer. The aims of this study were to explore the underlying metabolic mechanisms of gastric cancer and to identify biomarkers associated with morbidity. Gas chromatography/mass spectrometry (GC/MS) was used to analyze the serum metabolites of 30 Chinese gastric cancer patients and 30 healthy controls. Diagnostic models for gastric cancer were constructed using orthogonal partial least squares discriminant analysis (OPLS-DA). Acquired metabolomic data were analyzed by the nonparametric Wilcoxon test to find serum metabolic biomarkers for gastric cancer. The OPLS-DA model showed adequate discrimination between cancer and non-cancer cohorts while the model failed to discriminate different pathological stages (I-IV) of gastric cancer patients. A total of 44 endogenous metabolites such as amino acids, organic acids, carbohydrates, fatty acids, and steroids were detected, of which 18 differential metabolites were identified with significant differences. A total of 13 variables were obtained for their greatest contribution in the discriminating OPLS-DA model [variable importance in the projection (VIP) value >1.0], among which 11 metabolites were identified using both VIP values (VIP >1) and the Wilcoxon test. These metabolites potentially revealed perturbations of glycolysis and of amino acid, fatty acid, cholesterol, and nucleotide metabolism of gastric cancer patients. These results suggest that gastric cancer serum metabolic profiling has great potential in detecting this disease and helping to understand its metabolic mechanisms.

Molecular patterns behind immunological and metabolic alterations in lysinuric protein intolerance

Lysinuric protein intolerance (LPI) is a recessively inherited disorder characterised by reduced plasma and increased urinary levels of cationic amino acids (CAAs), protein malnutrition, growth failure and hyperlipidemia. Some patients develop severe immunological, renal and pulmonary complications. All Finnish patients share the same LPIFin mutation in the SLC7A7 gene that encodes CAA transporter y+LAT1. The aim of this study was to examine molecular factors contributing to the various symptoms, systemic metabolic and lipid profiles, and innate immune responses in LPI. The transcriptomes, metabolomes and lipidomes were analysed in whole-blood cells and plasma using RNA microarrays and gas or liquid chromatography-mass spectrometry techniques, respectively. Toll-like receptor (TLR) signalling in monocyte-derived macrophages exposed to pathogens was scrutinised using qRT-PCR and the Luminex technology. Altered levels of transcripts participating in amino acid transport, immune responses, apoptosis and pathways of hepatic and renal metabolism were identified in the LPI whole-blood cells. The patients had increased non-essential amino acid, triacylglycerol and fatty acid levels, and decreased plasma levels of phosphatidylcholines and practically all essential amino acids. In addition, elevated plasma levels of eight metabolites, long-chain triacylglycerols, two chemoattractant chemokines and nitric oxide correlated with the reduced glomerular function in the patients with kidney disease. Accordingly, it can be hypothesised that the patients have increased autophagy, inflammation, oxidative stress and apoptosis, leading to hepatic steatosis, uremic toxicity and altered intestinal microbe metabolism. Furthermore, the LPI macrophages showed disruption in the TLR2/1, TLR4 and TLR9 pathways, suggesting innate immune dysfunctions with an excessive response to bacterial infections but a deficient viral DNA response.

On the effect of molecular structure and composition on the photofragmentation of biomolecules

The research on the interaction between radiation and biomolecules pro-vides valuable information for both radiobiology and molecular physics. While radiobiology is interested in the damage inflicted on the molecule upon irradiation, molecular physics exploits these studies to obtain infor-mation about the physical properties of the molecule and the quantum me-chanical processes involved in the interaction. This thesis work investigated how a small change in the structure or composition of a biomolecule changes the response of the molecule to ioniz-ing radiation. Altogether eight different biomolecules were studied: nucleo-sides uridine, 5-methyluridine and thymidine; amino acids alanine, cysteine and serine; and halogenated acetic acids chloro- and bromoacetic acids. The effect of ionizing radiation on these molecules was studied on molecular level, investigating the samples in gas phase. Synchrotron radiation of VUV or soft x-ray range was used to ionize sample molecules, and the subsequent fragmentation processes were investigated with ion mass spectroscopy and ion-ion-electron coincidence spectroscopy. The comparison between the three nucleosides revealed that adding or removing a single functional group can affect not only the bonds from which the molecule ruptures upon ionization but also the charge localiza-tion in the formed fragments. Studies on amino acids and halogenated acetic acids indicated that one simple substitution in the molecule can dramatical-ly change the extent of fragmentation. This thesis work also demonstrates that in order to steer the radiation-induced fragmentation of the molecules, it is not always necessary to alter the amount of energy deposited on the molecules but selecting a suitable substitution may suffice.

Phonon spectra and thermodynamic properties of rare gas solids based on empirical and semi-empirical (ab initio) two-body potentials : a comparative study /

We study the phonon dispersion, cohesive and thermal properties of raxe gas solids Ne, Ar, Kr, and Xe, using a variety of potentials obtained from different approaches; such as, fitting to crystal properties, purely ab initio calculations for molecules and dimers or ab initio calculations for solid crystalline phase, a combination of ab initio calculations and fitting to either gas phase data or sohd state properties. We explore whether potentials derived with a certain approaxih have any obvious benefit over the others in reproducing the solid state properties. In particular, we study phonon dispersion, isothermal ajid adiabatic bulk moduli, thermal expansion, and elastic (shear) constants as a function of temperatiue. Anharmonic effects on thermal expansion, specific heat, and bulk moduli have been studied using A^ perturbation theory in the high temperature limit using the neaxest-neighbor central force (nncf) model as developed by Shukla and MacDonald [4]. In our study, we find that potentials based on fitting to the crystal properties have some advantage, particularly for Kr and Xe, in terms of reproducing the thermodynamic properties over an extended range of temperatiures, but agreement with the phonon frequencies with the measured values is not guaranteed. For the lighter element Ne, the LJ potential which is based on fitting to the gas phase data produces best results for the thermodynamic properties; however, the Eggenberger potential for Ne, where the potential is based on combining ab initio quantum chemical calculations and molecular dynamics simulations, produces results that have better agreement with the measured dispersion, and elastic (shear) values. For At, the Morse-type potential, which is based on M0ller-Plesset perturbation theory to fourth order (MP4) ab initio calculations, yields the best results for the thermodynamic properties, elastic (shear) constants, and the phonon dispersion curves.

Investigation of molecular polarizabilities and derivatives in halomethanes

The research undertaken was to obtain absolute Raman intensities for the symmetric stretching vibrations of the methyl halides, CH3X with (X=F, CI, Br), by experiment and theory. The intensities were experimentally measured using the Ar+ ion gas laser as excitation source, a Spex 14018 double monochromator and a RCA C-31034 photomultiplier tube as detector. These intensities arise from changes in the derivative of the polarizability (8 a'), with respect to vibration along a normal coordinate (8qi). It was intended that these derivatives obtained with respect to normal coordinates would be converted to derivatives with respect to internal coordinates, for a quantitative comparison with theory. Theoretical numerical polarizability derivatives for the stretching vibrations are obtained using the following procedure. A vibration was simulated in the molecule by increasi.ng and decreasing the respective bond by the amount ±o.oosA for the C-H bonds and ±o.oIA for the C-X (X=F, CI, Br) bond. The derivative was obtained by taking the difference in the polarizability for the equilibrium geometry and the geometry when a particular bond is changed. This difference, when divided by the amount of change in each bond and the number of bonds present results in the derivative of the polarizability with respect to internal coordinate i.e., !1u/!1r. These derivatives were obtained by two methods: I} ab initio molecular orbital calculation and 2} theory of atoms in molecules (AIM) analysis. Due to errors in the experimental setup only a qualitative analysis of the results was undertaken relative to the theory. Theoretically it is predicted that the symmetric carbonhalogen stretch vibrations are more intense than the respective carbon-hydrogen stretch, but only for the methyl chloride and bromide. The carbon fluorine stretch is less intense than the carbon-hydrogen stretch, a fact which is attributed to the small size and high electronegativity of the fluorine atom. The experimental observations are seen to agree qualitatively with the theory results. It is hoped that when the experiment is repeated, a quantitative comparison can be made. The analysis by the theory of atoms in molecules, along with providing polarizabilities and polarizability derivatives, gives additional information outlined below. The theory provides a pictorial description of the main factors contributing to the molecular polarizability and polarizability derivative. These contributions are from the charge transfer and atomic dipole terms i.e., transfer of charge from one atom to another and the reorganization of atomic electronic charge distribution due to presence of an electric field. The linear relationship between polarizability and molecular volume was also observed.

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.

Differential induction, isolation, physicochemical and molecular characterization of temperate phages of environmental Vibrio cholerae as evidence of phage mediated Horizontal Gene Transfer

The resurgence of the enteric pathogen Vibrio cholerae, the causative organism of epidemic cholera, remains a major health problem in many developing countries like India. The southern Indian state of Kerala is endemic to cholera. The outbreaks of cholera follow a seasonal pattern in regions of endemicity. Marine aquaculture settings and mangrove environments of Kerala serve as reservoirs for V. cholerae. The non-O1/non-O139 environmental isolates of V. cholerae with incomplete ‘virulence casette’ are to be dealt with caution as they constitute a major reservoir of diverse virulence genes in the marine environment and play a crucial role in pathogenicity and horizontal gene transfer. The genes coding cholera toxin are borne on, and can be infectiously transmitted by CTXΦ, a filamentous lysogenic vibriophages. Temperate phages can provide crucial virulence and fitness factors affecting cell metabolism, bacterial adhesion, colonization, immunity, antibiotic resistance and serum resistance. The present study was an attempt to screen the marine environments like aquafarms and mangroves of coastal areas of Alappuzha and Cochin, Kerala for the presence of lysogenic V. cholerae, to study their pathogenicity and also gene transfer potential. Phenotypic and molecular methods were used for identification of isolates as V. cholerae. The thirty one isolates which were Gram negative, oxidase positive, fermentative, with or without gas production on MOF media and which showed yellow coloured colonies on TCBS (Thiosulfate Citrate Bile salt Sucrose) agar were segregated as vibrios. Twenty two environmental V. cholerae strains of both O1 and non- O1/non-O139 serogroups on induction with mitomycin C showed the presence of lysogenic phages. They produced characteristic turbid plaques in double agar overlay assay using the indicator strain V. cholerae El Tor MAK 757. PCR based molecular typing with primers targeting specific conserved sequences in the bacterial genome, demonstrated genetic diversity among these lysogen containing non-O1 V. cholerae . Polymerase chain reaction was also employed as a rapid screening method to verify the presence of 9 virulence genes namely, ctxA, ctxB, ace, hlyA, toxR, zot,tcpA, ninT and nanH, using gene specific primers. The presence of tcpA gene in ALPVC3 was alarming, as it indicates the possibility of an epidemic by accepting the cholera. Differential induction studies used ΦALPVC3, ΦALPVC11, ΦALPVC12 and ΦEKM14, underlining the possibility of prophage induction in natural ecosystems, due to abiotic factors like antibiotics, pollutants, temperature and UV. The efficiency of induction of prophages varied considerably in response to the different induction agents. The growth curve of lysogenic V. cholerae used in the study drastically varied in the presence of strong prophage inducers like antibiotics and UV. Bacterial cell lysis was directly proportional to increase in phage number due to induction. Morphological characterization of vibriophages by Transmission Electron Microscopy revealed hexagonal heads for all the four phages. Vibriophage ΦALPVC3 exhibited isometric and contractile tails characteristic of family Myoviridae, while phages ΦALPVC11 and ΦALPVC12 demonstrated the typical hexagonal head and non-contractile tail of family Siphoviridae. ΦEKM14, the podophage was distinguished by short non-contractile tail and icosahedral head. This work demonstrated that environmental parameters can influence the viability and cell adsorption rates of V. cholerae phages. Adsorption studies showed 100% adsorption of ΦALPVC3 ΦALPVC11, ΦALPVC12 and ΦEKM14 after 25, 30, 40 and 35 minutes respectively. Exposure to high temperatures ranging from 50ºC to 100ºC drastically reduced phage viability. The optimum concentration of NaCl required for survival of vibriophages except ΦEKM14 was 0.5 M and that for ΦEKM14 was 1M NaCl. Survival of phage particles was maximum at pH 7-8. V. cholerae is assumed to have existed long before their human host and so the pathogenic clones may have evolved from aquatic forms which later colonized the human intestine by progressive acquisition of genes. This is supported by the fact that the vast majority of V. cholerae strains are still part of the natural aquatic environment. CTXΦ has played a critical role in the evolution of the pathogenicity of V. cholerae as it can transmit the ctxAB gene. The unusual transformation of V. cholerae strains associated with epidemics and the emergence of V. cholera O139 demonstrates the evolutionary success of the organism in attaining greater fitness. Genetic changes in pathogenic V. cholerae constitute a natural process for developing immunity within an endemically infected population. The alternative hosts and lysogenic environmental V. cholerae strains may potentially act as cofactors in promoting cholera phage ‘‘blooms’’ within aquatic environments, thereby influencing transmission of phage sensitive, pathogenic V. cholerae strains by aquatic vehicles. Differential induction of the phages is a clear indication of the impact of environmental pollution and global changes on phage induction. The development of molecular biology techniques offered an accessible gateway for investigating the molecular events leading to genetic diversity in the marine environment. Using nucleic acids as targets, the methods of fingerprinting like ERIC PCR and BOX PCR, revealed that the marine environment harbours potentially pathogenic group of bacteria with genetic diversity. The distribution of virulence associated genes in the environmental isolates of V. cholerae provides tangible material for further investigation. Nucleotide and protein sequence analysis alongwith protein structure prediction aids in better understanding of the variation inalleles of same gene in different ecological niche and its impact on the protein structure for attaining greater fitness of pathogens. The evidences of the co-evolution of virulence genes in toxigenic V. cholerae O1 from different lineages of environmental non-O1 strains is alarming. Transduction studies would indicate that the phenomenon of acquisition of these virulence genes by lateral gene transfer, although rare, is not quite uncommon amongst non-O1/non-O139 V. cholerae and it has a key role in diversification. All these considerations justify the need for an integrated approach towards the development of an effective surveillance system to monitor evolution of V. cholerae strains with epidemic potential. Results presented in this study, if considered together with the mechanism proposed as above, would strongly suggest that the bacteriophage also intervenes as a variable in shaping the cholera bacterium, which cannot be ignored and hinting at imminent future epidemics.

Molecular computations for reactions and phase transitions: applications to protein stabilization, hydrates and catalysis

In this work we have made significant contributions in three different areas of interest: therapeutic protein stabilization, thermodynamics of natural gas clathrate-hydrates, and zeolite catalysis. In all three fields, using our various computational techniques, we have been able to elucidate phenomena that are difficult or impossible to explain experimentally. More specifically, in mixed solvent systems for proteins we developed a statistical-mechanical method to model the thermodynamic effects of additives in molecular-level detail. It was the first method demonstrated to have truly predictive (no adjustable parameters) capability for real protein systems. We also describe a novel mechanism that slows protein association reactions, called the “gap effect.” We developed a comprehensive picture of methioine oxidation by hydrogen peroxide that allows for accurate prediction of protein oxidation and provides a rationale for developing strategies to control oxidation. The method of solvent accessible area (SAA) was shown not to correlate well with oxidation rates. A new property, averaged two-shell water coordination number (2SWCN) was identified and shown to correlate well with oxidation rates. Reference parameters for the van der Waals Platteeuw model of clathrate-hydrates were found for structure I and structure II. These reference parameters are independent of the potential form (unlike the commonly used parameters) and have been validated by calculating phase behavior and structural transitions for mixed hydrate systems. These calculations are validated with experimental data for both structures and for systems that undergo transitions from one structure to another. This is the first method of calculating hydrate thermodynamics to demonstrate predictive capability for phase equilibria, structural changes, and occupancy in pure and mixed hydrate systems. We have computed a new mechanism for the methanol coupling reaction to form ethanol and water in the zeolite chabazite. The mechanism at 400°C proceeds via stable intermediates of water, methane, and protonated formaldehyde.

Effect of Gas Sparging in Mammalian Cell Bioreactors

One of the major problems in the operations of mammalian cell bioreactors is the detrimental effect of gas sparging. Since the most convenient way to oxygenate any bioreactor is by gas sparging, this adverse effect has often been one of the limiting oxygen transport problems in both laboratory and industrial mammalian cell bioreactors. When one examines the literature on the effect of gas sparging on the death of mammalian cells, a great deal of confusions has been reported. It is not clear from the published literature as to the leading cause for gas-sparged related cell death. These confusions prevent the rational design and operations of mammalian cell bioreactors. In our laboratory, we have attempted to address this problem both fundamentally as well as attempt to obtain a general understanding on the adverse effect of gas sparging. Our analyses first examined the fluid shear associated with the various sections that the gas bubbles encounter during entrance, passage through the bioreactor and the final exit of the gas bubbles. Our analyses showed that the major damage of the mammalian cells by gas bubbles is due to the burst of the bubbles when exiting the bioreactor. It was also our hypothesis that the entrained cells in the liquid boundary layer of the gas bubble upon bursting is the major cause for cell death. We have corroborated this hypothesis by correlating the liquid entrainment with the cell death rate using results from our laboratory as well as other studies. Pluonic F-68, a weak surfactant, has routinely been used in laboratory and industrial bioreactors. In the past, the protective effect of Pluronic F-68 has never been shown as to why it is effective. In our research, we have data using microphotography which clearly demonstrated and corroborated our entrainment hypothesis is the major reason for the effectiveness of Pluronic F-68 in protecting the cells from gas-sparged related cell death.