Basin-internal derivation of hydrocarbons in the Witwatersrand Basin, South Africa: evidence from bulk and molecular δ13C data

Gold in the quartz-pebble conglomerates of the late Archean Witwatersrand Basin, South Africa, is often intimately associated with carbonaceous matter of organic/biogenic origin which occurs in the form of stratiform carbon seams and paragenetically late bitumen nodules. Both carbon forms are believed to be formed by solidification of migrating hydrocarbons. This paper presents bulk and molecular chemical and stable carbon isotope data for the carbonaceous matter, all of which are used to provide a clue to the source of the hydrocarbons. These data are compared with those from intra-basinal shales and overlying dolostone of the Transvaal Supergroup. The delta C-13 values of the extracts from the Witwatersrand carbonaceous material show small differences (up to 2.4 parts per thousand) compared to the associated insoluble organic matter. This suggests that the auriferous rocks were stained by mobile hydrocarbons produced by thermal and oxidative alteration of indigenous bitumens, a contribution from hydrocarbons derived from intra-basinal Witwatersrand shales cannot be excluded. Individual aliphatic hydrocarbons of the various carbonaceous materials were subjected to compound specific isotope analysis using on-line gas chromatography/combustion/stable isotope ratio mass spectrometry (GC/C/IRMS). The limited variability of the molecular parameters and uniform delta C-13 values of individual n-alkanes (-31.1 +/- 1.7 parts per thousand) and isoprenoids (-30.7 +/- 1.1 parts per thousand) in the Witwatersrand samples exclude the mixing of oils from different sources. Carbonaceous matter in the dolostones shows distinctly different bulk and molecular isotope characteristics and thus cannot have been the source of the hydrocarbons in the Witwatersrand deposits. All the various forms of Witwatersrand carbon appear indigenous to the Witwatersrand Basin, and the differences between them are explained by variable, in general probably short (centimeter- to meter-scale) hydrocarbon migration during diagenesis and subsequent hydrothermal infiltration. (C) 2001 Elsevier Science B.V. All rights reserved.

Fast gas chromatography and negative-ion chemical ionization tandem mass spectrometry for forensic analysis of cannabinoids in whole blood.

The present work describes a fast gas chromatography/negative-ion chemical ionization tandem mass spectrometric assay (Fast GC/NICI-MS/MS) for analysis of tetrahydrocannabinol (THC), 11-hydroxy-tetrahydrocannabinol (THC-OH) and 11-nor-9-carboxy-tetrahydrocannabinol (THC-COOH) in whole blood. The cannabinoids were extracted from 500 microL of whole blood by a simple liquid-liquid extraction (LLE) and then derivatized by using trifluoroacetic anhydride (TFAA) and hexafluoro-2-propanol (HFIP) as fluorinated agents. Mass spectrometric detection of the analytes was performed in the selected reaction-monitoring mode on a triple quadrupole instrument after negative-ion chemical ionization. The assay was found to be linear in the concentration range of 0.5-20 ng/mL for THC and THC-OH, and of 2.5-100 ng/mL for THC-COOH. Repeatability and intermediate precision were found less than 12% for all concentrations tested. Under standard chromatographic conditions, the run cycle time would have been 15 min. By using fast conditions of separation, the assay analysis time has been reduced to 5 min, without compromising the chromatographic resolution. Finally, a simple approach for estimating the uncertainty measurement is presented.

Computational Analysis and Optimization of Real Gas Flow In Small Centrifugal Compressors

Small centrifugal compressors are more and more widely used in many industrialsystems because of their higher efficiency and better off-design performance comparing to piston and scroll compressors as while as higher work coefficient perstage than in axial compressors. Higher efficiency is always the aim of the designer of compressors. In the present work, the influence of four partsof a small centrifugal compressor that compresses heavy molecular weight real gas has been investigated in order to achieve higher efficiency. Two parts concern the impeller: tip clearance and the circumferential position of the splitter blade. The other two parts concern the diffuser: the pinch shape and vane shape. Computational fluid dynamics is applied in this study. The Reynolds averaged Navier-Stokes flow solver Finflo is used. The quasi-steady approach is utilized. Chien's k-e turbulence model is used to model the turbulence. A new practical real gas model is presented in this study. The real gas model is easily generated, accuracy controllable and fairly fast. The numerical results and measurements show good agreement. The influence of tip clearance on the performance of a small compressor is obvious. The pressure ratio and efficiency are decreased as the size of tip clearance is increased, while the total enthalpy rise keeps almost constant. The decrement of the pressure ratio and efficiency is larger at higher mass flow rates and smaller at lower mass flow rates. The flow angles at the inlet and outlet of the impeller are increased as the size of tip clearance is increased. The results of the detailed flow field show that leakingflow is the main reason for the performance drop. The secondary flow region becomes larger as the size of tip clearance is increased and the area of the main flow is compressed. The flow uniformity is then decreased. A detailed study shows that the leaking flow rate is higher near the exit of the impeller than that near the inlet of the impeller. Based on this phenomenon, a new partiallyshrouded impeller is used. The impeller is shrouded near the exit of the impeller. The results show that the flow field near the exit of the impeller is greatly changed by the partially shrouded impeller, and better performance is achievedthan with the unshrouded impeller. The loading distribution on the impeller blade and the flow fields in the impeller is changed by moving the splitter of the impeller in circumferential direction. Moving the splitter slightly to the suction side of the long blade can improve the performance of the compressor. The total enthalpy rise is reduced if only the leading edge of the splitter ismoved to the suction side of the long blade. The performance of the compressor is decreased if the blade is bended from the radius direction at the leading edge of the splitter. The total pressure rise and the enthalpy rise of thecompressor are increased if pinch is used at the diffuser inlet. Among the fivedifferent pinch shape configurations, at design and lower mass flow rates the efficiency of a straight line pinch is the highest, while at higher mass flow rate, the efficiency of a concave pinch is the highest. The sharp corner of the pinch is the main reason for the decrease of efficiency and should be avoided. The variation of the flow angles entering the diffuser in spanwise direction is decreased if pinch is applied. A three-dimensional low solidity twisted vaned diffuser is designed to match the flow angles entering the diffuser. The numerical results show that the pressure recovery in the twisted diffuser is higher than in a conventional low solidity vaned diffuser, which also leads to higher efficiency of the twisted diffuser. Investigation of the detailed flow fields shows that the separation at lower mass flow rate in the twisted diffuser is later than in the conventional low solidity vaned diffuser, which leads to a possible wider flow range of the twisted diffuser.

CNDOL: A fast and reliable method for the calculation of electronic properties of very large systems. Applications to retinal binding pocket in rhodopsin and gas phase porphine.

Very large molecular systems can be calculated with the so called CNDOL approximate Hamiltonians that have been developed by avoiding oversimplifications and only using a priori parameters and formulas from the simpler NDO methods. A new diagonal monoelectronic term named CNDOL/21 shows great consistency and easier SCF convergence when used together with an appropriate function for charge repulsion energies that is derived from traditional formulas. It is possible to obtain a priori molecular orbitals and electron excitation properties after the configuration interaction of single excited determinants with reliability, maintaining interpretative possibilities even being a simplified Hamiltonian. Tests with some unequivocal gas phase maxima of simple molecules (benzene, furfural, acetaldehyde, hexyl alcohol, methyl amine, 2,5 dimethyl 2,4 hexadiene, and ethyl sulfide) ratify the general quality of this approach in comparison with other methods. The calculation of large systems as porphine in gas phase and a model of the complete retinal binding pocket in rhodopsin with 622 basis functions on 280 atoms at the quantum mechanical level show reliability leading to a resulting first allowed transition in 483 nm, very similar to the known experimental value of 500 nm of "dark state." In this very important case, our model gives a central role in this excitation to a charge transfer from the neighboring Glu(-) counterion to the retinaldehyde polyene chain. Tests with gas phase maxima of some important molecules corroborate the reliability of CNDOL/2 Hamiltonians.

Molecular Physics of Elementary Processes relevant to Hypersonics: atom-molecule, molecule-molecule and atom-surface processes.

In the present chapter some prototype gas and gas-surface processes occurring within the hypersonic flow layer surrounding spacecrafts at planetary entry are discussed. The discussion is based on microscopic dynamical calculations of the detailed cross sections and rate coefficients performed using classical mechanics treatments for atoms, molecules and surfaces. Such treatment allows the evaluation of the efficiency of thermal processes (both at equilibrium and nonequilibrium distributions) based on state-to-state and state specific calculations properly averaged over the population of the initial states. The dependence of the efficiency of the considered processes on the initial partitioning of energy among the various degrees of freedom is discussed.

Determinação da estrutura molecular do ciclooctano por métodos ab initio e difração de elétrons na fase gasosa

The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can make a significant contribution for an unambiguous determination of the geometrical parameters. In this article the determination of the molecular structure of the cyclooctane molecule by electron diffraction in the gas phase and ab initio calculations will be addressed, providing an example of a comparative analysis of theoretical and experimental predictions.

Composição molecular e origem paleobotânica de âmbares da bacia do Araripe, Formação Santana

The terpenoid composition of seven amber samples from Araripe Basin (Santana Formation, Crato Member) has been analyzed by gas chromatography-mass spectrometry to determine their botanical origin. The diterpenoids, which have been identified in the fossil resin extracts are derived primarily from the abietane class, e.g., dehydroabietane, 4-epidehydroabietol, 16,17,18-trisnorabieta-8,11,13-triene, 7-oxo-16,17,19-trisnorabieta-8,11,13-trieno, dehydroabietic acid, ferruginol, hinokiol and hinokione. Their composition is certainly typical for conifers, and angiosperms can be excluded as the botanical source, as no triterpene was identified. The terpenoid characteristics strongly support a relationship to the Araucariaceae or Podocarpaceae families. In addition, the fossil record of the embedding sediments (pollen and fossil leaves) also supports the proposal of these paleobotanical origins for the ambers.

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.

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.