Analysis of radicals and radical reaction products in cell signalling and biomolecular damage:the long hard road to gold-standard measures

The field of free radical biology and medicine continues to move at a tremendous pace, with a constant flow of ground-breaking discoveries. The following collection of papers in this issue of Biochemical Society Transactions highlights several key areas of topical interest, including the crucial role of validated measurements of radicals and reactive oxygen species in underpinning nearly all research in the field, the important advances being made as a result of the overlap of free radical research with the reinvigorated field of lipidomics (driven in part by innovations in MS-based analysis), the acceleration of new insights into the role of oxidative protein modifications (particularly to cysteine residues) in modulating cell signalling, and the effects of free radicals on the functions of mitochondria, extracellular matrix and the immune system. In the present article, we provide a brief overview of these research areas, but, throughout this discussion, it must be remembered that it is the availability of reliable analytical methodologies that will be a key factor in facilitating continuing developments in this exciting research area.

Low severity Fischer-Tropsch synthesis for the production of synthetic hydrocarbon fuels

Currently, the main source for the production of liquid transportation fuels is petroleum, the continued use of which faces many challenges including depleting oil reserves, significant oil price rises, and environmental concerns over global warming which is widely believed to be due to fossil fuel derived CO2 emissions and other greenhouse gases. In this respect, lignocellulosic or plant biomass is a particularly interesting resource as it is the only renewable source of organic carbon that can be converted into liquid transportation fuels. The gasification of biomass produces syngas which can then be converted into synthetic liquid hydrocarbon fuels by means of the Fischer-Tropsch (FT) synthesis. This process has been widely considered as an attractive option for producing clean liquid hydrocarbon fuels from biomass that have been identified as promising alternatives to conventional fossil fuels like diesel and kerosene. The resulting product composition in FT synthesis is influenced by the type of catalyst and the reaction conditions that are used in the process. One of the issues facing this conversion process is the development of a technology that can be scaled down to match the scattered nature of biomass resources, including lower operating pressures, without compromising liquid composition. The primary aims of this work were to experimentally explore FT synthesis at low pressures for the purpose of process down-scaling and cost reduction, and to investigate the potential for obtaining an intermediate FT synthetic crude liquid product that can be integrated into existing refineries under the range of process conditions employed. Two different fixed-bed micro-reactors were used for FT synthesis; a 2cm3 reactor at the University of Rio de Janeiro (UFRJ) and a 20cm3 reactor at Aston University. The experimental work firstly involved the selection of a suitable catalyst from three that were available. Secondly, a parameter study was carried out on the 20cm3 reactor using the selected catalyst to investigate the influence of reactor temperature, reactor pressure, space velocity, the H2/CO molar ratio in the feed syngas and catalyst loading on the reaction performance measured as CO conversion, catalyst stability, product distribution, product yields and liquid hydrocarbon product composition. From this parameter study a set of preferred operating conditions was identified for low pressure FT synthesis. The three catalysts were characterized using BET, XRD, TPR and SEM. The catalyst selected was an unpromoted Co/Al2O3 catalyst. FT synthesis runs on the 20cm3 reactor at Aston were conducted for 48 hours. Permanent gases and light hydrocarbons (C1-C5) were analysed in an online GC-TCD/FID at hourly intervals. The liquid hydrocarbons collected were analyzed offline using GC-MS for determination of fuel composition. The parameter study showed that CO conversion and liquid hydrocarbon yields increase with increasing reactor pressure up to around 8 bar, above which the effect of pressure is small. The parameters that had the most significant influence on CO conversion, product selectivity and liquid hydrocarbon yields were reactor temperature and catalyst loading. The preferred reaction conditions identified for this research were: T = 230ºC, P = 10 bar, H2/CO = 2.0, WHSV = 2.2 h-1, and catalyst loading = 2.0g. Operation in the low range of pressures studied resulted in low CO conversions and liquid hydrocarbon yields, indicating that low pressure BTL-FT operation may not be industrially viable as the trade off in lower CO conversions and once-through liquid hydrocarbon product yields has to be carefully weighed against the potential cost savings resulting from process operation at lower pressures.

Carbon nanotube-supported metal catalysts for NOx reduction using hydrocarbon reductants. Part 1:catalyst preparation, characterization and NOx reduction characteristics

A dual catalyst system for the Selective Catalytic Reduction of NOx with hydrocarbons (HC-SCR), including distinct low and high temperature formulations, is proposed as a means to abate NOx emissions from diesel engines. Given that satisfactory high temperature HC-SCR catalysts are already available, this work focuses on the development of an improved low temperature formulation. Pt supported on multiwalled carbon nantubes (MWCNTs) was found to exhibit superior NOx reduction activity in comparison with Pt/Al2O3, while the MWCNT support displayed a higher resistance to oxidation than activated carbon. Refluxing the MWCNT support in a 1:1 mixture of H2SO4 and HNO3 prior to the metal deposition step proved to be beneficial for the metal dispersion and the NOx reduction performance of the resulting catalysts. This support effect is ascribed to the increased Brønsted acidity of the acid-treated MWCNTs, which in turn enhances the partial oxidation of the hydrocarbon reductant. Further improvements in the HC-SCR performance of MWCNT-based formulations were achieved using a 3:1 Pt–Rh alloy as the supported phase.

A catalytic reactor for the trapping of free radicals from gas phase oxidation reactions

A catalytic reactor for the trapping of free radicals originating from gas phase catalytic reactions is described and discussed. Radical trapping and identification were initially carried out using a known radical generator such as dicumyl peroxide. The trapping of radicals was further demonstrated by investigating genuine radical oxidation processes, e.g., benzaldehyde oxidation over manganese and cobalt salts. The efficiency of the reactor was finally proven by the partial oxidation of cyclohexane over MoO3, Cr2O3, and WO3, which allowed the identification of all the radical intermediates responsible for the formation of the products cyclohexanol and cyclohexanone. Assignment of the trapped radicals was carried out using spin trapping technique and X -band electron paramagnetic resonance spectroscopy. © 2010 American Institute of Physics.

Sulphate-promotion and structure-sensitivity in hydrocarbon combustion over Rh2/AlO3 catalysts

A series of Rh2/AlO3 catalysts have been prepared using untreated or pre-sulphated alumina supports. The effect of support sulphation on catalyst activity towards propene and propane combustion has been explored as a function of Rh loading. Light-off temperatures for the total oxidation of both hydrocarbons decrease with increasing Rh content, associated with a transition from small oxidic clusters to large metallic Rh particles. Sulphate promotes both propene and propane combustion equally, with the magnitude of promotion exhibiting only a weak loading dependence. Enhanced catalytic performance is accompanied by Rh reduction and sintering. © 2006 Elsevier B.V. All rights reserved.

Promoter effects in the polymerisation of a mixed hydrocarbon feed with silica-supported BF3

The activity of a silica-supported BF3–methanol solid acid catalyst in the cationic polymerisation of an industrial aromatic C9 feedstock has been investigated. Reuse has been achieved under continuous conditions. Titration of the catalyst acid sites with triethylphosphine oxide (TEPO) in conjunction with 31P MAS NMR shows the catalyst to have two types of acid sites. Further analysis with 2,6 di-tert-butyl-4-methylpyridine (DBMP) has revealed the majority of these acid sites to be Brønsted in nature. The role of α-methylstyrene in promoting resin polymerisation via chain transfer is proposed.

Computational fluid dynamics (CFD) based approach to consequence assessment of accidental release of hydrocarbon during storage and transportation

This thesis investigated the risk of accidental release of hydrocarbons during transportation and storage. Transportation of hydrocarbons from an offshore platform to processing units through subsea pipelines involves risk of release due to pipeline leakage resulting from corrosion, plastic deformation caused by seabed shakedown or damaged by contact with drifting iceberg. The environmental impacts of hydrocarbon dispersion can be severe. Overall safety and economic concerns of pipeline leakage at subsea environment are immense. A large leak can be detected by employing conventional technology such as, radar, intelligent pigging or chemical tracer but in a remote location like subsea or arctic, a small chronic leak may be undetected for a period of time. In case of storage, an accidental release of hydrocarbon from the storage tank could lead pool fire; further it could escalate to domino effects. This chain of accidents may lead to extremely severe consequences. Analyzing past accident scenarios it is observed that more than half of the industrial domino accidents involved fire as a primary event, and some other factors for instance, wind speed and direction, fuel type and engulfment of the compound. In this thesis, a computational fluid dynamics (CFD) approach is taken to model the subsea pipeline leak and the pool fire from a storage tank. A commercial software package ANSYS FLUENT Workbench 15 is used to model the subsea pipeline leakage. The CFD simulation results of four different types of fluids showed that the static pressure and pressure gradient along the axial length of the pipeline have a sharp signature variation near the leak orifice at steady state condition. Transient simulation is performed to obtain the acoustic signature of the pipe near leak orifice. The power spectral density (PSD) of acoustic signal is strong near the leak orifice and it dissipates as the distance and orientation from the leak orifice increase. The high-pressure fluid flow generates more noise than the low-pressure fluid flow. In order to model the pool fire from the storage tank, ANSYS CFX Workbench 14 is used. The CFD results show that the wind speed has significant contribution on the behavior of pool fire and its domino effects. The radiation contours are also obtained from CFD post processing, which can be applied for risk analysis. The outcome of this study will be helpful for better understanding of the domino effects of pool fire in complex geometrical settings of process industries. The attempt to reduce and prevent risks is discussed based on the results obtained from the numerical simulations of the numerical models.

Efficient Computation of Electromagnetic Waves in Hydrocarbon Exploration Using the Improved Numerical Mode Matching (NMM) Method

In this study, we developed and improved the numerical mode matching (NMM) method which has previously been shown to be a fast and robust semi-analytical solver to investigate the propagation of electromagnetic (EM) waves in an isotropic layered medium. The applicable models, such as cylindrical waveguide, optical fiber, and borehole with earth geological formation, are generally modeled as an axisymmetric structure which is an orthogonal-plano-cylindrically layered (OPCL) medium consisting of materials stratified planarly and layered concentrically in the orthogonal directions.

In this report, several important improvements have been made to extend applications of this efficient solver to the anisotropic OCPL medium. The formulas for anisotropic media with three different diagonal elements in the cylindrical coordinate system are deduced to expand its application to more general materials. The perfectly matched layer (PML) is incorporated along the radial direction as an absorbing boundary condition (ABC) to make the NMM method more accurate and efficient for wave diffusion problems in unbounded media and applicable to scattering problems with lossless media. We manipulate the weak form of Maxwell's equations and impose the correct boundary conditions at the cylindrical axis to solve the singularity problem which is ignored by all previous researchers. The spectral element method (SEM) is introduced to more efficiently compute the eigenmodes of higher accuracy with less unknowns, achieving a faster mode matching procedure between different horizontal layers. We also prove the relationship of the field between opposite mode indices for different types of excitations, which can reduce the computational time by half. The formulas for computing EM fields excited by an electric or magnetic dipole located at any position with an arbitrary orientation are deduced. And the excitation are generalized to line and surface current sources which can extend the application of NMM to the simulations of controlled source electromagnetic techniques. Numerical simulations have demonstrated the efficiency and accuracy of this method.

Finally, the improved numerical mode matching (NMM) method is introduced to efficiently compute the electromagnetic response of the induction tool from orthogonal transverse hydraulic fractures in open or cased boreholes in hydrocarbon exploration. The hydraulic fracture is modeled as a slim circular disk which is symmetric with respect to the borehole axis and filled with electrically conductive or magnetic proppant. The NMM solver is first validated by comparing the normalized secondary field with experimental measurements and a commercial software. Then we analyze quantitatively the induction response sensitivity of the fracture with different parameters, such as length, conductivity and permeability of the filled proppant, to evaluate the effectiveness of the induction logging tool for fracture detection and mapping. Casings with different thicknesses, conductivities and permeabilities are modeled together with the fractures in boreholes to investigate their effects for fracture detection. It reveals that the normalized secondary field will not be weakened at low frequencies, ensuring the induction tool is still applicable for fracture detection, though the attenuation of electromagnetic field through the casing is significant. A hybrid approach combining the NMM method and BCGS-FFT solver based integral equation has been proposed to efficiently simulate the open or cased borehole with tilted fractures which is a non-axisymmetric model.

(Table 1) Summary of low-molecular-weight hydrocarbon concentrations, organic carbon contents, Rock-Eval pyrolysis and lithology at DSDP Leg 79 Holes

A series of core samples taken during Cruise 79 of Glomar Challenger, drilling offshore Morocco (Mazagan Plateau), is analyzed for their low-molecular-weight hydrocarbon contents. Fifty-four samples from DSDP Holes 544A, 545, 547A, and 547B, deep frozen on board immediately after recovery, are studied by a hydrogen-stripping/thermovaporization technique combined with capillary gas chromatography. Thirty-eight compounds in the C2-C8 molecular range, including saturated, olefinic, and aromatic hydrocarbons, are identified. Because of large differences in organic carbon contents, the total C2-C8 hydrocarbon concentrations vary from about 20 to 1500 ng/g dry sediment weight in the whole sample series. Organic-carbon normalized values are about 3.2 x 10**4 ng/g Corg for Lithologic Subunits IIIA and IIIB at Site 545 (Cenomanian to Aptian) and 1.0 x 10**5 ng/g Corg for Unit V at Site 547 (Cenomanian to Albian) reflecting the slightly more advanced maturity stage at the latter site. Values exceeding 10**5 ng/g Corg (Site 545) and 2 x 10**5 ng/g Corg (Site 547) are associated with samples that are very lean in organic carbon and are generally rich in carbonate. These samples are enriched by small amounts of gaseous hydrocarbons. A detailed study of individual hydrocarbon concentrations, plotted against depth, reveal additional indications for migration phenomena. At Site 547, for instance, the most mobile hydrocarbons studied (e.g., ethane) appear to migrate by diffusion or a related process from more than 700 m depth toward the surface.

(Table 1) Low molecular weight hydrocarbon concentrations and organic carbon contents at DSDP Hole 71-511

C2-C8 hydrocarbons (36 compounds identified) from 56 shipboard sealed, deep-frozen core samples of DSDP Leg 71, Site 511, Falkland Plateau, South Atlantic, were analyzed by a combined hydrogen stripping-thermovaporization method. Concentrations, which represent hydrocarbons dissolved in the pore water and adsorbed to the mineral surfaces of the sediment, vary from 24 ng/g of dry weight sediment in Lithologic Unit 4 to 17,400 ng/g in Lithologic Unit 6 ("black shale" unit). Likewise, the organic carbon normalized C2-C8 hydrocarbon concentrations range from 104 to 3.5 x 105 ng/g Corg. The latter value is more than one order of magnitude lower than expected for petroleum source beds in the main phase of oil generation. The low maturity at 600 meters depth is further supported by light hydrocarbon concentration ratios. The change of the kerogen type from Lithologic Unit 5 (Type III) to 6 (Type II) is evidenced by changes in the C6 and C7 hydrocarbon composition. Redistribution phenomena are observed close to the Tertiary-Cretaceous unconformity and at the contact between the "black shale" unit and the overlying Cretaceous chalks and claystones. Otherwise, the low molecular weight hydrocarbons in Hole 511 are formed in situ and remain at their place of formation. The core samples turned out to be contaminated by large quantities of acetone, which is routinely used as a solvent during sampling procedures onboard Glomar Challenger.

(Table 1) Hydrocarbon gas composition of sediment and gas hydrate collected in video-guided grabs from Chapopote

In the Campeche Knolls, in the southern Gulf of Mexico, lava-like flows of solidified asphalt cover more than 1 square kilometer of the rim of a dissected salt dome at a depth of 3000 meters below sea level. Chemosynthetic tubeworms and bivalves colonize the sea floor near the asphalt, which chilled and contracted after discharge. The site also includes oil seeps, gas hydrate deposits, locally anoxic sediments, and slabs of authigenic carbonate. Asphalt volcanism creates a habitat for chemosynthetic life that may be widespread at great depth in the Gulf of Mexico.