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In sediments, the diaromatic carotenoid isorenieratene can undergo a wide range of molecular transformations, including cyclisation reactions via a Diels–Alder mechanism resulting in either mono- and diaromatic compounds or tetracyclic isorenieratene derivatives. To study these complex diagenetic pathways, we have used molecular dynamics simulations, in concert with a newly developed reactive hydrocarbon force field (ReaxFF). This allows us to simulate the entire cyclisation pathway, including both stable intermediates as well as energy barriers related to transition states. Our simulations indicate that the formation of tetracyclic isorenieratene derivatives is likely to occur via an A-ring initiated reaction mechanism, as the reaction product resulting from A-ring closure is more stable than that derived from B-ring closure. Furtherm...
The basic structure and stereochemistry of the characteristic glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipid of cosmopolitan pelagic crenarchaeota has been identified by high field two-dimensional (2D)-NMR techniques. It contains one cyclohexane and four cyclopentane rings formed by internal cyclisation of the biphytanyl chains. Its structure is similar to that of GDGTs biosynthesized by (hyper)thermophilic crenarchaeota apart from the cyclohexane ring. These findings are consistent with the close phylogenetic relationship of (hyper)thermophilic and pelagic crenarchaeota based 16S rRNA. The latter group inherited the biosynthetic capabilities for a membrane composed of cyclopentane ring-containing GDGTs from the (hyper)thermophilic crenarchaeota. However, to cope with the much lower temperature of the ocean, a small bu...
Diagenetic pathways of bacteriohopanepolyol derivatives are proposed based on the concentrations and 13C contents of homohopanes, homohop-17(21)-enes, benzohopanes, hopanoid thiophenes and sulphides, and macromolecularly S-bound homohopanes present in the extracts of twelve composite one metre samples from a 120 m core recovered from the Upper Cretaceous Jurf ed Darawish Oil Shale (Jordan). A large part (>80–95%) of the pentakishomohopane skeleton occurs in a S-bound form. This reveals the selective preservation of the C35 hopane skeleton by sulphur sequestration and provides a theoretical basis for the homohopane index as an indicator of anoxia in past depositional environments. A smaller part (>50–80%) of the total extended hopane skeletons (C31–C35) occurs in a S-bound form. Of the non-sulphur-containing hopanoids the homohop-17(21)...
Hydrous pyrolysis, performed at relatively low temperatures, of an immature marl yielded artificial maturation data on changes in homohopane isomer compositions. At higher temperatures enhanced amounts of 17,21(H)- and 17,21-hopanes over 17,21(H)-hopanes are observed. The amounts of 22S epimers increase relative to those of their 22R counterparts with increasing temperature. These experimental data, as well as sedimentary data on homohopane concentrations, have been reproduced using a kinetic calculation method, based on the thermodynamic stabilities determined by molecular mechanics calculation, using a full isomerization scheme rather than a single direct chiral isomerization step. We need to caution, however, that agreement between the predictions from a theoretical scheme and quantitative measurements is not an unequivocal proof fo...
A novel sulfur-containing sterane, 4,7-epithio-5-cholestane, has been identified in a sediment extract from the Miocene Northern Apennines marl (Italy) after its isolation by column chromatography and high pressure liquid chromatography. The compound has been characterised by GC-MS and mild Nickel boride desulfurisation and one and two-dimensional 1H NMR techniques. C27-C29 homologs have been detected in sediment extracts of three different formations and in one petroleum sample. These sulfur-containing steroids are A novel sulfur-containing sterane, 4,7-epithio-5-cholestane, has been identified in a sediment extract from the Miocene Northern Apennines marl (Italy) after its isolation by column chromatography and high pressure liquid chromatography. The compound has been characterised by GC-MS and mild Nickel boride desulfurisation and...
The second coordination sphere around a transition metal catalyst can contribute to the activity and selectivity that it displays. In this paper we present encapsulated catalysts using a template-ligand assembly strategy based on Zn(II)salphen building blocks, and show that these have significantly different properties in catalysis than previously reported Zn(II)porphyrin-based analogues. The conformational properties of tris-Zn(II)salphen-based capsular catalysts were examined by a combination of solid state and solution phase analytical methods, as well as computational techniques. We found that as a result of the ability of the salphen-based capsules to adopt different conformations compared to porphyrin-based capsules, less stringent constraints are enforced to the catalytic centre, resulting in different catalyst selectivities dis...
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