Ability of the PM3 Quantum Mechanical Method to Model Intermolecular Hydrogen Bonding between Neutral Molecules

The PM3 semiempirical quantum-mechanical method was found to systematically describe intermolecular hydrogen bonding in small polar molecules. PM3 shows charge transfer from the donor to acceptor molecules on the order of 0.02-0.06 units of charge when strong hydrogen bonds are formed. The PM3 method is predictive; calculated hydrogen bond energies with an absolute magnitude greater than 2 kcal mol-' suggest that the global minimum is a hydrogen bonded complex; absolute energies less than 2 kcal mol-' imply that other van der Waals complexes are more stable. The geometries of the PM3 hydrogen bonded complexes agree with high-resolution spectroscopic observations, gas electron diffraction data, and high-level ab initio calculations. The main limitations in the PM3 method are the underestimation of hydrogen bond lengths by 0.1-0.2 for some systems and the underestimation of reliable experimental hydrogen bond energies by approximately 1-2 kcal mol-l. The PM3 method predicts that ammonia is a good hydrogen bond acceptor and a poor hydrogen donor when interacting with neutral molecules. Electronegativity differences between F, N, and 0 predict that donor strength follows the order F > 0 > N and acceptor strength follows the order N > 0 > F. In the calculations presented in this article, the PM3 method mirrors these electronegativity differences, predicting the F-H- - -N bond to be the strongest and the N-H- - -F bond the weakest. It appears that the PM3 Hamiltonian is able to model hydrogen bonding because of the reduction of two-center repulsive forces brought about by the parameterization of the Gaussian core-core interactions. The ability of the PM3 method to model intermolecular hydrogen bonding means reasonably accurate quantum-mechanical calculations can be applied to small biologic systems.

Radical Chain Reduction of Alkylboron Compounds with Catechols

The conversion of alkylboranes to the corresponding alkanes is classically performed via protonolysis of alkylboranes. This simple reaction requires the use of severe reaction conditions, that is, treatment with a carboxylic acid at high temperature (>150 degrees C). We report here a mild radical procedure for the transformation of organoboranes to alkalies. 4-tert-Butylcatechol, a well-established radical inhibitor and antioxidant, is acting as a source of hydrogen atoms. An efficient chain reaction is observed due to the exceptional reactivity of phenoxyl radicals toward alkylboranes. The reaction has been applied to a wide range of organoboron derivatives such as B-alkylcatecholboranes, trialkylboranes, pinacolboronates, and alkylboronic acids. Furthermore, the so far elusive rate constants for the hydrogen transfer between secondary alkyl radical and catechol derivatives have been experimentally determined. Interestingly, they are less than 1 order of magnitude slower than that of tin hydride at 80 degrees C, making catechols particularly attractive for a wide range of transformations involving C-C bond formation.

Quantitative depth profiling of Ce 3+ in Pt/CeO 2 by in situ high-energy XPS in a hydrogen atmosphere

The redox property of ceria is a key factor in the catalytic activity of ceria-based catalysts. The oxidation state of well-defined ceria nanocubes in gas environments was analysed in situ by a novel combination of near-ambient pressure X-ray Photoelectron Spectroscopy (XPS) and high-energy XPS at a synchrotron X-ray source. In situ high-energy XPS is a promising new tool to determine the electronic structure of matter under defined conditions. The aim was to quantitatively determine the degree of cerium reduction in a nano-structured ceria-supported platinum catalyst as a function of the gas environment. To obtain a non-destructive depth profile at near-ambient pressure, in situ high-energy XPS analysis was performed by varying the kinetic energy of photoelectrons from 1 to 5 keV, and, thus, the probing depth. In ceria nanocubes doped with platinum, oxygen vacancies formed only in the uppermost layers of ceria in an atmosphere of 1 mbar hydrogen and 403 K. For pristine ceria nanocubes, no change in the cerium oxidation state in various hydrogen or oxygen atmospheres was observed as a function of probing depth. In the absence of platinum, hydrogen does not dissociate and, thus, does not lead to reduction of ceria.

Methane and hydrogen sulfide in porewater of sediment cores from the upwelling area off Namibia

Porewater concentrations of sulfate, methane, and other relevant constituents were determined on four sediment cores from the high productivity upwelling area off Namibia which were recovered from the continental slope at water depths of 1300 and 2000 m. At all four stations a distinct sulfate-methane transition zone was observed several meters below the seafloor in which both sulfate and methane are consumed. Nutrient porewater concentration profiles do not show gradient slope changes at the depths of the transition zones. Flux calculations carried out on the basis of the determined porewater profiles revealed that anaerobic methane oxidation accounts for 100% of deep sulfate reduction within the sulfate-methane transition zone and consumes the total net diffusive sulfate flux. A significant contribution of organic carbon oxidation to the reduction of sulfate at these depths could, therefore, be excluded. We state that porewater profiles of sulfate with constant gradients above the transition zones are indicative for anaerobic methane oxidation controlling sulfate reduction.

Hydrogen, carbon, and oxygen isotope ratios of interstitial fluides of ODP Leg 104 holes

Carbon, hydrogen, and oxygen isotope ratios determined on 32 squeezed interstitial fluid samples show remarkable variations with depth. For the most part these variations are related to diagenetic and alteration reactions taking place in the sediments, and in the underlying basalts. delta13C SumCO2 depth distributions at Sites 642 and 643 are the result of mixing of original SumCO2 of the paleo bottom water with SumCO2 released by remineralization of organic matter. At Site 644, where sulfate exhaustion occurs, the processes of methanogenesis by CO2 reduction and anaerobic methanotrophy strongly influence the delta13C SumCO2 distribution. Hydrogen and oxygen isotopes roughly covary, and become enriched in 16O and1H with depth. This effect is most pronounced at Sites 642 and 643, possibly due to the influence of the directly underlying basalts. Isotope depletions at Site 644 are much lower, corresponding to the greater sediment depth to basement. The alternative, that the O, H isotope shifts are due primarily to autochthonous diagenetic and exchange reactions, is not supported by the data available.

Organic matter composition and sulfate reduction intensity in Oman Margin sediments

Petrographical and geochemical studies of Neogene marine sediments from the Oman Sea (Leg 117, Sites 720, 724, 726 and 730), show a close relationship between the nature and amount of the organic matter, and the degree of degradation of organic matter by sulfate reduction, i.e. pyritization. Petrographically, three major pyritization types were observed: (1) Finely dispersed pyrite framboids in sediments from Oman Margin and Indus Fan, enriched in autochthonous marine organic matter. (2) Infilling of pores by massive pyrite crystals in Oman Margin sediments with a low TOC and a high microfossil content. (3) Pyrite mineralization of lignaceous fragments in organic-depleted sediments from the Indus Fan leading to more massive pyrite. Geochemically, we can define a sulfate reduction index (SRI) as the percentage of initial organic carbon versus that of residual organic carbon. Finely laminated Pliocene-Pleistocene sediments from the Oman Margin exclusively contain organic matter deriving from organic phytoplankton, for which the quantity (TOC) positively correlates with the geochemical quality (Hydrogen Index). We think that the occurrence of this residual organic matter is linked mainly to a high primary paleo-productivity. The intensity of sulfate reduction is constant for sediments with TOC up to 2% and becomes more important when organic input decreases. This degradation process can destroy up to 50% of the initial organic matter, but is not sufficient to explain some of the encountered very low TOC values. It can be seen that sharp increases of certain plankton species (with mineral skeletons) are responsible for a pronounced degradation of organic matter, due to increased sulfate reduction. In that case, the organic matter may be strongly degraded (high SRI), although deposited in an oxygen-depleted environment. Conversely, Miocene-Pliocene sediments contain an autochthonous organic matter that is typical of both low productivity and oxic processes; their very low sulfate reduction index indicates that very little metabolizable organic matter was initially present.

Anaerobic oxidation of methane and sulphate reduction rates, hydrocarbons, sulphate and sulphide concentrations of sediment cores from the Larsen B embayment at the eastern site of the Antarctic Peninsula

First videographic indication of an Antarctic cold seep ecosystem was recently obtained from the collapsed Larsen B ice shelf, western Weddell Sea (Domack et al., 2005). Within the framework of the R/V Polarstern expedition ANTXXIII-8, we revisited this area for geochemical, microbiological and further videographical examinations. During two dives with ROV Cherokee (MARUM, Bremen), several bivalve shell agglomerations of the seep-associated, chemosynthetic clam Calyptogena sp. were found in the trough of the Crane and Evans glacier. The absence of living clam specimens indicates that the flux of sulphide and hence the seepage activity is diminished at present. This impression was further substantiated by our geochemical observations. Concentrations of thermogenic methane were moderately elevated with 2 µM in surface sediments of a clam patch, increasing up to 9 µM at a sediment depth of about 1 m in the bottom sections of the sediment cores. This correlated with a moderate decrease in sulphate from about 28 mM at the surface down to 23.4 mM, an increase in sulphide to up to 1.43 mM and elevated rates of the anaerobic oxidation of methane (AOM) of up to 600 pmol cm**-3 d**-1 at about 1 m below the seafloor. Molecular analyses indicate that methanotrophic archaea related to ANME-3 are the most likely candidates mediating AOM in sediments of the Larsen B seep.