Ab initio molecular orbital calculations for boron isotope fractionations on boric acids and borates

Ab initio quantum chemistry calculations have been performed on the isotopic exchange reaction between B(OH)₃ and B(OH)₄⁻. Several calculation methods have been carefully compared and evaluated. The “water-droplet” method is chosen to investigate this isotope exchange reaction using cluster models with up to 34 water molecules surrounding the solute. HF/6-31G* level calculations coupled with a 0.920 scaling factor are used for the frequency calculations. A larger K value (1.027) is obtained from this study compared to the commonly used 1.0194 (Kakihana et al., 1977).The fractionations for several boric acid polymers and boron minerals are also studied. Our results suggest that assuming the BO₄ bonding in B(OH)₄⁻ is identical to that in borosilicates is wrong. Tetrahedral boron in silicates has a significantly smaller reduced isotopic partition function ratio (RPFR) and hence will be much isotopically lighter than in B(OH)₄⁻.The new theoretical curve of pH vs. δ¹¹B composition of B(OH)₄⁻ using our calculated 1.027 can be used to predict pH values for equilibrium cases such as incorporation into inorganic calcite. We also find that the shape of this curve is very sensitive to both K and pK_a value, giving the possibility of also predicting salinity from the different shapes of the curve.     

Ab initio potentials for the calculation of the dynamical and elastic properties of α-quartz

Ab initio LDF theory has been used to derive interatomic potentials for the Si-O and O-O interaction in α-quartz. The potentials have been used to study the lattice dynamical properties of α-quartz from 1 atm to 12.5 Gpa pressure. The results are compared with other calculated and experimentally derived potentials.     

The carbon isotopic distribution of Murchison amino acids

The δ¹³C values of thirty-four individual amino acids and two pyridine carboxylic acids have been obtained fromthe Murchison meteorite. They were found to range from +4.9 to +52.8‰, with statistically significant differences observed both within and between amino acid subgroups. The ¹³C content of α-amino acids declines with increasing chain length, a trend similar to the ones previously observed for carboxylic acids and alkanes. Also 2-methyl-2-amino acids were found to be heavier in ¹³C than the corresponding 2-H homologues. The3-, 4-, and 5-amino acids do not show a comparable declining trend in δ¹³C values and neither do the amino dicarboxylic acids. This variability in δ ¹³C values can be interpreted as to indicate that the synthetic histories of soluble organics in meteorites may have been diverse even within groups of compounds with very similar functional group composition.     

微生物磷脂脂肪酸单体碳同位素示踪碳循环过程

碳循环对于维持地球生命和调控气候变化具有重要意义。微生物是碳循环的关键驱动者之一,微生物群落结构和碳代谢活动的变化,能够影响温室气体的释放和碳储量,并进一步对气候变化产生反馈作用。在当前全球变化和人类活动加剧的背景下,需要进一步了解不同环境中的微生物群落组成和碳代谢活动的特征和响应。磷脂脂肪酸（PLFA）因其快速的周转速率和多样的分子结构,已经被广泛用于原位识别不同环境中活体微生物的生物量和群落结构。在此基础上,PLFA的单体碳同位素组成进一步指示了微生物利用哪些碳源,以及通过何种方式同化这些碳源,从而揭示微生物介导的碳流通和碳循环过程。本文综述了PLFA单体稳定碳同位素组成（δ¹³C）和放射性碳同位素组成（Δ¹⁴C）在示踪微生物碳循环过程中的应用。对比了农田、草地、森林、湿地以及海洋沉积物中活体微生物的碳源利用和碳同化途径的差异,这些差异可能与不同微生物对碳源的偏好以及不同环境中底物碳的可用性有关。对比了岩石、地下水、表层和深层土壤环境中微生物对化石碳源和年轻碳源的差异利用,化石碳是岩石和地下水环境中活体微生物碳源的重要组成部分,表明现代活体微生物可以直接利用部分老碳;相反,表层和深层土壤微生物倾向于利用现代碳源,这些碳源可能来自根系分泌物和从表面垂直输送的溶解有机碳。随着加速器质谱和单个化合物制备技术的进一步发展,预计PLFA单体放射性碳同位素将在微生物碳循环过程中发挥更重要的作用,值得在不同环境中进一步探索。

     

Biogenic processes in crystalline bedrock fractures indicated by carbon isotope signatures of secondary calcite

Variation in ¹³C/¹²C-isotope ratios of fracture filling calcite was analyzed in situ to investigate carbon sources and cycling in fractured bedrock. The study was conducted by separating sections of fracture fillings, and analyzing the ¹³C/¹²C-ratios with secondary ion mass spectrometry (SIMS). Specifically, the study was aimed at fillings where previously published sulfur isotope data indicated the occurrence of bacterial sulfate reduction. The results showed that the δ¹³C values of calcite were highly variable, ranging from −53.8‰ to +31.6‰ (VPDB). The analysis also showed high variations within single fillings of up to 39‰. The analyzed calcite fillings were mostly associated with two calcite groups, of which Group 3 represents possible Paleozoic fluid circulation, based on comparison with similar dated coatings within the Baltic Shield and the succeeding Group 1–2 fillings represent late-stage, low temperature mineralization and are possibly late Paleozoic to Quaternary in age. Both generations were associated with pyrite with δ³⁴S values indicative of bacterial sulfate reduction. The δ¹³C values of calcite, however, were indicative of geochemical environments which were distinct for these generations. The δ¹³C values of Group 3 calcite varied from −22.1‰ to +11‰, with a distinct peak at −16‰ to −12‰. Furthermore, there were no observable depth dependent trends in the δ¹³C values of Group 3 calcite. The δ¹³C values of Group 3 calcite were indicative of organic matter degradation and methanogenesis. In contrast to the Group 3 fillings, the δ¹³C values of Group 1–2 calcite were highly variable, ranging from −53.8‰ to +31.6‰ and they showed systematic variation with depth. The near surface environment of <30 m (bsl) was characterized by δ¹³C values indicative of degradation of surface derived organic matter, with δ¹³C values ranging from −30.3‰ to −5.5‰. The intermediate depth of 34–54 m showed evidence of localized methanotrophic activity seen as anomalously ¹³C depleted calcite, having δ¹³C values as low as −53.8‰. At depths of ∼60–400 m, positive δ¹³C values of up to +31.6‰ in late-stage calcite of Group 1–2 indicated methanogenesis. In comparison, high CH₄ concentrations in present day groundwaters are found at depths of >300 m. One sample at a depth of 111 m showed a transition from methanogenetic conditions (calcite bearing methanogenetic signature) to sulfate reducing (precipitation of pyrite on calcite surface), however, the timing of this transition is so far unclear. The results from this study gives indications of the complex nature of sulfur and carbon cycling in fractured crystalline environments and highlights the usefulness of in situ stable isotope analysis.     

Ab initio study of the high-pressure behavior of CaSiO3 perovskite

Using density functional simulations, within the generalized gradient approximation and projector-augmented wave method, we study structures and energetics of CaSiO₃ perovskite in the pressure range of the Earths lower mantle (0–150 GPa). At zero Kelvin temperature the cubic CaSiO₃ perovskite structure is unstable in the whole pressure range, at low pressures the orthorhombic (Pnam) structure is preferred. At 14.2 GPa there is a phase transition to the tetragonal (I4/mcm) phase. The CaIrO₃-type structure is not stable for CaSiO₃. Our results also rule out the possibility of decomposition into oxides.

Diagnostic lipid biomarker and stable carbon isotope signatures of microbial communities mediating the anaerobic oxidation of methane with sulphate

The anaerobic oxidation of methane (AOM) with sulphate is the most important sink for methane in marine environments. This process is mediated by a consortium of methanotrophic archaea and sulphate reducing bacteria. So far, three groups of anaerobic methane oxidisers (ANME-1, -2 and -3) related to the methanogenic Methanosarcinales and Methanomicrobiales were discovered. The sulphate reducing partner of ANME-1 and -2 are two different eco-types of SRB related to the Desulfosarcina/Desulfococcus cluster (Seep-SRB1), whereas ANME-3 is associated with Desulfobulbus spp. (DBB). In this article, we reviewed literature data to assign statistically significant lipid biomarker signatures for a chemotaxonomic identification of the three known AOM communities. The lipid signatures of ANME-2/Seep-SRB1 and ANME-3/DBB are intriguingly similar, whereas ANME-1/Seep-SRB1 shows substantial differences to these AOM communities. ANME-1 can be distinguished from ANME-2 and -3 by a low ratio of the isoprenoidal dialkyl glycerol diethers sn2-hydroxyarchaeol and archaeol combined with a comparably low stable carbon isotope difference of archaeol relative to the source methane. Furthermore, only ANME-1 contains substantial amounts of isoprenoidal glycerol dialkyl glycerol tetraethers (GDGTs), however, with the probable exception of the ANME-2c sub-cluster. In contrast to the ANME-1 archaea, the tail to tail linked hydrocarbon tetramethylhexadecane (crocetane) is unique to ANME-2, whereas pentamethylicosenes (PMIs) with 4 and 5 double bonds without any higher saturated homologues were only found in ANME-3. The sulphate reducing partner of ANME-1 can be discerned from those of ANME-2 and -3 by a low ratio of the fatty acids (FAs) C_16:1ω5 relative to i-C_15:0 and, although to a lesser degree, by a high abundance of ai-C_15:0 relative to i-C_15:0. Furthermore, substantial amounts of ¹³C depleted non-isoprenoidal monoalkyl glycerol ethers (MAGEs) were only found in the sulphate reducing partners of ANME-2 and -3. A differentiation of these SRB is possible based on the characteristic presence of the FAs cy-C_17:0ω5,6 and C_17:1ω6, respectively. Generally, the data analysed here show overlaps between the different AOM communities, which highlights the need to use multiple lipid signatures for a robust identification of the dominating microbes involved.     

Ab initio thermochemistry of some geochemically relevant molecules in the system Cr-O-H-Cl

A complete theoretical model chemistry algorithm (TMCA) for the prediction of thermodynamic properties of geochemically relevant gaseous and aqueous complexes, based on molecular quantum mechanics, is presented and discussed. Cr species are selected as a case study due to the high nuclear mass and the complex electronic structure of this transition metal. The various derived magnitudes are internally consistent and sufficiently accurate to warrant comparison with the existing (and often conflictual) experimental data and literature estimates. The TMCA is based on density functional theory (DFT) B3LYP/6-31G(d,p) gas phase computations followed by computation of solvation effects by the integral polarized continuum model approach at HF/STO-3G level. Energy corrections due to relativistic effects and electron-electron correlation are accounted for by a newly developed periodic function based on computed ionization potentials and electron affinity of the central metal. Electrostatic entropy contributions to the bulk solvation entropy are accounted for by a Born-model equation based on the electrostatic component of the Integral Equation Formalism—Polarized Continuum Model (IEFPCM) coupling work. As an ancillary result, the TMCA model confirms the validity of the absolute solvation energy terms of the aqueous proton. The TMCA model is of general validity and could be eventually adopted as a standard procedure in the ab initio assessment of gas-phase and aqueous-phase energetics of geochemically relevant species.     

Ab initio investigation into the elasticity of ultrahigh-pressure phases of SiO2

In this study, we report the elastic properties of three ultrahigh-pressure phases of SiO₂: pyrite, cotunnite and Fe₂P types between 300 and 1,500 GPa calculated by means of the density functional ab initio method. It is generally thought that materials tend to be more compact and isotropic with increasing pressure. These three ultrahigh-pressure phases of silica are mechanically stable in the investigated pressure range according to the Born criteria, while the cotunnite and Fe₂P types are unstable at lower pressure. The elastic azimuthal anisotropy of these ultrahigh-pressure phases of silica shows that all the structures counterintuitively have considerable anisotropies even at multimegabar pressures. Among the three investigated structures, the cotunnite type of SiO₂ is the most elastically anisotropic phase due to a soft compression along the b axis combined with a large distortion of the polyhedrons that make the structure. This might also be related to its thermodynamic unfavorability compared to the Fe₂P type under extreme pressure condition. The bond property analyses clearly show that the Si–O bond remains an ionic-covalent mixed bond even at multimegabar pressures with an invariable ionicity with pressure. This argument can explain the monotonously pressure dependence of the elastic anisotropy in the case of pyrite, while the changes in the velocity distribution patterns out of the thermodynamic instability range largely contribute to those of the cotunnite and Fe₂P types.     

Intercolony variability of skeletal oxygen and carbon isotope signatures of cultured Porites corals: Temperature-controlled experiments

The skeletal oxygen isotope ratio of Porites corals is the most frequently used proxy of past seawater temperature and composition for tropical and subtropical oceans. However, field calibration of the proxy signals is often difficult owing to the dual dependence of skeletal oxygen isotope ratio on temperature and the oxygen isotope composition of water. We conducted tank experiments in which we grew Porites spp. colonies for 142 d in thermostated seawater at five temperature settings between 21°C and 29°C under moderate light intensity of 250 μmol m⁻² s⁻¹ with a 12:12 light:dark photoperiod. A skeletal isotope microprofiling technique applied along the major growth axis of each colony revealed that the oxygen isotope ratios of newly deposited skeleton in most colonies remained almost constant during tank incubation, thus providing an ideal situation for precise calibration of oxygen isotope ratio proxy signals. However, the oxygen isotope ratios displayed an unusually large intercolony variability (∼1‰) at each temperature setting although the mean slope (∼0.15‰ °C⁻¹) obtained for the temperature-skeletal oxygen isotope ratio relationship was close to previous results. The intercolony variations in the oxygen isotope ratios were apparently caused by kinetic isotope effects related to variations in the skeletal growth rate rather than by species-specific variability or genetic differences within species. No correlation was found between skeletal carbon isotope ratios and temperature. The carbon isotope ratios showed significantly inverse correlation with linear growth rates, suggesting a kinetic isotope control at low growth rates. Observed intercolony variability in skeletal carbon isotope ratios (∼5‰) can be partly attributed to growth-rate-related kinetic isotope effects.     

Ab initio studies of structural instabilities in magnesium silicate perovskite

Density-functional simulations are used to calculate structural properties and high-symmetry phonons of the hypothetical cubic phase, the stable orthorhombic phase and an intermediate tetragonal phase of magnesium silicate perovskite. We show that the structure of the stable phase is well described by freezing a small number of phonons into the cubic phase. We use the frequencies of these modes to estimate transition temperatures for cubic → tetragonal and tetragonal → orthorhombic phase transitions. Unstable modes are investigated further to find that the coupling with the strain suggests that phonons give a better representation than rigid unit modes. The phonons of an intermediate tetragonal phase were found to be stable except for two rotational modes. The eigenvectors of the most unstable mode of each of the cubic and tetragonal phases account for all the positional parameters of the orthorhombic phase. The phase boundary for the orthorhombic-tetragonal transition intersects possible mantle geotherms, suggesting that the tetragonal phase may be present in the lower mantle.     

Ab initio calculation of interatomic force constants in H6Si2O7 and the bulk modulus of α quartz and α cristobalite

Ab initio force constants calculated for Si-O stretch and Si...Si non-bonded interactions in H₆Si₂O₇ are found comparable with experimental values derived from the lattice dynamics of α quartz. The bulk moduli of α quartz and α cristobalite are calculated using the molecular Si...Si force constant and assuming rigid regular SiO₄ tetrahedra. In the case (α quartz) where data are available the calculation agrees well with experiment.     

Stable isotope mass fragmentography: identification and hydrogen-deuterium exchange studies of eight Murchison meteorite amino acids

The concentration of eight protein amino acids found in extracts of the Murchison carbonaceous chondrite has been measured by quadrupole mass fragmentography. This result was obtained by using deuterated amino acids as internal standards. In addition, hydrogendeuterium exchange in amino acids was studied by two methods. First, nondeuterated amino acids were added to the meteorite and the amount of deuterium incorporated after extraction with deuterium oxide was determined. Second, deuterated amino acids were added to the dry meteorite and the loss of deuterium after extraction with H₂O was measured. It was observed that the degree of hydrogen-deuterium exchange increased with increasing severity of extraction conditions. This exchange resulted in some racemization, presumably catalyzed by constituents of the meteorite. The degree of racemization for each amino acid was determined by gas chromatography of the corresponding N-trifluoroacetyl-O-( + )-2-butyl esters.     

Lead isotope signatures of Holocene fluvial sediments from the Loire River valley

The distribution of Mn, V, Th, Pb and isotopes of Pb in the labile fraction of sediments from a channel infill in the Middle Loire alluvial plain are used to highlight some aspects of the basin evolution over the period from 0 to 10 ka BP. The acid extractable matter (AEM) in the sediment samples is variable in amount and in trace element contents. Iron-Mn oxyhydroxides are the principle trace element carrying phase in the labile fraction and carbonates are a secondary carrier. Vanadium and Pb originate from the weathering of silicates and are used as a silicate erosion rate index in the fluviatile record. Most of the AEM data plot along a general trend between 3 endmembers (basalts, Cretaceous carbonate rocks and granites) in the relationship between ²⁰⁷Pb/²⁰⁶Pb and ²⁰⁶Pb/²⁰⁶Pb. These endmembers have been mixed in various proportions depending on natural Holocene inputs (erosion, volcanic events) or human influences (mining and smelting of ore).     

Ab initio study of MgSiO3 C2/c enstatite

We have used a newly developed ab initio constant-pressure molecular dynamics with variable cell shape technique to investigate the zero temperature behaviour of high pressure clinoenstatite (MgSiO₃-C2/c) from 0 up to 30 GPa. The optimum structure at 8 GPa, as well as structural trends under pressure, compare very well with experimental data. At this pressure, we find noticeable “fluctuations” in the chain configuration which suggests the structure is on the verge of a mechanical instability. Two distinct compressive behaviours then appear: one below and another above 8 GPa. This phenomenon may be related to the observed transition to a lower symmetry P2₁/c phase which involves a reconfiguration of the silicate chains, and suggests that the C2/c structure at low pressures found here, may be an artifact of the dynamical algorithm which preserves space group in the absence of symmetry breaking fluctuations. Comparison with calculations in other magnesium silicate phases, indicates that the size and shape of the silicate units (isolated and/or linked tetrahedra and octahedra) are generally well described by the local density approximation; however, the weaker linkages provided by the O-Mg-O bonds, are not as well described. This trend suggests that, as in the recently studied case of H₂O-ice, the structural properties of more inhomogeneous systems, like enstatite, may be improved by using gradientcorrected density functionals.     

Geodynamic impact on the stable isotope signatures in a shallow epicontinental sea

Analyses were made of a mollusc‐based meta dataset of 859 δ¹³C and δ¹⁸O data of Miocene nearshore settings in the European Paratethys Sea and its descendant Lake Pannon. The observed trends document a strong tie to geodynamics, which are largely decoupled from Miocene open ocean isotope curves. Semi‐ to fully enclosed, initially marine water bodies such as the Paratethys Sea are prone to switching seawater isotope signatures because they respond rapidly to changes in the evaporation/precipitation ratio. Two phases of positive deviations of oxygen isotope values of water (relative to the modern ocean value, SMOW) occurred during the Middle Miocene; both were initiated by tectonic constrictions of the seaways and became amplified by global warming and regionally decreasing precipitation. With the final disintegration of the Paratethys, the marine isotope signatures vanish. Instead, the observed isotope trends suggest a comparably simple system of an alkaline lake with steadily declining salinity. The ‘ocean‐derived’ Paratethys Sea may thus act as a key for understanding isotope trends in epicontinental seas.     

西藏西南部休古嘎布蛇绿岩的Sm-Nd年龄及Nd-Sr-Pb同位素特征

休古嘎布蛇绿岩位于雅鲁藏布江蛇绿岩带西段,属于SSZ型蛇绿岩。用Sm-Nd法测定了该蛇绿岩中辉长辉绿岩的结晶年龄,辉石、斜长石和两个全岩样品的等时线年龄为(126.2±9.1)Ma,代表新特提斯洋在该区俯冲消减的时限。同时,对辉长辉绿岩的Nd-Sr-Pb同位素的测定结果表明,辉长辉绿岩的初始εNd(t)值高(6.7～9.1),反映原始岩浆起源于强烈亏损的地幔源区,未受大陆地壳物质的混染;初始206Pb/204Pb比值较低(17.412～17.523),但初始208Pb/204Pb比值较高(37.352～37.706),并具有较高的ISr值(0.70278～0.70383),指示休古嘎布蛇绿岩源于印度洋MORB型地幔域。     

Ab initio calculation of H, O, Al and Si NMR parameters, vibrational frequencies and bonding energetics in hydrous silica and Na-aluminosilicate glasses

Ab initio, molecular orbital (MO) calculations were performed on model systems of SiO₂, NaAlSi₃O₈ (albite), H₂O-SiO₂ and H₂O-NaAlSi₃O₈ glasses. Model nuclear magnetic resonance (NMR) isotropic chemical shifts (δ_iso) for ¹H, ¹⁷O, ²⁷Al and ²⁹Si are consistent with experimental data for the SiO₂, NaAlSi₃O₈, H₂O-SiO₂ systems where structural interpretations of the NMR peak assignments are accepted. For H₂O-NaSi₃AlO₈ glass, controversy has surrounded the interpretation of NMR and infrared (IR) spectra. Calculated δ_iso¹H, δ_iso¹⁷O, δ_iso²⁷Al and δ_iso²⁹Si are consistent with the interpretation of Kohn et al. (1992) that Si-(OH)-Al linkages are responsible for the observed peaks in hydrous Na-aluminosilicate glasses. In addition, a theoretical vibrational frequency associated with the Kohn et al. (1992) model agrees well with the observed shoulder near 900 cm⁻¹ in the IR and Raman spectra of hydrous albite glasses. MO calculations suggest that breaking this Si-(OH)-Al linkage requires ∼+56 to +82 kJ/mol which is comparable to the activation energies for viscous flow in hydrous aluminosilicate melts.     

Lead isotope signatures of epithermal and porphyry-type ore deposits from the Romanian Carpathian Mountains

Lead isotope analyses have been performed on the two major Miocene mining districts of Romania, Baia Mare and Apuseni Mountains. These two districts have different non-overlapping ²⁰⁶Pb/²⁰⁴Pb isotopic signatures ranging from 18.752 to 18.876 and 18.497 to 18.740. In the Baia Mare district, epithermal deposits are overall homogeneous in their lead isotopic compositions and have values similar to the average of the calc-alkaline volcanic rocks. These results suggest a magmatic signature for the Pb (and possibly other metals) in the hydrothermal fluids. However, magmas in this district show isotopic evidence of crustal assimilation. In the southern Apuseni Mountains, the lead isotope compositions of sulfide minerals in porphyry copper deposits are clustered, confirming that Pb, and probably other metals, were derived principally from associated porphyry stocks. On the other hand, lead isotope data on sulfides in epithermal ore deposits are much more scattered, indicating a notable contribution of Pb from local country rocks. In the Apuseni Mountains, 'fertile' volcanics are few and appear to come from a more primitive mantle-derived source. Most of the analysed volcanic rocks seem 'barren'. Differences in lead isotopic compositions between the Baia Mare district and the Apuseni Mountains are due to a different basement, and probably to variations in crustal assimilation superimposed on variations in the mantle source composition. In the Apuseni Mountains, Pb may be partly inherited from the previous Mesozoic magmatic-hydrothermal stage. From a geodynamic point of view, it seems that the nature and the source of volcanic rocks and their position related to the collision area of the Carpathian arc are not the only factors controlling the 'fertility' of a volcanic district.