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1.
Carboxyl groups are abundant in natural organic molecules (NOM) and play a major role in their reactivity. The structural environments of carboxyl groups in IHSS soil and river humic samples were investigated using 2D NMR (heteronuclear and homonuclear correlation) spectroscopy. Based on the 1H-13C heteronuclear multiple-bond correlation (HMBC) spectroscopy results, the carboxyl environments in NOM were categorized as Type I (unsubstituted and alkyl-substituted aliphatic/alicyclic), Type II (functionalized carbon substituted), Type IIIa, b (heteroatom and olefin substituted), and Type IVa, b (5-membered heterocyclic aromatic and 6-membered aromatic). The most intense signal in the HMBC spectra comes from the Type I carboxyl groups, including the 2JCH and 3JCH couplings of unsubstituted aliphatic and alicyclic acids, though this spectral region also includes the 3JCH couplings of Type II and III structures. Type II and III carboxyls have small but detectable 2JCH correlations in all NOM samples except for the Suwannee River humic acid. Signals from carboxyls bonded to 5-membered aromatic heterocyclic fragments (Type IVa) are observed in the soil HA and Suwannee River FA, while correlations to 6-membered aromatics (Type IVb) are only observed in Suwannee River HA. In general, aromatic carboxylic acids may be present at concentrations lower than previously imagined in these samples. Vibrational spectroscopy results for these NOM samples, described in an accompanying paper [Hay M. B. and Myneni S. C. B. (2007) Structural environments of carboxyl groups in natural organic molecules from terrestrial systems. Part 1: Infrared spectroscopy. Geochim. Cosmochim. Acta (in press)], suggest that Type II and Type III carboxylic acids with α substituents (e.g., -OH, -OR, or -CO2H) constitute the majority of carboxyl structures in all humic substances examined. Furoic and salicylic acid structures (Type IV) are also feasible fragments, albeit as minor constituents. The vibrational spectroscopy results also suggest that much of the “Type I” signal observed in the HMBC spectrum is due to carboxylic acid esters and possibly α-substituted alicyclic acids.  相似文献   

2.
Copper biogeochemistry is largely controlled by its bonding to natural organic matter (NOM) for reasons not well understood. Using XANES and EXAFS spectroscopy, along with supporting thermodynamic equilibrium calculations and structural and steric considerations, we show evidence at pH 4.5 and 5.5 for a five-membered Cu(malate)2-like ring chelate at 100-300 ppm Cu concentration, and a six-membered Cu(malonate))1-2-like ring chelate at higher concentration. A “structure fingerprint” is defined for the 5.0-7.0 Å−1 EXAFS region which is indicative of the ring size and number (i.e., mono- vs. bis-chelate), and the distance and bonding of axial oxygens (Oax) perpendicular to the chelate plane formed by the four equatorial oxygens (Oeq) at 1.94 Å. The stronger malate-type chelate is a C4 dicarboxylate, and the weaker malonate-type chelate a C3 dicarboxylate. The malate-type chelate owes its superior binding strength to an -OH for -H substitution on the α carbon, thus offering additional binding possibilities. The two new model structures are consistent with the majority of carboxyl groups being clustered and α-OH substitutions common in NOM, as shown by recent infrared and NMR studies. The high affinity of NOM for Cu(II) is explained by the abundance and geometrical fit of the two types of structures to the size of the equatorial plane of Cu(II). The weaker binding abilities of functionalized aromatic rings also is explained, as malate-type and malonate-type structures are present only on aliphatic chains. For example, salicylate is a monocarboxylate which forms an unfavorable six-membered chelate, because the OH substitution is in the β position. Similarly, phthalate is a dicarboxylate forming a highly strained seven-membered chelate.Five-membered Cu(II) chelates can be anchored by a thiol α-SH substituent instead of an alcohol α-OH, as in thio-carboxylic acids. This type of chelate is seldom present in NOM, but forms rapidly when Cu(II) is photoreduced to Cu(I) at room temperature under the X-ray beam. When the sample is wet, exposure to the beam can reduce Cu(II) to Cu(0). Chelates with an α-amino substituent were not detected, suggesting that malate-like α-OH dicarboxylates are stronger ligands than amino acids at acidic pH, in agreement with the strong electronegativity of the COOH clusters. However, aminocarboxylate Cu(II) chelates may form after saturation of the strongest sites or at circumneutral pH, and could be observed in NOM fractions enriched in proteinaceous material. Overall, our results support the following propositions:
(1)
The most stable Cu-NOM chelates at acidic pH are formed with closely-spaced carboxyl groups and hydroxyl donors in the α-position; oxalate-type ring chelates are not observed.
(2)
Cu(II) bonds the four equatorial oxygens to the heuristic distance of 1.94 ± 0.01 Å, compared to 1.97 Å in water. This shortening increases the ligand field strength, and hence the covalency of the Cu-Oeq bond and stability of the chelate.
(3)
The chelate is further stabilized by the bonding of axial oxygens with intra- or inter-molecular carboxyl groups.
(4)
Steric hindrances in NOM are the main reason for the absence of Cu-Cu interactions, which otherwise are common in carboxylate coordination complexes.
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3.
Interaction of dissolved aqueous species with natural organic matter (NOM) is thought to be important in sequestering some species and enhancing the transport of others, but little is known about these interactions on a molecular scale. This paper describes a combined experimental 133Cs and 35Cl nuclear magnetic resonance (NMR) and computational molecular dynamics (MD) modeling study of the interaction of Cs+ and Cl− with Suwannee River NOM. The results provide a detailed picture of the molecular-scale structure and dynamics of these interactions. Individual NOM molecules are typically hundreds to thousands of Daltons in weight, and on the molecular scale their interaction with small dissolved species can be investigated in ways similar to those used to study the interaction of dissolved aqueous species with mineral surfaces. As for such surface interactions, understanding both the structural environments and the dynamics over a wide range of frequencies is essential. The NMR results show that Cs+ is associated with NOM at pH values from 3.4 ± 0.5 (unbuffered Suwannee River NOM solution) to 9.0 ± 0.5. The extent of interaction increases with decreasing CsCl concentration at constant pH. It also decreases with increasing pH at constant CsCl concentration due to pH-dependent negative structural charge development on the NOM caused by progressive deprotonation of carboxylic and phenolic groups. The presence of NOM has little effect on the 133Cs chemical shifts, demonstrating that its local coordination environment does not change significantly due to interaction with the NOM. Narrow, solution-like line widths indicate rapid exchange of Cs+ between the NOM and bulk solution at frequencies of >102 Hz. The MD simulations support these results and show that Cs+ is associated with the NOM principally as outer sphere complexes and that this interaction does not reduce the Cs+ diffusion coefficient sufficiently to cause NMR line broadening. The 35Cl NMR data and the MD results are consistent in demonstrating that there is no significant complexation between Cl− and NOM in the pH range investigated, consistent with negative structural charge on the NOM.  相似文献   

4.
The Nuclear Waste Management Organization (NWMO) is developing a Deep Geological Repository (DGR) to contain and isolate used nuclear fuel in a suitable rock formation at a depth of approximately 500 m. The design concept employs a multibarrier system, including the use of copper-coated used fuel containers, surrounded by a low-permeability, swelling clay buffer material within a low permeability, stable host rock environment. The natural organic matter (NOM) composition of the bentonite clays being considered for the buffer material is largely uncharacterized at the molecular-level. To gain a better understanding of the NOM in target clays from Wyoming and Saskatchewan, molecular-level methods (biomarker analysis, solid-state 13C NMR and solution-state 1H nuclear magnetic resonance (NMR)) were used to elucidate the structure and sources of NOM. Organic carbon content in three commercially available bentonites analyzed was low (0.11–0.41%). The aliphatic lipid distribution of the clay samples analyzed showed a predominance of higher concentration of lipids from vascular plants and low concentrations of lipids consistent with microbial origin. The lignin phenol vanillyl acid to aldehyde ratio (Ad/Al) for the National sample indicated an advanced state of lignin oxidation and NOM diagenesis. The 13C NMR spectra were dominated by signals in the aromatic and aliphatic regions. The ratio of alkyl/O-alkyl carbon ranged from 7.6 to 9.7, indicating that the NOM has undergone advanced diagenetic alteration. The absence lignin-derived phenols commonly observed in CuO oxidation extracts from contemporary soils and sediments as well as the lack of amino acids suggests that the material corresponding to the aromatic signal is not composed of lignin or proteins but may be derived from another source such as black carbon or some other non-extractable aromatic-rich NOM. The aliphatic signal appears to correspond to long-chain compounds with little side branching based on the results of the one-dimensional (1D) and two-dimensional (2D) solution-state 1H NMR analyses. Overall, the organic geochemical analyses suggest that the NOM is composed mainly of plant-derived waxes and highly aromatic carbon with low contributions from small molecules. The compounds identified by the molecular-level analysis of NOM in the clay samples are hypothesized to be recalcitrant but future studies should examine if these compounds may serve as a microbial substrate to further test the observations of this study. Furthermore, our study suggests that the NOM has undergone diagenesis and that marine NOM signatures are no longer recognizable or detectable. As such, future work may also examine the diagenesis of these deposits to further understand the NOM geochemistry and paleoenvironmental conditions in bentonite deposits.  相似文献   

5.
With a half-life of 15.7 Ma, a high mobility and the potential to accumulate in the biosphere, 129I is considered, in safety assessment calculations for radioactive waste repositories, to be one of the main contributors to the radiological dose. Several authors have reported that, at low concentration, I− is weakly retained on argillaceous rocks. This process is not yet well-understood and different hypotheses have been put forward as to whether reactive phases or experimental artifacts (e.g. pyrite oxidation) could be the reason for the retention of I− observed at low concentration. The aim of this study was to investigate the effect on I− mobility of (i) the redox conditions and (ii) the amount of pyrite and natural organic matter (NOM) contents of the rock. These questions were addressed by performing batch sorption, through-diffusion and out-diffusion experiments on rock samples of Toarcian argillaceous rock from Tournemire (Aveyron, France). One of the challenges faced during this study was to distinguish actual transport properties from experimental artifacts. A especially elaborate experimental set-up allowed limiting the (i) oxidation of both argillaceous rock and I−, and (ii) carbonate precipitation. A comparison of the batch sorption results obtained for two Toarcian clay specimens, that differed in their amount of pyrite and NOM, allowed relating I− sorption to pyrite oxidation. However, no evidence was found to associate the I− behavior to the NOM amounts. While the through-diffusion experiments showed a very slight sorption (distribution ratio (Rd) = 0.016 mL g−1) for the lowest I− concentration under oxic conditions, the out-diffusion tests performed after the through-diffusion experiments on the same cells showed significant sorption under both oxic and anoxic conditions, resulting in Rd ranging from 0.02 mL g−1 to 1.25 mL g−1. The range of Rd values was higher for the upstream reservoir under oxic conditions. The discrepancies observed between the through-diffusion and the out-diffusion experiments suggest a kinetic control of the I− uptake by argillaceous rocks under oxic and anoxic conditions.  相似文献   

6.
Cadmium (Cd) is a toxic trace element and due to human activities soils and waters are contaminated by Cd both on a local and global scale. It is widely accepted that chemical interactions with functional groups of natural organic matter (NOM) is vital for the bioavailability and mobility of trace elements. In this study the binding strength of cadmium (Cd) to soil organic matter (SOM) was determined in an organic (49% organic C) soil as a function of reaction time, pH and Cd concentration. In experiments conducted at native Cd concentrations in soil (0.23 μg g−1 dry soil), halides (Cl, Br) were used as competing ligands to functional groups in SOM. The concentration of Cd in the aqueous phase was determined by isotope-dilution (ID) inductively-coupled-plasma-mass-spectrometry (ICP-MS), and the activity of Cd2+ was calculated from the well-established Cd-halide constants. At higher Cd loading (500-54,000 μg g−1), the Cd2+ activity was directly determined by an ion-selective electrode (ISE). On the basis of results from extended X-ray absorption fine structure (EXAFS) spectroscopy, a model with one thiolate group (RS−) was used to describe the complexation (Cd2+ + RS− ? CdSR+; log KCdSR) at native Cd concentrations. The concentration of thiols (RSH; 0.047 mol kg−1 C) was independently determined by X-ray absorption near-edge structure (XANES) spectroscopy. Log KCdSR values of 11.2-11.6 (pKa for RSH = 9.96), determined in the pH range 3.1-4.6, compare favorably with stability constants for the association between Cd and well-defined thiolates like glutathione. In the concentration range 500-54,000 μg Cd g−1, a model consisting of one thiolate and one carboxylate (RCOO−) gave the best fit to data, indicating an increasing role for RCOOH groups as RSH groups become saturated. The determined log KCdOOCR of 3.2 (Cd2+ +  RCOO− ? CdOOCR+; log KCdOOCR; pKa for RCOOH = 4.5) is in accordance with stability constants determined for the association between Cd and well-defined carboxylates. Given a concentration of reduced sulfur groups of 0.2% or higher in NOM, we conclude that the complexation to organic RSH groups may control the speciation of Cd in soils, and most likely also in surface waters, with a total concentration less than 5 mg Cd g−1 organic C.  相似文献   

7.
Information on the particle size and reactive surface area of natural samples and its interaction with natural organic matter (NOM) is essential for the understanding bioavailability, toxicity, and transport of elements in the natural environment. In part I of this series (Hiemstra et al., 2010), a method is presented that allows the determination of the effective reactive surface area (A, m2/g soil) of the oxide particles of natural samples which uses a native probe ion (phosphate) and a model oxide (goethite) as proxy. In soils, the natural oxide particles are generally embedded in a matrix of natural organic matter (NOM) and this will affect the ion binding properties of the oxide fraction. A remarkably high variation in the natural phosphate loading of the oxide surfaces (Γ, μmol/m2) is observed in our soils and the present paper shows that it is due to surface complexation of NOM, acting as a competitor via site competition and electrostatic interaction. The competitive interaction of NOM can be described with the charge distribution (CD) model by defining a ≡NOM surface species. The interfacial charge distribution of this ≡NOM surface species can be rationalized based on calculations done with an evolved surface complexation model, known as the ligand and charge distribution (LCD) model. An adequate choice is the presence of a charge of −1 v.u. at the 1-plane and −0.5 v.u. at the 2-plane of the electrical double layer used (Extended Stern layer model).The effective interfacial NOM adsorption can be quantified by comparing the experimental phosphate concentration, measured under standardized field conditions (e.g. 0.01 M CaCl2), with a prediction that uses the experimentally derived surface area (A) and the reversibly bound phosphate loading (Γ, μmol/m2) of the sample (part I) as input in the CD model. Ignoring the competitive action of adsorbed NOM leads to a severe under-prediction of the phosphate concentration by a factor ∼10 to 1000. The calculated effective loading of NOM is low at a high phosphate loading (Γ) and vice versa, showing the mutual competition of both constituents. Both constituents in combination usually dominate the surface loading of natural oxide fraction of samples and form the backbone in modeling the fate of other (minor) ions in the natural environment.Empirically, the effective NOM adsorption is found to correlate well to the organic carbon content (OC) of the samples. The effective NOM adsorption can also be linked to DOC. For this, a Non-Ideal Competitive adsorption (NICA) model is used. DOC is found to be a major explaining factor for the interfacial loading of NOM as well as phosphate. The empirical NOM-OC relation or the parameterized NICA model can be used as an alternative for estimating the effective NOM adsorption to be implemented in the CD model for calculation of the surface complexation of field samples. The biogeochemical impact of the NOM-PO4 interaction is discussed.  相似文献   

8.
The hexa-aqua complexes [Fe(H2O)6−m−n(OH)n](2−n)+n = 0 → 3, m = 0 → 6 − n; [Fe(H2O)6−m−n(OH)n](3−n)+n = 0 → 4, m = 0 → 6 − n were investigated by ab-initio methods with the aim of determining their ground-state geometries, total energies and vibrational properties by treating their inner solvation shell as part of their gaseous precursor1 (or “hybrid approach”). After a gas-phase energy optimization within the Density Functional Theory (DFT), the molecules were surrounded by a dielectric representing the Reaction Field through an implicit Polarized Continuum Model (PCM). The exploration of several structural ligand arrangements allowed us to quantify the relative stabilities of the various ionic species and the role of the various forms of energy (solute-solvent electronic interaction, cavitation, dispersion, repulsion, liberation free energy) that contribute to stabilize the aqueous complexes. A comparison with experimental thermochemistries showed that ab-initio gas-phase + solvation energies are quite consistent with experimental evidence and allow the depiction of the most stable form in solution and the eventual configurational disorder of water/hydroxyl species around central cations. A vibrational analysis performed on the 54Fe, 56Fe, 57Fe and 58Fe isotopomers indicated important separative effects systematically affected by the extent of deprotonation. The role of the system’s redox state (fO2) and acidity (pH) on the isotopic imprinting of the aqueous species in solution was investigated by coupling the separative effects with speciation calculations. The observed systematics provided a tool of general utility in the interpretation of the iron isotopic signature of natural waters. Applications to the interpretation of isotopic fractionation in solution dictated by redox equilibria and to the significance of the Fe-isotopic imprinting of Banded Iron Formations are given.  相似文献   

9.
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10.
Rates of anaerobic respiration are of central importance for the long-term burial of carbon (C) in peatlands, which are a relevant sink in the global C cycle. To identify constraints on anaerobic peat decomposition, we determined detailed concentration depth profiles of decomposition end-products, i.e. methane (CH4) and dissolved inorganic carbon (DIC), along with concentrations of relevant decomposition intermediates at an ombrotrophic Canadian peat bog. The magnitude of in situ net production rates of DIC and CH4 was estimated by inverse pore-water modeling. Vertical transport in the peat was slow and dominated by diffusion leading to the buildup of DIC and CH4 with depth (5500 μmol L−1 DIC, 500 μmol L−1 CH4). Highest DIC and CH4 production rates occurred close to the water table (decomposition constant kd ∼ 10−3-10−4 a−1) or in some distinct zones at depth (kd ∼ 10−4 a−1). Deeper into the peat, decomposition proceeded very slowly at about kd = 10−7 a−1. This pattern could be related to thermodynamic and transport constraints. The accumulation of metabolic end-products diminished in situ energy yields of acetoclastic methanogenesis to the threshold for microbially mediated processes (−20 to −25 kJ mol−1 CH4). The methanogenic precursor acetate also accumulated (150 μmol L−1). In line with these findings, CH4 was formed by hydrogenotrophic methanogenesis at Gibbs free energies of −35 to −40 kJ mol−1 CH4. This was indicated by an isotopic fractionation αCO2-CH4 of 1.069-1.079. Fermentative degradation of acetate, propionate and butyrate attained Gibbs free energies close to 0 kJ mol−1 substrate. Although methanogenesis was apparently limited by some other factor in some peat layers, transport and thermodynamic constraints likely impeded respiratory processes in the deeper peat. Constraints on the removal of DIC and CH4 may thus slow decomposition and contribute to the sustained burial of C in northern peatlands.  相似文献   

11.
IR spectroscopy is one of the few techniques that can directly probe water molecules in rocks. This method has been used to characterize the mineralogy of hydrated/hydrous carbonaceous chondrites, and to link known meteorite families with spectroscopic observations of low albedo asteroids. In this paper, we present measurements of the infrared transmission spectra of matrix chunks from 3 CI and 9 CM chondrites. Spectra were measured at ambient conditions and then at different temperatures along a dehydration path toward high-T (∼300 °C) under primary vacuum. At ambient conditions, the 3-μm spectral range is always dominated by adsorbed atmospheric water molecules. Upon moderate (∼100 °C) and high (∼300 °C) heating under low pressure (P < 10−4 mbar), adsorbed water and then phyllosilicates interlayer water are removed, revealing a residual absorption band around 3 μm. This band is a characteristic IR feature of the phyllosilicate phases which dominate the mineralogical assemblage of hydrated carbonaceous chondrites. Among the CM chondrites, the high-T spectra reveal a strong variability that appears correlated with the alteration classification scheme of Rubin et al. (2007) and Howard et al. (2009a). The 3-μm band continuously evolves from a broad feature peaking at 3550-3600 cm−1 for the weakly altered CMs (Murchison-type) to a sharp asymmetric peak at ∼3675 cm−1 for the more extensively altered samples (Cold Bokkeveld-type). We attribute this spectral evolution to variations in the chemistry of the phyllosilicate phases from Fe-rich to Mg-rich. On the other hand, the 10-μm spectral region shows a single broad peak which does not compare with known terrestrial serpentine spectra, probably due to high structural disorder of the chondrite phyllosilicate phases. The present work clearly shows that previously published reflectance spectra of chondrites are biased by the presence of adsorbed terrestrial water molecules. Laboratory data collected under dry conditions are needed to reinterpret the chondrite-asteroid connection from the comparison of their 3-μm absorption features.  相似文献   

12.
The acid-base properties of 14 standard and reference materials from the International Humic Substances Society (IHSS) were investigated by potentiometric titration. Titrations were conducted in 0.1 M NaCl under a nitrogen atmosphere, averaging 30 min from start to finish. Concentrations of carboxyl groups and phenolic groups were estimated directly from titration curves. Titration data were also fit to a modified Henderson-Hasselbalch model for two classes of proton-binding sites to obtain “best fit” parameters that describe proton-binding curves for the samples. The model was chosen for its simplicity, its ease of implementation in computer spreadsheets, and its excellent ability to describe the shapes of the titration curves. The carboxyl contents of the IHSS samples are in the general order: terrestrial fulvic acids > aquatic fulvic acids > Suwannee River natural organic matter (NOM) > aquatic humic acids > terrestrial humic acids. Overall, fulvic acids and humic acids have similar phenolic contents; however, all of the aquatically derived samples have higher phenolic contents than the terrestrially derived samples. The acid-base properties of reference Suwannee River NOM are surprisingly similar to those of standard Suwannee River humic acid. Results from titrations in this study were compared with other published results from both direct and indirect titrations. Typically, carboxyl contents for the IHSS samples were in agreement with the results from both methods of titration. Phenolic contents for the IHSS samples were comparable to those determined by direct titrations, but were significantly less than estimates of phenolic content that were based on indirect titrations with Ba(OH)2 and Ca(OAc)2. The average phenolic-to-carboxylic ratio of the IHSS samples is approximately 1:4. Models that assume a 1:2 ratio of phenolic-to-carboxylic groups may overestimate the relative contribution of phenolic groups to the acid-base chemistry of humic substances.  相似文献   

13.
Detailed structural information on two humic acids extracted from two sinking particulate matter samples at a water depth of 20 m in the Saguenay Fjord (F-20-HA) and the St. Lawrence Estuary (E-20-HA) (Canada), was obtained by advanced solid-state NMR. Spectral-editing analyses provided numerous structural details rarely reported in geochemical studies. The NMR data account almost quantitatively for the elemental compositions. The two humic acids were found to be quite similar, consisting of four main structural components: peptides (ca. 39 ± 3% vs. 34 ± 3% of all C for E-20-HA and F-20-HA, respectively); aliphatic chains, 14-20 carbons long (ca. 25 ± 5% vs. 17 ± 5% of all C); aromatic structures (ca. 17 ± 2% vs. 26 ± 2% of all C); and sugar rings (14 ± 2% vs. 15 ± 2% of all C). Peptides were identified by 13C{14N} SPIDER NMR, which selects signals of carbons bonded to nitrogen, and by dipolar DEPT, which selects CH-group signals, in particular the NCH band of peptides. The SPIDER spectra also indicate that heterocycles constitute a significant fraction of the aromatic structures. The aliphatic (CH2)n chains, which are highly mobile, contain at least one double bond per two chains and end in methyl groups. 1H spin diffusion NMR experiments showed that these mobile aliphatic chains are in close (<10 nm) proximity to the other structural components. A major bacterial contribution to these two samples could explain why the samples, which have different dominant organic matter sources (terrestrial vs. marine), are similar to each other as well as to degraded algae and particles from other waters. The NMR data suggest structures containing mobile lipids in close proximity to peptides and carbohydrates (e.g., peptidoglycan) as found in bacterial cell walls. Measured yields of muramic acid and d-amino acids confirmed the presence of bacterial cell wall components in the studied samples.  相似文献   

14.
We examined stable carbon isotope fractionation in biosynthesis of fatty acids of a piezophilic bacterium Moritella japonica strain DSK1. The bacterium was grown to stationary phase at pressures of 0.1, 10, 20, and 50 MPa in media prepared using sterile-filtered natural seawater supplied with glucose as the sole carbon source. Strain DSK1 synthesized typical bacterial fatty acids (C14-19 saturated, monounsaturated, and cyclopropane fatty acids) as well as long-chain polyunsaturated fatty acids (PUFA) (20:6ω3). Bacterial cell biomass and individual fatty acids exhibited consistent pressure-dependent carbon isotope fractionations relative to glucose. The observed ΔδFA-glucose (−1.0‰ to −11.9‰) at 0.1 MPa was comparable to or slightly higher than fractionations reported in surface bacteria. However, bulk biomass and fatty acids became more depleted in 13C with pressure. Average carbon isotope fractionation (ΔδFA-glucose) at high pressures was much higher than that for surface bacteria: −15.7‰, −15.3‰, and −18.3‰ at 10, 20, and 50 MPa, respectively. PUFA were more 13C depleted than saturated and monounsaturated fatty acids at all pressures. The observed isotope effects may be ascribed to the kinetics of enzymatic reactions that are affected by hydrostatic pressure and to biosynthetic pathways that are different for short-chain and long-chain fatty acids. A simple quantitative calculation suggests that in situ piezophilic bacterial contribution of polyunsaturated fatty acids to marine sediments is nearly two orders of magnitude higher than that of marine phytoplankton and that the carbon isotope imprint of piezophilic bacteria can override that of surface phytoplankton. Our results have important implications for marine biogeochemistry. Depleted fatty acids reported in marine sediments and the water column may be derived simply from piezophilic bacteria resynthesis of organic matter, not from bacterial utilization of a 13C-depleted carbon source (i.e., methane). The interpretation of carbon isotope signatures of marine lipids must be based on principles derived from piezophilic bacteria.  相似文献   

15.
Recent experimental studies have reported the existence of two new Sb sulfide species, Sb2S52− and Sb2S62−, in alkaline sulfidic solutions in equilibrium with stibnite, Sb2S3, and orthorhombic S. These species contain Sb(V), which has also recently been identified in similar solutions using EXAFS by other researchers. This represents a significant change from the consensus a decade ago that sulfidic solutions of Sb contained only Sb(III) species. I have calculated from first principles of quantum mechanics the energetics for the oxidation of the Sb(III) sulfide dimer Sb2S42− to the mixed Sb(III,V) dimer Sb2S52− and then to the all Sb(V) dimer, Sb2S62−. Gas-phase reaction energies have been evaluated using polarized valence double zeta effective core potential basis sets and Moller-Plesset second order treatments of electron correlation. All translational, rotational and vibrational contributions to the gas-phase reaction free energy have been calculated. Hydration energies have been obtained using the COSMO version of the self-consistent reaction field polarizable continuum method. Negative free energy changes are calculated for the oxidation of the dianion of the III,III dimer to the III,V dimer by both small polysulfides, like S4H−, and elemental S, modeled as S8. For the further oxidation of the III,V dimer to the V,V dimer the reaction free energies are calculated to be close to zero. The partially protonated Sb III,III dimer monoanion HSb2S4− can also be oxidized, but the reaction is not so favorable as for the dianion. Comparison of the calculated aqueous deprotonation energies of H2Sb2S4, H2Sb2S5 and H2Sb2S6 and their dianions with values calculated for various oxyacids indicates that the III,V and V,V dimers will have pKa2 values <5, so that their dianions will be the dominant species in alkaline solutions. These results are thus consistent with the recent identification of Sb2S52− and Sb2S62− species. I have also calculated the Raman spectra of Sb2S52− and Sb2S62− to assist in their identification. The calculated vibrational frequencies of the III,V and V,V dimers are characteristically higher than those of the III,III dimer I previously studied. The III,V dimer may contribute shoulders to the Raman spectrum.  相似文献   

16.
Information on the particle size and reactive surface area of natural samples is essential for the application of surface complexation models (SCM) to predict bioavailability, toxicity, and transport of elements in the natural environment. In addition, this information will be of great help to enlighten views on the formation, stability, and structure of nanoparticle associations of natural organic matter (NOM) and natural oxide particles.Phosphate is proposed as a natively present probe ion to derive the effective reactive surface area of natural samples. In the suggested method, natural samples are equilibrated (?10 days) with 0.5 M NaHCO3 (pH = 8.5) at various solid-solution ratios. This matrix fixes the pH and ionic strength, suppresses the influence of Ca2+ and Mg2+ ions by precipitation these in solid carbonates, and removes NOM due to the addition of activated carbon in excess, collectively leading to the dominance of the PO4-CO3 interaction in the system. The data have been interpreted with the charge distribution (CD) model, calibrated for goethite, and the analysis results in an effective reactive surface area (SA) and a reversibly bound phosphate loading Γ for a series of top soils.The oxidic SA varies between about 3-30 m2/g sample for a large series of representative agricultural top soils. Scaling of our data to the total iron and aluminum oxide content (dithionite-citrate-bicarbonate extractable), results in the specific surface area between about 200-1200 m2/g oxide for most soils, i.e. the oxide particles are nano-sized with an equivalent diameter in the order of ∼1-10 nm if considered as non-porous spheres. For the top soils, the effective surface area and the soil organic carbon fraction are strongly correlated. The oxide particles are embedded in a matrix of organic carbon (OC), equivalent to ∼1.4 ± 0.2 mg OC/m2 oxide for many soils of the collection, forming a NOM-mineral nanoparticle association with an average NOM volume fraction of ∼80%. The average mass density of such a NOM-mineral association is ∼1700 ± 100 kg/m3 (i.e. high-density NOM). The amount of reversibly bound phosphate is rather close to the amount of phosphate that is extractable with oxalate. The phosphate loading varies remarkably (Γ ≈ 1-3 μmol/m2 oxide) in the samples. As discussed in part II of this paper series (Hiemstra et al., 2010), the phosphate loading (Γ) of field samples is suppressed by surface complexation of NOM, where hydrophilic, fulvic, and humic acids act as a competitor for (an)ions via site competition and electrostatic interaction.  相似文献   

17.
Synchrotron-based Fourier-transform infrared (SR-FTIR) micro-spectroscopy was used to determine the concentration-dependent response of the organic structure of live cyanobacterial cells to silicification. Mid-infrared (4000-600 cm−1) measurements carried out on single filaments and sheaths of the cyanobacteria Calothrix sp. (strain KC97) were used to monitor the interaction between a polymerizing silica solution and the organic functional groups of the cells during progressive silicification. Spectra of whole-cells and sheaths were analyzed and the spectral features were assigned to specific functional groups related to the cell: lipids (-CH2 and -CH3; at 2870-2960 cm−1), fatty acids (>C=O at 1740 cm−1), proteins (amides I and II at 1650 and 1540 cm−1), nucleic acids (>P=O 1240 cm−1), carboxylic acids (C-O at 1392 cm−1), and polysaccharides (C-O between 1165 and 1030 cm−1). These vibrations and the characteristic vibrations for silica (Si-O between 1190 and 1060 cm−1; to some extent overlapping with the C-O frequencies of polysaccharides and Si-O at 800 cm−1) were used to follow the progress of silicification. Relative to unsilicified samples, the intensity of the combined C-O/Si-O vibration band increased considerably over the course of the silicification (whole-cells by > 90% and sheath by ∼75%). This increase is a consequence of (1) extensive growth of the sheath in response to the silicification, and (2) the formation of thin amorphous silica layers on the sheath. The formation of a silica specific band (∼800 cm−1) indicates, however, that the precipitation of amorphous silica is controlled by the dehydroxylation of abiotically formed silanol groups.  相似文献   

18.
Chlorine-35 magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra were collected at 14.1 and 18.8 Tesla fields to determine the atomic scale structural environments of the chloride ions in anhydrous and hydrous silicate and aluminosilicate glasses containing 0.2 to 0.7 wt% Cl. NMR peaks are broad and featureless, but are much narrower than the total chemical shift range for the nuclide in inorganic chlorides. Peak widths are primarily due to quadrupole interactions and to a lesser extent to chemical shift distributions. Peak positions are quite different for the Na- and Ca-containing glasses, suggesting that most Cl− coordination environments contain network modifier cations. Comparison of peak positions and shapes for silicate and aluminosilicate glasses containing either Na or Ca suggests that there is no obvious contribution from Cl− bonded to Al, and relative quantitation of peak areas indicates that there is no systematic undercounting of 35Cl spins in the aluminous vs. the Al-free samples. In Ca-Na silicate glasses with varying Ca/(Ca + Na), the mixed-cation glasses have intermediate chemical shifts between those of the end members, implying that there is not a strong preference of either Ca2+ or of Na+ around Cl−. Hydrous Na-aluminosilicate glasses with H2O contents up to 5.9 wt% show a shift to higher frequency NMR signal with increasing H2O content, while the quadrupole coupling constant (CQ) remains constant at ∼3.3 MHz. However, the change in frequency is much smaller than that expected if H2O systematically replaced Na+ in the first-neighbor coordination shell around Cl−. A series of hydrous Ca-aluminosilicate glasses with H2O contents up to 5.5 wt% show no shift in NMR signal with increasing H2O content. The CQ remains constant at ∼4.4 MHz, again suggesting no direct interaction between Cl− and H2O in these samples.  相似文献   

19.
XANES analyses at the sulfur K-edge were used to determine the oxidation state of S species in natural and synthetic basaltic glasses and to constrain the fO2 conditions for the transition from sulfide (S2−) to sulfate (S6+) in silicate melts. XANES spectra of basaltic samples from the Galapagos spreading center, the Juan de Fuca ridge and the Lau Basin showed a dominant broad peak at 2476.8 eV, similar to the spectra obtained from synthetic sulfide-saturated basalts and pyrrhotite. An additional sharp peak at 2469.8 eV, similar to that of crystalline sulfides, was present in synthetic glasses quenched from hydrous melts but absent in anhydrous glasses and may indicate differences in sulfide species with hydration or presence of minute sulfide inclusions exsolved during quenching. The XANES spectra of a basalt from the 1991 eruption of Mount Pinatubo, Philippines, and absarokitic basalts from the Cascades Range, Oregon, USA, showed a sharp peak at 2482.8 eV, characteristic of synthetic sulfate-saturated basaltic glasses and crystalline sulfate-bearing minerals such as hauyne. Basaltic samples from the Lamont Seamount, the early submarine phase of Kilauea volcano and the Loihi Seamount showed unequivocal evidence of the coexistence of S2− and S6+ species, emphasizing the relevance of S6+ to these systems. XANES spectra of basaltic glasses synthesized in internally-heated pressure vessels and equilibrated at fO2 ranging from FMQ − 1.4 to FMQ + 2.7 showed systematic changes in the features related to S2− and S6+ with changes in fO2. No significant features related to sulfite (S4+) species were observed. These results were used to construct a function that allows estimates of S6+/ΣS from XANES data. Comparison of S6+/ΣS data obtained by S Kα shifts measured with electron probe microanalysis (EPMA), S6+/ΣS obtained from XANES spectra, and theoretical considerations show that data obtained from EPMA measurements underestimate S6+/ΣS in samples that are sulfate-dominated (most likely because of photo-reduction effects during analysis) whereas S6+/ΣS from XANES provide a close match to the expected theoretical values. The XANES-derived relationship for S6+/ΣS as a function of fO2 indicates that the transition from S2− to S6− with increasing fO2 occurs over a narrower interval than what is predicted by the EPMA-derived relationship. The implications for natural systems is that small variation of fO2 above FMQ + 1 will have a large effect on S behavior in basaltic systems, in particular regarding the amount of S that can be transported by basaltic melts before sulfide saturation can occur.  相似文献   

20.
The adsorption of two model siderophores, desferrioxamine B (DFOB) and aerobactin, to lepidocrocite (γ-FeOOH) was investigated by attenuated total reflection infrared spectroscopy (ATR-FTIR). The adsorption of DFOB was investigated between pH 4.0 and 10.6. The spectra of adsorbed DFOB indicated that two to three hydroxamic acid groups of adsorbed DFOB were deprotonated in the pH range 4.0-8.2. Deprotonation of hydroxamic acid groups of adsorbed DFOB at pH values well below the first acid dissociation constant of solution DFOB species (pKa = 8.3) and well below the point of zero charge of lepidocrocite (pHPZC = 7.4) suggested that the surface speciation at the lower end of this pH range (pH 4) is dominated by a surface DFOB species with inner-sphere coordination of two to three hydroxamic acids groups to the surface. Maximum adsorption of DFOB occurred at approximately pH 8.6, close to the first pKa value of the hydroxamic acid groups, and decreased at lower and higher pH values.The spectra of adsorbed aerobactin in the pH range 3-9 indicated at least three different surface species. Due to the small spectral contributions of the hydroxamic acid groups of aerobactin, the interactions of these functional groups with the surface could not be resolved. At high pH, the spectral similarity of adsorbed aerobactin with free aerobactin deprotonated at the carboxylic acid groups indicated outer-sphere complexation of the carboxylate groups. With decreasing pH, a significant peak shift of the asymmetric carboxylate stretch vibration was observed. This finding suggested that the (lateral) carboxylic acid groups are coordinated to the surface either as inner-sphere complexes or as outer-sphere complexes that are strongly stabilized at the surface by hydrogen bonding at low pH.  相似文献   

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