Molecular environment of iodine in naturally iodinated humic substances: Insight from X-ray absorption spectroscopy

The molecular environment of iodine in reference inorganic and organic compounds, and in dry humic and fulvic acids (HAs and FAs) extracted from subsurface and deep aquifers was probed by iodine L₃-edge X-ray absorption spectroscopy. The X-ray absorption near-edge structure (XANES) of iodine spectra from HAs and FAs resembled those of organic references and displayed structural features consistent with iodine forming covalent bonds with organic molecules. Simulation of XANES spectra by linear combination of reference spectra suggested the predominance of iodine forming covalent bonds to aromatic rings (aromatic-bound iodine). Comparison of extended X-ray absorption fine structure (EXAFS) spectra of reference and samples further showed that iodine was surrounded by carbon shells at distances comparables to those for references containing aromatic-bound iodine. Quantitative analysis of EXAFS spectra indicated that iodine was bound to about one carbon at a distance d (I-C) of 2.01(4)-2.04(9) Å, which was comparable to the distances observed for aromatic-bound iodine in references (1.99(1)-2.07(6) Å), and significantly shorter than that observed for aliphatic-bound iodine (2.15(2)-2.16(2) Å). These results are in agreement with previous conclusions from X-ray photoelectron spectroscopy and from electrospray ionization mass spectrometry. These results collectively suggest that the aromatic-bound iodine is stable in the various aquifers of this study.     

The structure of freshwater humic substances as revealed by 13C-NMR spectroscopy

Freshwater humic substances from Lake Celyn, Gwynedd, N. Wales have been investigated by ¹³C-NMR spectroscopy. Carboxyl, aromatic, o-alkyl and alkyl resonances can be recognised. Varying pulse delay from 0.43 s to 2.5 sec has little effect on the magnitude of the signal ascribed to aromatic carbon, but there is a small nuclear Overhauser effect (1.45 at a pulse delay of 0.8 sec).The results show-that 24% of the Lake Celyn humic acid carbon is carboxyl and 40% is aromatic. The high proportion of aromatic carbon suggests the Lake Celyn humic acid is largely formed from terrestrial humic substances from the surrounding peaty watershed.     

Comparative studies on compounds occluded inside asphaltenes hierarchically released by increasing amounts of H2O2/CH3COOH

Being the heaviest fraction of crude oils, asphaltenes are liable to aggregate, and other molecules in the oils can be steadily adsorbed onto, and even occluded inside the macromolecular structures of the asphaltenes. These occluded compounds inside the asphaltenes can survive over geological time in oil reservoirs owing to effective protection by the macromolecular structures of the asphaltenes. The asphaltenes of a crude oil (ZG31) from the central Tarim Basin, NW China, were hierarchically degraded by increasing the amount of H₂O₂/CH₃COOH to release the occluded compounds. Besides the common components, series of even numbered n-alk-1-enes and 3-ethylalkanes were detected among the occluded compounds. Comparison of the biomarker distributions and the compound-specific C isotopic results between the compounds from the maltenes and those from the occluded fraction, the ZG31 reservoir was suggested to have been charged multiple times, with different charges being derived from different strata of source rocks.     

Aggregation of aquatic humic substances

Humic substances (HS) were isolated from Penwhirn Reservoir (PR) and Esthwaite Water (EW) and their removal from solution by centrifugation was studied as a function of pH, humic concentration and molecular weight, and CaCl₂ concentration. Large amounts (up to 50%) of PR HS could be removed but only small amounts (? 3%) of EW HS. At pH ? 5 removal of PR HS by Ca²⁺ can be explained satisfactorily in terms of decreases in humic solubilities induced by complexation with the cation. However, removal induced by protonation of the PR HS is unusual in that it decreases with increasing humic concentration.The results suggest that PR HS comprise a range of molecules differing in solubility, with the high-molecular-weight (40,000) components being the least soluble. The EW HS consist of molecules of weight-average molecular weight 5000 and resemble similarly sized PR HS in that they remain unaggregated in solution even when highly complexed with Ca²⁺.     

The luminescent humic substances in speleothems

Calcite speleothems deposited in caves by seepage waters derived from the overlying soils of the epikarst are typically coarsely crystalline, colored various shades of brown through orange and white, and strongly luminescent. For most speleothems, the color and luminescence is due to humic substances incorporated in the calcite crystals. For a quantitative assessment of the luminescent properties of these materials, the organic content of the dissolved speleothems was separated by gel chromatography and spectra measured as a function of molecular weight. The most intense luminescence was obtained from molecular weight fractions in the range of 4000–6000 daltons, a range characteristic of fulvic acids. In addition, there was considerable variation in detail from sample to sample that would merit further investigation.     

Molecular size of aquatic humic substances

Aquatic humic substances, which account for 30 to 50% of the organic carbon in water, are a principal component of aquatic organic matter. The molecular size of aquatic humic substances, determined by small-angle X-ray scattering, varies from 4.7 to 33 Å in their radius of gyration, corresponding to a molecular weight range of 500 to greater than 10,000. The aquatic fulvic acid fraction contains substances with molecular weights ranging from 500 to 2000 and is monodisperse, whereas the aquatic humic acid fraction contains substances with molecular weights ranging from 1000 to greater than 10,000 and is generally polydisperse.     

Phosphorus in marine and non-marine humic substances

The phosphorus content of marine humic acids (HA) is in the range of 0.1–0.2%. The C/P ratios of the HA are 300 to 400. Marine fulvic acids (FA) contain 0.4–0.8% P and have C/P ratios of 80 to 100. High molecular weight organic matter dissolved in pore waters (DOM) contains 0.5% P and has C/P of 90. The data suggest that during the formation sequence: Plankton → DOM → FA → HA → Kerogen, phosphorus is lost, mainly in the FA → HA (and possibly also in the HA → Kerogen) step. Diagenesis of sedimentary humic acids is accompanied by loss of phosphorus (as well as of nitrogen) to form HA with C/P ratios of 1000.Soil humic substances resemble marine humates in P content (0.3%) and soil FA's are about three to fivefold enriched in P relative to HA. C/P ratios are lower in soil HA (ca. 200) as compared with marine HA. Humic acids from diagenetic products such as peat and lignite are highly depleted in P. Rough calculations indicate that humate bound P may account for 20–50% of the organic phosphorus reservoir in sediments. The chemical speciation of this P is unknown, but lack of correlation with ash, Fe, Ca or Al content (in marine humates, at least) indicates that it is organically bound.     

X-ray absorption spectroscopic studies of silicate glasses and minerals

Selected results of x-ray absorption spectroscopy (XAS) studies of amorphous silicates and minerals are presented in order to show their utility in providing short-and, in certain cases, medium-range structural and bonding information for cations and anions. EXAFS and XANES studies of amorphous silicates are reviewed with the objective of illustrating variations in structural environments of the various types of glass-forming cations, including Si, Al, Na, K, Ca, Ti, Fe, Yb, and U. Al is shown to occur in tetrahedral coordination in all aluminosilicate glasses examined, including peraluminous compositions. The weakly bonded Na and Ca cations are shown to occur in sites with observed coordination numbers (ranging from 6 to 7) and distances similar to those predicted by molecular dynamics simulations. Elements like Ti, which form bonds of intermediate strength, may show some order beyond the first coordination shell at low concentrations in silicate glasses. EXAFS studies of Yb and U in silicate glasses at trace to minor concentration levels provide unique structural information about the environments of these cations. K-edges and XANES of transition element sulfides, third-row tetrahedral oxyanions, and oxygen in minerals are interpreted in terms of band theory or molecular orbital theory.     

Assessing redox properties of standard humic substances

Redox properties of humic substances (HS) control important biogeochemical processes. Thus, accurate estimation of redox properties of HS is essential. However, there is no general consensus regarding the best available measurement method of HS redox properties. In this study, we compared several common HS redox property measurement methods using anthraquinone-2,6-disulfonate (AQDS) as model compound, and standard Elliot soil humic acid (1S102H, ESHA), reference Pahokee peat (1R103H, PPHA), and Suwannee River natural organic matter (1R101N, SRNOM) as representative HS. We found that the H₂/Pd reduction method followed by incubation with ferric citrate (FeCit) reagent was incomplete, and the H₂/Pd reduction method followed by incubation with potassium ferricyanide (K₃Fe(CN)₆) was insensitive. Stannous chloride (SnCl₂) reduction followed by titration of excess stannous (Sn²⁺) by potassium dichromate (K₂Cr₂O₇) was found to be most accurate. These findings will help in future investigations on detailed characterizations of functional groups of HS responsible for oxidation/reduction reactions.     

Unique properties of humic substances from sapropel

Doklady Earth Sciences - Sapropel from inland Russian water reservoirs is becoming a popular raw material for medicinal purposes, production of sorbents, organomineral fertilizers, and food...     

Pyrolysis-GC-MS and NMR studies of dissolved seawater humic substances and isolates of a marine diatom

¹³C- and ¹H-NMR spectra were obtained for humic substances isolated from a coastal marine environment and also for the intracellular and extracellular extracts of a marine diatom. Phaeodactylum tricornutum Bohlin. Highly branched alkyl chains constitute a large proportion of the structure of the marine humic material, whereas aromatic components are less important. Carbohydrate-type materials, possibly uronic acids, are also present in appreciable amounts. Furans (derived from carbohydrates). pyrroles and nitriles (derived from proteins, nucleic acids and/or tetrapyrroles) and phenols and methylphenols (non-lignin derived) are pyrolysis products derived from pyrolysis-gas chromatography-mass spectrometry of the extracts. The results indicate the similarities in chemical structure of P. tricornutum exudate and dissolved marine humic material.     

Thermodynamic modeling of binary CH4-H2O fluid inclusions

This work reports the application of thermodynamic models, including equations of state, to binary (salt-free) CH₄-H₂O fluid inclusions. A general method is presented to calculate the compositions of CH₄-H₂O inclusions using the phase volume fractions and dissolution temperatures of CH₄ hydrate. To calculate the homogenization pressures and isolines of the CH₄-H₂O inclusions, an improved activity-fugacity model is developed to predict the vapor-liquid phase equilibrium. The phase equilibrium model can predict methane solubility in the liquid phase and water content in the vapor phase from 273 to 623 K and from 1 to 1000 bar (up to 2000 bar for the liquid phase), within or close to experimental uncertainties. Compared to reliable experimental phase equilibrium data, the average deviation of the water content in the vapor phase and methane solubility in the liquid phase is 4.29% and 3.63%, respectively. In the near-critical region, the predicted composition deviations increase to over 10%. The vapor-liquid phase equilibrium model together with the updated volumetric model of homogenous (single-phase) CH₄-H₂O fluid mixtures (Mao S., Duan Z., Hu J. and Zhang D. (2010) A model for single-phase PVTx properties of CO₂-CH₄-C₂H₆-N₂-H₂O-NaCl fluid mixtures from 273 to 1273 K and from 1 to 5000 bar. Chem. Geol.275, 148-160), is applied to calculate the isolines, homogenization pressures, homogenization volumes, and isochores at specified homogenization temperatures and compositions. Online calculation is on the website: http://www.geochem-model.org/.     

Electronic environments in carrollite, CuCo2S4, determined by soft X-ray photoelectron and absorption spectroscopy

Fracture surfaces of a natural carrollite specimen have been characterised by synchrotron and conventional X-ray photoelectron spectroscopy and near-edge X-ray absorption spectroscopy. For the synchrotron X-ray measurements, the mineral surfaces were prepared under clean ultra high vacuum and were unoxidised. The characterisation was undertaken primarily to establish unequivocally the oxidation state of the Cu in the mineral, but also to obtain information on the electronic environments of the Co and S, and on the surface species. Experimental and simulated Cu L_2,3-edge absorption spectra confirmed an oxidation state of Cu^I, while Co 2p photoelectron and Co L_2,3 absorption spectra were largely consistent with the Co^III established previously by nuclear magnetic resonance spectroscopy. S 2p photoelectron spectra provided no evidence for S to be present in the bulk in more than one state, and were consistent with an oxidation state slightly less negative than S^-II. Therefore it was concluded that carrollite can be best represented by Cu^ICo^III₂(S₄)^-VII. The Cu^I oxidation state is in agreement with that expected for Cu tetrahedrally coordinated by S, but is in disagreement with the Cu^II deduced previously from some magnetic, magnetic resonance and Cu L-edge X-ray absorption spectroscopic measurements. A significant concentration of S species with core electron binding energies both lower and higher than the bulk value were formed at fracture surfaces, and these entities were assigned to monomeric and oligomeric surface S species. The density of Cu d states calculated for carrollite differed from that previously reported but was consistent with the observed Cu L₃ X-ray absorption spectrum. The initial oxidation of carrollite in air under ambient conditions was confirmed to be congruent, unlike the incongruent reaction undergone by a number of non-thiospinel sulfide minerals.     

Thermal characterization of natural and synthetic humic substances

Thermogravimetric technique was used for the characterization of natural (humic) and synthetic (melanoidins) substances. The influence of pH on the thermal stability of humic substances was studied. A similarity in thermal behaviour of natural humic substances and of melanoidins (prepared from an excess of sugar) and the unique thermal properties of melanoidins (prepared from basic amino acids) was observed. Thermal behavior of natural and synthetic substances was compared with model compounds of sugar, peptide and kerogen types.     

3d transition metal L-edge X-ray absorption studies of the dichalcogenides of Fe, Co and Ni

The X-ray absorption spectra of the transition metal L_3,2-edges of the dichalcogenides FeS₂ (pyrite), FeSe₂, FeTe₂, CoS₂, CoSe₂, CoTe₂, NiS₂, NiSe₂ and NiTe₂ have been studied. These spectra are compared with theoretical simulations make using the atomic multiplet approach assuming on octahedral site for the metal atoms. The Ni spectra can be closely simulated using this approach but the Fe and Co spectra show less good fits to the experimental data. The reasons for this and its implications for the use of L-edge spectra in the study of such minerals are discussed in terms of the covalency and the ground states of the compounds; these results indicate the mixing of the ground states increases in the order Ni<Co<Fe.     

Effects of key geological factors in the long-term transport of CH4 and the CH4-hydrate formation behavior with formation dip

Many locations with concentrated hydrates at vents have confirmed the presence of abundant thermogenic gas in the middle of the Qiongdongnan Basin (QDNB). However, the impact of deep structures on gas-bearing fluids migration and gas hydrates distribution in tectonically inactive regions is still unclear. In this study, the authors apply high-resolution 3D seismic and logging while drilling (LWD) data from the middle of the QDNB to investigate the influence of deep-large faults on gas chimneys and preferred gas-escape pipes. The findings reveal the following: (1) Two significant deep-large faults, F1 and F2, developed on the edge of the Songnan Low Uplift, control the dominant migration of thermogenic hydrocarbons and determine the initial locations of gas chimneys. (2) The formation of gas chimneys is likely related to fault activation and reactivation. Gas chimney 1 is primarily arises from convergent fluid migration resulting from the intersection of the two faults, while the gas chimney 2 benefits from a steeper fault plane and shorter migration distance of fault F2. (3) Most gas-escape pipes are situated near the apex of the two faults. Their reactivations facilitate free gas flow into the GHSZ and contribute to the formation of fracture‐filling hydrates.     

Formation and abundance of doubly-substituted methane isotopologues (CH3D) in natural gas systems

Formation of the Carbon-13 (¹³C) and deuterium (D) doubly-substituted methane isotopologues (¹³CH₃D) in natural gases is studied utilizing both first-principle quantum mechanism molecular calculation and direct FTIR laboratorial measurements of specifically synthesized high isotope concentration methane gas. For ¹³CH₃D, the symmetrically breathing mode A₀ emerges as IR-detectable attributed to the molecular symmetry lowering to C_3v from T_d of the non-isotopic methane (CH₄), along with a large vibrational frequency shift from ∼3000 to ∼2250 cm⁻¹. Our studies also indicate that the concentration of ¹³CH₃D is dependent on the environmental temperature through isotope exchanges among methane isotopologues; and the Gibbs’ Free Energy difference due to Quantum Mechanics Zero-Point vibrational motions has the major contribution to this temperature dependency. Potential geologic applications of the ¹³CH₃D measurement to natural gas exploration and assessments are also discussed. In order to detect the ¹³CH₃D concentration change of each 50 °C in the natural gas system, a 10⁻⁹ resolution is desirable. Such a measurement could provide important add-on information to distinguish natural gas origin and distribution.     

Coordination chemistry and hydrolysis of Fe(III) in a peat humic acid studied by X-ray absorption spectroscopy

The speciation of iron (Fe) in soils, sediments and surface waters is highly dependent on chemical interactions with natural organic matter (NOM). However, the molecular structure and hydrolysis of the Fe species formed in association with NOM is still poorly described. In this study extended X-ray absorption fine structure (EXAFS) spectroscopy was used to determine the coordination chemistry and hydrolysis of Fe(III) in solution of a peat humic acid (5010-49,200 μg Fe g⁻¹ dry weight, pH 3.0-7.2). Data were analyzed by both conventional EXAFS data fitting and by wavelet transforms in order to facilitate the identification of the nature of backscattering atoms. Our results show that Fe occurs predominantly in the oxidized form as ferric ions and that the speciation varies with pH and Fe concentration. At low Fe concentrations (5010-9920 μg g⁻¹; pH 3.0-7.2) mononuclear Fe(III)-NOM complexes completely dominates the speciation. The determined bond distances for the Fe(III)-NOM complexes are similar to distances obtained for Fe(III) complexed by desferrioxamine B and oxalate indicating the formation of a five-membered chelate ring structure. At higher Fe concentrations (49,200 μg g⁻¹; pH 4.2-6.9) we detect a mixture of mononuclear Fe(III)-NOM complexes and polymeric Fe(III) (hydr)oxides with an increasing amount of Fe(III) (hydr)oxides at higher pH. However, even at pH 6.9 and a Fe concentration of 49,200 μg g⁻¹ our data indicates that a substantial amount of the total Fe (>50%) is in the form of organic complexes. Thus, in environments with significant amounts of organic matter organic Fe complexes will be of great importance for the geochemistry of Fe. Furthermore, the formation of five-membered chelate ring structures is in line with the strong complexation and limited hydrolytic polymerization of Fe(III) in our samples and also agrees with EXAFS derived structures of Fe(III) in organic soils.     

1H and 13C NMR of marine humic acids

¹³C and ¹H NMR spectra were obtained for humic acids isolated from marine sediments. NMR shows great promise in identifying structural components of humic acids as some new and interesting structural features are identified. Aliphatic structures were found to constitute a much larger fraction of humic acids than previously thought, and they appeared to be highly branched. Although the aromatic content of terrestrial humic acid was found to be lower than expected, the aromaticity appears to be a specific discriminator of terrestrial/aquatic source types. A humic acid isolated from an anoxic algal sapropel was found to be composed predominantly of polyuronic acids and different than other aquatic sedimentary humic substances.