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USGS1999

Molecular aggregation of humic substances

Humic substances (HS) form molecular aggregates in solution and on mineral surfaces. Elucidation of the mechanism of formation of these aggregates is important for an understanding of the interactions of HS in soils arid natural waters. The HS are formed mainly by enzymatic depolymerization and oxidation of plant biopolymers. These reactions transform the aromatic and lipid plant components into amphiphilic molecules, that is, molecules that consist of separate hydrophobic (nonpolar) and hydrophilic (polar) parts. The nonpolar parts of the molecules are composed of relatively unaltered segments of plant polymers and the polar parts of carboxylic acid groups. These amphiphiles form membrane-like aggregates on mineral surfaces and micelle-like aggregates in solution. The exterior surfaces of these aggregates are hydrophilic, and the interiors constitute separate hydrophobic liquid-like phases.

Soil Science↗

USGS2003

Temperature dependence of polyhedral cage volumes in clathrate hydrates

The polyhedral cage volumes of structure I (sI) (carbon dioxide, methane, trimethylene oxide) and structure II (sII) (methane-ethane, propane, tetrahydrofuran, trimethylene oxide) hydrates are computed from atomic positions determined from neutron powder-diffraction data. The ideal structural formulas for sI and sII are, respectively, S2L6 ?? 46H2O and S16L???8 ?? 136H2O, where S denotes a polyhedral cage with 20 vertices, L a 24-cage, and L??? a 28-cage. The space-filling polyhedral cages are defined by the oxygen atoms of the hydrogen-bonded network of water molecules. Collectively, the mean cage volume ratio is 1.91 : 1.43 : 1 for the 28-cage : 24-cage : 20-cage, which correspond to equivalent sphere radii of 4.18, 3.79, and 3.37 A??, respectively. At 100 K, mean polyhedral volumes are 303.8, 227.8, and 158.8 A??3 for the 28-cage, 24-cage, and 20-cage, respectively. In general, the 20-cage volume for a sII is larger than that of a sI, although trimethylene oxide is an exception. The temperature dependence of the cage volumes reveals differences between apparently similar cages with similar occupants. In the case of trimethylene oxide hydrate, which forms both sI and sII, the 20-cages common to both structures contract quite differently. From 220 K, the sII 20-cage exhibits a smooth monotonic reduction in size, whereas the sI 20-cage initially expands upon cooling to 160 K, then contracts more rapidly to 10 K, and overall the sI 20-cage is larger than the sII 20-cage. The volumes of the large cages in both structures contract monotonically with decreasing temperature. These differences reflect reoriented motion of the trimethyelene oxide molecule in the 24-cage of sI, consistent with previous spectroscopic and calorimetric studies. For the 20-cages in methane hydrate (sI) and a mixed methane-ethane hydrate (sII), both containing methane as the guest molecule, the temperature dependence of the 20-cage volume in sII is much less than that in sI, but sII is overall larger in volume.

Canadian Journal of Physics↗

USGS2008

A genomic view of the NOD-like receptor family in teleost fish: Identification of a novel NLR subfamily in zebrafish

Background. A large multigene family of NOD-like receptor (NLR) molecules have been described in mammals and implicated in immunity and apoptosis. Little information, however, exists concerning this gene family in non-mammalian taxa. This current study, therefore, provides an in-depth investigation of this gene family in lower vertebrates including extensive phylogenetic comparison of zebrafish NLRs with orthologs in tetrapods, and analysis of their tissue-specific expression. Results. Three distinct NLR subfamilies were identified by mining genome databases of various non-mammalian vertebrates; the first subfamily (NLR-A) resembles mammalian NODs, the second (NLR-B) resembles mammalian NALPs, while the third (NLR-C) appears to be unique to teleost fish. In zebrafish, NLR-A and NLR-B subfamilies contain five and six genes respectively. The third subfamily is large, containing several hundred NLR-C genes, many of which are predicted to encode a C-terminal B30.2 domain. This subfamily most likely evolved from a NOD3-like molecule. Gene predictions for zebrafish NLRs were verified using sequence derived from ESTs or direct sequencing of cDNA. Reverse-transcriptase (RT)-PCR analysis confirmed expression of representative genes from each subfamily in selected tissues. Conclusion. Our findings confirm the presence of multiple NLR gene orthologs, which form a large multigene family in teleostei. Although the functional significance of the three major NLR subfamilies is unclear, we speculate that conservation and abundance of NLR molecules in all teleostei genomes, reflects an essential role in cellular control, apoptosis or immunity throughout bony fish. ?? 2008 Laing et al; licensee BioMed Central Ltd.

BMC Evolutionary Biology↗

USGS2024

Male lake char release taurocholic acid as part of a mating pheromone

The evolutionary origins of sexual preferences for chemical signals remain poorly understood, due, in part, to scant information on the molecules involved. In the current study, we identified a male pheromone in lake char ( Salvelinus namaycush ) to evaluate the hypothesis that it exploits a non-sexual preference for juvenile odour. In anadromous char species, the odour of stream-resident juveniles guides migratory adults into spawning streams. Lake char are also attracted to juvenile odour but have lost the anadromous phenotype and spawn on nearshore reefs, where juvenile odour does not persist long enough to act as a cue for spawning site selection by adults. Previous behavioural data raised the possibility that males release a pheromone that includes components of juvenile odour. Using metabolomics, we found that the most abundant molecule released by males was also released by juveniles but not females. Tandem mass spectrometry and nuclear magnetic resonance were used to identify the molecule as taurocholic acid (TCA), which was previously implicated as a component of juvenile odour. Additional chemical analyses revealed that males release TCA at high rates via their urine during the spawning season. Finally, picomolar concentrations of TCA attracted pre-spawning and spawning females but not males. Taken together, our results indicate that male lake char release TCA as a mating pheromone and support the hypothesis that the pheromone is a partial match of juvenile odour.

Journal of Experimental Biology↗

USGS1994

Membrane-micelle model for humus in soils and sediments and its relation to humification

Humification, the process whereby biomass consisting of dead plant and animal remains is converted into soil organic matter (humus), is one of the basic processes of the carbon cycle. The organic compounds that make up plant and animal tissue are thermodynamically unstable in the oxidizing atmosphere at the surface of the Earth. After the organisms in which they are incorporated die, the compounds are converted back to carbon dioxide and water by degradation reactions catalyzed by enzymes secreted by micro-organisms. However, not all the organic compounds in the dead biomass are immediately converted; some of the material is only partially oxidized. The residue left after partial oxidative degradation of the dead biomass is the source of the organic compounds that accumulate in soils and sediments as humus. Previously, humification was thought to involve a conversion of degradation products by a series of polymerization reactions into new types of polymeric species that are different from the precursor molecular species in the original biomass. However, it is proposed here that the depolymerization and oxidation reactions that take place during the enzymatic degradation of biopolymers produce amphiphiles--molecules that have a polar (hydrophilic) part and a nonpolar (hydrophobic) part. These amphiphiles that result from the partial oxidative degradation of dead biomass assemble spontaneously into ordered aggregates in which the hydrophobic parts of the molecules form the interiors and the hydrophilic parts of the molecules make up the exterior surfaces of the aggregates. These ordered aggregates constitute the humus in soils and sediments. Humus ordered aggregates most likely exist as bilayer membranes coating mineral grains and as micelles in solution.

Water Supply Paper↗

USGS2006

Evolution of the CD4 family: teleost fish possess two divergent forms of CD4 in addition to lymphocyte activation gene-3

The T cell coreceptor CD4 is a transmembrane glycoprotein belonging to the Ig superfamily and is essential for cell-mediated immunity. Two different genes were identified in rainbow trout that resemble mammalian CD4. One (trout CD4) encodes four extracellular Ig domains reminiscent off mammalian CD4, whereas the other (CD4REL) codes for two Ig domains. Structural motifs within the amino acid sequences suggest that the two Ig domains of CD4REL duplicated to generate the four-domain molecule of CD4 and the related gene, lymphocyte activation gene-3. Here we present evidence that both of these molecules in trout are homologous to mammalian CD4 and that teleosts encode an additional CD4 family member, lymphocyte activation gene-3, which is a marker for activated T cells. The syntenic relationships of similar genes in other teleost and non-fish genomes provide evidence for the likely evolution of CD4-related molecules in vertebrates, with CD4REL likely representing the primordial form in fish. Expression of both CD4 genes is highest in the thymus and spleen, and mRNA expression of these genes is limited to surface IgM- lymphocytes, consistent with a role for T cell functionality. Finally, the intracellular regions of both CD4 and CD4REL possess the canonical CXC motif involved in the interaction off CD4 with p56LCK, implying that similar mechanisms for CD4 + T cell activation are present in all vertebrates. Our results therefore raise new questions about T cell development and functionality in lower vertebrates that cannot be answered by current mammalian models and, thus, is of fundamental importance for understanding the evolution of cell-mediated immunity in gnathosomes. Copyright ?? 2006 by The American Association of Immunologists, Inc.

Journal of Immunology↗

USGS1977

Chemical structure of humic acids - Part 2, the molecular aggregation of some humic acid fractions in N, N-dimethylformamide

Humic acid fractions form molecular aggregates in solution. In previous studies we have shown by small angle X-ray scattering that the size of these aggregates is a function of pH. In this study we have found that the size of the aggregates of two humic acid fractions in water and buffers and in dimethylformamide solutions can be changed by oxidation with molecular oxygen and air. These results cast new light on the bonding mechanisms that cause aggregation of the humic acid particles in solution. We have interpreted the changes in aggregation sizes as being brought about by changes in intermolecular and intramolecular hydrogen bonding of the humic particles. Solvation of the humic molecules by dimethylformamide interferes with some of the hydrogen bonding reactions between proton donor and acceptor groups on the same humic acid molecules or on different molecules.

Journal of Research of the U.S. Geological Survey↗

USGS2003

Microbial degradation of atmospheric halocarbons

Halocarbons are present in the atmosphere at parts-per-trillion (ppt) mixing ratios and are represented by such substances as chlorofluorocarbons (CFCs), hydrochlolofluorocarbons (HCFCs), hydrofluorocarbons (HFCs), and methyl halides like methyl bromide (MeBr) and their further substituted halomethane analogues (e. g., dibromomethane, bromoform). Many Halocarbons have only an anthropogenic origin (e.g., CFCs, HCFCs, HFCs) whereas others are of mixed anthropogenic and natural origin (e.g., MeBr). The molecular composition of the various CFCs, HCFCs, and HFCs can be deduced from their numerical classification by adding 90 to their designated numbers. The first digit (hundreds place) refers to the number of carbon atoms, the second to the number of hydrogens, and the third to the number of fluorines. For example, the molecular structure of CFC-12 is obtained from the resultant number of 102, and refers to a one carbon molecule containing no hydrogens and two fluorines. By inference from its CFC designation two chlorines must also be included. Similarly, the compound HFC-134 has a resultant sum of 224, which implies a two carbon molecule containing two hydrogens and four fluorines (tetrafluoroethane).

Book chapter↗

USGS1956

Silica in hot-spring waters

The silica in hot-spring waters and in a few cold waters was studied by moans of the colorimetrie ammonium-molybdate method of analysis. Murata found in 1947 that only a part of the total silica in aged samples of high-silica waters was determinable by the colorimetric method. Weitz , franck And schuchard later showed that ammonium molybdate reacts readily with the monomeric form of silica (probably H 4 SiO 4 ) but very slowly with polymeric silica. If the colorimetric measurement is completed in two or three minutes, only the monomer is determined. Nearly all silica of hot springs is in the monomeric form. Solubility equilibrium exists between dissolved (monomeric) and amorphous silica. For the hot springs that were studied, the solubility is about 315 p.p.m. at 90°C and 110 p.p.m. at 25°C, which is very similar to Krauskopf's experimental data. Monomeric silica polymerizes so slowly to colloidal silica that many waters are supersaturated with respect to amorphous silica. The rate of polymerization is influenced by pH, temperature, degree of supersaturation, presence of previously formed colloidal and gelatinous silica and contact with opal and other substances. Supersaturated acid waters and alkaline waters with less than 100% supersaturation tend to remain supersaturated almost indefinitely, with little or no change. Precipitation of colloidal silica is favoured by high temperature and contact with opal. Many connate and other ground waters, including some thermal springs, are much below saturation with respect to amorphous silica, probably because low-solubility quartz and chalcedony have been precipitating. Quartz is favoured by relatively high temperature, slow rale of precipitation, and low degree of supersaturation, and is believed to form by deposition of monomeric molecules. Chalcedony is probably deposited when the degree of supersaturation is moderately high and the rate of deposition is relatively fast. The ranges of temperature over which quartz and chalcedony deposit no doubt overlap, but, if other factors are equal, quartz is favoured by high temperature. Opal is favoured by relatively low temperature and rapid rate of precipitation. Although opal has probably been deposited at temperatures as high as 140°C, it is unstable and is slowly converted to chalcedony or quartz. Water that is saturated with respect to opal is highly supersaturated with respect to quartz. Opal is probably formed from monomeric or more probably, the smaller polymeric molecules of silica, retaining some of their water content. Evidence is lacking for the direct conversion of gelatinous silica to opal. Some differences in solubility probably exist between amorphous opal and opal that shows X-ray patterns like that of cristobalite. The suggestion is made that clay minerals form by combination of monomeric silica and a comparable form of monomeric alumina, which must have very low solubility in waters within the pH range of 5 to 9. Because of the abundance and relatively high solubility of silica, the proposed reaction, dissolved alumina + dissolved silica ⇌ clay, is ordinarily displaced strongly to the right in hydrothermal alteration and in ordinary soil formation. With removal of free silica, aided by tropical rainfall and temperatures, the reaction may be displaced to the left by dissolution and removal of silica from the system. Alumina, because of its very low solubility, remains as bauxite.

Geochimica et Cosmochimica Acta↗

USGS1967

On the chemistry of Jupiter's upper atmosphere

We conduct a first investigation into the ion-molecule chemistry of the upper Jovian atmosphere. Experimental results show that intense ultraviolet radiation reacts with the constituents of the Jovian atmosphere to produce C 2 H 4 , C 2 H 6 , C 3 H 8 , and higher polymers. The general procedure for calculating both equilibrium and nonequilibrium abundances of these products is formulated and applied to the case of the surface passage of a satellite shadow. A specific example is made of ethylene, for which an analytical approximation gives 10 10 molecules in an atmospheric column of 1 cm 2 cross section after a very rapid rise to equilibrium. Such a concentration of ethylene does not substantially affect the infrared radiation in the shadow.

Icarus↗

USGS1996

Mechanism of formation of humus coatings on mineral surfaces 2. Attenuated total reflectance spectra of hydrophobic and hydrophilic fractions of organic acids from compost leachate on alumina

Hydrophobic and hydrophilic fractions were isolated from a compost leachate. The adsorption isotherms of both fractions on alumina were measured by attenuated total reflectance infrared spectroscopy. The shapes of the adsorption isotherms of the two fractions were different. The isotherms for the hydrophilic fraction showed little change in surface excess with increasing solution concentration above 4 mg L-1. The isotherms for the hydrophobic fraction, on the other hand, displayed a marked increase in surface excess with increasing solution concentration. This increase is evidence for the formation of aggregates (admicelles or hemimicelles) on the alumina surface. Linear dichroism calculations indicated that more of the carboxylate groups in the adsorbed hydrophobic molecules than in the absorbed hydrophilic fraction were free to rotate. The hindered rotation of the carboxylate groups in the adsorbed hydrophilic-fraction molecules probably indicates that these groups are bound to surface aluminum ions by a bidentate mechanism in which the two oxygen atoms of a single carboxylate group bind to separate aluminum ions.

Colloids and Surfaces A: Physicochemical and Engin↗

USGS2009

The structure and stability of aqueous rare-earth elements in hydrothermal fluids: New results on neodymium(III) aqua and chloroaqua complexes in aqueous solutions to 500 °C and 520 MPa

X-ray absorption spectroscopy (XAS) measurements were made at the Nd L3-edge on neodymium(III) aqua and chloroaqua complexes in low pH aqueous solutions from 25 to 500????C and up to 520??MPa. Analysis of the extended X-ray absorption fine structure of the XAS spectra measured from a 0.07??m Nd/0.16??m HNO3 aqueous solution reveals a contraction of the Nd-O distance of the Nd3+ aqua ion at a uniform rate of ~ 0.013????/100????C and a uniform reduction of the number of coordinated H2O molecules from 10.0 ?? 0.9 to 7.4 ?? 0.9 over the range from 25 to 500????C and up to 370??MPa. The rate of reduction of the first-shell water molecules with temperature for Nd3+ (26%) is intermediate between the rate for the Gd3+ aqua ion (22% from 25 to 500????C) and the rates for the Eu3+ (29% from 25 to 400????C) and the Yb3+ aqua ions (42% from 25 to 500????C) indicating an intermediate stability of the Nd3+ aqua ion consistent with the tetrad effect. Nd L3-edge XAS measurements of 0.05??m NdCl3 aqueous solution at 25 to 500????C and up to 520??MPa show that stepwise inner-sphere complexes most likely of the type Nd(H2O)?? - nCln+3 - n occur in the solution at elevated temperatures, where ?? ??? 9 at 150????C decreasing to ~ 6 at 500????C and the number of chloride ions (n) of the chloroaqua complexes increases uniformly with temperature from 1.2 ?? 0.2 to 2.0 ?? 0.2 in the solution upon increase of temperature from 150 to 500????C. Conversely, the number of H2O ligands of Nd(H2O)?? - nCln+3 - n complexes is uniformly reduced with temperature from 7.5 ?? 0.8 to 3.7 ?? 0.3 in the aqueous solution, in the same temperature range. These data show greater stability of neodymium(III) than gadolinium(III) and ytterbium(III) chloride complexes in low pH aqueous solutions at elevated temperatures. Our data suggest a greater stability of aqueous light REE than that of heavy REE chloride complexes in low pH fluids at elevated temperatures consistent with REE analysis of fluids from deep-sea hydrothermal vents. ?? 2008 Elsevier B.V.

Chemical Geology↗

USGS2014

Vibrational, X-ray absorption, and Mössbauer spectra of sulfate minerals from the weathered massive sulfide deposit at Iron Mountain, California

The Iron Mountain Mine Superfund site in California is a prime example of an acid mine drainage (AMD) system with well developed assemblages of sulfate minerals typical for such settings. Here we present and discuss the vibrational (infrared), X-ray absorption, and Mössbauer spectra of a number of these phases, augmented by spectra of a few synthetic sulfates related to the AMD phases. The minerals and related phases studied in this work are (in order of increasing Fe 2 O 3 /FeO): szomolnokite, rozenite, siderotil, halotrichite, römerite, voltaite, copiapite, monoclinic Fe 2 (SO 4 ) 3 , Fe 2 (SO 4 ) 3 ·5H 2 O, kornelite, coquimbite, Fe(SO 4 )(OH), jarosite and rhomboclase. Fourier transform infrared spectra in the region 750–4000 cm −1 are presented for all studied phases. Position of the FTIR bands is discussed in terms of the vibrations of sulfate ions, hydroxyl groups, and water molecules. Sulfur K-edge X-ray absorption near-edge structure (XANES) spectra were collected for selected samples. The feature of greatest interest is a series of weak pre-edge peaks whose position is determined by the number of bridging oxygen atoms between Fe 3+ octahedra and sulfate tetrahedra. Mössbauer spectra of selected samples were obtained at room temperature and 80 K for ferric minerals jarosite and rhomboclase and mixed ferric–ferrous minerals römerite, voltaite, and copiapite. Values of Fe 2+ /[Fe 2+ + Fe 3+ ] determined by Mössbauer spectroscopy agree well with those determined by wet chemical analysis. The data presented here can be used as standards in spectroscopic work where spectra of well-characterized compounds are required to identify complex mixtures of minerals and related phases.

California↗

USGS2010

Variations in coal characteristics and their possible implications for CO2 sequestration: Tanquary injection site, southeastern Illinois, USA

As part of the U.S. Department of Energy's Regional Sequestration Partnership program, the potential for sequestering CO2 in the largest bituminous coal reserve in United States - the Illinois Basin - is being assessed at the Tanquary site in Wabash County, southeastern Illinois. To accomplish the main project objectives, which are to determine CO2 injection rates and storage capacity, we developed a detailed coal characterization program. The targeted Springfield Coal occurs at 274m (900ft) depth, is 2.1m (7ft) thick, and is of high volatile B bituminous rank, having an average vitrinite reflectance (Ro) of 0.63%. Desorbed Springfield Coal gas content in cores from four wells ~15 to ~30m (50 to 100ft) apart varies from 4.7-6.6cm3/g (150 to 210scf/ton, dmmf) and consists, generally, of >92% CH4 with lesser amounts of N2 and then CO2. Adsorption isotherms indicate that at least three molecules of CO2 can be stored for each displaced CH4 molecule. Whole seam petrographic composition, which affects sequestration potential, averages 76.5% vitrinite, 4.2% liptinite, 11.6% inertinite, and 7.7% mineral matter. Sulfur content averages 1.59%. Well-developed coal cleats with 1 to 2cm spacing contain partial calcite and/or kaolinite fillings that may decrease coal permeability. The shallow geophysical induction log curves show much higher resistivity in the lower part of the Springfield Coal than the medium or deep curves because of invasion by freshwater drilling fluid, possibly indicating higher permeability. Gamma-ray and bulk density vary, reflecting differences in maceral, ash, and pyrite content. Because coal properties vary across the basin, it is critical to characterize injection site coals to best predict the potential for CO2 injection and storage capacity. ?? 2010 Elsevier B.V.

International Journal of Coal Geology↗

USGS2004

Calculation of individual isotope equilibrium constants for geochemical reactions

Theory is derived from the work of Urey (Urey H. C. [1947] The thermodynamic properties of isotopic substances. J. Chem. Soc . 562–581) to calculate equilibrium constants commonly used in geochemical equilibrium and reaction-transport models for reactions of individual isotopic species. Urey showed that equilibrium constants of isotope exchange reactions for molecules that contain two or more atoms of the same element in equivalent positions are related to isotope fractionation factors by α = (K ex ) 1/n , where n is the number of atoms exchanged. This relation is extended to include species containing multiple isotopes, for example 13 C 16 O 18 O and 1 H 2 H 18 O. The equilibrium constants of the isotope exchange reactions can be expressed as ratios of individual isotope equilibrium constants for geochemical reactions. Knowledge of the equilibrium constant for the dominant isotopic species can then be used to calculate the individual isotope equilibrium constants. Individual isotope equilibrium constants are calculated for the reaction CO 2g = CO 2aq for all species that can be formed from 12 C, 13 C, 16 O, and 18 O; for the reaction between 12 C 18 O 2aq and 1 H 2 18 O l ; and among the various 1 H, 2 H, 16 O, and 18 O species of H 2 O. This is a subset of a larger number of equilibrium constants calculated elsewhere (Thorstenson D. C. and Parkhurst D. L. [2002] Calculation of individual isotope equilibrium constants for implementation in geochemical models. Water-Resources Investigation Report 02-4172. U.S. Geological Survey). Activity coefficients, activity-concentration conventions for the isotopic variants of H 2 O in the solvent 1 H 2 16 O l , and salt effects on isotope fractionation have been included in the derivations. The effects of nonideality are small because of the chemical similarity of different isotopic species of the same molecule or ion. The temperature dependence of the individual isotope equilibrium constants can be calculated from the temperature dependence of the fractionation factors. The derivations can be extended to calculation of individual isotope equilibrium constants for ion pairs and equilibrium constants for isotopic species of other chemical elements. The individual isotope approach calculates the same phase isotopic compositions as existing methods, but also provides concentrations of individual species, which are needed in calculations of mass-dependent effects in transport processes. The equilibrium constants derived in this paper are used to calculate the example of gas-water equilibrium for CO 2 in an acidic aqueous solution.

Geochimica et Cosmochimica Acta↗

USGS2018

Position-specific 13C distributions within propane from experiments and natural gas samples

Site-specific carbon isotope measurements of organic compounds potentially recover information that is lost in a conventional, ‘bulk’ isotopic analysis. Such measurements are useful because isotopically fractionating processes may have distinct effects at different molecular sites, and thermodynamically equilibrated populations of molecules tend to concentrate heavy isotopes in one molecular site versus another. Most recent studies of site-specific 13 C in organics use specialized Nuclear Magnetic Resonance (NMR) techniques or complex chemical degradations prior to mass spectrometric measurements. Herein we present the first application of a new mass spectrometric technique that reconstructs the site-specific carbon isotope composition of propane based on measurements of the 13 C/ 12 C ratios of two or more fragment ions that sample different proportions of the terminal and central carbon sites. We apply this method to propane from laboratory experiments and natural gas samples to explore the relationships between site-specific carbon isotope composition, full-molecular δ 13 C, thermal maturity, and variation in organic matter precursors. Our goal is to advance the understanding of the sources and histories of short-chain alkanes within geologic systems. Our findings suggest that propane varies in its site-specific carbon isotope structure, which is correlated with increasing thermal maturity, first increasing in terminal position δ 13 C and then increasing in both center and terminal position δ 13 C. This pattern is observed in both experimental and natural samples, and is plausibly explained by a combination of site-specific, temperature-dependent isotope effects associated with conversion of different precursor molecules (kerogen, bitumen, and/or oil) to propane, differences in site-specific isotopic contents of those precursors, and possibly distillation of reactive components of those precursors with increasing maturity. We hypothesize that the largest changes in site-specific isotopic content of propane occur when bitumen and/or oil replace kerogen as the dominant precursors. If correct, this phenomenon could have significant utility for understanding gas generation in thermogenic petroleum systems.

Geochimica et Cosmochimica Acta↗

USGS2010

Carbon dioxide on the satellites of Saturn: Results from the Cassini VIMS investigation and revisions to the VIMS wavelength scale

Several of the icy satellites of Saturn show the spectroscopic signature of the asymmetric stretching mode of C-O in carbon dioxide (CO 2 ) at or near the nominal solid-phase laboratory wavelength of 4.2675 ??m (2343.3 cm -1 ), discovered with the Visible-Infrared Mapping Spectrometer (VIMS) on the Cassini spacecraft. We report here on an analysis of the variation in wavelength and width of the CO 2 absorption band in the spectra of Phoebe, Iapetus, Hyperion, and Dione. Comparisons are made to laboratory spectra of pure CO 2 , CO 2 clathrates, ternary mixtures of CO 2 with other volatiles, implanted and adsorbed CO 2 in non-volatile materials, and ab initio theoretical calculations of CO 2 * nH 2 O. At the wavelength resolution of VIMS, the CO 2 on Phoebe is indistinguishable from pure CO 2 ice (each molecule's nearby neighbors are also CO 2 ) or type II clathrate of CO 2 in H 2 O. In contrast, the CO 2 band on Iapetus, Hyperion, and Dione is shifted to shorter wavelengths (typically ???4.255 ??m (???2350.2 cm -1 )) and broadened. These wavelengths are characteristic of complexes of CO 2 with different near-neighbor molecules that are encountered in other volatile mixtures such as with H 2 O and CH 3 OH, and non-volatile host materials like silicates, some clays, and zeolites. We suggest that Phoebe's CO 2 is native to the body as part of the initial inventory of condensates and now exposed on the surface, while CO 2 on the other three satellites results at least in part from particle or UV irradiation of native H 2 O plus a source of C, implantation or accretion from external sources, or redistribution of native CO 2 from the interior. The analysis presented here depends on an accurate VIMS wavelength scale. In preparation for this work, the baseline wavelength calibration for the Cassini VIMS was found to be distorted around 4.3 ??m, apparently as a consequence of telluric CO 2 gas absorption in the pre-launch calibration. The effect can be reproduced by convolving a sequence of model detector response profiles with a deep atmospheric CO 2 absorption profile, producing distorted detector profile shapes and shifted central positions. In a laboratory blackbody spectrum used for radiance calibration, close examination of the CO 2 absorption profile shows a similar deviation from that expected from a model. These modeled effects appear to be sufficient to explain the distortion in the existing wavelength calibration now in use. A modification to the wavelength calibration for 13 adjacent bands is provided. The affected channels span about 0.2 ??m centered on 4.28 ??m. The maximum wavelength change is about 10 nm toward longer wavelength. This adjustment has implications for interpretation of some of the spectral features observed in the affected wavelength interval, such as from CO 2 , as discussed in this paper.

Icarus↗

USGS2018

Evidence for major input of riverine organic matter into the ocean

The changes in the structure of XAD-8 isolated dissolved organic matter (DOM) samples along a river (Penobscot River) to estuary (Penobscot Bay) to ocean (across the Gulf of Maine) transect and from the Pacific Ocean were investigated using selective and two dimensional (2D) nuclear magnetic resonance (NMR) spectroscopy coupled with elemental and carbon isotope analysis. The results provide important insights into the nature of relatively stable structures in the river-to-ocean continuum and the enigma of the fate of terrestrial DOM in the marine system. First, lignin and carboxyl-rich alicyclic molecules (CRAMs), which are indistinguishable from mass spectrometry, were clearly differentiated with NMR spectroscopy. NMR unambiguously showed that CRAMs persisted along the river-to-ocean transect and in the Pacific Ocean, while lignin residues dramatically decreased in abundance from the river to the coastal ocean and the Pacific Ocean. The results challenge a previous conclusion that lignin-derived compounds are refractory and can accumulate in the coastal ocean. The loss of terrestrial plant-derived aromatic compounds such as lignin and tannin residues throughout the sequence of riverine, coastal, and open ocean DOM extracts could also partially explain the decreasing organic carbon recovery by XAD-8 isolation and the change in carbon stable isotope composition from riverine DOM (δ 13 C −27.6‰) to ocean DOM (δ 13 C −23.0‰) extracts. The observation, from advanced NMR, of similar CRAM molecules in XAD-8 isolated DOM samples from the Penobscot River to the Penobscot Bay and from the ocean refutes a previous conclusion that XAD-isolated DOM samples from seawater and river are distinctly different. The alicyclic structural features of CRAMs and their presence as the major structural units in DOM extracts from the Penobscot River to Gulf of Maine transect, together with the deduced old 14 C age of CRAMs in the ocean, imply that terrestrial CRAMs may persist on timescales long enough to be transported into the ocean.

Organic Geochemistry↗