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USGS2012

Molecular dynamics simulation of nitric oxide in myoglobin

The infrared (IR) spectroscopy and ligand migration of photodissociated nitric oxide (NO) in and around the active sites in myoglobin (Mb) are investigated. A distributed multipolar model for open-shell systems is developed and used, which allows one to realistically describe the charge distribution around the diatomic probe molecule. The IR spectra were computed from the trajectories for two conformational substates at various temperatures. The lines are narrow (width of 3–7 cm –1 at 20–100 K), in agreement with the experimental observations where they have widths of 4–5 cm –1 at 4 K. It is found that within one conformational substate (B or C) the splitting of the spectrum can be correctly described compared with recent experiments. Similar to photodissociated CO in Mb, additional substates exist for NO in Mb, which are separated by barriers below 1 kcal/mol. Contrary to full quantum mechanical calculations, however, the force field and mixed QM/MM simulations do not correctly describe the relative shifts between the B- and C-states relative to gas-phase NO. Free energy simulations establish that NO preferably localizes in the distal site and the barrier for migration to the neighboring Xe4 pocket is Δ G B→C = 1.7–2.0 kcal/mol. The reverse barrier is Δ G B←C = 0.7 kcal/mol, which agrees well with the experimental value of 0.7 kcal/mol, estimated from kinetic data.

Journal of Physical Chemistry↗

USGS1998

Optical-cell evidence for superheated ice under gas-hydrate-forming conditions

We previously reported indirect but compelling evidence that fine-grained H 2 O ice under elevated CH 4 gas pressure can persist to temperatures well above its ordinary melting point while slowly reacting to form methane clathrate hydrate. This phenomenon has now been visually verified by duplicating these experiments in an optical cell while observing the very slow hydrate-forming process as the reactants were warmed from 250 to 290 K at methane pressures of 23 to 30 MPa. Limited hydrate growth occurred rapidly after initial exposure of the methane gas to the ice grains at temperatures well within the ice subsolidus region. No evidence for continued growth of the hydrate phase was observed until samples were warmed above the equilibrium H 2 O melting curve. With continued heating, no bulk melting of the ice grains or free liquid water was detected anywhere within the optical cell until hydrate dissociation conditions were reached (292 K at 30 MPa), even though full conversion of the ice grains to hydrate requires 6−8 h at temperatures approaching 290 K. In a separate experimental sequence, unreacted portions of H 2 O ice grains that had persisted to temperatures above their ordinary melting point were successfully induced to melt, without dissociating the coexisting hydrate in the sample tube, by reducing the pressure overstep of the equilibrium phase boundary and thereby reducing the rate of hydrate growth at the ice−hydrate interface. Results from similar tests using CO 2 as the hydrate-forming species demonstrated that this superheating effect is not unique to the CH 4 −H 2 O system.

Journal of Physical Chemistry B↗

USGS1967

Pressure derivatives of elastic moduli of fused quartz to 10 kb

Measurements of the longitudinal and shear moduli were made on fused quartz to 10 kb at 24·5°C. The anomalous behavior of the bulk modulus K at low pressure, ∂K ∂P < 0 "> ∂K∂P< 0 , begins to approach the “normal” behavior of solids, ∂K ∂P > 0 "> ∂K∂P> 0 , at higher pressures. The pressure derivative of the rigidity modulus ∂G ∂P "> ∂G∂P remains constant and negative for the pressure range covered. A 15-kb hydrostatic pressure vessel is described for use with ultrasonic pulse instrumentation for precise measurements of elastic moduli and density changes with pressure. The placing of the transducer outside the pressure medium, and the use of C -ring pressure seals result in ease of operation and simplicity of design.

Journal of Physics and Chemistry of Solids↗

USGS1977

Cell dimensions and antiferromagnetism of lunar and terrestrial ilmenite single crystals

X-Ray diffraction and anisotropic magnetic measurements have been made on single crystals of lunar ilmenite and on terrestrial ilmenite from Bancroft, Ontario, Canada and the Ilmen Mountains, U.S.S.R. The elongated c "> c -axis of lunar ilmenite, previously reported, is confirmed by new measurements. The shorter c "> c -axis found in terrestrial specimens is ascribed to Fe 3+ substitution for Ti 4+ in the titanium layer. Magnetic measurements on the same specimens show that, in agreement with the Ishikawa-Shirane et al . model, the initial shortening of the c "> c -axis by the above substitution of small amounts of Fe 3+ (<8%) causes an increase in Fe 2+ −Fe 2+ exchange coupling through Fe 3+ in the titanium layer that lowers the Néel transition temperature. The Weiss temperatures and other magnetic parameters confirm this model proposed by Ishikawa and Shirane et al . Additional transitions found in one of the terrestrial specimens (Bancroft) have been ascribed to a small amount of an exsolved spinel phase, possibly a solid solution phase of magnetite-ülvospinel. The spinel phase is localized in hematite-rich blebs which exsolved from the host ilmenite-rich phase.

Journal of Physics and Chemistry of Solids↗

USGS1977

Anisotropic magnetic susceptibility of erbium and ytterbium in zircon, ZrSiO4

Magnetic susceptibility measurements have been made for both Er- and Yb-doped (1̃0 3 ppm) zircon single crystals with the magnetic field perpendicular and parallel to the [001] axis. Large susceptibility anisotropies were found in both cases. Our observed anisotropies of ZrSiO 4 : Yb indicate small populations (1̃9%) of Yb ions at the axial (tetragonal) sites, as the susceptibility of ZrSiO 4 : Yb would be nearly isotropic if the Yb ions only occupied the orthorhombic sites. For Er 3+ in orthorhombic sites of zircon, our data indicate that the first excited state is paramagnetic with g x = 9 and g y 5̃ at 20 cm −1 above the ground state ( g x 0̃, g y 1̃5). The first excited state is quite similar to the ground states observed for Er 3+ in many host lattices

Journal of Physics and Chemistry of Solids↗

USGS1971

Magnetic susceptibility and triangular exchange coupling in the tourmaline mineral group

Magnetic susceptibilities of three iron-rich tourmaline crystals from Mexquitic (Mexico), Pierpont (New York), and Madagascar with different and known chemical compositions have been studied from 8° to 300°K. The iron atoms in the tourmaline crystal structure, space group R3m , a∼15·9, c∼7·2 , are situated at the three corners of an equilateral triangle and are close enough for magnetic exchange interaction. For buergerite, the Mexquitic sample, the susceptibility data lead to an exchange constant J/k of 7·5°K. Although the amount of aluminum would be sufficient to fill point position 18(c) exactly, the magnetic data are consistent with some substitution of ferric iron for aluminum, as previously determined from X-ray and neutron diffraction studies. Some aluminum thus replaces iron in position 9(b). Exchange constants were also estimated for the other two magnesium-iron specimens, of which the madagascar sample is aluminum deficient. The results agree with the evidence from optical spectra that there is considerable deviation from octahedral symmetry in the oxygen coordination polyhedra about the 9(b) and 18(c) point positions.

New York↗

USGS1984

Adsorption of goethite onto quartz and kaolinite

The adsorption of colloidal goethite onto quartz and kaolinite substrates has been studied as a function of pH and NaCl concentration. Goethite adsorption was measured quantitatively by Fourier-transform infrared spectroscopy. The results indicate that adsorption onto both substrates is due primarily to coulombic forces; however, the pH dependence of adsorption is very different for the two substrates. This is explained by the fact that the surface charge on quartz is entirely pH-dependent, while kaolinite has surface faces which carry a permanent negative charge. Adsorption of goethite on to kaolinite increases markedly with increasing NaCl concentration, while adsorption onto quartz is relatively independent of NaCl concentration. This can be explained by the influence of NaCl concentration upon the development of surface charge on the substrates. A method is described for separating surface-bound goethite from free goethite.

Journal of the Chemical Society, Faraday Transacti↗

USGS1989

Shape-selective adsorption of aromatic molecules from water by tetramethylammonium-smectite

The adsorption of aromatic compounds by smectite exchanged with tetramethylammonium (TMA) has been studied. Aromatic compounds adsorbed by TMA-smectite are assumed to adopt a tilted orientation in a face-to-face arrangment with the TMA tetrahedra. The sorptive characteristics of TMA-smectite were influenced strongly by the presence of water. The dry TMA-smectite showed little selectivity in the uptake of benzen, toluene and xylene. In the presence of water, TMA-smectite showed a high degree of selectivity based on molecular size/shape, resulting in high uptake of benzene and progressively lower uptake of larger aromatic molecules. This selectivity appeared to result from the shrinkage of interlamellar cavities by water.

Journal of the Chemical Society, Faraday Transacti↗

USGS1987

Mineralogy and petrology of the Cretaceous- Tertiary boundary clay bed and adjacent clay-rich rocks, Raton Basin, New Mexico and Colorado.

The Cretaceous-Tertiary (K-T) boundary is preserved in a sequence of coal-bearing, fluvial rocks in the lower part of the Raton Formation (Late Cretaceous and Paleocene) at several sites in the east-central part of the Raton Basin. The K-T boundary occurs at the top of a kaolinitic claystone layer, commonly referred to as the "boundary clay layer," in an interval of coal and carbonaceous shale. The boundary is defined by the disappearance of certain fossil-pollen taxa. The boundary clay layer also contains shocked quartz grains and abundance anomalies of iridium, chromium, and other elements. Each of these characteristics support the hypothesis of an asteroid impact at the end of the Cretaceous. Small goyazite spheres were also found in the boundary clay bed; however, their origin is uncertain. X-ray powder diffraction (XRD), scanning electron microscopy (SEM), and thin-section petrography have shown that the boundary clay bed exhibits unique mineralogic and petrologic characteristics not possessed by other clay-rich beds in coal-bearing rocks of the Raton Basin. The boundary clay bed is composed primarily of well-crystallized kaolinite but also contains subordinate, randomly interstratified, mixed-layer illite/smectite, both of which appear to have been formed by the alteration of vitreous material in a coal-swamp environment. The bulk mineralogy of the boundary clay bed is similar to that of other kaolinite-rich clay beds (tonsteins) that altered in coal swamps from airfall volcanic ash. The alteration process and diagenetic products of the host material in the boundary clay bed, however, differed from those of the tonsteins, resulting in a unique petrographic fabric. The boundary clay bed is characterized by an overall imbricate fabric that may reflect an original vitreous material that included shards, bubbles, and spheres. The original fallout material of the boundary clay bed first altered to "cabbage-like" microspherules, indicating a halloysite or allophane precursor, and then to well-crystallized kaolinite; the well-crystallized kaolinite is the diagenetic stable phase for these rocks at their maximum burial conditions. In comparison, the vitreous components of the tonsteins were altered directly to coarse vermicular and platey kaolinite. Alteration of the original fallout material in the boundary bed was probably rapid, leading to hydrated, disordered, fine-grained clay minerals that formed into curled spherical or tubular shapes. The factors that produced these unique fabrics in the boundary clay bed existed at all K-T sites in the Raton Basin and were much different from those that formed the coarse platey and vermicular fabrics of ordinary tonsteins. The distinctive character of the boundary clay may be due to the unique nature and chemistry of the fallout material and (or) physical or chemical conditions existing shortly after its deposition.

Journal of Sedimentary Petrology↗

USGS2003

Temperature, pressure, and compositional effects on anomalous or "self" preservation of gas hydrates

We previously reported on a thermal regime where pure, polycrystalline methane hydrate is preserved metastably in bulk at up to 75 K above its nominal temperature stability limit of 193 K at 0.1 MPa, following rapid release of the sample pore pressure. Large fractions (>50 vol.%) of methane hydrate can be preserved for 2-3 weeks by this method, reflecting the greatly suppressed rates of dissociation that characterize this "anomalous preservation" regime. This behavior contrasts that exhibited by methane hydrate at both colder (193-240 K) and warmer (272-290 K) isothermal test conditions, where dissociation rates increase monotonically with increasing temperature. Here, we report on recent experiments that further investigate the effects of temperature, pressure, and composition on anomalous preservation behavior. All tests conducted on sI methane hydrate yielded self-consistent results that confirm the highly temperature-sensitive but reproducible nature of anomalous preservation behavior. Temperature-stepping experiments conducted between 250 and 268 K corroborate the relative rates measured previously in isothermal preservation tests, and elevated pore-pressure tests showed that, as expected, dissociation rates are further reduced with increasing pressure. Surprisingly, sII methane-ethane hydrate was found to exhibit no comparable preservation effect when rapidly depressurized at 268 K, even though it is thermodynamically stable at higher temperatures and lower pressures than sI methane hydrate. These results, coupled with SEM imaging of quenched sample material from a variety of dissociation tests, strongly support our earlier arguments that ice-"shielding" effects provided by partial dissociation along hydrate grain surfaces do not serve as the primary mechanism for anomalous preservation. The underlying physical-chemistry mechanism(s) of anomalous preservation remains elusive, but appears to be based more on textural or morphological changes within the hydrate material itself, rather than on compositional zoning or ice-rind development.

Canadian Journal of Physics↗

USGS2006

Description, Properties, and Degradation of Selected Volatile Organic Compounds Detected in Ground Water--A Review of Selected Literature

This report provides abridged information describing the most salient properties and biodegradation of 27 chlorinated volatile organic compounds detected during ground-water studies in the United States. This information is condensed from an extensive list of reports, papers, and literature published by the U.S. Government, various State governments, and peer-reviewed journals. The list includes literature reviews, compilations, and summaries describing volatile organic compounds in ground water. This report cross-references common names and synonyms associated with volatile organic compounds with the naming conventions supported by the International Union of Pure and Applied Chemistry. In addition, the report describes basic physical characteristics of those compounds such as Henry's Law constant, water solubility, density, octanol-water partition (log Kow), and organic carbon partition (log Koc) coefficients. Descriptions and illustrations are provided for natural and laboratory biodegradation rates, chemical by-products, and degradation pathways.

Open-File Report↗

USGS1973

The chemistry of five accessory rock-forming apatites

Chemical and physical data are given for five samples of rock-forming apatite from diverse geologic environments in Nevada and Colorado. Four of these apatites contain rare-earth assemblages in which the cerium group is well represented but the yttrium group predominates. The fifth apatite contains a highly fractionated assemblage of the lighter (cerium group) rare earths similar to the assemblage typical of alkulic rocks.

Nevada, Colorado↗

USGS1990

Modelling streamwater chemistry as a mixture of soilwater end-members - An application to the Panola Mountain catchment, Georgia, U.S.A.

Streamwater chemistry at Panola Mountain research catchment, Georgia, U.S.A., is explained as a mixture of representative soilwater solutions that are considered to be temporally invariant to a first approximation. The selection of three end-members from all sampled soil waters is evaluated by comparing the observed and predicted streamwater concentration of six solutes (alkalinity, sulfate, sodium, magnesium, calcium and dissolved silica), which are assumed to mix conservatively, and by assessing the consistency of the implied hydrograph separation with the hydrological mechanisms that are believed to be operating in this catchment. The percentage of variation in the streamwater solute concentrations explained by the end-member mixing analysis (EMMA) ranges from 82 to >97%, and the hydrograph separation is, intuitively, physically reasonable. If the correct end-members have been identified, the streamwater chemical response to different levels of acidic deposition can be predicted by examining the change in each end-member under different loads; no hydrological model is required. If a traditional hydrochemical model, which is driven by rainfall quantity and quality, is desired, this analysis provides an indication of the model structure that would be necessary to reproduce both streamwater and soilwater chemistry.

Georgia↗

USGS2019

Discriminating among Pacific salmon, Rainbow Trout, and Atlantic Salmon species using common genetic screening methods

The five most common species of Pacific salmon, Rainbow Trout (steelhead) Oncorhynchus spp., and Atlantic Salmon Salmo salar intermingle in the North Pacific Ocean and its freshwater tributaries. Efficient morphological methods for distinguishing among these species are sometimes limited by condition of the specimen (degraded or missing morphology), life history stage, or training of the observer. Researchers have successfully applied various genetic methods to distinguish among these species when morphological analyses are not possible, but they cannot easily incorporate these methods into standard fish and wildlife population monitoring analysis workflows. Here we test five 5′–3′ exonuclease (TaqMan) assays developed from mitochondrial genes and provide novel methods that take advantage of TaqMan output to distinguish among these species. We found that combinations of as few as two of the five assays were adequate to distinguish all species. TaqMan chemistry is designed to interrogate a single nucleotide locus. We also explore the basis for the variation in the observed scatter plot distributions (variation in florescent signals) and show that this variation is due to nucleotide diversity in and near the probe site. Because the SNPs underlying the assays developed here are all physically close to one another along the mitochondrial genome, the potential exists to develop a single DNA sequence-based assay to discriminate among salmon species. This single assay can be added to a genotyping-by-sequencing panel to identify and exclude nontarget species from analyses.

Journal of Fish and Wildlife Management↗

USGS2000

Contaminant distribution and accumulation in the surface sediments of Long Island Sound

The distribution of contaminants in surface sediments has been measured and mapped as part of a U.S. Geological Survey study of the sediment quality and dynamics of Long Island Sound. Surface samples from 219 stations were analyzed for trace (Ag, Ba, Cd, Cr, Cu, Hg, Ni, Pb, V, Zn and Zr) and major (Al, Fe, Mn, Ca, and Ti) elements, grain size, and Clostridium perfringens spores. Principal Components Analysis was used to identify metals that may covary as a function of common sources or geochemistry. The metallic elements generally have higher concentrations in fine-grained deposits, and their transport and depositional patterns mimic those of small particles. Fine-grained particles are remobilized and transported from areas of high bottom energy and deposited in less dynamic regions of the Sound. Metal concentrations in bottom sediments are high in the western part of the Sound and low in the bottom-scoured regions of the eastern Sound. The sediment chemistry was compared to model results (Signell et al., 1998) and maps of sedimentary environments (Knebel et al., 1999) to better understand the processes responsible for contaminant distribution across the Sound. Metal concentrations were normalized to grain-size and the resulting ratios are uniform in the depositional basins of the Sound and show residual signals in the eastern end as well as in some local areas. The preferential transport of fine-grained material from regions of high bottom stress is probably the dominant factor controlling the metal concentrations in different regions of Long Island Sound. This physical redistribution has implications for environmental management in the region.

Long Island Sound↗

USGS2010

Regional and grain size influences on the geochemistry of soil at Gusev Crater

Congruous with earlier work, Martian soil along the Spirit Rover's traverse at Gusev crater can be divided into three broad groups by size: fines (<150 μ m), sand, and a mix of various grain sizes. The key chemical observation is greater homogeneity in fines relative to the other two, consistent with regional‐ and global‐scale sampling of chemical compositions by finer particle sizes. The mix class is generally more heterogeneous as are samples from the Columbia Hills within each class. Variation in the trace element Ni is consistent with a CI contribution not exceeding 3%, while that of Ti is compatible with Fe‐Ti oxide enrichment not exceeding 3%. Physical mixing models are poorly supported. Among many potential binary and three‐component mixing models, only two show some consistency with the soil data: typical fines with the opaline Si end‐member identified at Home Plate and typical fines with sulfates (bearing a variable mix of Ca, Fe, and Mg cations). We also infer that binary mixing transcends classes, contrasting strongly with terrestrial sediments, and that mixing trends are consistent with significant nonmixing contributions, perhaps including localized chemical alteration. The decoupling between chemistry and grain size classes also suggests that processes linking composition with grain size, such as heavy mineral sorting, may have been minimal or absent entirely. The primary exception to this is the correlation between Cl and Si, Cl‐S, and Al‐Si, which is strongest in the fines class.

Journal of Geophysical Research E: Planets↗

USGS1991

Capture myopathy in an endangered sandhill crane (Grus canadensis pulla)

Despite precautions to protect cranes, a 3-year-old endangered Mississippi sandhill crane ( Grus canadensis pulla ) was found caught in a leghold trap in Gautier, Mississippi, on 11 November 1987. The bird could have been in the trap for up to 16 hr and was standing and struggling to escape when it was discovered. Serum chemistries of the crane on 12 November revealed elevated lactic dehydrogenase (2,880 IU/L), alanine aminotransferase (ALT) (152 IU/L), and aspartate aminotransferase (AST) (>1,000 IU/L) values. Following surgical amputation of a fractured toe, the bird never attempted to stand and was unable to stand even when manually supported. Radiographic and physical examination of both legs did not reveal any anatomical abnormalities. Despite medical care, including supportive therapy, no improvement was observed in the bird's ability to stand and to support itself, and the bird died on 19 November. Serum chemistries and the postmortem and histopathologic findings were compatible with capture myopathy described in other species. Because of the possible susceptibility of long-legged birds such as the Mississippi sandhill crane to capture myopathy, special care must be taken when trapping, handling, chemically immobilizing, and transporting these species. In addition, precautions must be taken when conducting a predator-control program to ensure that nontarget wildlife are unlikely to encounter traps. Capture myopathy has only rarely been observed in wild birds, and this case represents the first report in a Mississippi sandhill crane.

Mississippi↗

USGS2013

Hydrologic controls on the transport and cycling of carbon and nitrogen in a boreal catchment underlain by continuous permafrost

Boreal ecosystems represent a large carbon (C) reservoir and a substantial source of greenhouse gases. Hydrologic conditions dictate whether C leached from boreal soils is processed in catchments or flushed to less productive environments via the stream. This study quantified hydrologic and biogeochemical C loss from a boreal catchment underlain by frozen silt, where flowpaths may deepen as the active layer thaws over the summer. We hypothesized a decrease in the magnitude of C mineralization over the summer associated with changing flowpaths and decreasing hydrologic connectivity, organic matter lability, and nitrogen (N) availability. Conservative tracers were used to partition C and N loss between catchment export and biogeochemical processing. Coupling tracers with tributary and porewater chemistry indicated C and N cycling in soil flowpaths, with an exponential decrease over the summer. Nitrate was primarily reduced in hillslope flowpaths and the lack of N reaching the stream appeared to limit C mineralization. Stream export accounted for the greatest loss of C, removing 247 and 113 mol hr −1 in the early and late summer, respectively. Reactivity was related to hydrologic connectivity between the soils and stream, which was greatest early in the summer and following a large flood. While a warming climate may increase storage potential in thawed soils, the early‐season flush of labile material and late‐season runoff through mineral flowpaths may maintain high C export rates. Therefore, we highlight physical export as a dominant cause of aqueous C loss from silty catchments as the Arctic continues to thaw.

Journal of Geophysical Research G: Biogeosciences↗