Science.gov

Sample records for adjacent water molecules

  1. Synthesis of a Molecule with Four Different Adjacent Pnictogens.

    PubMed

    Hinz, Alexander; Schulz, Axel; Villinger, Alexander

    2016-08-22

    The synthesis of a molecule containing four adjacent different pnictogens was attempted by conversion of a Group 15 allyl analogue anion [Mes*NAsPMes*](-) (Mes*=2,4,6-tri-tert-butylphenyl) with antimony(III) chloride. A suitable precursor is Mes*N(H)AsPMes* (1) for which several syntheses were investigated. The anions afforded by deprotonation of Mes*N(H)AsPMes* were found to be labile and, therefore, salts could not be isolated. However, the in situ generated anions could be quenched with SbCl3 , yielding Mes*N(SbCl2 )AsPMes* (4). PMID:27377437

  2. 33 CFR 80.1395 - Puget Sound and adjacent waters.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Puget Sound and adjacent waters... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Thirteenth District § 80.1395 Puget Sound and adjacent waters. The 72 COLREGS shall apply on all waters of Puget Sound and adjacent waters, including Lake...

  3. 33 CFR 80.1395 - Puget Sound and adjacent waters.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Puget Sound and adjacent waters... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Thirteenth District § 80.1395 Puget Sound and adjacent waters. The 72 COLREGS shall apply on all waters of Puget Sound and adjacent waters, including Lake...

  4. 33 CFR 80.1395 - Puget Sound and adjacent waters.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Puget Sound and adjacent waters... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Thirteenth District § 80.1395 Puget Sound and adjacent waters. The 72 COLREGS shall apply on all waters of Puget Sound and adjacent waters, including Lake...

  5. 33 CFR 80.1395 - Puget Sound and adjacent waters.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Puget Sound and adjacent waters... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Thirteenth District § 80.1395 Puget Sound and adjacent waters. The 72 COLREGS shall apply on all waters of Puget Sound and adjacent waters, including Lake...

  6. 33 CFR 80.1395 - Puget Sound and adjacent waters.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Puget Sound and adjacent waters... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Thirteenth District § 80.1395 Puget Sound and adjacent waters. The 72 COLREGS shall apply on all waters of Puget Sound and adjacent waters, including Lake...

  7. 7. VIEW OF WATER TREATMENT PLANT, ADJACENT TO THE COAL ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    7. VIEW OF WATER TREATMENT PLANT, ADJACENT TO THE COAL CONVEYOR; IN THE DISTANCE IS THE FREQUENCY CHANGER HOUSE, WHICH IS ATTACHED TO SWITCH HOUSE NO. 1; LOOKING WEST. - Commonwealth Electric Company, Fisk Street Electrical Generating Station, 1111 West Cermak Avenue, Chicago, Cook County, IL

  8. How subaerial salt extrusions influence water quality in adjacent aquifers

    NASA Astrophysics Data System (ADS)

    Mehdizadeh, Razieh; Zarei, Mehdi; Raeisi, Ezzat

    2015-12-01

    Brines supplied from salt extrusions cause significant groundwater salinization in arid and semi-arid regions where salt rock is exposed to dissolution by episodic rainfalls. Here we focus on 62 of the 122 diapirs of Hormuz salt emergent in the southern Iran. To consider managing the degradation effect that salt extrusions have on the quality of adjoining aquifers, it is first necessary to understand how they influence adjacent water resources. We evaluate here the impacts that these diapirs have on adjacent aquifers based on investigating their geomorphologies, geologies, hydrologies and hydrogeologies. The results indicate that 28/62 (45%) of our sample of salt diapirs have no significant impact on the quality of groundwater in adjoining aquifers (namely Type N), while the remaining 34/62 (55%) degrade nearby groundwater quality. We offer simple conceptual models that account for how brines flowing from each of these types of salt extrusions contaminate adjacent aquifers. We identify three main mechanisms that lead to contamination: surface impact (Type A), subsurface intrusion (Type B) and indirect infiltration (Type C). A combination of all these mechanisms degrades the water quality in nearby aquifers in 19/62 (31%) of the salt diapirs studied. Having characterized the mechanism(s) by which each diapir affects the adjacent aquifer, we suggest a few possible remediation strategies to be considered. For instance, engineering the surface runoff of diapirs Types A and C into nearby evaporation basins would improve groundwater quality.

  9. 33 CFR 110.140 - Buzzards Bay, Nantucket Sound, and adjacent waters, Mass.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ..., and adjacent waters, Mass. 110.140 Section 110.140 Navigation and Navigable Waters COAST GUARD..., Nantucket Sound, and adjacent waters, Mass. Link to an amendment published at 76 FR 35744, June 20, 2011. (a... adjacent waters, Mass. (a) * * * (2) Anchorage B. All waters bounded by a line beginning at 41°36′42.3″...

  10. Spectroscopic modeling of water molecule

    NASA Astrophysics Data System (ADS)

    Danylo, R. I.; Okhrimenko, B. A.

    2013-12-01

    This research is devoted to the vibrational spectroscopy inverse problem solution that gives a possibility to design a molecule and make conclusions about its geometry. The valence angle finding based on the usage of inverse spectral vibrational spectroscopy problem is a well-known task. 3N-matrix method was chosen to solve the proposed task. The usage of this method permits to make no assumptions about the molecule force field, besides it can be applied to molecules of matter in liquid state. Anharmonicity constants assessment is an important part of the valence angle finding. The reduction to zero vibrations is necessary because used matrix analytical expression were found in the harmonic approach. In order to find the single-valued inverse spectral problem of vibrational spectroscopy solution a shape parameter characterizing "mixing" of ω1 and ω2 vibrations forms must be found. The minimum of such a function Υ called a divergence parameter was found. This function characterizes method's accuracy. The valence angle assessment was reduced to the divergence parameter minimization. The β value concerning divergence parameter minimum was interpreted as the desired valence angle. The proposed method was applied for water molecule in liquid state: β = (88,8 ±1,7)° . The found angle fits the water molecule nearest surrounding tetrahedral model including hydrogen bond curvature in the first approximation.

  11. Water molecules orientation in surface layer

    NASA Astrophysics Data System (ADS)

    Klingo, V. V.

    2000-08-01

    The water molecules orientation has been investigated theoretically in the water surface layer. The surface molecule orientation is determined by the direction of a molecule dipole moment in relation to outward normal to the water surface. Entropy expressions of the superficial molecules in statistical meaning and from thermodynamical approach to a liquid surface tension have been found. The molecules share directed opposite to the outward normal that is hydrogen protons inside is equal 51.6%. 48.4% water molecules are directed along to surface outward normal that is by oxygen inside. A potential jump at the water surface layer amounts about 0.2 volts.

  12. 33 CFR 334.70 - Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 3 2011-07-01 2011-07-01 false Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations. 334.70 Section 334.70 Navigation and Navigable Waters CORPS... REGULATIONS § 334.70 Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations. (a)...

  13. 33 CFR 334.70 - Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 3 2013-07-01 2013-07-01 false Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations. 334.70 Section 334.70 Navigation and Navigable Waters CORPS... REGULATIONS § 334.70 Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations. (a)...

  14. 33 CFR 334.70 - Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 3 2012-07-01 2012-07-01 false Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations. 334.70 Section 334.70 Navigation and Navigable Waters CORPS... REGULATIONS § 334.70 Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations. (a)...

  15. 33 CFR 110.140 - Buzzards Bay, Nantucket Sound, and adjacent waters, Mass.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Buzzards Bay, Nantucket Sound, and adjacent waters, Mass. 110.140 Section 110.140 Navigation and Navigable Waters COAST GUARD..., Nantucket Sound, and adjacent waters, Mass. (a) New Bedford Outer Harbor—(1) Anchorage A. West of...

  16. 33 CFR 110.140 - Buzzards Bay, Nantucket Sound, and adjacent waters, Mass.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Buzzards Bay, Nantucket Sound, and adjacent waters, Mass. 110.140 Section 110.140 Navigation and Navigable Waters COAST GUARD..., Nantucket Sound, and adjacent waters, Mass. (a) New Bedford Outer Harbor—(1) Anchorage A. West of...

  17. 33 CFR 110.140 - Buzzards Bay, Nantucket Sound, and adjacent waters, Mass.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Buzzards Bay, Nantucket Sound, and adjacent waters, Mass. 110.140 Section 110.140 Navigation and Navigable Waters COAST GUARD..., Nantucket Sound, and adjacent waters, Mass. (a) New Bedford Outer Harbor—(1) Anchorage A. West of...

  18. 33 CFR 334.70 - Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 3 2014-07-01 2014-07-01 false Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations. 334.70 Section 334.70 Navigation and Navigable Waters CORPS... REGULATIONS § 334.70 Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations. (a)...

  19. 33 CFR 110.140 - Buzzards Bay, Nantucket Sound, and adjacent waters, Mass.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Buzzards Bay, Nantucket Sound, and adjacent waters, Mass. 110.140 Section 110.140 Navigation and Navigable Waters COAST GUARD..., Nantucket Sound, and adjacent waters, Mass. (a) New Bedford Outer Harbor—(1) Anchorage A. West of...

  20. 33 CFR 334.70 - Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations. 334.70 Section 334.70 Navigation and Navigable Waters CORPS... REGULATIONS § 334.70 Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations. (a)...

  1. 33 CFR 110.168 - Hampton Roads, Virginia and adjacent waters (Datum: NAD 83).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... explosives, as defined in 49 CFR 173.50. Dangerous cargo means “certain dangerous cargo” as defined in § 160... adjacent waters (Datum: NAD 83). 110.168 Section 110.168 Navigation and Navigable Waters COAST GUARD..., Virginia and adjacent waters (Datum: NAD 83). (a) Anchorage Grounds—(1) Anchorage A . The waters bounded...

  2. 33 CFR 165.1303 - Puget Sound and adjacent waters, WA-regulated navigation area.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Puget Sound and adjacent waters... § 165.1303 Puget Sound and adjacent waters, WA—regulated navigation area. (a) The following is a... Light to New Dungeness Light and all points in the Puget Sound area north and south of these lights....

  3. 33 CFR 165.1303 - Puget Sound and adjacent waters, WA-regulated navigation area.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 2 2011-07-01 2011-07-01 false Puget Sound and adjacent waters... § 165.1303 Puget Sound and adjacent waters, WA—regulated navigation area. (a) The following is a... Light to New Dungeness Light and all points in the Puget Sound area north and south of these lights....

  4. 33 CFR 165.1303 - Puget Sound and adjacent waters, WA-regulated navigation area.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 2 2013-07-01 2013-07-01 false Puget Sound and adjacent waters... § 165.1303 Puget Sound and adjacent waters, WA—regulated navigation area. (a) The following is a... Light to New Dungeness Light and all points in the Puget Sound area north and south of these lights....

  5. 33 CFR 165.1303 - Puget Sound and adjacent waters, WA-regulated navigation area.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 2 2014-07-01 2014-07-01 false Puget Sound and adjacent waters... § 165.1303 Puget Sound and adjacent waters, WA—regulated navigation area. (a) The following is a... Light to New Dungeness Light and all points in the Puget Sound area north and south of these lights....

  6. 33 CFR 165.1303 - Puget Sound and adjacent waters, WA-regulated navigation area.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 2 2012-07-01 2012-07-01 false Puget Sound and adjacent waters... § 165.1303 Puget Sound and adjacent waters, WA—regulated navigation area. (a) The following is a... Light to New Dungeness Light and all points in the Puget Sound area north and south of these lights....

  7. Design of water molecule and its surrounding

    NASA Astrophysics Data System (ADS)

    Danylo, R. I.; Okhrimenko, B. A.; Yablochkova, K. S.

    2015-02-01

    Hydrogen bonds and their fluctuations are one of the factors that determine the unique properties of water [1]. Building models of formation and rupture of hydrogen bonds due to non-eigen vibrations of a molecule of water is to a large extent determined by the availability of accurate information on the geometric structure of the water molecule. Geometric parameters of the water molecule have been well studied for the gaseous state. This was aided by the possibility of an experimental study of the regularities in the rotational spectra of molecules. However, some questions about the geometry of the water molecule in the liquid state remain unanswered. For example, many sources state that the valence angle of the water molecule decreases during the transition into the liquid state [2]. Based on the experimental data of molecular vibration spectra in D2O and H2O molecules [3], the authors have estimated valence angle of water in the liquid state. Consequently, the value of the valence angle of water in liquid state was determined to be (89 +/-2)°. A question of determination of libration vibrations of water molecule, as well as the analysis of its consequent inversion doubling, based on the new information on the equilibrium angle of the water molecules in the liquid state, constitutes an interest and is discussed in the present paper.

  8. Water resources of Okaloosa County and adjacent areas, Florida

    USGS Publications Warehouse

    Trapp, Henry; Pascale, C.A.; Foster, J.B.

    1977-01-01

    Okaloosa County, in the northwest Florida panhandle, uses the Floridan aquifer for water supply, although it also has abundant surface water and ground water in the surficial sand-and-gravel aquifer. Water levels have declined locally more than 90 feet in the upper limestone of the Floridan aquifer. The Floridan aquifer is overlain by the Pensacola clay confining bed, and the Bucatunna Clay subdivides it into two limestone units. Water in the upper limestone is generally of good quality. The lower limestone probably contains saline water. Average daily stream discharge is about 2,500 million gallons. Stream discharge does not diminish excessively during droughts, owing to high base runoff. Water levels in the Floridan aquifer will decline as long as pumping increases in the present areas of withdrawal. The decline could be alleviated by redistribution of pumping, artificial recharge, and the use of the sand-and-gravel aquifer or streams. (Woodard-USGS)

  9. Modelling water molecules inside cyclic peptide nanotubes

    NASA Astrophysics Data System (ADS)

    Tiangtrong, Prangsai; Thamwattana, Ngamta; Baowan, Duangkamon

    2016-03-01

    Cyclic peptide nanotubes occur during the self-assembly process of cyclic peptides. Due to the ease of synthesis and ability to control the properties of outer surface and inner diameter by manipulating the functional side chains and the number of amino acids, cyclic peptide nanotubes have attracted much interest from many research areas. A potential application of peptide nanotubes is their use as artificial transmembrane channels for transporting ions, biomolecules and waters into cells. Here, we use the Lennard-Jones potential and a continuum approach to study the interaction of a water molecule in a cyclo[(- D-Ala- L-Ala)_4-] peptide nanotube. Assuming that each unit of a nanotube comprises an inner and an outer tube and that a water molecule is made up of a sphere of two hydrogen atoms uniformly distributed over its surface and a single oxygen atom at the centre, we determine analytically the interaction energy of the water molecule and the peptide nanotube. Using this energy, we find that, independent of the number of peptide units, the water molecule will be accepted inside the nanotube. Once inside the nanotube, we show that a water molecule prefers to be off-axis, closer to the surface of the inner nanotube. Furthermore, our study of two water molecules inside the peptide nanotube supports the finding that water molecules form an array of a 1-2-1-2 file inside peptide nanotubes. The theoretical study presented here can facilitate thorough understanding of the behaviour of water molecules inside peptide nanotubes for applications, such as artificial transmembrane channels.

  10. Water and solute transfer between a prairie wetland and adjacent uplands, 1. Water balance

    NASA Astrophysics Data System (ADS)

    Hayashi, Masaki; van der Kamp, Garth; Rudolph, Dave L.

    1998-06-01

    The hydrology and water quality of lakes and wetlands are controlled by the exchange of water and solutes with adjacent uplands. We studied a small catchment in Saskatchewan, Canada, to evaluate the mechanisms of water and solute transfer between the wetland and the surrounding upland. Detailed measurements of hydrologic processes (precipitation, runoff, evapotranspiration, and subsurface flow) and chloride distribution are combined to improve the estimate of the transfer flux. This paper describes hydrologic processes and Part 2 describes the solute transport processes. Large snowmelt runoff occurs in the catchment, which transfer 30-60% of winter precipitation on the upland into the wetland to form a pond in the center. Snowmelt water and summer precipitation infiltrate under the central pond. Infiltration accounts for 75% of water leaving the central pond and evapotranspiration accounts for 25%. Most of the infiltrated water flows laterally in the shallow subsurface to the wet margin of the pond and further to the upland, where it is consumed by evapotranspiration without recharging deep groundwater. The net recharge rate of the aquifer underlying the catchment is only 1-3 mm year -1. Snowmelt runoff transfers water from the upland to the wetland, and shallow subsurface flow transfers water in the opposite direction. When the two processes are combined, they provide the paths for cyclic transport of solutes.

  11. Water molecule conformation outside a metal surface

    NASA Astrophysics Data System (ADS)

    Flores, F.; Gabbay, I.; March, N. H.

    1981-05-01

    The effect of a metal surface on the conformation of a water molecule has been analyzed by discussing two independent effects: (i) the screening of the proton-proton repulsion, (ii) the interaction of the lone-pair orbitals with the surface. Both effects tend to increase the HOH angle. However, the interaction between the lone-pairs with the surface is the dominant effect for a water molecule approaching the surface. In particular, for a chemisorbed state this interaction is responsible for the major part of the molecule deformation. We have estimated that for H 2O chemisorbed on Ru, the HOH angle must increase from the free molecule value of 104.5° by 3.1 ± 0.5° in good agreement with the experimental evidence.

  12. Flow and transport within a coastal aquifer adjacent to a stratified water body

    NASA Astrophysics Data System (ADS)

    Oz, Imri; Yechieli, Yoseph; Eyal, Shalev; Gavrieli, Ittai; Gvirtzman, Haim

    2016-04-01

    The existence of a freshwater-saltwater interface and the circulation flow of saltwater beneath the interface is a well-known phenomenon found at coastal aquifers. This flow is a natural phenomenon that occurs due to density differences between fresh groundwater and the saltwater body. The goals of this research are to use analytical, numerical, and physical models in order to examine the configuration of the freshwater-saltwater interface and the density-driven flow patterns within a coastal aquifer adjacent to long-term stratified saltwater bodies (e.g. meromictic lake). Such hydrological systems are unique, as they consist of three different water types: the regional fresh groundwater, and low and high salinity brines forming the upper and lower water layers of the stratified water body, respectively. This research also aims to examine the influence of such stratification on hydrogeological processes within the coastal aquifer. The coastal aquifer adjacent to the Dead Sea, under its possible future meromictic conditions, serves as an ideal example to examine these processes. The results show that adjacent to a stratified saltwater body three interfaces between three different water bodies are formed, and that a complex flow system, controlled by the density differences, is created, where three circulation cells are developed. These results are significantly different from the classic circulation cell that is found adjacent to non-stratified water bodies (lakes or oceans). In order to obtain a more generalized insight into the groundwater behavior adjacent to a stratified water body, we used the numerical model to perform sensitivity analysis. The hydrological system was found be sensitive to three dimensionless parameters: dimensionless density (i.e. the relative density of the three water bodies'); dimensionless thickness (i.e. the ratio between the relative thickness of the upper layer and the whole thickness of the lake); and dimensionless flux. The results

  13. 33 CFR 165.1301 - Puget Sound and Adjacent Waters in Northwestern Washington-Regulated Navigation Area.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Puget Sound and Adjacent Waters... Areas Thirteenth Coast Guard District § 165.1301 Puget Sound and Adjacent Waters in Northwestern... northwestern Washington waters under the jurisdiction of the Captain of the Port, Puget Sound: Puget...

  14. 33 CFR 165.1301 - Puget Sound and Adjacent Waters in Northwestern Washington-Regulated Navigation Area.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 2 2014-07-01 2014-07-01 false Puget Sound and Adjacent Waters... Areas Thirteenth Coast Guard District § 165.1301 Puget Sound and Adjacent Waters in Northwestern... northwestern Washington waters under the jurisdiction of the Captain of the Port, Puget Sound: Puget...

  15. 33 CFR 165.1301 - Puget Sound and Adjacent Waters in Northwestern Washington-Regulated Navigation Area.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 2 2011-07-01 2011-07-01 false Puget Sound and Adjacent Waters... Areas Thirteenth Coast Guard District § 165.1301 Puget Sound and Adjacent Waters in Northwestern... northwestern Washington waters under the jurisdiction of the Captain of the Port, Puget Sound: Puget...

  16. 33 CFR 165.1301 - Puget Sound and Adjacent Waters in Northwestern Washington-Regulated Navigation Area.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 2 2012-07-01 2012-07-01 false Puget Sound and Adjacent Waters... Areas Thirteenth Coast Guard District § 165.1301 Puget Sound and Adjacent Waters in Northwestern... northwestern Washington waters under the jurisdiction of the Captain of the Port, Puget Sound: Puget...

  17. 75 FR 65278 - Pamlico Sound and Adjacent Waters, NC; Danger Zones for Marine Corps Operations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-22

    ... of Engineers, Department of the Army 33 CFR Part 334 Pamlico Sound and Adjacent Waters, NC; Danger... its regulations to establish one new danger zone in Pamlico Sound near Marine Corps Air Station Cherry... existing 1.8 mile Danger Zone [as described in Sec. 334.420(b)(1)(i)] in the Pamlico Sound and...

  18. DISTRIBUTION OF CONTAMINANTS IN WATERS OF MONROE HARBOR (RIVER RAISIN), MICHIGAN AND ADJACENT LAKE ERIE

    EPA Science Inventory

    The report describes the results of surveys of selected organochlorines and metals in Monroe Harbor and adjacent Lake Erie. Seasonal surveys at 3 sites of contaminant distribution in the water column were designed to support exposure effects studies and mass balance modeling. Che...

  19. The Dipole Polarizability of a Water Molecule in Liquid Water

    NASA Astrophysics Data System (ADS)

    Distasio, Robert; Maitra, Rahul

    The dipole polarizability, α, provides a measure of the tendency of a molecule or material to deform (or polarize) in the presence of an electric field. Within the framework of density functional theory (DFT), we present a hierarchy of first principles based approaches for computing α of a molecule located in the condensed phase. This hierarchy includes a successive treatment of both short-range (hybridization, Pauli exchange-repulsion, etc.) and long-range (Coulomb) electrodynamical response screening in the computation of α, while simultaneously accounting for the surrounding condensed-phase environment. Utilizing highly accurate liquid water configurations generated from van der Waals inclusive hybrid DFT based ab initio molecular dynamics, we computed α for a given water molecule in liquid water as a first application of this approach. Our findings will be compared and contrasted with α computed for an isolated gas-phase water molecule.

  20. 33 CFR 165.1301 - Puget Sound and Adjacent Waters in Northwestern Washington-Regulated Navigation Area.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Sound Vessel Traffic Service (PSVTS) VHF-FM radio frequency for the area in which the vessel is... 33 Navigation and Navigable Waters 2 2013-07-01 2013-07-01 false Puget Sound and Adjacent Waters... Areas Thirteenth Coast Guard District § 165.1301 Puget Sound and Adjacent Waters in...

  1. 33 CFR 334.420 - Pamlico Sound and adjacent waters, N.C.; danger zones for Marine Corps operations.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 3 2011-07-01 2011-07-01 false Pamlico Sound and adjacent waters... REGULATIONS § 334.420 Pamlico Sound and adjacent waters, N.C.; danger zones for Marine Corps operations. (a) Bombing and rocket firing area in Pamlico Sound in vicinity of Brant Island—(1) The area. The...

  2. 33 CFR 334.420 - Pamlico Sound and adjacent waters, N.C.; danger zones for Marine Corps operations.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Pamlico Sound and adjacent waters... REGULATIONS § 334.420 Pamlico Sound and adjacent waters, N.C.; danger zones for Marine Corps operations. (a) Bombing and rocket firing area in Pamlico Sound in vicinity of Brant Island—(1) The area. The...

  3. Clusters of mobile molecules in supercooled water

    NASA Astrophysics Data System (ADS)

    Giovambattista, Nicolas; Buldyrev, Sergey V.; Stanley, H. Eugene; Starr, Francis W.

    2005-07-01

    We study the spatially heterogeneous dynamics in water via molecular dynamics simulations using the extended simple point charge potential. We identify clusters formed by mobile molecules and study their properties. We find that these clusters grow in size and become more compact as temperature decreases. We analyze the probability density function of cluster size, and we study the cluster correlation length. We find that clusters appear to be characterized by a fractal dimension consistent with that of lattice animals. We relate the cluster size and correlation length to the configurational entropy, Sconf . We find that these quantities depend weakly on 1/Sconf . In particular, the linearity found between the cluster mass n* and 1/Sconf suggests that n* may be interpreted as the mass of the cooperatively rearranging regions that form the basis of the Adam-Gibbs approach to the dynamics of supercooled liquids. We study the motion of molecules within a cluster, and find that each molecule preferentially follows a neighboring molecule in the same cluster. Based on this finding we hypothesize that stringlike cooperative motion may be a general mechanism for molecular rearrangement of complex, as well as simple liquids. By mapping each equilibrium configuration onto its corresponding local potential energy minimum or inherent structure (IS), we are able to compare the mobile molecule clusters in the equilibrium system with the molecules forming the clusters identified in the transitions between IS. We find that (i) mobile molecule clusters obtained by comparing different system configurations and (ii) clusters obtained by comparing the corresponding IS are completely different for short time scales, but are the same on the longer time scales of diffusive motion.

  4. Dynamics of water molecules in glucose solutions.

    SciTech Connect

    Talon, C.; Smith, L. J.; Brady, J. W.; Copley, J. R. D.; Price, D. L.; Saboungi, M. L.; Materials Science Division; Centre de Recherche sur la Matiyre Divisye; Cornell Univ.; NIST; Centre de Recherche sur les Matyriaux y Haute Tempyrature

    2004-04-22

    The effects of the solution of glucose molecules on the dynamics of solvent water have been studied by quasielastic neutron scattering (QENS) measurements on solutions of selectively deuterated glucose in natural water. The data are fitted to two Lorentzians ascribed to pure translational and mixed translational and rotational character, respectively. The addition of the glucose to the water causes a substantial slowing down, by a factor 10 for the translational diffusion and 3-4 for the rotational motion at the highest concentration studied, 1:11 C{sub 6}H{sub 12}O{sub 6}:H{sub 2}O. The values obtained for water diffusion constants are consistent with previous QENS and NMR experiments on monosaccharide solutions but an order of magnitude higher than those derived from a recent molecular dynamics simulation.

  5. 33 CFR 334.412 - Albemarle Sound, Pamlico Sound, Harvey Point and adjacent waters, NC; restricted area.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... REGULATIONS § 334.412 Albemarle Sound, Pamlico Sound, Harvey Point and adjacent waters, NC; restricted area. (a) The area. Beginning on the north shore of Albemarle Sound and the easternmost tip of Harvey Point..., Harvey Point and adjacent waters, NC; restricted area. 334.412 Section 334.412 Navigation and...

  6. 33 CFR 334.412 - Albemarle Sound, Pamlico Sound, Harvey Point and adjacent waters, NC; restricted area.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... REGULATIONS § 334.412 Albemarle Sound, Pamlico Sound, Harvey Point and adjacent waters, NC; restricted area. (a) The area. Beginning on the north shore of Albemarle Sound and the easternmost tip of Harvey Point..., Harvey Point and adjacent waters, NC; restricted area. 334.412 Section 334.412 Navigation and...

  7. 33 CFR 334.412 - Albemarle Sound, Pamlico Sound, Harvey Point and adjacent waters, NC; restricted area.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... REGULATIONS § 334.412 Albemarle Sound, Pamlico Sound, Harvey Point and adjacent waters, NC; restricted area. (a) The area. Beginning on the north shore of Albemarle Sound and the easternmost tip of Harvey Point..., Harvey Point and adjacent waters, NC; restricted area. 334.412 Section 334.412 Navigation and...

  8. 33 CFR 334.412 - Albemarle Sound, Pamlico Sound, Harvey Point and adjacent waters, NC; restricted area.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... REGULATIONS § 334.412 Albemarle Sound, Pamlico Sound, Harvey Point and adjacent waters, NC; restricted area. (a) The area. Beginning on the north shore of Albemarle Sound and the easternmost tip of Harvey Point..., Harvey Point and adjacent waters, NC; restricted area. 334.412 Section 334.412 Navigation and...

  9. 33 CFR 334.412 - Albemarle Sound, Pamlico Sound, Harvey Point and adjacent waters, NC; restricted area.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... REGULATIONS § 334.412 Albemarle Sound, Pamlico Sound, Harvey Point and adjacent waters, NC; restricted area. (a) The area. Beginning on the north shore of Albemarle Sound and the easternmost tip of Harvey Point..., Harvey Point and adjacent waters, NC; restricted area. 334.412 Section 334.412 Navigation and...

  10. 33 CFR 165.1310 - Strait of Juan de Fuca and adjacent coastal waters of Northwest Washington; Makah Whale Hunting...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... adjacent coastal waters of Northwest Washington; Makah Whale Hunting-Regulated Navigation Area. 165.1310... and adjacent coastal waters of Northwest Washington; Makah Whale Hunting—Regulated Navigation Area. (a.... Datum: NAD 1983. (b) During a whale hunt, while the international numeral pennant five (5) is flown by...

  11. 33 CFR 165.1310 - Strait of Juan de Fuca and adjacent coastal waters of Northwest Washington; Makah Whale Hunting...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... adjacent coastal waters of Northwest Washington; Makah Whale Hunting-Regulated Navigation Area. 165.1310... and adjacent coastal waters of Northwest Washington; Makah Whale Hunting—Regulated Navigation Area. (a.... Datum: NAD 1983. (b) During a whale hunt, while the international numeral pennant five (5) is flown by...

  12. 33 CFR 165.1310 - Strait of Juan de Fuca and adjacent coastal waters of Northwest Washington; Makah Whale Hunting...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... adjacent coastal waters of Northwest Washington; Makah Whale Hunting-Regulated Navigation Area. 165.1310... and adjacent coastal waters of Northwest Washington; Makah Whale Hunting—Regulated Navigation Area. (a.... Datum: NAD 1983. (b) During a whale hunt, while the international numeral pennant five (5) is flown by...

  13. 33 CFR 165.1310 - Strait of Juan de Fuca and adjacent coastal waters of Northwest Washington; Makah Whale Hunting...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... adjacent coastal waters of Northwest Washington; Makah Whale Hunting-Regulated Navigation Area. 165.1310... and adjacent coastal waters of Northwest Washington; Makah Whale Hunting—Regulated Navigation Area. (a.... Datum: NAD 1983. (b) During a whale hunt, while the international numeral pennant five (5) is flown by...

  14. Summary of ground-water data, Post Headquarters and adjacent areas, White Sands Missile Range

    USGS Publications Warehouse

    Kelly, T.E.

    1973-01-01

    Geohydrologic data have been obtained from more than 100 wells and test holes that have been drilled in the Post Headquarters and adjacent areas of White Sands Missile Range. Observation-well data show that, in general, a continuous decline of the water table has occurred in the vicinity of the well field since production began in 1949. Approximately 40,000 acre-feet of water has been produced from the aquifer to date (1972). A series of maps are presented which show the changes that have occurred in the well field as the result of development.

  15. Two new species in the family Axinellidae (Porifera, Demospongiae) from British Columbia and adjacent waters.

    PubMed

    Austin, William C; Ott, Bruce S; Reiswig, Henry M; Romagosa, Paula; McDaniel, Neil G

    2013-01-01

    Two new species of Demospongiae are described for British Columbia and adjacent waters in the family Axinellidae, Auletta krautteri sp. n. and Dragmacidon kishinensis sp. n. They represent range extensions for both of these genera. Both are fairly commonly encountered, Auletta krautteri below diving depths (87 to at least 300 m) and Dragmacidon kishinensis in shallow water (intertidal to 30 m). We propose an amended genus diagnosis for Auletta to account for the variability among species in principal spicules that form the ascending tracts to be either oxeas, styles or strongyles rather than just oxeas. PMID:24146581

  16. Two new species in the family Axinellidae (Porifera, Demospongiae) from British Columbia and adjacent waters

    PubMed Central

    Austin, William C.; Ott, Bruce S.; Reiswig, Henry M.; Romagosa, Paula; McDaniel, Neil G.

    2013-01-01

    Abstract Two new species of Demospongiae are described for British Columbia and adjacent waters in the family Axinellidae, Auletta krautteri sp. n. and Dragmacidon kishinensis sp. n. They represent range extensions for both of these genera. Both are fairly commonly encountered, Auletta krautteri below diving depths (87 to at least 300 m) and Dragmacidon kishinensis in shallow water (intertidal to 30 m). We propose an amended genus diagnosis for Auletta to account for the variability among species in principal spicules that form the ascending tracts to be either oxeas, styles or strongyles rather than just oxeas. PMID:24146581

  17. Rotational motion of a single water molecule in a buckyball.

    PubMed

    Farimani, A Barati; Wu, Yanbin; Aluru, N R

    2013-11-01

    Encapsulation of a single water molecule in a buckyball (C60) can provide fundamental insights into the properties of water. Investigation of a single water molecule is feasible through its solitary confinement in C60. In this paper, we performed a detailed study of the properties and dynamics of a single water molecule in a buckyball using DFT and MD simulations. We report on the enhancement of rotational diffusion and entropy of a water molecule in C60, compared to a bulk water molecule. H2O@C60 has zero translational diffusion and terahertz revolution frequency. The harmonic, high amplitude rotation of a single water molecule in C60 is compared to stochastic behavior of bulk water molecules. The combination of large rotational and negligible translational motion of water in C60 creates new opportunities in nanotechnology applications. PMID:24061613

  18. 33 CFR 165.501 - Chesapeake Bay entrance and Hampton Roads, VA and adjacent waters-Regulated Navigation Area.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Hampton Roads, VA and adjacent waters-Regulated Navigation Area. 165.501 Section 165.501 Navigation and... Areas Fifth Coast Guard District § 165.501 Chesapeake Bay entrance and Hampton Roads, VA and adjacent... Sector Hampton Roads. Designated representative of the Captain of the Port means a person, including...

  19. 33 CFR 165.501 - Chesapeake Bay entrance and Hampton Roads, VA and adjacent waters-Regulated Navigation Area.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Hampton Roads, VA and adjacent waters-Regulated Navigation Area. 165.501 Section 165.501 Navigation and... Areas Fifth Coast Guard District § 165.501 Chesapeake Bay entrance and Hampton Roads, VA and adjacent... Sector Hampton Roads. Designated representative of the Captain of the Port means a person, including...

  20. 33 CFR 165.501 - Chesapeake Bay entrance and Hampton Roads, VA and adjacent waters-Regulated Navigation Area.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Hampton Roads, VA and adjacent waters-Regulated Navigation Area. 165.501 Section 165.501 Navigation and... Areas Fifth Coast Guard District § 165.501 Chesapeake Bay entrance and Hampton Roads, VA and adjacent... Sector Hampton Roads. Designated representative of the Captain of the Port means a person, including...

  1. 33 CFR 165.501 - Chesapeake Bay entrance and Hampton Roads, VA and adjacent waters-Regulated Navigation Area.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Hampton Roads, VA and adjacent waters-Regulated Navigation Area. 165.501 Section 165.501 Navigation and... Areas Fifth Coast Guard District § 165.501 Chesapeake Bay entrance and Hampton Roads, VA and adjacent... Sector Hampton Roads. Designated representative of the Captain of the Port means a person, including...

  2. 33 CFR 165.501 - Chesapeake Bay entrance and Hampton Roads, VA and adjacent waters-Regulated Navigation Area.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Hampton Roads, VA and adjacent waters-Regulated Navigation Area. 165.501 Section 165.501 Navigation and... Areas Fifth Coast Guard District § 165.501 Chesapeake Bay entrance and Hampton Roads, VA and adjacent... Sector Hampton Roads. Designated representative of the Captain of the Port means a person, including...

  3. Measures of Water Quality in Merrit Island National Wildlife Refuge Impoundments and Adjacent Indian River Lagoon

    NASA Technical Reports Server (NTRS)

    Blum, Linda K.

    2000-01-01

    The goal of this project was to conduct preliminary investigations to determine appropriate sampling strategies to measure the flux of dissolved nutrients (specifically, NH4+, NO3-, NO2-, and PO4(3-)) and suspended particulate matter (TSS) between impoundments and the IRL in preparation for an intensive three-year monitoring program. In addition to nutrients and TSS, a variety of common water quality indicators were also measured during these preliminary studies. Six impoundments and a single restored marsh were selected for study. Over a month long period, water samples were collected weekly at selected impoundment culverts. Water was collected in duplicate as independent grab samples from both the lagoon side and within the perimeter ditch directly adjacent to the culverts. Water quality indicators inside and outside the marsh impoundments were different. Ammonium, salinity, bacteria, and chlorophyll-a were higher inside the impoundments as expected possibly as a result of the great affect of evaporation on impoundment water. Water quality indicators responded rapidly both inside and outside the impoundments as exemplified by the increase in NH4(+)-N concentrations during a horseshoe crab die-off. Water quality indicators were high variable during the month in which water samples were collected. Because the impoundments are widely spaced it is logistically unrealistic to sample each of the impoundments and associated seagrass beds on a single day, sampling must be stratified to allow patterns of material movement and the annual flux of materials to and from the impoundments to be determined.

  4. Contrasting microbial assemblages in adjacent water masses associated with the East Australian Current.

    PubMed

    Seymour, Justin R; Doblin, Martina A; Jeffries, Thomas C; Brown, Mark V; Newton, Kelly; Ralph, Peter J; Baird, Mark; Mitchell, James G

    2012-10-01

    Different oceanographic provinces host discrete microbial assemblages that are adapted to local physicochemical conditions. We sequenced and compared the metagenomes of two microbial communities inhabiting adjacent water masses in the Tasman Sea, where the recent strengthening of the East Australian Current (EAC) has altered the ecology of coastal environments. Despite the comparable latitude of the samples, significant phylogenetic differences were apparent, including shifts in the relative frequency of matches to Cyanobacteria, Crenarchaeota and Euryarchaeota. Fine-scale variability in the structure of SAR11, Prochlorococcus and Synechococcus populations, with more matches to 'warm-water' ecotypes observed in the EAC, indicates the EAC may drive an intrusion of tropical microbes into temperate regions of the Tasman Sea. Furthermore, significant shifts in the relative importance of 17 metabolic categories indicate that the EAC prokaryotic community has different physiological properties than surrounding waters. PMID:23760900

  5. Literature and data review for the surface-water pathway: Columbia River and adjacent coastal areas

    SciTech Connect

    Walters, W.H.; Dirkes, R.L.; Napier, B.A.

    1992-04-01

    As part of the Hanford Environmental Dose Reconstruction Project, Pacific Northwest Laboratory reviewed literature and data on radionuclide concentrations and distribution in the water, sediment, and biota of the Columbia River and adjacent coastal areas. Over 600 documents were reviewed including Hanford reports, reports by offsite agencies, journal articles, and graduate theses. Certain radionuclide concentration data were used in preliminary estimates of individual dose for the 1964--1966 time period. This report summarizes the literature and database review and the results of the preliminary dose estimates.

  6. Literature and data review for the surface-water pathway: Columbia River and adjacent coastal areas

    SciTech Connect

    Walters, W.H.; Dirkes, R.L.; Napier, B.A.

    1992-11-01

    As part of the Hanford Environmental Dose Reconstruction (HEDR) Project, Battelle, Pacific Northwest Laboratories reviewed literature and data on radionuclide concentrations and distribution in the water, sediment, and biota of the Columbia River and adjacent coastal areas. Over 600 documents were reviewed including Hanford reports, reports by offsite agencies, journal articles, and graduate theses. Radionuclide concentration data were used in preliminary estimates of individual dose for the period 1964 through 1966. This report summarizes the literature and database reviews and the results of the preliminary dose estimates.

  7. A new version of regional ocean reanalysis for coastal waters of China and adjacent seas

    NASA Astrophysics Data System (ADS)

    Han, Guijun; Li, Wei; Zhang, Xuefeng; Wang, Xidong; Wu, Xinrong; Fu, Hongli; Zhang, Xiaoshuang; Zhang, Lianxin; Li, Dong

    2013-07-01

    A new regional ocean reanalysis over multiple decades (1958-2008) for the coastal waters of China and adjacent seas has been completed by the National Marine Data and Information Service (NMDIS) under the CORA (China Ocean ReAnalysis) project. Evaluations were performed on three aspects: (1) the improvement of general reanalysis quality; (2) eddy structures; and (3) decadal variability of sea surface height anomalies (SSHAs). Results showed that the quality of the new reanalysis has been enhanced beyond ˜40% (39% for temperature, 44% for salinity) in terms of the reduction of root mean squared errors (RMSEs) for which the reanalysis values were compared to observed values in the observational space. Compared to the trial version released to public in 2009, the new reanalysis is able to reproduce more detailed eddy structures as seen in satellite and in situ observations. EOF analysis of the reanalysis SSHAs showed that the new reanalysis reconstructs the leading modes of SSHAs much better than the old version. These evaluations suggest that the new CORA regional reanalysis represents a much more useful dataset for the community of the coastal waters of China and adjacent seas.

  8. A regional ocean reanalysis system for coastal waters of China and adjacent seas

    NASA Astrophysics Data System (ADS)

    Han, Guijun; Li, Wei; Zhang, Xuefeng; Li, Dong; He, Zhongjie; Wang, Xidong; Wu, Xinrong; Yu, Ting; Ma, Jirui

    2011-05-01

    A regional ocean reanalysis system for the coastal waters of China and adjacent seas has been developed by the National Marine Data and Information Service (NMDIS). It produces a dataset package called CORA (China ocean reanalysis). The regional ocean model used is based on the Princeton Ocean Model with a generalized coordinate system (POMgcs). The model is parallelized by NMDIS with the addition of the wave breaking and tidal mixing processes into model parameterizations. Data assimilation is a sequential three-dimensional variational (3D-Var) scheme implemented within a multigrid framework. Observations include satellite remote sensing sea surface temperature (SST), altimetry sea level anomaly (SLA), and temperature/salinity profiles. The reanalysis fields of sea surface height, temperature, salinity, and currents begin with January 1986 and are currently updated every year. Error statistics and error distributions of temperature, salinity and currents are presented as a primary evaluation of the reanalysis fields using sea level data from tidal gauges, temperature profiles, as well as the trajectories of Argo floats. Some case studies offer the opportunity to verify the evolution of certain local circulations. These evaluations show that the reanalysis data produced provide a good representation of the ocean processes and phenomena in the coastal waters of China and adjacent seas.

  9. Estimated water use in the Southwest Florida Water Management District and adjacent areas, 1980

    USGS Publications Warehouse

    Duerr, A.D.; Trommer, J.T.

    1981-01-01

    Water-use data for 1980 are summarized in this report for 16 counties in the Southwest Florida Water Management District. Data include total use of ground water and surface water for each of five water-use categories. The 1980 withdrawals for each category were as follows: 290 million gallons per day for public supply, 63 million gallons per day for rural, 325 million gallons per day for industry, 416 million gallons per day for irrigation, and 6,605 million gallons per day for thermoelectric power generation. Withdrawals totaled 7,699 million gallons per day and included 983 million gallons per day of ground water and 6,716 million gallons per day of surface water. Excluding thermoelectric power generation, all water withdrawn was freshwater except 38 million gallons per day of saline ground water withdrawn for industrial use in Hillsborough County. (USGS)

  10. 33 CFR 165.1310 - Strait of Juan de Fuca and adjacent coastal waters of Northwest Washington; Makah Whale Hunting...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 2 2012-07-01 2012-07-01 false Strait of Juan de Fuca and adjacent coastal waters of Northwest Washington; Makah Whale Hunting-Regulated Navigation Area. 165.1310 Section 165.1310 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) PORTS AND WATERWAYS SAFETY...

  11. The large quadrupole of water molecules.

    PubMed

    Niu, Shuqiang; Tan, Ming-Liang; Ichiye, Toshiko

    2011-04-01

    Many quantum mechanical calculations indicate water molecules in the gas and liquid phase have much larger quadrupole moments than any of the common site models of water for computer simulations. Here, comparisons of multipoles from quantum mechanical∕molecular mechanical (QM∕MM) calculations at the MP2∕aug-cc-pVQZ level on a B3LYP∕aug-cc-pVQZ level geometry of a waterlike cluster and from various site models show that the increased square planar quadrupole can be attributed to the p-orbital character perpendicular to the molecular plane of the highest occupied molecular orbital as well as a slight shift of negative charge toward the hydrogens. The common site models do not account for the p-orbital type electron density and fitting partial charges of TIP4P- or TIP5P-type models to the QM∕MM dipole and quadrupole give unreasonable higher moments. Furthermore, six partial charge sites are necessary to account reasonably for the large quadrupole, and polarizable site models will not remedy the problem unless they account for the p-orbital in the gas phase since the QM calculations show it is present there too. On the other hand, multipole models by definition can use the correct multipoles and the electrostatic potential from the QM∕MM multipoles is much closer than that from the site models to the potential from the QM∕MM electron density. Finally, Monte Carlo simulations show that increasing the quadrupole in the soft-sticky dipole-quadrupole-octupole multipole model gives radial distribution functions that are in good agreement with experiment. PMID:21476758

  12. The Large Quadrupole of Water Molecules

    SciTech Connect

    Niu, Shuqiang; Tan, Ming-Liang; Ichiye, Toshhiko

    2011-04-07

    Many quantum mechanical calculations indicate water molecules in the gas and liquid phase have much larger quadrupole moments than any of the common site models of water for computer simulations. Here, comparisons of multipoles from quantum mechanical/molecular mechanical (QM/MM) calculations at the MP2/aug-cc-pVQZ level on a B3LYP/aug-cc-pVQZ level geometry of a waterlike cluster and from various site models show that the increased square planar quadrupole can be attributed to the p-orbital character perpendicular to the molecular plane of the highest occupied molecular orbital as well as a slight shift of negative charge toward the hydrogens. The common site models do not account for the p-orbital type electron density and fitting partial charges of TIP4P- or TIP5P-type models to the QM/MM dipole and quadrupole give unreasonable higher moments. Furthermore, six partial charge sites are necessary to account reasonably for the large quadrupole, and polarizable site models will not remedy the problem unless they account for the p-orbital in the gas phase since the QM calculations show it is present there too. On the other hand, multipole models by definition can use the correct multipoles and the electrostatic potential from the QM/MM multipoles is much closer than that from the site models to the potential from the QM/MM electron density. Finally, Monte Carlo simulations show that increasing the quadrupole in the soft-sticky dipole-quadrupole-octupole multipole model gives radial distribution functions that are in good agreement with experiment

  13. The large quadrupole of water molecules

    NASA Astrophysics Data System (ADS)

    Niu, Shuqiang; Tan, Ming-Liang; Ichiye, Toshiko

    2011-04-01

    Many quantum mechanical calculations indicate water molecules in the gas and liquid phase have much larger quadrupole moments than any of the common site models of water for computer simulations. Here, comparisons of multipoles from quantum mechanical/molecular mechanical (QM/MM) calculations at the MP2/aug-cc-pVQZ level on a B3LYP/aug-cc-pVQZ level geometry of a waterlike cluster and from various site models show that the increased square planar quadrupole can be attributed to the p-orbital character perpendicular to the molecular plane of the highest occupied molecular orbital as well as a slight shift of negative charge toward the hydrogens. The common site models do not account for the p-orbital type electron density and fitting partial charges of TIP4P- or TIP5P-type models to the QM/MM dipole and quadrupole give unreasonable higher moments. Furthermore, six partial charge sites are necessary to account reasonably for the large quadrupole, and polarizable site models will not remedy the problem unless they account for the p-orbital in the gas phase since the QM calculations show it is present there too. On the other hand, multipole models by definition can use the correct multipoles and the electrostatic potential from the QM/MM multipoles is much closer than that from the site models to the potential from the QM/MM electron density. Finally, Monte Carlo simulations show that increasing the quadrupole in the soft-sticky dipole-quadrupole-octupole multipole model gives radial distribution functions that are in good agreement with experiment.

  14. Concentration of hydrocarbons associated with particles in the shelf waters adjacent to the entrance of Chesapeake Bay

    NASA Technical Reports Server (NTRS)

    Wade, T. L.; Oertel, G. F.

    1981-01-01

    Particulate hydrocarbon concentrations were measured in 94 water samples. The concentrations ranged from below the detection limit ( 0.7 micro-G/L) to 32 micro-g/l. The mean for all samples was 5.6 micro-g/l. Particulate hydrocarbon concentrations are higher in the Bay mouth and lower in the shelf waters adjacent to the entrance of Chesapeake Bay. No coherent particulate hydrocarbon distribution is seen with depth in the water column. The Bay is postulated as one of the possible chronic sources of particulate hydrocarbons for the adjacent shelf waters.

  15. Adsorption structure of water molecules on the Be(0001) surface

    SciTech Connect

    Yang, Yu; Li, Yanfang; Wang, Shuangxi; Zhang, Ping

    2014-06-07

    By using density functional theory calculations, we systematically investigate the adsorption of water molecules at different coverages on the Be(0001) surface. The coverage dependence of the prototype water structures and energetics for water adlayer growth are systematically studied. The structures, energetics, and electronic properties are calculated and compared with other available studies. Through our systematic investigations, we find that water molecules form clusters or chains on the Be(0001) surface at low coverages. When increasing the water coverage, water molecules tend to form a 2 × 2 hexagonal network on the Be(0001) surface.

  16. [Functional groups of high trophic level communities in adjacent waters of Changjiang estuary].

    PubMed

    Zhang, Bo; Jin, Xian-Shi; Tang, Qi-Sheng

    2009-02-01

    Based on the three bottom trawl surveys in adjacent waters of Changjiang estuary in June, August and October 2006, the composition and variation of the functional groups of high trophic level communities in the waters were studied. According to diet analysis, the high trophic level communities in the waters included six functional groups, i.e., piscivore, shrimp predator, crab predator, benthivore, planktivore, and generalist predator. Due to the variation of marine environment and fish migration behavior, the composition and trophic level of the high trophic level communities had greater monthly change. In June, fishes, acetes, and crabs dominated the communities, and planktivore was the major functional group, with its trophic level being the lowest (3.06); in August, fishes were dominant, and shrimp predator was the major functional group, with its trophic level being the highest (3.78); and in October, fishes also dominated the communities, the proportion of shrimp and crab increased, and planktivore and benthivore were the major functional groups, with a trophic level of 3.58. PMID:19459374

  17. Pore water nutrient characteristics and the fluxes across the sediment in the Pearl River estuary and adjacent waters, China

    NASA Astrophysics Data System (ADS)

    Zhang, Ling; Wang, Lu; Yin, Kedong; Lü, Ying; Zhang, Derong; Yang, Yongqiang; Huang, Xiaoping

    2013-11-01

    Spatio-temporal distribution of pore water nutrients and the fluxes at the sediment-water interface (SWI) were investigated to probe into the geochemical behavior of nutrients associated with early diagenesis of organic matter (OM), and to study the accumulation and transformation processes of nutrients at the SWI, as well as to discuss the impact of riverine inputs on nutrients in the Pearl River estuary (PRE) and adjacent offshore areas. Nutrient concentrations decreased from the upper to the lower reaches of the estuary, suggesting that there was a high input of anthropogenic nutrients and the estuary was acting as a nutrient sink. Dissolved inorganic nitrogen (DIN: the sum of NH4-N, NO3-N and NO2-N) concentrations in the water column and the pore water were higher in the estuary than at offshore areas due to the riverine discharge and the high accumulation rate in the estuary. NO3-N concentration was the highest of the three forms of DIN in the overlying water and showed a sharp decrease from the surficial sediment with increasing sediment depth, indicating that there was strong denitrification at the SWI. NH4-N, mainly deriving from the anaerobic degradation of OM, was the main form of DIN in the pore water and increased with depth. Negative NO3-N fluxes (into the sediment) and positive NH4-N fluxes (from the sediment) were commonly observed from incubation experiments, indicating the denitrification occurred at the SWI. DIN flux suggested that the sediment was a sink of DIN in spring, however, the sediment was the source of DIN in summer and winter. Nutrients dominantly diffused out of the sediment, suggesting that the sediment was the source of nutrients in spring at adjacent offshore areas. The fluxes directed that PO4-P mainly diffused into the sediment while SiO4-Si mainly diffused out of the sediment.

  18. Microbial water quality before and after the repair of a failing onsite wastewater treatment system adjacent to coastal waters

    USGS Publications Warehouse

    Conn, K.E.; Habteselassie, M.Y.; Denene, Blackwood A.; Noble, R.T.

    2012-01-01

    Aims: The objective was to assess the impacts of repairing a failing onsite wastewater treatment system (OWTS, i.e., septic system) as related to coastal microbial water quality. Methods and Results: Wastewater, groundwater and surface water were monitored for environmental parameters, faecal indicator bacteria (total coliforms, Escherichia coli, enterococci) and the viral tracer MS2 before and after repairing a failing OWTS. MS2 results using plaque enumeration and quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) often agreed, but inhibition limited the qRT-PCR assay sensitivity. Prerepair, MS2 persisted in groundwater and was detected in the nearby creek; postrepair, it was not detected. In groundwater, total coliform concentrations were lower and E.??coli was not detected, while enterococci concentrations were similar to prerepair levels. E.??coli and enterococci surface water concentrations were elevated both before and after the repair. Conclusions: Repairing the failing OWTS improved groundwater microbial water quality, although persistence of bacteria in surface water suggests that the OWTS was not the singular faecal contributor to adjacent coastal waters. A suite of tracers is needed to fully assess OWTS performance in treating microbial contaminants and related impacts on receiving waters. Molecular methods like qRT-PCR have potential but require optimization. Significance and Impact of Study: This is the first before and after study of a failing OWTS and provides guidance on selection of microbial tracers and methods. ?? 2011 The Authors. Journal of Applied Microbiology ?? 2011 The Society for Applied Microbiology.

  19. 33 CFR 334.410 - Albemarle Sound, Pamlico Sound, and adjacent waters, NC; danger zones for naval aircraft operations.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 3 2014-07-01 2014-07-01 false Albemarle Sound, Pamlico Sound... AND RESTRICTED AREA REGULATIONS § 334.410 Albemarle Sound, Pamlico Sound, and adjacent waters, NC; danger zones for naval aircraft operations. (a) Target areas—(1) North Landing River (Currituck...

  20. 33 CFR 334.410 - Albemarle Sound, Pamlico Sound, and adjacent waters, NC; danger zones for naval aircraft operations.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Albemarle Sound, Pamlico Sound... AND RESTRICTED AREA REGULATIONS § 334.410 Albemarle Sound, Pamlico Sound, and adjacent waters, NC; danger zones for naval aircraft operations. (a) Target areas—(1) North Landing River (Currituck...

  1. 33 CFR 334.410 - Albemarle Sound, Pamlico Sound, and adjacent waters, NC; danger zones for naval aircraft operations.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 3 2012-07-01 2012-07-01 false Albemarle Sound, Pamlico Sound... AND RESTRICTED AREA REGULATIONS § 334.410 Albemarle Sound, Pamlico Sound, and adjacent waters, NC; danger zones for naval aircraft operations. (a) Target areas—(1) North Landing River (Currituck...

  2. 33 CFR 334.410 - Albemarle Sound, Pamlico Sound, and adjacent waters, NC; danger zones for naval aircraft operations.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 3 2011-07-01 2011-07-01 false Albemarle Sound, Pamlico Sound... AND RESTRICTED AREA REGULATIONS § 334.410 Albemarle Sound, Pamlico Sound, and adjacent waters, NC; danger zones for naval aircraft operations. (a) Target areas—(1) North Landing River (Currituck...

  3. [Distribution of picophytoplanktons in Qingdao offshore and its adjacent waters in winter].

    PubMed

    Wang, Min; Liang, Yan-tao; Bai, Xiao-ge; Jiang, Xue-jiao; Wang, Fang; Qiao, Qian

    2008-11-01

    Picophytoplankton (0.2-2.0 microm in size) is the smallest group of autotrophic plankton, being abundant and widespread in the world ocean and playing an important role in the organic matter cycling in ocean. By the method of epifluorescence microscopy (EFM), the abundance and its spatial and diurnal variations of the picophytoplanktons in Qingdao offshore and its adjacent waters in winter were investigated. The results showed that in the study area in winter, phycoerythrin-rich (PE) Synechococcus cells were dominant, followed by Picoeukaryote (Euk) cells, while the abundance of phycocyanin-rich (PC) Synechococcus cells was low and no Prochlorococcus (Pro) cells were observed. The abundance of Synechococcus (Syn) and Euk varied from 8.97 x 10(3) to 1.95 x 10(5) cells x ml(-1) (averaged 4.67 x 10(4) cells x ml(-1) and from 1.95 x 10(2) to 1.01 x 10(4) cells x m(l-1)(averaged 2.39 x 10(3) cells x ml(1) respectively. There was a high-value of Syn abundance in Jiaonan offshore and a low-value in Jimo and southeast Laoshan off-shores, while a high-value of Euk abundance in Rizhao offshore and a low-value in Laoshan offshore. No significant difference was observed in the vertical distribution of Syn and Euk abundance among four water layers (P>0.05) at a continuous station located in the center of Jiaozhou Bay, the abundance had an obvious diurnal fluctuation. Pearson correlation analysis indicated that Syn was positively correlated with water temperature and electrical conductivity (P<0.01) but negatively correlated with dissolved oxygen concentration (P<0.01) and Euk was negatively correlated with water salinity and dissolved oxygen concentration. In the study area in winter, picophytoplankton contributed about 20% to the total phytoplanktonic biomass. PMID:19238842

  4. Water and solute transfer between a prairie wetland and adjacent uplands, 2. Chloride cycle

    NASA Astrophysics Data System (ADS)

    Hayashi, Masaki; van der Kamp, Garth; Rudolph, Dave L.

    1998-06-01

    The quality of water in lakes and wetlands depends on the exchange of solutes with adjacent uplands. In many prairie wetlands, the input of water is dominated by snowmelt runoff and the outputis dominated by groundwater flow. We use chloride as a tracer to quantify the mass transfer processes associated with surface runoff and groundwater flow between a wetland in Saskatchewan, Canada and the surrounding upland. Snowmelt runoff transports 4-5 kg yr -1 of chloride from the upland to the wetland. Most of this chloride infiltrates under the wetland and moves laterally to the upland with shallow groundwater. Under the upland, chloride moves upward in the vadose zone with soil water, and accumulates near the surface as water is consumed by evapotranspiration. Part of this chloride mixes with snowmelt runoff and moves back to the wetland Therefore, chloride is cycled between the wetland and the upland at an approximate rate of 5 kg yr -1. The chloride cycle occurs within 5-6 m of the ground surface. A small amount of chloride escapes from the cycle with the downward flow of groundwater into the deep aquifer. The estimated flux of chloride leaving the cycle is 0.1-0.6 kg yr -1, which is of the same order of magnitude as the rate at which the catchment receives atmospheric deposition of chloride. Because the atmospheric input is reasonably well known over the prairie region, the concentration of chloride in groundwater under recharge wetlands can be used to estimate the recharge rate of deep aquifers.

  5. Giant pumping of single-file water molecules in a carbon nanotube.

    PubMed

    Wang, Y; Zhao, Y J; Huang, J P

    2011-11-17

    Achieving a fast, unidirectional flow of single-file water molecules (UFSWM) across nanochannels is important for membrane-based water purification or seawater desalination. For this purpose, electro-osmosis methods are recognized as a very promising approach and have been extensively discussed in the literature. Utilizing molecular dynamics simulations, here we propose a design for pumping water molecules in a single-walled carbon nanotube in the presence of a linearly gradient electric (GE) field. Such a GE field is inspired by GE fields generated from charged ions located adjacent to biological membrane water nanochannels that can conduct water in and out of cells and can be experimentally achieved by using the charged tip of an atomic force microscope. As a result, the maximum speed of the UFSWM can be 1 or 2 orders of magnitude larger than that in a uniform electric (UE) field. Also, inverse transportation of water molecules does not exist in case of the GE field but can appear for the UE field. Thus, the GE field yields a much more efficient UFSWM than the UE field. The giant pumping ability as revealed is attributed to the nonzero net electrostatic force acting on each water molecule confined in the nanotube. These observations have significance for the design of nanoscale devices for readily achieving controllable UFSWM at high speed. PMID:21977917

  6. Nutrient fluxes in the Changjiang River estuary and adjacent waters — a modified box model approach

    NASA Astrophysics Data System (ADS)

    Wang, Xiaohong; Yu, Zhiming; Fan, Wei; Song, Xiuxian; Cao, Xihua; Yuan, Yongquan

    2015-01-01

    To solve nutrient flux and budget among waters with distinct salinity difference for water-salt-nutrient budget, a traditional method is to build a stoichiometrically linked steady state model. However, the traditional way cannot cope appropriately with those without distinct salinity difference that parallel to coastline or in a complex current system, as the results would be highly affected by box division in time and space, such as the Changjiang (Yangtze) River estuary (CRE) and adjacent waters (30.75°2-31.75°N, 122°10'-123°20'E). Therefore, we developed a hydrodynamic box model based on the traditional way and the regional oceanic modeling system model (ROMS). Using data from four cruises in 2005, horizontal, vertical and boundary nutrient fluxes were calculated in the hydrodynamic box model, in which flux fields and the major controlling factors were studied. Results show that the nutrient flux varied greatly in season and space. Water flux outweighs the nutrient concentration in horizontal flux, and upwelling flux outweighs upward diffusion flux in vertical direction (upwelling flux and upward diffusion flux regions overlap largely all the year). Vertical flux in spring and summer are much greater than that in autumn and winter. The maximum vertical flux for DIP (dissolved inorganic phosphate) occurs in summer. Additional to the fluxes of the Changjiang River discharge, coastal currents, the Taiwan Warm Current, and the upwelling, nutrient flux inflow from the southern Yellow Sea and outflow southward are found crucial to nutrient budgets of the study area. Horizontal nutrient flux is controlled by physical dilution and confined to coastal waters with a little into the open seas. The study area acts as a conveyer transferring nutrients from the Yellow Sea to the East China Sea in the whole year. In addition, vertical nutrient flux in spring and summer is a main source of DIP. Therefore, the hydrodynamic ROMS-based box model is superior to the traditional

  7. [Temporal and spatial distribution of red tide in Yangtze River Estuary and adjacent waters].

    PubMed

    Liu, Lu-San; Li, Zi-Cheng; Zhou, Juan; Zheng, Bing-Hui; Tang, Jing-Liang

    2011-09-01

    The events of red tide were collected in Yangtze River Estuary and adjacent waters from 1972 to 2009. Based on geographic information system (GIS) analysis on the temporal and spatial distribution of red tide, the distribution map was generated accordingly. The results show: (1) There are three red tide-prone areas, which are outside the Yangtze River estuary and the eastern of Sheshan, Huaniaoshan-Shengshan-Gouqi, Zhoushan and the eastern of Zhujiajian. The red tide occurred 174 times in total, in which there were 25 times covered the area was larger than 1 000 km2. After 2000, the frequency of red tide were significantly increasing; (2) The frequent occurrence of red tide was in May (51% of total occurrence) and June (20% of total occurrence); (3) In all of the red tide plankton, the dominant species were Prorocentrum danghaiense, Skeletonema costatum, Prorocentrum dantatum, Nactiluca scientillans. The red tides caused by these species were 38, 35, 15, 10 times separately. PMID:22165212

  8. Distribution patterns of phytoplankton in the Changjiang River estuary and adjacent waters in spring 2009

    NASA Astrophysics Data System (ADS)

    Kong, Fanzhou; Xu, Zijun; Yu, Rencheng; Yuan, Yongquan; Zhou, Mingjiang

    2016-09-01

    The Changjiang River estuary and adjacent waters are one of the most notable regions for red tides/harmful algal blooms in China's coastal waters. In this study, phytoplankton samples were collected and analyzed during the outbreak stage of red tides in May 2009. It was found that dinoflagellates, Prorocentrum donghaiense and Karenia mikimotoi, and diatoms, Skeletonema spp. and Paralia sulcata, were the major taxa dominating the phytoplankton community. Cluster analysis, non-metric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) was conducted on a data matrix including taxa composition and cell abundance of the phytoplankton samples. The analyses categorized the samples into three groups at a similarity level of 30%. Group I was characterized by estuarine diatoms and distributed mainly in the highly turbid estuarine region. Group II, which was dominated by the diatom Skeletonema spp. and represented the red tide of Skeletonema spp., was situated around Group I in the sea area west of 122°50'E. Group III was characterized by a high proportion of dinoflagellates and was found further offshore compared with Groups I and II. Group III was further divided into two subgroups (III-S1 and III-S2) at a similarity level of 40%. Group III-S1 was characterized by the presence of the benthic diatom P. sulcata, representing phytoplankton samples collected either from the bottom or from the sea area affected by upwelling. Group III-S2 was dominated by dinoflagellates and represented red tides formed by P. donghaiense and K. mikimotoi. A gradual change of red-tide causative species was observed from the estuary to the offshore sea area, from diatoms to armored dinoflagellates and then unarmored dinoflagellates. Environmental factors associated with each group, and thus affecting the distribution of phytoplankton and red tides, are discussed.

  9. Distribution patterns of phytoplankton in the Changjiang River estuary and adjacent waters in spring 2009

    NASA Astrophysics Data System (ADS)

    Kong, Fanzhou; Xu, Zijun; Yu, Rencheng; Yuan, Yongquan; Zhou, Mingjiang

    2016-01-01

    The Changjiang River estuary and adjacent waters are one of the most notable regions for red tides/harmful algal blooms in China's coastal waters. In this study, phytoplankton samples were collected and analyzed during the outbreak stage of red tides in May 2009. It was found that dinoflagellates, Prorocentrum donghaiense and Karenia mikimotoi, and diatoms, Skeletonema spp. and Paralia sulcata, were the major taxa dominating the phytoplankton community. Cluster analysis, non-metric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) was conducted on a data matrix including taxa composition and cell abundance of the phytoplankton samples. The analyses categorized the samples into three groups at a similarity level of 30%. Group I was characterized by estuarine diatoms and distributed mainly in the highly turbid estuarine region. Group II, which was dominated by the diatom Skeletonema spp. and represented the red tide of Skeletonema spp., was situated around Group I in the sea area west of 122°50'E. Group III was characterized by a high proportion of dinoflagellates and was found further offshore compared with Groups I and II. Group III was further divided into two subgroups (III-S1 and III-S2) at a similarity level of 40%. Group III-S1 was characterized by the presence of the benthic diatom P. sulcata, representing phytoplankton samples collected either from the bottom or from the sea area affected by upwelling. Group III-S2 was dominated by dinoflagellates and represented red tides formed by P. donghaiense and K. mikimotoi. A gradual change of red-tide causative species was observed from the estuary to the offshore sea area, from diatoms to armored dinoflagellates and then unarmored dinoflagellates. Environmental factors associated with each group, and thus affecting the distribution of phytoplankton and red tides, are discussed.

  10. A benchmark-multi-disciplinary study of the interaction between the Chesapeake Bay and adjacent waters of the Virginian Sea

    NASA Technical Reports Server (NTRS)

    Hargis, W. J., Jr.

    1981-01-01

    The social and economic importance of estuaries are discussed. Major focus is on the Chesapeake Bay and its interaction with the adjacent waters of the Virginia Sea. Associated multiple use development and management problems as well as their internal physical, geological, chemical, and biological complexities are described.

  11. Amino acids in the Pearl River Estuary and adjacent waters: origins, transformation and degradation

    NASA Astrophysics Data System (ADS)

    Chen, Jianfang; Li, Yan; Yin, Kedong; Jin, Haiyan

    2004-10-01

    Two cruises were conducted in the Pearl River Estuary (PRE) and adjacent coastal waters during July 1999 and 2000 to investigate spatial variation, transformation and degradation of amino acids (AAs). Salinity, suspended sediments (SS), chl a, nutrients, dissolved organic carbon, particulate organic carbon, AAs, and hexosamines were measured and analyzed. Concentrations of particulate hydrolysable AAs (PHAAs), dissolved combined AAs and dissolved free AAs ranged from 0.41 to 12.6 μmol L-1, 1.1 to 4.0 μmol L-1 and 0.15 to 1.10 μmol L-1, respectively. AAs concentrations were low in waters of salinity <10, increased to the maximum in the estuarine and coastal plumes (salinity =10-25) and decreased beyond the coastal plume. There was a region where PHAAs were maximum, which coincided with the region of the chl a maximum and depletion of dissolved inorganic phosphorus in the coastal plume south of Hong Kong. This indicates that most of the AAs in estuarine and coastal waters were produced through phytoplankton production and AAs might be a temporary sink for inorganic nitrogen. The ratios of AAs/HAs and glucosamine/galactosamine (Glc-NH2/Gal-NH2) were on average, 26.0 and 3.8, respectively, in biogenic particulate matter (chl a >5 μg L-1 and SS<10 mg L-1), decreased in turbid particles (SS>20 mg L-1) and reached the lowest values of 5.8 and 1.4 in sediments. In particular, the ratios of AAs/HAs, Glc-NH2/Gal-NH2 were low in the upper or northwest side of the estuary where turbidity was high. This indicated that these AAs were "old", likely due to resuspension of refractory organic matter from sediments or zooplankton grazing modification and bacterial reworking as the salt wedge advanced upstream near the bottom. Apparently, the dynamics of AAs in the PRE appeared to be governed by biological production processes and estuarine circulation in the estuary. As the chl a maximum developed downstream in the estuarine and coastal plume and the salt wedge moved upstream at

  12. Clusterization of water molecules as deduced from statistical mechanical approach

    NASA Astrophysics Data System (ADS)

    Krasnoholovets, Volodymyr

    2004-12-01

    Using the methods of statistical mechanics we have shown that a homogeneous water network is unstable and spontaneously disintegrates to the nonhomogeneous state (i.e. peculiar clusters), which can be treated as an ordinary state of liquid water. The major peculiarity of the concept is that it separates the paired potential into two independent components—the attractive potential and the repulsive one, which in turn should feature a very different dependence on the distance from the particle (a water molecule in the present case). We choose the interaction potential as a combination of the ionic crystal potential and the vibratory potential associated with the elastic properties of the water system as a whole. The number ℵ of water molecules that enters a cluster is calculated as a function of several parameters, such as the dielectric constant, the mass of a water molecule, the distance between nearest molecules, and the vibrations of nearest molecules in their nodes. The number of H2O molecules that comprise a cluster is estimated as about ℵ ≈ 900, which agrees with the available experimental data.

  13. On the Several Molecules and Nanostructures of Water

    PubMed Central

    Whitney, Cynthia Kolb

    2012-01-01

    This paper investigates the water molecule from a variety of viewpoints. Water can involve different isotopes of Hydrogen and Oxygen, it can form differently shaped isomer molecules, and, when frozen, it occupies space differently than most other substances do. The tool for conducting the investigation of all this is called ‘Algebraic Chemistry’. This tool is a quantitative model for predicting the energy budget for all sorts of changes between different ionization states of atoms that are involved in chemical reactions and in changes of physical state. The model is based on consistent patterns seen in empirical data about ionization potentials, together with rational scaling laws that can interpolate and extrapolate for situations where no data are available. The results of the investigation of the water molecule include comments, both positive and negative, about technologies involving heavy water, poly water, Brown’s gas, and cold fusion. PMID:22312305

  14. On the several molecules and nanostructures of water.

    PubMed

    Whitney, Cynthia Kolb

    2012-01-01

    This paper investigates the water molecule from a variety of viewpoints. Water can involve different isotopes of Hydrogen and Oxygen, it can form differently shaped isomer molecules, and, when frozen, it occupies space differently than most other substances do. The tool for conducting the investigation of all this is called 'Algebraic Chemistry'. This tool is a quantitative model for predicting the energy budget for all sorts of changes between different ionization states of atoms that are involved in chemical reactions and in changes of physical state. The model is based on consistent patterns seen in empirical data about ionization potentials, together with rational scaling laws that can interpolate and extrapolate for situations where no data are available. The results of the investigation of the water molecule include comments, both positive and negative, about technologies involving heavy water, poly water, Brown's gas, and cold fusion. PMID:22312305

  15. Size, separation, structural order, and mass density of molecules packing in water and ice

    PubMed Central

    Huang, Yongli; Zhang, Xi; Ma, Zengsheng; Li, Wen; Zhou, Yichun; Zhou, Ji; Zheng, Weitao; Sun, Chang Q.

    2013-01-01

    The structural symmetry and molecular separation in water and ice remain uncertain. We present herewith a solution to unifying the density, the structure order and symmetry, the size (H-O length dH), and the separation (dOO = dL + dH or the O:H length dL) of molecules packing in water and ice in terms of statistic mean. This solution reconciles: i) the dL and the dH symmetrization of the O:H-O bond in compressed ice, ii) the dOO relaxation of cooling water and ice and, iii) the dOO expansion of a dimer and between molecules at water surface. With any one of the dOO, the density ρ(g·cm−3), the dL, and the dH, as a known input, one can resolve the rest quantities using this solution that is probing conditions or methods independent. We clarified that: i) liquid water prefers statistically the mono-phase of tetrahedrally-coordinated structure with fluctuation, ii) the low-density phase (supersolid phase as it is strongly polarized with even lower density) exists only in regions consisting molecules with fewer than four neighbors and, iii) repulsion between electron pairs on adjacent oxygen atoms dictates the cooperative relaxation of the segmented O:H-O bond, which is responsible for the performance of water and ice. PMID:24141643

  16. Quantum Behavior of Water Molecules Confined to Nanocavities in Gemstones.

    PubMed

    Gorshunov, Boris P; Zhukova, Elena S; Torgashev, Victor I; Lebedev, Vladimir V; Shakurov, Gil'man S; Kremer, Reinhard K; Pestrjakov, Efim V; Thomas, Victor G; Fursenko, Dimitry A; Dressel, Martin

    2013-06-20

    When water is confined to nanocavities, its quantum mechanical behavior can be revealed by terahertz spectroscopy. We place H2O molecules in the nanopores of a beryl crystal lattice and observe a rich and highly anisotropic set of absorption lines in the terahertz spectral range. Two bands can be identified, which originate from translational and librational motions of the water molecule isolated within the cage; they correspond to the analogous broad bands in liquid water and ice. In the present case of well-defined and highly symmetric nanocavities, the observed fine structure can be explained by macroscopic tunneling of the H2O molecules within a six-fold potential caused by the interaction of the molecule with the cavity walls. PMID:26283245

  17. Effects of water molecules on photoluminescence from hierarchical peptide nanotubes and water probing capability.

    PubMed

    Wang, Minjie; Xiong, Shijie; Wu, Xinglong; Chu, Paul K

    2011-10-01

    Photoluminescence (PL) spectra reveal that deficiency of water molecules in the channel cores of bioinspired hierarchical diphenylalanine ( L -Phe- L -Phe, FF) peptide nanotubes (PNTs) not only modifies the bandgap of the subnanometer crystalline structure formed by the self-assembly process, but also induces a characteristic ultraviolet PL peak the position of which is linearly proportional to the number of water molecules in the PNTs. Addition or loss of water molecules gives rise to the UV PL redshift or blueshift. Density functional theory calculation also confirms that addition of water molecules to the PNTs causes splitting of the valence-band peak, which corresponds to the shift and splitting of the observed UV PL peak. Water molecules play an important role in the biological properties of FF PNTs and the results demonstrate that the PL spectra can be used to probe the number of water molecules bonded to the FF molecules. PMID:22049551

  18. An interdisciplinary study of the estuarine and coastal oceanography of Block Island Sound and adjacent New York coastal waters

    NASA Technical Reports Server (NTRS)

    Yost, E. (Principal Investigator)

    1972-01-01

    The author has identified the following significant results. The synoptic repetitive coverage of the multispectral imagery from the ERTS-1 satellite, when photographically reprocessed using the state-of-the-art techniques, has given indication of spectral differences in Block Island and adjacent New England waters which were heretofore unknown. Of particular interest was the possible detection of relatively small amounts of phytoplankton prior to the occurrence of the red tide in Massachusetts waters. Preparation of spatial and temporal hydrographic charts using ERTS-1 imagery and ground truth analysis will hopefully determine the environmental impact on New York coastal waters.

  19. Molecules to Materials for PEC Water Splitting

    SciTech Connect

    Neale, N. R.; Ruddy, D. A.; Lee, K.; Seabold, J. A.; Deutsch, T. G.; Dukovic, G.

    2013-01-01

    Advances in heterogeneous catalysis are driven by the formation of structure-property relationships at solid-liquid and solid-gaseous interfaces. The establishment of these relationships relies on cooperative research efforts on several fronts: prediction and analysis using high-level theoretical models, the development of new synthetic methods to prepare specific solid-state compositions and structures, new analytical methods to identify the active site and define interfacial properties, and mechanistic analysis of functioning catalysts. However, customized materials that allow for fine control of the interfacial properties at solid-liquid boundaries represent difficult synthetic targets. We have been investigating molecular synthons as precursors to advanced materials to address this challenge. In this presentation, we will discuss (1) the chemistry of molecular inorganic complexes, (2) their conversion to mixed-metal oxides, and (3) structure-property relationships of the resulting oxides relevant to PEC water splitting.

  20. Dynamics of Confined Water Molecules in Aqueous Salt Hydrates

    SciTech Connect

    Werhahn, Jasper C.; Pandelov, S.; Yoo, Soohaeng; Xantheas, Sotiris S.; Iglev, H.

    2011-04-01

    The unusual properties of water are largely dictated by the dynamics of the H bond network. A single water molecule has more H bonding sites than atoms, hence new experimental and theoretical investigations about this peculiar liquid have not ceased to appear. Confinement of water to nanodroplets or small molecular clusters drastically changes many of the liquid’s properties. Such confined water plays a major role in the solvation of macro molecules such as proteins and can even be essential to their properties. Despite the vast results available on bulk and confined water, discussions about the correlation between spectral and structural properties continue to this day. The fast relaxation of the OH stretching vibration in bulk water, and the variance of sample geometries in the experiments on confined water obfuscate definite interpretation of the spectroscopic results in terms of structural parameters. We present first time-resolved investigations on a new model system that is ideally suited to overcome many of the problems faced in spectroscopical investigation of the H bond network of water. Aqueous hydrates of inorganic salts provide water molecules in a crystal grid, that enables unambiguous correlations of spectroscopic and structural features. Furthermore, the confined water clusters are well isolated from each other in the crystal matrix, so different degrees of confinement can be achieved by selection of the appropriate salt.

  1. Theoretical study of impulsive orientation of asymmetric top water molecules

    NASA Astrophysics Data System (ADS)

    Rangan, Chitra; Senchuk, Andrew

    2008-05-01

    We theoretically study the orientation of a polar, asymmetric top molecule by a terahertz half-cycle pulse. This study is motivated by recent experimental results by C. Herne and P.H. Bucksbaum on the orientation of water molecule using terahertz half-cycle pulses. The half-cycle pulse is modelled as an impulse. The degree of orientation is calculated. Our aim is to characterize the calculated orientation curves in terms of rotational spectroscopy constants.

  2. Unprecedentedly rapid transport of single-file rolling water molecules

    NASA Astrophysics Data System (ADS)

    Qiu, Tong; Huang, Ji-Ping

    2015-10-01

    The realization of rapid and unidirectional single-file water-molecule flow in nanochannels has posed a challenge to date. Here, we report unprecedentedly rapid unidirectional single-file water-molecule flow under a translational terahertz electric field, which is obtained by developing a Debye doublerelaxation theory. In addition, we demonstrate that all the single-file molecules undergo both stable translation and rotation, behaving like high-speed train wheels moving along a railway track. Independent molecular dynamics simulations help to confirm these theoretical results. The mechanism involves the resonant relaxation dynamics of H and O atoms. Further, an experimental demonstration is suggested and discussed. This work has implications for the design of high-efficiency nanochannels or smaller nanomachines in the field of nanotechnology, and the findings also aid in the understanding and control of water flow across biological nanochannels in biology-related research.

  3. How Many Water Molecules Does it Take to Dissociate HCl?

    PubMed

    Vargas-Caamal, Alba; Cabellos, Jose Luis; Ortiz-Chi, Filiberto; Rzepa, Henry S; Restrepo, Albeiro; Merino, Gabriel

    2016-02-18

    The potential energy surfaces of the HCl(H2O)n (n is the number of water molecules) clusters are systematically explored using density functional theory and high-level ab initio computations. On the basis of electronic energies, the number of water molecules needed for HCl dissociation is four as reported by some experimental groups. However, this number is five owing to the inclusion of entropic factors. Wiberg bond indices are calculated and analyzed, and the results provide a quadratic correlation and classification of clusters according to the nondissociated, partially dissociated, and fully dissociated character of the H-Cl bond. Our computations show that if temperature is not controlled during the experiment, the values obtained for the dipole moment (or for any measurable property) are susceptible to change, providing a different picture of the number of water molecules needed for HCl dissociation in a nanoscopic droplet. PMID:26774026

  4. Transport behavior of water molecules through two-dimensional nanopores

    SciTech Connect

    Zhu, Chongqin; Li, Hui; Meng, Sheng

    2014-11-14

    Water transport through a two-dimensional nanoporous membrane has attracted increasing attention in recent years thanks to great demands in water purification and desalination applications. However, few studies have been reported on the microscopic mechanisms of water transport through structured nanopores, especially at the atomistic scale. Here we investigate the microstructure of water flow through two-dimensional model graphene membrane containing a variety of nanopores of different size by using molecular dynamics simulations. Our results clearly indicate that the continuum flow transits to discrete molecular flow patterns with decreasing pore sizes. While for pores with a diameter ≥15 Å water flux exhibits a linear dependence on the pore area, a nonlinear relationship between water flux and pore area has been identified for smaller pores. We attribute this deviation from linear behavior to the presence of discrete water flow, which is strongly influenced by the water-membrane interaction and hydrogen bonding between water molecules.

  5. SPAM: A Simple Approach for Profiling Bound Water Molecules.

    PubMed

    Cui, Guanglei; Swails, Jason M; Manas, Eric S

    2013-12-10

    A method that identifies the hydration shell structure of proteins and estimates the relative free energies of water molecules within that hydration shell is described. The method, which we call "SPAM" (maps spelled in reverse), utilizes explicit solvent molecular dynamics (MD) simulations to capture discrete hydration sites at the water-protein interface and computes a local free energy measure from the distribution of interaction energies between water and the environment at a specific site. SPAM is able to provide a qualitative estimate of the thermodynamic profile of bound water molecules that correlates nicely with well-studied structure-activity relationships and observed binding "hot spots". This is demonstrated in retrospective analyses of HIV1 protease and hen egg white lysozyme, where the effects of water displacement and solvent binding have been studied extensively. The simplicity and effectiveness of SPAM allow for prospective application during the drug discovery process. PMID:26592287

  6. Assessment of water resources in lead-zinc mined areas in Cherokee County, Kansas, and adjacent areas

    USGS Publications Warehouse

    Spruill, T.B.

    1984-01-01

    A study was conducted to evaluate water-resource problems related to abandoned lead and zinc mines in Cherokee County, and adjacent areas in Oklahoma and Missouri. Discontinuities and perforations, which were produced by mining in the confining shale west of the Pennsylvanian-Mississippian geologic contact, have created artificial groundwater recharge and discharge areas. Abandoned wells and drill holes present the greatest contamination hazard to water supplies in the deep aquifer. There is a potential for downward movement from the shallow to the deep aquifer throughout the study area, with greatest potential in Ottawa County, Oklahoma. Principal effects of abandoned mines on groundwater quality are lowered pH and increased concentrations of sulfate and trace metals of water in the mines. No conclusive evidence of lateral migration of contaminated mine water from the mines into the water-supply wells adjacent to the mines was found. Analyses of water from the deep aquifer did not indicate trace-metal contamination. The effects of abandoned mines on streamwater quality are most severe in Short Creek and Tar Creek. Increased concentrations of zinc and manganese were observed in the Spring River below Short Creek Kansas. (USGS)

  7. Structures of water molecules in carbon nanotubes under electric fields

    SciTech Connect

    Winarto,; Takaiwa, Daisuke; Yamamoto, Eiji; Yasuoka, Kenji

    2015-03-28

    Carbon nanotubes (CNTs) are promising for water transport through membranes and for use as nano-pumps. The development of CNT-based nanofluidic devices, however, requires a better understanding of the properties of water molecules in CNTs because they can be very different from those in the bulk. Using all-atom molecular dynamics simulations, we investigate the effect of axial electric fields on the structure of water molecules in CNTs having diameters ranging from (7,7) to (10,10). The water dipole moments were aligned parallel to the electric field, which increases the density of water inside the CNTs and forms ordered ice-like structures. The electric field induces the transition from liquid to ice nanotubes in a wide range of CNT diameters. Moreover, we found an increase in the lifetime of hydrogen bonds for water structures in the CNTs. Fast librational motion breaks some hydrogen bonds, but the molecular pairs do not separate and the hydrogen bonds reform. Thus, hydrogen bonds maintain the water structure in the CNTs, and the water molecules move collectively, decreasing the axial diffusion coefficient and permeation rate.

  8. Structures of water molecules in carbon nanotubes under electric fields

    NASA Astrophysics Data System (ADS)

    Winarto, Takaiwa, Daisuke; Yamamoto, Eiji; Yasuoka, Kenji

    2015-03-01

    Carbon nanotubes (CNTs) are promising for water transport through membranes and for use as nano-pumps. The development of CNT-based nanofluidic devices, however, requires a better understanding of the properties of water molecules in CNTs because they can be very different from those in the bulk. Using all-atom molecular dynamics simulations, we investigate the effect of axial electric fields on the structure of water molecules in CNTs having diameters ranging from (7,7) to (10,10). The water dipole moments were aligned parallel to the electric field, which increases the density of water inside the CNTs and forms ordered ice-like structures. The electric field induces the transition from liquid to ice nanotubes in a wide range of CNT diameters. Moreover, we found an increase in the lifetime of hydrogen bonds for water structures in the CNTs. Fast librational motion breaks some hydrogen bonds, but the molecular pairs do not separate and the hydrogen bonds reform. Thus, hydrogen bonds maintain the water structure in the CNTs, and the water molecules move collectively, decreasing the axial diffusion coefficient and permeation rate.

  9. [Investigation of membrane permeability of carp spermatozoa for water molecules].

    PubMed

    Pugovkin, A Iu; Kopeĭka, E F; Nardid, O A; Cherkashina, Ia O

    2014-01-01

    The fundamentals of a photometry method for determination of membrane permeability of some fish spermatozoa for water molecules are presented. Osmotic tolerance of carp spermatozoa membranes was studied using EPR-spectroscopy and photometric analysis methods. It was shown that carp spermatozoa look like the ideal osmometers in their reaction on media of different osmolarity. The value of membrane permeability of carp spermatozoa for water molecules was determined. Data obtained can be used in cryobiology for creating cryoprotective media and regimes of fish sperm cryopreservation. PMID:25715589

  10. Chemical Interactions of Uranium in Water, Sediments, and Plants Along a Watershed Adjacent to the Abandoned Jackpile Mine

    NASA Astrophysics Data System (ADS)

    Blake, J.; De Vore, C. L.; Avasarala, S.; Ali, A.; Roldan, C.; Bowers, F.; Spilde, M.; Artyushkova, K.; Cerrato, J.

    2015-12-01

    The chemical interactions, mobility, and plant uptake of uranium (U) near abandoned mine wastes was investigated along the Rio Paguate, adjacent to the Jackpile Mine, located in Laguna Pueblo, New Mexico. Elevated U concentrations in surface water adjacent to mine waste range from 30 to 710 μg/L seasonally and decrease to 5.77 to 10.0 μg/L at a wetland 4.5 kilometers downstream of the mine. Although U concentrations in stream water are elevated, aqua regia acid digestions performed on co-located stream bed and stream bank sediments reveal that there is limited U accumulation on sediments along the reach between the mine and wetland, with most sediment concentrations being near the 3 mg/kg crustal average. However, U concentrations in sediments in the wetland are 4 times the background concentrations in the area. Individual results from salt cedar roots, stems, and leaves collected along the river transect show higher U concentrations in the roots adjacent to the mine waste (20 and 55 mg/kg) and lower in the stems and leaves. Translocation values calculated below 1 are evident in many of the plant samples, suggesting that U root to shoot translocation is minimal and U is accumulating in the roots. Concentrations of U in salt cedar roots from downstream of the mine waste decrease to 15 mg/kg. X-ray photoelectron spectroscopy analysis on sediment samples adjacent to the mine waste show a 75:25% ratio of Fe(III) to Fe(II), which can have an effect on adsorption properties. Electron microprobe results suggest that the ore in this area is present as a uranium-phosphate phase. Our results suggest that dilution, uptake by plants, and U sorption to wetland sediments are the dominant factors that help to decrease the U concentrations downstream of the mine.

  11. Visualizing Water Molecules in Transmembrane Proteins Using Radiolytic Labeling Methods

    SciTech Connect

    Orban, T.; Gupta, S; Palczewski, K; Chance, M

    2010-01-01

    Essential to cells and their organelles, water is both shuttled to where it is needed and trapped within cellular compartments and structures. Moreover, ordered waters within protein structures often colocalize with strategically placed polar or charged groups critical for protein function, yet it is unclear if these ordered water molecules provide structural stabilization, mediate conformational changes in signaling, neutralize charged residues, or carry out a combination of all these functions. Structures of many integral membrane proteins, including G protein-coupled receptors (GPCRs), reveal the presence of ordered water molecules that may act like prosthetic groups in a manner quite unlike bulk water. Identification of 'ordered' waters within a crystalline protein structure requires sufficient occupancy of water to enable its detection in the protein's X-ray diffraction pattern, and thus, the observed waters likely represent a subset of tightly bound functional waters. In this review, we highlight recent studies that suggest the structures of ordered waters within GPCRs are as conserved (and thus as important) as conserved side chains. In addition, methods of radiolysis, coupled to structural mass spectrometry (protein footprinting), reveal dynamic changes in water structure that mediate transmembrane signaling. The idea of water as a prosthetic group mediating chemical reaction dynamics is not new in fields such as catalysis. However, the concept of water as a mediator of conformational dynamics in signaling is just emerging, because of advances in both crystallographic structure determination and new methods of protein footprinting. Although oil and water do not mix, understanding the roles of water is essential to understanding the function of membrane proteins.

  12. Water-quality, water-level, and lake-bottom-sediment data collected from the defense fuel supply point and adjacent properties, Hanahan, South Carolina, 1990-96

    USGS Publications Warehouse

    Petkewich, M.D.; Vroblesky, D.A.; Robertson, J.F.; Bradley, P.M.

    1997-01-01

    A 9-year scientific investigation to determine the potential for biore-mediation of ground-water contamination and to monitor the effectiveness of an engineered bioremediation system located at the Defense Fuel Supply Point and adjacent properties in Hanahan, S.C., has culminated in the collection of abundant water-quality and water-level data.This report presents the analytical results of the study that monitored the changes in surface- and ground-water quality and water-table elevations in the study area from December 1990 to January 1996. This report also presents analytical results of lake-bottom sediments collected in the study area.

  13. Sources and growth dynamics of fecal indicator bacteria in a coastal wetland system and potential impacts to adjacent waters.

    PubMed

    Evanson, Melissa; Ambrose, Richard F

    2006-02-01

    Coastal wetlands are receiving increased attention as a putative source of fecal indicator bacteria (FIB) in Southern California coastal waters. We examined temporal trends of water and sediment-associated FIB after rain events along with spatial sediment characteristics at two sites within the Santa Ana River wetlands and made comparisons to FIB levels observed in adjacent surf zone waters. During the first two rain events, total coliforms (TC), Escherichia coli (EC) and enterococci (ENT) in wetland water and sediment samples peaked either on the same day or within several days of the rain event, while the third resulted in elevated wetlands sediment TC levels only. TC in adjacent coastal waters consistently peaked on the same day as the rain event and decreased quickly thereafter (within 1 day). The TC/EC ratios of surf zone samples consistently fell below 10, indicating an increased probability of human fecal contamination whereas wetland TC/EC ratios were higher, averaging approximately 60 and 14 at each site. These results suggest sediment-associated FIB populations may be distinct from those found in the water samples, or at least have internal dynamics independent of water-borne populations. Increases in sediment-associated FIB may be due to in situ population growth and/or increased survival due to changes in environmental parameters (salinity, moisture and nutrient input) resulting from the rain events. Spatial differences in between the two sites may be due to sediment differences such as organic content and finer grain size and/or discrete sources of FIB. PMID:16386284

  14. Interaction between water molecules and zinc sulfide nanoparticles studied by temperature-programmed desorption and molecular dynamics simulations.

    PubMed

    Zhang, Hengzhong; Rustad, James R; Banfield, Jillian F

    2007-06-14

    We have investigated the bonding of water molecules to the surfaces of ZnS nanoparticles (approximately 2-3 nm sphalerite) using temperature-programmed desorption (TPD). The activation energy for water desorption was derived as a function of the surface coverage through kinetic modeling of the experimental TPD curves. The binding energy of water equals the activation energy of desorption if it is assumed that the activation energy for adsorption is nearly zero. Molecular dynamics (MD) simulations of water adsorption on 3 and 5 nm sphalerite nanoparticles provided insights into the adsorption process and water binding at the atomic level. Water binds with the ZnS nanoparticle surface mainly via formation of Zn-O bonds. As compared with bulk ZnS crystals, ZnS nanoparticles can adsorb more water molecules per unit surface area due to the greatly increased curvature, which increases the distance between adjacent adsorbed molecules. Results from both TPD and MD show that the water binding energy increases with decreasing the water surface coverage. We attribute the increase in binding energy with decreasing surface water coverage to the increasing degree of surface under-coordination as removal of water molecules proceeds. MD also suggests that the water binding energy increases with decreasing particle size due to the further distance and hence lower interaction between adsorbed water molecules on highly curved smaller particle surfaces. Results also show that the binding energy, and thus the strength of interaction of water, is highest in isolated nanoparticles, lower in nanoparticle aggregates, and lowest in bulk crystals. Given that water binding is driven by surface energy reduction, we attribute the decreased binding energy for aggregated as compared to isolated particles to the decrease in surface energy that occurs as the result of inter-particle interactions. PMID:17518448

  15. Ground Water in Kilauea Volcano and Adjacent Areas of Mauna Loa Volcano, Island of Hawaii

    USGS Publications Warehouse

    Takasaki, Kiyoshi J.

    1993-01-01

    About 1,000 million gallons of water per day moves toward or into ground-water bodies of Kilauea Volcano from the lavas of Mauna Loa Volcano. This movement continues only to the northern boundaries of the east and southwest rift zones of Kilauea, where a substantial quantity of ground water is deflected downslope to other ground-water bodies or to the ocean. In the western part of Kilauea, the kaoiki fault system, which parallels the southwest rift zone, may be the main barrier to ground-water movement. The diversion of the ground water is manifested in the western part of Kilauea by the presence of large springs at the shore end of the Kaoiki fault system, and in the eastern part by the apparently large flow of unheated basal ground water north of the east rift zone. Thus, recharge to ground water in the rift zones of Kilauea and to the areas to the south of the rift zones may be largely by local rainfall. Recharge from rainfall for all of Kilauea is about 1,250 million gallons per day. Beneath the upper slopes of the Kilauea rift zones, ground-water levels are 2,000 feet or more above mean sea level, or more than 1,000 feet below land surface. Ground-water levels are at these high altitudes because numerous and closely spaced dikes at depth in the upper slopes impound the ground water. In the lower slopes, because the number of dikes decreases toward the surface, the presence of a sufficient number of dikes capable of impounding ground water at altitudes substantially above sea level is unlikely. In surrounding basal ground-water reservoirs, fresh basal ground water floats on seawater and, through a transition zone of mixed freshwater and seawater, discharges into the sea. The hydraulic conductivity of the dike-free lavas ranges from about 3,000 to about 7,000 feet per day. The conductivity in the upper slopes of the rift ranges from about 5 to 30 feet per day and that of the lower slopes of the east rift zone was calculated at about 7,000 feet per day. The

  16. 33 CFR 334.730 - Waters of Santa Rosa Sound and Gulf of Mexico adjacent to Santa Rosa Island, Air Force Proving...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Gulf of Mexico adjacent to Santa Rosa Island, Air Force Proving Ground Command, Eglin Air Force Base... Sound and Gulf of Mexico adjacent to Santa Rosa Island, Air Force Proving Ground Command, Eglin Air Force Base, Fla. (a) The danger zones—(1) Prohibited area. Waters of Santa Rosa Sound and Gulf of...

  17. 33 CFR 334.730 - Waters of Santa Rosa Sound and Gulf of Mexico adjacent to Santa Rosa Island, Air Force Proving...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Gulf of Mexico adjacent to Santa Rosa Island, Air Force Proving Ground Command, Eglin Air Force Base... Sound and Gulf of Mexico adjacent to Santa Rosa Island, Air Force Proving Ground Command, Eglin Air Force Base, Fla. (a) The danger zones—(1) Prohibited area. Waters of Santa Rosa Sound and Gulf of...

  18. Water quality at and adjacent to the south Dade County solid-waste disposal facility, Florida

    USGS Publications Warehouse

    McKenzie, D.J.

    1983-01-01

    A water-quality reconnaissance was conducted at the south Dade County solid-waste landfill near Goulds, Florida, from December 1977 through August 1978. The landfill is located directly on the unconfined Biscayne aquifer, which, in the study area, is affected by saltwater intrusion. Water samples collected from six monitor well sites at two depths and four surface-water sites were analyzed to determine the chemical, physical, and biological conditions of the ground water and surface water of the study area. Results indicated that water quality beneath the landfill was highly variable with location and depth. Leachate was generally more evident in the shallow wells and during the dry-season sampling, but was greatly diluted and dispersed in the deep wells and during the wet season. High concentrations of contaminants were generated primarily in areas of the landfill with the most recent waste deposits. Chloride (limited to the shallow wells and the dry season), alkalinity, ammonia, iron, manganese, lead, phosphorus, and organic nitrogen indicate leachate contamination of the aquifer. Water-quality characteristics in the surface waters were generally only slightly above background levels. (USGS)

  19. Ground-water resources in the tri-state region adjacent to the Lower Delaware River

    USGS Publications Warehouse

    Barksdale, Henry C.; Greenman, David W.; Lang, Solomon Max; Hilton, George Stockbridge; Outlaw, Donald E.

    1958-01-01

    The maximum beneficial utilization of the ground-water resources cannot be accomplished in haphazard fashion. It must be planned and controlled on the basis of sound, current information about the hydrology of the various aquifers. Continued and, in some areas, intensified investigations of the ground-water resources of the region should form the basis for such planning and control.

  20. Emergency ground-water supplies in the Seattle-Tacoma urban complex and adjacent areas, Washington

    USGS Publications Warehouse

    Foxworthy, B.L.

    1972-01-01

    Urban areas that are supplied from surface-water sources are especially vulnerable to major disruption of their water supplies. Such disruption could result from natural disasters such as earthquakes, floods, or landslides or from such other causes as dam failures fallout of radioactive material or other toxic substance from the atmosphere or other toxic substances from the atmosphere or direct introduction (either accidental or deliberate) of any substance that would render the water unfit for use. Prolonged disruption of public water supplies not only causes personal hardships but also endangers health and safety unless suitable alternative emergency supplies can be provided. The degree of hardship and danger generally increases in direct relation to the population density. Ground water because it occurs beneath protective soil and rock materials is less subject to sudden major contamination than are surface-water bodies. For this reason and also because of its widespread availability in the Puget Sound region ground water is especially desireable as a sources of emergency supplies for drinking or other uses requiring water of good quality. In much of the area existing wells would be suitable as safe sources of emergency supplies.

  1. Potentiometric surface of Floridan Aquifer, Southwest Florida Water Management District and adjacent areas, May 1979

    USGS Publications Warehouse

    Wolansky, R.M.; Mills, L.R.; Woodham, W.M.; Laughlin, C.P.

    1979-01-01

    A May 1979 potentiometric-surface map depicts the annual low water-level period. Potentiometric levels declined 4 to 21 feet between September 1978 and May 1979, in the citrus and farming sections of southern Hillsborough, northern Hardee, southwestern Polk, northwestern DeSoto, and Manatee Counties. Water levels in these areas are widely affected by pumping for irrigation and have the greatest range in fluctuations. Water-level declines ranged from 0 to 6 feet in coastal, northern, and southern areas of the Water Management District. Generally potentiometric levels were higher than previous May levels due to heavy rains in April and May. In parts of Hillsborough, Pasco, and Pinellas Counties, May 1979 potentiometric levels were 18 feet higher than those of September 1978. (USGS)

  2. Quantification of lincomycin resistance genes associated with lincomycin residues in waters and soils adjacent to representative swine farms in China

    PubMed Central

    Li, Liang; Sun, Jian; Liu, Baotao; Zhao, Donghao; Ma, Jun; Deng, Hui; Li, Xue; Hu, Fengyang; Liao, Xiaoping; Liu, Yahong

    2013-01-01

    Lincomycin is commonly used on swine farms for growth promotion as well as disease treatment and control. Consequently, lincomycin may accumulate in the environment adjacent to the swine farms in many ways, thereby influencing antibiotic resistance in the environment. Levels of lincomycin-resistance genes and lincomycin residues in water and soil samples collected from multiple sites near wastewater discharge areas were investigated in this study. Sixteen lincomycin-resistance and 16S rRNA genes were detected using real-time PCR. Three genes, lnu(F), erm(A), and erm(B), were detected in all water and soil samples except control samples. Lincomycin residues were determined by rapid resolution liquid chromatography-tandem mass spectrometry, with concentrations detected as high as 9.29 ng/mL in water and 0.97 ng/g in soil. A gradual reduction in the levels of lincomycin-resistance genes and lincomycin residues in the waters and soils were detected from multiple sites along the path of wastewater discharging to the surrounding environment from the swine farms. Significant correlations were found between levels of lincomycin-resistance genes in paired water and soil samples (r = 0.885, p = 0.019), and between lincomycin-resistance genes and lincomycin residues (r = 0.975, p < 0.01). This study emphasized the potential risk of dissemination of lincomycin-resistance genes such as lnu(F), erm(A), and erm(B), associated with lincomycin residues in surrounding environments adjacent to swine farms. PMID:24348472

  3. Hadronic chemistry applied to hydrogen and water molecules

    NASA Astrophysics Data System (ADS)

    Tangde, Vijay M.

    2012-09-01

    The decades of research of R M Santilli resulted into the formulation of iso-, geno- and hyper- mathematics [1, 2] that helped in understanding numerous diversified problems and removing inadequacies in most of the established and celebrated theories of 20th century physics and chemistry, for example, the theories of relativity, quantum mechanics (chemistry), astrophysics, particle physics, and so on. This involves the isotopic, genotopic, etc. lifting of Lie algebra that generated Lie admissible mathematics to properly describe irreversible processes. The studies on Hadronic m Mechanics based on Santilli's mathematics for the first time has removed the very fundamental limitations of quantum chemistry [3, 4] [2, 3, 4]. Herein, we review a Santilli-Shillady model[3, 4, 5] of hydrogen and water molecules characterized by a bond at short distances of the two valance electrons into a singlet quasi-particle state called isoelectronium for hydrogen molecule and two isoelctronia (one per H-O dimer) in case of water molecule. We especially emphasis on: the numerically exact representation of binding energies from unadulterated first axiomatic principle, the reduction of the hydrogen molecule to a restricted three body problem that admits exact analytic solutions and the reduction of computer time by at least a factor of 1000 folds due to a much faster convergent series.

  4. An ecological study of the KSC Turning Basin and adjacent waters

    NASA Technical Reports Server (NTRS)

    Nevin, T. A.; Lasater, J. A.; Clark, K. B.; Kalajian, E. H.

    1974-01-01

    The conditions existing in the waters and bottoms of the Turning Basin, the borrow pit near Pad 39A, and the Barge Canal connecting them were investigated to determine the ecological significance of the chemical, biological, and microbiological parameters. The water quality, biological, microbiological findings are discussed. It is recommended that future dredging activities be limited in depth, and that fill materials should not be removed down to the clay strata.

  5. Potential interactions among disease, pesticides, water quality and adjacent land cover in amphibian habitats in the United States.

    PubMed

    Battaglin, W A; Smalling, K L; Anderson, C; Calhoun, D; Chestnut, T; Muths, E

    2016-10-01

    To investigate interactions among disease, pesticides, water quality, and adjacent land cover, we collected samples of water, sediment, and frog tissue from 21 sites in 7 States in the United States (US) representing a variety of amphibian habitats. All samples were analyzed for >90 pesticides and pesticide degradates, and water and frogs were screened for the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) using molecular methods. Pesticides and pesticide degradates were detected frequently in frog breeding habitats (water and sediment) as well as in frog tissue. Fungicides occurred more frequently in water, sediment, and tissue than was expected based upon their limited use relative to herbicides or insecticides. Pesticide occurrence in water or sediment was not a strong predictor of occurrence in tissue, but pesticide concentrations in tissue were correlated positively to agricultural and urban land, and negatively to forested land in 2-km buffers around the sites. Bd was detected in water at 45% of sites, and on 34% of swabbed frogs. Bd detections in water were not associated with differences in land use around sites, but sites with detections had colder water. Frogs that tested positive for Bd were associated with sites that had higher total fungicide concentrations in water and sediment, but lower insecticide concentrations in sediments relative to frogs that were Bd negative. Bd concentrations on frog swabs were positively correlated to dissolved organic carbon, and total nitrogen and phosphorus, and negatively correlated to pH and water temperature. Data were collected from a range of locations and amphibian habitats and represent some of the first field-collected information aimed at understanding the interactions between pesticides, land use, and amphibian disease. These interactions are of particular interest to conservation efforts as many amphibians live in altered habitats and may depend on wetlands embedded in these landscapes to survive

  6. Paleoenvironments and hydrocarbon potential of Upper Jurassic Norphlet Formation of southwestern Alabama and adjacent coastal water area

    SciTech Connect

    Mancini, E.A.; Mink, R.M.; Bearden, B.L.

    1984-09-01

    Upper Jurassic Norphlet sediments in southwestern Alabama and the adjacent coastal water area accumulated under arid climatic conditions. The Appalachian Mountains of the eastern United States extended into southwestern Alabama, providing a barrier for air and water circulation during Norphlet deposition. Norphlet paleogeography was dominated by a broad desert plain rimmed to the north and east by the Appalachians and to the south by a developing shallow sea. Initiation of Norphlet sedimentation was a result of erosion of the southern Appalachians. Norphlet conglomerates were deposited in coalescing alluvial fans in proximity to an Appalachian source. The conglomeratic sandstones grade downdip into red-bed lithofacies that accumulated in distal portions of alluvial fan and wadi systems. Quartzose sandstones (Denkman Member) were deposited as dune and interdune sediments on a broad desert plain. The source of the sand was the updip and adjacent alluvial fan, plain, and wadi deposits. A marine transgression was initiated late in Denkman deposition, resulting in the reworking of previously deposited Norphlet sediments. Norphlet hydrocarbon potential in southwestern and offshore Alabama is excellent with four oil and gas fields already established. Petroleum traps discovered to date are primarily structural traps involving salt anticlines, faulted salt anticlines, and extensional fault traps associated with salt movement. Reservoir rocks consist of quartzose sandstones, which are principally eolian in origin. Smackover algal carbonate mudstones were probably the source for the Norphlet hydrocarbons.

  7. Study on the total water pollutant load allocation in the Changjiang (Yangtze River) Estuary and adjacent seawater area

    NASA Astrophysics Data System (ADS)

    Deng, Yixiang; Zheng, Binghui; Fu, Guo; Lei, Kun; Li, Zicheng

    2010-02-01

    With the rapid economic development, the water quality is worsening and red tide takes place frequently in the Changjiang Estuary and adjacent seawaters. To improve the marine water quality, the total inland pollutant load should be controlled effectively. With efficiency and fairness in consideration, the total maximum allowable loads of COD Mn, NH 3-N, inorganic nitrogen and active phosphate to the seawaters were calculated and allocated by the linear programming method based on the water quality response fields of the pollution sources. The maximum allowable loads are 2008 × 10 3 tons, 169 × 10 3 tons, 226 × 10 3 tons and 18 × 10 3 tons for COD Mn, NH 3-N, inorganic nitrogen and active phosphate when the water quality targets are requested to be achieved in the whole studied region, and 346 × 10 3 tons and 32 × 10 3 tons for inorganic nitrogen and active phosphate when the water quality targets to be achieved only in the red tide sensitive area. The cut task of COD Mn and NH 3-N is relatively easy and can be finished by the watershed environmental plan; while the cut task of inorganic nitrogen and active phosphate is tremendous. The coastal provinces should install more denitrification and dephosphorization facilities in the existing waste water treatment plants or build new ones to control the red tides in the concerned seawaters.

  8. Quantum behaviour of water molecule in gemstone: terahertz fingerprints

    NASA Astrophysics Data System (ADS)

    Zhukova, Elena S.; Gorshunov, Boris P.; Torgashev, Victor I.; Lebedev, Vladimir V.; Shakurov, Gil'man S.; Kremer, Reinhard K.; Pestrjakov, Efim V.; Thomas, Victor G.; Fursenko, Dimitry A.; Dressel, Martin

    2014-03-01

    We have shown that a weak interaction of a lone H2O molecule with the ''walls'' of nano-sized crystalline cage of gemstone (beryl) results in emergence of a rich set of molecular vibrational states. By analogy with translational and librational bands in liquid water and ice corresponding absorption bands are explained as due to translational (T) and librational (L) movements of the H2O molecule which is hydrogen bonded to the cage walls. In beryl crystal lattice, however, the six-fold symmetry of the cage brings about additional effect of splitting of the T and L bands into fine structure due to tunnelling within the six-well potential relief. The presented results will be of use for analysis of more complicated systems with confined water molecules like H2O chains in carbon nano-tubes, molecular clusters in e.g. zeolites, clays, silica gels and other natural or synthetic frameworks, as well as for interfacial water in biological systems.

  9. Picosecond water dynamics adjacent to charged paramagnetic ions measured by magnetic relaxation dispersion

    NASA Astrophysics Data System (ADS)

    Lisitza, Natasha; Bryant, Robert G.

    2007-03-01

    Measurements of water-proton spin-lattice relaxation rate constants as a function of magnetic field strength [magnetic relaxation dispersion (MRD)] in aqueous solutions of paramagnetic solutes reveal a peak in the MRD profile. These previously unobserved peaks require that the time correlation functions describing the water-proton-electron dipolar coupling have a periodic contribution. In aqueous solutions of iron(III) ion the peak corresponds to a frequency of 8.7cm-1, which the authors ascribe to the motion of water participating in the second coordination sphere of the triply charged solute ion. Similar peaks of weaker intensity in the same time range are observed for aqueous solutions of chromium(III) chloride as well as for ion pairs formed by ammonium ion with trioxalatochromate(III) ion. The widths of the dispersion peaks are consistent with a lifetime for the periodic motion in the range of 5ps or longer.

  10. Corals persisting in naturally turbid waters adjacent to a pristine catchment in Solomon Islands.

    PubMed

    Albert, Simon; Fisher, Paul L; Gibbes, Badin; Grinham, Alistair

    2015-05-15

    Few water quality measurements exist from pristine environments, with fewer reported studies of coastal water quality from Solomon Islands. Water quality benchmarks for the Solomons have relied on data from other geographic regions, often from quite different higher latitude developed nations, with large land masses. We present the first data of inshore turbidity and sedimentation rate for a pristine catchment on Isabel Island. Surveys recorded relatively high coral cover. The lowest cover was recorded at 22.7% (Jejevo) despite this site having a mean turbidity (continuous monitoring) of 32 NTU. However, a similar site (Jihro) was significantly less turbid (2.1 mean NTU) over the same period. This difference in turbidity is likely due to natural features of the Jihro River promoting sedimentation before reaching coastal sites. We provide an important baseline for Solomon Island inshore systems, whilst demonstrating the importance of continuous monitoring to capture episodic high turbidity events. PMID:25752531

  11. Trace Element Mobility in Water and Sediments in a Hyporheic Zone Adjacent to an Abandoned Uranium Mine

    NASA Astrophysics Data System (ADS)

    Roldan, C.; Blake, J.; Cerrato, J.; Ali, A.; Cabaniss, S.

    2015-12-01

    The legacy of abandoned uranium mines lead to community concerns about environmental and health effects. This study focuses on a cross section of the Rio Paguate, adjacent to the Jackpile Mine on the Laguna Reservation, west-central New Mexico. Often, the geochemical interactions that occur in the hyporheic zone adjacent to these abandoned mines play an important role in trace element mobility. In order to understand the mobility of uranium (U), arsenic (As), and vanadium (V) in the Rio Paguate; surface water, hyporheic zone water, and core sediment samples were analyzed using inductively coupled plasma mass spectroscopy (ICP-MS). All water samples were filtered through 0.45μm and 0.22μm filters and analyzed. The results show that there is no major difference in concentrations of U (378-496μg/L), As (0.872-6.78μg/L), and V (2.94-5.01μg/L) between the filter sizes or with depth (8cm and 15cm) in the hyporheic zone. The unfiltered hyporheic zone water samples were analyzed after acid digestion to assess the particulate fraction. These results show a decrease in U concentration (153-202μg/L) and an increase in As (33.2-219μg/L) and V (169-1130μg/L) concentrations compared to the filtered waters. Surface water concentrations of U(171-184μg/L) are lower than the filtered hyporheic zone waters while As(1.32-8.68μg/L) and V(1.75-2.38μg/L) are significantly lower than the hyporheic zone waters and particulates combined. Concentrations of As in the sediment core samples are higher in the first 15cm below the water-sediment interface (14.3-3.82μg/L) and decrease (0.382μg/L) with depth. Uranium concentrations are consistent (0.047-0.050μg/L) at all depths. The over all data suggest that U is mobile in the dissolved phase and both As and V are mobile in the particular phase as they travel through the system.

  12. Insight into water molecules bonding on 4d metal surfaces

    NASA Astrophysics Data System (ADS)

    Carrasco, Javier; Michaelides, Angelos; Scheffler, Matthias

    2008-03-01

    Water-metal interactions are of capital importance to a wide variety of phenomena in materials science, catalysis, corrosion, electrochemistry, etc. Here we address the nature of the bond between water molecules and metal surfaces through a careful systematic study. Specifically, the bonding of isolated water molecules to a series of close-packed transition metal surfaces - Ru(0001), Rh(111), Pd(111) and Ag(111) - has been examined in detail with density functional theory (DFT). Aiming to understand the origin behind energetic and structural trends along the 4d series we employ a range of analysis tools, such as decomposition of the density of states, electron density differences, electronic reactivity function and inspection of individual Kohn-Sham orbitals. The results obtained allow us to rationalize the bonding between water and transition metal surfaces as a balance of covalent and electrostatic interactions. A frontier orbital scheme based on so-called two-center four-electron interactions between molecular orbitals of water and d band states of the surface proves incisive in understanding these systems.

  13. Interaction Of Water Molecules With SiC(001) Surfaces

    SciTech Connect

    Cicero, G; Catellani, A; Galli, G

    2004-08-10

    We have investigated the interaction of water molecules with the polar Si- and C- terminated surfaces of cubic Silicon Carbide by means of ab initio molecular dynamics simulations at finite temperature. Different water coverages were considered, from {1/4} to a complete monolayer. Irrespective of coverage, we find that water dissociates on the silicon terminated surfaces, leading to important changes in both its structural and electronic properties. On the contrary, the carbon terminated surface remains inert when exposed to water. We propose experiments to reveal the ionic and electronic structure of wet Si-terminated surfaces predicted by our calculations, which at full coverage are notably different from those of hydrated Si(001) substrates. Finally, we discuss the implications of our results for SiC surface functionalization.

  14. Primary production of coral ecosystems in the Vietnamese coastal and adjacent marine waters

    NASA Astrophysics Data System (ADS)

    Tac-An, Nguyen; Minh-Thu, Phan; Cherbadji, I. I.; Propp, M. V.; Odintsov, V. S.; Propp, L. H.

    2013-11-01

    Coral reef ecosystems in coastal waters and islands of Vietnam have high primary production. Average gross primary production (GPP) in coral reef waters was 0.39 g C m-2 day-1. GPP of corals ranged from 3.12 to 4.37 g C m-2 day-1. GPP of benthic microalgae in coral reefs ranged from 2 to 10 g C m-2 day-1. GPP of macro-algae was 2.34 g C m-2 day-1. Therefore, the total of GPP of whole coral reef ecosystems could reach 7.85 to 17.10 g C m-2 day-1. Almost all values of the ratio of photosynthesis to respiration in the water bodies are higher than 1, which means these regions are autotrophic systems. Wire variation of GPP in coral reefs was contributed by species abundance of coral and organisms, nutrient supports and environmental characteristics of coral ecosystems. Coral reefs play an important ecological role of biogeochemical cycling of nutrients in waters around the reefs. These results contribute valuable information for the protection, conservation and sustainable exploitation of the natural resources in coral reef ecosystems in Vietnam.

  15. 33 CFR 110.168 - Hampton Roads, Virginia and adjacent waters (Datum: NAD 83).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... explosives, as defined in 49 CFR 173.50. Dangerous cargo means “certain dangerous cargo” as defined in § 160... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Hampton Roads, Virginia and..., DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.168 Hampton...

  16. Ground-water data in Orange County and adjacent counties, Texas, 1985-90

    USGS Publications Warehouse

    Kasmarek, Mark C.

    1999-01-01

    The lower unit of the Chicot aquifer is a major source of freshwater for Orange County, Texas. In 1989, the average rate of ground-water withdrawal from the lower unit of the Chicot aquifer in Orange County for municipal and industrial use was 13.8 million gallons per day, a substantial decrease from the historical high of 23.1 million gallons per day in 1972. The average withdrawal for industrial use decreased substantially from 14.4 million gallons per day during 1963?84 to 6.9 million gallons per day during 1985?89. The average withdrawal for municipal use during 1985?89 was 6.8 million gallons per day, similar to the average withdrawal of 5.8 million gallons per day during 1963?84. Water levels in wells in most of the study area rose during 1985?90. The largest rise in water levels was more than 10 feet in parts of Orange and Pinehurst, north of site B (one of three areas of ground-water withdrawal for industrial use), while the largest decline in water levels was a localized decline of more than 60 feet at site C in south-central Orange County (also an area of withdrawal for industrial use). Chemical analyses of ground-water samples from the lower Chicot aquifer during 1985?90 indicate that the aquifer contained mostly freshwater (dissolved solids concentrations less than 1,000 milligrams per liter). Dissolved chloride concentrations remained relatively constant in most wells during 1985?90 but could vary greatly between wells within short distances. Saline-water encroachment continued to occur during 1985?89 but at a slower rate than in the 1970s and early 1980s. On the basis of chemical data collected during 1985?89, a relation was determined between specific conductance and dissolved chloride concentration that can be used to estimate dissolved chloride by multiplying the specific conductance by different factors for low or high conductances.

  17. Hydrogeochemistry and stable isotopes of ground and surface waters from two adjacent closed basins, Atacama Desert, northern Chile

    USGS Publications Warehouse

    Alpers, C.N.; Whittemore, D.O.

    1990-01-01

    The geochemistry and stable isotopes of groundwaters, surface waters, and precipitation indicate different sources of some dissolved constituents, but a common source of recharge and other constituents in two adjacent closed basins in the Atacama Desert region of northern Chile (24??15???-24??45???S). Waters from artesian wells, trenches, and ephemeral streams in the Punta Negra Basin are characterized by concentrations of Na>Ca>Mg and Cl ???SO4, with TDS Mg ??? Ca and SO4 > Cl, with TDS also Mg ??? Ca and SO4 > Cl, but with TDS up to 40 g/l. The deep mine waters have pH between 3.2 and 3.9, and are high in dissolved CO2 (??13 C = -4.8%PDB), indicating probable interaction with oxidizing sulfides. The deep mine waters have ??18O values of ???-1.8%.compared with values < -3.5??? for other Hamburgo Basin waters; thus the mine waters may represent a mixture of meteoric waters with deeper "metamorphic" waters, which had interacted with rocks and exchanged oxygen isotopes at elevated temperatures. Alternatively, the deep mine waters may represent fossil meteoric waters which evolved isotopically along an evaporative trend starting from values quite depleted in ??18O and ??Dd relative to either precipitation or shallow groundwaters. High I/Br ratios in the Hamburgo Basin waters and La Escondida mine waters are consistent with regionally high I in surficial deposits in the Atacama Desert region and may represent dissolution of a wind-blown evaporite component. Rain and snow collected during June 1984, indicate systematic ??18O and ??D fractionation with increasing elevation between 3150 and 4180 m a.s.l. (-0.21??.??18O and -1.7??.??D per 100 m). Excluding the deep mine waters from La Escondida, the waters from the Hamburgo and Punta Negra Basins have similar ??D and ??18O values and together show a distinct evaporative trend (??D = 5.0 ??18O - 20.2). Snowmelt from the central Andes Cordillera to the east is the most likely source of recharge to both basins. Some of the

  18. Interannual to Decadal Variability of Atlantic Water in the Nordic and Adjacent Seas

    NASA Technical Reports Server (NTRS)

    Carton, James A.; Chepurin, Gennady A.; Reagan, James; Haekkinen, Sirpa

    2011-01-01

    Warm salty Atlantic Water is the main source water for the Arctic Ocean and thus plays an important role in the mass and heat budget of the Arctic. This study explores interannual to decadal variability of Atlantic Water properties in the Nordic Seas area where Atlantic Water enters the Arctic, based on a reexamination of the historical hydrographic record for the years 1950-2009, obtained by combining multiple data sets. The analysis shows a succession of four multi-year warm events where temperature anomalies at 100m depth exceed 0.4oC, and three cold events. Three of the four warm events lasted 3-4 years, while the fourth began in 1999 and persists at least through 2009. This most recent warm event is anomalous in other ways as well, being the strongest, having the broadest geographic extent, being surface-intensified, and occurring under exceptional meteorological conditions. Three of the four warm events were accompanied by elevated salinities consistent with enhanced ocean transport into the Nordic Seas, with the exception of the event spanning July 1989-July 1993. Of the three cold events, two lasted for four years, while the third lasted for nearly 14 years. Two of the three cold events are associated with reduced salinities, but the cold event of the 1960s had elevated salinities. The relationship of these events to meteorological conditions is examined. The results show that local surface heat flux variations act in some cases to reinforce the anomalies, but are too weak to be the sole cause.

  19. Anomalous water molecules and mechanistic effects of water nanotube clusters confined to molecular porous crystals.

    PubMed

    Tadokoro, Makoto; Ohhara, Takashi; Ohhata, Yuhki; Suda, Takaaki; Miyasato, Yuji; Yamada, Takeshi; Kikuchi, Tatsuya; Tanaka, Ichiro; Kurihara, Kazuo; Oguni, Masaharu; Nakasuji, Kazuhiro; Yamamuro, Osamu; Ryota, Kuroki

    2010-02-18

    The movement of water molecules in the limited space present within nanoscale regions, which is different from the molecular motion of bulk water, is significantly affected by strong interfacial interactions with the surrounding outer walls. Hence, most of the water molecules that are confined to nanochannel spaces having widths less than ca. 2 nm can generally be classified together as "structural water". Since the motions of such water molecules are limited by interfacial interactions with the outer wall, the nature of structural water, which is strongly influenced by the interactions, will have different characteristics from normal water. For our investigations on the characteristics of structural water, we have developed a nanoporous crystal with a diameter of ca. 1.6 nm; it was constructed from 1-D hydrophilic channels by self-organization of the designed molecules. A tubelike three-layered water cluster, called a water nanotube (WNT), is formed in each internal channel space and is regulated by H-bonds with the outer wall. The WNT undergoes a glass transition (T(g) = 107 K) and behaves as a liquid; it freezes at 234 K and changes into an icelike nanotube cluster. In this study, the structure of the WNT is investigated through neutron structure analysis, and it is observed to stabilize by a mechanistic anchor effect of structural water. Furthermore, from neutron-scattering experiments, it is seen that a few water molecules around the center of the WNT move approximately with the same diffusion constant as those in bulk water; however, the residence time and average jump length are longer, despite the restrictions imposed by the H-bonding with structural water. The behavior of mobile water within a WNT is investigated; this can be used to elucidate the mechanism for the effect of structural water on vital functions on the cell surface. PMID:20102158

  20. The spontaneous synchronized dance of pairs of water molecules

    SciTech Connect

    Roncaratti, Luiz F.; Cappelletti, David Pirani, Fernando

    2014-03-28

    Molecular beam scattering experiments have been performed to study the effect of long-range anisotropic forces on the collision dynamics of two small polar molecules. The main focus of this paper is on water, but also ammonia and hydrogen sulphide molecules have been investigated, and some results will be anticipated. The intermolecular distances mainly probed are of the order of 1 nm and therefore much larger than the molecular dimensions. In particular, we have found that the natural electric field gradient, generated by different spatial orientations of the permanent electric dipoles, is able to promote the transformation of free rotations into coupled pendular states, letting the molecular partners involved in the collision complex swinging to and fro around the field direction. This long-ranged concerted motion manifested itself as large increases of the magnitude of the total integral cross section. The experimental findings and the theoretical treatment developed to shed light on the details of the process suggest that the transformation from free rotations to pendular states depends on the rotational level of both molecules, on the impact parameter, on the relative collision velocity, on the dipole moment product and occurs in the time scale of picoseconds. The consequences of this intriguing phenomenon may be important for the interpretation and, in perspective, for the control of elementary chemical and biological processes, given by polar molecules, ions, and free radicals, occurring in several environments under various conditions.

  1. Sticking of Molecules on Nonporous Amorphous Water Ice

    NASA Astrophysics Data System (ADS)

    He, Jiao; Acharyya, Kinsuk; Vidali, Gianfranco

    2016-05-01

    Accurate modeling of physical and chemical processes in the interstellar medium (ISM) requires detailed knowledge of how atoms and molecules adsorb on dust grains. However, the sticking coefficient, a number between 0 and 1 that measures the first step in the interaction of a particle with a surface, is usually assumed in simulations of ISM environments to be either 0.5 or 1. Here we report on the determination of the sticking coefficient of H2, D2, N2, O2, CO, CH4, and CO2 on nonporous amorphous solid water. The sticking coefficient was measured over a wide range of surface temperatures using a highly collimated molecular beam. We showed that the standard way of measuring the sticking coefficient—the King–Wells method—leads to the underestimation of trapping events in which there is incomplete energy accommodation of the molecule on the surface. Surface scattering experiments with the use of a pulsed molecular beam are used instead to measure the sticking coefficient. Based on the values of the measured sticking coefficient, we suggest a useful general formula of the sticking coefficient as a function of grain temperature and molecule-surface binding energy. We use this formula in a simulation of ISM gas–grain chemistry to find the effect of sticking on the abundance of key molecules both on grains and in the gas phase.

  2. Spatial and seasonal patterns of ichthyoplankton assemblages in the Haizhou Bay and its adjacent waters of China

    NASA Astrophysics Data System (ADS)

    Li, Zengguang; Ye, Zhenjiang; Wan, Rong

    2015-12-01

    Surveys were conducted in five voyages in Haizhou Bay and its adjacent coastal area from March to December 2011 during full moon spring tides. The ichthyoplankton assemblages and the environmental factors that affect their spatial and seasonal patterns were determined. Totally 35 and 12 fish egg and larvae taxa were identified, respectively. Over the past several decades, the egg and larval species composition has significantly changed in Haizhou Bay and its adjacent waters, most likely corresponding with the alteration of fishery resources, which are strongly affected by anthropogenic activities and climate change. The Bray-Curtis dissimilarity index identified four assemblages: near-shore bay assemblage, middle bay assemblage and two closely related assemblages (near-shore/middle bay assemblage and middle/edge of bay assemblage). The primary species of each assemblage principally reflected the spawning strategies of adult fish. The near-shore bay assemblage generally occurred in near-shore bay, with depths measuring <20 m, and the middle bay assemblage generally occurred in the middle of bay, with depths measuring 20 to 40 m. Spatial and seasonal variations in ichthyoplankton in each assemblage were determined by interactions between biological behavioral traits and oceanographic features, particularly the variation of local conditions within the constraint of a general reproductive strategy. The results of Spearman's rank correlation analysis indicated that both fish egg and larval abundance were positively correlated with depth, which is critical to the oceanographic features in Haizhou Bay.

  3. Larval distribution pattern of Muraenesox cinereus (Anguilliformes: Muraenesocidae) leptocephali in waters adjacent to Korea

    NASA Astrophysics Data System (ADS)

    Ji, Hwan-Sung; Kim, Jin-Koo; Oh, Taeg Yun; Choi, Kwang Ho; Choi, Jung Hwa; Seo, Young Il; Lee, Dong Woo

    2015-09-01

    To understand the transport and recruitment processes of the daggertooth pike conger, Muraenesox cinereus, in the marginal seas of East Asia, we investigated the distribution pattern, estimated spawning areas and periods, and recruitment mechanisms of M. cinereus, based on 51 individuals of leptocephali collected from Korean waters during 2010-2014. Back-calculated hatching dates, determined from the daily incremental growth rates of the otoliths, indicated that the spawning period for M. cinereus was during July-September. The size range of M. cinereus leptocephali collected offshore of Jeju Island and southeast of the Korea-Japan intermediate zone was 16.6-20.9 mm TL (age, 18-23 d). We hypothesize that one of the spawning grounds of M. cinereus is located offshore in the East China Sea. In Korean waters, the ages and body lengths of M. cinereus leptocephali increased northward from latitude 31°30'N to 34°40'N, with metamorphosis occurring at latitude 34°40'N. Therefore, we surmised that the hatched preleptocephali of M. cinereus were transported from offshore areas in the East China Sea to Jeju Island and the Korea Strait (KS) by the Kuroshio and Tsushima Warm Current.

  4. Assessment of the fresh-and brackish-water resources underlying Dunedin and adjacent areas on northern Pinellas County, Florida

    USGS Publications Warehouse

    Knochenmus, L.A.; Swenson, E.S.

    1996-01-01

    The city of Dunedin is enhancing their potable ground-water resources through desalination of brackish ground water. An assessment of the fresh- and brackish-water resources in the Upper Floridan aquifer was needed to estimate the changes that may result from brackish-water development. The complex hydrogeologic framework underlying Dunedin and adjacent areas of northern Pinellas County is conceptualized as a multilayered sequence of permeable zones and confining and semiconfining units. The permeable zones contain vertically spaced, discrete, water-producing zones with differing water quality. Water levels, water-level responses, and water quality are highly variable among the different permeable zones. The Upper Floridan aquifer is best characterized as a local flow system in most of northern Pinellas County. Pumping from the Dunedin well field is probably not influencing water levels in the aquifer outside Dunedin, but has resulted in localized depressions in the potentiometric surface surrounding production-well clusters. The complex geologic layering combined with the effects of production-well distribution probably contribute to the spatial and temporal variability in chloride concentrations in the Dunedin well field. Chloride concentrations in ground water underlying the Dunedin well field vary both vertically and laterally. In general, water-quality rapidly changes below depths of 400 feet below sea level. Additionally, randomly distributed water-producing zones with higher chloride concentrations may occur at shallow, discrete intervals above 400 feet. A relation between chloride concentration and distance from St. Joseph Sound is not apparent; however, a possible relation exists between chloride concentration and production-well density. Chloride-concentration data from production wells show a consistently increasing pattern that has accelerated since the late 1980's. Chloride-concentration data from 15 observation wells show increasing trends for 6 wells

  5. Scanning electron microscopic investigations of fresh mortars: Well-defined water-filled layers adjacent to sand grains

    SciTech Connect

    Diamond, S. Kjellsen, K.O.

    2008-04-15

    SEM examinations are reported of freshly-mixed and early age mortar specimens prepared by fast freezing in liquid nitrogen followed by epoxy impregnation, and of companion specimens of early aged mortars prepared conventionally. Freshly-mixed mortars reveal complex features that appear to influence subsequent development of the hardened state microstructure. In particular, layers of entirely water-filled space a few micrometers thick are found adjacent to many of the sand grain surfaces. After a few hours sparse deposits of calcium hydroxide crystals (and later C-S-H) are found within these layers, but the layers persist as recognizable features for at least 12 h. The layers are identically recognizable in both fast-frozen and conventionally-prepared specimens. Another feature found in freshly-mixed mortars is the existence of patchy local areas of sparsely-packed and other areas of densely-packed cement particles.

  6. Hydrology of the coastal springs ground-water basin and adjacent parts of Pasco, Hernando, and Citrus Counties, Florida

    USGS Publications Warehouse

    Knochenmus, Lari A.; Yobbi, Dann K.

    2001-01-01

    The coastal springs in Pasco, Hernando, and Citrus Counties, Florida consist of three first-order magnitude springs and numerous smaller springs, which are points of substantial ground-water discharge from the Upper Floridan aquifer. Spring flow is proportional to the water-level altitude in the aquifer and is affected primarily by the magnitude and timing of rainfall. Ground-water levels in 206 Upper Floridan aquifer wells, and surface-water stage, flow, and specific conductance of water from springs at 10 gaging stations were measured to define the hydrologic variability (temporally and spatially) in the Coastal Springs Ground-Water Basin and adjacent parts of Pasco, Hernando, and Citrus Counties. Rainfall at 46 stations and ground-water withdrawals for three counties, were used to calculate water budgets, to evaluate long-term changes in hydrologic conditions, and to evaluate relations among the hydrologic components. Predictive equations to estimate daily spring flow were developed for eight gaging stations using regression techniques. Regression techniques included ordinary least squares and multiple linear regression techniques. The predictive equations indicate that ground-water levels in the Upper Floridan aquifer are directly related to spring flow. At tidally affected gaging stations, spring flow is inversely related to spring-pool altitude. The springs have similar seasonal flow patterns throughout the area. Water-budget analysis provided insight into the relative importance of the hydrologic components expected to influence spring flow. Four water budgets were constructed for small ground-water basins that form the Coastal Springs Ground-Water Basin. Rainfall averaged 55 inches per year and was the only source of inflow to the Basin. The pathways for outflow were evapotranspiration (34 inches per year), runoff by spring flow (8 inches per year), ground-water outflow from upward leakage (11 inches per year), and ground-water withdrawal (2 inches per year

  7. High-harmonic generation in aligned water molecules

    NASA Astrophysics Data System (ADS)

    Wang, Song; Devin, Julien; Hoffmann, Matthias; Cryan, James; Kaldun, Andreas; Bucksbaum, Philip

    2016-05-01

    In recent years, the use of high harmonic generation (HHG) in aligned molecular vapors has become a powerful tool to study ultrafast dynamics of electronic and nuclear wave packets. In our new experimental setup, we are able to orient H2 O and D2 O molecules using a single cycle terahertz (THz) pulse. Aligning water is especially interesting as the highest occupied molecular orbital (HOMO) of water contains a node in the xz plane of the molecular frame, allowing us to perform HHG from second highest occupied molecular orbital (HOMO-1) only, by setting the polarization of the fundamental laser along the z-axis of the aligned water molecules. We are particularly interested in the HOMO-1 state, as there is fast motion of the H-O-H angle leading to sub-wavelength dynamics. On this poster we present our all-optical alignment setup where HHG and single-cycle THz generation take place in high-vacuum, where measurements with arbitrary polarization angles between the two are possible. In addition, we discuss the effects of the molecular orientation on HHG, including symmetry breaking that could produce even harmonics and isotope effects between H2 O and D2 O due to different vibrational energies. This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division.

  8. Single ionization of water molecules in collisions with bare ions

    NASA Astrophysics Data System (ADS)

    Mondal, A.; Mandal, C. R.; Purkait, M.

    2016-04-01

    We present the double differential cross sections (DDCSs) for the direct ionization of water molecules by impact of fully stripped helium, carbon and oxygen atoms, respectively. In the present formalism, we have represented the wavefunction in the entrance channel as the product of a plane wave for the projectile and an accurate one-center-molecular wavefunction of the water molecule by Moccia (1964 J. Chem. Phys. 40 2186). In the exit channel, we have expressed the total wavefunction as the product of pair-wise Coulomb wavefunctions among the ejected electron, projectile ion and the residual target ion, respectively. The contributions of DDCSs for five different molecular orbitals of water to the spectrum of angular distributions have been analyzed for several electron emission energies. The present results for DDCSs are compared with existing experimental and theoretical findings. We find an overall good agreement between our calculated results and the experimental findings for electron emission cross sections. In addition, DDCS results for ionization from different orbitals at a few electron emission energies are given in tabular form.

  9. Electric Dipole Moments of Nanosolvated Acid Molecules in Water Clusters

    NASA Astrophysics Data System (ADS)

    Guggemos, Nicholas; Slavíček, Petr; Kresin, Vitaly V.

    2015-01-01

    The electric dipole moments of (H2O)nDCl (n =3 - 9 ) clusters have been measured by the beam-deflection method. Reflecting the (dynamical) charge distribution within the system, the dipole moment contributes information about the microscopic structure of nanoscale solvation. The addition of a DCl molecule to a water cluster results in a strongly enhanced susceptibility. There is evidence for a noticeable rise in the dipole moment occurring at n ≈5 - 6 . This size is consistent with predictions for the onset of ionic dissociation. Additionally, a molecular-dynamics model suggests that even with a nominally bound impurity an enhanced dipole moment can arise due to the thermal and zero-point motion of the proton and the water molecules. The experimental measurements and the calculations draw attention to the importance of fluctuations in defining the polarity of water-based nanoclusters and generally to the essential role played by motional effects in determining the response of fluxional nanoscale systems under realistic conditions.

  10. Comparison of fish communities in a clean-water stream and an adjacent polluted stream

    SciTech Connect

    Reash, R.J.; Berra, T.M. )

    1987-10-01

    Fish populations were studied in two parallel tributaries of the Mohican River, Ohio: Clear Fork, relatively undisturbed; and Rocky Fork, which receives industrial discharges and sewage effluent. Water quality in Rocky Fork was significantly worse than the control stream with respect to heavy metals (Cr, Cu, Fe, Ni, and Zn) and ammonia concentrations. Fish species richness and diversity increased downstream in Clear Fork but decreased downstream in Rocky Fork. Pollution-intolerant species were present in the headwaters of Rocky Fork and at all sites of Clear Fork. Fish community similarity of fish communities between corresponding headwater sites was significantly greater than similarity of corresponding downstream reaches, using polluted and unpolluted sites for comparison. Both headwater sites were dominated numerically by generalized invertebrate-feeding fish. At downstream sites in Clear Fork benthic insectivores became dominant in Rocky Fork, generalized invertebrate-feeding fish were present. Fish communities at polluted sites had comparatively lower variability of both trophic structure rank and relative abundance. The smaller populations of fish in these sites were dominated by a few pollution-tolerant species.

  11. Nocturnal water loss in mature subalpine Eucalyptus delegatensis tall open forests and adjacent E. pauciflora woodlands

    PubMed Central

    Buckley, Thomas N; Turnbull, Tarryn L; Pfautsch, Sebastian; Adams, Mark A

    2011-01-01

    We measured sap flux (S) and environmental variables in four monospecific stands of alpine ash (Eucalyptus delegatensis R. Baker, AA) and snowgum (E. pauciflora Sieb. ex Spreng., SG) in Australia's Victorian Alps. Nocturnal S was 11.8 ± 0.8% of diel totals. We separated transpiration (E) and refilling components of S using a novel modeling approach based on refilling time constants. The nocturnal fraction of diel water loss (fn) averaged 8.6 ± 0.6% for AA and 9.8 ± 1.7% for SG; fn differed among sites but not species. Evaporative demand (D) was the strongest driver of nocturnal E (En). The ratio En/D (Gn) was positively correlated to soil moisture in most cases, whereas correlations between wind speed and Gn varied widely in sign and strength. Our results suggest (1) the large, mature trees at our subalpine sites have greater fn than the few Australian native tree species that have been studied at lower elevations, (2) AA and SG exhibit similar fn despite very different size and life history, and (3) fn may differ substantially among sites, so future work should be replicated across differing sites. Our novel approach to quantifying fn can be applied to S measurements obtained by any method. PMID:22393512

  12. Dynamic factor modeling of ground and surface water levels in an agricultural area adjacent to Everglades National Park

    NASA Astrophysics Data System (ADS)

    Ritter, A.; Muñoz-Carpena, R.

    2006-02-01

    The extensive eastern boundary of Everglades National Park (ENP) in south Florida (USA) is subject to one the most expensive and ambitious environmental restoration projects in history. Understanding and predicting the interaction between the shallow aquifer and surface water is a key component for fine-tuning the process. The Frog Pond is an intensively instrumented agricultural 2023 ha area adjacent to ENP. The interactions among 21 multivariate daily time series (ground and surface water elevations, rainfall and evapotranspiration) available from this area were studied by means of dynamic factor analysis, a novel technique in the field of hydrology. This method is designed to determine latent or background effects governing variability or fluctuations in non-stationary time series. Water levels in 16 wells and two drainage ditch locations inside the area were selected as response variables, and canal levels and net recharge as explanatory variables. Elevations in the two canals delimiting the Frog Pond area were found to be the main factors explaining the response variables. This influence of canal elevations on water levels inside the area was complementary and inversely related to the distance between the observation point and each canal. Rainfall events do not affect daily water levels significantly but are responsible for instantaneous or localized groundwater responses that in some cases can be directly associated with the risk of flooding. This close coupling between surface and groundwater levels, that corroborates that found by other authors using different methods, could hinder on-going environmental restoration efforts in the area by bypassing the function of wetlands and other surface features. An empirical model with a reduced set of parameters was successfully developed and validated in the area by interpolating the results from the dynamic factor analysis across the spatial domain (coefficient of efficiency across the domain: 0.66-0.99). Although

  13. Ionization of water molecules by fast charged projectiles

    SciTech Connect

    Dubois, A.; Carniato, S.; Fainstein, P. D.; Hansen, J. P.

    2011-07-15

    Single-ionization cross sections of water molecules colliding with fast protons are calculated from lowest-order perturbation theory by taking all electrons and molecular orientations consistently into account. Explicit analytical formulas based on the peaking approximation are obtained for differential ionization cross sections with the partial contribution from the various electron orbitals accounted for. The results, which are in very good agreement with total and partial cross sections at high electron and projectile energies, display a strong variation on molecular orientation and molecular orbitals.

  14. Analysis and simulation of ground-water flow in Lake Wales Ridge and adjacent areas of central Florida

    USGS Publications Warehouse

    Yobbi, Dann K.

    1996-01-01

    The Lake Wales Ridge is an uplands recharge area in central Florida that contains many sinkhole lakes. Below-normal rainfall and increased pumping of ground water have resulted in declines both in ground-water levels and in the water levels of many of the ridge lakes. A digital flow model was developed for a 3,526 square-mile area to help understand the current (1990) ground-water flow system and its response to future ground-water withdrawals. The ground-water flow system in the Lake Wales Ridge and adjacent area of central Florida consists of a sequence of sedimentary aquifers and confining units. The uppermost water-bearing unit of the study area is the surficial aquifer. This aquifer is generally unconfined and is composed primarily of clastic deposits. The surficial aquifer is underlain by the confined intermediate aquifer and confining units which consists of up to three water-bearing units composed of interbedded clastics and carbonate rocks. The lowermost unit of the ground- water flow system, the confined Upper Floridan aquifer, consists of a thick, hydraulically connected sequence of carbonate rocks. The Upper Floridan aquifer is about 1,200 to 1,400 feet thick and is the primary source for ground-water withdrawals in the study area. The generalized ground-water flow system of the Lake Wales Ridge is that water moves downward from the surficial aquifer to the intermediate aquifer and the Upper Floridan aquifer in the central area, primarily under the ridges, with minor amounts of water flow under the flatlands. The water flows laterally away fromn the central area, downgradient to discharge areas to the west, east, and south, and locally along valleys of major streams. Upward leakage occurs along valleys of major streams. The model was initially calibrated to the steady-state conditions representing September 1989. The resulting calibrated hydrologic parameters were then tested by simulating transient conditions for the period October 1989 through 1990. A

  15. Geochemistry of waters from springs, wells, and snowpack on and adjacent to Medicine Lake volcano, northern California

    USGS Publications Warehouse

    Mariner, R.H.; Lowenstern, Jacob B.

    1999-01-01

    Chemical analyses of waters from cold springs and wells of the Medicine Lake volcano and surrounding region indicate small chloride anomalies that may be due to water-rock interaction or limited mixing with high-temperature geothermal fluids. The Fall River Springs (FRS) with a combined discharge of approximately 37 m3/s, show a negative correlation between chloride (Cl) and temperature, implying that the Cl is not derived from a high-temperature geothermal fluid. The high discharge from the FRS indicates recharge over a large geographic region. Chemical and isotopic variations in the FRS show that they contain a mixture of three distinct waters. The isotopic composition of recharge on and adjacent to the volcano are estimated from the isotopic composition of snow and precipitation amounts adjusted for evapotranspiration. Enough recharge of the required isotopic composition (-100 parts per thousand ??D) is available from a combination of the Medicine Lake caldera, the Fall River basin and the Long Bell basin to support the slightly warmer components of the FRS (32 m3/s). The cold-dilute part of the FRS (approximately 5 m3/s) may recharge in the Bear Creek basin or at lower elevations in the Fall River basin.

  16. 33 CFR 334.730 - Waters of Santa Rosa Sound and Gulf of Mexico adjacent to Santa Rosa Island, Armament Center...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... CFR part 329, including the waters of Santa Rosa Sound and Gulf of Mexico within a circle one nautical... defined at 33 CFR part 329, including the waters of Santa Rosa Sound and Gulf of Mexico, surrounding the... Gulf of Mexico adjacent to Santa Rosa Island, Armament Center, Eglin Air Force Base, Fla.......

  17. 33 CFR 334.730 - Waters of Santa Rosa Sound and Gulf of Mexico adjacent to Santa Rosa Island, Armament Center...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... CFR part 329, including the waters of Santa Rosa Sound and Gulf of Mexico within a circle one nautical... defined at 33 CFR part 329, including the waters of Santa Rosa Sound and Gulf of Mexico, surrounding the... Gulf of Mexico adjacent to Santa Rosa Island, Armament Center, Eglin Air Force Base, Fla.......

  18. 33 CFR 334.730 - Waters of Santa Rosa Sound and Gulf of Mexico adjacent to Santa Rosa Island, Armament Center...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... CFR part 329, including the waters of Santa Rosa Sound and Gulf of Mexico within a circle one nautical... defined at 33 CFR part 329, including the waters of Santa Rosa Sound and Gulf of Mexico, surrounding the... Gulf of Mexico adjacent to Santa Rosa Island, Armament Center, Eglin Air Force Base, Fla.......

  19. Geomorphic data collected within and adjacent to Nebraska Public Power District's Cottonwood Ranch Property, Platte River, Nebraska, Water Year 2001

    USGS Publications Warehouse

    Kinzel, Paul; Parker, Randolph; Nelson, Johnathan; Burman, R.; Heckman, Aashley

    2003-01-01

    River-channel topographic surveys were conducted and bed-material samples were collected along transects across the Platte River during water year 2001 (October 1, 2000 to September 30, 2001). A total of 57 transect lines or cross sections were established within three study reaches located along the middle channel of the Platte River in a 2,650-acre parcel of land owned by the Nebraska Public Power District (NPPD), hereinafter referred to as the Cottonwood Ranch Property. Five additional cross sections were established downstream of the Cottonwood Ranch Property across the entire width of the Platte River as a component of a proposed future general monitoring program. A development and enhancement plan is proposed by NPPD on the Cottonwood Ranch Property to satisfy their Federal Energy Regulatory Commission (FERC) relicensing guidelines. The goal of the plan is to improve habitat along this reach for endangered species. The United States Geological Survey (USGS) designed a monitoring and research program to study and detect what effects, if any, these channel management actions have on channel morphology and sediment transport within and adjacent to the Cottonwood Ranch Property. This report presents the data-collection methods and summarizes the geomorphic data collected in support of the monitoring program for water year 2001.

  20. Temporal and spatial distribution of red tide outbreaks in the Yangtze River Estuary and adjacent waters, China.

    PubMed

    Liu, Lusan; Zhou, Juan; Zheng, Binghui; Cai, Wenqian; Lin, Kuixuan; Tang, Jingliang

    2013-07-15

    Between 1972 and 2009, evidence of red tide outbreaks in the Yangtze River Estuary and adjacent waters was collected. A geographic information system (GIS) was used to analyze the temporal and spatial distribution of these red tides, and it was subsequently used to map the distribution of these events. The results show that the following findings. (1) There were three red tide-prone areas: outside the Yangtze River Estuary and the eastern coast of Sheshan, the Huaniaoshan-Shengshan-Gouqi waters, and the Zhoushan areas and eastern coast of Zhujiajian. In these areas, red tides occurred 174 total times, 25 of which were larger than 1000 km(2) in areal extent. After 2000, the frequency of red tide outbreaks increased significantly. (2) During the months of May and June, the red tide occurrence in these areas was 51% and 20%, respectively. (3) Outbreaks of the dominant red tide plankton species Prorocentrum dong-haiense, Skeletonema costatum, Prorocentrum dantatum, and Noctiluca scientillan occurred 38, 35, 15, and 10 times, respectively, during the study interval. PMID:23628547

  1. Water-molecule dissociation by proton and hydrogen impact

    NASA Astrophysics Data System (ADS)

    Luna, H.; de Barros, A. L. F.; Wyer, J. A.; Scully, S. W. J.; Lecointre, J.; Garcia, P. M. Y.; Sigaud, G. M.; Santos, A. C. F.; Senthil, V.; Shah, M. B.; Latimer, C. J.; Montenegro, E. C.

    2007-04-01

    Time-of-flight-based mass analysis of charged water fragments have been used to measure the dissociative and the nondissociative reaction pathways of water formed during collisions with 15to100keV and 500to3500keV H+ projectiles and with 8to100keV H0 projectiles. The fragmentation pathways resulting from the ionization and the electron capture collisions with the incident H+ and H0 projectiles, as well as collisions involving projectile electron loss by the incident H0 projectiles, were separately recorded by detecting the target product ions in coincidence with either the ejected target electrons or the charge-analyzed projectiles. The fragmentation profile shows that at high collision energies the ionization of water arises mainly through outer shell processes. At lower energies valence electron capture and ionization dominate and transfer ionization leads to substantially different fragmentation patterns. H0 and H+ projectiles are found to be equally efficient at ionizing the water molecule. These results are of particular interest to workers in astrophysics and those involved in cancer therapy with heavy particle ion beams.

  2. Ion condensation behavior and dynamics of water molecules surrounding the sodium poly(methacrylic acid) chain in water: a molecular dynamics study.

    PubMed

    Chung, Yung-Ting; Huang, Ching-I

    2012-03-28

    All-atom molecular dynamics simulations are used to study the condensation behavior of monovalent (Na(+)) and multivalent (Ca(2+)) salt counterions associated with the co-ions (Cl(-)) surrounding the charged poly(methacrylic acid) (PMAA) chain in water. The study is extended to the influences on chain conformation, local arrangement, and dynamics of water in the highly diluted aqueous solutions. We find that even when the salt ions are monovalent, they attract more than one charged monomer and act as a bridging agent within the chain, as the multivalent salt ions. In principle, the salt ions bridge between not only the "non-adjacent" but also the "adjacent" charged monomers, leading to a more coil-like and a locally stretched conformation, respectively. With an increase in the salt concentration, the amount of coiled-type condensed ions increase and reach a maximum when the chain conformation becomes the most collapsed; whereas, the stretched-type shows an opposite trend. Our results show that the attractive interactions through the condensed salt ions between the non-adjacent monomers are responsible for the conformational collapse. When the salt concentration increases high enough, a significant increase for the stretched-type condensed ions makes an expansion effect on the chain. These stretched-type salt ions, followed by the adsorption of the co-ions and water molecules, tend to form a multilayer organization outside surrounding the PMAA chain. Thus, the expansion degree of the chain conformation is greatly limited. When only the monovalent Na(+) ions are present in the solutions, water molecules are primarily adsorbed into either the condensed Na(+) ions or the COO(-) groups. These adsorbed water molecules form hydrogen bonds with each other and enhance the local bridging behavior associated with the Na(+) condensation on the resultant chain conformation. With an increase in the amount of multivalent Ca(2+) salt ions, more water molecules are bonded directly

  3. Quantum Tunneling of Water in Beryl: A New State of the Water Molecule

    NASA Astrophysics Data System (ADS)

    Kolesnikov, Alexander I.; Reiter, George F.; Choudhury, Narayani; Prisk, Timothy R.; Mamontov, Eugene; Podlesnyak, Andrey; Ehlers, George; Seel, Andrew G.; Wesolowski, David J.; Anovitz, Lawrence M.

    2016-04-01

    Using neutron scattering and ab initio simulations, we document the discovery of a new "quantum tunneling state" of the water molecule confined in 5 Å channels in the mineral beryl, characterized by extended proton and electron delocalization. We observed a number of peaks in the inelastic neutron scattering spectra that were uniquely assigned to water quantum tunneling. In addition, the water proton momentum distribution was measured with deep inelastic neutron scattering, which directly revealed coherent delocalization of the protons in the ground state.

  4. Shallow ground-water quality adjacent to burley tobacco fields in northeastern Tennessee and southwestern Virginia, spring 1997

    USGS Publications Warehouse

    Johnson, G.C.; Connell, J.F.

    2001-01-01

    In 1994, the U.S. Geological Survey began an assessment of the upper Tennessee River Basin as part of the National Water-Quality Assessment (NAWQA) Program. A ground-water land-use study conducted in 1996 focused on areas with burley tobacco production in northeastern Tennessee and southwestern Virginia. Land-use studies are designed to focus on specific land uses and to examine natural and human factors that affect the quality of shallow ground water underlying specific types of land use. Thirty wells were drilled in shallow regolith adjacent to and downgradient of tobacco fields in the Valley and Ridge Physiographic Province of the upper Tennessee River Basin. Ground-water samples were collected between June 4 and July 9, 1997, to coincide with the application of the majority of pesticides and fertilizers used in tobacco production. Ground-water samples were analyzed for nutrients, major ions, 79 pesticides, 7 pesticide degradation products, 86 volatile organic compounds, and dissolved organic carbon. Nutrient concentrations were lower than the levels found in similar NAWQA studies across the United States during 1993-95. Five of 30 upper Tennessee River Basin wells (16.7 percent) had nitrate levels exceeding 10 mg/L while 19 percent of agricultural land-use wells nationally and 7.9 percent in the Southeast had nitrate concentrations exceeding 10 mg/L. Median nutrient concentrations were equal to or less than national median concentrations. All pesticide concentrations in the basin were less than established drinking water standards, and pesticides were detected less frequently than average for other NAWQA study units. Atrazine was detected at 8 of 30 (27 percent) of the wells, and deethylatrazine (an atrazine degradation product) was found in 9 (30 percent) of the wells. Metalaxyl was found in 17 percent of the wells, and prometon, flumetralin, dimethomorph, 2,4,5-T, 2,4-D, dichlorprop, and silvex were detected once each (3 percent). Volatile organic compounds

  5. Characterization of surface-water resources in the Great Basin National Park area and their susceptibility to ground-water withdrawals in adjacent valleys, White Pine County, Nevada

    USGS Publications Warehouse

    Elliott, Peggy E.; Beck, David A.; Prudic, David E.

    2006-01-01

    Eight drainage basins and one spring within the Great Basin National Park area were monitored continually from October 2002 to September 2004 to quantify stream discharge and assess the natural variability in flow. Mean annual discharge for the stream drainages ranged from 0 cubic feet per second at Decathon Canyon to 9.08 cubic feet per second at Baker Creek. Seasonal variability in streamflow generally was uniform throughout the network. Minimum and maximum mean monthly discharges occurred in February and June, respectively, at all but one of the perennial streamflow sites. Synoptic-discharge, specific-conductance, and water- and air-temperature measurements were collected during the spring, summer, and autumn of 2003 along selected reaches of Strawberry, Shingle, Lehman, Baker, and Snake Creeks, and Big Wash to determine areas where surface-water resources would be susceptible to ground-water withdrawals in adjacent valleys. Comparison of streamflow and water-property data to the geology along each stream indicated areas where surface-water resources likely or potentially would be susceptible to ground-water withdrawals. These areas consist of reaches where streams (1) are in contact with permeable rocks or sediments, or (2) receive water from either spring discharge or ground-water inflow.

  6. Assessment of water resources in lead-zinc mined areas in Cherokee County, Kansas, and adjacent areas

    SciTech Connect

    Spruill, T.B.

    1987-01-01

    A study was conducted to evaluate water resources problems related to abandoned lead and zinc mines in Cherokee County, Kansas, and adjacent areas in Missouri and Oklahoma. Past mining activities have caused changes in the geohydrology of the area. Discharge of mine-contaminated groundwater to Tar Creek occurs in Oklahoma from drill holes and shafts where the potentiometric surface of the shallow aquifer is above the land surface. Pumping of the deep aquifer has resulted in a potential for downward movement of water from the shallow aquifer. Water from mines in the eastern area contained dissolved solids concentrations of < 500 mg/L a median pH of 3.9, sulfate concentrations that ranged between 98 and 290 mg/L, and median concentrations for zinc of 37,600 micrograms/L (ug/L) for lead of 240 ug/L, for cadmium of 180 ug/L, for iron of 70 ug/L, for manganese of 240 ug/L, and for silica of 15 mg/L. Water from mines in the western area contained dissolved solids concentrations of generally > 500 mg/L, a median pH of 6.8, sulfate concentrations that ranged between 170 and 2,150 mg/L, and median concentrations for zinc of 3,200 ug/L for lead of 0 ug/L. No conclusive evidence of lateral migration of water from the mines into domestic well water supplies in the shallow aquifer was found in the study area in Kansas. Effects of abandoned lead and zinc mines on tributaries of the Spring River in the eastern area are most severe in Short Creek. Drainage from tailings cause large concentrations of sulfate, zinc, and cadmium in Tar Creek in Kansas. Compared with four other major streams in the western area in Kansas, Tar Creek contained the largest low flow concentrations of sulfate (910 mg/L), zinc (5,800 ug/L), and cadmium (40 ug/L). 45 refs., 23 figs., 26 tabs.

  7. Searching for Water and Other Molecules with JWST

    NASA Astrophysics Data System (ADS)

    Valenti, Jeff

    2015-08-01

    The James Webb Space Telescope (JWST) will be a powerful tool for measuring water and other molecules in transiting exoplanets, warm circumstellar disks, brown dwarfs, and cool stars. In early 2019 the observatory is scheduled to begin science operations near the Sun-Earth L2 Lagrange point. The sunshield will allow the telescope and science instrument module to cool passively to approximately 40 K. The segmented primary mirror has 25 square meters of collecting area, giving the observatory unprecedented sensitivity in the infrared. JWST has four science instruments that cover wavelengths from 0.6 to 28 microns at spectral resolutions up to about R=3000. I will summarize relevant observatory constraints, instrument capabilities, and observing templates. I will illustrate practical issues with examples from the Science Operations Design Reference Mission. Finally, I will discuss the Cycle 1 proposal process, which begins in 2017.

  8. Taxonomic review of Hadromerida (Porifera, Demospongiae) from British Columbia, Canada, and adjacent waters, with the description of nine new species.

    PubMed

    Austin, William C; Ott, Bruce S; Reiswig, Henry M; Romagosa, Paula; Mcdaniel, Neil G

    2014-01-01

    The history of sponge collecting and systematics in British Columbia is reviewed over the period 1878 to 1966. Recent additions and changes are provided in an on-line species list: www.mareco/org/kml/projects/NEsponges.asp. Hadromerids are the focus of this paper as eight of 19 species in British Columbia are considered new. An additional new species is described from southern California to clarify the status of Tethya californiana in BC. An update is timely for hadromerids in BC as there is new material and renewed interest, while existing descriptions are often inadequate. We describe new species and provide additions to previous descriptions for sponges of the order Hadromerida (Porifera: Demospongiae) in the cold temperate NE Pacific off British Columbia and adjacent waters. We propose one range extension and one new species in Clionaidae; two range extensions and five new species in Polymastiidae; one range extension, two name changes and two new species in Suberitidae; and one new species in Tethyidae. New species include Pione gibraltarensis n.sp., Polymastia piscesae n. sp., Radiella endeavourensis n. sp., Sphaerotylus raphidophora n. sp., Sphaerotylus verenae n. sp., Weberella perlucida n. sp., Prosuberites saanichensis n. sp., Suberites lambei n. sp., and Tethya vacua n. sp.. PMID:24989879

  9. Water temperature, streamflow, and ground-water elevation in and adjacent to the Russian river between Hopland and Guerneville, California from 1998-2002

    USGS Publications Warehouse

    Cox, Marisa H.; Hatch, Christine

    2003-01-01

    Temperature, water level elevation, stage height, and river discharge data for this report were collected in and adjacent to the Russian River from Hopland to Guerneville, CA over a four-year period from 1998 to 2002 to establish baselines for long-term water quality, water supply and habitat. Data files presented in this report were collected by the USGS and the Sonoma County Water Agency's Engineering Resource and Planning, and Natural Resource Divisions. Temperature data were collected in single-channel submersible microloggers or temperature data were collected simultaneously with water-elevation data in dual-channel down-hole data loggers. Stream stage and streamflow data were collected at USGS stream gaging stations located near Hopland, Healdsburg, and Guerneville over a 130 km reach of the Russian River. During the period of record stream flow ranged from 3 to 1458 m3/s. Stream temperature ranged from 8 to 29 oC while groundwater temperature ranged from 10 to 38 oC. Stream stage varied 5 m seasonly, while ground-water level varied 19 m over the same time scale.

  10. Assessment of water resources in lead-zinc mined areas in Cherokee County, Kansas, and adjacent areas

    USGS Publications Warehouse

    Spruill, Timothy B.

    1987-01-01

    A study was conducted to evaluate water-resources problems related to abandoned lead and zinc mines in Cherokee County, Kansas, and adjacent areas in Missouri and Oklahoma. Past mining activities have caused changes in the hydrogeology of the area. Lead and zinc mining has caused discontinuities and perforations in the confining shale west of the Pennsylvanian-Mississippian geologic contact (referred to as the western area), which have created artificial ground-water recharge and discharge areas. Recharge to the shallow aquifer (rocks of Mississippian age) through collapses, shafts, and drill holes in the shale has caused the formation of a ground-water 'mound' in the vicinity of the Picher Field in Kansas and Oklahoma. Discharge of mine-contaminated ground water to Tar Creek occurs in Oklahoma from drill holes and shafts where the potentiometric surface of the shallow aquifer is above the land surface. Mining of ore in the shallow aquifer has resulted in extensive fracturing and removal of material, which has created highly transmissive zones and voids and increased ground-water storage properties of the aquifer. In the area east of the Pennsylvanian-Mississippian geologic contact (referred to as the eastern area), fractured rock and tailings on the land surface increased the amount of water available for infiltration to the shallow aquifer; in the western area, tailings on the impermeable shale created artificial, perched aquifer systems that slowly drain to surface streams. Pumping of the deep aquifer (rocks of Cambrian and Ordovician age) by towns and industries, which developed as a result of the mining industry, has resulted in a potential for downward movement of water from the shallow aquifer. The potential is greatest in Ottawa County, Oklahoma. Because of the large volume of water that may be transported from the shallow to the deep aquifer, open drill holes or casings present the greatest contamination hazard to water supplies in the deep aquifer. Mining

  11. From single molecules to water networks: Dynamics of water adsorption on Pt(111).

    PubMed

    Naderian, Maryam; Groß, Axel

    2016-09-01

    The adsorption dynamics of water on Pt(111) was studied using ab initio molecular dynamics simulations based on density functional theory calculations including dispersion corrections. Sticking probabilities were derived as a function of initial kinetic energy and water coverage. In addition, the energy distribution upon adsorption was monitored in order to analyze the energy dissipation process. We find that on the water pre-covered surface the sticking probability is enhanced because of the attractive water-water interaction and the additional effective energy dissipation channels to the adsorbed water molecules. The water structures forming directly after the adsorption on the pre-covered surfaces do not necessarily correspond to energy minimum structures. PMID:27609006

  12. Distribution of binding energies of a water molecule in the water liquid-vapor interface

    SciTech Connect

    Chempath, Shaji; Pratt, Lawrence R

    2008-01-01

    Distributions of binding energies of a water molecule in the water liquid-vapor interface are obtained on the basis of molecular simulation with the SPC/E model of water. These binding energies together with the observed interfacial density profile are used to test a minimally conditioned Gaussian quasi-chemical statistical thermodynamic theory. Binding energy distributions for water molecules in that interfacial region clearly exhibit a composite structure. A minimally conditioned Gaussian quasi-chemical model that is accurate for the free energy of bulk liquid water breaks down for water molecules in the liquid-vapor interfacial region. This breakdown is associated with the fact that this minimally conditioned Gaussian model would be inaccurate for the statistical thermodynamics of a dilute gas. Aggressive conditioning greatly improves the performance of that Gaussian quasi-chemical model. The analogy between the Gaussian quasi-chemical model and dielectric models of hydration free energies suggests that naive dielectric models without the conditioning features of quasi-chemical theory will be unreliable for these interfacial problems. Multi-Gaussian models that address the composite nature of the binding energy distributions observed in the interfacial region might provide a mechanism for correcting dielectric models for practical applications.

  13. Seasonal dynamics of particulate organic matter in the Changjiang Estuary and adjacent coastal waters illustrated by amino acid enantiomers

    NASA Astrophysics Data System (ADS)

    Wu, Ying; Liu, Zongguang; Hu, Jun; Zhu, Zhuoyi; Liu, Sumei; Zhang, Jing

    2016-02-01

    Total suspended matter (TSM) was collected in the Changjiang Estuary and adjacent areas of the East China Sea in July, August, and November 2011, to study the composition and fate of particulate organic nitrogen (PON) during an August typhoon event and bottom trawling activities. Concentrations of particulate organic carbon (POC), particulate nitrogen (PN), and hydrolyzable particulate amino acids (PAA, D- and L-enantiomers) were higher during July and August than during November; however, D-arginine and alanine levels were significantly higher in November. Seasonal trends in the composition of PAAs indicate that in situ production is a key factor in their temporal distribution. No significant increase in TSM or decrease in labile organic matter was observed during the transit period following a typhoon event in August. In contrast, higher primary production was observed at this time as a result of the penetration of Changjiang Diluted Water caused by the typhoon event. Trawling effects were studied by comparing the calm season (July) with the bottom-trawling period (November) at similar sampling sites. The effect of trawling on the composition of bottom organic matter was studied by comparing D-amino acids concentrations and C/N ratios in the calm season (July) with the bottom-trawling period (November). A substantial contribution of microbial organic matter during the November cruise was indicated by a decrease in glutamic acid, an increase in TSM and D-alanine, and a lower carbon/nitrogen (C/N) ratio. In shallow coastal regions, anthropogenic activities (bottom trawling) may enhance the transfer of low-nutritional-value particulate organic matter into the benthic food chain.

  14. Quantum Tunneling of Water in Beryl. A New State of the Water Molecule

    DOE PAGESBeta

    Kolesnikov, Alexander I.; Reiter, George F.; Choudhury, Narayani; Prisk, Timothy R.; Mamontov, Eugene; Podlesnyak, Andrey; Ehlers, George; Seel, Andrew G.; Wesolowski, David J.; Anovitz, Lawrence M.

    2016-04-22

    When using neutron scattering and ab initio simulations, we document the discovery of a new “quantum tunneling state” of the water molecule confined in 5 Å channels in the mineral beryl, characterized by extended proton and electron delocalization. We observed a number of peaks in the inelastic neutron scattering spectra that were uniquely assigned to water quantum tunneling. Additionally, the water proton momentum distribution was measured with deep inelastic neutron scattering, which directly revealed coherent delocalization of the protons in the ground state.

  15. Quantum Tunneling of Water in Beryl: A New State of the Water Molecule.

    PubMed

    Kolesnikov, Alexander I; Reiter, George F; Choudhury, Narayani; Prisk, Timothy R; Mamontov, Eugene; Podlesnyak, Andrey; Ehlers, George; Seel, Andrew G; Wesolowski, David J; Anovitz, Lawrence M

    2016-04-22

    Using neutron scattering and ab initio simulations, we document the discovery of a new "quantum tunneling state" of the water molecule confined in 5 Å channels in the mineral beryl, characterized by extended proton and electron delocalization. We observed a number of peaks in the inelastic neutron scattering spectra that were uniquely assigned to water quantum tunneling. In addition, the water proton momentum distribution was measured with deep inelastic neutron scattering, which directly revealed coherent delocalization of the protons in the ground state. PMID:27152824

  16. Disorder of Hydrofluorocarbon Molecules Entrapped in the Water Cages of Structure I Clathrate Hydrate.

    PubMed

    Takeya, Satoshi; Udachin, Konstantin A; Moudrakovski, Igor L; Ohmura, Ryo; Ripmeester, John A

    2016-05-23

    Water versus fluorine: Clathrate hydrates encaging hydrofluorocarbons as guests show both isotropic and anisotropic distributions within host water cages, depending on the number of fluorine atoms in the guest molecule; this is caused by changes in intermolecular interactions to host water molecules in the hydrates. PMID:27105807

  17. Electron capture by bare ions on water molecules

    NASA Astrophysics Data System (ADS)

    Rivarola, Roberto; Montenegro, Pablo; Monti, Juan; Fojón, Omar

    2016-05-01

    Single electron capture from water molecules by impact of bare ions is theoretically investigated at intermediate and high collision energies. This reaction is of fundamental importance to determine the deposition of energy in biological matter irradiated with ion beams (hadrontherapy), dominating other ionizing processes of the target at low-intermediate impact velocities and giving principal contributions to the energetic region where electronic stopping power maximizes. The dynamics of the interaction between the aggregates is described within the one active-electron continuum distorted wave-eikonal initial state theory. The orbitals of the target in the ground state are represented using the approximate self-consistent complete neglect of differential orbitals (SC-CNDO) model. The contribution of different molecular orbitals on the partial cross sections to selected n-principal quantum number projectile states is discriminated as well as the collaboration of these n-states on total cross sections. The latter ones are dominated by capture to n=1 states at high enough energies decreasing their contribution as n increases.

  18. Study of water molecule decomposition in plasma by diode laser spectroscopy and optical actinometry methods

    NASA Astrophysics Data System (ADS)

    Bernatskiy, A. V.; Lagunov, V. V.; Ochkin, V. N.; Tskhai, S. N.

    2016-07-01

    The methods of diode laser radiation absorption at vibrational–rotational molecule transitions and optical actinometry with measurements of its electron emission spectra are used independently to study water molecule dissociation in glow discharge plasma in a mixture of water vapor and inert gases at reduced pressure. The methods yield close results. The dissociation reaches 98%.

  19. Key Role of Active-Site Water Molecules in Bacteriorhodopsin Proton-Transfer Reactions

    SciTech Connect

    Bondar, A.N.; Baudry, Jerome Y; Suhai, Sandor; Fischer, S.; Smith, Jeremy C

    2008-10-01

    The functional mechanism of the light-driven proton pump protein bacteriorhodopsin depends on the location of water molecules in the active site at various stages of the photocycle and on their roles in the proton-transfer steps. Here, free energy computations indicate that electrostatic interactions favor the presence of a cytoplasmic-side water molecule hydrogen bonding to the retinal Schiff base in the state preceding proton transfer from the retinal Schiff base to Asp85. However, the nonequilibrium nature of the pumping process means that the probability of occupancy of a water molecule in a given site depends both on the free energies of insertion of the water molecule in this and other sites during the preceding photocycle steps and on the kinetic accessibility of these sites on the time scale of the reaction steps. The presence of the cytoplasmic-side water molecule has a dramatic effect on the mechanism of proton transfer: the proton is channeled on the Thr89 side of the retinal, whereas the transfer on the Asp212 side is hindered. Reaction-path simulations and molecular dynamics simulations indicate that the presence of the cytoplasmic-side water molecule permits a low-energy bacteriorhodopsin conformer in which the water molecule bridges the twisted retinal Schiff base and the proton acceptor Asp85. From this low-energy conformer, proton transfer occurs via a concerted mechanism in which the water molecule participates as an intermediate proton carrier.

  20. Adsorption of Small Molecules at Water--Hexane and Water--Membrane Interfaces

    NASA Astrophysics Data System (ADS)

    Wilson, Michael A.

    1996-03-01

    The interaction of solutes with aqueous interfaces plays a significant role in a variety of physical processes, including general anesthesia and atmospheric chemistry. We present molecular dynamics results for the transfer of several small solutes across water liquid--vapor, water--hexane and water--GMO bilayer membrane interfaces. (A. Pohorille and M. A. Wilson, J. Chem. Phys. (in press, 1995).)^, (A. Pohorille, P. CIeplak, and M. A. Wilson, Chem. Phys. (in press, 1995).) The free energies of transferring small polar molecules across the interface exhibit fairly deep minima while those of nonpolar molecules do not. This is due to a balance between nonelectrostatic contributions --- primarily the work required to create a cavity large enough to accommodate the solute --- and the solute--solvent electrostatic interactions.^1 The surface excess of solute is calculated and compared with experimental results from the Gibbs adsorption isotherm. The interfacial solubilities correlate with measured anesthetic potencies of these compounds, implying that the binding sites for anesthetics are located near the water--membrane interface.

  1. Chemical reactions of water molecules on Ru(0001) induced by selective excitation of vibrational modes

    SciTech Connect

    Mugarza, Aitor; Shimizu, Tomoko K.; Ogletree, D. Frank; Salmeron, Miquel

    2009-05-07

    Tunneling electrons in a scanning tunneling microscope were used to excite specific vibrational quantum states of adsorbed water and hydroxyl molecules on a Ru(0 0 0 1) surface. The excited molecules relaxed by transfer of energy to lower energy modes, resulting in diffusion, dissociation, desorption, and surface-tip transfer processes. Diffusion of H{sub 2}O molecules could be induced by excitation of the O-H stretch vibration mode at 445 meV. Isolated molecules required excitation of one single quantum while molecules bonded to a C atom required at least two quanta. Dissociation of single H{sub 2}O molecules into H and OH required electron energies of 1 eV or higher while dissociation of OH required at least 2 eV electrons. In contrast, water molecules forming part of a cluster could be dissociated with electron energies of 0.5 eV.

  2. Approximate changes in water levels in wells completed in the Chicot and Evangeline aquifers, 1990-94 and 1993-94, in Fort Bend County and adjacent areas, Texas

    USGS Publications Warehouse

    Coplin, L.S.; Santos, H.X.

    1994-01-01

    Measurements of water levels from wells completed in the Chicot and Evangeline aquifers were used to construct maps showing approximate changes of water levels in Fort Bend County and adjacent areas during 1990-94 and 1993-94.

  3. The impact of pumped water from a de-watered Magnesian limestone quarry on an adjacent wetland: Thrislington, County Durham, UK.

    PubMed

    Mayes, W M; Large, A R G; Younger, P L

    2005-12-01

    Although quarrying is often cited as a potential threat to wetland systems, there is a lack of relevant, quantitative case studies in the literature. The impact of pumped groundwater discharged from a quarry into a wetland area was assessed relative to reference conditions in an adjacent fen wetland that receives only natural runoff. Analysis of vegetation patterns at the quarry wetland site, using Detrended Correspondence Analysis and the species indicator values of Ellenberg, revealed a clear disparity between community transitions in the quarry wetland and the reference site. Limited establishment of moisture-sensitive taxa, the preferential proliferation of robust wetland species and an overall shift towards lower species diversity in the quarry wetland were explicable primarily by the physico-chemical environment created by quarry dewatering. This encompassed high pH (up to 12.8), sediment-rich effluent creating a nutrient-poor substrate with poor moisture retention in the quarry wetland, and large fluctuations in water levels. PMID:15993994

  4. Infrared Spectra of Water Bending Bands of Propylene Oxide-Water Complexes: Sequential Solvation of a Chiral Molecule in Water

    NASA Astrophysics Data System (ADS)

    Liu, Xunchen; Xu, Yunjie

    2011-06-01

    Sequential solvation of propylene oxide (C3H6O), an prototypical chiral molecule, with water has been investigated using high resolution infrared spectroscopy and ab initio methods. In a number of low resolution studies, the vibrational and vibrational circular dichroism spectral features at the water bending vibration region had been shown to be highly sensitive to the water solvation structures around propylene oxide in aqueous solution. The current study aims to provide quantitative information about solvation of a chiral molecule with water molecules at the molecular level and to provide the experimental benchmarks for calculations of vibrational frequencies in these larger molecular complexes. The high resolution infrared spectra of the propylene oxide-water complexes have been measured using a pulsed jet infrared spectrometer equipped with a room temperature external cavity quantum cascade laser and an astigmatic multi-pass cell. At least 6 bands have been observed from 1650 to 1680 Cm-1. Based on the previous microwave spectroscopic studies, these bands have been assigned to the blue-shifted water bending (ν_2) vibration modes associated with both the syn- and anti- conformers of the binary (C3H6O-H2O) and ternary (C3H6O-(H2O)2) complexes. This report shows the power of high resolution infrared spectroscopy to study multi-conformers of relatively large organic molecule complexes produced in a jet expansion. M. Losada, P. Nguyen, and Y .Xu, J. Phys. Chem. A, 112, 5621, (2008) Z. Su, Q. Wen, and Y. Xu, J. Am. Chem. Soc., 128, 6755, (2006) Z. Su and Y. Xu, Angew. Chem. Int. Ed., 46, 6163, (2007)

  5. Quasielastic neutron scattering from adsorbed water molecules on pyrogenic silica surfaces

    NASA Astrophysics Data System (ADS)

    Tumanov, A. A.; Zarko, V. I.

    1994-04-01

    Quasielastic neutron scattering (QNS) from hydrated samples of high dispersion (Aerosil) and of porous dioxide silicon was investigated. The broadening of the QNS peak analysis permits one to obtain the effective diffusion coefficient D of adsorbed water molecules. It was obtained that the D-value increases with silica hydration. The mean square displacement of the water molecules from equilibrium < x2> equals approximately 0.1 Å 2 and does not depend on the quantity of adsorbed water.

  6. Water disinfection: microbes versus molecules - an introduction of issues

    SciTech Connect

    Fowle, J.R. III, Kopfler, F.C.

    1986-11-01

    If the chemicals used to rid drinking water of disease-causing microbes are themselves potentially harmful, is drinking water safe. What trade-offs are acceptable with respect to microbial versus chemical water quality. This conference deals with current thinking about these topics. The subjects discussed reflect the evolution of thinking, both scientifically and socially, about how best to supply the public with safe, pure potable water. The goal of this paper is to introduce the issues associated with disinfectants and disinfectant by-products in water. This will be done by presenting a historical overview of the use of chemical disinfectants to purify drinking water and the subsequent awareness of potential health concerns. Historically, the major health issue associated with water has been the demonstrated role that water has played in spreading infectious disease. Waterborne infectious agents remain in the environment, and new ones emerge through evolution of humans and microorganisms and because of changing exposure patterns.

  7. Implication of crystal water molecules in inhibitor binding at ALR2 active site.

    PubMed

    Hymavati; Kumar, Vivek; Sobhia, M Elizabeth

    2012-01-01

    Water molecules play a crucial role in mediating the interaction between a ligand and a macromolecule. The solvent environment around such biomolecule controls their structure and plays important role in protein-ligand interactions. An understanding of the nature and role of these water molecules in the active site of a protein could greatly increase the efficiency of rational drug design approaches. We have performed the comparative crystal structure analysis of aldose reductase to understand the role of crystal water in protein-ligand interaction. Molecular dynamics simulation has shown the versatile nature of water molecules in bridge H bonding during interaction. Occupancy and life time of water molecules depend on the type of cocrystallized ligand present in the structure. The information may be useful in rational approach to customize the ligand, and thereby longer occupancy and life time for bridge H-bonding. PMID:22649481

  8. Quantifying the Entropy of Binding for Water Molecules in Protein Cavities by Computing Correlations

    PubMed Central

    Huggins, David J.

    2015-01-01

    Protein structural analysis demonstrates that water molecules are commonly found in the internal cavities of proteins. Analysis of experimental data on the entropies of inorganic crystals suggests that the entropic cost of transferring such a water molecule to a protein cavity will not typically be greater than 7.0 cal/mol/K per water molecule, corresponding to a contribution of approximately +2.0 kcal/mol to the free energy. In this study, we employ the statistical mechanical method of inhomogeneous fluid solvation theory to quantify the enthalpic and entropic contributions of individual water molecules in 19 protein cavities across five different proteins. We utilize information theory to develop a rigorous estimate of the total two-particle entropy, yielding a complete framework to calculate hydration free energies. We show that predictions from inhomogeneous fluid solvation theory are in excellent agreement with predictions from free energy perturbation (FEP) and that these predictions are consistent with experimental estimates. However, the results suggest that water molecules in protein cavities containing charged residues may be subject to entropy changes that contribute more than +2.0 kcal/mol to the free energy. In all cases, these unfavorable entropy changes are predicted to be dominated by highly favorable enthalpy changes. These findings are relevant to the study of bridging water molecules at protein-protein interfaces as well as in complexes with cognate ligands and small-molecule inhibitors. PMID:25692597

  9. Fast transport of water molecules across carbon nanotubes induced by static electric fields

    NASA Astrophysics Data System (ADS)

    Zhang, Qi-Lin; Yang, Rong-Yao

    2016-01-01

    Water permeation across a single-walled carbon nanotube has been studied in the presence of static electric fields (SEFs) with different directions under hydrostatic pressures. With the angle between the SEF direction and tube axis increasing from 0∘ to 90∘, the water flux decreases gradually until almost vanishes, and the maximum value at 0∘ is approximately four times the case without SEFs. The phenomenon is attributed to the alignment of the polar water molecules along the SEF direction. We also show that water permeation properties are dependent on the field strength due mainly to thermal fluctuations of water molecules.

  10. Development of ground-water resources in Orange County, Texas, and adjacent areas in Texas and Louisiana, 1971-80

    USGS Publications Warehouse

    Bonnet, C.W.; Gabrysch, R.K.

    1982-01-01

    Although saltwater encroachment is evident in parts of southern Orange County, the encroachment is not expected to be detrimental if the ground-water pumping remains stable and the projected increase in demands for water is met with surface-water supplies.

  11. Availability and chemistry of ground water on the Bruneau Plateau and adjacent eastern plain in Twin Falls County, south-central Idaho

    USGS Publications Warehouse

    Moffatt, R.L.; Jones, M.L.

    1984-01-01

    The Bruneau plateau in south-central Idaho consists of about 889 ,600 acres of potentially irrigable land. About 112,200 of these acres have been developed for agriculture; 11,200 acres are irrigated with ground water, and the remaining acreage is irrigated with water from the Snake and Bruneau rivers and Salmon Falls Creek. On the basis of present usage, about 158,000 acre-feet of water per year are needed to develop an additional 63,000 acres. About 438,000 acre-feet per year are needed to irrigate existing and newly developed lands in dry years when streamflow in the Snake River at Milner Dam is inadequate to meet appropriated needs. Pumping lifts of about 400-600 feet and low well yields on the Bruneau plateau probably preclude large-scale irrigation development solely from local ground-water resources. However, supplemental sources of irrigation water are available from a perched-water aquifer, a thermal aquifer, and the regional aquifer adjacent to the plateau. About 100,000-115,000 acre-feet per year of water probably could be withdrawn from the perched and regional aquifers and conveyed to the plateau without serious impact on local ground-water resources. The amount of water that could be safely withdrawn from the thermal aquifer was not determined. (USGS)

  12. Shape of a water molecule as function of OH separation

    NASA Astrophysics Data System (ADS)

    Gabbay, I.; March, N. H.

    1980-02-01

    For small O-H separation the water molecule becomes linear. The Murrell-Sorbie potential energy surface affords a basis to study the shape of the molecule for larger OH separation. The possible relevance to H 2O outside a metal surface is discussed.

  13. The putative role of some conserved water molecules in the structure and function of human transthyretin.

    PubMed

    Banerjee, Avik; Dasgupta, Subrata; Mukhopadhyay, Bishnu P; Sekar, Kanagaraj

    2015-11-01

    Human transthyretin (hTTR) is a multifunctional protein that is involved in several neurodegenerative diseases. Besides the transportation of thyroxin and vitamin A, it is also involved in the proteolysis of apolipoprotein A1 and Aβ peptide. Extensive analyses of 32 high-resolution X-ray and neutron diffraction structures of hTTR followed by molecular-dynamics simulation studies using a set of 15 selected structures affirmed the presence of 44 conserved water molecules in its dimeric structure. They are found to play several important roles in the structure and function of the protein. Eight water molecules stabilize the dimeric structure through an extensive hydrogen-bonding network. The absence of some of these water molecules in highly acidic conditions (pH ≤ 4.0) severely affects the interfacial hydrogen-bond network, which may destabilize the native tetrameric structure, leading to its dissociation. Three pairs of conserved water molecules contribute to maintaining the geometry of the ligand-binding cavities. Some other water molecules control the orientation and dynamics of different structural elements of hTTR. This systematic study of the location, absence, networking and interactions of the conserved water molecules may shed some light on various structural and functional aspects of the protein. The present study may also provide some rational clues about the conserved water-mediated architecture and stability of hTTR. PMID:26527142

  14. Unraveling the Sc(3+) Hydration Geometry: The Strange Case of the Far-Coordinated Water Molecule.

    PubMed

    Migliorati, Valentina; D'Angelo, Paola

    2016-07-01

    The hydration structure and dynamics of Sc(3+) in aqueous solution have been investigated using a combined approach based on quantum mechanical (QM) calculations, molecular dynamics (MD) simulations, and extended X-ray absorption fine structure (EXAFS) spectroscopy. An effective Sc-water two-body potential has been generated from QM calculations and then used in the MD simulation of Sc(3+) in water, and the reliability of the entire procedure has been assessed by comparing the theoretical structural results with the EXAFS experimental data. The outstanding outcome of this work is that the Sc(3+) ion forms a well-defined capped square antiprism (SAP) complex in aqueous solution, where the eight water molecules closest to the ion are located at the vertexes of a SAP polyhedron, while the ninth water molecule occupying the capping position is unusually found at a very long distance from the ion. This far-coordinated water molecule possesses a degree of structure comparable with the other first shell molecules surrounding the ion at much shorter distances, and its presence gave us the unique opportunity to easily identify the geometry of the Sc(3+) coordination polyhedron. Despite very strong ion-water interactions, the Sc(3+) hydration shell is very labile, as the far-coordinated ligand allows first shell water molecules to easily exchange their positions both inside the solvation shell and with the rest of the solvent molecules. PMID:27300102

  15. High physisorption affinity of water molecules to the hydroxylated aluminum oxide (001) surface.

    PubMed

    Kittaka, Shigeharu; Yamaguchi, Keisuke; Takahara, Shuichi

    2012-02-15

    The adsorption mechanism of water on the hydroxylated (001) plane of α-Al(2)O(3) was studied by measuring adsorption isotherms and GCMC simulations. The experimental adsorption isotherms for three α-Al(2)O(3) samples from different sources are typical type II, in which adsorption starts sharply at low pressures, suggesting a high affinity of water to the Al(2)O(3) surface. Water molecules are adsorbed in two registered forms (bilayer structure). In the first form, water is registered at the center of three surface hydroxyl groups by directing a proton of the water. In the second form, a water molecule is adsorbed by bridging two of the first-layer water molecules through hydrogen bonding, by which a hexagonal ring network is constructed over the hydroxylated surface. The network domains are spread over the surface, and their size decreases as the temperature increases. The simulated adsorption isotherms present a characteristic two-dimensional (2D) phase diagram including a 2D critical point at 365K, which is higher than that on the hydroxylated Cr(2)O(3) surface (319 K). This fact substantiates the high affinity of water molecules to the α-Al(2)O(3) surfaces, which enhances the adsorbability originating from higher heat of adsorption. The higher affinity of water molecules to the α-Al(2)O(3) (001) plane is ascribed to the high compatibility of the crystal plane to form a hexagonal ring network of (001) plane of ice Ih. PMID:22178567

  16. Relaxation dynamics of surface-adsorbed water molecules in nanoporous silica probed by terahertz spectroscopy

    NASA Astrophysics Data System (ADS)

    Huang, Yu-Ru; Liu, Kao-Hsiang; Mou, Chung-Yuan; Sun, Chi-Kuang

    2015-08-01

    Relaxation dynamics of an exclusively adsorbed water molecule in mesoporous silica MCM-41-S was studied by using terahertz spectroscopy. With the temperature controlled from 0 to 50 °C, we observed strongly frequency- and temperature-dependent dielectric relaxation responses, implying that, unlike ice, surface-adsorbed water molecules retained flourishing picosecond dynamics. Based on the Debye relaxation model, a relaxation time constant was found to increase from 1.77 to 4.83 ps when the water molecule was cooled from 50 to 0 °C. An activation energy of ˜15 kJ/mol, which was in close agreement with a hydrogen-bonding energy, was further extracted from the Arrhenius analysis. Combined with previous molecular dynamics simulations, our results indicate that the reorientation relaxation originated from the "flip-flop" rotation of a three hydrogen-bonded surface-adsorbed water molecule.

  17. Asymmetric self-diffusion with orientation-dependence of water molecule in finite timescale

    NASA Astrophysics Data System (ADS)

    Wei, Xu; Sheng, Nan; Wan, RongZheng; Hu, GuoHui; Fang, HaiPing

    2016-07-01

    Self-diffusion of water has been investigated by molecular dynamics simulations. It was found that the preference of the direction in self-diffusion of water is orientation dependent in a finite time. For a time of ~100 ps, there are more possibilities for water molecules moving along the initial dipole orientation than in the opposite direction. This reveals that self-diffusion of water molecules is asymmetric in a finite time. We tested four water models and found that they all show similar asymmetric diffusion, indicating that asymmetric diffusion of water is intrinsic behavior rather than induced by the water model. These results are important for understanding and application of asymmetric diffusion in research fields such as biological water and confined water in small dimensions.

  18. Free energy barriers for escape of water molecules from protein hydration layer.

    PubMed

    Roy, Susmita; Bagchi, Biman

    2012-03-01

    Free energy barriers separating interfacial water molecules from the hydration layer at the surface of a protein to the bulk are obtained by using the umbrella sampling method of free energy calculation. We consider hydration layer of chicken villin head piece (HP-36) which has been studied extensively by molecular dynamics simulations. The free energy calculations reveal a strong sensitivity to the secondary structure. In particular, we find a region near the junction of first and second helix that contains a cluster of water molecules which are slow in motion, characterized by long residence times (of the order of 100 ps or more) and separated by a large free energy barrier from the bulk water. However, these "slow" water molecules constitute only about 5-10% of the total number of hydration layer water molecules. Nevertheless, they play an important role in stabilizing the protein conformation. Water molecules near the third helix (which is the important helix for biological function) are enthalpically least stable and exhibit the fastest dynamics. Interestingly, barrier height distributions of interfacial water are quite broad for water surrounding all the three helices (and the three coils), with the smallest barriers found for those near the helix-3. For the quasi-bound water molecules near the first and second helices, we use well-known Kramers' theory to estimate the residence time from the free energy surface, by estimating the friction along the reaction coordinate from the diffusion coefficient by using Einstein relation. The agreement found is satisfactory. We discuss the possible biological function of these slow, quasi-bound (but transient) water molecules on the surface. PMID:22288939

  19. Depositional and diagenetic history and petroleum geology of the Jurassic Norphlet Formation of the Alabama coastal waters area and adjacent federal waters area

    USGS Publications Warehouse

    Kugler, R.L.; Mink, R.M.

    1999-01-01

    The discovery of deep (>20,000 ft) gas reservoirs in eolian sandstone of the Upper Jurassic Norphlet Formation in Mobile Bay and offshore Alabama in the late 1970s represents one of the most significant hydrocarbon discoveries in the nation during the past several decades. Estimated original proved gas from Norphlet reservoirs in the Alabama coastal waters and adjacent federal waters is 7.462 trillion ft3 (Tcf) (75% recovery factor). Fifteen fields have been established in the offshore Alabama area. Norphlet sediment was deposited in an arid environment in alluvial fans, alluvial plains, and wadis in updip areas. In downdip areas, the Norphlet was deposited in a broad desert plain, with erg development in some areas. Marine transgression, near the end of Norphlet deposition, resulted in reworking of the upper part of the Norphlet Formation. Norphlet reservoir sandstone is arkose and subarkose, consisting of a simple assemblage of three minerals, quartz, albite, and K-feldspar. The present framework grain assemblage of the Norphlet is dominantly diagenetic, owing to albitization and dissolution of feldspar. Despite the simple framework composition, the diagenetic character of the Norphlet is complex. Important authigenic minerals include carbonate phases (calcite, dolomite, Fe-dolomite, and breunnerite), feldspar (albite and K-feldspar), evaporite minerals (anhydrite and halite), clay minerals (illite and chlorite), quartz, and pyrobitumen. The abundance and distribution of these minerals varies significantly between onshore and offshore regions of Norphlet production. The lack of sufficient internal sources of components for authigenic minerals, combined with unusual chemical compositions of chloride (Mg-rich), breunnerite, and some minor authigenic minerals, suggests that Louann-derived fluids influenced Norphlet diagenesis. In offshore Alabama reservoirs, porosity is dominantly modified primary porosity. Preservation of porosity in deep Norphlet reservoirs is due

  20. Water-quality, bed-sediment, and discharge data for the Mississippi River-Gulf Outlet and adjacent waterways, southeastern Louisiana, August 2008 through December 2009

    USGS Publications Warehouse

    Swarzenski, Christopher M.; Mize, Scott V.; Lovelace, John K.

    2012-01-01

    The Mississippi River-Gulf Outlet navigation channel (MRGO) was constructed in the early 1960s to provide a safer and shorter route between the Gulf of Mexico and the Port of New Orleans for deep-draft, ocean-going vessels and to promote the economic development of the Port of New Orleans. In 2006, the U.S. Army Corps of Engineers developed a plan to de-authorize the MRGO. The plan called for a rock barrier to be constructed across the MRGO near Bayou La Loutre. In 2008, the U.S. Geological Survey, in cooperation with the Louisiana Coastal Area Science and Technology Program began a study to document the impacts of the rock barrier on water-quality and flow before, during, and after its construction. Water-quality, bed-sediment, and discharge data were collected in the MRGO and adjacent water bodies from August 2008 through December 2009.

  1. Literature and data review for the surface-water pathway: Columbia River and adjacent coastal areas. Hanford Environmental Dose Reconstruction Project

    SciTech Connect

    Walters, W.H.; Dirkes, R.L.; Napier, B.A.

    1992-04-01

    As part of the Hanford Environmental Dose Reconstruction Project, Pacific Northwest Laboratory reviewed literature and data on radionuclide concentrations and distribution in the water, sediment, and biota of the Columbia River and adjacent coastal areas. Over 600 documents were reviewed including Hanford reports, reports by offsite agencies, journal articles, and graduate theses. Certain radionuclide concentration data were used in preliminary estimates of individual dose for the 1964--1966 time period. This report summarizes the literature and database review and the results of the preliminary dose estimates.

  2. Literature and data review for the surface-water pathway: Columbia River and adjacent coastal areas. Hanford Environmental Dose Reconstruction Project

    SciTech Connect

    Walters, W.H.; Dirkes, R.L.; Napier, B.A.

    1992-11-01

    As part of the Hanford Environmental Dose Reconstruction (HEDR) Project, Battelle, Pacific Northwest Laboratories reviewed literature and data on radionuclide concentrations and distribution in the water, sediment, and biota of the Columbia River and adjacent coastal areas. Over 600 documents were reviewed including Hanford reports, reports by offsite agencies, journal articles, and graduate theses. Radionuclide concentration data were used in preliminary estimates of individual dose for the period 1964 through 1966. This report summarizes the literature and database reviews and the results of the preliminary dose estimates.

  3. 33 CFR 165.1317 - Security and Safety Zone; Large Passenger Vessel Protection, Puget Sound and adjacent waters...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... including publication in the Federal Register as practicable, in accordance with 33 CFR 165.7(a). Such means... Vessel does not include vessels inspected and certificated under 46 CFR, Chapter I, Subchapter T such as.... Navigable waters of the United States means those waters defined as such in 33 CFR part 2. Navigation...

  4. 33 CFR 165.1317 - Security and Safety Zone; Large Passenger Vessel Protection, Puget Sound and adjacent waters...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... including publication in the Federal Register as practicable, in accordance with 33 CFR 165.7(a). Such means... Vessel does not include vessels inspected and certificated under 46 CFR, Chapter I, Subchapter T such as.... Navigable waters of the United States means those waters defined as such in 33 CFR part 2. Navigation...

  5. 33 CFR 165.1313 - Security zone regulations, tank ship protection, Puget Sound and adjacent waters, Washington

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... CFR 165.7(a). Such means of notification may also include but are not limited to, Broadcast Notice to... United States. (2) Navigable waters of the United States means those waters defined as such in 33 CFR...), (d), (f), (g), (h), (j), and (k) of this section. (j) Exception. 33 CFR Part 161 promulgates...

  6. 33 CFR 165.1313 - Security zone regulations, tank ship protection, Puget Sound and adjacent waters, Washington

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... CFR 165.7(a). Such means of notification may also include but are not limited to, Broadcast Notice to... United States. (2) Navigable waters of the United States means those waters defined as such in 33 CFR...), (d), (f), (g), (h), (j), and (k) of this section. (j) Exception. 33 CFR Part 161 promulgates...

  7. 33 CFR 165.1313 - Security zone regulations, tank ship protection, Puget Sound and adjacent waters, Washington

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... CFR 165.7(a). Such means of notification may also include but are not limited to, Broadcast Notice to... United States. (2) Navigable waters of the United States means those waters defined as such in 33 CFR...), (d), (f), (g), (h), (j), and (k) of this section. (j) Exception. 33 CFR Part 161 promulgates...

  8. 33 CFR 165.1313 - Security zone regulations, tank ship protection, Puget Sound and adjacent waters, Washington

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... CFR 165.7(a). Such means of notification may also include but are not limited to, Broadcast Notice to... United States. (2) Navigable waters of the United States means those waters defined as such in 33 CFR...), (d), (f), (g), (h), (j), and (k) of this section. (j) Exception. 33 CFR Part 161 promulgates...

  9. 33 CFR 165.1313 - Security zone regulations, tank ship protection, Puget Sound and adjacent waters, Washington

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... CFR 165.7(a). Such means of notification may also include but are not limited to, Broadcast Notice to... United States. (2) Navigable waters of the United States means those waters defined as such in 33 CFR...), (d), (f), (g), (h), (j), and (k) of this section. (j) Exception. 33 CFR Part 161 promulgates...

  10. Roles of water molecules in bacteria and viruses

    NASA Astrophysics Data System (ADS)

    Cox, C. S.

    1993-02-01

    In addition to water, microbes mainly comprise lipids, carbohydrates, proteins and nucleic acids. Their structure and function singularly and conjointly is affected by water activity. Desiccation leads to dramatic lipid phase changes whereas carbohydrates, proteins and nucleic acids initially suffer spontaneous, reversible low activation energy Maillard reactions forming products that more slowly re-arrange, cross-link etc. to give non-native states. While initial products spontaneously may reverse to native states by raising water activity, later products only do so through energy consumption and enzymatic activity eg. repair. Yet, native states of lipid membranes and associated enzymes are required to generate energy. Consequently, good reserves of high energy compounds (e.g. ATP) and of membrane stabilisers (e.g. trehalose) may be expected to enhance survival following drying and rehydration (e.g. anhydrobiotic organisms).

  11. Water Resources of the Basin and Range Carbonate-Rock Aquifer System, White Pine County, Nevada, and Adjacent Areas in Nevada and Utah - Draft Report

    USGS Publications Warehouse

    Welch, Alan H., (Edited By); Bright, Daniel J.

    2007-01-01

    Summary of Major Findings This report summarizes results of a water-resources study for White Pine County, Nevada, and adjacent areas in east-central Nevada and western Utah. The Basin and Range carbonate-rock aquifer system (BARCAS) study was initiated in December 2004 through Federal legislation (Section 131 of the Lincoln County Conservation, Recreation, and Development Act of 2004) directing the Secretary of the Interior to complete a water-resources study through the U.S. Geological Survey, Desert Research Institute, and State of Utah. The study was designed as a regional water-resource assessment, with particular emphasis on summarizing the hydrogeologic framework and hydrologic processes that influence ground-water resources. The study area includes 13 hydrographic areas that cover most of White Pine County; in this report however, results for the northern and central parts of Little Smoky Valley were combined and presented as one hydrographic area. Hydrographic areas are the basic geographic units used by the State of Nevada and Utah and local agencies for water-resource planning and management, and are commonly defined on the basis of surface-water drainage areas. Hydrographic areas were further divided into subbasins that are separated by areas where bedrock is at or near the land surface. Subbasins represent subdivisions used in this study for estimating recharge, discharge, and water budget. Hydrographic areas represent the subdivision used for reporting summed and tabulated subbasin estimates.

  12. Water Resources of the Basin and Range Carbonate-Rock Aquifer System, White Pine County, Nevada, and Adjacent Areas in Nevada and Utah

    USGS Publications Warehouse

    Welch, Alan H., (Edited By); Bright, Daniel J.; Knochenmus, Lari A.

    2008-01-01

    INTRODUCTION This report summarizes results of a water-resources study for White Pine County, Nevada, and adjacent areas in east-central Nevada and western Utah. The Basin and Range carbonate-rock aquifer system (BARCAS) study was initiated in December 2004 through Federal legislation (Section 301(e) of the Lincoln County Conservation, Recreation, and Development Act of 2004; PL108-424) directing the Secretary of the Interior to complete a water-resources study through the U.S. Geological Survey, Desert Research Institute, and State of Utah. The study was designed as a regional water-resource assessment, with particular emphasis on summarizing the hydrogeologic framework and hydrologic processes that influence ground-water resources. The study area includes 13 hydrographic areas that cover most of White Pine County; in this report however, results for the northern and central parts of Little Smoky Valley were combined and presented as one hydrographic area. Hydrographic areas are the basic geographic units used by the State of Nevada and Utah and local agencies for water-resource planning and management, and are commonly defined on the basis of surface-water drainage areas. Hydrographic areas were further divided into subbasins that are separated by areas where bedrock is at or near the land surface. Subbasins are the subdivisions used in this study for estimating recharge, discharge, and water budget. Hydrographic areas are the subdivision used for reporting summed and tabulated subbasin estimates.

  13. Analytical model for three-dimensional Mercedes-Benz water molecules.

    PubMed

    Urbic, T

    2012-06-01

    We developed a statistical model which describes the thermal and volumetric properties of water-like molecules. A molecule is presented as a three-dimensional sphere with four hydrogen-bonding arms. Each water molecule interacts with its neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction. This model, which is largely analytical, is a variant of a model developed before for a two-dimensional Mercedes-Benz model of water. We explored properties such as molar volume, density, heat capacity, thermal expansion coefficient, and isothermal compressibility as a function of temperature and pressure. We found that the volumetric and thermal properties follow the same trends with temperature as in real water and are in good general agreement with Monte Carlo simulations, including the density anomaly, the minimum in the isothermal compressibility, and the decreased number of hydrogen bonds upon increasing the temperature. PMID:23005100

  14. Analytical model for three-dimensional Mercedes-Benz water molecules

    NASA Astrophysics Data System (ADS)

    Urbic, T.

    2012-06-01

    We developed a statistical model which describes the thermal and volumetric properties of water-like molecules. A molecule is presented as a three-dimensional sphere with four hydrogen-bonding arms. Each water molecule interacts with its neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction. This model, which is largely analytical, is a variant of a model developed before for a two-dimensional Mercedes-Benz model of water. We explored properties such as molar volume, density, heat capacity, thermal expansion coefficient, and isothermal compressibility as a function of temperature and pressure. We found that the volumetric and thermal properties follow the same trends with temperature as in real water and are in good general agreement with Monte Carlo simulations, including the density anomaly, the minimum in the isothermal compressibility, and the decreased number of hydrogen bonds upon increasing the temperature.

  15. Analytical model for three-dimensional Mercedes-Benz water molecules

    PubMed Central

    Urbic, T.

    2013-01-01

    We developed a statistical model which describes the thermal and volumetric properties of water-like molecules. A molecule is presented as a three-dimensional sphere with four hydrogen-bonding arms. Each water molecule interacts with its neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction. This model, which is largely analytical, is a variant of a model developed before for a two-dimensional Mercedes-Benz model of water. We explored properties such as molar volume, density, heat capacity, thermal expansion coefficient, and isothermal compressibility as a function of temperature and pressure. We found that the volumetric and thermal properties follow the same trends with temperature as in real water and are in good general agreement with Monte Carlo simulations, including the density anomaly, the minimum in the isothermal compressibility, and the decreased number of hydrogen bonds upon increasing the temperature. PMID:23005100

  16. Fish diversity in the Río de la Plata and adjacent waters: an overview of environmental influences on its spatial and temporal structure.

    PubMed

    Jaureguizar, A J; Solari, A; Cortés, F; Milessi, A C; Militelli, M I; Camiolo, M D; Luz Clara, M; García, M

    2016-07-01

    The fish diversity and the main environmental factors affecting the spatial distribution of species, life history stages and community structure in the Río de la Plata (RdP) and adjacent waters are reviewed and analysed, with emphasis on the functional guild classification. The functional guild classification indicated that most species in the RdP were marine stragglers, zoobenthivores and oviparous species, although the biomass was dominated by estuarine species. Salinity had a stronger influence than temperature on the spatial pattern for all life stages, shallower and fresher waters are the preferred habitats of neonates and juveniles. During the breeding season (spring-summer), adults showed an intrusion into the inner part of RdP or to its adjacent nearshore waters from the offshore waters for spawning or mating, respectively. Variations in river discharge and wind patterns greatly affected the spatial extent of estuarine water, which ultimately influenced the domain of the main life-history stages (juveniles or adults) for both marine and estuarine fishes, as well as species and fish assemblage composition. The strong environmental gradient restricts some species and life-history stages to a particular section and defines three main fish assemblage areas. The composition of the fish assemblage is indicative of the recruitment of freshwater and marine species to the estuary in opposite ways, determined by the vertical stratification. Seasonal changes in the species composition were related to migration as a result of salinity and temperature variations and reproductive migrations to spawning and mating areas. This overview reveals that the RdP is under environmental variations that are likely to produce modifications to fish distribution and abundance that affect its fisheries. This context plus fish stock declines and changes in exploitation patterns could amplify the magnitude of the variations in the fisheries resources availability and affect the

  17. Characteristics of the δ ^{15} N_{NO_3 } distribution and its drivers in the Changjiang River estuary and adjacent waters

    NASA Astrophysics Data System (ADS)

    Wang, Wentao; Yu, Zhiming; Song, Xiuxian; Wu, Zaixing; Yuan, Yongquan; Zhou, Peng; Cao, Xihua

    2016-05-01

    In this study, we conducted investigations in the Changjiang (Yangtze) River estuary and adjacent waters (CREAW) in June and November of 2014. We collected water samples from different depths to analyze the nitrogen isotopic compositions of nitrate, nutrient concentrations (including inorganic N, P, and Si), and other physical and biological parameters, along with the vertical distribution and seasonal variations of these parameters. The compositions of nitrogen isotope in nitrate were measured with the denitrifier method. Results show that the Changjiang River diluted water (CDW) was the main factor aff ecting the shallow waters (above 10 m) of the CREAW, and CDW tended to influence the northern areas in June and the southern areas in November. δ ^{15} N_{NO_3 } values in CDW ranged from 3.21‰-3.55‰. In contrast, the deep waters (below 30 m) were aff ected by the subsurface water of the Kuroshio Current, which intruded into the waters near 31°N in June. The δ ^{15} N_{NO_3 } values of these waters were 6.03‰-7.6‰, slightly higher than the values of the Kuroshio Current. Nitrate assimilation by phytoplankton in the shallow waters of the study area varied seasonally. Because of the favorable temperature and nutrient conditions in June, abundant phytoplankton growth resulted in harmful algae blooms (HABs). Therefore, nitrate assimilation was strong in June and weak in November. The δ ^{15} N_{NO_3 } fractionations caused by assimilation of phytoplankton were 4.57‰ and 4.41‰ in the shallow waters in June and November, respectively. These results are consistent with previous laboratory cultures and in situ investigations. Nitrification processes were observed in some deep waters of the study area, and they were more apparent in November than in June. The fractionation values of nitrification ranged from 24‰-25‰, which agrees with results for Nitrosospira tenuis reported by previous studies.

  18. Coprostanol as a potential tracer of particulate sewage effluent to shelf waters adjacent to the Chesapeake Bay

    NASA Technical Reports Server (NTRS)

    Brown, R. C.; Wade, T. L.

    1981-01-01

    Samples were collected in the Chesapeake Bay entrance and contiguous shelf waters and were subsequently analyzed for particulate coprostanol and cholesterol concentrations. Surface coprostanol concentrations were fairly uniform, with a slight increase with depth. This increase with depth may be due to sewage-associated particulates settling as they leave the Bay, or the resuspension of contaminated sediment. Preliminary findings indicate sewage-associated materials are being transported from the Chesapeake Bay to shelf waters, where they may have a detrimental affect on living marine resources.

  19. An interdisciplinary study of the estuarine and coastal oceanography of Block Island Sound and adjacent New York coastal waters

    NASA Technical Reports Server (NTRS)

    Yost, E. F. (Principal Investigator); Hollman, R.; Alexander, J.; Nuzzi, R.

    1974-01-01

    The author has identified the following significant results. Photo-optical additive color quantitative measurements were made of ERTS-1 reprocessed positives of New York Bight and Block Island Sound. Regression of these data on almost simultaneous ship sample data of water's physical, chemical, biological, and optical properties showed that ERTS bands 5 and 6 can be used to predict the absolute value of the total number of particles and bands 4 and 5 to predict the relative extinction coefficient in New York Bight. Water masses and mixing patterns in Block Island Sound heretofore considered transient were found to be persistent phenomena requiring revision of existing mathematical and hydraulic models.

  20. Disulfuric acid dissociated by two water molecules: ab initio and density functional theory calculations.

    PubMed

    Kim, Seong Kyu; Lee, Han Myoung; Kim, Kwang S

    2015-11-21

    We have studied geometries, energies and vibrational spectra of disulfuric acid (H2S2O7) and its anion (HS2O7(-)) hydrated by a few water molecules, using density functional theory (M062X) and ab initio theory (SCS-MP2 and CCSD(T)). The most noteworthy result is found in H2S2O7(H2O)2 in which the lowest energy conformer shows deprotonated H2S2O7. Thus, H2S2O7 requires only two water molecules, the fewest number of water molecules for deprotonation among various hydrated monomeric acids reported so far. Even the second deprotonation of the first deprotonated species HS2O7(-) needs only four water molecules. The deprotonation is supported by vibration spectra, in which acid O-H stretching peaks disappear and specific three O-H stretching peaks for H3O(+) (eigen structure) appear. We have also kept track of variations in several geometrical parameters, atomic charges, and hybrid orbital characters upon addition of water. As the number of water molecules added increases, the S-O bond weakens in the case of H2S2O7, but strengthens in the case of HS2O7(-). It implies that the decomposition leading to H2SO4 and SO3 hardly occurs prior to the 2nd deprotonation at low temperatures. PMID:26400266

  1. Whales, Dolphins, and Porpoises of the Eastern North Pacific and Adjacent Arctic Waters: A Guide to Their Identification.

    ERIC Educational Resources Information Center

    Leatherwood, Stephen; And Others

    This field guide is designed to permit observers to identify the cetaceans (whales, dolphins, and porpoises) they see in the waters of the eastern North Pacific, including the Gulf of California, Hawaii, and the western Arctic of North America. The animals described are grouped not by scientific relationships but by similarities in appearance in…

  2. 33 CFR 334.420 - Pamlico Sound and adjacent waters, N.C.; danger zones for Marine Corps operations.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...) Bombing and rocket firing area in Pamlico Sound in vicinity of Brant Island—(1) The area. The waters.... Upon being so warned vessels working in the area shall leave the area immediately. (b) Bombing, rocket... regulations. (i) The area described in paragraph (b)(1) of this section will be used as bombing, rocket...

  3. 33 CFR 334.420 - Pamlico Sound and adjacent waters, N.C.; danger zones for Marine Corps operations.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...) Bombing and rocket firing area in Pamlico Sound in vicinity of Brant Island—(1) The area. The waters.... Upon being so warned vessels working in the area shall leave the area immediately. (b) Bombing, rocket... regulations. (i) The area described in paragraph (b)(1) of this section will be used as bombing, rocket...

  4. 33 CFR 334.420 - Pamlico Sound and adjacent waters, N.C.; danger zones for Marine Corps operations.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...) Bombing and rocket firing area in Pamlico Sound in vicinity of Brant Island—(1) The area. The waters.... Upon being so warned vessels working in the area shall leave the area immediately. (b) Bombing, rocket... regulations. (i) The area described in paragraph (b)(1) of this section will be used as bombing, rocket...

  5. WATER-ROCK INTERACTIONS INFLUENCING MERCURY FATE AND TRANSPORT FROM AN ABANDONED MINE SITE TO AN ADJACENT AQUATIC ECOSYSTEM

    EPA Science Inventory

    Clear Lake, located 150 km north of San Francisco, is one of the largest fresh water lakes in California and is an important economic resource for the region. Elevated mercury levels in fish in Clear Lake were identified in the late 1970s, resulting in a fish consumption advisor...

  6. A study of the estuarine and coastal oceanography of Block Island Sound and adjacent New York coastal waters

    NASA Technical Reports Server (NTRS)

    Yost, E. (Principal Investigator)

    1972-01-01

    There are no author-identified significant results in this report. ERTS-1 imagery was received from NASA in both positive and negative form. This imagery was analyzed to determine the hydrologic features of the water mass, including current patterns, particulate in suspension, and the contacts between different water masses, as well as coastal marsh characteristics. A Spectral Data Model 64 multispectral projector/viewer was used for the analysis. Quick look analysis of the second generation negatives indicated that: (1) green spectral band lacked contrast and was overexposed; (2) red spectral had acceptable contrast, but somewhat overexposed; and (3) infrared bands overexposed for land areas, but exposure good for water. Analysis of second generation positives indicated that; (1) green spectral band extremely flat; (2) red spectral band of acceptable contrast, but too dense for projection; and (3) infrared bands lacked detail in both water and land areas. Photographs indicate that it is necessary to expose and process the multispectral imagery for the scene brightness range under consideration.

  7. Auger spectrum of a water molecule after single and double core ionization

    SciTech Connect

    Inhester, L.; Burmeister, C. F.; Groenhof, G.; Grubmueller, H.

    2012-04-14

    The high intensity of free electron lasers opens up the possibility to perform single-shot molecule scattering experiments. However, even for small molecules, radiation damage induced by absorption of high intense x-ray radiation is not yet fully understood. One of the striking effects which occurs under intense x-ray illumination is the creation of double core ionized molecules in considerable quantity. To provide insight into this process, we have studied the dynamics of water molecules in single and double core ionized states by means of electronic transition rate calculations and ab initio molecular dynamics (MD) simulations. From the MD trajectories, photoionization and Auger transition rates were computed based on electronic continuum wavefunctions obtained by explicit integration of the coupled radial Schroedinger equations. These rates served to solve the master equations for the populations of the relevant electronic states. To account for the nuclear dynamics during the core hole lifetime, the calculated electron emission spectra for different molecular geometries were incoherently accumulated according to the obtained time-dependent populations, thus neglecting possible interference effects between different decay pathways. We find that, in contrast to the single core ionized water molecule, the nuclear dynamics for the double core ionized water molecule during the core hole lifetime leaves a clear fingerprint in the resulting electron emission spectra. The lifetime of the double core ionized water was found to be significantly shorter than half of the single core hole lifetime.

  8. Fast phase transition of water molecules in a defective carbon nanotube under an electric field

    NASA Astrophysics Data System (ADS)

    Meng, Xianwen; Huang, Jiping

    2016-02-01

    We utilize molecular dynamics simulations to study the effect of an electric field on the permeation of water molecules through a defective single-walled carbon nanotube (DSWCNT). Compared with a perfect single-walled carbon nanotube (PSWCNT), the behaviors of water molecules respond more quickly under the same electric field in a DSWCNT. Wet-dry phase transition of water molecules occurs when the electric field reaches 0.32 V/nm, which is much lower than the case of the PSWCNT. Besides, the critical electric field is affected by the number of defects. These results pave a way for designing fast wet-dry transition devices and provide a new insight into water permeation through a defective nanochannel.

  9. Vibrational states of a water molecule in a nano-cavity of beryl crystal lattice

    NASA Astrophysics Data System (ADS)

    Zhukova, Elena S.; Torgashev, Victor I.; Gorshunov, Boris P.; Lebedev, Vladimir V.; Shakurov, Gil'man S.; Kremer, Reinhard K.; Pestrjakov, Efim V.; Thomas, Victor G.; Fursenko, Dimitry A.; Prokhorov, Anatoly S.; Dressel, Martin

    2014-06-01

    Low-energy excitations of a single water molecule are studied when confined within a nano-size cavity formed by the ionic crystal lattice. Optical spectra are measured of manganese doped beryl single crystal Mn:Be3Al2Si6O18, that contains water molecules individually isolated in 0.51 nm diameter voids within the crystal lattice. Two types of orientation are distinguished: water-I molecules have their dipole moments aligned perpendicular to the c axis and dipole moments of water-II molecules are parallel to the c-axis. The optical conductivity σ(ν) and permittivity ɛ'(ν) spectra are recorded in terahertz and infrared ranges, at frequencies from several wavenumbers up to ν = 7000 cm-1, at temperatures 5-300 K and for two polarizations, when the electric vector E of the radiation is parallel and perpendicular to the c-axis. Comparative experiments on as-grown and on dehydrated samples allow to identify the spectra of σ(ν) and ɛ'(ν) caused exclusively by water molecules. In the infrared range, well-known internal modes ν1, ν2, and ν3 of the H2O molecule are observed for both polarizations, indicating the presence of water-I and water-II molecules in the crystal. Spectra recorded below 1000 cm-1 reveal a rich set of highly anisotropic features in the low-energy response of H2O molecule in a crystalline nano-cavity. While for E∥c only two absorption peaks are detected, at ˜90 cm-1 and ˜160 cm-1, several absorption bands are discovered for E⊥c, each consisting of narrower resonances. The bands are assigned to librational (400-500 cm-1) and translational (150-200 cm-1) vibrations of water-I molecule that is weakly coupled to the nano-cavity "walls." A model is presented that explains the "fine structure" of the bands by a splitting of the energy levels due to quantum tunneling between the minima in a six-well potential relief felt by a molecule within the cavity.

  10. Ground-water quality and discharge to Chincoteague and Sinepuxent Bays adjacent to Assateague Island National Seashore, Maryland

    USGS Publications Warehouse

    Dillow, Jonathan J.A.; Banks, William S.L.; Smigaj, Michael J.

    2002-01-01

    The U.S. Geological Survey, in cooperation with the Maryland Department of the Environment and the Wisconsin State Laboratory of Hygiene, conducted a study to characterize the occurrence and distribution of viral contamination in small (withdrawing less than 10,000 gallons per day) public water-supply wells screened in the shallow aquifer in the Piedmont Physiographic Province in Baltimore and Harford Counties, Maryland. Two hundred sixty-three small public water-supply wells were in operation in these counties during the spring of 2000. Ninety-one of these sites were selected for sampling using a methodology that distributed the samples evenly over the population and the spatial extent of the study area. Each site, and its potential susceptibility to microbiological contamination, was evaluated with regard to hole depth, casing interval, and open interval. Each site was evaluated using characteristics such as on-site geology and on-site land use.Samples were collected by pumping between 200 and 400 gallons of untreated well water through an electropositive cartridge filter. Water concentrates were subjected to cell-culture assay for the detection of culturable viruses and reverse-transcription polymerase chain reaction/gene probe assays to detect viral ribonucleic acid; grab samples were analyzed for somatic and male-specific coliphages, Bacteroides fragilis, Clostridium perfringens, enterococci, Escherichia coli, total coliforms, total oxidized nitrogen, nitrite, organic nitrogen, total phosphate, ortho-phosphate, calcium, magnesium, sodium, potas-sium, chloride, sulfate, iron, acid-neutralizing capacity, pH, specific conductance, temperature, and dissolved oxygen.One sample tested positive for the presence of the ribonucleic acid of rotavirus through poly-merase chain-reaction analysis. Twenty-nine per-cent of the samples (26 of 90) had bacterial con-tamination. About 7 percent of the samples (6 of 90) were contaminated with either male-specific coliphage

  11. Water and Small-Molecule Permeation of Dormant Bacillus subtilis Spores

    PubMed Central

    Cermak, Nathan; Feijó Delgado, Francisco; Setlow, Barbara; Setlow, Peter

    2015-01-01

    ABSTRACT We use a suspended microchannel resonator to characterize the water and small-molecule permeability of Bacillus subtilis spores based on spores' buoyant mass in different solutions. Consistent with previous results, we found that the spore coat is not a significant barrier to small molecules, and the extent to which small molecules may enter the spore is size dependent. We have developed a method to directly observe the exchange kinetics of intraspore water with deuterium oxide, and we applied this method to wild-type spores and a panel of congenic mutants with deficiencies in the assembly or structure of the coat. Compared to wild-type spores, which exchange in approximately 1 s, several coat mutant spores were found to have relatively high water permeability with exchange times below the ∼200-ms temporal resolution of our assay. In addition, we found that the water permeability of the spore correlates with the ability of spores to germinate with dodecylamine and with the ability of TbCl3 to inhibit germination with l-valine. These results suggest that the structure of the coat may be necessary for maintaining low water permeability. IMPORTANCE Spores of Bacillus species cause food spoilage and disease and are extremely resistant to standard decontamination methods. This hardiness is partly due to spores' extremely low permeability to chemicals, including water. We present a method to directly monitor the uptake of molecules into B. subtilis spores by weighing spores in fluid. The results demonstrate the exchange of core water with subsecond resolution and show a correlation between water permeability and the rate at which small molecules can initiate or inhibit germination in coat-damaged spores. The ability to directly measure the uptake of molecules in the context of spores with known structural or genetic deficiencies is expected to provide insight into the determinants of spores' extreme resistance. PMID:26483518

  12. Hydroxyl and water molecule orientations in trypsin: Comparison to molecular dynamics structures

    SciTech Connect

    McDowell, R.S.; Kossiakoff, A.A.

    1994-12-31

    A comparison is presented of experimentally observed hydroxyl and water hydrogens in trypsin determined from neutron density maps with the results of a 140ps molecular dynamics (MD) simulation. Experimental determination of hydrogen and deuterium atom positions in molecules as large as proteins is a unique capability of neutron diffraction. The comparison addresses the degree to which a standard force-field approach can adequately describe the local electrostatic and van der Waals forces that determine the orientations of these hydrogens. Neutron densities, derived from 2.1{Angstrom} D{sub 2}O-H{sub 2}O difference Fourier maps, provide a database of 27 well-ordered hydroxyl hydrogens. Most of the simulated hydroxyl orientations are within a standard deviation of the experimentally-observed positions, including several examples in which both the simulation and the neutron density indicate that a hydroxyl group is shifted from a {open_quote}standard{close_quote} rotamer. For the most highly ordered water molecules, the hydrogen distributions calculated from the trajectory were in good agreement with neutron density; simulated water molecules that displayed multiple hydrogen bonding networks had correspondingly broadened neutron density profiles. This comparison was facilitated by development of a method to construct a pseudo 2{Angstrom} density map based on the hydrogen atom distributions from the simulation. The degree of disorder of internal water molecules is shown to result primarily from the electrostatic environment surrounding that water molecule as opposed to the cavity size available to the molecule. A method is presented for comparing the discrete observations sampled in a dynamics trajectory with the time- averaged data obtained from X-ray or neutron diffraction studies. This method is particularly useful for statically-disordered water molecules, in which the average location assigned from a trajectory may represent a site of relatively low occupancy.

  13. An interdisciplinary study of the estaurine and coastal oceanography of Block Island Sound and adjacent New York coastal waters

    NASA Technical Reports Server (NTRS)

    Yost, E.; Hollman, R.; Alexander, J.; Nuzzi, R.

    1974-01-01

    ERTS-1 photographic data products have been analyzed using additive color viewing and electronic image analysis techniques. Satellite data were compared to water sample data collected simultaneously with the data of ERTS-1 coverage in New York Bight. Prediction of the absolute value of total suspended particles can be made using composites of positives of MSS bands 5 and 6 which have been precisely made using the step wedge supplied on the imagery. Predictions of the relative value of the extinction coefficient can be made using bands 4 and 5. Thematic charts of total suspended particles (particles per litre) and extinction coefficient provide scientists conducting state and federal water sampling programs in New York Bight with data which improves the performance of these programs.

  14. Improving protein-ligand docking with flexible interfacial water molecules using SWRosettaLigand.

    PubMed

    Li, Linqing; Xu, Weiwei; Lü, Qiang

    2015-11-01

    Computational protein-ligand docking is of great importance in drug discovery and design. Conformational changes greatly affect the results of protein-ligand docking, especially when water molecules take part in mediating protein ligand interactions or when large conformational changes are observed in the receptor backbone interface. We have developed an improved protocol, SWRosettaLigand, based on the RosettaLigand protocol. This approach incorporates the flexibility of interfacial water molecules and modeling of the interface of the receptor into the original RosettaLigand. In a coarse sampling step, SWRosettaLigand pre-optimizes the initial position of the water molecules, docks the ligand to the receptor with explicit water molecules, and minimizes the predicted structure with water molecules. The receptor backbone interface is treated as a loop and perturbed and refined by kinematic closure, or cyclic coordinate descent algorithm, with the presence of the ligand. In two cross-docking test sets, it was identified that for 8 out of 14, and 16 out of 22, test instances, the top-ranked structures by SWRosettaLigand achieved better accuracy than other protocols. PMID:26515196

  15. Water molecules inside protein structure affect binding of monosaccharides with HIV-1 antibody 2G12.

    PubMed

    Ueno-Noto, Kaori; Takano, Keiko

    2016-10-01

    Water molecules inside biomolecules constitute integral parts of their structure and participate in the functions of the proteins. Some of the X-ray crystallographic data are insufficient for analyzing a series of ligand-protein complexes in the same condition. We theoretically investigated antibody binding abilities of saccharide ligands and the effects of the inner water molecules of ligand-antibody complexes. Classical molecular dynamics and quantum chemical simulations using a model with possible water molecules inside the protein were performed with saccharide ligands and Human Immunodeficiency Virus 1 neutralizing antibody 2G12 complexes to estimate how inner water molecules of the protein affect the dynamics of the complexes as well as the ligand-antibody interaction. Our results indicate the fact that d-fructose's strong affinity to the antibody was partly due to the good retentiveness of solvent water molecules of the ligand and its stability of the ligand's conformation and relative position in the active site. © 2016 Wiley Periodicals, Inc. PMID:27388036

  16. Enhanced permeation of single-file water molecules across a noncylindrical nanochannel

    NASA Astrophysics Data System (ADS)

    Meng, X. W.; Huang, J. P.

    2013-07-01

    We utilize molecular dynamics simulations to study the effect of noncylindrical shapes of a nanochannel (which are inspired from the shape of real biological water nanochannels) on the permeation of single-file water molecules across the nanochannel. Compared with the cylindrical shape that has been tremendously adopted in the literature, the noncylindrical shapes play a crucial role in enhancing water permeation. Remarkably, the maximal enhancement ratio reaches a value of 6.28 (enhancement behavior). Meanwhile, the enhancement becomes saturated when the volume of the noncylindrical shape continues to increase (saturation behavior). The analysis of average diffusivity of water molecules helps to reveal the mechanism underlying the two behaviors whereas Poiseuille's law fails to explain them. These results pave a way for designing high-flow nanochannels and provide insight into water permeation across biological water nanochannels.

  17. Formation of Organic Molecules and Water in Warm Disk Atmospheres

    NASA Astrophysics Data System (ADS)

    Najita, Joan R.; Ádámkovics, Máté; Glassgold, Alfred E.

    2011-12-01

    Observations from Spitzer and ground-based infrared spectroscopy reveal significant diversity in the molecular emission from the inner few AU of T Tauri disks. We explore theoretically the possible origin of this diversity by expanding on our earlier thermal-chemical model of disk atmospheres. We consider how variations in grain settling, X-ray irradiation, accretion-related mechanical heating, and the oxygen-to-carbon ratio can affect the thermal and chemical properties of the atmosphere at 0.25-40 AU. We find that these model parameters can account for many properties of the detected molecular emission. The column density of the warm (200-2000 K) molecular atmosphere is sensitive to grain settling and the efficiency of accretion-related heating, which may account, at least in part, for the large range in molecular emission fluxes that have been observed. The dependence of the atmospheric properties on the model parameters may also help to explain trends that have been reported in the literature between molecular emission strength and mid-infrared color, stellar accretion rate, and disk mass. We discuss whether some of the differences between our model results and the observations (e.g., for water) indicate a role for vertical transport and freezeout in the disk midplane. We also discuss how planetesimal formation in the outer disk (beyond the snowline) may imprint a chemical signature on the inner few AU of the disk and speculate on possible observational tracers of this process.

  18. Intracomplex {pi}-{pi} stacking interaction between adjacent phenanthroline molecules in complexes with rare-earth nitrates: Crystal and molecular structures of bis(1,10-Phenanthroline)trinitratoytterbium and bis(1,10-Phenanthroline)trinitratolanthanum

    SciTech Connect

    Sadikov, G. G. Antsyshkina, A. S.; Rodnikova, M. N.; Solonina, I. A.

    2009-01-15

    Crystals of the compounds Yb(NO{sub 3}){sub 3}(Phen){sub 2} and La(NO{sub 3}){sub 3}(Phen){sub 2} (Phen = 1,10-phenanthroline) are investigated using X-ray diffraction. It is established that there exist two different crystalline modifications: the main modification (phase 1) is characteristic of all members of the isostructural series, and the second modification (phase 2) is observed only for the Eu, Er, and Yb elements. It is assumed that the stability and universality of main phase 1 are associated with the occurrence of the nonbonded {pi}-{pi} stacking interactions between the adjacent phenanthroline ligands in the complexes. The indication of the interactions is a distortion of the planar shape of the Phen molecule (the folding of the metallocycle along the N-N line with a folding angle of 11{sup o}-13{sup o} and its 'boomerang' distortion). The assumption regarding the {pi}-{pi} stacking interaction is very consistent with the shape of the ellipsoids of atomic thermal vibrations, as well as with the data obtained from thermography and IR spectroscopy. An analysis of the structures of a number of rare-earth compounds has demonstrated that the intracomplex {pi}-{pi} stacking interactions directly contribute to the formation of supramolecular associates in the crystals, such as molecular dimers, supramolecules, chain and layered ensembles, and framework systems.

  19. Water-mediated influence of a crowded environment on internal vibrations of a protein molecule.

    PubMed

    Kuffel, Anna; Zielkiewicz, Jan

    2016-02-01

    The influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described. The cross-correlation function of the collective velocities of surface atoms of two proteins was decomposed into the Fourier series. The amplitude spectrum displays a peak at low frequencies. Also, the results of principal component analysis suggest that the close presence of an additional protein molecule influences the high-amplitude, low-frequency modes in the most prominent way. This part of the spectrum covers biologically important protein motions. The neighbor-induced changes in the inner dynamics of the protein may be connected with the changes in the velocity power spectrum of interfacial water. The additional protein molecule changes the properties of solvation water and in this way it can influence the dynamics of the second protein. It is suggested that this phenomenon may be described, at first approximation, by a damped oscillator driven by an external random force. This model was successfully applied to conformationally rigid Choristoneura fumiferana antifreeze protein molecules. PMID:26805932

  20. Review of samples of sediment, tailings, and waters adjacent to the Cactus Queen gold mine, Kern County, California

    USGS Publications Warehouse

    Rytuba, James J.; Kim, Christopher S.; Goldstein, Daniel N.

    2011-01-01

    The Cactus Queen Mine is located in the western Mojave Desert in Kern County, California. The Cactus Queen gold-silver (Au-Ag) deposit is similar to other Au-Ag deposits hosted in Miocene volcanic rocks that consist of silicic domes and associated flows, pyroclastic rocks, and subvolcanic intrusions. The volcanic rocks were emplaced onto a basement of Mesozoic silicic intrusive rocks. A part of the Cactus Queen Mine is located on Federal land managed by the U.S. Bureau of Land Management (BLM). Staff from the BLM initially sampled the mine area and documented elevated concentrations of arsenic (As) in tailings and sediment. BLM then requested that the U.S. Geological Survey (USGS), in collaboration with Chapman University, measure and characterize As and other geochemical constituents in sediment, tailings, and waters on the part of the mine on Federal lands. This report is made in response to the request by the BLM, the lead agency mandated to conduct a Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) - Removal Site Investigation (RSI). The RSI applies to the potential removal of As-contaminated mine waste from the Cactus Queen Mine as a means of reducing As release and exposure to humans and biota. This report summarizes data obtained from field sampling of sediments, mine tailings, and surface waters at the Cactus Queen Mine on January 27, 2008. Our results provide a preliminary assessment of the sources of As and associated chemical constituents that could potentially impact humans and biota.

  1. Turnover and release of P-, N-, Si-nutrients in the Mexicali Valley (Mexico): interactions between the lower Colorado River and adjacent ground- and surface water systems.

    PubMed

    Orozco-Durán, A; Daesslé, L W; Camacho-Ibar, V F; Ortiz-Campos, E; Barth, J A C

    2015-04-15

    A study on dissolved nitrate, ammonium, phosphate and silicate concentrations was carried out in various water compartments (rivers, drains, channels, springs, wetland, groundwater, tidal floodplains and ocean water) in the Mexicali Valley and the Colorado River delta between 2012 and 2013, to assess modern potential nutrient sources into the marine system after river damming. While nitrate and silicate appear to have a significant input into the coastal ocean, phosphate is rapidly transformed into a particulate phase. Nitrate is, in general, rapidly bio-consumed in the surface waters rich in micro algae, but its excess (up to 2.02 mg L(-1) of N from NO3 in winter) in the Santa Clara Wetland represents a potential average annual source to the coast of 59.4×10(3)kg N-NO3. Despite such localized inputs, continuous regional groundwater flow does not appear to be a source of nitrate to the estuary and coastal ocean. Silicate is associated with groundwaters that are also geothermally influenced. A silicate receiving agricultural drain adjacent to the tidal floodplain had maximum silicate concentrations of 16.1 mg L(-1) Si-SiO2. Seepage of drain water and/or mixing with seawater during high spring tides represents a potential source of dissolved silicate and nitrate into the Gulf of California. PMID:25617998

  2. The influence of climate cycles on the water regime and carbonate profile in chernozems of Central European Russia and adjacent territories

    NASA Astrophysics Data System (ADS)

    Bazykina, G. S.; Ovechkin, S. V.

    2016-04-01

    The influence of long-term "dry" and "wet" climatic cycles on the water regime, hydrological parameters, and carbonate profiles of chernozems in Central European Russia and adjacent territories was studied. The hydrological and carbonate profiles were found to change during the wet cycle. However, the upper part of the hydrological profile is basically unchanging, whereas in its lower part, the number of hydrological horizons and contrast in their moistening decrease in the forest-steppe chernozems and increase in the steppe chernozems. The frequency of through wetting of chernozems increases during the wet cycles. The vertical lithological heterogeneity of the parent material affects the soil moisture status. In the wet climatic cycle, the moisture content above the lithological contact increases resulting in the development of the features of soil hydromorphism. In the carbonate profile, the character of pedofeatures is changing: some carbonate neoformations disappear, while the other ones develop. Possible variations of the periodically percolative water regime were revealed in chernozems. The classification of water regime proposed by A.A. Rode may be updated based on the data obtained during the dry climatic cycle. Rode's hypothesis about cyclic variations in the soil water regime is confirmed.

  3. Study of environmental isotope distribution in the Aswan High Dam Lake (Egypt) for estimation of evaporation of lake water and its recharge to adjacent groundwater.

    PubMed

    Aly, A I; Froehlich, K; Nada, A; Awad, M; Hamza, M; Salem, W M

    1993-03-01

    Oxygen-18 ((18)0) and deuterium isotopes were used to estimate the evaporation from the Aswan High Dam Lake and to investigate the inter-relation between the lake water and adjacent groundwater.According to stable isotopic analysis of samples taken in 1988 and 1989, the lake can be divided into two sections. In the first section extending between Abu Simbel and a point between EI-Alaki and Krosko, a remarkable vertical gradient of (18)0 and deuterium isotopic composition was observed. The second northern sector extending to the High Dam is characterised by a lower vertical isotopic gradient. In this sector in general, higher values of (18)O and deuterium contents were found at the top and lower values at the bottom. Also a strong horizontal increase of the heavy isotope content was observed. Thus, in the northern section evaporation is of dominating influence on the isotopic composition of the lake water.With the help of an evaporation pan experiment it was possible to calibrate the evaporative isotope enrichment in the lake and to facilitate a preliminary estimate of evaporative losses of lake water. The evaporation from the lake was estimated to be about 19% of the input water flow rate.The groundwater around the lake was investigated and samples from production wells and piezometers were subjected to isotopic analysis. The results indicate that recent recharge to the groundwater aquifer is limited to wells near to the lake and up to a maximum distance of about 10 km. The contribution of recent Nile water to the groundwater in these wells was estimated to range between 23 and 70%. Beyond this distance, palaeowater was observed with highly depleted deuterium and (18)0 contents, which was also confirmed by 14c dating. The age of palaeo groundwater in this area can reach values of more than 26,000 years.Recommendations are given for efficient water management of the lake water. PMID:24198080

  4. Rotation of water molecules in plastic phase at extreme conditions from first principles molecular dynamics method

    NASA Astrophysics Data System (ADS)

    Tasaka, Tomofumi; Tsumuraya, Kazuo

    2014-03-01

    Water has a variety of polymorphs in wide ranges of temperature and pressure. Ice VII phase transforms to ice X with increased pressure. However the ice VII transforms to a superionic phase at higher temperatures around 2000K and pressure 30GPa in which the protons migrate in the body centered cubic lattice of oxygens. The ice VII transforms into rotator phase (so called plastic phase at lower temperatures around 600K and 5 to 50GPa. The formation of the phase has been confirmed only with the empirical potentials, whereas the experimental confirmation has been postponed until now. The present study elucidates the mechanism of the rotation of the water molecules and the correlation between the molecules during the rotation with the first principles molecular dynamics method. The water molecules rotate around each oxygen atom to conserve the ice VII positions of the protons.

  5. Interaction of water molecules with hexagonal 2D systems. A DFT study

    NASA Astrophysics Data System (ADS)

    Rojas, Ángela; Rey, Rafael

    Over the years water sources have been contaminated with many chemical agents, becoming issues that affect health of the world population. The advances of the nanoscience and nanotechnology in the development new materials constitute an alternative for design molecular filters with great efficiencies and low cost for water treatment and purification. In the nanoscale, the process of filtration or separation of inorganic and organic pollutants from water requires to study interactions of these atoms or molecules with different nano-materials. Specifically, it is necessary to understand the role of these interactions in physical and chemical properties of the nano-materials. In this work, the main interest is to do a theoretical study of interaction between water molecules and 2D graphene-like systems, such as silicene (h-Si) or germanene (h-Ge). Using Density Functional Theory we calculate total energy curves as function of separation between of water molecules and 2D systems. Different spatial configurations of water molecules relative to 2D systems are considered. Structural relaxation effects and changes of electronic charge density also are reported. Universidad Nacional de Colombia.

  6. The formation of acid rain in the atmosphere, adjacent to the TTP with the joint-condensing of sulfur dioxide and water vapor

    NASA Astrophysics Data System (ADS)

    Gvozdyakov, D. V.; Gubin, V. E.; Matveeva, A. A.

    2014-08-01

    Presents the results of mathematical simulation of the condensation process of sulphur dioxide and water vapor on the condensation nuclei surface under the action of natural factors. Numerical investigations were carried out for the summer at a moderate speed of the wind. The influence of the parameter of condensation on the speed of the process of sulfuric acid drops formation in the air space was analyzed. Time ranges, sufficient for the formation of the acid rain sedimentation in the atmosphere, adjacent to the areas of thermal power station work were established. It is shown that the speed of air masses movement effects on the process of acid anthropogenic admixtures dispersion in the atmosphere. Approbation of the obtained results was carried out by checking the difference scheme conservative and solution of test problems.

  7. Solvation of a probe molecule by fluid supercooled water in a hydrogel at 200 K.

    PubMed

    Santangelo, Maria Grazia; Levantino, Matteo; Cupane, Antonio; Jeschke, Gunnar

    2008-12-11

    By combining electron paramagnetic resonance (EPR) measurements on a nitroxide probe and differential scanning calorimetry (DSC), we demonstrate existence of liquid supercooled water in a silica hydrogel with high hydration level down to temperatures of at least 198 K. Besides the major fraction of liquid supercooled water, a minor fraction crystallizes at about 236 K during cooling and melts at 246 K during heating. The liquid domains are of sufficient size to solvate the nearly spherical paramagnetic probe molecule TEMPO with a diameter of about 6 A. Analysis of EPR spectra provides the rotational correlation time of the probe that is further used to compare the viscosity of the supercooled water with the one of bulk water. In the temperature interval investigated, the supercooled water behaves as a fragile liquid and eventually solidifies at 120 K to a glass that incorporates the probe molecules. PMID:19053683

  8. Shear-stress-induced structural arrangement of water molecules in nanoscale Couette flow with slipping at wall boundary

    SciTech Connect

    Lin, Jau-Wen

    2014-08-07

    This study investigated the structuring of water molecules in a nanoscale Couette flow with the upper plate subjected to lateral forces with various magnitudes and water slipping against a metal wall. It was found that when the upper plate is subjected to a force, the water body deforms into a parallelepiped. Water molecules in the channel are then gradually arranged into lattice positions, creating a layered structure. The structural arrangement of water molecules is caused by the water molecules accommodating themselves to the increase in energy under the application of a lateral force on the moving plate. The ordering arrangement of water molecules increases the rotational degree of freedom, allowing the molecules to increase their Coulomb potential energy through polar rotation that accounts for the energy input through the upper plate. With a force continuously applied to the upper plate, the water molecules in contact with the upper plate move forward until slip between the water and upper plate occurs. The relation between the structural arrangement of water molecules, slip at the wall, and the shear force is studied. The relation between the slip and the locking/unlocking of water molecules to metal atoms is also studied.

  9. Evaluation of cracking in feedwater piping adjacent to the steam generators in Nine Pressurized Water Reactor Plants

    SciTech Connect

    Goldberg, A.; Streit, R.D.; Scott, R.G.

    1980-06-25

    Cracking in ASTM A106-B and A106-C feedwater piping was detected near the inlet to the steam generators in a number of pressurized water reactor plants. We received sections with cracks from nine of the plants with the objective of identifying the cracking mechanism and assessing various factors that might contribute to this cracking. Variations were observed in piping surface irregularities, corrosion-product, pit, and crack morphology, surface elmental and crystal structure analyses, and steel microstructures and mechanical properties. However, with but two exceptions, namely, arrest bands and major surface irregularities, we were unable to relate the extent of cracking to any of these factors. Tensile and fracture toughness (J/sub Ic/ and tearing modulus) properties were measured over a range of temperatures and strain rates. No unusual properties or microstructures were observed that could be related to the cracking problem. All crack surfaces contained thick oxide deposits and showed evidence of cyclic events in the form of arrest bands. Transmission electron microscopy revealed fatigue striations on replicas of cleaned crack surfaces from one plant and possibly from three others. Calculations based on the observed striation spacings gave a value of ..delta..sigma = 150 MPa (22 ksi) for one of the major cracks. The direction of crack propagation was invariably related to the piping surface and not to the piping axis. These two factors are consistent with the proposed concept of thermally induced, cyclic, tensile surface stresses. Although surface irregularities and corrosion pits were sources for crack initiation and corrosion may have contributed to crack propagation, it is proposed that the overriding factor in the cracking problem is the presence of unforeseen cyclic loads.

  10. Distribution and relative abundance of humpback whales in relation to environmental variables in coastal British Columbia and adjacent waters

    NASA Astrophysics Data System (ADS)

    Dalla Rosa, Luciano; Ford, John K. B.; Trites, Andrew W.

    2012-03-01

    Humpback whales are common in feeding areas off British Columbia (BC) from spring to fall, and are widely distributed along the coast. Climate change and the increase in population size of North Pacific humpback whales may lead to increased anthropogenic impact and require a better understanding of species-habitat relationships. We investigated the distribution and relative abundance of humpback whales in relation to environmental variables and processes in BC waters using GIS and generalized additive models (GAMs). Six non-systematic cetacean surveys were conducted between 2004 and 2006. Whale encounter rates and environmental variables (oceanographic and remote sensing data) were recorded along transects divided into 4 km segments. A combined 3-year model and individual year models (two surveys each) were fitted with the mgcv R package. Model selection was based primarily on GCV scores. The explained deviance of our models ranged from 39% for the 3-year model to 76% for the 2004 model. Humpback whales were strongly associated with latitude and bathymetric features, including depth, slope and distance to the 100-m isobath. Distance to sea-surface-temperature fronts and salinity (climatology) were also constantly selected by the models. The shapes of smooth functions estimated for variables based on chlorophyll concentration or net primary productivity with different temporal resolutions and time lags were not consistent, even though higher numbers of whales seemed to be associated with higher primary productivity for some models. These and other selected explanatory variables may reflect areas of higher biological productivity that favor top predators. Our study confirms the presence of at least three important regions for humpback whales along the BC coast: south Dixon Entrance, middle and southwestern Hecate Strait and the area between La Perouse Bank and the southern edge of Juan de Fuca Canyon.

  11. Nd isotopic composition and REE pattern in the surface waters of the eastern Indian Ocean and its adjacent seas

    SciTech Connect

    Amakawa, Hiroshi; Alibo, D.S.; Nozaki, Yoshiyuki

    2000-05-01

    The Nd isotopic composition and dissolved rare earth elements (REEs) have been measured in the surface waters along the 1996/97 R.V. Hakuho-Maru Expedition route from Tokyo to the Southern Ocean, southwest of Australia, through the Philippine and Indonesian Archipelago, the eastern Indian Ocean, the Bay of Bengal and the South China Sea. The radiogenic {epsilon}{sub Nd} values of {minus}1.3 and {minus}1.4 were found in the Sulu Sea and near the Lombok Strait, indicating the strong influence of surrounding volcanic islands, whereas non-radiogenic {epsilon}{sub Nd} values of less than {minus}10 were found in the Southern Ocean and the Bay of Bengal suggesting Nd of continental origin. The dissolved Nd concentrations also showed a wide range of variation from 2.8 to 19.6 pmol/kg and the trivalent REE patterns exhibited characteristic features that can be grouped into each different oceanic province. The geographical distribution of dissolved Nd is different from that of atmospherically derived {sup 210}Pb, but generally resembles that of coastally derived {sup 228}Ra. This strongly suggests that fluvial and coastal input predominates over eolian input for dissolved Nd in the surface ocean. However, the riverine dissolved Nd flux appears to be relatively minor, and remobilization of Nd from coastal and shelf sediments may play an important role in the total Nd input to the ocean. By modeling the distributions of the isotopic composition and concentration of Nd together with the activity ratio of {sup 228}Ra/{sup 226}Ra in the southeastern Indian Ocean, the authors estimate a mean residence time of Nd in the surface mixed layer to be 1.5--2.6 years. The short mean residence time is comparable with, or slightly longer than that of {sup 210}Pb suggesting similar chemical reactivity.

  12. Modeling the Physical and Biochemical Influence of Ocean Thermal Energy Conversion Plant Discharges into their Adjacent Waters

    SciTech Connect

    PAT GRANDELLI, P.E.; GREG ROCHELEAU; JOHN HAMRICK, Ph.D.; MATT CHURCH, Ph.D.; BRIAN POWELL, Ph.D.

    2012-09-29

    This paper describes the modeling work by Makai Ocean Engineering, Inc. to simulate the biochemical effects of of the nutrient-enhanced seawater plumes that are discharged by one or several 100 megawatt OTEC plants. The modeling is needed to properly design OTEC plants that can operate sustainably with acceptably low biological impact. In order to quantify the effect of discharge configuration and phytoplankton response, Makai Ocean Engineering implemented a biological and physical model for the waters surrounding O`ahu, Hawai`i, using the EPA-approved Environmental Fluid Dynamics Code (EFDC). Each EFDC grid cell was approximately 1 square kilometer by 20 meters deep, and used a time step of three hours. The biological model was set up to simulate the biochemical response for three classes of organisms: Picoplankton (< 2 um) such as prochlorococccus, nanoplankton (2-20 um), and microplankton (> 20 um) e.g., diatoms. The dynamic biological phytoplankton model was calibrated using chemical and biological data collected for the Hawaii Ocean Time Series (HOTS) project. Peer review of the biological modeling was performed. The physical oceanography model uses boundary conditions from a surrounding Hawai'i Regional Ocean Model, (ROM) operated by the University of Hawai`i and the National Atmospheric and Oceanic Administration. The ROM provided tides, basin scale circulation, mesoscale variability, and atmospheric forcing into the edges of the EFDC computational domain. This model is the most accurate and sophisticated Hawai'ian Regional Ocean Model presently available, assimilating real-time oceanographic observations, as well as model calibration based upon temperature, current and salinity data collected during 2010 near the simulated OTEC site. The ROM program manager peer-reviewed Makai's implementation of the ROM output into our EFDC model. The supporting oceanographic data was collected for a Naval Facilities Engineering Command / Makai project. Results: The model

  13. Dynamics of water molecules adsorbed by silica and resin SGK-7

    NASA Astrophysics Data System (ADS)

    Lisichkin, Yu. V.; Sakharova, L. A.; Tumanov, A. A.

    2014-01-01

    This paper has presented neutron spectroscopy data on the dynamics of light water molecules adsorbed in the cation exchanger (ion-exchange resin) SGK-7 and on the surface of aerosils (highly dispersed pyrogenic silica) with different levels of hydration. The measurements have been performed on a DIN-2PI spectrometer (Frank Laboratory of Neutron Physics of the Joint Institute for Nuclear Research, Dubna, Russia). The characteristics of the diffusive and vibrational motions of adsorbed water molecules have been determined from the experimental neutron scattering spectra. The data obtained in the quasi-elastic neutron scattering region have been analyzed using a model accounting for the effects of restricted translational and rotational diffusion. The results have demonstrated a significant decrease in the diffusion mobility of adsorbed water molecules as compared to conventional (bulk) water. In particular, the self-diffusion coefficient decreases several times, and the diffusion rate is the lower, the smaller is the thickness of the hydration layer. The dependences of the intensity and half-width of the quasi-elastic scattering peak on the magnitude of the neutron momentum transfer q in the scattering process exhibit a nonmonotonic character. This indicates manifestation of the effects of restricted translational diffusion, rotational diffusion, and jump diffusion. The partial distributions of vibrational frequencies of hydrogen atoms of water molecules adsorbed by the cation exchanger and aerosils have been obtained from the inelastic neutron scattering data.

  14. Local lateral environment of the molecules at the surface of DMSO-water mixtures.

    PubMed

    Fábián, Balázs; Idrissi, Abdenacer; Marekha, Bogdan; Jedlovszky, Pál

    2016-10-12

    Molecular dynamics simulations of the liquid-vapour interface of dimethyl sulphoxide (DMSO)-water mixtures of 11 different compositions, including two neat systems are performed on the canonical (N, V, T) ensemble at 298 K. The molecules constituting the surface layer of these systems are selected by means of the identification of the truly interfacial molecules (ITIM) method, and their local lateral environment at the liquid surface is investigated by performing Voronoi analysis. The obtained results reveal that both molecules prefer to be in a mixed local environment, consisting of both kinds of molecules, at the liquid surface, and this preference is even stronger here than in the bulk liquid phase. Neat-like patches, in which a molecule is surrounded by like neighbours, are not found. However, vacancies that are surrounded solely by water molecules are observed at the liquid surface. Our results show that strongly hydrogen bonded DMSO·H2O complexes, known to exist in the bulk phase of these mixtures, are absent from the liquid surface. PMID:27506283

  15. An ab initio molecular dynamics study on hydrogen bonds between water molecules

    NASA Astrophysics Data System (ADS)

    Pan, Zhang; Chen, Jing; Lü, Gang; Geng, Yi-Zhao; Zhang, Hui; Ji, Qing

    2012-04-01

    The quantitative estimation of the total interaction energy of a molecular system containing hydrogen bonds (H bonds) depends largely on how to identify H bonding. The conventional geometric criteria of H bonding are simple and convenient in application, but a certain amount of non-H bonding cases are also identified as H bonding. In order to investigate the wrong identification, we carry out a systematic calculation on the interaction energy of two water molecules at various orientation angles and distances using ab initio molecular dynamics method with the dispersion correction for the Becke-Lee-Yang-Parr (BLYP) functionals. It is shown that, at many orientation angles and distances, the interaction energies of the two water molecules exceed the energy criterion of the H bond, but they are still identified as H-bonded by the conventional "distance-angle" criteria. It is found that in these non-H bonding cases the wrong identification is mainly caused by short-range interaction between the two neighbouring water molecules. We thus propose that, in addition to the conventional distance and angle criteria of H bonding, the distance dHṡṡṡH between the two neighbouring hydrogen atoms of the two water molecules should also be taken as a criterion, and the distance rOṡṡṡH between the hydrogen atom of the H-bond donor molecule and the oxygen atom of the acceptor molecule should be restricted by a lower limit. When dHṡṡṡH and rOṡṡṡH are small (e.g., dHṡṡṡH < 2.0 Å and rOṡṡṡH < 1.62 Å), the repulsion between the two neighbouring atoms increases the total energy of the two water molecules dramatically and apparently weakens the binding of the water dimer. A statistical analysis and comparison of the numbers of the H bonds identified by using different criteria have been conducted on a Car-Parrinello ab initio molecular dynamics simulation with dispersion correction for a system of 64 water molecules at near-ambient temperature. They

  16. DFTr optimization and DFTr-MD studies of glucose, ten explicit water molecules enclosed by an implicit solvent, COSMO

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DFTr optimization studies are carried out on alpha/beta-glucose surrounded by ten explicit water molecules and the glucose/water super-molecule completely enclosed by an implicit solvation model, COSMO. Twenty one starting configurations of the explicit waters were first optimized empirically with t...

  17. Distribution and ecological risk assessment of polycyclic aromatic hydrocarbons in water, suspended particulate matter and sediment from Daliao River estuary and the adjacent area, China.

    PubMed

    Zheng, Binghui; Wang, Liping; Lei, Kun; Nan, Bingxu

    2016-04-01

    Polycyclic aromatic hydrocarbons (PAHs) contamination was investigated in concurrently sampled surface water, suspended particulate matter (SPM) and sediment of Daliao River estuary and the adjacent area, China. The total concentrations of PAHs ranged from 71.12 to 4255.43 ng/L in water, from 1969.95 to 11612.21 ng/L in SPM, and from 374.84 to 11588.85 ng/g dry weight (dw) in sediment. Although the 2-3 ring PAHs were main PAH congeners in water and SPM, the 4-6 ring PAHs were also detected and their distribution was site-specific, indicating a very recent PAHs input around the area since they were hydrophobic. The PAHs pollution was identified as mixed combustion and petroleum sources. Based on species sensitivity distribution (SSD), the ecological risk in SPM from 82% stations was found to be higher obviously than that in water. The risk in water was basically ranked as medium, while the risk in SPM was ranked as high. Analysis with sediment quality guidelines (SQGs) indicated that negative eco-risk occasionally occurred in about 50% stations, while negative eco-risk frequently occurred in about 3% stations only caused by Phenanthrene(Phe) and Dibenzo(a,h)anthracene(DBA). Here freshwater acute effects data together with saltwater data were used for SSD model. And this method could quickly give the rational risk information, and achieved our objective that compared the spatial difference of risk levels among three compartments. The results confirmed that the use of freshwater acute effects data from the ECOTOX database together with saltwater effects data is acceptable for risk assessment purposes in estuary. PMID:26855211

  18. Chemically accurate energy barriers of small gas molecules moving through hexagonal water rings.

    PubMed

    Hjertenæs, Eirik; Trinh, Thuat T; Koch, Henrik

    2016-07-21

    We present chemically accurate potential energy curves of CH4, CO2 and H2 moving through hexagonal water rings, calculated by CCSD(T)/aug-cc-pVTZ with counterpoise correction. The barriers are extracted from a potential energy surface obtained by allowing the water ring to expand while the gas molecule diffuses through. State-of-the-art XC-functionals are evaluated against the CCSD(T) potential energy surface. PMID:27345929

  19. Structure of hydrated clusters of dibenzo-18-crown-6-ether in a supersonic jet--encapsulation of water molecules in the crown cavity.

    PubMed

    Kusaka, Ryoji; Inokuchi, Yoshiya; Ebata, Takayuki

    2008-11-01

    The structure of dibenzo-18-crown-6-ether (DB18C6) and its hydrated clusters has been investigated in a supersonic jet. Two conformers of bare DB18C6 and six hydrated clusters (DB18C6-(H(2)O)(n)) were identified by laser-induced fluorescence, fluorescence-detected UV-UV hole-burning and IR-UV double-resonance spectroscopy. The IR-UV double resonance spectra were compared with the IR spectra obtained by quantum chemical calculations at the B3LYP/6-31+G* level. The two conformers of bare DB18C6 are assigned to "boat" and "chair I" forms, respectively, among which the boat form is dominant. All the six DB18C6-(H(2)O)(n) clusters with n = 1-4 have a boat conformation in the DB18C6 part. The water molecules form a variety of hydration networks in the boat-DB18C6 cavity. In DB18C6-(H(2)O)(1), a water molecule forms the bidentate hydrogen bond with the O atoms adjacent to the benzene rings. In this cluster, the water molecule is preferentially hydrogen bonded from the bottom of boat-DB18C6. In the larger clusters, the hydration networks are developed on the basis of the DB18C6-(H(2)O)(1) cluster. PMID:18936847

  20. Theoretical study of the decomposition of formamide in the presence of water molecules.

    PubMed

    Nguyen, Vinh Son; Orlando, Thomas M; Leszczynski, Jerzy; Nguyen, Minh Tho

    2013-03-28

    Formamide (NH2CHO, FM) has been considered an active key precursor in prebiotic chemistry on early Earth. Under certain conditions such as dry lagoons, FM can decompose to produce reactants that lead to formation of more complex biomolecules. Specifically, FM decomposition follows many reactive channels producing small molecules such as H2, CO, H2O, HCN, HNC, NH3, and HNCO with comparable energy barriers in the range of 73-82 kcal/mol. Due to the likely presence of water on prebiotic Earth and the intrinsic presence of water following FM decomposition, we explore the effects of water oligomers, (H2O)n with n = 1-3, on its dehydration, dehydrogenation, and decarbonylation reactions using quantum chemical computations. Geometries are optimized using MP2/aug-cc-pVxZ calculations (x = D,T), and relative energies are evaluated using coupled-cluster theory CCSD(T) with the aug-cc-pVxZ basis sets (x = D, T, Q). Where possible the coupled-cluster energies are extrapolated to the complete basis set limit (CBS). Water classically acts as an efficient bifunctional catalyst for decomposition. With the presence of one water molecule, the dehydration pathway leading to HCN is favored. When two and three water molecules are involved, dehydration remains energetically favored over other channels and attains an energy barrier of ~30 kcal/mol. PMID:23461351

  1. Temperature dependence of the transport of single-file water molecules through a hydrophobic channel.

    PubMed

    Su, Jiaye; Yang, Keda

    2016-05-01

    Although great effort has been made on the transport properties of water molecules through nanometer channels, our understanding on the effect of some basic parameters are still rather poor. In this article, we use molecular dynamics simulations to study the temperature effect on the transport of single-file water molecules through a hydrophobic channel. Of particular interest is that the water flow and average translocation time both exhibit exponential relations with the temperature. Based on the continuous-time random-walk model and Arrhenius equation, we explore some new physical insights on these exponential behaviors. With the increase of temperature, the water dipoles flip more frequently, since the estimated flipping barrier is less than 2 kB T. Specifically, the flipping frequency also shows an exponential relation with the temperature. Furthermore, the water-water interaction and water occupancy demonstrate linear relations with the temperature, and the water density profiles along the channel axis can be slightly affected by the temperature. These results not only enhance our knowledge about the temperature effect on the single-file water transport, but also have potential implications for the design of controllable nanofluidic machines. © 2016 Wiley Periodicals, Inc. PMID:26777386

  2. The Dynamics, energetics and selectivity of water chain-containing aquapores created by the self-assembly of aquafoldamer molecules.

    PubMed

    Ma, Wenliang; Wang, Chunquan; Li, Juntong; Zhang, Kun; Lu, Yu-Jing; Huo, Yanping; Zeng, Huaqiang

    2015-11-21

    Through a series of crystallographic snapshots of water chain-containing aquapores formed from numerous one-dimensionally aligned aquafoldamer molecules 2, we demonstrated here (1) a preferential recognition of the water molecules over methanol molecules by the assembled cavity-containing aquapores with a selectivity factor of at least 17.7, (2) the dynamic nature of the water chains and the aquapores in response to varying external stimuli that exert the most influential impact on the aromatic π-π stacking in the aquapores and (3) the aquapores undergo a significant rearrangement in order to accommodate water, rather than methanol, molecules. PMID:26381358

  3. Effects of brush management on the hydrologic budget and water quality in and adjacent to Honey Creek State Natural Area, Comal County, Texas, 2001--10

    USGS Publications Warehouse

    Banta, J. Ryan; Slattery, Richard N.

    2012-01-01

    Woody vegetation, including ashe juniper (Juniperus ashei), has encroached on some areas in central Texas that were historically oak grassland savannah. Encroachment of woody vegetation is generally attributed to overgrazing and fire suppression. Removing the ashe juniper and allowing native grasses to reestablish in the area as a brush management conservation practice (hereinafter referred to as "brush management") might change the hydrology in the watershed. These hydrologic changes might include changes to surface-water runoff, evapotranspiration, or groundwater recharge. The U.S. Geological Survey (USGS), in cooperation with Federal, State, and local partners, examined the hydrologic effects of brush management in two adjacent watersheds in Comal County, Tex. Hydrologic data were collected in the watersheds for 3-4 years (pre-treatment) depending on the type of data, after which brush management occurred on one watershed (treatment watershed) and the other was left in its original condition (reference watershed). Hydrologic data were collected in the study area for another 6 years (post-treatment). These hydrologic data included rainfall, streamflow, evapotranspiration, and water quality. Groundwater recharge was not directly measured, but potential groundwater recharge was calculated by using a simplified mass balance approach. This fact sheet summarizes highlights of the study from the USGS Scientific Investigations Report on which it is based.

  4. Distributions of dissolved monosaccharides and polysaccharides in the surface microlayer and surface water of the Jiaozhou Bay and its adjacent area

    NASA Astrophysics Data System (ADS)

    Zhang, Yan-Ping; Yang, Gui-Peng; Lu, Xiao-Lan; Ding, Hai-Bing; Zhang, Hong-Hai

    2013-07-01

    Sea surface microlayer (SML) samples and corresponding bulk surface water (SW) samples were collected in the Jiaozhou Bay and its adjacent area in July and November 2008. The average concentrations of dissolved monosaccharides (MCHO) and polysaccharides (PCHO) revealed similar temporal variability, with higher concentrations during the green-tide period (in July) than during the non-green-tide period (in November). Average enrichment factors (EF) of MCHO and PCHO, defined as the ratio of the concentration in the SML to that in the SW, were 1.3 and 1.4 in July, respectively, while those values in November were 1.9 and 1.6. Our data also showed that the concentrations of MCHO and PCHO in the SML were strongly correlated with those in the SW, indicating that most of the organic materials in the SML came from the SW. The total dissolved carbohydrate concentrations (TDCHO) in the bulk surface water were closely correlated with salinity during the cruises (July: r=-0.580, n=18, P=0.01; November: r=-0.679, n=26, P<0.001), suggesting that riverine input had an important effect on the distribution of TDCHO in surface seawater of the study area.

  5. Trapped water molecule in the charge separation of a bacterial reaction center.

    PubMed

    Ivashin, Nikolai; Larsson, Sven

    2008-09-25

    Low-frequency oscillations in the absorption spectrum at 1020 nm, connected to the primary charge separation process in Rhodobacter sphaeroides, have been shown by Yakovlev et al. to be caused by rotational motion of an interstitial water molecule called "water-A". The same water molecule was shown by Potter et al. to increase the rate of charge separation by a factor of 8. We have carried out geometry optimization of water-A and its nearest atoms in the protein pocket, using density functional theory (DFT). There are strong hydrogen bonds to the axial imidazol group of the B part of the special pair (P=PAPB) and to the keto carbonyl group of ring V of the accessory chlorophyll (BA). Rotation of water-A is thus impossible in the electronic ground state. We have tried to support our speculations on other possible mechanisms by calculations. The P(+)BA(-) charge transfer state is stabilized by proton transfer from water-A and simultaneous proton transfer from the axial group of PB to water-A. After double proton transfer the hydrogen bond to the keto group disappears whereby a possibility opens up for almost free water rotation. The results therefore would explain the 32 cm(-1) oscillation of Yakovlev et al. The proposed mechanism assumes, however, that the general assumption that the activation energy disappears in the primary charge separation of bacterial photosynthesis, holds also for this special case. PMID:18761433

  6. Trapping and desorption of complex organic molecules in water at 20 K

    NASA Astrophysics Data System (ADS)

    Burke, Daren J.; Puletti, Fabrizio; Woods, Paul M.; Viti, Serena; Slater, Ben; Brown, Wendy A.

    2015-10-01

    The formation, chemical, and thermal processing of complex organic molecules (COMs) is currently a topic of much interest in interstellar chemistry. The isomers glycolaldehyde, methyl formate, and acetic acid are particularly important because of their role as pre-biotic species. It is becoming increasingly clear that many COMs are formed within interstellar ices which are dominated by water. Hence, the interaction of these species with water ice is crucially important in dictating their behaviour. Here, we present the first detailed comparative study of the adsorption and thermal processing of glycolaldehyde, methyl formate, and acetic acid adsorbed on and in water ices at astrophysically relevant temperatures (20 K). We show that the functional group of the isomer dictates the strength of interaction with water ice, and hence the resulting desorption and trapping behaviour. Furthermore, the strength of this interaction directly affects the crystallization of water, which in turn affects the desorption behaviour. Our detailed coverage and composition dependent data allow us to categorize the desorption behaviour of the three isomers on the basis of the strength of intermolecular and intramolecular interactions, as well as the natural sublimation temperature of the molecule. This categorization is extended to other C, H, and O containing molecules in order to predict and describe the desorption behaviour of COMs from interstellar ices.

  7. Disintegration of water molecules in a steam-plasma torch powered by microwaves

    SciTech Connect

    Uhm, Han S.; Kim, Jong H.; Hong, Yong C.

    2007-07-15

    A pure steam torch is generated by making use of 2.45 GHz microwave. Steam from a steam generator enters the discharge tube as a swirl gas at a temperature higher than 150 deg. C. This steam becomes a working gas and produces a stable steam torch. The torch volume is almost linearly proportional to the microwave power. The temperature of the torch flame is measured by making use of optical spectroscopy and a thermocouple device. Two distinctive regions are exhibited, a bright, whitish region of a high-temperature zone and a reddish, dimmer region of a relatively low-temperature zone. The bright, whitish region is a typical torch based on plasma species and the reddish, dimmer region is hydrogen burning in oxygen. Study of water molecule disintegration and gas temperature effects on the molecular fraction characteristics in steam-plasma of a microwave plasma torch at the atmospheric pressure is carried out. An analytical investigation of water disintegration indicates that a substantial fraction of water molecules disintegrate and form other compounds at high temperatures in the steam-plasma torch. Emission profiles of the hydroxide radical and water molecules confirm the theoretical predictions of water disintegration in the torch.

  8. A systematic method for studying the spatial distribution of water molecules around nucleic acid bases.

    PubMed Central

    Schneider, B; Cohen, D M; Schleifer, L; Srinivasan, A R; Olson, W K; Berman, H M

    1993-01-01

    A new method to analyze the distribution of water molecules around the bases in DNA is presented. This method relies on the notion of a "hydrated building block," which represents the joint observed hydration around all bases of a particular type, in structures of a particular conformation type. The hydrated building blocks were constructed using atomic coordinates from 40 structures contained in the Nucleic Acid Database. Pseudoelectron densities were calculated for water molecules in each hydrated building block using standard crystallographic procedures. The electron densities were fitted to obtain "average building blocks," which represent bases with waters only at average or probable positions. Both types of building blocks were used to construct models of hydrated DNA oligomers. The essential features of the solvent structure around d(CGCGAATTCGCG)2 in the B form and d(CGCGCG)2 in the Z form were reproduced. Images FIGURE 4 FIGURE 5 PMID:8312469

  9. Monte Carlo simulation of several biologically relevant molecules and zwitterions in water

    NASA Astrophysics Data System (ADS)

    Patuwo, Michael Y.; Bettens, Ryan P. A.

    2012-02-01

    In this work, we study the hydration free energies of butane, zwitterionic alanine, valine, serine, threonine, and asparagine, and two neuraminidase inhibitors by means of Monte Carlo (MC) simulation. The solute molecule, represented in the form of distributed multipoles and modified 6-12 potential, was varied from a non-interacting 'ghost' molecule to its full potential functions in TIP4P water. Intermediate systems with soft-core solute-solvent interaction potentials are simulated separately and then subjected to Bennett's Acceptance ratio (BAR) for the free energy calculation. Hydration shells surrounding the solute particles were used to assess the quality of potential functions.

  10. Structure detection in a libration vibration spectrum of water molecules by methods of nonlinear optics

    SciTech Connect

    Babenko, V A; Sychev, Andrei A

    2012-09-30

    In exciting water possessing an enhanced optical strength by the radiation of a YAG : Nd{sup 3+} laser with 20-ps pulses, nonlinear scattering of light was detected in the frequency range of the optical second harmonic. A relationship was established of the signal of the nonlinear scattering with a stimulated Raman scattering (SRS) of the laser radiation in water. Near the SRS threshold, the structure was observed in the spectrum of nonlinear scattering, which is related to intermolecular libration vibrations of water molecules. (laser applications and other topics in quantum electronics)

  11. Water-inducing molecular self-assembly of amphiphilic molecules into nanofibers

    SciTech Connect

    Zhang, Weiguang; Zhao, Pusu; Song, Jie

    2011-12-15

    Graphical abstract: TPDP nanofibers with smooth surfaces can be obtained by reprecipitation method using ethanol as good solvent and water as poor solvent. In the self-assembly process, during the water adding to the amphiphilic molecules' saturated solution, the amphiphilic molecules firstly assembled into needle-like small rods. With an increase in the self-assembled time, a large number of the nanofibers are produced. The assembly behavior was revealed in the course of direct in situ monitoring of its growth with optical microscopy. Highlights: Black-Right-Pointing-Pointer 2,3,6,7-Tetramethoxy-9,10-di(4-pyridyl)-9,10-dihydroanthracen (TPDP) was synthesized. Black-Right-Pointing-Pointer TPDP nanofibers can be obtained by reprecipitation method. Black-Right-Pointing-Pointer The assembly behavior was revealed in situ monitoring with optical microscopy. -- Abstract: We present investigations on the microcosmic self-assembly process of new synthesized amphiphilic TPDP molecules. It can be seen that pure TPDP nanofibers with smooth surfaces can be obtained by reprecipitation method using ethanol as good solvent and water as poor solvent. In the self-assembly process, during the water adding to the amphiphilic molecules' saturated solution, the amphiphilic molecules firstly assembled into needle-like small rods. With an increase in the self-assembled time, a large number of the nanofibers are produced. The assembly behavior was revealed in the course of direct in situ monitoring of its growth with optical microscopy. Field emission scanning electron microscopy was adopted to characterize the morphologies of the products.

  12. Geology and ground-water resources of the Two Medicine unit and adjacent areas, Blackfeet Indian Reservation, Montana, with a section on chemical quality of water

    USGS Publications Warehouse

    Paulson, Q.F.; Zimmerman, Tom V.; Langford, Russell H.

    1965-01-01

    The Two Medicine Irrigation Unit, on the Blackfeet Indian Reservation of northern Montana, is irrigated by water diverted from Two Medicine Creek. Waterlogging because of overapplication of water and locally inadequate subsurface drainage is a serious problem. This study was undertaken by the U.S. Geological Survey in cooperation with the U.S. Bureau of Indian Affairs to evaluate the problem and to suggest remedies. For this study, the geology was mapped, and data concerning 129 wells and test holes were gathered. The water level in 63 wells was measured periodically. Three test holes were drilled and 4 single-well and 1 multiple-well pump tests were made. Nineteen samples of ground water were collected and analyzed chemically, and applied irrigation water was analyzed periodically.

  13. Molecular mimicry of substrate oxygen atoms by water molecules in the beta-amylase active site.

    PubMed

    Pujadas, G; Palau, J

    2001-08-01

    Soybean beta-amylase (EC 3.2.1.2) has been crystallized both free and complexed with a variety of ligands. Four water molecules in the free-enzyme catalytic cleft form a multihydrogen-bond network with eight strategic residues involved in enzyme-ligand hydrogen bonds. We show here that the positions of these four water molecules are coincident with the positions of four potential oxygen atoms of the ligands within the complex. Some of these waters are displaced from the active site when the ligands bind to the enzyme. How many are displaced depends on the shape of the ligand. This means that when one of the four positions is not occupied by a ligand oxygen atom, the corresponding water remains. We studied the functional/structural role of these four waters and conclude that their presence means that the conformation of the eight side chains is fixed in all situations (free or complexed enzyme) and preserved from unwanted or forbidden conformational changes that could hamper the catalytic mechanism. The water structure at the active pocket of beta-amylase is therefore essential for providing the ligand recognition process with plasticity. It does not affect the protein active-site geometry and preserves the overall hydrogen-bonding network, irrespective of which ligand is bound to the enzyme. We also investigated whether other enzymes showed a similar role for water. Finally, we discuss the potential use of these results for predicting whether water molecules can mimic ligand atoms in the active center. PMID:11468361

  14. Single-molecule redox blinking of perylene diimide derivatives in water.

    PubMed

    Cordes, Thorben; Vogelsang, Jan; Anaya, Milena; Spagnuolo, Carla; Gietl, Andreas; Summerer, Wolfram; Herrmann, Andreas; Müllen, Klaus; Tinnefeld, Philip

    2010-02-24

    Dynamic developments in ultrasensitive and superresolution fluorescence microscopy call for improved fluorescence markers with increased photostability and new functionalities. We used single-molecule spectroscopy to study water-soluble perylene dicarboximide fluorophores (PDI), which were immobilized in aqueous buffer by attaching the fluorophore to DNA. Under these conditions bright fluorescence, comparable to that of single-molecule compatible organic fluorophores, is observed with homogeneous spectral and fluorescence decay time distributions. We additionally show how the fluorescence of the PDI can be controlled through photoinduced electron-transfer reactions by using different concentrations of reductants and oxidants, yielding either blinking or stable emission. We explain these properties by the redox potentials of PDI and the recently introduced ROXS (reducing and oxidizing system) concept. Finally, we evaluate how this fluorescence control of PDIs can be used for superresolution "Blink-Microscopy" in aqueous or organic media and more generally for single-molecule spectroscopy. PMID:20121094

  15. INTERSTELLAR ICES AS WITNESSES OF STAR FORMATION: SELECTIVE DEUTERATION OF WATER AND ORGANIC MOLECULES UNVEILED

    SciTech Connect

    Cazaux, S.; Spaans, M.; Caselli, P.

    2011-11-10

    Observations of star-forming environments revealed that the abundances of some deuterated interstellar molecules are markedly larger than the cosmic D/H ratio of 10{sup -5}. Possible reasons for this pointed to grain surface chemistry. However, organic molecules and water, which are both ice constituents, do not enjoy the same deuteration. For example, deuterated formaldehyde is very abundant in comets and star-forming regions, while deuterated water rarely is. In this paper, we explain this selective deuteration by following the formation of ices (using the rate equation method) in translucent clouds, as well as their evolution as the cloud collapses to form a star. Ices start with the deposition of gas-phase CO and O onto dust grains. While reaction of oxygen with atoms (H or D) or molecules (H{sub 2}) yields H{sub 2}O (HDO), CO only reacts with atoms (H and D) to form H{sub 2}CO (HDCO, D{sub 2}CO). As a result, the deuteration of formaldehyde is sensitive to the gas D/H ratio as the cloud undergoes gravitational collapse, while the deuteration of water strongly depends on the dust temperature at the time of ice formation. These results reproduce well the deuterium fractionation of formaldehyde observed in comets and star-forming regions and can explain the wide spread of deuterium fractionation of water observed in these environments.

  16. Bias-dependent local structure of water molecules at an electrochemical interface

    NASA Astrophysics Data System (ADS)

    Pedroza, Luana; Brandimarte, Pedro; Rocha, Alexandre R.; Fernandez-Serra, Marivi

    2015-03-01

    Following the need for new - and renewable - sources of energy worldwide, fuel cells using electrocatalysts can be thought of as a viable option. Understanding the local structure of water molecules at the interfaces of the metallic electrodes is a key problem. Notably the system is under an external potential bias, which makes the task of simulating this setup difficult. A first principle description of all components of the system is the most appropriate methodology in order to advance understanding of electrochemical processes. There, the metal is usually charged. To correctly compute the effect of an external bias potential applied to electrodes, we combine density functional theory (DFT) and non-equilibrium Green's functions methods (NEGF), with and without van der Waals interactions. In this work, we apply this methodology to study the electronic properties and forces of one water molecule and water monolayer at the interface of gold electrodes. We find that the water molecule has a different torque direction depending on the sign of the bias applied. We also show that it changes the position of the most stable configuration indicating that the external bias plays an important role in the structural properties of the interface. We acknowledge financial support from FAPESP.

  17. Theoretical and experimental investigation of the interactions between [emim]Ac and water molecules

    NASA Astrophysics Data System (ADS)

    Ding, Zhen-Dong; Chi, Zhen; Gu, Wen-Xiu; Gu, Sheng-Ming; Wang, Hai-Jun

    2012-05-01

    Density functional theory (DFT) calculations, atom in molecules (AIM) theory, natural bond orbital (NBO) analysis and infrared (IR) spectroscopy were performed to investigate the interactions between water molecules and ionic liquid 1-ethyl-3-methylimidazolium acetate ([emim]Ac). It was found that [emim]Ac interacts with water molecules mainly via H-bonds, and the anionic part of [emim]Ac plays a major role in the interaction with H2O. The energies of H-bonds were estimated from spectral shifts of hydroxy antisymmetric stretching vibration. Moreover, the experimental results also indicated that hydroxy of water mainly interacts with the COO- of [emim]Ac. Further studies indicated that the intensity of hydroxy stretching vibrations tend to be stronger with the increase of the concentration of water. In addition, the frequency of hydroxy stretching vibrations showed clearly red-shift, and the COO- vibrational frequency gradually shifted to the lower wavenumber region, which were indicative of extended hydrogen bonded network.

  18. Geologic Assessment of Undiscovered, Technically Recoverable Coalbed-Gas Resources in Cretaceous and Tertiary Rocks, North Slope and Adjacent State Waters, Alaska

    USGS Publications Warehouse

    Roberts, Stephen B., (compiler)

    2008-01-01

    The purpose of the U.S. Geological Survey's (USGS) National Oil and Gas Assessment is to develop geology-based hypotheses regarding the potential for additions to oil and gas reserves in priority areas of the United States, focusing on the distribution, quantity, and availability of oil and natural gas resources. The USGS has completed an assessment of the undiscovered, technically recoverable coalbed-gas resources in Cretaceous and Tertiary rocks underlying the North Slope and adjacent State waters of Alaska (USGS Northern Alaska Province 5001). The province is a priority Energy Policy and Conservation Act (EPCA) province for the National Assessment because of its potential for oil and gas resources. The assessment of this province is based on geologic principles and uses the total petroleum system concept. The geologic elements of a total petroleum system include hydrocarbon source rocks (source rock maturation, hydrocarbon generation and migration), reservoir rocks (stratigraphy, sedimentology, petrophysical properties), and hydrocarbon traps (trap formation and timing). In the Northern Alaska Province, the USGS used this geologic framework to define one composite coalbed gas total petroleum system and three coalbed gas assessment units within the petroleum system, and quantitatively estimated the undiscovered coalbed-gas resources within each assessment unit.

  19. Grand canonical Monte Carlo simulation of the adsorption isotherms of water molecules on model soot particles

    NASA Astrophysics Data System (ADS)

    Moulin, F.; Picaud, S.; Hoang, P. N. M.; Jedlovszky, P.

    2007-10-01

    The grand canonical Monte Carlo method is used to simulate the adsorption isotherms of water molecules on different types of model soot particles. The soot particles are modeled by graphite-type layers arranged in an onionlike structure that contains randomly distributed hydrophilic sites, such as OH and COOH groups. The calculated water adsorption isotherm at 298K exhibits different characteristic shapes depending both on the type and the location of the hydrophilic sites and also on the size of the pores inside the soot particle. The different shapes of the adsorption isotherms result from different ways of water aggregation in or/and around the soot particle. The present results show the very weak influence of the OH sites on the water adsorption process when compared to the COOH sites. The results of these simulations can help in interpreting the experimental isotherms of water adsorbed on aircraft soot.

  20. Adjacent segment disease.

    PubMed

    Virk, Sohrab S; Niedermeier, Steven; Yu, Elizabeth; Khan, Safdar N

    2014-08-01

    EDUCATIONAL OBJECTIVES As a result of reading this article, physicians should be able to: 1. Understand the forces that predispose adjacent cervical segments to degeneration. 2. Understand the challenges of radiographic evaluation in the diagnosis of cervical and lumbar adjacent segment disease. 3. Describe the changes in biomechanical forces applied to adjacent segments of lumbar vertebrae with fusion. 4. Know the risk factors for adjacent segment disease in spinal fusion. Adjacent segment disease (ASD) is a broad term encompassing many complications of spinal fusion, including listhesis, instability, herniated nucleus pulposus, stenosis, hypertrophic facet arthritis, scoliosis, and vertebral compression fracture. The area of the cervical spine where most fusions occur (C3-C7) is adjacent to a highly mobile upper cervical region, and this contributes to the biomechanical stress put on the adjacent cervical segments postfusion. Studies have shown that after fusion surgery, there is increased load on adjacent segments. Definitive treatment of ASD is a topic of continuing research, but in general, treatment choices are dictated by patient age and degree of debilitation. Investigators have also studied the risk factors associated with spinal fusion that may predispose certain patients to ASD postfusion, and these data are invaluable for properly counseling patients considering spinal fusion surgery. Biomechanical studies have confirmed the added stress on adjacent segments in the cervical and lumbar spine. The diagnosis of cervical ASD is complicated given the imprecise correlation of radiographic and clinical findings. Although radiological and clinical diagnoses do not always correlate, radiographs and clinical examination dictate how a patient with prolonged pain is treated. Options for both cervical and lumbar spine ASD include fusion and/or decompression. Current studies are encouraging regarding the adoption of arthroplasty in spinal surgery, but more long

  1. Effects of brush management on the hydrologic budget and water quality in and adjacent to Honey Creek State Natural Area, Comal County, Texas, 2001-10

    USGS Publications Warehouse

    Banta, J. Ryan; Slattery, Richard N.

    2011-01-01

    The U.S. Geological Survey, in cooperation with the U.S. Department of Agriculture Natural Resources Conservation Service, the Edwards Region Grazing Lands Conservation Initiative, the Texas State Soil and Water Conservation Board, the San Antonio River Authority, the Edwards Aquifer Authority, Texas Parks and Wildlife, the Guadalupe Blanco River Authority, and the San Antonio Water System, evaluated the hydrologic effects of ashe juniper (Juniperus ashei) removal as a brush management conservation practice in and adjacent to the Honey Creek State Natural Area in Comal County, Tex. By removing the ashe juniper and allowing native grasses to reestablish in the area as a brush management conservation practice, the hydrology in the watershed might change. Using a simplified mass balance approach of the hydrologic cycle, the incoming rainfall was distributed to surface water runoff, evapotranspiration, or groundwater recharge. After hydrologic data were collected in adjacent watersheds for 3 years, brush management occurred on the treatment watershed while the reference watershed was left in its original condition. Hydrologic data were collected for another 6 years. Hydrologic data include rainfall, streamflow, evapotranspiration, and water quality. Groundwater recharge was not directly measured but potential groundwater recharge was calculated using a simplified mass balance approach. The resulting hydrologic datasets were examined for differences between the watersheds and between pre- and post-treatment periods to assess the effects of brush management. The streamflow to rainfall relation (expressed as event unit runoff to event rainfall relation) did not change between the watersheds during pre- and post-treatment periods. The daily evapotranspiration rates at the reference watershed and treatment watershed sites exhibited a seasonal cycle during the pre- and post-treatment periods, with intra- and interannual variability. Statistical analyses indicate the mean

  2. Anomalous and anisotropic nanoscale diffusion of hydration water molecules in fluid lipid membranes.

    PubMed

    Toppozini, Laura; Roosen-Runge, Felix; Bewley, Robert I; Dalgliesh, Robert M; Perring, Toby; Seydel, Tilo; Glyde, Henry R; García Sakai, Victoria; Rheinstädter, Maikel C

    2015-11-14

    We have studied nanoscale diffusion of membrane hydration water in fluid-phase lipid bilayers made of 1,2-dimyristoyl-3-phosphocholine (DMPC) using incoherent quasi-elastic neutron scattering. Dynamics were fit directly in the energy domain using the Fourier transform of a stretched exponential. By using large, 2-dimensional detectors, lateral motions of water molecules and motions perpendicular to the membranes could be studied simultaneously, resulting in 2-dimensional maps of relaxation time, τ, and stretching exponent, β. We present experimental evidence for anomalous (sub-diffusive) and anisotropic diffusion of membrane hydration water molecules over nanometer distances. By combining molecular dynamics and Brownian dynamics simulations, the potential microscopic origins for the anomaly and anisotropy of hydration water were investigated. Bulk water was found to show intrinsic sub-diffusive motion at time scales of several picoseconds, likely related to caging effects. In membrane hydration water, however, the anisotropy of confinement and local dynamical environments leads to an anisotropy of relaxation times and stretched exponents, indicative of anomalous dynamics. PMID:26338138

  3. Structure and dynamics of water and lipid molecules in charged anionic DMPG lipid bilayer membranes

    NASA Astrophysics Data System (ADS)

    Rønnest, A. K.; Peters, G. H.; Hansen, F. Y.; Taub, H.; Miskowiec, A.

    2016-04-01

    Molecular dynamics simulations have been used to investigate the influence of the valency of counter-ions on the structure of freestanding bilayer membranes of the anionic 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol (DMPG) lipid at 310 K and 1 atm. At this temperature, the membrane is in the fluid phase with a monovalent counter-ion and in the gel phase with a divalent counter-ion. The diffusion constant of water as a function of its depth in the membrane has been determined from mean-square-displacement calculations. Also, calculated incoherent quasielastic neutron scattering functions have been compared to experimental results and used to determine an average diffusion constant for all water molecules in the system. On extrapolating the diffusion constants inferred experimentally to a temperature of 310 K, reasonable agreement with the simulations is obtained. However, the experiments do not have the sensitivity to confirm the diffusion of a small component of water bound to the lipids as found in the simulations. In addition, the orientation of the dipole moment of the water molecules has been determined as a function of their depth in the membrane. Previous indirect estimates of the electrostatic potential within phospholipid membranes imply an enormous electric field of 108-109 V m-1, which is likely to have great significance in controlling the conformation of translocating membrane proteins and in the transfer of ions and molecules across the membrane. We have calculated the membrane potential for DMPG bilayers and found ˜1 V (˜2 ṡ 108 V m-1) when in the fluid phase with a monovalent counter-ion and ˜1.4 V (˜2.8 ṡ 108 V m-1) when in the gel phase with a divalent counter-ion. The number of water molecules for a fully hydrated DMPG membrane has been estimated to be 9.7 molecules per lipid in the gel phase and 17.5 molecules in the fluid phase, considerably smaller than inferred experimentally for 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC

  4. Isotope geochemistry and fluxes of carbon and organic matter in tropical small mountainous river systems and adjacent coastal waters of the Caribbean

    USGS Publications Warehouse

    Moyer, Ryan; Bauer, James; Grottoli, Andrea

    2012-01-01

    Recent studies have shown that small mountainous rivers (SMRs) may act as sources of aged and/or refractory carbon (C) to the coastal ocean, which may increase organic C burial at sea and subsidize coastal food webs and heterotrophy. However, the characteristics and spatial and temporal variability of C and organic matter (OM) exported from tropical SMR systems remain poorly constrained. To address this, the abundance and isotopic character (δ13C and Δ14C) of the three major C pools were measured in two Puerto Rico SMRs with catchments dominated by different land uses (agricultural vs. non-agricultural recovering forest). The abundance and character of C pools in associated estuaries and adjacent coastal waters were also examined. Riverine dissolved and particulate organic C (DOC and POC, respectively) concentrations were highly variable with respect to land use and sampling month, while dissolved inorganic C (DIC) was significantly higher at all times in the agricultural catchment. In both systems, riverine DOC and POC ranged from modern to highly aged (2,340 years before present), while DIC was always modern. The agricultural river and irrigation canals contained very old DOC (1,184 and 2,340 years before present, respectively), which is consistent with findings in temperate SMRs and indicates that these tropical SMRs provide a source of aged DOC to the ocean. During months of high river discharge, OM in estuarine and coastal waters had C isotope signatures reflective of direct terrestrial input, indicating that relatively unaltered OM is transported to the coastal ocean at these times. This is also consistent with findings in temperate SMRs and indicates that C transported to the coastal ocean by SMRs may differ from that of larger rivers because it is exported from smaller catchments that have steeper terrains and fewer land-use types.

  5. Biodiversity and ecological composition of macrobenthos on cold-water coral mounds and adjacent off-mound habitat in the bathyal Porcupine Seabight, NE Atlantic

    NASA Astrophysics Data System (ADS)

    Henry, Lea-Anne; Roberts, J. Murray

    2007-04-01

    The cold-water scleractinian corals Lophelia pertusa and Madrepora oculata form mound structures on the continental shelf and slope in the NE Atlantic. This study is the first to compare the taxonomic biodiversity and ecological composition of the macrobenthos between on- and off-mound habitats. Seven box cores from the summits of three mounds and four cores from an adjacent off-mound area in the Belgica Mound Province in the Porcupine Seabight yielded 349 species, including 10 undescribed species. On-mound habitat was three times more speciose, and was richer with higher evenness and significantly greater Shannon's diversity than off-mound. Species composition differed significantly between habitats and the four best discriminating species were Pliobothrus symmetricus (more frequent off-mound), Crisia nov. sp, Aphrocallistes bocagei and Lophelia pertusa (all more frequent on-mound). Filter/suspension feeders were significantly more abundant on-mound, while deposit feeders were significantly more abundant off-mound. Species composition did not significantly differ between mounds, but similarity within replicates decreased from Galway Moundwater coral biodiversity across larger spatio-temporal scales.

  6. Versatile Small Molecule Motifs for Self-assembly in Water and Formation of Biofunctional Supramolecular Hydrogels

    PubMed Central

    Zhang, Ye; Kuang, Yi; Gao, Yuan; Xu, Bing

    2010-01-01

    This article introduces new structural motifs (referred as “samogen”) that serve as the building blocks of hydrogelators for molecular self-assembly in water to result in a series of supramolecular hydrogels. Using a compound that consists of two phenylalanine residues and a naphthyl group (also abbreviated as NapFF (1) in this text) as an example of the samogens, we demonstrated the ability of the samogens to convert bioactive molecules into molecular hydrogelators that self-assemble in water to result in nanofibers. By briefly summarizing the properties and applications (e.g., wound healing, drug delivery, controlling cell fate, typing bacteria, and catalysis) of these molecular hydrogelators derived from the samogens, we intend to illustrate the basic requirements and promises of the small molecule hydrogelators for applications in chemistry, materials science, and biomedicine. PMID:20608718

  7. Orientation and alignment effects in electron-induced ionization of a single oriented water molecule

    SciTech Connect

    Champion, C.; Rivarola, R. D.

    2010-10-15

    We here report a theoretical study about the orientation effect on the total ionization cross sections for a single oriented water molecule. The theoretical description of the ionization process is performed within the first Born framework with a collisional system including an initial state composed of a projectile and a water target molecule described by a plane wave and an accurate one-center molecular wave function, respectively, and a final state constituted by a slow ejected electron represented by a Coulomb wave and a scattered (fast) electron projectile described by a plane wave. Secondary electron energetic distributions as well as total cross sections are then compared for particular target configurations pointing out strong alignment and orientation effects on the description of the ionization process.

  8. Water molecule-enhanced CO{sub 2} insertion in lanthanide coordination polymers

    SciTech Connect

    Luo Liushan; Huang Xiaoyuan; Wang Ning; Wu Hongyan; Chen Wenbin; Feng Zihao; Zhu Huiping; Peng Xiaoling; Li Yongxian; Huang Ling; Yue Shantang; Liu Yingliang

    2009-08-15

    Two new lanthanide coordination polymers H{sub 2}N(CH{sub 3}){sub 2}.[Eu{sup III}{sub 2}(L{sub 1}){sub 3}(L{sub 2})] (1, L{sub 1}=isophthalic acid dianion, L{sub 2}=formic acid anion) and [La{sup III}(2,5-PDC)(L{sub 2})](2, 2,5-PDC=2,5-pyridinedicarboxylate dianion) were synthesized under solvothermal conditions. It is of interest that the formic ligand (L{sub 2}) is not contained in the stating materials, but arises from the water molecule-enhanced CO{sub 2} insertion during the solvothermal process. Both of the two compounds exhibit complicated three dimensional sandwich-like frameworks. - Graphical abstract: Two new lanthanide coordination polymers involving water molecule-enhanced CO{sub 2} insertion resulting in the formation of formic anion and dimethylammonium cation were synthesized under solvothermal conditions.

  9. Diagrammatic perturbation theory applied to the ground state of the water molecule

    NASA Technical Reports Server (NTRS)

    Silver, D. M.; Wilson, S.

    1977-01-01

    The diagrammatic many-body perturbation theory is applied to the ground state of the water molecule within the algebraic approximation. Using four different basis sets, the total energy, the equilibrium OH bond length, and the equilibrium HOH bond angle are examined. The latter is found to be a particularly sensitive test of the convergence of perturbation expansions. Certain third-order results, which incorporate all two-, three-, and four-body effects, show evidence of good convergence properties.

  10. Double ionization of single oriented water molecules by electron impact: Second-order Born description

    SciTech Connect

    Dal Cappello, C.; Champion, C.; Kada, I.; Mansouri, A.

    2011-06-15

    The double ionization of isolated water molecules fixed in space is investigated within a theoretical approach based on the second-order Born approximation. Electron angular distributions have been studied for specific kinematical conditions. The three usual mechanisms, the shake-off and the two two-step mechanisms, have been identified. A significant contribution of the two-step mechanism is clearly visible for some particular kinematics.

  11. Organic molecules and water in the planet formation region of young circumstellar disks.

    PubMed

    Carr, John S; Najita, Joan R

    2008-03-14

    The chemical composition of protoplanetary disks is expected to hold clues to the physical and chemical processes that influence the formation of planetary systems. However, characterizing the gas composition in the planet formation region of disks has been a challenge to date. We report here that the protoplanetary disk within 3 astronomical units of AA Tauri possesses a rich molecular emission spectrum in the mid-infrared, indicating a high abundance of simple organic molecules (HCN, C2H2, and CO2), water vapor, and OH. These results suggest that water is abundant throughout the inner disk and that the disk supports an active organic chemistry. PMID:18339932

  12. Infrared spectroscopy of water clusters co-adsorbed with hydrogen molecules on a sodium chloride film

    NASA Astrophysics Data System (ADS)

    Yamakawa, Koichiro; Fukutani, Katsuyuki

    2016-06-01

    Hydrogen gas containing a trace of water vapor was dosed on a vacuum-evaporated sodium chloride film at 13 K, and water clusters formed on the substrate were investigated by infrared absorption spectroscopy. Absorption bands due to (H2O)n clusters with n = 3-6 and an induced absorption band due to hydrogen were clearly observed. With increasing gas dosage, the intensities of the cluster bands increased linearly while the intensity of the hydrogen band was constant. This suggests that the water clusters were formed in two-dimensional matrices of hydrogen. We found that the water clusters did exist on the surface upon heating even after the hydrogen molecules had desorbed. A further rise of the substrate temperature up to 27 K yielded the formation of larger clusters, (H2O)n with n > 6 . We also discuss the origins of the two bands of the trimer in terms of pseudorotation and a metastable isomer.

  13. Experimental Evaluation of Proposed Small-Molecule Inhibitors of Water Channel Aquaporin-1.

    PubMed

    Esteva-Font, Cristina; Jin, Byung-Ju; Lee, Sujin; Phuan, Puay-Wah; Anderson, Marc O; Verkman, A S

    2016-06-01

    The aquaporin-1 (AQP1) water channel is a potentially important drug target, as AQP1 inhibition is predicted to have therapeutic action in edema, tumor growth, glaucoma, and other conditions. Here, we measured the AQP1 inhibition efficacy of 12 putative small-molecule AQP1 inhibitors reported in six recent studies, and one AQP1 activator. Osmotic water permeability was measured by stopped-flow light scattering in human and rat erythrocytes that natively express AQP1, in hemoglobin-free membrane vesicles from rat and human erythrocytes, and in plasma membrane vesicles isolated from AQP1-transfected Chinese hamster ovary cell cultures. As a positive control, 0.3 mM HgCl2 inhibited AQP1 water permeability by >95%. We found that none of the tested compounds at 50 µM significantly inhibited or increased AQP1 water permeability in these assays. Identification of AQP1 inhibitors remains an important priority. PMID:26993802

  14. WScore: A Flexible and Accurate Treatment of Explicit Water Molecules in Ligand-Receptor Docking.

    PubMed

    Murphy, Robert B; Repasky, Matthew P; Greenwood, Jeremy R; Tubert-Brohman, Ivan; Jerome, Steven; Annabhimoju, Ramakrishna; Boyles, Nicholas A; Schmitz, Christopher D; Abel, Robert; Farid, Ramy; Friesner, Richard A

    2016-05-12

    We have developed a new methodology for protein-ligand docking and scoring, WScore, incorporating a flexible description of explicit water molecules. The locations and thermodynamics of the waters are derived from a WaterMap molecular dynamics simulation. The water structure is employed to provide an atomic level description of ligand and protein desolvation. WScore also contains a detailed model for localized ligand and protein strain energy and integrates an MM-GBSA scoring component with these terms to assess delocalized strain of the complex. Ensemble docking is used to take into account induced fit effects on the receptor conformation, and protein reorganization free energies are assigned via fitting to experimental data. The performance of the method is evaluated for pose prediction, rank ordering of self-docked complexes, and enrichment in virtual screening, using a large data set of PDB complexes and compared with the Glide SP and Glide XP models; significant improvements are obtained. PMID:27054459

  15. Pesticides in surface water, bed sediment, and ground water adjacent to commercial cranberry bogs, Lac du Flambeau Reservation, Vilas County, Wisconsin

    USGS Publications Warehouse

    Saad, David A.

    2005-01-01

    In samples from the Trout River, which is used as a source of water to maintain lake levels in the Corn Lakes, the only pesticides detected were the non-targeted compounds atrazine and deethyl atrazine, indicating it was not a source of targeted compounds detected in the Corn Lakes. Only two pesticides (chlorpyrifos and metolachlor) were detected in bed-sediment samples collected from the lakes; chlorpyrifos from Little Trout Lake and metolachlor from the Corn Lakes. Four pesticides (the targeted compounds napropamide and norflurazon and the non-targeted compounds atrazine and deethyl atrazine) were detected in ground-water samples from two of four sampled monitor wells. The highest ground-water concentrations (up to 0.14 ?g/L napropamide and 0.56 ?g/L norflurazon) were measured in samples from the monitoring well located directly downgradient from the Corn Lakes and commercial cranberry operations. No pesticides were detected in samples from the reference well located upgradient from the Corn Lakes and cranberry operations. Further study is needed to identify additional pesticides as well as chronic effects on aquatic organisms to determine whether cranberry-related pesticides affect the lake ecosystems of the Lac du Flambeau Reservation.

  16. Size-fractionated phytoplankton biomass in autumn of the Changjiang (Yangtze) River Estuary and its adjacent waters after the Three Gorges Dam construction

    NASA Astrophysics Data System (ADS)

    Song, Shuqun; Sun, Jun; Luan, Qingshan; Shen, Zhiliang

    2008-08-01

    A cruise was undertaken from 3rd to 8th November 2004 in Changjiang (Yangtze) River Estuary and its adjacent waters to investigate the spatial biomass distribution and size composition of phytoplankton. Chlorophyll- a (Chl- a) concentration ranged 0.42-1.17 μg L-1 and 0.41-10.43 μg L-1 inside and outside the river mouth, with the mean value 0.73 μg L-1 and 1.86 μg L-1, respectively. Compared with the Chl- a concentration in summer of 2004, the mean value was much lower inside, and a little higher outside the river mouth. The maximal Chl- a was 10.43 μg L-1 at station 18 (122.67°E, 31.25°N), and the region of high Chl- a concentration was observed in the central survey area between 122.5°E and 123.0°E. In the stations located east of 122.5°E, Chl- a concentration was generally high in the upper layers above 5 m due to water stratification. In the survey area, the average Chl- a in sizes of >20 μm and <20 μm was 0.28 μg L-1 and 1.40 μg L-1, respectively. High Chl- a concentration of <20 μm size-fraction indicated that the nanophytoplankton and picophytoplankton contributed the most to the biomass of phytoplankton. Skeletonema costatum, Prorocentrum micans and Scrippsiella trochoidea were the dominant species in surface water. The spatial distribution of cell abundance of phytoplankton was patchy and did not agree well with that of Chl- a, as the cell abundance could not distinguish the differences in shape and size of phytoplankton cells. Nitrate and silicate behaved conservatively, but the former could probably be the limitation factor to algal biomass at offshore stations. The distribution of phosphate scattered considerably, and its relation to the phytoplankton biomass was complicated.

  17. Ultrafast Raman-induced Kerr-effect of water: Single molecule versus collective motions

    NASA Astrophysics Data System (ADS)

    Winkler, Kathrin; Lindner, Jörg; Bürsing, Helge; Vöhringer, Peter

    2000-09-01

    The ultrafast optical Kerr-response of water and heavy water has been measured at 1 bar in the temperature range between 273 and 373 K. The nuclear Kerr response of the liquid exhibits a pronounced double exponential decay on longer time scales after dephasing of impulsively perturbed acoustic modes is completed. The time constant, τ2, characterizing the slowly decaying exponential component of the Kerr-response function is in quantitative agreement with rotational diffusion time constants of the water molecules obtained form nuclear magnetic resonance (NMR) spin-lattice relaxation rates. A detailed comparison with THz time domain spectroscopy demonstrates that the reorientational dynamics responsible for the long time tail of the Kerr response are due to single molecule as opposed to collective effects. Furthermore, a good agreement between the single molecule rotational diffusion and the Stokes-Einstein-Debye equation is found in the temperature range of thermodynamic stability of the liquid. The time constant, τ1, characterizing the fast exponential component of the Kerr-response of water is found to be in qualitative agreement with central Lorentzian linewidths obtained from frequency-domain, depolarized Raman scattering experiments. The temperature dependence of τ2 does not follow an Arrhenius-type behavior, which was previously taken as evidence for thermally activated crossing of a librational barrier with concomitant hydrogen-bond breakage. Instead, the temperature dependence of the fast relaxation time constant can be represented adequately by the Speedy-Angell relation which has been shown to accurately describe a number of transport parameters and thermodynamic properties of water.

  18. Fall diets of red-breasted merganser (Mergus serrator) and walleye (Sander vitreus) in Sandusky Bay and adjacent waters of western Lake Erie

    USGS Publications Warehouse

    Bur, M.T.; Stapanian, M.A.; Bernhardt, G.; Turner, M.W.

    2008-01-01

    Although published studies indicate the contrary, there is concern among many sport anglers that migrating red-breasted mergansers (Mergus serrator) and other waterbirds pose a competitive threat to sport fish species such as walleye (Sander vitreus) in Lake Erie. We quantified the diet of autumn-migrant mergansers and walleye during 1998-2000 in Sandusky Bay and adjacent waters of western Lake Erie. We hypothesized that the diets of both predators would be similar in species composition, but because of different foraging ecologies their diets would differ markedly in size of prey consumed. In addition to predator samples, we used trawl data from the same general area as an index of prey availability. We found that mergansers fed almost exclusively on fish (nine species). Gizzard shad (Dorosoma cepedianum), emerald shiner (Notropis atherinoides) and round goby (Neogobius melanostomus) were consumed in the greatest numbers, most frequently and comprised the greatest biomass. Walleye fed exclusively on fish: gizzard shad, alewife (Alosa psuedoharengus) and emerald shiner were consumed in the greatest numbers, most frequently and comprised the greatest biomass. Diet overlap between mergansers and walleye was 67% by weight and 66% by species frequency. Mean total lengths of gizzard shad, emerald shiner and round goby found in walleye stomachs exceeded those captured in trawls by 47%, on average. Mean total lengths of gizzard shad, emerald shiner and round goby were greater in walleye stomachs than in merganser stomachs. Mean total lengths of emerald shiner and round goby were less in merganser stomachs than in trawls. Our results suggest that although the diets of walleye and mergansers overlapped considerably, mergansers generally consumed smaller fish than walleye. Given the abundance and diversity of prey species available, and the transient nature of mergansers on Lake Erie during migration, we conclude that competition for food between these species is minimal.

  19. Single-Molecule Imaging of DNAs with Sticky Ends at Water/Fused Silica Interface

    SciTech Connect

    Slavica Isailovic

    2005-12-17

    Total internal reflection fluorescence microscopy (TIRFM) was used to study intermolecular interactions of DNAs with unpaired (sticky) ends of different lengths at water/fused silica interface at the single-molecule level. Evanescent field residence time, linear velocity and adsorption/desorption frequency were measured in a microchannel for individual DNA molecules from T7, Lambda, and PSP3 phages at various pH values. The longest residence times and the highest adsorption/desorption frequencies at the constant flow at pH 5.5 were found for PSP3 DNA, followed by lower values for Lambda DNA, and the lowest values for T7 DNA. Since T7, Lambda, and PSP3 DNA molecules contain none, twelve and nineteen unpaired bases, respectively, it was concluded that the affinity of DNAs for the surface increases with the length of the sticky ends. This confirms that hydrophobic and hydrogen-bonding interactions between sticky ends and fused-silica surface are driving forces for DNA adsorption at the fused-silica surface. Described single-molecule methodology and results therein can be valuable for investigation of interactions in liquid chromatography, as well as for design of DNA hybridization sensors and drug delivery systems.

  20. Atomic force microscopy study of nitrogen molecule self-assembly at the HOPG-water interface

    NASA Astrophysics Data System (ADS)

    Lu, Yi-Hsien; Yang, Chih-Wen; Hwang, Ing-Shouh

    2014-06-01

    In this work, we investigated the evolution of the graphite-water interface in a nitrogen atmosphere by using frequency-modulation atomic force microscopy (FM-AFM). A highly ordered pyrolytic graphite (HOPG) sample was immersed in pre-degassed water and subsequently placed in the nitrogen environment. The dissolved nitrogen molecules diffused in water and self-assembled into ordered row-like structural domains at the interface. Nucleation and growth processes of the domains were observed. When the coverage of the ordered structure surpassed 50%, small clusters began to appear on the ordered structure. The number density of the clusters increases as the coverage of the ordered structures increases and these clusters may hop on the ordered structures. A model is proposed to explain the evolution of the nitrogen molecule self-assembly process at the interface. The observation of nitrogen clusters may shed light on the nature and nucleation of the so-called nanobubbles at hydrophobic-water interfaces.

  1. CVRQD ab initio ground-state adiabatic potential energy surfaces for the water molecule.

    PubMed

    Barletta, Paolo; Shirin, Sergei V; Zobov, Nikolai F; Polyansky, Oleg L; Tennyson, Jonathan; Valeev, Edward F; Császár, Attila G

    2006-11-28

    The high accuracy ab initio adiabatic potential energy surfaces (PESs) of the ground electronic state of the water molecule, determined originally by Polyansky et al. [Science 299, 539 (2003)] and called CVRQD, are extended and carefully characterized and analyzed. The CVRQD potential energy surfaces are obtained from extrapolation to the complete basis set of nearly full configuration interaction valence-only electronic structure computations, augmented by core, relativistic, quantum electrodynamics, and diagonal Born-Oppenheimer corrections. We also report ab initio calculations of several quantities characterizing the CVRQD PESs, including equilibrium and vibrationally averaged (0 K) structures, harmonic and anharmonic force fields, harmonic vibrational frequencies, vibrational fundamentals, and zero-point energies. They can be considered as the best ab initio estimates of these quantities available today. Results of first-principles computations on the rovibrational energy levels of several isotopologues of the water molecule are also presented, based on the CVRQD PESs and the use of variational nuclear motion calculations employing an exact kinetic energy operator given in orthogonal internal coordinates. The variational nuclear motion calculations also include a simplified treatment of nonadiabatic effects. This sophisticated procedure to compute rovibrational energy levels reproduces all the known rovibrational levels of the water isotopologues considered, H(2) (16)O, H(2) (17)O, H(2) (18)O, and D(2) (16)O, to better than 1 cm(-1) on average. Finally, prospects for further improvement of the ground-state adiabatic ab initio PESs of water are discussed. PMID:17144700

  2. Vibrational spectra and molecular dynamics of hydrogen peroxide molecules at quartz/water interfaces

    NASA Astrophysics Data System (ADS)

    Lv, Ye-qing; Zheng, Shi-li; Wang, Shao-na; Yan, Wen-yi; Zhang, Yi; Du, Hao

    2016-06-01

    The influence of H2O2 on the water vibration at quartz interface was examined using sum-frequency generation (SFG) spectroscopy, and the effect of H2O2 concentration has been systematically studied. Further, the number density and radical distribution of water molecules, H2O2 molecules, and quartz surface silanol groups were calculated using molecular dynamics (MD) simulation to provide molecular level interpretation for the SFG spectra. It is concluded from this study that the hydrogen peroxide molecules prefers to donate H-bonds to the in-plane silanol groups rather than accepting H-bonds from out-of-plane silanol groups, as evidenced by the strengthening of the peak located at 3400 cm-1 assigned to "liquid-like" hydrogen-bonding network. The SFG results have been supported by the MD calculation results, which demonstrate that the relative intensity of the peak located at 3400 cm-1 to that of located at 3200 cm-1 increases monotonously with the increase in the number of hydrogen peroxide in the first hydration shell of silanol.

  3. Patterns of deep-water coral diversity in the Caribbean Basin and adjacent southern waters: an approach based on records from the R/V Pillsbury expeditions.

    PubMed

    Hernández-Ávila, Iván

    2014-01-01

    The diversity of deep-water corals in the Caribbean Sea was studied using records from oceanographic expeditions performed by the R/V Pillsbury. Sampled stations were sorted according to broad depth ranges and ecoregions and were analyzed in terms of species accumulation curves, variance in the species composition and contributions to alpha, beta and gamma diversity. According to the analysis of species accumulation curves using the Chao2 estimator, more diversity occurs on the continental slope (200-2000 m depth) than on the upper continental shelf (60-200 m depth). In addition to the effect of depth sampling, differences in species composition related to depth ranges were detected. However, the differences between ecoregions are dependent on depth ranges, there were fewer differences among ecoregions on the continental slope than on the upper continental shelf. Indicator species for distinctness of ecoregions were, in general, Alcyonaria and Antipatharia for the upper continental shelf, but also the scleractinians Madracis myriabilis and Cladocora debilis. In the continental slope, the alcyonarian Placogorgia and the scleractinians Stephanocyathus and Fungiacyathus were important for the distinction of ecoregions. Beta diversity was the most important component of gamma diversity in the Caribbean Basin. The contribution of ecoregions to alpha, beta and gamma diversity differed with depth range. On the upper continental shelf, the Southern Caribbean ecoregion contributed substantially to all components of diversity. In contrast, the northern ecoregions contributed substantially to the diversity of the Continental Slope. Strategies for the conservation of deep-water coral diversity in the Caribbean Basin must consider the variation between ecoregions and depth ranges. PMID:24671156

  4. Patterns of Deep-Water Coral Diversity in the Caribbean Basin and Adjacent Southern Waters: An Approach based on Records from the R/V Pillsbury Expeditions

    PubMed Central

    Hernández-Ávila, Iván

    2014-01-01

    The diversity of deep-water corals in the Caribbean Sea was studied using records from oceanographic expeditions performed by the R/V Pillsbury. Sampled stations were sorted according to broad depth ranges and ecoregions and were analyzed in terms of species accumulation curves, variance in the species composition and contributions to alpha, beta and gamma diversity. According to the analysis of species accumulation curves using the Chao2 estimator, more diversity occurs on the continental slope (200–2000 m depth) than on the upper continental shelf (60–200 m depth). In addition to the effect of depth sampling, differences in species composition related to depth ranges were detected. However, the differences between ecoregions are dependent on depth ranges, there were fewer differences among ecoregions on the continental slope than on the upper continental shelf. Indicator species for distinctness of ecoregions were, in general, Alcyonaria and Antipatharia for the upper continental shelf, but also the scleractinians Madracis myriabilis and Cladocora debilis. In the continental slope, the alcyonarian Placogorgia and the scleractinians Stephanocyathus and Fungiacyathus were important for the distinction of ecoregions. Beta diversity was the most important component of gamma diversity in the Caribbean Basin. The contribution of ecoregions to alpha, beta and gamma diversity differed with depth range. On the upper continental shelf, the Southern Caribbean ecoregion contributed substantially to all components of diversity. In contrast, the northern ecoregions contributed substantially to the diversity of the Continental Slope. Strategies for the conservation of deep-water coral diversity in the Caribbean Basin must consider the variation between ecoregions and depth ranges. PMID:24671156

  5. Difference of Ecosystem and Hydrological control on Long-term water quality between adjacent subcatchments in a forested catchment in central Japan

    NASA Astrophysics Data System (ADS)

    Katsuyama, M.; Iwasaki, K.; Nagano, R.; Takaki, K.; Tanaka, Y.

    2014-12-01

    ecosystem. Therefore, it is important to continue the monitoring and to consider the mechanisms. We will discuss about the mechanisms and the differences between adjacent subcatchments considering the water quality of the precipitation and the groundwater as well as the hydrological parameters at the coming meeting.

  6. Effects of a single water molecule on the OH + H2O2 reaction.

    PubMed

    Buszek, Robert J; Torrent-Sucarrat, Miquel; Anglada, Josep M; Francisco, Joseph S

    2012-06-21

    The effect of a single water molecule on the reaction between H(2)O(2) and HO has been investigated by employing MP2 and CCSD(T) theoretical approaches in connection with the aug-cc-PVDZ, aug-cc-PVTZ, and aug-cc-PVQZ basis sets and extrapolation to an ∞ basis set. The reaction without water has two elementary reaction paths that differ from each other in the orientation of the hydrogen atom of the hydroxyl radical moiety. Our computed rate constant, at 298 K, is 1.56 × 10(-12) cm(3) molecule(-1) s(-1), in excellent agreement with the suggested value by the NASA/JPL evaluation. The influence of water vapor has been investigated by considering either that H(2)O(2) first forms a complex with water that reacts with hydroxyl radical or that H(2)O(2) reacts with a previously formed H(2)O·OH complex. With the addition of water, the reaction mechanism becomes much more complex, yielding four different reaction paths. Two pathways do not undergo the oxidation reaction but an exchange reaction where there is an interchange between H(2)O(2)·H(2)O and H(2)O·OH complexes. The other two pathways oxidize H(2)O(2), with a computed total rate constant of 4.09 × 10(-12) cm(3) molecule(-1) s(-1) at 298 K, 2.6 times the value of the rate constant of the unassisted reaction. However, the true effect of water vapor requires taking into account the concentration of the prereactive bimolecular complex, namely, H(2)O(2)·H(2)O. With this consideration, water can actually slow down the oxidation of H(2)O(2) by OH between 1840 and 20.5 times in the 240-425 K temperature range. This is an example that demonstrates how water could be a catalyst in an atmospheric reaction in the laboratory but is slow under atmospheric conditions. PMID:22455374

  7. Influence of water on the mobility of small molecules dispersed in a polymeric system.

    PubMed

    Le Meste, M; Voilley, A; Colas, B

    1991-01-01

    The rotational mobility of paramagnetic solutes dispersed in partially hydrated macromolecules (proteins, polysaccharides, synthetic polymers) was measured using Electron Spin Resonance. A critical minimum amount of water was observed to be necessary for these molecules to reach a level of mobility of the same order as in dilute solutions. This amount of water depended on the size of the diffusing solute and on the microporosity of the macromolecule. Above this critical moisture range, a progressive increase of the proportion of mobile solute occurred over a hydration range determined by the size of the diffusing solute. At the same time, the rotational diffusivity of the mobile solute increased linearly with water content. The mobilization pattern of spin-labelled side chains of caseinates was observed to be similar to that of the solute. Results are discussed with reference to free volume theory. PMID:1660672

  8. Interactions of water, methanol and diethyl ether molecules with the surface of oxidized activated carbon

    NASA Astrophysics Data System (ADS)

    Salame, Issa I.; Bandosz, Teresa J.

    Two samples of oxidized activated carbon of wood origin were used as adsorbents of water, methanol, and diethyl ether. Structural and chemical characteristics of the samples' surfaces were obtained using adsorption of nitrogen and Boehm titration. The adsorption isotherms of water and methanol were measured using a volumetric apparatus whereas the adsorption of diethyl ether was studied by means of inverse gas chromatography at finite concentration. Then the isotherms at three different temperatures were used to calculate the isosteric heats of adsorption. The results showed that the strength of interaction depends on the porosity of the sample and its surface chemistry. The effect of surface chemistry and the presence of oxygenated groups are predominant in the case of water and the least important in the case of diethyl ether. This is the result of the chemical nature of the molecules, their sizes, and the relative strengths of the dispersive interactions in small pores in comparison with hydrogen bonding to surface functional groups.

  9. Single molecule force spectroscopy by AFM indicates helical structure of poly(ethylene-glycol) in water

    NASA Astrophysics Data System (ADS)

    Oesterhelt, F.; Rief, M.; Gaub, H. E.

    1999-03-01

    We elongated individual poly(ethylene-glycol) (PEG) molecules tethered at one end to an AFM cantilever. We observed the resistive force as a function of elongation in different solvents. In all cases the molecular response was found to be fully reversible and thus in thermodynamic equilibrium. In hexadecane the stretched PEG acts like an ideal entropy spring and can be well described as a freely jointed chain. In water we observed marked deviations in the transition region from entropic to enthalpic elasticity, indicating the deformation of a supra-structure within the polymer. An analysis based on elastically coupled Markovian two-level systems agrees well with recent ab initio calculations predicting that PEG in water forms a non-planar supra-structure which is stabilized by water bridges. We obtained a binding free energy of 3.0+/-0.3 kT.

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

    USGS Publications Warehouse

    Lee, J.; Mortland, M.M.; Boyd, S.A.; Chiou, C.T.

    1989-01-01

    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.

  11. Influence of the water molecules near surface of viral protein on virus activation process

    NASA Astrophysics Data System (ADS)

    Shepelenko, S. O.; Salnikov, A. S.; Rak, S. V.; Goncharova, E. P.; Ryzhikov, A. B.

    2009-06-01

    The infection of a cell with influenza virus comprises the stages of receptor binding to the cell membrane, endocytosis of virus particle, and fusion of the virus envelope and cell endosome membrane, which is determined by the conformational changes in hemagglutinin, a virus envelope protein, caused by pH decrease within the endosome. The pH value that induces conformation rearrangements of hemagglutinin molecule considerably varies for different influenza virus strains, first and foremost, due to the differences in amino acid structure of the corresponding proteins. The main goal of this study was to construct a model making it possible to assess the critical pH value characterizing the fusogenic activity of influenza virus hemagglutinin from the data on hemagglutinin structure and experimental verification of this model. Under this model, we assume that when the electrostatic force between interacting hemagglutinin molecules in the virus envelop exceeds a certain value, the hemagglutinin HA1 subunits are arranged so that they form a cavity sufficient for penetration of water molecules. This event leads to an irreversible hydration of the inner fragments of hemagglutinin molecule in a trimer and to the completion of conformational changes. The geometry of electrostatic field in hemagglutinin trimer was calculated taking into account the polarization effects near the interface of two dielectrics, aqueous medium and protein macromolecule. The critical pH values for the conformational changes in hemagglutinin were measured by the erythrocyte hemolysis induced by influenza virus particles when decreasing pH. The critical pH value conditionally separating the pH range into the regions with and without the conformational changes was calculated for several influenza virus H1N1 and H3N2 strains based on the data on the amino acid structure of the corresponding hemagglutinin molecules. Comparison of the theoretical and experimental values of critical pH values for

  12. The Effect of Water Molecules on Mechanical Properties of Bamboo Microfibrils

    NASA Astrophysics Data System (ADS)

    Rahbar, Nima

    Bamboo fibers have higher strength-to-weight ratios than steel and concrete. The unique properties of bamboo fibers come from their natural composite structures that comprise mainly cellulose nanofibrils in a matrix of intertwined hemicellulose and lignin called lignin-carbohydrate complex (LCC). Here, we have utilized atomistic simulations to investigate the mechanical properties and mechanisms of interactions between these materials, in the presence of water molecules. Our results suggest that hemicellulose exhibits better mechanical properties and lignin shows greater tendency to adhere to cellulose nanofibrils. Consequently, the role of hemicellulose found to be enhancing the mechanical properties and lignin found to be providing the strength of bamboo fibers. The abundance of Hbonds in hemicellulose chains is responsible for improving the mechanical behavior of LCC. The strong van der Waals forces between lignin molecules and cellulose nanofibrils is responsible for higher adhesion energy between LCC/cellulose nanofibrils. We also found out that the amorphous regions of cellulose nanofibrils is the weakest interface in bamboo Microfibrils. In presence of water, the elastic modulus of lignin increases at low water content (less than 10 NSF CAREER Grant No. 1261284.

  13. Test conditions greatly influence permeation of water soluble molecules through the intestinal mucosa: need for standardisation.

    PubMed Central

    Peeters, M; Hiele, M; Ghoos, Y; Huysmans, V; Geboes, K; Vantrappen, G; Rutgeerts, P

    1994-01-01

    Permeability tests are widely used to investigate the pathogenesis of various gastrointestinal diseases including coeliac disease, infectious diarrhoea, and inflammatory bowel disease. In Crohn's disease they are used as activity parameters by some investigators. Lack of standardisation, however, makes it very difficult to compare data reported in different studies. The aim of this study was to gather permeation data in well controlled test conditions to standardise the methods. Nine healthy volunteers each received five consecutive permeability tests by mouth using polyethylene glycol-400 (PEG-400) and 51Cr-EDTA as probe molecules. The probes were dissolved in water, a glucose solution, a starch solution, a hyperosmolar lactulose-mannitol solution, and a liquid meal. A significantly decreased permeation for both probes was found when given with the hyperosmolar solution. The 51Cr-EDTA permeation was also decreased with water. The permeability index, 51Cr-EDTA/PEG-400, corrected for influencing factors, confirmed that the lactulose-mannitol solution and plain water yield lower values of macro-molecule permeation than starch, glucose or liquid meal. Hyperosmolarity was clearly accompanied by a decrease in permeability probably caused by reversed solvent drag. Interindividual variability of probe permeation and permeability index is very low with a standard liquid meal. It is proposed that for permeability studies a standard liquid meal is always used. PMID:7959195

  14. Test conditions greatly influence permeation of water soluble molecules through the intestinal mucosa: need for standardisation.

    PubMed

    Peeters, M; Hiele, M; Ghoos, Y; Huysmans, V; Geboes, K; Vantrappen, G; Rutgeerts, P

    1994-10-01

    Permeability tests are widely used to investigate the pathogenesis of various gastrointestinal diseases including coeliac disease, infectious diarrhoea, and inflammatory bowel disease. In Crohn's disease they are used as activity parameters by some investigators. Lack of standardisation, however, makes it very difficult to compare data reported in different studies. The aim of this study was to gather permeation data in well controlled test conditions to standardise the methods. Nine healthy volunteers each received five consecutive permeability tests by mouth using polyethylene glycol-400 (PEG-400) and 51Cr-EDTA as probe molecules. The probes were dissolved in water, a glucose solution, a starch solution, a hyperosmolar lactulose-mannitol solution, and a liquid meal. A significantly decreased permeation for both probes was found when given with the hyperosmolar solution. The 51Cr-EDTA permeation was also decreased with water. The permeability index, 51Cr-EDTA/PEG-400, corrected for influencing factors, confirmed that the lactulose-mannitol solution and plain water yield lower values of macro-molecule permeation than starch, glucose or liquid meal. Hyperosmolarity was clearly accompanied by a decrease in permeability probably caused by reversed solvent drag. Interindividual variability of probe permeation and permeability index is very low with a standard liquid meal. It is proposed that for permeability studies a standard liquid meal is always used. PMID:7959195

  15. Intramolecular cyclization of aspartic acid residues assisted by three water molecules: a density functional theory study

    NASA Astrophysics Data System (ADS)

    Takahashi, Ohgi; Kirikoshi, Ryota

    2014-01-01

    Aspartic acid (Asp) residues in peptides and proteins (l-Asp) are known to undergo spontaneous nonenzymatic reactions to form l-β-Asp, d-Asp, and d-β-Asp residues. The formation of these abnormal Asp residues in proteins may affect their three-dimensional structures and hence their properties and functions. Indeed, the reactions have been thought to contribute to aging and pathologies. Most of the above reactions of the l-Asp residues proceed via a cyclic succinimide intermediate. In this paper, a novel three-water-assisted mechanism is proposed for cyclization of an Asp residue (forming a gem-diol precursor of the succinimide) by the B3LYP/6-31 + G(d,p) density functional theory calculations carried out for an Asp-containing model compound (Ace-Asp-Nme, where Ace = acetyl and Nme = NHCH3). The three water molecules act as catalysts by mediating ‘long-range’ proton transfers. In the proposed mechanism, the amide group on the C-terminal side of the Asp residue is first converted to the tautomeric iminol form (iminolization). Then, reorientation of a water molecule and a conformational change occur successively, followed by the nucleophilic attack of the iminol nitrogen on the carboxyl carbon of the Asp side chain to form the gem-diol species. A satisfactory agreement was obtained between the calculated and experimental energetics.

  16. Two-dimensional interlocked pentagonal bilayer ice: how do water molecules form a hydrogen bonding network?

    PubMed

    Zhu, Weiduo; Zhao, Wen-Hui; Wang, Lu; Yin, Di; Jia, Min; Yang, Jinlong; Zeng, Xiao Cheng; Yuan, Lan-Feng

    2016-06-01

    The plethora of ice structures observed both in bulk and under nanoscale confinement reflects the extraordinary ability of water molecules to form diverse forms of hydrogen bonding networks. An ideal hydrogen bonding network of water should satisfy three requirements: (1) four hydrogen bonds connected with every water molecule, (2) nearly linear hydrogen bonds, and (3) tetrahedral configuration for the four hydrogen bonds around an O atom. However, under nanoscale confinement, some of the three requirements have to be unmet, and the selection of the specific requirement(s) leads to different types of hydrogen bonding structures. According to molecular dynamics (MD) simulations for water confined between two smooth hydrophobic walls, we obtain a phase diagram of three two-dimensional (2D) crystalline structures and a bilayer liquid. A new 2D bilayer ice is found and named the interlocked pentagonal bilayer ice (IPBI), because its side view comprises interlocked pentagonal channels. The basic motif in the top view of IPBI is a large hexagon composed of four small pentagons, resembling the top view of a previously reported "coffin" bilayer ice [Johnston, et al., J. Chem. Phys., 2010, 133, 154516]. First-principles optimizations suggest that both bilayer ices are stable. However, there are fundamental differences between the two bilayer structures due to the difference in the selection among the three requirements. The IPBI sacrifices the linearity of hydrogen bonds to retain locally tetrahedral configurations of the hydrogen bonds, whereas the coffin structure does the opposite. The tradeoff between the conditions of an ideal hydrogen bonding network can serve as a generic guidance to understand the rich phase behaviors of nanoconfined water. PMID:27063210

  17. Climatology of the oceanography in the northern South China Sea Shelf-sea (NoSoCS) and adjacent waters: Observations from satellite remote sensing

    NASA Astrophysics Data System (ADS)

    Pan, X.; Wong, G. T.; Tai, J.; Ho, T.

    2013-12-01

    By using the observations from multiple satellite sensors, the climatology of the oceanography, including the surface wind vector, sea surface temperature (SST), surface chlorophyll a concentration (Chl_a), and vertically integrated net primary production (PPeu), in the northern South China Sea Shelf-sea (NoSoCS) and adjacent waters is evaluated. Regional and sub-regional mechanisms in driving the coastal processes, which influence the spatial and temporal distributional patterns in water component, are assessed. Seasonal vertical convective mixing by wind and surface heating/cooling is the primary force in driving the annual changes in SST and Chl_a in the open South China Sea (SCS), in which highly negative correlation coefficients between Chl_a and SST and moderately positive correlation coefficients between Chl_a and wind speed are found. Together, the seasonal variations in SST and wind speed account for about 80% of the seasonal variation in Chl_a. In the NoSoCS as a whole, however, the contribution is reduced to about 40%, primarily due to the effect of the Pearl River plume. A tongue of water extending eastward from the mouth of the River into the middle shelf with positive correlation coefficients between Chl_a and SST and around zero or slightly negative correlation coefficients between Chl_a and wind is the most striking feature in the NoSoCS. The westward and eastward propagations of the Pearl River plume are both very small during the northeast monsoonal season, driven primarily by the Coriolis effect. The abrupt increase in the areal coverage of the River plume, which is much more pronounced in the eastward propagation, between June and August can be attributed to the prevailing southwest monsoon as well as the annual peak of the river flow. Coastal upwelling is another sub-regional phenomenon in the NoSoCS. The upwelling at the shelf edge off the Taiwan Bank may be characterized by its elevated Chl_a. Its areal coverage and average Chl_a do not vary

  18. Pseudorhabdosynochus species (Monogenoidea, Diplectanidae) parasitizing groupers (Serranidae, Epinephelinae, Epinephelini) in the western Atlantic Ocean and adjacent waters, with descriptions of 13 new species.

    PubMed

    Kritsky, Delane C; Bakenhaster, Micah D; Adams, Douglas H

    2015-01-01

    Seventeen of twenty-three species of groupers collected from the western Atlantic Ocean and adjacent waters were infected with 19 identified species (13 new) of Pseudorhabdosynochus Yamaguti, 1958 (Dactylogyridea, Diplectanidae); specimens of the Spanish flag Gonioplectrus hispanus, coney Cephalopholis fulva, marbled grouper Dermatolepis inermis, mutton hamlet Alphestes afer, and misty grouper Hyporthodus mystacinus were not infected; the yellowmouth grouper Mycteroperca interstitialis and yellowfin grouper Mycteroperca venenosa were infected with unidentified species of Pseudorhabdosynochus; the Atlantic creolefish Paranthias furcifer was infected with an unidentified species of Diplectanidae that could not be accommodated in Pseudorhabdosynochus. The following species of Pseudorhabdosynochus are described or redescribed based entirely or in part on new collections: Pseudorhabdosynochus americanus (Price, 1937) Kritsky & Beverley-Burton, 1986 from Atlantic goliath grouper Epinephelus itajara; Pseudorhabdosynochus yucatanensis Vidal-Martínez, Aguirre-Macedo & Mendoza-Franco, 1997 and Pseudorhabdosynochus justinella n. sp. from red grouper Epinephelus morio; Pseudorhabdosynochus kritskyi Dyer, Williams & Bunkley-Williams, 1995 from gag Mycteroperca microlepis; Pseudorhabdosynochus capurroi Vidal-Martínez & Mendoza-Franco, 1998 from black grouper Mycteroperca bonaci; Pseudorhabdosynochus hyphessometochus n. sp. from Mycteroperca interstitialis; Pseudorhabdosynochus sulamericanus Santos, Buchmann & Gibson, 2000 from snowy grouper Hyporthodus niveatus and Warsaw grouper Hyporthodus nigritus (new host record); Pseudorhabdosynochus firmicoleatus n. sp. from yellowedge grouper Hyporthodus flavolimbatus and snowy grouper H. niveatus; Pseudorhabdosynochus mcmichaeli n. sp., Pseudorhabdosynochus contubernalis n. sp., and Pseudorhabdosynochus vascellum n. sp. from scamp Mycteroperca phenax; Pseudorhabdosynochus meganmarieae n. sp. from graysby Cephalopholis cruentata

  19. Pseudorhabdosynochus species (Monogenoidea, Diplectanidae) parasitizing groupers (Serranidae, Epinephelinae, Epinephelini) in the western Atlantic Ocean and adjacent waters, with descriptions of 13 new species

    PubMed Central

    Kritsky, Delane C.; Bakenhaster, Micah D.; Adams, Douglas H.

    2015-01-01

    Seventeen of twenty-three species of groupers collected from the western Atlantic Ocean and adjacent waters were infected with 19 identified species (13 new) of Pseudorhabdosynochus Yamaguti, 1958 (Dactylogyridea, Diplectanidae); specimens of the Spanish flag Gonioplectrus hispanus, coney Cephalopholis fulva, marbled grouper Dermatolepis inermis, mutton hamlet Alphestes afer, and misty grouper Hyporthodus mystacinus were not infected; the yellowmouth grouper Mycteroperca interstitialis and yellowfin grouper Mycteroperca venenosa were infected with unidentified species of Pseudorhabdosynochus; the Atlantic creolefish Paranthias furcifer was infected with an unidentified species of Diplectanidae that could not be accommodated in Pseudorhabdosynochus. The following species of Pseudorhabdosynochus are described or redescribed based entirely or in part on new collections: Pseudorhabdosynochus americanus (Price, 1937) Kritsky & Beverley-Burton, 1986 from Atlantic goliath grouper Epinephelus itajara; Pseudorhabdosynochus yucatanensis Vidal-Martínez, Aguirre-Macedo & Mendoza-Franco, 1997 and Pseudorhabdosynochus justinella n. sp. from red grouper Epinephelus morio; Pseudorhabdosynochus kritskyi Dyer, Williams & Bunkley-Williams, 1995 from gag Mycteroperca microlepis; Pseudorhabdosynochus capurroi Vidal-Martínez & Mendoza-Franco, 1998 from black grouper Mycteroperca bonaci; Pseudorhabdosynochus hyphessometochus n. sp. from Mycteroperca interstitialis; Pseudorhabdosynochus sulamericanus Santos, Buchmann & Gibson, 2000 from snowy grouper Hyporthodus niveatus and Warsaw grouper Hyporthodus nigritus (new host record); Pseudorhabdosynochus firmicoleatus n. sp. from yellowedge grouper Hyporthodus flavolimbatus and snowy grouper H. niveatus; Pseudorhabdosynochus mcmichaeli n. sp., Pseudorhabdosynochus contubernalis n. sp., and Pseudorhabdosynochus vascellum n. sp. from scamp Mycteroperca phenax; Pseudorhabdosynochus meganmarieae n. sp. from graysby Cephalopholis cruentata

  20. Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water.

    PubMed

    Bannan, Caitlin C; Calabró, Gaetano; Kyu, Daisy Y; Mobley, David L

    2016-08-01

    Partition coefficients describe how a solute is distributed between two immiscible solvents. They are used in drug design as a measure of a solute's hydrophobicity and a proxy for its membrane permeability. We calculate partition coefficients from transfer free energies using molecular dynamics simulations in explicit solvent. Setup is done by our new Solvation Toolkit which automates the process of creating input files for any combination of solutes and solvents for many popular molecular dynamics software packages. We calculate partition coefficients between octanol/water and cyclohexane/water with the Generalized AMBER Force Field (GAFF) and the Dielectric Corrected GAFF (GAFF-DC). With similar methods in the past we found a root-mean-squared error (RMSE) of 6.3 kJ/mol in hydration free energies which would correspond to an error of around 1.6 log units in partition coefficients if solvation free energies in both solvents were estimated with comparable accuracy. Here we find an overall RMSE of about 1.2 log units with both force fields. Results from GAFF and GAFF-DC seem to exhibit systematic biases in opposite directions for calculated cyclohexane/water partition coefficients. PMID:27434695

  1. Explicit Consideration of Water Molecules to Study Vibrational Circular DICHROÎSM of Monosaccharide's

    NASA Astrophysics Data System (ADS)

    Moussi, Sofiane; Ouamerali, Ourida

    2014-06-01

    Carbohydrates have multiples roles in biological systems. It has been found that the glycoside bond is fundamentally important in many aspects of chemistry and biology and forms the basis of carbohydrate chemistry. That means the stereochemical information, namely, glycosidic linkages α or β, gives an significant features of the carbohydrate glycosidation position of the glycosylic acceptor. For these reasons, much effort was made for the synthesis and analysis of the glycoside bond. Vibrational circular dichroism VCD has some advantages over conventional electronic circular dichroism (ECD) due to the applicability to all organic molecules and the reliability of ab initio quantum calculation. However, for a molecule with many chiral centers such as carbohydrates, determination of the absolute configuration tends to be difficult because the information from each stereochemical center is mixed and averaged over the spectrum. In the CH stretching region, only two VCD studies on carbohydrates have been reported and spectra--structure correlation, as determined for the glycoside band, remains to be investigated. T. Taniguchi and collaborators report that methyl glycosides exhibit a characteristic VCD peak, the sign of which solely reflects the C-1 absolute configuration. This work is a theoretical contribution to study the behaviour of VCD spectrum's of the monosaccharides when the water molecules are taken explicitly. This study is focused on six different monosaccharides in theirs absolute configuration R and S. We used the method of density functional theory DFT by means of the B3LYP hybrid functional and 6-31G * basis set.

  2. Energy deposition model based on electron scattering cross section data from water molecules

    NASA Astrophysics Data System (ADS)

    Muñoz, A.; Oiler, J. C.; Blanco, F.; Gorfinkiel, J. D.; Limão-Vieira, P.; Maira-Vidal, A.; Borge, M. J. G.; Tengblad, O.; Huerga, C.; Téllez, M.; García, G.

    2008-10-01

    A complete set of electrons scattering cross sections by water molecules over a broad energy range, from the me V to the Me V ranges, is presented in this study. These data have been obtained by combining experiments and calculations and cover most relevant processes, both elastic and inelastic, which can take place in the considered energy range. A new Monte Carlo simulation programme has been developed using as input parameter these cross sectional data as well as experimental energy loss spectra. The simulation procedure has been applied to obtain electron tracks and energy deposition plots in water when irradiated by a Ru-106 plaque as those used for brachyteraphy of ocular tumours. Finally, the low energy electron tracks provided by the present model have been compared with those obtained with other codes available in the literature

  3. Dipole and quadrupole polarizabilities of the water molecule as a function of geometry.

    PubMed

    Loboda, Oleksandr; Ingrosso, Francesca; Ruiz-López, Manuel F; Reis, Heribert; Millot, Claude

    2016-09-01

    Dipolar, dipole-quadrupole and quadrupole-quadrupole static polarizabilities of the water molecule have been determined by ab initio calculations at coupled cluster level of theory with single, double and perturbative triple excitations CCSD(T) with an aug-cc-pVTZ basis set using a finite field and field-gradient method. The geometry dependence of polarizability tensor components has been explored and modeled by power series expansion in bond length and angle variations up to sum of powers equal to 4. The results provide a very detailed description of the static polarizability of water up to quadrupolar rank which can be used for the test and development of novel accurate polarizable interaction potentials for modeling aqueous solutions. © 2016 Wiley Periodicals, Inc. PMID:27354163

  4. Water and complex organic molecules in the warm inner regions of solar-type protostars

    NASA Astrophysics Data System (ADS)

    Coutens, A.; Jørgensen, J. K.; Persson, M. V.; Lykke, J. M.; Taquet, V.; van Dishoeck, E. F.; Vastel, C.; Wampfler, S. F.

    2015-12-01

    Water and complex organic molecules play an important role in the emergence of Life. They have been detected in different types of astrophysical environments (protostars, prestellar cores, outflows, protoplanetary disks, comets, etc). In particular, they show high abundances towards the warm inner regions of protostars, where the icy grain mantles thermally desorb. Can a part of the molecular content observed in these regions be preserved during the star formation process and incorporated into asteroids and comets, that can deliver it to planetary embryos through impacts? By comparison with cometary studies, interferometric observations of solar-type protostars can help to address this important question. We present recent results obtained with the Plateau de Bure interferometer about water deuteration, glycolaldehyde and ethylene glycol towards the low-mass protostar NGC 1333 IRAS2A.

  5. Tuning dissociation using isoelectronically doped graphene and hexagonal boron nitride: Water and other small molecules

    NASA Astrophysics Data System (ADS)

    Al-Hamdani, Yasmine S.; Alfè, Dario; von Lilienfeld, O. Anatole; Michaelides, Angelos

    2016-04-01

    Novel uses for 2-dimensional materials like graphene and hexagonal boron nitride (h-BN) are being frequently discovered especially for membrane and catalysis applications. Still however, a great deal remains to be understood about the interaction of environmentally and industrially relevant molecules such as water with these materials. Taking inspiration from advances in hybridising graphene and h-BN, we explore using density functional theory, the dissociation of water, hydrogen, methane, and methanol on graphene, h-BN, and their isoelectronic doped counterparts: BN doped graphene and C doped h-BN. We find that doped surfaces are considerably more reactive than their pristine counterparts and by comparing the reactivity of several small molecules, we develop a general framework for dissociative adsorption. From this a particularly attractive consequence of isoelectronic doping emerges: substrates can be doped to enhance their reactivity specifically towards either polar or non-polar adsorbates. As such, these substrates are potentially viable candidates for selective catalysts and membranes, with the implication that a range of tuneable materials can be designed.

  6. Tuning dissociation using isoelectronically doped graphene and hexagonal boron nitride: Water and other small molecules.

    PubMed

    Al-Hamdani, Yasmine S; Alfè, Dario; von Lilienfeld, O Anatole; Michaelides, Angelos

    2016-04-21

    Novel uses for 2-dimensional materials like graphene and hexagonal boron nitride (h-BN) are being frequently discovered especially for membrane and catalysis applications. Still however, a great deal remains to be understood about the interaction of environmentally and industrially relevant molecules such as water with these materials. Taking inspiration from advances in hybridising graphene and h-BN, we explore using density functional theory, the dissociation of water, hydrogen, methane, and methanol on graphene, h-BN, and their isoelectronic doped counterparts: BN dopedgraphene and C doped h-BN. We find that dopedsurfaces are considerably more reactive than their pristine counterparts and by comparing the reactivity of several small molecules, we develop a general framework for dissociative adsorption. From this a particularly attractive consequence of isoelectronic doping emerges: substrates can be doped to enhance their reactivity specifically towards either polar or non-polar adsorbates. As such, these substrates are potentially viable candidates for selective catalysts and membranes, with the implication that a range of tuneable materials can be designed. PMID:27389233

  7. Conserved hydrogen bonds and water molecules in MDR HIV-1 protease substrate complexes

    SciTech Connect

    Liu, Zhigang; Wang, Yong; Yedidi, Ravikiran S.; Dewdney, Tamaria G.; Reiter, Samuel J.; Brunzelle, Joseph S.; Kovari, Iulia A.; Kovari, Ladislau C.

    2012-12-19

    Success of highly active antiretroviral therapy (HAART) in anti-HIV therapy is severely compromised by the rapidly developing drug resistance. HIV-1 protease inhibitors, part of HAART, are losing their potency and efficacy in inhibiting the target. Multi-drug resistant (MDR) 769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, 90) was selected for the present study to understand the binding to its natural substrates. The nine crystal structures of MDR769 HIV-1 protease substrate hepta-peptide complexes were analyzed in order to reveal the conserved structural elements for the purpose of drug design against MDR HIV-1 protease. Our structural studies demonstrated that highly conserved hydrogen bonds between the protease and substrate peptides, together with the conserved crystallographic water molecules, played a crucial role in the substrate recognition, substrate stabilization and protease stabilization. Additionally, the absence of the key flap-ligand bridging water molecule might imply a different catalytic mechanism of MDR769 HIV-1 protease compared to that of wild type (WT) HIV-1 protease.

  8. The binding energies of one and two water molecules to the first transition-row metal positive ions. II

    NASA Technical Reports Server (NTRS)

    Rosi, Marzio; Bauschlicher, Charles W., Jr.

    1990-01-01

    The present investigation of H2O's binding energy to transition-metal ions proceeds from the D(2h) structure and bends the two water molecules out of plane. The molecule is constrained to have C(2v) symmetry, so that each water molecule and metal ion lies on a plane. The ground states are bent only for Mn(H2O)2(+) and Zn(H2O)2(+), where only 4s4p hybridization is energetically favorable; 4s4p hybridization reduces repulsion.

  9. Design, revision, and application of ground-water flow models for simulation of selected water-management scenarios in the coastal area of Georgia and adjacent parts of South Carolina and Florida

    USGS Publications Warehouse

    Clarke, John S.; Krause, Richard E.

    2000-01-01

    Ground-water flow models of the Floridan aquifer system in the coastal area of Georgia and adjacent parts of South Carolina and Florida, were revised and updated to ensure consistency among the various models used, and to facilitate evaluation of the effects of pumping on the ground-water level near areas of saltwater contamination. The revised models, developed as part of regional and areal assessments of ground-water resources in coastal Georgia, are--the Regional Aquifer-System Analysis (RASA) model, the Glynn County area (Glynn) model, and the Savannah area (Savannah) model. Changes were made to hydraulic-property arrays of the RASA and Glynn models to ensure consistency among all of the models; results of theses changes are evidenced in revised water budgets and calibration statistics. Following revision, the three models were used to simulate 32 scenarios of hypothetical changes in pumpage that ranged from about 82 million gallons per day (Mgal/d) lower to about 438 Mgal/d higher, than the May 1985 pumping rate of 308 Mgal/d. The scenarios were developed by the Georgia Department of Natural Resources, Environmental Protection Division and the Chatham County-Savannah Metropolitan Planning Commission to evaluate water-management alternatives in coastal Georgia. Maps showing simulated ground-water-level decline and diagrams presenting changes in simulated flow rates are presented for each scenario. Scenarios were grouped on the basis of pumping location--entire 24-county area, central subarea, Glynn-Wayne-Camden County subarea, and Savannah-Hilton Head Island subarea. For those scenarios that simulated decreased pumpage, the water level at both Brunswick and Hilton Head Island rose, decreasing the hydraulic gradient and reducing the potential for saltwater contamination. Conversely, in response to scenarios of increased pumpage, the water level at both locations declined, increasing the hydraulic gradient and increasing the potential for saltwater contamination

  10. The effects of water molecules on the electronic and structural properties of peptide nanotubes.

    PubMed

    Andrade-Filho, T; Ferreira, Fabio Furlan; Alves, Wendel Andrade; Rocha, Alexandre Reily

    2013-05-28

    The self-assembly of short amino acid chains appears to be one of the most promising strategies for the fabrication of nanostructures. Their solubility in water and the possibility of chemical modification by targeting the amino or carboxyl terminus give peptide-based nanostructures several advantages over carbon nanotube nanostructures. However, because these systems are synthesized in aqueous solution, a deeper understanding is needed on the effects of water especially with respect to the electronic, structural and transport properties. In this work, the electronic properties of L-diphenylalanine nanotubes (FF-NTs) have been studied using the Self-Consistent Charge Density-Functional-based Tight-Binding method augmented with dispersion interaction. The presence of water molecules in the central hydrophilic channel and their interaction with the nanostructures are addressed. We demonstrate that the presence of water leads to significant changes in the electronic properties of these systems decreasing the band gap which can lead to an increase in the hopping probability and the conductivity. PMID:23588391

  11. Hydrodynamic and nonhydrodynamic contributions to the bimolecular collision rates of solute molecules in supercooled bulk water.

    PubMed

    Peric, Ida; Merunka, Dalibor; Bales, Barney L; Peric, Miroslav

    2014-06-26

    Bimolecular collision rate constants of a model solute are measured in water at T = 259-303 K, a range encompassing both normal and supercooled water. A stable, spherical nitroxide spin probe, perdeuterated 2,2,6,6-tetramethyl-4-oxopiperidine-1-oxyl, is studied using electron paramagnetic resonance spectroscopy (EPR), taking advantage of the fact that the rotational correlation time, τ(R), the mean time between successive spin exchanges within a cage, τ(RE), and the long-time-averaged spin exchange rate constants, K(ex), of the same solute molecule may be measured independently. Thus, long- and short-time translational diffusion behavior may be inferred from K(ex) and τ(RE), respectively. In order to measure K(ex), the effects of dipole-dipole interactions (DD) on the EPR spectra must be separated, yielding as a bonus the DD broadening rate constants that are related to the dephasing rate constant due to DD, W(dd). We find that both K(ex) and W(dd) behave hydrodynamically; that is to say they vary monotonically with T/η or η/T, respectively, where η is the shear viscosity, as predicted by the Stokes-Einstein equation. The same is true of the self-diffusion of water. In contrast, τ(RE) does not follow hydrodynamic behavior, varying rather as a linear function of the density reaching a maximum at 276 ± 2 K near where water displays a maximum density. PMID:24874024

  12. Hydrodynamic and Nonhydrodynamic Contributions to the Bimolecular Collision Rates of Solute Molecules in Supercooled Bulk Water

    PubMed Central

    2015-01-01

    Bimolecular collision rate constants of a model solute are measured in water at T = 259–303 K, a range encompassing both normal and supercooled water. A stable, spherical nitroxide spin probe, perdeuterated 2,2,6,6-tetramethyl-4-oxopiperidine-1-oxyl, is studied using electron paramagnetic resonance spectroscopy (EPR), taking advantage of the fact that the rotational correlation time, τR, the mean time between successive spin exchanges within a cage, τRE, and the long-time-averaged spin exchange rate constants, Kex, of the same solute molecule may be measured independently. Thus, long- and short-time translational diffusion behavior may be inferred from Kex and τRE, respectively. In order to measure Kex, the effects of dipole–dipole interactions (DD) on the EPR spectra must be separated, yielding as a bonus the DD broadening rate constants that are related to the dephasing rate constant due to DD, Wdd. We find that both Kex and Wdd behave hydrodynamically; that is to say they vary monotonically with T/η or η/T, respectively, where η is the shear viscosity, as predicted by the Stokes–Einstein equation. The same is true of the self-diffusion of water. In contrast, τRE does not follow hydrodynamic behavior, varying rather as a linear function of the density reaching a maximum at 276 ± 2 K near where water displays a maximum density. PMID:24874024

  13. ORGANIC MOLECULES AND WATER IN THE INNER DISKS OF T TAURI STARS

    SciTech Connect

    Carr, John S.; Najita, Joan R. E-mail: najita@noao.edu

    2011-06-01

    We report high signal-to-noise Spitzer Infrared Spectrograph spectra of a sample of 11 classical T Tauri stars. Molecular emission from rotational transitions of H{sub 2}O and OH and rovibrational bands of simple organic molecules (CO{sub 2}, HCN, C{sub 2}H{sub 2}) is common among the sources in the sample. The emission shows a range in both flux and line-to-continuum ratio for each molecule and in the flux ratios of different molecular species. The gas temperatures (200-800 K) and emitting areas we derive are consistent with the emission originating in a warm disk atmosphere in the inner planet formation region at radii <2 AU. The H{sub 2}O emission appears to form under a limited range of excitation conditions, as demonstrated by the similarity in relative strengths of H{sub 2}O features from star to star and the narrow range in derived temperature and column density. Emission from highly excited rotational levels of OH is present in all stars; the OH emission flux increases with the stellar accretion rate, and the OH/H{sub 2}O flux ratio shows a relatively small scatter. We interpret these results as evidence for OH production via FUV photodissociation of H{sub 2}O in the disk surface layers. No obvious explanation is found for the observed range in the relative emission strengths of different organic molecules or in their strength with respect to water. We put forward the possibility that these variations reflect a diversity in organic abundances due to star-to-star differences in the C/O ratio of the inner disk gas. Stars with the largest HCN/H{sub 2}O flux ratios in our sample have the largest disk masses. While larger samples are required to confirm this, we speculate that such a trend could result if higher mass disks are more efficient at planetesimal formation and sequestration of water in the outer disk, leading to enhanced C/O ratios and abundances of organic molecules in the inner disk. A comparison of our derived HCN-to-H{sub 2}O column density ratio

  14. Dynamic and Static Water Molecules Complement the TN16 Conformational Heterogeneity inside the Tubulin Cavity.

    PubMed

    Majumdar, Sarmistha; Maiti, Satyabrata; Ghosh Dastidar, Shubhra

    2016-01-19

    TN16 is one of the most promising inhibitors of α, β dimer of tubulin that occupies the cavity in the β-subunit located at the dimeric interface, known as the colchicine binding site. The experimentally determined structure of the complex (Protein Data Bank entry 3HKD) presents the conformation and position of the ligand based on the "best fit", keeping the controversy of other significant binding modes open for further investigation. Computation has already revealed that TN16 experiences fluctuations within the binding pocket, but the insight from that previous report was limited by the shorter windows of sampling and by the approximations on the surrounding environment by implicit solvation. This article reports that in most of the cases straightforward MMGBSA calculations of binding energy revealed a gradual loss of stabilization that was inconsistent with the structural observations, and thus, it indicated the lack of consideration of stabilizing factors with appropriate weightage. Consideration of the structurally packed water molecules in the space between the ligand and receptor successfully eliminated such discrepancies between the structure and stability, serving as the "litmus test" of the importance of explicit consideration of such structurally packed water in the calculations. Such consideration has further evidenced a quasi-degenerate character of the different binding modes of TN16 that has rationalized the observed intrinsic fluctuations of TN16 within the pocket, which is likely to be the most critical insight into its entropy-dominated binding. Quantum mechanical calculations have revealed a relay of electron density from TN16 to the protein via a water molecule in a concerted manner. PMID:26666704

  15. Vasoactive properties of CORM-3, a novel water-soluble carbon monoxide-releasing molecule.

    PubMed

    Foresti, Roberta; Hammad, Jehad; Clark, James E; Johnson, Tony R; Mann, Brian E; Friebe, Andreas; Green, Colin J; Motterlini, Roberto

    2004-06-01

    1 Carbon monoxide (CO), one of the end products of heme catabolism by heme oxygenase, possesses antihypertensive and vasodilatory characteristics. We have recently discovered that certain transition metal carbonyls are capable of releasing CO in biological fluids and modulate physiological functions via the delivery of CO. Because the initial compounds identified were not water soluble, we have synthesized new CO-releasing molecules that are chemically modified to allow solubility in water. The aim of this study was to assess the vasoactive properties of tricarbonylchloro(glycinato)ruthenium(II) (CORM-3) in vitro and in vivo. 2 CORM-3 produced a concentration-dependent relaxation in vessels precontracted with phenylephrine, exerting significant vasodilatation starting at concentrations of 25-50 microm. Inactive CORM-3, which does not release CO, did not affect vascular tone. 3 Blockers of ATP-dependent potassium channels (glibenclamide) or guanylate cyclase activity (ODQ) considerably reduced CORM-3-dependent relaxation, confirming that potassium channels activation and cGMP partly mediate the vasoactive properties of CO. In fact, increased levels of cGMP were detected in aortas following CORM-3 stimulation. 4 The in vitro and in vivo vasorelaxant activities of CORM-3 were further enhanced in the presence of YC-1, a benzylindazole derivative which is known to sensitize guanylate cyclase to activation by CO. Interestingly, inhibiting nitric oxide production or removing the endothelium significantly decreased vasodilatation by CORM-3, suggesting that factors produced by the endothelium influence CORM-3 vascular activities. 5 These results, together with our previous findings on the cardioprotective functions of CORM-3, indicate that this molecule is an excellent prototype of water-soluble CO carriers for studying the pharmacological and biological features of CO. PMID:15148243

  16. Vasoactive properties of CORM-3, a novel water-soluble carbon monoxide-releasing molecule

    PubMed Central

    Foresti, Roberta; Hammad, Jehad; Clark, James E; Johnson, Tony R; Mann, Brian E; Friebe, Andreas; Green, Colin J; Motterlini, Roberto

    2004-01-01

    Carbon monoxide (CO), one of the end products of heme catabolism by heme oxygenase, possesses antihypertensive and vasodilatory characteristics. We have recently discovered that certain transition metal carbonyls are capable of releasing CO in biological fluids and modulate physiological functions via the delivery of CO. Because the initial compounds identified were not water soluble, we have synthesized new CO-releasing molecules that are chemically modified to allow solubility in water. The aim of this study was to assess the vasoactive properties of tricarbonylchloro(glycinato)ruthenium(II) (CORM-3) in vitro and in vivo. CORM-3 produced a concentration-dependent relaxation in vessels precontracted with phenylephrine, exerting significant vasodilatation starting at concentrations of 25–50 μM. Inactive CORM-3, which does not release CO, did not affect vascular tone. Blockers of ATP-dependent potassium channels (glibenclamide) or guanylate cyclase activity (ODQ) considerably reduced CORM-3-dependent relaxation, confirming that potassium channels activation and cGMP partly mediate the vasoactive properties of CO. In fact, increased levels of cGMP were detected in aortas following CORM-3 stimulation. The in vitro and in vivo vasorelaxant activities of CORM-3 were further enhanced in the presence of YC-1, a benzylindazole derivative which is known to sensitize guanylate cyclase to activation by CO. Interestingly, inhibiting nitric oxide production or removing the endothelium significantly decreased vasodilatation by CORM-3, suggesting that factors produced by the endothelium influence CORM-3 vascular activities. These results, together with our previous findings on the cardioprotective functions of CORM-3, indicate that this molecule is an excellent prototype of water-soluble CO carriers for studying the pharmacological and biological features of CO. PMID:15148243

  17. Unintended consequences? Water molecules at biological and crystallographic protein-protein interfaces.

    PubMed

    Ahmed, Mostafa H; Habtemariam, Mesay; Safo, Martin K; Scarsdale, J Neel; Spyrakis, Francesca; Cozzini, Pietro; Mozzarelli, Andrea; Kellogg, Glen E

    2013-12-01

    The importance of protein-protein interactions (PPIs) is becoming increasingly appreciated, as these interactions lie at the core of virtually every biological process. Small molecule modulators that target PPIs are under exploration as new therapies. One of the greatest obstacles faced in crystallographically determining the 3D structures of proteins is coaxing the proteins to form "artificial" PPIs that lead to uniform crystals suitable for X-ray diffraction. This work compares interactions formed naturally, i.e., "biological", with those artificially formed under crystallization conditions or "non-biological". In particular, a detailed analysis of water molecules at the interfaces of high-resolution (≤2.30 Å) X-ray crystal structures of protein-protein complexes, where 140 are biological protein-protein complex structures and 112 include non-biological protein-protein interfaces, was carried out using modeling tools based on the HINT forcefield. Surprisingly few and relatively subtle differences were observed between the two types of interfaces: (i) non-biological interfaces are more polar than biological interfaces, yet there is better organized hydrogen bonding at the latter; (ii) biological associations rely more on water-mediated interactions with backbone atoms compared to non-biological associations; (iii) aromatic/planar residues play a larger role in biological associations with respect to water, and (iv) Lys has a particularly large role at non-biological interfaces. A support vector machines (SVMs) classifier using descriptors from this study was devised that was able to correctly classify 84% of the two interface types. PMID:24076743

  18. Orbiting Water Molecules Dance to Tune Of Galaxy's "Central Engine," Astronomers Say

    NASA Astrophysics Data System (ADS)

    2000-01-01

    A disk of water molecules orbiting a supermassive black hole at the core of a galaxy 60 million light-years away is "reverberating" in response to variations in the energy output from the galaxy's powerful "central engine" close to the black hole, astronomers say. The team of astronomers used the National Science Foundation's (NSF) Very Large Array (VLA) radio telescope in New Mexico and the 100-meter-diameter radio telescope of the Max Planck Institute for Radio Astronomy at Effelsberg, Germany, to observe the galaxy NGC 1068 in the constellation Cetus. They announced their findings today at the American Astronomical Society's meeting in Atlanta. The water molecules, in a disk some 5 light-years in diameter, are acting as a set of giant cosmic radio-wave amplifiers, called masers. Using energy radiated by the galaxy's "central engine," the molecules strengthen, or brighten, radio emission at a particular frequency as seen from Earth. "We have seen variations in the radio 'brightness' of these cosmic amplifiers that we believe were caused by variations in the energy output of the central engine," said Jack Gallimore, an astronomer at the National Radio Astronomy Observatory (NRAO) in Charlottesville, VA. "This could provide us with a valuable new tool for learning about the central engine itself," he added. Gallimore worked with Stefi Baum of the Space Telescope Science Institute in Baltimore, MD; Christian Henkel of the Max Planck Institute for Radio Astronomy in Bonn, Germany; Ian Glass of the South African Astronomical Observatory; Mark Claussen of the NRAO in Socorro, NM; and Almudena Prieto of the European Southern Observatory in Munich, Germany. "Our observations show that NGC 1068 is the second-known case of a giant disk of water molecules orbiting a supermassive black hole at a galaxy's core," Gallimore said. The first case was the galaxy NGC 4258 (Messier 106), whose disk of radio-amplifying water molecules was measured by the NSF's Very Long Baseline

  19. Rotations and vibrations of water molecule inside the fullerene cage: infrared study of H2O@C60

    NASA Astrophysics Data System (ADS)

    Room, Toomas; Shugai, A.; Nagel, U.; Mamone, S.; Krachmalnicoff, A.; Whitby, R. J.; Levitt, M. H.; Nishida, T.; Murata, Y.; Lei, Xuegong; Li, Yongjun; Turro, N. J.

    2015-03-01

    Water is the second molecule after hydrogen what has been trapped inside the cage of a C60 molecule by the molucular surgery method. We studied isolated water molecule isotopologs H2O, D2O, and HDO in the solid phase at cryogenic temperatures using IR spectroscopy. The water molecule rotation transitions were observed in the THz and vibration-rotation transitions in the mid-IR range. The slow conversion between para and ortho water allowed us to record the time evolution of spectra and to separate ortho and para absorption lines of water. The similarity of the rotation spectrum of caged water to water in the gas phase indicates that water is free to rotate in the C60 cage even at temperature as low as 3 K. However, spectral lines show a splitting of about 0.5 meV what is not compatible with the icosahedral symmetry of C60. Different models (e.g. crystal field effects in solid C60, C60 cage distortions) will be discussed. This work was supported by institutional research funding IUT23-3 of the Estonian Ministry of Education and Research.

  20. Adsorption of apolar molecules at the water liquid-vapor interface: A Monte Carlo simulations study of the water-n-octane system

    NASA Astrophysics Data System (ADS)

    Jedlovszky, Pál; Varga, Imre; Gilányi, Tibor

    2003-07-01

    The adsorption of n-octane at the water liquid-vapor interface has been investigated by Monte Carlo computer simulation. For this purpose, simulation of five different water-apolar interfacial systems have been performed, in which the number of n-octane molecules has been varied. The results clearly show that the apolar n-octane molecules are adsorbed from the vapor phase at the interface. The adsorption is driven by the weak attraction due to the dispersion forces acting between the water molecules and the methyl and methylene groups of the octanes. This weak attraction is, however, amplified by the fact that it is added up for the CH2 and CH3 groups belonging to the same molecule. Consistently, the n-octane molecules located closest to the aqueous phase are found to prefer all-trans conformation and parallel alignment with the plane of the interface. On the other hand, entropic effects become more important among the molecules of the outer part of the adsorption layer. Hence, the preferred orientation of these molecules is perpendicular to the interface, as they can be extended toward the less dense region of the apolar phase; and gauche dihedrals appear more frequently here than among the molecules located next to the aqueous phase.

  1. Anisotropic conductivity tensor imaging in MREIT using directional diffusion rate of water molecules

    NASA Astrophysics Data System (ADS)

    In Kwon, Oh; Jeong, Woo Chul; Sajib, Saurav Z. K.; Kim, Hyung Joong; Woo, Eung Je

    2014-06-01

    Magnetic resonance electrical impedance tomography (MREIT) is an emerging method to visualize electrical conductivity and/or current density images at low frequencies (below 1 KHz). Injecting currents into an imaging object, one component of the induced magnetic flux density is acquired using an MRI scanner for isotropic conductivity image reconstructions. Diffusion tensor MRI (DT-MRI) measures the intrinsic three-dimensional diffusion property of water molecules within a tissue. It characterizes the anisotropic water transport by the effective diffusion tensor. Combining the DT-MRI and MREIT techniques, we propose a novel direct method for absolute conductivity tensor image reconstructions based on a linear relationship between the water diffusion tensor and the electrical conductivity tensor. We first recover the projected current density, which is the best approximation of the internal current density one can obtain from the measured single component of the induced magnetic flux density. This enables us to estimate a scale factor between the diffusion tensor and the conductivity tensor. Combining these values at all pixels with the acquired diffusion tensor map, we can quantitatively recover the anisotropic conductivity tensor map. From numerical simulations and experimental verifications using a biological tissue phantom, we found that the new method overcomes the limitations of each method and successfully reconstructs both the direction and magnitude of the conductivity tensor for both the anisotropic and isotropic regions.

  2. The hydrolytic water molecule in trypsin, revealed by time-resolved Laue crystallography

    SciTech Connect

    Singer, P.T. ); Smalaas, A. ); Carty, R.P. ); Mangel, W.F.; Sweet, R.M. )

    1993-01-29

    Crystals of bovine trypsin were acylated at the reactive residue, serine 195, to form the transiently stable p-guanidinobenzoate. Hydrolysis of this species was triggered in the crystals by a jump in pH. The hydrolysis was monitored by three-dimensional Laue crystallography, resulting in three x-ray diffraction structures, all from the same crystal and each representing approximately 5 seconds of x-ray exposure. The structures were analyzed at a nominal resolution of 1.8 angstroms and were of sufficient quality to reproduce subtle features in the electron-density maps for each of the structures. Comparison of the structures before and after the pH jump reveals that a water molecule has positioned itself to attack the acyl group in the initial step of the hydrolysis of this transient intermediate. 12 refs., 3 figs., 2 tabs.

  3. Switching of the magnetocaloric effect of Mn(II) glycolate by water molecules.

    PubMed

    Chen, Yan-Cong; Guo, Fu-Sheng; Liu, Jun-Liang; Leng, Ji-Dong; Vrábel, Peter; Orendáč, Martin; Prokleška, Jan; Sechovský, Vladimír; Tong, Ming-Liang

    2014-03-10

    The transformation of Mn(II) glycolates (glc) between the three-dimensional coordination polymer [Mn(glc)2]n (1) and discrete mononuclear phase [Mn(glc)2 (H2O)2] (2) can be reversibly switched by water molecules, which dramatically change the magnetocaloric effect (MCE) of Mn(II) glycolates from the maximum of 6.9 J kg(-1)  K(-1) in 1 to 60.3 J kg(-1)  K(-1) in 2. This case example reveals that the effect of magnetic coupling on MCE plays a dominant role over that of other factors such as magnetic density for 3d-type magnetic refrigerants. PMID:24532426

  4. Computing the energy of a water molecule using multideterminants: A simple, efficient algorithm

    NASA Astrophysics Data System (ADS)

    Clark, Bryan K.; Morales, Miguel A.; McMinis, Jeremy; Kim, Jeongnim; Scuseria, Gustavo E.

    2011-12-01

    Quantum Monte Carlo (QMC) methods such as variational Monte Carlo and fixed node diffusion Monte Carlo depend heavily on the quality of the trial wave function. Although Slater-Jastrow wave functions are the most commonly used variational ansatz in electronic structure, more sophisticated wave functions are critical to ascertaining new physics. One such wave function is the multi-Slater-Jastrow wave function which consists of a Jastrow function multiplied by the sum of Slater determinants. In this paper we describe a method for working with these wave functions in QMC codes that is easy to implement, efficient both in computational speed as well as memory, and easily parallelized. The computational cost scales quadratically with particle number making this scaling no worse than the single determinant case and linear with the total number of excitations. Additionally, we implement this method and use it to compute the ground state energy of a water molecule.

  5. Computing the energy of a water molecule using multideterminants: a simple, efficient algorithm.

    PubMed

    Clark, Bryan K; Morales, Miguel A; McMinis, Jeremy; Kim, Jeongnim; Scuseria, Gustavo E

    2011-12-28

    Quantum Monte Carlo (QMC) methods such as variational Monte Carlo and fixed node diffusion Monte Carlo depend heavily on the quality of the trial wave function. Although Slater-Jastrow wave functions are the most commonly used variational ansatz in electronic structure, more sophisticated wave functions are critical to ascertaining new physics. One such wave function is the multi-Slater-Jastrow wave function which consists of a Jastrow function multiplied by the sum of Slater determinants. In this paper we describe a method for working with these wave functions in QMC codes that is easy to implement, efficient both in computational speed as well as memory, and easily parallelized. The computational cost scales quadratically with particle number making this scaling no worse than the single determinant case and linear with the total number of excitations. Additionally, we implement this method and use it to compute the ground state energy of a water molecule. PMID:22225142

  6. Measurements of the number density of water molecules in plasma by using a combined spectral-probe method

    NASA Astrophysics Data System (ADS)

    Bernatskiy, A. V.; Ochkin, V. N.; Afonin, O. N.; Antipenkov, A. B.

    2015-09-01

    A novel method for measuring the number density of water molecules in low-temperature plasma is developed. The absolute intensities of rotational lines of the (0,0) band of the OH( A 2Σ- X 2П) transition are used. Lines with sufficiently large rotational quantum numbers referring to the so-called "hot" group of molecules produced by electron-impact dissociative excitation of water molecules are chosen for measurements. The excitation rate of a process with a known cross section is determined by measuring the parameters of plasma electrons by means of the probe method. The measured number densities of molecules are compared with those in the initial plasma-forming mixture. The time evolution of the particle densities in plasma is investigated. The problems of the sensitivity and applicability of the absolute spectral method are considered.

  7. Measurements of the number density of water molecules in plasma by using a combined spectral−probe method

    SciTech Connect

    Bernatskiy, A. V. Ochkin, V. N.; Afonin, O. N.; Antipenkov, A. B.

    2015-09-15

    A novel method for measuring the number density of water molecules in low-temperature plasma is developed. The absolute intensities of rotational lines of the (0,0) band of the OH(A{sup 2}Σ–X{sup 2}Π) transition are used. Lines with sufficiently large rotational quantum numbers referring to the so-called “hot” group of molecules produced by electron-impact dissociative excitation of water molecules are chosen for measurements. The excitation rate of a process with a known cross section is determined by measuring the parameters of plasma electrons by means of the probe method. The measured number densities of molecules are compared with those in the initial plasma-forming mixture. The time evolution of the particle densities in plasma is investigated. The problems of the sensitivity and applicability of the absolute spectral method are considered.

  8. How small polar molecules protect membrane systems against osmotic stress: the urea-water-phospholipid system.

    PubMed

    Costa-Balogh, Fátima O; Wennerström, Håkan; Wadsö, Lars; Sparr, Emma

    2006-11-30

    We investigate how a small polar molecule, urea, can act to protect a phospholipid bilayer system against osmotic stress. Osmotic stress can be caused by a dry environment, by freezing, or by exposure to aqueous systems with high osmotic pressure due to solutes like in saline water. A large number of organisms regularly experience osmotic stress, and it is a common response to produce small polar molecules intracellularly. We have selected a ternary system of urea-water-dimyristoyl phosphatidylcholine (DMPC) as a model to investigate the molecular mechanism behind this protective effect, in this case, of urea, and we put special emphasis on the applications of urea in skin care products. Using differential scanning calorimetry, X-ray diffraction, and sorption microbalance measurements, we studied the phase behavior of lipid systems exposed to an excess of solvent of varying compositions, as well as lipid systems exposed to water at reduced relative humidities. From this, we have arrived at a rather detailed thermodynamic characterization. The basic findings are as follows: (i) In excess solvent, the thermally induced lipid phase transitions are only marginally dependent on the urea content, with the exception being that the P(beta) phase is not observed in the presence of urea. (ii) For lipid systems with limited access to solvent, the phase behavior is basically determined by the amount (volume) of solvent irrespective of the urea content. (iii) The presence of urea has the effect of retaining the liquid crystalline phase at relative humidities down to 64% (at 27 degrees C), whereas, in the absence of urea, the transition to the gel phase occurs already at a relative humidity of 94%. This demonstrates the protective effect of urea against osmotic stress. (iv) In skin care products, urea is referred to as a moisturizer, which we find slightly misleading as it replaces the water while keeping the physical properties unaltered. (v) In other systems, urea is known to

  9. The local environment of the molecules in water-DMSO mixtures, as seen from computer simulations and Voronoi polyhedra analysis.

    PubMed

    Idrissi, Abdenacer; Marekha, B; Kiselev, M; Jedlovszky, Pál

    2015-02-01

    Molecular dynamics simulations of water-DMSO mixtures, containing 10, 20, 30, 40, 50, 60, 70, 80, and 90 mol% DMSO, respectively, have been performed on the isothermal-isobaric (N,p,T) ensemble at T = 298 K and at the pressure equal to the experimental vapor pressure at each mixture composition. In addition, simulations of the two neat systems have also been performed for reference. The potential models used in the simulations are known to excellently reproduce the mixing properties of these compounds. The simulation results have been analyzed in detail by means of the Voronoi polyhedra (VP) of the molecules. Distributions of the VP volume and the asphericity parameter as well as that of the radius of the spherical intermolecular voids have been calculated. Detailed analyses of these distributions have revealed that both molecules prefer to be in an environment consisting of both types of molecules, but the affinity of DMSO for mixing with water is clearly stronger than that of water for mixing with DMSO. As a consequence, the dilution of the two neat liquids by the other component has been found to follow different mechanisms: when DMSO is added to neat water small domains of neat-like water persist up to the equimolar composition, whereas no such domains are found when neat DMSO is diluted by water. The observed behaviour is also in line with the fact that the main thermodynamic driving force behind the full miscibility of water and DMSO is the energy change accompanying their mixing, and that the entropy change accompanying this mixing is negative in systems of low and positive in systems of high DMSO mole fractions. Finally, we have found a direct evidence for the existence of strong hydrogen bonded complexes formed by one DMSO and two water molecules, but it has also been shown that these complexes are in equilibrium with single (monomeric) water and DMSO molecules in the mixed systems. PMID:25533427

  10. Effect of nanotube-length on the transport properties of single-file water molecules: Transition from bidirectional to unidirectional

    NASA Astrophysics Data System (ADS)

    Su, Jiaye; Guo, Hongxia

    2011-06-01

    We use molecular dynamics (MD) simulations to study the transport of single-file water molecules through carbon nanotubes (CNTs) with various lengths in an electric field. Most importantly, we find that even the water dipoles inside the CNT are maintained along the field direction, a large amount of water molecules can still transport against the field direction for short CNTs, leading to a low unidirectional transport efficiency (η). As the CNT length increases, the efficiency η will increase remarkably, and achieves the maximum value of 1.0 at or exceeding a critical CNT length. Consequently, the transition from bidirectional to unidirectional transport is observed and is found to be relevant to thermal fluctuations of the two reservoirs, which is explored by the interaction between water molecules inside and outside the CNT. We also find that the water flow vs CNT length follows an exponential decay of f ˜ exp ( - L/L0), and the average translocation time of individual water molecules yields to a power law of τtrans ˜ Lυ, where L0 and ν are constant and slightly depend on the field strength. We further compare our results with the continuous-time random-walk (CTRW) model and find that the water flow can also be described by a power law of f ˜ L-μ modified from CTRW. Our results provide some new physical insights into the biased transport of single-file water molecules, which show the feasibility of using CNTs with any length to pump water in an electric field. The mechanism is important for designing efficient nanofluidic apparatuses.

  11. Transition energies of benzoquinone anions are immune to symmetry breaking by a single water molecule.

    PubMed

    Stockett, Mark H; Nielsen, Steen Brøndsted

    2016-03-14

    p-Benzoquinone is the prototypical member of the quinone class of molecules with a basic functionality relevant for the primary reactions of photosynthesis. As electronically excited quinone anions are formed in near-resonant electron transfer, key issues are how the local environment affects excited-state energy levels and deexcitation times. The former we address here with action spectroscopy of mass-selected bare radical anions (pBQ(-)) and one-water pBQ(-)·H2O complexes, isolated in vacuo. The complex represents a precursor for internal proton transfer to form the semiquinone free radical, the first chemical product in the light-driven electron transport chain. Both ions display bands in the visible and ultraviolet with, importantly, almost identical maxima. Despite localizing negative charge, thereby breaking the high orbital symmetries, water is surprisingly innocent. This finding implies that natural fluctuations in the quinone microenvironment cause only minor variations in excited-state energies and thus electron-transfer rates. Hence quinones are robust participants in electron transport. PMID:26490302

  12. A proactive role of water molecules in acceptor recognition by protein O-fucosyltransferase 2.

    PubMed

    Valero-González, Jessika; Leonhard-Melief, Christina; Lira-Navarrete, Erandi; Jiménez-Osés, Gonzalo; Hernández-Ruiz, Cristina; Pallarés, María Carmen; Yruela, Inmaculada; Vasudevan, Deepika; Lostao, Anabel; Corzana, Francisco; Takeuchi, Hideyuki; Haltiwanger, Robert S; Hurtado-Guerrero, Ramon

    2016-04-01

    Protein O-fucosyltransferase 2 (POFUT2) is an essential enzyme that fucosylates serine and threonine residues of folded thrombospondin type 1 repeats (TSRs). To date, the mechanism by which this enzyme recognizes very dissimilar TSRs has been unclear. By engineering a fusion protein, we report the crystal structure of Caenorhabditis elegans POFUT2 (CePOFUT2) in complex with GDP and human TSR1 that suggests an inverting mechanism for fucose transfer assisted by a catalytic base and shows that nearly half of the TSR1 is embraced by CePOFUT2. A small number of direct interactions and a large network of water molecules maintain the complex. Site-directed mutagenesis demonstrates that POFUT2 fucosylates threonine preferentially over serine and relies on folded TSRs containing the minimal consensus sequence C-X-X-S/T-C. Crystallographic and mutagenesis data, together with atomic-level simulations, uncover a binding mechanism by which POFUT2 promiscuously recognizes the structural fingerprint of poorly homologous TSRs through a dynamic network of water-mediated interactions. PMID:26854667

  13. State of Water Molecules and Silanol Groups in Opal Minerals: a Near Infrared Spectroscopic Study of Opals from Slovakia

    NASA Astrophysics Data System (ADS)

    Bobon, Miroslav; Christy, Alfred A.; Kluvanec, Daniel; Illasova, L'udmila

    2011-06-01

    Recently near infrared spectroscopy in combination with double derivative technique has been effectively used by Christy [1] to differentiate between free silanol groups and hydrogen bonded silanol groups on silica gel. The method has given some insight into the type of functionalities and their location in silica gel samples. The inportant information in this respect comes from the overtones of the OH groups of water molecules hydrogen bonded to free silanol groups, and hydrogen bonded silanol groups absorbing in the region 5500- 5100 Cm-1 region. The approach was adapted to study the state of water and silanol functionalities and their locations in opals from Slovakia. Twenty opal samples classified into CT and A classes and one quartz sample were used in this work. The samples were crushed using a hydrolic press and powderised. Each sample was then subjected to evacuation process to remove surface adsorbed water at 200°C and the near infrared spectrum of the sample was measured using a Perkin Elmer NTS near infrared spectrometer equipped with a transflectance accessory. The detailed analysis of the sample was carried out using the second derivative profile of the spectrum. The samples were also heated to 750°C to study the state of water molecules in Opal minerals. The results indicate that the opal samples contain 1) surface adsorbed water 2) free and hydrogen bonded silanol groups on the surface 3) Trapped water in the bulk 4) free and hydrogen bonded silanol groups in the cavity surfaces in the bulk. A part of the water molecules found in the bulk of opal minerals are free molecules and the rest are found in hydrogen bonded state to free and hydrogen bonded silanol groups. [1] A. A. Christy, New insights into the surface functionalities and adsorption evolution of water molecules on silica gel surface: A study by second derivative Near Infrared Spectroscopy, Vib. Spectrosc. 54 (2010) 42-49.

  14. Hyperfine coupling constants on inner-sphere water molecules of Gd(III)-based MRI contrast agents.

    PubMed

    Esteban-Gómez, David; de Blas, Andrés; Rodríguez-Blas, Teresa; Helm, Lothar; Platas-Iglesias, Carlos

    2012-11-12

    Herein we present a theoretical investigation of the hyperfine coupling constants (HFCCs) on the inner-sphere water molecules of [Gd(H(2)O)(8)](3+) and different Gd(III)-based magnetic resonance imaging contrast agents such as [Gd(DOTA)(H(2)O)](-), [Gd(DTPA)(H(2)O)](2-), [Gd(DTPA-BMA)(H(2)O)] and [Gd(HP-DO3A)(H(2)O)]. DFT calculations performed on the [Gd(H(2)O)(8)](3+) model system show that both hybrid-GGA functionals (BH&HLYP, B3PW91 and PBE1PBE) and the hybrid meta-GGA functional TPSSh provide (17)O HFCCs in close agreement with the experimental data. The use of all-electron relativistic approaches based on the DKH2 approximation and the use of relativistic effective core potentials (RECP) provide results of essentially the same quality. The accurate calculation of HFCCs on the [Gd(DOTA)(H(2)O)](-), [Gd(DTPA)(H(2)O)](2-), [Gd(DTPA-BMA)(H(2)O)] and [Gd(HP-DO3A)(H(2)O)] complexes requires an adequate description of solvent effects. This was achieved by using a mixed cluster/continuum approach that includes explicitly two second-sphere water molecules. The calculated isotropic (17)O HFCCs (A(iso)) fall within the range 0.40-0.56 MHz, and show deviations from the corresponding experimental values typically lower than 0.05 MHz. The A(iso) values are significantly affected by the distance between the oxygen atom of the coordinated water molecule and the Gd(III) ion, as well as by the orientation of the water molecule plane with respect to the Gd-O vector. (1)H HFCCs of coordinated water molecules and (17)O HFCCs of second-sphere water molecules take values close to zero. PMID:22927182

  15. Modeling the impacts of winter cover crops on water quality in two adjacent sub-watersheds within the Chesapeake Bay Watershed, Maryland, USA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Choptank River on Maryland’s Eastern Shore has been designated by the USEPA as “impaired waters” under Section 303(d) of the Federal Clean Water Act of 1972, mainly because of significant nutrient loads that resulted in not meeting the EPA water quality standards. This water quality deteriorati...

  16. Lance water injection tests adjacent to the 281-3H retention basin at the Savannah River Site, Aiken, South Carolina

    SciTech Connect

    Freifeld, B.; Myer, L.; Moridis, G.; Cook, P.; James, A.; Pellerin, L.; Pruess, K.

    1996-09-01

    A pilot-scale field demonstration of waste isolation using viscous- liquid containment barriers has been planned for the 281-3H retention basin at the Savannah River Site, Aiken, SC. The 281-3H basin is a shallow retention/seepage basin contaminated mainly by radionuclides. The viscous-liquid containment barrier utilizes the permeation of liquid grout to either entomb the contaminants within a monolithic grout structure or to isolate the waste by drastically reducing the permeability, of the soils around the plume. A clear understanding of the hydrogeologic setting of the retention basin is necessary for proper design of the viscous liquid barrier. To aid in the understanding of the hydrogeology of the 281-3H retention basin, and to obtain critical parameters necessary for grout injection design, a series of tests were undertaken in a region immediately adjacent to the basin. The objectives of the LWIT were: 1. To evaluate the general performance of the Lance Injection Technique for grout emplacement at the site, including the range and upper limits of injection pressures, the flow rates applicable for site conditions, as well as the mechanical forces needed for lance penetration. 2. To obtain detailed information on the injectability of the soils immediately adjacent to the H-area retention basin. 3. To identify any high permeability zones suitable for injection and evaluate their spatial distribution. 4. To perform ground penetrating radar (GPR) to gain information on the structure of the soil column and to compare the results with LWIT data. This report will focus on results pertinent to these objectives.

  17. Limnological characteristics of selected lakes in the Nebraska sandhills, U.S.A., and their relation to chemical characteristics of adjacent ground water

    NASA Astrophysics Data System (ADS)

    La Baugh, James W.

    1986-10-01

    Limnological characteristics of Crane, Hackberry, Island and Roundup Lakes, and chemical characteristics of shallow ground water, within the Crescent Lake National Wildlife Refuge, western Nebraska, were determined during a preliminary investigation of the interaction between lakes and ground water in this study area between 1980 and 1984. When ice cover was absent, the lakes were well-mixed vertically, regardless of season. Depth to which 1% of surface illumination penetrated was commonly less than 1m. Variability in light penetration, as measured by Secchidisk transparency, appeared to be unrelated to changes in algal biomass, even though algal biomass, measured as chlorophyll a, varied seasonally within a two-order-of-magnitude range. Blue-green algae were the most abundant phytoplankton; this condition occurred most often when the ratio of total nitrogen to total phosphorus in the lakes' water was less than 29. Although rotifers and copepod naupli commonly were the most abundant zooplankton in the lakes, cladocerans were dominant occasionally. Either sodium or calcium was the most abundant cation, and bicarbonate was the most abundant anion, in water from water-table wells and lakes sampled during the study. The second most abundant cation in the ground water was related to the location of the sampled well within the ground-water system. The lakes were a source of dissolved organic carbon seeping to ground water. Chemical and hydrologic data indicate there is interaction between lakes and ground water in the study area.

  18. The impact of variations in oceanographic conditions on distribution of redfish in the Irminger Sea and adjacent waters - the temperature is as major factor such cause according to analysis of climatic variability and SST Satellite Data

    NASA Astrophysics Data System (ADS)

    Vanyushin, Georgy; Melnikov, Sergey; Bulatova, Tatiana; Krovnin, Andrey; Troshkov, Anatoly

    2016-04-01

    In this study, for the first time, the data of satellite ("NOAA" and "Meteosat") monitoring of the Irminger Sea and adjacent waters were used to estimate the impact of the Sea surface temperature (SST) on distribution and density of redfish concentrations. We made analytical calculations of the average values of SST for the reference zone of the Irminger Sea, integral acoustic values (SA) for the reference zone, and the average values of the SA only for those sites on the reference zone where redfish were found in the layer 0-500 m. The strong correlation between SST and average values of redfish density for real situations shows that the lower SST values correspond to the lower integral and average values of redfish density. The area of the Irminger Sea and adjacent waters is characterized by considerable interannual and decadal climatic variability associated with the state of the NAO (the North Atlantic Oscillation) and phase of the AMO (the Atlantic Multidecadal Oscillation). This results in corresponding variations of the thermal parameters in the upper 500-m layer. The further investigations are needed to identify mechanisms of transfer of physical anomalies controlled by the NAO and AMO, from the sea surface into the intermediate and deep layers of water column. The climatic variability leads to permanent spatial redistribution of redfish concentrations. The results obtained confirm that environmental processes, rather than fishery, have the greater impact on estimates of redfish distribution. Key words: satellite monitoring of SST, climatic variability, the North Atlantic, the Irminger Sea, redfish distribution.

  19. State of water molecules and silanol groups in opal minerals: a near infrared spectroscopic study of opals from Slovakia

    NASA Astrophysics Data System (ADS)

    Boboň, Miroslav; Christy, Alfred A.; Kluvanec, Daniel; Illášová, L'udmila

    2011-12-01

    Recently, near infrared spectroscopy in combination with double derivative technique has been effectively used by Christy (Vib Spectrosc 54:42-49, 2010) to study and differentiate between free and hydrogen bonded silanol groups on silica gel surface. The method has given some insight into the type of functionalities, their location in silica gel samples, and the way the water molecules bind onto the silanol groups. The important information in this respect comes from the overtones of the OH groups of water molecules hydrogen-bonded to free silanol groups, and hydrogen-bonded silanol groups absorbing in the region 5,500-5,100 cm-1. Chemically, opal minerals are hydrated silica and the same approach was adapted to study the state of water molecules, silanol functionalities, and their locations in opal samples from Slovakia. Twenty opal samples classified into CT and A classes and one quartz sample were used in this work. The samples were crushed using a hydraulic press and powderized. Each sample was then subjected to evacuation process to remove surface-adsorbed water at 200°C, and the near infrared spectrum of each sample was measured using a Perkin Elmer NTS FT-NIR spectrometer equipped with a transflectance accessory and a DTGS detector. The samples were also heated to 750°C to remove the hydrogen-bonded silanol groups on the surface to reveal their locality. Second derivative profiles of the near infrared reflectance spectra were obtained using the instrument's software and used in the detailed analysis of the samples. The analysis of the near infrared spectra and their second derivative profiles had the aim in finding relationships between the surface chemical structure and the classification of opal samples. The dry opal samples were also tested for their surface adsorption effectivity toward water molecules. The results indicate that the opal samples contain (1) surface-adsorbed water, (2) free and hydrogen-bonded silanol groups on the surface, (3) trapped

  20. Hydrology and water quality of a field and riparian buffer adjacent to a mangrove wetland in Jobos Bay Watershed, Puerto Rico

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Models that estimate the effects of agricultural conservation practices on water quantity and quality have become increasingly important tools for short- and long-term assessments. In this study, we simulated the water quality and hydrology of a portion of the Jobos Bay watershed, Puerto Rico using...

  1. Two-dimensional description of surface-bounded exospheres with application to the migration of water molecules on the Moon

    NASA Astrophysics Data System (ADS)

    Schorghofer, Norbert

    2015-05-01

    On the Moon, water molecules and other volatiles are thought to migrate along ballistic trajectories. Here, this migration process is described in terms of a two-dimensional partial differential equation for the surface concentration, based on the probability distribution of thermal ballistic hops. A random-walk model, a corresponding diffusion coefficient, and a continuum description are provided. In other words, a surface-bounded exosphere is described purely in terms of quantities on the surface, which can provide computational and conceptual advantages. The derived continuum equation can be used to calculate the steady-state distribution of the surface concentration of volatile water molecules. An analytic steady-state solution is obtained for an equatorial ring; it reveals the width and mass of the pileup of molecules at the morning terminator.

  2. Single-molecule analysis of ultradilute solutions with guided streams of 1-{mu}m water droplets

    SciTech Connect

    Kung, C.; Barnes, M.D.; Lermer, N.; Whitten, W.B.; Ramsey, J.M.

    1999-03-01

    We describe instrumentation for real-time detection of single-molecule fluorescence in guided streams of 1-{mu}m (nominal) water droplets. In this technique, target molecules were confined to droplets whose volumes were comparable with illumination volumes in diffraction-limited fluorescence microscopy and guided to the waist of a cw probe laser with an electrostatic potential. Concentration detection limits for Rhodamine 6G in water were determined to be {approximately}1 fM, roughly 3 orders of magnitude lower than corresponding limits determined recently with diffraction-limited microscopy techniques for a chemical separation of similar dyes. In addition to its utility as a vehicle for probing single molecules, instrumentation for producing and focusing stable streams of 1{endash}2-{mu}m-diameter droplets may have other important analytical applications as well. {copyright} 1999 Optical Society of America

  3. Cardioprotective actions by a water-soluble carbon monoxide-releasing molecule.

    PubMed

    Clark, James E; Naughton, Patrick; Shurey, Sandra; Green, Colin J; Johnson, Tony R; Mann, Brian E; Foresti, Roberta; Motterlini, Roberto

    2003-07-25

    Carbon monoxide, which is generated in mammals during the degradation of heme by the enzyme heme oxygenase, is an important signaling mediator. Transition metal carbonyls have been recently shown to function as carbon monoxide-releasing molecules (CO-RMs) and to elicit distinct pharmacological activities in biological systems. In the present study, we report that a water-soluble form of CO-RM promotes cardioprotection in vitro and in vivo. Specifically, we found that tricarbonylchloro(glycinato)ruthenium(II) (CORM-3) is stable in water at acidic pH but in physiological buffers rapidly liberates CO in solution. Cardiac cells pretreated with CORM-3 (10 to 50 micromol/L) become more resistant to the damage caused by hypoxia-reoxygenation and oxidative stress. In addition, isolated hearts reperfused in the presence of CORM-3 (10 micromol/L) after an ischemic event displayed a significant recovery in myocardial performance and a marked and significant reduction in cardiac muscle damage and infarct size. The cardioprotective effects mediated by CORM-3 in cardiac cells and isolated hearts were totally abolished by 5-hydroxydecanoic acid, an inhibitor of mitochondrial ATP-dependent potassium channels. Predictably, cardioprotection is lost when CORM-3 is replaced by an inactive form (iCORM-3) that is incapable of liberating CO. Using a model of cardiac allograft rejection in mice, we also found that treatment of recipients with CORM-3 but not iCORM-3 considerably prolonged the survival rate of transplanted hearts. These data corroborate the notion that transition metal carbonyls could be used as carriers to deliver CO and highlight the bioactivity and potential therapeutic features of CO-RMs in the mitigation of cardiac dysfunction. The full text of this article is available online at http://www.circresaha.org. PMID:12842916

  4. Water-level data for the Albuquerque Basin and adjacent areas, central New Mexico, period of record through September 30, 2014

    USGS Publications Warehouse

    Beman, Joseph E.

    2015-01-01

    An initial network of wells was established by the U.S. Geological Survey (USGS) in cooperation with the City of Albuquerque from April 1982 through September 1983 to monitor changes in groundwater levels throughout the basin. This network consisted of 6 wells with analog-to-digital recorders and 27 wells where water levels were measured monthly in 1983. The network currently (2014) consists of 125 wells and piezometers. (A piezometer is a specialized well open to a specific depth in the aquifer, often of small diameter and nested with other piezometers open to different depths.) The USGS, in cooperation with the Albuquerque Bernalillo County Water Utility Authority, currently (2014) measures and reports water levels from the 125 wells and piezometers in the network; this report presents water-level data collected by USGS personnel at those 125 sites through water year 2014 (October 1, 2013, to September 30, 2014).

  5. Computing the energy of a water molecule using multideterminants: A simple, efficient algorithm

    SciTech Connect

    Clark, Bryan K.; Morales, Miguel A; Mcminis, Jeremy; Kim, Jeongnim; Scuseria, Gustavo E

    2011-01-01

    Quantum Monte Carlo (QMC) methods such as variational Monte Carlo and fixed node diffusion Monte Carlo depend heavily on the quality of the trial wave function. Although Slater-Jastrow wave functions are the most commonly used variational ansatz in electronic structure, more sophisticated wave functions are critical to ascertaining new physics. One such wave function is the multi-Slater- Jastrow wave function which consists of a Jastrow function multiplied by the sum of Slater deter- minants. In this paper we describe a method for working with these wave functions in QMC codes that is easy to implement, efficient both in computational speed as well as memory, and easily par- allelized. The computational cost scales quadratically with particle number making this scaling no worse than the single determinant case and linear with the total number of excitations. Addition- ally, we implement this method and use it to compute the ground state energy of a water molecule. 2011 American Institute of Physics. [doi:10.1063/1.3665391

  6. Association of Catechin Molecules in Water: Quantitative Binding Study and Complex Structure Analysis.

    PubMed

    Ujihara, Tomomi; Hayashi, Nobuyuki

    2016-01-22

    Associations between catechin molecules were investigated by (1)H NMR titration experiments. Eight green tea catechins formed self-assembled dimers in water, and gallate-type catechins had a greater tendency to self-associate than non-gallate-type catechins. All eight catechins also associated as 1:1 heterodimer complexes. Investigation of complex formation of epigallocatechin-3-O-gallate (EGCg) and epigallocatechin (EGC) with the other catechins showed that the affinity between EGCg and 2,3-trans-gallate-type catechins was remarkably high, and the binding affinity of EGCg for ECg was also rather strong. In contrast, the non-gallate-type catechin EGC exhibited generally low binding affinity for other catechins. Structural analyses of the complexes by ROESY experiments and density functional theory calculations demonstrated that the higher binding abilities of gallate-type catechins are due to providing multiple intermolecular interactions that remain effective in an aqueous environment, such as aromatic/aromatic or CH/π interactions. PMID:26720794

  7. About Some Of The Properties Of A Guest Molecule Confined In A Water Network, In Order To Form A Clathrate

    NASA Astrophysics Data System (ADS)

    Pérez, G. Bravo; Cruz-Torres, A.; Romero-Martínez, A.

    2008-03-01

    At conditions of high pressure and or low temperature, like a sea bottom from even 1 Km deep, hydrates formation may take place. Its presence is facilitated at the water/oil interface inside conducting oil pipelines. Once formed, the hydrates nucleate further to agglomerations, sticking to the inner surface of the tube. This represents a big problem to flow assurance. We present results contributing to a better understanding of the interaction of a guest molecule with a water cage confining it, that give rise to a hydrate formation. The hydrate structure, its formation energy, and the role that the H bond and its cooperative effect in the water network play in the electrostatic dipole moment of the hydrate, are presented. Molecular calculations using the HF/6-311g(d, p), B3LYP/6-311g(d, p), and B3LYP/6-311++g(d,p) methods, have been applied to compare three different hydrates, each one confining one, two CH4 molecules, and a CO2 molecule, requiring respectively n = 14, 35, and 15 water molecules for the confinement.

  8. Discharge, suspended sediment, and salinity in the Gulf Intracoastal Waterway and adjacent surface waters in South-Central Louisiana, 1997–2008

    USGS Publications Warehouse

    Swarzenski, Christopher M.; Perrien, Scott M.

    2015-01-01

    River water penetrates much of the Louisiana coast, as demonstrated by the large year-to-year fluctuations in salinity regimes of intradistributary basins in response to differences in flow regimes of the Mississippi and the Atchafalaya Rivers. This occurs directly through inflow along the GIWW and through controlled diversions and indirectly by transport into basin interiors after mixing with the Gulf of Mexico. The GIWW plays an important role in moderating salinity in intradistributary basins; for example, salinity in surface waters just south of the GIWW between Bayou Boeuf and the Houma Navigation Canal remained low even during a year with prolonged low water (2000).

  9. Potentiometric surface of Floridan aquifer May 1975, and change of potentiometric surface 1969 to 1975, Southwest Florida Water Management District and adjacent areas

    USGS Publications Warehouse

    Mills, L.R.; Laughlin, C.P.

    1976-01-01

    Maps showing the potentiometric surface of the Floridan aquifer for May 1975, and changes of potentiometric surface from 1964 to 1975 were prepared for areas in southwest Florida. Contours and color codes describe water-level changes. The larger map, scale 1:500,000, reflects the water-level changes from 1969-75. The smaller map shows the changes from January 1964 to May 1969. (Woodard-USGS)

  10. Water and Streambed Sediment Quality, and Ecotoxicology of a Stream along the Blue Ridge Parkway, Adjacent to a Closed Landfill, near Roanoke, Virginia: 1999

    USGS Publications Warehouse

    Ebner, Donna Belval; Cherry, Donald S.; Currie, Rebecca J.

    2004-01-01

    A study was done of the effects of a closed landfill on the quality of water and streambed sediment and the benthic macroinvertebrate community of an unnamed stream and its tributary that flow through Blue Ridge Parkway lands in west-central Virginia. The primary water source for the tributary is a 4-inch polyvinyl chloride (PVC) pipe that protrudes from the slope at the base of the embankment bordering the landfill. An unusual expanse of precipitate was observed in the stream near the PVC pipe. Stream discharge was measured and water and streambed sediment samples were collected at a nearby reference site and at three sites downstream of the landfill in April and September 1999. Water samples were analyzed for major ions, nitrate, total and dissolved metals, total dissolved solids, total organic carbon, and volatile and semivolatile organic compounds, including organochlorine pesticides and polychlorinated biphenyls (PCBs). Streambed sediment samples were analyzed for total metals, total organic carbon, percent moisture, and volatile and semivolatile organic compounds, including organochlorine pesticides and PCBs. The benthic macroinvertebrate community within the stream channel also was sampled at the four chemical sampling sites and at one additional site in April and September. Each of the five sites was assessed for physical habitat quality. Water collected periodically at the PVC pipe discharge between November 1998 and November 1999 was used to conduct 48-hour acute and 7-day chronic toxicity tests using selected laboratory test organisms. Two 10-day chronic toxicity tests of streambed sediments collected near the discharge pipe also were conducted. Analyses showed that organic and inorganic constituents in water from beneath the landfill were discharged into the sampled tributary. In April, 79 percent of inorganic constituents detected in water had their highest concentrations at the site closest to the landfill; at the same site, 59 percent of inorganic

  11. A reconnaissance of the water resources of the Shoalwater Bay Indian Reservation and adjacent areas, Pacific County, Washington, 1978-1979

    USGS Publications Warehouse

    Lum, W.E.

    1984-01-01

    A 1978-79 reconnaissance of the quantity and quality of water in the Shoalwater Bay Indian Reservation yielded information needed by the Shoalwater Bay Indian Tribe to plan future use of these resources. Ground water from the local artesian aquifer is suitable for most uses and it is estimated that yield can be as much as 100 to 500 gallons per minute. Long-term yields cannot be calculated from available data. Data from 1968-80 show no measurable declines in water levels or rates of flow due to pumping from the aquifer. Analysis of ground-water samples indicated no seawater intrusion into the aquifer. Mean monthly flows of two streams in the study area ranged from 0.53 to 3.28 cubic feet per second in February 1979. Estimated average 7-day low flows with a recurrance interval of 2 years ranged from 0.3 to 3.0 cubic feet per second. Analyses of surface-water samples indicated concentrations of Aldrin, DDD, DDT, Dieldrin, Diazinon , and Ethyl Parathion that exceeded EPA limits for protection of marine life. Samples of the stream-bottom material in one stream had high concentrations of Aldrin, DDD, DDE, DDT, Dichlobenil, and Dieldrin. Tribally owned tidelands into which these streams flow may be contaminated by these toxic chemicals. (USGS)

  12. Differential flexibility of the secondary structures of lysozyme and the structure and ordering of surrounding water molecules

    NASA Astrophysics Data System (ADS)

    Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy

    2011-03-01

    We have performed an atomistic molecular dynamics simulation of an aqueous solution of hen egg-white lysozyme at room temperature with explicit water molecules. Several analyses have been carried out to explore the differential flexibility of the secondary structural segments of the protein and the structure and ordering of water around them. It is found that the overall flexibility of the protein molecule is primarily controlled by few large-amplitude bistable motions exhibited by two coils; one connecting two α-helical segments in domain-1 and the other connecting a 310 helix and a β-sheet in domain-2 of the protein. The heterogeneous structuring of water around the segments of the protein has been found to depend on the degree of exposure of the segments to water. The ordering of water molecules around the protein segments and their tagged potential energies have been found to be anticorrelated with each other. Some of these findings can be verified by suitable experimental studies.

  13. Label-Free Fluctuation Spectroscopy Based on Coherent Anti-Stokes Raman Scattering from Bulk Water Molecules.

    PubMed

    Rabasovic, M D; Sisamakis, E; Wennmalm, S; Widengren, J

    2016-04-01

    Nanoparticles (NPs) and molecules can be analyzed by inverse fluorescence correlation spectroscopy (iFCS) as they pass through an open detection volume, displacing fractions of the fluorescence-emitting solution in which they are dissolved. iFCS does not require the NPs or molecules to be labeled. However, fluorophores in μm-mm concentrations are needed for the solution signal. Here, we instead use coherent anti-Stokes Raman scattering (CARS) from plain water molecules as the signal from the solution. By this fully label-free approach, termed inverse CARS-based correlation spectroscopy (iCARS-CS), NPs that are a few tenths of nm in diameter and at pM concentrations can be analyzed, and their absolute volumes/concentrations can be determined. Likewise, lipid vesicles can be analyzed as they diffuse/flow through the detection volume by using CARS fluctuations from the surrounding water molecules. iCARS-CS could likely offer a broadly applicable, label-free characterization technique of, for example, NPs, small lipid exosomes, or microparticles in biomolecular diagnostics and screening, and can also utilize CARS signals from biologically relevant media other than water. PMID:26819085

  14. The Formation of Oxygen-Containing Molecules in Liquid Water Environments on the Surface of Titan (Invited)

    NASA Astrophysics Data System (ADS)

    Neish, C.

    2010-12-01

    Saturn’s moon Titan represents a unique locale for studying prebiotic chemistry. Reactions occurring in its thick nitrogen - methane atmosphere produce a wide variety of organic molecules. Observations by the Voyager spacecraft found evidence for six gas-phase hydrocarbons and three nitriles, along with an enveloping haze layer shrouding the surface of the moon (Hanel et al., 1981; Kunde et al., 1981; Maguire et al., 1981). More recently, the INMS instrument on the Cassini spacecraft has found evidence for organic molecules up to its mass limit of 100 Da at altitudes as high as 1200 km (Waite et al., 2005; Vuitton et al. 2007). Laboratory experiments that simulate the reactions occurring in Titan’s atmosphere produce many of the same organic molecules observed by Voyager and Cassini, along with organic precipitates known as tholins. Tholins have the general formula CxHyNz and are spectrally similar to Titan’s haze (Khare et al., 1984). Though interesting from the point of view of organic chemistry, the molecules found in Titan’s atmosphere stop short of addressing questions related to the origins of life. Oxygen - a key element for most known biological molecules - is generally lacking in Titan’s atmosphere. The most abundant oxygenated molecule, CO, is present at only ~50 ppm (de Kok et al., 2007). However, if Titan’s atmospheric organic molecules mix with water found in cryovolcanic lavas or impact melts, they may react to produce oxygen-containing, prebiotic species. In this paper, I will show that reactions between Titan tholins and low temperature aqueous solutions produce a wide variety of oxygen-containing species. These reactions display first-order kinetic behaviour with half-lives between 0.4 to 7 days at 273 K (in water) and between 0.3 and 14 days at 253 K (in 13 wt. % ammonia-water). Tholin hydrolysis is thus very fast compared to the freezing timescales of impact melts and volcanic sites on Titan, which take hundreds to thousands of years

  15. Extraction of Organic Molecules from Terrestrial Material: Quantitative Yields from Heat and Water Extractions

    NASA Technical Reports Server (NTRS)

    Beegle, L. W.; Abbey, W. A.; Tsapin, A. T.; Dragoi, D.; Kanik, I.

    2004-01-01

    In the robotic search for life on Mars, different proposed missions will analyze the chemical and biological signatures of life using different platforms. The analysis of samples via analytical instrumentation on the surface of Mars has thus far only been attempted by the two Viking missions. Robotic arms scooped relogith material into a pyrolysis oven attached to a GC/MS. No trace of organic material was found on any of the two different samples at either of the two different landing sites. This null result puts an upper limit on the amount of organics that might be present in Martian soil/rocks, although the level of detection for each individual molecular species is still debated. Determining the absolute limit of detection for each analytical instrument is essential so that null results can be understood. This includes investigating the trade off of using pyrolysis versus liquid solvent extraction to release organic materials (in terms of extraction efficiencies and the complexity of the sample extraction process.) Extraction of organics from field samples can be accomplished by a variety of methods such utilizing various solvents including HCl, pure water, supercritical fluid and Soxhelt extraction. Utilizing 6N HCl is one of the most commonly used method and frequently utilized for extraction of organics from meteorites but it is probably infeasible for robotic exploration due to difficulty of storage and transport. Extraction utilizing H2O is promising, but it could be less efficient than 6N HCl. Both supercritical fluid and Soxhelt extraction methods require bulky hardware and require complex steps, inappropriate for inclusion on rover spacecraft. This investigation reports the efficiencies of pyrolysis and solvent extraction methods for amino acids for different terrestrial samples. The samples studied here, initially created in aqueous environments, are sedimentary in nature. These particular samples were chosen because they possibly represent one of the

  16. Evaluation of low-temperature geothermal potential in Utah and Goshen Valleys and adjacent areas, Utah. Part II. Water temperature and chemistry

    SciTech Connect

    Klauk, R.H.; Davis, D.A.

    1984-12-01

    Geothermal reconnaissance techniques have identified five areas in Utah County warranting further investigation for low-temperature geothermal resources. One area in northern Utah Valley is along Utah Lake fault zone and includes Saratoga Hot Springs. Water temperatures within this area range from 21 to 43/sup 0/C. Common ion analyses as well as B and Li concentrations indicate waters sampled in this area are anomalous when compared to other samples from the same aquifer. Two other areas in southern Utah Valley also coincide with the Utah Lake fault zone. Common ion analyses, trace element concentrations, and C1/HCO/sub 3/ ratios distinguish these areas from all other waters in this valley. Temperatures within these southern areas range from 21 to 32/sup 0/C. All three thermal areas are possibly the result of deep circulation of meteoric water being warmed and subsequently migrating upward within the Utah Lake fault zone. The Castilla Hot Springs area has been expanded by this study to include a spring located 3 mi further up Spanish Fork Canyon near the Thistle earthflow. A temperature of 50/sup 0/C was recorded for this spring and chemistry is similar to Castilla. In Goshen Valley, the fifth geothermal area identified, measured temperatures range from 20 to 27/sup 0/C for some wells and springs. Chemical analyses, however, do not discern the location of low-temperature geothermal reservoirs. 18 refs., 7 figs., 5 tabs.

  17. Conceptual evaluation of regional ground-water flow in the carbonate-rock province of the Great Basin, Nevada, Utah, and adjacent states

    USGS Publications Warehouse

    Prudic, D.E.; Harrill, J.R.; Burbey, T.J.

    1993-01-01

    The regional groundwater flow system in the carbonate rocks of Nevada and Utah is conceptualized as shallow systems superimposed on deeper systems, which transmit water primarily through carbonate rocks. A computer model was used to simulate the two systems. The regional model includes simplifying assumptions that are probably valid for parts of the province; however, the validity of each assumption is unknown for the province as a whole. Therefore, simulation results do not perfectly replicate actual groundwater flow; instead they provide a conceptual evaluation of regional groundwater flow. The model was calibrated by adjusting transmissivity and vertical leakance until simulated water levels and simulated discharge generally agreed with known water levels, mapped areas of discharge, and estimates of discharge. Simulated flow is about 1.5 million acre-ft/yr. Most groundwater flow is simulated in the upper model layer where about 45 shallow flow regions were identified. In the lower layer, 17 deep-flow subregions were identified and grouped into 5 large regions on the basis of water-flow patterns. Simulated flow in this layer is about 28 percent of the total inflow and about half is discharged as springflow. Interbasin flow to several large springs is through thick, continuous, permeable carbonate rocks; elsewhere deep consolidated rocks are not highly transmissive, suggesting that carbonate rocks are not highly permeable everywhere or are not present everywhere. (USGS)

  18. A look deep inside the a hillslope reveals a structured heterogeneity of isotopic reservoirs and distinct water use strategies for adjacent trees

    NASA Astrophysics Data System (ADS)

    Oshun, J.; Rempe, D. M.; Link, P.; Simonin, K. A.; Dietrich, W.; Dawson, T. E.; Fung, I.

    2012-12-01

    Whereas recent studies have begun to note the importance of weathered rock as a source of moisture for vegetation and, through transpiration, as a moderator of local and regional climate, no study has looked deeply into a hillslope in three-dimensions to explore dynamics in the hydrologic cycle and tree water use. Here, we use natural abundance stable isotope techniques to reveal distinct isotopic reservoirs within the hillslope, as well as quantify the movement of water from weathered rock and soil into vegetation. Our study site, at the Angelo Coast Range Reserve in Northern California, is a 4000 m2 unchanneled catchment that drains into Elder Creek, in the South Fork of the Eel River basin. Although average annual rainfall is 1900mm, 90% falls between October and May, forcing vegetation to find deep sources of moisture to survive the dry summer. An old-growth mixed conifer forest with trees as tall as 65 m grows on a 38° slope, with soils 10-60 cm thick underlain by vertically dipping, weathered turbidite sequences of the Coastal Franciscan Belt. A perched seasonally drains to unweathered bedrock. The water table fluctuates between 3 and 5 m below the surface near Elder Creek, and between 18 and 24 m below the surface at the hillslope divide. The site contains over 850 sensors monitoring the climatic variables and the movement of water through the subsurface, vegetation and into the atmosphere. Daily rainwater sampling during storm events from 2007-2012 shows a Local Meteoric Water Line, setting the context for our comparison of isotopic reservoirs. From Summer 2011 to Fall 2012, bi-weekly to tri-weekly samples were collected of tree xylem of over 30 individuals of Pseudotsuga menziesii, quercus agrifolia, arbutus menziesii, Umbellularia californica, Notholithocarpus densiflorus, acer macrophyllum, as well as from soil and rock to a depth of 1-1.3 m, and from the water table at 12 wells across the hillslope. Analysis reveals a structured heterogeneity of

  19. Cold crystallisation behaviour of water molecules in ionic liquids as a screening method to evaluate biocompatibility of the hydrated ionic liquids.

    PubMed

    Fujita, Kyoko; Nikawa, Yohsuke; Ohno, Hiroyuki

    2013-04-21

    Hydrated ionic liquids, exhibiting cold crystallisation behaviour of water molecules in a certain range of water contents, successfully dissolved cytochrome c maintaining the original spin state of heme. PMID:23486783

  20. Reaction Kinetics of Water Molecules with Oxygen Vacancies on Rutile TiO2(110)

    SciTech Connect

    Petrik, Nikolay G.; Kimmel, Gregory A.

    2015-09-16

    The formation of bridging hydroxyls (OHb) via reactions of water molecules with oxygen vacancies (VO) on reduced TiO2(110) surfaces is studied using infrared reflection-absorption spectroscopy (IRAS), electron-stimulated desorption (ESD), and photon-stimulated desorption (PSD). Narrow IRAS peaks at 2737 cm-1 and 3711 cm-1 are observed for stretching vibrations of ODb and OHb on TiO2(110), respectively. IRAS measurements with s- and p-polarized light demonstrate that the bridging hydroxyls are oriented normal to the (110) surface. The IR peaks disappear after the sample is exposed to O2 or annealed in the temperature range of 400 – 600 K (correlating with the temperature at which pairs of OHb’s reform water and then desorb), which is consistent with their identification as bridging hydroxyls. We have studied the kinetics of water reacting with the vacancies by monitoring the formation of bridging hydroxyls (using IRAS) as a function of the annealing temperature for a small amount of water initially dosed on the TiO2(110) at low temperature. Separate experiments have also monitored the loss of water molecules (using water ESD) and vacancies (using the CO photooxidation reaction) due to the reactions of water molecules with the vacancies. All three techniques show that the reaction rate becomes appreciable for T > 150 K and that the reactions largely complete for T > 250 K. The temperature-dependent water-VO reaction kinetics are consistent with a Gaussian distribution of activation energies with Ea = 0.545 eV, ΔEa(FWHM) = 0.125 eV, and a “normal” prefactor, v = 1012 s-1. In contrast, a single activation energy with a physically reasonable prefactor does not fit the data well. Our experimental activation energy is close to theoretical estimates for the diffusion of water molecules along the Ti5c rows on the reduced TiO2

  1. In situ spectroradiometric calibration of EREP imagery and estuarine and coastal oceanography of Block Island sound and adjacent New York coastal waters. [Willcox, Arizona

    NASA Technical Reports Server (NTRS)

    Yost, E. F. (Principal Investigator)

    1975-01-01

    The author has identified the following significant results. The first part of the study resulted in photographic procedures for making multispectral positive images which greatly enhance the color differences in land detail using an additive color viewer. An additive color analysis of the geologic features near Willcox, Arizona using enhanced black and white multispectral positives allowed compilation of a significant number of unmapped geologic units which do not appear on geologic maps of the area. The second part demonstrated the feasibility of utilizing Skylab remote sensor data to monitor and manage the coastal environment by relating physical, chemical, and biological ship sampled data to S190A, S190B, and S192 image characteristics. Photographic reprocessing techniques were developed which greatly enhanced subtle low brightness water detail. Using these photographic contrast-stretch techniques, two water masses having an extinction coefficient difference of only 0.07 measured simultaneously with the acquisition of S190A data were readily differentiated.

  2. Depth estimation for ordinary high water of streams in the Mobile District of the U.S. Army Corps of Engineers, Alabama and adjacent states

    USGS Publications Warehouse

    Harkins, Joe R.; Green, Mark E.

    1981-01-01

    Drainage areas for about 1,600 surface-water sites on streams and lakes in Florida are contained in this report. The sites are generally either U.S. Geological Survey gaging stations or the mouths of gaged streas. Each site is identified by latitude and longitude, by the general stream type, and by the U.S. Geological Survey 7.5-minute topographic map on which it can be located. The gaging stations are furhter identified by a downstream order number, a county code, and a nearby city or town. In addition to drainage areas, the surface areas of lakes are shown for the elevation given on the topographic map. These data were retrieved from the Surface Water Index developed and maintained by the Hydrologic Surveillance section of the Florida District Office, U.S. Geological Survey. (USGS)

  3. Properties of Poloxamer Molecules and Poloxamer Micelles Dissolved in Water and Next to Lipid Bilayers: Results from Computer Simulations.

    PubMed

    Adhikari, Upendra; Goliaei, Ardeshir; Tsereteli, Levan; Berkowitz, Max L

    2016-07-01

    To study the properties of poloxamer molecules P85 and P188 and micelles containing these poloxamers in bulk water and also next to lipid bilayers, we performed coarse-grained molecular dynamics computer simulations. We used MARTINI force-field and adjusted Lennard-Jones nonbonded interaction strength parameters for poloxamer beads to take into account the presence of polarizable water. Simulations of systems containing poloxamer molecules or micelles solvated in bulk water showed that structural properties, such as radii of gyration of the molecules and micelles, agree with the ones inferred from experiments. We observed that P85 micelle is almost spherical in shape, whereas the P188 micelle is distorted from being spherical. Simulations containing systems with the water-lipid bilayer interface showed that hydrophilic blocks of poloxamers interact with lipid headgroups of the bilayer and remain at the interface, whereas hydrophobic blocks prefer to insert into the central hydrophobic region of the bilayer. Simulations containing poloxamer micelles next to lipid bilayer showed no permeation of these micelles into the bilayer. To study the "healing" properties of P188 poloxamer, we performed simulations on a system containing a P188 micelle next to "damaged" lipid bilayer containing a pore. We observed that hydrophobic chains of poloxamers got inserted into the bilayer through the pore region, ultimately closing the pore. PMID:26719970

  4. Adsorption of a water molecule on the MgO(100) surface as described by cluster and slab models.

    PubMed

    Karalti, Ozan; Alfè, Dario; Gillan, Michael J; Jordan, Kenneth D

    2012-06-01

    The interaction of a water molecule with the (100) surface of MgO as described by cluster models is studied using MP2, coupled MP2 (MP2C) and symmetry-adapted perturbation theory (SAPT) methods. In addition, diffusion Monte Carlo (DMC) results are presented for several slab models as well as for the smallest, 2X2 cluster model. For the 2X2 model it is found that the MP2C, DMC, and CCSD(T) methods give nearly the same potential energy curve for the water-cluster interaction, whereas the potential energy curve from the SAPT calculations differs slightly from those of the other methods. The interaction of the water molecule with the cluster models of the MgO(100) surface is weakened upon expanding the number of layers from one to two and also upon expanding the description of the layers from 2X2 to 4X4 to 6X6. The SAPT calculations reveal that both these expansions of the cluster model are accompanied by reductions in the magnitudes of the induction and dispersion constributions. The best estimate of the energy for binding an isolated water molecule to the surface obtained from the cluster model calculations is in good agreement with that obtained from the DMC calculations using a 2-layer slab model with periodic boundary conditions. PMID:22535216

  5. Radical-Molecule Reaction C3H + H2O on Amorphous Water Ice: A Promising Route for Interstellar Propynal

    NASA Astrophysics Data System (ADS)

    Xie, Hong-bin; Shao, Chang-bin; Ding, Yi-hong

    2007-11-01

    Intriguing propynal (HCCCHO) has been attracting chemist's attention since 1955. However, to date, no satisfying conclusion concerning its formation mechanism in the interstellar medium (ISM) has been reached, although a variety of gas-reaction models, including ion-molecule, radical-molecule, and molecule-molecule, have been postulated. In this paper, we consider for the first time the gas-grain interaction model that involves heterogeneous reaction at the surface of dust grain or in the icy mantles to account for the propynal's formation. Based on the detailed density functional theory (DFT) and Gaussian-3 potential energy surface studies, we found that although the gaseous process C3H+H2O-->propynal+H must surmount a considerable entrance barrier (around 10 kcal mol-1), amorphous water ice can significantly catalyze the propynal's formation to be barrierless. So, this model should be a more reasonable one for propynal's formation in the low-temperature interstellar space. This result may also represent one rare case of the water-catalyzed reaction associated with a molecular radical in space. Future experimental studies are greatly desired to probe such interesting processes.

  6. Selenium and Other Elements in Water and Adjacent Rock and Sediment of Toll Gate Creek, Aurora, Arapahoe County, Colorado, December 2003 through March 2004

    USGS Publications Warehouse

    Herring, J.R.; Walton-Day, Katherine

    2007-01-01

    Streamwater and solid samples (rock, unconsolidated sediment, stream sediment, and efflorescent material) in the Toll Gate Creek watershed, Colorado, were collected and analyzed for major and trace elements to determine trace-element concentrations and stream loads from December 2003 through March 2004, a period of seasonally low flow. Special emphasis was given to selenium (Se) concentrations because historic Se concentrations exceeded current (2004) stream standards. The goal of the project was to assess the distribution of Se concentration and loads in Toll Gate Creek and to determine the potential for rock and unconsolidated sediment in the basin to be sources of Se to the streamwater. Streamwater samples and discharge measurements were collected during December 2003 and March 2004 along Toll Gate Creek and its two primary tributaries - West Toll Gate Creek and East Toll Gate Creek. During both sampling periods, discharge ranged from 2.5 liters per second to 138 liters per second in the watershed. Discharge was greater in March 2004 than December 2003, but both periods represent low flow in Toll Gate Creek, and results of this study should not be extended to periods of higher flow. Discharge decreased moving downstream in East Toll Gate Creek but increased moving downstream along West Toll Gate Creek and the main stem of Toll Gate Creek, indicating that these two streams gain flow from ground water. Se concentrations in streamwater samples ranged from 7 to 70 micrograms per liter, were elevated in the upstream-most samples, and were greater than the State stream standard of 4.6 micrograms per liter. Se loads ranged from 6 grams per day to 250 grams per day, decreased in a downstream direction along East Toll Gate Creek, and increased in a downstream direction along West Toll Gate Creek and Toll Gate Creek. The largest Se-load increases occurred between two sampling locations on West Toll Gate Creek during both sampling periods and between the two sampling

  7. How water molecules affect the catalytic activity of hydrolases - A XANES study of the local structures of peptide deformylase

    NASA Astrophysics Data System (ADS)

    Cui, Peixin; Wang, Yu; Chu, Wangsheng; Guo, Xiaoyun; Yang, Feifei; Yu, Meijuan; Zhao, Haifeng; Dong, Yuhui; Xie, Yaning; Gong, Weimin; Wu, Ziyu

    2014-12-01

    Peptide deformylase (PDF) is a prokaryotic enzyme that catalyzes the deformylation of nascent peptides generated during protein synthesis and water molecules play a key role in these hydrolases. Using X-ray absorption near edge spectroscopy (XANES) and ab initio calculations we accurately probe the local atomic environment of the metal ion binding in the active site of PDF at different pH values and with different metal ions. This new approach is an effective way to monitor existing correlations among functions and structural changes. We show for the first time that the enzymatic activity depends on pH values and metal ions via the bond length of the nearest coordinating water (Wat1) to the metal ion. Combining experimental and theoretical data we may claim that PDF exhibits an enhanced enzymatic activity only when the distance of the Wat1 molecule with the metal ion falls in the limited range from 2.15 to 2.55 Å.

  8. Molecular orientation effect on the differential cross sections for the electron-impact double ionization of oriented water molecules

    SciTech Connect

    Champion, C.; Dal Cappello, C.; Oubaziz, D.; Aouchiche, H.; Popov, Yu. V.

    2010-03-15

    Double ionization of isolated water molecules fixed in space is here investigated in a theoretical approach based on the first Born approximation. Secondary electron angular distributions are reported for particular (e,3e) kinematical conditions and compared in terms of shape and magnitude. Strong dependence of the fivefold differential cross sections on the molecular target orientation is clearly observed in (e,3-1e) as well as (e,3e) channels. Furthermore, for the major part of the kinematics considered, we identified the different mechanisms involved in the double ionization of water molecule, namely, the direct shake-off process as well as the two-step1 process. They are both discussed and analyzed with respect to the molecular target orientation.

  9. Chemical-quality reconnaissance of the water and surficial bed material in the Delaware River estuary and adjacent New Jersey tributaries, 1980-81

    USGS Publications Warehouse

    Hochreiter, Joseph J., Jr.

    1982-01-01

    This report presents chemical-quality data collected from May 1980 to January 1981 at several locations within the Delaware River estuary and selected New Jersey tributaries. Samples of surface water were analyzed Environmental Protection Agency ' priority pollutants, ' including acid extractable, base/neutral extractable and volatile organic compounds, in addition to selected dissolved inorganic constituents. Surficial bed material at selected locations was examined for trace metals, insecticides, polychlorinated biphenyls, and base/neutral extractable organic compounds. Trace levels (1-50 micrograms per liter) of purgeable organic compounds, particularly those associated with the occurrence of hydrocarbons, were found in about 60% of the water samples taken. DDT, DDD, DDE, PCB 's and chlordane are present in most surficial bed material samples. Diazinon was the only organophosphorous insecticide detected in the study (1.6 micrograms per kilogram at one location). High values for select trace metals in bed material were discovered at two locations. Of the 10 sites sampled, the surficial bed material containing the most contamination was found along one cross section of Raccoon Creek at Bridgeport. An additional analysis of Raccoon Creek revealed bed material containing toluene, oil and grease, and trace quantities of 15 base/neutral extractable organic compounds, including polynuclear aromatic hydrocarbons, phthalate esters, and chlorinated benzenes.

  10. Observing the water molecule in macromolecules using infrared spectrometry: structure of the hydrogen bond network and hydration mechanism

    NASA Astrophysics Data System (ADS)

    Maréchal, Y.

    2004-08-01

    The power and precision of IR spectrometry, or IR quantitative spectroscopy, to observe water molecules embedded in macromolecules, is illustrated, taking as examples the determination of the structures of the hydrogen-bond network of a dried polysaccharide, hyaluronan, of a dried protein, bovine serum albumine, and of a dried polymer, a sulfonated polyimide. We also indicate how IR spectrometry conveys original and precise information from which their hydration mechanisms can be precisely determined in terms of chemical reactions.

  11. Body condition of the deep water demersal resources at two adjacent oligotrophic areas of the western Mediterranean and the influence of the environmental features

    NASA Astrophysics Data System (ADS)

    Rueda, L.; Moranta, J.; Abelló, P.; Balbín, R.; Barberá, C.; Fernández de Puelles, M. L.; Olivar, M. P.; Ordines, F.; Ramón, M.; Torres, A. P.; Valls, M.; Massutí, E.

    2014-10-01

    Body condition indices not only are often used as reliable indicators of the nutritional status of individuals but also can they be utilized to provide insights regarding food availability and habitat quality. The aim of this study was to evaluate the connection between the body condition of the demersal species and the environmental features in the water column (i.e. the hydrographic conditions and the potential trophic resources) in two proximate areas, the north and south regions of the Balearic Islands (western Mediterranean), viz., the Balearic sub-basin (BsB) and the Algerian sub-basin (AsB), respectively, with different geomorphological and hydrodynamic features. Body condition indices were calculated for individuals of 21 demersal species including 11 teleosts, 4 elasmobranchs, 3 cephalopods and 3 crustaceans, which represented > 70-77% of the deep water resources, captured by bottom trawling. The morphometric indices, viz., Relative Condition Index (Kn) and Standardised Residuals (SR) from the length-weight relationship, were used. The results for each one of the 21 species indicated a significantly better condition in terms of Kn and SR in the BsB, for 7 and 9 species, respectively. In addition, a general model, including the 21 species together, showed better body condition in the BsB, and during the summer. The spatial and temporal differences in the body condition are discussed in the context of the environmental variables characterising both the study areas, which showed significant variations, for some of the hydrographic features (chlorophyll a, dissolved oxygen, salinity, potential density and temperature), as well as for some of the potential trophic resources (mesopelagic and epibenthic fauna). These findings suggest an environmental effect on the body condition of the deep-water resources in the Balearic Islands, one of the most oligotrophic areas of the western Mediterranean, and reveal more suitable environmental conditions for these species

  12. Determination of selected pesticides in water samples adjacent to agricultural fields and removal of organophosphorus insecticide chlorpyrifos using soil bacterial isolates

    NASA Astrophysics Data System (ADS)

    Hossain, M. S.; Chowdhury, M. Alamgir Zaman; Pramanik, Md. Kamruzzaman; Rahman, M. A.; Fakhruddin, A. N. M.; Alam, M. Khorshed

    2014-03-01

    The use of pesticide for crops leads to serious environmental pollution, therefore, it is essential to monitor and develop approaches to remove pesticide from contaminated environment. In this study, water samples were collected to monitor pesticide residues, and degradation of chlorpyrifos was also performed using soil bacteria. Identification of pesticide residues and determination of their levels were performed by high-performance liquid chromatography with photodiode array detector. Among 12 samples, 10 samples were found contaminated with pesticides. Chlorpyrifos was detected in four tested samples and concentrations ranged from 3.27 to 9.31 μg/l whereas fenitrothion ranging from (Below Detection Limit, <0.1 μg/l) to 33.41 μg/l in the tested samples. Parathion was found in two tested samples at the concentration of 0.73 and 6.23 μg/l. None of the tested samples was found contaminated with Methoxychlor, DDT and Ethion. Three soil bacterial isolates, Pseudomonas peli BG1, Burkholderia caryophylli BG4 and Brevundimonas diminuta PD6 degraded chlorpyrifos completely in 8, 10 and 10 days, respectively, when 20 mg/l chlorpyrifos was supplied as sole source of carbon. Whereas, BG1, BG4 and PD6 took 14, 16 and 16 days, respectively, for complete removal of 50 mg/l chlorpyrifos. Chlorpyrifos degradation rates were found maximum by all three isolates at 2nd day of incubation for both tested concentrations. The results of the present study suggest the need for regular monitoring of pesticide residues in water, to protect the aquatic environment. Chlorpyrifos degrading bacterial isolates can be used to clean up environmental samples contaminated with the organophosphate pesticides.

  13. Determination of selected pesticides in water samples adjacent to agricultural fields and removal of organophosphorus insecticide chlorpyrifos using soil bacterial isolates

    NASA Astrophysics Data System (ADS)

    Hossain, M. S.; Chowdhury, M. Alamgir Zaman; Pramanik, Md. Kamruzzaman; Rahman, M. A.; Fakhruddin, A. N. M.; Alam, M. Khorshed

    2015-06-01

    The use of pesticide for crops leads to serious environmental pollution, therefore, it is essential to monitor and develop approaches to remove pesticide from contaminated environment. In this study, water samples were collected to monitor pesticide residues, and degradation of chlorpyrifos was also performed using soil bacteria. Identification of pesticide residues and determination of their levels were performed by high-performance liquid chromatography with photodiode array detector. Among 12 samples, 10 samples were found contaminated with pesticides. Chlorpyrifos was detected in four tested samples and concentrations ranged from 3.27 to 9.31 μg/l whereas fenitrothion ranging from (Below Detection Limit, <0.1 μg/l) to 33.41 μg/l in the tested samples. Parathion was found in two tested samples at the concentration of 0.73 and 6.23 μg/l. None of the tested samples was found contaminated with Methoxychlor, DDT and Ethion. Three soil bacterial isolates, Pseudomonas peli BG1, Burkholderia caryophylli BG4 and Brevundimonas diminuta PD6 degraded chlorpyrifos completely in 8, 10 and 10 days, respectively, when 20 mg/l chlorpyrifos was supplied as sole source of carbon. Whereas, BG1, BG4 and PD6 took 14, 16 and 16 days, respectively, for complete removal of 50 mg/l chlorpyrifos. Chlorpyrifos degradation rates were found maximum by all three isolates at 2nd day of incubation for both tested concentrations. The results of the present study suggest the need for regular monitoring of pesticide residues in water, to protect the aquatic environment. Chlorpyrifos degrading bacterial isolates can be used to clean up environmental samples contaminated with the organophosphate pesticides.

  14. Velocity of a Molecule Evaporated from a Water Nanodroplet: Maxwell-Boltzmann Statistics versus Non-Ergodic Events.

    PubMed

    Abdoul-Carime, Hassan; Berthias, Francis; Feketeová, Linda; Marciante, Mathieu; Calvo, Florent; Forquet, Valérian; Chermette, Henry; Farizon, Bernadette; Farizon, Michel; Märk, Tilmann D

    2015-12-01

    The velocity of a molecule evaporated from a mass-selected protonated water nanodroplet is measured by velocity map imaging in combination with a recently developed mass spectrometry technique. The measured velocity distributions allow probing statistical energy redistribution in ultimately small water nanodroplets after ultrafast electronic excitation. As the droplet size increases, the velocity distribution rapidly approaches the behavior expected for macroscopic droplets. However, a distinct high-velocity contribution provides evidence of molecular evaporation before complete energy redistribution, corresponding to non-ergodic events. PMID:26473406

  15. Velocity of a Molecule Evaporated from a Water Nanodroplet: Maxwell–Boltzmann Statistics versus Non-Ergodic Events

    PubMed Central

    Abdoul-Carime, Hassan; Berthias, Francis; Feketeová, Linda; Marciante, Mathieu; Calvo, Florent; Forquet, Valérian; Chermette, Henry; Farizon, Bernadette; Farizon, Michel; Märk, Tilmann D

    2015-01-01

    The velocity of a molecule evaporated from a mass-selected protonated water nanodroplet is measured by velocity map imaging in combination with a recently developed mass spectrometry technique. The measured velocity distributions allow probing statistical energy redistribution in ultimately small water nanodroplets after ultrafast electronic excitation. As the droplet size increases, the velocity distribution rapidly approaches the behavior expected for macroscopic droplets. However, a distinct high-velocity contribution provides evidence of molecular evaporation before complete energy redistribution, corresponding to non-ergodic events. PMID:26473406

  16. Reduction of Local Stress Concentration on Nanosheet in Layered Nanoparticles with Water Molecules

    NASA Astrophysics Data System (ADS)

    Sato, Kiminori; Numata, Kazuomi; Fujimoto, Koichiro

    2014-01-01

    The local stress concentration on 2D nanosheets is investigated for saponite layered nanoparticles by means of X-ray diffraction (XRD) and positronium (Ps) annihilation spectroscopy. XRD experiments indicated that the layered structure for the mechanochemically milled sample is maintained in the presence of H2O molecules. Ps annihilation studies of self-assembly revealed that the 2D nanosheets are well in-plane ordered after uniaxial pressure compaction without H2O molecules due to the efficient propagation of stress concentration. The present results of both XRD and Ps lifetime spectroscopy clearly demonstrates that the stress concentration on the 2D nanosheets can be reduced in the presence of H2O molecules.

  17. Metagenomics of Water Column Microbes Near Brine Pool NR1 and adjacent regions of the Northern Gulf of Mexico Collected in Fall 2009

    NASA Astrophysics Data System (ADS)

    Wood, A. M.; Goodwin, K. D.; Brami, D.; Schwartz, A.; Toledo, G.

    2012-12-01

    High-throughput sequencing was applied to eight water column samples collected from the Gulf of Mexico in 2009 in regions SW and west of the 2010 Macondo oil spill. Samples were collected by Niskin-equipped CTD (~200 and ~650 m depths) at two locations, including a site over a methane brine pool (Brine Pool NR1). In addition, seawater was collected ~3m lateral of the pool (649m depth) via Niskin bottle equipped on the Johnson-Sea-Link submersible. Unassembled reads were submitted to the Synthetic Genomics bioinformatics pipeline for taxonomic analysis. The distribution of Bacteria (56-73%), Archae (7-16%), Eukaryotes (12-23%), and unclassified sequences (6-10%) were similar for all samples. However, certain taxonomic classifications were relatively more abundant in deeper samples, and differences were noted for samples collected by submersible. For example, Methylophaga was classified as 38% of the order Thiotrichales for the Niskin/submersible sample compared to 0% in the 200m-depth samples and 3-11% in the 650m samples. Methylophaga is a genus of indigenous methylotrophs reported to respond during the Deepwater Horizon event of 2010. In contrast, sequence abundance for Oceanospirillales, also reported to respond during the event, was similar for all samples (6-9% of the gamma-proteobacteria).

  18. Effects of water molecules on the chemical stability of MAGeI3 perovskite explored from a theoretical viewpoint.

    PubMed

    Sun, Ping-Ping; Chi, Wei-Jie; Li, Ze-Sheng

    2016-09-21

    The stability of perovskite in humid environments is one of the biggest obstacles for its potential applications in light harvesting and electroluminescent displays. Understanding the detailed degradation mechanism of MAGeI3 in moisture is a critical way to explore the practicability of MAGeI3 perovskite. In this study, we report a quantitative and systematic investigation of MAGeI3 degradation processes by exploring the effects of H2O molecules on the structural and electronic properties of the most stable MAGeI3(101) surface under various simulated environmental conditions with different water coverage based on first-principles calculations. The results show that H2O molecules can easily diffuse into the inner side of the perovskite and gradually corrode the structure as the number of H2O molecules increases. As a result of the interactions between perovskite and H2O molecules, a hydrated intermediate will be generated as the first step in the degradation mechanism; the perovskite will further decompose to HI and GeI2. In terms of one MAGeI3 molecule, it will be dissociated completely to GeI2 as a result of hydrolysis reactions with a minimum of 4H2O molecules. In addition, the degradation of the perovskite will also affect the electronic structure, causing a decrease in optical absorption across the visible region of the spectrum and a distinct deformation change in the crystal structure of the material. These findings further illustrate the degradation of the hydrolysis process of MAGeI3 perovskite in humid environments, which should be helpful to inspire experimentalists to take action to prolong the lifetimes of perovskite solar cells to achieve high conversion efficiency in their applications. PMID:27539944

  19. Control of water molecule aggregations in copper 1,4-cyclohexanedicarboxylate coordination polymers containing pyridyl-piperazine type ligands

    NASA Astrophysics Data System (ADS)

    Qiblawi, Sultan H.; LaDuca, Robert L.

    2014-01-01

    A series of layered divalent copper coordination polymers containing 1,4-cyclohexanedicarboxylate and long-spanning pyridyl-piperazine type ligands exhibits greatly different co-crystallized water molecule aggregations depending on the specific ligands used. Both [Cu(t-14cdc)(4-bpmp)]n (1, t-14cdc = trans-1,4-cyclohexanedicarboxylate, 4-bpmp = bis(4-pyridylmethyl)piperazine) and {[Cu(t-14cdc)(4-bpfp)(H2O)2]·6H2O}n (2, 4-bpfp = bis(4-pyridylformyl)piperazine) possess 2D (4,4) coordination polymer grids. However 1 lacks any co-crystallized water and has pinched grid apertures, while 2 manifests infinite water tapes with T6(2)4(2) classification and rectangular grid apertures. {[Cu2(c-14cdc)2(4-bpmp)]·2H2O}n (3, c-14cdc = cis-1,4-cyclohexanedicarboxylate) has [Cu2(c-14cdc)]2 ribbons with paddlewheel dimeric units linked into 2D slabs by 4-bpmp tethers, along with isolated water molecule pairs. In contrast, {[Cu2(c-14cdc)2(4-bpfp)]·10H2O}n (4) shows a very similar underlying coordination polymer topology but entrains unique decameric water molecule clusters. The minor product {[Cu2(c-14cdcH)2(t-1,4-cdc)(4-bpfp)2(H2O)2]·2H2O}n (5) was isolated along with 4; this compound underwent some in situ cis to trans cyclohexane-dicarboxylate ligand isomerization and exhibits a ladder polymer motif.

  20. Water-COOH Composite Structure with Enhanced Hydrophobicity Formed by Water Molecules Embedded into Carboxyl-Terminated Self-Assembled Monolayers.

    PubMed

    Guo, Pan; Tu, Yusong; Yang, Jinrong; Wang, Chunlei; Sheng, Nan; Fang, Haiping

    2015-10-30

    By combining molecular dynamics simulations and quantum mechanics calculations, we show the formation of a composite structure composed of embedded water molecules and the COOH matrix on carboxyl-terminated self-assembled monolayers (COOH SAMs) with appropriate packing densities. This composite structure with an integrated hydrogen bond network inside reduces the hydrogen bonds with the water above. This explains the seeming contradiction on the stability of the surface water on COOH SAMs observed in experiments. The existence of the composite structure at appropriate packing densities results in the two-step distribution of contact angles of water droplets on COOH SAMs, around 0° and 35°, which compares favorably to the experimental measurements of contact angles collected from forty research articles over the past 25 years. These findings provide a molecular-level understanding of water on surfaces (including surfaces on biomolecules) with hydrophilic functional groups. PMID:26565476

  1. Water-COOH Composite Structure with Enhanced Hydrophobicity Formed by Water Molecules Embedded into Carboxyl-Terminated Self-Assembled Monolayers

    NASA Astrophysics Data System (ADS)

    Guo, Pan; Tu, Yusong; Yang, Jinrong; Wang, Chunlei; Sheng, Nan; Fang, Haiping

    2015-10-01

    By combining molecular dynamics simulations and quantum mechanics calculations, we show the formation of a composite structure composed of embedded water molecules and the COOH matrix on carboxyl-terminated self-assembled monolayers (COOH SAMs) with appropriate packing densities. This composite structure with an integrated hydrogen bond network inside reduces the hydrogen bonds with the water above. This explains the seeming contradiction on the stability of the surface water on COOH SAMs observed in experiments. The existence of the composite structure at appropriate packing densities results in the two-step distribution of contact angles of water droplets on COOH SAMs, around 0° and 35°, which compares favorably to the experimental measurements of contact angles collected from forty research articles over the past 25 years. These findings provide a molecular-level understanding of water on surfaces (including surfaces on biomolecules) with hydrophilic functional groups.

  2. All-electron scalar relativistic calculation of water molecule adsorption onto small gold clusters.

    PubMed

    Kuang, Xiang-Jun; Wang, Xin-Qiang; Liu, Gao-Bin

    2011-08-01

    An all-electron scalar relativistic calculation was performed on Au( n )H(2)O (n = 1-13) clusters using density functional theory (DFT) with the generalized gradient approximation at PW91 level. The calculation results reveal that, after adsorption, the small gold cluster would like to bond with oxygen and the H(2)O molecule prefers to occupy the single fold coordination site. Reflecting the strong scalar relativistic effect, Au( n ) geometries are distorted slightly but still maintain a planar structure. The Au-Au bond is strengthened and the H-O bond is weakened, as manifested by the shortening of the Au-Au bond-length and the lengthening of the H-O bond-length. The H-O-H bond angle becomes slightly larger. The enhancement of reactivity of the H(2)O molecule is obvious. The Au-O bond-lengths, adsorption energies, VIPs, HLGs, HOMO (LUMO) energy levels, charge transfers and the highest vibrational frequencies of the Au-O mode for Au( n )H(2)O clusters exhibit an obvious odd-even oscillation. The most favorable adsorption between small gold clusters and the H(2)O molecule takes place when the H(2)O molecule is adsorbed onto an even-numbered Au( n ) cluster and becomes an Au( n )H(2)O cluster with an even number of valence electrons. The odd-even alteration of magnetic moments is observed in Au( n )H(2)O clusters and may serve as material with a tunable code capacity of "0" and "1" by adsorbing a H(2)O molecule onto an odd or even-numbered small gold cluster. PMID:21140279

  3. Nucleation of Mixed Nitric Acid-Water Ice Nanoparticles in Molecular Beams that Starts with a HNO3 Molecule.

    PubMed

    Lengyel, Jozef; Pysanenko, Andriy; Kočišek, Jaroslav; Poterya, Viktoriya; Pradzynski, Christoph C; Zeuch, Thomas; Slavíček, Petr; Fárník, Michal

    2012-11-01

    Mixed (HNO3)m(H2O)n clusters generated in supersonic expansion of nitric acid vapor are investigated in two different experiments, (1) time-of-flight mass spectrometry after electron ionization and (2) Na doping and photoionization. This combination of complementary methods reveals that only clusters containing at least one acid molecule are generated, that is, the acid molecule serves as the nucleation center in the expansion. The experiments also suggest that at least four water molecules are needed for HNO3 acidic dissociation. The clusters are undoubtedly generated, as proved by electron ionization; however, they are not detected by the Na doping due to a fast charge-transfer reaction between the Na atom and HNO3. This points to limitations of the Na doping recently advocated as a general method for atmospheric aerosol detection. On the other hand, the combination of the two methods introduces a tool for detecting molecules with sizable electron affinity in clusters. PMID:26296012

  4. Tailoring 1H spin dynamics in small molecules via supercooled water: a promising approach for metabolite identification and validation.

    PubMed

    Farooq, Hashim; Soong, Ronald; Courtier-Murias, Denis; Anklin, Clemens; Simpson, André

    2012-08-01

    Metabolic mixtures are often analyzed via NMR spectroscopy as it provides a metabolic profile without sample alteration in a noninvasive manner. These mixtures however tend to be very complex and demonstrate considerable spectral overlap resulting in assignments that are sometimes ambiguous given the range of current NMR methods available. De novo molecular identification in these mixtures is generally accomplished using chemical shift information and J-coupling based experiments to determine spin connectivity information, but these techniques fall short when a molecule of interest contains nonrelaying centers. A method is presented here that enhances intramolecular spatial interactions via supercooled water and uses the resulting spatial correlations to edit mixtures. This is accomplished by utilizing nuclear Overhauser effect spectroscopy (NOESY) at subzero temperatures in capillaries to enhance NOE and provide more complete spin systems. This technique is applied to a standard mixture of three known molecules in D(2)O with overlapping resonances and is further demonstrated to assign molecules in a worm tissue extract. The current method proves to be a powerful complement to existing methods such as total correlation spectroscopy (TOCSY) to expand the range of molecules that can be assigned in situ without physical separation of mixtures. PMID:22788933

  5. Fast rotational motion of water molecules increases ordering of hydrophobes in solutions and may cause hydrophobic chains to collapse

    NASA Astrophysics Data System (ADS)

    Mohorič, Tomaž; Bren, Urban; Vlachy, Vojko

    2015-12-01

    Using the molecular dynamics simulations with separate thermostats for translational and rotational degrees of freedom, we investigate the effects of water's rotational motion on the interaction among Lennard-Jones solutes. The situation with rotational temperature higher than the translational one (TR > TT) is mimicking the effects of microwaves on model solutions. Molecular dynamics simulations suggest that solutions of Lennard-Jones solutes become increasingly more structured with the rise in TR, while keeping the TT constant. This is evidenced by an increase of the first and the second peak of the solute-solute radial distribution function. In addition, the first peak moves toward slightly larger distances; the effect seems to be caused by the destabilization of water molecules in the first hydration shell around hydrophobic solutes. More evidence of strong effects of the rotationally excited water is provided by the simulations of short hydrophobic polymers, which upon an increase in TR assume more compact conformations. In these simulations, we see the re-distribution of water molecules, which escape from hydrophobic "pockets" to better solvate the solvent exposed monomers.

  6. Effects of water molecules on tribological behavior and property measurements in nano-indentation processes - a numerical analysis

    PubMed Central

    2013-01-01

    Nano/micro-manufacturing under wet condition is an important consideration for various tool-based processes such as indentation, scratching, and machining. The existence of liquids adds complexity to the system, changes the tool/work interfacial condition, and affects material behaviors. For indentation, it may also affect material property measurements. However, little effort has been made to study this challenging issue at nano- or atomistic scale. In this study, we tackle this challenge by investigating nano-indentation processes submerged in water using the molecular dynamics (MD) simulation approach. Compared with dry indentation in which no water molecules are present, the existence of water molecules causes the increase of indentation force in initial penetration, but the decrease of indentation force in full penetration. It also reduces the sticking phenomenon between the work and tool atoms during indenter retraction, such that the indentation geometry can be better retained. Meanwhile, nano-indentation under wet condition exhibits the indentation size effect, while dry nano-indentation exhibits the reverse indentation size effect. The existence of water leads to higher computed hardness values at low indentation loads and a smaller value of Young's modulus. In addition, the friction along the tool/work interface is significantly reduced under wet indentation. PMID:24044504

  7. Fast rotational motion of water molecules increases ordering of hydrophobes in solutions and may cause hydrophobic chains to collapse.

    PubMed

    Mohorič, Tomaž; Bren, Urban; Vlachy, Vojko

    2015-12-28

    Using the molecular dynamics simulations with separate thermostats for translational and rotational degrees of freedom, we investigate the effects of water's rotational motion on the interaction among Lennard-Jones solutes. The situation with rotational temperature higher than the translational one (TR > TT) is mimicking the effects of microwaves on model solutions. Molecular dynamics simulations suggest that solutions of Lennard-Jones solutes become increasingly more structured with the rise in TR, while keeping the TT constant. This is evidenced by an increase of the first and the second peak of the solute-solute radial distribution function. In addition, the first peak moves toward slightly larger distances; the effect seems to be caused by the destabilization of water molecules in the first hydration shell around hydrophobic solutes. More evidence of strong effects of the rotationally excited water is provided by the simulations of short hydrophobic polymers, which upon an increase in TR assume more compact conformations. In these simulations, we see the re-distribution of water molecules, which escape from hydrophobic "pockets" to better solvate the solvent exposed monomers. PMID:26723695

  8. SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation

    SciTech Connect

    Del Rizzo, Paul A.; Couture, Jean-François; Dirk, Lynnette M.A.; Strunk, Bethany S.; Roiko, Marijo S.; Brunzelle, Joseph S.; Houtz, Robert L.; Trievel, Raymond C.

    2010-11-15

    SET domain lysine methyltransferases (KMTs) methylate specific lysine residues in histone and non-histone substrates. These enzymes also display product specificity by catalyzing distinct degrees of methylation of the lysine {epsilon}-amino group. To elucidate the molecular mechanism underlying this specificity, we have characterized the Y245A and Y305F mutants of the human KMT SET7/9 (also known as KMT7) that alter its product specificity from a monomethyltransferase to a di- and a trimethyltransferase, respectively. Crystal structures of these mutants in complex with peptides bearing unmodified, mono-, di-, and trimethylated lysines illustrate the roles of active site water molecules in aligning the lysine {epsilon}-amino group for methyl transfer with S-adenosylmethionine. Displacement or dissociation of these solvent molecules enlarges the diameter of the active site, accommodating the increasing size of the methylated {epsilon}-amino group during successive methyl transfer reactions. Together, these results furnish new insights into the roles of active site water molecules in modulating lysine multiple methylation by SET domain KMTs and provide the first molecular snapshots of the mono-, di-, and trimethyl transfer reactions catalyzed by these enzymes.

  9. 52. EASTSIDE PLANT: GENERAL VIEW OF GOVERNOR ADJACENT TO GENERATOR ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    52. EASTSIDE PLANT: GENERAL VIEW OF GOVERNOR ADJACENT TO GENERATOR - American Falls Water, Power & Light Company, Island Power Plant, Snake River, below American Falls Dam, American Falls, Power County, ID

  10. Relationships between membrane water molecules and Patman equilibration kinetics at temperatures far above the phosphatidylcholine melting point.

    PubMed

    Vaughn, Alexandra R; Bell, Thomas A; Gibbons, Elizabeth; Askew, Caitlin; Franchino, Hannabeth; Hirsche, Kelsey; Kemsley, Linea; Melchor, Stephanie; Moulton, Emma; Schwab, Morgan; Nelson, Jennifer; Bell, John D

    2015-04-01

    The naphthalene-based fluorescent probes Patman and Laurdan detect bilayer polarity at the level of the phospholipid glycerol backbone. This polarity increases with temperature in the liquid-crystalline phase of phosphatidylcholines and was observed even 90°C above the melting temperature. This study explores mechanisms associated with this phenomenon. Measurements of probe anisotropy and experiments conducted at 1M NaCl or KCl (to reduce water permittivity) revealed that this effect represents interactions of water molecules with the probes without proportional increases in probe mobility. Furthermore, comparison of emission spectra to Monte Carlo simulations indicated that the increased polarity represents elevation in probe access to water molecules rather than increased mobility of relevant bilayer waters. Equilibration of these probes with the membrane involves at least two steps which were distinguished by the membrane microenvironment reported by the probe. The difference in those microenvironments also changed with temperature in the liquid-crystalline phase in that the equilibrium state was less polar than the initial environment detected by Patman at temperatures near the melting point, more polar at higher temperatures, and again less polar as temperature was raised further. Laurdan also displayed this level of complexity during equilibration, although the relationship to temperature differed quantitatively from that experienced by Patman. This kinetic approach provides a novel way to study in molecular detail basic principles of what happens to the membrane environment around an individual amphipathic molecule as it penetrates the bilayer. Moreover, it provides evidence of unexpected and interesting membrane behaviors far from the phase transition. PMID:25559316

  11. Density Functional Theory Study of the Complexation of the Uranyl Dication with Anionic Phosphate Ligands with and without Water Molecules

    SciTech Connect

    Jackson, Virgil E.; Gutowski, Keith E.; Dixon, David A.

    2013-08-01

    The structures, vibrational frequencies and energetics of anhydrous and hydrated complexes of UO2 2+ with the phosphate anions H2PO4 -, HPO4 2-, and PO4 3- were predicted at the density functional theory (DFT) and MP2 molecular orbital theory levels as isolated gas phase species and in aqueous solution by using self-consistent reaction field (SCRF) calculations with different solvation models. The geometries and vibrational frequencies of the major binding modes for these complexes are compared to experiment where possible and good agreement is found. The uranyl moiety is nonlinear in many of the complexes, and the coordination number (CN) 5 in the equatorial plane is the predominant binding motif. The phosphates are found to bind in both monodentate and bidentate binding modes depending on the charge and the number of water molecules. The SCRF calculations were done with a variety of approaches, and different SCRF approaches were found to be optimal for different reaction types. The acidities of HxPO4 3-x in HxPO4 3-x(H2O)4, x = 0-3 complexes were calculated with different SCRF models and compared to experiment. Phosphate anions can displace water molecules from the first solvation shell at the uranyl exothermically. The addition of water molecules can cause the bonding of H2PO4 - and HPO4 2- to change from bidentate to monodentate exothermically while maintaining CN 5. The addition of water can generate monodentate structures capable of cross-linking to other uranyl phosphates to form the types of structures found in the solid state. [UO2(HPO4)(H2O)3] is predicted to be a strong base in the gas phase and in aqueous solution. It is predicted to be a much weaker acid than H3PO4 in the gas phase and in solution.

  12. Subpicosecond energy transfer from a highly intense THz pulse to water: A computational study based on the TIP4P/2005 rigid-water-molecule model

    NASA Astrophysics Data System (ADS)

    Mishra, Pankaj Kr.; Vendrell, Oriol; Santra, Robin

    2016-03-01

    The dynamics of ultrafast energy transfer to water clusters and to bulk water by a highly intense, subcycle THz pulse of duration ≈150 fs is investigated in the context of force-field molecular dynamics simulations. We focus our attention on the mechanisms by which rotational and translational degrees of freedom of the water monomers gain energy from these subcycle pulses with an electric field amplitude of up to about 0.6 V/Å. It has been recently shown that pulses with these characteristics can be generated in the laboratory [C. Vicario, B. Monoszlai, and C. P. Hauri, Phys. Rev. Lett. 112, 213901 (2014), 10.1103/PhysRevLett.112.213901]. Through their permanent dipole moment, water molecules are acted upon by the electric field and forced off their preferred hydrogen-bond network conformation. This immediately sets them in motion with respect to one another as energy quickly transfers to their relative center of mass displacements. We find that, in the bulk, the operation of these mechanisms is strongly dependent on the initial temperature and density of the system. In low density systems, the equilibration between rotational and translational modes is slow due to the lack of collisions between monomers. As the initial density of the system approaches 1 g/cm3 , equilibration between rotational and translational modes after the pulse becomes more efficient. In turn, low temperatures hinder the direct energy transfer from the pulse to rotational motion owing to the resulting stiffness of the hydrogen bond network. For small clusters of just a few water molecules we find that fragmentation due to the interaction with the pulse is faster than equilibration between rotations and translations, meaning that the latter remain colder than the former after the pulse. In contrast, clusters with more than a few tens of water molecules already display energy gain dynamics similar to water in condensed phases owing to inertial confinement of the internal water molecules by

  13. An aspartate and a water molecule mediate efficient acid-base catalysis in a tailored antibody pocket

    SciTech Connect

    Debler, Erik W.; Müller, Roger; Hilvert, Donald; Wilson, Ian A.

    2009-12-01

    Design of catalysts featuring multiple functional groups is a desirable, yet formidable goal. Antibody 13G5, which accelerates the cleavage of unactivated benzisoxazoles, is one of few artificial enzymes that harness an acid and a base to achieve efficient proton transfer. X-ray structures of the Fab-hapten complexes of wild-type 13G5 and active-site variants now afford detailed insights into its mechanism. The parent antibody preorganizes Asp{sup H35} and Glu{sup L34} to abstract a proton from substrate and to orient a water molecule for leaving group stabilization, respectively. Remodeling the environment of the hydrogen bond donor with a compensatory network of ordered waters, as seen in the Glu{sup L34} to alanine mutant, leads to an impressive 10{sup 9}-fold rate acceleration over the nonenzymatic reaction with acetate, illustrating the utility of buried water molecules in bifunctional catalysis. Generalization of these design principles may aid in creation of catalysts for other important chemical transformations.

  14. Binding site identification and role of permanent water molecule of PIM-3 kinase: A molecular dynamics study.

    PubMed

    Ul-Haq, Zaheer; Gul, Sana; Usmani, Saman; Wadood, Abdul; Khan, Waqasuddin

    2015-11-01

    The kinome is a protein kinase complement of the human genome, categorized as serine/threonine and tyrosine kinases. These kinases catalyze phosphorylation reaction by using ATP as phosphoryl donor. Proviral Integration Site for Moloney Murine Leukemia Virus (PIM) kinase encodes serine/threonine protein kinases that recognized as proto-oncogene, responsible for rapid growth of cancerous cells. It is implicated in cell survival and function via cell cycle progression and its metabolism. PIM-3, sub-member of PIM kinases is a proto-oncogene, its overexpression inhibits apoptosis, and results in progression of hepatocellular carcinoma. PIM-3 is considered as a promising drug target but attempts to develop its specific inhibitors is slowed down due to the lack of 3D structure by any experimental technique. In silico techniques generally facilitate scientist to explore hidden structural features in order to improve drug discovery. In the present study, homology modeling, molecular docking and MD simulation techniques were utilized to explore the structure and dynamics of PIM-3 kinase. Induction of water molecules during molecular docking simulation explored differences in the hinge region between PIM-1 and PIM-3 kinases that may be responsible for specificity. Furthermore, role of water molecules in the active site was also explored via radial distribution function (RDF) after a 10 ns molecular dynamics (MD) simulations. Generated RDF plots exhibited the importance of water for inhibitor binding through their bridging capability that links the ligand with binding site residues. PMID:26529487

  15. H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin.

    PubMed

    Nicoletti, Francesco P; Droghetti, Enrica; Howes, Barry D; Bustamante, Juan P; Bonamore, Alessandra; Sciamanna, Natascia; Estrin, Darío A; Feis, Alessandro; Boffi, Alberto; Smulevich, Giulietta

    2013-09-01

    The ferric form of truncated hemoglobin II from Thermobifida fusca (Tf-trHb) and its triple mutant WG8F-YB10F-YCD1F at neutral and alkaline pH, and in the presence of CN(-) have been characterized by resonance Raman spectroscopy, electron paramagnetic resonance spectroscopy, and molecular dynamics simulations. Tf-trHb contains three polar residues in the distal site, namely TrpG8, TyrCD1 and TyrB10. Whereas TrpG8 can act as a potential hydrogen-bond donor, the tyrosines can act as donors or acceptors. Ligand binding in heme-containing proteins is determined by a number of factors, including the nature and conformation of the distal residues and their capability to stabilize the heme-bound ligand via hydrogen-bonding and electrostatic interactions. Since both the RR Fe-OH(-) and Fe-CN(-) frequencies are very sensitive to the distal environment, detailed information on structural variations has been obtained. The hydroxyl ligand binds only the WT protein giving rise to two different conformers. In form 1 the anion is stabilized by H-bonds with TrpG8, TyrCD1 and a water molecule, in turn H-bonded to TyrB10. In form 2, H-bonding with TyrCD1 is mediated by a water molecule. Unlike the OH(-) ligand, CN(-) binds both WT and the triple mutant giving rise to two forms with similar spectroscopic characteristics. The overall results clearly indicate that H-bonding interactions both with distal residues and water molecules are important structural determinants in the active site of Tf-trHb. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins. PMID:23467007

  16. Water-soluble carbon monoxide-releasing molecules: helping to elucidate the vascular activity of the 'silent killer'.

    PubMed

    Chatterjee, Prabal Kumar

    2004-06-01

    Carbon monoxide (CO) is formed during the degradation of haeme by haeme oxygenase (HO). As well as being an important signalling molecule and vasodilator, CO also possesses antihypertensive, anti-inflammatory and antiapoptotic qualities and protects against ischaemic tissue injury. Several approaches have been used to investigate the therapeutic potential of CO, ranging from direct administration of CO gas to the use of prodrugs, which generate CO upon metabolism. A novel approach involves the use of specific CO carriers, which will release measurable, controllable and effective amounts of CO into biological systems. Transitional metal carbonyls based around iron, manganese or ruthenium have recently been developed as CO-releasing molecules (CO-RMs) that, under appropriate conditions, will release CO. Such molecules have been shown to provide cardioprotection in both ex vivo and in vivo experiments. To date, CO-RMs have been largely incompatible with biological systems in that they are only soluble in organic solvents or have to be preactivated either by physical or chemical stimuli. However, the recent development of water-soluble CO-RMs has provided new opportunities to investigate the pharmacological and biological features of CO without such confounding influences. CORM-3, a novel water-soluble CO-RM, has recently been used to confirm the cardioprotective actions of CO. In this issue of British Journal of Pharmacology, Foresti and co-workers report that CORM-3 delivers CO, produces aortic vasodilation ex vivo and reduces blood pressure in vivo via modulation of the same cGMP and potassium channels utilised by endogenous and exogenous CO. These findings suggest that CORM-3 has the potential for use as a modulator of vascular function and hypertension. However, the use of water-soluble CO-RMs raises several questions of their own which will need to be addressed if CO-RMs are to be of future use therapeutically. PMID:15148242

  17. Water-soluble carbon monoxide-releasing molecules: helping to elucidate the vascular activity of the ‘silent killer'

    PubMed Central

    Chatterjee, Prabal Kumar

    2004-01-01

    Carbon monoxide (CO) is formed during the degradation of haeme by haeme oxygenase (HO). As well as being an important signalling molecule and vasodilator, CO also possesses antihypertensive, anti-inflammatory and antiapoptotic qualities and protects against ischaemic tissue injury. Several approaches have been used to investigate the therapeutic potential of CO, ranging from direct administration of CO gas to the use of prodrugs, which generate CO upon metabolism. A novel approach involves the use of specific CO carriers, which will release measurable, controllable and effective amounts of CO into biological systems. Transitional metal carbonyls based around iron, manganese or ruthenium have recently been developed as CO-releasing molecules (CO-RMs) that, under appropriate conditions, will release CO. Such molecules have been shown to provide cardioprotection in both ex vivo and in vivo experiments. To date, CO-RMs have been largely incompatible with biological systems in that they are only soluble in organic solvents or have to be preactivated either by physical or chemical stimuli. However, the recent development of water-soluble CO-RMs has provided new opportunities to investigate the pharmacological and biological features of CO without such confounding influences. CORM-3, a novel water-soluble CO-RM, has recently been used to confirm the cardioprotective actions of CO. In this issue of British Journal of Pharmacology, Foresti and co-workers report that CORM-3 delivers CO, produces aortic vasodilation ex vivo and reduces blood pressure in vivo via modulation of the same cGMP and potassium channels utilised by endogenous and exogenous CO. These findings suggest that CORM-3 has the potential for use as a modulator of vascular function and hypertension. However, the use of water-soluble CO-RMs raises several questions of their own which will need to be addressed if CO-RMs are to be of future use therapeutically. PMID:15148242

  18. DFT studies of carbohydrate solvation: II. MD-DFTr of a super-molecule complex of glucose, explicit waters, and an implicit solvent (COSMO)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    MD-DFTr studies are carried out on the super-molecule solvated complexes of glucose described in paper I. Included were ten explicit water molecules and an implicit solvation model, COSMO, superimposed upon the complex. Starting configurations were taken from DFTr optimized complexes resulting from ...

  19. Investigation of N-acyl homoserine lactone (AHL) molecule production in Gram-negative bacteria isolated from cooling tower water and biofilm samples.

    PubMed

    Haslan, Ezgi; Kimiran-Erdem, Ayten

    2013-09-01

    In this study, 99 Gram-negative rod bacteria were isolated from cooling tower water, and biofilm samples were examined for cell-to-cell signaling systems, N-acyl homoserine lactone (AHL) signal molecule types, and biofilm formation capacity. Four of 39 (10 %) strains isolated from water samples and 14 of 60 (23 %) strains isolated from biofilm samples were found to be producing a variety of AHL signal molecules. It was determined that the AHL signal molecule production ability and the biofilm formation capacity of sessile bacteria is higher than planktonic bacteria, and there was a statistically significant difference between the AHL signal molecule production of these two groups (p < 0.05). In addition, it was found that bacteria belonging to the same species isolated from cooling tower water and biofilm samples produced different types of AHL signal molecules and that there were different types of AHL signal molecules in an AHL extract of bacteria. In the present study, it was observed that different isolates of the same strains did not produce the same AHLs or did not produce AHL molecules, and bacteria known as AHL producers did not produce AHL. These findings suggest that detection of signal molecules in bacteria isolated from cooling towers may contribute to prevention of biofilm formation, elimination of communication among bacteria in water systems, and blockage of quorum-sensing controlled virulence of these bacteria. PMID:23250628

  20. Possible interstellar formation of glycine from the reaction of CH2=NH, CO and H2O: catalysis by extra water molecules through the hydrogen relay transport.

    PubMed

    Nhlabatsi, Zanele P; Bhasi, Priya; Sitha, Sanyasi

    2016-01-01

    "How the fundamental life elements are created in the interstellar medium (ISM)?" is one of the intriguing questions related to the genesis of life. Using computational calculations, we have discussed the reaction of CH2=NH, CO and H2O for the formation of glycine, the simplest life element. This reaction proceeds through a concerted mechanism with reasonably large barriers for the cases with one and two water molecules as reactants. For the two water case we found that the extra water molecule exhibits some catalytic role through the hydrogen transport relay effect and the barrier height is reduced substantially compared to the case with one water molecule. These two cases can be treated as ideal cases for the hot-core formation of the interstellar glycine. With an increasing number of water molecules as the reactants, we found that when the numbers of water molecules are three or more than three, the barrier height reduced so drastically that the transition states were more stable than the reactants. Such a situation gives a clear indication that with excess water molecules as the reactants, this reaction will be feasible even under the low temperature conditions existing in the cold interstellar clouds and the exothermic nature of the reaction will be the driving force. PMID:26616741

  1. Product distributions and rate constants for ion-molecule reactions in water, hydrogen sulfide, ammonia, and methane

    NASA Technical Reports Server (NTRS)

    Huntress, W. T., Jr.; Pinizzotto, R. F., Jr.

    1973-01-01

    The thermal energy, bimolecular ion-molecule reactions occurring in gaseous water, hydrogen sulfide, ammonia, and methane have been identified and their rate constants determined using ion cyclotron resonance methods. Absolute rate constants were determined for the disappearance of the primary ions by using the trapped ion method, and product distributions were determined for these reactions by using the cyclotron ejection method. Previous measurements are reviewed and compared with the results using the present methods. The relative rate constants for hydrogen-atom abstraction, proton transfer, and charge transfer are also determined for reactions of the parent ions.

  2. Double ionization of the water molecule: Influence of the target orientation on the secondary-electron angular distributions

    SciTech Connect

    Oubaziz, D.; Aouchiche, H.; Champion, C.

    2011-01-15

    Fivefold differential cross sections for electron-induced double ionization of isolated oriented water molecules are reported. The theoretical investigation is performed within the first Born approximation by describing the initial molecular state by means of single-center wave functions. The contributions of each final state to the double-ionization process, i.e., with target electrons ejected from similar and/or different molecular subshells, are studied and compared in terms of shape and magnitude. Furthermore, for the particular target orientations investigated, we identify clearly the signature of the main scenarios involved in (e,3e) reactions, namely, the shake-off and the two-step 1 mechanisms.

  3. Quantum-chemical study of the interactions between cyanide ions and water molecules

    SciTech Connect

    Baranovskii, V.I.; Fomicheva, V.P.; Ivanova, N.V.; Sizova, O.V.

    1986-05-01

    Nonempirical MO SCF calculations have been performed in the 4-31 G basis to examine the interactions of CN/sup -/ ions with H/sub 2/O molecules. The most stable geometrical configurations have been used in calculating the force constants of the C-N and hydrogen-bond stretching vibrations and of the deformation vibration for the H...N-C (H...C-N) angle. The frequencies of the corresponding vibrations have been determined. The results are compared with data obtained for the uncharged HCN x H/sub 2/O system.

  4. Boltzmann equation analysis of electron-molecule collision cross sections in water vapor and ammonia

    SciTech Connect

    Yousfi, M.; Benabdessadok, M.D.

    1996-12-01

    Sets of electron-molecule collision cross sections for H{sub 2}O and NH{sub 3} have been determined from a classical technique of electron swarm parameter unfolding. This deconvolution method is based on a simplex algorithm using a powerful multiterm Boltzmann equation analysis established in the framework of the classical hydrodynamic approximation. It is well adapted for the simulation of the different classes of swarm experiments (i.e., time resolved, time of flight, and steady state experiments). The sets of collision cross sections that exist in the literature are reviewed and analyzed. Fitted sets of cross sections are determined for H{sub 2}O and NH{sub 3} which exhibit features characteristic of polar molecules such as high rotational excitation collision cross sections. The hydrodynamic swarm parameters (i.e., drift velocity, longitudinal and transverse diffusion coefficients, ionization and attachment coefficients) calculated from the fitted sets are in excellent agreement with the measured ones. These sets are finally used to calculate the transport and reaction coefficients needed for discharge modeling in two cases of typical gas mixtures for which experimental swarm data are very sparse or nonexistent (i.e., flue gas mixtures and gas mixtures for rf plasma surface treatment). {copyright} {ital 1996 American Institute of Physics.}

  5. Rotational dynamics of water molecules near biological surfaces with implications for nuclear quadrupole relaxation.

    PubMed

    Braun, Daniel; Schmollngruber, Michael; Steinhauser, Othmar

    2016-09-21

    Based on Molecular Dynamics simulations of two different systems, the protein ubiquitin dissolved in water and an AOT reverse micelle, we present a broad analysis of the single particle rotational dynamics of water. A comprehensive connection to NQR, which is a prominent experimental method in this field, is developed, based on a reformulation of its theoretical framework. Interpretation of experimental NQR results requires a model which usually assumes that the NQR experiences retardation only in the first hydration shell. Indeed, the present study shows that this first-shell model is correct. Moreover, previous experimental retardation factors are quantitatively reproduced. All of this is seemingly contradicted by results of other methods, e.g., dielectric spectroscopy, responsible for a long-standing debate in this field. Our detailed analysis shows that NQR omits important information contained in overall water dynamics, most notably, the retardation of the water dipole axis in the electric field exerted by a biological surface. PMID:27546227

  6. Assessments of aquifer sensitivity on Navajo Nation and adjacent lands and ground-water vulnerability to pesticide contamination on the Navajo Indian Irrigation Project, Arizona, New Mexico, and Utah

    USGS Publications Warehouse

    Blanchard, Paul J.

    2002-01-01

    The U.S. Environmental Protection Agency requested that the Navajo Nation conduct an assessment of aquifer sensitivity on Navajo Nation lands and an assessment of ground-water vulnerability to pesticide contamination on the Navajo Indian Irrigation Project. Navajo Nation lands include about 17,000 square miles in northeastern Arizona, northwestern New Mexico, and southeastern Utah. The Navajo Indian Irrigation Project in northwestern New Mexico is the largest area of agriculture on the Navajo Nation. The Navajo Indian Irrigation Project began operation in 1976; presently (2001) about 62,000 acres are available for irrigated agriculture. Numerous pesticides have been used on the Navajo Indian Irrigation Project during its operation. Aquifer sensitivity is defined by the U.S. Environmental Protection Agency as 'The relative ease with which a contaminant [pesticide] applied on or near a land surface can migrate to the aquifer of interest. Aquifer sensitivity is a function of the intrinsic characteristics of the geologic material in question, any underlying saturated materials, and the overlying unsaturated zone. Sensitivity is not dependent on agronomic practices or pesticide characteristics.' Ground-water vulnerability is defined by the U.S. Environmental Protection Agency as 'The relative ease with which a contaminant [pesticide] applied on or near a land surface can migrate to the aquifer of interest under a given set of agronomic management practices, pesticide characteristics, and aquifer sensitivity conditions.' The results of the aquifer sensitivity assessment on Navajo Nation and adjacent lands indicated relative sensitivity within the boundaries of the study area. About 22 percent of the study area was not an area of recharge to bedrock aquifers or an area of unconsolidated deposits and was thus assessed to have an insignificant potential for contamination. About 72 percent of the Navajo Nation study area was assessed to be in the categories of most potential

  7. Size-dependent molecule-like to plasmonic transition in water-soluble glutathione stabilized gold nanomolecules

    NASA Astrophysics Data System (ADS)

    Kothalawala, Nuwan; Lee West, James, IV; Dass, Amala

    2013-12-01

    A size-dependent transition from molecule-like to plasmonic behaviour is demonstrated in the case of water soluble Au:SG nanomolecules. This was achieved using PAGE separation of smaller and larger nanomolecules, resulting in an unprecedented 26 bands, in a wide-range from 10's to 1000's of Au-atoms. PAGE separation of larger plasmonic nanomolecules is demonstrated for the first time. High resolution ESI-MS, with isotopic resolution, of smaller nanoparticles is reported, including the first time report of Au43(SG)26. This report will aid in the fundamental understanding of size-dependent properties of nanomolecules. The synthetic procedure employs a green approach with non-toxic chemicals and processes. The water solubility, non-toxicity and biocompatibility will lead to applications in biomedicine.A size-dependent transition from molecule-like to plasmonic behaviour is demonstrated in the case of water soluble Au:SG nanomolecules. This was achieved using PAGE separation of smaller and larger nanomolecules, resulting in an unprecedented 26 bands, in a wide-range from 10's to 1000's of Au-atoms. PAGE separation of larger plasmonic nanomolecules is demonstrated for the first time. High resolution ESI-MS, with isotopic resolution, of smaller nanoparticles is reported, including the first time report of Au43(SG)26. This report will aid in the fundamental understanding of size-dependent properties of nanomolecules. The synthetic procedure employs a green approach with non-toxic chemicals and processes. The water solubility, non-toxicity and biocompatibility will lead to applications in biomedicine. Electronic supplementary information (ESI) available: Detailed synthetic conditions, expanded MS, and optical spectra. This material is available free of charge via the Internet at http://pubs.acs.org. See DOI: 10.1039/c3nr03657j

  8. What interactions can distort the orientational distribution of interfacial water molecules as probed by second harmonic and sum frequency generation?

    NASA Astrophysics Data System (ADS)

    de Beer, Alex G. F.; Roke, Sylvie

    2016-07-01

    Aqueous interfaces are omnipresent in nature. Nonlinear optical methods such as second harmonic and sum frequency generation (SHG/SFG) are valuable techniques to access molecular level information from these interfaces. In the interpretation of SHG and SFG data for both scattering and reflection mode experiments, the relation between the second-order hyperpolarizability tensor β(2), a molecular property, and the surface second-order susceptibility (" separators=" χ(2), a surface averaged property, plays a central role. To correctly describe the molecular details of the interface, it needs to be determined how molecules are oriented, and what the influence is of interfacial electrostatic fields and H-bonding on the orientational distribution. Here, we revisit the relations between β(2) and χ(2) and show, by means of a Boltzmann average, that significant energy differences are needed to generate measurable changes in the molecular orientational distribution at the interface. In practice, H-bonding and surface pressure such as applied in a Langmuir trough can be strong enough to alter the shape of the orientational distribution function of water. In contrast, electrostatic fields, such as those present in the Stern layer, will not have a significant impact on the shape of the orientational distribution function of water molecules.

  9. Hydrogen-bonding changes of internal water molecules upon the actions of microbial rhodopsins studied by FTIR spectroscopy.

    PubMed

    Furutani, Yuji; Kandori, Hideki

    2014-05-01

    Microbial rhodopsins are classified into type-I rhodopsins, which utilize light energy to perform wide varieties of function, such as proton pumping, ion pumping, light sensing, cation channels, and so on. The crystal structures of several type-I rhodopsins were solved and the molecular mechanisms have been investigated based on the atomic structures. However, the crystal structures of proteins of interest are not always available and the basic architectures are sometimes quite similar, which obscures how the proteins achieve different functions. Stimulus-induced difference FTIR spectroscopy is a powerful tool to detect minute structural changes providing a clue for elucidating the molecular mechanisms. In this review, the studies on type-I rhodopsins from fungi and marine bacteria, whose crystal structures have not been solved yet, were summarized. Neurospora rhodopsin and Leptosphaeria rhodopsin found from Fungi have sequence similarity. The former has no proton pumping function, while the latter has. Proteorhodopsin is another example, whose proton pumping machinery is altered at alkaline and acidic conditions. We described how the structural changes of protein were different and how water molecules were involved in them. We reviewed the results on dynamics of the internal water molecules in pharaonis halorhodopsin as well. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks. PMID:24041645

  10. How water molecules affect the catalytic activity of hydrolases--a XANES study of the local structures of peptide deformylase.

    PubMed

    Cui, Peixin; Wang, Yu; Chu, Wangsheng; Guo, Xiaoyun; Yang, Feifei; Yu, Meijuan; Zhao, Haifeng; Dong, Yuhui; Xie, Yaning; Gong, Weimin; Wu, Ziyu

    2014-01-01

    Peptide deformylase (PDF) is a prokaryotic enzyme that catalyzes the deformylation of nascent peptides generated during protein synthesis and water molecules play a key role in these hydrolases. Using X-ray absorption near edge spectroscopy (XANES) and ab initio calculations we accurately probe the local atomic environment of the metal ion binding in the active site of PDF at different pH values and with different metal ions. This new approach is an effective way to monitor existing correlations among functions and structural changes. We show for the first time that the enzymatic activity depends on pH values and metal ions via the bond length of the nearest coordinating water (Wat1) to the metal ion. Combining experimental and theoretical data we may claim that PDF exhibits an enhanced enzymatic activity only when the distance of the Wat1 molecule with the metal ion falls in the limited range from 2.15 to 2.55 Å. PMID:25503313

  11. What interactions can distort the orientational distribution of interfacial water molecules as probed by second harmonic and sum frequency generation?

    PubMed

    de Beer, Alex G F; Roke, Sylvie

    2016-07-28

    Aqueous interfaces are omnipresent in nature. Nonlinear optical methods such as second harmonic and sum frequency generation (SHG/SFG) are valuable techniques to access molecular level information from these interfaces. In the interpretation of SHG and SFG data for both scattering and reflection mode experiments, the relation between the second-order hyperpolarizability tensor β(2), a molecular property, and the surface second-order susceptibility χ(2), a surface averaged property, plays a central role. To correctly describe the molecular details of the interface, it needs to be determined how molecules are oriented, and what the influence is of interfacial electrostatic fields and H-bonding on the orientational distribution. Here, we revisit the relations between β(2) and χ(2) and show, by means of a Boltzmann average, that significant energy differences are needed to generate measurable changes in the molecular orientational distribution at the interface. In practice, H-bonding and surface pressure such as applied in a Langmuir trough can be strong enough to alter the shape of the orientational distribution function of water. In contrast, electrostatic fields, such as those present in the Stern layer, will not have a significant impact on the shape of the orientational distribution function of water molecules. PMID:27475384

  12. Ligand uptake in Mycobacterium tuberculosis truncated hemoglobins is controlled by both internal tunnels and active site water molecules

    PubMed Central

    Davidge, Kelly S; Singh, Sandip; Bowman, Lesley AH; Tinajero-Trejo, Mariana; Carballal, Sebastián; Radi, Rafael; Poole, Robert K; Dikshit, Kanak; Estrin, Dario A; Marti, Marcelo A; Boechi, Leonardo

    2015-01-01

    Mycobacterium tuberculosis, the causative agent of human tuberculosis, has two proteins belonging to the truncated hemoglobin (trHb) family. Mt-trHbN presents well-defined internal hydrophobic tunnels that allow O 2 and •NO to migrate easily from the solvent to the active site, whereas Mt-trHbO possesses tunnels that are partially blocked by a few bulky residues, particularly a tryptophan at position G8. Differential ligand migration rates allow Mt-trHbN to detoxify •NO, a crucial step for pathogen survival once under attack by the immune system, much more efficiently than Mt-trHbO. In order to investigate the differences between these proteins, we performed experimental kinetic measurements, •NO decomposition, as well as molecular dynamics simulations of the wild type Mt-trHbN and two mutants, VG8F and VG8W. These mutations introduce modifications in both tunnel topologies and affect the incoming ligand capacity to displace retained water molecules at the active site. We found that a single mutation allows Mt-trHbN to acquire ligand migration rates comparable to those observed for Mt-trHbO, confirming that ligand migration is regulated by the internal tunnel architecture as well as by water molecules stabilized in the active site. PMID:26478812

  13. Ligand uptake in Mycobacterium tuberculosis truncated hemoglobins is controlled by both internal tunnels and active site water molecules.

    PubMed

    Boron, Ignacio; Bustamante, Juan Pablo; Davidge, Kelly S; Singh, Sandip; Bowman, Lesley Ah; Tinajero-Trejo, Mariana; Carballal, Sebastián; Radi, Rafael; Poole, Robert K; Dikshit, Kanak; Estrin, Dario A; Marti, Marcelo A; Boechi, Leonardo

    2015-01-01

    Mycobacterium tuberculosis, the causative agent of human tuberculosis, has two proteins belonging to the truncated hemoglobin (trHb) family. Mt-trHbN presents well-defined internal hydrophobic tunnels that allow O 2 and (•)NO to migrate easily from the solvent to the active site, whereas Mt-trHbO possesses tunnels that are partially blocked by a few bulky residues, particularly a tryptophan at position G8. Differential ligand migration rates allow Mt-trHbN to detoxify (•)NO, a crucial step for pathogen survival once under attack by the immune system, much more efficiently than Mt-trHbO. In order to investigate the differences between these proteins, we performed experimental kinetic measurements, (•)NO decomposition, as well as molecular dynamics simulations of the wild type Mt-trHbN and two mutants, VG8F and VG8W. These mutations introduce modifications in both tunnel topologies and affect the incoming ligand capacity to displace retained water molecules at the active site. We found that a single mutation allows Mt-trHbN to acquire ligand migration rates comparable to those observed for Mt-trHbO, confirming that ligand migration is regulated by the internal tunnel architecture as well as by water molecules stabilized in the active site. PMID:26478812

  14. Prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium: DFT and Car-Parrinello molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Dutta, Bipan; De, Rina; Chowdhury, Joydeep

    2015-12-01

    The ground state prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium has been investigated with the aid of DFT and Car-Parrinello molecular dynamics (CPMD) simulation studies. The CPMD simulations envisage the possibility of proton transfer reactions of the molecule through the solvent water medium. Probable proton transfer pathways have been predicted from the DFT calculations which are substantiated by the natural bond orbital analyses. The evolution and breaking of the concerned bonds of the molecule for different proton transfer reaction pathways are also estimated.

  15. Dynamics of molecules in a supercooled water nanoparticle during the ice accretion on the aircraft surface

    NASA Astrophysics Data System (ADS)

    Amelyushkin, I. A.; Stasenko, A. L.

    2015-06-01

    The principal aim of this work is to elaborate a robust physical model and the corresponding numerical code for prediction of the icing startup due to numerous water nanoparticles in the supercooled humid air. For this purpose, a scientified approach was used which is based not on the quantum-mechanics considerations but on the information about intermolecular potentials (especially, Lennard-Jones (LJ), etc.) tightly connected with the state equations of the corresponding specie (e. g., van der Waals for air and water and Mie-Grünaisen for circumfluent body). u In other words, the principal idea of this work is to adequately ascribe certain macroscopic characteristics of a water nanoparticle which may significantly differ from those indicated in physical reference books for bulk materials.

  16. Effect of anodizing voltage on the sorption of water molecules on porous alumina

    NASA Astrophysics Data System (ADS)

    Vrublevsky, I.; Chernyakova, K.; Bund, A.; Ispas, A.; Schmidt, U.

    2012-05-01

    The amount of water adsorbed on different centers on the surface of oxalic acid alumina films is a function of the anodizing voltage. It is decreased with increasing the anodizing voltage from 20 up to 50 V, came up to maximum value at 20-30 V and slightly increased at voltages above 50 V. Water adsorption by oxide films formed at voltages below 50 V can be due to the negative surface charge that is present on the alumina surface. The negative surface charge disappears in the films formed at voltages higher than 50 V, and thus, the water is adsorbed on aluminum ions in a tetrahedral and octahedral environment. The correlation between anodizing conditions of aluminum in oxalic acid and the structure and composition of anodic alumina was established by Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM), thermogravimetric and differential thermal analyses (TG/DTA).

  17. Mercedes–Benz water molecules near hydrophobic wall: Integral equation theories vs Monte Carlo simulations

    PubMed Central

    Urbic, T.; Holovko, M. F.

    2011-01-01

    Associative version of Henderson-Abraham-Barker theory is applied for the study of Mercedes–Benz model of water near hydrophobic surface. We calculated density profiles and adsorption coefficients using Percus-Yevick and soft mean spherical associative approximations. The results are compared with Monte Carlo simulation data. It is shown that at higher temperatures both approximations satisfactory reproduce the simulation data. For lower temperatures, soft mean spherical approximation gives good agreement at low and at high densities while in at mid range densities, the prediction is only qualitative. The formation of a depletion layer between water and hydrophobic surface was also demonstrated and studied. PMID:21992334

  18. Mercedes-Benz water molecules near hydrophobic wall: Integral equation theories vs Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Urbic, T.; Holovko, M. F.

    2011-10-01

    Associative version of Henderson-Abraham-Barker theory is applied for the study of Mercedes-Benz model of water near hydrophobic surface. We calculated density profiles and adsorption coefficients using Percus-Yevick and soft mean spherical associative approximations. The results are compared with Monte Carlo simulation data. It is shown that at higher temperatures both approximations satisfactory reproduce the simulation data. For lower temperatures, soft mean spherical approximation gives good agreement at low and at high densities while in at mid range densities, the prediction is only qualitative. The formation of a depletion layer between water and hydrophobic surface was also demonstrated and studied.

  19. Mercedes-Benz water molecules near hydrophobic wall: integral equation theories vs Monte Carlo simulations.

    PubMed

    Urbic, T; Holovko, M F

    2011-10-01

    Associative version of Henderson-Abraham-Barker theory is applied for the study of Mercedes-Benz model of water near hydrophobic surface. We calculated density profiles and adsorption coefficients using Percus-Yevick and soft mean spherical associative approximations. The results are compared with Monte Carlo simulation data. It is shown that at higher temperatures both approximations satisfactory reproduce the simulation data. For lower temperatures, soft mean spherical approximation gives good agreement at low and at high densities while in at mid range densities, the prediction is only qualitative. The formation of a depletion layer between water and hydrophobic surface was also demonstrated and studied. PMID:21992334

  20. Recombination time of an RF discharge plasma in the presence of water molecules

    SciTech Connect

    Protasevich, E.T.

    1986-05-01

    The authors show that the introduction of water vapor into an electrodeless rf discharge noticeably reduces the excitation temperature and substantially increases the recombination time of the plasma. An attempt is made to explain the physical processes associated with these phenomena.

  1. Hierarchical assembly of an achiral pi-conjugated molecule into a chiral nanotube through the air/water interface.

    PubMed

    Yao, Pingping; Wang, Haifeng; Chen, Penglei; Zhan, Xiaowei; Kuang, Xun; Zhu, Daoben; Liu, Minghua

    2009-06-16

    An achiral pi-conjugated fluorinated fused pyrazine derivative has been spread at the air/water interface, and its assembling property is investigated. It has been found that the compound, although without any long alkyl chain, could be spread as a floating film on water surface, the surface pressure of which can be compressed up to ca. 70 mN/m. An inflection point has been observed in the isotherm of the floating film on water surface. The atomic force microscope (AFM), scanning electron microscope (SEM) as well as the transmission electron microscope (TEM) observations revealed that the floating film first formed a multilayer structure and then was compressed into nanotubes after the inflection region as a result of the rolling of the ultrathin film. Interestingly, the rolled nanotubes show circular dichroism although the molecule itself is an achiral species, suggesting the chiral nanotube is predominantly produced on the water surface. The investigation provides an effective way to fabricate supramolecular-based organic chiral nanotubes through an interfacial supramolecular assembly process. PMID:19459675

  2. Structural and atoms-in-molecules analysis of hydrogen-bond network around nitroxides in liquid water.

    PubMed

    Houriez, Céline; Masella, Michel; Ferré, Nicolas

    2010-09-28

    In this study, we investigated the hydrogen-bond network patterns involving the NO moieties of five small nitroxides in liquid water by analyzing nanosecond scale molecular dynamics trajectories. To this end, we implemented two types of hydrogen-bond definitions, based on electronic structure, using Bader's atoms-in-molecules analysis and based on geometric criteria. In each definition framework, the nitroxide/water hydrogen-bond networks appear very variable from a nitroxide to another. Moreover, each definition clearly leads to a different picture of nitroxide hydration. For instance, the electronic structure-based definition predicts a number of hydrogen bonds around the nitroxide NO moiety usually larger than geometric structure-based ones. One particularly interesting result is that the strength of a nitroxide/water hydrogen bond does not depend on its linearity, leading us to question the relevance of geometric definition based on angular cutoffs to study this type of hydrogen bond. Moreover, none of the hydrogen-bond definitions we consider in the present study is able to quantitatively correlate the strength of nitroxide/water hydrogen-bond networks with the aqueous nitroxide spin properties. This clearly exhibits that the hydrogen-bonding concept is not reliable enough to draw quantitative conclusions concerning such properties. PMID:20886951

  3. Structural and atoms-in-molecules analysis of hydrogen-bond network around nitroxides in liquid water

    NASA Astrophysics Data System (ADS)

    Houriez, Céline; Masella, Michel; Ferré, Nicolas

    2010-09-01

    In this study, we investigated the hydrogen-bond network patterns involving the NO moieties of five small nitroxides in liquid water by analyzing nanosecond scale molecular dynamics trajectories. To this end, we implemented two types of hydrogen-bond definitions, based on electronic structure, using Bader's atoms-in-molecules analysis and based on geometric criteria. In each definition framework, the nitroxide/water hydrogen-bond networks appear very variable from a nitroxide to another. Moreover, each definition clearly leads to a different picture of nitroxide hydration. For instance, the electronic structure-based definition predicts a number of hydrogen bonds around the nitroxide NO moiety usually larger than geometric structure-based ones. One particularly interesting result is that the strength of a nitroxide/water hydrogen bond does not depend on its linearity, leading us to question the relevance of geometric definition based on angular cutoffs to study this type of hydrogen bond. Moreover, none of the hydrogen-bond definitions we consider in the present study is able to quantitatively correlate the strength of nitroxide/water hydrogen-bond networks with the aqueous nitroxide spin properties. This clearly exhibits that the hydrogen-bonding concept is not reliable enough to draw quantitative conclusions concerning such properties.

  4. Structure and energetics of model amphiphilic molecules at the water liquid-vapor interface - A molecular dynamics study

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; Benjamin, Ilan

    1993-01-01

    A molecular dynamics study of adsorption of p-n-pentylphenol at infinite dilution at the water liquid-vapor interface is reported. The calculated free energy of adsorption is -8.8 +/- 0.7 kcal/mol, in good agreement with the experimental value of -7.3 kcal/mol. The transition between the interfacial region and the bulk solution is sharp and well-defined by energetic, conformational, and orientational criteria. At the water surface, the phenol head group is mostly immersed in aqueous solvent. The most frequent orientation of the hydrocarbon tail is parallel to the interface, due to dispersion interactions with the water surface. This arrangement of the phenol ring and the alkyl chain requires that the chain exhibits a kink. As the polar head group is being moved into the solvent, the chain length increases and the tail becomes increasingly aligned toward the surface normal, such that the nonpolar part of the molecule exposed to water is minimized. The same effect was achieved when phenol was replaced by a more polar head group, phenolate.

  5. The signatures of stable isotopes δ 15N and δ 13C in anadromous and non-anadromous Coilia nasus living in the Yangtze River, and the adjacent sea waters

    NASA Astrophysics Data System (ADS)

    Wang, Lei; Tang, Wenqiao; Dong, Wenxia

    2015-12-01

    Stable isotopes are increasingly used to investigate seasonal migrations of aquatic organisms. This study employed stable isotopes ( δ 13C and δ 15N) for Coilia nasus from the lower Yangtze River and the adjacent East China Sea to distinguish different ecotypic groups, ascertain trophic nutrition positions, and reflect environmental influences on C. nasus. δ 13C signatures of C. nasus sampled from Zhoushan (ZS), Chongming (CM), and Jingjiang (JJ) waters were significantly higher than those from the Poyang Lake (PYL) ( P < 0.05). By contrast, δ 15N signatures of C. nasus in ZS, CM, and JJ groups were significantly lower than those in PYL group ( P < 0.05). Basing on δ 13C and δ 15N signatures, we could distinguish anadromous (ZS, CM, and JJ) and non-anadromous (PYL) groups. The trophic level (TL) of anadromous C. nasus ranged from 2.90 to 3.04, whereas that of non-anadromous C. nasus was 4.38. C. nasus occupied the middle and top nutrition positions in the marine and Poyang Lake food webs, respectively. C. nasus in Poyang Lake were significantly more enriched in δ 15N but depleted in δ 13C, suggesting that anthropogenic nutrient inputs and terrigenous organic carbon are important to the Poyang Lake food web. This study is the first to apply δ 15N and δ 13C to population assignment studies of C. nasus in the Yangtze River and its affiliated waters. Analysis of stable isotopes ( δ 15N and δ 13C) is shown to be a useful tool for discriminating anadromous and non-anadromous C. nasus.

  6. Infrared photodissociation of a water molecule from a flexible molecule-H{sub 2}O complex: Rates and conformational product yields following XH stretch excitation

    SciTech Connect

    Clarkson, Jasper R.; Herbert, John M.; Zwier, Timothy S.

    2007-04-07

    Infrared-ultraviolet hole-burning and hole-filling spectroscopies have been used to study IR-induced dissociation of the tryptamine{center_dot}H{sub 2}O and tryptamine{center_dot}D{sub 2}O complexes. Upon complexation of a single water molecule, the seven conformational isomers of tryptamine collapse to a single structure that retains the same ethylamine side chain conformation present in the most highly populated conformer of tryptamine monomer. Infrared excitation of the tryptamine{center_dot}H{sub 2}O complex was carried out using a series of infrared absorptions spanning the range of 2470-3715 cm{sup -1}. The authors have determined the conformational product yield over this range and the dissociation rate near threshold, where it is slow enough to be measured by our methods. The observed threshold for dissociation occurred at 2872 cm{sup -1} in tryptamine{center_dot}H{sub 2}O and at 2869 cm{sup -1} in tryptamine{center_dot}D{sub 2}O, with no dissociation occurring on the time scale of the experiment ({approx}2 {mu}s) at 2745 cm{sup -1}. The dissociation time constants varied from {approx}200 ns for the 2869 cm{sup -1} band of tryptamine{center_dot}D{sub 2}O to {approx}25 ns for the 2872 cm{sup -1} band of tryptamine{center_dot}H{sub 2}O. This large isotope dependence is associated with a zero-point energy effect that increases the binding energy of the deuterated complex by {approx}190 cm{sup -1}, thereby reducing the excess energy available at the same excitation energy. At all higher energies, the dissociation lifetime was shorter than the pulse duration of our lasers (8 ns). At all wavelengths, the observed products in the presence of collisions are dominated by conformers A and B of tryptamine monomer, with small contributions from the other minor conformers. In addition, right at threshold (2869 cm{sup -1}), tryptamine{center_dot}D{sub 2}O dissociates exclusively to conformer A in the absence of collisions with helium, while both A and B conformational

  7. [DOTA-bis(amide)]lanthanide complexes: NMR evidence for differences in water-molecule exchange rates for coordination isomers.

    PubMed

    Zhang, S; Kovacs, Z; Burgess, S; Aime, S; Terreno, E; Sherry, A D

    2001-01-01

    Two derivatives of 1,4,7,10-tetraazacyclododecane with trans-acetate and trans-amide side-chain ligating groups have been prepared and their complexes with lanthanide cations examined by multinuclear NMR spectroscopy. These lanthanide complexes exist in aqueous solution as a mixture of slowly interconverting coordination isomers with 1H chemical shifts similar to those reported previously for the major (M) and minor (m) forms of the tetraacetate ([Ln(dota)]-) and tetraamide ([Ln(dtma)]3+) complexes. As in the [Ln(dota)]- and [Ln(dtma)]3+ complexes, the m/M ratio proved to be a sensitive function of lanthanide size and temperature. An analysis of 1H hyperfine shifts in spectra of the Yb3+ complexes revealed significant differences between the axial (D1) and non-axial (D2) components of the magnetic susceptibility tensor anisotropy in the m and M coordination isomers and the energetics of ring inversion and m <==> M isomerization as determined by two-dimensional exchange spectroscopy (EXSY). (17)O shift data for the Dy3+ complexes showed that both have one inner-sphere water molecule. A temperature-dependent (17)O NMR study of bulk water linewidths for solutions of the Gd3+ complexes provided direct evidence for differences in water exchange rates for the two coordination isomers. The bound-water lifetimes (tauM298) in the M and m isomers of the Gd3+ complexes ranged from 1.4-2.4 micros and 3-14 ns, respectively. This indicates that 1) the inner-sphere water lifetimes for the complexes with a single positive charge reported here are considerably shorter for both coordination isomers than the corresponding values for the [Gd(dtma)]3+ complex with three positive charges, and 2) the difference in water lifetimes for M and m isomers in these two series is magnified in the [Gd[dota-bis(amide)

  8. The reaction of clean Li surfaces with small molecules in ultrahigh vacuum. 2: Water

    SciTech Connect

    Zhuang, G.; Ross, P.N. Jr.; Kong, F.P.; McLarnon, F. |

    1998-01-01

    Reactions at the Li/H{sub 2}O interface were studied at 160 to 290 K in ultrahigh vacuum by a combination of spectroscopic ellipsometry and Auger electron spectroscopy. Ice multilayers, ca. 100 ML thick, were deposited on clean Li at 160 K. The evaporation rate of water at 160 K is sufficiently slow that the ice layer remains on the surface for about 1 h. After 10 min at 160 k, a pure LiOH layer ca. 70 {angstrom} thick is produced, and after 1 h there is evidence of a slow conversion to LiOH to Li{sub 2}O in the layer, probably at the Li/LiOH interface. Raising the temperature to 240 K results in desorption of the adsorbed water and conversion of all the LiOH to a porous (60% void) layer composed mostly of Li{sub 2}O (35%) with some metallic Li mixed in. Raising the temperature further to 290 K results in densification of the layer by both collapse of the voids and by diffusion of Li into the interstices of the Li{sub 2}O, increasing the Li content to 27% and shrinking the film thickness to 26 {angstrom}. Based on these results, a model for the behavior of small amounts of water in Li battery electrolyte is presented.

  9. Proposed photosynthesis method for producing hydrogen from dissociated water molecules using incident near-infrared light.

    PubMed

    Li, Xingxing; Li, Zhenyu; Yang, Jinlong

    2014-01-10

    Highly efficient solar energy utilization is very desirable in photocatalytic water splitting. However, until now, the infrared part of the solar spectrum, which constitutes almost half of the solar energy, has not been used, resulting in significant loss in the efficiency of solar energy utilization. Here, we propose a new mechanism for water splitting in which near-infrared light can be used to produce hydrogen. This ability is a result of the unique electronic structure of the photocatalyst, in which the valence band and conduction band are distributed on two opposite surfaces with a large electrostatic potential difference produced by the intrinsic dipole of the photocatalyst. This surface potential difference, acting as an auxiliary booster for photoexcited electrons, can effectively reduce the photocatalyst's band gap required for water splitting in the infrared region. Our electronic structure and optical property calculations on a surface-functionalized hexagonal boron-nitride bilayer confirm the existence of such photocatalysts and verify the reaction mechanism. PMID:24483934

  10. Ion hydration and associated defects in hydrogen bond network of water: Observation of reorientationally slow water molecules beyond first hydration shell in aqueous solutions of MgCl 2

    NASA Astrophysics Data System (ADS)

    Baul, Upayan; Vemparala, Satyavani

    2015-01-01

    Effects of the presence of ions, at moderate to high concentrations, on dynamical properties of water molecules are investigated through classical molecular dynamics simulations using two well-known nonpolarizable water models. Simulations reveal that the presence of magnesium chloride (MgCl2) induces perturbations in the hydrogen bond network of water leading to the formation of bulklike domains with ``defect sites'' on boundaries of such domains: water molecules at such defect sites have less number of hydrogen bonds than those in bulk water. Reorientational autocorrelation functions for dipole vectors of such defect water molecules are computed at different concentrations of ions and compared with system of pure water. Earlier experimental and simulation studies indicate significant differences in reorientational dynamics for water molecules in the first hydration shell of many dissolved ions. Results of this study suggest that defect water molecules, which are beyond the first hydration shells of ions, also experience significant slowing of reorientation times as a function of concentration in the case of MgCl2. However, addition of cesium chloride (CsCl) to water does not perturb the hydrogen bond network of water significantly even at higher concentrations. This difference in behavior between MgCl2 and CsCl is consistent with the well-known Hofmeister series.

  11. Photo-electrochemical Oxidation of Organic C1 Molecules over WO3 Films in Aqueous Electrolyte: Competition Between Water Oxidation and C1 Oxidation.

    PubMed

    Reichert, Robert; Zambrzycki, Christian; Jusys, Zenonas; Behm, R Jürgen

    2015-11-01

    To better understand organic-molecule-assisted photo-electrochemical water splitting, photo-electrochemistry and on-line mass spectrometry measurements are used to investigate the photo-electrochemical oxidation of the C1 molecules methanol, formaldehyde, and formic acid over WO3 film anodes in aqueous solution and its competition with O2 evolution from water oxidation O2 (+) and CO2 (+) ion currents show that water oxidation is strongly suppressed by the organic species. Photo-electro-oxidation of formic acid is dominated by formation of CO2 , whereas incomplete oxidation of formaldehyde and methanol prevails, with the selectivity for CO2 formation increasing with increasing potential and light intensity. The mechanistic implications for the photo-electro-oxidation of the organic molecules and its competition with water oxidation, which could be derived from this novel approach, are discussed. PMID:26382643

  12. Binding Energy of Molecules on Water Ice: Laboratory Measurements and Modeling

    NASA Astrophysics Data System (ADS)

    He, Jiao; Acharyya, Kinsuk; Vidali, Gianfranco

    2016-07-01

    We measured the binding energy of N2, CO, O2, CH4, and CO2 on non-porous (compact) amorphous solid water (np-ASW), of N2 and CO on porous ASW, and of NH3 on crystalline water ice. We were able to measure binding energies down to a fraction of 1% of a layer, thus making these measurements more appropriate for astrochemistry than the existing values. We found that CO2 forms clusters on the np-ASW surface even at very low coverages. The binding energies of N2, CO, O2, and CH4 decrease with coverage in the submonolayer regime. Their values at the low coverage limit are much higher than what is commonly used in gas-grain models. An empirical formula was used to describe the coverage dependence of the binding energies. We used the newly determined binding energy distributions in a simulation of gas-grain chemistry for cold cloud and hot-core models. We found that owing to the higher value of binding energy in the submonolayer regime, a fraction of all these ices remains for much longer and up to higher temperatures on the grain surface compared to the single value energies currently used in the astrochemical models.

  13. Confined Water Determines Transport Properties of Guest Molecules in Narrow Pores.

    PubMed

    Phan, Anh; Cole, David R; Weiß, R Gregor; Dzubiella, Joachim; Striolo, Alberto

    2016-08-23

    We computed the transport of methane through 1 nm wide slit-shaped pores carved out of solid substrates. Models for silica, magnesium oxide, and alumina were used as solid substrates. The pores were filled with water. The results show that the methane permeability through the hydrated pores is strongly dependent on the solid substrate. Detailed analysis of the simulated systems reveals that local properties of confined water, including its structure, and more importantly, evolution of solvation free energy and hydrogen bond structure are responsible for the pronounced differences observed. The simulations are extended to multicomponent systems representative of natural gas, containing methane, ethane, and H2S. The results show that all pores considered have high affinity for H2S, moderate affinity for methane, and low affinity for ethane. The H2S/methane transport selectivity through the hydrated alumina pore is comparable, or superior, to that reported for existing commercial membranes. A multiscale approach was then implemented to demonstrate that a Smoluchowski one-dimensional model is able to reproduce the molecular-level results for short pores when appropriate values for the local self-diffusion coefficients are used as input parameters. We propose that the model can be extended to predict methane transport through uniform hydrated pores of macroscopic length. When verified by experiments, our simulation results could have important implications in applications such as natural gas sweetening and predictions of methane migration through hydraulically fractured shale formations. PMID:27490280

  14. Theoretical investigation of hydrogen bonding between water and platinum(II): an atom in molecule (AIM) study

    NASA Astrophysics Data System (ADS)

    Li, Yan; Zhang, Guiqiu; Chen, Dezhan

    2012-02-01

    Recently, Rizzato et al. [Angew. Chem. Int. Ed. 49, 7440 (2010)] [1] reported a hydrogen-bonding-like interaction between a water molecule and a d8 metal ion (PtII) based on neutron diffraction, and provided the first crystallographic evidence for this interaction. We studied the hydrogen bonding of the O-H ... Pt interaction theoretically using atoms in molecule (AIM) and natural bond orbital analysis (NBO) in the crystallographic geometries. The method used density functional theory (DFT) with the hybrid B3LYP function. For platinum atoms, we used the Los Alamos National Laboratory 2-Double-Zeta (LANL2DZ) basis set, and for the other atoms we used 6-311++G(d,p) basis sets. Criteria based on a topological analysis of the electron density were used in order to characterize the nature of interactions in the complexes. The main purpose of the present work is to provide an answer to the following questions: Why can a filled d orbital of square-planar d8 metal ions such as platinum(II) also act as hydrogen-bond acceptors? Can a study based on the electron charge density answer this question? A good correlation between the density at the intermolecular bond critical point and the energy interaction was found. The interaction is mainly closed-shell and there is some charge transfer in this system.

  15. Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description.

    PubMed

    Spyrakis, Francesca; Cavasotto, Claudio N

    2015-10-01

    Structure-based virtual screening is currently an established tool in drug lead discovery projects. Although in the last years the field saw an impressive progress in terms of algorithm development, computational performance, and retrospective and prospective applications in ligand identification, there are still long-standing challenges where further improvement is needed. In this review, we consider the conceptual frame, state-of-the-art and recent developments of three critical "structural" issues in structure-based drug lead discovery: the use of homology modeling to accurately model the binding site when no experimental structures are available, the necessity of accounting for the dynamics of intrinsically flexible systems as proteins, and the importance of considering active site water molecules in lead identification and optimization campaigns. PMID:26271444

  16. Rotationally resolved photoelectron spectroscopy of a triatomic molecule: Photoionization of the C (0.0.0) state of water

    SciTech Connect

    Glab, W.L.; Glynn, P.T.; Dehmer, P.M.; Dehmer, J.L.

    1996-05-01

    The authors have used a magnetic bottle photoelectron spectrometer to study the distribution of ion rotational states following photoionization of selected rotational states of the {tilde C}(0,0,0) state of water by 355 nm light. The spectrometer`s kinetic energy resolution of about 4 meV was sufficient to yield rotationally resolved time-of-flight photoelectron spectra. Comparison of the measured and calculated photoelectron spectra is encouraging and reveals unusual photoionization dynamics due to very nonatomic-like behavior in the photoionization continuum and to the presence of Cooper minima. This is the first time that such a test of photoionization theory for a polyatomic molecule at finite kinetic energy has been possible.

  17. Internal water molecules and H-bonding in biological macromolecules: a review of structural features with functional implications.

    PubMed Central

    Meyer, E.

    1992-01-01

    Conserved structural patterns of internal water molecules and/or H-bond chains were observed and are here correlated in this review, which then describes two functional properties: equilibration of hydrostatic pressure and proton transport. Available evidence in support of these hypotheses is presented, together with suggested experiments to test them. High-resolution crystal structures of a variety of proteins were studied with interactive computer graphics. Conserved H-bonding linkages may be used as a paradigm for a rationalization of proton transport in membranes. The concept of the "proton wire," which links buried active-site amino acids with the surface of the protein raises the more general question of the functional role of the various molecular components. PMID:1304887

  18. CO2 and C2H2 in cold nanodroplets of oxygenated organic molecules and water.

    PubMed

    Devlin, J Paul; Balcı, F Mine; Maşlakcı, Zafer; Uras-Aytemiz, Nevin

    2014-11-14

    Recent demonstrations of subsecond and microsecond timescales for formation of clathrate hydrate nanocrystals hint at future methods of control of environmental and industrial gases such as CO2 and methane. Combined results from cold-chamber and supersonic-nozzle [A. S. Bhabhe, "Experimental study of condensation and freezing in a supersonic nozzle," Ph.D. thesis (Ohio State University, 2012), Chap. 7] experiments indicate extremely rapid encagement of components of all-vapor pre-mixtures. The extreme rates are derived from (a) the all-vapor premixing of the gas-hydrate components and (b) catalytic activity of certain oxygenated organic large-cage guests. Premixing presents no obvious barrier to large-scale conditions of formation. Further, from sequential efforts of the groups of Trout and Buch, a credible defect-based model of the catalysis mechanism exists for guidance. Since the catalyst-generated defects are both mobile and abundant, it is often unnecessary for a high percentage of the cages to be occupied by a molecular catalyst. Droplets represent the liquid phase that bridges the premixed vapor and clathrate hydrate phases but few data exist for the droplets themselves. Here we describe a focused computational and FTIR spectroscopic effort to characterize the aerosol droplets of the all-vapor cold-chamber methodology. Computational data for CO2 and C2H2, hetero-dimerized with each of the organic catalysts and water, closely match spectroscopic redshift patterns in both magnitude and direction. Though vibrational frequency shifts are an order of magnitude greater for the acetylene stretch mode, both CO2 and C2H2 experience redshift values that increase from that for an 80% water-methanol solvent through the solvent series to approximately doubled values for tetrahydrofuran and trimethylene oxide (TMO) droplets. The TMO solvent properties extend to a 50 mol.% solution of CO2, more than an order of magnitude greater than for the water-methanol solvent mixture

  19. CO2 and C2H2 in cold nanodroplets of oxygenated organic molecules and water

    NASA Astrophysics Data System (ADS)

    Devlin, J. Paul; Balcı, F. Mine; Maşlakcı, Zafer; Uras-Aytemiz, Nevin

    2014-11-01

    Recent demonstrations of subsecond and microsecond timescales for formation of clathrate hydrate nanocrystals hint at future methods of control of environmental and industrial gases such as CO2 and methane. Combined results from cold-chamber and supersonic-nozzle [A. S. Bhabhe, "Experimental study of condensation and freezing in a supersonic nozzle," Ph.D. thesis (Ohio State University, 2012), Chap. 7] experiments indicate extremely rapid encagement of components of all-vapor pre-mixtures. The extreme rates are derived from (a) the all-vapor premixing of the gas-hydrate components and (b) catalytic activity of certain oxygenated organic large-cage guests. Premixing presents no obvious barrier to large-scale conditions of formation. Further, from sequential efforts of the groups of Trout and Buch, a credible defect-based model of the catalysis mechanism exists for guidance. Since the catalyst-generated defects are both mobile and abundant, it is often unnecessary for a high percentage of the cages to be occupied by a molecular catalyst. Droplets represent the liquid phase that bridges the premixed vapor and clathrate hydrate phases but few data exist for the droplets themselves. Here we describe a focused computational and FTIR spectroscopic effort to characterize the aerosol droplets of the all-vapor cold-chamber methodology. Computational data for CO2 and C2H2, hetero-dimerized with each of the organic catalysts and water, closely match spectroscopic redshift patterns in both magnitude and direction. Though vibrational frequency shifts are an order of magnitude greater for the acetylene stretch mode, both CO2 and C2H2 experience redshift values that increase from that for an 80% water-methanol solvent through the solvent series to approximately doubled values for tetrahydrofuran and trimethylene oxide (TMO) droplets. The TMO solvent properties extend to a 50 mol.% solution of CO2, more than an order of magnitude greater than for the water-methanol solvent mixture

  20. 22. Float located adjacent to entry stair in filtration bed. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    22. Float located adjacent to entry stair in filtration bed. The float actuates a valve that maintains water level over the bed. - Lake Whitney Water Filtration Plant, Filtration Plant, South side of Armory Street between Edgehill Road & Whitney Avenue, Hamden, New Haven County, CT

  1. Ubiquitous Water-Soluble Molecules in Aquatic Plant Exudates Determine Specific Insect Attraction

    PubMed Central

    Sérandour, Julien; Reynaud, Stéphane; Willison, John; Patouraux, Joëlle; Gaude, Thierry; Ravanel, Patrick; Lempérière, Guy; Raveton, Muriel

    2008-01-01

    Plants produce semio-chemicals that directly influence insect attraction and/or repulsion. Generally, this attraction is closely associated with herbivory and has been studied mainly under atmospheric conditions. On the other hand, the relationship between aquatic plants and insects has been little studied. To determine whether the roots of aquatic macrophytes release attractive chemical mixtures into the water, we studied the behaviour of mosquito larvae using olfactory experiments with root exudates. After testing the attraction on Culex and Aedes mosquito larvae, we chose to work with Coquillettidia species, which have a complex behaviour in nature and need to be attached to plant roots in order to obtain oxygen. This relationship is non-destructive and can be described as commensal behaviour. Commonly found compounds seemed to be involved in insect attraction since root exudates from different plants were all attractive. Moreover, chemical analysis allowed us to identify a certain number of commonly found, highly water-soluble, low-molecular-weight compounds, several of which (glycerol, uracil, thymine, uridine, thymidine) were able to induce attraction when tested individually but at concentrations substantially higher than those found in nature. However, our principal findings demonstrated that these compounds appeared to act synergistically, since a mixture of these five compounds attracted larvae at natural concentrations (0.7 nM glycerol, <0.5 nM uracil, 0.6 nM thymine, 2.8 nM uridine, 86 nM thymidine), much lower than those found for each compound tested individually. These results provide strong evidence that a mixture of polyols (glycerol), pyrimidines (uracil, thymine), and nucleosides (uridine, thymidine) functions as an efficient attractive signal in nature for Coquillettidia larvae. We therefore show for the first time, that such commonly found compounds may play an important role in plant-insect relationships in aquatic eco-systems. PMID:18841203

  2. Boundary Layers of Air Adjacent to Cylinders

    PubMed Central

    Nobel, Park S.

    1974-01-01

    Using existing heat transfer data, a relatively simple expression was developed for estimating the effective thickness of the boundary layer of air surrounding cylinders. For wind velocities from 10 to 1000 cm/second, the calculated boundary-layer thickness agreed with that determined for water vapor diffusion from a moistened cylindrical surface 2 cm in diameter. It correctly predicted the resistance for water vapor movement across the boundary layers adjacent to the (cylindrical) inflorescence stems of Xanthorrhoea australis R. Br. and Scirpus validus Vahl and the leaves of Allium cepa L. The boundary-layer thickness decreased as the turbulence intensity increased. For a turbulence intensity representative of field conditions (0.5) and for νwindd between 200 and 30,000 cm2/second (where νwind is the mean wind velocity and d is the cylinder diameter), the effective boundary-layer thickness in centimeters was equal to [Formula: see text]. PMID:16658855

  3. Crystal Structure of Fatty Acid Amide Hydrolase Bound to the Carbamate Inhibitor URB597: Discovery of a Deacylating Water Molecule and Insight into Enzyme Inactivation

    SciTech Connect

    Mileni, Mauro; Kamtekar, Satwik; Wood, David C.; Benson, Timothy E.; Cravatt, Benjamin F.; Stevens, Raymond C.

    2010-08-12

    The endocannabinoid system regulates a wide range of physiological processes including pain, inflammation, and cognitive/emotional states. URB597 is one of the best characterized covalent inhibitors of the endocannabinoid-degrading enzyme fatty acid amide hydrolase (FAAH). Here, we report the structure of the FAAH-URB597 complex at 2.3 {angstrom} resolution. The structure provides insights into mechanistic details of enzyme inactivation and experimental evidence of a previously uncharacterized active site water molecule that likely is involved in substrate deacylation. This water molecule is part of an extensive hydrogen-bonding network and is coordinated indirectly to residues lining the cytosolic port of the enzyme. In order to corroborate our hypothesis concerning the role of this water molecule in FAAH's catalytic mechanism, we determined the structure of FAAH conjugated to a urea-based inhibitor, PF-3845, to a higher resolution (2.4 {angstrom}) than previously reported. The higher-resolution structure confirms the presence of the water molecule in a virtually identical location in the active site. Examination of the structures of serine hydrolases that are non-homologous to FAAH, such as elastase, trypsin, or chymotrypsin, shows a similarly positioned hydrolytic water molecule and suggests a functional convergence between the amidase signature enzymes and serine proteases.

  4. Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules

    SciTech Connect

    Chakraborty, Kaushik; Bandyopadhyay, Sanjoy

    2015-07-28

    Single-stranded DNA (ss-DNA) binding proteins specifically bind to the single-stranded regions of the DNA and protect it from premature annealing, thereby stabilizing the DNA structure. We have carried out atomistic molecular dynamics simulations of the aqueous solutions of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein complexed with two short ss-DNA segments. Attempts have been made to explore the influence of the formation of such complex structures on the microscopic dynamics and hydrogen bond properties of the interfacial water molecules. It is found that the water molecules involved in bridging the ss-DNA segments and the protein domains form a highly constrained thin layer with extremely retarded mobility. These water molecules play important roles in freezing the conformational oscillations of the ss-DNA oligomers and thereby forming rigid complex structures. Further, it is demonstrated that the effect of complexation on the slow long-time relaxations of hydrogen bonds at the interface is correlated with hindered motions of the surrounding water molecules. Importantly, it is observed that the highly restricted motions of the water molecules bridging the protein and the DNA components in the complexed forms originate from more frequent hydrogen bond reformations.

  5. Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules

    NASA Astrophysics Data System (ADS)

    Chakraborty, Kaushik; Bandyopadhyay, Sanjoy

    2015-07-01

    Single-stranded DNA (ss-DNA) binding proteins specifically bind to the single-stranded regions of the DNA and protect it from premature annealing, thereby stabilizing the DNA structure. We have carried out atomistic molecular dynamics simulations of the aqueous solutions of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein complexed with two short ss-DNA segments. Attempts have been made to explore the influence of the formation of such complex structures on the microscopic dynamics and hydrogen bond properties of the interfacial water molecules. It is found that the water molecules involved in bridging the ss-DNA segments and the protein domains form a highly constrained thin layer with extremely retarded mobility. These water molecules play important roles in freezing the conformational oscillations of the ss-DNA oligomers and thereby forming rigid complex structures. Further, it is demonstrated that the effect of complexation on the slow long-time relaxations of hydrogen bonds at the interface is correlated with hindered motions of the surrounding water molecules. Importantly, it is observed that the highly restricted motions of the water molecules bridging the protein and the DNA components in the complexed forms originate from more frequent hydrogen bond reformations.

  6. Water Splitting: Strongly Coupled Nafion Molecules and Ordered Porous CdS Networks for Enhanced Visible-Light Photoelectrochemical Hydrogen Evolution (Adv. Mater. 24/2016).

    PubMed

    Zheng, Xue-Li; Song, Ji-Peng; Ling, Tao; Hu, Zhen Peng; Yin, Peng-Fei; Davey, Kenneth; Du, Xi-Wen; Qiao, Shi-Zhang

    2016-06-01

    T. Ling, X.-W. Du, S. Z. Qiao, and co-workers report strongly coupled Nafion molecules and ordered-porous CdS networks for visible-light water splitting. The image conceptually shows how the three-dimensional ordered structure effectively harvests incoming light. As described on page 4935, the inorganic CdS skeleton is homogeneously passivated by the organic Nafion molecules to facilitate hydrogen generation. PMID:27311095

  7. Response to memorandum by Rowley and Dixon regarding U.S. Geological Survey report titled "Characterization of Surface-Water Resources in the Great Basin National Park Area and Their Susceptibility to Ground-Water Withdrawals in Adjacent Valleys, White Pine County, Nevada"

    USGS Publications Warehouse

    Prudic, David E.

    2006-01-01

    Applications pending for permanent permits to pump large quantities of ground water in Spring and Snake Valleys adjacent to Great Basin National Park (the Park) prompted the National Park Service to request a study by the U.S. Geological Survey to evaluate the susceptibility of the Park's surface-water resources to pumping. The result of this study was published as U.S. Geological Survey Scientific Investigations Report 2006-5099 'Characterization of Surface-Water Resources in the Great Basin National Park Area and Their Susceptibility to Ground-Water Withdrawals in Adjacent Valleys, White Pine County, Nevada,' by P.E. Elliott, D.A. Beck, and D.E. Prudic. That report identified areas within the Park where surface-water resources are susceptible to ground-water pumping; results from the study showed that three streams and several springs near the eastern edge of the Park were susceptible. However, most of the Park's surface-water resources likely would not be affected by pumping because of either low-permeability rocks or because ground water is sufficiently deep as to not be directly in contact with the streambeds. A memorandum sent by Peter D. Rowley and Gary L. Dixon, Consulting Geologists, to the Southern Nevada Water Authority (SNWA) on June 29, 2006 was critical of the report. The memorandum by Rowley and Dixon was made available to the National Park Service, the U.S. Geological Survey, and the public during the Nevada State Engineer's 'Evidentiary Exchange' process for the recent hearing on applications for ground-water permits by SNWA in Spring Valley adjacent to Great Basin National Park. The U.S. Geological Survey was asked by the National Park Service to assess the validity of the concerns and comments contained in the Rowley and Dixon memorandum. An Administrative Letter Report responding to Rowley and Dixon's concerns and comments was released to the National Park Service on October 30, 2006. The National Park Service subsequently requested that the

  8. Reflections on Small Molecule Manganese Models that Seek to Mimic Photosynthetic Water Oxidation Chemistry

    PubMed Central

    Mullins, Christopher S.

    2008-01-01

    Recent advances in the study of the Oxygen Evolving Complex (OEC) of Photosystem II (PSII) include structural information attained from several X-ray crystallographic (XRD) and spectroscopic (XANES and EXAFS) investigations. The possible structural features gleaned from these studies have enabled synthetic chemists to design more accurate model complexes, which in turn, offer better insight into the possible pathways used by PSII to drive photosynthetic water oxidation catalysis. Mononuclear model compounds have been used to advance the knowledge base regarding the physical properties and reactivity of high-valent (MnIV or MnV) complexes. Such investigations have been especially important in regard to the manganyl (MnIV=O or MnV≡O) species, as there are no reports, to date, of any structural characterized multinuclear model compounds that incorporate such a functionality. Dinuclear and trinuclear model compounds have also been thoroughly studied in attempts to draw further comparison to the physical properties observed in the natural system and to design systems of catalytic relevance. As the reactive center of the OEC has been shown to contain an oxo-Mn4Ca cluster, exact structural models necessitate a tetranuclear Mn core. The number of models that make use of Mn4 clusters has risen substantially in recent years, and these models have provided evidence to support and refute certain mechanistic proposals. Further work is needed to adequately address the rationale for Ca (and Cl) in the OEC and to determine the sequence of events that lead to O2 evolution. PMID:19081816

  9. Groundwater and surface-water resources in the Bureau of Land Management Moab Master Leasing Plan area and adjacent areas, Grand and San Juan Counties, Utah, and Mesa and Montrose Counties, Colorado

    USGS Publications Warehouse

    Masbruch, Melissa D.; Shope, Christopher L.

    2014-01-01

    The Bureau of Land Management (BLM) Canyon Country District Office is preparing a leasing plan known as the Moab Master Leasing Plan (Moab MLP) for oil, gas, and potash mineral rights in an area encompassing 946,469 acres in southeastern Utah. The BLM has identified water resources as being potentially affected by oil, gas, and potash development and has requested that the U.S. Geological Survey prepare a summary of existing water-resources information for the Moab MLP area. This report includes a summary and synthesis of previous and ongoing investigations conducted in the Moab MLP and adjacent areas in Utah and Colorado from the early 1930s through the late 2000s. Eight principal aquifers and six confining units were identified within the study area. Permeability is a function of both the primary permeability from interstitial pore connectivity and secondary permeability created by karst features or faults and fractures. Vertical hydraulic connection generally is restricted to strongly folded and fractured zones, which are concentrated along steeply dipping monoclines and in narrow regions encompassing igneous and salt intrusive masses. Several studies have identified both an upper and lower aquifer system separated by the Pennsylvanian age Paradox Member of the Hermosa Formation evaporite, which is considered a confining unit and is present throughout large parts of the study area. Surface-water resources of the study area are dominated by the Colorado River. Several perennial and ephemeral or intermittent tributaries join the Colorado River as it flows from northeast to southwest across the study area. An annual spring snowmelt and runoff event dominates the hydrology of streams draining mountainous parts of the study area, and most perennial streams in the study area are snowmelt-dominated. A bimodal distribution is observed in hydrographs from some sites with a late-spring snowmelt-runoff peak followed by smaller peaks of shorter duration during the late

  10. The rates of exchange of water molecules from Al(III)-methylmalonate complexes: The effect of chelate ring size

    SciTech Connect

    Casey, W.H.; Phillips, B.L.; Nordin, J.P.; Sullivan, D.J.

    1998-08-01

    Rate coefficients are reported for exchange of hydration waters in the inner-coordination-sphere of Al(III)-methylmalonate complexes with bulk solution as determined via {sup 17}O-NMR. Surprisingly, water molecules in the thermodynamically less-stable complexes containing six-membered chelates are much more labile than those in five-membered oxalate-A(III) complexes. The surprising trend in reactivity is attributable either to differences in the Lewis basicities of oxygens in bidentate oxalate and methylmalonate ligands, or to rapid dissociation/reassociation of one of the acetate groups to the metal center. These results identify a useful case where trends in the apparent labilities of dissolved and presumed surface complexes deviate sharply. This deviation could be usefully exploited to probe surfaces if ligand-promoted dissolution rates could be compared at conditions where inner-sphere and outer-sphere chelate complexes could be distinguished spectroscopically. The authors expect inner-sphere oxalate to have a smaller labilizing effect than malonate or methylmalonate. A contrary result would indicate structural dissimilarity between complexes on the surface and in solution, or perhaps steric hindrance.

  11. Double differential distribution of electron emission in the ionization of water molecules by fast bare oxygen ions

    NASA Astrophysics Data System (ADS)

    Bhattacharjee, Shamik; Biswas, Shubhadeep; Bagdia, Chandan; Roychowdhury, Madhusree; Nandi, Saikat; Misra, Deepankar; Monti, J. M.; Tachino, C. A.; Rivarola, R. D.; Champion, C.; Tribedi, Lokesh C.

    2016-03-01

    The doubly differential distributions of low-energy electron emission in the ionization of water molecules under the impact of fast bare oxygen ions with energy of 48 MeV are measured. The measured data are compared with two quantum-mechanical models, i.e. the post and prior versions of the continuum distorted wave-eikonal initial state (CDW-EIS) approximation, and the first-order Born approximation with initial and final wavefunctions verifying correct boundary conditions (CB1). An overall excellent qualitative agreement is found between the data and the CDW-EIS models whereas the CB1 model showed substantial deviation. However, the detailed angular distributions display some discrepancies with both CDW-EIS models. The single differential and total cross-sections exhibit good agreement with the CDW-EIS models. The present detailed data set could also be used as an input for modeling highly charged ion induced radiation damage in living tissues, whose most abundant component is water. Similar measurements are also carried out for a projectile energy of 60 MeV. However, since the double differential cross-section data show similar results the details are not provided here, except for the total ionization cross-sections results.

  12. Theoretical predictions of the spectroscopic parameters in noble-gas molecules: HXeOH and its complex with water.

    PubMed

    Cukras, Janusz; Sadlej, Joanna

    2011-09-14

    We employ state-of-the-art methods and basis sets to study the effect of inserting the Xe atom into the water molecule and the water dimer on their NMR parameters. Our aim is to obtain predictions for the future experimental investigation of novel xenon complexes by NMR spectroscopy. Properties such as molecular structure and energetics have been studied by supermolecular approaches using HF, MP2, CCSD, CCSD(T) and MP4 methods. The bonding in HXeOH···H(2)O complexes has been analyzed by Symmetry-Adapted Perturbation Theory to provide the intricate insight into the nature of the interaction. We focus on vibrational spectra, NMR shielding and spin-spin coupling constants-experimental signals that reflect the electronic structures of the compounds. The parameters have been calculated at electron-correlated and Dirac-Hartree-Fock relativistic levels. This study has elucidated that the insertion of the Xe atom greatly modifies the NMR properties, including both the electron correlation and relativistic effects, the (129)Xe shielding constants decrease in HXeOH and HXeOH···H(2)O in comparison to Xe atom; the (17)O, as a neighbour of Xe, is deshielded too. The HXeOH···H(2)O complex in its most stable form is stabilized mainly by induction and dispersion energies. PMID:21804992

  13. The dynamics of some metal-organic and organic molecules in water solution studied by molecular mechanical and molecular dynamical methods

    NASA Astrophysics Data System (ADS)

    Broo, Anders

    1993-07-01

    A force field is developed to reproduce geometries and vibration spectra of rutheniumhexaamine(III) and rutheniumhexamine(II) complexes. The force constants for ruthenium were then used in molecular dynamics simulation of a Ru 2+ ion, a Ru 3+ ion and Ru(NH 3) 5-pyrazine 2+ in water solution. Simulations of pyrazine and 1,3-dimethyluracile in water solution were also performed. A comparison of different ways of how to include solvation effects in quantum chemical calculations is discussed using the results from the simulations. The MD simulations show that the solvent surrounding a small charged ion, such as a Ru 2+ ion, have a pronounced shell structure and the first layer of solvent molecules is stable during a 61 ps simulation. For a metal-organic molecule as Ru(NH 3) 5-pyrazine the solvent shows shell structure, but the water molecules are exchanged frequently. In the relatively charge-symmetric pyrazine the solvent is not polarized around the molecule. In a molecule like 1,3-dimethyluracile, which is non-symmetric in the charge distribution, the water is strongly polarized.

  14. Translational and rotational energy measurements of desorbed water molecules in their vibrational ground state following 157 nm irradiation of amorphous solid water

    NASA Astrophysics Data System (ADS)

    Hama, Tetsuya; Yokoyama, Masaaki; Yabushita, Akihiro; Kawasaki, Masahiro; Watanabe, Naoki

    2011-05-01

    Water ice is the major solid component in a variety of astrophysical environments, e.g., cold and dense molecular clouds. Photodesorption plays a dominant role in consuming ice in such cold regions. In this study, photodesorption of vibrationally ground-state H 2O( v = 0) from amorphous solid water has been investigated at 157 nm. Using a resonance-enhanced multiphoton ionization technique, the translational and rotational energy distributions of photodesorbed H 2O( v = 0) were measured, i.e., Boltzmann distributions at 1800 and 300 K, respectively. These energies are in good accordance with those predicted by classical molecular calculations for water photodesorption due to a kick-out mechanism following absorption of a single photon; hot H atom released by photodissociation of H 2O in ice transfers enough momentum to another H 2O molecule to kick it off the surface. Desorption of D 2O( v = 0) following 193 nm photoirradiation of a D 2O/H 2S mixed ice was investigated to provide further direct evidence for the operation of a kick-out mechanism. The other desorption mechanisms were also discussed in the context of possible photodesorption of vibrationally excited H 2O.

  15. Mixed-metal molecular complexes: Single-molecule nanomagnets and bioinorganic models of the water oxidizing complex of photosystem II

    NASA Astrophysics Data System (ADS)

    Mishra, Abhudaya

    2006-12-01

    The current burgeoning research in high nuclearity manganese-containing carboxylate clusters is primarily due to their relevance in areas as diverse as magnetic materials and bioinorganic chemistry. In the former, the ability of single molecules to retain, below a critical temperature (T B), their magnetization vector, resulting in the observation of bulk magnetization in the absence of a field and without long-range ordering of the spins, has termed such molecules as Single-Molecule Magnets (SMMs), or molecular nanomagnets. These molecules display superparamagnet like slow magnetization relaxation arising from the combination of a large molecular spin, S, and a large and negative magnetoanisotropy, D. Traditionally, these nanomagnets have been Mn containing species. An out of the box approach towards synthesizing SMMs is engineering mixed-metal Mn-containing compounds. An attractive choice towards this end is the use of Lanthanides (Ln), which possess both a high spin, S, and a large D. A family of related MnIII8Ce IV SMMs has been synthesized. However, the Ce ion of these complexes is diamagnetic (CeIV). Thus, further investigation has led to the isolation of a family of MnIII11Ln III4 complexes in which all but the Ln = Eu complex function as single-molecule nanomagnets. The mixed-metal synthetic effort has been extended to include actinides with the successful isolation of a Mn IV10ThIV6 complex, albeit this homovalent complex is not a SMM. In the bioinorganic research, the Water Oxidizing Complex (WOC) in Photosystem II (PS II) catalyzes the oxidation of H2O to O2 in green plants, algae and cyanobacteria. Recent crystal structures of the WOC confirm it to be a Mn4CaOx cluster with primarily carboxylate ligation. To date, various multinuclear Mn complexes have been synthesized as putative models of the WOC. On the contrary, there have been no synthetic MnCa(Sr) mixed-metal complexes. Thus, in this bioinorganic modeling research of the WOC, various synthetic

  16. Chemical interaction of water molecules with framework Al in acid zeolites: a periodic ab initio study on H-clinoptilolite.

    PubMed

    Valdiviés-Cruz, Karell; Lam, Anabel; Zicovich-Wilson, Claudio M

    2015-09-28

    Periodic quantum-chemistry methods as implemented in the CRYSTAL14 code were considered to analyse the interaction of acid clinoptilolite with water. Initially adsorbed molecules hydrolyse the Al-O bonds, giving rise to defective dealuminated materials. A suitable and representative periodic model of the partially disordered hydrated H-zeolite is the primitive cell (18 T sites) of a decahydrated trialuminated structure of HEU topology. The water distribution inside the material cavities was initially investigated. The model considered for further dealumination was the most stable one from those generated through a combined force field Monte Carlo and ab initio optimization strategy. Optimizations and energy estimations were made at the hybrid DFT level of theory (PBE0 functional) with an atomic basis set of VDZP quality. The energetics of the different pathways involved in the dealumination process was addressed by considering the Gibbs free energy with thermal and zero-point corrections through phonon analysis. It arises that hydrated models exhibit protonated water clusters stabilized by different kinds of H-bonds. The first Al extraction is slightly more energetically favourable from T3 than T2 sites, but at the same time the latter is more probable owing to its larger Al population. However, concerning the second dealumination step, it is more favourable removing the Al atom from both remaining sites after a starting abstraction from T2 rather than T3. These facts determine that the most probable overall pathways go through a first Al removal from T2. The agreement with experimental results is discussed. PMID:26299763

  17. 46 CFR 148.445 - Adjacent spaces.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 5 2013-10-01 2013-10-01 false Adjacent spaces. 148.445 Section 148.445 Shipping COAST... THAT REQUIRE SPECIAL HANDLING Additional Special Requirements § 148.445 Adjacent spaces. When... following requirements must be met: (a) Each space adjacent to a cargo hold must be ventilated by...

  18. 46 CFR 148.445 - Adjacent spaces.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 5 2014-10-01 2014-10-01 false Adjacent spaces. 148.445 Section 148.445 Shipping COAST... THAT REQUIRE SPECIAL HANDLING Additional Special Requirements § 148.445 Adjacent spaces. When... following requirements must be met: (a) Each space adjacent to a cargo hold must be ventilated by...

  19. 46 CFR 148.445 - Adjacent spaces.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 5 2012-10-01 2012-10-01 false Adjacent spaces. 148.445 Section 148.445 Shipping COAST... THAT REQUIRE SPECIAL HANDLING Additional Special Requirements § 148.445 Adjacent spaces. When... following requirements must be met: (a) Each space adjacent to a cargo hold must be ventilated by...

  20. 46 CFR 148.445 - Adjacent spaces.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 5 2011-10-01 2011-10-01 false Adjacent spaces. 148.445 Section 148.445 Shipping COAST... THAT REQUIRE SPECIAL HANDLING Additional Special Requirements § 148.445 Adjacent spaces. When... following requirements must be met: (a) Each space adjacent to a cargo hold must be ventilated by...

  1. Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory.

    PubMed

    Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Tama, Florence; Miyashita, Osamu; Nakano, Shu-Ichi; Sugimoto, Naoki

    2015-12-01

    In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water-water interactions, (ii) ethylene glycol more effectively disrupted water-water interactions around Watson-Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson-Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions. PMID:26538600

  2. Tracking all-vapor instant gas-hydrate formation and guest molecule populations: a possible probe for molecules trapped in water nanodroplets.

    PubMed

    Uras-Aytemiz, Nevin; Cwiklik, Lukasz; Paul Devlin, J

    2012-11-28

    Quantitative Fourier-transform infrared spectra for low-temperature (160-200 K) aerosols of clathrate-hydrate nanoparticles that contain large-cage catalysts and small-cage nonpolar guests have been extended to a broad range of vapor compositions and sampling conditions. The data better reveal the stages by which room-temperature vapor mixtures, when cooled below ∼220 K, instantly generate aerosols with particles composed exclusively of the corresponding clathrate hydrates. In particular the quantitative data help relate the nature of the hydrates that form to the composition of the aqueous nanodroplets of the first stages of the rapid transition from the all-vapor mixture. The overall transition from an all-vapor mixture to "gas"-hydrate nanocrystals is a multistage one that has been characterized as homogeneous nucleation and growth of solution nanodroplets (∼240 K) followed by nucleation and growth of the gas-hydrate particles (∼220 K); all occurring within a subsecond that follows pulsing of the warm vapor into a sampling cold chamber. This may serve well as a general description of the instantaneous generation of the gas-hydrate aerosols, but closer consideration of the nature of the sampling method, in context with recent computation-based insights to (a) gas-hydrate nucleation stages∕rates and (b) the lifetimes of trapped small nonpolar molecules in cold aqueous nanodroplets, suggests a more complex multistage transition. The simulated lifetimes and extensive new quantitative infrared data significantly broaden the knowledge base in which the instantaneous transition from vapor to crystalline hydrate particles is viewed. The apparent need for a high occupancy of large-cage catalytic guest molecules currently limits the practical value of the all-vapor method. Only through greater clarity in the molecular-level description of the transition will the ultimate limits be defined. PMID:23206013

  3. Tracking all-vapor instant gas-hydrate formation and guest molecule populations: A possible probe for molecules trapped in water nanodroplets

    NASA Astrophysics Data System (ADS)

    Uras-Aytemiz, Nevin; Cwiklik, Lukasz; Paul Devlin, J.

    2012-11-01

    Quantitative Fourier-transform infrared spectra for low-temperature (160-200 K) aerosols of clathrate-hydrate nanoparticles that contain large-cage catalysts and small-cage nonpolar guests have been extended to a broad range of vapor compositions and sampling conditions. The data better reveal the stages by which room-temperature vapor mixtures, when cooled below ˜220 K, instantly generate aerosols with particles composed exclusively of the corresponding clathrate hydrates. In particular the quantitative data help relate the nature of the hydrates that form to the composition of the aqueous nanodroplets of the first stages of the rapid transition from the all-vapor mixture. The overall transition from an all-vapor mixture to "gas"-hydrate nanocrystals is a multistage one that has been characterized as homogeneous nucleation and growth of solution nanodroplets (˜240 K) followed by nucleation and growth of the gas-hydrate particles (˜220 K); all occurring within a subsecond that follows pulsing of the warm vapor into a sampling cold chamber. This may serve well as a general description of the instantaneous generation of the gas-hydrate aerosols, but closer consideration of the nature of the sampling method, in context with recent computation-based insights to (a) gas-hydrate nucleation stages/rates and (b) the lifetimes of trapped small nonpolar molecules in cold aqueous nanodroplets, suggests a more complex multistage transition. The simulated lifetimes and extensive new quantitative infrared data significantly broaden the knowledge base in which the instantaneous transition from vapor to crystalline hydrate particles is viewed. The apparent need for a high occupancy of large-cage catalytic guest molecules currently limits the practical value of the all-vapor method. Only through greater clarity in the molecular-level description of the transition will the ultimate limits be defined.

  4. 1H NMR detection of immobilized water molecules within a strong distal hydrogen-bonding network of substrate-bound human heme oxygenase-1.

    PubMed

    Syvitski, Ray T; Li, Yiming; Auclair, Karine; Ortiz De Montellano, Paul R; La Mar, Gerd N

    2002-12-01

    Solution 1H NMR is used to probe the environments of the donor protons of eight strong hydrogen bonds on the distal side of the heme substrate in the cyanide-inhibited, substrate-bound complex of human heme oxygenase, hHO. It is demonstrated that significant magnetization transfer from the bulk water signal to the eight labile protons does not result from chemical exchange, but from direct nuclear Overhauser effect due to the dipolar interaction of these labile protons with "ordered" water molecules. The enzyme labile proton to water proton distances are estimated at approximately 3 A. It is proposed that the role of the strong hydrogen-bonding network is to immobilize numerous water molecules which both stabilize the activated hydroperoxy species and funnel protons to the active site. PMID:12452690

  5. Maximizing T2-exchange in Dy3+DOTA-(amide)X chelates: Fine-tuning the water molecule exchange rate for enhanced T2 contrast in MRI

    PubMed Central

    Soesbe, Todd C.; Ratnakar, S. James; Milne, Mark; Zhang, Shanrong; Do, Quyen N.; Kovacs, Zoltan; Sherry, A. Dean

    2014-01-01

    Purpose The water molecule exchange rates in a series of DyDOTA-(amide)X chelates were fine-tuned to maximize the effects of T2-exchange line broadening and improve T2 contrast. Methods Four DyDOTA-(amide)X chelates having a variable number of glycinate side-arms were prepared and characterized as T2-exchange agents. The non-exchanging DyTETA chelate was also used to measure the bulk water T2 reduction due solely to T2*. The total transverse relaxivity (r2tot) at 22, 37, and 52 °C for each chelate was measured in vitro at 9.4 T (400 MHz) by fitting plots of total T2−1 versus concentration. The water molecule exchange rates for each complex were measured by fitting 17O line-width versus temperature data taken at 9.4 T (54.3 MHz). Results The measured transverse relaxivities due to water molecule exchange (r2ex) and bound water lifetimes (τM) were in excellent agreement with Swift-Connick theory, with DyDOTA-(gly)3 giving the largest r2ex = 11.8 s−1 mM−1 at 37 °C. Conclusion By fine-tuning the water molecule exchange rate at 37 °C, the transverse relaxivity has been increased by 2 to 30 times compared to previously studied Dy3+-based chelates. Polymerization or dendrimerization of the optimal chelate could yield a highly sensitive, molecule-sized T2 contrast agent for improved molecular imaging applications. PMID:24390729

  6. Mono/bimetallic water-stable lanthanide coordination polymers as luminescent probes for detecting cations, anions and organic solvent molecules.

    PubMed

    Wang, Huarui; Qin, Jianhua; Huang, Chao; Han, Yanbing; Xu, Wenjuan; Hou, Hongwei

    2016-08-01

    Eleven water-stable isostructural mono/bimetallic lanthanide coordination polymers (Ln-CPs) {[EuxTb1-x (HL)(H2O)3]·H2O}n (x = 1.0 (1), 0.9 (3), 0.8 (4), 0.7 (5), 0.6 (6), 0.4 (7), 0.3 (8), 0.2 (9), 0.1 (10), 0.05 (11), 0 (2), H4L = 5,5'-(1H-2,3,5-triazole-1,4-diyl)diisophthalic acid) with uncoordinated Lewis basic triazole sites within the pores were prepared. The Ln-CPs represented by 1 showed a rapid and drastic emission quenching induced by external Fe(3+) and Cr(3+) cations and CrO4(2-) and CO3(2-) anions in aqueous solution. In addition, because of the comparable emission intensities of Eu(3+) and Tb(3+) ions, bimetallic CP 8 can be used as a ratiometric luminescent sensor for organic solvent molecules. Moreover, the luminescent color of the 8 sensor in pyridine and in other guest solvents undergoes obvious changes that can be clearly distinguished by the naked eye. PMID:27443408

  7. Improved Estimation of Protein-Ligand Binding Free Energy by Using the Ligand-Entropy and Mobility of Water Molecules

    PubMed Central

    Fukunishi, Yoshifumi; Nakamura, Haruki

    2013-01-01

    We previously developed the direct interaction approximation (DIA) method to estimate the protein-ligand binding free energy (ΔG). The DIA method estimates the ΔG value based on the direct van der Waals and electrostatic interaction energies between the protein and the ligand. In the current study, the effect of the entropy of the ligand was introduced with protein dynamic properties by molecular dynamics simulations, and the interaction between each residue of the protein and the ligand was also weighted considering the hydration of each residue. The molecular dynamics simulation of the apo target protein gave the hydration effect of each residue, under the assumption that the residues, which strongly bind the water molecules, are important in the protein-ligand binding. These two effects improved the reliability of the DIA method. In fact, the parameters used in the DIA became independent of the target protein. The averaged error of ΔG estimation was 1.3 kcal/mol and the correlation coefficient between the experimental ΔG value and the calculated ΔG value was 0.75. PMID:24276169

  8. Interactions of carbon nanotubes with the nitromethane-water mixture governing selective adsorption of energetic molecules from aqueous solution.

    PubMed

    Liu, Yingzhe; Lai, Weipeng; Yu, Tao; Kang, Ying; Ge, Zhongxue

    2015-03-14

    The structure and dynamics of the nitromethane-water (NM-WT) binary mixture surrounding single walled carbon nanotubes (SWNTs) have been investigated by molecular dynamics simulations. The simulation trajectories show that the NM molecules can be selectively adsorbed both outside the surface and inside the cavity of SWNTs mainly dominated by van der Waals attractions because SWNTs have a higher binding affinity for NM than WT. The binding energies of SWNTs with NM and WT obtained from electronic structure calculations at the M06-2X/6-31+G* level are 15.31 and 5.51 kcal mol(-1), respectively. Compared with the SWNT exterior, the selective adsorption of NM is preferentially occurred in the SWNT interior due to the hydrophobic interactions and the dipole-dipole interactions, which induces the decrease of the hydrogen-bond number of NM with WT and ordered structures of NM with preferred intermolecular orientation in the SWNT cavity. Furthermore, the selective adsorption dynamics of NM from the aqueous solution is regardless of the chirality and radius of SWNTs. The SWNT radius plays a negligible role in the mass density distributions of NM outside the SWNTs, while the mass density of NM in the SWNT interior decreases gradually as the SWNT radius increases. The structural arrangements and intermolecular orientations of NM in the SWNT cavity are greatly dependent on the SWNT radius due to the size effect. PMID:25684688

  9. The role of water molecules in the binding of class I and II peptides to the SH3 domain of the Fyn tyrosine kinase.

    PubMed

    Camara-Artigas, Ana; Ortiz-Salmeron, Emilia; Andujar-Sánchez, Montserrrat; Bacarizo, Julio; Martin-Garcia, Jose Manuel

    2016-09-01

    Interactions of proline-rich motifs with SH3 domains are present in signal transduction and other important cell processes. Analysis of structural and thermodynamic data suggest a relevant role of water molecules in these protein-protein interactions. To determine whether or not the SH3 domain of the Fyn tyrosine kinase shows the same behaviour, the crystal structures of its complexes with two high-affinity synthetic peptides, VSL12 and APP12, which are class I and II peptides, respectively, have been solved. In the class I complexes two water molecules were found at the binding interface that were not present in the class II complexes. The structures suggest a role of these water molecules in facilitating conformational changes in the SH3 domain to allow the binding of the class I or II peptides. In the third binding pocket these changes modify the cation-π and salt-bridge interactions that determine the affinity of the binding. Comparison of the water molecules involved in the binding of the peptides with previous reported hydration spots suggests a different pattern for the SH3 domains of the Src tyrosine kinase family. PMID:27599862

  10. Dissecting the Influence of Protein Flexibility on the Location and Thermodynamic Profile of Explicit Water Molecules in Protein-Ligand Binding.

    PubMed

    Yang, Ying; Lill, Markus A

    2016-09-13

    Explicit water molecules in the binding site of proteins play a crucial role for protein-ligand association. Recent advances in computer-aided drug discovery methodology allow for an accurate prediction of the localized position and thermodynamic profile of water molecules (i.e., hydration sites) in the binding site. The underlying calculations are based on MD simulations of explicit water molecules in a restrained protein structure. However, the ligand-binding process is typically associated with protein conformational change that influences the position and thermodynamic properties of the hydration site. In this manuscript, we present the developments of two methods to incorporate the influence of protein conformational change on hydration sites either by following the conformational transition step-by-step (method I) or to match the hydration sites of the two transition end states using local coordinate systems (method II). Using these methods, we highlight the difference in the estimated protein desolvation free energy with and without inclusion of protein flexibility. To the best of our knowledge, this is the first study that explicitly studies the influence of protein conformational change on the position and thermodynamic profiles of water molecules and provides methodology to incorporate protein flexibility into the estimation of the desolvation free energy. PMID:27494046

  11. 33 CFR 162.215 - Lake Tahoe, Nev.; restricted area adjacent to Nevada Beach.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 2 2013-07-01 2013-07-01 false Lake Tahoe, Nev.; restricted area adjacent to Nevada Beach. 162.215 Section 162.215 Navigation and Navigable Waters COAST GUARD, DEPARTMENT... § 162.215 Lake Tahoe, Nev.; restricted area adjacent to Nevada Beach. (a) The restricted area....

  12. 33 CFR 162.215 - Lake Tahoe, Nev.; restricted area adjacent to Nevada Beach.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Lake Tahoe, Nev.; restricted area adjacent to Nevada Beach. 162.215 Section 162.215 Navigation and Navigable Waters COAST GUARD, DEPARTMENT... § 162.215 Lake Tahoe, Nev.; restricted area adjacent to Nevada Beach. (a) The restricted area....

  13. 33 CFR 162.215 - Lake Tahoe, Nev.; restricted area adjacent to Nevada Beach.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 2 2011-07-01 2011-07-01 false Lake Tahoe, Nev.; restricted area adjacent to Nevada Beach. 162.215 Section 162.215 Navigation and Navigable Waters COAST GUARD, DEPARTMENT... § 162.215 Lake Tahoe, Nev.; restricted area adjacent to Nevada Beach. (a) The restricted area....

  14. 33 CFR 162.215 - Lake Tahoe, Nev.; restricted area adjacent to Nevada Beach.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 2 2012-07-01 2012-07-01 false Lake Tahoe, Nev.; restricted area adjacent to Nevada Beach. 162.215 Section 162.215 Navigation and Navigable Waters COAST GUARD, DEPARTMENT... § 162.215 Lake Tahoe, Nev.; restricted area adjacent to Nevada Beach. (a) The restricted area....

  15. 33 CFR 162.215 - Lake Tahoe, Nev.; restricted area adjacent to Nevada Beach.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 2 2014-07-01 2014-07-01 false Lake Tahoe, Nev.; restricted area adjacent to Nevada Beach. 162.215 Section 162.215 Navigation and Navigable Waters COAST GUARD, DEPARTMENT... § 162.215 Lake Tahoe, Nev.; restricted area adjacent to Nevada Beach. (a) The restricted area....

  16. Environmental swap energy and role of configurational entropy in transfer of small molecules from water into alkanes

    NASA Astrophysics Data System (ADS)

    Smejtek, Pavel; Word, Robert C.

    2004-01-01

    We studied the effect of segmented solvent molecules on the free energy of transfer of small molecules from water into alkanes (hexane, heptane, octane, decane, dodecane, tetradecane, and hexadecane). For these alkanes we measured partition coefficients of benzene, 3-methylindole (3MI), 2,3,4,6-tetrachlorophenol (TeCP), and 2,4,6-tribromophenol (TriBP) at 3, 11, 20, 3, and 47 °C. For 3MI, TeCP, and TriBP the dependence of free energy of transfer on length of alkane chains was found to be very different from that for benzene. In contrast to benzene, the energy of transfer for 3MI, TeCP, and TriBP was independent of the number of carbons in alkanes. To interpret data, we used the classic Flory-Huggins (FH) theory of concentrated polymer solutions for the alkane phase. For benzene, the measured dependence of energy of transfer on the number of carbons in alkanes agreed well with predictions based on FH model in which the size of alkane segments was obtained from the ratio of molar volumes of alkanes and the solute. We show that for benzene, the energy of transfer can be divided into two components, one called environmental swap energy (ESE), and one representing the contribution of configurational entropy of alkane chains. For 3MI, TeCP, and TriBP the contribution of configurational entropy was not measurable even though the magnitude of the effect predicted from the FH model for short chain alkanes was as much as 20 times greater than experimental uncertainties. From the temperature dependence of ESE we obtained enthalpy and entropy of transfer for benzene, 3MI, TeCP, and TriBP. Experimental results are discussed in terms of a thermodynamic cycle considering creation of cavity, insertion of solute, and activation of solute-medium attractive interactions. Our results suggest that correcting experimental free energy of transfer by Flory-Huggins configurational entropy term is not generally appropriate and cannot be applied indiscriminately.

  17. 1. OVERVIEW SHOWING FIRING CONTROL BLOCKHOUSE 0502 AND ADJACENT OBSERVATION ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. OVERVIEW SHOWING FIRING CONTROL BLOCKHOUSE 0502 AND ADJACENT OBSERVATION TOWER. WATER BRAKE TROUGH SEGMENT AT LOWER RIGHT. Looking north northeast. - Edwards Air Force Base, South Base Sled Track, Firing & Control Blockhouse for 10,000-foot Track, South of Sled Track at midpoint of 20,000-foot track, Lancaster, Los Angeles County, CA

  18. Effects of protonation state of Asp181 and position of active site water molecules on the conformation of PTP1B.

    PubMed

    Ozcan, Ahmet; Olmez, Elif Ozkirimli; Alakent, Burak

    2013-05-01

    In protein tyrosine phosphatase 1B (PTP1B), the flexible WPD loop adopts a closed conformation (WPDclosed ) in the active state of PTP1B, bringing the catalytic Asp181 close to the active site pocket, while WPD loop is in an open conformation (WPDopen ) in the inactive state. Previous studies showed that Asp181 may be protonated at physiological pH, and ordered water molecules exist in the active site. In the current study, molecular dynamics simulations are employed at different Asp181 protonation states and initial positions of active site water molecules, and compared with the existing crystallographic data of PTP1B. In WPDclosed conformation, the active site is found to maintain its conformation only in the protonated state of Asp181 in both free and liganded states, while Asp181 is likely to be deprotonated in WPDopen conformation. When the active site water molecule network that is a part of the free WPDclosed crystal structure is disrupted, intermediate WPD loop conformations, similar to that in the PTPRR crystal structure, are sampled in the MD simulations. In liganded PTP1B, one active site water molecule is found to be important for facilitating the orientation of Cys215 and the phosphate ion, thus may play a role in the reaction. In conclusion, conformational stability of WPD loop, and possibly catalytic activity of PTP1B, is significantly affected by the protonation state of Asp181 and position of active site water molecules, showing that these aspects should be taken into consideration both in MD simulations and inhibitor design. PMID:23239271

  19. Effect of plasticizers (water and glycerol) on the diffusion of a small molecule in iota-carrageenan biopolymer films for edible coating application.

    PubMed

    Karbowiak, Thomas; Hervet, Hubert; Léger, Liliane; Champion, Dominique; Debeaufort, Frédéric; Voilley, Andrée

    2006-06-01

    Translational diffusion of a fluorescein probe has been measured in iota-carrageenan edible films containing different amounts of glycerol (0, 15, 30, and 45%), using fluorescence recovery after photobleaching (FRAP) experiments. The effects of this plasticizer as well as the plasticizing effect of water on the diffusion of fluorescein have been studied in this edible coating mainly composed of natural biopolymer. Diffusion coefficients of about 10(-13) m2 s(-1) have been measured in these films for water activity (aw) lower than 0.7. Above this water content threshold, fluorescein translational diffusion coefficient increases up to 10(-12) m2 s(-1). Another interesting information obtained from FRAP experiments on this system is the ratio of the diffusing molecules which are immobilized in the carrageenan matrix at aw lower than 0.98. Moreover, films containing more than 30% glycerol (w/w carrageenan) present a huge increase of the diffusion coefficient of fluorescein at high water activity (about 2 orders of magnitude), this effect being less pronounced at low water activity. The increase of diffusion seems to be only related to the water content, and glycerol only acts through the enhancement of water adsorption. Therefore, in biopolymer films containing polyol plasticizers, the gain in mobility could be devoted to the effect of the ubiquitous plasticizing molecule, water, whose adsorption is increased by the plasticizer. PMID:16768427

  20. Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory

    PubMed Central

    Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Tama, Florence; Miyashita, Osamu; Nakano, Shu-ichi; Sugimoto, Naoki

    2015-01-01

    In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water–water interactions, (ii) ethylene glycol more effectively disrupted water–water interactions around Watson–Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson–Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions. PMID:26538600