Water resources of the Waccasassa River Basin and adjacent areas, Florida

USGS Publications Warehouse

Taylor, G.F.; Snell, L.J.

1978-01-01

This map report was prepared in cooperation with the Southwest Florida Water Management District which, with the Waccasassa River Basin Board, had jurisdiction over waters within the Waccasassa River basin, the coastal areas adjacent to the basin, and other adjacent areas outside the basin. New water management district boundaries, effective January 1977, place most of the Waccasassa River basin in the Suwannee River Water Management District. The purpose of the report is to provide water information for consideration in land-use and water development which is accelerating, especially in the northeastern part of the study area. It is based largely on existing data in the relatively undeveloped area. Of the total area included in the topographic drainage basin for the Waccasassa River about 72 percent is in Levy County, 18 percent in Alachua County, 9 percent in Gilchrist County, and 1 percent in Marion County. The elongated north-south drainage basin is approximately 50 mi in length, averages 13 mi in width, and lies between the Suwannee River, the St. Johns River, and the Withlacoochee River basins. (Woodard-USGS)

View from water showing south facade and adjacent boat slips ...

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

View from water showing south facade and adjacent boat slips (Facility Nos. S375 & S376) - U.S. Naval Base, Pearl Harbor, Boat House, Hornet Avenue at Independence Street, Pearl City, Honolulu County, HI

What is the minimum number of water molecules required to dissolve a potassium chloride molecule?

PubMed

Sen, Anik; Ganguly, Bishwajit

2010-12-01

This work answers an unsolved question that consists of determining the least number of water molecules necessary to separate a potassium chloride molecule. The answer based on accurate quantum chemical calculations suggests that tetramers are the smallest clusters necessary to dissociate KCl molecules. The study was made with Møller-Plesset second-order perturbation theory modified with the cluster theory having single, double, and perturbative triple excitations. With this extensive study, the dissociation of KCl molecule in different water clusters was evaluated. The calculated results show that four water molecules stabilize a solvent separated K(+)/Cl(-) ion-pair in prismatic structure and with six water molecules further dissociation was observed. Attenuated total reflection infrared spectroscopy of KCl dissolved in water establishes that clusters are made of closely bound ions with a mean of five water molecules per ion-pair [K(+)(H(2)O)(5)Cl(-)]. (Max and Chapados, Appl Spectrosc 1999, 53, 1601; Max and Chapados, J Chem Phys 2001, 115, 2664.) The calculated results tend to support that five water molecules leads toward the formation of contact ion-pair. The structures, energies, and infrared spectra of KCl molecules in different water clusters are also discussed. © 2010 Wiley Periodicals, Inc.

Regional Jurassic geologic framework of Alabama coastal waters area and adjacent Federal waters area

USGS Publications Warehouse

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

1989-01-01

To date, numerous Jurassic hydrocarbon fields and pools have been discovered in the Cotton Valley Group, Haynesville Formation, Smackover Formation and Norphlet Formation in the tri-state area of Mississippi, Alabama and Florida, and in Alabama State coastal waters and adjacent Federal waters area. Petroleum traps are basement highs, salt anticlines, faulted salt anticlines and extensional faults associated with salt movement. Reservoirs include continental and marine sandstones, limestones and dolostones. Hydrocarbon types are oil, condensate and natural gas. The onshore stratigraphic and structural information can be used to establish a regional geologic framework for the Jurassic for the State coastal waters and adjacent Federal waters areas. Evaluation of the geologic information along with the hydrocarbon data from the tri-state area indicates that at least three Jurassic hydrocarbon trends (oil, oil and gas condensate, and deep natural gas) can be identified onshore. These onshore hydrocarbon trends can be projected into the Mobile area in the Central Gulf of Mexico and into the Pensacola, Destin Dome and Apalachicola areas in the Eastern Gulf of Mexico. Substantial reserves of natural gas are expected to be present in Alabama State waters and the northern portion of the Mobile area. Significant accumulations of oil and gas condensate may be encountered in the Pensacola, Destin Dome, and Apalachicola areas. ?? 1989.

Water-assisted dehalogenation of thionyl chloride in the presence of water molecules.

PubMed

Yeung, Chi Shun; Ng, Ping Leung; Guan, Xiangguo; Phillips, David Lee

2010-04-01

A second-order Møller-Plesset perturbation theory (MP2) and density functional theory (DFT) investigation of the dehalogenation reactions of thionyl chloride is reported, in which water molecules (up to seven) were explicitly involved in the reaction complex. The dehalogenation processes of thionyl chloride were found to be dramatically catalyzed by water molecules. The reaction rate became significantly faster as more water molecules became involved in the reaction complex. The dehalogenation processes can be reasonably simulated by the gas-phase water cluster models, which reveals that water molecules can help to solvate the thionyl chloride molecules and activate the release of the Cl(-) leaving group. The computed activation energies were used to compare the calculations to available experimental data.

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

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

... ship protection, Puget Sound and adjacent waters, Washington 165.1313 Section 165.1313 Navigation and... Sound and adjacent waters, Washington (a) Notice of enforcement or suspension of enforcement. The tank... Port Puget Sound. Captain of the Port Puget Sound will cause notice of the enforcement of the tank ship...

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

... ship protection, Puget Sound and adjacent waters, Washington 165.1313 Section 165.1313 Navigation and... Sound and adjacent waters, Washington (a) Notice of enforcement or suspension of enforcement. The tank... Port Puget Sound. Captain of the Port Puget Sound will cause notice of the enforcement of the tank ship...

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

Code of Federal Regulations, 2012 CFR

2012-07-01

... Passenger Vessel Protection, Puget Sound and adjacent waters, Washington. 165.1317 Section 165.1317... Vessel Protection, Puget Sound and adjacent waters, Washington. (a) Notice of enforcement or suspension... be enforced only upon notice by the Captain of the Port Puget Sound. Captain of the Port Puget Sound...

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

Code of Federal Regulations, 2011 CFR

2011-07-01

... Passenger Vessel Protection, Puget Sound and adjacent waters, Washington. 165.1317 Section 165.1317... Vessel Protection, Puget Sound and adjacent waters, Washington. (a) Notice of enforcement or suspension... be enforced only upon notice by the Captain of the Port Puget Sound. Captain of the Port Puget Sound...

Transfer of lipid molecules and polycyclic aromatic hydrocarbons to open marine waters by dense water cascading events

NASA Astrophysics Data System (ADS)

Salvadó, Joan A.; Grimalt, Joan O.; López, Jordi F.; Palanques, Albert; Heussner, Serge; Pasqual, Catalina; Sanchez-Vidal, Anna; Canals, Miquel

2017-12-01

Settling particles were collected by a set of moored sediment traps deployed during one year in the western Gulf of Lion along Cap de Creus and Lacaze-Duthiers submarine canyons and on the adjacent southern open slope. These traps collected particles during periods of pelagic settling and also during events of deep water flushing by dense shelf water cascading (DSWC). Analyses of lipid biomarkers (n-alkanes, n-alkan-1-ols, sterols and C37-C38 alkenones) and polycyclic aromatic hydrocarbons (PAHs) showed much higher transfer of terrestrial lipids and PAHs to open deep waters during DSWC than in the absence of cascading. The area of highest lateral fluxes was mostly located at 1000 m depth but also at 1500 m depth and extended along the canyons and to the adjacent slope. Higher fluxes were observed near the bottom (30 m above bottom; mab) than at intermediate waters (500 mab) which is consistent with the formation and sinking of dense water over the continental shelf, and its transport through the canyons towards the continental slope and deep basin. DSWC involved the highest settling fluxes of terrestrial lipids and PAHs ever described in marine continental slopes and the pelagic domain, as illustrated by peak values of C23-C33 odd carbon numbered alkanes (405 ng m-2 d-1), C22-C32 even carbon numbered alkan-1-ols (850 ng m-2 d-1), β-sitosterol+sitostanol (4800 ng m-2 d-1) and PAHs (55 μg m-2 d-1). The algal lipids also showed higher transfer to deep waters during DSWC but to a lower extent than the terrigenous compounds. However, the C37-C38 alkenones constituted an exception and their settling fluxes were not influenced by DSWC. The lack of influence of the DSWC on the C37-C38 alkenone settling is consistent with absence of haptophyte algal inputs from the continental shelf and reinforces the reliability of these molecules for palaeothermometry and palaeoproductivity measurements in pelagic systems.

Sequential evaporation of water molecules from protonated water clusters: measurement of the velocity distributions of the evaporated molecules and statistical analysis.

PubMed

Berthias, F; Feketeová, L; Abdoul-Carime, H; Calvo, F; Farizon, B; Farizon, M; Märk, T D

2018-06-22

Velocity distributions of neutral water molecules evaporated after collision induced dissociation of protonated water clusters H+(H2O)n≤10 were measured using the combined correlated ion and neutral fragment time-of-flight (COINTOF) and velocity map imaging (VMI) techniques. As observed previously, all measured velocity distributions exhibit two contributions, with a low velocity part identified by statistical molecular dynamics (SMD) simulations as events obeying the Maxwell-Boltzmann statistics and a high velocity contribution corresponding to non-ergodic events in which energy redistribution is incomplete. In contrast to earlier studies, where the evaporation of a single molecule was probed, the present study is concerned with events involving the evaporation of up to five water molecules. In particular, we discuss here in detail the cases of two and three evaporated molecules. Evaporation of several water molecules after CID can be interpreted in general as a sequential evaporation process. In addition to the SMD calculations, a Monte Carlo (MC) based simulation was developed allowing the reconstruction of the velocity distribution produced by the evaporation of m molecules from H+(H2O)n≤10 cluster ions using the measured velocity distributions for singly evaporated molecules as the input. The observed broadening of the low-velocity part of the distributions for the evaporation of two and three molecules as compared to the width for the evaporation of a single molecule results from the cumulative recoil velocity of the successive ion residues as well as the intrinsically broader distributions for decreasingly smaller parent clusters. Further MC simulations were carried out assuming that a certain proportion of non-ergodic events is responsible for the first evaporation in such a sequential evaporation series, thereby allowing to model the entire velocity distribution.

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

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.

Dynamics of bound water molecules in fullerenol at different hydration levels

NASA Astrophysics Data System (ADS)

Wang, Yilin; Robey, Steven; Reutt-Robey, Janice

Fullerenols, polyhydroxylated fullerenes, are of great interest as promising materials in medical application because of their high water solubility and biocompatibility. Fullerenols are highly responsive to their environment, for example, they readily undergo hydration under ambient conditions. Understanding the dynamics of water molecules bound to fullerenols, and the interplay between water molecules and fullerenols is important in realizing biological function. Here, broadband dielectric spectroscopy (BDS), was performed on a fullerenol with 44 hydroxyl groups, C60(OH)44, between 300 K and 340 K. At room temperature and under ambient conditions, C60(OH)44 is hydrated, releasing bound water molecules with increasing temperature, as quantified by thermal gravimetric analysis (TGA) measurements. At room temperature, a dielectric band due to collective bulk-like dynamics of the bound water molecules is observed. The relaxation peak of the water molecules shifts to higher frequency with increasing of temperature, reflecting the dynamics of bound water. Upon loss of water molecules, either thermally induced or vacuum induced, the relaxation peak shifts to lower frequency. The stoichiometric relationship between the dielectric properties of the hydrated fullerenol and the interplay between the bound water molecules and C60(OH)44 will be discussed. This work was supported by the National Science Foundation (NSF) under Award Number 1310380.

Free enthalpies of replacing water molecules in protein binding pockets.

PubMed

Riniker, Sereina; Barandun, Luzi J; Diederich, François; Krämer, Oliver; Steffen, Andreas; van Gunsteren, Wilfred F

2012-12-01

Water molecules in the binding pocket of a protein and their role in ligand binding have increasingly raised interest in recent years. Displacement of such water molecules by ligand atoms can be either favourable or unfavourable for ligand binding depending on the change in free enthalpy. In this study, we investigate the displacement of water molecules by an apolar probe in the binding pocket of two proteins, cyclin-dependent kinase 2 and tRNA-guanine transglycosylase, using the method of enveloping distribution sampling (EDS) to obtain free enthalpy differences. In both cases, a ligand core is placed inside the respective pocket and the remaining water molecules are converted to apolar probes, both individually and in pairs. The free enthalpy difference between a water molecule and a CH(3) group at the same location in the pocket in comparison to their presence in bulk solution calculated from EDS molecular dynamics simulations corresponds to the binding free enthalpy of CH(3) at this location. From the free enthalpy difference and the enthalpy difference, the entropic contribution of the displacement can be obtained too. The overlay of the resulting occupancy volumes of the water molecules with crystal structures of analogous ligands shows qualitative correlation between experimentally measured inhibition constants and the calculated free enthalpy differences. Thus, such an EDS analysis of the water molecules in the binding pocket may give valuable insight for potency optimization in drug design.

Free enthalpies of replacing water molecules in protein binding pockets

NASA Astrophysics Data System (ADS)

Riniker, Sereina; Barandun, Luzi J.; Diederich, François; Krämer, Oliver; Steffen, Andreas; van Gunsteren, Wilfred F.

2012-12-01

Water molecules in the binding pocket of a protein and their role in ligand binding have increasingly raised interest in recent years. Displacement of such water molecules by ligand atoms can be either favourable or unfavourable for ligand binding depending on the change in free enthalpy. In this study, we investigate the displacement of water molecules by an apolar probe in the binding pocket of two proteins, cyclin-dependent kinase 2 and tRNA-guanine transglycosylase, using the method of enveloping distribution sampling (EDS) to obtain free enthalpy differences. In both cases, a ligand core is placed inside the respective pocket and the remaining water molecules are converted to apolar probes, both individually and in pairs. The free enthalpy difference between a water molecule and a CH3 group at the same location in the pocket in comparison to their presence in bulk solution calculated from EDS molecular dynamics simulations corresponds to the binding free enthalpy of CH3 at this location. From the free enthalpy difference and the enthalpy difference, the entropic contribution of the displacement can be obtained too. The overlay of the resulting occupancy volumes of the water molecules with crystal structures of analogous ligands shows qualitative correlation between experimentally measured inhibition constants and the calculated free enthalpy differences. Thus, such an EDS analysis of the water molecules in the binding pocket may give valuable insight for potency optimization in drug design.

Structured Water Layers Adjacent to Biological Membranes

PubMed Central

Higgins, Michael J.; Polcik, Martin; Fukuma, Takeshi; Sader, John E.; Nakayama, Yoshikazu; Jarvis, Suzanne P.

2006-01-01

Water amid the restricted space of crowded biological macromolecules and at membrane interfaces is essential for cell function, though the structure and function of this “biological water” itself remains poorly defined. The force required to remove strongly bound water is referred to as the hydration force and due to its widespread importance, it has been studied in numerous systems. Here, by using a highly sensitive dynamic atomic force microscope technique in conjunction with a carbon nanotube probe, we reveal a hydration force with an oscillatory profile that reflects the removal of up to five structured water layers from between the probe and biological membrane surface. Further, we find that the hydration force can be modified by changing the membrane fluidity. For 1,2-dipalmitoyl-sn-glycero-3-phosphocholine gel (Lβ) phase bilayers, each oscillation in the force profile indicates the force required to displace a single layer of water molecules from between the probe and bilayer. In contrast, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine fluid (Lα) phase bilayers at 60°C and 1,2-dioleoyl-sn-glycero-3-phosphocholine fluid (Lα) phase bilayers at 24°C seriously disrupt the molecular ordering of the water and result predominantly in a monotonic force profile. PMID:16798815

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

Code of Federal Regulations, 2013 CFR

2013-07-01

..., Mass.; danger zones for naval operations. 334.70 Section 334.70 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.70 Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations. (a) Atlantic...

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

Code of Federal Regulations, 2012 CFR

2012-07-01

..., Mass.; danger zones for naval operations. 334.70 Section 334.70 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.70 Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations. (a) Atlantic...

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

Code of Federal Regulations, 2010 CFR

2010-07-01

..., Mass.; danger zones for naval operations. 334.70 Section 334.70 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.70 Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations. (a) Atlantic...

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

Code of Federal Regulations, 2011 CFR

2011-07-01

..., Mass.; danger zones for naval operations. 334.70 Section 334.70 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.70 Buzzards Bay, and adjacent waters, Mass.; danger zones for naval operations. (a) Atlantic...

Use of carbonated water in reduction of adjacent gastric activity in 456 consecutive technetium-99m myocardial perfusion imaging studies.

PubMed

Thomas, Dustin M; Lee, Joshua S; Charmforoush, Anthony; Rubal, Bernard J; Rosenblatt, Stephen A; Butler, Joshua T; Clemenshaw, Michael; Cheezum, Michael K; Slim, Ahmad M

2015-12-01

Small, observational trials have suggested a reduction in adjacent gastric activity with ingestion of soda water in myocardial perfusion imaging (MPI). We report our findings prior to and after implementation of soda water in 467 consecutive MPI studies. Consecutive MPI studies performed at a high-volume facility referred for vasodilator (VD) or exercise treadmill testing (ETT) were retrospectively reviewed before and after implementation of the soda water protocol. Patients undergoing the soda water protocol received 100 ml of soda water administered 30 min prior to image acquisition and after stress. Studies were performed using a same day rest/stress protocol. Incidence of adjacent gastric activity, diaphragmatic attenuation, stress and rest perfusion defects, and major adverse cardiovascular events (MACE) outcomes defined as death, myocardial infarction, stroke, reevaluation for chest pain, and late revascularization (>90 days from MPI) were abstracted using International Classification of Diseases, Ninth Revision (ICD-9) search. Two hundred and eighteen studies were performed prior to implementation of the soda water protocol and 249 studies were performed with the use of soda water. Baseline demographic data were equal between the groups with the exception of more patients undergoing VD stress receiving soda water (p < 0.001). Soda water was not associated with a decreased incidence of adjacent gastric activity with stress (54.7% versus 61.9% with no soda water, p = 0.129) or rest (68.6% versus 69.5% with no soda water, p = 0.919) imaging. Less adjacent gastric activity was observed with patients undergoing ETT who received soda water (42.5% versus 56.9% with no soda water, p = 0.031), but no difference was observed between the groups with VD stress (69.0% versus 68.1% with no soda water, p = 1.000). The use of soda water prior to technetium-99m MPI was associated with lower rates of adjacent gastric activity only in patients undergoing ETT stress but not

Femtosecond spectroscopic study of the solvation of amphiphilic molecules by water

NASA Astrophysics Data System (ADS)

Rezus, Y. L. A.; Bakker, H. J.

2008-06-01

We use polarization-resolved mid-infrared pump-probe spectroscopy to study the aqueous solvation of proline and N-methylacetamide. These molecules serve as models to study the solvation of proteins. We monitor the orientational dynamics of partly deuterated water molecules (HDO) that are present at a low concentration in the water. We find that the OD vibration of HDO relaxes via an intermediate level, that is characterized by a hydrogen-bond that is stronger than in the ground state. With increasing concentration the lifetime of the excited state increases from 1.8 ps to 2.4 ps and the lifetime of the intermediate level from 0.6 ps to 1.0 ps. Regarding the orientational dynamics we observe biexponential behavior, which finds its origin in the presence of two classes of water molecules. There is a fraction of water molecules that has bulk-like orientational dynamics ( τrot = 2.5 ps) and a fraction of immobilized water molecules ( τrot > 10 ps). The relative abundance of the two fractions is determined by the nature and concentration of the solute. We find that the hydrophobic solute groups are responsible for the immobilization of water molecules. Every methyl group causes the immobilization of approximately 4 water OH groups. The hydrophilic solute groups, on the other hand, do not hinder the reorientation and the water molecules solvating them reorient with the same rate as in the bulk liquid.

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.

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.

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

Rapid and accurate prediction and scoring of water molecules in protein binding sites.

PubMed

Ross, Gregory A; Morris, Garrett M; Biggin, Philip C

2012-01-01

Water plays a critical role in ligand-protein interactions. However, it is still challenging to predict accurately not only where water molecules prefer to bind, but also which of those water molecules might be displaceable. The latter is often seen as a route to optimizing affinity of potential drug candidates. Using a protocol we call WaterDock, we show that the freely available AutoDock Vina tool can be used to predict accurately the binding sites of water molecules. WaterDock was validated using data from X-ray crystallography, neutron diffraction and molecular dynamics simulations and correctly predicted 97% of the water molecules in the test set. In addition, we combined data-mining, heuristic and machine learning techniques to develop probabilistic water molecule classifiers. When applied to WaterDock predictions in the Astex Diverse Set of protein ligand complexes, we could identify whether a water molecule was conserved or displaced to an accuracy of 75%. A second model predicted whether water molecules were displaced by polar groups or by non-polar groups to an accuracy of 80%. These results should prove useful for anyone wishing to undertake rational design of new compounds where the displacement of water molecules is being considered as a route to improved affinity.

Influence of Molecular Oxygen on Ortho-Para Conversion of Water Molecules

NASA Astrophysics Data System (ADS)

Valiev, R. R.; Minaev, B. F.

2017-07-01

The mechanism of influence of molecular oxygen on the probability of ortho-para conversion of water molecules and its relation to water magnetization are considered within the framework of the concept of paramagnetic spin catalysis. Matrix elements of the hyperfine ortho-para interaction via the Fermi contact mechanism are calculated, as well as the Maliken spin densities on water protons in H2O and O2 collisional complexes. The mechanism of penetration of the electron spin density into the water molecule due to partial spin transfer from paramagnetic oxygen is considered. The probability of ortho-para conversion of the water molecules is estimated by the quantum chemistry methods. The results obtained show that effective ortho-para conversion of the water molecules is possible during the existence of water-oxygen dimers. An external magnetic field affects the ortho-para conversion rate given that the wave functions of nuclear spin sublevels of the water protons are mixed in the complex with oxygen.

Different effects of water molecules on CO oxidation with different reaction mechanisms.

PubMed

Liu, Shan Ping; Zhao, Ming; Sun, Guo En; Gao, Wang; Jiang, Qing

2018-03-28

The effects of water molecules (promotion/prohibition) on CO oxidation remain debated. Herein, using density functional theory calculations, we demonstrate that water molecules can facilitate the CO + O/O 2 oxidation process, but prohibit the CO + OH oxidation process, which is consistent with the experimental finding that water molecules have two distinct effects on CO oxidation. For the CO + O/O 2 oxidation mechanisms, we find that the reactants were pushed towards each other due to the steric effect of the water molecules, which decreases the reaction barriers and promotes the CO + O/O 2 oxidation process. For the CO + OH oxidation mechanisms, water molecules increase the stability of the COOH* intermeditae by H-bonds and van der Waals forces, which increase the barriers of the COOH* transformation process and the COOH*-tra dissociation process, and prohibit the CO + OH oxidation process. These results clarify the different effects of water molecules on CO oxidation and shed light on catalyst usage in the CO oxidation industry.

Origin of the blueshift of water molecules at interfaces of hydrophilic cyclic compounds

PubMed Central

Tomobe, Katsufumi; Yamamoto, Eiji; Kojić, Dušan; Sato, Yohei; Yasui, Masato; Yasuoka, Kenji

2017-01-01

Water molecules at interfaces of materials exhibit enigmatic properties. A variety of spectroscopic studies have observed a high-frequency motion in these water molecules, represented by a blueshift, at both hydrophobic and hydrophilic interfaces. However, the molecular mechanism behind this blueshift has remained unclear. Using Raman spectroscopy and ab initio molecular dynamics simulations, we reveal the molecular mechanism of the blueshift of water molecules around six monosaccharide isomers. In the first hydration shell, we found weak hydrogen-bonded water molecules that cannot have a stable tetrahedral water network. In the water molecules, the vibrational state of the OH bond oriented toward the bulk solvent strongly contributes to the observed blueshift. Our work suggests that the blueshift in various solutions originates from the vibrational motions of these observed water molecules. PMID:29282448

The role of water molecules in computational drug design.

PubMed

de Beer, Stephanie B A; Vermeulen, Nico P E; Oostenbrink, Chris

2010-01-01

Although water molecules are small and only consist of two different atom types, they play various roles in cellular systems. This review discusses their influence on the binding process between biomacromolecular targets and small molecule ligands and how this influence can be modeled in computational drug design approaches. Both the structure and the thermodynamics of active site waters will be discussed as these influence the binding process significantly. Structurally conserved waters cannot always be determined experimentally and if observed, it is not clear if they will be replaced upon ligand binding, even if sufficient space is available. Methods to predict the presence of water in protein-ligand complexes will be reviewed. Subsequently, we will discuss methods to include water in computational drug research. Either as an additional factor in automated docking experiments, or explicitly in detailed molecular dynamics simulations, the effect of water on the quality of the simulations is significant, but not easily predicted. The most detailed calculations involve estimates of the free energy contribution of water molecules to protein-ligand complexes. These calculations are computationally demanding, but give insight in the versatility and importance of water in ligand binding.

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.

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

... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Security and Safety Zone; Large Passenger Vessel Protection, Puget Sound and adjacent waters, Washington. 165.1317 Section 165.1317 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) PORTS AND WATERWAYS...

Interplay between translational diffusion and large-amplitude angular jumps of water molecules

NASA Astrophysics Data System (ADS)

Liu, Chao; Zhang, Yangyang; Zhang, Jian; Wang, Jun; Li, Wenfei; Wang, Wei

2018-05-01

Understanding the microscopic mechanism of water molecular translational diffusion is a challenging topic in both physics and chemistry. Here, we report an investigation on the interplay between the translational diffusion and the large-amplitude angular jumps of water molecules in bulk water using molecular dynamics simulations. We found that large-amplitude angular jumps are tightly coupled to the translational diffusions. Particularly, we revealed that concurrent rotational jumps of spatially neighboring water molecules induce inter-basin translational jumps, which contributes to the fast component of the water translational diffusion. Consequently, the translational diffusion shows positional heterogeneity; i.e., the neighbors of the water molecules with inter-basin translational jumps have larger probability to diffuse by inter-basin translational jumps. Our control simulations showed that a model water molecule with moderate hydrogen bond strength can diffuse much faster than a simple Lennard-Jones particle in bulk water due to the capability of disturbing the hydrogen bond network of the surrounding water molecules. Our results added to the understanding of the microscopic picture of the water translational diffusion and demonstrated the unique features of water diffusion arising from their hydrogen bond network structure compared with those of the simple liquids.

Protein-bound water molecules in primate red- and green-sensitive visual pigments.

PubMed

Katayama, Kota; Furutani, Yuji; Imai, Hiroo; Kandori, Hideki

2012-02-14

Protein-bound water molecules play crucial roles in the structure and function of proteins. The functional role of water molecules has been discussed for rhodopsin, the light sensor for twilight vision, on the basis of X-ray crystallography, Fourier transform infrared (FTIR) spectroscopy, and a radiolytic labeling method, but nothing is known about the protein-bound waters in our color visual pigments. Here we apply low-temperature FTIR spectroscopy to monkey red (MR)- and green (MG)-sensitive color pigments at 77 K and successfully identify water vibrations using D(2)O and D(2)(18)O in the whole midinfrared region. The observed water vibrations are 6-8 for MR and MG, indicating that several water molecules are present near the retinal chromophore and change their hydrogen bonds upon retinal photoisomerization. In this sense, color visual pigments possess protein-bound water molecules essentially similar to those of rhodopsin. The absence of strongly hydrogen-bonded water molecules (O-D stretch at <2400 cm(-1)) is common between rhodopsin and color pigments, which greatly contrasts with the case of proton-pumping microbial rhodopsins. On the other hand, two important differences are observed in water signal between rhodopsin and color pigments. First, the water vibrations are identical between the 11-cis and 9-cis forms of rhodopsin, but different vibrational bands are observed at >2550 cm(-1) for both MR and MG. Second, strongly hydrogen-bonded water molecules (2303 cm(-1) for MR and 2308 cm(-1) for MG) are observed for the all-trans form after retinal photoisomerization, which is not the case for rhodopsin. These specific features of MR and MG can be explained by the presence of water molecules in the Cl(-)-biding site, which are located near positions C11 and C9 of the retinal chromophore. The averaged frequencies of the observed water O-D stretching vibrations for MR and MG are lower as the λ(max) is red-shifted, suggesting that water molecules are involved in

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

... Areas Thirteenth Coast Guard District § 165.1313 Security zone regulations, tank ship protection, Puget... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Security zone regulations, tank ship protection, Puget Sound and adjacent waters, Washington 165.1313 Section 165.1313 Navigation and...

Internally bridging water molecule in transmembrane alpha-helical kink.

PubMed

Miyano, Masashi; Ago, Hideo; Saino, Hiromichi; Hori, Tetsuya; Ida, Koh

2010-08-01

There are hundreds of membrane protein atomic coordinates in the Protein Data Bank (PDB), and high-resolution structures of better than 2.5 A enable the visualization of a sizable number of amphiphiles (lipid and/or detergent) and bound water molecules as essential parts of the structure. Upon scrutinizing these high-resolution structures, water molecules were found to 'wedge' and stabilize large kink angle (30-40 degrees) in a simple cylindrical model at the transmembrane helical kinks so as to form an inter-helical cavity to accommodate a ligand binding or active site as a crucial structural feature in alpha-helical integral membrane proteins. Furthermore, some of these water molecules are proposed to play a pivotal role of their conformational change to exert their functional regulation. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

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.

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

PubMed

Roy, Susmita; Bagchi, Biman

2012-03-08

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.

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

... 33 Navigation and Navigable Waters 3 2013-07-01 2013-07-01 false Albemarle Sound, Pamlico Sound... 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...

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

... 33 Navigation and Navigable Waters 3 2014-07-01 2014-07-01 false Albemarle Sound, Pamlico Sound... 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...

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

... 33 Navigation and Navigable Waters 3 2012-07-01 2012-07-01 false Albemarle Sound, Pamlico Sound... 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...

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

... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Albemarle Sound, Pamlico Sound... 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...

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

... 33 Navigation and Navigable Waters 3 2011-07-01 2011-07-01 false Albemarle Sound, Pamlico Sound... 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...

Quantum Electric Dipole Lattice - Water Molecules Confined to Nanocavities in Beryl

NASA Astrophysics Data System (ADS)

Dressel, Martin; Zhukova, Elena S.; Thomas, Victor G.; Gorshunov, Boris P.

2018-02-01

Water is subject to intense investigations due to its importance in biological matter but keeps many of its secrets. Here, we unveil an even other aspect by confining H2O molecules to nanosize cages. Our THz and infrared spectra of water in the gemstone beryl evidence quantum tunneling of H2O molecules in the crystal lattice. The water molecules are spread out when confined in a nanocage. In combination with low-frequency dielectric measurements, we were also able to show that dipolar coupling among the H2O molecules leads towards a ferroelectric state at low temperatures. Upon cooling, a ferroelectric soft mode shifts through the THz range. Only quantum fluctuations prevent perfect macroscopic order to be fully achieved. Beside the significance to life science and possible application, nanoconfined water may become the prime example of a quantum electric dipolar lattice.

What Can Interfacial Water Molecules Tell Us About Solute Structure?

NASA Astrophysics Data System (ADS)

Willard, Adam

The molecular structure of bulk liquid water reflects a molecular tendency to engage in tetrahedrally coordinated hydrogen bonding. At a solute interface waters preferred three-dimensional hydrogen bonding network must conform to a locally anisotropy interfacial environment. Interfacial water molecules adopt configurations that balance water-solute and water-water interactions. The arrangements of interfacial water molecules, therefore encode information about the effective solute-water interactions. This solute-specific information is difficult to extract, however, because interfacial structure also reflects waters collective response to an anisotropic hydrogen bonding environment. Here I present a methodology for characterizing the molecular-level structure of liquid water interface from simulation data. This method can be used to explore waters static and/or dynamic response to a wide range of chemically and topologically heterogeneous solutes such as proteins.

Structures of water molecules in carbon nanotubes under electric fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Winarto,; Takaiwa, Daisuke; Yamamoto, Eiji

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 electricmore » 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.« less

Radium Isotope Ratios as Tracers for Estimating the Influence of Changjiang Outflow Water to the Adjacent Seas

NASA Astrophysics Data System (ADS)

Kim, K.; Kim, S.

2006-12-01

In order to understand the influence of Changjiang (Yangtze River) outflow water to the adjacent seas during rainy and draught seasons, we studied the origin and mixing of surface water masses in the East China Sea and the South Sea of Korea. We used Ra-228/Ra-226 activity ratio and salinity as two conservative tracers in three end-members: Changjiang water (CW); Yellow Sea water (YSW); and Kuroshio water (KW). Radium isotopes in each 300-liter of surface water samples were extracted by passing through manganese-fiber cartridges, dissolved in hydroxylamine hydrochloride solution, coprecipitated as barium sulfate, dried and measured by gamma-ray spectroscopy. Results show that surface water of the East China Sea includes all three end-member waters during the rainy season, in the order of KW (50-80%), YSW (20-50%) and CW (5-15%). Surface water of the South Sea of Korea, however, includes a little fraction of, or almost no, CW in drought season. These are the preliminary results from an ongoing 6-year project ending in 2009 which aims to predict the influence of heavily polluted Changjiang outflow water to the adjacent seas after the completion of the gigantic Three Gorges (Sanxia) Dam.

Ground-water hydrology of Pahvant Valley and adjacent areas, Utah

USGS Publications Warehouse

1990-01-01

The primary ground-water reservoir in Pahvant Valley and adjacent areas is in the unconsolidated basin fill and interbedded basalt. Recharge in 1959 was estimated to be about 70,000 acre-feet per year and was mostly by seepage from streams, canals, and unconsumed irrigation water and by infiltration of precipitation. Discharge in 1959 was estimated to be about 109,000 acre-feet and was mostly from springs, evapotranspiration, and wells.Water-level declines of more than 50 feet occurred in some areas between 1953 and 1980 because of less-than-normal precipitation and extensive pumping for irrigation. Water levels recovered most of these declines between 1983 and 1986 because of reduced withdrawals and record quantities of precipitation.The quality of ground water in the area west of Kanosh has deteriorated since large ground-water withdrawals began in about 1953. The cause of the deterioration probably is movement of poor quality water into the area from the southwest and possibly the west during periods of large ground-water withdrawals and recycling of irrigation water. The quality of water from some wells has improved since 1983, due to increased recharge and decreased withdrawals for irrigation.Water-level declines of m:>re than 80 feet in some parts of Pahvant Valley are projected if ground-water withdrawals continue for 20 years at the 1977 rate of about 96,000 acre-feet. Rises of as much as 58 feet and declines of as much as 47 feet are projected with withdrawals of 48,000 acre-feet per year for 20 years. The elimination of recharge from the Central Utah Canal is projected to cause water-level declines of up to 8 feet near the canal.

Ground-water resources of southern Tangipahoa Parish and adjacent areas, Louisiana

USGS Publications Warehouse

Rapp, T.R.

1994-01-01

Groundwater resources in southern Tangipahoa Parish and adjacent areas were studied to determine their potential for development as an alternative to the Mississippi River as a water-supply source for Jefferson Parish. Eight major aquifers consisting of thick sand units that underlie the study area are, in descending order: (1) shallow, (2) upper Ponchatoula, (3) lower Ponchatoula, (4) Abita, (5) Covington, (6) Tchefuncta, (7) Hammond, and (8) Amite. A fault zone, referred to as the Baton Rouge fault, crosses southern Tangipahoa Parish. Analyses of geophysical logs indicated that the deep aquifers south of the fault zone had been displaced from 350 to 400 feet, and that the deeper aquifers were not in hydraulic connection with the flow system north of the fault. The groundwater resources of southeastern Louisiana are immense and the quality of groundwater in Tangipahoa Parish is suitable for most uses. The quality of water in these aquifers generally meets the U.S. Environmental Protection Agency's standards for public supply. The hydrologic system underlying Tangipahoa Parish and adjacent areas in 1990 supplied about 19 Mgal/d of water that was suitable for public supply. However, substantial increases in pumping from the aquifer system would result in renewed water-level declines throughout the hydrologic system until a new equilibrium is established. A test we11 in southern Tangipahoa Parish, penetrated all eight aquifers. Total thickness of freshwater sand beds penetrated by the 3003-ft test hole was more than 1900 ft. Resistivity values from an electric log of the test typically averaged 200 ohm-meters, which indicates that the water has low dissolved-solids and chloride concentrations. An analysis of the Abita aquifer at Ruddock in St. John the Baptist Parish, for two of three hypothetical well fields, indicated that for a hypothetical we11 field with a pumping rate of 112 Mgal/d, the freshwater/saltwater interface could arrive at the outer perimeter we11 in

Comparative water relations of adjacent california shrub and grassland communities.

PubMed

Davis, S D; Mooney, H A

1985-07-01

Much of the coastal mountains and foothills of central and southern California are covered by a mosaic of grassland, coastal sage scrub, and evergreen sclerophyllous shrubs (chaparral). In many cases, the borders between adjacent plant communities are stable. The cause of this stability is unknown. The purpose of our study was to examine the water use patterns of representative grasses, herbs, and shrubs across a grassland/chaparrel ecotone and determine the extent to which patterns of water use contribute to ecotone stability. In addition, we examined the effects of seed dispersal and animal herbivory. We found during spring months, when water was not limited, grassland species had a much higher leaf conductance to water vapor diffusion than chaparral plants. As the summer drought progressed, grassland species depleted available soil moisture first, bare zone plants second, and chaparral third, with one chaparral species (Quercus durata) showing no evidence of water stress. Soil moisture depletion patterns with depth and time corresponded to plant water status and root depth. Rabbit herbivory was highest in the chaparral and bare zone as indicated by high densities of rabbit pellets. Dispersal of grassland seeds into the chaparral and bare zone was low. Our results support the hypothesis that grassland species deplete soil moisture in the upper soil horizon early in the drought, preventing the establishment of chaparral seedlings or bare zone herbs. Also, grassland plants are prevented from invading the chaparral because of low seed dispersability and high animal herbivory in these regions.

The role of water molecules in stereoselectivity of glucose/galactose-binding protein

NASA Astrophysics Data System (ADS)

Kim, Minsup; Cho, Art E.

2016-11-01

Using molecular dynamics (MD) simulation methods, we attempted to explain the experimental results on ligand specificity of glucose/galactose-binding protein (GGBP) to β-D-glucose and β-D-galactose. For the simulation, a three-dimensional structure of GGBP was prepared, and homology modeling was performed to generate variant structures of GGBP with mutations at Asp14. Then, docking was carried out to find a reasonable β-D-glucose and β-D-galactose binding conformations with GGBP. Subsequent molecular dynamics simulations of β-D-glucose-GGBP and β-D-galactose-GGBP complexes and estimation of the orientation and stability of water molecules at the binding site revealed how water molecules influence ligand specificity. In our simulation, water molecules mediated interactions of β-D-glucose or β-D-galactose with residue 14 of GGBP. In this mechanism, the Phe16Ala mutant leaves both sugar molecules free to move, and the specific role of water molecules were eliminated, while the wild type, Asp14Asn mutant, and Asp14Glu mutant make hydrogen bond interactions with β-D-glucose more favorable. Our results demonstrate that bound water molecules at the binding site of GGBP are related to localized conformational change, contributing to ligand specificity of GGBP for β-D-glucose over β-D-galactose.

Hydration of polar and nonpolar molecules at the surface of amorphous solid water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Souda, Ryutaro

2004-10-15

On the basis of time-of-flight secondary ion mass spectrometry, properties of amorphous solid water above the glass transition temperature (136 K) and the hydration of polar (HCOOH,C{sub 3}H{sub 7}OH) and nonpolar (C{sub 6}H{sub 14},C{sub 6}F{sub 14}) molecules on the D{sub 2}O-ice surface have been investigated. No evidence was obtained for the irreversible transition of the amorphous solid water into the crystalline phase: the self-diffusion of water molecules occurs above 140 K irrespective of the preparation temperatures of the water-ice film ranging from 15 K to 165 K, whereas the morphology of the film changes drastically at 165 K due tomore » the evolution of liquidlike water. It is also demonstrated that the change in conformation of the hydrated HCOOH molecule, as well as the occurrence of hydrophilic/hydrophobic hydration of the C{sub 3}H{sub 7}OH molecule, can be analyzed successfully from the temperature evolutions of the secondary-ion intensities. These polar molecules basically stay on the surface and tend to quench the morphological change of the water film due to the reduction of surface tension. The nonpolar C{sub 6}H{sub 14} and C{sub 6}F{sub 14} molecules readily dissolve in the D{sub 2}O layer below 100 K and dehydration of the incorporated molecules occurs at 165 K concomitantly with the evolution of the liquidlike water. It is thus concluded that the hydrophobic hydration of nonpolar molecules is intimately related to the properties of water films.« less

Confinement of water molecule inside (2, 2) graphyne nanotube

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deb, Jyotirmoy; Bhattacharya, Barnali; Sarkar, Utpal, E-mail: utpalchemiitkgp@yahoo.com

2016-05-23

Using density functional theory (DFT) calculations with generalized gradient approximation, the interaction between H{sub 2}O molecule and (2, 2) graphyne nanotube (GNT) has been investigated. The stable configuration due to the insertion of H{sub 2}O molecule inside (2, 2) GNT is determined on the basis of binding energy. The band gap of the GNT decreases due to the confinement of H{sub 2}O molecule. The charge analysis reveals that electrons are shifted from the H{sub 2}O molecule to the GNT. The electronic property of the GNT is highly influenced by the presence of H{sub 2}O molecule; thus, we may design amore » GNT based sensor for the detection of water molecule.« less

The Effect of Water Molecules on Mechanical Properties of Cell Walls

NASA Astrophysics Data System (ADS)

Rahbar, Nima; Youssefian, Sina

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. 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 are 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 and decreases in higher water content, whereas the hemicellulose elastic modulus constantly decreases. The variations of Radial Distribution Function and Free Fractional Volume of these materials with water suggest that water molecules enhance the mechanical properties of lignin by filling voids in the system and creating Hbond bridges between polymer chains. For hemicellulose, however, the effect is always regressive due to the destructive effect of water molecules on the Hbond of its dense structure.

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.

Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins

NASA Astrophysics Data System (ADS)

Poornima, C. S.; Dean, P. M.

1995-12-01

Water molecules are known to play an important rôle in mediating protein-ligand interactions. If water molecules are conserved at the ligand-binding sites of homologous proteins, such a finding may suggest the structural importance of water molecules in ligand binding. Structurally conserved water molecules change the conventional definition of `binding sites' by changing the shape and complementarity of these sites. Such conserved water molecules can be important for site-directed ligand/drug design. Therefore, five different sets of homologous protein/protein-ligand complexes have been examined to identify the conserved water molecules at the ligand-binding sites. Our analysis reveals that there are as many as 16 conserved water molecules at the FAD binding site of glutathione reductase between the crystal structures obtained from human and E. coli. In the remaining four sets of high-resolution crystal structures, 2-4 water molecules have been found to be conserved at the ligand-binding sites. The majority of these conserved water molecules are either bound in deep grooves at the protein-ligand interface or completely buried in cavities between the protein and the ligand. All these water molecules, conserved between the protein/protein-ligand complexes from different species, have identical or similar apolar and polar interactions in a given set. The site residues interacting with the conserved water molecules at the ligand-binding sites have been found to be highly conserved among proteins from different species; they are more conserved compared to the other site residues interacting with the ligand. These water molecules, in general, make multiple polar contacts with protein-site residues.

76 FR 30023 - Pamlico Sound and Adjacent Waters, NC; Danger Zones for Marine Corps Operations

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-24

... DEPARTMENT OF DEFENSE Corps of Engineers, Department of the Army 33 CFR Part 334 Pamlico Sound and Adjacent Waters, NC; Danger Zones for Marine Corps Operations AGENCY: United States Army Corps of Engineers, DoD. ACTION: Final rule. SUMMARY: The U.S. Army Corps of Engineers is amending its regulations to...

Fast Rotational Diffusion of Water Molecules in a 2D Hydrogen Bond Network at Cryogenic Temperatures

NASA Astrophysics Data System (ADS)

Prisk, T. R.; Hoffmann, C.; Kolesnikov, A. I.; Mamontov, E.; Podlesnyak, A. A.; Wang, X.; Kent, P. R. C.; Anovitz, L. M.

2018-05-01

Individual water molecules or small clusters of water molecules contained within microporous minerals present an extreme case of confinement where the local structure of hydrogen bond networks are dramatically altered from bulk water. In the zinc silicate hemimorphite, the water molecules form a two-dimensional hydrogen bond network with hydroxyl groups in the crystal framework. Here, we present a combined experimental and theoretical study of the structure and dynamics of water molecules within this network. The water molecules undergo a continuous phase transition in their orientational configuration analogous to a two-dimensional Ising model. The incoherent dynamic structure factor reveals two thermally activated relaxation processes, one on a subpicosecond timescale and another on a 10-100 ps timescale, between 70 and 130 K. The slow process is an in-plane reorientation of the water molecule involving the breaking of hydrogen bonds with a framework that, despite the low temperatures involved, is analogous to rotational diffusion of water molecules in the bulk liquid. The fast process is a localized motion of the water molecule with no apparent analogs among known bulk or confined phases of water.

Fast Rotational Diffusion of Water Molecules in a 2D Hydrogen Bond Network at Cryogenic Temperatures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prisk, Timothy; Hoffmann, Christina; Kolesnikov, Alexander I.

Individual water molecules or small clusters of water molecules contained within microporous minerals present an extreme case of confinement where the local structure of hydrogen bond networks are dramatically altered from bulk water. In the zinc silicate hemimorphite, the water molecules form a two-dimensional hydrogen bond network with hydroxyl groups in the crystal framework. Here in this paper, we present a combined experimental and theoretical study of the structure and dynamics of water molecules within this network. The water molecules undergo a continuous phase transition in their orientational configuration analogous to a two-dimensional Ising model. The incoherent dynamic structure factormore » reveals two thermally activated relaxation processes, one on a subpicosecond timescale and another on a 10–100 ps timescale, between 70 and 130 K. The slow process is an in-plane reorientation of the water molecule involving the breaking of hydrogen bonds with a framework that, despite the low temperatures involved, is analogous to rotational diffusion of water molecules in the bulk liquid. The fast process is a localized motion of the water molecule with no apparent analogs among known bulk or confined phases of water.« less

Fast Rotational Diffusion of Water Molecules in a 2D Hydrogen Bond Network at Cryogenic Temperatures

DOE PAGES

Prisk, Timothy; Hoffmann, Christina; Kolesnikov, Alexander I.; ...

2018-05-09

Individual water molecules or small clusters of water molecules contained within microporous minerals present an extreme case of confinement where the local structure of hydrogen bond networks are dramatically altered from bulk water. In the zinc silicate hemimorphite, the water molecules form a two-dimensional hydrogen bond network with hydroxyl groups in the crystal framework. Here in this paper, we present a combined experimental and theoretical study of the structure and dynamics of water molecules within this network. The water molecules undergo a continuous phase transition in their orientational configuration analogous to a two-dimensional Ising model. The incoherent dynamic structure factormore » reveals two thermally activated relaxation processes, one on a subpicosecond timescale and another on a 10–100 ps timescale, between 70 and 130 K. The slow process is an in-plane reorientation of the water molecule involving the breaking of hydrogen bonds with a framework that, despite the low temperatures involved, is analogous to rotational diffusion of water molecules in the bulk liquid. The fast process is a localized motion of the water molecule with no apparent analogs among known bulk or confined phases of water.« less

Variability of adjacency effects in sky reflectance measurements.

PubMed

Groetsch, Philipp M M; Gege, Peter; Simis, Stefan G H; Eleveld, Marieke A; Peters, Steef W M

2017-09-01

Sky reflectance R sky (λ) is used to correct in situ reflectance measurements in the remote detection of water color. We analyzed the directional and spectral variability in R sky (λ) due to adjacency effects against an atmospheric radiance model. The analysis is based on one year of semi-continuous R sky (λ) observations that were recorded in two azimuth directions. Adjacency effects contributed to R sky (λ) dependence on season and viewing angle and predominantly in the near-infrared (NIR). For our test area, adjacency effects spectrally resembled a generic vegetation spectrum. The adjacency effect was weakly dependent on the magnitude of Rayleigh- and aerosol-scattered radiance. The reflectance differed between viewing directions 5.4±6.3% for adjacency effects and 21.0±19.8% for Rayleigh- and aerosol-scattered R sky (λ) in the NIR. Under which conditions in situ water reflectance observations require dedicated correction for adjacency effects is discussed. We provide an open source implementation of our method to aid identification of such conditions.

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

... Gulf of Mexico adjacent to Santa Rosa Island, Armament Center, Eglin Air Force Base, Fla. 334.730... Mexico adjacent to Santa Rosa Island, Armament Center, Eglin Air Force Base, Fla. (a) The areas—(1) The... CFR part 329, including the waters of Santa Rosa Sound and Gulf of Mexico within a circle one nautical...

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

... Gulf of Mexico adjacent to Santa Rosa Island, Armament Center, Eglin Air Force Base, Fla. 334.730... Mexico adjacent to Santa Rosa Island, Armament Center, Eglin Air Force Base, Fla. (a) The areas—(1) The... CFR part 329, including the waters of Santa Rosa Sound and Gulf of Mexico within a circle one nautical...

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

... Gulf of Mexico adjacent to Santa Rosa Island, Armament Center, Eglin Air Force Base, Fla. 334.730... Mexico adjacent to Santa Rosa Island, Armament Center, Eglin Air Force Base, Fla. (a) The areas—(1) The... CFR part 329, including the waters of Santa Rosa Sound and Gulf of Mexico within a circle one nautical...

Transport of water molecules through noncylindrical pores in multilayer nanoporous graphene.

PubMed

Shahbabaei, Majid; Kim, Daejoong

2017-08-09

In this study, molecular dynamics (MD) simulations are used to examine the water transport properties through asymmetric hourglass-shaped pores in multilayer nanoporous graphene with a constant interlayer separation of 6 Å. The properties of the tested asymmetric hourglass-shaped pores [with the models having long cone (l 1 , -P) and short cone (l 2 , +P) entrances] are compared to a symmetric pore model. The study findings indicate that the water occupancy increases across the asymmetric pore (l 1 , -P) compared to (l 2 , +P), because of the length effect. The asymmetric pore, (l 1 , -P), yields higher flux compared to (l 2 , +P) and even the symmetric model, which can be attributed to the increase in the hydrogen bonds. In addition, the single-file water molecules across the narrowest pore diameter inside the (l 2 , +P) pore exhibit higher viscosity compared to those in the (l 1 , -P) pore because of the increase in the water layering effect. Moreover, it is found that the permeability inside the multilayer hourglass-shaped pore depends on the length of the flow path of the water molecules before approaching the layer with the smallest pore diameter. The probability of dipole orientation exhibits wider distribution inside the (l 1 , -P) system compared to (l 2 , +P), implying an enhanced formation of hydrogen bonding of water molecules. This results in the fast flow of water molecules. The MD trajectory shows that the dipole orientation across the single-layer graphene has frequently flipped compared to the dipole orientation across the pores in multilayer graphene, which is maintained during the whole simulation time (although the dipole orientation has flipped for a few picoseconds at the beginning of the simulation). This can be attributed to the energy barrier induced by the individual layer. The diffusion coefficient of water molecules inside the (l 2 , +P) system increases with pressure difference, however, it decreases inside the (l 1 , -P) system because

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

... DEPARTMENT OF DEFENSE Corps of Engineers, Department of the Army 33 CFR Part 334 Pamlico Sound and... (Corps) is proposing to amend its regulations to establish one new danger zone in Pamlico Sound near... described in Sec. 334.420(b)(1)(i)] in the Pamlico Sound and adjacent waters in Carteret County, North...

On influencing factors of hypoxia in waters adjacent to the Changjiang estuary

NASA Astrophysics Data System (ADS)

Luo, Xiaofan; Wei, Hao; Fan, Renfu; Liu, Zhe; Zhao, Liang; Lu, Youyu

2018-01-01

Based on observational data from ten cruises carried out in 2012 and 2013, the distribution of dissolved oxygen (DO) and the evolution of hypoxia (DO concentrations < 2.0 mg L-1) in waters adjacent to the Changjiang estuary are studied. The linkage between summer hypoxia and hydrodynamic conditions is explored. The results suggest that hypoxia frequently occurred from June to October to the south of the Changjiang estuary near the 30-50 m isobaths and was prone to happening under strong stratification without the presence of the Kuroshio Subsurface Water (KSW). Over the Changjiang Bank, hypoxia mainly occurred in July, August and September. Low-oxygen areas initially appeared under strong stratification induced by the spreading of the Changjiang Diluted Water (CDW), and developed into hypoxic zones due to lack of DO replenishment from the relatively DO-rich Yellow Sea Water and the KSW. The yearly evolution of hypoxia was influenced by shelf circulation especially the path of the KSW in the bottom layer of the water to the south of the Changjiang estuary, and the extension of the CDW in the surface layer over the Changjiang Bank.

Incipient ferroelectricity of water molecules confined to nano-channels of beryl

NASA Astrophysics Data System (ADS)

Gorshunov, B. P.; Torgashev, V. I.; Zhukova, E. S.; Thomas, V. G.; Belyanchikov, M. A.; Kadlec, C.; Kadlec, F.; Savinov, M.; Ostapchuk, T.; Petzelt, J.; Prokleška, J.; Tomas, P. V.; Pestrjakov, E. V.; Fursenko, D. A.; Shakurov, G. S.; Prokhorov, A. S.; Gorelik, V. S.; Kadyrov, L. S.; Uskov, V. V.; Kremer, R. K.; Dressel, M.

2016-09-01

Water is characterized by large molecular electric dipole moments and strong interactions between molecules; however, hydrogen bonds screen the dipole-dipole coupling and suppress the ferroelectric order. The situation changes drastically when water is confined: in this case ordering of the molecular dipoles has been predicted, but never unambiguously detected experimentally. In the present study we place separate H2O molecules in the structural channels of a beryl single crystal so that they are located far enough to prevent hydrogen bonding, but close enough to keep the dipole-dipole interaction, resulting in incipient ferroelectricity in the water molecular subsystem. We observe a ferroelectric soft mode that causes Curie-Weiss behaviour of the static permittivity, which saturates below 10 K due to quantum fluctuations. The ferroelectricity of water molecules may play a key role in the functioning of biological systems and find applications in fuel and memory cells, light emitters and other nanoscale electronic devices.

Incipient ferroelectricity of water molecules confined to nano-channels of beryl

PubMed Central

Gorshunov, B. P.; Torgashev, V. I.; Zhukova, E. S.; Thomas, V. G.; Belyanchikov, M. A.; Kadlec, C.; Kadlec, F.; Savinov, M.; Ostapchuk, T.; Petzelt, J.; Prokleška, J.; Tomas, P. V.; Pestrjakov, E. V.; Fursenko, D. A.; Shakurov, G. S.; Prokhorov, A. S.; Gorelik, V. S.; Kadyrov, L. S.; Uskov, V. V.; Kremer, R. K.; Dressel, M.

2016-01-01

Water is characterized by large molecular electric dipole moments and strong interactions between molecules; however, hydrogen bonds screen the dipole–dipole coupling and suppress the ferroelectric order. The situation changes drastically when water is confined: in this case ordering of the molecular dipoles has been predicted, but never unambiguously detected experimentally. In the present study we place separate H2O molecules in the structural channels of a beryl single crystal so that they are located far enough to prevent hydrogen bonding, but close enough to keep the dipole–dipole interaction, resulting in incipient ferroelectricity in the water molecular subsystem. We observe a ferroelectric soft mode that causes Curie–Weiss behaviour of the static permittivity, which saturates below 10 K due to quantum fluctuations. The ferroelectricity of water molecules may play a key role in the functioning of biological systems and find applications in fuel and memory cells, light emitters and other nanoscale electronic devices. PMID:27687693

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 Mexico...

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhukova, Elena S., E-mail: zhukovaelenka@gmail.com; Gorshunov, Boris P.; 1. Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart

2014-06-14

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:Be{sub 3}Al{sub 2}Si{sub 6}O{sub 18}, 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 ε{sup ′}(ν) spectra are recorded in terahertz and infrared ranges, at frequencies from severalmore » wavenumbers up to ν = 7000 cm{sup −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 ε{sup ′}(ν) caused exclusively by water molecules. In the infrared range, well-known internal modes ν{sub 1}, ν{sub 2}, and ν{sub 3} of the H{sub 2}O molecule are observed for both polarizations, indicating the presence of water-I and water-II molecules in the crystal. Spectra recorded below 1000 cm{sup −1} reveal a rich set of highly anisotropic features in the low-energy response of H{sub 2}O molecule in a crystalline nano-cavity. While for E∥c only two absorption peaks are detected, at ∼90 cm{sup −1} and ∼160 cm{sup −1}, several absorption bands are discovered for E⊥c, each consisting of narrower resonances. The bands are assigned to librational (400–500 cm{sup −1}) and translational (150–200 cm{sup −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

Detection of magnetic dipolar coupling of water molecules at the nanoscale using quantum magnetometry

NASA Astrophysics Data System (ADS)

Yang, Zhiping; Shi, Fazhan; Wang, Pengfei; Raatz, Nicole; Li, Rui; Qin, Xi; Meijer, Jan; Duan, Changkui; Ju, Chenyong; Kong, Xi; Du, Jiangfeng

2018-05-01

It is a crucial issue to study interactions among water molecules and hydrophobic interfacial water at the nanoscale. Here we succeed in measuring the nuclear magnetic resonance spectrum of a diamond-water interfacial ice with a detection volume of about 2.2 ×10-22 L. More importantly, the magnetic dipolar coupling between the two protons of a water molecule is resolved by measuring the signal contributed from about 7000 water molecules at the nanoscale. The resolved intramolecule magnetic dipolar interactions are about 15 and 33 kHz with spectral resolution of 5 kHz. This work provides a platform for hydrophobic interfacial water study under ambient conditions, with further applications in more general nanoscale structural analysis.

[Estuary health assessment using a benthic-index of biotic integrity in Yangtze Estuary and its adjacent waters].

PubMed

Zhou, Xiao-wei; Wang, Li-ping; Zheng, Bing-hui; Liu, Lu-san; Fu, Qing

2009-01-01

A benthic index of biotic integrity (B-IBI) was developed for application in estuaries health assessment of the Yangtze Estuary and its adjacent waters. Benthic macro-invertebrate samples were collected from 41 stream sites (13 non-degraded stations and 28 degraded stations) in the Yangtze Estuary and its adjacent waters in July, 2005. The analyses of the range of index value distribution, Pearson correlation and judgment ability were performed on fourteen candidate metrics. Six biological metrics were selected for the establishment of B-IBI, which were Shannon-Wiener index, the species number, total density, total biomass, Carapace Animals density percentage and Echinoderms density percentage. B-IBI was obtained by sum up all these indices after which were transformed into a uniform score by using the ratio scoring method. Base on 50 percentile of B-IBI value in reference sites, the criteria of health ranking was determined. The proposed criteria of benthic-index of biotic integrity were as follows: B-IBI > 2.48 was regarded as health, 1.86-2.48 sub-health, 1.24-1.86 fair, 0.62-1.24 poor, and B-IBI < 0.62 very poor. Assessing with these criteria, the results showed that among the 41 sites in Yangtze Estuary and its adjacent waters, 7 sites were health, 2 sites were sub-health, 8 sites were fair, 8 sites were poor and 16 sites were very poor. An independent data set sampled in June of 2006 was used to validate the index, the results indicated that final combined index correctly classified 89% of stations in the validation data set.

Investigation of the Hydantoin Monomer and its Interaction with Water Molecules

NASA Astrophysics Data System (ADS)

Gruet, Sébastien; Perez, Cristobal; Schnell, Melanie

2017-06-01

Hydantoin (Imidazolidine-2,4-dione, C_3H_4N_2O_2) is a five-membered heterocyclic compound of astrobiological interest. This molecule has been detected in carbonaceous chondrites [1], and its formation can rise from the presence of glycolic acid and urea, two prebiotic molecules [2]. The hydrolysis of hydantoin under acidic conditions can also produce glycine [3], an amino acid actively searched for in the interstellar medium. Spectroscopic data of hydantoin is very limited and mostly dedicated to the solid phase. The high resolution study in gas phase is restricted to the work recently published by Ozeki et al. reporting the pure rotational spectra of the ground state and two vibrational states of the molecule in the millimeter-wave region (90-370 GHz)[4]. Using chirped-pulse Fourier-transform microwave (CP-FTMW) spectroscopy, we recorded the jet-cooled rotational spectra of hydantoin with water between 2 to 8 GHz. We observed the ground state of hydantoin monomer and several water complexes with one or two water molecules. All the observed species exhibit a hyperfine structure due to the two nitrogen atoms present in the molecule, which were fully resolved and analyzed. Additional experiments with a ^{18}O enriched water sample were realized to determine the oxygen-atom positions of the water monomers. These experiments yielded accurate structural information on the preferred water binding sites. The observed complexes and the interactions that hold them together, mainly strong directional hydrogen bonds, will be presented and discussed. [1] Shimoyama, A. and Ogasawara, R., Orig. Life Evol. Biosph., 32, 165-179, 2002. DOI:10.1023/A:1016015319112. [2] Menor-Salván, C. and Marín-Yaseli, M.R., Chem. Soc. Rev., 41(16), 5404-5415, 2012. DOI:10.1039/c2cs35060b. [3] De Marcellus P., Bertrand M., Nuevo M., Westall F. and Le Sergeant d'Hendecourt L., Astrobiology. 11(9), 847-854, 2011. DOI:10.1089/ast.2011.0677. [4] Ozeki, H., Miyahara R., Ihara H., Todaka S., Kobayashi

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.

Thermodynamics of hydrogen bond patterns in supramolecular assemblies of water molecules.

PubMed

Henry, Marc

2002-07-02

The PACHA (Partial Atomic Charges and Hardnesses Analysis) formalism is applied to various supramolecular assemblies of water molecules. After a detailed study of all available crystal structures for ice polymorphs, we shown that the hydrogen bond strength is roughly constant below 1 GPa and considerably weakened above that value. New hydrogen bond patterns are proposed for ice IV, V, and VI after (EB) (electrostatic balance) minimization. For other polymorphs, there is an almost perfect coincidence between experimental and predicted hydrogen bond patterns. The evolution of hydrogen bond energy as a function of molecular geometry in water clusters with up to 280 water molecules and in large supramolecular compounds is quantitatively described. Intermolecular hydrogen bonds are found to lie between -9 and -32 kJ mol-1, the stronger interaction occurs within the spherical fully disordered water droplet buried at the heart of Müller's superfullerene keplerate. The weakest one occurs in a chiral molecular snub cube built from six calix[4]resorcinarene and eight water molecules. Intramolecular hydrogen bonds are found in the range -10-100 kJ mol-1 and can thus be considerably stronger than intermolecular bonds. Finally, through the investigation of a clathrate type I compound, it was possible to obtain a deep insight of the host-guest interactions and self-assembly rules of water cages in these materials.

Water: a responsive small molecule.

PubMed

Shultz, Mary Jane; Vu, Tuan Hoang; Meyer, Bryce; Bisson, Patrick

2012-01-17

Unique among small molecules, water forms a nearly tetrahedral yet flexible hydrogen-bond network. In addition to its flexibility, this network is dynamic: bonds are formed or broken on a picosecond time scale. These unique features make probing the local structure of water challenging. Despite the challenges, there is intense interest in developing a picture of the local water structure due to water's fundamental importance in many fields of chemistry. Understanding changes in the local network structure of water near solutes likely holds the key to unlock problems from analyzing parameters that determine the three dimensional structure of proteins to modeling the fate of volatile materials released into the atmosphere. Pictures of the local structure of water are heavily influenced by what is known about the structure of ice. In hexagonal I(h) ice, the most stable form of solid water under ordinary conditions, water has an equal number of donor and acceptor bonds; a kind of symmetry. This symmetric tetrahedral coordination is only approximately preserved in the liquid. The most obvious manifestation of this altered tetrahedral bonding is the greater density in the liquid compared with the solid. Formation of an interface or addition of solutes further modifies the local bonding in water. Because the O-H stretching frequency is sensitive to the environment, vibrational spectroscopy provides an excellent probe for the hydrogen-bond structure in water. In this Account, we examine both local interactions between water and small solutes and longer range interactions at the aqueous surface. Locally, the results suggest that water is not a symmetric donor or acceptor, but rather has a propensity to act as an acceptor. In interactions with hydrocarbons, action is centered at the water oxygen. For soluble inorganic salts, interaction is greater with the cation than the anion. The vibrational spectrum of the surface of salt solutions is altered compared with that of neat

Capacitive Sensing of Intercalated H2O Molecules Using Graphene.

PubMed

Olson, Eric J; Ma, Rui; Sun, Tao; Ebrish, Mona A; Haratipour, Nazila; Min, Kyoungmin; Aluru, Narayana R; Koester, Steven J

2015-11-25

Understanding the interactions of ambient molecules with graphene and adjacent dielectrics is of fundamental importance for a range of graphene-based devices, particularly sensors, where such interactions could influence the operation of the device. It is well-known that water can be trapped underneath graphene and its host substrate; however, the electrical effect of water beneath graphene and the dynamics of how the interfacial water changes with different ambient conditions has not been quantified. Here, using a metal-oxide-graphene variable-capacitor (varactor) structure, we show that graphene can be used to capacitively sense the intercalation of water between graphene and HfO2 and that this process is reversible on a fast time scale. Atomic force microscopy is used to confirm the intercalation and quantify the displacement of graphene as a function of humidity. Density functional theory simulations are used to quantify the displacement of graphene induced by intercalated water and also explain the observed Dirac point shifts as being due to the combined effect of water and oxygen on the carrier concentration in the graphene. Finally, molecular dynamics simulations indicate that a likely mechanism for the intercalation involves adsorption and lateral diffusion of water molecules beneath the graphene.

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

DOE PAGES

Kolesnikov, Alexander I.; Reiter, George F.; Choudhury, Narayani; ...

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolesnikov, Alexander I.; Reiter, George F.; Choudhury, Narayani

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.

On the dynamics of water molecules at the protein solute interfaces.

PubMed

Bernini, A; Spiga, O; Ciutti, A; Chiellini, S; Menciassi, N; Venditti, V; Niccolai, N

2004-10-01

Proteins, with the large variety of chemical groups they present at their molecular surface, are a class of molecules which can be very informative on most of the possible solute-solvent interactions. Hen egg white lysozyme has been used as a probe to investigate the complex solvent dynamics occurring at the protein surface, by analysing the results obtained from Nuclear Magnetic Resonance, X-ray diffractometry and Molecular Dynamics simulations. A consistent overall picture for the dynamics of water molecules close to the protein is obtained, suggesting that a rapid exchange occurs, in a picosecond timescale, among all the possible hydration surface sites both in solution and the solid state, excluding the possibility that solvent molecules can form liquid-crystal-like supramolecular adducts, which have been proposed as a molecular basis of 'memory of water'.

Structural, spectroscopic and electronic properties of hydrogen-bonded water molecules in crystals. Ab initio calculations and experimental data of MC1 2· n(H,D) 2O, M = Sr or Ba

NASA Astrophysics Data System (ADS)

Möller, H.; Niu, J. E.; Lutz, H. D.; Schwarz, W. H. E.

1997-12-01

Structural, spectroscopic and electronic properties of (more or less deuterated) water molecules in the crystal fields of SrCl 2·2H 2O, SrCl 2·H 2O and BaCl 2·H 2O, previously investigated by experimental techniques, were calculated by ab initio SCF-MP methods. The H 2O molecules of each compound are asymmetrically surrounded by three adjacent chloride ions, one hydrogen atom being attached to a nearby Cl -, the other less perturbed hydrogen atom bridging the two less near Cl -. The diversity of structural and spectroscopic features found experimentally, for instance the trends from free H 2O to H 2O in BaCl 2·H 2OSrCl 2·H 2OSrCl 2·2H 2O, are well reproduced by the model calculations, which provide the correct assignment and physical interpretation. The differences between the compounds and the asymmetry of the hydrate water molecules can be rationalized with the help of crystal fields. The crystal environment expands the internuclear distances of H 2O by up to 3 pm. The change of vibrational frequencies can be explained qualitatively by only taking the coupling and anharmonicity of the free water molecule and its modified structure in the crystals into account. The infra-red intensities, however, are strongly influenced by the electronic polarization.

Hydrology of Cache Valley, Cache County, Utah, and adjacent part of Idaho, with emphasis on simulation of ground-water flow

USGS Publications Warehouse

Kariya, Kim A.; Roark, D. Michael; Hanson, Karen M.

1994-01-01

A hydrologic investigation of Cache Valley was done to better understand the ground-water system in unconsolidated basin-fill deposits and the interaction between ground water and surface water. Ground-water recharge occurs by infiltration of precipitation and unconsumed irrigation water, seepage from canals and streams, and subsurface inflow from adjacent consolidated rock and adjacent unconsolidated basin-fill deposit ground-water systems. Ground-water discharge occurs as seepage to streams and reservoirs, spring discharge, evapotranspiration, and withdrawal from wells.Water levels declined during 1984-90. Less-than-average precipitation during 1987-90 and increased pumping from irrigation and public-supply wells contributed to the declines.A ground-water-flow model was used to simulate flow in the unconsolidated basin-fill deposits. Data primarily from 1969 were used to calibrate the model to steady-state conditions. Transient-state calibration was done by simulating ground-water conditions on a yearly basis for 1982-90.A hypothetical simulation in which the dry conditions of 1990 were continued for 5 years projected an average lO-foot water-level decline between Richmond and Hyrum. When increased pumpage was simulated by adding three well fields, each pumping 10 cubic feet per second, in the Logan, Smithfield, and College Ward areas, water-level declines greater than 10 feet were projected in most of the southeastern part of the valley and discharge from springs and seepage to streams and reservoirs decreased.

Multivalent small molecule pan-RAS inhibitors

PubMed Central

Welsch, Matthew E.; Kaplan, Anna; Chambers, Jennifer M.; Stokes, Michael E.; Bos, Pieter H.; Zask, Arie; Zhang, Yan; Sanchez-Martin, Marta; Badgley, Michael A.; Huang, Christine S.; Tran, Timothy H.; Akkiraju, Hemanth; Brown, Lewis M.; Nandakumar, Renu; Cremers, Serge; Yang, Wan S.; Tong, Liang; Olive, Kenneth P.; Ferrando, Adolfo; Stockwell, Brent R.

2017-01-01

SUMMARY Design of small molecules that disrupt protein-protein interactions, including the interaction of RAS proteins and their effectors, have potential use as chemical probes and therapeutic agents. We describe here the synthesis and testing of potential small molecule pan-RAS ligands, which were designed to interact with adjacent sites on the surface of oncogenic KRAS. One compound, termed 3144, was found to bind to RAS proteins using microscale thermophoresis, nuclear magnetic resonance spectroscopy and isothermal titration calorimetry, and to exhibit lethality in cells partially dependent on expression of RAS proteins. This compound was metabolically stable in liver microsomes and displayed anti-tumor activity in xenograft mouse cancer models. These findings suggest that pan-RAS inhibition may be an effective therapeutic strategy for some cancers, and that structure-based design of small molecules targeting multiple adjacent sites to create multivalent inhibitors may be effective for some proteins. PMID:28235199

Reversible geminate recombination of hydrogen-bonded water molecule pair

NASA Astrophysics Data System (ADS)

Markovitch, Omer; Agmon, Noam

2008-08-01

The (history independent) autocorrelation function for a hydrogen-bonded water molecule pair, calculated from classical molecular dynamics trajectories of liquid water, exhibits a t-3/2 asymptotic tail. Its whole time dependence agrees quantitatively with the solution for reversible diffusion-influenced geminate recombination derived by Agmon and Weiss [J. Chem. Phys. 91, 6937 (1989)]. Agreement with diffusion theory is independent of the precise definition of the bound state. Given the water self-diffusion constant, this theory enables us to determine the dissociation and bimolecular recombination rate parameters for a water dimer. (The theory is indispensable for obtaining the bimolecular rate coefficient.) Interestingly, the activation energies obtained from the temperature dependence of these rate coefficients are similar, rather than differing by the hydrogen-bond (HB) strength. This suggests that recombination requires displacing another water molecule, which meanwhile occupied the binding site. Because these activation energies are about twice the HB strength, cleavage of two HBs may be required to allow pair separation. The autocorrelation function without the HB angular restriction yields a recombination rate coefficient that is larger than that for rebinding to all four tetrahedral water sites (with angular restrictions), suggesting the additional participation of interstitial sites. Following dissociation, the probability of the pair to be unbound but within the reaction sphere rises more slowly than expected, possibly because binding to the interstitial sites delays pair separation. An extended diffusion model, which includes an additional binding site, can account for this behavior.

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.

Advances in the treatment of explicit water molecules in docking and binding free energy calculations.

PubMed

Hu, Xiao; Maffucci, Irene; Contini, Alessandro

2018-05-13

The inclusion of direct effects mediated by water during the ligand-receptor recognition is a hot-topic of modern computational chemistry applied to drug discovery and development. Docking or virtual screening with explicit hydration is still debatable, despite the successful cases that have been presented in the last years. Indeed, how to select the water molecules that will be included in the docking process or how the included waters should be treated remain open questions. In this review, we will discuss some of the most recent methods that can be used in computational drug discovery and drug development when the effect of a single water, or of a small network of interacting waters, needs to be explicitly considered. Here, we analyse software to aid the selection, or to predict the position, of water molecules that are going to be explicitly considered in later docking studies. We also present software and protocols able to efficiently treat flexible water molecules during docking, including examples of applications. Finally, we discuss methods based on molecular dynamics simulations that can be used to integrate docking studies or to reliably and efficiently compute binding energies of ligands in presence of interfacial or bridging water molecules. Software applications aiding the design of new drugs that exploit water molecules, either as displaceable residues or as bridges to the receptor, are constantly being developed. Although further validation is needed, workflows that explicitly consider water will probably become a standard for computational drug discovery soon. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Visualizing water molecules in transmembrane proteins using radiolytic labeling methods†

PubMed Central

Orban, Tivadar; Gupta, Sayan; Palczewski, Krzysztof; Chance, Mark R.

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 co-localize 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, owing to 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. PMID:20047303

Electric dipole moments of nanosolvated acid molecules in water clusters.

PubMed

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

2015-01-30

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.

Neuroscience of water molecules: a salute to professor Linus Carl Pauling.

PubMed

Nakada, Tsutomu

2009-04-01

More than 35 years ago double Nobel laureate Linus Carl Pauling published a powerful model of the molecular mechanism of general anesthesia, generally referred to as the hydrate-microcrystal (aqueous-phase) theory. This hypothesis, based on the molecular behavior of water molecules, did not receive serious attention during Pauling's life time, when scientific tools for examining complex systems such as the brain were still in their infancy. The situation has since drastically changed, and, now, in the twenty first century, many scientific tools are available for examining different types of complex systems. The discovery of aquaporin-4, a subtype of water channel abundantly expressed in glial systems, further highlighted the concept that the dynamics of water molecules in the cerebral cortex play an important role in important physiological brain functions including consciousness and information processing.

Influence of Aromatic Molecules on the Structure and Spectroscopy of Water Clusters

NASA Astrophysics Data System (ADS)

Tabor, Daniel P.; Sibert, Edwin; Walsh, Patrick S.; Zwier, Timothy S.

2016-06-01

Isomer-specific resonant ion-dip infrared spectra are presented for benzene-(water)_n, 1-2-diphenoxyethane-(water)_n, and tricyclophane-(water)_n clusters. The IR spectra are modeled with a local mode Hamiltonian that was originally formulated for the analysis of benzene-(water)_n clusters with up to seven waters. The model accounts for stretch-bend Fermi coupling, which can complicate the IR spectra in the 3150-3300 cm-1 region. When the water clusters interact with each of the solutes, the hydrogen bond lengths between the water molecules change in a characteristic way, reflecting the strength of the solute-water interaction. These structural effects are also reflected spectroscopically in the shifts of the local mode OH stretch frequencies. When diphenoxyethane is the solute, the water clusters distort more significantly than when bound to benzene. Tricyclophane's structure provides an aromatic-rich binding pocket for the water clusters. The local mode model is used to extract Hamiltonians for individual water molecules. These monomer Hamiltonians divide into groups based on their local H-bonding architecture, allowing for further classification of the wide variety of water environments encountered in this study.

Geometry-dependent distributed polarizability models for the water molecule

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loboda, Oleksandr; Ingrosso, Francesca; Ruiz-López, Manuel F.

2016-01-21

Geometry-dependent distributed polarizability models have been constructed by fits to ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set for the water molecule in the field of a point charge. The investigated models include (i) charge-flow polarizabilities between chemically bonded atoms, (ii) isotropic or anisotropic dipolar polarizabilities on oxygen atom or on all atoms, and (iii) combinations of models (i) and (ii). For each model, the polarizability parameters have been optimized to reproduce the induction energy of a water molecule polarized by a point charge successivelymore » occupying a grid of points surrounding the molecule. The quality of the models is ascertained by examining their ability to reproduce these induction energies as well as the molecular dipolar and quadrupolar polarizabilities. The geometry dependence of the distributed polarizability models has been explored by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For each considered model, the distributed polarizability components have been fitted as a function of the geometry by a Taylor expansion in monomer coordinate displacements up to the sum of powers equal to 4.« less

Clustering of water molecules in ultramicroporous carbon: In-situ small-angle neutron scattering

DOE PAGES

Bahadur, Jitendra; Contescu, Cristian I.; Rai, Durgesh K.; ...

2016-10-19

The adsorption of water is central to most of the applications of microporous carbon as adsorbent material. We report early kinetics of water adsorption in the microporous carbon using in-situ small-angle neutron scattering. It is observed that adsorption of water occurs via cluster formation of molecules. Interestingly, the cluster size remains constant throughout the adsorption process whereas number density of clusters increases with time. The role of surface chemistry of microporous carbon on the early kinetics of adsorption process was also investigated. Lastly, the present study provides direct experimental evidence for cluster assisted adsorption of water molecules in microporous carbonmore » (Do-Do model).« less

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.

A programmable DNA origami nanospring that reveals force-induced adjacent binding of myosin VI heads

PubMed Central

Iwaki, M.; Wickham, S. F.; Ikezaki, K.; Yanagida, T.; Shih, W. M.

2016-01-01

Mechanosensitive biological nanomachines such as motor proteins and ion channels regulate diverse cellular behaviour. Combined optical trapping with single-molecule fluorescence imaging provides a powerful methodology to clearly characterize the mechanoresponse, structural dynamics and stability of such nanomachines. However, this system requires complicated experimental geometry, preparation and optics, and is limited by low data-acquisition efficiency. Here we develop a programmable DNA origami nanospring that overcomes these issues. We apply our nanospring to human myosin VI, a mechanosensory motor protein, and demonstrate nanometre-precision single-molecule fluorescence imaging of the individual motor domains (heads) under force. We observe force-induced transitions of myosin VI heads from non-adjacent to adjacent binding, which correspond to adapted roles for low-load and high-load transport, respectively. Our technique extends single-molecule studies under force and clarifies the effect of force on biological processes. PMID:27941751

A programmable DNA origami nanospring that reveals force-induced adjacent binding of myosin VI heads.

PubMed

Iwaki, M; Wickham, S F; Ikezaki, K; Yanagida, T; Shih, W M

2016-12-12

Mechanosensitive biological nanomachines such as motor proteins and ion channels regulate diverse cellular behaviour. Combined optical trapping with single-molecule fluorescence imaging provides a powerful methodology to clearly characterize the mechanoresponse, structural dynamics and stability of such nanomachines. However, this system requires complicated experimental geometry, preparation and optics, and is limited by low data-acquisition efficiency. Here we develop a programmable DNA origami nanospring that overcomes these issues. We apply our nanospring to human myosin VI, a mechanosensory motor protein, and demonstrate nanometre-precision single-molecule fluorescence imaging of the individual motor domains (heads) under force. We observe force-induced transitions of myosin VI heads from non-adjacent to adjacent binding, which correspond to adapted roles for low-load and high-load transport, respectively. Our technique extends single-molecule studies under force and clarifies the effect of force on biological processes.

Dinitrogen Fixation Within and Adjacent to Oxygen Deficient Waters of the Eastern Tropical South Pacific Ocean

NASA Astrophysics Data System (ADS)

Widner, B.; Mulholland, M. R.; Bernhardt, P. W.; Chang, B. X.; Jayakumar, A.

2016-02-01

Recent work suggests that planktonic diazotrophs are geographically more widely distributed than previously thought including relatively warm (14-23oC) aphotic oxygenated pelagic waters and in aphotic waters within oxygen deficient zones. Because the volume of aphotic water in the ocean is large and may increase in the future, if dinitrogen (N2) fixation is widely occurring at sub-euphotic depths, this could result in a dramatic upward revision of global nitrogen (N) inputs via this process. N2 fixation rates were measured during a cruise in the Eastern Tropical South Pacific using stable isotope tracer techniques that account for slow gas dissolution. Results are compared with light, nutrient, and oxygen gradients (and necessarily temperature gradients). In addition, rates of N2 fixation made in vertical profiles within and above oxygen deficient waters are compared with those measured in vertical profiles adjacent to oxygen deficient waters. Results suggest that while rates of N2 fixation were measurable in deeper anoxic waters, volumetric N2 fixation rates were higher in surface waters.

A Raman spectroscopy study on the effects of intermolecular hydrogen bonding on water molecules absorbed by borosilicate glass surface

NASA Astrophysics Data System (ADS)

Li, Fabing; Li, Zhanlong; Wang, Ying; Wang, Shenghan; Wang, Xiaojun; Sun, Chenglin; Men, Zhiwei

2018-05-01

The structural forms of water/deuterated water molecules located on the surface of borosilicate capillaries have been first investigated in this study on the basis of the Raman spectral data obtained at different temperatures and under atmospheric pressure for molecules in bulk and also for molecules absorbed by borosilicate glass surface. The strongest two fundamental bands locating at 3063 cm-1 (2438 cm-1) in the recorded Raman spectra are assigned here to the Osbnd H (Osbnd D) bond stretching vibrations and they are compared with the corresponding bands observed at 3124 cm-1 (2325 cm-1) in the Raman spectrum of ice Ih. Our spectroscopic observations have indicated that the structure of water and deuterated water molecules on borosilicate surface is similar to that of ice Ih (hexagonal phase of ice). These observations have also indicated that water molecules locate on the borosilicate surface so as to construct a bilayer structure and that strong and weak intermolecular hydrogen bonds are formed between water/deuterated molecules and silanol groups on borosilicate surface. In accordance with these findings, water and deuterated water molecules at the interface of capillary have a higher melting temperature.

Weakly bound water structure, bond valence saturation and water dynamics at the goethite (100) surface/aqueous interface: ab initio dynamical simulations.

PubMed

Chen, Ying; Bylaska, Eric J; Weare, John H

2017-03-31

Many important geochemical and biogeochemical reactions occur in the mineral/formation water interface of the highly abundant mineral, goethite [α-Fe(OOH)]. Ab initio molecular dynamics (AIMD) simulations of the goethite α-FeOOH (100) surface and the structure, water bond formation and dynamics of water molecules in the mineral/aqueous interface are presented. Several exchange correlation functionals were employed (PBE96, PBE96 + Grimme, and PBE0) in the simulations of a (3 × 2) goethite surface with 65 absorbed water molecules in a 3D-periodic supercell (a = 30 Å, FeOOH slab ~12 Å thick, solvation layer ~18 Å thick). The lowest energy goethite (100) surface termination model was determined to have an exposed surface Fe 3+ that was loosely capped by a water molecule and a shared hydroxide with a neighboring surface Fe 3+ . The water molecules capping surface Fe 3+ ions were found to be loosely bound at all DFT levels with and without Grimme corrections, indicative that each surface Fe 3+ was coordinated with only five neighbors. These long bonds were supported by bond valence theory calculations, which showed that the bond valence of the surface Fe 3+ was saturated and surface has a neutral charge. The polarization of the water layer adjacent to the surface was found to be small and affected only the nearest water. Analysis by density difference plots and localized Boys orbitals identified three types of water molecules: those loosely bound to the surface Fe 3+ , those hydrogen bonded to the surface hydroxyl, and bulk water with tetrahedral coordination. Boys orbital analysis showed that the spin down lone pair orbital of the weakly absorbed water interact more strongly with the spin up Fe 3+ ion. These weakly bound surface water molecules were found to rapidly exchange with the second water layer (~0.025 exchanges/ps) using a dissociative mechanism. Water molecules adjacent to the surface were found to only weakly interact with the surface and as a

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.

The molecular inventory around protostars: water, organic molecules, and the missing oxygen problem

NASA Astrophysics Data System (ADS)

Neufeld, David A.

2018-06-01

Massive star formation is accompanied by significant chemical evolution in the surrounding interstellar gas. Here, grains are heated up and icy mantles evaporate, releasing a rich inventory of water and organic molecules into the gas-phase within “hot core” regions surrounding massive protostars. Because molecules on the grain surface present broad infrared features without rotational structure, only the most abundant molecules can be identified unambiguously in the solid phase; once released into the gas-phase, however, where they are free to rotate, the constituents of grain mantles can be identified easily by means of rotational spectroscopy at millimeter and submillimeter wavelengths or through rovibrational spectroscopy in the mid-infrared. While observations of pure-rotational emission lines provide a broad view of hot core chemistry, absorption line spectroscopy of rovibrational transitions can probe the very hottest material closest to the protostar. With access to the mid-infrared spectral region from above 99% of Earth’s water vapor, SOFIA provides a unique platform for high-resolution rovibrational spectroscopy of water and organic molecules, many of which have vibrational transitions in the 5 – 8 micron spectral region that is unobservable from the ground. High spectral resolution is essential for disentangling the rotational structure and providing reliable measurements of the molecular column densities and temperatures. Future SOFIA observations will help elucidate the inventory of water and organic molecules around young protostars, and can address a puzzle related to the “oxygen budget” in the interstellar medium: surprisingly, the main interstellar reservoirs of the third-most abundant element in the Universe have yet to be identified.

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.

Monitoring for a specific management objective: protection of shorebird foraging habitat adjacent to a waste water treatment plant.

PubMed

Morris, Liz; Petch, David; May, David; Steele, William K

2017-05-01

Intertidal invertebrates are often used in environmental monitoring programs as they are good indicators of water quality and an important food source for many species of fish and birds. We present data from a monitoring program where the primary aim is to report on the condition of the potential invertebrate prey abundance, biomass and diversity for migrating shorebirds on mudflats adjacent to a waste water treatment plant in a Ramsar listed wetland in Victoria, Australia. A key threat to the foraging habitat at this site has been assessed as a reduction in potential prey items as a result of the changes to the waste water treatment processes. We use control charts, which summarise data from intertidal mudflats across the whole shoreline of the adjacent waste water treatment plant, to elicit a management response when trigger levels are reached. We then examine data from replicate discharge and control sites to determine the most appropriate management response. The monitoring program sits within an adaptive management framework where management decisions are reviewed and the data is examined at different scales to evaluate and modify our models of the likely outcomes of management actions. This study provides a demonstration of the process undertaken in a year when trigger levels were reached and a management decision was required. This highlights the importance of monitoring data from a range of scales in reducing uncertainty and improving decision making in complex systems.

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

PubMed

Kuffel, Anna; Zielkiewicz, Jan

2016-02-14

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.

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.

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. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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.

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.

Building better water models using the shape of the charge distribution of a water molecule

NASA Astrophysics Data System (ADS)

Dharmawardhana, Chamila Chathuranga; Ichiye, Toshiko

2017-11-01

The unique properties of liquid water apparently arise from more than just the tetrahedral bond angle between the nuclei of a water molecule since simple three-site models of water are poor at mimicking these properties in computer simulations. Four- and five-site models add partial charges on dummy sites and are better at modeling these properties, which suggests that the shape of charge distribution is important. Since a multipole expansion of the electrostatic potential describes a charge distribution in an orthogonal basis set that is exact in the limit of infinite order, multipoles may be an even better way to model the charge distribution. In particular, molecular multipoles up to the octupole centered on the oxygen appear to describe the electrostatic potential from electronic structure calculations better than four- and five-site models, and molecular multipole models give better agreement with the temperature and pressure dependence of many liquid state properties of water while retaining the computational efficiency of three-site models. Here, the influence of the shape of the molecular charge distribution on liquid state properties is examined by correlating multipoles of non-polarizable water models with their liquid state properties in computer simulations. This will aid in the development of accurate water models for classical simulations as well as in determining the accuracy needed in quantum mechanical/molecular mechanical studies and ab initio molecular dynamics simulations of water. More fundamentally, this will lead to a greater understanding of how the charge distribution of a water molecule leads to the unique properties of liquid water. In particular, these studies indicate that p-orbital charge out of the molecular plane is important.

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.

Reaction Kinetics of Water Molecules with Oxygen Vacancies on Rutile TiO 2(110)

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 TiO 2(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 OD b and OH b on TiO 2(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 O 2 or annealed in the temperature range of 400 – 600more » 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 TiO 2(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 E a = 0.545 eV, ΔE a(FWHM) = 0.125 eV, and a “normal” prefactor, v = 10 12 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 Ti 5c rows on the reduced TiO 2(110) surface, which suggests that the diffusion of water controls the water – V O reaction rate.« less

Measurements of water molecule density by tunable diode laser absorption spectroscopy in dielectric barrier discharges with gas-water interface

NASA Astrophysics Data System (ADS)

Tachibana, Kunihide; Nakamura, Toshihiro; Kawasaki, Mitsuo; Morita, Tatsuo; Umekawa, Toyofumi; Kawasaki, Masahiro

2018-01-01

We measured water molecule (H2O) density by tunable diode-laser absorption spectroscopy (TDLAS) for applications in dielectric barrier discharges (DBDs) with a gas-water interface. First, the effects of water temperature and presence of gas flow were tested using a Petri dish filled with water and a gas injection nozzle. Second, the TDLAS system was applied to the measurements of H2O density in two types of DBDs; one was a normal (non-inverted) type with a dielectric-covered electrode above a water-filled counter electrode and the other was an inverted type with a water-suspending mesh electrode above a dielectric-covered counter electrode. The H2O density in the normal DBD was close to the density estimated from the saturated vapor pressure, whereas the density in the inverted DBD was about half of that in the former type. The difference is attributed to the upward gas flow in the latter type, that pushes the water molecules up towards the gas-water interface.

STICKING OF MOLECULES ON NONPOROUS AMORPHOUS WATER ICE

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Jiao; Vidali, Gianfranco; Acharyya, Kinsuk, E-mail: gvidali@syr.edu

2016-05-20

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 H{sub 2}, D{sub 2}, N{sub 2}, O{sub 2}, CO, CH{sub 4}, and CO{sub 2} on nonporous amorphous solid water. The sticking coefficient was measured over a widemore » 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.« less

Different catalytic effects of a single water molecule: the gas-phase reaction of formic acid with hydroxyl radical in water vapor.

PubMed

Anglada, Josep M; Gonzalez, Javier

2009-12-07

The effect of a single water molecule on the reaction mechanism of the gas-phase reaction between formic acid and the hydroxyl radical was investigated with high-level quantum mechanical calculations using DFT-B3LYP, MP2 and CCSD(T) theoretical approaches in concert with the 6-311+G(2df,2p) and aug-cc-pVTZ basis sets. The reaction between HCOOH and HO has a very complex mechanism involving a proton-coupled electron transfer process (pcet), two hydrogen-atom transfer reactions (hat) and a double proton transfer process (dpt). The hydroxyl radical predominantly abstracts the acidic hydrogen of formic acid through a pcet mechanism. A single water molecule affects each one of these reaction mechanisms in different ways, depending on the way the water interacts. Very interesting is also the fact that our calculations predict that the participation of a single water molecule results in the abstraction of the formyl hydrogen of formic acid through a hydrogen atom transfer process (hat).

Geometry-dependent atomic multipole models for the water molecule.

PubMed

Loboda, O; Millot, C

2017-10-28

Models of atomic electric multipoles for the water molecule have been optimized in order to reproduce the electric potential around the molecule computed by ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set. Different models of increasing complexity, from atomic charges up to models containing atomic charges, dipoles, and quadrupoles, have been obtained. The geometry dependence of these atomic multipole models has been investigated by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For several models, the atomic multipole components have been fitted as a function of the geometry by a Taylor series of fourth order in monomer coordinate displacements.

Geometry-dependent atomic multipole models for the water molecule

NASA Astrophysics Data System (ADS)

Loboda, O.; Millot, C.

2017-10-01

Models of atomic electric multipoles for the water molecule have been optimized in order to reproduce the electric potential around the molecule computed by ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set. Different models of increasing complexity, from atomic charges up to models containing atomic charges, dipoles, and quadrupoles, have been obtained. The geometry dependence of these atomic multipole models has been investigated by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For several models, the atomic multipole components have been fitted as a function of the geometry by a Taylor series of fourth order in monomer coordinate displacements.

Contrasting stream water NO3- and Ca2+ in two nearly adjacent catchments: the role of soil Ca and forest vegetation

Treesearch

Sheila F. Christopher; Blair D. Page; John L. Campbell; Myron J. Mitchell

2006-01-01

Two nearly adjacent subcatchments, located in the Adirondack Mountains of New York State, US, with similar atmospheric inputs of N (0.6 kmol ha-1 yr-1), but markedly different stream water solute concentrations, provided a unique opportunity to evaluate the mechanisms causing this variation.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo Liushan; Huang Xiaoyuan; Wang Ning

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 weremore » synthesized under solvothermal conditions.« less

Control of unidirectional transport of single-file water molecules through carbon nanotubes in an electric field.

PubMed

Su, Jiaye; Guo, Hongxia

2011-01-25

The transport of water molecules through nanopores is not only crucial to biological activities but also useful for designing novel nanofluidic devices. Despite considerable effort and progress that has been made, a controllable and unidirectional water flow is still difficult to achieve and the underlying mechanism is far from being understood. In this paper, using molecular dynamics simulations, we systematically investigate the effects of an external electric field on the transport of single-file water molecules through a carbon nanotube (CNT). We find that the orientation of water molecules inside the CNT can be well-tuned by the electric field and is strongly coupled to the water flux. This orientation-induced water flux is energetically due to the asymmetrical water-water interaction along the CNT axis. The wavelike water density profiles are disturbed under strong field strengths. The frequency of flipping for the water dipoles will decrease as the field strength is increased, and the flipping events vanish completely for the relatively large field strengths. Most importantly, a critical field strength E(c) related to the water flux is found. The water flux is increased as E is increased for E ≤ E(c), while it is almost unchanged for E > E(c). Thus, the electric field offers a level of governing for unidirectional water flow, which may have some biological applications and provides a route for designing efficient nanopumps.

Cavity mutants of Savinase. Crystal structures and differential scanning calorimetry experiments give hints of the function of the buried water molecules in subtilisins.

PubMed

Pedersen, J T; Olsen, O H; Betzel, C; Eschenburg, S; Branner, S; Hastrup, S

1994-09-23

The subtilisin molecule possesses several internal water molecules, which may be characterised as an integral part of the protein structure. We have introduced specific mutations (T71I, T71S, T71V, T71A and T71G) at position 71 in the subtilisin variant Savinase from Bacillus lentus. This position is involved in a hydrogen bonded network with several internal water molecules, forming a water channel. The water channel and most of the other internal water molecules are positioned in the interface between two half-domains of the subtilisin molecule. The data presented here indicate that the internal water molecules are structural, and may be the result of trapping during the folding process.

[Characteristics of ichthyoplankton assemblages in Yangtze Estuary and adjacent waters in spring].

PubMed

Liu, Shu-De; Xian, Wei-Wei; Liu, Dong

2008-10-01

Based on the investigation data of ichthyoplankton assemblages and environmental factors in Yangtze Estuary and adjacent waters in May 1999 and 2001, the characteristics of ichthyoplankton assemblages in these areas in spring were studied by using TWINSPAN (two-way indicator species analysis) and CCA (canonical correspondence analysis). A total of 11 540 ichthyoplankton individuals were taxonomically identified, belonging to 11 orders, 18 families and 32 species, of which, Coilia mystus, Engraulis japonicus, Chaeturichthys hexanema, Allanetta bleekeri, and Trachidermis fasciatus were the dominant species. The ichthyoplankton communities were classified into three assemblages by using TWINSPAN, i.e., estuarine assemblage dominated by C. mystus, coastal assemblage dominated by A. bleekeri and T. fasciatus; and shelf assemblage featured by E. japonicus and C. hexanema. The CCA ordination of the interrelations among the three assemblages and their correlations to the environmental variables revealed that salinity, depth, dissolved oxygen, and total suspended particulate matter were the major factors affecting the ichthyoplankton assemblages in the study areas.

What Gives an Insulin Hexamer Its Unique Shape and Stability? Role of Ten Confined Water Molecules.

PubMed

Mukherjee, Saumyak; Mondal, Sayantan; Deshmukh, Ashish Anilrao; Gopal, Balasubramanian; Bagchi, Biman

2018-02-08

Self-assembly of proteins often gives rise to interesting quasi-stable structures that serve important biological purposes. Insulin hexamer is such an assembly. While monomer is the biologically active form of insulin, hexamer serves as the storehouse of the hormone. The hexamer also prevents the formation of higher order aggregates. While several studies explored the role of bivalent metal ions like Zn 2+ , Ca 2+ , etc., in the stabilization of the hexameric form, the role of water molecules has been ignored. We combine molecular dynamics simulations, quantum calculations, and X-ray analyses to discover that a team of approximately 10 water molecules confined inside a barrel-shaped nanocavity at the center of insulin hexamer is one of the major causes that account for the unusual stability of the biomolecular assembly. These cavity water molecules exhibit interesting dynamical features like intermittent escape and reentrance. We find that these water molecules are dynamically slower than the bulk and weave an intricate hydrogen bond network among themselves and with neighboring protein residues to generate a robust backbone at the center of the hexamer that holds the association strongly from inside and maintains the barrel shape.

Specific intermolecular interactions of conserved water molecules with amino acids in the Galectin-1 carbohydrate recognition domain

NASA Astrophysics Data System (ADS)

Di Lella, Santiago; Petruk, Ariel A.; Armiño, Diego J. Alonso de; Álvarez, Rosa M. S.

2010-08-01

Water molecules, rigidly associated to protein surfaces, play a key role in stabilizing biomolecules and participating in their biological functions. Recent studies on the solvation properties of the carbohydrate recognition domain of Galectin-1 by means of molecular dynamic simulations have revealed the existence of several water sites which were well correlated to both the bound water molecules observed in the crystal structure of the protein in the free state and to some of the hydroxyl groups of the carbohydrate ligand observed in the crystal structure of the complexed protein. In this work, we present a study using quantum mechanical methods (B3LYP/6-311++G(3df,3dp)//B3LYP/6-31+G(d)) to determine the energy involved in the binding of these water molecules to specific amino acids in the carbohydrate recognition domain of the protein. By modeling the hydroxyl groups of the carbohydrate by methanol, the energies associated to the local interactions between the ligand and the protein have been evaluated by replacing specific water molecules with methanol. The values of the binding energies have been compared to those previously obtained by the molecular dynamic method.

Water Molecules and Hydrogen-Bonded Networks in Bacteriorhodopsin—Molecular Dynamics Simulations of the Ground State and the M-Intermediate

PubMed Central

Grudinin, Sergei; Büldt, Georg; Gordeliy, Valentin; Baumgaertner, Artur

2005-01-01

Protein crystallography provides the structure of a protein, averaged over all elementary cells during data collection time. Thus, it has only a limited access to diffusive processes. This article demonstrates how molecular dynamics simulations can elucidate structure-function relationships in bacteriorhodopsin (bR) involving water molecules. The spatial distribution of water molecules and their corresponding hydrogen-bonded networks inside bR in its ground state (G) and late M intermediate conformations were investigated by molecular dynamics simulations. The simulations reveal a much higher average number of internal water molecules per monomer (28 in the G and 36 in the M) than observed in crystal structures (18 and 22, respectively). We found nine water molecules trapped and 19 diffusive inside the G-monomer, and 13 trapped and 23 diffusive inside the M-monomer. The exchange of a set of diffusive internal water molecules follows an exponential decay with a 1/e time in the order of 340 ps for the G state and 460 ps for the M state. The average residence time of a diffusive water molecule inside the protein is ∼95 ps for the G state and 110 ps for the M state. We have used the Grotthuss model to describe the possible proton transport through the hydrogen-bonded networks inside the protein, which is built up in the picosecond-to-nanosecond time domains. Comparing the water distribution and hydrogen-bonded networks of the two different states, we suggest possible pathways for proton hopping and water movement inside bR. PMID:15731388

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.

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

[Interactions of DNA bases with individual water molecules. Molecular mechanics and quantum mechanics computation results vs. experimental data].

PubMed

Gonzalez, E; Lino, J; Deriabina, A; Herrera, J N F; Poltev, V I

2013-01-01

To elucidate details of the DNA-water interactions we performed the calculations and systemaitic search for minima of interaction energy of the systems consisting of one of DNA bases and one or two water molecules. The results of calculations using two force fields of molecular mechanics (MM) and correlated ab initio method MP2/6-31G(d, p) of quantum mechanics (QM) have been compared with one another and with experimental data. The calculations demonstrated a qualitative agreement between geometry characteristics of the most of local energy minima obtained via different methods. The deepest minima revealed by MM and QM methods correspond to water molecule position between two neighbor hydrophilic centers of the base and to the formation by water molecule of hydrogen bonds with them. Nevertheless, the relative depth of some minima and peculiarities of mutual water-base positions in' these minima depend on the method used. The analysis revealed insignificance of some differences in the results of calculations performed via different methods and the importance of other ones for the description of DNA hydration. The calculations via MM methods enable us to reproduce quantitatively all the experimental data on the enthalpies of complex formation of single water molecule with the set of mono-, di-, and trimethylated bases, as well as on water molecule locations near base hydrophilic atoms in the crystals of DNA duplex fragments, while some of these data cannot be rationalized by QM calculations.

On the Role of Water Models in Quantifying the Binding Free Energy of Highly Conserved Water Molecules in Proteins: The Case of Concanavalin A.

PubMed

Fadda, Elisa; Woods, Robert J

2011-10-11

The ability of ligands to displace conserved water molecules in protein binding sites is of significant interest in drug design and is particularly pertinent in the case of glycomimetic drugs. This concept was explored in previous work [ Clarke et al. J. Am. Chem. Soc. 2001 , 123 , 12238 - 12247 and Kadirvelraj et al. J. Am. Chem. Soc. 2008 , 130 , 16933 - 16942 ] for a highly conserved water molecule located in the binding site of the prototypic carbohydrate-binding protein Concanavalin A (Con A). A synthetic ligand was designed with the aim of displacing such water. While the synthetic ligand bound to Con A in an analogous manner to that of the natural ligand, crystallographic analysis demonstrated that it did not displace the conserved water. In order to quantify the affinity of this particular water for the Con A surface, we report here the calculated standard binding free energy for this water in both ligand-bound and free Con A, employing three popular water models: TIP3P, TIP4P, and TIP5P. Although each model was developed to perform well in simulations of bulk-phase water, the computed binding energies for the isolated water molecule displayed a high sensitivity to the model. Both molecular dynamics simulation and free energy results indicate that the choice of water model may greatly influence the characterization of surface water molecules as conserved (TIP5P) or not (TIP3P) in protein binding sites, an observation of considerable significance to rational drug design. Structural and theoretical aspects at the basis of the different behaviors are identified and discussed.

Dynamic water patterns change the stability of the collapsed filter conformation of the KcsA K+ channel

PubMed Central

2017-01-01

The selectivity filter of the KcsA K+ channel has two typical conformations—the conductive and the collapsed conformations, respectively. The transition from the conductive to the collapsed filter conformation can represent the process of inactivation that depends on many environmental factors. Water molecules permeating behind the filter can influence the collapsed filter stability. Here we perform the molecular dynamics simulations to study the stability of the collapsed filter of the KcsA K+ channel under the different water patterns. We find that the water patterns are dynamic behind the collapsed filter and the filter stability increases with the increasing number of water molecules. In addition, the stability increases significantly when water molecules distribute uniformly behind the four monomeric filter chains, and the stability is compromised if water molecules only cluster behind one or two adjacent filter chains. The altered filter stabilities thus suggest that the collapsed filter can inactivate gradually under the dynamic water patterns. We also demonstrate how the different water patterns affect the filter recovery from the collapsed conformation. PMID:29049423

Dynamic water patterns change the stability of the collapsed filter conformation of the KcsA K+ channel.

PubMed

Wu, Di

2017-01-01

The selectivity filter of the KcsA K+ channel has two typical conformations-the conductive and the collapsed conformations, respectively. The transition from the conductive to the collapsed filter conformation can represent the process of inactivation that depends on many environmental factors. Water molecules permeating behind the filter can influence the collapsed filter stability. Here we perform the molecular dynamics simulations to study the stability of the collapsed filter of the KcsA K+ channel under the different water patterns. We find that the water patterns are dynamic behind the collapsed filter and the filter stability increases with the increasing number of water molecules. In addition, the stability increases significantly when water molecules distribute uniformly behind the four monomeric filter chains, and the stability is compromised if water molecules only cluster behind one or two adjacent filter chains. The altered filter stabilities thus suggest that the collapsed filter can inactivate gradually under the dynamic water patterns. We also demonstrate how the different water patterns affect the filter recovery from the collapsed conformation.

Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules.

PubMed

Haider, Kamran; Huggins, David J

2013-10-28

Intermolecular interactions in the aqueous phase must compete with the interactions between the two binding partners and their solvating water molecules. In biological systems, water molecules in protein binding sites cluster at well-defined hydration sites and can form strong hydrogen-bonding interactions with backbone and side-chain atoms. Displacement of such water molecules is only favorable when the ligand can form strong compensating hydrogen bonds. Conversely, water molecules in hydrophobic regions of protein binding sites make only weak interactions, and the requirements for favorable displacement are less stringent. The propensity of water molecules for displacement can be identified using inhomogeneous fluid solvation theory (IFST), a statistical mechanical method that decomposes the solvation free energy of a solute into the contributions from different spatial regions and identifies potential binding hotspots. In this study, we employed IFST to study the displacement of water molecules from the ATP binding site of Hsp90, using a test set of 103 ligands. The predicted contribution of a hydration site to the hydration free energy was found to correlate well with the observed displacement. Additionally, we investigated if this correlation could be improved by using the energetic scores of favorable probe groups binding at the location of hydration sites, derived from a multiple copy simultaneous search (MCSS) method. The probe binding scores were not highly predictive of the observed displacement and did not improve the predictivity when used in combination with IFST-based hydration free energies. The results show that IFST alone can be used to reliably predict the observed displacement of water molecules in Hsp90. However, MCSS can augment IFST calculations by suggesting which functional groups should be used to replace highly displaceable water molecules. Such an approach could be very useful in improving the hit-to-lead process for new drug targets.

The spontaneous synchronized dance of pairs of water molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roncaratti, Luiz F.; Instituto de Física, Universidade de Brasília, 70910-900 Brasília; Cappelletti, David, E-mail: david.cappelletti@unipg.it

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 coupledmore » 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.« less

The spontaneous synchronized dance of pairs of water molecules

NASA Astrophysics Data System (ADS)

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

2014-03-01

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.

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.

The δ18O of Atmospheric Water Vapour is Recorded in the Oxygen Isotope Ratios of Leaf water and Organic Molecules at High Relative Humidity

NASA Astrophysics Data System (ADS)

Lehmann, M. M.; Goldsmith, G. R.; Schmid, L.; Siegwolf, R. T.; Gessler, A.; Saurer, M.

2016-12-01

The oxygen stable isotope ratios (δ18O) of water and organic molecules in plants hold information about plant physiology, ecohydrology, and environmental conditions. For instance, the δ18O ratio of leaf water reflects both the δ18O ratios of water in the soil and in the atmosphere. This water, which is incorporated into organic molecules at the time of synthesis, thus serves to record the environment in which the plant was growing. However, how δ18O of atmospheric water vapour affects the δ18O ratio of organic molecules remains poorly understood. In order to investigate the effects of fog and rain (e.g. high atmospheric water availability) on δ18O ratios of leaf water and organic molecules, we exposed oak tree saplings (Quercus robur) in wet and dry soil treatments to 18O-depleted water vapour at ca. 90% relative humidity for 5 h. We harvested plant material over 24 h to trace the movement of the isotopic label in water and organics throughout the plant from the leaves to the stem. The atmospheric water vapour caused a strong 18O-depletion in leaf and xylem water, as well as in leaf carbohydrates, with the most negative ratios observed at the end of the fogging. Moreover, the label was clearly observed in twig and stem phloem carbohydrates following a short delay. A detailed compound-specific isotope analysis of the leaf carbohydrates revealed that the label caused an 18O-depletion in fructose, glucose, and sucrose. Quercitol, an oak-specific alditol, did not show 18O-depletion. Clear soil moisture treatment effects were only observed for twig phloem carbohydrates, with a stronger 18O-depletion in wet plants than in dry plants, suggesting retarded leaf-to-phloem sugar export in trees under drought. We demonstrate that labelling with 18O-depleted water is a potential tool to trace the movement and incorporation of oxygen stable isotopes in plants. We clearly show that changes in δ18O of atmospheric water vapour are quickly imprinted on leaf water and

Effects of Water Molecule on CO Oxidation by OH: Reaction Pathways, Kinetic Barriers, and Rate Constants.

PubMed

Zhang, Linyao; Yang, Li; Zhao, Yijun; Zhang, Jiaxu; Feng, Dongdong; Sun, Shaozeng

2017-07-06

The water dilute oxy-fuel combustion is a clean combustion technology for near-zero emission power; and the presence of water molecule could have both kinetic and dynamic effects on combustion reactions. The reaction OH + CO → CO 2 + H, one of the most important elementary reactions, has been investigated by extensive electronic structure calculations. And the effects of a single water molecule on CO oxidation have been studied by considering the preformed OH(H 2 O) complex reacts with CO. The results show little change in the reaction pathways, but the additional water molecule actually increases the vibrationally adiabatic energy barriers (V a G ). Further thermal rate constant calculations in the temperature range of 200 to 2000 K demonstrate that the total low-pressure limit rate constant for the water assisted OH(H 2 O) + CO → CO 2 + H 2 O + H reaction is 1-2 orders lower than that of the water unassisted one, which is consistent with the change of V a G . Therefore, the hydrated radical OH(H 2 O) would actually slow down the oxidation of CO. Meanwhile, comparisons show that the M06-2X/aug-cc-pVDZ method gives a much better estimation in energy and thus is recommended to be employed for direct dynamics simulations.

Water quality in the lower Puyallup River valley and adjacent uplands, Pierce County, Washington

USGS Publications Warehouse

Ebbert, J.C.; Bortleson, Gilbert C.; Fuste, L.A.; Prych, E.A.

1987-01-01

The quality of most ground and surface water within and adjacent to the lower Puyallup River valley is suitable for most typical uses; however, some degradation of shallow groundwater quality has occurred. High concentrations of iron and manganese were found in groundwater, sampled at depths of < 40 ft, from wells tapping alluvial aquifers and in a few wells tapping deeper aquifers. Volatile and acid- and base/neutral-extractable organic compounds were not detected in either shallow or deep groundwater samples. The quality of shallow groundwater was generally poorer than that of deep water. Deep ground water (wells set below 100 ft) appears suitable as a supplementary water supply for fish-hatchery needs. Some degradation of water quality, was observed downstream from river mile 1.7 where a municipal wastewater-treatment plant discharges into the river. In the Puyallup River, the highest concentrations of most trace elements were found in bed sediments collected downstream from river mile 1.7. Median concentrations of arsenic, lead, and zinc were higher in bed sediments from small streams compared with those from the Puyallup River, possibly because the small stream drainages, which are almost entirely within developed areas, receive more urban runoff as a percentage of total flow. Total-recoverable trace-element concentrations exceeded water-quality criteria for acute toxicity in the Puyallup River and in some of the small streams. In most cases, high concentrations of total-recoverable trace elements occurred when suspended-sediment concentrations were high. Temperatures in all streams except Wapato Creek and Fife Dutch were within limits (18 C) for Washington State class A water. Minimum dissolved oxygen concentrations were relatively low at 5.6 and 2.0 mg/L, respectively, for Wapato Creek and Fife Dutch. The poorest surface-water quality, which can be characterized as generally unsuitable for fish, was in Fife Dutch, a manmade channel and therefore

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.

Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks.

PubMed

Rudling, Axel; Orro, Adolfo; Carlsson, Jens

2018-02-26

Water plays a major role in ligand binding and is attracting increasing attention in structure-based drug design. Water molecules can make large contributions to binding affinity by bridging protein-ligand interactions or by being displaced upon complex formation, but these phenomena are challenging to model at the molecular level. Herein, networks of ordered water molecules in protein binding sites were analyzed by clustering of molecular dynamics (MD) simulation trajectories. Locations of ordered waters (hydration sites) were first identified from simulations of high resolution crystal structures of 13 protein-ligand complexes. The MD-derived hydration sites reproduced 73% of the binding site water molecules observed in the crystal structures. If the simulations were repeated without the cocrystallized ligands, a majority (58%) of the crystal waters in the binding sites were still predicted. In addition, comparison of the hydration sites obtained from simulations carried out in the absence of ligands to those identified for the complexes revealed that the networks of ordered water molecules were preserved to a large extent, suggesting that the locations of waters in a protein-ligand interface are mainly dictated by the protein. Analysis of >1000 crystal structures showed that hydration sites bridged protein-ligand interactions in complexes with different ligands, and those with high MD-derived occupancies were more likely to correspond to experimentally observed ordered water molecules. The results demonstrate that ordered water molecules relevant for modeling of protein-ligand complexes can be identified from MD simulations. Our findings could contribute to development of improved methods for structure-based virtual screening and lead optimization.

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

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.

Simulation and analysis of soil-water conditions in the Great Plains and adjacent areas, central United States, 1951-80

USGS Publications Warehouse

Dugan, Jack T.; Zelt, Ronald B.

2000-01-01

Ground-water recharge and consumptive-irrigation requirements in the Great Plains and adjacent areas largely depend upon an environment extrinsic to the ground-water system. This extrinsic environment, which includes climate, soils, and vegetation, determines the water demands of evapotranspiration, the availability of soil water to meet these demands, and the quantity of soil water remaining for potential ground-water recharge after these demands are met. The geographic extent of the Great Plains contributes to large regional differences among all elements composing the extrinsic environment, particularly the climatic factors. A soil-water simulation program, SWASP, which synthesizes selected climatic, soil, and vegetation factors, was used to simulate the regional soil-water conditions during 1951-80. The output from SWASP consists of several soil-water characteristics, including surface runoff, infiltration, consumptive water requirements, actual evapotranspiration, potential recharge or deep percolation under various conditions, consumptive irrigation requirements, and net fluxes from the ground-water system under irrigated conditions. Simulation results indicate that regional patterns of potential recharge, consumptive irrigation requirements, and net fluxes from the ground-water system under irrigated conditions are largely determined by evapotranspiration and precipitation. The local effects of soils and vegetation on potential recharge cause potential recharge to vary by more than 50 percent in some areas having similar climatic conditions.

Spatial variability in the response of surface-water extent to climate extremes across the Prairie Pothole Region and adjacent Northern Prairie, United States

NASA Astrophysics Data System (ADS)

Vanderhoof, M.; Lane, C.; McManus, M.; Alexander, L. C.; Christensen, J.

2017-12-01

Surface-water extent, duration and movement will depend not only on climatic inputs but also the relative importance of different hydrologic pathways (e.g., surface storage, infiltration, evapotranspiration, stream outflows). We mapped surface-water extent from historic drought years to historic wet years spanning 1985 - 2015 across eleven Landsat path/rows representing the Prairie Pothole Region (PPR) and adjacent Northern Prairie of the United States. The PPR not only experienced a greater surface water extent under median conditions (2.6 times more) relative to the adjacent Northern Prairie, but showed a greater difference between drought and deluge conditions as well (range averaged 8.5 ha surface water km-2 relative to 2.5 ha surface water km-2 for the PPR and Northern Prairie, respectively). To explain the spatial variability in the amount of surface water expansion and contraction we used a two-stage modeling approach. First, surface-water extent was regressed on accumulated water availability (precipitation minus potential evapotranspiration). The slope of surface-water extent to climate inputs (per watershed) was our dependent variable in the second stage. That slope was regressed against independent variables representing hydrology-related landscape characteristics (e.g., infiltration capacity, surface storage capacity, stream density). Stream-connected surface water can leave via stream flow, influencing the rate at which surface-water may leave a location, therefore stream-connected and disconnected surface water were analyzed separately. Stream-connected surface water responded more strongly to wetter climatic conditions (i.e., accumulated) in landscapes with more lakes and less artificial drainage (e.g., ditching, tile drainage). Disconnected surface water responded more strongly to wetter climatic conditions when landscapes contained greater wetland density, fewer streams and a lower predicted rate of infiltration. From these findings, we can expect

Relationship between diffusivity of water molecules inside hydrating tablets and their drug release behavior elucidated by magnetic resonance imaging.

PubMed

Kikuchi, Shingo; Onuki, Yoshinori; Kuribayashi, Hideto; Takayama, Kozo

2012-01-01

We reported previously that sustained release matrix tablets showed zero-order drug release without being affected by pH change. To understand drug release mechanisms more fully, we monitored the swelling and erosion of hydrating tablets using magnetic resonance imaging (MRI). Three different types of tablets comprised of polyion complex-forming materials and a hydroxypropyl methylcellulose (HPMC) were used. Proton density- and diffusion-weighted images of the hydrating tablets were acquired at intervals. Furthermore, apparent self-diffusion coefficient maps were generated from diffusion-weighted imaging to evaluate the state of hydrating tablets. Our findings indicated that water penetration into polyion complex tablets was faster than that into HPMC matrix tablets. In polyion complex tablets, water molecules were dispersed homogeneously and their diffusivity was relatively high, whereas in HPMC matrix tablets, water molecule movement was tightly restricted within the gel. An optimal tablet formulation determined in a previous study had water molecule penetration and diffusivity properties that appeared intermediate to those of polyion complex and HPMC matrix tablets; water molecules were capable of penetrating throughout the tablets and relatively high diffusivity was similar to that in the polyion complex tablet, whereas like the HPMC matrix tablet, it was well swollen. This study succeeded in characterizing the tablet hydration process. MRI provides profound insight into the state of water molecules in hydrating tablets; thus, it is a useful tool for understanding drug release mechanisms at a molecular level.

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.

Rotational spectra of tetracyclic quinolizidine alkaloids: does a water molecule flip sparteine?

PubMed

Lesarri, Alberto; Pinacho, Ruth; Enríquez, Lourdes; Rubio, José E; Jaraíz, Martín; Abad, José L; Gigosos, Marco A

2017-07-21

Sparteine is a quinolizidine alkaloid used as a chiral auxiliary in asymmetric synthesis. We examine whether hydration by a single molecule can flip sparteine from the most stable trans conformation to the bidentate cis arrangement observed in catalytic complexation to a metal center. Sparteine and the sparteine-water dimer were generated in a supersonic jet expansion with H 2 16 O and H 2 18 O, and characterized by broadband chirped-pulse microwave spectroscopy. Even though the bidentate water dimer was predicted with larger binding energy, a single isomer was observed for the monohydrated cluster, with sparteine retaining the trans conformation observed for the free molecule. The absence of the bidentate dimer is attributed to the kinetic control of cluster formation, favoring the pre-expansion most abundant monomer. The structural properties of the O-HN hydrogen bond in the dimer are compared with those of complexes of other secondary and tertiary amines.

Sensitivity of polarization fluctuations to the nature of protein-water interactions: Study of biological water in four different protein-water systems

NASA Astrophysics Data System (ADS)

Ghosh, Rikhia; Banerjee, Saikat; Hazra, Milan; Roy, Susmita; Bagchi, Biman

2014-12-01

Since the time of Kirkwood, observed deviations in magnitude of the dielectric constant of aqueous protein solution from that of neat water (˜80) and slower decay of polarization have been subjects of enormous interest, controversy, and debate. Most of the common proteins have large permanent dipole moments (often more than 100 D) that can influence structure and dynamics of even distant water molecules, thereby affecting collective polarization fluctuation of the solution, which in turn can significantly alter solution's dielectric constant. Therefore, distance dependence of polarization fluctuation can provide important insight into the nature of biological water. We explore these aspects by studying aqueous solutions of four different proteins of different characteristics and varying sizes, chicken villin headpiece subdomain (HP-36), immunoglobulin binding domain protein G (GB1), hen-egg white lysozyme (LYS), and Myoglobin (MYO). We simulate fairly large systems consisting of single protein molecule and 20000-30000 water molecules (varied according to the protein size), providing a concentration in the range of ˜2-3 mM. We find that the calculated dielectric constant of the system shows a noticeable increment in all the cases compared to that of neat water. Total dipole moment auto time correlation function of water ⟨δMW(0)δMW(t)⟩ is found to be sensitive to the nature of the protein. Surprisingly, dipole moment of the protein and total dipole moment of the water molecules are found to be only weakly coupled. Shellwise decomposition of water molecules around protein reveals higher density of first layer compared to the succeeding ones. We also calculate heuristic effective dielectric constant of successive layers and find that the layer adjacent to protein has much lower value (˜50). However, progressive layers exhibit successive increment of dielectric constant, finally reaching a value close to that of bulk 4-5 layers away. We also calculate shellwise

Energy-switching potential energy surface for the water molecule revisited: A highly accurate singled-sheeted form.

PubMed

Galvão, B R L; Rodrigues, S P J; Varandas, A J C

2008-07-28

A global ab initio potential energy surface is proposed for the water molecule by energy-switching/merging a highly accurate isotope-dependent local potential function reported by Polyansky et al. [Science 299, 539 (2003)] with a global form of the many-body expansion type suitably adapted to account explicitly for the dynamical correlation and parametrized from extensive accurate multireference configuration interaction energies extrapolated to the complete basis set limit. The new function mimics also the complicated Sigma/Pi crossing that arises at linear geometries of the water molecule.

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.

Direct numerical solution of the Ornstein-Zernike integral equation and spatial distribution of water around hydrophobic molecules

NASA Astrophysics Data System (ADS)

Ikeguchi, Mitsunori; Doi, Junta

1995-09-01

The Ornstein-Zernike integral equation (OZ equation) has been used to evaluate the distribution function of solvents around solutes, but its numerical solution is difficult for molecules with a complicated shape. This paper proposes a numerical method to directly solve the OZ equation by introducing the 3D lattice. The method employs no approximation the reference interaction site model (RISM) equation employed. The method enables one to obtain the spatial distribution of spherical solvents around solutes with an arbitrary shape. Numerical accuracy is sufficient when the grid-spacing is less than 0.5 Å for solvent water. The spatial water distribution around a propane molecule is demonstrated as an example of a nonspherical hydrophobic molecule using iso-value surfaces. The water model proposed by Pratt and Chandler is used. The distribution agrees with the molecular dynamics simulation. The distribution increases offshore molecular concavities. The spatial distribution of water around 5α-cholest-2-ene (C27H46) is visualized using computer graphics techniques and a similar trend is observed.

33 CFR 150.35 - How may an adjacent coastal State request an amendment to the operations manual?

Code of Federal Regulations, 2010 CFR

2010-07-01

... provide equivalent or improved protection and safety. The adjacent coastal State may petition the... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false How may an adjacent coastal State... § 150.35 How may an adjacent coastal State request an amendment to the operations manual? (a) An...

33 CFR 150.35 - How may an adjacent coastal State request an amendment to the operations manual?

Code of Federal Regulations, 2012 CFR

2012-07-01

... provide equivalent or improved protection and safety. The adjacent coastal State may petition the... 33 Navigation and Navigable Waters 2 2012-07-01 2012-07-01 false How may an adjacent coastal State... § 150.35 How may an adjacent coastal State request an amendment to the operations manual? (a) An...

33 CFR 150.35 - How may an adjacent coastal State request an amendment to the operations manual?

Code of Federal Regulations, 2011 CFR

2011-07-01

... provide equivalent or improved protection and safety. The adjacent coastal State may petition the... 33 Navigation and Navigable Waters 2 2011-07-01 2011-07-01 false How may an adjacent coastal State... § 150.35 How may an adjacent coastal State request an amendment to the operations manual? (a) An...

Selected ground-water information for the Pasco basin and adjacent areas, Washington, 1986-1989

USGS Publications Warehouse

Drost, B.W.; Schurr, K.M.; Lum, W. E.

1989-01-01

The U.S. Geological Survey, in cooperation with the United States Department of Energy, conducted a study of the Pasco basin and adjacent areas, Washington, in support of the Basalt Waste Isolation Project at the Hanford site, Washington. The purpose of the study was to develop a data set that would help define the groundwater-flow system of the Pasco Basin. This report contains the basic data, without interpretation, that were collected from the start of the project in February 1986 through January 1989. Information presented is from the U.S. Bureau of Reclamation, State of Washington Department of Ecology , US Army Corps of Engineers, Kennewick Irrigation District, and the Survey, and consists of well location and construction data, records of water levels in the wells, and aquifer designations for each well. The aquifer designation represents the geohydrologic unit to which the well is reported to be open. (USGS)

Dynamic properties of individual water molecules in a hydrophobic pore lined with acyl chains: a molecular dynamics study.

PubMed

Qi, Z; Sokabe, M

1998-03-30

Recently, a certain class of synthetic molecules has been shown to form ion channels, the pore of which is lined with hydrophobic acyl chains [M. Sokabe, in: F. Oosawa, H. Hayashi, T. Yoshioka (Eds.), Transmembrane Signaling and Sensation, JSSP/VNU Science Press BV, Tokyo, 1984, p. 119; F. Hayashi, M. Sokabe, M. Takagi, K. Hayashi, U. Kishimoto, Biochim. Biophys. Acta, 510 (1978) 305; M.J. Pregel, L. Jullien, J. Canceill, L. Lacombe, J.M. Lehn, J. Chem. Soc. Perkin Trans., 2 (1995) 417; Y. Tanaka, Y. Kobuke, M. Sokabe, Angew. Chem. Int. Ed. Engl., 34 (1995) 693; M. Sokabe, Z. Qi, K. Donowaki, H. Ishida, K. Okubo, Biophys. J., 70 (1996) A201; H. Ishida, K. Donowaki, Y. Inoue, Z. Qi, M. Sokabe, Chem. Lett. (1997) p. 953]. As an initial step towards understanding the physical mechanisms of ion permeation across such a hydrophobic pore, systematic molecular dynamics simulations were performed to investigate dynamic and energetic properties of water molecules inside the pore using a dimer of alanine-N'-acylated cyclic peptide as a channel model. Dynamic energy profiles for water molecules indicated that the energy barrier at the middle region of the pore is approximately 2-3 kcal/mol higher than that in the cap water region which was defined as a vicinity region of the channel entrance. Energetics analyses demonstrated that the mutual interactions among intrapore water molecules are the major factor to give favorable interaction (negative energy contribution) for themselves. The pore, despite being lined with acyl chains, has a favorable van der Waals interaction with intrapore water molecules. These results may help to explain why water-filled channels can be formed by the hydrophobic helices in natural channels.

Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding

PubMed Central

2013-01-01

Background Human triosephosphate isomerase (HsTIM) deficiency is a genetic disease caused often by the pathogenic mutation E104D. This mutation, located at the side of an abnormally large cluster of water in the inter-subunit interface, reduces the thermostability of the enzyme. Why and how these water molecules are directly related to the excessive thermolability of the mutant have not been investigated in structural biology. Results This work compares the structure of the E104D mutant with its wild type counterparts. It is found that the water topology in the dimer interface of HsTIM is atypical, having a "wet-core-dry-rim" distribution with 16 water molecules tightly packed in a small deep region surrounded by 22 residues including GLU104. These water molecules are co-conserved with their surrounding residues in non-archaeal TIMs (dimers) but not conserved across archaeal TIMs (tetramers), indicating their importance in preserving the overall quaternary structure. As the structural permutation induced by the mutation is not significant, we hypothesize that the excessive thermolability of the E104D mutant is attributed to the easy propagation of atoms' flexibility from the surface into the core via the large cluster of water. It is indeed found that the B factor increment in the wet region is higher than other regions, and, more importantly, the B factor increment in the wet region is maintained in the deeply buried core. Molecular dynamics simulations revealed that for the mutant structure at normal temperature, a clear increase of the root-mean-square deviation is observed for the wet region contacting with the large cluster of interfacial water. Such increase is not observed for other interfacial regions or the whole protein. This clearly suggests that, in the E104D mutant, the large water cluster is responsible for the subunit interface flexibility and overall thermolability, and it ultimately leads to the deficiency of this enzyme. Conclusions Our study

Pollution patterns and characteristics of perfluorinated compounds in surface water adjacent potential industrial emission categories of Shanghai, China.

PubMed

Chai, Jian-Fei; Lei, Peng-Hui; Xia, Xiao-Yu; Xu, Gang; Wang, De-Jin; Sun, Rui; Gu, Jian-Zhong; Tang, Liang

2017-11-01

Perfluorinated compounds (PFCs) have received increasing attention worldwide recently because of potential risk to aquatic environment and living organisms. Herein, occurrence and spatial distributions of 17 selected PFCs were investigated in surface water adjacent to potential industrial emission categories in Shanghai. The results showed the distributions of PFCs in the ambient rivers were greatly affected by those industrial sources. Perfluorooctanoic acid (PFOA) and other short-chain PFCs such as perfluoropentanoic acid (PFPeA) and perfluorooctanesulfonate (PFBS) were detected as the predominant species in all samples. Specifically, the total concentrations of PFCs (∑PFCs) near the airport ranged from 142 to 264ngL -1 , with PFOA, PFPeA, and PFBS as most prevalent. While near the fluorochemical plant and metal plating, concentrations of ∑PFCs ranged from 200 to 2143ngL -1 and 211ngL -1 to 705ngL -1 ; and PFOA was the predominant individual PFCs, with the highest concentration of 1985ngL -1 . However, concentrations of PFOS were found at relatively low level, which ranged from < 0.06 to 4.44ngL -1 . The Spearman correlation analysis of concentration of individual PFCs showed that PFOA and perfluorohexanoic acid (PFHxA) was positive, while the correlation between PFOA and perfluorohexansulfonate (PFHxS) was negative near the airport, indicating PFOA and PFHxA may share common sources. Preliminary ecological risk evaluation of PFCs in adjacent water of the industrial emission areas suggested these emission categories posed higher risks than other area, although the risk level was still relatively safe. Copyright © 2017 Elsevier Inc. All rights reserved.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rønnest, A. K.; Peters, G. H.; Hansen, F. Y., E-mail: flemming@kemi.dtu.dk

2016-04-14

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 allmore » 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 10{sup 8}–10{sup 9} V m{sup −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 ⋅ 10{sup 8} V m{sup −1}) when in the fluid phase with a monovalent counter-ion and ∼1.4 V (∼2.8 ⋅ 10{sup 8} V m{sup −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

Application of differential scanning calorimetry to measure the differential binding of ions, water and protons in the unfolding of DNA molecules.

PubMed

Olsen, Chris M; Shikiya, Ronald; Ganugula, Rajkumar; Reiling-Steffensmeier, Calliste; Khutsishvili, Irine; Johnson, Sarah E; Marky, Luis A

2016-05-01

The overall stability of DNA molecules globally depends on base-pair stacking, base-pairing, polyelectrolyte effect and hydration contributions. In order to understand how they carry out their biological roles, it is essential to have a complete physical description of how the folding of nucleic acids takes place, including their ion and water binding. To investigate the role of ions, water and protons in the stability and melting behavior of DNA structures, we report here an experimental approach i.e., mainly differential scanning calorimetry (DSC), to determine linking numbers: the differential binding of ions (Δnion), water (ΔnW) and protons (ΔnH(+)) in the helix-coil transition of DNA molecules. We use DSC and temperature-dependent UV spectroscopic techniques to measure the differential binding of ions, water, and protons for the unfolding of a variety of DNA molecules: salmon testes DNA (ST-DNA), one dodecamer, one undecamer and one decamer duplexes, nine hairpin loops, and two triplexes. These methods can be applied to any conformational transition of a biomolecule. We determined complete thermodynamic profiles, including all three linking numbers, for the unfolding of each molecule. The favorable folding of a DNA helix results from a favorable enthalpy-unfavorable entropy compensation. DSC thermograms and UV melts as a function of salt, osmolyte and proton concentrations yielded releases of ions and water. Therefore, the favorable folding of each DNA molecule results from the formation of base-pair stacks and uptake of both counterions and water molecules. In addition, the triplex with C(+)GC base triplets yielded an uptake of protons. Furthermore, the folding of a DNA duplex is accompanied by a lower uptake of ions and a similar uptake of four water molecules as the DNA helix gets shorter. In addition, the oligomer duplexes and hairpin thermodynamic data suggest ion and water binding depends on the DNA sequence rather than DNA composition. Copyright �

Reactions of water and C1 molecules on carbide and metal-modified carbide surfaces

DOE PAGES

Wan, Weiming; Tackett, Brian M.; Chen, Jingguang G.

2017-02-23

The formation of carbides can significantly modify the physical and chemical properties of the parent metals. In the current review, we summarize the general trends in the reactions of water and C1 molecules over transition metal carbide (TMC) and metal-modified TMC surfaces and thin films. Although the primary focus of the current review is on the theoretical and experimental studies of reactions of C1 molecules (CO, CO 2, CH 3OH, etc.), the reactions of water will also be reviewed because water plays an important role in many of the C1 transformation reactions. This review is organized by discussing separately thermalmore » reactions and electrochemical reactions, which provides insights into the application of TMCs in heterogeneous catalysis and electrocatalysis, respectively. In thermal reactions, we discuss the thermal decomposition of water and methanol, as well as the reactions of CO and CO 2 over TMC surfaces. In electrochemical reactions, we summarize recent studies in the hydrogen evolution reaction, electrooxidation of methanol and CO, and electroreduction of CO 2. Lastly, future research opportunities and challenges associated with using TMCs as catalysts and electrocatalysts are also discussed.« less

[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.

Preliminary Geologic Map of the Southern Funeral Mountains and Adjacent Ground-Water Discharge Sites, Inyo County, California, and Nye County, Nevada

USGS Publications Warehouse

Fridrich, Christopher J.; Thompson, Ren A.; Slate, Janet L.; Berry, M.E.; Machette, Michael N.

2008-01-01

This map covers the southern part of the Funeral Mountains, and adjacent parts of four structural basins - Furnace Creek, Amargosa Valley, Opera House, and central Death Valley. It extends over three full 7.5-minute quadrangles, and parts of eleven others - a total area of about 950 square kilometers. The boundaries of this map were drawn to include all of the known proximal hydrogeologic features that may affect the flow of ground water that discharges from the springs of the Furnace Creek wash area, in the west-central part of the map. These springs provide the major potable water supply for Death Valley National Park.

Molecular conformation of linear alkane molecules: From gas phase to bulk water through the interface

NASA Astrophysics Data System (ADS)

Murina, Ezequiel L.; Fernández-Prini, Roberto; Pastorino, Claudio

2017-08-01

We studied the behavior of long chain alkanes (LCAs) as they were transferred from gas to bulk water, through the liquid-vapor interface. These systems were studied using umbrella sampling molecular dynamics simulation and we have calculated properties like free energy profiles, molecular orientation, and radius of gyration of the LCA molecules. The results show changes in conformation of the solutes along the path. LCAs adopt pronounced molecular orientations and the larger ones extend appreciably when partially immersed in the interface. In bulk water, their conformations up to dodecane are mainly extended. However, larger alkanes like eicosane present a more stable collapsed conformation as they approach bulk water. We have characterized the more probable configurations in all interface and bulk regions. The results obtained are of interest for the study of biomatter processes requiring the transfer of hydrophobic matter, especially chain-like molecules like LCAs, from gas to bulk aqueous systems through the interface.

Distribution of oil and natural-gas wells in relation to ground-water flow systems in the Great Basin region of Nevada and Utah, and adjacent states

USGS Publications Warehouse

Schaefer, Donald H.

1996-01-01

This map publication is one of several in a series concerning various aspects of the ground-water hydrology of the Great Basin in Nevada, Utah, and adjacent States.  One report in the series describes the hydrogeologic framework of the Great Basin (Plume and Carlton, 1988).  Another shows the ground-water levels for the aquifer systems of the Great Basin (Thomas and others, 1986).  A third report in the series describes the regional ground-water flow patterns in the Great Basin (Harrill and others, 1988).

Adsorption Study of a Water Molecule on Vacancy-Defected Nonpolar CdS Surfaces

PubMed Central

2017-01-01

A detailed understanding of the water–semiconductor interface is of major importance for elucidating the molecular interactions at the photocatalyst’s surface. Here, we studied the effect of vacancy defects on the adsorption of a water molecule on the (101̅0) and (112̅0) CdS surfaces, using spin-polarized density functional theory. We observed that the local spin polarization did not persist for most of the cationic vacancies on the surfaces, unlike in bulk, owing to surface reconstructions caused by displaced S atoms. This result suggests that cationic vacancies on these surfaces may not be the leading cause of the experimentally observed magnetism in CdS nanostructures. The surface vacancies are predominantly nonmagnetic except for one case, where a magnetic cationic vacancy is relatively stable due to constraints posed by the (101̅0) surface geometry. At this particular magnetic defect site, we found a very strong interaction with the H2O molecule leading to a case of chemisorption, where the local spin polarization vanishes concurrently. At the same defect site, adsorption of an O2 molecule was also simulated, and the results were found to be consistent with experimental electron paramagnetic resonance findings for powdered CdS. The anion vacancies on these surfaces were always found to be nonmagnetic and did not affect the water adsorption at these surfaces. PMID:28539988

Structure of the myotonic dystrophy type 2 RNA and designed small molecules that reduce toxicity.

PubMed

Childs-Disney, Jessica L; Yildirim, Ilyas; Park, HaJeung; Lohman, Jeremy R; Guan, Lirui; Tran, Tuan; Sarkar, Partha; Schatz, George C; Disney, Matthew D

2014-02-21

Myotonic dystrophy type 2 (DM2) is an incurable neuromuscular disorder caused by a r(CCUG) expansion (r(CCUG)(exp)) that folds into an extended hairpin with periodically repeating 2×2 nucleotide internal loops (5'CCUG/3'GUCC). We designed multivalent compounds that improve DM2-associated defects using information about RNA-small molecule interactions. We also report the first crystal structure of r(CCUG) repeats refined to 2.35 Å. Structural analysis of the three 5'CCUG/3'GUCC repeat internal loops (L) reveals that the CU pairs in L1 are each stabilized by one hydrogen bond and a water-mediated hydrogen bond, while CU pairs in L2 and L3 are stabilized by two hydrogen bonds. Molecular dynamics (MD) simulations reveal that the CU pairs are dynamic and stabilized by Na(+) and water molecules. MD simulations of the binding of the small molecule to r(CCUG) repeats reveal that the lowest free energy binding mode occurs via the major groove, in which one C residue is unstacked and the cross-strand nucleotides are displaced. Moreover, we modeled the binding of our dimeric compound to two 5'CCUG/3'GUCC motifs, which shows that the scaffold on which the RNA-binding modules are displayed provides an optimal distance to span two adjacent loops.

Structure of the Myotonic Dystrophy Type 2 RNA and Designed Small Molecules That Reduce Toxicity

PubMed Central

Park, HaJeung; Lohman, Jeremy R.; Guan, Lirui; Tran, Tuan; Sarkar, Partha; Schatz, George C.; Disney, Matthew D.

2014-01-01

Myotonic dystrophy type 2 (DM2) is an untreatable neuromuscular disorder caused by a r(CCUG) expansion (r(CCUG)exp) that folds into an extended hairpin with periodically repeating 2×2 nucleotide internal loops (5’CCUG/3’GUCC). We designed multivalent compounds that improve DM2-associated defects using information about RNA-small molecule interactions. We also report the first crystal structure of r(CCUG)exp refined to 2.35 Å. Structural analysis of the three 5’CCUG/3’GUCC repeat internal loops (L) reveals that the CU pairs in L1 are each stabilized by one hydrogen bond and a water-mediated hydrogen bond while CU pairs in L2 and L3 are stabilized by two hydrogen bonds. Molecular dynamics (MD) simulations reveal that the CU pairs are dynamic and stabilized by Na+ and water molecules. MD simulations of the binding of the small molecule to r(CCUG) repeats reveal that the lowest free energy binding mode occurs via the major groove, in which one C residue is unstacked and the cross-strand nucleotides are displaced. Moreover, we modeled the binding of our dimeric compound to two 5’CCUG/3’GUCC motifs, which shows that the scaffold on which the RNA-binding modules are displayed provides an optimal distance to span two adjacent loops. PMID:24341895

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

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

Role of water molecules in structure and energetics of Pseudomonas aeruginosa lectin I interacting with disaccharides.

PubMed

Nurisso, Alessandra; Blanchard, Bertrand; Audfray, Aymeric; Rydner, Lina; Oscarson, Stefan; Varrot, Annabelle; Imberty, Anne

2010-06-25

Calcium-dependent lectin I from Pseudomonas aeruginosa (PA-IL) binds specifically to oligosaccharides presenting an alpha-galactose residue at their nonreducing end, such as the disaccharides alphaGal1-2betaGalOMe, alphaGal1-3betaGalOMe, and alphaGal1-4betaGalOMe. This provides a unique model for studying the effect of the glycosidic linkage of the ligands on structure and thermodynamics of the complexes by means of experimental and theoretical tools. The structural features of PA-IL in complex with the three disaccharides were established by docking and molecular dynamics simulations and compared with those observed in available crystal structures, including PA-IL.alphaGal1-2betaGalOMe complex, which was solved at 2.4 A resolution and reported herein. The role of a structural bridge water molecule in the binding site of PA-IL was also elucidated through molecular dynamics simulations and free energy calculations. This water molecule establishes three very stable hydrogen bonds with O6 of nonreducing galactose, oxygen from Pro-51 main chain, and nitrogen from Gln-53 main chain of the lectin binding site. Binding free energies for PA-IL in complex with the three disaccharides were investigated, and the results were compared with the experimental data determined by titration microcalorimetry. When the bridge water molecule was included in the free energy calculations, the simulations predicted the correct binding affinity trends with the 1-2-linked disaccharide presenting three times stronger affinity ligand than the other two. These results highlight the role of the water molecule in the binding site of PA-IL and indicate that it should be taken into account when designing glycoderivatives active against P. aeruginosa adhesion.

Structures and Spectroscopic Properties of F-(H2O) n with n = 1-10 Clusters from a Global Search Based On Density Functional Theory.

PubMed

Shi, Ruili; Wang, Pengju; Tang, Lingli; Huang, Xiaoming; Chen, Yonggang; Su, Yan; Zhao, Jijun

2018-04-05

Using a genetic algorithm incorporated in density functional theory, we explore the ground state structures of fluoride anion-water clusters F - (H 2 O) n with n = 1-10. The F - (H 2 O) n clusters prefer structures in which the F - anion remains at the surface of the structure and coordinates with four water molecules, as the F - (H 2 O) n clusters have strong F - -H 2 O interactions as well as strong hydrogen bonds between H 2 O molecules. The strong interaction between the F - anion and adjacent H 2 O molecule leads to a longer O-H distance in the adjacent molecule than in an individual water molecule. The simulated infrared (IR) spectra of the F - (H 2 O) 1-5 clusters obtained via second-order vibrational perturbation theory (VPT2) and including anharmonic effects reproduce the experimental results quite well. The strong interaction between the F - anion and water molecules results in a large redshift (600-2300 cm -1 ) of the adjacent O-H stretching mode. Natural bond orbital (NBO) analysis of the lowest-energy structures of the F - (H 2 O) 1-10 clusters illustrates that charge transfer from the lone pair electron orbital of F - to the antibonding orbital of the adjacent O-H is mainly responsible for the strong interaction between the F - anion and water molecules, which leads to distinctly different geometric and vibrational properties compared with neutral water clusters.

Utilization by fishes of the Alviso Island ponds and adjacent waters in south san francisco bay following restoration to tidal influence

USGS Publications Warehouse

Saiki, M.K.; Mejia, F.H.

2009-01-01

Earthen levees of three isolated salt ponds known locally as the Alviso Island Ponds were intentionally breached in March 2006 to allow tidal exchange of the ponds with water from Coyote Creek. The water exchange transformed the previously fishless hypersaline ponds into lower salinity habitats suitable for fish life. This study documented fish utilization of the ponds, adjacent reaches of Coyote Creek, and an upstream reach in nearby Artesian Slough during May-July 2006. By the time the study was initiated, water quality conditions in the ponds were similar to conditions in adjacent reaches of Coyote Creek. The only variable exhibiting a strong gradient within the study area was salinity, which increased progressively from upstream to downstream in Coyote Creek. A total of 4,034 fish represented by 18 species from 14 families was caught during the study. Judging from cluster analysis of presence-absence data that excluded rare fish species, the 10 sampling units (3 ponds, 6 reaches in Coyote Creek, and 1 reach in Artesian Slough) formed two clusters or groups, suggesting two species assemblages. The existence of two groups was also suggested by ordination with non-metric multidimensional scaling (NMS). One group, which was composed of the three ponds and four of the lowermost reaches of Coyote Creek, was characterized by mostly estuarine or marine species (e.g., topsmelt, Atherinops affinis; northern anchovy, Engraulis mordax; and longjaw mudsucker, Gillichthys mirabilis). The second group, which was composed of the two uppermost reaches of Coyote Creek and the one reach of Artesian Slough, was characterized by freshwater species (e.g., Sacramento sucker, Catostomus occidentalis) and by an absence of the estuarine/marine species noted in the first assemblage. Judging from a joint plot of selected water quality variables overlaying the ordination results, salinity was the only important variable associated with spatial distribution of fish species. Water

Water-soluble conductive polymers

DOEpatents

Aldissi, Mahmoud

1989-01-01

Polymers which are soluble in water and are electrically conductive. The monomer repeat unit is a thiophene or pyrrole molecule having an alkyl group substituted for the hydrogen atom located in the beta position of the thiophene or pyrrole ring and having a surfactant molecule at the end of the alkyl chain. Polymers of this class having 8 or more carbon atoms in the alkyl chain exhibit liquid crystalline behavior, resulting in high electrical anisotropy. The monomer-to-monomer bonds are located between the carbon atoms which are adjacent to the sulfur or nitrogen atoms. The number of carbon atoms in the alkyl group may vary from 1 to 20 carbon atoms. The surfactant molecule consists of a sulfonate group, or a sulfate group, or a carboxylate group, and hydrogen or an alkali metal. Negative ions from a supporting electrolyte which may be used in the electrochemical synthesis of a polymer may be incorporated into the polymer during the synthesis and serve as a dopant to increase the conductivity.

Water-soluble conductive polymers

DOEpatents

Aldissi, Mahmoud

1990-01-01

Polymers which are soluble in water and are electrically conductive. The monomer repeat unit is a thiophene or pyrrole molecule having an alkyl group substituted for the hydrogen atom located in the beta position of the thiophene or pyrrole ring and having a surfactant molecule at the end of the alkyl chain. Polymers of this class having 8 or more carbon atoms in the alkyl chain exhibit liquid crystalline behavior, resulting in high electrical anisotropy. The monomer-to-monomer bonds are located between the carbon atoms which are adjacent to the sulfur or nitrogen atoms. The number of carbon atoms in the alkyl group may vary from 1 to 20 carbon atoms. The surfactant molecule consists of a sulfonate group, or a sulfate group, or a carboxylate group, and hydrogen or an alkali metal. Negative ions from a supporting electrolyte which may be used in the electrochemical synthesis of a polymer may be incorporated into the polymer during the synthesis and serve as a dopant to increase the conductivity.

Water-soluble conductive polymers

DOEpatents

Aldissi, M.

1988-02-12

Polymers which are soluble in water and are electrically conductive. The monomer repeat unit is a thiophene or pyrrole molecule having an alkyl group substituted for the hydrogen atom located in the beta position of the thiophene or pyrrole ring and having a surfactant molecule at the end of the alkyl chain. Polymers of this class having 8 or more carbon atoms in the alkyl chain exhibit liquid crystalline behavior, resulting in high electrical anisotropy. The monomer-to-monomer bonds are located between the carbon atoms which are adjacent to the sulfur or nitrogen atoms. The number of carbon atoms in the alkyl group may vary from 1 to 20 carbon atoms. The surfactant molecule consists of a sulfonate group, or a sulfate group, or a carboxylate group, and hydrogen or an alkali metal. Negative ions from a supporting electrolyte which may be used in the electrochemical synthesis of a polymer may be incorporated into the polymer during the synthesis and serve as a dopant to increase the conductivity.

Origins of Protons in C-H Bond Insertion Products of Phenols: Proton-Self-Sufficient Function via Water Molecules.

PubMed

Luo, Zhoujie; Gao, Ya; Zhu, Tong; Zhang, John Zenghui; Xia, Fei

2017-08-31

Water molecules can serve as proton shuttles for proton transfer in the C-H bond insertion reactions catalyzed by transition metal complexes. Recently, the control experiments performed for C-H bond insertion of phenol and anisol by gold carbenes show that large discrepancy exists in the yields of hydrogenated and deuterated products. Thus, we conducted a detailed theoretical analysis on the function of water molecules in the C-H bond insertion reactions. The comparison of calculated results and control experiments indicates that the solution water molecules play a crucial role of proton shuttle in C-H bond insertion. In particular, it was found that the hydroxyl groups in phenols were capable of donating protons via water shuttles for the production of C-H products, which had a substantial influence on the yields of inserted products. The hydroxyl groups instead of C-H bonds in phenols function like "proton reservoirs" in the C-H bond insertion, which we call the "proton self-sufficient" (PSS) function of phenol. The PSS function of phenol indicates that the substrates with and without proton reservoirs will lead to different C-H bond insertion products.

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

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

USGS Publications Warehouse

Battaglin, William A.; Smalling, Kelly L.; Anderson, Chauncey; Calhoun, Daniel L.; Chestnut, Tara E.; Muths, Erin L.

2016-01-01

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

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.

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. Copyright © 2013 Elsevier Ltd. All rights reserved.

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)

33 CFR 150.35 - How may an Adjacent Coastal State request an amendment to the deepwater port operations manual?

Code of Federal Regulations, 2014 CFR

2014-07-01

... equivalent or improved protection and safety. The Adjacent Coastal State may petition the Commandant (CG-5P... 33 Navigation and Navigable Waters 2 2014-07-01 2014-07-01 false How may an Adjacent Coastal State...: OPERATIONS General § 150.35 How may an Adjacent Coastal State request an amendment to the deepwater port...

33 CFR 150.35 - How may an Adjacent Coastal State request an amendment to the deepwater port operations manual?

Code of Federal Regulations, 2013 CFR

2013-07-01

... equivalent or improved protection and safety. The Adjacent Coastal State may petition the Commandant (CG-5P... 33 Navigation and Navigable Waters 2 2013-07-01 2013-07-01 false How may an Adjacent Coastal State...: OPERATIONS General § 150.35 How may an Adjacent Coastal State request an amendment to the deepwater port...

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.

Change of the isoelectric point of hemoglobin at the air/water interface probed by the orientational flip-flop of water molecules.

PubMed

Devineau, Stéphanie; Inoue, Ken-Ichi; Kusaka, Ryoji; Urashima, Shu-Hei; Nihonyanagi, Satoshi; Baigl, Damien; Tsuneshige, Antonio; Tahara, Tahei

2017-04-19

Elucidation of the molecular mechanisms of protein adsorption is of essential importance for further development of biotechnology. Here, we use interface-selective nonlinear vibrational spectroscopy to investigate protein charge at the air/water interface by probing the orientation of interfacial water molecules. We measured the Im χ (2) spectra of hemoglobin, myoglobin, serum albumin and lysozyme at the air/water interface in the CH and OH stretching regions using heterodyne-detected vibrational sum frequency generation (HD-VSFG) spectroscopy, and we deduced the isoelectric point of the protein by monitoring the orientational flip-flop of water molecules at the interface. Strikingly, our measurements indicate that the isoelectric point of hemoglobin is significantly lowered (by about one pH unit) at the air/water interface compared to that in the bulk. This can be predominantly attributed to the modifications of the protein structure at the air/water interface. Our results also suggest that a similar mechanism accounts for the modification of myoglobin charge at the air/water interface. This effect has not been reported for other model proteins at interfaces probed by conventional VSFG techniques, and it emphasizes the importance of the structural modifications of proteins at the interface, which can drastically affect their charge profiles in a protein-specific manner. The direct experimental approach using HD-VSFG can unveil the changes of the isoelectric point of adsorbed proteins at various interfaces, which is of major relevance to many biological applications and sheds new light on the effect of interfaces on protein charge.

An ab initio MO study on the hydrolysis of methyl chloride with explicit consideration of 13 water molecules

NASA Astrophysics Data System (ADS)

Yamataka, Hiroshi; Aida, Misako

1998-06-01

Ab initio MO calculations (HF/3-21G, HF/6-31G, HF/6-31+G* and MP2/6-31+G*) were carried out on the hydrolysis of CH 3Cl in which up to 13 water solvent molecules were explicitly considered. For n⩾3, three important stationary points ( cmp1, TS, and cmp2) were detected in the course of the reaction. The calculations for the n=13 system at the HF/6-31+G* level reproduced the experimental activation enthalpy and the secondary deuterium kinetic isotope effect. The two reacting bond lengths in the transition state are 1.975 Å (O-C) and 2.500 Å (C-Cl), and CH 3Cl is surrounded by 13 water molecules without any apparent vacant space. The proton transfer from the attacking water to the water cluster occurs after TS is reached.

Sampling and Analysis of Organic Molecules in the Plumes of Enceladus

NASA Astrophysics Data System (ADS)

Monroe, A. A.; Williams, P.; Anbar, A. D.; Tsou, P.

2012-12-01

The recent detection of organic molecules in the plumes of Enceladus, which also contain water and nitrogen (Waite et al., 2006; Matson et al., 2007), suggests that the geologically active South polar region contains habitable, subsurface water (McKay et al., 2008). Characterizing these molecules will be a high priority for any future mission to Enceladus. Sample return is highly desirable, but can it capture useful samples at Enceladus? Using Stardust mission parameters for comparison, we consider the survival of complex organic molecules during collection to assess the feasibility of one aspect of a sample return mission. A successful sample return mission must include the capability to capture and recover intact or partly intact molecules of particular astrobiological interest: lipids, amino and nucleic acids, polypeptides, and polynucleotides. The Stardust mission to comet Wild 2 successfully captured amino acids, amines, and PAHs using a combination of aerogel and Al foil (Sandford et al., 2006, 2010). For larger and more fragile molecules, particularly polypeptides and polynucleotides, low collisional damage is achieved by impact on low molecular weight surfaces. A particularly intriguing possibility is a capture surface pre-coated with organic matrices identified as ideal for analysis of various biomolecules using MALDI-MS (matrix-assisted laser desorption/ionization mass spectrometry) (Hillenkamp and Karas, 2007). MALDI is a standard technique with attomole sensitivity, exceptional mass resolution, and (bio)molecular specificity (Vestal, 2011). Capture surfaces appropriate for MALDI-MS analysis could be analyzed directly without post-return manipulation, minimizing post-capture damage to these molecules and the risk of contamination during handling. A hypothetical sample collection encounter speed of ~ 5 km/s corresponds to ~0.13 eV kinetic energy per amu. Studies of molecule survival and fragmentation exist for free hexapeptides impacting hydrocarbon

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.

Single molecule tracking

DOEpatents

Shera, E. Brooks

1988-01-01

A detection system is provided for identifying individual particles or molecules having characteristic emission in a flow train of the particles in a flow cell. A position sensitive sensor is located adjacent the flow cell in a position effective to detect the emissions from the particles within the flow cell and to assign spatial and temporal coordinates for the detected emissions. A computer is then enabled to predict spatial and temporal coordinates for the particle in the flow train as a function of a first detected emission. Comparison hardware or software then compares subsequent detected spatial and temporal coordinates with the predicted spatial and temporal coordinates to determine whether subsequently detected emissions originate from a particle in the train of particles. In one embodiment, the particles include fluorescent dyes which are excited to fluoresce a spectrum characteristic of the particular particle. Photones are emitted adjacent at least one microchannel plate sensor to enable spatial and temporal coordinates to be assigned. The effect of comparing detected coordinates with predicted coordinates is to define a moving sample volume which effectively precludes the effects of background emissions.

Single molecule tracking

DOEpatents

Shera, E.B.

1987-10-07

A detection system is provided for identifying individual particles or molecules having characteristic emission in a flow train of the particles in a flow cell. A position sensitive sensor is located adjacent the flow cell in a position effective to detect the emissions from the particles within the flow cell and to assign spatial and temporal coordinates for the detected emissions. A computer is then enabled to predict spatial and temporal coordinates for the particle in the flow train as a function of a first detected emission. Comparison hardware or software then compares subsequent detected spatial and temporal coordinates with the predicted spatial and temporal coordinates to determine whether subsequently detected emissions originate from a particle in the train of particles. In one embodiment, the particles include fluorescent dyes which are excited to fluoresce a spectrum characteristic of the particular particle. Photons are emitted adjacent at least one microchannel plate sensor to enable spatial and temporal coordinates to be assigned. The effect of comparing detected coordinates with predicted coordinates is to define a moving sample volume which effectively precludes the effects of background emissions. 3 figs.

An aspartate and a water molecule mediate efficient acid-base catalysis in a tailored antibody pocket

PubMed Central

Debler, Erik W.; Müller, Roger; Hilvert, Donald; Wilson, Ian A.

2009-01-01

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 AspH35 and GluL34 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 GluL34 to alanine mutant, leads to an impressive 109-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. PMID:19846764

An aspartate and a water molecule mediate efficient acid-base catalysis in a tailored antibody pocket.

PubMed

Debler, Erik W; Müller, Roger; Hilvert, Donald; Wilson, Ian A

2009-11-03

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(H35) and Glu(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(L34) to alanine mutant, leads to an impressive 10(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.

Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chakraborty, Kaushik; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in

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 themore » 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.« less

33 CFR 334.1080 - San Francisco Bay adjacent to northeast corner of Treasure Island; naval restricted area.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false San Francisco Bay adjacent to northeast corner of Treasure Island; naval restricted area. 334.1080 Section 334.1080 Navigation and... RESTRICTED AREA REGULATIONS § 334.1080 San Francisco Bay adjacent to northeast corner of Treasure Island...

Size cues and the adjacency principle.

DOT National Transportation Integrated Search

1963-11-01

The purpose of the present study was to apply the adjacency principle to the perception of relative depth from size cues. In agreement with the adjacency principle, it was found that the size cue between adjacent objects was more effective than the s...

Effects of Withdrawals on Ground-Water Levels in Southern Maryland and the Adjacent Eastern Shore, 1980-2005

USGS Publications Warehouse

Soeder, Daniel J.; Raffensperger, Jeff P.; Nardi, Mark R.

2007-01-01

Ground water is the primary source of water supply in most areas of Maryland?s Atlantic Coastal Plain, including Southern Maryland. The counties in this area are experiencing some of the most rapid growth and development in the State, resulting in an increased demand for ground-water production. The cooperative, basic water-data program of the U.S. Geological Survey and the Maryland Geological Survey has collected long-term observations of ground-water levels in Southern Maryland and parts of the Eastern Shore for many decades. Additional water-level observations were made by both agencies beginning in the 1970s, under the Power Plant Research Program of the Maryland Department of Natural Resources. These long-term water levels commonly show significant declines over several decades, which are attributed to ground-water withdrawals. Ground-water-level trends since 1980 in major Coastal Plain aquifers such as the Piney Point-Nanjemoy, Aquia, Magothy, upper Patapsco, lower Patapsco, and Patuxent were compared to water use and withdrawal data. Potentiometric surface maps show that most of the declines in ground-water levels can be directly related to effects from major pumping centers. There is also evidence that deep drawdowns in some pumped aquifers may be causing declines in adjacent, unpumped aquifers. Water-level hydrographs of many wells in Southern Maryland show linear declines in levels year after year, instead of the gradual leveling-off that would be expected as the aquifers equilibrate with pumping. A continual increase in the volumes of water being withdrawn from the aquifers is one explanation for why they are not reaching equilibrium. Although reported ground-water production in Southern Maryland has increased somewhat over the past several decades, the reported increases are often not large enough to account for the observed water-level declines. Numerical modeling simulations indicate that a steady, annual increase in the number of small wells could

Tuning the Redox Properties of a Nonheme Iron(III)-Peroxo Complex Binding Redox-Inactive Zinc Ions by Water Molecules.

PubMed

Lee, Yong-Min; Bang, Suhee; Yoon, Heejung; Bae, Seong Hee; Hong, Seungwoo; Cho, Kyung-Bin; Sarangi, Ritimukta; Fukuzumi, Shunichi; Nam, Wonwoo

2015-07-20

Redox-inactive metal ions play important roles in tuning chemical properties of metal-oxygen intermediates. Herein we report the effect of water molecules on the redox properties of a nonheme iron(III)-peroxo complex binding redox-inactive metal ions. The coordination of two water molecules to a Zn(2+) ion in (TMC)Fe(III) -(O2 )-Zn(CF3 SO3 )2 (1-Zn(2+) ) decreases the Lewis acidity of the Zn(2+) ion, resulting in the decrease of the one-electron oxidation and reduction potentials of 1-Zn(2+) . This further changes the reactivities of 1-Zn(2+) in oxidation and reduction reactions; no reaction occurred upon addition of an oxidant (e.g., cerium(IV) ammonium nitrate (CAN)) to 1-Zn(2+) , whereas 1-Zn(2+) coordinating two water molecules, (TMC)Fe(III) -(O2 )-Zn(CF3 SO3 )2 -(OH2 )2 [1-Zn(2+) -(OH2 )2 ], releases the O2 unit in the oxidation reaction. In the reduction reactions, 1-Zn(2+) was converted to its corresponding iron(IV)-oxo species upon addition of a reductant (e.g., a ferrocene derivative), whereas such a reaction occurred at a much slower rate in the case of 1-Zn(2+) -(OH2 )2 . The present results provide the first biomimetic example showing that water molecules at the active sites of metalloenzymes may participate in tuning the redox properties of metal-oxygen intermediates. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tuning the Redox Properties of a Nonheme Iron(III)-Peroxo Complex Binding Redox-Inactive Zinc Ions by Water Molecules

DOE PAGES

Lee, Yong-Min; Bang, Suhee; Yoon, Heejung; ...

2015-06-19

Here we report redox-inactive metal ions play important roles in tuning chemical properties of metal–oxygen intermediates. We describe the effect of water molecules on the redox properties of a nonheme iron(III)–peroxo complex binding redox-inactive metal ions. The coordination of two water molecules to a Zn 2+ ion in (TMC)Fe III-(O 2)-Zn(CF 3SO 3) 2 (1-Zn 2+) decreases the Lewis acidity of the Zn 2+ ion, resulting in the decrease of the one-electron oxidation and reduction potentials of 1-Zn 2+. This further changes the reactivities of 1-Zn 2+ in oxidation and reduction reactions; no reaction occurred upon addition of an oxidantmore » (e.g., cerium(IV) ammonium nitrate (CAN)) to 1-Zn 2+, whereas 1-Zn 2+ coordinating two water molecules, (TMC)Fe III-(O 2)-Zn(CF 3SO 3) 2-(OH 2) 2 [1-Zn 2+-(OH 2) 2], releases the O 2 unit in the oxidation reaction. In the reduction reactions, 1-Zn 2+ was converted to its corresponding iron(IV)–oxo species upon addition of a reductant (e.g., a ferrocene derivative), whereas such a reaction occurred at a much slower rate in the case of 1-Zn 2+-(OH 2) 2. Finally, the present results provide the first biomimetic example showing that water molecules at the active sites of metalloenzymes may participate in tuning the redox properties of metal–oxygen intermediates.« less

Satellite observations of rainfall effect on sea surface salinity in the waters adjacent to Taiwan

NASA Astrophysics Data System (ADS)

Ho, Chung-Ru; Hsu, Po-Chun; Lin, Chen-Chih; Huang, Shih-Jen

2017-10-01

Changes of oceanic salinity are highly related to the variations of evaporation and precipitation. To understand the influence of rainfall on the sea surface salinity (SSS) in the waters adjacent to Taiwan, satellite remote sensing data from the year of 2012 to 2014 are employed in this study. The daily rain rate data obtained from Special Sensor Microwave Imager (SSM/I), Tropical Rainfall Measuring Mission's Microwave Imager (TRMM/TMI), Advanced Microwave Scanning Radiometer (AMSR), and WindSat Polarimetric Radiometer. The SSS data was derived from the measurements of radiometer instruments onboard the Aquarius satellite. The results show the average values of SSS in east of Taiwan, east of Luzon and South China Sea are 33.83 psu, 34.05 psu, and 32.84 psu, respectively, in the condition of daily rain rate higher than 1 mm/hr. In contrast to the rainfall condition, the average values of SSS are 34.07 psu, 34.26 psu, and 33.09 psu in the three areas, respectively at no rain condition (rain rate less than 1 mm/hr). During the cases of heavy rainfall caused by spiral rain bands of typhoon, the SSS is diluted with an average value of -0.78 psu when the average rain rate is higher than 4 mm/hr. However, the SSS was increased after temporarily decreased during the typhoon cases. A possible reason to explain this phenomenon is that the heavy rainfall caused by the spiral rain bands of typhoon may dilute the sea surface water, but the strong winds can uplift the higher salinity of subsurface water to the sea surface.

Hydrogen bonding directed self-assembly of small-molecule amphiphiles in water.

PubMed

Xu, Jiang-Fei; Niu, Li-Ya; Chen, Yu-Zhe; Wu, Li-Zhu; Tung, Chen-Ho; Yang, Qing-Zheng

2014-08-01

Compounds comprising one or two quadruply hydrogen bonding units, 2-ureido-4[1H]-pyrimidinone (UPy) and tris(tetraethylene glycol monomethyl ether) moieties, were reported to form highly stable hydrogen-bonded assemblies in water. Compound 1, containing one UPy, assembles into vesicles, and compound 2, containing two UPy units, forms micelles. The aggregates disassemble reversibly when the solution pH is raised to 9.0 or above. The results demonstrate the utility of hydrogen bonding to direct the self-assembly of small-molecule building blocks in aqueous media.

Bond-based linear indices of the non-stochastic and stochastic edge-adjacency matrix. 1. Theory and modeling of ChemPhys properties of organic molecules.

PubMed

Marrero-Ponce, Yovani; Martínez-Albelo, Eugenio R; Casañola-Martín, Gerardo M; Castillo-Garit, Juan A; Echevería-Díaz, Yunaimy; Zaldivar, Vicente Romero; Tygat, Jan; Borges, José E Rodriguez; García-Domenech, Ramón; Torrens, Francisco; Pérez-Giménez, Facundo

2010-11-01

Novel bond-level molecular descriptors are proposed, based on linear maps similar to the ones defined in algebra theory. The kth edge-adjacency matrix (E(k)) denotes the matrix of bond linear indices (non-stochastic) with regard to canonical basis set. The kth stochastic edge-adjacency matrix, ES(k), is here proposed as a new molecular representation easily calculated from E(k). Then, the kth stochastic bond linear indices are calculated using ES(k) as operators of linear transformations. In both cases, the bond-type formalism is developed. The kth non-stochastic and stochastic total linear indices are calculated by adding the kth non-stochastic and stochastic bond linear indices, respectively, of all bonds in molecule. First, the new bond-based molecular descriptors (MDs) are tested for suitability, for the QSPRs, by analyzing regressions of novel indices for selected physicochemical properties of octane isomers (first round). General performance of the new descriptors in this QSPR studies is evaluated with regard to the well-known sets of 2D/3D MDs. From the analysis, we can conclude that the non-stochastic and stochastic bond-based linear indices have an overall good modeling capability proving their usefulness in QSPR studies. Later, the novel bond-level MDs are also used for the description and prediction of the boiling point of 28 alkyl-alcohols (second round), and to the modeling of the specific rate constant (log k), partition coefficient (log P), as well as the antibacterial activity of 34 derivatives of 2-furylethylenes (third round). The comparison with other approaches (edge- and vertices-based connectivity indices, total and local spectral moments, and quantum chemical descriptors as well as E-state/biomolecular encounter parameters) exposes a good behavior of our method in this QSPR studies. Finally, the approach described in this study appears to be a very promising structural invariant, useful not only for QSPR studies but also for similarity

Toxicity and bioavailability of metals in the Missouri River adjacent to a lead refinery

USGS Publications Warehouse

Chapman, Duane C.; Allert, Ann L.; Fairchild, James F.; May, Thomas W.; Schmitt, Christopher J.; Callahan, Edward V.

2001-01-01

This study is an evaluation of the potential environmental impacts of contaminated groundwater from the ASARCO metals refining facility adjacent to the Missouri River in Omaha, Nebraska. Surface waters, sediments, and sediment pore waters were collected from the Burt-Izard drain, which transects the facility, and from the Missouri River adjacent to the facility. Groundwater was also collected from the facility. Waters and sediments were analyzed for inorganic contaminants, and the toxicity of the waters was evaluated with the Ceriodaphnia dubia 7-day test. Concentrations of several elemental contaminants were highly elevated in the groundwater, but not in river sediment pore waters. Lead concentrations were moderately elevated in whole sediment at one site, but lead concentrations in pore waters were low due to apparent sequestration by acid-volatile sulfides. The groundwater sample was highly toxic to C. dubia, causing 100% mortality. Even at the lowest groundwater concentration tested (6.25%) C. dubia survival was reduced; however, at that concentration, reproduction was not significantly different from upstream porewater reference samples. Sediment pore waters were not toxic, except reproduction in pore water collected from one downstream site was somewhat reduced. The decrease in reproduction could not be attributed to measured elemental contaminants.

Cell Motility by Labile Association of Molecules

PubMed Central

Inoué, Shinya; Sato, Hidemi

1967-01-01

This article summarizes our current views on the dynamic structure of the mitotic spindle and its relation to mitotic chromosome movements. The following statements are based on measurements of birefringence of spindle fibers in living cells, normally developing or experimentally modified by various physical and chemical agents, including high and low temperatures, antimitotic drugs, heavy water, and ultraviolet microbeam irradiation. Data were also obtained concomitantly with electron microscopy employing a new fixative and through measurements of isolated spindle protein. Spindle fibers in living cells are labile dynamic structures whose constituent filaments (microtubules) undergo cyclic breakdown and reformation. The dynamic state is maintained by an equilibrium between a pool of protein molecules and their linearly aggregated polymers, which constitute the microtubules or filaments. In living cells under physiological conditions, the association of the molecules into polymers is very weak (absolute value of ΔF 25°C < 1 kcal), and the equilibrium is readily shifted to dissociation by low temperature or by high hydrostatic pressure. The equilibrium is shifted toward formation of polymer by increase in temperature (with a large increase in entropy: ΔS 25°C ≃ 100 eu) or by the addition of heavy water. The spindle proteins tend to polymerize with orienting centers as their geometrical foci. The centrioles, kinetochores, and cell plate act as orienting centers successively during mitosis. Filaments are more concentrated adjacent to an orienting center and yield higher birefringence. Astral rays, continuous fibers, chromosomal fibers, and phragmoplast fibers are thus formed by successive reorganization of the same protein molecules. During late prophase and metaphase, polymerization takes place predominantly at the kinetochores; in metaphase and anaphase, depolymerization is prevalent near the spindle poles. When the concentration of spindle protein is high

Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase.

PubMed

Woods, Christopher J; Shaw, Katherine E; Mulholland, Adrian J

2015-01-22

The applicability of combined quantum mechanics/molecular mechanics (QM/MM) methods for the calculation of absolute binding free energies of conserved water molecules in protein/ligand complexes is demonstrated. Here, we apply QM/MM Monte Carlo simulations to investigate binding of water molecules to influenza neuraminidase. We investigate five different complexes, including those with the drugs oseltamivir and peramivir. We investigate water molecules in two different environments, one more hydrophobic and one hydrophilic. We calculate the free-energy change for perturbation of a QM to MM representation of the bound water molecule. The calculations are performed at the BLYP/aVDZ (QM) and TIP4P (MM) levels of theory, which we have previously demonstrated to be consistent with one another for QM/MM modeling. The results show that the QM to MM perturbation is significant in both environments (greater than 1 kcal mol(-1)) and larger in the more hydrophilic site. Comparison with the same perturbation in bulk water shows that this makes a contribution to binding. The results quantify how electronic polarization differences in different environments affect binding affinity and also demonstrate that extensive, converged QM/MM free-energy simulations, with good levels of QM theory, are now practical for protein/ligand complexes.

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

2015-12-02

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. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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 natural...

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 natural...

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 natural...

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 natural...

Dynamics of copper-phthalocyanine molecules on Au/Ge(001).

PubMed

Sotthewes, K; Heimbuch, R; Zandvliet, H J W

2015-10-07

Spatially resolved current-time scanning tunneling spectroscopy combined with current-distance spectroscopy has been used to characterize the dynamic behavior of copper-phthalocyanine (CuPc) molecules adsorbed on a Au-modified Ge(001) surface. The analyzed CuPc molecules are adsorbed in a "molecular bridge" configuration, where two benzopyrrole groups (lobes) are connected to a Au-induced nanowire, whereas the other two lobes are connected to the adjacent nanowire. Three types of lobe configurations are found: a bright lobe, a dim lobe, and a fuzzy lobe. The dim and fuzzy lobes exhibit a well-defined switching behavior between two discrete levels, while the bright lobe shows a broad oscillation band. The observed dynamic behavior is induced by electrons that are injected into the LUMO+1 orbital of the CuPc molecule. By precisely adjusting the tip-molecule distance, the switching frequency of the lobes can be tuned accurately.

Simulation of single-molecule trapping in a nanochannel

PubMed Central

Robinson, William Neil; Davis, Lloyd M.

2010-01-01

The detection and trapping of single fluorescent molecules in solution within a nanochannel is studied using numerical simulations. As optical forces are insufficient for trapping molecules much smaller than the optical wavelength, a means for sensing a molecule’s position along the nanochannel and adjusting electrokinetic motion to compensate diffusion is assessed. Fluorescence excitation is provided by two adjacently focused laser beams containing temporally interleaved laser pulses. Photon detection is time-gated, and the displacement of the molecule from the middle of the two foci alters the count rates collected in the two detection channels. An algorithm for feedback control of the electrokinetic motion in response to the timing of photons, to reposition the molecule back toward the middle for trapping and to rapidly reload the trap after a molecule photobleaches or escapes, is evaluated. While accommodating the limited electrokinetic speed and the finite latency of feedback imposed by experimental hardware, the algorithm is shown to be effective for trapping fast-diffusing single-chromophore molecules within a micron-sized confocal region. Studies show that there is an optimum laser power for which loss of molecules from the trap due to either photobleaching or shot-noise fluctuations is minimized. PMID:20799801

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. Copyright © 2013 Wiley Periodicals, Inc.

Docking ligands into flexible and solvated macromolecules. 7. Impact of protein flexibility and water molecules on docking-based virtual screening accuracy.

PubMed

Therrien, Eric; Weill, Nathanael; Tomberg, Anna; Corbeil, Christopher R; Lee, Devin; Moitessier, Nicolas

2014-11-24

The use of predictive computational methods in the drug discovery process is in a state of continual growth. Over the last two decades, an increasingly large number of docking tools have been developed to identify hits or optimize lead molecules through in-silico screening of chemical libraries to proteins. In recent years, the focus has been on implementing protein flexibility and water molecules. Our efforts led to the development of Fitted first reported in 2007 and further developed since then. In this study, we wished to evaluate the impact of protein flexibility and occurrence of water molecules on the accuracy of the Fitted docking program to discriminate active compounds from inactive compounds in virtual screening (VS) campaigns. For this purpose, a total of 171 proteins cocrystallized with small molecules representing 40 unique enzymes and receptors as well as sets of known ligands and decoys were selected from the Protein Data Bank (PDB) and the Directory of Useful Decoys (DUD), respectively. This study revealed that implementing displaceable crystallographic or computationally placed particle water molecules and protein flexibility can improve the enrichment in active compounds. In addition, an informed decision based on library diversity or research objectives (hit discovery vs lead optimization) on which implementation to use may lead to significant improvements.

Role of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl.

PubMed

Palencia, Andres; Camara-Artigas, Ana; Pisabarro, M Teresa; Martinez, Jose C; Luque, Irene

2010-01-22

The interaction of Abl-Src homology 3 domain (SH3) with the high affinity peptide p41 is the most notable example of the inconsistency existing between the currently accepted description of SH3 complexes and their binding thermodynamic signature. We had previously hypothesized that the presence of interfacial water molecules is partially responsible for this thermodynamic behavior. We present here a thermodynamic, structural, and molecular dynamics simulation study of the interaction of p41 with Abl-SH3 and a set of mutants designed to alter the water-mediated interaction network. Our results provide a detailed description of the dynamic properties of the interfacial water molecules and a molecular interpretation of the thermodynamic effects elicited by the mutations in terms of the modulation of the water-mediated hydrogen bond network. In the light of these results, a new dual binding mechanism is proposed that provides a better description of proline-rich ligand recognition by Abl-SH3 and that has important implications for rational design.

Toxicity and Bioavailability of Metals in the Missouri River Adjacent to a Lead Refinery

DTIC Science & Technology

2001-12-01

Missouri River adjacent to the facility. Groundwater was also collected from the facility. Waters and sediments were analyzed for inorganic...highly elevated in the groundwater , but not in river sediment pore waters . Lead concentrations were moderately elevated in whole sediment at one site...but lead concentrations in pore waters were low due to apparent sequestration by acid-volatile sulfides. The groundwater sample was highly toxic to

Forecasters Handbook for Japan and Adjacent Sea Areas

DTIC Science & Technology

1988-06-01

a strengthening Siberian high pressure cell. 4.5.1.1 Synoptic Patterns Summer is a season of reduced extratropical storm activity over the East China...the waters adjacent to eastern Asia, summer is a period of reduced extratropical storm activity over the Yellow Sea. Figure 2-6 (page 2-23) depicts...since the southeastern part of the sea is 6-15 closer to the extratropical storm tracks discussed in section 6.3.1.1 above. 6.3.1.3 Upper Level Winds

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

Intuitive, but not simple: including explicit water molecules in protein-protein docking simulations improves model quality.

PubMed

Parikh, Hardik I; Kellogg, Glen E

2014-06-01

Characterizing the nature of interaction between proteins that have not been experimentally cocrystallized requires a computational docking approach that can successfully predict the spatial conformation adopted in the complex. In this work, the Hydropathic INTeractions (HINT) force field model was used for scoring docked models in a data set of 30 high-resolution crystallographically characterized "dry" protein-protein complexes and was shown to reliably identify native-like models. However, most current protein-protein docking algorithms fail to explicitly account for water molecules involved in bridging interactions that mediate and stabilize the association of the protein partners, so we used HINT to illuminate the physical and chemical properties of bridging waters and account for their energetic stabilizing contributions. The HINT water Relevance metric identified the "truly" bridging waters at the 30 protein-protein interfaces and we utilized them in "solvated" docking by manually inserting them into the input files for the rigid body ZDOCK program. By accounting for these interfacial waters, a statistically significant improvement of ∼24% in the average hit-count within the top-10 predictions the protein-protein dataset was seen, compared to standard "dry" docking. The results also show scoring improvement, with medium and high accuracy models ranking much better than incorrect ones. These improvements can be attributed to the physical presence of water molecules that alter surface properties and better represent native shape and hydropathic complementarity between interacting partners, with concomitantly more accurate native-like structure predictions. © 2013 Wiley Periodicals, Inc.

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

The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood-Buff approaches.

PubMed

Kobayashi, Takeshi; Reid, Joshua E S J; Shimizu, Seishi; Fyta, Maria; Smiatek, Jens

2017-07-26

We study the properties of residual water molecules at different mole fractions in dialkylimidazolium based ionic liquids (ILs), namely 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM/BF 4 ) and 1-butyl-3-methylimidazolium tetrafluoroborate (BMIM/BF 4 ) by means of atomistic molecular dynamics (MD) simulations. The corresponding Kirkwood-Buff (KB) integrals for the water-ion and ion-ion correlation behavior are calculated by a direct evaluation of the radial distribution functions. The outcomes are compared to the corresponding KB integrals derived by an inverse approach based on experimental data. Our results reveal a quantitative agreement between both approaches, which paves a way towards a more reliable comparison between simulation and experimental results. The simulation outcomes further highlight that water even at intermediate mole fractions has a negligible influence on the ion distribution in the solution. More detailed analysis on the local/bulk partition coefficients and the partial structure factors reveal that water molecules at low mole fractions mainly remain in the monomeric state. A non-linear increase of higher order water clusters can be found at larger water concentrations. For both ILs, a more pronounced water coordination around the cations when compared to the anions can be observed, which points out that the IL cations are mainly responsible for water pairing mechanisms. Our simulations thus provide detailed insights in the properties of dialkylimidazolium based ILs and their effects on water binding.

Aqueous solvation of polyalanine α-helices with specific water molecules and with the CPCM and SM5.2 aqueous continuum models using density functional theory.

PubMed

Marianski, Mateusz; Dannenberg, J J

2012-02-02

We present density functional theory (DFT) calculations at the X3LYP/D95(d,p) level on the solvation of polyalanine α-helices in water. The study includes the effects of discrete water molecules and the CPCM and AMSOL SM5.2 solvent continuum model both separately and in combination. We find that individual water molecules cooperatively hydrogen-bond to both the C- and N-termini of the helix, which results in increases in the dipole moment of the helix/water complex to more than the vector sum of their individual dipole moments. These waters are found to be more stable than in bulk solvent. On the other hand, individual water molecules that interact with the backbone lower the dipole moment of the helix/water complex to below that of the helix itself. Small clusters of waters at the termini increase the dipole moments of the helix/water aggregates, but the effect diminishes as more waters are added. We discuss the somewhat complex behavior of the helix with the discrete waters in the continuum models.

Gibbs Free Energy of Hydrolytic Water Molecule in Acyl-Enzyme Intermediates of a Serine Protease: A Potential Application for Computer-Aided Discovery of Mechanism-Based Reversible Covalent Inhibitors.

PubMed

Masuda, Yosuke; Yamaotsu, Noriyuki; Hirono, Shuichi

2017-01-01

In order to predict the potencies of mechanism-based reversible covalent inhibitors, the relationships between calculated Gibbs free energy of hydrolytic water molecule in acyl-trypsin intermediates and experimentally measured catalytic rate constants (k cat ) were investigated. After obtaining representative solution structures by molecular dynamics (MD) simulations, hydration thermodynamics analyses using WaterMap™ were conducted. Consequently, we found for the first time that when Gibbs free energy of the hydrolytic water molecule was lower, logarithms of k cat were also lower. The hydrolytic water molecule with favorable Gibbs free energy may hydrolyze acylated serine slowly. Gibbs free energy of hydrolytic water molecule might be a useful descriptor for computer-aided discovery of mechanism-based reversible covalent inhibitors of hydrolytic enzymes.

Hydrophobic fluorine mediated switching of the hydrogen bonding site as well as orientation of water molecules in the aqueous mixture of monofluoroethanol: IR, molecular dynamics and quantum chemical studies.

PubMed

Mondal, Saptarsi; Biswas, Biswajit; Nandy, Tonima; Singh, Prashant Chandra

2017-09-20

The local structures between water-water, alcohol-water and alcohol-alcohol have been investigated for aqueous mixtures of ethanol (ETH) and monofluoroethanol (MFE) by the deconvolution of IR bands in the OH stretching region, molecular dynamics simulation and quantum chemical calculations. It has been found that the addition of a small amount of ETH into the aqueous medium increases the strength of the hydrogen bonds between water molecules. In an aqueous mixture of MFE, the substitution of a single fluorine induces a change in the orientation as well as the hydrogen bonding site of water molecules from the oxygen to the fluorine terminal of MFE. The switching of the hydrogen bonding site of water in the aqueous mixture of MFE results in comparatively strong hydrogen bonds between MFE and water molecules as well as less clustering of water molecules, unlike the case of the aqueous mixture of ETH. These findings about the modification of a hydrogen bond network by the hydrophobic fluorine group probably make fluorinated molecules useful for pharmaceutical as well as biological applications.

Aqueous turbulence structure immediately adjacent to the air - water interface and interfacial gas exchange

NASA Astrophysics Data System (ADS)

Wang, Binbin

Air-sea interaction and the interfacial exchange of gas across the air-water interface are of great importance in coupled atmospheric-oceanic environmental systems. Aqueous turbulence structure immediately adjacent to the air-water interface is the combined result of wind, surface waves, currents and other environmental forces and plays a key role in energy budgets, gas fluxes and hence the global climate system. However, the quantification of turbulence structure sufficiently close to the air-water interface is extremely difficult. The physical relationship between interfacial gas exchange and near surface turbulence remains insufficiently investigated. This dissertation aims to measure turbulence in situ in a complex environmental forcing system on Lake Michigan and to reveal the relationship between turbulent statistics and the CO2 flux across the air-water interface. The major objective of this dissertation is to investigate the physical control of the interfacial gas exchange and to provide a universal parameterization of gas transfer velocity from environmental factors, as well as to propose a mechanistic model for the global CO2 flux that can be applied in three dimensional climate-ocean models. Firstly, this dissertation presents an advanced measurement instrument, an in situ free floating Particle Image Velocimetry (FPIV) system, designed and developed to investigate the small scale turbulence structure immediately below the air-water interface. Description of hardware components, design of the system, measurement theory, data analysis procedure and estimation of measurement error were provided. Secondly, with the FPIV system, statistics of small scale turbulence immediately below the air-water interface were investigated under a variety of environmental conditions. One dimensional wave-number spectrum and structure function sufficiently close to the water surface were examined. The vertical profiles of turbulent dissipation rate were intensively studied

Dynamics of copper-phthalocyanine molecules on Au/Ge(001)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sotthewes, K.; Heimbuch, R.; Zandvliet, H. J. W.

2015-10-07

Spatially resolved current-time scanning tunneling spectroscopy combined with current-distance spectroscopy has been used to characterize the dynamic behavior of copper-phthalocyanine (CuPc) molecules adsorbed on a Au-modified Ge(001) surface. The analyzed CuPc molecules are adsorbed in a “molecular bridge” configuration, where two benzopyrrole groups (lobes) are connected to a Au-induced nanowire, whereas the other two lobes are connected to the adjacent nanowire. Three types of lobe configurations are found: a bright lobe, a dim lobe, and a fuzzy lobe. The dim and fuzzy lobes exhibit a well-defined switching behavior between two discrete levels, while the bright lobe shows a broad oscillationmore » band. The observed dynamic behavior is induced by electrons that are injected into the LUMO+1 orbital of the CuPc molecule. By precisely adjusting the tip-molecule distance, the switching frequency of the lobes can be tuned accurately.« less

Seep and stream nitrogen dynamics in two adjacent mixed land use watersheds

USDA-ARS?s Scientific Manuscript database

In many headwater catchments, streamflow originates from surface seeps and springs. The objective of this study was to determine the influence of seeps on nitrogen (N) dynamics within the stream and at the outlet of two adjacent mixed land use watersheds. Nitrogen concentrations in stream water were...

Facilitation of the PED analysis of large molecules by using global coordinates.

PubMed

Jamróz, Michał H; Ostrowski, Sławomir; Dobrowolski, Jan Cz

2015-10-05

Global coordinates have been found to be useful in the potential energy distribution (PED) analyses of the following large molecules: [13]-acene and [33]-helicene. The global coordinate is defined based on much distanced fragments of the analysed molecule, whereas so far, the coordinates used in the analysis were based on stretchings, bendings, or torsions of the adjacent atoms. It has been shown that the PED analyses performed using the global coordinate and the classical ones can lead to exactly the same PED contributions. The global coordinates may significantly improve the facility of the analysis of the vibrational spectra of large molecules. Copyright © 2015 Elsevier B.V. All rights reserved.

Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection

PubMed Central

Maciag, Joseph J.; Mackenzie, Sarah H.; Tucker, Matthew B.; Schipper, Joshua L.; Swartz, Paul; Clark, A. Clay

2016-01-01

The native ensemble of caspases is described globally by a complex energy landscape where the binding of substrate selects for the active conformation, whereas targeting an allosteric site in the dimer interface selects an inactive conformation that contains disordered active-site loops. Mutations and posttranslational modifications stabilize high-energy inactive conformations, with mostly formed, but distorted, active sites. To examine the interconversion of active and inactive states in the ensemble, we used detection of related solvent positions to analyze 4,995 waters in 15 high-resolution (<2.0 Å) structures of wild-type caspase-3, resulting in 450 clusters with the most highly conserved set containing 145 water molecules. The data show that regions of the protein that contact the conserved waters also correspond to sites of posttranslational modifications, suggesting that the conserved waters are an integral part of allosteric mechanisms. To test this hypothesis, we created a library of 19 caspase-3 variants through saturation mutagenesis in a single position of the allosteric site of the dimer interface, and we show that the enzyme activity varies by more than four orders of magnitude. Altogether, our database consists of 37 high-resolution structures of caspase-3 variants, and we demonstrate that the decrease in activity correlates with a loss of conserved water molecules. The data show that the activity of caspase-3 can be fine-tuned through globally desolvating the active conformation within the native ensemble, providing a mechanism for cells to repartition the ensemble and thus fine-tune activity through conformational selection. PMID:27681633

Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection.

PubMed

Maciag, Joseph J; Mackenzie, Sarah H; Tucker, Matthew B; Schipper, Joshua L; Swartz, Paul; Clark, A Clay

2016-10-11

The native ensemble of caspases is described globally by a complex energy landscape where the binding of substrate selects for the active conformation, whereas targeting an allosteric site in the dimer interface selects an inactive conformation that contains disordered active-site loops. Mutations and posttranslational modifications stabilize high-energy inactive conformations, with mostly formed, but distorted, active sites. To examine the interconversion of active and inactive states in the ensemble, we used detection of related solvent positions to analyze 4,995 waters in 15 high-resolution (<2.0 Å) structures of wild-type caspase-3, resulting in 450 clusters with the most highly conserved set containing 145 water molecules. The data show that regions of the protein that contact the conserved waters also correspond to sites of posttranslational modifications, suggesting that the conserved waters are an integral part of allosteric mechanisms. To test this hypothesis, we created a library of 19 caspase-3 variants through saturation mutagenesis in a single position of the allosteric site of the dimer interface, and we show that the enzyme activity varies by more than four orders of magnitude. Altogether, our database consists of 37 high-resolution structures of caspase-3 variants, and we demonstrate that the decrease in activity correlates with a loss of conserved water molecules. The data show that the activity of caspase-3 can be fine-tuned through globally desolvating the active conformation within the native ensemble, providing a mechanism for cells to repartition the ensemble and thus fine-tune activity through conformational selection.

Enamel remineralization on teeth adjacent to Class II glass ionomer restorations.

PubMed

Segura, A; Donly, K J; Stratmann, R G

1997-10-01

To examine the in vitro remineralization of incipient carious lesions on teeth adjacent interproximally to teeth with Class II glass ionomer cement restorations. Artificial carious lesions were created at the contact area of 30 teeth. Ten teeth had Class II glass ionomer cement/resin composite restorations placed, 10 teeth had Class II glass ionomer silver cermet restorations placed and 10 teeth had Class II amalgam restorations placed. Sections 100 microns thick were obtained longitudinally through the caries sites and polarized photomicrographs were taken in imbibition media of water and Thoulet's (R.I. 1.41 and 1.47) solutions, representing 5%, 10% and 25% pore volume respectively. Varnish was placed on the section, leaving only the external section site exposed, then sections were situated back into the original tooth. The restored teeth were abutted to the carious tooth so that the restorations came into contact with the adjacent restoration. The specimens were placed into closed environments of artificial saliva for 14 days, then were photographed again under polarized light and areas of the carious lesions were quantitated. An ANOVA indicated significant variance in adjacent tooth remineralization, when comparing the experimental groups, in imbibition media of water (P < 0.05), Thoulet's 1.41 solution (P < 0.008) and Thoulet's 1.47 solution (P < 0.006). Duncan's multiple range test demonstrated the glass ionomer cement/resin composite group to have significantly greater decrease in pore volume (P < 0.05) than the amalgam control group in water imbibition media and Thoulet's 1.47 media. There was no statistically significant difference between the glass ionomer cement/resin composite and glass ionomer silver cermet groups in these two imbibition media. The glass ionomer cement/resin composite group demonstrated significantly more (P < 0.05) decrease in pore volume than both the glass ionomer silver cermet group and amalgam control group in Thoulet's 1

An optical conveyor for molecules.

PubMed

Weinert, Franz M; Braun, Dieter

2009-12-01

Trapping single ions under vacuum allows for precise spectroscopy in atomic physics. The confinement of biological molecules in bulk water is hindered by the lack of comparably strong forces. Molecules have been immobilized to surfaces, however often with detrimental effects on their function. Here, we optically trap molecules by creating the microscale analogue of a conveyor belt: a bidirectional flow is combined with a perpendicular thermophoretic molecule drift. Arranged in a toroidal geometry, the conveyor accumulates a hundredfold excess of 5-base DNA within seconds. The concentrations of the trapped DNA scale exponentially with length, reaching trapping potential depths of 14 kT for 50 bases. The mechanism does not require microfluidics, electrodes, or surface modifications. As a result, the trap can be dynamically relocated. The optical conveyor can be used to enhance diffusion-limited surface reactions, redirect cellular signaling, observe individual biomolecules over a prolonged time, or approach single-molecule chemistry in bulk water.

Crystal Structures of Fatty Acid Amide Hydrolase Bound to the Carbamate Inhibitor URB597: Discovery of a Deacylating Water Molecule and Insight into Enzyme Inactivation

PubMed Central

Mileni, Mauro; Kamtekar, Satwik; Wood, David C.; Benson, Timothy E.; Cravatt, Benjamin F.; Stevens, Raymond C.

2010-01-01

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 Å 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 Å) 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 suggest a functional convergence between the amidase signature enzymes and serine proteases. PMID:20493882

Crystal structure of fatty acid amide hydrolase bound to the carbamate inhibitor URB597: discovery of a deacylating water molecule and insight into enzyme inactivation.

PubMed

Mileni, Mauro; Kamtekar, Satwik; Wood, David C; Benson, Timothy E; Cravatt, Benjamin F; Stevens, Raymond C

2010-07-23

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 A 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 A) 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. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

USGS Publications Warehouse

Alpers, Charles N.; Whittemore, Donald 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

Seep and stream nitrogen dynamics in two adjacent mixed land use watersheds

USDA-ARS?s Scientific Manuscript database

In many headwater catchments, stream flow originates from surface seeps and springs. The objective of this study was to determine the influence of seeps on nitrogen (N) dynamics within the stream and at the outlet of two adjacent mixed land use watersheds. Nitrogen concentrations in stream water wer...

Role of Interfacial Water Molecules in Proline-rich Ligand Recognition by the Src Homology 3 Domain of Abl*

PubMed Central

Palencia, Andres; Camara-Artigas, Ana; Pisabarro, M. Teresa; Martinez, Jose C.; Luque, Irene

2010-01-01

The interaction of Abl-Src homology 3 domain (SH3) with the high affinity peptide p41 is the most notable example of the inconsistency existing between the currently accepted description of SH3 complexes and their binding thermodynamic signature. We had previously hypothesized that the presence of interfacial water molecules is partially responsible for this thermodynamic behavior. We present here a thermodynamic, structural, and molecular dynamics simulation study of the interaction of p41 with Abl-SH3 and a set of mutants designed to alter the water-mediated interaction network. Our results provide a detailed description of the dynamic properties of the interfacial water molecules and a molecular interpretation of the thermodynamic effects elicited by the mutations in terms of the modulation of the water-mediated hydrogen bond network. In the light of these results, a new dual binding mechanism is proposed that provides a better description of proline-rich ligand recognition by Abl-SH3 and that has important implications for rational design. PMID:19906645

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.

Displacement of disordered water molecules from hydrophobic pocket creates enthalpic signature: binding of phosphonamidate to the S₁'-pocket of thermolysin.

PubMed

Englert, L; Biela, A; Zayed, M; Heine, A; Hangauer, D; Klebe, G

2010-11-01

Prerequisite for the design of tight binding protein inhibitors and prediction of their properties is an in-depth understanding of the structural and thermodynamic details of the binding process. A series of closely related phosphonamidates was studied to elucidate the forces underlying their binding affinity to thermolysin. The investigated inhibitors are identical except for the parts penetrating into the hydrophobic S₁'-pocket. A correlation of structural, kinetic and thermodynamic data was carried out by X-ray crystallography, kinetic inhibition assay and isothermal titration calorimetry. Binding affinity increases with larger ligand hydrophobic P₁'-moieties accommodating the S₁'-pocket. Surprisingly, larger P₁'-side chain modifications are accompanied by an increase in the enthalpic contribution to binding. In agreement with other studies, it is suggested that the release of largely disordered waters from an imperfectly hydrated pocket results in an enthalpically favourable integration of these water molecules into bulk water upon inhibitor binding. This enthalpically favourable process contributes more strongly to the binding energetics than the entropy increase resulting from the release of water molecules from the S₁'-pocket or the formation of apolar interactions between protein and inhibitor. Displacement of highly disordered water molecules from a rather imperfectly hydrated and hydrophobic specificity pocket can reveal an enthalpic signature of inhibitor binding. Copyright © 2010 Elsevier B.V. All rights reserved.

Miscibility at the immiscible liquid/liquid interface: A molecular dynamics study of thermodynamics and mechanism

NASA Astrophysics Data System (ADS)

Karnes, John J.; Benjamin, Ilan

2018-01-01

Molecular dynamics simulations are used to study the dissolution of water into an adjacent, immiscible organic liquid phase. Equilibrium thermodynamic and structural properties are calculated during the transfer of water molecule(s) across the interface using umbrella sampling. The net free energy of transfer agrees reasonably well with experimental solubility values. We find that water molecules "prefer" to transfer into the adjacent phase one-at-a-time, without co-transfer of the hydration shell, as in the case of evaporation. To study the dynamics and mechanism of transfer of water to liquid nitrobenzene, we collected over 400 independent dissolution events. Analysis of these trajectories suggests that the transfer of water is facilitated by interfacial protrusions of the water phase into the organic phase, where one water molecule at the tip of the protrusion enters the organic phase by the breakup of a single hydrogen bond.

The cellular environment of cancerous human tissue. Interfacial and dangling water as a "hydration fingerprint".

PubMed

Abramczyk, Halina; Brozek-Pluska, Beata; Krzesniak, Marta; Kopec, Monika; Morawiec-Sztandera, Alina

2014-08-14

Despite a large number of publications, the role of water in the cellular environment of biological tissue has not been clarified. Characterizing the biological interface is a key challenge in understanding the interactions of water in the tissue. Although we often assume that the properties of the bulk water can be translated to the crowded biological environment, this approach must be considerably revised when considering the biological interface. To our knowledge, few studies have directly monitored the interactions and accumulation of water in the restricted environments of the biological tissue upon realistic crowding conditions. The present study focuses on a molecular picture of water molecules at the biological interface, or specifically, water molecules adjacent to the hydrophobic and hydrophilic surfaces of normal and cancerous tissues. We recorded and analyzed the IR and Raman spectra of the νs(OH) stretching modes of water at the biological interfaces of the human breast and neck tissues. The results revealed dramatic changes in the water content in the tissue and are potentially relevant to both the fundamental problems of interfacial water modeling and the molecular diagnostics of cancer as a 'hydration fingerprint'. Herein, we will discuss the origin of the vibrational substructures observed for the νs(OH) stretching modes of water, showing that the interfacial water interacting via H-bond with other water molecules and biomolecules at the biological surface and free OH vibration of the dangling water are sensitive indicators of the pathology between the normal (noncancerous) and cancerous tissue and cancer types. Copyright © 2014 Elsevier B.V. All rights reserved.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Al-Hamdani, Yasmine S.; Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ; Alfè, Dario

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 doped graphene and C doped h-BN. We find that doped surfaces are considerably more reactive than their pristine counterparts and by comparingmore » 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.« less

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.

Changes in the hydrogen-bonding strength of internal water molecules and cysteine residues in the conductive state of channelrhodopsin-1

NASA Astrophysics Data System (ADS)

Lórenz-Fonfría, Víctor A.; Muders, Vera; Schlesinger, Ramona; Heberle, Joachim

2014-12-01

Water plays an essential role in the structure and function of proteins, particularly in the less understood class of membrane proteins. As the first of its kind, channelrhodopsin is a light-gated cation channel and paved the way for the new and vibrant field of optogenetics, where nerve cells are activated by light. Still, the molecular mechanism of channelrhodopsin is not understood. Here, we applied time-resolved FT-IR difference spectroscopy to channelrhodopsin-1 from Chlamydomonas augustae. It is shown that the (conductive) P2380 intermediate decays with τ ≈ 40 ms and 200 ms after pulsed excitation. The vibrational changes between the closed and the conductive states were analyzed in the X-H stretching region (X = O, S, N), comprising vibrational changes of water molecules, sulfhydryl groups of cysteine side chains and changes of the amide A of the protein backbone. The O-H stretching vibrations of "dangling" water molecules were detected in two different states of the protein using H218O exchange. Uncoupling experiments with a 1:1 mixture of H2O:D2O provided the natural uncoupled frequencies of the four O-H (and O-D) stretches of these water molecules, each with a very weakly hydrogen-bonded O-H group (3639 and 3628 cm-1) and with the other O-H group medium (3440 cm-1) to moderately strongly (3300 cm-1) hydrogen-bonded. Changes in amide A and thiol vibrations report on global and local changes, respectively, associated with the formation of the conductive state. Future studies will aim at assigning the respective cysteine group(s) and at localizing the "dangling" water molecules within the protein, providing a better understanding of their functional relevance in CaChR1.

33 CFR 334.85 - New York Harbor, adjacent to the Stapleton Naval Station, Staten Island, New York; restricted area.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false New York Harbor, adjacent to the Stapleton Naval Station, Staten Island, New York; restricted area. 334.85 Section 334.85 Navigation and... RESTRICTED AREA REGULATIONS § 334.85 New York Harbor, adjacent to the Stapleton Naval Station, Staten Island...

Cooperation between bound waters and hydroxyls in controlling isotope-exchange rates

NASA Astrophysics Data System (ADS)

Panasci, Adele F.; McAlpin, J. Gregory; Ohlin, C. André; Christensen, Shauna; Fettinger, James C.; Britt, R. David; Rustad, James R.; Casey, William H.

2012-02-01

Mineral oxides differ from aqueous ions in that the bound water molecules are usually attached to different metal centers, or vicinal, and thus separated from one another. In contrast, for most monomeric ions used to establish kinetic reactivity trends, such as octahedral aquo ions (e.g., Al(H 2O) 63+), the bound waters are closely packed, or geminal. Because of this structural difference, the existing literature about ligand substitution in monomer ions may be a poor guide to the reactions of geochemical interest. To understand how coordination of the reactive functional groups might affect the rates of simple water-exchange reactions, we synthesized two structurally similar Rh(III) complexes, [Rh(phen) 2(H 2O) 2] 3+ [ 1] and [Rh(phen) 2(H 2O)Cl] 2+ [ 2] where (phen) = 1,10-phenanthroline. Complex [ 1] has two adjacent, geminal, bound waters in the inner-coordination sphere and [ 2] has a single bound water adjacent to a bound chloride ion. We employed Rh(III) as a trivalent metal rather than a more geochemically relevant metal like Fe(III) or Al(III) to slow the rate of reaction, which makes possible measurement of the rates of isotopic substitution by simple mass spectrometry. We prepared isotopically pure versions of the molecules, dissolved them into isotopically dissimilar water, and measured the rates of exchange from the extents of 18O and 16O exchange at the bound waters. The pH dependency of rates differ enormously between the two complexes. Pseudo-first-order rate coefficients at 298 K for water exchanges from the fully protonated molecules are close: k0298 = 5 × 10 -8(±0.5 × 10 -8) s -1 for [ 1] and k0298 = 2.5 × 10 -9(±1 × 10 -9) for [ 2]. Enthalpy and entropy activation parameters (Δ H‡ and Δ S‡) were measured to be 119(±3) kJ mol -1, and 14(±1) J mol -1 K -1, respectively for [ 1]. The corresponding parameters for the mono-aquo complex, [ 2], are 132(±3) kJ mol -1 and 41.5(±2) J mol -1 K -1. Rates increase by many orders of magnitude

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

[Permeability of isolated rat hepatocyte plasma membranes for molecules of dimethyl sulfoxide].

PubMed

Kuleshova, L G; Gordienko, E A; Kovalenko, I F

2014-01-01

We have studied permeability of isolated rat hepatocyte membranes for molecules of dimethyl sulfoxide (DMSO) at different hypertonicity of a cryoprotective medium. The permeability coefficient of hepatocyte membranes κ1 for DMSO molecules was shown to be the differential function of osmotic pressure between a cell and an extracellular medium. Ten-fold augmentation of DMSO concentration in the cryoprotective medium causes the decrease of permeability coefficients κ1 probably associated with the increased viscosity in membrane-adjacent liquid layers as well as partial limitations appeared as a result of change in cell membrane shape after hepatocyte dehydration. We have found out that in aqueous solutions of NaCl (2246 mOsm/l) and DMSO (2250 mOsm/l) the filtration coefficient L(p) in the presence of a penetrating cryoprotectant (L(pDMSO) = (4.45 ± 0.04) x 10(-14) m3/Ns) is 3 orders lower compared to the case with electrolyte (L(pNaCl) = (2.25 ± 0.25) x 10(-11) m3/Ns). This phenomenon is stipulated by the cross impact of flows of a cryoprotectant and water at the stage of cell dehydration. Pronounced lipophilicity of DMSO, geometric parameters of its molecule as well as the presence of large aqueous pores in rat hepatocyte membranes allow of suggesting the availability of two ways of penetrating this cryoprotectant into the cells by non-specific diffusion through membrane lipid areas and hydrophilic channels.

Redhead duck behavior on lower Laguna Madre and adjacent ponds of southern Texas

USGS Publications Warehouse

Mitchell, C.A.; Custer, T.W.; Zwank, P.J.

1992-01-01

Behavior of redheads (Aythya americana) during winter was studied on the hypersaline lower Laguna Madre and adjacent freshwater to brackish water ponds of southern Texas. On Laguna Madre, feeding (46%) and sleeping (37%) were the most common behaviors. Redheads fed more during early morning (64%) than during the rest of the day (40%); feeding activity was negatively correlated with temperature. Redheads fed more often by dipping (58%) than by tipping (25%), diving (16%), or gleaning (0.1%). Water depth was least where they fed by dipping (16 cm), greatest where diving (75 cm), and intermediate where tipping (26 cm). Feeding sequences averaged 5.3 s for dipping, 8.1 s for tipping, and 19.2 s for diving. Redheads usually were present on freshwater to brackish water ponds adjacent to Laguna Madre only during daylight hours, and use of those areas declined as winter progressed. Sleeping (75%) was the most frequent behavior at ponds, followed by preening (10%), swimming (10%), and feeding (0.4%). Because redheads fed almost exclusively on shoalgrass while dipping and tipping in shallow water and shoalgrass meadows have declined in the lower Laguna Madre, proper management of the remaining shoalgrass habitat is necessary to ensure that this area remains the major wintering area for redheads.

33 CFR 334.830 - Lake Michigan; small-arms range adjacent to U.S. Naval Training Center, Great Lakes, Ill.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 33 Navigation and Navigable Waters 3 2014-07-01 2014-07-01 false Lake Michigan; small-arms range adjacent to U.S. Naval Training Center, Great Lakes, Ill. 334.830 Section 334.830 Navigation and Navigable... REGULATIONS § 334.830 Lake Michigan; small-arms range adjacent to U.S. Naval Training Center, Great Lakes, Ill...

33 CFR 334.830 - Lake Michigan; small-arms range adjacent to U.S. Naval Training Center, Great Lakes, Ill.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 33 Navigation and Navigable Waters 3 2012-07-01 2012-07-01 false Lake Michigan; small-arms range adjacent to U.S. Naval Training Center, Great Lakes, Ill. 334.830 Section 334.830 Navigation and Navigable... REGULATIONS § 334.830 Lake Michigan; small-arms range adjacent to U.S. Naval Training Center, Great Lakes, Ill...

33 CFR 334.830 - Lake Michigan; small-arms range adjacent to U.S. Naval Training Center, Great Lakes, Ill.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Lake Michigan; small-arms range adjacent to U.S. Naval Training Center, Great Lakes, Ill. 334.830 Section 334.830 Navigation and Navigable... REGULATIONS § 334.830 Lake Michigan; small-arms range adjacent to U.S. Naval Training Center, Great Lakes, Ill...

33 CFR 334.830 - Lake Michigan; small-arms range adjacent to U.S. Naval Training Center, Great Lakes, Ill.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 33 Navigation and Navigable Waters 3 2011-07-01 2011-07-01 false Lake Michigan; small-arms range adjacent to U.S. Naval Training Center, Great Lakes, Ill. 334.830 Section 334.830 Navigation and Navigable... REGULATIONS § 334.830 Lake Michigan; small-arms range adjacent to U.S. Naval Training Center, Great Lakes, Ill...

33 CFR 334.830 - Lake Michigan; small-arms range adjacent to U.S. Naval Training Center, Great Lakes, Ill.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 33 Navigation and Navigable Waters 3 2013-07-01 2013-07-01 false Lake Michigan; small-arms range adjacent to U.S. Naval Training Center, Great Lakes, Ill. 334.830 Section 334.830 Navigation and Navigable... REGULATIONS § 334.830 Lake Michigan; small-arms range adjacent to U.S. Naval Training Center, Great Lakes, Ill...

Photoionization of water molecules by a train of attosecond pulses assisted by a near-infrared laser: delay and polarization control

NASA Astrophysics Data System (ADS)

Martini, Lara; Boll, Diego I. R.; Fojón, Omar A.

2017-08-01

Basic reactions involving water molecules are essential to understand the interaction between radiation and the biological tissue because living cells are composed mostly by water. Therefore, the knowledge of ionization of the latter is crucial in many domains of Biology and Physics. So, we study theoretically the photoionization of water molecules by extreme ultraviolet attopulse trains assisted by lasers in the near-infrared range. We use a separable Coulomb-Volkov model in which the temporal evolution of the system can be divided into three stages allowing spatial and temporal separation for the Coulomb and Volkov final state wavefunctions. First, we analyze photoelectron angular distributions for different delays between the attopulse train and the assistant laser field. We compare our results for water and Ne atoms as they belong to the same isoelectronic series. Moreover, we contrast our calculations with previous theoretical and experimental work for Ar atoms due to the similarities of the orbitals involved in the reaction. Second, we study the effect of varying the relative orientations of the attopulse and laser field polarizations and we compare our predictions with other theories and experiments. We expect these studies contribute to the improvement of polarization experiments and the development of the attopulse trains and assistant laser fields technologies. Finally, we hope our work promote progress on the control of the chemical reactivity of water molecules since this could be useful in different fields such as radiobiology and medical physics.

30 CFR 816.57 - Hydrologic balance: Activities in or adjacent to perennial or intermittent streams.

Code of Federal Regulations, 2012 CFR

2012-07-01

... or adjacent to perennial or intermittent streams. (a)(1) Buffer requirement. Except as provided in... section 402 or 404 of the Clean Water Act. (b) Exception. The buffer requirement of paragraph (a) of this...

30 CFR 816.57 - Hydrologic balance: Activities in or adjacent to perennial or intermittent streams.

Code of Federal Regulations, 2014 CFR

2014-07-01

... or adjacent to perennial or intermittent streams. (a)(1) Buffer requirement. Except as provided in... section 402 or 404 of the Clean Water Act. (b) Exception. The buffer requirement of paragraph (a) of this...

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.

Variability in physical and biological exchange among coastal wetlands and their adjacent Great Lakes

EPA Science Inventory

Hydrology is a major governor of physically-driven exchange among coastal wetlands and the adjacent Great Lake, whereas fish movement is a major governor of biologically-driven exchange. We use data describing coastal wetland morphology, hydrology, water quality, and fish tissue...

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

Correlation between macrobenthic structure (biotic) and water-sediment characteristics (abiotic) adjacent aquaculture areas at Tembelas Island, indonesia

NASA Astrophysics Data System (ADS)

Sharani, Jeanny; Hidayat, Jafron W.; Putro, Sapto P.

2018-05-01

Macrobenthic community play important role in sedimentary habitats as a part of food chain. Their structure may be influenced by environmental characteristic spatially and temporally. The purpose of this study is to access the correlation between macrobenthic structure (biotic) and water-sediment characteristics (abiotic) adjacent aquaculture areas at Tembelas Island, Indonesia. Water and sediments samples were taken twice, where the first and second sampling time were taken in June and October 2016, respectively. Samples were taken in the area of fish farming at coastal area of policulture/IMTA (as Location I), site of 1 km away from fish farming area as a reference site (as Location II), and monoculture sites (as Location III), with three stations for each location. Data of abiotic parameters included the composition of sediment substrate and DO, pH, salinity, temperature, and. Sediment samples were taken using Ekman grab. The organisms were 1 mm -size sieved and fixed using 10% formalin for further analysis, i.e. sorting, preserving, enumerating, identifying, and grouping. The relationship between biotics (macrobentos) and abiotics (physical-chemical factors) was assessed using a non-parametric multivariate procedure (BIOENV). This study found 61 species consisting of 46 families and 5 classes of macrobenthos. The most common classes were member of Mollusca and Polychaeta. Total nitrogen, silt, and clay were the abiotic factors most influencing macrobenthic structure (BIO-ENV; r = 0.46; R2 = 21.16%).

Endothelin-1 stimulates colon cancer adjacent fibroblasts.

PubMed

Knowles, Jonathan P; Shi-Wen, Xu; Haque, Samer-ul; Bhalla, Ashish; Dashwood, Michael R; Yang, Shiyu; Taylor, Irving; Winslet, Marc C; Abraham, David J; Loizidou, Marilena

2012-03-15

Endothelin-1 (ET-1) is produced by and stimulates colorectal cancer cells. Fibroblasts produce tumour stroma required for cancer development. We investigated whether ET-1 stimulated processes involved in tumour stroma production by colonic fibroblasts. Primary human fibroblasts, isolated from normal tissues adjacent to colon cancers, were cultured with or without ET-1 and its antagonists. Cellular proliferation, migration and contraction were measured. Expression of enzymes involved in tumour stroma development and alterations in gene transcription were determined by Western blotting and genome microarrays. ET-1 stimulated proliferation, contraction and migration (p < 0.01 v control) and the expression of matrix degrading enzymes TIMP-1 and MMP-2, but not MMP-3. ET-1 upregulated genes for profibrotic growth factors and receptors, signalling molecules, actin modulators and extracellular matrix components. ET-1 stimulated colonic fibroblast cellular processes in vitro that are involved in developing tumour stroma. Upregulated genes were consistent with these processes. By acting as a strong stimulus for tumour stroma creation, ET-1 is proposed as a target for adjuvant cancer therapy. Copyright © 2011 UICC.

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

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.; 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.

Petroleum hydrocarbons in a water-sediment system from Yellow River estuary and adjacent coastal area, China: Distribution pattern, risk assessment and sources.

PubMed

Wang, Min; Wang, Chuanyuan; Li, Yuanwei

2017-09-15

Aliphatic hydrocarbons (AHs), biomarker and polycyclic aromatic hydrocarbons (PAHs) concentrations of surface water and sediment samples collected from Yellow River Estuary and adjacent coastal area in China were measured to determine their spatial distributions, analyze their sources and evaluate the ecological risk of PAHs in the water-sediment system. The spatial distributions of n-alkane in sediments are mainly controlled by the mixing inputs of terrigenous and marine components. In comparison with AHs, the total concentrations of Σ16PAHs in surface sediments from a transect of the offshore area were noticeably higher than that of the riverine and estuary areas. Additionally, the AHs and total PAHs concentrations all indicated an overall pattern of a seaward decrease. The PAHs concentrations during the dry season (mainly in the form of dissolved phase) were higher than that of PAHs (mainly dissolved phase and particulate phase form) in the flooding season. In comparison with global concentration levels of PAHs, the level of PAHs in suspended particulate matter and sediments from the Yellow River Estuary was lower than those from other countries, while the concentration of PAHs in the dissolved phase were in the middle range. Petroleum contamination, mainly from oil exploration and discharge of pollutants from rivers, was the main source of n-alkanes. The PAHs in the river were mostly of petrogenic origin, while those in the estuarial and marine areas originated mainly from pyrogenic sources. The results of the toxicology assessment suggested that the PAHs in sediments from Yellow River Estuary and adjacent coastal area exhibited a low potential eco-toxicological contamination level. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular dynamics approach to probe PKCβII-ligand interactions and influence of crystal water molecules on these interactions.

PubMed

Grewal, Baljinder K; Bhat, Jyotsna; Sobhia, Masilamani Elizabeth

2015-01-01

PKCβII is a potential target for therapeutic intervention against pandemic diabetic complications. Present study probes the molecular interactions of PKCβII with its clinically important ligands, viz. ruboxistaurin, enzastaurin and co-crystallized ligand, 2-methyl-1H-indol-3-yl-BIM-1. The essentials of PKCβII-ligand interaction, crystal water-induced alterations in these interactions and key interacting flexible residues are analyzed. Computational methodologies, viz. molecular docking and molecular simulation coupled with molecular mechanics-Poisson-Boltzmann surface area and generalized born surface area (MM-PB[GB]SA) are employed. The structural changes in the presence and absence of crystal water molecules in PKCβII ATP binding site residues, and its interaction with bound ligand, are identified. Difference in interaction of selective and nonselective ligand with ATP binding site residues of PKCβII is reported. The study showed that the nonbonding interactions contribute significantly in PKCβII-ligand binding and presence of crystal water molecules affects the interactions. The findings of present work may integrate the new aspects in the drug design process of PKCβII inhibitors.

Generation of Chimeric RNAs by cis-splicing of adjacent genes (cis-SAGe) in mammals.

PubMed

Zhuo, Jian-Shu; Jing, Xiao-Yan; Du, Xin; Yang, Xiu-Qin

2018-02-20

Chimeric RNA molecules, possessing exons from two or more independent genes, are traditionally believed to be produced by chromosome rearrangement. However, recent studies revealed that cis-splicing of adjacent genes (cis- SAGe) is one of the major mechanisms underlying the formation of chimeric RNAs. cis-SAGe refers to intergenic splicing of directly adjacent genes with the same transcriptional orientation, resulting in read-through transcripts, termed chimeric RNAs, which contain sequences from two or more parental genes. cis-SAGe was first identified in tumor cells, since then its potential in carcinogenesis has attracted extensive attention. More and more scientists are focusing on it. With the development of research, cis-SAGe was found to be ubiquitous in various normal tissues, and might make a crucial contribution to the formation of novel genes in the evolution of genomes. In this review, we summarize the splicing pattern, expression characteristics, possible mechanisms, and significance of cis-SAGe in mammals. This review will be helpful for general understanding of the current status and development tendency of cis-SAGe.

Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization.

PubMed

Beuming, Thijs; Che, Ye; Abel, Robert; Kim, Byungchan; Shanmugasundaram, Veerabahu; Sherman, Woody

2012-03-01

Water plays an essential role in determining the structure and function of all biological systems. Recent methodological advances allow for an accurate and efficient estimation of the thermodynamic properties of water molecules at the surface of proteins. In this work, we characterize these thermodynamic properties and relate them to various structural and functional characteristics of the protein. We find that high-energy hydration sites often exist near protein motifs typically characterized as hydrophilic, such as backbone amide groups. We also find that waters around alpha helices and beta sheets tend to be less stable than waters around loops. Furthermore, we find no significant correlation between the hydration site-free energy and the solvent accessible surface area of the site. In addition, we find that the distribution of high-energy hydration sites on the protein surface can be used to identify the location of binding sites and that binding sites of druggable targets tend to have a greater density of thermodynamically unstable hydration sites. Using this information, we characterize the FKBP12 protein and show good agreement between fragment screening hit rates from NMR spectroscopy and hydration site energetics. Finally, we show that water molecules observed in crystal structures are less stable on average than bulk water as a consequence of the high degree of spatial localization, thereby resulting in a significant loss in entropy. These findings should help to better understand the characteristics of waters at the surface of proteins and are expected to lead to insights that can guide structure-based drug design efforts. Copyright © 2011 Wiley Periodicals, Inc.

New biochemical insight of conserved water molecules at catalytic and structural Zn2+ ions in human matrix metalloproteinase-I: a study by MD-simulation.

PubMed

Chakrabarti, Bornali; Bairagya, Hridoy R; Mukhopadhyay, Bishnu P; Sekar, K

2017-02-01

Human matrix metalloproteinase (MMP)-1 or collagenase-1 plays a significant role in embryonic development, tissue remodeling, and is also involved in several diseases like arthritis, metastasis, etc. Molecular dynamics simulation studies on hMMP-1 X-ray structures (PDB Id. 1CGE, 1CGF, 1CGL, 1HFC, and 2TCL) suggest that the three conserved water molecules (W H/1 , W I , W S ) are coordinated with catalytic zinc (Zn C ), and one water molecule (W) is associated at structural zinc ion (Zn S ). Transition of the coordination geometry around Zn C from tetrahedral to octahedral and tetrahedral to trigonal bipyramidal at Zn S are also observed during the dynamics. Recognition of two zinc ions through water mediated bridges (Zn C - W H (W 1 )…W 2 ….H 183 - Zn S ) and stabilization of secondary coordination zone around the metal ions indicates the possibility of Zn C …Zn S coupled catalytic mechanism in hMMP-I. This study not only reveals a functionally important role of conserved water molecules in hMMP-I but also highlights the involvement of other non catalytic residues, such as S172 and D170 in the catalytic mechanism. The results obtained in this study could be relevant for importance of conserved water mediated recognition site of the sequence residue id. 202(RWTNNFREY)210, interaction of W(tryptophan)203 to zinc bound histidine, their influence on the water molecules that are involved in bridging between Zn C and Zn S , and structure-based design of specific hMMP inhibitors. Graphical abstract Water mediated recognition of structural and catalytic zinc ions of hMMP-1 structure (MD simulatated conformation).

A delicate case of unidirectional proton transfer from water to an aromatic heterocyclic anion.

PubMed

Biswas, Sohag; Mallik, Bhabani S

2016-11-21

We present the characteristic proton transfer process from water to the pyrazole anion, infrared signatures of hydroxyl groups and the free energy profile of the process in aqueous solution combining first principles simulations, wavelet analysis and metadynamics. Our results show that the presence of minimum three water molecules in the gas phase cluster with a particular arrangement is sufficient to facilitate the proton transfer process from water to the anion. The overall reaction is very rapid in aqueous solution, and the free energy barrier for this process is found to be 4.2 kcal mol -1 . One of the earlier reported fundamental reasons for the transfer of proton from water to the anion is the change in the acidity of OH groups surrounding the anion. We have correlated the stretching frequencies of the surrounding OH groups with this acidity. We find that the development of less energetic vibrational states, and the OH mode having lowest average stretching frequency contains the most acidic proton. A large frequency shift of the OH mode belonging to one of the surrounding water molecules is observed during the transfer of proton from water to the anion; this shift is due to the change in acidity of the adjacent hydroxyl groups in the vicinity of the anion.

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.

30 CFR 817.57 - Hydrologic balance: Surface activities in or adjacent to perennial or intermittent streams.

Code of Federal Regulations, 2014 CFR

2014-07-01

... activities in or adjacent to perennial or intermittent streams. (a)(1) Buffer requirement. Except as provided... section 402 or 404 of the Clean Water Act. (b) Exception. The buffer requirement of paragraph (a) of this...

30 CFR 817.57 - Hydrologic balance: Surface activities in or adjacent to perennial or intermittent streams.

Code of Federal Regulations, 2012 CFR

2012-07-01

... activities in or adjacent to perennial or intermittent streams. (a)(1) Buffer requirement. Except as provided... section 402 or 404 of the Clean Water Act. (b) Exception. The buffer requirement of paragraph (a) of this...

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.

Detection of water molecules in inert gas based plasma by the ratios of atomic spectral lines

NASA Astrophysics Data System (ADS)

Bernatskiy, A. V.; Ochkin, V. N.

2017-01-01

A new approach is considered to detect the water leaks in inert plasma-forming gas present in the reactor chamber. It is made up of the intensity ratio of D α and H α spectral lines in combination with O, Ar and Xe lines intensity. The concentrations of H2O, O, H and D particles have been measured with high sensitivity. At the D2 admixture pressure {{p}{{\\text{D}\\text{2}}}}   =  0.025 mbar, we used the acquisition time of 10 s to measure the rate of water molecules injected from the outside, Γ0  =  1.4 · 10-9 mbar · m3 · s-1, and the incoming water molecules to plasma, Γ  =  5 ·10-11 mbar · m3 · s-1. The scaling proves that at small D2 admixtures (10-4 mbar), the leaks with the rates Γ0  ≈  6 · 10-12 mbar · m3 · s-1 and Γ  ≈  2 · 10-13 mbar · m3 · s-1 can be detected and measured. The difference between Γ0 and Γ values is due to the high degree of H2O dissociation, which can be up to 97-98%.

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)

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

Flight of a cytidine deaminase complex with an imperfect transition state analogue inhibitor: mass spectrometric evidence for the presence of a trapped water molecule.

PubMed

Schroeder, Gottfried K; Zhou, Li; Snider, Mark J; Chen, Xian; Wolfenden, Richard

2012-08-14

Cytidine deaminase (CDA) binds the inhibitor zebularine as its 3,4-hydrate (K(d) ~ 10(-12) M), capturing all but ~5.6 kcal/mol of the free energy of binding expected of an ideal transition state analogue (K(tx) ~ 10(-16) M). On the basis of its entropic origin, that shortfall was tentatively ascribed to the trapping of a water molecule in the enzyme-inhibitor complex, as had been observed earlier for product uridine [Snider, M. J., and Wolfenden, R. (2001) Biochemistry 40, 11364-11371]. Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) of CDA nebularized in the presence of saturating 5-fluorozebularine reveals peaks corresponding to the masses of E(2)Zn(2)W(2) (dimeric Zn-CDA with two water molecules), E(2)Zn(2)W(2)Fz, and E(2)Zn(2)W(2)Fz(2), where Fz represents the 3,4-hydrate of 5-fluorozebularine. In the absence of an inhibitor, E(2)Zn(2) is the only dimeric species detected, with no additional water molecules. Experiments conducted in H(2)(18)O indicate that the added mass W represents a trapped water molecule rather than an isobaric ammonium ion. This appears to represent the first identification of an enzyme-bound water molecule at a subunit interface (active site) using FTICR-MS. The presence of a 5-fluoro group appears to retard the decomposition of the inhibitory complex kinetically in the vapor phase, as no additional dimeric complexes (other than E(2)Zn(2)) are observed when zebularine is used in place of 5-fluorozebularine. Substrate competition assays show that in solution zebularine is released from CDA (k(off) > 0.14 s(-1)) much more rapidly than is 5-fluorozebularine (k(off) = 0.014 s(-1)), despite the greater thermodynamic stability of the zebularine complex.

NON-NAVIGABLE STREAMS AND ADJACENT WETLANDS: ADDRESSING SCIENCE NEEDS FOLLOWING THE SUPREME COURT'S RAPANOS DECISION

EPA Science Inventory

In June of 2006, the US Supreme Court ruled in two cases concerning jurisdiction under the Clean Water Act (CWA). The decisions suggest that hydrological permanence of non-navigable streams and adjacent wetlands (NNSAWs) and their effects on the chemical, physical, and biological...

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.; 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.

Charge-specific size-dependent separation of water-soluble organic molecules by fluorinated nanoporous networks

NASA Astrophysics Data System (ADS)

Byun, Jeehye; Patel, Hasmukh A.; Thirion, Damien; Yavuz, Cafer T.

2016-11-01

Molecular architecture in nanoscale spaces can lead to selective chemical interactions and separation of species with similar sizes and functionality. Substrate specific sorbent chemistry is well known through highly crystalline ordered structures such as zeolites, metal organic frameworks and widely available nanoporous carbons. Size and charge-dependent separation of aqueous molecular contaminants, on the contrary, have not been adequately developed. Here we report a charge-specific size-dependent separation of water-soluble molecules through an ultra-microporous polymeric network that features fluorines as the predominant surface functional groups. Treatment of similarly sized organic molecules with and without charges shows that fluorine interacts with charges favourably. Control experiments using similarly constructed frameworks with or without fluorines verify the fluorine-cation interactions. Lack of a σ-hole for fluorine atoms is suggested to be responsible for this distinct property, and future applications of this discovery, such as desalination and mixed matrix membranes, may be expected to follow.

Charge-specific size-dependent separation of water-soluble organic molecules by fluorinated nanoporous networks

PubMed Central

Byun, Jeehye; Patel, Hasmukh A.; Thirion, Damien; Yavuz, Cafer T.

2016-01-01

Molecular architecture in nanoscale spaces can lead to selective chemical interactions and separation of species with similar sizes and functionality. Substrate specific sorbent chemistry is well known through highly crystalline ordered structures such as zeolites, metal organic frameworks and widely available nanoporous carbons. Size and charge-dependent separation of aqueous molecular contaminants, on the contrary, have not been adequately developed. Here we report a charge-specific size-dependent separation of water-soluble molecules through an ultra-microporous polymeric network that features fluorines as the predominant surface functional groups. Treatment of similarly sized organic molecules with and without charges shows that fluorine interacts with charges favourably. Control experiments using similarly constructed frameworks with or without fluorines verify the fluorine-cation interactions. Lack of a σ-hole for fluorine atoms is suggested to be responsible for this distinct property, and future applications of this discovery, such as desalination and mixed matrix membranes, may be expected to follow. PMID:27830697

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

Hyperfine coupling constants on inner-sphere water molecules of a triazacyclononane-based Mn(II) complex and related systems relevant as MRI contrast agents.

PubMed

Patinec, Véronique; Rolla, Gabriele A; Botta, Mauro; Tripier, Raphaël; Esteban-Gómez, David; Platas-Iglesias, Carlos

2013-10-07

We report the synthesis of the ligand H2MeNO2A (1,4-bis(carboxymethyl)-7-methyl-1,4,7-triazacyclononane) and a detailed experimental and computational study of the hyperfine coupling constants (HFCCs) on the inner-sphere water molecules of [Mn(MeNO2A)] and related Mn(2+) complexes relevant as potential contrast agents in magnetic resonance imaging (MRI). Nuclear magnetic relaxation dispersion (NMRD) profiles, (17)O NMR chemical shifts, and transverse relaxation rates of aqueous solutions of [Mn(MeNO2A)] were recorded to determine the parameters governing the relaxivity in this complex and the (17)O and (1)H HFCCs. DFT calculations (TPSSh model) performed in aqueous solution (PCM model) on the [Mn(MeNO2A)(H2O)]·xH2O and [Mn(EDTA)(H2O)](2-)·xH2O (x = 0-4) systems were used to determine theoretically the (17)O and (1)H HFCCs responsible for the (17)O NMR chemical shifts and the scalar contributions to (17)O and (1)H NMR relaxation rates. The use of a mixed cluster/continuum approach with the explicit inclusion of a few second-sphere water molecules is critical for an accurate calculation of HFCCs of coordinated water molecules. The impact of complex dynamics on the calculated HFCCs was evaluated with the use of molecular dynamics simulations within the atom-centered density matrix propagation (ADMP) approach. The (17)O and (1)H HFCCs calculated for these complexes and related systems show an excellent agreement with the experimental data. Both the (1)H and (17)O HFCCs (A(iso) values) are dominated by the spin delocalization mechanism. The A(iso) values are significantly affected by the distance between the oxygen atom of the coordinated water molecule and the Mn(2+) ion, as well as by the orientation of the water molecule plane with respect to the Mn-O vector.

How Properties of Solid Surfaces Modulate the Nucleation of Gas Hydrate

PubMed Central

Bai, Dongsheng; Chen, Guangjin; Zhang, Xianren; Sum, Amadeu K.; Wang, Wenchuan

2015-01-01

Molecular dynamics simulations were performed for CO2 dissolved in water near silica surfaces to investigate how the hydrophilicity and crystallinity of solid surfaces modulate the local structure of adjacent molecules and the nucleation of CO2 hydrates. Our simulations reveal that the hydrophilicity of solid surfaces can change the local structure of water molecules and gas distribution near liquid-solid interfaces, and thus alter the mechanism and dynamics of gas hydrate nucleation. Interestingly, we find that hydrate nucleation tends to occur more easily on relatively less hydrophilic surfaces. Different from surface hydrophilicity, surface crystallinity shows a weak effect on the local structure of adjacent water molecules and on gas hydrate nucleation. At the initial stage of gas hydrate growth, however, the structuring of molecules induced by crystalline surfaces are more ordered than that induced by amorphous solid surfaces. PMID:26227239

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.

Relative Sizes of Organic Molecules

NASA Technical Reports Server (NTRS)

2000-01-01

This computer graphic depicts the relative complexity of crystallizing large proteins in order to study their structures through x-ray crystallography. Insulin is a vital protein whose structure has several subtle points that scientists are still trying to determine. Large molecules such as insuline are complex with structures that are comparatively difficult to understand. For comparison, a sugar molecule (which many people have grown as hard crystals in science glass) and a water molecule are shown. These images were produced with the Macmolecule program. Photo credit: NASA/Marshall Space Flight Center (MSFC)

Conceptualization and analysis of ground-water flow system in the Coastal Plain of Virginia and adjacent parts of Maryland and North Carolina

USGS Publications Warehouse

Harsh, John F.; Laczniak, Randell J.

1990-01-01

The ground-water flow system in the Coastal Plain of Virginia and adjacent parts of Maryland and North Carolina consists of a water table aquifer and an underlying sequence of confined aquifers and intervening confining units composed of unconsolidated sand and clay. A digital flow model was developed to enhance knowledge of the behavior of the ground-water flow system in response to its development. Ten pumping periods covering 90 yr of withdrawal simulated the history of ground-water development. Simulated potentiometric-surface maps for 1980 show lowered water levels and the development of coalescing cones of depression around the cities of Franklin, Suffolk, and Williamsburg and the town of West Point, all in Virginia. The largest simulated decline in water level, about 210 ft was near Franklin. Water budgets indicate that over the period of simulation (1891-1980): (1) pumpage from the model area increased by about 105 Mgal/d; (2) lateral boundary outflow increased by about 5 Mgal/d; (3) ground-water flow to streams and coastal water decreased by about 107.5 Mgal/d; (4) lateral boundary inflow increased by about 0.7 Mgal/d, and (5) water released from aquifer storage increased by about 1.6 Mgal/d. Simulated rates of recharge into the confined aquifer system at the end of the final pumping period (1980) varied up to 3.8 in/yr. and simulated rates of discharge out of the confined system varied up to 2.2 in/yr. Results of simulations show an increase of about 110 Mgal/d into the confined system from the unconfined system over the period of simulation. This increase in flow into the confined system affected local discharge of ground water to streams and regional discharge to coastal water. Lowering the storage coefficient of the aquifer had a minimal effect simulated water levels, whereas increasing the storage coefficient had a much more significant effect.

Quantification of the Intracellular Life Time of Water Molecules to Measure Transport Rates of Human Aquaglyceroporins.

PubMed

Palmgren, Madelene; Hernebring, Malin; Eriksson, Stefanie; Elbing, Karin; Geijer, Cecilia; Lasič, Samo; Dahl, Peter; Hansen, Jesper S; Topgaard, Daniel; Lindkvist-Petersson, Karin

2017-12-01

Orthodox aquaporins are transmembrane channel proteins that facilitate rapid diffusion of water, while aquaglyceroporins facilitate the diffusion of small uncharged molecules such as glycerol and arsenic trioxide. Aquaglyceroporins play important roles in human physiology, in particular for glycerol metabolism and arsenic detoxification. We have developed a unique system applying the strain of the yeast Pichia pastoris, where the endogenous aquaporins/aquaglyceroporins have been removed and human aquaglyceroporins AQP3, AQP7, and AQP9 are recombinantly expressed enabling comparative permeability measurements between the expressed proteins. Using a newly established Nuclear Magnetic Resonance approach based on measurement of the intracellular life time of water, we propose that human aquaglyceroporins are poor facilitators of water and that the water transport efficiency is similar to that of passive diffusion across native cell membranes. This is distinctly different from glycerol and arsenic trioxide, where high glycerol transport efficiency was recorded.

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

Site-specific binding of a water molecule to the sulfa drugs sulfamethoxazole and sulfisoxazole: a laser-desorption isomer-specific UV and IR study.

PubMed

Uhlemann, Thomas; Seidel, Sebastian; Müller, Christian W

2018-03-07

To determine the preferred water molecule binding sites of the polybasic sulfa drugs sulfamethoxazole (SMX) and sulfisoxazole (SIX), we have studied their monomers and monohydrated complexes through laser-desorption conformer-specific UV and IR spectroscopy. Both the SMX and SIX monomer adopt a single conformer in the molecular beam. On the basis of their conformer-specific IR spectra in the NH stretch region, these conformers were assigned to the SMX and SIX global minimum structures, both exhibiting a staggered sulfonamide group and an intramolecular C-HO[double bond, length as m-dash]S hydrogen bond. The SMX-H 2 O and SIX-H 2 O complexes each adopt a single isomer in the molecular beam. Their isomeric structures were determined based on their isomer-specific IR spectra in the NH/OH stretch region. Quantum Theory of Atoms in Molecules analysis of the calculated electron densities revealed that in the SMX-H 2 O complex the water molecule donates an O-HN hydrogen bond to the heterocycle nitrogen atom and accepts an N-HO hydrogen bond from the sulfonamide NH group. In the SIX-H 2 O complex, however, the water molecule does not bind to the heterocycle but instead donates an O-HO[double bond, length as m-dash]S hydrogen bond to the sulfonamide group and accepts an N-HO hydrogen bond from the sulfonamide NH group. Both water complexes are additionally stabilized by a C ph -HOH 2 hydrogen bond. Interacting Quantum Atoms analysis suggests that all intermolecular hydrogen bonds are dominated by the short-range exchange-correlation contribution.

Aqueous Solvation of Polyalanine α-Helices with Specific Water Molecules and with the CPCM and SM5.2 Aqueous Continuum Models using Density Functional Theory

PubMed Central

Marianski, Mateusz

2012-01-01

We present density functional theory (DFT) calculations at the X3LYP/D95(d,p) level on the solvation of polyalanine α-helices in water. The study includes the effects of discrete water molecules and the CPCM and AMSOL SM5.2 solvent continuum model both separately and in combination. We find that individual water molecules cooperatively hydrogen-bond to both the C- and N-termini of the helix, which results in increases in the dipole moment of the helix/water complex to more than the vector sum of their individual dipole moments. These waters are found to be more stable than in bulk solvent. On the other hand, individual water that interact with the backbone lower the dipole moment of the helix/water complex to below that of the helix, itself. Small clusters of waters at the termini increase the dipole moments of the helix/water aggregates, but the effect diminishes as more waters are added. We discuss the somewhat complex behavior of the helix with the discrete waters in the continuum models. PMID:22201227

Groundwater recharge to the Gulf Coast aquifer system in Montgomery and Adjacent Counties, Texas

USGS Publications Warehouse

Oden, Timothy D.; Delin, Geoffrey N.

2013-01-01

Simply stated, groundwater recharge is the addition of water to the groundwater system. Most of the water that is potentially available for recharging the groundwater system in Montgomery and adjacent counties in southeast Texas moves relatively rapidly from land surface to surface-water bodies and sustains streamflow, lake levels, and wetlands. Recharge in southeast Texas is generally balanced by evapotranspiration, discharge to surface waters, and the downward movement of water into deeper parts of the groundwater system; however, this balance can be altered locally by groundwater withdrawals, impervious surfaces, land use, precipitation variability, or climate, resulting in increased or decreased rates of recharge. Recharge rates were compared to the 1971–2000 normal annual precipitation measured Cooperative Weather Station 411956, Conroe, Tex.

Adsorption of squaraine molecules to Au(111) and Ag(001) surfaces

NASA Astrophysics Data System (ADS)

Luft, Maike; Groß, Boris; Schulz, Matthias; Lützen, Arne; Schiek, Manuela; Nilius, Niklas

2018-02-01

The adsorption of anilino squaraines, an important chromophore for the use in organic solar cells, to Ag(001) and Au(111) has been studied with scanning tunneling microscopy. Self-assembly into square building blocks with eight molecules per unit cell is revealed on the Ag surface, while no ordering effects occur on gold. The squaraine-silver interaction is mediated by the carbonyl and hydroxyl oxygens located in the center of the molecule. The intermolecular coupling, on the other hand, is governed by hydrogen bonds formed between the terminal isobutyl groups and oxygen species of adjacent molecules. The latter gets maximized by rotating the molecules by a few degrees against a perfect square alignment. A similar molecular pattern does not form on Au(111) due to symmetry mismatch. Moreover, the high electronegativity of gold reduces the directing effect of oxygen-metal bonds that trigger the ordering process on silver. As a consequence, only frustrated three-fold symmetric units that do not expand into an ordered molecular network are present on the gold surface.

47 CFR 101.1421 - Coordination of adjacent area MVDDS stations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... SPECIAL RADIO SERVICES FIXED MICROWAVE SERVICES Multichannel Video Distribution and Data Service Rules for... compatible with adjacent and co-channel operations in the adjacent areas on all its frequencies; and (2... adjacent and co-channel operations in adjacent areas. (b) Harmful interference to public safety stations...

FISH-MEDIATED NUTRIENT AND ENERGY EXCHANGE BETWEEN A LAKE SUPERIOR COASTAL WETLAND AND ITS ADJACENT BAY

EPA Science Inventory

Little has been done to quantify fluxes of organisms, nutrients, and energy between freshwater coastal habitats and adjacent offshore waters or to evaluate the ecological implications of these exchanges on a whole-lake basis. To test the hypothesis that fish-mediated transport m...

Changes in NMR relaxation times of adjacent muscle after implantation of malignant and normal tissue.

PubMed Central

Ling, C. R.; Foster, M. A.; Mallard, J. R.

1979-01-01

In separate experiments, normal foreign tissue and malignant tumour were implanted s.c. into the rat thigh. NMR T1 values of the adjacent normal muscle, resulting from local inflammatory reactions or from malignant invasion, were measured. Elevations in T1 of the underlying muscle occurred within 24 h in both experiments, and it is believed these were caused by rapid inflammatory and immunological reactions to the implants. However the T1 values of muscle samples adjacent to the non-malignant implants decreased during the 11 days after implantation, dropping to values within the normal range. In the second experiment there was progressive malignant invasion into the normal adjacent tissue and the elevated T1 values were maintained throughout the 12-day period. The effects of the implantation on tissue water content are discussed in relation to NMR T1 relaxation times, and the relevance to whole-body NMR imaging of elevated T1 values due to nonmalignant pathological states is considered. PMID:526431

33 CFR 334.1060 - Oakland Outer Harbor adjacent to the Oakland Army Base; restricted area.

Code of Federal Regulations, 2013 CFR

2013-07-01

... the Oakland Army Base; restricted area. 334.1060 Section 334.1060 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.1060 Oakland Outer Harbor adjacent to the Oakland Army Base; restricted area. (a) The area...

33 CFR 334.1060 - Oakland Outer Harbor adjacent to the Oakland Army Base; restricted area.

Code of Federal Regulations, 2012 CFR

2012-07-01

... the Oakland Army Base; restricted area. 334.1060 Section 334.1060 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.1060 Oakland Outer Harbor adjacent to the Oakland Army Base; restricted area. (a) The area...

33 CFR 334.1060 - Oakland Outer Harbor adjacent to the Oakland Army Base; restricted area.

Code of Federal Regulations, 2010 CFR

2010-07-01

... the Oakland Army Base; restricted area. 334.1060 Section 334.1060 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.1060 Oakland Outer Harbor adjacent to the Oakland Army Base; restricted area. (a) The area...

Water solvent effects using continuum and discrete models: The nitromethane molecule, CH3NO2.

PubMed

Modesto-Costa, Lucas; Uhl, Elmar; Borges, Itamar

2015-11-15

The first three valence transitions of the two nitromethane conformers (CH3NO2) are two dark n → π* transitions and a very intense π → π* transition. In this work, these transitions in gas-phase and solvated in water of both conformers were investigated theoretically. The polarizable continuum model (PCM), two conductor-like screening (COSMO) models, and the discrete sequential quantum mechanics/molecular mechanics (S-QM/MM) method were used to describe the solvation effect on the electronic spectra. Time dependent density functional theory (TDDFT), configuration interaction including all single substitutions and perturbed double excitations (CIS(D)), the symmetry-adapted-cluster CI (SAC-CI), the multistate complete active space second order perturbation theory (CASPT2), and the algebraic-diagrammatic construction (ADC(2)) electronic structure methods were used. Gas-phase CASPT2, SAC-CI, and ADC(2) results are in very good agreement with published experimental and theoretical spectra. Among the continuum models, PCM combined either with CASPT2, SAC-CI, or B3LYP provided good agreement with available experimental data. COSMO combined with ADC(2) described the overall trends of the transition energy shifts. The effect of increasing the number of explicit water molecules in the S-QM/MM approach was discussed and the formation of hydrogen bonds was clearly established. By including explicitly 24 water molecules corresponding to the complete first solvation shell in the S-QM/MM approach, the ADC(2) method gives more accurate results as compared to the TDDFT approach and with similar computational demands. The ADC(2) with S-QM/MM model is, therefore, the best compromise for accurate solvent calculations in a polar environment. © 2015 Wiley Periodicals, Inc.

Denitrification in sediments from the hyporheic zone adjacent to a small forested stream

USGS Publications Warehouse

Duff, J.H.; Triska, F.J.

1990-01-01

Denitrifying potentials increased with increasing distance from the stream channel. Dissolved oxygen was 100% of the concentration expected in equilibrium with the atmosphere in water obtained from monitoring wells immediately adjacent to the stream but was as low as 7% of the expected value in water 11.4 m inland. Both nitrate and dissolved organic carbon decreased over summer in wells at the base of the alder-forested slope. A 48-h injection of nitrate-amended stream water into hyporheic water 8.4 m inland stimulated nitrous oxide production in the presence of acetylene. Nitrous oxide was generated as nitrate and acetylene were co-transported to a well 13 m down-gradient. Acetylene-block experiments coupled with the chemistry data suggest that denitrification can modify the chemistry of water during passage through the hyporheic zone. -from Authors

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..., Headquarters Air Proving Ground Command, Eglin Air Force Base, Florida, and such agencies as he may designate...

Promotion of Homogeneous Ice Nucleation by Soluble Molecules.

PubMed

Mochizuki, Kenji; Qiu, Yuqing; Molinero, Valeria

2017-11-29

Atmospheric aerosols nucleate ice in clouds, strongly impacting precipitation and climate. The prevailing consensus is that ice nucleation is promoted heterogeneously by the surface of ice nucleating particles in the aerosols. However, recent experiments indicate that water-soluble molecules, such as polysaccharides of pollen and poly(vinyl alcohol) (PVA), increase the ice freezing temperature. This poses the question of how do flexible soluble molecules promote the formation of water crystals, as they do not expose a well-defined surface to ice. Here we use molecular simulations to demonstrate that PVA promotes ice nucleation through a homogeneous mechanism: PVA increases the nucleation rate by destabilizing water in the solution. This work demonstrates a novel paradigm for understanding ice nucleation by soluble molecules and provides a new handle to design additives that promote crystallization.

The Ortho-to-para Ratio of Water Molecules Desorbed from Ice Made from Para-water Monomers at 11 K

NASA Astrophysics Data System (ADS)

Hama, Tetsuya; Kouchi, Akira; Watanabe, Naoki

2018-04-01

Water has two nuclear-spin isomers: ortho- and para-H2O. Some observations of interstellar space and cometary comae have reported the existence of gaseous H2O molecules with anomalous ortho-to-para ratios (OPRs) less than the statistical value of three. This has been often used to estimate the formation temperature of ice on dust, which is inferred to be below 50 K. The relation between the nuclear-spin dynamics of H2O in ice at low temperatures and the OPR of gaseous H2O desorbed from the ice has yet to be explored in a laboratory. Consequently, the true meaning of the observed OPRs remains debated. We measure the OPR of H2O photodesorbed from ice made from para-H2O monomers at 11 K, which was prepared by the sublimation of Ne from a para-H2O/Ne matrix. The photodesorbed H2O molecules from the ice have the statistical OPR value of three, demonstrating the immediate nuclear-spin-state mixing of H2O toward the statistical value of ice even at 11 K. The OPR of H2O thermally desorbed from the ice also shows the expected statistical value. Our results indicate that the OPR of H2O desorbed from interstellar ice should be the statistical value regardless of the formation process of the ice, which cannot be used to deduce the ice-formation temperature. This study highlights the importance of interstellar gas-phase processes in understanding anomalous abundance ratios of nuclear-spin isomers of molecules in space.

Effects of Bt-transgenic rice cultivation on planktonic communities in paddy fields and adjacent ditches.

PubMed

Liu, Yongbo; Liu, Fang; Wang, Chao; Quan, Zhanjun; Li, Junsheng

2016-09-15

The non-target effects of transgenic plants are issues of concern; however, their impacts in cultivated agricultural fields and adjacent natural aquatic ecosystems are poorly understood. We conducted field experiments during two growing seasons to determine the effects of cultivating Bacillus thuringiensis (Bt)-transgenic rice on the phytoplankton and zooplankton communities in a paddy field and an adjacent ditch. Bt toxin was detected in soil but not in water. Water quality was not significantly different between non-Bt and Bt rice fields, but varied among up-, mid- and downstream locations in the ditch. Cultivation of Bt-transgenic rice had no effects on zooplankton communities. Phytoplankton abundance and biodiversity were not significantly different between transgenic and non-transgenic rice fields in 2013; however, phytoplankton were more abundant in the transgenic rice field than in the non-transgenic rice field in 2014. Water quality and rice type explained 65.9% and 12.8% of this difference in 2014, respectively. Phytoplankton and zooplankton were more abundant in mid- and downstream, than upstream, locations in the ditch, an effect that we attribute to water quality differences. Thus, the release of Bt toxins into field water during the cultivation of transgenic crops had no direct negative effects on plankton community composition, but indirect effects that alter environmental conditions should be taken into account during the processes of management planning and policymaking. Copyright © 2016 Elsevier B.V. All rights reserved.

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.

33 CFR 334.880 - San Diego Harbor, Calif.; naval restricted area adjacent to Point Loma.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 33 Navigation and Navigable Waters 3 2012-07-01 2012-07-01 false San Diego Harbor, Calif.; naval....880 San Diego Harbor, Calif.; naval restricted area adjacent to Point Loma. (a) The area. That portion of San Diego Bay southerly of Ballast Point, exclusive of the southwesterly portion of the restricted...

33 CFR 334.880 - San Diego Harbor, Calif.; naval restricted area adjacent to Point Loma.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 33 Navigation and Navigable Waters 3 2011-07-01 2011-07-01 false San Diego Harbor, Calif.; naval....880 San Diego Harbor, Calif.; naval restricted area adjacent to Point Loma. (a) The area. That portion of San Diego Bay southerly of Ballast Point, exclusive of the southwesterly portion of the restricted...

33 CFR 334.880 - San Diego Harbor, Calif.; naval restricted area adjacent to Point Loma.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 33 Navigation and Navigable Waters 3 2014-07-01 2014-07-01 false San Diego Harbor, Calif.; naval....880 San Diego Harbor, Calif.; naval restricted area adjacent to Point Loma. (a) The area. That portion of San Diego Bay southerly of Ballast Point, exclusive of the southwesterly portion of the restricted...

33 CFR 334.880 - San Diego Harbor, Calif.; naval restricted area adjacent to Point Loma.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 33 Navigation and Navigable Waters 3 2013-07-01 2013-07-01 false San Diego Harbor, Calif.; naval....880 San Diego Harbor, Calif.; naval restricted area adjacent to Point Loma. (a) The area. That portion of San Diego Bay southerly of Ballast Point, exclusive of the southwesterly portion of the restricted...

Effects of a Single Water Molecule on the Reaction Barrier of Interstellar CO2 Formation Reaction.

PubMed

Tachikawa, Hiroto; Kawabata, Hiroshi

2016-08-25

The mechanism by which CO2 is formed in the interstellar space remains a mystery. The most likely reaction is collision between CO and OH; however, previous theoretical works have shown that the activation barrier for CO2 formation is high enough to prevent the reaction at the low thermal conditions of space (∼10 K). The effects of single water molecule on the reaction barrier of CO2 formation from reaction between CO and OH have been investigated here by means of ab initio calculation. The barrier height along the lowest-energy pathway in the reaction between CO and OH in the absence of the H2O molecule was calculated to be 2.3 kcal/mol when CCSD(T) energy corrections are combined with the MP2 basis set limit. In the case of the hydrated (H2O-CO-OH) system, the inclusion of a single H2O molecule into the system significantly decreased the barrier height to 0.2 kcal/mol. This suggests that CO2 can be formed when CO and OH react in the presence of H2O, even under thermal conditions as low as 10 K.

Deprotonation states of the two active site water molecules regulate the binding of protein phosphatase 5 with its substrate: A molecular dynamics study.

PubMed

Wang, Lingyun; Yan, Feng

2017-10-01

Protein phosphatase 5 (PP5), mainly localized in human brain, can dephosphorylate tau protein whose high level of phosphorylation is related to Alzheimer's disease. Similar to other protein phosphatases, PP5 has a conserved motif in the catalytic domain that contains two binding sites for manganese (Mn 2+ ) ions. Structural data indicate that two active site water molecules, one bridging the two Mn 2+ ions and the other terminally coordinated with one of the Mn 2+ ions (Mn1), are involved in catalysis. Recently, a density functional theory study revealed that the two water molecules can be both deprotonated to keep a neutral active site for catalysis. The theoretical study gives us an insight into the catalytic mechanism of PP5, but the knowledge of how the deprotonation states of the two water molecules affect the binding of PP5 with its substrate is still lacking. To approach this problem, molecular dynamics simulations were performed to model the four possible deprotonation states. Through structural, dynamical and energetic analyses, the results demonstrate that the deprotonation states of the two water molecules affect the structure of the active site including the distance between the two Mn 2+ ions and their coordination, impact the interaction energy of residues R275, R400 and H304 which directly interact with the substrate phosphoserine, and mediate the dynamics of helix αJ which is involved in regulation of the enzyme's activity. Furthermore, the deprotonation state that is preferable for PP5 binding of its substrate has been identified. These findings could provide new design strategy for PP5 inhibitor. © 2017 The Protein Society.

The effects of metabolite molecules produced by drinking water-isolated bacteria on their single and multispecies biofilms.

PubMed

Simões, Lúcia Chaves; Simões, Manuel; Vieira, Maria João

2011-08-01

The elucidation of the mechanisms by which diverse species survive and interact in drinking water (DW) biofilm communities may allow the identification of new biofilm control strategies. The purpose of the present study was to investigate the effects of metabolite molecules produced by bacteria isolated from DW on biofilm formation. Six opportunistic bacteria, viz. Acinetobacter calcoaceticus, Burkholderia cepacia, Methylobacterium sp., Mycobacterium mucogenicum, Sphingomonas capsulata and Staphylococcus sp. isolated from a drinking water distribution systems (DWDS) were used to form single and multispecies biofilms in the presence and absence of crude cell-free supernatants produced by the partner bacteria. Biofilms were characterized in terms of mass and metabolic activity. Additionally, several physiological aspects regulating interspecies interactions (sessile growth rates, antimicrobial activity of cell-free supernatants, and production of iron chelators) were studied to identify bacterial species with biocontrol potential in DWDS. Biofilms of Methylobacterium sp. had the highest growth rate and M. mucogenicum biofilms the lowest. Only B. cepacia was able to produce extracellular iron-chelating molecules. A. calcoaceticus, B. cepacia, Methylobacterium sp. and M. mucogenicum biofilms were strongly inhibited by crude cell-free supernatants from the other bacteria. The crude cell-free supernatants of M. mucogenicum and S. capsulata demonstrated a high potential for inhibiting the growth of counterpart biofilms. Multispecies biofilm formation was strongly inhibited in the absence of A. calcoaceticus. Only crude cell-free supernatants produced by B. cepacia and A. calcoaceticus had no inhibitory effects on multispecies biofilm formation, while metabolite molecules of M. mucogenicum showed the most significant biocontrol potential.

Cryopreserved embryo transfer: adjacent or non-adjacent to failed fresh long GnRH-agonist protocol IVF cycle.

PubMed

Volodarsky-Perel, Alexander; Eldar-Geva, Talia; Holzer, Hananel E G; Schonberger, Oshrat; Reichman, Orna; Gal, Michael

2017-03-01

The optimal time to perform cryopreserved embryo transfer (CET) after a failed oocyte retrieval-embryo transfer (OR-ET) cycle is unknown. Similar clinical pregnancy rates were recently reported in immediate and delayed CET, performed after failed fresh OR-ET, in cycles with the gonadotrophin-releasing hormone (GnRH) antagonist protocol. This study compared outcomes of CET performed adjacently (<50 days, n = 67) and non-adjacently (≥50 to 120 days, n = 62) to the last OR-day of cycles with the GnRH agonist down-regulation protocol. Additional inclusion criteria were patients' age 20-38 years, the transfer of only 1-2 cryopreserved embryos, one treatment cycle per patient and artificial preparation for CET. Significantly higher implantation, clinical pregnancy and live birth rates were found in the non-adjacent group than in the adjacent group: 30.5% versus 11.3% (P = 0.001), 41.9% versus 17.9% (P = 0.003) and 32.3% versus 13.4% (P = 0.01), respectively. These results support the postponement of CET after a failed OR-ET for at least one menstrual cycle, when a preceding long GnRH-agonist protocol is used. Copyright © 2016 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

Sediment load from major rivers into Puget Sound and its adjacent waters

USGS Publications Warehouse

Czuba, Jonathan A.; Magirl, Christopher S.; Czuba, Christiana R.; Grossman, Eric E.; Curran, Christopher A.; Gendaszek, Andrew S.; Dinicola, Richard S.

2011-01-01

Each year, an estimated load of 6.5 million tons of sediment is transported by rivers to Puget Sound and its adjacent waters—enough to cover a football field to the height of six Space Needles. This estimated load is highly uncertain because sediment studies and available sediment-load data are sparse and historically limited to specific rivers, short time frames, and a narrow range of hydrologic conditions. The largest sediment loads are carried by rivers with glaciated volcanoes in their headwaters. Research suggests 70 percent of the sediment load delivered to Puget Sound is from rivers and 30 percent is from shoreline erosion, but the magnitude of specific contributions is highly uncertain. Most of a river's sediment load occurs during floods.

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

2014-12-12

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.

Precise small molecule recognition of a toxic CUG RNA repeat expansion

PubMed Central

Rzuczek, Suzanne G; Colgan, Lesley A; Nakai, Yoshio; Cameron, Michael D; Furling, Denis; Yasuda, Ryohei; Disney, Matthew D

2017-01-01

Excluding the ribosome and riboswitches, developing small molecules that selectively target RNA is a longstanding problem in chemical biology. A typical cellular RNA is difficult to target because it has little tertiary, but abundant secondary structure. We designed allele-selective compounds that target such an RNA, the toxic noncoding repeat expansion (r(CUG)exp) that causes myotonic dystrophy type 1 (DM1). We developed several strategies to generate allele-selective small molecules, including non-covalent binding, covalent binding, cleavage and on-site probe synthesis. Covalent binding and cleavage enabled target profiling in cells derived from individuals with DM1, showing precise recognition of r(CUG)exp. In the on-site probe synthesis approach, small molecules bound adjacent sites in r(CUG)exp and reacted to afford picomolar inhibitors via a proximity-based click reaction only in DM1-affected cells. We expanded this approach to image r(CUG)exp in its natural context. PMID:27941760

Precise small-molecule recognition of a toxic CUG RNA repeat expansion.

PubMed

Rzuczek, Suzanne G; Colgan, Lesley A; Nakai, Yoshio; Cameron, Michael D; Furling, Denis; Yasuda, Ryohei; Disney, Matthew D

2017-02-01

Excluding the ribosome and riboswitches, developing small molecules that selectively target RNA is a longstanding problem in chemical biology. A typical cellular RNA is difficult to target because it has little tertiary, but abundant secondary structure. We designed allele-selective compounds that target such an RNA, the toxic noncoding repeat expansion (r(CUG) exp ) that causes myotonic dystrophy type 1 (DM1). We developed several strategies to generate allele-selective small molecules, including non-covalent binding, covalent binding, cleavage and on-site probe synthesis. Covalent binding and cleavage enabled target profiling in cells derived from individuals with DM1, showing precise recognition of r(CUG) exp . In the on-site probe synthesis approach, small molecules bound adjacent sites in r(CUG) exp and reacted to afford picomolar inhibitors via a proximity-based click reaction only in DM1-affected cells. We expanded this approach to image r(CUG) exp in its natural context.

Optimizing electrostatic field calculations with the Adaptive Poisson-Boltzmann Solver to predict electric fields at protein-protein interfaces II: explicit near-probe and hydrogen-bonding water molecules.

PubMed

Ritchie, Andrew W; Webb, Lauren J

2014-07-17

We have examined the effects of including explicit, near-probe solvent molecules in a continuum electrostatics strategy using the linear Poisson-Boltzmann equation with the Adaptive Poisson-Boltzmann Solver (APBS) to calculate electric fields at the midpoint of a nitrile bond both at the surface of a monomeric protein and when docked at a protein-protein interface. Results were compared to experimental vibrational absorption energy measurements of the nitrile oscillator. We examined three methods for selecting explicit water molecules: (1) all water molecules within 5 Å of the nitrile nitrogen; (2) the water molecule closest to the nitrile nitrogen; and (3) any single water molecule hydrogen-bonding to the nitrile. The correlation between absolute field strengths with experimental absorption energies were calculated and it was observed that method 1 was only an improvement for the monomer calculations, while methods 2 and 3 were not significantly different from the purely implicit solvent calculations for all protein systems examined. Upon taking the difference in calculated electrostatic fields and comparing to the difference in absorption frequencies, we typically observed an increase in experimental correlation for all methods, with method 1 showing the largest gain, likely due to the improved absolute monomer correlations using that method. These results suggest that, unlike with quantum mechanical methods, when calculating absolute fields using entirely classical models, implicit solvent is typically sufficient and additional work to identify hydrogen-bonding or nearest waters does not significantly impact the results. Although we observed that a sphere of solvent near the field of interest improved results for relative field calculations, it should not be consider a panacea for all situations.

33 CFR 334.880 - San Diego Harbor, Calif.; naval restricted area adjacent to Point Loma.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false San Diego Harbor, Calif.; naval....880 San Diego Harbor, Calif.; naval restricted area adjacent to Point Loma. (a) The area. That portion... Commander, Naval Base, San Diego, Calif. (3) The regulations in this section shall be enforced by the...

Activation of a water molecule using a mononuclear Mn complex: from Mn-aquo, to Mn-hydroxo, to Mn-oxyl via charge compensation.

PubMed

Lassalle-Kaiser, Benedikt; Hureau, Christelle; Pantazis, Dimitrios A; Pushkar, Yulia; Guillot, Régis; Yachandra, Vittal K; Yano, Junko; Neese, Frank; Anxolabéhère-Mallart, Elodie

2010-07-01

Activation of a water molecule by the electrochemical oxidation of a Mn-aquo complex accompanied by the loss of protons is reported. The sequential (2 × 1 electron/1 proton) and direct (2 electron/2 proton) proton-coupled electrochemical oxidation of a non-porphyrinic six-coordinated Mn(II)OH 2 complex into a mononuclear Mn(O) complex is described. The intermediate Mn(III)OH 2 and Mn(III)OH complexes are electrochemically prepared and analysed. Complete deprotonation of the coordinated water molecule in the Mn(O) complex is confirmed by electrochemical data while the analysis of EXAFS data reveals a gradual shortening of an Mn-O bond upon oxidation from Mn(II)OH 2 to Mn(III)OH and Mn(O). Reactivity experiments, DFT calculations and XANES pre-edge features provide strong evidence that the bonding in Mn(O) is best characterized by a Mn(III)-oxyl description. Such oxyl species could play a crucial role in natural and artificial water splitting reactions. We provide here a synthetic example for such species, obtained by electrochemical activation of a water ligand.

Activation of a water molecule using a mononuclear Mn complex: from Mn-aquo, to Mn-hydroxo, to Mn-oxyl via charge compensation†

PubMed Central

Lassalle-Kaiser, Benedikt; Hureau, Christelle; Pantazis, Dimitrios A.; Pushkar, Yulia; Guillot, Régis; Yachandra, Vittal K.; Yano, Junko; Neese, Frank; Anxolabéhère-Mallart, Elodie

2014-01-01

Activation of a water molecule by the electrochemical oxidation of a Mn-aquo complex accompanied by the loss of protons is reported. The sequential (2 × 1 electron/1 proton) and direct (2 electron/2 proton) proton-coupled electrochemical oxidation of a non-porphyrinic six-coordinated Mn(II)OH2 complex into a mononuclear Mn(O) complex is described. The intermediate Mn(III)OH2 and Mn(III)OH complexes are electrochemically prepared and analysed. Complete deprotonation of the coordinated water molecule in the Mn(O) complex is confirmed by electrochemical data while the analysis of EXAFS data reveals a gradual shortening of an Mn–O bond upon oxidation from Mn(II)OH2 to Mn(III)OH and Mn(O). Reactivity experiments, DFT calculations and XANES pre-edge features provide strong evidence that the bonding in Mn(O) is best characterized by a Mn(III)-oxyl description. Such oxyl species could play a crucial role in natural and artificial water splitting reactions. We provide here a synthetic example for such species, obtained by electrochemical activation of a water ligand. PMID:24772190

Open-framework gallium borate with boric and metaboric acid molecules inside structural channels showing photocatalysis to water splitting.

PubMed

Gao, Wenliang; Jing, Yan; Yang, Jia; Zhou, Zhengyang; Yang, Dingfeng; Sun, Junliang; Lin, Jianhua; Cong, Rihong; Yang, Tao

2014-03-03

An open-framework gallium borate with intrinsic photocatalytic activities to water splitting has been discovered. Small inorganic molecules, H3BO3 and H3B3O6, are confined inside structural channels by multiple hydrogen bonds. It is the first example to experimentally show the structural template effect of boric acid in flux synthesis.

Molecular dynamics simulations of amphiphilic graft copolymer molecules at a water/air interface.

PubMed

Anderson, Philip M; Wilson, Mark R

2004-11-01

Fully atomistic molecular dynamics simulations of amphiphilic graft copolymer molecules have been performed at a range of surface concentrations at a water/air interface. These simulations are compared to experimental results from a corresponding system over a similar range of surface concentrations. Neutron reflectivity data calculated from the simulation trajectories agrees well with experimentally acquired profiles. In particular, excellent agreement in neutron reflectivity is found for lower surface concentration simulations. A simulation of a poly(ethylene oxide) (PEO) chain in aqueous solution has also been performed. This simulation allows the conformational behavior of the free PEO chain and those tethered to the interface in the previous simulations to be compared. (c) 2004 American Institute of Physics.

Stem and leaf hydraulics of congeneric tree species from adjacent tropical savanna and forest ecosystems

Treesearch

Guang You Hao; William A. Hoffmann; Fabian G. Scholz; Sandra J. Bucci; Frederick C. Meinzer; Augusto C. Franco; Kun Fang Cao; Guillermo Goldstein

2008-01-01

Leaf and stem functional traits related to plant water relations were studied for six congeneric species pairs, each composed of one tree species typical of savanna habitats and another typical of adjacent forest habitats, to determine whether there were intrinsic differences in plant hydraulics between these two functional types. Only individuals growing in savanna...

Development of improved connection details for adjacent prestressed member bridges.

DOT National Transportation Integrated Search

2017-06-01

Adjacent prestressed member girder bridges are economical systems for short spans and generally come in two types: adjacent box beam bridges and adjacent voided slab bridges. Each type provides the advantages of having low clearances because of their...

Atomistic investigation on the detachment of oil molecules from defective alumina surface

NASA Astrophysics Data System (ADS)

Xie, W. K.; Sun, Y. Z.; Liu, H. T.

2017-12-01

The mechanism of oil detachment from defective alumina surface in aqueous solution was investigated via atomistic molecular dynamics (MD) simulations. Special attention was focused on the effect of surface defect on the oil detachment. Our simulation results suggest that compared with perfect Al2O3 surface, defective substrate surface provides much more sites for the adsorption of oil molecules, thus it has higher oil adsorption energy. However, higher oil-solid adsorption energy does not mean that oil contaminants are much more difficult to be detached. It is found that surface defect could induce the spontaneous imbibition of water molecules, effectively promoting the detachment of oil molecules. Thus, compared with perfect alumina surface, the detachment of oil molecules from defective alumina surface tends to be much easier. Moreover, surface defect could lead to the oil residues inside surface defect. In water solution, the entire detachment process of oil molecules on defective surface consists of following stages, including the early detachment of oil molecules inside surface defect induced by capillary-driven spontaneous imbibition of water molecules, the following conformational change of oil molecules on topmost surface and the final migration of detached oil molecules from solid surface. These findings may help to sufficiently enrich the removal mechanism of oil molecules adhered onto defective solid surface.

Cadmium in the Coastal Upwelling Area Adjacent to the California Mexico Border

NASA Astrophysics Data System (ADS)

Segovia-Zavala, J. A.; Delgadillo-Hinojosa, F.; Alvarez-Borrego, S.

1998-04-01

Cadmium concentrations ([Cd]) were measured in samples from the water column of the coastal upwelling zone adjacent to the California - Mexico border. Temperature and nutrient distributions showed an intense upwelling event during our sampling. Lowest [Cd] were found at locations offshore (50 km) (0·03-0·058 nM), whereas the maximum concentrations were found inshore (0·14-0·166 nM). Both nutrients and [Cd] were enriched in coastal waters. Our inshore [Cd] values are about 25% of those reported for waters off central California. This is possibly due to the intrusion of oligotrophic waters from the eastern edge of the North Pacific Central Gyre to the Southern California Bight. Multivariate analysis indicates that high [Cd]s were associated with high phytoplankton biomass, nutrients and low temperature. Our data present no evidence of a [Cd] gradient due to the San Diego and Tijuana sewage discharges, which indicates that they maintain a very local effect.

Improved connection details for adjacent prestressed bridge beams.

DOT National Transportation Integrated Search

2015-03-01

Bridges with adjacent box beams and voided slabs are simply and rapidly constructed, and are well suited to : short to medium spans. The traditional connection between the adjacent members is a shear key lled with a : conventional non-shrink grout...

CHEMICAL TRANSPORT FACILITATED BY COLLOIDAL-SIZED ORGANIC MOLECULES

EPA Science Inventory

The fluid passing through the pores of soils and geologic materials is not just water with dissolved inorganic chemicals, but a complex mixture of organic and inorganic molecules. Large organic molecules such as humic and fulvic materials may impact the movement of contaminants. ...

Macrobenthos of Yenisei Bay and the adjacent Kara Sea shelf

NASA Astrophysics Data System (ADS)

Galkin, S. V.; Vedenin, A. A.

2015-07-01

Trawl samples were collected in the northern region of Yenisei Bay and adjacent parts of the Kara Sea shelf. A total of eight stations were taken. We found more than 200 species of benthic organisms. A consecutive replacement of benthic communities is observed when going to the north from the Ob and Yenisei estuaries to the open parts of the sea. We could distinguish four different species complexes in the investigated area: a brackish-water complex where Saduria entomon is dominant; an intermediate complex where S. sibirica, S. sabini and Portlandia aestuariorum are dominant; a transitional complex with P. arctica as a dominant species and with a small amount of Ophiocten sericeum; a marine complex where O. sericeum is dominant. When salinity increased, some brackish-water species were replaced by related euryhaline species. One such example was the replacement of brackish-water Saduria entomon isopods by two euryhaline species: S. sibirica and S. sabini. The consecutive replacement of benthic communities showed a break near Sverdrup Island. In this area the marine complex was replaced by a transitional complex with P. arctica.

Contribution of the upper river, the estuarine region, and the adjacent sea to the heavy metal pollution in the Yangtze Estuary.

PubMed

Yin, Su; Wu, Yuehan; Xu, Wei; Li, Yangyang; Shen, Zhenyao; Feng, Chenghong

2016-07-01

To determine whether the discharge control of heavy metals in the Yangtze River basin can significantly change the pollution level in the estuary, this study analyzed the sources (upper river, the estuarine region, and the adjacent sea) of ten heavy metals (As, Cd, Co, Cr, Cu, Hg, Ni, Pb, Sb, and Zn) in dissolved and particulate phases in the surface water of the estuary during wet, normal, and dry seasons. Metal sources inferred from section fluxes agree with those in statistical analysis methods. Heavy metal pollution in the surface water of Yangtze Estuary primarily depends on the sediment suspension and the wastewater discharge from estuary cities. Upper river only constitutes the main source of dissolved heavy metals during the wet season, while the estuarine region and the adjacent sea (especially the former) dominate the dissolved metal pollution in the normal and dry seasons. Particulate metals are mainly derived from sediment suspension in the estuary and the adjacent sea, and the contribution of the upper river can be neglected. Compared with the hydrologic seasons, flood-ebb tides exert a more obvious effect on the water flow directions in the estuary. Sediment suspension, not the upper river, significantly affects the suspended particulate matter concentration in the estuary. Copyright © 2016 Elsevier Ltd. All rights reserved.

Chemical Recycling of Molecules in Cometary Comae

NASA Astrophysics Data System (ADS)

Boice, Daniel C.; Kawakita, Hideyo; Shinnaka, Yoshiharu; Kobayashi, Hitomi

2015-08-01

Modeling is essential to understand the important physical and chemical processes that occur in cometary comae, especially the relationship between native and sibling molecules, such as, HCN and CN. Photochemistry is a major source of ions and electrons that further initiate key gas-phase reactions, leading to the plethora of molecules and atoms observed in comets. The effects of photoelectrons that react via impacts are important to the overall ionization in the inner coma. We have found that many molecules undergo protonation reactions with primarily water, followed by electron recombination resulting in the original molecules in a vibrationally excited state. These excited molecules spontaneously emit photons back to the ground state. We identify this series of reactions as chemical “recycling.” We discuss the importance of this mechanism for HCN, NH3, and water in comets. We also identify other relevant processes in the collision-dominated, inner coma of a comet within a global modeling framework to better understand observations and in situ measurements of cometary species, especially relationships between native and sibling molecules for the Rosetta Mission to Comet 67P/Churyumov-Gerasimenko.Acknowledgements: We appreciate support from the NSF Planetary Astronomy Program under Grant No. 0908529. This program is partially supported by the MEXT Supported Program for the Strategic Research Foundation at Private Universities, 2014-2018.

Cell adhesion molecules, the extracellular matrix and oral squamous carcinoma.

PubMed

Lyons, A J; Jones, J

2007-08-01

Carcinomas are characterized by invasion of malignant cells into the underlying connective tissue and migration of malignant cells to form metastases at distant sites. These processes require alterations in cell-cell and cell-extracellular matrix interactions. As cell adhesion molecules play a role in cell-cell and cell-extracellular matrix adhesion and interactions they are involved in the process of tumour invasion and metastases. In epithelial tissues, receptors of the integrin family mediate adhesion to the adjacent matrix whereas cadherins largely mediate intercellular adhesion. These and other cell adhesion molecules such as intercellular adhesion molecule-1, CD44, dystroglycans and selectins, are involved and undergo changes in carcinomas, which provide possible targets for anti-cancer drug treatments. In the extracellular matrix that is associated with tumours, laminin 5, oncofetal fibronectin and tenascin C appear. The degree of expression of some of these moieties indicates prognosis in oral cancer and offer targets for antibody-directed radiotherapy. Metalloproteases which degrade the extracellular matrix are increased in carcinomas, and their activity is necessary for tumour angiogenesis and consequent invasion and metastases. Metalloprotease inhibitors have begun to produce decreases in mortality in clinical trials. This report provides a brief overview of our current understanding of cell adhesion molecules, the extracellular matrix, tumour invasion and metastasis.

Phase-Transfer Energetics of Small-Molecule Alcohols Across the Water-Hexane Interface: Molecular Dynamics Simulation Using Charge Equilibration Models

PubMed Central

Bauer, Brad A.; Zhong, Yang; Meninger, David J.; Davis, Joseph E.; Patel, Sandeep

2010-01-01

We study the water-hexane interface using molecular dynamics (MD) and polarizable charge equilibration (CHEQ) force fields. Bulk densities for TIP4P-FQ water and hexane, 1.0086±0.0002 g/cm3 and 0.6378±0.0001 g/cm3, demonstrate excellent agreement with experiment. Interfacial width and interfacial tension are consistent with previously reported values. The in-plane component of the dielectric permittivity (ε∥) for water is shown to decrease from 81.7±0.04 to unity, transitioning longitudinally from bulk water to bulk hexane. ε∥ for hexane reaches a maximum in the interface, but this term represents only a small contribution to the total dielectric constant (as expected for a non-polar species). Structurally, net orientations of the molecules arise in the interfacial region such that hexane lies slightly parallel to the interface and water reorients to maximize hydrogen bonding. Interfacial potentials due to contributions of the water and hexane are calculated to be -567.9±0.13mV and 198.7±0.01mV, respectively, giving rise to a total potential in agreement with the range of values reported from previous simulations of similar systems. Potentials of mean force (PMF) calculated for methanol, ethanol, and 1-propanol for the transfer from water to hexane indicate an interfacial free energy minimum, corresponding to the amphiphilic nature of the molecules. The magnitudes of transfer free energies were further characterized from the solvation free energies of alcohols in water and hexane using thermodynamic integration. This analysis shows that solvation free energies for alcohols in hexane are 0.2-0.3 kcal/mol too unfavorable, whereas solvation of alcohols in water is approximately 1 kcal/mol too favorable. For the pure hexane-water interfacial simulations, we observe a monotonic decrease of the water dipole moment to near-vacuum values. This suggests that the electrostatic component of the desolvation free energy is not as severe for polarizable models than

New approximate orientation averaging of the water molecule interacting with the thermal neutron

DOE Office of Scientific and Technical Information (OSTI.GOV)

Markovic, M.I.; Minic, D.M.; Rakic, A.D.

1992-02-01

This paper reports that exactly describing the time of thermal neutron collisions with water molecules, orientation averaging is performed by an exact method (EOA{sub k}) and four approximate methods (two well known and two less known). Expressions for the microscopic scattering kernel are developed. The two well-known approximate orientation averaging methods are Krieger-Nelkin (K-N) and Koppel-Young (K-Y). The results obtained by one of the two proposed approximate orientation averaging methods agree best with the corresponding results obtained by EOA{sub k}. The largest discrepancies between the EOA{sub k} results and the results of the approximate methods are obtained using the well-knowmore » K-N approximate orientation averaging method.« less

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

USGS Publications Warehouse

Spruill, Timothy B.

1984-01-01

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 groundwater "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

33 CFR 334.710 - The Narrows and Gulf of Mexico adjacent to Santa Rosa Island, Air Force Proving Ground Command...

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false The Narrows and Gulf of Mexico... DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.710 The Narrows and Gulf of Mexico adjacent to.... The waters of The Narrows and the Gulf of Mexico easterly of the periphery of a circular area 5...

Oxidative damage to DNA: counterion-assisted addition of water to ionized DNA.

PubMed

Barnett, Robert N; Bongiorno, Angelo; Cleveland, Charles L; Joy, Abraham; Landman, Uzi; Schuster, Gary B

2006-08-23

Oxidative damage to DNA, implicated in mutagenesis, aging, and cancer, follows electron loss that generates a radical cation that migrates to a guanine, where it may react with water to form 8-oxo-7,8-dihydroguanine (8-OxoG). Molecular dynamics and ab initio quantum simulations on a B-DNA tetradecamer reveal activated reaction pathways that depend on the local counterion arrangement. The lowest activation barrier, 0.73 eV, is found for a reaction that starts from a configuration where a Na(+) resides in the major groove near the N7 atoms of adjacent guanines, and evolves through a transition state where a bond between a water oxygen atom and a carbon atom forms concurrently with displacement of a proton toward a neighboring water molecule. Subsequently, a bonded complex of a hydronium ion and the nearest backbone phosphate group forms. This counterion-assisted proton shuttle mechanism is supported by experiments exploiting selective substitution of backbone phosphates by methylphosphonates.

Learning Non-Adjacent Regularities at Age 0 ; 7

ERIC Educational Resources Information Center

Gervain, Judit; Werker, Janet F.

2013-01-01

One important mechanism suggested to underlie the acquisition of grammar is rule learning. Indeed, infants aged 0 ; 7 are able to learn rules based on simple identity relations (adjacent repetitions, ABB: "wo fe fe" and non-adjacent repetitions, ABA: "wo fe wo", respectively; Marcus et al., 1999). One unexplored issue is…

Light absorption properties of colored dissolved organic matter (CDOM) in adjacent waters of the Changjiang Estuary during a flood season: implication for DOC estimation

NASA Astrophysics Data System (ADS)

Liu, Yangyang; Shen, Fang; Li, Xiuzhen

2014-11-01

Light absorption properties of colored dissolved organic matter (CDOM) in adjacent waters of the Changjiang Estuary were investigated during the summer of 2013. CDOM absorption showed a substantial portion of the total absorption and clearly dominant among most investigation stations. It generally decreased from the northwest to the southeast, which controlled by physical mixing of fresh water and seawater as was indicated by a conservative behaviour of CDOM. CDOM absorption sharply increased during phytoplankton blooms. Similarly, dissolved organic carbon (DOC) also peaked during blooms period. However, DOC exhibited a more complex behavior relative to a simple conservative mixing, possibly attributed to multiple origins of DOC. CDOM absorption and DOC co-varied to some degree, implying a potential way of DOC estimation from CDOM absorption. However, more detailed information such as CDOM and DOC composition and more validation data were required to obtain a stable CDOM - DOC pattern. Lastly, empirical algorithms with limited data were developed to retrieve CDOM absorption. Further validation of the algorithms were needed when they were to be commonly applied.

Distributions and Relationships of CO2, O2, and Dimethylsulfide in the Changjiang (Yangtze) Estuary and Its Adjacent Waters in Summer

NASA Astrophysics Data System (ADS)

Wu, Xi; Tan, Tingting; Liu, Chunying; Li, Tie; Liu, Xiaoshou; Yang, Guipeng

2018-04-01

The distributions and relationships of O2, CO2, and dimethylsulfide (DMS) in the Changjiang (Yangtze) Estuary and its adjacent waters were investigated in June 2014. In surface water, mean O2 saturation level, partial pressure of CO2 (pCO2), and DMS concentrations (and ranges) were 110% (89%-167%), 374 μatm (91-640 μatm), and 8.53 nmol L-1 (1.10-27.50 nmol L-1), respectively. The sea-to-air fluxes (and ranges) of DMS and CO2 were 8.24 μmol m-2 d-1 (0.26-62.77 μmol m-2 d-1), and -4.7 mmol m-2 d-1 (-110.8-31.7 mmol m-2 d-1), respectively. Dissolved O2 was oversaturated, DMS concentrations were relatively high, and this region served as a sink of atmospheric CO2. The pCO2 was significantly and negatively correlated with the O2 saturation level, while the DMS concentration showed different positive relationships with the O2 saturation level in different water masses. In vertical profiles, a hypoxic zone existed below 20 m at a longitude of 123°E. The stratification of temperature and salinity caused by the Taiwan Warm Current suppressed seawater exchange between upper and lower layers, resulting in the formation of a hypoxic zone. Oxidative decomposition of organic detritus carried by the Changjiang River Diluted Water (CRDW) consumed abundant O2 and produced additional CO2. The DMS concentrations decreased because of low phytoplankton biomass in the hypoxic zone. Strong correlations appeared between the O2 saturation level, pCO2 and DMS concentrations in vertical profiles. Our results strongly suggested that CRDW played an important role in the distributions and relationships of O2, CO2, and DMS.

Sewage effluent clean-up reduces phosphorus but not phytoplankton in lowland chalk stream (River Kennet, UK) impacted by water mixing from adjacent canal.

PubMed

Neal, Colin; Martin, Ellie; Neal, Margaret; Hallett, John; Wickham, Heather D; Harman, Sarah A; Armstrong, Linda K; Bowes, Mike J; Wade, Andrew J; Keay, David

2010-10-15

Information is provided on phosphorus in the River Kennet and the adjacent Kennet and Avon Canal in southern England to assess their interactions and the changes following phosphorus reductions in sewage treatment work (STW) effluent inputs. A step reduction in soluble reactive phosphorus (SRP) concentration within the effluent (5 to 13 fold) was observed from several STWs discharging to the river in the mid-2000s. This translated to over halving of SRP concentrations within the lower Kennet. Lower Kennet SRP concentrations change from being highest under base-flow to highest under storm-flow conditions. This represented a major shift from direct effluent inputs to a within-catchment source dominated system characteristic of the upper part to the catchment. Average SRP concentrations in the lower Kennet reduced over time towards the target for good water quality. Critically, there was no corresponding reduction in chlorophyll-a concentration, the waters remaining eutrophic when set against standards for lakes. Following the up gradient input of the main water and SRP source (Wilton Water), SRP concentrations in the canal reduced down gradient to below detection limits at times near its junction with the Kennet downstream. However, chlorophyll concentrations in the canal were in an order of magnitude higher than in the river. This probably resulted from long water residence times and higher temperatures promoting progressive algal and suspended sediment generations that consumed SRP. The canal acted as a point source for sediment, algae and total phosphorus to the river especially during the summer months when boat traffic disturbed the canal's bottom sediments and the locks were being regularly opened. The short-term dynamics of this transfer was complex. For the canal and the supply source at Wilton Water, conditions remained hypertrophic when set against standards for lakes even when SRP concentrations were extremely low. Copyright © 2010 Elsevier B.V. All

Correlation analysis of expressions of PTEN and p53 with the value obtained by magnetic resonance spectroscopy and apparent diffusion coefficient in the tumor and the tumor-adjacent area in magnetic resonance imaging for glioblastoma.

PubMed

Li, Yunyun; Ji, Feng; Jiang, Yuzhi; Zhao, Ting; Xu, Chongfu

2018-01-01

To explore the correlation of the expression levels of phosphate and tension homology deleted on chromosome ten (PTEN) and p53 of glioblastoma multiforme (GBM) with the value obtained by magnetic resonance spectroscopy (MRS) and apparent diffusion coefficient (ADC) in the tumor and the tumor-adjacent area in magnetic resonance imaging (MRI). A total of 38 patients were operated for GBM. All the patients had received diffusion-weighted imaging (DWI) and MRS prior to surgery. ADC of water molecules and values of metabolite indexes of MRS, including n-acetyl aspartate (NAA), choline (Cho) and creatine (Cr), were recorded, and the ratios of Cho/NAA, Cho/Cr and NAA/Cr were calculated. Hematoxylin-eosin (H&E) staining was done to examine the morphology of tumor and of tumor-adjacent tissues; immunohistochemistry (IHC) was performed to examine the expressions of PTEN and p53 in the tumor and the tumor-adjacent area. Finally, the correlations of the expressions of PTEN and p53 with ADC, Cho/NAA, Cho/Cr and NAA/Cr of the tumor and the tumor-adjacent area were analyzed. H&E staining showed that GBM tissues had disordered morphology, different sizes of cells, large cell nuclei and significant cell heterogeneity. IHC indicated that the expression level of p53 protein in the tumor was significantly higher than in the tumor-adjacent tissues (p<0.05). The expression level of PTEN protein was high in the tumor-adjacent tissues, but significantly deficient in the tumor. DWI showed that the signal of DWI in the tumor was significantly increased, but ADC was decreased compared with the tumor-adjacent area. MRS indicated that the wave band of Cho in the tumor was significantly increased, NAA was significantly lowered, and Cr section was decreased compared with the tumor-adjacent area, while NAA/Cr in the tumor was significantly decreased compared with the tumoradjacent area (p<0.05). Correlation analysis indicated that PTEN levels in the tumor and the tumor-adjacent area were

Interactions of Oxygen and Water Molecules with Pyrite Surface: A New Insight.

PubMed

Li, Yuqiong; Chen, Jianhua; Chen, Ye; Zhao, Cuihua; Zhang, Yibing; Ke, Baolin

2018-02-06

Pyrite is the most common sulfide in nature, and it is well-known for its roles in acid mine drainage, flotation separation of useful metal (Cu, Pb, Zn, and Mo) sulfide minerals, optoelectronic and photovoltaic application, pneumoconiosis, and even in the origin of life. However, the detailed oxidation behaviors of pyrite are still unclear and not well-understood. New oxidation pathways by O 2 on the pyrite (100) surface have been found in this work for the first time using density functional theory simulation; that is, besides Fe sites, S sites are also possible oxidation sites in the initial oxidation state of pyrite, where easier and stronger oxidation may occur. This is the first time to confirm the other researchers' conjecture on the direct oxidation of S sites, which explains the isotopic composition experiments that a minor amount of O 2 is permanently incorporated into SO 4 2- during pyrite oxidation (O in SO 4 2- is mainly derived from water). We constructed various H 2 O-O 2 coadsorption models on the pyrite surface by considering the adsorption sequence of H 2 O and O 2 . It is found that the H 2 O molecule undergoes step-wise dissociation in the presence of the O 2 molecule. Hydroxyl radical •OH is the reactive oxygen species during H 2 O dissociation. Cyclic voltammetric measurements confirm the presence of •OH. In addition, H 2 O 2 may also be formed on the surface in terms of H 2 O-then-O 2 sequence adsorption.

Single-molecule nanopore enzymology

PubMed Central

Wloka, Carsten; Maglia, Giovanni

2017-01-01

Biological nanopores are a class of membrane proteins that open nanoscale water-conduits in biological membranes. When they are reconstituted in artificial membranes and a bias voltage is applied across the membrane, the ionic current passing through individual nanopores can be used to monitor chemical reactions, to recognize individual molecules and, of most interest, to sequence DNA. More recently, proteins and enzymes have started being analysed with nanopores. Monitoring enzymatic reactions with nanopores, i.e. nanopore enzymology, has the unique advantage that it allows long-timescale observations of native proteins at the single-molecule level. Here we describe the approaches and challenges in nanopore enzymology. PMID:28630164

A systematic review of definitions and classification systems of adjacent segment pathology.

PubMed

Kraemer, Paul; Fehlings, Michael G; Hashimoto, Robin; Lee, Michael J; Anderson, Paul A; Chapman, Jens R; Raich, Annie; Norvell, Daniel C

2012-10-15

Systematic review. To undertake a systematic review to determine how "adjacent segment degeneration," "adjacent segment disease," or clinical pathological processes that serve as surrogates for adjacent segment pathology are classified and defined in the peer-reviewed literature. Adjacent segment degeneration and adjacent segment disease are terms referring to degenerative changes known to occur after reconstructive spine surgery, most commonly at an immediately adjacent functional spinal unit. These can include disc degeneration, instability, spinal stenosis, facet degeneration, and deformity. The true incidence and clinical impact of degenerative changes at the adjacent segment is unclear because there is lack of a universally accepted classification system that rigorously addresses clinical and radiological issues. A systematic review of the English language literature was undertaken and articles were classified using the Grades of Recommendation Assessment, Development, and Evaluation criteria. RESULTS.: Seven classification systems of spinal degeneration, including degeneration at the adjacent segment, were identified. None have been evaluated for reliability or validity specific to patients with degeneration at the adjacent segment. The ways in which terms related to adjacent segment "degeneration" or "disease" are defined in the peer-reviewed literature are highly variable. On the basis of the systematic review presented in this article, no formal classification system for either cervical or thoracolumbar adjacent segment disorders currently exists. No recommendations regarding the use of current classification of degeneration at any segments can be made based on the available literature. A new comprehensive definition for adjacent segment pathology (ASP, the now preferred terminology) has been proposed in this Focus Issue, which reflects the diverse pathology observed at functional spinal units adjacent to previous spinal reconstruction and balances

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.

Controls on the interannual variability of hypoxia in a subtropical embayment and its adjacent waters in the Guangdong coastal upwelling system, northern South China Sea

NASA Astrophysics Data System (ADS)

Zhang, Heng; Cheng, Weicong; Chen, Yuren; Yu, Liuqian; Gong, Wenping

2018-06-01

Coastal embayments located downwind of large rivers under an upwelling-favorable wind are prone to develop low-oxygen or hypoxic conditions in their bottom water. One such embayment is Mirs Bay, off the Guangdong coast, which is affected by upwelling and the Pearl River Estuary (PRE) plume during summer. The relative importance of physical and biochemical processes on the interannual variability of hypoxia in Mirs Bay and its adjacent waters was investigated using statistical analyses of monthly hydrographic and water quality monitoring data from 2001 to 2015. The results reveal that the southwesterly wind duration and the PRE river discharge together explain 49% of the interannual variability in the size of the hypoxic area, whereas inclusion of the nutrient concentrations inside Mirs Bay and phytoplankton on the shelf explains 75% of the interannual variability in the size of the hypoxic area. This finding suggests that the interannual variability of hypoxia in Mirs Bay is regulated by coupled physical and biochemical processes. Increase of the hypoxic area under a longer-lasting southwesterly wind is caused by increased stratification, extended bottom water residence time, and onshore transport of a low-oxygen water mass induced by stable upwelling. In contrast, a reduction in the size of the hypoxic area may be attributed to a decrease in the surface water residence time of the particulate organic matter outside Mirs Bay due to increased discharge from the PRE. The results also show that the effects of allochthonous particulate organic matter outside Mirs Bay on bottom hypoxia cannot be neglected.

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

Delayed Acquisition of Non-Adjacent Vocalic Distributional Regularities

ERIC Educational Resources Information Center

Gonzalez-Gomez, Nayeli; Nazzi, Thierry

2016-01-01

The ability to compute non-adjacent regularities is key in the acquisition of a new language. In the domain of phonology/phonotactics, sensitivity to non-adjacent regularities between consonants has been found to appear between 7 and 10 months. The present study focuses on the emergence of a posterior-anterior (PA) bias, a regularity involving two…

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.

Geochemistry of ground water in alluvial basins of Arizona and adjacent parts of Nevada, New Mexico, and California

USGS Publications Warehouse

Robertson, Frederick N.

1991-01-01

Chemical and isotope analyses of ground water from 28 basins in the Basin and Range physiographic province of Arizona and parts of adjacent States were used to evaluate ground-water quality, determine processes that control ground-water chemistry, provide independent insight into the hydrologic flow system, and develop information transfer. The area is characterized by north- to northwest-trending mountains separated by alluvial basins that form a regional topography of alternating mountains and valleys. On the basis of ground-water divides or zones of minimal basin interconnection, the area was divided into 72 basins, each representing an individual aquifer system. These systems are joined in a dendritic pattern and collectively constitute the major water resource in the region. Geochemical models were developed to identify reactions and mass transfer responsible for the chemical evolution of the ground water. On the basis of mineralogy and chemistry of the two major rock associations of the area, a felsic model and a mafic model were developed to illustrate geologic, climatic, and physiographic effects on ground-water chemistry. Two distinct hydrochemical processes were identified: (1) reactions of meteoric water with minerals and gases in recharge areas and (2) reactions of ground water as it moves down the hydraulic gradient. Reactions occurring in recharge and downgradient areas can be described by a 13-component system. Major reactions are the dissolution and precipitation of calcite and dolomite, the weathering of feldspars and ferromagnesian minerals, the formation of montmorillonite, iron oxyhydroxides, and probably silica, and, in some basins, ion exchange. The geochemical modeling demonstrated that relatively few phases are required to derive the ground-water chemistry; 14 phases-12 mineral and 2 gas-consistently account for the chemical evolution in each basin. The final phases were selected through analysis of X-ray diffraction and fluorescence data

NITROGEN CONCENTRATIONS IN LOADING SOURCES FOR THREE COASTAL LAGOONS FROM ATMOSPHERIC AND WATERSHED SOURCES, ADJACENT COASTAL MARSHES, TIDAL EXCHANGES

EPA Science Inventory

Abstract and Oral Presentation Gulf Estuarine Research Society.

Standing stocks and inputs of total dissolved nitrogen (TDN) to three coastal lagoons, hereafter referred to as Kee's Bayou, Gongora, and State Park, with varying adjacent land-use, geomorphology, and water re...

Anomalous diffusion of water molecules at grain boundaries in ice Ih.

PubMed

Moreira, Pedro Augusto Franco Pinheiro; Veiga, Roberto Gomes de Aguiar; Ribeiro, Ingrid de Almeida; Freitas, Rodrigo; Helfferich, Julian; de Koning, Maurice

2018-05-23

Using ab initio and classical molecular dynamics simulations, we study pre-melting phenomena in pristine coincident-site-lattice grain boundaries (GBs) in proton-disordered hexagonal ice Ih at temperatures just below the melting point Tm. Concerning pre-melt-layer thicknesses, the results are consistent with the available experimental estimates for low-disorder impurity-free GBs. With regard to molecular mobility, the simulations provide a key new insight: the translational motion of the water molecules is found to be subdiffusive for time scales from ∼10 ns up to at least 0.1 μs. Moreover, the fact that the anomalous diffusion occurs even at temperatures just below Tm where the bulk supercooled liquid still diffuses normally suggests that it is related to the confinement of the GB pre-melt layers by the surrounding crystalline environment. Furthermore, we show that this behavior can be characterized by continuous-time random walk models in which the waiting-time distributions decay according to power-laws that are very similar to those describing dynamics in glass-forming systems.

Intercalated Water and Organic Molecules for Electrode Materials of Rechargeable Batteries.

PubMed

Lee, Hyeon Jeong; Shin, Jaeho; Choi, Jang Wook

2018-03-24

The intrinsic limitations of lithium-ion batteries (LIBs) with regard to safety, cost, and the availability of raw materials have promoted research on so-called "post-LIBs". The recent intense research of post-LIBs provides an invaluable lesson that existing electrode materials used in LIBs may not perform as well in post-LIBs, calling for new material designs compliant with emerging batteries based on new chemistries. One promising approach in this direction is the development of materials with intercalated water or organic molecules, as these materials demonstrate superior electrochemical performance in emerging battery systems. The enlarged ionic channel dimensions and effective shielding of the electrostatic interaction between carrier ions and the lattice host are the origins of the observed electrochemical performance. Moreover, these intercalants serve as interlayer pillars to sustain the framework for prolonged cycles. Representative examples of such intercalated materials applied to batteries based on Li + , Na + , Mg 2+ , and Zn 2+ ions and supercapacitors are considered, along with their impact in materials research. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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 interrupted 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 affect both the tunnels accessibility as well as the affinity of distal site water molecules, thus modifying the ligand access to the iron. 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

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 interrupted 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 affect both the tunnels accessibility as well as the affinity of distal site water molecules, thus modifying the ligand access to the iron. 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.

Synthesis of ZnO particles using water molecules generated in esterification reaction

NASA Astrophysics Data System (ADS)

Šarić, Ankica; Gotić, Marijan; Štefanić, Goran; Dražić, Goran

2017-07-01

Zinc oxide particles were synthesized without the addition of water by autoclaving (anhydrous) zinc acetate/alcohol and zinc acetate/acetic acid/alcohol solutions at 160 °C. The solvothermal synthesis was performed in ethanol or octanol. The structural, optical and morphological characteristics of ZnO particles were investigated by X-ray diffraction (XRD), UV-Vis spectroscopy, FE-SEM and TEM/STEM microscopy. 13C NMR spectroscopy revealed the presence of ester (ethyl- or octyl-acetate) in the supernatants which directly indicate the reaction mechanism. The formation of ester in this esterification reaction generated water molecule in situ, which hydrolyzed anhydrous zinc acetate and initiated nucleation and formation of ZnO. It was found that the size and shape of ZnO particles depend on the type of alcohol used as a solvent and on the presence of acetic acid in solution. The presence of ethanol in the ;pure; system without acetic acid favoured the formation of fine and uniform spherical ZnO nanoparticles (∼20 nm). With the addition of small amount of acetic acid the size of these small nanoparticles increased significantly up to a few hundred nanometers. The addition of small amount of acetic acid in the presence of octanol caused even more radical changes in the shape of ZnO particles, favouring the growth of huge rod-like particles (∼3 μm).

Electronic origin of the dependence of hydrogen bond strengths on nearest-neighbor and next-nearest-neighbor hydrogen bonds in polyhedral water clusters (H 2 O) n , n = 8, 20 and 24

DOE Office of Scientific and Technical Information (OSTI.GOV)

Iwata, Suehiro; Akase, Dai; Aida, Misako

2016-01-01

The relative stability and the characteristics of the hydrogen bond networks in the cubic cages of (H2O)8, dodecahedral cages of (H2O)20,and tetrakaidodecahedral cages of (H2O)24 are studied. The charge-transfer and dispersion interaction terms of every pair of the hydrogen bonds are evaluated by using the perturbation theory based on the locally-projected molecular orbital (LPMO PT). Every water molecule and every hydrogen-bonded pair in polyhedral clusters are classified by the types of the adjacent molecules and hydrogen bonds. The relative binding energies among the polyhedral clusters are grouped by these classifications. The necessary condition for the stable conformers and the rulesmore » of the ordering of the relative stability among the isomers are derived from the analysis. The O–O distances and the pair-wise charge-transfer terms are dependent not only on the types of the hydrogen donor and acceptor waters but also on the types of the adjacent waters. This dependence is analyzed with Mulliken’s charge-transfer theory. The work is partially supported by the Grant-in-Aid for Science Research of JSPS (SI, DA, MA). SSX was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Battelle operates the Pacific Northwest National Laboratory for the US Department of Energy.« less

4,4'-([4,4'-Bipyridine]-1,1'-diium-1,1'-diyl)dibenzoate dihydrate

DOE PAGES

Rodriguez, Mark A.; Sava Gallis, Dorina F.; Chavez, James S.; ...

2016-06-01

We report here the synthesis of a neutral viologen derivative, C 24H 16N 2O 4·2H 2O. The non-solvent portion of the structure (Z-Lig) is a zwitterion, consisting of two positively charged pyridinium cations and two negatively charged carboxylate anions. The carboxylate group is almost coplanar [dihedral angle = 2.04 (11)°] with the benzene ring, whereas the dihedral angle between pyridine and benzene rings is 46.28 (5)°. TheZ-Lig molecule is positioned on a center of inversion (Fig. 1). The presence of the twofold axis perpendicular to thec-glide plane in space groupC2/c generates a screw-axis parallel to thebaxis that is shifted from themore » origin by 1/4 in theaandcdirections. This screw-axis replicates the molecule (and solvent water molecules) through space. TheZ-Lig molecule links to adjacent moleculesviaO—H...O hydrogen bonds involving solvent water molecules as well as intermolecular C—H...O interactions. There are also π–π interactions between benzene rings on adjacent molecules.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodriguez, Mark A.; Sava Gallis, Dorina F.; Chavez, James S.

We report here the synthesis of a neutral viologen derivative, C 24H 16N 2O 4·2H 2O. The non-solvent portion of the structure (Z-Lig) is a zwitterion, consisting of two positively charged pyridinium cations and two negatively charged carboxylate anions. The carboxylate group is almost coplanar [dihedral angle = 2.04 (11)°] with the benzene ring, whereas the dihedral angle between pyridine and benzene rings is 46.28 (5)°. TheZ-Lig molecule is positioned on a center of inversion (Fig. 1). The presence of the twofold axis perpendicular to thec-glide plane in space groupC2/c generates a screw-axis parallel to thebaxis that is shifted from themore » origin by 1/4 in theaandcdirections. This screw-axis replicates the molecule (and solvent water molecules) through space. TheZ-Lig molecule links to adjacent moleculesviaO—H...O hydrogen bonds involving solvent water molecules as well as intermolecular C—H...O interactions. There are also π–π interactions between benzene rings on adjacent molecules.« less

Probing the dynamic nature of water molecules and their influences on ligand binding in a model binding site.

PubMed

Cappel, Daniel; Wahlström, Rickard; Brenk, Ruth; Sotriffer, Christoph A

2011-10-24

The model binding site of the cytochrome c peroxidase (CCP) W191G mutant is used to investigate the structural and dynamic properties of the water network at the buried cavity using computational methods supported by crystallographic analysis. In particular, the differences of the hydration pattern between the uncomplexed state and various complexed forms are analyzed as well as the differences between five complexes of CCP W191G with structurally closely related ligands. The ability of docking programs to correctly handle the water molecules in these systems is studied in detail. It is found that fully automated prediction of water replacement or retention upon docking works well if some additional preselection is carried out but not necessarily if the entire water network in the cavity is used as input. On the other hand, molecular interaction fields for water calculated from static crystal structures and hydration density maps obtained from molecular dynamics simulations agree very well with crystallographically observed water positions. For one complex, the docking and MD results sensitively depend on the quality of the starting structure, and agreement is obtained only after redetermination of the crystal structure and refinement at higher resolution.

Electron and fluorescence spectra of a water molecule irradiated by an x-ray free-electron laser pulse

NASA Astrophysics Data System (ADS)

Schäfer, Julia M.; Inhester, Ludger; Son, Sang-Kil; Fink, Reinhold F.; Santra, Robin

2018-05-01

With the highly intense x-ray light generated by x-ray free-electron lasers (XFELs), molecular samples can be ionized many times in a single pulse. Here we report on a computational study of molecular spectroscopy at the high x-ray intensity provided by XFELs. Calculated photoelectron, Auger electron, and x-ray fluorescence spectra are presented for a single water molecule that reaches many electronic hole configurations through repeated ionization steps. The rich details shown in the spectra depend on the x-ray pulse parameters in a nonintuitive way. We discuss how the observed trends can be explained by the competition of microscopic electronic transition processes. A detailed comparison between spectra calculated within the independent-atom model and within the molecular-orbital framework highlights the chemical sensitivity of the spectral lines of multiple-hole configurations. Our results demonstrate how x-ray multiphoton ionization-related effects such as charge-rearrangement-enhanced x-ray ionization of molecules and frustrated absorption manifest themselves in the electron and fluorescence spectra.

Objectifying the adjacent and opposite angles: a cultural historical analysis

NASA Astrophysics Data System (ADS)

Daher, Wajeeh; Musallam, Nadera

2018-02-01

The angle topic is central to the development of geometric knowledge. Two of the basic concepts associated with this topic are the adjacent and opposite angles. It is the goal of the present study to analyze, based on the cultural historical semiotics framework, how high-achieving seventh grade students objectify the adjacent and opposite angles' concepts. We videoed the learning of a group of three high-achieving students who used technology, specifically GeoGebra, to explore geometric relations related to the adjacent and opposite angles' concepts. To analyze students' objectification of these concepts, we used the categories of objectification of knowledge (attention and awareness) and the categories of generalization (factual, contextual and symbolic), developed by Radford. The research results indicate that teacher's and students' verbal and visual signs, together with the software dynamic tools, mediated the students' objectification of the adjacent and opposite angles' concepts. Specifically, eye and gestures perceiving were part of the semiosis cycles in which the participating students were engaged and which related to the mathematical signs that signified the adjacent and the opposite angles. Moreover, the teacher's suggestions/requests/questions included/suggested semiotic signs/tools, including verbal signs that helped the students pay attention, be aware of and objectify the adjacent and opposite angles' concepts.

The bubble method of water purification

NASA Astrophysics Data System (ADS)

Smirnov, B. M.; Babaeva, N. Yu.; Naidis, G. V.; Panov, V. A.; Saveliev, A. S.; Son, E. E.; Tereshonok, D. V.

2018-02-01

The processes of water purification from admixture molecules are analyzed. The purification rate is limited due to a low diffusion coefficient of the admixture molecules in water. At non-small concentrations of the admixture molecules, the water purication can proceed through association of molecules in condensed nanoparticles which fall on the bottom of the water volume. The rate of association may be increased in an external electric field, but in reality this cannot change significantly the rate of the purification process. The bubble method of water purification is considered, where air bubbles formed at the bottom of the water volume, transfer admixture molecules to the interface. This method allows one to clean small water volumes fast. This mechanism of water purification is realized experimentally and exhibits the promises of the bubble purification method.

Fine-scale characteristics of fluvial bull trout redds and adjacent sites in Rapid River, Idaho, 1993-2007

Treesearch

John W. Guzevich; Russell F. Thurow

2017-01-01

From 1993 to 2007, we used single pass, September surveys to locate and measure fluvial bull trout (Salvelinus confluentus) redds in Rapid River, Idaho. Here we describe substrate sizes, redd dimensions, and water depths, velocities, and temperatures within and adjacent to 337 redds. Most (79%) spawning sites had fewer than 20% surface fines (< 2 mm) and mean,...

Intermolecular interaction in nucleobases and dimethyl sulfoxide/water molecules: A DFT, NBO, AIM and NCI analysis.

PubMed

Venkataramanan, Natarajan Sathiyamoorthy; Suvitha, Ambigapathy; Kawazoe, Yoshiyuki

2017-11-01

This study aims to cast light on the physico-chemical nature and energetics of interactions between the nucleobases and water/DMSO molecules which occurs through the non-conventional CH⋯O/N-H bonds using a comprehensive quantum-chemical approach. The computed interaction energies do not show any appreciable change for all the nucleobase-solvent complexes, conforming the experimental findings on the hydration enthalpies. Compared to water, DMSO form complexes with high interaction energies. The quantitative molecular electrostatic potentials display a charge transfer during the complexation. NBO analysis shows the nucleobase-DMSO complexes, have higher stabilization energy values than the nucleobase-water complexes. AIM analysis illustrates that the in the nucleobase-DMSO complexes, SO⋯H-N type interaction have strongest hydrogen bond strength with high E HB values. Furthermore, the Laplacian of electron density and total electron density were negative indicating the partial covalent nature of bonding in these systems, while the other bonds are classified as noncovalent interactions. EDA analysis indicates, the electrostatic interaction is more pronounced in the case of nucleobase-water complexes, while the dispersion contribution is more dominant in nucleobase-DMSO complexes. NCI-RDG analysis proves the existence of strong hydrogen bonding in nucleobase-DMSO complex, which supports the AIM results. Copyright © 2017 Elsevier Inc. All rights reserved.

Phytoparasitic Nematodes Adjacent to Established Strawberry Plantations

PubMed Central

Crow, R. V.; MacDonald, D. H.

1978-01-01

Plant-nematode populations associated with uncultivated vegetation, adjacent strawberry plants, and alternate crop sites were studied at three locations in Minnesota. At one site (Forest Lake), Paratylenchus projectus, Meloidogyne hapla, and Pratylenchus tenuis were frequently associated with the roots of native vegetation. These nematode species were also present in adjacent strawberry beds. Among alternate crops observed, oats and muskmelon usually supported the fewest nematodes although moderate densities of Xiphinema americanum and P. tenuis were found at one location in plots planted to oats. Pratylenchus tenuis was also found on rye at one location. PMID:19305841

Self-Assemblies of novel molecules, VECAR

NASA Astrophysics Data System (ADS)

Shrestha, Bijay; Kim, Hye-Young; Lee, Soojin; Novak, Brian; Moldovan, Dorel

2015-03-01

VECAR is a newly synthesized molecule, which is an amphiphilic antioxidant molecule that consists of two molecular groups, vitamin-E and Carnosine, linked by a hydrocarbon chain. The hydrocarbon chain is hydrophobic and both vitamin-E and Carnosine ends are hydrophilic. In the synthesis process, the length of the hydrophobic chain of VECAR molecules can vary from the shortest (n =0) to the longest (n =18), where n indicates the number of carbon atoms in the chain. We conducted MD simulation studies of self-assembly of VECAR molecules in water using GROMACS on LONI HPC resources. Our study shows that there is a strong correlation between the shape and atomistic structure of the self-assembled nano-structures (SANs) and the chain-length (n) of VECAR molecules. We will report the results of data analyses including the atomistic structure of each SANs and the dynamic and energetic mechanisms of their formation as function of time. In summary, both VECAR molecules of chain-length n =18 and 9 form worm-like micelles, which may be used as a drug delivery system. This research is supported by the Louisiana Board of Regents-RCS Grant (LEQSF(2012-15)-RD-A-19).

A Revision of the Stylasteridae (Cnidaria, Hydrozoa, Filifera) from Alaska and Adjacent Waters

PubMed Central

Cairns, Stephen D.; Lindner, Alberto

2011-01-01

Abstract The stylasterid fauna of Alaska is revised, consisting of the description or redescription and illustration of 21 species, one additional subspecies, and a geographically adjacent species: Stylaster venustus. Six new species and one new subspecies are described: Errinopora fisheri, Errinopora undulata, Errinopora disticha, Errinopora dichotoma, Stylaster crassiseptum, Stylaster repandus, and Stylaster parageus columbiensis. Four subspecies are raised to species rank: Stylaster leptostylus, Stylaster trachystomus, Stylaster parageus, and Distichopora japonica, and five species and one subspecies were synonymized. A dichotomous key to the Errinopora species and tabular keys to the Errinopora and Alaskan Stylaster species are provided. The focus of the study was on the stylasterids from Alaska, primarily those from the diverse Aleutian Islands, but also including records from British Columbia. This is the first revisionary work on this fauna since the seminal report by Fisher in 1938. PMID:22303109

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. Copyright © 2015 Elsevier B.V. All rights reserved.

[Dynamics of Irreversible Evaporation of a Water-Protein Droplet and a Problem of Structural and Dynamical Experiments with Single Molecules].

PubMed

Shaitan, K V; Armeev, G A; Shaytan, A K

2016-01-01

We discuss the effect of isothermal and adiabatic evaporation of water on the state of a water-protein droplet. The discussed problem is of current importance due to development of techniques to perform single molecule experiments using free electron lasers. In such structure-dynamic experiments the delivery of a sample into the X-ray beam is performed using the microdroplet injector. The time between the injection and delivery is in the order of microseconds. In this paper we developed a specialized variant of all-atom molecular dynamics simulations for the study of irreversible isothermal evaporation of the droplet. Using in silico experiments we determined the parameters of isothermal evaporation of the water-protein droplet with the sodium and chloride ions in the concentration range of 0.3 M at different temperatures. The energy of irreversible evaporation determined from in silico experiments at the initial stages of evaporation virtually coincides with the specific heat of evaporation for water. For the kinetics of irreversible adiabatic evaporation an exact analytical solution was obtained in the limit of high thermal conductivity of the droplet (or up to the droplet size of -100 Å). This analytical solution incorporates parameters that are determined using in silico. experiments on isothermal droplet evaporation. We show that the kinetics of adiabatic evaporation and cooling of the droplet scales with the droplet size. Our estimates of the water-protemi droplet. freezing rate in the adiabatic regime in a vacuum chamber show that additional techniques for stabilizing the temperature inside the droplet should be used in order to study the conformational transitions of the protein in single molecules. Isothermal and quasi-isothermal conditions are most suitable for studying the conformational transitions upon object functioning. However, in this case it is necessary to take into account the effects of dehydration and rapid increase of ionic strength in an

[Ortho/para spin-isomers of H2O molecules as a factor responsible for formation of two structural motifs in water].

PubMed

Zakharov, S D

2013-01-01

According to the last results obtained by small-angle X-ray scattering and X-ray spectroscopy it was suggested that water within the nanometer scale represents a fluctuating mixture of clusters with tetrahedral structure and a subphase with partially broken hydrogen bonds whereas the nuclear configuration of the H20 molecule corresponds to single tetrahedral coordination. The basic reason of such structural partition is not clear until now. Here we show that it can be associated with the existence of two nuclear H2O spin-isomers which have different probability to be in one or another subphase. The para-molecule can transfer an excess of its rotational energy to the environment up to the complete stopping of rotation because its rotational quantum number J = 0 in the basic state. This property is favorable for the formation of clusters with closed H-bonds. Ortho-molecules with odd-numbered J states lack for this property and thus should be predominantly present in the surrounding with distorted bonds.

Variable length adjacent partitioning for PTS based PAPR reduction of OFDM signal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ibraheem, Zeyid T.; Rahman, Md. Mijanur; Yaakob, S. N.

2015-05-15

Peak-to-Average power ratio (PAPR) is a major drawback in OFDM communication. It leads the power amplifier into nonlinear region operation resulting into loss of data integrity. As such, there is a strong motivation to find techniques to reduce PAPR. Partial Transmit Sequence (PTS) is an attractive scheme for this purpose. Judicious partitioning the OFDM data frame into disjoint subsets is a pivotal component of any PTS scheme. Out of the existing partitioning techniques, adjacent partitioning is characterized by an attractive trade-off between cost and performance. With an aim of determining effects of length variability of adjacent partitions, we performed anmore » investigation into the performances of a variable length adjacent partitioning (VL-AP) and fixed length adjacent partitioning in comparison with other partitioning schemes such as pseudorandom partitioning. Simulation results with different modulation and partitioning scenarios showed that fixed length adjacent partition had better performance compared to variable length adjacent partitioning. As expected, simulation results showed a slightly better performance of pseudorandom partitioning technique compared to fixed and variable adjacent partitioning schemes. However, as the pseudorandom technique incurs high computational complexities, adjacent partitioning schemes were still seen as favorable candidates for PAPR reduction.« less

A discrete water hexamer with a new planar tetrameric water moiety trapped in the crystal host of [Ag(azelate)(4,4‧-bipyridine)]·(H2O)3

NASA Astrophysics Data System (ADS)

Luo, Geng-Geng; Wu, Dong-Liang; Liu, Li; Xia, Jiu-Xu; Li, Dong-Xu; Dai, Jing-Cao; Xiao, Zi-Jing

2011-11-01

The ultrasonic reaction of Ag 2O, bipy and H 2aze gave rise to a novel Ag(I) mixed-ligand coordination polymer, namely [Ag(aze)(bipy)]·(H 2O) 3 ( 1) (bipy = 4,4'-bipyridine, H 2aze = azelaic acid). In 1, Ag(I) ions are linked by bipy and aze ligands to form a single two-dimensional (2D) undulated net with a (6,3) topology, incorporating Ag 6(bipy) 4(aze) 2 windows of 22.58 × 11.06 Å based on Ag⋯Ag distances. A pair of identical 2D single nets are interconnected via π⋯π stacking and unsupported Ag⋯Ag interactions to generate a 2D double-layered net. A discrete water hexamer composed of a new planar tetrameric water ring and two pendent water molecules is perpendicularly located in each hydrophilic cavity of the 2D bilayer and acts as a 'glue' to assemble adjacent 2D double-layered nets into a three-dimensional (3D) structure.

The use of Chironomus riparius larvae to assess effects of pesticides from rice fields in adjacent freshwater ecosystems.

PubMed

Faria, Mafalda S; Nogueira, António J A; Soares, Amadeu M V M

2007-06-01

A bioassay with Chironomus riparius larvae, using larval development and growth as endpoints, was carried out inside a rice field and in the adjacent wetland channel in Portugal, during pesticide treatments (molinate, endosulfan and propanil) to determine impact caused by pesticide contamination in freshwater ecosystems. The bioassay was also performed under laboratory conditions, to assess whether in situ and laboratory bioassays demonstrated comparable results. Growth was inhibited by concentrations of endosulfan (2.3 and 1.9 microgL(-1) averages) in water from rice field in both the field and laboratory, and by concentrations of endosulfan (0.55 and 0.76 microgL(-1) averages) in water from the wetland channel in the laboratory bioassay, while development was not affected. C. riparius larvae were not affected by molinate and propanil concentrations. The results indicate that endosulfan treatments in rice fields may cause an ecological impairment in adjacent freshwater ecosystems. The results also indicate that laboratory testing can be used to assess in situ toxicity caused by pesticide contamination.

Long-term effects of vertebroplasty: adjacent vertebral fractures.

PubMed

Baroud, Gamal; Vant, Christianne; Wilcox, Ruth

2006-01-01

In today's aging population, osteoporosis-related fractures are an ever-growing concern. Vertebroplasty, a promising yet cost-effective treatment for vertebral compression fractures, has an increasing role. The first vertebroplasty procedures were reported by Deramond and Galibert in France in 1987, and international interest grew with continued development of clinical techniques and augmentation materials in Europe and the United States. Initial publications and presentations at peer review meetings demonstrated 60-90% success rates in providing immediate and significant pain relief. The objective of this review is to assemble experimental and computational biomechanical research whose goal is determining and preventing the negative long-term effects ofvertebroplasty, with a specific focus on adjacent vertebral fractures. Biomechanical studies using isolated cancellous bone cylinders have shown that osteoporotic cancellous bone samples augmented by the rigid bone cement were at least 12 times stiffer and 35 times stronger than the untreated osteoporotic cancellous bone samples. The biomechanical efficacy of the procedure to repair the fractured vertebrae and prevent further collapse is determined using single-vertebra models. The strength or load-bearing capacity of a single vertebra is significantly increased following augmentation when compared to the intact strength. However, there is no dear result regarding the overall stiffness of the single vertebra, with studies reporting contradictorily that the stiffness increases, decreases, or does not significantly alter following augmentation. The effects of vertebroplasty on adjacent structures are studied via multisegment models, whose results plainly oppose the findings of the single-vertebra and intravertebral models. Here, augmentation was shown to decrease the overall segment strength by 19% when compared to the matched controls. As well, there is a significant increase in disc pressure compared to the pre

Synthetic fermentation of bioactive molecules.

PubMed

Stepek, Iain A; Bode, Jeffrey W