CuCl Complexation in the Vapor Phase: Insights from Ab Initio Molecular Dynamics Simulations

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

Mei, Yuan; Liu, Weihua; Migdiov, A. A.

We invesmore » tigated the hydration of the CuCl 0 complex in HCl-bearing water vapor at 350°C and a vapor-like fluid density between 0.02 and 0.09 g/cm 3 using ab initio molecular dynamics (MD) simulations. The simulations reveal that one water molecule is strongly bonded to Cu(I) (first coordination shell), forming a linear [H 2O-Cu-Cl] 0 moiety. The second hydration shell is highly dynamic in nature, and individual configurations have short life-spans in such low-density vapors, resulting in large fluctuations in instantaneous hydration numbers over a timescale of picoseconds. The average hydration number in the second shell (m) increased from ~0.5 to ~3.5 and the calculated number of hydrogen bonds per water molecule increased from 0.09 to 0.25 when fluid density (which is correlated to water activity) increased from 0.02 to 0.09 g/cm 3 ( f H 2O 1.72 to 2.05). These changes of hydration number are qualitatively consistent with previous solubility studies under similar conditions, although the absolute hydration numbers from MD were much lower than the values inferred by correlating experimental Cu fugacity with water fugacity. This could be due to the uncertainties in the MD simulations and uncertainty in the estimation of the fugacity coefficients for these highly nonideal “vapors” in the experiments. Finally, our study provides the first theoretical confirmation that beyond-first-shell hydrated metal complexes play an important role in metal transport in low-density hydrothermal fluids, even if it is highly disordered and dynamic in nature.« less

CuCl Complexation in the Vapor Phase: Insights from Ab Initio Molecular Dynamics Simulations

DOE PAGES

Mei, Yuan; Liu, Weihua; Migdiov, A. A.; ...

2018-05-02

We invesmore » tigated the hydration of the CuCl 0 complex in HCl-bearing water vapor at 350°C and a vapor-like fluid density between 0.02 and 0.09 g/cm 3 using ab initio molecular dynamics (MD) simulations. The simulations reveal that one water molecule is strongly bonded to Cu(I) (first coordination shell), forming a linear [H 2O-Cu-Cl] 0 moiety. The second hydration shell is highly dynamic in nature, and individual configurations have short life-spans in such low-density vapors, resulting in large fluctuations in instantaneous hydration numbers over a timescale of picoseconds. The average hydration number in the second shell (m) increased from ~0.5 to ~3.5 and the calculated number of hydrogen bonds per water molecule increased from 0.09 to 0.25 when fluid density (which is correlated to water activity) increased from 0.02 to 0.09 g/cm 3 ( f H 2O 1.72 to 2.05). These changes of hydration number are qualitatively consistent with previous solubility studies under similar conditions, although the absolute hydration numbers from MD were much lower than the values inferred by correlating experimental Cu fugacity with water fugacity. This could be due to the uncertainties in the MD simulations and uncertainty in the estimation of the fugacity coefficients for these highly nonideal “vapors” in the experiments. Finally, our study provides the first theoretical confirmation that beyond-first-shell hydrated metal complexes play an important role in metal transport in low-density hydrothermal fluids, even if it is highly disordered and dynamic in nature.« less

Structure and dynamics of the CrIII ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation.

PubMed

Kritayakornupong, Chinapong; Plankensteiner, Kristof; Rode, Bernd M

2004-10-01

Structural and dynamical properties of the Cr(III) ion in aqueous solution have been investigated using a combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation. The hydration structure of Cr(III) was determined in terms of radial distribution functions, coordination numbers, and angular distributions. The QM/MM simulation gives coordination numbers of 6 and 15.4 for the first and second hydration shell, respectively. The first hydration shell is kinetically very inert but by no means rigid and variations of the first hydration shell geometry lead to distinct splitting in the vibrational spectra of Cr(H(2)O)(6) (3+). A mean residence time of 22 ps was obtained for water ligands residing in the second hydration shell, which is remarkably shorter than the experimentally estimated value. The hydration energy of -1108 +/- 7 kcal/mol, obtained from the QM/MM simulation, corresponds well to the experimental hydration enthalpy value. Copyright 2004 Wiley Periodicals, Inc.

Interruption of Hydrogen Bonding Networks of Water in Carbon Nanotubes Due to Strong Hydration Shell Formation.

PubMed

Oya, Yoshifumi; Hata, Kenji; Ohba, Tomonori

2017-10-24

We present the structures of NaCl aqueous solution in carbon nanotubes with diameters of 1, 2, and 3 nm based on an analysis performed using X-ray diffraction and canonical ensemble Monte Carlo simulations. Anomalously longer nearest-neighbor distances were observed in the electrolyte for the 1-nm-diameter carbon nanotubes; in contrast, in the 2 and 3 nm carbon nanotubes, the nearest-neighbor distances were shorter than those in the bulk electrolyte. We also observed similar properties for water in carbon nanotubes, which was expected because the main component of the electrolyte was water. However, the nearest-neighbor distances of the electrolyte were longer than those of water in all of the carbon nanotubes; the difference was especially pronounced in the 2-nm-diameter carbon nanotubes. Thus, small numbers of ions affected the entire structure of the electrolyte in the nanopores of the carbon nanotubes. The formation of strong hydration shells between ions and water molecules considerably interrupted the hydrogen bonding between water molecules in the nanopores of the carbon nanotubes. The hydration shell had a diameter of approximately 1 nm, and hydration shells were thus adopted for the nanopores of the 2-nm-diameter carbon nanotubes, providing an explanation for the large difference in the nearest-neighbor distances between the electrolyte and water in these nanopores.

Neutron Scattering Studies of the Hydration Structure of Li +

DOE PAGES

Mason, P. E.; Ansell, S.; Neilson, G. W.; ...

2015-01-05

New results derived from the experimental method of neutron diffraction and isotopic substitution (NDIS) are presented for the hydration structure of the lithium cation (Li +) in aqueous solutions of lithium chloride in heavy water (D 2O) at concentrations of 6, 3 and 1 molal and at 1.5 molal lithium sulphate. By introducing new and more accurate data reduction procedures than in our earlier studies (Howell and Neilson, (1996)), we find in the first hydration shell of Li +,~4.3(2) water molecules at 6 molal, 4.9(3) at 3 molal, 4.8(3) at 1 molal in the LiCl solutions, and 5.0(3) water moleculesmore » in the case of Li 2SO 4 solution. The general form of the first hydration shell is similar in all four solutions, with the correlations for Li-O and Li-D sited at 1.96 (0.02) Å and 2.58 (0.02) Å, respectively. The results resemble those presented in 1996 in terms of ion-water distances and local coordination, but the hydration number is significantly lower for the case at 1 molal than the 6.5 (1.0) given at that time. Thus, experimental and theoretical results now agree that lithium is hydrated by a small number of waters (4-5) in the nearest coordination shell.« less

Molecular mechanisms of decomposition of hydrated Na+Cl- ion pairs under planar nanopore conditions

NASA Astrophysics Data System (ADS)

Shevkunov, S. V.

2017-02-01

The decomposition of Na+Cl- ion pairs under the conditions of a nanoscopic planar pore with structureless walls in a material contact with water vapor at 298 K is simulated by Monte Carlo method. The transition from the state of a contact ion pair (CIP) to the state of solvent-separated ion pair (SSIP) is shown to occur as a result of an increase in the vapor pressure over a pore after exceeding the threshold number of molecules in a hydrate shell. It is found that the planar form of a molecular cluster under the conditions of a narrow pore does not level an abrupt structural transition and the formation of hydrogen bonds in the hydrate shell starts after three molecules are added. The hydrogen bond length under pore conditions is found to be resistant to variations in the hydrate shell size and coincides with that in water under normal conditions.

Hydrophobic hydration and the anomalous partial molar volumes in ethanol-water mixtures

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

Tan, Ming-Liang; Te, Jerez; Cendagorta, Joseph R.

2015-02-14

The anomalous behavior in the partial molar volumes of ethanol-water mixtures at low concentrations of ethanol is studied using molecular dynamics simulations. Previous work indicates that the striking minimum in the partial molar volume of ethanol V{sub E} as a function of ethanol mole fraction X{sub E} is determined mainly by water-water interactions. These results were based on simulations that used one water model for the solute-water interactions but two different water models for the water-water interactions. This is confirmed here by using two more water models for the water-water interactions. Furthermore, the previous work indicates that the initial decreasemore » is caused by association of the hydration shells of the hydrocarbon tails, and the minimum occurs at the concentration where all of the hydration shells are touching each other. Thus, the characteristics of the hydration of the tail that cause the decrease and the features of the water models that reproduce this type of hydration are also examined here. The results show that a single-site multipole water model with a charge distribution that mimics the large quadrupole and the p-orbital type electron density out of the molecular plane has “brittle” hydration with hydrogen bonds that break as the tails touch, which reproduces the deep minimum. However, water models with more typical site representations with partial charges lead to flexible hydration that tends to stay intact, which produces a shallow minimum. Thus, brittle hydration may play an essential role in hydrophobic association in water.« less

Structure and dynamics of phosphate ion in aqueous solution: an ab initio QMCF MD study.

PubMed

Pribil, Andreas B; Hofer, Thomas S; Randolf, Bernhard R; Rode, Bernd M

2008-11-15

A simulation of phosphate in aqueous solution was carried out employing the new QMCF MD approach which offers the possibility to investigate composite systems with the accuracy of a QMMM method but without the time consuming creation of solute-solvent potential functions. The data of the simulations give a clear picture of the hydration shells of the phosphate anion. The first shell consists of 13 water molecules and each oxygen of the phosphate forms in average three hydrogens bonds to different solvent molecules. Several structural parameters such as radial distribution functions and coordination number distributions allow to fully characterize the embedding of the highly charged phosphate ion in the solvent water. The dynamics of the hydration structure of phosphate are described by mean residence times of the solvent molecules in the first hydration shell and the water exchange rate. 2008 Wiley Periodicals, Inc.

High-temperature stability of the hydrate shell of a Na+ cation in a flat nanopore with hydrophobic walls

NASA Astrophysics Data System (ADS)

Shevkunov, S. V.

2017-11-01

The effect of elevated temperature has on the hydrate shell of a singly charged sodium cation inside a flat nanopore with smooth walls is studied using the Monte Carlo method. The free energy and the entropy of vapor molecule attachment are calculated by means of a bicanonical statistical ensemble using a detailed model of interactions. The nanopore has a stabilizing effect on the hydrate shell with respect to fluctuations and a destabilizing effect with respect to complete evaporation. At the boiling point of water, behavior is observed that is qualitatively similar to behavior at room temperature, but with a substantial shift in the vapor pressure and shell size.

Water in the hydration shell of halide ions has significantly reduced Fermi resonance and moderately enhanced Raman cross section in the OH stretch regions.

PubMed

Ahmed, Mohammed; Singh, Ajay K; Mondal, Jahur A; Sarkar, Sisir K

2013-08-22

Water in the presence of electrolytes plays an important role in biological and industrial processes. The properties of water, such as the intermolecular coupling, Fermi resonance (FR), hydrogen-bonding, and Raman cross section were investigated by measuring the Raman spectra in the OD and OH stretch regions in presence of alkali halides (NaX; X = F, Cl, Br, I). It is observed that the changes in spectral characteristics by the addition of NaX in D2O are similar to those obtained by the addition of H2O in D2O. The spectral width decreases significantly by the addition of NaX in D2O (H2O) than that in the isotopically diluted water. Quantitative estimation, on the basis of integrated Raman intensity, revealed that the relative Raman cross section, σ(H)/σ(b) (σ(H) and σ(b) are the average Raman cross section of water in the first hydration shell of X(-) and in bulk, respectively), in D2O and H2O is higher than those in the respective isotopically diluted water. These results suggest that water in the hydration shell has reduced FR and intermolecular coupling compared to those in bulk. In the isotopically diluted water, the relative Raman cross section increases with increase in size of the halide ions (σ(H)/σ(b) = 0.6, 1.1, 1.5, and 1.9 for F(-), Cl(-), Br(-), and I(-), respectively), which is assignable to the enhancement of Raman cross section by charge transfer from halide ions to the hydrating water. Nevertheless, the experimentally determined σ(H)/σ(b) is lower than the calculated values obtained on the basis of the energy of the charge transfer state of water. The weak enhancement of σ(H)/σ(b) signifies that the charge transfer transition in the hydration shell of halide ions causes little change in the OD (OH) bond lengths of hydrating water.

Hydration energies and structures of alkaline earth metal ions, M2+(H2O)n, n = 5-7, M = Mg, Ca, Sr, and Ba.

PubMed

Rodriguez-Cruz, S E; Jockusch, R A; Williams, E R

1999-09-29

The evaporation of water from hydrated alkaline earth metal ions, produced by electrospray ionization, was studied in a Fourier transform mass spectrometer. Zero-pressure-limit dissociation rate constants for loss of a single water molecule from the hydrated divalent metal ions, M(2+)(H(2)O)(n) (M = Mg, Ca, and Sr for n = 5-7, and M = Ba for n = 4-7), are measured as a function of temperature using blackbody infrared radiative dissociation. From these values, zero-pressure-limit Arrhenius parameters are obtained. By modeling the dissociation kinetics using a master equation formalism, threshold dissociation energies (E(o)) are determined. These reactions should have a negligible reverse activation barrier; therefore, E(o) values should be approximately equal to the binding energy or hydration enthalpy at 0 K. For the hepta- and hexahydrated ions at low temperature, binding energies follow the trend expected on the basis of ionic radii: Mg > Ca > Sr > Ba. For the hexahydrated ions at high temperature, binding energies follow the order Ca > Mg > Sr > Ba. The same order is observed for the pentahydrated ions. Collisional dissociation experiments on the tetrahydrated species result in relative dissociation rates that directly correlate with the size of the metals. These results indicate the presence of two isomers for hexahydrated magnesium ions: a low-temperature isomer in which the six water molecules are located in the first solvation shell, and a high-temperature isomer with the most likely structure corresponding to four water molecules in the inner shell and two water molecules in the second shell. These results also indicate that the pentahydrated magnesium ions have a structure with four water molecules in the first solvation shell and one in the outer shell. The dissociation kinetics for the hexa- and pentahydrated clusters of Ca(2+), Sr(2+), and Ba(2+) are consistent with structures in which all the water molecules are located in the first solvation shell.

Inner and Outer Coordination Shells of Mg(2+) in CorA Selectivity Filter from Molecular Dynamics Simulations.

PubMed

Kitjaruwankul, Sunan; Wapeesittipan, Pattama; Boonamnaj, Panisak; Sompornpisut, Pornthep

2016-01-28

Structural data of CorA Mg(2+) channels show that the five Gly-Met-Asn (GMN) motifs at the periplasmic loop of the pentamer structure form a molecular scaffold serving as a selectivity filter. Unfortunately, knowledge about the cation selectivity of Mg(2+) channels remains limited. Since Mg(2+) in aqueous solution has a strong first hydration shell and apparent second hydration sphere, the coordination structure of Mg(2+) in a CorA selectivity filter is expected to be different from that in bulk water. Hence, this study investigated the hydration structure and ligand coordination of Mg(2+) in a selectivity filter of CorA using molecular dynamics (MD) simulations. The simulations reveal that the inner-shell structure of Mg(2+) in the filter is not significantly different from that in aqueous solution. The major difference is the characteristic structural features of the outer shell. The GMN residues engage indirectly in the interactions with the metal ion as ligands in the second shell of Mg(2+). Loss of hydrogen bonds between inner- and outer-shell waters observed from Mg(2+) in bulk water is mostly compensated by interactions between waters in the first solvation shell and the GMN motif. Some water molecules in the second shell remain in the selectivity filter and become less mobile to support the metal binding. Removal of Mg(2+) from the divalent cation sensor sites of the protein had an impact on the structure and metal binding of the filter. From the results, it can be concluded that the GMN motif enhances the affinity of the metal binding site in the CorA selectivity filter by acting as an outer coordination ligand.

Compressibility of the protein-water interface

NASA Astrophysics Data System (ADS)

Persson, Filip; Halle, Bertil

2018-06-01

The compressibility of a protein relates to its stability, flexibility, and hydrophobic interactions, but the measurement, interpretation, and computation of this important thermodynamic parameter present technical and conceptual challenges. Here, we present a theoretical analysis of protein compressibility and apply it to molecular dynamics simulations of four globular proteins. Using additively weighted Voronoi tessellation, we decompose the solution compressibility into contributions from the protein and its hydration shells. We find that positively cross-correlated protein-water volume fluctuations account for more than half of the protein compressibility that governs the protein's pressure response, while the self correlations correspond to small (˜0.7%) fluctuations of the protein volume. The self compressibility is nearly the same as for ice, whereas the total protein compressibility, including cross correlations, is ˜45% of the bulk-water value. Taking the inhomogeneous solvent density into account, we decompose the experimentally accessible protein partial compressibility into intrinsic, hydration, and molecular exchange contributions and show how they can be computed with good statistical accuracy despite the dominant bulk-water contribution. The exchange contribution describes how the protein solution responds to an applied pressure by redistributing water molecules from lower to higher density; it is negligibly small for native proteins, but potentially important for non-native states. Because the hydration shell is an open system, the conventional closed-system compressibility definitions yield a pseudo-compressibility. We define an intrinsic shell compressibility, unaffected by occupation number fluctuations, and show that it approaches the bulk-water value exponentially with a decay "length" of one shell, less than the bulk-water compressibility correlation length. In the first hydration shell, the intrinsic compressibility is 25%-30% lower than in bulk water, whereas its self part is 15%-20% lower. These large reductions are caused mainly by the proximity to the more rigid protein and are not a consequence of the perturbed water structure.

Compressibility of the protein-water interface.

PubMed

Persson, Filip; Halle, Bertil

2018-06-07

The compressibility of a protein relates to its stability, flexibility, and hydrophobic interactions, but the measurement, interpretation, and computation of this important thermodynamic parameter present technical and conceptual challenges. Here, we present a theoretical analysis of protein compressibility and apply it to molecular dynamics simulations of four globular proteins. Using additively weighted Voronoi tessellation, we decompose the solution compressibility into contributions from the protein and its hydration shells. We find that positively cross-correlated protein-water volume fluctuations account for more than half of the protein compressibility that governs the protein's pressure response, while the self correlations correspond to small (∼0.7%) fluctuations of the protein volume. The self compressibility is nearly the same as for ice, whereas the total protein compressibility, including cross correlations, is ∼45% of the bulk-water value. Taking the inhomogeneous solvent density into account, we decompose the experimentally accessible protein partial compressibility into intrinsic, hydration, and molecular exchange contributions and show how they can be computed with good statistical accuracy despite the dominant bulk-water contribution. The exchange contribution describes how the protein solution responds to an applied pressure by redistributing water molecules from lower to higher density; it is negligibly small for native proteins, but potentially important for non-native states. Because the hydration shell is an open system, the conventional closed-system compressibility definitions yield a pseudo-compressibility. We define an intrinsic shell compressibility, unaffected by occupation number fluctuations, and show that it approaches the bulk-water value exponentially with a decay "length" of one shell, less than the bulk-water compressibility correlation length. In the first hydration shell, the intrinsic compressibility is 25%-30% lower than in bulk water, whereas its self part is 15%-20% lower. These large reductions are caused mainly by the proximity to the more rigid protein and are not a consequence of the perturbed water structure.

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

Chatterjee, Anupam; Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076; Higham, Jonathan

A range of methods are presented to calculate a solute’s hydration shell from computer simulations of dilute solutions of monatomic ions and noble gas atoms. The methods are designed to be parameter-free and instantaneous so as to make them more general, accurate, and consequently applicable to disordered systems. One method is a modified nearest-neighbor method, another considers solute-water Lennard-Jones overlap followed by hydrogen-bond rearrangement, while three methods compare various combinations of water-solute and water-water forces. The methods are tested on a series of monatomic ions and solutes and compared with the values from cutoffs in the radial distribution function, themore » nearest-neighbor distribution functions, and the strongest-acceptor hydrogen bond definition for anions. The Lennard-Jones overlap method and one of the force-comparison methods are found to give a hydration shell for cations which is in reasonable agreement with that using a cutoff in the radial distribution function. Further modifications would be required, though, to make them capture the neighboring water molecules of noble-gas solutes if these weakly interacting molecules are considered to constitute the hydration shell.« less

Unraveling halide hydration: A high dilution approach.

PubMed

Migliorati, Valentina; Sessa, Francesco; Aquilanti, Giuliana; D'Angelo, Paola

2014-07-28

The hydration properties of halide aqua ions have been investigated combining classical Molecular Dynamics (MD) with Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy. Three halide-water interaction potentials recently developed [M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144104 (2011)], along with three plausible choices for the value of the absolute hydration free energy of the proton (ΔG [minus sign in circle symbol]hyd[H+]), have been checked for their capability to properly describe the structural properties of halide aqueous solutions, by comparing the MD structural results with EXAFS experimental data. A very good agreement between theory and experiment has been obtained with one parameter set, namely LE, thus strengthening preliminary evidences for a ΔG [minus sign in circle symbol]hyd[H] value of -1100 kJ mol(-1) [M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144104 (2011)]. The Cl(-), Br(-), and I(-) ions have been found to form an unstructured and disordered first hydration shell in aqueous solution, with a broad distribution of instantaneous coordination numbers. Conversely, the F(-) ion shows more ordered and defined first solvation shell, with only two statistically relevant coordination geometries (six and sevenfold complexes). Our thorough investigation on the effect of halide ions on the microscopic structure of water highlights that the perturbation induced by the Cl(-), Br(-), and I(-) ions does not extend beyond the ion first hydration shell, and the structure of water in the F(-) second shell is also substantially unaffected by the ion.

Hydration Energies and Structures of Alkaline Earth Metal Ions, M2+ (H2O)n, n = 5–7, M = Mg, Ca, Sr, and Ba

PubMed Central

Rodriguez-Cruz, Sandra E.; Jockusch, Rebecca A.

2005-01-01

The evaporation of water from hydrated alkaline earth metal ions, produced by electrospray ionization, was studied in a Fourier transform mass spectrometer. Zero-pressure-limit dissociation rate constants for loss of a single water molecule from the hydrated divalent metal ions, M2+(H2O)n (M = Mg, Ca, and Sr for n = 5–7, and M = Ba for n = 4–7), are measured as a function of temperature using blackbody infrared radiative dissociation. From these values, zero-pressure-limit Arrhenius parameters are obtained. By modeling the dissociation kinetics using a master equation formalism, threshold dissociation energies (Eo) are determined. These reactions should have a negligible reverse activation barrier; therefore, Eo values should be approximately equal to the binding energy or hydration enthalpy at 0 K. For the hepta- and hexahydrated ions at low temperature, binding energies follow the trend expected on the basis of ionic radii: Mg > Ca > Sr > Ba. For the hexahydrated ions at high temperature, binding energies follow the order Ca > Mg > Sr > Ba. The same order is observed for the pentahydrated ions. Collisional dissociation experiments on the tetrahydrated species result in relative dissociation rates that directly correlate with the size of the metals. These results indicate the presence of two isomers for hexahydrated magnesium ions: a low-temperature isomer in which the six water molecules are located in the first solvation shell, and a high-temperature isomer with the most likely structure corresponding to four water molecules in the inner shell and two water molecules in the second shell. These results also indicate that the pentahydrated magnesium ions have a structure with four water molecules in the first solvation shell and one in the outer shell. The dissociation kinetics for the hexa- and pentahydrated clusters of Ca2+, Sr2+, and Ba2+ are consistent with structures in which all the water molecules are located in the first solvation shell. PMID:16429612

Search for memory effects in methane hydrate: structure of water before hydrate formation and after hydrate decomposition.

PubMed

Buchanan, Piers; Soper, Alan K; Thompson, Helen; Westacott, Robin E; Creek, Jefferson L; Hobson, Greg; Koh, Carolyn A

2005-10-22

Neutron diffraction with HD isotope substitution has been used to study the formation and decomposition of the methane clathrate hydrate. Using this atomistic technique coupled with simultaneous gas consumption measurements, we have successfully tracked the formation of the sI methane hydrate from a water/gas mixture and then the subsequent decomposition of the hydrate from initiation to completion. These studies demonstrate that the application of neutron diffraction with simultaneous gas consumption measurements provides a powerful method for studying the clathrate hydrate crystal growth and decomposition. We have also used neutron diffraction to examine the water structure before the hydrate growth and after the hydrate decomposition. From the neutron-scattering curves and the empirical potential structure refinement analysis of the data, we find that there is no significant difference between the structure of water before the hydrate formation and the structure of water after the hydrate decomposition. Nor is there any significant change to the methane hydration shell. These results are discussed in the context of widely held views on the existence of memory effects after the hydrate decomposition.

Methanogenic calcite, 13C-depleted bivalve shells, and gas hydrate from a mud volcano offshore southern California

USGS Publications Warehouse

Hein, J.R.; Normark, W.R.; McIntyre, B.R.; Lorenson, T.D.; Powell, C.L.

2006-01-01

Methane and hydrogen sulfide vent from a cold seep above a shallowly buried methane hydrate in a mud volcano located 24 km offshore southern California in?? 800 m of water. Bivalves, authigenic calcite, and methane hydrate were recovered in a 2.1 m piston core. Aragonite shells of two bivalve species are unusually depleted in 13C (to -91??? ??13C), the most 13C-depleted shells of marine macrofauna yet discovered. Carbon isotopes for both living and dead specimens indicate that they used, in part, carbon derived from anaerobically oxidized methane to construct their shells. The ??13C values are highly variable, but most are within the range -12??? to -91???. This variability may be diagnostic for identifying cold-seep-hydrate systems in the geologic record. Authigenic calcite is abundant in the cores down to ???1.5 m subbottom, the top of the methane hydrate. The calcite is depleted in 13C (??13C = -46??? to -58???), indicating that carbon produced by anaerobically oxidized methane is the main source of the calcite. Methane sources include a geologic hydrocarbon reservoir from Miocene source rocks, and biogenic and thermogenic degradation of organic matter in basin sediments. Oxygen isotopes indicate that most calcite formed out of isotopic equilibrium with ambient bottom water, under the influence of gas hydrate dissociation and strong methane flux. High metal content in the mud volcano sediment indicates leaching of basement rocks by fluid circulating along an underlying fault, which also allows for a high flux of fossil methane. ?? 2006 Geological Society of America.

Anomalously enhanced hydration of aqueous electrolyte solution in hydrophobic carbon nanotubes to maintain stability.

PubMed

Ohba, Tomonori

2014-02-24

An understanding of the structure and behavior of electrolyte solutions in nanoenvironements is crucial not only for a wide variety of applications, but also for the development of physical, chemical, and biological processes. We demonstrate the structure and stability of electrolyte in carbon nanotubes using hybrid reverse Monte Carlo simulations of X-ray diffraction patterns. Hydrogen bonds between water are adequately formed in carbon nanotubes, although some hydrogen bonds are restricted by the interfaces of carbon nanotubes. The hydrogen bonding network of water in electrolyte in the carbon nanotubes is further weakened. On the other hand, formation of the ion hydration shell is significantly enhanced in the electrolyte in the carbon nanotubes in comparison to ion hydration in bulk electrolyte. The significant hydrogen bond and hydration shell formation are a result of gaining stability in the hydrophobic nanoenvironment. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular dynamics of ion hydration in the presence of small carboxylated molecules and implications for calcification.

PubMed

Hamm, Laura M; Wallace, Adam F; Dove, Patricia M

2010-08-19

The aspartate-rich macromolecules found at nucleation sites of calcifying organisms are widely implicated in regulating biomineral formation. Anecdotal evidence suggests that their ability to influence the onset of nucleation and composition of calcified structures may arise from effects on ion hydration. This study investigates the interactions of acidic amino acids and dipeptides with hydrated cations using molecular dynamics. By monitoring the hydration states of Mg2+, Ca2+, and Sr2+ during their approach to negatively charged molecules, we show that carboxylate moieties of Asp promote dehydration of Ca2+ and Sr2+. A contact ion pair (CIP) is not required to disrupt cation hydration, and we demonstrate that reductions and rearrangements of first shell water can begin at ion-Asp separation distances as large as approximately 4.9 A for Ca2+ and approximately 5.1 A for Sr2+. CIP formation between Ca2+ and Sr2+ and carboxylate groups decreases the total first shell coordination number from an average of 8.0 and 8.4 in bulk water to 7.5 and 8.0, respectively. The energy barrier to physically replacing waters about Ca2+ with carboxylate oxygen atoms is small (approximately 2 kcal/mol) as compared to a somewhat larger barrier for Sr2+ (approximately 4 kcal/mol). This may be explained by differences in the strength of Coulombic interactions between the cations and the Asp, resulting in different paths of approach toward Asp for Ca2+ and Sr2+. In contrast, the primary solvation shell of Mg2+ remains largely unchanged during interactions with Asp until the abrupt physical replacement of water by carboxylate oxygen atoms, which comes at a high energetic cost. These insights support the claim that carboxylated biomolecules increase the growth rate of calcite by lowering the energy barrier to Ca2+ dehydration. The findings also suggest a physical basis for the idea that ion-specific behaviors of Ca2+ and Mg2+ in cellular systems arise from a critical balance between water binding in the ion hydration shells versus their interactions with ligands present in intracellular environments.

Hydrogen bond breaking in aqueous solutions near the critical point

USGS Publications Warehouse

Mayanovic, Robert A.; Anderson, Alan J.; Bassett, William A.; Chou, I.-Ming

2001-01-01

The nature of water-anion bonding is examined using X-ray absorption fine structure spectroscopy on a 1mZnBr2/6m NaBr aqueous solution, to near critical conditions. Analyses show that upon heating the solution from 25??C to 500??C, a 63% reduction of waters occurs in the solvation shell of ZnBr42-, which is the predominant complex at all pressure-temperature conditions investigated. A similar reduction in the hydration shell of waters in the Br- aqua ion was found. Our results indicate that the water-anion and water-water bond breaking mechanisms occurring at high temperatures are essentially the same. This is consistent with the hydration waters being weakly hydrogen bonded to halide anions in electrolyte solutions. ?? 2001 Elsevier Science B.V.

An experimental point of view on hydration/solvation in halophilic proteins

PubMed Central

Talon, Romain; Coquelle, Nicolas; Madern, Dominique; Girard, Eric

2014-01-01

Protein-solvent interactions govern the behaviors of proteins isolated from extreme halophiles. In this work, we compared the solvent envelopes of two orthologous tetrameric malate dehydrogenases (MalDHs) from halophilic and non-halophilic bacteria. The crystal structure of the MalDH from the non-halophilic bacterium Chloroflexus aurantiacus (Ca MalDH) solved, de novo, at 1.7 Å resolution exhibits numerous water molecules in its solvation shell. We observed that a large number of these water molecules are arranged in pentagonal polygons in the first hydration shell of Ca MalDH. Some of them are clustered in large networks, which cover non-polar amino acid surface. The crystal structure of MalDH from the extreme halophilic bacterium Salinibacter ruber (Sr) solved at 1.55 Å resolution shows that its surface is strongly enriched in acidic amino acids. The structural comparison of these two models is the first direct observation of the relative impact of acidic surface enrichment on the water structure organization between a halophilic protein and its non-adapted counterpart. The data show that surface acidic amino acids disrupt pentagonal water networks in the hydration shell. These crystallographic observations are discussed with respect to halophilic protein behaviors in solution PMID:24600446

An experimental point of view on hydration/solvation in halophilic proteins.

PubMed

Talon, Romain; Coquelle, Nicolas; Madern, Dominique; Girard, Eric

2014-01-01

Protein-solvent interactions govern the behaviors of proteins isolated from extreme halophiles. In this work, we compared the solvent envelopes of two orthologous tetrameric malate dehydrogenases (MalDHs) from halophilic and non-halophilic bacteria. The crystal structure of the MalDH from the non-halophilic bacterium Chloroflexus aurantiacus (Ca MalDH) solved, de novo, at 1.7 Å resolution exhibits numerous water molecules in its solvation shell. We observed that a large number of these water molecules are arranged in pentagonal polygons in the first hydration shell of Ca MalDH. Some of them are clustered in large networks, which cover non-polar amino acid surface. The crystal structure of MalDH from the extreme halophilic bacterium Salinibacter ruber (Sr) solved at 1.55 Å resolution shows that its surface is strongly enriched in acidic amino acids. The structural comparison of these two models is the first direct observation of the relative impact of acidic surface enrichment on the water structure organization between a halophilic protein and its non-adapted counterpart. The data show that surface acidic amino acids disrupt pentagonal water networks in the hydration shell. These crystallographic observations are discussed with respect to halophilic protein behaviors in solution.

Crustal fingering: solidification on a viscously unstable interface

NASA Astrophysics Data System (ADS)

Fu, Xiaojing; Jimenez-Martinez, Joaquin; Cueto-Felgueroso, Luis; Porter, Mark; Juanes, Ruben

2017-11-01

Motivated by the formation of gas hydrates in seafloor sediments, here we study the volumetric expansion of a less viscous gas pocket into a more viscous liquid when the gas-liquid interfaces readily solidify due to hydrate formation. We first present a high-pressure microfluidic experiment to study the depressurization-controlled expansion of a Xenon gas pocket in a water-filled Hele-Shaw cell. The evolution of the pocket is controlled by three processes: (1) volumetric expansion of the gas; (2) rupturing of existing hydrate films on the gas-liquid interface; and (3) formation of new hydrate films. These result in gas fingering leading to a complex labyrinth pattern. To reproduce these observations, we propose a phase-field model that describes the formation of hydrate shell on viscously unstable interfaces. We design the free energy of the three-phase system to rigorously account for interfacial effects, gas compressibility and phase transitions. We model the hydrate shell as a highly viscous fluid with shear-thinning rheology to reproduce shell-rupturing behavior. We present high-resolution numerical simulations of the model, which illustrate the emergence of complex crustal fingering patterns as a result of gas expansion dynamics modulated by hydrate growth at the interface.

Polarization and charge transfer in the hydration of chloride ions

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

Zhao Zhen; Rogers, David M.; Beck, Thomas L.

2010-01-07

A theoretical study of the structural and electronic properties of the chloride ion and water molecules in the first hydration shell is presented. The calculations are performed on an ensemble of configurations obtained from molecular dynamics simulations of a single chloride ion in bulk water. The simulations utilize the polarizable AMOEBA force field for trajectory generation and MP2-level calculations are performed to examine the electronic structure properties of the ions and surrounding waters in the external field of more distant waters. The ChelpG method is employed to explore the effective charges and dipoles on the chloride ions and first-shell waters.more » The quantum theory of atoms in molecules (QTAIM) is further utilized to examine charge transfer from the anion to surrounding water molecules. The clusters extracted from the AMOEBA simulations exhibit high probabilities of anisotropic solvation for chloride ions in bulk water. From the QTAIM analysis, 0.2 elementary charges are transferred from the ion to the first-shell water molecules. The default AMOEBA model overestimates the average dipole moment magnitude of the ion compared to the quantum mechanical value. The average magnitude of the dipole moment of the water molecules in the first shell treated at the MP2-level, with the more distant waters handled with an AMOEBA effective charge model, is 2.67 D. This value is close to the AMOEBA result for first-shell waters (2.72 D) and is slightly reduced from the bulk AMOEBA value (2.78 D). The magnitude of the dipole moment of the water molecules in the first solvation shell is most strongly affected by the local water-water interactions and hydrogen bonds with the second solvation shell, rather than by interactions with the ion.« less

Importance of counteranions on the hydration structure of the curium ion

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

Atta Fynn, Raymond; Bylaska, Eric J.; De Jong, Wibe A.

2013-07-04

Using density functional theory based ab initio molecular dynamics and metadynamics we show that counter ions can trigger noticeable changes in the hydration shell structure of the curium ion. The free energies of curium-water coordination and the solvent hydrogen bond (HB) lifetimes in the absence and presence the counter anions predict that chloride and bromide counter anions strengthen the first shell and consequently the 8-fold coordination state is dominant by at least 98%. In contrast, the perchlorate counter anions are found to weaken the coordination shell and the HB network, with the 9-fold and 8-fold states existing in an 8:1more » ratio, which is in good agreement with reported 9:1 ratio seen in time resolved fluorescence spectroscopy experiments. To our knowledge this is the first time molecular simulations have shown that counter anions can directly affect the first hydration shell structure of a cation.« less

Animated molecular dynamics simulations of hydrated caesium-smectite interlayers

PubMed Central

Sutton, Rebecca; Sposito, Garrison

2002-01-01

Computer animation of center of mass coordinates obtained from 800 ps molecular dynamics simulations of Cs-smectite hydrates (1/3 and 2/3 water monolayers) provided information concerning the structure and dynamics of the interlayer region that could not be obtained through traditional simulation analysis methods. Cs+ formed inner sphere complexes with the mineral surface, and could be seen to jump from one attracting location near a layer charge site to the next, while water molecules were observed to migrate from the hydration shell of one ion to that of another. Neighboring ions maintained a partial hydration shell by sharing water molecules, such that a single water molecule hydrated two ions simultaneously for hundreds of picoseconds. Cs-montmorillonite hydrates featured the largest extent of this sharing interaction, because interlayer ions were able to inhabit positions near surface cavities as well as at their edges, close to oxygen triads. The greater positional freedom of Cs+ within the montmorillonite interlayer, a result of structural hydroxyl orientation and low tetrahedral charge, promoted the optimization of distances between cations and water molecules required for water sharing. Preference of Cs+ for locations near oxygen triads was observed within interlayer beidellite and hectorite. Water molecules also could be seen to interact directly with the mineral surface, entering its surface cavities to approach attracting charge sites and structural hydroxyls. With increasing water content, water molecules exhibited increased frequency and duration of both cavity habitation and water sharing interactions. Competition between Cs+ and water molecules for surface sites was evident. These important cooperative and competitive features of interlayer molecular behavior were uniquely revealed by animation of an otherwise highly complex simulation output.

On the structure and dynamics of the hydrated sulfite ion in aqueous solution--an ab initio QMCF MD simulation and large angle X-ray scattering study.

PubMed

Eklund, Lars; Hofer, Thomas S; Pribil, Andreas B; Rode, Bernd M; Persson, Ingmar

2012-05-07

Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism has been applied in conjunction to experimental large angle X-ray scattering to study the structure and dynamics of the hydrated sulfite ion in aqueous solution. The results show that there is a considerable effect of the lone electron-pair on sulfur concerning structure and dynamics in comparison with the sulfate ion with higher oxidation number and symmetry of the hydration shell. The S-O bond distance in the hydrated sulfite ion has been determined to 1.53(1) Å by both methods. The hydrogen bonds between the three water molecules bound to each sulfite oxygen are only slightly stronger than those in bulk water. The sulfite ion can therefore be regarded as a weak structure maker. The water exchange rate is somewhat slower for the sulfite ion than for the sulfate ion, τ(0.5) = 3.2 and 2.6 ps, respectively. An even more striking observation in the angular radial distribution (ARD) functions is that the for sulfite ion the water exchange takes place in close vicinity of the lone electron-pair directed at its sides, while in principle no water exchange did take place of the water molecules hydrogen bound to sulfite oxygens during the simulation time. This is also confirmed when detailed pathway analysis is conducted. The simulation showed that the water molecules hydrogen bound to the sulfite oxygens can move inside the hydration shell to the area outside the lone electron-pair and there be exchanged. On the other hand, for the hydrated sulfate ion in aqueous solution one can clearly see from the ARD that the distribution of exchange events is symmetrical around the entire hydration sphere.

Differences in Hydration Structure Around Hydrophobic and Hydrophilic Model Peptides Probed by THz Spectroscopy

NASA Astrophysics Data System (ADS)

Wirtz, Hanna; Schäfer, Sarah; Hoberg, Claudius; Havenith, Martina

2018-03-01

We have recorded the THz spectra of the peptides NALA and NAGA as well as the amino acid leucine as model systems for hydrophobic and hydrophilic hydration. The spectra were recorded as a function of temperature and concentration and were analyzed in terms of a principal component analysis approach. NAGA shows positive absorptions with an increasing effective absorption coefficient for increasing concentrations. We conclude that NAGA due to its polar and hydrophilic structure does not have a significant influence on the surrounding water network, but is instead integrated into the water network forming a supramolecular complex. In contrast, for NALA, one hydrogen atom is substituted by a hydrophobic iso-butyl chain. We observe for NALA a decrease in absorption below 1.5 THz and a nonlinearity with a turning point around 0.75 M. Our measurements indicate that the first hydration shell of NALA is still intact at 0.75 M (corresponding to 65 water molecules per NALA). However, for larger concentrations the hydration shells can overlap, which explains the nonlinearity. For leucine, the changes in the spectrum occur at smaller concentrations. This might indicate that leucine exhibits a long-range effect on the solvating water network.

Hydration Dynamics of Hyaluronan and Dextran

PubMed Central

Hunger, Johannes; Bernecker, Anja; Bakker, Huib J.; Bonn, Mischa; Richter, Ralf P.

2012-01-01

Hyaluronan is a polysaccharide, which is ubiquitous in vertebrates and has been reported to be strongly hydrated in a biological environment. We study the hydration of hyaluronan in solution using the rotational dynamics of water as a probe. We measure these dynamics with polarization-resolved femtosecond-infrared and terahertz time-domain spectroscopies. Both experiments reveal that a subensemble of water molecules is slowed down in aqueous solutions of hyaluronan amounting to ∼15 water molecules per disaccharide unit. This quantity is consistent with what would be expected for the first hydration shell. Comparison of these results to the water dynamics in aqueous dextran solution, a structurally similar polysaccharide, yields remarkably similar results. This suggests that the observed interaction with water is a common feature for hydrophilic polysaccharides and is not specific to hyaluronan. PMID:22828349

Dynamics of Hydration Water in Sugars and Peptides Solutions

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

Perticaroli, Stefania; Nakanishi, Masahiro; Pashkovski, Eugene

2013-01-01

We analyzed solute and solvent dynamics of sugars and peptides aqueous solutions using extended epolarized light scattering (EDLS) and broadband dielectric spectroscopies (BDS). Spectra measured with both techniques reveal the same mechanism of rotational diffusion of peptides molecules. In the case of sugars, this solute reorientational relaxation can be isolated by EDLS measurements, whereas its ontribution to the dielectric spectra is almost negligible. In the presented analysis, we characterize the hydration water in terms of hydration number and retardation ratio between relaxation times of hydration and bulk water. Both techniques provide similar estimates of . The retardation imposed on themore » hydration water by sugars is 3.3 1.3 and involves only water molecules hydrogen-bonded (HB) to solutes ( 3 water molecules per sugar OH-group). In contrast, polar peptides cause longer range erturbations beyond the first hydration shell, and between 2.8 and 8, increasing with the number of chemical groups engaged in HB formation. We demonstrate that chemical heterogeneity and specific HB interactions play a crucial role in hydration dynamics around polar solutes. The obtained results help to disentangle the role of excluded volume and enthalpic contributions in dynamics of hydration water at the interface with biological molecules.« less

Solvation of Na^+ in water from first-principles molecular dynamics

NASA Astrophysics Data System (ADS)

White, J. A.; Schwegler, E.; Galli, G.; Gygi, F.

2000-03-01

We have carried out ab initio molecular dynamics (MD) simulations of the Na^+ ion in water with an MD cell containing a single alkali ion and 53 water molecules. The electron-electron and electron-ion interactions were modeled by density functional theory with a generalized gradient approximation for the exchange-correlation functional. The computed radial distribution functions, coordination numbers, and angular distributions are consistent with available experimental data. The first solvation shell contains 5.2±0.6 water molecules, with some waters occasionally exchanging with those of the second shell. The computed Na^+ hydration number is larger than that from calculations for water clusters surrounding an Na^+ ion, but is consistent with that derived from x-ray measurements. Our results also indicate that the first hydration shell is better defined for Na^+ than for K^+ [1], as indicated by the first minimum in the Na-O pair distribution function. [1] L.M. Ramaniah, M. Bernasconi, and M. Parrinello, J. Chem. Phys. 111, 1587 (1999). This work was performed for DOE under contract W-7405-ENG-48.

Nuclear quantum effects in water exchange around lithium and fluoride ions

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

Wilkins, David M.; Manolopoulos, David E.; Dang, Liem X.

2015-02-14

We employ classical and ring polymer molecular dynamics simulations to study the effect of nuclear quantum fluctuations on the structure and the water exchange dynamics of aqueous solutions of lithium and fluoride ions. While we obtain reasonably good agreement with experimental data for solutions of lithium by augmenting the Coulombic interactions between the ion and the water molecules with a standard Lennard-Jones ion-oxygen potential, the same is not true for solutions of fluoride, for which we find that a potential with a softer repulsive wall gives much better agreement. A small degree of destabilization of the first hydration shell ismore » found in quantum simulations of both ions when compared with classical simulations, with the shell becoming less sharply defined and the mean residence time of the water molecules in the shell decreasing. In line with these modest differences, we find that the mechanisms of the exchange processes are unaffected by quantization, so a classical description of these reactions gives qualitatively correct and quantitatively reasonable results. We also find that the quantum effects in solutions of lithium are larger than in solutions of fluoride. This is partly due to the stronger interaction of lithium with water molecules, partly due to the lighter mass of lithium and partly due to competing quantum effects in the hydration of fluoride, which are absent in the hydration of lithium.« less

Methane hydrate formation and decomposition: structural studies via neutron diffraction and empirical potential structure refinement.

PubMed

Thompson, Helen; Soper, Alan K; Buchanan, Piers; Aldiwan, Nawaf; Creek, Jefferson L; Koh, Carolyn A

2006-04-28

Neutron diffraction studies with hydrogen/deuterium isotope substitution measurements are performed to investigate the water structure at the early, medium, and late periods of methane clathrate hydrate formation and decomposition. These measurements are coupled with simultaneous gas consumption measurements to track the formation of methane hydrate from a gas/water mixture, and then the complete decomposition of hydrate. Empirical potential structure refinement computer simulations are used to analyze the neutron diffraction data and extract from the data the water structure in the bulk methane hydrate solution. The results highlight the significant changes in the water structure of the remaining liquid at various stages of hydrate formation and decomposition, and give further insight into the way in which hydrates form. The results also have important implications on the memory effect, suggesting that the water structure in the presence of hydrate crystallites is significantly different at equivalent stages of forming compared to decomposing. These results are in sharp contrast to the previously reported cases when all remaining hydrate crystallites are absent from the solution. For these systems there is no detectable change in the water structure or the methane hydration shell before hydrate formation and after decomposition. Based on the new results presented in this paper, it is clear that the local water structure is affected by the presence of hydrate crystallites, which may in turn be responsible for the "history" or "memory" effect where the production of hydrate from a solution of formed and then subsequently melted hydrate is reportedly much quicker than producing hydrate from a fresh water/gas mixture.

TMAO and urea in the hydration shell of the protein SNase.

PubMed

Smolin, Nikolai; Voloshin, Vladimir P; Anikeenko, Alexey V; Geiger, Alfons; Winter, Roland; Medvedev, Nikolai N

2017-03-01

We performed all-atom MD simulations of the protein SNase in aqueous solution and in the presence of two major osmolytes, trimethylamine-N-oxide (TMAO) and urea, as cosolvents at various concentrations and compositions and at different pressures and temperatures. The distributions of the cosolvent molecules and their orientation in the surroundings of the protein were analyzed in great detail. The distribution of urea is largely conserved near the protein. It varies little with pressure and temperature, and does practically not depend on the addition of TMAO. The slight decrease with temperature of the number of urea molecules that are in contact with the SNase molecule is consistent with the view that the interaction of the protein with urea is mainly of enthalpic nature. Most of the TMAO molecules tend to be oriented to the protein by its methyl groups, a small amount of these molecules contact the protein by its oxygen, forming hydrogen bonds with the protein, only. Unlike urea, the fraction of TMAO in the hydration shell of SNase slightly increases with temperature (a signature of a prevailing hydrophobic interaction between TMAO and SNase), and decreases significantly upon the addition of urea. This behavior reflects the diverse nature of the interaction of the two osmolytes with the protein. Using the Voronoi volume of the atoms of the solvent molecules (water, urea, TMAO), we compared the fraction of the volume occupied by a given type of solvent molecule in the hydration shell and in the bulk solvent. The volume fraction of urea in the hydration shell is more than two times larger than in the bulk, whereas the volume fraction of TMAO in the hydration shell is only slightly larger in the binary solvent (TMAO + water) and becomes even less than in the bulk in the ternary solvent (TMAO + water + urea). Thus, TMAO tends to be excluded from the hydration shell of the protein. The behavior of the two cosolvents in the vicinity of the protein does not change much with pressure (from 1 to 5000 bar) and temperature (from 280 to 330 K). This is also in line with the conception of the "osmophobic effect" of TMAO to protect proteins from denaturation also at harsh environmental conditions. We also calculated the volumetric parameters of SNase and found that the cosolvents have a small but significant effect on the apparent volume and its contributions, i.e. the intrinsic, molecular and thermal volumes.

Structure, Kinetics, and Thermodynamics of the Aqueous Uranyl(VI) Cation

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

Kerisit, Sebastien N.; Liu, Chongxuan

2013-08-20

Molecular simulation techniques are employed to gain insights into the structural, kinetic, and thermodynamic properties of the uranyl(VI) cation (UO22+) in aqueous solution. The simulations make use of an atomistic potential model (force field) derived in this work and based on the model of Guilbaud and Wipff (Guilbaud, P.; Wipff, G. J. Mol. Struct. (THEOCHEM) 1996, 366, 55-63). Reactive flux and thermodynamic integration calculations show that the derived potential model yields predictions for the water exchange rate and free energy of hydration, respectively, that are in agreement with experimental data. The water binding energies, hydration shell structure, and self-diffusion coefficientmore » are also calculated and discussed. Finally, a combination of metadynamics and transition path sampling simulations is employed to probe the mechanisms of water exchange reactions in the first hydration shell of the uranyl ion. These atomistic simulations indicate, based on two-dimensional free energy surfaces, that water exchanges follow an associative interchange mechanism. The nature and structure of the water exchange transition states are also determined. The improved potential model is expected to lead to more accurate predictions of uranyl adsorption energies at mineral surfaces using potential-based molecular dynamics simulations.« less

Dual reorientation relaxation routes of water molecules in oxyanion’s hydration shell: A molecular geometry perspective

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

Xie, Wen Jun; Yang, Yi Isaac; Gao, Yi Qin, E-mail: gaoyq@pku.edu.cn

2015-12-14

In this study, we examine how complex ions such as oxyanions influence the dynamic properties of water and whether differences exist between simple halide anions and oxyanions. Nitrate anion is taken as an example to investigate the hydration properties of oxyanions. Reorientation relaxation of its hydration water can occur through two different routes: water can either break its hydrogen bond with the nitrate to form one with another water or switch between two oxygen atoms of the same nitrate. The latter molecular mechanism increases the residence time of oxyanion’s hydration water and thus nitrate anion slows down the translational motionmore » of neighbouring water. But it is also a “structure breaker” in that it accelerates the reorientation relaxation of hydration water. Such a result illustrates that differences do exist between the hydration of oxyanions and simple halide anions as a result of different molecular geometries. Furthermore, the rotation of the nitrate solute is coupled with the hydrogen bond rearrangement of its hydration water. The nitrate anion can either tilt along the axis perpendicularly to the plane or rotate in the plane. We find that the two reorientation relaxation routes of the hydration water lead to different relaxation dynamics in each of the two above movements of the nitrate solute. The current study suggests that molecular geometry could play an important role in solute hydration and dynamics.« less

Glacigenic sedimentation pulses triggered post-glacial gas hydrate dissociation.

PubMed

Karstens, Jens; Haflidason, Haflidi; Becker, Lukas W M; Berndt, Christian; Rüpke, Lars; Planke, Sverre; Liebetrau, Volker; Schmidt, Mark; Mienert, Jürgen

2018-02-12

Large amounts of methane are stored in continental margins as gas hydrates. They are stable under high pressure and low, but react sensitively to environmental changes. Bottom water temperature and sea level changes were considered as main contributors to gas hydrate dynamics after the last glaciation. However, here we show with numerical simulations that pulses of increased sedimentation dominantly controlled hydrate stability during the end of the last glaciation offshore mid-Norway. Sedimentation pulses triggered widespread gas hydrate dissociation and explains the formation of ubiquitous blowout pipes in water depths of 600 to 800 m. Maximum gas hydrate dissociation correlates spatially and temporally with the formation or reactivation of pockmarks, which is constrained by radiocarbon dating of Isorropodon nyeggaensis bivalve shells. Our results highlight that rapid changes of sedimentation can have a strong impact on gas hydrate systems affecting fluid flow and gas seepage activity, slope stability and the carbon cycle.

Reconsideration on Hydration of Sodium Ion: From Micro-Hydration to Bulk Hydration

NASA Astrophysics Data System (ADS)

Yongquan, Zhou; Chunhui, Fang; Yan, Fang; Fayan, Zhu; Haiwen, Ge; Hongyan, Liu

2017-12-01

Micro hydration structures of the sodium ion, [Na(H2O) n ]+, n = 1-12, were probed by density functional theory (DFT) at B3LYP/aug-cc-pVDZ level in both gaseous and aqueous phase. The predicted equilibrium sodium-oxygen distance of 0.240 nm at the present level of theory. The four-, five- and six-coordinated cluster can transform from each other at the ambient condition. The analysis of the successive water binding energy and natural charge population (NBO) on Na+ clearly shows that the influence of Na+ on the surrounding water molecules goes beyond the first hydration shell with the hydration number of 6. The Car-Parrinello molecular dynamic simulation shows that only the first hydration sphere can be found, and the hydration number of Na+ is 5.2 and the hydration distance ( r Na-O) is 0.235 nm. All our simulations mentioned in the present paper show an excellent agreement with the diffraction result from X-ray scattering study.

Nuclear quantum effects in water exchange around lithium and fluoride ions

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

Wilkins, David M.; Manolopoulos, David; Dang, Liem X.

2015-02-14

We employ classical and ring polymer molecular dynamics simulations to study the effect of nuclear quantum fluctuations on the structure and the water exchange dynamics of aqueous solutions of lithium and fluoride ions. While we obtain reasonably good agreement with experimental data for solutions of lithium by augmenting the Coulombic interactions between the ion and the water molecules with a standard Lennard-Jones ion-oxygen potential, the same is not true for solutions of fluoride, for which we find that a potential with a softer repulsive wall gives much better agreement. A small degree of destabilization of the first hydration shell ismore » found in quantum simulations of both ions when compared with classical simulations, with the shell becoming less sharply defined and the mean residence time of the water molecules in the shell decreasing. In line with these modest differences, we find that the mechanisms of the water exchange reactions are unaffected by quantization, so a classical description of these reactions gives qualitatively correct and quantitatively reasonable results. We also find that the quantum effects in solutions of lithium are larger than in solutions of fluoride. This is partly due to the stronger interaction of lithium with water molecules, partly due to the lighter mass of lithium, and partly due to competing quantum effects in the hydration of fluoride, which are absent in the hydration of lithium. LXD was supported by US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.« less

WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations.

PubMed

Černý, Jiří; Schneider, Bohdan; Biedermannová, Lada

2017-07-14

Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function. WatAA is a newly developed, web-based atlas of amino-acid hydration in proteins. The atlas provides information about the ordered first hydration shell of the most populated amino-acid conformers in proteins. The data presented in the atlas are drawn from two sources: experimental data and ab initio quantum-mechanics calculations. The experimental part is based on a data-mining study of a large set of high-resolution protein crystal structures. The crystal-derived data include 3D maps of water distribution around amino-acids and probability of occurrence of each of the identified hydration sites. The quantum mechanics calculations validate and extend this primary description by optimizing the water position for each hydration site, by providing hydrogen atom positions and by quantifying the interaction energy that stabilizes the water molecule at the particular hydration site position. The calculations show that the majority of experimentally derived hydration sites are positioned near local energy minima for water, and the calculated interaction energies help to assess the preference of water for the individual hydration sites. We propose that the atlas can be used to validate water placement in electron density maps in crystallographic refinement, to locate water molecules mediating protein-ligand interactions in drug design, and to prepare and evaluate molecular dynamics simulations. WatAA: Atlas of Protein Hydration is freely available without login at .

Molecular dynamics study of the solvation of calcium carbonate in water.

PubMed

Bruneval, Fabien; Donadio, Davide; Parrinello, Michele

2007-10-25

We performed molecular dynamics simulations of diluted solutions of calcium carbonate in water. To this end, we combined and tested previous polarizable models. The carbonate anion forms long-living hydrogen bonds with water and shows an amphiphilic character, in which the water molecules are expelled in a region close to its C(3) symmetry axis. The calcium cation forms a strongly bound ion pair with the carbonate. The first hydration shell around the CaCO(3) pair is found to be very similar to the location of the water molecules surrounding CaCO(3) in ikaite, the hydrated mineral.

Preferential solvation, ion pairing, and dynamics of concentrated aqueous solutions of divalent metal nitrate salts

NASA Astrophysics Data System (ADS)

Yadav, Sushma; Chandra, Amalendu

2017-12-01

We have investigated the characteristics of preferential solvation of ions, structure of solvation shells, ion pairing, and dynamics of aqueous solutions of divalent alkaline-earth metal nitrate salts at varying concentration by means of molecular dynamics simulations. Hydration shell structures and the extent of preferential solvation of the metal and nitrate ions in the solutions are investigated through calculations of radial distribution functions, tetrahedral ordering, and also spatial distribution functions. The Mg2+ ions are found to form solvent separated ion-pairs while the Ca2+ and Sr2+ ions form contact ion pairs with the nitrate ions. These findings are further corroborated by excess coordination numbers calculated through Kirkwood-Buff G factors for different ion-ion and ion-water pairs. The ion-pairing propensity is found to be in the order of Mg(NO3) 2 < C a (NO3) 2 < S r (NO3) 2, and it follows the trend given by experimental activity coefficients. It is found that proper modeling of these solutions requires the inclusion of electronic polarization of the ions which is achieved in the current study through electronic continuum correction force fields. A detailed analysis of the effects of ion-pairs on the structure and dynamics of water around the hydrated ions is done through classification of water into different subspecies based on their locations around the cations or anions only or bridged between them. We have looked at the diffusion coefficients, relaxation of orientational correlation functions, and also the residence times of different subspecies of water to explore the dynamics of water in different structural environments in the solutions. The current results show that the water molecules are incorporated into fairly well-structured hydration shells of the ions, thus decreasing the single-particle diffusivities and increasing the orientational relaxation times of water with an increase in salt concentration. The different structural motifs also lead to the presence of substantial dynamical heterogeneity in these solutions of strongly interacting ions. The current study helps us to understand the molecular details of hydration structure, ion pairing, and dynamics of water in the solvation shells and also of ion diffusion in aqueous solutions of divalent metal nitrate salts.

How proteins modify water dynamics

NASA Astrophysics Data System (ADS)

Persson, Filip; Söderhjelm, Pär; Halle, Bertil

2018-06-01

Much of biology happens at the protein-water interface, so all dynamical processes in this region are of fundamental importance. Local structural fluctuations in the hydration layer can be probed by 17O magnetic relaxation dispersion (MRD), which, at high frequencies, measures the integral of a biaxial rotational time correlation function (TCF)—the integral rotational correlation time. Numerous 17O MRD studies have demonstrated that this correlation time, when averaged over the first hydration shell, is longer than in bulk water by a factor 3-5. This rotational perturbation factor (RPF) has been corroborated by molecular dynamics simulations, which can also reveal the underlying molecular mechanisms. Here, we address several outstanding problems in this area by analyzing an extensive set of molecular dynamics data, including four globular proteins and three water models. The vexed issue of polarity versus topography as the primary determinant of hydration water dynamics is resolved by establishing a protein-invariant exponential dependence of the RPF on a simple confinement index. We conclude that the previously observed correlation of the RPF with surface polarity is a secondary effect of the correlation between polarity and confinement. Water rotation interpolates between a perturbed but bulk-like collective mechanism at low confinement and an exchange-mediated orientational randomization (EMOR) mechanism at high confinement. The EMOR process, which accounts for about half of the RPF, was not recognized in previous simulation studies, where only the early part of the TCF was examined. Based on the analysis of the experimentally relevant TCF over its full time course, we compare simulated and measured RPFs, finding a 30% discrepancy attributable to force field imperfections. We also compute the full 17O MRD profile, including the low-frequency dispersion produced by buried water molecules. Computing a local RPF for each hydration shell, we find that the perturbation decays exponentially with a decay "length" of 0.3 shells and that the second and higher shells account for a mere 3% of the total perturbation measured by 17O MRD. The only long-range effect is a weak water alignment in the electric field produced by an electroneutral protein (not screened by counterions), but this effect is negligibly small for 17O MRD. By contrast, we find that the 17O TCF is significantly more sensitive to the important short-range perturbations than the other two TCFs examined here.

The Role of Concentration and Solvent Character in the Molecular Organization of Humic Acids.

PubMed

Klučáková, Martina; Věžníková, Kateřina

2016-10-27

The molecular organization of humic acids in different aqueous solutions was studied over a wide concentration range (0.01-10 g·dm -3 ). Solutions of humic acids were prepared in three different media: NaOH, NaCl, and NaOH neutralized by HCl after dissolution of the humic sample. Potentiometry, conductometry, densitometry, and high resolution ultrasound spectrometry were used in order to investigate conformational changes in the humic systems. The molecular organization of humic acids in the studied systems could be divided into three concentration ranges. The rearrangements were observed at concentrations of ~0.02 g·dm -3 and ~1 g·dm -3 . The first "switch-over point" was connected with changes in the hydration shells of humic particles resulting in changes in their elasticity. The compressibility of water in the hydration shells is less than the compressibility of bulk water. The transfer of hydration water into bulk water increased the total compressibility of the solution, reducing the ultrasonic velocity. The aggregation of humic particles and the formation of rigid structures in systems with concentrations higher than 1 g·dm -3 was detected.

On the influence of hydrated ionic liquids on the dynamical structure of model proteins: a computational study.

PubMed

Haberler, Michael; Steinhauser, Othmar

2011-10-28

The solvation of the protein ubiquitin (PDB entry "1UBQ") in hydrated molecular ionic liquids was studied for varying water content or, equivalently, a diversity of ionic strengths. The cations and anions were 1-ethyl-3-methylimidazolium and trifluoromethanesulfonate, respectively. The protein's shape and stability as well as the solvation structure, the shell dynamics and the shell resolved dielectric properties were investigated by means of molecular dynamics simulations. The respective simulation trajectories covered 200 nanoseconds. Besides the characteristic point already found for the zinc finger motif at the transition from the pure aqueous environment to the ionic solution an even more pronounced state is found where several properties show extremal behaviour (maximum or minimum). This second characteristic point occurs at the transition from the ionic solution to the hydrated ionic melt where water changes its role from a solvent to a co-solvent. Most of the data analysis presented here is based on the Voronoi decomposition of space. This journal is © the Owner Societies 2011

Influence of drug binding on DNA hydration: acoustic and densimetric characterizations of netropsin binding to the poly(dAdT).poly(dAdT) and poly(dA).poly(dT) duplexes and the poly(dT).poly(dA).poly(dT) triplex at 25 degrees C.

PubMed

Chalikian, T V; Plum, G E; Sarvazyan, A P; Breslauer, K J

1994-07-26

We use high-precision acoustic and densimetric techniques to determine, at 25 degrees C, the changes in volume, delta V, and adiabatic compressibility, delta Ks, that accompany the binding of netropsin to the poly(dAdT).poly(dAdT) and poly(dA).poly(dT) duplexes, as well as to the poly(dT).poly(dA).poly(dT) triplex. We find that netropsin binding to the heteropolymeric poly(dAdT).poly(dAdT) duplex is accompanied by negative changes in volume, delta V, and small positive changes in compressibility, delta Ks. By contrast, netropsin binding to the homopolymeric poly(dA).poly(dT) duplex is accompanied by large positive changes in both volume, delta V, and compressibility, delta Ks. Furthermore, netropsin binding to the poly(dT).poly(dA).poly(dT) triplex causes changes in both volume and compressibility that are nearly twice as large as those observed when netropsin binds to the poly(dA).poly(dT) duplex. We interpret these macroscopic data in terms of binding-induced microscopic changes in the hydration of the DNA structures and the drug. Specifically, we find that netropsin binding induces the release of approximately 22 waters from the hydration shell of the poly(dAdT).poly(dAdT) heteropolymeric duplex, approximately 40 waters from the hydration shell of the poly(dA).poly(dT) homopolymeric duplex, and about 53 waters from the hydration shell of the poly(dA).poly(dT), induces the release of 18 more water molecules than netropsin binding to the heteropolymeric duplex, poly(dAdT).poly(dAdT). On the basis of apparent molar volume, phi V, and apparent molar adiabatic compressibility, phi Ks, values for the initial drug-free and final drug-bound states of the two all-AT duplexes, we propose that the larger dehydration of the poly(dA).poly(dT) duplex reflects, in part, the formation of a less hydrated poly(dA).poly(dT)-netropsin complex compared with the corresponding poly(dAdT).poly(dAdT)-netropsin complex. In conjunction with our previously published entropy data [Marky, L. A., & Breslauer, K. J. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 4359-4363], we calculate that each water of hydration released to the bulk solvent by ligand binding contributes 1.6 cal K-1 mol-1 to the entropy of binding. This value corresponds to the average difference between the partial molar entropy of water in the bulk state and water in the hydration shells of the two all-AT duplexes. When netropsin binds to the poly(dT).poly(dA).poly(dT) triplex, the changes in both volume and compressibility suggest that the binding event induces more dehydration of the triplex than of the duplex state. Specifically, we calculate that netropsin binding to the poly(dT).poly(dA).poly(dT) triplex causes the release of 13 more waters than netropsin binding to the poly(dA).poly(dT) duplex.(ABSTRACT TRUNCATED AT 400 WORDS)

Role of specific cations and water entropy on the stability of branched DNA motif structures.

PubMed

Pascal, Tod A; Goddard, William A; Maiti, Prabal K; Vaidehi, Nagarajan

2012-10-11

DNA three-way junctions (TWJs) are important intermediates in various cellular processes and are the simplest of a family of branched nucleic acids being considered as scaffolds for biomolecular nanotechnology. Branched nucleic acids are stabilized by divalent cations such as Mg(2+), presumably due to condensation and neutralization of the negatively charged DNA backbone. However, electrostatic screening effects point to more complex solvation dynamics and a large role of interfacial waters in thermodynamic stability. Here, we report extensive computer simulations in explicit water and salt on a model TWJ and use free energy calculations to quantify the role of ionic character and strength on stability. We find that enthalpic stabilization of the first and second hydration shells by Mg(2+) accounts for 1/3 and all of the free energy gain in 50% and pure MgCl(2) solutions, respectively. The more distorted DNA molecule is actually destabilized in pure MgCl(2) compared to pure NaCl. Notably, the first shell, interfacial waters have very low translational and rotational entropy (i.e., mobility) compared to the bulk, an entropic loss that is overcompensated by increased enthalpy from additional electrostatic interactions with Mg(2+). In contrast, the second hydration shell has anomalously high entropy as it is trapped between an immobile and bulklike layer. The nonmonotonic entropic signature and long-range perturbations of the hydration shells to Mg(2+) may have implications in the molecular recognition of these motifs. For example, we find that low salt stabilizes the parallel configuration of the three-way junction, whereas at normal salt we find antiparallel configurations deduced from the NMR. We use the 2PT analysis to follow the thermodynamics of this transition and find that the free energy barrier is dominated by entropic effects that result from the decreased surface area of the antiparallel form which has a smaller number of low entropy waters in the first monolayer.

Study of lysozyme mobility and binding free energy during adsorption on a graphene surface

NASA Astrophysics Data System (ADS)

Nakano, C. Masato; Ma, Heng; Wei, Tao

2015-04-01

Understanding protein adsorption is a key to the development of biosensors and anti-biofouling materials. Hydration essentially controls the adsorption process on hydrophobic surfaces, but its effect is complicated by various factors. Here, we present an ideal model system to isolate hydration effects—lysozyme adsorption on a flat hydrophobic graphene surface. Our all-atom molecular dynamics and molecular-mechanics/Poisson-Boltzmann surface area computation study reveal that lysozyme on graphene displays much larger diffusivity than in bulk water. Protein's hydration free energy within the first hydration shell is dominated by the protein-water electrostatic interactions and acts as an energy barrier for protein adsorption. On the other hand, the surface tension, especially that from the hydrophobic graphene, can effectively weaken the barrier to promote adsorption.

Hydration and dielectrical properties of aqueous pyrrolidinium trifluoroacetate solutions

NASA Astrophysics Data System (ADS)

Lyashchenko, A. K.; Balakaeva, I. V.; Simonova, Yu. A.; Timofeeva, L. M.

2017-10-01

Results from microwave measurements of the dielectrical properties of aqueous pyrrolidinium trifluoroacetate solutions at maximum water dispersion frequencies (13-25 GHz) and temperatures of 288, 298, and 308 K are given. The static dielectrical constants, times, and activation parameters of the dielectrical relaxation of solutions are calculated. The enthalpy and time of dielectrical relaxation activation are increased by deceleration of the motion of water molecules in the hydrate shells of ions. The changes in dielectrical parameters are in this case minimal in a series of aqueous solutions of diallylammonium salts with cations of different structures and degrees of substitution. It is shown that pyrrolidinium ions are characterized by weak hydrophobic hydration.

Ion Association in AlCl3 Aqueous Solutions from Constrained First-Principles Molecular Dynamics

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

Cauet, Emilie L.; Bogatko, Stuart A.; Bylaska, Eric J.

2012-10-15

Ab initio molecular dynamics was used to investigate the ion pairing behavior between Cl- and the Al3+ ion in an aqueous AlCl3 solution containing 63 water molecules. A series of constrained simulations was carried out at 300 K for up to 16 ps each, by fixing the inter-nuclear separation (rAl-Cl) between the Al3+ ion and one of the Cl- ions. The calculated potential of mean force of the Al3+-Cl- ion pair shows a pronounced minimum at rAl-Cl = 2.3 Å corresponding to a contact ion pair (CIP). Two local minima assigned to solvent separated ion pairs (SSIP) are identified atmore » rAl-Cl= 4.4 and 6.0 Å. The positions of the free energy minima coincide with the hydration shell intervals of the Al3+ cation suggesting that the Cl- ion is inclined to reside in regions of low concentration of waters, i.e. between the 1st and 2nd shells of Al3+ and between the 2nd shell and bulk. A detailed analysis of solvent structure around the Al3+ and Cl- ions as a function of rAl-Cl is presented. The results are compared to structure data from X-ray measurements and unconstrained AIMD simulations of single ions Al3+ and Cl- and AlCl3 solutions. The dipole moment of the water molecules inside the 1st and 2nd hydration shells of Al3+ and in the bulk region and those of the Clion were calculated as a function of rAl-Cl. Major changes in the electronic structure of the system result from the removal of Cl- from the 1st hydration shell of the Al3+ cation. Finally, two unconstrained AIMD simulations of aqueous AlCl3 solutions corresponding to CIP and SSIP configurations were performed (17 ps, 300 K). Only minor structural changes are observed in these systems, confirming their stability.« less

Stabilizing effects of hydrated fullerenes C₆₀ in a wide range of concentrations on luciferase, alkaline phosphatase, and peroxidase in vitro.

PubMed

Voeikov, Vladimir L; Yablonskaya, Olga I

2015-01-01

Hydrated fullerene (HyFnC60) is a highly hydrophilic supra-molecular complex consisting of unmodified С60 fullerene molecule enclosed into a hydrated shell. It has been shown in numerous experiments that aqueous solutions of HyFnC60 manifest a wide range of biological activities both in vivo and in vitro even at very low concentrations of HyFnC60. We used a spectrophotometric method and a method of biochemoluminescence to demonstrate that HyFnC60 in concentrations below 10(-9) M down to 10(-23) M stabilizes peroxidase, alkaline phosphatase, and bacterial luciferase against inactivation due to long-term incubation of the enzymes at room temperature and also against heat inactivation. In addition, HyFnC60 was able to "revive" heat inactivated enzymes. These effects cannot be explained by the direct action of the fullerene molecules upon the enzymes. We suggest that the effects of HyFnC60 on the enzymes are related to the ability of hydrated fullerene C60 molecules to organize thick aqueous shells around them. One of the specific properties of water phase in these shells is its ability to optimize redox reactions, which can support enzyme stability against factors deteriorating their structure.

Study of lysozyme mobility and binding free energy during adsorption on a graphene surface

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

Nakano, C. Masato; Ma, Heng; Wei, Tao, E-mail: twei@lamar.edu

Understanding protein adsorption is a key to the development of biosensors and anti-biofouling materials. Hydration essentially controls the adsorption process on hydrophobic surfaces, but its effect is complicated by various factors. Here, we present an ideal model system to isolate hydration effects—lysozyme adsorption on a flat hydrophobic graphene surface. Our all-atom molecular dynamics and molecular-mechanics/Poisson-Boltzmann surface area computation study reveal that lysozyme on graphene displays much larger diffusivity than in bulk water. Protein's hydration free energy within the first hydration shell is dominated by the protein-water electrostatic interactions and acts as an energy barrier for protein adsorption. On the othermore » hand, the surface tension, especially that from the hydrophobic graphene, can effectively weaken the barrier to promote adsorption.« less

Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

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

Biedermannová, Lada, E-mail: lada.biedermannova@ibt.cas.cz; Schneider, Bohdan

2015-10-27

The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined. Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. Themore » results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.« less

Can xenon in water inhibit ice growth? Molecular dynamics of phase transitions in water-Xe system.

PubMed

Artyukhov, Vasilii I; Pulver, Alexander Yu; Peregudov, Alex; Artyuhov, Igor

2014-07-21

Motivated by recent experiments showing the promise of noble gases as cryoprotectants, we perform molecular dynamics modeling of phase transitions in water with xenon under cooling. We follow the structure and dynamics of xenon water solution as a function of temperature. Homogeneous nucleation of clathrate hydrate phase is observed and characterized. As the temperature is further reduced we observe hints of dissociation of clathrate due to stronger hydrophobic hydration, pointing towards a possible instability of clathrate at cryogenic temperatures and conversion to an amorphous phase comprised of "xenon + hydration shell" Xe·(H2O)21.5 clusters. Simulations of ice-xenon solution interface in equilibrium and during ice growth reveal the effects of xenon on the ice-liquid interface, where adsorbed xenon causes roughening of ice surface but does not preferentially form clathrate. These results provide evidence against the ice-blocker mechanism of xenon cryoprotection.

Water adsorption on TiO2 surfaces probed by soft X-ray spectroscopies: bulk materials vs. isolated nanoparticles

PubMed Central

Benkoula, Safia; Sublemontier, Olivier; Patanen, Minna; Nicolas, Christophe; Sirotti, Fausto; Naitabdi, Ahmed; Gaie-Levrel, François; Antonsson, Egill; Aureau, Damien; Ouf, François-Xavier; Wada, Shin-Ichi; Etcheberry, Arnaud; Ueda, Kiyoshi; Miron, Catalin

2015-01-01

We describe an experimental method to probe the adsorption of water at the surface of isolated, substrate-free TiO2 nanoparticles (NPs) based on soft X-ray spectroscopy in the gas phase using synchrotron radiation. To understand the interfacial properties between water and TiO2 surface, a water shell was adsorbed at the surface of TiO2 NPs. We used two different ways to control the hydration level of the NPs: in the first scheme, initially solvated NPs were dried and in the second one, dry NPs generated thanks to a commercial aerosol generator were exposed to water vapor. XPS was used to identify the signature of the water layer shell on the surface of the free TiO2 NPs and made it possible to follow the evolution of their hydration state. The results obtained allow the establishment of a qualitative determination of isolated NPs’ surface states, as well as to unravel water adsorption mechanisms. This method appears to be a unique approach to investigate the interface between an isolated nano-object and a solvent over-layer, paving the way towards new investigation methods in heterogeneous catalysis on nanomaterials. PMID:26462615

The hydration structure of the heavy-alkalines Rb+ and Cs+ through molecular dynamics and X-ray absorption spectroscopy: surface clusters and eccentricity.

PubMed

Caralampio, Daniel Z; Martínez, José M; Pappalardo, Rafael R; Marcos, Enrique Sánchez

2017-11-01

Physicochemical properties of the two heaviest stable alkaline cations, Rb + and Cs + , in water have been examined from classical molecular dynamics (MD) simulations. Alkaline cation-water intermolecular potentials have been built from ab initio interaction energies of [M(H 2 O) n ] + clusters. Unlike in the case of other monatomic metal cations, the sampling needed the inclusion of surface clusters to properly describe the interactions. The first coordination shell is found at an average M-O distance of 2.87 Å and 3.12 Å for Rb + and Cs + , respectively, with coordination numbers of 8 and 10. Structural, dynamical and energetic properties are discussed on the basis of the delicate compromise among the ion-water and water-water interactions which contribute almost on the same foot to the definition of the solvent structure around the ions. A significant asymmetry is detected in the Rb + and Cs + first hydration shell. Reorientational times of first-shell water molecules for Cs + support a clear structure-breaking nature for this cation, whereas the Rb + values do not differ from pure water behavior. Experimental EXAFS and XANES spectra have been compared to simulated ones, obtained by means of application of the FEFF code to a set of statistically significant structures taken from the MD simulations. Due to the presence of multi-excitations in the absorption spectra, theoretical-experimental agreement for the EXAFS spectra is reached when the multi-excitations are removed from the experimental spectra.

Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates

NASA Astrophysics Data System (ADS)

Zhang, Junfang; Rivero, Mayela; Choi, S. K.

2007-02-01

We present molecular dynamics simulation results for polyacrylamide in potassium montmorillonite clay-aqueous systems. Interlayer molecular structure and dynamics properties are investigated. The number density profile, radial distribution function, root-mean-square deviation (RMSD), mean-square displacement (MSD) and diffusion coefficient are reported. The calculations are conducted in constant NVT ensembles, at T = 300 K and with layer spacing of 40 Å. Our simulation results showed that polyacrylamides had little impact on the structure of interlayer water. Density profiles and radial distribution function indicated that hydration shells were formed. In the presence of polyacrylamides more potassium counterions move close to the clay surface while water molecules move away, indicating that potassium counterions are hydrated to a lesser extent than the system in which no polyacrylamides were added. The diffusion coefficients for potassium and water decreased when polyacrylamides were added.

The spatial range of protein hydration

NASA Astrophysics Data System (ADS)

Persson, Filip; Söderhjelm, Pär; Halle, Bertil

2018-06-01

Proteins interact with their aqueous surroundings, thereby modifying the physical properties of the solvent. The extent of this perturbation has been investigated by numerous methods in the past half-century, but a consensus has still not emerged regarding the spatial range of the perturbation. To a large extent, the disparate views found in the current literature can be traced to the lack of a rigorous definition of the perturbation range. Stating that a particular solvent property differs from its bulk value at a certain distance from the protein is not particularly helpful since such findings depend on the sensitivity and precision of the technique used to probe the system. What is needed is a well-defined decay length, an intrinsic property of the protein in a dilute aqueous solution, that specifies the length scale on which a given physical property approaches its bulk-water value. Based on molecular dynamics simulations of four small globular proteins, we present such an analysis of the structural and dynamic properties of the hydrogen-bonded solvent network. The results demonstrate unequivocally that the solvent perturbation is short-ranged, with all investigated properties having exponential decay lengths of less than one hydration shell. The short range of the perturbation is a consequence of the high energy density of bulk water, rendering this solvent highly resistant to structural perturbations. The electric field from the protein, which under certain conditions can be long-ranged, induces a weak alignment of water dipoles, which, however, is merely the linear dielectric response of bulk water and, therefore, should not be thought of as a structural perturbation. By decomposing the first hydration shell into polarity-based subsets, we find that the hydration structure of the nonpolar parts of the protein surface is similar to that of small nonpolar solutes. For all four examined proteins, the mean number of water-water hydrogen bonds in the nonpolar subset is within 1% of the value in bulk water, suggesting that the fragmentation and topography of the nonpolar protein-water interface has evolved to minimize the propensity for protein aggregation by reducing the unfavorable free energy of hydrophobic hydration.

Why are ionic liquid ions mainly associated in water? A Car-Parrinello study of 1-ethyl-3-methyl-imidazolium chloride water mixture

NASA Astrophysics Data System (ADS)

Spickermann, C.; Thar, J.; Lehmann, S. B. C.; Zahn, S.; Hunger, J.; Buchner, R.; Hunt, P. A.; Welton, T.; Kirchner, B.

2008-09-01

In this study we present the results of a first principles molecular dynamics simulation of a single 1-ethyl-3-methyl-imidazolium chloride [C2C1im][Cl] ion pair dissolved in 60 water molecules. We observe a preference of the in plane chloride coordination with respect to the cation ring plane as compared to the energetic slightly more demanding on top coordination. Evaluation of the different radial distribution functions demonstrates that the structure of the hydration shell around the ion pair differs significantly from bulk water and that no true ion pair dissociation in terms of completely autonomous solvation shells takes place on the timescale of the simulation. In addition, dipole moment distributions of the solvent in distinct solvation shells around different functional parts of the [C2C1im][Cl] ion pair are calculated from maximally localized Wannier functions. The analysis of these distributions gives evidence for a depolarization of water molecules close to the hydrophobic parts of the cation as well as close to the anion. Examination of the angular distribution of different OH(H2O )-X angles in turn shows a linear coordination of chloride accompanied by a tangential orientation of water molecules around the hydrophobic groups, being a typical feature of hydrophobic hydration. Based on these orientational aspects, a structural model for the obvious preference of ion pair association is developed, which justifies the associating behavior of solvated [C2C1im][Cl] ions in terms of an energetically favorable interface between the solvation shells of the anion and the hydrophobic parts of the cation.

Why are ionic liquid ions mainly associated in water? A Car-Parrinello study of 1-ethyl-3-methyl-imidazolium chloride water mixture.

PubMed

Spickermann, C; Thar, J; Lehmann, S B C; Zahn, S; Hunger, J; Buchner, R; Hunt, P A; Welton, T; Kirchner, B

2008-09-14

In this study we present the results of a first principles molecular dynamics simulation of a single 1-ethyl-3-methyl-imidazolium chloride [C(2)C(1)im][Cl] ion pair dissolved in 60 water molecules. We observe a preference of the in plane chloride coordination with respect to the cation ring plane as compared to the energetic slightly more demanding on top coordination. Evaluation of the different radial distribution functions demonstrates that the structure of the hydration shell around the ion pair differs significantly from bulk water and that no true ion pair dissociation in terms of completely autonomous solvation shells takes place on the timescale of the simulation. In addition, dipole moment distributions of the solvent in distinct solvation shells around different functional parts of the [C(2)C(1)im][Cl] ion pair are calculated from maximally localized Wannier functions. The analysis of these distributions gives evidence for a depolarization of water molecules close to the hydrophobic parts of the cation as well as close to the anion. Examination of the angular distribution of different OH(H(2)O)-X angles in turn shows a linear coordination of chloride accompanied by a tangential orientation of water molecules around the hydrophobic groups, being a typical feature of hydrophobic hydration. Based on these orientational aspects, a structural model for the obvious preference of ion pair association is developed, which justifies the associating behavior of solvated [C(2)C(1)im][Cl] ions in terms of an energetically favorable interface between the solvation shells of the anion and the hydrophobic parts of the cation.

Dynamics of confined water reconstructed from inelastic x-ray scattering measurements of bulk response functions

NASA Astrophysics Data System (ADS)

Coridan, Robert H.; Schmidt, Nathan W.; Lai, Ghee Hwee; Abbamonte, Peter; Wong, Gerard C. L.

2012-03-01

Nanoconfined water and surface-structured water impacts a broad range of fields. For water confined between hydrophilic surfaces, measurements and simulations have shown conflicting results ranging from “liquidlike” to “solidlike” behavior, from bulklike water viscosity to viscosity orders of magnitude higher. Here, we investigate how a homogeneous fluid behaves under nanoconfinement using its bulk response function: The Green's function of water extracted from a library of S(q,ω) inelastic x-ray scattering data is used to make femtosecond movies of nanoconfined water. Between two confining surfaces, the structure undergoes drastic changes as a function of surface separation. For surface separations of ≈9 Å, although the surface-associated hydration layers are highly deformed, they are separated by a layer of bulklike water. For separations of ≈6 Å, the two surface-associated hydration layers are forced to reconstruct into a single layer that modulates between localized “frozen’ and delocalized “melted” structures due to interference of density fields. These results potentially reconcile recent conflicting experiments. Importantly, we find a different delocalized wetting regime for nanoconfined water between surfaces with high spatial frequency charge densities, where water is organized into delocalized hydration layers instead of localized hydration shells, and are strongly resistant to `freezing' down to molecular distances (<6 Å).

Deoxyribonucleoprotein structure and radiation injury - Cellular radiosensitivity is determined by LET-infinity-dependent DNA damage in hydrated deoxyribonucleoproteins and the extent of its repair

NASA Technical Reports Server (NTRS)

Lett, J. T.; Peters, E. L.

1992-01-01

Until recently, OH radicals formed in bulk nuclear water were believed to be the major causes of DNA damage that results in cell death, especially for sparsely ionizing radiations. That hypothesis has now been challenged, if not refuted. Lethal genomic DNA damage is determined mainly by energy deposition in deoxyribonucleoproteins, and their hydration shells, and charge (energy) transfer processes within those structures.

Adsorption of insulin peptide on charged single-walled carbon nanotubes: significant role of ordered water molecules.

PubMed

Shen, Jia-Wei; Wu, Tao; Wang, Qi; Kang, Yu; Chen, Xin

2009-06-02

Ordered hydration shells: The more ordered hydration shells outside the charged CNT surfaces prevent more compact adsorption of the peptide in the charged CNT systems [picture: see text], but peptide binding strengths on the charged CNT surfaces are stronger due to the electrostatic interaction.Studies of adsorption dynamics and stability for peptides/proteins on single-walled carbon nanotubes (SWNTs) are of great importance for a better understanding of the properties and nature of nanotube-based biosystems. Herein, the dynamics and mechanism of the adsorption of the insulin chain B peptide on different charged SWNTs are investigated by explicit solvent molecular dynamics simulations. The results show that all types of surfaces effectively attract the model peptide. Water molecules play a significant role in peptide adsorption on the surfaces of charged carbon nanotubes (CNTs). Compared to peptide adsorption on neutral CNT surfaces, the more ordered hydration shells outside the tube prevent more compact adsorption of the peptide in charged CNT systems. This shield effect leads to a smaller conformational change and van der Waals interaction between the peptide and surfaces, but peptide binding strengths on charged CNT surfaces are stronger than those on the neutral CNT surface due to the strong electrostatic interaction. The result of these simulations implies the possibility of improving the binding strength of peptides/proteins on CNT surfaces, as well as keeping the integrity of the peptide/protein conformation in peptide/protein-CNT complexes by charging the CNTs.

Aqueous solvation of Mg(ii) and Ca(ii): A Born-Oppenheimer molecular dynamics study of microhydrated gas phase clusters

NASA Astrophysics Data System (ADS)

León-Pimentel, C. I.; Amaro-Estrada, J. I.; Hernández-Cobos, J.; Saint-Martin, H.; Ramírez-Solís, A.

2018-04-01

The hydration features of [Mg(H2O)n ] 2 + and [Ca(H2O)n ] 2 + clusters with n = 3-6, 8, 18, and 27 were studied by means of Born-Oppenheimer molecular dynamics simulations at the B3LYP/6-31+G** level of theory. For both ions, it is energetically more favorable to have all water molecules in the first hydration shell when n ≤ 6, but stable lower coordination average structures with one water molecule not directly interacting with the ion were found for Mg2+ at room temperature, showing signatures of proton transfer events for the smaller cation but not for the larger one. A more rigid octahedral-type structure for Mg2+ than for Ca2+ was observed in all simulations, with no exchange of water molecules to the second hydration shell. Significant thermal effects on the average structure of clusters were found: while static optimizations lead to compact, spherically symmetric hydration geometries, the effects introduced by finite-temperature dynamics yield more prolate configurations. The calculated vibrational spectra are in agreement with infrared spectroscopy results. Previous studies proposed an increase in the coordination number (CN) from six to eight water molecules for [Ca(H2O)n ] 2 + clusters when n ≥ 12; however, in agreement with recent measurements of binding energies, no transition to a larger CN was found when n > 8. Moreover, the excellent agreement found between the calculated extended X-ray absorption fine structure spectroscopy spectra for the larger cluster and the experimental data of the aqueous solution supports a CN of six for Ca2+.

Molecular-dynamics simulations of alkaline-earth metal cations in water by atom-bond electronegativity equalization method fused into molecular mechanics.

PubMed

Yang, Zhong-Zhi; Li, Xin

2005-09-01

Intermolecular potential for alkaline-earth metal (Be(2+), Mg(2+), and Ca(2+)) cations in water has been derived using the atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM), and it is consistent with what was previously applied to the hydration study of the monovalent cations. Parameters for the effective interaction between a cation and a water molecule were determined, reproducing the ab initio results. The static, dynamic, and thermodynamic properties of Be(2+)(aq), Mg(2+)(aq), and Ca(2+)(aq) were studied using these potential parameters. Be(2+) requires a more complicated form of the potential function than Mg(2+) and Ca(2+) in order to obtain better fits. Strong influences of the twofold charged cations on the structures of the hydration shells and some other properties of aqueous ionic solutions are discussed and compared with the results of a previous study of monovalent cations in water. At the same time, comparative study of the hydration properties of each cation is also discussed. This work demonstrates that ABEEM/MM provides a useful tool in the exploration of the hydration of double-charged cations in water.

Global minimum-energy structure and spectroscopic properties of I2(*-) x n H2O clusters: a Monte Carlo simulated annealing study.

PubMed

Pathak, Arup Kumar; Mukherjee, Tulsi; Maity, Dilip Kumar

2010-01-18

The vibrational (IR and Raman) and photoelectron spectral properties of hydrated iodine-dimer radical-anion clusters, I(2)(*-) x n H(2)O (n=1-10), are presented. Several initial guess structures are considered for each size of cluster to locate the global minimum-energy structure by applying a Monte Carlo simulated annealing procedure including spin-orbit interaction. In the Raman spectrum, hydration reduces the intensity of the I-I stretching band but enhances the intensity of the O-H stretching band of water. Raman spectra of more highly hydrated clusters appear to be simpler than the corresponding IR spectra. Vibrational bands due to simultaneous stretching vibrations of O-H bonds in a cyclic water network are observed for I(2)(*-) x n H(2)O clusters with n > or = 3. The vertical detachment energy (VDE) profile shows stepwise saturation that indicates closing of the geometrical shell in the hydrated clusters on addition of every four water molecules. The calculated VDE of finite-size small hydrated clusters is extrapolated to evaluate the bulk VDE value of I(2)(*-) in aqueous solution as 7.6 eV at the CCSD(T) level of theory. Structure and spectroscopic properties of these hydrated clusters are compared with those of hydrated clusters of Cl(2)(*-) and Br(2)(*-).

Cellulose Aggregation under Hydrothermal Pretreatment Conditions.

PubMed

Silveira, Rodrigo L; Stoyanov, Stanislav R; Kovalenko, Andriy; Skaf, Munir S

2016-08-08

Cellulose, the most abundant biopolymer on Earth, represents a resource for sustainable production of biofuels. Thermochemical treatments make lignocellulosic biomaterials more amenable to depolymerization by exposing cellulose microfibrils to enzymatic or chemical attacks. In such treatments, the solvent plays fundamental roles in biomass modification, but the molecular events underlying these changes are still poorly understood. Here, the 3D-RISM-KH molecular theory of solvation has been employed to analyze the role of water in cellulose aggregation under different thermodynamic conditions. The results show that, under ambient conditions, highly structured hydration shells around cellulose create repulsive forces that protect cellulose microfibrils from aggregating. Under hydrothermal pretreatment conditions, however, the hydration shells lose structure, and cellulose aggregation is favored. These effects are largely due to a decrease in cellulose-water interactions relative to those at ambient conditions, so that cellulose-cellulose attractive interactions become prevalent. Our results provide an explanation to the observed increase in the lateral size of cellulose crystallites when biomass is subject to pretreatments and deepen the current understanding of the mechanisms of biomass modification.

Dynamics of water solutions of natural polysaccharides by fast field cycling nmr relaxometry

NASA Astrophysics Data System (ADS)

Prusova, Alena; Conte, Pellegrino; Kucerik, Jiri; de Pasquale, Claudio; Alonzo, Giuseppe

2010-05-01

Cryobiology studies the effect of low temperatures on living systems such as microorganisms and plants. In particular, plants growing in cold or frozen environments can survive such extreme conditions due to the cold hardening process. Hardening is a three step process during which, first, translocation of polysaccharides to the plant roots affects water structure in the cell-soil surface. For this reason, increase of cell-membrane permeability and resistance to temperatures from -5°C to -10°C is achieved. In a second step, chemical alteration of cell membrane arises and resistance to temperatures up to -20°C is obtained. The last hardening step consists in the vitrification of the plant tissues which allow plants to survive at temperatures as low as -50°C. Since polysaccharides play a very important role in the initial part of the cold hardening process, it is of paramount importance to study the effect of such natural biopolymers on water structure. Here, we present preliminary data obtained by fast field cycling NMR relaxometry on the effect of hyaluronan (an anionic, non-sulfated glycosaminoglycan) on water structure at different concentrations of the polysaccharide. Although hyaluronan is a polysaccharide found exceptionally in animal, human or bacterial bodies, in the present work it was used as a model "pilot" compound. In fact, it has an unique ability to hold water and it contains both polysaccharide and protein-like acetamido functionalities. For this reason, hyaluronan promotes the future research on other plant biopolymers such as, for instance, starch and other very specific proteins. Results revealed that different water-structure systems surround the molecule of hyaluronan in diluted and semidiluted systems. Namely, at the lowest hyaluronan concentration, three hydration shells can be recognized. The first hydration shell is made by bound water (BW) which is strongly fixed to the hyaluronan surface mainly through electrostatic interactions. A second hydration shell contains water molecules, also recognized as partly-bound (PBW), which are not directly interacting with the hyaluronan chains but with BW. Finally, water molecules, which dynamics is resembling that of the pure and undisturbed water, are indicated either as a bulk water or free water (FW). As hyaluronan concentration is increased the third FW hydration shell is lost and all water molecules are affected by the presence of hyaluronan molecules. This work showed the great potential of FFC-NMR relaxometry in revealing water nature in polysaccharide solutions and the possibility for future applications on complex biological systems. Acknowledgements A.P. gratefully acknowledges a bilateral Erasmus project between Brno University of Technology and University of Palermo which provided grant sustainment for working in Italy. Ministry of Education of the Czech Republic, project MSM 0021630501 is also acknwledged. This work was partially funded by Ce.R.T.A. s.c.r.l. (Centri Regionali per le Tecnologie Alimentari; Italy). Authors kindly acknowledge Dr. Vladimír Velebný (CPN company, Dolní Dobrouč, Czech Republic) for providing of hyaluronan sample.

Hydration properties of adenosine phosphate series as studied by microwave dielectric spectroscopy.

PubMed

Mogami, George; Wazawa, Tetsuichi; Morimoto, Nobuyuki; Kodama, Takao; Suzuki, Makoto

2011-02-01

Hydration properties of adenine nucleotides and orthophosphate (Pi) in aqueous solutions adjusted to pH=8 with NaOH were studied by high-resolution microwave dielectric relaxation (DR) spectroscopy at 20 °C. The dielectric spectra were analyzed using a mixture theory combined with a least-squares Debye decomposition method. Solutions of Pi and adenine nucleotides showed qualitatively similar dielectric properties described by two Debye components. One component was characterized by a relaxation frequency (f(c)=18.8-19.7 GHz) significantly higher than that of bulk water (17 GHz) and the other by a much lower f(c) (6.4-7.6 GHz), which are referred to here as hyper-mobile water and constrained water, respectively. By contrast, a hydration shell of only the latter type was found for adenosine (f(c)~6.7 GHz). The present results indicate that phosphoryl groups are mostly responsible for affecting the structure of the water surrounding the adenine nucleotides by forming one constrained water layer and an additional three or four layers of hyper-mobile water. Copyright © 2010 Elsevier B.V. All rights reserved.

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

Flow strength of highly hydrated Mg- and Na-sulfate hydrate salts, pure and in mixtures with water ice, with application to Europa

USGS Publications Warehouse

Durham, W.B.; Stern, L.A.; Kubo, T.; Kirby, S.H.

2005-01-01

We selected two Europan-ice-shell candidate highly hydrated sulfate salts for a laboratory survey of ductile flow properties: MgSO4 ?? 7H2O (epsomite) and Na2SO4 ?? 10H2O (mirabilite), called MS7 and NS10, respectively. Polycrystalline samples in pure form and in mixtures with water ice I were tested using our cryogenic high-pressure creep apparatus at temperatures 232 ??? T ??? 294 K, confining pressures P = 50 and 100 MPa, and strain rates 4 ?? 10-8 ??? ???dot;e ??? 7 ?? 10-5 s-1. Grain size of NS10 samples was > 100 ??m. The flow strength ?? of pure MS7 was over 100 times that of polycrystalline ice I at comparable conditions; that of pure NS10 over 20 times that of ice. In terms of the creep law ???dot;e = A??n e-Q/RT, where R is the gas constant, we determine parameter values of A = 1012.1 MPa-ns-1, n = 5.4, and Q = 128 kJ/mol for pure NS10. Composites of ice I and NS10 of volume fraction ?? NS10 have flow strength ??c = [??NS10??NS10J + (1 - ?? NS10)??iceIJ]1/J where J ??? -0.5, making the effect on the flow of ice with low volume fractions of NS10 much like that of virtually undeformable hard rock inclusions. Being much stronger and denser than ice, massive sulfate inclusions in the warmer, ductile layer of the Europan ice shell are less likely to be entrained in convective ice flow and more likely to be drawn to the base of the ice shell by gravitational forces and eventually expelled. With only smaller, dispersed sulfate inclusions, at probable sulfate ?? < 0.2, the shell may be treated rheologically as pure, polycrystalline ice, with boundary conditions perhaps influenced by the high density and low thermal conductivity of the hydrated salts. Copyright 2005 by the American Geophysical Union.

Water Mediated Ligand Functional Group Cooperativity: The Contribution of a Methyl Group to Binding Affinity is Enhanced by a COO− Group Through Changes in the Structure and Thermo dynamics of the Hydration Waters of Ligand-Thermolysin Complexes

PubMed Central

Nasief, Nader N; Tan, Hongwei; Kong, Jing; Hangauer, David

2012-01-01

Ligand functional groups can modulate the contributions of one another to the ligand-protein binding thermodynamics, producing either positive or negative cooperativity. Data presented for four thermolysin phosphonamidate inhibitors demonstrate that the differential binding free energy and enthalpy caused by replacement of a H with a Me group, which binds in the well-hydrated S2′ pocket, are more favorable in presence of a ligand carboxylate. The differential entropy is however less favorable. Dissection of these differential thermodynamic parameters, X-ray crystallography, and density-functional theory calculations suggest that these cooperativities are caused by variations in the thermodynamics of the complex hydration shell changes accompanying the H→Me replacement. Specifically, the COO− reduces both the enthalpic penalty and the entropic advantage of displacing water molecules from the S2′ pocket, and causes a subsequent acquisition of a more enthalpically, less entropically, favorable water network. This study contributes to understanding the important role water plays in ligand-protein binding. PMID:22894131

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.

The importance of dehydration in determining ion transport in narrow pores.

PubMed

Richards, Laura A; Schäfer, Andrea I; Richards, Bryce S; Corry, Ben

2012-06-11

The transport of hydrated ions through narrow pores is important for a number of processes such as the desalination and filtration of water and the conductance of ions through biological channels. Here, molecular dynamics simulations are used to systematically examine the transport of anionic drinking water contaminants (fluoride, chloride, nitrate, and nitrite) through pores ranging in effective radius from 2.8 to 6.5 Å to elucidate the role of hydration in excluding these species during nanofiltration. Bulk hydration properties (hydrated size and coordination number) are determined for comparison with the situations inside the pores. Free energy profiles for ion transport through the pores show energy barriers depend on pore size, ion type, and membrane surface charge and that the selectivity sequence can change depending on the pore size. Ion coordination numbers along the trajectory showed that partial dehydration of the transported ion is the main contribution to the energy barriers. Ion transport is greatly hindered when the effective pore radius is smaller than the hydrated radius, as the ion has to lose some associated water molecules to enter the pore. Small energy barriers are still observed when pore sizes are larger than the hydrated radius due to re-orientation of the hydration shell or the loss of more distant water. These results demonstrate the importance of ion dehydration in transport through narrow pores, which increases the current level of mechanistic understanding of membrane-based desalination and transport in biological channels. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simulation of water solutions of Ni 2+ at infinite dilution

NASA Astrophysics Data System (ADS)

Natália, M.; Cordeiro, D. S.; Ignaczak, Anna; Gomes, José A. N. F.

1993-10-01

A new ab initio pair potential is developed to describe the nickel—water interactions in Ni(II) aqueous solutions. Results of Monte Carlo simulations for the Ni(II)(H 2O) 200 system are presented for this pair potential with and without three-body classical polarization terms (the water—water interaction is described by the ab initio MCY potential). The structure of the solution around Ni(II) is discussed in terms of radial distribution functions, coordination numbers and thermal ellipsoids. The results show that the three-body terms have a non-negligible effect on the simulated solution. In fact, the experimental coordination number of six is reproduced with the full potential while a higher value is predicted when the simple pairwise-additive potential is used. The equilibrium NiO distance for the first hydration shell is also dependent on the use of the three-body terms. Comparison of our distribution functions with those obtained by neutron-diffraction experiments shows a reasonable quantitative agreement. Statistical pattern recognition analysis has also been applied to our simulations in order to better understand the local thermal motion of the water molecules around the metal ion. In this way, thermal ellipsoids have been computed (and graphically displayed) for each atom of the water molecules belonging to the Ni(II) first hydration shell. This analysis revealed that the twisting and bending motions are greater than the radial motion, and that the hydrogens have a higher mobility than the oxygens. In addition, a thermodynamic perturbation method has been incorporated in our Monte Carlo procedure in order to compute the free energy of hydration for the Ni(II) ion. Agreement between these results and the experimental ones is also sufficiently reasonable to demonstrate the feasibility of this new potential for the nickel—water interactions.

The anomalous halogen bonding interactions between chlorine and bromine with water in clathrate hydrates.

PubMed

Dureckova, Hana; Woo, Tom K; Udachin, Konstantin A; Ripmeester, John A; Alavi, Saman

2017-10-13

Clathrate hydrate phases of Cl 2 and Br 2 guest molecules have been known for about 200 years. The crystal structure of these phases was recently re-determined with high accuracy by single crystal X-ray diffraction. In these structures, the water oxygen-halogen atom distances are determined to be shorter than the sum of the van der Waals radii, which indicates the action of some type of non-covalent interaction between the dihalogens and water molecules. Given that in the hydrate phases both lone pairs of each water oxygen atom are engaged in hydrogen bonding with other water molecules of the lattice, the nature of the oxygen-halogen interactions may not be the standard halogen bonds characterized recently in the solid state materials and enzyme-substrate compounds. The nature of the halogen-water interactions for the Cl 2 and Br 2 molecules in two isolated clathrate hydrate cages has recently been studied with ab initio calculations and Natural Bond Order analysis (Ochoa-Resendiz et al. J. Chem. Phys. 2016, 145, 161104). Here we present the results of ab initio calculations and natural localized molecular orbital analysis for Cl 2 and Br 2 guests in all cage types observed in the cubic structure I and tetragonal structure I clathrate hydrates to characterize the orbital interactions between the dihalogen guests and water. Calculations with isolated cages and cages with one shell of coordinating molecules are considered. The computational analysis is used to understand the nature of the halogen bonding in these materials and to interpret the guest positions in the hydrate cages obtained from the X-ray crystal structures.

Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration.

PubMed

Hofer, Thomas S; Hünenberger, Philippe H

2018-06-14

The absolute intrinsic hydration free energy G H + ,wat ◦ of the proton, the surface electric potential jump χ wat ◦ upon entering bulk water, and the absolute redox potential V H + ,wat ◦ of the reference hydrogen electrode are cornerstone quantities for formulating single-ion thermodynamics on absolute scales. They can be easily calculated from each other but remain fundamentally elusive, i.e., they cannot be determined experimentally without invoking some extra-thermodynamic assumption (ETA). The Born model provides a natural framework to formulate such an assumption (Born ETA), as it automatically factors out the contribution of crossing the water surface from the hydration free energy. However, this model describes the short-range solvation inaccurately and relies on the choice of arbitrary ion-size parameters. In the present study, both shortcomings are alleviated by performing first-principle calculations of the hydration free energies of the sodium (Na + ) and potassium (K + ) ions. The calculations rely on thermodynamic integration based on quantum-mechanical molecular-mechanical (QM/MM) molecular dynamics (MD) simulations involving the ion and 2000 water molecules. The ion and its first hydration shell are described using a correlated ab initio method, namely resolution-of-identity second-order Møller-Plesset perturbation (RIMP2). The next hydration shells are described using the extended simple point charge water model (SPC/E). The hydration free energy is first calculated at the MM level and subsequently increased by a quantization term accounting for the transformation to a QM/MM description. It is also corrected for finite-size, approximate-electrostatics, and potential-summation errors, as well as standard-state definition. These computationally intensive simulations provide accurate first-principle estimates for G H + ,wat ◦ , χ wat ◦ , and V H + ,wat ◦ , reported with statistical errors based on a confidence interval of 99%. The values obtained from the independent Na + and K + simulations are in excellent agreement. In particular, the difference between the two hydration free energies, which is not an elusive quantity, is 73.9 ± 5.4 kJ mol -1 (K + minus Na + ), to be compared with the experimental value of 71.7 ± 2.8 kJ mol -1 . The calculated values of G H + ,wat ◦ , χ wat ◦ , and V H + ,wat ◦ (-1096.7 ± 6.1 kJ mol -1 , 0.10 ± 0.10 V, and 4.32 ± 0.06 V, respectively, averaging over the two ions) are also in remarkable agreement with the values recommended by Reif and Hünenberger based on a thorough analysis of the experimental literature (-1100 ± 5 kJ mol -1 , 0.13 ± 0.10 V, and 4.28 ± 0.13 V, respectively). The QM/MM MD simulations are also shown to provide an accurate description of the hydration structure, dynamics, and energetics.

Hydration Repulsion between Carbohydrate Surfaces Mediated by Temperature and Specific Ions

PubMed Central

Chen, Hsieh; Cox, Jason R.; Ow, Hooisweng; Shi, Rena; Panagiotopoulos, Athanassios Z.

2016-01-01

Stabilizing colloids or nanoparticles in solution involves a fine balance between surface charges, steric repulsion of coating molecules, and hydration forces against van der Waals attractions. At high temperature and electrolyte concentrations, the colloidal stability of suspensions usually decreases rapidly. Here, we report a new experimental and simulation discovery that the polysaccharide (dextran) coated nanoparticles show ion-specific colloidal stability at high temperature, where we observed enhanced colloidal stability of nanoparticles in CaCl2 solution but rapid nanoparticle-nanoparticle aggregation in MgCl2 solution. The microscopic mechanism was unveiled in atomistic simulations. The presence of surface bound Ca2+ ions increases the carbohydrate hydration and induces strongly polarized repulsive water structures beyond at least three hydration shells which is farther-reaching than previously assumed. We believe leveraging the binding of strongly hydrated ions to macromolecular surfaces represents a new paradigm in achieving absolute hydration and colloidal stability for a variety of materials, particularly under extreme conditions. PMID:27334145

Hydration Repulsion between Carbohydrate Surfaces Mediated by Temperature and Specific Ions

NASA Astrophysics Data System (ADS)

Chen, Hsieh; Cox, Jason R.; Ow, Hooisweng; Shi, Rena; Panagiotopoulos, Athanassios Z.

2016-06-01

Stabilizing colloids or nanoparticles in solution involves a fine balance between surface charges, steric repulsion of coating molecules, and hydration forces against van der Waals attractions. At high temperature and electrolyte concentrations, the colloidal stability of suspensions usually decreases rapidly. Here, we report a new experimental and simulation discovery that the polysaccharide (dextran) coated nanoparticles show ion-specific colloidal stability at high temperature, where we observed enhanced colloidal stability of nanoparticles in CaCl2 solution but rapid nanoparticle-nanoparticle aggregation in MgCl2 solution. The microscopic mechanism was unveiled in atomistic simulations. The presence of surface bound Ca2+ ions increases the carbohydrate hydration and induces strongly polarized repulsive water structures beyond at least three hydration shells which is farther-reaching than previously assumed. We believe leveraging the binding of strongly hydrated ions to macromolecular surfaces represents a new paradigm in achieving absolute hydration and colloidal stability for a variety of materials, particularly under extreme conditions.

Fate of Methane Emitted from Dissociating Marine Hydrates: Modeling, Laboratory, and Field Constraints

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

Juanes, Ruben

The overall goals of this research are: (1) to determine the physical fate of single and multiple methane bubbles emitted to the water column by dissociating gas hydrates at seep sites deep within the hydrate stability zone or at the updip limit of gas hydrate stability, and (2) to quantitatively link theoretical and laboratory findings on methane transport to the analysis of real-world field-scale methane plume data placed within the context of the degrading methane hydrate province on the US Atlantic margin. The project is arranged to advance on three interrelated fronts (numerical modeling, laboratory experiments, and analysis of field-basedmore » plume data) simultaneously. The fundamental objectives of each component are the following: Numerical modeling: Constraining the conditions under which rising bubbles become armored with hydrate, the impact of hydrate armoring on the eventual fate of a bubble’s methane, and the role of multiple bubble interactions in survival of methane plumes to very shallow depths in the water column. Laboratory experiments: Exploring the parameter space (e.g., bubble size, gas saturation in the liquid phase, “proximity” to the stability boundary) for formation of a hydrate shell around a free bubble in water, the rise rate of such bubbles, and the bubble’s acoustic characteristics using field-scale frequencies. Field component: Extending the results of numerical modeling and laboratory experiments to the field-scale using brand new, existing, public-domain, state-of-the-art real world data on US Atlantic margin methane seeps, without acquiring new field data in the course of this particular project. This component quantitatively analyzes data on Atlantic margin methane plumes and place those new plumes and their corresponding seeps within the context of gas hydrate degradation processes on this margin.« less

Molecular Friction-Induced Electroosmotic Phenomena in Thin Neutral Nanotubes.

PubMed

Vuković, Lela; Vokac, Elizabeth; Král, Petr

2014-06-19

We reveal by classical molecular dynamics simulations electroosmotic flows in thin neutral carbon (CNT) and boron nitride (BNT) nanotubes filled with ionic solutions of hydrated monovalent atomic ions. We observe that in (12,12) BNTs filled with single ions in an electric field, the net water velocity increases in the order of Na(+) < K(+) < Cl(-), showing that different ions have different power to drag water in thin nanotubes. However, the effect gradually disappears in wider nanotubes. In (12,12) BNTs containing neutral ionic solutions in electric fields, we observe net water velocities going in the direction of Na(+) for (Na(+), Cl(-)) and in the direction of Cl(-) for (K(+), Cl(-)). We hypothesize that the electroosmotic flows are caused by different strengths of friction between ions with different hydration shells and the nanotube walls.

Ab initio atomic recombination reaction energetics on model heat shield surfaces

NASA Technical Reports Server (NTRS)

Senese, Fredrick; Ake, Robert

1992-01-01

Ab initio quantum mechanical calculations on small hydration complexes involving the nitrate anion are reported. The self-consistent field method with accurate basis sets has been applied to compute completely optimized equilibrium geometries, vibrational frequencies, thermochemical parameters, and stable site labilities of complexes involving 1, 2, and 3 waters. The most stable geometries in the first hydration shell involve in-plane waters bridging pairs of nitrate oxygens with two equal and bent hydrogen bonds. A second extremely labile local minimum involves out-of-plane waters with a single hydrogen bond and lies about 2 kcal/mol higher. The potential in the region of the second minimum is extremely flat and qualitatively sensitive to changes in the basis set; it does not correspond to a true equilibrium structure.

Function and biotechnology of extremophilic enzymes in low water activity

PubMed Central

2012-01-01

Enzymes from extremophilic microorganisms usually catalyze chemical reactions in non-standard conditions. Such conditions promote aggregation, precipitation, and denaturation, reducing the activity of most non-extremophilic enzymes, frequently due to the absence of sufficient hydration. Some extremophilic enzymes maintain a tight hydration shell and remain active in solution even when liquid water is limiting, e.g. in the presence of high ionic concentrations, or at cold temperature when water is close to the freezing point. Extremophilic enzymes are able to compete for hydration via alterations especially to their surface through greater surface charges and increased molecular motion. These properties have enabled some extremophilic enzymes to function in the presence of non-aqueous organic solvents, with potential for design of useful catalysts. In this review, we summarize the current state of knowledge of extremophilic enzymes functioning in high salinity and cold temperatures, focusing on their strategy for function at low water activity. We discuss how the understanding of extremophilic enzyme function is leading to the design of a new generation of enzyme catalysts and their applications to biotechnology. PMID:22480329

Dynamics of Uncrystallized Water, Ice, and Hydrated Protein in Partially Crystallized Gelatin-Water Mixtures Studied by Broadband Dielectric Spectroscopy.

PubMed

Sasaki, Kaito; Panagopoulou, Anna; Kita, Rio; Shinyashiki, Naoki; Yagihara, Shin; Kyritsis, Apostolos; Pissis, Polycarpos

2017-01-12

The glass transition of partially crystallized gelatin-water mixtures was investigated using broadband dielectric spectroscopy (BDS) over a wide range of frequencies (10 mHz to 10 MHz), temperatures (113-298 K), and concentrations (10-45 wt %). Three dielectric relaxation processes (processes I, II, and III) were clearly observed. Processes I, II, and III originate from uncrystallized water (UCW) in the hydration shells of gelatin, ice, and hydrated gelatin, respectively. A dynamic crossover, called the Arrhenius to non-Arrhenius transition of UCW, was observed at the glass transition temperature of the relaxation process of hydrated gelatin for all mixtures. The amount of UCW increases with increasing gelatin content. However, above 35 wt % gelatin, the amount of UCW became more dependent on the gelatin concentration. This increase in UCW causes a decrease in the glass transition temperature of the cooperative motion of gelatin and UCW, which appears to result from a change in the aggregation structure of gelatin in the mixture at a gelatin concentration of approximately 35 wt %. The temperature dependence of the relaxation time of process II has nearly the same activation energy as pure ice made by slow crystallization of ice Ih. This implies that process II originates from the dynamics of slowly crystallized ice Ih.

K/T spherules from Haiti and Wyoming: Origin, diagenesis, and similarity to some microtektites

NASA Technical Reports Server (NTRS)

Bohor, B. F.; Glass, B. P.; Betterton, W. J.

1993-01-01

Spherules with relict glass cores in the K/T boundary bed of Haiti allow for a comparison of these bodies with hollow goyazite shells in the K/T boundary claystone of Wyoming and with younger microtektites of the Ivory Coast strewn field. Samples of the Haitian beds from undisturbed sections at Beloc, as determined by Jehanno et al., contain both hollow shells and relict glass cores rimmed by palagonite that has been partially converted to smectite. These palagonite rims developed from hydration zones formed when hot, splash-form droplets of andesitic impact glass were deposited into water. Mutual collisions between these droplets in the ejecta curtain may have formed point-source stresses on their surfaces. Initiation of hydration would be facilitated at these surface stress points and propagated radially into the glass. The inner surface of these merged hemispherical fronts appears mammillary, which is reflected as scalloping in Haitian relict glass cores.

Region-specific role of water in collagen unwinding and assembly.

PubMed

Ravikumar, Krishnakumar M; Hwang, Wonmuk

2008-09-01

Conformational stability of the collagen triple helix affects its turnover and determines tissue homeostasis. Although it is known that the presence of imino acids (prolines or hydroxyprolines) confer stability to the molecule, little is known regarding the stability of the imino-poor region lacking imino acids, which plays a key role in collagen cleavage. In particular, there have been continuing debates about the role of water in collagen stability. We addressed these issues using molecular dynamics simulations on 30-residue long collagen triple helices, including a structure that has a biologically relevant 9-residue imino-poor region from type III collagen (PDB ID: 1BKV). A torsional map approach was used to characterize the conformational motion of the molecule that differ between imino-rich and imino-poor regions. At temperatures 300 K and above, unwinding initiates at a common cleavage site, the glycine-isoleucine bond in the imino-poor region. This provides a linkage between previous observations that unwinding of the imino-poor region is a requirement for collagenase cleavage, and that isolated collagen molecules are unstable at body temperature. We found that unwinding of the imino-poor region is controlled by dynamic water bridges between backbone atoms with average lifetimes on the order of a few picoseconds, as the degree of unwinding strongly correlated with the loss of water bridges, and unwinding could be either prevented or enhanced, respectively by enforcing or forbidding water bridge formation. While individual water bridges were short-lived in the imino-poor region, the hydration shell surrounding the entire molecule was stable even at 330 K. The diameter of the hydrated collagen including the first hydration shell was about 14 A, in good agreement with the experimentally measured inter-collagen distances. These results elucidate the general role of water in collagen turnover: water not only affects collagen cleavage by controlling its torsional motion, but it also forms a larger-scale lubrication layer mediating collagen self-assembly. 2008 Wiley-Liss, Inc.

Neutron Nucleic Acid Crystallography.

PubMed

Chatake, Toshiyuki

2016-01-01

The hydration shells surrounding nucleic acids and hydrogen-bonding networks involving water molecules and nucleic acids are essential interactions for the structural stability and function of nucleic acids. Water molecules in the hydration shells influence various conformations of DNA and RNA by specific hydrogen-bonding networks, which often contribute to the chemical reactivity and molecular recognition of nucleic acids. However, X-ray crystallography could not provide a complete description of structural information with respect to hydrogen bonds. Indeed, X-ray crystallography is a powerful tool for determining the locations of water molecules, i.e., the location of the oxygen atom of H2O; however, it is very difficult to determine the orientation of the water molecules, i.e., the orientation of the two hydrogen atoms of H2O, because X-ray scattering from the hydrogen atom is very small.Neutron crystallography is a specialized tool for determining the positions of hydrogen atoms. Neutrons are not diffracted by electrons, but are diffracted by atomic nuclei; accordingly, neutron scattering lengths of hydrogen and its isotopes are comparable to those of non-hydrogen atoms. Therefore, neutron crystallography can determine both of the locations and orientations of water molecules. This chapter describes the current status of neutron nucleic acid crystallographic research as well as the basic principles of neutron diffraction experiments performed on nucleic acid crystals: materials, crystallization, diffraction experiments, and structure determination.

Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration

NASA Astrophysics Data System (ADS)

Hofer, Thomas S.; Hünenberger, Philippe H.

2018-06-01

The absolute intrinsic hydration free energy GH+,w a t ◦ of the proton, the surface electric potential jump χwa t ◦ upon entering bulk water, and the absolute redox potential VH+,w a t ◦ of the reference hydrogen electrode are cornerstone quantities for formulating single-ion thermodynamics on absolute scales. They can be easily calculated from each other but remain fundamentally elusive, i.e., they cannot be determined experimentally without invoking some extra-thermodynamic assumption (ETA). The Born model provides a natural framework to formulate such an assumption (Born ETA), as it automatically factors out the contribution of crossing the water surface from the hydration free energy. However, this model describes the short-range solvation inaccurately and relies on the choice of arbitrary ion-size parameters. In the present study, both shortcomings are alleviated by performing first-principle calculations of the hydration free energies of the sodium (Na+) and potassium (K+) ions. The calculations rely on thermodynamic integration based on quantum-mechanical molecular-mechanical (QM/MM) molecular dynamics (MD) simulations involving the ion and 2000 water molecules. The ion and its first hydration shell are described using a correlated ab initio method, namely resolution-of-identity second-order Møller-Plesset perturbation (RIMP2). The next hydration shells are described using the extended simple point charge water model (SPC/E). The hydration free energy is first calculated at the MM level and subsequently increased by a quantization term accounting for the transformation to a QM/MM description. It is also corrected for finite-size, approximate-electrostatics, and potential-summation errors, as well as standard-state definition. These computationally intensive simulations provide accurate first-principle estimates for GH+,w a t ◦, χwa t ◦, and VH+,w a t ◦, reported with statistical errors based on a confidence interval of 99%. The values obtained from the independent Na+ and K+ simulations are in excellent agreement. In particular, the difference between the two hydration free energies, which is not an elusive quantity, is 73.9 ± 5.4 kJ mol-1 (K+ minus Na+), to be compared with the experimental value of 71.7 ± 2.8 kJ mol-1. The calculated values of GH+,w a t ◦, χwa t ◦, and VH+,w a t ◦ (-1096.7 ± 6.1 kJ mol-1, 0.10 ± 0.10 V, and 4.32 ± 0.06 V, respectively, averaging over the two ions) are also in remarkable agreement with the values recommended by Reif and Hünenberger based on a thorough analysis of the experimental literature (-1100 ± 5 kJ mol-1, 0.13 ± 0.10 V, and 4.28 ± 0.13 V, respectively). The QM/MM MD simulations are also shown to provide an accurate description of the hydration structure, dynamics, and energetics.

Near-membrane electric field calcium ion dehydration.

PubMed

Barger, James P; Dillon, Patrick F

2016-12-01

The dehydration of ion-water complexes prior to ion channel transit has focused on channel protein-mediated dissociation of water. Ion dehydration by the membrane electric field has not previously been considered. Near membrane electric fields have previously been shown to cause the disassociation of non-covalently bound small molecule-small molecule, small molecule-protein, and protein-protein complexes. It is well known that cosmotropic, structure making ions such as calcium and sodium significantly bind multiple water ions in solution. It is also known that these ions are often not hydrated as they pass through membrane ion channels. Using capillary electrophoresis, the range of electric fields needed to strip water molecules from calcium ions has been measured. Ion migration velocity is a linear function of the electric field. At low electric fields, the migration rate of calcium ion was shown to be linearly related to the applied electric field. Using a form of the Stoke's equation applicable to ion migration, the hydrated calcium radius was found to be 0.334nm, corresponding to a water hydration shell of 5.09 water molecules. At higher electric fields, the slope of the calcium migration velocity as a function of the electric field increased, which was modeled as a decrease in the radius of the migrating ion as the water was removed. Using a tanh function to model the transition of the ion from a hydrated to a stripped state, the transition had a midpoint at 446V/cm, and was 88% complete at 587V/cm with a correlation coefficient of 0.9996. The migration velocity of the stripped calcium ion was found to be a function of both the decrease in radius and an increase in the effective, electronic viscosity of the dipole medium through which the dehydrated ion moved. The size of the electric field needed to dehydrate calcium occurs 6-7nm from the cell membrane. Calcium ions within this distance from the membrane will be devoid of water molecules when they reach the calcium selective channel pore entrances, all known to be approximately 1-2nm from the membrane. No matter what the calcium pore structure, calcium ions reaching the channel entrance will be devoid of a water shell. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dynamical transition, hydrophobic interface, and the temperature dependence of electrostatic fluctuations in proteins.

PubMed

Lebard, David N; Matyushov, Dmitry V

2008-12-01

Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of electrostatic fluctuations, expressed in terms of the reorganization energy of changing the redox state of the protein, is related to the formation of the hydrophobic protein-water interface, allowing large-amplitude collective fluctuations of the water density in the protein's first solvation shell. On top of the monotonic increase of the reorganization energy with increasing temperature, we have observed a spike at approximately 220 K also accompanied by a significant slowing of the exponential collective Stokes shift dynamics. In contrast to the local density fluctuations of the hydration-shell waters, these spikes might be related to the global property of the water solvent crossing the Widom line or undergoing a weak first-order transition.

A Study of the Hydration of the Alkali Metal Ions in Aqueous Solution

PubMed Central

2011-01-01

The hydration of the alkali metal ions in aqueous solution has been studied by large angle X-ray scattering (LAXS) and double difference infrared spectroscopy (DDIR). The structures of the dimethyl sulfoxide solvated alkali metal ions in solution have been determined to support the studies in aqueous solution. The results of the LAXS and DDIR measurements show that the sodium, potassium, rubidium and cesium ions all are weakly hydrated with only a single shell of water molecules. The smaller lithium ion is more strongly hydrated, most probably with a second hydration shell present. The influence of the rubidium and cesium ions on the water structure was found to be very weak, and it was not possible to quantify this effect in a reliable way due to insufficient separation of the O–D stretching bands of partially deuterated water bound to these metal ions and the O–D stretching bands of the bulk water. Aqueous solutions of sodium, potassium and cesium iodide and cesium and lithium hydroxide have been studied by LAXS and M–O bond distances have been determined fairly accurately except for lithium. However, the number of water molecules binding to the alkali metal ions is very difficult to determine from the LAXS measurements as the number of distances and the temperature factor are strongly correlated. A thorough analysis of M–O bond distances in solid alkali metal compounds with ligands binding through oxygen has been made from available structure databases. There is relatively strong correlation between M–O bond distances and coordination numbers also for the alkali metal ions even though the M–O interactions are weak and the number of complexes of potassium, rubidium and cesium with well-defined coordination geometry is very small. The mean M–O bond distance in the hydrated sodium, potassium, rubidium and cesium ions in aqueous solution have been determined to be 2.43(2), 2.81(1), 2.98(1) and 3.07(1) Å, which corresponds to six-, seven-, eight- and eight-coordination. These coordination numbers are supported by the linear relationship of the hydration enthalpies and the M–O bond distances. This correlation indicates that the hydrated lithium ion is four-coordinate in aqueous solution. New ionic radii are proposed for four- and six-coordinate lithium(I), 0.60 and 0.79 Å, respectively, as well as for five- and six-coordinate sodium(I), 1.02 and 1.07 Å, respectively. The ionic radii for six- and seven-coordinate K+, 1.38 and 1.46 Å, respectively, and eight-coordinate Rb+ and Cs+, 1.64 and 1.73 Å, respectively, are confirmed from previous studies. The M–O bond distances in dimethyl sulfoxide solvated sodium, potassium, rubidium and cesium ions in solution are very similar to those observed in aqueous solution. PMID:22168370

Surfactants at Single-Walled Carbon Nanotube-Water Interface: Physics of Surfactants, Counter-Ions, and Hydration Shell

NASA Astrophysics Data System (ADS)

Khare, Ketan S.; Phelan, Frederick R., Jr.

Specialized applications of single-walled carbon nanotubes (SWCNTs) require an efficient and reliable method to sort these materials into monodisperse fractions with respect to their defining metrics (chirality, length, etc.) while retaining their physical and chemical integrity. A popular method to achieve this goal is to use surfactants that individually disperse SWCNTs in water and then to separate the resulting colloidal mixture into fractions that are enriched in monodisperse SWCNTs. Recently, experiments at NIST have shown that subtle point mutations of chemical groups in bile salt surfactants have a large impact on the hydrodynamic properties of SWCNT-surfactant complexes during ultracentrifugation. These results provide strong motivation for understanding the rich physics underlying the assembly of surfactants around SWCNTs, the structure and dynamics of counter ions around the resulting complex, and propagation of these effects into the first hydration shell. Here, all-atom molecular dynamics simulations are used to investigate the thermodynamics of SWCNT-bile salt surfactant complexes in water with an emphasis on the buoyant characteristics of the SWCNT-surfactant complexes. Simulation results will be presented along with a comparison with experimental data. Official contribution of the National Institute of Standards and Technology; not subject to copyright in the United States.

Surfactant Effect on Hydrate Crystallization at the Oil-Water Interface.

PubMed

Dann, Kevin; Rosenfeld, Liat

2018-05-29

Gas hydrates pose economic and environmental risks to the oil and gas industry when plug formation occurs in pipelines. A novel approach was applied to understand cyclopentane clathrate hydrate formation in the presence of nonionic surfactant to achieve hydrate inhibition at low percent weight compared to thermodynamic inhibitors. The hydrate-inhibiting performance of low (CMC) concentrations of Span 20, Span 80, Pluronic L31, and Tween 65 at 2 °C on a manually nucleated 2 μL droplet showed a morphological shift in crystallization from planar shell growth to conical growth. Monitoring the internal pressure of the water droplet undergoing hydrate crystallization provides information on the change in interfacial tension during the crystallization process. The results of this study will provide information on the surfactant effect on hydrate crystallization and inhibition. At low surfactant concentrations (below CMC), a planar hydrate crystal was formed. Decreasing interfacial tension was observed, which can be related to the shrinking area of the water-cyclopentane interface. At high surfactant concentration, the crystal morphology was shifted to conical. Interfacial tension measurements reveal oscillations of the interfacial tension during the crystallization process. The oscillations of the interfacial tension result from the fact that once the crystal has reached a critical size a portion of the cone breaks free from the droplet surface, which results in a sudden increase in the available surface for the surfactant molecules. Hence, a temporary increase in the interfacial tension can be observed. The oscillatory behavior of the interfacial tension is a result of the growth and release of the hydrate cones from the surface of the droplet. We have found that the most efficient surfactant in hydrate inhibition would be the one with HLB closest to 10 (equal hydrophilic-hydrophobic parts). In this way, the surfactant molecules will stay at the interface as they observe equal affinities for both the oil and water phases. Surfactant molecules that have the strongest affinity to the interface will be able to inhibit the growth of the crystal as they will force the cones to break and will not allow them to grow.

Deep Sea Shell Taphonomy: Interactive benthic experiments in hydrate environments of Barkley Canyon, Ocean Networks Canada.

NASA Astrophysics Data System (ADS)

Best, Mairi; Purser, Autun

2015-04-01

In order to quantify and track the rates and processes of modification of biogenic carbonate in gas hydrate environments, and their possible environmental/ecological correlates, ongoing observations of experimentally deployed specimens are being made using a remotely controlled crawler with camera and sensors. The crawler is connected to NEPTUNE Canada, an 800km, 5-node, regional cabled ocean network across the northern Juan de Fuca Plate, northeastern Pacific, part of Ocean Networks Canada. One of 15 study areas is an environment of exposed hydrate mounds along the wall of Barkley Canyon, at ˜865m water depth. This is the home of a benthic crawler developed by Jacobs University of Germany, who is affectionately known as Wally. Wally is equipped with a range of sensors including cameras, methane sensor, current meter, fluorometer, turbidity meter, CTD, and a sediment microprofiler with probes for oxygen, methane, sulphide, pH, temperature, and conductivity. In conjunction with this sensor suite, a series of experiments have been designed to assess the cycling of biogenic carbon and carbonate in this complex environment. The biota range from microbes, to molluscs, to large fish, and therefore the carbon inputs include both a range of organic carbon compounds as well as the complex materials that are "biogenic carbonate". Controlled experimental specimens were deployed of biogenic carbonate (Mytilus edulis fresh shells) and cellulose (pieces of untreated pine lumber) that had been previously well characterized (photographed, weighed, and numbered, matching valves and lumber kept as controls). Deployment at the sediment/water interface was in such a way to maximize natural burial exhumation cycles but to minimize specimen interaction. 10 replicate specimens of each material were deployed in two treatments: 1) adjacent to a natural life and death assemblage of chemosynthetic bivalves and exposed hydrate on a hydrate mound and 2) on the muddy seafloor at a distance from the mound. On retrieval, the specimens are being further studied for net material loss, surface alteration, microbial recruitment, endo- and epibionts, and microstructural and chemical modification. Understanding the production and cycling of carbon across the sediment/water interface in this environment will help elucidate the formation and evolution of these hydrate deposits, their distribution through time, and the ecological and taphonomic feedbacks they generate.

Infrared light-induced protein crystallization. Structuring of protein interfacial water and periodic self-assembly

NASA Astrophysics Data System (ADS)

Kowacz, Magdalena; Marchel, Mateusz; Juknaité, Lina; Esperança, José M. S. S.; Romão, Maria João; Carvalho, Ana Luísa; Rebelo, Luís Paulo N.

2017-01-01

We show that a physical trigger, a non-ionizing infrared (IR) radiation at wavelengths strongly absorbed by liquid water, can be used to induce and kinetically control protein (periodic) self-assembly in solution. This phenomenon is explained by considering the effect of IR light on the structuring of protein interfacial water. Our results indicate that the IR radiation can promote enhanced mutual correlations of water molecules in the protein hydration shell. We report on the radiation-induced increase in both the strength and cooperativeness of H-bonds. The presence of a structured dipolar hydration layer can lead to attractive interactions between like-charged biomacromolecules in solution (and crystal nucleation events). Furthermore, our study suggests that enveloping the protein within a layer of structured solvent (an effect enhanced by IR light) can prevent the protein non-specific aggregation favoring periodic self-assembly. Recognizing the ability to affect protein-water interactions by means of IR radiation may have important implications for biological and bio-inspired systems.

Cations Form Sequence Selective Motifs within DNA Grooves via a Combination of Cation-Pi and Ion-Dipole/Hydrogen Bond Interactions

PubMed Central

Stewart, Mikaela; Dunlap, Tori; Dourlain, Elizabeth; Grant, Bryce; McFail-Isom, Lori

2013-01-01

The fine conformational subtleties of DNA structure modulate many fundamental cellular processes including gene activation/repression, cellular division, and DNA repair. Most of these cellular processes rely on the conformational heterogeneity of specific DNA sequences. Factors including those structural characteristics inherent in the particular base sequence as well as those induced through interaction with solvent components combine to produce fine DNA structural variation including helical flexibility and conformation. Cation-pi interactions between solvent cations or their first hydration shell waters and the faces of DNA bases form sequence selectively and contribute to DNA structural heterogeneity. In this paper, we detect and characterize the binding patterns found in cation-pi interactions between solvent cations and DNA bases in a set of high resolution x-ray crystal structures. Specifically, we found that monovalent cations (Tl+) and the polarized first hydration shell waters of divalent cations (Mg2+, Ca2+) form cation-pi interactions with DNA bases stabilizing unstacked conformations. When these cation-pi interactions are combined with electrostatic interactions a pattern of specific binding motifs is formed within the grooves. PMID:23940752

Cations form sequence selective motifs within DNA grooves via a combination of cation-pi and ion-dipole/hydrogen bond interactions.

PubMed

Stewart, Mikaela; Dunlap, Tori; Dourlain, Elizabeth; Grant, Bryce; McFail-Isom, Lori

2013-01-01

The fine conformational subtleties of DNA structure modulate many fundamental cellular processes including gene activation/repression, cellular division, and DNA repair. Most of these cellular processes rely on the conformational heterogeneity of specific DNA sequences. Factors including those structural characteristics inherent in the particular base sequence as well as those induced through interaction with solvent components combine to produce fine DNA structural variation including helical flexibility and conformation. Cation-pi interactions between solvent cations or their first hydration shell waters and the faces of DNA bases form sequence selectively and contribute to DNA structural heterogeneity. In this paper, we detect and characterize the binding patterns found in cation-pi interactions between solvent cations and DNA bases in a set of high resolution x-ray crystal structures. Specifically, we found that monovalent cations (Tl⁺) and the polarized first hydration shell waters of divalent cations (Mg²⁺, Ca²⁺) form cation-pi interactions with DNA bases stabilizing unstacked conformations. When these cation-pi interactions are combined with electrostatic interactions a pattern of specific binding motifs is formed within the grooves.

Resolving Nonadiabatic Dynamics of Hydrated Electrons Using Ultrafast Photoemission Anisotropy.

PubMed

Karashima, Shutaro; Yamamoto, Yo-Ichi; Suzuki, Toshinori

2016-04-01

We have studied ultrafast nonadiabatic dynamics of excess electrons trapped in the band gap of liquid water using time- and angle-resolved photoemission spectroscopy. Anisotropic photoemission from the first excited state was discovered, which enabled unambiguous identification of nonadiabatic transition to the ground state in 60 fs in H_{2}O and 100 fs in D_{2}O. The photoelectron kinetic energy distribution exhibited a rapid spectral shift in ca. 20 fs, which is ascribed to the librational response of a hydration shell to electronic excitation. Photoemission anisotropy indicates that the electron orbital in the excited state is depolarized in less than 40 fs.

Hydrate-melt electrolytes for high-energy-density aqueous batteries

NASA Astrophysics Data System (ADS)

Yamada, Yuki; Usui, Kenji; Sodeyama, Keitaro; Ko, Seongjae; Tateyama, Yoshitaka; Yamada, Atsuo

2016-10-01

Aqueous Li-ion batteries are attracting increasing attention because they are potentially low in cost, safe and environmentally friendly. However, their low energy density (<100 Wh kg-1 based on total electrode weight), which results from the narrow operating potential window of water and the limited selection of suitable negative electrodes, is problematic for their future widespread application. Here, we explore optimized eutectic systems of several organic Li salts and show that a room-temperature hydrate melt of Li salts can be used as a stable aqueous electrolyte in which all water molecules participate in Li+ hydration shells while retaining fluidity. This hydrate-melt electrolyte enables a reversible reaction at a commercial Li4Ti5O12 negative electrode with a low reaction potential (1.55 V versus Li+/Li) and a high capacity (175 mAh g-1). The resultant aqueous Li-ion batteries with high energy density (>130 Wh kg-1) and high voltage (˜2.3-3.1 V) represent significant progress towards performance comparable to that of commercial non-aqueous batteries (with energy densities of ˜150-400 Wh kg-1 and voltages of ˜2.4-3.8 V).

Observations of different core water cluster ions Y-(H2O)n (Y = O2, HOx, NOx, COx) and magic number in atmospheric pressure negative corona discharge mass spectrometry.

PubMed

Sekimoto, Kanako; Takayama, Mitsuo

2011-01-01

Reliable mass spectrometry data from large water clusters Y(-)(H(2)O)(n) with various negative core ions Y(-) such as O(2)(-), HO(-), HO(2)(-), NO(2)(-), NO(3)(-), NO(3)(-)(HNO(3))(2), CO(3)(-) and HCO(4)(-) have been obtained using atmospheric pressure negative corona discharge mass spectrometry. All the core Y(-) ions observed were ionic species that play a central role in tropospheric ion chemistry. These mass spectra exhibited discontinuities in ion peak intensity at certain size clusters Y(-)(H(2)O)(m) indicating specific thermochemical stability. Thus, Y(-)(H(2)O)(m) may correspond to the magic number or first hydrated shell in the cluster series Y(-)(H(2)O)(n). The high intensity discontinuity at HO(-)(H(2)O)(3) observed was the first mass spectrometric evidence for the specific stability of HO(-)(H(2)O)(3) as the first hydrated shell which Eigen postulated in 1964. The negative ion water clusters Y(-)(H(2)O)(n) observed in the mass spectra are most likely to be formed via core ion formation in the ambient discharge area (760 torr) and the growth of water clusters by adiabatic expansion in the vacuum region of the mass spectrometers (≈1 torr). The detailed mechanism of the formation of the different core water cluster ions Y(-)(H(2)O)(n) is described. Copyright © 2010 John Wiley & Sons, Ltd.

Strengthening of the Coordination Shell by Counter Ions in Aqueous Th 4+ Solutions

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

Atta-Fynn, Raymond; Bylaska, Eric J.; de Jong, Wibe A.

The presence of counter ions in solutions containing highly charged metal cations can trigger processes such as ion-pair formation, hydrogen bond breakages and subsequent reformation, and ligand exchanges. In this work, it is shown how halide (Cl-, Br-) and perchlorate (ClO4-) anions affect the strength of the primary solvent coordination shells around Th4+ using explicit solvent and finite temperature ab initio molecular dynamics modeling methods. The 9-fold solvent geometry was found to be the most stable hydration structure in each aqueous solution. Relative to the dilute aqueous solution, the presence of the counter ions did not significantly alter the geometrymore » of the primary hydration shell. However, the free energy analyses indicated that the 10-fold hydrated states were thermodynamically accessible in dilute and bromide aqueous solutions within 1 kcal/mol. Analysis of the results showed that the hydrogen bond lifetimes were longer and solvent exchange energy barriers were larger in solutions with counter ions in comparison with the solution with no counter ions. This implies that the presence of the counter ions induces a strengthening of the Th4+ hydration shell.« less

Hydration behavior of casein micelles in thin film geometry: a GISANS study?

PubMed

Metwalli, E; Moulin, J F; Gebhardt, R; Cubitt, R; Tolkach, A; Kulozik, U; Müller-Buschbaum, P

2009-04-07

The water content of casein micelle films in water vapor atmosphere is investigated using time-resolved grazing incidence small-angle neutron scattering (GISANS). Initial dry casein films are prepared with a spin-coating method. At 30 degrees C, the formation of a water-equilibrated casein protein film is reached after 11 min with a total content of 0.36 g of water/g of protein. With increasing water vapor temperature up to 70 degrees C, an increase in the water content is found. With GISANS, lateral structures on the nanometer scale are resolved during the swelling experiment at different temperatures and modeled using two types of spheres: micelles and mini-micelles. Upon water uptake, molecular assemblies in the size range of 15 nm (mini-micelles) are attributed to the formation of a high-contrast D2O outer shell on the small objects that already exist in the protein film. For large objects (>100 nm), the mean size increases at high D2O vapor temperature because of possible aggregation between hydrated micelles. These results are discussed and compared with various proposed models for casein micelle structures.

Quantum Calculations on Salt Bridges with Water: Potentials, Structure, and Properties

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

Liao, Sing; Green, Michael E.

2011-01-01

Salt bridges are electrostatic links between acidic and basic amino acids in a protein; quantum calculations are used here to determine the energetics and other properties of one form of these species, in the presence of water molecules. The acidic groups are carboxylic acids (aspartic and glutamic acids); proteins have two bases with pK above physiological pH: one, arginine, with a guanidinium basic group, the other lysine, which is a primary amine. Only arginine is modeled here, by ethyl guanidinium, while propionic acid is used as a model for either carboxylic acid. The salt bridges are accompanied by 0-12 watermore » molecules; for each of the 13 systems, the energy-bond distance relation, natural bond orbitals (NBO), frequency calculations allowing thermodynamic corrections to room temperature, and dielectric constant dependence, were all calculated. The water molecules were found to arrange themselves in hydrogen bonded rings anchored to the oxygens of the salt bridge components. This was not surprising in itself, but it was found that the rings lead to a periodicity in the energy, and to a 'water addition' rule. The latter shows that the initial rings, with four oxygen atoms, become five member rings when an additional water molecule becomes available, with the additional water filling in at the bond with the lowest Wiberg index, as calculated using NBO. The dielectric constant dependence is the expected hyperbola, and the fit of the energy to the inverse dielectric constant is determined. There is an energy periodicity related to ring formation upon addition of water molecules. When 10 water molecules have been added, all spaces near the salt bridge are filled, completing the first hydration shell, and a second shell starts to form. The potentials associated with salt bridges depend on their hydration, and potentials assigned without regard to local hydration are likely to cause errors as large as or larger than kBT, thus suggesting a serious problem if these potentials are used in Molecular Dynamics simulations.« less

Solvent Electrostatic Response: From Simple Solutes to Proteins

NASA Astrophysics Data System (ADS)

Dinpajooh, Mohammadhasan

How water behaves at interfaces is relevant to many scientific and technological applications; however, many subtle phenomena are unknown in aqueous solutions. In this work, interfacial structural transition in hydration shells of a polarizable solute at critical polarizabilities is discovered. The transition is manifested in maximum water response, the reorientation of the water dipoles at the interface, and an increase in the density of dangling OH bonds. This work also addresses the role of polarizability of the active site of proteins in biological catalytic reactions. For proteins, the hydration shell becomes very heterogeneous and involves a relatively large number of water molecules. The molecular dynamics simulations show that the polarizability, along with the atomic charge distribution, needs to be a part of the picture describing how enzymes work. Non Gaussian dynamics in time-resolved linear and nonlinear (correlation) 2D spectra are also analyzed. Additionally, a theoretical formalism is presented to show that when preferential orientations of water dipoles exist at the interface, electrophoretic charges can be produced without free charge carriers, i.e., neutral solutes can move in a constant electric field due to the divergence of polarization at the interface. Furthermore, the concept of interface susceptibility is introduced. It involves the fluctuations of the surface charge density caused by thermal motion and its correlation over the characteristic correlation length with the fluctuations of the solvent charge density. Solvation free energy and interface dielectric constant are formulated accordingly. Unlike previous approaches, the solvation free energy scales quite well in a broad range of ion sizes, namely in the range of 2-14 A. Interface dielectric constant is defined such that the boundary conditions in the Laplace equation describing a micro- or mesoscopic interface are satisfied. The effective dielectric constant of interfacial water is found to be significantly lower than its bulk value. Molecular dynamics simulation results show that the interface dielectric constant for a TIP3P water model changes from nine to four when the effective solute radius is increased from 5 Ato 18 A. The small value of the interface dielectric constant of water has potentially dramatic consequences for hydration.

Tuning the tetrahedrality of the hydrogen-bonded network of water: Comparison of the effects of pressure and added salts

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

Prasad, Saurav, E-mail: saurav7188@gmail.com, E-mail: cyz118212@chemistry.iitd.ac.in; Chakravarty, Charusita

Experiments and simulations demonstrate some intriguing equivalences in the effect of pressure and electrolytes on the hydrogen-bonded network of water. Here, we examine the extent and nature of equivalence effects between pressure and salt concentration using relationships between structure, entropy, and transport properties based on two key ideas: first, the approximation of the excess entropy of the fluid by the contribution due to the atom-atom pair correlation functions and second, Rosenfeld-type excess entropy scaling relations for transport properties. We perform molecular dynamics simulations of LiCl–H{sub 2}O and bulk SPC/E water spanning the concentration range 0.025–0.300 molefraction of LiCl at 1more » atm and pressure range from 0 to 7 GPa, respectively. The temperature range considered was from 225 to 350 K for both the systems. To establish that the time-temperature-transformation behaviour of electrolyte solutions and water is equivalent, we use the additional observation based on our simulations that the pair entropy behaves as a near-linear function of pressure in bulk water and of composition in LiCl–H{sub 2}O. This allows for the alignment of pair entropy isotherms and allows for a simple mapping of pressure onto composition. Rosenfeld-scaling implies that pair entropy is semiquantitatively related to the transport properties. At a given temperature, equivalent state points in bulk H{sub 2}O and LiCl–H{sub 2}O (at 1 atm) are defined as those for which the pair entropy, diffusivity, and viscosity are nearly identical. The microscopic basis for this equivalence lies in the ability of both pressure and ions to convert the liquid phase into a pair-dominated fluid, as demonstrated by the O–O–O angular distribution within the first coordination shell of a water molecule. There are, however, sharp differences in local order and mechanisms for the breakdown of tetrahedral order by pressure and electrolytes. Increasing pressure increases orientational disorder within the first neighbour shell while addition of ions shifts local orientational order from tetrahedral to close-packed as water molecules get incorporated in ionic hydration shells. The variations in local order within the first hydration shell may underlie ion-specific effects, such as the Hofmeister series.« less

Tuning the tetrahedrality of the hydrogen-bonded network of water: Comparison of the effects of pressure and added salts

NASA Astrophysics Data System (ADS)

Prasad, Saurav; Chakravarty, Charusita

2016-06-01

Experiments and simulations demonstrate some intriguing equivalences in the effect of pressure and electrolytes on the hydrogen-bonded network of water. Here, we examine the extent and nature of equivalence effects between pressure and salt concentration using relationships between structure, entropy, and transport properties based on two key ideas: first, the approximation of the excess entropy of the fluid by the contribution due to the atom-atom pair correlation functions and second, Rosenfeld-type excess entropy scaling relations for transport properties. We perform molecular dynamics simulations of LiCl-H2O and bulk SPC/E water spanning the concentration range 0.025-0.300 molefraction of LiCl at 1 atm and pressure range from 0 to 7 GPa, respectively. The temperature range considered was from 225 to 350 K for both the systems. To establish that the time-temperature-transformation behaviour of electrolyte solutions and water is equivalent, we use the additional observation based on our simulations that the pair entropy behaves as a near-linear function of pressure in bulk water and of composition in LiCl-H2O. This allows for the alignment of pair entropy isotherms and allows for a simple mapping of pressure onto composition. Rosenfeld-scaling implies that pair entropy is semiquantitatively related to the transport properties. At a given temperature, equivalent state points in bulk H2O and LiCl-H2O (at 1 atm) are defined as those for which the pair entropy, diffusivity, and viscosity are nearly identical. The microscopic basis for this equivalence lies in the ability of both pressure and ions to convert the liquid phase into a pair-dominated fluid, as demonstrated by the O-O-O angular distribution within the first coordination shell of a water molecule. There are, however, sharp differences in local order and mechanisms for the breakdown of tetrahedral order by pressure and electrolytes. Increasing pressure increases orientational disorder within the first neighbour shell while addition of ions shifts local orientational order from tetrahedral to close-packed as water molecules get incorporated in ionic hydration shells. The variations in local order within the first hydration shell may underlie ion-specific effects, such as the Hofmeister series.

Terahertz response of dipolar impurities in polar liquids: On anomalous dielectric absorption of protein solutions

NASA Astrophysics Data System (ADS)

Matyushov, Dmitry V.

2010-02-01

A theory of radiation absorption by dielectric mixtures is presented. The coarse-grained formulation is based on the wave-vector-dependent correlation functions of molecular dipoles of the host polar liquid and a density structure factor of the solutes. A nonlinear dependence of the dielectric absorption coefficient on the solute concentration is predicted and originates from the mutual polarization of the liquid surrounding the solutes by the collective field of the solute dipoles aligned along the radiation field. The theory is applied to terahertz absorption of hydrated saccharides and proteins. While the theory gives an excellent account of the observations for saccharides, without additional assumptions and fitting parameters, experimental absorption coefficient of protein solutions significantly exceeds theoretical calculations with dipole moment of the bare protein assigned to the solute and shows a peak against the protein concentration. A substantial polarization of protein’s hydration shell, resulting in a net dipole moment, is required to explain the disagreement between theory and experiment. When the correlation function of the total dipole moment of the protein with its hydration shell from numerical simulations is used in the analytical model, an absorption peak, qualitatively similar to that seen in experiment, is obtained. The existence and position of the peak are sensitive to the specifics of the protein-protein interactions. Numerical testing of the theory requires the combination of dielectric and small-angle scattering measurements. The calculations confirm that “elastic ferroelectric bag” of water shells observed in previous numerical simulations is required to explain terahertz dielectric measurements.

The importance of dissolved salts to the in vivo efficacy of antifreeze proteins.

PubMed

Evans, Robert P; Hobbs, Rod S; Goddard, Sally V; Fletcher, Garth L

2007-11-01

Antifreeze proteins (AFP) and antifreeze glycoproteins (AFGP) lower the freezing point of marine fish plasma non-colligatively by specifically adsorbing to certain surfaces of ice crystals, modifying their structure and inhibiting further growth. While the freezing point is lowered, the melting point is unaltered and the difference between the two is termed thermal hysteresis (TH). In pure water, the level of TH is directly related to the intrinsic activity of the specific AF(G)P in solution and to their concentration. Results of this study indicate that when AF(G)P are dissolved in salt solutions, such as NaCl, encompassing the range they could encounter in nature, there is a synergistic enhancement of basal TH that is positively related to the salt concentration. This enhancement is likely a result of the hydration shell surrounding the dissolved ions and, as a consequence, reducing freezable water. A secondary reason for the enhancement is that the salt could be influencing the hydration shell surrounding the AF(G)P, increasing their solubility and thus the protein surface area available to adsorb to the ice/water interface. The former hypothesis for the salt enhanced TH has implications for the in vivo function of AF(G)P, particularly at the seawater/external epithelia (gills, skin, stomach) interface. The latter hypothesis is likely only relevant to in vitro situations where freeze dried protein is dissolved in low salt solutions.

Lutetium(iii) aqua ion: On the dynamical structure of the heaviest lanthanoid hydration complex

NASA Astrophysics Data System (ADS)

Sessa, Francesco; Spezia, Riccardo; D'Angelo, Paola

2016-05-01

The structure and dynamics of the lutetium(iii) ion in aqueous solution have been investigated by means of a polarizable force field molecular dynamics (MD). An 8-fold square antiprism (SAP) geometry has been found to be the dominant configuration of the lutetium(iii) aqua ion. Nevertheless, a low percentage of 9-fold complexes arranged in a tricapped trigonal prism (TTP) geometry has been also detected. Dynamic properties have been explored by carrying out six independent MD simulations for each of four different temperatures: 277 K, 298 K, 423 K, 632 K. The mean residence time of water molecules in the first hydration shell at room temperature has been found to increase as compared to the central elements of the lanthanoid series in agreement with previous experimental findings. Water exchange kinetic rate constants at each temperature and activation parameters of the process have been determined from the MD simulations. The obtained structural and dynamical results suggest that the water exchange process for the lutetium(iii) aqua ion proceeds with an associative mechanism, in which the SAP hydration complex undergoes temporary structural changes passing through a 9-fold TTP intermediate. Such results are consistent with the water exchange mechanism proposed for heavy lanthanoid atoms.

Lutetium(iii) aqua ion: On the dynamical structure of the heaviest lanthanoid hydration complex.

PubMed

Sessa, Francesco; Spezia, Riccardo; D'Angelo, Paola

2016-05-28

The structure and dynamics of the lutetium(iii) ion in aqueous solution have been investigated by means of a polarizable force field molecular dynamics (MD). An 8-fold square antiprism (SAP) geometry has been found to be the dominant configuration of the lutetium(iii) aqua ion. Nevertheless, a low percentage of 9-fold complexes arranged in a tricapped trigonal prism (TTP) geometry has been also detected. Dynamic properties have been explored by carrying out six independent MD simulations for each of four different temperatures: 277 K, 298 K, 423 K, 632 K. The mean residence time of water molecules in the first hydration shell at room temperature has been found to increase as compared to the central elements of the lanthanoid series in agreement with previous experimental findings. Water exchange kinetic rate constants at each temperature and activation parameters of the process have been determined from the MD simulations. The obtained structural and dynamical results suggest that the water exchange process for the lutetium(iii) aqua ion proceeds with an associative mechanism, in which the SAP hydration complex undergoes temporary structural changes passing through a 9-fold TTP intermediate. Such results are consistent with the water exchange mechanism proposed for heavy lanthanoid atoms.

Electrostatics of the protein-water interface and the dynamical transition in proteins.

PubMed

Matyushov, Dmitry V; Morozov, Alexander Y

2011-07-01

Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent experiments indicate a connection between the dynamical transition and the dielectric response of the hydrated protein. We analyze two mechanisms of the coupling between the protein atomic motions and the protein-water interface. The first mechanism considers viscoelastic changes in the global shape of the protein plasticized by its coupling to the hydration shell. The second mechanism involves modulations of the local motions of partial charges inside the protein by electrostatic fluctuations. The model is used to analyze mean-square displacements of iron of metmyoglobin reported by Mössbauer spectroscopy. We show that high displacement of heme iron at physiological temperatures is dominated by electrostatic fluctuations. Two onsets, one arising from the viscoelastic response and the second from electrostatic fluctuations, are seen in the temperature dependence of the mean-square displacements when the corresponding relaxation times enter the instrumental resolution window.

Electrostatics of the protein-water interface and the dynamical transition in proteins

NASA Astrophysics Data System (ADS)

Matyushov, Dmitry V.; Morozov, Alexander Y.

2011-07-01

Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent experiments indicate a connection between the dynamical transition and the dielectric response of the hydrated protein. We analyze two mechanisms of the coupling between the protein atomic motions and the protein-water interface. The first mechanism considers viscoelastic changes in the global shape of the protein plasticized by its coupling to the hydration shell. The second mechanism involves modulations of the local motions of partial charges inside the protein by electrostatic fluctuations. The model is used to analyze mean-square displacements of iron of metmyoglobin reported by Mössbauer spectroscopy. We show that high displacement of heme iron at physiological temperatures is dominated by electrostatic fluctuations. Two onsets, one arising from the viscoelastic response and the second from electrostatic fluctuations, are seen in the temperature dependence of the mean-square displacements when the corresponding relaxation times enter the instrumental resolution window.

Vibrational Properties of Anhydrous and Partially Hydrated Uranyl Fluoride

DOE PAGES

Anderson, Brian B.; Kirkegaard, Marie C.; Miskowiec, Andrew J.; ...

2017-01-01

Uranyl fluoride (UO 2F 2) is a hygroscopic powder with two main structural phases: an anhydrous crystal and a partially hydrated crystal of the same R¯3m symmetry. The formally closed-shell electron structure of anhydrous UO 2F 2 is amenable to density functional theory calculations. We use density functional perturbation theory (DFPT) to calculate the vibrational frequencies of the anhydrous crystal structure and employ complementary inelastic neutron scattering and temperature-dependent Raman scattering to validate those frequencies. As a model closed-shell actinide, we investigated the effect of LDA, GGA, and non-local vdW functionals as well as the spherically-averaged Hubbard +U correction onmore » vibrational frequencies, electronic structure, and geometry of anhydrous UO 2F 2. A particular choice of U eff = 5.5 eV yields the correct U Oyl bond distance and vibrational frequencies for the characteristic Eg and A1g modes that are within the resolution of experiment. Inelastic neutron scattering and Raman scattering suggest a degree of water coupling to the lattice vibrations in the more experimentally accessible partially hydrated UO 2F 2 system, with the symmetric O-U-O stretching vibration shifted approximately 47 cm -1 lower in energy compared to the anhydrous structure. Evidence of water interaction with the uranyl ion is present from a two-peak decomposition of the uranyl stretching vibration in the Raman spectra and anion hydrogen stretching vibrations in the inelastic neutron scattering spectra. A first-order dehydration phase transition temperature is definitively identified to be 125 °C using temperature-dependent Raman scattering.« less

Hydrate Formation in Gas-Rich Marine Sediments: A Grain-Scale Model

NASA Astrophysics Data System (ADS)

Holtzman, R.; Juanes, R.

2009-12-01

We present a grain-scale model of marine sediment, which couples solid- and multiphase fluid-mechanics together with hydrate kinetics. The model is applied to investigate the spatial distribution of the different methane phases - gas and hydrate - within the hydrate stability zone. Sediment samples are generated from three-dimensional packs of spherical grains, mapping the void space into a pore network by tessellation. Gas invasion into the water-saturated sample is simulated by invasion-percolation, coupled with a discrete element method that resolves the grain mechanics. The coupled model accounts for forces exerted by the fluids, including cohesion associated with gas-brine surface tension. Hydrate growth is represented by a hydrate film along the gas-brine interface, which increases sediment cohesion by cementing the grain contacts. Our model of hydrate growth includes the possible rupture of the hydrate layer, which leads to the creation of new gas-water interface. In previous work, we have shown that fine-grained sediments (FGS) exhibit greater tendency to fracture, whereas capillary invasion is the preferred mode of methane gas transport in coarse-grained sediments (CGS). The gas invasion pattern has profound consequences on the hydrate distribution: a larger area-to-volume ratio of the gas cluster leads to a larger drop in gas pressure inside the growing hydrate shell, causing it to rupture. Repeated cycles of imbibition and hydrate growth accompanied by trapping of gas allow us to determine the distribution of hydrate and gas within the sediment as a function of time. Our pore-scale model suggests that, even when film rupture takes place, the conversion of gas to hydrate is slow. This explains two common field observations: the coexistence of gas and hydrate within the hydrate stability zone in CGS, and the high methane fluxes through fracture conduits in FGS. These results demonstrate the importance of accounting for the strong coupling among multiphase flow, sediment mechanics, and hydrate formation. Our model explains the remarkable differences in hydrate distribution and saturation between fine- and coarse-grained sediments, and promotes the quantitative understanding of the role of methane hydrate in seafloor stability and the global carbon cycle, including the size of the hydrate energy resource, and estimates of methane fluxes into the ocean and the atmosphere.

Conformational relaxation and water penetration coupled to ionization of internal groups in proteins.

PubMed

Damjanović, Ana; Brooks, Bernard R; García-Moreno, Bertrand

2011-04-28

Molecular dynamics simulations were used to examine the effects of ionization of internal groups on the structures of eighteen variants of staphylococcal nuclease (SNase) with internal Lys, Asp, or Glu. In most cases the RMSD values of internal ionizable side chains were larger when the ionizable moieties were charged than when they were neutral. Calculations of solvent-accessible surface area showed that the internal ionizable side chains were buried in the protein interior when they were neutral and moved toward crevices and toward the protein-water interface when they were charged. The only exceptions are Lys-36, Lys-62, and Lys-103, which remained buried even after charging. With the exception of Lys-38, the number of internal water molecules surrounding the ionizable group increased upon charging: the average number of water oxygen atoms within the first hydration shell increased by 1.7 for Lys residues, by 5.2 for Asp residues, and by 3.2 for Glu residues. The polarity of the microenvironment of the ionizable group also increased when the groups were charged: the average number of polar atoms of any kind within the first hydration shell increased by 2.7 for Lys residues, by 4.8 for Asp residues, and by 4.0 for Glu residues. An unexpected correlation was observed between the absolute value of the shifts in pK(a) values measured experimentally, and several parameters of structural relaxation: the net difference in the polarity of the microenvironment of the charged and neutral forms of the ionizable groups, the net difference in hydration of the charged and neutral forms of the ionizable groups, and the difference in RMSD values of the charged and neutral forms of the ionizable groups. The effects of ionization of internal groups on the conformation of the backbone were noticeable but mostly small and localized to the area immediately next to the internal ionizable moiety. Some variants did exhibit local unfolding.

Probe conformational dynamics of proteins in aqueous solutions by terahertz spectroscopy

NASA Astrophysics Data System (ADS)

Vinh, Nguyen Q.

2016-10-01

Proteins solvated in their biologically milieu are expected to exhibit strong absorption in the terahertz frequencies, that contain information on their global and sub-global collective vibrational modes (conformational dynamics) and global dynamic correlations among solvent water and proteins. The dynamics play an important role in enzymatic activities of proteins, but obtaining an accurate and quantitative pictures of these activities, however, is challenging due to the strong absorption of water. In response, we have developed the world's highest precision, highest sensitivity terahertz-frequency domain spectrometer and a standard terahertz-time domain system to probe the collective dynamics of proteins in aqueous solutions. Operating over the frequency range from 5 GHz up to 3 THz, our spectrometers provide an unparalleled ability to probe directly such questions as the hydration level, the dynamics of water and hydrated proteins over the 100 fs to 1 ns timescale. Employing an effective medium approximation to describe the complex dielectric response of the solvated proteins in solution we find that proteins are surrounded by a loosely and tightly held layers of water molecules that behave as if they are an integral part of the protein. The number of water molecules in the protein hydration shells varies with proteins, which can tell us the average surface structure of proteins. These measurements shed light on the macromolecular motions of proteins in their biologically relevant environment.

Theoretical modeling of magnesium ion imprints in the Raman scattering of water.

PubMed

Kapitán, Josef; Dracínský, Martin; Kaminský, Jakub; Benda, Ladislav; Bour, Petr

2010-03-18

Hydration envelopes of metallic ions significantly influence their chemical properties and biological functioning. Previous computational studies, nuclear magnetic resonance (NMR), and vibrational spectra indicated a strong affinity of the Mg(2+) cation to water. We find it interesting that, although monatomic ions do not vibrate themselves, they cause notable changes in the water Raman signal. Therefore, in this study, we used a combination of Raman spectroscopy and computer modeling to analyze the magnesium hydration shell and origin of the signal. In the measured spectra of several salts (LiCl, NaCl, KCl, MgCl(2), CaCl(2), MgBr(2), and MgI(2) water solutions), only the spectroscopic imprint of the hydrated Mg(2+) cation could clearly be identified as an exceptionally distinct peak at approximately 355 cm(-1). The assignment of this band to the Mg-O stretching motion could be confirmed on the basis of several models involving quantum chemical computations on metal/water clusters. Minor Raman spectral features could also be explained. Ab initio and Fourier transform (FT) techniques coupled with the Car-Parrinello molecular dynamics were adapted to provide the spectra from dynamical trajectories. The results suggest that even in concentrated solutions magnesium preferentially forms a [Mg(H(2)O)(6)](2+) complex of a nearly octahedral symmetry; nevertheless, the Raman signal is primarily associated with the relatively strong metal-H(2)O bond. Partially covalent character of the Mg-O bond was confirmed by a natural bond orbital analysis. Computations on hydrated chlorine anion did not provide a specific signal. The FT techniques gave good spectral profiles in the high-frequency region, whereas the lowest-wavenumber vibrations were better reproduced by the cluster models. Both dynamical and cluster computational models provided a useful link between spectral shapes and specific ion-water interactions.

The catalytic effect of H2O on the hydrolysis of CO32- in hydrated clusters and its implication in the humidity driven CO2 air capture.

PubMed

Xiao, Hang; Shi, Xiaoyang; Zhang, Yayun; Liao, Xiangbiao; Hao, Feng; Lackner, Klaus S; Chen, Xi

2017-10-18

The hydration of ions in nanoscale hydrated clusters is ubiquitous and essential in many physical and chemical processes. Here we show that the hydrolysis reaction is strongly affected by relative humidity. The hydrolysis of CO 3 2- with n = 1-8 water molecules is investigated using an ab initio method. For n = 1-5 water molecules, all the reactants follow a stepwise pathway to the transition state. For n = 6-8 water molecules, all the reactants undergo a direct proton transfer to the transition state with overall lower activation free energy. The activation free energy of the reaction is dramatically reduced from 10.4 to 2.4 kcal mol -1 as the number of water molecules increases from 1 to 6. Meanwhile, the degree of hydrolysis of CO 3 2- is significantly increased compared to the bulk water solution scenario. Incomplete hydration shells facilitate the hydrolysis of CO 3 2- with few water molecules to be not only thermodynamically favorable but also kinetically favorable. We showed that the chemical kinetics is not likely to constrain the speed of CO 2 air capture driven by the humidity-swing. Instead, the pore-diffusion of ions is expected to be the time-limiting step in the humidity driven CO 2 air capture. The effect of humidity on the speed of CO 2 air capture was studied by conducting a CO 2 absorption experiment using IER with a high ratio of CO 3 2- to H 2 O molecules. Our result is able to provide valuable insights into designing efficient CO 2 air-capture sorbents.

Ultrafast phosphate hydration dynamics in bulk H{sub 2}O

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

Costard, Rene, E-mail: costard@mbi-berlin.de; Tyborski, Tobias; Fingerhut, Benjamin P., E-mail: fingerhut@mbi-berlin.de

2015-06-07

Phosphate vibrations serve as local probes of hydrogen bonding and structural fluctuations of hydration shells around ions. Interactions of H{sub 2}PO{sub 4}{sup −} ions and their aqueous environment are studied combining femtosecond 2D infrared spectroscopy, ab-initio calculations, and hybrid quantum-classical molecular dynamics (MD) simulations. Two-dimensional infrared spectra of the symmetric (ν{sub S}(PO{sub 2}{sup −})) and asymmetric (ν{sub AS}(PO{sub 2}{sup −})) PO{sub 2}{sup −} stretching vibrations display nearly homogeneous lineshapes and pronounced anharmonic couplings between the two modes and with the δ(P-(OH){sub 2}) bending modes. The frequency-time correlation function derived from the 2D spectra consists of a predominant 50 fs decaymore » and a weak constant component accounting for a residual inhomogeneous broadening. MD simulations show that the fluctuating electric field of the aqueous environment induces strong fluctuations of the ν{sub S}(PO{sub 2}{sup −}) and ν{sub AS}(PO{sub 2}{sup −}) transition frequencies with larger frequency excursions for ν{sub AS}(PO{sub 2}{sup −}). The calculated frequency-time correlation function is in good agreement with the experiment. The ν(PO{sub 2}{sup −}) frequencies are mainly determined by polarization contributions induced by electrostatic phosphate-water interactions. H{sub 2}PO{sub 4}{sup −}/H{sub 2}O cluster calculations reveal substantial frequency shifts and mode mixing with increasing hydration. Predicted phosphate-water hydrogen bond (HB) lifetimes have values on the order of 10 ps, substantially longer than water-water HB lifetimes. The ultrafast phosphate-water interactions observed here are in marked contrast to hydration dynamics of phospholipids where a quasi-static inhomogeneous broadening of phosphate vibrations suggests minor structural fluctuations of interfacial water.« less

Study of transmittance and reflectance spectra of the cornea and the sclera in the THz frequency range

NASA Astrophysics Data System (ADS)

Iomdina, Elena N.; Goltsman, Gregory N.; Seliverstov, Sergey V.; Sianosyan, Alisa A.; Teplyakova, Kseniya O.; Rusova, Anastasia A.

2016-09-01

An adequate water balance (hydration extent) is one of the basic factors of normal eye function, including its external shells: the cornea and the sclera. Adequate control of corneal and scleral hydration is very important for early diagnosis of a variety of eye diseases, stating indications for and contraindications against keratorefractive surgeries and the choice of contact lens correction solutions. THz systems of creating images in reflected beams are likely to become ideal instruments of noninvasive control of corneal and scleral hydration degrees. This paper reports on the results of a study involving transmittance and reflectance spectra for the cornea and the sclera of rabbit and human eyes, as well as those of the rabbit eye, in the frequency range of 0.13 to 0.32 THz. The dependence of the reflectance coefficient of these tissues on water mass percentage content was determined. The experiments were performed on three corneas, three rabbit scleras, two rabbit eyes, and three human scleras. The preliminary results demonstrate that the proposed technique, based on the use of a continuous THz radiation, may be utilized to create a device for noninvasive control of corneal and scleral hydration, which has clear potential of broad practical application.

Scalable Graphene-Based Membranes for Ionic Sieving with Ultrahigh Charge Selectivity.

PubMed

Hong, Seunghyun; Constans, Charlotte; Surmani Martins, Marcos Vinicius; Seow, Yong Chin; Guevara Carrió, Juan Alfredo; Garaj, Slaven

2017-02-08

Nanostructured graphene-oxide (GO) laminate membranes, exhibiting ultrahigh water flux, are excellent candidates for next generation nanofiltration and desalination membranes, provided the ionic rejection could be further increased without compromising the water flux. Using microscopic drift-diffusion experiments, we demonstrated the ultrahigh charge selectivity for GO membranes, with more than order of magnitude difference in the permeabilities of cationic and anionic species of equivalent hydration radii. Measuring diffusion of a wide range of ions of different size and charge, we were able to clearly disentangle different physical mechanisms contributing to the ionic sieving in GO membranes: electrostatic repulsion between ions and charged chemical groups; and the compression of the ionic hydration shell within the membrane's nanochannels, following the activated behavior. The charge-selectivity allows us to rationally design membranes with increased ionic rejection and opens up the field of ion exchange and electrodialysis to the GO membranes.

Characteristics of gas hydrate-bearing sediments of the northern South China Sea: insight into past hydrate episodic dissociations and intensities of seepage

NASA Astrophysics Data System (ADS)

Chen, F.; Su, X.; Zhou, Y.; Zhang, G.; Zhuang, C.; Lu, H.

2016-12-01

In 2013 the second China's major gas hydrate expedition, GMGS2, cored and recovered abundant gas hydrates at five sites, which were located in the South China Sea.Site GMGS08 (95m long) contained two gas hydrate intervals and five authigenic carbonate intervals. We analyzed carbon and oxygen isotopes of authigenic carbonates and foraminifera shells in sediments recovered at this site, in order to understanding of features of hydrate-bearing sediments and timing of gas hydrate dissociation and methane seepage at this site. An age of younger than 0.27 Ma was estimated for the 95 m sedimentary sequences at Site GMGS08. A detailed age model was further established by employing of U/Th and AMS14C dating of authigenic carbonates and seep bivalve fragments. These carbonates are featured by 13C-depleted (with a range from -38.9‰ to 56.7‰ δ13C) and positive δ18O (from 2.94‰ to 5.66‰ δ18O) values. A further analysis indicated the formation of carbonates were correlated to methane seepages derived from gas hydrate dissociation. Subsequently, these five authigenic carbonates intervals were seen as five hydrate episodic dissociation events since last 0.27Ma at this site. The most significant event during the period of 0.11 Ma to 0.13 Ma were account for the formation of thick authigenic carbonate (with the lowest -56.8‰ δ13C value) platform on paleo-seafloor at this site. The upmost authigenic carbonates interval is just overlying on the top of the upper gas hydrate occurrence zone, and it represents the latest methane seepage event with an age of 26ka to 36ka. Well correlated to these five events, it existed five intervals with strongly 13C-depleted carbon (-15.85‰ PDB) of foraminifera shells both from benthic and planktonic. The anomalous δ13C depletion records of planktonic G. ruber shells should be caused by formation of secondary authigenic carbonates on the shells, which were derived from the anaerobic oxidation of methane (AOM). The analyses on carbonate samples indicated varied intensity of methane flux in each event. The most intensive methane venting flux occurred during the event of 0.11 Ma to 0.13 Ma, which is correlated to a warm and relative high sea level period of MIS stage 5. These records obtained at Site GMGS08 implied much complicated causes for formation of authigenic carbonates and gas hydrate episodic dissociation.

Analysis of the detailed configuration of hydrated lanthanoid(III) ions in aqueous solution and crystalline salts by using K- and L(3)-edge XANES spectroscopy.

PubMed

D'Angelo, Paola; Zitolo, Andrea; Migliorati, Valentina; Persson, Ingmar

2010-01-11

The structural properties of the hydrated lanthanoid(III) ions in aqueous solution and in the isostructural trifluoromethanesulfonate salts have been investigated by a quantitative analysis of the X-ray absorption near-edge structure (XANES) spectra at the K- and L(3)-edges. The XANES analysis has provided a clear description of the variation of lanthanoid(III) hydration properties across the series. It was found that all of the lanthanoid(III) hydration complexes retain a tricapped trigonal prism (TTP) geometry, and along the series two of the capping water molecules become less and less strongly bound, before finally, on average, one of them leaves the hydration cluster. This gives rise to an eight-coordinated distorted bicapped trigonal prism with two different Ln--O capping distances for the smallest lanthanoid(III) ions. This systematic study has shown that for lanthanoid compounds more accurate structural information is obtained from the analysis of the L(3)-edge than from K-edge XANES data. Moreover, whereas the second hydration shells provide a detectable contribution to the L(3)-edge XANES spectra of the lighter lanthanoid ions, the K-edge spectra are insensitive to the more distant coordination spheres.

Quantum mechanical effects in zwitterionic amino acids: The case of proline, hydroxyproline, and alanine in water

NASA Astrophysics Data System (ADS)

Ulman, Kanchan; Busch, Sebastian; Hassanali, Ali A.

2018-06-01

In this work, we use ab initio molecular dynamics simulations to elucidate the electronic properties of three hydrated zwitterionic amino acids, namely proline, hydroxyproline, and alanine, the former two forming an important constituent of collagen. In all three systems, we find a substantial amount of charge transfer between the amino acids and surrounding solvent, which, rather surprisingly, also involves the reorganization of electron density near the hydrophobic non-polar groups. Water around proline appears to be slightly more polarized, as reflected by the enhanced water dipole moment in its hydration shell. This observation is also complemented by an examination of the IR spectra of the three systems where there is a subtle red and blue shift in the O-H stretch and bend regions, respectively, for proline. We show that polarizability of these amino acids as revealed by a dipole moment analysis involves a significant enhancement from the solvent and that this also involves non-polar groups. Our results suggest that quantum mechanical effects are likely to be important in understanding the coupling between biomolecules and water in general and in hydrophobic interactions.

The unfolding effects on the protein hydration shell and partial molar volume: a computational study.

PubMed

Del Galdo, Sara; Amadei, Andrea

2016-10-12

In this paper we apply the computational analysis recently proposed by our group to characterize the solvation properties of a native protein in aqueous solution, and to four model aqueous solutions of globular proteins in their unfolded states thus characterizing the protein unfolded state hydration shell and quantitatively evaluating the protein unfolded state partial molar volumes. Moreover, by using both the native and unfolded protein partial molar volumes, we obtain the corresponding variations (unfolding partial molar volumes) to be compared with the available experimental estimates. We also reconstruct the temperature and pressure dependence of the unfolding partial molar volume of Myoglobin dissecting the structural and hydration effects involved in the process.

Hydrophilic Solvation Dominates the Terahertz Fingerprint of Amino Acids in Water.

PubMed

Esser, Alexander; Forbert, Harald; Sebastiani, Federico; Schwaab, Gerhard; Havenith, Martina; Marx, Dominik

2018-02-01

Spectroscopy in the terahertz frequency regime is a sensitive tool to probe solvation-induced effects in aqueous solutions. Yet, a systematic understanding of spectral lineshapes as a result of distinct solvation contributions remains terra incognita. We demonstrate that modularization of amino acids in terms of functional groups allows us to compute their distinct contributions to the total terahertz response. Introducing the molecular cross-correlation analysis method provides unique access to these site-specific contributions. Equivalent groups in different amino acids lead to look-alike spectral contributions, whereas side chains cause characteristic but additive complexities. Specifically, hydrophilic solvation of the zwitterionic groups in valine and glycine leads to similar terahertz responses which are fully decoupled from the side chain. The terahertz response due to H-bonding within the large hydrophobic solvation shell of valine turns out to be nearly indistinguishable from that in bulk water in direct comparison to the changes imposed by the charged functional groups that form strong H-bonds with their hydration shells. Thus, the hydrophilic groups and their solvation shells dominate the terahertz absorption difference, while on the same intensity scale, the influence of hydrophobic water can be neglected.

Studies of protein-protein and protein-water interactions by small angle x-ray scattering, terahertz spectroscopy, ASMOS, and computer simulation

NASA Astrophysics Data System (ADS)

Kim, Seung Joong

The protein folding problem has been one of the most challenging subjects in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very important for describing the energy landscape surface of proteins correctly. At first, we present a new method for computing protein-protein interaction potentials of solvated proteins directly from SAXS data. An ensemble of proteins was modeled by Metropolis Monte Carlo and Molecular Dynamics simulations, and the global X-ray scattering of the whole model ensemble was computed at each snapshot of the simulation. The interaction potential model was optimized and iterated by a Levenberg-Marquardt algorithm. Secondly, we report that terahertz spectroscopy directly probes hydration dynamics around proteins and determines the size of the dynamical hydration shell. We also present the sequence and pH-dependence of the hydration shell and the effect of the hydrophobicity. On the other hand, kinetic terahertz absorption (KITA) spectroscopy is introduced to study the refolding kinetics of ubiquitin and its mutants. KITA results are compared to small angle X-ray scattering, tryptophan fluorescence, and circular dichroism results. We propose that KITA monitors the rearrangement of hydrogen bonding during secondary structure formation. Finally, we present development of the automated single molecule operating system (ASMOS) for a high throughput single molecule detector, which levitates a single protein molecule in a 10 microm diameter droplet by the laser guidance. I also have performed supporting calculations and simulations with my own program codes.

Selective Permeability of Uranyl Peroxide Nanocages to Different Alkali Ions: Influences from Surface Pores and Hydration Shells

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

Gao, Yunyi; Haso, Fadi; Szymanowski, Jennifer E. S.

2015-11-16

The precise guidance to different ions across the biological channels is essential for many biological processes. An artificial nanopore system will facilitate the study of the ion-transport mechanism through nanosized channels and offer new views for designing nanodevices. Herein we reveal that a 2.5 nm-sized, fullerene-shaped molecular cluster Li48+mK12(OH)m[UO2(O2)(OH)]60-(H2O)n (m≈20 and n≈310) (U60) shows selective permeability to different alkali ions. The subnanometer pores on the water–ligand-rich surface of U60 are able to block Rb+ and Cs+ ions from passing through, while allowing Na+ and K+ ions, which possess larger hydrated sizes, to enter the interior space of U60. An interestinglymore » high entropy gain during the binding process between U60 and alkali ions suggests that the hydration shells of Na+/K+ and U60 are damaged during the interaction. The ion selectivity of U60 is greatly influenced by both the morphologies of the surface nanopores and the dynamics of the hydration shells.« less

Exploration of the Ca2+ interaction modes of the nifedipine calcium channel antagonist.

PubMed

Liu, Huichun; Zhang, Liang; Li, Ping; Cukier, Robert I; Bu, Yuxiang

2007-02-02

A comprehensive study is carried out using quantum chemical computation and molecular dynamics (MD) simulations to gain insight into the interaction between Ca(2+) ions and the most important class of calcium channel antagonists--nifedipine. First, the chelating structures and energetic characters of nifedipine-Ca(2+) in the gas phase are explored, and 25 isomers are found. The most favorable chelating mode is a tridentate one, that is, Ca(2+) binds to two carbonyl O atoms and one nitryl O atom, where Ca(2+) is above the plane of the three O atoms to form a pyramidal structure. Accurate geometric structures, relative stabilities, vertical and adiabatic binding energies, and charge distributions are discussed. The differences in the geometries and energies among these isomers are analyzed from the contributions of chelating sites, electrostatics and polarizations, steric repulsions, and charge distributions. The interconversions among isomers with similar geometries and energies are also investigated because of the importance of the geometric transformation in the biological system. Furthermore, certain numbers of water molecules are added to the nifedipine-Ca(2+) system to probe the effect of water. A detailed study is performed on the hydrated geometries on the basis of the most stable isomer 1. Stepwise hydration can weaken the nifedipine-Ca(2+) interaction, and the chelating sites of nifedipine are gradually replaced by the added water molecules. Hexacoordination is found to be the most favorable geometry no matter how many water molecules were added, which can be verified by the MD simulations. The transfer of water molecules from the inner shell to the outer shell is also supported by MD simulations of the hexahydrated complexes.

Beaufort Sea deep-water gas hydrate recovery from a seafloor mound in a region of widespread BSR occurrence

USGS Publications Warehouse

Hart, Patrick E.; Pohlman, John W.; Lorenson, T.D.; Edwards, Brian D.

2011-01-01

Gas hydrate was recovered from the Alaskan Beaufort Sea slope north of Camden Bay in August 2010 during a U.S. Coast Guard Cutter Healy expedition (USCG cruise ID HLY1002) under the direction of the U.S. Geological Survey (USGS). Interpretation of multichannel seismic (MCS) reflection data collected in 1977 by the USGS across the Beaufort Sea continental margin identified a regional bottom simulating reflection (BSR), indicating that a large segment of the Beaufort Sea slope is underlain by gas hydrate. During HLY1002, gas hydrate was sampled by serendipity with a piston core targeting a steep-sided bathymetric high originally thought to be an outcrop of older, exposed strata. The feature cored is an approximately 1100m diameter, 130 m high conical mound, referred to here as the Canning Seafloor Mound (CSM), which overlies the crest of a buried anticline in a region of sub-parallel compressional folds beneath the eastern Beaufort outer slope. An MCS profile shows a prominent BSR upslope and downslope from the mound. The absence of a BSR beneath the CSM and occurrence of gas hydrate near the summit indicates that free gas has migrated via deep-rooted thrust faults or by structural focusing up the flanks of the anticline to the seafloor. Gas hydrate recovered from near the CSM summit at a subbottom depth of about 5.7 meters in a water depth of 2538 m was of nodular and vein-filling morphology. Although the hydrate was not preserved, residual gas from the core liner contained >95% methane by volume when corrected for atmospheric contamination. The presence of trace C4+hydrocarbons (<0.1% by volume) confirms at least a minor thermogenic component. Authigenic carbonates and mollusk shells found throughout the core indicate sustained methane-rich fluid advection and possible sediment extrusion contributing to the development of the mound. Blister-like inflation of the seafloor caused by formation and accumulation of shallow hydrate lenses is also a likely factor in CSM growth. Pore water analysis shows the sulfate-methane transition to be very shallow (0-1 mbsf), also supporting an active high-flux interpretation. Pore water with chloride concentrations as low as 160 mM suggest fluid migration pathways may extend to the mound from buried non-marine sediments containing low-salinity fluids.

Competing Insertion and External Binding Motifs in Hydrated Neurotransmitters: Infrared Spectra of Protonated Phenylethylamine Monohydrate.

PubMed

Bouchet, Aude; Schütz, Markus; Dopfer, Otto

2016-01-18

Hydration has a drastic impact on the structure and function of flexible biomolecules, such as aromatic ethylamino neurotransmitters. The structure of monohydrated protonated phenylethylamine (H(+) PEA-H2 O) is investigated by infrared photodissociation (IRPD) spectroscopy of cold cluster ions by using rare-gas (Rg=Ne and Ar) tagging and dispersion-corrected density functional theory calculations at the B3LYP-D3/aug-cc-pVTZ level. Monohydration of this prototypical neurotransmitter gives an insight into the first step of the formation of its solvation shell, especially regarding the competition between intra- and intermolecular interactions. The spectra of Rg-tagged H(+) PEA-H2 O reveal the presence of a stable insertion structure in which the water molecule is located between the positively charged ammonium group and the phenyl ring of H(+) PEA, acting both as a hydrogen bond acceptor (NH(+) ⋅⋅⋅O) and donor (OH⋅⋅⋅π). Two other nearly equivalent isomers, in which water is externally H bonded to one of the free NH groups, are also identified. The balance between insertion and external hydration strongly depends on temperature. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular Dynamics Studies of Overbased Detergents on a Water Surface.

PubMed

Bodnarchuk, M S; Dini, D; Heyes, D M; Breakspear, A; Chahine, S

2017-07-25

Molecular dynamics (MD) simulations are reported of model overbased detergent nanoparticles on a model water surface which mimic their behavior on a Langmuir trough or large water droplet in engine oil. The simulations predict that the structure of the nanoparticle on a water surface is different to when it is immersed in a bulk hydrophobic solvent. The surfactant tails are partly directed out of the water, while the carbonate core maximizes its extent of contact with the water. Umbrella sampling calculations of the potential of mean force between two particles showed that they are associated with varying degrees with a maximum binding free energy of ca. 10 k B T for the salicylate stabilized particle, ca. 8 k B T for a sulfurized alkyl phenate stabilized particle, and ca. 5 k B T for a sulfonate stabilized particle. The differences in the strength of attraction depend on the proximity of nearest approach and the energy penalty associated with the disruption of the hydration shell of water molecules around the calcium carbonate core when the two particles approach. This is greatest for the sulfonate particle, which partially loses the surfactant ions to the solution, and least for the salicylate, which forms the weakest water "cage". The particles are separated by a water hydration layer, even at the point of closest approach.

Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties

NASA Astrophysics Data System (ADS)

Fogarty, Aoife C.; Potestio, Raffaello; Kremer, Kurt

2015-05-01

A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydration shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspects of the AdResS methodology peculiar to biomolecular simulations.

Nucleation pathways of clathrate hydrates: effect of guest size and solubility.

PubMed

Jacobson, Liam C; Hujo, Waldemar; Molinero, Valeria

2010-11-04

Understanding the microscopic mechanism of nucleation of clathrate hydrates is important for their use in hydrogen storage, CO(2) sequestration, storage and transport of natural gas, and the prevention of the formation of hydrate plugs in oil and gas pipelines. These applications involve hydrate guests of varied sizes and solubility in water that form different hydrate crystal structures. Nevertheless, molecular studies of the mechanism of nucleation of hydrates have focused on the single class of small hydrophobic guests that stabilize the sI crystal. In this work, we use molecular dynamics simulations with a very efficient coarse-grained model to elucidate the mechanisms of nucleation of clathrate hydrates of four model guests that span a 2 orders of magnitude range in solubility in water and that encompass sizes which stabilize each one a different hydrate structure (sI and sII, with and without occupancy of the dodecahedral cages). We find that the overall mechanism of clathrate nucleation is similar for all guests and involves a first step of formation of blobs, dense clusters of solvent-separated guest molecules that are the birthplace of the clathrate cages. Blobs of hydrophobic guests are rarer and longer-lived than those for soluble guests. For each guest, we find multiple competing channels to form the critical nuclei, filled dodecahedral (5(12)) cages, empty 5(12) cages, and a variety of filled large (5(12)6(n) with n = 2, 3, and 4) clathrate cages. Formation of empty dodecahedra is an important nucleation channel for all but the smallest guest. The empty 5(12) cages are stabilized by the presence of guests from the blob in their first solvation shell. Under conditions of high supercooling, the structure of the critical and subcritical nuclei is mainly determined by the size of the guest and does not reflect the cage composition or ordering of the stable or metastable clathrate crystals.

The effect of the condensed-phase environment on the vibrational frequency shift of a hydrogen molecule inside clathrate hydrates

NASA Astrophysics Data System (ADS)

Powers, Anna; Scribano, Yohann; Lauvergnat, David; Mebe, Elsy; Benoit, David M.; Bačić, Zlatko

2018-04-01

We report a theoretical study of the frequency shift (redshift) of the stretching fundamental transition of an H2 molecule confined inside the small dodecahedral cage of the structure II clathrate hydrate and its dependence on the condensed-phase environment. In order to determine how much the hydrate water molecules beyond the confining small cage contribute to the vibrational frequency shift, quantum five-dimensional (5D) calculations of the coupled translation-rotation eigenstates are performed for H2 in the v =0 and v =1 vibrational states inside spherical clathrate hydrate domains of increasing radius and a growing number of water molecules, ranging from 20 for the isolated small cage to over 1900. In these calculations, both H2 and the water domains are treated as rigid. The 5D intermolecular potential energy surface (PES) of H2 inside a hydrate domain is assumed to be pairwise additive. The H2-H2O pair interaction, represented by the 5D (rigid monomer) PES that depends on the vibrational state of H2, v =0 or v =1 , is derived from the high-quality ab initio full-dimensional (9D) PES of the H2-H2O complex [P. Valiron et al., J. Chem. Phys. 129, 134306 (2008)]. The H2 vibrational frequency shift calculated for the largest clathrate domain considered, which mimics the condensed-phase environment, is about 10% larger in magnitude than that obtained by taking into account only the small cage. The calculated splittings of the translational fundamental of H2 change very little with the domain size, unlike the H2 j = 1 rotational splittings that decrease significantly as the domain size increases. The changes in both the vibrational frequency shift and the j = 1 rotational splitting due to the condensed-phase effects arise predominantly from the H2O molecules in the first three complete hydration shells around H2.

Effect of the conditions of REM microalloying of steel on the corrosion activity of nonmetallic inclusions

NASA Astrophysics Data System (ADS)

Movenko, D. A.; Kotel'nikov, G. I.; Pavlov, A. V.; Bytsenko, O. A.

2015-11-01

Experimental heats of low-alloy steel are performed under various conditions of rare-earth metal microalloying and aluminum and calcium deoxidation. Electron-probe microanalysis of nonmetallic inclusions and a metallographic investigation of a metal are used to show that, when interacting with water, nonmetallic cerium oxide inclusions do not form hydrates and, correspondingly, are not aggressive. When aluminum, calcium, and cerium additions are sequentially introduced into a melt, a continuous cerium oxide shell forms on calcium aluminates, protects corrosive nonmetallic inclusions against interaction with water, and weakens local metal corrosion.

Dipolar response of hydrated proteins

NASA Astrophysics Data System (ADS)

Matyushov, Dmitry V.

2012-02-01

The paper presents an analytical theory and numerical simulations of the dipolar response of hydrated proteins in solution. We calculate the effective dielectric constant representing the average dipole moment induced at the protein by a uniform external field. The dielectric constant shows a remarkable variation among the proteins, changing from 0.5 for ubiquitin to 640 for cytochrome c. The former value implies a negative dipolar susceptibility, that is a dia-electric dipolar response and negative dielectrophoresis. It means that ubiquitin, carrying an average dipole of ≃240 D, is expected to repel from the region of a stronger electric field. This outcome is the result of a negative cross-correlation between the protein and water dipoles, compensating for the positive variance of the intrinsic protein dipole in the overall dipolar susceptibility. In contrast to the neutral ubiquitin, charged proteins studied here show para-electric dipolar response and positive dielectrophoresis. The study suggests that the dipolar response of proteins in solution is strongly affected by the coupling of the protein surface charge to the hydration water. The protein-water dipolar cross-correlations are long-ranged, extending ˜2 nm from the protein surface into the bulk. A similar correlation length of about 1 nm is seen for the electrostatic potential produced by the hydration water inside the protein. The analysis of numerical simulations suggests that the polarization of the protein-water interface is highly heterogeneous and does not follow the standard dielectric results for cavities carved in dielectrics. The polarization of the water shell gains in importance, relative to the intrinsic protein dipole, at high frequencies, above the protein Debye peak. The induced interfacial dipole can be either parallel or antiparallel to the protein dipole, depending on the distribution of the protein surface charge. As a result, the high-frequency absorption of the protein solution can be either higher or lower than the absorption of water. Both scenarios have been experimentally observed in the THz window of radiation.

Dipolar response of hydrated proteins.

PubMed

Matyushov, Dmitry V

2012-02-28

The paper presents an analytical theory and numerical simulations of the dipolar response of hydrated proteins in solution. We calculate the effective dielectric constant representing the average dipole moment induced at the protein by a uniform external field. The dielectric constant shows a remarkable variation among the proteins, changing from 0.5 for ubiquitin to 640 for cytochrome c. The former value implies a negative dipolar susceptibility, that is a dia-electric dipolar response and negative dielectrophoresis. It means that ubiquitin, carrying an average dipole of ≃240 D, is expected to repel from the region of a stronger electric field. This outcome is the result of a negative cross-correlation between the protein and water dipoles, compensating for the positive variance of the intrinsic protein dipole in the overall dipolar susceptibility. In contrast to the neutral ubiquitin, charged proteins studied here show para-electric dipolar response and positive dielectrophoresis. The study suggests that the dipolar response of proteins in solution is strongly affected by the coupling of the protein surface charge to the hydration water. The protein-water dipolar cross-correlations are long-ranged, extending ~2 nm from the protein surface into the bulk. A similar correlation length of about 1 nm is seen for the electrostatic potential produced by the hydration water inside the protein. The analysis of numerical simulations suggests that the polarization of the protein-water interface is highly heterogeneous and does not follow the standard dielectric results for cavities carved in dielectrics. The polarization of the water shell gains in importance, relative to the intrinsic protein dipole, at high frequencies, above the protein Debye peak. The induced interfacial dipole can be either parallel or antiparallel to the protein dipole, depending on the distribution of the protein surface charge. As a result, the high-frequency absorption of the protein solution can be either higher or lower than the absorption of water. Both scenarios have been experimentally observed in the THz window of radiation.

Deconstructing Free Energies in the Law of Matching Water Affinities.

PubMed

Shi, Yu; Beck, Thomas

2017-03-09

The law of matching water affinities (LMWA) is explored in classical molecular dynamics simulations of several alkali halide ion pairs, spanning the size range from small kosmotropes to large chaotropes. The ion-ion potentials of mean force (PMFs) are computed using three methods: the local molecular field theory (LMFT), the weighted histogram analysis method (WHAM), and integration of the average force. All three methods produce the same total PMF for a given ion pair. In addition, LMFT-based partitioning into van der Waals and local and far-field electrostatic free energies and assessment of the enthalpic, entropic, and ion-water components yield insights into the origins of the observed free energy profiles in water. The results highlight the importance of local electrostatic interactions in determining the shape of the PMFs, while longer-ranged interactions enhance the overall ion-ion attraction, as expected in a dielectric continuum model. The association equilibrium constants are estimated from the smooth WHAM curves and compared to available experimental conductance data. By examining the variations in the average hydration numbers of ions with ion-ion distance, a correlation of the water structure in the hydration shells with the free energy features is found.

Dynamical properties of the hydration shell of fully deuterated myoglobin

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

Achterhold, Klaus; Parak, Fritz G.; Ostermann, Andreas

2011-10-15

Freeze-dried perdeuterated sperm whale myoglobin was kept in a water-saturated atmosphere in order to obtain a hydration degree of 335 {sup 1}H{sub 2}O molecules per one myoglobin molecule. Incoherent neutron scattering was performed at the neutron spectrometer TOFTOF at the FRM II in an angular range of q from 0.6 to 1.8 A{sup -1} and a temperature range from 4 to 297 K. We used neutrons with a wavelength of {lambda}{alpha}E 6 A and an energy resolution of about 65 {mu}eV corresponding to motions faster than 10 ps. At temperatures above 225 K, broad lines appear in the spectra causedmore » by quasielastic scattering. For an explanation of these lines, we assumed that there are only two types of protons, those that are part of the hydration water (72%) and those that belong to the protein (28%). The protons of the hydration water were analyzed with the diffusion model of Singwi and Sjoelander [Phys. Rev. 119, 863 (1960)]. In this model, a water molecule stays for a time {tau}{sub 0} in a bound state performing oscillatory motions. Thereafter, the molecule performs free diffusion for the time {tau}{sub 1} in a nonbound state followed again by the oscillatory motions for {tau}{sub 0} and so forth. We used the general formulation with no simplifications as {tau}{sub 0}>>{tau}{sub 1} or {tau}{sub 1}>>{tau}{sub 0}. At room temperature, we obtained {tau}{sub 0} {alpha}E 104 ps and {tau}{sub 1} {alpha}E 37 ps. For the protein bound hydrogen, the dynamics is described by a Brownian oscillator where the protons perform overdamped motions in limited space.« less

Methane-derived authigenic carbonates from the northern Gulf of Mexico - MD02 Cruise

USGS Publications Warehouse

Chen, Y.; Matsumoto, R.; Paull, C.K.; Ussler, W.; Lorenson, T.; Hart, P.; Winters, W.

2007-01-01

Authigenic carbonates were sampled in piston cores collected from both the Tunica Mound and the Mississippi Canyon area on the continental slope of the northern Gulf of Mexico during a Marion Dufresne cruise in July 2002. The carbonates are present as hardgrounds, porous crusts, concretions or nodules and shell fragments with or without carbonate cements. Carbonates occurred at gas venting sites which are likely to overlie gas hydrates bearing sediments. Electron microprobe, X-ray diffraction (XRD) and thinsection investigations show that these carbonates are high-Mg calcite (6-21??mol% MgCO3), with significant presence of framboidal pyrite. All carbonates are depleted in 13C (??13C = - 61.9 to - 31.5??? PDB) indicating that the carbon is derived mainly from anaerobic methane oxidation (AMO). Age estimates based on 14C dating of shell fragments and on regional sedimentation rates indicate that these authigenic carbonates formed within the last 1000??yr in the Mississippi Canyon and within 5500??yr at the Tunica Mound. The oxygen isotopic composition of carbonates ranges from + 3.4 to + 5.9??? PDB. Oxygen isotopic compositions and Mg2+ contents of carbonates, and present in-situ temperatures of bottom seawater/sediments, show that some of these carbonates, especially from a core associated with underlying massive gas hydrates precipitated in or near equilibrium with bottom-water. On the other hand, those carbonates more enriched in 18O are interpreted to have precipitated from 18O-rich fluids which are thought to have been derived from the dissociation of gas hydrates. The dissociation of gas hydrates in the northern Gulf of Mexico within the last 5500??yr may be caused by nearby salt movement and related brines. ?? 2007 Elsevier B.V. All rights reserved.

Non-cooperative immobilization of residual water bound in lyophilized photosynthetic lamellae.

PubMed

Harańczyk, Hubert; Baran, Ewelina; Nowak, Piotr; Florek-Wojciechowska, Małgorzata; Leja, Anna; Zalitacz, Dorota; Strzałka, Kazimierz

2015-12-01

This study applied 1H-NMR in time and in frequency domain measurements to monitor the changes that occur in bound water dynamics at decreased temperature and with increased hydration level in lyophilizates of native wheat photosynthetic lamellae and in photosynthetic lamellae reconstituted from lyophilizate. Proton relaxometry (measured as free induction decay = FID) distinguishes a Gaussian component S within the NMR signal (o). This comes from protons of the solid matrix of the lamellae and consists of (i) an exponentially decaying contribution L1 from mobile membrane protons, presumably from lipids, and from water that is tightly bound to the membrane surface and thus restricted in mobility; and (ii) an exponentially decaying component L2 from more mobile, loosely bound water pool. Both proton relaxometry data and proton spectroscopy show that dry lyophilizate incubated in dry air, i.e., at a relative humidity (p/p0) of 0% reveals a relatively high hydration level. The observed liquid signal most likely originates from mobile membrane protons and a tightly bound water fraction that is sealed in pores of dry lyophilizate and thus restricted in mobility. The estimations suggest that the amount of sealed water does not exceed the value characteristic for the main hydration shell of a phospholipid. Proton spectra collected for dry lyophilizate of photosynthetic lamellae show a continuous decrease in the liquid signal component without a distinct freezing transition when it is cooled down to -60ºC, which is significantly lower than the homogeneous ice nucleation temperature [Bronshteyn, V.L. et al. Biophys. J. 65 (1993) 1853].

Hydrogen bonding in hydrates with one acetic acid molecule.

PubMed

Pu, Liang; Sun, Yueming; Zhang, Zhibing

2010-10-14

Hydrogen bonding (H-bond) interaction significantly influences the separation of acetic acid (HAc) from the HAc/H(2)O mixtures, especially the dilute solution, in distillation processes. It has been examined from the HAc mono-, di-, tri-, and tetrahydrates by analyzing the structures, binding energies, and infrared vibrational frequencies from quantum chemical calculations. For the first coordinate shell the 6-membered head-on ring is surely the most favorable structure because it has (1) the most favorable H-bonding parameters, (2) almost the largest binding energy per H-bond, (3) the biggest wavenumber shifts, and (4) the highest ring distribution (the AIMD simulations). Moreover, the comparison of the calculations with the experiments (the X-ray scattering data and IR frequencies) suggests that the possible structures in dilute aqueous solution are those involving two or more coordinate shells. The H-bonding in these water-surrounded HAc hydrates are the origin of the low-efficiency problem of isolating HAc from the dilute HAc/H(2)O mixtures. It is apparently a tougher work to break the H-bonds among HAc and the surrounded H(2)O molecules with respect to the case of more concentrated solutions, where the dominant structures are HAc or H(2)O aggregates.

Protein hydration in solution: Experimental observation by x-ray and neutron scattering

PubMed Central

Svergun, D. I.; Richard, S.; Koch, M. H. J.; Sayers, Z.; Kuprin, S.; Zaccai, G.

1998-01-01

The structure of the protein–solvent interface is the subject of controversy in theoretical studies and requires direct experimental characterization. Three proteins with known atomic resolution crystal structure (lysozyme, Escherichia coli thioredoxin reductase, and protein R1 of E. coli ribonucleotide reductase) were investigated in parallel by x-ray and neutron scattering in H2O and D2O solutions. The analysis of the protein–solvent interface is based on the significantly different contrasts for the protein and for the hydration shell. The results point to the existence of a first hydration shell with an average density ≈10% larger than that of the bulk solvent in the conditions studied. Comparisons with the results of other studies suggest that this may be a general property of aqueous interfaces. PMID:9482874

Modeling the interactions of phthalocyanines in water: from the Cu(II)-tetrasulphonate to the metal-free phthalocyanine.

PubMed

Martín, Elisa I; Martínez, Jose M; Sánchez Marcos, Enrique

2011-01-14

A quantum and statistical study on the effects of the ions Cu(2+) and SO(3)(-) in the solvent structure around the metal-free phthalocyanine (H(2)Pc) is presented. We developed an ab initio interaction potential for the system CuPc-H(2)O based on quantum chemical calculations and studied its transferability to the H(2)Pc-H(2)O and [CuPc(SO(3))(4)](4-)-H(2)O interactions. The use of the molecular dynamics technique allows the determination of energetic and structural properties of CuPc, H(2)Pc, and [CuPc(SO(3))(4)](4-) in water and the understanding of the keys for the different behaviors of the three phthalocyanine (Pc) derivatives in water. The inclusion of the Cu(2+) cation in the Pc structure reinforces the appearance of two axial water molecules and second-shell water molecules in the solvent structure, whereas the presence of SO(3)(-) anions implies a well defined hydration shell of about eight water molecules around them making the macrocycle soluble in water. Debye-Waller factors for axial water molecules have been obtained in order to examine the potential sensitivity of the extended x-ray absorption fine structure technique to detect the axial water molecules.

Unraveling the role of water in the stereoselective step of aqueous proline-catalyzed aldol reactions.

PubMed

Ribas-Arino, Jordi; Carvajal, Maria Angels; Chaumont, Alain; Masia, Marco

2012-12-03

A multiscale computational study was performed with the aim of tracing the source of stereoselectivity and disclosing the role of water in the stereoselective step of propionaldehyde aldol self-condensation catalyzed by proline amide in water, a reaction that serves as a model for aqueous organocatalytic aldol condensations. Solvent mixing and hydration behavior were assessed by classical molecular dynamics simulations, which show that the reaction between propanal and the corresponding enamine takes place in a fully hydrated environment. First-principles molecular dynamics simulations were used to study the free-energy profile of four possible reaction paths, each of which yields a different stereoisomer, and high-level static first-principles calculations were employed to characterize the transition states for microsolvated species. The first solvation shell of the oxygen atom of the electrophilic aldehyde at the transition states contains two water molecules, each of which donates one hydrogen bond to the nascent alkoxide and thereby largely stabilizes its excess electron density. The stereoselectivity originates in an extra hydrogen bond donated by the amido group of proline amide in two reaction paths. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Dissecting the THz spectrum of liquid water from first principles via correlations in time and space.

PubMed

Heyden, Matthias; Sun, Jian; Funkner, Stefan; Mathias, Gerald; Forbert, Harald; Havenith, Martina; Marx, Dominik

2010-07-06

Solvation of molecules in water is at the heart of a myriad of molecular phenomena and of crucial importance to understanding such diverse issues as chemical reactivity or biomolecular function. Complementing well-established approaches, it has been shown that laser spectroscopy in the THz frequency domain offers new insights into hydration from small solutes to proteins. Upon introducing spatially-resolved analyses of the absorption cross section by simulations, the sensitivity of THz spectroscopy is traced back to characteristic distance-dependent modulations of absorption intensities for bulk water. The prominent peak at approximately 200 cm(-1) is dominated by first-shell dynamics, whereas a concerted motion involving the second solvation shell contributes most significantly to the absorption at about 80 cm(-1) approximately 2.4 THz. The latter can be understood in terms of an umbrella-like motion of two hydrogen-bonded tetrahedra along the connecting hydrogen bond axis. Thus, a modification of the hydrogen bond network, e.g., due to the presence of a solute, is expected to affect vibrational motion and THz absorption intensity at least on a length scale that corresponds to two layers of solvating water molecules. This result provides a molecular mechanism explaining the experimentally determined sensitivity of absorption changes in the THz domain in terms of distinct, solute-induced dynamical properties in solvation shells of (bio)molecules--even in the absence of well-defined resonances.

Study of lithium cation in water clusters: based on atom-bond electronegativity equalization method fused into molecular mechanics.

PubMed

Li, Xin; Yang, Zhong-Zhi

2005-05-12

We present a potential model for Li(+)-water clusters based on a combination of the atom-bond electronegativity equalization and molecular mechanics (ABEEM/MM) that is to take ABEEM charges of the cation and all atoms, bonds, and lone pairs of water molecules into the intermolecular electrostatic interaction term in molecular mechanics. The model allows point charges on cationic site and seven sites of an ABEEM-7P water molecule to fluctuate responding to the cluster geometry. The water molecules in the first sphere of Li(+) are strongly structured and there is obvious charge transfer between the cation and the water molecules; therefore, the charge constraint on the ionic cluster includes the charged constraint on the Li(+) and the first-shell water molecules and the charge neutrality constraint on each water molecule in the external hydration shells. The newly constructed potential model based on ABEEM/MM is first applied to ionic clusters and reproduces gas-phase state properties of Li(+)(H(2)O)(n) (n = 1-6 and 8) including optimized geometries, ABEEM charges, binding energies, frequencies, and so on, which are in fair agreement with those measured by available experiments and calculated by ab initio methods. Prospects and benefits introduced by this potential model are pointed out.

How the shape of an H-bonded network controls proton-coupled water activation in HONO formation.

PubMed

Relph, Rachael A; Guasco, Timothy L; Elliott, Ben M; Kamrath, Michael Z; McCoy, Anne B; Steele, Ryan P; Schofield, Daniel P; Jordan, Kenneth D; Viggiano, Albert A; Ferguson, Eldon E; Johnson, Mark A

2010-01-15

Many chemical reactions in atmospheric aerosols and bulk aqueous environments are influenced by the surrounding solvation shell, but the precise molecular interactions underlying such effects have rarely been elucidated. We exploited recent advances in isomer-specific cluster vibrational spectroscopy to explore the fundamental relation between the hydrogen (H)-bonding arrangement of a set of ion-solvating water molecules and the chemical activity of this ensemble. We find that the extent to which the nitrosonium ion (NO+)and water form nitrous acid (HONO) and a hydrated proton cluster in the critical trihydrate depends sensitively on the geometrical arrangement of the water molecules in the network. Theoretical analysis of these data details the role of the water network in promoting charge delocalization.

Variations of water's local-structure induced by solvation of NaCl

NASA Astrophysics Data System (ADS)

Gu, Bin; Zhang, Feng-Shou; Huang, Yu-Gai; Fang, Xia

2010-03-01

The researches on the structure of water and its changes induced by solutes are of enduring interests. The changes of the local structure of liquid water induced by NaCl solute under ambient conditions are studied and presented quantitatively with some order parameters and visualized with 2-body and 3-body correlation functions. The results show that, after the NaCl are solvated, the translational order t of water is decreased for the suppression of the second hydration shells around H2O molecules; the tetrahedral order (q) of water is also decreased and its favorite distribution peak moves from 0.76 to 0.5. In addition, the orientational freedom k and the diffusion coefficient D of water molecules are reduced because of new formed hydrogen-bonding structures between water and solvated ions.

Hydration of Li+ -ion in atom-bond electronegativity equalization method-7P water: a molecular dynamics simulation study.

PubMed

Li, Xin; Yang, Zhong-Zhi

2005-02-22

We have carried out molecular dynamics simulations of a Li(+) ion in water over a wide range of temperature (from 248 to 368 K). The simulations make use of the atom-bond electronegativity equalization method-7P water model, a seven-site flexible model with fluctuating charges, which has accurately reproduced many bulk water properties. The recently constructed Li(+)-water interaction potential through fitting to the experimental and ab initio gas-phase binding energies and to the measured structures for Li(+)-water clusters is adopted in the simulations. ABEEM was proposed and developed in terms of partitioning the electron density into atom and bond regions and using the electronegativity equalization method (EEM) and the density functional theory (DFT). Based on a combination of the atom-bond electronegativity equalization method and molecular mechanics (ABEEM/MM), a new set of water-water and Li(+)-water potentials, successfully applied to ionic clusters Li(+)(H(2)O)(n)(n=1-6,8), are further investigated in an aqueous solution of Li(+) in the present paper. Two points must be emphasized in the simulations: first, the model allows for the charges on the interacting sites fluctuating as a function of time; second, the ABEEM-7P model has applied the parameter k(lp,H)(R(lp,H)) to explicitly describe the short-range interaction of hydrogen bond in the hydrogen bond interaction region, and has a new description for the hydrogen bond. The static, dynamic, and thermodynamic properties have been studied in detail. In addition, at different temperatures, the structural properties such as radial distribution functions, and the dynamical properties such as diffusion coefficients and residence times of the water molecules in the first hydration shell of Li(+), are also simulated well. These simulation results show that the ABEEM/MM-based water-water and Li(+)-water potentials appear to be robust giving the overall characteristic hydration properties in excellent agreement with experiments and other molecular dynamics simulations on similar system.

Structure of aqueous cesium metaborate solutions by X-ray scattering and DFT calculation

NASA Astrophysics Data System (ADS)

Zhang, W. Q.; Fang, C. H.; Fang, Y.; Zhu, F. Y.; Zhou, Y. Q.; Liu, H. Y.; Li, W.

2018-05-01

In the present work, precise radial distribution function (RDF) of cesium metaborate solutions with salt-water molar ratio of 1:25, 1:30 and 1:35 in large scattering vector range (3.91-214.26 nm-1) were obtained by X-ray scattering. Polyborate species were given using Newton iteration method with measured pH and literature equilibrium constants. In model calculation, structural parameters such as the coordination number, interatomic distance and Debye-Waller factor were given through model calculation. The B-O(H2O) distance was determined to be ∼0.37 nm with the hydration number of ∼7.8 for B(OH)4-. The Cs-B distance of the contact ions CsB(OH)40 was measured to be ∼0.46 nm with interaction number of ∼0.77. The interaction distances and coordination number for the first shell and the second shell of Cs-O(W) are ∼0.325 nm, ∼0.517 nm and ∼8.0, ∼11, respectively. Five low-energy configurations of [Cs(H2O)8]+ were given with DFT calculation, including the first and the second hydration shell, and the most stable eight-coordinated one is close to the model calculation. Furthermore, the effect of concentration is discussed in the X-ray scattering analysis part, showing that hydration degree changes with the concentration. For the coordination number and distance of Cs-O(H2O) and H-bonding decrease with the increasing concentration. The coordination number of Cs-O(H2O) keep stable, and the coordination distance changes from 3.25 nm to 3.30 nm. For H-bonding, which the coordination number varies from 2.20 to 2.24, and the coordination distance varies from 2.76 nm to 2.78 nm with the decreasing concentration.

Temperature effects on prevalent structures of hydrated Fe{sup +} complexes: Infrared spectroscopy and DFT calculations of Fe{sup +}(H{sub 2}O){sub n} (n = 3–8)

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

Ohashi, Kazuhiko, E-mail: kazu@chem.kyushu-univ.jp; Sekiya, Hiroshi; Sasaki, Jun

2014-12-07

Hydrated Fe{sup +} ions are produced in a laser-vaporization cluster source of a triple quadrupole mass spectrometer. The Fe{sup +}(H{sub 2}O){sub n} (n = 3–8) complexes are mass-selected and probed with infrared (IR) photodissociation spectroscopy in the OH-stretch region. Density functional theory (DFT) calculations are also carried out for analyzing the experimental IR spectra and for evaluating thermodynamic quantities of low-lying isomers. Solvation through H-bonding instead of direct coordination to Fe{sup +} is observed already at n = 3, indicating the completion of the first hydration shell with two H{sub 2}O molecules. Size dependent variations in the spectra for nmore » = 5–7 provide evidence for the second-shell completion at n = 6, where a linearly coordinated Fe{sup +}(H{sub 2}O){sub 2} subunit is solvated with four H{sub 2}O molecules. Overall spectral features for n = 3–8 agree well with those predicted for 2-coordinated structures. DFT calculations predict that such 2-coordinated structures are lowest in energy for smaller n. However, 4-coordinated isomers are predicted to be more stable for n = 7 and 8; the energy ordering is in conflict with the IR spectroscopic observation. Examination of free energy as a function of temperature suggests that the ordering of the isomers at warmer temperatures can be different from the ordering near 0 K. For n = 7 and 8, the 4-coordinated isomers should be observed at low temperatures because they are lowest in enthalpy. Meanwhile, outer-shell waters in the 2-coordinated structures are bound less rigidly; their contribution to entropy is rather large. The 2-coordinated structures become abundant at warmer temperatures, owing to the entropy effect.« less

Amino Acid Side Chain Interactions in the Presence of Salts

PubMed Central

Hassan, Sergio A.

2005-01-01

The effects of salt on the intermolecular interactions between polar/charged amino acids are investigated through molecular dynamics simulations. The mean forces and associated potentials are calculated for NaCl salt in the 0–2 M concentration range at 298 K. It is found that the addition of salt may stabilize or destabilize the interactions, depending on the nature of the interacting molecules. The degree of (de)stabilization is quantified, and the origin of the salt-dependent modulation is discussed based upon an analysis of solvent density profiles. To gain insight into the molecular origin of the salt modulation, spatial distribution functions (sdf’s) are calculated, revealing a high degree of solvent structuredness in all cases. The peaks in the sdf’s are consistent with long-range hydrogen-bonding networks connecting the solute hydrophilic groups, and that contribute to their intermolecular solvent-induced forces. The restructuring of water around the solutes as they dissociate from close contact is analyzed. This analysis offers clues on how the solvent structure modulates the effective intermolecular interactions in complex solutes. This modulation results from a critical balance between bulk electrostatic forces and those exerted by (i) the water molecules in the structured region between the monomers, which is disrupted by ions that transiently enter the hydration shells, and (ii) the ions in the hydration shells in direct interactions with the solutes. The implications of these findings in protein/ligand (noncovalent) association/dissociation mechanisms are briefly discussed. PMID:16479276

Interactions between Hofmeister anions and the binding pocket of a protein.

PubMed

Fox, Jerome M; Kang, Kyungtae; Sherman, Woody; Héroux, Annie; Sastry, G Madhavi; Baghbanzadeh, Mostafa; Lockett, Matthew R; Whitesides, George M

2015-03-25

This paper uses the binding pocket of human carbonic anhydrase II (HCAII, EC 4.2.1.1) as a tool to examine the properties of Hofmeister anions that determine (i) where, and how strongly, they associate with concavities on the surfaces of proteins and (ii) how, upon binding, they alter the structure of water within those concavities. Results from X-ray crystallography and isothermal titration calorimetry show that most anions associate with the binding pocket of HCAII by forming inner-sphere ion pairs with the Zn(2+) cofactor. In these ion pairs, the free energy of anion-Zn(2+) association is inversely proportional to the free energetic cost of anion dehydration; this relationship is consistent with the mechanism of ion pair formation suggested by the "law of matching water affinities". Iodide and bromide anions also associate with a hydrophobic declivity in the wall of the binding pocket. Molecular dynamics simulations suggest that anions, upon associating with Zn(2+), trigger rearrangements of water that extend up to 8 Å away from their surfaces. These findings expand the range of interactions previously thought to occur between ions and proteins by suggesting that (i) weakly hydrated anions can bind complementarily shaped hydrophobic declivities, and that (ii) ion-induced rearrangements of water within protein concavities can (in contrast with similar rearrangements in bulk water) extend well beyond the first hydration shells of the ions that trigger them. This study paints a picture of Hofmeister anions as a set of structurally varied ligands that differ in size, shape, and affinity for water and, thus, in their ability to bind to—and to alter the charge and hydration structure of—polar, nonpolar, and topographically complex concavities on the surfaces of proteins.

First Principles Simulations fo the Supercritical Behavior of Ore Forming Fluids

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

Weare, John H

2013-04-19

Abstract of Selected Research Progress: I. First-principles simulation of solvation structure and deprotonation reactions of ore forming metal ions in very nonideal solutions: Advances in algorithms and computational performance achieved in this grant period have allowed the atomic level dynamical simulation of complex nanoscale materials using interparticle forces calculated directly from an accurate density functional solution to the electronic Schr dinger equation (ab-initio molecular dynamics, AIMD). Focus of this program was on the prediction and analysis of the properties of environmentally important ions in aqueous solutions. AIMD methods have provided chemical interpretations of these very complex systems with an unprecedentedmore » level of accuracy and detail. The structure of the solvation region neighboring a highly charged metal ion (e.g., 3+) in an aqueous solution is very different from that of bulk water. The many-body behaviors (polarization, charge transfer, etc.) of the ion-water and water-water interactions in this region are difficult to capture with conventional empirical potentials. However, a large numbers of waters (up to 128 waters) are required to fully describe chemical events in the extended hydrations shells and long simulation times are needed to reliably sample the system. Taken together this makes simulation at the 1st principles level a very large computational problem. Our AIMD simulation results using these methods agree with the measured octahedral structure of the 1st solvation shell of Al3+ at the 1st shell boundary and a calculated radius of 1.937 (exp. 1.9). Our calculated average 2nd shell radius agrees remarkably well with the measured radius, 4.093 calculated vs. the measured value of 4.0-4.15 . Less can be experimentally determined about the structure of the 2nd shell. Our simulations show that this shell contains roughly 12 water molecules, which are trigonally coordinated to the 1st shell waters. This structure cannot be measured directly. However, the number of 2nd shell water molecules predicted by the simulation is consistent with experimental estimates. Tetrahedral bulk water coordination reappears just after the 2nd shell. Simulations with 128 waters are close to the maximum size that can effectively be performed with present day methods. While the time scale of our simulation are not long enough to observe transfers of waters from the 1st to the 2nd shell, we do see transfers occurring on a picosecond time scale between the 2nd shell and 3rd shell via an associative mechanism. This is faster than, but consistent with, the results of measurements on the more tightly bound Cr3+ system. For high temperature simulations, proton transfers occur in the solvation shells leading to transient hydrolysis species. The reaction coordinate for proton transfer involves the coordinates of neighboring solvent waters as in the Grotis mechanism for proton transfer in bulk water. Directly removing a proton from the hexaqua Al3+ ion leads to a much more labile solvation shell and to a five coordinated Al3+ ion. This is consistent with very recent rate measurements of ligand exchange and the conjugate base labilization effect. For the Al3+-H2O system results for high but subcritical temperatures are qualitatively similar to room temperature simulations. However, preliminary simulations for supercritical temperatures (750K) suggest that there may be a dramatic change in behavior in the hydration structure of ions for these temperatures. For transition metal ions the presence of d valence electrons plays a significant role in the behavior of the system. Our preliminary results for the Fe3+ ion suggest that this ion which is larger radius than the Al3+ ion has somewhat less rigid 1st and 2nd solvation shell. II. Gibbs Ensemble Monte Carlo Simulation of Vapor/Liquid and Metastable Liquid/Liquid Phase Equilibria in the CO2-CH4-N2 System Many fluid inclusions have compositions in the system CO2-CH4-N2. Estimates of the saturation pressures, compositions and volumetric properties of coexisting phases in the unaries, binaries and the ternary of this system have been obtained from simulations using the Gibbs Ensemble Monte Carlo method. The temperature and pressure range considered include liquid/vapor, gas/gas and metastable liquid/liquid regions. All the molecular interactions in the system were described with two-body Lennard-Jones potentials requiring only two temperature independent parameters for interactions between like molecules. The Berthhelot-Lorentz rules are used to define the Lennard-Jones interactions for unlike molecules with one additional temperature independent mixing parameter. The equilibrium compositions and molar volumes of the coexisting phases in all the mixtures are predicted with accuracy close to that of the data. These results, particularly for the phase densities and critical parameters, are considerably closer to the observed values than those that have been reported using equation of state methods(116). For very low temperatures liquid/metastable liquid/vapor coexistence was observed for the CO2-N2 and the CH4-CO2 systems, e.g. the L1L2V line. The possibility of gas-gas coexistence for the binary N2-CO2 at high temperatures and pressures was also investigated but not observed.« less

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

Varanasi, S. R., E-mail: s.raovaranasi@uq.edu.au, E-mail: guskova@ipfdd.de; John, A.; Guskova, O. A., E-mail: s.raovaranasi@uq.edu.au, E-mail: guskova@ipfdd.de

Fullerene C{sub 60} sub-colloidal particle with diameter ∼1 nm represents a boundary case between small and large hydrophobic solutes on the length scale of hydrophobic hydration. In the present paper, a molecular dynamics simulation is performed to investigate this complex phenomenon for bare C{sub 60} fullerene and its amphiphilic/charged derivatives, so called shape amphiphiles. Since most of the unique properties of water originate from the pattern of hydrogen bond network and its dynamics, spatial, and orientational aspects of water in solvation shells around the solute surface having hydrophilic and hydrophobic regions are analyzed. Dynamical properties such as translational-rotational mobility, reorientationalmore » correlation and occupation time correlation functions of water molecules, and diffusion coefficients are also calculated. Slower dynamics of solvent molecules—water retardation—in the vicinity of the solutes is observed. Both the topological properties of hydrogen bond pattern and the “dangling” –OH groups that represent surface defects in water network are monitored. The fraction of such defect structures is increased near the hydrophobic cap of fullerenes. Some “dry” regions of C{sub 60} are observed which can be considered as signatures of surface dewetting. In an effort to provide molecular level insight into the thermodynamics of hydration, the free energy of solvation is determined for a family of fullerene particles using thermodynamic integration technique.« less

Water reorientation in the hydration shells of hydrophilic and hydrophobic solutes

NASA Astrophysics Data System (ADS)

Laage, Damien; Stirnemann, Guillaume; Hynes, James T.

2010-06-01

We discuss some key aspects of our recent theoretical work on water reorientation dynamics, which is important in a wide range of phenomena, including aqueous phase chemical reactions, protein folding, and drug binding to proteins and DNA. It is shown that, contrary to the standard conception that these dynamics are diffusional, the reorientation of a water molecule occurs by sudden, large amplitude angular jumps. The mechanism involves the exchange of one hydrogen bond for another by the reorienting water, and the process can be fruitfully viewed as a chemical reaction. The results for reorientation times, which can be well described analytically, are discussed in the context of the molecular level interpretation of recent ultrafast infrared spectroscopic results, focusing on the concepts of structure making/breaking and solvent ‘icebergs’.

The influence of ion hydration on nucleation and growth of LiF crystals in aqueous solution.

PubMed

Lanaro, G; Patey, G N

2018-01-14

Molecular dynamics (MD) simulations are employed to investigate crystal nucleation and growth in oversaturated aqueous LiF solutions. Results obtained for a range of temperatures provide evidence that the rate of crystal growth is determined by a substantial energy barrier (∼49 kJ mol -1 ) related to the loss of water from the ion hydration shells. Employing direct MD simulations, we do not observe spontaneous nucleation of LiF crystals at 300 K, but nucleation is easily observable in NVT simulations at 500 K. This contrasts with the NaCl case, where crystal nucleation is directly observed in similar simulations at 300 K. Based on these observations, together with a detailed analysis of ion clustering in metastable LiF solutions, we argue that the ion dehydration barrier also plays a key role in crystal nucleation. The hydration of the relatively small Li + and F - ions strongly influences the probability of forming large, crystal-like ion clusters, which are a necessary precursor to nucleation. This important factor is not accounted for in classical nucleation theory.

The influence of ion hydration on nucleation and growth of LiF crystals in aqueous solution

NASA Astrophysics Data System (ADS)

Lanaro, G.; Patey, G. N.

2018-01-01

Molecular dynamics (MD) simulations are employed to investigate crystal nucleation and growth in oversaturated aqueous LiF solutions. Results obtained for a range of temperatures provide evidence that the rate of crystal growth is determined by a substantial energy barrier (˜49 kJ mol-1) related to the loss of water from the ion hydration shells. Employing direct MD simulations, we do not observe spontaneous nucleation of LiF crystals at 300 K, but nucleation is easily observable in NVT simulations at 500 K. This contrasts with the NaCl case, where crystal nucleation is directly observed in similar simulations at 300 K. Based on these observations, together with a detailed analysis of ion clustering in metastable LiF solutions, we argue that the ion dehydration barrier also plays a key role in crystal nucleation. The hydration of the relatively small Li+ and F- ions strongly influences the probability of forming large, crystal-like ion clusters, which are a necessary precursor to nucleation. This important factor is not accounted for in classical nucleation theory.

Interfacial Properties and Mechanisms Dominating Gas Hydrate Cohesion and Adhesion in Liquid and Vapor Hydrocarbon Phases.

PubMed

Hu, Sijia; Koh, Carolyn A

2017-10-24

The interfacial properties and mechanisms of gas hydrate systems play a major role in controlling their interparticle and surface interactions, which is desirable for nearly all energy applications of clathrate hydrates. In particular, preventing gas hydrate interparticle agglomeration and/or particle-surface deposition is critical to the prevention of gas hydrate blockages during the exploration and transportation of oil and gas subsea flow lines. These agglomeration and deposition processes are dominated by particle-particle cohesive forces and particle-surface adhesive force. In this study, we present the first direct measurements on the cohesive and adhesive forces studies of the CH 4 /C 2 H 6 gas hydrate in a liquid hydrocarbon-dominated system utilizing a high-pressure micromechanical force (HP-MMF) apparatus. A CH 4 /C 2 H 6 gas mixture was used as the gas hydrate former in the model liquid hydrocarbon phase. For the cohesive force baseline test, it was found that the addition of liquid hydrocarbon changed the interfacial tension and contact angle of water in the liquid hydrocarbon compared to water in the gas phase, resulting in a force of 23.5 ± 2.5 mN m -1 at 3.45 MPa and 274 K for a 2 h annealing time period in which hydrate shell growth occurs. It was observed that the cohesive force was inversely proportional to the annealing time, whereas the force increased with increasing contact time. For a longer contact time (>12 h), the force could not be measured because the two hydrate particles adhered permanently to form one large particle. The particle-surface adhesive force in the model liquid hydrocarbon was measured to be 5.3 ± 1.1 mN m -1 under the same experimental condition. Finally, with a 1 h contact time, the hydrate particle and the carbon steel (CS) surface were sintered together and the force was higher than what could be measured by the current apparatus. A possible mechanism is presented in this article to describe the effect of contact time on the particle-particle cohesive force based on the capillary liquid bridge model. A model adapted from the capillary liquid bridge equation has been used to predict the particle-particle cohesive force as a function of contact time, showing close agreement with the experimental data. By comparing the cohesive forces results from gas hydrates for both gas and liquid bulk phases, the surface free energy of a hydrate particle was calculated and found to dominate the changes in the interaction forces with different continuous bulk phases.

Simulation study of sulfonate cluster swelling in ionomers

NASA Astrophysics Data System (ADS)

Allahyarov, Elshad; Taylor, Philip L.; Löwen, Hartmut

2009-12-01

We have performed simulations to study how increasing humidity affects the structure of Nafion-like ionomers under conditions of low sulfonate concentration and low humidity. At the onset of membrane hydration, the clusters split into smaller parts. These subsequently swell, but then maintain constant the number of sulfonates per cluster. We find that the distribution of water in low-sulfonate membranes depends strongly on the sulfonate concentration. For a relatively low sulfonate concentration, nearly all the side-chain terminal groups are within cluster formations, and the average water loading per cluster matches the water content of membrane. However, for a relatively higher sulfonate concentration the water-to-sulfonate ratio becomes nonuniform. The clusters become wetter, while the intercluster bridges become drier. We note the formation of unusual shells of water-rich material that surround the sulfonate clusters.

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.

Characterization via atomic force microscopy of discrete plasticity in collagen fibrils from mechanically overloaded tendons: Nano-scale structural changes mimic rope failure.

PubMed

Baldwin, Samuel J; Kreplak, Laurent; Lee, J Michael

2016-07-01

Tendons exposed to tensile overload show a structural alteration at the fibril scale termed discrete plasticity. Serial kinks appear along individual collagen fibrils that are susceptible to enzymatic digestion and are thermally unstable. Using atomic force microscopy we mapped the topography and mechanical properties in dehydrated and hydrated states of 25 control fibrils and 25 fibrils displaying periodic kinks, extracted from overloaded bovine tail tendons. Using the measured modulus of the hydrated fibrils as a probe of molecular density, we observed a non-linear negative correlation between molecular density and kink density of individual fibrils. This is accompanied by an increase in water uptake with kink density and a doubling of the coefficient of variation of the modulus between kinked, and control fibrils. The mechanical property maps of kinked collagen fibrils show radial heterogeneity that can be modeled as a high-density core surrounded by a low-density shell. The core of the fibril contains the kink structures characteristic of discrete plasticity; separated by inter-kink regions, which often retain the D-banding structure. We propose that the shell and kink structures mimic characteristic damage motifs observed in laid rope strands. Copyright © 2016 Elsevier Ltd. All rights reserved.

Anisotropic mechanical behaviors and their structural dependences of crossed-lamellar structure in a bivalve shell.

PubMed

Jiao, D; Liu, Z Q; Qu, R T; Zhang, Z F

2016-02-01

Crossed-lamellar structure is one of the most common organizations found in mollusk shells and may serve as a natural mimetic model for designing bio-inspired synthetic materials. Nonetheless, the mechanical behaviors and corresponding mechanisms have rarely been investigated for individual macro-layer of such structure. The integrated effects of orientation and hydration also remain unclear. In this study, the mechanical behaviors and their structural dependences of pure crossed-lamellar structure in Saxidomus purpuratus shell were systematically examined by three-point bending and compression tests. Mechanical properties and fracture mechanisms were revealed to depend strongly on the orientation, hydration state and loading condition. Three basic cracking modes of inter-platelet, trans-platelet, and along the interfaces between first-order lamellae were identified, and the interfacial separation was enhanced by hydration. Macroscopic compressive fracture was accomplished through axial splitting during which multiple toughening mechanisms were activated. The competition among different cracking modes was quantitatively evaluated by analyzing their driving stresses and resistances from fundamental mechanics. This study helps to clarify the mechanical behaviors of naturally occurring crossed-lamellar structure, and accordingly, aids in designing new bio-inspired synthetic materials by mimicking it. Copyright © 2015 Elsevier B.V. All rights reserved.

Transport of ions through a (6,6) carbon nanotube under electric fields

NASA Astrophysics Data System (ADS)

Shen, Li; Xu, Zhen; Zhou, Zhe-Wei; Hu, Guo-Hui

2014-11-01

The transport of water and ions through carbon nanotubes (CNTs) is crucial in nanotechnology and biotechnology. Previous investigation indicated that the ions can hardly pass through (6,6) CNTs due to their hydrated shells. In the present study, utilizing molecular dynamics simulation, it is shown that the energy barrier mainly originating from the hydrated water molecules could be overcome by applying an electric field large enough in the CNT axis direction. Potential of mean force is calculated to show the reduction of energy barrier when the electric field is present for (Na+, K+, Cl-) ions. Consequently, ionic flux through (6,6) CNTs can be found once the electric field becomes larger than a threshold value. The variation of the coordination numbers of ions at different locations from the bulk to the center of the CNT is also explored to elaborate this dynamic process. The thresholds of the electric field are different for Na+, K+, and Cl- due to their characteristics. This consequence might be potentially applied in ion selectivity in the future.

Influence of Hydration on Proton Transfer in the Guanine-Cytosine Radical Cation (G•+-C) Base Pair: A Density Functional Theory Study

PubMed Central

Kumar, Anil; Sevilla, Michael D.

2009-01-01

On one-electron oxidation all molecules including DNA bases become more acidic in nature. For the GC base pair experiments suggest that a facile proton transfer takes place in the G•+-C base pair from N1 of G•+ to N3 of cytosine. This intra-base pair proton transfer reaction has been extensively considered using theoretical methods for the gas phase and it is predicted that the proton transfer is slightly unfavorable in disagreement with experiment. In the present study, we consider the effect of the first hydration layer on the proton transfer reaction in G•+-C by the use of density functional theory (DFT), B3LYP/6-31+G** calculations of the G•+-C base pair in the presence of 6 and 11 water molecules. Under the influence of hydration of 11 waters, a facile proton transfer from N1 of G•+ to N3 of C is predicted. The zero point energy (ZPE) corrected forward and backward energy barriers, for the proton transfer from N1 of G•+ to N3 of C, was found to be 1.4 and 2.6 kcal/mol, respectively. The proton transferred G•-(H+)C + 11H2O was found to be 1.2 kcal/mol more stable than G•+-C + 11H2O in agreement with experiment. The present calculation demonstrates that the inclusion of the first hydration shell around G•+-C base pair has an important effect on the internal proton transfer energetics. PMID:19485319

Direct measurements of the interactions between clathrate hydrate particles and water droplets.

PubMed

Liu, Chenwei; Li, Mingzhong; Zhang, Guodong; Koh, Carolyn A

2015-08-14

Clathrate hydrate particle agglomeration is often considered to be one of the key limiting factors in plug formation. The hydrate particle-water interaction can play a critical role in describing hydrate agglomeration, yet is severely underexplored. Therefore, this work investigates the interactions between water droplets and cyclopentane hydrate particles using a micromechanical force (MMF) apparatus. Specifically, the effect of contact time, temperature/subcooling, contact area, and the addition of Sorbitane monooleate (Span 80) surfactant on the water droplet-hydrate particle interaction behavior are studied. The measurements indicate that hydrate formation during the measurement would increase the water-hydrate interaction force significantly. The results also indicate that the contact time, subcooling and concentration of cyclopentane, which determine the hydrate formation rate and hydrate amount, will affect the hydrate-water interaction force. In addition, the interaction forces also increase with the water-hydrate contact area. The addition of Span 80 surfactant induces a change in the hydrate morphology and renders the interfaces stable versus unstable (leading to coalescence), and the contact force can affect the hydrate-water interaction behavior significantly. Compared with the hydrate-hydrate cohesion force (measured in cyclopentane), the hydrate-water adhesion force is an order of magnitude larger. These new measurements can help to provide new and critical insights into the hydrate agglomeration process and potential strategies to control this process.

Aqueous solubility diagrams for cementitious waste stabilization systems. 3. Mechanism of zinc immobilizaton by calcium silicate hydrate.

PubMed

Tommaseo, C E; Kersten, M

2002-07-01

Zinc oxide was added during hydration of alite (C3S) as an analogue for solidification/stabilization by cement of metal-bearing hazardous waste. Curing of samples was stopped at various intervals between 8 h and 100 d, and the reaction products were analyzed by both X-ray diffraction (XRD) and X-ray absorption spectroscopy (EXAFS at Zn, Ca, and Si K-edges). Calcium zincate hydrate (CaZn2(OH)6 x 2H2O) initially formed together with calcium silicate hydrate (CSH) vanishes from X-ray diffractograms after 14 d, and no other crystalline Zn-bearing phase could be detected thereafter. EXAFS Zn K-edge data analysis reveals that Zn(O,OH)4 tetrahedra continue to determine the first shell coordination. However, a new Zn-Si bond appears in the second coordination shell as indicated by both Zn K-edge and Si K-edge EXAFS. Together with the Ca-Zn and Ca-Ca shells derived from the Ca K-edge EXAFS spectra, a structural model for the site occupation of Zn in CSH is proposed, whereby the Zn(O,OH)4 tetrahedra are bound in layer rather than interlayer positions substituting for the silicate bridging tetrahedra and/or at terminal silicate chain sites. This structural model enables ultimately the formulation of a thermodyamic Lippmann model to predict the aqueous solubility of Zn in solid solution with a CSH phase of a Ca/Si ratio fixed to unity.

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

Anderson, Brian B.; Kirkegaard, Marie C.; Miskowiec, Andrew J.

Uranyl fluoride (UO 2F 2) is a hygroscopic powder with two main structural phases: an anhydrous crystal and a partially hydrated crystal of the same R¯3m symmetry. The formally closed-shell electron structure of anhydrous UO 2F 2 is amenable to density functional theory calculations. We use density functional perturbation theory (DFPT) to calculate the vibrational frequencies of the anhydrous crystal structure and employ complementary inelastic neutron scattering and temperature-dependent Raman scattering to validate those frequencies. As a model closed-shell actinide, we investigated the effect of LDA, GGA, and non-local vdW functionals as well as the spherically-averaged Hubbard +U correction onmore » vibrational frequencies, electronic structure, and geometry of anhydrous UO 2F 2. A particular choice of U eff = 5.5 eV yields the correct U Oyl bond distance and vibrational frequencies for the characteristic Eg and A1g modes that are within the resolution of experiment. Inelastic neutron scattering and Raman scattering suggest a degree of water coupling to the lattice vibrations in the more experimentally accessible partially hydrated UO 2F 2 system, with the symmetric O-U-O stretching vibration shifted approximately 47 cm -1 lower in energy compared to the anhydrous structure. Evidence of water interaction with the uranyl ion is present from a two-peak decomposition of the uranyl stretching vibration in the Raman spectra and anion hydrogen stretching vibrations in the inelastic neutron scattering spectra. A first-order dehydration phase transition temperature is definitively identified to be 125 °C using temperature-dependent Raman scattering.« less

Reduced Point Charge Models of Proteins: Effect of Protein-Water Interactions in Molecular Dynamics Simulations of Ubiquitin Systems.

PubMed

Leherte, Laurence; Vercauteren, Daniel P

2017-10-26

We investigate the influence of various solvent models on the structural stability and protein-water interface of three ubiquitin complexes (PDB access codes: 1Q0W , 2MBB , 2G3Q ) modeled using the Amber99sb force field (FF) and two different point charge distributions. A previously developed reduced point charge model (RPCM), wherein each amino acid residue is described by a limited number of point charges, is tested and compared to its all-atom (AA) version. The complexes are solvated in TIP4P-Ew or TIP3P type water molecules, involving either the scaling of the Lennard-Jones protein-O water interaction parameters, or the coarse-grain (CG) SIRAH water description. The best agreements between the RPCM and AA models were obtained for structural, protein-water, and ligand-ubiquitin properties when using the TIP4P-Ew water FF with a scaling factor γ of 0.7. At the RPCM level, a decrease in γ, or the inclusion of SIRAH particles, allows weakening of the protein-water interactions. It results in a slight collapse of the protein structure and a less compact hydration shell and, thus, in a decrease in the number of protein-water and water-water H-bonds. The dynamics of the surface protein atoms and of the water shell molecules are also slightly refrained, which allow the generation of stable RPCM trajectories.

The water retention curve and relative permeability for gas production from hydrate-bearing sediments: pore-network model simulation

NASA Astrophysics Data System (ADS)

Mahabadi, Nariman; Dai, Sheng; Seol, Yongkoo; Sup Yun, Tae; Jang, Jaewon

2016-08-01

The water retention curve and relative permeability are critical to predict gas and water production from hydrate-bearing sediments. However, values for key parameters that characterize gas and water flows during hydrate dissociation have not been identified due to experimental challenges. This study utilizes the combined techniques of micro-focus X-ray computed tomography (CT) and pore-network model simulation to identify proper values for those key parameters, such as gas entry pressure, residual water saturation, and curve fitting values. Hydrates with various saturation and morphology are realized in the pore-network that was extracted from micron-resolution CT images of sediments recovered from the hydrate deposit at the Mallik site, and then the processes of gas invasion, hydrate dissociation, gas expansion, and gas and water permeability are simulated. Results show that greater hydrate saturation in sediments lead to higher gas entry pressure, higher residual water saturation, and steeper water retention curve. An increase in hydrate saturation decreases gas permeability but has marginal effects on water permeability in sediments with uniformly distributed hydrate. Hydrate morphology has more significant impacts than hydrate saturation on relative permeability. Sediments with heterogeneously distributed hydrate tend to result in lower residual water saturation and higher gas and water permeability. In this sense, the Brooks-Corey model that uses two fitting parameters individually for gas and water permeability properly capture the effect of hydrate saturation and morphology on gas and water flows in hydrate-bearing sediments.

Complex admixtures of clathrate hydrates in a water desalination method

DOEpatents

Simmons, Blake A [San Francisco, CA; Bradshaw, Robert W [Livermore, CA; Dedrick, Daniel E [Berkeley, CA; Anderson, David W [Riverbank, CA

2009-07-14

Disclosed is a method that achieves water desalination by utilizing and optimizing clathrate hydrate phenomena. Clathrate hydrates are crystalline compounds of gas and water that desalinate water by excluding salt molecules during crystallization. Contacting a hydrate forming gaseous species with water will spontaneously form hydrates at specific temperatures and pressures through the extraction of water molecules from the bulk phase followed by crystallite nucleation. Subsequent dissociation of pure hydrates yields fresh water and, if operated correctly, allows the hydrate-forming gas to be efficiently recycled into the process stream.

Seeding hydrate formation in water-saturated sand with dissolved-phase methane obtained from hydrate dissolution: A progress report

USGS Publications Warehouse

Waite, William F.; Osegovic, J.P.; Winters, William J.; Max, M.D.; Mason, David H.

2008-01-01

An isobaric flow loop added to the Gas Hydrate And Sediment Test Laboratory Instrument (GHASTLI) is being investigated as a means of rapidly forming methane hydrate in watersaturated sand from methane dissolved in water. Water circulates through a relatively warm source chamber, dissolving granular methane hydrate that was pre-made from seed ice, then enters a colder hydrate growth chamber where hydrate can precipitate in a water-saturated sand pack. Hydrate dissolution in the source chamber imparts a known methane concentration to the circulating water, and hydrate particles from the source chamber entrained in the circulating water can become nucleation sites to hasten the onset of hydrate formation in the growth chamber. Initial results suggest hydrate grows rapidly near the growth chamber inlet. Techniques for establishing homogeneous hydrate formation throughout the sand pack are being developed.

Enzyme microheterogeneous hydration and stabilization in supercritical carbon dioxide.

PubMed

Silveira, Rodrigo L; Martínez, Julian; Skaf, Munir S; Martínez, Leandro

2012-05-17

Supercritical carbon dioxide is a promising green-chemistry solvent for many enzyme-catalyzed chemical reactions, yet the striking stability of some enzymes in such unconventional environments is not well understood. Here, we investigate the stabilization of the Candida antarctica Lipase B (CALB) in supercritical carbon dioxide-water biphasic systems using molecular dynamics simulations. The preservation of the enzyme structure and optimal activity depend on the presence of small amounts of water in the supercritical dispersing medium. When the protein is at least partially hydrated, water molecules bind to specific sites on the enzyme surface and prevent carbon dioxide from penetrating its catalytic core. Strikingly, water and supercritical carbon dioxide cover the protein surface quite heterogeneously. In the first solvation layer, the hydrophilic residues at the surface of the protein are able to pin down patches of water, whereas carbon dioxide solvates preferentially hydrophobic surface residues. In the outer solvation shells, water molecules tend to cluster predominantly on top of the larger water patches of the first solvation layer instead of spreading evenly around the remainder of the protein surface. For CALB, this exposes the substrate-binding region of the enzyme to carbon dioxide, possibly facilitating diffusion of nonpolar substrates into the catalytic funnel. Therefore, by means of microheterogeneous solvation, enhanced accessibility of hydrophobic substrates to the active site can be achieved, while preserving the functional structure of the enzyme. Our results provide a molecular picture on the nature of the stability of proteins in nonaqueous media.

Evaluation of the possible presence of clathrate hydrates in Europa's icy shell or seafloor

NASA Astrophysics Data System (ADS)

Prieto-Ballesteros, Olga; Kargel, Jeffrey S.; Fernández-Sampedro, Maite; Selsis, Franck; Martínez, Eduardo Sebastián; Hogenboom, David L.

2005-10-01

Several substances besides water ice have been detected on the surface of Europa by spectroscopic sensors, including CO 2, SO 2, and H 2S. These substances might occur as pure crystalline ices, as vitreous mixtures, or as clathrate hydrate phases, depending on the system conditions and the history of the material. Clathrate hydrates are crystalline compounds in which an expanded water ice lattice forms cages that contain gas molecules. The molecular gases that may constitute Europan clathrate hydrates may have two possible ultimate origins: they might be primordial condensates from the interstellar medium, solar nebula, or jovian subnebula, or they might be secondary products generated as a consequence of the geological evolution and complex chemical processing of the satellite. Primordial ices and volatile-bearing compounds would be difficult to preserve in pristine form in Europa without further processing because of its active geological history. But dissociated volatiles derived from differentiation of a chondritic rock or cometary precursor may have produced secondary clathrates that may be present now. We have evaluated the current stability of several types of clathrate hydrates in the crust and the ocean of Europa. The depth at which the clathrates of SO 2, CO 2, H 2S, and CH 4 are stable have been obtained using both the temperatures observed in the surface [Spencer, J.R., Tamppari, L.K., Martin, T.Z., Travis, L.D., 1999. Temperatures on Europa from Galileo photopolarimeter-radiometer: Nighttime thermal anomalies. Science 284, 1514-1516] and thermal models for the crust. In addition, their densities have been calculated in order to determine their buoyancy in the ocean, obtaining different results depending upon the salinity of the ocean and type of clathrate. For instance, assuming a eutectic composition of the system MgSO 4sbnd H 2O for the ocean, CO 2, H 2S, and CH 4 clathrates would float but SO 2 clathrate would sink to the seafloor; an ocean of much lower salinity would allow all these clathrates to sink, except that CH 4 clathrate would still float. Many geological processes may be driven or affected by the formation, presence, and destruction of clathrates in Europa such as explosive cryomagmatic activity [Stevenson, D.J., 1982. Volcanism and igneous processes in small icy satellites. Nature 298, 142-144], partial differentiation of the crust driven by its clathration, or the local retention of heat within or beneath clathrate-rich layers because of the low thermal conductivity of clathrate hydrates [Ross, R.G., Kargel, J.S., 1998. Thermal conductivity of Solar System ices, with special reference to martian polar caps. In: Schmitt, B., De Berg, C., Festou, M. (Eds.), Solar System Ices. Kluwer Academic, Dordrecht, pp. 33-62]. On the surface, destabilization of these minerals and compounds, triggered by fracture decompression or heating could result in formation of chaotic terrain morphologies, a mechanism that also has been proposed for some martian chaotic terrains [Tanaka, K.L., Kargel, J.S., MacKinnon, D.J., Hare, T.M., Hoffman, N., 2002. Catastrophic erosion of Hellas basin rim on Mars induced by magmatic intrusion into volatile-rich rocks. Geophys. Res. Lett. 29 (8); Kargel, J.S., Prieto-Ballesteros, O., Tanaka K.L., 2003. Is clathrate hydrate dissociation responsible for chaotic terrains on Earth, Mars, Europa, and Triton? Geophys. Res. 5. Abstract 14252]. Models of the evolution of the ice shell of Europa might take into account the presence of clathrate hydrates because if gases are vented from the silicate interior to the water ocean, they first would dissolve in the ocean and then, if the gas concentrations are sufficient, may crystallize. If any methane releases occur in Europa by hydrothermal or biological activity, they also might form clathrates. Then, from both geological and astrobiological perspectives, future missions to Europa should carry instrumentation capable of clathrate hydrate detection.

Synthesis of core-shell AlOOH hollow nanospheres by reacting Al nanoparticles with water

NASA Astrophysics Data System (ADS)

Lozhkomoev, A. S.; Glazkova, E. A.; Bakina, O. V.; Lerner, M. I.; Gotman, I.; Gutmanas, E. Y.; Kazantsev, S. O.; Psakhie, S. G.

2016-05-01

A novel route for the synthesis of boehmite nanospheres with a hollow core and the shell composed of highly crumpled AlOOH nanosheets by oxidizing Al nanopowder in pure water under mild processing conditions is described. The stepwise events of Al transformation into boehmite are followed by monitoring the pH in the reaction medium. A mechanism of formation of hollow AlOOH nanospheres with a well-defined shape and crystallinity is proposed which includes the hydration of the Al oxide passivation layer, local corrosion of metallic Al accompanied by hydrogen evolution, the rupture of the protective layer, the dissolution of Al from the particle interior and the deposition of AlOOH nanosheets on the outer surface. In contrast to previously reported methods of boehmite nanoparticle synthesis, the proposed method is simple, and environmentally friendly and allows the generation of hydrogen gas as a by-product. Due to their high surface area and high, slit-shaped nanoporosity, the synthesized AlOOH nanostructures hold promise for the development of more effective catalysts, adsorbents, vaccines and drug carriers.

Polymeric microcapsules with switchable mechanical properties for self-healing concrete: synthesis, characterisation and proof of concept

NASA Astrophysics Data System (ADS)

Kanellopoulos, A.; Giannaros, P.; Palmer, D.; Kerr, A.; Al-Tabbaa, A.

2017-04-01

Microcapsules, with sodium silicate solution as core, were produced using complex coacervation in a double, oil-in-water-in oil, emulsion system. The shell material was a gelatin-acacia gum crosslinked coacervate and the produced microcapsules had diameters ranging from 300 to 700 μm. The shell material designed with switchable mechanical properties. When it is hydrated exhibits soft and ‘rubbery’ behaviour and, when dried, transitions to a stiff and ‘glassy’ material. The microcapsules survived drying and rehydrating cycles and preserved their structural integrity when exposed to highly alkaline solutions that mimic the pH environment of concrete. Microscopy revealed that the shell thickness of the microcapsules varies across their perimeter from 5 to 20 μm. Thermal analysis showed that the produced microcapsules were very stable up to 190 °C. Proof of concept investigation has demonstrated that the microcapsules successfully survive and function when exposed to a cement-based matrix. Observations showed that the microcapsules survive mixing with cement and rupture successfully upon crack formation releasing the encapsulated sodium silicate solution.

Elucidating hydrogen oxidation/evolution kinetics in base and acid by enhanced activities at the optimized Pt shell thickness on the Ru core

DOE PAGES

Elbert, Katherine; Hu, Jue; Ma, Zhong; ...

2015-10-05

Hydrogen oxidation and evolution on Pt in acid are facile processes, while in alkaline electrolytes, they are 2 orders of magnitude slower. Thus, developing catalysts that are more active than Pt for these two reactions is important for advancing the performance of anion exchange membrane fuel cells and water electrolyzers. Herein, we detail a 4-fold enhancement of Pt mass activity that we achieved using single-crystalline Ru@Pt core–shell nanoparticles with two-monolayer-thick Pt shells, which doubles the activity on Pt–Ru alloy nanocatalysts. For Pt specific activity, the two- and one-monolayer-thick Pt shells exhibited enhancement factors of 3.1 and 2.3, respectively, compared tomore » the Pt nanocatalysts in base, differing considerably from the values of 1 and 0.4, respectively, in acid. To explain such behavior and the orders of magnitude difference in activity on going from acid to base, we performed kinetic analyses of polarization curves over a wide range of potential from –250 to 250 mV using the dual-pathway kinetic equation. From acid to base, the activation free energies increase the most for the Volmer reaction, resulting in a switch of the rate-determining step from the Tafel to the Volmer reaction, and a shift to a weaker optimal hydrogen binding energy. Furthermore, the much higher activation barrier for the Volmer reaction in base than in acid is ascribed to one or both of the two catalyst-insensitive factors: slower transport of OH – than H + in water and a stronger O–H bond in water molecules (HO–H) than in hydrated protons (H 2O–H +).« less

Structural Interpretation of the Large Slowdown of Water Dynamics at Stacked Phospholipid Membranes for Decreasing Hydration Level: All-Atom Molecular Dynamics

DOE PAGES

Calero, Carles; Stanley, H.; Franzese, Giancarlo

2016-04-27

Hydration water determines the stability and function of phospholipid membranes as well as the interaction of membranes with other molecules. Experiments and simulations have shown that water dynamics slows down dramatically as the hydration decreases, suggesting that the interfacial water that dominates the average dynamics at low hydration is slower than water away from the membrane. Here, based on all-atom molecular dynamics simulations, we provide an interpretation of the slowdown of interfacial water in terms of the structure and dynamics of water–water and water–lipid hydrogen bonds (HBs). We calculate the rotational and translational slowdown of the dynamics of water confinedmore » in stacked phospholipid membranes at different levels of hydration, from completely hydrated to poorly hydrated membranes. For all hydrations, we analyze the distribution of HBs and find that water–lipids HBs last longer than water–water HBs and that at low hydration most of the water is in the interior of the membrane. We also show that water–water HBs become more persistent as the hydration is lowered. We attribute this effect (i) to HBs between water molecules that form, in turn, persistent HBs with lipids; (ii) to the hindering of the H-bonding switching between water molecules due to the lower water density at the interface; and (iii) to the higher probability of water–lipid HBs as the hydration decreases. Lastly, our interpretation of the large dynamic slowdown in water under dehydration is potentially relevant in understanding membrane biophysics at different hydration levels.« less

On the molecular origin of the cooperative coil-to-globule transition of poly(N-isopropylacrylamide) in water† †Electronic supplementary information (ESI) available: Stereochemistry and initial conformation of PNIPAM 30-mer; pair distribution functions of PNIPAM methyl groups; average time of transitions of dihedral angles; distribution of methyl dihedral angles; temperature dependence of average number of hydration water molecules; correlation between hydrogen bonding of water molecules per repeating unit in the FHS and end to end distance and correlation between PNIPAM–water hydrogen bonding and end to end distance. Time evolution of PNIPAM with the first hydration shell: movie FHSpnipam.avi. See DOI: 10.1039/c8cp00537k

PubMed Central

Zaccarelli, E.

2018-01-01

By means of atomistic molecular dynamics simulations we investigate the behaviour of poly(N-isopropylacrylamide), PNIPAM, in water at temperatures below and above the lower critical solution temperature (LCST), including the undercooled regime. The transition between water soluble and insoluble states at the LCST is described as a cooperative process involving an intramolecular coil-to-globule transition preceding the aggregation of chains and the polymer precipitation. In this work we investigate the molecular origin of such cooperativity and the evolution of the hydration pattern in the undercooled polymer solution. The solution behaviour of an atactic 30-mer at high dilution is studied in the temperature interval from 243 to 323 K with a favourable comparison to available experimental data. In the water soluble states of PNIPAM we detect a correlation between polymer segmental dynamics and diffusion motion of bound water, occurring with the same activation energy. Simulation results show that below the coil-to-globule transition temperature PNIPAM is surrounded by a network of hydrogen bonded water molecules and that the cooperativity arises from the structuring of water clusters in proximity to hydrophobic groups. Differently, the perturbation of the hydrogen bond pattern involving water and amide groups occurs above the transition temperature. Altogether these findings reveal that even above the LCST PNIPAM remains largely hydrated and that the coil-to-globule transition is related with a significant rearrangement of the solvent in the proximity of the surface of the polymer. The comparison between the hydrogen bonding of water in the surrounding of PNIPAM isopropyl groups and in the bulk displays a decreased structuring of solvent at the hydrophobic polymer–water interface across the transition temperature, as expected because of the topological extension along the chain of such interface. No evidence of an upper critical solution temperature behaviour, postulated in theoretical and thermodynamics studies of PNIPAM aqueous solution, is observed in the low temperature domain. PMID:29619464

SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomolecules.

PubMed

Bardhan, Jaydeep; Park, Sanghyun; Makowski, Lee

2009-10-01

This paper describes a computational approach to estimating wide-angle X-ray solution scattering (WAXS) from proteins, which has been implemented in a computer program called SoftWAXS. The accuracy and efficiency of SoftWAXS are analyzed for analytically solvable model problems as well as for proteins. Key features of the approach include a numerical procedure for performing the required spherical averaging and explicit representation of the solute-solvent boundary and the surface of the hydration layer. These features allow the Fourier transform of the excluded volume and hydration layer to be computed directly and with high accuracy. This approach will allow future investigation of different treatments of the electron density in the hydration shell. Numerical results illustrate the differences between this approach to modeling the excluded volume and a widely used model that treats the excluded-volume function as a sum of Gaussians representing the individual atomic excluded volumes. Comparison of the results obtained here with those from explicit-solvent molecular dynamics clarifies shortcomings inherent to the representation of solvent as a time-averaged electron-density profile. In addition, an assessment is made of how the calculated scattering patterns depend on input parameters such as the solute-atom radii, the width of the hydration shell and the hydration-layer contrast. These results suggest that obtaining predictive calculations of high-resolution WAXS patterns may require sophisticated treatments of solvent.

Stepwise microhydration of aromatic amide cations: water solvation networks revealed by the infrared spectra of acetanilide+-(H2O)n clusters (n ≤ 3).

PubMed

Klyne, Johanna; Schmies, Matthias; Miyazaki, Mitsuhiko; Fujii, Masaaki; Dopfer, Otto

2018-01-31

The structure and activity of peptides and proteins strongly rely on their charge state and the interaction with their hydration environment. Here, infrared photodissociation (IRPD) spectra of size-selected microhydrated clusters of cationic acetanilide (AA + , N-phenylacetamide), AA + -(H 2 O) n with n ≤ 3, are analysed by dispersion-corrected density functional theory calculations at the ωB97X-D/aug-cc-pVTZ level to determine the stepwise microhydration process of this aromatic peptide model. The IRPD spectra are recorded in the informative X-H stretch (ν OH , ν NH , ν CH , amide A, 2800-3800 cm -1 ) and fingerprint (amide I-II, 1000-1900 cm -1 ) ranges to probe the preferred hydration motifs and the cluster growth. In the most stable AA + -(H 2 O) n structures, the H 2 O ligands solvate the acidic NH proton of the amide by forming a hydrogen-bonded solvent network, which strongly benefits from cooperative effects arising from the excess positive charge. Comparison with neutral AA-H 2 O reveals the strong impact of ionization on the acidity of the NH proton and the topology of the interaction potential. Comparison with related hydrated formanilide clusters demonstrates the influence of methylation of the amide group (H → CH 3 ) on the shape of the intermolecular potential and the structure of the hydration shell.

Modeling the hydration of mono-atomic anions from the gas phase to the bulk phase: the case of the halide ions F-, Cl-, and Br-.

PubMed

Trumm, Michael; Martínez, Yansel Omar Guerrero; Réal, Florent; Masella, Michel; Vallet, Valérie; Schimmelpfennig, Bernd

2012-01-28

In this work, we investigate the hydration of the halide ions fluoride, chloride, and bromide using classical molecular dynamics simulations at the 10 ns scale and based on a polarizable force-field approach, which treats explicitly the cooperative bond character of strong hydrogen bond networks. We have carried out a thorough analysis of the ab initio data at the MP2 or CCSD(T) level concerning anion/water clusters in gas phase to adjust the force-field parameters. In particular, we consider the anion static polarizabilities computed in gas phase using large atomic basis sets including additional diffuse functions. The information extracted from trajectories in solution shows well structured first hydration shells formed of 6.7, 7.0, and 7.6 water molecules at about 2.78 Å, 3.15 Å, and 3.36 Å for fluoride, chloride, and bromide, respectively. These results are in excellent agreement with the latest neutron- and x-ray diffraction studies. In addition, our model reproduces several other properties of halide ions in solution, such as diffusion coefficients, description of hydration processes, and exchange reactions. Moreover, it is also able to reproduce the electrostatic properties of the anions in solution (in terms of anion dipole moment) as reported by recent ab initio quantum simulations. All the results show the ability of the proposed model in predicting data, as well as the need of accounting explicitly for the cooperative character of strong hydrogen bonds to reproduce ab initio potential energy surfaces in a mean square sense and to build up a reliable force field. © 2012 American Institute of Physics

Dehydration of multilamellar fatty acid membranes: Towards a computational model of the stratum corneum

NASA Astrophysics Data System (ADS)

MacDermaid, Christopher M.; DeVane, Russell H.; Klein, Michael L.; Fiorin, Giacomo

2014-12-01

The level of hydration controls the cohesion between apposed lamellae of saturated free fatty acids found in the lipid matrix of stratum corneum, the outermost layer of mammalian skin. This multilamellar lipid matrix is highly impermeable to water and ions, so that the local hydration shell of its fatty acids may not always be in equilibrium with the acidity and relative humidity, which significantly change over a course of days during skin growth. The homeostasis of the stratum corneum at each moment of its growth likely requires a balance between two factors, which affect in opposite ways the diffusion of hydrophilic species through the stratum corneum: (i) an increase in water order as the lipid lamellae come in closer contact, and (ii) a decrease in water order as the fraction of charged fatty acids is lowered by pH. Herein molecular dynamics simulations are employed to estimate the impact of both effects on water molecules confined between lamellae of fatty acids. Under conditions where membrane undulations are energetically favorable, the charged fatty acids are able to sequester cations around points of contact between lamellae that are fully dehydrated, while essentially maintaining a multilamellar structure for the entire system. This observation suggests that the undulations of the fatty acid lamellae control the diffusion of hydrophilic species through the water phase by altering the positional and rotational order of water molecules in the embedded/occluded "droplets."

Influence of Sodium Chloride on the Formation and Dissociation Behavior of CO2 Gas Hydrates.

PubMed

Holzammer, Christine; Schicks, Judith M; Will, Stefan; Braeuer, Andreas S

2017-09-07

We present an experimental study on the formation and dissociation characteristics of carbon dioxide (CO 2 ) gas hydrates using Raman spectroscopy. The CO 2 hydrates were formed from sodium chloride/water solutions with salinities of 0-10 wt %, which were pressurized with liquid CO 2 in a stirred vessel at 6 MPa and a subcooling of 9.5 K. The formation of the CO 2 hydrate resulted in a hydrate gel where the solid hydrate can be considered as the continuous phase that includes small amounts of a dispersed liquid water-rich phase that has not been converted to hydrate. During the hydrate formation process we quantified the fraction of solid hydrate, x H , and the fraction of the dispersed liquid water-rich phase, x L , from the signature of the hydroxyl (OH)-stretching vibration of the hydrate gel. We found that the fraction of hydrate x H contained in the hydrate gel linearly depends on the salinity of the initial liquid water-rich phase. In addition, the ratio of CO 2 and water was analyzed in the liquid water-rich phase before hydrate formation, in the hydrate gel during growth and dissociation, and after its complete dissociation again in the liquid water-rich phase. We observed a supersaturation of CO 2 in the water-rich phase after complete dissociation of the hydrate gel and were able to show that the excess CO 2 exists as dispersed micro- or nanoscale liquid droplets in the liquid water-rich phase. These residual nano- and microdroplets could be a possible explanation for the so-called memory effect.

Revisiting a many-body model for water based on a single polarizable site: from gas phase clusters to liquid and air/liquid water systems.

PubMed

Réal, Florent; Vallet, Valérie; Flament, Jean-Pierre; Masella, Michel

2013-09-21

We present a revised version of the water many-body model TCPE [M. Masella and J.-P. Flament, J. Chem. Phys. 107, 9105 (1997)], which is based on a static three charge sites and a single polarizable site to model the molecular electrostatic properties of water, and on an anisotropic short range many-body energy term specially designed to accurately model hydrogen bonding in water. The parameters of the revised model, denoted TCPE/2013, are here developed to reproduce the ab initio energetic and geometrical properties of small water clusters (up to hexamers) and the repulsive water interactions occurring in cation first hydration shells. The model parameters have also been refined to reproduce two liquid water properties at ambient conditions, the density and the vaporization enthalpy. Thanks to its computational efficiency, the new model range of applicability was validated by performing simulations of liquid water over a wide range of temperatures and pressures, as well as by investigating water liquid/vapor interfaces over a large range of temperatures. It is shown to reproduce several important water properties at an accurate enough level of precision, such as the existence liquid water density maxima up to a pressure of 1000 atm, the water boiling temperature, the properties of the water critical point (temperature, pressure, and density), and the existence of a "singularity" temperature at about 225 K in the supercooled regime. This model appears thus to be particularly well-suited for characterizing ion hydration properties under different temperature and pressure conditions, as well as in different phases and interfaces.

Free energies and mechanisms of water exchange around Uranyl from first principles molecular dynamics

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

Atta-Fynn, Raymond; Bylaska, Eric J.; De Jong, Wibe A.

2012-02-01

From density functional theory (DFT) based ab initio (Car-Parrinello) metadynamics, we compute the activation energies and mechanisms of water exchange between the first and second hydration shells of aqueous Uranyl (UO{sub 2}{sup 2+}) using the primary hydration number of U as the reaction coordinate. The free energy and activation barrier of the water dissociation reaction [UO{sub 2}(OH{sub 2}){sub 5}]{sup 2+}(aq) {yields} [UO{sub 2}(OH{sub 2})4]{sup 2+}(aq) + H{sub 2}O are 0.7 kcal and 4.7 kcal/mol respectively. The free energy is in good agreement with previous theoretical (-2.7 to +1.2 kcal/mol) and experimental (0.5 to 2.2 kcal/mol) data. The associative reaction [UO{submore » 2}(OH{sub 2}){sub 5}]{sup 2+}(aq) + H{sub 2}O {yields} [UO{sub 2}(OH{sub 2})6]{sup 2+}(aq) is short-lived with a free energy and activation barrier of +7.9 kcal/mol and +8.9 kca/mol respectively; it is therefore classified as associative-interchange. On the basis of the free energy differences and activation barriers, we predict that the dominant exchange mechanism between [UO{sub 2}(OH{sub 2}){sub 5}]{sup 2+}(aq) and bulk water is dissociative.« less

Visual observation of gas hydrates nucleation and growth at a water - organic liquid interface

NASA Astrophysics Data System (ADS)

Stoporev, Andrey S.; Semenov, Anton P.; Medvedev, Vladimir I.; Sizikov, Artem A.; Gushchin, Pavel A.; Vinokurov, Vladimir A.; Manakov, Andrey Yu.

2018-03-01

Visual observation of nucleation sites of methane and methane-ethane-propane hydrates and their further growth in water - organic liquid - gas systems with/without surfactants was carried out. Sapphire Rocking Cell RCS6 with transparent sapphire cells was used. The experiments were conducted at the supercooling ΔTsub = 20.2 °C. Decane, toluene and crude oils were used as organics. Gas hydrate nucleation occurred on water - metal - gas and water - sapphire - organic liquid three-phase contact lines. At the initial stage of growth hydrate crystals rapidly covered the water - gas or water - organics interfaces (depending on the nucleation site). Further hydrate phase accrete on cell walls (sapphire surface) and into the organics volume. At this stage, growth was accompanied by water «drawing out» from under initial hydrate film formed at water - organic interface. Apparently, it takes place due to water capillary inflow in the reaction zone. It was shown that the hydrate crystal morphology depends on the organic phase composition. In the case of water-in-decane emulsion relay hydrate crystallization was observed in the whole sample, originating most likely due to the hydrate crystal intergrowth through decane. Contacts of such crystals with adjacent water droplets result in rapid hydrate crystallization on this droplet.

Damage to cellular DNA from particulate radiations, the efficacy of its processing and the radiosensitivity of mammalian cells. Emphasis on DNA double strand breaks and chromatin breaks

NASA Technical Reports Server (NTRS)

Lett, J. T.

1992-01-01

For several years, it has been evident that cellular radiation biology is in a necessary period of consolidation and transition (Lett 1987, 1990; Lett et al. 1986, 1987). Both changes are moving apace, and have been stimulated by studies with heavy charged particles. From the standpoint of radiation chemistry, there is now a consensus of opinion that the DNA hydration shell must be distinguished from bulk water in the cell nucleus and treated as an integral part of DNA (chromatin) (Lett 1987). Concomitantly, sentiment is strengthening for the abandonment of the classical notions of "direct" and "indirect" action (Fielden and O'Neill 1991; O'Neill 1991; O'Neill et al. 1991; Schulte-Frohlinde and Bothe 1991 and references therein). A layer of water molecules outside, or in the outer edge of, the DNA (chromatin) hydration shell influences cellular radiosensitivity in ways not fully understood. Charge and energy transfer processes facilitated by, or involving, DNA hydration must be considered in rigorous theories of radiation action on cells. The induction and processing of double stand breaks (DSBs) in DNA (chromatin) seem to be the predominant determinants of the radiotoxicity of normally radioresistant mammalian cells, the survival curves of which reflect the patterns of damage induced and the damage present after processing ceases, and can be modelled in formal terms by the use of reaction (enzyme) kinetics. Incongruities such as sublethal damage are neither scientifically sound nor relevant to cellular radiation biology (Calkins 1991; Lett 1990; Lett et al. 1987a). Increases in linear energy transfer (LET infinity) up to 100-200 keV micron-1 cause increases in the extents of neighboring chemical and physical damage in DNA denoted by the general term DSB. Those changes are accompanied by decreasing abilities of cells normally radioresistant to sparsely ionizing radiations to process DSBs in DNA and chromatin and to recover from radiation exposure, so they make significant contributions to the relative biological effectiveness (RBE) of a given radiation.(ABSTRACT TRUNCATED AT 400 WORDS).

Influence of Sodium Chloride on the Formation and Dissociation Behavior of CO2 Gas Hydrates

PubMed Central

2017-01-01

We present an experimental study on the formation and dissociation characteristics of carbon dioxide (CO2) gas hydrates using Raman spectroscopy. The CO2 hydrates were formed from sodium chloride/water solutions with salinities of 0–10 wt %, which were pressurized with liquid CO2 in a stirred vessel at 6 MPa and a subcooling of 9.5 K. The formation of the CO2 hydrate resulted in a hydrate gel where the solid hydrate can be considered as the continuous phase that includes small amounts of a dispersed liquid water-rich phase that has not been converted to hydrate. During the hydrate formation process we quantified the fraction of solid hydrate, xH, and the fraction of the dispersed liquid water-rich phase, xL, from the signature of the hydroxyl (OH)-stretching vibration of the hydrate gel. We found that the fraction of hydrate xH contained in the hydrate gel linearly depends on the salinity of the initial liquid water-rich phase. In addition, the ratio of CO2 and water was analyzed in the liquid water-rich phase before hydrate formation, in the hydrate gel during growth and dissociation, and after its complete dissociation again in the liquid water-rich phase. We observed a supersaturation of CO2 in the water-rich phase after complete dissociation of the hydrate gel and were able to show that the excess CO2 exists as dispersed micro- or nanoscale liquid droplets in the liquid water-rich phase. These residual nano- and microdroplets could be a possible explanation for the so-called memory effect. PMID:28817275

Microscopic diffusion in hydrated encysted eggs of brine shrimp

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

Mamontov, Eugene

We have studied microscopic diffusion of water in fully hydrated encysted eggs of brine shrimp (Artemia). We utilized quasielastic neutron scattering. Dry eggs of brine shrimp were rehydrated using (1) water without additives, (2) eutectic mixture of water and dimethyl sulfoxide, and (3) a concentrated aqueous solution of lithium chloride. Despite the complexity of the hydrated multicellular organism, measurable microscopic diffusivity of water is rather well defined. Pure hydration water in eggs exhibits freezing temperature depression, whereas hydration water in eggs mixed with dimethyl sulfoxide or lithium chloride does not crystallize at all. The characteristic size of the voids occupiedmore » by water or aqueous solvents in hydrated brine shrimp eggs is between 2 and 10 nm. Those voids are accessible to co-solvents such as dimethyl sulfoxide and lithium chloride. There is no evidence of intracellular water in the hydrated eggs. The lack of intracellular water in the fully hydrated (but still under arrested development) state must be linked to the unique resilience against adverse environmental factors documented not only for the anhydrous, but also hydrated encysted eggs of brine shrimp.« less

Microscopic diffusion in hydrated encysted eggs of brine shrimp

DOE PAGES

Mamontov, Eugene

2017-05-24

We have studied microscopic diffusion of water in fully hydrated encysted eggs of brine shrimp (Artemia). We utilized quasielastic neutron scattering. Dry eggs of brine shrimp were rehydrated using (1) water without additives, (2) eutectic mixture of water and dimethyl sulfoxide, and (3) a concentrated aqueous solution of lithium chloride. Despite the complexity of the hydrated multicellular organism, measurable microscopic diffusivity of water is rather well defined. Pure hydration water in eggs exhibits freezing temperature depression, whereas hydration water in eggs mixed with dimethyl sulfoxide or lithium chloride does not crystallize at all. The characteristic size of the voids occupiedmore » by water or aqueous solvents in hydrated brine shrimp eggs is between 2 and 10 nm. Those voids are accessible to co-solvents such as dimethyl sulfoxide and lithium chloride. There is no evidence of intracellular water in the hydrated eggs. The lack of intracellular water in the fully hydrated (but still under arrested development) state must be linked to the unique resilience against adverse environmental factors documented not only for the anhydrous, but also hydrated encysted eggs of brine shrimp.« less

Methane Hydrate Recovered From A Mud Volcano in Santa Monica Basin, Offshore Southern California

NASA Astrophysics Data System (ADS)

Normark, W. R.; Hein, J. R.; Powell, C. L.; Lorenson, T. D.; Lee, H. J.; Edwards, B. D.

2003-12-01

In July 2003, a short (2.1 m) piston core from the summit of a mud volcano recovered methane hydrate at a water depth of 813 m in Santa Monica Basin. The discovery core penetrated into in the hydrate as evidenced by chunks of ice and violent degassing of the core section between 162 and 212 cm depth. The core consists of shell hash and carbonate clasts (to 7-cm long) in silty mud. The methanogenic carbonates are of two types: massive, recrystallized nodular masses with an outer mm-thick sugary patina and a bivalve coquina with carbonate cement. Living clams including the genus Vesicomya, commonly found at cold-seep sites elsewhere, were recovered from the top of the core. Further sampling attempts using piston, gravity, and box corers, all of which were obtained within 15 m of the discovery core, recovered olive-brown silty mud with variable amounts of whole and fragmented bivalve shells and methanogenic carbonate fragments characteristic of cold-seep environments. Gases collected in cores adjacent to the discovery core contain elevated amounts of methane and trace amounts of heavier hydrocarbon gases, indicating some component from thermogenic sources. Hydrogen sulfide was also detected in these sediment samples. Vertical channels in one core may have served as fluid pathways. The existence of hydrate at such a shallow depth in the sediment was unexpected, however, the presence of Vesicomya and hydrogen sulfide indicate that the mud volcano is a site of active methane venting. The mud volcano, which is about 24 km west-southwest of Redondo Beach, is about 300 m in diameter at the base. No internal structure is resolved on either high resolution deep-tow boomer or single-channel air-gun profiles, most likely as a result of the gas content and sediment deformation. The diapiric structure has ascended through well-bedded sediment on the lower slope of the basin, producing as much as 30 m of bathymetric relief. It is located in an area where strike-slip motion along the San Pedro Basin fault zone to the south is replaced by convergent motion to the north. The source horizon for the gas in the hydrate is unknown but appears to be collecting in beds as shallow as 200 m below the regional seafloor based on the presence of a strong and irregular reflection interval.

Water retention curve for hydrate-bearing sediments

NASA Astrophysics Data System (ADS)

Dai, Sheng; Santamarina, J. Carlos

2013-11-01

water retention curve plays a central role in numerical algorithms that model hydrate dissociation in sediments. The determination of the water retention curve for hydrate-bearing sediments faces experimental difficulties, and most studies assume constant water retention curves regardless of hydrate saturation. This study employs network model simulation to investigate the water retention curve for hydrate-bearing sediments. Results show that (1) hydrate in pores shifts the curve to higher capillary pressures and the air entry pressure increases as a power function of hydrate saturation; (2) the air entry pressure is lower in sediments with patchy rather than distributed hydrate, with higher pore size variation and pore connectivity or with lower specimen slenderness along the flow direction; and (3) smaller specimens render higher variance in computed water retention curves, especially at high water saturation Sw > 0.7. Results are relevant to other sediment pore processes such as bioclogging and mineral precipitation.

CH4 Hydrate Formation between Silica and Graphite Surfaces: Insights from Microsecond Molecular Dynamics Simulations.

PubMed

He, Zhongjin; Linga, Praveen; Jiang, Jianwen

2017-10-31

Microsecond simulations have been performed to investigate CH 4 hydrate formation from gas/water two-phase systems between silica and graphite surfaces, respectively. The hydrophilic silica and hydrophobic graphite surfaces exhibit substantially different effects on CH 4 hydrate formation. The graphite surface adsorbs CH 4 molecules to form a nanobubble with a flat or negative curvature, resulting in a low aqueous CH 4 concentration, and hydrate nucleation does not occur during 2.5 μs simulation. Moreover, an ordered interfacial water bilayer forms between the nanobubble and graphite surface thus preventing their direct contact. In contrast, the hydroxylated-silica surface prefers to be hydrated by water, with a cylindrical nanobubble formed in the solution, leading to a high aqueous CH 4 concentration and hydrate nucleation in the bulk region; during hydrate growth, the nanobubble is gradually covered by hydrate solid and separated from the water phase, hence slowing growth. The silanol groups on the silica surface can form strong hydrogen bonds with water, and hydrate cages need to match the arrangements of silanols to form more hydrogen bonds. At the end of the simulation, the hydrate solid is separated from the silica surface by liquid water, with only several cages forming hydrogen bonds with the silica surface, mainly due to the low CH 4 aqueous concentrations near the surface. To further explore hydrate formation between graphite surfaces, CH 4 /water homogeneous solution systems are also simulated. CH 4 molecules in the solution are adsorbed onto graphite and hydrate nucleation occurs in the bulk region. During hydrate growth, the adsorbed CH 4 molecules are gradually converted into hydrate solid. It is found that the hydrate-like ordering of interfacial water induced by graphite promotes the contact between hydrate solid and graphite. We reveal that the ability of silanol groups on silica to form strong hydrogen bonds to stabilize incipient hydrate solid, as well as the ability of graphite to adsorb CH 4 molecules and induce hydrate-like ordering of the interfacial water, are the key factors to affect CH 4 hydrate formation between silica and graphite surfaces.

New Model for Europa's Tidal Response Based after Laboratory Measurements

NASA Astrophysics Data System (ADS)

Castillo, J. C.; McCarthy, C.; Choukroun, M.; Rambaux, N.

2009-12-01

We explore the application of the Andrade model to the modeling of Europa’s tidal response at the orbital period and for different librations. Previous models have generally assumed that the satellite behaves as a Maxwell body. However, at the frequencies exciting Europa’s tides and librations, material anelasticity tends to dominate the satellite’s response for a wide range of temperatures, a feature that is not accounted for by the Maxwell model. Many experimental studies on the anelasticity of rocks, ice, and hydrates, suggest that the Andrade model usually provides a good fit to the dissipation spectra obtained for a wide range of frequencies, encompassing the tidal frequencies of most icy satellites. These data indicate that, at Europa’s orbital frequency, the Maxwell model overestimates water ice attenuation at temperature warmer than ~240 K, while it tends to significantly underestimate it at lower temperatures. Based on the available data we suggest an educated extrapolation of available data to Europa’s conditions. We compute the tidal response of a model of Europa differentiated in a rocky core and a water-rich shell. We assume various degrees of stratification of the core involving hydrated and anhydrous silicates, as well as an iron core. The water-rich shell of Europa is assumed to be fully frozen, or to have preserved a deep liquid layer. In both cases we consider a range of thermal structures, based on existing models. These structures take into account the presence of non-ice materials, especially hydrated salts. This new approach yields a greater tidal response (amplitude and phase lag) than previously expected. This is due to the fact that a greater volume of material dissipates tidal energy in comparison to models assuming a Maxwell body. Another feature of interest is that the tidal stress expected in Europa is at about the threshold between a linear and non-linear mechanical response of water ice as a function of stress. Increased stress at a time when Europa’s eccentricity was greater than its current value is likely to have resulted in significant dissipation increase. We will assess how this new approach affects our understanding of Europa, and we will quantify the tidal response of this satellite and the amount of tidal heating available to its evolution. Acknowledgements: Part of this work has been conducted at the Jet Propulsion Laboratory, California Institute of Technology, under contract with NASA. Government sponsorship acknowledged. Part of the experimental work was conducted at Brown University, funded by NASA. MC is supported by a NASA Postdoctoral Fellowship, administered by Oak Ridge Associated Universities.

A molecular dynamics study of model SI clathrate hydrates: the effect of guest size and guest-water interaction on decomposition kinetics.

PubMed

Das, Subhadip; Baghel, Vikesh Singh; Roy, Sudip; Kumar, Rajnish

2015-04-14

One of the options suggested for methane recovery from natural gas hydrates is molecular replacement of methane by suitable guests like CO2 and N2. This approach has been found to be feasible through many experimental and molecular dynamics simulation studies. However, the long term stability of the resultant hydrate needs to be evaluated; the decomposition rate of these hydrates is expected to depend on the interaction between these guest and water molecules. In this work, molecular dynamics simulation has been performed to illustrate the effect of guest molecules with different sizes and interaction strengths with water on structure I (SI) hydrate decomposition and hence the stability. The van der Waals interaction between water of hydrate cages and guest molecules is defined by Lennard Jones potential parameters. A wide range of parameter spaces has been scanned by changing the guest molecules in the SI hydrate, which acts as a model gas for occupying the small and large cages of the SI hydrate. All atomistic simulation results show that the stability of the hydrate is sensitive to the size and interaction of the guest molecules with hydrate water. The increase in the interaction of guest molecules with water stabilizes the hydrate, which in turn shows a slower rate of hydrate decomposition. Similarly guest molecules with a reasonably small (similar to Helium) or large size increase the decomposition rate. The results were also analyzed by calculating the structural order parameter to understand the dynamics of crystal structure and correlated with the release rate of guest molecules from the solid hydrate phase. The results have been explained based on the calculation of potential energies felt by guest molecules in amorphous water, hydrate bulk and hydrate-water interface regions.

Preliminary Experimental Examination Of Controls On Methane Expulsion During Melting Of Natural Gas Hydrate Systems

NASA Astrophysics Data System (ADS)

Kneafsey, T. J.; Flemings, P. B.; Bryant, S. L.; You, K.; Polito, P. J.

2013-12-01

Global climate change will cause warming of the oceans and land. This will affect the occurrence, behavior, and location of subseafloor and subterranean methane hydrate deposits. We suggest that in many natural systems local salinity, elevated by hydrate formation or freshened by hydrate dissociation, may control gas transport through the hydrate stability zone. We are performing experiments and modeling the experiments to explore this behavior for different warming scenarios. Initially, we are exploring hydrate association/dissociation in saline systems with constant water mass. We compare experiments run with saline (3.5 wt. %) water vs. distilled water in a sand mixture at an initial water saturation of ~0.5. We increase the pore fluid (methane) pressure to 1050 psig. We then stepwise cool the sample into the hydrate stability field (~3 degrees C), allowing methane gas to enter as hydrate forms. We measure resistivity and the mass of methane consumed. We are currently running these experiments and we predict our results from equilibrium thermodynamics. In the fresh water case, the modeled final hydrate saturation is 63% and all water is consumed. In the saline case, the modeled final hydrate saturation is 47%, the salinity is 12.4 wt. %, and final water saturation is 13%. The fresh water system is water-limited: all the water is converted to hydrate. In the saline system, pore water salinity is elevated and salt is excluded from the hydrate structure during hydrate formation until the salinity drives the system to three phase equilibrium (liquid, gas, hydrate) and no further hydrate forms. In our laboratory we can impose temperature gradients within the column, and we will use this to investigate equilibrium conditions in large samples subjected to temperature gradients and changing temperature. In these tests, we will quantify the hydrate saturation and salinity over our meter-long sample using spatially distributed temperature sensors, spatially distributed resistivity probes, compressional wave velocities, and X-ray computed tomography scanning. Modeling of hydrate formation and dissociation for these conditions indicates that the transport of bulk fluid phases (gas and water) plays a crucial role in the overall behavior, and we will explore open-system boundary conditions in the experiments to test this prediction.

Analysis of experimental heats of dilution of aqueous solutions of NaBPh 4 by use of the mean spherical approximation and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

M'halla, Jalel; M'halla, Sondes; Wipff, Georges

2003-03-01

Calorimetric measurements of heats of dilution: QDC→0 =- nsφL,sexp, of aqueous solutions of NaBPh 4 are determined at 25 °C in the concentration range: 0

Sedimentological Control on Hydrate Saturation Distribution in Arctic Gas-Hydrate-Bearing Deposits

NASA Astrophysics Data System (ADS)

Behseresht, J.; Peng, Y.; Bryant, S. L.

2010-12-01

Grain size variations along with the relative rates of fluid phases migrating into the zone of hydrate stability, plays an important role in gas-hydrate distribution and its morphologic characteristics. In the Arctic, strata several meters thick containing large saturations of gas hydrate are often separated by layers containing small but nonzero hydrate saturations. Examples are Mt. Elbert, Alaska and Mallik, NW Territories. We argue that this sandwich type hydrate saturation distribution is consistent with having a gas phase saturation within the sediment when the base of gas hydrate stability zone (BGHSZ) was located above the sediment package. The volume change during hydrate formation process derives movement of fluid phases into the GHSZ. We show that this fluid movement -which is mainly governed by characteristic relative permeability curves of the host sediment-, plays a crucial role in the amount of hydrate saturation in the zone of major hydrate saturation. We develop a mechanistic model that enables estimating the final hydrate saturation from an initial gas/water saturation in sediment with known relative permeability curves. The initial gas/water saturation is predicted using variation of capillary entry pressure with depth, which in turn depends on the variation in grain-size distribution. This model provides a mechanistic approach for explaining large hydrate saturations (60%-75%) observed in zones of major hydrate saturation considering the governing characteristic relative permeability curves of the host sediments. We applied the model on data from Mount Elbert well on the Alaskan North Slope. It is shown that, assuming a cocurrent flow of gas and water into the GHSZ, such large hydrate saturations (up to 75%) cannot result from large initial gas saturations (close to 1-Sw,irr) due to limitations on water flux imposed by typical relative permeability curves. They could however result from modest initial gas saturations (ca. 40%) at which we have reasonable phase mobility ratios required for appropriate relative rates of gas and water transporting into GHSZ to form large hydrate saturations. Nevertheless, from the profile of capillary entry pressure vs. depth, we expect large initial gas saturations and thus the final high hydrate saturation suggests another form of water flow: water moves down through accumulated hydrate from the unfrozen water above. For this to happen the water phase must remain connected within the hydrate-bearing sediment. This seems plausible in hydrate bearing sediments because hydrate formation will be stopped before water saturation gets to very low values (lower than Sw,irr) due to salinity build up. The location of small hydrate saturations (10-15%) is consistent with the location of the residual gas phase established during water imbibition into these locations while they serve as a gas source to the layers above.

Molecular modeling of the dissociation of methane hydrate in contact with a silica surface.

PubMed

Bagherzadeh, S Alireza; Englezos, Peter; Alavi, Saman; Ripmeester, John A

2012-03-15

We use constant energy, constant volume (NVE) molecular dynamics simulations to study the dissociation of the fully occupied structure I methane hydrate in a confined geometry between two hydroxylated silica surfaces between 36 and 41 Å apart, at initial temperatures of 283, 293, and 303 K. Simulations of the two-phase hydrate/water system are performed in the presence of silica, with and without a 3 Å thick buffering water layer between the hydrate phase and silica surfaces. Faster decomposition is observed in the presence of silica, where the hydrate phase is prone to decomposition from four surfaces, as compared to only two sides in the case of the hydrate/water simulations. The existence of the water layer between the hydrate phase and the silica surface stabilizes the hydrate phase relative to the case where the hydrate is in direct contact with silica. Hydrates bound between the silica surfaces dissociate layer-by-layer in a shrinking core manner with a curved decomposition front which extends over a 5-8 Å thickness. Labeling water molecules shows that there is exchange of water molecules between the surrounding liquid and intact cages in the methane hydrate phase. In all cases, decomposition of the methane hydrate phase led to the formation of methane nanobubbles in the liquid water phase. © 2012 American Chemical Society

Dielectric constant of ionic solutions: a field-theory approach.

PubMed

Levy, Amir; Andelman, David; Orland, Henri

2012-06-01

We study the variation of the dielectric response of a dielectric liquid (e.g. water) when a salt is added to the solution. Employing field-theoretical methods, we expand the Gibbs free energy to first order in a loop expansion and calculate self-consistently the dielectric constant. We predict analytically the dielectric decrement which depends on the ionic strength in a complex way. Furthermore, a qualitative description of the hydration shell is found and is characterized by a single length scale. Our prediction fits rather well a large range of concentrations for different salts using only one fit parameter related to the size of ions and dipoles.

Effect of Electric Field on Gas Hydrate Nucleation Kinetics: Evidence for the Enhanced Kinetics of Hydrate Nucleation by Negatively Charged Clay Surfaces.

PubMed

Park, Taehyung; Kwon, Tae-Hyuk

2018-03-06

Natural gas hydrates are found widely in oceanic clay-rich sediments, where clay-water interactions have a profound effect on the formation behavior of gas hydrates. However, it remains unclear why and how natural gas hydrates are formed in clay-rich sediments in spite of factors that limit gas hydrate formation, such as small pore size and high salinity. Herein, we show that polarized water molecules on clay surfaces clearly promote gas hydrate nucleation kinetics. When water molecules were polarized with an electric field of 10 4 V/m, gas hydrate nucleation occurred significantly faster with an induction time reduced by 5.8 times. Further, the presence of strongly polarized water layers at the water-gas interface hindered gas uptake and thus hydrate formation, when the electric field was applied prior to gas dissolution. Our findings expand our understanding of the formation habits of naturally occurring gas hydrates in clay-rich sedimentary deposits and provide insights into gas production from natural hydrate deposits.

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

Elbert, Katherine; Hu, Jue; Ma, Zhong

Hydrogen oxidation and evolution on Pt in acid are facile processes, while in alkaline electrolytes, they are 2 orders of magnitude slower. Thus, developing catalysts that are more active than Pt for these two reactions is important for advancing the performance of anion exchange membrane fuel cells and water electrolyzers. Herein, we detail a 4-fold enhancement of Pt mass activity that we achieved using single-crystalline Ru@Pt core–shell nanoparticles with two-monolayer-thick Pt shells, which doubles the activity on Pt–Ru alloy nanocatalysts. For Pt specific activity, the two- and one-monolayer-thick Pt shells exhibited enhancement factors of 3.1 and 2.3, respectively, compared tomore » the Pt nanocatalysts in base, differing considerably from the values of 1 and 0.4, respectively, in acid. To explain such behavior and the orders of magnitude difference in activity on going from acid to base, we performed kinetic analyses of polarization curves over a wide range of potential from –250 to 250 mV using the dual-pathway kinetic equation. From acid to base, the activation free energies increase the most for the Volmer reaction, resulting in a switch of the rate-determining step from the Tafel to the Volmer reaction, and a shift to a weaker optimal hydrogen binding energy. Furthermore, the much higher activation barrier for the Volmer reaction in base than in acid is ascribed to one or both of the two catalyst-insensitive factors: slower transport of OH – than H + in water and a stronger O–H bond in water molecules (HO–H) than in hydrated protons (H 2O–H +).« less

Bioinspired Diatomite Membrane with Selective Superwettability for Oil/Water Separation.

PubMed

Lo, Yu-Hsiang; Yang, Ching-Yu; Chang, Haw-Kai; Hung, Wei-Chen; Chen, Po-Yu

2017-05-03

Membranes with selective superwettability for oil/water separation have received significant attention during the past decades. Hierarchical structures and surface roughness are believed to improve the oil repellency and the stability of Cassie-Baxter state. Diatoms, unicellular photosynthetic algae, possess sophisticated skeletal shells (called frustules) which are made of hydrated silica. Motivated by the hierarchical micro- and nanoscale features of diatom, we fabricate a hierarchical diatomite membrane which consists of aligned micro-sized channels by the freeze casting process. The fine nano-porous structures of frustules are well preserved after the post sintering process. The bioinspired diatomite membrane performs both underwater superoleophobicity and superhydrophobicity under various oils. Additionally, we demonstrate the highly efficient oil/water separation capabililty of the membranes in various harsh environments. The water flux can be further adjusted by tuning the cooling rates. The eco-friendly and robust bioinspired membranes produced by the simple, cost-effective freeze casting method can be potentially applied for large scale and efficient oil/water separation.

Two-state protein model with water interactions: Influence of temperature on the intrinsic viscosity of myoglobin

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

Bakk, Audun

2001-06-01

We describe a single-domain protein as a two-state system with water interactions. Around the unfolded apolar parts of the protein we incorporate the hydration effect by introducing hydrogen bonds between the water molecules in order to mimic the {open_quotes}icelike{close_quotes} shell structure. Intrinsic viscosity, proportional to the effective hydrodynamic volume, for sperm whale metmyoglobin is assigned from experimental data in the folded and in the denaturated state. By weighing statistically the two states against the degree of folding, we express the total intrinsic viscosity. The temperature dependence of the intrinsic viscosity, for different chemical potentials, is in good correspondence with experimentalmore » data [P. L. Privalov , J. Mol. Biol. >190, 487 (1986)]. Cold and warm unfolding, common to small globular proteins, is also a result of the model.« less

Increasing Gas Hydrate Formation Temperature for Desalination of High Salinity Produced Water with Secondary Guests

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

Cha, Jong-Ho; Seol, Yongkoo

We suggest a new gas hydrate-based desalination process using water-immiscible hydrate formers; cyclopentane (CP) and cyclohexane (CH) as secondary hydrate guests to alleviate temperature requirements for hydrate formation. The hydrate formation reactions were carried out in an isobaric condition of 3.1 MPa to find the upper temperature limit of CO2 hydrate formation. Simulated produced water (8.95 wt % salinity) mixed with the hydrate formers shows an increased upper temperature limit from -2 °C for simple CO2 hydrate to 16 and 7 °C for double (CO2 + CP) and (CO2 + CH) hydrates, respectively. The resulting conversion rate to double hydratemore » turned out to be similar to that with simple CO2 hydrate at the upper temperature limit. Hydrate formation rates (Rf) for the double hydrates with CP and CH are shown to be 22 and 16 times higher, respectively, than that of the simple CO2 hydrate at the upper temperature limit. Such mild hydrate formation temperature and fast formation kinetics indicate increased energy efficiency of the double hydrate system for the desalination process. Dissociated water from the hydrates shows greater than 90% salt removal efficiency for the hydrates with the secondary guests, which is also improved from about 70% salt removal efficiency for the simple hydrates.« less

Gas hydrates (clathrates) causing pore-water freshening and oxygen isotope fractionation in deep-water sedimentary sections of terrigenous continental margins

USGS Publications Warehouse

Hesse, R.; Harrison, W.E.

1981-01-01

The occurrence of gas hydrates in deep-water sections of the continental margins predicted from anomalous acoustic reflectors on seismic profiles has been confirmed by recent deep-sea drilling results. On the Pacific continental slope off Guatemala gas hydrates were brought up for the first time from two holes (497, 498A) drilled during Leg 67 of the DSDP in water depths of 2360 and 5500 m, respectively. The hydrates occur in organic matter-rich Pleistocene to Miocene terrigenous sediments. In the hydrate-bearing zone a marked decrease in interstitial water chlorinities was observed starting at about 10-20 m subbottom depth. Pore waters at the bottom of the holes (near 400 m subbottom) have as little as half the chlorinity of seawater (i.e. 9???). Similar, but less pronounced, trends were observed during previous legs of the DSDP in other hydrate-prone segments of the continental margins where recharge of fresh water from the continent can be excluded (e.g. Leg 11). The crystallization of hydrates, like ice, excludes salt ions from the crystal structure. During burial the dissolved salts are separated from the solids. Subsidence results in a downward motion of the solids (including hydrates) relative to the pore fluids. Thawing of hydrates during recovery releases fresh water which is remixed with the pore fluid not involved in hydrate formation. The volume of the latter decreases downhole thus causing downward decreasing salinity (chlorinity). Hydrate formation is responsible for oxygen isotope fractionation with 18O-enrichment in the hydrate explaining increasingly more positive ??18O values in the pore fluids recovered (after hydrate dissociation) with depth. ?? 1981.

Near-infrared studies of glucose and sucrose in aqueous solutions: water displacement effect and red shift in water absorption from water-solute interaction.

PubMed

Jung, Youngeui; Hwang, Jungseek

2013-02-01

We used near infrared spectroscopy to obtain concentration dependent glucose absorption spectra in aqueous solutions in the near-infrared range (3800-7500 cm(-1)). Here we introduce a new method to obtain reliable glucose absorption bands from aqueous glucose solutions without measuring the water displacement coefficients of glucose separately. Additionally, we were able to extract the water displacement coefficients of glucose, and this may offer a new general method using spectroscopy techniques applicable to other water-soluble materials. We also observed red shifts in the absorption bands of water in the hydration shell around solute molecules, which comes from the contribution of the interacting water molecules around the glucose molecules in solutions. The intensity of the red shift gets larger as the concentration increases, which indicates that as the concentration increases more water molecules are involved in the interaction. However, the red shift in frequency does not seem to depend significantly on the concentration. We also performed the same measurements and analysis with sucrose instead of glucose as solute and compared.

Water-wetting surfaces as hydrate promoters during transport of carbon dioxide with impurities.

PubMed

Kuznetsova, Tatiana; Jensen, Bjørnar; Kvamme, Bjørn; Sjøblom, Sara

2015-05-21

Water condensing as liquid drops within the fluid bulk has traditionally been the only scenario accepted in the industrial analysis of hydrate risks. We have applied a combination of absolute thermodynamics and molecular dynamics modeling to analyze the five primary routes of hydrate formation in a rusty pipeline carrying dense carbon dioxide with methane, hydrogen sulfide, argon, and nitrogen as additional impurities. We have revised the risk analysis of all possible routes in accordance with the combination of the first and the second laws of thermodynamics to determine the highest permissible content of water. It was found that at concentrations lower than five percent, hydrogen sulfide will only support the formation of carbon dioxide-dominated hydrate from adsorbed water and hydrate formers from carbon dioxide phase rather than formation in the aqueous phase. Our results indicate that hydrogen sulfide leaving carbon dioxide for the aqueous phase will be able to create an additional hydrate phase in the aqueous region adjacent to the first adsorbed water layer. The growth of hydrate from different phases will decrease the induction time by substantially reducing the kinetically limiting mass transport across the hydrate films. Hydrate formation via adsorption of water on rusty walls will play the decisive role in hydrate formation risk, with the initial concentration of hydrogen sulfide being the critical factor. We concluded that the safest way to eliminate hydrate risks is to ensure that the water content of carbon dioxide is low enough to prevent water dropout via the adsorption mechanism.

Thermosensitive behavior of poly(ethylene glycol)-based block copolymer (PEG-b-PADMO) controlled via self-assembled microstructure.

PubMed

Cui, Qianling; Wu, Feipeng; Wang, Erjian

2011-05-19

Stimuli-responsive, well-defined diblock copolymers (PEG-b-PADMO) comprising poly(ethylene glycol) (PEG, DP (degree of polymerization)=45) as the hydrophilic and temperature-sensitive part and poly(N-acryloyl-2,2-dimethyl-1,3-oxazolidine) (PADMO, DP=18-47) as the hydrophobic and acid-labile part self-assembled in water into spherical micelles with high aggregation number. The micellar structures and thermally induced phase transitions of the copolymers were investigated with (1)H NMR spectroscopy, light scattering, microscopy, turbidimetry, and fluorescence techniques. Thermoresponsive phase transitions of the copolymers in water were controlled via formation of core-shell-type micelles with densely compact PEG corona. Their lower critical solution temperatures (LCSTs) were modulated within the range 40-72 °C by varying PADMO block length. This unusually low LCST was attributed to the densely packed PEG structure in the polymer micelles, which resulted in strong n-clustering attractive interactions and insufficient hydration of PEG chains in the shell and greatly enhanced the thermosensitivity. The LCST behavior can also be modulated by partial acid hydrolysis of PADMO segments through the resulting change of hydrophobicity. © 2011 American Chemical Society

Thermodynamic and structural signatures of water-driven methane-methane attraction in coarse-grained mW water.

PubMed

Song, Bin; Molinero, Valeria

2013-08-07

Hydrophobic interactions are responsible for water-driven processes such as protein folding and self-assembly of biomolecules. Microscopic theories and molecular simulations have been used to study association of a pair of methanes in water, the paradigmatic example of hydrophobic attraction, and determined that entropy is the driving force for the association of the methane pair, while the enthalpy disfavors it. An open question is to which extent coarse-grained water models can still produce correct thermodynamic and structural signatures of hydrophobic interaction. In this work, we investigate the hydrophobic interaction between a methane pair in water at temperatures from 260 to 340 K through molecular dynamics simulations with the coarse-grained monatomic water model mW. We find that the coarse-grained model correctly represents the free energy of association of the methane pair, the temperature dependence of free energy, and the positive change in entropy and enthalpy upon association. We investigate the relationship between thermodynamic signatures and structural order of water through the analysis of the spatial distribution of the density, energy, and tetrahedral order parameter Qt of water. The simulations reveal an enhancement of tetrahedral order in the region between the first and second hydration shells of the methane molecules. The increase in tetrahedral order, however, is far from what would be expected for a clathrate-like or ice-like shell around the solutes. This work shows that the mW water model reproduces the key signatures of hydrophobic interaction without long ranged electrostatics or the need to be re-parameterized for different thermodynamic states. These characteristics, and its hundred-fold increase in efficiency with respect to atomistic models, make mW a promising water model for studying water-driven hydrophobic processes in more complex systems.

Hydration level dependence of the microscopic dynamics of water adsorbed in ultramicroporous carbon

DOE PAGES

Mamontov, Eugene; Yue, Yanfeng; Bahadur, Jitendra; ...

2016-10-20

Even when not functionalized intentionally, most carbon materials are not hydrophobic and readily adsorb water molecules from atmospheric water vapor. We have equilibrated an ultramicroporous carbon at several levels of relative humidity, thereby attaining various hydration levels. The water molecules were adsorbed on the pore walls (but did not fill completely the pore volume) and thus could be better described as hydration, or surface, rather than confined, water. We used quasielastic neutron scattering to perform a detailed investigation of the dependence of microscopic dynamics of these adsorbed water species on the hydration level and temperature. The behavior of hydration watermore » in ultramicroporous carbon clearly demonstrates the same universal traits that characterize surface (hydration) water in other materials that are surface-hydrated. In addition, unless special treatment is intentionally applied to ultramicroporous carbon, the species filling its pores in various applications, ranging from hydrogen molecules to electrolytes, likely find themselves in contact with non-freezing water molecules characterized by rich microscopic dynamics.« less

Water isotope effect on the thermostability of a polio viral RNA hairpin: A metadynamics study.

PubMed

Pathak, Arup K; Bandyopadhyay, Tusar

2017-04-28

Oral polio vaccine is considered to be the most thermolabile of all the common childhood vaccines. Despite heavy water (D 2 O) having been known for a long time to stabilise attenuated viral RNA against thermodegradation, the molecular underpinnings of its mechanism of action are still lacking. Whereas, understanding the basis of D 2 O action is an important step that might reform the way other thermolabile drugs are stored and could possibly minimize the cold chain problem. Here using a combination of parallel tempering and well-tempered metadynamics simulation in light water (H 2 O) and in D 2 O, we have fully described the free energy surface associated with the folding/unfolding of a RNA hairpin containing a non-canonical basepair motif, which is conserved within the 3'-untranslated region of poliovirus-like enteroviruses. Simulations reveal that in heavy water (D 2 O) there is a considerable increase of the stability of the folded basin as monitored through an intramolecular hydrogen bond (HB), size, shape, and flexibility of RNA structures. This translates into a higher melting temperature in D 2 O by 41 K when compared with light water (H 2 O). We have explored the hydration dynamics of the RNA, hydration shell around the RNA surface, and spatial dependence of RNA-solvent collective HB dynamics in the two water systems. Simulation in heavy water clearly showed that D 2 O strengthens the HB network in the solvent, lengthens inter-residue water-bridge lifetime, and weakens dynamical coupling of the hairpin to its solvation environment, which enhances the rigidity of solvent exposed sites of the native configurations. The results might suggest that like other added osmoprotectants, D 2 O can act as a thermostabilizer when used as a solvent.

Water isotope effect on the thermostability of a polio viral RNA hairpin: A metadynamics study

NASA Astrophysics Data System (ADS)

Pathak, Arup K.; Bandyopadhyay, Tusar

2017-04-01

Oral polio vaccine is considered to be the most thermolabile of all the common childhood vaccines. Despite heavy water (D2O) having been known for a long time to stabilise attenuated viral RNA against thermodegradation, the molecular underpinnings of its mechanism of action are still lacking. Whereas, understanding the basis of D2O action is an important step that might reform the way other thermolabile drugs are stored and could possibly minimize the cold chain problem. Here using a combination of parallel tempering and well-tempered metadynamics simulation in light water (H2O) and in D2O, we have fully described the free energy surface associated with the folding/unfolding of a RNA hairpin containing a non-canonical basepair motif, which is conserved within the 3'-untranslated region of poliovirus-like enteroviruses. Simulations reveal that in heavy water (D2O) there is a considerable increase of the stability of the folded basin as monitored through an intramolecular hydrogen bond (HB), size, shape, and flexibility of RNA structures. This translates into a higher melting temperature in D2O by 41 K when compared with light water (H2O). We have explored the hydration dynamics of the RNA, hydration shell around the RNA surface, and spatial dependence of RNA-solvent collective HB dynamics in the two water systems. Simulation in heavy water clearly showed that D2O strengthens the HB network in the solvent, lengthens inter-residue water-bridge lifetime, and weakens dynamical coupling of the hairpin to its solvation environment, which enhances the rigidity of solvent exposed sites of the native configurations. The results might suggest that like other added osmoprotectants, D2O can act as a thermostabilizer when used as a solvent.

Molecular simulation study on Hofmeister cations and the aqueous solubility of benzene.

PubMed

Ganguly, Pritam; Hajari, Timir; van der Vegt, Nico F A

2014-05-22

We study the ion-specific salting-out process of benzene in aqueous alkali chloride solutions using Kirkwood-Buff (KB) theory of solutions and molecular dynamics simulations with different empirical force field models for the ions and benzene. Despite inaccuracies in the force fields, the simulations indicate that the decrease of the Setchenow salting-out coefficient for the series NaCl > KCl > RbCl > CsCl is determined by direct benzene-cation correlations, with the larger cations showing weak interactions with benzene. Although ion-specific aqueous solubilities of benzene may be affected by indirect ion-ion, ion-water, and water-water correlations, too, these correlations are found to be unimportant, with little to no effect on the Setchenow salting-out coefficients of the various salts. We further considered LiCl, which is experimentally known to be a weaker salting-out agent than NaCl and KCl and, therefore, ranks at an unusual position within the Hofmeister cation series. The simulations indicate that hydrated Li(+) ions can take part of the benzene hydration shell while the other cations are repelled by it. This causes weaker Li(+) exclusion around the solute and a resulting, weaker salting-out propensity of LiCl compared to that of the other salts. Removing benzene-water and benzene-salt electrostatic interactions in the simulations does not affect this mechanism, which may therefore also explain the smaller effect of LiCl, as compared to that of NaCl or KCl, on aqueous solvation and hydrophobic interaction of nonpolar molecules.

Competitive Sorption of CO2 and H2O in 2:1 Layer Phyllosilicates

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

Schaef, Herbert T.; Loring, John S.; Glezakou, Vassiliki Alexandra

The salting out effect, where increasing the ionic strength of aqueous solutions decreases the solubility of dissolved gases is a well-known phenomenon. Less explored is the opposite process where an initially anhydrous system containing a volatile, relatively non-polar component and inorganic ions is systematically hydrated. Expandable clays such as montmorillonite are ideal systems for exploring this scenario as they have readily accessible exchange sites containing cations that can be systematically dehydrated or hydrated, from near anhydrous to almost bulk-like water conditions. This phenomenon has new significance with the simultaneous implementation of geological sequestration and secondary utilization of CO2 to bothmore » mitigate climate warming and enhance extraction of methane from hydrated clay-rich formations. Here, the partitioning of CO2 and H2O between Na-, Ca-, and Mg-exchanged montmorillonite and variably hydrated supercritical CO2 (scCO2) was investigated using in situ X-ray diffraction, infrared (IR)spectroscopic titrations, and quartz crystal microbalance (QCM) measurements. Density functional theory calculations provided mechanistic insights. Structural volumetric changes were correlated to quantified changes in sorbed H2O and CO2 concentrations as a function of %H2O saturated in scCO2. Intercalation of CO2 is favored at low H2O/CO2 ratios in the interlayer region, where CO2 can solvate the interlayer cation. As the clay becomes more hydrated and the H2O/CO2 ratio increases, H2O displaces CO2 from the solvation shell of the cation and CO2 tends to segregate. This transition decreases both the entropic and enthalpic driving force for CO2 intercalation, consistent with experimentally observed loss of intercalated CO2.« less

α-chymotrypsin in water-acetone and water-dimethyl sulfoxide mixtures: Effect of preferential solvation and hydration.

PubMed

Sirotkin, Vladimir A; Kuchierskaya, Alexandra A

2017-10-01

We investigated water/organic solvent sorption and residual enzyme activity to simultaneously monitor preferential solvation/hydration of protein macromolecules in the entire range of water content at 25°C. We applied this approach to estimate protein destabilization/stabilization due to the preferential interactions of bovine pancreatic α-chymotrypsin with water-acetone (moderate-strength H-bond acceptor) and water-DMSO (strong H-bond acceptor) mixtures. There are three concentration regimes for the dried α-chymotrypsin. α-Chymotrypsin is preferentially hydrated at high water content. The residual enzyme activity values are close to 100%. At intermediate water content, the dehydrated α-chymotrypsin has a higher affinity for acetone/DMSO than for water. Residual enzyme activity is minimal in this concentration range. The acetone/DMSO molecules are preferentially excluded from the protein surface at the lowest water content, resulting in preferential hydration. The residual catalytic activity in the water-poor acetone is ∼80%, compared with that observed after incubation in pure water. This effect is very small for the water-poor DMSO. Two different schemes are operative for the hydrated enzyme. At high and intermediate water content, α-chymotrypsin exhibits preferential hydration. However, at intermediate water content, in contrast to the dried enzyme, the initially hydrated α-chymotrypsin possesses increased preferential hydration parameters. At low water content, no residual enzyme activity was observed. Preferential binding of DMSO/acetone to α-chymotrypsin was detected. Our data clearly demonstrate that the hydrogen bond accepting ability of organic solvents and the protein hydration level constitute key factors in determining the stability of protein-water-organic solvent systems. © 2017 Wiley Periodicals, Inc.

Influence of surfactants on gas-hydrate formation' kinetics in water-oil emulsion

NASA Astrophysics Data System (ADS)

Zemenkov, Yu D.; Shirshova, A. V.; Arinstein, E. A.; Shuvaev, A. N.

2018-05-01

The kinetics of gas hydrate formation of propane in a water-oil emulsion is experimentally studied when three types of surfactants (SAA (surface acting agent)) - anionic type emulsifiers - are added to the aqueous phase. It is shown that all three types of surfactants decelerate the growth of the gas-hydrate in the emulsion and can be considered as anti-agglutinating and kinetic low-dose inhibitors. The most effective inhibitor of hydrate formation in water-oil emulsion of SV-102 surfactant was revealed. For comparison, experimental studies of gas-hydrate formation under the same conditions for bulk water have been carried out. It is shown that in bulk water, all the surfactants investigated act as promoters (accelerators) of hydrate formation. A qualitative explanation of the action mechanisms of emulsifiers in the process of gas-hydrate formation in water-oil emulsion is given.

Clathrate hydrate stability models for Titan: implications for a global subsurface ocean

NASA Astrophysics Data System (ADS)

Basu Sarkar, D.; Elwood Madden, M.

2013-12-01

Titan is the only planetary body in the solar system, apart from the Earth, with liquid at its surface. Titan's changing rotational period suggests that a global subsurface ocean decouples the icy crust from the interior. Several studies predict the existence of such an internal ocean below an Ice I layer, ranging in depth between a few tens of kilometers to a few hundreds of kilometers, depending on the composition of the icy crust and liquid-ocean. While the overall density of Titan is well constrained, the degree of differentiation within the interior is unclear. These uncertainties lead to poor understanding of the volatile content of the moon. However, unlike other similar large icy moons like Ganymede and Callisto, Titan has a thick nitrogen atmosphere, with methane as the second most abundant constituent - 5% near the surface. Titan's atmosphere, surface, and interior are likely home to various compounds such as C2H6, CO2, Ar, N2 and CH4, capable of forming clathrate hydrates. In addition, the moon has low temperature and low-to-high pressure conditions required for clathrate formation. Therefore the occurrence of extensive multicomponent hydrates may effect the composition of near-surface materials, the subsurface ocean, as well as the atmosphere. This work uses models of hydrate stability for a number of plausible hydrate formers including CH4, C2H6, CH4 + C2H6 and CH4 + NH3, and equilibrium geothermal gradients for probable near-surface materials to delineate the lateral and vertical extent of clathrate hydrate stability zones for Titan. By comparing geothermal gradients with clathrate stability fields for these systems we investigate possible compositions of Titan's global subsurface ocean. Preliminary model results indicate that ethane hydrates or compound hydrates of ethane and methane could be destabilized within the proposed depth range of the internal ocean, while methane/ammonia or pure methane hydrates may not be affected. Therefore, ethane or ethane-methane clathrates may be a major component of Titan's icy shell. Modeled geothermal gradients and stability fields of possible clathrate formers with three different scenarios for an internal ocean from the recent literature. Geothermal gradients obtained from thermal conductivity and density representing water ice and pure CH4-C2H6 hydrate. Clathrate stability field determined using HYDOFF and recent publications of NH3 clathrate stability.

Integrated experimental and theoretical approach for the structural characterization of Hg2+ aqueous solutions

NASA Astrophysics Data System (ADS)

D'Angelo, Paola; Migliorati, Valentina; Mancini, Giordano; Barone, Vincenzo; Chillemi, Giovanni

2008-02-01

The structural and dynamic properties of the solvated Hg2+ ion in aqueous solution have been investigated by a combined experimental-theoretical approach employing x-ray absorption spectroscopy and molecular dynamics (MD) simulations. This method allows one to perform a quantitative analysis of the x-ray absorption near-edge structure (XANES) spectra of ionic solutions using a proper description of the thermal and structural fluctuations. XANES spectra have been computed starting from the MD trajectory, without carrying out any minimization in the structural parameter space. The XANES experimental data are accurately reproduced by a first-shell heptacoordinated cluster only if the second hydration shell is included in the calculations. These results confirm at the same time the existence of a sevenfold first hydration shell for the Hg2+ ion in aqueous solution and the reliability of the potentials used in the MD simulations. The combination of MD and XANES is found to be very helpful to get important new insights into the quantitative estimation of structural properties of disordered systems.

Protein-solvent preferential interactions, protein hydration, and the modulation of biochemical reactions by solvent components.

PubMed

Timasheff, Serge N

2002-07-23

Solvent additives (cosolvents, osmolytes) modulate biochemical reactions if, during the course of the reaction, there is a change in preferential interactions of solvent components with the reacting system. Preferential interactions can be expressed in terms of preferential binding of the cosolvent or its preferential exclusion (preferential hydration). The driving force is the perturbation by the protein of the chemical potential of the cosolvent. It is shown that the measured change of the amount of water in contact with protein during the course of the reaction modulated by an osmolyte is a change in preferential hydration that is strictly a measure of the cosolvent chemical potential perturbation by the protein in the ternary water-protein-cosolvent system. It is not equal to the change in water of hydration, because water of hydration is a reflection strictly of protein-water forces in a binary system. There is no direct relation between water of preferential hydration and water of hydration.

Supramolecular Organization of Nonstoichiometric Drug Hydrates: Dapsone

NASA Astrophysics Data System (ADS)

Braun, Doris E.; Griesser, Ulrich J.

2018-02-01

The observed moisture- and temperature dependent transformations of the dapsone (4,4'-diaminodiphenyl sulfone, DDS) 0.33-hydrate were correlated to its structure and the number and strength of the water-DDS intermolecular interactions. A combination of characterization techniques was used, including thermal analysis (hot-stage microscopy, differential scanning calorimetry and thermogravimetric analysis), gravimetric moisture sorption/desorption studies and variable humidity powder X-ray diffraction, along with computational modeling (crystal structure prediction and pair-wise intermolecular energy calculations). Depending on the relative humidity the hydrate contains between 0 and 0.33 molecules of water per molecule DDS. The crystal structure is retained upon dehydration indicating that DDS hydrate shows a non-stoichiometric (de)hydration behavior. Unexpectedly, the water molecules are not located in structural channels but at isolated-sites of the host framework, which is counterintuitively for a hydrate with non-stoichiometric behavior. The water-DDS interactions were estimated to be weaker than water-host interactions that are commonly observed in stoichiometric hydrates and the lattice energies of the isomorphic dehydration product (hydrate structure without water molecules) and a stable anhydrate at room temperature (form III) differ only by approximately 1 kJ mol–1. The computational generation of hypothetical monohydrates confirms that the hydrate with the unusual DDS:water ratio of 3:1 is more stable than a feasible monohydrate structure. Overall, this study addresses the critical class of non-stoichiometric hydrates, highlighting that only a multidisciplinary investigation can unravel hydrate formation at a molecular level, knowledge which is a requirement in modern drug development.

Experimental investigation of gas hydrate formation, plugging and transportability in partially dispersed and water continuous systems

NASA Astrophysics Data System (ADS)

Vijayamohan, Prithvi

As oil/gas subsea fields mature, the amount of water produced increases significantly due to the production methods employed to enhance the recovery of oil. This is true especially in the case of oil reservoirs. This increase in the water hold up increases the risk of hydrate plug formation in the pipelines, thereby resulting in higher inhibition cost strategies. A major industry concern is to reduce the severe safety risks associated with hydrate plug formation, and significantly extending subsea tieback distances by providing a cost effective flow assurance management/safety tool for mature fields. Developing fundamental understanding of the key mechanistic steps towards hydrate plug formation for different multiphase flow conditions is a key challenge to the flow assurance community. Such understanding can ultimately provide new insight and hydrate management guidelines to diminish the safety risks due to hydrate formation and accumulation in deepwater flowlines and facilities. The transportability of hydrates in pipelines is a function of the operating parameters, such as temperature, pressure, fluid mixture velocity, liquid loading, and fluid system characteristics. Specifically, the hydrate formation rate and plugging onset characteristics can be significantly different for water continuous, oil continuous, and partially dispersed systems. The latter is defined as a system containing oil/gas/water, where the water is present both as a free phase and partially dispersed in the oil phase (i.e., entrained water in the oil). Since hydrate formation from oil dispersed in water systems and partially dispersed water systems is an area which is poorly understood, this thesis aims to address some key questions in these systems. Selected experiments have been performed at the University of Tulsa flowloop to study the hydrate formation and plugging characteristics for the partially dispersed water/oil/gas systems as well as systems where the oil is completely dispersed in water. These experiments indicate that the partially dispersed systems tend to be problematic and are more severe cases with respect to flow assurance when compared to systems where the water is completely dispersed in oil. We have found that the partially dispersed systems are distinct, and are not an intermediate case between water dominated, and water-in-oil emulsified systems. Instead the experiments indicate that the hydrate formation and plugging mechanism for these systems are very complex. Hydrate growth is very rapid for such systems when compared to 100% water cut systems. The plugging mechanism for these systems is a combination of various phenomena (wall growth, agglomeration, bedding/settling, etc). Three different oils with different viscosities have been used to investigate the transportability of hydrates with respect to oil properties. The experiments indicate that the transportability of hydrates increases with increase in oil viscosity. The data from the tests performed provide the basis for a mechanistic model for hydrate formation and plugging in partially dispersed systems. It is found that in systems that were in stratified flow regime before hydrate onset, the hydrates eventually settled on the pipe walls thereby decreasing the flow area for the flow of fluids. In systems that were in the slug flow regime before hydrate formation, moving beds of hydrates were the main cause for plugging. In both the flow regimes, the systems studied entered a plugging regime beyond a certain hydrate concentration. This is termed as φplugging onset and can be used as an indicator to calculate the amount of hydrates that can be transported safely without requiring any additional treatment for a given set of flow characteristics. A correlation to calculate this hydrate concentration based on easily accessible parameters is developed in terms of flow characteristics and oil properties. The work performed in this thesis has enhanced the understanding of the hydrate plug mechanism in pipelines having high amounts of water. This work has also shown the effect of hydrate formation in different flow regimes thereby shedding light on the effects of hydrates on multiphase flow and vice versa. Lessons resulting from this work could be incorporated into flow assurance models, as well as operating company production strategies to reduce or mitigate hydrate plugging risks in complex multiphase systems.

Theoretical and computational studies of renewable energy materials: Room temperature ionic liquids and proton exchange membranes

NASA Astrophysics Data System (ADS)

Feng, Shulu

2011-12-01

Two kinds of renewable energy materials, room temperature ionic liquids (RTILs) and proton exchange membranes (PEMs), especially Nafion, are studied by computational and theoretical approaches. The ultimate purpose of the present research is to design novel materials to meet the future energy demands. To elucidate the effect of alkyl side chain length and anion on the structure and dynamics of the mixtures, molecular dynamics (MD) simulations of three RTILs/water mixtures at various water mole fractions: 1-butyl-3-methylimidazolium (BMIM+)/BF4-, 1-octyl-3-methylimidazolium (OMIM+)/BF4-, and OMIM +/Cl- are performed. Replacing the BMIM + cation with OMIM+ results in stronger aggregation of the cations as well as a slower diffusion of the anions, and replacing the BF4- anion with Cl- alters the water distribution at low water mole fractions and slows diffusion of the mixtures. Potential experimental manifestations of these behaviors in both cases are provided. Proton solvation properties and transport mechanisms are studied in hydrated Nafion, by using the self-consistent multistate empirical valence bond (SCI-MS-EVB) method. It is found that by stabilizing a more Zundel-like (H5O 2+) structure in the first solvation shells, the solvation of excess protons, as well as the proton hydration structure are both influenced by the sulfonate groups. Hydrate proton-related hydrogen bond networks are observed to be more stable than those with water alone. In order to characterize the nature of the proton transport (PT), diffusive motion, Arrhenius activation energies, and transport pathways are calculated and analyzed. Analysis of diffusive motion suggests that (1) a proton-hopping mechanism dominates the proton transport for the studied water loading levels and (2) there is an obvious degree of anti-correlation between the proton hopping and the vehicular transport. The activation energy drops rapidly with an increasing water content when the water loading level is smaller than ˜ 10 H2O/SO 3-, which is consistent with experimental observations. The sulfonate groups are also found to have influence on the proton hopping directions. The temperature and water content effects on the PT pathways are also investigated. The morphological effects on proton solvation and transport in hydrated Nafion are investigated, by using the SCI-MS-EVB method. Two of the most significant morphological models of Nafion, the lamellar model and the cylinder model, are selected. The two models exhibit distinct PT patterns, which result in different proton diffusion rates. In both models, the interaction between protons and the sulfonate groups are proven to be the key to determining PT behavior. The proton solvation structure change as a function of the distance between protons and sulfonate groups has been analyzed. It is found that the increase of water cylinder radius or water layer height leads to the presence of more protons around the sulfonate groups. Furthermore, at a lower hydration level, the increased amount of protons around the sulfonate groups consists of more Zundel-like structures, which is influenced by the distinct morphological structures of Nafion.

Inhibition of methane and natural gas hydrate formation by altering the structure of water with amino acids.

PubMed

Sa, Jeong-Hoon; Kwak, Gye-Hoon; Han, Kunwoo; Ahn, Docheon; Cho, Seong Jun; Lee, Ju Dong; Lee, Kun-Hong

2016-08-16

Natural gas hydrates are solid hydrogen-bonded water crystals containing small molecular gases. The amount of natural gas stored as hydrates in permafrost and ocean sediments is twice that of all other fossil fuels combined. However, hydrate blockages also hinder oil/gas pipeline transportation, and, despite their huge potential as energy sources, our insufficient understanding of hydrates has limited their extraction. Here, we report how the presence of amino acids in water induces changes in its structure and thus interrupts the formation of methane and natural gas hydrates. The perturbation of the structure of water by amino acids and the resulting selective inhibition of hydrate cage formation were observed directly. A strong correlation was found between the inhibition efficiencies of amino acids and their physicochemical properties, which demonstrates the importance of their direct interactions with water and the resulting dissolution environment. The inhibition of methane and natural gas hydrate formation by amino acids has the potential to be highly beneficial in practical applications such as hydrate exploitation, oil/gas transportation, and flow assurance. Further, the interactions between amino acids and water are essential to the equilibria and dynamics of many physical, chemical, biological, and environmental processes.

Inhibition of methane and natural gas hydrate formation by altering the structure of water with amino acids

PubMed Central

Sa, Jeong-Hoon; Kwak, Gye-Hoon; Han, Kunwoo; Ahn, Docheon; Cho, Seong Jun; Lee, Ju Dong; Lee, Kun-Hong

2016-01-01

Natural gas hydrates are solid hydrogen-bonded water crystals containing small molecular gases. The amount of natural gas stored as hydrates in permafrost and ocean sediments is twice that of all other fossil fuels combined. However, hydrate blockages also hinder oil/gas pipeline transportation, and, despite their huge potential as energy sources, our insufficient understanding of hydrates has limited their extraction. Here, we report how the presence of amino acids in water induces changes in its structure and thus interrupts the formation of methane and natural gas hydrates. The perturbation of the structure of water by amino acids and the resulting selective inhibition of hydrate cage formation were observed directly. A strong correlation was found between the inhibition efficiencies of amino acids and their physicochemical properties, which demonstrates the importance of their direct interactions with water and the resulting dissolution environment. The inhibition of methane and natural gas hydrate formation by amino acids has the potential to be highly beneficial in practical applications such as hydrate exploitation, oil/gas transportation, and flow assurance. Further, the interactions between amino acids and water are essential to the equilibria and dynamics of many physical, chemical, biological, and environmental processes. PMID:27526869

Inhibition of methane and natural gas hydrate formation by altering the structure of water with amino acids

NASA Astrophysics Data System (ADS)

Sa, Jeong-Hoon; Kwak, Gye-Hoon; Han, Kunwoo; Ahn, Docheon; Cho, Seong Jun; Lee, Ju Dong; Lee, Kun-Hong

2016-08-01

Natural gas hydrates are solid hydrogen-bonded water crystals containing small molecular gases. The amount of natural gas stored as hydrates in permafrost and ocean sediments is twice that of all other fossil fuels combined. However, hydrate blockages also hinder oil/gas pipeline transportation, and, despite their huge potential as energy sources, our insufficient understanding of hydrates has limited their extraction. Here, we report how the presence of amino acids in water induces changes in its structure and thus interrupts the formation of methane and natural gas hydrates. The perturbation of the structure of water by amino acids and the resulting selective inhibition of hydrate cage formation were observed directly. A strong correlation was found between the inhibition efficiencies of amino acids and their physicochemical properties, which demonstrates the importance of their direct interactions with water and the resulting dissolution environment. The inhibition of methane and natural gas hydrate formation by amino acids has the potential to be highly beneficial in practical applications such as hydrate exploitation, oil/gas transportation, and flow assurance. Further, the interactions between amino acids and water are essential to the equilibria and dynamics of many physical, chemical, biological, and environmental processes.

Methane hydrate formation in partially water-saturated Ottawa sand

USGS Publications Warehouse

Waite, W.F.; Winters, W.J.; Mason, D.H.

2004-01-01

Bulk properties of gas hydrate-bearing sediment strongly depend on whether hydrate forms primarily in the pore fluid, becomes a load-bearing member of the sediment matrix, or cements sediment grains. Our compressional wave speed measurements through partially water-saturated, methane hydrate-bearing Ottawa sands suggest hydrate surrounds and cements sediment grains. The three Ottawa sand packs tested in the Gas Hydrate And Sediment Test Laboratory Instrument (GHASTLI) contain 38(1)% porosity, initially with distilled water saturating 58, 31, and 16% of that pore space, respectively. From the volume of methane gas produced during hydrate dissociation, we calculated the hydrate concentration in the pore space to be 70, 37, and 20% respectively. Based on these hydrate concentrations and our measured compressional wave speeds, we used a rock physics model to differentiate between potential pore-space hydrate distributions. Model results suggest methane hydrate cements unconsolidated sediment when forming in systems containing an abundant gas phase.

Near-infrared detection of potential evidence for microscopic organisms on Europa

NASA Technical Reports Server (NTRS)

Dalton, J. Brad; Mogul, Rakesh; Kagawa, Hiromi K.; Chan, Suzanne L.; Jamieson, Corey S.

2003-01-01

The possibility of an ocean within the icy shell of Jupiter's moon Europa has established that world as a primary candidate in the search for extraterrestrial life within our Solar System. This paper evaluates the potential to detect evidence for microbial life by comparing laboratory studies of terrestrial microorganisms with measurements from the Galileo Near Infrared Imaging Spectrometer (NIMS). If the interior of Europa at one time harbored life, some evidence may remain in the surface materials. Examination of laboratory spectra of terrestrial extremophiles measured at cryogenic temperatures reveals distorted, asymmetric nearinfrared absorption features due to water of hydration. The band centers, widths, and shapes of these features closely match those observed in the Europa spectra. These features are strongest in reddish-brown, disrupted terrains such as linea and chaos regions. Narrow spectral features due to amide bonds in the microbe proteins provide a means of constraining the abundances of such materials using the NIMS data. The NIMS data of disrupted terrains exhibit distorted, asymmetric near-infrared absorption features consistent with the presence of water ice, sulfuric acid octahydrate, hydrated salts, and possibly as much as 0.2 mg cm(-3) of carbonaceous material that could be of biological origin. However, inherent noise in the observations and limitations of spectral sampling must be taken into account when discussing these findings.

Near-infrared detection of potential evidence for microscopic organisms on Europa.

PubMed

Dalton, J Brad; Mogul, Rakesh; Kagawa, Hiromi K; Chan, Suzanne L; Jamieson, Corey S

2003-01-01

The possibility of an ocean within the icy shell of Jupiter's moon Europa has established that world as a primary candidate in the search for extraterrestrial life within our Solar System. This paper evaluates the potential to detect evidence for microbial life by comparing laboratory studies of terrestrial microorganisms with measurements from the Galileo Near Infrared Imaging Spectrometer (NIMS). If the interior of Europa at one time harbored life, some evidence may remain in the surface materials. Examination of laboratory spectra of terrestrial extremophiles measured at cryogenic temperatures reveals distorted, asymmetric nearinfrared absorption features due to water of hydration. The band centers, widths, and shapes of these features closely match those observed in the Europa spectra. These features are strongest in reddish-brown, disrupted terrains such as linea and chaos regions. Narrow spectral features due to amide bonds in the microbe proteins provide a means of constraining the abundances of such materials using the NIMS data. The NIMS data of disrupted terrains exhibit distorted, asymmetric near-infrared absorption features consistent with the presence of water ice, sulfuric acid octahydrate, hydrated salts, and possibly as much as 0.2 mg cm(-3) of carbonaceous material that could be of biological origin. However, inherent noise in the observations and limitations of spectral sampling must be taken into account when discussing these findings.

Interior Structure of Ceres Artist Concept

NASA Image and Video Library

2016-08-03

This artist's concept shows a diagram of how the inside of Ceres could be structured, based on data about the dwarf planet's gravity field from NASA's Dawn mission. Using information about Ceres' gravity and topography, scientists found that Ceres is "differentiated," which means that it has compositionally distinct layers at different depths. The densest layer is at the core, which scientists suspect is made of hydrated silicates. Above that is a volatile-rich shell, topped with a crust of mixed materials. This research teaches scientists about what internal processes could have occurred during the early history of Ceres. It appears that, during a heating phase early in the history of Ceres, water and other light materials partially separated from rock. These light materials and water then rose to the outer layer of Ceres. http://photojournal.jpl.nasa.gov/catalog/PIA20867

Understanding decomposition and encapsulation energies of structure I and II clathrate hydrates

NASA Astrophysics Data System (ADS)

Alavi, Saman; Ohmura, Ryo

2016-10-01

When compressed with water or ice under high pressure and low temperature conditions, some gases form solid gas hydrate inclusion compounds which have higher melting points than ice under those pressures. In this work, we study the balance of the guest-water and water-water interaction energies that lead to the formation of the clathrate hydrate phases. In particular, molecular dynamics simulations with accurate water potentials are used to study the energetics of the formation of structure I (sI) and II (sII) clathrate hydrates of methane, ethane, and propane. The dissociation enthalpy of the clathrate hydrate phases, the encapsulation enthalpy of methane, ethane, and propane guests in the corresponding phases, and the average bonding enthalpy of water molecules are calculated and compared with accurate calorimetric measurements and previous classical and quantum mechanical calculations, when available. The encapsulation energies of methane, ethane, and propane guests stabilize the small and large sI and sII hydrate cages, with the larger molecules giving larger encapsulation energies. The average water-water interactions are weakened in the sI and sII phases compared to ice. The relative magnitudes of the van der Waals potential energy in ice and the hydrate phases are similar, but in the ice phase, the electrostatic interactions are stronger. The stabilizing guest-water "hydrophobic" interactions compensate for the weaker water-water interactions and stabilize the hydrate phases. A number of common assumptions regarding the guest-cage water interactions are used in the van der Waals-Platteeuw statistical mechanical theory to predict the clathrate hydrate phase stability under different pressure-temperature conditions. The present calculations show that some of these assumptions may not accurately reflect the physical nature of the interactions between guest molecules and the lattice waters.

Understanding decomposition and encapsulation energies of structure I and II clathrate hydrates.

PubMed

Alavi, Saman; Ohmura, Ryo

2016-10-21

When compressed with water or ice under high pressure and low temperature conditions, some gases form solid gas hydrate inclusion compounds which have higher melting points than ice under those pressures. In this work, we study the balance of the guest-water and water-water interaction energies that lead to the formation of the clathrate hydrate phases. In particular, molecular dynamics simulations with accurate water potentials are used to study the energetics of the formation of structure I (sI) and II (sII) clathrate hydrates of methane, ethane, and propane. The dissociation enthalpy of the clathrate hydrate phases, the encapsulation enthalpy of methane, ethane, and propane guests in the corresponding phases, and the average bonding enthalpy of water molecules are calculated and compared with accurate calorimetric measurements and previous classical and quantum mechanical calculations, when available. The encapsulation energies of methane, ethane, and propane guests stabilize the small and large sI and sII hydrate cages, with the larger molecules giving larger encapsulation energies. The average water-water interactions are weakened in the sI and sII phases compared to ice. The relative magnitudes of the van der Waals potential energy in ice and the hydrate phases are similar, but in the ice phase, the electrostatic interactions are stronger. The stabilizing guest-water "hydrophobic" interactions compensate for the weaker water-water interactions and stabilize the hydrate phases. A number of common assumptions regarding the guest-cage water interactions are used in the van der Waals-Platteeuw statistical mechanical theory to predict the clathrate hydrate phase stability under different pressure-temperature conditions. The present calculations show that some of these assumptions may not accurately reflect the physical nature of the interactions between guest molecules and the lattice waters.

Atomistic details of protein dynamics and the role of hydration water

DOE PAGES

Khodadadi, Sheila; Sokolov, Alexei P.

2016-05-04

The importance of protein dynamics for their biological activity is nowwell recognized. Different experimental and computational techniques have been employed to study protein dynamics, hierarchy of different processes and the coupling between protein and hydration water dynamics. But, understanding the atomistic details of protein dynamics and the role of hydration water remains rather limited. Based on overview of neutron scattering, molecular dynamic simulations, NMR and dielectric spectroscopy results we present a general picture of protein dynamics covering time scales from faster than ps to microseconds and the influence of hydration water on different relaxation processes. Internal protein dynamics spread overmore » a wide time range fromfaster than picosecond to longer than microseconds. We suggest that the structural relaxation in hydrated proteins appears on the microsecond time scale, while faster processes present mostly motion of side groups and some domains. Hydration water plays a crucial role in protein dynamics on all time scales. It controls the coupled protein-hydration water relaxation on 10 100 ps time scale. Our process defines the friction for slower protein dynamics. Analysis suggests that changes in amount of hydration water affect not only general friction, but also influence significantly the protein's energy landscape.« less

Atomistic details of protein dynamics and the role of hydration water

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

Khodadadi, Sheila; Sokolov, Alexei P.

The importance of protein dynamics for their biological activity is nowwell recognized. Different experimental and computational techniques have been employed to study protein dynamics, hierarchy of different processes and the coupling between protein and hydration water dynamics. But, understanding the atomistic details of protein dynamics and the role of hydration water remains rather limited. Based on overview of neutron scattering, molecular dynamic simulations, NMR and dielectric spectroscopy results we present a general picture of protein dynamics covering time scales from faster than ps to microseconds and the influence of hydration water on different relaxation processes. Internal protein dynamics spread overmore » a wide time range fromfaster than picosecond to longer than microseconds. We suggest that the structural relaxation in hydrated proteins appears on the microsecond time scale, while faster processes present mostly motion of side groups and some domains. Hydration water plays a crucial role in protein dynamics on all time scales. It controls the coupled protein-hydration water relaxation on 10 100 ps time scale. Our process defines the friction for slower protein dynamics. Analysis suggests that changes in amount of hydration water affect not only general friction, but also influence significantly the protein's energy landscape.« less

Gas processing developments. Why not use methanol for hydrate control

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

Nielsen, R.B.; Bucklin, R.W.

1983-04-01

Hydrate formation in turboexpander plants can be avoided more economically by using methanol than by using solid bed dehydration. Although the first turboexpander plant used methanol, most expander installations now have used solid bed dehydration. The reasons are obscure, since methanol often grants greater ease of operation as well as lower capital and operating costs, especially when the water in the feed gas is low or when recompression is required. Natural gas generally contains water before processing. High pressure, low temperature, or both favor the combination of water with light gases to form hydrates. Free water always must be presentmore » for hydrates to form. Hydrates cause problems by plugging pipelines, valves, and other process equipment. Therefore, proper equipment design requires accurate prediction of the limiting conditions at which hydrates are formed anytime a gas stream containing hydrate formers and free water is cooled below 80 F. (16 refs.)« less

Seepage from an arctic shallow marine gas hydrate reservoir is insensitive to momentary ocean warming

PubMed Central

Hong, Wei-Li; Torres, Marta E.; Carroll, JoLynn; Crémière, Antoine; Panieri, Giuliana; Yao, Haoyi; Serov, Pavel

2017-01-01

Arctic gas hydrate reservoirs located in shallow water and proximal to the sediment-water interface are thought to be sensitive to bottom water warming that may trigger gas hydrate dissociation and the release of methane. Here, we evaluate bottom water temperature as a potential driver for hydrate dissociation and methane release from a recently discovered, gas-hydrate-bearing system south of Spitsbergen (Storfjordrenna, ∼380 m water depth). Modelling of the non-steady-state porewater profiles and observations of distinct layers of methane-derived authigenic carbonate nodules in the sediments indicate centurial to millennial methane emissions in the region. Results of temperature modelling suggest limited impact of short-term warming on gas hydrates deeper than a few metres in the sediments. We conclude that the ongoing and past methane emission episodes at the investigated sites are likely due to the episodic ventilation of deep reservoirs rather than warming-induced gas hydrate dissociation in this shallow water seep site. PMID:28589962

Seepage from an arctic shallow marine gas hydrate reservoir is insensitive to momentary ocean warming

DOE PAGES

Hong, Wei-Li; Torres, Marta E.; Carroll, JoLynn; ...

2017-06-07

Arctic gas hydrate reservoirs located in shallow water and proximal to the sediment-water interface are thought to be sensitive to bottom water warming that may trigger gas hydrate dissociation and the release of methane. Here, we evaluate bottom water temperature as a potential driver for hydrate dissociation and methane release from a recently discovered, gas-hydrate-bearing system south of Spitsbergen (Storfjordrenna, ~380m water depth). Modelling of the non-steady-state porewater profiles and observations of distinct layers of methane-derived authigenic carbonate nodules in the sediments indicate centurial to millennial methane emissions in the region. The results of temperature modelling suggest limited impact ofmore » short-term warming on gas hydrates deeper than a few metres in the sediments. We conclude that the ongoing and past methane emission episodes at the investigated sites are likely due to the episodic ventilation of deep reservoirs rather than warming-induced gas hydrate dissociation in this shallow water seep site.« less

Seepage from an arctic shallow marine gas hydrate reservoir is insensitive to momentary ocean warming.

PubMed

Hong, Wei-Li; Torres, Marta E; Carroll, JoLynn; Crémière, Antoine; Panieri, Giuliana; Yao, Haoyi; Serov, Pavel

2017-06-07

Arctic gas hydrate reservoirs located in shallow water and proximal to the sediment-water interface are thought to be sensitive to bottom water warming that may trigger gas hydrate dissociation and the release of methane. Here, we evaluate bottom water temperature as a potential driver for hydrate dissociation and methane release from a recently discovered, gas-hydrate-bearing system south of Spitsbergen (Storfjordrenna, ∼380 m water depth). Modelling of the non-steady-state porewater profiles and observations of distinct layers of methane-derived authigenic carbonate nodules in the sediments indicate centurial to millennial methane emissions in the region. Results of temperature modelling suggest limited impact of short-term warming on gas hydrates deeper than a few metres in the sediments. We conclude that the ongoing and past methane emission episodes at the investigated sites are likely due to the episodic ventilation of deep reservoirs rather than warming-induced gas hydrate dissociation in this shallow water seep site.

Seepage from an arctic shallow marine gas hydrate reservoir is insensitive to momentary ocean warming

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

Hong, Wei-Li; Torres, Marta E.; Carroll, JoLynn

Arctic gas hydrate reservoirs located in shallow water and proximal to the sediment-water interface are thought to be sensitive to bottom water warming that may trigger gas hydrate dissociation and the release of methane. Here, we evaluate bottom water temperature as a potential driver for hydrate dissociation and methane release from a recently discovered, gas-hydrate-bearing system south of Spitsbergen (Storfjordrenna, ~380m water depth). Modelling of the non-steady-state porewater profiles and observations of distinct layers of methane-derived authigenic carbonate nodules in the sediments indicate centurial to millennial methane emissions in the region. The results of temperature modelling suggest limited impact ofmore » short-term warming on gas hydrates deeper than a few metres in the sediments. We conclude that the ongoing and past methane emission episodes at the investigated sites are likely due to the episodic ventilation of deep reservoirs rather than warming-induced gas hydrate dissociation in this shallow water seep site.« less

NMR Studies of Protein Hydration and Protein-Ligand Interactions

NASA Astrophysics Data System (ADS)

Chong, Yuan

Water on the surface of a protein is called hydration water. Hydration water is known to play a crucial role in a variety of biological processes including protein folding, enzymatic activation, and drug binding. Although the significance of hydration water has been recognized, the underlying mechanism remains far from being understood. This dissertation employs a unique in-situ nuclear magnetic resonance (NMR) technique to study the mechanism of protein hydration and the role of hydration in alcohol-protein interactions. Water isotherms in proteins are measured at different temperatures via the in-situ NMR technique. Water is found to interact differently with hydrophilic and hydrophobic groups on the protein. Water adsorption on hydrophilic groups is hardly affected by the temperature, while water adsorption on hydrophobic groups strongly depends on the temperature around 10 C, below which the adsorption is substantially reduced. This effect is induced by the dramatic decrease in the protein flexibility below 10 C. Furthermore, nanosecond to microsecond protein dynamics and the free energy, enthalpy, and entropy of protein hydration are studied as a function of hydration level and temperature. A crossover at 10 C in protein dynamics and thermodynamics is revealed. The effect of water at hydrophilic groups on protein dynamics and thermodynamics shows little temperature dependence, whereas water at hydrophobic groups has stronger effect above 10 C. In addition, I investigate the role of water in alcohol binding to the protein using the in-situ NMR detection. The isotherms of alcohols are first measured on dry proteins, then on proteins with a series of controlled hydration levels. The free energy, enthalpy, and entropy of alcohol binding are also determined. Two distinct types of alcohol binding are identified. On the one hand, alcohols can directly bind to a few specific sites on the protein. This type of binding is independent of temperature and can be facilitated by hydration. On the other hand, alcohols can bind to many nonspecific sites on the protein. In dry proteins, this type of binding only occurs above a threshold of alcohol vapor pressure. Such a threshold is gradually reduced by increasing the hydration level and can be removed above a critical hydration level. Hydration also shifts the nonspecific alcohol binding from an entropy-driven to an enthalpy-driven process. This dissertation reveals the mechanism of protein hydration and the detailed roles of hydration in ligand binding, with important implications for the understanding of protein functions.

Measurements of gas hydrate formation probability distributions on a quasi-free water droplet

NASA Astrophysics Data System (ADS)

Maeda, Nobuo

2014-06-01

A High Pressure Automated Lag Time Apparatus (HP-ALTA) can measure gas hydrate formation probability distributions from water in a glass sample cell. In an HP-ALTA gas hydrate formation originates near the edges of the sample cell and gas hydrate films subsequently grow across the water-guest gas interface. It would ideally be desirable to be able to measure gas hydrate formation probability distributions of a single water droplet or mist that is freely levitating in a guest gas, but this is technically challenging. The next best option is to let a water droplet sit on top of a denser, immiscible, inert, and wall-wetting hydrophobic liquid to avoid contact of a water droplet with the solid walls. Here we report the development of a second generation HP-ALTA which can measure gas hydrate formation probability distributions of a water droplet which sits on a perfluorocarbon oil in a container that is coated with 1H,1H,2H,2H-Perfluorodecyltriethoxysilane. It was found that the gas hydrate formation probability distributions of such a quasi-free water droplet were significantly lower than those of water in a glass sample cell.

Supramolecular Organization of Nonstoichiometric Drug Hydrates: Dapsone.

PubMed

Braun, Doris E; Griesser, Ulrich J

2018-01-01

The observed moisture- and temperature dependent transformations of the dapsone (4,4'-diaminodiphenyl sulfone, DDS) 0. 33-hydrate were correlated to its structure and the number and strength of the water-DDS intermolecular interactions. A combination of characterization techniques was used, including thermal analysis (hot-stage microscopy, differential scanning calorimetry and thermogravimetric analysis), gravimetric moisture sorption/desorption studies and variable humidity powder X-ray diffraction, along with computational modeling (crystal structure prediction and pair-wise intermolecular energy calculations). Depending on the relative humidity the hydrate contains between 0 and 0.33 molecules of water per molecule DDS. The crystal structure is retained upon dehydration indicating that DDS hydrate shows a non-stoichiometric (de)hydration behavior. Unexpectedly, the water molecules are not located in structural channels but at isolated-sites of the host framework, which is counterintuitively for a hydrate with non-stoichiometric behavior. The water-DDS interactions were estimated to be weaker than water-host interactions that are commonly observed in stoichiometric hydrates and the lattice energies of the isomorphic dehydration product (hydrate structure without water molecules) and (form III ) differ only by ~1 kJ mol -1 . The computational generation of hypothetical monohydrates confirms that the hydrate with the unusual DDS:water ratio of 3:1 is more stable than a feasible monohydrate structure. Overall, this study highlights that a deeper understanding of the formation of hydrates with non-stoichiometric behavior requires a multidisciplinary approach including suitable experimental and computational methods providing a firm basis for the development and manufacturing of high quality drug products.

Method for excluding salt and other soluble materials from produced water

DOEpatents

Phelps, Tommy J [Knoxville, TN; Tsouris, Costas [Oak Ridge, TN; Palumbo, Anthony V [Oak Ridge, TN; Riestenberg, David E [Knoxville, TN; McCallum, Scott D [Knoxville, TN

2009-08-04

A method for reducing the salinity, as well as the hydrocarbon concentration of produced water to levels sufficient to meet surface water discharge standards. Pressure vessel and coflow injection technology developed at the Oak Ridge National Laboratory is used to mix produced water and a gas hydrate forming fluid to form a solid or semi-solid gas hydrate mixture. Salts and solids are excluded from the water that becomes a part of the hydrate cage. A three-step process of dissociation of the hydrate results in purified water suitable for irrigation.

Density functional theory based molecular dynamics study of hydration and electronic properties of aqueous La(3+).

PubMed

Terrier, Cyril; Vitorge, Pierre; Gaigeot, Marie-Pierre; Spezia, Riccardo; Vuilleumier, Rodolphe

2010-07-28

Structural and electronic properties of La(3+) immersed in bulk water have been assessed by means of density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations. Correct structural properties, i.e., La(III)-water distances and La(III) coordination number, can be obtained within the framework of Car-Parrinello simulations providing that both the La pseudopotential and conditions of the dynamics (fictitious mass and time step) are carefully set up. DFT-MD explicitly treats electronic densities and is shown here to provide a theoretical justification to the necessity of including polarization when studying highly charged cations such as lanthanoids(III) with classical MD. La(3+) was found to strongly polarize the water molecules located in the first shell, giving rise to dipole moments about 0.5 D larger than those of bulk water molecules. Finally, analyzing Kohn-Sham orbitals, we found La(3+) empty 4f orbitals extremely compact and to a great extent uncoupled from the water conduction band, while the 5d empty orbitals exhibit mixing with unoccupied states of water.

Solution influence on biomolecular equilibria - Nucleic acid base associations

NASA Technical Reports Server (NTRS)

Pohorille, A.; Pratt, L. R.; Burt, S. K.; Macelroy, R. D.

1984-01-01

Various attempts to construct an understanding of the influence of solution environment on biomolecular equilibria at the molecular level using computer simulation are discussed. First, the application of the formal statistical thermodynamic program for investigating biomolecular equilibria in solution is presented, addressing modeling and conceptual simplications such as perturbative methods, long-range interaction approximations, surface thermodynamics, and hydration shell. Then, Monte Carlo calculations on the associations of nucleic acid bases in both polar and nonpolar solvents such as water and carbon tetrachloride are carried out. The solvent contribution to the enthalpy of base association is positive (destabilizing) in both polar and nonpolar solvents while negative enthalpies for stacked complexes are obtained only when the solute-solute in vacuo energy is added to the total energy. The release upon association of solvent molecules from the first hydration layer around a solute to the bulk is accompanied by an increase in solute-solvent energy and decrease in solvent-solvent energy. The techniques presented are expectd to displace less molecular and more heuristic modeling of biomolecular equilibria in solution.

Raman studies of methane-ethane hydrate metastability.

PubMed

Ohno, Hiroshi; Strobel, Timothy A; Dec, Steven F; Sloan, E Dendy; Koh, Carolyn A

2009-03-05

The interconversion of methane-ethane hydrate from metastable to stable structures was studied using Raman spectroscopy. sI and sII hydrates were synthesized from methane-ethane gas mixtures of 65% or 93% methane in ethane and water, both with and without the kinetic hydrate inhibitor, poly(N-vinylcaprolactam). The observed faster structural conversion rate in the higher methane concentration atmosphere can be explained in terms of the differences in driving force (difference in chemical potential of water in sI and sII hydrates) and kinetics (mass transfer of gas and water rearrangement). The kinetic hydrate inhibitor increased the conversion rate at 65% methane in ethane (sI is thermodynamically stable) but retards the rate at 93% methane in ethane (sII is thermodynamically stable), implying there is a complex interaction between the polymer, water, and hydrate guests at crystal surfaces.

Adsorption isotherms of water on mica: redistribution and film growth.

PubMed

Malani, Ateeque; Ayappa, K G

2009-01-29

Adsorption isotherms of water on muscovite mica are obtained using grand canonical Monte Carlo simulations over a wide range of relative vapor pressures, p/p(0) at 298 K. Three distinct stages are observed in the adsorption isotherm. A sharp rise in the water coverage occurs for 0 < p/p(0) < 0.1. This is followed by a relatively slow increase in the coverage for 0.1 < or = p/p(0) < or = 0.7. Above p/p(0) = 0.7, a second increase in the coverage occurs due to the adsorption of water with bulklike features. The derived film thickness and isotherm shape for the simple point charge (SPC) water model is in excellent agreement with recent experiments of Balmer et al. [ Langmuir 2008 , 24 , 1566 ]. A novel observation is the significant redistribution of water between adsorbed layers as the water film develops. This redistribution is most pronounced for 0.1 < or = p/p(0) < or = 0.7, where water is depleted from the inner layers and film growth is initiated on the outer layer. During this stage, potassium hydration is found to play a dominant role in the rearrangement of water near the mica surface. The analysis of structural features reveals a strongly bound first layer of water molecules occupying the ditrigonal cavities between the potassium ions. In-plane structure of oxygen in the second layer, which forms part of the first hydration shell of potassium, reveals a liquidlike structure with the oxygen-oxygen pair correlation function displaying features similar to bulk water. Isosteric heats of adsorption were found to be in good agreement with the differential microcalorimetric data of Rakhmatkariev ( Clays Clay Miner. 2006 , 54 , 402 ), over the entire range of pressures investigated. Both SPC and extended simple point charge (SPC/E) water models were found to yield qualitatively similar adsorption and structural characteristics, with the SPC/E model predicting lower coverages than the SPC model for p/p(0) > 0.7.

Surfactant process for promoting gas hydrate formation and application of the same

DOEpatents

Rogers, Rudy E.; Zhong, Yu

2002-01-01

This invention relates to a method of storing gas using gas hydrates comprising forming gas hydrates in the presence of a water-surfactant solution that comprises water and surfactant. The addition of minor amounts of surfactant increases the gas hydrate formation rate, increases packing density of the solid hydrate mass and simplifies the formation-storage-decomposition process of gas hydrates. The minor amounts of surfactant also enhance the potential of gas hydrates for industrial storage applications.

Simultaneous determination of thermal conductivity, thermal diffusivity and specific heat in sI methane hydrate

USGS Publications Warehouse

Waite, W.F.; Stern, L.A.; Kirby, S.H.; Winters, W.J.; Mason, D.H.

2007-01-01

Thermal conductivity, thermal diffusivity and specific heat of sI methane hydrate were measured as functions of temperature and pressure using a needle probe technique. The temperature dependence was measured between −20°C and 17°C at 31.5 MPa. The pressure dependence was measured between 31.5 and 102 MPa at 14.4°C. Only weak temperature and pressure dependencies were observed. Methane hydrate thermal conductivity differs from that of water by less than 10 per cent, too little to provide a sensitive measure of hydrate content in water-saturated systems. Thermal diffusivity of methane hydrate is more than twice that of water, however, and its specific heat is about half that of water. Thus, when drilling into or through hydrate-rich sediment, heat from the borehole can raise the formation temperature more than 20 per cent faster than if the formation's pore space contains only water. Thermal properties of methane hydrate should be considered in safety and economic assessments of hydrate-bearing sediment.

Adhesion force interactions between cyclopentane hydrate and physically and chemically modified surfaces.

PubMed

Aman, Zachary M; Sloan, E Dendy; Sum, Amadeu K; Koh, Carolyn A

2014-12-07

Interfacial interactions between liquid-solid and solid-solid phases/surfaces are of fundamental importance to the formation of hydrate deposits in oil and gas pipelines. This work establishes the effect of five categories of physical and chemical modification to steel on clathrate hydrate adhesive force: oleamide, graphite, citric acid ester, nonanedithiol, and Rain-X anti-wetting agent. Hydrate adhesive forces were measured using a micromechanical force apparatus, under both dry and water-wet surface conditions. The results show that the graphite coating reduced hydrate-steel adhesion force by 79%, due to an increase in the water wetting angle from 42 ± 8° to 154 ± 7°. Two chemical surface coatings (nonanedithiol and the citric acid ester) induced rapid hydrate growth in the hydrate particles; nonanedithiol increased hydrate adhesive force by 49% from the baseline, while the citric acid ester coating reduced hydrate adhesion force by 98%. This result suggests that crystal growth may enable a strong adhesive pathway between hydrate and other crystalline structures, however this effect may be negated in cases where water-hydrocarbon interfacial tension is minimised. When a liquid water droplet was placed on the modified steel surfaces, the graphite and citric acid ester became less effective at reducing adhesive force. In pipelines containing a free water phase wetting the steel surface, chemical or physical surface modifications alone may be insufficient to eliminate hydrate deposition risk. In further tests, the citric acid ester reduced hydrate cohesive forces by 50%, suggesting mild activity as a hybrid anti-agglomerant suppressing both hydrate deposition and particle agglomeration. These results demonstrate a new capability to develop polyfunctional surfactants, which simultaneously limit the capability for hydrate particles to aggregate and deposit on the pipeline wall.

Shifting Focus: From Hydration for Performance to Hydration for Health.

PubMed

Perrier, Erica T

2017-01-01

Over the past 10 years, literature on hydration biomarkers has evolved considerably - from (de)hydration assessment towards a more global definition of biomarkers of hydration in daily life. This shift in thinking about hydration markers was largely driven by investigating the differences that existed between otherwise healthy individuals whose habitual, ad-libitum drinking habits differ, and by identifying physiological changes in low-volume drinkers who subsequently increase their water intake. Aside from obvious differences in urinary volume and concentration, a growing body of evidence is emerging that links differences in fluid intake with small, but biologically significant, differences in vasopressin (copeptin), glomerular filtration rate, and markers of metabolic dysfunction or disease. Taken together, these pieces of the puzzle begin to form a picture of how much water intake should be considered adequate for health, and represent a shifting focus from hydration for performance, toward hydration for health outcomes. This narrative review outlines the key areas of research in which the global hydration process - including water intake, urinary hydration markers, and vasopressin - has been associated with health outcomes, focusing on kidney and metabolic endpoints. It will also provide a commentary on how various hydration biomarkers may be used in hydration for health assessment. Finally, if adequate water intake can play a role in maintaining health, how might we tell if we are drinking enough? Urine output is easily measured, and can take into account differences in daily physical activity, climate, dietary solute load, and other factors that influence daily water needs. Today, targets have been proposed for urine osmolality, specific gravity, and color that may be used by researchers, clinicians, and individuals as simple indicators of optimal hydration. However, there remain a large number of incomplete or unanswered research questions regarding the relationships between water intake, hydration, vasopressin, and health outcomes. Thus, this emerging field represents an excellent opportunity, particularly for young researchers, to develop relevant and novel lines of research. © 2017 The Author(s) Published by S. Karger AG, Basel.

Basin-Wide Temperature Constraints On Gas Hydrate Stability In The Gulf Of Mexico

NASA Astrophysics Data System (ADS)

MacDonald, I. R.; Reagan, M. T.; Guinasso, N. L.; Garcia-Pineda, O. G.

2012-12-01

Gas hydrate deposits commonly occur at the seafloor-water interface on marine margins. They are especially prevalent in the Gulf of Mexico where they are associated with natural oil seeps. The stability of these deposits is potentially challenged by fluctuations in bottom water temperature, on an annual time-scale, and under the long-term influence of climate change. We mapped the locations of natural oil seeps where shallow gas hydrate deposits are known to occur across the entire Gulf of Mexico basin based on a comprehensive review of synthetic aperture radar (SAR) data (~200 images). We prepared a bottom water temperature map based on the archive of CTD casts from the Gulf (~6000 records). Comparing the distribution of gas hydrate deposits with predicted bottom water temperature, we find that a broad area of the upper slope lies above the theoretical stability horizon for structure 1 gas hydrate, while all sites where gas hydrate deposits occur are within the stability horizon for structure 2 gas hydrate. This is consistent with analytical results that structure 2 gas hydrates predominate on the upper slope (Klapp et al., 2010), where bottom water temperatures fluctuate over a 7 to 10 C range (approx. 600 m depth), while pure structure 1 hydrates are found at greater depths (approx. 3000 m). Where higher hydrocarbon gases are available, formation of structure 2 gas hydrate should significantly increase the resistance of shallow gas hydrate deposits to destabilizing effects variable or increasing bottom water temperature. Klapp, S.A., Bohrmann, G., Kuhs, W.F., Murshed, M.M., Pape, T., Klein, H., Techmer, K.S., Heeschen, K.U., and Abegg, F., 2010, Microstructures of structure I and II gas hydrates from the Gulf of Mexico: Marine and Petroleum Geology, v. 27, p. 116-125.Bottom temperature and pressure for Gulf of Mexico gas hydrate outcrops and stability horizons for sI and sII hydrate.

Supramolecular Organization of Nonstoichiometric Drug Hydrates: Dapsone

PubMed Central

Braun, Doris E.; Griesser, Ulrich J.

2018-01-01

The observed moisture- and temperature dependent transformations of the dapsone (4,4′-diaminodiphenyl sulfone, DDS) 0. 33-hydrate were correlated to its structure and the number and strength of the water-DDS intermolecular interactions. A combination of characterization techniques was used, including thermal analysis (hot-stage microscopy, differential scanning calorimetry and thermogravimetric analysis), gravimetric moisture sorption/desorption studies and variable humidity powder X-ray diffraction, along with computational modeling (crystal structure prediction and pair-wise intermolecular energy calculations). Depending on the relative humidity the hydrate contains between 0 and 0.33 molecules of water per molecule DDS. The crystal structure is retained upon dehydration indicating that DDS hydrate shows a non-stoichiometric (de)hydration behavior. Unexpectedly, the water molecules are not located in structural channels but at isolated-sites of the host framework, which is counterintuitively for a hydrate with non-stoichiometric behavior. The water-DDS interactions were estimated to be weaker than water-host interactions that are commonly observed in stoichiometric hydrates and the lattice energies of the isomorphic dehydration product (hydrate structure without water molecules) and (form III) differ only by ~1 kJ mol−1. The computational generation of hypothetical monohydrates confirms that the hydrate with the unusual DDS:water ratio of 3:1 is more stable than a feasible monohydrate structure. Overall, this study highlights that a deeper understanding of the formation of hydrates with non-stoichiometric behavior requires a multidisciplinary approach including suitable experimental and computational methods providing a firm basis for the development and manufacturing of high quality drug products. PMID:29520359

The onset of calcium carbonate nucleation: a density functional theory molecular dynamics and hybrid microsolvation/continuum study.

PubMed

Di Tommaso, Devis; de Leeuw, Nora H

2008-06-12

Density functional theory (Perdew-Burke-Ernzerhof) based methods have been used to study the structure and hydration environment of the building blocks of CaCO 3 in aqueous solutions of calcium bicarbonate and calcium carbonate. Car-Parrinello molecular dynamics simulations of Ca(2+)/CO3(2-) and Ca (2+)/HCO3(-) in explicit water were performed to investigate the formation of CaCO3 and the hydration shell of the solvated hetero-ion pair. Our simulations show that the formation of the monomer of CaCO3 occurs with an associative mechanism and that the dominant building block of calcium (bi)carbonate in aqueous solution is Ca[eta(1)-(H)CO3](H2O)5, i.e., the preferred hydration number is five, while the (bi)carbonate is coordinated to the calcium in a monodentate mode. This result agrees with static calculations, where a hybrid approach using a combination of explicit solvent molecules and a polarizable continuum model has been applied to compute the solvation free energies of calcium bicarbonate species. Furthermore, the discrete-continuum calculations predict that the Ca(HCO3)2 and Ca(HCO3)3(-) species are stable in an aqueous environment preferentially as Ca(HCO3)2(H2O)4 and Ca(HCO3)3(H2O)2(-), respectively.

Reflective terahertz (THz) imaging: system calibration using hydration phantoms

NASA Astrophysics Data System (ADS)

Bajwa, Neha; Garritano, James; Lee, Yoon Kyung; Tewari, Priyamvada; Sung, Shijun; Maccabi, Ashkan; Nowroozi, Bryan; Babakhanian, Meghedi; Sanghvi, Sajan; Singh, Rahul; Grundfest, Warren; Taylor, Zachary

2013-02-01

Terahertz (THz) hydration sensing continues to gain traction in the medical imaging community due to its unparalleled sensitivity to tissue water content. Rapid and accurate detection of fluid shifts following induction of thermal skin burns as well as remote corneal hydration sensing have been previously demonstrated in vivo using reflective, pulsed THz imaging. The hydration contrast sensing capabilities of this technology were recently confirmed in a parallel 7 Tesla Magnetic Resonance (MR) imaging study, in which burn areas are associated with increases in local mobile water content. Successful clinical translation of THz sensing, however, still requires quantitative assessments of system performance measurements, specifically hydration concentration sensitivity, with tissue substitutes. This research aims to calibrate the sensitivity of a novel, reflective THz system to tissue water content through the use of hydration phantoms for quantitative comparisons of THz hydration imagery.Gelatin phantoms were identified as an appropriate tissue-mimicking model for reflective THz applications, and gel composition, comprising mixtures of water and protein, was varied between 83% to 95% hydration, a physiologically relevant range. A comparison of four series of gelatin phantom studies demonstrated a positive linear relationship between THz reflectivity and water concentration, with statistically significant hydration sensitivities (p < .01) ranging between 0.0209 - 0.038% (reflectivity: %hydration). The THz-phantom interaction is simulated with a three-layer model using the Transfer Matrix Method with agreement in hydration trends. Having demonstrated the ability to accurately and noninvasively measure water content in tissue equivalent targets with high sensitivity, reflective THz imaging is explored as a potential tool for early detection and intervention of corneal pathologies.

Analysis of Decomposition for Structure I Methane Hydrate by Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Wei, Na; Sun, Wan-Tong; Meng, Ying-Feng; Liu, An-Qi; Zhou, Shou-Wei; Guo, Ping; Fu, Qiang; Lv, Xin

2018-05-01

Under multi-nodes of temperatures and pressures, microscopic decomposition mechanisms of structure I methane hydrate in contact with bulk water molecules have been studied through LAMMPS software by molecular dynamics simulation. Simulation system consists of 482 methane molecules in hydrate and 3027 randomly distributed bulk water molecules. Through analyses of simulation results, decomposition number of hydrate cages, density of methane molecules, radial distribution function for oxygen atoms, mean square displacement and coefficient of diffusion of methane molecules have been studied. A significant result shows that structure I methane hydrate decomposes from hydrate-bulk water interface to hydrate interior. As temperature rises and pressure drops, the stabilization of hydrate will weaken, decomposition extent will go deep, and mean square displacement and coefficient of diffusion of methane molecules will increase. The studies can provide important meanings for the microscopic decomposition mechanisms analyses of methane hydrate.

Water permeability in hydrate-bearing sediments: A pore-scale study

NASA Astrophysics Data System (ADS)

Dai, Sheng; Seol, Yongkoo

2014-06-01

Permeability is a critical parameter governing methane flux and fluid flow in hydrate-bearing sediments; however, limited valid data are available due to experimental challenges. Here we investigate the relationship between apparent water permeability (k') and hydrate saturation (Sh), accounting for hydrate pore-scale growth habit and meso-scale heterogeneity. Results from capillary tube models rely on cross-sectional tube shapes and hydrate pore habits, thus are appropriate only for sediments with uniform hydrate distribution and known hydrate pore character. Given our pore network modeling results showing that accumulating hydrate in sediments decreases sediment porosity and increases hydraulic tortuosity, we propose a modified Kozeny-Carman model to characterize water permeability in hydrate-bearing sediments. This model agrees well with experimental results and can be easily implemented in reservoir simulators with no empirical variables other than Sh. Results are also relevant to flow through other natural sediments that undergo diagenesis, salt precipitation, or bio-clogging.

Structure and Hydration of Highly-Branched, Monodisperse Phytoglycogen Nanoparticles

DOE PAGES

Nickels, Jonathan D.; Atkinson, John; Papp-Szabo, Erzsebet; ...

2016-01-30

Phytoglycogen is a naturally occurring polysaccharide nanoparticle made up of extensively branched glucose monomers. It has a number of unusual and advantageous properties, such as high water retention, low viscosity, and high stability in water, which make this biomaterial a promising candidate for a wide variety of applications. For this paper, we have characterized the structure and hydration of aqueous dispersions of phytoglycogen nanoparticles using neutron scattering. Small angle neutron scattering results suggest that the phytoglycogen nanoparticles behave similar to hard sphere colloids and are hydrated by a large number of water molecules (each nanoparticle contains between 250% and 285%more » of its mass in water). This suggests that phytoglycogen is an ideal sample in which to study the dynamics of hydration water. To this end, we used quasielastic neutron scattering (QENS) to provide an independent and consistent measure of the hydration number, and to estimate the retardation factor (or degree of water slow-down) for hydration water translational motions. These data demonstrate a length-scale dependence in the measured retardation factors that clarifies the origin of discrepancies between retardation factor values reported for hydration water using different experimental techniques. Finally, the present approach can be generalized to other systems containing nanoconfined water.« less

Combustion of Methane Hydrate

NASA Astrophysics Data System (ADS)

Roshandell, Melika

A significant methane storehouse is in the form of methane hydrates on the sea floor and in the arctic permafrost. Methane hydrates are ice-like structures composed of water cages housing a guest methane molecule. This caged methane represents a resource of energy and a potential source of strong greenhouse gas. Most research related to methane hydrates has been focused on their formation and dissociation because they can form solid plugs that complicate transport of oil and gas in pipelines. This dissertation explores the direct burning of these methane hydrates where heat from the combustion process dissociates the hydrate into water and methane, and the released methane fuels the methane/air diffusion flame heat source. In contrast to the pipeline applications, very little research has been done on the combustion and burning characteristics of methane hydrates. This is the first dissertation on this subject. In this study, energy release and combustion characteristics of methane hydrates were investigated both theoretically and experimentally. The experimental study involved collaboration with another research group, particularly in the creation of methane hydrate samples. The experiments were difficult because hydrates form at high pressure within a narrow temperature range. The process can be slow and the resulting hydrate can have somewhat variable properties (e.g., extent of clathration, shape, compactness). The experimental study examined broad characteristics of hydrate combustion, including flame appearance, burning time, conditions leading to flame extinguishment, the amount of hydrate water melted versus evaporated, and flame temperature. These properties were observed for samples of different physical size. Hydrate formation is a very slow process with pure water and methane. The addition of small amounts of surfactant increased substantially the hydrate formation rate. The effects of surfactant on burning characteristics were also studied. One finding from the experimental component of the research was that hydrates can burn completely, and that they burn most rapidly just after ignition and then burn steadily when some of the water in the dissociated zone is allowed to drain away. Excessive surfactant in the water creates a foam layer around the hydrate that acts as an insulator. The layer prevents sufficient heat flux from reaching the hydrate surface below the foam to release additional methane and the hydrate flame extinguishes. No self-healing or ice-freezing processes were observed in any of the combustion experiments. There is some variability, but a typical hydrate flame is receiving between one and two moles of water vapor from the liquid dissociated zone of the hydrate for each mole of methane it receives from the dissociating solid region. This limits the flame temperature to approximately 1800 K. In the theoretical portion of the study, a physical model using an energy balance from methane combustion was developed to understand the energy transfer between the three phases of gas, liquid and solid during the hydrate burn. Also this study provides an understanding of the different factors impacting the hydrate's continuous burn, such as the amount of water vapor in the flame. The theoretical study revealed how the water layer thickness on the hydrate surface, and its effect on the temperature gradient through the dissociated zone, plays a significant role in the hydrate dissociation rate and methane release rate. Motivated by the above mentioned observation from the theoretical analysis, a 1-D two-phase numerical simulation based on a moving front model for hydrate dissociation from a thermal source was developed. This model was focused on the dynamic growth of the dissociated zone and its effect on the dissociation rate. The model indicated that the rate of hydrate dissociation with a thermal source is a function of the dissociated zone thickness. It shows that in order for a continuous dissociation and methane release, some of the water from the dissociated zone needs to be drained. The results are consistent with the experimental observations. The understanding derived from the experiments and the numerical model permitted a brief exploration into the potential effects of pressure on the combustion of methane hydrates. The prediction is that combustion should improve under high pressure conditions because the evaporation of water is suppressed allowing more energy into the dissociation. Future experiments are needed to validate these initial findings.

Gas hydrate inhibition by perturbation of liquid water structure

NASA Astrophysics Data System (ADS)

Sa, Jeong-Hoon; Kwak, Gye-Hoon; Han, Kunwoo; Ahn, Docheon; Lee, Kun-Hong

2015-06-01

Natural gas hydrates are icy crystalline materials that contain hydrocarbons, which are the primary energy source for this civilization. The abundance of naturally occurring gas hydrates leads to a growing interest in exploitation. Despite their potential as energy resources and in industrial applications, there is insufficient understanding of hydrate kinetics, which hinders the utilization of these invaluable resources. Perturbation of liquid water structure by solutes has been proposed to be a key process in hydrate inhibition, but this hypothesis remains unproven. Here, we report the direct observation of the perturbation of the liquid water structure induced by amino acids using polarized Raman spectroscopy, and its influence on gas hydrate nucleation and growth kinetics. Amino acids with hydrophilic and/or electrically charged side chains disrupted the water structure and thus provided effective hydrate inhibition. The strong correlation between the extent of perturbation by amino acids and their inhibition performance constitutes convincing evidence for the perturbation inhibition mechanism. The present findings bring the practical applications of gas hydrates significantly closer, and provide a new perspective on the freezing and melting phenomena of naturally occurring gas hydrates.

Gas hydrate inhibition by perturbation of liquid water structure.

PubMed

Sa, Jeong-Hoon; Kwak, Gye-Hoon; Han, Kunwoo; Ahn, Docheon; Lee, Kun-Hong

2015-06-17

Natural gas hydrates are icy crystalline materials that contain hydrocarbons, which are the primary energy source for this civilization. The abundance of naturally occurring gas hydrates leads to a growing interest in exploitation. Despite their potential as energy resources and in industrial applications, there is insufficient understanding of hydrate kinetics, which hinders the utilization of these invaluable resources. Perturbation of liquid water structure by solutes has been proposed to be a key process in hydrate inhibition, but this hypothesis remains unproven. Here, we report the direct observation of the perturbation of the liquid water structure induced by amino acids using polarized Raman spectroscopy, and its influence on gas hydrate nucleation and growth kinetics. Amino acids with hydrophilic and/or electrically charged side chains disrupted the water structure and thus provided effective hydrate inhibition. The strong correlation between the extent of perturbation by amino acids and their inhibition performance constitutes convincing evidence for the perturbation inhibition mechanism. The present findings bring the practical applications of gas hydrates significantly closer, and provide a new perspective on the freezing and melting phenomena of naturally occurring gas hydrates.

Methane hydrate induced permeability modification for multiphase flow in unsaturated porous media

NASA Astrophysics Data System (ADS)

Seol, Yongkoo; Kneafsey, Timothy J.

2011-08-01

An experimental study was performed using X-ray computed tomography (CT) scanning to capture three-dimensional (3-D) methane hydrate distributions and potential discrete flow pathways in a sand pack sample. A numerical study was also performed to develop and analyze empirical relations that describe the impacts of hydrate accumulation habits within pore space (e.g., pore filling or grain cementing) on multiphase fluid migration. In the experimental study, water was injected into a hydrate-bearing sand sample that was monitored using an X-ray CT scanner. The CT images were converted into numerical grid elements, providing intrinsic sample data including porosity and phase saturations. The impacts of hydrate accumulation were examined by adapting empirical relations into the flow simulations as additional relations governing the evolution of absolute permeability of hydrate bearing sediment with hydrate deposition. The impacts of pore space hydrate accumulation habits on fluid migration were examined by comparing numerical predictions with experimentally measured water saturation distributions and breakthrough curves. A model case with 3-D heterogeneous initial conditions (hydrate saturation, porosity, and water saturation) and pore body-preferred hydrate accumulations best captured water migration behavior through the hydrate-bearing sample observed in the experiment. In the best matching model, absolute permeability in the hydrate bearing sample does not decrease significantly with increasing hydrate saturation until hydrate saturation reaches about 40%, after which it drops rapidly, and complete blockage of flow through the sample can occur as hydrate accumulations approach 70%. The result highlights the importance of permeability modification due to hydrate accumulation habits when predicting multiphase flow through high-saturation, reservoir quality hydrate-bearing sediments.

Waters of Hydration of Cupric Hydrates: A Comparison between Heating and Absorbance Methods

ERIC Educational Resources Information Center

Barlag, Rebecca; Nyasulu, Frazier

2011-01-01

The empirical formulas of four cupric hydrates are determined by measuring the absorbance in aqueous solution. The Beer-Lambert Law is verified by constructing a calibration curve of absorbance versus known Cu[superscript 2+](aq) concentration. A solution of the unknown hydrate is prepared by using 0.2-0.3 g of hydrate, and water is added such…

Structure, hydrolysis, and diffusion of aqueous vanadium ions from Car-Parrinello molecular dynamics

NASA Astrophysics Data System (ADS)

Jiang, Zhen; Klyukin, Konstantin; Alexandrov, Vitaly

2016-09-01

A molecular level understanding of the properties of electroactive vanadium species in aqueous solution is crucial for enhancing the performance of vanadium redox flow batteries. Here, we employ Car-Parrinello molecular dynamics simulations based on density functional theory to investigate the hydration structures, first hydrolysis reaction, and diffusion of aqueous V2+, V3+, VO2+, and VO 2+ ions at 300 K. The results indicate that the first hydration shell of both V2+ and V3+ contains six water molecules, while VO2+ is coordinated to five and VO 2+ to three water ligands. The first acidity constants (pKa) estimated using metadynamics simulations are 2.47, 3.06, and 5.38 for aqueous V3+, VO 2+ , and VO2+, respectively, while V2+ is predicted to be a fairly weak acid in aqueous solution with a pKa value of 6.22. We also show that the presence of chloride ions in the first coordination sphere of the aqueous VO 2+ ion has a significant impact on water hydrolysis leading to a much higher pKa value of 4.8. This should result in a lower propensity of aqueous VO 2+ for oxide precipitation reaction in agreement with experimental observations for chloride-based electrolyte solutions. The computed diffusion coefficients of vanadium species in water at room temperature are found to increase as V 3 + < VO 2 + < V O 2 + < V 2 + and thus correlate with the simulated hydrolysis constants, namely, the higher the pKa value, the greater the diffusion coefficient.

Organic ion association in aqueous phase and ab initio-based force fields: The case of carboxylate/ammonium salts

NASA Astrophysics Data System (ADS)

Houriez, Céline; Vallet, Valérie; Réal, Florent; Meot-Ner Mautner, Michael; Masella, Michel

2017-10-01

We performed molecular dynamics simulations of carboxylate/methylated ammonium ion pairs solvated in bulk water and of carboxylate/methylated ammonium salt solutions at ambient conditions using an ab initio-based polarizable force field whose parameters are assigned to reproduce only high end quantum computations, at the Møller-Plesset second-order perturbation theory/complete basis set limit level, regarding single ions and ion pairs as isolated and micro-hydrated in gas phase. Our results agree with the available experimental results regarding carboxylate/ammonium salt solutions. For instance, our force field approach predicts the percentage of acetate associated with ammonium ions in CH3 COO-/CH3 NH3+ solutions at the 0.2-0.8M concentration scale to range from 14% to 35%, in line with the estimates computed from the experimental ion association constant in liquid water. Moreover our simulations predict the number of water molecules released from the ion first hydration shell to the bulk upon ion association to be about 2.0 ± 0.6 molecules for acetate/protonated amine ion pairs, 3.1 ± 1.5 molecules for the HCOO-/NH4+ pair and 3.3 ± 1.2 molecules for the CH3COO-/(CH3)4N+ pair. For protonated amine-based ion pairs, these values are in line with experiment for alkali/halide pairs solvated in bulk water. All these results demonstrate the promising feature of ab initio-based force fields, i.e., their capacity in accurately modeling chemical systems that cannot be readily investigated using available experimental techniques.

Molecular basis for polyol-induced protein stability revealed by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Liu, Fu-Feng; Ji, Luo; Zhang, Lin; Dong, Xiao-Yan; Sun, Yan

2010-06-01

Molecular dynamics simulations of chymotrypsin inhibitor 2 in different polyols (glycerol, xylitol, sorbitol, trehalose, and sucrose) at 363 K were performed to probe the molecular basis of the stabilizing effect, and the data in water, ethanol, and glycol were compared. It is found that protein protection by polyols is positively correlated with both the molecular volume and the fractional polar surface area, and the former contributes more significantly to the protein's stability. Polyol molecules have only a few direct hydrogen bonds with the protein, and the number of hydrogen bonds between a polyol and the protein is similar for different polyols. Thus, it is concluded that the direct interactions contribute little to the stabilizing effect. It is clarified that the preferential exclusion of the polyols is the origin of their protective effects, and it increases with increasing polyol size. Namely, there is preferential hydration on the protein surface (2 Å), and polyol molecules cluster around the protein at a distance of about 4 Å. The preferential exclusion of polyols leads to indirect interactions that prevent the protein from thermal unfolding. The water structure becomes more ordered with increasing the polyol size. So, the entropy of water in the first hydration shell decreases, and a larger extent of decrease is observed with increasing polyol size, leading to larger transfer free energy. The findings suggest that polyols protect the protein from thermal unfolding via indirect interactions. The work has thus elucidated the molecular mechanism of structural stability of the protein in polyol solutions.

Role of naturally occurring gas hydrates in sediment transport

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

McIver, R.D.

1982-06-01

Naturally occurring gas hydrates have the potential to store enormous volumes of both gas and water in semi-solid form in ocean-bottom sediments and then to release that gas and water when the hydrate's equilibrium condition are disturbed. Therefore, hydrates provide a potential mechanism for transporting large volumes of sediments. Under the combined low bottom-water temperatures and moderate hydrostatic pressures that exist over most of the continental slopes and all of the continental rises and abyssal plains, hydrocarbon gases at or near saturation in the interstitial waters of the near-bottom sediments will form hydrates. The gas can either be autochthonous, microbiallymore » produced gas, or allochthonous, catagenic gas from deeper sediments. Equilibrium conditions that stabilize hydrated sediments may be disturbed, for example, by continued sedimentation or by lowering of sea level. In either case, some of the solid gas-water matrix decomposes. Released gas and water volume exceeds the volume occupied by the hydrate, so the internal pressure rises - drastically if large volumes of hydrate are decomposed. Part of the once rigid sediment is converted to a gas- and water-rich, relatively low density mud. When the internal pressure, due to the presence of the compressed gas or to buoyancy, is sufficiently high, the overlying sediment may be lifted and/or breached, and the less dense, gas-cut mud may break through. Such hydrate-related phenomena can cause mud diapirs, mud volcanos, mud slides, or turbidite flows, depending on sediment configuration and bottom topography. 4 figures.« less

Identification of Clathrate Hydrates, Hexagonal Ice, Cubic Ice, and Liquid Water in Simulations: the CHILL+ Algorithm.

PubMed

Nguyen, Andrew H; Molinero, Valeria

2015-07-23

Clathrate hydrates and ice I are the most abundant crystals of water. The study of their nucleation, growth, and decomposition using molecular simulations requires an accurate and efficient algorithm that distinguishes water molecules that belong to each of these crystals and the liquid phase. Existing algorithms identify ice or clathrates, but not both. This poses a challenge for cases in which ice and hydrate coexist, such as in the synthesis of clathrates from ice and the formation of ice from clathrates during self-preservation of methane hydrates. Here we present an efficient algorithm for the identification of clathrate hydrates, hexagonal ice, cubic ice, and liquid water in molecular simulations. CHILL+ uses the number of staggered and eclipsed water-water bonds to identify water molecules in cubic ice, hexagonal ice, and clathrate hydrate. CHILL+ is an extension of CHILL (Moore et al. Phys. Chem. Chem. Phys. 2010, 12, 4124-4134), which identifies hexagonal and cubic ice but not clathrates. In addition to the identification of hydrates, CHILL+ significantly improves the detection of hexagonal ice up to its melting point. We validate the use of CHILL+ for the identification of stacking faults in ice and the nucleation and growth of clathrate hydrates. To our knowledge, this is the first algorithm that allows for the simultaneous identification of ice and clathrate hydrates, and it does so in a way that is competitive with respect to existing methods used to identify any of these crystals.

Proton transfer reactions and dynamics in CH(3)OH-H(3)O(+)-H(2)O complexes.

PubMed

Sagarik, Kritsana; Chaiwongwattana, Sermsiri; Vchirawongkwin, Viwat; Prueksaaroon, Supakit

2010-01-28

Proton transfer reactions and dynamics in hydrated complexes formed from CH(3)OH, H(3)O(+) and H(2)O were studied using theoretical methods. The investigations began with searching for equilibrium structures at low hydration levels using the DFT method, from which active H-bonds in the gas phase and continuum aqueous solution were characterized and analyzed. Based on the asymmetric stretching coordinates (Deltad(DA)), four H-bond complexes were identified as potential transition states, in which the most active unit is represented by an excess proton nearly equally shared between CH(3)OH and H(2)O. These cannot be definitive due to the lack of asymmetric O-H stretching frequencies (nu(OH)) which are spectral signatures of transferring protons. Born-Oppenheimer molecular dynamics (BOMD) simulations revealed that, when the thermal energy fluctuations and dynamics were included in the model calculations, the spectral signatures at nu(OH) approximately 1000 cm(-1) appeared. In continuum aqueous solution, the H-bond complex with incomplete water coordination at charged species turned out to be the only active transition state. Based on the assumption that the thermal energy fluctuations and dynamics could temporarily break the H-bonds linking the transition state complex and water molecules in the second hydration shell, elementary reactions of proton transfer were proposed. The present study showed that, due to the coupling among various vibrational modes, the discussions on proton transfer reactions cannot be made based solely on static proton transfer potentials. Inclusion of thermal energy fluctuations and dynamics in the model calculations, as in the case of BOMD simulations, together with systematic IR spectral analyses, have been proved to be the most appropriate theoretical approaches.

"Structure-making" ability of Na+ in dilute aqueous solution: an ONIOM-XS MD simulation study.

PubMed

Sripa, Pattrawan; Tongraar, Anan; Kerdcharoen, Teerakiat

2013-02-28

An ONIOM-XS MD simulation has been performed to characterize the "structure-making" ability of Na(+) in dilute aqueous solution. The region of most interest, i.e., a sphere that includes Na(+) and its surrounding water molecules, was treated at the HF level of accuracy using LANL2DZ and DZP basis sets for the ion and waters, respectively, whereas the rest of the system was described by classical pair potentials. Detailed analyzes of the ONIOM-XS MD trajectories clearly show that Na(+) is able to order the structure of waters in its surroundings, forming two prevalent Na(+)(H(2)O)(5) and Na(+)(H(2)O)(6) species. Interestingly, it is observed that these 5-fold and 6-fold coordinated complexes can convert back and forth with some degrees of flexibility, leading to frequent rearrangements of the Na(+) hydrates as well as numerous attempts of inner-shell water molecules to interchange with waters in the outer region. Such a phenomenon clearly demonstrates the weak "structure-making" ability of Na(+) in aqueous solution.

Consequences of CO2 solubility for hydrate formation from carbon dioxide containing water and other impurities.

PubMed

Kvamme, Bjørn; Kuznetsova, Tatiana; Jensen, Bjørnar; Stensholt, Sigvat; Bauman, Jordan; Sjøblom, Sara; Nes Lervik, Kim

2014-05-14

Deciding on the upper bound of water content permissible in a stream of dense carbon dioxide under pipeline transport conditions without facing the risks of hydrate formation is a complex issue. In this work, we outline and analyze ten primary routes of hydrate formation inside a rusty pipeline, with hydrogen sulfide, methane, argon, and nitrogen as additional impurities. A comprehensive treatment of equilibrium absolute thermodynamics as applied to multiple hydrate phase transitions is provided. We also discuss in detail the implications of the Gibbs phase rule that make it necessary to consider non-equilibrium thermodynamics. The analysis of hydrate formation risk has been revised for the dominant routes, including the one traditionally considered in industrial practice and hydrate calculators. The application of absolute thermodynamics with parameters derived from atomistic simulations leads to several important conclusions regarding the impact of hydrogen sulfide. When present at studied concentrations below 5 mol%, the presence of hydrogen sulfide will only support the carbon-dioxide-dominated hydrate formation on the phase interface between liquid water and hydrate formers entering from the carbon dioxide phase. This is in contrast to a homogeneous hydrate nucleation and growth inside the aqueous solution bulk. Our case studies indicate that hydrogen sulfide at higher than 0.1 mol% concentration in carbon dioxide can lead to growth of multiple hydrate phases immediately adjacent to the adsorbed water layers. We conclude that hydrate formation via water adsorption on rusty pipeline walls will be the dominant contributor to the hydrate formation risk, with initial concentration of hydrogen sulfide being the critical factor.

Microwave absorption in substances that form hydration layers with water

NASA Astrophysics Data System (ADS)

Garner, H. R.; Ohkawa, T.; Tuason, O.; Lee, R. L.

1990-12-01

The microwave absorption of certain water soluble polymers (polyethylene glycol, polyvinyl pyrrolidone, proteins, and DNA) in solution is composed of three parts: absorption in the free water, absorption in the substance, and absorption in the hydration layer. Ethanol, sucrose, glycerol, and sodium acetate, which form weak hydrogen bonds or have an ionic nature in aqueous solutions, also have microwave absorption signatures similar to polymers that form hydration layers. The frequency-dependent absorption of the free water and of the hydration layer water is described by a simple Debye relaxation model. The absorption per unit sample volume attributable to the hydration layer is solute concentration dependent, and a simple model is used to describe the dependence. The hydration-layer relaxation time was found to vary from substance to substance and with solute concentration. The relaxation time was also found to be independent of solute length.

Formation of Structured Water and Gas Hydrate by the Use of Xenon Gas in Vegetable Tissue

NASA Astrophysics Data System (ADS)

Ando, Hiroko; Suzuki, Toru; Kawagoe, Yoshinori; Makino, Yoshio; Oshita, Seiichi

Freezing is a valuable technique for food preservation. However, vegetables are known to be softening remarkably after freezing and thawing process. It is expected to find alternative technique instead of freezing. Recently, the application of structured water and/or gas hydrate had been attempted to prolong the preservation of vegetable. In this study, the formation process of structure water and/or gas hydrate in pure water and carrot tissue was investigated by using NMR relaxation times, T1 and T2, of which applying condition was up to 0.4MPa and 0.8MPa at 5oC. Under the pressure of 0.4MPa, no gas hydrate was appeared, however, at 0.8MPa, formation of gas hydrate was recognized in both water and carrot tissue. Once the gas hydrate formation process in carrot tissue started, T1 and T2 increased remarkably. After that, as the gas hydrate developed, then T1 and T2 turned to decrease. Since this phenomenon was not observed in pure water, it is suggested that behavior of NMR relaxation time just after the formation of gas hydrate in carrot tissue may be peculiar to compartment system such as inter and intracellular spaces.

Optimization of linear and branched alkane interactions with water to simulate hydrophobic hydration

NASA Astrophysics Data System (ADS)

Ashbaugh, Henry S.; Liu, Lixin; Surampudi, Lalitanand N.

2011-08-01

Previous studies of simple gas hydration have demonstrated that the accuracy of molecular simulations at capturing the thermodynamic signatures of hydrophobic hydration is linked both to the fidelity of the water model at replicating the experimental liquid density at ambient pressure and an accounting of polarization interactions between the solute and water. We extend those studies to examine alkane hydration using the transferable potentials for phase equilibria united-atom model for linear and branched alkanes, developed to reproduce alkane phase behavior, and the TIP4P/2005 model for water, which provides one of the best descriptions of liquid water for the available fixed-point charge models. Alkane site/water oxygen Lennard-Jones cross interactions were optimized to reproduce the experimental alkane hydration free energies over a range of temperatures. The optimized model reproduces the hydration free energies of the fitted alkanes with a root mean square difference between simulation and experiment of 0.06 kcal/mol over a wide temperature range, compared to 0.44 kcal/mol for the parent model. The optimized model accurately reproduces the temperature dependence of hydrophobic hydration, as characterized by the hydration enthalpies, entropies, and heat capacities, as well as the pressure response, as characterized by partial molar volumes.

Multi-scale model for the hierarchical architecture of native cellulose hydrogels.

PubMed

Martínez-Sanz, Marta; Mikkelsen, Deirdre; Flanagan, Bernadine; Gidley, Michael J; Gilbert, Elliot P

2016-08-20

The structure of protiated and deuterated cellulose hydrogels has been investigated using a multi-technique approach combining small-angle scattering with diffraction, spectroscopy and microscopy. A model for the multi-scale structure of native cellulose hydrogels is proposed which highlights the essential role of water at different structural levels characterised by: (i) the existence of cellulose microfibrils containing an impermeable crystalline core surrounded by a partially hydrated paracrystalline shell, (ii) the creation of a strong network of cellulose microfibrils held together by hydrogen bonding to form cellulose ribbons and (iii) the differential behaviour of tightly bound water held within the ribbons compared to bulk solvent. Deuterium labelling provides an effective platform on which to further investigate the role of different plant cell wall polysaccharides in cellulose composite formation through the production of selectively deuterated cellulose composite hydrogels. Copyright © 2016 Elsevier Ltd. All rights reserved.

Coupling of the hydration water dynamics and the internal dynamics of actin detected by quasielastic neutron scattering

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

Fujiwara, Satoru, E-mail: fujiwara.satoru@jaea.go.jp; Plazanet, Marie; Oda, Toshiro

2013-02-15

Highlights: ► Quasielastic neutron scattering spectra of F-actin and G-actin were measured. ► Analysis of the samples in D{sub 2}O and H{sub 2}O provided the spectra of hydration water. ► The first layer hydration water around F-actin is less mobile than around G-actin. ► This difference in hydration water is in concert with the internal dynamics of actin. ► Water outside the first layer behaves bulk-like but influenced by the first layer. -- Abstract: In order to characterize dynamics of water molecules around F-actin and G-actin, quasielastic neutron scattering experiments were performed on powder samples of F-actin and G-actin, hydratedmore » either with D{sub 2}O or H{sub 2}O, at hydration ratios of 0.4 and 1.0. By combined analysis of the quasielastic neutron scattering spectra, the parameter values characterizing the dynamics of the water molecules in the first hydration layer and those of the water molecules outside of the first layer were obtained. The translational diffusion coefficients (D{sub T}) of the hydration water in the first layer were found to be 1.2 × 10{sup −5} cm{sup 2}/s and 1.7 × 10{sup −5} cm{sup 2}/s for F-actin and G-actin, respectively, while that for bulk water was 2.8 × 10{sup −5} cm{sup 2}/s. The residence times were 6.6 ps and 5.0 ps for F-actin and G-actin, respectively, while that for bulk water was 0.62 ps. These differences between F-actin and G-actin, indicating that the hydration water around G-actin is more mobile than that around F-actin, are in concert with the results of the internal dynamics of F-actin and G-actin, showing that G-actin fluctuates more rapidly than F-actin. This implies that the dynamics of the hydration water is coupled to the internal dynamics of the actin molecules. The D{sub T} values of the water molecules outside of the first hydration layer were found to be similar to that of bulk water though the residence times are strongly affected by the first hydration layer. This supports the recent observation on intracellular water that shows bulk-like behavior.« less

Observations related to tetrahydrofuran and methane hydrates for laboratory studies of hydrate-bearing sediments

USGS Publications Warehouse

Lee, J.Y.; Yun, T.S.; Santamarina, J.C.; Ruppel, C.

2007-01-01

The interaction among water molecules, guest gas molecules, salts, and mineral particles determines the nucleation and growth behavior of gas hydrates in natural sediments. Hydrate of tetrahydrofuran (THF) has long been used for laboratory studies of gas hydrate-bearing sediments to provide close control on hydrate concentrations and to overcome the long formation history of methane hydrate from aqueous phase methane in sediments. Yet differences in the polarizability of THF (polar molecule) compared to methane (nonpolar molecule) raise questions about the suitability of THF as a proxy for methane in the study of hydrate-bearing sediments. From existing data and simple macroscale experiments, we show that despite its polar nature, THF's large molecular size results in low permittivity, prevents it from dissolving precipitated salts, and hinders the solvation of ions on dry mineral surfaces. In addition, the interfacial tension between water and THF hydrate is similar to that between water and methane hydrate. The processes that researchers choose for forming hydrate in sediments in laboratory settings (e.g., from gas, liquid, or ice) and the pore-scale distribution of the hydrate that is produced by each of these processes likely have a more pronounced effect on the measured macroscale properties of hydrate-bearing sediments than do differences between THF and methane hydrates themselves.

Detecting gas hydrate behavior in crude oil using NMR.

PubMed

Gao, Shuqiang; House, Waylon; Chapman, Walter G

2006-04-06

Because of the associated experimental difficulties, natural gas hydrate behavior in black oil is poorly understood despite its grave importance in deep-water flow assurance. Since the hydrate cannot be visually observed in black oil, traditional methods often rely on gas pressure changes to monitor hydrate formation and dissociation. Because gases have to diffuse through the liquid phase for hydrate behavior to create pressure responses, the complication of gas mass transfer is involved and hydrate behavior is only indirectly observed. This pressure monitoring technique encounters difficulties when the oil phase is too viscous, the amount of water is too small, or the gas phase is absent. In this work we employ proton nuclear magnetic resonance (NMR) spectroscopy to observe directly the liquid-to-solid conversion of the water component in black oil emulsions. The technique relies on two facts. The first, well-known, is that water becomes essentially invisible to liquid state NMR as it becomes immobile, as in hydrate or ice formation. The second, our recent finding, is that in high magnetic fields of sufficient homogeneity, it is possible to distinguish water from black oil spectrally by their chemical shifts. By following changes in the area of the water peak, the process of hydrate conversion can be measured, and, at lower temperatures, the formation of ice. Taking only seconds to accomplish, this measurement is nearly direct in contrast to conventional techniques that measure the pressure changes of the whole system and assume these changes represent formation or dissociation of hydrates - rather than simply changes in solubility. This new technique clearly can provide accurate hydrate thermodynamic data in black oils. Because the technique measures the total mobile water with rapidity, extensions should prove valuable in studying the dynamics of phase transitions in emulsions.

Nuclear Well Log Properties of Natural Gas Hydrate Reservoirs

NASA Astrophysics Data System (ADS)

Burchwell, A.; Cook, A.

2015-12-01

Characterizing gas hydrate in a reservoir typically involves a full suite of geophysical well logs. The most common method involves using resistivity measurements to quantify the decrease in electrically conductive water when replaced with gas hydrate. Compressional velocity measurements are also used because the gas hydrate significantly strengthens the moduli of the sediment. At many gas hydrate sites, nuclear well logs, which include the photoelectric effect, formation sigma, carbon/oxygen ratio and neutron porosity, are also collected but often not used. In fact, the nuclear response of a gas hydrate reservoir is not known. In this research we will focus on the nuclear log response in gas hydrate reservoirs at the Mallik Field at the Mackenzie Delta, Northwest Territories, Canada, and the Gas Hydrate Joint Industry Project Leg 2 sites in the northern Gulf of Mexico. Nuclear logs may add increased robustness to the investigation into the properties of gas hydrates and some types of logs may offer an opportunity to distinguish between gas hydrate and permafrost. For example, a true formation sigma log measures the thermal neutron capture cross section of a formation and pore constituents; it is especially sensitive to hydrogen and chlorine in the pore space. Chlorine has a high absorption potential, and is used to determine the amount of saline water within pore spaces. Gas hydrate offers a difference in elemental composition compared to water-saturated intervals. Thus, in permafrost areas, the carbon/oxygen ratio may vary between gas hydrate and permafrost, due to the increase of carbon in gas hydrate accumulations. At the Mallik site, we observe a hydrate-bearing sand (1085-1107 m) above a water-bearing sand (1107-1140 m), which was confirmed through core samples and mud gas analysis. We observe a decrease in the photoelectric absorption of ~0.5 barnes/e-, as well as an increase in the formation sigma readings of ~5 capture units in the water-bearing sand as compared to the hydrate sand interval. This is further correlated with the carbon/oxygen ratio showing a decrease of 20% in the water sand compared to the hydrate sand above. In future research, we will quantify the effect of gas hydrate on the nuclear logs at the Mallik well and compare it to wells in the Gulf of Mexico.

Vibrational spectroscopy of water in hydrated lipid multi-bilayers. II. Two-dimensional infrared and peak shift observables within different theoretical approximations.

PubMed

Gruenbaum, Scott M; Pieniazek, Piotr A; Skinner, J L

2011-10-28

In a previous report, we calculated the infrared absorption spectrum and both the isotropic and anisotropic pump-probe signals for the OD stretch of isotopically dilute water in dilauroylphosphatidylcholine (DLPC) multi-bilayers as a function of the lipid hydration level. These results were then compared to recent experimental measurements and are in generally good agreement. In this paper, we will further investigate the structure and dynamics of hydration water using molecular dynamics simulations and calculations of the two-dimensional infrared and vibrational echo peak shift observables for hydration water in DLPC membranes. These observables have not yet been measured experimentally, but future comparisons may provide insight into spectral diffusion processes and hydration water heterogeneity. We find that at low hydration levels the motion of water molecules inside the lipid membrane is significantly arrested, resulting in very slow spectral diffusion. At higher hydration levels, spectral diffusion is more rapid, but still slower than in bulk water. We also investigate the effects of several common approximations on the calculation of spectroscopic observables by computing these observables within multiple levels of theory. The impact of these approximations on the resulting spectra affects our interpretation of these measurements and reveals that, for example, the cumulant approximation, which may be valid for certain systems, is not a good approximation for a highly heterogeneous environment such as hydration water in lipid multi-bilayers.

New in Situ Measurements of the Viscosity of Gas Clathrate Hydrate Slurries Formed from Model Water-in-Oil Emulsions.

PubMed

Majid, Ahmad A A; Wu, David T; Koh, Carolyn A

2017-10-24

In situ rheological measurements for clathrate hydrate slurries were performed using a high pressure rheometer to determine the effect of hydrate particles on the viscosity and transportability of these slurries. These measurements were conducted using a well-characterized model water-in-oil emulsion ( Delgado-Linares et al. Model Water in-Oil Emulsions for Gas Hydrate Studies in Oil Continuous Systems . Energy Fuels 2013 , 27 , 4564 - 4573 ). The emulsion consists of a model liquid hydrocarbon, water, and a surfactant mixture of sorbitane monooleate 80 (Span 80) and sodium di-2-ethylhexylsulfosuccinate (Aerosol OT, AOT). This emulsion was used as an analog to water-in-crude oil (w/o) emulsions and provides reproducible results. The flow properties of the model w/o emulsion prior to hydrate formation were investigated in terms of several parameters including water percentage, temperature and pressure. A general equation that describes the viscosity of the emulsion as a function of the aforementioned parameters was developed. This general equation was able to predict the viscosity of a saturated emulsion at various temperatures and water percentages to within ±13% error. The general equation was then used to analyze the effect of hydrate formation on the transportability of gas hydrate slurries. As for hydrate slurries investigation, measurements were performed using methane gas as the hydrate former and a straight vane impeller as a stirring system. Tests were conducted at constant temperature and pressure (1 °C and 1500 psig of methane) and water percentages ranging from 5 to 30 vol %. Results of this work were analyzed and presented in terms of relative values, i.e., viscosities of the slurries relative to the viscosities of the continuous phase at similar temperature and pressure. In this work, a correlation to predict the relative viscosity of a hydrate slurry at various hydrate volume fractions was developed. Analysis of the developed correlation showed that the model was able to predict the relative viscosity of a hydrate slurry to within ±17% error.

Hydrophobic amino acids as a new class of kinetic inhibitors for gas hydrate formation

PubMed Central

Sa, Jeong-Hoon; Kwak, Gye-Hoon; Lee, Bo Ram; Park, Da-Hye; Han, Kunwoo; Lee, Kun-Hong

2013-01-01

As the foundation of energy industry moves towards gas, flow assurance technology preventing pipelines from hydrate blockages becomes increasingly significant. However, the principle of hydrate inhibition is still poorly understood. Here, we examined natural hydrophobic amino acids as novel kinetic hydrate inhibitors (KHIs), and investigated hydrate inhibition phenomena by using them as a model system. Amino acids with lower hydrophobicity were found to be better KHIs to delay nucleation and retard growth, working by disrupting the water hydrogen bond network, while those with higher hydrophobicity strengthened the local water structure. It was found that perturbation of the water structure around KHIs plays a critical role in hydrate inhibition. This suggestion of a new class of KHIs will aid development of KHIs with enhanced biodegradability, and the present findings will accelerate the improved control of hydrate formation for natural gas exploitation and the utilization of hydrates as next-generation gas capture media. PMID:23938301

Modeling dynamic accumulation of gas hydrates in Shenhu area, northern South China Sea

NASA Astrophysics Data System (ADS)

Su, Z.; Cao, Y.; Wu, N.

2013-12-01

The accumulation of the hydrates in Shenhu area on northern continental slope of the South China Sea (SCS) could not be well quantified by the numerical models. The formation mechanism of the hydrate deposits remains an open question. Here, a conceptual model was applied for illustrating the formation pattern of hydrate accumulation in Shenhu area based on the studies of sedimentary and tectonic geologies. Our results indicated that the present hydrate deposits were a development of 'ancient hydrates' in the faulted sediment. The dynamic accumulation of the hydrates was further quantified by using a numerical model with two controlling parameters of seafloor sedimentation rate and water flow rate. The model results were testified with the hydrate saturations derived from the chloride abnormalities at site SH2 in Shenhu area. It suggested that the hydrate accumulation in Shenhu area had experienced two typical stages. In the first stage, the gas hydrates grew in the fractured sediment ~1.5 Ma. High permeability of the fractured sediment permitted rapid water flow that carrying methane gas toward the seafloor. Massive gas transformed to gas hydrate in the gas hydrate stability zone (GHSZ) at water flow rate of 50m/kyr within 40kyrs. The 'ancient hydrate' filled 20% volume of the sediment pores in the stage. The second stage was initiated after ending of the last faulting activity. The water flow rate dropped to 0.7m/kyr due to quick burial of fine-grained sediments. Inadequate gas supply could merely sustain hydrate growth slowly at the base of GHSZ, and ultimately yielded the current hydrate deposits in Shenhu area after a subsequent evolution of 1.5 Myrs.

Examination of Hydrate Formation Methods: Trying to Create Representative Samples

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

Kneafsey, T.J.; Rees, E.V.L.; Nakagawa, S.

2011-04-01

Forming representative gas hydrate-bearing laboratory samples is important so that the properties of these materials may be measured, while controlling the composition and other variables. Natural samples are rare, and have often experienced pressure and temperature changes that may affect the property to be measured [Waite et al., 2008]. Forming methane hydrate samples in the laboratory has been done a number of ways, each having advantages and disadvantages. The ice-to-hydrate method [Stern et al., 1996], contacts melting ice with methane at the appropriate pressure to form hydrate. The hydrate can then be crushed and mixed with mineral grains under controlledmore » conditions, and then compacted to create laboratory samples of methane hydrate in a mineral medium. The hydrate in these samples will be part of the load-bearing frame of the medium. In the excess gas method [Handa and Stupin, 1992], water is distributed throughout a mineral medium (e.g. packed moist sand, drained sand, moistened silica gel, other porous media) and the mixture is brought to hydrate-stable conditions (chilled and pressurized with gas), allowing hydrate to form. This method typically produces grain-cementing hydrate from pendular water in sand [Waite et al., 2004]. In the dissolved gas method [Tohidi et al., 2002], water with sufficient dissolved guest molecules is brought to hydrate-stable conditions where hydrate forms. In the laboratory, this is can be done by pre-dissolving the gas of interest in water and then introducing it to the sample under the appropriate conditions. With this method, it is easier to form hydrate from more soluble gases such as carbon dioxide. It is thought that this method more closely simulates the way most natural gas hydrate has formed. Laboratory implementation, however, is difficult, and sample formation is prohibitively time consuming [Minagawa et al., 2005; Spangenberg and Kulenkampff, 2005]. In another version of this technique, a specified quantity of gas is placed in a sample, then the sample is flooded with water and cooled [Priest et al., 2009]. We have performed a number of tests in which hydrate was formed and the uniformity of the hydrate formation was examined. These tests have primarily used a variety of modifications of the excess gas method to make the hydrate, although we have also used a version of the excess water technique. Early on, we found difficulties in creating uniform samples with a particular sand/ initial water saturation combination (F-110 Sand, {approx} 35% initial water saturation). In many of our tests we selected this combination intentionally to determine whether we could use a method to make the samples uniform. The following methods were examined: Excess gas, Freeze/thaw/form, Freeze/pressurize/thaw, Excess gas followed by water saturation, Excess water, Sand and kaolinite, Use of a nucleation enhancer (SnoMax), and Use of salt in the water. Below, each method, the underlying hypothesis, and our results are briefly presented, followed by a brief conclusion. Many of the hypotheses investigated are not our own, but were presented to us. Much of the data presented is from x-ray CT scanning our samples. The x-ray CT scanner provides a three-dimensional density map of our samples. From this map and the physics that is occurring in our samples, we are able to gain an understanding of the spatial nature of the processes that occur, and attribute them to the locations where they occur.« less

Evaluation of hydrate-screening methods.

PubMed

Cui, Yong; Yao, Erica

2008-07-01

The purpose of this work is to evaluate the effectiveness and reliability of several common hydrate-screening techniques, and to provide guidelines for designing hydrate-screening programs for new drug candidates. Ten hydrate-forming compounds were selected as model compounds and six hydrate-screening approaches were applied to these compounds in an effort to generate their hydrate forms. The results prove that no screening approach is universally effective in finding hydrates for small organic compounds. Rather, a combination of different methods should be used to improve screening reliability. Among the approaches tested, the dynamic water vapor sorption/desorption isotherm (DVI) method and storage under high humidity (HH) yielded 60-70% success ratios, the lowest among all techniques studied. The risk of false negatives arises in particular for nonhygroscopic compounds. On the other hand, both slurry in water (Slurry) and temperature cycling of aqueous suspension (TCS) showed high success rates (90%) with some exceptions. The mixed solvent systems (MSS) procedure also achieved high success rates (90%), and was found to be more suitable for water-insoluble compounds. For water-soluble compounds, MSS may not be the best approach because recrystallization is difficult in solutions with high water activity. Finally, vapor diffusion (VD) yielded a reasonably high success ratio in finding hydrates (80%). However, this method suffers from experimental difficulty and unreliable results for either highly water-soluble or water-insoluble compounds. This study indicates that a reliable hydrate-screening strategy should take into consideration the solubility and hygroscopicity of the compounds studied. A combination of the Slurry or TCS method with the MSS procedure could provide a screening strategy with reasonable reliability.

Thermodynamic properties of methane hydrate in quartz powder.

PubMed

Voronov, Vitaly P; Gorodetskii, Evgeny E; Safonov, Sergey S

2007-10-04

Using the experimental method of precision adiabatic calorimetry, the thermodynamic (equilibrium) properties of methane hydrate in quartz sand with a grain size of 90-100 microm have been studied in the temperature range of 260-290 K and at pressures up to 10 MPa. The equilibrium curves for the water-methane hydrate-gas and ice-methane hydrate-gas transitions, hydration number, latent heat of hydrate decomposition along the equilibrium three-phase curves, and the specific heat capacity of the hydrate have been obtained. It has been experimentally shown that the equilibrium three-phase curves of the methane hydrate in porous media are shifted to the lower temperature and high pressure with respect to the equilibrium curves of the bulk hydrate. In these experiments, we have found that the specific heat capacity of the hydrate, within the accuracy of our measurements, coincides with the heat capacity of ice. The latent heat of the hydrate dissociation for the ice-hydrate-gas transition is equal to 143 +/- 10 J/g, whereas, for the transition from hydrate to water and gas, the latent heat is 415 +/- 15 J/g. The hydration number has been evaluated in the different hydrate conditions and has been found to be equal to n = 6.16 +/- 0.06. In addition, the influence of the water saturation of the porous media and its distribution over the porous space on the measured parameters has been experimentally studied.

Challenges and Early Results: Interactive benthic experiments in hydrate environments of Barkley Canyon, NEPTUNE Canada.

NASA Astrophysics Data System (ADS)

Best, M.; Thomsen, L.; de Beer, D.

2012-04-01

NEPTUNE Canada, operating and online since 2009, is an 800km, 5-node, regional cabled ocean network across the northern Juan de Fuca Plate, northeastern Pacific, part of the Ocean Networks Canada Observatory. One of 15 study areas is an environment of exposed hydrate mounds along the wall of Barkley Canyon, at ~865m water depth. This is the home of a benthic crawler developed by Jacobs University of Germany, who is affectionately known as Wally. Wally is equipped with a range of sensors including a camera, methane sensor, current meter, fluorometer, turbidity meter, CTD, and a sediment microprofiler developed at the Max Planck Institute with probes for oxygen, methane, sulphide, pH, temperature, and conductivity. In conjunction with this sensor suite, a series of experiments have been designed to assess the cycling of biogenic carbon and carbonate in this complex environment. The biota range from microbes, to molluscs, to large fish, and therefore the carbon inputs include both a range of organic carbon compounds as well as the complex materials that are "biogenic carbonate". Controlled experimental specimens were deployed of biogenic carbonate (Mytilus edulis fresh shells) and cellulose (pieces of untreated pine lumber) that had been previously well characterized (photographed, weighed, and numbered, matching valves and lumber kept as controls). Deployment at the sediment/water interface was in such a way to maximize natural burial exhumation cycles but to minimize specimen interaction. 10 replicate specimens of each material were deployed in two treatments: 1) adjacent to a natural life and death assemblage of chemosynthetic bivalves and exposed hydrate on a hydrate mound and 2) on the muddy seafloor at a distance from the mound. In order to quantify and track the rates and processes of modification of the natural materials, and their possible environmental/ecological correlates, observations of the experimental specimens are being made on a regular basis using the crawler camera and sensors. On retrieval, the specimens will be further studied for net material loss, surface alteration, microbial recruitment, endo- and epibionts, and microstructural and chemical modification. The complex coordination of hardware, software, and people is challenging such that the ideal of frequent and timely observations of these poorly known processes is realized. Understanding the production and cycling of carbon across the sediment/water interface in this environment will help elucidate the formation and evolution of these hydrate deposits, their distribution through time, and the ecological and taphonomic feedbacks they generate.

Gas hydrate formation rates from dissolved-phase methane in porous laboratory specimens

USGS Publications Warehouse

Waite, William F.; Spangenberg, E.K.

2013-01-01

Marine sands highly saturated with gas hydrates are potential energy resources, likely forming from methane dissolved in pore water. Laboratory fabrication of gas hydrate-bearing sands formed from dissolved-phase methane usually requires 1–2 months to attain the high hydrate saturations characteristic of naturally occurring energy resource targets. A series of gas hydrate formation tests, in which methane-supersaturated water circulates through 100, 240, and 200,000 cm3 vessels containing glass beads or unconsolidated sand, show that the rate-limiting step is dissolving gaseous-phase methane into the circulating water to form methane-supersaturated fluid. This implies that laboratory and natural hydrate formation rates are primarily limited by methane availability. Developing effective techniques for dissolving gaseous methane into water will increase formation rates above our observed (1 ± 0.5) × 10−7 mol of methane consumed for hydrate formation per minute per cubic centimeter of pore space, which corresponds to a hydrate saturation increase of 2 ± 1% per day, regardless of specimen size.

Phase diagram and high-pressure boundary of hydrate formation in the ethane-water system.

PubMed

Kurnosov, Alexander V; Ogienko, Andrey G; Goryainov, Sergei V; Larionov, Eduard G; Manakov, Andrey Y; Lihacheva, Anna Y; Aladko, Eugeny Y; Zhurko, Fridrikh V; Voronin, Vladimir I; Berger, Ivan F; Ancharov, Aleksei I

2006-11-02

Dissociation temperatures of gas hydrate formed in the ethane-water system were studied at pressures up to 1500 MPa. In situ neutron diffraction analysis and X-ray diffraction analysis in a diamond anvil cell showed that the gas hydrate formed in the ethane-water system at 340, 700, and 1840 MPa and room temperature belongs to the cubic structure I (CS-I). Raman spectra of C-C vibrations of ethane molecules in the hydrate phase, as well as the spectra of solid and liquid ethane under high-pressure conditions were studied at pressures up to 6900 MPa. Within 170-3600 MPa Raman shift of the C-C vibration mode of ethane in the hydrate phase did not show any discontinuities, which could be evidence of possible phase transformations. The upper pressure boundary of high-pressure hydrate existence was discovered at the pressure of 3600 MPa. This boundary corresponds to decomposition of the hydrate to solid ethane and ice VII. The type of phase diagram of ethane-water system was proposed in the pressure range of hydrate formation (0-3600 MPa).

Structural properties of hydration shell around various conformations of simple polypeptides.

PubMed

Czapiewski, Dariusz; Zielkiewicz, Jan

2010-04-08

In this paper we investigate structural properties of water within the solvation shell around the peptide core created by a well-defined conformation of polypeptide chain. The following secondary structures are investigated: linear (straight chain), and three helices PII (polyproline-like), 3(10), and alpha. We propose using the two-particle contribution to entropy as a rational measure of the water structural ordering within the solvation layer. This contribution divides into two terms, depending on the peptide-water and water-water interactions, respectively, and in this paper both terms are investigated. The structure of "solvation" water is described by the second term, and therefore it mainly attracts our attention. Determination of this term, however, is not an easy task, requiring some controversial approximations. Therefore, we have transformed this term to the form of some rational parameter which measures the local structural ordering of water within the solvation shell. Moreover, the results of several independent investigations are reported: we adopt the harmonic approximation for an independent estimation of the water entropy within the solvation shell, and we also study structure of the water-water hydrogen bond network, mean geometry of a single hydrogen bond, the self-diffusion coefficients (both translational and rotational) of water, and the mean lifetimes of water-water and water-peptide hydrogen bonds. All the obtained results lead to the conclusion that the local structure of water within the solvation shell changes only slightly in comparison to the bulk one. If so, the measure of local water ordering proposed by us is exploited with the aim to gain the deeper insight on the structural properties of "solvation" water. It has been shown that this parameter can be factored into three terms, which measure translational, configurational, and orientational ordering, respectively. Using this factoring, the ordering map for a precise description of the water local ordering has been built. An interesting correlation is observed: the points on this map lie approximately on the straight line, while the linear conformations clearly deviate from the general tendency. Further analysis of the obtained results allows us to express the supposition that an increasing local ordering of water around given secondary structure corresponds to an increasing relative stability of this structure in aqueous solution. Analyzing the geometry of the water-water hydrogen bond network within the solvation layer, we find some systematic deviations of this geometry from the bulk water properties. We also observe that the alanine peptides (excluding the linear form) disturb the hydrogen bond network in the less range, and in another way than the various conformations of polyglycine, while the linear form of polyalanine behaves very similarly to the glycine ones. Next, investigating the dynamic properties, we also conclude that water near the peptide surface creates a pseudorigid structure, a "halo" around the peptide core. This "halo" is stabilized by slightly higher energy of the hydrogen bonds network: we have found that within this region the hydrogen bonds network is slightly less distorted, the water-water hydrogen bonds are a little more stable and their mean lifetime is clearly longer that that of bulk water. Significant differences between the alanine- and glycine-based polypeptides are also visible. It has also been found that this solvation layer interacts with the polyalanine in another way than with polyglycine. Although in the case of the glycine-based polypeptide this layer slides relatively freely over the peptide surface, for the alanine-based polypeptide this sliding is strongly hindered by the presence of the methyl groups, and this effect is additionally enhanced by a rise in the solvation layer rigidity. Thus, the survey of various dynamic properties allows us to perceive and to explain distinct differences in behavior of water within the solvation shell around both glycine and alanine peptides.

Water Transport and the Evolution of CM Parent Bodies

NASA Technical Reports Server (NTRS)

Coker, Rob; Cohen, Barbara

2014-01-01

Meteorites have amino acids and hydrated minerals which constrain the peak temperature ranges they have experienced. CMs in particular have a narrow range (273-325K). Bulk fluid motion during hydration constrained to small scales (less than mm). Some asteroids are known to have hydrated minerals on their surfaces. It is presumed these two facts may be related. Problem: hydration only occurs (significantly) with liquid water; melting water only occurs early on in nebula (1-10 Myrs ANC); in nebula asteroid surface temperature very cold (approximately 150K). Can indigenous alteration produce CMs and/or surface hydration?

Gas hydrate property measurements in porous sediments with resonant ultrasound spectroscopy

NASA Astrophysics Data System (ADS)

McGrail, B. P.; Ahmed, S.; Schaef, H. T.; Owen, A. T.; Martin, P. F.; Zhu, T.

2007-05-01

Resonant ultrasound spectroscopy was used to characterize a natural geological core sample obtained from the Mallik 5L-38 gas hydrate research well at high pressure and subambient temperatures. Using deuterated methane gas to form gas hydrate in the core sample, it was discovered that resonance amplitudes are correlated with the fraction of the pore space occupied by the gas hydrate crystals. A pore water freezing model was developed that utilizes the known pore size distribution and pore water chemistry to predict gas hydrate saturation as a function of pressure and temperature. The model showed good agreement with the experimental measurements and demonstrated that pore water chemistry is the most important factor controlling equilibrium gas hydrate saturations in these sediments when gas hydrates are formed artificially in laboratory pressure vessels. With further development, the resonant ultrasound technique can provide a rapid, nondestructive, field portable means of measuring the equilibrium P-T properties and dissociation kinetics of gas hydrates in porous media, determining gas hydrate saturations, and may provide new insights into the nature of gas hydrate formation mechanisms in geologic materials.

Oceanic methane hydrate: The character of the Blake Ridge hydrate stability zone, and the potential for methane extraction

USGS Publications Warehouse

Max, M.D.; Dillon, William P.

1998-01-01

Oceanic methane hydrates are mineral deposits formed from a crystalline 'ice' of methane and water in sea-floor sediments (buried to less than about 1 km) in water depths greater than about 500 m; economic hydrate deposits are probably restricted to water depths of between 1.5 km and 4 km. Gas hydrates increase a sediment's strength both by 'freezing' the sediment and by filling the pore spaces in a manner similar to water-ice in permafrost. Concentrated hydrate deposits may be underlain by significant volumes of methane gas, and these localities are the most favourable sites for methane gas extraction operations. Seismic reflection records indicate that trapped gas may blow-out naturally, causing large-scale seafloor collapse. In this paper, we consider both the physical properties and the structural integrity of the hydrate stability zone and the associated free gas deposits, with special reference to the Blake Ridge area, SE US offshore, in order to help establish a suitable framework for the safe, efficient, and economic recovery of methane from oceanic gas hydrates. We also consider the potential effects of the extraction of methane from hydrate (such as induced sea-floor faulting, gas venting, and gas-pocket collapse). We assess the ambient pressure effect on the production of methane by hydrate dissociation, and attempt to predict the likelihood of spontaneous gas flow in a production situation.Oceanic methane hydrates are mineral sits formed from a crystalline `ice' of methane and water in sea-floor sediments (buried to less than about 1 km) in water depths greater than about 500 m; economic hydrate deposits are probably restricted to water depths of between 1.5 km and 4 km. Gas hydrates increase a sediment's strength both by `freezing' the sediment and by filling the pore spaces in a manner similar to water-ice in permafrost. Concentrated hydrate deposits may be underlain by significant volumes of methane gas, and these localities are the most favourable sites for methane gas extraction operations. Seismic reflection records indicate that trapped gas may blow-out naturally, causing large-scale seafloor collapse. In this paper, we consider both the physical properties and the structural integrity of the hydrate stability zone and the associated free gas deposits, with special reference to the Blake Ridge area, SE US offshore, in order to help establish a suitable framework for the safe, efficient, and economic recovery of methane from oceanic gas hydrates. We also consider the potential effects of the extraction of methane from hydrate (such as induced sea-floor faulting, gas venting, and gas-pocket collapse). We assess the ambient pressure effect on the production of methane by hydrate dissociation, and attempt to predict the likelihood of spontaneous gas flow in a production situation.

Modulators of heterogeneous protein surface water dynamics

NASA Astrophysics Data System (ADS)

Han, Songi

The hydration water that solvates proteins is a major factor in driving or enabling biological events, including protein-protein and protein-ligand interactions. We investigate the role of the protein surface in modulating the hydration water fluctuations on both the picosecond and nanosecond timescale with an emerging experimental NMR technique known as Overhauser Dynamic Nuclear Polarization (ODNP). We carry out site-specific ODNP measurements of the hydration water fluctuations along the surface of Chemotaxis Y (CheY), and correlate the measured fluctuations to hydropathic and topological properties of the CheY surface as derived from molecular dynamics (MD) simulation. Furthermore, we compare hydration water fluctuations measured on the CheY surface to that of other globular proteins, as well as intrinsically disordered proteins, peptides, and liposome surfaces to systematically test characteristic effects of the biomolecular surface on the hydration water dynamics. Our results suggest that the labile (ps) hydration water fluctuations are modulated by the chemical nature of the surface, while the bound (ns) water fluctuations are present on surfaces that feature a rough topology and chemical heterogeneity such as the surface of a folded and structured protein. In collaboration with: Ryan Barnes, Dept of Chemistry and Biochemistry, University of California Santa Barbara

Clinical, biochemical, and hygiene assessment of stabled horses provided continuous or intermittent access to drinking water.

PubMed

Freeman, D A; Cymbaluk, N F; Schott, H C; Hinchcliff, K; McDonnell, S M; Kyle, B

1999-11-01

To compare health, hydration status, and management of stabled pregnant mares provided drinking water continuously or via 1 of 3 intermittent delivery systems. 22 Quarter Horse (QH) or QH-crossbred mares and 18 Belgian or Belgian-crossbred mares (study 1); 24 QH or QH-crossbred mares and 18 Belgian or Belgian-crossbred mares (study 2). Stabled horses were provided water continuously or via 1 of 3 intermittent water delivery systems in 2 study periods during a 2-year period. Body temperature, attitude, appetite, water intake, and urine output were recorded daily. Hygiene of each horse and the stable were assessed weekly. Clinical and biochemical measures of hydration were determined 3 times during each study. Clinical measures of hydration included skin turgor, gum moisture, capillary refill time, and fecal consistency. Biochemical measures of hydration included PCV, plasma total protein concentration, serum osmolality, plasma vasopressin concentration, urine specific gravity, and urine osmolality. All horses remained healthy. Stable hygiene was worse when horses had continuous access to water. Clinical and biochemical measures of hydration did not differ among water delivery systems. Various continuous and intermittent water delivery systems provided adequate amounts of water to stabled horses to maintain health and hydration status. Providing intermittent access to water may be preferable on the basis of stable hygiene.

Racial/Ethnic and Socioeconomic Disparities in Hydration Status Among US Adults and the Role of Tap Water and Other Beverage Intake

PubMed Central

Gortmaker, Steven L.; Long, Michael W.; Cradock, Angie L.; Kenney, Erica L.

2017-01-01

Objectives. To evaluate whether differences in tap water and other beverage intake explain differences in inadequate hydration among US adults by race/ethnicity and income. Methods. We estimated the prevalence of inadequate hydration (urine osmolality ≥ 800 mOsm/kg) by race/ethnicity and income of 8258 participants aged 20 to 74 years in the 2009 to 2012 National Health and Nutrition Examination Survey. Using multivariable regression models, we estimated associations between demographic variables, tap water intake, and inadequate hydration. Results. The prevalence of inadequate hydration among US adults was 29.5%. Non-Hispanic Blacks (adjusted odds ratio [AOR] = 1.44; 95% confidence interval [CI] = 1.17, 1.76) and Hispanics (AOR = 1.42; 95% CI = 1.21, 1.67) had a higher risk of inadequate hydration than did non-Hispanic Whites. Lower-income adults had a higher risk of inadequate hydration than did higher-income adults (AOR = 1.23; 95% CI = 1.04, 1.45). Differences in tap water intake partially attenuated racial/ethnic differences in hydration status. Differences in total beverage and other fluid intake further attenuated sociodemographic disparities. Conclusions. Racial/ethnic and socioeconomic disparities in inadequate hydration among US adults are related to differences in tap water and other beverage intake. Policy action is needed to ensure equitable access to healthy beverages. PMID:28727528

Racial/Ethnic and Socioeconomic Disparities in Hydration Status Among US Adults and the Role of Tap Water and Other Beverage Intake.

PubMed

Brooks, Carolyn J; Gortmaker, Steven L; Long, Michael W; Cradock, Angie L; Kenney, Erica L

2017-09-01

To evaluate whether differences in tap water and other beverage intake explain differences in inadequate hydration among US adults by race/ethnicity and income. We estimated the prevalence of inadequate hydration (urine osmolality ≥ 800 mOsm/kg) by race/ethnicity and income of 8258 participants aged 20 to 74 years in the 2009 to 2012 National Health and Nutrition Examination Survey. Using multivariable regression models, we estimated associations between demographic variables, tap water intake, and inadequate hydration. The prevalence of inadequate hydration among US adults was 29.5%. Non-Hispanic Blacks (adjusted odds ratio [AOR] = 1.44; 95% confidence interval [CI] = 1.17, 1.76) and Hispanics (AOR = 1.42; 95% CI = 1.21, 1.67) had a higher risk of inadequate hydration than did non-Hispanic Whites. Lower-income adults had a higher risk of inadequate hydration than did higher-income adults (AOR = 1.23; 95% CI = 1.04, 1.45). Differences in tap water intake partially attenuated racial/ethnic differences in hydration status. Differences in total beverage and other fluid intake further attenuated sociodemographic disparities. Racial/ethnic and socioeconomic disparities in inadequate hydration among US adults are related to differences in tap water and other beverage intake. Policy action is needed to ensure equitable access to healthy beverages.

Hydration forces between aligned DNA helices undergoing B to A conformational change: In-situ X-ray fiber diffraction studies in a humidity and temperature controlled environment.

PubMed

Case, Ryan; Schollmeyer, Hauke; Kohl, Phillip; Sirota, Eric B; Pynn, Roger; Ewert, Kai E; Safinya, Cyrus R; Li, Youli

2017-12-01

Hydration forces between DNA molecules in the A- and B-Form were studied using a newly developed technique enabling simultaneous in situ control of temperature and relative humidity. X-ray diffraction data were collected from oriented calf-thymus DNA fibers in the relative humidity range of 98%-70%, during which DNA undergoes the B- to A-form transition. Coexistence of both forms was observed over a finite humidity range at the transition. The change in DNA separation in response to variation in humidity, i.e. change of chemical potential, led to the derivation of a force-distance curve with a characteristic exponential decay constant of∼2Å for both A- and B-DNA. While previous osmotic stress measurements had yielded similar force-decay constants, they were limited to B-DNA with a surface separation (wall-to-wall distance) typically>5Å. The current investigation confirms that the hydration force remains dominant even in the dry A-DNA state and at surface separation down to∼1.5Å, within the first hydration shell. It is shown that the observed chemical potential difference between the A and B states could be attributed to the water layer inside the major and minor grooves of the A-DNA double helices, which can partially interpenetrate each other in the tightly packed A phase. The humidity-controlled X-ray diffraction method described here can be employed to perform direct force measurements on a broad range of biological structures such as membranes and filamentous protein networks. Copyright © 2017 Elsevier Inc. All rights reserved.

Dominant Alcohol-Protein Interaction via Hydration-Enabled Enthalpy-Driven Binding Mechanism

PubMed Central

Chong, Yuan; Kleinhammes, Alfred; Tang, Pei; Xu, Yan; Wu, Yue

2015-01-01

Water plays an important role in weak associations of small drug molecules with proteins. Intense focus has been on binding-induced structural changes in the water network surrounding protein binding sites, especially their contributions to binding thermodynamics. However, water is also tightly coupled to protein conformations and dynamics, and so far little is known about the influence of water-protein interactions on ligand binding. Alcohols are a type of low-affinity drugs, and it remains unclear how water affects alcohol-protein interactions. Here, we present alcohol adsorption isotherms under controlled protein hydration using in-situ NMR detection. As functions of hydration level, Gibbs free energy, enthalpy, and entropy of binding were determined from the temperature dependence of isotherms. Two types of alcohol binding were found. The dominant type is low-affinity nonspecific binding, which is strongly dependent on temperature and the level of hydration. At low hydration levels, this nonspecific binding only occurs above a threshold of alcohol vapor pressure. An increased hydration level reduces this threshold, with it finally disappearing at a hydration level of h~0.2 (g water/g protein), gradually shifting alcohol binding from an entropy-driven to an enthalpy-driven process. Water at charged and polar groups on the protein surface was found to be particularly important in enabling this binding. Although further increase in hydration has smaller effects on the changes of binding enthalpy and entropy, it results in significant negative change in Gibbs free energy due to unmatched enthalpy-entropy compensation. These results show the crucial role of water-protein interplay in alcohol binding. PMID:25856773

Determination of Protein Surface Hydration by Systematic Charge Mutations

NASA Astrophysics Data System (ADS)

Yang, Jin; Jia, Menghui; Qin, Yangzhong; Wang, Dihao; Pan, Haifeng; Wang, Lijuan; Xu, Jianhua; Zhong, Dongping; Dongping Zhong Collaboration; Jianhua Xu Collaboration

Protein surface hydration is critical to its structural stability, flexibility, dynamics and function. Recent observations of surface solvation on picosecond time scales have evoked debate on the origin of such relatively slow motions, from hydration water or protein charged sidechains, especially with molecular dynamics simulations. Here, we used a unique nuclease with a single tryptophan as a local probe and systematically mutated neighboring three charged residues to differentiate the contributions from hydration water and charged sidechains. By mutations of alternative one and two and all three charged residues, we observed slight increases in the total tryptophan Stokes shifts with less neighboring charged residue(s) and found insensitivity of charged sidechains to the relaxation patterns. The dynamics is correlated with hydration water relaxation with the slowest time in a dense charged environment and the fastest time at a hydrophobic site. On such picosecond time scales, the protein surface motion is restricted. The total Stokes shifts are dominantly from hydration water relaxation and the slow dynamics is from water-driven relaxation, coupled with local protein fluctuations.

Physical Chemical Controls of Methane and other Hydrocarbon gases in Outer Solar System Water-Ice Systems

NASA Astrophysics Data System (ADS)

Osegovic, J. P.; Max, M. D.

2012-12-01

Saturn's moon Enceladus appear to have liquid water under its thin icy surface that has venting water and complex hydrocarbons. Jupiter's moon Europa is locked under a very thick layer of surface ice. Because Saturn's moon Titan contains abundant hydrocarbon gasses and liquids and both Saturn and Jupiter contain abundant hydrocarbon gases, it is likely that Europa also may have significant quantities of hydrocarbon gases in their water-ice systems. Both of these moons have the potential for life. We have begun to explore the impact that gas hydrate, which is a crystalline material composed of water and gas molecules, has on the availability of liquid water on a planet's surface: what conditions need to be present to initiate hydrate formation from a primordial selection of gases, salts, and water, how isolated hydrate systems evolve under the condition of mass transfer from ex-hydrate stability conditions to pro-hydrate stability conditions, the timespan of conditions that hydrate formation can host liquid solutions in an otherwise cooling regime; and the impact that additional chemistry, such as primitive chemosynthesis, may have on the sequestered hydrocarbon gases in hydrate. The analog for gas hydrate on these moons is the Permafrost hydrate system of Earth. Gas hydrate and water ice are stable in a compound cryosphere with ice extending downward from cold surface conditions to about the 273 K isotherm. Hydrate, depending on the mixture of gases in it, is stable from some depth below the surface to some isotherm that could be considerably in excess of 273 K. Salinity may strongly affect stability conditions. In order to estimate the thickness of the gas hydrate stability zone and its effect on 'planetary' heat flow, we model heat production as a function of mass flow. Variables are gravity, ice thickness, temperature of the surrounding medium (space, ice, and water), the thickness of the "ocean", the and the thermophysical properties of the gas being transferred. The model is constrained by the molecular diffusion rate of gas approaching the hydrate phase boundary. The heat produced or consumed by the hydrate system will affect the ice system and phase boundary. Fick's law can be used to model steady state diffusion. Flux is related to the diffusivity of the component and as a function of concentration and the distance over which the reactions take place. Initial model calculations indicate that in some cases, methane (ΔH = -56 kJ/mol for small molecules (CH4, N2, CO2, H2S) may affect the water-ice energy balance sufficiently to contribute to the maintenance of a deep ocean below ice. The effect of the presence of higher density hydrocarbons (ΔH = -72 kJ/mol for ethane and -126 kJ/mol for propane) accentuate the thermal transfer effect but may diffuse too slowly to be a thermal forcing agent in the hydrate system.

Molecular mechanisms responsible for hydrate anti-agglomerant performance.

PubMed

Phan, Anh; Bui, Tai; Acosta, Erick; Krishnamurthy, Pushkala; Striolo, Alberto

2016-09-28

Steered and equilibrium molecular dynamics simulations were employed to study the coalescence of a sI hydrate particle and a water droplet within a hydrocarbon mixture. The size of both the hydrate particle and the water droplet is comparable to that of the aqueous core in reverse micelles. The simulations were repeated in the presence of various quaternary ammonium chloride surfactants. We investigated the effects due to different groups on the quaternary head group (e.g. methyl vs. butyl groups), as well as different hydrophobic tail lengths (e.g. n-hexadecyl vs. n-dodecyl tails) on the surfactants' ability to prevent coalescence. Visual inspection of sequences of simulation snapshots indicates that when the water droplet is not covered by surfactants it is more likely to approach the hydrate particle, penetrate the protective surfactant film, reach the hydrate surface, and coalesce with the hydrate than when surfactants are present on both surfaces. Force-distance profiles obtained from steered molecular dynamics simulations and free energy profiles obtained from umbrella sampling suggest that surfactants with butyl tripods on the quaternary head group and hydrophobic tails with size similar to the solvent molecules can act as effective anti-agglomerants. These results qualitatively agree with macroscopic experimental observations. The simulation results provide additional insights, which could be useful in flow assurance applications: the butyl tripod provides adhesion between surfactants and hydrates; when the length of the surfactant tail is compatible with that of the hydrocarbon in the liquid phase a protective film can form on the hydrate; however, once a molecularly thin chain of water molecules forms through the anti-agglomerant film, connecting the water droplet and the hydrate, water flows to the hydrate and coalescence is inevitable.

Sugar-influenced water diffusion, interaction, and retention in clay interlayer nanopores probed by theoretical simulations and experimental spectroscopies

NASA Astrophysics Data System (ADS)

Aristilde, Ludmilla; Galdi, Stephen M.; Kelch, Sabrina E.; Aoki, Thalia G.

2017-08-01

Understanding the hydrodynamics in clay nanopores is important for gaining insights into the trapping of water, nutrients, and contaminants in natural and engineered soils. Previous investigations have focused on the interlayer organization and molecular diffusion coefficients (D) of cations and water molecules in cation-saturated interlayer nanopores of smectite clays. Little is known, however, about how these interlayer dynamic properties are influenced by the ubiquitous presence of small organic compounds such as sugars in the soil environment. Here we probed the effects of glucose molecules on montmorillonite interlayer properties. Molecular dynamics simulations revealed re-structuring of the interlayer organization of the adsorptive species. Water-water interactions were disrupted by glucose-water H-bonding interactions. ;Dehydration; of the glucose-populated nanopore led to depletion in the Na solvation shell, which resulted in the accumulation of both Na ions (as inner-sphere complexes) and remaining hydrated water molecules at the mineral surface. This accumulation led to a decrease in both DNa and Dwater. In addition, the reduction in Dglucose as a function of increasing glucose content can be explained by the aggregation of glucose molecules into organic clusters H-bonded to the mineral surface on both walls of the nanopore. Experimental nuclear magnetic resonance and X-ray diffraction data were consistent with the theoretical predictions. Compared to clay interlayers devoid of glucose, increased intensities and new peaks in the 23Na nuclear magnetic resonance spectra confirmed increasing immobilization of Na as a function of increasing glucose content. And, the X-ray diffraction data indicated a reduced collapse of glucose-populated interlayers exposed to decreasing moisture conditions, which led to the maintenance of hydrated clay nanopores. The coupling of theoretical and experimental findings sheds light on the molecular to nanoscale mechanisms that control the enhanced trapping of water molecules and solutes within sugar-enriched clay nanopores.

Screening and Characterization of Hydrate Forms of T-3256336, a Novel Inhibitor of Apoptosis (IAP) Protein Antagonist.

PubMed

Takeuchi, Shoko; Kojima, Takashi; Hashimoto, Kentaro; Saito, Bunnai; Sumi, Hiroyuki; Ishikawa, Tomoyasu; Ikeda, Yukihiro

2015-01-01

Different crystal packing of hydrates from anhydrate crystals leads to different physical properties, such as solubility and stability. Investigation of the potential of varied hydrate formation, and understanding the stability in an anhydrous/hydrate system, are crucial to prevent an undesired transition during the manufacturing process and storage. Only one anhydrous form of T-3256336, a novel inhibitor of apoptosis (IAP) protein antagonist, was discovered during synthesis, and no hydrate form has been identified. In this study, we conducted hydrate screening such as dynamic water vapor sorption/desorption (DVS), and the slurry experiment, and characterized the solid-state properties of anhydrous/hydrate forms to determine the most desirable crystalline form for development. New hydrate forms, both mono-hydrate and hemi-hydrate forms, were discovered as a result of this hydrate screening. The characterization of two new hydrate forms was conducted, and the anhydrous form was determined to be the most desirable development form of T-3256336 in terms of solid-state stability. In addition, the stability of the anhydrous form was investigated using the water content and temperature controlled slurry experiment to obtain the desirable crystal form in the crystallization process. The water content regions of the stable phase of the desired form, the anhydrous form, were identified for the cooling crystallization process.

Influence of ion size and charge on osmosis.

PubMed

Cannon, James; Kim, Daejoong; Maruyama, Shigeo; Shiomi, Junichiro

2012-04-12

Osmosis is fundamental to many processes, such as in the function of biological cells and in industrial desalination to obtain clean drinking water. The choice of solute in industrial applications of osmosis is highly important in maximizing efficiency and minimizing costs. The macroscale process of osmosis originates from the nanoscale properties of the solvent, and therefore an understanding of the mechanisms of how these properties determine osmotic strength can be highly useful. For this reason, we have undertaken molecular dynamics simulations to systematically study the influence of ion size and charge on the strength of osmosis of water through carbon nanotube membranes. Our results show that strong osmosis occurs under optimum conditions of ion placement near the region of high water density near the membrane wall and of maintenance of a strong water hydration shell around the ions. The results in turn allow greater insight into the origin of the strong osmotic strength of real ions such as NaCl. Finally, in terms of practical simulation, we highlight the importance of avoiding size effects that can occur if the simulation cell is too small.

Low-δD hydration rinds in Yellowstone perlites record rapid syneruptive hydration during glacial and interglacial conditions

USGS Publications Warehouse

Bindeman, Ilya N.; Lowenstern, Jacob B.

2016-01-01

Hydration of silicic volcanic glass forms perlite, a dusky, porous form of altered glass characterized by abundant “onion-skin” fractures. The timing and temperature of perlite formation are enigmatic and could plausibly occur during eruption, during post-eruptive cooling, or much later at ambient temperatures. To learn more about the origin of natural perlite, and to fingerprint the hydration waters, we investigated perlitic glass from several synglacial and interglacial rhyolitic lavas and tuffs from the Yellowstone volcanic system. Perlitic cores are surrounded by a series of conchoidal cracks that separate 30- to 100-µm-thick slivers, likely formed in response to hydration-induced stress. H2O and D/H profiles confirm that most D/H exchange happens together with rapid H2O addition but some smoother D/H variations may suggest separate minor exchange by deuterium atom interdiffusion following hydration. The hydrated rinds (2–3 wt% H2O) transition rapidly (within 30 µm, or by 1 wt% H2O per 10 µm) to unhydrated glass cores. This is consistent with quenched “hydration fronts” where H2O diffusion coefficients are strongly dependent on H2O concentrations. The chemical, δ18O, and δD systematics of bulk glass records last equilibrium between ~110 and 60 °C without chemical exchange but with some δ18O exchange. Similarly, the δ18O of water extracted from glass by rapid heating suggests that water was added to the glass during cooling at <200 °C. Our observations support fast hydration at temperatures as low as 60 °C; prolonged exposure to high temperature of 175°–225° during water addition is less likely as the glass would lose alkalies and should alter to clays within days. A compilation of low-temperature hydration diffusion coefficients suggests ~2 orders of magnitude higher rates of diffusion at 60–110 °C temperatures, compared with values expected from extrapolation of high-temperature (>400 °C) experimental data. The thick hydration rinds in perlites, measuring hundreds of microns, preserve the original D/H values of hydrating water as a recorder of paleoclimate conditions. Measured δD values in perlitic lavas are −150 to −191 or 20–40 ‰ lower than glass hydrated by modern Yellowstone waters. This suggests that Yellowstone perlites record the low-δD signature of glacial ice. Cooling calculations, combined with the observed high water diffusion coefficients noted for 60–150 °C, suggest that if sufficient hot water or steam is available, any rhyolite flow greater than ~5 m thick can develop the observed ~250-µm hydration rinds within the expected timescale of cooling (weeks–years). As the process of hydration involves shattering of 30- to 100-µm-thick slivers to expose unhydrated rhyolite glass, the time required for hydration may be even shorter. Rapid hydration and formation of relatively thick-walled glass shards allow perlites to provide a snapshot view of the meteoric water (and thus climate) at the time of initial alteration. Perlites retain their initial hydration D/H signal better than thin-walled ash, which in contrast hydrates over many thousands of years with time-averaged precipitation.

Low-δD hydration rinds in Yellowstone perlites record rapid syneruptive hydration during glacial and interglacial conditions

NASA Astrophysics Data System (ADS)

Bindeman, Ilya N.; Lowenstern, Jacob B.

2016-11-01

Hydration of silicic volcanic glass forms perlite, a dusky, porous form of altered glass characterized by abundant "onion-skin" fractures. The timing and temperature of perlite formation are enigmatic and could plausibly occur during eruption, during post-eruptive cooling, or much later at ambient temperatures. To learn more about the origin of natural perlite, and to fingerprint the hydration waters, we investigated perlitic glass from several synglacial and interglacial rhyolitic lavas and tuffs from the Yellowstone volcanic system. Perlitic cores are surrounded by a series of conchoidal cracks that separate 30- to 100-µm-thick slivers, likely formed in response to hydration-induced stress. H2O and D/H profiles confirm that most D/H exchange happens together with rapid H2O addition but some smoother D/H variations may suggest separate minor exchange by deuterium atom interdiffusion following hydration. The hydrated rinds (2-3 wt% H2O) transition rapidly (within 30 µm, or by 1 wt% H2O per 10 µm) to unhydrated glass cores. This is consistent with quenched "hydration fronts" where H2O diffusion coefficients are strongly dependent on H2O concentrations. The chemical, δ18O, and δD systematics of bulk glass records last equilibrium between 110 and 60 °C without chemical exchange but with some δ18O exchange. Similarly, the δ18O of water extracted from glass by rapid heating suggests that water was added to the glass during cooling at <200 °C. Our observations support fast hydration at temperatures as low as 60 °C; prolonged exposure to high temperature of 175°-225° during water addition is less likely as the glass would lose alkalies and should alter to clays within days. A compilation of low-temperature hydration diffusion coefficients suggests 2 orders of magnitude higher rates of diffusion at 60-110 °C temperatures, compared with values expected from extrapolation of high-temperature (>400 °C) experimental data. The thick hydration rinds in perlites, measuring hundreds of microns, preserve the original D/H values of hydrating water as a recorder of paleoclimate conditions. Measured δD values in perlitic lavas are -150 to -191 or 20-40 ‰ lower than glass hydrated by modern Yellowstone waters. This suggests that Yellowstone perlites record the low-δD signature of glacial ice. Cooling calculations, combined with the observed high water diffusion coefficients noted for 60-150 °C, suggest that if sufficient hot water or steam is available, any rhyolite flow greater than 5 m thick can develop the observed 250-µm hydration rinds within the expected timescale of cooling (weeks-years). As the process of hydration involves shattering of 30- to 100-µm-thick slivers to expose unhydrated rhyolite glass, the time required for hydration may be even shorter. Rapid hydration and formation of relatively thick-walled glass shards allow perlites to provide a snapshot view of the meteoric water (and thus climate) at the time of initial alteration. Perlites retain their initial hydration D/H signal better than thin-walled ash, which in contrast hydrates over many thousands of years with time-averaged precipitation.

Water in volcanic glass: From volcanic degassing to secondary hydration

NASA Astrophysics Data System (ADS)

Seligman, Angela N.; Bindeman, Ilya N.; Watkins, James M.; Ross, Abigail M.

2016-10-01

Volcanic glass is deposited with trace amounts (0.1-0.6 wt.%) of undegassed magmatic water dissolved in the glass. After deposition, meteoric water penetrates into the glass structure mostly as molecular H2O. Due to the lower δD (‰) values of non-tropical meteoric waters and the ∼30‰ offset between volcanic glass and environmental water during hydration, secondary water imparts lighter hydrogen isotopic values during secondary hydration up to a saturation concentration of 3-4 wt.% H2O. We analyzed compositionally and globally diverse volcanic glass from 0 to 10 ka for their δD and H2Ot across different climatic zones, and thus different δD of precipitation, on a thermal conversion elemental analyzer (TCEA) furnace attached to a mass spectrometer. We find that tephrachronologically coeval rhyolite glass is hydrated faster than basaltic glass, and in the majority of glasses an increase in age and total water content leads to a decrease in δD (‰), while a few equatorial glasses have little change in δD (‰). We compute a magmatic water correction based on our non-hydrated glasses, and calculate an average 103lnαglass-water for our hydrated felsic glasses of -33‰, which is similar to the 103lnαglass-water determined by Friedman et al. (1993a) of -34‰. We also determine a smaller average 103lnαglass-water for all our mafic glasses of -23‰. We compare the δD values of water extracted from our glasses to local meteoric waters following the inclusion of a -33‰ 103lnαglass-water. We find that, following a correction for residual magmatic water based on an average δD and wt.% H2Ot of recently erupted ashes from our study, the δD value of water extracted from hydrated volcanic glass is, on average, within 4‰ of local meteoric water. To better understand the difference in hydration rates of mafic and felsic glasses, we imaged 6 tephra clasts ranging in age and chemical composition with BSE (by FEI SEM) down to a submicron resolution. Mafic tephra have more bubbles per unit area (25-77 mm-2) than felsic tephra (736 mm-2) and thicker average bubble walls (0.07 mm) than felsic tephra (0.02 mm). We use a simplified diffusion model to quantify the hydration rate of vesicular glass as a function of the diffusivity of water and the average bubble wall thickness. Based on fits to our hydration rate data, we estimate the initial low-temperature diffusivity at 0.1 wt.% H2Ot in volcanic glass (mafic and felsic) to be on the order of 10-3 to 10-4 μm2/year and find that differences in hydration rates between mafic and felsic tephra can be attributed primarily to differences in vesicularity, although slightly slower hydration of basalt cannot be precluded. We also observe no consistent temporal difference in secondary meteoric water uptake in wet versus dry and hot versus cold climates.

Impacts of Hydrate Distribution on the Hydro-Thermo-Mechanical Properties of Hydrate-Bearing Sediments

NASA Astrophysics Data System (ADS)

Dai, S.; Seol, Y.

2015-12-01

In general, hydrate makes the sediments hydraulically less conductive, thermally more conductive, and mechanically stronger; yet the dependency of these physical properties on hydrate saturation varies with hydrate distribution and morphology. Hydrate distribution in sediments may cause the bulk physical properties of their host sediments varying several orders of magnitude even with the same amount of hydrate. In natural sediments, hydrate morphology is inherently governed by the burial depth and the grain size of the host sediments. Compare with patchy hydrate, uniformly distributed hydrate is more destructive to fluid flow, yet leads to higher gas and water permeability during hydrate dissociation due to the easiness of forming percolation paths. Water and hydrate have similar thermal conductivity values; the bulk thermal conductivity of hydrate-bearing sediments depends critically on gas-phase saturation. 60% of gas saturation may result in evident thermal conductivity drop and hinder further gas production. Sediments with patchy hydrate yield lower stiffness than that with cementing hydrate but higher stiffness than that with pore filling and loading bearing hydrate. Besides hydrate distribution, the stress state and loading history also play an important role in the mechanical behavior of hydrate-bearing sediments.

Hydration-Dependent Dynamical Modes in Xyloglucan from Molecular Dynamics Simulation of 13C NMR Relaxation Times and Their Distributions.

PubMed

Chen, Pan; Terenzi, Camilla; Furó, István; Berglund, Lars A; Wohlert, Jakob

2018-05-15

Macromolecular dynamics in biological systems, which play a crucial role for biomolecular function and activity at ambient temperature, depend strongly on moisture content. Yet, a generally accepted quantitative model of hydration-dependent phenomena based on local relaxation and diffusive dynamics of both polymer and its adsorbed water is still missing. In this work, atomistic-scale spatial distributions of motional modes are calculated using molecular dynamics simulations of hydrated xyloglucan (XG). These are shown to reproduce experimental hydration-dependent 13 C NMR longitudinal relaxation times ( T 1 ) at room temperature, and relevant features of their broad distributions, which are indicative of locally heterogeneous polymer reorientational dynamics. At low hydration, the self-diffusion behavior of water shows that water molecules are confined to particular locations in the randomly aggregated XG network while the average polymer segmental mobility remains low. Upon increasing water content, the hydration network becomes mobile and fully accessible for individual water molecules, and the motion of hydrated XG segments becomes faster. Yet, the polymer network retains a heterogeneous gel-like structure even at the highest level of hydration. We show that the observed distribution of relaxations times arises from the spatial heterogeneity of chain mobility that in turn is a result of heterogeneous distribution of water-chain and chain-chain interactions. Our findings contribute to the picture of hydration-dependent dynamics in other macromolecules such as proteins, DNA, and synthetic polymers, and hold important implications for the mechanical properties of polysaccharide matrixes in plants and plant-based materials.

Microstructural evolution of gas hydrates in sedimentary matrices observed with synchrotron X-ray computed tomographic microscopy

NASA Astrophysics Data System (ADS)

Chaouachi, Marwen; Falenty, Andrzej; Sell, Kathleen; Enzmann, Frieder; Kersten, Michael; Haberthür, David; Kuhs, Werner F.

2015-06-01

The formation process of gas hydrates in sedimentary matrices is of crucial importance for the physical and transport properties of the resulting aggregates. This process has never been observed in situ at submicron resolution. Here we report on synchrotron-based microtomographic studies by which the nucleation and growth processes of gas hydrate were observed at 276 K in various sedimentary matrices such as natural quartz (with and without admixtures of montmorillonite type clay) or glass beads with different surface properties, at varying water saturation. Both juvenile water and metastably gas-enriched water obtained from gas hydrate decomposition was used. Xenon gas was employed to enhance the density contrast between gas hydrate and the fluid phases involved. The nucleation sites can be easily identified and the various growth patterns are clearly established. In sediments under-saturated with juvenile water, nucleation starts at the water-gas interface resulting in an initially several micrometer thick gas hydrate film; further growth proceeds to form isometric single crystals of 10-20 µm size. The growth of gas hydrate from gas-enriched water follows a different pattern, via the nucleation in the bulk of liquid producing polyhedral single crystals. A striking feature in both cases is the systematic appearance of a fluid phase film of up to several micron thickness between gas hydrates and the surface of the quartz grains. These microstructural findings are relevant for future efforts of quantitative rock physics modeling of gas hydrates in sedimentary matrices and explain the anomalous attenuation of seismic/sonic waves.

Effect of Sodium Dodecyl Sulfate Surfactant on Methane Hydrate Formation: A Molecular Dynamics Study.

PubMed

Choudhary, Nilesh; Hande, Vrushali R; Roy, Sudip; Chakrabarty, Suman; Kumar, Rajnish

2018-06-28

In experimental studies, it has been observed that the presence of sodium dodecyl sulfate (SDS) significantly increases the kinetics of hydrate formation and the final water-to-hydrate conversion ratio. In this study, we intend to understand the molecular mechanism behind the effect of SDS on the formation of methane hydrate through molecular dynamics simulation. Hydrate formation conditions similar to that of laboratory experiments were chosen to study hydrate growth kinetics in 1 wt % SDS solution. We also investigate the effect of interactions with isolated SDS molecules on methane hydrate growth. It was observed that the hydrophobic tail part of the SDS molecule favorably interacts with the growing hydrate surface and may occupy the partial hydrate cages while the head groups remain exposed to water.

Phase equilibria and thermodynamic modeling of ethane and propane hydrates in porous silica gels.

PubMed

Seo, Yongwon; Lee, Seungmin; Cha, Inuk; Lee, Ju Dong; Lee, Huen

2009-04-23

In the present study, we examined the active role of porous silica gels when used as natural gas storage and transportation media. We adopted the dispersed water in silica gel pores to substantially enhance active surface for contacting and encaging gas molecules. We measured the three-phase hydrate (H)-water-rich liquid (L(W))-vapor (V) equilibria of C(2)H(6) and C(3)H(8) hydrates in 6.0, 15.0, 30.0, and 100.0 nm silica gel pores to investigate the effect of geometrical constraints on gas hydrate phase equilibria. At specified temperatures, the hydrate stability region is shifted to a higher pressure region depending on pore size when compared with those of bulk hydrates. Through application of the Gibbs-Thomson relationship to the experimental data, we determined the values for the C(2)H(6) hydrate-water and C(3)H(8) hydrate-water interfacial tensions to be 39 +/- 2 and 45 +/- 1 mJ/m(2), respectively. By using these values, the calculation values were in good agreement with the experimental ones. The overall results given in this study could also be quite useful in various fields, such as exploitation of natural gas hydrate in marine sediments and sequestration of carbon dioxide into the deep ocean.

Infrared signature of micro-hydration in the organophosphate sarin: An ab initio study

DOE PAGES

Alam, Todd M.; Pearce, Charles Joseph

2015-06-28

The infrared (IR) spectra of micro-hydrated Sarin•(H 2O) n clusters containing between one and four explicit waters have been studied using ab initio density functional theory (DFT) methods. The phosphate group P=O bond vibration region (~1270 to 1290 cm –1) revealed the largest frequency variation with hydration, with a frequency red shift reflecting the direct hydrogen bond formation between the P=O of Sarin and water. Small variations to the P-F stretch (~810 to 815 cm –1) and the C-O-P vibrational modes (~995 to 1004 cm –1) showed that the water interactions with these functional groups were minor, and that themore » structures of Sarin were not extensively perturbed in the hydrated complexes. Increasing the number of explicit hydration waters produced only small vibrational changes in the lowest free energy complexes. These minor changes were consistent with a single water-phosphate hydrogen bond being the dominant structure, though a second water-phosphate hydrogen bond was observed in some complexes and was identified by an additional red shift of the P=O bond vibration. As a result, the H 2O•H 2O vibrational modes (~3450 to 3660 cm –1) increased in complexity with higher hydration levels and reflect the extended hydrogen bonding networks formed between the explicit waters in the hydrated Sarin clusters.« less

Structure of cellulose microfibrils in mature cotton fibres.

PubMed

Martínez-Sanz, Marta; Pettolino, Filomena; Flanagan, Bernadine; Gidley, Michael J; Gilbert, Elliot P

2017-11-01

The structure of cellulose microfibrils in mature cotton fibres from three varieties - Gossypium hirsutum, G. barbadense and G. arboreum - has been investigated by a multi-technique approach combining small angle scattering techniques with spectroscopy and diffraction. Cellulose microfibrils present a Iβ-rich crystalline structure with limited surface disorder. Small angle scattering (SAXS and SANS) data have been successfully fitted using a core-shell model and the results obtained indicate that the cellulose microfibrils, formed by the association of 2-3 elementary fibrils, are composed of a ca. 2nm impermeable crystalline core, surrounded by a partially hydrated paracrystalline shell, with overall cross-sections of ca. 3.6-4.7nm. Different low levels of cell wall matrix components have a strong impact on the microfibril architecture and enable moisture penetration upon hydration. Furthermore, the higher amounts of non-cellulosic components in G. barbadense result in a less dense packing of cellulose microfibrils and increased solvent accessibility. Copyright © 2017 Elsevier Ltd. All rights reserved.

Label-free detection and characterization of the binding of hemagglutinin protein and broadly neutralizing monoclonal antibodies using terahertz spectroscopy

NASA Astrophysics Data System (ADS)

Sun, Yiwen; Zhong, Junlan; Zhang, Cunlin; Zuo, Jian; Pickwell-MacPherson, Emma

2015-03-01

Hemagglutinin (HA) is the main surface glycoprotein of the influenza A virus. The H9N2 subtype influenza A virus is recognized as the most possible pandemic strain as it has crossed the species barrier, infecting swine and humans. We use terahertz spectroscopy to study the hydration shell formation around H9 subtype influenza A virus's HA protein (H9 HA) as well as the detection of antigen binding of H9 HA with the broadly neutralizing monoclonal antibody. We observe a remarkable concentration dependent nonlinear response of the H9 HA, which reveals the formation process of the hydration shell around H9 HA molecules. Furthermore, we show that terahertz dielectric properties of the H9 HA are strongly affected by the presence of the monoclonal antibody F10 and that the terahertz dielectric loss tangent can be used to detect the antibody binding at lower concentrations than the standard ELISA test.

Phase diagram and high-pressure boundary of hydrate formation in the carbon dioxide-water system.

PubMed

Manakov, Andrej Yu; Dyadin, Yuriy A; Ogienko, Andrey G; Kurnosov, Alexander V; Aladko, Eugeny Ya; Larionov, Eduard G; Zhurko, Fridrih V; Voronin, Vladimir I; Berger, Ivan F; Goryainov, Sergei V; Lihacheva, Anna Yu; Ancharov, Aleksei I

2009-05-21

Experimental investigation of the phase diagram of the system carbon dioxide-water at pressures up to 2.7 GPa has been carried out in order to explain earlier controversial results on the decomposition curves of the hydrates formed in this system. According to X-ray diffraction data, solid and/or liquid phases of water and CO2 coexist in the system at room temperature within the pressure range from 0.8 to 2.6 GPa; no clathrate hydrates are observed. The results of neutron diffraction experiments involving the samples with different CO2/H2O molar ratios, and the data on the phase diagram of the system carbon dioxide-water show that CO2 hydrate of cubic structure I is the only clathrate phase present in this system under studied P-T conditions. We suppose that in the cubic structure I hydrate of CO2 multiple occupation of the large hydrate cavities with CO2 molecules takes place. At pressure of about 0.8 GPa this hydrate decomposes into components indicating the presence of the upper pressure boundary of the existence of clathrate hydrates in the system.

Sequence Dependencies of DNA Deformability and Hydration in the Minor Groove

PubMed Central

Yonetani, Yoshiteru; Kono, Hidetoshi

2009-01-01

Abstract DNA deformability and hydration are both sequence-dependent and are essential in specific DNA sequence recognition by proteins. However, the relationship between the two is not well understood. Here, systematic molecular dynamics simulations of 136 DNA sequences that differ from each other in their central tetramer revealed that sequence dependence of hydration is clearly correlated with that of deformability. We show that this correlation can be illustrated by four typical cases. Most rigid basepair steps are highly likely to form an ordered hydration pattern composed of one water molecule forming a bridge between the bases of distinct strands, but a few exceptions favor another ordered hydration composed of two water molecules forming such a bridge. Steps with medium deformability can display both of these hydration patterns with frequent transition. Highly flexible steps do not have any stable hydration pattern. A detailed picture of this correlation demonstrates that motions of hydration water molecules and DNA bases are tightly coupled with each other at the atomic level. These results contribute to our understanding of the entropic contribution from water molecules in protein or drug binding and could be applied for the purpose of predicting binding sites. PMID:19686662

Evaluation of water displacement energetics in protein binding sites with grid cell theory.

PubMed

Gerogiokas, G; Southey, M W Y; Mazanetz, M P; Heifetz, A; Hefeitz, A; Bodkin, M; Law, R J; Michel, J

2015-04-07

Excess free energies, enthalpies and entropies of water in protein binding sites were computed via classical simulations and Grid Cell Theory (GCT) analyses for three pairs of congeneric ligands in complex with the proteins scytalone dehydratase, p38α MAP kinase and EGFR kinase respectively. Comparative analysis is of interest since the binding modes for each ligand pair differ in the displacement of one binding site water molecule, but significant variations in relative binding affinities are observed. Protocols that vary in their use of restraints on protein and ligand atoms were compared to determine the influence of protein-ligand flexibility on computed water structure and energetics, and to assess protocols for routine analyses of protein-ligand complexes. The GCT-derived binding affinities correctly reproduce experimental trends, but the magnitude of the predicted changes in binding affinities is exaggerated with respect to results from a previous Monte Carlo Free Energy Perturbation study. Breakdown of the GCT water free energies into enthalpic and entropic components indicates that enthalpy changes dominate the observed variations in energetics. In EGFR kinase GCT analyses revealed that replacement of a pyrimidine by a cyanopyridine perturbs water energetics up three hydration shells away from the ligand.

Unexpected inhibition of CO 2 gas hydrate formation in dilute TBAB solutions and the critical role of interfacial water structure

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

Nguyen, Ngoc N.; Nguyen, Anh V.; Nguyen, Khoi T.

Gas hydrates formed under moderated conditions open up novel approaches to tackling issues related to energy supply, gas separation, and CO 2 sequestration. Several additives like tetra-n-butylammonium bromide (TBAB) have been empirically developed and used to promote gas hydrate formation. Here we report unexpected experimental results which show that TBAB inhibits CO 2 gas hydrate formation when used at minuscule concentration. We also used spectroscopic techniques and molecular dynamics simulation to gain further insights and explain the experimental results. They have revealed the critical role of water alignment at the gas-water interface induced by surface adsorption of tetra-n-butylammonium cation (TBAmore » +) which gives rise to the unexpected inhibition of dilute TBAB solution. The water perturbation by TBA + in the bulk is attributed to the promotion effect of high TBAB concentration on gas hydrate formation. We explain our finding using the concept of activation energy of gas hydrate formation. Our results provide a step toward to mastering the control of gas hydrate formation.« less

Effects of protein conformational flexibilities and electrostatic interactions on the low-frequency vibrational spectrum of hydration water.

PubMed

Pal, Somedatta; Bandyopadhyay, Sanjoy

2013-05-16

The conformational flexibility of a protein and its ability to form hydrogen bonds with water are expected to influence the microscopic properties of water layer hydrating the protein. Detailed molecular dynamics simulations with an aqueous solution of the globular protein barstar have been carried out to explore such influence on the low-frequency vibrational spectrum of the hydration water molecules. The calculations reveal that enhanced degree of confinement at the protein surface on freezing its local motions leads to increasingly restricted oscillatory motions of the hydration water molecules as evident from larger blue shifts of the corresponding band. Interestingly, conformational fluctuations of the protein and electrostatic component of its interaction with the solvent have been found to affect the transverse and longitudinal oscillations of hydration water molecules in a nonuniform manner. It is further noticed that the distributions of the low-frequency modes for the water molecules hydrogen bonded to the residues of different segments of the protein are heterogeneously altered. The effect is more around the frozen protein matrix and agrees well with slower protein-water hydrogen bond relaxations.

Gas hydrate in nature

USGS Publications Warehouse

Ruppel, Carolyn D.

2018-01-17

Gas hydrate is a naturally occurring, ice-like substance that forms when water and gas combine under high pressure and at moderate temperatures. Methane is the most common gas present in gas hydrate, although other gases may also be included in hydrate structures, particularly in areas close to conventional oil and gas reservoirs. Gas hydrate is widespread in ocean-bottom sediments at water depths greater than 300–500 meters (m; 984–1,640 feet [ft]) and is also present in areas with permanently frozen ground (permafrost). Several countries are evaluating gas hydrate as a possible energy resource in deepwater or permafrost settings. Gas hydrate is also under investigation to determine how environmental change may affect these deposits.

Laboratory formation of non-cementing, methane hydrate-bearing sands

USGS Publications Warehouse

Waite, William F.; Bratton, Peter M.; Mason, David H.

2011-01-01

Naturally occurring hydrate-bearing sands often behave as though methane hydrate is acting as a load-bearing member of the sediment. Mimicking this behavior in laboratory samples with methane hydrate likely requires forming hydrate from methane dissolved in water. To hasten this formation process, we initially form hydrate in a free-gas-limited system, then form additional hydrate by circulating methane-supersaturated water through the sample. Though the dissolved-phase formation process can theoretically be enhanced by increasing the pore pressure and flow rate and lowering the sample temperature, a more fundamental concern is preventing clogs resulting from inadvertent methane bubble formation in the circulation lines. Clog prevention requires careful temperature control throughout the circulation loop.

Probing methane hydrate nucleation through the forward flux sampling method.

PubMed

Bi, Yuanfei; Li, Tianshu

2014-11-26

Understanding the nucleation of hydrate is the key to developing effective strategies for controlling methane hydrate formation. Here we present a computational study of methane hydrate nucleation, by combining the forward flux sampling (FFS) method and the coarse-grained water model mW. To facilitate the application of FFS in studying the formation of methane hydrate, we developed an effective order parameter λ on the basis of the topological analysis of the tetrahedral network. The order parameter capitalizes the signature of hydrate structure, i.e., polyhedral cages, and is capable of efficiently distinguishing hydrate from ice and liquid water while allowing the formation of different hydrate phases, i.e., sI, sII, and amorphous. Integration of the order parameter λ with FFS allows explicitly computing hydrate nucleation rates and obtaining an ensemble of nucleation trajectories under conditions where spontaneous hydrate nucleation becomes too slow to occur in direct simulation. The convergence of the obtained hydrate nucleation rate was found to depend crucially on the convergence of the spatial distribution for the spontaneously formed hydrate seeds obtained from the initial sampling of FFS. The validity of the approach is also verified by the agreement between the calculated nucleation rate and that inferred from the direct simulation. Analyzing the obtained large ensemble of hydrate nucleation trajectories, we show hydrate formation at 220 K and 500 bar is initiated by the nucleation events occurring in the vicinity of water-methane interface, and facilitated by a gradual transition from amorphous to crystalline structure. The latter provides the direct support to the proposed two-step nucleation mechanism of methane hydrate.

The effects of salt, particle and pore size on the process of carbon dioxide hydrate formation: A critical review

NASA Astrophysics Data System (ADS)

Ghaedi, Hosein; Ayoub, Muhammad; Bhat, A. H.; Mahmood, Syed Mohammad; Akbari, Saeed; Murshid, Ghulam

2016-11-01

Hydration is an alternative method for CO2 capture. In doing so, some researchers use porous media on an experimental scale. This paper tries to gather the researches on the formation of CO2 hydrate in different types of porous media such as silica sand, quartz sand, Toyoura, pumice, and fire hardened red clay. This review has attempted to examine the effects of salt and particle sizes as two major factors on the induction time, water to hydrate conversion, gas uptake (or gas consumption), and the rate of CO2 hydrate formation. By performing a critical assessment of previous research works, it was observed that the figure for the gas uptake (or gas consumption) and water to hydrate conversion in porous media was decreased by increasing the particle size provided that the pore size was constant. Although, salt can play a role in hydrate formation as the thermodynamic inhibitor, the results show that salt can be regarded as the kinetic growth inhibitor and kinetic promoter. Because of the fact that the gas uptake in seawater is lower than pure water at the end of experiment, the salt can act as a kinetic growth inhibitor. However, since gas uptake (after the nucleation period and for a short period) and the initial rate of hydrate formation in saline water were more than that of pure water, salt can play a promoter role in the kinetic reaction, too. Besides these, in the case of pure water and within a certain particle size, the amount of the hydrate formation rate has been seen to be greater in smaller particles (provided that the pore size is constant), however this has not been observed for seawater.

Electrical properties of methane hydrate + sediment mixtures: The σ of CH 4 Hydrate + Sediment

DOE PAGES

Du Frane, Wyatt L.; Stern, Laura A.; Constable, Steven; ...

2015-07-30

Knowledge of the electrical properties of multicomponent systems with gas hydrate, sediments, and pore water is needed to help relate electromagnetic (EM) measurements to specific gas hydrate concentration and distribution patterns in nature. We built a pressure cell capable of measuring in situ electrical properties of multicomponent systems such that the effects of individual components and mixing relations can be assessed. We first established the temperature-dependent electrical conductivity (σ) of pure, single-phase methane hydrate to be ~5 orders of magnitude lower than seawater, a substantial contrast that can help differentiate hydrate deposits from significantly more conductive water-saturated sediments in EMmore » field surveys. We report σ measurements of two-component systems in which methane hydrate is mixed with variable amounts of quartz sand or glass beads. Sand by itself has low σ but is found to increase the overall σ of mixtures with well-connected methane hydrate. Alternatively, the overall σ decreases when sand concentrations are high enough to cause gas hydrate to be poorly connected, indicating that hydrate grains provide the primary conduction path. Our measurements suggest that impurities from sand induce chemical interactions and/or doping effects that result in higher electrical conductivity with lower temperature dependence. Finally, these results can be used in the modeling of massive or two-phase gas-hydrate-bearing systems devoid of conductive pore water. Further experiments that include a free water phase are the necessary next steps toward developing complex models relevant to most natural systems.« less

Electrical properties of methane hydrate + sediment mixtures: The σ of CH 4 Hydrate + Sediment

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

Du Frane, Wyatt L.; Stern, Laura A.; Constable, Steven

Knowledge of the electrical properties of multicomponent systems with gas hydrate, sediments, and pore water is needed to help relate electromagnetic (EM) measurements to specific gas hydrate concentration and distribution patterns in nature. We built a pressure cell capable of measuring in situ electrical properties of multicomponent systems such that the effects of individual components and mixing relations can be assessed. We first established the temperature-dependent electrical conductivity (σ) of pure, single-phase methane hydrate to be ~5 orders of magnitude lower than seawater, a substantial contrast that can help differentiate hydrate deposits from significantly more conductive water-saturated sediments in EMmore » field surveys. We report σ measurements of two-component systems in which methane hydrate is mixed with variable amounts of quartz sand or glass beads. Sand by itself has low σ but is found to increase the overall σ of mixtures with well-connected methane hydrate. Alternatively, the overall σ decreases when sand concentrations are high enough to cause gas hydrate to be poorly connected, indicating that hydrate grains provide the primary conduction path. Our measurements suggest that impurities from sand induce chemical interactions and/or doping effects that result in higher electrical conductivity with lower temperature dependence. Finally, these results can be used in the modeling of massive or two-phase gas-hydrate-bearing systems devoid of conductive pore water. Further experiments that include a free water phase are the necessary next steps toward developing complex models relevant to most natural systems.« less

Numerical studies of gas production from several CH4 hydrate zones at the Mallik site, Mackenzie Delta, Canada

USGS Publications Warehouse

Moridis, G.J.; Collett, T.S.; Dallimore, S.R.; Satoh, T.; Hancock, S.; Weatherill, B.

2004-01-01

The Mallik site represents an onshore permafrost-associated gas hydrate accumulation in the Mackenzie Delta, Northwest Territories, Canada. A gas hydrate research well was drilled at the site in 1998. The objective of this study is the analysis of various gas production scenarios from five methane hydrate-bearing zones at the Mallik site. In Zone #1, numerical simulations using the EOSHYDR2 model indicated that gas production from hydrates at the Mallik site was possible by depressurizing a thin free gas zone at the base of the hydrate stability field. Horizontal wells appeared to have a slight advantage over vertical wells, while multiwell systems involving a combination of depressurization and thermal stimulation offered superior performance, especially when a hot noncondensible gas was injected. Zone #2, which involved a gas hydrate layer with an underlying aquifer, could yield significant amounts of gas originating entirely from gas hydrates, the volumes of which increased with the production rate. However, large amounts of water were also produced. Zones #3, #4 and #5 were lithologically isolated gas hydrate-bearing deposits with no underlying zones of mobile gas or water. In these zones, thermal stimulation by circulating hot water in the well was used to induce dissociation. Sensitivity studies indicated that the methane release from the hydrate accumulations increased with the gas hydrate saturation, the initial formation temperature, the temperature of the circulating water in the well, and the formation thermal conductivity. Methane production appears to be less sensitive to the specific heat of the rock and of the hydrate, and to the permeability of the formation. ?? 2004 Published by Elsevier B.V.

Theory of gas hydrates: effect of the approximation of rigid water lattice.

PubMed

Pimpalgaonkar, Hrushikesh; Veesam, Shivanand K; Punnathanam, Sudeep N

2011-08-25

One of the assumptions of the van der Waals and Platteeuw theory for gas hydrates is that the host water lattice is rigid and not distorted by the presence of guest molecules. In this work, we study the effect of this approximation on the triple-point lines of the gas hydrates. We calculate the triple-point lines of methane and ethane hydrates via Monte Carlo molecular simulations and compare the simulation results with the predictions of van der Waals and Platteeuw theory. Our study shows that even if the exact intermolecular potential between the guest molecules and water is known, the dissociation temperatures predicted by the theory are significantly higher. This has serious implications to the modeling of gas hydrate thermodynamics, and in spite of the several impressive efforts made toward obtaining an accurate description of intermolecular interactions in gas hydrates, the theory will suffer from the problem of robustness if the issue of movement of water molecules is not adequately addressed. © 2011 American Chemical Society

A molecular dynamics study of ethanol-water hydrogen bonding in binary structure I clathrate hydrate with CO2

NASA Astrophysics Data System (ADS)

Alavi, Saman; Ohmura, Ryo; Ripmeester, John A.

2011-02-01

Guest-host hydrogen bonding in clathrate hydrates occurs when in addition to the hydrophilic moiety which causes the molecule to form hydrates under high pressure-low temperature conditions, the guests contain a hydrophilic, hydrogen bonding functional group. In the presence of carbon dioxide, ethanol clathrate hydrate has been synthesized with 10% of large structure I (sI) cages occupied by ethanol. In this work, we use molecular dynamics simulations to study hydrogen bonding structure and dynamics in this binary sI clathrate hydrate in the temperature range of 100-250 K. We observe that ethanol forms long-lived (>500 ps) proton-donating and accepting hydrogen bonds with cage water molecules from both hexagonal and pentagonal faces of the large cages while maintaining the general cage integrity of the sI clathrate hydrate. The presence of the nondipolar CO2 molecules stabilizes the hydrate phase, despite the strong and prevalent alcohol-water hydrogen bonding. The distortions of the large cages from the ideal form, the radial distribution functions of the guest-host interactions, and the ethanol guest dynamics are characterized in this study. In previous work through dielectric and NMR relaxation time studies, single crystal x-ray diffraction, and molecular dynamics simulations we have observed guest-water hydrogen bonding in structure II and structure H clathrate hydrates. The present work extends the observation of hydrogen bonding to structure I hydrates.

Role of Polymeric Excipients in the Stabilization of Olanzapine when Exposed to Aqueous Environments.

PubMed

Paisana, Maria; Wahl, Martin; Pinto, João

2015-12-12

Hydrate formation is a phase transition which can occur during manufacturing processes involving water. This work considers the prevention of hydration of anhydrous olanzapine and hydrate conversions in the presence of water and polymers (polyethyleneglycol; hydroxypropylcellulose; polyvinylpyrrolidone) in forming pellets by wet extrusion and spheronisation. Anhydrous olanzapine was added to water with or without those polymers prior to extrusion with microcrystalline cellulose. Assessment of olanzapine conversion was made by XRP-Diffraction; FTIR spectroscopy; calorimetry (DSC) and microscopy (SEM for crystal size and shape). The addition of water converted the anhydrous form into dihydrate B and higher hydrate; whereas polyethyleneglycol promoted a selective hydrate conversion into the higher hydrate olanzapine form. Both polyvinylpyrrolidone and hydroxypropylcellulose prevented the hydrate transformations of the anhydrous drug; the latter even in the presence of hydrate seeds. This may be explained by the higher H-bond ability; higher network association and higher hydrophobicity of hydroxypropylcellulose by comparison with polyethyleneglycol and polyvinylpyrrolidone; which could contribute to its higher affinity to the crystal surfaces of the hydrate nuclei/initial crystals and promoting steric hindrance to the incorporation of other drug molecules into the crystal lattice; thus, preventing the crystal growth. The addition of microcrystalline cellulose needed for the pellets production (final product) did not eliminate the protector effect of both hydroxypropylcellulose and polyvinylpyrrolidone during pellets' processing and dissolution evaluation.

The role of water in gas hydrate dissociation

USGS Publications Warehouse

Circone, S.; Stern, L.A.; Kirby, S.H.

2004-01-01

When raised to temperatures above the ice melting point, gas hydrates release their gas in well-defined, reproducible events that occur within self-maintained temperature ranges slightly below the ice point. This behavior is observed for structure I (carbon dioxide, methane) and structure II gas hydrates (methane-ethane, and propane), including those formed with either H2O- or D2O-host frameworks, and dissociated at either ambient or elevated pressure conditions. We hypothesize that at temperatures above the H2O (or D2O) melting point: (1) hydrate dissociation produces water + gas instead of ice + gas, (2) the endothermic dissociation reaction lowers the temperature of the sample, causing the water product to freeze, (3) this phase transition buffers the sample temperatures within a narrow temperature range just below the ice point until dissociation goes to completion, and (4) the temperature depression below the pure ice melting point correlates with the average rate of dissociation and arises from solution of the hydrate-forming gas, released by dissociation, in the water phase at elevated concentrations. In addition, for hydrate that is partially dissociated to ice + gas at lower temperatures and then heated to temperatures above the ice point, all remaining hydrate dissociates to gas + liquid water as existing barriers to dissociation disappear. The enhanced dissociation rates at warmer temperatures are probably associated with faster gas transport pathways arising from the formation of water product.

Inhibited phase behavior of gas hydrates in graphene oxide: influences of surface and geometric constraints.

PubMed

Kim, Daeok; Kim, Dae Woo; Lim, Hyung-Kyu; Jeon, Jiwon; Kim, Hyungjun; Jung, Hee-Tae; Lee, Huen

2014-11-07

Porous materials have provided us unprecedented opportunities to develop emerging technologies such as molecular storage systems and separation mechanisms. Pores have also been used as supports to contain gas hydrates for the application in gas treatments. Necessarily, an exact understanding of the properties of gas hydrates in confining pores is important. Here, we investigated the formation of CO2, CH4 and N2 hydrates in non-interlamellar voids in graphene oxide (GO), and their thermodynamic behaviors. For that, low temperature XRD and P-T traces were conducted to analyze the water structure and confirm hydrate formation, respectively, in GO after its exposure to gaseous molecules. Confinement and strong interaction of water with the hydrophilic surface of graphene oxide reduce water activity, which leads to the inhibited phase behavior of gas hydrates.

Effect of Chitin Isolated from Crustaceans and Cephalopods on Denaturation of Fish Myofibrillar Protein and the State of Water during Frozen Storage

NASA Astrophysics Data System (ADS)

Yamashita, Yasumitsu; Zhang, Nong; Nozaki, Yukinori

The effect of chitin hydrolysate made from shell of crustaceans and cartilage of cephalopods on the denaturation and the state of water of lizard fish myofibrillar protein (Mf) during frozen storage at -250°C for 120 days were investigated. 5.0% chitin hydrolysate (dried matter) added Mf samples were frozen at -25°C and storage for 120 days, and the change of inactivation of Mf Ca-ATPase and the change of unfrozen water in Mf were examined during the frozen storage. The decrease of Mf Ca-ATPase during frozen storage were slow by addition of chitin hydrolysate. The amount of unfrozen water in Mf were increased by addition of chitin hydrolysate, and decreaced gradually during frozen storage. On the other hand, the amount of unfrozen water of the control were decreaced suddenly during frozen storage. Above results suggest that chitin hydrolysate has cryoprotective effect on Mf. It is guessed that the mechanism of cryoprotective effect of chitin hydrolysate may be caused by an interaction between hydration sphere of Mf and equatorial OH groups in the molecular structure of chitin hydrolysate.

Correlation Between Chain Architecture and Hydration Water Structure in Polysaccharides

NASA Astrophysics Data System (ADS)

Grossutti, Michael; Dutcher, John

The physical properties of confined water can differ dramatically from those of bulk water. Hydration water associated with polysaccharides provides a particularly important example of confined water, with differences in polysaccharide structure providing different spatially confined environments for water adsorption. We have used attenuated total reflection infrared (ATR-IR) spectroscopy to investigate the structure of hydration water in films of three different polysaccharides under controlled relative humidity (RH) conditions. We compare the results obtained for films of highly branched, monodisperse phytoglycogen nanoparticles to those obtained for two unbranched polysaccharides, hyaluronic acid (HA) and chitosan. We find similarities between water structuring in the two linear polysaccharides, and significant differences for phytoglycogen. In particular, the phytoglycogen nanoparticles exhibited high network water connectivity, and a large increase in the fraction of multimer water clusters with increasing RH, whereas the water structure for HA and chitosan was found to be insensitive to changes in RH. These measurements provide unique insight into the relationship between the chain architecture and hydration of polysaccharides.

Fracturing Behavior of Methane-Hydrate-Bearing Sediment

NASA Astrophysics Data System (ADS)

Konno, Y.; Jin, Y.; Yoneda, J.; Uchiumi, T.; Shinjou, K.; Nagao, J.

2016-12-01

As a part of a Japanese national hydrate research program (MH21, funded by the Ministry of Economy, Trade, and Industry), we performed laboratory experiments of hydraulic fracturing in methane-hydrate-bearing sediment. Distilled water was injected into methane-hydrate-bearing sand which was artificially made in a tri-axial pressure cell. X-ray computed tomography revealed that tensile failure was occurred after a rapid drop in the injection pressure. It was found that generated fractures cause a significant increase in the effective water permeability of hydrate-bearing sand. The result contributes fundamental understanding of the accumulation mechanism of gas hydrates in sediments and shows that hydraulic fracturing is one of promising enhanced recovery methods for low-permeable gas hydrate reservoirs.

Development of hydrate risk quantification in oil and gas production

NASA Astrophysics Data System (ADS)

Chaudhari, Piyush N.

Subsea flowlines that transport hydrocarbons from wellhead to the processing facility face issues from solid deposits such as hydrates, waxes, asphaltenes, etc. The solid deposits not only affect the production but also pose a safety concern; thus, flow assurance is significantly important in designing and operating subsea oil and gas production. In most subsea oil and gas operations, gas hydrates form at high pressure and low temperature conditions, causing the risk of plugging flowlines, with a undesirable impact on production. Over the years, the oil and gas industry has shifted their perspective from hydrate avoidance to hydrate management given several parameters such as production facility, production chemistry, economic and environmental concerns. Thus, understanding the level of hydrate risk associated with subsea flowlines is an important in developing efficient hydrate management techniques. In the past, hydrate formation models were developed for various flow-systems (e.g., oil dominated, water dominated, and gas dominated) present in the oil and gas production. The objective of this research is to extend the application of the present hydrate prediction models for assessing the hydrate risk associated with subsea flowlines that are prone to hydrate formation. It involves a novel approach for developing quantitative hydrate risk models based on the conceptual models built from the qualitative knowledge obtained from experimental studies. A comprehensive hydrate risk model, that ranks the hydrate risk associated with the subsea production system as a function of time, hydrates, and several other parameters, which account for inertial, viscous, interfacial forces acting on the flow-system, is developed for oil dominated and condensate systems. The hydrate plugging risk for water dominated systems is successfully modeled using The Colorado School of Mines Hydrate Flow Assurance Tool (CSMHyFAST). It is found that CSMHyFAST can be used as a screening tool in order to reduce the parametric study that may require a long duration of time using The Colorado School of Mines Hydrate Kinetic Model (CSMHyK). The evolution of the hydrate plugging risk along flowline-riser systems is modeled for steady state and transient operations considering the effect of several critical parameters such as oil-hydrate slip, duration of shut-in, and water droplet size on a subsea tieback system. This research presents a novel platform for quantification of the hydrate plugging risk, which in-turn will play an important role in improving and optimizing current hydrate management strategies. The predictive strength of the hydrate risk quantification and hydrate prediction models will have a significant impact on flow assurance engineering and design with respect to building safe and efficient hydrate management techniques for future deep-water developments.

Interfacial Water at Protein Surfaces: Wide-Line NMR and DSC Characterization of Hydration in Ubiquitin Solutions

PubMed Central

Tompa, Kálmán; Bánki, Péter; Bokor, Mónika; Kamasa, Pawel; Lasanda, György; Tompa, Péter

2009-01-01

Wide-line 1H-NMR and differential scanning calorimetry measurements were done in aqueous solutions and on lyophilized samples of human ubiquitin between −70°C and +45°C. The measured properties (size, thermal evolution, and wide-line NMR spectra) of the protein-water interfacial region are substantially different in the double-distilled and buffered-water solutions of ubiquitin. The characteristic transition in water mobility is identified as the melting of the nonfreezing/hydrate water. The amount of water in the low-temperature mobile fraction is 0.4 g/g protein for the pure water solution. The amount of mobile water is higher and its temperature dependence more pronounced for the buffered solution. The specific heat of the nonfreezing/hydrate water was evaluated using combined differential scanning calorimetry and NMR data. Considering the interfacial region as an independent phase, the values obtained are 5.0–5.8 J·g−1·K−1, and the magnitudes are higher than that of pure/bulk water (4.2 J·g−1·K−1). This unexpected discrepancy can only be resolved in principle by assuming that hydrate water is in tight H-bond coupling with the protein matrix. The specific heat for the system composed of the protein molecule and its hydration water is 2.3 J·g−1·K−1. It could be concluded that the protein ubiquitin and its hydrate layer behave as a highly interconnected single phase in a thermodynamic sense. PMID:19348762

Studying pressure denaturation of a protein by molecular dynamics simulations.

PubMed

Sarupria, Sapna; Ghosh, Tuhin; García, Angel E; Garde, Shekhar

2010-05-15

Many globular proteins unfold when subjected to several kilobars of hydrostatic pressure. This "unfolding-up-on-squeezing" is counter-intuitive in that one expects mechanical compression of proteins with increasing pressure. Molecular simulations have the potential to provide fundamental understanding of pressure effects on proteins. However, the slow kinetics of unfolding, especially at high pressures, eliminates the possibility of its direct observation by molecular dynamics (MD) simulations. Motivated by experimental results-that pressure denatured states are water-swollen, and theoretical results-that water transfer into hydrophobic contacts becomes favorable with increasing pressure, we employ a water insertion method to generate unfolded states of the protein Staphylococcal Nuclease (Snase). Structural characteristics of these unfolded states-their water-swollen nature, retention of secondary structure, and overall compactness-mimic those observed in experiments. Using conformations of folded and unfolded states, we calculate their partial molar volumes in MD simulations and estimate the pressure-dependent free energy of unfolding. The volume of unfolding of Snase is negative (approximately -60 mL/mol at 1 bar) and is relatively insensitive to pressure, leading to its unfolding in the pressure range of 1500-2000 bars. Interestingly, once the protein is sufficiently water swollen, the partial molar volume of the protein appears to be insensitive to further conformational expansion or unfolding. Specifically, water-swollen structures with relatively low radii of gyration have partial molar volume that are similar to that of significantly more unfolded states. We find that the compressibility change on unfolding is negligible, consistent with experiments. We also analyze hydration shell fluctuations to comment on the hydration contributions to protein compressibility. Our study demonstrates the utility of molecular simulations in estimating volumetric properties and pressure stability of proteins, and can be potentially extended for applications to protein complexes and assemblies. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

Structural, dynamical, and transport properties of the hydrated halides: How do At{sup −} bulk properties compare with those of the other halides, from F{sup −} to I{sup −}?

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

Réal, Florent, E-mail: florent.real@univ-lille1.fr; Severo Pereira Gomes, André; Guerrero Martínez, Yansel Omar

2016-03-28

The properties of halides from the lightest, fluoride (F{sup −}), to the heaviest, astatide (At{sup −}), have been studied in water using a polarizable force-field approach based on molecular dynamics (MD) simulations at the 10 ns scale. The selected force-field explicitly treats the cooperativity within the halide-water hydrogen bond networks. The force-field parameters have been adjusted to ab initio data on anion/water clusters computed at the relativistic Möller-Plesset second-order perturbation theory level of theory. The anion static polarizabilities of the two heaviest halides, I{sup −} and At{sup −}, were computed in the gas phase using large and diffuse atomic basis sets,more » and taking into account both electron correlation and spin-orbit coupling within a four-component framework. Our MD simulation results show the solvation properties of I{sup −} and At{sup −} in aqueous phase to be very close. For instance, their first hydration shells are structured and encompass 9.2 and 9.1 water molecules at about 3.70 ± 0.05 Å, respectively. These values have to be compared to the F{sup −}, Cl{sup −}, and Br{sup −} ones, i.e., 6.3, 8.4, and 9.0 water molecules at 2.74, 3.38, and 3.55 Å, respectively. Moreover our computations predict the solvation free energy of At{sup −} in liquid water at ambient conditions to be 68 kcal mol{sup −1}, a value also close the I{sup −} one, about 70 kcal mol{sup −1}. In all, our simulation results for I{sup −} are in excellent agreement with the latest neutron- and X-ray diffraction studies. Those for the At{sup −} ion are predictive, as no theoretical or experimental data are available to date.« less

Dynamical Coupling of Intrinsically Disordered Proteins and Their Hydration Water: Comparison with Folded Soluble and Membrane Proteins

PubMed Central

Gallat, F.-X.; Laganowsky, A.; Wood, K.; Gabel, F.; van Eijck, L.; Wuttke, J.; Moulin, M.; Härtlein, M.; Eisenberg, D.; Colletier, J.-P.; Zaccai, G.; Weik, M.

2012-01-01

Hydration water is vital for various macromolecular biological activities, such as specific ligand recognition, enzyme activity, response to receptor binding, and energy transduction. Without hydration water, proteins would not fold correctly and would lack the conformational flexibility that animates their three-dimensional structures. Motions in globular, soluble proteins are thought to be governed to a certain extent by hydration-water dynamics, yet it is not known whether this relationship holds true for other protein classes in general and whether, in turn, the structural nature of a protein also influences water motions. Here, we provide insight into the coupling between hydration-water dynamics and atomic motions in intrinsically disordered proteins (IDP), a largely unexplored class of proteins that, in contrast to folded proteins, lack a well-defined three-dimensional structure. We investigated the human IDP tau, which is involved in the pathogenic processes accompanying Alzheimer disease. Combining neutron scattering and protein perdeuteration, we found similar atomic mean-square displacements over a large temperature range for the tau protein and its hydration water, indicating intimate coupling between them. This is in contrast to the behavior of folded proteins of similar molecular weight, such as the globular, soluble maltose-binding protein and the membrane protein bacteriorhodopsin, which display moderate to weak coupling, respectively. The extracted mean square displacements also reveal a greater motional flexibility of IDP compared with globular, folded proteins and more restricted water motions on the IDP surface. The results provide evidence that protein and hydration-water motions mutually affect and shape each other, and that there is a gradient of coupling across different protein classes that may play a functional role in macromolecular activity in a cellular context. PMID:22828339

Hydrogen-bond dynamics at the bio-water interface in hydrated proteins: a molecular-dynamics study.

PubMed

Nandi, Prithwish K; English, Niall J; Futera, Zdenek; Benedetto, Antonio

2016-12-21

Water is fundamental to the biochemistry of enzymes. It is well known that without a minimum amount of water, enzymes are not biologically active. Bare minimal solvation for biological function corresponds to about a single layer of water covering enzymes' surfaces. Many contradictory studies on protein-hydration-water-coupled dynamics have been published in recent decades. Following prevailing wisdom, a dynamical crossover in hydration water (at around 220 K for hydrated lysozymes) can trigger larger-amplitude motions of the protein, activating, in turn, biological functions. Here, we present a molecular-dynamics-simulation study on a solvated model protein (hen egg-white lysozyme), in which we determine, inter alia, the relaxation dynamics of the hydrogen-bond network between the protein and its hydration water molecules on a residue-per-residue basis. Hydrogen-bond breakage/formation kinetics is rather heterogeneous in temperature dependence (due to the heterogeneity of the free-energy surface), and is driven by the magnitude of thermal motions of various different protein residues which provide enough thermal energy to overcome energy barriers to rupture their respective hydrogen bonds with water. In particular, arginine residues exhibit the highest number of such hydrogen bonds at low temperatures, losing almost completely such bonding above 230 K. This suggests that hydration water's dynamical crossover, observed experimentally for hydrated lysozymes at ∼220 K, lies not at the origin of the protein residues' larger-amplitude motions, but rather arises as a consequence thereof. This highlights the need for new experimental investigations, and new interpretations to link protein dynamics to functions, in the context of key interrelationships with the solvation layer.

Effects of water activity and low molecular weight humectants on skin permeability and hydration dynamics - a double-blind, randomized and controlled study.

PubMed

Albèr, C; Buraczewska-Norin, I; Kocherbitov, V; Saleem, S; Lodén, M; Engblom, J

2014-10-01

The mammalian skin is a barrier that effectively separates the water-rich interior of the body from the normally dryer exterior. Changes in the external conditions, for example ambient humidity, have been shown to affect the skin barrier properties. The prime objective of this study was to evaluate the effect of water activity of a topical formulation on skin hydration and permeability. A second objective was to gain more understanding on how two commonly used humectants, urea and glycerol, affect skin barrier function in vivo. Simple aqueous formulations were applied under occlusion to the volar forearm of healthy volunteers. Following 4-h exposure, skin water loss (by transepidermal water loss measurements), skin hydration (by Corneometry) and skin permeability (by time to vasodilation due to benzyl nicotinate exposure) were monitored. The results demonstrate that a relatively small change in the water activity of a topical formulation is sufficient to induce considerable effects on stratum corneum hydration and permeability to exogenous substances. Exposing the skin to high water activity leads to increased skin hydration and also increased permeability. Furthermore, urea and glycerol promote skin hydration and permeability even at reduced water activity of the applied formulation. These results highlight the importance of considering the water activity in topically applied formulations and the potential benefit of using humectants. The results may impact formulation optimization in how to facilitate skin hydration and to modify skin permeability by temporarily open and close the skin barrier. © 2014 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

Formation of natural gas hydrates in marine sediments 1. Conceptual model of gas hydrate growth conditioned by host sediment properties

USGS Publications Warehouse

Clennell, M.B.; Hovland, M.; Booth, J.S.; Henry, P.; Winters, W.J.

1999-01-01

The stability of submarine gas hydrates is largely dictated by pressure and temperature, gas composition, and pore water salinity. However, the physical properties and surface chemistry of deep marine sediments may also affect the thermodynamic state, growth kinetics, spatial distributions, and growth forms of clathrates. Our conceptual model presumes that gas hydrate behaves in a way analogous to ice in a freezing soil. Hydrate growth is inhibited within fine-grained sediments by a combination of reduced pore water activity in the vicinity of hydrophilic mineral surfaces, and the excess internal energy of small crystals confined in pores. The excess energy can be thought of as a "capillary pressure" in the hydrate crystal, related to the pore size distribution and the state of stress in the sediment framework. The base of gas hydrate stability in a sequence of fine sediments is predicted by our model to occur at a lower temperature (nearer to the seabed) than would be calculated from bulk thermodynamic equilibrium. Capillary effects or a build up of salt in the system can expand the phase boundary between hydrate and free gas into a divariant field extending over a finite depth range dictated by total methane content and pore-size distribution. Hysteresis between the temperatures of crystallization and dissociation of the clathrate is also predicted. Growth forms commonly observed in hydrate samples recovered from marine sediments (nodules, and lenses in muds; cements in sands) can largely be explained by capillary effects, but kinetics of nucleation and growth are also important. The formation of concentrated gas hydrates in a partially closed system with respect to material transport, or where gas can flush through the system, may lead to water depletion in the host sediment. This "freeze-drying" may be detectable through physical changes to the sediment (low water content and overconsolidation) and/or chemical anomalies in the pore waters and metastable presence of free gas within the normal zone of hydrate stability. 

In-situ gas hydrate hydrate saturation estimated from various well logs at the Mount Elbert Gas Hydrate Stratigraphic Test Well, Alaska North Slope

USGS Publications Warehouse

Lee, M.W.; Collett, T.S.

2011-01-01

In 2006, the U.S. Geological Survey (USGS) completed detailed analysis and interpretation of available 2-D and 3-D seismic data and proposed a viable method for identifying sub-permafrost gas hydrate prospects within the gas hydrate stability zone in the Milne Point area of northern Alaska. To validate the predictions of the USGS and to acquire critical reservoir data needed to develop a long-term production testing program, a well was drilled at the Mount Elbert prospect in February, 2007. Numerous well log data and cores were acquired to estimate in-situ gas hydrate saturations and reservoir properties.Gas hydrate saturations were estimated from various well logs such as nuclear magnetic resonance (NMR), P- and S-wave velocity, and electrical resistivity logs along with pore-water salinity. Gas hydrate saturations from the NMR log agree well with those estimated from P- and S-wave velocity data. Because of the low salinity of the connate water and the low formation temperature, the resistivity of connate water is comparable to that of shale. Therefore, the effect of clay should be accounted for to accurately estimate gas hydrate saturations from the resistivity data. Two highly gas hydrate-saturated intervals are identified - an upper ???43 ft zone with an average gas hydrate saturation of 54% and a lower ???53 ft zone with an average gas hydrate saturation of 50%; both zones reach a maximum of about 75% saturation. ?? 2009.

Structure and water exchange dynamics of hydrated oxo halo ions in aqueous solution using QMCF MD simulation, large angle X-ray scattering and EXAFS.

PubMed

Eklund, Lars; Hofer, Tomas S; Persson, Ingmar

2015-01-28

Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) has been applied in conjunction with experimental large angle X-ray scattering (LAXS) and EXAFS measurements to study structure and dynamics of the hydrated oxo chloro anions chlorite, ClO2(-), chlorate, ClO3(-), and perchlorate, ClO4(-). In addition, the structures of the hydrated hypochlorite, ClO(-), bromate, BrO3(-), iodate, IO3(-) and metaperiodate, IO4(-), ions have been determined in aqueous solution by means of LAXS. The structures of the bromate, metaperiodate, and orthoperiodate, H2IO6(3-), ions have been determined by EXAFS as solid sodium salts and in aqueous solution as well. The results show clearly that the only form of periodate present in aqueous solution is metaperiodate. The Cl-O bond distances in the hydrated oxo chloro anions as determined by LAXS and obtained in the QMCF MD simulations are in excellent agreement, being 0.01-0.02 Å longer than in solid anhydrous salts due to hydration through hydrogen bonding to water molecules. The oxo halo anions, all with unit negative charge, have low charge density making them typical structure breakers, thus the hydrogen bonds formed to the hydrating water molecules are weaker and more short-lived than those between water molecules in pure water. The water exchange mechanism of the oxo chloro anions resembles those of the oxo sulfur anions with a direct exchange at the oxygen atoms for perchlorate and sulfate. The water exchange rate for the perchlorate ion is significantly faster, τ0.5 = 1.4 ps, compared to the hydrated sulfate ion and pure water, τ0.5 = 2.6 and 1.7 ps, respectively. The angular radial distribution functions show that the chlorate and sulfite ions have a more complex water exchange mechanism. As the chlorite and chlorate ions are more weakly hydrated than the sulfite ion the spatial occupancy is less well-defined and it is not possible to follow any well-defined migration pattern as it is difficult to distinguish between hydrating water molecules and bulk water in the region close to the ions.

Structure and water exchange dynamics of hydrated oxo halo ions in aqueous solution using QMCF MD simulation, large angle X-ray scattering and EXAFS

PubMed Central

Eklund, Lars; Hofer, Tomas S.

2014-01-01

Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) has been applied in conjunction with experimental large angle X-ray scattering (LAXS) and EXAFS measurements to study structure and dynamics of the hydrated oxo chloro anions chlorite, ClO2−, chlorate, ClO3−, and perchlorate, ClO4−. In addition, the structures of the hydrated hypochlorite, ClO−, bromate, BrO3−, iodate, IO3− and metaperiodate, IO4−, ions have been determined in aqueous solution by means of LAXS. The structures of the bromate, metaperiodate, and orthoperiodate, H2IO63−, ions have been determined by EXAFS as solid sodium salts and in aqueous solution as well. The results show clearly that the only form of periodate present in aqueous solution is metaperiodate. The Cl-O bond distances in the hydrated oxo chloro anions as determined by LAXS and obtained in the QMCF MD simulations are in excellent agreement, being 0.01–0.02 Å longer than in solid anhydrous salts due to hydration through hydrogen bonding to water molecules. The oxo halo anions, all with unit negative charge, have low charge density making them typical structure breakers, thus the hydrogen bonds formed to the hydrating water molecules are weaker and more short-lived than those between water molecules in pure water. The water exchange mechanism of the oxo chloro anions resembles those of the oxo sulfur anions with a direct exchange at the oxygen atoms for perchlorate and sulfate. The water exchange rate for the perchlorate ion is significantly faster, τ0.5=1.4 ps, compared to the hydrated sulfate ion and pure water, τ0.5=2.6 and 1.7 ps, respectively. The angular radial distribution functions show that the chlorate and sulfite ions have a more complex water exchange mechanism. As the chlorite and chlorate ions are more weakly hydrated than the sulfite ion the spatial occupancy is less well-defined and it is not possible to follow any well-defined migration pattern as it is difficult to distinguish between hydrating water molecules and bulk water in the region close to the ions. PMID:25473816

Structure and water exchange dynamics of hydrated oxo halo ions in aqueous solution using QMCF MD simulation, large angle X-ray scattering and EXAFS

DOE PAGES

Eklund, Lars; Hofer, Tomas S.; Persson, Ingmar

2014-11-26

Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) has been applied in conjunction with experimental large angle X-ray scattering (LAXS) and EXAFS measurements to study structure and dynamics of the hydrated oxo chloro anions chlorite, ClO 2 –, chlorate, ClO 3 –, and perchlorate, ClO 4 –. In addition, the structures of the hydrated hypochlorite, ClO –, bromate, BrO 3 –, iodate, IO 3 – and metaperiodate, IO 4 –, ions have been determined in aqueous solution by means of LAXS. The structures of the bromate, metaperiodate, and orthoperiodate, H 2IO 6 3–, ions have been determinedmore » by EXAFS as solid sodium salts and in aqueous solution as well. The results show clearly that the only form of periodate present in aqueous solution is metaperiodate. The Cl–O bond distances in the hydrated oxo chloro anions as determined by LAXS and obtained in the QMCF MD simulations are in excellent agreement, being 0.01–0.02 Å longer than in solid anhydrous salts due to hydration through hydrogen bonding to water molecules. The oxo halo anions, all with unit negative charge, have low charge density making them typical structure breakers, thus the hydrogen bonds formed to the hydrating water molecules are weaker and more short-lived than those between water molecules in pure water. The water exchange mechanism of the oxo chloro anions resembles those of the oxo sulfur anions with a direct exchange at the oxygen atoms for perchlorate and sulfate. Here, the water exchange rate for the perchlorate ion is significantly faster, τ 0.5 = 1.4 ps, compared to the hydrated sulfate ion and pure water, τ 0.5 = 2.6 and 1.7 ps, respectively. The angular radial distribution functions show that the chlorate and sulfite ions have a more complex water exchange mechanism. As the chlorite and chlorate ions are more weakly hydrated than the sulfite ion the spatial occupancy is less well-defined and it is not possible to follow any well-defined migration pattern as it is difficult to distinguish between hydrating water molecules and bulk water in the region close to the ions.« less

Geochemistry of a naturally occurring massive marine gas hydrate

USGS Publications Warehouse

Kvenvolden, K.A.; Claypool, G.E.; Threlkeld, C.N.; Dendy, Sloan E.

1984-01-01

During Deep Sea Drilling Project (DSDP) Leg 84 a core 1 m long and 6 cm in diameter of massive gas hydrate was unexpectedly recovered at Site 570 in upper slope sediment of the Middle America Trench offshore of Guatemala. This core contained only 5-7% sediment, the remainder being the solid hydrate composed of gas and water. Samples of the gas hydrate were decomposed under controlled conditions in a closed container maintained at 4??C. Gas pressure increased and asymptotically approached the equilibrium decomposition pressure for an ideal methane hydrate, CH4.5-3/4H2O, of 3930 kPa and approached to this pressure after each time gas was released, until the gas hydrate was completely decomposed. The gas evolved during hydrate decomposition was 99.4% methane, ???0.2% ethane, and ???0.4% CO2. Hydrocarbons from propane to heptane were also present, but in concentrations of less than 100 p.p.m. The carbon-isotopic composition of methane was -41 to -44 permil(( 0 00), relative to PDB standard. The observed volumetric methane/water ratio was 64 or 67, which indicates that before it was stored and analyzed, the gas hydrate probably had lost methane. The sample material used in the experiments was likely a mixture of methane hydrate and water ice. Formation of this massive gas hydrate probably involved the following processes: (i) upward migration of gas and its accumulation in a zone where conditions favored the growth of gas hydrates, (ii) continued, unusually rapid biological generation of methane, and (iii) release of gas from water solution as pressure decreased due to sea level lowering and tectonic uplift. ?? 1984.

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

Investigation on the effect of THF on Nitrogen Hydrate formation under isobaric condition

NASA Astrophysics Data System (ADS)

Jamil, N.; Husin, H.; Aman, Z.; Hassan, Z.

2018-03-01

In this paper, we studied nitrogen (N2) hydrate formation in the presence of tetrahydrofuran (THF) under 3 different conditions; different concentration of THF (0, 3 and 30 %(v/v), different temperature setting (room temperature and induced temperature) and different water content (15, 35 and 55 mL) in an isobaric condition. We found that in the presence of THF which acting as an enhancer, hydrate formation kinetic is highly influenced by these parameters. We observed a striking contrast in hydrate formation behaviour observed at room temperature (RT) and induced temperature (IT) with and without the presence of THF under similar operating conditions. At the presence of 30 %(v/v) of THF in 15 mL water, it can be seen that, hydrate tend to form faster than other samples. Visual observation of N2hydrates are also conducted at 30 %(v/v) of THF in 15 mL water.

Gravimetric analysis and differential scanning calorimetric studies on glycerin-induced skin hydration.

PubMed

Lee, Ae-Ri Cho; Moon, Hee Kyung

2007-11-01

A thermal gravimetric analysis (TGA) and a differential scanning calorimetry (DSC) were carried out to characterize the water property and an alteration of lipid phase transition of stratum corneum (SC) by glycerin. In addition, the relationship between steady state skin permeation rate and skin hydration in various concentrations of glycerin was investigated. Water vapor absorption-desorption was studied in the hairless mouse stratum corneum. Dry SC samples were exposed to different conc. of glycerin (0-50%) followed by exposure to dry air and the change in weight property was monitored over time by use of TGA. In DSC study, significant decrease in DeltaH of the lipid transition in 10% glycerin and water treated sample: the heat of lipid transition of normal, water, 10% glycerin treated SC were 6.058, 4.412 and 4.316 mJ/mg, respectively. In 10% glycerin treated SCs, the Tc of water shifts around 129 degrees C, corresponding to the weakly bound secondary water. In 40% glycerin treated SC, the Tc of water shifts to 144 degrees C corresponding to strongly bound primary water. There was a good correlation between the hydration property of the skin and the steady state skin flux with the correlation coefficient (r2=0.94). As the hydration increased, the steady state flux increased. As glycerin concentration increased, hydration property decreased. High diffusivity induced by the hydration effect of glycerin and water could be the major contributing factor for the enhanced skin permeation of nicotinic acid (NA).

The Effects of Hydration on Growth of the House Cricket, Acheta domesticus

PubMed Central

McCluney, Kevin E; Date, Rishabh C

2008-01-01

Maintenance of biochemical gradients, membrane fluidity, and sustained periods of activity are key physiological and behavioral functions of water for animals living in desiccating environments. Water stress may reduce the organism's ability to maintain these functions and as such, may reduce an organism's growth. However, few studies have examined this potential effect. The effects of altered hydration state of the house cricket, Acheta domesticus L. (Orthoptera: Gryllidae) on individual growth were studied under laboratory conditions. Crickets were permitted access to water for three different durations each day, resulting in significant differences in hydration state (32% greater hydration for maximum than minimum duration of water availability). Growth was 59% and 72% greater in dry mass and length, respectively, between the lowest and highest hydration state treatments. These findings may be representative for a variety of animal species and environments and could have important ecological implications. PMID:20302456

Characterizing Natural Gas Hydrates in the Deep Water Gulf of Mexico: Applications for Safe Exploration and Production Activities

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

Bent, Jimmy

2014-05-31

In 2000 Chevron began a project to learn how to characterize the natural gas hydrate deposits in the deep water portion of the Gulf of Mexico (GOM). Chevron is an active explorer and operator in the Gulf of Mexico and is aware that natural gas hydrates need to be understood to operate safely in deep water. In August 2000 Chevron worked closely with the National Energy Technology Laboratory (NETL) of the United States Department of Energy (DOE) and held a workshop in Houston, Texas to define issues concerning the characterization of natural gas hydrate deposits. Specifically, the workshop was meantmore » to clearly show where research, the development of new technologies, and new information sources would be of benefit to the DOE and to the oil and gas industry in defining issues and solving gas hydrate problems in deep water.« less

Polyethylene oxide hydration in grafted layers

NASA Astrophysics Data System (ADS)

Dormidontova, Elena; Wang, Zilu

Hydration of water soluble polymers is one of the key-factors defining their conformation and properties, similar to biopolymers. Polyethylene oxide (PEO) is one of the most important biomedical-applications polymers and is known for its reverse temperature solubility due to hydrogen bonding with water. As in many practical applications PEO chains are grafted to surfaces, e.g. of nanoparticles or planar surfaces, it is important to understand PEO hydration in such grafted layers. Using atomistic molecular dynamic simulations we investigate the details of molecular conformation and hydration of PEO end-grafted to gold surfaces. We analyze polymer and water density distribution as a function of distance from the surface for different grafting densities. Based on a detailed analysis of hydrogen bonding between polymer and water in grafted PEO layers, we will discuss the extent of PEO hydration and its implication for polymer conformation, mobility and layer properties. This research is supported by NSF (DMR-1410928).

Sulfate content of Europa's ocean and shell: evolutionary considerations and some geological and astrobiological implications.

PubMed

McKinnon, William B; Zolensky, Michael E

2003-01-01

Recent models for the origin of Jupiter indicate that the Galilean satellites were mostly derived from largely unprocessed solar nebula solids and planetesimals. In the jovian subnebula the solids that built Europa were first heated and then cooled, but the major effect was most likely partial or total devolatilization, and less likely to have been wholesale thermochemical reprocessing of rock + metal compositions (e.g., oxidation of Fe and hydration of silicates). Ocean formation and substantial alteration of interior rock by accreted water and ice would occur during and after accretion, but none of the formation models predicts or implies accretion of sulfates. Europa's primordial ocean was most likely sulfidic. After accretion and later radiogenic and tidal heating, the primordial ocean would have interacted hydrothermally with subjacent rock. It has been hypothesized that sulfides could be converted to sulfates if sufficient hydrogen was lost to space, but pressure effects and the impermeability of serpentinite imply that extraction of sulfate from thoroughly altered Europa-rock would have been inefficient (if indeed Mg sulfates formed at all). Permissive physical limits on the extent of alteration limit the sulfate concentration of Europa's evolved ocean to 10% by weight MgSO(4) or equivalent. Later oxidation of the deep interior of Europa may have also occurred because of water released by the breakdown of hydrated silicates, ultimately yielding S magma and/or SO(2) gas. Geological and astrobiological implications are considered.

Hydration measured by doubly labeled water in ALS and its effects on survival.

PubMed

Scagnelli, Connor N; Howard, Diantha B; Bromberg, Mark B; Kasarskis, Edward J; Matthews, Dwight E; Mitsumoto, Hiroshi M; Simmons, Zachary; Tandan, Rup

2018-05-01

We present a study of hydration in ALS patients and its effects on survival. This was a multicenter study over 48 weeks in 80 ALS patients who underwent 250 individual measurements using doubly labeled water (DLW). Total body water (TBW) and water turnover (a surrogate for water intake) were 3.4% and 8.6% lower, respectively, in patients compared to age- and gender-matched healthy controls, and both significantly decreased over study duration. In 20% of patients, water turnover measured over 10 d was 2 standard deviations below the mean value in healthy controls. In a separate clinic cohort of 208 patients, water intake estimated from a de novo equation created from common clinical endpoints was a prognostic indicator of survival. Regardless of nutritional state assessed by BMI, survival was two-fold longer in the group above the median for estimated water intake, suggesting that hydration may be a more important predictor of survival than malnutrition. Risk factors for poor hydration were identified. Water intake equations recommended by US Centers for Medicare and Medicaid Services in healthy elderly were inaccurate for use in ALS patients. We developed equations to estimate TBW and water intake in ALS patients for use in clinics to accurately estimate hydration and improve clinical care.

Cell hydration as a biomarker for estimation of biological effects of nonionizing radiation on cells and organisms.

PubMed

Ayrapetyan, Sinerik; De, Jaysankar

2014-01-01

"Changes in cell hydration" have been hypothesized as an input signal for intracellular metabolic cascade responsible for biological effects of nonionizing radiation (NIR). To test this hypothesis a comparative study on the impacts of different temperature and NIR (infrasound frequency mechanical vibration (MV), static magnetic field (SMF), extremely low frequency electromagnetic field (ELF EMF), and microwave (MW)) pretreated water on the hydration of barley seeds in its dormant and germination periods was performed. In dormant state temperature sensitivity (Q 10) of seed hydration in distilled water (DW) was less than 2, and it was nonsensitive to NIR treated DW, whereas during the germination period (48-72 hours) seeds hydration exhibited temperature sensitivity Q 10 > 2 and higher sensitivity to NIR treated DW. Obtained data allow us to suggest that the metabolic driving of intracellular water dynamics accompanied by hydrogen bonding and breaking is more sensitive to NIR-induced water structure changes in seed bathing aqua medium than the simple thermodynamic processes such as osmotic gradient driven water absorption by seeds in dormant state. Therefore, cell hydration is suggested to be a universal and extrasensitive biomarker for detection of biological effects of NIR on cells and organisms.

Parametric study of the physical properties of hydrate-bearing sand, silt, and clay sediments: 1. Electromagnetic properties

USGS Publications Warehouse

Lee, J.Y.; Santamarina, J.C.; Ruppel, C.

2010-01-01

The marked decrease in bulk electrical conductivity of sediments in the presence of gas hydrates has been used to interpret borehole electrical resistivity logs and, to a lesser extent, the results of controlled source electromagnetic surveys to constrain the spatial distribution and predicted concentration of gas hydrate in natural settings. Until now, an exhaustive laboratory data set that could be used to assess the impact of gas hydrate on the electromagnetic properties of different soils (sand, silt, and clay) at different effective stress and with different saturations of hydrate has been lacking. The laboratory results reported here are obtained using a standard geotechnical cell and the hydrate-formed tetrahydrofuran (THF), a liquid that is fully miscible in water and able to produce closely controlled saturations of hydrate from dissolved phase. Both permittivity and electrical conductivity are good indicators of the volume fraction of free water in the sediment, which is in turn dependent on hydrate saturation. Permittivity in the microwave frequency range is particularly predictive of free water content since it is barely affected by ionic concentration, pore structure, and surface conduction. Electrical conductivity (or resistivity) is less reliable for constraining water content or hydrate saturation: In addition to fluid-filled porosity, other factors, such as the ionic concentration of the pore fluid and possibly other conduction effects (e.g., surface conduction in high specific surface soils having low conductivity pore fluid), also influence electrical conductivity.

Electrical properties of methane hydrate + sediment mixtures

USGS Publications Warehouse

Du Frane, Wyatt L.; Stern, Laura A.; Constable, Steven; Weitemeyer, Karen A.; Smith, Megan M; Roberts, Jeffery J.

2015-01-01

Knowledge of the electrical properties of multicomponent systems with gas hydrate, sediments, and pore water is needed to help relate electromagnetic (EM) measurements to specific gas hydrate concentration and distribution patterns in nature. Toward this goal, we built a pressure cell capable of measuring in situ electrical properties of multicomponent systems such that the effects of individual components and mixing relations can be assessed. We first established the temperature-dependent electrical conductivity (σ) of pure, single-phase methane hydrate to be ~5 orders of magnitude lower than seawater, a substantial contrast that can help differentiate hydrate deposits from significantly more conductive water-saturated sediments in EM field surveys. Here we report σ measurements of two-component systems in which methane hydrate is mixed with variable amounts of quartz sand or glass beads. Sand by itself has low σ but is found to increase the overall σ of mixtures with well-connected methane hydrate. Alternatively, the overall σ decreases when sand concentrations are high enough to cause gas hydrate to be poorly connected, indicating that hydrate grains provide the primary conduction path. Our measurements suggest that impurities from sand induce chemical interactions and/or doping effects that result in higher electrical conductivity with lower temperature dependence. These results can be used in the modeling of massive or two-phase gas-hydrate-bearing systems devoid of conductive pore water. Further experiments that include a free water phase are the necessary next steps toward developing complex models relevant to most natural systems.

In situ DMSO hydration measurements of HTS compound libraries.

PubMed

Ellson, R; Stearns, R; Mutz, M; Brown, C; Browning, B; Harris, D; Qureshi, S; Shieh, J; Wold, D

2005-09-01

Compounds used in high throughput screening (HTS) are typically dissolved in DMSO. These solutions are stored automation-friendly racks of wells or tubes. DMSO is hygroscopic and quickly absorbs water from the atmosphere. When present in DMSO compound solutions, water can accelerate degradation and precipitation. Understanding DMSO hydration in an HTS compound library can improve storage and screening methods by managing the impact of water on compound stability. A non-destructive, acoustic method compatible with HTS has been developed to measure water content in DMSO solutions. Performance of this acoustic method was compared with an optical technique and found to be in good agreement. The accuracy and precision of acoustic measurements was shown to be under 3% over the tested range of DMSO solutions (0% to 35% water by volume) and insensitive to the presence of HTS compounds at typical storage concentrations. Time course studies of hydration for wells in 384-well and 1536-well microplates were performed. Well geometry, fluid volume, well position and atmospheric conditions were all factors in hydration rate. High rates of hydration were seen in lower-volume fills, higher-density multi-well plates and when there was a large differential between the humidity of the lab and the water content of the DMSO. For example, a 1536-well microplate filled with 2microL of 100% DMSO exposed for one hour to a laboratory environment with approximately 40% relative humidity will absorb over 6% water by volume. Understanding DMSO hydration rates as well as the ability to reverse library hydration are important steps towards managing stability and availability of compound libraries.

Numerical analysis of wellbore instability in gas hydrate formation during deep-water drilling

NASA Astrophysics Data System (ADS)

Zhang, Huaiwen; Cheng, Yuanfang; Li, Qingchao; Yan, Chuanliang; Han, Xiuting

2018-02-01

Gas hydrate formation may be encountered during deep-water drilling because of the large amount and wide distribution of gas hydrates under the shallow seabed of the South China Sea. Hydrates are extremely sensitive to temperature and pressure changes, and drilling through gas hydrate formation may cause dissociation of hydrates, accompanied by changes in wellbore temperatures, pore pressures, and stress states, thereby leading to wellbore plastic yield and wellbore instability. Considering the coupling effect of seepage of drilling fluid into gas hydrate formation, heat conduction between drilling fluid and formation, hydrate dissociation, and transformation of the formation framework, this study established a multi-field coupling mathematical model of the wellbore in the hydrate formation. Furthermore, the influences of drilling fluid temperatures, densities, and soaking time on the instability of hydrate formation were calculated and analyzed. Results show that the greater the temperature difference between the drilling fluid and hydrate formation is, the faster the hydrate dissociates, the wider the plastic dissociation range is, and the greater the failure width becomes. When the temperature difference is greater than 7°C, the maximum rate of plastic deformation around the wellbore is more than 10%, which is along the direction of the minimum horizontal in-situ stress and associated with instability and damage on the surrounding rock. The hydrate dissociation is insensitive to the variation of drilling fluid density, thereby implying that the change of the density of drilling fluids has a minimal effect on the hydrate dissociation. Drilling fluids that are absorbed into the hydrate formation result in fast dissociation at the initial stage. As time elapses, the hydrate dissociation slows down, but the risk of wellbore instability is aggravated due to the prolonged submersion in drilling fluids. For the sake of the stability of the wellbore in deep-water drilling through hydrate formation, the drilling fluid with low temperatures should be given priority. The drilling process should be kept under balanced pressures, and the drilling time should be shortened.

Thermodynamic properties of water solvating biomolecular surfaces

NASA Astrophysics Data System (ADS)

Heyden, Matthias

Changes in the potential energy and entropy of water molecules hydrating biomolecular interfaces play a significant role for biomolecular solubility and association. Free energy perturbation and thermodynamic integration methods allow calculations of free energy differences between two states from simulations. However, these methods are computationally demanding and do not provide insights into individual thermodynamic contributions, i.e. changes in the solvent energy or entropy. Here, we employ methods to spatially resolve distributions of hydration water thermodynamic properties in the vicinity of biomolecular surfaces. This allows direct insights into thermodynamic signatures of the hydration of hydrophobic and hydrophilic solvent accessible sites of proteins and small molecules and comparisons to ideal model surfaces. We correlate dynamic properties of hydration water molecules, i.e. translational and rotational mobility, to their thermodynamics. The latter can be used as a guide to extract thermodynamic information from experimental measurements of site-resolved water dynamics. Further, we study energy-entropy compensations of water at different hydration sites of biomolecular surfaces. This work is supported by the Cluster of Excellence RESOLV (EXC 1069) funded by the Deutsche Forschungsgemeinschaft.

Photocatalytic activity of Ag/ZnO core-shell nanoparticles with shell thickness as controlling parameter under green environment

NASA Astrophysics Data System (ADS)

Rajbongshi, Himanshu; Bhattacharjee, Suparna; Datta, Pranayee

2017-02-01

Plasmonic Ag/ZnO core-shell nanoparticles have been synthesized via a simple two-step wet chemical method for application in Photocatalysis. The morphology, size, crystal structure, composition and optical properties of the nanoparticles are investigated by x-ray diffraction, transmission electron microscopy (TEM), FTIR spectroscopy, ultraviolet-visible (UV-Vis) absorption spectroscopy and photoluminescence (PL) spectroscopy. The shell thicknesses are varied by varying the concentration of zinc nitrate hexa-hydrate and triethanolamine. The ZnO shell coating over Ag core enhances the charge separation, whereas the larger shell thickness and increased refractive index of surrounding medium cause red shifts of surface Plasmon resonance (SPR) peak of Ag core. The photoluminescence (PL) spectra of Ag/ZnO core-shell show that the larger shell thickness quenches the near band edge UV emission of ZnO. The electrochemical impedance spectra (EIS) i.e. Nyquist plots also confirm the higher charge transfer efficiency of the Ag/ZnO core-shell nanoparticles. The Photocatalytic activities of Ag/ZnO core-shell nanoparticles are investigated by the degradation of methylene blue (MB) dye under direct sunlight irradiation. Compared to pure ZnO nanoparticles (NPs), Ag/ZnO core-shell NPs display efficient sunlight plasmonic photocatalytic activity because of the influence of SPR of Ag core and the electron sink effect. The photocatalytic activity of Ag/ZnO core-shell NPs is found to be enhanced with increase in shell thickness.

Gas content and composition of gas hydrate from sediments of the southeastern North American continental margin

USGS Publications Warehouse

Lorenson, T.D.; Collett, T.S.

2000-01-01

Gas hydrate samples were recovered from four sites (Sites 994, 995, 996, and 997) along the crest of the Blake Ridge during Ocean Drilling Program (ODP) Leg 164. At Site 996, an area of active gas venting, pockmarks, and chemosynthetic communities, vein-like gas hydrate was recovered from less than 1 meter below seafloor (mbsf) and intermittently through the maximum cored depth of 63 mbsf. In contrast, massive gas hydrate, probably fault filling and/or stratigraphically controlled, was recovered from depths of 260 mbsf at Site 994, and from 331 mbsf at Site 997. Downhole-logging data, along with geochemical and core temperature profiles, indicate that gas hydrate at Sites 994, 995, and 997 occurs from about 180 to 450 mbsf and is dispersed in sediment as 5- to 30-m-thick zones of up to about 15% bulk volume gas hydrate. Selected gas hydrate samples were placed in a sealed chamber and allowed to dissociate. Evolved gas to water volumetric ratios measured on seven samples from Site 996 ranged from 20 to 143 mL gas/mL water to 154 mL gas/mL water in one sample from Site 994, and to 139 mL gas/mL water in one sample from Site 997, which can be compared to the theoretical maximum gas to water ratio of 216. These ratios are minimum gas/water ratios for gas hydrate because of partial dissociation during core recovery and potential contamination with pore waters. Nonetheless, the maximum measured volumetric ratio indicates that at least 71% of the cages in this gas hydrate were filled with gas molecules. When corrections for pore-water contamination are made, these volumetric ratios range from 29 to 204, suggesting that cages in some natural gas hydrate are nearly filled. Methane comprises the bulk of the evolved gas from all sites (98.4%-99.9% methane and 0%-1.5% CO2). Site 996 hydrate contained little CO2 (0%-0.56%). Ethane concentrations differed significantly from Site 996, where they ranged from 720 to 1010 parts per million by volume (ppmv), to Sites 994 and 997, which contained much less ethane (up to 86 ppmv). Up to 19 ppmv propane and other higher homologues were noted; however, these gases are likely contaminants derived from sediment in some hydrate samples. CO2 concentrations are less in gas hydrate than in the surrounding sediment, likely an artifact of core depressurization, which released CO2 derived from dissolved organic carbon (DIC) into sediment. The isotopic composition of methane from gas hydrate ranges from ??13C of -62.5??? to -70.7??? and ??D of -175??? to -200??? and is identical to the isotopic composition of methane from surrounding sediment. Methane of this isotopic composition is mainly microbial in origin and likely produced by bacterial reduction of bicarbonate. The hydrocarbon gases here are likely the products of early microbial diagenesis. The isotopic composition of CO2 from gas hydrate ranges from ??13C of -5.7 to -6.9, about 15??? lighter than CO2 derived from nearby sediment.

Water-network percolation transitions in hydrated yeast

NASA Astrophysics Data System (ADS)

Sokołowska, Dagmara; Król-Otwinowska, Agnieszka; Mościcki, Józef K.

2004-11-01

We discovered two percolation processes in succession in dc conductivity of bulk baker’s yeast in the course of dehydration. Critical exponents characteristic for the three-dimensional network for heavily hydrated system, and two dimensions in the light hydration limit, evidenced a dramatic change of the water network dimensionality in the dehydration process.

Acoustical Method of Whole-Body Hydration Status Monitoring.

PubMed

Sarvazyan, A P; Tsyuryupa, S N; Calhoun, M; Utter, A

2016-07-01

An acoustical handheld hydration monitor (HM) for assessing the water balance of the human body was developed. Dehydration is a critical public health problem. Many elderly over age of 65 are particularly vulnerable as are infants and young children. Given that dehydration is both preventable and reversible, the need for an easy-to-perform method for the detection of water imbalance is of the utmost clinical importance. The HM is based on an experimental fact that ultrasound velocity in muscle is a linear function of water content and can be referenced to the hydration status of the body. Studies on the validity of HM for the assessment of whole-body hydration status were conducted in the Appalachian State University, USA, on healthy young adults and on elderly subjects residing at an assisted living facility. The HM was able to track changes in total body water during periods of acute dehydration and rehydration in athletes and day-to-day and diurnal variability of hydration in elderly. Results of human studies indicate that HM has a potential to become an efficient tool for detecting abnormal changes in the body hydration status.

DSC investigation of bovine hide collagen at varying degrees of crosslinking and humidities.

PubMed

Schroepfer, Michaela; Meyer, Michael

2017-10-01

Bovine hide collagen (nonCLC; non-CrossLinked Collagen) was analysed by differential scanning calorimetry (DSC) at different hydration degrees and compared with hide collagen samples crosslinked with glutaraldehyde (CLC-GA) and chromium(III) ions (CLC-Cr), respectively. Crosslinking and drying were confirmed to increase the denaturation temperature. Different regions were assigned, that reflect the variation of the influence of water on the denaturation temperature. Furthermore, at moderate hydration degrees, the enthalpies of non-crosslinked collagen increase compared to the fully hydrated state. This reflects a glue-like action of water in the range of 25% hydration. Crosslinking of bovine hide collagen decreases the enthalpy by 25% in the fully hydrated state, even at very low levels of crosslinking This can be explained by intensive effects of the crosslinking agent on the hydration network of the collagen molecules, assuming that the enthalpies are principally a result of hydrogen bonding. At very low water contents DSC peaks of CLC-Cr completely disappear. This could be explained by competition between hydroxosulfochromate(III) complexes and collagen for water. Copyright © 2017 Elsevier B.V. All rights reserved.

Acoustical method of whole-body hydration status monitoring

NASA Astrophysics Data System (ADS)

Sarvazyan, A. P.; Tsyuryupa, S. N.; Calhoun, M.; Utter, A.

2016-07-01

An acoustical handheld hydration monitor (HM) for assessing the water balance of the human body was developed. Dehydration is a critical public health problem. Many elderly over age of 65 are particularly vulnerable as are infants and young children. Given that dehydration is both preventable and reversible, the need for an easy-to-perform method for the detection of water imbalance is of the utmost clinical importance. The HM is based on an experimental fact that ultrasound velocity in muscle is a linear function of water content and can be referenced to the hydration status of the body. Studies on the validity of HM for the assessment of whole-body hydration status were conducted in the Appalachian State University, USA, on healthy young adults and on elderly subjects residing at an assisted living facility. The HM was able to track changes in total body water during periods of acute dehydration and rehydration in athletes and day-to-day and diurnal variability of hydration in elderly. Results of human studies indicate that HM has a potential to become an efficient tool for detecting abnormal changes in the body hydration status.

Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures.

PubMed

Kirillova, Svetlana; Carugo, Oliviero

2011-10-19

Hydration is crucial for RNA structure and function. X-ray crystallography is the most commonly used method to determine RNA structures and hydration and, therefore, statistical surveys are based on crystallographic results, the number of which is quickly increasing. A statistical analysis of the water molecule distribution in high-resolution X-ray structures of unpaired RNA nucleotides showed that: different bases have the same penchant to be surrounded by water molecules; clusters of water molecules indicate possible hydration sites, which, in some cases, match those of the major and minor grooves of RNA and DNA double helices; complex hydrogen bond networks characterize the solvation of the nucleotides, resulting in a significant rigidity of the base and its surrounding water molecules. Interestingly, the hydration sites around unpaired RNA bases do not match, in general, the positions that are occupied by the second nucleotide when the base-pair is formed. The hydration sites around unpaired RNA bases were found. They do not replicate the atom positions of complementary bases in the Watson-Crick pairs.

Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures

PubMed Central

2011-01-01

Background Hydration is crucial for RNA structure and function. X-ray crystallography is the most commonly used method to determine RNA structures and hydration and, therefore, statistical surveys are based on crystallographic results, the number of which is quickly increasing. Results A statistical analysis of the water molecule distribution in high-resolution X-ray structures of unpaired RNA nucleotides showed that: different bases have the same penchant to be surrounded by water molecules; clusters of water molecules indicate possible hydration sites, which, in some cases, match those of the major and minor grooves of RNA and DNA double helices; complex hydrogen bond networks characterize the solvation of the nucleotides, resulting in a significant rigidity of the base and its surrounding water molecules. Interestingly, the hydration sites around unpaired RNA bases do not match, in general, the positions that are occupied by the second nucleotide when the base-pair is formed. Conclusions The hydration sites around unpaired RNA bases were found. They do not replicate the atom positions of complementary bases in the Watson-Crick pairs. PMID:22011380

Hydration: certain basic aspects for developing technical and scientific parameters into the nutrition knowledge

PubMed

Perales-García, Aránzazu; Estévez-Martínez, Isabel; Urrialde, Rafael

2016-07-12

Introduction: Hydration is defined as the water intake coming from food and beverages. Its study has become an area by itself, within the nutrition field. Meaning that in 2010 the European Food Safety Authority (EFSA) approved the water intake recommendations, but the study of this topic implies a rigorous methodology, which represents several issues. Objective: Showing as a glance the main methodological issues in hydration studies. Material and methods: Bibliographic revision of scientific literature. Results: The main methodological issues presented are: sample selection (investigation field and sample design), selection of the method to evaluate hydration status (dilution techniques, bioelectrical impedance, plasmatic and urinary indicators, changes in body composition, water losses and clinic symptoms) selection of the method to evaluate water intake (biomarker, questionnaires, informatics programs, smartphone use, 24-h register, dietary history and food frequency questionnaire), and the main sources of hydration. Conclusions: Hydration status should be understood as a routine model, with daily frequency, according to gender, age, physical activity and environmental conditions. Furthermore, the correct design of the methodology has a special importance in order to take into account all the aspects

High pressure rheology of gas hydrate formed from multiphase systems using modified Couette rheometer.

PubMed

Pandey, Gaurav; Linga, Praveen; Sangwai, Jitendra S

2017-02-01

Conventional rheometers with concentric cylinder geometries do not enhance mixing in situ and thus are not suitable for rheological studies of multiphase systems under high pressure such as gas hydrates. In this study, we demonstrate the use of modified Couette concentric cylinder geometries for high pressure rheological studies during the formation and dissociation of methane hydrate formed from pure water and water-decane systems. Conventional concentric cylinder Couette geometry did not produce any hydrates in situ and thus failed to measure rheological properties during hydrate formation. The modified Couette geometries proposed in this work observed to provide enhanced mixing in situ, thus forming gas hydrate from the gas-water-decane system. This study also nullifies the use of separate external high pressure cell for such measurements. The modified geometry was observed to measure gas hydrate viscosity from an initial condition of 0.001 Pa s to about 25 Pa s. The proposed geometries also possess the capability to measure dynamic viscoelastic properties of hydrate slurries at the end of experiments. The modified geometries could also capture and mimic the viscosity profile during the hydrate dissociation as reported in the literature. The present study acts as a precursor for enhancing our understanding on the rheology of gas hydrate formed from various systems containing promoters and inhibitors in the context of flow assurance.

High pressure rheology of gas hydrate formed from multiphase systems using modified Couette rheometer

NASA Astrophysics Data System (ADS)

Pandey, Gaurav; Linga, Praveen; Sangwai, Jitendra S.

2017-02-01

Conventional rheometers with concentric cylinder geometries do not enhance mixing in situ and thus are not suitable for rheological studies of multiphase systems under high pressure such as gas hydrates. In this study, we demonstrate the use of modified Couette concentric cylinder geometries for high pressure rheological studies during the formation and dissociation of methane hydrate formed from pure water and water-decane systems. Conventional concentric cylinder Couette geometry did not produce any hydrates in situ and thus failed to measure rheological properties during hydrate formation. The modified Couette geometries proposed in this work observed to provide enhanced mixing in situ, thus forming gas hydrate from the gas-water-decane system. This study also nullifies the use of separate external high pressure cell for such measurements. The modified geometry was observed to measure gas hydrate viscosity from an initial condition of 0.001 Pa s to about 25 Pa s. The proposed geometries also possess the capability to measure dynamic viscoelastic properties of hydrate slurries at the end of experiments. The modified geometries could also capture and mimic the viscosity profile during the hydrate dissociation as reported in the literature. The present study acts as a precursor for enhancing our understanding on the rheology of gas hydrate formed from various systems containing promoters and inhibitors in the context of flow assurance.

Structural Basis for the Inhibition of Gas Hydrates by α-Helical Antifreeze Proteins

PubMed Central

Sun, Tianjun; Davies, Peter L.; Walker, Virginia K.

2015-01-01

Kinetic hydrate inhibitors (KHIs) are used commercially to inhibit gas hydrate formation and growth in pipelines. However, improvement of these polymers has been constrained by the lack of verified molecular models. Since antifreeze proteins (AFPs) act as KHIs, we have used their solved x-ray crystallographic structures in molecular modeling to explore gas hydrate inhibition. The internal clathrate water network of the fish AFP Maxi, which extends to the protein’s outer surface, is remarkably similar to the {100} planes of structure type II (sII) gas hydrate. The crystal structure of this water web has facilitated the construction of in silico models for Maxi and type I AFP binding to sII hydrates. Here, we have substantiated our models with experimental evidence of Maxi binding to the tetrahydrofuran sII model hydrate. Both in silico and experimental evidence support the absorbance-inhibition mechanism proposed for KHI binding to gas hydrates. Based on the Maxi crystal structure we suggest that the inhibitor adsorbs to the gas hydrate lattice through the same anchored clathrate water mechanism used to bind ice. These results will facilitate the rational design of a next generation of effective green KHIs for the petroleum industry to ensure safe and efficient hydrocarbon flow. PMID:26488661

Time-dependent water dynamics in hydrated uranyl fluoride

DOE PAGES

Miskowiec, Andrew J.; Anderson, Brian B.; Herwig, Kenneth W.; ...

2015-09-15

In this study, uranyl fluoride is a three-layer, hexagonal structure with significant stacking disorder in the c-direction. It supports a range of unsolved ‘thermodynamic’ hydrates with 0–2.5 water molecules per uranium atom, and perhaps more. However, the relationship between water, hydrate crystal structures, and thermodynamic results, collectively representing the chemical pathway through these hydrate structures, has not been sufficiently elucidated. We used high-resolution quasielastic neutron scattering to study the dynamics of water in partially hydrated uranyl fluoride powder over the course of 4 weeks under closed conditions. The spectra are composed of two quasielastic components: one is associated with translationalmore » diffusive motion of water that is approximately five to six times slower than bulk water, and the other is a slow (on the order of 2–300 ps), spatially bounded water motion. The translational component represents water diffusing between the weakly bonded layers in the crystal, while the bounded component may represent water trapped in subnanometre ‘pockets’ formed by the space between uranium-centred polymerisation units. Complementary neutron diffraction measurements do not show any significant structural changes, suggesting that a chemical conversion of the material does not occur in the thermodynamically isolated system on this timescale.« less

Growth Kinetics and Mechanics of Hydrate Films by Interfacial Rheology.

PubMed

Leopércio, Bruna C; de Souza Mendes, Paulo R; Fuller, Gerald G

2016-05-03

A new approach to study and understand the kinetics and mechanical properties of hydrates by interfacial rheology is presented. This is made possible using a "double wall ring" interfacial rheology cell that has been designed to provide the necessary temperature control. Cyclopentane and water are used to form hydrates, and this model system forms these structures at ambient pressures. Different temperature and water/hydrocarbon contact protocols are explored. Of particular interest is the importance of first contacting the hydrocarbon against ice crystals in order to initiate hydrate formation. Indeed, this is found to be the case, even though the hydrates may be created at temperatures above the melting point of ice. Once hydrates completely populate the hydrocarbon/water interface, strain sweeps of the interfacial elastic and viscous moduli are conducted to interrogate the mechanical response and fragility of the hydrate films. The dependence on temperature, Tf, by the kinetics of formation and the mechanical properties is reported, and the cyclopentane hydrate dissociation temperature was found to be between 6 and 7 °C. The formation time (measured from the moment when cyclopentane first contacts ice crystals) as well as the elastic modulus and the yield strain increase as Tf increases.

Hydration index--a better parameter for explaining small molecule hydration in inhibition of ice recrystallization.

PubMed

Tam, Roger Y; Ferreira, Sandra S; Czechura, Pawel; Chaytor, Jennifer L; Ben, Robert N

2008-12-24

Several simple mono- and disaccharides have been assessed for their ability to inhibit ice recrystallization. Two carbohydrates were found to be effective recrystallization inhibitors. D-galactose (1) was the best monosaccharide and D-melibiose (5) was the most active disaccharide. The ability of each carbohydrate to inhibit ice growth was correlated to its respective hydration number reported in the literature. A hydration number reflects the number of tightly bound water molecules to the carbohydrate and is a function of carbohydrate stereochemistry. It was discovered that using the absolute hydration number of a carbohydrate does not allow one to accurately predict its ability to inhibit ice recrystallization. Consequently, we have defined a hydration index in which the hydration number is divided by the molar volume of the carbohydrate. This new parameter not only takes into account the number of water molecules tightly bound to a carbohydrate but also the size or volume of a particular solute and ultimately the concentration of hydrated water molecules. The hydration index of both mono- and disaccharides correlates well with experimentally measured RI activity. C-Linked derivatives of the monosaccharides appear to have RI activity comparable to that of their O-linked saccharides but a more thorough investigation is required. The relationship between carbohydrate concentration and RI activity was shown to be noncolligative and a 0.022 M solution of D-galactose (1) and C-linked galactose derivative (10) inhibited recrystallization as well as a 3% DMSO solution. The carbohydrates examined in this study did not possess any thermal hysteresis activity (selective depression of freezing point relative to melting point) or dynamic ice shaping. As such, we propose that they are inhibiting recrystallization at the interface between bulk water and the quasi liquid layer (a semiordered interface between ice and bulk water) by disrupting the preordering of water.

CO2 hydrate formation and dissociation in cooled porous media: a potential technology for CO2 capture and storage.

PubMed

Yang, Mingjun; Song, Yongchen; Jiang, Lanlan; Zhu, Ningjun; Liu, Yu; Zhao, Yuechao; Dou, Binlin; Li, Qingping

2013-09-03

The purpose of this study was to investigate the hydrate formation and dissociation with CO2 flowing through cooled porous media at different flow rates, pressures, temperatures, and flow directions. CO2 hydrate saturation was quantified using the mean intensity of water. The experimental results showed that the hydrate block appeared frequently, and it could be avoided by stopping CO2 flooding early. Hydrate formed rapidly as the temperature was set to 274.15 or 275.15 K, but the hydrate formation delayed when it was 276.15 K. The flow rate was an important parameter for hydrate formation; a too high or too low rate was not suitable for CO2 hydration formation. A low operating pressure was also unacceptable. The gravity made hydrate form easily in the vertically upward flow direction. The pore water of the second cycle converted to hydrate more completely than that of the first cycle, which was a proof of the hydrate "memory effect". When the pressure was equal to atmospheric pressure, hydrate did not dissociate rapidly and abundantly, and a long time or reduplicate depressurization should be used in industrial application.

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

Conte, F.P.; Droukas, P.C.; Ewing, R.D.

The development of brine shrimp embryos, A. salina, incubated in media of increasing salinity is delayed as evidenced by decreased emergence and lengthening of the time for excystment. Prehydration of cysts at low temperature (3/sup 0/C) for four to ten hours in distilled water eliminates asynchrony of the population in regard to emergency and hatching times. Internal concentration glycerol, which controls the rate of hydration of the cyst stage, is markedly affected by external salinity. Water balance in the cyst stage is maintained via the trehalose-glycerol mechanism which generates a simple passive diffusional gradient across the chitinous shell allowing watermore » to pass. Non-gaseous solutes, such as sodium and glycerol, do not pass through the chitin-membrane barrier. Rupturing the shell by emergence initiates the onset of the prenaupliar stage; it is accompanied by the appearance of large amounts of free glycerol in the external media, decreasing levels of internal glycerol, increased concentrations of internal sodium and the first detectable levels of the cationic transport enzyme, Na + K-ATPase. Continual loss of free glycerol through the cellular and hatching membranes causes the excysting embryo to convert from a trehalose-glycerol mechanism to a sodium-mediated transport system in order to maintain larval water balance. Ontogeny of the sodium regulating mechanism requires formation of Na + K-ATPase. The production of new Na + K-ATPase, as evidenced by incorporation of /sup 14/C-amino acids into polypeptide subunits and density-gradient centrifugation of radioactive membrane vesicles rich in Na + K-ATPase, may play an important role and, if so, it appears to be initiated between E-1 and E-2 stages.« less

Cyclic formation and dissociation of methane hydrate within partially water saturated sand

NASA Astrophysics Data System (ADS)

Kneafsey, T. J.; Nakagawa, S.

2010-12-01

For partially water-saturated sediments, laboratory experiments have shown that methane hydrate forms heterogeneously within a sample at the core scale. The heterogeneous distribution of hydrate in combination with grain-scale hydrate location (eg. grain cementing, load bearing, and pore filling), determines the overall mechanical properties of hydrate-bearing sediments including shear strength and seismic properties. For this reason, understanding the heterogeneity of hydrate-bearing sample is essential when the bulk properties of the sample are examined in the laboratory. We present a series of laboratory methane hydrate formation and dissociation experiments with concurrent x-ray CT imaging and low-frequency (near 1 kHz) seismic measurements. The seismic measurements were conducted using a new acoustic resonant bar technique called the Split Hopkinson Resonant Bar method, which allows using a small sediment core (3.75 cm diameter, 7.5 cm length). The experiment was conducted using a jacketed, pre-compacted, fine-grain silica sand sample with a 40% distilled water saturation. Under isotropic confining stress of 6.9 MPa and a temperature 4 oC, the hydrate was formed in the sample by injecting pure methane gas at 5.6 MPa. Once the hydrate formed, it was dissociated by reducing the pore pressure to 2.8 MPa. This cycle was repeated by three times (dissociation test for the third cycle was not done) to examine the resulting changes in the hydrate distribution and seismic signatures. The repeated formation of hydrate resulted in significant changes in its distribution, which resulted in differences in the overall elastic properties of the sample, determined from the seismic measurements. Interestingly, the time intervals between the dissociation and subsequent formation of hydrate affected the rate of hydrate formation, shorter intervals resulting in faster formation. This memory effect, possibly caused by the presence of residual “seed crystals” in the pore water providing nucleation points for hydrate formation, did not result in rapid formation at all locations in the sample. In spite of heterogeneity, observed seismic properties were very similar for the two measurements during dissociation.

Is the U-B color sufficient for identifying water of hydration on solar system bodies?

NASA Technical Reports Server (NTRS)

Vilas, Faith

1995-01-01

The U-B color has been suggested as a predictor of the presence of water of hydration on asteroids. Photometry from the Eight-Color Asteroid Survey (ECAS) was used to test this concept. An overlap in U-B color prevents this magnitude difference from distinguishing between surface material that was thermally processed at higher temperatures and surface material that was aqueously altered. Two tests of the presence of water of hydration using visible spectral region photometry failed to flag those few higher albedo M- and E-class asteroids having photometry that shows a 3.0-micrometers water of hydration absorption. These asteroids probably contain little or no oxidized iron in their surface material.

Gas hydrate saturation from acoustic impedance and resistivity logs in the shenhu area, south china sea

USGS Publications Warehouse

Wang, X.; Wu, S.; Lee, M.; Guo, Y.; Yang, S.; Liang, J.

2011-01-01

During the China's first gas hydrate drilling expedition -1 (GMGS-1), gas hydrate was discovered in layers ranging from 10 to 25 m above the base of gas hydrate stability zone in the Shenhu area, South China Sea. Water chemistry, electrical resistivity logs, and acoustic impedance were used to estimate gas hydrate saturations. Gas hydrate saturations estimated from the chloride concentrations range from 0 to 43% of the pore space. The higher gas hydrate saturations were present in the depth from 152 to 177 m at site SH7 and from 190 to 225 m at site SH2, respectively. Gas hydrate saturations estimated from the resistivity using Archie equation have similar trends to those from chloride concentrations. To examine the variability of gas hydrate saturations away from the wells, acoustic impedances calculated from the 3 D seismic data using constrained sparse inversion method were used. Well logs acquired at site SH7 were incorporated into the inversion by establishing a relation between the water-filled porosity, calculated using gas hydrate saturations estimated from the resistivity logs, and the acoustic impedance, calculated from density and velocity logs. Gas hydrate saturations estimated from acoustic impedance of seismic data are ???10-23% of the pore space and are comparable to those estimated from the well logs. The uncertainties in estimated gas hydrate saturations from seismic acoustic impedances were mainly from uncertainties associated with inverted acoustic impedance, the empirical relation between the water-filled porosities and acoustic impedances, and assumed background resistivity. ?? 2011 Elsevier Ltd.

Scanning electron microscopy investigations of laboratory-grown gas clathrate hydrates formed from melting ice, and comparison to natural hydrates

USGS Publications Warehouse

Stern, L.A.; Kirby, S.H.; Circone, S.; Durham, W.B.

2004-01-01

Scanning electron microscopy (SEM) was used to investigate grain texture and pore structure development within various compositions of pure sI and sII gas hydrates synthesized in the laboratory, as well as in natural samples retrieved from marine (Gulf of Mexico) and permafrost (NW Canada) settings. Several samples of methane hydrate were also quenched after various extents of partial reaction for assessment of mid-synthesis textural progression. All laboratory-synthesized hydrates were grown under relatively high-temperature and high-pressure conditions from rounded ice grains with geometrically simple pore shapes, yet all resulting samples displayed extensive recrystallization with complex pore geometry. Growth fronts of mesoporous methane hydrate advancing into dense ice reactant were prevalent in those samples quenched after limited reaction below and at the ice point. As temperatures transgress the ice point, grain surfaces continue to develop a discrete "rind" of hydrate, typically 5 to 30 ??m thick. The cores then commonly melt, with rind microfracturing allowing migration of the melt to adjacent grain boundaries where it also forms hydrate. As the reaction continues under progressively warmer conditions, the hydrate product anneals to form dense and relatively pore-free regions of hydrate grains, in which grain size is typically several tens of micrometers. The prevalence of hollow, spheroidal shells of hydrate, coupled with extensive redistribution of reactant and product phases throughout reaction, implies that a diffusion-controlled shrinking-core model is an inappropriate description of sustained hydrate growth from melting ice. Completion of reaction at peak synthesis conditions then produces exceptional faceting and euhedral crystal growth along exposed pore walls. Further recrystallization or regrowth can then accompany even short-term exposure of synthetic hydrates to natural ocean-floor conditions, such that the final textures may closely mimic those observed in natural samples of marine origin. Of particular note, both the mesoporous and highly faceted textures seen at different stages during synthetic hydrate growth were notably absent from all examined hydrates recovered from a natural marine-environment setting.

Correlation Between Chain Architecture and Hydration Water Structure in Polysaccharides.

PubMed

Grossutti, Michael; Dutcher, John R

2016-03-14

The physical properties of confined water can differ dramatically from those of bulk water. Hydration water associated with polysaccharides provides a particularly interesting example of confined water, because differences in polysaccharide structure provide different spatially confined environments for water sorption. We have used attenuated total reflection infrared (ATR-IR) spectroscopy to investigate the structure of hydration water in films of three different polysaccharides under controlled relative humidity (RH) conditions. We compare the results obtained for films of highly branched, dendrimer-like phytoglycogen nanoparticles to those obtained for two unbranched polysaccharides, hyaluronic acid (HA), and chitosan. We find similarities between the water structuring in the two linear polysaccharides and significant differences for phytoglycogen. In particular, the results suggest that the high degree of branching in phytoglycogen leads to a much more well-ordered water structure (low density, high connectivity network water), indicating the strong influence of chain architecture on the structuring of water. These measurements provide unique insight into the relationship between the structure and hydration of polysaccharides, which is important for understanding and exploiting these sustainable nanomaterials in a wide range of applications.

Gas hydrates of outer continental margins

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

Kvenvolden, K.A.

1990-05-01

Gas hydrates are crystalline substances in which a rigid framework of water molecules traps molecules of gas, mainly methane. Gas-hydrate deposits are common in continental margin sediment in all major oceans at water depths greater than about 300 m. Thirty-three localities with evidence for gas-hydrate occurrence have been described worldwide. The presence of these gas hydrates has been inferred mainly from anomalous lacoustic reflectors seen on marine seismic records. Naturally occurring marine gas hydrates have been sampled and analyzed at about tensites in several regions including continental slope and rise sediment of the eastern Pacific Ocean and the Gulf ofmore » Mexico. Except for some Gulf of Mexico gas hydrate occurrences, the analyzed gas hydrates are composed almost exclusively of microbial methane. Evidence for the microbial origin of methane in gas hydrates includes (1) the inverse relation between methane occurence and sulfate concentration in the sediment, (2) the subparallel depth trends in carbon isotopic compositions of methane and bicarbonate in the interstitial water, and (3) the general range of {sup 13}C depletion ({delta}{sub PDB}{sup 13}C = {minus}90 to {minus}60 {per thousand}) in the methane. Analyses of gas hydrates from the Peruvian outer continental margin in particular illustrate this evidence for microbially generated methane. The total amount of methane in gas hydrates of continental margins is not known, but estimates of about 10{sup 16} m{sup 3} seem reasonable. Although this amount of methane is large, it is not yet clear whether methane hydrates of outer continental margins will ever be a significant energy resource; however, these gas hydrates will probably constitute a drilling hazard when outer continental margins are explored in the future.« less

Dynamic morphology of gas hydrate on a methane bubble in water: Observations and new insights for hydrate film models

NASA Astrophysics Data System (ADS)

Warzinski, Robert P.; Lynn, Ronald; Haljasmaa, Igor; Leifer, Ira; Shaffer, Frank; Anderson, Brian J.; Levine, Jonathan S.

2014-10-01

Predicting the fate of subsea hydrocarbon gases escaping into seawater is complicated by potential formation of hydrate on rising bubbles that can enhance their survival in the water column, allowing gas to reach shallower depths and the atmosphere. The precise nature and influence of hydrate coatings on bubble hydrodynamics and dissolution is largely unknown. Here we present high-definition, experimental observations of complex surficial mechanisms governing methane bubble hydrate formation and dissociation during transit of a simulated oceanic water column that reveal a temporal progression of deep-sea controlling mechanisms. Synergistic feedbacks between bubble hydrodynamics, hydrate morphology, and coverage characteristics were discovered. Morphological changes on the bubble surface appear analogous to macroscale, sea ice processes, presenting new mechanistic insights. An inverse linear relationship between hydrate coverage and bubble dissolution rate is indicated. Understanding and incorporating these phenomena into bubble and bubble plume models will be necessary to accurately predict global greenhouse gas budgets for warming ocean scenarios and hydrocarbon transport from anthropogenic or natural deep-sea eruptions.

Crystal structures of hydrates of simple inorganic salts. III. Water-rich aluminium halide hydrates: AlCl3 · 15H2O, AlBr3 · 15H2O, AlI3 · 15H2O, AlI3 · 17H2O and AlBr3 · 9H2O.

PubMed

Schmidt, Horst; Hennings, Erik; Voigt, Wolfgang

2014-09-01

Water-rich aluminium halide hydrate structures are not known in the literature. The highest known water content per Al atom is nine for the perchlorate and fluoride. The nonahydrate of aluminium bromide, stable pentadecahydrates of aluminium chloride, bromide and iodide, and a metastable heptadecahydrate of the iodide have now been crystallized from low-temperature solutions. The structures of these hydrates were determined and are discussed in terms of the development of cation hydration spheres. The pentadecahydrate of the chloride and bromide are isostructural. In AlI(3) · 15H2O, half of the Al(3+) cations are surrounded by two complete hydration spheres, with six H2O in the primary and 12 in the secondary. For the heptadecahydrate of aluminium iodide, this hydration was found for every Al(3+).

Comparison of skin hydration in combination and single use of common moisturizers (cream, toner, and spray water).

PubMed

Yuanxi, Li; Wei, Hua; Lidan, Xiiong; Li, Li

2016-01-01

This study aims to assess the moisturization in combination or single use (including seven general applications) of three common moisturizers: cream, toner, and spray water. Groups were set as C: cream only; T: toner only; C+T, T+C: cream or toner applied successively within a few minutes; C-T, C-S: cream applied with repeated toner or spray water every 2 h; T-T: toner applied with repeated toner every 2 h; and N: untreated group. Outcomes were the change in skin hydration from baseline at 2, 4, 6, and 8 h after applications. All treated zones displayed a significantly higher degree of hydration compared with the untreated zone ( p < 0.05). For normal skin (hydration value at baseline >35 a.u.), C-T led to greatest hydration change rate compared with others, followed by C+T, T+C, and C. Those three applications exhibited analogous hydration at each test point ( p > 0.05). The hydration rate of C-S differed slightly from T-T, followed by those four mentioned above, with T being the last. For dry skin (hydration value at baseline <35 a.u.), no statistical significance could be detected between C-T zone and C+T, T+C, and C zones ( p > 0.05), the other results were identical. When cream and toner were applied successively, the application order has little effect on skin hydration. The application of cream only was an effective and brief way to achieve favorable moisturization especially for dry skin. As a complement, repeated application of toner rather than spray water is efficacious for skin hydration.

A computer simulation study of the temperature dependence of the hydrophobic hydration

NASA Astrophysics Data System (ADS)

Guillot, B.; Guissani, Y.

1993-11-01

The test particle method is used to evaluate by molecular dynamics calculations the solubility of rare gases and of methane in water between the freezing point and the critical point. A quantitative agreement is obtained between solubility data and simulation results when the simulated water is modeled by the extended simple point charge model (SPCE). From a thermodynamical point of view, it is shown that the hierarchy of rare gases solubilities in water is governed by the solute-water interaction energy while an entropic term of cavity formation is found to be responsible for the peculiar temperature dependence of the solubility along the coexistence curve, and more precisely, of the solubility minimum exhibited by all the investigated solutes. Near the water critical point, the asymptotic behaviors of the Henry's constant and of the vapor-liquid partition coefficient, respectively, as deduced from the simulation data follow with a good accuracy the critical laws recently proposed in the literature for these quantities. Moreover, the calculated partial molar volume of the solute shows a steep increase above 473 K and becomes proportional to the isothermal compressibility of the pure solvent in the vicinity of the critical point as it is observed experimentally. From a microscopic point of view, the evaluation of the solute-solvent pair distribution functions permits to establish a relationship between the increase of the solubility with the decrease of the temperature in cold water on the one hand, and the formation of cages of the clathrate-type around the solute on the other hand. Nevertheless, as soon as the boiling point of water is reached the computer simulation shows that the water molecules of the first hydration shell are no longer oriented tangentially to the solute and tend to reorientate towards the bulk. At higher temperatures a deficit of water molecules progressively appears around the solute, a deficit which is directly associated with an increase of the partial molar volume. Although this phenomenon could be related to what is observed in supercritical mixtures it is emphasized that no long range critical fluctuation is present in the simulated sample.

Physical properties of northern Gulf of Mexico sediment and laboratory samples containing natural and synthetic methane gas hydrate

NASA Astrophysics Data System (ADS)

Winters, W. J.; Waite, W. F.; Mason, D. H.; Lorenson, T. L.; Paull, C. K.; Novosel, I.; Boldina, O. M.; Dallimore, S. R.; Collett, T. S.; Page 127 Shipboard Sc. Party

2003-04-01

The U.S. Geological Survey (USGS) has been involved in oceanographic and Arctic field programs and laboratory studies to better understand the relationship between natural gas hydrate and physical properties of surrounding sediment. Recently, the Institut Polaire Francais, Paul-Emile Victor (IPEV) and the USGS jointly conducted a cruise aboard the Marion Dufresne to collect giant piston cores to determine the distribution of gas hydrate in the northern Gulf of Mexico. Hydrates recovered during the cruise did not appear to be lithologically controlled (unlike Canadian Arctic cores) and were either disseminated or were massive layers. Sediment water content typically decreases rapidly to a subbottom depth of about 8 to 9 m, but then decreases at a lower rate. At-sea help was provided by the IMAGES (International Marine Past Global Changes Study) and PAGE (Paleoceanography of the Atlantic and Geochemistry) programs, and funding was provided by the U.S. Dept. of Energy. We have used the Gas Hydrate And Sediment Test Laboratory Instrument (GHASTLI) to analyze sediment containing natural gas hydrate and to examine hydrate formed within (a) initially water-saturated and (b) partly-water saturated sieved Ottawa sand specimens at a pore pressure of 12 MPa and 250 kPa confining stress. Hydrate is formed when methane gas is slowly percolated into a 70-mm diameter by 140-mm long cylindrical specimen and subsequently the temperature is lowered to about 6 degrees C. We have found that acoustic velocity, shear strength, and permeability of samples containing different initial water contents are significantly affected by (a) the amount of hydrate present, (b) its distribution, (c) its position within pores, and (d) concentration at key locations. Acoustic P-wave velocities can increase from 1.7 km/s to 4.0 km/s using different hydrate and synthetic sample formation techniques. Although acoustic properties are significantly affected by hydrate at grain boundaries, the mere presence of hydrate in pores (but not necessarily at grain contacts) causes strength to significantly increase because dilation during undrained shear results in greater negative pore pressures. Recently determined strengths of three Ottawa sand samples are exponentially related to the degree of water saturation, bulk density, and hydrate content.

THE EFFECT OF GAS HYDRATES DISSOCIATION AND DRILLING FLUIDS INVASION UPON BOREHOLE STABILITY IN OCEANIC GAS HYDRATES-BEARING SEDIMENT

NASA Astrophysics Data System (ADS)

Ning, F.; Wu, N.; Jiang, G.; Zhang, L.

2009-12-01

Under the condition of over-pressure drilling, the solid-phase and liquid-phase in drilling fluids immediately penetrate into the oceanic gas hydrates-bearing sediment, which causes the water content surrounding the borehole to increase largely. At the same time, the hydrates surrounding borehole maybe quickly decompose into water and gas because of the rapid change of temperature and pressure. The drilling practices prove that this two factors may change the rock characteristics of wellbore, such as rock strength, pore pressure, resistivity, etc., and then affect the logging response and evaluation, wellbore stability and well safty. The invasion of filtrate can lower the angle of friction and weaken the cohesion of hydrates-bearing sediment,which is same to the effect of invading into conventional oil and gas formation on borehole mechnical properties. The difference is that temperature isn’t considered in the invasion process of conventional formations while in hydrates-bearing sediments, it is a factor that can not be ignored. Temperature changes can result in hydrates dissociating, which has a great effect on mechanical properties of borehole. With the application of numerical simulation method, we studied the changes of pore pressure and variation of water content in the gas hydrates-bearing sediment caused by drilling fluid invasion under pressure differential and gas hydrate dissociation under temperature differential and analyzed their influence on borehole stability.The result of simulation indicated that the temperature near borehole increased quickly and changed hardly any after 6 min later. About 1m away from the borehole, the temperature of formation wasn’t affected by the temperature change of borehole. At the place near borehole, as gas hydrate dissociated dramatically and drilling fluid invaded quickly, the pore pressure increased promptly. The degree of increase depends on the permeability and speed of temperature rise of formation around bohole. If the formation has a low permeability and is heated quickly, the dissociated gas and water couldn’t flow away in time, which is likely to bring a hazard of excess pore pressure. Especially in the area near the wall of borehole, the increase degree of pore pressure is high than other area because the dissociation of gas hydrates is relatively violent and hydraulic gradient is bigger. We also studied the distribution of water saturation around borehole after 10min, 30min and 60min respectively. It revealed that along with the invasion of drilling fluid and dissociation of gas hydrate, the degree of water saturation increased gradually. The effect of gas hydrate dissociation and drilling fluids invasion on borehole stability is to weaken mechanical properties of wellbore and change the pore pressure, then changes the effective stress of gas hydrates-bearing sediment. So temperature, pressure in the borehole and filter loss of drilling fluids should be controlled strictly to prevent gas hydrates from decomposing largely and in order to keep the borehole stability in the gas hydrates-bearing formations.

Hydrated interfacial ions and electrons.

PubMed

Abel, Bernd

2013-01-01

Charged particles such as hydrated ions and transient hydrated electrons, the simplest anionic reducing agents in water, and the special hydronium and hydroxide ions at water interfaces play an important role in many fields of science, such as atmospheric chemistry, radiation chemistry, and biology, as well as biochemistry. This article focuses on these species near hydrophobic interfaces of water, such as the air or vacuum interface of water or water protein/membrane interfaces. Ions at interfaces as well as solvated electrons have been reviewed frequently during the past decade. Although all species have been known for some time with seemingly familiar features, recently the picture in all cases became increasingly diffuse rather than clearer. The current account gives a critical state-of-the art overview of what is known and what remains to be understood and investigated about hydrated interfacial ions and electrons.

Water cavities of sH clathrate hydrate stabilized by molecular hydrogen.

PubMed

Strobel, Timothy A; Koh, Carolyn A; Sloan, E Dendy

2008-02-21

X-ray diffraction and Raman spectroscopic measurements confirm that molecular hydrogen can be contained within the small water cavities of a binary sH clathrate hydrate using large guest molecules that stabilize the large cavity. The potential increase in hydrogen storage could be more than 40% when compared with binary sII hydrates. This work demonstrates the stabilization of hydrogen in a hydrate structure previously unknown for encapsulating molecular hydrogen, indicating the potential for other inclusion compound materials with even greater hydrogen storage capabilities.

Microstructural characteristics of natural gas hydrates hosted in various sand sediments.

PubMed

Zhao, Jiafei; Yang, Lei; Liu, Yu; Song, Yongchen

2015-09-21

Natural gas hydrates have aroused worldwide interest due to their energy potential and possible impact on climate. The occurrence of natural gas hydrates hosted in the pores of sediments governs the seismic exploration, resource assessment, stability of deposits, and gas production from natural gas hydrate reserves. In order to investigate the microstructure of natural gas hydrates occurring in pores, natural gas hydrate-bearing sediments were visualized using microfocus X-ray computed tomography (CT). Various types of sands with different grain sizes and wettability were used to study the effect of porous materials on the occurrence of natural gas hydrates. Spatial distributions of methane gas, natural gas hydrates, water, and sands were directly identified. This work indicates that natural gas hydrates tend to reside mainly within pore spaces and do not come in contact with adjacent sands. Such an occurring model of natural gas hydrates is termed the floating model. Furthermore, natural gas hydrates were observed to nucleate at gas-water interfaces as lens-shaped clusters. Smaller sand grain sizes contribute to higher hydrate saturation. The wetting behavior of various sands had little effect on the occurrence of natural gas hydrates within pores. Additionally, geometric properties of the sediments were collected through CT image reconstructions. These findings will be instructive for understanding the microstructure of natural gas hydrates within major global reserves and for future resource utilization of natural gas hydrates.

Liquid Water on Enceladus from Observations of Ammonia and Ar-40 in the Plume

NASA Technical Reports Server (NTRS)

Waite, J. H., Jr.; Lewis, W. S.; Magee, B. A.; Lunine, J. I.; McKinnon, W. B.; Glein, C. R.; Mousis, O.; Young, D. T.; Brockwell, T.; Westlake, J.;

Skin hydration analysis by experiment and computer simulations and its implications for diapered skin.

PubMed

Saadatmand, M; Stone, K J; Vega, V N; Felter, S; Ventura, S; Kasting, G; Jaworska, J

2017-11-01

Experimental work on skin hydration is technologically challenging, and mostly limited to observations where environmental conditions are constant. In some cases, like diapered baby skin, such work is practically unfeasible, yet it is important to understand potential effects of diapering on skin condition. To overcome this challenge, in part, we developed a computer simulation model of reversible transient skin hydration effects. Skin hydration model by Li et al. (Chem Eng Sci, 138, 2015, 164) was further developed to simulate transient exposure conditions where relative humidity (RH), wind velocity, air, and skin temperature can be any function of time. Computer simulations of evaporative water loss (EWL) decay after different occlusion times were compared with experimental data to calibrate the model. Next, we used the model to investigate EWL and SC thickness in different diapering scenarios. Key results from the experimental work were: (1) For occlusions by RH=100% and free water longer than 30 minutes the absorbed amount of water is almost the same; (2) Longer occlusion times result in higher water absorption by the SC. The EWL decay and skin water content predictions were in agreement with experimental data. Simulations also revealed that skin under occlusion hydrates mainly because the outflux is blocked, not because it absorbs water from the environment. Further, simulations demonstrated that hydration level is sensitive to time, RH and/or free water on skin. In simulated diapering scenarios, skin maintained hydration content very close to the baseline conditions without a diaper for the entire duration of a 24 hours period. Different diapers/diaper technologies are known to have different profiles in terms of their ability to provide wetness protection, which can result in consumer-noticeable differences in wetness. Simulation results based on published literature using data from a number of different diapers suggest that diapered skin hydrates within ranges considered reversible. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Controlling the hydration of the skin though the application of occluding barrier creams

PubMed Central

Sparr, Emma; Millecamps, Danielle; Isoir, Muriel; Burnier, Véronique; Larsson, Åsa; Cabane, Bernard

2013-01-01

The skin is a barrier membrane that separates environments with profoundly different water contents. The barrier properties are assured by the outer layer of the skin, the stratum corneum (SC), which controls the transepidermal water loss. The SC acts as a responding membrane, since its hydration and permeability vary with the boundary condition, which is the activity of water at the outer surface of the skin. We show how this boundary condition can be changed by the application of a barrier cream that makes a film with a high resistance to the transport of water. We present a quantitative model that predicts hydration and water transport in SC that is covered by such a film. We also develop an experimental method for measuring the specific resistance to water transport of films made of occluding barrier creams. Finally, we combine the theoretical model with the measured properties of the barrier creams to predict how a film of cream changes the activity of water at the outer surface of the SC. Using the known variations of SC permeability and hydration with the water activity in its environment (i.e. the relative humidity), we can thus predict how a film of barrier cream changes SC hydration. PMID:23269846

Controlling the hydration of the skin though the application of occluding barrier creams.

PubMed

Sparr, Emma; Millecamps, Danielle; Isoir, Muriel; Burnier, Véronique; Larsson, Åsa; Cabane, Bernard

2013-03-06

The skin is a barrier membrane that separates environments with profoundly different water contents. The barrier properties are assured by the outer layer of the skin, the stratum corneum (SC), which controls the transepidermal water loss. The SC acts as a responding membrane, since its hydration and permeability vary with the boundary condition, which is the activity of water at the outer surface of the skin. We show how this boundary condition can be changed by the application of a barrier cream that makes a film with a high resistance to the transport of water. We present a quantitative model that predicts hydration and water transport in SC that is covered by such a film. We also develop an experimental method for measuring the specific resistance to water transport of films made of occluding barrier creams. Finally, we combine the theoretical model with the measured properties of the barrier creams to predict how a film of cream changes the activity of water at the outer surface of the SC. Using the known variations of SC permeability and hydration with the water activity in its environment (i.e. the relative humidity), we can thus predict how a film of barrier cream changes SC hydration.

In silico studies of the properties of water hydrating a small protein

NASA Astrophysics Data System (ADS)

Sinha, Sudipta Kumar; Jana, Madhurima; Chakraborty, Kausik; Bandyopadhyay, Sanjoy

2014-12-01

Atomistic molecular dynamics simulation of an aqueous solution of the small protein HP-36 has been carried out with explicit solvent at room temperature. Efforts have been made to explore the influence of the protein on the relative packing and ordering of water molecules around its secondary structures, namely, three α-helices. The calculations reveal that the inhomogeneous water ordering and density distributions around the helices are correlated with their relative hydrophobicity. Importantly, we have identified the existence of a narrow relatively dehydrated region containing randomly organized "quasi-free" water molecules beyond the first layer of "bound" waters at the protein surface. These water molecules with relatively weaker binding energies form the transition state separating the "bound" and "free" water molecules at the interface. Further, increased contribution of solid-like caging motions of water molecules around the protein is found to be responsible for reduced fluidity of the hydration layer. Interestingly, we notice that the hydration layer of helix-3 is more fluidic with relatively higher entropy as compared to the hydration layers of the other two helical segments. Such characteristics of helix-3 hydration layer correlate well with the activity of HP-36, as helix-3 contains the active site of the protein.

Comparing effectiveness of rhamnolipid biosurfactant with a quaternary ammonium salt surfactant for hydrate anti-agglomeration.

PubMed

York, J Dalton; Firoozabadi, Abbas

2008-01-24

Natural gas is projected to be the premium fuel of the 21st century because of availability, as well as economical and environmental considerations. Natural gas is coproduced with water from the subsurface forming gas hydrates. Hydrate formation may result in shutdown of onshore and offshore operations. Industry practice has been usage of alcohols--which have undesirable environmental impacts--to affect bulk-phase properties and inhibit hydrate formation. An alternative to alcohols is changing the surface properties through usage of polymers and surfactants, effective at 0.5-3 wt % of coproduced water. One group of low-dosage hydrate inhibitors (LDHI) are kinetic inhibitors, which affect nucleation rate and growth. A second group of LDHI are anti-agglomerants, which prevent agglomeration of small hydrate crystallites. Despite great potential, reported work on hydrate anti-agglomeration is very limited. In this paper, our focus is on the use of two vastly different surfactants as anti-agglomerants. We use a model oil, water, and tetrahydrofuran as a hydrate-forming species. We examine the effectiveness of a quaternary ammonium salt (i.e., quat). Visual observation measurements show that a small concentration of the quat (0.01%) can prevent agglomeration. However, a quat is not a green chemical and therefore may be undesirable. We show that a rhamnolipid biosurfactant can be effective to a concentration of 0.05 wt %. One difference between the two surfactants is the stability of the water-in-oil emulsions created. The biosurfactant forms a less stable emulsion, which makes it very desirable for hydrate application.

Fabrication of Silica-Coated Hollow Carbon Nanospheres Encapsulating Fe3O4 Cluster for Magnetical and MR Imaging Guided NIR Light Triggering Hyperthermia and Ultrasound Imaging.

PubMed

Huang, Yun-Kai; Su, Chia-Hao; Chen, Jiu-Jeng; Chang, Chun-Ting; Tsai, Yu-Hsin; Syu, Sheng-Fu; Tseng, Tsu-Ting; Yeh, Chen-Sheng

2016-06-15

Iron oxide nanoparticles (IONPs)-carbon (C) hybrid zero-dimensional nanostructures normally can be categorized into core-shell and yolk-shell architectures. Although IONP-C is a promising theranostic nanoagent, the in vivo study has surprisingly been less described. In addition, little effort has strived toward the fabrication of yolk-shell compared to the core-shell structures. In this context, we synthesized a yolk-shell type of the silica-coated hollow carbon nanospheres encapsulating IONPs cluster, which can be dispersed in aqueous solution for systemic studies in vivo, via the preparation involving the mixed micellization, polymerization/hollowing, sol-gel (hydration-condensation), and pyrolysis processes. Through a surface modification of the polyethylenimine followed by the sol-gel process, the silica shell coating was able to escape from condensing and sintering courses resulting in aggregation, due to the annealing. Not limited to the well-known functionalities in magnetical targeting and magnetic resonance (MR) imaging for IONP-C hybrid structures, we expanded this yolk-shell NPs as a near-infrared (NIR) light-responsive echogenic nanoagent giving an enhanced ultrasound imaging. Overall, we fabricated the NIR sensitive yolk-shell IONP-C to activate ultrasound imaging and photothermal ablation under magnetically and MR imaging guided therapy.

Biomineral shell formation under ocean acidification: a shift from order to chaos.

PubMed

Fitzer, Susan C; Chung, Peter; Maccherozzi, Francesco; Dhesi, Sarnjeet S; Kamenos, Nicholas A; Phoenix, Vernon R; Cusack, Maggie

2016-02-15

Biomineral production in marine organisms employs transient phases of amorphous calcium carbonate (ACC) in the construction of crystalline shells. Increasing seawater pCO2 leads to ocean acidification (OA) with a reduction in oceanic carbonate concentration which could have a negative impact on shell formation and therefore survival. We demonstrate significant changes in the hydrated and dehydrated forms of ACC in the aragonite and calcite layers of Mytilus edulis shells cultured under acidification conditions (1000 μatm pCO2) compared to present day conditions (380 μatm pCO2). In OA conditions, Mytilus edulis has more ACC at crystalisation sites. Here, we use the high-spatial resolution of synchrotron X-ray Photo Emission Electron Microscopy (XPEEM) combined with X-ray Absorption Spectroscopy (XAS) to investigate the influence of OA on the ACC formation in the shells of adult Mytilus edulis. Electron Backscatter Diffraction (EBSD) confirms that OA reduces crystallographic control of shell formation. The results demonstrate that OA induces more ACC formation and less crystallographic control in mussels suggesting that ACC is used as a repair mechanism to combat shell damage under OA. However, the resultant reduced crystallographic control in mussels raises concerns for shell protective function under predation and changing environments.

Biomineral shell formation under ocean acidification: a shift from order to chaos

PubMed Central

Fitzer, Susan C.; Chung, Peter; Maccherozzi, Francesco; Dhesi, Sarnjeet S.; Kamenos, Nicholas A.; Phoenix, Vernon R.; Cusack, Maggie

2016-01-01

Biomineral production in marine organisms employs transient phases of amorphous calcium carbonate (ACC) in the construction of crystalline shells. Increasing seawater pCO2 leads to ocean acidification (OA) with a reduction in oceanic carbonate concentration which could have a negative impact on shell formation and therefore survival. We demonstrate significant changes in the hydrated and dehydrated forms of ACC in the aragonite and calcite layers of Mytilus edulis shells cultured under acidification conditions (1000 μatm pCO2) compared to present day conditions (380 μatm pCO2). In OA conditions, Mytilus edulis has more ACC at crystalisation sites. Here, we use the high-spatial resolution of synchrotron X-ray Photo Emission Electron Microscopy (XPEEM) combined with X-ray Absorption Spectroscopy (XAS) to investigate the influence of OA on the ACC formation in the shells of adult Mytilus edulis. Electron Backscatter Diffraction (EBSD) confirms that OA reduces crystallographic control of shell formation. The results demonstrate that OA induces more ACC formation and less crystallographic control in mussels suggesting that ACC is used as a repair mechanism to combat shell damage under OA. However, the resultant reduced crystallographic control in mussels raises concerns for shell protective function under predation and changing environments. PMID:26876022

Biomineral shell formation under ocean acidification: a shift from order to chaos

NASA Astrophysics Data System (ADS)

Fitzer, Susan C.; Chung, Peter; Maccherozzi, Francesco; Dhesi, Sarnjeet S.; Kamenos, Nicholas A.; Phoenix, Vernon R.; Cusack, Maggie

2016-02-01

Biomineral production in marine organisms employs transient phases of amorphous calcium carbonate (ACC) in the construction of crystalline shells. Increasing seawater pCO2 leads to ocean acidification (OA) with a reduction in oceanic carbonate concentration which could have a negative impact on shell formation and therefore survival. We demonstrate significant changes in the hydrated and dehydrated forms of ACC in the aragonite and calcite layers of Mytilus edulis shells cultured under acidification conditions (1000 μatm pCO2) compared to present day conditions (380 μatm pCO2). In OA conditions, Mytilus edulis has more ACC at crystalisation sites. Here, we use the high-spatial resolution of synchrotron X-ray Photo Emission Electron Microscopy (XPEEM) combined with X-ray Absorption Spectroscopy (XAS) to investigate the influence of OA on the ACC formation in the shells of adult Mytilus edulis. Electron Backscatter Diffraction (EBSD) confirms that OA reduces crystallographic control of shell formation. The results demonstrate that OA induces more ACC formation and less crystallographic control in mussels suggesting that ACC is used as a repair mechanism to combat shell damage under OA. However, the resultant reduced crystallographic control in mussels raises concerns for shell protective function under predation and changing environments.

Vibrational spectroscopy of water in hydrated lipid multi-bilayers. I. Infrared spectra and ultrafast pump-probe observables.

PubMed

Gruenbaum, S M; Skinner, J L

2011-08-21

The vibrational spectroscopy of hydration water in dilauroylphosphatidylcholine lipid multi-bilayers is investigated using molecular dynamics simulations and a mixed quantum/classical model for the OD stretch spectroscopy of dilute HDO in H(2)O. FTIR absorption spectra, and isotropic and anisotropic pump-probe decay curves have been measured experimentally as a function of the hydration level of the lipid multi-bilayer, and our goal is to make connection with these experiments. To this end, we use third-order response functions, which allow us to include non-Gaussian frequency fluctuations, non-Condon effects, molecular rotations, and a fluctuating vibrational lifetime, all of which we believe are important for this system. We calculate the response functions using existing transition frequency and dipole maps. From the experiments it appears that there are two distinct vibrational lifetimes corresponding to HDO molecules in different molecular environments. In order to obtain these lifetimes, we consider a simple two-population model for hydration water hydrogen bonds. Assuming a different lifetime for each population, we then calculate the isotropic pump-probe decay, fitting to experiment to obtain the two lifetimes for each hydration level. With these lifetimes in hand, we then calculate FTIR spectra and pump-probe anisotropy decay as a function of hydration. This approach, therefore, permits a consistent calculation of all observables within a unified computational scheme. Our theoretical results are all in qualitative agreement with experiment. The vibrational lifetime of lipid-associated OD groups is found to be systematically shorter than that of the water-associated population, and the lifetimes of each population increase with decreasing hydration, in agreement with previous analysis. Our theoretical FTIR absorption spectra successfully reproduce the experimentally observed red-shift with decreasing lipid hydration, and we confirm a previous interpretation that this shift results from the hydrogen bonding of water to the lipid phosphate group. From the pump-probe anisotropy decay, we confirm that the reorientational motions of water molecules slow significantly as hydration decreases, with water bound in the lipid carbonyl region undergoing the slowest rotations. © 2011 American Institute of Physics

Vibrational spectroscopy of water in hydrated lipid multi-bilayers. I. Infrared spectra and ultrafast pump-probe observables

PubMed Central

Gruenbaum, S. M.; Skinner, J. L.

2011-01-01

The vibrational spectroscopy of hydration water in dilauroylphosphatidylcholine lipid multi-bilayers is investigated using molecular dynamics simulations and a mixed quantum∕classical model for the OD stretch spectroscopy of dilute HDO in H2O. FTIR absorption spectra, and isotropic and anisotropic pump-probe decay curves have been measured experimentally as a function of the hydration level of the lipid multi-bilayer, and our goal is to make connection with these experiments. To this end, we use third-order response functions, which allow us to include non-Gaussian frequency fluctuations, non-Condon effects, molecular rotations, and a fluctuating vibrational lifetime, all of which we believe are important for this system. We calculate the response functions using existing transition frequency and dipole maps. From the experiments it appears that there are two distinct vibrational lifetimes corresponding to HDO molecules in different molecular environments. In order to obtain these lifetimes, we consider a simple two-population model for hydration water hydrogen bonds. Assuming a different lifetime for each population, we then calculate the isotropic pump-probe decay, fitting to experiment to obtain the two lifetimes for each hydration level. With these lifetimes in hand, we then calculate FTIR spectra and pump-probe anisotropy decay as a function of hydration. This approach, therefore, permits a consistent calculation of all observables within a unified computational scheme. Our theoretical results are all in qualitative agreement with experiment. The vibrational lifetime of lipid-associated OD groups is found to be systematically shorter than that of the water-associated population, and the lifetimes of each population increase with decreasing hydration, in agreement with previous analysis. Our theoretical FTIR absorption spectra successfully reproduce the experimentally observed red-shift with decreasing lipid hydration, and we confirm a previous interpretation that this shift results from the hydrogen bonding of water to the lipid phosphate group. From the pump-probe anisotropy decay, we confirm that the reorientational motions of water molecules slow significantly as hydration decreases, with water bound in the lipid carbonyl region undergoing the slowest rotations. PMID:21861584

Structural and dynamical properties of the V(3+) ion in dilute aqueous solution: An ab initio QM/MM molecular dynamics simulation.

PubMed

Kritayakornupong, Chinapong

2009-12-01

A hybrid ab initio QM/MM molecular dynamics simulation at the Hartree-Fock level has been performed to investigate structural and dynamical parameters of the V(3+) ion in dilute aqueous solution. A distorted octahedral structure with the average V(3+)-O distance of 1.99 A is evaluated from the QM/MM simulation, which is in good agreement with the X-ray data. Several structural parameters such as angular distribution functions, theta- and tilt-angle distributions have been determined to obtain the full description of the hydration structure of the hydrated V(3+). The Jahn-Teller distortions of the V(3+) ion are pronounced in the QM/MM simulation. The mean residence time of 14.5 ps is estimated for the ligand exchange processes in the second hydration shell. (c) 2009 Wiley Periodicals, Inc.

Poly(2,6-dimethyl-1,4-phenylene oxide) Blended with Poly (vinylbenzyl chloride)-b-polystyrene for the Formation of Anion Exchange Membranes

DTIC Science & Technology

2014-08-14

show improved mechanical properties compared to the styrenic copolymer, particularly in a hydrated condition. The membranes were subjected to...AEMs) show improved mechanical properties compared to the styrenic copolymer, particularly in a hydrated condition. The membranes were subjected to...deionized water, and after 24 h of soaking, the fully hydrated membranes were removed from the water; any residual bulk water on the membrane surface was

A temperature and photographic time-series from a seafloor gas hydrate deposit on the Gulf of Mexico Slope

NASA Astrophysics Data System (ADS)

MacDonald, I. R.; Vararo, M.; Bender, L.

2003-04-01

Under laboratory conditions, gas hydrates are highly sensitive to changes in water temperature. MacDonald et al. (1994) and Roberts et al. (1999) have monitored in-situ deposits and recorded rapid changes in gas flux from vents partially plugged with gas hydrate; the changes appear to correlate with fluctuation in bottom temperature over ranges of <0.2 to 1.0 C. To study this process in a different way, a monitoring array consisting of a time lapse camera and two thermistor probes was deployed at a hydrocarbon seep known as Bush Hill. Every 6 hours for 96 days (until battery power was exhausted), the camera recorded a digital image of a prominent gas hydrate mound consisting of Structure II hydrate with gas vents, chemosynthetic tube worms, and a number of mobile species. The temperature probes comprised two autonomous Antares thermistors, one at each end of a 50-cm PVC wand, which recorded temperatures with precision of better than 0.1 C at 30-min intervals over 327 d. One probe was implanted with a tight seal into a drill hole about 7 cm deep in the top of the gas hydrate mound. The second was inserted about 50 cm deep into the adjacent sediments. For each probe, the top thermistor recorded the ambient water temperature while the bottom thermistor recorded the internal temperature of the hydrate or sediment. Photographic results show no dramatic changes in the size, shape, or gas venting from the mound during the 96 day time-series. There were subtle increases in the amount of hydrate exposed to the water between the end of the photographic time series and the recovery of the monitoring array. Mean temperatures (SDEV) and temperature range recorded by the probes were as follows: In-water: 7.87 ( 0.44) and 6.64-9.73 C In-hydrate: 7.81 ( 0.34) and 6.87-9.18 C In-sediment: 7.81 ( 0.16) and 7.79-9.18 C Spectra of the temperature records showed significant high-frequency peaks for in-water data corresponding to K1, M2 and M3 lunar tides. Of these peaks, only the K1 (23.9 h) was evident for in-hydrate records and none of the tidal peaks were evident for in-sediment records. All three records showed significant low-frequency periodicity at about 288 h. In-hydrate temperatures lagged the in-water temperatures by 6 h with high correlation. In-sediment temperatures lagged in-water temperatures by 288 h with weak correlation. These results constrain the response of shallow gas hydrate deposits to changing water temperature. MacDonald, I. R., N. L. Guinasso, Jr., et al. (1994). Gas hydrate that breaches the sea floor on the continental slope of the Gulf of Mexico. Geology 22: 699-702. Roberts, H., W. Wiseman Jr., et al. (1999). Surficial gas hydrates of the Louisiana continental slope--initial results of direct observations and in situ data collection. Offshore Technology Conference, Houston, TX, 10770: 259-272

Hydrogen speciation in hydrated layers on nuclear waste glass

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

Aines, R.D.; Weed, H.C.; Bates, J.K.

1987-12-31

The hydration of an outer layer on nuclear waste glasses in known to occur during leaching, but the actual speciation of hydrogen (as water or hydroxyl groups) in these layers has not been determined. As part of the Nevada Nuclear Waste Storage Investigations Project, we have used infrared spectroscopy to determine hydrogen speciations in three nuclear waste glass compositions (SRL-131 & 165, and PNL 76-68), which were leached at 90{sup 0}C (all glasses) or hydrated in a vapor-saturated atmosphere at 202{sup 0}C (SRL-131 only). Hydroxyl groups were found in the surface layers of all the glasses. In addition, molecular watermore » was found in the surface of SRL-131 and PNL 76-68 glasses that had been leached for several months in deionized water, and in the vapor-hydrated sample. The water/hydroxyl ratio increases with increasing reaction time; molecular water makes up most of the hydrogen in the thick reaction layers on vapor-phase hydrated glass while only hydroxyl occurs in the least reacted samples. The hydrated layer on the nuclear waste glasses appears to be of relatively low water content (4 to 7% by weight) and is not substantially hydroxylated. Thus, these layers do not have many of the properties associated with gel layers.« less

NMR relaxation studies on the hydrate layer of intrinsically unstructured proteins.

PubMed

Bokor, Mónika; Csizmók, Veronika; Kovács, Dénes; Bánki, Péter; Friedrich, Peter; Tompa, Peter; Tompa, Kálmán

2005-03-01

Intrinsically unstructured/disordered proteins (IUPs) exist in a disordered and largely solvent-exposed, still functional, structural state under physiological conditions. As their function is often directly linked with structural disorder, understanding their structure-function relationship in detail is a great challenge to structural biology. In particular, their hydration and residual structure, both closely linked with their mechanism of action, require close attention. Here we demonstrate that the hydration of IUPs can be adequately approached by a technique so far unexplored with respect to IUPs, solid-state NMR relaxation measurements. This technique provides quantitative information on various features of hydrate water bound to these proteins. By freezing nonhydrate (bulk) water out, we have been able to measure free induction decays pertaining to protons of bound water from which the amount of hydrate water, its activation energy, and correlation times could be calculated. Thus, for three IUPs, the first inhibitory domain of calpastatin, microtubule-associated protein 2c, and plant dehydrin early responsive to dehydration 10, we demonstrate that they bind a significantly larger amount of water than globular proteins, whereas their suboptimal hydration and relaxation parameters are correlated with their differing modes of function. The theoretical treatment and experimental approach presented in this article may have general utility in characterizing proteins that belong to this novel structural class.

On the formation and structure of rare-earth element complexes in aqueous solutions under hydrothermal conditions with new data on gadolinium aqua and chloro complexes

USGS Publications Warehouse

Mayanovic, Robert A.; Anderson, Alan J.; Bassett, William A.; Chou, I.-Ming

2007-01-01

Synchrotron X-ray spectroscopy experiments were made on the Gd(III) aqua and chloro complexes in low pH aqueous solutions at temperatures ranging from 25 to 500????C and at pressures up to 480??MPa using a hydrothermal diamond anvil cell. Analysis of fluorescence Gd L3-edge X-ray absorption fine structure (XAFS) spectra measured from a 0.006m Gd/0.16m HNO3 aqueous solution at temperatures up to 500????C and at pressures up to 260??MPa shows that the Gd-O distance of the Gd3+ aqua ion decreases steadily at a rate of ??? 0.007??A??/100????C whereas the number of coordinated H2O molecules decreases from 9.0 ?? 0.5 to 7.0 ?? 0.4. The loss of water molecules in the Gd3+ aqua ion inner hydration shell over this temperature range (a 22% reduction) is smaller than exhibited by the Yb3+ aqua ion (42% reduction) indicating that the former is significantly more stable than the later. We conjecture that the anomalous enrichment of Gd reported from measurement of REE concentrations in ocean waters may be attributed to the enhanced stability of the Gd3+ aqua ion relative to other REEs. Gd L3-edge XAFS measurements of 0.006m and 0.1m GdCl3 aqueous solutions at temperatures up to 500????C and pressures up to 480??MPa reveal that the onset of significant Gd3+-Cl- association occurs around 300????C. Partially-hydrated stepwise inner-sphere complexes most likely of the type Gd(H2O)??-nCln+3-n occur in the chloride solutions at higher temperatures, where ?? ??? 8 at 300????C decreasing slightly to an intermediate value between 7 and 8 upon approaching 500????C. This is the first direct evidence for the occurrence of partially-hydrated REE Gd (this study) and Yb [Mayanovic, R.A., Jayanetti, S., Anderson, A.J., Bassett, W.A., Chou, I-M., 2002a. The structure of Yb3+ aquo ion and chloro complexes in aqueous solutions at up to 500 ??C and 270 MPa. J. Phys. Chem. A 106, 6591-6599.] chloro complexes in hydrothermal solutions. The number of chlorides (n) of the partially-hydrated Gd(III) chloro complexes increases steadily with temperature from 0.4 ?? 0.2 to 1.7 ?? 0.3 in the 0.006m chloride solution and from 0.9 ?? 0.7 to 1.8 ?? 0.7 in the 0.1m GdCl3 aqueous solution in the 300-500????C range. Conversely, the number of H2O ligands of Gd(H2O)??-nCln+3-n complexes decreases steadily from 8.9 ?? 0.4 to 5.8 ?? 0.7 in the 0.006m GdCl3 aqueous solution and from 9.0 ?? 0.5 to 5.3 ?? 1.0 in the 0.1m GdCl3 aqueous solution at temperatures from 25 to 500????C. Analysis of our results shows that the chloride ions partially displace the inner-shell water molecules during Gd(III) complex formation under hydrothermal conditions. The Gd-OH2 bond of the partially-hydrated Gd(III) chloro complexes exhibits slightly smaller rates of length contraction (??? 0.005??A??/100????C) for both solutions. The structural aspects of chloride speciation of Gd(III) as measured from this study and of Yb(III) as measured from our previous experiments are consistent with the solubility of these and other REE in deep-sea hydrothermal fluids. ?? 2006 Elsevier B.V. All rights reserved.

Critical pressure and multiphase flow in Blake Ridge gas hydrates

USGS Publications Warehouse

Flemings, P.B.; Liu, Xiuying; Winters, W.J.

2003-01-01

We use core porosity, consolidation experiments, pressure core sampler data, and capillary pressure measurements to predict water pressures that are 70% of the lithostatic stress, and gas pressures that equal the lithostatic stress beneath the methane hydrate layer at Ocean Drilling Program Site 997, Blake Ridge, offshore North Carolina. A 29-m-thick interconnected free-gas column is trapped beneath the low-permeability hydrate layer. We propose that lithostatic gas pressure is dilating fractures and gas is migrating through the methane hydrate layer. Overpressured gas and water within methane hydrate reservoirs limit the amount of free gas trapped and may rapidly export methane to the seafloor.

Effects of various vehicles on skin hydration in vivo.

PubMed

Wiedersberg, S; Leopold, C S; Guy, R H

2009-01-01

The stratum corneum, the outermost layer of the skin, regulates the passive loss of water to the environment. Furthermore, it is well accepted that drug penetration is influenced by skin hydration, which may be manipulated by the application of moisturizing or oleaginous vehicles. Measurements of transepidermal water loss (TEWL), and of skin hydration using a corneometer, were used to assess the effect of different vehicles on stratum corneum barrier function in vivo in human volunteers. A microemulsion significantly increased skin hydration relative to a reference vehicle based on medium chain triglycerides; in contrast, Transcutol(R) lowered skin hydration. TEWL measurements confirmed these observations. Copyright 2009 S. Karger AG, Basel.

Enhanced Hydrate Nucleation Near the Limit of Stability.

PubMed

Jimenez-Angeles, Felipe; Firoozabadi, Abbas

2015-03-30

Clathrate hydrates are crystalline structures composed of small guest molecules trapped into cages formed by hydrogen-bonded water molecules. In hydrate nucleation, water and the guest molecules may stay in a metastable fluid mixture for a long period. Metastability is broken if the concentration of the guest is above certain limit. We perform molecular dynamics (MD) simulations of supersaturated water-propane solutions close to the limit of stability. We show that hydrate nucleation can be very fast in a very narrow range of composition at moderate temperatures. Propane density fluctuations near the fluid-fluid demixing are coupled with crystallization producing en- hanced nucleation rates. This is the first report of propane-hydrate nucleation by MD simulations. We observe motifs of the crystalline structure II in line with experiments and new hydrate cages not reported in the literature. Our study relates nucleation to the fluid-fluid spinodal decomposition and demonstration that the enhanced nucleation phenomenon is more general than short range attractive interactions as suggested in nucleation of proteins.

Absorbing a Little Water: The Structural, Thermodynamic, and Kinetic Relationship between Pyrogallol and Its Tetarto-Hydrate

PubMed Central

2013-01-01

The anhydrate and the stoichiometric tetarto-hydrate of pyrogallol (0.25 mol water per mol pyrogallol) are both storage stable at ambient conditions, provided that they are phase pure, with the system being at equilibrium at aw (water activity) = 0.15 at 25 °C. Structures have been derived from single crystal and powder X-ray diffraction data for the anhydrate and hydrate, respectively. It is notable that the tetarto-hydrate forms a tetragonal structure with water in channels, a framework that although stabilized by water, is found as a higher energy structure on a computationally generated crystal energy landscape, which has the anhydrate crystal structure as the most stable form. Thus, a combination of slurry experiments, X-ray diffraction, spectroscopy, moisture (de)sorption, and thermo-analytical methods with the computationally generated crystal energy landscape and lattice energy calculations provides a consistent picture of the finely balanced hydration behavior of pyrogallol. In addition, two monotropically related dimethyl sulfoxide monosolvates were found in the accompanying solid form screen. PMID:24027438

Absorbing a Little Water: The Structural, Thermodynamic, and Kinetic Relationship between Pyrogallol and Its Tetarto-Hydrate.

PubMed

Braun, Doris E; Bhardwaj, Rajni M; Arlin, Jean-Baptiste; Florence, Alastair J; Kahlenberg, Volker; Griesser, Ulrich J; Tocher, Derek A; Price, Sarah L

2013-09-04

The anhydrate and the stoichiometric tetarto-hydrate of pyrogallol (0.25 mol water per mol pyrogallol) are both storage stable at ambient conditions, provided that they are phase pure, with the system being at equilibrium at a w (water activity) = 0.15 at 25 °C. Structures have been derived from single crystal and powder X-ray diffraction data for the anhydrate and hydrate, respectively. It is notable that the tetarto-hydrate forms a tetragonal structure with water in channels, a framework that although stabilized by water, is found as a higher energy structure on a computationally generated crystal energy landscape, which has the anhydrate crystal structure as the most stable form. Thus, a combination of slurry experiments, X-ray diffraction, spectroscopy, moisture (de)sorption, and thermo-analytical methods with the computationally generated crystal energy landscape and lattice energy calculations provides a consistent picture of the finely balanced hydration behavior of pyrogallol. In addition, two monotropically related dimethyl sulfoxide monosolvates were found in the accompanying solid form screen.

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.

Sticky ions in biological systems.

PubMed Central

Collins, K D

1995-01-01

Aqueous gel sieving chromatography on Sephadex G-10 of the Group IA cations (Li+, Na+, K+, Rb+, Cs+) plus NH4+ as the Cl- salts, in combination with previous results for the halide anions (F-, Cl-, Br-, I-) as the Na+ salts [Washabaugh, M.W. & Collins, K.D. (1986) J. Biol. Chem. 261, 12477-12485], leads to the following conclusions. (i) The small monovalent ions (Li+, Na+, F-) flow through the gel with water molecules attached, whereas the large monovalent ions (K+, Rb+, Cs+, Cl-, Br-, I-) adsorb to the nonpolar surface of the gel, a process requiring partial dehydration of the ion and implying that these ions bind the immediately adjacent water molecules weakly. (ii) The transition from strong to weak hydration occurs at a radius of about 1.78 A for the monovalent anions, compared with a radius of about 1.06 A for the monovalent cations (using ionic radii), indicating that the anions are more strongly hydrated than the cations for a given charge density. (iii) The anions show larger deviations from ideal behavior (an elution position corresponding to the anhydrous molecular weight) than do the cations and dominate the chromatographic behavior of the neutral salts. These results are interpreted to mean that weakly hydrated ions (chaotropes) are "pushed" onto weakly hydrated surfaces by strong water-water interactions and that the transition from strong ionic hydration to weak ionic hydration occurs where the strength of ion-water interactions approximately equals the strength of water-water interactions in bulk solution. PMID:7539920

Confined Water in Layered Silicates: The Origin of Anomalous Thermal Expansion Behavior in Calcium-Silicate-Hydrates

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

Krishnan, N. M. Anoop; Wang, Bu; Falzone, Gabriel

Water, under conditions of nanoscale confinement, exhibits anomalous dynamics, and enhanced thermal deformations, which may be further enhanced when such water is in contact with hydrophilic surfaces. Such heightened thermal deformations of water could control the volume stability of hydrated materials containing nanoconfined structural water. Understanding and predicting the thermal deformation coefficient (TDC, often referred to as the CTE, coefficient of thermal expansion), which represents volume changes induced in materials under conditions of changing temperature, is of critical importance for hydrated solids including: hydrogels, biological tissues, and calcium silicate hydrates, as changes in their volume can result in stress development,more » and cracking. By pioneering atomistic simulations, we examine the physical origin of thermal expansion in calcium-silicate-hydrates (C–S–H), the binding agent in concrete that is formed by the reaction of cement with water. We report that the TDC of C–S–H shows a sudden increase when the CaO/SiO 2 (molar ratio; abbreviated as Ca/Si) exceeds 1.5. This anomalous behavior arises from a notable increase in the confinement of water contained in the C–S–H’s nanostructure. We identify that confinement is dictated by the topology of the C–S–H’s atomic network. Altogether, the results suggest that thermal deformations of hydrated silicates can be altered by inducing compositional changes, which in turn alter the atomic topology and the resultant volume stability of the solids.« less

Confined Water in Layered Silicates: The Origin of Anomalous Thermal Expansion Behavior in Calcium-Silicate-Hydrates.

PubMed

Krishnan, N M Anoop; Wang, Bu; Falzone, Gabriel; Le Pape, Yann; Neithalath, Narayanan; Pilon, Laurent; Bauchy, Mathieu; Sant, Gaurav

2016-12-28

Water, under conditions of nanoscale confinement, exhibits anomalous dynamics, and enhanced thermal deformations, which may be further enhanced when such water is in contact with hydrophilic surfaces. Such heightened thermal deformations of water could control the volume stability of hydrated materials containing nanoconfined structural water. Understanding and predicting the thermal deformation coefficient (TDC, often referred to as the CTE, coefficient of thermal expansion), which represents volume changes induced in materials under conditions of changing temperature, is of critical importance for hydrated solids including: hydrogels, biological tissues, and calcium silicate hydrates, as changes in their volume can result in stress development, and cracking. By pioneering atomistic simulations, we examine the physical origin of thermal expansion in calcium-silicate-hydrates (C-S-H), the binding agent in concrete that is formed by the reaction of cement with water. We report that the TDC of C-S-H shows a sudden increase when the CaO/SiO 2 (molar ratio; abbreviated as Ca/Si) exceeds 1.5. This anomalous behavior arises from a notable increase in the confinement of water contained in the C-S-H's nanostructure. We identify that confinement is dictated by the topology of the C-S-H's atomic network. Taken together, the results suggest that thermal deformations of hydrated silicates can be altered by inducing compositional changes, which in turn alter the atomic topology and the resultant volume stability of the solids.

Confined Water in Layered Silicates: The Origin of Anomalous Thermal Expansion Behavior in Calcium-Silicate-Hydrates

DOE PAGES

Krishnan, N. M. Anoop; Wang, Bu; Falzone, Gabriel; ...

2016-12-06

Water, under conditions of nanoscale confinement, exhibits anomalous dynamics, and enhanced thermal deformations, which may be further enhanced when such water is in contact with hydrophilic surfaces. Such heightened thermal deformations of water could control the volume stability of hydrated materials containing nanoconfined structural water. Understanding and predicting the thermal deformation coefficient (TDC, often referred to as the CTE, coefficient of thermal expansion), which represents volume changes induced in materials under conditions of changing temperature, is of critical importance for hydrated solids including: hydrogels, biological tissues, and calcium silicate hydrates, as changes in their volume can result in stress development,more » and cracking. By pioneering atomistic simulations, we examine the physical origin of thermal expansion in calcium-silicate-hydrates (C–S–H), the binding agent in concrete that is formed by the reaction of cement with water. We report that the TDC of C–S–H shows a sudden increase when the CaO/SiO 2 (molar ratio; abbreviated as Ca/Si) exceeds 1.5. This anomalous behavior arises from a notable increase in the confinement of water contained in the C–S–H’s nanostructure. We identify that confinement is dictated by the topology of the C–S–H’s atomic network. Altogether, the results suggest that thermal deformations of hydrated silicates can be altered by inducing compositional changes, which in turn alter the atomic topology and the resultant volume stability of the solids.« less

The hydration structure at yttria-stabilized cubic zirconia (110)-water interface with sub-Ångström resolution

DOE PAGES

Hou, Binyang; Kim, Seunghyun; Kim, Taeho; ...

2016-06-15

The interfacial hydration structure of yttria-stabilized cubic zirconia (110) surface in contact with water was determined with ~0.5 Å resolution by high-resolution X-ray reflectivity measurement. The terminal layer shows a reduced electron density compared to the following substrate lattice layers, which indicates there are additional defects generated by metal depletion as well as intrinsic oxygen vacancies, both of which are apparently filled by water species. Above this top surface layer, two additional adsorbed layers are observed forming a characteristic interfacial hydration structure. The first adsorbed layer shows abnormally high density as pure water and likely includes metal species, whereas themore » second layer consists of pure water. The observed interfacial hydration structure seems responsible for local equilibration of the defective surface in water and eventually regulating the long-term degradation processes. As a result, the multitude of water interactions with the zirconia surface results in the complex but highly ordered interfacial structure constituting the reaction front.« less

Gel phase in hydrated calcium dipicolinate

NASA Astrophysics Data System (ADS)

Rajak, Pankaj; Mishra, Ankit; Sheng, Chunyang; Tiwari, Subodh; Krishnamoorthy, Aravind; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

2017-11-01

The mineralization of dipicolinic acid (DPA) molecules in bacterial spore cores with Ca2+ ions to form Ca-DPA is critical to the wet-heat resistance of spores. This resistance to "wet-heat" also depends on the physical properties of water and DPA in the hydrated Ca-DPA-rich protoplasm. Using reactive molecular dynamics simulations, we have determined the phase diagram of hydrated Ca-DPA as a function of temperature and water concentration, which shows the existence of a gel phase along with distinct solid-gel and gel-liquid phase transitions. Simulations reveal monotonically decreasing solid-gel-liquid transition temperatures with increasing hydration, which explains the experimental trend of wet-heat resistance of bacterial spores. Our observation of different phases of water also reconciles previous conflicting experimental findings on the state of water in bacterial spores. Further comparison with an unmineralized hydrated DPA system allows us to quantify the importance of Ca mineralization in decreasing diffusivity and increasing the heat resistance of the spore.

Hydration-reduced lattice thermal conductivity of olivine in Earth's upper mantle.

PubMed

Chang, Yun-Yuan; Hsieh, Wen-Pin; Tan, Eh; Chen, Jiuhua

2017-04-18

Earth's water cycle enables the incorporation of water (hydration) in mantle minerals that can influence the physical properties of the mantle. Lattice thermal conductivity of mantle minerals is critical for controlling the temperature profile and dynamics of the mantle and subducting slabs. However, the effect of hydration on lattice thermal conductivity remains poorly understood and has often been assumed to be negligible. Here we have precisely measured the lattice thermal conductivity of hydrous San Carlos olivine (Mg 0.9 Fe 0.1 ) 2 SiO 4 (Fo90) up to 15 gigapascals using an ultrafast optical pump-probe technique. The thermal conductivity of hydrous Fo90 with ∼7,000 wt ppm water is significantly suppressed at pressures above ∼5 gigapascals, and is approximately 2 times smaller than the nominally anhydrous Fo90 at mantle transition zone pressures, demonstrating the critical influence of hydration on the lattice thermal conductivity of olivine in this region. Modeling the thermal structure of a subducting slab with our results shows that the hydration-reduced thermal conductivity in hydrated oceanic crust further decreases the temperature at the cold, dry center of the subducting slab. Therefore, the olivine-wadsleyite transformation rate in the slab with hydrated oceanic crust is much slower than that with dry oceanic crust after the slab sinks into the transition zone, extending the metastable olivine to a greater depth. The hydration-reduced thermal conductivity could enable hydrous minerals to survive in deeper mantle and enhance water transportation to the transition zone.

Widespread gas hydrate instability on the upper U.S. Beaufort margin

NASA Astrophysics Data System (ADS)

Phrampus, Benjamin J.; Hornbach, Matthew J.; Ruppel, Carolyn D.; Hart, Patrick E.

2014-12-01

The most climate-sensitive methane hydrate deposits occur on upper continental slopes at depths close to the minimum pressure and maximum temperature for gas hydrate stability. At these water depths, small perturbations in intermediate ocean water temperatures can lead to gas hydrate dissociation. The Arctic Ocean has experienced more dramatic warming than lower latitudes, but observational data have not been used to study the interplay between upper slope gas hydrates and warming ocean waters. Here we use (a) legacy seismic data that constrain upper slope gas hydrate distributions on the U.S. Beaufort Sea margin, (b) Alaskan North Slope borehole data and offshore thermal gradients determined from gas hydrate stability zone thickness to infer regional heat flow, and (c) 1088 direct measurements to characterize multidecadal intermediate ocean warming in the U.S. Beaufort Sea. Combining these data with a three-dimensional thermal model shows that the observed gas hydrate stability zone is too deep by 100 to 250 m. The disparity can be partially attributed to several processes, but the most important is the reequilibration (thinning) of gas hydrates in response to significant (~0.5°C at 2σ certainty) warming of intermediate ocean temperatures over 39 years in a depth range that brackets the upper slope extent of the gas hydrate stability zone. Even in the absence of additional ocean warming, 0.44 to 2.2 Gt of methane could be released from reequilibrating gas hydrates into the sediments underlying an area of ~5-7.5 × 103 km2 on the U.S. Beaufort Sea upper slope during the next century.

Hydro-bio-geomechanical properties of hydrate-bearing sediments from Nankai Trough

USGS Publications Warehouse

Santamarina, J.C.; Dai, Shifeng; Terzariol, M.; Jang, Jeonghwan; Waite, William F.; Winters, William J.; Nagao, J.; Yoneda, J.; Konno, Y.; Fujii, T.; Suzuki, K.

2015-01-01

Natural hydrate-bearing sediments from the Nankai Trough, offshore Japan, were studied using the Pressure Core Characterization Tools (PCCTs) to obtain geomechanical, hydrological, electrical, and biological properties under in situ pressure, temperature, and restored effective stress conditions. Measurement results, combined with index-property data and analytical physics-based models, provide unique insight into hydrate-bearing sediments in situ. Tested cores contain some silty-sands, but are predominantly sandy- and clayey-silts. Hydrate saturations Sh range from 0.15 to 0.74, with significant concentrations in the silty-sands. Wave velocity and flexible-wall permeameter measurements on never-depressurized pressure-core sediments suggest hydrates in the coarser-grained zones, the silty-sands where Sh exceeds 0.4, contribute to soil-skeletal stability and are load-bearing. In the sandy- and clayey-silts, where Sh < 0.4, the state of effective stress and stress history are significant factors determining sediment stiffness. Controlled depressurization tests show that hydrate dissociation occurs too quickly to maintain thermodynamic equilibrium, and pressure–temperature conditions track the hydrate stability boundary in pure-water, rather than that in seawater, in spite of both the in situ pore water and the water used to maintain specimen pore pressure prior to dissociation being saline. Hydrate dissociation accompanied with fines migration caused up to 2.4% vertical strain contraction. The first-ever direct shear measurements on never-depressurized pressure-core specimens show hydrate-bearing sediments have higher sediment strength and peak friction angle than post-dissociation sediments, but the residual friction angle remains the same in both cases. Permeability measurements made before and after hydrate dissociation demonstrate that water permeability increases after dissociation, but the gain is limited by the transition from hydrate saturation before dissociation to gas saturation after dissociation. In a proof-of-concept study, sediment microbial communities were successfully extracted and stored under high-pressure, anoxic conditions. Depressurized samples of these extractions were incubated in air, where microbes exhibited temperature-dependent growth rates.

Electrical Conductive Mechanism of Gas Hydrate-Bearing Reservoirs in the Permafrost Region of Qilian Mountain

NASA Astrophysics Data System (ADS)

Peng, C.; Zou, C.; Tang, Y.; Liu, A.; Hu, X.

2017-12-01

In the Qilian Mountain, gas hydrates not only occur in pore spaces of sandstones, but also fill in fractures of mudstones. This leads to the difficulty in identification and evaluation of gas hydrate reservoir from resistivity and velocity logs. Understanding electrical conductive mechanism is the basis for log interpretation. However, the research is insufficient in this area. We have collected well logs from 30 wells in this area. Well logs and rock samples from DK-9, DK-11 and DK-12 wells were used in this study. The experiments including SEM, thin section, NMR, XRD, synthesis of gas hydrate in consolidated rock cores under low temperature and measurement of their resistivity and others were performed for understanding the effects of pore structure, rock composition, temperature and gas hydrate on conductivity. The results show that the porosity of reservoir of pore filling type is less than 10% and its clay mineral content is high. As good conductive passages, fractures can reduce resistivity of water-saturated rock. If fractures in the mudstone are filled by calcite, resistivity increases significantly. The resistivity of water-saturated rock at 2°C is twice of that at 18°C. The gas hydrate formation process in the sandstone was studied by resistivity recorded in real time. In the early stage of gas hydrate formation, the increase of residual water salinity may lead to the decrease of resistivity. In the late stage of gas hydrate formation, the continuity decrease of water leads to continuity increase of resistivity. In summary, fractures, rock composition, temperature and gas hydrate are important factors influencing resistivity of formation. This study is helpful for more accurate evaluation of gas hydrate from resistivity log. Acknowledgment: We acknowledge the financial support of the National Special Program for Gas Hydrate Exploration and Test-production (GZH201400302).

Evaluation of Gas Hydrate at Alaminos Canyon 810, Northern Gulf of Mexico Slope

NASA Astrophysics Data System (ADS)

Yang, C.; Cook, A.; Sawyer, D.; Hillman, J. I. T.

2016-12-01

We characterize the gas hydrate reservoir in Alaminos Canyon Block 810 (AC810) on the northern Gulf of Mexico slope, approximately 400 km southeast of Houston, Texas, USA. Three-dimensional seismic data shows a bottom-simulating-reflection (BSR), over 30 km2, which suggests that a significant gas hydrate accumulation may occur at AC810. Furthermore, logging while drilling (LWD) data acquired from a Statoil well located that penetrated the BSR near the crest of the regional anticline indicates two possible gas hydrate units (Hydrate Unit A and Hydrate Unit B). LWD data in this interval are limited to gamma ray and resistivity only. Resistivity curve separations are observed in Hydrate Unit A (131 to 253 mbsf) suggesting hydrate-filled fractures in marine mud. A spiky high resistivity response in Hydrate Unit B (308 to 354 mbsf) could either be a marine mud or a sand-prone interval. The abrupt decrease (from 7 to 1 Ωm) in resistivity logs at 357 mbsf generally corresponds with the interpreted base of hydrate stability, as the BSR is observed near 350 mbsf on the seismic data. To further investigate the formation characteristics, we generate synthetic traces using general velocity and density trends for marine sediments to match the seismic trace extracted at the Statoil well. We consider models with 1) free gas and 2) water only below the base of hydrate stability. In our free gas-below models, we find the velocity of Hydrate Unit A and Hydrate Unit B is generally low and does not deviate significantly from the general velocity trends, suggesting that gas hydrate is present in a marine mud. In the water-below model, the compressional velocity of Hydrate Unit B ranges from 2450 m/s to 3150 m/s. This velocity is similar to the velocity of high hydrate saturation in sand; typically greater than 2500 m/s. This may indicate that Hydrate Unit B is sand with high hydrate saturation; however, to achieve a suitable match between the water-below synthetic seismogram and the trace, a high velocity layer was required below the base of hydrate stability, which is not indicated by the well logs. Our models indicate that at AC810, Hydrate Unit A probably contains hydrate filled fractures in a marine mud. For Hydrate Unit B, our models suggest hydrate may occur in a sand-prone interval, but is more likely to be gas hydrate filled fractures in marine mud.

Thermogenic methane injection via bubble transport into the upper Arctic Ocean from the hydrate-charged Vestnesa Ridge, Svalbard

NASA Astrophysics Data System (ADS)

Smith, Andrew J.; Mienert, Jürgen; Bünz, Stefan; Greinert, Jens

2014-05-01

We use new gas-hydrate geochemistry analyses, echosounder data, and three-dimensional P-Cable seismic data to study a gas-hydrate and free-gas system in 1200 m water depth at the Vestnesa Ridge offshore NW Svalbard. Geochemical measurements of gas from hydrates collected at the ridge revealed a thermogenic source. The presence of thermogenic gas and temperatures of ˜3.3°C result in a shallow top of the hydrate stability zone (THSZ) at ˜340 m below sea level (mbsl). Therefore, hydrate-skinned gas bubbles, which inhibit gas-dissolution processes, are thermodynamically stable to this shallow water depth. This was confirmed by hydroacoustic observations of flares in 2010 and 2012 reaching water depths between 210 and 480 mbsl. At the seafloor, bubbles are released from acoustically transparent zones in the seismic data, which we interpret as regions where free gas is migrating through the hydrate stability zone (HSZ). These intrusions result in vertical variations in the base of the HSZ (BHSZ) of up to ˜150 m, possibly making the shallow hydrate reservoir more susceptible to warming. Such Arctic gas-hydrate and free-gas systems are important because of their potential role in climate change and in fueling marine life, but remain largely understudied due to limited data coverage in seasonally ice-covered Arctic environments.

Gender- and hydration- associated differences in the physiological response to spinning.

PubMed

Ramos-Jiménez, Arnulfo; Hernández-Torres, Rosa Patricia; Wall-Medrano, Abraham; Torres-Durán, Patricia Victoria; Juárez-Oropeza, Marco Antonio; Viloria, María; Villalobos-Molina, Rafael

2014-03-01

There is scarce and inconsistent information about gender-related differences in the hydration of sports persons, as well as about the effects of hydration on performance, especially during indoor sports. To determine the physiological differences between genders during in indoor physical exercise, with and without hydration. 21 spinning sportspeople (12 men and 9 women) participated in three controlled, randomly assigned and non-sequential hydration protocols, including no fluid intake and hydration with plain water or a sports drink (volume adjusted to each individual every 15 min), during 90 min of spinning exercise. The response variables included body mass, body temperature, heart rate and blood pressure. During exercise without hydration, men and women lost ~2% of body mass, and showed higher body temperature (~0.2°C), blood pressure (~4 mmHg) and heart rate (~7 beats/min) compared to exercises with hydration. Body temperature and blood pressure were higher for men than for women during exercise without hydration, differences not observed during exercise with hydration. Between 42-99% of variance in body temperature, blood pressure and heart rate could be explained by the physical characteristics of subjects and the work done. During exercise with hydration (either with water or sport drink), the physiological response was similar for both genders. Exercise without hydration produced physical stress, which could be prevented with either of the fluids (plain water was sufficient). Gender differences in the physiological response to spinning (body temperature, mean blood pressure and heart rate) can be explained in part by the distinct physical characteristics of each individual. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Seismic reflections identify finite differences in gas hydrate resources

USGS Publications Warehouse

Dillon, William P.; Max, M.

1999-01-01

Gas hydrate is a gas-bearing, ice-like crystalline solid. The substance's build ing blocks consist of a gas molecule (generally methane) sur-rounded by a cage of water molecules. The total amount of methane in hydrate in the world is immense - the most recent speculative estimate centers on values of 21x1015 cu meters. Thus, it may represent a future energy resource. This estimate was presented by Keith Kvenvolden at the International Symposium on Methane Hydrates, Resources in the Near Future, sponsor ed by Japanese National Oil Company (Tokyo, October, 1998).But, as with any natural resource, there is a need to find naturally occurring concentrations in order to effectively extract gas. We need to answer four basic questions:Do methane hydrate concentrations suitable for methane extraction exist?How can we recognize these concentrations?Where are concentrations located?What processes control methane hydrate concentrations?Gas hydrate occurs naturally at the pressure/ temperature/chemical conditions that are present within ocean floor sediments at water depths greater than about 500 meters. The gas hydrate stability zone (GHSZ) extends from the sea bottom downward to a depth where the natural increase in temperature causes the hydrate to melt (dissociate), even though the downward pressure increase is working to increase gas hydrate stability.Thus, the base of the GHSZ tends to parallel the seafloor at any given water depth (pressure), because the sub-seafloor isotherms (depths of constant temperature) generally parallel the seafloor. The layer at which gas hydrate is stable commonly extends from the sea floor to several hundred meters below it. The gas in most gas hydrates is methane, generated by bacteria in the sediments. In some cases, it can be higher carbon-number, thermogenic hydrocarbon gases that rise from greater depths.

The Dependence of Water Permeability in Quartz Sand on Gas Hydrate Saturation in the Pore Space

NASA Astrophysics Data System (ADS)

Kossel, E.; Deusner, C.; Bigalke, N.; Haeckel, M.

2018-02-01

Transport of fluids in gas hydrate bearing sediments is largely defined by the reduction of the permeability due to gas hydrate crystals in the pore space. Although the exact knowledge of the permeability behavior as a function of gas hydrate saturation is of crucial importance, state-of-the-art simulation codes for gas production scenarios use theoretically derived permeability equations that are hardly backed by experimental data. The reason for the insufficient validation of the model equations is the difficulty to create gas hydrate bearing sediments that have undergone formation mechanisms equivalent to the natural process and that have well-defined gas hydrate saturations. We formed methane hydrates in quartz sand from a methane-saturated aqueous solution and used magnetic resonance imaging to obtain time-resolved, three-dimensional maps of the gas hydrate saturation distribution. These maps were fed into 3-D finite element method simulations of the water flow. In our simulations, we tested the five most well-known permeability equations. All of the suitable permeability equations include the term (1-SH)n, where SH is the gas hydrate saturation and n is a parameter that needs to be constrained. The most basic equation describing the permeability behavior of water flow through gas hydrate bearing sand is k = k0 (1-SH)n. In our experiments, n was determined to be 11.4 (±0.3). Results from this study can be directly applied to bulk flow analysis under the assumption of homogeneous gas hydrate saturation and can be further used to derive effective permeability models for heterogeneous gas hydrate distributions at different scales.

Origin of 1/f noise in hydration dynamics on lipid membrane surfaces

PubMed Central

Yamamoto, Eiji; Akimoto, Takuma; Yasui, Masato; Yasuoka, Kenji

2015-01-01

Water molecules on lipid membrane surfaces are known to contribute to membrane stability by connecting lipid molecules and acting as a water bridge. Although water structures and diffusivities near the membrane surfaces have been extensively studied, hydration dynamics on the surfaces has remained an open question. Here we investigate residence time statistics of water molecules on the surface of lipid membranes using all-atom molecular dynamics simulations. We show that hydration dynamics on the lipid membranes exhibits 1/f noise. Constructing a dichotomous process for the hydration dynamics, we find that residence times in each state follow a power-law with exponential cutoff and that the process can be regarded as a correlated renewal process where interoccurrence times are correlated. The results imply that the origin of the 1/f noise in hydration dynamics on the membrane surfaces is a combination of a power-law distribution with cutoff of interoccurrence times of switching events and a long-term correlation between the interoccurrence times. These results suggest that the 1/f noise attributed to the correlated renewal process may contribute to the stability of the hydration layers and lipid membranes. PMID:25743377

Gas hydrate dissociation off Svalbard induced by isostatic rebound rather than global warming.

PubMed

Wallmann, Klaus; Riedel, M; Hong, W L; Patton, H; Hubbard, A; Pape, T; Hsu, C W; Schmidt, C; Johnson, J E; Torres, M E; Andreassen, K; Berndt, C; Bohrmann, G

2018-01-08

Methane seepage from the upper continental slopes of Western Svalbard has previously been attributed to gas hydrate dissociation induced by anthropogenic warming of ambient bottom waters. Here we show that sediment cores drilled off Prins Karls Foreland contain freshwater from dissociating hydrates. However, our modeling indicates that the observed pore water freshening began around 8 ka BP when the rate of isostatic uplift outpaced eustatic sea-level rise. The resultant local shallowing and lowering of hydrostatic pressure forced gas hydrate dissociation and dissolved chloride depletions consistent with our geochemical analysis. Hence, we propose that hydrate dissociation was triggered by postglacial isostatic rebound rather than anthropogenic warming. Furthermore, we show that methane fluxes from dissociating hydrates were considerably smaller than present methane seepage rates implying that gas hydrates were not a major source of methane to the oceans, but rather acted as a dynamic seal, regulating methane release from deep geological reservoirs.

Rapid gas hydrate formation process

DOEpatents

Brown, Thomas D.; Taylor, Charles E.; Unione, Alfred J.

2013-01-15

The disclosure provides a method and apparatus for forming gas hydrates from a two-phase mixture of water and a hydrate forming gas. The two-phase mixture is created in a mixing zone which may be wholly included within the body of a spray nozzle. The two-phase mixture is subsequently sprayed into a reaction zone, where the reaction zone is under pressure and temperature conditions suitable for formation of the gas hydrate. The reaction zone pressure is less than the mixing zone pressure so that expansion of the hydrate-forming gas in the mixture provides a degree of cooling by the Joule-Thompson effect and provides more intimate mixing between the water and the hydrate-forming gas. The result of the process is the formation of gas hydrates continuously and with a greatly reduced induction time. An apparatus for conduct of the method is further provided.

The Relative Rates of Secondary Hydration in Basalt and Rhyolite, and the use of δD as a Paleoclimate Indicator: Implications for Paleoenvironmental and Volcanic Degassing Studies

NASA Astrophysics Data System (ADS)

Seligman, A. N.; Bindeman, I. N.

2014-12-01

The δD-H2O correlation is important for volcanic degassing and secondary hydration trends. We utilize the caibration of the TC/EA - MAT 253 continuous flow system, which permits us to analyze wt.% H2O and its δD extracted from 1-8 mg of glass with as little as 0.1 wt% H2O. Tephra that has been secondarily hydrated with meteoric water is widely used as a paleoenvironmental tool, but the rate of secondary hydration, the relative amounts of primary magmatic (degassed) and secondary meteoric water, and the retention of primary and secondary δD values are not well understood. To quantify these processes, we use a natural experiment involving dated Holocene tepha in Kamchatka and Oregon. Our research illustrates the drastic difference in hydration rates between silicic (hydrated after ~1.5 ka) and mafic tephra, which is not hydrated in the Holocene (similar to results for submarine volcanic glasses), and andesitic tephra with intermediate degrees of hydration. The 0.05-7.3 ka basaltic scoria from Klyuchevskoy volcano retains ≤0.45 wt.% primary magmatic H2O, with δD values from -99 to -121 ‰. Four other 0.05-7.6 ka basaltic tephra units from Kamchatka with <57 wt.% SiO2 all have wt.% H2O 0.21-0.84 and δD values ranging from -90 - -145 ‰. The 1.0-7.6 ka andesitic tephra have slightly higher water contents (0.9-3.0 %) and slightly lower δD values (-113 - -146 ‰). Seven 0.3-7.9 ka silicic samples with SiO2 >65 wt.% have higher (1.5 -3.4) wt.% H2O and δD values between -115 - -160 ‰. We interpret the lower δD values and higher water contents (opposite of the magmatic degassing trend) to be a characteristic of secondary hydration in regions of higher latitude such as Kamchatka and Oregon. We are also investigating 7.7 ka Mt. Mazama tephra in Oregon that are known to be fully hydrated and cover nearly 5000 km2 northeast of Crater Lake and range in elevation from ~1.3-1.9 km to understand the δD and δ18O details of the hydrated water's correspondence with local Holocene meteoric waters. In the future, we plan to use a combination of δD in mid-high latitude precipitation to delineate δD-H2O hydration trends to better understand the distinction between primary magmatic and secondary meteoric water in volcanic glass, and the exchange of hydrogen isotopes between OH- and H2Omol sites in volcanic glass.

Coarse-grained model of water diffusion and proton conductivity in hydrated polyelectrolyte membrane

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

Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V., E-mail: aneimark@rutgers.edu

2016-01-07

Using dissipative particle dynamics (DPD), we simulate nanoscale segregation, water diffusion, and proton conductivity in hydrated sulfonated polystyrene (sPS). We employ a novel model [Lee et al. J. Chem. Theory Comput. 11(9), 4395-4403 (2015)] that incorporates protonation/deprotonation equilibria into DPD simulations. The polymer and water are modeled by coarse-grained beads interacting via short-range soft repulsion and smeared charge electrostatic potentials. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with the base beads representing water and sulfonate anions. Morse bond formation and breakup artificially mimics the Grotthuss mechanism of proton hopping between the bases. Themore » DPD model is parameterized by matching the proton mobility in bulk water, dissociation constant of benzenesulfonic acid, and liquid-liquid equilibrium of water-ethylbenzene solutions. The DPD simulations semi-quantitatively predict nanoscale segregation in the hydrated sPS into hydrophobic and hydrophilic subphases, water self-diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from isolated water clusters to a 3D network. The analysis of hydrophilic subphase connectivity and water diffusion demonstrates the importance of the dynamic percolation effect of formation and breakup of temporary junctions between water clusters. The proposed DPD model qualitatively predicts the ratio of proton to water self-diffusion and its dependence on the hydration level that is in reasonable agreement with experiments.« less

Concentration of Natural Gas Hydrate Beneath the Permafrost Zone: Implications for Geochemical and Hydrologic Investigations

NASA Astrophysics Data System (ADS)

Uchida, T.; Waseda, A.; Namikawa, T.

2004-12-01

Gas hydrates are ice-like solids made of water molecules containing various gas molecules. The geological evaluations have suggested worldwide methane contents of gas hydrate beneath deep sea floors as well as permafrost-related zones to about twice the total reserves of conventional and unconventional hydrocarbon. Scientific and economic interests are increasing in gas hydrate as a new energy resource and a potential greenhouse gas. In 1998 and 2002 Mallik wells were drilled in the Canadian Arctic that clarified the characteristics of gas hydrate-dominant layers at depths from 890 to 1110 m beneath the permafrost zone. Continuous downhole well log data, anomalies of chloride contents in pore waters, core temperature depression as well as visible gas hydrates have confirmed the highly saturated pore-space hydrate as intergranular pore filling within sandy layers, whose saturations are higher than 70% in pore volume. Muddy sediments scarcely contain gas hydrate. The Nankai Trough runs along the Japanese Island, where forearc basins and accretionary prisms developed extensively and BSRs (bottom simulating reflectors) have been recognized widely. The METI Nankai Trough wells in 2000 also revealed the presence of pore-space hydrate filling intergranular pore of sandy layers. It is remarked that there are many similar features in appearance and characteristics between the Mallik and Nankai Trough areas with observations of well-interconnected and highly saturated pore-space hydrate. It is necessary for evaluating subsurface fluid flow behaviors to know both porosity and permeability of gas hydrate-bearing sandy sediments, and measurements of water permeability for them indicate that highly saturated sands may have permeability of a few millidarcies. Subsequent analyses in sedimentology and geochemistry performed on gas hydrate-bearing sands revealed important geologic and sedimentologic controls on the formation and concentration of gas hydrate. It is suggested that the distribution of a porous and coarser-grained sandy sediments is one of the most important factors to control the occurrence of gas hydrates, as well as physicochemical conditions.

New hydrate formation methods in a liquid-gas medium

NASA Astrophysics Data System (ADS)

Chernov, A. A.; Pil'Nik, A. A.; Elistratov, D. S.; Mezentsev, I. V.; Meleshkin, A. V.; Bartashevich, M. V.; Vlasenko, M. G.

2017-01-01

Conceptually new methods of hydrate formation are proposed. The first one is based on the shock wave impact on a water-bubble medium. It is shown that the hydrate formation rate in this process is typically very high. A gas hydrate of carbon dioxide was produced. The process was experimentally studied using various initial conditions, as well as different external action magnitudes. The obtained experimental data are in good agreement with the proposed model. Other methods are based on the process of boiling liquefied gas in an enclosed volume of water (explosive boiling of a hydrating agent and the organization of cyclic boiling-condensation process). The key features of the methods are the high hydrate formation rate combined with a comparatively low power consumption leading to a great expected efficiency of the technologies based on them. The set of experiments was carried out. Gas hydrates of refrigerant R134a, carbon dioxide and propane were produced. The investigation of decomposition of a generated gas hydrate sample was made. The criteria of intensification of the hydrate formation process are formulated.

New hydrate formation methods in a liquid-gas medium.

PubMed

Chernov, A A; Pil'nik, A A; Elistratov, D S; Mezentsev, I V; Meleshkin, A V; Bartashevich, M V; Vlasenko, M G

2017-01-18

Conceptually new methods of hydrate formation are proposed. The first one is based on the shock wave impact on a water-bubble medium. It is shown that the hydrate formation rate in this process is typically very high. A gas hydrate of carbon dioxide was produced. The process was experimentally studied using various initial conditions, as well as different external action magnitudes. The obtained experimental data are in good agreement with the proposed model. Other methods are based on the process of boiling liquefied gas in an enclosed volume of water (explosive boiling of a hydrating agent and the organization of cyclic boiling-condensation process). The key features of the methods are the high hydrate formation rate combined with a comparatively low power consumption leading to a great expected efficiency of the technologies based on them. The set of experiments was carried out. Gas hydrates of refrigerant R134a, carbon dioxide and propane were produced. The investigation of decomposition of a generated gas hydrate sample was made. The criteria of intensification of the hydrate formation process are formulated.

New hydrate formation methods in a liquid-gas medium

PubMed Central

Chernov, A. A.; Pil’nik, A. A.; Elistratov, D. S.; Mezentsev, I. V.; Meleshkin, A. V.; Bartashevich, M. V.; Vlasenko, M. G.

2017-01-01

Conceptually new methods of hydrate formation are proposed. The first one is based on the shock wave impact on a water-bubble medium. It is shown that the hydrate formation rate in this process is typically very high. A gas hydrate of carbon dioxide was produced. The process was experimentally studied using various initial conditions, as well as different external action magnitudes. The obtained experimental data are in good agreement with the proposed model. Other methods are based on the process of boiling liquefied gas in an enclosed volume of water (explosive boiling of a hydrating agent and the organization of cyclic boiling-condensation process). The key features of the methods are the high hydrate formation rate combined with a comparatively low power consumption leading to a great expected efficiency of the technologies based on them. The set of experiments was carried out. Gas hydrates of refrigerant R134a, carbon dioxide and propane were produced. The investigation of decomposition of a generated gas hydrate sample was made. The criteria of intensification of the hydrate formation process are formulated. PMID:28098194

Constraints of gas venting activity for the interstitial water geochemistry at the shallow gas hydrate site, eastern margin of the Japan Sea; results from high resolution time-series fluid sampling by OsmoSampler

NASA Astrophysics Data System (ADS)

Owari, S.; Tomaru, H.; Matsumoto, R.

2016-12-01

We have conducted ROV researches in the eastern margin of the Japan Sea where active gas venting and outcropping of gas hydrates were observed near the seafloor and have found the strength and location of venting had changed within a few days. These observations indicate the seafloor environments with the shallow gas hydrate system could have changed for short period compared to a geological time scale. We have applied a long-term osmotic fluid sampling system "OsmoSampler" on the active gas hydrate system for one year in order to document how the gas venting and gas hydrate activity have changed the geochemical environments near the seafloor. All the major ion concentrations in the interstitial water show synchronous increase and decrease repeatedly in three to five days, reflecting the incorporation and release of fresh water in gas hydrates in response to the gas concentration change near the sampling site. Dissolved methane concentration increases rapidly and excessively (over several mM) in the first 40 days corresponding to the active gas venting. The increases of methane concentration are often associated with high ion concentration during high water pressure period, indicating excess gas release from shallow gas pockets. Contrarily, enhanced gas hydrate growth may plug the fluid-gas paths in shallow sediment, reducing gas hydrate formation due to the decrease of methane flux. This study was conducted under the commission from AIST as a part of the methane hydrate research project funded by METI (the Ministry of Economy, Trade and Industry, Japan).

Hydration of dimethyldodecylamine-N-oxide: enthalpy and entropy driven processes.

PubMed

Kocherbitov, Vitaly; Söderman, Olle

2006-07-13

Dimethyldodecylamine-N-oxide (DDAO) has only one polar atom that is able to interact with water. Still, this surfactant shows very hydrophilic properties: in mixtures with water, it forms normal liquid crystalline phases and micelles. Moreover, there is data in the literature indicating that the hydration of this surfactant is driven by enthalpy while other studies show that hydration of surfactants and lipids typically is driven by entropy. Sorption calorimetry allows resolving enthalpic and entropic contributions to the free energy of hydration at constant temperature and thus directly determines the driving forces of hydration. The results of the present sorption calorimetric study show that the hydration of liquid crystalline phases of DDAO is driven by entropy, except for the hydration of the liquid crystalline lamellar phase which is co-driven by enthalpy. The exothermic heat effect of the hydration of the lamellar phase arises from formation of strong hydrogen bonds between DDAO and water. Another issue is the driving forces of the phase transitions caused by the hydration. The sorption calorimetric results show that the transitions from the lamellar to cubic and from the cubic to the hexagonal phase are driven by enthalpy. Transitions from solid phases to the liquid crystalline lamellar phase are entropically driven, while the formation of the monohydrate from the dry surfactant is driven by enthalpy. The driving forces of the transition from the hexagonal phase to the isotropic solution are close to zero. These sorption calorimetric results are in good agreement with the analysis of the binary phase diagram based on the van der Waals differential equation. The phase diagram of the DDAO-water system determined using DSC and sorption calorimetry is presented.

Water binding in legume seeds

NASA Technical Reports Server (NTRS)

Vertucci, C. W.; Leopold, A. C.

1987-01-01

The physical status of water in seeds has a pivotal role in determining the physiological reactions that can take place in the dry state. Using water sorption isotherms from cotyledon and axis tissue of five leguminous seeds, the strength of water binding and the numbers of binding sites have been estimated using van't Hoff analyses and the D'Arcy/Watt equation. These parameters of water sorption are calculated for each of the three regions of water binding and for a range of temperatures. Water sorption characteristics are reflective of the chemical composition of the biological materials as well as the temperature at which hydration takes place. Changes in the sorption characteristics with temperature and hydration level may suggest hydration-induced structural changes in cellular components.

Characterization of water in hydrated Bombyx mori silk fibroin fiber and films by 2H NMR relaxation and 13C solid state NMR.

PubMed

Asakura, Tetsuo; Isobe, Kotaro; Kametani, Shunsuke; Ukpebor, Obehi T; Silverstein, Moshe C; Boutis, Gregory S

2017-03-01

The mechanical properties of Bombyx mori silk fibroin (SF), such as elasticity and tensile strength, change remarkably upon hydration. However, the microscopic interaction with water is not currently well understood on a molecular level. In this work, the dynamics of water molecules interacting with SF was studied by 2 H solution NMR relaxation and exchange measurements. Additionally, the conformations of hydrated [3- 13 C]Ala-, [3- 13 C]Ser-, and [3- 13 C]Tyr-SF fibers and films were investigated by 13 C DD/MAS NMR. Using an inverse Laplace transform algorithm, we were able to identify four distinct components in the relaxation times for water in SF fiber. Namely, A: bulk water outside the fiber, B: water molecules trapped weakly on the surface of the fiber, C: bound water molecules located in the inner surface of the fiber, and D: bound water molecules located in the inner part of the fiber were distinguishable. In addition, four components were also observed for water in the SF film immersed in methanol for 30s, while only two components for the film immersed in methanol for 24h. The effects of hydration on the conformation of Ser and Tyr residues in the site-specific crystalline and non-crystalline domains of 13 C selectively labeled SF, respectively, could be determined independently. Our measurements provide new insight relating the characteristics of water and the hydration structure of silk, which are relevant in light of current interest in the design of novel silk-based biomaterials. The mechanical properties of Bombyx mori silk fibroin (SF) change remarkably upon hydration. However, the microscopic interaction between SF and water is not currently well understood on a molecular level. We were able to identify four distinct components in the relaxation times for water in SF fiber by 2 H solution NMR relaxation and exchange measurements. In addition, the effects of hydration on the conformation of Ser and Tyr residues in the site-specific crystalline and non-crystalline domains of 13 C selectively labeled SF, respectively, could be determined independently. Thus, our measurements provide new insight relating the characteristics of water and the hydration structure of silk, which are relevant in light of current interest in the design of novel silk-based biomaterials. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Hydrogen-Bonding System in Barium Nitroprusside 6.5-Hydrate

NASA Astrophysics Data System (ADS)

Navaza, A.; Chevrier, G.; Guida, J. A.

1995-01-01

The hydrogen-bond system in barium nitroprusside 6.5-hydrate, [Ba 2(H 2O) 10][Fe(CN) 5NOl 23H 2O], has been determined by neutron diffraction on monocrystals. Results show the compound to be orthorhombic, space group Cmc2 1 (36), a = 16.008(43), b = 11.550(3), c = 16.648(5) Å, V = 3078(3) Å 3, Z = 4. Refinement of the structure, using 973 observed structure factors, converged to the final RW factor of 0.058. The 2 independent barium atoms, separated 4.60 Å, share a plane of three water molecules forming dimeric tetravalent units. The nitroprusside anions deviate from the C4r ideal symmetry, but this deviation is less than that observed in other nitroprussides. The 10 crystallographically independent water molecules have been classified according to their coordination. Analysis of the H-bond strength, together with a comparison of the packing of the two known barium nitroprusside hydrates (3-hydrate and 6.5-hydrate), suggests that the water molecules labeled as W(1), W(7), W(8), and W(9) could be lost during the partial dehydration of 6.5-hydrate into 3-hydrate.

Clathrate hydrates in the solar system

NASA Technical Reports Server (NTRS)

Miller, S. L.

1985-01-01

Clathrate hydrates are crystalline compounds in which an expanded ice lattice forms cages that contain gas molecules. There are two principal hydrate structures. Structure I, with a 12 A cubic unit cell, contains 46 water molecules and 8 cages of two types, giving an ideal formula (for CH4) of CH4.5.75H2O. The actual formula contains somewhat more water as the cages are not completely filled. Other examples that form Structure I hydrates are C2H6, C2H4, C2H2, CO2, SO2, OCS, Xe, H2S. Structure II, with a 17 A cubic unit cell, contains 136 water molecules, and 8 large and 16 small cages. The ideal formula for CHCl3 is CHCL3.17H2O. Other examples of Structure II hydrates include C3H8, C2H5Cl, acetone, and tetrahydrofuran. Small molecules such as Ar, Kr and probably N2 and O2 also form a Structure II hydrate. The small molecules occupy both the large and small cages, giving an ideal formula of Ar.5.67H2O. The conditions of pressure and temperature for hydrate formation are discussed.

Numerical simulations of CO2 -assisted gas production from hydrate reservoirs

NASA Astrophysics Data System (ADS)

Sridhara, P.; Anderson, B. J.; Myshakin, E. M.

2015-12-01

A series of experimental studies over the last decade have reviewed the feasibility of using CO2 or CO2+N2 gas mixtures to recover CH4 gas from hydrates deposits. That technique would serve the dual purpose of CO2 sequestration and production of CH4 while maintaining the geo-mechanical stability of the reservoir. In order to analyze CH4 production process by means of CO2 or CO2+N2 injection into gas hydrate reservoirs, a new simulation tool, Mix3HydrateResSim (Mix3HRS)[1], was previously developed to account for the complex thermodynamics of multi-component hydrate phase and to predict the process of CH4 substitution by CO2 (and N2) in the hydrate lattice. In this work, Mix3HRS is used to simulate the CO2 injection into a Class 2 hydrate accumulation characterized by a mobile aqueous phase underneath a hydrate bearing sediment. That type of hydrate reservoir is broadly confirmed in permafrost and along seashore. The production technique implies a two-stage approach using a two-well design, one for an injector and one for a producer. First, the CO2 is injected into the mobile aqueous phase to convert it into immobile CO2 hydrate and to initiate CH4 release from gas hydrate across the hydrate-water boundary (generally designating the onset of a hydrate stability zone). Second, CH4 hydrate decomposition is induced by the depressurization method at a producer to estimate gas production potential over 30 years. The conversion of the free water phase into the CO2 hydrate significantly reduces competitive water production in the second stage, thereby improving the methane gas production. A base case using only the depressurization stage is conducted to compare with enhanced gas production predicted by the CO2-assisted technique. The approach also offers a possibility to permanently store carbon dioxide in the underground formation to greater extent comparing to a direct injection of CO2 into gas hydrate sediment. Numerical models are based on the hydrate formations at the Prudhoe Bay L-Pad region on the Alaska North Slope. References [1] N.Garapati, "Reservoir Simulation for Production of CH4 from Gas Hydrate Reservoirs Using CO2/CO2+N2 by HydrateResSim", Ph.D. thesis, West Virginia University, 2013.

Freshwater lake to salt-water sea causing widespread hydrate dissociation in the Black Sea.

PubMed

Riboulot, Vincent; Ker, Stephan; Sultan, Nabil; Thomas, Yannick; Marsset, Bruno; Scalabrin, Carla; Ruffine, Livio; Boulart, Cédric; Ion, Gabriel

2018-01-09

Gas hydrates, a solid established by water and gas molecules, are widespread along the continental margins of the world. Their dynamics have mainly been regarded through the lens of temperature-pressure conditions. A fluctuation in one of these parameters may cause destabilization of gas hydrate-bearing sediments below the seafloor with implications in ocean acidification and eventually in global warming. Here we show throughout an example of the Black Sea, the world's most isolated sea, evidence that extensive gas hydrate dissociation may occur in the future due to recent salinity changes of the sea water. Recent and forthcoming salt diffusion within the sediment will destabilize gas hydrates by reducing the extension and thickness of their thermodynamic stability zone in a region covering at least 2800 square kilometers which focus seepages at the observed sites. We suspect this process to occur in other world regions (e.g., Caspian Sea, Sea of Marmara).

Diamond-anvil cell observations of a new methane hydrate phase in the 100-MPa pressure range

USGS Publications Warehouse

Chou, I.-Ming; Sharma, A.; Burruss, R.C.; Hemley, R.J.; Goncharov, A.F.; Stern, L.A.; Kirby, S.H.

2001-01-01

A new high-pressure phase of methane hydrate has been identified based on its high optical relief, distinct pressure-temperature phase relations, and Raman spectra. In-situ optical observations were made in a hydrothermal diamond-anvil cell at temperatures between -40?? and 60 ??C and at pressures up to 900 MPa. Two new invariant points were located at -8.7 ??C and 99 MPa for the assemblage consisting of the new phase, structure I methane hydrate, ice Ih, and water, and at 35.3 ??C and 137 MPa for the new phase-structure I methane hydrate-water-methane vapor. Existence of the new phase is critical for understanding the phase relations among the hydrates at low to moderate pressures, and may also have important implications for understanding the hydrogen bonding in H2O and the behavior of water in the planetary bodies, such as Europa, of the outer solar system.

Hydration states of AFm cement phases

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

Baquerizo, Luis G., E-mail: luis.baquerizoibarra@holcim.com; Matschei, Thomas; Scrivener, Karen L.

2015-07-15

The AFm phase, one of the main products formed during the hydration of Portland and calcium aluminate cement based systems, belongs to the layered double hydrate (LDH) family having positively charged layers and water plus charge-balancing anions in the interlayer. It is known that these phases present different hydration states (i.e. varying water content) depending on the relative humidity (RH), temperature and anion type, which might be linked to volume changes (swelling and shrinkage). Unfortunately the stability conditions of these phases are insufficiently reported. This paper presents novel experimental results on the different hydration states of the most important AFmmore » phases: monocarboaluminate, hemicarboaluminate, strätlingite, hydroxy-AFm and monosulfoaluminate, and the thermodynamic properties associated with changes in their water content during absorption/desorption. This data opens the possibility to model the response of cementitious systems during drying and wetting and to engineer systems more resistant to harsh external conditions.« less

Water Sorption in Electron-Beam Evaporated SiO2 on QCM Crystals and Its Influence on Polymer Thin Film Hydration Measurements.

PubMed

Kushner, Douglas I; Hickner, Michael A

2017-05-30

Spectroscopic ellipsometry (SE) and quartz crystal microbalance (QCM) measurements are two critical characterization techniques routinely employed for hydration studies of polymer thin films. Water uptake by thin polymer films is an important area of study to investigate antifouling surfaces, to probe the swelling of thin water-containing ionomer films, and to conduct fundamental studies of polymer brush hydration and swelling. SiO 2 -coated QCM crystals, employed as substrates in many of these hydration studies, show porosity in the thin electron-beam (e-beam) evaporated SiO 2 layer. The water sorption into this porous SiO 2 layer requires correction of the optical and mass characterization of the hydrated polymer due to changes in the SiO 2 layer as it sorbs water. This correction is especially important when experiments on SiO 2 -coated QCM crystals are compared to measurements on Si wafers with dense native SiO 2 layers. Water adsorption filling void space during hydration in ∼200-260 nm thick SiO 2 layers deposited on a QCM crystal resulted in increased refractive index of the layer during water uptake experiments. The increased refractive index led to artificially higher polymer swelling in the optical modeling of the hydration experiments. The SiO 2 -coated QCM crystals showed between 6 and 8% void as measured by QCM and SE, accounting for 60%-85% of the measured polymer swelling in the low humidity regime (<20% RH) and 25%-40% of the polymer swelling in the high humidity regime (>70% RH) from optical modeling for 105 and 47 nm thick sulfonated polymer films. Correcting the refractive index of the SiO 2 layer for its water content resulted in polymer swelling that successfully resembled swelling measured on a silicon wafer with nonporous native oxide.

Bacterial methane oxidation in sea-floor gas hydrate: Significance to life in extreme environments

NASA Astrophysics Data System (ADS)

Sassen, Roger; MacDonald, Ian R.; Guinasso, Norman L., Jr.; Joye, Samantha; Requejo, Adolfo G.; Sweet, Stephen T.; Alcalá-Herrera, Javier; Defreitas, Debra A.; Schink, David R.

1998-09-01

Samples of thermogenic hydrocarbon gases, from vents and gas hydrate mounds within a sea-floor chemosynthetic community on the Gulf of Mexico continental slope at about 540 m depth, were collected by research submersible. Our study area is characterized by low water temperature (mean =7 °C), high pressure (about 5400 kPa), and abundant structure II gas hydrate. Bacterial oxidation of hydrate-bound methane (CH4) is indicated by three isotopic properties of gas hydrate samples. Relative to the vent gas from which the gas hydrate formed, (1) methane-bound methane is enriched in 13C by as much as 3.8‰ PDB (Peedee belemnite), (2) hydrate-bound methane is enriched in deuterium (D) by as much as 37‰ SMOW (standard mean ocean water), and (3) hydrate-bound carbon dioxide (CO2) is depleted in 13C by as much as 22.4‰ PDB. Hydrate-associated authigenic carbonate rock is also depleted in 13C. Bacterial oxidation of methane is a driving force in chemosynthetic communities, and in the concomitant precipitation of authigenic carbonate rock that modifies sea-floor geology. Bacterial oxidation of hydrate-bound methane expands the potential boundaries of life in extreme environments.

Apparatus for recovering gaseous hydrocarbons from hydrocarbon-containing solid hydrates

DOEpatents

Elliott, Guy R. B.; Barraclough, Bruce L.; Vanderborgh, Nicholas E.

1984-01-01

A method and apparatus are provided for producing gaseous hydrocarbons from formations comprising solid hydrocarbon hydrates located under either a body of land or a body of water. The vast natural resources of such hydrocarbon hydrates can thus now be economically mined. Relatively warm brine or water is brought down from an elevation above that of the hydrates through a portion of the apparatus and passes in contact with the hydrates, thus melting them. The liquid then continues up another portion of the apparatus, carrying entrained hydrocarbon vapors in the form of bubbles, which can easily be separated from the liquid. After a short startup procedure, the process and apparatus are substantially self-powered.

Squirt flow due to interfacial water films in hydrate bearing sediments

NASA Astrophysics Data System (ADS)

Sell, Kathleen; Quintal, Beatriz; Kersten, Michael; Saenger, Erik H.

2018-05-01

Sediments containing gas hydrate dispersed in the pore space are known to show a characteristic seismic anomaly which is a high attenuation along with increasing seismic velocities. Currently, this observation cannot be fully explained albeit squirt-flow type mechanisms on the microscale have been speculated to be the cause. Recent major findings from in situ experiments, using the gas in excess and water in excess formation method, and coupled with high-resolution synchrotron-based X-ray micro-tomography, have revealed the systematic presence of thin water films between the quartz grains and the encrusting hydrate. The data obtained from these experiments underwent an image processing procedure to quantify the thicknesses and geometries of the aforementioned interfacial water films. Overall, the water films vary from sub-micrometer to a few micrometers in thickness. In addition, some of the water films interconnect through water bridges. This geometrical analysis is used to propose a new conceptual squirt flow model for hydrate bearing sediments. A series of numerical simulations is performed considering variations of the proposed model to study seismic attenuation caused by such thin water films. Our results support previous speculation that squirt flow can explain high attenuation at seismic frequencies in hydrate bearing sediments, but based on a conceptual squirt flow model which is geometrically different than those previously considered.

The mechanism of vapor phase hydration of calcium oxide: implications for CO2 capture.

PubMed

Kudłacz, Krzysztof; Rodriguez-Navarro, Carlos

2014-10-21

Lime-based sorbents are used for fuel- and flue-gas capture, thereby representing an economic and effective way to reduce CO2 emissions. Their use involves cyclic carbonation/calcination which results in a significant conversion reduction with increasing number of cycles. To reactivate spent CaO, vapor phase hydration is typically performed. However, little is known about the ultimate mechanism of such a hydration process. Here, we show that the vapor phase hydration of CaO formed after calcination of calcite (CaCO3) single crystals is a pseudomorphic, topotactic process, which progresses via an intermediate disordered phase prior to the final formation of oriented Ca(OH)2 nanocrystals. The strong structural control during this solid-state phase transition implies that the microstructural features of the CaO parent phase predetermine the final structural and physicochemical (reactivity and attrition) features of the product hydroxide. The higher molar volume of the product can create an impervious shell around unreacted CaO, thereby limiting the efficiency of the reactivation process. However, in the case of compact, sintered CaO structures, volume expansion cannot be accommodated in the reduced pore volume, and stress generation leads to pervasive cracking. This favors complete hydration but also detrimental attrition. Implications of these results in carbon capture and storage (CCS) are discussed.

3D pore-type digital rock modeling of natural gas hydrate for permafrost and numerical simulation of electrical properties

NASA Astrophysics Data System (ADS)

Dong, Huaimin; Sun, Jianmeng; Lin, Zhenzhou; Fang, Hui; Li, Yafen; Cui, Likai; Yan, Weichao

2018-02-01

Natural gas hydrate is being considered as an alternative energy source for sustainable development and has become a focus of research throughout the world. In this paper, based on CT scanning images of hydrate reservoir rocks, combined with the microscopic distribution of hydrate, a diffusion limited aggregation (DLA) model was used to construct 3D hydrate digital rocks of different distribution types, and the finite-element method was used to simulate their electrical characteristics in order to study the influence of different hydrate distribution types, hydrate saturation and formation of water salinity on electrical properties. The results show that the hydrate digital rocks constructed using the DLA model can be used to characterize the microscopic distribution of different types of hydrates. Under the same conditions, the resistivity of the adhesive hydrate digital rock is higher than the cemented and scattered type digital rocks, and the resistivity of the scattered hydrate digital rock is the smallest among the three types. Besides, the difference in the resistivity of the different types of hydrate digital rocks increases with an increase in hydrate saturation, especially when the saturation is larger than 55%, and the rate of increase of each of the hydrate types is quite different. Similarly, the resistivity of the three hydrate types decreases with an increase in the formation of water salinity. The single distribution hydrate digital rock constructed, combined with the law of microscopic distribution and influence of saturation on the electrical properties, can effectively improve the accuracy of logging identification of hydrate reservoirs and is of great significance for the estimation of hydrate reserves.

The mechanism of CO2 hydration: a porous metal oxide nanocapsule catalyst can mimic the biological carbonic anhydrase role.

PubMed

Bandeira, Nuno A G; Garai, Somenath; Müller, Achim; Bo, Carles

2015-11-04

The mechanism for the hydration of CO2 within a Keplerate nanocapsule is presented. A network of hydrogen bonds across the water layers in the first metal coordination sphere facilitates the proton abstraction and nucleophilic addition of water. The highly acidic properties of the polyoxometalate cluster are crucial for explaining the catalysed hydration.

Hydration water dynamics and instigation of protein structuralrelaxation

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

Russo, Daniela; Hura, Greg; Head-Gordon, Teresa

2003-09-01

Until a critical hydration level is reached, proteins do not function. This critical level of hydration is analogous to a similar lack of protein function observed for temperatures below a dynamical temperature range of 180-220K that also is connected to the dynamics of protein surface water. Restoration of some enzymatic activity is observed in partially hydrated protein powders, sometimes corresponding to less than a single hydration layer on the protein surface, which indicates that the dynamical and structural properties of the surface water is intimately connected to protein stability and function. Many elegant studies using both experiment and simulation havemore » contributed important information about protein hydration structure and timescales. The molecular mechanism of the solvent motion that is required to instigate the protein structural relaxation above a critical hydration level or transition temperature has yet to be determined. In this work we use experimental quasi-elastic neutron scattering (QENS) and molecular dynamics simulation to investigate hydration water dynamics near a greatly simplified protein system. We consider the hydration water dynamics near the completely deuterated N-acetyl-leucine-methylamide (NALMA) solute, a hydrophobic amino acid side chain attached to a polar blocked polypeptide backbone, as a function of concentration between 0.5M-2.0M under ambient conditions. We note that roughly 50-60% of a folded protein's surface is equally distributed between hydrophobic and hydrophilic domains, domains whose lengths are on the order of a few water diameters, that justify our study of hydration dynamics of this simple model protein system. The QENS experiment was performed at the NIST Center for Neutron Research, using the disk chopper time of flight spectrometer (DCS). In order to separate the translational and rotational components in the spectra, two sets of experiments were carried out using different incident neutron wavelengths of 7.5{angstrom} and 5.5{angstrom} to give two different time resolutions. All the spectra have been measure at room temperature. The spectra were corrected for the sample holder contribution and normalized using the vanadium standard. The resulting data were analyzed with DAVE programs (http://www.ncnr.nist.gov/dave/). The AMBER force field and SPCE water model were used for modeling the NALMA solute and water, respectively. For the analysis of the water dynamics in the NALMA aqueous solutions, we performed simulations of a dispersed solute configuration consistent with our previous structural analysis, where we had primarily focused on the structural organization of these peptide solutions and their connection to protein folding. Further details of the QENS experiment and molecular dynamics simulations are reported elsewhere.« less

Ab initio molecular dynamics simulations reveal localization and time evolution dynamics of an excess electron in heterogeneous CO2-H2O systems.

PubMed

Liu, Ping; Zhao, Jing; Liu, Jinxiang; Zhang, Meng; Bu, Yuxiang

2014-01-28

In view of the important implications of excess electrons (EEs) interacting with CO2-H2O clusters in many fields, using ab initio molecular dynamics simulation technique, we reveal the structures and dynamics of an EE associated with its localization and subsequent time evolution in heterogeneous CO2-H2O mixed media. Our results indicate that although hydration can increase the electron-binding ability of a CO2 molecule, it only plays an assisting role. Instead, it is the bending vibrations that play the major role in localizing the EE. Due to enhanced attraction of CO2, an EE can stably reside in the empty, low-lying π(*) orbital of a CO2 molecule via a localization process arising from its initial binding state. The localization is completed within a few tens of femtoseconds. After EE trapping, the ∠OCO angle of the core CO2 (-) oscillates in the range of 127°∼142°, with an oscillation period of about 48 fs. The corresponding vertical detachment energy of the EE is about 4.0 eV, which indicates extreme stability of such a CO2-bound solvated EE in [CO2(H2O)n](-) systems. Interestingly, hydration occurs not only on the O atoms of the core CO2 (-) through formation of O⋯H-O H-bond(s), but also on the C atom, through formation of a C⋯H-O H-bond. In the latter binding mode, the EE cloud exhibits considerable penetration to the solvent water molecules, and its IR characteristic peak is relatively red-shifted compared with the former. Hydration on the C site can increase the EE distribution at the C atom and thus reduce the C⋯H distance in the C⋯H-O H-bonds, and vice versa. The number of water molecules associated with the CO2 (-) anion in the first hydration shell is about 4∼7. No dimer-core (C2O4 (-)) and core-switching were observed in the double CO2 aqueous media. This work provides molecular dynamics insights into the localization and time evolution dynamics of an EE in heterogeneous CO2-H2O media.

Overview: Nucleation of clathrate hydrates

NASA Astrophysics Data System (ADS)

Warrier, Pramod; Khan, M. Naveed; Srivastava, Vishal; Maupin, C. Mark; Koh, Carolyn A.

2016-12-01

Molecular level knowledge of nucleation and growth of clathrate hydrates is of importance for advancing fundamental understanding on the nature of water and hydrophobic hydrate formers, and their interactions that result in the formation of ice-like solids at temperatures higher than the ice-point. The stochastic nature and the inability to probe the small length and time scales associated with the nucleation process make it very difficult to experimentally determine the molecular level changes that lead to the nucleation event. Conversely, for this reason, there have been increasing efforts to obtain this information using molecular simulations. Accurate knowledge of how and when hydrate structures nucleate will be tremendously beneficial for the development of sustainable hydrate management strategies in oil and gas flowlines, as well as for their application in energy storage and recovery, gas separation, carbon sequestration, seawater desalination, and refrigeration. This article reviews various aspects of hydrate nucleation. First, properties of supercooled water and ice nucleation are reviewed briefly due to their apparent similarity to hydrates. Hydrate nucleation is then reviewed starting from macroscopic observations as obtained from experiments in laboratories and operations in industries, followed by various hydrate nucleation hypotheses and hydrate nucleation driving force calculations based on the classical nucleation theory. Finally, molecular simulations on hydrate nucleation are discussed in detail followed by potential future research directions.

Towards understanding the role of amines in the SO2 hydration and the contribution of the hydrated product to new particle formation in the Earth's atmosphere.

PubMed

Lv, Guochun; Nadykto, Alexey B; Sun, Xiaomin; Zhang, Chenxi; Xu, Yisheng

2018-08-01

By theoretical calculations, the gas-phase SO 2 hydration reaction assisted by methylamine (MA) and dimethylamine (DMA) was investigated, and the potential contribution of the hydrated product to new particle formation (NPF) also was evaluated. The results show that the energy barrier for aliphatic amines (MA and DMA) assisted SO 2 hydration reaction is lower than the corresponding that of water and ammonia assisted SO 2 hydration. In these hydration reactions, nearly barrierless reaction (only a barrier of 0.1 kcal mol -1 ) can be found in the case of SO 2  + 2H 2 O + DMA. These lead us to conclude that the SO 2 hydration reaction assisted by MA and DMA is energetically facile. The temporal evolution for hydrated products (CH 3 NH 3 + -HSO 3 - -H 2 O or (CH 3 ) 2 NH 2 + -HSO 3 - -H 2 O) in molecular dynamics simulations indicates that these complexes can self-aggregate into bigger clusters and can absorb water and amine molecules, which means that these hydrated products formed by the hydration reaction may serve as a condensation nucleus to initiate the NPF. Copyright © 2018 Elsevier Ltd. All rights reserved.

Overview: Nucleation of clathrate hydrates.

PubMed

Warrier, Pramod; Khan, M Naveed; Srivastava, Vishal; Maupin, C Mark; Koh, Carolyn A

2016-12-07

Molecular level knowledge of nucleation and growth of clathrate hydrates is of importance for advancing fundamental understanding on the nature of water and hydrophobic hydrate formers, and their interactions that result in the formation of ice-like solids at temperatures higher than the ice-point. The stochastic nature and the inability to probe the small length and time scales associated with the nucleation process make it very difficult to experimentally determine the molecular level changes that lead to the nucleation event. Conversely, for this reason, there have been increasing efforts to obtain this information using molecular simulations. Accurate knowledge of how and when hydrate structures nucleate will be tremendously beneficial for the development of sustainable hydrate management strategies in oil and gas flowlines, as well as for their application in energy storage and recovery, gas separation, carbon sequestration, seawater desalination, and refrigeration. This article reviews various aspects of hydrate nucleation. First, properties of supercooled water and ice nucleation are reviewed briefly due to their apparent similarity to hydrates. Hydrate nucleation is then reviewed starting from macroscopic observations as obtained from experiments in laboratories and operations in industries, followed by various hydrate nucleation hypotheses and hydrate nucleation driving force calculations based on the classical nucleation theory. Finally, molecular simulations on hydrate nucleation are discussed in detail followed by potential future research directions.

Widespread gas hydrate instability on the upper U.S. Beaufort margin

USGS Publications Warehouse

Phrampus, Benjamin J.; Hornbach, Matthew J.; Ruppel, Carolyn D.; Hart, Patrick E.

2014-01-01

The most climate-sensitive methane hydrate deposits occur on upper continental slopes at depths close to the minimum pressure and maximum temperature for gas hydrate stability. At these water depths, small perturbations in intermediate ocean water temperatures can lead to gas hydrate dissociation. The Arctic Ocean has experienced more dramatic warming than lower latitudes, but observational data have not been used to study the interplay between upper slope gas hydrates and warming ocean waters. Here we use (a) legacy seismic data that constrain upper slope gas hydrate distributions on the U.S. Beaufort Sea margin, (b) Alaskan North Slope borehole data and offshore thermal gradients determined from gas hydrate stability zone thickness to infer regional heat flow, and (c) 1088 direct measurements to characterize multidecadal intermediate ocean warming in the U.S. Beaufort Sea. Combining these data with a three-dimensional thermal model shows that the observed gas hydrate stability zone is too deep by 100 to 250 m. The disparity can be partially attributed to several processes, but the most important is the reequilibration (thinning) of gas hydrates in response to significant (~0.5°C at 2σ certainty) warming of intermediate ocean temperatures over 39 years in a depth range that brackets the upper slope extent of the gas hydrate stability zone. Even in the absence of additional ocean warming, 0.44 to 2.2 Gt of methane could be released from reequilibrating gas hydrates into the sediments underlying an area of ~5–7.5 × 103 km2 on the U.S. Beaufort Sea upper slope during the next century.

Synergistic hydrate inhibition of monoethylene glycol with poly(vinylcaprolactam) in thermodynamically underinhibited system.

PubMed

Kim, Jakyung; Shin, Kyuchul; Seo, Yutaek; Cho, Seong Jun; Lee, Ju Dong

2014-07-31

This study investigates the hydrate inhibition performance of monoethylene glycol (MEG) with poly(vinylcaprolactam) (PVCap) for retarding the hydrate onset as well as preventing the agglomeration of hydrate particles. A high-pressure autoclave was used to determine the hydrate onset time, subcooling temperature, hydrate fraction in the liquid phase, and torque changes during hydrate formation in pure water, 0.2 wt % PVCap solution, and 20 and 30 wt % MEG solutions. In comparison to water with no inhibitors, the addition of PVCap delays the hydrate onset time but cannot reduce the hydrate fraction, leading to a sharp increase in torque. The 20 and 30 wt % MEG solutions also delay the hydrate onset time slightly and reduce the hydrate fraction to 0.15. The addition of 0.2 wt % PVCap to the 20 wt % MEG solution, however, delays the hydrate onset time substantially, and the hydrate fraction was less than 0.19. The torque changes were negligible during the hydrate formation, suggesting the homogeneous dispersion of hydrate particles in the liquid phase. The well-dispersed hydrate particles do not agglomerate or deposit under stirring. Moreover, when 0.2 wt % PVCap was added to the 30 wt % MEG solution, no hydrate formation was observed for at least 24 h. These results suggest that mixing of MEG with a small amount of PVCap in underinhibited conditions will induce the synergistic inhibition of hydrate by delaying the hydrate onset time as well as preventing the agglomeration and deposition of hydrate particles. Decreasing the hydrate fraction in the liquid phase might be the reason for negligible torque changes during the hydrate formation in the 0.2 wt % PVCap and 20 wt % MEG solution. Simple structure II was confirmed by in situ Raman spectroscopy for the synergistic inhibition system, while coexisting structures I and II are observed in 0.2 wt % PVCap solution.

Entrapment of Hydrate-coated Gas Bubbles into Oil and Separation of Gas and Hydrate-film; Seafloor Experiments with ROV

NASA Astrophysics Data System (ADS)

Hiruta, A.; Matsumoto, R.

2015-12-01

We trapped gas bubbles emitted from the seafloor into oil-containing collector and observed an unique phenomena. Gas hydrate formation needs water for the crystal lattice; however, gas hydrates in some areas are associated with hydrophobic crude oil or asphalt. In order to understand gas hydrate growth in oil-bearing sediments, an experiment with cooking oil was made at gas hydrate stability condition. We collected venting gas bubbles into a collector with canola oil during ROV survey at a gas hydrate area in the eastern margin of the Sea of Japan. When the gas bubbles were trapped into collector with oil, gas phase appeared above the oil and gas hydrates, between oil and gas phase. At this study area within gas hydrate stability condition, control experiment with oil-free collector suggested that gas bubbles emitted from the seafloor were quickly covered with gas hydrate film. Therefore it is improbable that gas bubbles entered into the oil phase before hydrate skin formation. After the gas phase formation in oil-containing collector, the ROV floated outside of hydrate stability condition for gas hydrate dissociation and re-dived to the venting site. During the re-dive within hydrate stability condition, gas hydrate was not formed. The result suggests that moisture in the oil is not enough for hydrate formation. Therefore gas hydrates that appeared at the oil/gas phase boundary were already formed before bubbles enter into the oil. Hydrate film is the only possible origin. This observation suggests that hydrate film coating gas hydrate was broken at the sea water/oil boundary or inside oil. Further experiments may contribute for revealing kinetics of hydrate film and formation. This work was a part of METI (Ministry of Economy, Trade and Industry)'s project entitled "FY2014 Promoting research and development of methane hydrate". We also appreciate support of AIST (National Institute of Advanced Industrial Science and Technology).

Deep-ocean field test of methane hydrate formation from a remotely operated vehicle

USGS Publications Warehouse

Brewer, P.G.; Orr, F.M.; Friederich, G.; Kvenvolden, K.A.; Orange, D.L.; McFarlane, J.; Kirkwood, W.

1997-01-01

We have observed the process of formation of clathrate hydrates of methane in experiments conducted on the remotely operated vehicle (ROY) Ventana in the deep waters of Monterey Bay. A tank of methane gas, acrylic tubes containing seawater, and seawater plus various types of sediment were carried down on Ventana to a depth of 910 m where methane gas was injected at the base of the acrylic tubes by bubble stream. Prior calculations had shown that the local hydrographic conditions gave an upper limit of 525 m for the P-T boundary defining methane hydrate formation or dissociation at this site, and thus our experiment took place well within the stability range for this reaction to occur. Hydrate formation in free sea-water occurred within minutes as a buoyant mass of translucent hydrate formed at the gas-water interface. In a coarse sand matrix the Filling of the pore spaces with hydrate turned the sand column into a solidified block, which gas pressure soon lifted and ruptured. In a fine-grained black mud the gas flow carved out flow channels, the walls of which became coated and then filled with hydrate in larger discrete masses. Our experiment shows that hydrate formation is rapid in natural seawater, that sediment type strongly influences the patterns of hydrate formation, and that the use of ROV technologies permits the synthesis of large amounts of hydrate material in natural systems under a variety of conditions so that fundamental research on the stability and growth of these substances is possible.

Molecular simulation of a model of dissolved organic matter.

PubMed

Sutton, Rebecca; Sposito, Garrison; Diallo, Mamadou S; Schulten, Hans-Rolf

2005-08-01

A series of atomistic simulations was performed to assess the ability of the Schulten dissolved organic matter (DOM) molecule, a well-established model humic molecule, to reproduce the physical and chemical behavior of natural humic substances. The unhydrated DOM molecule had a bulk density value appropriate to humic matter, but its Hildebrand solubility parameter was lower than the range of current experimental estimates. Under hydrated conditions, the DOM molecule went through conformational adjustments that resulted in disruption of intramolecular hydrogen bonds (H-bonds), although few water molecules penetrated the organic interior. The radius of gyration of the hydrated DOM molecule was similar to those measured for aquatic humic substances. To simulate humic materials under aqueous conditions with varying pH levels, carboxyl groups were deprotonated, and hydrated Na+ or Ca2+ were added to balance the resulting negative charge. Because of intrusion of the cation hydrates, the model metal-humic structures were more porous, had greater solvent-accessible surface areas, and formed more H-bonds with water than the protonated, hydrated DOM molecule. Relative to Na+, Ca2+ was both more strongly bound to carboxylate groups and more fully hydrated. This difference was attributed to the higher charge of the divalent cation. The Ca-DOM hydrate, however, featured fewer H-bonds than the Na-DOM hydrate, perhaps because of the reduced orientational freedom of organic moieties and water molecules imposed by Ca2+. The present work is, to our knowledge, the first rigorous computational exploration regarding the behavior of a model humic molecule under a range of physical conditions typical of soil and water systems.

Hydration-reduced lattice thermal conductivity of olivine in Earth’s upper mantle

PubMed Central

Chang, Yun-Yuan; Hsieh, Wen-Pin; Tan, Eh; Chen, Jiuhua

2017-01-01

Earth’s water cycle enables the incorporation of water (hydration) in mantle minerals that can influence the physical properties of the mantle. Lattice thermal conductivity of mantle minerals is critical for controlling the temperature profile and dynamics of the mantle and subducting slabs. However, the effect of hydration on lattice thermal conductivity remains poorly understood and has often been assumed to be negligible. Here we have precisely measured the lattice thermal conductivity of hydrous San Carlos olivine (Mg0.9Fe0.1)2SiO4 (Fo90) up to 15 gigapascals using an ultrafast optical pump−probe technique. The thermal conductivity of hydrous Fo90 with ∼7,000 wt ppm water is significantly suppressed at pressures above ∼5 gigapascals, and is approximately 2 times smaller than the nominally anhydrous Fo90 at mantle transition zone pressures, demonstrating the critical influence of hydration on the lattice thermal conductivity of olivine in this region. Modeling the thermal structure of a subducting slab with our results shows that the hydration-reduced thermal conductivity in hydrated oceanic crust further decreases the temperature at the cold, dry center of the subducting slab. Therefore, the olivine−wadsleyite transformation rate in the slab with hydrated oceanic crust is much slower than that with dry oceanic crust after the slab sinks into the transition zone, extending the metastable olivine to a greater depth. The hydration-reduced thermal conductivity could enable hydrous minerals to survive in deeper mantle and enhance water transportation to the transition zone. PMID:28377520

Enhancing capacitance behaviour of CoOOH nanostructures using transition metal dopants by ambient oxidation.

PubMed

Chen, Yanhui; Zhou, Junfeng; Maguire, Pierce; O'Connell, Robert; Schmitt, Wolfgang; Li, Yonghe; Yan, Zhengguang; Zhang, Yuefei; Zhang, Hongzhou

2016-02-08

Cobalt hydrate and doped binary Co0.9M0.1OOH (M = Ni, Mn, Fe) nanorings of 100-300 nm were fabricated in solution through a facile ambient oxidation method. A transformation from Co0.9Ni0.1(OH)2 nanodiscs to hollow Co0.9Ni0.1OOH nanorings was observed with prolonged reaction time. Core-shell nanodiscs have elemental segregation with a Co(OH)2 core and Ni(OH)2 shell. Co0.9Ni0.1OOH nanorings displayed a higher electrochemical capacitance than Mn and Fe doped nanorings materials or materials with disc-like geometries.

Perspective: Watching low-frequency vibrations of water in biomolecular recognition by THz spectroscopy.

PubMed

Xu, Yao; Havenith, Martina

2015-11-07

Terahertz (THz) spectroscopy has turned out to be a powerful tool which is able to shed new light on the role of water in biomolecular processes. The low frequency spectrum of the solvated biomolecule in combination with MD simulations provides deep insights into the collective hydrogen bond dynamics on the sub-ps time scale. The absorption spectrum between 1 THz and 10 THz of solvated biomolecules is sensitive to changes in the fast fluctuations of the water network. Systematic studies on mutants of antifreeze proteins indicate a direct correlation between biological activity and a retardation of the (sub)-ps hydration dynamics at the protein binding site, i.e., a "hydration funnel." Kinetic THz absorption studies probe the temporal changes of THz absorption during a biological process, and give access to the kinetics of the coupled protein-hydration dynamics. When combined with simulations, the observed results can be explained in terms of a two-tier model involving a local binding and a long range influence on the hydration bond dynamics of the water around the binding site that highlights the significance of the changes in the hydration dynamics at recognition site for biomolecular recognition. Water is shown to assist molecular recognition processes.

Hydration and conformational equilibria of simple hydrophobic and amphiphilic solutes.

PubMed Central

Ashbaugh, H S; Kaler, E W; Paulaitis, M E

1998-01-01

We consider whether the continuum model of hydration optimized to reproduce vacuum-to-water transfer free energies simultaneously describes the hydration free energy contributions to conformational equilibria of the same solutes in water. To this end, transfer and conformational free energies of idealized hydrophobic and amphiphilic solutes in water are calculated from explicit water simulations and compared to continuum model predictions. As benchmark hydrophobic solutes, we examine the hydration of linear alkanes from methane through hexane. Amphiphilic solutes were created by adding a charge of +/-1e to a terminal methyl group of butane. We find that phenomenological continuum parameters fit to transfer free energies are significantly different from those fit to conformational free energies of our model solutes. This difference is attributed to continuum model parameters that depend on solute conformation in water, and leads to effective values for the free energy/surface area coefficient and Born radii that best describe conformational equilibrium. In light of these results, we believe that continuum models of hydration optimized to fit transfer free energies do not accurately capture the balance between hydrophobic and electrostatic contributions that determines the solute conformational state in aqueous solution. PMID:9675177