The dynamics of water in hydrated white bread investigated using quasielastic neutron scattering

NASA Astrophysics Data System (ADS)

Sjöström, J.; Kargl, F.; Fernandez-Alonso, F.; Swenson, J.

2007-10-01

The dynamics of water in fresh and in rehydrated white bread is studied using quasielastic neutron scattering (QENS). A diffusion constant for water in fresh bread, without temperature gradients and with the use of a non-destructive technique, is presented here for the first time. The self-diffusion constant for fresh bread is estimated to be Ds = 3.8 × 10-10 m2 s-1 and the result agrees well with previous findings for similar systems. It is also suggested that water exhibits a faster dynamics than previously reported in the literature using equilibration of a hydration-level gradient monitored by vibrational spectroscopy. The temperature dependence of the dynamics of low hydration bread is also investigated for T = 280-350 K. The average relaxation time at constant momentum transfer (Q) shows an Arrhenius behavior in the temperature range investigated.

Protein-Style Dynamical Transition in a Non-Biological Polymer and a Non-Aqueous Solvent.

PubMed

Mamontov, E; Sharma, V K; Borreguero, J M; Tyagi, M

2016-03-31

Temperature-dependent onset of apparent anharmonicity in the microscopic dynamics of hydrated proteins and other biomolecules has been known as protein dynamical transition for the last quarter of a century. Using neutron scattering and molecular dynamics simulation, techniques most often associated with protein dynamical transition studies, we have investigated the microscopic dynamics of one of the most common polymers, polystyrene, which was exposed to toluene vapor, mimicking the process of protein hydration from water vapor. Polystyrene with adsorbed toluene is an example of a solvent-solute system, which, unlike biopolymers, is anhydrous and lacks hydrogen bonding. Nevertheless, it exhibits the essential traits of the dynamical transition in biomolecules, such as a specific dependence of the microscopic dynamics of both solvent and host on the temperature and the amount of solvent adsorbed. We conclude that the protein dynamical transition is a manifestation of a universal solvent-solute dynamical relationship, which is not specific to either biomolecules as solute, or aqueous media as solvent, or even a particular type of interactions between solvent and solute.

The molecular mechanism of the inhibition effects of PVCaps on the growth of sI hydrate: an unstable adsorption mechanism.

PubMed

Xu, Jiafang; Li, Liwen; Liu, Jinxiang; Wang, Xiaopu; Yan, Youguo; Zhang, Jun

2018-03-28

The inhibition properties of kinetic hydrate inhibitor (KHI) molecules on the dynamic growth of a hydrate/water interface are investigated by using molecular dynamics simulations. The shape of the hydrate interface is transformed from laminar to funnel by PVCaps. Results indicate that the inhibition effects not only depend on the adsorption capacity which was believed to determine inhibition, but also on the fact that PVCaps must have some non-binding-hydrate sites that don't tend to combine with hydrate. By observing the time evolution of the distance between each component of PVCaps and hydrate, the heterocyclic ring of PVCaps mainly contributes to adsorption and can preferentially adjust itself to come into contact with a hydrate semi-large-cage. The distance between the amide of PVCaps and hydrate is about 4 Å and exceeds the range of a general hydrogen bond (3.5 Å), which proves that the non-binding-hydrate sites of PVCaps exist. On the other hand, the amide of PVCaps is at the intersection of the solid-liquid interface but has no adsorption affinity for hydrate, so this adsorption pattern indicates that the PVCaps at the hydrate interface are not stable. Due to this unstable adsorption, a repeated hydrate destruction phenomenon was revealed by the identification algorithm of hydrate and the calculation of the local number density of methane. The statistical evolution of water rings further proved the existence of non-binding-hydrate sites in PVCaps and the inhibition mechanism to destroy the hydrate cages by PVCaps. This unstable adsorption mechanism may shed light on the development of novel efficient KHIs.

Confocal spectroscopic imaging measurements of depth dependent hydration dynamics in human skin in-vivo

NASA Astrophysics Data System (ADS)

Behm, P.; Hashemi, M.; Hoppe, S.; Wessel, S.; Hagens, R.; Jaspers, S.; Wenck, H.; Rübhausen, M.

2017-11-01

We present confocal spectroscopic imaging measurements applied to in-vivo studies to determine the depth dependent hydration profiles of human skin. The observed spectroscopic signal covers the spectral range from 810 nm to 2100 nm allowing to probe relevant absorption signals that can be associated with e.g. lipid and water-absorption bands. We employ a spectrally sensitive autofocus mechanism that allows an ultrafast focusing of the measurement spot on the skin and subsequently probes the evolution of the absorption bands as a function of depth. We determine the change of the water concentration in m%. The water concentration follows a sigmoidal behavior with an increase of the water content of about 70% within 5 μm in a depth of about 14 μm. We have applied our technique to study the hydration dynamics of skin before and after treatment with different concentrations of glycerol indicating that an increase of the glycerol concentration leads to an enhanced water concentration in the stratum corneum. Moreover, in contrast to traditional corneometry we have found that the application of Aluminium Chlorohydrate has no impact to the hydration of skin.

Temperature dependence of the hydrated electron's excited-state relaxation. II. Elucidating the relaxation mechanism through ultrafast transient absorption and stimulated emission spectroscopy

NASA Astrophysics Data System (ADS)

Farr, Erik P.; Zho, Chen-Chen; Challa, Jagannadha R.; Schwartz, Benjamin J.

2017-08-01

The structure of the hydrated electron, particularly whether it exists primarily within a cavity or encompasses interior water molecules, has been the subject of much recent debate. In Paper I [C.-C. Zho et al., J. Chem. Phys. 147, 074503 (2017)], we found that mixed quantum/classical simulations with cavity and non-cavity pseudopotentials gave different predictions for the temperature dependence of the rate of the photoexcited hydrated electron's relaxation back to the ground state. In this paper, we measure the ultrafast transient absorption spectroscopy of the photoexcited hydrated electron as a function of temperature to confront the predictions of our simulations. The ultrafast spectroscopy clearly shows faster relaxation dynamics at higher temperatures. In particular, the transient absorption data show a clear excess bleach beyond that of the equilibrium hydrated electron's ground-state absorption that can only be explained by stimulated emission. This stimulated emission component, which is consistent with the experimentally known fluorescence spectrum of the hydrated electron, decreases in both amplitude and lifetime as the temperature is increased. We use a kinetic model to globally fit the temperature-dependent transient absorption data at multiple temperatures ranging from 0 to 45 °C. We find the room-temperature lifetime of the excited-state hydrated electron to be 137 ±40 fs, in close agreement with recent time-resolved photoelectron spectroscopy (TRPES) experiments and in strong support of the "non-adiabatic" picture of the hydrated electron's excited-state relaxation. Moreover, we find that the excited-state lifetime is strongly temperature dependent, changing by slightly more than a factor of two over the 45 °C temperature range explored. This temperature dependence of the lifetime, along with a faster rate of ground-state cooling with increasing bulk temperature, should be directly observable by future TRPES experiments. Our data also suggest that the red side of the hydrated electron's fluorescence spectrum should significantly decrease with increasing temperature. Overall, our results are not consistent with the nearly complete lack of temperature dependence predicted by traditional cavity models of the hydrated electron but instead agree qualitatively and nearly quantitatively with the temperature-dependent structural changes predicted by the non-cavity hydrated electron model.

Molecular dynamics study of structure H clathrate hydrates of methane and large guest molecules.

PubMed

Susilo, Robin; Alavi, Saman; Ripmeester, John A; Englezos, Peter

2008-05-21

Methane storage in structure H (sH) clathrate hydrates is attractive due to the relatively higher stability of sH as compared to structure I methane hydrate. The additional stability is gained without losing a significant amount of gas storage density as happens in the case of structure II (sII) methane clathrate. Our previous work has showed that the selection of a specific large molecule guest substance (LMGS) as the sH hydrate former is critical in obtaining the optimum conditions for crystallization kinetics, hydrate stability, and methane content. In this work, molecular dynamics simulations are employed to provide further insight regarding the dependence of methane occupancy on the type of the LMGS and pressure. Moreover, the preference of methane molecules to occupy the small (5(12)) or medium (4(3)5(6)6(3)) cages and the minimum cage occupancy required to maintain sH clathrate mechanical stability are examined. We found that thermodynamically, methane occupancy depends on pressure but not on the nature of the LMGS. The experimentally observed differences in methane occupancy for different LMGS may be attributed to the differences in crystallization kinetics and/or the nonequilibrium conditions during the formation. It is also predicted that full methane occupancies in both small and medium clathrate cages are preferred at higher pressures but these cages are not fully occupied at lower pressures. It was found that both small and medium cages are equally favored for occupancy by methane guests and at the same methane content, the system suffers a free energy penalty if only one type of cage is occupied. The simulations confirm the instability of the hydrate when the small and medium cages are empty. Hydrate decomposition was observed when less than 40% of the small and medium cages are occupied.

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

Mamontov, Eugene; O'Neil, Hugh

In this paper, we have studied microscopic dynamics of a protein in carbon disulfide, a non-glass forming solvent, down to its freezing temperature of ca. 160 K. We have utilized quasielastic neutron scattering. A comparison of lysozyme hydrated with water and dissolved in carbon disulfide reveals a stark difference in the temperature dependence of the protein's microscopic relaxation dynamics induced by the solvent. In the case of hydration water, the common protein glass-forming solvent, the protein relaxation slows down in response to a large increase in the water viscosity on cooling down, exhibiting a well-known protein dynamical transition. The dynamicalmore » transition disappears in non-glass forming carbon disulfide, whose viscosity remains a weak function of temperature all the way down to freezing at just below 160 K. The microscopic relaxation dynamics of lysozyme dissolved in carbon disulfide is sustained down to the freezing temperature of its solvent at a rate similar to that measured at ambient temperature. Finally, our results demonstrate that protein dynamical transition is not merely solvent-assisted, but rather solvent-induced, or, more precisely, is a reflection of the temperature dependence of the solvent's glass-forming dynamics.« less

Water dynamics in protein hydration shells: the molecular origins of the dynamical perturbation.

PubMed

Fogarty, Aoife C; Laage, Damien

2014-07-17

Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra.

Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation

PubMed Central

2014-01-01

Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585

Dynamics of confined reactive water in smectite clay-zeolite composites.

PubMed

Pitman, Michael C; van Duin, Adri C T

2012-02-15

The dynamics of water confined to mesoporous regions in minerals such as swelling clays and zeolites is fundamental to a wide range of resource management issues impacting many processes on a global scale, including radioactive waste containment, desalination, and enhanced oil recovery. Large-scale atomic models of freely diffusing multilayer smectite particles at low hydration confined in a silicalite cage are used to investigate water dynamics in the composite environment with the ReaxFF reactive force field over a temperature range of 300-647 K. The reactive capability of the force field enabled a range of relevant surface chemistry to emerge, including acid/base equilibria in the interlayer calcium hydrates and silanol formation on the edges of the clay and inner surface of the zeolite housing. After annealing, the resulting clay models exhibit both mono- and bilayer hydration structures. Clay surface hydration redistributed markedly and yielded to silicalite water loading. We find that the absolute rates and temperature dependence of water dynamics compare well to neutron scattering data and pulse field gradient measures from relevant samples of Ca-montmorillonite and silicalite, respectively. Within an atomistic, reactive context, our results distinguish water dynamics in the interlayer Ca(OH)(2)·nH(2)O environment from water flowing over the clay surface, and from water diffusing within silicalite. We find that the diffusion of water when complexed to Ca hydrates is considerably slower than freely diffusing water over the clay surface, and the reduced mobility is well described by a difference in the Arrhenius pre-exponential factor rather than a change in activation energy.

6,7-dimethoxy-coumarin as a probe of hydration dynamics in biologically relevant systems

NASA Astrophysics Data System (ADS)

Ghose, Avisek; Amaro, Mariana; Kovaricek, Petr; Hof, Martin; Sykora, Jan

2018-04-01

Coumarin derivatives are well known fluorescence reporters for investigating biological systems due to their strong micro-environment sensitivity. Despite having wide range of environment sensitive fluorescence probes, the potential of 6,7-dimethoxy-coumarin has not been studied extensively so far. With a perspective of its use in protein studies, namely using the unnatural amino acid technology or as a substrate for hydrolase enzymes, we study acetyloxymethyl-6,7-dimethoxycoumarin (Ac-DMC). We investigate the photophysics and hydration dynamics of this dye in aerosol-OT (AOT) reverse micelles at various water contents using the time dependent fluorescence shift (TDFS) method. The TDFS response in AOT reverse micelles from water/surfactant ratio of 0 to 20 confirms its sensitivity towards the hydration and mobility of its microenvironment. Moreover, we show that the fluorophore can be efficiently quenched by halide ions. Hence, we conclude that the 6,7-dimethoxy-methylcoumarin fluorophore is useful for studying hydration parameters in biologically relevant systems.

Molecular-dynamics study of propane-hydrate dissociation: Fluctuation-dissipation and non-equilibrium analysis.

PubMed

Ghaani, Mohammad Reza; English, Niall J

2018-03-21

Equilibrium and non-equilibrium molecular-dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar propane-hydrate interfaces in contact with liquid water over the 260-320 K range. Two types of hydrate-surface water-lattice molecular termination were adopted, at the hydrate edge with water, for comparison: a 001-direct surface cleavage and one with completed cages. Statistically significant differences in melting temperatures and initial break-up rates were observed between both interface types. Dissociation rates were observed to be strongly dependent on temperature, with higher rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model, developed previously, was applied to fit the observed dissociation profiles, and this helps us to identify clearly two distinct hydrate-decomposition régimes; following a highly temperature-dependent break-up phase, a second well-defined stage is essentially independent of temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. Further equilibrium MD-analysis of the two-phase systems at their melting point, with consideration of the relaxation times gleaned from the auto-correlation functions of fluctuations in a number of enclathrated guest molecules, led to statistically significant differences between the two surface-termination cases; a consistent correlation emerged in both cases between the underlying, non-equilibrium, thermal-driven dissociation rates sampled directly from melting with that from an equilibrium-MD fluctuation-dissipation approach.

Molecular-dynamics study of propane-hydrate dissociation: Fluctuation-dissipation and non-equilibrium analysis

NASA Astrophysics Data System (ADS)

Ghaani, Mohammad Reza; English, Niall J.

2018-03-01

Equilibrium and non-equilibrium molecular-dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar propane-hydrate interfaces in contact with liquid water over the 260-320 K range. Two types of hydrate-surface water-lattice molecular termination were adopted, at the hydrate edge with water, for comparison: a 001-direct surface cleavage and one with completed cages. Statistically significant differences in melting temperatures and initial break-up rates were observed between both interface types. Dissociation rates were observed to be strongly dependent on temperature, with higher rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model, developed previously, was applied to fit the observed dissociation profiles, and this helps us to identify clearly two distinct hydrate-decomposition régimes; following a highly temperature-dependent break-up phase, a second well-defined stage is essentially independent of temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. Further equilibrium MD-analysis of the two-phase systems at their melting point, with consideration of the relaxation times gleaned from the auto-correlation functions of fluctuations in a number of enclathrated guest molecules, led to statistically significant differences between the two surface-termination cases; a consistent correlation emerged in both cases between the underlying, non-equilibrium, thermal-driven dissociation rates sampled directly from melting with that from an equilibrium-MD fluctuation-dissipation approach.

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

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

Effect of skin hydration on the dynamics of fingertip gripping contact.

PubMed

André, T; Lévesque, V; Hayward, V; Lefèvre, P; Thonnard, J-L

2011-11-07

The dynamics of fingertip contact manifest themselves in the complex skin movements observed during the transition from a stuck state to a fully developed slip. While investigating this transition, we found that it depended on skin hydration. To quantify this dependency, we asked subjects to slide their index fingertip on a glass surface while keeping the normal component of the interaction force constant with the help of visual feedback. Skin deformation inside the contact region was imaged with an optical apparatus that allowed us to quantify the relative sizes of the slipping and sticking regions. The ratio of the stuck skin area to the total contact area decreased linearly from 1 to 0 when the tangential force component increased from 0 to a maximum. The slope of this relationship was inversely correlated to the normal force component. The skin hydration level dramatically affected the dynamics of the contact encapsulated in the course of evolution from sticking to slipping. The specific effect was to reduce the tendency of a contact to slip, regardless of the variations of the coefficient of friction. Since grips were more unstable under dry skin conditions, our results suggest that the nervous system responds to dry skin by exaggerated grip forces that cannot be simply explained by a change in the coefficient of friction.

Effect of skin hydration on the dynamics of fingertip gripping contact

PubMed Central

André, T.; Lévesque, V.; Hayward, V.; Lefèvre, P.; Thonnard, J.-L.

2011-01-01

The dynamics of fingertip contact manifest themselves in the complex skin movements observed during the transition from a stuck state to a fully developed slip. While investigating this transition, we found that it depended on skin hydration. To quantify this dependency, we asked subjects to slide their index fingertip on a glass surface while keeping the normal component of the interaction force constant with the help of visual feedback. Skin deformation inside the contact region was imaged with an optical apparatus that allowed us to quantify the relative sizes of the slipping and sticking regions. The ratio of the stuck skin area to the total contact area decreased linearly from 1 to 0 when the tangential force component increased from 0 to a maximum. The slope of this relationship was inversely correlated to the normal force component. The skin hydration level dramatically affected the dynamics of the contact encapsulated in the course of evolution from sticking to slipping. The specific effect was to reduce the tendency of a contact to slip, regardless of the variations of the coefficient of friction. Since grips were more unstable under dry skin conditions, our results suggest that the nervous system responds to dry skin by exaggerated grip forces that cannot be simply explained by a change in the coefficient of friction. PMID:21490002

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

Microscopic relaxations in a protein sustained down to 160 K in a non-glass forming organic solvent

DOE PAGES

Mamontov, Eugene; O'Neil, Hugh

2016-05-03

In this paper, we have studied microscopic dynamics of a protein in carbon disulfide, a non-glass forming solvent, down to its freezing temperature of ca. 160 K. We have utilized quasielastic neutron scattering. A comparison of lysozyme hydrated with water and dissolved in carbon disulfide reveals a stark difference in the temperature dependence of the protein's microscopic relaxation dynamics induced by the solvent. In the case of hydration water, the common protein glass-forming solvent, the protein relaxation slows down in response to a large increase in the water viscosity on cooling down, exhibiting a well-known protein dynamical transition. The dynamicalmore » transition disappears in non-glass forming carbon disulfide, whose viscosity remains a weak function of temperature all the way down to freezing at just below 160 K. The microscopic relaxation dynamics of lysozyme dissolved in carbon disulfide is sustained down to the freezing temperature of its solvent at a rate similar to that measured at ambient temperature. Finally, our results demonstrate that protein dynamical transition is not merely solvent-assisted, but rather solvent-induced, or, more precisely, is a reflection of the temperature dependence of the solvent's glass-forming dynamics.« less

Temperature dependence of the hydrated electron's excited-state relaxation. I. Simulation predictions of resonance Raman and pump-probe transient absorption spectra of cavity and non-cavity models

NASA Astrophysics Data System (ADS)

Zho, Chen-Chen; Farr, Erik P.; Glover, William J.; Schwartz, Benjamin J.

2017-08-01

We use one-electron non-adiabatic mixed quantum/classical simulations to explore the temperature dependence of both the ground-state structure and the excited-state relaxation dynamics of the hydrated electron. We compare the results for both the traditional cavity picture and a more recent non-cavity model of the hydrated electron and make definite predictions for distinguishing between the different possible structural models in future experiments. We find that the traditional cavity model shows no temperature-dependent change in structure at constant density, leading to a predicted resonance Raman spectrum that is essentially temperature-independent. In contrast, the non-cavity model predicts a blue-shift in the hydrated electron's resonance Raman O-H stretch with increasing temperature. The lack of a temperature-dependent ground-state structural change of the cavity model also leads to a prediction of little change with temperature of both the excited-state lifetime and hot ground-state cooling time of the hydrated electron following photoexcitation. This is in sharp contrast to the predictions of the non-cavity model, where both the excited-state lifetime and hot ground-state cooling time are expected to decrease significantly with increasing temperature. These simulation-based predictions should be directly testable by the results of future time-resolved photoelectron spectroscopy experiments. Finally, the temperature-dependent differences in predicted excited-state lifetime and hot ground-state cooling time of the two models also lead to different predicted pump-probe transient absorption spectroscopy of the hydrated electron as a function of temperature. We perform such experiments and describe them in Paper II [E. P. Farr et al., J. Chem. Phys. 147, 074504 (2017)], and find changes in the excited-state lifetime and hot ground-state cooling time with temperature that match well with the predictions of the non-cavity model. In particular, the experiments reveal stimulated emission from the excited state with an amplitude and lifetime that decreases with increasing temperature, a result in contrast to the lack of stimulated emission predicted by the cavity model but in good agreement with the non-cavity model. Overall, until ab initio calculations describing the non-adiabatic excited-state dynamics of an excess electron with hundreds of water molecules at a variety of temperatures become computationally feasible, the simulations presented here provide a definitive route for connecting the predictions of cavity and non-cavity models of the hydrated electron with future experiments.

Characterizing heterogeneous dynamics at hydrated electrode surfaces.

PubMed

Willard, Adam P; Limmer, David T; Madden, Paul A; Chandler, David

2013-05-14

In models of Pt 111 and Pt 100 surfaces in water, motions of molecules in the first hydration layer are spatially and temporally correlated. To interpret these collective motions, we apply quantitative measures of dynamic heterogeneity that are standard tools for considering glassy systems. Specifically, we carry out an analysis in terms of mobility fields and distributions of persistence times and exchange times. In so doing, we show that dynamics in these systems is facilitated by transient disorder in frustrated two-dimensional hydrogen bonding networks. The frustration is the result of unfavorable geometry imposed by strong metal-water bonding. The geometry depends upon the structure of the underlying metal surface. Dynamic heterogeneity of water on the Pt 111 surface is therefore qualitatively different than that for water on the Pt 100 surface. In both cases, statistics of this ad-layer dynamic heterogeneity responds asymmetrically to applied voltage.

Characterizing heterogeneous dynamics at hydrated electrode surfaces

NASA Astrophysics Data System (ADS)

Willard, Adam P.; Limmer, David T.; Madden, Paul A.; Chandler, David

2013-05-01

In models of Pt 111 and Pt 100 surfaces in water, motions of molecules in the first hydration layer are spatially and temporally correlated. To interpret these collective motions, we apply quantitative measures of dynamic heterogeneity that are standard tools for considering glassy systems. Specifically, we carry out an analysis in terms of mobility fields and distributions of persistence times and exchange times. In so doing, we show that dynamics in these systems is facilitated by transient disorder in frustrated two-dimensional hydrogen bonding networks. The frustration is the result of unfavorable geometry imposed by strong metal-water bonding. The geometry depends upon the structure of the underlying metal surface. Dynamic heterogeneity of water on the Pt 111 surface is therefore qualitatively different than that for water on the Pt 100 surface. In both cases, statistics of this ad-layer dynamic heterogeneity responds asymmetrically to applied voltage.

Dynamical behaviors of structural, constrained and free water in calcium- and magnesium-silicate-hydrate gels

DOE PAGES

Le, Peisi; Fratini, Emiliano; Ito, Kanae; ...

2016-01-28

We present the hypothesis that the mechanical properties of cement pastes depend strongly on their porosities. In a saturated paste, the porosity links to the free water volume after hydration. Structural water, constrained water, and free water have different dynamical behavior. Hence, it should be possible to extract information on pore system by exploiting the water dynamics. With our experiments we investigated the slow dynamics of hydration water confined in calcium- and magnesium-silicate-hydrate (C-S-H and M-S-H) gels using high-resolution quasi-elastic neutron scattering (QENS) technique. C-S-H and M-S-H are the chemical binders present in calcium rich and magnesium rich cements. Wemore » measured three M-S-H samples: pure M-S-H, M-S-H with aluminum-silicate nanotubes (ASN), and M-S-H with carboxyl group functionalized ASN (ASN-COOH). A C-S-H sample with the same water content (i.e. 0.3) is also studied for comparison. We found that structural water in the gels contributes to the elastic component of the QENS spectrum, while constrained water and free water contribute the quasi-elastic component. The quantitative analysis suggests that the three components vary for different samples and indicate the variance in the system porosity, which controls the mechanical properties of cement pastes.« less

Dynamical behaviors of structural, constrained and free water in calcium- and magnesium-silicate-hydrate gels

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

Le, Peisi; Fratini, Emiliano; Ito, Kanae

We present the hypothesis that the mechanical properties of cement pastes depend strongly on their porosities. In a saturated paste, the porosity links to the free water volume after hydration. Structural water, constrained water, and free water have different dynamical behavior. Hence, it should be possible to extract information on pore system by exploiting the water dynamics. With our experiments we investigated the slow dynamics of hydration water confined in calcium- and magnesium-silicate-hydrate (C-S-H and M-S-H) gels using high-resolution quasi-elastic neutron scattering (QENS) technique. C-S-H and M-S-H are the chemical binders present in calcium rich and magnesium rich cements. Wemore » measured three M-S-H samples: pure M-S-H, M-S-H with aluminum-silicate nanotubes (ASN), and M-S-H with carboxyl group functionalized ASN (ASN-COOH). A C-S-H sample with the same water content (i.e. 0.3) is also studied for comparison. We found that structural water in the gels contributes to the elastic component of the QENS spectrum, while constrained water and free water contribute the quasi-elastic component. The quantitative analysis suggests that the three components vary for different samples and indicate the variance in the system porosity, which controls the mechanical properties of cement pastes.« less

Impact of hydration and temperature history on the structure and dynamics of lignin

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

Vural, Derya; Gainaru, C.; O'Neill, Hugh Michael

The full utilization of plant biomass for the production of energy and novel materials often involves high temperature treatment. Examples include melt spinning of lignin for manufacturing low-cost carbon fiber and the relocalization of lignin to increase the accessibility of cellulose for production of biofuels. These temperature-induced effects arise from poorly understood changes in lignin flexibility. Here, we combine molecular dynamics simulations with neutron scattering and dielectric spectroscopy experiments to probe the dependence of lignin dynamics on hydration and thermal history. We find a dynamical and structural hysteresis: at a given temperature, the lignin molecules are more expanded and theirmore » dynamics faster when the lignin is cooled than when heated. The structural hysteresis is more pronounced for dry lignin. The difference in dynamics, however, follows a different trend, it is found to be more significant at high temperatures and high hydration levels. The simulations also reveal syringyl units to be more dynamic than guiacyl. The results provide an atomic-detailed description of lignin dynamics, important for understanding lignin role in plant cell wall mechanics and for rationally improving lignin processing. The lignin glass transition, at which the polymer softens, is lower when lignin is cooled than when heated, therefore extending the cooling phase of processing and shortening the heating phase may offer ways to lower processing costs.« less

Impact of hydration and temperature history on the structure and dynamics of lignin

DOE PAGES

Vural, Derya; Gainaru, C.; O'Neill, Hugh Michael; ...

2018-03-16

The full utilization of plant biomass for the production of energy and novel materials often involves high temperature treatment. Examples include melt spinning of lignin for manufacturing low-cost carbon fiber and the relocalization of lignin to increase the accessibility of cellulose for production of biofuels. These temperature-induced effects arise from poorly understood changes in lignin flexibility. Here, we combine molecular dynamics simulations with neutron scattering and dielectric spectroscopy experiments to probe the dependence of lignin dynamics on hydration and thermal history. We find a dynamical and structural hysteresis: at a given temperature, the lignin molecules are more expanded and theirmore » dynamics faster when the lignin is cooled than when heated. The structural hysteresis is more pronounced for dry lignin. The difference in dynamics, however, follows a different trend, it is found to be more significant at high temperatures and high hydration levels. The simulations also reveal syringyl units to be more dynamic than guiacyl. The results provide an atomic-detailed description of lignin dynamics, important for understanding lignin role in plant cell wall mechanics and for rationally improving lignin processing. The lignin glass transition, at which the polymer softens, is lower when lignin is cooled than when heated, therefore extending the cooling phase of processing and shortening the heating phase may offer ways to lower processing costs.« less

Adsorption Mechanism of Inhibitor and Guest Molecules on the Surface of Gas Hydrates.

PubMed

Yagasaki, Takuma; Matsumoto, Masakazu; Tanaka, Hideki

2015-09-23

The adsorption of guest and kinetic inhibitor molecules on the surface of methane hydrate is investigated by using molecular dynamics simulations. We calculate the free energy profile for transferring a solute molecule from bulk water to the hydrate surface for various molecules. Spherical solutes with a diameter of ∼0.5 nm are significantly stabilized at the hydrate surface, whereas smaller and larger solutes exhibit lower adsorption affinity than the solutes of intermediate size. The range of the attractive force is subnanoscale, implying that this force has no effect on the macroscopic mass transfer of guest molecules in crystal growth processes of gas hydrates. We also examine the adsorption mechanism of a kinetic hydrate inhibitor. It is found that a monomer of the kinetic hydrate inhibitor is strongly adsorbed on the hydrate surface. However, the hydrogen bonding between the amide group of the inhibitor and water molecules on the hydrate surface, which was believed to be the driving force for the adsorption, makes no contribution to the adsorption affinity. The preferential adsorption of both the kinetic inhibitor and the spherical molecules to the surface is mainly due to the entropic stabilization arising from the presence of cavities at the hydrate surface. The dependence of surface affinity on the size of adsorbed molecules is also explained by this mechanism.

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.

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

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

Molecular Gibbs Surface Excess and CO2-Hydrate Density Determine the Strong Temperature- and Pressure-Dependent Supercritical CO2-Brine Interfacial Tension.

PubMed

Ji, Jiayuan; Zhao, Lingling; Tao, Lu; Lin, Shangchao

2017-06-29

In CO 2 geological storage, the interfacial tension (IFT) between supercritical CO 2 and brine is critical for the storage capacitance design to prevent CO 2 leakage. IFT relies not only on the interfacial molecule properties but also on the environmental conditions at different storage sites. In this paper, supercritical CO 2 -NaCl solution systems are modeled at 343-373 K and 6-35 MPa under the salinity of 1.89 mol/L using molecular dynamics simulations. After computing and comparing the molecular density profile across the interface, the atomic radial distribution function, the molecular orientation distribution, the molecular Gibbs surface excess (derived from the molecular density profile), and the CO 2 -hydrate number density under the above environmental conditions, we confirm that only the molecular Gibbs surface excess of CO 2 molecules and the CO 2 -hydrate number density correlate strongly with the temperature- and pressure-dependent IFTs. We also compute the populations of two distinct CO 2 -hydrate structures (T-type and H-type) and attribute the observed dependence of IFTs to the dominance of the more stable, surfactant-like T-type CO 2 -hydrates at the interface. On the basis of these new molecular mechanisms behind IFT variations, this study could guide the rational design of suitable injecting environmental pressure and temperature conditions. We believe that the above two molecular-level metrics (Gibbs surface excess and hydrate number density) are of great fundamental importance for understanding the supercritical CO 2 -water interface and engineering applications in geological CO 2 storage.

Some thermodynamical aspects of protein hydration water

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

Mallamace, Francesco, E-mail: francesco.mallamace@unime.it; Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215

2015-06-07

We study by means of nuclear magnetic resonance the self-diffusion of protein hydration water at different hydration levels across a large temperature range that includes the deeply supercooled regime. Starting with a single hydration shell (h = 0.3), we consider different hydrations up to h = 0.65. Our experimental evidence indicates that two phenomena play a significant role in the dynamics of protein hydration water: (i) the measured fragile-to-strong dynamic crossover temperature is unaffected by the hydration level and (ii) the first hydration shell remains liquid at all hydrations, even at the lowest temperature.

Inhibition of insulin amyloid fibrillation by Morin hydrate.

PubMed

Patel, Palak; Parmar, Krupali; Das, Mili

2018-03-01

We report here the inhibition of amyloid fibrillation of human insulin in vitro by Morin hydrate, a naturally occurring small molecule. Using spectroscopic assays and transmission electron microscopy, we found that Morin hydrate effectively inhibits insulin amyloid fibrillation in a dose dependent manner with more than 80% inhibition occurring even at only a 1:1 concentration. As suggested by fluorescence spectroscopic titration studies, Morin hydrate binds to insulin with a fairly strong affinity of -26.436kJmol -1 . Circular dichroism (CD) spectroscopy was used to analyse structural changes of insulin in the presence of Morin hydrate demonstrating the ability of Morin hydrate to bind with the native monomeric protein and/or its near native state, intermediate oligomeric species and amyloid fibrils. Based on computational docking and molecular dynamics study, we propose that Morin hydrate binds to residues having greater aggregation propensity and prevent structural and/or conformational changes leading to amyloid fibrillation. Morin hydrate should also bind to fibrils by hydrogen bonding and/or hydrophobic forces throughout the surface, stabilize them and inhibit the release of oligomeric species which could be nuclei or template for further fibrillation. Overall results provide an insight into the mechanism of inhibition of insulin amyloid fibrillation by Morin hydrate. Copyright © 2017 Elsevier B.V. All rights reserved.

Controls on the physical properties of gas-hydrate-bearing sediments because of the interaction between gas hydrate and porous media

USGS Publications Warehouse

Lee, Myung W.; Collett, Timothy S.

2005-01-01

Physical properties of gas-hydrate-bearing sediments depend on the pore-scale interaction between gas hydrate and porous media as well as the amount of gas hydrate present. Well log measurements such as proton nuclear magnetic resonance (NMR) relaxation and electromagnetic propagation tool (EPT) techniques depend primarily on the bulk volume of gas hydrate in the pore space irrespective of the pore-scale interaction. However, elastic velocities or permeability depend on how gas hydrate is distributed in the pore space as well as the amount of gas hydrate. Gas-hydrate saturations estimated from NMR and EPT measurements are free of adjustable parameters; thus, the estimations are unbiased estimates of gas hydrate if the measurement is accurate. However, the amount of gas hydrate estimated from elastic velocities or electrical resistivities depends on many adjustable parameters and models related to the interaction of gas hydrate and porous media, so these estimates are model dependent and biased. NMR, EPT, elastic-wave velocity, electrical resistivity, and permeability measurements acquired in the Mallik 5L-38 well in the Mackenzie Delta, Canada, show that all of the well log evaluation techniques considered provide comparable gas-hydrate saturations in clean (low shale content) sandstone intervals with high gas-hydrate saturations. However, in shaly intervals, estimates from log measurement depending on the pore-scale interaction between gas hydrate and host sediments are higher than those estimates from measurements depending on the bulk volume of gas hydrate.

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 and rotational diffusion of levoglucosan in aqueous solutions

NASA Astrophysics Data System (ADS)

Corezzi, S.; Sassi, P.; Paolantoni, M.; Comez, L.; Morresi, A.; Fioretto, D.

2014-05-01

Extended frequency range depolarized light scattering measurements of water-levoglucosan solutions are reported at different concentrations and temperatures to assess the effect of the presence and distribution of hydroxyl groups on the dynamics of hydration water. The anhydro bridge, reducing from five to three the number of hydroxyl groups with respect to glucose, considerably affects the hydration properties of levoglucosan with respect to those of mono and disaccharides. In particular, we find that the average retardation of water dynamics is ≈3-4, that is lower than ≈5-6 previously found in glucose, fructose, trehalose, and sucrose. Conversely, the average number of retarded water molecules around levoglucosan is 24, almost double that found in water-glucose mixtures. These results suggest that the ability of sugar molecules to form H-bonds through hydroxyl groups with surrounding water, while producing a more effective retardation, it drastically reduces the spatial extent of the perturbation on the H-bond network. In addition, the analysis of the concentration dependence of the hydration number reveals the aptitude of levoglucosan to produce large aggregates in solution. The analysis of shear viscosity and rotational diffusion time suggests a very short lifetime for these aggregates, typically faster than ≈20 ps.

Effect of Methylation on Local Mechanics and Hydration Structure of DNA.

PubMed

Teng, Xiaojing; Hwang, Wonmuk

2018-04-24

Cytosine methylation affects mechanical properties of DNA and potentially alters the hydration fingerprint for recognition by proteins. The atomistic origin for these effects is not well understood, and we address this via all-atom molecular dynamics simulations. We find that the stiffness of the methylated dinucleotide step changes marginally, whereas the neighboring steps become stiffer. Stiffening is further enhanced for consecutively methylated steps, providing a mechanistic origin for the effect of hypermethylation. Steric interactions between the added methyl groups and the nonpolar groups of the neighboring nucleotides are responsible for the stiffening in most cases. By constructing hydration maps, we found that methylation also alters the surface hydration structure in distinct ways. Its resistance to deformation may contribute to the stiffening of DNA for deformational modes lacking steric interactions. These results highlight the sequence- and deformational-mode-dependent effects of cytosine methylation. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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.

Water Dynamics in the Hydration Shells of Biomolecules

PubMed Central

2017-01-01

The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water. PMID:28248491

Dehydration process in NaCl solutions under various external electric fields

NASA Astrophysics Data System (ADS)

Kadota, Kazunori; Shimosaka, Atsuko; Shirakawa, Yoshiyuki; Hidaka, Jusuke

2007-06-01

Ionic motions at solid-liquid interface in supersaturated NaCl solutions have been investigated by molecular dynamics (MD) simulation for understanding crystal growth processes. The density profile in the vicinity of the interfaces between NaCl(100) and the supersaturated NaCl solution was calculated. Diffusion coefficients of water molecules in the solution were estimated as a function of distance from the crystal interface. It turned out that the structure and dynamics of the solution in the interfaces was different from those of bulk solution owing to electric fields depending on the surface charge. Therefore, the electric field was applied to the supersaturated solutions and dehydration phenomenon occurring in the process of the crystal growth was discussed. As the electric field increased, it was observed that the Na+ keeping strongly hydration structure broke out by the electric force. In supersaturated concentration, the solution structure is significantly different from that of dilution and has a complicated structure with hydration ions and clusters of NaCl. If the electric fields were applied to the solutions, the breakout of hydration structure was not affected with increasing the supersaturated ratio. This reason is that the cluster structures are destroyed by the electric force. The situation depends on the electric field or crystal surface structure.

Origin of diverse time scales in the protein hydration layer solvation dynamics: A simulation study

NASA Astrophysics Data System (ADS)

Mondal, Sayantan; Mukherjee, Saumyak; Bagchi, Biman

2017-10-01

In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics, we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems, namely, lysozyme, myoglobin, and sweet protein monellin. In these experiments, we mutate the charges of the neighbouring amino acid side chains of certain natural probes (tryptophan) and also freeze the side chain motions. In order to distinguish between different contributions, we decompose the total solvation energy response in terms of various components present in the system. This allows us to capture the interplay among different self- and cross-energy correlation terms. Freezing the protein motions removes the slowest component that results from side chain fluctuations, but a part of slowness remains. This leads to the conclusion that the slow component approximately in the 20-80 ps range arises from slow water molecules present in the hydration layer. While the more than 100 ps component has multiple origins, namely, adjacent charges in amino acid side chains, hydrogen bonded water molecules and a dynamically coupled motion between side chain and water. In addition, the charges enforce a structural ordering of nearby water molecules and helps to form a local long-lived hydrogen bonded network. Further separation of the spatial and temporal responses in solvation dynamics reveals different roles of hydration and bulk water. We find that the hydration layer water molecules are largely responsible for the slow component, whereas the initial ultrafast decay arises predominantly (approximately 80%) due to the bulk. This agrees with earlier theoretical observations. We also attempt to rationalise our results with the help of a molecular hydrodynamic theory that was developed using classical time dependent density functional theory in a semi-quantitative manner.

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.

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.

Mapping hydration dynamics around a protein surface

PubMed Central

Zhang, Luyuan; Wang, Lijuan; Kao, Ya-Ting; Qiu, Weihong; Yang, Yi; Okobiah, Oghaghare; Zhong, Dongping

2007-01-01

Protein surface hydration is fundamental to its structure and activity. We report here the direct mapping of global hydration dynamics around a protein in its native and molten globular states, using a tryptophan scan by site-specific mutations. With 16 tryptophan mutants and in 29 different positions and states, we observed two robust, distinct water dynamics in the hydration layer on a few (≈1–8 ps) and tens to hundreds of picoseconds (≈20–200 ps), representing the initial local relaxation and subsequent collective network restructuring, respectively. Both time scales are strongly correlated with protein's structural and chemical properties. These results reveal the intimate relationship between hydration dynamics and protein fluctuations and such biologically relevant water–protein interactions fluctuate on picosecond time scales. PMID:18003912

Structure and collective dynamics of hydrated anti-freeze protein type III from 180 K to 298 K by X-ray diffraction and inelastic X-ray scattering

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

Yoshida, Koji; Baron, Alfred Q. R.; Uchiyama, Hiroshi

We investigated hydrated antifreeze protein type III (AFP III) powder with a hydration level h (=mass of water/mass of protein) of 0.4 in the temperature range between 180 K and 298 K using X-ray diffraction and inelastic X-ray scattering (IXS). The X-ray diffraction data showed smooth, largely monotonic changes between 180 K and 298 K without freezing water. Meanwhile, the collective dynamics observed by IXS showed a strong change in the sound velocity at 180 K, after being largely temperature independent at higher temperatures (298–220 K). We interpret this change in terms of the dynamic transition previously discussed using othermore » probes including THz IR absorption spectroscopy and incoherent elastic and quasi-elastic neutron scattering. This finding suggests that the dynamic transition of hydrated proteins is observable on the subpicosecond time scale as well as nano- and pico-second scales, both in collective dynamics from IXS and single particle dynamics from neutron scattering. Moreover, it is most likely that the dynamic transition of hydrated AFP III is not directly correlated with its hydration structure.« less

Structure and collective dynamics of hydrated anti-freeze protein type III from 180 K to 298 K by X-ray diffraction and inelastic X-ray scattering

NASA Astrophysics Data System (ADS)

Yoshida, Koji; Baron, Alfred Q. R.; Uchiyama, Hiroshi; Tsutsui, Satoshi; Yamaguchi, Toshio

2016-04-01

We investigated hydrated antifreeze protein type III (AFP III) powder with a hydration level h (=mass of water/mass of protein) of 0.4 in the temperature range between 180 K and 298 K using X-ray diffraction and inelastic X-ray scattering (IXS). The X-ray diffraction data showed smooth, largely monotonic changes between 180 K and 298 K without freezing water. Meanwhile, the collective dynamics observed by IXS showed a strong change in the sound velocity at 180 K, after being largely temperature independent at higher temperatures (298-220 K). We interpret this change in terms of the dynamic transition previously discussed using other probes including THz IR absorption spectroscopy and incoherent elastic and quasi-elastic neutron scattering. This finding suggests that the dynamic transition of hydrated proteins is observable on the subpicosecond time scale as well as nano- and pico-second scales, both in collective dynamics from IXS and single particle dynamics from neutron scattering. Moreover, it is most likely that the dynamic transition of hydrated AFP III is not directly correlated with its hydration structure.

Structure and collective dynamics of hydrated anti-freeze protein type III from 180 K to 298 K by X-ray diffraction and inelastic X-ray scattering.

PubMed

Yoshida, Koji; Baron, Alfred Q R; Uchiyama, Hiroshi; Tsutsui, Satoshi; Yamaguchi, Toshio

2016-04-07

We investigated hydrated antifreeze protein type III (AFP III) powder with a hydration level h (=mass of water/mass of protein) of 0.4 in the temperature range between 180 K and 298 K using X-ray diffraction and inelastic X-ray scattering (IXS). The X-ray diffraction data showed smooth, largely monotonic changes between 180 K and 298 K without freezing water. Meanwhile, the collective dynamics observed by IXS showed a strong change in the sound velocity at 180 K, after being largely temperature independent at higher temperatures (298-220 K). We interpret this change in terms of the dynamic transition previously discussed using other probes including THz IR absorption spectroscopy and incoherent elastic and quasi-elastic neutron scattering. This finding suggests that the dynamic transition of hydrated proteins is observable on the subpicosecond time scale as well as nano- and pico-second scales, both in collective dynamics from IXS and single particle dynamics from neutron scattering. Moreover, it is most likely that the dynamic transition of hydrated AFP III is not directly correlated with its hydration structure.

Dynamics of biopolymers on nanomaterials studied by quasielastic neutron scattering and MD simulations

NASA Astrophysics Data System (ADS)

Dhindsa, Gurpreet K.

Neutron scattering has been proved to be a powerful tool to study the dynamics of biological systems under various conditions. This thesis intends to utilize neutron scattering techniques, combining with MD simulations, to develop fundamental understanding of several biologically interesting systems. Our systems include a drug delivery system containing Nanodiamonds with nucleic acid (RNA), and two specific model proteins, beta-Casein and Inorganic Pyrophosphatase (IPPase). RNA and nanodiamond (ND) both are suitable for drug-delivery applications in nano-biotechnology. The architecturally flexible RNA with catalytic functionality forms nanocomposites that can treat life-threatening diseases. The non-toxic ND has excellent mechanical and optical properties and functionalizable high surface area, and thus actively considered for biomedical applications. In this thesis, we utilized two tools, quasielastic neutron scattering (QENS) and Molecular Dynamics Simulations to probe the effect of ND on RNA dynamics. Our work provides fundamental understanding of how hydrated RNA motions are affected in the RNA-ND nanocomposites. From the experimental and Molecular Dynamics Simulation (MD), we found that hydrated RNA motion is faster on ND surface than a freestanding one. MD Simulation results showed that the failure of Stokes Einstein relation results the presence of dynamic heterogeneities in the biomacromolecules. Radial pair distribution function from MD Simulation confirmed that the hydrophilic nature of ND attracts more water than RNA results the de-confinement of RNA on ND. Therefore, RNA exhibits faster motion in the presence of ND than freestanding RNA. In the second project, we studied the dynamics of a natively disordered protein beta-Casein which lacks secondary structures. In this study, the temperature and hydration effects on the dynamics of beta-Casein are explored by Quasielastic Neutron Scattering (QENS). We investigated the mean square displacement (MSD) of hydrated and dry beta-Casein as a function of temperature, to study the effect of hydration on their flexibility. The Elastic Incoherent Structure Factor (EISF) in the energy domain reveals the fraction of hydrogen atoms participating in motion in a sphere of diffusion. In the time domain analysis, a logarithmic-like decay is observed in the range of picosecond to nanosecond (beta-relaxation time) in the dynamics of hydrated beta-Casein. Our temperature dependent QENS experiments provide evidence that lack of secondary structure in beta-Casein results in higher flexibility in its dynamics and easier reversible thermal unfolding compared to other rigid biomolecules. Lastly, we studied the domain motion of IPPase protein by Neutron Spin Echo Spectroscopy (NSE). We found that decrease in diffusion coefficient belongs to domain motion of IPPase. Moreover, Rg is varied by temperature and concentration.

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

Molecular dynamics simulations of methane hydrate using polarizable force fields

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

Jiang, H.N.; Jordan, K.D.; Taylor, C.E.

2007-03-01

Molecular dynamics simulations of methane hydrate have been carried out using the AMOEBA and COS/G2 polarizable force fields. Properties examined include the temperature dependence of the lattice constant, the OC and OO radial distribution functions and the vibrational spectra. Both the AMOEBA and COS/G2 models are found to successfully account for the available experimental data, with overall slightly better agreement with experiment being found for the AMOEBA model. Several properties calculated using the AMOEBA and COS/G2 models differ appreciable from the corresponding results obtained previously using the polarizable TIP4P-FQ model. This appears to be due to the inadequacy of themore » treatment of polarization, especially, the restriction of polarization to in-plane only, in the TIP4P-FQ model.« less

Microscopic relaxations in a protein sustained down to 160K in a non-glass forming organic solvent.

PubMed

Mamontov, E; O'Neill, H

2017-01-01

We have studied microscopic dynamics of a protein in carbon disulfide, a non-glass forming solvent, down to its freezing temperature of ca. 160K. We have utilized quasielastic neutron scattering. A comparison of lysozyme hydrated with water and dissolved in carbon disulfide reveals a stark difference in the temperature dependence of the protein's microscopic relaxation dynamics induced by the solvent. In the case of hydration water, the common protein glass-forming solvent, the protein relaxation slows down in response to a large increase in the water viscosity on cooling down, exhibiting a well-known protein dynamical transition. The dynamical transition disappears in non-glass forming carbon disulfide, whose viscosity remains a weak function of temperature all the way down to freezing at just below 160K. The microscopic relaxation dynamics of lysozyme dissolved in carbon disulfide is sustained down to the freezing temperature of its solvent at a rate similar to that measured at ambient temperature. Our results demonstrate that protein dynamical transition is not merely solvent-assisted, but rather solvent-induced, or, more precisely, is a reflection of the temperature dependence of the solvent's glass-forming dynamics. We hypothesize that, if the long debated idea regarding the direct link between the microscopic relaxations and the biological activity in proteins is correct, then not only the microscopic relaxations, but also the activity, could be sustained in proteins all the way down to the freezing temperature of a non-glass forming solvent with a weak temperature dependence of its viscosity. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo. Copyright © 2016 Elsevier B.V. All rights reserved.

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

Origin of Self-preservation Effect for Hydrate Decomposition: Coupling of Mass and Heat Transfer Resistances

PubMed Central

Bai, Dongsheng; Zhang, Diwei; Zhang, Xianren; Chen, Guangjin

2015-01-01

Gas hydrates could show an unexpected high stability at conditions out of thermodynamic equilibrium, which is called the self-preservation effect. The mechanism of the effect for methane hydrates is here investigated via molecular dynamics simulations, in which an NVT/E method is introduced to represent different levels of heat transfer resistance. Our simulations suggest a coupling between the mass transfer resistance and heat transfer resistance as the driving mechanism for self-preservation effect. We found that the hydrate is initially melted from the interface, and then a solid-like water layer with temperature-dependent structures is formed next to the hydrate interface that exhibits fractal feature, followed by an increase of mass transfer resistance for the diffusion of methane from hydrate region. Furthermore, our results indicate that heat transfer resistance is a more fundamental factor, since it facilitates the formation of the solid-like layer and hence inhibits the further dissociation of the hydrates. The self-preservation effect is found to be enhanced with the increase of pressure and particularly the decrease of temperature. Kinetic equations based on heat balance calculations is also developed to describe the self-preservation effect, which reproduces our simulation results well and provides an association between microscopic and macroscopic properties. PMID:26423519

Origin of Self-preservation Effect for Hydrate Decomposition: Coupling of Mass and Heat Transfer Resistances.

PubMed

Bai, Dongsheng; Zhang, Diwei; Zhang, Xianren; Chen, Guangjin

2015-10-01

Gas hydrates could show an unexpected high stability at conditions out of thermodynamic equilibrium, which is called the self-preservation effect. The mechanism of the effect for methane hydrates is here investigated via molecular dynamics simulations, in which an NVT/E method is introduced to represent different levels of heat transfer resistance. Our simulations suggest a coupling between the mass transfer resistance and heat transfer resistance as the driving mechanism for self-preservation effect. We found that the hydrate is initially melted from the interface, and then a solid-like water layer with temperature-dependent structures is formed next to the hydrate interface that exhibits fractal feature, followed by an increase of mass transfer resistance for the diffusion of methane from hydrate region. Furthermore, our results indicate that heat transfer resistance is a more fundamental factor, since it facilitates the formation of the solid-like layer and hence inhibits the further dissociation of the hydrates. The self-preservation effect is found to be enhanced with the increase of pressure and particularly the decrease of temperature. Kinetic equations based on heat balance calculations is also developed to describe the self-preservation effect, which reproduces our simulation results well and provides an association between microscopic and macroscopic properties.

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.

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

Dynamics of Model Hydraulic Fracturing Liquid Studied by Two-Dimensional Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Daley, Kim; Kubarych, Kevin J.

2014-06-01

The technique of two-dimensional infrared (2DIR) spectroscopy is used to expose the chemical dynamics of various concentrations of polymers and their monomers in heterogeneous mixtures. An environmentally relevant heterogeneous mixture, which inspires this study, is hydraulic fracturing liquid (HFL). Hydraulic fracking is a technique used to extract natural gas from shale deposits. HFL consists of mostly water, proppant (sand), an emulsifier (guar), and other chemicals specific to the drilling site. Utilizing a metal carbonyl as a probe, we observe the spectral dynamics of the polymer, guar, and its monomer, mannose, and compare the results to see how hydration dynamics change with varying concentration. Another polymer, Ficoll, and its monomer, sucrose, are also compared to see how polymer size affects hydration dynamics. The two results are as follows: (1) Guar experiences collective hydration at high concentrations, where as mannose experiences independent hydration; (2) no collective hydration is observed for Ficoll in the same concentration range as guar, possibly due to polymer shape and size. HFL experiences extremely high pressure during natural gas removal, so future studies will focus on how increased pressure affects the hydration dynamics of polymers and monomers.

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.

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

Individual-Based Model of Microbial Life on Hydrated Rough Soil Surfaces

PubMed Central

Kim, Minsu; Or, Dani

2016-01-01

Microbial life in soil is perceived as one of the most interesting ecological systems, with microbial communities exhibiting remarkable adaptability to vast dynamic environmental conditions. At the same time, it is a notoriously challenging system to understand due to its complexity including physical, chemical, and biological factors in synchrony. This study presents a spatially-resolved model of microbial dynamics on idealised rough soil surfaces represented as patches with different (roughness) properties that preserve the salient hydration physics of real surfaces. Cell level microbial interactions are considered within an individual-based formulation including dispersion and various forms of trophic dependencies (competition, mutualism). The model provides new insights into mechanisms affecting microbial community dynamics and gives rise to spontaneous formation of microbial community spatial patterns. The framework is capable of representing many interacting species and provides diversity metrics reflecting surface conditions and their evolution over time. A key feature of the model is its spatial scalability that permits representation of microbial processes from cell-level (micro-metric scales) to soil representative volumes at sub-metre scales. Several illustrative examples of microbial trophic interactions and population dynamics highlight the potential of the proposed modelling framework to quantitatively study soil microbial processes. The model is highly applicable in a wide range spanning from quantifying spatial organisation of multiple species under various hydration conditions to predicting microbial diversity residing in different soils. PMID:26807803

Coupling between the Dynamics of Water and Surfactants in Lyotropic Liquid Crystals.

PubMed

McDaniel, Jesse G; Yethiraj, Arun

2017-05-18

Bilayers composed of lipid or surfactant molecules are central to biological membranes and lamellar lyotropic liquid crystalline (LLC) phases. Common to these systems are phases that exhibit either ordered or disordered packing of the hydrophobic tails. In this work, we study the impact of surfactant ordering, i.e., disordered L α and ordered L β LLC phases, on the dynamics of water and sodium ions in the lamellar phases of dicarboxylate gemini surfactants. We study the different phases at identical hydration levels by changing the length of the hydrophobic tails; surfactants with shorter tails form L α phases and those with longer tails form L β phases. We find that the L α phases exhibit lower density and greater compressibility than the L β phases, with a hydration-dependent headgroup surface area. These structural differences significantly affect the relative dynamic properties of the phases, primarily the mobility of the surfactant molecules tangential to the bilayer surface, as well as the rates of water and ion diffusion. We find ∼20-50% faster water diffusion in the L α phases compared to the L β phases, with the differences most pronounced at low hydration. This coupling between water dynamics and surfactant mobility is verified using additional simulations in which the surfactant tails are frozen. Our study indicates that gemini surfactant LLCs provide an important prototypical system for characterizing properties shared with more complex biological lipid membranes.

Unique rheological behavior of chitosan-modified nanoclay at highly hydrated state.

PubMed

Liang, Songmiao; Liu, Linshu; Huang, Qingrong; Yam, Kit L

2009-04-30

This work attempts to explore the dynamic and steady-state rheological properties of chitosan modified clay (CMCs) at highly hydrated state. CMCs with different initial chitosan/clay weight ratios (s) were prepared from pre-exfoliated clay via electrostatic adsorption process. Thermogravimetric analysis and optical microscopy were used to determine the adsorbed content of chitosan (m) in CMCs and the microstructure of CMCs at highly hydrated state, respectively. Dynamic rheological results indicate that both stress-strain behavior and moduli of CMCs exhibit strong dependence on m. Shear-thinning behavior for all of CMCs is observed and further confirmed by steady-state shear test. Interestingly, two unique transitions, denoted as a small peak region of the shear viscosity for CMCs with m > 2.1% and a sharp drop region of the shear viscosity for CMCs with m

Methanol incorporation in clathrate hydrates and the implications for oil and gas pipeline flow assurance and icy planetary bodies

PubMed Central

Shin, Kyuchul; Udachin, Konstantin A.; Moudrakovski, Igor L.; Leek, Donald M.; Alavi, Saman; Ratcliffe, Christopher I.; Ripmeester, John A.

2013-01-01

One of the best-known uses of methanol is as antifreeze. Methanol is used in large quantities in industrial applications to prevent methane clathrate hydrate blockages from forming in oil and gas pipelines. Methanol is also assigned a major role as antifreeze in giving icy planetary bodies (e.g., Titan) a liquid subsurface ocean and/or an atmosphere containing significant quantities of methane. In this work, we reveal a previously unverified role for methanol as a guest in clathrate hydrate cages. X-ray diffraction (XRD) and NMR experiments showed that at temperatures near 273 K, methanol is incorporated in the hydrate lattice along with other guest molecules. The amount of included methanol depends on the preparative method used. For instance, single-crystal XRD shows that at low temperatures, the methanol molecules are hydrogen-bonded in 4.4% of the small cages of tetrahydrofuran cubic structure II hydrate. At higher temperatures, NMR spectroscopy reveals a number of methanol species incorporated in hydrocarbon hydrate lattices. At temperatures characteristic of icy planetary bodies, vapor deposits of methanol, water, and methane or xenon show that the presence of methanol accelerates hydrate formation on annealing and that there is unusually complex phase behavior as revealed by powder XRD and NMR spectroscopy. The presence of cubic structure I hydrate was confirmed and a unique hydrate phase was postulated to account for the data. Molecular dynamics calculations confirmed the possibility of methanol incorporation into the hydrate lattice and show that methanol can favorably replace a number of methane guests. PMID:23661058

Methanol incorporation in clathrate hydrates and the implications for oil and gas pipeline flow assurance and icy planetary bodies.

PubMed

Shin, Kyuchul; Udachin, Konstantin A; Moudrakovski, Igor L; Leek, Donald M; Alavi, Saman; Ratcliffe, Christopher I; Ripmeester, John A

2013-05-21

One of the best-known uses of methanol is as antifreeze. Methanol is used in large quantities in industrial applications to prevent methane clathrate hydrate blockages from forming in oil and gas pipelines. Methanol is also assigned a major role as antifreeze in giving icy planetary bodies (e.g., Titan) a liquid subsurface ocean and/or an atmosphere containing significant quantities of methane. In this work, we reveal a previously unverified role for methanol as a guest in clathrate hydrate cages. X-ray diffraction (XRD) and NMR experiments showed that at temperatures near 273 K, methanol is incorporated in the hydrate lattice along with other guest molecules. The amount of included methanol depends on the preparative method used. For instance, single-crystal XRD shows that at low temperatures, the methanol molecules are hydrogen-bonded in 4.4% of the small cages of tetrahydrofuran cubic structure II hydrate. At higher temperatures, NMR spectroscopy reveals a number of methanol species incorporated in hydrocarbon hydrate lattices. At temperatures characteristic of icy planetary bodies, vapor deposits of methanol, water, and methane or xenon show that the presence of methanol accelerates hydrate formation on annealing and that there is unusually complex phase behavior as revealed by powder XRD and NMR spectroscopy. The presence of cubic structure I hydrate was confirmed and a unique hydrate phase was postulated to account for the data. Molecular dynamics calculations confirmed the possibility of methanol incorporation into the hydrate lattice and show that methanol can favorably replace a number of methane guests.

Computational solvation dynamics of oxyquinolinium betaine linked to trehalose.

PubMed

Heid, Esther; Schröder, Christian

2016-10-28

Studying the changed water dynamics in the hydration layers of biomolecules is an important step towards fuller understanding of their function and mechanisms, but has shown to be quite difficult. The measurement of the time-dependent Stokes shift of a chromophore attached to the biomolecule is a promising method to achieve this goal, as published in Sajadi et al. [J. Phys. Chem. Lett., 5, 1845 (2014).] where trehalose was used as biomolecule, 1-methyl-6-oxyquinolinium betaine as chromophore, and water as solvent. An overall retardation of solvent molecules is then obtained by comparison of the linked system to the same system without trehalose, but contributions from different subgroups of solvent molecules, for example, molecules close to or far from trehalose, are unknown. The difficulty arising from these unknown contributions of retarded and possibly unretarded solvent molecules is overcome in this work by conducting computer simulations on this system and decomposing the overall signal into the contributions from various molecules at different locations. We performed non-equilibrium molecular dynamics simulation using a polarizable water model and a non-polarizable solute model and could reproduce the experimental time-dependent Stokes shift accurately for the linked trehalose-oxyquinolinium and the pure oxyquinolinium over a wide temperature range, indicating the correctness of our employed models. Decomposition of the shift into contributions from different solvent subgroups showed that the amplitude of the measured shift is made up only half by the desired retarded solvent molecules in the hydration layer, but to another half by unretarded bulk water, so that measured relaxation times of the overall Stokes shift are only a lower boundary for the true relaxation times in the hydration layer of trehalose. As a side effect, the results on the effect of trehalose on solvation dynamics contribute to the long standing debate on the range of influence of trehalose on water dynamics, the number of retarded solvent molecules, and the observed retardation factor when compared to bulk water.

Computational solvation dynamics of oxyquinolinium betaine linked to trehalose

NASA Astrophysics Data System (ADS)

Heid, Esther; Schröder, Christian

2016-10-01

Studying the changed water dynamics in the hydration layers of biomolecules is an important step towards fuller understanding of their function and mechanisms, but has shown to be quite difficult. The measurement of the time-dependent Stokes shift of a chromophore attached to the biomolecule is a promising method to achieve this goal, as published in Sajadi et al. [J. Phys. Chem. Lett., 5, 1845 (2014).] where trehalose was used as biomolecule, 1-methyl-6-oxyquinolinium betaine as chromophore, and water as solvent. An overall retardation of solvent molecules is then obtained by comparison of the linked system to the same system without trehalose, but contributions from different subgroups of solvent molecules, for example, molecules close to or far from trehalose, are unknown. The difficulty arising from these unknown contributions of retarded and possibly unretarded solvent molecules is overcome in this work by conducting computer simulations on this system and decomposing the overall signal into the contributions from various molecules at different locations. We performed non-equilibrium molecular dynamics simulation using a polarizable water model and a non-polarizable solute model and could reproduce the experimental time-dependent Stokes shift accurately for the linked trehalose-oxyquinolinium and the pure oxyquinolinium over a wide temperature range, indicating the correctness of our employed models. Decomposition of the shift into contributions from different solvent subgroups showed that the amplitude of the measured shift is made up only half by the desired retarded solvent molecules in the hydration layer, but to another half by unretarded bulk water, so that measured relaxation times of the overall Stokes shift are only a lower boundary for the true relaxation times in the hydration layer of trehalose. As a side effect, the results on the effect of trehalose on solvation dynamics contribute to the long standing debate on the range of influence of trehalose on water dynamics, the number of retarded solvent molecules, and the observed retardation factor when compared to bulk water.

Temperature-dependent dynamical transitions of different classes of amino acid residue in a globular protein.

PubMed

Miao, Yinglong; Yi, Zheng; Glass, Dennis C; Hong, Liang; Tyagi, Madhusudan; Baudry, Jerome; Jain, Nitin; Smith, Jeremy C

2012-12-05

The temperature dependences of the nanosecond dynamics of different chemical classes of amino acid residue have been analyzed by combining elastic incoherent neutron scattering experiments with molecular dynamics simulations on cytochrome P450cam. At T = 100-160 K, anharmonic motion in hydrophobic and aromatic residues is activated, whereas hydrophilic residue motions are suppressed because of hydrogen-bonding interactions. In contrast, at T = 180-220 K, water-activated jumps of hydrophilic side chains, which are strongly coupled to the relaxation rates of the hydrogen bonds they form with hydration water, become apparent. Thus, with increasing temperature, first the hydrophobic core awakens, followed by the hydrophilic surface.

Striped gold nanoparticles: New insights from molecular dynamics simulations

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

Velachi, Vasumathi, E-mail: vasuphy@gmail.com; Cordeiro, M. Natália D. S., E-mail: ncordeir@fc.up.pt; Bhandary, Debdip

Recent simulations have improved our knowledge of the molecular-level structure and hydration properties of mixed self-assembled monolayers (SAMs) with equal and unequal alkyl thiols at three different arrangements, namely, random, patchy, and Janus. In our previous work [V. Vasumathi et al., J. Phys. Chem. C 119, 3199–3209 (2015)], we showed that the bending of longer thiols over shorter ones clearly depends on the thiols’ arrangements and chemical nature of their terminal groups. In addition, such a thiol bending revealed to have a strong impact on the structural and hydration properties of SAMs coated on gold nanoparticles (AuNPs). In this paper,more » we extend our previous atomistic simulation study to investigate the bending of longer thiols by increasing the stripe thickness of mixed SAMs of equal and unequal lengths coated on AuNPs. We study also the effect of stripe thickness on the structural morphology and hydration of the coated SAMs. Our results show that the structural and hydration properties of SAMs are affected by the stripe thickness for mixtures of alkyl thiols with unequal chain length but not for equal length. Hence, the stability of the stripe configuration depends on the alkyl’s chain length, the length difference between the thiol mixtures, and solvent properties.« less

Does fluoride disrupt hydrogen bond network in cationic lipid bilayer? Time-dependent fluorescence shift of Laurdan and molecular dynamics simulations

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

Pokorna, Sarka; Jurkiewicz, Piotr; Hof, Martin, E-mail: martin.hof@jh-inst.cas.cz

2014-12-14

Time-dependent fluorescence shift (TDFS) of Laurdan embedded in phospholipid bilayers reports on hydration and mobility of the phospholipid acylgroups. Exchange of H{sub 2}O with D{sub 2}O prolongs the lifetime of lipid-water and lipid-water-lipid interactions, which is reflected in a significantly slower TDFS kinetics. Combining TDFS measurements in H{sub 2}O and D{sub 2}O hydrated bilayers with atomistic molecular dynamics (MD) simulations provides a unique tool for characterization of the hydrogen bonding at the acylgroup level of lipid bilayers. In this work, we use this approach to study the influence of fluoride anions on the properties of cationic bilayers composed of trimethylammonium-propanemore » (DOTAP). The results obtained for DOTAP are confronted with those for neutral phosphatidylcholine (DOPC) bilayers. Both in DOTAP and DOPC H{sub 2}O/D{sub 2}O exchange prolongs hydrogen-bonding lifetime and does not disturb bilayer structure. These results are confirmed by MD simulations. TDFS experiments show, however, that for DOTAP this effect is cancelled in the presence of fluoride ions. We interpret these results as evidence that strongly hydrated fluoride is able to steal water molecules that bridge lipid carbonyls. Consequently, when attracted to DOTAP bilayer, fluoride disrupts the local hydrogen-bonding network, and the differences in TDFS kinetics between H{sub 2}O and D{sub 2}O hydrated bilayers are no longer observed. A distinct behavior of fluoride is also evidenced by MD simulations, which show different lipid-ion binding for Cl{sup −} and F{sup −}.« less

Hydration dynamics promote bacterial coexistence on rough surfaces

PubMed Central

Wang, Gang; Or, Dani

2013-01-01

Identification of mechanisms that promote and maintain the immense microbial diversity found in soil is a central challenge for contemporary microbial ecology. Quantitative tools for systematic integration of complex biophysical and trophic processes at spatial scales, relevant for individual cell interactions, are essential for making progress. We report a modeling study of competing bacterial populations cohabiting soil surfaces subjected to highly dynamic hydration conditions. The model explicitly tracks growth, motion and life histories of individual bacterial cells on surfaces spanning dynamic aqueous networks that shape heterogeneous nutrient fields. The range of hydration conditions that confer physical advantages for rapidly growing species and support competitive exclusion is surprisingly narrow. The rapid fragmentation of soil aqueous phase under most natural conditions suppresses bacterial growth and cell dispersion, thereby balancing conditions experienced by competing populations with diverse physiological traits. In addition, hydration fluctuations intensify localized interactions that promote coexistence through disproportional effects within densely populated regions during dry periods. Consequently, bacterial population dynamics is affected well beyond responses predicted from equivalent and uniform hydration conditions. New insights on hydration dynamics could be considered in future designs of soil bioremediation activities, affect longevity of dry food products, and advance basic understanding of bacterial diversity dynamics and its role in global biogeochemical cycles. PMID:23051694

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.

A molecular dynamics study on sI hydrogen hydrate.

PubMed

Mondal, S; Ghosh, S; Chattaraj, P K

2013-07-01

A molecular dynamics simulation is carried out to explore the possibility of using sI clathrate hydrate as hydrogen storage material. Metastable hydrogen hydrate structures are generated using the LAMMPS software. Different binding energies and radial distribution functions provide important insights into the behavior of the various types of hydrogen and oxygen atoms present in the system. Clathrate hydrate cages become more stable in the presence of guest molecules like hydrogen.

Uncoupled poroelastic and intrinsic viscoelastic dissipation in cartilage.

PubMed

Han, Guebum; Hess, Cole; Eriten, Melih; Henak, Corinne R

2018-04-26

This paper studies uncoupled poroelastic (flow-dependent) and intrinsic viscoelastic (flow-independent) energy dissipation mechanisms via their dependence on characteristic lengths to understand the root of cartilage's broadband dissipation behavior. Phase shift and dynamic modulus were measured from dynamic microindentation tests conducted on hydrated cartilage at different contact radii, as well as on dehydrated cartilage. Cartilage weight and thickness were recorded during dehydration. Phase shifts revealed poroelastic- and viscoelastic-dominant dissipation regimes in hydrated cartilage. Specifically, phase shift at a relatively small radius was governed by poroviscoelasticity, while phase shift at a relatively large radius was dominantly governed by intrinsic viscoelasticity. The uncoupled dissipation mechanisms demonstrated that intrinsic viscoelastic dissipation provided sustained broadband dissipation for all length scales, and additional poroelastic dissipation increased total dissipation at small length scales. Dehydration decreased intrinsic viscoelastic dissipation of cartilage. The findings demonstrated a possibility to measure poroelastic and intrinsic viscoelastic properties of cartilage at similar microscale lengths. Also they encouraged development of broadband cartilage like-dampers and provided important design parameters to maximize their performance. Copyright © 2018 Elsevier Ltd. All rights reserved.

Influence of hydrostatic pressure on dynamics and spatial distribution of protein partial molar volume: time-resolved surficial Kirkwood-Buff approach.

PubMed

Yu, Isseki; Tasaki, Tomohiro; Nakada, Kyoko; Nagaoka, Masataka

2010-09-30

The influence of hydrostatic pressure on the partial molar volume (PMV) of the protein apomyoglobin (AMb) was investigated by all-atom molecular dynamics (MD) simulations. Using the time-resolved Kirkwood-Buff (KB) approach, the dynamic behavior of the PMV was identified. The simulated time average value of the PMV and its reduction by 3000 bar pressurization correlated with experimental data. In addition, with the aid of the surficial KB integral method, we obtained the spatial distributions of the components of PMV to elucidate the detailed mechanism of the PMV reduction. New R-dependent PMV profiles identified the regions that increase or decrease the PMV under the high pressure condition. The results indicate that besides the hydration in the vicinity of the protein surface, the outer space of the first hydration layer also significantly influences the total PMV change. These results provide a direct and detailed picture of pressure induced PMV reduction.

Solvation and thermal effects on the optical properties of naturaldyes: a case study on the flavylium cyanin

NASA Astrophysics Data System (ADS)

Calzolari, Arrigo; Malcioglu, Baris; Gebauer, Ralph; Varsano, Daniele; Baroni, Stefano

2011-03-01

We present a first-principles study of the effects of both hydration and thermal dynamics on the optical properties of a natural anthocyanin dye, namely, cyanin (Cya), in aqueous solution. We combine Car-Parrinello molecular dynamics and time-dependent density functional theory (TDDFT) approaches to simulate the time evolution of UV-vis spectrum of the hydrated Cya molecule at room temperature [2,3]. The spectrum of the dye calculated in the gas phase is characterized by two peaks in the red and in the blue, which would bring about a greenish hue incompatible with the dark purple coloration observed in nature. Describing the effect of the water solvent through a polarizable continuum model does not modify qualitatively the resulting picture. An explicit simulation of both solvent and thermal effects using ab-initio molecular dynamics results instead in a spectrum that is compatible with the observed coloration. This result is analyzed in terms of the spectroscopic effects of molecular distortions, induced by thermal fluctuations.

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

From hydration repulsion to dry adhesion between asymmetric hydrophilic and hydrophobic surfaces

PubMed Central

Kanduč, Matej; Netz, Roland R.

2015-01-01

Using all-atom molecular dynamics (MD) simulations at constant water chemical potential in combination with basic theoretical arguments, we study hydration-induced interactions between two overall charge-neutral yet polar planar surfaces with different wetting properties. Whether the water film between the two surfaces becomes unstable below a threshold separation and cavitation gives rise to long-range attraction, depends on the sum of the two individual surface contact angles. Consequently, cavitation-induced attraction also occurs for a mildly hydrophilic surface interacting with a very hydrophobic surface. If both surfaces are very hydrophilic, hydration repulsion dominates at small separations and direct attractive force contribution can—if strong enough—give rise to wet adhesion in this case. In between the regimes of cavitation-induced attraction and hydration repulsion we find a narrow range of contact angle combinations where the surfaces adhere at contact in the absence of cavitation. This dry adhesion regime is driven by direct surface–surface interactions. We derive simple laws for the cavitation transition as well as for the transition between hydration repulsion and dry adhesion, which favorably compare with simulation results in a generic adhesion state diagram as a function of the two surface contact angles. PMID:26392526

Hydration-dependent dynamics of water in calcium-silicate-hydrate: A QENS study by global model.

PubMed

Le, Peisi; Fratini, Emiliano; Chen, Sow-Hsin

2018-02-02

In a saturated cement paste, there are three different types of water: the structural water chemically reacted with cement, the constrained water absorbed to the surface of the pores, and the free water in the center of the pores. Each type has different physicochemical state and unique relation to cement porosity. The different water types have different dynamics which can be detected using quasi-elastic neutron scattering (QENS). Since the porosity of a hardened cement paste is impacted strongly by the water to cement ratio (w/c), it should be possible to extract the hydration dependence of the pores by exploiting the dynamical parameters of the confined water. Three C-S-H samples with different water levels, 8%, 17% and 30% were measured using QENS. The measurements were carried out in the scattering vector, Q, range from 0.5 Å -1 to 1.3 Å -1 , and in the temperature interval from 230 K to 280 K. The data were analyzed using a novel global model developed for cement QENS spectra. The results show that while increasing the water content, the structural water index (SWI) decreases and the confining radius, a, increases. Both SWI and a have a linear relationship with the water content. The Arrhenius plot of the translational relaxation time shows that the constrained water dominates the non-structural water at water contents lower than 17%. The rotational activation energy is smaller for lower water content. The analysis demonstrated that our newly proposed global model is practical and useful for analyzing cement QENS data. Copyright © 2018 Elsevier B.V. All rights reserved.

Collective hydration dynamics in some amino acid solutions: A combined GHz-THz spectroscopic study

NASA Astrophysics Data System (ADS)

Samanta, Nirnay; Das Mahanta, Debasish; Choudhury, Samiran; Barman, Anjan; Kumar Mitra, Rajib

2017-03-01

A detailed understanding of hydration of amino acids, the building units of protein, is a key step to realize the overall solvation processes in proteins. In the present contribution, we have made a combined GHz (0.2-50) to THz (0.3-2.0) experimental spectroscopic study to investigate the dynamics of water at room temperature in the presence of different amino acids (glycine, L-serine, L-lysine, L-tryptophan, L-arginine, and L-aspartic acid). The THz absorption coefficient, α(ν), of amino acids follows a trend defined by their solvent accessible surface area. The imaginary and real dielectric constants obtained in GHz and THz regions are fitted into multiple Debye model to obtain various relaxation times. The ˜100 ps time scale obtained in the GHz frequency region is attributed to the rotational motion of the amino acids. In the THz region, we obtain ˜8 ps and ˜200 fs time scales which are related to the cooperative dynamics of H-bond network and partial rotation or sudden jump of the under-coordinated water molecules. These time scales are found to be dependent on the amino acid type and the cooperative motion is found to be dependent on both the hydrophobic as well as the hydrophilic residue of amino acids.

Coupling between the Dynamics of Water and Surfactants in Lyotropic Liquid Crystals

DOE PAGES

McDaniel, Jesse G.; Yethiraj, Arun

2017-04-26

Bilayers composed of lipid or surfactant molecules are central to biological membranes and lamellar lyotropic liquid crystalline (LLC) phases. Common to these systems are phases that exhibit either ordered or disordered packing of the hydrophobic tails. In this work, we study the impact of surfactant ordering, i.e., disordered L α and ordered L β LLC phases, on the dynamics of water and sodium ions in the lamellar phases of dicarboxylate gemini surfactants. We study the different phases at identical hydration levels by changing the length of the hydrophobic tails; surfactants with shorter tails form L α phases and those withmore » longer tails form L β phases. We find that the L α phases exhibit lower density and greater compressibility than the L β phases, with a hydration-dependent headgroup surface area. These structural differences significantly affect the relative dynamic properties of the phases, primarily the mobility of the surfactant molecules tangential to the bilayer surface, as well as the rates of water and ion diffusion. We find ~20–50% faster water diffusion in the L α phases compared to the L β phases, with the differences most pronounced at low hydration. This coupling between water dynamics and surfactant mobility is verified using additional simulations in which the surfactant tails are frozen. Our study indicates that gemini surfactant LLCs provide an important prototypical system for characterizing properties shared with more complex biological lipid membranes.« less

Nanoscopic Dynamic Mechanical Properties of Intertubular and Peritubular Dentin

PubMed Central

Ryou, Heon; Romberg, Elaine; Pashley, David H.; Tay, Franklin R.; Arola, Dwayne

2011-01-01

An experimental evaluation of intertubular and peritubular dentin was performed using nanoindentation and Dynamic Mechanical Analysis (DMA). The objective of the investigation was to evaluate the differences in dynamic mechanical behavior of these two constituents and to assess if their response is frequency dependent. Specimens of hydrated coronal dentin were evaluated by DMA using single indents over a range in parametric conditions and using scanning probe microscopy. The complex (E*), storage (E’) and loss moduli (E”) of the intertubular and peritubular dentin were evaluated as a function of the dynamic loading frequency and static load in the fully hydrated condition. The mean complex E* (19.6 GPa) and storage E’ (19.2 GPa) moduli of the intertubular dentin were significantly lower than those quantities of peritubular dentin (E* = 31.1 GPa, p< 0.05; E’ = 30.3 GPa, p< 0.05). There was no significant influence of dynamic loading frequency on these measures. Though there was no significant difference in the loss modulus (E”) between the two materials (p> 0.05), both constituents exhibited a significant increase in E” with dynamic load frequency and reduction in the quasi-static component of indentation load. The largest difference in dynamic behavior of the two tissues was noted at small quasi-static indentation loads and the highest frequency. PMID:22340680

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

Water circulation and global mantle dynamics: Insight from numerical modeling

NASA Astrophysics Data System (ADS)

Nakagawa, Takashi; Nakakuki, Tomoeki; Iwamori, Hikaru

2015-05-01

We investigate water circulation and its dynamical effects on global-scale mantle dynamics in numerical thermochemical mantle convection simulations. Both dehydration-hydration processes and dehydration melting are included. We also assume the rheological properties of hydrous minerals and density reduction caused by hydrous minerals. Heat transfer due to mantle convection seems to be enhanced more effectively than water cycling in the mantle convection system when reasonable water dependence of viscosity is assumed, due to effective slab dehydration at shallow depths. Water still affects significantly the global dynamics by weakening the near-surface oceanic crust and lithosphere, enhancing the activity of surface plate motion compared to dry mantle case. As a result, including hydrous minerals, the more viscous mantle is expected with several orders of magnitude compared to the dry mantle. The average water content in the whole mantle is regulated by the dehydration-hydration process. The large-scale thermochemical anomalies, as is observed in the deep mantle, is found when a large density contrast between basaltic material and ambient mantle is assumed (4-5%), comparable to mineral physics measurements. Through this study, the effects of hydrous minerals in mantle dynamics are very important for interpreting the observational constraints on mantle convection.

Molecular dynamics simulations of methane hydrate using polarizable force fields

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

Jiang, H.N.; Jordan, K.D.; Taylor, C.E.

2007-06-14

Molecular dynamics simulations of methane hydrate have been carried out using the polarizable AMOEBA and COS/G2 force fields. Properties calculated include the temperature dependence of the lattice constant, the OC and OO radial distribution functions, and the vibrational spectra. Both the AMOEBA and COS/G2 force fields are found to successfully account for the available experimental data, with overall somewhat better agreement with experiment being found for the AMOEBA model. Comparison is made with previous results obtained using TIP4P and SPC/E effective two-body force fields and the polarizable TIP4P-FQ force field, which allows for in-plane polarization only. Significant differences are foundmore » between the properties calculated using the TIP4P-FQ model and those obtained using the other models, indicating an inadequacy of restricting explicit polarization to in-plane onl« less

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

Water of Hydration Dynamics in Minerals Gypsum and Bassanite: Ultrafast 2D IR Spectroscopy of Rocks.

PubMed

Yan, Chang; Nishida, Jun; Yuan, Rongfeng; Fayer, Michael D

2016-08-03

Water of hydration plays an important role in minerals, determining their crystal structures and physical properties. Here ultrafast nonlinear infrared (IR) techniques, two-dimensional infrared (2D IR) and polarization selective pump-probe (PSPP) spectroscopies, were used to measure the dynamics and disorder of water of hydration in two minerals, gypsum (CaSO4·2H2O) and bassanite (CaSO4·0.5H2O). 2D IR spectra revealed that water arrangement in freshly precipitated gypsum contained a small amount of inhomogeneity. Following annealing at 348 K, water molecules became highly ordered; the 2D IR spectrum became homogeneously broadened (motional narrowed). PSPP measurements observed only inertial orientational relaxation. In contrast, water in bassanite's tubular channels is dynamically disordered. 2D IR spectra showed a significant amount of inhomogeneous broadening caused by a range of water configurations. At 298 K, water dynamics cause spectral diffusion that sampled a portion of the inhomogeneous line width on the time scale of ∼30 ps, while the rest of inhomogeneity is static on the time scale of the measurements. At higher temperature, the dynamics become faster. Spectral diffusion accelerates, and a portion of the lower temperature spectral diffusion became motionally narrowed. At sufficiently high temperature, all of the dynamics that produced spectral diffusion at lower temperatures became motionally narrowed, and only homogeneous broadening and static inhomogeneity were observed. Water angular motions in bassanite exhibit temperature-dependent diffusive orientational relaxation in a restricted cone of angles. The experiments were made possible by eliminating the vast amount of scattered light produced by the granulated powder samples using phase cycling methods.

Communication: modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions.

PubMed

Bardhan, Jaydeep P; Knepley, Matthew G

2014-10-07

We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley "bracelet" and "rod" test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, "Charge asymmetries in hydration of polar solutes," J. Phys. Chem. B 112, 2405-2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry.

Communication: Modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions

PubMed Central

Bardhan, Jaydeep P.; Knepley, Matthew G.

2014-01-01

We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley “bracelet” and “rod” test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, “Charge asymmetries in hydration of polar solutes,” J. Phys. Chem. B 112, 2405–2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry. PMID:25296776

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

Diffusional dynamics of an active rhodamine-labeled 1,4-dihydropyridine in sarcolemmal lipid multibilayers.

PubMed Central

Mason, R P; Chester, D W

1989-01-01

A "membrane bilayer pathway" model, involving ligand partition into the bilayer, lateral diffusion, and receptor binding has been invoked to describe the 1,4-dihydropyridine (DHP) calcium channel antagonist receptor binding mechanism. In an earlier study (Chester et al. 1987. Biophys. J. 52:1021-1030), the diffusional component of this model was examined using an active fluorescence labeled DHP calcium channel antagonist, nisoldipine-lissamine rhodamine B (Ns-R), in purified cardiac sarcolemmal (CSL) lipid multibilayers. Diffusion coefficient measurements on membrane-bound drug and phospholipid at maximum bilayer hydration yielded similar values (3.8 x 10(-8) cm2/s). However, decreases in bilayer hydration resulted in dramatically reduced diffusion coefficient values for both probes with substantially greater impact on Ns-R diffusion. These data suggested that hydration dependent diffusional differences could be a function of relative probe location along the bilayer normal. In this communication, we have addressed the relative effect of the rhodamine substituent on Ns-R diffusion complex by examining the diffusional dynamics of free rhodamine B under the same conditions used to evaluate Ns-R complex and phospholipid diffusion. X-ray diffraction studies were performed to determine the Ns-R location in the membrane and model the CSL lipid bilayer profile structure to give a rationale for the differences in probe diffusional dynamics as a function of interbilayer water space. PMID:2611332

Temperature effect on the small-to-large crossover lengthscale of hydrophobic hydration

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

Djikaev, Y. S., E-mail: idjikaev@buffalo.edu; Ruckenstein, E.

2013-11-14

The thermodynamics of hydration is expected to change gradually from entropic for small solutes to enthalpic for large ones. The small-to-large crossover lengthscale of hydrophobic hydration depends on the thermodynamic conditions of the solvent such as temperature, pressure, presence of additives, etc. We attempt to shed some light on the temperature dependence of the crossover lengthscale by using a probabilistic approach to water hydrogen bonding that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of both its distance to a solute and solute radius. Incorporating that approach into the densitymore » functional theory, one can examine the solute size effects on its hydration over the entire small-to-large lengthscale range at a series of different temperatures. Knowing the dependence of the hydration free energy on the temperature and solute size, one can also obtain its enthalpic and entropic contributions as functions of both temperature and solute size. These functions can provide some interesting insight into the temperature dependence of the crossover lengthscale of hydrophobic hydration. The model was applied to the hydration of spherical particles of various radii in water in the temperature range from T = 293.15 K to T = 333.15 K. The model predictions for the temperature dependence of the hydration free energy of small hydrophobes are consistent with the experimental and simulational data on the hydration of simple molecular solutes. Three alternative definitions for the small-to-large crossover length-scale of hydrophobic hydration are proposed, and their temperature dependence is obtained. Depending on the definition and temperature, the small-to-large crossover in the hydration mechanism is predicted to occur for hydrophobes of radii from one to several nanometers. Independent of its definition, the crossover length-scale is predicted to decrease with increasing temperature.« less

Shallow methane hydrate system controls ongoing, downslope sediment transport in a low-velocity active submarine landslide complex, Hikurangi Margin, New Zealand

NASA Astrophysics Data System (ADS)

Mountjoy, Joshu J.; Pecher, Ingo; Henrys, Stuart; Crutchley, Gareth; Barnes, Philip M.; Plaza-Faverola, Andreia

2014-11-01

Morphological and seismic data from a submarine landslide complex east of New Zealand indicate flow-like deformation within gas hydrate-bearing sediment. This "creeping" deformation occurs immediately downslope of where the base of gas hydrate stability reaches the seafloor, suggesting involvement of gas hydrates. We present evidence that, contrary to conventional views, gas hydrates can directly destabilize the seafloor. Three mechanisms could explain how the shallow gas hydrate system could control these landslides. (1) Gas hydrate dissociation could result in excess pore pressure within the upper reaches of the landslide. (2) Overpressure below low-permeability gas hydrate-bearing sediments could cause hydrofracturing in the gas hydrate zone valving excess pore pressure into the landslide body. (3) Gas hydrate-bearing sediment could exhibit time-dependent plastic deformation enabling glacial-style deformation. We favor the final hypothesis that the landslides are actually creeping seafloor glaciers. The viability of rheologically controlled deformation of a hydrate sediment mix is supported by recent laboratory observations of time-dependent deformation behavior of gas hydrate-bearing sands. The controlling hydrate is likely to be strongly dependent on formation controls and intersediment hydrate morphology. Our results constitute a paradigm shift for evaluating the effect of gas hydrates on seafloor strength which, given the widespread occurrence of gas hydrates in the submarine environment, may require a reevaluation of slope stability following future climate-forced variation in bottom-water temperature.

Theory of the milieu dependent isomerisation dynamics of reducing sugars applied to d-erythrose.

PubMed

Kaufmann, Martin; Mügge, Clemens; Kroh, Lothar W

2015-12-11

Quantitative (1)H selective saturation transfer NMR spectroscopy ((1)H SST qNMR) was used to fully describe the milieu dependent dynamics of the isomeric system of d-erythrose. Thermodynamic activation parameters are calculated for acidic as well as for basic catalysis combining McConnell's modified Bloch equations for the chemical exchange solved for the constraint of saturating the non-hydrated acyclic isomer, the Eyring equation and Hudson's equation for pH dependent catalysis. A detailed mathematical examination describing the milieu dependent dynamics of sugar isomerisation is provided. Thermodynamic data show evidence that photo-catalysed sugar isomerisation as well as degradation has to be considered. Approximations describing the pH and temperature dependence of thermodynamic activation parameters are derived that indicate the possibility of photo-affecting equilibrium constants. Moreover, the results show that isomerisation dynamics are closely related to degradation kinetics and that sugars' reactivities are altered by the concentration of acyclic carbonyl isomer and the sum of its ring closing rate constants. Additionally, it is concluded that sugar solutions show a limited self-stabilising behaviour. Copyright © 2015 Elsevier Ltd. All rights reserved.

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.

Perspective: Watching low-frequency vibrations of water in biomolecular recognition by THz spectroscopy

NASA Astrophysics Data System (ADS)

Xu, Yao; Havenith, Martina

2015-11-01

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.

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.

Lattice constants of pure methane and carbon dioxide hydrates at low temperatures. Implementing quantum corrections to classical molecular dynamics studies

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

Costandy, Joseph; Michalis, Vasileios K.; Economou, Ioannis G., E-mail: i.tsimpanogiannis@qatar.tamu.edu, E-mail: ioannis.economou@qatar.tamu.edu

2016-03-28

We introduce a simple correction to the calculation of the lattice constants of fully occupied structure sI methane or carbon dioxide pure hydrates that are obtained from classical molecular dynamics simulations using the TIP4PQ/2005 water force field. The obtained corrected lattice constants are subsequently used in order to obtain isobaric thermal expansion coefficients of the pure gas hydrates that exhibit a trend that is significantly closer to the experimental behavior than previously reported classical molecular dynamics studies.

Electrostatic, elastic and hydration-dependent interactions in dermis influencing volume exclusion and macromolecular transport.

PubMed

Øien, Alf H; Wiig, Helge

2016-07-07

Interstitial exclusion refers to the limitation of space available for plasma proteins and other macromolecules based on collagen and negatively charged glycosaminoglycans (GAGs) in the interstitial space. It is of particular importance to interstitial fluid and plasma volume regulation. Here we present a novel mechanical and mathematical model of the dynamic interactions of structural elements within the interstitium of the dermis at the microscopic level that may explain volume exclusion of charged and neutral macroparticles. At this level, the interstitium is considered to consist of elements called extracellular matrix (ECM) cells, again containing two main interacting structural components on a fluid background including anions and cations setting up osmotic forces: one smaller GAG component, having an intrinsic expansive electric force, and one bigger collagen component, having an intrinsic elastic force. Because of size differences, the GAG component interacts with a fraction of the collagen component only at normal hydration. This fraction, however, increases with rising hydration as a consequence of the modeled form of the interaction force between the GAGs and collagen. Collagen is locally displaced at variable degrees as hydration changes. Two models of GAGs are considered, having largely different geometries which demands different, but related, forms of GAG-collagen interaction forces. The effects of variable fixed charges on GAGs and of GAG density in tissue are evaluated taking into account observed volume exclusion properties of charged macromolecules as a function of tissue hydration. The presented models may improve our biophysical understanding of acting forces influencing tissue fluid dynamics. Such knowledge is significant when evaluating the transport of electrically charged and neutral macromolecules into and through the interstitium, and therefore to drug uptake and the therapeutic effects of macromolecular agents. Copyright © 2016 Elsevier Ltd. All rights reserved.

Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

USGS Publications Warehouse

Lee, M.W.; Meuwly, M.

2013-01-01

The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

Hydration water dynamics in biopolymers from NMR relaxation in the rotating frame.

PubMed

Blicharska, Barbara; Peemoeller, Hartwig; Witek, Magdalena

2010-12-01

Assuming dipole-dipole interaction as the dominant relaxation mechanism of protons of water molecules adsorbed onto macromolecule (biopolymer) surfaces we have been able to model the dependences of relaxation rates on temperature and frequency. For adsorbed water molecules the correlation times are of the order of 10(-5)s, for which the dispersion region of spin-lattice relaxation rates in the rotating frame R(1)(ρ)=1/T(1)(ρ) appears over a range of easily accessible B(1) values. Measurements of T(1)(ρ) at constant temperature and different B(1) values then give the "dispersion profiles" for biopolymers. Fitting a theoretical relaxation model to these profiles allows for the estimation of correlation times. This way of obtaining the correlation time is easier and faster than approaches involving measurements of the temperature dependence of R(1)=1/T(1). The T(1)(ρ) dispersion approach, as a tool for molecular dynamics study, has been demonstrated for several hydrated biopolymer systems including crystalline cellulose, starch of different origins (potato, corn, oat, wheat), paper (modern, old) and lyophilized proteins (albumin, lysozyme). Copyright © 2010 Elsevier Inc. All rights reserved.

"Cooking the sample": radiofrequency induced heating during solid-state NMR experiments.

PubMed

d'Espinose de Lacaillerie, Jean-Baptiste; Jarry, Benjamin; Pascui, Ovidiu; Reichert, Detlef

2005-09-01

Dissipation of radiofrequency (RF) energy as heat during continuous wave decoupling in solid-state NMR experiment was examined outside the conventional realm of such phenomena. A significant temperature increase could occur while performing dynamic NMR measurements provided the sample contains polar molecules and the sequence calls for relatively long applications of RF power. It was shown that the methyl flip motion in dimethylsulfone (DMS) is activated by the decoupling RF energy conversion to heat during a CODEX pulse sequence. This introduced a significant bias in the correlation time-temperature dependency measurement used to obtain the activation energy of the motion. By investigating the dependency of the temperature increase in hydrated lead nitrate on experimental parameters during high-power decoupling one-pulse experiments, the mechanisms for the RF energy deposition was identified. The samples were heated due to dissipation of the energy absorbed by dielectric losses, a phenomenon commonly known as "microwave" heating. It was thus established that during solid-state NMR experiments at moderate B0 fields, RF heating could lead to the heating of samples containing polar molecules such as hydrated polymers and inorganic solids. In particular, this could result in systematic errors for slow dynamics measurements by solid-state NMR.

Experimental and theoretical study on the excited-state dynamics of ortho-, meta-, and para-methoxy methylcinnamate.

PubMed

Miyazaki, Yasunori; Yamamoto, Kanji; Aoki, Jun; Ikeda, Toshiaki; Inokuchi, Yoshiya; Ehara, Masahiro; Ebata, Takayuki

2014-12-28

The S1 state dynamics of methoxy methylcinnamate (MMC) has been investigated under supersonic jet-cooled conditions. The vibrationally resolved S1-S0 absorption spectrum was recorded by laser induced fluorescence and mass-resolved resonant two-photon ionization spectroscopy and separated into conformers by UV-UV hole-burning (UV-UV HB) spectroscopy. The S1 lifetime measurements revealed different dynamics of para-methoxy methylcinnamate from ortho-methoxy methylcinnamate and meta-methoxy methylcinnamate (hereafter, abbreviated as p-, o-, and m-MMCs, respectively). The lifetimes of o-MMC and m-MMC are on the nanosecond time scale and exhibit little tendency of excess energy dependence. On the other hand, p-MMC decays much faster and its lifetime is conformer and excess energy dependent. In addition, the p-MMC-H2O complex was studied to explore the effect of hydration on the S1 state dynamics of p-MMC, and it was found that the hydration significantly accelerates the nonradiative decay. Quantum chemical calculation was employed to search the major decay route from S1(ππ(∗)) for three MMCs and p-MMC-H2O in terms of (i) trans → cis isomerization and (ii) internal conversion to the (1)nπ(∗) state. In o-MMC and m-MMC, the large energy barrier is created for the nonradiative decay along (i) the double-bond twisting coordinate (∼1000 cm(-1)) in S1 as well as (ii) the linear interpolating internal coordinate (∼1000 cm(-1)) from S1 to (1)nπ(∗) states. The calculation on p-MMC decay dynamics suggests that both (i) and (ii) are available due to small energy barrier, i.e., 160 cm(-1) by the double-bond twisting and 390 cm(-1) by the potential energy crossing. The hydration of p-MMC raises the energy barrier of the IC route to the S1/(1)nπ(∗) conical intersection, convincing that the direct isomerization is more likely to occur.

Determining the mechanism and parameters of hydrate formation and loss in glucose.

PubMed

Scholl, Sarah K; Schmidt, Shelly J

2014-11-01

Water-solid interactions are known to play a major role in the chemical and physical stability of food materials. Despite its extensive use throughout the food industry, the mechanism and parameters of hydrate formation and loss in glucose are not well characterized. Hydrate formation in alpha-anhydrous glucose (α-AG) and hydrate loss in glucose monohydrate (GM) were studied under equilibrium conditions at various relative humidity (RH) values using saturated salt slurries for 1 y. The mechanism of hydrate formation and hydrate loss were determined through mathematical modeling of Dynamic Vapor Sorption data and Raman spectroscopy was used to confirm the mechanisms. The critical temperature for hydrate loss in GM was determined using thermogravimetric analysis (TGA). The moisture sorption profiles of α-AG and GM were also studied under dynamic conditions using an AquaSorp Isotherm Generator. Hydrate formation was observed at and above 68% RH at 25 °C and the conversion of α-AG to GM can best be described as following a nucleation mechanism, however, diffusion and/or geometric contraction mechanisms were also observed by Raman spectroscopy subsequent to the coalescence of initial nucleation sites. Hydrate loss was observed to occur at and below 11% RH at 25 °C during RH storage and at 70 °C during TGA. The conversion of GM to α-AG follows nucleation and diffusion mechanisms. Hydrate formation was evident under dynamic conditions in α-AG and GM prior to deliquescence. This research is the first to report hydrate formation and loss parameters for crystalline α-AG and GM during extended storage at 25 ˚C. © 2014 Institute of Food Technologists®

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

Properties of inhibitors of methane hydrate formation via molecular dynamics simulations.

PubMed

Anderson, Brian J; Tester, Jefferson W; Borghi, Gian Paolo; Trout, Bernhardt L

2005-12-21

Within the framework of a proposed two-step mechanism for hydrate inhibition, the energy of binding of four inhibitor molecules (PEO, PVP, PVCap, and VIMA) to a hydrate surface is estimated with molecular dynamic simulations. One key feature of this proposed mechanism is that the binding of an inhibitor molecule to the surface of an ensuing hydrate crystal disrupts growth and therein crystallization. It is found through the molecular dynamic simulations that inhibitor molecules that experimentally exhibit better inhibition strength also have higher free energies of binding, an indirect confirmation of our proposed mechanism. Inhibitors increasing in effectiveness, PEO < PVP < PVCap < VIMA, have increasingly negative (exothermic) binding energies of -0.2 < -20.6 < -37.5 < -45.8 kcal/mol and binding free energies of increasing favorability (+0.4 approximately = +0.5 < -9.4 < -15.1 kcal/mol). Furthermore, the effect of an inhibitor molecule on the local liquid water structure under hydrate-forming conditions was examined and correlated to the experimental effectiveness of the inhibitors. Two molecular characteristics that lead to strongly binding inhibitors were found: (1) a charge distribution on the edge of the inhibitor that mimics the charge separation in the water molecules on the surface of the hydrate and (2) the congruence of the size of the inhibitor with respect to the available space at the hydrate-surface binding site. Equipped with this molecular-level understanding of the process of hydrate inhibition via low-dosage kinetic hydrate inhibitors we can design new, more effective inhibitor molecules.

Analysis of factors influencing hydration site prediction based on molecular dynamics simulations.

PubMed

Yang, Ying; Hu, Bingjie; Lill, Markus A

2014-10-27

Water contributes significantly to the binding of small molecules to proteins in biochemical systems. Molecular dynamics (MD) simulation based programs such as WaterMap and WATsite have been used to probe the locations and thermodynamic properties of hydration sites at the surface or in the binding site of proteins generating important information for structure-based drug design. However, questions associated with the influence of the simulation protocol on hydration site analysis remain. In this study, we use WATsite to investigate the influence of factors such as simulation length and variations in initial protein conformations on hydration site prediction. We find that 4 ns MD simulation is appropriate to obtain a reliable prediction of the locations and thermodynamic properties of hydration sites. In addition, hydration site prediction can be largely affected by the initial protein conformations used for MD simulations. Here, we provide a first quantification of this effect and further indicate that similar conformations of binding site residues (RMSD < 0.5 Å) are required to obtain consistent hydration site predictions.

Signature of hydrophobic hydration in a single polymer

PubMed Central

Li, Isaac T. S.; Walker, Gilbert C.

2011-01-01

Hydrophobicity underpins self-assembly in many natural and synthetic molecular and nanoscale systems. A signature of hydrophobicity is its temperature dependence. The first experimental evaluation of the temperature and size dependence of hydration free energy in a single hydrophobic polymer is reported, which tests key assumptions in models of hydrophobic interactions in protein folding. Herein, the hydration free energy required to extend three hydrophobic polymers with differently sized aromatic side chains was directly measured by single molecule force spectroscopy. The results are threefold. First, the hydration free energy per monomer is found to be strongly dependent on temperature and does not follow interfacial thermodynamics. Second, the temperature dependence profiles are distinct among the three hydrophobic polymers as a result of a hydrophobic size effect at the subnanometer scale. Third, the hydration free energy of a monomer on a macromolecule is different from a free monomer; corrections for the reduced hydration free energy due to hydrophobic interaction from neighboring units are required. PMID:21911397

Adsorption of Dissolved Gases (CH4, CO2, H2, Noble Gases) by Water-Saturated Smectite Clay Minerals

NASA Astrophysics Data System (ADS)

Bourg, I. C.; Gadikota, G.; Dazas, B.

2016-12-01

Adsorption of dissolved gases by water-saturated clay minerals plays important roles in a range of fields. For example, gas adsorption in on clay minerals may significantly impact the formation of CH4 hydrates in fine-grained sediments, the behavior of CH4 in shale, CO2 leakage across caprocks of geologic CO2 sequestration sites, H2 leakage across engineered clay barriers of high-level radioactive waste repositories, and noble gas geochemistry reconstructions of hydrocarbon migration in the subsurface. Despite its importance, the adsorption of gases on clay minerals remains poorly understood. For example, some studies have suggested that clay surfaces promote the formation of CH4 hydrates, whereas others indicate that clay surfaces inhibit the formation of CH4 hydrates. Here, we present molecular dynamics (MD) simulations of the adsorption of a range of gases (CH4, CO2, H2, noble gases) on clay mineral surfaces. Our results indicate that the affinity of dissolved gases for clay mineral surfaces has a non-monotone dependence on the hydrated radius of the gas molecules. This non-monotone dependence arises from a combination of two effects: the polar nature of certain gas molecules (in particular, CO2) and the templating of interfacial water structure by the clay basal surface, which results in the presence of interfacial water "cages" of optimal size for intermediate-size gas molecules (such as Ne or Ar).

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

Role of Adsorbed Water on Charge Carrier Dynamics in Photoexcited TiO2

PubMed Central

2017-01-01

Overall photocatalytic water splitting is one of the most sought after processes for sustainable solar-to-chemical energy conversion. The efficiency of this process strongly depends on charge carrier recombination and interaction with surface adsorbates at different time scales. Here, we investigated how hydration of TiO2 P25 affects dynamics of photogenerated electrons at the millisecond to minute time scale characteristic for chemical reactions. We used rapid scan diffuse-reflectance infrared Fourier transform spectroscopy (DRIFTS). The decay of photogenerated electron absorption was substantially slower in the presence of associated water. For hydrated samples, the charge carrier recombination rates followed an Arrhenius-type behavior in the temperature range of 273–423 K; these became temperature-independent when the material was dehydrated at temperatures above 423 K or cooled below 273 K. A DFT+U analysis revealed that hydrogen bonding with adsorbed water stabilizes surface-trapped holes at anatase TiO2(101) facet and lowers the barriers for hole migration. Hence, hole mobility should be higher in the hydrated material than in the dehydrated system. This demonstrates that adsorbed associated water can efficiently stabilize photogenerated charge carriers in nanocrystalline TiO2 and suppress their recombination at the time scale up to minutes. PMID:28413570

High-pressure dynamics of hydrated protein in bioprotective trehalose environment

DOE PAGES

Diallo, S. O.; Zhang, Q.; O'Neill, H.; ...

2014-10-30

Here we present a pressure-dependence study of the dynamics of lysozyme protein powder immersed in deuterated , α-trehalose environment via quasielastic neutron scattering (QENS). The goal is to assess the baroprotective benefits of trehalose on biomolecules by comparing the findings with those of a trehalose-free reference study. While the mean-square displacement of the trehalose-free protein (hydrated to d D₂O ≃40 w%) as a whole, is reduced by increasing pressure, the actual observable relaxation dynamics in the picoseconds to nanoseconds time range remains largely unaffected by pressure up to the maximum investigated pressure of 2.78(2) Kbar. Our observation is independent ofmore » whether or not the protein is mixed with the deuterated sugar. This suggests that the hydrated protein s conformational states at atmospheric pressure remain unaltered by hydrostatic pressures, below 2.78 Kbar. We also found the QENS response to be totally recoverable after ambient pressure conditions are restored. Small-angle neutron diffraction measurements confirm that the protein-protein correlation remains undisturbed.We observe, however, a clear narrowing of the QENS response as the temperature is decreased from 290 to 230 K in both cases, which we parametrize using the Kohlrausch-Williams-Watts stretched exponential model. Finally, only the fraction of protons that are immobile on the accessible time window of the instrument, referred to as the elastic incoherent structure factor, is observably sensitive to pressure, increasing only marginally but systematically with increasing pressure.« less

High-pressure dynamics of hydrated protein in bioprotective trehalose environment

NASA Astrophysics Data System (ADS)

Diallo, S. O.; Zhang, Q.; O'Neill, H.; Mamontov, E.

2014-10-01

We present a pressure-dependence study of the dynamics of lysozyme protein powder immersed in deuterated α ,α -trehalose environment via quasielastic neutron scattering (QENS). The goal is to assess the baroprotective benefits of trehalose on biomolecules by comparing the findings with those of a trehalose-free reference study. While the mean-square displacement of the trehalose-free protein (hydrated to dD2O≃ 40 w%) as a whole, is reduced by increasing pressure, the actual observable relaxation dynamics in the picoseconds to nanoseconds time range remains largely unaffected by pressure—up to the maximum investigated pressure of 2.78(2) Kbar. Our observation is independent of whether or not the protein is mixed with the deuterated sugar. This suggests that the hydrated protein's conformational states at atmospheric pressure remain unaltered by hydrostatic pressures, below 2.78 Kbar. We also found the QENS response to be totally recoverable after ambient pressure conditions are restored. Small-angle neutron diffraction measurements confirm that the protein-protein correlation remains undisturbed. We observe, however, a clear narrowing of the QENS response as the temperature is decreased from 290 to 230 K in both cases, which we parametrize using the Kohlrausch-Williams-Watts stretched exponential model. Only the fraction of protons that are immobile on the accessible time window of the instrument, referred to as the elastic incoherent structure factor, is observably sensitive to pressure, increasing only marginally but systematically with increasing pressure.

Invasion of drilling mud into gas-hydrate-bearing sediments. Part I: effect of drilling mud properties

NASA Astrophysics Data System (ADS)

Ning, Fulong; Zhang, Keni; Wu, Nengyou; Zhang, Ling; Li, Gang; Jiang, Guosheng; Yu, Yibing; Liu, Li; Qin, Yinghong

2013-06-01

To our knowledge, this study is the first to perform a numerical simulation and analysis of the dynamic behaviour of drilling mud invasion into oceanic gas-hydrate-bearing sediment (GHBS) and to consider the effects of such an invasion on borehole stability and the reliability of well logging. As a case study, the simulation background sets up the conditions of mud temperature over hydrate equilibrium temperature and overbalanced drilling, considering the first Chinese expedition to drill gas hydrate (GMGS-1). The results show that dissociating gas may form secondary hydrates in the sediment around borehole by the combined effects of increased pore pressure (caused by mud invasion and flow resistance), endothermic cooling that accompanies hydrate dissociation compounded by the Joule-Thompson effect and the lagged effect of heat transfer in sediments. The secondary hydrate ring around the borehole may be more highly saturated than the in situ sediment. Mud invasion in GHBS is a dynamic process of thermal, fluid (mud invasion), chemical (hydrate dissociation and reformation) and mechanical couplings. All of these factors interact and influence the pore pressure, flow ability, saturation of fluid and hydrates, mechanical parameters and electrical properties of sediments around the borehole, thereby having a strong effect on borehole stability and the results of well logging. The effect is particularly clear in the borehole SH7 of GMGS-1 project. The borehole collapse and resistivity distortion were observed during practical drilling and wireline logging operations in borehole SH7 of the GMGS-1.mud density (i.e. the corresponding borehole pressure), temperature and salinity have a marked influence on the dynamics of mud invasion and on hydrate stability. Therefore, perhaps well-logging distortion caused by mud invasion, hydrate dissociation and reformation should be considered for identifying and evaluating gas hydrate reservoirs. And some suitable drilling measurements need to be adopted to reduce the risk of well-logging distortion and borehole instability.

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.

Hydrate morphology: Physical properties of sands with patchy hydrate saturation

USGS Publications Warehouse

Dai, S.; Santamarina, J.C.; Waite, William F.; Kneafsey, T.J.

2012-01-01

The physical properties of gas hydrate-bearing sediments depend on the volume fraction and spatial distribution of the hydrate phase. The host sediment grain size and the state of effective stress determine the hydrate morphology in sediments; this information can be used to significantly constrain estimates of the physical properties of hydrate-bearing sediments, including the coarse-grained sands subjected to high effective stress that are of interest as potential energy resources. Reported data and physical analyses suggest hydrate-bearing sands contain a heterogeneous, patchy hydrate distribution, whereby zones with 100% pore-space hydrate saturation are embedded in hydrate-free sand. Accounting for patchy rather than homogeneous hydrate distribution yields more tightly constrained estimates of physical properties in hydrate-bearing sands and captures observed physical-property dependencies on hydrate saturation. For example, numerical modeling results of sands with patchy saturation agree with experimental observation, showing a transition in stiffness starting near the series bound at low hydrate saturations but moving toward the parallel bound at high hydrate saturations. The hydrate-patch size itself impacts the physical properties of hydrate-bearing sediments; for example, at constant hydrate saturation, we find that conductivity (electrical, hydraulic and thermal) increases as the number of hydrate-saturated patches increases. This increase reflects the larger number of conductive flow paths that exist in specimens with many small hydrate-saturated patches in comparison to specimens in which a few large hydrate saturated patches can block flow over a significant cross-section of the specimen.

An experimental challenge: Unraveling the dependencies of ultrasonic and electrical properties of sandy sediments with pore-filling gas hydrates

NASA Astrophysics Data System (ADS)

Heeschen, Katja; Spangenberg, Erik; Seyberth, Karl; Priegnitz, Mike; Schicks, Judith M.

2016-04-01

The accuracy of gas hydrate quantification using seismic or electric measurements fundamentally depends on the knowledge of any factor describing the dependencies of physical properties on gas hydrate saturation. Commonly, these correlations are the result of laboratory measurements on artificially produced gas hydrates of exact saturation. Thus, the production of gas hydrates and accurate determination of gas hydrate concentrations or those of a substitute are a major concern. Here we present data of both, seismic and electric measurements on accurately quantified pore-filling ice as a substitute for natural gas hydrates. The method was validated using selected gas hydrate saturations in the same experimental set-up as well as literature data from glass bead samples [Spangenberg and Kulenkampff, 2006]. The environmental parameters were chosen to fit those of a possible gas hydrate reservoir in the Danube Delta, which is in the focus of models for joint inversions of seismic and electromagnetic data in the SUGAR III project. The small effective pressures present at this site proved to be yet another challenge for the experiments. Using a more powerful pulse generator and a 4 electrode electric measurement, respectively, models for a wide range of gas hydrate saturations between 20 - 90 % vol. could be established. Spangenberg, E. and Kulenkampff, J., Influence of methane hydrate content on electrical sediment properties. Geophysical Research Letters 2006, 33, (24).

Molecular Dynamics Simulation of the Crystal Nucleation and Growth Behavior of Methane Hydrate in the Presence of the Surface and Nanopores of Porous Sediment.

PubMed

Yan, Ke-Feng; Li, Xiao-Sen; Chen, Zhao-Yang; Xia, Zhi-Ming; Xu, Chun-Gang; Zhang, Zhiqiang

2016-08-09

The behavior of hydrate formation in porous sediment has been widely studied because of its importance in the investigation of reservoirs and in the drilling of natural gas hydrate. However, it is difficult to understand the hydrate nucleation and growth mechanism on the surface and in the nanopores of porous media by experimental and numerical simulation methods. In this work, molecular dynamics simulations of the nucleation and growth of CH4 hydrate in the presence of the surface and nanopores of clay are carried out. The molecular configurations and microstructure properties are analyzed for systems containing one H2O hydrate layer (System A), three H2O hydrate layers (System B), and six H2O hydrate layers (System C) in both clay and the bulk solution. It is found that hydrate formation is more complex in porous media than in the pure bulk solution and that there is cooperativity between hydrate growth and molecular diffusion in clay nanopores. The hydroxylated edge sites of the clay surface could serve as a source of CH4 molecules to facilitate hydrate nucleation. The diffusion velocity of molecules is influenced by the growth of the hydrate that forms a block in the throats of the clay nanopore. Comparing hydrate growth in different clay pore sizes reveals that the pore size plays an important role in hydrate growth and molecular diffusion in clay. This simulation study provides the microscopic mechanism of hydrate nucleation and growth in porous media, which can be favorable for the investigation of the formation of natural gas hydrate in sediments.

Direct characterization of hydrophobic hydration during cold and pressure denaturation.

PubMed

Das, Payel; Matysiak, Silvina

2012-05-10

Cold and pressure denaturation are believed to have their molecular origin in hydrophobic interactions between nonpolar groups and water. However, the direct characterization of the temperature- and pressure-dependent variations of those interactions with atomistic simulations remains challenging. We investigated the role of solvent in the cold and pressure denaturation of a model hydrophobic 32-mer polymer by performing extensive coarse-grained molecular dynamics simulations including explicit solvation. Our simulations showed that the water-excluded folded state of this polymer is marginally stable and can be unfolded by heating or cooling, as well as by applying pressure, similar to globular proteins. We further detected essential population of a hairpin-like configuration prior to the collapse, which is consistently accompanied by a vapor bubble at the elbow of the kink. Increasing pressure suppresses formation of this vapor bubble by reducing water fluctuations in the hydration shell of the polymer, thus promoting unfolding. Further analysis revealed a slight reduction of water tetrahedrality in the polymer hydration shell compared to the bulk. Cold denaturation is driven by an enhanced tetrahedral ordering of hydration shell water than bulk water. At elevated pressures, the strikingly reduced fluctuations combined with the increase in interstitial water molecules in the polymer hydration shell contribute to weakening of hydrophobic interactions, thereby promoting pressure unfolding. These findings provide critical molecular insights into the changes in hydrophobic hydration during cold and pressure unfolding of a hydrophobic polymer, which is strongly related to the cold and pressure denaturation of globular proteins.

Communication: Modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions

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

Bardhan, Jaydeep P.; Knepley, Matthew G.

2014-10-07

We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley “bracelet” and “rod” test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, “Charge asymmetries in hydration of polar solutes,” J. Phys.more » Chem. B 112, 2405–2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry.« less

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.

Water Dynamics in Nafion Fuel Cell Membranes: the Effects of Confinement and Structural Changes on the Hydrogen Bond Network

PubMed Central

Moilanen, David E.; Piletic, Ivan R.; Fayer, Michael D.

2008-01-01

The complex environments experienced by water molecules in the hydrophilic channels of Nafion membranes are studied by ultrafast infrared pump-probe spectroscopy. A wavelength dependent study of the vibrational lifetime of the O-D stretch of dilute HOD in H2O confined in Nafion membranes provides evidence of two distinct ensembles of water molecules. While only two ensembles are present at each level of membrane hydration studied, the characteristics of the two ensembles change as the water content of the membrane changes. Time dependent anisotropy measurements show that the orientational motions of water molecules in Nafion membranes are significantly slower than in bulk water and that lower hydration levels result in slower orientational relaxation. Initial wavelength dependent results for the anisotropy show no clear variation in the time scale for orientational motion across a broad range of frequencies. The anisotropy decay is analyzed using a model based on restricted orientational diffusion within a hydrogen bond configuration followed by total reorientation through jump diffusion. PMID:18728757

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.

The dynamical crossover phenomenon in bulk water, confined water and protein hydration water.

PubMed

Mallamace, Francesco; Corsaro, Carmelo; Baglioni, Piero; Fratini, Emiliano; Chen, Sow-Hsin

2012-02-15

We discuss a phenomenon regarding water that was until recently a subject of scientific controversy, i.e. the dynamical crossover from fragile-to-strong glass-forming material, for both bulk and protein hydration water. Such a crossover is characterized by a temperature T(L) at which significant dynamical changes occur, such as violation of the Stokes-Einstein relation and changes of behaviour of homologous transport parameters such as the density relaxation time and the viscosity. In this respect we will consider carefully the dynamic properties of water-protein systems. More precisely, we will study proteins and their hydration water as far as bulk and confined water. In order to clarify the controversy we will discuss in a comparative way many previous and new experimental data that have emerged using different techniques and molecular dynamic simulation (MD). We point out the reasons for the different dynamical findings from the use of different experimental techniques.

Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water

PubMed Central

Athawale, Manoj V.; Goel, Gaurav; Ghosh, Tuhin; Truskett, Thomas M.; Garde, Shekhar

2007-01-01

We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on folding. Hydrophobic polymers display parabolic, protein-like, temperature-dependent free energy of unfolding. Folded states of small attractive polymers are marginally stable at 300 K and can be unfolded by heating or cooling. Increasing the lengthscale or decreasing the polymer–water attractions stabilizes folded states significantly, the former dominated by the hydration contribution. That hydration contribution can be described by the surface tension model, ΔG = γ(T)ΔA, where the surface tension, γ, is lengthscale-dependent and decreases monotonically with temperature. The resulting variation of the hydration entropy with polymer lengthscale is consistent with theoretical predictions of Huang and Chandler [Huang DM, Chandler D (2000) Proc Natl Acad Sci USA 97:8324–8327] that explain the blurring of entropy convergence observed in protein folding thermodynamics. Analysis of water structure shows that the polymer–water hydrophobic interface is soft and weakly dewetted, and is characterized by enhanced interfacial density fluctuations. Formation of this interface, which induces polymer folding, is strongly opposed by enthalpy and favored by entropy, similar to the vapor–liquid interface. PMID:17215352

Formation and decomposition of ethane, propane, and carbon dioxide hydrates in silica gel mesopores under high pressure.

PubMed

Aladko, E Ya; Dyadin, Yu A; Fenelonov, V B; Larionov, E G; Manakov, A Yu; Mel'gunov, M S; Zhurko, F V

2006-10-05

The experimental data on decomposition temperatures for the gas hydrates of ethane, propane, and carbon dioxide dispersed in silica gel mesopores are reported. The studies were performed at pressures up to 1 GPa. It is shown that the experimental dependence of hydrate decomposition temperature on the size of pores that limit the size of hydrate particles can be described on the basis of the Gibbs-Thomson equation only if one takes into account changes in the shape coefficient that is present in the equation; in turn, the value of this coefficient depends on a method of mesopore size determination. A mechanism of hydrate formation in mesoporous medium is proposed. Experimental data providing evidence of the possibility of the formation of hydrate compounds in hydrophobic matrixes under high pressure are reported. Decomposition temperature of those hydrate compounds is higher than that for the bulk hydrates of the corresponding gases.

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.

Dynamics of proteins at low temperatures: fibrous vs. globular

NASA Astrophysics Data System (ADS)

Foucat, L.; Renou, J.-P.; Tengroth, C.; Janssen, S.; Middendorf, H. D.

We have measured quasielastic neutron scattering from H2O-hydrated collagen and haemoglobin at T<=270K. The data consist of sets of nearly elastic peaks showing (i) Q,T-dependent decreases in window-integrated intensities Sqe(Q;T) proportional to effective Debye-Waller factors and (ii) small line-shape changes due to various types of proton motions with ns>τ>10 ps. Relative to haemoglobin, the 200-K dynamic transition is shifted upward by 20-25 K in collagen, and the T-dependence of m.-sq. displacements derived from Sqe(Q;T) suggests that in triple-helical systems there are three rather than two regimes: one up to around 120K (probably purely harmonic), an intermediate quasiharmonic region with a linear dependence up to 240K, followed by a steeper nonlinear rise similar to that in globular proteins.

Nucleation and growth constraints and outcome in the natural gas hydrate system

NASA Astrophysics Data System (ADS)

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

2016-12-01

Hydrate formation processes are functions of energy distribution constrained by physical and kinetic parameters. The generation of energy and energy derivative plots of a constrained growth crucible are used to demonstrate nucleation probability zones (phase origin(s)). Nucleation sets the stage for growth by further constraining the pathways through changes in heat capacity, heat flow coefficient, and enthalpy which in turn modify the mass and energy flow into the hydrate formation region. Nucleation events result from the accumulation of materials and energy relative to pressure, temperature, and composition. Nucleation induction is predictive (a frequency parameter) rather than directly dependent on time. Growth, as mass tranfer into a new phase, adds time as a direct parameter. Growth has direct feedback on phase transfer, energy dynamics, and mass export/import rates. Many studies have shown that hydrate growth is largely an equilibrium process controlled by either mass or energy flows. Subtle changes in the overall energy distribution shift the equilibrium in a predictable fashion. We will demonstrate the localization of hydrate nucleation in a reservoir followed by likely evolution of growth in a capped, sand filled environment. The gas hydrate stability zone (GHSZ) can be characterized as a semi-batch crystallizer in which nucleation and growth of natural gas hydrate (NGH) is a continuous process that may result in very large concentrations of NGH. Gas flux, or the relative concentration of hydrate-forming gas is the critical factor in a GHSZ. In an open groundwater system in which flow rate exceeds diffusion transport rate, dissolved natural gas is transported into and through the GHSZ. In a closed system, such as a geological trap, diffusion of hydrate-forming gas from a free gas zone below the GHSZ is the primary mechanism for movement of gas reactants. Because of the lower molecular weight of methane, where diffusion is the principal transport mechanism, the natural system can be a purification process for formation of increasingly pure NGH from a mixed gas solution over time.

Adsorption of Kinetic Hydrate Inhibitors on Growing Surfaces: A Molecular Dynamics Study.

PubMed

Yagasaki, Takuma; Matsumoto, Masakazu; Tanaka, Hideki

2018-04-05

We investigate the mechanism of a typical kinetic hydrate inhibitor (KHI), polyvinylcaprolactam (PVCap), which has been applied to prevent hydrate plugs from forming in gas pipe lines, using molecular dynamics simulations of crystal growth of ethylene oxide hydrate. Water-soluble ethylene oxide is chosen as a guest species to avoid problems associated with the presence of the gas phase in the simulation cell such as slow crystal growth. A PVCap dodecamer adsorbs irreversibly on the hydrate surface which grows at supercooling of 3 K when the hydrophobic part of two pendent groups are trapped in open cages at the surface. The amide hydrogen bonds make no contribution to the adsorption. PVCap can adsorb on various crystallographic planes of sI hydrate. This is in contrast to antifreeze proteins, each of which prefers a specific plane of ice. The trapped PVCap gives rise to necessarily the concave surface of the hydrate. The crystal growth rate decreases with increasing surface curvature, indicating that the inhibition by PVCap is explained by the Gibbs-Thomson effect.

Analysis of Factors Influencing Hydration Site Prediction Based on Molecular Dynamics Simulations

PubMed Central

2015-01-01

Water contributes significantly to the binding of small molecules to proteins in biochemical systems. Molecular dynamics (MD) simulation based programs such as WaterMap and WATsite have been used to probe the locations and thermodynamic properties of hydration sites at the surface or in the binding site of proteins generating important information for structure-based drug design. However, questions associated with the influence of the simulation protocol on hydration site analysis remain. In this study, we use WATsite to investigate the influence of factors such as simulation length and variations in initial protein conformations on hydration site prediction. We find that 4 ns MD simulation is appropriate to obtain a reliable prediction of the locations and thermodynamic properties of hydration sites. In addition, hydration site prediction can be largely affected by the initial protein conformations used for MD simulations. Here, we provide a first quantification of this effect and further indicate that similar conformations of binding site residues (RMSD < 0.5 Å) are required to obtain consistent hydration site predictions. PMID:25252619

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.

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

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

PubMed

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

2011-10-24

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

Determination of pore-scale hydrate phase equilibria in sediments using lab-on-a-chip technology.

PubMed

Almenningen, Stian; Flatlandsmo, Josef; Kovscek, Anthony R; Ersland, Geir; Fernø, Martin A

2017-11-21

We present an experimental protocol for fast determination of hydrate stability in porous media for a range of pressure and temperature (P, T) conditions. Using a lab-on-a-chip approach, we gain direct optical access to dynamic pore-scale hydrate formation and dissociation events to study the hydrate phase equilibria in sediments. Optical pore-scale observations of phase behavior reproduce the theoretical hydrate stability line with methane gas and distilled water, and demonstrate the accuracy of the new method. The procedure is applicable for any kind of hydrate transitions in sediments, and may be used to map gas hydrate stability zones in nature.

The effects of ice on methane hydrate nucleation: a microcanonical molecular dynamics study.

PubMed

Zhang, Zhengcai; Guo, Guang-Jun

2017-07-26

Although ice powders are widely used in gas hydrate formation experiments, the effects of ice on hydrate nucleation and what happens in the quasi-liquid layer of ice are still not well understood. Here, we used high-precision constant energy molecular dynamics simulations to study methane hydrate nucleation from vapor-liquid mixtures exposed to the basal, prismatic, and secondary prismatic planes of hexagonal ice (ice Ih). Although no significant difference is observed in hydrate nucleation processes for these different crystal planes, it is found, more interestingly, that methane hydrate can nucleate either on the ice surface heterogeneously or in the bulk solution phase homogeneously. Several factors are mentioned to be able to promote the heterogeneous nucleation of hydrates, including the adsorption of methane molecules at the solid-liquid interface, hydrogen bonding between hydrate cages and the ice structure, the stronger ability of ice to transfer heat than that of the aqueous solution, and the higher occurrence probability of hydrate cages in the vicinity of the ice surface than in the bulk solution. Meanwhile, however, the other factors including the hydrophilicity of ice and the ice lattice mismatch with clathrate hydrates can inhibit heterogeneous nucleation on the ice surface and virtually promote homogeneous nucleation in the bulk solution. Certainly, the efficiency of ice as a promoter and as an inhibitor for heterogeneous nucleation is different. We estimate that the former is larger than the latter under the working conditions. Additionally, utilizing the benefit of ice to absorb heat, the NVE simulation of hydrate formation with ice can mimic the phenomenon of ice shrinking during the heterogeneous nucleation of hydrates and lower the overly large temperature increase during homogeneous nucleation. These results are helpful in understanding the nucleation mechanism of methane hydrate in the presence of ice.

Pressure effects on collective density fluctuations in water and protein solutions

PubMed Central

Russo, Daniela; Laloni, Alessio; Filabozzi, Alessandra; Heyden, Matthias

2017-01-01

Neutron Brillouin scattering and molecular dynamics simulations have been used to investigate protein hydration water density fluctuations as a function of pressure. Our results show significant differences between the pressure and density dependence of collective dynamics in bulk water and in concentrated protein solutions. Pressure-induced changes in the tetrahedral order of the water HB network have direct consequences for the high-frequency sound velocity and damping coefficients, which we find to be a sensitive probe for changes in the HB network structure as well as the wetting of biomolecular surfaces. PMID:29073065

Dynamic nuclear polarization methods in solids and solutions to explore membrane proteins and membrane systems.

PubMed

Cheng, Chi-Yuan; Han, Songi

2013-01-01

Membrane proteins regulate vital cellular processes, including signaling, ion transport, and vesicular trafficking. Obtaining experimental access to their structures, conformational fluctuations, orientations, locations, and hydration in membrane environments, as well as the lipid membrane properties, is critical to understanding their functions. Dynamic nuclear polarization (DNP) of frozen solids can dramatically boost the sensitivity of current solid-state nuclear magnetic resonance tools to enhance access to membrane protein structures in native membrane environments. Overhauser DNP in the solution state can map out the local and site-specific hydration dynamics landscape of membrane proteins and lipid membranes, critically complementing the structural and dynamics information obtained by electron paramagnetic resonance spectroscopy. Here, we provide an overview of how DNP methods in solids and solutions can significantly increase our understanding of membrane protein structures, dynamics, functions, and hydration in complex biological membrane environments.

Ultrafast Hydration Dynamics and Coupled Water-Protein Fluctuations in Apomyoglobin

NASA Astrophysics Data System (ADS)

Yang, Yi; Zhang, Luyuan; Wang, Lijuan; Zhong, Dongping

2009-06-01

Protein hydration dynamics are of fundamental importance to its structure and function. Here, we characterize the global solvation dynamics and anisotropy dynamics around the apomyoglobin surface in different conformational states (native and molten globule) by measuring the Stokes shift and anisotropy decay of tryptophan with femtosecond-resolved fluorescence upconversion. With site-directed mutagenesis, we designed sixteen mutants with one tryptophan in each, and placed the probe at a desirable position ranging from buried in the protein core to fully solvent-exposed on the protein surface. In all protein sites studied, two distinct solvation relaxations (1-8 ps and 20-200 ps) were observed, reflecting the initial collective water relaxation and subsequent hydrogen-bond network restructuring, respectively, and both are strongly correlated with protein's local structures and chemical properties. The hydration dynamics of the mutants in molten globule state are faster than those observed in native state, indicating that the protein becomes more flexible and less structured when its conformation is converted from fully-folded native state to partially-folded molten globule state. Complementary, fluorescence anisotropy dynamics of all mutants in native state show an increasing trend of wobbling times (40-260 ps) when the location of the probe is changed from a loop, to a lateral helix, and then, to the compact protein core. Such an increase in wobbling times is related to the local protein structural rigidity, which relates the interaction of water with side chains. The ultrafast hydration dynamics and related side-chain motion around the protein surface unravel the coupled water-protein fluctuations on the picosecond time scales and indicate that the local protein motions are slaved by hydrating water fluctuations.

Experimental and theoretical study on the excited-state dynamics of ortho-, meta-, and para-methoxy methylcinnamate

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

Miyazaki, Yasunori; Yamamoto, Kanji; Aoki, Jun

The S{sub 1} state dynamics of methoxy methylcinnamate (MMC) has been investigated under supersonic jet-cooled conditions. The vibrationally resolved S{sub 1}-S{sub 0} absorption spectrum was recorded by laser induced fluorescence and mass-resolved resonant two-photon ionization spectroscopy and separated into conformers by UV-UV hole-burning (UV-UV HB) spectroscopy. The S{sub 1} lifetime measurements revealed different dynamics of para-methoxy methylcinnamate from ortho-methoxy methylcinnamate and meta-methoxy methylcinnamate (hereafter, abbreviated as p-, o-, and m-MMCs, respectively). The lifetimes of o-MMC and m-MMC are on the nanosecond time scale and exhibit little tendency of excess energy dependence. On the other hand, p-MMC decays much faster andmore » its lifetime is conformer and excess energy dependent. In addition, the p-MMC-H{sub 2}O complex was studied to explore the effect of hydration on the S{sub 1} state dynamics of p-MMC, and it was found that the hydration significantly accelerates the nonradiative decay. Quantum chemical calculation was employed to search the major decay route from S{sub 1}(ππ{sup ∗}) for three MMCs and p-MMC-H{sub 2}O in terms of (i) trans → cis isomerization and (ii) internal conversion to the {sup 1}nπ{sup ∗} state. In o-MMC and m-MMC, the large energy barrier is created for the nonradiative decay along (i) the double-bond twisting coordinate (∼1000 cm{sup −1}) in S{sub 1} as well as (ii) the linear interpolating internal coordinate (∼1000 cm{sup −1}) from S{sub 1} to {sup 1}nπ{sup ∗} states. The calculation on p-MMC decay dynamics suggests that both (i) and (ii) are available due to small energy barrier, i.e., 160 cm{sup −1} by the double-bond twisting and 390 cm{sup −1} by the potential energy crossing. The hydration of p-MMC raises the energy barrier of the IC route to the S{sub 1}/{sup 1}nπ{sup ∗} conical intersection, convincing that the direct isomerization is more likely to occur.« less

Temperature- and pressure-dependent structural transformation of methane hydrates in salt environments

NASA Astrophysics Data System (ADS)

Shin, Donghoon; Cha, Minjun; Yang, Youjeong; Choi, Seunghyun; Woo, Yesol; Lee, Jong-Won; Ahn, Docheon; Im, Junhyuck; Lee, Yongjae; Han, Oc Hee; Yoon, Ji-Ho

2017-03-01

Understanding the stability of volatile species and their compounds under various surface and subsurface conditions is of great importance in gaining insights into the formation and evolution of planetary and satellite bodies. We report the experimental results of the temperature- and pressure-dependent structural transformation of methane hydrates in salt environments using in situ synchrotron X-ray powder diffraction, solid-state nuclear magnetic resonance, and Raman spectroscopy. We find that under pressurized and concentrated brine solutions methane hydrate forms a mixture of type I clathrate hydrate, ice, and hydrated salts. Under a low-pressure condition, however, the methane hydrates are decomposed through a rapid sublimation of water molecules from the surface of hydrate crystals, while NaCl · 2H2O undergoes a phase transition into a crystal growth of NaCl via the migration of salt ions. In ambient pressure conditions, the methane hydrate is fully decomposed in brine solutions at temperatures above 252 K, the eutectic point of NaCl · 2H2O.

Protein-style dynamical transition in a non-biological polymer and a non-aqueous solvent

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

Mamontov, E.; Sharma, V. K.; Borreguero, J. M.

Using neutron scattering and molecular dynamics simulation, techniques most often associated with protein dynamical transition studies, we have investigated the microscopic dynamics of one of the most common polymers, polystyrene, which was exposed to toluene vapor, mimicking the process of protein hydration from water vapor. Polystyrene with adsorbed toluene is an example of a solvent-solute system, which, unlike biopolymers, is anhydrous and lacks hydrogen bonding. Nevertheless, it exhibits the essential traits of the dynamical transition in biomolecules, such as a specific dependence of the microscopic dynamics of both solvent and host on the temperature and the amount of solvent adsorbed.more » Ultimately, we conclude that the protein dynamical transition is a manifestation of a universal solvent-solute dynamical relationship, which is not specific to either biomolecules as solute, or aqueous media as solvent, or even a particular type of interactions between solvent and solute.« less

Protein-style dynamical transition in a non-biological polymer and a non-aqueous solvent

DOE PAGES

Mamontov, E.; Sharma, V. K.; Borreguero, J. M.; ...

2016-03-15

Using neutron scattering and molecular dynamics simulation, techniques most often associated with protein dynamical transition studies, we have investigated the microscopic dynamics of one of the most common polymers, polystyrene, which was exposed to toluene vapor, mimicking the process of protein hydration from water vapor. Polystyrene with adsorbed toluene is an example of a solvent-solute system, which, unlike biopolymers, is anhydrous and lacks hydrogen bonding. Nevertheless, it exhibits the essential traits of the dynamical transition in biomolecules, such as a specific dependence of the microscopic dynamics of both solvent and host on the temperature and the amount of solvent adsorbed.more » Ultimately, we conclude that the protein dynamical transition is a manifestation of a universal solvent-solute dynamical relationship, which is not specific to either biomolecules as solute, or aqueous media as solvent, or even a particular type of interactions between solvent and solute.« less

Coarse-grained model of nanoscale segregation, water diffusion, and proton transport in Nafion membranes

NASA Astrophysics Data System (ADS)

Vishnyakov, Aleksey; Mao, Runfang; Lee, Ming-Tsung; Neimark, Alexander V.

2018-01-01

We present a coarse-grained model of the acid form of Nafion membrane that explicitly includes proton transport. This model is based on a soft-core bead representation of the polymer implemented into the dissipative particle dynamics (DPD) simulation framework. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with water beads. Morse bond formation and breakup artificially mimics the Grotthuss hopping mechanism of proton transport. The proposed DPD model is parameterized to account for the specifics of the conformations and flexibility of the Nafion backbone and sidechains; it treats electrostatic interactions in the smeared charge approximation. The simulation results qualitatively, and in many respects quantitatively, predict the specifics of nanoscale segregation in the hydrated Nafion membrane into hydrophobic and hydrophilic subphases, water diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from a collection of isolated water clusters to a 3D network of pores filled with water embedded in the hydrophobic matrix. The segregated morphology is characterized in terms of the pore size distribution with the average size growing with hydration from ˜1 to ˜4 nm. Comparison of the predicted water diffusivity with the experimental data taken from different sources shows good agreement at high and moderate hydration and substantial deviation at low hydration, around and below the percolation threshold. This discrepancy is attributed to the dynamic percolation effects of formation and rupture of merging bridges between the water clusters, which become progressively important at low hydration, when the coarse-grained model is unable to mimic the fine structure of water network that includes singe molecule bridges. Selected simulations of water diffusion are performed for the alkali metal substituted membrane which demonstrate the effects of the counter-ions on membrane self-assembly and transport. The hydration dependence of the proton diffusivity reproduces semi-qualitatively the trend of the diverse experimental data, showing a sharp decrease around the percolation threshold. Overall, the proposed model opens up an opportunity to study self-assembly and water and proton transport in polyelectrolytes using computationally efficient DPD simulations, and, with further refinement, it may become a practical tool for theory informed design and optimization of perm-selective and ion-conducting membranes with improved properties.

Nonequilibrium adiabatic molecular dynamics simulations of methane clathrate hydrate decomposition

NASA Astrophysics Data System (ADS)

Alavi, Saman; Ripmeester, J. A.

2010-04-01

Nonequilibrium, constant energy, constant volume (NVE) molecular dynamics simulations are used to study the decomposition of methane clathrate hydrate in contact with water. Under adiabatic conditions, the rate of methane clathrate decomposition is affected by heat and mass transfer arising from the breakup of the clathrate hydrate framework and release of the methane gas at the solid-liquid interface and diffusion of methane through water. We observe that temperature gradients are established between the clathrate and solution phases as a result of the endothermic clathrate decomposition process and this factor must be considered when modeling the decomposition process. Additionally we observe that clathrate decomposition does not occur gradually with breakup of individual cages, but rather in a concerted fashion with rows of structure I cages parallel to the interface decomposing simultaneously. Due to the concerted breakup of layers of the hydrate, large amounts of methane gas are released near the surface which can form bubbles that will greatly affect the rate of mass transfer near the surface of the clathrate phase. The effects of these phenomena on the rate of methane hydrate decomposition are determined and implications on hydrate dissociation in natural methane hydrate reservoirs are discussed.

Nonequilibrium adiabatic molecular dynamics simulations of methane clathrate hydrate decomposition.

PubMed

Alavi, Saman; Ripmeester, J A

2010-04-14

Nonequilibrium, constant energy, constant volume (NVE) molecular dynamics simulations are used to study the decomposition of methane clathrate hydrate in contact with water. Under adiabatic conditions, the rate of methane clathrate decomposition is affected by heat and mass transfer arising from the breakup of the clathrate hydrate framework and release of the methane gas at the solid-liquid interface and diffusion of methane through water. We observe that temperature gradients are established between the clathrate and solution phases as a result of the endothermic clathrate decomposition process and this factor must be considered when modeling the decomposition process. Additionally we observe that clathrate decomposition does not occur gradually with breakup of individual cages, but rather in a concerted fashion with rows of structure I cages parallel to the interface decomposing simultaneously. Due to the concerted breakup of layers of the hydrate, large amounts of methane gas are released near the surface which can form bubbles that will greatly affect the rate of mass transfer near the surface of the clathrate phase. The effects of these phenomena on the rate of methane hydrate decomposition are determined and implications on hydrate dissociation in natural methane hydrate reservoirs are discussed.

Polymorphic Protein Crystal Growth: Influence of Hydration and Ions in Glucose Isomerase

PubMed Central

Gillespie, C. M.; Asthagiri, D.; Lenhoff, A. M.

2014-01-01

Crystal polymorphs of glucose isomerase were examined to characterize the properties and to quantify the energetics of protein crystal growth. Transitions of polymorph stability were measured in poly(ethylene glycol)/NaCl solutions, and one transition point was singled out for more detailed quantitative analysis. Single crystal x-ray diffraction was used to confirm space groups and identify complementary crystal structures. Crystal polymorph stability was found to depend on the NaCl concentration, with stability transitions requiring > 1 M NaCl combined with a low concentration of PEG. Both salting-in and salting-out behavior was observed and was found to differ for the two polymorphs. For NaCl concentrations above the observed polymorph transition, the increase in solubility of the less stable polymorph together with an increase in the osmotic second virial coefficient suggests that changes in protein hydration upon addition of salt may explain the experimental trends. A combination of atomistic and continuum models was employed to dissect this behavior. Molecular dynamics simulations of the solvent environment were interpreted using quasi-chemical theory to understand changes in protein hydration as a function of NaCl concentration. The results suggest that protein surface hydration and Na+ binding may introduce steric barriers to contact formation, resulting in polymorph selection. PMID:24955067

Control of the geomorphology and gas hydrate extent on widespread gas emissions offshore Romania (Black Sea)

NASA Astrophysics Data System (ADS)

Riboulot, V.; Cattaneo, A.; Sultan, N.; Ker, S.; Scalabrin, C.; Gaillot, A.; Jouet, G.; Marsset, B.; Thomas, Y.; Ballas, G.; Marsset, T.; Garziglia, S.; Ruffine, L.; Boulart, C.

2016-12-01

The Romanian sector of the Black Sea deserves attention because the Danube deep-sea fan is one of the largest sediment depositional systems worldwide and is considered the world's most isolated sea, the largest anoxic water body on the planet and a unique energy-rich sea. Due to the high sediment accumulation rate, presence of organic matter and anoxic conditions, the Black sea sediment offshore the Danube delta is rich in gas and thus show BSR. The cartography of the BSR over the last 20 years, exhibits its widespread occurrence, indicative of extensive development of hydrate accumulations and a huge gas hydrate potential. By combining old and new datasets acquired in 2015 during the GHASS expedition, we performed a geomorphological analysis of the continental slope north-east of the Danube canyon that reveals the presence of several landslides inside and outside several canyons incising the seafloor. It is a complex study area presenting sedimentary processes such as seafloor erosion and instability, mass wasting, formation of gas hydrates, fluid migration, gas escape, where the imprint of geomorphology seems to dictate the location where gas seep occurs. . Some 1409 gas seeps within the water column acoustic records are observed between 200 m and 800 m water depth. No gas flares were detected in deeper areas where gas hydrates are stable. Overall, 93% of the all gas seeps observed are above geomorphological structures. 78% are right above escarpment induced by sedimentary destabilizations inside or outside canyons. The results suggest a geomorphological control of degassing at the seafloor and gas seeps are thus constrained by the gas hydrates stability zone. The stability of the gas hydrates is dependent on the salinity gradient through the sedimentary column and thus on the Black Sea recent geological history. The extent and the dynamics of gas hydrates have a probable impact on the sedimentary destabilization observed at the seafloor.

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.

Dielectric method of high-resolution gas hydrate estimation

NASA Astrophysics Data System (ADS)

Sun, Y. F.; Goldberg, D.

2005-02-01

In-situ dielectric properties of natural gas hydrate are measured for the first time in the Mallik 5L-38 Well in the Mackenzie Delta, Canada. The average dielectric constant of the hydrate zones is 9, ranging from 5 to 20. The average resistivity is >5 ohm.m in the hydrate zones, ranging from 2 to 10 ohm.m at a 1.1 GHz dielectric tool frequency. The dielectric logs show similar trends with sonic and induction resistivity logs, but exhibits inherently higher vertical resolution (<5 cm). The average in-situ hydrate saturation in the well is about 70%, ranging from 20% to 95%. The dielectric estimates are overall in agreement with induction estimates but the induction log tends to overestimate hydrate content up to 15%. Dielectric estimates could be used as a better proxy of in-situ hydrate saturation in modeling hydrate dynamics. The fine-scale structure in hydrate zones could help reveal hydrate formation history.

Dynamics of lipid saccharide nanoparticles by quasielastic neutron scattering

NASA Astrophysics Data System (ADS)

Di Bari, M. T.; Gerelli, Y.; Sonvico, F.; Deriu, A.; Cavatorta, F.; Albanese, G.; Colombo, P.; Fernandez-Alonso, F.

2008-04-01

Nano- and microparticles composed of saccharide and lipid systems are extensively investigated for applications as highly biocompatible drug carriers. A detailed understanding of particle-solvent interactions is of key importance in order to tailor their characteristics for delivering drugs with specific chemical properties. Here we report results of a quasielastic neutron scattering (QENS) investigation on lecithin/chitosan nanoparticles prepared by autoassembling the two components in an aqueous solution. The measurements were performed at room temperature on lyophilized and H 2O hydrated nanoparticles ( h = 0.47 w H 2O/w hydrated sample). In the latter, hydration water is mostly enclosed inside the nanoparticles; its dynamics is similar to that of bulk water but with a significant decrease in diffusivity. The scattering from the nanoparticles can be described by a simple model of confined diffusion. In the lyophilized state only hydrogens belonging to the polar heads are seen as mobile within the experimental time-window. In the hydrated sample the diffusive dynamics involves also a significant part of the hydrogens in the lipid tails.

A molecular dynamic study on the dissociation mechanism of SI methane hydrate in inorganic salt aqueous solutions.

PubMed

Xu, Jiafang; Chen, Zhe; Liu, Jinxiang; Sun, Zening; Wang, Xiaopu; Zhang, Jun

2017-08-01

Gas hydrate is not only a potential energy resource, but also almost the biggest challenge in oil/gas flow assurance. Inorganic salts such as NaCl, KCl and CaCl 2 are widely used as the thermodynamic inhibitor to reduce the risk caused by hydrate formation. However, the inhibition mechanism is still unclear. Therefore, molecular dynamic (MD) simulation was performed to study the dissociation of structure I (SI) methane hydrate in existence of inorganic salt aqueous solution on a micro-scale. The simulation results showed that, the dissociation became stagnant due to the presence of liquid film formed by the decomposed water molecules, and more inorganic ions could shorten the stagnation-time. The diffusion coefficients of ions and water molecules were the largest in KCl system. The structures of ion/H 2 O and H 2 O/H 2 O were the most compact in hydrate/NaCl system. The ionic ability to decompose hydrate cells followed the sequence of: Ca 2+ >2K + >2Cl - >2Na + . Copyright © 2017 Elsevier Inc. All rights reserved.

Molecular dynamics study of methane hydrate formation at a water/methane interface.

PubMed

Zhang, Junfang; Hawtin, R W; Yang, Ye; Nakagava, Edson; Rivero, M; Choi, S K; Rodger, P M

2008-08-28

We present molecular dynamics simulation results of a liquid water/methane interface, with and without an oligomer of poly(methylaminoethylmethacrylate), PMAEMA. PMAEMA is an active component of a commercial low dosage hydrate inhibitor (LDHI). Simulations were performed in the constant NPT ensemble at temperatures of 220, 235, 240, 245, and 250 K and a pressure of 300 bar. The simulations show the onset of methane hydrate growth within 30 ns for temperatures below 245 K in the methane/water systems; at 240 K there is an induction period of ca. 20 ns, but at lower temperatures growth commences immediately. The simulations were analyzed to calculate hydrate content, the propensity for hydrogen bond formation, and how these were affected by both temperature and the presence of the LDHI. As expected, both the hydrogen bond number and hydrate content decreased with increasing temperature, though little difference was observed between the lowest two temperatures considered. In the presence of PMAEMA, the temperature below which sustained hydrate growth occurred was observed to decrease. Some of the implications for the role of PMAEMA in LDHIs are discussed.

Capturing Transient Endoperoxide in the Singlet Oxygen Oxidation of Guanine.

PubMed

Lu, Wenchao; Liu, Jianbo

2016-02-24

The chemistry of singlet O2 toward the guanine base of DNA is highly relevant to DNA lesion, mutation, cell death, and pathological conditions. This oxidative damage is initiated by the formation of a transient endoperoxide through the Diels-Alder cycloaddition of singlet O2 to the guanine imidazole ring. However, no endoperoxide formation was directly detected in native guanine or guanosine, even at -100 °C. Herein, gas-phase ion-molecule scattering mass spectrometry was utilized to capture unstable endoperoxides in the collisions of hydrated guanine ions (protonated or deprotonated) with singlet O2 at ambient temperature. Corroborated by results from potential energy surface exploration, kinetic modeling, and dynamics simulations, various aspects of endoperoxide formation and transformation (including its dependence on guanine ionization and hydration states, as well as on collision energy) were determined. This work has pieced together reaction mechanisms, kinetics, and dynamics data concerning the early stage of singlet O2 induced guanine oxidation, which is missing from conventional condensed-phase studies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

CO2 Capture by Injection of Flue Gas or CO2-N2 Mixtures into Hydrate Reservoirs: Dependence of CO2 Capture Efficiency on Gas Hydrate Reservoir Conditions.

PubMed

Hassanpouryouzband, Aliakbar; Yang, Jinhai; Tohidi, Bahman; Chuvilin, Evgeny; Istomin, Vladimir; Bukhanov, Boris; Cheremisin, Alexey

2018-04-03

Injection of flue gas or CO 2 -N 2 mixtures into gas hydrate reservoirs has been considered as a promising option for geological storage of CO 2 . However, the thermodynamic process in which the CO 2 present in flue gas or a CO 2 -N 2 mixture is captured as hydrate has not been well understood. In this work, a series of experiments were conducted to investigate the dependence of CO 2 capture efficiency on reservoir conditions. The CO 2 capture efficiency was investigated at different injection pressures from 2.6 to 23.8 MPa and hydrate reservoir temperatures from 273.2 to 283.2 K in the presence of two different saturations of methane hydrate. The results showed that more than 60% of the CO 2 in the flue gas was captured and stored as CO 2 hydrate or CO 2 -mixed hydrates, while methane-rich gas was produced. The efficiency of CO 2 capture depends on the reservoir conditions including temperature, pressure, and hydrate saturation. For a certain reservoir temperature, there is an optimum reservoir pressure at which the maximum amount of CO 2 can be captured from the injected flue gas or CO 2 -N 2 mixtures. This finding suggests that it is essential to control the injection pressure to enhance CO 2 capture efficiency by flue gas or CO 2 -N 2 mixtures injection.

Hydration of non-polar anti-parallel β-sheets

NASA Astrophysics Data System (ADS)

Urbic, Tomaz; Dias, Cristiano L.

2014-04-01

In this work we focus on anti-parallel β-sheets to study hydration of side chains and polar groups of the backbone using all-atom molecular dynamics simulations. We show that: (i) water distribution around the backbone does not depend significantly on amino acid sequence, (ii) more water molecules are found around oxygen than nitrogen atoms of the backbone, and (iii) water molecules around nitrogen are highly localized in the planed formed by peptide backbones. To study hydration around side chains we note that anti-parallel β-sheets exhibit two types of cross-strand pairing: Hydrogen-Bond (HB) and Non-Hydrogen-Bond (NHB) pairing. We show that distributions of water around alanine, leucine, and valine side chains are very different at HB compared to NHB faces. For alanine pairs, the space between side chains has a higher concentration of water if residues are located in the NHB face of the β-sheet as opposed to the HB face. For leucine residues, the HB face is found to be dry while the space between side chains at the NHB face alternates between being occupied and non-occupied by water. Surprisingly, for valine residues the NHB face is dry, whereas the HB face is occupied by water. We postulate that these differences in water distribution are related to context dependent propensities observed for β-sheets.

Hydration of non-polar anti-parallel β-sheets

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

Urbic, Tomaz; Dias, Cristiano L., E-mail: cld@njit.edu

2014-04-28

In this work we focus on anti-parallel β-sheets to study hydration of side chains and polar groups of the backbone using all-atom molecular dynamics simulations. We show that: (i) water distribution around the backbone does not depend significantly on amino acid sequence, (ii) more water molecules are found around oxygen than nitrogen atoms of the backbone, and (iii) water molecules around nitrogen are highly localized in the planed formed by peptide backbones. To study hydration around side chains we note that anti-parallel β-sheets exhibit two types of cross-strand pairing: Hydrogen-Bond (HB) and Non-Hydrogen-Bond (NHB) pairing. We show that distributions ofmore » water around alanine, leucine, and valine side chains are very different at HB compared to NHB faces. For alanine pairs, the space between side chains has a higher concentration of water if residues are located in the NHB face of the β-sheet as opposed to the HB face. For leucine residues, the HB face is found to be dry while the space between side chains at the NHB face alternates between being occupied and non-occupied by water. Surprisingly, for valine residues the NHB face is dry, whereas the HB face is occupied by water. We postulate that these differences in water distribution are related to context dependent propensities observed for β-sheets.« 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 .

Skin Membrane Electrical Impedance Properties under the Influence of a Varying Water Gradient

PubMed Central

Björklund, Sebastian; Ruzgas, Tautgirdas; Nowacka, Agnieszka; Dahi, Ihab; Topgaard, Daniel; Sparr, Emma; Engblom, Johan

2013-01-01

The stratum corneum (SC) is an effective permeability barrier. One strategy to increase drug delivery across skin is to increase the hydration. A detailed description of how hydration affects skin permeability requires characterization of both macroscopic and molecular properties and how they respond to hydration. We explore this issue by performing impedance experiments on excised skin membranes in the frequency range 1 Hz to 0.2 MHz under the influence of a varying gradient in water activity (aw). Hydration/dehydration induces reversible changes of membrane resistance and effective capacitance. On average, the membrane resistance is 14 times lower and the effective capacitance is 1.5 times higher when the outermost SC membrane is exposed to hydrating conditions (aw = 0.992), as compared to the case of more dehydrating conditions (aw = 0.826). Molecular insight into the hydration effects on the SC components is provided by natural-abundance 13C polarization transfer solid-state NMR and x-ray diffraction under similar hydration conditions. Hydration has a significant effect on the dynamics of the keratin filament terminals and increases the interchain spacing of the filaments. The SC lipids are organized into lamellar structures with ∼ 12.6 nm spacing and hexagonal hydrocarbon chain packing with mainly all-trans configuration of the acyl chains, irrespective of hydration state. Subtle changes in the dynamics of the lipids due to mobilization and incorporation of cholesterol and long-chain lipid species into the fluid lipid fraction is suggested to occur upon hydration, which can explain the changes of the impedance response. The results presented here provide information that is useful in explaining the effect of hydration on skin permeability. PMID:23790372

Thermal conductivity and thermal diffusivity of methane hydrate formed from compacted granular ice

NASA Astrophysics Data System (ADS)

Zhao, Jie; Sun, Shicai; Liu, Changling; Meng, Qingguo

2018-05-01

Thermal conductivity and thermal diffusivity of pure methane hydrate samples, formed from compacted granular ice (0-75 μm), and were measured simultaneously by the transient plane source (TPS) technique. The temperature dependence was measured between 263.15 and 283.05 K, and the gas-phase pressure dependence was measured between 2 and 10 MPa. It is revealed that the thermal conductivity of pure methane hydrate exhibits a positive trend with temperature and increases from 0.4877 to 0.5467 W·m-1·K-1. The thermal diffusivity of methane hydrate has inverse dependence on temperature and the values in the temperature range from 0.2940 to 0.3754 mm2·s-1, which is more than twice that of water. The experimental results show that the effects of gas-phase pressure on the thermal conductivity and thermal diffusivity are very small. Thermal conductivity of methane hydrate is found to have weakly positive gas-phase pressure dependence, whereas the thermal diffusivity has slightly negative trend with gas-phase pressure.

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.

Preferential solvation of lysozyme in dimethyl sulfoxide/water binary mixture probed by terahertz spectroscopy.

PubMed

Das, Dipak Kumar; Patra, Animesh; Mitra, Rajib Kumar

2016-09-01

We report the changes in the hydration dynamics around a model protein hen egg white lysozyme (HEWL) in water-dimethyl sulfoxide (DMSO) binary mixture using THz time domain spectroscopy (TTDS) technique. DMSO molecules get preferentially solvated at the protein surface, as indicated by circular dichroism (CD) and Fourier transform infrared (FTIR) study in the mid-infrared region, resulting in a conformational change in the protein, which consequently modifies the associated hydration dynamics. As a control we also study the collective hydration dynamics of water-DMSO binary mixture and it is found that it follows a non-ideal behavior owing to the formation of DMSO-water clusters. It is observed that the cooperative dynamics of water at the protein surface does follow the DMSO-mediated conformational modulation of the protein. Copyright © 2016 Elsevier B.V. All rights reserved.

Hydration status and diurnal trophic interactions shape microbial community function in desert biocrusts

NASA Astrophysics Data System (ADS)

Kim, Minsu; Or, Dani

2017-12-01

Biological soil crusts (biocrusts) are self-organised thin assemblies of microbes, lichens, and mosses that are ubiquitous in arid regions and serve as important ecological and biogeochemical hotspots. Biocrust ecological function is intricately shaped by strong gradients of water, light, oxygen, and dynamics in the abundance and spatial organisation of the microbial community within a few millimetres of the soil surface. We report a mechanistic model that links the biophysical and chemical processes that shape the functioning of biocrust representative microbial communities that interact trophically and respond dynamically to cycles of hydration, light, and temperature. The model captures key features of carbon and nitrogen cycling within biocrusts, such as microbial activity and distribution (during early stages of biocrust establishment) under diurnal cycles and the associated dynamics of biogeochemical fluxes at different hydration conditions. The study offers new insights into the highly dynamic and localised processes performed by microbial communities within thin desert biocrusts.

Dissipation at the angstrom scale: Probing the surface and interior of an enzyme

NASA Astrophysics Data System (ADS)

Alavi, Zahra; Zocchi, Giovanni

2018-05-01

Pursuing a materials science approach to understanding the deformability of enzymes, we introduce measurements of the phase of the mechanical response function within the nanorheology paradigm. Driven conformational motion of the enzyme is dissipative as characterized by the phase measurements. The dissipation originates both from the surface hydration layer and the interior of the molecule, probed by examining the effect of point mutations on the mechanics. We also document changes in the mechanics of the enzyme examined, guanylate kinase, upon binding its four substrates. GMP binding stiffens the molecule, ATP and ADP binding softens it, while there is no clear mechanical signature of GDP binding. A hyperactive two-Gly mutant is found to possibly trade specificity for speed. Global deformations of enzymes are shown to be dependent on both hydration layer and polypeptide chain dynamics.

Along - Strike Analysis of Contemporary Ocean Temperature Change on the Cascadia Margin and Implications to Upper Slope Hydrate Instability

NASA Astrophysics Data System (ADS)

Phrampus, B.; Harris, R. N.; Trehu, A. M.; Embley, R. W.; Merle, S. G.

2017-12-01

Gas hydrates are found globally on continental margins and due to the large amount of sequestered carbon in hydrate reservoirs, whether these deposits are dynamic or stable has significant implications for slope stability, ocean/atmosphere carbon budget, and deep-water energy exploration. Recent studies indicate that upper slope hydrate degradation may be relatively widespread on passive margins due to recent ocean temperature warming between 0.012 and 0.033 °C/yr (e.g. Svalbard, North Alaska, and US Atlantic margin). However, the potential and breadth of warming induced hydrate instability remains contentious based on multiple observations including: 1) seep locations not consistent with locations of hydrate dissociation, 2) a lack of hydrate in regions of warming, and 3) evidence for long-lived seepage in regions associated with contemporary warming-induced hydrate dissociation. At the Cascadia margin, a recent study suggests that contemporary warming of intermediate water intersects the hydrate stability zone leading to hydrate dissociation that feeds upper slope seeps. Here, we provide a systematic analysis of along-strike variations in hydrate distribution along the Cascadia margin combined with a multivariable regression of ocean temperatures to characterize the potential of upper slope hydrate instability. Preliminary seep locations reveal upper slope seeps and observed regions of hydrate are correlated spatially between 42.5 and 48.0 °N, outside this region there is a dearth of identified upper slope hydrate and seeps. Between 44.5 and 48.0 °N a contemporary warming trend is as large as 0.006 °C/yr and is collocated with upper slope hydrate and gas seepage. This warming rate is relatively small, 2-5x smaller than warming trends identified in the Arctic where temperature induced hydrate instability remains uncertain. Additionally, we identify a region between 42.5 and 44.5 °N with collocated upper slope seepage and hydrate but no evidence of ocean warming, suggesting upper slope seepage is not driven by temperature induced hydrate instability, but maybe driven by tectonic uplift. These results highlight the absence of temperature driven seepage and slope instability on the Cascadia margin and deemphasize the impact of lower latitude warming on global hydrate dynamics and carbon budget.

On the hydration of subnanometric antifouling organosilane adlayers: a molecular dynamics simulation.

PubMed

Sheikh, Sonia; Blaszykowski, Christophe; Nolan, Robert; Thompson, Damien; Thompson, Michael

2015-01-01

The connection between antifouling and surface hydration is a fascinating but daunting question to answer. Herein, we use molecular dynamics (MD) computer simulations to gain further insight into the role of surface functionalities in the molecular-level structuration of water (surface kosmotropicity)--within and atop subnanometric organosilane adlayers that were shown in previous experimental work to display varied antifouling behavior. Our simulations support the hypothesized intimate link between surface hydration and antifouling, in particular the importance of both internal and interfacial hydrophilicity and kosmotropicity. The antifouling mechanism is also discussed in terms of surface dehydration energy and water dynamicity (lability and mobility), notably the crucial requirement for clustered water molecules to remain tightly bound for extensive periods of time--i.e. exhibit slow exchange dynamics. A substrate effect on surface hydration, which would also participate in endowing antifouling adlayers with hydrogel-like characteristics, is also proposed. In contrast, the role of adlayer flexibility, if any, is assigned a secondary role in these ultrathin structures made of short building blocks. The conclusions from this work are well in line with those previously drawn in the literature. Copyright © 2014 Elsevier Inc. All rights reserved.

Mechanical instability of monocrystalline and polycrystalline methane hydrates

PubMed Central

Wu, Jianyang; Ning, Fulong; Trinh, Thuat T.; Kjelstrup, Signe; Vlugt, Thijs J. H.; He, Jianying; Skallerud, Bjørn H.; Zhang, Zhiliang

2015-01-01

Despite observations of massive methane release and geohazards associated with gas hydrate instability in nature, as well as ductile flow accompanying hydrate dissociation in artificial polycrystalline methane hydrates in the laboratory, the destabilising mechanisms of gas hydrates under deformation and their grain-boundary structures have not yet been elucidated at the molecular level. Here we report direct molecular dynamics simulations of the material instability of monocrystalline and polycrystalline methane hydrates under mechanical loading. The results show dislocation-free brittle failure in monocrystalline hydrates and an unexpected crossover from strengthening to weakening in polycrystals. Upon uniaxial depressurisation, strain-induced hydrate dissociation accompanied by grain-boundary decohesion and sliding destabilises the polycrystals. In contrast, upon compression, appreciable solid-state structural transformation dominates the response. These findings provide molecular insight not only into the metastable structures of grain boundaries, but also into unusual ductile flow with hydrate dissociation as observed during macroscopic compression experiments. PMID:26522051

Transport Mechanism of Guest Methane in Water-Filled Nanopores

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

Bui, Tai; Phan, Anh; Cole, David R.

We computed the transport of methane through 1 nm wide slit-shaped pores carved out of selected solid substrates using classical molecular dynamics simulations. The transport mechanism was elucidated via the implementation of the well-tempered metadynamics algorithm, which allowed for the quantification and visualization of the free energy landscape sampled by the guest molecule. Models for silica, magnesium oxide, alumina, muscovite, and calcite were used as solid substrates. Slit-shaped pores of width 1 nm were carved out of these materials and filled with liquid water. Methane was then inserted at low concentration. The results show that the diffusion of methane throughmore » the hydrated pores is strongly dependent on the solid substrate. While methane molecules diffuse isotropically along the directions parallel to the pore surfaces in most of the pores considered, anisotropic diffusion was observed in the hydrated calcite pore. The differences observed in the various pores are due to local molecular properties of confined water, including molecular structure and solvation free energy. The transport mechanism and the diffusion coefficients are dependent on the free energy barriers encountered by one methane molecule as it migrates from one preferential adsorption site to a neighboring one. It was found that the heterogeneous water distribution in different hydration layers and the low free energy pathways in the plane parallel to the pore surfaces yield the anisotropic diffusion of methane molecules in the hydrated calcite pore. Our observations contribute to an ongoing debate on the relation between local free energy profiles and diffusion coefficients and could have important practical consequences in various applications, ranging from the design of selective membranes for gas separations to the sustainable deployment of shale gas.« less

Transport Mechanism of Guest Methane in Water-Filled Nanopores

DOE PAGES

Bui, Tai; Phan, Anh; Cole, David R.; ...

2017-05-11

We computed the transport of methane through 1 nm wide slit-shaped pores carved out of selected solid substrates using classical molecular dynamics simulations. The transport mechanism was elucidated via the implementation of the well-tempered metadynamics algorithm, which allowed for the quantification and visualization of the free energy landscape sampled by the guest molecule. Models for silica, magnesium oxide, alumina, muscovite, and calcite were used as solid substrates. Slit-shaped pores of width 1 nm were carved out of these materials and filled with liquid water. Methane was then inserted at low concentration. The results show that the diffusion of methane throughmore » the hydrated pores is strongly dependent on the solid substrate. While methane molecules diffuse isotropically along the directions parallel to the pore surfaces in most of the pores considered, anisotropic diffusion was observed in the hydrated calcite pore. The differences observed in the various pores are due to local molecular properties of confined water, including molecular structure and solvation free energy. The transport mechanism and the diffusion coefficients are dependent on the free energy barriers encountered by one methane molecule as it migrates from one preferential adsorption site to a neighboring one. It was found that the heterogeneous water distribution in different hydration layers and the low free energy pathways in the plane parallel to the pore surfaces yield the anisotropic diffusion of methane molecules in the hydrated calcite pore. Our observations contribute to an ongoing debate on the relation between local free energy profiles and diffusion coefficients and could have important practical consequences in various applications, ranging from the design of selective membranes for gas separations to the sustainable deployment of shale gas.« less

Collective hydration dynamics of guanidinium chloride solutions and its possible role in protein denaturation: a terahertz spectroscopic study.

PubMed

Samanta, Nirnay; Mahanta, Debasish Das; Mitra, Rajib Kumar

2014-11-14

The remarkable ability of guanidinium chloride (GdmCl) to denature proteins is a well studied yet controversial phenomenon; the exact molecular mechanism is still debatable, especially the role of hydration dynamics, which has been paid less attention. In the present contribution, we have addressed the issue of whether the collective hydrogen bond dynamics of water gets perturbed in the presence of GdmCl and its possible impact on the denaturation of a globular protein human serum albumin (HSA), using terahertz (THz) time domain spectroscopy (TTDS) in the frequency range of 0.3-2.0 THz. The collective hydrogen bond dynamics is determined by fitting the obtained complex dielectric response in a multiple Debye relaxation model. To compare the results, the studies were extended to two more salts: tetramethylguanidinium chloride (TMGdmCl) and sodium chloride (NaCl). It was concluded that the change in hydration dynamics plays a definite role in the protein denaturation process.

Steps Towards Understanding Large-scale Deformation of Gas Hydrate-bearing Sediments

NASA Astrophysics Data System (ADS)

Gupta, S.; Deusner, C.; Haeckel, M.; Kossel, E.

2016-12-01

Marine sediments bearing gas hydrates are typically characterized by heterogeneity in the gas hydrate distribution and anisotropy in the sediment-gas hydrate fabric properties. Gas hydrates also contribute to the strength and stiffness of the marine sediment, and any disturbance in the thermodynamic stability of the gas hydrates is likely to affect the geomechanical stability of the sediment. Understanding mechanisms and triggers of large-strain deformation and failure of marine gas hydrate-bearing sediments is an area of extensive research, particularly in the context of marine slope-stability and industrial gas production. The ultimate objective is to predict severe deformation events such as regional-scale slope failure or excessive sand production by using numerical simulation tools. The development of such tools essentially requires a careful analysis of thermo-hydro-chemo-mechanical behavior of gas hydrate-bearing sediments at lab-scale, and its stepwise integration into reservoir-scale simulators through definition of effective variables, use of suitable constitutive relations, and application of scaling laws. One of the focus areas of our research is to understand the bulk coupled behavior of marine gas hydrate systems with contributions from micro-scale characteristics, transport-reaction dynamics, and structural heterogeneity through experimental flow-through studies using high-pressure triaxial test systems and advanced tomographical tools (CT, ERT, MRI). We combine these studies to develop mathematical model and numerical simulation tools which could be used to predict the coupled hydro-geomechanical behavior of marine gas hydrate reservoirs in a large-strain framework. Here we will present some of our recent results from closely co-ordinated experimental and numerical simulation studies with an objective to capture the large-deformation behavior relevant to different gas production scenarios. We will also report on a variety of mechanically relevant test scenarios focusing on effects of dynamic changes in gas hydrate saturation, highly uneven gas hydrate distributions, focused fluid migration and gas hydrate production through depressurization and CO2 injection.

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.

Preliminary Measurements on the Mechanical Properties of Clathrate Hydrates with Implications for the Internal Dynamics of Icy Satellites

NASA Astrophysics Data System (ADS)

Choukroun, M.; Barmatz, M. B.; Castillo, J. C.; Sotin, C.

2008-12-01

Surface features potentially associated with cryovolcanism have been identified on Titan, and the processes taking place beneath the surface are likely associated with the dissociation of clathrate hydrates and the release of methane. On Enceladus, the South Pole plume discovered by the Cassini-Huygens mission contains a large proportion of volatiles, in amounts consistent with models of clathrate hydrates dissociation at depth (Kieffer et al., Science 314, 1764-1766, 2006). The stability of clathrate hydrates is relatively well constrained in pure and mixed gas systems (e.g., Sloan, Clathrate hydrates of natural gases, Marcel Dekker, New York, 1998). Recent measurements of clathrate destabilization in presence of ammonia, a likely component of Titan's interior, led to the development of a new model of cryovolcanism (Choukroun et al., Lunar Planet. Sci. Conf., #1837, Houston, 2008). Internal dynamics relies on ice convection at depth on Titan and Enceladus (e.g., Tobie et al., Icarus 175, 496-502, 2005), and on relatively large tidal stresses on Enceladus. Clathrates are expected to destabilize when subject to stress (Durham et al., J. Geophys. Res. 108 (B4), 2182, 2003). Therefore, addressing the mechanical properties of clathrate hydrates in these environments is a necessary step toward better understanding cryovolcanic processes. We have developed a new apparatus for growing clathrate hydrates samples with controlled geometry, composition, and grain size. This system consists of a high-pressure autoclave and a cooling system and supports gas pressures up to 500 bars, and temperatures within the range -50 - 150 °C. We have started the production of clathrate hydrates of CH4, CO2, and N2 with this system, with the purpose to test their mechanical properties using an Instron compression system (Castillo-Rogez et al., submitted to J. Geophys. Res.; Castillo-Rogez et al., this meeting). We will present initial measurements on the creep response and on the viscoelastic response of clathrate hydrates as a function of frequency. These measurements will provide new information on the behavior of clathrate hydrates during dynamic motions within icy satellites.

The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR

PubMed Central

Walsh, Scott T.R.; Cheng, Richard P.; Wright, Wayne W.; Alonso, Darwin O.V.; Daggett, Valerie; Vanderkooi, Jane M.; DeGrado, William F.

2003-01-01

We examined the hydration of amides of α3D, a simple, designed three-helix bundle protein. Molecular dynamics calculations show that the amide carbonyls on the surface of the protein tilt away from the helical axis to interact with solvent water, resulting in a lengthening of the hydrogen bonds on this face of the helix. Water molecules are bonded to these carbonyl groups with partial occupancy (∼50%–70%), and their interaction geometries show a large variation in their hydrogen bond lengths and angles on the nsec time scale. This heterogeneity is reflected in the carbonyl stretching vibration (amide I′ band) of a group of surface Ala residues. The surface-exposed amides are broad, and shift to lower frequency (reflecting strengthening of the hydrogen bonds) as the temperature is decreased. By contrast, the amide I′ bands of the buried 13C-labeled Leu residues are significantly sharper and their frequencies are consistent with the formation of strong hydrogen bonds, independent of temperature. The rates of hydrogen-deuterium exchange and the proton NMR chemical shifts of the helical amide groups also depend on environment. The partial occupancy of the hydration sites on the surface of helices suggests that the interaction is relatively weak, on the order of thermal energy at room temperature. One unexpected feature that emerged from the dynamics calculations was that a Thr side chain subtly disrupted the helical geometry 4–7 residues N-terminal in sequence, which was reflected in the proton chemical shifts and the rates of amide proton exchange for several amides that engage in a mixed 310/α/π-helical conformation. PMID:12592022

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.

Dynamical cage behaviour and hydrogen migration in hydrogen and hydrogen-tetrahydrofuran clathrate hydrates

NASA Astrophysics Data System (ADS)

Gorman, Paul D.; English, Niall J.; MacElroy, J. M. D.

2012-01-01

Classical equilibrium molecular dynamics simulations have been performed to investigate dynamical properties of cage radial breathing modes and intra- and inter-cage hydrogen migration in both pure hydrogen and mixed hydrogen-tetrahydrofuran sII hydrates at 0.05 kbar and up to 250 K. For the mixed H2-THF system in which there is single H2 occupation of the small cage (labelled "1SC 1LC"), we find that no H2 migration occurs, and this is also the case for pure H2 hydrate with single small-cavity occupation and quadruple occupancy for large cages (dubbed "1SC 4LC"). However, for the more densely filled H2-THF and pure-H2 systems, in which there is double H2 occupation in the small cage (dubbed "2SC 1LC" and "2SC 4LC," respectively), there is an onset of inter-cage H2 migration events from the small cages to neighbouring cavities at around 200 K, with an approximate Arrhenius temperature-dependence for the migration rate from 200 to 250 K. It was found that these "cage hopping" events are facilitated by temporary openings of pentagonal small-cage faces with the relaxation and reformation of key stabilising hydrogen bonds during and following passage. The cages remain essentially intact up to 250 K, save for transient hydrogen bond weakening and reformation during and after inter-cage hydrogen diffusion events in the 200-250 K range. The "breathing modes," or underlying frequencies governing the variation in the cavities' radii, exhibit a certain overlap with THF rattling motion in the case of large cavities, while there is some overlap of small cages' radial breathing modes with lattice acoustic modes.

Hydrogen-Bonded Network and Water Dynamics in the D-channel of Cytochrome c Oxidase.

PubMed

Ghane, Tahereh; Gorriz, Rene F; Wrzalek, Sandro; Volkenandt, Senta; Dalatieh, Ferand; Reidelbach, Marco; Imhof, Petra

2018-02-12

Proton transfer in cytochrome c oxidase (CcO) from the cellular inside to the binuclear redox centre as well as proton pumping through the membrane takes place through proton entrance via two distinct pathways, the D- and K-channel. Both channels show a dependence of their hydration level on the protonation states of their key residues, K362 for the K-channel, and E286 or D132 for the D-channel. In the oxidative half of CcO's catalytic cycle the D-channel is the proton-conducting path. For this channel, an interplay of protonation state of the D-channel residues with the water and hydrogen-bond dynamics has been observed in molecular dynamics simulations of the CcO protein, embedded in a lipid bi-layer, modelled in different protonation states. Protonation of residue E286 at the end of the D-channel results in a hydrogen-bonded network pointing from E286 to N139, that is against proton transport, and favouring N139 conformations which correspond to a closed asparagine gate (formed by residues N121 and N139). Consequently, the hydration level is lower than with unprotonated E286. In those models, the Asn gate is predominantly open, allowing water molecules to pass and thus increase the hydration level. The hydrogen-bonded network in these states exhibits longer life times of the Asn residues with water than other models and shows the D-channel to be traversable from the entrance, D132, to exit, E286. The D-channel can thus be regarded as auto-regulated with respect to proton transport, allowing proton passage only when required, that is the proton is located at the lower part of the D-channel (D132 to Asn gate) and not at the exit (E286).

Decomposition of total solvation energy into core, side-chains and water contributions: Role of cross correlations and protein conformational fluctuations in dynamics of hydration layer

NASA Astrophysics Data System (ADS)

Mondal, Sayantan; Mukherjee, Saumyak; Bagchi, Biman

2017-09-01

Dynamical coupling between water and amino acid side-chain residues in solvation dynamics is investigated by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on protein surface. Such differently placed residues are found to exhibit different timescales of relaxation. The total solvation response measured by the probe is decomposed in terms of its interactions with (i) protein core, (ii) side-chain and (iii) water. Significant anti cross-correlation among these contributions are observed. When the motion of the protein side-chains is quenched, solvation either becomes faster or slower depending on the location of the probe.

Surface hydration amplifies single-well protein atom diffusion propagating into the macromolecular core

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

Hong, Liang; Cheng, Xiaolin; Glass, Dennis C.

2012-06-05

The effect of surface hydration water on internal protein motion is of fundamental interest in molecular biophysics. Here, by decomposing the picosecond to nanosecond atomic motion in molecular dynamics simulations of lysozyme at different hydration levels into three components localized single-well diffusion, methyl group rotation, and nonmethyl jumps we show that the effect of surface hydration is mainly to increase the volume of the localized single-well diffusion. As a result, these diffusive motions are coupled in such a way that the hydration effect propagates from the protein surface into the dry core.

Quantifying Hydrate Formation in Gas-rich Environments Using the Method of Characteristics

NASA Astrophysics Data System (ADS)

You, K.; Flemings, P. B.; DiCarlo, D. A.

2015-12-01

Methane hydrates hold a vast amount of methane globally, and have huge energy potential. Methane hydrates in gas-rich environments are the most promising production targets. We develop a one-dimensional analytical solution based on the method of characteristics to explore hydrate formation in such environments (Figure 1). Our solution shows that hydrate saturation is constant with time and space in a homogeneous system. Hydrate saturation is controlled by the initial thermodynamic condition of the system, and changed by the gas fractional flow. Hydrate saturation increases with the initial distance from the hydrate phase boundary. Different gas fractional flows behind the hydrate solidification front lead to different gas saturations at the hydrate solidification front. The higher the gas saturation at the front, the less the volume available to be filled by hydrate, and hence the lower the hydrate saturation. The gas fractional flow depends on the relative permeability curves, and the forces that drive the flow. Viscous forces (the drive for flow induced from liquid pressure gradient) dominate the flow, and hydrate saturation is independent on the gas supply rates and the flow directions at high gas supply rates. Hydrate saturation can be estimated as one minus the ratio of the initial to equilibrium salinity. Gravity forces (the drive for flow induced from the gravity) dominate the flow, and hydrate saturation depends on the flow rates and the flow directions at low gas supply rates. Hydrate saturation is highest for upward flow, and lowest for downward flow. Hydrate saturation decreases with the flow rate for upward flow, and increases with the flow rate for downward flow. This analytical solution illuminates how hydrate is formed by gas (methane, CO2, ethane, propane) flowing into brine-saturated sediments at both the laboratory and geological scales (Figure 1). It provides an approach to generalize the understanding of hydrate solidification in gas-rich environments, although complicated numerical models have been developed previously. Examples of gas expulsion into hydrate stability zones and the associated hydrate formation in both laboratory and geological scales, and CO2 sequestration into CO2-hydrates near the seafloor and under the permafrost will be presented.

Protein Conformational Entropy is Independent of Solvent

NASA Astrophysics Data System (ADS)

Nucci, Nathaniel; Moorman, Veronica; Gledhill, John; Valentine, Kathleen; Wand, A. Joshua

Proteins exhibit most of their conformational entropy in individual bond vector motions on the ps-ns timescale. These motions can be examined through determination of the Lipari-Szabo generalized squared order parameter (O2) using NMR spin relaxation measurements. It is often argued that most protein motions are intimately dependent on the nature of the solvating environment. Here the solvent dependence of the fast protein dynamics is directly assessed. Using the model protein ubiquitin, the order parameters of the backbone and methyl groups are shown to be generally unaffected by up to a six-fold increase in bulk viscosity or by encapsulation in the nanoscale interior of a reverse micelle. In addition, the reverse micelle condition permits direct comparison of protein dynamics to the mobility of the hydration layer; no correlation is observed. The dynamics of aromatic side chains are also assessed and provide an estimate of the length- and timescale of protein motions where solvent dependence is seen. These data demonstrate the solvent independence of conformational entropy, clarifying a long-held misconception in the fundamental behavior of biological macromolecules. Supported by the National Science Foundation.

Skin hydration: interplay between molecular dynamics, structure and water uptake in the stratum corneum.

PubMed

Mojumdar, Enamul Haque; Pham, Quoc Dat; Topgaard, Daniel; Sparr, Emma

2017-11-16

Hydration is a key aspect of the skin that influences its physical and mechanical properties. Here, we investigate the interplay between molecular and macroscopic properties of the outer skin layer - the stratum corneum (SC) and how this varies with hydration. It is shown that hydration leads to changes in the molecular arrangement of the peptides in the keratin filaments as well as dynamics of C-H bond reorientation of amino acids in the protruding terminals of keratin protein within the SC. The changes in molecular structure and dynamics occur at a threshold hydration corresponding to ca. 85% relative humidity (RH). The abrupt changes in SC molecular properties coincide with changes in SC macroscopic swelling properties as well as mechanical properties in the SC. The flexible terminals at the solid keratin filaments can be compared to flexible polymer brushes in colloidal systems, creating long-range repulsion and extensive swelling in water. We further show that the addition of urea to the SC at reduced RH leads to similar molecular and macroscopic responses as the increase in RH for SC without urea. The findings provide new molecular insights to deepen the understanding of how intermediate filament organization responds to changes in the surrounding environment.

Stepwise hydration and evaporation of adenosine monophosphate nucleotide anions: a multiscale theoretical study.

PubMed

Calvo, F; Douady, J

2010-04-14

The structure and finite-temperature properties of hydrated nucleotide anion adenosine 5'-monophosphate (AMP) have been theoretically investigated with a variety of methods. Using a polarizable version of the Amber force field and replica-exchange molecular dynamics simulations, putative lowest-energy structures have been located for the AMP(-)(H(2)O)(n) cluster anions with n = 0-20. The hydration energies obtained with the molecular mechanics potential slightly overestimate experimental measurements. However, closer values are found after reoptimizing the structures locally at more sophisticated levels, namely semi-empirical (PM6) and density-functional theory (B3LYP/6-31+G*). Upon heating the complexes, various indicators such as the heat capacity, number of hydrogen bonds or surface area provide evidence that the water cluster melts below 200 K but remains bonded to the AMP anion. The sequential loss of water molecules after sudden heating has been studied using a statistical approach in which unimolecular evaporation is described using the orbiting transition state version of phase space theory, together with anharmonic densities of vibrational states. The evaporation rates are calibrated based on the results of molecular dynamics trajectories at high internal energy. Our results indicate that between 4 and 10 water molecules are lost from AMP(-)(H(2)O)(20) after one second depending on the initial heating in the 250-350 K range, with a concomitant cooling of the remaining cluster by 75-150 K.

Toward the Understanding of MNEI Sweetness from Hydration Map Surfaces

PubMed Central

De Simone, Alfonso; Spadaccini, Roberta; Temussi, Piero A.; Fraternali, Franca

2006-01-01

The binding mechanism of sweet proteins to their receptor, a G-protein-coupled receptor, is not supported by direct structural information. In principle, the key groups responsible for biological activity (glucophores) can be localized on a small structural unit (sweet finger) or spread on a larger surface area. A recently proposed model, called “wedge model”, implies a large surface of interaction with the receptor. To explore this model in greater detail, it is necessary to examine the physicochemical features of the surfaces of sweet proteins, since their interaction with the receptor, with respect to that of small sweeteners, is more dependent on general physicochemical properties of the interface, such as electrostatic potential and hydration. In this study, we performed exhaustive molecular dynamics simulations in explicit water of the sweet protein MNEI and of its structural mutant G-16A, whose sweetness is one order of magnitude lower than that of MNEI. Solvent density and self-diffusion calculated from molecular dynamics simulations suggest a likely area of interaction delimited by four stretches arranged as a tetrahedron whose shape is complementary to that of a cavity on the surface of the receptor, in agreement with the wedge model. The suggested area of interaction is amazingly consistent with known mutagenesis data. In addition, the asymmetric hydration of the only helix in both proteins hints at a specific role for this secondary structure element in orienting the protein during the binding process. PMID:16461400

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

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.

Hydration shell parameters of aqueous alcohols: THz excess absorption and packing density.

PubMed

Matvejev, V; Zizi, M; Stiens, J

2012-12-06

Solvation in water requires minimizing the perturbations in its hydrogen bonded network. Hence solutes distort water molecular motions in a surrounding domain, forming a molecule-specific hydration shell. The properties of those hydration shells impact the structure and function of the solubilized molecules, both at the single molecule and at higher order levels. The size of the hydration shell and the picoseconds time-scale water dynamics retardation are revealed by terahertz (THz) absorption coefficient measurements. Room-temperature absorption coefficient at f = 0.28 [THz] is measured as a function of alcohol concentration in aqueous methanol, ethanol, 1,2-propanol, and 1-butanol solutions. Highly diluted alcohol measurements and enhanced overall measurement accuracy are achieved with a THz absorption measurement technique of nL-volume liquids in a capillary tube. In the absorption analysis, bulk and interfacial molecular domains of water and alcohol are considered. THz ideal and excess absorption coefficients are defined in accordance with thermodynamics mixing formulations. The parameter extraction method is developed based on a THz excess absorption model and hydrated solute molecule packing density representation. First, the hydration shell size is deduced from the hydrated solute packing densities at two specific THz excess absorption nonlinearity points: at infinite alcohol dilution (IAD) and at the THz excess absorption extremum (EAE). Consequently, interfacial water and alcohol molecular domain absorptions are deduced from the THz excess absorption model. The hydration shell sizes obtained at the THz excess absorption extremum are in excellent agreement with other reports. The hydration shells of methanol, ethanol, 1- and 2-propanol consist of 13.97, 22.94, 22.99, and 31.10 water molecules, respectively. The hydration shell water absorption is on average 0.774 ± 0.028 times the bulk water absorption. The hydration shell parameters might shed light on hydration dynamics of biomolecules.

CO2 injection into submarine, CH4-hydrate bearing sediments: Parameter studies towards the development of a hydrate conversion technology

NASA Astrophysics Data System (ADS)

Deusner, Christian; Bigalke, Nikolaus; Kossel, Elke; Haeckel, Matthias

2013-04-01

In the recent past, international research efforts towards exploitation of submarine and permafrost hydrate reservoirs have increased substantially. Until now, findings indicate that a combination of different technical means such as depressurization, thermal stimulation and chemical activation is the most promising approach for producing gas from natural hydrates. Moreover, emission neutral exploitation of CH4-hydrates could potentially be achieved in a combined process with CO2 injection and storage as CO2-hydrate. In the German gas hydrate initiative SUGAR, a combination of experimental and numerical studies is used to elucidate the process mechanisms and technical parameters on different scales. Experiments were carried out in the novel high-pressure flow-through system NESSI (Natural Environment Simulator for sub-Seafloor Interactions). Recent findings suggest that the injection of heated, supercritical CO2 is beneficial for both CH4 production and CO2 retention. Among the parameters tested so far are the CO2 injection regime (alternating vs. continuous injection) and the reservoir pressure / temperature conditions. Currently, the influence of CO2 injection temperature is investigated. It was shown that CH4 production is optimal at intermediate reservoir temperatures (8 ° C) compared to lower (2 ° C) and higher temperatures (10 ° C). The reservoir pressure, however, was of minor importance for the production efficiency. At 8 ° C, where CH4- and CO2-hydrates are thermodynamically stable, CO2-hydrate formation appears to be slow. Eventual clogging of fluid conduits due to CO2-rich hydrate formation force open new conduits, thereby tapping different regions inside the CH4-hydrate sample volume for CH4gas. In contrast, at 2 ° C immediate formation of CO2-hydrate results in rapid and irreversible obstruction of the entire pore space. At 10 ° C pure CO2-hydrates can no longer be formed. Consequently the injected CO2 flows through quickly and interaction with the reservoir is minimized. Our results clearly indicate that the formation of mixed CH4-CO2-hydrates is an important aspect in the conversion process. The experimental studies have shown that the injection of heated CO2 into the hydrate reservoir induces a variety of spatial and temporal processes which result in substantial bulk heterogeneity. Current numerical simulators are not able to predict these process dynamics and it is important to improve available transport-reaction models (e.g. to include the effect of bulk sediment permeability on the conversion dynamics). Our results confirm that experimental studies are important to better understand the mechanisms of hydrate dissociation and conversion at CO2-injection conditions as a basis towards the development of a suitable hydrate conversion technology. The application of non-invasive analytical methods such as Magnetic Resonance Imaging (MRI) and Raman microscopy are important tools, which were applied to resolve process dynamics on the pore scale. Additionally, the NESSI system is being modified to allow high-pressure flow-through experiments under triaxial loading to better simulate hydrate-sediment mechanics. This aspect is important for overall process development and evaluation of process safety issues.

Effect of Glycerol Water Binary Mixtures on the Structure and Dynamics of Protein Solutions

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

Ghattyvenkatakrishna, Pavan K; Carri, Gustavo A.

We have performed 20ns of fully atomistic molecular dynamics simulations of Hen Egg-White Lysozyme in 0, 10, 20, 30 and 100% by weight of glycerol in water to better understand the microscopic physics behind the bioprotection offered by glycerol to naturally occuring biological systems. The sovlent exposure of protein surface residues changes when glycerol is introduced. The dynamic behavior of the protein, as quantified by the Incoherent Intermediate Scattering Function, shows a non-monotonic dependence on glycerol content. The fluctuations of the protein residues with respect to each other were found to be similar in all water containing solvents; but differentmore » from the pure glycerol case. The increase in the number of protein glycerol hydrogen bonds in glycerol water binary mixtures explains the slowing down of protein dynamics as the glycerol content increases. We also explored the dynamic behavior of the hydration layer. We show that the short-length scale dynamics of this layer are insenstive to glycerol concentration. However, the long-length scale behavior shows a significant dependence on glycerol content. We also provide insights into the behavior of bound and mobile water molecules.« less

Navigating the Waters of Unconventional Crystalline Hydrates

PubMed Central

2015-01-01

Elucidating the crystal structures, transformations, and thermodynamics of the two zwitterionic hydrates (Hy2 and HyA) of 3-(4-dibenzo[b,f][1,4]oxepin-11-yl-piperazin-1-yl)-2,2-dimethylpropanoic acid (DB7) rationalizes the complex interplay of temperature, water activity, and pH on the solid form stability and transformation pathways to three neutral anhydrate polymorphs (Forms I, II°, and III). HyA contains 1.29 to 1.95 molecules of water per DB7 zwitterion (DB7z). Removal of the essential water stabilizing HyA causes it to collapse to an amorphous phase, frequently concomitantly nucleating the stable anhydrate Forms I and II°. Hy2 is a stoichiometric dihydrate and the only known precursor to Form III, a high energy disordered anhydrate, with the level of disorder depending on the drying conditions. X-ray crystallography, solid state NMR, and H/D exchange experiments on highly crystalline phase pure samples obtained by exquisite control over crystallization, filtration, and drying conditions, along with computational modeling, provided a molecular level understanding of this system. The slow rates of many transformations and sensitivity of equilibria to exact conditions, arising from its varying static and dynamic disorder and water mobility in different phases, meant that characterizing DB7 hydration in terms of simplified hydrate classifications was inappropriate for developing this pharmaceutical. PMID:26075319

Molecular simulations and density functional theory calculations of bromine in clathrate hydrate phases

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

Dureckova, Hana, E-mail: houci059@uottawa.ca; Woo, Tom K., E-mail: tom.woo@uottawa.ca; Alavi, Saman, E-mail: saman.alavi@nrc-cnrc.gc.ca

Bromine forms a tetragonal clathrate hydrate structure (TS-I) very rarely observed in clathrate hydrates of other guest substances. The detailed structure, energetics, and dynamics of Br{sub 2} and Cl{sub 2} in TS-I and cubic structure I (CS-I) clathrate hydrates are studied in this work using molecular dynamics and quantum chemical calculations. X-ray diffraction studies show that the halogen-water–oxygen distances in the cages of these structures are shorter than the sum of the van der Waals radii of halogen and oxygen atoms. This suggests that the stabilizing effects of halogen bonding or other non-covalent interactions (NCIs) may contribute to the formationmore » of the unique tetragonal bromine hydrate structure. We performed molecular dynamics simulations of Br{sub 2} and Cl{sub 2} clathrate hydrates using our previously developed five-site charge models for the dihalogen molecules [Dureckova et al. Can. J. Chem. 93, 864 (2015)] which reproduce the computed electrostatic potentials of the dihalogens and account for the electropositive σ-hole of the halogen bond donor (the dihalogen). Analysis of the radial distribution functions, enthalpies of encapsulation, velocity and orientation autocorrelation functions, and polar angle distributions are carried out for Br{sub 2} and Cl{sub 2} guests in various cages to contrast the properties of these guests in the TS-I and CS-I phases. Quantum chemical partial geometry optimizations of Br{sub 2} and Cl{sub 2} guests in the hydrate cages using the M06-2X functional give short halogen-water distances compatible with values observed in X-ray diffraction experiments. NCI plots of guest-cage structures are generated to qualitatively show the relative strength of the non-bonding interactions between dihalogens and water molecules. The differences between behaviors of Br{sub 2} and Cl{sub 2} guests in the hydrate cages may explain why bromine forms the unique TS-I phase.« less

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.

Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes

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

Yang, J.; Martí, J., E-mail: jordi.marti@upc.edu; Calero, C.

2014-03-14

Microscopic structure and dynamics of water and lipids in a fully hydrated dimyristoylphosphatidylcholine phospholipid lipid bilayer membrane in the liquid-crystalline phase have been analyzed with all-atom molecular dynamics simulations based on the recently parameterized CHARMM36 force field. The diffusive dynamics of the membrane lipids and of its hydration water, their reorientational motions as well as their corresponding spectral densities, related to the absorption of radiation, have been considered for the first time using the present force field. In addition, structural properties such as density and pressure profiles, a deuterium-order parameter, surface tension, and the extent of water penetration in themore » membrane have been analyzed. Molecular self-diffusion, reorientational motions, and spectral densities of atomic species reveal a variety of time scales playing a role in membrane dynamics. The mechanisms of lipid motion strongly depend on the time scale considered, from fast ballistic translation at the scale of picoseconds (effective diffusion coefficients of the order of 10{sup −5} cm{sup 2}/s) to diffusive flow of a few lipids forming nanodomains at the scale of hundreds of nanoseconds (diffusion coefficients of the order of 10{sup −8} cm{sup 2}/s). In the intermediate regime of sub-diffusion, collisions with nearest neighbors prevent the lipids to achieve full diffusion. Lipid reorientations along selected directions agree well with reported nuclear magnetic resonance data and indicate two different time scales, one about 1 ns and a second one in the range of 2–8 ns. We associated the two time scales of reorientational motions with angular distributions of selected vectors. Calculated spectral densities corresponding to lipid and water reveal an overall good qualitative agreement with Fourier transform infrared spectroscopy experiments. Our simulations indicate a blue-shift of the low frequency spectral bands of hydration water as a result of its interaction with lipids. We have thoroughly analyzed the physical meaning of all spectral features from lipid atomic sites and correlated them with experimental data. Our findings include a “wagging of the tails” frequency around 30 cm{sup −1}, which essentially corresponds to motions of the tail-group along the instantaneous plane formed by the two lipid tails, i.e., in-plane oscillations are clearly of bigger importance than those along the normal-to-the plane direction.« less

Mechanical features of various silkworm crystalline considering hydration effect via molecular dynamics simulations.

PubMed

Kim, Yoonjung; Lee, Myeongsang; Choi, Hyunsung; Baek, Inchul; Kim, Jae In; Na, Sungsoo

2018-04-01

Silk materials are receiving significant attention as base materials for various functional nanomaterials and nanodevices, due to its exceptionally high mechanical properties, biocompatibility, and degradable characteristics. Although crystalline silk regions are composed of various repetitive motifs with differing amino acid sequences, how the effect of humidity works differently on each of the motifs and their structural characteristics remains unclear. We report molecular dynamics (MD) simulations on various silkworm fibroins composed of major motifs (i.e. (GAGAGS) n , (GAGAGA) n , and (GAGAGY) n ) at varying degrees of hydration, and reveal how each major motifs of silk fibroins change at each degrees of hydration using MD simulations and their structural properties in mechanical perspective via steered molecular dynamics simulations. Our results explain what effects humidity can have on nanoscale materials and devices consisting of crystalline silk materials.

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.

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.

Theoretical modeling insights into elastic wave attenuation mechanisms in marine sediments with pore-filling methane hydrate

NASA Astrophysics Data System (ADS)

Marín-Moreno, H.; Sahoo, S. K.; Best, A. I.

2017-03-01

The majority of presently exploitable marine methane hydrate reservoirs are likely to host hydrate in disseminated form in coarse grain sediments. For hydrate concentrations below 25-40%, disseminated or pore-filling hydrate does not increase elastic frame moduli, thus making impotent traditional seismic velocity-based methods. Here, we present a theoretical model to calculate frequency-dependent P and S wave velocity and attenuation of an effective porous medium composed of solid mineral grains, methane hydrate, methane gas, and water. The model considers elastic wave energy losses caused by local viscous flow both (i) between fluid inclusions in hydrate and pores and (ii) between different aspect ratio pores (created when hydrate grows); the inertial motion of the frame with respect to the pore fluid (Biot's type fluid flow); and gas bubble damping. The sole presence of pore-filling hydrate in the sediment reduces the available porosity and intrinsic permeability of the sediment affecting Biot's type attenuation at high frequencies. Our model shows that attenuation maxima due to fluid inclusions in hydrate are possible over the entire frequency range of interest to exploration seismology (1-106 Hz), depending on the aspect ratio of the inclusions, whereas maxima due to different aspect ratio pores occur only at sonic to ultrasound frequencies (104-106 Hz). This frequency response imposes further constraints on possible hydrate saturations able to reproduce broadband elastic measurements of velocity and attenuation. Our results provide a physical basis for detecting the presence and amount of pore-filling hydrate in seafloor sediments using conventional seismic surveys.

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.

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.

Dynamics of bound water molecules in fullerenol at different hydration levels

NASA Astrophysics Data System (ADS)

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

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

Nonequilibrium Thermodynamics of Hydrate Growth on a Gas-Liquid Interface

NASA Astrophysics Data System (ADS)

Fu, Xiaojing; Cueto-Felgueroso, Luis; Juanes, Ruben

2018-04-01

We develop a continuum-scale phase-field model to study gas-liquid-hydrate systems far from thermodynamic equilibrium. We design a Gibbs free energy functional for methane-water mixtures that recovers the isobaric temperature-composition phase diagram under thermodynamic equilibrium conditions. The proposed free energy is incorporated into a phase-field model to study the dynamics of hydrate formation on a gas-liquid interface. We elucidate the role of initial aqueous concentration in determining the direction of hydrate growth at the interface, in agreement with experimental observations. Our model also reveals two stages of hydrate growth at an interface—controlled by a crossover in how methane is supplied from the gas and liquid phases—which could explain the persistence of gas conduits in hydrate-bearing sediments and other nonequilibrium phenomena commonly observed in natural methane hydrate systems.

Microscopic Origin of Strain Hardening in Methane Hydrate

PubMed Central

Jia, Jihui; Liang, Yunfeng; Tsuji, Takeshi; Murata, Sumihiko; Matsuoka, Toshifumi

2016-01-01

It has been reported for a long time that methane hydrate presents strain hardening, whereas the strength of normal ice weakens with increasing strain after an ultimate strength. However, the microscopic origin of these differences is not known. Here, we investigated the mechanical characteristics of methane hydrate and normal ice by compressive deformation test using molecular dynamics simulations. It is shown that methane hydrate exhibits strain hardening only if the hydrate is confined to a certain finite cross-sectional area that is normal to the compression direction. For normal ice, it does not present strain hardening under the same conditions. We show that hydrate guest methane molecules exhibit no long-distance diffusion when confined to a finite-size area. They appear to serve as non-deformable units that prevent hydrate structure failure, and thus are responsible for the strain-hardening phenomenon. PMID:27009239

Nonequilibrium Thermodynamics of Hydrate Growth on a Gas-Liquid Interface.

PubMed

Fu, Xiaojing; Cueto-Felgueroso, Luis; Juanes, Ruben

2018-04-06

We develop a continuum-scale phase-field model to study gas-liquid-hydrate systems far from thermodynamic equilibrium. We design a Gibbs free energy functional for methane-water mixtures that recovers the isobaric temperature-composition phase diagram under thermodynamic equilibrium conditions. The proposed free energy is incorporated into a phase-field model to study the dynamics of hydrate formation on a gas-liquid interface. We elucidate the role of initial aqueous concentration in determining the direction of hydrate growth at the interface, in agreement with experimental observations. Our model also reveals two stages of hydrate growth at an interface-controlled by a crossover in how methane is supplied from the gas and liquid phases-which could explain the persistence of gas conduits in hydrate-bearing sediments and other nonequilibrium phenomena commonly observed in natural methane hydrate systems.

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.

Thermodynamic properties of hydrate phases immersed in ice phase

NASA Astrophysics Data System (ADS)

Belosludov, V. R.; Subbotin, O. S.; Krupskii, D. S.; Ikeshoji, T.; Belosludov, R. V.; Kawazoe, Y.; Kudoh, J.

2006-01-01

Thermodynamic properties and the pressure of hydrate phases immersed in the ice phase with the aim to understand the nature of self-preservation effect of methane hydrate in the framework of macroscopic and microscopic molecular models was studied. It was show that increasing of pressure is happen inside methane hydrate phases immersed in the ice phase under increasing temperature and if the ice structure does not destroy, the methane hydrate will have larger pressure than ice phase. This is because of the thermal expansion of methane hydrate in a few times larger than ice one. The thermal expansion of the hydrate is constrained by the thermal expansion of ice because it can remain in a region of stability within the methane hydrate phase diagram. The utter lack of preservation behavior in CS-II methane- ethane hydrate can be explain that the thermal expansion of ethane-methane hydrate coincide with than ice one it do not pent up by thermal expansion of ice. The pressure and density during the crossing of interface between ice and hydrate was found and dynamical and thermodynamic stability of this system are studied in accordance with relation between ice phase and hydrate phase.

Mapping hydration dynamics and coupled water-protein fluctuations around a protein surface

NASA Astrophysics Data System (ADS)

Zhang, Luyuan; Wang, Lijuan; Kao, Ya-Ting; Qiu, Weihong; Yang, Yi; Okobiah, Oghaghare; Zhong, Dongping

2009-03-01

Elucidation of the molecular mechanism of water-protein interactions is critical to understanding many fundamental aspects of protein science, such as protein folding and misfolding and enzyme catalysis. We recently carried out a global mapping of protein-surface hydration dynamics around a globular α-helical protein apomyoglobin. The intrinsic optical probe tryptophan was employed to scan the protein surface one at a time by site-specific mutagenesis. With femtosecond resolution, we mapped out the dynamics of water-protein interactions with more than 20 mutants and for two states, native and molten globular. A robust bimodal distribution of time scales was observed, representing two types of water motions: local relaxation and protein-coupled fluctuations. The time scales show a strong correlation with the local protein structural rigidity and chemical identity. We also resolved two distinct contributions to the overall Stokes-shifts from the two time scales. These results are significant to understanding the role of hydration water on protein structural stability, dynamics and function.

Steric Effects of Solvent Molecules on SN2 Substitution Dynamics.

PubMed

Liu, Xu; Xie, Jing; Zhang, Jiaxu; Yang, Li; Hase, William L

2017-04-20

Influences of solvent molecules on S N 2 reaction dynamics of microsolvated F - (H 2 O) n with CH 3 I, for n = 0-3, are uncovered by direct chemical dynamics simulations. The direct substitution mechanism, which is important without microsolvation, is quenched dramatically upon increasing hydration. The water molecules tend to force reactive encounters to proceed through the prereaction collision complex leading to indirect reaction. In contrast to F - (H 2 O), reaction with higher hydrated ions shows a strong propensity for ion desolvation in the entrance channel, diminishing steric hindrance for nucleophilic attack. Thus, nucleophilic substitution avoids the potential energy barrier with all of the solvent molecules intact and instead occurs through the less solvated barrier, which is energetically unexpected because the former barrier has a lower energy. The work presented here reveals a trade-off between reaction energetics and steric effects, with the latter found to be crucial in understanding how hydration influences microsolvated S N 2 dynamics.

Vibrational Dynamics and Guest-Host Coupling in Clathrate Hydrates

NASA Astrophysics Data System (ADS)

Koza, Michael M.; Schober, Helmut

Clathrate hydrates may turn out either a blessing or a curse for mankind. On one hand, they constitute a huge reservoir of fossil fuel. On the other hand, their decomposition may liberate large amounts of green house gas and have disastrous consequences on sea floor stability. It is thus of paramount importance to understand the formation and stability of these guest-host compounds. Neutron diffraction has successfully occupied a prominent place on the stage of these scientific investigations. Complete understanding, however, is not achieved without an explanation for the thermal properties of clathrates. In particular, the thermal conductivity has a large influence on clathrate formation and conservation. Neutron spectroscopy allows probing the microscopic dynamics of clathrate hydrates. We will show how comparative studies of vibrations in clathrate hydrates give insight into the coupling of the guest to the host lattice. This coupling together with the anharmonicity of the vibrational modes is shown to lay the foundations for the peculiar thermodynamic properties of clathrate hydrates. The results obtained reach far beyond the specific clathrate system. Similar mechanisms are expected to be at work in any guest-host complex.

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.

Mathematical model of the methane replacement by carbon dioxide in the gas hydrate reservoir taking into account the diffusion kinetics

NASA Astrophysics Data System (ADS)

Musakaev, N. G.; Khasanov, M. K.; Rafikova, G. R.

2018-03-01

The problem of the replacement of methane in its hydrate by carbon dioxide in a porous medium is considered. The gas-exchange kinetics scheme is proposed in which the intensity of the process is limited by the diffusion of CO2 through the hydrate layer formed between the gas mixture flow and the CH4 hydrate. Dynamics of the main parameters of the process is numerically investigated. The main characteristic stages of the process are determined.

On the hydration and conformation of cocaine in solution

NASA Astrophysics Data System (ADS)

Gillams, Richard J.; Lorenz, Christian D.; McLain, Sylvia E.

2017-05-01

In order to develop theories relating to the mechanism through which cocaine can diffuse across the blood-brain barrier, it is important to understand the interplay between the hydration of the molecule and the adopted conformation. Here key differences in the hydration of cocaine hydrochloride (CHC) and freebase cocaine (CFB) are highlighted on the atomic scale in solution, through the use of molecular dynamics simulations. By adopting different conformations, CHC and CFB experience differing hydration environments. The interplay between these two factors may account for the vast difference in solubility of these two molecules.

Ferric citrate hydrate for the treatment of hyperphosphatemia in nondialysis-dependent CKD.

PubMed

Yokoyama, Keitaro; Hirakata, Hideki; Akiba, Takashi; Fukagawa, Masafumi; Nakayama, Masaaki; Sawada, Kenichi; Kumagai, Yuji; Block, Geoffrey A

2014-03-01

Ferric citrate hydrate is a novel iron-based phosphate binder being developed for hyperphosphatemia in patients with CKD. A phase 3, multicenter, randomized, double blind, placebo-controlled study investigated the efficacy and safety of ferric citrate hydrate in nondialysis-dependent patients with CKD. Starting in April of 2011, 90 CKD patients (eGFR=9.21±5.72 ml/min per 1.73 m(2)) with a serum phosphate≥5.0 mg/dl were randomized 2:1 to ferric citrate hydrate or placebo for 12 weeks. The primary end point was change in serum phosphate from baseline to the end of treatment. Secondary end points included the percentage of patients achieving target serum phosphate levels (2.5-4.5 mg/dl) and change in fibroblast growth factor-23 at the end of treatment. The mean change in serum phosphate was -1.29 mg/dl (95% confidence interval, -1.63 to -0.96 mg/dl) in the ferric citrate hydrate group and 0.06 mg/dl (95% confidence interval, -0.20 to 0.31 mg/dl) in the placebo group (P<0.001 for difference between groups). The percentage of patients achieving target serum phosphate levels was 64.9% in the ferric citrate hydrate group and 6.9% in the placebo group (P<0.001). Fibroblast growth factor-23 concentrations were significantly lower in patients treated with ferric citrate hydrate versus placebo (change from baseline [median], -142.0 versus 67.0 pg/ml; P<0.001). Ferric citrate hydrate significantly increased serum iron, ferritin, and transferrin saturation compared with placebo (P=0.001 or P<0.001). Five patients discontinued active treatment because of treatment-emergent adverse events with ferric citrate hydrate treatment versus one patient with placebo. Overall, adverse drug reactions were similar in patients receiving ferric citrate hydrate or placebo, with gastrointestinal disorders occurring in 30.0% of ferric citrate hydrate patients and 26.7% of patients receiving placebo. In patients with nondialysis-dependent CKD, 12-week treatment with ferric citrate hydrate resulted in significant reductions in serum phosphate and fibroblast growth factor-23 while simultaneously increasing serum iron parameters.

Structure of hydrophobic hydration of benzene and hexafluorobenzene from first principles

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

Allesch, M; Schwegler, E; Galli, G

We report on the aqueous hydration of benzene and hexafluorobenzene, as obtained by carrying out extensive (>100 ps) first principles molecular dynamics simulations. Our results show that benzene and hexafluorobenzene do not behave as ordinary hydrophobic solutes, but rather present two distinct regions, one equatorial and the other axial, that exhibit different solvation properties. While in both cases the equatorial regions behave as typical hydrophobic solutes, the solvation properties of the axial regions depend strongly on the nature of the {pi}-water interaction. In particular, {pi}-hydrogen and {pi}-lone pair interactions are found to dominate in benzene and hexafluorobenzene, respectively, which leadsmore » to substantially different orientations of water near the two solutes. We present atomic and electronic structure results (in terms of Maximally Localized Wannier Functions) providing a microscopic description of benzene- and hexafluorobenzene-water interfaces, as well as a comparative study of the two solutes. Our results point at the importance of an accurate description of interfacial water in order to characterize hydration properties of apolar molecules, as these are strongly influenced by subtle charge rearrangements and dipole moment redistributions in interfacial regions.« less

Cavity hydration dynamics in cytochrome c oxidase and functional implications

PubMed Central

Son, Chang Yun; Cui, Qiang

2017-01-01

Cytochrome c oxidase (CcO) is a transmembrane protein that uses the free energy of O2 reduction to generate the proton concentration gradient across the membrane. The regulation of competitive proton transfer pathways has been established to be essential to the vectorial transport efficiency of CcO, yet the underlying mechanism at the molecular level remains lacking. Recent studies have highlighted the potential importance of hydration-level change in an internal cavity that connects the proton entrance channel, the site of O2 reduction, and the putative proton exit route. In this work, we use atomistic molecular dynamics simulations to investigate the energetics and timescales associated with the volume fluctuation and hydration-level change in this central cavity. Extensive unrestrained molecular dynamics simulations (accumulatively ∼4 μs) and free energy computations for different chemical states of CcO support a model in which the volume and hydration level of the cavity are regulated by the protonation state of a propionate group of heme a3 and, to a lesser degree, the redox state of heme a and protonation state of Glu286. Markov-state model analysis of ∼2-μs trajectories suggests that hydration-level change occurs on the timescale of 100–200 ns before the proton-loading site is protonated. The computed energetic and kinetic features for the cavity wetting transition suggest that reversible hydration-level change of the cavity can indeed be a key factor that regulates the branching of proton transfer events and therefore contributes to the vectorial efficiency of proton transport. PMID:28973914

Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: H2 NMR studies on perdeuterated C-phycocyanin

NASA Astrophysics Data System (ADS)

Kämpf, Kerstin; Kremmling, Beke; Vogel, Michael

2014-03-01

Using a combination of H2 nuclear magnetic resonance (NMR) methods, we study internal rotational dynamics of the perdeuterated protein C-phycocyanin (CPC) in dry and hydrated states over broad temperature and dynamic ranges with high angular resolution. Separating H2 NMR signals from methyl deuterons, we show that basically all backbone deuterons exhibit highly restricted motion occurring on time scales faster than microseconds. The amplitude of this motion increases when a hydration shell exists, while it decreases upon cooling and vanishes near 175 K. We conclude that the vanishing of the highly restricted motion marks a dynamical transition, which is independent of the time window and of a fundamental importance. This conclusion is supported by results from experimental and computational studies of the proteins myoglobin and elastin. In particular, we argue based on findings in molecular dynamics simulations that the behavior of the highly restricted motion of proteins at the dynamical transition resembles that of a characteristic secondary relaxation of liquids at the glass transition, namely the nearly constant loss. Furthermore, H2 NMR studies on perdeuterated CPC reveal that, in addition to highly restricted motion, small fractions of backbone segments exhibit weakly restricted dynamics when temperature and hydration are sufficiently high.

Dynamic impact indentation of hydrated biological tissues and tissue surrogate gels

NASA Astrophysics Data System (ADS)

Ilke Kalcioglu, Z.; Qu, Meng; Strawhecker, Kenneth E.; Shazly, Tarek; Edelman, Elazer; VanLandingham, Mark R.; Smith, James F.; Van Vliet, Krystyn J.

2011-03-01

For both materials engineering research and applied biomedicine, a growing need exists to quantify mechanical behaviour of tissues under defined hydration and loading conditions. In particular, characterisation under dynamic contact-loading conditions can enable quantitative predictions of deformation due to high rate 'impact' events typical of industrial accidents and ballistic insults. The impact indentation responses were examined of both hydrated tissues and candidate tissue surrogate materials. The goals of this work were to determine the mechanical response of fully hydrated soft tissues under defined dynamic loading conditions, and to identify design principles by which synthetic, air-stable polymers could mimic those responses. Soft tissues from two organs (liver and heart), a commercially available tissue surrogate gel (Perma-Gel™) and three styrenic block copolymer gels were investigated. Impact indentation enabled quantification of resistance to penetration and energy dissipative constants under the rates and energy densities of interest for tissue surrogate applications. These analyses indicated that the energy dissipation capacity under dynamic impact increased with increasing diblock concentration in the styrenic gels. Under the impact rates employed (2 mm/s to 20 mm/s, corresponding to approximate strain energy densities from 0.4 kJ/m3 to 20 kJ/m3), the energy dissipation capacities of fully hydrated soft tissues were ultimately well matched by a 50/50 triblock/diblock composition that is stable in ambient environments. More generally, the methodologies detailed here facilitate further optimisation of impact energy dissipation capacity of polymer-based tissue surrogate materials, either in air or in fluids.

Dynamics of Permafrost Associated Methane Hydrate in Response to Climate Change

NASA Astrophysics Data System (ADS)

You, K.; Flemings, P. B.

2014-12-01

The formation and melting of methane hydrate and ice are intertwined in permafrost regions. A shortage of methane supply leads to formation of hydrate only at depth, below the base of permafrost. We consider a system with the ground surface initially at 0 oC with neither ice nor hydrate present. We abruptly decrease the temperature from 0 to -10 oC to simulate the effect of marine regression/ global cooling. A low methane supply rate of 0.005 kg m-2 yr-1 from depth leads to distinct ice and hydrate layers: a 100 m continuous hydrate layer is present beneath 850 m at 80 k.y.. However, a high methane supply rate of 0.1 kg m-2 yr-1 leads to 50 m ice-bonded methane hydrate at the base of permafrost, and the hydrate layer distributes between the depth of 350 and 700 m at 80 k.y.. We apply our model to illuminate future melting of hydrate at Mallik, a known Arctic hydrate accumulation. We assume a 600 m thick ice saturated (average 90%) layer extending downward from the ground surface. We increase the surface temperature linearly from -6 to 0 oC for 300 yr and then keep the surface temperature at 0 oC to reflect future climate warming caused by doubling of CO2. Hydrate melting is initiated at the base of the hydrate layer after 15 k.y.. Methane gas starts to vent to the atmosphere at 38 k.y. with an average flux of ~ 0.35 g m-2 yr-1. If the 600 m thick average ice saturation is decreased to half (45%) (or to zero), methane gas starts to vent to the atmosphere at 29 k.y. (or at 20 k.y.) with the same average flux. These results are found by a newly-developed fully-coupled multiphase multicomponent fluid flow and heat transport model. Our thermodynamic equilibrium-based model emphasizes the role of salinity in both ice and hydrate dynamics.

Dynamics of meso and thermo citrate synthases with implicit solvation

NASA Astrophysics Data System (ADS)

Cordeiro, J. M. M.

The dynamics of hydration of meso and thermo citrate synthases has been investigated using the EEF1 methodology implemented with the CHARMM program. The native enzymes are composed of two identical subunits, each divided into a small and large domain. The dynamics behavior of both enzymes at 30°C and 60°C has been compared. The results of simulations show that during the hydration process, each subunit follows a different pathway of hydration, in spite of the identical sequence. The hydrated structures were compared with the crystalline structure, and the root mean square deviation (RMSD) of each residue along the trajectory was calculated. The regions with larger and smaller mobility were identified. In particular, helices belonging to the small domain are more mobile than those of the large domain. In contrast, the residues that constitute the active site show a much lower displacement compared with the crystalline structure. Hydration free energy calculations point out that Thermoplasma acidophilum citrate synthase (TCS) is more stable than chicken citrate synthase (CCS), at high temperatures. Such result has been ascribed to the higher number of superficial charges in the thermophilic homologue, which stabilizes the enzyme, while the mesophilic homologue denatures. These results are in accord with the experimental found that TCS keeps activity at temperatures farther apart from the catalysis regular temperature than the CCS.

Rethinking the global carbon cycle with a large, dynamic and microbially mediated gas hydrate capacitor

NASA Astrophysics Data System (ADS)

Dickens, Gerald R.

2003-08-01

Prominent negative δ13C excursions characterize several past intervals of abrupt (<100 kyr) environmental change. These anomalies, best exemplified by the >2.5‰ drop across the Paleocene/Eocene thermal maximum (PETM) ca. 55.5 Ma, command our attention because they lack explanation with conventional models for global carbon cycling. Increasingly, Earth scientists have argued that they signify massive release of CH4 from marine gas hydrates, although typically without considering the underlying process or the ensuing ramifications of such an interpretation. At the most basic level, a large, dynamic 'gas hydrate capacitor' stores and releases 13C-depleted carbon at rates linked to external conditions such as deep ocean temperature. The capacitor contains three internal reservoirs: dissolved gas, gas hydrate, and free gas. Carbon enters and leaves these reservoirs through microbial decomposition of organic matter, anaerobic oxidation of CH4 in shallow sediment, and seafloor gas venting; carbon cycles between these reservoirs through several processes, including fluid flow, precipitation and dissolution of gas hydrate, and burial. Numerical simulations show that simple gas hydrate capacitors driven by inferred changes in bottom water warming during the PETM can generate a global δ13C excursion that mimics observations. The same modeling extended over longer time demonstrates that variable CH4 fluxes to and from gas hydrates can partly explain other δ13C excursions, rapid and slow, large and small, negative and positive. Although such modeling is rudimentary (because processes and variables in modern and ancient gas hydrate systems remain poorly constrained), acceptance of a vast, externally regulated gas hydrate capacitor forces us to rethink δ13C records and the operation of the global carbon cycle throughout time.

Nucleation Rate Analysis of Methane Hydrate from Molecular Dynamics Simulations

DOE PAGES

Yuhara, Daisuke; Barnes, Brian C.; Suh, Donguk; ...

2015-01-06

Clathrate hydrates are solid crystalline structures most commonly formed from solutions that have nucleated to form a mixed solid composed of water and gas. Understanding the mechanism of clathrate hydrate nucleation is essential to grasp the fundamental chemistry of these complex structures and their applications. Molecular dynamics (MD) simulation is an ideal method to study nucleation at the molecular level because the size of the critical nucleus and formation rate occur on the nano scale. Moreover, various analysis methods for nucleation have been developed through MD to analyze nucleation. In particular, the mean first-passage time (MFPT) and survival probability (SP)more » methods have proven to be effective in procuring the nucleation rate and critical nucleus size for monatomic systems. This study assesses the MFPT and SP methods, previously used for monatomic systems, when applied to analyzing clathrate hydrate nucleation. Because clathrate hydrate nucleation is relatively difficult to observe in MD simulations (due to its high free energy barrier), these methods have yet to be applied to clathrate hydrate systems. In this study, we have analyzed the nucleation rate and critical nucleus size of methane hydrate using MFPT and SP methods from data generated by MD simulations at 255 K and 50 MPa. MFPT was modified for clathrate hydrate from the original version by adding the maximum likelihood estimate and growth effect term. The nucleation rates were calculated by MFPT and SP methods and are within 5%; the critical nucleus size estimated by the MFPT method was 50% higher, than values obtained through other more rigorous but computationally expensive estimates. These methods can also be extended to the analysis of other clathrate hydrates.« less

Nucleation Rate Analysis of Methane Hydrate from Molecular Dynamics Simulations

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

Yuhara, Daisuke; Barnes, Brian C.; Suh, Donguk

Clathrate hydrates are solid crystalline structures most commonly formed from solutions that have nucleated to form a mixed solid composed of water and gas. Understanding the mechanism of clathrate hydrate nucleation is essential to grasp the fundamental chemistry of these complex structures and their applications. Molecular dynamics (MD) simulation is an ideal method to study nucleation at the molecular level because the size of the critical nucleus and formation rate occur on the nano scale. Moreover, various analysis methods for nucleation have been developed through MD to analyze nucleation. In particular, the mean first-passage time (MFPT) and survival probability (SP)more » methods have proven to be effective in procuring the nucleation rate and critical nucleus size for monatomic systems. This study assesses the MFPT and SP methods, previously used for monatomic systems, when applied to analyzing clathrate hydrate nucleation. Because clathrate hydrate nucleation is relatively difficult to observe in MD simulations (due to its high free energy barrier), these methods have yet to be applied to clathrate hydrate systems. In this study, we have analyzed the nucleation rate and critical nucleus size of methane hydrate using MFPT and SP methods from data generated by MD simulations at 255 K and 50 MPa. MFPT was modified for clathrate hydrate from the original version by adding the maximum likelihood estimate and growth effect term. The nucleation rates were calculated by MFPT and SP methods and are within 5%; the critical nucleus size estimated by the MFPT method was 50% higher, than values obtained through other more rigorous but computationally expensive estimates. These methods can also be extended to the analysis of other clathrate hydrates.« less

Primary radical yields in pulse irradiated alkaline aqueous solution

NASA Technical Reports Server (NTRS)

Fielden, E. M.; Hart, E. J.

1969-01-01

Primary radical yields of hydrated electrons, H atoms, and OH radicals are determined by measuring hydrated electron formation following a 4 microsecond pulse of X rays. The pH dependence of free radical yields beyond pH 12 is determined by observation of the hydrated electrons.

Ab initio investigation of the first hydration shell of protonated glycine

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

Wei, Zhichao; Chen, Dong, E-mail: dongchen@henu.edu.cn, E-mail: boliu@henu.edu.cn; Zhao, Huiling

2014-02-28

The first hydration shell of the protonated glycine is built up using Monte Carlo multiple minimum conformational search analysis with the MMFFs force field. The potential energy surfaces of the protonated glycine and its hydration complexes with up to eight water molecules have been scanned and the energy-minimized structures are predicted using the ab initio calculations. First, three favorable structures of protonated glycine were determined, and the micro-hydration processes showed that water can significantly stabilize the unstable conformers, and then their first hydration shells were established. Finally, we found that seven water molecules are required to fully hydrate the firstmore » hydration shell for the most stable conformer of protonated glycine. In order to analyse the hydration process, the dominant hydration sites located around the ammonium and carboxyl groups are studied carefully and systemically. The results indicate that, water molecules hydrate the protonated glycine in an alternative dynamic hydration process which is driven by the competition between different hydration sites. The first three water molecules are strongly attached by the ammonium group, while only the fourth water molecule is attached by the carboxyl group in the ultimate first hydration shell of the protonated glycine. In addition, the first hydration shell model has predicted most identical structures and a reasonable accord in hydration energy and vibrational frequencies of the most stable conformer with the conductor-like polarizable continuum model.« less

Multiscale Molecular Dynamics Simulations of Model Hydrophobically Modified Ethylene Oxide Urethane Micelles.

PubMed

Yuan, Fang; Larson, Ronald G

2015-09-24

The flower-like micelles of various aggregation numbers of a model hydrophobically modified ethylene oxide urethane (HEUR) molecule, C16E45C16, and their corresponding starlike micelles, containing the surfactants C16E22 and C16E23, were studied by atomistic and coarse-grained molecular dynamic (MD) simulations. We used free energies from umbrella sampling to calculate the size distribution of micelle sizes and the average time for escape of a hydrophobic group from the micelle. Using the coarse-grained MARTINI force field, the most probable size of the model HEUR molecule was thereby determined to be about 80 hydrophobes per micelle and the average hydrophobe escape time to be about 0.1 s, both of which are consistent with previous experimental studies. Atomistic simulations reveal that hydrogen bond formation and the mean lifetime of hydration waters of the poly(ethylene oxide) (or PEO) groups are location-dependent in the HEUR micelle, with PEO groups immediately adjacent to the C16 groups forming the fewest hydrogen bonds with water and having hydration waters with longer lifetimes than those of the PEO groups located further away from the C16 groups.

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.

Hydrated Ordinary Portland Cement as a Carbonic Cement: The Mechanisms, Dynamics, and Implications of Self-Sealing and CO 2 Resistance in Wellbore Cements

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

Guthrie, George Drake Jr.; Pawar, Rajesh J.; Carey, James William

2017-07-28

This report analyzes the dynamics and mechanisms of the interactions of carbonated brine with hydrated Portland cement. The analysis is based on a recent set of comprehensive reactive-transport simulations, and it relies heavily on the synthesis of the body of work on wellbore integrity that we have conducted for the Carbon Storage Program over the past decade.

Evolution of mechanical response of sodium montmorillonite interlayer with increasing hydration by molecular dynamics.

PubMed

Schmidt, Steven R; Katti, Dinesh R; Ghosh, Pijush; Katti, Kalpana S

2005-08-16

The mechanical response of the interlayer of hydrated montmorillonite was evaluated using steered molecular dynamics. An atomic model of the sodium montmorillonite was previously constructed. In the current study, the interlayer of the model was hydrated with multiple layers of water. Using steered molecular dynamics, external forces were applied to individual atoms of the clay surface, and the response of the model was studied. The displacement versus applied stress and stress versus strain relationships of various parts of the interlayer were studied. The paper describes the construction of the model, the simulation procedure, and results of the simulations. Some results of the previous work are further interpreted in the light of the current research. The simulations provide quantitative stress deformation relationships as well as an insight into the molecular interactions taking place between the clay surface and interlayer water and cations.

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.

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

Impact of Ionic Liquids on the Structure and Dynamics of Collagen.

PubMed

Tarannum, Aafiya; Adams, Alina; Blümich, Bernhard; Fathima, Nishter Nishad

2018-01-25

The changes in the structure and dynamics of collagen treated with two different classes of ionic liquids, bis-choline sulfate (CS) and 1-butyl-3-methyl imidazolium dimethyl phosphate (IDP), have been studied at the molecular and fibrillar levels. At the molecular level, circular dichroic studies revealed an increase in molar ellipticity values for CS when compared with native collagen, indicating cross-linking, albeit pronounced conformational changes for IDP were witnessed indicating denaturation. The impedance was analyzed to correlate the conformational changes with the hydration dynamics of protein. Changes in the dielectric properties of collagen observed upon treatment with CS and IDP reported molecular reorientation in the surrounding water milieu, suggesting compactness or destabilization of the collagen. This was further confirmed by proton transverse NMR relaxation time measurements, which demonstrated that the water mobility changes in the presence of the ILs. At the fibrillar level, differential scanning calorimetry thermograms for rat tail tendon collagen fibers treated with CS show a 5 °C increase in denaturation temperature, suggesting imparted stability. On the contrary, a significant temperature decrease was noticed for IDP, indicating the destabilization of collagen fibers. The obtained results clearly indicate that the changes in the secondary structure of protein are due to the changes in the hydration dynamics of collagen upon interaction with ILs. Thus, this study on the interaction of collagen with ionic liquids unfolds the propensity of ILs to stabilize or destabilize collagen depending on the changes invoked at the molecular level in terms of structure and dynamics of protein, which also got manifested at the fibrillar level.

Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics.

PubMed

Abriata, Luciano A; Spiga, Enrico; Peraro, Matteo Dal

2016-08-23

Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known effects on coarse protein traits like stability, diffusion, and shape, but likely also perturb other traits through finer effects pertinent at the residue and atomic levels. Here, NMR and molecular dynamics investigations on ubiquitin disclose variable interactions with concentrated solutes that lead to localized perturbations of the protein's surface, hydration, electrostatics, and dynamics, all dependent on solute size and chemical properties. Most strikingly, small polar uncharged molecules are sticky on the protein surface, whereas charged small molecules are not, but the latter still perturb the internal protein electrostatics as they diffuse nearby. Meanwhile, interactions with macromolecular crowders are favored mainly through hydrophobic, but not through polar, surface patches. All the tested small solutes strongly slow down water exchange at the protein surface, whereas macromolecular crowders do not exert such strong perturbation. Finally, molecular dynamics simulations predict that unspecific interactions slow down microsecond- to millisecond-timescale protein dynamics despite having only mild effects on pico- to nanosecond fluctuations as corroborated by NMR. We discuss our results in the light of recent advances in understanding proteins inside living cells, focusing on the physical chemistry of quinary structure and cellular organization, and we reinforce the idea that proteins should be studied in native-like media to achieve a faithful description of their function. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Dynamics of hydrocarbon vents: Focus on primary porosity

NASA Astrophysics Data System (ADS)

Johansen, C.; Shedd, W.; Abichou, T.; Pineda-Garcia, O.; Silva, M.; MacDonald, I. R.

2012-12-01

This study investigated the dynamics of hydrocarbon release by monitoring activity of a single vent at a 1215m deep site in the Gulf of Mexico (GC600). An autonomous camera, deployed by the submersible ALVIN, was programmed to capture a close-up image every 4 seconds for approximately 3.5 hours. The images provided the ability to study the gas hydrate outcrop site (that measured 5.2x16.3cm3) in an undisturbed state. The outcrop included an array of 38 tube-like vents through which dark brown oil bubbles are released at a rate ranging from 8 bubbles per minute to 0 bubbles per minute. The average release of bubbles from all the separate vents was 59.5 bubbles per minute, equating the total volume released to 106.38cm per minute. The rate of bubble release decreased toward the end of the observation interval, which coincided approximately with the tidal minimum. Ice worms (Hesiocaeca methanicola, Desbruyères & Toulmond, 1998) were abundant at the vent site. The image sequence showed the ice-worms actively moving in and out of burrows in the mound. It has been speculated that Hesiocaeca methanicola contribute to gas hydrate decomposition by creating burrows and depressions in the gas hydrate matrix (Fisher et al, 2000). Ice worm burrows could generate pathways for the passage of oil and gas through the gas hydrate mound. Gas hydrates commonly occur along active and/or passive continental margins (Kennicutt et al, 1988a). The release of oil and gas at this particular hydrocarbon seep site is along a passive continental margin, and controlled primarily by active salt tectonics as opposed to the movement of continental tectonic plates (Salvador, 1987). We propose a descriptive model governing the release of gas and oil from deep sub-bottom reservoirs at depths of 3000-5000m (MacDonald, 1998), through consolidated and unconsolidated sediments, and finally through gas hydrate deposits at the sea floor. The oil and gas escape from the source rock and/or reservoir through at least three degrees of porosity (i.e. traveling through faulted consolidated sediment, unconsolidated sediment, and finally the gas hydrate outcroppings as described here). The oil and gas travel from the sub-bottom reservoir along, what is thought, an interface between the salt and sediment, and then up a fault in the consolidated sediment. When it reaches the unconsolidated sediments, vertical pathways bifurcate due to lack of sediment strength to allow for the oil and gas to reach different clusters of hydrocarbon vents at the sea floor. Hydrocarbon vents are formed and sustained by a combination of pressure, temperature, and gas solubility (Peltzer & Brewer, 2000) creating persistent primary porosity conduits, from which the bubbles escape at different rates depending on the size of the tubes. Previous research has been carried out in order to determine the effect of temperature fluxes on hydrocarbon outcroppings (MacDonald et al, 2005), however, a focus on the dynamics at this level of primary porosity is lacking. By determining the rate and size of bubbles and pore size distribution of the hydrocarbon outcropping, we can explore the hydraulic properties. Therefore, examination of biological and physical effects, such as the role of ice-worms, and the effect of tides, allow for a better understanding of the dynamics and persistency of hydrocarbon vent outcroppings.

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.

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.

Thermodynamic Changes in the Coal Matrix - Gas - Moisture System Under Pressure Release and Phase Transformations of Gas Hydrates

NASA Astrophysics Data System (ADS)

Dyrdin, V. V.; Smirnov, V. G.; Kim, T. L.; Manakov, A. Yu.; Fofanov, A. A.; Kartopolova, I. S.

2017-06-01

The physical processes occurring in the coal - natural gas system under the gas pressure release were studied experimentally. The possibility of gas hydrates presence in the inner space of natural coal was shown, which decomposition leads to an increase in the amount of gas passing into the free state. The decomposition of gas hydrates can be caused either by the seam temperature increase or the pressure decrease to lower than the gas hydrates equilibrium curve. The contribution of methane released during gas hydrates decomposition should be taken into account in the design of safe mining technologies for coal seams prone to gas dynamic phenomena.

Elasticity and Stability of Clathrate Hydrate: Role of Guest Molecule Motions.

PubMed

Jia, Jihui; Liang, Yunfeng; Tsuji, Takeshi; Murata, Sumihiko; Matsuoka, Toshifumi

2017-05-02

Molecular dynamic simulations were performed to determine the elastic constants of carbon dioxide (CO 2 ) and methane (CH 4 ) hydrates at one hundred pressure-temperature data points, respectively. The conditions represent marine sediments and permafrost zones where gas hydrates occur. The shear modulus and Young's modulus of the CO 2 hydrate increase anomalously with increasing temperature, whereas those of the CH 4 hydrate decrease regularly with increase in temperature. We ascribe this anomaly to the kinetic behavior of the linear CO 2 molecule, especially those in the small cages. The cavity space of the cage limits free rotational motion of the CO 2 molecule at low temperature. With increase in temperature, the CO 2 molecule can rotate easily, and enhance the stability and rigidity of the CO 2 hydrate. Our work provides a key database for the elastic properties of gas hydrates, and molecular insights into stability changes of CO 2 hydrate from high temperature of ~5 °C to low decomposition temperature of ~-150 °C.

Nonlinear fluid dynamics of nanoscale hydration water layer

NASA Astrophysics Data System (ADS)

Jhe, Wonho; Kim, Bongsu; Kim, Qhwan; An, Sangmin

In nature, the hydration water layer (HWL) ubiquitously exists in ambient conditions or aqueous solutions, where water molecules are tightly bound to ions or hydrophilic surfaces. It plays an important role in various mechanisms such as biological processes, abiotic materials, colloidal interaction, and friction. The HWL, for example, can be easily formed between biomaterials since most biomaterials are covered by hydrophilic molecules such as lipid bilayers, and this HWL is expected to be significant to biological and physiological functions. Here (1) we present the general stress tensor of the hydration water layer. The hydration stress tensor provided the platform form for holistic understanding of the dynamic behaviors of the confined HWL including tapping and shear dynamics which are until now individually studied. And, (2) through fast shear velocity ( 1mm/s) experiments, the elastic turbulence caused by elastic property of the HWL is indirectly observed. Our results may contribute to a deeper study of systems where the HWL plays an important role such as biomolecules, colloidal particles, and the MEMS. This work was supported by the National Research Foundation of Korea(NRF) Grant funded by the Korea government(MSIP) (2016R1A3B1908660).

Challenges of biological sample preparation for SIMS imaging of elements and molecules at subcellular resolution

NASA Astrophysics Data System (ADS)

Chandra, Subhash

2008-12-01

Secondary ion mass spectrometry (SIMS) based imaging techniques capable of subcellular resolution characterization of elements and molecules are becoming valuable tools in many areas of biology and medicine. Due to high vacuum requirements of SIMS, the live cells cannot be analyzed directly in the instrument. The sample preparation, therefore, plays a critical role in preserving the native chemical composition for SIMS analysis. This work focuses on the evaluation of frozen-hydrated and frozen freeze-dried sample preparations for SIMS studies of cultured cells with a CAMECA IMS-3f dynamic SIMS ion microscope instrument capable of producing SIMS images with a spatial resolution of 500 nm. The sandwich freeze-fracture method was used for fracturing the cells. The complimentary fracture planes in the plasma membrane were characterized by field-emission secondary electron microscopy (FESEM) in the frozen-hydrated state. The cells fractured at the dorsal surface were used for SIMS analysis. The frozen-hydrated SIMS analysis of individual cells under dynamic primary ion beam (O 2+) revealed local secondary ion signal enhancements correlated with the water image signals of 19(H 3O) +. A preferential removal of water from the frozen cell matrix in the Z-axis was also observed. These complications render the frozen-hydrated sample type less desirable for subcellular dynamic SIMS studies. The freeze-drying of frozen-hydrated cells, either inside the instrument or externally in a freeze-drier, allowed SIMS imaging of subcellular chemical composition. Morphological evaluations of fractured freeze-dried cells with SEM and confocal laser scanning microscopy (CLSM) revealed well-preserved mitochondria, Golgi apparatus, and stress fibers. SIMS analysis of fractured freeze-dried cells revealed well-preserved chemical composition of even the most highly diffusible ions like K + and Na + in physiologically relevant concentrations. The high K-low Na signature in individual cells provided a rule-of-thumb criterion for the validation of sample preparation. The fractured freeze-dried cells allowed 3-D SIMS imaging and localization of 13C 15N labeled molecules and therapeutic drugs containing an elemental tag. Examples are shown to demonstrate that both diffusible elements and molecules are prone to artifact-induced relocation at subcellular scale if the sample preparation is compromised. The sample preparation is problem dependent and may vary widely between the diverse sample types of biological systems and the type of instrument used for SIMS analysis. The sample preparation, however, must be validated so that SIMS can be applied with confidence in biology and medicine.

Study on small-strain behaviours of methane hydrate sandy sediments using discrete element method

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

Yu Yanxin; Cheng Yipik; Xu Xiaomin

Methane hydrate bearing soil has attracted increasing interest as a potential energy resource where methane gas can be extracted from dissociating hydrate-bearing sediments. Seismic testing techniques have been applied extensively and in various ways, to detect the presence of hydrates, due to the fact that hydrates increase the stiffness of hydrate-bearing sediments. With the recognition of the limitations of laboratory and field tests, wave propagation modelling using Discrete Element Method (DEM) was conducted in this study in order to provide some particle-scale insights on the hydrate-bearing sandy sediment models with pore-filling and cementation hydrate distributions. The relationship between shear wavemore » velocity and hydrate saturation was established by both DEM simulations and analytical solutions. Obvious differences were observed in the dependence of wave velocity on hydrate saturation for these two cases. From the shear wave velocity measurement and particle-scale analysis, it was found that the small-strain mechanical properties of hydrate-bearing sandy sediments are governed by both the hydrate distribution patterns and hydrate saturation.« less

Prediction of glass transition temperature of freeze-dried formulations by molecular dynamics simulation.

PubMed

Yoshioka, Sumie; Aso, Yukio; Kojima, Shigeo

2003-06-01

To examine whether the glass transition temperature (Tg) of freeze-dried formulations containing polymer excipients can be accurately predicted by molecular dynamics simulation using software currently available on the market. Molecular dynamics simulations were carried out for isomaltodecaose, a fragment of dextran, and alpha-glucose, the repeated unit of dextran. in the presence or absence of water molecules. Estimated values of Tg were compared with experimental values obtained by differential scanning calorimetry (DSC). Isothermal-isobaric molecular dynamics simulations (NPTMD) and isothermal molecular dynamics simulations at a constant volume (NVTMD) were carried out using the software package DISCOVER (Material Studio) with the Polymer Consortium Force Field. Mean-squared displacement and radial distribution function were calculated. NVTMD using the values of density obtained by NPTMD provided the diffusivity of glucose-ring oxygen and water oxygen in amorphous alpha-glucose and isomaltodecaose, which exhibited a discontinuity in temperature dependence due to glass transition. Tg was estimated to be approximately 400K and 500K for pure amorphous a-glucose and isomaltodecaose, respectively, and in the presence of one water molecule per glucose unit, Tg was 340K and 360K, respectively. Estimated Tg values were higher than experimentally determined values because of the very fast cooling rates in the simulations. However, decreases in Tg on hydration and increases in Tg associated with larger fragment size could be demonstrated. The results indicate that molecular dynamics simulation is a useful method for investigating the effects of hydration and molecular weight on the Tg of lyophilized formulations containing polymer excipients. although the relationship between cooling rates and Tg must first be elucidated to predict Tg vales observed by DSC measurement. January 16.

A multivariable model for predicting the frictional behaviour and hydration of the human skin.

PubMed

Veijgen, N K; van der Heide, E; Masen, M A

2013-08-01

The frictional characteristics of skin-object interactions are important when handling objects, in the assessment of perception and comfort of products and materials and in the origins and prevention of skin injuries. In this study, based on statistical methods, a quantitative model is developed that describes the friction behaviour of human skin as a function of the subject characteristics, contact conditions, the properties of the counter material as well as environmental conditions. Although the frictional behaviour of human skin is a multivariable problem, in literature the variables that are associated with skin friction have been studied using univariable methods. In this work, multivariable models for the static and dynamic coefficients of friction as well as for the hydration of the skin are presented. A total of 634 skin-friction measurements were performed using a recently developed tribometer. Using a statistical analysis, previously defined potential influential variables were linked to the static and dynamic coefficient of friction and to the hydration of the skin, resulting in three predictive quantitative models that descibe the friction behaviour and the hydration of human skin respectively. Increased dynamic coefficients of friction were obtained from older subjects, on the index finger, with materials with a higher surface energy at higher room temperatures, whereas lower dynamic coefficients of friction were obtained at lower skin temperatures, on the temple with rougher contact materials. The static coefficient of friction increased with higher skin hydration, increasing age, on the index finger, with materials with a higher surface energy and at higher ambient temperatures. The hydration of the skin was associated with the skin temperature, anatomical location, presence of hair on the skin and the relative air humidity. Predictive models have been derived for the static and dynamic coefficient of friction using a multivariable approach. These two coefficients of friction show a strong correlation. Consequently the two multivariable models resemble, with the static coefficient of friction being on average 18% lower than the dynamic coefficient of friction. The multivariable models in this study can be used to describe the data set that was the basis for this study. Care should be taken when generalising these results. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

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.

Theoretical study of gas hydrate decomposition kinetics: model predictions.

PubMed

Windmeier, Christoph; Oellrich, Lothar R

2013-11-27

In order to provide an estimate of intrinsic gas hydrate dissolution and dissociation kinetics, the Consecutive Desorption and Melting Model (CDM) was developed in a previous publication (Windmeier, C.; Oellrich, L. R. J. Phys. Chem. A 2013, 117, 10151-10161). In this work, an extensive summary of required model data is given. Obtained model predictions are discussed with respect to their temperature dependence as well as their significance for technically relevant areas of gas hydrate decomposition. As a result, an expression for determination of the intrinsic gas hydrate decomposition kinetics for various hydrate formers is given together with an estimate for the maximum possible rates of gas hydrate decomposition.

Variable Lysozyme Transport Dynamics on Oxidatively Functionalized Polystyrene Films.

PubMed

Moringo, Nicholas A; Shen, Hao; Tauzin, Lawrence J; Wang, Wenxiao; Bishop, Logan D C; Landes, Christy F

2017-10-17

Tuning protein adsorption dynamics at polymeric interfaces is of great interest to many biomedical and material applications. Functionalization of polymer surfaces is a common method to introduce application-specific surface chemistries to a polymer interface. In this work, single-molecule fluorescence microscopy is utilized to determine the adsorption dynamics of lysozyme, a well-studied antibacterial protein, at the interface of polystyrene oxidized via UV exposure and oxygen plasma and functionalized by ligand grafting to produce varying degrees of surface hydrophilicity, surface roughness, and induced oxygen content. Single-molecule tracking indicates lysozyme loading capacities, and surface mobility at the polymer interface is hindered as a result of all functionalization techniques. Adsorption dynamics of lysozyme depend on the extent and the specificity of the oxygen functionalities introduced to the polystyrene surface. Hindered adsorption and mobility are dominated by hydrophobic effects attributed to water hydration layer formation at the functionalized polystyrene surfaces.

Development of media for dynamic latent heat storage for the low-temperature range. Part 1: Thermal analyses of selected salt hydrate systems

NASA Technical Reports Server (NTRS)

Kanwischer, H.; Tamme, R.

1985-01-01

Phase change temperatures and phase change enthalpies of seventeen salt hydrates, three double salts, and four eutectics were measured thermodynamically and the results reported herein. Good results were obtained, especially for congruently melting salt hydrates. Incongruently melting salt hydrates appear less suitable for heat storage applications. The influence of the second phase - water, acid and hydroxide - to the latent heat is described. From these results, basic values of the working temperatures and storage capabilities of various storage media compositions may be derived.

Does the "sleeping Dragon" Really Sleep?: the Case for Continuous Long-Term Monitoring at a Gulf of Mexico Cold Seep Site

NASA Astrophysics Data System (ADS)

Wilson, R. M.; Lapham, L.; Farr, N.; Lutken, C.; MacDonald, I. R.; Macelloni, L.; Riedel, M.; Sleeper, K.; Chanton, J.

2011-12-01

Continuous porewater monitoring indicates that the methane flux away from exposed hydrate mounds can vary considerably over time. Recently, we retrieved a Pore Fluid Array instrument pack from a hydrate outcrop adjacent to a NEPTUNE Canada observatory node. The sampler was designed to continuously collect and store sediment pore fluids over the course of 9 months. On analysis, we observed a 35mM variation in methane concentrations corresponding with an abrupt shift in current direction at the site. Video and resistivity data have led to previous speculation that hydrate growth and dissolution/dissociation may be seasonally variable. Cumulatively, these findings suggest that the persistence of hydrate outcrops may be extremely dynamic, driven by fluctuations in physical conditions on short time scales. Short-term monitoring in the Gulf of Mexico within Mississippi Canyon lease block 118 (MC118), a known hydrate-bearing site, indicates that physical conditions even at these depths (~540-890m) may be highly variable. Pressure can vary within hours, and recorded temperature changes of ~1.5°C have been associated with passing storms. Moreover, increased particle abundance was observed at the site in 2007 suggesting that organic matter flux to the sediments may vary on the scale of months to years. These inputs have the potential to alter the chemical environment surrounding the hydrate, thereby affecting dissolution rates. Continuous, long-term observations of physical conditions at MC118 could provide information about the potential for natural perturbations to impact hydrate dynamics on the scale of weeks or even days necessary for assessing the long-term persistence of hydrate outcrops. Sleeping Dragon is a massive hydrate outcrop at MC118 that has been monitored since 2006. Three years ago, researchers returning to the site found it visibly diminished relative to previous observations. This apparent shift toward net dissolution of the mound may have been precipitated by changes in physical and chemical conditions at the site. We propose that the dynamics of hydrate stability may be compared to an oscillating "see-saw" where fluctuations in physical conditions tip the balance alternately in favor of dissociation/dissolution or hydrate growth. The chemical environment at MC118 results from the interaction among physical parameters, fluid/particle flux, and biological processes occurring near the hydrate surface. Given that these parameters may be varying on the scale of days, weeks, months, and possibly even years, long-term continuous monitoring will play a key role in understanding the stability conditions at MC118 and the potential for gas release from this methane reservoir should the dragon be awakened.

Ferroelectric hydration shells around proteins: electrostatics of the protein-water interface.

PubMed

LeBard, David N; Matyushov, Dmitry V

2010-07-22

Numerical simulations of hydrated proteins show that protein hydration shells are polarized into a ferroelectric layer with large values of the average dipole moment magnitude and the dipole moment variance. The emergence of the new polarized mesophase dramatically alters the statistics of electrostatic fluctuations at the protein-water interface. The linear response relation between the average electrostatic potential and its variance breaks down, with the breadth of the electrostatic fluctuations far exceeding the expectations of the linear response theories. The dynamics of these non-Gaussian electrostatic fluctuations are dominated by a slow (approximately = 1 ns) component that freezes in at the temperature of the dynamical transition of proteins. The ferroelectric shell propagates 3-5 water diameters into the bulk.

Scale-dependent gas hydrate saturation estimates in sand reservoirs in the Ulleung Basin, East Sea of Korea

USGS Publications Warehouse

Lee, Myung Woong; Collett, Timothy S.

2013-01-01

Through the use of 2-D and 3-D seismic data, several gas hydrate prospects were identified in the Ulleung Basin, East Sea of Korea and thirteen drill sites were established and logging-while-drilling (LWD) data were acquired from each site in 2010. Sites UBGH2–6 and UBGH2–10 were selected to test a series of high amplitude seismic reflections, possibly from sand reservoirs. LWD logs from the UBGH2–6 well indicate that there are three significant sand reservoirs with varying thickness. Two upper sand reservoirs are water saturated and the lower thinly bedded sand reservoir contains gas hydrate with an average saturation of 13%, as estimated from the P-wave velocity. The well logs at the UBGH2–6 well clearly demonstrated the effect of scale-dependency on gas hydrate saturation estimates. Gas hydrate saturations estimated from the high resolution LWD acquired ring resistivity (vertical resolution of about 5–8 cm) reaches about 90% with an average saturation of 28%, whereas gas hydrate saturations estimated from the low resolution A40L resistivity (vertical resolution of about 120 cm) reaches about 25% with an average saturation of 11%. However, in the UBGH2–10 well, gas hydrate occupies a 5-m thick sand reservoir near 135 mbsf with a maximum saturation of about 60%. In the UBGH2–10 well, the average and a maximum saturation estimated from various well logging tools are comparable, because the bed thickness is larger than the vertical resolution of the various logging tools. High resolution wireline log data further document the role of scale-dependency on gas hydrate calculations.

Kinetic effects of sulfur oxidation on catalytic nitrile hydration: nitrile hydratase insights from bioinspired ruthenium(II) complexes.

PubMed

Kumar, Davinder; Nguyen, Tho N; Grapperhaus, Craig A

2014-12-01

Kinetic investigations inspired by the metalloenzyme nitrile hydratase were performed on a series of ruthenium(II) complexes to determine the effect of sulfur oxidation on catalytic nitrile hydration. The rate of benzonitrile hydration was quantified as a function of catalyst, nitrile, and water concentrations. Precatalysts L(n)RuPPh3 (n = 1-3; L(1) = 4,7-bis(2'-methyl-2'-mercapto-propyl)-1-thia-4,7-diazacyclononane; L(2) = 4-(2'-methyl-2'-sulfinatopropyl)-7-(2'-methyl-2'-mercapto-propyl)-1-thia-4,7-diazacyclononane; L(3) = 4-(2'-methyl-2'-sulfinatopropyl)-7-(2'-methyl-2'-sulfenato-propyl)-1-thia-4,7-diazacyclononane) were activated by substitution of triphenylphosphine with substrate in hot dimethylformamide solution. Rate measurements are consistent with a dynamic equilibrium between inactive aqua (L(n)Ru-OH2) and active nitrile (L(n)Ru-NCR) derivatives with K = 21 ± 1, 9 ± 0.9, and 23 ± 3 for L(1) to L(3), respectively. Subsequent hydration of the L(n)Ru-NCR intermediate yields the amide product with measured hydration rate constants (k's) of 0.37 ± 0.01, 0.82 ± 0.07, and 1.59 ± 0.12 M(-1) h(-1) for L(1) to L(3), respectively. Temperature dependent studies reveal that sulfur oxidation lowers the enthalpic barrier by 27 kJ/mol, but increases the entropic barrier by 65 J/(mol K). Density functional theory (DFT) calculations (B3LYP/LanL2DZ (Ru); 6-31G(d) (all other atoms)) support a nitrile bound catalytic cycle with lowering of the reaction barrier as a consequence of sulfur oxidation through enhanced nitrile binding and attack of the water nucleophile through a highly organized transition state.

Ductile flow of methane hydrate

USGS Publications Warehouse

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

2003-01-01

Compressional creep tests (i.e., constant applied stress) conducted on pure, polycrystalline methane hydrate over the temperature range 260-287 K and confining pressures of 50-100 MPa show this material to be extraordinarily strong compared to other icy compounds. The contrast with hexagonal water ice, sometimes used as a proxy for gas hydrate properties, is impressive: over the thermal range where both are solid, methane hydrate is as much as 40 times stronger than ice at a given strain rate. The specific mechanical response of naturally occurring methane hydrate in sediments to environmental changes is expected to be dependent on the distribution of the hydrate phase within the formation - whether arranged structurally between and (or) cementing sediments grains versus passively in pore space within a sediment framework. If hydrate is in the former mode, the very high strength of methane hydrate implies a significantly greater strain-energy release upon decomposition and subsequent failure of hydrate-cemented formations than previously expected.

Effect of Temperature and Hydration Level on Purple Membrane Dynamics Studied Using Broadband Dielectric Spectroscopy from Sub-GHz to THz Regions.

PubMed

Yamamoto, Naoki; Ito, Shota; Nakanishi, Masahiro; Chatani, Eri; Inoue, Keiichi; Kandori, Hideki; Tominaga, Keisuke

2018-02-01

To investigate the effects of temperature and hydration on the dynamics of purple membrane (PM), we measured the broadband complex dielectric spectra from 0.5 GHz to 2.3 THz using a vector network analyzer and terahertz time-domain spectroscopy from 233 to 293 K. In the lower temperature region down to 83 K, the complex dielectric spectra in the THz region were also obtained. The complex dielectric spectra were analyzed through curve fitting using several model functions. We found that the hydrated states of one relaxational mode, which was assigned as the coupled motion of water molecules with the PM surface, began to overlap with the THz region at approximately 230 K. On the other hand, the relaxational mode was not observed for the dehydrated state. On the basis of this result, we conclude that the protein-dynamical-transition-like behavior in the THz region is due to the onset of the overlap of the relaxational mode with the THz region. Temperature hysteresis was observed in the dielectric spectrum at 263 K when the hydration level was high. It is suggested that the hydration water behaves similarly to supercooled liquid at that temperature. The third hydration layer may be partly formed to observe such a phenomenon. We also found that the relaxation time is slower than that of a globular protein, lysozyme, and the microscopic environment in the vicinity of the PM surface is suggested to be more heterogeneous than lysozyme. It is proposed that the spectral overlap of the relaxational mode and the low-frequency vibrational mode is necessary for the large conformational change of protein.

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.

Microcanonical molecular simulations of methane hydrate nucleation and growth: evidence that direct nucleation to sI hydrate is among the multiple nucleation pathways.

PubMed

Zhang, Zhengcai; Walsh, Matthew R; Guo, Guang-Jun

2015-04-14

The results of six high-precision constant energy molecular dynamics (MD) simulations initiated from methane-water systems equilibrated at 80 MPa and 250 K indicate that methane hydrates can nucleate via multiple pathways. Five trajectories nucleate to an amorphous solid. One trajectory nucleates to a structure-I hydrate template with long-range order which spans the simulation box across periodic boundaries despite the presence of several defects. While experimental and simulation data for hydrate nucleation with different time- and length-scales suggest that there may exist multiple pathways for nucleation, including metastable intermediates and the direct formation of the globally-stable phase, this work provides the most compelling evidence that direct formation to the globally stable crystalline phase is one of the multiple pathways available for hydrate nucleation.

Structure and water exchange of the hydrated thiosulfate ion in aqueous solution using QMCF MD simulation and large angle X-ray scattering.

PubMed

Eklund, Lars; Hofer, Tomas S; Weiss, Alexander K H; Tirler, Andreas O; Persson, Ingmar

2014-09-07

Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) has been applied in conjunction with experimental large angle X-ray scattering (LAXS) to study the structure and dynamics of the hydrated thiosulfate ion, S2O3(2-), in aqueous solution. The S-O and SC-ST bond distances have been determined to be 1.479(5) and 2.020(6) Å by LAXS and to be 1.478 and 2.017 Å by QMCF MD simulations, which are slightly longer than the mean values found in the solid state, 1.467 and 2.002 Å, respectively. This is due to the hydrogen bonds formed at hydration. The water dynamics show that water molecules are exchanged at the hydrated oxygen and sulfur atoms, and that the water exchange is ca. 50% faster at the sulfur atom than at the oxygen atoms with mean residence times, τ0.5, of 2.4 and 3.6 ps, respectively. From this point of view the water exchange dynamics mechanism resembles the sulfate ion, while it is significantly different from the sulfite ion. This shows that the lone electron-pair in the sulfite ion has a much larger impact on the water exchange dynamics than a substitution of an oxygen atom for a sulfur one. The LAXS data did give mean SCOaq1 and SCOaq2 distances of 3.66(2) and 4.36(10) Å, respectively, and SC-Othio and OthioOaq1, SC-ST and STOaq2 distances of 1.479(5), 2.845(10), 2.020(6) and 3.24(5) Å, respectively, giving SC-OthioOaq1 and SC-STOaq2 angles close to 110°, strongly indicating a tetrahedral geometry around the terminal thiosulfate sulfur and the oxygens, and thereby, three water molecules are hydrogen bound to each of them. The hydrogen bonds between thiosulfate oxygens and the hydrating water molecules are stronger and with longer mean residence times than those between water molecules in the aqueous bulk, while the opposite is true for the hydrogen bonds between the terminal thiosulfate sulfur and the hydrating water molecules. The hydration of all oxo sulfur ions is discussed using the detailed observations for the sulfate, thiosulfate and sulfite ions, and the structure of the hydrated peroxodisulfate ion, S2O8(2-), in aqueous solution has been determined by means of LAXS to support the general observations. The mean S-O bond distances are 1.448(2) and 1.675(5) Å to the oxo and peroxo oxygens, respectively.

Modeling the Formation of Hydrate-Filled Veins in Fine-Grained Sediments from in Situ Microbial Methane

NASA Astrophysics Data System (ADS)

Malinverno, A.; Cook, A.; Daigle, H.

2016-12-01

Continental margin sediments are dominantly fine-grained silt and clay, and methane hydrates in these sediments are often found in semi-vertical veins and fractures. In several instances, these hydrate veins occupy discrete depth intervals that are a few tens of meters thick and are surrounded by hydrate-free sediments. As they are not connected with gas sources beneath the base of the gas hydrate stability zone (GHSZ), these isolated hydrate-bearing intervals have been interpreted as formed by in situ microbial methane. To investigate the formation of these hydrate deposits, we applied a time-dependent advection-diffusion-reaction model that includes the effects of sedimentation, compaction, solute diffusion, and microbial methane generation. Microbial methane generation depends on the amount of metabolizable organic carbon deposited at the seafloor, whose progressive degradation produces methane beneath the sulfate reduction zone. If the amount of organic carbon entering the methanogenic zone is kept constant in time, we found that the computed amounts of hydrate formed in discrete intervals within the GHSZ are well below those estimated from observations. On the other hand, if the deposition of organic carbon is higher in a given time interval, methane generation during burial is more intense in the corresponding sediment interval, resulting in enhanced hydrate formation. With variations in organic carbon deposition comparable to those generally observed in continental margins, our model was able to reproduce the methane hydrate contents that were estimated from drilling. These results support the suggestion that in situ microbial generation associated with transient organic carbon deposition is the source of methane that forms isolated intervals of hydrate-filled veins in fine-grained sediments.

Modeling the Formation of Hydrate-Filled Veins in Fine-Grained Sediments from in Situ Microbial Methane

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

Malinverno, Alberto; Cook, Ann; Daigle, Hugh

Continental margin sediments are dominantly fine-grained silt and clay, and methane hydrates in these sediments are often found in semi-vertical veins and fractures. In several instances, these hydrate veins occupy discrete depth intervals that are a few tens of meters thick and are surrounded by hydrate-free sediments. As they are not connected with gas sources beneath the base of the gas hydrate stability zone (GHSZ), these isolated hydrate-bearing intervals have been interpreted as formed by in situ microbial methane. To investigate the formation of these hydrate deposits, we applied a time-dependent advection-diffusion-reaction model that includes the effects of sedimentation, compaction,more » solute diffusion, and microbial methane generation. Microbial methane generation depends on the amount of metabolizable organic carbon deposited at the seafloor, whose progressive degradation produces methane beneath the sulfate reduction zone. If the amount of organic carbon entering the methanogenic zone is kept constant in time, we found that the computed amounts of hydrate formed in discrete intervals within the GHSZ are well below those estimated from observations. On the other hand, if the deposition of organic carbon is higher in a given time interval, methane generation during burial is more intense in the corresponding sediment interval, resulting in enhanced hydrate formation. With variations in organic carbon deposition comparable to those generally observed in continental margins, our model was able to reproduce the methane hydrate contents that were estimated from drilling. These results support the suggestion that in situ microbial generation associated with transient organic carbon deposition is the source of methane that forms isolated intervals of hydrate-filled veins in fine-grained sediments.« less

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

Modeling the formation of methane hydrate-bearing intervals in fine-grained sediments

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

Malinverno, Alberto; Cook, Ann; Daigle, Hugh

Sediment grain size exerts a fundamental control on how methane hydrates are distributed within the pore space. Fine-grained muds are the predominant sediments in continental margins, and hydrates in these sediments have often been observed in semi-vertical veins and fractures. In several instances, these hydrate veins/fractures are found in discrete depth intervals a few tens meters thick within the gas hydrate stability zone (GHSZ) surrounded by hydrate-free sediments above and below. As they are not obviously connected with free gas occurring beneath the base of the GHSZ, these isolated hydrate-bearing intervals have been interpreted as formed by microbial methane generatedmore » in situ. To investigate further the formation of these hydrate deposits, we applied a time-dependent advection-diffusion-reaction model that includes the effects of sedimentation, solute diffusion, and microbial methane generation. The microbial methane generation term depends on the amount of metabolizable organic carbon deposited at the seafloor, which is degraded at a prescribed rate resulting in methane formation beneath the sulfate reduction zone. In the model, methane hydrate precipitates once the dissolved methane concentration is greater than solubility, or hydrate dissolves if concentration goes below solubility. If the deposition of organic carbon at the seafloor is kept constant in time, we found that the predicted amounts of hydrate formed in discrete intervals within the GHSZ are much less than those estimated from observations. We then investigated the effect of temporal variations in the deposition of organic carbon. If greater amounts of organic carbon are deposited during some time interval, methane generation is enhanced during burial in the corresponding sediment interval. With variations in organic carbon deposition that are consistent with observations in continental margin sediments, we were able to reproduce the methane hydrate contents estimated in discrete depth intervals. Our results support the suggestion that in situ microbial methane generation is the source for hydrates within fine-grained sediments.« less

Effects of CO2 adsorption on proton migration on a hydrated ZrO2 surface: an ab initio molecular dynamics study.

PubMed

Sato, Ryuhei; Shibuta, Yasushi; Shimojo, Fuyuki; Yamaguchi, Shu

2017-08-02

Hydration reactions on a carbonate-terminated cubic ZrO 2 (110) surface were analyzed using ab initio molecular dynamics (AIMD) simulations. After hydration reactions, carbonates were still present on the surface at 500 K. However, these carbonates are very weak conjugate bases and only act as steric hindrance in proton hopping processes between acidic chemisorbed H 2 O molecules (Zr-OH 2 ) and monodentate hydroxyl groups (Zr-OH - ). Similar to a carbonate-free hydrated surface, Zr-OH 2 , Zr-OH - , and polydentate hydroxyl groups ([double bond splayed left]OH + ) were observed, while the ratio of acidic Zr-OH 2 was significantly larger than that on the carbonate-free hydrated surface. A thermodynamic discussion and bond property analysis reveal that CO 2 adsorption significantly decreases the basicity of surface oxide ions ([double bond splayed left]O), whereas the acidity of Zr-OH 2 is not affected. As a result, protons released from [double bond splayed left]OH + react with Zr-OH - to form Zr-OH 2 , leading to a deficiency of proton acceptor sites, which decreases the proton conductivity by the hopping mechanism.

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.

About one discrete model of splitting by the physical processes of a piezoconductive medium with gas hydrate inclusions

NASA Astrophysics Data System (ADS)

Poveshchenko, Yu A.; Podryga, V. O.; Rahimly, P. I.; Sharova, Yu S.

2018-01-01

The thermodynamically equilibrium model for splitting by the physical processes of a two-component three-phase filtration fluid dynamics with gas hydrate inclusions is considered in the paper, for which a family of two-layer completely conservative difference schemes of the support operators method with time weights profiled in space is constructed. On the irregular grids of the theory of the support-operators method applied to the specifics of the processes of transfer of saturations and internal energies of water and gas in a medium with gas hydrate inclusions, methods of directwind approximation of these processes are considered. These approximations preserve the continual properties of divergence-gradient operations in their difference form and are related to the velocity field providing saturations transfer and internal energies of fluids. Fluid dynamics with gas hydrate inclusions are also calculated on the basis of the proposed approach, in particular, in areas of severe pressure depression in the collector space.

Linking pore-scale and basin-scale effects on diffusive methane transport in hydrate bearing environments through multi-scale reservoir simulations

NASA Astrophysics Data System (ADS)

Nole, M.; Daigle, H.; Cook, A.; Malinverno, A.; Hillman, J. I. T.

2016-12-01

We explore the gas hydrate-generating capacity of diffusive methane transport induced by solubility gradients due to pore size contrasts in lithologically heterogeneous marine sediments. Through the use of 1D, 2D, and 3D reactive transport simulations, we investigate scale-dependent processes in diffusion-dominated gas hydrate systems. These simulations all track a sand body, or series of sands, surrounded by clays as they are buried through the gas hydrate stability zone. Methane is sourced by microbial methanogenesis in the clays surrounding the sand layers. In 1D, simulations performed in a Lagrangian reference frame demonstrate that gas hydrate in thin sands (3.6 m thick) can occur in high saturations (upward of 70%) at the edges of sand bodies within the upper 400 meters below the seafloor. Diffusion of methane toward the center of the sand layer depends on the concentration gradient within the sand: broader sand pore size distributions with smaller median pore sizes enhance diffusive action toward the sand's center. Incorporating downhole log- and laboratory-derived sand pore size distributions, gas hydrate saturations in the center of the sand can reach 20% of the hydrate saturations at the sand's edges. Furthermore, we show that hydrate-free zones exist immediately above and below the sand and are approximately 5 m thick, depending on the sand-clay solubility contrast. A moving reference frame is also adopted in 2D, and the angle of gravity is rotated relative to the grid system to simulate a dipping sand layer. This is important to minimize diffusive edge effects or numerical diffusion that might be associated with a dipping sand in an Eulerian grid system oriented orthogonal to gravity. Two-dimensional simulations demonstrate the tendency for gas hydrate to accumulate downdip in a sand body because of greater methane transport at depth due to larger sand-clay solubility contrasts. In 3D, basin-scale simulations illuminate how convergent sand layers in a multilayered system can compete for diffusion from clays between them, resulting in relatively low hydrate saturations. All simulations suggest that when hydrate present in clays dissociates with burial, the additional dissolved methane is soaked up by nearby sands preserving high hydrate saturations.

Linking pore-scale and basin-scale effects on diffusive methane transport in hydrate bearing environments through multi-scale reservoir simulations

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

Nole, Michael; Daigle, Hugh; Cook, Ann

We explore the gas hydrate-generating capacity of diffusive methane transport induced by solubility gradients due to pore size contrasts in lithologically heterogeneous marine sediments. Through the use of 1D, 2D, and 3D reactive transport simulations, we investigate scale-dependent processes in diffusion-dominated gas hydrate systems. These simulations all track a sand body, or series of sands, surrounded by clays as they are buried through the gas hydrate stability zone. Methane is sourced by microbial methanogenesis in the clays surrounding the sand layers. In 1D, simulations performed in a Lagrangian reference frame demonstrate that gas hydrate in thin sands (3.6 m thick)more » can occur in high saturations (upward of 70%) at the edges of sand bodies within the upper 400 meters below the seafloor. Diffusion of methane toward the center of the sand layer depends on the concentration gradient within the sand: broader sand pore size distributions with smaller median pore sizes enhance diffusive action toward the sand’s center. Incorporating downhole log- and laboratory-derived sand pore size distributions, gas hydrate saturations in the center of the sand can reach 20% of the hydrate saturations at the sand’s edges. Furthermore, we show that hydrate-free zones exist immediately above and below the sand and are approximately 5 m thick, depending on the sand-clay solubility contrast. A moving reference frame is also adopted in 2D, and the angle of gravity is rotated relative to the grid system to simulate a dipping sand layer. This is important to minimize diffusive edge effects or numerical diffusion that might be associated with a dipping sand in an Eulerian grid system oriented orthogonal to gravity. Two-dimensional simulations demonstrate the tendency for gas hydrate to accumulate downdip in a sand body because of greater methane transport at depth due to larger sand-clay solubility contrasts. In 3D, basin-scale simulations illuminate how convergent sand layers in a multilayered system can compete for diffusion from clays between them, resulting in relatively low hydrate saturations. All simulations suggest that when hydrate present in clays dissociates with burial, the additional dissolved methane is soaked up by nearby sands preserving high hydrate saturations.« less

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

Thermal conductivity measurements in porous mixtures of methane hydrate and quartz sand

USGS Publications Warehouse

Waite, W.F.; deMartin, B.J.; Kirby, S.H.; Pinkston, J.; Ruppel, C.D.

2002-01-01

Using von Herzen and Maxwell's needle probe method, we measured thermal conductivity in four porous mixtures of quartz sand and methane gas hydrate, with hydrate composing 0, 33, 67 and 100% of the solid volume. Thermal conductivities were measured at a constant methane pore pressure of 24.8 MPa between -20 and +15??C, and at a constant temperature of -10??C between 3.5 and 27.6 MPa methane pore pressure. Thermal conductivity decreased with increasing temperature and increased with increasing methane pore pressure. Both dependencies weakened with increasing hydrate content. Despite the high thermal conductivity of quartz relative to methane hydrate, the largest thermal conductivity was measured in the mixture containing 33% hydrate rather than in hydrate-free sand. This suggests gas hydrate enhanced grain-to-grain heat transfer, perhaps due to intergranular contact growth during hydrate synthesis. These results for gas-filled porous mixtures can help constrain thermal conductivity estimates in porous, gas hydrate-bearing systems.

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.

Gas-hydrate occurrence on the W-Svalbard margin at the gateway to the Arctic Ocean

NASA Astrophysics Data System (ADS)

Bünz, Stefan; Mienert, Jürgen

2010-05-01

Gas hydrates contain more carbon than does any other global reservoir and are abundant on continental margins worldwide. These two facts make gas hydrates important as a possible future energy resource, in submarine landsliding and in global climate change. With the ongoing global warming, there is a need for a better understanding of the distribution of gas hydrates and their sensitivity to environmental changes. Gas hydrate systems in polar latitudes may be of particular importance due to the fact that environmental changes will be felt here first and most likely are more extreme than elsewhere. The gas-hydrate systems offshore western Svalbard are far more extensive (~4000km^2) than previously assumed and include the whole Vestnesa Ridge, an elongated sediment drift north of the Molloy Transform and just east of the Molloy Ridge, one of the shortest segments of the slow spreading North-Atlantic Ridge system. However, in this peculiar setting gas hydrates also occur within few km of a mid-oceanic ridge and transform fault, which makes this gas hydrate system unique on Earth. The close proximity to the spreading centre and its hydrothermal circulation system affects the dynamics of the gas hydrate system. A strong cross-cutting BSR is visible, especially in areas of dipping seafloor. Other places show a weak almost subtle BSR. The base of gas-hydrate stability varies with distance from the ridge system, suggesting a strong temperature-controlled subsurface depth as the underlying young oceanic crust cools off eastward. High amplitude reflections over a depth range of up to 150m underneath the BSR indicate the presence of a considerable amount of free gas. The free gas is focused laterally upwards by the less-permeable hydrated sediments as the only fluid-escape features occur at the crest of the Vestnesa Ridge. The fluid migration system and its active plumbing system at the crest provide an efficient mechanism for gas escape from the base of the hydrate stability zone. The high heat flow together with the high tectonic activity of this region, a thick sedimentary cover, a shallow maturation window and an accelerated rate of biogenic and thermogenic gas production cause substantial disturbance to the gas hydrate system leading to high variability in gas hydrate build up and dissociation. This young and dynamic system allows studying gas hydrate formation in marine sediments, their governing parameters and their relationship with the fluid flow in great detail.

Theoretical and Experimental Approaches towards study of Methane Occupation Dynamics within Gas Hydrates

NASA Astrophysics Data System (ADS)

Mendonca, P.; Shemella, P.; Nayak, S.; Sharma, A.

2006-12-01

Hydrate structures of hydrocarbon (commonly methane hydrates) within the continental shelf regions are considered a huge energy resource since they are a significant reservoir for terrestrial carbon. Any changes, abrupt or continual, will have an impact on the carbon (as well as water) cycle. However, tapping into this reservoir for energy resource has been challenging from both technical and scientific fronts primarily because any rapid release of methane (CH4) will likely have serious impact on the global climate of Earth as well as the stability of the continental shelf. While fossil fuel combustion derived CO2 in the atmosphere is considered a major contributor to global warming, the massive amounts of methane release from the gas hydrates has been a point of debate for its impact on the global climate. Due to the lack of a clear physical mechanism for such structural destabilization, environmental changes within the ocean setting (viz. temperature, salinity or biology) are typically assigned as possible causes. A good kinetic model that ties into structural instability of these essentially non-stoichiometric compounds at both the macromolecular (thermodynamic) and nanometric scale is essential. Preliminary experiments on single crystal methane hydrate high pressure phase (~1.0GPa) indicate a measurable kinetics of methane diffusion upon bringing structural disorder to the single crystal. Although there have been several kinetic studies of gas-hydrate nucleation and dissociation, systematic study of kinetics (and dynamics) of diffusion based changes within the gas hydrates has been lacking. In addition to experimental data on single crystal methane hydrates, we will present a first principle study on the structure, energetic, and dynamics of sI phase methane hydrate. We use density functional theory to study the energetic effect of the occupancy of neighboring cages in a cluster model system consisting of two sI gas hydrates. In this situation there can be two, one, or no methane, and we find that the binding for the first methane is exothermic. The second methane binding is endothermic, suggesting that the stability of a methane molecule is determined by the occupancy of adjacent cages. Using these results, we will present the calculated binding energies of a periodic system based on crystal structure data and compare them to the cluster method. This combined experimental and theoretical investigation is aimed at generating fundamental dataset that can be tested for the broader impact of such processes on the global carbon cycle.

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

Direction-specific van der Waals attraction between rutile TiO2 nanocrystals

NASA Astrophysics Data System (ADS)

Zhang, Xin; He, Yang; Sushko, Maria L.; Liu, Jia; Luo, Langli; De Yoreo, James J.; Mao, Scott X.; Wang, Chongmin; Rosso, Kevin M.

2017-04-01

Mutual lattice orientations dictate the types and magnitudes of forces between crystalline particles. When lattice polarizability is anisotropic, the van der Waals dispersion attraction can, in principle, contribute to this direction dependence. We report measurement of this attraction between rutile nanocrystals, as a function of their mutual orientation and surface hydration extent. At tens of nanometers of separation, the attraction is weak and shows no dependence on azimuthal alignment or surface hydration. At separations of approximately one hydration layer, the attraction is strongly dependent on azimuthal alignment and systematically decreases as intervening water density increases. Measured forces closely agree with predictions from Lifshitz theory and show that dispersion forces can generate a torque between particles interacting in solution and between grains in materials.

Submarine slope failures due to pipe structure formation.

PubMed

Elger, Judith; Berndt, Christian; Rüpke, Lars; Krastel, Sebastian; Gross, Felix; Geissler, Wolfram H

2018-02-19

There is a strong spatial correlation between submarine slope failures and the occurrence of gas hydrates. This has been attributed to the dynamic nature of gas hydrate systems and the potential reduction of slope stability due to bottom water warming or sea level drop. However, 30 years of research into this process found no solid supporting evidence. Here we present new reflection seismic data from the Arctic Ocean and numerical modelling results supporting a different link between hydrates and slope stability. Hydrates reduce sediment permeability and cause build-up of overpressure at the base of the gas hydrate stability zone. Resulting hydro-fracturing forms pipe structures as pathways for overpressured fluids to migrate upward. Where these pipe structures reach shallow permeable beds, this overpressure transfers laterally and destabilises the slope. This process reconciles the spatial correlation of submarine landslides and gas hydrate, and it is independent of environmental change and water depth.

The structure of aqueous sodium hydroxide solutions: a combined solution x-ray diffraction and simulation study.

PubMed

Megyes, Tünde; Bálint, Szabolcs; Grósz, Tamás; Radnai, Tamás; Bakó, Imre; Sipos, Pál

2008-01-28

To determine the structure of aqueous sodium hydroxide solutions, results obtained from x-ray diffraction and computer simulation (molecular dynamics and Car-Parrinello) have been compared. The capabilities and limitations of the methods in describing the solution structure are discussed. For the solutions studied, diffraction methods were found to perform very well in describing the hydration spheres of the sodium ion and yield structural information on the anion's hydration structure. Classical molecular dynamics simulations were not able to correctly describe the bulk structure of these solutions. However, Car-Parrinello simulation proved to be a suitable tool in the detailed interpretation of the hydration sphere of ions and bulk structure of solutions. The results of Car-Parrinello simulations were compared with the findings of diffraction experiments.

Glacial Cycles Influence Marine Methane Hydrate Formation

NASA Astrophysics Data System (ADS)

Malinverno, A.; Cook, A. E.; Daigle, H.; Oryan, B.

2018-01-01

Methane hydrates in fine-grained continental slope sediments often occupy isolated depth intervals surrounded by hydrate-free sediments. As they are not connected to deep gas sources, these hydrate deposits have been interpreted as sourced by in situ microbial methane. We investigate here the hypothesis that these isolated hydrate accumulations form preferentially in sediments deposited during Pleistocene glacial lowstands that contain relatively large amounts of labile particulate organic carbon, leading to enhanced microbial methanogenesis. To test this hypothesis, we apply an advection-diffusion-reaction model with a time-dependent organic carbon deposition controlled by glacioeustatic sea level variations. In the model, hydrate forms in sediments with greater organic carbon content deposited during the penultimate glacial cycle ( 120-240 ka). The model predictions match hydrate-bearing intervals detected in three sites drilled on the northern Gulf of Mexico continental slope, supporting the hypothesis of hydrate formation driven by enhanced organic carbon burial during glacial lowstands.

Impact of pore-water freshening on clays and the compressibility of hydrate-bearing reservoirs during production

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

Jang, Junbong; Cao, Shuang; Waite, William

Gas production efficiency from natural hydrate-bearing sediments depends in part on geotechnical properties of fine-grained materials, which are ubiquitous even in sandy hydrate-bearing sediments. The responses of fine-grained material to pore fluid chemistry changes due to freshening during hydrate dissociation could alter critical sediment characteristics during gas production activities. We investigate the electrical sensitivity of fine grains to pore fluid freshening and the implications of freshening on sediment compression and recompression parameters.

The alteration of lipid bilayer dynamics by phloretin and 6-ketocholestanol.

PubMed

Przybylo, M; Procek, J; Hof, M; Langner, M

2014-02-01

Lipid bilayer properties are quantified with a variety of arbitrary selected parameters such as molecular packing and dynamics, electrostatic potentials or permeability. In the paper we determined the effect of phloretin and 6-ketocholestanol (dipole potential modifying agents) on the membrane hydration and efficiency of the trans-membrane water flow. The dynamics of water molecules within the lipid bilayer interface was evaluated using solvent relaxation method, whereas the osmotically induced trans-membrane water flux was estimated with the stopped-flow method using the liposome shrinkage kinetics. The presence of phloretin or 6-ketocholestanol resulted in a change of both, the interfacial hydration level and osmotically driven water fluxes. Specifically, the presence of 6-ketocholestanol reduced the amount and mobility of water in the membrane interface. It also slows the osmotically induced water flow. The interfacial hydration change caused by phloretin was much smaller and the effect on osmotically induced water flow was opposite to that of 6-ketocholestanol. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

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

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.

Mathematical model reveals role of nucleotide signaling in airway surface liquid homeostasis and its dysregulation in cystic fibrosis

PubMed Central

Sandefur, Conner I.; Boucher, Richard C.; Elston, Timothy C.

2017-01-01

Mucociliary clearance is composed of three components (i.e., mucin secretion, airway surface hydration, and ciliary-activity) which function coordinately to clear inhaled microbes and other foreign particles from airway surfaces. Airway surface hydration is maintained by water fluxes driven predominantly by active chloride and sodium ion transport. The ion channels that mediate electrogenic ion transport are regulated by extracellular purinergic signals that signal through G protein-coupled receptors. These purinoreceptors and the signaling pathways they activate have been identified as possible therapeutic targets for treating lung disease. A systems-level description of airway surface liquid (ASL) homeostasis could accelerate development of such therapies. Accordingly, we developed a mathematical model to describe the dynamic coupling of ion and water transport to extracellular purinergic signaling. We trained our model from steady-state and time-dependent experimental measurements made using normal and cystic fibrosis (CF) cultured human airway epithelium. To reproduce CF conditions, reduced chloride secretion, increased potassium secretion, and increased sodium absorption were required. The model accurately predicted ASL height under basal normal and CF conditions and the collapse of surface hydration due to the accelerated nucleotide metabolism associated with CF exacerbations. Finally, the model predicted a therapeutic strategy to deliver nucleotide receptor agonists to effectively rehydrate the ASL of CF airways. PMID:28808008

Gas hydrate saturations estimated from fractured reservoir at Site NGHP-01-10, Krishna-Godavari Basin, India

USGS Publications Warehouse

Lee, M.W.; Collett, T.S.

2009-01-01

During the Indian National Gas Hydrate Program Expedition 01 (NGHP-Ol), one of the richest marine gas hydrate accumulations was discovered at Site NGHP-01-10 in the Krishna-Godavari Basin. The occurrence of concentrated gas hydrate at this site is primarily controlled by the presence of fractures. Assuming the resistivity of gas hydratebearing sediments is isotropic, th?? conventional Archie analysis using the logging while drilling resistivity log yields gas hydrate saturations greater than 50% (as high as ???80%) of the pore space for the depth interval between ???25 and ???160 m below seafloor. On the other hand, gas hydrate saturations estimated from pressure cores from nearby wells were less than ???26% of the pore space. Although intrasite variability may contribute to the difference, the primary cause of the saturation difference is attributed to the anisotropic nature of the reservoir due to gas hydrate in high-angle fractures. Archie's law can be used to estimate gas hydrate saturations in anisotropic reservoir, with additional information such as elastic velocities to constrain Archie cementation parameters m and the saturation exponent n. Theory indicates that m and n depend on the direction of the measurement relative to fracture orientation, as well as depending on gas hydrate saturation. By using higher values of m and n in the resistivity analysis for fractured reservoirs, the difference between saturation estimates is significantly reduced, although a sizable difference remains. To better understand the nature of fractured reservoirs, wireline P and S wave velocities were also incorporated into the analysis.

Mechanisms Leading to Co-Existence of Gas Hydrate in Ocean Sediments [Part 1 of 2

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

Bryant, Steven; Juanes, Ruben

In this project we have sought to explain the co-existence of gas and hydrate phases in sediments within the gas hydrate stability zone. We have focused on the gas/brine interface at the scale of individual grains in the sediment. The capillary forces associated with a gas/brine interface play a dominant role in many processes that occur in the pores of sediments and sedimentary rocks. The mechanical forces associated with the same interface can lead to fracture initiation and propagation in hydrate-bearing sediments. Thus the unifying theme of the research reported here is that pore scale phenomena are key to understandingmore » large scale phenomena in hydrate-bearing sediments whenever a free gas phase is present. Our analysis of pore-scale phenomena in this project has delineated three regimes that govern processes in which the gas phase pressure is increasing: fracturing, capillary fingering and viscous fingering. These regimes are characterized by different morphology of the region invaded by the gas. On the other hand when the gas phase pressure is decreasing, the corresponding regimes are capillary fingering and compaction. In this project, we studied all these regimes except compaction. Many processes of interest in hydrate-bearing sediments can be better understood when placed in the context of the appropriate regime. For example, hydrate formation in sub-permafrost sediments falls in the capillary fingering regime, whereas gas invasion into ocean sediments is likely to fall into the fracturing regime. Our research provides insight into the mechanisms by which gas reservoirs are converted to hydrate as the base of the gas hydrate stability zone descends through the reservoir. If the reservoir was no longer being charged, then variation in grain size distribution within the reservoir explain hydrate saturation profiles such as that at Mt. Elbert, where sand-rich intervals containing little hydrate are interspersed between intervals containing large hydrate saturations. Large volumes (of order one pore volume) of gaseous and aqueous phases must be transported into the gas hydrate stability zone. The driver for this transport is the pressure sink induced by a reduction in occupied pore volume that accompanies the formation of hydrate from gas and water. Pore-scale imbibition models and bed-scale multiphase flow models indicate that the rate-limiting step in converting gas to hydrate is the supply of water to the hydrate stability zone. Moreover, the water supply rate is controlled by capillarity-driven flux for conditions typical of the Alaska North Slope. A meter-scale laboratory experiment confirms that significant volumes of fluid phases move into the hydrate stability zone and that capillarity is essential for the water flux. The model shows that without capillarity-driven flux, large saturations of hydrate cannot form. The observations of thick zones of large saturation at Mallik and Mt Elbert thus suggest that the primary control on these systems is the rate of transport of gaseous and aqueous phases, driven by the pressure sink at the base of the gas hydrate stability zone. A key finding of our project is the elucidation of ?capillary fracturing? as a dominant gas transport mechanism in low-permeability media. We initially investigate this phenomenon by means of grain-scale simulations in which we extended a discrete element mechanics code (PFC, by Itasca) to incorporate the dynamics of first single-phase and then multiphase flow. A reductionist model on a square lattice allows us to determine some of the fundamental dependencies of the mode of gas invasion (capillary fingering, viscous fingering, and fracturing) on the parameters of the system. We then show that the morphology of the gas-invaded region exerts a fundamental control on the fabric of methane hydrate formation, and on the overpressures caused by methane hydrate dissociation. We demonstrate the existence of the different invasion regimes by means of controlled laboratory experiments in a radial cell. We collapse the behavior in the form of a phase diagram fully characterized by two dimensionless groups: a modified capillary number and a ?fracturing number? that reflects the balance between the pressure forces that act to open conduits in the granular pack, and frictional forces that resist it. We use all this small-scale knowledge to propose simple mechanistic models of gas migration and hydrate formation at the geologic bed scale. We propose that methane transport in lake and oceanic sediments is controlled by dynamic conduits, which dilate and release gas as the falling hydrostatic pressure reduces the effective stress below the tensile strength of the sediments. We test our model against a four-month record of hydrostatic load and methane flux in Upper Mystic Lake, Mass., USA, and show that it captures the complex episodicity of methane ebullition. Our quantitative conceptualization opens the door to integrated modeling of methane transport to constrain global methane release from lakes and other methane-rich sediment systems, and to assess its climate feedbacks.« less

Mechanisms Leading to Co-Existence of Gas Hydrate in Ocean Sediments [Part 2 of 2

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

Bryant, Steven; Juanes, Ruben

In this project we have sought to explain the co-existence of gas and hydrate phases in sediments within the gas hydrate stability zone. We have focused on the gas/brine interface at the scale of individual grains in the sediment. The capillary forces associated with a gas/brine interface play a dominant role in many processes that occur in the pores of sediments and sedimentary rocks. The mechanical forces associated with the same interface can lead to fracture initiation and propagation in hydrate-bearing sediments. Thus the unifying theme of the research reported here is that pore scale phenomena are key to understandingmore » large scale phenomena in hydrate-bearing sediments whenever a free gas phase is present. Our analysis of pore-scale phenomena in this project has delineated three regimes that govern processes in which the gas phase pressure is increasing: fracturing, capillary fingering and viscous fingering. These regimes are characterized by different morphology of the region invaded by the gas. On the other hand when the gas phase pressure is decreasing, the corresponding regimes are capillary fingering and compaction. In this project, we studied all these regimes except compaction. Many processes of interest in hydrate-bearing sediments can be better understood when placed in the context of the appropriate regime. For example, hydrate formation in sub-permafrost sediments falls in the capillary fingering regime, whereas gas invasion into ocean sediments is likely to fall into the fracturing regime. Our research provides insight into the mechanisms by which gas reservoirs are converted to hydrate as the base of the gas hydrate stability zone descends through the reservoir. If the reservoir was no longer being charged, then variation in grain size distribution within the reservoir explain hydrate saturation profiles such as that at Mt. Elbert, where sand-rich intervals containing little hydrate are interspersed between intervals containing large hydrate saturations. Large volumes (of order one pore volume) of gaseous and aqueous phases must be transported into the gas hydrate stability zone. The driver for this transport is the pressure sink induced by a reduction in occupied pore volume that accompanies the formation of hydrate from gas and water. Pore-scale imbibition models and bed-scale multiphase flow models indicate that the rate-limiting step in converting gas to hydrate is the supply of water to the hydrate stability zone. Moreover, the water supply rate is controlled by capillarity-driven flux for conditions typical of the Alaska North Slope. A meter-scale laboratory experiment confirms that significant volumes of fluid phases move into the hydrate stability zone and that capillarity is essential for the water flux. The model shows that without capillarity-driven flux, large saturations of hydrate cannot form. The observations of thick zones of large saturation at Mallik and Mt Elbert thus suggest that the primary control on these systems is the rate of transport of gaseous and aqueous phases, driven by the pressure sink at the base of the gas hydrate stability zone. A key finding of our project is the elucidation of ?capillary fracturing? as a dominant gas transport mechanism in low-permeability media. We initially investigate this phenomenon by means of grain-scale simulations in which we extended a discrete element mechanics code (PFC, by Itasca) to incorporate the dynamics of first singlephase and then multiphase flow. A reductionist model on a square lattice allows us to determine some of the fundamental dependencies of the mode of gas invasion (capillary fingering, viscous fingering, and fracturing) on the parameters of the system. We then show that the morphology of the gas-invaded region exerts a fundamental control on the fabric of methane hydrate formation, and on the overpressures caused by methane hydrate dissociation. We demonstrate the existence of the different invasion regimes by means of controlled laboratory experiments in a radial cell. We collapse the behavior in the form of a phase diagram fully characterized by two dimensionless groups: a modified capillary number and a ?fracturing number? that reflects the balance between the pressure forces that act to open conduits in the granular pack, and frictional forces that resist it. We use all this small-scale knowledge to propose simple mechanistic models of gas migration and hydrate formation at the geologic bed scale. We propose that methane transport in lake and oceanic sediments is controlled by dynamic conduits, which dilate and release gas as the falling hydrostatic pressure reduces the effective stress below the tensile strength of the sediments. We test our model against a four-month record of hydrostatic load and methane flux in Upper Mystic Lake, Mass., USA, and show that it captures the complex episodicity of methane ebullition. Our quantitative conceptualization opens the door to integrated modeling of methane transport to constrain global methane release from lakes and other methane-rich sediment systems, and to assess its climate feedbacks.« less

Structure and dynamics of single hydrophobic/ionic heteropolymers at the vapor-liquid interface of water.

PubMed

Vembanur, Srivathsan; Venkateshwaran, Vasudevan; Garde, Shekhar

2014-04-29

We focus on the conformational stability, structure, and dynamics of hydrophobic/charged homopolymers and heteropolymers at the vapor-liquid interface of water using extensive molecular dynamics simulations. Hydrophobic polymers collapse into globular structures in bulk water but unfold and sample a broad range of conformations at the vapor-liquid interface of water. We show that adding a pair of charges to a hydrophobic polymer at the interface can dramatically change its conformations, stabilizing hairpinlike structures, with molecular details depending on the location of the charged pair in the sequence. The translational dynamics of homopolymers and heteropolymers are also different, whereas the homopolymers skate on the interface with low drag, the tendency of charged groups to remain hydrated pulls the heteropolymers toward the liquid side of the interface, thus pinning them, increasing drag, and slowing the translational dynamics. The conformational dynamics of heteropolymers are also slower than that of the homopolymer and depend on the location of the charged groups in the sequence. Conformational dynamics are most restricted for the end-charged heteropolymer and speed up as the charge pair is moved toward the center of the sequence. We rationalize these trends using the fundamental understanding of the effects of the interface on primitive pair-level interactions between two hydrophobic groups and between oppositely charged ions in its vicinity.

Backbone hydration determines the folding signature of amino acid residues.

PubMed

Bignucolo, Olivier; Leung, Hoi Tik Alvin; Grzesiek, Stephan; Bernèche, Simon

2015-04-08

The relation between the sequence of a protein and its three-dimensional structure remains largely unknown. A lasting dream is to elucidate the side-chain-dependent driving forces that govern the folding process. Different structural data suggest that aromatic amino acids play a particular role in the stabilization of protein structures. To better understand the underlying mechanism, we studied peptides of the sequence EGAAXAASS (X = Gly, Ile, Tyr, Trp) through comparison of molecular dynamics (MD) trajectories and NMR residual dipolar coupling (RDC) measurements. The RDC data for aromatic substitutions provide evidence for a kink in the peptide backbone. Analysis of the MD simulations shows that the formation of internal hydrogen bonds underlying a helical turn is key to reproduce the experimental RDC values. The simulations further reveal that the driving force leading to such helical-turn conformations arises from the lack of hydration of the peptide chain on either side of the bulky aromatic side chain, which can potentially act as a nucleation point initiating the folding process.

Microscopic origin of gating current fluctuations in a potassium channel voltage sensor.

PubMed

Freites, J Alfredo; Schow, Eric V; White, Stephen H; Tobias, Douglas J

2012-06-06

Voltage-dependent ion channels open and close in response to changes in membrane electrical potential due to the motion of their voltage-sensing domains (VSDs). VSD charge displacements within the membrane electric field are observed in electrophysiology experiments as gating currents preceding ionic conduction. The elementary charge motions that give rise to the gating current cannot be observed directly, but appear as discrete current pulses that generate fluctuations in gating current measurements. Here we report direct observation of gating-charge displacements in an atomistic molecular dynamics simulation of the isolated VSD from the KvAP channel in a hydrated lipid bilayer on the timescale (10-μs) expected for elementary gating charge transitions. The results reveal that gating-charge displacements are associated with the water-catalyzed rearrangement of salt bridges between the S4 arginines and a set of conserved acidic side chains on the S1-S3 transmembrane segments in the hydrated interior of the VSD. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition

PubMed Central

Blatter, Markus; Cléry, Antoine; Damberger, Fred F.

2017-01-01

Abstract The Fox-1 RNA recognition motif (RRM) domain is an important member of the RRM protein family. We report a 1.8 Å X-ray structure of the free Fox-1 containing six distinct monomers. We use this and the nuclear magnetic resonance (NMR) structure of the Fox-1 protein/RNA complex for molecular dynamics (MD) analyses of the structured hydration. The individual monomers of the X-ray structure show diverse hydration patterns, however, MD excellently reproduces the most occupied hydration sites. Simulations of the protein/RNA complex show hydration consistent with the isolated protein complemented by hydration sites specific to the protein/RNA interface. MD predicts intricate hydration sites with water-binding times extending up to hundreds of nanoseconds. We characterize two of them using NMR spectroscopy, RNA binding with switchSENSE and free-energy calculations of mutant proteins. Both hydration sites are experimentally confirmed and their abolishment reduces the binding free-energy. A quantitative agreement between theory and experiment is achieved for the S155A substitution but not for the S122A mutant. The S155 hydration site is evolutionarily conserved within the RRM domains. In conclusion, MD is an effective tool for predicting and interpreting the hydration patterns of protein/RNA complexes. Hydration is not easily detectable in NMR experiments but can affect stability of protein/RNA complexes. PMID:28505313

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.

Molecular dynamics study of CO2 hydrate dissociation: Fluctuation-dissipation and non-equilibrium analysis.

PubMed

English, Niall J; Clarke, Elaine T

2013-09-07

Equilibrium and non-equilibrium molecular dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar CO2 hydrate interfaces in liquid water at 300-320 K. Different guest compositions, at 85%, 95%, and 100% of maximum theoretical occupation, led to statistically-significant differences in the observed initial dissociation rates. The melting temperatures of each interface were estimated, and dissociation rates were observed to be strongly dependent on temperature, with higher dissociation rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model developed previously was applied to fit the observed dissociation profiles, and this helps to identify clearly two distinct régimes of break-up; a second well-defined region is essentially independent of composition and temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. From equilibrium MD of the two-phase systems at their melting point, the relaxation times of the auto-correlation functions of fluctuations in number of enclathrated guest molecules were used as a basis for comparison of the variation in the underlying, non-equilibrium, thermal-driven dissociation rates via Onsager's hypothesis, and statistically significant differences were found, confirming the value of a fluctuation-dissipation approach in this case.

O-H anharmonic vibrational motions in Cl(-)···(CH3OH)(1-2) ionic clusters. Combined IRPD experiments and AIMD simulations.

PubMed

Beck, Jordan P; Cimas, Alvaro; Lisy, James M; Gaigeot, Marie-Pierre

2014-02-05

The structures of Cl(-)-(Methanol)1,2 clusters have been unraveled combining Infrared Predissociation (IR-PD) experiments and DFT-based molecular dynamics simulations (DFT-MD) at 100 K. The dynamical IR spectra extracted from DFT-MD provide the initial 600 cm(-1) large anharmonic red-shift of the O-H stretch from uncomplexed methanol (3682 cm(-1)) to Cl(-)-(Methanol)1 complex (3085 cm(-1)) as observed in the IR-PD experiment, as well as the subtle supplementary blue- and red-shifts of the O-H stretch in Cl(-)-(Methanol)2 depending on the structure. The anharmonic vibrational calculations remarkably provide the 100 cm(-1) O-H blue-shift when the two methanol molecules are simultaneously organized in the anion first hydration shell (conformer 2A), while they provide the 240 cm(-1) O-H red-shift when the second methanol is in the second hydration shell of Cl(-) (conformer 2B). RRKM calculations have also shown that 2A/2B conformers interconvert on a nanosecond time-scale at the estimated 100 K temperature of the clusters formed by evaporative cooling of argon prior to the IR-PD process. Copyright © 2013 Elsevier B.V. All rights reserved.

A Circuit Model of Real Time Human Body Hydration.

PubMed

Asogwa, Clement Ogugua; Teshome, Assefa K; Collins, Stephen F; Lai, Daniel T H

2016-06-01

Changes in human body hydration leading to excess fluid losses or overload affects the body fluid's ability to provide the necessary support for healthy living. We propose a time-dependent circuit model of real-time human body hydration, which models the human body tissue as a signal transmission medium. The circuit model predicts the attenuation of a propagating electrical signal. Hydration rates are modeled by a time constant τ, which characterizes the individual specific metabolic function of the body part measured. We define a surrogate human body anthropometric parameter θ by the muscle-fat ratio and comparing it with the body mass index (BMI), we find theoretically, the rate of hydration varying from 1.73 dB/min, for high θ and low τ to 0.05 dB/min for low θ and high τ. We compare these theoretical values with empirical measurements and show that real-time changes in human body hydration can be observed by measuring signal attenuation. We took empirical measurements using a vector network analyzer and obtained different hydration rates for various BMI, ranging from 0.6 dB/min for 22.7 [Formula: see text] down to 0.04 dB/min for 41.2 [Formula: see text]. We conclude that the galvanic coupling circuit model can predict changes in the volume of the body fluid, which are essential in diagnosing and monitoring treatment of body fluid disorder. Individuals with high BMI would have higher time-dependent biological characteristic, lower metabolic rate, and lower rate of hydration.

The effect of hydrate promoters on gas uptake.

PubMed

Xu, Chun-Gang; Yu, Yi-Song; Ding, Ya-Long; Cai, Jing; Li, Xiao-Sen

2017-08-16

Gas hydrate technology is considered as a promising technology in the fields of gas storage and transportation, gas separation and purification, seawater desalination, and phase-change thermal energy storage. However, to date, the technology is still not commercially used mainly due to the low gas hydrate formation rate and the low gas uptake. In this study, the effect of hydrate promoters on gas uptake was systematically studied and analyzed based on hydrate-based CH 4 storage and CO 2 capture from CO 2 /H 2 gas mixture experiments. Raman spectroscopy, Fourier transform infrared spectroscopy (FTIR) and gas chromatography (GC) were employed to analyze the microstructures and gas compositions. The results indicate that the effect of the hydrate promoter on the gas uptake depends on the physical and chemical properties of the promoter and gas. A strong polar ionic promoter is not helpful towards obtaining the ideal gas uptake because a dense hydrate layer is easily formed at the gas-liquid interface, which hinders gas diffusion from the gas phase to the bulk solution. For a weak polar or non-polar promoter, the gas uptake depends on the dissolution characteristics among the different substances in the system. The lower the mutual solubility among the substances co-existing in the system, the higher the independence among the substances in the system; this is so that each phase has an equal chance to occupy the hydrate cages without or with small interactions, finally leading to a relatively high gas uptake.

A view on thermodynamics of concentrated electrolytes: Modification necessity for electrostatic contribution of osmotic coefficient

NASA Astrophysics Data System (ADS)

Sahu, Jyoti; Juvekar, Vinay A.

2018-05-01

Prediction of the osmotic coefficient of concentrated electrolytes is needed in a wide variety of industrial applications. There is a need to correctly segregate the electrostatic contribution to osmotic coefficient from nonelectrostatic contribution. This is achieved in a rational way in this work. Using the Robinson-Stokes-Glueckauf hydrated ion model to predict non-electrostatic contribution to the osmotic coefficient, it is shown that hydration number should be independent of concentration so that the observed linear dependence of osmotic coefficient on electrolyte concentration in high concentration range could be predicted. The hydration number of several electrolytes (LiCl, NaCl, KCl, MgCl2, and MgSO4) has been estimated by this method. The hydration number predicted by this model shows correct dependence on temperature. It is also shown that the electrostatic contribution to osmotic coefficient is underpredicted by the Debye-Hückel theory at concentration beyond 0.1 m. The Debye-Hückel theory is modified by introducing a concentration dependent hydrated ionic size. Using the present analysis, it is possible to correctly estimate the electrostatic contribution to the osmotic coefficient, beyond the range of validation of the D-H theory. This would allow development of a more fundamental model for electrostatic interaction at high electrolyte concentrations.

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

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

Sessa, Francesco; D’Angelo, Paola, E-mail: p.dangelo@uniroma1.it; Spezia, Riccardo

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 shellmore » 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.« less

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.

Picosecond to nanosecond dynamics provide a source of conformational entropy for protein folding.

PubMed

Stadler, Andreas M; Demmel, Franz; Ollivier, Jacques; Seydel, Tilo

2016-08-03

Myoglobin can be trapped in fully folded structures, partially folded molten globules, and unfolded states under stable equilibrium conditions. Here, we report an experimental study on the conformational dynamics of different folded conformational states of apo- and holomyoglobin in solution. Global protein diffusion and internal molecular motions were probed by neutron time-of-flight and neutron backscattering spectroscopy on the picosecond and nanosecond time scales. Global protein diffusion was found to depend on the α-helical content of the protein suggesting that charges on the macromolecule increase the short-time diffusion of protein. With regard to the molten globules, a gel-like phase due to protein entanglement and interactions with neighbouring macromolecules was visible due to a reduction of the global diffusion coefficients on the nanosecond time scale. Diffusion coefficients, residence and relaxation times of internal protein dynamics and root mean square displacements of localised internal motions were determined for the investigated structural states. The difference in conformational entropy ΔSconf of the protein between the unfolded and the partially or fully folded conformations was extracted from the measured root mean square displacements. Using thermodynamic parameters from the literature and the experimentally determined ΔSconf values we could identify the entropic contribution of the hydration shell ΔShydr of the different folded states. Our results point out the relevance of conformational entropy of the protein and the hydration shell for stability and folding of myoglobin.

Dielectric relaxation spectroscopy shows a sparingly hydrated interface and low counterion mobility in triflate micelles.

PubMed

Lima, Filipe S; Chaimovich, Hernan; Cuccovia, Iolanda M; Buchner, Richard

2013-08-13

The properties of ionic micelles are affected by the nature of the counterion. Specific ion effects can be dramatic, inducing even shape and phase changes in micellar solutions, transitions apparently related to micellar hydration and counterion binding at the micellar interface. Thus, determining the hydration and dynamics of ions in micellar systems capable of undergoing such transitions is a crucial step in understanding shape and phase changes. For cationic micelles, such transitions are common with large organic anions as counterions. Interestingly, however, phase separation also occurs for dodecyltrimethylammonium triflate (DTATf) micelles in the presence of sodium triflate (NaTf). Specific ion effects for micellar solutions of dodecyltrimethylammonium chloride (DTAC), bromide (DTAB), methanesulfonate (DTAMs), and triflate (DTATf) were studied with dielectric relaxation spectroscopy (DRS), a technique capable of monitoring hydration and counterion dynamics of micellar aggregates. In comparison to DTAB, DTAC, and DTAMs, DTATf micelles were found to be considerably less hydrated and showed reduced counterion mobility at the micellar interface. The obtained DTATf and DTAMs data support the reported central role of the anion's -CF3 moiety with respect to the properties of DTATf micelles. The reduced hydration observed for DTATf micelles was rationalized in terms of the higher packing of this surfactant compared to that of other DTA-based systems. The decreased mobility of Tf(-) anions condensed at the DTATf interface strongly suggests the insertion of Tf(-) in the micellar interface, which is apparently driven by the strong hydrophobicity of -CF3.

On the origin of the phase-space diffusion limit in (dis)ordered protein aggregation

NASA Astrophysics Data System (ADS)

Gadomski, A.; Siódmiak, J.; Santamaría-Holek, I.

2013-08-01

Derivation of a phase-space diffusion limit (D-L) allows to obtain a useful formula for a characteristic width of the macroion-channeling filter, controlling model (dis)ordered protein aggregations in a non-ideal aqueous solution. The channel’s width is estimated at the order of an inner half-width of the Stern-type double layer circumventing the growing object and depends in turn on an interplay of the local thermal and electrostatic conditions. The interfacial channeling effect manifests at the edge of biomolecular hydration-duration dependent (non)Markovianity of the system. The interface vs. solution aggregation late-time dynamics are discussed in such local (non)isothermal context with the aim to suggest their experimental assessment.

Stability of Gas Hydrates on Continental Margins: Implications of Subsurface Fluid Flow

NASA Astrophysics Data System (ADS)

Nunn, J. A.

2008-12-01

Gas hydrates are found at or just below the sediment-ocean interface in continental margins settings throughout the world. They are also found on land in high latitude regions such as the north slope of Alaska. While gas hydrate occurrence is common, gas hydrates are stable under a fairly restricted range of temperatures and pressures. In a purely conductive thermal regime, near surface temperatures depend on basal heat flow, thermal conductivity of sediments, and temperature at the sediment-water or sediment-air interface. Thermal conductivity depends on porosity and sediment composition. Gas hydrates are most stable in areas of low heat flow and high thermal conductivity which produce low temperature gradients. Older margins with thin continental crust and coarse grained sediments would tend to be colder. Another potentially important control on subsurface temperatures is advective heat transport by recharge/discharge of groundwater. Upward fluid flow depresses temperature gradients over a purely conductive regime with the same heat flow which would make gas hydrates more stable. Downward fluid flow would have the opposite effect. However, regional scale fluid flow may substantially increase heat flow in discharge areas which would destabilize gas hydrates. For example, discharge of topographically driven groundwater along the coast in the Central North Slope of Alaska has increased surface heat flow in some areas by more than 50% over a purely conductive thermal regime. Fluid flow also alters the pressure regime which can affect gas hydrate stability. Modeling results suggest a positive feedback between gas hydrate formation/disassociation and fluid flow. Disassociation of gas hydrates or permafrost due to global warming could increase permeability. This could enhance fluid flow and associated heat transport causing a more rapid and/or more spatially extensive gas hydrate disassociation than predicted solely from conductive propagation of temporal changes in surface or water bottom temperature. Model results from both the North Slope of Alaska and the Gulf of Mexico are compared.

Communication: Charge transfer dominates over proton transfer in the reaction of nitric acid with gas-phase hydrated electrons

NASA Astrophysics Data System (ADS)

Lengyel, Jozef; Med, Jakub; Slavíček, Petr; Beyer, Martin K.

2017-09-01

The reaction of HNO3 with hydrated electrons (H2O)n- (n = 35-65) in the gas phase was studied using Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry and ab initio molecular dynamics simulations. Kinetic analysis of the experimental data shows that OH-(H2O)m is formed primarily via a reaction of the hydrated electron with HNO3 inside the cluster, while proton transfer is not observed and NO3-(H2O)m is just a secondary product. The reaction enthalpy was determined using nanocalorimetry, revealing a quite exothermic charge transfer with -241 ± 69 kJ mol-1. Ab initio molecular dynamics simulations indicate that proton transfer is an allowed reaction pathway, but the overall thermochemistry favors charge transfer.

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.

Glasslike dynamical behavior of the plastocyanin hydration water

NASA Astrophysics Data System (ADS)

Bizzarri, Anna Rita; Paciaroni, Alessandro; Cannistraro, Salvatore

2000-09-01

The dynamical behavior of water around plastocyanin has been investigated in a wide temperature range by molecular dynamics simulation. The mean square displacements of water oxygen atoms show, at long times, a tα trend for all temperatures. Below 150 K, α is constant and equal to 1; at higher temperatures it drops to a value significantly smaller than 1, and thereafter decreases with increasing temperature. The occurrence of such an anomalous diffusion matches the onset of the dynamical transition observed in the protein. The intermediate scattering function of water is characterized, at high temperature, by a stretched exponential decay evolving, at low temperature, toward a two step relaxation behavior, which becomes more evident on increasing the exchanged wave vector q. Both the mean square displacements and the intermediate scattering functions show, beyond the ballistic regime, a plateau, which progressively extends for longer times as long as the temperature is lowered, such behavior reflecting trapping of water molecules within a cage formed by the nearest neighbors. At low temperature, a low frequency broad inelastic peak is observed in the dynamical structure factor of hydration water; such an excess of vibrational modes being reminiscent of the boson peak, characteristic of disordered, amorphous systems. All these features, which are typical of complex systems, can be traced back to the glassy character of the hydration water and suggest a dynamical coupling occurring at the macromolecule-solvent interface.

Effect of clathrate hydrate formation and decomposition on NMR parameters in THF-D2O solution.

PubMed

Rousina-Webb, Alexander; Leek, Donald M; Ripmeester, John

2012-06-28

The NMR spin-lattice relaxation time (T(1)), spin-spin relaxation time (T(2)) and the diffusion coefficient D were measured for (1)H in a 1:17 mol % solution of tetrahydrofuran (THF) in D(2)O. The aim of the work was to clarify some earlier points raised regarding the utility of these measurements to convey structural information on hydrate formation and reformation. A number of irregularities in T(1) and T(2) measurements during hydrate processes reported earlier are explained in terms of the presence of interfaces and possible temperature gradients. We observe that T(1) and T(2) in solution are exactly the same before and after hydrate formation, thus confirming that the solution is isotropic. This is inconsistent with the presence of memory effects, at least those that may affect the dynamics to which T(1) and T(2) are sensitive. The measurement of the diffusion coefficient for a number of hours in the subcooled solution before nucleation proved invariant with time, again suggesting that the solution remains isotropic without affecting the guest dynamics and diffusion.

Graph-Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions.

PubMed

Han, Kyungreem; Venable, Richard M; Bryant, Anne-Marie; Legacy, Christopher J; Shen, Rong; Li, Hui; Roux, Benoît; Gericke, Arne; Pastor, Richard W

2018-02-01

All-atom molecular dynamics simulations combined with graph-theoretic analysis reveal that clustering of monomethyl phosphate dianion (MMP 2- ) is strongly influenced by the types and combinations of cations in the aqueous solution. Although Ca 2+ promotes the formation of stable and large MMP 2- clusters, K + alone does not. Nonetheless, clusters are larger and their link lifetimes are longer in mixtures of K + and Ca 2+ . This "synergistic" effect depends sensitively on the Lennard-Jones interaction parameters between Ca 2+ and the phosphorus oxygen and correlates with the hydration of the clusters. The pronounced MMP 2- clustering effect of Ca 2+ in the presence of K + is confirmed by Fourier transform infrared spectroscopy. The characterization of the cation-dependent clustering of MMP 2- provides a starting point for understanding cation-dependent clustering of phosphoinositides in cell membranes.

Offshore gas hydrate sample database with an overview and preliminary analysis

USGS Publications Warehouse

Booth, James S.; Rowe, Mary M.; Fisher, Kathleen M.

1996-01-01

Synopsis -- A database of offshore gas hydrate samples was constructed from published observations and measurements. More than 90 samples from 15 distinct regions are represented in 13 data categories. This database has permitted preliminary description of gas hydrate (chiefly methane hydrate) tendencies and associations with respect to their geological environment. Gas hydrates have been recovered from offshore sediment worldwide and from total depths (water depth plus subseabed depth) ranging from 500 m to nearly 6,000 m. Samples have come from subbottom depths ranging from 0 to 400 m. Various physiographic provinces are represented in the data set including second order landforms such as continental margins and deep-sea trenches, and third order forms such as submarine canyons, continental slopes, continental margin ridges and intraslope basins. There is a clear association between fault zones and other manifestations of local, tectonic-related processes, and hydrate-bearing sediment. Samples of gas hydrate frequently consist of individual grains or particles. These types of hydrates are often further described as inclusions or disseminated in the sediment. Moreover, hydrates occur as a cement, as nodules, or as layers (mostly laminae) or in veins. The preponderance of hydrates that could be characterized as 2- dimensional (planar) were associated with fine sediment, either as intercalated layers or in fractures. Hydrate cements were commonly associated with coarser sediment. Hydrates have been found in association with grain sizes ranging from clay through gravel. More hydrates are associated with the more abundant finer-grained sediment than with coarser sediment, and many were discovered in the presence of both fine (silt and clay) and coarse sediment. The thickness of hydrate zones (i. e., sections of hydrate-bearing sediment) varies from a few centimeters to as much as 30 m. In contrast, the thickness of layers of pure hydrate or the dimensions of individual hydrate grains were most often characterized in terms of millimeters or centimeters, although a pure hydrate layer discovered in the Middle America Trench off Guatemala was as much as 3-4-m-thick. The data suggest that grains, or thin veins or laminae of pure gas hydrate may be ubiquitous in many hydrate zones but that typically they may only comprise a minor component of the thicker zones. In more than 80 percent of the hydrate samples the methane was of biogenic origin. The methane in the remainder was either classified as (or may be at least part) thermogenic. Each site where thermogenic gas was identified is characterized by faults or other manifestions of a dynamic geological environment (e.g., diapirs, mud volcanoes, gas seeps). Every sample in the database came from within the zone of theoretical methane hydrate stability, as determined on the basis of assumed regional pressure and temperature gradients. Most show that they were situated --- expressed in terms of depth --- well above the phase boundary and about 70% of the samples were located more than 100 m above the assumed regional position of that boundary. The calculated subseabed positions of the phase boundaries and the BSRs (bottom simulating reflector) are essentially identical. This may be taken as general corroboration of the regional phase boundary calculations and the concept of the BSR. Three provocative aspects of marine gas hydrates have been disclosed by the database: gas hydrates are frequently situated at much shallower subseabed depths than the assumed contemporary position of the regional phase boundary hydrates are often found in areas typified by faults or other indicators of a dynamic geological environment zones of gas hydrate-bearing sediment tend to be tens of centimeters to tens of meters thick but the hydrate within the thicker zones tends to be only a minor constituent. Whether existing as dispersed particles, cements, or pure layers or vein

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.

Rotational dynamics of trehalose in aqueous solutions studied by depolarized light scattering

NASA Astrophysics Data System (ADS)

Gallina, M. E.; Comez, L.; Morresi, A.; Paolantoni, M.; Perticaroli, S.; Sassi, P.; Fioretto, D.

2010-06-01

High resolution depolarized light scattering spectra, extended from 0.5 to 2×104 GHz by the combined used of a dispersive and an interferometric setup, give evidence of separated solute and solvent dynamics in diluted trehalose aqueous solutions. The slow relaxation process, located in the gigahertz frequency region, is analyzed as a function of temperature and concentration and assigned to the rotational diffusion of the sugar molecule. The results are discussed in comparison with the data obtained on glucose solutions and they are used to clarify the molecular origin of some among the several relaxation processes reported in literature for oligosaccharides solutions. The concentration dependence of relaxation time and of shear viscosity are also discussed, suggesting that the main effect of carbohydrate molecules on the structural relaxation of diluted aqueous solutions is the perturbation induced on the dynamics of the first hydration shell of each solute molecule.

The conversion process of hydrocarbon hydrates into CO2 hydrates and vice versa: thermodynamic considerations.

PubMed

Schicks, J M; Luzi, M; Beeskow-Strauch, B

2011-11-24

Microscopy, confocal Raman spectroscopy and powder X-ray diffraction (PXRD) were used for in situ investigations of the CO(2)-hydrocarbon exchange process in gas hydrates and its driving forces. The study comprises the exposure of simple structure I CH(4) hydrate and mixed structure II CH(4)-C(2)H(6) and CH(4)-C(3)H(8) hydrates to gaseous CO(2) as well as the reverse reaction, i.e., the conversion of CO(2)-rich structure I hydrate into structure II mixed hydrate. In the case of CH(4)-C(3)H(8) hydrates, a conversion in the presence of gaseous CO(2) from a supposedly more stable structure II hydrate to a less stable structure I CO(2)-rich hydrate was observed. PXRD data show that the reverse process requires longer initiation times, and structural changes seem to be less complete. Generally, the exchange process can be described as a decomposition and reformation process, in terms of a rearrangement of molecules, and is primarily induced by the chemical potential gradient between hydrate phase and the provided gas phase. The results show furthermore the dependency of the conversion rate on the surface area of the hydrate phase, the thermodynamic stability of the original and resulting hydrate phase, as well as the mobility of guest molecules and formation kinetics of the resulting hydrate phase.

Fundamentals and applications of gas hydrates.

PubMed

Koh, Carolyn A; Sloan, E Dendy; Sum, Amadeu K; Wu, David T

2011-01-01

Fundamental understanding of gas hydrate formation and decomposition processes is critical in many energy and environmental areas and has special importance in flow assurance for the oil and gas industry. These areas represent the core of gas hydrate applications, which, albeit widely studied, are still developing as growing fields of research. Discovering the molecular pathways and chemical and physical concepts underlying gas hydrate formation potentially can lead us beyond flowline blockage prevention strategies toward advancing new technological solutions for fuel storage and transportation, safely producing a new energy resource from natural deposits of gas hydrates in oceanic and arctic sediments, and potentially facilitating effective desalination of seawater. The state of the art in gas hydrate research is leading us to new understanding of formation and dissociation phenomena that focuses on measurement and modeling of time-dependent properties of gas hydrates on the basis of their well-established thermodynamic properties.

Effects of ensembles on methane hydrate nucleation kinetics.

PubMed

Zhang, Zhengcai; Liu, Chan-Juan; Walsh, Matthew R; Guo, Guang-Jun

2016-06-21

By performing molecular dynamics simulations to form a hydrate with a methane nano-bubble in liquid water at 250 K and 50 MPa, we report how different ensembles, such as the NPT, NVT, and NVE ensembles, affect the nucleation kinetics of the methane hydrate. The nucleation trajectories are monitored using the face-saturated incomplete cage analysis (FSICA) and the mutually coordinated guest (MCG) order parameter (OP). The nucleation rate and the critical nucleus are obtained using the mean first-passage time (MFPT) method based on the FS cages and the MCG-1 OPs, respectively. The fitting results of MFPT show that hydrate nucleation and growth are coupled together, consistent with the cage adsorption hypothesis which emphasizes that the cage adsorption of methane is a mechanism for both hydrate nucleation and growth. For the three different ensembles, the hydrate nucleation rate is quantitatively ordered as follows: NPT > NVT > NVE, while the sequence of hydrate crystallinity is exactly reversed. However, the largest size of the critical nucleus appears in the NVT ensemble, rather than in the NVE ensemble. These results are helpful for choosing a suitable ensemble when to study hydrate formation via computer simulations, and emphasize the importance of the order degree of the critical nucleus.

Investigation of C3S hydration by environmental scanning electron microscope.

PubMed

Sakalli, Y; Trettin, R

2015-07-01

Tricalciumsilicate (C(3)S, Alite) is the major component of the Portland cement clinker, The hydration of the Alite is decisive for the properties of the resulting material due to the high content in cement. The mechanism of the hydration of C(3)S is very complicated and not yet fully understood. There are some models that describe the hydration of C(3)S in various ways. The Environmental Scanning Electron Microscopy (ESEM) working in gaseous atmosphere enables high-resolution dynamic observations of structure of materials, from micrometre to nanometre scale. This provides a new perspective in material research. ESEM significantly allows imaging of specimen in their natural state without the need for special preparation (coating, drying, etc.) that can alter the physical properties. This paper presents the results of our experimental studies of hydration of C(3)S using ESEM. The ESEM turned out to be an important extension of the conventional scanning microscopy. The purpose of these investigations is to gain insight of hydration mechanism to determine which hydration products are formed and to analyze if there are any differences in the composition of the hydration products. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Temporal Characterization of Hydrates System Dynamics beneath Seafloor Mounds. Integrating Time-Lapse Electrical Resistivity Methods and In Situ Observations of Multiple Oceanographic Parameters

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

Lutken, Carol; Macelloni, Leonardo; D'Emidio, Marco

This study was designed to investigate temporal variations in hydrate system dynamics by measuring changes in volumes of hydrate beneath hydrate-bearing mounds on the continental slope of the northern Gulf of Mexico, the landward extreme of hydrate occurrence in this region. Direct Current Resistivity (DCR) measurements were made contemporaneously with measurements of oceanographic parameters at Woolsey Mound, a carbonate-hydrate complex on the mid-continental slope, where formation and dissociation of hydrates are most vulnerable to variations in oceanographic parameters affected by climate change, and where changes in hydrate stability can readily translate to loss of seafloor stability, impacts to benthic ecosystems,more » and venting of greenhouse gases to the water-column, and eventually, the atmosphere. We focused our study on hydrate within seafloor mounds because the structurally-focused methane flux at these sites likely causes hydrate formation and dissociation processes to occur at higher rates than at sites where the methane flux is less concentrated and we wanted to maximize our chances of witnessing association/dissociation of hydrates. We selected a particularly well-studied hydrate-bearing seafloor mound near the landward extent of the hydrate stability zone, Woolsey Mound (MC118). This mid-slope site has been studied extensively and the project was able to leverage considerable resources from the team’s research experience at MC118. The site exhibits seafloor features associated with gas expulsion, hydrates have been documented at the seafloor, and changes in the outcropping hydrates have been documented, photographically, to have occurred over a period of months. We conducted observatory-based, in situ measurements to 1) characterize, geophysically, the sub-bottom distribution of hydrate and its temporal variability, and 2) contemporaneously record relevant environmental parameters (temperature, pressure, salinity, turbidity, bottom currents) to detect short-term changes within the hydrates system, identify relationships/impacts of local oceanographic parameters on the hydrates system, and improve our understanding of how seafloor instability is affected by hydrates-driven changes. A 2009 DCR survey of MC118 demonstrated that we could image resistivity anomalies to a depth of 75m below the seafloor in water depths of 1km. We reconfigured this system to operate autonomously on the seafloor in a pre-programmed mode, for periods of months. We designed and built a novel seafloor lander and deployment capability that would allow us to investigate the seafloor at potential deployment sites and deploy instruments only when conditions met our criteria. This lander held the DCR system, controlling computers, and battery power supply, as well as instruments to record oceanographic parameters. During the first of two cruises to the study site, we conducted resistivity surveying, selected a monitoring site, and deployed the instrumented lander and DCR, centered on what appeared to be the most active locations within the site, programmed to collect a DCR profile, weekly. After a 4.5-month residence on the seafloor, the team recovered all equipment. Unfortunately, several equipment failures occurred prior to recovery of the instrument packages. Prior to the failures, however, two resistivity profiles were collected together with oceanographic data. Results show, unequivocally, that significant changes can occur in both hydrate volume and distribution during time periods as brief as one week. Occurrences appear to be controlled by both deep and near-surface structure. Results have been integrated with seismic data from the area and show correspondence in space of hydrate and structures, including faults and gas chimneys.« 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.

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

Chemical imaging of molecular changes in a hydrated single cell by dynamic secondary ion mass spectrometry and super-resolution microscopy

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

Hua, Xin; Szymanski, Craig; Wang, Zhaoying

2016-01-01

Chemical imaging of single cells is important in capturing biological dynamics. Single cell correlative imaging is realized between structured illumination microscopy (SIM) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) using System for Analysis at the Liquid Vacuum Interface (SALVI), a multimodal microreactor. SIM characterized cells and guided subsequent ToF-SIMS analysis. Dynamic ToF-SIMS provided time- and space-resolved cell molecular mapping. Lipid fragments were identified in the hydrated cell membrane. Principal component analysis was used to elucidate chemical component differences among mouse lung cells that uptake zinc oxide nanoparticles. Our results provided submicron chemical spatial mapping for investigations of cell dynamics atmore » the molecular level.« less

Glacial cycles influence marine methane hydrate formation

DOE PAGES

Malinverno, A.; Cook, A. E.; Daigle, H.; ...

2018-01-12

Methane hydrates in fine-grained continental slope sediments often occupy isolated depth intervals surrounded by hydrate-free sediments. As they are not connected to deep gas sources, these hydrate deposits have been interpreted as sourced by in situ microbial methane. We investigate here the hypothesis that these isolated hydrate accumulations form preferentially in sediments deposited during Pleistocene glacial lowstands that contain relatively large amounts of labile particulate organic carbon, leading to enhanced microbial methanogenesis. To test this hypothesis, we apply an advection-diffusion-reaction model with a time-dependent organic carbon deposition controlled by glacioeustatic sea level variations. In the model, hydrate forms in sedimentsmore » with greater organic carbon content deposited during the penultimate glacial cycle (~120-240 ka). As a result, the model predictions match hydrate-bearing intervals detected in three sites drilled on the northern Gulf of Mexico continental slope, supporting the hypothesis of hydrate formation driven by enhanced organic carbon burial during glacial lowstands.« less

Glacial cycles influence marine methane hydrate formation

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

Malinverno, A.; Cook, A. E.; Daigle, H.

Methane hydrates in fine-grained continental slope sediments often occupy isolated depth intervals surrounded by hydrate-free sediments. As they are not connected to deep gas sources, these hydrate deposits have been interpreted as sourced by in situ microbial methane. We investigate here the hypothesis that these isolated hydrate accumulations form preferentially in sediments deposited during Pleistocene glacial lowstands that contain relatively large amounts of labile particulate organic carbon, leading to enhanced microbial methanogenesis. To test this hypothesis, we apply an advection-diffusion-reaction model with a time-dependent organic carbon deposition controlled by glacioeustatic sea level variations. In the model, hydrate forms in sedimentsmore » with greater organic carbon content deposited during the penultimate glacial cycle (~120-240 ka). As a result, the model predictions match hydrate-bearing intervals detected in three sites drilled on the northern Gulf of Mexico continental slope, supporting the hypothesis of hydrate formation driven by enhanced organic carbon burial during glacial lowstands.« less

RH-temperature phase diagrams of hydrate forming deliquescent crystalline ingredients.

PubMed

Allan, Matthew; Mauer, Lisa J

2017-12-01

Several common deliquescent crystalline food ingredients (including glucose and citric acid) are capable of forming crystal hydrate structures. The propensity of such crystals to hydrate/dehydrate or deliquesce is dependent on the environmental temperature and relative humidity (RH). As an anhydrous crystal converts to a crystal hydrate, water molecules internalize into the crystal structure resulting in different physical properties. Deliquescence is a solid-to-solution phase transformation. RH-temperature phase diagrams of the food ingredients alpha-d-glucose and citric acid, along with sodium sulfate, were produced using established and newly developed methods. Each phase diagram included hydrate and anhydrate deliquescence boundaries, the anhydrate-hydrate phase boundary, and the peritectic temperature (above which the hydrate was no longer stable). This is the first report of RH-temperature phase diagrams of glucose and citric acid, information which is beneficial for selecting storage and processing conditions to promote or avoid hydrate formation or loss and/or deliquescence. Copyright © 2017 Elsevier Ltd. All rights reserved.

Oxidation Dynamics of Methionine with Singlet Oxygen: Effects of Methionine Ionization and Microsolvation.

PubMed

Liu, Fangwei; Liu, Jianbo

2015-06-25

We report an in-depth study on the gas-phase reactions of singlet O2[a(1)Δg] with methionine (Met) at different ionization and hydration states (including deprotonated [Met - H](-), hydrated deprotonated [Met - H](-)(H2O)1,2, and hydrated protonated MetH(+)(H2O)1,2), using guided-ion-beam scattering mass spectrometry. The measurements include the effects of collision energy (Ecol) on reaction cross sections over a center-of-mass Ecol range from 0.05 to 1.0 eV. The aim of this study is to probe the influences of Met ionization and hydration on its oxidation mechanism and dynamics. Density functional theory calculations, Rice-Ramsperger-Kassel-Marcus modeling, and quasi-classical, direct dynamics trajectory simulations were performed to examine the properties of various complexes and transition states that might be important along reaction coordinates, probe reaction potential energy surfaces, and to establish the atomic-level mechanism for the Met oxidation process. No oxidation products were observed for the reaction of [Met - H](-) with (1)O2 due to the high-energy barriers located in the product channels for this system. However, this nonreactive property was altered by the microsolvation of [Met - H](-); as a result, hydroperoxides were captured as the oxidation products for [Met - H](-)(H2O)1,2 + (1)O2. For the reaction of MetH(+)(H2O)1,2 + (1)O2, besides formation of hydroperoxides, an H2O2 elimination channel was observed. The latter channel is similar to what was found in the reaction of dehydrated MetH(+) with (1)O2 (J. Phys. Chem. B 2011, 115, 2671). The reactions of hydrated protonated and deprotonated Met are all inhibited by Ecol, becoming negligible at Ecol ≥ 0.5 eV. The kinetic and dynamical consequences of microsolvation on Met oxidation and their biological implications are discussed.

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.

Unified Stress Tensor of the Hydration Water Layer

NASA Astrophysics Data System (ADS)

Kim, Bongsu; Kim, QHwan; Kwon, Soyoung; An, Sangmin; Lee, Kunyoung; Lee, Manhee; Jhe, Wonho

2013-12-01

We present the general stress tensor of the ubiquitous hydration water layer (HWL), based on the empirical hydration force, by combining the elasticity and hydrodynamics theories. The tapping and shear component of the tensor describe the elastic and damping properties of the HWL, respectively, in good agreement with experiments. In particular, a unified understanding of HWL dynamics provides the otherwise unavailable intrinsic parameters of the HWL, which offer additional but unexplored aspects to the supercooled liquidity of the confined HWL. Our results may allow deeper insight on systems where the HWL is critical.

Unified stress tensor of the hydration water layer.

PubMed

Kim, Bongsu; Kim, Qhwan; Kwon, Soyoung; An, Sangmin; Lee, Kunyoung; Lee, Manhee; Jhe, Wonho

2013-12-13

We present the general stress tensor of the ubiquitous hydration water layer (HWL), based on the empirical hydration force, by combining the elasticity and hydrodynamics theories. The tapping and shear component of the tensor describe the elastic and damping properties of the HWL, respectively, in good agreement with experiments. In particular, a unified understanding of HWL dynamics provides the otherwise unavailable intrinsic parameters of the HWL, which offer additional but unexplored aspects to the supercooled liquidity of the confined HWL. Our results may allow deeper insight on systems where the HWL is critical.

Numerical simulations of sand production in interbedded hydrate-bearing sediments during depressurization

USGS Publications Warehouse

Uchida, Shun; Lin, Jeen-Shang; Myshakin, Evgeniy; Seol, Yongkoo; Collett, Timothy S.; Boswell, Ray

2017-01-01

Geomechanical behavior of hydrate-bearing sediments during gas production is complex, involving changes in hydrate-dependent mechanical properties. When interbedded clay layers are present, the complexity is more pronounced because hydrate dissociation tends to occur preferentially in the sediments adjacent to the clay layers due to clay layers acting as a heat source. This would potentially lead to shearing deformation along the sand/clay contacts and may contribute to solid migration, which hindered past field-scale gas production tests. This paper presents a near-wellbore simulation of sand/clay interbedded hydrate-bearing sediments that have been subjected to depressurization and discusses the effect of clay layers on sand production.

Clathrate structure-type recognition: Application to hydrate nucleation and crystallisation

NASA Astrophysics Data System (ADS)

Lauricella, Marco; Meloni, Simone; Liang, Shuai; English, Niall J.; Kusalik, Peter G.; Ciccotti, Giovanni

2015-06-01

For clathrate-hydrate polymorphic structure-type (sI versus sII), geometric recognition criteria have been developed and validated. These are applied to the study of the rich interplay and development of both sI and sII motifs in a variety of hydrate-nucleation events for methane and H2S hydrate studied by direct and enhanced-sampling molecular dynamics (MD) simulations. In the case of nucleation of methane hydrate from enhanced-sampling simulation, we notice that already at the transition state, ˜80% of the enclathrated CH4 molecules are contained in a well-structured (sII) clathrate-like crystallite. For direct MD simulation of nucleation of H2S hydrate, some sI/sII polymorphic diversity was encountered, and it was found that a realistic dissipation of the nucleation energy (in view of non-equilibrium relaxation to either microcanonical (NVE) or isothermal-isobaric (NPT) distributions) is important to determine the relative propensity to form sI versus sII motifs.

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.

Models for Gas Hydrate-Bearing Sediments Inferred from Hydraulic Permeability and Elastic Velocities

USGS Publications Warehouse

Lee, Myung W.

2008-01-01

Elastic velocities and hydraulic permeability of gas hydrate-bearing sediments strongly depend on how gas hydrate accumulates in pore spaces and various gas hydrate accumulation models are proposed to predict physical property changes due to gas hydrate concentrations. Elastic velocities and permeability predicted from a cementation model differ noticeably from those from a pore-filling model. A nuclear magnetic resonance (NMR) log provides in-situ water-filled porosity and hydraulic permeability of gas hydrate-bearing sediments. To test the two competing models, the NMR log along with conventional logs such as velocity and resistivity logs acquired at the Mallik 5L-38 well, Mackenzie Delta, Canada, were analyzed. When the clay content is less than about 12 percent, the NMR porosity is 'accurate' and the gas hydrate concentrations from the NMR log are comparable to those estimated from an electrical resistivity log. The variation of elastic velocities and relative permeability with respect to the gas hydrate concentration indicates that the dominant effect of gas hydrate in the pore space is the pore-filling characteristic.

Relationship between the mobility of phosphocholine headgroups of liposomes and the hydrophobicity at the membrane interface: a characterization with spectrophotometric measurements.

PubMed

Shimanouchi, Toshinori; Sasaki, Masashi; Hiroiwa, Azusa; Yoshimoto, Noriko; Miyagawa, Kazuya; Umakoshi, Hiroshi; Kuboi, Ryoichi

2011-11-01

In this study, we investigated the dynamics of a membrane interface of liposomes prepared by eight zwitterionic phosphatidylcholines in terms of their headgroup mobility, with spectroscopic methods such as dielectric dispersion analysis (DDA), fluorescence spectroscopy. The DDA measurement is based on the response of the permanent dipole moment to a driving electric field and could give the information on the axial rotational Brownian motion of a headgroup with the permanent dipole moment. This motion depended on kinds of phospholipids, the diameter of the liposomes, and the temperature. The activation energy required to overcome the intermolecular force between headgroups of phospholipids depended on the strength of the interaction between headgroups such as hydrogen bonds and/or dipole-dipole interaction. Hydration at the phosphorous group of phospholipid and the molecular order of lipid membrane impaired the interaction between headgroups. Furthermore, the hydrophobicity of membrane surface increased parallel to the increase in headgroup mobility. It is, therefore, concluded that hydration of headgroup promoted its mobility to make the membrane surface hydrophobic. The lipid membrane in liquid crystalline phase or the lipid membrane with the larger curvature was more hydrophobic. Copyright © 2011 Elsevier B.V. All rights reserved.

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.

Inelastic neutron scattering and molecular simulation of the dynamics of interlayer water in smectite clay minerals

DOE PAGES

Cygan, Randall T.; Daemen, Luke L.; Ilgen, Anastasia G.; ...

2015-11-16

The study of mineral–water interfaces is of great importance to a variety of applications including oil and gas extraction, gas subsurface storage, environmental contaminant treatment, and nuclear waste repositories. Understanding the fundamentals of that interface is key to the success of those applications. Confinement of water in the interlayer of smectite clay minerals provides a unique environment to examine the interactions among water molecules, interlayer cations, and clay mineral surfaces. Smectite minerals are characterized by a relatively low layer charge that allows the clay to swell with increasing water content. Montmorillonite and beidellite varieties of smectite were investigated to comparemore » the impact of the location of layer charge on the interlayer structure and dynamics. Inelastic neutron scattering of hydrated and dehydrated cation-exchanged smectites was used to probe the dynamics of the interlayer water (200–900 cm –1 spectral region) and identify the shift in the librational edge as a function of the interlayer cation. Molecular dynamics simulations of equivalent phases and power spectra, derived from the resulting molecular trajectories, indicate a general shift in the librational behavior with interlayer cation that is generally consistent with the neutron scattering results for the monolayer hydrates. Both neutron scattering and power spectra exhibit librational structures affected by the location of layer charge and by the charge of the interlayer cation. Furthermore, divalent cations (Ba 2+ and Mg 2+) characterized by large hydration enthalpies typically exhibit multiple broad librational peaks compared to monovalent cations (Cs + and Na +), which have relatively small hydration enthalpies.« less

The Limitations of an Exclusively Colloidal View of Protein Solution Hydrodynamics and Rheology

PubMed Central

Sarangapani, Prasad S.; Hudson, Steven D.; Migler, Kalman B.; Pathak, Jai A.

2013-01-01

Proteins are complex macromolecules with dynamic conformations. They are charged like colloids, but unlike colloids, charge is heterogeneously distributed on their surfaces. Here we overturn entrenched doctrine that uncritically treats bovine serum albumin (BSA) as a colloidal hard sphere by elucidating the complex pH and surface hydration-dependence of solution viscosity. We measure the infinite shear viscosity of buffered BSA solutions in a parameter space chosen to tune competing long-range repulsions and short-range attractions (2 mg/mL ≤ [BSA] ≤ 500 mg/mL and 3.0 ≤ pH ≤ 7.4). We account for surface hydration through partial specific volume to define volume fraction and determine that the pH-dependent BSA intrinsic viscosity never equals the classical hard sphere result (2.5). We attempt to fit our data to the colloidal rheology models of Russel, Saville, and Schowalter (RSS) and Krieger-Dougherty (KD), which are each routinely and successfully applied to uniformly charged suspensions and to hard-sphere suspensions, respectively. We discover that the RSS model accurately describes our data at pH 3.0, 4.0, and 5.0, but fails at pH 6.0 and 7.4, due to steeply rising solution viscosity at high concentration. When we implement the KD model with the maximum packing volume fraction as the sole floating parameter while holding the intrinsic viscosity constant, we conclude that the model only succeeds at pH 6.0 and 7.4. These findings lead us to define a minimal framework for models of crowded protein solution viscosity wherein critical protein-specific attributes (namely, conformation, surface hydration, and surface charge distribution) are addressed. PMID:24268154

Chloral Hydrate Treatment Induced Apoptosis of Macrophages via Fas Signaling Pathway.

PubMed

Cai, Jun; Peng, Yanxia; Chen, Ting; Liao, Huanjin; Zhang, Lifang; Chen, Qiuhua; He, Yiming; Wu, Ping; Xie, Tong; Pan, Qingjun

2016-12-10

BACKGROUND There are recent reports on several anesthetics that have anti-inflammatory and anti-infective effects apart from their uses for pain relief and muscle relaxation. Chloral hydrate is a clinical anesthetic drug and sedative that has also been reported to attenuate inflammatory response, but the mechanisms are not clearly understood. MATERIAL AND METHODS This study investigated the effect of chloral hydrate treatment on the apoptosis of macrophages and explored the underlying mechanisms. RAW264.7 macrophages were treated with various concentrations of chloral hydrate for various lengths of time. Morphological changes were observed under a light microscope and apoptosis was detected with annexin-V-FITC/PI double-staining assay, Hochest 33258 and DNA ladder assay, the expression of Fas/FasL was detected with a flow cytometer, and the Fas signaling pathway was assessed by Western blotting. RESULTS The results showed that chloral hydrate treatment induced the morphology of RAW264.7 macrophages to change shape from typical fusiform to round in a concentration- and time-dependent manner, and was finally suspended in the supernatant. For the induction of apoptosis, chloral hydrate treatment induced the apoptosis of RAW264.7 macrophages from early-to-late stage apoptosis in a concentration- and time-dependent manner. For the mechanism, chloral hydrate treatment induced higher expression of Fas on RAW264.7 macrophages, and was also associated with changes in the expression of proteins involved in Fas signaling pathways. CONCLUSIONS Chloral hydrate treatment can induce the apoptosis of RAW264.7 macrophages through the Fas signaling pathway, which may provide new options for adjunctive treatment of acute inflammation.

Chloral Hydrate Treatment Induced Apoptosis of Macrophages via Fas Signaling Pathway

PubMed Central

Cai, Jun; Peng, Yanxia; Chen, Ting; Liao, Huanjin; Zhang, Lifang; Chen, Qiuhua; He, Yiming; Wu, Ping; Xie, Tong; Pan, Qingjun

2016-01-01

Background There are recent reports on several anesthetics that have anti-inflammatory and anti-infective effects apart from their uses for pain relief and muscle relaxation. Chloral hydrate is a clinical anesthetic drug and sedative that has also been reported to attenuate inflammatory response, but the mechanisms are not clearly understood. Material/Methods This study investigated the effect of chloral hydrate treatment on the apoptosis of macrophages and explored the underlying mechanisms. RAW264.7 macrophages were treated with various concentrations of chloral hydrate for various lengths of time. Morphological changes were observed under a light microscope and apoptosis was detected with annexin-V-FITC/PI double-staining assay, Hochest 33258 and DNA ladder assay, the expression of Fas/FasL was detected with a flow cytometer, and the Fas signaling pathway was assessed by Western blotting. Results The results showed that chloral hydrate treatment induced the morphology of RAW264.7 macrophages to change shape from typical fusiform to round in a concentration- and time-dependent manner, and was finally suspended in the supernatant. For the induction of apoptosis, chloral hydrate treatment induced the apoptosis of RAW264.7 macrophages from early-to-late stage apoptosis in a concentration- and time-dependent manner. For the mechanism, chloral hydrate treatment induced higher expression of Fas on RAW264.7 macrophages, and was also associated with changes in the expression of proteins involved in Fas signaling pathways. Conclusions Chloral hydrate treatment can induce the apoptosis of RAW264.7 macrophages through the Fas signaling pathway, which may provide new options for adjunctive treatment of acute inflammation. PMID:27941708

Direction-specific van der Waals attraction between rutile TiO2 nanocrystals.

PubMed

Zhang, Xin; He, Yang; Sushko, Maria L; Liu, Jia; Luo, Langli; De Yoreo, James J; Mao, Scott X; Wang, Chongmin; Rosso, Kevin M

2017-04-28

Mutual lattice orientations dictate the types and magnitudes of forces between crystalline particles. When lattice polarizability is anisotropic, the van der Waals dispersion attraction can, in principle, contribute to this direction dependence. We report measurement of this attraction between rutile nanocrystals, as a function of their mutual orientation and surface hydration extent. At tens of nanometers of separation, the attraction is weak and shows no dependence on azimuthal alignment or surface hydration. At separations of approximately one hydration layer, the attraction is strongly dependent on azimuthal alignment and systematically decreases as intervening water density increases. Measured forces closely agree with predictions from Lifshitz theory and show that dispersion forces can generate a torque between particles interacting in solution and between grains in materials. Copyright © 2017, American Association for the Advancement of Science.

Direction-specific van der Waals attraction between rutile TiO 2 nanocrystals

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

Zhang, Xin; He, Yang; Sushko, Maria L.

Mutual lattice orientations dictate the types and magnitudes of forces between crystalline particles. When lattice polarizability is anisotropic, the van der Waals dispersion attraction can, in principle, contribute to this direction dependence. Here we report direct measurement of this attraction between rutile nanocrystals, as a function of their mutual orientation and surface hydration extent. At tens of nanometers of separation the attraction is weak and shows no dependence on azimuthal alignment nor surface hydration. At separations of approximately one hydration layer the attraction is strongly dependent on azimuthal alignment, and systematically decreases as intervening water density increases. Measured forces aremore » in close agreement with predictions from Lifshitz theory, and show that dispersion forces are capable of generating a torque between particles interacting in solution and between grains in materials.« less

Equilibrium, Kinetics, and Spectroscopic Studies of SF6 Hydrate in NaCl Electrolyte Solution.

PubMed

Seo, Youngrok; Moon, Donghyun; Lee, Changho; Park, Jeong-Woo; Kim, Byeong-Soo; Lee, Gang-Woo; Dotel, Pratik; Lee, Jong-Won; Cha, Minjun; Yoon, Ji-Ho

2015-05-19

Many studies have focused on desalination via hydrate formation; however, for their potential application, knowledge pertaining to thermodynamic stability, formation kinetics, and guest occupation behavior in clathrate hydrates needs to be determined. Herein, the phase equilibria of SF6 hydrates in the presence of NaCl solutions (0, 2, 4, and 10 wt %) were monitored in the temperature range of 277-286 K and under pressures of up to 1.4 MPa. The formation kinetics of SF6 hydrates in the presence of NaCl solutions (0, 2, and 4 wt %) was also investigated. Gas consumption curves of SF6 hydrates showed that a pure SF6 hydrate system allowed fast hydrate growth as well as high conversion yield, whereas SF6 hydrate in the presence of NaCl solutions showed retarded hydrate growth rate as well as low conversion yield. In addition, structural identification of SF6 hydrates with and without NaCl solutions was performed using spectroscopic tools such as Raman spectroscopy and X-ray diffraction. The Raman spectrometer was also used to evaluate the temperature-dependent release behavior of guest molecules in SF6 and SF6 + 4 wt % NaCl hydrates. The results indicate that whereas SF6 hydrate starts to decompose at around 240 K, the escape of SF6 molecules in SF6 + 4 wt % NaCl hydrate is initiated rapidly at around 205 K. The results of this study can provide a better understanding of guest-host interaction in electrolyte-containing systems.

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.

Investigating a dynamic gas hydrate system in disequilibrium in the Danube Delta, Black Sea

NASA Astrophysics Data System (ADS)

Hillman, Jess; Bialas, Joerg; Klaucke, Ingo; Feldman, Howard; Drexler, Tina

2017-04-01

Gas hydrates are known to be extensive across the Danube Delta, as indicated by the presence of bottom simulating reflections (BSRs). The shelf break in this region is characterised by several incised submarine canyons, the largest of which is the Viteaz Canyon, and numerous slope failures. BSRs often coincide with submarine landslides, and it has been proposed that hydrates may play a role in triggering, or facilitating such events. This study focuses on a seafloor canyon (the S2 Canyon) to the north-east of the main Viteaz Canyon, where geophysical survey data and sediment cores were acquired in 2014. Active venting from the seafloor is known to be occurring at this site as multiple flares were been imaged in the water column. The location of these flares coincides with a significant slope failure adjacent to the canyon, and some can be correlated to subsurface gas chimneys, indicating a complex 'plumbing system' of gas migration pathways. This site is of particular interest as the 'present-day' BSR imaged in seismic data is not at equilibrium with the present-day seafloor conditions. Using high resolution 2D seismic data, a P-cable 3D seismic volume and ocean bottom seismometer data we investigate potential gas migration pathways and the complex gas hydrate system in the vicinity of the S2 Canyon. In addition, we use stratigraphic interpretation based on regional 2D seismic lines to constrain the relative ages of the channel levee systems. Through detailed mapping of the BSR, possible paleo-seafloor surfaces and gas migration features we are able to provide estimates of equilibrium conditions for the hydrate system, and examine the controlling factors affecting gas migration pathways and hydrate formation. The results of this study provide new insight into a geologically complex setting with a dynamic hydrate system. Characterising the hydrate system here may help to explain why it is in disequilibrium with the present day seafloor, and provide a better understanding of any potential implications for slope stability in the future as the hydrate system moves towards equilibrium.

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).

Computational study of the interplay between intermolecular interactions and CO2 orientations in type I hydrates.

PubMed

Pérez-Rodríguez, M; Vidal-Vidal, A; Míguez, J M; Blas, F J; Torré, J-P; Piñeiro, M M

2017-01-25

Carbon dioxide (CO 2 ) molecules show a rich orientation landscape when they are enclathrated in type I hydrates. Previous studies have described experimentally their preferential orientations, and some theoretical works have explained, but only partially, these experimental results. In the present paper, we use classical molecular dynamics and electronic density functional theory to advance in the theoretical description of CO 2 orientations within type I hydrates. Our results are fully compatible with those previously reported, both theoretical and experimental, the geometric shape of the cavities in hydrate being, and therefore, the steric constraints, responsible for some (but not all) preferential angles. In addition, our calculations also show that guest-guest interactions in neighbouring cages are a key factor to explain the remaining experimental angles. Besides the implication concerning equation of state hydrate modeling approximations, the conclusion is that these guest-guest interactions should not be neglected, contrary to the usual practice.

Ab initio electron correlated studies on the intracluster reaction of NO+ (H2O)(n) → H3O+ (H2O)(n-2) (HONO) (n = 4 and 5).

PubMed

Asada, Toshio; Nagaoka, Masataka; Koseki, Shiro

2011-01-28

Hydrated nitrosonium ion clusters NO(+)(H(2)O)(n) (n = 4 and 5) were investigated by using MP2/aug-cc-pVTZ level of theory to clarify isomeric reaction pathways for formation of HONO and fully hydrated hydride ions. We found some new isomers and transition state structures in each hydration number, whose lowest activation energies of the intracluster reactions were found to be 4.1 and 3.4 kcal mol(-1) for n = 4 and n = 5, respectively. These thermodynamic properties and full quantum mechanical molecular dynamics simulation suggest that product isomers with HONO and fully hydrated hydride ions can be obtained at n = 4 and n = 5 in terms of excess hydration binding energies which can overcome these activation barriers.

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).

Dynamics of Hydrophobic Core Phenylalanine Residues Probed by Solid-State Deuteron NMR

PubMed Central

Vugmeyster, Liliya; Ostrovsky, Dmitry; Villafranca, Toni; Sharp, Janelle; Xu, Wei; Lipton, Andrew S.; Hoatson, Gina L.; Vold, Robert L.

2016-01-01

We conducted a detailed investigation of the dynamics of two phenylalanine side chains in the hydrophobic core of the villin headpiece subdomain protein (HP36) in the hydrated powder state over the 298–80 K temperature range. Our main tools were static deuteron NMR measurements of longitudinal relaxation and line shapes supplemented with computational modeling. The temperature dependence of the relaxation times reveals the presence of two main mechanisms that can be attributed to the ring-flips, dominating at high temperatures, and small-angle fluctuations, dominating at low temperatures. The relaxation is non-exponential at all temperatures with the extent of non-exponentiality increasing from higher to lower temperatures. This behavior suggests a distribution of conformers with unique values of activation energies. The central values of the activation energies for the ring-flipping motions are among the smallest reported for aromatic residues in peptides and proteins and point to a very mobile hydrophobic core. The analysis of the widths of the distributions, in combination with the earlier results on the dynamics of flanking methyl groups (Vugmeyster et al., J. Phys. Chem. B 2013, 117, 6129–6137), suggests that the hydrophobic core undergoes slow concerted fluctuations. There is a pronounced effect of dehydration on the ring-flipping motions, which shifts the distribution toward more rigid conformers. The cross-over temperature between the regions of dominance of the small-angle fluctuations and ring-flips shifts from 195 K in the hydrated protein to 278 K in the dry one. This result points to the role of solvent in softening the core and highlights aromatic residues as markers of the protein dynamical transitions. PMID:26529128

Dynamics of Hydrophobic Core Phenylalanine Residues Probed by Solid-State Deuteron NMR

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

Vugmeyster, Liliya; Ostrovsky, Dmitry; Villafranca, Toni

We conducted a detailed investigation of the dynamics of two phenylalanine side chains in the hydrophobic core of the villin headpiece subdomain protein (HP36) in the hydrated powder state over the 298–80 K temperature range. We utilized static deuteron NMR measurements of longitudinal relaxation and line shapes supplemented with computational modeling. The temperature dependence of the relaxation times reveals the presence of two main mechanisms that can be attributed to the ring-flips, dominating at high temperatures, and small-angle fluctuations, dominating at low temperatures. The relaxation is non- exponential at all temperatures with the extent of non-exponentiality increasing from higher tomore » lower temperatures. This behavior suggests a distribution of conformers with unique values of activation energies. The central values of the activation energies for the ring-flipping motions are among the smallest reported for aromatic residues in peptides and proteins and point to a very mobile hydrophobic core. The analysis of the widths of the distributions, in combination with the earlier results on the dynamics of flanking methyl groups (Vugmeyster et al., J. Phys. Chem. 2013, 117, 6129–6137), suggests that the hydrophobic core undergoes concerted fluctuations. There is a pronounced effect of dehydration on the ring-flipping motions, which shifts the distribution toward more rigid conformers. The cross-over temperature between the regions of dominance of the small-angle fluctuations and ring-flips shifts from 195 K in the hydrated protein to 278 K in the dry one. This result points to the role of solvent in the onset of the concerted fluctuations of the core and highlights aromatic residues as markers of the protein dynamical transitions.« less

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.

Reservoir Models for Gas Hydrate Numerical Simulation

NASA Astrophysics Data System (ADS)

Boswell, R.

2016-12-01

Scientific and industrial drilling programs have now providing detailed information on gas hydrate systems that will increasingly be the subject of field experiments. The need to carefully plan these programs requires reliable prediction of reservoir response to hydrate dissociation. Currently, a major emphasis in gas hydrate modeling is the integration of thermodynamic/hydrologic phenomena with geomechanical response for both reservoir and bounding strata. However, also critical to the ultimate success of these efforts is the appropriate development of input geologic models, including several emerging issues, including (1) reservoir heterogeneity, (2) understanding of the initial petrophysical characteristics of the system (reservoirs and seals), the dynamic evolution of those characteristics during active dissociation, and the interdependency of petrophysical parameters and (3) the nature of reservoir boundaries. Heterogeneity is ubiquitous aspect of every natural reservoir, and appropriate characterization is vital. However, heterogeneity is not random. Vertical variation can be evaluated with core and well log data; however, core data often are challenged by incomplete recovery. Well logs also provide interpretation challenges, particularly where reservoirs are thinly-bedded due to limitation in vertical resolution. This imprecision will extend to any petrophysical measurements that are derived from evaluation of log data. Extrapolation of log data laterally is also complex, and should be supported by geologic mapping. Key petrophysical parameters include porosity, permeability and it many aspects, and water saturation. Field data collected to date suggest that the degree of hydrate saturation is strongly controlled by/dependant upon reservoir quality and that the ratio of free to bound water in the remaining pore space is likely also controlled by reservoir quality. Further, those parameters will also evolve during dissociation, and not necessary in a simple/linear way. Significant progress has also occurred in recent years with regard to the geologic characterization of reservoir boundaries. Vertical boundaries with overlying clay-rich "seals" are now widely-appreciated to have non-zero permeability, and lateral boundaries are sources of potential lateral fluid flow.

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.

Gradual Crossover from Subdiffusion to Normal Diffusion: A Many-Body Effect in Protein Surface Water

NASA Astrophysics Data System (ADS)

Tan, Pan; Liang, Yihao; Xu, Qin; Mamontov, Eugene; Li, Jinglai; Xing, Xiangjun; Hong, Liang

2018-06-01

Dynamics of hydration water is essential for the function of biomacromolecules. Previous studies have demonstrated that water molecules exhibit subdiffusion on the surface of biomacromolecules; yet the microscopic mechanism remains vague. Here, by performing neutron scattering, molecular dynamics simulations, and analytic modeling on hydrated perdeuterated protein powders, we found water molecules jump randomly between trapping sites on protein surfaces, whose waiting times obey a broad distribution, resulting in subdiffusion. Moreover, the subdiffusive exponent gradually increases with observation time towards normal diffusion due to a many-body volume-exclusion effect.

Mass fractionation of noble gases in synthetic methane hydrate: Implications for naturally occurring gas hydrate dissociation

USGS Publications Warehouse

Hunt, Andrew G.; Stern, Laura; Pohlman, John W.; Ruppel, Carolyn; Moscati, Richard J.; Landis, Gary P.

2013-01-01

As a consequence of contemporary or longer term (since 15 ka) climate warming, gas hydrates in some settings may presently be dissociating and releasing methane and other gases to the ocean-atmosphere system. A key challenge in assessing the impact of dissociating gas hydrates on global atmospheric methane is the lack of a technique able to distinguish between methane recently released from gas hydrates and methane emitted from leaky thermogenic reservoirs, shallow sediments (some newly thawed), coal beds, and other sources. Carbon and deuterium stable isotopic fractionation during methane formation provides a first-order constraint on the processes (microbial or thermogenic) of methane generation. However, because gas hydrate formation and dissociation do not cause significant isotopic fractionation, a stable isotope-based hydrate-source determination is not possible. Here, we investigate patterns of mass-dependent noble gas fractionation within the gas hydrate lattice to fingerprint methane released from gas hydrates. Starting with synthetic gas hydrate formed under laboratory conditions, we document complex noble gas fractionation patterns in the gases liberated during dissociation and explore the effects of aging and storage (e.g., in liquid nitrogen), as well as sampling and preservation procedures. The laboratory results confirm a unique noble gas fractionation pattern for gas hydrates, one that shows promise in evaluating modern natural gas seeps for a signature associated with gas hydrate dissociation.

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.

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.

Alchemical prediction of hydration free energies for SAMPL

PubMed Central

Mobley, David L.; Liu, Shaui; Cerutti, David S.; Swope, William C.; Rice, Julia E.

2013-01-01

Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report results of alchemical hydration free energy calculations for the set of small molecules comprising the 2011 Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenge. Our calculations are largely based on the Generalized Amber Force Field (GAFF) with several different charge models, and we achieved RMS errors in the 1.4-2.2 kcal/mol range depending on charge model, marginally higher than what we typically observed in previous studies1-5. The test set consists of ethane, biphenyl, and a dibenzyl dioxin, as well as a series of chlorinated derivatives of each. We found that, for this set, using high-quality partial charges from MP2/cc-PVTZ SCRF RESP fits provided marginally improved agreement with experiment over using AM1-BCC partial charges as we have more typically done, in keeping with our recent findings5. Switching to OPLS Lennard-Jones parameters with AM1-BCC charges also improves agreement with experiment. We also find a number of chemical trends within each molecular series which we can explain, but there are also some surprises, including some that are captured by the calculations and some that are not. PMID:22198475

Evaporative concentration of skimmed milk: effect on casein micelle hydration, composition, and size.

PubMed

Liu, Dylan Z; Dunstan, David E; Martin, Gregory J O

2012-10-01

Understanding the effect of evaporative concentration on casein micelle composition is of high importance for milk processing. Alterations to the hydration, composition and size of casein micelles were investigated in skimmed milk evaporated to concentrations of 12-45% total solids content. The size of casein micelles was determined by dynamic light scattering, and the water content and composition determined by analysis of supernatants and pellets obtained by ultracentrifugation. The mass balance and hydration results showed that during the evaporation process, while micelles were dehydrated, water was removed preferentially from the serum. The amount of soluble casein and calcium in the serum decreased as a function of increasing solids content, indicating a shift of these components to the micelles. The formation of a small proportion of micelle aggregates at high concentrations appeared dependent on the time kept at these concentrations. Upon redilution with water, casein micelles were immediately rehydrated and aggregates were broken up in a matter of minutes. Soluble calcium and pH returned to their original state over a number of hours; however, only a small percentage of original soluble casein returned to the serum over the 5h period investigated. These results showed that casein micelles are significantly affected by evaporative concentration and that the alterations are not completely and rapidly reversible. Copyright © 2012. Published by Elsevier Ltd.

Microscopic mechanism of protein cryopreservation in an aqueous solution with trehalose

PubMed Central

Corradini, Dario; Strekalova, Elena G.; Stanley, H. Eugene; Gallo, Paola

2013-01-01

In order to investigate the cryoprotective mechanism of trehalose on proteins, we use molecular dynamics computer simulations to study the microscopic dynamics of water upon cooling in an aqueous solution of lysozyme and trehalose. We find that the presence of trehalose causes global retardation of the dynamics of water. Comparing aqueous solutions of lysozyme with/without trehalose, we observe that the dynamics of water in the hydration layers close to the protein is dramatically slower when trehalose is present in the system. We also analyze the structure of water and trehalose around the lysozyme and find that the trehalose molecules form a cage surrounding the protein that contains very slow water molecules. We conclude that the transient cage of trehalose molecules that entraps and slows the water molecules prevents the crystallisation of protein hydration water upon cooling. PMID:23390573

Microscopic mechanism of protein cryopreservation in an aqueous solution with trehalose.

PubMed

Corradini, Dario; Strekalova, Elena G; Stanley, H Eugene; Gallo, Paola

2013-01-01

In order to investigate the cryoprotective mechanism of trehalose on proteins, we use molecular dynamics computer simulations to study the microscopic dynamics of water upon cooling in an aqueous solution of lysozyme and trehalose. We find that the presence of trehalose causes global retardation of the dynamics of water. Comparing aqueous solutions of lysozyme with/without trehalose, we observe that the dynamics of water in the hydration layers close to the protein is dramatically slower when trehalose is present in the system. We also analyze the structure of water and trehalose around the lysozyme and find that the trehalose molecules form a cage surrounding the protein that contains very slow water molecules. We conclude that the transient cage of trehalose molecules that entraps and slows the water molecules prevents the crystallisation of protein hydration water upon cooling.

Observation of Water-Protein Interaction Dynamics with Broadband Two-Dimensional Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

De Marco, Luigi; Haky, Andrew; Tokmakoff, Andrei

Two-dimensional infrared (2D IR) spectroscopy has proven itself an indispensable tool for studying molecular dynamics and intermolecular interactions on ultrafast timescales. Using a novel source of broadband mid-IR pulses, we have collected 2D IR spectra of protein films at varying levels of hydration. With 2D IR, we can directly observe coupling between water's motions and the protein's. Protein films provide us with the ability to discriminate hydration waters from bulk water and thus give us access to studying water dynamics along the protein backbone, fluctuations in the protein structure, and the interplay between the molecular dynamics of the two. We present two representative protein films: poly-L-proline (PLP) and hen egg-white lysozyme (HEWL). Having no N-H groups, PLP allows us to look at water dynamics without interference from resonant energy transfer between the protein N-H stretch and the water O-H stretch. We conclude that at low hydration levels water-protein interactions dominate, and the water's dynamics are tied to those of the protein. In HEWL films, we take advantage of the robust secondary structure to partially deuterate the film, allowing us to spectrally distinguish the protein core from the exterior. From this, we show that resonant energy transfer to water provides an effective means of dissipating excess energy within the protein, while maintaining the structure. These methods are general and can easily be extended to studying specific protein-water interactions.

Pre-conditioned place preference treatment of chloral hydrate interrupts the rewarding effect of morphine.

PubMed

Sun, YongMei; Zong, Wei; Zhou, MuRu; Ma, YuanYe; Wang, JianHong

2015-08-01

The medical use of morphine as a pain killer is hindered by its side effects including dependence and further addiction. As the prototypical μ receptor agonist, morphine's rewarding effect can be measured by conditioned place preference (CPP) paradigms in animals. Chloral hydrate is a clinical sedative. Using a morphine CPP paradigm that mainly contains somatosensory cues, we found that pre-CPP treatment in rats using chloral hydrate for 6 consecutive days could disrupt the establishment of CPP in a U shape. Chloral hydrate had no effect on the body weight of rats. Our results indicate that prior treatment with chloral hydrate can interrupt the rewarding effect of morphine. Copyright © 2015 Elsevier Inc. All rights reserved.

Frequency Dependent Non- Thermal Effects of Oscillating Electric Fields in the Microwave Region on the Properties of a Solvated Lysozyme System: A Molecular Dynamics Study

PubMed Central

Floros, Stelios; Liakopoulou-Kyriakides, Maria; Karatasos, Kostas

2017-01-01

The use of microwaves in every day’s applications raises issues regarding the non thermal biological effects of microwaves. In this work we employ molecular dynamics simulations to advance further the dielectric studies of protein solutions in the case of lysozyme, taking into consideration possible frequency dependent changes in the structural and dynamic properties of the system upon application of electric field in the microwave region. The obtained dielectric spectra are identical with those derived in our previous work using the Fröhlich-Kirkwood approach in the framework of the linear response theory. Noticeable structural changes in the protein have been observed only at frequencies near its absorption maximum. Concerning Cα position fluctuations, different frequencies affected different regions of the protein sequence. Furthermore, the influence of the field on the kinetics of protein-water as well as on the water-water hydrogen bonds in the first hydration shell has been studied; an extension of the Luzar-Chandler kinetic model was deemed necessary for a better fit of the applied field results and for the estimation of more accurate hydrogen bond lifetime values. PMID:28129348

Structure and dynamics of water in nonionic reverse micelles: a combined time-resolved infrared and small angle x-ray scattering study.

PubMed

van der Loop, Tibert H; Panman, Matthijs R; Lotze, Stephan; Zhang, Jing; Vad, Thomas; Bakker, Huib J; Sager, Wiebke F C; Woutersen, Sander

2012-07-28

We study the structure and reorientation dynamics of nanometer-sized water droplets inside nonionic reverse micelles (water/Igepal-CO-520/cyclohexane) with time-resolved mid-infrared pump-probe spectroscopy and small angle x-ray scattering. In the time-resolved experiments, we probe the vibrational and orientational dynamics of the O-D bonds of dilute HDO:H(2)O mixtures in Igepal reverse micelles as a function of temperature and micelle size. We find that even small micelles contain a large fraction of water that reorients at the same rate as water in the bulk, which indicates that the polyethylene oxide chains of the surfactant do not penetrate into the water volume. We also observe that the confinement affects the reorientation dynamics of only the first hydration layer. From the temperature dependent surface-water dynamics, we estimate an activation enthalpy for reorientation of 45 ± 9 kJ mol(-1) (11 ± 2 kcal mol(-1)), which is close to the activation energy of the reorientation of water molecules in ice.

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.

Molecular Dynamics Simulations of Hydration Effects on Solvation, Diffusivity, and Permeability in Chitosan/Chitin Films.

PubMed

McDonnell, Marshall T; Greeley, Duncan A; Kit, Kevin M; Keffer, David J

2016-09-01

The effects of hydration on the solvation, diffusivity, solubility, and permeability of oxygen molecules in sustainable, biodegradable chitosan/chitin food packaging films were studied via molecular dynamics and confined random walk simulations. With increasing hydration, the membrane has a more homogeneous water distribution with the polymer chains being fully solvated. The diffusivity increased by a factor of 4 for oxygen molecules and by an order of magnitude for water with increasing the humidity. To calculate the Henry's constant and solubility of oxygen in the membranes with changing hydration, the excess chemical potential was calculated via free energy perturbation, thermodynamic integration and direct particle deletion methods. The simulations predicted a higher solubility and permeability for the lower humidity, in contradiction to experimental results. All three methods for calculating the solubility were in good agreement. It was found that the Coulombic interactions in the potential caused the oxygen to bind too strongly to the protonated amine group. Insight from this work will help guide molecular modeling of chitosan/chitin membranes, specifically permeability measurements for small solute molecules. Efforts to chemically tailor chitosan/chitin membranes to favor discrete as opposed to continuous aqueous domains could reduce oxygen permeability.

Elastic-wave velocity in marine sediments with gas hydrates: Effective medium modeling

USGS Publications Warehouse

Helgerud, M.B.; Dvorkin, J.; Nur, A.; Sakai, A.; Collett, T.

1999-01-01

We offer a first-principle-based effective medium model for elastic-wave velocity in unconsolidated, high porosity, ocean bottom sediments containing gas hydrate. The dry sediment frame elastic constants depend on porosity, elastic moduli of the solid phase, and effective pressure. Elastic moduli of saturated sediment are calculated from those of the dry frame using Gassmann's equation. To model the effect of gas hydrate on sediment elastic moduli we use two separate assumptions: (a) hydrate modifies the pore fluid elastic properties without affecting the frame; (b) hydrate becomes a component of the solid phase, modifying the elasticity of the frame. The goal of the modeling is to predict the amount of hydrate in sediments from sonic or seismic velocity data. We apply the model to sonic and VSP data from ODP Hole 995 and obtain hydrate concentration estimates from assumption (b) consistent with estimates obtained from resistivity, chlorinity and evolved gas data. Copyright 1999 by the American Geophysical Union.

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.

Atomic Resolution of Calcium and Oxygen Sublattices of Calcite in Ambient Conditions by Atomic Force Microscopy Using qPlus Sensors with Sapphire Tips.

PubMed

Wastl, Daniel S; Judmann, Michael; Weymouth, Alfred J; Giessibl, Franz J

2015-01-01

Characterization and imaging at the atomic scale with atomic force microscopy in biocompatible environments is an ongoing challenge. We demonstrate atomically resolved imaging of the calcite (101̅4) surface plane using stiff quartz cantilevers ("qPlus sensors", stiffness k = 1280 N/m) equipped with sapphire tips in ambient conditions without any surface preparation. With 10 atoms in one surface unit cell, calcite has a highly complex surface structure comprising three different chemical elements (Ca, C, and O). We obtain true atomic resolution of calcite in air at relative humidity ranging from 20% to 40%, imaging atomic steps and single atomic defects. We observe a great durability of sapphire tips with their Mohs hardness of 9, only one step below diamond. Depending on the state of the sapphire tip, we resolve either the calcium or the oxygen sublattice. We determine the tip termination by comparing the experimental images with simulations and discuss the possibility of chemical tip identification in air. The main challenges for imaging arise from the presence of water layers, which form on almost all surfaces and have the potential to dissolve the crystal surface. Frequency shift versus distance spectra show the presence of at least three ordered hydration layers. The measured height of the first hydration layer corresponds well to X-ray diffraction data and molecular dynamic simulations, namely, ∼220 pm. For the following hydration layers we measure ∼380 pm for the second and third layer, ending up in a total hydration layer thickness of at least 1 nm. Understanding the influence of water layers and their structure is important for surface segregation, surface reactions including reconstructions, healing of defects, and corrosion.

Physical properties and rock physics models of sediment containing natural and laboratory-formed methane gas hydrate

USGS Publications Warehouse

Winters, W.J.; Pecher, I.A.; Waite, W.F.; Mason, D.H.

2004-01-01

This paper presents results of shear strength and acoustic velocity (p-wave) measurements performed on: (1) samples containing natural gas hydrate from the Mallik 2L-38 well, Mackenzie Delta, Northwest Territories; (2) reconstituted Ottawa sand samples containing methane gas hydrate formed in the laboratory; and (3) ice-bearing sands. These measurements show that hydrate increases shear strength and p-wave velocity in natural and reconstituted samples. The proportion of this increase depends on (1) the amount and distribution of hydrate present, (2) differences, in sediment properties, and (3) differences in test conditions. Stress-strain curves from the Mallik samples suggest that natural gas hydrate does not cement sediment grains. However, stress-strain curves from the Ottawa sand (containing laboratory-formed gas hydrate) do imply cementation is present. Acoustically, rock physics modeling shows that gas hydrate does not cement grains of natural Mackenzie Delta sediment. Natural gas hydrates are best modeled as part of the sediment frame. This finding is in contrast with direct observations and results of Ottawa sand containing laboratory-formed hydrate, which was found to cement grains (Waite et al. 2004). It therefore appears that the microscopic distribution of gas hydrates in sediment, and hence the effect of gas hydrate on sediment physical properties, differs between natural deposits and laboratory-formed samples. This difference may possibly be caused by the location of water molecules that are available to form hydrate. Models that use laboratory-derived properties to predict behavior of natural gas hydrate must account for these differences.

Solute rotational dynamics at the water liquid/vapor interface.

PubMed

Benjamin, Ilan

2007-11-28

The rotational dynamics of a number of diatomic molecules adsorbed at different locations at the interface between water and its own vapors are studied using classical molecular dynamics computer simulations. Both equilibrium orientational and energy correlations and nonequilibrium orientational and energy relaxation correlations are calculated. By varying the dipole moment of the molecule and its location, and by comparing the results with those in bulk water, the effects of dielectric and mechanical frictions on reorientation dynamics and on rotational energy relaxation can be studied. It is shown that for nonpolar and weekly polar solutes, the equilibrium orientational relaxation is much slower in the bulk than at the interface. As the solute becomes more polar, the rotation slows down and the surface and bulk dynamics become similar. The energy relaxation (both equilibrium and nonequilibrium) has the opposite trend with the solute dipole (larger dipoles relax faster), but here again the bulk and surface results converge as the solute dipole is increased. It is shown that these behaviors correlate with the peak value of the solvent-solute radial distribution function, which demonstrates the importance of the first hydration shell structure in determining the rotational dynamics and dependence of these dynamics on the solute dipole and location.

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

Diallo, S. O.; Zhang, Q.; O'Neill, H.

Here we present a pressure-dependence study of the dynamics of lysozyme protein powder immersed in deuterated , α-trehalose environment via quasielastic neutron scattering (QENS). The goal is to assess the baroprotective benefits of trehalose on biomolecules by comparing the findings with those of a trehalose-free reference study. While the mean-square displacement of the trehalose-free protein (hydrated to d D₂O ≃40 w%) as a whole, is reduced by increasing pressure, the actual observable relaxation dynamics in the picoseconds to nanoseconds time range remains largely unaffected by pressure up to the maximum investigated pressure of 2.78(2) Kbar. Our observation is independent ofmore » whether or not the protein is mixed with the deuterated sugar. This suggests that the hydrated protein s conformational states at atmospheric pressure remain unaltered by hydrostatic pressures, below 2.78 Kbar. We also found the QENS response to be totally recoverable after ambient pressure conditions are restored. Small-angle neutron diffraction measurements confirm that the protein-protein correlation remains undisturbed.We observe, however, a clear narrowing of the QENS response as the temperature is decreased from 290 to 230 K in both cases, which we parametrize using the Kohlrausch-Williams-Watts stretched exponential model. Finally, only the fraction of protons that are immobile on the accessible time window of the instrument, referred to as the elastic incoherent structure factor, is observably sensitive to pressure, increasing only marginally but systematically with increasing pressure.« less

Ammonia clathrate hydrates as new solid phases for Titan, Enceladus, and other planetary systems.

PubMed

Shin, Kyuchul; Kumar, Rajnish; Udachin, Konstantin A; Alavi, Saman; Ripmeester, John A

2012-09-11

There is interest in the role of ammonia on Saturn's moons Titan and Enceladus as the presence of water, methane, and ammonia under temperature and pressure conditions of the surface and interior make these moons rich environments for the study of phases formed by these materials. Ammonia is known to form solid hemi-, mono-, and dihydrate crystal phases under conditions consistent with the surface of Titan and Enceladus, but has also been assigned a role as water-ice antifreeze and methane hydrate inhibitor which is thought to contribute to the outgassing of methane clathrate hydrates into these moons' atmospheres. Here we show, through direct synthesis from solution and vapor deposition experiments under conditions consistent with extraterrestrial planetary atmospheres, that ammonia forms clathrate hydrates and participates synergistically in clathrate hydrate formation in the presence of methane gas at low temperatures. The binary structure II tetrahydrofuran + ammonia, structure I ammonia, and binary structure I ammonia + methane clathrate hydrate phases synthesized have been characterized by X-ray diffraction, molecular dynamics simulation, and Raman spectroscopy methods.

Formation of methane nano-bubbles during hydrate decomposition and their effect on hydrate growth.

PubMed

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

2015-06-07

Molecular dynamic simulations are performed to study the conditions for methane nano-bubble formation during methane hydrate dissociation in the presence of water and a methane gas reservoir. Hydrate dissociation leads to the quick release of methane into the liquid phase which can cause methane supersaturation. If the diffusion of methane molecules out of the liquid phase is not fast enough, the methane molecules agglomerate and form bubbles. Under the conditions of our simulations, the methane-rich quasi-spherical bubbles grow to become cylindrical with a radius of ∼11 Å. The nano-bubbles remain stable for about 35 ns until they are gradually and homogeneously dispersed in the liquid phase and finally enter the gas phase reservoirs initially set up in the simulation box. We determined that the minimum mole fraction for the dissolved methane in water to form nano-bubbles is 0.044, corresponding to about 30% of hydrate phase composition (0.148). The importance of nano-bubble formation to the mechanism of methane hydrate formation, growth, and dissociation is discussed.

Ammonia clathrate hydrates as new solid phases for Titan, Enceladus, and other planetary systems

PubMed Central

Shin, Kyuchul; Kumar, Rajnish; Udachin, Konstantin A.; Alavi, Saman; Ripmeester, John A.

2012-01-01

There is interest in the role of ammonia on Saturn’s moons Titan and Enceladus as the presence of water, methane, and ammonia under temperature and pressure conditions of the surface and interior make these moons rich environments for the study of phases formed by these materials. Ammonia is known to form solid hemi-, mono-, and dihydrate crystal phases under conditions consistent with the surface of Titan and Enceladus, but has also been assigned a role as water-ice antifreeze and methane hydrate inhibitor which is thought to contribute to the outgassing of methane clathrate hydrates into these moons’ atmospheres. Here we show, through direct synthesis from solution and vapor deposition experiments under conditions consistent with extraterrestrial planetary atmospheres, that ammonia forms clathrate hydrates and participates synergistically in clathrate hydrate formation in the presence of methane gas at low temperatures. The binary structure II tetrahydrofuran + ammonia, structure I ammonia, and binary structure I ammonia + methane clathrate hydrate phases synthesized have been characterized by X-ray diffraction, molecular dynamics simulation, and Raman spectroscopy methods. PMID:22908239

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.

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

[Cevimeline hydrochloride hydrate (Saligren capsule 30 mg): a review of its pharmacological profiles and clinical potential in xerostomia].

PubMed

Shiozawa, Akira

2002-10-01

Cevimeline hydrochloride hydrate is a muscarinic receptor agonist with a chemical structure of a quinuclidine. Intraduodenal administration of cevimeline hydrochloride hydrate dose-dependently increased salivary secretion in normal mice and rats, two strains of autoimmune disease mice, and X-irradiated rats. The clinical efficacy of the cevimeline hydrochlide hydrate at 30 mg t.i.d. during 4 weeks has been demonstrated in double blind comparative study with placebo. In addition, its treatments in 52 weeks have increased salivary flow and improved subjective and objective symptoms of patients with xerostomia in Sjögren's syndrome.

Effect of the crystal chemistry on the hydration mechanism of swelling micas

NASA Astrophysics Data System (ADS)

Pavón, Esperanza; Alba, María D.; Castro, Miguel A.; Cota, A.; Osuna, Francisco J.; Pazos, M. Carolina

2017-11-01

Swelling and dehydration under minor changes in temperature and water vapor pressure is an important property that clays and clay minerals exhibit. In particular, their interlayer space, the solid-water interface and the layers' collapse and re-expansion have received much attention because it affects to the dynamical properties of interlayer cations and thus the transfer and fate of water and pollutants. In this contribution, the dehydration and rehydration mechanism of a swelling high-charge mica family is examined by in situ X-ray Diffraction. The effect of the aluminosilicate layer charge and the physicochemical properties of the interlayer cations on these processes are analyzed. The results showed that the dehydration temperature and the number of steps involved in this process are related to the layer charge of the silicate and the physicochemical properties of the interlayer cations. Moreover, the ability to adsorb water molecules in a confined space with high electric field by the interlayer cations does not only depend on their hydration enthalpy but also on the electrostatic parameters of these cations.

Molecular dynamics simulations of poly (ethylene oxide) hydration and conformation in solutions

NASA Astrophysics Data System (ADS)

Dahal, Udaya; Dormidontova, Elena

Polyethylene oxide (PEO) is one of the most actively used polymers, especially in biomedical applications due to its high hydrophilicity, biocompatibility and potency to inhibit protein adsorption. PEO solubility and conformation in water depends on its capability to form hydrogen bonds. Using atomistic molecular dynamics simulations we investigated the details of water packing around PEO chain and characterized the type and lifetime of hydrogen bonds in aqueous and mixed solvent solutions. The observed polymer chain conformation varies from an extended coil in pure water to collapsed globule in hexane and a helical-like conformation in pure isobutyric acid or isobutyric acid -water mixture in agreement with experimental observations. We'll discuss the implications of protic solvent arrangement and stability of hydrogen bonds on PEO chain conformation and mobility. This research is supported by NSF (DMR-1410928).

Role of Quantum Vibrations on the Structural, Electronic, and Optical Properties of 9-Methylguanine.

PubMed

Law, Yu Kay; Hassanali, Ali A

2015-11-05

In this work, we report theoretical predictions of the UV-absorption spectra of 9-methylguanine using time dependent density functional theory (TDDFT). Molecular dynamics simulations of the hydrated DNA base are peformed using an empirical force field, Born-Oppenheimer ab initio molecular dynamics (AIMD), and finally path-integral AIMD to understand the role of the underlying electronic potential, solvation, and nuclear quantum vibrations on the absorption spectra. It is shown that the conformational distributions, including hydrogen bonding interactions, are perturbed by the inclusion of nuclear quantum effects, leading to significant changes in the total charge and dipole fluctuations of the DNA base. The calculated absorption spectra using the different sampling protocols shows that the inclusion of nuclear quantum effects causes a significant broadening and red shift of the spectra bringing it into closer agreement with experiments.

Cyclic AMP-dependent signaling system is a primary metabolic target for non-thermal effect of microwaves on heart muscle hydration.

PubMed

Narinyan, Lilia; Ayrapetyan, Sinerik

2017-01-01

Previously, we have suggested that cell hydration is a universal and extra-sensitive sensor for the structural changes of cell aqua medium caused by the impact of weak chemical and physical factors. The aim of present work is to elucidate the nature of the metabolic messenger through which physiological solution (PS) treated by non-thermal (NT) microwaves (MW) could modulate heart muscle hydration of rats. For this purpose, the effects of NT MW-treated PS on heart muscle hydration, [ 3 H]-ouabain binding with cell membrane, 45 Ca 2+ uptake and intracellular cyclic nucleotides contents in vivo and in vitro experiments were studied. It is shown that intraperitoneal injections of both Sham-treated PS and NT MW-treated PS elevate heart muscle hydration. However, the effect of NT MW-treated PS on muscle hydration is more pronounced than the effect of Sham-treated PS. In vitro experiments NT MW-treated PS has dehydration effect on muscle, which is not changed by decreasing Na + gradients on membrane. Intraperitoneal injection of Sham- and NT MW-treated PS containing 45 Ca 2+ have similar dehydration effect on muscle, while NT MW-treated PS has activation effect on Na + /Ca 2+ exchange in reverse mode. The intraperitoneal injection of NT MW-treated PS depresses [ 3 H]-ouabain binding with its high-affinity membrane receptors, elevates intracellular cAMP and decreases cGMP contents. Based on the obtained data, it is suggested that cAMP-dependent signaling system serves as a primary metabolic target for NT MW effect on heart muscle hydration.

In Situ Temperature Measurements at the Svalbard Continental Margin: Implications for Gas Hydrate Dynamics

NASA Astrophysics Data System (ADS)

Riedel, M.; Wallmann, K.; Berndt, C.; Pape, T.; Freudenthal, T.; Bergenthal, M.; Bünz, S.; Bohrmann, G.

2018-04-01

During expedition MARIA S. MERIAN MSM57/2 to the Svalbard margin offshore Prins Karls Forland, the seafloor drill rig MARUM-MeBo70 was used to assess the landward termination of the gas hydrate system in water depths between 340 and 446 m. The study region shows abundant seafloor gas vents, clustered at a water depth of ˜400 m. The sedimentary environment within the upper 100 m below seafloor (mbsf) is dominated by ice-berg scours and glacial unconformities. Sediments cored included glacial diamictons and sheet-sands interbedded with mud. Seismic data show a bottom simulating reflector terminating ˜30 km seaward in ˜760 m water depth before it reaches the theoretical limit of the gas hydrate stability zone (GHSZ) at the drilling transect. We present results of the first in situ temperature measurements conducted with MeBo70 down to 28 mbsf. The data yield temperature gradients between ˜38°C km-1 at the deepest site (446 m) and ˜41°C km-1 at a shallower drill site (390 m). These data constrain combined with in situ pore-fluid data, sediment porosities, and thermal conductivities the dynamic evolution of the GHSZ during the past 70 years for which bottom water temperature records exist. Gas hydrate is not stable in the sediments at sites shallower than 390 m water depth at the time of acquisition (August 2016). Only at the drill site in 446 m water depth, favorable gas hydrate stability conditions are met (maximum vertical extent of ˜60 mbsf); however, coring did not encounter any gas hydrates.

Molecular dynamics studies of interfacial water at the alumina surface.

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

Argyris, Dr. Dimitrios; Ho, Thomas; Cole, David

2011-01-01

Interfacial water properties at the alumina surface were investigated via all-atom equilibrium molecular dynamics simulations at ambient temperature. Al-terminated and OH-terminated alumina surfaces were considered to assess the structural and dynamic behavior of the first few hydration layers in contact with the substrates. Density profiles suggest water layering up to {approx}10 {angstrom} from the solid substrate. Planar density distribution data indicate that water molecules in the first interfacial layer are organized in well-defined patterns dictated by the atomic terminations of the alumina surface. Interfacial water exhibits preferential orientation and delayed dynamics compared to bulk water. Water exhibits bulk-like behavior atmore » distances greater than {approx}10 {angstrom} from the substrate. The formation of an extended hydrogen bond network within the first few hydration layers illustrates the significance of water?water interactions on the structural properties at the interface.« less

Protein dynamics in organic media at varying water activity studied by molecular dynamics simulation.

PubMed

Wedberg, Rasmus; Abildskov, Jens; Peters, Günther H

2012-03-01

In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method relies on determining the water content of the bulk phase and uses a combination of Kirkwood-Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents methanol, tert-butyl alcohol, methyl tert-butyl ether, and hexane, each mixture at five different water activities. It is shown that similar water activity yields similar enzyme hydration in the different solvents. However, both solvent and water activity are shown to have profound effects on enzyme structure and flexibility.

Structural characteristics of hydrated protons in the conductive channels: effects of confinement and fluorination studied by molecular dynamics simulation.

PubMed

Zhang, Ning; Song, Yuechun; Ruan, Xuehua; Yan, Xiaoming; Liu, Zhao; Shen, Zhuanglin; Wu, Xuemei; He, Gaohong

2016-09-21

The relationship between the proton conductive channel and the hydrated proton structure is of significant importance for understanding the deformed hydrogen bonding network of the confined protons which matches the nanochannel. In general, the structure of hydrated protons in the nanochannel of the proton exchange membrane is affected by several factors. To investigate the independent effect of each factor, it is necessary to eliminate the interference of other factors. In this paper, a one-dimensional carbon nanotube decorated with fluorine was built to investigate the independent effects of nanoscale confinement and fluorination on the structural properties of hydrated protons in the nanochannel using classical molecular dynamics simulation. In order to characterize the structure of hydrated protons confined in the channel, the hydrogen bonding interaction between water and the hydrated protons has been studied according to suitable hydrogen bond criteria. The hydrogen bond criteria were proposed based on the radial distribution function, angle distribution and pair-potential energy distribution. It was found that fluorination leads to an ordered hydrogen bonding structure of the hydrated protons near the channel surface, and confinement weakens the formation of the bifurcated hydrogen bonds in the radial direction. Besides, fluorination lowers the free energy barrier of hydronium along the nanochannel, but slightly increases the barrier for water. This leads to disintegration of the sequential hydrogen bond network in the fluorinated CNTs with small size. In the fluorinated CNTs with large diameter, the lower degree of confinement produces a spiral-like sequential hydrogen bond network with few bifurcated hydrogen bonds in the central region. This structure might promote unidirectional proton transfer along the channel without random movement. This study provides the cooperative effect of confinement dimension and fluorination on the structure and hydrogen bonding of the slightly acidic water in the nanoscale channel.

Observed correlation between the depth to base and top of gas hydrate occurrence from review of global drilling data

NASA Astrophysics Data System (ADS)

Riedel, M.; Collett, T. S.

2017-07-01

A global inventory of data from gas hydrate drilling expeditions is used to develop relationships between the base of structure I gas hydrate stability, top of gas hydrate occurrence, sulfate-methane transition depth, pressure (water depth), and geothermal gradients. The motivation of this study is to provide first-order estimates of the top of gas hydrate occurrence and associated thickness of the gas hydrate occurrence zone for climate-change scenarios, global carbon budget analyses, or gas hydrate resource assessments. Results from publically available drilling campaigns (21 expeditions and 52 drill sites) off Cascadia, Blake Ridge, India, Korea, South China Sea, Japan, Chile, Peru, Costa Rica, Gulf of Mexico, and Borneo reveal a first-order linear relationship between the depth to the top and base of gas hydrate occurrence. The reason for these nearly linear relationships is believed to be the strong pressure and temperature dependence of methane solubility in the absence of large difference in thermal gradients between the various sites assessed. In addition, a statistically robust relationship was defined between the thickness of the gas hydrate occurrence zone and the base of gas hydrate stability (in meters below seafloor). The relationship developed is able to predict the depth of the top of gas hydrate occurrence zone using observed depths of the base of gas hydrate stability within less than 50 m at most locations examined in this study. No clear correlation of the depth to the top and base of gas hydrate occurrences with geothermal gradient and sulfate-methane transition depth was identified.

Observed correlation between the depth to base and top of gas hydrate occurrence from review of global drilling data

USGS Publications Warehouse

Riedel, Michael; Collett, Timothy S.

2017-01-01

A global inventory of data from gas hydrate drilling expeditions is used to develop relationships between the base of structure I gas hydrate stability, top of gas hydrate occurrence, sulfate-methane transition depth, pressure (water depth), and geothermal gradients. The motivation of this study is to provide first-order estimates of the top of gas hydrate occurrence and associated thickness of the gas hydrate occurrence zone for climate-change scenarios, global carbon budget analyses, or gas hydrate resource assessments. Results from publically available drilling campaigns (21 expeditions and 52 drill sites) off Cascadia, Blake Ridge, India, Korea, South China Sea, Japan, Chile, Peru, Costa Rica, Gulf of Mexico, and Borneo reveal a first-order linear relationship between the depth to the top and base of gas hydrate occurrence. The reason for these nearly linear relationships is believed to be the strong pressure and temperature dependence of methane solubility in the absence of large difference in thermal gradients between the various sites assessed. In addition, a statistically robust relationship was defined between the thickness of the gas hydrate occurrence zone and the base of gas hydrate stability (in meters below seafloor). The relationship developed is able to predict the depth of the top of gas hydrate occurrence zone using observed depths of the base of gas hydrate stability within less than 50 m at most locations examined in this study. No clear correlation of the depth to the top and base of gas hydrate occurrences with geothermal gradient and sulfate-methane transition depth was identified.

Communication: Heterogeneous water dynamics on a clathrate hydrate lattice detected by multidimensional oxygen nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Adjei-Acheamfour, Mischa; Storek, Michael; Böhmer, Roland

2017-05-01

Previous deuteron nuclear magnetic resonance studies revealed conflicting evidence regarding the possible motional heterogeneity of the water dynamics on the hydrate lattice of an ice-like crystal. Using oxygen-17 nuclei as a sensitive quadrupolar probe, the reorientational two-time correlation function displays a clear nonexponentiality. To check whether this dispersive behavior is a consequence of dynamic heterogeneity or rather of an intrinsic nonexponentiality, a multidimensional, four-time magnetic resonance experiment was devised that is generally applicable to strongly quadrupolarly perturbed half-integer nuclei such as oxygen-17. Measurements of an appropriate four-time function demonstrate that it is possible to select a subensemble of slow water molecules. Its mean time scale is compared to theoretical predictions and evidence for significant motional heterogeneity is found.

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.

Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies.

PubMed Central

Feller, S E; Yin, D; Pastor, R W; MacKerell, A D

1997-01-01

A potential energy function for unsaturated hydrocarbons is proposed and is shown to agree well with experiment, using molecular dynamics simulations of a water/octene interface and a dioleoyl phosphatidylcholine (DOPC) bilayer. The simulation results verify most of the assumptions used in interpreting the DOPC experiments, but suggest a few that should be reconsidered. Comparisons with recent results of a simulation of a dipalmitoyl phosphatidylcholine (DPPC) lipid bilayer show that disorder is comparable, even though the temperature, hydration level, and surface area/lipid for DOPC are lower. These observations highlight the dramatic effects of unsaturation on bilayer structure. Images FIGURE 3 PMID:9370424

Competing quantum effects in the free energy profiles and diffusion rates of hydrogen and deuterium molecules through clathrate hydrates.

PubMed

Cendagorta, Joseph R; Powers, Anna; Hele, Timothy J H; Marsalek, Ondrej; Bačić, Zlatko; Tuckerman, Mark E

2016-11-30

Clathrate hydrates hold considerable promise as safe and economical materials for hydrogen storage. Here we present a quantum mechanical study of H 2 and D 2 diffusion through a hexagonal face shared by two large cages of clathrate hydrates over a wide range of temperatures. Path integral molecular dynamics simulations are used to compute the free-energy profiles for the diffusion of H 2 and D 2 as a function of temperature. Ring polymer molecular dynamics rate theory, incorporating both exact quantum statistics and approximate quantum dynamical effects, is utilized in the calculations of the H 2 and D 2 diffusion rates in a broad temperature interval. We find that the shape of the quantum free-energy profiles and their height relative to the classical free energy barriers at a given temperature, as well as the rate of diffusion, are strongly affected by competing quantum effects: above 25 K, zero-point energy (ZPE) perpendicular to the reaction path for diffusion between cavities decreases the quantum rate compared to the classical rate, whereas at lower temperatures tunneling outcompetes the ZPE and as a result the quantum rate is greater than the classical rate.

Hydrate kinetics study in the presence of nonaqueous liquid by nuclear magnetic resonance spectroscopy and imaging.

PubMed

Susilo, Robin; Moudrakovski, Igor L; Ripmeester, John A; Englezos, Peter

2006-12-28

The dynamics of methane hydrate growth and decomposition were studied by nuclear magnetic resonance (NMR) spectroscopy and imaging (MRI). Three well-known large molecule guest substances (LMGS) were used as structure H hydrate formers: 2,2-dimethylbutane (NH), methylcyclohexane (MCH), tert-butyl methyl ether (TBME). In addition, the impact of a non-hydrate former (n-heptane/nC7) was studied. The methane diffusion and hydrate growth were monitored by recording the 2H NMR spectra at 253 K and approximately 4.5 MPa for 20 h. The results revealed that methane diffuses faster in TBME and NH, slower in nC7, and slowest in MCH. The TBME system gives the fastest hydrate formation kinetics followed by NH, MCH, and nC7. The conversion of water into hydrate was also observed. The imaging study showed that TBME has a strong affinity toward ice, which is not the case for the NH and MCH systems. The degree of ice packing was also found to affect the LMGS distribution between ice particles. Highly packed ice increases the mass transfer resistance and hence limits the contact between LMGS and ice. It was also found that "temperature ramping" above the ice point improves the conversion significantly. Finally, hydrates were found to dissociate quickly within the first hour at atmospheric pressure and subsequently at a much slower rate. Methane dissolved in LMGS was also seen. The residual methane in hydrate phase and dissolved in LMGS phase explain the faster kinetics during hydrate re-formation.

Instability of buried hydration sites increases protein subdomains fluctuations in the human prion protein by the pathogenic mutation T188R

NASA Astrophysics Data System (ADS)

Tomobe, Katsufumi; Yamamoto, Eiji; Akimoto, Takuma; Yasui, Masato; Yasuoka, Kenji

2016-05-01

The conformational change from the cellular prion protein (PrPc) to scrapie prion protein (PrPsc) is a key process in prion diseases. The prion protein has buried water molecules which significantly contribute to the stability of the protein; however, there has been no report investigating the influence on the buried hydration sites by a pathogenic mutation not adjacent to the buried hydration sites. Here, we perform molecular dynamics simulations of wild type (WT) PrPc and pathogenic point mutant T188R to investigate conformational changes and the buried hydration sites. In WT-PrPc, four buried hydration sites are identified by residence time and rotational relaxation analysis. However, there are no stable buried hydration sites in one of T188R simulations, which indicates that T188R sometimes makes the buried hydration sites fragile. We also find that fluctuations of subdomains S1-H1-S2 and H1-H2 increase in T188R when the buried hydration sites become unstable. Since the side chain of arginine which is replaced from threonine in T188R is larger than of threonine, the side chain cannot be embedded in the protein, which is one of the causes of the instability of subdomains. These results show correlations between the buried hydration sites and the mutation which is far from them, and provide a possible explanation for the instability by mutation.

Volume change associated with formation and dissociation of hydrate in sediment

USGS Publications Warehouse

Ruppel, Carolyn D.; Lee, J.Y.; Santamarina, J. Carlos

2017-01-01

Gas hydrate formation and dissociation in sediments are accompanied by changes in the bulk volume of the sediment and can lead to changes in sediment properties, loss of integrity for boreholes, and possibly regional subsidence of the ground surface over areas where methane might be produced from gas hydrate in the future. Experiments on sand, silts, and clay subject to different effective stress and containing different saturations of hydrate formed from dissolved phase tetrahydrofuran are used to systematically investigate the impact of gas hydrate formation and dissociation on bulk sediment volume. Volume changes in low specific surface sediments (i.e., having a rigid sediment skeleton like sand) are much lower than those measured in high specific surface sediments (e.g., clay). Early hydrate formation is accompanied by contraction for all soils and most stress states in part because growing gas hydrate crystals buckle skeletal force chains. Dilation can occur at high hydrate saturations. Hydrate dissociation under drained, zero lateral strain conditions is always associated with some contraction, regardless of soil type, effective stress level, or hydrate saturation. Changes in void ratio during formation-dissociation decrease at high effective stress levels. The volumetric strain during dissociation under zero lateral strain scales with hydrate saturation and sediment compressibility. The volumetric strain during dissociation under high shear is a function of the initial volume average void ratio and the stress-dependent critical state void ratio of the sediment. Other contributions to volume reduction upon hydrate dissociation are related to segregated hydrate in lenses and nodules. For natural gas hydrates, some conditions (e.g., gas production driven by depressurization) might contribute to additional volume reduction by increasing the effective stress.

Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles - upscaling an aggregate biophysical model.

PubMed

Ebrahimi, Ali; Or, Dani

2016-09-01

Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Recent mechanistic models of microbial processes in unsaturated aggregate-like pore networks revealed a highly dynamic interplay between oxic and anoxic microsites jointly shaped by hydration conditions and by aerobic and anaerobic microbial community abundance and self-organization. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support substantial anaerobic microbial activity even in aerated soil profiles. We employed an individual-based model for microbial community life in soil aggregate assemblies represented by 3D angular pore networks. Model aggregates of different sizes were subjected to variable water, carbon and oxygen contents that varied with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain estimates of biogeochemical fluxes from the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2 O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of practical interest for hydrological and climate models. © 2016 John Wiley & Sons Ltd.

Observation of interstitial molecular hydrogen in clathrate hydrates.

PubMed

Grim, R Gary; Barnes, Brian C; Lafond, Patrick G; Kockelmann, Winfred A; Keen, David A; Soper, Alan K; Hiratsuka, Masaki; Yasuoka, Kenji; Koh, Carolyn A; Sum, Amadeu K

2014-09-26

The current knowledge and description of guest molecules within clathrate hydrates only accounts for occupancy within regular polyhedral water cages. Experimental measurements and simulations, examining the tert-butylamine + H2 + H2O hydrate system, now suggest that H2 can also be incorporated within hydrate crystal structures by occupying interstitial sites, that is, locations other than the interior of regular polyhedral water cages. Specifically, H2 is found within the shared heptagonal faces of the large (4(3)5(9)6(2)7(3)) cage and in cavities formed from the disruption of smaller (4(4)5(4)) water cages. The ability of H2 to occupy these interstitial sites and fluctuate position in the crystal lattice demonstrates the dynamic behavior of H2 in solids and reveals new insight into guest-guest and guest-host interactions in clathrate hydrates, with potential implications in increasing overall energy storage properties. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Formation of Methane Hydrate in the Presence of Natural and Synthetic Nanoparticles

PubMed Central

2018-01-01

Natural gas hydrates occur widely on the ocean-bed and in permafrost regions, and have potential as an untapped energy resource. Their formation and growth, however, poses major problems for the energy sector due to their tendency to block oil and gas pipelines, whereas their melting is viewed as a potential contributor to climate change. Although recent advances have been made in understanding bulk methane hydrate formation, the effect of impurity particles, which are always present under conditions relevant to industry and the environment, remains an open question. Here we present results from neutron scattering experiments and molecular dynamics simulations that show that the formation of methane hydrate is insensitive to the addition of a wide range of impurity particles. Our analysis shows that this is due to the different chemical natures of methane and water, with methane generally excluded from the volume surrounding the nanoparticles. This has important consequences for our understanding of the mechanism of hydrate nucleation and the design of new inhibitor molecules. PMID:29401390

In vivo skin imaging for hydration and micro relief-measurement.

PubMed

Kardosova, Z; Hegyi, V

2013-01-01

We present the results of our work with device used for measurement of skin capacitance before and after application of moisturizing creams and results of experiment performed on cellulose filter papers soaked with different solvents. The measurements were performed by a device built on capacitance sensor, which provides an investigator with a capacitance image of the skin. The capacitance values are coded in a range of 256 gray levels then the skin hydration can be characterized using parameters derived from gray level histogram by specific software. The images obtained by device allow a highly precise observation of skin topography. Measuring of skin capacitance brings new, objective, reliable information about topographical, physical and chemical parameters of the skin. The study shows that there is a good correlation between the average grayscale values and skin hydration. In future works we need to complete more comparison studies, interpret the average grayscale values to skin hydration levels and use it for follow-up of dynamics of skin micro-relief and hydration changes (Fig. 6, Ref. 15).

Microcrystalline dolomite within massive Japan Sea methane hydrate: origin and development ascertained by inclusions within inclusions.

NASA Astrophysics Data System (ADS)

Snyder, G. T.; Kakizaki, Y.; Matsumoto, R.; Suzuki, Y.; Takahata, N.; Sano, Y.; Tanaka, K.; Tomaru, H.; Imajo, T.; Iguchi, A.

2017-12-01

Microcrystalline dolomite grains were recently discovered as inclusions within relatively pure massive gas hydrate recovered from the Joetsu Basin area of the Japan Sea. These grains presumably formed as a consequence of the highly saline conditions in fluid inclusions which developed between coalescing grain boundaries within the growing hydrate. Stable carbon and oxygen isotopic composition of the dolomite is consistent with crystal growth occurring within such fluids. In addition to stable isotopes, we investigate trends in Mg/Ca ratios of the grains as well as the composition of inclusions which exist within the dolomites. Preliminary research shows that these inclusions retain valuable information as to the conditions which existed at the time of formation, as well as the dynamics of these extensive hydrate deposits over time. 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).

Solubility of aqueous methane under metastable conditions: implications for gas hydrate nucleation.

PubMed

Guo, Guang-Jun; Rodger, P Mark

2013-05-30

To understand the prenucleation stage of methane hydrate formation, we measured methane solubility under metastable conditions using molecular dynamics simulations. Three factors that influence solubility are considered: temperature, pressure, and the strength of the modeled van der Waals attraction between methane and water. Moreover, the naturally formed water cages and methane clusters in the methane solutions are analyzed. We find that both lowering the temperature and increasing the pressure increase methane solubility, but lowering the temperature is more effective than increasing the pressure in promoting hydrate nucleation because the former induces more water cages to form while the latter makes them less prevalent. With an increase in methane solubility, the chance of forming large methane clusters increases, with the distribution of cluster sizes being exponential. The critical solubility, beyond which the metastable solutions spontaneously form hydrate, is estimated to be ~0.05 mole fraction in this work, corresponding to the concentration of 1.7 methane molecules/nm(3). This value agrees well with the cage adsorption hypothesis of hydrate nucleation.

Leaf water dynamics of Arabidopsis thaliana monitored in-vivo using terahertz time-domain spectroscopy

NASA Astrophysics Data System (ADS)

Castro-Camus, E.; Palomar, M.; Covarrubias, A. A.

2013-10-01

The declining water availability for agriculture is becoming problematic for many countries. Therefore the study of plants under water restriction is acquiring extraordinary importance. Botanists currently follow the dehydration of plants comparing the fresh and dry weight of excised organs, or measuring their osmotic or water potentials; these are destructive methods inappropriate for in-vivo determination of plants' hydration dynamics. Water is opaque in the terahertz band, while dehydrated biological tissues are partially transparent. We used terahertz spectroscopy to study the water dynamics of Arabidopsis thaliana by comparing the dehydration kinetics of leaves from plants under well-irrigated and water deficit conditions. We also present measurements of the effect of dark-light cycles and abscisic acid on its water dynamics. The measurements we present provide a new perspective on the water dynamics of plants under different external stimuli and confirm that terahertz can be an excellent non-contact probe of in-vivo tissue hydration.

Traditional Portland cement and MgO-based cement: a promising combination?

NASA Astrophysics Data System (ADS)

Tonelli, Monica; Martini, Francesca; Calucci, Lucia; Geppi, Marco; Borsacchi, Silvia; Ridi, Francesca

2017-06-01

MgO/SiO2 cements are materials potentially very useful for radioactive waste disposal, but knowledge about their physico-chemical properties is still lacking. In this paper we investigated the hydration kinetics of cementitious formulations prepared by mixing MgO/SiO2 and Portland cement in different proportions and the structural properties of the hydrated phases formed in the first month of hydration. In particular, the hydration kinetics was investigated by measuring the free water index on pastes by means of differential scanning calorimetry, while the structural characterization was carried out by combining thermal (DTA), diffractometric (XRD), and spectroscopic (FTIR, 29Si solid state NMR) techniques. It was found that calcium silicate hydrate (C-S-H) and magnesium silicate hydrate (M-S-H) gels mainly form as separate phases, their relative amount and structural characteristics depending on the composition of the hydrated mixture. Moreover, the composition of the mixtures strongly affects the kinetics of hydration and the pH of the aqueous phase in contact with the cementitious materials. The results here reported show that suitable mixtures of Portland cement and MgO/SiO2 could be used to modify the properties of hydrated phases with potential application in the storage of nuclear waste in clayey disposal.

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.

Assessment of corneal hydration sensing in the terahertz band: in vivo results at 100 GHz

PubMed Central

Taylor, Zachary; Tewari, Pria; Sung, Shijun; Maccabi, Ashkan; Singh, Rahul; Culjat, Martin; Grundfest, Warren; Hubschman, Jean-Pierre; Brown, Elliott

2012-01-01

Abstract. Terahertz corneal hydration sensing has shown promise in ophthalmology applications and was recently shown to be capable of detecting water concentration changes of about two parts in a thousand in ex vivo corneal tissues. This technology may be effective in patient monitoring during refractive surgery and for early diagnosis and treatment monitoring in diseases of the cornea. In this work, Fuchs dystrophy, cornea transplant rejection, and keratoconus are discussed, and a hydration sensitivity of about one part in a hundred is predicted to be needed to successfully distinguish between diseased and healthy tissues in these applications. Stratified models of corneal tissue reflectivity are developed and validated using ex vivo spectroscopy of harvested porcine corneas that are hydrated using polyethylene glycol solutions. Simulation of the cornea’s depth-dependent hydration profile, from 0.01 to 100 THz, identifies a peak in intrinsic reflectivity contrast for sensing at 100 GHz. A 100 GHz hydration sensing system is evaluated alongside the current standard ultrasound pachymetry technique to measure corneal hydration in vivo in four rabbits. A hydration sensitivity, of three parts per thousand or better, was measured in all four rabbits under study. This work presents the first in vivo demonstration of remote corneal hydration sensing. PMID:23085925

Assessment of corneal hydration sensing in the terahertz band: in vivo results at 100 GHz

NASA Astrophysics Data System (ADS)

Bennett, David; Taylor, Zachary; Tewari, Pria; Sung, Sijun; Maccabi, Ashkan; Singh, Rahul; Culjat, Martin; Grundfest, Warren; Hubschman, Jean-Pierre; Brown, Elliott

2012-09-01

Terahertz corneal hydration sensing has shown promise in ophthalmology applications and was recently shown to be capable of detecting water concentration changes of about two parts in a thousand in ex vivo corneal tissues. This technology may be effective in patient monitoring during refractive surgery and for early diagnosis and treatment monitoring in diseases of the cornea. In this work, Fuchs dystrophy, cornea transplant rejection, and keratoconus are discussed, and a hydration sensitivity of about one part in a hundred is predicted to be needed to successfully distinguish between diseased and healthy tissues in these applications. Stratified models of corneal tissue reflectivity are developed and validated using ex vivo spectroscopy of harvested porcine corneas that are hydrated using polyethylene glycol solutions. Simulation of the cornea's depth-dependent hydration profile, from 0.01 to 100 THz, identifies a peak in intrinsic reflectivity contrast for sensing at 100 GHz. A 100 GHz hydration sensing system is evaluated alongside the current standard ultrasound pachymetry technique to measure corneal hydration in vivo in four rabbits. A hydration sensitivity, of three parts per thousand or better, was measured in all four rabbits under study. This work presents the first in vivo demonstration of remote corneal hydration sensing.

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.

Elastic wave speeds and moduli in polycrystalline ice Ih, si methane hydrate, and sll methane-ethane hydrate

USGS Publications Warehouse

Helgerud, M.B.; Waite, W.F.; Kirby, S.H.; Nur, A.

2009-01-01

We used ultrasonic pulse transmission to measure compressional, P, and shear, S, wave speeds in laboratory-formed polycrystalline ice Ih, si methane hydrate, and sll methane-ethane hydrate. From the wave speed's linear dependence on temperature and pressure and from the sample's calculated density, we derived expressions for bulk, shear, and compressional wave moduli and Poisson's ratio from -20 to 15??C and 22.4 to 32.8 MPa for ice Ih, -20 to 15??C and 30.5 to 97.7 MPa for si methane hydrate, and -20 to 10??C and 30.5 to 91.6 MPa for sll methane-ethane hydrate. All three materials had comparable P and S wave speeds and decreasing shear wave speeds with increasing applied pressure. Each material also showed evidence of rapid intergranular bonding, with a corresponding increase in wave speed, in response to pauses in sample deformation. There were also key differences. Resistance to uniaxial compaction, indicated by the pressure required to compact initially porous samples, was significantly lower for ice Ih than for either hydrate. The ice Ih shear modulus decreased with increasing pressure, in contrast to the increase measured in both hydrates ?? 2009.

Morin hydrate augments phagocytosis mechanism and inhibits LPS induced autophagic signaling in murine macrophage.

PubMed

Jakhar, Rekha; Paul, Souren; Chauhan, Anil Kumar; Kang, Sun Chul

2014-10-01

Morin, a natural flavonoid that is the primary bioactive constituent of the family Moraceae, has been found to be associated with many therapeutic properties. In this study, we evaluated the immunomodulatory activities of increasing concentration of morin hydrate in vitro. Three different concentrations of morin hydrate (5, 10, and 15μM) were used to evaluate their effect on splenocyte proliferation, phagocytic activity of macrophages, cytokine secretion and complement inhibition. We also evaluated the role of morin hydrate on lipopolysaccharide (LPS) induced autophagy. Our study demonstrated that morin hydrate elicited a significant increase in splenocyte proliferation, phagocytic capacity and suppressed the production of cytokines and nitric oxide in activated macrophages. Humoral immunity measured by anti-complement activity showed an increase in inhibition of the complement system after the addition of morin hydrate, where morin hydrate at 15μM concentration induced a significant inhibition. Depending on our results, we can also conclude that morin hydrate protects macrophages from LPS induced autophagic cell death. Our findings suggest that morin hydrate represents a structurally diverse class of flavonoid and this structural variability can profoundly affect its cell-type specificity and its biological activities. Supplementation of immune cells with morin hydrate has an upregulating and immunoprotective effect that shows potential as a countermeasure to the immune dysfunction and suggests an interesting use in inflammation related diseases. Copyright © 2014 Elsevier B.V. All rights reserved.

A spectroscopic study of the structure and occupancies of clathrate hydrates incorporating hydrogen

NASA Astrophysics Data System (ADS)

Grim, R. Gary

With the ability to store and concentrate gases inside a clean and abundant water framework, clathrate hydrates are considered to be a promising material for many applications related to gas storage, separation, and sequestration. Hydrates of hydrogen are particularly interesting, for in addition to these potential applications, the small molecular size provides an opportunity for use as a model guest in many fundamental studies such as guest diffusion, multiple guest occupancy, and quantum mechanical effects upon confinement. In attempt to study these effects and the viability of H 2 hydrates as an energy storage material, a combined experimental and theoretical approach incorporating Raman spectroscopy, X-ray and neutron diffraction, nuclear magnetic resonance, ab-initio calculations, and molecular dynamic simulations was performed. One of the most significant challenges in the application of H2 clathrate hydrates is the demanding thermodynamic requirements needed for stability. In recent years, a mechanism known as the `tuning' effect had reportedly solved this issue where thermodynamic requirements could be reduced while simultaneously maintaining high storage capacities. In this work, the viability and validity of this technique is explored and alternative explanations in the form of epitaxial hydrate growth under high driving force conditions are discussed. A second, and equally important challenge facing clathrate hydrates as a future storage material is the overall storage capacity of H2. In previous work, H2 has only been experimentally verified to occupy the small 512 and 43566 3 cages and also in the large 51264 cages of the type II clathrate, often with an energy deficient promoter. In order to achieve more robust energy densities, other hydrate cages must be accessible. Herein a new method for increasing overall hydrate energy densities is presented involving the incorporation of H2 in the large cages of the type I clathrate with CH4 as a co-guest molecule. Finally, for all of the collective research on gas hydrates since their discovery in 1810 by Sir Humphrey Davy, the one common theme that unites them is the assumption that guest molecules are trapped at the center (or near center) of the host water cages that makes up the respective crystal structure. For the first time, this work provides evidence suggesting that this definition of clathrate hydrate guest occupancy is possibly incomplete, and should include the addition of interstitial sites within the water crystal lattice. Specifically, H2 is found within the shared heptagonal faces of the large (4 3596273) cage and in cavities formed from the disruption of smaller (445 4) water cages in structure VI hydrates. The ability of H2 to occupy these interstitial sites and fluctuate position in the crystal lattice demonstrates the dynamic behavior of H2 in solids and reveals new insight into guest-guest and guest-host interactions in clathrate hydrates with potential implications in increasing overall energy storage properties.

HCO3(-) formation from CO2 at high pH: ab initio molecular dynamics study.

PubMed

Stirling, András

2011-12-15

Ab initio molecular dynamics simulations have been performed to study the dissolution of CO2 in water at high pH. The CO2 + OH(-) --> HCO3(-) forward and the HCO3(-) --> CO2 + OH(-) reverse paths have been simulated by employing the metadynamics technics. We have found that the free energy barrier along the forward direction is predominantly hydration related and significantly entropic in origin, whereas the backward barrier is primarily enthalpic. The main motifs in the forward mechanism are the structural diffusion of the hydroxyl ion to the first hydration sphere of CO2, its desolvation, and the C-O bond formation in concert with the CO2 bending within the hydrate cavity. In the reverse reaction, the origin of the barrier is the rupture of the strong C-O(H) bond. The present findings support the notion that the free energy barrier of the bicarbonate formation is strongly solvation related but provide also additional mechanistic details at the molecular level.

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

Lopez, Murielle; Kurkal-Siebert, V; Dunn, Rachel V.

Water is widely assumed to be essential for life, although the exact molecular basis of this requirement is unclear. Water facilitates protein motions, and although enzyme activity has been demonstrated at low hydrations in organic solvents, such nonaqueous solvents may allow the necessary motions for catalysis. To examine enzyme function in the absence of solvation and bypass diffusional constraints we have tested the ability of an enzyme, pig liver esterase, to catalyze alcoholysis as an anhydrous powder, in a reaction system of defined water content and where the substrates and products are gaseous. At hydrations of 3 ( 2) moleculesmore » of water per molecule of enzyme, activity is several orders-of-magnitude greater than nonenzymatic catalysis. Neutron spectroscopy indicates that the fast ( nanosecond) global anharmonic dynamics of the anhydrous functional enzyme are suppressed. This indicates that neither hydration water nor fast anharmonic dynamics are required for catalysis by this enzyme, implying that one of the biological requirements of water may lie with its role as a diffusion medium rather than any of its more specific properties.« less

Hydration property of globular proteins: An analysis of solvation free energy by energy representation method

NASA Astrophysics Data System (ADS)

Saito, Hiroaki; Matubayasi, Nobuyuki; Nishikawa, Kiyoshi; Nagao, Hidemi

2010-09-01

Molecular dynamics simulations and solvation free energy calculations of five globular proteins (BPTI, RNase A, Lysozyme, β-lactoglobulin A, and α-chymotrypsinogen A) have been carried out to elucidate the hydration properties. Solvation free energies of the proteins with explicit solvent were estimated by energy representation (ER) method. The calculated solvation free energies were correlated with the solvent accessible surface area of hydrophilic portion, being consistent with the hydrophilic property of the proteins. These results showed that the ER method should be a powerful tool for estimating the hydration property of proteins, showing a progress of the free energy calculation with explicit solvent.

The analysis of axisymmetric viscoelasticity, time-dependent recovery, and hydration in rat tail intervertebral discs by radial compression test.

PubMed

Lin, Leou-Chyr; Hedman, Thomas P; Wang, Shyu-Jye; Huoh, Michael; Chang, Shih-Youeng

2009-05-01

The goal of this study was to develop a nondestructive radial compression technique and to investigate the viscoelastic behavior of the rat tail disc under repeated radial compression. Rat tail intervertebral disc underwent radial compression relaxation testing and creep testing using a custom-made gravitational creep machine. The axisymmetric viscoelasticity and time-dependent recovery were determined. Different levels of hydration (with or without normal saline spray) were supplied to evaluate the effect of changes in viscoelastic properties. Viscoelasticity was found to be axisymmetric in rat-tail intervertebral discs at four equidistant locations. Complete relaxation recovery was found to take 20 min, whereas creep recovery required 25 min. Hydration was required for obtaining viscoelastic axisymmetry and complete viscoelastic recovery.

The coexistence temperature of hydrogen clathrates: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Luis, D. P.; Romero-Ramirez, I. E.; González-Calderón, A.; López-Lemus, J.

2018-03-01

Extensive molecular dynamics simulations in the equilibrium isobaric-isothermal (NPT) ensemble were developed to determine the coexistence temperatures of the water hydrogen mixture using the direct coexistence method. The water molecules were modeled using the four-site TIP4P/Ice analytical potential, and the hydrogen molecules were described using a three-site potential. The simulations were performed at different pressures (p = 900, 1500, 3000, and 4000 bars). At each pressure, a series of simulations were developed at different temperatures (from 230 to 270 K). Our results followed a line parallel to the experimental coexistence temperatures and underestimated these temperatures by approximately 25 K in the investigated range. The final configurations could or could not contain a fluid phase depending on the pressure, in accordance with the phase diagram. In addition, we explored the dynamics of the H2 molecules through clathrate hydrate cages and observed different behaviors of the H2 molecules in the small cages and the large cages of the sII structure.

Preliminary report on the commercial viability of gas production from natural gas hydrates

USGS Publications Warehouse

Walsh, M.R.; Hancock, S.H.; Wilson, S.J.; Patil, S.L.; Moridis, G.J.; Boswell, R.; Collett, T.S.; Koh, C.A.; Sloan, E.D.

2009-01-01

Economic studies on simulated gas hydrate reservoirs have been compiled to estimate the price of natural gas that may lead to economically viable production from the most promising gas hydrate accumulations. As a first estimate, $CDN2005 12/Mscf is the lowest gas price that would allow economically viable production from gas hydrates in the absence of associated free gas, while an underlying gas deposit will reduce the viability price estimate to $CDN2005 7.50/Mscf. Results from a recent analysis of the simulated production of natural gas from marine hydrate deposits are also considered in this report; on an IROR basis, it is $US2008 3.50-4.00/Mscf more expensive to produce marine hydrates than conventional marine gas assuming the existence of sufficiently large marine hydrate accumulations. While these prices represent the best available estimates, the economic evaluation of a specific project is highly dependent on the producibility of the target zone, the amount of gas in place, the associated geologic and depositional environment, existing pipeline infrastructure, and local tariffs and taxes. ?? 2009 Elsevier B.V.

Comparative atomic-scale hydration of the ceramide and phosphocholine headgroup in solution and bilayer environments

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

Gillams, Richard J.; McLain, Sylvia E., E-mail: sylvia.mclain@bioch.ox.ac.uk; Lorenz, Christian D., E-mail: chris.lorenz@kcl.ac.uk

2016-06-14

Previous studies have used neutron diffraction to elucidate the hydration of the ceramide and the phosphatidylcholine headgroup in solution. These solution studies provide bond-length resolution information on the system, but are limited to liquid samples. The work presented here investigates how the hydration of ceramide and phosphatidylcholine headgroups in a solution compares with that found in a lipid bilayer. This work shows that the hydration patterns seen in the solution samples provide valuable insight into the preferential location of hydrating water molecules in the bilayer. There are certain subtle differences in the distribution, which result from a combination of themore » lipid conformation and the lipid-lipid interactions within the bilayer environment. The lipid-lipid interactions in the bilayer will be dependent on the composition of the bilayer, whereas the restricted exploration of conformational space is likely to be applicable in all membrane environments. The generalized description of hydration gathered from the neutron diffraction studies thus provides good initial estimation for the hydration pattern, but this can be further refined for specific systems.« less

Electrical properties of polycrystalline methane hydrate

USGS Publications Warehouse

Du Frane, W. L.; Stern, L.A.; Weitemeyer, K.A.; Constable, S.; Pinkston, J.C.; Roberts, J.J.

2011-01-01

Electromagnetic (EM) remote-sensing techniques are demonstrated to be sensitive to gas hydrate concentration and distribution and complement other resource assessment techniques, particularly seismic methods. To fully utilize EM results requires knowledge of the electrical properties of individual phases and mixing relations, yet little is known about the electrical properties of gas hydrates. We developed a pressure cell to synthesize gas hydrate while simultaneously measuring in situ frequency-dependent electrical conductivity (σ). Synthesis of methane (CH4) hydrate was verified by thermal monitoring and by post run cryogenic scanning electron microscope imaging. Impedance spectra (20 Hz to 2 MHz) were collected before and after synthesis of polycrystalline CH4 hydrate from polycrystalline ice and used to calculate σ. We determined the σ of CH4 hydrate to be 5 × 10−5 S/m at 0°C with activation energy (Ea) of 30.6 kJ/mol (−15 to 15°C). After dissociation back into ice, σ measurements of samples increased by a factor of ~4 and Ea increased by ~50%, similar to the starting ice samples.

Sensitivity of the global submarine hydrate inventory to scenarios of future climate change

NASA Astrophysics Data System (ADS)

Hunter, S. J.; Goldobin, D. S.; Haywood, A. M.; Ridgwell, A.; Rees, J. G.

2013-04-01

The global submarine inventory of methane hydrate is thought to be considerable. The stability of marine hydrates is sensitive to changes in temperature and pressure and once destabilised, hydrates release methane into sediments and ocean and potentially into the atmosphere, creating a positive feedback with climate change. Here we present results from a multi-model study investigating how the methane hydrate inventory dynamically responds to different scenarios of future climate and sea level change. The results indicate that a warming-induced reduction is dominant even when assuming rather extreme rates of sea level rise (up to 20 mm yr-1) under moderate warming scenarios (RCP 4.5). Over the next century modelled hydrate dissociation is focussed in the top ˜100m of Arctic and Subarctic sediments beneath <500m water depth. Predicted dissociation rates are particularly sensitive to the modelled vertical hydrate distribution within sediments. Under the worst case business-as-usual scenario (RCP 8.5), upper estimates of resulting global sea-floor methane fluxes could exceed estimates of natural global fluxes by 2100 (>30-50TgCH4yr-1), although subsequent oxidation in the water column could reduce peak atmospheric release rates to 0.75-1.4 Tg CH4 yr-1.

Biomechanical effects of hydration in vocal fold tissues.

PubMed

Chan, Roger W; Tayama, Niro

2002-05-01

It has often been hypothesized, with little empirical support, that vocal fold hydration affects voice production by mediating changes in vocal fold tissue rheology. To test this hypothesis, we attempted in this study to quantify the effects of hydration on the viscoelastic shear properties of vocal fold tissues in vitro. Osmotic changes in hydration (dehydration and rehydration) of 5 excised canine larynges were induced by sequential incubation of the tissues in isotonic, hypertonic, and hypotonic solutions. Elastic shear modulus (G'), dynamic viscosity eta' and the damping ratio zeta of the vocal fold mucosa (lamina propria) were measured as a function of frequency (0.01 to 15 Hz) with a torsional rheometer. Vocal fold tissue stiffness (G') and viscosity (eta) increased significantly (by 4 to 7 times) with the osmotically induced dehydration, whereas they decreased by 22% to 38% on the induced rehydration. Damping ratio (zeta) also increased with dehydration and decreased with rehydration, but the detected differences were not statistically significant at all frequencies. These findings support the long-standing hypothesis that hydration affects vocal fold vibration by altering tissue rheologic (or viscoelastic) properties. Our results demonstrated the biomechanical importance of hydration in vocal fold tissues and suggested that hydration approaches may potentially improve the biomechanics of phonation in vocal fold lesions involving disordered fluid balance.

In situ Low-temperature Pair Distribution Function (PDF) Analysis of CH4 and CO2 Hydrates

NASA Astrophysics Data System (ADS)

Cladek, B.; Everett, M.; McDonnell, M.; Tucker, M.; Keffer, D.; Rawn, C.

2017-12-01

Gas hydrates occur in ocean floor and sub-surface permafrost deposits and are stable at moderate to high pressures and low temperatures. They are a clathrate structure composed of hydrogen bonded water cages that accommodate a wide variety of guest molecules. CO2 and CH4 hydrates both crystallize as the cubic sI hydrate and can form a solid solution. Natural gas hydrates are interesting as a potential methane source and for CO2 sequestration. Long-range diffraction studies on gas hydrates give valuable structural information but do not provide a detailed understanding of the disordered gas molecule interactions with the host lattice. In-situ low temperature total scattering experiments combined with pair distribution function (PDF) analysis are used to investigate the gas molecule motions and guest-cage interactions. CO2 and methane hydrates exhibit different decomposition behavior, and CO2 hydrate has a smaller lattice parameter despite it being a relatively larger molecule. Total scattering studies characterizing both the short- and long-range order simultaneously help to elucidate the structural source of these phenomena. Low temperature neutron total scattering data were collected using the Nanoscale Ordered MAterials Diffractometer (NOMAD) beamline at the Spallation Neutron Source (SNS) on CO2 and CH4 hydrates synthesized with D2O. Guest molecule motion within cages and interactions between gases and cages are investigated through the hydrate stability and decomposition regions. Data were collected from 2-80 K at a pressure of 55 mbar on CO2 and CH4 hydrates, and from 80-270 K at 25 bar on CH4 hydrate. The hydrate systems were modeled with classical molecular dynamic (MD) simulations to provide an analysis of the total energy into guest-guest, guest-host and host-host contributions. Combined Reitveld and Reverse Monte Carlo (RMC) structure refinement were used to fit models of the data. This combined modeling and simulation characterizes the effects of CO2 and CH4 as guest molecules on the structure and decomposition of gas hydrates. Structure and thermodynamic studies will provide a more comprehensive understanding of CO2-CH4 solid solutions, exchange kinetics, and implications on hydrate 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

LASER BIOLOGY: Optomechanical tests of hydrated biological tissues subjected to laser shaping

NASA Astrophysics Data System (ADS)

Omel'chenko, A. I.; Sobol', E. N.

2008-03-01

The mechanical properties of a matrix are studied upon changing the size and shape of biological tissues during dehydration caused by weak laser-induced heating. The cartilage deformation, dehydration dynamics, and hydraulic conductivity are measured upon laser heating. The hydrated state and the shape of samples of separated fascias and cartilaginous tissues were controlled by using computer-aided processing of tissue images in polarised light.

High-Order Ca(II)-Chloro Complexes in Mixed CaCl2-LiCl Aqueous Solution: Insights from Density Functional Theory and Molecular Dynamics Simulations.

PubMed

Wang, Yu-Lin; Wang, Ying; Yi, Hai-Bo

2016-07-21

In this study, the structural characteristics of high-coordinated Ca-Cl complexes present in mixed CaCl2-LiCl aqueous solution were investigated using density functional theory (DFT) and molecular dynamics (MD) simulations. The DFT results show that [CaClx](2-x) (x = 4-6) clusters are quite unstable in the gas phase, but these clusters become metastable when hydration is considered. The MD simulations show that high-coordinated Ca-chloro complexes are possible transient species that exist for up to nanoseconds in concentrated (11.10 mol·kg(-1)) Cl(-) solution at 273 and 298 K. As the temperature increases to 423 K, these high-coordinated structures tend to disassociate and convert into smaller clusters and single free ions. The presence of high-order Ca-Cl species in concentrated LiCl solution can be attributed to their enhanced hydration shell and the inadequate hydration of ions. The probability of the [CaClx](2-x)aq (x = 4-6) species being present in concentrated LiCl solution decreases greatly with increasing temperature, which also indicates that the formation of the high-coordinated Ca-Cl structure is related to its hydration characteristics.

Molecular dynamics simulations reveal that water diffusion between graphene oxide layers is slow

DOE PAGES

Devanathan, Ram; Chase-Woods, Dylan; Shin, Yongsoon; ...

2016-07-08

Membranes made of stacked layers of graphene oxide (GO) hold the tantalizing promise of revolutionizing desalination and water filtration if selective transport of molecules can be controlled. We present the findings of a molecular dynamics simulation study of water intercalated between GO layers that have a C/O ratio of 4. We simulated a range of hydration levels from 1 wt.% to 23.3 wt.% water. The interlayer spacing increased upon hydration from 0.8 nm to 1.1 nm. We also synthesized GO membranes that showed an increase in spacing from about 0.7 nm to 0.8 nm and an increase in mass ofmore » about 14% on hydration. Water diffusion through GO layers is an order of magnitude slower than that in bulk water, because of strong hydrogen bonded interactions. Most of the water molecules are bound to OH groups even at the highest hydration level. We observed large water clusters that could span graphitic regions, oxidized regions and holes that have been experimentally observed in GO. As a result, slow interlayer diffusion can be consistent with experimentally observed water transport in GO if holes lead to a shorter path length than previously assumed and sorption serves as a key rate-limiting step.« less

Protein dynamics in a broad frequency range: Dielectric spectroscopy studies

DOE PAGES

Nakanishi, Masahiro; Sokolov, Alexei P.

2014-09-17

We present detailed dielectric spectroscopy studies of dynamics in two hydrated proteins, lysozyme and myoglobin. We emphasize the importance of explicit account for possible Maxwell-Wagner (MW) polarization effects in protein powder samples. Combining our data with earlier literature results, we demonstrate the existence of three major relaxation processes in globular proteins. To understand the mechanisms of these relaxations we involve literature data on neutron scattering, simulations and NMR studies. The faster process is ascribed to coupled protein-hydration water motions and has relaxation time similar to 10-50 Ps at room temperature. The intermediate process is similar to 10(2)-10(3) times slower thanmore » the faster process and might be strongly affected by MW polarizations. Based on the analysis of data obtained by different experimental techniques and simulations, we ascribe this process to large scale domain-like motions of proteins. The slowest observed process is similar to 10(6)-10(7) times slower than the faster process and has anomalously large dielectric amplitude Delta epsilon similar to 10(2)-10(4). The microscopic nature of this process is not clear, but it seems to be related to the glass transition of hydrated proteins. The presentedresults suggest a general classification of the relaxation processes in hydrated proteins. (c) 2014 Elsevier B.V. All rights reserved.« less

Molecular Packing, Hydrogen Bonding, and Fast Dynamics in Lysozyme/Trehalose/Glycerol and Trehalose/Glycerol Glasses at Low Hydration.

PubMed

Lerbret, Adrien; Affouard, Frédéric

2017-10-12

Water and glycerol are well-known to facilitate the structural relaxation of amorphous protein matrices. However, several studies evidenced that they may also limit fast (∼picosecond-nanosecond, ps-ns) and small-amplitude (∼Å) motions of proteins, which govern their stability in freeze-dried sugar mixtures. To determine how they interact with proteins and sugars in glassy matrices and, thereby, modulate their fast dynamics, we performed molecular dynamics (MD) simulations of lysozyme/trehalose/glycerol (LTG) and trehalose/glycerol (TG) mixtures at low glycerol and water concentrations. Upon addition of glycerol and/or water, the glass transition temperature, T g , of LTG and TG mixtures decreases, the molecular packing of glasses is improved, and the mean-square displacements (MSDs) of lysozyme and trehalose either decrease or increase, depending on the time scale and on the temperature considered. A detailed analysis of the hydrogen bonds (HBs) formed between species reveals that water and glycerol may antiplasticize the fast dynamics of lysozyme and trehalose by increasing the total number and/or the strength of the HBs they form in glassy matrices.

Natural-gas hydrates: Resource of the twenty-first century?

USGS Publications Warehouse

Collett, T.S.

2001-01-01

Although considerable uncertainty and disagreement prevail concerning the world's gas-hydrate resources, the estimated amount of gas in those gas-hydrate accumulations greatly exceeds the volume of known conventional gas reserves. However, the role that gas hydrates will play in contributing to the world's energy requirements will ultimately depend less on the volume of gas-hydrate resources than on the cost to extract them. Gas hydrates occur in sedimentary deposits under conditions of pressure and temperature present in permafrost regions and beneath the sea in outer continental margins. The combined information from arctic gas-hydrate studies shows that in permafrost regions, gas hydrates may exist at subsurface depths ranging from about 130 m to 2000 m. The presence of gas hydrates in offshore continental margins has been inferred mainly from anomalous seismic reflectors (known as bottom-simulating reflectors) that have been mapped at depths below the seafloor ranging from approximately 100 m to 1100 m. Current estimates of the amount of gas in the world's marine and permafrost gas-hydrate accumulations are in rough accord at about 20,000 trillion m3. Gas hydrate as an energy commodity is often grouped with other unconventional hydrocarbon resources. In most cases, the evolution of a nonproducible unconventional resource to a producible energy resource has relied on significant capital investment and technology development. To evaluate the energy-resource potential of gas hydrates will also require the support of sustained research and development programs. Despite the fact that relatively little is known about the ultimate resource potential of gas hydrates, it is certain that they are a vast storehouse of natural gas, and significant technical challenges will need to be met before this enormous resource can be considered an economically producible reserve.

Methane gas hydrate effect on sediment acoustic and strength properties

USGS Publications Warehouse

Winters, W.J.; Waite, W.F.; Mason, D.H.; Gilbert, L.Y.; Pecher, I.A.

2007-01-01

To improve our understanding of the interaction of methane gas hydrate with host sediment, we studied: (1) the effects of gas hydrate and ice on acoustic velocity in different sediment types, (2) effect of different hydrate formation mechanisms on measured acoustic properties (3) dependence of shear strength on pore space contents, and (4) pore pressure effects during undrained shear.A wide range in acoustic p-wave velocities (Vp) were measured in coarse-grained sediment for different pore space occupants. Vp ranged from less than 1 km/s for gas-charged sediment to 1.77–1.94 km/s for water-saturated sediment, 2.91–4.00 km/s for sediment with varying degrees of hydrate saturation, and 3.88–4.33 km/s for frozen sediment. Vp measured in fine-grained sediment containing gas hydrate was substantially lower (1.97 km/s). Acoustic models based on measured Vp indicate that hydrate which formed in high gas flux environments can cement coarse-grained sediment, whereas hydrate formed from methane dissolved in the pore fluid may not.The presence of gas hydrate and other solid pore-filling material, such as ice, increased the sediment shear strength. The magnitude of that increase is related to the amount of hydrate in the pore space and cementation characteristics between the hydrate and sediment grains. We have found, that for consolidation stresses associated with the upper several hundred meters of sub-bottom depth, pore pressures decreased during shear in coarse-grained sediment containing gas hydrate, whereas pore pressure in fine-grained sediment typically increased during shear. The presence of free gas in pore spaces damped pore pressure response during shear and reduced the strengthening effect of gas hydrate in sands.

Selective Encaging of N2O in N2O-N2 Binary Gas Hydrates via Hydrate-Based Gas Separation.

PubMed

Yang, Youjeong; Shin, Donghoon; Choi, Seunghyun; Woo, Yesol; Lee, Jong-Won; Kim, Dongseon; Shin, Hee-Young; Cha, Minjun; Yoon, Ji-Ho

2017-03-21

The crystal structure and guest inclusion behaviors of nitrous oxide-nitrogen (N 2 O-N 2 ) binary gas hydrates formed from N 2 O/N 2 gas mixtures are determined through spectroscopic analysis. Powder X-ray diffraction results indicate that the crystal structure of all the N 2 O-N 2 binary gas hydrates is identified as the structure I (sI) hydrate. Raman spectra for the N 2 O-N 2 binary gas hydrate formed from N 2 O/N 2 (80/20, 60/40, 40/60 mol %) gas mixtures reveal that N 2 O molecules occupy both large and small cages of the sI hydrate. In contrast, there is a single Raman band of N 2 O molecules for the N 2 O-N 2 binary gas hydrate formed from the N 2 O/N 2 (20/80 mol %) gas mixture, indicating that N 2 O molecules are trapped in only large cages of the sI hydrate. From temperature-dependent Raman spectra and the Predictive Soave-Redlich-Kwong (PSRK) model calculation, we confirm the self-preservation of N 2 O-N 2 binary gas hydrates in the temperature range of 210-270 K. Both the experimental measurements and the PSRK model calculations demonstrate the preferential occupation of N 2 O molecules rather than N 2 molecules in the hydrate cages, leading to a possible process for separating N 2 O from gas mixtures via hydrate formation. The phase equilibrium conditions, pseudo-pressure-composition (P-x) diagram, and gas storage capacity of N 2 O-N 2 binary gas hydrates are discussed in detail.

The characteristics of gas hydrates occurring in natural environment

NASA Astrophysics Data System (ADS)

Lu, H.; Moudrakovski, I.; Udachin, K.; Enright, G.; Ratcliffe, C.; Ripmeester, J.

2009-12-01

In the past few years, extensive analyses have been carried out for characterizing the natural gas hydrate samples from Cascadia, offshore Vancouver Island; Mallik, Mackenzie Delta; Mount Elbert, Alaska North Slope; Nankai Trough, offshore Japan; Japan Sea and offshore India. With the results obtained, it is possible to give a general picture of the characteristics of gas hydrates occurring in natural environment. Gas hydrate can occur in sediments of various types, from sands to clay, although it is preferentially enriched in sediments of certain types, for example coarse sands and fine volcanic ash. Most of the gas hydrates in sediments are invisible, occurring in the pores of the sediments, while some hydrates are visible, appearing as massive, nodular, planar, vein-like forms and occurring around the seafloor, in the fractures related to fault systems, or any other large spaces available in sediments. Although methane is the main component of most of the natural gas hydrates, C2 to C7 hydrocarbons have been recognized in hydrates, sometimes even in significant amounts. Shallow marine gas hydrates have been found generally to contain minor amounts of hydrogen sulfide. Gas hydrate samples with complex gas compositions have been found to have heterogeneous distributions in composition, which might reflect changes in the composition of the available gas in the surrounding environment. Depending on the gas compositions, the structure type of a natural gas hydrate can be structure I, II or H. For structure I methane hydrate, the large cages are almost fully occupied by methane molecules, while the small cages are only partly occupied. Methane hydrates occurring in different environments have been identified with almost the same crystallographic parameters.

The impacts of surface polarity on the solubility of nanoparticle

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

Zhu, Jianzhuo; Su, Jiguo, E-mail: jiguosu@ysu.edu.cn; Ou, Xinwen

In order to study the dependence of water solubility and hydration behavior of nanoparticles on their surface polarity, we designed polar nanoparticles with varying surface polarity by assigning atomic partial charge to the surface of C60. The water solubility of the nanoparticle is enhanced by several orders of magnitude after the introduction of surface polarity. Nevertheless, when the atomic partial charge grows beyond a certain value (q{sub M}), the solubility continuously decreases to the level of nonpolar nanoparticle. It should be noted that such q{sub M} is comparable with atomic partial charge of a variety of functional groups. The hydrationmore » behaviors of nanoparticles were then studied to investigate the non-monotonic dependence of solubility on the surface polarity. The interaction between the polar nanoparticle and the hydration water is stronger than the nonpolar counterpart, which should facilitate the dissolution of the nanoparticles. On the other hand, the surface polarity also reduces the interaction of hydration water with the other water molecules and enhances the interaction between the nanoparticles which may hinder their dispersion. Besides, the introduction of surface polarity disturbs and even rearranges the hydration structure of nonpolar nanoparticle. Interestingly, the polar nanoparticle with less ordered hydration structure tends to have higher water solubility.« less

Impact of Compound Hydrate Dynamics on Phase Boundary Changes

NASA Astrophysics Data System (ADS)

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

2006-12-01

Compound hydrate reactions are affected by the local concentration of hydrate forming materials (HFM). The relationship between HFM composition and the phase boundary is as significant as temperature and pressure. Selective uptake and sequestration of preferred hydrate formers (PF) has wide ranging implications for the state and potential use of natural hydrate formation, including impact on climate. Rising mineralizing fluids of hydrate formers (such as those that occur on Earth and are postulated to exist elsewhere in the solar system) will sequester PF before methane, resulting in a positive relationship between depth and BTU content as ethane and propane are removed before methane. In industrial settings the role of preferred formers can separate gases. When depressurizing gas hydrate to release the stored gas, the hydrate initial composition will set the decomposition phase boundary because the supporting solution takes on the composition of the hydrate phase. In other settings where hydrate is formed, transported, and then dissociated, similar effects can control the process. The behavior of compound hydrate systems can primarily fit into three categories: 1) In classically closed systems, all the material that can form hydrate is isolated, such as in a sealed laboratory vessel. In such systems, formation and decomposition are reversible processes with observed hysteresis related to mass or heat transfer limitations, or the order and magnitude in which individual hydrate forming gases are taken up from the mixture and subsequently released. 2) Kinetically closed systems are exposed to a solution mass flow across a hydrate mass. These systems can have multiple P-T phase boundaries based on the local conditions at each face of the hydrate mass. A portion of hydrate that is exposed to fresh mineralizing solution will contain more preferred hydrate formers than another portion that is exposed to a partially depleted solution. Examples of kinetically closed systems include pipeline blockages and natural hydrate concentrations associated with upwelling fluids in marine sediments. 3) In open systems, mass can either flow into or out of a system. In such situations compound hydrate will form or decompose to re-establish chemical equilibrium. This is accomplished by 1) loading/consuming a preferred hydrate former to/from the surroundings, 2) lowering/raising the temperature of the system, and 3) increasing the local pressure. Examples of this type of system include hydrate produced for low pressure transport, depressurized or superheated hydrate settings (pipeline remediation or energy recovery), or in an industrial process where formation of compound hydrates may be used to separate and concentrate gases from a mixture. The relationship between composition and the phase boundary is as important as pressure and temperature effects. Composition is less significant for simple hydrates where the hydrate behaves as a one-component mineral, but for compound hydrate, feedback between pressure, temperature, and composition can result in complex system behavior.

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.

Spatial and temporal dependencies of structure II to structure I methane hydrate transformation in porous media under moderate pressure and temperature conditions

NASA Astrophysics Data System (ADS)

Dong, T.; Lin, J. F.; Gu, J. T.; Polito, P. J.; O'Connell, J.; Flemings, P. B.

2017-12-01

We used Raman spectroscopy to monitor methane hydrates transforming from structure II to structure I at the pore scale as a function of space and time. It is well documented that structure I hydrate is the thermodynamically stable phase for pure methane hydrate (<100 MPa, < 20 °C), but due to kinetic limitation, initial methane hydrate formation produces a mixture of structure I and structure II hydrates. We observed that the structure transformation originated around the porous medium grains and over time slowly migrated into the pore space. We synthesized methane hydrates in spherical glass beads (210-297 µm in diameter) in a pressure cell with a sapphire window to integrate optical observations with Raman measurements. We injected CH4 vapor into the cell and supplied only deionized water thereafter to maintain a constant pressure of 14.6 MPa at 3.5 °C, with 14.5 °C subcooling. We used Raman spectroscopy to map the methane hydrates in pore spaces at 5-25 µm resolution, in order to monitor the occupancy ratio of CH4 in large cages to CH4 in small cages, by their Raman peak intensity ratio, i.e., I( 2905 cm-1)/I( 2915 cm-1). We identified 3 stages of hydrate formation at the pore scale: (1) after the initial hydrate formation, Raman mapping revealed that the occupancy ratio ranged from 0.5 to 3, indicating a mixture of structure I and II hydrates; (2) within 1 week, we observed that all structure I hydrates occurred on the glass bead surfaces and structure II hydrates occupied the pore spaces; (3) over the following 2 weeks, structure II hydrates gradually recrystallized into structure I hydrates from glass bead surfaces towards the pore space. These results imply that (1) due to kinetics, the formation of methane hydrate in porous media is more complex than previously thought, and (2) the bulk physical and chemical properties of laboratory-synthesized methane hydrates in porous media may drift over time, as methane hydrates recrystallize from a metastable phase (structure II) to the thermodynamically stable phase (structure I).

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.

Hydro-mechanical properties of pressure core sediments recovered from the Krishna-Godavari Basin during India's National Gas Hydrate Program Expedition NGHP-02

NASA Astrophysics Data System (ADS)

Yoneda, J.; Oshima, M.; Kida, M.; Kato, A.; Konno, Y.; Jin, Y.; Waite, W. F.; Jang, J.; Kumar, P.; Tenma, N.

2017-12-01

Pressure coring and analysis technology allows for gas hydrate to be recovered from the deep seabed, transferred to the laboratory and characterized while continuously maintaining gas hydrate stability. For this study, dozens of hydrate-bearing pressure core sediment subsections recovered from the Krishna-Godavari Basin during India's National Gas Hydrate Program Expedition NGHP-02 were tested with Pressure Core Non-destructive Analysis Tools (PNATs) through a collaboration between Japan and India. PNATs, originally developed by AIST as a part of the Japanese National hydrate research program (MH21, funded by METI) conducted permeability, compression and consolidation tests under various effective stress conditions, including the in situ stress state estimated from downhole bulk density measurements. At the in situ effective stress, gas hydrate-bearing sediments had an effective permeability range of 0.01-10mD even at pore-space hydrate saturations above 60%. Permeability increased by 10 to 100 times after hydrate dissociation at the same effective stress, but these post-dissociation gains were erased when effective stress was increased from in situ values ( 1 MPa) to 10MPa in a simulation of the depressurization method for methane extraction from hydrate. Vertical-to-horizontal permeability anisotropy was also investigated. First-ever multi-stage loading tests and strain-rate alternation compression tests were successfully conducted for evaluating sediment strengthening dependence on the rate and magnitude of effective confining stress changes. In addition, oedometer tests were performed up to 40MPa of consolidation stress to simulate the depressurization method in ultra-deep sea environments. Consolidation curves measured with and without gas hydrate were investigated over a wide range of effective confining stresses. Compression curves for gas hydrate-bearing sediments were convex downward due to high hydrate saturations. Consolidation tests show that, regardless of the consolidation history with hydrate in place, the consolidation behavior after dissociation will first return to, then follow, the original normal consolidation curve for the hydrate-free host sediment.

Crystal structure, stability and spectroscopic properties of methane and CO2 hydrates.

PubMed

Martos-Villa, Ruben; Francisco-Márquez, Misaela; Mata, M Pilar; Sainz-Díaz, C Ignacio

2013-07-01

Methane hydrates are highly present in sea-floors and in other planets and their moons. Hence, these compounds are of great interest for environment, global climate change, energy resources, and Cosmochemistry. The knowledge of stability and physical-chemical properties of methane hydrate crystal structure is important for evaluating some new green becoming technologies such as, strategies to produce natural gas from marine methane hydrates and simultaneously store CO2 as hydrates. However, some aspects related with their stability, spectroscopic and other chemical-physical properties of both hydrates are not well understood yet. The structure and stability of crystal structure of methane and CO2 hydrates have been investigated by means of calculations with empirical interatomic potentials and quantum-mechanical methods based on Hartree-Fock and Density Functional Theory (DFT) approximations. Molecular Dynamic simulations have been also performed exploring different configurations reproducing the experimental crystallographic properties. Spectroscopic properties have also been studied. Frequency shifts of the main vibration modes were observed upon the formation of these hydrates, confirming that vibration stretching peaks of C-H at 2915cm(-1) and 2905cm(-1) are due to methane in small and large cages, respectively. Similar effect is observed in the CO2 clathrates. The guest-host binding energy in these clathrates calculated with different methods are compared and discussed in terms of adequacy of empirical potentials and DFT methods for describing the interactions between gas guest and the host water cage, proving an exothermic nature of methane and CO2 hydrates formation process. Copyright © 2013 Elsevier Inc. All rights reserved.

CO2 Injection Into CH4 Hydrate Reservoirs: Quantifying Controls of Micro-Scale Processes

NASA Astrophysics Data System (ADS)

Bigalke, N. K.; Deusner, C.; Kossel, E.; Haeckel, M.

2014-12-01

The exchangeability of methane for carbon dioxide in gas hydrates opens the possibility of producing emission-neutral hydrocarbon energy. Recent field tests have shown that the production of natural gas from gas hydrates is feasible via injection of carbon dioxide into sandy, methane-hydrate-bearing sediment strata. Industrial-scale application of this method requires identification of thermo- and fluid-dynamic as well as kinetic controls on methane yield from and carbon dioxide retention within the reservoir. Extraction of gas via injection of carbon dioxide into the hydrate reservoir triggers a number of macroscopic effects, which are revealed for example by changes of the hydraulic conductivity and geomechanical stability. Thus far, due to analytical limitations, localized reactions and fluid-flow phenomena held responsible for these effects remain unresolved on the microscale (1 µm - 1 mm) and at near-natural reservoir conditions. We address this deficit by showing results from high-resolution, two-dimensional Raman spectroscopy mappings of an artificial hydrate reservoir during carbon dioxide injection under realistic reservoir conditions. The experiments allow us to resolve hydrate conversion rate and efficiency as well as activation of fluid pathways in space and time and their effect on methane yield, carbon-dioxide retention and hydraulic conductivity of the reservoir. We hypothesize that the conversion of single hydrate grains is a diffusion-controlled process which starts at the grain surface before continuing into the grain interior and show that the conversion can be modeled simply by using published permeation coefficients for CO2 and CH4 in hydrate and grain size as only input parameters.

Methane sources in gas hydrate-bearing cold seeps: Evidence from radiocarbon and stable isotopes

USGS Publications Warehouse

Pohlman, J.W.; Bauer, J.E.; Canuel, E.A.; Grabowski, K.S.; Knies, D.L.; Mitchell, C.S.; Whiticar, Michael J.; Coffin, R.B.

2009-01-01

Fossil methane from the large and dynamic marine gas hydrate reservoir has the potential to influence oceanic and atmospheric carbon pools. However, natural radiocarbon (14C) measurements of gas hydrate methane have been extremely limited, and their use as a source and process indicator has not yet been systematically established. In this study, gas hydrate-bound and dissolved methane recovered from six geologically and geographically distinct high-gas-flux cold seeps was found to be 98 to 100% fossil based on its 14C content. Given this prevalence of fossil methane and the small contribution of gas hydrate (??? 1%) to the present-day atmospheric methane flux, non-fossil contributions of gas hydrate methane to the atmosphere are not likely to be quantitatively significant. This conclusion is consistent with contemporary atmospheric methane budget calculations. In combination with ??13C- and ??D-methane measurements, we also determine the extent to which the low, but detectable, amounts of 14C (~ 1-2% modern carbon, pMC) in methane from two cold seeps might reflect in situ production from near-seafloor sediment organic carbon (SOC). A 14C mass balance approach using fossil methane and 14C-enriched SOC suggests that as much as 8 to 29% of hydrate-associated methane carbon may originate from SOC contained within the upper 6??m of sediment. These findings validate the assumption of a predominantly fossil carbon source for marine gas hydrate, but also indicate that structural gas hydrate from at least certain cold seeps contains a component of methane produced during decomposition of non-fossil organic matter in near-surface sediment.

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.

Sensitivity Analysis of Methane Hydrate Reservoirs: Effects of Reservoir Parameters on Gas Productivity and Economics

NASA Astrophysics Data System (ADS)

Anderson, B. J.; Gaddipati, M.; Nyayapathi, L.

2008-12-01

This paper presents a parametric study on production rates of natural gas from gas hydrates by the method of depressurization, using CMG STARS. Seven factors/parameters were considered as perturbations from a base-case hydrate reservoir description based on Problem 7 of the International Methane Hydrate Reservoir Simulator Code Comparison Study led by the Department of Energy and the USGS. This reservoir is modeled after the inferred properties of the hydrate deposit at the Prudhoe Bay L-106 site. The included sensitivity variables were hydrate saturation, pressure (depth), temperature, bottom-hole pressure of the production well, free water saturation, intrinsic rock permeability, and porosity. A two-level (L=2) Plackett-Burman experimental design was used to study the relative effects of these factors. The measured variable was the discounted cumulative gas production. The discount rate chosen was 15%, resulting in the gas contribution to the net present value of a reservoir. Eight different designs were developed for conducting sensitivity analysis and the effects of the parameters on the real and discounted production rates will be discussed. The breakeven price in various cases and the dependence of the breakeven price on the production parameters is given in the paper. As expected, initial reservoir temperature has the strongest positive effect on the productivity of a hydrate deposit and the bottom-hole pressure in the production well has the strongest negative dependence. Also resulting in a positive correlation is the intrinsic permeability and the initial free water of the formation. Negative effects were found for initial hydrate saturation (at saturations greater than 50% of the pore space) and the reservoir porosity. These negative effects are related to the available sensible heat of the reservoir, with decreasing productivity due to decreasing available sensible heat. Finally, we conclude that for the base case reservoir, the break-even price (BEP) for natural gas is approximately 7/mcf and for warmer and deeper reservoirs the BEP can approach 5.33/mcf.

The impact of flow focusing on gas hydrate accumulations in overpressured marine sediments

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

Nole, Michael; Daigle, Hugh; Cook, Ann

This study demonstrates the potential for flow focusing due to overpressuring in marine sedimentary environments to act as a significant methane transport mechanism from which methane hydrate can precipitate in large quantities in dipping sandstone bodies. Traditionally, gas hydrate accumulations in nature are discussed as resulting from either short-range diffusive methane migration or from long-range advective fluid transport sourced from depth. However, 3D simulations performed in this study demonstrate that a third migration mechanism, short-range advective transport, can provide a significant methane source that is unencumbered by limitations of the other two end-member mechanisms. Short-range advective sourcing is advantageous overmore » diffusion because it can convey greater amounts of methane to sands over shorter timespans, yet it is not necessarily limited by down-dip pore blocking in sands as is typical of updip advection from a deep source. These results are novel because they integrate pore size impacts on spatial solubility gradients, grid block properties that evolve through time, and methane sourcing through microbial methanogenesis into a holistic characterization of environments exposed to multiple methane hydrate sourcing mechanisms. We show that flow focusing toward sand bodies transports large quantities of methane, the magnitude of which are determined by the sand-clay solubility contrast, and generates larger quantities of hydrate in sands than a solely diffusive system; after depositing methane as hydrate, fluid exiting a sand body is depleted in methane and leaves a hydrate free region in its wake above the sand. Additionally, we demonstrate that in overpressured environments, hydrate growth is initially diffusively dominated before transitioning to an advection-dominated regime. The timescale and depth at which this transition takes place depends primarily on the rate of microbial metabolism and the sedimentation rate but only depends loosely on the degree of overpressuring.« less

Calculation of Derivative Thermodynamic Hydration and Aqueous Partial Molar Properties of Ions Based on Atomistic Simulations.

PubMed

Dahlgren, Björn; Reif, Maria M; Hünenberger, Philippe H; Hansen, Niels

2012-10-09

The raw ionic solvation free energies calculated on the basis of atomistic (explicit-solvent) simulations are extremely sensitive to the boundary conditions and treatment of electrostatic interactions used during these simulations. However, as shown recently [Kastenholz, M. A.; Hünenberger, P. H. J. Chem. Phys.2006, 124, 224501 and Reif, M. M.; Hünenberger, P. H. J. Chem. Phys.2011, 134, 144104], the application of an appropriate correction scheme allows for a conversion of the methodology-dependent raw data into methodology-independent results. In this work, methodology-independent derivative thermodynamic hydration and aqueous partial molar properties are calculated for the Na(+) and Cl(-) ions at P° = 1 bar and T(-) = 298.15 K, based on the SPC water model and on ion-solvent Lennard-Jones interaction coefficients previously reoptimized against experimental hydration free energies. The hydration parameters considered are the hydration free energy and enthalpy. The aqueous partial molar parameters considered are the partial molar entropy, volume, heat capacity, volume-compressibility, and volume-expansivity. Two alternative calculation methods are employed to access these properties. Method I relies on the difference in average volume and energy between two aqueous systems involving the same number of water molecules, either in the absence or in the presence of the ion, along with variations of these differences corresponding to finite pressure or/and temperature changes. Method II relies on the calculation of the hydration free energy of the ion, along with variations of this free energy corresponding to finite pressure or/and temperature changes. Both methods are used considering two distinct variants in the application of the correction scheme. In variant A, the raw values from the simulations are corrected after the application of finite difference in pressure or/and temperature, based on correction terms specifically designed for derivative parameters at P° and T(-). In variant B, these raw values are corrected prior to differentiation, based on corresponding correction terms appropriate for the different simulation pressures P and temperatures T. The results corresponding to the different calculation schemes show that, except for the hydration free energy itself, accurate methodological independence and quantitative agreement with even the most reliable experimental parameters (ion-pair properties) are not yet reached. Nevertheless, approximate internal consistency and qualitative agreement with experimental results can be achieved, but only when an appropriate correction scheme is applied, along with a careful consideration of standard-state issues. In this sense, the main merit of the present study is to set a clear framework for these types of calculations and to point toward directions for future improvements, with the ultimate goal of reaching a consistent and quantitative description of single-ion hydration thermodynamics in molecular dynamics simulations.

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

Femtosecond movies of water near interfaces at sub-Angstrom resolution

NASA Astrophysics Data System (ADS)

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

2010-03-01

The behavior of liquid water near interfaces with nanoscopic variations in chemistry influences a broad range of phenomena in biology. Using inelastic x-ray scattering (IXS) data from 3rd-generation synchrotron x-ray sources, we reconstruct the Greens function of liquid water, which describes the å-scale spatial and femtosecond-scale temporal evolution of density fluctuations. We extend this response function formalism to reconstruct the evolution of hydration structures near dynamic surfaces with different charge distributions, in order to define more precisely the molecular signature of hydrophilicity and hydrophobicity. Moreover, we investigate modifications to surface hydration structures and dynamics as the size of hydrophilic and hydrophobic patches are varied.

Investigation of the structure and stability of SnO2 nanocrystal and its surface-bound water

NASA Astrophysics Data System (ADS)

Wang, H.; Wesolowski, D. J.; Proffen, T. E.; Kolesnikov, A. I.; Vlcek, L.; Wang, W.; Feygenson, M.; Sofo, J. O.; Anovitz, L.

2012-12-01

Driven partly by a myriad use of engineered metal oxide nanoparticles, understanding their stabilities and interactions with environmental matrix during and after applications are desired. SnO2 (cassiterite) is one of the frequently used oxides in solid-state gas sensors and oxidation catalysts. A close relationship between the gas sensitivity and catalysis of oxides with their surface chemistry ensures continuous interests in the study of SnO2-water interfacial complexity (unavoidable "contamination" in which water can potentially participate in reactions and change SnO2 conductivity). Such information is important, as the existence of hydration layers on the surface of SnO2 nanoparticles not only play a critical role in stabilizing the nanoparticle but also affect its selectivity/sensitivity, as a nanosensor. SnO2 nanoparticles (2-5 nm) synthesized by a wet chemical route are dominated by {110} faces and are capped with H2O or D2O water molecules (after purification), depending on isotopic composition of water used for syntheses. When water is in direct contact with terminal Sn and O atoms, there is a controversial argument as to whether or not dissociative adsorption occurs (i.e., formation of hydroxyl groups). Although theoretical studies point toward a tendency for dissociative configuration in the direct contact layer, experimental studies have not unambiguously confirmed this conclusion. We present combined investigations using neutron total scattering (NPDF at the NOMAD beamline, SNS) and inelastic neutron scattering (INS at the SEQUOIA beamline, SNS) techniques as static and dynamic probes to reveal structure and dynamics of water and SnO2 nanocrystalline stability upon dehydration. The NPDF results (measured with deuterated samples) suggest layered water configurations with G(r) signals dominated by O-D bonds at 0.98 Å, and the second hydration layer that gives a broad peak at 2.5-4 Å. There is no evidence of a third hydration layer at 5-7 Å as shown by our previous molecular dynamic (MD) simulations, perhaps because this outermost hydration layer is not laterally-ordered parallel to the oxide surface and thus contributes a much weaker G(r) signal than the first two layers. Additionally, due to the relatively broad distribution of D-D distances and Fourier termination ripples, NPDF results cannot provide unambiguous evidence about the formation of hydroxylated surfaces, even though the dissociative MD model gives a better fitted result. Upon heating to 250 °C (at 10-7 bar), SnO2 nanoparticles start to show surface transformation and increased crystallinity before completion of dehydration. This likely corresponds to the minimum concentration of surface-bound groups required to stabilize the nanoparticles (i.e., < 0.7 monolayer coverage). Attempts to remove D2O/OD- groups below this threshold lead to rapidly increase of crystallinity. INS experiments on SnO2 nanoparticles with a minimum threshold coverage and with those from a fully hydrated sample clearly suggested dissociated water configurations with no observations of H2O bending modes in the sample with a minimum threshold coverage. Corresponding ab initio MD simulation on SnO2 (110) surface for a comparison with INS results is underway to provide a complete picture of SnO2-water surface dynamics.

Interfacial Connection Mechanisms in Calcium-Silicate-Hydrates/Polymer Nanocomposites: A Molecular Dynamics Study.

PubMed

Zhou, Yang; Hou, Dongshuai; Manzano, Hegoi; Orozco, Carlos A; Geng, Guoqing; Monteiro, Paulo J M; Liu, Jiaping

2017-11-22

Properties of organic/inorganic composites can be highly dependent on the interfacial connections. In this work, molecular dynamics, using pair-potential-based force fields, was employed to investigate the structure, dynamics, and stability of interfacial connections between calcium-silicate-hydrates (C-S-H) and organic functional groups of three different polymer species. The calculation results suggest that the affinity between C-S-H and polymers is influenced by the polarity of the functional groups and the diffusivity and aggregation tendency of the polymers. In the interfaces, the calcium counterions from C-S-H act as the coordination atoms in bridging the double-bonded oxygen atoms in the carboxyl groups (-COOH), and the Ca-O connection plays a dominant role in binding poly(acrylic acid) (PAA) due to the high bond strength defined by time-correlated function. The defective calcium-silicate chains provide significant numbers of nonbridging oxygen sites to accept H-bonds from -COOH groups. As compared with PAA, the interfacial interactions are much weaker between C-S-H and poly(vinyl alcohol) (PVA) or poly(ethylene glycol) (PEG). Predominate percentage of the -OH groups in the PVA form H-bonds with inter- and intramolecule, which results in the polymer intertwining and reduces the probability of H-bond connections between PVA and C-S-H. On the other hand, the inert functional groups (C-O-C) in poly(ethylene glycol) (PEG) make this polymer exhibit unfolded configurations and move freely with little restrictions. The interaction mechanisms interpreted in this organic-inorganic interface can give fundamental insights into the polymer modification of C-S-H and further implications to improving cement-based materials from the genetic level.

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.

A tribo-mechanical analysis of PVA-based building-blocks for implementation in a 2-layered skin model.

PubMed

Morales Hurtado, M; de Vries, E G; Zeng, X; van der Heide, E

2016-09-01

Poly(vinyl) alcohol hydrogel (PVA) is a well-known polymer widely used in the medical field due to its biocompatibility properties and easy manufacturing. In this work, the tribo-mechanical properties of PVA-based blocks are studied to evaluate their suitability as a part of a structure simulating the length scale dependence of human skin. Thus, blocks of pure PVA and PVA mixed with Cellulose (PVA-Cel) were synthesised via freezing/thawing cycles and their mechanical properties were determined by Dynamic Mechanical Analysis (DMA) and creep tests. The dynamic tests addressed to elastic moduli between 38 and 50kPa for the PVA and PVA-Cel, respectively. The fitting of the creep compliance tests in the SLS model confirmed the viscoelastic behaviour of the samples with retardation times of 23 and 16 seconds for the PVA and PVA-Cel, respectively. Micro indentation tests were also achieved and the results indicated elastic moduli in the same range of the dynamic tests. Specifically, values between 45-55 and 56-81kPa were obtained for the PVA and PVA-Cel samples, respectively. The tribological results indicated values of 0.55 at low forces for the PVA decreasing to 0.13 at higher forces. The PVA-Cel blocks showed lower friction even at low forces with values between 0.2 and 0.07. The implementation of these building blocks in the design of a 2-layered skin model (2LSM) is also presented in this work. The 2LSM was stamped with four different textures and their surface properties were evaluated. The hydration of the 2LSM was also evaluated with a corneometer and the results indicated a gradient of hydration comparable to the human skin. Copyright © 2016 Elsevier Ltd. All rights reserved.

Origins of saccharide-dependent hydration at aluminate, silicate, and aluminosilicate surfaces.

PubMed

Smith, Benjamin J; Rawal, Aditya; Funkhouser, Gary P; Roberts, Lawrence R; Gupta, Vijay; Israelachvili, Jacob N; Chmelka, Bradley F

2011-05-31

Sugar molecules adsorbed at hydrated inorganic oxide surfaces occur ubiquitously in nature and in technologically important materials and processes, including marine biomineralization, cement hydration, corrosion inhibition, bioadhesion, and bone resorption. Among these examples, surprisingly diverse hydration behaviors are observed for oxides in the presence of saccharides with closely related compositions and structures. Glucose, sucrose, and maltodextrin, for example, exhibit significant differences in their adsorption selectivities and alkaline reaction properties on hydrating aluminate, silicate, and aluminosilicate surfaces that are shown to be due to the molecular architectures of the saccharides. Solid-state (1)H, (13)C, (29)Si, and (27)Al nuclear magnetic resonance (NMR) spectroscopy measurements, including at very high magnetic fields (19 T), distinguish and quantify the different molecular species, their chemical transformations, and their site-specific adsorption on different aluminate and silicate moieties. Two-dimensional NMR results establish nonselective adsorption of glucose degradation products containing carboxylic acids on both hydrated silicates and aluminates. In contrast, sucrose adsorbs intact at hydrated silicate sites and selectively at anhydrous, but not hydrated, aluminate moieties. Quantitative surface force measurements establish that sucrose adsorbs strongly as multilayers on hydrated aluminosilicate surfaces. The molecular structures and physicochemical properties of the saccharides and their degradation species correlate well with their adsorption behaviors. The results explain the dramatically different effects that small amounts of different types of sugars have on the rates at which aluminate, silicate, and aluminosilicate species hydrate, with important implications for diverse materials and applications.

On the intermolecular vibrational coupling, hydrogen bonding, and librational freedom of water in the hydration shell of mono- and bivalent anions.

PubMed

Ahmed, Mohammed; Namboodiri, V; Singh, Ajay K; Mondal, Jahur A

2014-10-28

The hydration energy of an ion largely resides within the first few layers of water molecules in its hydration shell. Hence, it is important to understand the transformation of water properties, such as hydrogen-bonding, intermolecular vibrational coupling, and librational freedom in the hydration shell of ions. We investigated these properties in the hydration shell of mono- (Cl(-) and I(-)) and bivalent (SO4(2-) and CO3(2-)) anions by using Raman multivariate curve resolution (Raman-MCR) spectroscopy in the OH stretch, HOH bend, and [bend+librational] combination bands of water. Raman-MCR of aqueous Na-salt (NaCl, NaI, Na2SO4, and Na2CO3) solutions provides ion-correlated spectra (IC-spectrum) which predominantly bear the vibrational characteristics of water in the hydration shell of respective anions. Comparison of these IC-spectra with the Raman spectrum of bulk water in different spectral regions reveals that the water is vibrationally decoupled with its neighbors in the hydration shell. Hydrogen-bond strength and librational freedom also vary with the nature of anion: hydrogen-bond strength, for example, decreases as CO3(2-) > SO4(2-) > bulk water ≈ Cl(-) > I(-); and the librational freedom increases as CO3(2-) ≈ SO4(2-) < bulk water < Cl(-) < I(-). It is believed that these structural perturbations influence the dynamics of coherent energy transfer and librational reorientation of water in the hydration shell of anions.

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.

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.

Coupled numerical modeling of gas hydrates bearing sediments from laboratory to field-scale conditions

NASA Astrophysics Data System (ADS)

Sanchez, M. J.; Santamarina, C.; Gai, X., Sr.; Teymouri, M., Sr.

2017-12-01

Stability and behavior of Hydrate Bearing Sediments (HBS) are characterized by the metastable character of the gas hydrate structure which strongly depends on thermo-hydro-chemo-mechanical (THCM) actions. Hydrate formation, dissociation and methane production from hydrate bearing sediments are coupled THCM processes that involve, amongst other, exothermic formation and endothermic dissociation of hydrate and ice phases, mixed fluid flow and large changes in fluid pressure. The analysis of available data from past field and laboratory experiments, and the optimization of future field production studies require a formal and robust numerical framework able to capture the very complex behavior of this type of soil. A comprehensive fully coupled THCM formulation has been developed and implemented into a finite element code to tackle problems involving gas hydrates sediments. Special attention is paid to the geomechanical behavior of HBS, and particularly to their response upon hydrate dissociation under loading. The numerical framework has been validated against recent experiments conducted under controlled conditions in the laboratory that challenge the proposed approach and highlight the complex interaction among THCM processes in HBS. The performance of the models in these case studies is highly satisfactory. Finally, the numerical code is applied to analyze the behavior of gas hydrate soils under field-scale conditions exploring different features of material behavior under possible reservoir conditions.

Dependence of phonatory effort on hydration level.

PubMed

Verdolini, K; Titze, I R; Fennell, A

1994-10-01

In this study, a double-blind placebo-controlled approach was used to assess the relation between hydration level and phonatory effort. Twelve adult, untrained voice users with normal voices participated as subjects. Each subject received a 4-hour hydration treatment, a 4-hour dehydration treatment, and a 4-hour placebo (control) treatment. Following each treatment, phonatory effort was measured with a physiological measure, phonation threshold pressure (PTP), and with a psychological measure, direct magnitude estimation of perceived phonatory effort (DMEPPE). Summarizing the results across these measures, the findings indicated an inverse relation between phonatory effort and hydration level, but primarily for high-pitched phonation tasks. The findings for PTPs replicated those from an earlier study conducted without double-blind experimental manipulations (Verdolini-Marston, Titze, & Druker, 1990). Theoretical discussion focuses on the possible role of vocal fold tissue viscosity for hydration and dehydration effects, although direct measures of tissue viscosity are lacking.

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

Sensitivity Studies on Productivity Performance from 3D Heterogeneous Reservoir Model Based on the L-Pad Gas Hydrate Accumulation in Prudhoe Bay Unit, North Slope Alaska

NASA Astrophysics Data System (ADS)

Myshakin, E. M.; Ajayi, T.; Seol, Y.; Boswell, R.

2016-12-01

Three-dimensional reservoir model of the "L-Pad" hydrate deposit located in the Prudhoe Bay region of the Alaska's North Slope was created including four stratigraphic units; silty shale overburden, hydrate-bearing D sand, inter-reservoir silty shale, hydrate-bearing C sand, and silty shale underburden. The model incorporates the actual geological settings, accounts for the presence of faults, reservoir dip, the hydrate-water contact in the C sand. Geostatistical porosity distributions in D and C sands conditioned to log data from 78 wells drilled in the vicinity of the Prudhoe Bay "L-pad" were developed providing vertical and lateral 3D heterogeneity in porosity and porosity-dependent hydrate saturation and intrinsic permeability. Gas production potential was estimated using a conventional vertical wellbore completion and a deviated toe-down wellbore perforated through both sand units to induce hydrate depressurization at a constant bottom-hole pressure. The results have shown the greater performance of the deviated well design over the vertical one. The scenarios involving simultaneous and sequential hydrate dissociation in sand units were explored and the effect of the underlying aquifer in the C sand was estimated. Sensitivity analysis has demonstrated that hydraulic communication with over- and underlying shale units affects production in the beginning of depressurization due to competitive water influx into producing mobile flow and could suppress efficient hydrate decomposition resulting in production lag. Another important factor greatly influencing the productivity performance is the effective permeability of hydrate-bearing sediment controlled by the relative permeability function. The results call for the necessity of thorough fundamental studies to understand multi-phase flow in hydrate-bearing sediments with different hydrate precipitation habits.

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.

A new estimate of the volume and distribution of gas hydrate in the northern Gulf of Mexico

NASA Astrophysics Data System (ADS)

Majumdar, U.; Cook, A.

2016-12-01

In spite of the wealth of information gained over the last several decades about gas hydrate in the northern Gulf of Mexico, there is still considerable uncertainty about the distribution and volume of gas hydrate. In our assessment we build a dataset of basin-wide gas hydrate distribution and thickness, as appraised from publicly available petroleum industry well logs within the gas hydrate stability zone (HSZ), and subsequently develop a Monte Carlo to determine the volumetric estimate of gas hydrate using the dataset. We evaluate the presence of gas hydrate from electrical resistivity well logs, and categorized possible reservoir type (either sand or clay) based on the gamma ray response and resistivity curve characteristics. Out of the 798 wells with resistivity well log data within the HSZ we analyzed, we found evidence of gas hydrate in 124 wells. In this research we present a new stochastic estimate of the gas hydrate volume in the northern Gulf of Mexico guided by our well log dataset. For our Monte Carlo simulation, we divided our assessment area of 200,000 km2 into 1 km2 grid cells. Our volume assessment model incorporates variables unique to our well log dataset such as the likelihood of gas hydrate occurrence, fraction of the HSZ occupied by gas hydrate, reservoir type, and gas hydrate saturation depending on the reservoir, in each grid cell, in addition to other basic variables such as HSZ thickness and porosity. Preliminary results from our model suggests that the total volume of gas at standard temperature and pressure in gas hydrate in the northern Gulf of Mexico is in the range of 430 trillion cubic feet (TCF) to 730 TCF, with a mean volume of 585 TCF. While the reservoir distribution from our well log dataset found gas hydrate in sand reservoirs in 30 wells out of the 124 wells with evidence of gas hydrate ( 24%), we find sand reservoirs contain over half of the total volume of gas hydrate in the Gulf of Mexico, as a result of the relatively high gas hydrate saturation in sand.

Mechanical Performance of Asphalt Mortar Containing Hydrated Lime and EAFSS at Low and High Temperatures.

PubMed

Moon, Ki Hoon; Falchetto, Augusto Cannone; Wang, Di; Riccardi, Chiara; Wistuba, Michael P

2017-07-03

In this paper, the possibility of improving the global response of asphalt materials for pavement applications through the use of hydrated lime and Electric Arc-Furnace Steel Slag (EAFSS) was investigated. For this purpose, a set of asphalt mortars was prepared by mixing two different asphalt binders with fine granite aggregate together with hydrated lime or EAFSS at three different percentages. Bending Beam Rheometer (BBR) creep tests and Dynamic Shear Rheometer (DSR) complex modulus tests were performed to evaluate the material response both at low and high temperature. Then, the rheological Huet model was fitted to the BBR creep results for estimating the impact of filler content on the model parameters. It was found that an addition of hydrated lime and EAFSS up to 10% and 5%, respectively, results in satisfactory low-temperature performance with a substantial improvement of the high-temperature behavior.

Mechanical Performance of Asphalt Mortar Containing Hydrated Lime and EAFSS at Low and High Temperatures

PubMed Central

Moon, Ki Hoon; Wang, Di; Riccardi, Chiara; Wistuba, Michael P.

2017-01-01

In this paper, the possibility of improving the global response of asphalt materials for pavement applications through the use of hydrated lime and Electric Arc-Furnace Steel Slag (EAFSS) was investigated. For this purpose, a set of asphalt mortars was prepared by mixing two different asphalt binders with fine granite aggregate together with hydrated lime or EAFSS at three different percentages. Bending Beam Rheometer (BBR) creep tests and Dynamic Shear Rheometer (DSR) complex modulus tests were performed to evaluate the material response both at low and high temperature. Then, the rheological Huet model was fitted to the BBR creep results for estimating the impact of filler content on the model parameters. It was found that an addition of hydrated lime and EAFSS up to 10% and 5%, respectively, results in satisfactory low-temperature performance with a substantial improvement of the high-temperature behavior. PMID:28773100

Simulations of single-particle imaging of hydrated proteins with x-ray free-electron lasers

NASA Astrophysics Data System (ADS)

Fortmann-Grote, C.; Bielecki, J.; Jurek, Z.; Santra, R.; Ziaja-Motyka, B.; Mancuso, A. P.

2017-08-01

We employ start-to-end simulations to model coherent diffractive imaging of single biomolecules using x-ray free electron lasers. This technique is expected to yield new structural information about biologically relevant macromolecules thanks to the ability to study the isolated sample in its natural environment as opposed to crystallized or cryogenic samples. The effect of the solvent on the diffraction pattern and interpretability of the data is an open question. We present first results of calculations where the solvent is taken into account explicitly. They were performed with a molecular dynamics scheme for a sample consisting of a protein and a hydration layer of varying thickness. Through R-factor analysis of the simulated diffraction patterns from hydrated samples, we show that the scattering background from realistic hydration layers of up to 3 Å thickness presents no obstacle for the resolution of molecular structures at the sub-nm level.

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.

Importance of the rate of hydration of pharmaceutical preparations of guar gum; a new in vitro monitoring method.

PubMed

Ellis, P R; Morris, E R

1991-05-01

Dietary supplements of guar gum are known to improve blood glucose control in diabetic patients. The efficacy of guar is probably dependent mainly upon its capacity to hydrate rapidly and thus to increase viscosity in the small intestine post-prandially. Measurement of the rate of hydration in vitro might therefore be a useful index of the effectiveness of guar formulations. A simple method for monitoring the hydration rate of guar gum has been developed, which involves measuring the changes in viscosity at discrete time intervals over a period of 5 h using a Brookfield RVT rotoviscometer. Six different samples of guar gum (four pharmaceutical preparations and two food grades of guar flour) were hydrated in sealed glass jars rotated at 6 rev min-1 in order to prevent particle aggregation. Marked differences in hydration rate and ultimate (maximum) viscosity between the different guar samples were observed. Three of the four pharmaceutical preparations were lower in viscosity than the food grades of guar flour during the first 60 min of hydration. Two of the preparations hydrated so slowly that even after 5 h they attained viscosity levels of only 60% of their ultimate viscosity. These results may explain why some guar gum preparations are clinically ineffective.

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.

In situ Raman and X-ray diffraction studies on the high pressure and temperature stability of methane hydrate up to 55 GPa.

PubMed

Kadobayashi, Hirokazu; Hirai, Hisako; Ohfuji, Hiroaki; Ohtake, Michika; Yamamoto, Yoshitaka

2018-04-28

High-temperature and high-pressure experiments were performed under 2-55 GPa and 298-653 K using in situ Raman spectroscopy and X-ray diffraction combined with externally heated diamond anvil cells to investigate the stability of methane hydrate. Prior to in situ experiments, the typical C-H vibration modes of methane hydrate and their pressure dependence were measured at room temperature using Raman spectroscopy to make a clear discrimination between methane hydrate and solid methane which forms through the decomposition of methane hydrate at high temperature. The sequential in situ Raman spectroscopy and X-ray diffraction revealed that methane hydrate survives up to 633 K and 40.3 GPa and then decomposes into solid methane and ice VII above the conditions. The decomposition curve of methane hydrate estimated by the present experiments is >200 K lower than the melting curves of solid methane and ice VII, and moderately increases with increasing pressure. Our result suggests that although methane hydrate may be an important candidate for major constituents of cool exoplanets and other icy bodies, it is unlikely to be present in the ice mantle of Neptune and Uranus, where the temperature is expected to be far beyond the decomposition temperatures.

In situ Raman and X-ray diffraction studies on the high pressure and temperature stability of methane hydrate up to 55 GPa

NASA Astrophysics Data System (ADS)

Kadobayashi, Hirokazu; Hirai, Hisako; Ohfuji, Hiroaki; Ohtake, Michika; Yamamoto, Yoshitaka

2018-04-01

High-temperature and high-pressure experiments were performed under 2-55 GPa and 298-653 K using in situ Raman spectroscopy and X-ray diffraction combined with externally heated diamond anvil cells to investigate the stability of methane hydrate. Prior to in situ experiments, the typical C-H vibration modes of methane hydrate and their pressure dependence were measured at room temperature using Raman spectroscopy to make a clear discrimination between methane hydrate and solid methane which forms through the decomposition of methane hydrate at high temperature. The sequential in situ Raman spectroscopy and X-ray diffraction revealed that methane hydrate survives up to 633 K and 40.3 GPa and then decomposes into solid methane and ice VII above the conditions. The decomposition curve of methane hydrate estimated by the present experiments is >200 K lower than the melting curves of solid methane and ice VII, and moderately increases with increasing pressure. Our result suggests that although methane hydrate may be an important candidate for major constituents of cool exoplanets and other icy bodies, it is unlikely to be present in the ice mantle of Neptune and Uranus, where the temperature is expected to be far beyond the decomposition temperatures.

Estimating Atomic Contributions to Hydration and Binding Using Free Energy Perturbation.

PubMed

Irwin, Benedict W J; Huggins, David J

2018-06-12

We present a general method called atom-wise free energy perturbation (AFEP), which extends a conventional molecular dynamics free energy perturbation (FEP) simulation to give the contribution to a free energy change from each atom. AFEP is derived from an expansion of the Zwanzig equation used in the exponential averaging method by defining that the system total energy can be partitioned into contributions from each atom. A partitioning method is assumed and used to group terms in the expansion to correspond to individual atoms. AFEP is applied to six example free energy changes to demonstrate the method. Firstly, the hydration free energies of methane, methanol, methylamine, methanethiol, and caffeine in water. AFEP highlights the atoms in the molecules that interact favorably or unfavorably with water. Finally AFEP is applied to the binding free energy of human immunodeficiency virus type 1 protease to lopinavir, and AFEP reveals the contribution of each atom to the binding free energy, indicating candidate areas of the molecule to improve to produce a more strongly binding inhibitor. FEP gives a single value for the free energy change and is already a very useful method. AFEP gives a free energy change for each "part" of the system being simulated, where part can mean individual atoms, chemical groups, amino acids, or larger partitions depending on what the user is trying to measure. This method should have various applications in molecular dynamics studies of physical, chemical, or biochemical phenomena, specifically in the field of computational drug discovery.

Measured temperature and pressure dependence of Vp and Vs in compacted, polycrystalline sI methane and sII methane-ethane hydrate

USGS Publications Warehouse

Helgerud, M.B.; Waite, W.F.; Kirby, S.H.; Nur, A.

2003-01-01

We report on compressional- and shear-wave-speed measurements made on compacted polycrystalline sI methane and sII methane-ethane hydrate. The gas hydrate samples are synthesized directly in the measurement apparatus by warming granulated ice to 17??C in the presence of a clathrate-forming gas at high pressure (methane for sI, 90.2% methane, 9.8% ethane for sII). Porosity is eliminated after hydrate synthesis by compacting the sample in the synthesis pressure vessel between a hydraulic ram and a fixed end-plug, both containing shear-wave transducers. Wave-speed measurements are made between -20 and 15??C and 0 to 105 MPa applied piston pressure.

Localised electrochemical impedance measurements of a polymer electrolyte fuel cell using a reference electrode array to give cathode-specific measurements and examine membrane hydration dynamics

NASA Astrophysics Data System (ADS)

Engebretsen, Erik; Hinds, Gareth; Meyer, Quentin; Mason, Tom; Brightman, Edward; Castanheira, Luis; Shearing, Paul R.; Brett, Daniel J. L.

2018-04-01

Advances in bespoke diagnostic techniques for polymer electrolyte fuel cells continue to provide unique insight into the internal operation of these devices and lead to improved performance and durability. Localised measurements of current density have proven to be extremely useful in designing better fuel cells and identifying optimal operating strategies, with electrochemical impedance spectroscopy (EIS) now routinely used to deconvolute the various losses in fuel cells. Combining the two techniques provides another dimension of understanding, but until now each localised EIS has been based on 2-electrode measurements, composed of both the anode and cathode responses. This work shows that a reference electrode array can be used to give individual electrode-specific EIS responses, in this case the cathode is focused on to demonstrate the approach. In addition, membrane hydration dynamics are studied under current load steps from open circuit voltage. A three-stage process is identified associated with an initial rapid reduction in membrane resistance after 10 s of applying a current step, followed by a slower ramp to approximately steady state, which was achieved after ∼250 s. These results support previously published work that has looked at membrane swelling dynamics and reveal that membrane hydration/membrane resistance is highly heterogeneous.

A Molecular Dynamics-Quantum Mechanics Theoretical Study of DNA-Mediated Charge Transport in Hydrated Ionic Liquids.

PubMed

Meng, Zhenyu; Kubar, Tomas; Mu, Yuguang; Shao, Fangwei

2018-05-08

Charge transport (CT) through biomolecules is of high significance in the research fields of biology, nanotechnology, and molecular devices. Inspired by our previous work that showed the binding of ionic liquid (IL) facilitated charge transport in duplex DNA, in silico simulation is a useful means to understand the microscopic mechanism of the facilitation phenomenon. Here molecular dynamics simulations (MD) of duplex DNA in water and hydrated ionic liquids were employed to explore the helical parameters. Principal component analysis was further applied to capture the subtle conformational changes of helical DNA upon different environmental impacts. Sequentially, CT rates were calculated by a QM/MM simulation of the flickering resonance model based upon MD trajectories. Herein, MD simulation illustrated that the binding of ionic liquids can restrain dynamic conformation and lower the on-site energy of the DNA base. Confined movement among the adjacent base pairs was highly related to the increase of electronic coupling among base pairs, which may lead DNA to a CT facilitated state. Sequentially combining MD and QM/MM analysis, the rational correlations among the binding modes, the conformational changes, and CT rates illustrated the facilitation effects from hydrated IL on DNA CT and supported a conformational-gating mechanism.

Strontium and barium in aqueous solution and a potassium channel binding site

NASA Astrophysics Data System (ADS)

Chaudhari, Mangesh I.; Rempe, Susan B.

2018-06-01

Ion hydration structure and free energy establish criteria for understanding selective ion binding in potassium (K+) ion channels and may be significant to understanding blocking mechanisms as well. Recently, we investigated the hydration properties of Ba2+, the most potent blocker of K+ channels among the simple metal ions. Here, we use a similar method of combining ab initio molecular dynamics simulations, statistical mechanical theory, and electronic structure calculations to probe the fundamental hydration properties of Sr2+, which does not block bacterial K+ channels. The radial distribution of water around Sr2+ suggests a stable 8-fold geometry in the local hydration environment, similar to Ba2+. While the predicted hydration free energy of -331.8 kcal/mol is comparable with the experimental result of -334 kcal/mol, the value is significantly more favorable than the -305 kcal/mol hydration free energy of Ba2+. When placed in the innermost K+ channel blocking site, the solvation free energies and lowest energy structures of both Sr2+ and Ba2+ are nearly unchanged compared with their respective hydration properties. This result suggests that the block is not attributable to ion trapping due to +2 charge, and differences in blocking behavior arise due to free energies associated with the exchange of water ligands for channel ligands instead of free energies of transfer from water to the binding site.

Postglacial response of Arctic Ocean gas hydrates to climatic amelioration

PubMed Central

Serov, Pavel; Mienert, Jürgen; Patton, Henry; Portnov, Alexey; Silyakova, Anna; Panieri, Giuliana; Carroll, Michael L.; Carroll, JoLynn; Andreassen, Karin; Hubbard, Alun

2017-01-01

Seafloor methane release due to the thermal dissociation of gas hydrates is pervasive across the continental margins of the Arctic Ocean. Furthermore, there is increasing awareness that shallow hydrate-related methane seeps have appeared due to enhanced warming of Arctic Ocean bottom water during the last century. Although it has been argued that a gas hydrate gun could trigger abrupt climate change, the processes and rates of subsurface/atmospheric natural gas exchange remain uncertain. Here we investigate the dynamics between gas hydrate stability and environmental changes from the height of the last glaciation through to the present day. Using geophysical observations from offshore Svalbard to constrain a coupled ice sheet/gas hydrate model, we identify distinct phases of subglacial methane sequestration and subsequent release on ice sheet retreat that led to the formation of a suite of seafloor domes. Reconstructing the evolution of this dome field, we find that incursions of warm Atlantic bottom water forced rapid gas hydrate dissociation and enhanced methane emissions during the penultimate Heinrich event, the Bølling and Allerød interstadials, and the Holocene optimum. Our results highlight the complex interplay between the cryosphere, geosphere, and atmosphere over the last 30,000 y that led to extensive changes in subseafloor carbon storage that forced distinct episodes of methane release due to natural climate variability well before recent anthropogenic warming. PMID:28584081

Influence of electrolytes on the microenvironment of F127 triblock copolymer micelles: a solvation and rotational dynamics study of coumarin dyes.

PubMed

Kumbhakar, Manoj; Ganguly, Rajib

2007-04-19

Dynamic Stokes' shift and fluorescence anisotropy measurements of coumarin 153 (C153) and coumarin 151 (C151) as fluorescence probes have been carried out to understand the influence of electrolytes (NaCl and LiCl) on the hydration behavior of aqueous (ethylene oxide)100-(propylene oxide)70-(ethylene oxide)100 (EO100-PO70-EO100, F127) block copolymer micelles. A small blue shift in the fluorescence spectra of C153 has been observed in presence of electrolytes due to the dehydration of the oxyethylene chains in the PEO-PPO region, although fluorescence spectra of C151 remain unaltered. The close vicinity of bulk water for C151 probably negates the effect of dehydration in the PEO region. Fluorescence anisotropy measurements indicate a gradual increase in microviscosity with electrolyte concentrations. The partial collapse of copolymer blocks in the presence of electrolytes has been suggested as a reason for the increase in microviscosity along with the strong hydration of ions in the corona region. The interplay between the ion hydration and the mechanically trapped water content, and specific interaction of ions, such as complexation of Li+ ions with the copolymer block, is found to control solvation dynamics in the corona region. In addition to that, it has been established that Na+ ions reside deep into the corona region whereas Li+ ions prefer to reside closer to the surface. Owing to its higher lyotropicity, LiCl influences the corona hydration to a greater extent than NaCl and sets in micelle-micelle interaction above the 2 M LiCl concentration, as reflected in the saturation of solvation time constants. The formation of larger clusters of F127 micelles above 2 M LiCl has been confirmed by dynamic light scattering measurements; however, such cluster formation is not evident with NaCl.

Swelling properties of montmorillonite and beidellite clay minerals from molecular simulation: Comparison of temperature interlayer cation, and charge location effects

DOE PAGES

Teich-McGoldrick, Stephanie L.; Greathouse, Jeffery A.; Jove-Colon, Carlos F.; ...

2015-08-27

In this study, the swelling properties of smectite clay minerals are relevant to many engineering applications including environmental remediation, repository design for nuclear waste disposal, borehole stability in drilling operations, and additives for numerous industrial processes and commercial products. We used molecular dynamics and grand canonical Monte Carlo simulations to study the effects of layer charge location, interlayer cation, and temperature on intracrystalline swelling of montmorillonite and beidellite clay minerals. For a beidellite model with layer charge exclusively in the tetrahedral sheet, strong ion–surface interactions shift the onset of the two-layer hydrate to higher water contents. In contrast, for amore » montmorillonite model with layer charge exclusively in the octahedral sheet, weaker ion–surface interactions result in the formation of fully hydrated ions (two-layer hydrate) at much lower water contents. Clay hydration enthalpies and interlayer atomic density profiles are consistent with the swelling results. Water adsorption isotherms from grand canonical Monte Carlo simulations are used to relate interlayer hydration states to relative humidity, in good agreement with experimental findings.« 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.

[Skin hydration and hydrating products].

PubMed

Duplan, H; Nocera, T

2018-05-01

One of the skin's principal functions is to protect the body against its environment by maintaining an effective epidermal barrier, not only against external factors, but also to prevent water loss from the body. Indeed, water homeostasis is vital for the normal physiological functioning of skin. Hydration levels affect not only visible microscopic parameters such as the suppleness and softness of skin, but also molecular parameters, enzyme activities and cellular signalling within the epidermis. The body is continually losing some of its water, but this phenomenon is limited and the optimal hydration gradient in skin is ensured via a set of sophisticated regulatory processes that rely on the functional and dynamic properties of the uppermost level of the skin consisting of the stratum corneum. The present article brings together data recently acquired in the fields of skin hydration and the characterisation of dehydrated or dry skin, whether through study of the regulatory processes involved or as a result of changes in the techniques used for in situ measurement, and thus in optimisation of management. Copyright © 2018. Published by Elsevier Masson SAS.