Pf1 bacteriophage hydration by magic angle spinning solid-state NMR

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

Sergeyev, Ivan V.; Bahri, Salima; McDermott, Ann E., E-mail: aem5@columbia.edu

2014-12-14

High resolution two- and three-dimensional heteronuclear correlation spectroscopy ({sup 1}H–{sup 13}C, {sup 1}H–{sup 15}N, and {sup 1}H–{sup 13}C–{sup 13}C HETCOR) has provided a detailed characterization of the internal and external hydration water of the Pf1 virion. This long and slender virion (2000 nm × 7 nm) contains highly stretched DNA within a capsid of small protein subunits, each only 46 amino acid residues. HETCOR cross-peaks have been unambiguously assigned to 25 amino acids, including most external residues 1–21 as well as residues 39–40 and 43–46 deep inside the virion. In addition, the deoxyribose rings of the DNA near the virionmore » axis are in contact with water. The sets of cross-peaks to the DNA and to all 25 amino acid residues were from the same hydration water {sup 1}H resonance; some of the assigned residues do not have exchangeable side-chain protons. A mapping of the contacts onto structural models indicates the presence of water “tunnels” through a highly hydrophobic region of the capsid. The present results significantly extend and modify results from a lower resolution study, and yield a comprehensive hydration surface map of Pf1. In addition, the internal water could be distinguished from external hydration water by means of paramagnetic relaxation enhancement. The internal water population may serve as a conveniently localized magnetization reservoir for structural studies.« less

Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory.

PubMed

Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Tama, Florence; Miyashita, Osamu; Nakano, Shu-Ichi; Sugimoto, Naoki

2015-12-02

In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water-water interactions, (ii) ethylene glycol more effectively disrupted water-water interactions around Watson-Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson-Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Structure, stability and behaviour of nucleic acids in ionic liquids

PubMed Central

Tateishi-Karimata, Hisae; Sugimoto, Naoki

2014-01-01

Nucleic acids have become a powerful tool in nanotechnology because of their conformational polymorphism. However, lack of a medium in which nucleic acid structures exhibit long-term stability has been a bottleneck. Ionic liquids (ILs) are potential solvents in the nanotechnology field. Hydrated ILs, such as choline dihydrogen phosphate (choline dhp) and deep eutectic solvent (DES) prepared from choline chloride and urea, are ‘green’ solvents that ensure long-term stability of biomolecules. An understanding of the behaviour of nucleic acids in hydrated ILs is necessary for developing DNA materials. We here review current knowledge about the structures and stabilities of nucleic acids in choline dhp and DES. Interestingly, in choline dhp, A–T base pairs are more stable than G–C base pairs, the reverse of the situation in buffered NaCl solution. Moreover, DNA triplex formation is markedly stabilized in hydrated ILs compared with aqueous solution. In choline dhp, the stability of Hoogsteen base pairs is comparable to that of Watson–Crick base pairs. Moreover, the parallel form of the G-quadruplex is stabilized in DES compared with aqueous solution. The behaviours of various DNA molecules in ILs detailed here should be useful for designing oligonucleotides for the development of nanomaterials and nanodevices. PMID:25013178

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

PubMed

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

2017-12-01

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

Cisplatin intrastrand adducts sensitize DNA to base damage by hydrated electrons.

PubMed

Behmand, B; Wagner, J R; Sanche, L; Hunting, D J

2014-05-08

The oligonucleotide TTTTTGTGTTT with or without a cisplatin adduct was reacted with hydrated electrons generated by ionizing radiation. Hydroxyl radicals were quenched with ethylenediaminetetraacetic acid (EDTA), and the solutions were bubbled with wet nitrogen to eliminate oxygen, a scavenger of hydrated electrons. Prior to irradiation, the structure of the initial cisplatin adduct was identified by mass spectrometry as G-cisplatin-G. Radiation damage to DNA bases was quantified by high-performance liquid chromatography (HPLC), after enzymatic digestion of the TTTTTGTGTTT-cisplatin complex to deoxyribonucleosides. The masses of the platinum adducts following digestion and separation by HPLC were measured by mass spectrometry. Our results demonstrate that hydrated electrons induce damage to thymines as well as detachment of the cisplatin moiety from both guanines in the oligonucleotide. This detachment regenerates both unmodified guanine and damaged guanine, in equimolar amounts. At 1000 Gy, a net average of 2.5 thymines and 1 guanine are damaged for each platinum lost from the oligonucleotide. Given the extensive base damage that occurs for each cisplatin adduct lost, it is clear that, prior to undergoing detachment, these adducts must catalyze several cycles of reactions of hydrated electrons with DNA bases. It is likely that a single reaction leads to the loss of the cisplatin adduct and the damage observed on the guanine base; however, the damage to the thymine bases must require the continued presence of the cisplatin adduct, acting as a catalyst. To our knowledge, this is the first time that platinum-DNA adducts have been shown to have catalytic activity. We propose two pathways for the interaction of hydrated electrons with TTTTTGTGTTT-cisplatin: (1) the hydrated electron is initially captured by a thymine base and transferred by base to base electron hopping to the guanine site, where the cisplatin moiety detaches from the oligonucleotide via dissociative electron attachment, and (2) the hydrated electron interacts directly with the platinum-guanine adduct and induces detachment of the cisplatin moiety via dissociative electron attachment. Although the precise mechanism remains to be elucidated, our results provide important insights into the radiosensitization of DNA by cisplatin.

Cisplatin Intrastrand Adducts Sensitize DNA to Base Damage by Hydrated Electrons

PubMed Central

Behmand, B.; Wagner, J. R.; Sanche, L.; Hunting, D. J.

2015-01-01

The oligonucleotide TTTTTGTGTTT with or without a cisplatin adduct was reacted with hydrated electrons generated by ionizing radiation. Hydroxyl radicals were quenched with ethylenediaminetetraacetic acid (EDTA), and the solutions were bubbled with wet nitrogen to eliminate oxygen, a scavenger of hydrated electrons. Prior to irradiation, the structure of the initial cisplatin adduct was identified by mass spectrometry as G-cisplatin-G. Radiation damage to DNA bases was quantified by high-performance liquid chromatography (HPLC), after enzymatic digestion of the TTTTTGTGTTT-cisplatin complex to deoxyribonucleosides. The masses of the platinum adducts following digestion and separation by HPLC were measured by mass spectrometry. Our results demonstrate that hydrated electrons induce damage to thymines as well as detachment of the cisplatin moiety from both guanines in the oligonucleotide. This detachment regenerates both unmodified guanine and damaged guanine, in equimolar amounts. At 1000 Gy, a net average of 2.5 thymines and 1 guanine are damaged for each platinum lost from the oligonucleotide. Given the extensive base damage that occurs for each cisplatin adduct lost, it is clear that, prior to undergoing detachment, these adducts must catalyze several cycles of reactions of hydrated electrons with DNA bases. It is likely that a single reaction leads to the loss of the cisplatin adduct and the damage observed on the guanine base; however, the damage to the thymine bases must require the continued presence of the cisplatin adduct, acting as a catalyst. To our knowledge, this is the first time that platinum-DNA adducts have been shown to have catalytic activity. We propose two pathways for the interaction of hydrated electrons with TTTTTGTGTTT-cisplatin: (1) the hydrated electron is initially captured by a thymine base and transferred by base to base electron hopping to the guanine site, where the cisplatin moiety detaches from the oligonucleotide via dissociative electron attachment, and (2) the hydrated electron interacts directly with the platinum-guanine adduct and induces detachment of the cisplatin moiety via dissociative electron attachment. Although the precise mechanism remains to be elucidated, our results provide important insights into the radiosensitization of DNA by cisplatin. PMID:24779712

Effect of pH and temperature on the stability of UV-induced repairable pyrimidine hydrates in DNA.

PubMed

O'Donnell, R E; Boorstein, R J; Cunningham, R P; Teebor, G W

1994-08-23

UV irradiation of cytosine yields 6-hydroxy-5,6-dihydrocytosine (cytosine hydrate) whether the cytosine is in solution as base, nucleoside, or nucleotide or on the DNA backbone. Cytosine hydrate decomposes by elimination of water, yielding cytosine, or by irreversible deamination, yielding uracil hydrate, which, in turn, decomposes by dehydration yielding uracil. To determine how pH and temperature affect these decomposition reactions, alternating poly(dG-[3H]dC) copolymer was irradiated at 254 nm and incubated under different conditions of pH and temperature. The cytosine hydrate and uracil hydrate content of the DNA was determined by the use of Escherichia coli endonuclease III, which releases pyrimidine hydrates from DNA by virtue of its DNA glycosylase activity. Uracil content was determined by using uracil-DNA glycosylase. The rate of decomposition of cytosine hydrate to cytosine was determined at 4 temperatures at pH 3.1, 5.4, and 7.4. The Ea was determined from the rates by using the Arrhenius equation and proved to be the same at pH 5.4 and 7.4, although the decomposition rate at pH 5.4 was faster at all temperatures. At pH 3.1, the Ea was reduced. These results suggest that the dehydration reaction is affected by two discrete protonations, most probably of the N-3 and the OH group of C-6 of cytosine hydrate. The deamination of cytosine hydrate to uracil hydrate was maximal at pH 3.1 at all temperatures. The doubly protonated cytosine hydrate probably is the common intermediate for both competing decomposition reactions, explaining why cytosine hydrate is prone to deamination at acid pH.(ABSTRACT TRUNCATED AT 250 WORDS)

Silicon supported lipid-DNA thin film structures at varying temperature studied by energy dispersive X-ray diffraction and neutron reflectivity.

PubMed

Domenici, F; Castellano, C; Dell'Unto, F; Albinati, A; Congiu, A

2011-11-01

Non-viral gene transfection by means of lipid-based nanosystems, such as solid supported lipid assemblies, is often limited due to their lack of stability and the consequent loss of efficiency. Therefore not only a detailed thermo-lyotropic study of these DNA-lipid complexes is necessary to understand their interaction mechanisms, but it can also be considered as a first step in conceiving and developing new transfection biosystems. The aim of our study is a structural characterization of 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC)-dimethyl-dioctadecyl-ammonium bromide (DDAB)-DNA complex at varying temperature using the energy dispersive X-ray diffraction (EDXD) and neutron reflectivity (NR) techniques. We have shown the formation of a novel thermo-lyotropic structure of DOPC/DDAB thin film self-organized in multi-lamellar planes on (100)-oriented silicon support by spin coating, thus enlightening its ability to include DNA strands. Our NR measurements indicate that the DOPC/DDAB/DNA complex forms temperature-dependent structures. At 65°C and relative humidity of 100% DNA fragments are buried between single lamellar leaflets constituting the hydrocarbon core of the lipid bilayers. This finding supports the consistency of the hydrophobic interaction model, which implies that the coupling between lipid tails and hypo-hydrated DNA single strands could be the driving force of DNA-lipid complexation. Upon cooling to 25°C, EDXD analysis points out that full-hydrated DOPC-DDAB-DNA can switch in a different metastable complex supposed to be driven by lipid heads-DNA electrostatic interaction. Thermotropic response analysis also clarifies that DOPC has a pivotal role in promoting the formation of our observed thermophylic silicon supported lipids-DNA assembly. Copyright © 2011 Elsevier B.V. All rights reserved.

Crystal structure of the Msx-1 homeodomain/DNA complex.

PubMed

Hovde, S; Abate-Shen, C; Geiger, J H

2001-10-09

The Msx-1 homeodomain protein plays a crucial role in craniofacial, limb, and nervous system development. Homeodomain DNA-binding domains are comprised of 60 amino acids that show a high degree of evolutionary conservation. We have determined the structure of the Msx-1 homeodomain complexed to DNA at 2.2 A resolution. The structure has an unusually well-ordered N-terminal arm with a unique trajectory across the minor groove of the DNA. DNA specificity conferred by bases flanking the core TAAT sequence is explained by well ordered water-mediated interactions at Q50. Most interactions seen at the TAAT sequence are typical of the interactions seen in other homeodomain structures. Comparison of the Msx-1-HD structure to all other high resolution HD-DNA complex structures indicate a remarkably well-conserved sphere of hydration between the DNA and protein in these complexes.

Sequence Dependencies of DNA Deformability and Hydration in the Minor Groove

PubMed Central

Yonetani, Yoshiteru; Kono, Hidetoshi

2009-01-01

Abstract DNA deformability and hydration are both sequence-dependent and are essential in specific DNA sequence recognition by proteins. However, the relationship between the two is not well understood. Here, systematic molecular dynamics simulations of 136 DNA sequences that differ from each other in their central tetramer revealed that sequence dependence of hydration is clearly correlated with that of deformability. We show that this correlation can be illustrated by four typical cases. Most rigid basepair steps are highly likely to form an ordered hydration pattern composed of one water molecule forming a bridge between the bases of distinct strands, but a few exceptions favor another ordered hydration composed of two water molecules forming such a bridge. Steps with medium deformability can display both of these hydration patterns with frequent transition. Highly flexible steps do not have any stable hydration pattern. A detailed picture of this correlation demonstrates that motions of hydration water molecules and DNA bases are tightly coupled with each other at the atomic level. These results contribute to our understanding of the entropic contribution from water molecules in protein or drug binding and could be applied for the purpose of predicting binding sites. PMID:19686662

Hydration of protein–RNA recognition sites

PubMed Central

Barik, Amita; Bahadur, Ranjit Prasad

2014-01-01

We investigate the role of water molecules in 89 protein–RNA complexes taken from the Protein Data Bank. Those with tRNA and single-stranded RNA are less hydrated than with duplex or ribosomal proteins. Protein–RNA interfaces are hydrated less than protein–DNA interfaces, but more than protein–protein interfaces. Majority of the waters at protein–RNA interfaces makes multiple H-bonds; however, a fraction do not make any. Those making H-bonds have preferences for the polar groups of RNA than its partner protein. The spatial distribution of waters makes interfaces with ribosomal proteins and single-stranded RNA relatively ‘dry’ than interfaces with tRNA and duplex RNA. In contrast to protein–DNA interfaces, mainly due to the presence of the 2′OH, the ribose in protein–RNA interfaces is hydrated more than the phosphate or the bases. The minor groove in protein–RNA interfaces is hydrated more than the major groove, while in protein–DNA interfaces it is reverse. The strands make the highest number of water-mediated H-bonds per unit interface area followed by the helices and the non-regular structures. The preserved waters at protein–RNA interfaces make higher number of H-bonds than the other waters. Preserved waters contribute toward the affinity in protein–RNA recognition and should be carefully treated while engineering protein–RNA interfaces. PMID:25114050

Investigation of the electrostatic and hydration properties of DNA minor groove-binding by a heterocyclic diamidine by osmotic pressure.

PubMed

Erlitzki, Noa; Huang, Kenneth; Xhani, Suela; Farahat, Abdelbasset A; Kumar, Arvind; Boykin, David W; Poon, Gregory M K

2017-12-01

Previous investigations of sequence-specific DNA binding by model minor groove-binding compounds showed that the ligand/DNA complex was destabilized in the presence of compatible co-solutes. Inhibition was interpreted in terms of osmotic stress theory as the uptake of significant numbers of excess water molecules from bulk solvent upon complex formation. Here, we interrogated the AT-specific DNA complex formed with the symmetric heterocyclic diamidine DB1976 as a model for minor groove DNA recognition using both ionic (NaCl) and non-ionic cosolutes (ethylene glycol, glycine betaine, maltose, nicotinamide, urea). While the non-ionic cosolutes all destabilized the ligand/DNA complex, their quantitative effects were heterogeneous in a cosolute- and salt-dependent manner. Perturbation with NaCl in the absence of non-ionic cosolute showed that preferential hydration water was released upon formation of the DB1976/DNA complex. As salt probes counter-ion release from charged groups such as the DNA backbone, we propose that the preferential hydration uptake in DB1976/DNA binding observed in the presence of osmolytes reflects the exchange of preferentially bound cosolute with hydration water in the environs of the bound DNA, rather than a net uptake of hydration waters by the complex. Copyright © 2017 Elsevier B.V. All rights reserved.

Sensitivity of hydrogen bonds of DNA and RNA to hydration, as gauged by 1JNH measurements in ethanol-water mixtures.

PubMed

Manalo, Marlon N; Kong, Xiangming; LiWang, Andy

2007-04-01

Hydrogen-bond lengths of nucleic acids are (1) longer in DNA than in RNA, and (2) sequence dependent. The physicochemical basis for these variations in hydrogen-bond lengths is unknown, however. Here, the notion that hydration plays a significant role in nucleic acid hydrogen-bond lengths is tested. Watson-Crick N1...N3 hydrogen-bond lengths of several DNA and RNA duplexes are gauged using imino 1J(NH) measurements, and ethanol is used as a cosolvent to lower water activity. We find that 1J(NH) values of DNA and RNA become less negative with added ethanol, which suggests that mild dehydration reduces hydrogen-bond lengths even as the overall thermal stabilities of these duplexes decrease. The 1J(NH) of DNA are increased in 8 mol% ethanol to those of RNA in water, which suggests that the greater hydration of DNA plays a significant role in its longer hydrogen bonds. The data also suggest that ethanol-induced dehydration is greater for the more hydrated G:C base pairs and thereby results in greater hydrogen-bond shortening than for the less hydrated A:T/U base pairs of DNA and RNA.

Sequence and Structure Dependent DNA-DNA Interactions

NASA Astrophysics Data System (ADS)

Kopchick, Benjamin; Qiu, Xiangyun

Molecular forces between dsDNA strands are largely dominated by electrostatics and have been extensively studied. Quantitative knowledge has been accumulated on how DNA-DNA interactions are modulated by varied biological constituents such as ions, cationic ligands, and proteins. Despite its central role in biology, the sequence of DNA has not received substantial attention and ``random'' DNA sequences are typically used in biophysical studies. However, ~50% of human genome is composed of non-random-sequence DNAs, particularly repetitive sequences. Furthermore, covalent modifications of DNA such as methylation play key roles in gene functions. Such DNAs with specific sequences or modifications often take on structures other than the canonical B-form. Here we present series of quantitative measurements of the DNA-DNA forces with the osmotic stress method on different DNA sequences, from short repeats to the most frequent sequences in genome, and to modifications such as bromination and methylation. We observe peculiar behaviors that appear to be strongly correlated with the incurred structural changes. We speculate the causalities in terms of the differences in hydration shell and DNA surface structures.

Signatures of DNA target selectivity by ETS transcription factors

PubMed Central

Kim, Hye Mi

2017-01-01

ABSTRACT The ETS family of transcription factors is a functionally heterogeneous group of gene regulators that share a structurally conserved, eponymous DNA-binding domain. DNA target specificity derives from combinatorial interactions with other proteins as well as intrinsic heterogeneity among ETS domains. Emerging evidence suggests molecular hydration as a fundamental feature that defines the intrinsic heterogeneity in DNA target selection and susceptibility to epigenetic DNA modification. This perspective invokes novel hypotheses in the regulation of ETS proteins in physiologic osmotic stress, their pioneering potential in heterochromatin, and the effects of passive and pharmacologic DNA demethylation on ETS regulation. PMID:28301293

Signatures of DNA target selectivity by ETS transcription factors.

PubMed

Poon, Gregory M K; Kim, Hye Mi

2017-05-27

The ETS family of transcription factors is a functionally heterogeneous group of gene regulators that share a structurally conserved, eponymous DNA-binding domain. DNA target specificity derives from combinatorial interactions with other proteins as well as intrinsic heterogeneity among ETS domains. Emerging evidence suggests molecular hydration as a fundamental feature that defines the intrinsic heterogeneity in DNA target selection and susceptibility to epigenetic DNA modification. This perspective invokes novel hypotheses in the regulation of ETS proteins in physiologic osmotic stress, their pioneering potential in heterochromatin, and the effects of passive and pharmacologic DNA demethylation on ETS regulation.

Complex between triple helix of collagen and double helix of DNA in aqueous solution.

PubMed

Mrevlishvili, George M; Svintradze, David V

2005-06-01

We demonstrate in this paper that one example of a biologically important and molecular self-assembling complex system is a collagen-DNA ordered aggregate which spontaneously forms in aqueous solutions. Interaction between the collagen and the DNA leads to destruction of the hydration shell of the triple helix and stabilization of the double helix structure. From a molecular biology point of view this nano-scale self-assembling superstructure could increase the stability of DNA against the nucleases during collagen diseases and the growth of collagen fibrills in the presence of DNA.

Hydrated electrons react with high specificity with cisplatin bound to single-stranded DNA.

PubMed

Behmand, B; Cloutier, P; Girouard, S; Wagner, J R; Sanche, L; Hunting, D J

2013-12-19

Short oligonucleotides TTTTTGTGTTT and TTTTTTTGTTT in solution with and without cisplatin (cisPt) bound to the guanine bases were irradiated with γ-rays at doses varying from 0 to 2500 Gy. To determine the effect of hydrated electrons from water radiolysis on the oligonucleotides, we quenched (•)OH radicals with ethylenediaminetetraacetic acid (EDTA) and displaced oxygen, which reacts with hydrated electrons, by bubbling the solution with wet nitrogen. DNA strand breaks and platinum detachment were quantified by gel electrophoresis. Our results demonstrate that hydrated electrons react almost exclusively at the position of the cisPt adduct, where they induce cisPt detachment from one or both guanines in the oligonucleotide. Given the high yield of hydrated electrons in irradiated tissues, this reaction may be an important step in the mechanism of radiosensitization of DNA by cisPt.

Cisplatin enhances the formation of DNA single- and double-strand breaks by hydrated electrons and hydroxyl radicals.

PubMed

Rezaee, Mohammad; Sanche, Léon; Hunting, Darel J

2013-03-01

The synergistic interaction of cisplatin with ionizing radiation is the clinical rationale for the treatment of several cancers including head and neck, cervical and lung cancer. The underlying molecular mechanism of the synergy has not yet been identified, although both DNA damage and repair processes are likely involved. Here, we investigate the indirect effect of γ rays on strand break formation in a supercoiled plasmid DNA (pGEM-3Zf-) covalently modified by cisplatin. The yields of single- and double-strand breaks were determined by irradiation of DNA and cisplatin/DNA samples with (60)Co γ rays under four different scavenging conditions to examine the involvement of hydrated electrons and hydroxyl radicals in inducing the DNA damage. At 5 mM tris in an N2 atmosphere, the presence of an average of two cisplatins per plasmid increased the yields of single- and double-strand breaks by factors of 1.9 and 2.2, respectively, relative to the irradiated unmodified DNA samples. Given that each plasmid of 3,200 base pairs contained an average of two cisplatins, this represents an increase in radiosensitivity of 3,200-fold on a per base pair basis. When hydrated electrons were scavenged by saturating the samples with N2O, these enhancement factors decreased to 1.5 and 1.2, respectively, for single- and double-strand breaks. When hydroxyl radicals were scavenged using 200 mM tris, the respective enhancement factors were 1.2 and 1.6 for single- and double-strand breaks, respectively. Furthermore, no enhancement in DNA damage by cisplatin was observed after scavenging both hydroxyl radicals and hydrated electrons. These findings show that hydrated electrons can induce both single- and double-strand breaks in the platinated DNA, but not in unmodified DNA. In addition, cisplatin modification is clearly an extremely efficient means of increasing the formation of both single- and double-strand breaks by the hydrated electrons and hydroxyl radicals created by ionizing radiation.

Controlled dehydration of a ruthenium complex-DNA crystal induces reversible DNA kinking.

PubMed

Hall, James P; Sanchez-Weatherby, Juan; Alberti, Cora; Quimper, Caroline Hurtado; O'Sullivan, Kyra; Brazier, John A; Winter, Graeme; Sorensen, Thomas; Kelly, John M; Cardin, David J; Cardin, Christine J

2014-12-17

Hydration-dependent DNA deformation has been known since Rosalind Franklin recognized that the relative humidity of the sample had to be maintained to observe a single conformation in DNA fiber diffraction. We now report for the first time the crystal structure, at the atomic level, of a dehydrated form of a DNA duplex and demonstrate the reversible interconversion to the hydrated form at room temperature. This system, containing d(TCGGCGCCGA) in the presence of Λ-[Ru(TAP)2(dppz)](2+) (TAP = 1,4,5,8-tetraazaphenanthrene, dppz = dipyrido[3,2-a:2',3'-c]phenazine), undergoes a partial transition from an A/B hybrid to the A-DNA conformation, at 84-79% relative humidity. This is accompanied by an increase in kink at the central step from 22° to 51°, with a large movement of the terminal bases forming the intercalation site. This transition is reversible on rehydration. Seven data sets, collected from one crystal at room temperature, show the consequences of dehydration at near-atomic resolution. This result highlights that crystals, traditionally thought of as static systems, are still dynamic and therefore can be the subject of further experimentation.

An optical microscopy study of the swelling of wet-spun films of CsDNA as a function of hydration and CsCl concentration

NASA Astrophysics Data System (ADS)

Schwenker, Megan; Marlowe, Robert; Lee, Scott; Rupprecht, Allan

2005-03-01

Highly oriented, wet-spun films of DNA expand in the direction perpendicular to the helical axis as the hydration of the film is increased. CsDNA films with a high CsCl content show an unexpected shrinkage at a relative humidity of 92%. Our most recent experiments have been to measure the perpendicular dimension of CsDNA as a function of both hydration and concentration of CsCl. Our preliminary results show that no shrinkage is observed at low contents of CsCl, showing that the CsCl plays an integral role in the shrinkage phenomenon.

Kr-86 Ion-Beam Irradiation of Hydrated DNA: Free Radical and Unaltered Base Yields

PubMed Central

Becker, David; Adhikary, Amitava; Tetteh, Smedley T.; Bull, Arthur W.; Sevilla, Michael D.

2012-01-01

This work reports an ESR and product analysis investigation of Kr-86 ion-beam irradiation of hydrated DNA at 77 K. The irradiation results in the formation and trapping of both base radicals and sugar phosphate radicals (DNA backbone radicals). The absolute yields (G, μmol/J) of the base radicals are smaller than the yields found in similarly prepared γ-irradiated DNA samples, and the relative yields of backbone radicals relative to base radicals are much higher than that found in γ-irradiated samples. From these results, we have elaborated our radiation chemical model of the track structure for ion-beam irradiated DNA as it applies to krypton ion-beams. The base radicals, which are trapped as ion radicals or reversibly protonated or deprotonated ion radicals, are formed almost entirely in the track penumbra, a region in which radiation chemical effects are similar to those found in γ-irradiated samples. By comparing the yields of base radicals in ion-beam samples to the yields of the same radicals in γ-irradiated samples, the partition of energy between the low-LET region (penumbra) and the core is experimentally determined. The neutral sugar and other backbone radicals, which are not as susceptible to recombination as are ion radicals, are formed largely in the track core. The backbone radicals show a linear dose response up to very high doses. Unaltered base release yields in Kr-86 irradiated hydrated DNA are equal to sugar radical yields within experimental error limits, consistent with radiation-chemical processes in which all base release originates with sugar radicals. Two phosphorus-centered radicals from fragmentation of the DNA backbone are found in low yields. PMID:23106211

Kr-86 ion-beam irradiation of hydrated DNA: free radical and unaltered base yields.

PubMed

Becker, David; Adhikary, Amitava; Tetteh, Smedley T; Bull, Arthur W; Sevilla, Michael D

2012-12-01

This work reports an ESR and product analysis investigation of Kr-86 ion-beam irradiation of hydrated DNA at 77 K. The irradiation results in the formation and trapping of both base radicals and sugar phosphate radicals (DNA backbone radicals). The absolute yields (G, μmol/J) of the base radicals are smaller than the yields found in similarly prepared γ-irradiated DNA samples, and the relative yields of backbone radicals relative to base radicals are much higher than that found in γ-irradiated samples. From these results, we have elaborated our radiation chemical model of the track structure for ion-beam irradiated DNA as it applies to krypton ion-beams. The base radicals, which are trapped as ion radicals or reversibly protonated or deprotonated ion radicals, are formed almost entirely in the track penumbra, a region in which radiation chemical effects are similar to those found in γ-irradiated samples. By comparing the yields of base radicals in ion-beam samples to the yields of the same radicals in γ-irradiated samples, the partition of energy between the low-LET region (penumbra) and the core is experimentally determined. The neutral sugar and other backbone radicals, which are not as susceptible to recombination as are ion radicals, are formed largely in the track core. The backbone radicals show a linear dose response up to very high doses. Unaltered base release yields in Kr-86 irradiated hydrated DNA are equal to sugar radical yields within experimental error limits, consistent with radiation-chemical processes in which all base release originates with sugar radicals. Two phosphorus-centered radicals from fragmentation of the DNA backbone are found in low yields.

The structure and intermolecular forces of DNA condensates.

PubMed

Yoo, Jejoong; Aksimentiev, Aleksei

2016-03-18

Spontaneous assembly of DNA molecules into compact structures is ubiquitous in biological systems. Experiment has shown that polycations can turn electrostatic self-repulsion of DNA into attraction, yet the physical mechanism of DNA condensation has remained elusive. Here, we report the results of atomistic molecular dynamics simulations that elucidated the microscopic structure of dense DNA assemblies and the physics of interactions that makes such assemblies possible. Reproducing the setup of the DNA condensation experiments, we measured the internal pressure of DNA arrays as a function of the DNA-DNA distance, showing a quantitative agreement between the results of our simulations and the experimental data. Analysis of the MD trajectories determined the DNA-DNA force in a DNA condensate to be pairwise, the DNA condensation to be driven by electrostatics of polycations and not hydration, and the concentration of bridging cations, not adsorbed cations, to determine the magnitude and the sign of the DNA-DNA force. Finally, our simulations quantitatively characterized the orientational correlations of DNA in DNA arrays as well as diffusive motion of DNA and cations. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Life Origination Hydrate Hypothesis (LOH-Hypothesis)

PubMed Central

Ostrovskii, Victor; Kadyshevich, Elena

2012-01-01

The paper develops the Life Origination Hydrate Hypothesis (LOH-hypothesis), according to which living-matter simplest elements (LMSEs, which are N-bases, riboses, nucleosides, nucleotides), DNA- and RNA-like molecules, amino-acids, and proto-cells repeatedly originated on the basis of thermodynamically controlled, natural, and inevitable processes governed by universal physical and chemical laws from CH4, niters, and phosphates under the Earth's surface or seabed within the crystal cavities of the honeycomb methane-hydrate structure at low temperatures; the chemical processes passed slowly through all successive chemical steps in the direction that is determined by a gradual decrease in the Gibbs free energy of reacting systems. The hypothesis formulation method is based on the thermodynamic directedness of natural movement and consists ofan attempt to mentally backtrack on the progression of nature and thus reveal principal milestones alongits route. The changes in Gibbs free energy are estimated for different steps of the living-matter origination process; special attention is paid to the processes of proto-cell formation. Just the occurrence of the gas-hydrate periodic honeycomb matrix filled with LMSEs almost completely in its final state accounts for size limitation in the DNA functional groups and the nonrandom location of N-bases in the DNA chains. The slowness of the low-temperature chemical transformations and their “thermodynamic front” guide the gross process of living matter origination and its successive steps. It is shown that the hypothesis is thermodynamically justified and testable and that many observed natural phenomena count in its favor. PMID:25382120

Hydrated Electrons React with High Specificity with Cisplatin Bound to Single-Stranded DNA

PubMed Central

Behmand, B.; Cloutier, P.; Girouard, S.; Wagner, J. R.; Sanche, L.; Hunting, D. J.

2015-01-01

Short oligonucleotides TTTTTGTGTTT and TTTTTTTGTTT in solution with and without cisplatin (cisPt) bound to the guanine bases were irradiated with γ-rays at doses varying from 0 to 2500 Gy. To determine the effect of hydrated electrons from water radiolysis on the oligonucleotides, we quenched •OH radicals with ethylenediaminetetraacetic acid (EDTA) and displaced oxygen, which reacts with hydrated electrons, by bubbling the solution with wet nitrogen. DNA strand breaks and platinum detachment were quantified by gel electrophoresis. Our results demonstrate that hydrated electrons react almost exclusively at the position of the cisPt adduct, where they induce cisPt detachment from one or both guanines in the oligonucleotide. Given the high yield of hydrated electrons in irradiated tissues, this reaction may be an important step in the mechanism of radiosensitization of DNA by cisPt. PMID:24205952

DNA under Force: Mechanics, Electrostatics, and Hydration.

PubMed

Li, Jingqiang; Wijeratne, Sithara S; Qiu, Xiangyun; Kiang, Ching-Hwa

2015-02-25

Quantifying the basic intra- and inter-molecular forces of DNA has helped us to better understand and further predict the behavior of DNA. Single molecule technique elucidates the mechanics of DNA under applied external forces, sometimes under extreme forces. On the other hand, ensemble studies of DNA molecular force allow us to extend our understanding of DNA molecules under other forces such as electrostatic and hydration forces. Using a variety of techniques, we can have a comprehensive understanding of DNA molecular forces, which is crucial in unraveling the complex DNA functions in living cells as well as in designing a system that utilizes the unique properties of DNA in nanotechnology.

Small terminase couples viral DNA-binding to genome-packaging ATPase activity

PubMed Central

Roy, Ankoor; Bhardwaj, Anshul; Datta, Pinaki; Lander, Gabriel C.; Cingolani, Gino

2012-01-01

SUMMARY Packaging of viral genomes into empty procapsids is powered by a large DNA-packaging motor. In most viruses, this machine is composed of a large (L) and a small (S) terminase subunit complexed with a dodecamer of portal protein. Here, we describe the 1.75 Å crystal structure of the bacteriophage P22 S-terminase in a nonameric conformation. The structure presents a central channel ~23 Å in diameter, sufficiently large to accommodate hydrated B-DNA. The last 23 residues of S-terminase are essential for binding to DNA and assembly to L-terminase. Upon binding to its own DNA, S-terminase functions as a specific activator of L-terminase ATPase activity. The DNA-dependent stimulation of ATPase activity thus rationalizes the exclusive specificity of genome-packaging motors for viral DNA in the crowd of host DNA, ensuring fidelity of packaging and avoiding wasteful ATP hydrolysis. This posits a model for DNA-dependent activation of genome-packaging motors of general interest in virology. PMID:22771211

Structural basis for stabilization of Z-DNA by cobalt hexaammine and magnesium cations

NASA Technical Reports Server (NTRS)

Gessner, R. V.; Quigley, G. J.; Wang, A. H.; van der Marel, G. A.; van Boom, J. H.; Rich, A.

1985-01-01

In the equilibrium between B-DNA and Z-DNA in poly(dC-dG), the [Co(NH3)6]3+ ion stabilizes the Z form 4 orders of magnitude more effectively than the Mg2+ ion. The structural basis of this difference is revealed in Z-DNA crystal structures of d(CpGpCpGpCpG) stabilized by either Na+/Mg2+ or Na+/Mg2+ plus [Co(NH3)6]3+. The crystals diffract X-rays to high resolution, and the structures were refined at 1.25 A. The [Co(NH3)6]3+ ion forms five hydrogen bonds onto the surface of Z-DNA, bonding to a guanine O6 and N7 as well as to a phosphate group in the ZII conformation. The Mg2+ ion binds through its hydration shell with up to three hydrogen bonds to guanine N7 and O6. Higher charge, specific fitting of more hydrogen bonds, and a more stable complex all contribute to the great effectiveness of [Co(NH3)6]3+ in stabilizing Z-DNA.

Potential-of-mean-force description of ionic interactions and structural hydration in biomolecular systems

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

Hummer, G.; Garcia, A.E.; Soumpasis, D.M.

1994-10-01

To understand the functioning of living organisms on a molecular level, it is crucial to dissect the intricate interplay of the immense number of biological molecules. Most of the biochemical processes in cells occur in a liquid environment formed mainly by water and ions. This solvent environment plays an important role in biological systems. The potential-of-mean-force (PMF) formalism attempts to describe quantitatively the interactions of the solvent with biological macromolecules on the basis of an approximate statistical-mechanical representation. At its current status of development, it deals with ionic effects on the biomolecular structure and with the structural hydration of biomolecules.more » The underlying idea of the PMF formalism is to identify the dominant sources of interactions and incorporate these interactions into the theoretical formalism using PMF`s (or particle correlation functions) extracted from bulk-liquid systems. In the following, the authors shall briefly outline the statistical-mechanical foundation of the PMF formalism and introduce the PMF expansion formalism, which is intimately linked to superposition approximations for higher-order particle correlation functions. The authors shall then sketch applications, which describe the effects of the ionic environment on nucleic-acid structure. Finally, the authors shall present the more recent extension of the PMF idea to describe quantitatively the structural hydration of biomolecules. Results for the interface of ice and water and for the hydration of deoxyribonucleic acid (DNA) will be discussed.« less

Thermodynamics-hydration relationships within loops that affect G-quadruplexes under molecular crowding conditions.

PubMed

Fujimoto, Takeshi; Nakano, Shu-ichi; Sugimoto, Naoki; Miyoshi, Daisuke

2013-01-31

We systematically investigated the effects of loop length on the conformation, thermodynamic stability, and hydration of DNA G-quadruplexes under dilute and molecular crowding conditions in the presence of Na(+). Structural analysis showed that molecular crowding induced conformational switches of oligonucleotides with the longer guanine stretch and the shorter thymine loop. Thermodynamic parameters further demonstrated that the thermodynamic stability of G-quadruplexes increased by increasing the loop length from two to four, whereas it decreased by increasing the loop length from four to six. Interestingly, we found by osmotic pressure analysis that the number of water molecules released from the G-quadruplex decreased with increasing thermodynamic stability. We assumed that base-stacking interactions within the loops not only stabilized the whole G-quadruplex structure but also created hydration sites by accumulating nucleotide functional groups. The molecular crowding effects on the stability of G-quadruplexes composed of abasic sites, which reduce the stacking interactions at the loops, further demonstrated that G-quadruplexes with fewer stacking interactions within the loops released a larger number of water molecules upon folding. These results showed that the stacking interactions within the loops determined the thermodynamic stability and hydration of the whole G-quadruplex.

Sivelestat sodium hydrate improves post-traumatic knee osteoarthritis through nuclear factor-κB in a rat model.

PubMed

Yu, Xiaofeng; Zhao, Lijun; Yu, Zhiping; Yu, Changzheng; Bi, Jianfei; Sun, Binglong; Cong, Haibo

2017-08-01

As a specific inhibitor of neutrophil elastase, sivelestat sodium hydrate has primarily been used in the treatment of acute lung injury caused by various factors since its approval in 2002. Sivelestat sodium hydrate also improves post-traumatic knee osteoarthritis (KOA), although its underlying mechanisms of action have yet to be elucidated. The aim of the current study was to determine if sivelestat sodium hydrate improves post-traumatic KOA through nuclear factor (NF)-κB in a rat model. Treatment with sivelestat sodium hydrate significantly inhibited the induction of structural changes and significantly increased the vertical episode count and ipsilateral static weight bearing of the joint in KOA rats (all P<0.01). Sivelestat sodium hydrate significantly inhibited tumor necrosis factor-α and interleukin-6 production, serum nitrite levels, inducible nitric oxide synthase protein expression and high mobility group box 1 (HMGB1) secretion in KOA rats compared with the model group (all P<0.01). Sivelestat sodium hydrate also significantly suppressed p50/p65 DNA binding activity and NF-κB and phosphorylated inhibitor of κB protein expression in the joints of KOA rats compared with the model group (all P<0.01). These results suggest that sivelestat sodium hydrate improves post-traumatic KOA through HMGB1 and NF-κB in rats.

Sivelestat sodium hydrate improves post-traumatic knee osteoarthritis through nuclear factor-κB in a rat model

PubMed Central

Yu, Xiaofeng; Zhao, Lijun; Yu, Zhiping; Yu, Changzheng; Bi, Jianfei; Sun, Binglong; Cong, Haibo

2017-01-01

As a specific inhibitor of neutrophil elastase, sivelestat sodium hydrate has primarily been used in the treatment of acute lung injury caused by various factors since its approval in 2002. Sivelestat sodium hydrate also improves post-traumatic knee osteoarthritis (KOA), although its underlying mechanisms of action have yet to be elucidated. The aim of the current study was to determine if sivelestat sodium hydrate improves post-traumatic KOA through nuclear factor (NF)-κB in a rat model. Treatment with sivelestat sodium hydrate significantly inhibited the induction of structural changes and significantly increased the vertical episode count and ipsilateral static weight bearing of the joint in KOA rats (all P<0.01). Sivelestat sodium hydrate significantly inhibited tumor necrosis factor-α and interleukin-6 production, serum nitrite levels, inducible nitric oxide synthase protein expression and high mobility group box 1 (HMGB1) secretion in KOA rats compared with the model group (all P<0.01). Sivelestat sodium hydrate also significantly suppressed p50/p65 DNA binding activity and NF-κB and phosphorylated inhibitor of κB protein expression in the joints of KOA rats compared with the model group (all P<0.01). These results suggest that sivelestat sodium hydrate improves post-traumatic KOA through HMGB1 and NF-κB in rats. PMID:28810618

On the electron affinity of cytosine in bulk water and at hydrophobic aqueous interfaces.

PubMed

Vöhringer-Martinez, Esteban; Dörner, Ciro; Abel, Bernd

2014-10-01

In the past one possible mechanism of DNA damage in bulk water has been attributed to the presence of hydrated electrons in water. Recently, one important property of hydrated electrons, namely their binding energy, was reported to be smaller at hydrophobic interfaces than in bulk aqueous solution. This possibly opens up new reaction possibilities with different solutes such as the DNA at hydrophobic, aqueous interfaces. Here, we use QM/MM molecular dynamics simulation to study how the molecular environment at the vacuum-water interface and in the bulk alters the electron affinity of cytosine being a characteristic part of the DNA. The electron affinity at the interface is closer to the corresponding binding energy of the partially hydrated electron. The increased energy resonance makes the electron capture process more probable and suggests that hydrated electrons at hydrophobic interfaces may be more reactive than the fully hydrated ones. Additionally, we found that the relaxation of the anionic form after electron attachment also induces a proton transfer from the surrounding solvent that was confirmed by comparison with the experimental reduction potential.

Quantitative Analysis of Nucleic Acid Stability with Ligands Under High Pressure to Design Novel Drugs Targeting G-Quadruplexes.

PubMed

Takahashi, Shuntaro; Sugimoto, Naoki

2017-09-18

Nucleic acids (DNA and RNA) can form various non-canonical structures. Because some serious diseases are caused by the conformational change of G-quadruplex DNA structures, the development of ligands that bind and stabilize G-quadruplex DNA is of interest to the field of nucleic acid chemistry. Volumetric changes (ΔV) in the biomolecular reaction include the structural change of biomolecules and hydration behaviors, which provide information about the tertiary interaction between G-quadruplex DNA and ligands. Thus, it is valuable to investigate ΔV values to understand the mechanism of interaction between non-canonical structures and their ligands. This unit describes methods that can be used to quantitatively analyze the interaction between G-quadruplex DNA and ligands by using high-pressure UV melting. The combination of thermodynamic parameters (ΔG, ΔH, ΔS, and ΔV) is a powerful tool to elucidate the mechanism of ligand binding to G-quadruplex without real structural analysis by NMR and X-ray spectroscopy, and gives useful information to design novel drugs. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

DNA octaplex formation with an I-motif of water-mediated A-quartets: reinterpretation of the crystal structure of d(GCGAAAGC).

PubMed

Sato, Yoshiteru; Mitomi, Kenta; Sunami, Tomoko; Kondo, Jiro; Takénaka, Akio

2006-12-01

The crystal structure of the tetragonal form of d(gcGAAAgc) has been revised and reasonably refined including the disordered residues. The two DNA strands form a base-intercalated duplex, and the four duplexes are assembled according to the crystallographic 222 symmetry to form an octaplex. In the central region, the eight strands are associated by I-motif of double A-quartets. Furthermore, eight hydrated-magnesium cations link the four duplexes to support the octaplex formation. Based on these structural features, a proposal that folding of d(GAAA)n, found in the non-coding region of genomes, into an octaplex can induce slippage during replication to facilitate length polymorphism is presented.

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

PubMed

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

2018-05-15

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

Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

PubMed

Fenn, Timothy D; Schnieders, Michael J; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S; Brunger, Axel T

2011-04-13

Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints, and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here, we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen-bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. Copyright © 2011 Elsevier Ltd. All rights reserved.

Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration

PubMed Central

Fenn, Timothy D.; Schnieders, Michael J.; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S.; Brunger, Axel T.

2011-01-01

Summary Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. PMID:21481775

Mg2+ in the Major Groove Modulates B-DNA Structure and Dynamics

PubMed Central

Guéroult, Marc; Boittin, Olivier; Mauffret, Oliver; Etchebest, Catherine; Hartmann, Brigitte

2012-01-01

This study investigates the effect of Mg2+ bound to the DNA major groove on DNA structure and dynamics. The analysis of a comprehensive dataset of B-DNA crystallographic structures shows that divalent cations are preferentially located in the DNA major groove where they interact with successive bases of (A/G)pG and the phosphate group of 5′-CpA or TpG. Based on this knowledge, molecular dynamics simulations were carried out on a DNA oligomer without or with Mg2+ close to an ApG step. These simulations showed that the hydrated Mg2+ forms a stable intra-strand cross-link between the two purines in solution. ApG generates an electrostatic potential in the major groove that is particularly attractive for cations; its intrinsic conformation is well-adapted to the formation of water-mediated hydrogen bonds with Mg2+. The binding of Mg2+ modulates the behavior of the 5′-neighboring step by increasing the BII (ε-ζ>0°) population of its phosphate group. Additional electrostatic interactions between the 5′-phosphate group and Mg2+ strengthen both the DNA-cation binding and the BII character of the 5′-step. Cation binding in the major groove may therefore locally influence the DNA conformational landscape, suggesting a possible avenue for better understanding how strong DNA distortions can be stabilized in protein-DNA complexes. PMID:22844516

Comparable stability of Hoogsteen and Watson-Crick base pairs in ionic liquid choline dihydrogen phosphate.

PubMed

Tateishi-Karimata, Hisae; Nakano, Miki; Sugimoto, Naoki

2014-01-08

The instability of Hoogsteen base pairs relative to Watson-Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson-Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson-Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo.

Comparable Stability of Hoogsteen and Watson–Crick Base Pairs in Ionic Liquid Choline Dihydrogen Phosphate

PubMed Central

Tateishi-Karimata, Hisae; Nakano, Miki; Sugimoto, Naoki

2014-01-01

The instability of Hoogsteen base pairs relative to Watson–Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson–Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson–Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo. PMID:24399194

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.

SAXS Study of Sterically Stabilized Lipid Nanocarriers Functionalized by DNA

NASA Astrophysics Data System (ADS)

Angelov, Borislav; Angelova, Angelina; Filippov, Sergey; Karlsson, Göran; Terrill, Nick; Lesieur, Sylviane; Štěpánek, Petr

2012-03-01

The structure of novel spontaneously self-assembled plasmid DNA/lipid complexes is investigated by means of synchrotron radiation small-angle X-ray scattering (SAXS) and Cryo-TEM imaging. Liquid crystalline (LC) hydrated lipid systems are prepared using the non-ionic lipids monoolein and DOPE-PEG2000 and the cationic amphiphile CTAB. The employed plasmid DNA (pDNA) is encoding for the human protein brain-derived neurotrophic factor (BDNF). A coexistence of nanoparticulate objects with different LC inner organizations is established. A transition from bicontinuous membrane sponges, cubosome intermediates and unilamelar liposomes to multilamellar vesicles, functionalized by pDNA, is favoured upon binding and compaction of pBDNF onto the cationic PEGylated lipid nanocarriers. The obtained sterically stabilized multicompartment nanoobjects, with confined supercoiled plasmid DNA (pBDNF), are important in the context of multicompartment lipid nanocarriers of interest for gene therapy of neurodegenerative diseases.

Structure and stability of the consecutive stereoregulated chiral phosphorothioate DNA duplex.

PubMed

Kanaori, K; Tamura, Y; Wada, T; Nishi, M; Kanehara, H; Morii, T; Tajima, K; Makino, K

1999-12-07

The duplex structures of the stereoregulated phosphorothioate DNAs, [R(p),R(p)]- and [S(p),S(p)]-[d(GC(ps)T(ps)ACG)] (ps, phosphorothioate; PS-DNA), with their complementary RNA have been investigated by combined use of (1)H NMR and restrained molecular dynamics calculation. Compared to those obtained for the unmodified duplex structures (PO-DNA.RNA), the NOE cross-peak intensities are virtually identical for the PS-DNA.RNA hybrid duplexes. The structural analysis on the basis of the NOE restraints reveals that all of the three DNA.RNA duplexes take a A-form conformation and that there is no significant difference in the base stacking for the DNA.RNA hybrid duplexes. On the other hand, the NOE cross-peak intensities of the protons around the central T(ps)A step of the PS-DNA.DNA duplexes are apparently different from those of PO-DNA. DNA. The chemical shifts of H8/6 and H1' at the T(ps)A step are also largely different among PS-DNA.DNAs and PO-DNA.DNA, suggesting that the DNA.DNA structure is readily changed by the introduction of the phosphorothioate groups to the central T(p)A step. The structure calculations indicate that all of these DNA.DNA duplexes are B-form although there exist some small differences in helical parameters between the [R(p),R(p)]- and [S(p),S(p)]PS-DNA.DNA duplexes. The melting temperatures (T(m)) were determined for all of the duplexes by plotting the chemical shift change of isolated peaks as a function of temperature. For the PS-DNA.RNA hybrid duplexes, the [S(p),S(p)] isomer is less stable than the [R(p),R(p)] isomer while this trend is reversed for the PS-DNA.DNA duplexes. Consequently, although the PS-DNA.RNA duplexes take the similar A-form structure, the duplex stability is different between PS-DNA.RNA duplexes. The stability of the DNA.RNA duplexes may not be governed by the A-form structure itself but by some other factors such as the hydration around the phosphorothioate backbone, although the T(m) difference of the DNA.DNA duplexes could be explained by the structural factor.

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).

Differential scanning calorimetric study of the binding between native DNA and its primary water of hydration.

NASA Astrophysics Data System (ADS)

Marlowe, R. L.; Lukan, A. M.; Lee, S. A.; Anthony, L.; Rupprecht, A.

1996-03-01

Differential scanning calorimetry was used to measure the binding strength between calf-thymus DNA and its primary water of hydration. The specific heat of wet-spun films was found to have a broad endothermic transition near 80 ^oC and a sharp exothermic transition near 250 ^oC. The broad transition is believed to be mainly due to the breaking of the bonds of the strongly bound water of hydration. This transition was found to be reversible, as expected. Kissinger analysis indicates that the activation barrier for breaking the bonds of these water molecules is about 0.6 eV. The sharp transition appeared to be an indication of a thermal decomposition of the DNA. Samples taken above this transition lost mass, showed evidence of having melted, and had turned black in color. This transition is irreversible.

Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters.

PubMed

Jasiński, Maciej; Feig, Michael; Trylska, Joanna

2018-06-06

Peptide nucleic acids are promising nucleic acid analogs for antisense therapies as they can form stable duplex and triplex structures with DNA and RNA. Computational studies of PNA-containing duplexes and triplexes are an important component for guiding their design, yet existing force fields have not been well validated and parametrized with modern computational capabilities. We present updated CHARMM and Amber force fields for PNA that greatly improve the stability of simulated PNA-containing duplexes and triplexes in comparison with experimental structures and allow such systems to be studied on microsecond time scales. The force field modifications focus on reparametrized PNA backbone torsion angles to match high-level quantum mechanics reference energies for a model compound. The microsecond simulations of PNA-PNA, PNA-DNA, PNA-RNA, and PNA-DNA-PNA complexes also allowed a comprehensive analysis of hydration and ion interactions with such systems.

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

PubMed

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

2006-04-28

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

Measurement of intercolumnar forces between parallel guanosine four-stranded helices.

PubMed Central

Mariani, P; Saturni, L

1996-01-01

The deoxyguanosine-5'-monophosphate in aqueous solution self-associates into stable structures, which include hexagonal and cholesteric columnar phases. The structural unit is a four-stranded helix, composed of a stacked array of Hoogsteen-bonded guanosine quartets. We have measured by osmotic stress method the force per unit length versus interaxial distance between helices in the hexagonal phase under various ionic conditions. Two contributions have been recognized: the first one is purely electrostatic, is effective at large distances, and shows a strong dependence on the salt concentration of the solution. The second contribution is short range, dominates at interaxial separations smaller than about 30-32 A, and rises steeply as the columns approach each other, preventing the coalescence of the helices. This repulsion has an exponential nature and shows a magnitude and a decay length insensitive to the ionic strength of the medium. Because these features are distinctive of the hydration force detected between phospholipid bilayers or between several linear macromolecules (DNA, polysaccharides, collagen), we conclude that the dominant force experienced by deoxyguanosine helices approaching contact is hydration repulsion. The observed decay length of about 0.7 A has been rationalized to emerge from the coupling between the 3-A decay length of water solvent and the helically ordered structure of the hydrophilic groups on the opposing surfaces. The present results agree with recent measurements, also showing the dependence of the hydration force decay on the structure of interacting surfaces and confirm the correlations between force and structure. Images FIGURE 1 PMID:8744324

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.

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

PubMed

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

2005-10-22

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

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

PubMed

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

2012-10-11

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

Analysis of DNA repair and protection in the Tardigrade Ramazzottius varieornatus and Hypsibius dujardini after exposure to UVC radiation.

PubMed

Horikawa, Daiki D; Cumbers, John; Sakakibara, Iori; Rogoff, Dana; Leuko, Stefan; Harnoto, Raechel; Arakawa, Kazuharu; Katayama, Toshiaki; Kunieda, Takekazu; Toyoda, Atsushi; Fujiyama, Asao; Rothschild, Lynn J

2013-01-01

Tardigrades inhabiting terrestrial environments exhibit extraordinary resistance to ionizing radiation and UV radiation although little is known about the mechanisms underlying the resistance. We found that the terrestrial tardigrade Ramazzottius varieornatus is able to tolerate massive doses of UVC irradiation by both being protected from forming UVC-induced thymine dimers in DNA in a desiccated, anhydrobiotic state as well as repairing the dimers that do form in the hydrated animals. In R. varieornatus accumulation of thymine dimers in DNA induced by irradiation with 2.5 kJ/m(2) of UVC radiation disappeared 18 h after the exposure when the animals were exposed to fluorescent light but not in the dark. Much higher UV radiation tolerance was observed in desiccated anhydrobiotic R. varieornatus compared to hydrated specimens of this species. On the other hand, the freshwater tardigrade species Hypsibius dujardini that was used as control, showed much weaker tolerance to UVC radiation than R. varieornatus, and it did not contain a putative phrA gene sequence. The anhydrobiotes of R. varieornatus accumulated much less UVC-induced thymine dimers in DNA than hydrated one. It suggests that anhydrobiosis efficiently avoids DNA damage accumulation in R. varieornatus and confers better UV radiation tolerance on this species. Thus we propose that UV radiation tolerance in tardigrades is due to the both high capacities of DNA damage repair and DNA protection, a two-pronged survival strategy.

Analysis of DNA Repair and Protection in the Tardigrade Ramazzottius varieornatus and Hypsibius dujardini after Exposure to UVC Radiation

PubMed Central

Horikawa, Daiki D.; Cumbers, John; Sakakibara, Iori; Rogoff, Dana; Leuko, Stefan; Harnoto, Raechel; Arakawa, Kazuharu; Katayama, Toshiaki; Kunieda, Takekazu; Toyoda, Atsushi; Fujiyama, Asao; Rothschild, Lynn J.

2013-01-01

Tardigrades inhabiting terrestrial environments exhibit extraordinary resistance to ionizing radiation and UV radiation although little is known about the mechanisms underlying the resistance. We found that the terrestrial tardigrade Ramazzottius varieornatus is able to tolerate massive doses of UVC irradiation by both being protected from forming UVC-induced thymine dimers in DNA in a desiccated, anhydrobiotic state as well as repairing the dimers that do form in the hydrated animals. In R. varieornatus accumulation of thymine dimers in DNA induced by irradiation with 2.5 kJ/m2 of UVC radiation disappeared 18 h after the exposure when the animals were exposed to fluorescent light but not in the dark. Much higher UV radiation tolerance was observed in desiccated anhydrobiotic R. varieornatus compared to hydrated specimens of this species. On the other hand, the freshwater tardigrade species Hypsibius dujardini that was used as control, showed much weaker tolerance to UVC radiation than R. varieornatus, and it did not contain a putative phrA gene sequence. The anhydrobiotes of R. varieornatus accumulated much less UVC-induced thymine dimers in DNA than hydrated one. It suggests that anhydrobiosis efficiently avoids DNA damage accumulation in R. varieornatus and confers better UV radiation tolerance on this species. Thus we propose that UV radiation tolerance in tardigrades is due to the both high capacities of DNA damage repair and DNA protection, a two-pronged survival strategy. PMID:23762256

First determination of volume changes and enthalpies of the high-pressure decomposition reaction of the structure H methane hydrate to the cubic structure I methane hydrate and fluid methane.

PubMed

Ogienko, Andrey G; Tkacz, Marek; Manakov, Andrey Yu; Lipkowski, Janusz

2007-11-08

Pressure-temperature (P-T) conditions of the decomposition reaction of the structure H high-pressure methane hydrate to the cubic structure I methane hydrate and fluid methane were studied with a piston-cylinder apparatus at room temperature. For the first time, volume changes accompanying this reaction were determined. With the use of the Clausius-Clapeyron equation the enthalpies of the decomposition reaction of the structure H high-pressure methane hydrate to the cubic structure I methane hydrate and fluid methane have been calculated.

Effects of Near Infrared Radiation on DNA. DLS and ATR-FTIR Study

NASA Astrophysics Data System (ADS)

Szymborska-Małek, Katarzyna; Komorowska, Małgorzata; Gąsior-Głogowska, Marlena

2018-01-01

We presume that the primary effect of Near Infrared (NIR) radiation on aqueous solutions of biological molecules concerns modification of hydrogen bonded structures mainly the global and the hydration shell water molecules. Since water has a significant influence on the DNA structure, we expect that the thermal stability of DNA could be modified by NIR radiation. The herring sperm DNA was exposed to NIR radiation (700-1100 nm) for 5, 10, and 20 min periods. The temperature dependent infrared measurements were done for the thin films formed on the diamond ATR crystal from evaporated DNA solutions exposed and unexposed to NIR radiation. For the NIR-treated samples (at room temperature) the B form was better conserved than in the control sample independently of the irradiation period. Above 50 °C a considerable increase in the A form was only observed for 10 min NIR exposed samples. The hydrodynamic radius, (Rh), studied by the dynamic light scattering, showed drastic decrease with the increasing irradiation time. Principal components analysis (PCA) allowed to detect the spectral features correlated with the NIR effect and thermal stability of the DNA films. Obtained results strongly support the idea that the photoionization of water by NIR radiation in presence of DNA molecules is the main factor influencing on its physicochemical properties.

Hydration properties of natural and synthetic DNA sequences with methylated adenine or cytosine bases in the R.DpnI target and BDNF promoter studied by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Shanak, Siba; Helms, Volkhard

2014-12-01

Adenine and cytosine methylation are two important epigenetic modifications of DNA sequences at the levels of the genome and transcriptome. To characterize the differential roles of methylating adenine or cytosine with respect to their hydration properties, we performed conventional MD simulations and free energy perturbation calculations for two particular DNA sequences, namely the brain-derived neurotrophic factor (BDNF) promoter and the R.DpnI-bound DNA that are known to undergo methylation of C5-methyl cytosine and N6-methyl adenine, respectively. We found that a single methylated cytosine has a clearly favorable hydration free energy over cytosine since the attached methyl group has a slightly polar character. In contrast, capping the strongly polar N6 of adenine with a methyl group gives a slightly unfavorable contribution to its free energy of solvation. Performing the same demethylation in the context of a DNA double-strand gave quite similar results for the more solvent-accessible cytosine but much more unfavorable results for the rather buried adenine. Interestingly, the same demethylation reactions are far more unfavorable when performed in the context of the opposite (BDNF or R.DpnI target) sequence. This suggests a natural preference for methylation in a specific sequence context. In addition, free energy calculations for demethylating adenine or cytosine in the context of B-DNA vs. Z-DNA suggest that the conformational B-Z transition of DNA transition is rather a property of cytosine methylated sequences but is not preferable for the adenine-methylated sequences investigated here.

Hydration properties of natural and synthetic DNA sequences with methylated adenine or cytosine bases in the R.DpnI target and BDNF promoter studied by molecular dynamics simulations.

PubMed

Shanak, Siba; Helms, Volkhard

2014-12-14

Adenine and cytosine methylation are two important epigenetic modifications of DNA sequences at the levels of the genome and transcriptome. To characterize the differential roles of methylating adenine or cytosine with respect to their hydration properties, we performed conventional MD simulations and free energy perturbation calculations for two particular DNA sequences, namely the brain-derived neurotrophic factor (BDNF) promoter and the R.DpnI-bound DNA that are known to undergo methylation of C5-methyl cytosine and N6-methyl adenine, respectively. We found that a single methylated cytosine has a clearly favorable hydration free energy over cytosine since the attached methyl group has a slightly polar character. In contrast, capping the strongly polar N6 of adenine with a methyl group gives a slightly unfavorable contribution to its free energy of solvation. Performing the same demethylation in the context of a DNA double-strand gave quite similar results for the more solvent-accessible cytosine but much more unfavorable results for the rather buried adenine. Interestingly, the same demethylation reactions are far more unfavorable when performed in the context of the opposite (BDNF or R.DpnI target) sequence. This suggests a natural preference for methylation in a specific sequence context. In addition, free energy calculations for demethylating adenine or cytosine in the context of B-DNA vs. Z-DNA suggest that the conformational B-Z transition of DNA transition is rather a property of cytosine methylated sequences but is not preferable for the adenine-methylated sequences investigated here.

Ultrahigh-resolution crystal structures of Z-DNA in complex with Mn(2+) and Zn(2+) ions.

PubMed

Drozdzal, Pawel; Gilski, Miroslaw; Kierzek, Ryszard; Lomozik, Lechoslaw; Jaskolski, Mariusz

2013-06-01

X-ray crystal structures of the spermine(4+) form of the Z-DNA duplex with the self-complementary d(CG)3 sequence in complexes with Mn(2+) and Zn(2+) cations have been determined at the ultrahigh resolutions of 0.75 and 0.85 Å, respectively. Stereochemical restraints were only used for the sperminium cation (in both structures) and for nucleotides with dual conformation in the Zn(2+) complex. The Mn(2+) and Zn(2+) cations at the major site, designated M(2+)(1), bind at the N7 position of G6 by direct coordination. The coordination geometry of this site was octahedral, with complete hydration shells. An additional Zn(2+)(2) cation was bis-coordinated in a tetrahedral fashion by the N7 atoms of G10 and G12 from a symmetry-related molecule. The coordination distances of Zn(2+)(1) and Zn(2+)(2) to the O6 atom of the guanine residues were 3.613 (6) and 3.258 (5) Å, respectively. Moreover, a chloride ion was also identified in the coordination sphere of Zn(2+)(2). Alternate conformations were observed in the Z-DNA-Zn(2+) structure not only at internucleotide linkages but also at the terminal C3'-OH group of G12. The conformation of the sperminium chain in the Z-DNA-Mn(2+) complex is similar to the spermine(4+) conformation in analogous Z-DNA-Mg(2+) structures. In the Z-DNA-Zn(2+) complex the sperminium cation is disordered and partially invisible in electron-density maps. In the Z-DNA-Zn(2+) complex the sperminium cation only interacts with the phosphate groups of the Z-DNA molecules, while in the Z-DNA-Mn(2+) structure it forms hydrogen bonds to both the phosphate groups and DNA bases.

Low temperature structures of dCpG-proflavine. Conformational and hydration effects.

PubMed Central

Schneider, B; Ginell, S L; Berman, H M

1992-01-01

The structure of the complex of dCpG with proflavine was determined using x-ray data taken at -130 degrees C (low temperature) and at -2 degrees C (cold temperature) and compared with the structure of the complex determined previously at room temperature (Shieh, H. S., H. M. Berman, M. Dabrow, and S. Neidle. 1980. Nucleic Acids Res. 8:85-97). Low temperature was refined with 5,125 reflections between 8.0 and 0.93 A, Anisotropically modeled temperature factors were used for DNA/drug atoms and isotropic ones for water oxygens to R factor of 12.2% in P2(1)2(1)2; a = 32.853, b = 21.760, c = 13.296 A. Cold temperature was refined isotropically with 2,846 reflections 8.0-0.89 A to R = 15.1% in P2(1)2(1)2; a = 32.867, b = 22.356, c = 13.461 A. Both structures are very similar to the room temperature one, though some important differences were observed: one guanine sugar moiety is disordered and additional water molecules have been located that give rise to infinite polyhedral hydration networks. Images FIGURE 2 PMID:1489914

Selenium Derivatization of Nucleic Acids for Crystallography

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

Jiang,J.; Sheng, J.; Carrasco, N.

2007-01-01

The high-resolution structure of the DNA (5'-GTGTACA-C-3') with the selenium derivatization at the 2'-position of T2 was determined via MAD and SAD phasing. The selenium-derivatized structure (1.28 {angstrom} resolution) with the 2'-Se modification in the minor groove is isomorphorous to the native structure (2.0 {angstrom}). To directly compare with the conventional bromine derivatization, we incorporated bromine into the 5-postion of T4, determined the bromine-derivatized DNA structure at 1.5 {angstrom} resolution, and found that the local backbone torsion angles and solvent hydration patterns were altered in the structure with the Br incorporation in the major groove. Furthermore, while the native andmore » Br-derivatized DNAs needed over a week to form reasonable-size crystals, we observed that the Se-derivatized DNAs grew crystals overnight with high-diffraction quality, suggesting that the Se derivatization facilitated the crystal formation. In addition, the Se-derivatized DNA sequences crystallized under a broader range of buffer conditions, and generally had a faster crystal growth rate. Our experimental results indicate that the selenium derivatization of DNAs may facilitate the determination of nucleic acid X-ray crystal structures in phasing and high-quality crystal growth. In addition, our results suggest that the Se derivatization can be an alternative to the conventional Br derivatization.« less

Effects of cyclic structure inhibitors on the morphology and growth of tetrahydrofuran hydrate crystals

NASA Astrophysics Data System (ADS)

Li, Sijia; Wang, Yanhong; Lang, Xuemei; Fan, Shuanshi

2013-08-01

Morphology and growth of hydrate crystals with cyclic structure inhibitors at a hydrate-liquid interface were directly observed through a microscopic manipulating apparatus. Tetrahydrofuran (THF) hydrate was employed as an objective. The effects of four kind of cyclic structure inhibitors, polyvinylpyrrolidone (PVP), poly(N-vinyl-2-pyrrolidone-co-2-vinyl pyridine) (PVPP), poly(2-vinyl pyridine-co-N-vinylcaprolactam) (PVPC) and poly(N-vinylcaprolactam) (PVCap), were investigated. Morphological patterns between each hydrate crystal growth from hydrate-liquid interface into droplet were found differ significantly. Lamellar structure growth of hydrate crystal was observed without inhibitor, while with PVP was featheriness-like, PVPP was like long dendritic crystal, PVPC was Mimosa pudica leaf-like and PVCap was like weeds. The growth rate of hydrate crystal without inhibitor was 0.00498 mm3/s, while with PVPP, PVPC and PVCap, were 0.00339 mm3/s, 0.00350 mm3/s, 0.00386 mm3/s and 0.00426 mm3/s, respectively. Cyclic structure inhibitors can decrease the growth rate, degree of reduction in growth rate of hydrate crystals decrease with the increase of cylinder number.

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.

Gas composition and isotopic geochemistry of cuttings, core, and gas hydrate from the JAPEX/JNOC/GSC Mallik 2L-38 gas hydrate research well

USGS Publications Warehouse

Lorenson, T.D.

1999-01-01

Molecular and isotopic composition of gases from the JAPEX/JNOC/GSC Mallik 2L-38 gas hydrate research well demonstrate that the in situ gases can be divided into three zones composed of mixtures of microbial and thermogenic gases. Sediments penetrated by the well are thermally immature; thus the sediments are probably not a source of thermogenic gas. Thermogenic gas likely migrated from depths below 5000 m. Higher concentrations of gas within and beneath the gas hydrate zone suggest that gas hydrate is a partial barrier to gas migration. Gas hydrate accumulations occur wholly within zone 3, below the base of permafrost. The gas in gas hydrate resembles, in part, the thermogenic gas in surrounding sediments and gas desorbed from lignite. Gas hydrate composition implies that the primary gas hydrate form is Structure I. However, Structure II stabilizing gases are more concentrated and isotopically partitioned in gas hydrate relative to the sediment hosting the gas hydrate, implying that Structure II gas hydrate may be present in small quantities.

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

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.

Improvement of hydration and epidermal barrier function in human skin by a novel compound isosorbide dicaprylate.

PubMed

Chaudhuri, R K; Bojanowski, K

2017-10-01

The study involved the synthesis of a novel derivative of caprylic acid - isosorbide dicaprylate (IDC) - and the evaluation of its potential in improving water homoeostasis and epidermal barrier function in human skin. The effect of IDC on gene expression was assayed in skin organotypic cultures by DNA microarrays. The results were then confirmed for a few key genes by quantitative PCR, immuno- and cytochemistry. Final validation of skin hydration properties was obtained by four separate clinical studies. Level of hydration was measured by corneometer either by using 2% IDC lotion alone vs placebo or in combination with 2% glycerol lotion vs 2% glycerol only. A direct comparison in skin hydration between 2% IDC and 2% glycerol lotions was also carried out. The epidermal barrier function improvement was assessed by determining changes in transepidermal water loss (TEWL) on the arms before and after treatment with 2% IDC lotion versus placebo. IDC was found to upregulate the expression of AQP3, CD44 and proteins involved in keratinocyte differentiation as well as the formation and function of stratum corneum. A direct comparison between 2% IDC versus 2% glycerol lotions revealed a three-fold advantage of IDC in providing skin hydration. Severely dry skin treated with 2% IDC in combination with 2% glycerol showed 133% improvement, whereas 35% improvement was observed with moderately dry human skin. Topical isosorbide dicaprylate favourably modulates genes involved in the maintenance of skin structure and function, resulting in superior clinical outcomes. By improving skin hydration and epidermal permeability barrier, it offers therapeutic applications in skin ageing. © 2017 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

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

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.

Transformations in methane hydrates

USGS Publications Warehouse

Chou, I.-Ming; Sharma, A.; Burruss, R.C.; Shu, J.; Mao, Ho-kwang; Hemley, R.J.; Goncharov, A.F.; Stern, L.A.; Kirby, S.H.

2000-01-01

Detailed study of pure methane hydrate in a diamond cell with in situ optical, Raman, and x-ray microprobe techniques reveals two previously unknown structures, structure II and structure H, at high pressures. The structure II methane hydrate at 250 MPa has a cubic unit cell of a = 17.158(2) A?? and volume V = 5051.3(13) A??3; structure H at 600 MPa has a hexagonal unit cell of a = 11.980(2) A??, c = 9.992(3) A??, and V = 1241.9(5) A??3. The compositions of these two investigated phases are still not known. With the effects of pressure and the presence of other gases in the structure, the structure II phase is likely to dominate over the known structure I methane hydrate within deep hydrate-bearing sediments underlying continental margins.

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

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.

Study of intermolecular contacts in the proline-rich homeodomain (PRH)-DNA complex using molecular dynamics simulations.

PubMed

Jalili, Seifollah; Karami, Leila

2012-03-01

The proline-rich homeodomain (PRH)-DNA complex consists of a protein with 60 residues and a 13-base-pair DNA. The PRH protein is a transcription factor that plays a key role in the regulation of gene expression. PRH is a significant member of the Q50 class of homeodomain proteins. The homeodomain section of PRH is essential for binding to DNA and mediates sequence-specific DNA binding. Three 20-ns molecular dynamics (MD) simulations (free protein, free DNA and protein-DNA complex) in explicit solvent water were performed to elucidate the intermolecular contacts in the PRH-DNA complex and the role of dynamics of water molecules forming water-mediated contacts. The simulation provides a detailed explanation of the trajectory of hydration water molecules. The simulations show that some water molecules in the protein-DNA interface exchange with bulk waters. The simulation identifies that most of the contacts consisted of direct interactions between the protein and DNA including specific and non-specific contacts, but several water-mediated polar contacts were also observed. The specific interaction between Gln50 and C18 and water-mediated hydrogen bond between Gln50 and T7 were found to be present during almost the entire time of the simulation. These results show good consistency with experimental and previous computational studies. Structural properties such as root-mean-square deviations (RMSD), root-mean-square fluctuations (RMSF) and secondary structure were also analyzed as a function of time. Analyses of the trajectories showed that the dynamic fluctuations of both the protein and the DNA were lowered by the complex formation.

Investigating the Metastability of Clathrate Hydrates for Energy Storage

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

Koh, Carolyn Ann

2014-11-18

Important breakthrough discoveries have been achieved from the DOE award on the key processes controlling the synthesis and structure-property relations of clathrate hydrates, which are critical to the development of clathrate hydrates as energy storage materials. Key achievements include: (i) the discovery of key clathrate hydrate building blocks (stable and metastable) leading to clathrate hydrate nucleation and growth; (ii) development of a rapid clathrate hydrate synthesis route via a seeding mechanism; (iii) synthesis-structure relations of H2 + CH4/CO2 binary hydrates to control thermodynamic requirements for energy storage and sequestration applications; (iv) discovery of a new metastable phase present during clathratemore » hydrate structural transitions. The success of our research to-date is demonstrated by the significant papers we have published in high impact journals, including Science, Angewandte Chemie, J. Am. Chem. Soc. Intellectual Merits of Project Accomplishments: The intellectual merits of the project accomplishments are significant and transformative, in which the fundamental coupled computational and experimental program has provided new and critical understanding on the key processes controlling the nucleation, growth, and thermodynamics of clathrate hydrates containing hydrogen, methane, carbon dioxide, and other guest molecules for energy storage. Key examples of the intellectual merits of the accomplishments include: the first discovery of the nucleation pathways and dominant stable and metastable structures leading to clathrate hydrate formation; the discovery and experimental confirmation of new metastable clathrate hydrate structures; the development of new synthesis methods for controlling clathrate hydrate formation and enclathration of molecular hydrogen. Broader Impacts of Project Accomplishments: The molecular investigations performed in this project on the synthesis (nucleation & growth)-structure-stability relations of clathrate hydrate systems are pivotal in the fundamental understanding of crystalline clathrate hydrates and the discovery of new clathrate hydrate properties and novel materials for a broad spectrum of energy applications, including: energy storage (hydrogen, natural gas); carbon dioxide sequestration; controlling hydrate formation in oil/gas transportation in subsea pipelines. The Project has also enabled the training of undergraduate, graduate and postdoctoral students in computational methods, molecular spectroscopy and diffraction, and measurement methods at extreme conditions of high pressure and low temperature.« less

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

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

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

2015-10-27

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

Gas hydrate inhibition by perturbation of liquid water structure

NASA Astrophysics Data System (ADS)

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

2015-06-01

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

Gas hydrate inhibition by perturbation of liquid water structure.

PubMed

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

2015-06-17

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

Molecular dynamics simulations of electrostatics and hydration distributions around RNA and DNA motifs

NASA Astrophysics Data System (ADS)

Marlowe, Ashley E.; Singh, Abhishek; Semichaevsky, Andrey V.; Yingling, Yaroslava G.

2009-03-01

Nucleic acid nanoparticles can self-assembly through the formation of complementary loop-loop interactions or stem-stem interactions. Presence and concentration of ions can significantly affect the self-assembly process and the stability of the nanostructure. In this presentation we use explicit molecular dynamics simulations to examine the variations in cationic distributions and hydration environment around DNA and RNA helices and loop-loop interactions. Our simulations show that the potassium and sodium ionic distributions are different around RNA and DNA motifs which could be indicative of ion mediated relative stability of loop-loop complexes. Moreover in RNA loop-loop motifs ions are consistently present and exchanged through a distinct electronegative channel. We will also show how we used the specific RNA loop-loop motif to design a RNA hexagonal nanoparticle.

Knowledge-Based Elastic Potentials for Docking Drugs or Proteins with Nucleic Acids

PubMed Central

Ge, Wei; Schneider, Bohdan; Olson, Wilma K.

2005-01-01

Elastic ellipsoidal functions defined by the observed hydration patterns around the DNA bases provide a new basis for measuring the recognition of ligands in the grooves of double-helical structures. Here a set of knowledge-based potentials suitable for quantitative description of such behavior is extracted from the observed positions of water molecules and amino acid atoms that form hydrogen bonds with the nitrogenous bases in high resolution crystal structures. Energies based on the displacement of hydrogen-bonding sites on drugs in DNA-crystal complexes relative to the preferred locations of water binding around the heterocyclic bases are low, pointing to the reliability of the potentials and the apparent displacement of water molecules by drug atoms in these structures. The validity of the energy functions has been further examined in a series of sequence substitution studies based on the structures of DNA bound to polyamides that have been designed to recognize the minor-groove edges of Watson-Crick basepairs. The higher energies of binding to incorrect sequences superimposed (without conformational adjustment or displacement of polyamide ligands) on observed high resolution structures confirm the hypothesis that the drug subunits associate with specific DNA bases. The knowledge-based functions also account satisfactorily for the measured free energies of DNA-polyamide association in solution and the observed sites of polyamide binding on nucleosomal DNA. The computations are generally consistent with mechanisms by which minor-groove binding ligands are thought to recognize DNA basepairs. The calculations suggest that the asymmetric distributions of hydrogen-bond-forming atoms on the minor-groove edge of the basepairs may underlie ligand discrimination of G·C from C·G pairs, in addition to the commonly believed role of steric hindrance. The analysis of polyamide-bound nucleosomal structures reveals other discrepancies in the expected chemical design, including unexpected contacts to DNA and modified basepair targets of some ligands. The ellipsoidal potentials thus appear promising as a mathematical tool for the study of drug- and protein-DNA interactions and for gaining new insights into DNA-binding mechanisms. PMID:15501936

Ambient water and visible-light irradiation drive changes in graphene morphology, structure, surface chemistry, aggregation, and toxicity.

PubMed

Hu, Xiangang; Zhou, Ming; Zhou, Qixing

2015-03-17

The environmental behaviors and risks associated with graphene have attracted considerable attention. However, the fundamental effects of ambient water and visible-light irradiation on the properties and toxicity of graphene remain unknown. This work revealed that hydration and irradiation result in the transformation of large-sheet graphene to long-ribbon graphene. The thickness of the treated graphene decreased, and oxides were formed through the generation of singlet oxygen. In addition, hydration and irradiation resulted in greater disorder in the graphene structure and in the expansion of the d-spacing of the structure due to the introduction of water molecules and modifications of the functional groups. Oxidative modifications with two-stage (fast and low) kinetics enhanced the number of negative surface charges on the graphene and enhanced graphene aggregation. The above property alterations reduced the nanotoxicity of graphene to algal cells by reducing the generation of reactive oxygen species, diminishing protein carbonylation and decreasing tail DNA. A comparative study using graphene oxide suggested that oxidative modifications could play an important role in inhibiting toxicological activity. This study provides a preliminary approach for understanding the environmental behaviors of graphene and avoids overestimating the risks of graphene in the natural environment.

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.

Standard atomic volumes in double-stranded DNA and packing in protein–DNA interfaces

PubMed Central

Nadassy, Katalin; Tomás-Oliveira, Isabel; Alberts, Ian; Janin, Joël; Wodak, Shoshana J.

2001-01-01

Standard volumes for atoms in double-stranded B-DNA are derived using high resolution crystal structures from the Nucleic Acid Database (NDB) and compared with corresponding values derived from crystal structures of small organic compounds in the Cambridge Structural Database (CSD). Two different methods are used to compute these volumes: the classical Voronoi method, which does not depend on the size of atoms, and the related Radical Planes method which does. Results show that atomic groups buried in the interior of double-stranded DNA are, on average, more tightly packed than in related small molecules in the CSD. The packing efficiency of DNA atoms at the interfaces of 25 high resolution protein–DNA complexes is determined by computing the ratios between the volumes of interfacial DNA atoms and the corresponding standard volumes. These ratios are found to be close to unity, indicating that the DNA atoms at protein–DNA interfaces are as closely packed as in crystals of B-DNA. Analogous volume ratios, computed for buried protein atoms, are also near unity, confirming our earlier conclusions that the packing efficiency of these atoms is similar to that in the protein interior. In addition, we examine the number, volume and solvent occupation of cavities located at the protein–DNA interfaces and compared them with those in the protein interior. Cavities are found to be ubiquitous in the interfaces as well as inside the protein moieties. The frequency of solvent occupation of cavities is however higher in the interfaces, indicating that those are more hydrated than protein interiors. Lastly, we compare our results with those obtained using two different measures of shape complementarity of the analysed interfaces, and find that the correlation between our volume ratios and these measures, as well as between the measures themselves, is weak. Our results indicate that a tightly packed environment made up of DNA, protein and solvent atoms plays a significant role in protein–DNA recognition. PMID:11504874

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

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.

Biophysical and transfection studies of the diC(14)-amidine/DNA complex.

PubMed Central

Cherezov, Vadim; Qiu, Hong; Pector, Veronique; Vandenbranden, Michel; Ruysschaert, Jean-Marie; Caffrey, Martin

2002-01-01

Liposomes of the synthetic cationic lipid, N-t-butyl-N'-tetradecylamino-propionamidine (diC(14)-amidine), efficiently ports DNA into mammalian cells in the absence of other (neutral) lipids. The compositional simplicity of this transfection mix makes it attractive from a formulation perspective. We have used low- and wide-angle x-ray diffraction and polarized light microscopy to characterize the thermotropic phase behavior and microstructure of diC(14)-amidine and of the lipid/DNA (circular plasmid, 5.4 kb) complex with a view to understanding the structure of the complex and its role in transfection. Upon heating, the lipid in buffer undergoes a lamellar crystalline (L(c), d(001) = 41.7 A)-to-lamellar liquid crystal (L(c)(alpha), d(001) depends on hydration and T) transition at approximately 40 degrees C. Sonicated lipid vesicles with a reported transition temperature of approximately 23 degrees C complex with DNA. Complex formation is complete at a DNA/lipid mole ratio (rho) of 0.8. Adding DNA to the lipid causes d(001) of the multilayered complex to drop from 52 to 49 A as rho rises from 0.03 to 1.64. The minimal DNA-DNA duplex separation observed is 26 A, consistent with the close packing of B-DNA. Lipid bilayers in the complex undergo a lamellar gel (L(c)(beta))-to-L(c)(alpha) (superscript c refers to complex) transition at approximately 23 degrees C. Transfection efficiency was maximized at rho = 0.4. The structure and transfection data combined suggest that densely packaged DNA in a net positively charged complex is essential for transfection. PMID:12023234

Monitoring the reversible B to A-like transition of DNA in eukaryotic cells using Fourier transform infrared spectroscopy

PubMed Central

Whelan, Donna R.; Bambery, Keith R.; Heraud, Philip; Tobin, Mark J.; Diem, Max; McNaughton, Don; Wood, Bayden R.

2011-01-01

The ability to detect DNA conformation in eukaryotic cells is of paramount importance in understanding how some cells retain functionality in response to environmental stress. It is anticipated that the B to A transition might play a role in resistance to DNA damage such as heat, desiccation and toxic damage. To this end, conformational detail about the molecular structure of DNA has been derived primarily from in vitro experiments on extracted or synthetic DNA. Here, we report that a B- to A-like DNA conformational change can occur in the nuclei of intact cells in response to dehydration. This transition is reversible upon rehydration in air-dried cells. By systematically monitoring the dehydration and rehydration of single and double-stranded DNA, RNA, extracted nuclei and three types of eukaryotic cells including chicken erythrocytes, mammalian lymphocytes and cancerous rodent fibroblasts using Fourier transform infrared (FTIR) spectroscopy, we unequivocally assign the important DNA conformation marker bands within these cells. We also demonstrate that by applying FTIR spectroscopy to hydrated samples, the DNA bands become sharper and more intense. This is anticipated to provide a methodology enabling differentiation of cancerous from non-cancerous cells based on the increased DNA content inherent to dysplastic and neoplastic tissue. PMID:21447564

Structural Basis for the Inhibition of Gas Hydrates by α-Helical Antifreeze Proteins

PubMed Central

Sun, Tianjun; Davies, Peter L.; Walker, Virginia K.

2015-01-01

Kinetic hydrate inhibitors (KHIs) are used commercially to inhibit gas hydrate formation and growth in pipelines. However, improvement of these polymers has been constrained by the lack of verified molecular models. Since antifreeze proteins (AFPs) act as KHIs, we have used their solved x-ray crystallographic structures in molecular modeling to explore gas hydrate inhibition. The internal clathrate water network of the fish AFP Maxi, which extends to the protein’s outer surface, is remarkably similar to the {100} planes of structure type II (sII) gas hydrate. The crystal structure of this water web has facilitated the construction of in silico models for Maxi and type I AFP binding to sII hydrates. Here, we have substantiated our models with experimental evidence of Maxi binding to the tetrahydrofuran sII model hydrate. Both in silico and experimental evidence support the absorbance-inhibition mechanism proposed for KHI binding to gas hydrates. Based on the Maxi crystal structure we suggest that the inhibitor adsorbs to the gas hydrate lattice through the same anchored clathrate water mechanism used to bind ice. These results will facilitate the rational design of a next generation of effective green KHIs for the petroleum industry to ensure safe and efficient hydrocarbon flow. PMID:26488661

Highly porous CO 2 hydrate generation aided by silica nanoparticles for potential secure storage of CO 2 and desalination

DOE PAGES

Kim, Ijung; Nole, Michael; Jang, Sunghyun; ...

2017-01-31

Here in this paper, we report a new way of storing CO 2 in a highly porous hydrate structure, stabilized by silica nanoparticles (NPs). Such a porous CO 2 hydrate structure was generated either by cooling down NP-stabilized CO 2-in-seawater foams, or by gently mixing CO 2 and seawater that contains silica NPs under CO 2 hydrate-generating conditions. With the highly porous structure, enhanced desalination was also achievable when the partial meltdown of CO 2 hydrate was allowed.

Highly porous CO 2 hydrate generation aided by silica nanoparticles for potential secure storage of CO 2 and desalination

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

Kim, Ijung; Nole, Michael; Jang, Sunghyun

Here in this paper, we report a new way of storing CO 2 in a highly porous hydrate structure, stabilized by silica nanoparticles (NPs). Such a porous CO 2 hydrate structure was generated either by cooling down NP-stabilized CO 2-in-seawater foams, or by gently mixing CO 2 and seawater that contains silica NPs under CO 2 hydrate-generating conditions. With the highly porous structure, enhanced desalination was also achievable when the partial meltdown of CO 2 hydrate was allowed.

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

Experimental investigations about the effect of trace amount of propane on the formation of mixed hydrates of methane and propane

NASA Astrophysics Data System (ADS)

Cai, W.; Lu, H.; Huang, X.

2016-12-01

In natural gas hydrates, some heavy hydrocarbons are always detected in addition to methane. However, it is still not well understood how the trace amount of heavy gas affect the hydrate properties. Intensive studies have been carried out to study the thermodynamic properties and structure types of mixed gases hydrates, but comparatively few investigations have been carried out on the cage occupancies of guest molecules in mixed gases hydrates. For understanding how trace amount of propane affects the formation of mixed methane-propane hydrates, X-ray diffraction, Raman spectroscopy, and gas chromatography were applied to the synthesized mixed methane-propane hydrate specimens, to get their structural characteristics (structure type, structural parameters, cage occupancy, etc.) and gas compositions. The mixed methane-propane hydrates were prepared by reacting fine ice powders with various gas mixtures of methane and propane. When the propane content was below 0.4%, the hydrates synthesized were found containing both sI methane hydrate and sII methane-propane hydrate; while the hydrates were found always sII when propane was over certain content. Detail studies about the cage occupancies of propane and methane in sII hydrate revealed that: 1) with the increase in propane content of methane-propane mixture, the occupancy of propane in large cage increased as accompanied with the decrease in methane occupancy in large cage, however the occupancy of methane in small cage didn't experience significant change; 2) temperature and pressure seemed no obvious influence on cage occupancy.

Thermodynamics of complex structures formed between single-stranded DNA oligomers and the KH domains of the far upstream element binding protein

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

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

The noncovalent interaction between protein and DNA is responsible for regulating the genetic activities in living organisms. The most critical issue in this problem is to understand the underlying driving force for the formation and stability of the complex. To address this issue, we have performed atomistic molecular dynamics simulations of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein (FBP) complexed with two single-stranded DNA (ss-DNA) oligomers in aqueous media. Attempts have been made to calculate the individual components of the net entropy change for the complexation process by adopting suitablemore » statistical mechanical approaches. Our calculations reveal that translational, rotational, and configurational entropy changes of the protein and the DNA components have unfavourable contributions for this protein-DNA association process and such entropy lost is compensated by the entropy gained due to the release of hydration layer water molecules. The free energy change corresponding to the association process has also been calculated using the Free Energy Perturbation (FEP) method. The free energy gain associated with the KH4–DNA complex formation has been found to be noticeably higher than that involving the formation of the KH3–DNA complex.« less

RECENT ADVANCES IN MACROMOLECULAR HYDRODYNAMIC MODELING

PubMed Central

Aragon, Sergio R.

2010-01-01

The modern implementation of the boundary element method (S.R. Aragon, J. Comput. Chem. 25(2004)1191–12055) has ushered unprecedented accuracy and precision for the solution of the Stokes equations of hydrodynamics with stick boundary conditions. This article begins by reviewing computations with the program BEST of smooth surface objects such as ellipsoids, the dumbbell, and cylinders that demonstrate that the numerical solution of the integral equation formulation of hydrodynamics yields very high precision and accuracy. When BEST is used for macromolecular computations, the limiting factor becomes the definition of the molecular hydrodynamic surface and the implied effective solvation of the molecular surface. Studies on 49 different proteins, ranging in molecular weight from 9 to over 400 kDa, have shown that a model using a 1.1 A thick hydration layer describes all protein transport properties very well for the overwhelming majority of them. In addition, this data implies that the crystal structure is an excellent representation of the average solution structure for most of them. In order to investigate the origin of a handful of significant discrepancies in some multimeric proteins (over −20% observed in the intrinsic viscosity), the technique of Molecular Dynamics simulation (MD) has been incorporated into the research program. A preliminary study of dimeric α-chymotrypsin using approximate implicit water MD is presented. In addition I describe the successful validation of modern protein force fields, ff03 and ff99SB, for the accurate computation of solution structure in explicit water simulation by comparison of trajectory ensemble average computed transport properties with experimental measurements. This work includes small proteins such as lysozyme, ribonuclease and ubiquitin using trajectories around 10 ns duration. We have also studied a 150 kDa flexible monoclonal IgG antibody, trastuzumab, with multiple independent trajectories encompassing over 320 ns of simulation. The close agreement within experimental error of the computed and measured properties allows us to conclude that MD does produce structures typical of those in solution, and that flexible molecules can be properly described using the method of ensemble averaging over a trajectory. We review similar work on the study of a transfer RNA molecule and DNA oligomers that demonstrate that within 3% a simple uniform hydration model 1.1 A thick provides agreement with experiment for these nucleic acids. In the case of linear oligomers, the precision can be improved close to 1% by a non-uniform hydration model that hydrates mainly in the DNA grooves, in agreement with high resolution x-ray diffraction. We conclude with a vista on planned improvements for the BEST program to decrease its memory requirements and increase its speed without sacrificing accuracy. PMID:21073955

Clathrate hydrates in the solar system

NASA Technical Reports Server (NTRS)

Miller, S. L.

1985-01-01

Clathrate hydrates are crystalline compounds in which an expanded ice lattice forms cages that contain gas molecules. There are two principal hydrate structures. Structure I, with a 12 A cubic unit cell, contains 46 water molecules and 8 cages of two types, giving an ideal formula (for CH4) of CH4.5.75H2O. The actual formula contains somewhat more water as the cages are not completely filled. Other examples that form Structure I hydrates are C2H6, C2H4, C2H2, CO2, SO2, OCS, Xe, H2S. Structure II, with a 17 A cubic unit cell, contains 136 water molecules, and 8 large and 16 small cages. The ideal formula for CHCl3 is CHCL3.17H2O. Other examples of Structure II hydrates include C3H8, C2H5Cl, acetone, and tetrahydrofuran. Small molecules such as Ar, Kr and probably N2 and O2 also form a Structure II hydrate. The small molecules occupy both the large and small cages, giving an ideal formula of Ar.5.67H2O. The conditions of pressure and temperature for hydrate formation are discussed.

Ionization energies of aqueous nucleic acids: photoelectron spectroscopy of pyrimidine nucleosides and ab initio calculations.

PubMed

Slavícek, Petr; Winter, Bernd; Faubel, Manfred; Bradforth, Stephen E; Jungwirth, Pavel

2009-05-13

Vertical ionization energies of the nucleosides cytidine and deoxythymidine in water, the lowest ones amounting in both cases to 8.3 eV, are obtained from photoelectron spectroscopy measurements in aqueous microjets. Ab initio calculations employing a nonequilibrium polarizable continuum model quantitatively reproduce the experimental spectra and provide molecular interpretation of the individual peaks of the photoelectron spectrum, showing also that lowest ionization originates from the base. Comparison of calculated vertical ionization potentials of pyrimidine bases, nucleosides, and nucleotides in water and in the gas phase underlines the dramatic effect of bulk hydration on the electronic structure. In the gas phase, the presence of sugar and, in particular, of phosphate has a strong effect on the energetics of ionization of the base. Upon bulk hydration, the ionization potential of the base in contrast becomes rather insensitive to the presence of the sugar and phosphate, which indicates a remarkable screening ability of the aqueous solvent. Accurate aqueous-phase vertical ionization potentials provide a significant improvement to the corrected gas-phase values used in the literature and represent important information in assessing the threshold energies for photooxidation and oxidation free energies of solvent-exposed DNA components. Likewise, such energetic data should allow improved assessment of delocalization and charge-hopping mechanisms in DNA ionized by radiation.

Micromechanical cohesion force between gas hydrate particles measured under high pressure and low temperature conditions.

PubMed

Lee, Bo Ram; Sum, Amadeu K

2015-04-07

To prevent hydrate plugging conditions in the transportation of oil/gas in multiphase flowlines, one of the key processes to control is the agglomeration/deposition of hydrate particles, which are determined by the cohesive/adhesive forces. Previous studies reporting measurements of the cohesive/adhesive force between hydrate particles used cyclopentane hydrate particles in a low-pressure micromechanical force apparatus. In this study, we report the cohesive forces of particles measured in a new high-pressure micromechanical force (MMF) apparatus for ice particles, mixed (methane/ethane, 74.7:25.3) hydrate particles (Structure II), and carbon dioxide hydrate particles (Structure I). The cohesive forces are measured as a function of the contact time, contact force, temperature, and pressure, and determined from pull-off measurements. For the measurements performed of the gas hydrate particles in the gas phase, the determined cohesive force is about 30-35 mN/m, about 8 times higher than the cohesive force of CyC5 hydrates in the liquid CyC5, which is about 4.3 mN/m. We show from our results that the hydrate structure (sI with CO2 hydrates and sII with CH4/C2H6 hydrates) has no influence on the cohesive force. These results are important in the deposition of a gas-dominated system, where the hydrate particles formed in the liquid phase can then stick to the hydrate deposited in the wall exposed to the gas phase.

Dissociation behavior of methane--ethane mixed gas hydrate coexisting structures I and II.

PubMed

Kida, Masato; Jin, Yusuke; Takahashi, Nobuo; Nagao, Jiro; Narita, Hideo

2010-09-09

Dissociation behavior of methane-ethane mixed gas hydrate coexisting structures I and II at constant temperatures less than 223 K was studied with use of powder X-ray diffraction and solid-state (13)C NMR techniques. The diffraction patterns at temperatures less than 203 K showed both structures I and II simultaneously convert to Ih during the dissociation, but the diffraction pattern at temperatures greater than 208 K showed different dissociation behavior between structures I and II. Although the diffraction peaks from structure II decreased during measurement at constant temperatures greater than 208 K, those from structure I increased at the initial step of dissociation and then disappeared. This anomalous behavior of the methane-ethane mixed gas hydrate coexisting structures I and II was examined by using the (13)C NMR technique. The (13)C NMR spectra revealed that the anomalous behavior results from the formation of ethane-rich structure I. The structure I hydrate formation was associated with the dissociation rate of the initial methane-ethane mixed gas hydrate.

Monitoring early hydration of reinforced concrete structures using structural parameters identified by piezo sensors via electromechanical impedance technique

NASA Astrophysics Data System (ADS)

Talakokula, Visalakshi; Bhalla, Suresh; Gupta, Ashok

2018-01-01

Concrete is the most widely used material in civil engineering construction. Its life begins when the hydration process is activated after mixing the cement granulates with water. In this paper, a non-dimensional hydration parameter, obtained from piezoelectric ceramic (PZT) patches bonded to rebars embedded inside concrete, is employed to monitor the early age hydration of concrete. The non-dimensional hydration parameter is derived from the equivalent stiffness determined from the piezo-impedance transducers using the electro-mechanical impedance (EMI) technique. The focus of the study is to monitor the hydration process of cementitious materials commencing from the early hours and continue till 28 days using single non-dimensional parameter. The experimental results show that the proposed piezo-based non-dimensional hydration parameter is very effective in monitoring the early age hydration, as it has been derived from the refined structural impedance parameters, obtained by eliminating the PZT contribution, and using both the real and imaginary components of the admittance signature.

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

The Role of Natural Hydrate on the Strength of Sands: Load-bearing or Cementing?

NASA Astrophysics Data System (ADS)

Priest, J. A.; Hayley, J. L.

2017-12-01

The strength of hydrate bearing sands is a key parameter for simulating the long-term performance of hydrate reservoirs during gas production and assessing reservoir and wellbore stability. Historically this parameter has been determined from testing synthesized hydrate sand samples, which has led to significant differences in measured strength that appears to reflect different formation methods adopted. At present, formation methods can be grouped into either those that form hydrate at grain contacts leading to a high strength `cemented' sand, or those where the hydrate forms a `load-bearing' structure in which the hydrate grains reside in the pore space resulting in more subtle changes in strength. Recovered natural hydrate-bearing cores typically exhibit this `load-bearing' behavior, although these cores have generally undergone significant changes in temperature and pressure during recovery, which may have altered the structure of the hydrate and sediment. Recent drilling expeditions using pressure coring, such as NGHP2 offshore India, have enabled intact hydrate bearing sediments to be recovered that have maintained hydrostatic stresses minimizing any changes in the hydrate structure within the core. Triaxial testing on these samples highlight enhanced strength even at zero effective stresses. This suggests that the hydrate forms a connected framework within the pore space apparently `cementing' the sand grains in place: we differentiate here between true cementation where hydrate is sintered onto the sand grains and typical observed behavior for cemented sands (cohesion, peak strength, post-peak strain softening). This inter-connected hydrate, and its ability to increase strength of the sands, appears to occur even at hydrate saturations as low as 30%, where typical `load-bearing' hydrates just start to increase strength. The results from pressure cores suggest that hydrate formation techniques that lead to `load-bearing' behavior may not capture the true interaction between the hydrate and sand and thus further research is needed to form synthesized hydrate bearing samples that more realistically mimic the observed strength behavior of natural hydrate bearing cores.

High-resolution resistivity imaging of marine gas hydrate structures by combined inversion of CSEM towed and ocean-bottom receiver data

NASA Astrophysics Data System (ADS)

Attias, Eric; Weitemeyer, Karen; Hölz, Sebastian; Naif, Samer; Minshull, Tim A.; Best, Angus I.; Haroon, Amir; Jegen-Kulcsar, Marion; Berndt, Christian

2018-06-01

We present high-resolution resistivity imaging of gas hydrate pipe-like structures, as derived from marine controlled-source electromagnetic (CSEM) inversions that combine towed and ocean-bottom electric field receiver data, acquired from the Nyegga region, offshore Norway. Two-dimensional CSEM inversions applied to the towed receiver data detected four new prominent vertical resistive features that are likely gas hydrate structures, located in proximity to a major gas hydrate pipe-like structure, known as the CNE03 pockmark. The resistivity model resulting from the CSEM data inversion resolved the CNE03 hydrate structure in high resolution, as inferred by comparison to seismically constrained inversions. Our results indicate that shallow gas hydrate vertical features can be delineated effectively by inverting both ocean-bottom and towed receiver CSEM data simultaneously. The approach applied here can be utilised to map and monitor seafloor mineralisation, freshwater reservoirs, CO2 sequestration sites and near-surface geothermal systems.

The structural response of the cornea to changes in stromal hydration

PubMed Central

White, Tomas; Boote, Craig; Kamma-Lorger, Christina S.; Bell, James; Sorenson, Thomas; Terrill, Nick; Shebanova, Olga; Meek, Keith M.

2017-01-01

The primary aim of this study was to quantify the relationship between corneal structure and hydration in humans and pigs. X-ray scattering data were collected from human and porcine corneas equilibrated with polyethylene glycol (PEG) to varying levels of hydration, to obtain measurements of collagen fibril diameter, interfibrillar spacing (IFS) and intermolecular spacing. Both species showed a strong positive linear correlation between hydration and IFS2 and a nonlinear, bi-phasic relationship between hydration and fibril diameter, whereby fibril diameter increased up to approximately physiological hydration, H = 3.0, with little change thereafter. Above H = 3.0, porcine corneas exhibited a larger fibril diameter than human corneas (p < 0.001). Intermolecular spacing also varied with hydration in a bi-phasic manner but reached a maximum value at a lower hydration (H = 1.5) than fibril diameter. Human corneas displayed a higher intermolecular spacing than porcine corneas at all hydrations (p < 0.0001). Human and porcine corneas required a similar PEG concentration to reach physiological hydration, suggesting that the total fixed charge that gives rise to the swelling pressure is the same. The difference in their structural responses to hydration can be explained by variations in molecular cross-linking and intra/interfibrillar water partitioning. PMID:28592658

The structural response of the cornea to changes in stromal hydration.

PubMed

Hayes, Sally; White, Tomas; Boote, Craig; Kamma-Lorger, Christina S; Bell, James; Sorenson, Thomas; Terrill, Nick; Shebanova, Olga; Meek, Keith M

2017-06-01

The primary aim of this study was to quantify the relationship between corneal structure and hydration in humans and pigs. X-ray scattering data were collected from human and porcine corneas equilibrated with polyethylene glycol (PEG) to varying levels of hydration, to obtain measurements of collagen fibril diameter, interfibrillar spacing (IFS) and intermolecular spacing. Both species showed a strong positive linear correlation between hydration and IFS 2 and a nonlinear, bi-phasic relationship between hydration and fibril diameter, whereby fibril diameter increased up to approximately physiological hydration, H = 3.0, with little change thereafter. Above H = 3.0, porcine corneas exhibited a larger fibril diameter than human corneas ( p < 0.001). Intermolecular spacing also varied with hydration in a bi-phasic manner but reached a maximum value at a lower hydration ( H = 1.5) than fibril diameter. Human corneas displayed a higher intermolecular spacing than porcine corneas at all hydrations ( p < 0.0001). Human and porcine corneas required a similar PEG concentration to reach physiological hydration, suggesting that the total fixed charge that gives rise to the swelling pressure is the same. The difference in their structural responses to hydration can be explained by variations in molecular cross-linking and intra/interfibrillar water partitioning. © 2017 The Authors.

Structural changes and preferential cage occupancy of ethane hydrate and methane-ethane mixed gas hydrate under very high pressure.

PubMed

Hirai, Hisako; Takahara, Naoya; Kawamura, Taro; Yamamoto, Yoshitaka; Yagi, Takehiko

2008-12-14

High-pressure experiments of ethane hydrate and methane-ethane mixed hydrates with five compositions were performed using a diamond anvil cell in a pressure range of 0.1-2.8 GPa at room temperature. X-ray diffractometry and Raman spectroscopy showed structural changes as follows. The initial structure, structure I (sI), of ethane hydrate was retained up to 2.1 GPa without any structural change. For the mixed hydrates, sI was widely distributed throughout the region examined except for the methane-rich and lower pressure regions. For the ethane-rich and intermediate composition regions (73 mol % ethane sample and 53% sample), sI was maintained up to 2.1 GPa. With increasing methane component (34% and 30% samples), sI existed at pressures from 0.1 to about 1.0 GPa. Hexagonal structure (sH) appeared in addition to sI at 1.3 GPa for the 34% sample and at 1.1 GPa for the 30% sample. By further increasing the methane component (22% sample), structure II (sII) existed solely up to 0.3 GPa. From 0.3 to 0.6 GPa, sII and sI coexisted, and from 0.6 to 1.0 GPa only sI existed. At 1.2 GPa sH appeared, and sH and sI coexisted up to 2.1 GPa. Above 2.1 GPa, ethane hydrate and all of the mixed hydrates decomposed into ice VI and ethane fluid or methane-ethane fluid, respectively. The Raman study revealed that occupation of the small cages by ethane molecules occurred above 0.1 GPa in ethane hydrate and continued up to decomposition at 2.1 GPa, although it is thought that ethane molecules are contained only in the large cage.

[Raman Characterization of Hydrate Crystal Structure Influenced by Mine Gas Concentration].

PubMed

Zhang, Bao-yong; Zhou, Hong-ji; Wu, Qiang; Gao, Xia

2016-01-01

CH4 /C2H6/N2 mixed hydrate formation experiments were performed at 2 degrees C and 5 MPa for three different mine gas concentrations (CH4/C2H6/N2, G1 = 54 : 36 : 10, G2 = 67.5 : 22.5 : 10, G3 = 81 : 9 : 10). Raman spectra for hydration products were obtained by using Microscopic Raman Spectrometer. Hydrate structure is determined by the Raman shift of symmetric C-C stretching vibration mode of C2H6 in the hydrate phase. This work is focused on the cage occupancies and hydration numbers, calculated by the fitting methods of Raman peaks. The results show that structure I (s I) hydrate forms in the G1 and G2 gas systems, while structure II (s II) hydrate forms in the G3 gas system, concentration variation of C2H6 in the gas samples leads to a change in hydrate structure from s I to s II; the percentages of CH4 and C2H6 in s I hydrate phase are less affected by the concentration of gas samples, the percentages of CH4 are respectively 34.4% and 35.7%, C2H6 are respectively 64.6% and 63.9% for gas systems of G1 and G2, the percentages of CH4 and 2 H6 are respectively 73.5% and 22.8% for gas systems of G3, the proportions of object molecules largely depend on the hydrate structure; CH4 and C2H6 molecules occupy 98%, 98% and 92% of the large cages and CH4 molecules occupy 80%, 60% and 84% of the small cages for gas systems of G1, G2 and G3, respectively; additionally, N2 molecules occupy less than 5% of the small cages is due to its weak adsorption ability and the lower partial pressure.

Probing the electrostatics and pharmacologic modulation of sequence-specific binding by the DNA-binding domain of the ETS-family transcription factor PU.1: a binding affinity and kinetics investigation

PubMed Central

Munde, Manoj; Poon, Gregory M. K.; Wilson, W. David

2013-01-01

Members of the ETS family of transcription factors regulate a functionally diverse array of genes. All ETS proteins share a structurally-conserved but sequence-divergent DNA-binding domain, known as the ETS domain. Although the structure and thermodynamics of the ETS-DNA complexes are well known, little is known about the kinetics of sequence recognition, a facet that offers potential insight into its molecular mechanism. We have characterized DNA binding by the ETS domain of PU.1 by biosensor-surface plasmon resonance (SPR). SPR analysis revealed a striking kinetic profile for DNA binding by the PU.1 ETS domain. At low salt concentrations, it binds high-affinity cognate DNA with a very slow association rate constant (≤105 M−1 s−1), compensated by a correspondingly small dissociation rate constant. The kinetics are strongly salt-dependent but mutually balance to produce a relatively weak dependence in the equilibrium constant. This profile contrasts sharply with reported data for other ETS domains (e.g., Ets-1, TEL) for which high-affinity binding is driven by rapid association (>107 M−1 s−1). We interpret this difference in terms of the hydration properties of ETS-DNA binding and propose that at least two mechanisms of sequence recognition are employed by this family of DNA-binding domain. Additionally, we use SPR to demonstrate the potential for pharmacological inhibition of sequence-specific ETS-DNA binding, using the minor groove-binding distamycin as a model compound. Our work establishes SPR as a valuable technique for extending our understanding of the molecular mechanisms of ETS-DNA interactions as well as developing potential small-molecule agents for biotechnological and therapeutic purposes. PMID:23416556

Structural stability of methane hydrate at high pressures

USGS Publications Warehouse

Shu, J.; Chen, X.; Chou, I-Ming; Yang, W.; Hu, Jiawen; Hemley, R.J.; Mao, Ho-kwang

2011-01-01

The structural stability of methane hydrate under pressure at room temperature was examined by both in-situ single-crystal and powder X-ray diffraction techniques on samples with structure types I, II, and H in diamond-anvil cells. The diffraction data for types II (sII) and H (sH) were refined to the known structures with space groups Fd3m and P63/mmc, respectively. Upon compression, sI methane hydrate transforms to the sII phase at 120 MPa, and then to the sH phase at 600 MPa. The sII methane hydrate was found to coexist locally with sI phase up to 500 MPa and with sH phase up to 600 MPa. The pure sH structure was found to be stable between 600 and 900 MPa. Methane hydrate decomposes at pressures above 3 GPa to form methane with the orientationally disordered Fm3m structure and ice VII (Pn3m). The results highlight the role of guest (CH4)-host (H2O) interactions in the stabilization of the hydrate structures under pressure.

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

NASA Technical Reports Server (NTRS)

Lett, J. T.

1992-01-01

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

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

PubMed

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

2015-04-14

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

Radiosensitization of DNA by Cisplatin Adducts Results from an Increase in the Rate Constant for the Reaction with Hydrated Electrons and Formation of Pt(I).

PubMed

Behmand, B; Marignier, J-L; Mostafavi, M; Wagner, J R; Hunting, D J; Sanche, L

2015-07-30

Pulse radiolysis measurements of the decay of hydrated electrons in solutions containing different concentrations of the oligonucleotide GTG with and without a cisplatin adduct show that the presence of a cisplatin moiety accelerates the reaction between hydrated electrons and the oligonucleotide. The rate constant of the reaction is found to be 2.23 × 10(10) mol(-1) L s(-1), which indicates that it is diffusion controlled. In addition, we show for the first time the formation of a Pt(I) intermediate as a result of the reaction of hydrated electrons with GTG-cisplatin. A putative reaction mechanism is proposed, which may form the basis of the radiosensitization of cancer cells in concomitant chemoradiation therapy with cisplatin.

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.

Synthesis and reversible hydration behavior of the thiosulfate intercalated layered double hydroxide of Zn and Al

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

Radha, S.; Milius, Wolfgang; Breu, Josef, E-mail: josef.breu@uni-bayreuth.de

2013-08-15

The thiosulfate-intercalated layered double hydroxide of Zn and Al undergoes reversible hydration with a variation in the relative humidity of the ambient. The hydrated and dehydrated phases, which represent the end members of the hydration cycle, both adopt the structure of the 3R{sub 1} polytype. In the intermediate range of relative humidity values (40–60%), the hydrated and dehydrated phases coexist. The end members of the hydration cycle adopt the structure of the same polytype, and vary only in their basal spacings. This points to the possibility that all the intermediate phases have a kinetic origin. - Graphical abstract: Basal spacingmore » evolution of the thiosulfate ion intercalated [Zn–Al] LDH during one complete hydration–dehydration cycle as a function of relative humidity. Display Omitted - Highlights: • Thiosulfate intercalated [Zn–Al] LDHs were synthesized by co-precipitation. • The LDH exhibits reversible hydration with variation in humidity. • Both the end members of the hydration cycle adopt the same polytype structure. • The interstratified intermediates observed are kinetic in origin.« less

[Laser Raman Spectroscopy and Its Application in Gas Hydrate Studies].

PubMed

Fu, Juan; Wu, Neng-you; Lu, Hai-long; Wu, Dai-dai; Su, Qiu-cheng

2015-11-01

Gas hydrates are important potential energy resources. Microstructural characterization of gas hydrate can provide information to study the mechanism of gas hydrate formation and to support the exploitation and application of gas hydrate technology. This article systemly introduces the basic principle of laser Raman spectroscopy and summarizes its application in gas hydrate studies. Based on Raman results, not only can the information about gas composition and structural type be deduced, but also the occupancies of large and small cages and even hydration number can be calculated from the relative intensities of Raman peaks. By using the in-situ analytical technology, laser Raman specstropy can be applied to characterize the formation and decomposition processes of gas hydrate at microscale, for example the enclathration and leaving of gas molecules into/from its cages, to monitor the changes in gas concentration and gas solubility during hydrate formation and decomposition, and to identify phase changes in the study system. Laser Raman in-situ analytical technology has also been used in determination of hydrate structure and understanding its changing process under the conditions of ultra high pressure. Deep-sea in-situ Raman spectrometer can be employed for the in-situ analysis of the structures of natural gas hydrate and their formation environment. Raman imaging technology can be applied to specify the characteristics of crystallization and gas distribution over hydrate surface. With the development of laser Raman technology and its combination with other instruments, it will become more powerful and play a more significant role in the microscopic study of gas hydrate.

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.

Three-dimensional distribution of gas hydrate beneath southern Hydrate Ridge: Constraints from ODP Leg 204

USGS Publications Warehouse

Trehu, A.M.; Long, P.E.; Torres, M.E.; Bohrmann, G.; Rack, F.R.; Collett, T.S.; Goldberg, D.S.; Milkov, A.V.; Riedel, M.; Schultheiss, P.; Bangs, N.L.; Barr, S.R.; Borowski, W.S.; Claypool, G.E.; Delwiche, M.E.; Dickens, G.R.; Gracia, E.; Guerin, G.; Holland, M.; Johnson, J.E.; Lee, Y.-J.; Liu, C.-S.; Su, X.; Teichert, B.; Tomaru, H.; Vanneste, M.; Watanabe, M. E.; Weinberger, J.L.

2004-01-01

Large uncertainties about the energy resource potential and role in global climate change of gas hydrates result from uncertainty about how much hydrate is contained in marine sediments. During Leg 204 of the Ocean Drilling Program (ODP) to the accretionary complex of the Cascadia subduction zone, we sampled the gas hydrate stability zone (GHSZ) from the seafloor to its base in contrasting geological settings defined by a 3D seismic survey. By integrating results from different methods, including several new techniques developed for Leg 204, we overcome the problem of spatial under-sampling inherent in robust methods traditionally used for estimating the hydrate content of cores and obtain a high-resolution, quantitative estimate of the total amount and spatial variability of gas hydrate in this structural system. We conclude that high gas hydrate content (30-40% of pore space or 20-26% of total volume) is restricted to the upper tens of meters below the seafloor near the summit of the structure, where vigorous fluid venting occurs. Elsewhere, the average gas hydrate content of the sediments in the gas hydrate stability zone is generally <2% of the pore space, although this estimate may increase by a factor of 2 when patchy zones of locally higher gas hydrate content are included in the calculation. These patchy zones are structurally and stratigraphically controlled, contain up to 20% hydrate in the pore space when averaged over zones ???10 m thick, and may occur in up to ???20% of the region imaged by 3D seismic data. This heterogeneous gas hydrate distribution is an important constraint on models of gas hydrate formation in marine sediments and the response of the sediments to tectonic and environmental change. ?? 2004 Published by Elsevier B.V.

The role of correlation and solvation in ion interactions with B-DNA

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

Sushko, Maria L.; Thomas, Dennis G.; Pabit, Suzette

Ionic atmosphere around nucleic acids plays important roles in biological function. Large-scale explicit solvent simulations coupled to experimental assays such as anomalous small-angle X-ray scattering (ASAXS) can provide important insights into the structure and energetics of the ionic atmosphere but are time- and resource-intensive. In this paper, we demonstrate the use of classical density functional theory to model DNA-ion interactions and explore the balance between ion-DNA, ion-water, and ion-ion interactions. In particular, we compute the distribution of RbCl, SrCl2, and CoHexCl3 (cobalt hexammine chlo- ride) around a B-form DNA molecule. The accuracy of the DFT calculations was assessed by comparisonmore » between simulated and experimental ASAXS curves. As expected, these calculations revealed significant differences between the monovalent, divalent, and trivalent cations. About half of the DNA-bound Rb+ ions penetrate into the minor groove of the DNA and half adsorb on the DNA strands. The fraction of cations in the minor groove decreases for the larger Sr2+ ions and becomes zero for CoHex3+ ions, which all adsorb on the DNA strands. The distribution of CoHex3+ ions is mainly determined by Coulomb interactions, while ion-correlation forces play a central role in the monovalent Rb+ distribution and a combination of ion-correlation and hydration forces affect the Sr2+ distribution around DNA.« less

States of phage T3/T7 capsids: buoyant density centrifugation and cryo-EM.

PubMed

Serwer, Philip; Wright, Elena T; Demeler, Borries; Jiang, Wen

2018-04-01

Mature double-stranded DNA bacteriophages have capsids with symmetrical shells that typically resist disruption, as they must to survive in the wild. However, flexibility and associated dynamism assist function. We describe biochemistry-oriented procedures used to find previously obscure flexibility for capsids of the related phages, T3 and T7. The primary procedures are hydration-based buoyant density ultracentrifugation and purified particle-based cryo-electron microscopy (cryo-EM). We review the buoyant density centrifugation in detail. The mature, stable T3/T7 capsid is a shell flexibility-derived conversion product of an initially assembled procapsid (capsid I). During DNA packaging, capsid I expands and loses a scaffolding protein to form capsid II. The following are observations made with capsid II. (1) The in vivo DNA packaging of wild type T3 generates capsid II that has a slight (1.4%), cryo-EM-detected hyper-expansion relative to the mature phage capsid. (2) DNA packaging in some altered conditions generates more extensive hyper-expansion of capsid II, initially detected by hydration-based preparative buoyant density centrifugation in Nycodenz density gradients. (3) Capsid contraction sometimes occurs, e.g., during quantized leakage of DNA from mature T3 capsids without a tail.

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

PubMed Central

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

2013-01-01

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

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.

Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

NASA Astrophysics Data System (ADS)

Vlasic, Thomas M.; Servio, Phillip; Rey, Alejandro D.

2016-08-01

This work uses density functional theory (DFT) to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane), at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS) for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu) were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

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

Vlasic, Thomas M.; Servio, Phillip; Rey, Alejandro D., E-mail: alejandro.rey@mcgill.ca

2016-08-15

This work uses density functional theory (DFT) to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane), at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS) for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu) were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better thanmore » the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.« less

Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS.

PubMed

Grindon, Christina; Harris, Sarah; Evans, Tom; Novik, Keir; Coveney, Peter; Laughton, Charles

2004-07-15

Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.

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.

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.

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.

Molecular level studies on interfacial hydration of zwitterionic and other antifouling polymers in situ.

PubMed

Leng, Chuan; Sun, Shuwen; Zhang, Kexin; Jiang, Shaoyi; Chen, Zhan

2016-08-01

Antifouling polymers have wide applications in biomedical engineering and marine industry. Recently, zwitterionic materials have been reported as promising candidates for antifouling applications, while strong hydration is believed to be the key antifouling mechanism. Zwitterionic materials can be designed with various molecular structures, which affect their hydration and antifouling performance. Although strong hydration has been proposed to occur at the material surfaces, probing the solid material/water interfaces is challenging with traditional analytical techniques. Here in this review, we will review our studies on surface hydration of zwitterionic materials and other antifouling materials by using sum frequency generation (SFG) vibrational spectroscopy, which provides molecular understanding of the water structures at various material surfaces. The materials studied include zwitterionic polymer brushes with different molecular structures, amphiphilic polymers with zwitterionic groups, uncharged hydrophilic polymer brushes, amphiphilic polypeptoids, and widely used antifouling material poly(ethylene glycol). We will compare the differences among zwitterionic materials with various molecular structures as well as the differences between antifouling materials and fouling surfaces of control samples. We will also discuss the effects of pH and biological molecules like proteins on the surface hydration of the zwitterionic materials. Using SFG spectroscopy, we have measured the hydration layers of antifouling materials and found that strong hydrogen bonds are key to the formation of strong hydration layers preventing protein fouling at the polymer interfaces. Antifouling polymers have wide applications in biomedical engineering and marine industry. Recently, zwitterionic materials have been reported as promising candidates for antifouling applications, while strong hydration is believed to be the key antifouling mechanism. However, zwitterionic materials can be designed with various molecular structures, which affect their hydration and antifouling performance. Moreover, although strong hydration has been proposed to occur at the material surfaces, probing the solid material/water interfaces is challenging with traditional analytical techniques. Here in this manuscript, we will review our studies on surface hydration of zwitterionic materials and other antifouling materials by using sum frequency generation (SFG) vibrational spectroscopy, which provides molecular understanding of the water structures at various material surfaces. The materials studied include zwitterionic polymer brushes with different molecular structures, amphiphilic polymers with zwitterionic groups, uncharged hydrophilic polymer brushes, amphiphilic polypeptoids, and widely used antifouling material poly(ethylene glycol). We will compare the differences among zwitterionic materials with various molecular structures as well as the differences between antifouling materials and fouling surfaces of control samples. We will also discuss the effects of pH and biological molecules like proteins on the surface hydration of the zwitterionic materials. All the SFG results indicate that strongly hydrogen-bonded water at the materials' surfaces (strong surface hydration) is closely correlated to the good antifouling properties of the materials. This review will be widely interested by readers of Acta Biomaterialia and will impact many different research fields in chemistry, materials, engineering, and beyond. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Radiosensitization of DNA by Cisplatin Adducts Results from an Increase in the Rate Constant for the Reaction with Hydrated Electrons and Formation of PtI

PubMed Central

Behmand, B.; Marignier, J.-L.; Mostafavi, M.; Wagner, J. R.; Hunting, D. J.; Sanche, L.

2015-01-01

Pulse radiolysis measurements of the decay of hydrated electrons in solutions containing different concentrations of the oligonucleotide GTG with and without a cisplatin adduct show that the presence of a cisplatin moiety accelerates the reaction between hydrated electrons and the oligonucleotide. The rate constant of the reaction is found to be 2.23 × 1010 mol−1 L s−1, which indicates that it is diffusion controlled. In addition, we show for the first time the formation of a PtI intermediate as a result of the reaction of hydrated electrons with GTG-cisplatin. A putative reaction mechanism is proposed, which may form the basis of the radiosensitization of cancer cells in concomitant chemoradiation therapy with cisplatin. PMID:26098937

Raman studies of methane-ethane hydrate metastability.

PubMed

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

2009-03-05

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

Structural and spectroscopic features of proton hydrates in the crystalline state. Solid-state DFT study on HCl and triflic acid hydrates

NASA Astrophysics Data System (ADS)

Vener, M. V.; Chernyshov, I. Yu.; Rykounov, A. A.; Filarowski, A.

2018-01-01

Crystalline HCl and CF3SO3H hydrates serve as excellent model systems for protonated water and perfluorosulphonic acid membranes, respectively. They contain characteristic H3O+, H5О+2, H7О+3 and H3O+(H2O)3 (the Eigen cation) structures. The properties of these cations in the crystalline hydrates of strong monobasic acids are studied by solid-state density function theory (DFT). Simultaneous consideration of the HCl and CF3SO3H hydrates reveals the impact of the size of a counter ion and the crystalline environment on the structure and infrared active bands of the simplest proton hydrates. The H7O+3 structure is very sensitive to the size of the counter ion and symmetry of the local environment. This makes it virtually impossible to identify the specific features of H7O+3 in molecular crystals. The H3O+ ion can be treated as the Eigen-like cation in the crystalline state. Structural, infrared and electron-density features of H5О+2 and the Eigen cation are virtually insensitive to the size of the counter ion and the symmetry of the local crystalline environment. These cations can be considered as the simplest stable proton hydrates in the condensed phase. Finally, the influence of the Grimme correction on the structure and harmonic frequencies of the molecular crystals with short (strong) intermolecular O-H···O bonds is discussed.

NMR relaxation studies on the hydrate layer of intrinsically unstructured proteins.

PubMed

Bokor, Mónika; Csizmók, Veronika; Kovács, Dénes; Bánki, Péter; Friedrich, Peter; Tompa, Peter; Tompa, Kálmán

2005-03-01

Intrinsically unstructured/disordered proteins (IUPs) exist in a disordered and largely solvent-exposed, still functional, structural state under physiological conditions. As their function is often directly linked with structural disorder, understanding their structure-function relationship in detail is a great challenge to structural biology. In particular, their hydration and residual structure, both closely linked with their mechanism of action, require close attention. Here we demonstrate that the hydration of IUPs can be adequately approached by a technique so far unexplored with respect to IUPs, solid-state NMR relaxation measurements. This technique provides quantitative information on various features of hydrate water bound to these proteins. By freezing nonhydrate (bulk) water out, we have been able to measure free induction decays pertaining to protons of bound water from which the amount of hydrate water, its activation energy, and correlation times could be calculated. Thus, for three IUPs, the first inhibitory domain of calpastatin, microtubule-associated protein 2c, and plant dehydrin early responsive to dehydration 10, we demonstrate that they bind a significantly larger amount of water than globular proteins, whereas their suboptimal hydration and relaxation parameters are correlated with their differing modes of function. The theoretical treatment and experimental approach presented in this article may have general utility in characterizing proteins that belong to this novel structural class.

The influence of porosity and structural parameters on different kinds of gas hydrate dissociation

PubMed Central

Misyura, S. Y.

2016-01-01

Methane hydrate dissociation at negative temperatures was studied experimentally for different artificial and natural samples, differing by macro- and micro-structural parameters. Four characteristic dissociation types are discussed in the paper. The internal kinetics of artificial granule gas hydrates and clathrate hydrates in coal is dependent on the porosity, defectiveness and gas filtration rate. The density of pores distribution in the crust of formed ice decreases by the several orders of magnitude and this change significantly the rate of decay. Existing models for describing dissociation at negative temperatures do not take into account the structural parameters of samples. The dissociation is regulated by internal physical processes that must be considered in the simulation. Non-isothermal dissociation with constant external heat flux was simulated numerically. The dissociation is simulated with consideration of heat and mass transfer, kinetics of phase transformation and gas filtering through a porous medium of granules for the negative temperatures. It is shown that the gas hydrate dissociation in the presence of mainly microporous structures is fundamentally different from the disintegration of gas hydrates containing meso and macropores. PMID:27445113

Crystal structures of hydrates of simple inorganic salts. III. Water-rich aluminium halide hydrates: AlCl3 · 15H2O, AlBr3 · 15H2O, AlI3 · 15H2O, AlI3 · 17H2O and AlBr3 · 9H2O.

PubMed

Schmidt, Horst; Hennings, Erik; Voigt, Wolfgang

2014-09-01

Water-rich aluminium halide hydrate structures are not known in the literature. The highest known water content per Al atom is nine for the perchlorate and fluoride. The nonahydrate of aluminium bromide, stable pentadecahydrates of aluminium chloride, bromide and iodide, and a metastable heptadecahydrate of the iodide have now been crystallized from low-temperature solutions. The structures of these hydrates were determined and are discussed in terms of the development of cation hydration spheres. The pentadecahydrate of the chloride and bromide are isostructural. In AlI(3) · 15H2O, half of the Al(3+) cations are surrounded by two complete hydration spheres, with six H2O in the primary and 12 in the secondary. For the heptadecahydrate of aluminium iodide, this hydration was found for every Al(3+).

CO2 hydrate: Synthesis, composition, structure, dissociation behavior, and a comparison to structure I CH4 hydrate

USGS Publications Warehouse

Circone, S.; Stern, L.A.; Kirby, S.H.; Durham, W.B.; Chakoumakos, B.C.; Rawn, C.J.; Rondinone, A.J.; Ishii, Y.

2003-01-01

Structure I (sI) carbon dioxide (CO2) hydrate exhibits markedly different dissociation behavior from sI methane (CH4) hydrate in experiments in which equilibrated samples at 0.1 MPa are heated isobarically at 13 K/h from 210 K through the H2O melting point (273.15 K). The CO2 hydrate samples release only about 3% of their gas content up to temperatures of 240 K, which is 22 K above the hydrate phase boundary. Up to 20% is released by 270 K, and the remaining CO2 is released at 271.0 plusmn; 0.5 K, where the sample temperature is buffered until hydrate dissociation ceases. This reproducible buffering temperature for the dissociation reaction CO2??nH2O = CO2(g) + nH2O(1 to s) is measurably distinct from the pure H2O melting point at 273.15 K, which is reached as gas evolution ceases. In contrast, when si CH4 hydrate is heated at the same rate at 0.1 MPa, >95% of the gas is released within 25 K of the equilibrium temperature (193 K at 0.1 MPa). In conjunction with the dissociation study, a method for efficient and reproducible synthesis of pure polycrystalline CO2 hydrate with suitable characteristics for material properties testing was developed, and the material was characterized. CO2 hydrate was synthesized from CO2 liquid and H2O solid and liquid reactants at pressures between 5 and 25 MPa and temperatures between 250 and 281 K. Scanning electron microscopy (SEM) examination indicates that the samples consist of dense crystalline hydrate and 50-300 ??m diameter pores that are lined with euhedral cubic hydrate crystals. Deuterated hydrate samples made by this same procedure were analyzed by neutron diffraction at temperatures between 4 and 215 K; results confirm that complete conversion of water to hydrate has occurred and that the measured unit cell parameter and thermal expansion are consistent with previously reported values. On the basis of measured weight gain after synthesis and gas yields from the dissociation experiments, approximately all cages in the hydrate structure are filled such that n ??? 5.75.

Anti-NGF Local Therapy for Autonomic Dysreflexia in Spinal Cord Injury

DTIC Science & Technology

2012-10-01

propyl ]-N,N,N trimethylammonium methylsulfate) were made by thin film hydration method and hydrated with nuclease free water with the final lipid...isolation method (Qiagen, Valencia CA). Synthesis of cDNA was performed as described previously (Takimoto et al., 2002). These primers were designed to...probe synthesis . Primers used for the cloning were as follows: Kv4.1 5’-cacagacgagctaactttcag-3′ and 5′-tcacagggaagagatcttgac-3′ (GenBank ID: 116695

In Situ Raman Detection of Gas Hydrates Exposed on the Seafloor of the South China Sea

NASA Astrophysics Data System (ADS)

Zhang, Xin; Du, Zengfeng; Luan, Zhendong; Wang, Xiujuan; Xi, Shichuan; Wang, Bing; Li, Lianfu; Lian, Chao; Yan, Jun

2017-10-01

Gas hydrates are usually buried in sediments. Here we report the first discovery of gas hydrates exposed on the seafloor of the South China Sea. The in situ chemical compositions and cage structures of these hydrates were measured at the depth of 1,130 m below sea level using a Raman insertion probe (RiP-Gh) that was carried and controlled by a remotely operated vehicle (ROV) Faxian. This in situ analytical technique can avoid the physical and chemical changes associated with the transport of samples from the deep sea to the surface. Natural gas hydrate samples were analyzed at two sites. The in situ spectra suggest that the newly formed hydrate was Structure I but contains a small amount of C3H8 and H2S. Pure gas spectra of CH4, C3H8, and H2S were also observed at the SCS-SGH02 site. These data represent the first in situ proof that free gas can be trapped within the hydrate fabric during rapid hydrate formation. We provide the first in situ confirmation of the hydrate growth model for the early stages of formation of crystalline hydrates in a methane-rich seafloor environment. Our work demonstrates that natural hydrate deposits, particularly those in the early stages of formation, are not monolithic single structures but instead exhibit significant small-scale heterogeneities due to inclusions of free gas and the surrounding seawater, there inclusions also serve as indicators of the likely hydrate formation mechanism. These data also reinforce the importance of correlating visual and in situ measurements when characterizing a sampling site.

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.

The binding of the primary water of hydration to nucleosides, CsDNA and potassium hyaluronate

NASA Astrophysics Data System (ADS)

Lukan, A. M.; Cavanaugh, D.; Whitson, K. B.; Marlowe, R. L.; Lee, S. A.; Anthony, L.; Rupprecht, A.; Mohan, V.

1998-03-01

Differential scanning calorimetry (DSC) has been used to study the eight nucleosides, CsDNA and KHA hydrated at 59% relative humidity. Thermograms were measured between 25 and 180 ^oC for scan rates of 1, 2, 5, 10 and 20 K/min. A broad endothermic transition (due to the desorption of the water) near 80 ^oC was observed for all runs. The average enthalpy of desorption per water molecule was evaluated from the area under the peak. A Kissinger analysis of these data yielded the net activation energy for desorption. Both parameters were very similar for the two biopolymers. Rayleigh scattering of Mossbauer radiation (RSMR) data(G. Albanese et al. ) Hyperfine Int. 95, 97 (1995) were analyzed via a simple harmonic oscillator model to evaluate the effective force constant of the water bound to the biopolymer. This analysis suggests that the effective force constant of water bound to HA is much larger (about 5 times) than for water bound to DNA.

Binding of the water of primary hydration to the sodium and cesium salts of deoxyribonucleic acid and potassium hyaluronate

NASA Astrophysics Data System (ADS)

Whitson, K. B.; Lukan, A. M.; Marlowe, R. L.; Lee, S. A.; Anthony, L.; Rupprecht, A.

1998-08-01

Differential scanning calorimetry (DSC) has been used to evaluate the average enthalpy of desorption of the water of primary hydration bound to wet-spun films of potassium hyaluronate (KHA) and CsDNA. The enthalpies were measured to be 0.24+/-0.08 eV/H2O molecule for KHA and 0.32+/-0.10 eV/H2O molecule for CsDNA. A Kissinger analysis was used to extract the net activation energy (0.61+/-0.04 eV) for the desorption of this water from KHA by analyzing DSC data acquired at different heating rates. The average effective force constants at 295 K of this water bound to KHA (63+/-3 μdyn/Å) and NaDNA (17+/-4 μdyn/Å) are determined from Rayleigh scattering of Mossbauer radiation data [G. Albanese, A. Deriu, F. Cavatorta, and A. Rupprecht, Hyperfine Interact. 95, 97 (1995)] via a harmonic approximation.

Synergistic hydrate inhibition of monoethylene glycol with poly(vinylcaprolactam) in thermodynamically underinhibited system.

PubMed

Kim, Jakyung; Shin, Kyuchul; Seo, Yutaek; Cho, Seong Jun; Lee, Ju Dong

2014-07-31

This study investigates the hydrate inhibition performance of monoethylene glycol (MEG) with poly(vinylcaprolactam) (PVCap) for retarding the hydrate onset as well as preventing the agglomeration of hydrate particles. A high-pressure autoclave was used to determine the hydrate onset time, subcooling temperature, hydrate fraction in the liquid phase, and torque changes during hydrate formation in pure water, 0.2 wt % PVCap solution, and 20 and 30 wt % MEG solutions. In comparison to water with no inhibitors, the addition of PVCap delays the hydrate onset time but cannot reduce the hydrate fraction, leading to a sharp increase in torque. The 20 and 30 wt % MEG solutions also delay the hydrate onset time slightly and reduce the hydrate fraction to 0.15. The addition of 0.2 wt % PVCap to the 20 wt % MEG solution, however, delays the hydrate onset time substantially, and the hydrate fraction was less than 0.19. The torque changes were negligible during the hydrate formation, suggesting the homogeneous dispersion of hydrate particles in the liquid phase. The well-dispersed hydrate particles do not agglomerate or deposit under stirring. Moreover, when 0.2 wt % PVCap was added to the 30 wt % MEG solution, no hydrate formation was observed for at least 24 h. These results suggest that mixing of MEG with a small amount of PVCap in underinhibited conditions will induce the synergistic inhibition of hydrate by delaying the hydrate onset time as well as preventing the agglomeration and deposition of hydrate particles. Decreasing the hydrate fraction in the liquid phase might be the reason for negligible torque changes during the hydrate formation in the 0.2 wt % PVCap and 20 wt % MEG solution. Simple structure II was confirmed by in situ Raman spectroscopy for the synergistic inhibition system, while coexisting structures I and II are observed in 0.2 wt % PVCap solution.

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.

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.

Anhydrobiosis-Associated Nuclear DNA Damage and Repair in the Sleeping Chironomid: Linkage with Radioresistance

PubMed Central

Vanyagina, Veronica; Malutina, Ludmila; Cornette, Richard; Sakashita, Tetsuya; Hamada, Nobuyuki; Kikawada, Takahiro; Kobayashi, Yasuhiko; Okuda, Takashi

2010-01-01

Anhydrobiotic chironomid larvae can withstand prolonged complete desiccation as well as other external stresses including ionizing radiation. To understand the cross-tolerance mechanism, we have analyzed the structural changes in the nuclear DNA using transmission electron microscopy and DNA comet assays in relation to anhydrobiosis and radiation. We found that dehydration causes alterations in chromatin structure and a severe fragmentation of nuclear DNA in the cells of the larvae despite successful anhydrobiosis. Furthermore, while the larvae had restored physiological activity within an hour following rehydration, nuclear DNA restoration typically took 72 to 96 h. The DNA fragmentation level and the recovery of DNA integrity in the rehydrated larvae after anhydrobiosis were similar to those of hydrated larvae irradiated with 70 Gy of high-linear energy transfer (LET) ions (4He). In contrast, low-LET radiation (gamma-rays) of the same dose caused less initial damage to the larvae, and DNA was completely repaired within within 24 h. The expression of genes encoding the DNA repair enzymes occurred upon entering anhydrobiosis and exposure to high- and low-LET radiations, indicative of DNA damage that includes double-strand breaks and their subsequent repair. The expression of antioxidant enzymes-coding genes was also elevated in the anhydrobiotic and the gamma-ray-irradiated larvae that probably functions to reduce the negative effect of reactive oxygen species upon exposure to these stresses. Indeed the mature antioxidant proteins accumulated in the dry larvae and the total activity of antioxidants increased by a 3–4 fold in association with anhydrobiosis. We conclude that one of the factors explaining the relationship between radioresistance and the ability to undergo anhydrobiosis in the sleeping chironomid could be an adaptation to desiccation-inflicted nuclear DNA damage. There were also similarities in the molecular response of the larvae to damage caused by desiccation and ionizing radiation. PMID:21103355

Raman spectroscopic investigations on natural samples from the Integrated Ocean Drilling Program (IODP) Expedition 311: indications for heterogeneous compositions in hydrate crystals.

PubMed

Schicks, J M; Ziemann, M A; Lu, H; Ripmeester, J A

2010-12-01

Natural gas hydrates usually are found in the form of structure I, encasing predominantly methane in the hydrate lattices as guest molecules, sometimes also minor amount of higher hydrocarbons, CO2 or H2S. Raman spectroscopy is an approved tool to determine the composition of the hydrate phase. Thus, in this study Raman spectroscopic analyses have been applied to hydrate samples obtained from Integrated Ocean Drilling Program (IODP) Expedition 311 in two different approaches: studying the samples randomly taken from the hydrate core, and--as a new application--mapping small areas on the surface of clear hydrate crystals. The results obtained imply that the gas composition of hydrate, in terms of relative concentrations of CH4 and H2S, is not homogeneous over a core or even within a crystal. The mapping method yielded results with very high lateral resolution, indicating the coexistence of different phases with the same structure but different compositions within a hydrate crystal. Copyright © 2010 Elsevier B.V. All rights reserved.

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.

DNA oligonucleotide duplexes containing intramolecular platinated cross-links: energetics, hydration, sequence, and ionic effects.

PubMed

Kankia, Besik I; Soto, Ana Maria; Burns, Nicole; Shikiya, Ronald; Tung, Chang-Shung; Marky, Luis A

2002-11-05

The anticancer activity of cisplatin arises from its ability to bind covalently to DNA, forming primarily intrastrand cross-links to adjacent purine residues; the most common adducts involve d(GpG) (65%) and d(ApG) (25%) intrastrand cross-links. The incorporation of these platinum adducts in a B-DNA helix induces local distortions, causing bending and unwinding of the DNA. In this work, we used temperature-dependent UV spectroscopy to investigate the unfolding thermodynamics, and associated ionic effects, of two sets of DNA decamer duplexes containing either cis-[Pt(NH(3))(2)[d(GpG

Morphological and transcriptional response of an anhydrobiotic insect to ionizing radiation and desiccation: steps forward in understanding molecular background of extreme radioresistance in higher eukaryotes

NASA Astrophysics Data System (ADS)

Gusev, Oleg; Novikova, Nataliya; Sychev, Vladimir; Okuda, Takashi; Kikawada, Takahiro; Sakashita, Tetsuya; Mukae, Kyosuke

2012-07-01

Life in extreme or drastically changing environments in many cases leads to evolutionary evolvement of mechanisms of cross-resistance to different abiotic stresses, often never actually faced by the organism in its natural habitat. Larvae of the sleeping chironomidPolypedilum vanderplanki (Diptera) are able to resist complete desiccation and in the dry form survive under excess of various abiotic stresses, including exposure to space environment. One of the most intriguing features of the anhydrobiotic larvae is resistance to extremely high doses of different types of ionizing radiation. To understand the cross-tolerance mechanism, we have analyzed the structural changes in the nuclear DNA using transmission electron microscopy and DNA comet assays in relation to anhydrobiosis and radiation. We find that dehydration causes alterations in chromatin structure and a severe fragmentation of nuclear DNA in the cells of the larvae despite successful anhydrobiosis. The DNA fragmentation level and the recovery of DNA integrity in the rehydrated after anhydrobiosis larvae were similar to those of hydrated larvae irradiated with 70 Gy of high-linear energy transfer (LET) ions (4He+). In comparison, low-LET radiation (gamma rays) of the same dose causes less initial damage to the larvae, and recovery of DNA repair is complete within 24 h. Genome-wide analysis of mRNA expression in the larvae revealed that a large group of genes (including antioxidants, anhydrobiosis-specific biomolecules and protein-reparation enzymes) showed a similar patterns of activity in response to both desiccation and ionizing radiation. We conclude that t one of the factors explaining the relationship between the resistance to ionizing radiation and the ability to undergo anhydrobiosis in the sleeping chironomid would be an adaptation to desiccation-inflicted proteins and nuclear DNA damage.

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

NASA Astrophysics Data System (ADS)

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

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

Neutron Nucleic Acid Crystallography.

PubMed

Chatake, Toshiyuki

2016-01-01

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

Hydration water and bulk water in proteins have distinct properties in radial distributions calculated from 105 atomic resolution crystal structures.

PubMed

Chen, Xianfeng; Weber, Irene; Harrison, Robert W

2008-09-25

Water plays a critical role in the structure and function of proteins, although the experimental properties of water around protein structures are not well understood. The water can be classified by the separation from the protein surface into bulk water and hydration water. Hydration water interacts closely with the protein and contributes to protein folding, stability, and dynamics, as well as interacting with the bulk water. Water potential functions are often parametrized to fit bulk water properties because of the limited experimental data for hydration water. Therefore, the structural and energetic properties of the hydration water were assessed for 105 atomic resolution (

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.

Data for exploring the effect of parameters on decomposition of gas hydrate structure I.

PubMed

Kheshty, Mohammad Fani; Varaminian, Farshad; Farhadian, Nafiseh

2018-06-01

This article describes initial and final configurations of methane hydrate structure I as PDB file at various cage occupancies and different temperatures. Cage occupancies from full occupancy to 75% at three temperatures of 290 K, 300 K and 310 K are presented. Dissociation behavior of gas hydrate structure I at the temperature of 300 K is shown in changing the potential energy and radial distribution function.

Crystal structure of zwitterionic bisimidazolium sulfonates

NASA Astrophysics Data System (ADS)

Kohmoto, Shigeo; Okuyama, Shinpei; Yokota, Nobuyuki; Takahashi, Masahiro; Kishikawa, Keiki; Masu, Hyuma; Azumaya, Isao

2012-05-01

Crystal structures of three zwitterionic bisimidazolium salts 1-3 in which imidazolium sulfonate moieties were connected with aromatic linkers, p-xylylene, 4,4'-dimethylenebiphenyl, and phenylene, respectively, were examined. The latter two were obtained as hydrates. An S-shaped molecular structure in which the sulfonate moiety was placed on the imidazolium ring was observed for 1. A helical array of hydrated water molecules was obtained for 2 while a linear array of hydrated water molecules was observed for 3.

Geologic controls on gas hydrate occurrence in the Mount Elbert prospect, Alaska North Slope

USGS Publications Warehouse

Boswell, R.; Rose, K.; Collett, T.S.; Lee, M.; Winters, W.; Lewis, K.A.; Agena, W.

2011-01-01

Data acquired at the BPXA-DOE-USGS Mount Elbert Gas Hydrate Stratigraphic Test Well, drilled in the Milne Point area of the Alaska North Slope in February, 2007, indicates two zones of high gas hydrate saturation within the Eocene Sagavanirktok Formation. Gas hydrate is observed in two separate sand reservoirs (the D and C units), in the stratigraphically highest portions of those sands, and is not detected in non-sand lithologies. In the younger D unit, gas hydrate appears to fill much of the available reservoir space at the top of the unit. The degree of vertical fill with the D unit is closely related to the unit reservoir quality. A thick, low-permeability clay-dominated unit serves as an upper seal, whereas a subtle transition to more clay-rich, and interbedded sand, silt, and clay units is associated with the base of gas hydrate occurrence. In the underlying C unit, the reservoir is similarly capped by a clay-dominated section, with gas hydrate filling the relatively lower-quality sands at the top of the unit leaving an underlying thick section of high-reservoir quality sands devoid of gas hydrate. Evaluation of well log, core, and seismic data indicate that the gas hydrate occurs within complex combination stratigraphic/structural traps. Structural trapping is provided by a four-way fold closure augmented by a large western bounding fault. Lithologic variation is also a likely strong control on lateral extent of the reservoirs, particularly in the D unit accumulation, where gas hydrate appears to extend beyond the limits of the structural closure. Porous and permeable zones within the C unit sand are only partially charged due most likely to limited structural trapping in the reservoir lithofacies during the period of primary charging. The occurrence of the gas hydrate within the sands in the upper portions of both the C and D units and along the crest of the fold is consistent with an interpretation that these deposits are converted free gas accumulations formed prior to the imposition of gas hydrate stability conditions. ?? 2009.

Absorbing a Little Water: The Structural, Thermodynamic, and Kinetic Relationship between Pyrogallol and Its Tetarto-Hydrate

PubMed Central

2013-01-01

The anhydrate and the stoichiometric tetarto-hydrate of pyrogallol (0.25 mol water per mol pyrogallol) are both storage stable at ambient conditions, provided that they are phase pure, with the system being at equilibrium at aw (water activity) = 0.15 at 25 °C. Structures have been derived from single crystal and powder X-ray diffraction data for the anhydrate and hydrate, respectively. It is notable that the tetarto-hydrate forms a tetragonal structure with water in channels, a framework that although stabilized by water, is found as a higher energy structure on a computationally generated crystal energy landscape, which has the anhydrate crystal structure as the most stable form. Thus, a combination of slurry experiments, X-ray diffraction, spectroscopy, moisture (de)sorption, and thermo-analytical methods with the computationally generated crystal energy landscape and lattice energy calculations provides a consistent picture of the finely balanced hydration behavior of pyrogallol. In addition, two monotropically related dimethyl sulfoxide monosolvates were found in the accompanying solid form screen. PMID:24027438

Absorbing a Little Water: The Structural, Thermodynamic, and Kinetic Relationship between Pyrogallol and Its Tetarto-Hydrate.

PubMed

Braun, Doris E; Bhardwaj, Rajni M; Arlin, Jean-Baptiste; Florence, Alastair J; Kahlenberg, Volker; Griesser, Ulrich J; Tocher, Derek A; Price, Sarah L

2013-09-04

The anhydrate and the stoichiometric tetarto-hydrate of pyrogallol (0.25 mol water per mol pyrogallol) are both storage stable at ambient conditions, provided that they are phase pure, with the system being at equilibrium at a w (water activity) = 0.15 at 25 °C. Structures have been derived from single crystal and powder X-ray diffraction data for the anhydrate and hydrate, respectively. It is notable that the tetarto-hydrate forms a tetragonal structure with water in channels, a framework that although stabilized by water, is found as a higher energy structure on a computationally generated crystal energy landscape, which has the anhydrate crystal structure as the most stable form. Thus, a combination of slurry experiments, X-ray diffraction, spectroscopy, moisture (de)sorption, and thermo-analytical methods with the computationally generated crystal energy landscape and lattice energy calculations provides a consistent picture of the finely balanced hydration behavior of pyrogallol. In addition, two monotropically related dimethyl sulfoxide monosolvates were found in the accompanying solid form screen.

Pore Effect on the Occurrence and Formation of Gas Hydrate in Permafrost of Qilian Mountain, Qinghai-Tibet Plateau, China

NASA Astrophysics Data System (ADS)

Gao, H.; Lu, H.; Lu, Z.

2014-12-01

Gas hydrates were found in the permafrost of Qilian Mountain, Qinghai- Tibet Plateau, China in 2008. It has been found that gas hydrates occur in Jurassic sedimentary rocks, and the hydrated gases are mainly thermogenic. Different from the gas hydrates existing in loose sands in Mallik, Mackenzie Delta, Canada and North Slope, Alaska, USA, the gas hydrates in Qilian Mountain occurred in hard rocks. For understanding the occurrence and formation mechanism of gas hydrate in hard rcok, extensive experimental investigations have been conducted to study the pore features and hydrate formation in the rocks recovered from the hydrate layers in Qilian Mountain. The structures of sedimentary rock were observed by high-resolution X-ray CT, and pore size distribution of a rock specimen was measured with the mercury-injection method. Methane hydrate was synthesized in water-saturated rocks, and the saturations of hydrate in sedimentary rocks of various types were estimated from the amount of gas released from certain volume of rock. X-ray CT observation revealed that fractures were developed in the rocks associated with faults, while those away from faults were generally with massive structure. The mercury-injection analysis of pore features found that the porosities of the hydrate-existing rocks were generally less than 3%, and the pore sizes were generally smaller than 100 nm. The synthesizing experiments found that the saturation of methane hydrate were generally lower than 6% of pore space in rocks, but up to 16% when fractures developed. The low hydrate saturation in Qilian sedimentary rocks has been found mainly due to the small pore size of rock. The low hydrate saturation in the rocks might be the reason for the failure of regional seismic and logging detections of gas hydrates in Qilian Mountain.

An effective medium inversion algorithm for gas hydrate quantification and its application to laboratory and borehole measurements of gas hydrate-bearing sediments

NASA Astrophysics Data System (ADS)

Chand, Shyam; Minshull, Tim A.; Priest, Jeff A.; Best, Angus I.; Clayton, Christopher R. I.; Waite, William F.

2006-08-01

The presence of gas hydrate in marine sediments alters their physical properties. In some circumstances, gas hydrate may cement sediment grains together and dramatically increase the seismic P- and S-wave velocities of the composite medium. Hydrate may also form a load-bearing structure within the sediment microstructure, but with different seismic wave attenuation characteristics, changing the attenuation behaviour of the composite. Here we introduce an inversion algorithm based on effective medium modelling to infer hydrate saturations from velocity and attenuation measurements on hydrate-bearing sediments. The velocity increase is modelled as extra binding developed by gas hydrate that strengthens the sediment microstructure. The attenuation increase is modelled through a difference in fluid flow properties caused by different permeabilities in the sediment and hydrate microstructures. We relate velocity and attenuation increases in hydrate-bearing sediments to their hydrate content, using an effective medium inversion algorithm based on the self-consistent approximation (SCA), differential effective medium (DEM) theory, and Biot and squirt flow mechanisms of fluid flow. The inversion algorithm is able to convert observations in compressional and shear wave velocities and attenuations to hydrate saturation in the sediment pore space. We applied our algorithm to a data set from the Mallik 2L-38 well, Mackenzie delta, Canada, and to data from laboratory measurements on gas-rich and water-saturated sand samples. Predictions using our algorithm match the borehole data and water-saturated laboratory data if the proportion of hydrate contributing to the load-bearing structure increases with hydrate saturation. The predictions match the gas-rich laboratory data if that proportion decreases with hydrate saturation. We attribute this difference to differences in hydrate formation mechanisms between the two environments.

An effective medium inversion algorithm for gas hydrate quantification and its application to laboratory and borehole measurements of gas hydrate-bearing sediments

USGS Publications Warehouse

Chand, S.; Minshull, T.A.; Priest, J.A.; Best, A.I.; Clayton, C.R.I.; Waite, W.F.

2006-01-01

The presence of gas hydrate in marine sediments alters their physical properties. In some circumstances, gas hydrate may cement sediment grains together and dramatically increase the seismic P- and S-wave velocities of the composite medium. Hydrate may also form a load-bearing structure within the sediment microstructure, but with different seismic wave attenuation characteristics, changing the attenuation behaviour of the composite. Here we introduce an inversion algorithm based on effective medium modelling to infer hydrate saturations from velocity and attenuation measurements on hydrate-bearing sediments. The velocity increase is modelled as extra binding developed by gas hydrate that strengthens the sediment microstructure. The attenuation increase is modelled through a difference in fluid flow properties caused by different permeabilities in the sediment and hydrate microstructures. We relate velocity and attenuation increases in hydrate-bearing sediments to their hydrate content, using an effective medium inversion algorithm based on the self-consistent approximation (SCA), differential effective medium (DEM) theory, and Biot and squirt flow mechanisms of fluid flow. The inversion algorithm is able to convert observations in compressional and shear wave velocities and attenuations to hydrate saturation in the sediment pore space. We applied our algorithm to a data set from the Mallik 2L–38 well, Mackenzie delta, Canada, and to data from laboratory measurements on gas-rich and water-saturated sand samples. Predictions using our algorithm match the borehole data and water-saturated laboratory data if the proportion of hydrate contributing to the load-bearing structure increases with hydrate saturation. The predictions match the gas-rich laboratory data if that proportion decreases with hydrate saturation. We attribute this difference to differences in hydrate formation mechanisms between the two environments.

Kinetics of methane-ethane gas replacement in clathrate-hydrates studied by time-resolved neutron diffraction and Raman spectroscopy.

PubMed

Murshed, M Mangir; Schmidt, Burkhard C; Kuhs, Werner F

2010-01-14

The kinetics of CH(4)-C(2)H(6) replacement in gas hydrates has been studied by in situ neutron diffraction and Raman spectroscopy. Deuterated ethane structure type I (C(2)H(6) sI) hydrates were transformed in a closed volume into methane-ethane mixed structure type II (CH(4)-C(2)H(6) sII) hydrates at 5 MPa and various temperatures in the vicinity of 0 degrees C while followed by time-resolved neutron powder diffraction on D20 at ILL, Grenoble. The role of available surface area of the sI starting material on the formation kinetics of sII hydrates was studied. Ex situ Raman spectroscopic investigations were carried out to crosscheck the gas composition and the distribution of the gas species over the cages as a function of structure type and compared to the in situ neutron results. Raman micromapping on single hydrate grains showed compositional and structural gradients between the surface and core of the transformed hydrates. Moreover, the observed methane-ethane ratio is very far from the one expected for a formation from a constantly equilibrated gas phase. The results also prove that gas replacement in CH(4)-C(2)H(6) hydrates is a regrowth process involving the nucleation of new crystallites commencing at the surface of the parent C(2)H(6) sI hydrate with a progressively shrinking core of unreacted material. The time-resolved neutron diffraction results clearly indicate an increasing diffusion limitation of the exchange process. This diffusion limitation leads to a progressive slowing down of the exchange reaction and is likely to be responsible for the incomplete exchange of the gases.

Self-preservation and structural transition of gas hydrates during dissociation below the ice point: an in situ study using Raman spectroscopy

NASA Astrophysics Data System (ADS)

Zhong, Jin-Rong; Zeng, Xin-Yang; Zhou, Feng-He; Ran, Qi-Dong; Sun, Chang-Yu; Zhong, Rui-Qin; Yang, Lan-Ying; Chen, Guang-Jin; Koh, Carolyn A.

2016-12-01

The hydrate structure type and dissociation behavior for pure methane and methane-ethane hydrates at temperatures below the ice point and atmospheric pressure were investigated using in situ Raman spectroscopic analysis. The self-preservation effect of sI methane hydrate is significant at lower temperatures (268.15 to 270.15 K), as determined by the stable C-H region Raman peaks and AL/AS value (Ratio of total peak area corresponding to occupancies of guest molecules in large cavities to small cavities) being around 3.0. However, it was reduced at higher temperatures (271.15 K and 272.15 K), as shown from the dramatic change in Raman spectra and fluctuations in AL/AS values. The self-preservation effect for methane-ethane double hydrate is observed at temperatures lower than 271.15 K. The structure transition from sI to sII occurred during the methane-ethane hydrate decomposition process, which was clearly identified by the shift in peak positions and the change in relative peak intensities at temperatures from 269.15 K to 271.15 K. Further investigation shows that the selectivity for self-preservation of methane over ethane leads to the structure transition; this kind of selectivity increases with decreasing temperature. This work provides new insight into the kinetic behavior of hydrate dissociation below the ice point.

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

PubMed

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

2010-01-18

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

Insights into Hydrate Formation and Stability of Morphinanes from a Combination of Experimental and Computational Approaches

PubMed Central

2014-01-01

Morphine, codeine, and ethylmorphine are important drug compounds whose free bases and hydrochloride salts form stable hydrates. These compounds were used to systematically investigate the influence of the type of functional groups, the role of water molecules, and the Cl– counterion on molecular aggregation and solid state properties. Five new crystal structures have been determined. Additionally, structure models for anhydrous ethylmorphine and morphine hydrochloride dihydrate, two phases existing only in a very limited humidity range, are proposed on the basis of computational dehydration modeling. These match the experimental powder X-ray diffraction patterns and the structural information derived from infrared spectroscopy. All 12 structurally characterized morphinane forms (including structures from the Cambridge Structural Database) crystallize in the orthorhombic space group P212121. Hydrate formation results in higher dimensional hydrogen bond networks. The salt structures of the different compounds exhibit only little structural variation. Anhydrous polymorphs were detected for all compounds except ethylmorphine (one anhydrate) and its hydrochloride salt (no anhydrate). Morphine HCl forms a trihydrate and dihydrate. Differential scanning and isothermal calorimetry were employed to estimate the heat of the hydrate ↔ anhydrate phase transformations, indicating an enthalpic stabilization of the respective hydrate of 5.7 to 25.6 kJ mol–1 relative to the most stable anhydrate. These results are in qualitative agreement with static 0 K lattice energy calculations for all systems except morphine hydrochloride, showing the need for further improvements in quantitative thermodynamic prediction of hydrates having water···water interactions. Thus, the combination of a variety of experimental techniques, covering temperature- and moisture-dependent stability, and computational modeling allowed us to generate sufficient kinetic, thermodynamic and structural information to understand the principles of hydrate formation of the model compounds. This approach also led to the detection of several new crystal forms of the investigated morphinanes. PMID:25036525

Methane hydrate formation in confined nanospace can surpass nature

DOE PAGES

Casco, Mirian E.; Silvestre-Albero, Joaquín; Ramírez-Cuesta, Anibal J.; ...

2015-03-02

Natural methane hydrates are believed to be the largest source of hydrocarbons on Earth. These structures are formed in specific locations such as deep-sea sediments and the permafrost based on demanding conditions of high pressure and low temperature. We report that, by taking advantage of the confinement effects on nanopore space, synthetic methane hydrates grow under mild conditions (3.5 MPa and 2 degrees C), with faster kinetics (within minutes) than nature, fully reversibly and with a nominal stoichiometry that mimics nature. Furthermore, the formation of the hydrate structures in nanospace and their similarity to natural hydrates is confirmed using inelasticmore » neutron scattering experiments and synchrotron X-ray powder diffraction. Our findings may be a step towards the application of a smart synthesis of methane hydrates in energy-demanding applications (for example, transportation).« less

Isomers and energy landscapes of micro-hydrated sulfite and chlorate clusters

NASA Astrophysics Data System (ADS)

Hey, John C.; Doyle, Emily J.; Chen, Yuting; Johnston, Roy L.

2018-03-01

We present putative global minima for the micro-hydrated sulfite SO32-(H2O)N and chlorate ClO32(H2O)N systems in the range 3≤N≤15 found using basin-hopping global structure optimization with an empirical potential. We present a structural analysis of the hydration of a large number of minimized structures for hydrated sulfite and chlorate clusters in the range 3≤N≤50. We show that sulfite is a significantly stronger net acceptor of hydrogen bonding within water clusters than chlorate, completely suppressing the appearance of hydroxyl groups pointing out from the cluster surface (dangling OH bonds), in low-energy clusters. We also present a qualitative analysis of a highly explored energy landscape in the region of the global minimum of the eight water hydrated sulfite and chlorate systems. This article is part of the theme issue `Modern theoretical chemistry'.

Isomers and energy landscapes of micro-hydrated sulfite and chlorate clusters.

PubMed

Hey, John C; Doyle, Emily J; Chen, Yuting; Johnston, Roy L

2018-03-13

We present putative global minima for the micro-hydrated sulfite SO 3 2- (H 2 O) N and chlorate ClO 3 - (H 2 O) N systems in the range 3≤ N ≤15 found using basin-hopping global structure optimization with an empirical potential. We present a structural analysis of the hydration of a large number of minimized structures for hydrated sulfite and chlorate clusters in the range 3≤ N ≤50. We show that sulfite is a significantly stronger net acceptor of hydrogen bonding within water clusters than chlorate, completely suppressing the appearance of hydroxyl groups pointing out from the cluster surface (dangling OH bonds), in low-energy clusters. We also present a qualitative analysis of a highly explored energy landscape in the region of the global minimum of the eight water hydrated sulfite and chlorate systems.This article is part of the theme issue 'Modern theoretical chemistry'. © 2018 The Authors.

Chromatin organization and radio resistance in the bacterium Gemmata obscuriglobus.

PubMed

Lieber, Arnon; Leis, Andrew; Kushmaro, Ariel; Minsky, Abraham; Medalia, Ohad

2009-03-01

The organization of chromatin has a major impact on cellular activities, such as gene expression. For bacteria, it was suggested that the spatial organization of the genetic material correlates with transcriptional levels, implying a specific architecture of the chromosome within the cytoplasm. Accordingly, recent technological advances have emphasized the organization of the genetic material within nucleoid structures. Gemmata obscuriglobus, a member of the phylum Planctomycetes, exhibits a distinctive nucleoid structure in which chromatin is encapsulated within a discrete membrane-bound compartment. Here, we show that this soil and freshwater bacterium tolerates high doses of UV and ionizing radiation. Cryoelectron tomography of frozen hydrated sections and electron microscopy of freeze-substituted cells have indicated a more highly ordered condensed-chromatin organization in actively dividing and stationary-phase G. obscuriglobus cells. These three-dimensional analyses revealed a complex network of double membranes that engulf the condensed DNA. Bioinformatics analysis has revealed the existence of a putative component involved in nonhomologous DNA end joining that presumably plays a role in maintaining chromatin integrity within the bacterium. Thus, our observations further support the notion that packed chromatin organization enhances radiation tolerance.

The structure of CO 2 hydrate between 0.7 and 1.0 GPa

DOE PAGES

Tulk, Chris A.; Machida, Shinichi; Klug, Dennis D.; ...

2014-11-05

A deuterated sample of CO 2 structure I (sI) clathrate hydrate (CO 2 ∙ 8.3 D 2O) has been formed and neutron diffraction experiments up to 1.0 GPa at 240 K were performed. The sI CO 2 hydrate transformed at 0.7 GPa into the high pressure phase that had been observed previously by Hirai, et al. (J. Phys. Chem. 133, 124511 (2010)) and O. Bollengier et al. (Geochim. Cosmochim. AC. 119, 322 (2013)), but which had not been structurally identified. The current neutron diffraction data were successfully fitted to a filled ice structure with CO 2 molecules filling the watermore » channels. This CO 2+water system has also been investigated using classical molecular dynamics and density functional ab initio methods to provide additional characterization of the high pressure structure. Both models indicate the water network adapts an MH-III ‘like’ filled ice structure with considerable disorder of the orientations of the CO 2molecule. Furthermore, the disorder appears be a direct result of the level of proton disorder in the water network. In contrast to the conclusions of Bollengier et al. our neutron diffraction data shows that the filled ice phase can be recovered to ambient pressure (0.1 MPa) at 96 K, and recrystallization to sI hydrate occurs upon subsequent heating to 150 K, possibly by first forming low density amorphous ice. Unlike other clathrate hydrate systems, which transform from the sI or sII structure to the hexagonal structure (sH) then to the filled ice structure, CO 2 hydrate transforms directly from the sI form to the filled ice structure.« less

The structure of CO 2 hydrate between 0.7 and 1.0 GPa

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

Tulk, C. A.; Machida, S.; Klug, D. D.

A deuterated sample of CO2 structure I (sI) clathrate hydrate (CO2·8.3 D2O) has been formed and neutron diffraction experiments up to 1.0 GPa at 240 K were performed. The sI CO2 hydrate transformed at 0.7 GPa into the high pressure phase that had been observed previously by Hirai et al. [J. Phys. Chem. 133, 124511 (2010)] and Bollengier et al. [Geochim. Cosmochim. Acta 119, 322 (2013)], but which had not been structurally identified. The current neutron diffraction data were successfully fitted to a filled ice structure with CO2 molecules filling the water channels. This CO2+water system has also been investigatedmore » using classical molecular dynamics and density functional ab initio methods to provide additional characterization of the high pressure structure. Both models indicate the water network adapts a MH-III “like” filled ice structure with considerable disorder of the orientations of the CO2 molecule. Furthermore, the disorder appears to be a direct result of the level of proton disorder in the water network. In contrast to the conclusions of Bollengier et al., our neutron diffraction data show that the filled ice phase can be recovered to ambient pressure (0.1 MPa) at 96 K, and recrystallization to sI hydrate occurs upon subsequent heating to 150 K, possibly by first forming low density amorphous ice. Unlike other clathrate hydrate systems, which transform from the sI or sII structure to the hexagonal structure (sH) then to the filled ice structure, CO2 hydrate transforms directly from the sI form to the filled ice structure.« less

The structure of CO{sub 2} hydrate between 0.7 and 1.0 GPa

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

Tulk, C. A.; Molaison, J. J.; Machida, S.

A deuterated sample of CO{sub 2} structure I (sI) clathrate hydrate (CO{sub 2}·8.3 D{sub 2}O) has been formed and neutron diffraction experiments up to 1.0 GPa at 240 K were performed. The sI CO{sub 2} hydrate transformed at 0.7 GPa into the high pressure phase that had been observed previously by Hirai et al. [J. Phys. Chem. 133, 124511 (2010)] and Bollengier et al. [Geochim. Cosmochim. Acta 119, 322 (2013)], but which had not been structurally identified. The current neutron diffraction data were successfully fitted to a filled ice structure with CO{sub 2} molecules filling the water channels. This CO{submore » 2}+water system has also been investigated using classical molecular dynamics and density functional ab initio methods to provide additional characterization of the high pressure structure. Both models indicate the water network adapts a MH-III “like” filled ice structure with considerable disorder of the orientations of the CO{sub 2} molecule. Furthermore, the disorder appears to be a direct result of the level of proton disorder in the water network. In contrast to the conclusions of Bollengier et al., our neutron diffraction data show that the filled ice phase can be recovered to ambient pressure (0.1 MPa) at 96 K, and recrystallization to sI hydrate occurs upon subsequent heating to 150 K, possibly by first forming low density amorphous ice. Unlike other clathrate hydrate systems, which transform from the sI or sII structure to the hexagonal structure (sH) then to the filled ice structure, CO{sub 2} hydrate transforms directly from the sI form to the filled ice structure.« less

The structure of CO 2 hydrate between 0.7 and 1.0 GPa

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

Tulk, Chris A.; Machida, Shinichi; Klug, Dennis D.

A deuterated sample of CO 2 structure I (sI) clathrate hydrate (CO 2 ∙ 8.3 D 2O) has been formed and neutron diffraction experiments up to 1.0 GPa at 240 K were performed. The sI CO 2 hydrate transformed at 0.7 GPa into the high pressure phase that had been observed previously by Hirai, et al. (J. Phys. Chem. 133, 124511 (2010)) and O. Bollengier et al. (Geochim. Cosmochim. AC. 119, 322 (2013)), but which had not been structurally identified. The current neutron diffraction data were successfully fitted to a filled ice structure with CO 2 molecules filling the watermore » channels. This CO 2+water system has also been investigated using classical molecular dynamics and density functional ab initio methods to provide additional characterization of the high pressure structure. Both models indicate the water network adapts an MH-III ‘like’ filled ice structure with considerable disorder of the orientations of the CO 2molecule. Furthermore, the disorder appears be a direct result of the level of proton disorder in the water network. In contrast to the conclusions of Bollengier et al. our neutron diffraction data shows that the filled ice phase can be recovered to ambient pressure (0.1 MPa) at 96 K, and recrystallization to sI hydrate occurs upon subsequent heating to 150 K, possibly by first forming low density amorphous ice. Unlike other clathrate hydrate systems, which transform from the sI or sII structure to the hexagonal structure (sH) then to the filled ice structure, CO 2 hydrate transforms directly from the sI form to the filled ice structure.« less

Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges.

PubMed

Lara, A; Riquelme, M; Vöhringer-Martinez, E

2018-05-11

Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases, the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account, and when the energy needed to polarize the electron density of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogs. Comparison of the two partitioning methods, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS), revealed some deficiencies in the Hirshfeld-I method related to the unstable isolated anionic nitrogen pro-atom used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Natural gas hydrates; vast resource, uncertain future

USGS Publications Warehouse

Collett, T.S.

2001-01-01

Gas hydrates are naturally occurring icelike solids in which water molecules trap gas molecules in a cagelike structure known as a clathrate. Although many gases form hydrates in nature, methane hydrate is by far the most common; methane is the most abundant natural gas. The volume of carbon contained in methane hydrates worldwide is estimated to be twice the amount contained in all fossil fuels on Earth, including coal.

Occurrence and structural characterization of gas hydrates associated with a cold vent field, offshore Vancouver Island

NASA Astrophysics Data System (ADS)

Lu, Hailong; Moudrakovski, Igor; Riedel, Michael; Spence, George; Dutrisac, Regent; Ripmeester, John; Wright, Fred; Dallimore, Scott

2005-10-01

Gas hydrate samples recovered from a cold vent field offshore Vancouver Island were studied in detail both by macroscopic observations and instrumental methods (powder X-ray diffraction method (PXRD), nuclear magnetic resonance (NMR), and Raman spectroscopy). It was found that gas hydrates were massive from 2.64 to 2.94 m below seafloor (mbsf), elongated, nodular and tabular from 4.60 to 4.81 mbsf, and vein-like from 5.48 to 5.68 mbsf, showing a trend of decreasing hydrate content with increasing depth. All samples were determined to be structure I hydrate from PXRD, NMR, and Raman spectroscopies. The hydration numbers were estimated to be 6.1 ± 0.2 on average as determined from the methane distribution over the cage sites from NMR and Raman analytical results. Estimates of conversion levels indicated that ˜78% of the water in the massive samples was hydrate, down to a low value of ˜0.4% for the pore hydrate samples. The results are compared with measurements on synthetic hydrates and samples recovered from below the permafrost on the Mallik site. Differences in methane content and lattice parameters for synthetic and natural samples are relatively minor. Additional work is needed to address the presence of minor gas components and the heterogeneity of natural hydrate samples.

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

Dehydration-induced amorphous phases of calcium carbonate.

PubMed

Saharay, Moumita; Yazaydin, A Ozgur; Kirkpatrick, R James

2013-03-28

Amorphous calcium carbonate (ACC) is a critical transient phase in the inorganic precipitation of CaCO3 and in biomineralization. The calcium carbonate crystallization pathway is thought to involve dehydration of more hydrated ACC to less hydrated ACC followed by the formation of anhydrous ACC. We present here computational studies of the transition of a hydrated ACC with a H2O/CaCO3 ratio of 1.0 to anhydrous ACC. During dehydration, ACC undergoes reorganization to a more ordered structure with a significant increase in density. The computed density of anhydrous ACC is similar to that of calcite, the stable crystalline phase. Compared to the crystalline CaCO3 phases, calcite, vaterite, and aragonite, the computed local structure of anhydrous ACC is most-similar to those of calcite and vaterite, but the overall structure is not well described by either. The strong hydrogen bond interaction between the carbonate ions and water molecules plays a crucial role in stabilizing the less hydrated ACC compositions compared to the more hydrated ones, leading to a progressively increasing hydration energy with decreasing water content.

Insights into the structure of mixed CO 2/CH 4 in gas hydrates

DOE PAGES

Everett, S. Michelle; Rawn, Claudia J.; Chakoumakos, Bryan C.; ...

2015-05-12

The exchange of carbon dioxide for methane in natural gas hydrates is an attractive approach to harvesting CH 4 for energy production while simultaneously sequestering CO 2. In addition to the energy and environmental implications, the solid solution of clathrate hydrate (CH 4) 1-x(CO 2) x·5.75H 2O provides a model system to study how the distinct bonding and shapes of CH 4 and CO 2 influence the structure and properties of the compound. In this paper, high-resolution neutron diffraction was used to examine mixed CO 2/CH 4 gas hydrates. CO 2-rich hydrates had smaller lattice parameters, which were attributed tomore » the higher affinity of the CO 2 molecule interacting with H 2O molecules that form the surrounding cages, and resulted in a reduction in the unit-cell volume. Experimental nuclear scattering densities illustrate how the cage occupants and energy landscape change with composition. Finally, these results provide important insights on the impact and mechanisms for the structure of mixed CH 4/CO 2 gas hydrate.« 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.

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

Spectral phasor analysis of LAURDAN fluorescence in live A549 lung cells to study the hydration and time evolution of intracellular lamellar body-like structures.

PubMed

Malacrida, Leonel; Astrada, Soledad; Briva, Arturo; Bollati-Fogolín, Mariela; Gratton, Enrico; Bagatolli, Luis A

2016-11-01

Using LAURDAN spectral imaging and spectral phasor analysis we concurrently studied the growth and hydration state of subcellular organelles (lamellar body-like, LB-like) from live A549 lung cancer cells at different post-confluence days. Our results reveal a time dependent two-step process governing the size and hydration of these intracellular LB-like structures. Specifically, a first step (days 1 to 7) is characterized by an increase in their size, followed by a second one (days 7 to 14) where the organelles display a decrease in their global hydration properties. Interestingly, our results also show that their hydration properties significantly differ from those observed in well-characterized artificial lamellar model membranes, challenging the notion that a pure lamellar membrane organization is present in these organelles at intracellular conditions. Finally, these LB-like structures show a significant increase in their hydration state upon secretion, suggesting a relevant role of entropy during this process. Copyright © 2016 Elsevier B.V. All rights reserved.

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

PubMed

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

1994-07-26

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

Microbial diversity in methane hydrate-bearing deep marine sediments core preserved in the original pressure.

NASA Astrophysics Data System (ADS)

Takahashi, Y.; Hata, T.; Nishida, H.

2017-12-01

In normal coring of deep marine sediments, the sampled cores are exposed to the pressure of the atmosphere, which results in dissociation of gas-hydrates and might change microbial diversity. In this study, we analyzed microbial composition in methane hydrate-bearing sediment core sampled and preserved by Hybrid-PCS (Pressure Coring System). We sliced core into three layers; (i) outside layer, which were most affected by drilling fluids, (ii) middle layer, and (iii) inner layer, which were expected to be most preserved as the original state. From each layer, we directly extracted DNA, and amplified V3-V4 region of 16S rRNA gene. We determined at least 5000 of nucleotide sequences of the partial 16S rDNA from each layer by Miseq (Illumina). In the all layers, facultative anaerobes, which can grow with or without oxygen because they can metabolize energy aerobically or anaerobically, were detected as majority. However, the genera which are often detected anaerobic environment is abundant in the inner layer compared to the outside layer, indicating that condition of drilling and preservation affect the microbial composition in the deep marine sediment core. This study was conducted as a part of the activity of the Research Consortium for Methane Hydrate Resources in Japan [MH21 consortium], and supported by JOGMEC (Japan Oil, Gas and Metals National Corporation). The sample was provided by AIST (National Institute of Advanced Industrial Science and Technology).

Vibrational Spectroscopy and Astrobiology

NASA Technical Reports Server (NTRS)

Chaban, Galina M.; Kwak, D. (Technical Monitor)

2001-01-01

Role of vibrational spectroscopy in solving problems related to astrobiology will be discussed. Vibrational (infrared) spectroscopy is a very sensitive tool for identifying molecules. Theoretical approach used in this work is based on direct computation of anharmonic vibrational frequencies and intensities from electronic structure codes. One of the applications of this computational technique is possible identification of biological building blocks (amino acids, small peptides, DNA bases) in the interstellar medium (ISM). Identifying small biological molecules in the ISM is very important from the point of view of origin of life. Hybrid (quantum mechanics/molecular mechanics) theoretical techniques will be discussed that may allow to obtain accurate vibrational spectra of biomolecular building blocks and to create a database of spectroscopic signatures that can assist observations of these molecules in space. Another application of the direct computational spectroscopy technique is to help to design and analyze experimental observations of ice surfaces of one of the Jupiter's moons, Europa, that possibly contains hydrated salts. The presence of hydrated salts on the surface can be an indication of a subsurface ocean and the possible existence of life forms inhabiting such an ocean.

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.

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

On Deterioration Mechanism of Concrete Exposed to Freeze-Thaw Cycles

NASA Astrophysics Data System (ADS)

Trofimov, B. Ya; Kramar, L. Ya; Schuldyakov, K. V.

2017-11-01

At present, concrete and reinforced concrete are gaining ground in all sectors of construction including construction in the extreme north, on shelves, etc. Under harsh service conditions, the durability of reinforced concrete structures is related to concrete frost resistance. Frost resistance tests are accompanied by the accumulation of residual dilation deformations affected by temperature-humidity stresses, ice formation and other factors. Porosity is an integral part of the concrete structure which is formed as a result of cement hydration. The prevailing hypothesis of a deterioration mechanism of concrete exposed to cyclic freezing, i.e. the hypothesis of hydraulic pressure of unfrozen water in microcapillaries, does not take into account a number of phenomena that affect concrete resistance to frost aggression. The main structural element of concrete, i.e. hardened cement paste, contains various hydration products, such as crystalline, semicrystalline and gel-like products, pores and non-hydrated residues of clinker nodules. These structural elements in service can gain thermodynamic stability which leads to the concrete structure coarsening, decrease in the relaxation capacity of concrete when exposed to cycling. Additional destructive factors are leaching of portlandite, the difference in thermal dilation coefficients of hydration products, non-hydrated relicts, aggregates and ice. The main way to increase concrete frost resistance is to reduce the macrocapillary porosity of hardened cement paste and to form stable gel-like hydration products.

Structure-based analysis reveals hydration changes induced by arginine hydrochloride.

PubMed

Nakakido, Makoto; Tanaka, Yoshikazu; Mitsuhori, Mariko; Kudou, Motonori; Ejima, Daisuke; Arakawa, Tsutomu; Tsumoto, Kouhei

2008-10-01

Arginine hydrochloride has been used to suppress protein aggregation during refolding and in various other applications. We investigated the structure of hen egg-white lysozyme (HEL) and solvent molecules in arginine hydrochloride solution by X-ray crystallography. Neither the backbone nor side-chain structure of HEL was altered by the presence of arginine hydrochloride. In addition, no stably bound arginine molecules were observed. The number of hydration water molecules, however, changed with the arginine hydrochloride concentration. We suggest that arginine hydrochloride suppresses protein aggregation by altering the hydration structure and the transient binding of arginine molecules that could not be observed.

Neutron powder diffraction studies as a function of temperature of structure II hydrate formed from propane

USGS Publications Warehouse

Rawn, C.J.; Rondinone, A.J.; Chakoumakos, B.C.; Circone, S.; Stern, L.A.; Kirby, S.H.; Ishii, Y.

2003-01-01

Neutron powder diffraction data confirm that hydrate samples synthesized with propane crystallize as structure type II hydrate. The structure has been modeled using rigid-body constraints to describe C3H8 molecules located in the eight larger polyhedral cavities of a deuterated host lattice. Data were collected at 12, 40, 100, 130, 160, 190, 220, and 250 K and used to calculate the thermal expansivity from the temperature dependence of the lattice parameters. The data collected allowed for full structural refinement of atomic coordinates and the atomic-displacement parameters.

Transient Electromagnetic Modelling and Imaging of Thin Resistive Structures: Applications for Gas Hydrate Assessment

NASA Astrophysics Data System (ADS)

Swidinsky, Andrei

Gas hydrates are a solid, ice-like mixture of water and low molecular weight hydrocarbons. They are found under the permafrost and to a far greater extent under the ocean, usually at water depths greater than 300m. Hydrates are a potential energy resource, a possible factor in climate change, and a geohazard. For these reasons, it is critical that gas hydrate deposits are quantitatively assessed so that their concentrations, locations and distributions may be established. Due to their ice-like nature, hydrates are electrically insulating. Consequently, a method which remotely detects changes in seafloor electrical conductivity, such as marine controlled source electromagnetics (CSEM), is a useful geophysical tool for marine gas hydrate exploration. Hydrates are geometrically complex structures. Advanced electromagnetic modelling and imaging techniques are crucial for proper survey design and data interpretation. I develop a method to model thin resistive structures in conductive host media which may be useful in building approximate geological models of gas hydrate deposits using arrangements of multiple, bent sheets. I also investigate the possibility of interpreting diffusive electromagnetic data using seismic imaging techniques. To be processed in this way, such data must first be transformed into its non-diffusive, seismic-like counterpart. I examine such a transform from both an analytical and a numerical point of view, focusing on methods to overcome inherent numerical instabilities. This is the first step to applying seismic processing techniques to CSEM data to rapidly and efficiently image resistive gas hydrate structures. The University of Toronto marine electromagnetics group has deployed a permanent marine CSEM array offshore Vancouver Island, in the framework of the NEPTUNE Canada cabled observatory, for the purposes of monitoring gas hydrate deposits. In this thesis I also propose and examine a new CSEM survey technique for gas hydrate which would make use of the stationary seafloor transmitter already on the seafloor, along with a cabled receiver array, towed from a ship. I furthermore develop a modelling algorithm to examine the electromagnetic effects of conductive borehole casings which have been proposed to be placed in the vicinity of this permanent marine CSEM array, and make preliminary recommendations about their locations.

Structural transformations of sVI tert-butylamine hydrates to sII binary hydrates with methane.

PubMed

Prasad, Pinnelli S R; Sugahara, Takeshi; Sloan, E Dendy; Sum, Amadeu K; Koh, Carolyn A

2009-10-22

Binary clathrate hydrates with methane (CH(4), 4.36 A) and tert-butylamine (t-BuNH(2), 6.72 A) as guest molecules were synthesized at different molar concentrations of t-BuNH(2) (1.00-9.31 mol %) with methane at 7.0 MPa and 250 K, and were characterized by powder X-ray diffraction (PXRD) and Raman microscopy. A structural transformation from sVI to sII of t-BuNH(2) hydrate was clearly observed on pressurizing with methane. The PXRD showed sII signatures and the remnant sVI signatures were insignificant, implying the metastable nature of sVI binary hydrates. Raman spectroscopic data on these binary hydrates suggest that the methane molecules occupy the small cages and vacant large cages. The methane storage capacity in this system was nearly doubled to approximately 6.86 wt % for 5.56 mol % > t-BuNH(2) > 1.0 mol %.

On the structure of an aqueous propylene glycol solution.

PubMed

Rhys, Natasha H; Gillams, Richard J; Collins, Louise E; Callear, Samantha K; Lawrence, M Jayne; McLain, Sylvia E

2016-12-14

Using a combination of neutron diffraction and empirical potential structure refinement computational modelling, the interactions in a 30 mol. % aqueous solution of propylene glycol (PG), which govern both the hydration and association of this molecule in solution, have been assessed. From this work it appears that PG is readily hydrated, where the most prevalent hydration interactions were found to be through both the PG hydroxyl groups but also alkyl groups typically considered hydrophobic. Hydration interactions of PG dominate the solution over PG self-self interactions and there is no evidence of more extensive association. This hydration behavior for PG in solutions suggests that the preference of PG to be hydrated rather than to be self-associated may translate into a preference for PG to bind to lipids rather than itself, providing a potential explanation for how PG is able to enhance the apparent solubility of drug molecules in vivo.

On the structure of an aqueous propylene glycol solution

NASA Astrophysics Data System (ADS)

Rhys, Natasha H.; Gillams, Richard J.; Collins, Louise E.; Callear, Samantha K.; Lawrence, M. Jayne; McLain, Sylvia E.

2016-12-01

Using a combination of neutron diffraction and empirical potential structure refinement computational modelling, the interactions in a 30 mol. % aqueous solution of propylene glycol (PG), which govern both the hydration and association of this molecule in solution, have been assessed. From this work it appears that PG is readily hydrated, where the most prevalent hydration interactions were found to be through both the PG hydroxyl groups but also alkyl groups typically considered hydrophobic. Hydration interactions of PG dominate the solution over PG self-self interactions and there is no evidence of more extensive association. This hydration behavior for PG in solutions suggests that the preference of PG to be hydrated rather than to be self-associated may translate into a preference for PG to bind to lipids rather than itself, providing a potential explanation for how PG is able to enhance the apparent solubility of drug molecules in vivo.

Cooperativity effect involving drug-DNA/RNA intermolecular interaction: A B3LYP-D3 and MP2 theoretical investigation on ketoprofen⋯cytosine⋯H2O system.

PubMed

Zhen, Jun-Ping; Wei, Xiao-Chun; Shi, Wen-Jing; Huang, Zhu-Yuan; Jin, Bo; Zhou, Yu-Kun

2017-11-14

In order to examine the origin of the drug action and design new DNA/RNA-targeted drugs, the cooperativity effect involving drug-DNA/RNA intermolecular interaction in ketoprofen⋯cytosine⋯H 2 O ternary system were investigated by the B3LYP, B3LYP-D3, and MP2 methods with the 6-311++G(2d,p) basis set. The thermodynamic cooperativity was also evaluated at 310.15 K. The N-H⋯O, O-H⋯O, O-H⋯N, C-H⋯N, and C-H⋯O H bonds coexist in ternary complexes. The intermolecular interactions obtained by B3LYP-D3 are close to those calculated by MP2. The steric effects and van der Waals interactions have little influence on the cooperativity effects. The anti-cooperativity effect in ket⋯cyt⋯H 2 O is far more notable than the cooperativity effect, and the stability of the cyclic structure with anti-cooperativity effect is higher than that of the linear structure with cooperativity effect, as is confirmed by the AIM (atoms in molecules) and RDG (reduced density gradient) analysis. Thus, it can be inferred that, in the presence of H 2 O, the anti-cooperativity effect plays a dominant role in the drug-DNA/RNA interaction, and the nature of the hydration in the binding of drugs to DNA/RNA bases is the H-bonding anti-cooperativity effect. Furthermore, the drug always links simultaneously with DNA/RNA base and H 2 O, and only in this way can the biological activity of drugs play a role. In most cases, the enthalpy change is the major factor driving the cooperativity, as is different from most of biomacromolecule complexes.

Novel Hydrogen Hydrate Structures under Pressure

PubMed Central

Qian, Guang-Rui; Lyakhov, Andriy O.; Zhu, Qiang; Oganov, Artem R.; Dong, Xiao

2014-01-01

Gas hydrates are systems of prime importance. In particular, hydrogen hydrates are potential materials of icy satellites and comets, and may be used for hydrogen storage. We explore the H2O–H2 system at pressures in the range 0–100 GPa with ab initio variable-composition evolutionary simulations. According to our calculation and previous experiments, the H2O–H2 system undergoes a series of transformations with pressure, and adopts the known open-network clathrate structures (sII, C0), dense “filled ice” structures (C1, C2) and two novel hydrate phases. One of these is based on the hexagonal ice framework and has the same H2O:H2 ratio (2:1) as the C0 phase at low pressures and similar enthalpy (we name this phase Ih-C0). The other newly predicted hydrate phase has a 1:2 H2O:H2 ratio and structure based on cubic ice. This phase (which we name C3) is predicted to be thermodynamically stable above 38 GPa when including van der Waals interactions and zero-point vibrational energy, and explains previously mysterious experimental X-ray diffraction and Raman measurements. This is the hydrogen-richest hydrate and this phase has a remarkable gravimetric density (18 wt.%) of easily extractable hydrogen. PMID:25001502

Measurement of clathrate hydrates via Raman spectroscopy

USGS Publications Warehouse

Sum, A.K.; Burruss, R.C.; Sloan, E.D.

1997-01-01

Raman spectra of clathrate hydrate guest molecules are presented for three known structures (I (sI), II (sII), and H (sH)) in the following systems: CH4 (sI), CO2 (sI), C3H8 (sII), CH4 + CO2 (sI), CD4 + C3H8 (sII), CH4 + N2 (sI), CH4 + THF-d8 (sII), and CH4 + C7D14 (sH). Relative occupancy of CH4 in the large and small cavities of sI were determined by deconvoluting the ??1 symmetric bands, resulting in hydration numbers of 6.04 ?? 0.03. The frequency of the ??1 bands for CH4 in structures I, II, and H differ statistically, so that Raman spectroscopy is a potential tool to identify hydrate crystal structure. Hydrate guest compositions were also measured for two vapor compositions of the CH4 + CO2 system, and they compared favorably with predictions. The large cavities were measured to be almost fully occupied by CH4 and CO2, whereas only a small fraction of the small cavities are occupied by CH4. No CO2 was found in the small cavities. Hydration numbers from 7.27 to 7.45 were calculated for the mixed hydrate.

Luminescence and ESR studies of relationships between O(-)-centres and structural iron in natural and synthetically hydrated kaolinites

NASA Technical Reports Server (NTRS)

Coyne, L. M.; Costanzo, P. M.; Theng, B. K.

1989-01-01

Luminescence, induced by dehydration and by wetting with hydrazine and unsymmetrically substituted hydrazine, and related ESR spectra have been observed from several kaolinites, synthetically hydrated kaolinites, and metahalloysites. The amine-wetting luminescence results suggest that intercalation, not a chemiluminescence reaction, is the luminescence trigger. Correlation between hydration-induced luminescence and g = 2 ESR signals associated with O(-)-centres in several natural halloysites, and concurrent diminution of the intensity of both these signal types as a function of aging in two 8.4 angstroms synthetically hydrated, kaolinites, confirm a previously-reported relationship between the luminescence induced by dehydration and in the presence of O(-)-centres (holes, i.e., electron vacancies) in the tetrahedral sheet. Furthermore, the ESR spectra of the 8.4 angstroms hydrate showed a concurrent change in the line shape of the g = 4 signal from a shape usually associated with structural Fe in an ordered kaolinite, to a simpler one typically observed in more disordered kaolinite, halloysite, and montmorillonite. Either structural Fe centres and the O(-)-centres interact, or both are subject to factors previously associated with degree of order. The results question the long-term stability of the 8.4 angstroms hydrate, although XRD does not indicate interlayer collapse over this period. Complex inter-relationships are shown between intercalation, stored energy, structural Fe, and the degree of hydration which may be reflected in catalytic as well as spectroscopic properties of the clays.

Self-preservation and structural transition of gas hydrates during dissociation below the ice point: an in situ study using Raman spectroscopy

PubMed Central

Zhong, Jin-Rong; Zeng, Xin-Yang; Zhou, Feng-He; Ran, Qi-Dong; Sun, Chang-Yu; Zhong, Rui-Qin; Yang, Lan-Ying; Chen, Guang-Jin; Koh, Carolyn A.

2016-01-01

The hydrate structure type and dissociation behavior for pure methane and methane-ethane hydrates at temperatures below the ice point and atmospheric pressure were investigated using in situ Raman spectroscopic analysis. The self-preservation effect of sI methane hydrate is significant at lower temperatures (268.15 to 270.15 K), as determined by the stable C-H region Raman peaks and AL/AS value (Ratio of total peak area corresponding to occupancies of guest molecules in large cavities to small cavities) being around 3.0. However, it was reduced at higher temperatures (271.15 K and 272.15 K), as shown from the dramatic change in Raman spectra and fluctuations in AL/AS values. The self-preservation effect for methane-ethane double hydrate is observed at temperatures lower than 271.15 K. The structure transition from sI to sII occurred during the methane-ethane hydrate decomposition process, which was clearly identified by the shift in peak positions and the change in relative peak intensities at temperatures from 269.15 K to 271.15 K. Further investigation shows that the selectivity for self-preservation of methane over ethane leads to the structure transition; this kind of selectivity increases with decreasing temperature. This work provides new insight into the kinetic behavior of hydrate dissociation below the ice point. PMID:27941857

Self-preservation and structural transition of gas hydrates during dissociation below the ice point: an in situ study using Raman spectroscopy.

PubMed

Zhong, Jin-Rong; Zeng, Xin-Yang; Zhou, Feng-He; Ran, Qi-Dong; Sun, Chang-Yu; Zhong, Rui-Qin; Yang, Lan-Ying; Chen, Guang-Jin; Koh, Carolyn A

2016-12-12

The hydrate structure type and dissociation behavior for pure methane and methane-ethane hydrates at temperatures below the ice point and atmospheric pressure were investigated using in situ Raman spectroscopic analysis. The self-preservation effect of sI methane hydrate is significant at lower temperatures (268.15 to 270.15 K), as determined by the stable C-H region Raman peaks and A L /A S value (Ratio of total peak area corresponding to occupancies of guest molecules in large cavities to small cavities) being around 3.0. However, it was reduced at higher temperatures (271.15 K and 272.15 K), as shown from the dramatic change in Raman spectra and fluctuations in A L /A S values. The self-preservation effect for methane-ethane double hydrate is observed at temperatures lower than 271.15 K. The structure transition from sI to sII occurred during the methane-ethane hydrate decomposition process, which was clearly identified by the shift in peak positions and the change in relative peak intensities at temperatures from 269.15 K to 271.15 K. Further investigation shows that the selectivity for self-preservation of methane over ethane leads to the structure transition; this kind of selectivity increases with decreasing temperature. This work provides new insight into the kinetic behavior of hydrate dissociation below the ice point.

Hydrate-Bearing Clayey Sediments: Morphology, Physical Properties, Production and Engineering/Geological Implications

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

Dai, Sheng; Santamarina, J. Carlos

Fine-grained sediments host more than 90 percent of global gas hydrate accumulation. However, hydrate formation in clay-dominated sediments is less understood and characterized than other types of hydrate occurrence. There is an inadequate understanding of hydrate formation mechanisms, segregation structures, hydrate lens topology, system connectivity, and physical macro-scale properties of clay-dominated hydrate-bearing sediments. This situation hinders further analyses of the global carbon budget as well as engineering challenges/solutions related to hydrate instability and production. This project studies hydrate-bearing clay-dominated sediments with emphasis on the enhanced fundamental understanding of hydrate formation and resulting morphology, the development laboratory techniques to emulate naturalmore » hydrate formations, the assessment of analytical tools to predict physical properties, the evaluation of engineering and geological implications, and the advanced understanding of gas production potential from finegrained sediments.« less

Infrared and swelling study of wet-spun films of DNA\\cdot[(bipy)Pt(en)]^2+ as a function of hydration

NASA Astrophysics Data System (ADS)

Kuebler, A.; Whitson, K. B.; Marlowe, R. L.; Lee, S. A.; Rupprecht, A.

1997-11-01

A ladder-like conformation of DNA has been induced by the binding of bipyridyl-Pt(II)-ethylenediamine (denoted as [(bipy)Pt(en)]^2+) at a relative humidity (RH) of 75%.(Arnott et al.,) Nature 287, (1980) 561. We report the first study of oriented films of this complex as a function of hydration by using Fourier transform infrared (IR) spectroscopy and optical microscopy. Vibrational modes between 800 and 1000 cm-1 are localized in the phosphodiester backbone and are sensitive to changes in the geometry of the molecule. The IR spectrum of this region is substantially different at 59% RH than at higher humidities, implying that a conformational change occurs as the RH is lowered below 75%. Optical microscopy measurements of small pieces of films of the complex also show changes at low RH. These trends are consistent with an order-disorder transition occurring as the RH is lowered The measurements also show that the DNA\\cdot[(bipy)Pt(en)]^2+) are very stable at the highest humidities.

Hydration and Thermal Expansion in Anatase Nanoparticles

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

Zhu, He; Li, Qiang; Ren, Yang

A tunable thermal expansion is reported in nanosized anatase by taking advantage of surface hydration. The coefficient of thermal expansion of 4 nm TiO2 along a-axis is negative with a hydrated surface and is positive without a hydrated surface. High-energy synchrotron X-ray pair distribution function analysis combined with ab initio calculations on the specific hydrated surface are carried out to reveal the local structure distortion that is responsible for the unusual negative thermal expansion.

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.

Uniform manganese hexacyanoferrate hydrate nanocubes featuring superior performance for low-cost supercapacitors and nonenzymatic electrochemical sensors

NASA Astrophysics Data System (ADS)

Pang, Huan; Zhang, Yizhou; Cheng, Tao; Lai, Wen-Yong; Huang, Wei

2015-09-01

Uniform manganese hexacyanoferrate hydrate nanocubes are prepared via a simple chemical precipitation method at room temperature. Due to both micro/mesopores of the Prussian blue analogue and nanocubic structures, the manganese hexacyanoferrate hydrate nanocubes allow the efficient charge transfer and mass transport for electrolyte solution and chemical species. Thus, the manganese hexacyanoferrate hydrate nanocube electrode shows a good rate capability and cycling stability for electrochemical capacitors. Furthermore, electrodes modified with manganese hexacyanoferrate hydrate nanocubes demonstrate a sensitive electrochemical response to hydrogen peroxide (H2O2) in buffer solutions with a high selectivity.Uniform manganese hexacyanoferrate hydrate nanocubes are prepared via a simple chemical precipitation method at room temperature. Due to both micro/mesopores of the Prussian blue analogue and nanocubic structures, the manganese hexacyanoferrate hydrate nanocubes allow the efficient charge transfer and mass transport for electrolyte solution and chemical species. Thus, the manganese hexacyanoferrate hydrate nanocube electrode shows a good rate capability and cycling stability for electrochemical capacitors. Furthermore, electrodes modified with manganese hexacyanoferrate hydrate nanocubes demonstrate a sensitive electrochemical response to hydrogen peroxide (H2O2) in buffer solutions with a high selectivity. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr04322k

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.

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

Cement hydration from hours to centuries controlled by diffusion through barrier shells of C-S-H

NASA Astrophysics Data System (ADS)

Rahimi-Aghdam, Saeed; Bažant, Zdeněk P.; Abdolhosseini Qomi, M. J.

2017-02-01

Although a few good models for cement hydration exist, they have some limitations. Some do not take into account the complete range of variation of pore relative humidity and temperature, and apply over durations limited from up a few months to up to about a year. The ones that are applicable for long durations are either computationally too intensive for use in finite element programs or predict the hydration to terminate after few months. However, recent tests of autogenous shrinkage and swelling in water imply that the hydration may continue, at decaying rate, for decades, provided that a not too low relative pore humidity (above 0.7) persists for a long time, as expected for the cores of thick concrete structural members. Therefore, and because design lifetimes of over hundred years are required for large concrete structures, a new hydration model for a hundred year lifespan and beyond is developed. The new model considers that, after the first day of hydration, the remnants of anhydrous cement grains, gradually consumed by hydration, are enveloped by contiguous, gradually thickening, spherical barrier shells of calcium-silicate hydrate (C-S-H). The hydration progress is controlled by transport of water from capillary pores through the barrier shells toward the interface with anhydrous cement. The transport is driven by a difference of humidity, defined by equivalence with the difference in chemical potential of water. Although, during the period of 4-24 h, the C-S-H forms discontinuous nano-globules around the cement grain, an equivalent barrier shell control was formulated for this period, too, for ease and effectiveness of calculation. The entire model is calibrated and validated by published test data on the evolution of hydration degree for various cement types, particle size distributions, water-cement ratios and temperatures. Computationally, this model is sufficiently effective for calculating the evolution of hydration degree (or aging) at every integration point of every finite element in a large structure.

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

PubMed

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

2009-05-21

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

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

Casco, Mirian E.; Silvestre-Albero, Joaquín; Ramírez-Cuesta, Anibal J.

Natural methane hydrates are believed to be the largest source of hydrocarbons on Earth. These structures are formed in specific locations such as deep-sea sediments and the permafrost based on demanding conditions of high pressure and low temperature. We report that, by taking advantage of the confinement effects on nanopore space, synthetic methane hydrates grow under mild conditions (3.5 MPa and 2 degrees C), with faster kinetics (within minutes) than nature, fully reversibly and with a nominal stoichiometry that mimics nature. Furthermore, the formation of the hydrate structures in nanospace and their similarity to natural hydrates is confirmed using inelasticmore » neutron scattering experiments and synchrotron X-ray powder diffraction. Our findings may be a step towards the application of a smart synthesis of methane hydrates in energy-demanding applications (for example, transportation).« less

Effect of Hydration and Confinement on Micro-Structure of Calcium-Silicate-Hydrate Gels

NASA Astrophysics Data System (ADS)

Gadde, Harish Kumar

Calcium-silicate-hydrate(C-S-H) gel is a primary nano-crystalline phase present in hydrated Ordinary Portland Cement (OPC) responsible for its strength and creep behavior. Our reliance on cement for infrastructure is global, and there is a need to improve infrastructure life-times. A way forward is to engineer the cement with more durability and long-term strength. The main purpose of this research is to quantify the micro-structure of C-S-H to see if cement can be engineered at various length scales to improve long-term behavior by spatial arrangement. We investigate the micro-structure evolution of C-S-H in cement as a function of hydration time and confinement. Scanning electron microscopy (SEM) and Energy Dispersive X-ray Spectroscopy (EDS) were used to quantify the material and spatial properties of C-S-H as a function of hydration time. The data obtained from these experiments was used to identify C-S-H phases in cement sample. Pair Distribution Function (PDF) analysis of HD C-S-H phase with different hydration times was done at Advanced Photon Source, Argonne National Laboratory, beamline 11-ID-B. Only nonlinear trends in the atomic ordering of C-S-H gel as a function of hydration time were observed. Solid state 29Si Nuclear Magnetic Resonance (NMR) was used to quantify the effect of confinement on two types of C-S-H: white cement C-S-H and synthetic C-S-H. NMR spectra revealed that there is no significant difference in the structure of C-S-H due to confinement when compared with unconfined C-S-H. It is also found that there is significant difference in the Si environments of these two types of C-S-H. Though it does seem possible to engineer the cement on atomic scales, all these studies reveal that engineering cement on such a scale requires a more statistically accurate understanding of intricate structure of C-S-H than is currently available.

Correlation Between Chain Architecture and Hydration Water Structure in Polysaccharides.

PubMed

Grossutti, Michael; Dutcher, John R

2016-03-14

The physical properties of confined water can differ dramatically from those of bulk water. Hydration water associated with polysaccharides provides a particularly interesting example of confined water, because differences in polysaccharide structure provide different spatially confined environments for water sorption. We have used attenuated total reflection infrared (ATR-IR) spectroscopy to investigate the structure of hydration water in films of three different polysaccharides under controlled relative humidity (RH) conditions. We compare the results obtained for films of highly branched, dendrimer-like phytoglycogen nanoparticles to those obtained for two unbranched polysaccharides, hyaluronic acid (HA), and chitosan. We find similarities between the water structuring in the two linear polysaccharides and significant differences for phytoglycogen. In particular, the results suggest that the high degree of branching in phytoglycogen leads to a much more well-ordered water structure (low density, high connectivity network water), indicating the strong influence of chain architecture on the structuring of water. These measurements provide unique insight into the relationship between the structure and hydration of polysaccharides, which is important for understanding and exploiting these sustainable nanomaterials in a wide range of applications.

Investigation of shallow gas hydrate occurrence and gas seep activity on the Sakhalin continental slope, Russia

NASA Astrophysics Data System (ADS)

Jin, Young Keun; Baranov, Boris; Obzhirov, Anatoly; Salomatin, Alexander; Derkachev, Alexander; Hachikubo, Akihiro; Minami, Hrotsugu; Kuk Hong, Jong

2016-04-01

The Sakhalin continental slope has been a well-known gas hydrate area since the first finding of gas hydrate in 1980's. This area belongs to the southernmost glacial sea in the northern hemisphere where most of the area sea is covered by sea ice the winter season. Very high organic carbon content in the sediment, cold sea environment, and active tectonic regime in the Sakhalin slope provide a very favorable condition for occurring shallow gas hydrate accumulation and gas emission phenomena. Research expeditions under the framework of a Korean-Russian-Japanese long-term international collaboration projects (CHAOS, SSGH-I, SSGH-II projects) have been conducted to investigate gas hydrate occurrence and gas seepage activities on the Sakhalin continental slope, Russia from 2003 to 2015. During the expeditions, near-surface gas hydrate samples at more than 30 sites have been retrieved and hundreds of active gas seepage structures on the seafloor were newly registered by multidisciplinary surveys. The gas hydrates occurrence at the various water depths from about 300 m to 1000 m in the study area were accompanied by active gas seepage-related phenomena in the sub-bottom, on the seafloor, and in the water column: well-defined upward gas migration structures (gas chimney) imaged by high-resolution seismic, hydroacoustic anomalies of gas emissions (gas flares) detected by echosounders, seafloor high backscatter intensities (seepage structures) imaged by side-scan sonar and bathymetric structures (pockmarks and mounds) mapped by single/multi-beam surveys, and very shallow SMTZ (sulphate-methane transition zone) depths, strong microbial activities and high methane concentrations measured in sediment/seawater samples. The highlights of the expeditions are shallow gas hydrate occurrences around 300 m in the water depth which is nearly closed to the upper boundary of gas hydrate stability zone in the area and a 2,000 m-high gas flare emitted from the deep seafloor.

The impact of fire suppression tasks on firefighter hydration: a critical review with consideration of the utility of reported hydration measures.

PubMed

Walker, Adam; Pope, Rodney; Orr, Robin Marc

2016-01-01

Firefighting is a highly stressful occupation with unique physical challenges, apparel and environments that increase the potential for dehydration. Dehydration leaves the firefighter at risk of harm to their health, safety and performance. The purpose of this review was to critically analyse the current literature investigating the impact of fighting 'live' fires on firefighter hydration. A systematic search was performed of four electronic databases for relevant published studies investigating the impact of live fire suppression on firefighter hydration. Study eligibility was assessed using strict inclusion and exclusion criteria. The included studies were critically appraised using the Downs and Black protocol and graded according to the Kennelly grading system. Ten studies met the eligibility criteria for this review. The average score for methodological quality was 55 %, ranging from 50 % ('fair' quality) to 61 % ('good' quality) with a 'substantial agreement' between raters ( k  = .772). Wildfire suppression was considered in five studies and structural fire suppression in five studies. Results varied across the studies, reflecting variations in outcome measures, hydration protocols and interventions. Three studies reported significant indicators of dehydration resulting from structural fire suppression, while two studies found mixed results, with some measures indicating dehydration and other measures an unchanged hydration status. Three studies found non-significant changes in hydration resulting from wildfire firefighting and two studies found significant improvements in markers of hydration. Ad libitum fluid intake was a common factor across the studies finding no, or less severe, dehydration. The evidence confirms that structural and wildfire firefighting can cause dehydration. Ad libitum drinking may be sufficient to maintain hydration in many wildfire environments but possibly not during intense, longer duration, hot structural fire operations. Future high quality research better quantifying the effects of these influences on the degree of dehydration is required to inform policies and procedures that ensure firefighter health and safety.

The effect of S-substitution at the O6-guanine site on the structure and dynamics of a DNA oligomer containing a G:T mismatch

PubMed Central

2017-01-01

The effect of S-substitution on the O6 guanine site of a 13-mer DNA duplex containing a G:T mismatch is studied using molecular dynamics. The structure, dynamic evolution and hydration of the S-substituted duplex are compared with those of a normal duplex, a duplex with S-substitution on guanine, but no mismatch and a duplex with just a G:T mismatch. The S-substituted mismatch leads to cell death rather than repair. One suggestion is that the G:T mismatch recognition protein recognises the S-substituted mismatch (GS:T) as G:T. This leads to a cycle of futile repair ending in DNA breakage and cell death. We find that some structural features of the helix are similar for the duplex with the G:T mismatch and that with the S-substituted mismatch, but differ from the normal duplex, notably the helical twist. These differences arise from the change in the hydrogen-bonding pattern of the base pair. However a marked feature of the S-substituted G:T mismatch duplex is a very large opening. This showed considerable variability. It is suggested that this enlarged opening would lend support to an alternative model of cell death in which the mismatch protein attaches to thioguanine and activates downstream damage-response pathways. Attack on the sulphur by reactive oxygen species, also leading to cell death, would also be aided by the large, variable opening. PMID:28910418

Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields.

PubMed

Yoo, Jejoong; Wilson, James; Aksimentiev, Aleksei

2016-10-01

Calcium ions (Ca(2+) ) play key roles in various fundamental biological processes such as cell signaling and brain function. Molecular dynamics (MD) simulations have been used to study such interactions, however, the accuracy of the Ca(2+) models provided by the standard MD force fields has not been rigorously tested. Here, we assess the performance of the Ca(2+) models from the most popular classical force fields AMBER and CHARMM by computing the osmotic pressure of model compounds and the free energy of DNA-DNA interactions. In the simulations performed using the two standard models, Ca(2+) ions are seen to form artificial clusters with chloride, acetate, and phosphate species; the osmotic pressure of CaAc2 and CaCl2 solutions is a small fraction of the experimental values for both force fields. Using the standard parameterization of Ca(2+) ions in the simulations of Ca(2+) -mediated DNA-DNA interactions leads to qualitatively wrong outcomes: both AMBER and CHARMM simulations suggest strong inter-DNA attraction whereas, in experiment, DNA molecules repel one another. The artificial attraction of Ca(2+) to DNA phosphate is strong enough to affect the direction of the electric field-driven translocation of DNA through a solid-state nanopore. To address these shortcomings of the standard Ca(2+) model, we introduce a custom model of a hydrated Ca(2+) ion and show that using our model brings the results of the above MD simulations in quantitative agreement with experiment. Our improved model of Ca(2+) can be readily applied to MD simulations of various biomolecular systems, including nucleic acids, proteins and lipid bilayer membranes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 752-763, 2016. © 2016 Wiley Periodicals, Inc.

Geological and geochemical implications of gas hydrates in the Gulf of Mexico. Final report

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

Brooks, J.M.; Bryant, W.R.

1985-09-01

This document presents the results of a study of the geological and geochemical implications of gas hydrates in the Gulf of Mexico. The report is based primarily on data obtained from available seismic surveys of the Green Canyon, Garden Banks, Mississippi Canyon, and Orca Basins areas of the northern continental margin of the Gulf of Mexico. The study also includes the data and analysis obtained from several gas hydrate cores recovered in these areas. The report provides new data relevant to gas hydrate research for more in-depth research of the Gulf of Mexico gas hydrates and provides significant information whichmore » advances the knowledge and understanding of gas hydrate formations in the natural environment. The report contains several high resolution seismic surveys. In the four hydrate sites studied in detail, the seismic ''wipeout'' zones were all associated with collapsed structures, fault scarps, and/or salt piercement structures. These features provide conduits for the upward migration of either biogenic or thermogenic gas from depth. 35 refs., 47 figs., 9 tabs.« less

Physical properties of repressurized samples recovered during the 2006 National Gas Hydrate Program expedition offshore India

USGS Publications Warehouse

Winters, William J.; Waite, William F.; Mason, David H.; Kumar, P.

2008-01-01

As part of an international cooperative research program, the U.S. Geological Survey (USGS) and researchers from the National Gas Hydrate Program (NGHP) of India are studying the physical properties of sediment recovered during the NGHP-01 cruise conducted offshore India during 2006. Here we report on index property, acoustic velocity, and triaxial shear test results for samples recovered from the Krishna-Godavari Basin. In addition, we discuss the effects of sample storage temperature, handling, and change in structure of fine-grained sediment. Although complex, sub-vertical planar gas-hydrate structures were observed in the silty clay to clayey silt samples prior to entering the Gas Hydrate And Sediment Test Laboratory Instrument (GHASTLI), the samples yielded little gas post test. This suggests most, if not all, gas hydrate dissociated during sample transfer. Mechanical properties of hydrate-bearing marine sediment are best measured by avoiding sample depressurization. By contrast, mechanical properties of hydrate-free sediments, that are shipped and stored at atmospheric pressure can be approximated by consolidating core material to the original in situ effective stress.

[In situ Raman spectroscopic observation of micro-processes of methane hydrate formation and dissociation].

PubMed

Liu, Chang-Ling; Ye, Yu-Guang; Meng, Qing-Guo; Lü, Wan-Jun; Wang, Fei-Fei

2011-06-01

Micro laser Raman spectroscopic technique was used for in situ observation of the micro-processes of methane hydrate formed and decomposed in a high pressure transparent capillary. The changes in clathrate structure of methane hydrate were investigated during these processes. The results show that, during hydrate formation, the Raman peak (2 917 cm(-1)) of methane gas gradually splits into two peaks (2 905 and 2 915 cm(-1)) representing large and small cages, respectively, suggesting that the dissolved methane molecules go into two different chemical environments. In the meantime, the hydrogen bonds interaction is strengthened because water is changing from liquid to solid state gradually. As a result, the O-H stretching vibrations of water shift to lower wavenumber. During the decomposition process of methane hydrates, the Raman peaks of the methane molecules both in the large and small cages gradually clear up, and finally turn into a single peak of methane gas. The experimental results show that laser Raman spectroscopy can accurately demonstrate some relevant information of hydrate crystal structure changes during the formation and dissociation processes of methane hydrate.

Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate.

PubMed

Resat, H; Mezei, M

1996-09-01

The grand canonical ensemble Monte Carlo molecular simulation method is used to investigate hydration patterns in the crystal hydrate structure of the dCpG/proflavine intercalated complex. The objective of this study is to show by example that the recently advocated grand canonical ensemble simulation is a computationally efficient method for determining the positions of the hydrating water molecules in protein and nucleic acid structures. A detailed molecular simulation convergence analysis and an analogous comparison of the theoretical results with experiments clearly show that the grand ensemble simulations can be far more advantageous than the comparable canonical ensemble simulations.

Transition mechanism of sH to filled-ice Ih structure of methane hydrate under fixed pressure condition

NASA Astrophysics Data System (ADS)

Kadobayashi, H.; Hirai, H.; Ohfuji, H.; Kojima, Y.; Ohishi, Y.; Hirao, N.; Ohtake, M.; Yamamoto, Y.

2017-10-01

The phase transition mechanism of methane hydrate from sH to filled-ice Ih structure was examined using a combination of time-resolved X-ray diffractometry (XRD) and Raman spectroscopy in conjunction with charge-coupled device (CCD) camera observation under fixed pressure conditions. Prior to time-resolved Raman experiments, the typical C-H vibration modes and their pressure dependence of three methane hydrate structures, fluid methane and solid methane were measured using Raman spectroscopy to distinguish the phase transitions of methane hydrates from decomposition to solid methane and ice VI or VII. Experimental results by XRD, Raman spectroscopy and CCD camera observation revealed that the structural transition of sH to filled-ice Ih occurs through a collapse of the sH framework followed by the release of fluid methane that is then gradually incorporated into the filled-ice Ih to reconstruct its structure. These observations suggest that the phase transition of sH to filled-ice Ih takes place by a typical reconstructive mechanism.

The hydration structure at yttria-stabilized cubic zirconia (110)-water interface with sub-Ångström resolution

DOE PAGES

Hou, Binyang; Kim, Seunghyun; Kim, Taeho; ...

2016-06-15

The interfacial hydration structure of yttria-stabilized cubic zirconia (110) surface in contact with water was determined with ~0.5 Å resolution by high-resolution X-ray reflectivity measurement. The terminal layer shows a reduced electron density compared to the following substrate lattice layers, which indicates there are additional defects generated by metal depletion as well as intrinsic oxygen vacancies, both of which are apparently filled by water species. Above this top surface layer, two additional adsorbed layers are observed forming a characteristic interfacial hydration structure. The first adsorbed layer shows abnormally high density as pure water and likely includes metal species, whereas themore » second layer consists of pure water. The observed interfacial hydration structure seems responsible for local equilibration of the defective surface in water and eventually regulating the long-term degradation processes. As a result, the multitude of water interactions with the zirconia surface results in the complex but highly ordered interfacial structure constituting the reaction front.« less

Correlation Between Chain Architecture and Hydration Water Structure in Polysaccharides

NASA Astrophysics Data System (ADS)

Grossutti, Michael; Dutcher, John

The physical properties of confined water can differ dramatically from those of bulk water. Hydration water associated with polysaccharides provides a particularly important example of confined water, with differences in polysaccharide structure providing different spatially confined environments for water adsorption. We have used attenuated total reflection infrared (ATR-IR) spectroscopy to investigate the structure of hydration water in films of three different polysaccharides under controlled relative humidity (RH) conditions. We compare the results obtained for films of highly branched, monodisperse phytoglycogen nanoparticles to those obtained for two unbranched polysaccharides, hyaluronic acid (HA) and chitosan. We find similarities between water structuring in the two linear polysaccharides, and significant differences for phytoglycogen. In particular, the phytoglycogen nanoparticles exhibited high network water connectivity, and a large increase in the fraction of multimer water clusters with increasing RH, whereas the water structure for HA and chitosan was found to be insensitive to changes in RH. These measurements provide unique insight into the relationship between the chain architecture and hydration of polysaccharides.

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

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.

Grain-scale imaging and compositional characterization of cryo-preserved India NGHP 01 gas-hydrate-bearing cores

USGS Publications Warehouse

Stern, Laura A.; Lorenson, T.D.

2014-01-01

We report on grain-scale characteristics and gas analyses of gas-hydrate-bearing samples retrieved by NGHP Expedition 01 as part of a large-scale effort to study gas hydrate occurrences off the eastern-Indian Peninsula and along the Andaman convergent margin. Using cryogenic scanning electron microscopy, X-ray spectroscopy, and gas chromatography, we investigated gas hydrate grain morphology and distribution within sediments, gas hydrate composition, and methane isotopic composition of samples from Krishna–Godavari (KG) basin and Andaman back-arc basin borehole sites from depths ranging 26 to 525 mbsf. Gas hydrate in KG-basin samples commonly occurs as nodules or coarse veins with typical hydrate grain size of 30–80 μm, as small pods or thin veins 50 to several hundred microns in width, or disseminated in sediment. Nodules contain abundant and commonly isolated macropores, in some places suggesting the original presence of a free gas phase. Gas hydrate also occurs as faceted crystals lining the interiors of cavities. While these vug-like structures constitute a relatively minor mode of gas hydrate occurrence, they were observed in near-seafloor KG-basin samples as well as in those of deeper origin (>100 mbsf) and may be original formation features. Other samples exhibit gas hydrate grains rimmed by NaCl-bearing material, presumably produced by salt exclusion during original hydrate formation. Well-preserved microfossil and other biogenic detritus are also found within several samples, most abundantly in Andaman core material where gas hydrate fills microfossil crevices. The range of gas hydrate modes of occurrence observed in the full suite of samples suggests a range of formation processes were involved, as influenced by local in situconditions. The hydrate-forming gas is predominantly methane with trace quantities of higher molecular weight hydrocarbons of primarily microbial origin. The composition indicates the gas hydrate is Structure I.

Irreversible electron attachment--a key to DNA damage by solvated electrons in aqueous solution.

PubMed

Westphal, K; Wiczk, J; Miloch, J; Kciuk, G; Bobrowski, K; Rak, J

2015-11-07

The TYT and TXT trimeric oligonucleotides, where X stands for a native nucleobase, T (thymine), C (cytosine), A (adenine), or G (guanine), and Y indicates a brominated analogue of the former, were irradiated with ionizing radiation generated by a (60)Co source in aqueous solutions containing Tris as a hydroxyl radical scavenger. In the past, these oligomers were bombarded with low energy electrons under an ultra-high vacuum and significant damage to TXT trimers was observed. However, in aqueous solution, hydrated electrons do not produce serious damage to TXT trimers although the employed radiation dose exceeded many times the doses used in radiotherapy. Thus, our studies demonstrate unequivocally that hydrated electrons, which are the major form of electrons generated during radiotherapy, are a negligible factor in damage to native DNA. It was also demonstrated that all the studied brominated nucleobases have a potential to sensitize DNA under hypoxic conditions. Strand breaks, abasic sites and the products of hydroxyl radical attachment to nucleobases have been identified by HPLC and LC-MS methods. Although all the bromonucleobases lead to DNA damage under the experimental conditions of the present work, bromopyrimidines seem to be the radiosensitizers of choice since they lead to more strand breaks than bromopurines.

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.

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.

Raman study of CaDNA films as a function of water content and excess CaCl2 concentration: Stability of the B conformation.

NASA Astrophysics Data System (ADS)

Schwenker, Megan; Marlowe, Robert; Lee, Scott; Rupprecht, Allan

2006-03-01

Highly oriented, wet-spun films of CaDNA expand in the direction perpendicular to the helical axis as the hydration of the film is increased. CaDNA films with a high CaCl2 content show an unexpected shrinkage at a relative humidity of about 93%. We have performed Raman experiments on CaDNA films as a function of both water content and excess CaCl2 concentration in order to determine if this unexpected shrinkage might be related to a conformational transition of the DNA molecules. We find that the DNA molecules remain in the B conformation for all salt contents down to a relative humidity of 59%.

Quantification of DNA in simple eukaryotic cells using Fourier transform infrared spectroscopy.

PubMed

Whelan, Donna R; Bambery, Keith R; Puskar, Ljiljana; McNaughton, Don; Wood, Bayden R

2013-10-01

A technique capable of detecting and monitoring nucleic acid concentration offers potential in diagnosing cancer and further developing an understanding of the biochemistry of disease. The application of Fourier transform infrared (FTIR) spectroscopy has previously been hindered by the supposed non-Beer-Lambert absorption behavior of DNA in intact cells making elucidation of the DNA bands difficult. We use known composition DNA/hemoglobin standards to successfully estimate the DNA content in avian erythrocyte nuclei (44.2%) and intact erythrocytes (12.8%). Furthermore we demonstrate that the absorption of cellular DNA does follow the Beer-Lambert Law and highlights the role of conformation and hydration in FTIR spectroscopy of biological samples. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lattice constants and expansivities of gas hydrates from 10 K up to the stability limit

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

Hansen, T. C.; Falenty, A.; Kuhs, W. F.

2016-02-07

The lattice constants of hydrogenated and deuterated CH{sub 4}-, CO{sub 2}-, Xe- (clathrate structure type I) and N{sub 2}-hydrates (clathrate structure type II) from 10 K up to the stability limit were established in neutron- and synchrotron diffraction experiments and were used to derive the related thermal expansivities. The following results emerge from this analysis: (1) The differences of expansivities of structure type I and II hydrates are fairly small. (2) Despite the larger guest-size of CO{sub 2} as compared to methane, CO{sub 2}-hydrate has the smaller lattice constants at low temperatures, which is ascribed to the larger attractive guest-hostmore » interaction of the CO{sub 2}-water system. (3) The expansivity of CO{sub 2}-hydrate is larger than for CH{sub 4}-hydrate which leads to larger lattice constants for the former at temperatures above ∼150 K; this is likely due to the higher motional degrees of freedom of the CO{sub 2} guest molecules. (4) The cage occupancies of Xe- and CO{sub 2}-hydrates affect significantly the lattice constants. (5) Similar to ice Ih, the deuterated compounds have generally slightly larger lattice constants which can be ascribed to the somewhat weaker H-bonding. (6) Compared to ice Ih, the high temperature expansivities are about 50% larger; in contrast to ice Ih and the empty hydrate, there is no negative thermal expansion at low temperature. (7) A comparison of the experimental results with lattice dynamical work, with models based on an Einstein oscillator model, and results from inelastic neutron scattering suggest that the contribution of the guest atoms’ vibrational energy to thermal expansion is important, most prominently for CO{sub 2}- and Xe-hydrates.« less

Experimental Equipment Validation for Methane (CH4) and Carbon Dioxide (CO2) Hydrates

NASA Astrophysics Data System (ADS)

Saad Khan, Muhammad; Yaqub, Sana; Manner, Naathiya; Ani Karthwathi, Nur; Qasim, Ali; Mellon, Nurhayati Binti; Lal, Bhajan

2018-04-01

Clathrate hydrates are eminent structures regard as a threat to the gas and oil industry in light of their irritating propensity to subsea pipelines. For natural gas transmission and processing, the formation of gas hydrate is one of the main flow assurance delinquent has led researchers toward conducting fresh and meticulous studies on various aspects of gas hydrates. This paper highlighted the thermodynamic analysis on pure CH4 and CO2 gas hydrates on the custom fabricated equipment (Sapphire cell hydrate reactor) for experimental validation. CO2 gas hydrate formed at lower pressure (41 bar) as compared to CH4 gas hydrate (70 bar) while comparison of thermodynamic properties between CH4 and CO2 also presented in this study. This preliminary study could provide pathways for the quest of potent hydrate inhibitors.

Gas hydrate in nature

USGS Publications Warehouse

Ruppel, Carolyn D.

2018-01-17

Gas hydrate is a naturally occurring, ice-like substance that forms when water and gas combine under high pressure and at moderate temperatures. Methane is the most common gas present in gas hydrate, although other gases may also be included in hydrate structures, particularly in areas close to conventional oil and gas reservoirs. Gas hydrate is widespread in ocean-bottom sediments at water depths greater than 300–500 meters (m; 984–1,640 feet [ft]) and is also present in areas with permanently frozen ground (permafrost). Several countries are evaluating gas hydrate as a possible energy resource in deepwater or permafrost settings. Gas hydrate is also under investigation to determine how environmental change may affect these deposits.

The occurrence of macro- and mesoscopic methane hydrate in the eastern margin of Japan Sea

NASA Astrophysics Data System (ADS)

Matsumoto, R.; Kakuwa, Y.; Tanahashi, M.; Hiruta, A.

2016-12-01

Shallow methane hydrate is known to occur in muddy sediments that were deposited in the eastern margin of Japan Sea. In such settings, the hydrate occurs just below the seabed or is exposed directly on the seabed. Its presence is quite different from the pore-filling type of hydrate typically found in sandstone of the Pacific Ocean side of the Japanese islands. This presentation focuses on categorizing the distribution of gas hydrate in Japan Sea which, until recently, has been poorly understood. Macroscopic occurrence: Numerous gas chimney structures, which are characterized by an acoustic blanking on sub-bottom profiler images, have been discovered in the eastern margin of Japan Sea. We carried out seafloor drilling at several topographic highs that showed gas chimney structures. The results confirm that, while methane hydrate does not occur in the well-stratified part of SBP images, it does occur uniquely in the gas chimney structure-bearing mounds and pockmarks. Several horizons of methane hydrate-concentrated layers are identified by our LWD data and are traceable over lateral distances of as much as a kilometer.. In another case, the methane hydrate-concentrated layers occur stratigraphically in a regular manner with methane-derived carbonate nodules. We interpret the second case as one in which methane gas was supplied by regularly repeated movements of active fault(s). Mesoscopic occurrence: Methane hydrate is classified into 5 types that are readily observable in drilled cores: granular, nodular, platy, veiny and massive. The granular type is common over shallower intervals, while platy and veiny types are more common in the deeper intervals. Nevertheless, a significant fraction of the granular type may have possibly originated from the destruction and dissociation of other types during drilling and recovery. The massive type hydrate that characterizes highly-concentrated layers transitions to other types laterally as methane hydrate becomes poorly concentrated. 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).

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.

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.

Free energy landscape and molecular pathways of gas hydrate nucleation.

PubMed

Bi, Yuanfei; Porras, Anna; Li, Tianshu

2016-12-07

Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p B histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p B histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.

Free energy landscape and molecular pathways of gas hydrate nucleation

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

Bi, Yuanfei; Porras, Anna; Li, Tianshu, E-mail: tsli@gwu.edu

Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p{sub B} histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage ordermore » parameter (H-COP) which we developed for driving FFS, through conducting the p{sub B} histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.« less

Kinetic studies of methane-ethane mixed gas hydrates by neutron diffraction and Raman spectroscopy.

PubMed

Murshed, M Mangir; Kuhs, Werner F

2009-04-16

In situ formations of CH(4)-C(2)H(6) mixed gas hydrates were made using high flux neutron diffraction at 270 K and 5 MPa. For this purpose, a feed gas composition of CH(4) and C(2)H(6) (95 mol% CH(4)) was employed. The rates of transformation of spherical grains of deuterated ice Ih into hydrates were measured by time-resolved neutron powder diffraction on D20 at ILL, Grenoble. Phase fractions of the crystalline constituents were obtained from Rietveld refinements. A concomitant formation of structure type I (sI) and structure type II (sII) hydrates were observed soon after the gas pressure was applied. The initial fast formation of sII hydrate reached its maximum volume and started declining very slowly. The formation of sI hydrate followed a sigmoid growth kinetics that slowed down due to diffusion limitation. This observation has been interpreted in terms of a kinetically favored nucleation of the sII hydrate along with a slow transformation into sI. Both powder diffraction and Raman spectroscopic results suggest that a C(2)H(6)-rich sII hydrate was formed at the early part of the clathration, which slowly decreased to approximately 3% after a reaction of 158 days as confirmed by synchrotron XRD. The final persistence of a small portion of sII hydrate points to a miscibility gap between CH(4)-rich sI and C(2)H(6)-rich sII hydrates.

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.

Discussion of "Hydrates off Brazil" by Rogerio L. Fontana and Alexandre Mussumeci

USGS Publications Warehouse

Dillon, William P.

1994-01-01

The paper "Hydrates Offshore Brazil" by Rogerio L. Fontana and Alexandre Mussumeci presents some important information that strongly indicates the presence of gas hydrates on the southern Brazilian continental margin. However, the acoustic compressional wave velocity structure reported for the Brazilian margin sediments is highly unusual and quite puzzling. We will discuss a possible explanation related to the presence of gas hydrate and free gas in sediements.

Discussion of the paper 'Hydrates offshore Brazil'

USGS Publications Warehouse

Dillon, William P.

1994-01-01

The paper “Hydrates Offshore Brazil” by Rogerio L. Fontana and Alexandre Mussumeci presents some important information that strongly indicates the presence of gas hydrates on the southern Brazilian continental margin. However, the acoustic compressional wave velocity structure reported for the Brazilian margin sediments is highly unusual and quite puzzling. We will discuss a possible explanation related to the presence of gas hydrate and free gas in the sediments.

Development of a DNA-liposome complex for gene delivery applications.

PubMed

Rasoulianboroujeni, M; Kupgan, G; Moghadam, F; Tahriri, M; Boughdachi, A; Khoshkenar, P; Ambrose, J J; Kiaie, N; Vashaee, D; Ramsey, J D; Tayebi, L

2017-06-01

The association structures formed by cationic liposomes and DNA (Deoxyribonucleic acid)-liposome have been effectively utilized as gene carriers in transfection assays. In this research study, cationic liposomes were prepared using a modified lipid film hydration method consisting of a lyophilization step for gene delivery applications. The obtained results demonstrated that the mean particle size had no significant change while the polydispersity (PDI) increased after lyophilization. The mean particle size slightly reduced after lyophilization (520±12nm to 464±25nm) while the PDI increased after lyophilization (0.094±0.017 to 0.220±0.004). In addition. The mean particle size of vesicles increases when DNA is incorporated to the liposomes (673±27nm). According to the Scanning Electron Microscopy (SEM) and transmission electron microscopy (TEM) images, the spherical shape of liposomes confirmed their successful preservation and reconstitution from the powder. It was found that liposomal formulation has enhanced transfection considerably compared to the naked DNA as negative control. Finally, liposomal formulation in this research had a better function than Lipofectamine® 2000 as a commercialized product because the cellular activity (cellular protein) was higher in the prepared lipoplex than Lipofectamine® 2000. Copyright © 2017 Elsevier B.V. All rights reserved.

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 high intensity ultrasound on the mesostructure of hydrated zirconia

NASA Astrophysics Data System (ADS)

Kopitsa, G. P.; Baranchikov, A. E.; Ivanova, O. S.; Yapryntsev, A. D.; Grigoriev, S. V.; Pranzas, P. Klaus; Ivanov, V. K.

2012-02-01

We report structural changes in amorphous hydrated zirconia caused by high intensity ultrasonic treatment studied by means of small-angle neutron scattering (SANS) and X-ray diffraction (XRD). It was established that sonication affects the mesostructure of ZrO2×xH2O gels (i.e. decreases their homogeneity, increases surface fractal dimension and the size of monomer particles). Ultrasound induced structural changes in hydrated zirconia governs its thermal behaviour, namely decreases the rate of tetragonal to monoclinic zirconia phase transition.

Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate.

PubMed Central

Resat, H; Mezei, M

1996-01-01

The grand canonical ensemble Monte Carlo molecular simulation method is used to investigate hydration patterns in the crystal hydrate structure of the dCpG/proflavine intercalated complex. The objective of this study is to show by example that the recently advocated grand canonical ensemble simulation is a computationally efficient method for determining the positions of the hydrating water molecules in protein and nucleic acid structures. A detailed molecular simulation convergence analysis and an analogous comparison of the theoretical results with experiments clearly show that the grand ensemble simulations can be far more advantageous than the comparable canonical ensemble simulations. Images FIGURE 5 FIGURE 7 PMID:8873992

Study of Electron Ionization and Fragmentation of Non-hydrated and Hydrated Tetrahydrofuran Clusters

NASA Astrophysics Data System (ADS)

Neustetter, Michael; Mahmoodi-Darian, Masoomeh; Denifl, Stephan

2017-05-01

Mass spectroscopic investigations on tetrahydrofuran (THF, C4H8O), a common model molecule of the DNA-backbone, have been carried out. We irradiated isolated THF and (hydrated) THF clusters with low energy electrons (electron energy 70 eV) in order to study electron ionization and ionic fragmentation. For elucidation of fragmentation pathways, deuterated TDF (C4D8O) was investigated as well. One major observation is that the cluster environment shows overall a protective behavior on THF. However, also new fragmentation channels open in the cluster. In this context, we were able to solve a discrepancy in the literature about the fragment ion peak at mass 55 u in the electron ionization mass spectrum of THF. We ascribe this ion yield to the fragmentation of ionized THF clusters.

Failure of cement hydrates: freeze-thaw and fracture

NASA Astrophysics Data System (ADS)

Ioannidou, Katerina; Del Gado, Emanuela; Ulm, Franz-Josef; Pellenq, Roland

Mechanical and viscoelastic behavior of concrete crucially depends on cement hydrates, the ``glue'' of cement. Even more than the atomistic structure, the mesoscale amorphous texture of cement hydrates over hundreds of nanometers plays a crucial role for material properties. We use simulations that combine information of the nano-scale building units of cement hydrates and on their effective interactions, obtained from atomistic simulations and experiments, into a statistical physics framework for aggregating nanoparticles.Our mesoscale model was able to reconcile different experimental results ranging from small-angle neutron scattering, SEM, adsorption/desorption of N2, and water to nanoindentation and gain the new fundamental insights into the microscopic origin of the properties measured. Our results suggest that heterogeneities developed during the early stages of hydration persist in the structure of C-S-H, impacting the rheological and mechanical performance of the hardened cement paste. In this talk I discuss recent investigation on failure mechanism at the mesoscale of hardened cement paste such as freeze-thaw and fracture. Using correlations between local volume fractions and local stress we provide a link between structural and mechanical heterogeneities during the failure mechanisms.

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

PubMed

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

2010-01-11

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

Substituent effect on the thermodynamic solubility of structural analogs: relative contribution of crystal packing and hydration.

PubMed

Ozaki, Shunsuke; Nakagawa, Yoshiaki; Shirai, Osamu; Kano, Kenji

2014-11-01

Thermodynamic analysis of the solubility of benzoylphenylurea (BPU) derivatives was conducted to investigate the relative importance of crystal packing and hydration for improving solubility with minor structural modification. The contribution of crystal packing to solubility was evaluated from the change in Gibbs energy on the transition from the crystalline to liquid state. Hydration Gibbs energy was estimated using a linear free-energy relationship between octanol-water partition coefficients and gas-water partition coefficients. The established solubility model satisfactorily explained the relative thermodynamic solubility of the model compounds and revealed that crystal packing and hydration equally controlled solubility of the structural analogs. All hydrophobic substituents were undesirable for solubility in terms of hydration, as expected. On the other hand, some of these hydrophobic substituents destabilized crystal packing and improved the solubility of the BPU derivatives when their impact on crystal packing exceeded their negative influence on hydration. The replacement of a single substituent could cause more than a 10-fold enhancement in thermodynamic solubility; this degree of improvement was comparable to that generally achieved by amorphous formulations. Detailed analysis of thermodynamic solubility will allow us to better understand the true substituent effect and design drug-like candidates efficiently. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Investigation of the effect of hydration on dermal collagen in ex vivo human skin tissue using second harmonic generation microscopy

NASA Astrophysics Data System (ADS)

Samatham, Ravikant; Wang, Nicholas K.; Jacques, Steven L.

2016-02-01

Effect of hydration on the dermal collagen structure in human skin was investigated using second harmonic generation microscopy. Dog ears from the Mohs micrographic surgery department were procured for the study. Skin samples with subject aged between 58-90 years old were used in the study. Three dimensional Multiphoton (Two-photon and backward SHG) control data was acquired from the skin samples. After the control measurement, the skin tissue was either soaked in deionized water for 2 hours (Hydration) or kept at room temperature for 2 hours (Desiccation), and SHG data was acquired. The data was normalized for changes in laser power and detector gain. The collagen signal per unit volume from the dermis was calculated. The desiccated skin tissue gave higher backward SHG compared to respective control tissue, while hydration sample gave a lower backward SHG. The collagen signal decreased with increase in hydration of the dermal collagen. Hydration affected the packing of the collagen fibrils causing a change in the backward SHG signal. In this study, the use of multiphoton microscopy to study the effect of hydration on dermal structure was demonstrated in ex vivo tissue.

Hydrogen-Bonding System in Barium Nitroprusside 6.5-Hydrate

NASA Astrophysics Data System (ADS)

Navaza, A.; Chevrier, G.; Guida, J. A.

1995-01-01

The hydrogen-bond system in barium nitroprusside 6.5-hydrate, [Ba 2(H 2O) 10][Fe(CN) 5NOl 23H 2O], has been determined by neutron diffraction on monocrystals. Results show the compound to be orthorhombic, space group Cmc2 1 (36), a = 16.008(43), b = 11.550(3), c = 16.648(5) Å, V = 3078(3) Å 3, Z = 4. Refinement of the structure, using 973 observed structure factors, converged to the final RW factor of 0.058. The 2 independent barium atoms, separated 4.60 Å, share a plane of three water molecules forming dimeric tetravalent units. The nitroprusside anions deviate from the C4r ideal symmetry, but this deviation is less than that observed in other nitroprussides. The 10 crystallographically independent water molecules have been classified according to their coordination. Analysis of the H-bond strength, together with a comparison of the packing of the two known barium nitroprusside hydrates (3-hydrate and 6.5-hydrate), suggests that the water molecules labeled as W(1), W(7), W(8), and W(9) could be lost during the partial dehydration of 6.5-hydrate into 3-hydrate.

Cage Occupation of Light Hydrocarbons in Gas Hydrate Crystals

NASA Astrophysics Data System (ADS)

Kida, M.; Watanabe, M.; Konno, Y.; Yoneda, J.; Jin, Y.; Nagao, J.

2016-12-01

Naturally occurring gas hydrates in marine or permafrost environments can trap methane and heavier hydrocarbons within its host lattice structure built up with hydrogen-bonded water molecules. Naturally occurring gas hydrates have been expected as new natural gas resources. It is important to reveal the distribution of guest hydrocarbons in host hydrate framework from viewpoint of assessment of gas capacity. In this study, we assessed cage occupancies of guest hydrocarbons in host hydrate framework of synthetic and natural gas hydrates using solid-state 13C NMR technique. As synthetic samples, gas hydrates formed from gas mixtures including C1 to C5 were investigated. As a natural sample, the pore-space gas hydrate sample recovered from the eastern Nankai Trough area during the 2012 JOGMEC/JAPEX Pressure coring operation was studied. As a result, it revealed that all heavier hydrocarbons than ethane are preferentially incorporated into the larger cage cavities in hydrate frameworks. We performed this study as a part of a Japanese National hydrate research program (MH21, funded by METI).

Diamond-anvil cell observations of a new methane hydrate phase in the 100-MPa pressure range

USGS Publications Warehouse

Chou, I.-Ming; Sharma, A.; Burruss, R.C.; Hemley, R.J.; Goncharov, A.F.; Stern, L.A.; Kirby, S.H.

2001-01-01

A new high-pressure phase of methane hydrate has been identified based on its high optical relief, distinct pressure-temperature phase relations, and Raman spectra. In-situ optical observations were made in a hydrothermal diamond-anvil cell at temperatures between -40?? and 60 ??C and at pressures up to 900 MPa. Two new invariant points were located at -8.7 ??C and 99 MPa for the assemblage consisting of the new phase, structure I methane hydrate, ice Ih, and water, and at 35.3 ??C and 137 MPa for the new phase-structure I methane hydrate-water-methane vapor. Existence of the new phase is critical for understanding the phase relations among the hydrates at low to moderate pressures, and may also have important implications for understanding the hydrogen bonding in H2O and the behavior of water in the planetary bodies, such as Europa, of the outer solar system.

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

Mendoza, Oscar, E-mail: oamendoz@unal.edu.co; Giraldo, Carolina; Camargo, Sergio S.

This research evaluates the effect of sodium and potassium hydroxide on the structure and nano-mechanical properties of Calcium Silicate Hydrate (C-S-H) formed from the hydration of pure alite. Monoclinic (MIII) alite was synthesized and hydrated, using water-to-alite ratios of 0.5 and 0.6 and additions of 10% NaOH and KOH by weight of alite. Based on results of X-ray diffraction, isothermal calorimetry, thermogravimetric analysis, Nuclear Magnetic Resonance and nanoindentation, two different effects of the alkaline hydroxides on the hydration reaction of alite, both at early and later ages, can be identified: (i) a differentiated hydration process, attributed to an enhancement inmore » calcium hydroxide (CH) precipitation and a stimulation of the C-S-H nuclei; and (ii) an increase in the elastic modulus of the C-S-H aggregations, attributed to an electrostatic attraction between positive charges from the alkaline cations and negative charges from the C-S-H structure.« less

Interaction of Nanostructured Calcium Silicate Hydrate with Ibuprofen Drug Molecules: X-ray Absorption Near Edge Structure (XANES) Study at the Ca, Si and O K-edge

NASA Astrophysics Data System (ADS)

Guo, X. X.; Sham, T. K.; Zhu, Y. J.; Hu, Y. F.

2013-04-01

Mesoporous calcium silicate hydrate (CSH) nanostructure has been proven to be bioactive and biocompatible, and has a bright future in the application of bone treatment among other applications. X-ray absorption near edge structure (XANES) is a powerful tool for the study of the interactions of calcium silicate hydrates with drug molecules because it is element specific and it probes the unoccupied electronic states. Herein, we report the use of the calcium, silicon and oxygen K-edge XANES spectroscopy to identify how drug molecules interact with different groups in calcium silicate hydrate mesoporous nano-carriers with different morphologies. Significant changes are observed in XANES spectra after drug loading into the calcium silicate hydrate system, especially at the Si and O K-edge. The implications of these findings are discussed.

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.

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.

Structure of Hydrated Poly(d,l-lactic acid) Studied with X-ray Diffraction and Molecular Simulation Methods

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

Li, Xianfeng; Murthy, N. Sanjeeva; Latour, Robert A.

2012-10-10

The effect of hydration on the molecular structure of amorphous poly(D,L-lactic acid) (PDLLA) with 50:50 L-to-D ratio has been studied by combining experiments with molecular simulations. X-ray diffraction measurements revealed significant changes upon hydration in the structure functions of the copolymer. Large changes in the structure functions at 10 days of incubation coincided with the large increase in the water uptake from {approx} 1 to {approx} 40% and the formation of voids in the film. Computer modeling based on the recently developed TIGER2/TIGER3 mixed sampling scheme was used to interpret these changes by efficiently equilibrating both dry and hydrated modelsmore » of PDLLA. Realistic models of bulk amorphous PDLLA structure were generated as demonstrated by close agreement between the calculated and the experimental structure functions. These molecular simulations were used to identify the interactions between water and the polymer at the atomic level including the change of positional order between atoms in the polymer due to hydration. Changes in the partial O-O structure functions, about 95% of which were due to water-polymer interactions, were apparent in the radial distribution functions. These changes, and somewhat smaller changes in the C-C and C-O partial structure functions, clearly demonstrated the ability of the model to capture the hydrogen-bonding interactions between water and the polymer, with the probability of water forming hydrogen bonds with the carbonyl oxygen of the ester group being about 4 times higher than with its ether oxygen.« less

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.

Methane rising from the Deep: Hydrates, Bubbles, Oil Spills, and Global Warming

NASA Astrophysics Data System (ADS)

Leifer, I.; Rehder, G. J.; Solomon, E. A.; Kastner, M.; Asper, V. L.; Joye, S. B.

2011-12-01

Elevated methane concentrations in near-surface waters and the atmosphere have been reported for seepage from depths of nearly 1 km at the Gulf of Mexico hydrate observatory (MC118), suggesting that for some methane sources, deepsea methane is not trapped and can contribute to atmospheric greenhouse gas budgets. Ebullition is key with important sensitivity to the formation of hydrate skins and oil coatings, high-pressure solubility, bubble size and bubble plume processes. Bubble ROV tracking studies showed survival to near thermocline depths. Studies with a numerical bubble propagation model demonstrated that consideration of structure I hydrate skins transported most methane only to mid-water column depths. Instead, consideration of structure II hydrates, which are stable to far shallower depths and appropriate for natural gas mixtures, allows bubbles to survive to far shallower depths. Moreover, model predictions of vertical methane and alkane profiles and bubble size evolution were in better agreement with observations after consideration of structure II hydrate properties as well as an improved implementation of plume properties, such as currents. These results demonstrate the importance of correctly incorporating bubble hydrate processes in efforts to predict the impact of deepsea seepage as well as to understand the fate of bubble-transported oil and methane from deepsea pipeline leaks and well blowouts. Application to the DWH spill demonstrated the importance of deepsea processes to the fate of spilled subsurface oil. Because several of these parameters vary temporally (bubble flux, currents, temperature), sensitivity studies indicate the importance of real-time monitoring data.

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

Synthesis, crystal structure, and structural conversion of Ni molybdate hydrate NiMoO 4· nH 2O

NASA Astrophysics Data System (ADS)

Eda, Kazuo; Kato, Yasuyuki; Ohshiro, Yu; Sugitani, Takamitu; Whittingham, M. Stanley

2010-06-01

The synthesis and crystal structure of NiMoO 4· nH 2O were investigated. The hydrate crystallized in the triclinic system with space group P-1, Z=4 with unit cell parameters of a=6.7791(2) Å, b=6.8900(2) Å, c=9.2486(2) Å, α=76.681(2)°, β=83.960(2)°, γ=74.218(2)°. Its ideal chemical composition was NiMoO 4·3/4H 2O rather than NiMoO 4·1H 2O. Under hydrothermal conditions the hydrate turned directly into α-NiMoO 4 above 483 K, giving nanorods thinner than the crystallites of the mother hydrate. On the other hand, it turned into Anderson type of polyoxomolybdate via a solid-solution process in a molybdate solution at room temperature.

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.

A crystal-chemical classification of borate structures with emphasis on hydrated borates

USGS Publications Warehouse

Christ, C.L.; Clark, J.R.

1977-01-01

The rules governing formation of hydrated borate polyanions that were proposed by C.L. Christ in 1960 are critically reviewed and new rules added on the basis of recent crystal structure determinations. Principles and classifications previously published by others are also critically reviewed briefly. The fundamental building blocks from which borate polyanions can be constructed are defined on the basis of the number n of boron atoms, and the fully hydrated polyanions are illustrated. Known structures are grouped accordingly, and a shorthand notation using n and symbols ?? = triangle, T = tetrahedron is introduced so that the polyanions can be easily characterized. For example, 3:??+2T describes [B3O3(OH)5]2-. Correct structural formulas are assigned borates with known structures whereas borates of unknown structure are grouped separately. ?? 1977 Springer-Verlag.

The characteristics of gas hydrates recovered from the Mount Elbert Gas Hydrate Stratigraphic Test Well, Alaska North Slope

USGS Publications Warehouse

Lu, H.; Lorenson, T.D.; Moudrakovski, I.L.; Ripmeester, J.A.; Collett, T.S.; Hunter, R.B.; Ratcliffe, C.I.

2011-01-01

Systematic analyses have been carried out on two gas hydrate-bearing sediment core samples, HYPV4, which was preserved by CH4 gas pressurization, and HYLN7, which was preserved in liquid-nitrogen, recovered from the BPXA-DOE-USGS Mount Elbert Stratigraphic Test Well. Gas hydrate in the studied core samples was found by observation to have developed in sediment pores, and the distribution of hydrate saturation in the cores imply that gas hydrate had experienced stepwise dissociation before it was stabilized by either liquid nitrogen or pressurizing gas. The gas hydrates were determined to be structure Type I hydrate with hydration numbers of approximately 6.1 by instrumentation methods such as powder X-ray diffraction, Raman spectroscopy and solid state 13C NMR. The hydrate gas composition was predominantly methane, and isotopic analysis showed that the methane was of thermogenic origin (mean ??13C=-48.6??? and ??D=-248??? for sample HYLN7). Isotopic analysis of methane from sample HYPV4 revealed secondary hydrate formation from the pressurizing methane gas during storage. ?? 2010 Elsevier Ltd.

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 .

Temperature and pressure correlation for volume of gas hydrates with crystal structures sI and sII

NASA Astrophysics Data System (ADS)

Vinš, Václav; Jäger, Andreas; Hielscher, Sebastian; Span, Roland; Hrubý, Jan; Breitkopf, Cornelia

The temperature and pressure correlations for the volume of gas hydrates forming crystal structures sI and sII developed in previous study [Fluid Phase Equilib. 427 (2016) 268-281], focused on the modeling of pure gas hydrates relevant in CCS (carbon capture and storage), were revised and modified for the modeling of mixed hydrates in this study. A universal reference state at temperature of 273.15 K and pressure of 1 Pa is used in the new correlation. Coefficients for the thermal expansion together with the reference lattice parameter were simultaneously correlated to both the temperature data and the pressure data for the lattice parameter. A two-stage Levenberg Marquardt algorithm was employed for the parameter optimization. The pressure dependence described in terms of the bulk modulus remained unchanged compared to the original study. A constant value for the bulk modulus B0 = 10 GPa was employed for all selected hydrate formers. The new correlation is in good agreement with the experimental data over wide temperature and pressure ranges from 0 K to 293 K and from 0 to 2000 MPa, respectively. Compared to the original correlation used for the modeling of pure gas hydrates the new correlation provides significantly better agreement with the experimental data for sI hydrates. The results of the new correlation are comparable to the results of the old correlation in case of sII hydrates. In addition, the new correlation is suitable for modeling of mixed hydrates.

Insights into a hydration regulating system in Cupressus pollen grains

PubMed Central

Danti, R.; Della Rocca, G.; Calamassi, R.; Mori, B.; Mariotti Lippi, M.

2011-01-01

Background and Aims Hydration, rupture and exine opening due to the sudden and large expansion of intine are typical of taxoid-type pollen grains. A hemispheric outgrowth external to the exine was observed on Cupressus and Juniperus pollen grains before the intine swelling and exine release. However, the actual existence of this permanent or temporary structure and its precise role in pollen hydration is still being debated. The aim of this paper is to collect information on the actual presence of this peculiar outgrowth on the surface of the Cupressus pollen grain, its structure, composition and function. Methods Pollen grains of several Cupressus species were observed using various techniques and methodologies, under light and fluorescence microscopy, phase-contrast microscopy, confocal microscopy, scanning electron microscopy, and an environmental scanning electron microscope. Observations were also performed on other species with taxoid-type pollen grains. Key Results A temporary structure located just above the pore was observed on Cupressus pollen grains, as well as on other taxoid-type pollens. It is hemispheric, layered, and consists of polysaccharides and proteins. The latter are confined to its inner part. Its presence seems to regulate the entrance of water into the grains at the beginning of pollen hydration. Conclusions The presence of a temporary structure over the pore of taxoid-type pollen grains was confirmed and its structure was resolved using several stains and observation techniques. This structure plays a role in the first phases of pollen hydration. PMID:21685430

Deep-Subsurface Marine Methane Hydrate Microbial Communities: Who's There and What Are They Doing?

NASA Astrophysics Data System (ADS)

Colwell, F.; Reed, D.; Fujita, Y.; Delwiche, M.; Blackwelder, D.; Uchida, T.; Fujii, T.; Lu, H.

2001-12-01

Natural gas hydrates are crystalline deposits of freshwater and primarily methane. They are estimated to represent a potentially vast reservoir of energy. Relatively little is known regarding microbial communities surrounding deep [>100 meters below sea floor (mbsf)] hydrate-bearing sediments. Deep sediment cores were collected in zones above, within, and below the hydrate bearing strata in an accretionary prism off the coast of Japan. Microorganisms were characterized using cultivation- and non-cultivation-based microbiological techniques to better understand the role that they play in the production and distribution of methane in gas hydrates. Direct counts show cell density at 105 cells/g throughout the hydrate strata. Lipid and 16S rDNA analyses indicate that diverse bacterial and archaeal microorganisms are represented throughout the strata. Acetate and hydrogen were utilized as an energy source for methane-producing microorganisms from each sediment depth. Although the methanogenic biomarker coenzyme M was not present above the detection limit in any of the samples, cloning and characterization of amplified 16S ribosomal RNA genes indicated the presence of methanogenic microorganisms related to the Methanobacteriales and Methanococcales. In addition, archaeal clones closely related to the hyperthermophilic Pyrodictiales were detected. Analysis of eubacterial clones indicated a more diverse eubacterial community compared to the archaea, including members from the groups of cyanobacteria, proteobacteria, gram positive bacteria, and flexibacter-cytophaga-bacteriodes. This study suggests that the diversity of microbial communities associated with the presence of methane in gas hydrate-rich deep marine sediments is greater than previously estimated.

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

A composite phase diagram of structure H hydrates using Schreinemakers' geometric approach

USGS Publications Warehouse

Mehta, A.P.; Makogon, T.Y.; Burruss, R.C.; Wendlandt, R.F.; Sloan, E.D.

1996-01-01

A composite phase diagram is presented for Structure H (sH) clathrate hydrates. In this work, we derived the reactions occurring among the various phases along each four-phase (Ice/Liquid water, liquid hydrocarbon, vapor, and hydrate) equilibrium line. A powerful method (though seldom used in chemical engineering) for multicomponent equilibria developed by Schreinemakers is applied to determine the relative location of all quadruple (four-phase) lines emanating from three quintuple (five-phase) points. Experimental evidence validating the approximate phase diagram is also provided. The use of Schreinemakers' rules for the development of the phase diagram is novel for hydrates, but these rules may be extended to resolve the phase space of other more complex systems commonly encountered in chemical engineering.

Differential Scanning Calorimetric Study and Potential Model of the Binding of the Primary Water of Hydration to K-Hyaluronate

NASA Astrophysics Data System (ADS)

Whitson, K. B.; Marlowe, R. L.; Lukan, A. M.; Lee, S. A.; Anthony, L.; Rupprecht, A.

1997-11-01

DSC was performed on samples of K-hyaluronate (KHA) through a temperature range of 25-180^oC. A transition peak was observed which is due to the desorption of the primary water of hydration. The maximum position of the peak was observed to change with different scan rates. The average energy of activation, E_A, and enthalpy for desorption of the primary water of hydration was determined to be 0.62 and 0.17 eV per water molecule, respectively. Analysis of Mossbauer data(G. Albanese et al., Hyperfine Int.,) 95, 97 (1995) allowed us to determine the effective force constant, k_eff, of the water bound to KHA to be approximately 19.4 eV/nm^2. The parameters E_A, ΔH,and k_eff allow us to construct a potential model for the primary water of hydration of KHA. Comparison of these parameters with the same parameters for HA and DNA with different counterions reveal that the energy of activation is similar, as well as the enthalpy change.

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.

Direct Measurements of 3D Structure, Chemistry and Mass Density During the Induction Period of C3S Hydration

PubMed Central

Hu, Qinang; Aboustait, Mohammed; Kim, Taehwan; Ley, M. Tyler; Bullard, Jeffrey W.; Scherer, George; Hanan, Jay C.; Rose, Volker; Winarski, Robert; Gelb, Jeffrey

2017-01-01

The reasons for the start and end of the induction period of cement hydration remain topic of controversy. One long-standing hypothesis is that a thin metastable hydrate forming on the surface of cement grains significantly reduces the particle dissolution rate; the eventual disappearance of this layer re-establishes higher dissolution rates at the beginning of the acceleration period. However, the importance, or even the existence, of this metastable layer has been questioned because it cannot be directly detected in most experiments. In this work, a combined analysis using nano-tomography and nano-X-ray fluorescence makes the direct imaging of early hydration products possible. These novel X-ray imaging techniques provide quantitative measurements of 3D structure, chemical composition, and mass density of the hydration products during the induction period. This work does not observe a low density product on the surface of the particle, but does provide insights into the formation of etch pits and the subsequent hydration products that fill them. PMID:28919638

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

Mechanisms of free radical-induced damage to DNA.

PubMed

Dizdaroglu, Miral; Jaruga, Pawel

2012-04-01

Endogenous and exogenous sources cause free radical-induced DNA damage in living organisms by a variety of mechanisms. The highly reactive hydroxyl radical reacts with the heterocyclic DNA bases and the sugar moiety near or at diffusion-controlled rates. Hydrated electron and H atom also add to the heterocyclic bases. These reactions lead to adduct radicals, further reactions of which yield numerous products. These include DNA base and sugar products, single- and double-strand breaks, 8,5'-cyclopurine-2'-deoxynucleosides, tandem lesions, clustered sites and DNA-protein cross-links. Reaction conditions and the presence or absence of oxygen profoundly affect the types and yields of the products. There is mounting evidence for an important role of free radical-induced DNA damage in the etiology of numerous diseases including cancer. Further understanding of mechanisms of free radical-induced DNA damage, and cellular repair and biological consequences of DNA damage products will be of outmost importance for disease prevention and treatment.

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.

Uniform manganese hexacyanoferrate hydrate nanocubes featuring superior performance for low-cost supercapacitors and nonenzymatic electrochemical sensors.

PubMed

Pang, Huan; Zhang, Yizhou; Cheng, Tao; Lai, Wen-Yong; Huang, Wei

2015-10-14

Uniform manganese hexacyanoferrate hydrate nanocubes are prepared via a simple chemical precipitation method at room temperature. Due to both micro/mesopores of the Prussian blue analogue and nanocubic structures, the manganese hexacyanoferrate hydrate nanocubes allow the efficient charge transfer and mass transport for electrolyte solution and chemical species. Thus, the manganese hexacyanoferrate hydrate nanocube electrode shows a good rate capability and cycling stability for electrochemical capacitors. Furthermore, electrodes modified with manganese hexacyanoferrate hydrate nanocubes demonstrate a sensitive electrochemical response to hydrogen peroxide (H2O2) in buffer solutions with a high selectivity.

On the origin of the decrease in stability of the DNA hairpin d(GCGAAGC) on complexation with aromatic drugs.

PubMed

Kostjukov, V V; Lantushenko, A O; Davies, D B; Evstigneev, M P

2007-08-01

Molecular dynamics simulations of drug-DNA complexes have been carried out in order to explain the experimentally observed decrease in thermal stability of the DNA hairpin d(GCGAAGC) on binding the aromatic drug molecules, daunomycin, ethidium bromide, novantrone and proflavine. This complexation behavior is in contrast to the stabilizing effect of the same aromatic drug molecules on DNA duplexes. Analysis of the energy parameters and the hydration properties of the complexes shows that the main factor correlating with the decrease in melting temperatures of the drug-hairpin complexes is the number of water bridges, with a reduction of at least 40% on ligand binding.

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

PubMed

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

2017-10-13

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

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.

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

PubMed

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

2016-05-01

The overall stability of DNA molecules globally depends on base-pair stacking, base-pairing, polyelectrolyte effect and hydration contributions. In order to understand how they carry out their biological roles, it is essential to have a complete physical description of how the folding of nucleic acids takes place, including their ion and water binding. To investigate the role of ions, water and protons in the stability and melting behavior of DNA structures, we report here an experimental approach i.e., mainly differential scanning calorimetry (DSC), to determine linking numbers: the differential binding of ions (Δnion), water (ΔnW) and protons (ΔnH(+)) in the helix-coil transition of DNA molecules. We use DSC and temperature-dependent UV spectroscopic techniques to measure the differential binding of ions, water, and protons for the unfolding of a variety of DNA molecules: salmon testes DNA (ST-DNA), one dodecamer, one undecamer and one decamer duplexes, nine hairpin loops, and two triplexes. These methods can be applied to any conformational transition of a biomolecule. We determined complete thermodynamic profiles, including all three linking numbers, for the unfolding of each molecule. The favorable folding of a DNA helix results from a favorable enthalpy-unfavorable entropy compensation. DSC thermograms and UV melts as a function of salt, osmolyte and proton concentrations yielded releases of ions and water. Therefore, the favorable folding of each DNA molecule results from the formation of base-pair stacks and uptake of both counterions and water molecules. In addition, the triplex with C(+)GC base triplets yielded an uptake of protons. Furthermore, the folding of a DNA duplex is accompanied by a lower uptake of ions and a similar uptake of four water molecules as the DNA helix gets shorter. In addition, the oligomer duplexes and hairpin thermodynamic data suggest ion and water binding depends on the DNA sequence rather than DNA composition. Copyright © 2015. Published by Elsevier B.V.

The Exchange Reaction Between Methane Hydrate and Carbon Dioxide: An Oceanic Feasibility Test

NASA Astrophysics Data System (ADS)

Dunk, R. M.; Brewer, P. G.; Peltzer, E. T.; Walz, P. M.; Hester, K. C.; Sloan, E. D.

2006-12-01

The conversion of CH4 hydrate to CO2 hydrate offers, in principle, a way of sequestering CO2, with the additional recovery of CH4 gas as an energy source. We report results from the first in-situ oceanic experiment on this reaction, carried out in August 2006 at the massive thermogenic hydrate mounds in 850 m water depth, Barkley Canyon, offshore from Vancouver Island (48° 18.642' N, 126° 3.903' W), using MBARI's ROV Tiburon deployed from the R/V Western Flyer. Two small cores (10 cm length, 4 cm diameter) of white hydrate were collected from exposed outcrops using an ROV operated tool and hydraulically ejected into a glass walled, closed top, reaction chamber. Approximately 2 L of liquid CO2 were dispensed into the chamber, and the chamber transferred to an aluminium base plate to seal the system. Under ambient conditions (P = 870 dbar, T = 4.0 °C, S = 34.2), the densities of natural gas hydrate and liquid CO2 are closely matched and less than that of seawater, where the hydrate cores floated at the top of the chamber fully immersed within the buoyant liquid CO2. Over the following ~48 hours, the system was inspected periodically with the ROV HDTV camera prior to examination with the sea-going laser Raman spectrometer, DORISS II. For this, the chamber was transferred to a Precision Underwater Positioner (PUP) that enabled focusing of the laser beam with sub- mm precision. Our choice of where to focus the laser was based upon the need to explore all phases the cored natural gas hydrate, liquid CO2, any created CO2 hydrate, and any liberated CH4 gas. The natural gas hydrate was composed primarily of CH4, with minor amounts of C2H6 and C3H8, indicating the presence of Structure II hydrate. To date, laboratory experiments have focused on the reaction between pure Structure I CH4 hydrate and CO2 vapour, where the difference in free energy between the CH4 and CO2 hydrate states provides a thermodynamic argument in favour of conversion. However for a Structure II hydrate with a complex guest gas composition immersed in liquid CO2 there are multiple pathways for the reaction to proceed. If the hydrate cage occupancy is 100% then we suspect on thermodynamic grounds that the reaction may proceed slowly; nevertheless if cage occupancy is <100%, and/or a mixture of Structure I and II is present, then substitution could occur rapidly. In addition, dissolution of the natural gas hydrate in the unsaturated liquid CO2 will liberate water molecules that are then available to form CO2 hydrate. Obviously, grain size and porosity (surface area) will have profound effects on reaction rate and extent. We also note that the solubility of CH4 in CO2 is significant, and we may not expect liberation of a free CH4 gas phase until the saturation condition has been met. Given the complexity of this system, the only way to know what will occur is to do the experiment. Indeed, spectra were obtained of a commingled CO2 and CH4 hydrate. The CO2 fermi-diad peaks in the hydrate phase are distinguishable from the liquid, and are shifted to lower wavenumbers by ~~3 cm-1. We also observed the presence of dissolved CH4 within the liquid CO2, and free CH4 gas in a small but visually identifiable bubble layer at the top of the chamber. The initial success of this pilot study bodes well for future investigations both in the laboratory and in ROV based experiments.

Superposition of two tRNA{sup Ser} acceptor stem crystal structures: Comparison of structure, ligands and hydration

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

Eichert, Andre; Fuerste, Jens P.; Ulrich, Alexander

2010-05-07

We solved the X-ray structures of two Escherichia coli tRNA{sup Ser} acceptor stem microhelices. As both tRNAs are aminoacylated by the same seryl-tRNA-synthetase, we performed a comparative structure analysis of both duplexes to investigate the helical conformation, the hydration patterns and magnesium binding sites. It is well accepted, that the hydration of RNA plays an important role in RNA-protein interactions and that the extensive solvent content of the minor groove has a special function in RNA. The detailed comparison of both tRNA{sup Ser} microhelices provides insights into the structural arrangement of the isoacceptor tRNA aminoacyl stems with respect to themore » surrounding water molecules and may eventually help us to understand their biological function at atomic resolution.« less

Determination of the hydrate structure of an isolated alcoholic OH in hydrophobic medium by infrared and near-infrared spectroscopy.

PubMed

Iwamoto, Reikichi; Kusanagi, Hiroshi

2009-05-07

This paper reports the structure of the hydrate complex of an isolated alcoholic OH, produced in a small amount in hydrophobic solution in heptane. The structure was determined from the changes, caused by hydration, in the infrared and near-infrared spectra of 2-nonanol in the solution. The changes were exhibited in the "difference" spectrum, in which the spectrum of the solution before hydration was subtracted from that after hydration. The difference spectrum showed a "plus" or "minus" peak at the frequency of the stretching band of a free OH, depending on whether the concentration was below or above about 2%(v/v), respectively. The plus peak appears because the OH stretching band of the isolated OH that acts as an acceptor does not change in frequency but significantly increases in intensity, in agreement with theoretical calculations. In contrast, the stretching band of an isolated OH that acts as a donor shifts downward. This shift decreases the intensity at the stretching frequency of a free OH, giving rise to a minus peak at the frequency in the difference spectrum. It was concluded that an isolated OH is hydrated in the manner as HO...HOH and OH...OH(2) at a concentration below and above about 2%, respectively, in the hydrophobic solution of 2-nonanol.

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

From Black Hole to Hydrate Hole: Gas hydrates, authigenic carbonates and vent biota as indicators of fluid migration at pockmark sites of the Northern Congo Fan

NASA Astrophysics Data System (ADS)

Kasten, S.; Schneider, R.; Spiess, V.; Cruise Participants Of M56b

2003-04-01

A recent high-resolution seismic, echosounder and video survey combined with detailed geological and geochemical sampling of pockmark sites on the Northern Congo Fan was carried out with RV Meteor in November/December 2002 in the frame of the project "CONGO" (BMBF/BEO "Geotechnologien"). These investigations revealed the extensive occurrence of surface and sub-surface gas hydrates as well as characteristic features of fluid venting such as clams (Calyptogena), tube worms (Pogonophera) and huge amounts of authigenic carbonates. In a first approach the patchyness in the occurrence of these features was mapped in relation to pockmark structure and seismic reflectors. Detailed sampling of three pockmarks by gravity corer showed that gas hydrates are present at and close to the sediment surface and often occur as several distinct layers and/or veins intercalated with hemipelagic muds. The depth of the upper boundary of these hydrate-bearing sediments increases from the center towards the edge of the pockmark structures. Pore water concentration profiles of sulfate and methane document the process of anaerobic methane oxidation above the hydrate-bearing layers. For those cores which contained several gas hydrate layers preliminary pore water profiles suggest the occurrence of more than one zone of anaerobic methane oxidation. Authigenic carbonates are found in high abundance, irregularly distributed within the pockmarks close to the sediment surface. These carbonates occur in a wide variety with respect to size, shape, structure and mineralogy. Their formation is associated with high amounts of bicarbonate released by the process of anaerobic methane oxidation. In the gravity cores authigenic carbonates are always present above hydrate-bearing sections. However, the quantities and characteristics of these authigenic minerals in relation to venting and microbial activity as well as to gas hydrate dissociation are not clear yet. Unraveling this relationship will be a major target of further investigation. By means of detailed studies of the sedimentary solid-phase, authigenic carbonates, clam layers and molecular biomarkers we will also try to reconstruct the history of venting and the dynamics of gas hydrate formation and decomposition in the Northern Congo fan area.

[Progress in Raman spectroscopic measurement of methane hydrate].

PubMed

Xu, Feng; Zhu, Li-hua; Wu, Qiang; Xu, Long-jun

2009-09-01

Complex thermodynamics and kinetics problems are involved in the methane hydrate formation and decomposition, and these problems are crucial to understanding the mechanisms of hydrate formation and hydrate decomposition. However, it was difficult to accurately obtain such information due to the difficulty of measurement since methane hydrate is only stable under low temperature and high pressure condition, and until recent years, methane hydrate has been measured in situ using Raman spectroscopy. Raman spectroscopy, a non-destructive and non-invasive technique, is used to study vibrational modes of molecules. Studies of methane hydrate using Raman spectroscopy have been developed over the last decade. The Raman spectra of CH4 in vapor phase and in hydrate phase are presented in this paper. The progress in the research on methane hydrate formation thermodynamics, formation kinetics, decomposition kinetics and decomposition mechanism based on Raman spectroscopic measurements in the laboratory and deep sea are reviewed. Formation thermodynamic studies, including in situ observation of formation condition of methane hydrate, analysis of structure, and determination of hydrate cage occupancy and hydration numbers by using Raman spectroscopy, are emphasized. In the aspect of formation kinetics, research on variation in hydrate cage amount and methane concentration in water during the growth of hydrate using Raman spectroscopy is also introduced. For the methane hydrate decomposition, the investigation associated with decomposition mechanism, the mutative law of cage occupancy ratio and the formulation of decomposition rate in porous media are described. The important aspects for future hydrate research based on Raman spectroscopy are discussed.

Interaction of Simple Ions with Water: Theoretical Models for the Study of Ion Hydration

ERIC Educational Resources Information Center

Gancheff, Jorge S.; Kremer, Carlos; Ventura, Oscar N.

2009-01-01

A computational experiment aimed to create and systematically analyze models of simple cation hydrates is presented. The changes in the structure (bond distances and angles) and the electronic density distribution of the solvent and the thermodynamic parameters of the hydration process are calculated and compared with the experimental data. The…

Microstructure, Porosity and Mechanical Property Relationships of Calcium-Silicate-Hydrate

DTIC Science & Technology

1991-02-15

feasibility of producing S ,,zeolite-cement composites . calcium silicate hydrate (C-S-H) structure, NAS NMR, C3S, pH, zeolites, aluminosilicate hydrate...3 S pH- Composition Plots......................................... 6 X-ray Diffraction...6 The System CaO-A1203-SiO 2 -H2 0................................. 8 pH- Composition Plots......................................... 8 MASNMR

Water cavities of sH clathrate hydrate stabilized by molecular hydrogen.

PubMed

Strobel, Timothy A; Koh, Carolyn A; Sloan, E Dendy

2008-02-21

X-ray diffraction and Raman spectroscopic measurements confirm that molecular hydrogen can be contained within the small water cavities of a binary sH clathrate hydrate using large guest molecules that stabilize the large cavity. The potential increase in hydrogen storage could be more than 40% when compared with binary sII hydrates. This work demonstrates the stabilization of hydrogen in a hydrate structure previously unknown for encapsulating molecular hydrogen, indicating the potential for other inclusion compound materials with even greater hydrogen storage capabilities.

Sebum and Hydration Levels in Specific Regions of Human Face Significantly Predict the Nature and Diversity of Facial Skin Microbiome

PubMed Central

Mukherjee, Souvik; Mitra, Rupak; Maitra, Arindam; Gupta, Satyaranjan; Kumaran, Srikala; Chakrabortty, Amit; Majumder, Partha P.

2016-01-01

The skin microbiome varies across individuals. The causes of these variations are inadequately understood. We tested the hypothesis that inter-individual variation in facial skin microbiome can be significantly explained by variation in sebum and hydration levels in specific facial regions of humans. We measured sebum and hydration from forehead and cheek regions of healthy female volunteers (n = 30). Metagenomic DNA from skin swabs were sequenced for V3-V5 regions of 16S rRNA gene. Altogether, 34 phyla were identified; predominantly Actinobacteria (66.3%), Firmicutes (17.7%), Proteobacteria (13.1%) and Bacteroidetes (1.4%). About 1000 genera were identified; predominantly Propionibacterium (58.6%), Staphylococcus (8.6%), Streptococcus (4.0%), Corynebacterium (3.6%) and Paracoccus (3.3%). A subset (n = 24) of individuals were sampled two months later. Stepwise multiple regression analysis showed that cheek sebum level was the most significant predictor of microbiome composition and diversity followed by forehead hydration level; forehead sebum and cheek hydration levels were not. With increase in cheek sebum, the prevalence of Actinobacteria (p = 0.001)/Propionibacterium (p = 0.002) increased, whereas microbiome diversity decreased (Shannon Index, p = 0.032); this was opposite for other phyla/genera. These trends were reversed for forehead hydration levels. Therefore, the nature and diversity of facial skin microbiome is jointly determined by site-specific lipid and water levels in the stratum corneum. PMID:27786295

Sebum and Hydration Levels in Specific Regions of Human Face Significantly Predict the Nature and Diversity of Facial Skin Microbiome.

PubMed

Mukherjee, Souvik; Mitra, Rupak; Maitra, Arindam; Gupta, Satyaranjan; Kumaran, Srikala; Chakrabortty, Amit; Majumder, Partha P

2016-10-27

The skin microbiome varies across individuals. The causes of these variations are inadequately understood. We tested the hypothesis that inter-individual variation in facial skin microbiome can be significantly explained by variation in sebum and hydration levels in specific facial regions of humans. We measured sebum and hydration from forehead and cheek regions of healthy female volunteers (n = 30). Metagenomic DNA from skin swabs were sequenced for V3-V5 regions of 16S rRNA gene. Altogether, 34 phyla were identified; predominantly Actinobacteria (66.3%), Firmicutes (17.7%), Proteobacteria (13.1%) and Bacteroidetes (1.4%). About 1000 genera were identified; predominantly Propionibacterium (58.6%), Staphylococcus (8.6%), Streptococcus (4.0%), Corynebacterium (3.6%) and Paracoccus (3.3%). A subset (n = 24) of individuals were sampled two months later. Stepwise multiple regression analysis showed that cheek sebum level was the most significant predictor of microbiome composition and diversity followed by forehead hydration level; forehead sebum and cheek hydration levels were not. With increase in cheek sebum, the prevalence of Actinobacteria (p = 0.001)/Propionibacterium (p = 0.002) increased, whereas microbiome diversity decreased (Shannon Index, p = 0.032); this was opposite for other phyla/genera. These trends were reversed for forehead hydration levels. Therefore, the nature and diversity of facial skin microbiome is jointly determined by site-specific lipid and water levels in the stratum corneum.

Clathrate type 2 hydrate formation in vacuo under astrophysical conditions

NASA Technical Reports Server (NTRS)

Blake, D. F.; Allamandola, L. J.; Sandford, S. A.; Freund, F.

1991-01-01

The properties of clathrate hydrates were used to explain the complex and poorly understood physical processes taking place within cometary nuclei and other icy solar system bodies. Most of all the experiments previously conducted used starting compositions which would yield clathrate types I hydrates. The main criterion for type I vs. type II clathrate hydrate formation is the size of the guest molecule. The stoichiometry of the two structure types is also quite different. In addition, the larger molecules which would form type II clathrate hydrates typically have lower vapor pressures. The result of these considerations is that at temperatures where we identified clathrate formation (120-130 K), it is more likely that type II clathrate hydrates will form. We also formed clathrate II hydrates of methanol by direct vapor deposition in the temperature range 125-135 K.

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

Structural characterization and cytotoxicity studies of different forms of a combretastatin A4 analogue

NASA Astrophysics Data System (ADS)

de Figueiredo, Laysa P.; Ibiapino, Amanda L.; do Amaral, Daniel N.; Ferraz, Letícia S.; Rodrigues, Tiago; Barreiro, Eliezer J.; Lima, Lídia M.; Ferreira, Fabio F.

2017-11-01

It is well known that combretastatin A4 (CA-4), which is a natural stilbene isolated from Combretum caffrum, is used to inhibit angiogenesis. However, depending on the dose administered to the patient, it can cause some side-effects. Herein, we present the synthesis and structural characterization of a novel N-acylhydrazone derivative - LASSBio-1735 - a CA-4 analogue. LASSBio-1735 has displayed in vitro antiproliferative activity against HL-60 (human leukemia), SF-295 (human glioblastoma), MDA-MB435 (melanoma) and HCT-8 (ileocecal adenocarcinoma) tumor cells. We found different hydration levels in two batches of the as-synthesized compound. As a consequence, we could successfully determine the crystal structures - by using X-ray powder diffraction data and a simulated annealing procedure - of the anhydrous and hydrated forms. The effects on cell viability of anhydrous and hydrated forms of LASSBio-1735 were comparatively evaluated in different tumor cell lines, and the hydrated form exhibited higher cytotoxicity in human leukemia K562 cells. These findings lead us to perform a quantitative phase analysis on one of the samples and may shed some light on the search for possible new solvates and/or hydrates.

Influence of Carbon Nanotubes on the Structure Formation of Cement Matrix

NASA Astrophysics Data System (ADS)

Petrunin, S.; Vaganov, V.; Reshetniak, V.; Zakrevskaya, L.

2015-11-01

The potential of application of CNTs as a reinforcing agent in cement composites is governed by their unique mechanical and electronic properties. The analysis of concrete strength changes under CNTs introduction shows non-uniformity and sometimes inconsistency of results. Due to the fact that CNTs influence the hydration kinetics, structure and phase composition of concrete, an idea concerning the importance of interaction between the surface of CNTs and hydrate ions formed by the dissolution of the clinker phases has been suggested. In this paper, the theoretical and experimental study of interaction between hydrate ions and CNTs surface is discussed. Reference nanotubes and nanotubes functionalized by carboxylic groups are used in this research. Phase composition was determined by X-Ray analysis according to the Rietveld method. It was found that the presence of oxygen-containing functional groups on CNTs surface leads to intensification of the hydration process and increase in concentration of C-S-H gel from 65.9% to 74.4%. Special attention is usually paid to interactions between Ca2+ ions and CNTs, because the hardening rate and structure of cement stone are determined by principle of Ca2+ localization in the solution. In this paper the possible binding mechanisms are discussed. Based on the experimental results, the hypothesis regarding the formation of cement composite structure for different CNTs surface functionalizations is considered. According to this hypothesis, the CNTs act as the centers of crystallization for hydration products contributing to the acceleration of hydration, increase of the concentration of C-S-H gel and strength improvement of CNTs based composites.

Structure and interactions in biomaterials based on membrane-biopolymer self-assembly

NASA Astrophysics Data System (ADS)

Koltover, Ilya

Physical and chemical properties of artificial pure lipid membranes have been extensively studied during the last two decades and are relatively well understood. However, most real membrane systems of biological and biotechnological importance incorporate macromolecules either embedded into the membranes or absorbed onto their surfaces. We have investigated three classes of self-assembled membrane-biopolymer biomaterials: (i) Structure, interactions and stability of the two-dimensional crystals of the integral membrane protein bacteriorhodopsin (bR). We have conducted a synchrotron x-ray diffraction study of oriented bR multilayers. The important findings were as follows: (1) the protein 2D lattice exhibited diffraction patterns characteristic of a 2D solid with power-law decay of in-plane positional correlations, which allowed to measure the elastic constants of protein crystal; (2) The crystal melting temperature was a function of the multilayer hydration, reflecting the effect of inter-membrane repulsion on the stability of protein lattice; (3) Preparation of nearly perfect (mosaicity < 0.04° ) multilayers of fused bR membranes permitted, for the first time, application of powerful interface-sensitive x-ray scattering techniques to a membrane-protein system. (ii) Interactions between the particles chemically attached or absorbed onto the surfaces of flexible giant phospholipid vesicles. Using video-enhanced light microscopy we have observed a membrane-distortion induced attraction between the particles with the interaction range of the order of particle diameter. Fluid membranes decorated with many particles exhibited: (i) a finite-sized two-dimensional closed packed aggregates and (ii) a one-dimensional ring-like aggregates. (iii) Structure, stability and interactions in the cationic lipid-DNA complexes. Cationic liposomes complexed with DNA are among the most promising synthetic non-viral carriers of DNA vectors currently used in gene therapy applications. We have established that DNA complexes with cationic lipid (DOTAP) and a neutral lipid (DOPC) have a compact multilayer liquid crystalline structure ( L ca ) with DNA intercalated between the lipid bilayers in a periodic 2D smectic phase. Furthermore, a different 2D columnar phase of complexes was found in mixtures with a transfectionen-hancing lipid DOPE. This structure ( HcII ) derived from synchrotron x-ray diffraction consists of DNA coated by cationic lipid monolayers and arranged on a two-dimensional hexagonal lattice. Optical microscopy revealed that the L ca complexes bind stably to anionic vesicles (models of cellular membranes), whereas the more transfectant HcII complexes are unstable, rapidly fusing and releasing DNA upon adhering to anionic vesicles.

Phase transitions in mixed gas hydrates: experimental observations versus calculated data.

PubMed

Schicks, Judith M; Naumann, Rudolf; Erzinger, Jörg; Hester, Keith C; Koh, Carolyn A; Sloan, E Dendy

2006-06-15

This paper presents the phase behavior of multicomponent gas hydrate systems formed from primarily methane with small amounts of ethane and propane. Experimental conditions were typically in a pressure range between 1 and 6 MPa, and the temperature range was between 260 and 290 K. These multicomponent systems have been investigated using a variety of techniques including microscopic observations, Raman spectroscopy, and X-ray diffraction. These techniques, used in combination, allowed for measurement of the hydrate structure and composition, while observing the morphology of the hydrate crystals measured. The hydrate formed immediately below the three-phase line (V-L --> V-L-H) and contained crystals that were both light and dark in appearance. The light crystals, which visually were a single solid phase, showed a spectroscopic indication for the presence of occluded free gas in the hydrate. In contrast, the dark crystals were measured to be structure II (sII) without the presence of these occluded phases. Along with hydrate measurements near the decomposition line, an unexpected transformation process was visually observed at P-T-conditions in the stability field of the hydrates. Larger crystallites transformed into a foamy solid upon cooling over this transition line (between 5 and 10 K below the decomposition temperature). Below the transition line, a mixture of sI and sII was detected. This is the first time that these multicomponent systems have been investigated at these pressure and temperature conditions using both visual and spectroscopic techniques. These techniques enabled us to observe and measure the unexpected transformation process showing coexistence of different gas hydrate phases.

DNA adsorption onto glass surfaces

NASA Astrophysics Data System (ADS)

Carlson, Krista Lynn

Streaming potential measurements were performed on microspheres of silica, lime silicate (SLS) and calcium aluminate (CA) glasses containing silica and iron oxide (CASi and CAFe). The silicate based glasses exhibited acidic surfaces with isoelectric points (IEP) around a pH of 3 while the calcium aluminates displayed more basic surfaces with IEP ranging from 8--9.5. The surface of the calcium aluminate microspheres containing silica reacted with the background electrolyte, altering the measured zeta potential values and inhibiting electrolyte flow past the sample at ˜ pH 4 due to formation of a solid plug. DNA adsorption experiments were performed using the microspheres and a commercially available silicate based DNA isolation filter using a known quantity of DNA suspended in a chaotropic agent free 0.35 wt% Tris(hydroxymethyl)aminomethane (Tris) buffer solution. The microspheres and commercial filter were also used to isolate DNA from macrophage cells in the presence of chaotropic agents. UV absorbance at ˜260 nm and gel electrophoresis were used to quantify the amount and size of the DNA strands that adsorbed to the microsphere surfaces. In both experiments, the 43--106 microm CAFe microspheres adsorbed the largest quantity of DNA. However, the 43--106 microm SLS microspheres isolated more DNA from the cells than the <43 microm CAFe microspheres, indicating that microsphere size contributes to isolation ability. The UV absorbance of DNA at ˜260 nm was slightly altered due to the dissolution of the calcium aluminate glasses during the adsorption process. Inductively coupled plasma-optical emission spectroscopy (ICP-OES) determined that calcium and aluminum ions leached from the CA and CAFe microsphere surfaces during these experiments. Circular dichroism (CD) spectroscopy showed that the leached ions had no effect on the conformation of the DNA, and therefore would not be expected to interfere in downstream applications such as DNA replication. The 0.35 wt% Tris solution completely inhibited the formation of the hydrated crystalline layer that develops when the calcium aluminate glassess are incubated in deionized water. A Tris concentration of 0.24 wt% allowed for the formation of both hexagonal and cubic hydrates, however they were severely distorted and present in low amounts such that they were undectable by XRD.

Types and Evolution of Gas Hydrate System along the Tectonically Active Zones of the Western Pacific: Nankai Trough vs. Eastern Margin of Japan Sea

NASA Astrophysics Data System (ADS)

Matsumoto, R.; Tomaru, H.; Takeuchi, L.; Hiruta, A.; Ishizaki, O.; Aoyama, C.; Machiyama, H.; Goto, T.

2007-12-01

A series of sea-going surveys of marine gas hydrates around Japan Islands for more than a decade has revealed characteristic and contrasting features and evolution of gas hydrate system between the Nankai subduction zone and the Joetsu Basin of Japan Sea. Gas hydrate of the Nankai trough largely occurs as pore-filling type, laterally extending in turbidites. Methane is depleted in C-13, mostly derived from microbial brake-down of organic matters. Strong and continuous BSRs occur at around 270 mbsf, corresponding to the base of gas hydrate stability (BGHS). Furthermore, double BSRs with weak reflector (BSR-2) 20-30 m below BSR appear in uplifting knolls. BSR-2 is explained as a relic BSR, which coincides with BGHS. Combination effects of uplifting of gas hydrate bearing sediments and sea-level fall are likely to have caused shoaling of BGHS and BSRs, dissociation of gas hydrate between old and new BRSs, and further accumulation of gas hydrates above BSR. Thus the recycling of methane at BGHS triggered by glacial sea level fall contributed for the development of subsurface gas hydrate deposits. Joetsu basin is located on a newly formed convergent boundary between Eurasia and Philippine Sea Plates. Well-defined circular pockmarks with ca.500 m in diameter develop on the folded and faulted Umitaka spur and Joetsu knoll in the basin. A number of circular swells and mounds, 200-500 m in diameter, have been also recognized nearby the pockmarks. Thus the Umitaka spur and perhaps Joetsu knoll are characterized by rough topography of pockmarks and mounds. Methane of plumes and gas hydrate originates in deep-seated thermogenic gases with relatively heavy carbon. 3D seismic profiles clearly depict gas chimney structures below pockmark-mound zones, and gigantic methane plumes stand on the mounds not in the pockmarks. Pockmarks are often considered as vent holes, however, those of the Joestu Basin are quite. BSRs occur at about 150 mbsr, corresponding to very high heat flow, and are widely distributed throughout the area, while no double BSRs are observed. BSRs within gas chimneys are very strong and often exhibit pull-up structure. A number of piston corers have recovered chunks of massive gas hydrate from the mounds. ROV dives observed gas hydrates exposed atop the mounds. Furthermore, electric ocean floor survey has revealed that sediments below the pockmark-mound zones were not conductive. These lines of evidence suggest that the mounds are more-or-less composed of or at least contain significant amounts of methane. Sea-level fall during the last glacial, 120 m in Japan Sea, should have caused instability of gas hydrate, in particular, those within pockmarks. Pull-up structures within the chimney seem to support the model that the mounds are gas hydrate dome and the pockmark, probably a relic hydrate mound. Glacial sea level fall should have caused massive dissociation of subsurface methane hydrate as in case of the Nankai trough. However the methane from the dissociation of massive hydrate in the chimney should escape to seawater to form a crater-like depression pockmarks. Considering active venting, gigantic plumes, inferred violent venting and perhaps floating of massive gas hydrates, gas hydrate deposits are to be formed during warmer, high-sea level periods, and episodic dissociation and massive emission of methane to ocean/atmosphere system.

Verification and recovery of thick deposits of massive gas hydrate from chimney structures, eastern margin of Japan Sea

NASA Astrophysics Data System (ADS)

Matsumoto, R.; Kakuwa, Y.; Snyder, G. T.; Tanahashi, M.; Yanagimoto, Y.; Morita, S.

2016-12-01

The initial scientific research that was carried out between 2004 and 2013 has provided us with invaluable evidence that gas hydrates occur widely on and below the sea floor down to approximately 30 mbsf within gas chimney structures in Japan Sea (Matsumoto, 2005; 2009). In 2013, METI (Ministry of Economy, Trade and Industry) launched a 3-year exploration project to assess the resource potential of shallow gas hydrates in Japan Sea. During the course of the project, Meiji University and AIST conducted: sea-going geophysical surveys with AUV, and high resolution 3D seismic and CSEM. These were followed by LWD and coring down to BSR depths, and coupled with a number of analyses and experiments. Regional mapping by MBES and SBP has confirmed 1742 gas chimneys in an area of 64,000km2 along the eastern margin of Japan Sea and around Hokkaido. Multiple LWD operations have revealed anomalous profiles such as extremely low natural gamma ray, high velocity Vp, and high resistivity Ro down to BSR depths, providing a strong indication that thick and massive gas hydrates exist throughout gas chimneys above the BSR. In several cases, conventional coring using 6-m long core liners recovered nearly 6 m long massive gas hydrates in several horizons adjacent to the anomalous LWD sites.The PCTB pressure coring system (Geotek Ltd) successfully cored 2-m long intervals of undisturbed, pressurized hydrate-bearing cores, providing valuable information about the in-situ occurrence and textural relations of hydrate and surrounding sediments. Full dissociation and slow degassing experiments of pressurized cores were conducted using onboard PCATS (Pressure core analysis and transfer system) to measure the amount of gases from hydrates. The mean volume fraction of gas hydrates in well-developed gas chimney structures is estimated to be 30 to 86 vol.% based on coupled PCATS and chloride anomaly profiles. Such an unusually high accumulation of gas hydrates in gas chimneys is assumed to have been caused by high TOC accumulation in rifted basins, followed by enhanced thermal maturation by high heat flow of young Japan Sea and, the subsequent migration of deep seated thermogenic gases as a consequence of the tectonic inversion some million years ago. This study was conducted under the commission from AIST as a part of the methane hydrate project of METI.

Unraveling halide hydration: A high dilution approach.

PubMed

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

2014-07-28

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

Hydration 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

Spectroscopic studies of the binding of Cu(II) complexes of oxicam NSAIDs to alternating G-C and homopolymeric G-C sequences

NASA Astrophysics Data System (ADS)

Chakraborty, Sreeja; Bose, Madhuparna; Sarkar, Munna

2014-03-01

Drugs belonging to the Non-steroidal anti-inflammatory (NSAID) group are not only used as anti-inflammatory, analgesic and anti-pyretic agents, but also show anti-cancer effects. Complexing them with a bioactive metal like copper, show an enhancement in their anti-cancer effects compared to the bare drugs, whose exact mechanism of action is not yet fully understood. For the first time, it was shown by our group that Cu(II)-NSAIDs can directly bind to the DNA backbone. The ability of the copper complexes of NSAIDs namely meloxicam and piroxicam to bind to the DNA backbone could be a possible molecular mechanism behind their enhanced anticancer effects. Elucidating base sequence specific interaction of Cu(II)-NSAIDs to the DNA will provide information on their possible binding sites in the genome sequence. In this work, we present how these complexes respond to differences in structure and hydration pattern of GC rich sequences. For this, binding studies of Cu(II) complexes of piroxicam [Cu(II)-(Px)2 (L)2] and meloxicam [Cu(II)-(Mx)2 (L)] with alternating GC (polydG-dC) and homopolymeric GC (polydG-polydC) sequences were carried out using a combination of spectroscopic techniques that include UV-Vis absorption, fluorescence and circular dichroism (CD) spectroscopy. The Cu(II)-NSAIDs show strong binding affinity to both polydG-dC and polydG-polydC. The role reversal of Cu(II)-meloxicam from a strong binder of polydG-dC (Kb = 11.5 × 103 M-1) to a weak binder of polydG-polydC (Kb = 5.02 × 103 M-1), while Cu(II)-piroxicam changes from a strong binder of polydG-polydC (Kb = 8.18 × 103 M-1) to a weak one of polydG-dC (Kb = 2.18 × 103 M-1), point to the sensitivity of these complexes to changes in the backbone structures/hydration. Changes in the profiles of UV absorption band and CD difference spectra, upon complex binding to polynucleotides and the results of competitive binding assay using ethidium bromide (EtBr) fluorescence indicate different binding modes in each case.

Site selection for DOE/JIP gas hydrate drilling in the northern Gulf of Mexico

USGS Publications Warehouse

Hutchinson, Deborah; Shelander, Dianna; Dai, J.; McConnell, D.; Shedd, William; Frye, Matthew; Ruppel, Carolyn D.; Boswell, R.; Jones, Emrys; Collett, Timothy S.; Rose, Kelly K.; Dugan, Brandon; Wood, Warren T.

2008-01-01

n the late spring of 2008, the Chevron-led Gulf of Mexico Gas Hydrate Joint Industry Project (JIP) expects to conduct an exploratory drilling and logging campaign to better understand gas hydrate-bearing sands in the deepwater Gulf of Mexico. The JIP Site Selection team selected three areas to test alternative geological models and geophysical interpretations supporting the existence of potential high gas hydrate saturations in reservoir-quality sands. The three sites are near existing drill holes which provide geological and geophysical constraints in Alaminos Canyon (AC) lease block 818, Green Canyon (GC) 955, and Walker Ridge (WR) 313. At the AC818 site, gas hydrate is interpreted to occur within the Oligocene Frio volcaniclastic sand at the crest of a fold that is shallow enough to be in the hydrate stability zone. Drilling at GC955 will sample a faulted, buried Pleistocene channel-levee system in an area characterized by seafloor fluid expulsion features, structural closure associated with uplifted salt, and abundant seismic evidence for upward migration of fluids and gas into the sand-rich parts of the sedimentary section. Drilling at WR313 targets ponded sheet sands and associated channel/levee deposits within a minibasin, making this a non-structural play. The potential for gas hydrate occurrence at WR313 is supported by shingled phase reversals consistent with the transition from gas-charged sand to overlying gas-hydrate saturated sand. Drilling locations have been selected at each site to 1) test geological methods and models used to infer the occurrence of gas hydrate in sand reservoirs in different settings in the northern Gulf of Mexico; 2) calibrate geophysical models used to detect gas hydrate sands, map reservoir thicknesses, and estimate the degree of gas hydrate saturation; and 3) delineate potential locations for subsequent JIP drilling and coring operations that will collect samples for comprehensive physical property, geochemical and other analyses

In-situ Micro-structural Studies of Gas Hydrate Formation in Sedimentary Matrices

NASA Astrophysics Data System (ADS)

Kuhs, Werner F.; Chaouachi, Marwen; Falenty, Andrzej; Sell, Kathleen; Schwarz, Jens-Oliver; Wolf, Martin; Enzmann, Frieder; Kersten, Michael; Haberthür, David

2015-04-01

The formation process of gas hydrates in sedimentary matrices is of crucial importance for the physical and transport properties of the resulting aggregates. This process has never been observed in-situ with sub-micron resolution. Here, we report on synchrotron-based micro-tomographic studies by which the nucleation and growth processes of gas hydrate were observed in different sedimentary matrices (natural quartz, glass beds with different surface properties, with and without admixtures of kaolinite and montmorillonite) at varying water saturation. The nucleation sites can be easily identified and the growth pattern is clearly established. In under-saturated sediments the nucleation starts at the water-gas interface and proceeds from there to form predominantly isometric single crystals of 10-20μm size. Using a newly developed synchrotron-based method we have determined the crystallite size distributions (CSD) of the gas hydrate in the sedimentary matrix confirming in a quantitative and statistically relevant manner the impressions from the tomographic reconstructions. It is noteworthy that the CSDs from synthetic hydrates are distinctly smaller than those of natural gas hydrates [1], which suggest that coarsening processes take place in the sedimentary matrix after the initial hydrate formation. Understanding the processes of formation and coarsening may eventually permit the determination of the age of gas hydrates in sedimentary matrices [2], which are largely unknown at present. Furthermore, the full micro-structural picture and its evolution will enable quantitative digital rock physics modeling to reveal poroelastic properties and in this way to support the exploration and exploitation of gas hydrate resources in the future. [1] Klapp S.A., Hemes S., Klein H., Bohrmann G., McDonald I., Kuhs W.F. Grain size measurements of natural gas hydrates. Marine Geology 2010; 274(1-4):85-94. [2] Klapp S.A., Klein H, Kuhs W.F. First determination of gas hydrate crystallite size distribution using high-energy synchrotron radiation. Geophys.Res.Letters, 2007 ; 34 : L13608, DOI:10.1029/2006GL029134

Thermodynamics of Small Alkali Metal Halide Cluster Ions: Comparison of Classical Molecular Simulations with Experiment and Quantum Chemistry

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

Vlcek, Lukas; Uhlik, Filip; Moucka, Filip

We evaluate the ability of selected classical molecular models to describe the thermodynamic and structural aspects of gas-phase hydration of alkali halide ions and the formation of small water clusters. To understand the effect of many-body interactions (polarization) and charge penetration effects on the accuracy of a force field, we perform Monte Carlo simulations with three rigid water models using different functional forms to account for these effects: (i) point charge non-polarizable SPC/E, (ii) Drude point charge polarizable SWM4- DP, and (iii) Drude Gaussian charge polarizable BK3. Model predictions are compared with experimental Gibbs free energies and enthalpies of ionmore » hydration, and with microscopic structural properties obtained from quantum DFT calculations. We find that all three models provide comparable predictions for pure water clusters and cation hydration, but differ significantly in their description of anion hydration. None of the investigated classical force fields can consistently and quantitatively reproduce the experimental gas phase hydration thermodynamics. The outcome of this study highlights the relation between the functional form that describes the effective intermolecular interactions and the accuracy of the resulting ion hydration properties.« 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

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.

Exploring the possibility to store the mixed oxygen-hydrogen cluster in clathrate hydrate in molar ratio 1:2 (O2+2H2).

PubMed

Qin, Yan; Du, Qi-Shi; Xie, Neng-Zhong; Li, Jian-Xiu; Huang, Ri-Bo

2017-05-01

An interesting possibility is explored: storing the mixture of oxygen and hydrogen in clathrate hydrate in molar ratio 1:2. The interaction energies between oxygen, hydrogen, and clathrate hydrate are calculated using high level quantum chemical methods. The useful conclusion points from this study are summarized as follows. (1) The interaction energies of oxygen-hydrogen mixed cluster are larger than the energies of pure hydrogen molecular cluster. (2) The affinity of oxygen molecules with water molecules is larger than that of the hydrogen molecules with water molecules. (3) The dimension of O 2 -2H 2 interaction structure is smaller than the dimension of CO 2 -2H 2 interaction structure. (4) The escaping energy of oxygen molecules from the hydrate cell is larger than that of the hydrogen molecules. (5) The high affinity of the oxygen molecules with both the water molecules and the hydrogen molecules may promote the stability of oxygen-hydrogen mixture in the clathrate hydrate. Therefore it is possible to store the mixed (O 2 +2H 2 ) cluster in clathrate hydrate. Copyright © 2017 Elsevier Inc. All rights reserved.

IR reflectance spectroscopy of carbon dioxide clathrate hydrates. Implications for Saturn's icy moons.

NASA Astrophysics Data System (ADS)

Oancea, A.; Grasset, O.; Le Menn, E.; Bezacier, L.; Bollengier, O.; Le Mouélic, S.; Tobie, G.

2012-04-01

A CO2 spectral band was discovered by VIMS on the Saturn's satellites Dione, Hyperion, Iapetus and Phoebe [1]. The band position on the three first satellites corresponds to CO2 trapped in a complex material, but no indication exists whether this latter is water ice or some mineral or complex organic compound [1]. On Phoebe, the CO2 spectral band is consistent with solid CO2 or CO2 molecules trapped in the small cages of a clathrate hydrate structure [2]. It is thought that clathrate hydrates could play a significant role in the chemistry of the solar nebula [3] and in the physical evolution of astrophysical objects [4]. But so far, no clathrate hydrate structure has been observed in astrophysical environments. Moreover, identification of molecules trapped in a clathrate hydrate structure is extremely difficult because of the strong IR vibration modes of the water ice matrix. In this work, experimental IR reflectance spectra for CO2 clathrate hydrates are studied on grains and films. Clathrates are synthesized in a high pressure autoclave at low temperatures. IR spectral analysis is made with a low pressure and low temperature cryostat. These experimental conditions - 80 < T < 110 K, P~10-5 bar - are relevant to icy moons' surfaces. We have observed that the IR reflectance, in the spectral region (3 - 5 μm) characterized by H2O and CO2 high absorption coefficients, is strongly dependent on physical (size, surface) and optical (n and k) properties of the samples. The impact of these parameters on the CO2 clathrate IR reflectance spectrum will be presented. A comparison between the absorption bands of CO2 clathrate hydrates obtained in our lab and CO2 absorption bands as detected by VIMS on the icy satellites of Saturn will be shown. This experimental work confirms that VIMS data are not consistent with the presence of structure I CO2 clathrate hydrates on the surface of the icy moons. Possibility of having metastable structure II still remains unsolved and will be discussed. [1] Dalton et al., Space Sci. Rev. 2010, 153 : 113-154. [2] Cruikshank D.P. et al, Icarus, 2010, 206: 561-572. [3] Mousis O. et al , Ap. J. 2009, 691: 1780-1786. [4] Choukroun M. et al, in Solar System Ices, edited by Castillo-Rogez, J. et al., 2011.

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.

Plasmid Stability in Dried Cells of the Desert Cyanobacterium Chroococcidiopsis and its Potential for GFP Imaging of Survivors on Earth and in Space

NASA Astrophysics Data System (ADS)

Billi, Daniela

2012-06-01

Two GFP-based plasmids, namely pTTQ18-GFP-pDU1mini and pDUCA7-GFP, of about 7 kbp and 15 kbp respectively, able to replicate in Chroococcidiopsis sp. CCMEE 029 and CCMEE 123, were developed. Both plasmids were maintained in Chroococcidiopsis cells after 18 months of dry storage as demonstrated by colony PCR, plasmid restriction analysis, GFP imaging and colony-forming ability under selection of dried transformants; thus suggesting that strategies employed by this cyanobacterium to stabilize dried chromosomal DNA, must have protected plasmid DNA. The suitability of pDU1mini-plasmid for GFP tagging in Chroococcidiopsis was investigated by using the RecA homolog of Synechocystis sp. PCC 6803. After 2 months of dry storage, the presence of dried cells with a GFP-RecASyn distribution resembling that of hydrated cells, supported its capability of preventing desiccation-induced genome damage, whereas the rewetted cells with filamentous GFP-RecASyn structures revealed sub-lethal DNA damage. The long-term stability of plasmid DNA in dried Chroococcidiopsis has implication for space research, for example when investigating the recovery of dried cells after Martian and space simulations or when developing life support systems based on phototrophs with genetically enhanced stress tolerance and stored in the dry state for prolonged periods.

Plasmid stability in dried cells of the desert cyanobacterium Chroococcidiopsis and its potential for GFP imaging of survivors on Earth and in space.

PubMed

Billi, Daniela

2012-06-01

Two GFP-based plasmids, namely pTTQ18-GFP-pDU1(mini) and pDUCA7-GFP, of about 7 kbp and 15 kbp respectively, able to replicate in Chroococcidiopsis sp. CCMEE 029 and CCMEE 123, were developed. Both plasmids were maintained in Chroococcidiopsis cells after 18 months of dry storage as demonstrated by colony PCR, plasmid restriction analysis, GFP imaging and colony-forming ability under selection of dried transformants; thus suggesting that strategies employed by this cyanobacterium to stabilize dried chromosomal DNA, must have protected plasmid DNA. The suitability of pDU1(mini)-plasmid for GFP tagging in Chroococcidiopsis was investigated by using the RecA homolog of Synechocystis sp. PCC 6803. After 2 months of dry storage, the presence of dried cells with a GFP-RecA(Syn) distribution resembling that of hydrated cells, supported its capability of preventing desiccation-induced genome damage, whereas the rewetted cells with filamentous GFP-RecA(Syn) structures revealed sub-lethal DNA damage. The long-term stability of plasmid DNA in dried Chroococcidiopsis has implication for space research, for example when investigating the recovery of dried cells after Martian and space simulations or when developing life support systems based on phototrophs with genetically enhanced stress tolerance and stored in the dry state for prolonged periods.

Characterization and physical properties of hydrate bearing sediments

NASA Astrophysics Data System (ADS)

Terzariol, M.; Santamarina, C.

2016-12-01

The amount of carbon trapped in hydrates is estimated to be larger than in conventional oil and gas reservoirs, thus methane hydrate is a promising energy resource. The high water pressure and the relatively low temperature needed for hydrate stability restrict the distribution of methane hydrates to continental shelves and permafrost regions. Stability conditions add inherent complexity to coring, sampling, handling, testing and data interpretation, have profound implications on potential production strategies. Thus a novel technology is developed for handling, transferring, and testing of natural hydrate bearing sediments without depressurization in order to preserve the sediment structure. Results from the first deployment of these tools on natural samples from Nankai Trough, Japan will also be summarized. Finally, to avoid consequences of poor sampling, a new multi-sensor in-situ characterization tool will be introduced.

Synergistic Effect of the Flavonoid Catechin, Quercetin, or Epigallocatechin Gallate with Fluconazole Induces Apoptosis in Candida tropicalis Resistant to Fluconazole

PubMed Central

da Silva, Cecília Rocha; de Andrade Neto, João Batista; de Sousa Campos, Rosana; Figueiredo, Narjara Silvestre; Sampaio, Letícia Serpa; Magalhães, Hemerson Iury Ferreira; Cavalcanti, Bruno Coêlho; Gaspar, Danielle Macêdo; de Andrade, Geanne Matos; Lima, Iri Sandro Pampolha; de Barros Viana, Glauce Socorro; de Moraes, Manoel Odorico; Lobo, Marina Duarte Pinto; Grangeiro, Thalles Barbosa

2014-01-01

Flavonoids are a class of phenolic compounds commonly found in fruits, vegetables, grains, flowers, tea, and wine. They differ in their chemical structures and characteristics. Such compounds show various biological functions and have antioxidant, antimicrobial, anti-inflammatory, and antiapoptotic properties. The aim of this study was to evaluate the in vitro interactions of flavonoids with fluconazole against Candida tropicalis strains resistant to fluconazole, investigating the mechanism of synergism. Three combinations formed by the flavonoids (+)-catechin hydrated, hydrated quercetin, and (−)-epigallocatechin gallate at a fixed concentration with fluconazole were tested. Flavonoids alone had no antifungal activity within the concentration range tested, but when they were used as a cotreatment with fluconazole, there was significant synergistic activity. From this result, we set out to evaluate the possible mechanisms of cell death involved in this synergism. Isolated flavonoids did not induce morphological changes or changes in membrane integrity in the strains tested, but when they were used as a cotreatment with fluconazole, these changes were quite significant. When evaluating mitochondrial damage and the production of reactive oxygen species (ROS) only in the cotreatment, changes were observed. Flavonoids combined with fluconazole were shown to cause a significant increase in the rate of damage and the frequency of DNA damage in the tested strains. The cotreatment also induced an increase in the externalization of phosphatidylserine, an important marker of early apoptosis. It is concluded that flavonoids, when combined with fluconazole, show activity against strains of C. tropicalis resistant to fluconazole, promoting apoptosis by exposure of phosphatidylserine in the plasma membrane and morphological changes, mitochondrial depolarization, intracellular accumulation of ROS, condensation, and DNA fragmentation. PMID:24366745

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.

Bacterial methane oxidation in sea-floor gas hydrate: Significance to life in extreme environments

NASA Astrophysics Data System (ADS)

Sassen, Roger; MacDonald, Ian R.; Guinasso, Norman L., Jr.; Joye, Samantha; Requejo, Adolfo G.; Sweet, Stephen T.; Alcalá-Herrera, Javier; Defreitas, Debra A.; Schink, David R.

1998-09-01

Samples of thermogenic hydrocarbon gases, from vents and gas hydrate mounds within a sea-floor chemosynthetic community on the Gulf of Mexico continental slope at about 540 m depth, were collected by research submersible. Our study area is characterized by low water temperature (mean =7 °C), high pressure (about 5400 kPa), and abundant structure II gas hydrate. Bacterial oxidation of hydrate-bound methane (CH4) is indicated by three isotopic properties of gas hydrate samples. Relative to the vent gas from which the gas hydrate formed, (1) methane-bound methane is enriched in 13C by as much as 3.8‰ PDB (Peedee belemnite), (2) hydrate-bound methane is enriched in deuterium (D) by as much as 37‰ SMOW (standard mean ocean water), and (3) hydrate-bound carbon dioxide (CO2) is depleted in 13C by as much as 22.4‰ PDB. Hydrate-associated authigenic carbonate rock is also depleted in 13C. Bacterial oxidation of methane is a driving force in chemosynthetic communities, and in the concomitant precipitation of authigenic carbonate rock that modifies sea-floor geology. Bacterial oxidation of hydrate-bound methane expands the potential boundaries of life in extreme environments.

P-Wave and S-Wave Velocity Structure of Submarine Landslide Associated With Gas Hydrate Layer on Frontal Ridge of Northern Cascadia Margin

NASA Astrophysics Data System (ADS)

He, T.; Lu, H.; Yelisetti, S.; Spence, G.

2015-12-01

The submarine landslide associated with gas hydrate is a potential risk for environment and engineering projects, and thus from long time ago it has been a hot topic of hydrate research. The study target is Slipstream submarine landslide, one of the slope failures observed on the frontal ridges of the Northern Cascadia accretionary margin off Vancouver Island. The previous studies indicated a possible connection between this submarine landslide feature and gas hydrate, whose occurrence is indicated by a prominent bottom-simulating reflector (BSR), at a depth of ~265-275 m beneath the seafloor (mbsf). The OBS (Ocean Bottom Seismometer) data collected during SeaJade (Seafloor Earthquake Array - Japan Canada Cascadia Experiment) project were used to derive the subseafloor velocity structure for both P- and S-wave using travel times picked from refraction and reflection events. The P-wave velocity structure above the BSR showed anomalous high velocities of about 2.0 km/s at shallow depths of 100 mbsf, closely matching the estimated depth of the glide plane (100 ± 10 m). Forward modelling of S-waves was carried out using the data from the OBS horizontal components. The S-wave velocities, interpreted in conjunction with the P-wave results, provide the key constraints on the gas hydrate distribution within the pores. The hydrate distribution in the pores is important for determining concentrations, and also for determining the frame strength which is critical for controlling slope stability of steep frontal ridges. The increase in S-wave velocity suggests that the hydrate is distributed as part of the load-bearing matrix to increase the rigidity of the sediment.

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

Architecture and Assembly of the Bacillus subtilis Spore Coat

DTIC Science & Technology

2014-09-26

with chromosomal DNA was as described [32]. Table 1. 8. subtifis strains used in this study. Stra in Genotype Phenotype• PS832 wild type PS3394...of the morphology of fully hydrated and air dried spores demonstrate that surface ridges on dehydrated spores mostly disappear or decrease in size

In Situ Soft X-ray Spectromicroscopy of Early Tricalcium Silicate Hydration

DOE PAGES

Bae, Sungchul; Kanematsu, Manabu; Hernandez-Cruz, Daniel; ...

2016-12-01

The understanding and control of early hydration of tricalcium silicate (C 3S) is of great importance to cement science and concrete technology. However, traditional characterization methods are incapable of providing morphological and spectroscopic information about in situ hydration at the nanoscale. Using soft X-ray spectromicroscopy, we report the changes in morphology and molecular structure of C 3S at an early stage of hydration. In situ C 3S hydration in a wet cell, beginning with induction (~1 h) and acceleration (~4 h) periods of up to ~8 h, was studied and compared with ex situ measurements in the deceleration period aftermore » 15 h of curing. Analysis of the near-edge X-ray absorption fine structure showed that the Ca binding energy and energy splitting of C 3S changed rapidly in the early age of hydration and exhibited values similar to calcium silicate hydrate (C–S–H). The formation of C–S–H nanoseeds in the C 3S solution and the development of a fibrillar C–S–H morphology on the C 3S surface were visualized. Following this, silicate polymerization accompanied by C–S–H precipitation produced chemical shifts in the peaks of the main Si K edge and in multiple scattering. However, the silicate polymerization process did not significantly affect the Ca binding energy of C–S–H.« less

In Situ Soft X-ray Spectromicroscopy of Early Tricalcium Silicate Hydration

PubMed Central

Bae, Sungchul; Kanematsu, Manabu; Hernández-Cruz, Daniel; Moon, Juhyuk; Kilcoyne, David; Monteiro, Paulo J. M.

2016-01-01

The understanding and control of early hydration of tricalcium silicate (C3S) is of great importance to cement science and concrete technology. However, traditional characterization methods are incapable of providing morphological and spectroscopic information about in situ hydration at the nanoscale. Using soft X-ray spectromicroscopy, we report the changes in morphology and molecular structure of C3S at an early stage of hydration. In situ C3S hydration in a wet cell, beginning with induction (~1 h) and acceleration (~4 h) periods of up to ~8 h, was studied and compared with ex situ measurements in the deceleration period after 15 h of curing. Analysis of the near-edge X-ray absorption fine structure showed that the Ca binding energy and energy splitting of C3S changed rapidly in the early age of hydration and exhibited values similar to calcium silicate hydrate (C–S–H). The formation of C–S–H nanoseeds in the C3S solution and the development of a fibrillar C–S–H morphology on the C3S surface were visualized. Following this, silicate polymerization accompanied by C–S–H precipitation produced chemical shifts in the peaks of the main Si K edge and in multiple scattering. However, the silicate polymerization process did not significantly affect the Ca binding energy of C–S–H. PMID:28774096

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

DOE PAGES

Alam, Todd M.; Pearce, Charles Joseph

2015-06-28

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

The role of water in gas hydrate dissociation

USGS Publications Warehouse

Circone, S.; Stern, L.A.; Kirby, S.H.

2004-01-01

When raised to temperatures above the ice melting point, gas hydrates release their gas in well-defined, reproducible events that occur within self-maintained temperature ranges slightly below the ice point. This behavior is observed for structure I (carbon dioxide, methane) and structure II gas hydrates (methane-ethane, and propane), including those formed with either H2O- or D2O-host frameworks, and dissociated at either ambient or elevated pressure conditions. We hypothesize that at temperatures above the H2O (or D2O) melting point: (1) hydrate dissociation produces water + gas instead of ice + gas, (2) the endothermic dissociation reaction lowers the temperature of the sample, causing the water product to freeze, (3) this phase transition buffers the sample temperatures within a narrow temperature range just below the ice point until dissociation goes to completion, and (4) the temperature depression below the pure ice melting point correlates with the average rate of dissociation and arises from solution of the hydrate-forming gas, released by dissociation, in the water phase at elevated concentrations. In addition, for hydrate that is partially dissociated to ice + gas at lower temperatures and then heated to temperatures above the ice point, all remaining hydrate dissociates to gas + liquid water as existing barriers to dissociation disappear. The enhanced dissociation rates at warmer temperatures are probably associated with faster gas transport pathways arising from the formation of water product.

Volumetric analysis of formation of the complex of G-quadruplex DNA with hemin using high pressure.

PubMed

Takahashi, Shuntaro; Bhowmik, Sudipta; Sugimoto, Naoki

2017-01-01

DNA guanine-quadruplexes (G-quadruplexes) complexed with the Fe-containing porphyrin, hemin (iron(III)-protoporphyrin IX), can catalyze oxidation reactions. This so-called DNAzyme has been widely used in the field of DNA nanotechnology. To improve DNAzyme properties, we sought to elucidate the interaction mechanism between G-quadruplex DNA and hemin. Here, we performed volumetric analyses of formation of the complex between an oligonucleotide with the sequence of human telomeric DNA (h-telo) and hemin. The G-quadruplex DNA alone and the G-quadruplex DNA-hemin complex were destabilized with increasing pressure in Na + buffer. The pressure required to destabilize the h-telo-hemin complex was less in K + -containing buffer than in buffer with Na + , which indicates that there was a smaller volumetric change upon h-telo formation in K + buffer than in Na + buffer. The calculated change in h-telo-hemin binding volume (∆V b ) in the Na + buffer was 2.5mLmol -1 , whereas it was -41.7 in mLmol -1 the K + buffer. The DNAzyme activity in the K + buffer was higher than that in the Na + buffer at atmospheric pressure. Interestingly, the pressure effect on the destabilization of the h-telo-hemin complex in the presence of poly(ethylene glycol)200 (PEG200) was repressed compared to that in the absence of PEG200. These results suggest that differences in volumetric parameters reflect different mechanisms of interaction between hemin and h-telo due to differences in both the fit of hemin into the h-telo structure and hydration. Thus, the pressure-based thermodynamic analysis provided important information about complex formation and could be a useful index to improve function of DNAzymes. Copyright © 2016 Elsevier Inc. All rights reserved.

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

PubMed

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

2010-11-04

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

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

NASA Astrophysics Data System (ADS)

Alavi, Saman; Ohmura, Ryo

2016-10-01

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

Occurrence of near-seafloor gas hydrates and associated cold vents in the Ulleung Basin, East Sea

NASA Astrophysics Data System (ADS)

Bahk, J.-J.; Kong, G.-S.; Park, Y.; Kim, J.-H.; Lee, H.; Park, Y.; Park, K.-P.

2009-04-01

During the site survey cruise for proposed drill sites of the Ulleung Basin Gas Hydrate Expedition 01, near-seafloor gas hydrates were discovered in core sediments from both regions of basin plain (2066-2012 m water depth) and southern slope (898 m) of the Ulleung Basin. The gas hydrate-bearing cores were exclusively retrieved from high backscatter intensity areas in processed 13 kHz multi-beam data, implying high seafloor reflectivity. In high-resolution (2-7 kHz) sub-bottom profiles, the coring sites are also characterized by narrow (< about 500 m wide) acoustic blank zones reaching seafloor, where they have surface expressions of low-relief (< about 5 m high) mound. In the data from a 38 kHz split-beam echosounder, which was deployed for acoustic characterization of gas bubbles, there are no apparent gas flares associated with the blank zones. The recovered gas hydrates mainly consist of disseminated nodules or veins in clayey mud, which normally occur from 5-6 m below the seafloor to the maximum penetration depth (<8 m) of the cores. In some cases, they were associated with abundant scattered authigenic carbonate nodules. Compositional and structural analyses of selected gas hydrate samples revealed that they consist of structure I hydrates which contain more than 99% methane with carbon isotope values ranging from -64 to -80 per mil (PDB). The preliminary results of the site survey cruise collectively suggest that the near-seafloor gas hydrates are related to cold vents, where high seafloor reflectivity is caused by presence of gas hydrates and authigenic carbonates. Gas seeping activity in the cold vents appears to be currently dormant.

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

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

PubMed

Alavi, Saman; Ohmura, Ryo

2016-10-21

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

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

Overview: Nucleation of clathrate hydrates

NASA Astrophysics Data System (ADS)

Warrier, Pramod; Khan, M. Naveed; Srivastava, Vishal; Maupin, C. Mark; Koh, Carolyn A.

2016-12-01

Molecular level knowledge of nucleation and growth of clathrate hydrates is of importance for advancing fundamental understanding on the nature of water and hydrophobic hydrate formers, and their interactions that result in the formation of ice-like solids at temperatures higher than the ice-point. The stochastic nature and the inability to probe the small length and time scales associated with the nucleation process make it very difficult to experimentally determine the molecular level changes that lead to the nucleation event. Conversely, for this reason, there have been increasing efforts to obtain this information using molecular simulations. Accurate knowledge of how and when hydrate structures nucleate will be tremendously beneficial for the development of sustainable hydrate management strategies in oil and gas flowlines, as well as for their application in energy storage and recovery, gas separation, carbon sequestration, seawater desalination, and refrigeration. This article reviews various aspects of hydrate nucleation. First, properties of supercooled water and ice nucleation are reviewed briefly due to their apparent similarity to hydrates. Hydrate nucleation is then reviewed starting from macroscopic observations as obtained from experiments in laboratories and operations in industries, followed by various hydrate nucleation hypotheses and hydrate nucleation driving force calculations based on the classical nucleation theory. Finally, molecular simulations on hydrate nucleation are discussed in detail followed by potential future research directions.

Overview: Nucleation of clathrate hydrates.

PubMed

Warrier, Pramod; Khan, M Naveed; Srivastava, Vishal; Maupin, C Mark; Koh, Carolyn A

2016-12-07

Molecular level knowledge of nucleation and growth of clathrate hydrates is of importance for advancing fundamental understanding on the nature of water and hydrophobic hydrate formers, and their interactions that result in the formation of ice-like solids at temperatures higher than the ice-point. The stochastic nature and the inability to probe the small length and time scales associated with the nucleation process make it very difficult to experimentally determine the molecular level changes that lead to the nucleation event. Conversely, for this reason, there have been increasing efforts to obtain this information using molecular simulations. Accurate knowledge of how and when hydrate structures nucleate will be tremendously beneficial for the development of sustainable hydrate management strategies in oil and gas flowlines, as well as for their application in energy storage and recovery, gas separation, carbon sequestration, seawater desalination, and refrigeration. This article reviews various aspects of hydrate nucleation. First, properties of supercooled water and ice nucleation are reviewed briefly due to their apparent similarity to hydrates. Hydrate nucleation is then reviewed starting from macroscopic observations as obtained from experiments in laboratories and operations in industries, followed by various hydrate nucleation hypotheses and hydrate nucleation driving force calculations based on the classical nucleation theory. Finally, molecular simulations on hydrate nucleation are discussed in detail followed by potential future research directions.

The Lithological Constraint To Gas Hydrate Formation: Evidence OF Grain Size Of Sediments From IODP 311 On CASCADIA Margin

NASA Astrophysics Data System (ADS)

Wang, J.

2006-12-01

A total of 614 sediment samples at intervals of about 1.5 m from all 5 sites of the Integrated Ocean Drilling Program (IODP) Expedition 311 on Cascadia Margin were analyzed using a Beckman Coulter LS-230 Particle Analyzer. The grain-size data were then plotted in depth and compared with other proxies of gas hydrate- occurrence such as soupy/mousse-like structures in sediments, gas hydrate concentration (Sh) derived from LWD data using Archie's relation, IR core images (infrared image) and the recovered samples of gas hydrate¨Cbearing sediments. A good relationship between the distribution of coarse grains in size of 31-63¦Ìm and 63-125¦Ìm sediments and the potential occurrence of gas hydrate was found across the entire gas hydrate stability zone. The depth distribution of grain size from the Site U1326 shows clear excursions at depths of 5-8, 21-26, 50- 123, 132-140, 167-180, 195-206 and 220-240 mbsf, which coincide with the potential occurrence of gas hydrate suggested by soupy/mousse-like structures, logging-derived gas hydrate concentrations (Sh) and the recovered samples of the gas hydrate¨Cbearing sand layers. The lithology of sediments significantly affects the formation of gas hydrate. Gas hydrate forms preferentially within relatively coarse grain-size sediments above 31 ¦Ìm. Key words: grain size of sediments, constraint, occurrence of gas hydrate, IODP 311 IODP Expedition 311 Scientists: Michael Riedel (Co-chief Scientist), Timothy S. Collett (Co-chief Scientist), Mitchell Malone (Expedition Project Manager/Staff Scientist), Gilles Gu¨¨rin, Fumio Akiba, Marie-Madeleine Blanc-Valleron, Michelle Ellis, Yoshitaka Hashimoto, Verena Heuer, Yosuke Higashi, Melanie Holland, Peter D. Jackson, Masanori Kaneko, Miriam Kastner, Ji-Hoon Kim, Hiroko Kitajima, Philip E. Long, Alberto Malinverno, Greg Myers, Leena D. Palekar, John Pohlman, Peter Schultheiss, Barbara Teichert, Marta E. Torres, Anne M. Tr¨¦hu, Jiasheng Wang, Ulrich G. Wortmann, Hideyoshi Yoshioka. Acknowledgement: This study was supported by the IODP/JOI Alliance, IODP-China 863 Project (grant 2004AA615030) and NSFC Project (grant 40472063).

Reaction mechanism of Ru(II) piano-stool complexes: umbrella sampling QM/MM MD study.

PubMed

Futera, Zdeněk; Burda, Jaroslav V

2014-07-15

Biologically relevant interactions of piano-stool ruthenium(II) complexes with ds-DNA are studied in this article by hybrid quantum mechanics-molecular mechanics (QM/MM) computational technique. The whole reaction mechanism is divided into three phases: (i) hydration of the [Ru(II) (η(6) -benzene)(en)Cl](+) complex, (ii) monoadduct formation between the resulting aqua-Ru(II) complex and N7 position of one of the guanines in the ds-DNA oligomer, and (iii) formation of the intrastrand Ru(II) bridge (cross-link) between two adjacent guanines. Free energy profiles of all the reactions are explored by QM/MM MD umbrella sampling approach where the Ru(II) complex and two guanines represent a quantum core, which is described by density functional theory methods. The combined QM/MM scheme is realized by our own software, which was developed to couple several quantum chemical programs (in this study Gaussian 09) and Amber 11 package. Calculated free energy barriers of the both ruthenium hydration and Ru(II)-N7(G) DNA binding process are in good agreement with experimentally measured rate constants. Then, this method was used to study the possibility of cross-link formation. One feasible pathway leading to Ru(II) guanine-guanine cross-link with synchronous releasing of the benzene ligand is predicted. The cross-linking is an exergonic process with the energy barrier lower than for the monoadduct reaction of Ru(II) complex with ds-DNA. Copyright © 2014 Wiley Periodicals, Inc.

Study of the effect of simulated space environment on nucleoprotein and DNA thin films

NASA Astrophysics Data System (ADS)

Fekete, A.; Módos, K.; Hegedüs, M.; Rontó, Gy.; Kovács, G.; Bérces, A.; Kargl, G.; Kömle, N. I.; Lammer, H.

2002-11-01

The main goal of PUR experiment (phage and uracil response) is to examine and quantify the effect of specific space conditions on nucleic acid models. To achieve this an improved method was elaborated for the preparation of DNA and bacteriophage thin films. The homogeneity of the films was controlled by UV spectroscopy and microscopy. To provide experimental evidence for the hypothesis that interplanetary transfer of life is possible, phage T7 and isolated T7 DNA thin films have been exposed to selected space conditions: intense UVC radiation (λ = 254 nm) and high vacuum (10-5 mbar). The effects of DNA hydration, conformation and packing on UV radiation damage were examined. Characteristic changes in the absorption spectrum, in the electrophoretic pattern of DNA and the decrease of the amount of PCR products have been detected indicating the photodamage of isolated and intraphage DNA.

Simulation experiments of the effect of space environment on bacteriophage and DNA thin films

NASA Astrophysics Data System (ADS)

Fekete, A.; Rontó, Gy.; Hegedüs, M.; Módos, K.; Bérces, A.; Kovács, G.; Lammer, H.; Panitz, C.

2004-01-01

The main goal of PUR experiment (phage and uracil response) is to examine and quantify the effect of specific space conditions on nucleic acid models. To achieve this an improved method was elaborated for the preparation of DNA and bacteriophage thin films. The homogeneity of the films was controlled by UV spectroscopy and microscopy. To provide experimental evidence for the hypothesis that interplanetary transfer of the genetic material is possible, phage T7 and isolated T7 DNA thin films have been exposed to selected space conditions: intense UVC radiation ( λ=254 nm) and high vacuum (10 -4 Pa). The effects of DNA hydration, conformation and packing on UV radiation damage were examined. Characteristic changes in the absorption spectrum, in the electrophoretic pattern of DNA and the decrease of the amount of PCR products have been detected indicating the photodamage of isolated and intraphage DNA.

The mechanism of vapor phase hydration of calcium oxide: implications for CO2 capture.

PubMed

Kudłacz, Krzysztof; Rodriguez-Navarro, Carlos

2014-10-21

Lime-based sorbents are used for fuel- and flue-gas capture, thereby representing an economic and effective way to reduce CO2 emissions. Their use involves cyclic carbonation/calcination which results in a significant conversion reduction with increasing number of cycles. To reactivate spent CaO, vapor phase hydration is typically performed. However, little is known about the ultimate mechanism of such a hydration process. Here, we show that the vapor phase hydration of CaO formed after calcination of calcite (CaCO3) single crystals is a pseudomorphic, topotactic process, which progresses via an intermediate disordered phase prior to the final formation of oriented Ca(OH)2 nanocrystals. The strong structural control during this solid-state phase transition implies that the microstructural features of the CaO parent phase predetermine the final structural and physicochemical (reactivity and attrition) features of the product hydroxide. The higher molar volume of the product can create an impervious shell around unreacted CaO, thereby limiting the efficiency of the reactivation process. However, in the case of compact, sintered CaO structures, volume expansion cannot be accommodated in the reduced pore volume, and stress generation leads to pervasive cracking. This favors complete hydration but also detrimental attrition. Implications of these results in carbon capture and storage (CCS) are discussed.

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

Random and Block Sulfonated Polyaramides as Advanced Proton Exchange Membranes

DOE PAGES

Kinsinger, Corey L.; Liu, Yuan; Liu, Feilong; ...

2015-10-09

We present here the experimental and computational characterization of two novel copolyaramide proton exchange membranes (PEMs) with higher conductivity than Nafion at relatively high temperatures, good mechanical properties, high thermal stability, and the capability to operate in low humidity conditions. The random and block copolyaramide PEMs are found to possess different ion exchange capacities (IEC) in addition to subtle structural and morphological differences, which impact the stability and conductivity of the membranes. SAXS patterns indicate the ionomer peak for the dry block copolymer resides at q = 0.1 Å –1, which increases in amplitude when initially hydrated to 25% relativemore » humidity, but then decrease in amplitude with additional hydration. This pattern is hypothesized to signal the transport of water into the polymer matrix resulting in a reduced degree of phase separation. Coupled to these morphological changes, the enhanced proton transport characteristics and structural/mechanical stability for the block copolymer are hypothesized to be primarily due to the ordered structure of ionic clusters that create connected proton transport pathways while reducing swelling upon hydration. Interestingly, the random copolymer did not possess an ionomer peak at any of the hydration levels investigated, indicating a lack of any significant ionomer structure. The random copolymer also demonstrated higher proton conductivity than the block copolymer, which is opposite to the trend normally seen in polymer membranes. However, it has reduced structural/mechanical stability as compared to the block copolymer. In conclusion, this reduction in stability is due to the random morphology formed by entanglements of polymer chains and the adverse swelling characteristics upon hydration. Therefore, the block copolymer with its enhanced proton conductivity characteristics, as compared to Nafion, and favorable structural/mechanical stability, as compared to the random copolymer, represents a viable alternative to current proton exchange membranes.« less

Structure and hydration of membranes embedded with voltage-sensing domains.

PubMed

Krepkiy, Dmitriy; Mihailescu, Mihaela; Freites, J Alfredo; Schow, Eric V; Worcester, David L; Gawrisch, Klaus; Tobias, Douglas J; White, Stephen H; Swartz, Kenton J

2009-11-26

Despite the growing number of atomic-resolution membrane protein structures, direct structural information about proteins in their native membrane environment is scarce. This problem is particularly relevant in the case of the highly charged S1-S4 voltage-sensing domains responsible for nerve impulses, where interactions with the lipid bilayer are critical for the function of voltage-activated ion channels. Here we use neutron diffraction, solid-state nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics simulations to investigate the structure and hydration of bilayer membranes containing S1-S4 voltage-sensing domains. Our results show that voltage sensors adopt transmembrane orientations and cause a modest reshaping of the surrounding lipid bilayer, and that water molecules intimately interact with the protein within the membrane. These structural findings indicate that voltage sensors have evolved to interact with the lipid membrane while keeping energetic and structural perturbations to a minimum, and that water penetrates the membrane, to hydrate charged residues and shape the transmembrane electric field.

Structure and hydration of membranes embedded with voltage-sensing domains

PubMed Central

Krepkiy, Dmitriy; Mihailescu, Mihaela; Freites, J. Alfredo; Schow, Eric V.; Worcester, David L.; Gawrisch, Klaus; Tobias, Douglas; White, Stephen H.; Swartz, Kenton J.

2009-01-01

Despite the growing number of atomic-resolution membrane protein structures, direct structural information about proteins in their native membrane environment is scarce. This problem is particularly relevant in the case of the highly-charged S1–S4 voltage-sensing domains responsible for nerve impulses, where interactions with the lipid bilayer are critical for the function of voltage-activated potassium channels. Here we use neutron diffraction, solid-state nuclear magnetic resonance spectroscopy, and molecular dynamics simulations to investigate the structure and hydration of bilayer membranes containing S1–S4 voltage-sensing domains. Our results show that voltage sensors adopt transmembrane orientations, cause a modest reshaping of the surrounding lipid bilayer, and that water molecules intimately interact with the protein within the membrane. These structural findings reveal that voltage sensors have evolved to interact with the lipid membrane while keeping the energetic and structural perturbations to a minimum, and that water penetrates into the membrane to hydrate charged residues and shape the transmembrane electric field. PMID:19940918

X-ray investigation of molten crystal hydrates H2SO4(nH2O) and HNO3(nH2O)

NASA Technical Reports Server (NTRS)

Romanova, A. V.; Skryshevskiy, A. F.

1979-01-01

Integral analysis of the intensity of the electron density distribution curve in molten crystal hydrates provided by X-ray analysis, permits the following conclusions on the structure of the complex SO and NO ions, and the short-range order in the structure of the solution. The SO4 ion in the solution has a tetrahedral structure with an S to O distance equal to 1.5 A. For the NO3 in the solution, a planar triangular shape is probable, with an N to O distance equal to 1.2 A. Preferential distances between each of the oxygens of the SO ion and the nearest molecules of water proved near to the corresponding distances in solid crystal hydrates. For an (H2SO4)(H2O) solution, the average number of water molecules surrounding each oxygen atom of the SO4 (--) ion was on the order of 1.3 molecules. Hence the preferential distances between the water molecules and the oxygen atoms of the SO ion, and the preference of their mutual position, correspond to the fixed position of these same elements of the structure in the solid crystal hydrate.

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.

Inhibited phase behavior of gas hydrates in graphene oxide: influences of surface and geometric constraints.

PubMed

Kim, Daeok; Kim, Dae Woo; Lim, Hyung-Kyu; Jeon, Jiwon; Kim, Hyungjun; Jung, Hee-Tae; Lee, Huen

2014-11-07

Porous materials have provided us unprecedented opportunities to develop emerging technologies such as molecular storage systems and separation mechanisms. Pores have also been used as supports to contain gas hydrates for the application in gas treatments. Necessarily, an exact understanding of the properties of gas hydrates in confining pores is important. Here, we investigated the formation of CO2, CH4 and N2 hydrates in non-interlamellar voids in graphene oxide (GO), and their thermodynamic behaviors. For that, low temperature XRD and P-T traces were conducted to analyze the water structure and confirm hydrate formation, respectively, in GO after its exposure to gaseous molecules. Confinement and strong interaction of water with the hydrophilic surface of graphene oxide reduce water activity, which leads to the inhibited phase behavior of gas hydrates.

The thermal structure of the mud diapir/volcano and its influence on gas hydrate stability in northern South China Sea

NASA Astrophysics Data System (ADS)

Wan, Z.; Xu, X.; Wang, X.

2016-12-01

The mud diapir/volcano is an important indicator for gas hydrate exploration, which develops widely in continental slopes. There are many mud diapirs/volcanoes developed in northern South China Sea continental slope. Guangzhou Marine Geological Survey (GMGS) of the Chinese Ministry of Land and Resources targeted mud diapirs/volcanoes and deployed gas hydrate drilling in the Shenhu area. An obvious mud diapir developed below borehole number SH5, and bottom-simulating reflection (BSR) was also detected, but no gas hydrates were found at this borehole. We analyzed the thermal structure of mud diapirs and their relationship to the occurrence of gas hydrates. The in situ temperature at the seafloor is approximately 2.2 2.5oC in the study area. Seafloor heat flow values of SH5 is 71.4mW/m2. Temperature increases rapidly to 17oC from 40 m to 100 m and stays in the range of 17 to 19oC below 100 m. And the thermal conductivity value of SH5 is approximately 1.0 W/m·k from top to bottom. The evolution of the mud diapir/volcanoes can be divided into three stages within a continuous geological process controlling the gas hydrate reservoir. During the late stage, liquid from the mud diapir/volcanoes begins to invade the gas hydrate stability zone . Because of the high unit heat capacity of liquid, the whole temperature field of the surrounding layers increases significantly when the mud diapir/volcanoes pierces upwards. This high heat flow leads to decomposition of the gas hydrates. Therefore, the reason of SH5 did not find gas hydrates may be that the mud diapir had pierced through during the late stage, leading to gas hydrate decomposition, even though there is an obvious BSR. This work was supported by Science and Technology Program of Guangzhou (No. 201607010214) and National Nature Science Foundation of China (No. 91128203,41102077).

Humidity-controlled preparation of frozen-hydrated biological samples for cryogenic coherent x-ray diffraction microscopy

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

Takayama, Yuki; Nakasako, Masayoshi; RIKEN Harima Institute/SPring-8, 1-1-1 Kouto, Mikaduki, Sayo, Hyogo 679-5148

2012-05-15

Coherent x-ray diffraction microscopy (CXDM) has the potential to visualize the structures of micro- to sub-micrometer-sized biological particles, such as cells and organelles, at high resolution. Toward advancing structural studies on the functional states of such particles, here, we developed a system for the preparation of frozen-hydrated biological samples for cryogenic CXDM experiments. The system, which comprised a moist air generator, microscope, micro-injector mounted on a micromanipulator, custom-made sample preparation chamber, and flash-cooling device, allowed for the manipulation of sample particles in the relative humidity range of 20%-94%rh at 293 K to maintain their hydrated and functional states. Here, wemore » report the details of the system and the operation procedure, including its application to the preparation of a frozen-hydrated chloroplast sample. Sample quality was evaluated through a cryogenic CXDM experiment conducted at BL29XUL of SPring-8. Taking the performance of the system and the quality of the sample, the system was suitable to prepare frozen-hydrated biological samples for cryogenic CXDM experiments.« less

Influence of Countercation Hydration Enthalpies on the Formation of Molecular Complexes: A Thorium–Nitrate Example

DOE PAGES

Jin, Geng Bang; Lin, Jian; Estes, Shanna L.; ...

2017-11-17

Here, the influence of countercations (A n+) in directing the composition of monomeric metal–ligand (ML) complexes that precipitate from solution are often overlooked despite the wide usage of A n+ in materials synthesis. Herein, we describe a correlation between the composition of ML complexes and A + hydration enthalpies found for two related series of thorium (Th)–nitrate molecular compounds obtained by evaporating acidic aqueous Th–nitrate solutions in the presence of A + counterions. Analyses of their chemical composition and solid-state structures demonstrate that A + not only affects the overall solid-state packing of the Th–nitrato complexes but also influences themore » composition of the Th–nitrato monomeric anions themselves. Trends in composition and structure are found to correlate with A + hydration enthalpies, such that the A + with smaller hydration enthalpies associate with less hydrated and more anionic Th–nitrato complexes. This perspective, broader than the general assumption of size and charge as the dominant influence of A n+, opens a new avenue for the design and synthesis of targeted metal–ligand complexes.« less

Influence of Countercation Hydration Enthalpies on the Formation of Molecular Complexes: A Thorium–Nitrate Example

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

Jin, Geng Bang; Lin, Jian; Estes, Shanna L.

Here, the influence of countercations (A n+) in directing the composition of monomeric metal–ligand (ML) complexes that precipitate from solution are often overlooked despite the wide usage of A n+ in materials synthesis. Herein, we describe a correlation between the composition of ML complexes and A + hydration enthalpies found for two related series of thorium (Th)–nitrate molecular compounds obtained by evaporating acidic aqueous Th–nitrate solutions in the presence of A + counterions. Analyses of their chemical composition and solid-state structures demonstrate that A + not only affects the overall solid-state packing of the Th–nitrato complexes but also influences themore » composition of the Th–nitrato monomeric anions themselves. Trends in composition and structure are found to correlate with A + hydration enthalpies, such that the A + with smaller hydration enthalpies associate with less hydrated and more anionic Th–nitrato complexes. This perspective, broader than the general assumption of size and charge as the dominant influence of A n+, opens a new avenue for the design and synthesis of targeted metal–ligand complexes.« less

Synthesis of New Hydrated Geranylphenols and in Vitro Antifungal Activity against Botrytis cinerea

PubMed Central

Soto, Mauricio; Espinoza, Luis; Chávez, María I.; Díaz, Katy; Olea, Andrés F.; Taborga, Lautaro

2016-01-01

Geranylated hydroquinones and other geranylated compounds isolated from Aplydium species have shown interesting biological activities. This fact has prompted a number of studies where geranylated phenol derivatives have been synthesized in order to assay their bioactivities. In this work, we report the synthesis of a series of new hydrated geranylphenols using two different synthetic approaches and their inhibitory effects on the mycelial growth of Botrytis cinerea. Five new hydrated geranylphenols were obtained by direct coupling reaction between geraniol and phenol in dioxane/water and using BF3·Et2O as the catalyst or by the reaction of a geranylated phenol with BF3·Et2O. Two new geranylated quinones were also obtained. The synthesis and structural elucidation of all new compounds is presented. All hydrated geranylphenols efficiently inhibit the mycelial growth of B. cinerea. Their activity is higher than that observed for non-hydrated compounds. These results indicate that structural modification on the geranyl chain brings about an enhancement of the inhibition effect of geranylated phenol derivatives. PMID:27271604

Structures and energetics of hydrated deprotonated cis-pinonic acid anion clusters and their atmospheric relevance

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

Hou, Gao-Lei; Zhang, Jun; Valiev, Marat

2017-01-01

Pinonic acid, a C10-monocarboxylic acid with a hydrophilic –CO 2H group and a hydrophobic hydrocarbon backbone, is a key intermediate oxidation product of α-pinene – an important monoterpene compound in biogenic emission processes that influences the atmosphere. Molecular interaction between cis-pinonic acid and water is essential for understanding its role in the formation and growth of pinene-derived secondary organic aerosols. In this work, we studied the structures, energetics, and optical properties of hydrated clusters of cis-pinonate anion (cPA–), the deprotonated form of cis-pinonic acid, by negative ion photoelectron spectroscopy and ab initio theoretical calculations. Our results show that cPA– canmore » adopt two different structural configurations – open and folded. In the absence of waters, the open configuration has the lowest energy and provides the best agreement with the experiment. The addition waters, which mainly interact with the negatively charged -CO 2– group, gradually stabilize the folded configuration and lower its energy difference relative to the most stable open-configured structure. Thermochemical and equilibrium hydrate distribution analysis suggests that the mono- and di- hydrates are likely to exist in humid atmospheric environment with high populations. The detailed molecular description of cPA– hydrated clusters unraveled in this study provides a valuable reference for understanding the initial nucleation process and aerosol formation involving organics containing both hydrophilic and hydrophobic groups, as well as for analyzing the optical properties of those organic aerosols.« less

Effect of Surface Hydration on Antifouling Properties of Mixed Charged Polymers.

PubMed

Leng, Chuan; Huang, Hao; Zhang, Kexin; Hung, Hsiang-Chieh; Xu, Yao; Li, Yaoxin; Jiang, Shaoyi; Chen, Zhan

2018-05-07

Interfacial water structure on a polymer surface in water (or surface hydration) is related to the antifouling activity of the polymer. Zwitterionic polymer materials exhibit excellent antifouling activity due to their strong surface hydration. It was proposed to replace zwitterionic polymers using mixed charged polymers because it is much easier to prepare mixed charged polymer samples with much lower costs. In this study, using sum frequency generation (SFG) vibrational spectroscopy, we investigated interfacial water structures on mixed charged polymer surfaces in water, and how such structures change while exposing to salt solutions and protein solutions. The 1:1 mixed charged polymer exhibits excellent antifouling property while other mixed charged polymers with different ratios of the positive/negative charges do not. It was found that on the 1:1 mixed charged polymer surface, SFG water signal is dominated by the contribution of the strongly hydrogen bonded water molecules, indicating strong hydration of the polymer surface. The responses of the 1:1 mixed charged polymer surface to salt solutions are similar to those of zwitterionic polymers. Interestingly, exposure to high concentrations of salt solutions leads to stronger hydration of the 1:1 mixed charged polymer surface after replacing the salt solution with water. Protein molecules do not substantially perturb the interfacial water structure on the 1:1 mixed charged polymer surface and do not adsorb to the surface, showing that this mixed charged polymer is an excellent antifouling material.

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.

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

PubMed

Ohba, Tomonori

2014-02-24

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

Analysis of protein structures and interactions in complex food by near-infrared spectroscopy. 2. Hydrated gluten.

PubMed

Bruun, Susanne Wrang; Søndergaard, Ib; Jacobsen, Susanne

2007-09-05

Hydrated gluten, treated with various salts, was analyzed by near-infrared (NIR) spectroscopy to assess the ability of this method to reveal protein structure and interaction changes in perturbed food systems. The spectra were pretreated with second-derivative transformation and extended multiplicative signal correction for improving the band resolution and removing physical and quantitative spectral variations. Principal component analysis of the preprocessed spectra showed spectral effects that depended on salt type and concentration. Although both gluten texture and the NIR spectra were little influenced by treatment with salt solutions of low concentrations (0.1-0.2 M), they were significantly and diversely affected by treatment with 1.0 M salt solutions. Compared to hydration in water, hydration in 1.0 M sulfate salts caused spectral effects similar to a drying-out effect, which could be explained by salting-out.

High-Performance of Gas Hydrates in Confined Nanospace for Reversible CH4 /CO2 Storage.

PubMed

Casco, Mirian E; Jordá, José L; Rey, Fernando; Fauth, François; Martinez-Escandell, Manuel; Rodríguez-Reinoso, Francisco; Ramos-Fernández, Enrique V; Silvestre-Albero, Joaquín

2016-07-11

The molecular exchange of CH4 for CO2 in gas hydrates grown in confined nanospace has been evaluated for the first time using activated carbons as a host structure. The nano-confinement effects taking place inside the carbon cavities and the exceptional physicochemical properties of the carbon structure allows us to accelerate the formation and decomposition process of the gas hydrates from the conventional timescale of hours/days in artificial bulk systems to minutes in confined nanospace. The CH4 /CO2 exchange process is fully reversible with high efficiency at practical temperature and pressure conditions. Furthermore, these activated carbons can be envisaged as promising materials for long-distance natural gas and CO2 transportation because of the combination of a high storage capacity, a high reversibility, and most important, with extremely fast kinetics for gas hydrate formation and release. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Electron attachment to the guanine-cytosine nucleic acid base pair and the effects of monohydration and proton transfer.

PubMed

Gupta, Ashutosh; Jaeger, Heather M; Compaan, Katherine R; Schaefer, Henry F

2012-05-17

The guanine-cytosine (GC) radical anion and its interaction with a single water molecule is studied using ab initio and density functional methods. Z-averaged second-order perturbation theory (ZAPT2) was applied to GC radical anion for the first time. Predicted spin densities show that the radical character is localized on cytosine. The Watson-Crick monohydrated GC anion is compared to neutral GC·H2O, as well as to the proton-transferred analogue on the basis of structural and energetic properties. In all three systems, local minima are identified that correspond to water positioned in the major and minor grooves of macromolecular DNA. On the anionic surface, two novel structures have water positioned above or below the GC plane. On the neutral and anionic surfaces, the global minimum can be described as water interacting with the minor groove. These structures are predicted to have hydration energies of 9.7 and 11.8 kcal mol(-1), respectively. Upon interbase proton-transfer (PT), the anionic global minimum has water positioned in the major groove, and the hydration energy increases to 13.4 kcal mol(-1). PT GC·H2O(•-) has distonic character; the radical character resides on cytosine, while the negative charge is localized on guanine. The effects of proton transfer are further investigated through the computed adiabatic electron affinities (AEA) of GC and monohydrated GC, and the vertical detachment energies (VDE) of the corresponding anions. Monohydration increases the AEAs and VDEs by only 0.1 eV, while proton-transfer increases the VDEs substantially (0.8 eV). The molecular charge distribution of monohydrated guanine-cytosine radical anion depends heavily on interbase proton transfer.

Environmentally Controlled Infrared Spectroscopy System for Fundamental Studies of Polymer Electrolyte Membranes

DTIC Science & Technology

2015-10-15

to state-of- hydration . Polarization modulated infrared reflection- absorption spectroscopy experiments are enabled by the use of a spin-coater to coat...NAME(S) AND ADDRESS (ES) U.S. Army Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 SPEEK, Nafion, Ionomers, state-of- hydration ...enabled correlation of the exchange site structure to state-of- hydration . Polarization modulated infrared reflection-absorption spectroscopy experiments

Multimodal approach to characterization of hydrophilic matrices manufactured by wet and dry granulation or direct compression methods.

PubMed

Kulinowski, Piotr; Woyna-Orlewicz, Krzysztof; Obrał, Jadwiga; Rappen, Gerd-Martin; Haznar-Garbacz, Dorota; Węglarz, Władysław P; Jachowicz, Renata; Wyszogrodzka, Gabriela; Klaja, Jolanta; Dorożyński, Przemysław P

2016-02-29

The purpose of the research was to investigate the effect of the manufacturing process of the controlled release hydrophilic matrix tablets on their hydration behavior, internal structure and drug release. Direct compression (DC) quetiapine hemifumarate matrices and matrices made of powders obtained by dry granulation (DG) and high shear wet granulation (HS) were prepared. They had the same quantitative composition and they were evaluated using X-ray microtomography, magnetic resonance imaging and biorelevant stress test dissolution. Principal results concerned matrices after 2 h of hydration: (i) layered structure of the DC and DG hydrated tablets with magnetic resonance image intensity decreasing towards the center of the matrix was observed, while in HS matrices layer of lower intensity appeared in the middle of hydrated part; (ii) the DC and DG tablets retained their core and consequently exhibited higher resistance to the physiological stresses during simulation of small intestinal passage than HS formulation. Comparing to DC, HS granulation changed properties of the matrix in terms of hydration pattern and resistance to stress in biorelevant dissolution apparatus. Dry granulation did not change these properties-similar hydration pattern and dissolution in biorelevant conditions were observed for DC and DG matrices. Copyright © 2015 Elsevier B.V. All rights reserved.

Direct Imaging of Individual Intrinsic Hydration Layers on Lipid Bilayers at Ångstrom Resolution

PubMed Central

Fukuma, Takeshi; Higgins, Michael J.; Jarvis, Suzanne P.

2007-01-01

The interactions between water and biological molecules have the potential to influence the structure, dynamics, and function of biological systems, hence the importance of revealing the nature of these interactions in relation to the local biochemical environment. We have investigated the structuring of water at the interface of supported dipalmitoylphosphatidylcholine bilayers in the gel phase in phosphate buffer solution using frequency modulation atomic force microscopy (FM-AFM). We present experimental results supporting the existence of intrinsic (i.e., surface-induced) hydration layers adjacent to the bilayer. The force versus distance curves measured between the bilayer and the AFM tip show oscillatory force profiles with a peak spacing of 0.28 nm, indicative of the existence of up to two hydration layers next to the membrane surface. These oscillatory force profiles reveal the molecular-scale origin of the hydration force that has been observed between two apposing lipid bilayers. Furthermore, FM-AFM imaging at the water/lipid interface visualizes individual hydration layers in three dimensions, with molecular-scale corrugations corresponding to the lipid headgroups. The results demonstrate that the intrinsic hydration layers are stable enough to present multiple energy barriers to approaching nanoscale objects, such as proteins and solvated ions, and are expected to affect membrane permeability and transport. PMID:17325013

A predictive numerical model for potential mapping of the gas hydrate stability zone in the Gulf of Cadiz

NASA Astrophysics Data System (ADS)

Leon, R.; Somoza, L.

2009-04-01

This comunication presents a computational model for mapping the regional 3D distribution in which seafloor gas hydrates would be stable, that is carried out in a Geographical Information System (GIS) environment. The construction of the model is comprised of three primary steps, namely (1) the construction of surfaces for the various variables based on available 3D data (seafloor temperature, geothermal gradient and depth-pressure); (2) the calculation of the gas function equilibrium functions for the various hydrocarbon compositions reported from hydrate and sediment samples; and (3) the calculation of the thickness of the hydrate stability zone. The solution is based on a transcendental function, which is solved iteratively in a GIS environment. The model has been applied in the northernmost continental slope of the Gulf of Cadiz, an area where an abundant supply for hydrate formation, such as extensive hydrocarbon seeps, diapirs and fault structures, is combined with deep undercurrents and a complex seafloor morphology. In the Gulf of Cadiz, model depicts the distribution of the base of the gas hydrate stability zone for both biogenic and thermogenic gas compositions, and explains the geometry and distribution of geological structures derived from gas venting in the Tasyo Field (Gulf of Cadiz) and the generation of BSR levels on the upper continental slope.

Chloral hydrate alters the organization of the ciliary basal apparatus and cell organelles in sea urchin embryos

NASA Technical Reports Server (NTRS)

Chakrabarti, A.; Schatten, H.; Mitchell, K. D.; Crosser, M.; Taylor, M.

1998-01-01

The mitotic inhibitor, chloral hydrate, induces ciliary loss in the early embryo phase of Lytechinus pictus. It causes a breakdown of cilia at the junction of the cilium and the basal body known as the basal plate. This leaves the plasma membrane temporarily unsealed. The basal apparatus accessory structures, consisting of the basal body, basal foot, basal foot cap, striated side arm, and striated rootlet, are either misaligned or disintegrated by treatment with chloral hydrate. Furthermore, microtubules which are associated with the basal apparatus are disassembled. Mitochondria accumulate at the base of cilia - underneath the plasma membrane - and show alterations in their structural organization. The accumulation of mitochondria is observed in 40% of all electron micrograph sections while 60% show the areas mostly devoid of mitochondria. The microvilli surrounding a cilium and striated rootlet remain intact in the presence of chloral hydrate. These results suggest that deciliation in early sea urchin embryos by chloral hydrate is caused by combined effects on the ciliary membrane and on microtubules in the cilia. Furthermore, it is suggested that chloral hydrate can serve as a tool to explore the cytoskeletal mechanisms that are involved in cilia motility in the developing sea urchin embryo.

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

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

PubMed

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

2006-11-02

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

Predictive Mechanical Characterization of Macro-Molecular Material Chemistry Structures of Cement Paste at Nano Scale - Two-phase Macro-Molecular Structures of Calcium Silicate Hydrate, Tri-Calcium Silicate, Di-Calcium Silicate and Calcium Hydroxide

NASA Astrophysics Data System (ADS)

Padilla Espinosa, Ingrid Marcela

Concrete is a hierarchical composite material with a random structure over a wide range of length scales. At submicron length scale the main component of concrete is cement paste, formed by the reaction of Portland cement clinkers and water. Cement paste acts as a binding matrix for the other components and is responsible for the strength of concrete. Cement paste microstructure contains voids, hydrated and unhydrated cement phases. The main crystalline phases of unhydrated cement are tri-calcium silicate (C3S) and di-calcium silicate (C2S), and of hydrated cement are calcium silicate hydrate (CSH) and calcium hydroxide (CH). Although efforts have been made to comprehend the chemical and physical nature of cement paste, studies at molecular level have primarily been focused on individual components. Present research focuses on the development of a method to model, at molecular level, and analysis of the two-phase combination of hydrated and unhydrated phases of cement paste as macromolecular systems. Computational molecular modeling could help in understanding the influence of the phase interactions on the material properties, and mechanical performance of cement paste. Present work also strives to create a framework for molecular level models suitable for potential better comparisons with low length scale experimental methods, in which the sizes of the samples involve the mixture of different hydrated and unhydrated crystalline phases of cement paste. Two approaches based on two-phase cement paste macromolecular structures, one involving admixed molecular phases, and the second involving cluster of two molecular phases are investigated. The mechanical properties of two-phase macromolecular systems of cement paste consisting of key hydrated phase CSH and unhydrated phases C3S or C2S, as well as CSH with the second hydrated phase CH were calculated. It was found that these cement paste two-phase macromolecular systems predicted an isotropic material behavior. Also, these systems exhibited a high bulk modulus, compared to the elastic modulus. These results are an indication and concur with the high compression strength of cement paste seen at engineering length scale. In addition, the bulk modulus of two-phase systems consisting of hydrated CSH and unhydrated C3S or C2S was found to increase with higher levels of unhydrated components. The interaction energies of two-phase cement paste molecular structures studied in the present work were calculated, showing that a higher interaction is attained when the two phases are admixed as small components instead of cluster of phases. Finally, the mechanical behavior under shear deformation was predicted by using a quasi-static deformation method and analyzed for a representative two-phase (CSH and C2S) macromolecular structure of cement paste.

Water reorientation in the hydration shells of hydrophilic and hydrophobic solutes

NASA Astrophysics Data System (ADS)

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

2010-06-01

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

CO₂ processing and hydration of fruit and vegetable tissues by clathrate hydrate formation.

PubMed

Takeya, Satoshi; Nakano, Kohei; Thammawong, Manasikan; Umeda, Hiroki; Yoneyama, Akio; Takeda, Tohoru; Hyodo, Kazuyuki; Matsuo, Seiji

2016-08-15

CO2 hydrate can be used to preserve fresh fruits and vegetables, and its application could contribute to the processing of carbonated frozen food. We investigated water transformation in the frozen tissue of fresh grape samples upon CO2 treatment at 2-3 MPa and 3°C for up to 46 h. Frozen fresh bean, radish, eggplant and cucumber samples were also investigated for comparison. X-ray diffraction indicated that after undergoing CO2 treatment for several hours, structure I CO2 hydrate formed within the grape tissue. Phase-contrast X-ray imaging using the diffraction-enhanced imaging technique revealed the presence of CO2 hydrate within the intercellular spaces of these tissues. The carbonated produce became effervescent because of the dissociation of CO2 hydrate through the intercellular space, especially above the melting point of ice. In addition, suppressed metabolic activity resulting from CO2 hydrate formation, which inhibits water and nutrient transport through intercellular space, can be expected. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

Thermodynamic and hydration effects for the incorporation of a cationic 3-aminopropyl chain into DNA

PubMed Central

Soto, Ana Maria; Kankia, Besik I.; Dande, Prasad; Gold, Barry; Marky, Luis A.

2002-01-01

The introduction of cationic 5-(ω-aminoalkyl)-2′-deoxypyrimidines into duplex DNA has been shown to induce DNA bending. In order to understand the energetic and hydration contributions for the incorporation of a cationic side chain in DNA a combination of spectroscopy, calorimetry and density techniques were used. Specifically, the temperature unfolding and isothermal formation was studied for a pair of duplexes with sequence d(CGTAGUCG TGC)/d(GCACGACTACG), where U represents 2′-deoxyuridine (‘control’) or 5-(3-aminopropyl)-2′-deoxyuridine (‘modified’). Continuous variation experiments confirmed 1:1 stoichiometries for each duplex and the circular dichroism spectra show that both duplexes adopted the B conformation. UV and differential scanning calorimetry melting experiments reveal that each duplex unfolds in two-state transitions. In low salt buffer, the ‘modified’ duplex is more stable and unfolds with a lower endothermic heat and lower release of counterion and water. This electrostatic stabilization is entropy driven and disappears at higher salt concentrations. Complete thermodynamic profiles at 15°C show that the favorable formation of each duplex results from the compensation of a favorable exothermic heat with an unfavorable entropy contribution. However, the isothermal profiles yielded a differential enthalpy of 8.8 kcal/mol, which is 4.3 kcal/mol higher than the differential enthalpy observed in the unfolding profiles. This indicates that the presence of the aminopropyl chain induces an increase in base stacking interactions in the modified single strand and a decrease in base stacking interactions in the modified duplex. Furthermore, the formation of the ‘control’ duplex releases water while the ‘modified’ duplex takes up water. Relative to the control duplex, formation of the modified duplex at 15°C yielded a marginal differential ΔG° term, positive ΔΔHITC–Δ(TΔS) compensation, negative ΔΔV and a net release of counterions. The opposite signs of the differential enthalpy–entropy compensation and differential volume change terms show a net uptake of structural water around polar and non-polar groups. This indicates that incorporation of the aminopropyl chain induces a higher exposure of aromatic bases to the solvent, which may be consistent with a small and local bend in the ‘modified’ duplex. PMID:12136099

Thick massive gas hydrate deposits were revealed by LWD in Off-Joetsu area, eastern margin of Japan Sea.

NASA Astrophysics Data System (ADS)

Tanahashi, M.; Morita, S.; Matsumoto, R.

2016-12-01

GR14 and HR15 survey cruises, which were dedicated to the LWD (Logging While Drilling), were carried out in summers of 2014 and 2015, respectively, by Meiji University and Geological Survey of Japan, AIST to explore the "gas chimney" structures in eastern margin of Japan Sea. Shallow (33 to 172m-bsf, average 136m-bsf) 33 LWD drilling were performed in Oki Trough, Off-Joetsu, and Mogami Trough areas along eastern margin of Japan Sea during two cruises. Schlumberger LWD tools, GeoVISION (resistivity), TeleScope, ProVISION (NMR) and SonicVISION were used during GR14. NeoScope (neutron) was added and SonicScope was replaced for SonicVISION during HR14. The data quality was generally good. "Gas chimney" structures with acoustic blanking columns on the high frequency seismic sections with mound and pockmark morphologic features on the sea bottom, are well developed within survey areas. Every LWD records taken from gas chimney structures during the cruises show high resistivity and acoustic velocity anomalies which suggest the development of gas hydrate. Characteristic development of massive gas hydrate was interpreted at the Umitaka CW mound structure, Off-Joetsu. The mound lies at 890-910m in water depth and has very rough bottom surface, regional high resistivity, regional high heat flow, several natural seep sites, 200m x 300m area, and 10-20m height. 8 LWD holes, J18L to J21L and J23L to J26L, were drilled on and around the mound. There are highly anomalous intervals which suggest the development of massive gas hydrate at J24L, with high resistivity, high Vp and Vs, high neutron porosity, low natural gamma ray intensity, low neutron gamma density, low NMR porosity, low NMR permeability, low formation sigma, from 10 to 110m-bsf with intercalating some thin less hydrate layers. It is interpreted that there is several tens of meter thick massive gas hydrate in the gas chimney mound. It is partly confirmed by the later nearby coring result which showed the repetition of the several meter thick massive hydrate recovery (Matsumoto et al., in this conference). Other LWD data at the sites on the mound shows lesser than J24L but still highly concentrated gas hydrate deposits. This study was conducted as a part of the methane hydrate research project funded by METI (the Ministry of Economy, Trade and Industry, Japan).

Effects of Incorporating High-Volume Fly Ash into Tricalcium Silicate on the Degree of Silicate Polymerization and Aluminum Substitution for Silicon in Calcium Silicate Hydrate

DOE PAGES

Bae, Sungchul; Taylor, Rae; Kilcoyne, David; ...

2017-02-04

This study assesses the quantitative effects of incorporating high-volume fly ash (HVFA) into tricalcium silicate (C 3S) paste on the hydration, degree of silicate polymerization, and Al substitution for Si in calcium silicate hydrate (C–S–H). Thermogravimetric analysis and isothermal conduction calorimetry showed that, although the induction period of C 3S hydration was significantly extended, the degree of hydration of C 3S after the deceleration period increased due to HVFA incorporation. Synchrotron-sourced soft X-ray spectromicroscopy further showed that most of the C 3S in the C 3S-HVFA paste was fully hydrated after 28 days of hydration, while that in the puremore » C 3S paste was not. The chemical shifts of the Si K edge peaks in the near-edge X-ray fine structure of C–S–H in the C 3S-HVFA paste directly indicate that Al substitutes for Si in C–S–H and that the additional silicate provided by the HVFA induces an enhanced degree of silicate polymerization. This new spectromicroscopic approach, supplemented with 27Al and 29Si magic-angle spinning nuclear magnetic resonance spectroscopy and transmission electron microscopy, turned out to be a powerful characterization tool for studying a local atomic binding structure of C–S–H in C 3S-HVFA system and presented results consistent with previous literature.« less

Effects of Incorporating High-Volume Fly Ash into Tricalcium Silicate on the Degree of Silicate Polymerization and Aluminum Substitution for Silicon in Calcium Silicate Hydrate

PubMed Central

Bae, Sungchul; Taylor, Rae; Kilcoyne, David; Moon, Juhyuk; Monteiro, Paulo J. M.

2017-01-01

This study assesses the quantitative effects of incorporating high-volume fly ash (HVFA) into tricalcium silicate (C3S) paste on the hydration, degree of silicate polymerization, and Al substitution for Si in calcium silicate hydrate (C–S–H). Thermogravimetric analysis and isothermal conduction calorimetry showed that, although the induction period of C3S hydration was significantly extended, the degree of hydration of C3S after the deceleration period increased due to HVFA incorporation. Synchrotron-sourced soft X-ray spectromicroscopy further showed that most of the C3S in the C3S-HVFA paste was fully hydrated after 28 days of hydration, while that in the pure C3S paste was not. The chemical shifts of the Si K edge peaks in the near-edge X-ray fine structure of C–S–H in the C3S-HVFA paste directly indicate that Al substitutes for Si in C–S–H and that the additional silicate provided by the HVFA induces an enhanced degree of silicate polymerization. This new spectromicroscopic approach, supplemented with 27Al and 29Si magic-angle spinning nuclear magnetic resonance spectroscopy and transmission electron microscopy, turned out to be a powerful characterization tool for studying a local atomic binding structure of C–S–H in C3S-HVFA system and presented results consistent with previous literature. PMID:28772490

Effects of Incorporating High-Volume Fly Ash into Tricalcium Silicate on the Degree of Silicate Polymerization and Aluminum Substitution for Silicon in Calcium Silicate Hydrate

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

Bae, Sungchul; Taylor, Rae; Kilcoyne, David

This study assesses the quantitative effects of incorporating high-volume fly ash (HVFA) into tricalcium silicate (C 3S) paste on the hydration, degree of silicate polymerization, and Al substitution for Si in calcium silicate hydrate (C–S–H). Thermogravimetric analysis and isothermal conduction calorimetry showed that, although the induction period of C 3S hydration was significantly extended, the degree of hydration of C 3S after the deceleration period increased due to HVFA incorporation. Synchrotron-sourced soft X-ray spectromicroscopy further showed that most of the C 3S in the C 3S-HVFA paste was fully hydrated after 28 days of hydration, while that in the puremore » C 3S paste was not. The chemical shifts of the Si K edge peaks in the near-edge X-ray fine structure of C–S–H in the C 3S-HVFA paste directly indicate that Al substitutes for Si in C–S–H and that the additional silicate provided by the HVFA induces an enhanced degree of silicate polymerization. This new spectromicroscopic approach, supplemented with 27Al and 29Si magic-angle spinning nuclear magnetic resonance spectroscopy and transmission electron microscopy, turned out to be a powerful characterization tool for studying a local atomic binding structure of C–S–H in C 3S-HVFA system and presented results consistent with previous literature.« less

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.

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

USGS Publications Warehouse

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

1998-01-01

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

Structural determinants of hydration, mechanics and fluid flow in freeze-dried collagen scaffolds.

PubMed

Offeddu, G S; Ashworth, J C; Cameron, R E; Oyen, M L

2016-09-01

Freeze-dried scaffolds provide regeneration templates for a wide range of tissues, due to their flexibility in physical and biological properties. Control of structure is crucial for tuning such properties, and therefore scaffold functionality. However, the common approach of modeling these scaffolds as open-cell foams does not fully account for their structural complexity. Here, the validity of the open-cell model is examined across a range of physical characteristics, rigorously linking morphology to hydration and mechanical properties. Collagen scaffolds with systematic changes in relative density were characterized using Scanning Electron Microscopy, X-ray Micro-Computed Tomography and spherical indentation analyzed in a time-dependent poroelastic framework. Morphologically, all scaffolds were mid-way between the open- and closed-cell models, approaching the closed-cell model as relative density increased. Although pore size remained constant, transport pathway diameter decreased. Larger collagen fractions also produced greater volume swelling on hydration, although the change in pore diameter was constant, and relatively small at ∼6%. Mechanically, the dry and hydrated scaffold moduli varied quadratically with relative density, as expected of open-cell materials. However, the increasing pore wall closure was found to determine the time-dependent nature of the hydrated scaffold response, with a decrease in permeability producing increasingly elastic rather than viscoelastic behavior. These results demonstrate that characterizing the deviation from the open-cell model is vital to gain a full understanding of scaffold biophysical properties, and provide a template for structural studies of other freeze-dried biomaterials. Freeze-dried collagen sponges are three-dimensional microporous scaffolds that have been used for a number of exploratory tissue engineering applications. The characterization of the structure-properties relationships of these scaffolds is necessary to understand their biophysical behavior in vivo. In this work, the relationship between morphology and physical properties in the dry and hydrated states was investigated across a range of solid concentrations in the scaffolds. The quantitative results provided can aid the design of scaffolds with a target trade-off between mechanical properties and structural features important for their biological activity. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. 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.

Quasielastic and inelastic neutron scattering study of the hydration of monoclinic and triclinic tricalcium silicate

NASA Astrophysics Data System (ADS)

Peterson, Vanessa K.; Brown, Craig M.; Livingston, Richard A.

2006-08-01

The hydration of Mg-stabilized triclinic and monoclinic tricalcium silicate samples were studied using quasielastic neutron scattering to follow the fixation of hydrogen into the reaction products and by applying hydration models to the data. The quantity of Ca(OH) 2 produced during hydration was also determined using inelastic neutron scattering. The monoclinic form was found to be intrinsically less reactive that the triclinic form. The monoclinic form was also confirmed to produce more product than the triclinic form after 50 h, a process found to occur through a longer, rather than earlier, nucleation and growth regime. Results indicated an increase in the permeability of the hydration layer product relative to the triclinic form and the increase in the length of the nucleation and growth regime was thus attributed to an alteration in morphology or structure of the hydration layer product, extending the time for diffusion limited mechanics to be reached.

Hydration of sulfonated polyimide membranes. I. Na + and NH +(C 2H 5) 3 homopolymers

NASA Astrophysics Data System (ADS)

Jamróz, Dorota; Maréchal, Yves

2004-05-01

Hydration of Na + and HN +(C 2H 5) 3 sulfonated polyimide membranes is probed by infrared spectrometry using a recently described method. These membranes consist of identical sulfonated repeat unit (homopolymers) and form a good starting point to study more elaborated membranes, composed of these units plus similar ones with no sulfonic groups (block copolymers). These latter membranes may be used in fuel cells and will be described in a forthcoming article. We first identify the bands of hydrophilic groups, which will be anchor points for hydration. We then define three 'elementary hydration spectra' onto which all hydration spectra can be decomposed. Their analysis allows us to measure the water uptake of these membranes as a function of the hygrometry of the ambient atmosphere and to determine the structures of the dried membranes and their hydration mechanisms in terms of chemical reactions.

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.

Theoretical studies of UO(2)(OH)(H(2)O)(n) (+), UO(2)(OH)(2)(H(2)O)(n), NpO(2)(OH)(H(2)O)(n), and PuO(2)(OH)(H(2)O)(n) (+) (n

PubMed

Cao, Zhiji; Balasubramanian, K

2009-10-28

Extensive ab initio calculations have been carried out to study equilibrium structures, vibrational frequencies, and the nature of chemical bonds of hydrated UO(2)(OH)(+), UO(2)(OH)(2), NpO(2)(OH), and PuO(2)(OH)(+) complexes that contain up to 21 water molecules both in first and second hydration spheres in both aqueous solution and the gas phase. The structures have been further optimized by considering long-range solvent effects through a polarizable continuum dielectric model. The hydrolysis reaction Gibbs free energy of UO(2)(H(2)O)(5) (2+) is computed to be 8.11 kcal/mol at the MP2 level in good agreement with experiments. Our results reveal that it is necessary to include water molecules bound to the complex in the first hydration sphere for proper treatment of the hydrated complex and the dielectric cavity although water molecules in the second hydration sphere do not change the coordination complex. Structural reoptimization of the complex in a dielectric cavity seems inevitable to seek subtle structural variations in the solvent and to correlate with the observed spectra and thermodynamic properties in the aqueous environment. Our computations reveal dramatically different equilibrium structures in the gas phase and solution and also confirm the observed facile exchanges between the complex and bulk solvent. Complete active space multiconfiguration self-consistent field followed by multireference singles+doubles CI (MRSDCI) computations on smaller complexes confirm predominantly single-configurational nature of these species and the validity of B3LYP and MP2 techniques for these complexes in their ground states.

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

PubMed

Rudling, Axel; Orro, Adolfo; Carlsson, Jens

2018-02-26

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

Cationic lipids bearing succinic-based, acyclic and macrocyclic hydrophobic domains: Synthetic studies and in vitro gene transfer.

PubMed

Jubeli, Emile; Maginty, Amanda B; Khalique, Nada Abdul; Raju, Liji; Nicholson, David G; Larsen, Helge; Pungente, Michael D; Goldring, William P D

2017-01-05

In this communication we describe the construction of four succinic-based cationic lipids, their formulation with plasmid DNA (pDNA), and an evaluation of their in vitro gene delivery into Chinese hamster ovarian (CHO-K1) cells. The cationic lipids employed in this work possess either a dimethylamine or trimethylamine headgroup, and a macrocyclic or an acyclic hydrophobic domain composed of, or derived from two 16-atom, succinic-based acyl chains. The synthesized lipids and a co-lipid of neutral charge, either cholesterol or 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), were formulated in an overall 3:2 cationic-to-neutral lipid molar ratio, then complexed with plasmid DNA (pDNA). The relative transfection performance was evaluated via a comparison between matched versus mismatched formulations defined by the rigidity relationship between the lipids employed. Gel electrophoresis was used to characterize the binding of the lipid formulations with plasmid DNA and the relative degree of plasmid degradation using a DNase I degradation assay. Small angle X-ray diffraction (SAXD) was employed to characterize the packing morphology of the lipid-DNA complexes. In general, the succinic unit embedded within the hydrophobic domain of the cationic lipids was found to improve lipid hydration. The transfection assays revealed a general trend in which mismatched formulations that employed a rigid lipid combined with a non-rigid (or flexible) lipid, outperformed the matched formulations. The results from this work suggest that the design of the cationic lipid structure and the composition of the lipoplex formulation play key roles in governing the transfection performance of nonviral gene delivery agents. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

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

PubMed

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

2014-12-07

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

Magnetic Tracking of Gas Hydrate Deposits.

NASA Astrophysics Data System (ADS)

Lowe, C.; Enkin, R. J.; Judith, B.; Dallimore, S. R.

2005-12-01

Analysis of recovered core from the Mallik gas hydrate field in the Mackenzie Delta, Northwest Territories, Canada demonstrates that the magnetic properties of hydrate-bearing strata differ significantly from those strata lacking gas hydrate. The recovered core, which extends from just above (885 m) to just below (1152 m) observed gas hydrate occurrences (891-1107 m), comprises a series of six stratigraphic units that are either sand or silt dominated. Gas hydrate is preferentially concentrated in the higher porosity, sand-dominated units. Although the sediment source region for the Mackenzie Delta is sufficiently large that silts and sands have similar primary mineralogy, their magnetic properties are distinct. Magnetite, apparent in silt units with porosities too low to accommodate significant gas hydrate deposits, is reduced to iron sulphide in the gas hydrate-bearing sand horizons. The degree of the observed magnetic reduction increases with increasing gas hydrate concentration. Furthermore, silts retain their primary magnetism, whereas sands are remagnetized. Two independent investigations of marine gas hydrate occurrences (Blake Ridge, offshore eastern USA and Cascadia, offshore western Canada) demonstrate similar magnetic reduction within known gas hydrate fields, and an even larger depletion of magnetic minerals in vent zones where methane is actively fluxing to surface. Collectively, the findings from these three regions indicate that porosity and structure are fundamental controls on methane pathways. Investigations are presently underway to determine the precise triggers and chemical pathways of the observed magnetic reductions. However, findings to date indicate that magnetic studies of host sediments in gas hydrate systems provide a powerful lithologic correlation tool, a window into the processes associated with gas hydrate formation, and form the basis of quantitative analysis of magnetic surveys over gas hydrate deposits.

Distributional prediction of Pleistocene forearc minibasin turbidites in the NE Nankai Trough area (off central Japan)

NASA Astrophysics Data System (ADS)

Egawa, K.; Furukawa, T.; Saeki, T.; Suzuki, K.; Narita, H.

2011-12-01

Natural gas hydrate-related sequences commonly provide unclear seismic images due to bottom simulating reflector, a seismic indicator of the theoretical base of gas hydrate stability zone, which usually causes problems for fully analyzing the detailed sedimentary structures and seismic facies. Here we propose an alternative technique to predict the distributional pattern of gas hydrate-related deep-sea turbidites with special reference to a Pleistocene forearc minibasin in the northeastern Nankai Trough area, off central Japan, from the integrated 3D structural and sedimentologic modeling. Structural unfolding and stratigraphic backstripping successively modeled a simple horseshoe-shaped paleobathymetry of the targeted turbidite sequence. Based on best-fit matching of net-to-gross ratio (or sand fraction) between the model and wells, subsequent turbidity current modeling on the restored paleobathymetric surface during a single flow event demonstrated excellent prediction results showing the morphologically controlled turbidity current evolution and selective turbidite sand distribution within the modeled minibasin. Also, multiple turbidity current modeling indicated the stacking sheet turbidites with regression and proximal/distal onlaps in the minibasin due to reflections off an opposing slope, whose sedimentary features are coincident with the seismic interpretation. Such modeling works can help us better understand the depositional pattern of gas hydrate-related, unconsolidated turbidites and also can improve gas hydrate reservoir characterization. This study was financially supported by MH21 Research Consortium.

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.

Chemical determination of free radical-induced damage to DNA.

PubMed

Dizdaroglu, M

1991-01-01

Free radical-induced damage to DNA in vivo can result in deleterious biological consequences such as the initiation and promotion of cancer. Chemical characterization and quantitation of such DNA damage is essential for an understanding of its biological consequences and cellular repair. Methodologies incorporating the technique of gas chromatography/mass spectrometry (GC/MS) have been developed in recent years for measurement of free radical-induced DNA damage. The use of GC/MS with selected-ion monitoring (SIM) facilitates unequivocal identification and quantitation of a large number of products of all four DNA bases produced in DNA by reactions with hydroxyl radical, hydrated electron, and H atom. Hydroxyl radical-induced DNA-protein cross-links in mammalian chromatin, and products of the sugar moiety in DNA are also unequivocally identified and quantitated. The sensitivity and selectivity of the GC/MS-SIM technique enables the measurement of DNA base products even in isolated mammalian chromatin without the necessity of first isolating DNA, and despite the presence of histones. Recent results reviewed in this article demonstrate the usefulness of the GC/MS technique for chemical determination of free radical-induced DNA damage in DNA as well as in mammalian chromatin under a vast variety of conditions of free radical production.

Hydration structure of the α-chymotrypsin substrate binding pocket: the impact of constrained geometry

NASA Astrophysics Data System (ADS)

Carey, Christina; Cheng, Yuen-Kit; Rossky, Peter J.

2000-08-01

The concave substrate binding pocket of α-chymotrypsin binds specifically hydrophobic side chains. In order to understand the hydration structure present in the absence of substrate, and elucidate the character of the solvent displaced on binding, molecular dynamics computer simulation of the solvent in a fully hydrated protein has been carried out and analyzed. The pocket is found to be characterized in terms of a mixed polar and apolar macromolecular surface. It is shown that the simulated solvent structure within it is spatially consistent with that seen via crystallography. The solvent structure is energetically characterized by large losses in hydrogen bonding among solvent molecules except at the mouth of the pocket where exposure to bulk-like solvent is possible. The loss in hydrogen bonding is attributed to the highly constrained geometry available to the solvent, preventing formation of a hydrogen bonding network, with only partial compensation by interactions with the macromolecular surface. The solvent displacement concomitant with substrate binding will therefore be associated with a large enthalpic driving force. This result is at the extreme of a continuum of variable cases of "hydrophobic" hydration, which differ most basically in surface curvature. These range from convex solute surfaces, inducing clathrate-like structures, with negligible hydrogen bond loss, to flat surfaces with significant interfacial loss, to the present concave case with hydrogen bonding losses exceeding 50%.

Detailed Gas Chimney Structures in Joetsu Area at Southeastern Margin of Japan Sea, Revealed by High-Resolution 3D Seismic Survey (HR3D)

NASA Astrophysics Data System (ADS)

Ohkawa, S.; Hiruta, A.; Yanagimoto, Y.; Matsumoto, R.; Asakawa, E.

2016-12-01

To delineate the detailed structure of the gas chimneys, a high-resolution three-dimensional seismic survey (HR3D) was carried out in Joetsu area, at the southeastern margin of Japan Sea where hydrate-related mound and pockmark systems with gas chimneys are widely developed. HR3D data have successfully revealed the fine structure of gas chimneys which were not clearly imaged by the existing seismic data, such as sub-bottom profilers and conventional large-scale 3D surveys for petroleum exploration. HR3D data are also useful to interpolate and extrapolate spatially the geological/geophysical information obtained at wells most of which were drilled into the gas hydrate concentrated zones (GHCZs.) In the areas of low hydrate concentration, the reflections show a parallel-stratified pattern and the bottom simulating reflector (BSR) is parallel to the sea floor reflections. On the other hand, GHCZs are seismologically characterized by (1) strong sea floor reflections on the chimney mounds, (2) chaotic reflection patterns in the chimneys, and (3) pull-up of bottom simulating reflector (BSR) as shown in the attached figure. Strong sea floor reflections suggest that solid hydrates deposit in the very shallow part beneath the sea floor and the chaotic reflections indicate the hydrates are not continuously layered but interspersedly distributed. The BSR pull-up phenomena as much as 70 80msec are caused by high-velocity materials existing between the sea floor and the BSR. The sonic logs acquired by LWD at wells drilled into GHCZs show high velocity up to 3,800 m/s in the massive hydrates. The pull-up times estimated from the sonic data are consistent in general with the observed pull-up times on HR3D sections, suggesting the pull-up times could be useful for a preliminary evaluation of hydrate zones before drilling and/or in the areas without well data. 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.)

Characterization of Gas Hydrate Samples from IODP 311 using High Resolution Raman Spectroscopy, X-ray Diffraction and Differential Scanning Calorimetry

NASA Astrophysics Data System (ADS)

Schicks, J. M.; Ziemann, M. A.; Naumann, R.; Erzinger, J.

2006-12-01

Investigations on hydrate bearing sediments taken from different locations (Gulf of Mexico, Sea of Okhotsk, etc.) lead to the conclusion that the coexistence of gas hydrates with different structures and compositions in nature is possible (Sassen et al. 2000, Takeya et al 2006). The aim of this study is to get more information about the variation in local composition of gas hydrates in samples from IODP Leg 311 (Hole 1328) using Raman spectroscopy. Therefore, in addition to investigations performed at the same samples by Lu et al., experiments in this study have been carried out with a confocal Raman microprobe in high lateral and spectral resolution mode. The samples have been analysed at 153 K and at atmospheric pressure (single spots, line scans, area mapping). The specified structure I hydrates contain methane and H2S. The Raman bands at 2569 cm-1 and 2593 cm-1 indicate H2S in large and small cages, respectively. Further information is provided about the variation of the CH4-H2S- composition and the cage occupancy of the sample. The samples have also been investigated with X-ray diffraction and differential scanning calorimetry (DSC). DSC measurements hint at the coexistence of two different gas hydrates with significantly different decomposition temperatures at atmospheric pressure (206 K and 247 K). This could be caused by variable amounts of H2S incorporated in the hydrate lattice. The results from the investigation on the IODP Leg 311 samples are compared and discussed with results of similar investigations on samples of structure I hydrate from Mallik 5L-38 drill hole in the permafrost of NW Canada. References: R. Sassen, S.T. Sweet, D.A. DeFreitas, A.V. Milkov, 2000. Organic Geochemistry, 31, 1257-1262. S. Takeya, M. Kida, H. Minami, H. Sakagami, A. Hachikubo, N. Takahashi, H. Shoji, V. Soloviev, K. Wallmann, N. Biebow, A. Obzhirov, A Salomatin, J. Poort, 2006. Chemical Engineering Science, 61, 2670- 2674.

Structures of Hydrated Alkali Metal Cations, M+(H2O)nAr (m = Li, Na, K, rb and Cs, n = 3-5), Using Infrared Photodissociation Spectroscopy and Thermodynamic Analysis

NASA Astrophysics Data System (ADS)

Ke, Haochen; van der Linde, Christian; Lisy, James M.

2014-06-01

Alkali metal cations play vital roles in chemical and biochemical systems. Lithium is widely used in psychiatric treatment of manic states and bipolar disorder; Sodium and potassium are essential elements, having major biological roles as electrolytes, balancing osmotic pressure on body cells and assisting the electroneurographic signal transmission; Rubidium has seen increasing usage as a supplementation for manic depression and depression treatment; Cesium doped compounds are used as essential catalysts in chemical production and organic synthesis. Since hydrated alkali metal cations are ubiquitous and the basic form of the alkali metal cations in chemical and biochemical systems, their structural and thermodynamic properties serve as the foundation for modeling more complex chemical and biochemical processes, such as ion transport and ion size-selectivity of ionophores and protein channels. By combining mass spectrometry and infrared photodissociation spectroscopy, we have characterized the structures and thermodynamic properties of the hydrated alkali metal cations, i.e. M+(H2O)nAr, (M = Li, Na, K, Rb and Cs, n = 3-5). Ab initio calculations and RRKM-EE (evaporative ensemble) calculations were used to assist in the spectral assignments and thermodynamic analysis. Results showed that the structures of hydrated alkali metal cations were determined predominantly by the competition between non-covalent interactions, i.e. the water---water hydrogen bonding interactions and the water---cation electrostatic interactions. This balance, however, is very delicate and small changes, i.e. different cations, different levels of hydration and different effective temperatures clearly impact the balance.

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

PubMed

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

2012-03-01

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

Mg-Sulfate Salts as Possible Water Reservoirs in Martian Regolith

NASA Astrophysics Data System (ADS)

Vaniman, D. T.; Bish, D. L.; Chipera, S. J.; Carey, J. W.; Feldman, W. C.

2003-12-01

Neutron spectrometer data from the Mars Odyssey orbiter provide evidence of high water-equivalent hydrogen abundance in some near-equatorial locations on Mars. In broad regions shallow (<1 m) regolith appears to have water abundances of up to ˜13 wt%. Water ice is predicted to be unstable at the present time at all depths below the surface in these equatorial regions. If present in hydrous silicate minerals such as clays or zeolites, which may contain water in abundances of ˜10-20% at Martian surface conditions, the Odyssey data require a regolith very enriched in hydrous silicates - an unlikely proposition. Viking X-ray fluorescence data and alteration assemblages in martian meteorites suggest the presence of sulfate salts in martian regolith. Viking data from excavated duricrust indicate that Mg and S are correlated and that ˜10% of an Mg-sulfate salt is a likely cementing agent. However, the range of possible Mg sulfates is large. Epsomite (7-hydrate, 51% water) and hexahydrite (6-hydrate, 47% water) are the most hydrated; both form structures of isolated SO4 tetrahedra with isolated octahedral sites consisting of Mg coordinated by six H2O molecules (epsomite has an extra H2O in addition to the six required to coordinate with Mg). Pentahydrite (5-hydrate, 43% water) has infinite chains of alternating SO4 tetrahedra and Mg octahedra, with 4/5 of the water forming apices in octahedral sites. Starkeyite (4-hydrate, 37% water) has clusters of two SO4 tetrahedra and two Mg octahedra, linked only by hydrogen bonds. The Mg-sulfate sanderite (2-hydrate, 23% water) is rare and has poorly known structure. Kieserite (1-hydrate, 13% water) is relatively common in evaporite deposits and has a framework structure of infinite tetrahedral-octahedral chains cross-linked by hydrogen bonds. The stability of Mg-sulfate hydrates under martian near-surface conditions depends on their structures; those with excess water beyond that required to form the octahedral Mg site (e.g., epsomite, pentahydrite) lose that excess readily. Experiments with epsomite and hexahydrite indicate great sensitivity to environmental conditions; epsomite is not stable at 295 K at relative humidity (RH) values less than about 55%, below which hexahydrite is the observed phase. More importantly, hexahydrite - with all water coordinated to Mg in octahedral sites - is unstable at pressures less than ˜20 mtorr. X-ray diffraction analysis of hexahydrite held at 20 mtorr for six hours shows that structural degradation is slow at 100 K but becomes obvious in 1 hour at 273 K. Thermogravimetric analysis of this amorphous solid shows that it contains ˜26% H2O (compared with 47% in crystalline hexahydrite), and its observed macroscopic expansion behavior suggests that it can reversibly hydrate and dehydrate. Although neither epsomite nor hexahydrite is likely to be stable near the surface of Mars, their amorphous derivatives or crystalline forms of the lower hydrates might be present (preliminary thermogravimetric data indicate that kieserite is likely to be stable). However, the limited rehydration of structurally degraded hexahydrite indicates that unrealistically large amounts ( ˜50%) would be required in the upper meter of regolith to account for the higher water contents ( ˜13%) suggested for some martian equatorial regions; even larger amounts of kieserite ( ˜100%) would be required. A more important role for sulfates may be in the formation of a low-permeability salt crust that could restrict dewatering of underlying soil horizons.

Liquefaction of Biopolymers: Solvent-free Liquids and Liquid Crystals from Nucleic Acids and Proteins.

PubMed

Liu, Kai; Ma, Chao; Göstl, Robert; Zhang, Lei; Herrmann, Andreas

2017-05-16

Biomacromolecules, such as nucleic acids, proteins, and virus particles, are persistent molecular entities with dimensions that exceed the range of their intermolecular forces hence undergoing degradation by thermally induced bond-scission upon heating. Consequently, for this type of molecule, the absence of a liquid phase can be regarded as a general phenomenon. However, certain advantageous properties usually associated with the liquid state of matter, such as processability, flowability, or molecular mobility, are highly sought-after features for biomacromolecules in a solvent-free environment. Here, we provide an overview over the design principles and synthetic pathways to obtain solvent-free liquids of biomacromolecular architectures approaching the topic from our own perspective of research. We will highlight the milestones in synthesis, including a recently developed general surfactant complexation method applicable to a large variety of biomacromolecules as well as other synthetic principles granting access to electrostatically complexed proteins and DNA. These synthetic pathways retain the function and structure of the biomacromolecules even under extreme, nonphysiological conditions at high temperatures in water-free melts challenging the existing paradigm on the role of hydration in structural biology. Under these conditions, the resulting complexes reveal their true potential for previously unthinkable applications. Moreover, these protocols open a pathway toward the assembly of anisotropic architectures, enabling the formation of solvent-free biomacromolecular thermotropic liquid crystals. These ordered biomaterials exhibit vastly different mechanical properties when compared to the individual building blocks. Beyond the preparative aspects, we will shine light on the unique potential applications and technologies resulting from solvent-free biomacromolecular fluids: From charge transport in dehydrated liquids to DNA electrochromism to biocatalysis in the absence of a protein hydration shell. Moreover, solvent-free biological liquids containing viruses can be used as novel storage and process media serving as a formulation technology for the delivery of highly concentrated bioactive compounds. We are confident that this new class of hybrid biomaterials will fuel further studies and applications of biomacromolecules beyond water and other solvents and in a much broader context than just the traditional physiological conditions.

Conformation, structure and molecular solvation: a spectroscopic and computational study of 2-phenoxy ethanol and its singly and multiply hydrated clusters

NASA Astrophysics Data System (ADS)

Macleod, Neil A.; Simons, John P.

2002-10-01

The conformational landscapes of 2-phenoxy ethanol (POX) and its hydrated clusters have been studied in the gas-phase, providing a model for pharmaceutical β-blockers. A combination of experimental techniques, including resonant two-photon ionisation (R2PI), laser-induced-fluorescence (LIF) and resonant ion-dip infra-red spectroscopy (RIDIRS), coupled with high-level ab initio calculations has allowed the assignment of the individually resolved spectral features to discrete conformational and supra-molecular structures. Assignments were made by comparison of experimental vibrational spectra and partially resolved ultra-violet rotational band contours with those predicted from quantum chemical calculations. The isolated molecule displays a solitary structure with an extended geometry of the side-chain which is stabilised by an intramolecular hydrogen-bond between the alcohol (proton donor) and the ether (proton acceptor) groups of the side-chain. In singly hydrated clusters the water molecule is accommodated by insertion into the intramolecular hydrogen-bond. In the doubly hydrated and higher clusters cyclic structures are generated which incorporate both the water molecules and the terminal OH group of the side-chain; additional (weak) hydrogen bonded interactions with the phenoxy group provide a degree of selectivity but essentially, the water 'droplet' forms on the end of the alcohol side-chain.

A relationship between three-dimensional surface hydration structures and force distribution measured by atomic force microscopy.

PubMed

Miyazawa, Keisuke; Kobayashi, Naritaka; Watkins, Matthew; Shluger, Alexander L; Amano, Ken-ichi; Fukuma, Takeshi

2016-04-07

Hydration plays important roles in various solid-liquid interfacial phenomena. Very recently, three-dimensional scanning force microscopy (3D-SFM) has been proposed as a tool to visualise solvated surfaces and their hydration structures with lateral and vertical (sub) molecular resolution. However, the relationship between the 3D force map obtained and the equilibrium water density, ρ(r), distribution above the surface remains an open question. Here, we investigate this relationship at an interface of an inorganic mineral, fluorite, and water. The force maps measured in pure water are directly compared to force maps generated using the solvent tip approximation (STA) model and from explicit molecular dynamics simulations. The results show that the simulated STA force map describes the major features of the experimentally obtained force image. The agreement between the STA data and the experiment establishes the correspondence between the water density used as an input to the STA model and the experimental hydration structure and thus provides a tool to bridge the experimental force data and atomistic solvation structures. Further applications of this method should improve the accuracy and reliability of both interpretation of 3D-SFM force maps and atomistic simulations in a wide range of solid-liquid interfacial phenomena.

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

A reusable PZT transducer for monitoring initial hydration and structural health of concrete.

PubMed

Yang, Yaowen; Divsholi, Bahador Sabet; Soh, Chee Kiong

2010-01-01

During the construction of a concrete structure, strength monitoring is important to ensure the safety of both personnel and the structure. Furthermore, to increase the efficiency of in situ casting or precast of concrete, determining the optimal time of demolding is important for concrete suppliers. Surface bonded lead zirconate titanate (PZT) transducers have been used for damage detection and parameter identification for various engineering structures over the last two decades. In this work, a reusable PZT transducer setup for monitoring initial hydration of concrete and structural health is developed, where a piece of PZT is bonded to an enclosure with two bolts tightened inside the holes drilled in the enclosure. An impedance analyzer is used to acquire the admittance signatures of the PZT. Root mean square deviation (RMSD) is employed to associate the change in concrete strength with changes in the PZT admittance signatures. The results show that the reusable setup is able to effectively monitor the initial hydration of concrete and the structural health. It can also be detached from the concrete for future re-use.

A Reusable PZT Transducer for Monitoring Initial Hydration and Structural Health of Concrete

PubMed Central

Yang, Yaowen; Divsholi, Bahador Sabet; Soh, Chee Kiong

2010-01-01

During the construction of a concrete structure, strength monitoring is important to ensure the safety of both personnel and the structure. Furthermore, to increase the efficiency of in situ casting or precast of concrete, determining the optimal time of demolding is important for concrete suppliers. Surface bonded lead zirconate titanate (PZT) transducers have been used for damage detection and parameter identification for various engineering structures over the last two decades. In this work, a reusable PZT transducer setup for monitoring initial hydration of concrete and structural health is developed, where a piece of PZT is bonded to an enclosure with two bolts tightened inside the holes drilled in the enclosure. An impedance analyzer is used to acquire the admittance signatures of the PZT. Root mean square deviation (RMSD) is employed to associate the change in concrete strength with changes in the PZT admittance signatures. The results show that the reusable setup is able to effectively monitor the initial hydration of concrete and the structural health. It can also be detached from the concrete for future re-use. PMID:22399929

Quantitative estimation of massive gas hydrate in gas chimney structures, the eastern margin of Japan Sea, from the physical property anomalies obtained by LWD.

NASA Astrophysics Data System (ADS)

Tanahashi, M.; Morita, S.; Matsumoto, R.

2017-12-01

Two dedicated LWD (Logging While Drilling) cruises, GR14 and HR15, were conducted in summers of 2014 and 2015, respectively, by Meiji University and Geological Survey of Japan, AIST to explore the gas chimney structures, which are characterized by the columnar acoustic blanking below the topographic mound and/or pockmarks in eastern margin of Japan Sea. Shallow (33 to 172m-bsf, average 136m-bsf) 33 LWD drillings were carried out generally in and around gas chimney structures which are in Oki Trough, Off-Joetsu, and Mogami Trough areas, eastern margin of Japan Sea, during two cruises. Schlumberger LWD tools, GeoVISION (resistivity), TeleScope, ProVISION (NMR) and SonicVISION (sonic) were applied during GR14. NeoScope (neutron) was added and SonicScope was replaced for SonicVISION during HR15. The presence of thick highly-anomalous intervals within the LWD data at site J24L suggests the development of massive gas hydrate within Off-Joetsu, by very high resistivity ( 10,000 Ωm), high Vp ( 3,700 m/s) and Vs (370-1,839 m/s), high neutron porosity ( 1.2), low natural gamma ray intensity ( 0 API), low neutron gamma density ( 0.8 g/cm3), low NMR porosity ( 0.0), low permeability (10-2-10-4 mD), low formation neutron sigma (26-28). The extreme physical properties intervals suggest the development of the almost pure hydrate. Because of the clear contrast between pure hydrate and seawater saturated fine sediments, the hydrate amount can be estimated quantitatively based on the assumptions as the two component system of pure hydrate and the monotonous seawater saturated fine sediments. This study was conducted as a part of the methane hydrate research project funded by METI (the Ministry of Economy, Trade and Industry, Japan).

Is DNA a metal, semiconductor or insulator? A theoretical approach

NASA Astrophysics Data System (ADS)

Rey-Gonzalez, Rafael; Fonseca-Romero, Karen; Plazas, Carlos; Grupo de Óptica e Información Cuántica Team

Over the last years, scientific interest for designing and making low dimensional electronic devices with traditional or novel materials has been increased. These experimental and theoretical researches in electronic properties at molecular scale are looking for developing efficient devices able to carry out tasks which are currently done by silicon transistors and devices. Among the new materials DNA strands are highlighted, but the experimental results have been contradictories pointing to behaviors as conductor, semiconductor or insulator. To contribute to the understanding of the origin of the disparity of the measurements, we perform a numerical calculation of the electrical conductance of DNA segments, modeled as 1D disordered finite chains. The system is described into a Tight binding model with nearest neighbor interactions and a s orbital per site. Hydration effects are included as random variations of self-energies. The electronic current as a function of applied bias is calculated using Launder formalism, where the transmission probability is determined into the transfer matrix formalism. We find a conductor-to-semiconductor-to-insulator transition as a function of the three effects taken into account: chain size, intrinsic disorder, and hydration We thank Fundación para la Promoción de la Investigación y la Tecnología, Colombia, and Dirección de Investigación de Bogotá, Universidad Nacional de Colombia, for partial financial support.

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

Finley, P.D.; Krason, J.; Dominic, K.

Multichannel and selected single-channel seismic lines of the continental margin sediments of the Colombia basin display compelling evidence for large accumulations of natural gas hydrate. Seismic bottom simulating reflectors (BSRs), interpreted to mark the base of the hydrate stability zone, are pronounced and very widespread along the entire Panama-Colombia lower continental slope. BSRs have also been identified at two locations on the abyssal plain. Water depths for these suspected hydrate occurrences range from 900 to 4000 m. Although no gas hydrate samples have been recovered from this area, biogenic methane is abundant in Pliocene turbidites underlying the abyssal plain. Moremore » deeply buried rocks beneath the abyssal plain are thermally mature. Thermogenic gas from these rocks may migrate upward along structural pathways into the hydrate stability zone and form hydrate. Impermeable hydrate layers may form caps over large accumulations of free gas, accounting for the very well-defined BSRs in the area. The abyssal plain and the deformed continental margin hold the highest potential for major economic accumulations of gas hydrate in the basin. The extensive continuity of BSRs, relatively shallow water depths, and promixity to onshore production facilities render the marginal deformed belt sediments the most favorable target for future economic development of the gas hydrate resource within the Colombia basin. The widespread evidence of gas hydrates in the Colombia basin suggests a high potential for conventional hydrocarbon deposits offshore of Panama and Colombia.« less

The effect of a solid surface on the segregation and melting of salt hydrates.

PubMed

Zhang, Yu; Anim-Danso, Emmanuel; Dhinojwala, Ali

2014-10-22

Considering the importance of salt and water on earth, the crystallization of salt hydrates next to solid surfaces has important implications in physical and biological sciences. Heterogeneous nucleation is driven by surface interactions, but our understanding of hydrate formation near surfaces is limited. Here, we have studied the hydrate formation of three commonly prevalent salts, MgCl2, CaCl2, and NaCl, next to a sapphire substrate using surface sensitive infrared-visible sum frequency generation (SFG) spectroscopy. SFG spectroscopy can detect the crystallization and melting of salt hydrates at the interface by observing the changes in the intensity and the location of the cocrystallized water hydroxyl peaks (3200-3600 cm(-1)). The results indicate that the surface crystal structures of these three hydrates are similar to those in the bulk. For the NaCl solution, the brine solution is segregated next to the sapphire substrate after the formation of the ice phase. In contrast, the MgCl2 and CaCl2 surface hydrate crystals are interdispersed with nanometer-size ice crystals. The nanosize ice crystals melt at much lower temperatures than bulk ice crystals. For NaCl and MgCl2 solution, the NaCl hydrates prefer to crystallize next to the sapphire substrate instead of the ice crystals and MgCl2 hydrates.

Kinetics of methane hydrate replacement with carbon dioxide and nitrogen gas mixture using in situ NMR spectroscopy.

PubMed

Cha, Minjun; Shin, Kyuchul; Lee, Huen; Moudrakovski, Igor L; Ripmeester, John A; Seo, Yutaek

2015-02-03

In this study, the kinetics of methane replacement with carbon dioxide and nitrogen gas in methane gas hydrate prepared in porous silica gel matrices has been studied by in situ (1)H and (13)C NMR spectroscopy. The replacement process was monitored by in situ (1)H NMR spectra, where about 42 mol % of the methane in the hydrate cages was replaced in 65 h. Large amounts of free water were not observed during the replacement process, indicating a spontaneous replacement reaction upon exposing methane hydrate to carbon dioxide and nitrogen gas mixture. From in situ (13)C NMR spectra, we confirmed that the replacement ratio was slightly higher in small cages, but due to the composition of structure I hydrate, the amount of methane evolved from the large cages was larger than that of the small cages. Compositional analysis of vapor and hydrate phases was also carried out after the replacement reaction ceased. Notably, the composition changes in hydrate phases after the replacement reaction would be affected by the difference in the chemical potential between the vapor phase and hydrate surface rather than a pore size effect. These results suggest that the replacement technique provides methane recovery as well as stabilization of the resulting carbon dioxide hydrate phase without melting.

[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.

A significant role of non-thermal equilibrated electrons in the formation of deleterious complex DNA damage.

PubMed

Kai, Takeshi; Yokoya, Akinari; Ukai, Masatoshi; Fujii, Kentaro; Toigawa, Tomohiro; Watanabe, Ritsuko

2018-01-24

Although most of the radiation damage to genomic DNA could be rendered harmless using repair enzymes in a living cell, a certain fraction of the damage is persistent resulting in serious genetic effects, such as mutation induction. In order to understand the mechanisms of the deleterious DNA damage formation in terms of its earliest physical stage at the radiation track end, dynamics of low energy electrons and their thermalization processes around DNA molecules were investigated using a dynamic Monte Carlo code. The primary incident (1 keV) electrons multiply collide within 1 nm (equivalent to three DNA-base-pairs, 3bp) and generate secondary electrons which show non-Gaussian and non-thermal equilibrium distributions within 300 fs. On the other hand, the secondary electrons are mainly distributed within approximately 10 nm from their parent cations although approximately 5% of the electrons are localized within 1 nm of the cations owing to the interaction of their Coulombic fields. The mean electron energy is 0.7 eV; however, more than 10% of the electrons fall into a much lower-energy region than 0.1 eV at 300 fs. These results indicate that pre-hydrated electrons are formed from the extremely decelerated electrons over a few nm from the cations. DNA damage sites comprising multiple nucleobase lesions or single strand breaks can therefore be formed by multiple collisions of these electrons within 3bp. This multiple damage site is hardly processed by base excision repair enzymes. However, pre-hydrated electrons can also be produced resulting in an additional base lesion (or a strand break) more than 3bp away from the multi-damage site. These damage sites may be finally converted into a double strand break (DSB) when base excision enzymes process the additional base lesions. This DSB includes another base lesion(s) at their termini, and may introduce miss-rejoining by DSB repair enzymes, and hence may result in biological effects such as mutation in surviving cells.

Design Concept of Dialyzer Biomaterials: How to Find Biocompatible Polymers Based on the Biointerfacial Water Structure.

PubMed

Tanaka, Masaru

2017-01-01

Although various types of materials have been used widely in dialyzers, most biomaterials lack the desired functional properties to interface with blood and have not been engineered for optimum performance. Therefore, there is increasing demand to develop novel materials to address such problems in the dialysis arena. Numerous parameters of polymeric biomaterials can affect biocompatibility in a controlled manner. The mechanisms responsible for the biocompatibility of polymers at the molecular level have not been clearly demonstrated, although many theoretical and experimental efforts have been made to try and understand them. Moreover, water interactions have been recognized as fundamental for the blood response to contact with polymers. We have proposed the 'intermediate water' concept and hypothesized that intermediate water, which prevents the proteins and blood cells from directly contacting the polymer surface, or nonfreezing water on the polymer surface, plays an important role in the biocompatibility of polymers. This chapter provides an overview of the recent experimental progress of biocompatible polymers measured by thermal, spectroscopic, and surface force techniques. Additionally, it highlights recent developments in the use of biocompatible polymeric biomaterials for dialyzers and provides an overview of the progress made in the design of multifunctional biomedical polymers by controlling the biointerfacial water structure through precision polymer synthesis. Key Messages: Intermediate water was found only in hydrated biopolymers (proteins, polysaccharides, and nucleic acids, DNA and RNA) and hydrated biocompatible synthetic polymers. Intermediate water could be one of the main screening factors for the design of appropriate dialyzer materials. © 2017 S. Karger AG, Basel.

Divalent counterion-induced condensation of triple-strand DNA.

PubMed

Qiu, Xiangyun; Parsegian, V Adrian; Rau, Donald C

2010-12-14

Understanding and manipulation of the forces assembling DNA/RNA helices have broad implications for biology, medicine, and physics. One subject of significance is the attractive force between dsDNA mediated by polycations of valence ≥ 3. Despite extensive studies, the physical origin of the "like-charge attraction" remains unsettled among competing theories. Here we show that triple-strand DNA (tsDNA), a more highly charged helix than dsDNA, is precipitated by alkaline-earth divalent cations that are unable to condense dsDNA. We further show that our observation is general by examining several cations (Mg(2+), Ba(2+), and Ca(2+)) and two distinct tsDNA constructs. Cation-condensed tsDNA forms ordered hexagonal arrays that redissolve upon adding monovalent salts. Forces between tsDNA helices, measured by osmotic stress, follow the form of hydration forces observed with condensed dsDNA. Probing a well-defined system of point-like cations and tsDNAs with more evenly spaced helical charges, the counterintuitive observation that the more highly charged tsDNA (vs. dsDNA) is condensed by cations of lower valence provides new insights into theories of polyelectrolytes and the biological and pathological roles of tsDNA. Cations and tsDNAs also hold promise as a model system for future studies of DNA-DNA interactions and electrostatic interactions in general.

Influence of nucleotide modifications at the C2’ position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA

PubMed Central

Copp, William; Denisov, Alexey Y.; Xie, Jingwei; Noronha, Anne M.; Liczner, Christopher; Safaee, Nozhat

2017-01-01

Abstract Polyadenylate (poly(A)) has the ability to form a parallel duplex with Hoogsteen adenine:adenine base pairs at low pH or in the presence of ammonium ions. In order to evaluate the potential of this structural motif for nucleic acid-based nanodevices, we characterized the effects on duplex stability of substitutions of the ribose sugar with 2′-deoxyribose, 2′-O-methyl-ribose, 2′-deoxy-2′-fluoro-ribose, arabinose and 2′-deoxy-2′-fluoro-arabinose. Deoxyribose substitutions destabilized the poly(A) duplex both at low pH and in the presence of ammonium ions: no duplex formation could be detected with poly(A) DNA oligomers. Other sugar C2’ modifications gave a variety of effects. Arabinose and 2′-deoxy-2′-fluoro-arabinose nucleotides strongly destabilized poly(A) duplex formation. In contrast, 2′-O-methyl and 2′-deoxy-2′-fluoro-ribo modifications were stabilizing either at pH 4 or in the presence of ammonium ions. The differential effect suggests they could be used to design molecules selectively responsive to pH or ammonium ions. To understand the destabilization by deoxyribose, we determined the structures of poly(A) duplexes with a single DNA residue by nuclear magnetic resonance spectroscopy and X-ray crystallography. The structures revealed minor structural perturbations suggesting that the combination of sugar pucker propensity, hydrogen bonding, pKa shifts and changes in hydration determine duplex stability. PMID:28973475

Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA.

PubMed

Copp, William; Denisov, Alexey Y; Xie, Jingwei; Noronha, Anne M; Liczner, Christopher; Safaee, Nozhat; Wilds, Christopher J; Gehring, Kalle

2017-09-29

Polyadenylate (poly(A)) has the ability to form a parallel duplex with Hoogsteen adenine:adenine base pairs at low pH or in the presence of ammonium ions. In order to evaluate the potential of this structural motif for nucleic acid-based nanodevices, we characterized the effects on duplex stability of substitutions of the ribose sugar with 2'-deoxyribose, 2'-O-methyl-ribose, 2'-deoxy-2'-fluoro-ribose, arabinose and 2'-deoxy-2'-fluoro-arabinose. Deoxyribose substitutions destabilized the poly(A) duplex both at low pH and in the presence of ammonium ions: no duplex formation could be detected with poly(A) DNA oligomers. Other sugar C2' modifications gave a variety of effects. Arabinose and 2'-deoxy-2'-fluoro-arabinose nucleotides strongly destabilized poly(A) duplex formation. In contrast, 2'-O-methyl and 2'-deoxy-2'-fluoro-ribo modifications were stabilizing either at pH 4 or in the presence of ammonium ions. The differential effect suggests they could be used to design molecules selectively responsive to pH or ammonium ions. To understand the destabilization by deoxyribose, we determined the structures of poly(A) duplexes with a single DNA residue by nuclear magnetic resonance spectroscopy and X-ray crystallography. The structures revealed minor structural perturbations suggesting that the combination of sugar pucker propensity, hydrogen bonding, pKa shifts and changes in hydration determine duplex stability. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Brookian sequence well log correlation sections and occurrence of gas hydrates, north-central North Slope, Alaska

USGS Publications Warehouse

Lewis, Kristen A.; Collett, Timothy S.

2013-01-01

Gas hydrates are naturally occurring crystalline, ice-like substances that consist of natural gas molecules trapped in a solid-water lattice. Because of the compact nature of their structure, hydrates can effectively store large volumes of gas and, consequently, have been identified as a potential unconventional energy source. First recognized to exist geologically in the 1960s, significant accumulations of gas hydrate have been found throughout the world. Gas hydrate occurrence is limited to environments such as permafrost regions and subsea sediments because of the pressure and temperature conditions required for their formation and stability. Permafrost-associated gas hydrate accumulations have been discovered in many regions of the Arctic, including Russia, Canada, and the North Slope of Alaska. Gas hydrate research has a long history in northern Alaska. This research includes the drilling, coring, and well log evaluation of two gas hydrate stratigraphic test wells and two resource assessments of gas hydrates on the Alaska North Slope. Building upon these previous investigations, this report provides a summary of the pertinent well log, gas hydrate, and stratigraphic data for key wells related to gas hydrate occurrence in the north-central North Slope. The data are presented in nine well log correlation sections with 122 selected wells to provide a regional context for gas hydrate accumulations and the relation of the accumulations to key stratigraphic horizons and to the base of the ice-bearing permafrost. Also included is a well log database that lists the location, available well logs, depths, and other pertinent information for each of the wells on the correlation section.

Neutron Scattering Studies of the Hydration Structure of Li +

DOE PAGES

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

2015-01-05

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

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

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.

Correlating the properties of different carioca bean cultivars (Phaseolus vulgaris) with their hydration kinetics.

PubMed

Miano, Alberto Claudio; Saldaña, Erick; Campestrini, Luciano Henrique; Chiorato, Alisson Fernando; Augusto, Pedro Esteves Duarte

2018-05-01

This work explained how the intrinsic properties of beans affects the hydration process. For that, different properties of six cultivars of carioca bean (a variety of common bean) were analyzed to verify the correlation with their hydration kinetics characteristics (hydration rate, lag phase time and equilibrium moisture content), using a Multiple Factorial Analysis (MFA): the chemical composition (starch, protein, lipids, minerals (Mg, P, S, K, Ca, Mn, Fe, Cu, Zn), functional groups from the seed coat analyzed by FT-IR), physical properties (size, 1000 grain weight, seed coat thickness, energy to penetrate the bean) and microstructure. Only few properties correlated with the hydration kinetics characteristics of the studied bean, comprising both composition and structure. The fat content, potassium content, specific surface, and the protein to lipids ratio correlated with the lag phase time, which is related with the seed coat impermeability to water. The necessary energy to perforate the seed coat correlated negatively with the hydration rate. It was concluded that the hydration of beans process is a complex phenomenon and that despite being from the same variety of legume, any change due to agronomic enhancement may affect their hydration process kinetics. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

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

Assembling tungsten oxide hydrate nanocrystal colloids formed by laser ablation in liquid into fast-response electrochromic films.

PubMed

Wang, Shalong; Dou, Kang; Zou, Yousheng; Dong, Yuhang; Li, Jubin; Ju, Dan; Zeng, Haibo

2017-03-01

High-performance electrochromic films based on tungsten oxide hydrate ([WO 2 (O 2 )H 2 O]·1.66H 2 O) colloidal nanocrystals with fast switching speed were fabricated by laser ablation in a mixture of water and hydrogen peroxide followed by electrophoretic methods. Through electrophoretic deposition, the nanoparticles in the colloids synthesized by laser ablation aggregated onto the FTO coated glass substrate forming a lager cell with a uniform size of around 200nm, which subsequently self-assembled into a porous tungsten oxide hydrate film. By optimizing the electrophoretic time (800s) and voltage (-0.5V), the mesh-like porous tungsten oxide hydrate film achieved a wide optical modulation of 32% at 632nm, fast coloration and bleaching response speed of 7.8 s and 1.7s respectively due to the synergetic effect of the unique atomic structure of [WO 2 (O 2 )H 2 O]·1.66H 2 O and porous structure with large surface area that facilitates the ion insertion/extraction. Thus the tungsten oxide hydrate can be a promising electrochromic material for practical applications. Copyright © 2016 Elsevier Inc. All rights reserved.

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

USGS Publications Warehouse

Hesse, R.; Harrison, W.E.

1981-01-01

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

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.

Hydraulic and Mechanical Effects from Gas Hydrate Conversion and Secondary Gas Hydrate Formation during Injection of CO2 into CH4-Hydrate-Bearing Sediments

NASA Astrophysics Data System (ADS)

Bigalke, N.; Deusner, C.; Kossel, E.; Schicks, J. M.; Spangenberg, E.; Priegnitz, M.; Heeschen, K. U.; Abendroth, S.; Thaler, J.; Haeckel, M.

2014-12-01

The injection of CO2 into CH4-hydrate-bearing sediments has the potential to drive natural gas production and simultaneously sequester CO2 by hydrate conversion. The process aims at maintaining the in situ hydrate saturation and structure and causing limited impact on soil hydraulic properties and geomechanical stability. However, to increase hydrate conversion yields and rates it must potentially be assisted by thermal stimulation or depressurization. Further, secondary formation of CO2-rich hydrates from pore water and injected CO2 enhances hydrate conversion and CH4 production yields [1]. Technical stimulation and secondary hydrate formation add significant complexity to the bulk conversion process resulting in spatial and temporal effects on hydraulic and geomechanical properties that cannot be predicted by current reservoir simulation codes. In a combined experimental and numerical approach, it is our objective to elucidate both hydraulic and mechanical effects of CO2 injection and CH4-CO2-hydrate conversion in CH4-hydrate bearing soils. For the experimental approach we used various high-pressure flow-through systems equipped with different online and in situ monitoring tools (e.g. Raman microscopy, MRI and ERT). One particular focus was the design of triaxial cell experimental systems, which enable us to study sample behavior even during large deformations and particle flow. We present results from various flow-through high-pressure experimental studies on different scales, which indicate that hydraulic and geomechanical properties of hydrate-bearing sediments are drastically altered during and after injection of CO2. We discuss the results in light of the competing processes of hydrate dissociation, hydrate conversion and secondary hydrate formation. Our results will also contribute to the understanding of effects of temperature and pressure changes leading to dissociation of gas hydrates in ocean and permafrost systems. [1] Deusner C, Bigalke N, Kossel E, Haeckel M. Methane Production from Gas Hydrate Deposits through Injection of Supercritical CO2. Energies 2012:5(7): 2112-2140.

The impact of permafrost-associated microorganisms on hydrate formation kinetics

NASA Astrophysics Data System (ADS)

Luzi-Helbing, Manja; Liebner, Susanne; Spangenberg, Erik; Wagner, Dirk; Schicks, Judith M.

2016-04-01

The relationship between gas hydrates, microorganisms and the surrounding sediment is extremely complex: On the one hand, microorganisms producing methane provide the prerequisite for gas hydrate formation. As it is known most of the gas incorporated into natural gas hydrates originates from biogenic sources. On the other hand, as a result of microbial activity gas hydrates are surrounded by a great variety of organic compounds which are not incorporated into the hydrate structure but may influence the formation or degradation process. For gas hydrate samples from marine environments such as the Gulf of Mexico a direct association between microbes and gas hydrates was shown by Lanoil et al. 2001. It is further assumed that microorganisms living within the gas hydrate stability zone produce biosurfactants which were found to enhance the hydrate formation process significantly and act as nucleation centres (Roger et al. 2007). Another source of organic compounds is sediment organic matter (SOM) originating from plant material or animal remains which may also enhance hydrate growth. So far, the studies regarding this relationship were focused on a marine environment. The scope of this work is to extend the investigations to microbes originating from permafrost areas. To understand the influence of microbial activity in a permafrost environment on the methane hydrate formation process and the stability conditions of the resulting hydrate phase we will perform laboratory studies. Thereby, we mimic gas hydrate formation in the presence and absence of methanogenic archaea (e.g. Methanosarcina soligelidi) and other psychrophilic bacteria isolated from permafrost environments of the Arctic and Antarctic to investigate their impact on hydrate induction time and formation rates. Our results may contribute to understand and predict the occurrences and behaviour of potential gas hydrates within or adjacent to the permafrost. Lanoil BD, Sassen R, La Duc MT, Sweet ST, Nealson KH (2001). Bacteria and Archaea Physically Associated with Gulf of Mexico Gas Hydrates. Appl Environ Microbiol 67: 5143-5153. Rogers R, Zhang G, Dearman J, Woods C (2007). Investigations into surfactant/gas hydrate relationship. J Petrol Sci Eng 56: 82-88.

Characterization of protein hydration by solution NMR spectroscopy

NASA Astrophysics Data System (ADS)

Wand, Joshua

A comprehensive understanding of the interactions between protein molecules and hydration water remains elusive. Solution nuclear magnetic resonance (NMR) spectroscopy has been proposed as a means to characterize these interactions but is plagued with artifacts when employed in bulk aqueous solution. Encapsulation of proteins in reverse micelles prepared in short chain alkane solvents can overcome these technical limitations. Application of this approach has revealed that the interaction of water with the surface of protein molecules is quite heterogeneous with some regions of the protein having long-lived interactions while other regions show relatively transient hydration. Results from several proteins will be presented including ubiquitin, staphylococcal nuclease, interleukin 1beta, hen egg white lysozyme (HEWL) and T4 lysozyme. Ubiquitin and interleukin 1beta are signaling proteins and interact with other proteins through formation of dry protein-protein interfaces. Interestingly, the protein surfaces of the free proteins show relatively slowed (restricted) motion at the surface, which is indicative of low residual entropy. Other regions of the protein surface have relatively high mobility water. These results are consistent with the idea that proteins have evolved to maximize the hydrophobic effect in optimization of binding with protein partners. As predicted by simulation and theory, we find that hydration of internal hydrophobic cavities of interleukin 1beta and T4 lysozyme is highly disfavored. In contrast, the hydrophilic polar cavity of HEWL is occupied by water. Initial structural correlations suggest that hydration of alpha helical structure is characterized by relatively mobile water while those of beta strands and loops are more ordered and slowed. These and other results from this set of proteins reveals that the dynamical and structural character of hydration of proteins is heterogeneous and complex. Supported by the National Science Foundation.

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.

5-(Halomethyl)uridine derivatives as potential antitumor radiosensitizers: A DFT study

NASA Astrophysics Data System (ADS)

Wang, Shoushan; Zhang, Min; Liu, Peng; Xie, Shilei; Cheng, Faliang; Wang, Lishi

2018-01-01

Considering the fact that the efficiency of the uridine-5-methyl radical in producing cytotoxic DNA intrastrand cross-link lesions is greatly higher than that of the uridine-5-yl radical, the radiosensitizing action of 5-(halomethyl)uridines (5-XCH2U, X = F, Cl, or Br) is studied in the present work. It is found that 5-XCH2U has sufficient electron affinity to capture a pre-hydrated or a hydrated electron, and electron attachment leads to significantly facile X- elimination forming the uridine-5-methyl radical. All these three halogenated uridine derivatives are shown to be potential radiosensitizers, with their radiosensitizing abilities increased in an order 5-FCH2U < 5-ClCH2U ≈ 5-BrCH2U.

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

Investigation of hydrate formation in the system H2-CH4-H2O at a pressure up to 250 MPa.

PubMed

Skiba, Sergei S; Larionov, Eduard G; Manakov, Andrey Y; Kolesov, Boris A; Kosyakov, Viktor I

2007-09-27

Phase equilibria in the system H2-CH4-H2O are investigated by means of differential thermal analysis within hydrogen concentration range 0-70 mol % and at a pressure up to 250 MPa. All the experiments were carried out under the conditions of gas excess. With an increase in hydrogen concentration in the initial gas mixture, decomposition temperature of the formed hydrates decreased. X-ray diffraction patterns and Raman spectra of the quenched hydrate samples obtained at a pressure of 20 MPA from a gas mixture containing 40 mol % hydrogen were recorded. It turned out that the hydrate has cubic structure I under these conditions. The Raman spectra showed that hydrogen molecules are not detected in the hydrate within the sensitivity of the method, that is, almost pure methane hydrate is formed. The general view of the phase diagram of the investigated system is proposed. A thermodynamic model was proposed to explain a decrease in hydrate decomposition temperature in the system with an increase in the concentration of hydrogen in the initial mixture.

Micro-Tomographic Investigation of Ice and Clathrate Formation and Decomposition under Thermodynamic Monitoring.

PubMed

Arzbacher, Stefan; Petrasch, Jörg; Ostermann, Alexander; Loerting, Thomas

2016-08-08

Clathrate hydrates are inclusion compounds in which guest molecules are trapped in a host lattice formed by water molecules. They are considered an interesting option for future energy supply and storage technologies. In the current paper, time lapse 3D micro computed tomographic (µCT) imaging with ice and tetrahydrofuran (THF) clathrate hydrate particles is carried out in conjunction with an accurate temperature control and pressure monitoring. µCT imaging reveals similar behavior of the ice and the THF clathrate hydrate at low temperatures while at higher temperatures (3 K below the melting point), significant differences can be observed. Strong indications for micropores are found in the ice as well as the THF clathrate hydrate. They are stable in the ice while unstable in the clathrate hydrate at temperatures slightly below the melting point. Significant transformations in surface and bulk structure can be observed within the full temperature range investigated in both the ice and the THF clathrate hydrate. Additionally, our results point towards an uptake of molecular nitrogen in the THF clathrate hydrate at ambient pressures and temperatures from 230 K to 271 K.

Relation of submarine landslide to hydrate occurrences in Baiyun Depression, South China Sea

NASA Astrophysics Data System (ADS)

Sun, Yunbao; Zhang, Xiaohua; Wu, Shiguo; Wang, Lei; Yang, Shengxiong

2018-02-01

Submarine landslides have been observed in the Baiyun Depression of the South China Sea. The occurrence of hydrates below these landslides indicates that these slope instabilities may be closely related to the massive release of methane. In this study, we used a simple Monte-Carlo model to determine the first-order deformation pattern of a gravitationally destabilizing slope. The results show that a stress concentration occurs due to hydrate dissociation on the nearby glide surface and on top of a gas chimney structure. Upon the dissolution of the gas hydrate, slope failure occurs due to the excess pore pressure generated by the dissociation of the gas hydrates. When gas hydrates dissociate at shallow depths, the excess pore pressure generated can be greater than the total stress acting at those points, along with the forces that resist sliding. Initially, the failure occurs at the toe of the slope, then extends to the interior. Although our investigation focused only on the contribution of hydrate decomposition to submarine landslide, this process is also affected by both the slope material properties and topography.

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

Stability of CO2 hydrate under very high pressure and low temperature

NASA Astrophysics Data System (ADS)

Hirai, H.; Honda, M.; Kawamura, T.; Yamamoto, Y.; Yagi, T.

2009-12-01

CO2 hydrate is a clathrate compound and the crystal structure type is sI at low pressure. CO2-reduction in the atmosphere is one of the most urgent subjects for mankind. Some technical developments to seclude CO2 as CO2 hydrate in ocean floor have been proceeded. Looking around the solar system, existence of CO2 hydrate in and beneath Martian permafrost has been predicted from spacecraft probes and theoretical studies. Thus, its stability and properties under high pressures and low temperatures are of great interest for fundamental understanding of clathrate hydrate, for the ocean sequestration technology, and for planetary science. CO2 hydrate exhibits characteristic properties different from those of other gas hydrate such as methane hydrate. For example, phase boundary between hydrate and gas + water for many gas hydrates shows positive slope in pressure versus temperature field, and the gas hydrates are kept at pressures up to several GPa at room temperature. On the other hand, for CO2 hydrate, the phase boundary turns to negative slope from positive one at a certain critical point [Nakano et al., 1998], and it can exist only at low temperature regions. And, a theoretical study predicted that CO2 hydrate decompose at low temperature region [Longhi, 2005]. In this study, high pressure and low temperature experiments were performed to examine stability and phase changes of CO2 hydrate using diamond anvil cell in a pressure range from 0.1 to 2.5 GPa and a the temperature range from 65 to 265 K. X-ray diffractometry and Raman spectroscopy revealed that the known phase boundary was extended into lower temperature region, and that CO2 hydrate was kept at low temperature regions at least 65 K despite the theoretical prediction of decomposition. References [1] S. Nakano, M. Moritoki, K. Ohgaki, J. Chem. Eng. Data, 43, 807 (1998). [2] J. Longhi, Geochim. Cosmochim. Acta, 69, 529 (2005)

Simulation experiments of the effect of space environment on bacteriophage and DNA thin films

NASA Technical Reports Server (NTRS)

Fekete, A.; Ronto, Gy; Hegedus, M.; Modos, K.; Berces, A.; Kovacs, G.; Lammer, H.; Panitz, C.

2004-01-01

The main goal of PUR experiment (phage and uracil response) is to examine and quantify the effect of specific space conditions on nucleic acid models. To achieve this an improved method was elaborated for the preparation of DNA and bacteriophage thin films. The homogeneity of the films was controlled by UV spectroscopy and microscopy. To provide experimental evidence for the hypothesis that interplanetary transfer of the genetic material is possible, phage T7 and isolated T7 DNA thin films have been exposed to selected space conditions: intense UVC radiation (lambda=254 nm) and high vacuum (10(-4) Pa). The effects of DNA hydration, conformation and packing on UV radiation damage were examined. Characteristic changes in the absorption spectrum, in the electrophoretic pattern of DNA and the decrease of the amount of PCR products have been detected indicating the photodamage of isolated and intraphage DNA. c2004 COSPAR. Published by Elsevier Ltd. All rights reserved.

General synthesis and structural evolution of a layered family of Ln8(OH)20Cl4 x nH2O (Ln = Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, and Y).

PubMed

Geng, Fengxia; Matsushita, Yoshitaka; Ma, Renzhi; Xin, Hao; Tanaka, Masahiko; Izumi, Fujio; Iyi, Nobuo; Sasaki, Takayoshi

2008-12-03

The synthesis process and crystal structure evolution for a family of stoichiometric layered rare-earth hydroxides with general formula Ln(8)(OH)(20)Cl(4) x nH(2)O (Ln = Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, and Y; n approximately 6-7) are described. Synthesis was accomplished through homogeneous precipitation of LnCl(3) x xH(2)O with hexamethylenetetramine to yield a single-phase product for Sm-Er and Y. Some minor coexisting phases were observed for Nd(3+) and Tm(3+), indicating a size limit for this layered series. Light lanthanides (Nd, Sm, Eu) crystallized into rectangular platelets, whereas platelets of heavy lanthanides from Gd tended to be of quasi-hexagonal morphology. Rietveld profile analysis revealed that all phases were isostructural in an orthorhombic layered structure featuring a positively charged layer, [Ln(8)(OH)(20)(H(2)O)(n)](4+), and interlayer charge-balancing Cl(-) ions. In-plane lattice parameters a and b decreased nearly linearly with a decrease in the rare-earth cation size. The interlamellar distance, c, was almost constant (approximately 8.70 A) for rare-earth elements Nd(3+), Sm(3+), and Eu(3+), but it suddenly decreased to approximately 8.45 A for Tb(3+), Dy(3+), Ho(3+), and Er(3+), which can be ascribed to two different degrees of hydration. Nd(3+) typically adopted a phase with high hydration, whereas a low-hydration phase was preferred for Tb(3+), Dy(3+), Ho(3+), Er(3+), and Tm(3+). Sm(3+), Eu(3+), and Gd(3+) samples were sensitive to humidity conditions because high- and low-hydration phases were interconvertible at a critical humidity of 10%, 20%, and 50%, respectively, as supported by both X-ray diffraction and gravimetry as a function of the relative humidity. In the phase conversion process, interlayer expansion or contraction of approximately 0.2 A also occurred as a possible consequence of absorption/desorption of H(2)O molecules. The hydration difference was also evidenced by refinement results. The number of coordinated water molecules per formula weight, n, changed from 6.6 for the high-hydration Gd sample to 6.0 for the low-hydration Gd sample. Also, the hydration number usually decreased with increasing atomic number; e.g., n = 7.4, 6.3, 7.2, and 6.6 for high-hydration Nd, Sm, Eu, and Gd, and n = 6.0, 5.8, 5.6, 5.4, and 4.9 for low-hydration Gd, Tb, Dy, Ho, and Er. The variation in the average Ln-O bond length with decreasing size of the lanthanide ions is also discussed. This family of layered lanthanide compounds highlights a novel chemistry of interplay between crystal structure stability and coordination geometry with water molecules.

The crucial effect of early-stage gelation on the mechanical properties of cement hydrates

NASA Astrophysics Data System (ADS)

Ioannidou, Katerina; Kanduč, Matej; Li, Lunna; Frenkel, Daan; Dobnikar, Jure; Del Gado, Emanuela

2016-07-01

Gelation and densification of calcium-silicate-hydrate take place during cement hydration. Both processes are crucial for the development of cement strength, and for the long-term evolution of concrete structures. However, the physicochemical environment evolves during cement formation, making it difficult to disentangle what factors are crucial for the mechanical properties. Here we use Monte Carlo and Molecular Dynamics simulations to study a coarse-grained model of cement formation, and investigate the equilibrium and arrested states. We can correlate the various structures with the time evolution of the interactions between the nano-hydrates during the preparation of cement. The novel emerging picture is that the changes of the physicochemical environment, which dictate the evolution of the effective interactions, specifically favour the early gel formation and its continuous densification. Our observations help us understand how cement attains its unique strength and may help in the rational design of the properties of cement and related materials.

A modeling study of methane hydrate decomposition in contact with the external surface of zeolites.

PubMed

Smirnov, Konstantin S

2017-08-30

The behavior of methane hydrate (MH) enclosed between the (010) surfaces of the silicalite-1 zeolite was studied by means of molecular dynamics simulations at temperatures of 150 and 250 K. Calculations reveal that the interaction with the hydrophilic surface OH groups destabilizes the clathrate structure of hydrate. While MH mostly conserves the structure in the simulation at the low temperature, thermal motion at the high temperature breaks the fragilized cages of H-bonded water molecules, thus leading to the release of methane. The dissociation proceeds in a layer-by-layer manner starting from the outer parts of the MH slab until complete hydrate decomposition. The released CH 4 molecules are absorbed by the microporous solid, whereas water is retained at the surfaces of hydrophobic silicalite and forms a meniscus in the interlayer space. Methane uptake reaches 70% of the silicalite sorption capacity. The energy necessary for the endothermic MH dissociation is supplied by the exothermic methane absorption by the zeolite.

Feasibility of using phase change materials to control the heat of hydration in massive concrete structures.

PubMed

Choi, Won-Chang; Khil, Bae-Soo; Chae, Young-Seok; Liang, Qi-Bo; Yun, Hyun-Do

2014-01-01

This paper presents experimental results that can be applied to select a possible phase change material (PCM), such as a latent heat material (LHM), to control the hydration heat in mass concrete structures. Five experimental tests (microconduction, simplified adiabatic temperature rise, heat, and compressive strength tests) were conducted to select the most desirable LHM out of seven types of inorganic PCM used in cement mortar and to determine the most suitable mix design. The results of these experimental tests were used to assess the feasibility of using PCM to reduce hydration heat in mass concrete that was examined. The experimental results show that cement mortar containing barium- [Ba(OH)2 · 8H2O] based PCM has the lowest amount of total hydration heat of the cement pastes. The barium-based PCM provides good latent heat properties that help to prevent volume change and microcracks caused by thermal stress in mass concrete.

Noninvasive optical coherence tomography monitoring of structure and hydration changes of human corneas in different preservation media

NASA Astrophysics Data System (ADS)

Wu, Yicong; Clarke, Dominic; Mathew, Aby; Nicoud, Ian; Li, Xingde

2011-02-01

The influence of different tissue preservation (a test solution under development and a standard storage solution) on human cornea morphology, refractive index and hydration was assessed noninvasively by ultrahigh-resolution optical coherence tomography (OCT) over time. For 28 days' or 15 days' storage in the preservation media, corneas in the two media exhibited different structural changes with different onset times including epithelial desquamation, edema-induced cornea thickening and change in tissue refractive index. It was found that the variation of the group refractive index over time was only about 2%, while 25% variation of hydration was observed in the storage and subsequent return to normothermic conditions in both preservation media. The results suggest the two media involved different but correlated preservation mechanisms. This study demonstrates that the noncontact, noninvasive, and high-resolution OCT is a powerful tool for noninvasive characterization of tissue morphological changes and hydration process and for assessment of the effects of preservation media on stored tissue integrity. Engineers.

The crucial effect of early-stage gelation on the mechanical properties of cement hydrates

PubMed Central

Ioannidou, Katerina; Kanduč, Matej; Li, Lunna; Frenkel, Daan; Dobnikar, Jure; Del Gado, Emanuela

2016-01-01

Gelation and densification of calcium–silicate–hydrate take place during cement hydration. Both processes are crucial for the development of cement strength, and for the long-term evolution of concrete structures. However, the physicochemical environment evolves during cement formation, making it difficult to disentangle what factors are crucial for the mechanical properties. Here we use Monte Carlo and Molecular Dynamics simulations to study a coarse-grained model of cement formation, and investigate the equilibrium and arrested states. We can correlate the various structures with the time evolution of the interactions between the nano-hydrates during the preparation of cement. The novel emerging picture is that the changes of the physicochemical environment, which dictate the evolution of the effective interactions, specifically favour the early gel formation and its continuous densification. Our observations help us understand how cement attains its unique strength and may help in the rational design of the properties of cement and related materials. PMID:27417911

Imaging fully hydrated whole cells by coherent x-ray diffraction microscopy.

PubMed

Nam, Daewoong; Park, Jaehyun; Gallagher-Jones, Marcus; Kim, Sangsoo; Kim, Sunam; Kohmura, Yoshiki; Naitow, Hisashi; Kunishima, Naoki; Yoshida, Takashi; Ishikawa, Tetsuya; Song, Changyong

2013-03-01

Nanoscale imaging of biological specimens in their native condition is of long-standing interest, in particular with direct, high resolution views of internal structures of intact specimens, though as yet progress has been limited. Here we introduce wet coherent x-ray diffraction microscopy capable of imaging fully hydrated and unstained biological specimens. Whole cell morphologies and internal structures better than 25 nm can be clearly visualized without contrast degradation.

Importance of counteranions on the hydration structure of the curium ion

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

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

2013-07-04

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

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.

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

Ryabova, N. Yu., E-mail: rny03@nf.jinr.ru; Kiselev, M. A.; Balagurov, A. M.

The structural changes in the multilamellar lipid membranes of dipalmitoylphosphatidylcholine (DPPC)/cholesterol and DPPC/ceramide VI binary systems during hydration and dehydration have been studied by neutron diffraction. The effect of cholesterol and ceramide on the kinetics of water exchange in DPPC membranes is characterized. Compared to pure DPPC, membranes of binary systems swell faster during hydration (with a characteristic time of {approx}30 min). Both compounds, ceramide VI and cholesterol, similarly affect the hydration of DPPC membranes, increasing the repeat distance due to the bilayer growth. However, in contrast to cholesterol, ceramide significantly reduces the thickness of the membrane water layer. Themore » introduction of cholesterol into a DPPC membrane slows down the change in the parameters of the bilayer internal structure during dehydration. In the DPPC/ceramide VI/cholesterol ternary system (with a molar cholesterol concentration of 40%), cholesterol is partially released from the lamellar membrane structure into the crystalline phase.« less

Crystal chemistry and structure refinement of five hydrated calcium borates

USGS Publications Warehouse

Clark, J.R.; Appleman, D.E.; Christ, C.L.

1964-01-01

The crystal structures of the five known members of the series Ca2B6O11??xH2O (x = 1, 5, 5, 7, 9, and 13) have been refined by full-matrix least-squares techniques, yielding bond distances and angles with standard errors of less than 0??01 A?? and 0??5??, respectively. The results illustrate the crystal chemical principles that govern the structures of hydrated borate compounds. The importance of hydrogen bonding in the ferroelectric transition of colemanite is confirmed by more accurate proton assignments. ?? 1964.

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

PubMed

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

2016-02-01

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

Influence of PNA containing 8-aza-7-deazaadenine on structure stability and binding affinity of PNA·DNA duplex: insights from thermodynamics, counter ion, hydration and molecular dynamics analysis.

PubMed

Gupta, Sharad K; Sur, Souvik; Prasad Ojha, Rajendra; Tandon, Vibha

2013-07-01

This paper describes the synthesis of a novel 8-aza-7-deazapurin-2,6-diamine (DPP)-containing peptide nucleic acid (PNA) monomer and Boc protecting group-based oligomerization of PNA, replacing adenine (A) with DPP monomers in the PNA strand. The PNA oligomers were synthesized against the biologically relevant SV40 promoter region (2494-AATTTTTTTTATTTA-2508) of pEGFP-N3 plasmid. The DPP-PNA·DNA duplex showed enhanced stability as compared to normal duplex (A-PNA·DNA). The electronic distribution of DPP monomer suggested that DPP had better electron donor properties over 2,6-diamino purine. UV melting and thermodynamic analysis revealed that the PNA oligomer containing a diaminopyrazolo(3,4-d)pyrimidine moiety (DPP) stabilized the PNA·DNA hybrids compared to A-PNA·DNA. DPP-PNA·DNA duplex showed higher water activity (Δnw = 38.5) in comparison to A-PNA·DNA duplex (Δnw = 14.5). The 50 ns molecular dynamics simulations of PNA·DNA duplex containing DPP or unmodified nucleobase-A showed average H-bond distances in the DPP-dT base pair of 2.90 Å (OH-N bond) and 2.91 Å (NH-N bond), which were comparably shorter than in the A-dT base pair, in which the average distances were 3.18 Å (OH-N bond) and 2.97 Å (NH-N bond), and there was one additional H-bond in the DPP-dT base pair of around 2.98 Å (O2H-N2 bond), supporting the higher stability of DPP-PNA·DNA. The analysis of molecular dynamics simulation data showed that the system binding free energy increased at a rate of approximately -4.5 kcal mol(-1) per DPP base of the PNA·DNA duplex. In summary, increased thermal stability, stronger hydrogen bonding and more stable conformation in the DPP-PNA·DNA duplex make it a better candidate as antisense/antigene therapeutic agents.

Seismic-reflection surveys of the Blake Ridge, R/V Cape Hatteras, 1992 and 1995; data acquisition, navigation and processing

USGS Publications Warehouse

Taylor, Michael H.; Dillon, William P.; Anton, Christopher H.; Danforth, William W.

1999-01-01

As part of an ongoing study, seismic-reflection profiles were collected over the Blake Ridge in 1992 and 1995, in order to map the volume and distribution of methane hydrate. Faulting and seafloor instabilities appear to be related to methane hydrate processes at the Blake Ridge. Seismic profiles display a prominent collapse structure at the crest, which is inferred to have resulted from the mobilization of sediment that was associated with methane hydrate dissociation.

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.

Hydration Repulsion between Carbohydrate Surfaces Mediated by Temperature and Specific Ions

PubMed Central

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

2016-01-01

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

Methods to determine hydration states of minerals and cement hydrates

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

Baquerizo, Luis G., E-mail: luis.baquerizoibarra@holcim.com; Matschei, Thomas; Scrivener, Karen L.

2014-11-15

This paper describes a novel approach to the quantitative investigation of the impact of varying relative humidity (RH) and temperature on the structure and thermodynamic properties of salts and crystalline cement hydrates in different hydration states (i.e. varying molar water contents). The multi-method approach developed here is capable of deriving physico-chemical boundary conditions and the thermodynamic properties of hydrated phases, many of which are currently missing from or insufficiently reported in the literature. As an example the approach was applied to monosulfoaluminate, a phase typically found in hydrated cement pastes. New data on the dehydration and rehydration of monosulfoaluminate aremore » presented. Some of the methods used were validated with the system Na{sub 2}SO{sub 4}–H{sub 2}O and new data related to the absorption of water by anhydrous sodium sulfate are presented. The methodology and data reported here should permit better modeling of the volume stability of cementitious systems exposed to various different climatic conditions.« less

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.

Morin Hydrate Mitigates Cisplatin-Induced Renal and Hepatic Injury by Impeding Oxidative/Nitrosative Stress and Inflammation in Mice.

PubMed

K V, Athira; Madhana, Rajaram Mohanrao; Kasala, Eshvendar Reddy; Samudrala, Pavan Kumar; Lahkar, Mangala; Gogoi, Ranadeep

2016-12-01

Cisplatin is a widely used chemotherapeutic drug; however, it induces damage on kidney and liver at clinically effective higher doses. Morin hydrate possesses antioxidant, anti-inflammatory, and anticancer properties. Therefore, we aimed to investigate the effects of morin hydrate (50 and 100 mg/kg, orally) against the renohepatic toxicity induced by a high dose of cisplatin (20 mg/kg, intraperitoneally). Renal and hepatic function, oxidative/nitrosative stress, and inflammatory markers along with histopathology were evaluated. Morin hydrate ameliorated cisplatin-induced renohepatic toxicity significantly at 100 mg/kg as evidenced from the significant reversal of cisplatin-induced body weight loss, mortality, functional and structural alterations of kidney, and liver. The protective role offered by morin hydrate against cisplatin-induced renohepatic toxicity is by virtue of its free radical scavenging property, thereby abating the depletion of cellular antioxidant defense components and through modulation of inflammatory cytokines. We speculate morin hydrate as a protective candidate against renohepatic toxicity of cisplatin. © 2016 Wiley Periodicals, Inc.

Hydration Repulsion between Carbohydrate Surfaces Mediated by Temperature and Specific Ions

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

[Hydration in clinical practice].

PubMed

Maristany, Cleofé Pérez-Portabella; Segurola Gurruchaga, Hegoi

2011-01-01

Water is an essential foundation for life, having both a regulatory and structural function. The former results from active and passive participation in all metabolic reactions, and its role in conserving and maintaining body temperature. Structurally speaking it is the major contributer to tissue mass, accounting for 60% of the basis of blood plasma, intracellular and intersticial fluid. Water is also part of the primary structures of life such as genetic material or proteins. Therefore, it is necessary that the nurse makes an early assessment of patients water needs to detect if there are signs of electrolyte imbalance. Dehydration can be a very serious problem, especially in children and the elderly. Dehydrations treatment with oral rehydration solution decreases the risk of developing hydration disorders, but even so, it is recommended to follow preventive measures to reduce the incidence and severity of dehydration. The key to having a proper hydration is prevention. Artificial nutrition encompasses the need for precise calculation of water needs in enteral nutrition as parenteral, so the nurse should be part of this process and use the tools for calculating the patient's requirements. All this helps to ensure an optimal nutritional status in patients at risk. Ethical dilemmas are becoming increasingly common in clinical practice. On the subject of artificial nutrition and hydration, there isn't yet any unanimous agreement regarding hydration as a basic care. It is necessary to take decisions in consensus with the health team, always thinking of the best interests of the patient.

Structural Phase Transitions and Water Dynamics in Uranyl Fluoride Hydrates

DOE PAGES

Miskowiec, Andrew J.; Kirkegaard, Marie C.; Huq, Ashfia; ...

2015-11-17

We report a novel production method for uranium oxy uoride [(UO 2) 7F 14(H 2O) 7] 4H 2O, referred to as structure D. Structure D is produced as a product of hydrating anhydrous uranyl uoride, UO 2F 2, through the gas phase at ambient temperatures fol- lowed by desiccation by equilibration with a dry environment. We follow the structure of [(UO 2) 7F 14(H 2O) 7] 4H 2O through an intermediate, liquid-like phase, wherein the coordination number of the uranyl ion is reduced to 5 (from 6 in the anhydrous struc- ture), and a water molecule binds as an equatorialmore » ligand to the uranyl ion. Quasielas- tic neutron scattering results compare well with previous measurements of mineral hydrates. The two groups of structurally distinct water molecules in D perform re- stricted motion on a length scale commensurate with the O{H bond (r = 0.92 A). The more tightly bound equatorial ligand waters rotate slower (Dr = 2.2 ps -1) than their hydrogen-bonded partners (Dr = 28.7 ps -1).« less

Metal Cations in G-Quadruplex Folding and Stability

NASA Astrophysics Data System (ADS)

Bhattacharyya, Debmalya; Mirihana Arachchilage, Gayan; Basu, Soumitra

2016-09-01

This review is focused on the structural and physico-chemical aspects of metal cation coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G-Quadruplex structures are non-canonical secondary structures formed by both DNA and RNA. G-quadruplexes regulate a wide range of important biochemical processes. Besides the sequence requirements, the coordination of monovalent cations in the GQ is essential for its formation and determines the stability and polymorphism of GQ structures. The nature, location and dynamics of the cation coordination and their impact on the overall GQ stability are dependent on several factors such as the ionic radii, hydration energy and the bonding strength to the O6 of guanines. The intracellular monovalent cation concentration and the localized ion concentrations determine the formation of GQs and can potentially dictate their regulatory roles. A wide range of biochemical and biophysical studies on an array of GQ enabling sequences have generated at a minimum the knowledge base that allows us to often predict the stability of GQs in presence of the physiologically relevant metal ions, however, prediction of conformation of such GQs is still out of the realm.

Low temperature structures of dCpG-proflavine.

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

Schneider, B.; Ginell, S. L.; Berman, H. M.

1992-12-01

The structure of the complex of dCpG with proflavine was determined using x-ray data taken at -130 degrees C (low temperature) and at -2 degrees C (cold temperature) and compared with the structure of the complex determined previously at room temperature (Shieh, H. S., H. M. Berman, M. Dabrow, and S. Neidle. 1980. Nucleic Acids Res. 8:85-97). Low temperature was refined with 5,125 reflections between 8.0 and 0.93 A, Anisotropically modeled temperature factors were used for DNA/drug atoms and isotropic ones for water oxygens to R factor of 12.2% in P2(1)2(1)2; a = 32.853, b = 21.760, c = 13.296more » A. Cold temperature was refined isotropically with 2,846 reflections 8.0-0.89 A to R = 15.1% in P2(1)2(1)2; a = 32.867, b = 22.356, c = 13.461 A. Both structures are very similar to the room temperature one, though some important differences were observed: one guanine sugar moiety is disordered and additional water molecules have been located that give rise to infinite polyhedral hydration networks.« less

Computational Recreation of Carbon Dioxide Hydrates at Habitable Planetary Conditions

NASA Astrophysics Data System (ADS)

Recio, J. M.; Izquierdo-Ruiz, F.; Prieto-Ballesteros, O.

2017-12-01

Gas clathrate hydrates are proposed as constituents of the icy moons of the giant planets in the Solar System [1]. Carbon dioxide has been detected on the surface of the moons of Jupiter, supposedly originated by internal degasification. In Ganymede, an aqueous ocean is proposed to exist under a thick ice crust in coexistence with several forms of ice, with pressure reaching up to 1.3 GPa [2]. Due to the limited available data on these systems under these conditions, we propose a combination of computational and experimental studies to describe microscopically and macroscopically the structural and chemical behavior of CO2@H2O polymorphs. This will allow us to understand how their presence affects the geophysical structure and activity and their impact on the habitability of the icy moon. A transition from the sI cubic structure to a high pressure phase at around 0.7 GPa has been found for CO2@H2O. In spite of different attempts to characterize the new structure, a definite answer has not been provided yet. A MH-III Filled Ice Structure type was proposed after neutron diffraction experiments in contrast with an alternative structure similar to the hexagonal C0 type for H2 hydrates [3]. It has an estimated hydration level ratio up to 2H2O:1CO2 and 6 water molecules per unit cell. In the figure below, our optimized unit cell based on this hexagonal C0 structure is displayed. Ab initio calculations using the XDM approximation to include van der Waals effects are performed in our search for the pressure evolution of the equilibrium geometries of the C0-CO2@H2O phase and those of a close related structure to this one called Ih-C0, with 8 water molecules per unit cell. We obtain occupation energies at different hydration ratios, densities, equations of state parameters, and stability energies with respect to decomposition. Raman and IR frequencies are also computed in the 0-2 GPa range. High pressure experiments are also being done in a newly designed chamber able to reach 1 GPa. It is equipped with a sapphire window to allow the measurements of Raman spectra. We believe that these results may throw light into gas hydrates of the habitable bodies of our Solar System. [1] Buffet B. A., Ann. Rev. Earth Plan. Sci. 28, 477, 2010. [2] Bland, M.T. et al. Icarus 200, 207, 2009. [3] Smirnov G. S. et al., J. Phys. Chem. Lett., 2013, 4, 3560

Major occurrences and reservoir concepts of marine clathrate hydrates: Implications of field evidence

USGS Publications Warehouse

Booth, J.S.; Winters, W.J.; Dillon, William P.; Clennell, M.B.; Rowe, M.M.

1998-01-01

This paper is part of the special publication Gas hydrates: relevance to world margin stability and climatic change (eds J.P. Henriet and J. Mienert). Questions concerning clathrate hydrate as an energy resource, as a factor in modifying global climate and as a triggering mechanism for mass movements invite consideration of what factors promote hydrate concentration, and what the quintessential hydrate-rich sediment may be. Gas hydrate field data, although limited, provide a starting point for identifying the environments and processes that lead to more massive concentrations. Gas hydrate zones are up to 30 m thick and the vertical range of occurrence at a site may exceed 200 m. Zones typically occur more than 100m above the phase boundary. Thicker zones are overwhelmingly associated with structural features and tectonism, and often contain sand. It is unclear whether an apparent association between zone thickness and porosity represents a cause-and-effect relationship. The primary control on the thickness of a potential gas hydrate reservoir is the geological setting. Deep water and low geothermal gradients foster thick gas hydrate stability zones (GHSZs). The presence of faults, fractures, etc. can favour migration of gas-rich fluids. Geological processes, such as eustacy or subsidence, may alter the thickness of the GHSZ or affect hydrate concentratiion. Tectonic forces may promote injection of gas into the GHSZ. More porous and permeable sediment, as host sediment properties, increase storage capacity and fluid conductivity, and thus also enhance reservoir potential.

Methane Hydrate Concentrations at GC955 and WR313 Drilling Sites in the Gulf of Mexico Determined from Seismic Prestack Waveform Inversion

NASA Astrophysics Data System (ADS)

Fortin, W.; Goldberg, D.; Küçük, H. M.

2016-12-01

Gas hydrates are naturally occurring compounds, which, at a molecular scale, are lattice structures of ice embedded with various gas molecules in the lattice voids. Volumetric estimates of associated hydrocarbons vary greatly due to the difficulty in remotely estimating hydrate concentrations in marine sediments but embedded hydrocarbon stores are thought to represent a significant portion of global deposits. The unstable nature of methane hydrates has been linked to submarine landslides and the subsequent release of large quantities of methane can accelerate global climate change. Understanding the details of gas hydrate systems is important for potential economic production and assessing natural hazards risks. Seismic reflection techniques are uniquely capable of detecting gas hydrates. Often, hydrate layers appear as bottom simulating reflectors (BSRs); however, BSRs are not present everywhere gas hydrates are known to occur. Using recently reprocessed prestack time migrated data and prestack waveform inversion (PWI) techniques, we produce velocity models at high vertical and horizontal resolution in order to investigate the presence of gas hydrates in the Gulf of Mexico. Coupling our PWI results with known velocity-property relationships and data from nearby well controls, we determine the viability of recently collected high-resolution seismic data and outline small-scale heterogeneities at GC955 and WR313. We outline where PWI techniques are capable of identifying gas hydrates in seismic reflection data where BSRs are not present.

Prestack Waveform Inversion and Well Log Examination at GC955 and WR313 in the Gulf of Mexico for Estimation of Methane Hydrate Concentrations

NASA Astrophysics Data System (ADS)

Fortin, W.; Goldberg, D.; Kucuk, H. M.

2017-12-01

Gas hydrates are naturally occurring compounds, which, at a molecular scale, are lattice structures of ice embedded with various gas molecules in the lattice voids. Volumetric estimates of associated hydrocarbons vary greatly due to the difficulty in remotely estimating hydrate concentrations in marine sediments but embedded hydrocarbon stores are thought to represent a significant portion of global deposits. Inherent hydrate instabilities obscure our understanding of and complicates processes related to resource extraction and hydrate response to disturbances in the local environment. Understanding the spatial extent and variability of hydrate deposits have important implications for potential economic production, climate change, and assessing natural hazards risks. Seismic reflection techniques are capable of determining the extent of gas hydrate deposits, often through the observation of bottom simulating reflectors (BSRs). However, BSRs are not present everywhere gas hydrates exist. Using high resolution prestack time migrated seismic data and prestack waveform inversion (PWI) we produce highly resolved velocity models and compare them to co-located well logs. Coupling our PWI results with velocity-porosity relationships and nearby well control, we map hydrate properties at GC955 and WR313. Integrating small scale heterogeneities and variations along the velocity model with in-situ measurements, we develop a workflow aimed to quantify hydrate concentrations observed in seismic data over large areas in great detail regardless of the existence of a BSR.

Gas hydrate characterization and grain-scale imaging of recovered cores from the Mount Elbert Gas Hydrate Stratigraphic Test Well, Alaska North Slope

USGS Publications Warehouse

Stern, Laura A.; Lorenson, T.D.; Pinkston, John C.

2011-01-01

Using cryogenic scanning electron microscopy (CSEM), powder X-ray diffraction, and gas chromatography methods, we investigated the physical states, grain characteristics, gas composition, and methane isotopic composition of two gas-hydrate-bearing sections of core recovered from the BPXA–DOE–USGS Mount Elbert Gas Hydrate Stratigraphic Test Well situated on the Alaska North Slope. The well was continuously cored from 606.5 m to 760.1 m depth, and sections investigated here were retrieved from 619.9 m and 661.0 m depth. X-ray analysis and imaging of the sediment phase in both sections shows it consists of a predominantly fine-grained and well-sorted quartz sand with lesser amounts of feldspar, muscovite, and minor clays. Cryogenic SEM shows the gas-hydrate phase forming primarily as a pore-filling material between the sediment grains at approximately 70–75% saturation, and more sporadically as thin veins typically several tens of microns in diameter. Pore throat diameters vary, but commonly range 20–120 microns. Gas chromatography analyses of the hydrate-forming gas show that it is comprised of mainly methane (>99.9%), indicating that the gas hydrate is structure I. Here we report on the distribution and articulation of the gas-hydrate phase within the cores, the grain morphology of the hydrate, the composition of the sediment host, and the composition of the hydrate-forming gas.

Gas hydrate characterization and grain-scale imaging of recovered cores from the Mount Elbert Gas Hydrate Stratigraphic Test Well, Alaska North Slope

USGS Publications Warehouse

Stern, L.A.; Lorenson, T.D.; Pinkston, J.C.

2011-01-01

Using cryogenic scanning electron microscopy (CSEM), powder X-ray diffraction, and gas chromatography methods, we investigated the physical states, grain characteristics, gas composition, and methane isotopic composition of two gas-hydrate-bearing sections of core recovered from the BPXA-DOE-USGS Mount Elbert Gas Hydrate Stratigraphic Test Well situated on the Alaska North Slope. The well was continuously cored from 606.5. m to 760.1. m depth, and sections investigated here were retrieved from 619.9. m and 661.0. m depth. X-ray analysis and imaging of the sediment phase in both sections shows it consists of a predominantly fine-grained and well-sorted quartz sand with lesser amounts of feldspar, muscovite, and minor clays. Cryogenic SEM shows the gas-hydrate phase forming primarily as a pore-filling material between the sediment grains at approximately 70-75% saturation, and more sporadically as thin veins typically several tens of microns in diameter. Pore throat diameters vary, but commonly range 20-120 microns. Gas chromatography analyses of the hydrate-forming gas show that it is comprised of mainly methane (>99.9%), indicating that the gas hydrate is structure I. Here we report on the distribution and articulation of the gas-hydrate phase within the cores, the grain morphology of the hydrate, the composition of the sediment host, and the composition of the hydrate-forming gas. ?? 2009.

Structural charge site influence on the interlayer hydration of expandable three-sheet clay minerals

USGS Publications Warehouse

Kerns, Raymond L.; Mankin, Charles J.

1968-01-01

Previous investigations have demonstrated the influences of interlayer cation composition, relative humidity, temperature, and magnitude of interlayer surface charge on the interlayer hydration of montmorillonites and vermiculites. It has been suggested that the sites of layer charge deficiencies may also have an influence upon the amount of hydration that can take place in the interlayers of expandable clay minerals. If the interlayer cation-to-layer bonds are considered as ideally electrostatic, the magnitude of the forces resisting expansion may be expressed as a form of Coulomb's law. If this effect is significant, expandable structures in which the charge-deficiency sites are predominantly in the tetrahedral sheet should have less pronounced swelling properties than should structures possessing charge deficiencies located primarily in the octahedral sheet.Three samples that differed in location of layer charge sites were selected for study. An important selection criterion was a non-correlation between tetrahedral charge sites and high surface-charge density, and between octahedral charge sites and low surface-charge density.The effects of differences in interlayer cation composition were eliminated by saturating portions of each sample with the same cations. Equilibrium (001) d values at controlled constant humidities were used as a measure of the relative degree of interlayer hydration.Although no correlation could be made between the degree of interlayer hydration and total surface-charge density, the investigation does not eliminate total surface-charge density as being significant to the swelling properties of three-sheet clay-mineral structures. The results do indicate a correlation between more intense expandability and predominance of charge deficiencies in the octahedral sheet. Conversely, less intense swelling behavior is associated with predominantly tetrahedral charge deficiencies.

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.

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.

CO2 capture from simulated fuel gas mixtures using semiclathrate hydrates formed by quaternary ammonium salts.

PubMed

Park, Sungwon; Lee, Seungmin; Lee, Youngjun; Seo, Yongwon

2013-07-02

In order to investigate the feasibility of semiclathrate hydrate-based precombustion CO2 capture, thermodynamic, kinetic, and spectroscopic studies were undertaken on the semiclathrate hydrates formed from a fuel gas mixture of H2 (60%) + CO2 (40%) in the presence of quaternary ammonium salts (QASs) such as tetra-n-butylammonium bromide (TBAB) and fluoride (TBAF). The inclusion of QASs demonstrated significantly stabilized hydrate dissociation conditions. This effect was greater for TBAF than TBAB. However, due to the presence of dodecahedral cages that are partially filled with water molecules, TBAF showed a relatively lower gas uptake than TBAB. From the stability condition measurements and compositional analyses, it was found that with only one step of semiclathrate hydrate formation with the fuel gas mixture from the IGCC plants, 95% CO2 can be enriched in the semiclathrate hydrate phase at room temperature. The enclathration of both CO2 and H2 in the cages of the QAS semiclathrate hydrates and the structural transition that results from the inclusion of QASs were confirmed through Raman and (1)H NMR measurements. The experimental results obtained in this study provide the physicochemical background required for understanding selective partitioning and distributions of guest gases in the QAS semiclathrate hydrates and for investigating the feasibility of a semiclathrate hydrate-based precombustion CO2 capture process.