The Stability of Clathrate Hydrates: Temperature Dependence of Dissociation Pressure in Xe and Ar Hydrate

Abstract

The thermodynamic stability of clathrate hydrates I and II encaging xenon or argon has been investigated by examining the temperature dependence of the dissociation pressure. The evaluation of the stability is made based on the generalized van der Waals and Platteeuw theory developed by Tanaka and Kiyohara [J. Chem. Phys. 98, 4098 (1993)]. In the new treatment, the free energy of formation of hydrates in equilibrium with ice is calculated by taking the coupling of the host lattice vibrations with guests into consideration. The predicted dissociation pressures of Xe and Ar hydrates agree well with experiments in higher temperature range. A poor agreement between experiment and calculation for Ar clathrate hydrate at low temperature is improved by the use of a quantum mechanical partition function for a harmonic oscillator in evaluating the free energy difference between ice and empty hydrate.     

Microbial Stabilization and Kinetic Enhancement of Marine Methane Hydrates

Abstract

In clathrate hydrates, a water host lattice encages small guest molecules in cavities. Methane hydrates are the most widespread in-situ clathrate in the permafrost and continental-shelf ocean regions, constituting a significant energy resource, and prompting recent marine-hydrate gas-production trials. Despite exciting engineering advances and a few marine-mimicking laboratory studies of methane-hydrate kinetics and stabilization, from microbial perspectives, little is known about a potential microbial origin of marine hydrates, nor their possible formation kinetics or potential stabilization by microbial sources. Here, for the first time, we show that an exported, extra-cytoplasmic porin – produced by a marine methylotrophic bacterium culture – provides the basis for kinetic enhancement and stabilization of methane hydrates under conditions simulating the seabed environment. We then identify the key protein at play, and we therefore suggest microbe-based stabilization of marine hydrates is evidently a property likely to be found in many marine bacteria. Our research opens the possibility of managing marine-hydrate deposits using microbiological strategies for environmental and societal benefit.     

The thermal properties of binary structure sI clathrate hydrate from molecular dynamics simulation

In this work, we present temperature dependence of lattice parameter and normalised lattice parameter in the atmospheric pressure and 120 bar and also pressure dependence of unit cell volume and normalised unit cell volume at 150 and 250?K for variety guests with different size, polarity and guest–host hydrogen bonding capability such as trimethylene oxide (TMO), ethylene oxide (EO), formaldehyde (FA), cyclobutane (CB), cyclopropane (CP) and ethane (Et) in the large cages with CH₄ in small cages of sI clathrate hydrates by molecular dynamics simulations. The obtained values of lattice parameters for the guest species are compatible with the experimental values. These clathrate hydrates are simulated with TIP4P/ice four-site water potential. Herein, isobaric thermal expansivity and isothermal compressibility are calculated at a temperature range of 50–250?K and a wide pressure range. These structural properties have been compared for guests which they are isoelectronic and have similar masses but with different size and polarity. We use molecular dynamics simulations to relate microscopic guest properties, like guest–host hydrogen bonding to macroscopic sI clathrate hydrate properties. The temperature dependence of thermodynamic properties such as constant-volume and constant-pressure heat capacity is presented in the atmospheric pressure for these guest species.     

Rearrangement of the Hydrogen-Bonded Network of the Clathrate Hydrates Encaging Polar Guest

Abstract

Rearrangement process of the hydrogen-bonded network of clathrate hydrate of the polar guest ethylamine is examined by the molecular dynamics simulation. The hydrogen-bonded network rearrangements with reorientation of water or migration of water are observed in the 10 ns trajectories and analyzed in term of a representative connectivity pattern of a time zone longer than a time scale of vibrational motion of molecules. The most frequent rearrangement is the reorientation of single water molecule rotating 180° around its twofold axis in the network unlike Bjerrum's picture of molecular rotation in ice. Migration of water in the host lattice rarely occurs and very long time (several hundred pico second) is required to complete the rearrangement process since cooperative reorientation of many neighboring water is necessarily accompanied. The correlation of reorientational motion of water appears to decay not with the Debye type but rather with a power-law behavior.     

Dissociation mechanism of gas hydrates (I,II, H) of alkane molecules: a comparative molecular dynamics simulation

Employing NPT molecular dynamics method with consistent valence force field, the dissociation processes of sI, sII and sH gas hydrates are simulated at different temperatures and at a constant pressure of 100 MPa. The dissociation mechanisms of gas hydrates are revealed by analysing the structural snapshots, radial distribution functions and diffusion coefficients at different temperatures. As temperature increases, the diffusion rates of water molecules and guest molecules increase; thus the clathrate skeleton formed by water molecules with hydrogen bonds distorts and breaks down; meanwhile the guest molecules encapsulated in the water cavities are released. The size of guest molecules affects the dissociation behaviour of gas hydrate. In addition, the dissociation behaviour also relies on the structural phase of gas hydrates.     

The Structure of Liquid Methanol: A Molecular Dynamics Study Using Three-Site Models

Abstract

The structure of liquid methanol at 298.15 K is investigated by performing molecular dynamics (MD) simulations in NVE ensemble using two 3-site force field models. The simulated structural results are compared with the recent neutron diffraction (ND) results obtained at the partial pair distribution function (pdf) level by employing H/D substitution on the hydroxyl hydrogen, Ho. Overall agreement is found between the simulated and experimental total intermolecular radial distribution functions (rdfs). The ability of the 3-site model simulations to satisfactorily reproduce experimental X—X (X = C, O or H- a methyl hydrogen) intermolecular partial distribution function, dominated by contributions from the methyl group. demonstrates that the methyl group does not participate in any bonding in the liquid. However, a comparison between the simulated and experimental Ho—Ho and X—Ho functions reveals that discrepancies still exist at a quantitative level.     

Hydration of Cytidine, 2′-Deoxycytidine and their Phosphate Salts in the Aqueous Solutions. A Molecular Dynamics Computer Simulation Study

Abstract

To compare the hydration pattern of the cytidine (Cyd) and 2′-deoxycytidine (dCyd) in the aqueous solutions at the level of microscopic interactions, Molecular Dynamics (MD) computer simulations have been undertaken. The results indicate that the hydration of the heterocyclic base moiety in cytidine and 2′-deoxycytidine has a hydrophobic character. None of the three potential Watson—;Crick base pair centres hydrogen bonds with the water molecules and the formation of something akin to a clathrate cage structure of water around base moieties of nucleosides in the aqueous solution is suggested. In contrast, the hydration of Cyd and dCyd sugar moieties shows a hydrophilic character and the three-dimensional networks of H-bonds involving all hydrophilic centres are formed differently around the ribose and 2′-deoxyribose. The sugar hydroxyl groups participate in the hydrogen bonding with water both as H-donor and as H-acceptor. Their donor-acceptor abilities have been evaluated and compared. The coordination numbers, the geometrical data of the first hydration shell, and the number of hydrogen bonds have been calculated. The changes in the pattern of hydration with the increased concentration of nucleosides and upon nucleoside protonation are discussed. The analysis of the pairwise interaction energies are also presented.     

The energy metabolism of <Emphasis Type="Italic">Methanomicrococcus blatticola</Emphasis>: physiological and biochemical aspects

Methanomicrococcus blatticola, a methanogenic archaeon isolated from the cockroach Periplaneta americana, is specialised in methane formation by the hydrogen-dependent reduction of methanol, monomethyl-, dimethyl- or trimethylamine. Experiments with resting cells demonstrated that the capability to utilise the methylated one-carbon compounds was growth substrate dependent. Methanol-grown cells were unable of methylamine conversion, while cells cultured on one of the methylated amines did not metabolise methanol. Unlike trimethylamine, monomethyl- and dimethylamine metabolism appeared to be co-regulated. The central reaction in the energy metabolism of all methanogens studied so far, the reduction of CoM-S-S-CoB, was catalysed with high specific activity by a cell-free system. Activity was associated with the membrane fraction. Phenazine was an efficient artificial substrate in partial reactions, suggesting that the recently discovered methanophenazine might act in the organism as the physiological intermediary electron carrier. Our experiments also showed that M. blatticola apparently lacks the pathway for methyl-coenzyme oxidation to CO₂, explaining the strict requirement for hydrogen in methanogenesis and the obligately heterotrophic character of the organism.     

Ultrafast Cleavage and Deprotection of Oligonucleotides Synthesis and Use of CAc Derivatives

Abstract

We have investigated the use of alkylamines as fast cleavage and deprotection reagents for the solid phase synthesis of oligonucleotides and found methylamine/ammonium hydroxide (or methylamine) as an efficient reagent. The transamination side product formed with the commonly used dC^bz has been eliminated by the use of dC^Ac phosphoramidite. This system has successfully been used in the synthesis of oligonucleotides and oligonucleoside phosphorothioates. DMT dC^Ac hydrogen phosphonate and DMT ribo C^Ac-2′-O Me phosphoramidite also have been prepared and used in the synthesis of oligonucleotides.     

Molecular dynamics simulation on the decomposition of type SII hydrogen hydrate and the performance of tetrahydrofuran as a stabiliser

Molecular dynamics simulation is used to study the decomposition and stability of SII hydrogen and hydrogen/tetrahydrofuran (THF) hydrates at 150 K, 220 K and 100 bar. The modelling of the microscopic decomposition process of hydrogen hydrate indicates that the decomposition of hydrogen hydrate is led by the diffusive behaviour of H₂ molecules. The hydrogen/THF hydrate presents higher stability, by comparing the distributions of the tetrahedral angle of H₂O molecules, radial distribution functions of H₂O molecules and mean square displacements or diffusion coefficients of H₂O and H₂ molecules in hydrogen hydrate with those in hydrogen/THF hydrate. It is also found that the resistance of the diffusion behaviour of H₂O and H₂ molecules can be enhanced by encaging THF molecules in the (5¹²6⁴) cavities. Additionally, the motion of THF molecules is restricted due to its high interaction energy barrier. Accordingly, THF, as a stabiliser, is helpful in increasing the stability of hydrogen hydrate.     

Alteration of the groove width of DNA induced by the multimodal hydrogen bonding of denaturants with DNA bases in its grooves affects their stability

BackgroundDenaturants, namely, urea and guanidinium chloride (GdmCl) affect the stability as well as structure of DNA. Critical assessment of the role of hydrogen bonding of these denaturants with the different regions of DNA is essential in terms of its stability and structural aspect. However, the understanding of the mechanistic aspects of structural change of DNA induced by the denaturants is not yet well understood.MethodsIn this study, various spectroscopic along with molecular dynamics (MD) simulation techniques were employed to understand the role of hydrogen bonding of these denaturants with DNA bases in their stability and structural change.Results and conclusionIt has been found that both, GdmCl and urea intrude into groove region of DNA by striping surrounding water. The hydrogen bonding pattern of Gdm⁺ and urea with DNA bases in its groove region is multimodal and distinctly different from each other. The interaction of GdmCl with DNA is stabilized by electrostatic interaction whereas electrostatic and Lennard-Jones interactions both contribute for urea. Gdm⁺ forms direct hydrogen bond with the bases in the minor groove of DNA whereas direct and water assisted hydrogen bond takes place with urea. The hydrogen bond formed between Gdm⁺ with bases in the groove region of DNA is stronger than urea due to strong electrostatic interaction along with less self-aggregation of Gdm⁺ than urea. The distinct hydrogen bonding capability of Gdm⁺ and urea with DNA bases in its groove region affects its width differently. The interaction of Gdm⁺ decreases the width of the minor and major groove which probably increases the strength of hydrogen bond between the Watson-Crick base pairs of DNA leading to its stability. In contrast, the interaction of urea does not affect much to the width of the grooves except the marginal increase in the minor groove width which probably decreases the strength of hydrogen bond between Watson Crick base pairs leading to the destabilization of DNA.General significanceOur study clearly depicts the role of hydrogen bonding between DNA bases and denaturants in their stability and structural change which can be used further for designing of the guanidinium based drug molecules.     

Vibrational spectra of deuterated methane and water molecules in structure I clathrate hydrate from ab initio MD simulation

The deuteration of the lattice molecules in clathrate hydrates is a widely used experimental technique to clearly separate the vibrational modes. However, the effect of the deuteration on the vibrational spectra and molecular motions is not fully understood. Since the guest–host coupling may change the vibrational spectra, a detailed analysis of the vibrational spectra of deuterated clathrate hydrate is significant in the understanding of the mechanism of the vibrational shift. In this study, the vibrational spectra of the deuterated methane hydrates were calculated by ab initio molecular dynamics simulation. The intramolecular vibrational frequency of the methane in D₂O lattice and deuterated methane in H₂O lattice was calculated and compared with the pure methane hydrate. The bending, rocking and overtone of the bending mode was also reported. The effect of coupling of the rattling motions of guest and host molecules on the vibrational spectra was revealed.     

Structural properties of sH hydrate: a DFT study of anisotropy and equation of state

ABSTRACT

Structure-H (sH) hydrate is one of the canonical gas hydrates with significant potential applications and scarce characterised material properties despite the wide knowledge available on other gas hydrates. In this work we characterise some of the important physical properties of this hydrate at the atomistic level using Density Functional Theory. Two exchange-correlation functionals (revPBE and DRSLL) were used to simulate six sH hydrate systems encapsulating neohexane and different help gas molecules. The important role of dispersion forces is quantified. The density and isothermal bulk modulus of sH hydrate are higher when dispersion interactions are considered. The presence of those interactions imposes a direct relationship between the hydrate density and its bulk modulus, while their absence reveals the bulk modulus dependency on hydrogen bond density. Anisotropy is a distinguishing feature of this hydrate in distinction to nearly isotropic sI and sII hydrates. Structure-H hydrate experiences a compressional anisotropy in which the a-lattice and the c-lattice constants respond differently to applied pressure showing less compressibility along the c-axis. This compressional anisotropy was found dependant on the chemistry of help gas molecules. Taken together, these property characterisation results and analysis are a significant and novel contribution to the material physics of sH hydrates.     

Two-component system that regulates methanol and formaldehyde oxidation in Paracoccus denitrificans

A chromosomal region encoding a two-component regulatory system, FlhRS, has been isolated from Paracoccus denitrificans. FlhRS-deficient mutants were unable to grow on methanol, methylamine, or choline as the carbon and energy source. Expression of the gene encoding glutathione-dependent formaldehyde dehydrogenase (fhlA) was undetectable in the mutant, and expression of the S-formylglutathione hydrolase gene (fghA) was reduced in the mutant background. In addition, methanol dehydrogenase was immunologically undetectable in cell extracts of FhlRS mutants. These results indicate that the FlhRS sensor-regulator pair is involved in the regulation of formaldehyde, methanol, and methylamine oxidation. The effect that the FlhRS proteins exert on the regulation of C₁ metabolism might be essential to maintain the internal concentration of formaldehyde below toxic levels.     

Msn5p is involved in formaldehyde resistance but not in oxidative stress response in the methylotrophic yeast Candida boidinii

Methylotrophic yeasts, which can utilize methanol as sole carbon and energy source, are exposed to two toxic metabolic intermediates, formaldehyde and hydrogen peroxide, during growth on methanol. Here we report that Msn5p, an importin-β family nuclear exporter, participated in the formaldehyde resistance mechanism but not in the hydrogen peroxide resistance mechanism in Candida boidinii. Disruption of the MSN5 gene in this yeast caused retardation of growth on formaldehyde-generating growth substrates such as methanol and methylamine, but the expression levels of the methanol-metabolizing enzymes did not fall. The Msn5p-depleted strain was sensitive to formaldehyde but not to hydrogen peroxide. Furthermore, a yellow fluorescent protein-tagged Msn5p was diffuse in the cytoplasm of C. boidinii when the cells were treated with high concentrations of formaldehyde or ethanol, but was predominantly associated with the nuclei following treatment with hydrogen peroxide.     

Factors affecting the production of pyrroloquinoline quinone by the methylotrophic bacterium W3A1

Two variants of the methylotrophic bacterium W3A1, designated W3A1-S (slimy) and W3A1-NS (nonslimy), were compared with respect to their ability to grow in batch culture on the C1 substrates methylamine, methanol, and trimethylamine. Substrate utilization, cell density, pH, cellular and soluble polysaccharide production, and concentrations of the enzymes methylamine dehydrogenase, trimethylamine dehydrogenase, and methanol dehydrogenase produced were measured as a function of growth. The ability of the two bacterial variants to excrete the redox cofactor pyrroloquinoline quinone into the growth medium was also investigated. The two variants were similar with respect to all properties measured, except that W3A1-S produced significantly more capsular polysaccharides than variant W3A1-NS. Pyrroloquinoline quinone was excreted when either variant was grown on any of the C1 substrates investigated but was maximally produced when the methylamine concentration was 0.45% (wt/vol). This cofactor is excreted only as bacterial growth enters the stationary phase, a time when the levels of trimethylamine dehydrogenase and the quinoproteins methanol dehydrogenase and methylamine dehydrogenase begin to decline. It is not known whether the pyrroloquinoline quinone found in the medium is made de novo for excretion, derived from the quinoprotein pool, or both. Pyrroloquinoline quinone excretion has been observed with other methylotrophs, but this is the first instance where the excretion was observed with substrates other than methanol.     

Packing Features of the all-AT Oligonucleotide d(AAATTT)

Abstract

We describe the packing features of the oligonucleotide duplex d(AAATTT)₂, as determined by X-ray diffraction. There is little information on sequences that only contain A and T bases. The present structure confirms that these sequences tend to pack as a helical arrangement of stacked oligonucleotides in a B conformation with Watson-Crick hydrogen bonding. Our results demonstrate that the virtual TA base step between stacked duplexes has a negative twist that improves base stacking. This observation is consistent with the low stability of TA base steps in B-form DNA.     

Factors affecting the production of pyrroloquinoline quinone by the methylotrophic bacterium W3A1.

Two variants of the methylotrophic bacterium W3A1, designated W3A1-S (slimy) and W3A1-NS (nonslimy), were compared with respect to their ability to grow in batch culture on the C1 substrates methylamine, methanol, and trimethylamine. Substrate utilization, cell density, pH, cellular and soluble polysaccharide production, and concentrations of the enzymes methylamine dehydrogenase, trimethylamine dehydrogenase, and methanol dehydrogenase produced were measured as a function of growth. The ability of the two bacterial variants to excrete the redox cofactor pyrroloquinoline quinone into the growth medium was also investigated. The two variants were similar with respect to all properties measured, except that W3A1-S produced significantly more capsular polysaccharides than variant W3A1-NS. Pyrroloquinoline quinone was excreted when either variant was grown on any of the C1 substrates investigated but was maximally produced when the methylamine concentration was 0.45% (wt/vol). This cofactor is excreted only as bacterial growth enters the stationary phase, a time when the levels of trimethylamine dehydrogenase and the quinoproteins methanol dehydrogenase and methylamine dehydrogenase begin to decline. It is not known whether the pyrroloquinoline quinone found in the medium is made de novo for excretion, derived from the quinoprotein pool, or both. Pyrroloquinoline quinone excretion has been observed with other methylotrophs, but this is the first instance where the excretion was observed with substrates other than methanol.     

Mechanisms for Stabilising Water Clathrates

Molecular dynamics computer simulations are used to examine various possible mechanisms for stabilising water clathrates. It is found that the attractive interactions between guest and host molecules are not sufficient to explain the clathrate's stability; nor is there any significant dynamic coupling between the guest and host molecules in the clathrate. Instead, it appears that the repulsive guest-host interactions provide the mechanical stability of the clathrate, and that they are even sufficient to define its structure. Some of the thermodynamic implications of these observations are discussed.