On the Stability of Clathrate Hydrates Encaging Polar Guest Molecules: Contrast in the Hydrogen Bonds of Methylamine and Methanol Hydrates

Abstract

The stability of clathrate hydrates encaging highly polar guests has been investigated in order to explain the experimental observation that some amines form clathrate hydrates but alcohols act as inhibitor to hydrate formation. We choose methylamine and methanol as guest species and examine the stable structure, at which the total potential energy has a minimum value. At the local minima of those two hydrates, the potential energies of water-water and guest-water, and their hydrogen bonded networks are compared. It is found that methanol does not retain the host lattice structure, while the host-network structure is kept in the presence of methylamine. It is shown that the difference in the magnitude of the partial charge on the hydrogen atom between the hydroxyl and amino groups plays a much more significant role on the stability of both clathrate hydrates than the difference in molecular geometry. This is supported from the result of a methylamine-like model that has the same partial charges on the atoms in the hydrophilic site as methanol.     

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 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.     

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.     

Ternary systems with 1,2-propanediol—A new gain in the stability of the amorphous state in the system water-1,2-propanediol-1-propanol

Three ternary systems with water and 1,2-propanediol were investigated, where the third component is 1-propanol, ethanol, or glycerol. 1-Propanol and ethanol give hydrates in their aqueous solutions as well as in these ternary systems, while glycerol gives none. No gain in the stability of the amorphous state and glass-formation tendency is obtained, for the same water contents, when 1,2-propanediol is partially replaced by ethanol. The gain is negligible when it is partially replaced by glycerol. On the contrary, a large maximum in the stability of the amorphous state is obtained, with a critical warming rate dropping from 10⁸ to 10⁴ °C/min in the presence of 65% (w/w) water when 15% (w/w) of the 1,2-propanediol is replaced by 1-propanol. The decrease in the glass formation tendency due to this replacement and corresponding to a few hydrate crystallization is small. Not only the higher stability of the amorphous state, but also in some cases the replacement of ice crystallization by clathrate crystallization at lower temperatures could perhaps contribute to a better cryoprotection of cells for some cooling and warming rates. The similarities observed between the ternary systems investigated gives an idea of the general behaviour of these systems     

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.     

Analysis of dissociation process for gas hydrates by molecular dynamics simulation

The dissociation processes of methane and carbon dioxide hydrates were investigated by molecular dynamics simulation. The simulations were performed with 368 water molecules and 64 gas molecules using NPT ensembles. The TraPPE (single-site) and 5-site models were adopted for methane molecules. The EPM2 (3-site) and SPC/E models were used for carbon dioxide and water molecules, respectively. The simulations were carried out at 270 K and 5.0 MPa for hydrate stabilisation. Then, temperature was increased up to 370 K. The temperature increasing rates were 0.1–20 TK/s. The gas hydrates dissociated during increasing temperature or at 370 K. The potential models of methane molecule did not much influence the dissociation process of methane hydrate. The mechanisms of dissociation process were analysed with the coordination numbers and mean square displacements. It was found that the water cages break down first, then the gas molecules escape from the water cages. The methane hydrate was more stable than the carbon dioxide hydrate at the calculated conditions.     

Clathrate hydrates are poor models of biomolecule hydration

Clathrate hydrates form the basis of a general model of biomolecule hydration. In clathrate hydrate crystal structures, the size of hydrogen-bonded water rings is highly constrained to five members. The clathrate hydrate model predicts that the size of water rings near biomolecule surfaces is similarly constrained to five members. This report describes a test of this model of biomolecule hydration. We have demonstrated that five-membered water rings are not a general feature of protein or nucleic acid hydration. The clathrate hydrate model appears to be inappropriate for biomolecules. © 1996 John Wiley & Sons, Inc.     

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.     

Free energy simulations for protein ligand binding and stability

Abstract

We summarize several computational techniques to determine relative free energies for condensed-phase systems. The focus is on practical considerations which are capable of making direct contact with experiments. Particular applications include the thermodynamic stability of apo- and holo-myoglobin, insulin dimerization free energy, ligand binding in lysozyme, and ligand diffusion in globular proteins. In addition to provide differential free energies between neighboring states, converged umbrella sampling simulations provide insight into migration barriers and ligand dissociation barriers and analysis of the trajectories yield additional insight into the structural dynamics of fundamental processes. Also, such simulations are useful tools to quantify relative stability changes for situations where experiments are difficult. This is illustrated for NO-bound myoglobin. For the dissociation of benzonitrile from lysozyme it is found that long umbrella sampling simulations are required to approximately converge the free energy profile. Then, however, the resulting differential free energy between the bound and unbound state is in good agreement with estimates from molecular mechanics with generalized Born surface area simulations. Furthermore, comparing the barrier height for ligand escape suggests that ligand dissociation contains a non-equilibrium component.     

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.     

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.     

Protein recovery from reversed micellar solutions through contact with a pressurized gas phase.

We describe a new process for the recovery of encapsulated protein from reversed micellar solution in concentrated form. The method involves desolubilization of the protein by decreasing solvent density through gas dissolution. Under appropriate thermodynamic conditions, the micellar water pool can be converted to clathrate hydrates. Protein recovery is facilitated by clathrate hydrate formation, which causes the desolubilized protein to exist in a solid phase, distinct from the micellar supernatant. The process is carried out without any ionic strength or pH modification.     

Molecular simulations as a tool for selection of kinetic hydrate inhibitors

Natural gas hydrates are ice-like structures in which water molecules form a cage around gas molecules. They have been a problem in the petroleum industry. The heavy cost of alcohol and glycol injections needed to suppress the formation of hydrates has spurred an interest in so-called “kinetic inhibitors”, able to slow down the hydrate formation rather than prevent it. An earlier work (Kvamme, B. et al. 1997, Mol. Phys., 90, p. 979) proposed a simulation-based scheme to assess the comparative performance of prospective inhibitors and select the best candidates for experimental testing. In this work, we employed molecular dynamics simulations to test several kinetic inhibitors in a multiphase water–hydrate system with rigid hydrate interface. In addition, a long-scale run was implemented for a system where the hydrate was free to melt and reform. Our conclusion that PVCap inhibitor will outperform PVP as a kinetic hydrate inhibitor is supported by experimental data. We demonstrate that numerical experiments can be a valuable tool for selecting kinetic inhibitors as well as provide insight into mechanisms of kinetic inhibition and hydrate melting and reformation.     

Hydration of krypton and consideration of clathrate models of hydrophobic effects from the perspective of quasi-chemical theory

Ab initio molecular dynamics (AIMD) results on a krypton-water liquid solution are presented and compared to recent XAFS results for the radial hydration structure for a Kr atom in liquid water solution. Though these AIMD calculations have important limitations of scale, the comparisons with the liquid solution results are satisfactory and significantly different from the radial distributions extracted from the data on the solid Kr/H(2)O clathrate hydrate phase. The calculations also produce the coordination number distribution that can be examined for metastable coordination structures suggesting possibilities for clathrate-like organization; none are seen in these results. Clathrate pictures of hydrophobic hydration are discussed, as is the quasi-chemical theory that should provide a basis for clathrate pictures. Outer shell contributions are discussed and estimated; they are positive and larger than the positive experimental hydration free energy of Kr(aq), implying that inner shell contributions must be negative and of comparable size. Clathrate-like inner shell hydration structures on a Kr atom solute are obtained for some, but not all, of the coordination number cases observed in the simulation. The structures found have a delicate stability. Inner shell coordination structures extracted from the simulation of the liquid, and then subjected to quantum chemical optimization, always decomposed. Interactions with the outer shell material are decisive in stabilizing coordination structures observed in liquid solution and in clathrate phases. The primitive quasi-chemical estimate that uses a dielectric model for the influence of the outer shell material on the inner shell equilibria gives a contribution to hydration free energy that is positive and larger than the experimental hydration free energy. The 'what are we to tell students' question about hydrophobic hydration, often answered with structural clathrate pictures, is then considered; we propose an alternative answer that is consistent with successful molecular theories of hydrophobic effects and based upon distinctive observable properties of liquid water. Considerations of parsimony, for instance Ockham's razor, then suggest that additional structural hypotheses in response to 'what are we to tell students' are not required at this stage.     

Quantized Water Clusters Around Apolar Molecules

Abstract

In order to understand the mechanism of gas hydrate kinetics and to explore the existance of other new cavities in the hydrate structure, we have used Molecular Dynamics (MD) simulation to study a system comprising two Lennard-Jones particles and 214 water molecules. Equilibrium structure and properties of twelve cases have been investigated. Our findings were as follows: ? Apolar molecules promote spherical liquid water clusters in a hydrate-like labile cavity.

? The size of the cavity and the coordination number is dependent upon the size of the apolar molecule.

? The coordination number of water molecules is quantized in jumps of four.

? Similarities are observed between the labile cavities and cavities in solid hydrates and in other chemical structures such as Buckminsterfullerene.

? Such a simulation procedure suggests the possibility of other clusters which may exist in yet-to-be-found hydrates. A separate question involves whether such suggested cavities can be combined with other cavities into a space-filling crystal.

     

Ab initio DFT study of structural and mechanical properties of methane and carbon dioxide hydrates

The structural and mechanical properties of methane and carbon dioxide hydrates were investigated using density functional theory simulations. Well-established equations of state of solids and exchange-correlation functionals were used for fitting the unit lattice total energy as a function of volume, and the full second-order elastic constants of these two gas hydrates were determined by energy–strain analyses. The polycrystalline elastic properties were also calculated from the unit lattice results. The final results for methane hydrate agree well with available experimental data and with other theoretical results. The two gas hydrates were found to be highly elastically isotropic, but they differed significantly in shear properties. The presented results for carbon dioxide hydrates are the first complete set reported so far. The results are a significant contribution to the ab initio material characterisation of gas hydrates required for ongoing fundamental studies and technological applications.     

Stability of DNA thymine hydrates.

Pyrimidine hydrates are products of ultraviolet irradiation of DNA. We have already demonstrated the formation of both cis-thymine hydrate and trans-thymine hydrate (6-hydroxy-5,6-dihydrothymine) in irradiated poly(dA-dT):poly(dA-dT). These are released from DNA as free bases by bacterial or human glycosylases. Thymine hydrate stabilities were studied in irradiated DNA substrates using purified E. coli endonuclease III as a reagent for their removal. After irradiation, substrate poly(dA-dT):poly(dA-dT), radiolabeled in thymine, was incubated at 50, 60, 70 or 80 degrees C, cooled, and then reacted with the enzyme under standard conditions. Thymine hydrates were assayed by enzymic release of labeled material into the ethanol-soluble fraction. Their identities were confirmed by high performance liquid chromatography. The decay of thymine hydrates in heated DNA followed first-order kinetics with a k = 2.8 x 10(-5)/sec at 80 degrees C. These hydrates were also detected in lesser quantities in the unirradiated, control substrate. Extrapolation from an Arrhenius plot yields an estimated half-life of 33.3 hours at 37 degrees C for DNA thymine hydrates. Such stability, together with their formation in unirradiated DNA, suggest thymine hydrates to be formed under physiological conditions and to be sufficiently stable in DNA to be potentially genotoxic. This necessitates their constant removal from DNA by the excision-repair system.     

Inhibition of DNA polymerase activity by thymine hydrates.

Ultraviolet irradiation of DNA results in various pyrimidine modifications. We have demonstrated formation of both cis-thymine hydrate and trans-thymine hydrate (6-hydroxy-5,6-dihydrothymine) in UV-irradiated poly(dA-dT):poly(dA-dT). Both are released from DNA as free bases by bacterial and human glycosylases. Thymine hydrates are stable in DNA and can be detected in control, unirradiated substrates. We examined the effects of thymine hydrates in UV-irradiated substrate poly(dA-dT):poly(dA-dT) on E. coli DNA polymerase I activity. Enzymic incorporation of labeled thymidine-5'-monophosphate significantly decreased with increasing UV dose. Reversal of DNA thymine hydrates to thymines by mild heating of the substrate prior to enzymic reaction resulted in partial recovery of nucleotide incorporation. Cyclobutane thymine dimers are formed between non-adjacent thymines in UV-irradiated poly(dA-dT):poly(dA-dT). These are responsible for the incomplete recovery of DNA polymerase activity following heating due to their heat stability. Analyses of the irradiated and hydrolyzed substrate also demonstrated formation of minor yields of photoproducts formed by covalent linkage of adjacent thymines and adenines by UV-irradiation. Therefore, the thymine hydrates formed in UV-irradiated DNA partially inhibit polymerase activity during DNA synthesis and thus could be potentially lethal if unrepaired.