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.     

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.     

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.     

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.     

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.     

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.     

Microhydration of caesium compounds: Cs,CsOH, CsI and Cs2I2 complexes with one to three H2O molecules of nuclear safety interest

The structure and properties of natural gas hydrates containing hydrocarbons, CO₂, and N₂ molecules were studied by using computational quantum chemistry methods via the density functional theory approach. All host cages involved in I, II, and H types structures where filled with hydrocarbons up to pentanes, CO₂ and N₂ molecules, depending on their size, and the structures of these host–guest systems optimized. Structural properties, vibrational spectra, and density of states were analyzed together with results from atoms-in-a-molecule and natural bond orbitals methods. The inclusion of dispersion terms in the used functional plays a vital role for obtaining reliable information, and thus, B97D functional was shown to be useful for these systems. Results showed remarkable interaction energies, not strongly affected by the type of host cage, with molecules tending to be placed at the center of the cavities when host cages and guest molecules cavities are of similar size, but with molecules approaching hexagonal faces for larger cages. Vibrational properties show remarkable features in certain regions, with shiftings rising from host-guest interactions, and useful patterns in the terahertz region rising from water surface vibrations strongly coupled with guest molecules. Likewise, calculations on crystal systems for the I and H types were carried out using a pseudopotential approach combined with Grimme’s method to take account of dispersion.

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.     

Molecular dynamics simulation of replacement of methane hydrate with carbon dioxide

Molecular dynamics simulation was performed to analyse the phenomena of replacement of methane hydrate with carbon dioxide (CO₂) at 270 K and 5.0 MPa for 5300 ps. The methane hydrate phase was constructed with 16 unit cells of hydrate. Every cage in the hydrate was occupied by one methane molecule. The methane hydrate phase was sandwiched between two CO₂ phases. During the simulation the hydrate partially melted and liquid water phase appeared, and CO₂ dissolved in the liquid water phase. The replacements were observed three times at the hydrate–liquid water interface during the simulation. In the first case, the replacement occurred at a S-cage without changing the structure. In the second case, an M-cage of methane hydrate partially collapsed, and methane and CO₂ molecules exchanged. After the exchange, the cage occupied by CO₂ remained in the M-cage structure. In the third case, a S-cage of methane hydrate partially collapsed, and methane and CO₂ molecules exchanged. After the exchange, the cage occupied by CO₂ changed to an M-cage-like structure.     

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.     

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.     

A molecular dynamics study on sI hydrogen hydrate

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.

Monte Carlo study of sI hydrogen hydrates

In this study, we perform grand canonical Monte Carlo simulations to evaluate the hydrogen storage capacity of structure I (sI) hydrogen hydrates at pressures up to 500 MPa. Initially, we calculate the upper limit of H₂ content of sI hydrates by studying the hypothetical sI hydrate, where H₂ is the single guest component. It is found that the storage capacity of the hypothetical pure H₂ sI hydrate could reach 3.5 wt% at 500 MPa and 274 K. Depending on pressure, the large cavities of the pure H₂ hydrate can accommodate up to three H₂ molecules while the small ones are singly occupied at most, even at pressures as high as 500 MPa, without any double occupancy being observed. Subsequently, the binary H₂–ethylene oxide (EO) hydrate is examined. In this case, the large cavities are occupied by a single EO molecule while the small cavities can accommodate at most a single H₂ molecule. Such configuration results in a maximum H₂ content of only 0.37 wt%. The hydrogen storage capacity does not improve significantly even in case when EO is replaced by a component with smaller molecular weight.     

Dynamic properties of methane,water and methane hydrates using computational simulations

In this study, the vibrational spectrum of methane hydrates is calculated through dynamic molecular simulations based on two different methods. The spectra obtained using the proposed procedure allow the differentiation of the contributions of different inter- and intramolecular motion types in the spectrum, which cannot be produced with the traditional method based on atomic velocities. Simulations were carried out at different composition, pressure and temperature conditions to observe the effect of these variables on the vibrational spectrum. The proposed method allowed the observation of a difference in the frequencies for the C–H stretching vibrations between small and large cavities, which agrees with reported experimental values.     

Analysis of crystal growth of methane hydrate using molecular dynamics simulation

Methane hydrate is a crystalline compound with methane molecules enclosed in cages formed by hydrogen-bonded water molecules. Understanding the mechanism of nucleation and crystal growth from methane vapour and liquid water is important for all hydrate applications. However, processes near the water/methane interface are still unclear. In this work, we focused on the crystal growth of methane hydrate seeds located near the water/methane interface. We performed molecular dynamics (MD) simulation and analysed the crystal growth of the hydrate seed at the interface. New cages formed in the liquid water phase were stabilised when they shared faces with the hydrate seed. We also investigated the crystal growth rate as the time development of the number of methane molecules trapped in hydrate cages, based on the trajectory of the MD simulation. The calculated growth rate in the direction that covers the interface was 1.38 times that in the direction towards the inside of the water phase.     

Molecular dynamics simulation of methane hydrate dissociation by depressurisation

Methane (CH₄) hydrate dissociation and the mechanism by depressurisation are investigated by molecular dynamics (MD) simulation. The hydrate decomposition processes are studied by the ‘vacuum removal method’ and the normal method. It is found that the hydrate decomposition is promoted by depressurisation. The quasi-liquid layer is formed in the hydrate surface layer. The driving force of dissociation is found to be controlled by the concentration gradient between the H₂O molecules of the hydrate surface layer and the H₂O molecules of the hydrate inner layer. The clathrates collapse gradually, and the hydrate decomposes layer by layer. Relative to our previous MD simulation results, this study shows that the rate of the hydrate dissociation by depressurisation is slower than that by the thermal stimulation and the inhibitor injection. This study illustrated that MD simulation can play a significant role in investigating the hydrate decomposition mechanisms.     

Evidence of protein collective motions on the picosecond timescale

We investigate the presence of structural collective motions on a picosecond timescale for the heme protein, cytochrome c, as a function of oxidation and hydration, using terahertz (THz) time domain spectroscopy and molecular dynamics simulations. The THz response dramatically increases with oxidation, with the largest increase for lowest hydrations, and highest frequencies. For both oxidation states the THz response rapidly increases with hydration saturating above ∼25% (g H₂O/g protein). Quasiharmonic vibrational modes and dipole-dipole correlation functions were calculated from molecular dynamics trajectories. The collective mode density of states alone reproduces the measured hydration dependence, providing strong evidence of the existence of these motions. The large oxidation dependence is reproduced only by the dipole-dipole correlation function, indicating the contrast arises from diffusive motions consistent with structural changes occurring in the vicinity of buried internal water molecules. This source for the observed oxidation dependence is consistent with the lack of an oxidation dependence in nuclear resonant vibrational spectroscopy measurements.