Molecular dynamics study of the stability of methane structure H clathrate hydrates

Molecular dynamics simulations are used to study the stability of structure H (sH) methane clathrate hydrates in a 3 x 3 x 3 sH unit cell replica. Simulations are performed at experimental conditions of 300 K and 2 GPa for three methane intermolecular potentials. The five small cages of the sH unit cell are assigned methane guest occupancies of one and large cage guest occupancies of one to five are considered. Radial distribution functions, unit cell volumes, and configurational energies are studied as a function of large cage CH(4) occupancy. Free energy calculations are carried out to determine the stability of clathrates for large cage occupancies. Large cage occupancy of five is the most stable configuration for a Lennard-Jones united-atom potential and the Tse-Klein-McDonald potential parametrized for condensed methane phases and two for the most stable configuation for the Murad and Gubbins potential.     

Molecular dynamics simulations of binary structure H hydrogen and methyl-tert-butylether clathrate hydrates

Binary structure H (sH) hydrogen and methyl-tert-butylether (MTBE) clathrate hydrates are studied with molecular dynamics simulations. Simulations on a 3 x 3 x 3 sH unit cell with up to 4.7 mass % hydrogen gas are run at pressures of 100 bars and 2 kbars at 100 and 273 K. For the small and medium cages of the sH unit cell, H2 guest molecule occupancies of 0, 1 (single occupancy), and 2 (double occupancy) are considered with the MTBE molecule occupying all of the large cages. An increase of the small and medium cage occupancies from 1 to 2 leads to a jump in the unit cell volume and configurational energy. Calculations are also set up with 13, 23, and 89 of the MTBE molecules in the large cages replaced by sets of three to six H2 molecules, and the effects on the configurational energy and volume of the simulation cell are determined. As MTBE molecules are replaced with sets of H2 guests in the large cages, the configurational energy of the unit cell increases. At the lower temperature, the energy and volume of the clathrate are not sensitive to the number of hydrogen guests in the large cages; however, at higher temperatures the repulsions among the H2 guest molecules in the large cages cause an increase in the system energy and volume.     

Molecular dynamics simulation of structure H clathrate-hydrates of binary guest molecules

Molecular dynamics (MD) simulations are performed to study the stability of structure H clathrate-hydrates of methane+large-molecule guest substance (LMGS) at temperatures of 270, 273, 278 and 280 K under canonical (NVT-) ensemble condition in a 3×3×3 structure H unit cell replica with 918 TIP4P water molecules. The studied LMGS are 2-methylbutane (2-MB), 2,3-dimethylbutane (2,3-DMB), neohexane (NH), methylcyclohexane (MCH), adamantane and tert-butyl methyl ether (TBME). In the process of MD simulation, achieving equilibrium of the studied system is recognized by stability in calculated pressure for NVT-ensemble. So, for the accuracy of MD simulations, the obtained pressures are compared with the experimental phase diagrams. Therefore, the obtained equilibrium pressures by MD simulations are presented for studying the structure H clathrate-hydrates. The results show that the calculated temperature and pressure conditions by MD simulations are consistent with the experimental phase diagrams. Also, the radial distribution functions (RDFs) of host-host, host-guest and guest-guest molecules are used to analysis the characteristic configurations of the structure H clathrate-hydrate.     

Molecular dynamics simulation for studying the stability of structure H clathrate-hydrates of argon and large guest molecules

The aim of present paper is to study the stability of (argon + large guest molecules) structure H clathrate-hydrates by using molecular dynamics simulations and with employing the COMPASS force field to consider the molecular interactions. The simulations are performed by embedding the structure H clathrate-hydrates in a simulation cell under isobaric-isothermal (NPT) conditions. The obtained equilibrium lattice parameters are compared with the experimental data, where a good consistency is observed. The results show that the size and dipole moment of the guest molecules enclosed in the hydrate cages play the main role in the interactions between the guest molecules and the water molecules, which constitute the surrounding walls of the hydrate cage and these interactions would stabilize the hydrate structure. The characteristics of the clathrate-hydrate structure are analyzed by evaluating the radial distribution function, where the agreement between the results obtained in this work and other similar theoretical and experimental investigations validates the simulation procedure and related interpretations.     

2H and13C NMR study of guest molecule orientation in clathrate hydrates

At relatively high temperatures (200–270K), clathrate hydrate cages achieve their full crystallographic symmetry because of time averaging of different cage configurations which exist because of disorder in the water molecule orientations. The average orientation of guest molecules in the cages can be obtained from the NMR spectrum, in case of spin 1/2 nuclei from the nuclear shielding tensor, in case of spin 1 nuclei from the quadrupole coupling tensor. Guest molecules studied include carbon dioxide, carbonyl sulphide, methyl-d₃ fluoride, methyl-d₃ chloride, methyl-d₃ bromide, ethane-d₆, acetylene-d₂ in the structure I hydrates, and methyl-d₃ iodide in the structure II hydrate.For the slightly flattened large cage of structure I hydrate, the guest molecules rotate so that the plane which contains the long axis of the molecule is confined to be nearer to the equatorial plane of the cage than the axial regions.Since the structure II large cage has tetrahedral symmetry on time average, it exerts no orienting effect on guest molecules.NRCC no. 32722.     

Structure transition and swapping pattern of clathrate hydrates driven by external guest molecules

We first report here that under strong surrounding gas of external CH4 guest molecules the sII and sH methane hydrates are structurally transformed to the crystalline framework of sI, leading to a favorable change of the lattice dimension of the host-guest networks. The high power decoupling 13C NMR and Raman spectroscopies were used to identify structure transitions of the mixed CH4 + C2H6 hydrates (sII) and hydrocarbons (methylcyclohexane, isopentane) + CH4 hydrates (sH). The present findings might be expected to provide rational evidences regarding the preponderant occurrence of naturally occurring sI methane hydrates in marine sediments. More importantly, we note that the unique and cage-specific swapping pattern of multiguests is expected to provide a new insight for better understanding the inclusion phenomena of clathrate materials.     

Vibrational spectra of methane clathrate hydrates from molecular dynamics simulation

Molecular dynamics simulations were performed on methane clathrate hydrates at ambient conditions. Thermal expansion results over the temperature range 60-300 K show that the unit cell volume increases with temperature in agreement with experiment. Power spectra were obtained at 273 K from velocity autocorrelation functions for selected atoms, and normal modes were assigned. The spectra were further classified according to individual atom types, allowing the assignment of contributions from methane molecules located in small and large cages within the structure I unit cell. The symmetric C-H stretch of methane in the small cages occurs at a higher frequency than for methane located in the large cages, with a peak separation of 14 cm(-1). Additionally, we determined that the symmetric C-H stretch in methane gas occurs at the same frequency as methane in the large cages. Results of molecular dynamics simulations indicate the use of power spectra obtained from the velocity autocorrelation function is a reliable method to investigate the vibrational behavior of guest molecules in clathrate hydrates.     

Stability of rare gas structure H clathrate hydrates

Molecular dynamics simulations are used to study the stability of structure H (sH) clathrate hydrates with the rare gases Ne, Ar, Kr, and Xe. Simulations on a 3 x 3 x 3 sH unit cell replica are performed at ambient pressure at 40 and 100 K temperatures. The small and medium (s+m) cages of the sH unit cell are assigned rare gas guest occupancies of 1 and for large (l) cages guest occupancies of 1-6 are considered. Radial distribution functions for guest pairs with occupancies in the l-l, l-(s+m), and (s+m)-(s+m) cages are presented. The unit cell volumes and configurational energies are studied as a function of large cage occupancy for the rare gases. Free energy calculations are carried out to determine the stability of clathrates for large cage occupancies at 100 K and 1 bar and 20 kbar pressures. These studies show that the most stable argon clathrate has five guests in the large cages. For krypton and xenon the most stable configurations have three and two guests in the large cages, respectively.     

Molecular vibrations of methane molecules in the structure I clathrate hydrate from ab initio molecular dynamics simulation

Vibrational frequencies of guest molecules in clathrate hydrates reflect the molecular environment and dynamical behavior of molecules. A detailed understanding of the mechanism for the vibrational frequency changes of the guest molecules in the clathrate hydrate cages is still incomplete. In this study, molecular vibrations of methane molecules in a structure I clathrate hydrate are calculated from ab initio molecular dynamics simulation. The vibrational spectra of methane are computed by Fourier transform of autocorrelation functions, which reveal distinct separation of each vibrational mode. Calculated symmetric and asymmetric stretching vibrational frequencies of methane molecules are lower in the large cages than in the small cages (8 and 16 cm(-1) for symmetric and asymmetric stretching, respectively). These changes are closely linked with the C-H bond length. The vibrational frequencies for the bending and rocking vibrational modes nearly overlap in each of the cages.     

The cages, dynamics, and structuring of incipient methane clathrate hydrates

Interest in describing clathrate hydrate formation mechanisms spans multiple fields of science and technical applications. Here, we report findings from multiple molecular dynamics simulations of spontaneous methane clathrate hydrate nucleation and growth from fully demixed and disordered two-phase fluid systems of methane and water. Across a range of thermodynamic conditions and simulation geometries and sizes, a set of seven cage types comprises approximately 95% of all cages formed in the nucleated solids. This set includes the ubiquitous 5(12) cage, the 5(12)6(n) subset (where n ranges from 2-4), and the 4(1)5(10)6(n) subset (where n also ranges from 2-4). Transformations among these cages occur via water pair insertions/removals and rotations, and may elucidate the mechanisms of solid-solid structural rearrangements observed experimentally. Some consistency is observed in the relative abundance of cages among all nucleation trajectories. 5(12) cages are always among the two most abundant cage types in the nucleated solids and are usually the most abundant cage type. In all simulations, the 5(12)6(n) cages outnumber their 4(1)5(10)6(n) counterparts with the same number of water molecules. Within these consistent features, some stochasticity is observed in certain cage ratios and in the long-range ordering of the nucleated solids. Even when comparing simulations performed at the same conditions, some trajectories yield swaths of multiple adjacent sI unit cells and long-range order over 5 nm, while others yield only isolated sI unit cells and little long-range order. The nucleated solids containing long-range order have higher 5(12)6(2)/5(12) and 5(12)6(3)/4(1)5(10)6(2) cage ratios when compared to systems that nucleate with little long-range order. The formation of multiple adjacent unit cells of sI hydrate at high driving forces suggests an alternative or addition to the prevailing hydrate nucleation hypotheses which involve formation through amorphous intermediates.     

Structural and dynamical properties of methane clathrate hydrates

Equilibrium molecular dynamics (MD) simulations have been performed in both the NVT and NPT ensembles to study the structural and dynamical properties of fully occupied methane clathrate hydrates at 50, 125, and 200 K. Five atomistic potential models were used for water, ranging from fully flexible to rigid polarizable and nonpolarizable. A flexible and a rigid model were utilized for methane. The phonon densities of states were evaluated and the localized rattling modes for the methane molecules were found to couple to the acoustic phonons of the host lattice. The calculated methane density of states was found to be in reasonable agreement with available experimental data.     

Molecular dynamics simulation of NMR powder lineshapes of linear guests in structure I clathrate hydrates

We perform molecular dynamics simulations (up to 6 ns) for the structure I clathrate hydrates of linear molecules CS, CS(2), OCS, and C(2)H(2) in large cages at different temperatures in the stability range to determine the angular distribution and dynamics of the guests in the large cages. The long axes of linear guest molecules in the oblate large structure I clathrate hydrate cages are primarily confined near the equatorial plane of the cage rather than axial regions. This non-uniform spatial distribution leads to well-known anisotropic lineshapes in the solid-state NMR spectra of the guest species. We use the dynamic distribution of guest orientations in the cages during the MD simulations at different temperatures to predict the (13)C NMR powder lineshapes of the guests in the large cages. The length of the guests and intermolecular interactions of the guests in the water cages determine the angular distribution and the mobility of the guests in the sI large cages at different temperatures. At low temperatures the range of motion of the guests in the cages are limited and this is reflected in the skew of the predicted (13)C lineshapes. As the guest molecules reach the fast motion limit at higher temperatures, the lineshapes for CS, OCS, and C(2)H(2) are predicted to have the "standard" powder lineshapes of guest molecules.     

Crystal lattice size and stability of type H clathrate hydrates with various large-molecule guest substances

To gain a better understanding of the effects of guest molecules on the lattice and stability of type H hydrates, we performed powder X-ray diffraction (PXRD) measurements and semiempirical molecular orbital calculations. The unit cell parameters and cohesive energies of various type H hydrates that contain methane (CH4) were analyzed. PXRD measurements indicated that an increase in the large-molecule guest volume caused the unit cell volume to increase. It was also indicated that a large-molecule guest substance caused the a-axis-direction of the unit cell to increase with little decrease in the c-axis direction. Calculations of cohesive energy by means of a semiempirical molecular orbital method indicated that the functional group and configuration of large-molecule guest substances affects the stability of type H hydrates. It was concluded that the icosahedron (5(12)6(8)) cages do not easily increase in length along the c-axis direction when larger guest molecules are used to form the hydrate, but the 5(12)6(8) cage and the layer of dodecahedron (5(12)) cages can easily increase in length along the a-axis direction due to interactions of the guest-host molecule.     

Critical guest concentration and complete tuning pattern appearing in the binary clathrate hydrates

The concept of tuning phenomenon in binary hydrate systems has been suggested to enhance the gas storage capacity through molecular interactions. In this report, the existence of critical guest concentration (CGC) is investigated by means of spectroscopic methods. The existence of the critical guest concentration can act as a limiting factor in the application areas of binary hydrates. Therefore, it should be taken into account before applying this concept to application fields. In addition, further research on this concept using other hydrate systems is required to clarify the present findings.     

Molecular motion and phase transitions of clathrate hydrates**

Abstract

Heat capacities and complex dielectric permittivities of three clathrate hydrates of type II, encaging tetrahydrofuran (THF), acetone (Ac), and trimethylene oxide (TMO), were measured at low temperatures. The heat capacity measurement was done in the temperature range 13–300 K by using an adiabatic calorimeter with a built-in cryorefrigerator. The permittivities were measured in the temperature range 20–260 K and in the frequency range 20 Hz-1 MHz. For pure samples, with a glass transition due to freezing out of water, reorientational motion of the host lattice was observed calorimetrically at 85 K for THF and at 90 K for Ac hydrates, respectively. Spontaneous temperature drift rates of the calorimetric cell were measured under adiabatic conditions to derive the characteristic time for enthalpy relaxation. The enthalpy relaxation times thus derived were well correlated in an Arrhenius plot with the dielectric relaxation times derived from the dielectric relaxation of orientation polarization. The situation is the same as hexagonal ice which has a similar four co-ordinated hydrogen-bonded network.     

Structure, dynamics and ordering in structure i ether clathrate hydrates from single-crystal X-ray diffraction and 2H NMR spectroscopy

The structure and dynamics of trimethylene oxide (TMO) and ethylene oxide (EO) structure I (sI) hydrates are reported from single-crystal X-ray diffraction and 2H NMR spectroscopic measurements. The guest molecule positions in the large cage were determined with considerable improvement over previous diffraction work so that a dynamic model that was consistent with these orientations could be developed to explain the 2H NMR data. Reorientations are shown to take place among both symmetry-related and symmetry-independent sites, 16 positions in all. Because of the prochiral nature of the molecules, both guests show 2H NMR line shapes with large asymmetry parameters, rather unusual for guest molecules in the sI hydrate large cage. The results also show that the dipolar axis of the TMO molecule lies close to the 4 bar axis of the cage on average, whereas for EO, this is not the case. For TMO, progressive alignment of the polar axis with decrease of temperature then allows the dipoles to interact more strongly until dipole reversal is quenched at the ordering transition. The lack of ordering of EO is consistent with the much weaker alignment of the molecular dipoles along the 4 bar axis. With the new complementary information on the structure and dynamics from crystallography and NMR, it is possible to understand why the large cage guests order in the large cage of sI hydrate for TMO hydrate but not for EO hydrate.     

Thermal expansivity of tetrahydrofuran clathrate hydrate with diatomic guest molecules

The guest dynamics and thermal behavior occurring in the cages of clathrate hydrates appear to be too complex to be clearly understood through various structural and spectroscopic approaches, even for the well-known structures of sI, sII, and sH. Neutron diffraction studies have recently been carried out to clarify the special role of guests in expanding the host water lattices and have contributed to revealing the influence factors on thermal expansivity. Through this letter we attempt to address three noteworthy features occurring in guest inclusion: (1) the effect of guest dimension on host water lattice expansion; (2) the effect of thermal history on host water lattice expansion; and (3) the effect of coherent/incoherent scattering cross sections on guest thermal patterns. The diatomic guests of H 2, D 2, N 2, and O 2 have been selected for study, and their size and mass dependence on the degree of lattice expansion have been examined, and four sII clathrate hydrates with tetrahydrofuran (THF) have been synthesized in order to determine their neutron powder diffraction patterns. After thermal cycling, the THF + H 2 clathrate hydrate is observed to exhibit an irreversible plastic deformation-like pattern, implying that the expanded lattices fail to recover the original state by contraction. The host-water cage dimension after degassing the guest molecules remains as it was expanded, and thus host-guest as well as guest-guest interactions will be altered if guest uptake reoccurs.     

Free energies of carbon dioxide sequestration and methane recovery in clathrate hydrates

Classical molecular dynamics simulations are used to compare the stability of methane, carbon dioxide, nitrogen, and mixed CO(2)N(2) structure I (sI) clathrates under deep ocean seafloor temperature and pressure conditions (275 K and 30 MPa) which were considered suitable for CO(2) sequestration. Substitution of methane guests in both the small and large sI cages by CO(2) and N(2) fluids are considered separately to determine the separate contributions to the overall free energy of substitution. The structure I clathrate with methane in small cages and carbon dioxide in large cages is determined to be the most stable. Substitutions of methane in the small cages with CO(2) and N(2) have positive free energies. Substitution of methane with CO(2) in the large cages has a large negative free energy and substitution of the methane in the large cages with N(2) has a small positive free energy. The calculations show that under conditions where storage is being considered, carbon dioxide spontaneously replaces methane from sI clathrates, causing the release of methane. This process must be considered if there are methane clathrates present where CO(2) sequestration is to be attempted. The calculations also indicate that N(2) does not directly compete with CO(2) during methane substitution or clathrate formation and therefore can be used as a carrier gas or may be present as an impurity. Simulations further reveal that the replacement of methane with CO(2) in structure II (sII) cages also has a negative free energy. In cases where sII CO(2) clathrates are formed, only single occupancy of the large cages will be observed.