A molecular dynamics study of ethanol-water hydrogen bonding in binary structure I clathrate hydrate with CO2

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 CO(2) 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.     

Some structural and thermodynamic studies of clathrate hydrates

X-ray and neutron diffraction studies show argon and krypton to preferentially form clathrate hydrates of structure II, rather than structure I as previously assumed; methane and hydrogen sulphide do form structure I. Re-examination of solid-solution thermodynamic theory shows that structure II is basically the more stable; structure I is generally formed only when the guest molecule is in the size range that favours occupancy of the 14-hedral over the 12-hedral cages. For molecules too large to enter the 12-hedra the relative stability of structure II is greatest at 0°C, in agreement with the observed sequence of change of stability of cyclopropane hydrate: I to II at –16° and II to I at 1.5°. Carbon dioxide hydrate is observed to decompose on prolonged standing at 105K in accord with the low-temperature instability predicted by Miller.     

Multiple H2 occupancy of cages of clathrate hydrate under mild conditions

Experiments were carried out by reacting H(2) gas with N(2) hydrate at a temperature of 243 K and a pressure of 15 MPa. The characterizations of the reaction products indicated that multiple H(2) molecules can be loaded into both large and small cages of structure II clathrate hydrates. The realization of multiple H(2) occupancy of hydrate cages under moderate conditions not only brings new insights into hydrogen clathrates but also refreshes the perspective of clathrate hydrates as hydrogen storage media.     

Kinetics and stability of CH4-CO2 mixed gas hydrates during formation and long-term storage.

The formation of CH4-CO2 mixed gas hydrates was observed by measuring the change of vapor-phase composition using gas chromatography and Raman spectroscopy. Preferential consumption of carbon dioxide molecules was found during hydrate formation, which agreed well with thermodynamic calculations. Both Raman spectroscopic analysis and the thermodynamic calculation indicated that the kinetics of this mixed gas hydrate system was controlled by the competition of both molecules to be enclathrated into the hydrate cages. However, the methane molecules were preferentially crystallized in the early stages of hydrate formation when the initial methane concentration was much less than that of carbon dioxide. According to the Roman spectra, pure methane hydrates first formed under this condition. This unique phenomenon suggested that methane molecules play important roles in the hydrate formation process. These mixed gas hydrates were stored at atmospheric pressure and 190 K for over two months to examine the stability of the encaged gases. During storage, CO2 was preferentially released. According to our thermodynamic analysis, this CO2 release was due to the instability of CO2 in the hydrate structure under the storage conditions.     

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.     

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.     

The conversion process of hydrocarbon hydrates into CO2 hydrates and vice versa: thermodynamic considerations

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.     

13C NMR studies of hydrocarbon guests in synthetic structure H gas hydrates: experiment and computation

(13)C NMR chemical shifts were measured for pure (neat) liquids and synthetic binary hydrate samples (with methane help gas) for 2-methylbutane, 2,2-dimethylbutane, 2,3-dimethylbutane, 2-methylpentane, 3-methylpentane, methylcyclopentane, and methylcyclohexane and ternary structure H (sH) clathrate hydrates of n-pentane and n-hexane with methane and 2,2-dimethylbutane, all of which form sH hydrates. The (13)C chemical shifts of the guest atoms in the hydrate are different from those in the free form, with some carbon atoms shifting specifically upfield. Such changes can be attributed to conformational changes upon fitting the large guest molecules in hydrate cages and/or interactions between the guests and the water molecules of the hydrate cages. In addition, powder X-ray diffraction measurements revealed that for the hexagonal unit cell, the lattice parameter along the a-axis changes with guest hydrate former molecule size and shape (in the range of 0.1 ?) but a much smaller change in the c-axis (in the range of 0.01 ?) is observed. The (13)C NMR chemical shifts for the pure hydrocarbons and all conformers were calculated using the gauge invariant atomic orbital method at the MP2/6-311+G(2d,p) level of theory to quantify the variation of the chemical shifts with the dihedral angles of the guest molecules. Calculated and measured chemical shifts are compared to determine the relative contribution of changes in the conformation and guest-water interactions to the change in chemical shift of the guest upon clathrate hydrate formation. Understanding factors that affect experimental chemical shifts for the enclathrated hydrocarbons will help in assigning spectra for complex hydrates recovered from natural sites.     

Ordering and Clathrate Hydrate Formation in Co‐deposits of Xenon and Water at Low Temperatures

Local ordering in co‐deposits of water and xenon atoms produced at low temperatures can be followed uniquely by ¹²⁹Xe NMR spectroscopy. In water‐rich samples deposited at 10 K and observed at 77 K, xenon NMR results show that there is a wide distribution of arrangements of water molecules around xenon atoms. This starts to order into the definite coordination for the structure I, large and small cages, when samples are annealed at ～140 K, although the process is not complete until a temperature of 180 K is reached, as shown by powder Xray diffraction. There is evidence that Xe ? 20 H₂O clusters are prominent in the early stages of crystallization. In xenon‐rich deposits at 77 K there is evidence of xenon atoms trapped in Xe ? 20 H₂O clusters, which are similar to the small hydration shells or cages observed in hydrate structures, but not in the larger water clusters consisting of 24 or 28 water molecules. These observations are in agreement with results obtained on the formation of Xe hydrate on the surface of ice surfaces by using hyperpolarized Xe NMR spectroscopy. The results indicate that for the various different modes of hydrate formation, both from Xe reacting with amorphous water and with crystalline ice surfaces, versions of the small cage are important structures in the early stages of crystallization.     

Mechanisms for thermal conduction in hydrogen hydrate

Extensive equilibrium molecular dynamics simulations have been performed to investigate thermal conduction mechanisms via the Green-Kubo approach for (type II) hydrogen hydrate, at 0.05 kbar and between 30 and 250 K, for both lightly filled H(2) hydrates (1s4l) and for more densely filled H(2) systems (2s4l), in which four H(2) molecules are present in the large cavities, with respective single- and double-occupation of the small cages. The TIP4P water model was used in conjunction with a fully atomistic hydrogen potential along with long-range Ewald electrostatics. It was found that substantially less damping in guest-host energy transfer is present in hydrogen hydrate as is observed in common type I clathrates (e.g., methane hydrate), but more akin in to previous results for type II and H methane hydrate polymorphs. This gives rise to larger thermal conductivities relative to common type I hydrates, and also larger than type II and H methane hydrate polymorphs, and a more crystal-like temperature dependence of the thermal conductivity.     

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.     

Phase equilibrium measurements and crystallographic analyses on structure-H type gas hydrate formed from the CH4-CO2-neohexane-water system

Phase equilibrium conditions and the crystallographic properties of structure-H type gas hydrates containing various amounts of methane (CH4), carbon dioxide (CO2), neohexane (2,2-dimethylbutane; NH), and liquid water were investigated. When the CH4 concentration was as high as approximately 70%, the phase equilibrium pressure of the structure-H hydrate, which included NH, was about 1 MPa lower at a given temperature than that of the structure-I hydrate with the same composition (except for a lack of NH). However, as the CO2 concentration increased, the pressure difference between the structures became smaller and, at CO2 concentrations below 50%, the phase equilibrium line for the structure-H hydrate crossed that for the structure I. This cross point occurred at a lower temperature at higher CO2 concentration. Extrapolating this relation between the cross point and the CO2 concentration to 100% CO2 suggests that the cross-point temperature would be far below 273.2 K. It is then difficult to form structure-H hydrates in the CO2-NH-liquid water system. To examine the structure, guest composition, and formation process of structure-H hydrates at various CH4-CO2 compositions, we used the methods of Raman spectroscopy, X-ray diffraction, and gas chromatography. Raman spectroscopic analyses indicated that the CH4 molecules were found to occupy both 5(12) and 4(3)5(6)6(3) cages, but they preferably occupied only the 5(12) cages. On the other hand, the CO2 molecules appeared to be trapped only in the 4(3)5(6)6(3) cages. Thus, the CO2 molecules aided the formation of structure-H hydrates even though they reduced the stability of that structure. This encaged condition of guest molecules was also compared with the theoretical calculations. In the batch-type reactor, this process may cause the fractionation of the remaining vapor composition in the opposite sense as that for CH4-CO2 hydrate (structure-I), and thus may result in an alternating formation of structure-H hydrates and structure-I in the same batch-type reactor.     

Hydrogen encapsulation in a silicon clathrate type I structure: Na5.5(H2)2.15Si46: synthesis and characterization

A hydrogen-encapsulated inorganic clathrate, which is stable at ambient temperature and pressure, has been prepared in high yield. Na5.5(H2)2.15Si46 is a sodium-deficient, hydrogen-encapsulated, type I silicon clathrate. It was prepared by the reaction between NaSi and NH4Br under dynamic vacuum at 300 degrees C. The Rietveld refinement of the powder X-ray diffraction data is consistent with the clathrate type I structure. The type I clathrate structure has two types of cages where the guest species, in this case Na and H2, can reside: a large cage composed of 24 Si, in which the guest resides in the 6d crystallographic position, and a smaller one composed of 20 Si, in which the guest occupies the 2a position. Solid-state 23Na, 1H, and 29Si MAS NMR confirmed the presence of both sodium and hydrogen in the clathrate cages. 23Na NMR shows that sodium completely fills the small cage and is deficient in the larger cage. The 1H NMR spectrum shows a pattern consistent with mobile hydrogen in the large cage. 29Si NMR spectrum is consistent with phase pure type I clathrate framework. Elemental analysis is consistent with the stoichiometry Na5.5(H2.15)2Si46. The sodium occupancy was also examined using spherical aberration (Cs) corrected scanning transmission electron microscopy (STEM). The high-angle annular dark-field (HAADF) STEM experimental and simulated images indicated that the Na occupancy of the large cage, 6d sites, is less than 2/3, consistent with the NMR and elemental analysis.     

用分子动力学模拟水合物储氢

用分子动力学(MD)模拟方法系统研究了结构Ⅰ型(SⅠ)和结构H型(SH)氢气水合物中氢气的占据情况并确定了氢气水合物的稳定结构: SⅠ水合物氢气分子数小胞中为2, 大胞中为3; SH水合物氢气分子数小胞中为2, 中胞中为2, 大胞中为11. 分析了稳定情况下水合物各胞腔内氢气分子之间的径向分布函数(RDF), 得出了氢气分子在各胞腔内的稳定位置. 由稳定位置得到了稳定结构下氢气水合物的储氢质量分数: SⅠ为5.085%, SH为6.467%. 与实验对比得出结论: SH水合物稳定结构下的储氢能力最强.     

Effect of small cage guests on hydrogen bonding of tetrahydrofuran in binary structure II clathrate hydrates

Molecular dynamics simulations of the pure structure II tetrahydrofuran clathrate hydrate and binary structure II tetrahydrofuran clathrate hydrate with CO(2), CH(4), H(2)S, and Xe small cage guests are performed to study the effect of the shape, size, and intermolecular forces of the small cages guests on the structure and dynamics of the hydrate. The simulations show that the number and nature of the guest in the small cage affects the probability of hydrogen bonding of the tetrahydrofuran guest with the large cage water molecules. The effect on hydrogen bonding of tetrahydrofuran occurs despite the fact that the guests in the small cage do not themselves form hydrogen bonds with water. These results indicate that nearest neighbour guest-guest interactions (mediated through the water lattice framework) can affect the clathrate structure and stability. The implications of these subtle small guest effects on clathrate hydrate stability are discussed.     

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.     

NMR shielding constants for hydrogen guest molecules in structure II clathrates

Proton NMR shielding constants and chemical shifts for hydrogen guests in small and large cages of structure II clathrates are calculated using density-functional theory and the gauge-invariant atomic-orbital method. Shielding constants are calculated at the B3LYP level with the 6-311++G(d,p) basis set. The calculated chemical shifts are corrected with a linear regression to reproduce the experimental chemical shifts of a set of standard molecules. The calculated chemical shifts of single hydrogen molecules in the small and large structure II cages are 4.94 and 4.84 ppm, respectively, which show that within the error range of the method the H2 guest molecules in the small and large cages cannot be distinguished. Chemical shifts are also calculated for double occupancy of the hydrogen guests in small cages, and double, triple, and quadruple occupancy in large cages. Multiple occupancy changes the chemical shift of the hydrogen guests by approximately 0.2 ppm. The relative effects of other guest molecules and the cage on the chemical shift are studied for the cages with multiple occupancies.     

Investigation of hydrate formation in the system H2-CH4-H2O at a pressure up to 250 MPa

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.     

Molecular-dynamics study of structure II hydrogen clathrates

Molecular-dynamics simulations are used to study the stability of structure II hydrogen clathrates with different H2 guest occupancies. Simulations are done at pressures of 2.5 kbars and 1.013 bars and for temperatures ranging from 100 to 250 K. For a structure II unit cell with 136 water molecules, H2 guest molecule occupancies of 0-64 are studied with uniform occupancies among each type of cage. The simulations show that at 100 K and 2.5 kbars, the most stable configurations have single occupancy in the small cages and quadruple occupancy in the large cages. The optimum occupancy for the large cages decreases as the temperature is raised. Double occupancy in the small cages increases the energy of the structures and causes tetragonal distortion in the unit cell. The spatial distribution of the hydrogen guest molecules in the cages is determined by studying the guest-water and guest-guest radial distribution functions at various temperatures.