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.     

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.     

Communication: Single crystal x-ray diffraction observation of hydrogen bonding between 1-propanol and water in a structure II clathrate hydrate

Single crystal x-ray crystallography is used to detect guest-host hydrogen bonding in structure II (sII) binary clathrate hydrate of 1-propanol and methane. X-ray structural analysis shows that the 1-propanol oxygen atom is at a distance of 2.749 and 2.788 ? from the closest clathrate hydrate water oxygen atoms from a hexagonal face of the large sII cage. The 1-propanol hydroxyl hydrogen atom is disordered and at distances of 1.956 and 2.035 ? from the closest cage water oxygen atoms. These distances are compatible with guest-water hydrogen bonding. The C-C-C-O torsional angle in 1-propanol in the cage is 91.47° which corresponds to a staggered conformation for the guest. Molecular dynamics studies of this system demonstrated guest-water hydrogen bonding in this hydrate. The molecular dynamics simulations predict most probable distances for the 1-propanol-water oxygen atoms to be 2.725 ?, and the average C-C-C-O torsional angle to be ~59° consistent with a gauche conformation. The individual cage distortions resulting from guest-host hydrogen bonding from the simulations are rather large, but due to the random nature of the hydrogen bonding of the guest with the 24 water molecules making up the hexagonal faces of the large sII cages, these distortions are not observed in the x-ray structure.     

Nucleation of the CO2 hydrate from three-phase contact lines

Using molecular dynamics simulations on the microsecond time scale, we investigate the nucleation and growth mechanisms of CO(2) hydrates in a water/CO(2)/silica three-phase system. Our simulation results indicate that the CO(2) hydrate nucleates near the three-phase contact line rather than at the two-phase interfaces and then grows along the contact line to form an amorphous crystal. In the nucleation stage, the hydroxylated silica surface can be understand as a stabilizer to prolong the lifetime of adsorbed hydrate cages that interact with the silica surface by hydrogen bonding, and the adsorbed cages behave as the nucleation sites for the formation of an amorphous CO(2) hydrate. After nucleation, the nucleus grows along the three-phase contact line and prefers to develop toward the CO(2) phase as a result of the hydrophilic nature of the modified solid surface and the easy availability of CO(2) molecules. During the growth process, the population of sI cages in the formed amorphous crystal is found to increase much faster than that of sII cages, being in agreement with the fact that only the sI hydrate can be formed in nature for CO(2) molecules.     

Determination of NMR Lineshape Anisotropy of Guest Molecules within Inclusion Complexes from Molecular Dynamics Simulations

Nonspherical cages in inclusion compounds can result in non‐uniform motion of guest species in these cages and anisotropic lineshapes in NMR spectra of the guest. Herein, we develop a methodology to calculate lineshape anisotropy of guest species in cages based on molecular dynamics simulations of the inclusion compound. The methodology is valid for guest atoms with spin 1/2 nuclei and does not depend on the temperature and type of inclusion compound or guest species studied. As an example, the nonspherical shape of the structure I (sI) clathrate hydrate large cages leads to preferential alignment of linear CO₂ molecules in directions parallel to the two hexagonal faces of the cages. The angular distribution of the CO₂ guests in terms of a polar angle θ and azimuth angle ? and small amplitude vibrational motions in the large cage are characterized by molecular dynamics simulations at different temperatures in the stability range of the CO₂ sI clathrate. The experimental ¹³C NMR lineshapes of CO₂ guests in the large cages show a reversal of the skew between the low temperature (77 K) and the high temperature (238 K) limits of the stability of the clathrate. We determine the angular distributions of the guests in the cages by classical MD simulations of the sI clathrate and calculate the ¹³C NMR lineshapes over a range of temperatures. Good agreement between experimental lineshapes and calculated lineshapes is obtained. No assumptions regarding the nature of the guest motions in the cages are required.     

Molecular dynamics study of structure H clathrate hydrates of methane and large guest molecules

Methane storage in structure H (sH) clathrate hydrates is attractive due to the relatively higher stability of sH as compared to structure I methane hydrate. The additional stability is gained without losing a significant amount of gas storage density as happens in the case of structure II (sII) methane clathrate. Our previous work has showed that the selection of a specific large molecule guest substance (LMGS) as the sH hydrate former is critical in obtaining the optimum conditions for crystallization kinetics, hydrate stability, and methane content. In this work, molecular dynamics simulations are employed to provide further insight regarding the dependence of methane occupancy on the type of the LMGS and pressure. Moreover, the preference of methane molecules to occupy the small (5(12)) or medium (4(3)5(6)6(3)) cages and the minimum cage occupancy required to maintain sH clathrate mechanical stability are examined. We found that thermodynamically, methane occupancy depends on pressure but not on the nature of the LMGS. The experimentally observed differences in methane occupancy for different LMGS may be attributed to the differences in crystallization kinetics and/or the nonequilibrium conditions during the formation. It is also predicted that full methane occupancies in both small and medium clathrate cages are preferred at higher pressures but these cages are not fully occupied at lower pressures. It was found that both small and medium cages are equally favored for occupancy by methane guests and at the same methane content, the system suffers a free energy penalty if only one type of cage is occupied. The simulations confirm the instability of the hydrate when the small and medium cages are empty. Hydrate decomposition was observed when less than 40% of the small and medium cages are occupied.     

Molecular Dynamics Simulation of Structure II Clathrate Hydrates of Xenon and Large Hydrocarbon Guest Molecules

Molecular dynamics (MD) simulations of structure II clathrate hydrates are performed under canonical (NVT) and isobaric–isothermal (NPT) ensembles. The guest molecule as a small help gas is xenon and gases such as cyclopropane, isobutane and propane are used as large hydrocarbon guest molecule (LHGM). The dynamics of structure II clathrate hydrate is considered in two cases: empty small cages and small cages containing xenon. Therefore, the MD results for structure II clathrate hydrates of LHGM and LHGM + Xe are obtained to clarify the effects of guest molecules on host lattice structure. To understand the characteristic configurations of structure II clathrate hydrate the radial distribution functions (RDFs) are calculated for the studied hydrate system. The obtained results indicate the significance of interactions of the guest molecules on stabilizing the hydrate host lattice and these results is consistent with most previous experimental and theoretical investigations.     

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.     

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.     

Effect of Guest–Host Hydrogen Bonding on the Structures and Properties of Clathrate Hydrates

To provide improved understanding of guest–host interactions in clathrate hydrates, we present some correlations between guest chemical structures and observations on the corresponding hydrate properties. From these correlations it is clear that directional interactions such as hydrogen bonding between guest and host are likely, although these have been ignored to greater or lesser degrees because there has been no direct structural evidence for such interactions. For the first time, single‐crystal X‐ray crystallography has been used to detect guest–host hydrogen bonding in structure II (sII) and structure H (sH) clathrate hydrates. The clathrates studied are the tert‐butylamine (tBA) sII clathrate with H₂S/Xe help gases and the pinacolone + H₂S binary sH clathrate. X‐ray structural analysis shows that the tBA nitrogen atom lies at a distance of 2.64 Å from the closest clathrate hydrate water oxygen atom, whereas the pinacolone oxygen atom is determined to lie at a distance of 2.96 Å from the closest water oxygen atom. These distances are compatible with guest–water hydrogen bonding. Results of molecular dynamics simulations on these systems are consistent with the X‐ray crystallographic observations. The tBA guest shows long‐lived guest–host hydrogen bonding with the nitrogen atom tethered to a water HO group that rotates towards the cage center to face the guest nitrogen atom. Pinacolone forms thermally activated guest–host hydrogen bonds with the lattice water molecules; these have been studied for temperatures in the range of 100–250 K. Guest–host hydrogen bonding leads to the formation of Bjerrum L‐defects in the clathrate water lattice between two adjacent water molecules, and these are implicated in the stabilities of the hydrate lattices, the water dynamics, and the dielectric properties. The reported stable hydrogen‐bonded guest–host structures also tend to blur the longstanding distinction between true clathrates and semiclathrates.     

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.     

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.     

Intermolecular hydrogen transfer between guest species in small and large cages of methane + propane mixed gas hydrates

To investigate the molecular interaction between guest species inside of the small and large cages of methane + propane mixed gas hydrates, thermal stabilities of the methyl radical (possibly induced in small cages) and the normal propyl and isopropyl radicals (induced in large cages) were investigated by means of electron spin resonance measurements. The increase of the total amount of the normal propyl and isopropyl radicals reveals that the methyl radical in the small cage withdraws one hydrogen atom from the propane molecule enclathrated in the adjacent large cage of the structure-II hydrate. A guest species in a hydrate cage has the ability to interact closely with the other one in the adjacent cages. The clathrate hydrate may be utilized as a possible nanoscale reaction field.     

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.     

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.     

Heterogeneous crystal growth of methane hydrate on its sII [001] crystallographic face

This paper presents a systematic molecular simulation study of the heterogeneous crystal growth of methane hydrate sII from supersaturated aqueous methane solutions. The growth of sII hydrate on the [001] crystallographic face is achieved through utilization of a recently proposed methodology, and rates of crystal growth of 1 A/ns were sustained for the molecular models and specific conditions employed in this work. Characteristics of the crystals grown as well as properties and structure of the interface are examined. Water cages with a 5(12)6(3) arrangement, which are improper to both sI and sII structures, are identified during the heterogeneous growth of sII methane hydrate. We show that the growth of a [001] face of sII hydrate can produce an sI crystalline structure, confirming that cross-nucleation of methane hydrate structures is possible. Defects consisting of two methane molecules trapped in large 5(12)6(4) cages and water molecules trapped in small and large cages are observed, where in one instance we have found a large 5(12)6(4) cage containing three water molecules.     

Micro-Raman investigations of mixed gas hydrates

We report laser Raman spectroscopic measurements on mixed hydrates (clathrates), with guest molecules tetrahydrofuran (THF) and methane (CH₄), at ambient pressure and at temperatures from 175 to 280 K. Gas hydrates were synthesized with different concentrations of THF ranging from 5.88 to 1.46 mol%. In all cases THF molecules occupied the large cages of sII hydrate. The present studies demonstrate formation of sII clathrates with CH₄ molecules occupying unfilled cages for concentrations of THF ranging from 5.88 to 2.95 mol%. The Raman spectral signature of hydrates with 1.46 mol% THF are distinctly different; hydrate growth was non-uniform and structural transformation occurred from sII to sI prior to clathrate melting.     

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.     

Molecular dynamics simulations for the growth of CH_4-CO_2 mixed hydrate

Molecular dynamics simulations are performed to study the growth mechanism of CH4-CO2 mixed hydrate in xCO2= 75%, xCO2= 50%, and xCO2= 25% systems at T = 250 K, 255 K and 260 K, respectively. Our simulation results show that the growth rate of CH4-CO2 mixed hydrate increases as the CO2 concentration in the initial solution phase increases and the temperature decreases. Via hydrate formation, the composition of CO2 in hydrate phase is higher than that in initial solution phase and the encaging capacity of CO2 in hydrates increases with the decrease in temperature. By analysis of the cage occupancy ratio of CH4 molecules and CO2 molecules in large cages to small cages, we find that CO2 molecules are preferably encaged into the large cages of the hydrate crystal as compared with CH4 molecules. Interestingly, CH4 molecules and CO2 molecules frequently replace with each other in some particular cage sites adjacent to hydrate/solution interface during the crystal growth process. These two species of guest molecules eventually act to stabilize the newly formed hydrates, with CO2 molecules occupying large cages and CH4 molecules occupying small cages in hydrate.     

Molecular dynamics simulations for the growth of CH4-CO2 mixed hydrate

Molecular dynamics simulations are performed to study the growth mechanism of CH4-CO2 mixed hydrate in xco2 = 75%, xco2 = 50%, and zco2 = 25% systems at T = 250 K, 255 K and 260 K, respectively. Our simulation results show that the growth rate of CH4-CO2 mixed hydrate increases as the CO2 concentration in the initial solution phase increases and the temperature decreases. Via hydrate formation, the composition of CO2 in hydrate phase is higher than that in initial solution phase and the encaging capacity of CO2 in hydrates increases with the decrease in temperature. By analysis of the cage occupancy ratio of CH4 molecules and CO2 molecules in large cages to small cages, we find that CO2 molecules are preferably encaged into the large cages of the hydrate crystal as compared with CH4 molecules. Interestingly, CH4 molecules and CO2 molecules frequently replace with each other in some particular cage sites adjacent to hydrate/solution interface during the crystal growth process. These two species of guest molecules eventually act to stabilize the newly formed hydrates, with CO2 molecules occupying large cages and CH4 molecules occupying small cages in hydrate.