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.     

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.     

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.     

Formation of ice nanotube with hydrophobic guests inside carbon nanotube

A composite ice nanotube inside a carbon nanotube has been explored by molecular-dynamics and grand canonical Monte Carlo simulations. It is made from an octagonal ice nanotube whose hollow space contains hydrophobic guest molecules such as neon, argon, and methane. It is shown that the attractive interaction of the guest molecules stabilizes the ice nanotube. The guest occupancy of the hollow space is calculated by the same method as applied to clathrate hydrates.     

On the thermodynamic stability of clathrate hydrates IV: double occupancy of cages

We have extended the van der Waals and Platteeuw theory to treat multiple occupancy of a single cage of clathrate hydrates, which has not been taken into account in the original theory but has been experimentally confirmed as a real entity. We propose a simple way to calculate the free energy of multiple cage occupancy and apply it to argon clathrate structure II in which a larger cage can be occupied by two argon atoms. The chemical potential of argon is calculated treating it as an imperfect gas, which is crucial to predict accurate pressure dependence of double occupancy expected at high pressure. It is found that double occupancy dominates over single occupancy when the guest pressure in equilibrium with the clathrate hydrate exceeds 270 MPa.     

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.     

Phase equilibrium measurements and the tuning behavior of new sII clathrate hydrates

We suggest two types of new amine-type sII formers: pyrrolidine and piperidine. These guest compounds fail to form clathrate hydrate structures with host water, but instead have to combine with light gaseous guest molecules (methane) for enclathration. First, two binary clathrate hydrates of (pyrrolidine + methane) and (piperidine + methane) were synthesized at various amine concentrations. ¹³C NMR and Raman analysis were done to identify the clathrate hydrate structure and guest distribution over sII-S and sII-L cages. XRD was also used to find the exact structure and corresponding cell parameters. At a dilute pyrrolidine concentration of less than 5.56 mol%, the tuning phenomenon is observed such that methane molecules surprisingly occupy sII-L cages. At the critical guest concentration of about 0.1 mol%, the cage occupancy ratio reaches the maximum of approximately 0.5. At very dilute guest concentration below 0.1 mol%, the methane molecules fail to occupy large cages on account of their rarefied distribution in the network. Direct-release experiments were performed to determine the actual guest compositions in the clathrate hydrate phases. Finally, we measured the clathrate hydrate phase equilibria of (pyrrolidine + methane) and (piperidine + methane).     

Calorimetric study on pure and KOH-doped argon clathrate hydrates

Pure and KOH (x=1.3×10^?3)-doped argon clathrate hydrates were synthesized in an adiabatic high-pressure calorimetric cell from one mole of water and 200 MPa of Ar gas. The heat capacities of the hydrates were measured from 12 to 130 K. No anomaly was found in the pure sample but a glass transition considered to be related to a proton-configurational mode of the host hydrogen-bonded lattice was observed for the first time at 55 K in the doped sample. Comparison with the results on pure and KOH-doped tetrahydrofuran clathrate hydrates indicated that the thermodynamic properties of a hydrogen-bonded system depend on the kind of guest molecule. The heat capacity of argon in the hydrate cages was adequately analyzed with the one-dimensional Pöschl-Teller potential as used in the Ar-β-quinol clathrate and the addivity of heat capacities of the guest and host was shown to be valid in the temperature range 12–130 K.     

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.     

Double clathrate hydrates of tetrabutylammonium fluoride + helium, neon, hydrogen and argon at high pressures

Decomposition curves of double ionic clathrate hydrates of tetrabutylammonium fluoride with helium, neon, hydrogen and argon were studied at pressures up to 800 MPa. Formation of double hydrates with helium, neon and hydrogen does not lead to any significant increase of the temperatures of decomposition of these hydrates; at high temperatures the hydrates may decompose even at lower temperatures than the hydrate of pure tetraalkylammonium salt does. Decomposition temperatures of double hydrates with argon in all cases were 4–8 °C higher in comparison with the decomposition temperature of ionic clathrate hydrates of tetrabutylammonium fluoride. We suppose that this behavior is caused by simultaneous effect of three factors on hydrate decomposition temperature: (1) partial filling of the small cavities in the framework of the hydrate with water molecules, (2) weakness of the van der Waals interactions between the gas molecules and the host water molecules, and (3) dissolution of helium, hydrogen and neon in the solution of tetrabutylammonium salt causing a decrease of melting temperatures of the hydrates formed from these solutions.     

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.     

常见客体分子对笼型水合物晶格常数的影响

Natural gas hydrates are considered as ideal alternative energy resources for the future, and the relevant basic and applied research has become more attractive in recent years. The influence of guest molecules on the hydrate crystal lattice parameters is of great significances to the understanding of hydrate structural characteristics, hydrate formation/decomposition mechanisms, and phase stability behaviors. In this study, we test a series of artificial hydrate samples containing different guest molecules (e.g. methane, ethane, propane, iso-butane, carbon dioxide, tetrahydrofuran, methane + 2, 2-dimethylbutane, and methane + methyl cyclohexane) by a low-temperature powder X-ray diffraction (PXRD). Results show that PXRD effectively elucidates structural characteristics of the natural gas hydrate samples, including crystal lattice parameters and structure types. The relationships between guest molecule sizes and crystal lattice parameters reveal that different guest molecules have different controlling behaviors on the hydrate types and crystal lattice constants. First, a positive correlation between the lattice constants and the van der Waals diameters of homologous hydrocarbon gases was observed in the single-guest-component hydrates. Small hydrocarbon homologous gases, such as methane and ethane, tended to form sI hydrates, whereas relatively larger molecules, such as propane and iso-butane, generated sⅡ hydrates. The hydrate crystal lattice constants increased with increasing guest molecule size. The types of hydrates composed of oxygen-containing guest molecules (such as CO₂ and THF) were also controlled by the van der Waals diameters. However, no positive correlation between the lattice constants and the van der Waals diameters of guest molecules in hydrocarbon hydrates was observed for CO₂ hydrate and THF hydrate, probably due to the special interactions between the guest oxygen atoms and hydrate "cages". Furthermore, the influences of the macromolecules and auxiliary small molecules on the lengths of the different crystal axes of the sH hydrates showed inverse trends. Compared to the methane + 2, 2-dimethylbutane hydrate sample, the length of the a-axis direction of the methane + methyl cyclohexane hydrate sample was slightly smaller, whereas the length of the c-axis direction was slightly longer. The crystal a-axis length of the sH hydrate sample formed with nitrogen molecules was slightly longer, whereas the c-axis was shorter than that of the methane + 2, 2-dimethylbutane hydrate sample at the same temperature.     

Formation and spectra of clathrate hydrates of methanol and methanol-ether mixtures

Infrared spectra of mixed clathrate hydrates, with either ethylene oxide (EO) or tetrahydrofuran (THF) and methanol molecules as the guest species, have been obtained from thin films prepared by vapor deposition of D₂O mixtures in the 115–130 K range. Although methanol acts as a suppressant to the direct vapor deposition of a type I clathrate with EO, nearly complete conversion of 115 K amorphous codeposits, to the crystalline mixed clathrate, occurs upon warming near 150 K. By contrast, the type II clathrate of THF shows an increased crystalline quality when methanol is included in the vapor deposits of the mixed clathrate hydrate at 130 K. The observation of the O---D stretch-mode band of weakly bonded CD₃OD near 2575 cm⁻¹ is part of the evidence that the methanol molecules are encaged. However, as shown theoretically by Tanaka, the clathrate hydrates of methanol, even when mixed with an ether help gas, are not stable structures but form at low temperatures because of kinetic factors, only to decompose in the 140–160 K range. Attempts to prepare a simple type I or type II clathrate hydrate of methanol have produced mixed results. Limited amounts of clathrate hydrate form during deposition but annealing does not result in complete conversion to crystalline clathrates, particularly for host : guest ratios of 17 : 1.     

Controlling nonclassical content of clathrate hydrates through the choice of molecular guests and temperature

Low-temperature, low-pressure studies of clathrate hydrates (CHs) have revealed that small ether and other proton-acceptor guests greatly enhance rates of clathrate hydrate nucleation and growth; rapid formation and transformations are enabled at temperatures as low as 110 K, and cool moist vapors containing small ether molecules convert to mixed-gas CHs on a subsecond time scale. More recently, FTIR spectroscopic studies of the tetrahydrofuran (THF)-HCN double clathrate hydrate revealed a sizable frequency shift accompanied by a four-fold intensification of the C-N stretch-mode absorption of the small cage HCN, behavior that is enhanced by cooling and which correlates precisely with similar significant changes of the ether C-O/C-C stretch modes. These temperature-dependent correlated changes in the infrared spectra have been attributed to equilibrated extensive hydrogen bonding of neighboring large- and small-cage guest molecules with water molecules of the intervening wall. An ether guest functions as a proton acceptor, particularly so when complemented by the action of a proton-donor (HCN)/electron-acceptor (SO(2)) small-cage guest. Because guest molecules of the classic clathrate hydrates do not participate in hydrogen bonds with the host water, this H-bonding of guests has been labeled "nonclassical". The present study has been enriched by comparing observed FTIR spectra with high-level molecular orbital computational results for guests and hydrogen-bonded guest-water dimers. Vibrational frequency shifts, from heterodimerization of ethers and water, correlate well with the corresponding observed classical to nonclassical shifts. The new spectroscopic data reveal that the nonclassical structures can contribute at observable levels to CH infrared spectra for a remarkable range of temperatures and choice of guest molecules. By the choice of guest molecules, it is now possible to select the abundance levels of nonclassical configurations, ranging from ～0 to 100%, for a given temperature. This ability is expected to hasten understanding of the role of guest-induced nonclassical structures in the acceleration or inhibition of the rates of CH formation and transformation.     

Structure transition and tuning pattern in the double (tetramethylammonium hydroxide + gaseous guests) clathrate hydrates

In this study, we present an extraordinary structural transition accompanying the occurrence of more than two coexisting clathrate hydrate phases in the double (CH4 + tetramethylammonium hydroxide (Me(4)NOH)) and (H2 + Me(4)NOH) ionic clathrate hydrates using solid-state NMR spectroscopy (high-powered decoupling and CP/MAS) and powder X-ray diffraction. It was confirmed that structure-I (sI) and structure-II (sII) hydrates coexist as the water concentration increases. In the Me(4)NOH-depleted region, the unique tuning phenomenon was first observed at a chemical shift of -8.4 ppm where relatively small gaseous CH4 molecules partly occupy the sII large cages (sII-L), pulling out large cationic Me(4)N+ that is considered to be strongly bound with the surrounding host lattices. Moreover, we note that, while pure Me(4)NOH.16H(2)O clathrate hydrates melted at 249 K under atmospheric pressure conditions, the double (CH4 + Me(4)NOH) clathrate hydrate maintained a solid state up to approximately 283 K under 120 bar of CH4 with a conductivity of 0.065 S cm(-1), suggesting its potential use as a solid electrolyte. The present results indicate that ionic contributions must be taken into account for ionic clathrate hydrate systems because of their distinctive guest dynamic behavior and structural patterns. In particular, microscopic analyses of ionic clathrate hydrates for identifying physicochemical characteristics are expected to provide new insights into inclusion chemistry.     

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.     

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.     

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.     

On the thermodynamic stability and structural transition of clathrate hydrates

Gas mixtures of methane and ethane form structure II clathrate hydrates despite the fact that each of pure methane and pure ethane gases forms the structure I hydrate. Optimization of the interaction potential parameters for methane and ethane is attempted so as to reproduce the dissociation pressures of each simple hydrate containing either methane or ethane alone. An account for the structural transitions between type I and type II hydrates upon changing the mole fraction of the gas mixture is given on the basis of the van der Waals and Platteeuw theory with these optimized potentials. Cage occupancies of the two kinds of hydrates are also calculated as functions of the mole fraction at the dissociation pressure and at a fixed pressure well above the dissociation pressure.     

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.