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.     

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.     

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.     

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.     

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.     

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.     

On the thermodynamic stability of hydrogen clathrate hydrates

The cage occupancy of hydrogen clathrate hydrate has been examined by grand canonical Monte Carlo (GCMC) simulations for wide ranges of temperature and pressure. The simulations are carried out with a fixed number of water molecules and a fixed chemical potential of the guest species so that hydrogen molecules can be created or annihilated in the clathrate. Two types of the GCMC simulations are performed; in one the volume of the clathrate is fixed and in the other it is allowed to adjust itself under a preset pressure so as to take account of compression by a hydrostatic pressure and expansion due to multiple cage occupancy. It is found that the smaller cage in structure II is practically incapable of accommodating more than a single guest molecule even at pressures as high as 500 MPa, which agrees with the recent experimental investigations. The larger cage is found to encapsulate at most 4 hydrogen molecules, but its occupancy is dependent significantly on the pressure of hydrogen.     

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.     

13C chemical shifts of propane molecules encaged in structure II clathrate hydrate

Experimental NMR measurements for (13)C chemical shifts of propane molecules encaged in 16-hedral cages of structure II clathrate hydrate were conducted to investigate the effects of guest-host interaction of pure propane clathrate on the (13)C chemical shifts of propane guests. Experimental (13)C NMR measurements revealed that the clathrate hydration of propane reverses the (13)C chemical shifts of methyl and methylene carbons in propane guests to gaseous propane at room temperature and atmospheric pressure or isolated propane, suggesting a change in magnetic environment around the propane guest by the clathrate hydration. Inversion of the (13)C chemical shifts of propane clathrate suggests that the deshielding effect of the water cage on the methyl carbons of the propane molecule encaged in the 16-hedral cage is greater than that on its methylene carbon.     

Spectroscopic Observation of the Hydroxy Position in Butanol Hydrates and Its Effect on Hydrate Stability

In this study, we investigate the crystal structures and phase equilibria of butanols+CH₄+H₂O systems to reveal the hydroxy group positioning and its effects on hydrate stability. Four clathrate hydrates formed by structural butanol isomers are identified with powder X‐ray diffraction (PXRD). In addition, Raman spectroscopy is used to analyze the guest distributions and inclusion behaviors of large alcohol molecules in these hydrate systems. The existence of a free OH indicates that guest molecules can be captured in the large cages of structure II hydrates without any hydrogen‐bonding interactions between the hydroxy group of the guests and the water‐host framework. However, Raman spectra of the binary (1‐butanol+CH₄) hydrate do not show the free OH signal, indicating that there could be possible hydrogen‐bonding interactions between the guests and hosts. We also measure the four‐phase equilibrium conditions of the butanols+CH₄+H₂O systems.     

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.     

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.     

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.     

How much carbon dioxide can be stored in the structure H clathrate hydrates?: a molecular dynamics study

The stability of structure H (sH) carbon dioxide clathrate hydrates at three temperature-pressure conditions are determined by molecular dynamics simulations on a 3x3x3 sH unit cell replica. Simulations are performed at 100 K at ambient pressure, 273 K at 100 bars and also 300 K and 5.0 kbars. The small and medium cages of the sH unit cell are occupied by a single carbon dioxide guest and large cage guest occupancies of 1-5 are considered. Radial distribution functions are given for guests in the large cages and unit cell volumes and configurational energies are studied as a function of large cage CO(2) occupancy. Free energy calculations are carried out to determine the stability of clathrates for large cage occupancies at three temperature/pressure conditions stated above. At the low temperature, large cage occupancy of 5 is the most stable while at the higher temperature, the occupancy of 3 is the most favored. Calculations are also performed to show that the CO(2) sH clathrate is more stable than the methane clathrate analog. Implications on CO(2) sequestration by clathrate formation are discussed.     

Molecular-dynamics simulations of binary structure II hydrogen and tetrahydrofurane clathrates

The binary structure II hydrogen and tetrahydrofurane (THF) clathrates are studied with molecular-dynamics simulations. Simulations are done at pressures of 120 and 1.013 bars for temperatures ranging from 100 to 273 K. For the small cages of the structure II unit cell, H2 guest molecule occupancies of 0, 16 (single occupancy), and 32 (double occupancy) are considered. THF occupancies of 0-8 in the large cages are studied. For cases in which THF does not occupy all large cages in a unit cell, the remaining large cages can be occupied with sets of four H2 guest molecules. The unit-cell volumes and configurational energies are compared in the different occupancy cases. Increasing the small cage occupancy leads to an increase in the unit-cell volume and thermal-expansion coefficient. Among simulations with the same small cage occupancy, those with the large cages containing 4H2 guests have the largest volumes. The THF guest molecules have a stabilizing effect on the clathrate and the configurational energy of the unit cell decreases linearly as the THF content increases. For binary THF + H2 clathrates, the substitution of the THF molecules in the large cages with sets of 4H2 molecules increases the configurational energy. For the binary clathrates, various combinations of THF and H2 occupancies have similar configurational energies.     

Guest-Host Interaction Study in Clathrate Hydrates Using Lattice Dynamics Simulation

Lattice dynamics simulation of several gas hydrates （helium, argon, and methane） with different occupancy rates has been performed using TIP3P potential model. Results show that the coupling between the guest and host is not simple as depicted by the conventional viewpoints. For clathrate hydrate enclosing small guest, the small cages are dominantly responsible for the thermodynamic stability of clathrate hydrates. And the spectrum of methane hydrate is studied compared with argon hydrate, then as a result, shrink effect from positive hydrogen shell is proposed.     

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.     

The thermodynamic stability of clathrate hydrate. Encaging non-spherical propane molecules

The thermodynamic stability of a clathrate hydrate encaging non-spherical molecules has been investigated by examining the free energy of cage occupancy. In the present study, a generalized van der Waals and Platteeuw theory is extended to treat the rotational motion of guest molecules in clathrate hydrate cages. The vibrational free energy of both guest and host molecules is divided into harmonic and anharmonic contributions. The anharmonic free energy associated with the non-spherical nature of the guest molecules is evaluated as a perturbation from the spherical guest. Predicted thermodynamic properties are compared with measured values. It is shown that this anharmonic contribution is important in the free energy of the hindered rotation of the guests.     

用分子动力学模拟天然气水合物的抑制效应

用分子动力学模拟方法确定了结构H型(SH)天然气水合物的稳定晶体生长面为(001), 系统研究了277 K时三种动力学抑制剂对此晶面的影响. 模拟显示抑制剂中的氧与表面水分子形成氢键, 从而破坏原有的稳定结构, 造成水合物笼型结构坍塌, 达到抑制水合物形成的效果. 比较三种不同动力学抑制剂对SH的抑制效果得出: PVCap＞PEO＞PVP. 在此基础上研究了PVCap对天然气水合物结构I型(SI), 结构II型(SII)和SH三种不同晶型的抑制效应. 模拟发现抑制效果的次序为: SH＞SI＞SII.