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.     

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

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

Molecular-dynamics 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.     

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.     

1H NMR chemical shift calculations as a probe of supramolecular host-guest geometry

The self-assembled supramolecular host [Ga(4)L(6)](12-) (1; L = 1,5-bis[2,3-dihydroxybenzamido]naphthalene) can encapsulate cationic guest molecules within its hydrophobic cavity and catalyze the chemical transformations of bound guests. The cavity of host 1 is lined with aromatic naphthalene groups, which create a magnetically shielded interior environment, resulting in upfield shifted (1-3 ppm) NMR resonances for encapsulated guest molecules. Using gauge independent atomic orbital (GIAO) DFT computations, we show that (1)H NMR chemical shifts for guests encapsulated in 1 can be efficiently and accurately calculated and that valuable structural information is obtained by comparing calculated and experimental chemical shifts. The (1)H NMR chemical shift calculations are used to map the magnetic environment of the interior of 1, discriminate between different host-guest geometries, and explain the unexpected downfield chemical shift observed for a particular guest molecule interacting with host 1.     

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.     

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.     

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 identification of the mixed hydrogen and carbon dioxide clathrate hydrate

In this contribution, we first found the novel clathrate hydrate containing two gaseous guests of hydrogen and carbon dioxide by spectroscopic analysis. X-ray powder diffraction and NMR spectroscopy were used to identify structure and guest distribution of the mixed H2 + CO2 hydrate. X-ray diffraction result confirmed that the unit cell parameter was 11.8602 +/- 0.0010 A, and the formed hydrate was identified as structure I hydrate. 1H magic angle spinning (MAS) NMR and 13C cross-polarization (CP) NMR spectroscopy were used to examine the distribution of hydrogen and carbon dioxide molecules in the cages of structure I, respectively. These NMR spectra showed that carbon dioxide molecules occupied both small 512 cages and large 51262 cages, and hydrogen molecules only were occluded in small 512 cages of structure I. The new finding of the mixed hydrogen hydrate is expected to contribute toward the development of hydrogen production technology and, particularly, inclusion chemistry.     

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.     

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.     

Simulations of structure II H2 and D2 clathrates: potentials incorporating quantum corrections

Molecular dynamics simulations are used to study the stability of structure II H(2) and D(2) clathrates with different large and small guest occupancies at 160 and 250 K and 2.0 kbars. Simulations are performed with the recently proposed anisotropic site-site potentials of Wang for H2 and D2 [J. Quant. Spectrosc. Radiat. Transf. 76, 23 (2003)] which are parameterized to account for quantum corrections of order variant Planck's over 2pi(2) in the second virial coefficient. Occupancies of 0-2 in the small cages and 2-5 in the large cages are considered. Thermodynamic integration is used to determine the most stable guest occupancy at each temperature. Since lattice free energy and configurational energy differences are small for a number of different combinations of cage occupancies, one must expect that in bulk samples various combinations will indeed be observed. Special attention is given to the differences between H(2) and D(2) guests and implications on the hydrogen storage capacity of the clathrates are discussed.     

Nuclear magnetic resonance parameters for methane molecule trapped in clathrate hydrates

The calculations of the nuclear shielding and spin-spin coupling constants were carried out for two models of clathrate hydrates, 5(12) and 5(12)6(8), using the density functional theory three-parameter Becke-Lee-Yang-Parr method with the basis set aug-cc-pVDZ (optimization) and HuzIII-su3 (NMR parameters). Particular attention has been devoted to evaluate the influence of a geometrical arrangement, the effect of long-range interactions on the NMR shielding of methane molecule, and to predict whether (13)C and (1)H chemical shifts can distinguish between guests in two clathrate hydrates cages. The correlation of the changes in the (17)O shielding constants depend strongly on the hydrogen-bonding topology. The intermolecular hydrogen-bond transmitted (1h)J(OH) spin-spin coupling constants are substantial. The increase of their values is connected with the elongation of the intramolecular O-H bond and the shortening of the intermolecular O···H distance. These data suggests that hydrogen bonds between double donor-single acceptor (DDA)-type water molecules acting as a proton acceptor from single donor-double acceptor (DAA)-type water molecules are stronger than ones formed by DAA-type water molecules acting as an acceptor for a DDA water proton. These state-of-the-art calculations confirmed the earlier experimental findings of the cage-dependency of (13)C chemical shift of methane.     

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.     

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 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.     

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.     

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.     

Redox active macrocyclic receptors for neutral guests

A novel series of triazine-appended macrocyclic complexes has been investigated as potential hydrogen bonding receptors for complementarily disposed heterocycles. Cocrystallization of a melamine-appended azacyclam complex of Cu(II) has been achieved with barbitone, the barbiturate anion and thymine. In each case, a complementary DAD/ADA hydrogen bonding motif between the melamine group and the heterocycle has been identified by X-ray crystallography. Electrochemical studies of the copper macrocycles in both nonaqueous and aqueous solution show anodic shifts of the Cu(II/)(I) redox couple of more than 60 mV upon addition of guest molecules with matching H-bonding motifs. The Zn(II) analogues have been synthesized via transmetalation of the Cu(II) complex, and their guest binding properties investigated by NMR spectroscopy. (1)H NMR shifts of up to 0.8 ppm were observed upon addition of guest, and stability constants are similar to those obtained electrochemically.     

Metal-assembled cobalt(II) resorc[4]arene-based cage molecules that reversibly capture organic molecules from water and act as NMR shift reagents

The complex Co4 1(2)8- is a tetranuclear cobalt(II) cage compound that assembles in aqueous solutions above pH 4 and is capable of encapsulating a variety of organic guest molecules, for example, benzene, hexane, chlorobutane, butanol, and ethyl acetate. Ligand 1 is a resorc[4]arene-based molecule with iminodiacetate moieties appended to its upper rim. 1H NMR studies of Co4 1(2)8-.guest complexes demonstrate inclusion of nonpolar hydrocarbons, substituted phenyls, alcohols, halogen-containing hydrocarbons, and polar organic molecules. The complex Co4 1(2)8- acts as an NMR shift reagent and causes substantial upfield isotropic hydrogen shifts (-30 to -40 ppm) in the guest molecule and separation of the guest hydrogen chemical shifts by typically 12 ppm. The complex Co4 1(2)8- will encapsulate molecules with fewer than eight atoms in a linear chain, mono- and disubstituted benzenes, and polar molecules with greater than two carbon atoms. The solid-state structure of Ba4[Co4 1(2).C6H5C2H5] shows a disordered guest molecule encapsulated within the cavity of Co4 1(2)8-. The cavity dimensions, bond lengths, and bond angles of Ba4[Co4 1(2).C6H5C2H5] are very similar to those determined in Ba4[Co4 1(2).6H2O].