Ammonia clathrate hydrates as new solid phases for Titan, Enceladus, and other planetary systems

A DFT Computational Study of Type-I Clathrates A8Sn46-x (A = Cs or NH4, x = 0 or 2)

Semiconducting clathrates have attracted considerable interest in the field of thermoelectric materials. We report here a computational study on the crystal structure, the enthalpy of formation, and the physical properties of the following type-I clathrates: (a) experimentally studied Cs8Sn44 and hypothetical Cs8Sn46 and (b) hypothetical (NH4)8Sn46-x (x = 0 or 2). The ab initio VASP calculations for the nominal stoichiometries include the geometry optimization of the initial structural models, enthalpies of formation, and the electronic and phonon density of states. Comparison of the chemical bonding of the structural models is performed via the electron localization function. The results show that the presence and distribution of defects in the Sn framework for both Cs8Sn46-x and (NH4)8Sn46-x systems significantly alters the formation energy and its electrical properties, ranging from metallic to semiconducting behavior. In particular, one defect per six-membered Sn ring in a 3D spiro-network is the thermodynamically preferred configuration that results in the Cs8Sn44 and (NH4)8Sn44 stoichiometries with narrow-band gap semiconducting behavior. Moreover, the rotation of the ammonium cation in the polyhedral cavities is an interesting feature that may promote the use of ammonium or other small molecular cations as guests in clathrates for thermoelectric applications; this is due to the decrease in the lattice thermal conductivity.

The structure of water-ammonia mixtures from classical and ab initio molecular dynamics

The structure of aqueous ammonia solutions is investigated through classical molecular dynamics (MD) and ab initio molecular dynamics (AIMD) simulations. We have preliminarily compared three well-known classical force fields for liquid water (SPC, SPC/E, and TIP4P) in order to identify the most accurate one in reproducing AIMD results obtained at the Generalized Gradient Approximation (GGA) and meta-GGA levels of theory. Liquid ammonia has been simulated by implementing an optimized force field recently developed by Chettiyankandy et al. [Fluid Phase Equilib. 511, 112507 (2020)]. Analysis of the radial distribution functions for different ammonia concentrations reveals that the three water force fields provide comparable estimates of the mixture structure, with the SPC/E performing slightly better. Although a fairly good agreement between MD and AIMD is observed for conditions close to the equimolarity, at lower ammonia concentrations, important discrepancies arise, with classical force fields underestimating the number and strength of H-bonds between water molecules and between water and ammonia moieties. Here, we prove that these drawbacks are rooted in a poor sampling of the configurational space spanned by the hydrogen atoms lying in the H-bonds of H2O⋯H2O and, more critically, H2O⋯NH3 neighbors due to the lack of polarization and charge transfer terms. This way, non-polarizable classical force fields underestimate the proton affinity of the nitrogen atom of ammonia in aqueous solutions, which plays a key role under realistic dilute ammonia conditions. Our results witness the need for developing more suited polarizable models that are able to take into account these effects properly.

Interfacial Ice Density Fluctuations Inform Surface Ice-Philicity

The propensity of a surface to nucleate ice or bind to ice is governed by its ice-philicity─its relative preference for ice over liquid water. However, the relationship between the features of a surface and its ice-philicity is not well understood, and for surfaces with chemical or topographical heterogeneity, such as proteins, their ice-philicity is not even well-defined. In the analogous problem of surface hydrophobicity, it has been shown that hydrophobic surfaces display enhanced low water-density (vapor-like) fluctuations in their vicinity. To interrogate whether enhanced ice-like fluctuations are similarly observed near ice-philic surfaces, here we use molecular simulations and enhanced sampling techniques. Using a family of model surfaces for which the wetting coefficient, k, has previously been characterized, we show that the free energy of observing rare interfacial ice-density fluctuations decreases monotonically with increasing k. By utilizing this connection, we investigate a set of fcc systems and find that the (110) surface is more ice-philic than the (111) or (100) surfaces. By additionally analyzing the structure of interfacial ice, we find that all surfaces prefer to bind to the basal plane of ice, and the topographical complementarity of the (110) surface to the basal plane explains its higher ice-philicity. Using enhanced interfacial ice-like fluctuations as a measure of surface ice-philicity, we then characterize the ice-philicity of chemically heterogeneous and topologically complex systems. In particular, we study the spruce budworm antifreeze protein (sbwAFP), which binds to ice using a known ice-binding site (IBS) and resists engulfment using nonbinding sites of the protein (NBSs). We find that the IBS displays enhanced interfacial ice-density fluctuations and is therefore more ice-philic than the two NBSs studied. We also find the two NBSs are similarly ice-phobic. By establishing a connection between interfacial ice-like fluctuations and surface ice-philicity, our findings thus provide a way to characterize the ice-philicity of heterogeneous surfaces.

Ab Initio Studies of Structural and Mechanical Properties of NH3, NO, and N2O Hydrates

The investigation on the mechanical properties of clathrate hydrate is closely related to the exploitation of hydrates and gas transportation. In this article, the structural and mechanical properties of some nitride gas hydrates were studied using DFT calculations. First, the equilibrium lattice structure is obtained by geometric structure optimization; then, the complete second-order elastic constant is determined by energy-strain analysis, and the polycrystalline elasticity is predicted. It is found that the NH₃, N₂O, and NO hydrates all have high elastic isotropy but are different in shear characteristics. This work may lay a theoretical foundation for studying the structural evolution of clathrate hydrates under the mechanical field.

Reply to the 'Comment on Cage occupancy of methane clathrate hydrates in the ternary H2O-NH3-CH4 system' by S. Alavi and J. Ripmeester, Chem. Commun., 2022, , DOI: 10.1039/D1CC06526B

Our recent Communication suggested that ammonia in aqueous solution may preferentially destabilize large cages in methane clathrate hydrates. A Comment favored ammonia incorporation instead, but it did not accurately describe our proposed mechanism and relied primarily on studies conducted in different chemical systems and/or which used other preparation methods.

Comment on “Cage occupancy of methane clathrate hydrates in the ternary H2O–NH3–CH4 system” by C. Petuya, M. Choukroun, T. H. Vu, A. Desmedt, A. G. Davies, and C. Sotin, Chem. Commun., 2020, , 12391

Alternative interpretations of the experimental results given in the cited Communication are presented. There is evidence that under certain conditions, ammonia can be incorporated into clathrate hydrate cages.

Managing hydrogen bonding in the clathrate hydrate of the 1-pentanol guest molecule

1-pentanol, long-chain alcohol molecule, can be encaged in the clathrate hydrate by managing the destabilizing influence of guest–host hydrogen bonding.

Effect of Ammonia on Methane Hydrate Stability under High-Pressure and High-Temperature Conditions

High-pressure experiments were conducted to investigate the stability and phase transition of methane hydrate (MH) in the water-methane-ammonia system at room-to-high temperatures employing Raman spectroscopy and synchrotron X-ray powder diffraction, in combination with an externally heated diamond anvil cell. The results revealed that, at room temperature, MH undergoes phase transitions from MH-I to MH-II at ∼1.0 GPa and from MH-II to MH-III at ∼2.0 GPa. These transition behaviors are consistent with those in the water-methane system, which indicates that ammonia has a negligible effect on a series of phase transitions of MH. Contrarily, a sequential in situ Raman spectroscopy revealed that ammonia affects the stability of MH-III under high pressure and high temperature: the dissociation temperature of MH-III was more than 10 K lower in the water-methane-ammonia system than in the water-methane system. These findings aid in improving the internal structural models of icy bodies and estimating the origin of their atmospheric methane.

Cage occupancy of methane clathrate hydrates in the ternary H2O-NH3-CH4 system

The incorporation of ammonia inside methane clathrate hydrate is of great interest to the hydrate chemistry community. We investigated the phase behavior of methane clathrate formed from aqueous ammonia solution. Ammonia's presence decreases methane occupancy in the large cages, without definitive Raman spectroscopic evidence for its incorporation inside the structure.

Gas hydrates in sustainable chemistry

This review includes the current state of the art understanding and advances in technical developments about various fields of gas hydrates, which are combined with expert perspectives and analyses.

Unraveling the metastability of the SI and SII carbon monoxide hydrate with a combined DFT-neutron diffraction investigation

Clathrate hydrates are crystalline compounds consisting of water molecules forming cages (so-called "host") inside of which "guest" molecules are encapsulated depending on the thermodynamic conditions of formation (systems stable at low temperature and high pressure). These icelike systems are naturally abundant on Earth and are generally expected to exist on icy celestial bodies. Carbon monoxide hydrate might be considered an important component of the carbon cycle in the solar system since CO gas is one of the predominant forms of carbon. Intriguing fundamental properties have also been reported: the CO hydrate initially forms in the sI structure (kinetically favored) and transforms into the sII structure (thermodynamically stable). Understanding and predicting the gas hydrate structural stability then become essential. The aim of this work is, thereby, to study the structural and energetic properties of the CO hydrate using density functional theory (DFT) calculations together with neutron diffraction measurements. In addition to the comparison of DFT-derived structural properties with those from experimental neutron diffraction, the originality of this work lies in the DFT-derived energy calculations performed on a complete unit cell (sI and sII) and not only by considering guest molecules confined in an isolated water cage (as usually performed for extracting the binding energies). Interestingly, an excellent agreement (within less than 1% error) is found between the measured and DFT-derived unit cell parameters by considering the Perdew-Burke-Ernzerhof (denoted PBE) functional. Moreover, a strategy is proposed for evaluating the hydrate structural stability on the basis of potential energy analysis of the total nonbonding energies (i.e., binding energy and water substructure nonbonding energy). It is found that the sII structure is the thermodynamically stable hydrate phase. In addition, increasing the CO content in the large cages has a stabilizing effect on the sII structure, while it destabilizes the sI structure. Such findings are in agreement with the recent experimental results evidencing the structural metastability of the CO hydrate.

NH3 as simple clathrate-hydrate catalyst: Experiment and theory

The catalytic action of NH₃ within the all-vapor approach for instant clathrate hydrate (CH) formation is studied using both FTIR spectroscopy and ab initio molecular dynamics simulations. A unique property of NH₃, namely, the rapid abundant penetration and occupation of the water network, creates defects, particularly Bjerrum D-defects, in the hydrate frame that are generally stabilized by guest NH₃ molecules in the cages. Furthermore, insertion of NH₃ seriously disturbs the hydrate network where the guest NH₃ molecules also make fluxional H-bonds with the host water molecules. These defects strongly facilitate a sub-second formation of the simple NH₃ s-II gas hydrate at 160 K. FTIR spectra of aerosols of the NH₃ s-II CH have been measured, and the displacement of both small and large cage NH₃ guests by CO₂ and tetrahydrofuran is examined.

In situ Raman and X-ray diffraction studies on the high pressure and temperature stability of methane hydrate up to 55 GPa

High-temperature and high-pressure experiments were performed under 2-55 GPa and 298-653 K using in situ Raman spectroscopy and X-ray diffraction combined with externally heated diamond anvil cells to investigate the stability of methane hydrate. Prior to in situ experiments, the typical C-H vibration modes of methane hydrate and their pressure dependence were measured at room temperature using Raman spectroscopy to make a clear discrimination between methane hydrate and solid methane which forms through the decomposition of methane hydrate at high temperature. The sequential in situ Raman spectroscopy and X-ray diffraction revealed that methane hydrate survives up to 633 K and 40.3 GPa and then decomposes into solid methane and ice VII above the conditions. The decomposition curve of methane hydrate estimated by the present experiments is >200 K lower than the melting curves of solid methane and ice VII, and moderately increases with increasing pressure. Our result suggests that although methane hydrate may be an important candidate for major constituents of cool exoplanets and other icy bodies, it is unlikely to be present in the ice mantle of Neptune and Uranus, where the temperature is expected to be far beyond the decomposition temperatures.

NH3 as unique non-classical content-former within clathrate hydrates

High quality FTIR spectra of aerosols of NH₃-THF and NH₃-TMO binary clathrate hydrates (CHs) have been measured. Our recently developed all-vapor sub-second approach to clathrate-hydrate formation combined with computational studies has been used to identify vibrational spectroscopic signatures of NH₃ within the gas hydrates. The present study shows that there are three distinct NH₃ types, namely, classical small-cage NH₃, nonclassical small-cage NH₃, and NH₃ within the hydrate network. The network ammonia does not directly trigger the non-classical CH structure. Rather, the ammonia within the network structure perturbs the water bonding, introducing orientational defects that are stabilized by small and/or large cage guest molecules through H-bonding. This unusual behavior of NH₃ within CHs opens a possibility for catalytic action of NH₃ during CH-formation. Furthermore, impacts over time of the small-cage NH₃-replacement molecules CO₂ and CH₄ on the structure and composition of the ternary CHs have been noted.

Ab Initio Studies on the Clathrate Hydrates of Some Nitrogen- and Sulfur-Containing Gases

Ab initio calculations are performed to investigate the host-guest interactions and multiple occupancies of some sulfur- (H₂S, CS₂) and nitrogen-containing (N₂, NO, and NH₃) molecules in dodecahedral, tetrakaidecahedral, and hexakaidecahedral water cages in this work. Five functionals in the framework of density functional theory are compared, and the M06-2X method appears to be the best to predict the binding energies as well as the geometries. Results show that N₂ and NO molecules are more stable in the 5¹²6⁴ cage, while NH₃ and H₂S prefer to stabilize in the 5¹²6² cage. This suggests that the sI hydrates of NH₃ and H₂S exhibit higher stability than the sII structures and that sII NO hydrate is more stable than sI NO hydrate. N₂ is found to be more stable in type II structure with single occupancy and to form type I hydrate with multiple occupancy, which is consistent with the experimental observations. As to the guest molecule CS₂, it may undergo severe structural deformation in the 5¹² and 5¹²6² cage. For multiple occupancies, the 5¹², 5¹²6², and 5¹²6⁴ water cages can trap up to two N₂ molecules, and the 5¹²6⁴ water cage can accommodate two H₂S molecules. This work is expected to provide new insight into the formation mechanism of clathrate hydrates for atmospherically important molecules.

Towards Clathrates: Frozen States of Hydration of tert-Butylamine

The dilution of tert-butylamine (tBA) with water and subsequent cooling leads to a large series of different crystalline hydrates by an in situ IR laser melting-zone procedure. The crystal structures were determined for tBA⋅n H2 O, with n=0, 1/4, 1, 7 1/4, 7 3/4, 9 3/4, 11, and 17. For the two lower hydrates (n= 1/4, 1), one- and two-dimensional hydrogen-bonded networks are formed, respectively. The higher hydrates (n>1) exhibit a clathrate-like three-dimensional water framework with the tBA molecules as part of, or sitting inside, the cages. In all cases, tBA is hydrogen-bonded to the H2 O framework. In the intermediate range (1<n<7 1/4), crystallization is hindered, and no crystalline phases could be observed. The crystal structures that are achieved from the dilution of tBA with water are considered to be frozen stages of hydration, describing the genesis of such clathrate-like structures, finally ending at ice as an example of an infinitely diluted hydrate.

A molecular dynamics study of guest-host hydrogen bonding in alcohol clathrate hydrates

Clathrate hydrates are typically stabilized by suitably sized hydrophobic guest molecules. However, it has been experimentally reported that isomers of amyl-alcohol C5H11OH can be enclosed into the 5(12)6(4) cages in structure II (sII) clathrate hydrates, even though the effective radii of the molecules are larger than the van der Waals radii of the cages. To reveal the mechanism of the anomalous enclathration of hydrophilic molecules, we performed ab initio and classical molecular dynamics simulations (MD) and analyzed the structure and dynamics of a guest-host hydrogen bond for sII 3-methyl-1-butanol and structure H (sH) 2-methyl-2-butanol clathrate hydrates. The simulations clearly showed the formation of guest-host hydrogen bonds and the incorporation of the O-H group of 3-methyl-1-butanol guest molecules into the framework of the sII 5(12)6(4) cages, with the remaining hydrophobic part of the amyl-alcohol molecule well accommodated into the cages. The calculated vibrational spectra of alcohol O-H bonds showed large frequency shifts due to the strong guest-host hydrogen bonding. The 2-methyl-2-butanol guests form strong hydrogen bonds with the cage water molecules in the sH clathrate, but are not incorporated into the water framework. By comparing the structures of the alcohols in the hydrate phases, the effect of the location of O-H groups in the butyl chain of the guest molecules on the crystalline structure of the clathrate hydrates is indicated.

Structural transformation and tuning behavior induced by the propylamine concentration in hydrogen clathrate hydrates

The structures and the guest–host distributions of propylamine hydrates provide useful information on the hydrophilic guest–host interactions in clathrate hydrates.

Calculations of NMR properties for sI and sII clathrate hydrates of methane, ethane and propane

Calculations of NMR parameters (the absolute shielding constants and the spin-spin coupling constants) for 5(12), 5(12)6(2) and 5(12)6(4) cages enclathrating CH4, C2H6 and C3H8 molecules are presented. The DFT/B3LYP/HuzIII-su3 level of theory was employed. The (13)C shielding constants of guest molecules are close to available experimental data. In two cases (the ethane in 5(12) and the propane in 5(12)6(2) cages) the (13)C shielding constants are reported for the first time. Inversion of the methyl/methylene (13)C and (1)H shielding constants order is found for propane in the 5(12)6(2) cage. Topological criteria are used to interpret the changes of values of NMR parameters of water molecules and they establish a connection between single cages and bulk crystal.

Antifreezes act as catalysts for methane hydrate formation from ice

Contrary to the thermodynamic inhibiting effect of methanol on methane hydrate formation from aqueous phases, hydrate forms quickly at high yield by exposing frozen water-methanol mixtures with methanol concentrations ranging from 0.6-10 wt% to methane gas at pressures from 125 bars at 253 K. Formation rates are some two orders of magnitude greater than those obtained for samples without methanol and conversion of ice is essentially complete. Ammonia has a similar catalytic effect when used in concentrations of 0.3-2.7 wt%. The structure I methane hydrate formed in this manner was characterized by powder X-ray diffraction and Raman spectroscopy. Steps in the possible mechanism of action of methanol were studied with molecular dynamics simulations of the Ih (0001) basal plane exposed to methanol and methane gas. Simulations show that methanol from a surface aqueous layer slowly migrates into the ice lattice. Methane gas is preferentially adsorbed into the aqueous methanol surface layer. Possible consequences of the catalytic methane hydrate formation on hydrate plug formation in gas pipelines, on large scale energy-efficient gas hydrate formation, and in planetary science are discussed.

Methanol incorporation in clathrate hydrates and the implications for oil and gas pipeline flow assurance and icy planetary bodies

One of the best-known uses of methanol is as antifreeze. Methanol is used in large quantities in industrial applications to prevent methane clathrate hydrate blockages from forming in oil and gas pipelines. Methanol is also assigned a major role as antifreeze in giving icy planetary bodies (e.g., Titan) a liquid subsurface ocean and/or an atmosphere containing significant quantities of methane. In this work, we reveal a previously unverified role for methanol as a guest in clathrate hydrate cages. X-ray diffraction (XRD) and NMR experiments showed that at temperatures near 273 K, methanol is incorporated in the hydrate lattice along with other guest molecules. The amount of included methanol depends on the preparative method used. For instance, single-crystal XRD shows that at low temperatures, the methanol molecules are hydrogen-bonded in 4.4% of the small cages of tetrahydrofuran cubic structure II hydrate. At higher temperatures, NMR spectroscopy reveals a number of methanol species incorporated in hydrocarbon hydrate lattices. At temperatures characteristic of icy planetary bodies, vapor deposits of methanol, water, and methane or xenon show that the presence of methanol accelerates hydrate formation on annealing and that there is unusually complex phase behavior as revealed by powder XRD and NMR spectroscopy. The presence of cubic structure I hydrate was confirmed and a unique hydrate phase was postulated to account for the data. Molecular dynamics calculations confirmed the possibility of methanol incorporation into the hydrate lattice and show that methanol can favorably replace a number of methane guests.