Vibrational modes of methane in the structure H clathrate hydrate from ab initio molecular dynamics simulation

Effect of Cage Occupancies on Molecular Vibrations of Methane in Structure H Clathrate Hydrate: Ab Initio Molecular Dynamics Simulation

The structure H (sH) of methane hydrate, which has a distinctive structure with large (LL) cages capable of encapsulating multiple methane molecules, has been suggested as a methane reservoir in large icy bodies such as Titan, making it important in planetary science. This high-pressure phase, which exists in the GPa range, lends itself to the study of methane states and dynamics using powerful experimental techniques such as IR and Raman spectroscopy. However, the interpretation of the vibrational spectra of methane in the sH structure has been challenging because of the spectral complexities. The signals attributed to the methane molecules in the LL cage, as well as those of the other two cage types, overlap in the spectra. In this study, we investigated the microscopic origins of the shape of the C-H stretching vibration spectrum of methane in the LL cage using ab initio molecular dynamics (AIMD) simulations. For a single methane molecule in the LL cage, the ν3 band of the C-H stretching mode was observed at a higher frequency typical of isolated molecules in vacuum due to the large size of the LL cage. As the number of methane molecules in the LL cage increased beyond one, a tendency to blue-shift with increasing methane occupancy was observed, consistent with a loose-cage-tight-cage model. By characterizing the time correlation function of methane stretching vibrations based on the solvation number of methane and water molecules proximal to methane within the LL cage, we showed that the complicated spectral line shape observed in cases of higher methane occupancy in the LL cage resulted from the wider variation of the solvation shell states. Analysis of the solvation structures of the AIMD trajectories provided interpretations of the experimental spectral line shape, demonstrating the complementary nature of AIMD to the experiment and its effectiveness in analysis.

Modeling of Structure H Carbon Dioxide Clathrate Hydrates: Guest-Lattice Energies, Crystal Structure, and Pressure Dependencies

We performed first-principles computations to investigate the complex interplay of molecular interaction energies in determining the lattice structure and stability of CO₂@sH clathrate hydrates. Density functional theory computations using periodic boundary conditions were employed to characterize energetics and the key structural properties of the sH clathrate crystal under pressure, such as equilibrium lattice volume and bulk modulus. The performance of exchange-correlation functionals together with recently developed dispersion-corrected schemes was evaluated in describing interactions in both short-range and long-range regions of the potential. Structural relaxations of the fully CO₂-filled and empty sH unit cells yield crystal structure and lattice energies, while their compressibility parameters were derived by including the pressure dependencies. The present quantum chemistry computations suggest anisotropy in the compressibility of the sH clathrate hydrates, with the crystal being less compressible along the a-axis direction than along the c-axis one, in distinction from nearly isotropic sI and sII structures. The detailed results presented here give insight into the complex nature of the underlying guest-host interactions, checking earlier assumptions, providing critical tests, and improving estimates. Such entries may eventually lead to better predictions of thermodynamic properties and formation conditions, with a direct impact on emerging hydrate-based technologies.

From Infrared Spectra to Macroscopic Mechanical Properties of sH Gas Hydrates through Atomistic Calculations

The vibrational characteristics of gas hydrates are key identifying molecular features of their structure and chemical composition. Density functional theory (DFT)-based IR spectra are one of the efficient tools that can be used to distinguish the vibrational signatures of gas hydrates. In this work, ab initio DFT-based IR technique is applied to analyze the vibrational and mechanical features of structure-H (sH) gas hydrate. IR spectra of different sH hydrates are obtained at 0 K at equilibrium and under applied pressure. Information about the main vibrational modes of sH hydrates and the factors that affect them such as guest type and pressure are revealed. The obtained IR spectra of sH gas hydrates agree with experimental/computational literature values. Hydrogen bond’s vibrational frequencies are used to determine the hydrate’s Young’s modulus which confirms the role of these bonds in defining sH hydrate’s elasticity. Vibrational frequencies depend on pressure and hydrate’s O···O interatomic distance. OH vibrational frequency shifts are related to the OH covalent bond length and present an indication of sH hydrate’s hydrogen bond strength. This work presents a new route to determine mechanical properties for sH hydrate based on IR spectra and contributes to the relatively small database of gas hydrates’ physical and vibrational properties.

Effect of temperature and large guest molecules on the C-H symmetric stretching vibrational frequencies of methane in structure H and I clathrate hydrates

Large molecules such as 2-methylbutane (C₅H₁₂) or 2,2-dimethylbutane (C₆H₁₄) form structure H (sH) hydrates with methane (CH₄) as a help gas. In this study, the Raman spectra of the C–H symmetric stretch region of CH₄ enclathrated within various sH hydrates and structure I CH₄ hydrates were analyzed in the temperature range 137.7–205.4 K. Thermal expansions of these sH hydrate samples were also measured using powder X-ray diffraction. Symmetric stretch vibrational frequencies of CH₄ in host–water cages increased because of varying temperature, and the sizes of the host–water cages also increased; variation of CH₄ in small cages was less than in larger cages. Comparing the variations of the C–H symmetric stretching frequencies of CH₄ in gas hydrates with varying pressure and temperature, we suggest that the observed trend is caused by thermal vibrations of the CH₄ molecule in water cages.

Temperature effect on C–H symmetric stretching frequencies of CH₄ in water cages of sI and sH clathrate hydrates were clarified.

Cage fusion from bi-cages to tri-cages during nucleation of methane hydrate: a DFT-D simulation

Water-cage clusters encapsulating guest molecules are the basic components of hydrate crystal structures. Herein, we investigated the fusion process from bi-cages to tri-cages to probe the nucleation mechanism at the initial stage of CH4 hydrate formation by employing dispersion-corrected density functional theory. We found that tri-cages possess high stability by sharing three, rather than two, polygonal faces. In addition, any mono-cage combined with a nonstandard 4151062 cage could achieve considerable stability regardless of which face is shared; this finding illustrates that 4151062 cages are more likely to appear at the early stages of CH4 hydrate nucleation than other nonstandard cages. We then simulated the Raman spectra of CH4 molecules in water-cage to characterize the spectral characteristics of the CH4 hydrate. The C-H symmetric stretching frequency of encapsulated CH4 molecules red-shifted with increasing mono-cage size, which follows the prediction of the "loose cage-tight cage" model. The symmetric stretching vibrational frequencies of trapped CH4 molecules in the tri-cage revealed a clear red-shift compared with those in the component mono- and bi-cages. The cage fusion process and spectroscopic properties described in this work are expected to provide new atomistic insights into CH4 hydrates at the initial nucleation stage.

Infrared Spectra of Gas Hydrates from First-Principles

The infrared spectra of sII gas hydrates have been computed using density functional theory for the first time, at equilibrium, and under pressure. It is also the first account of a full vibrational analysis (both guest and host vibrations) for gas hydrates with hydrocarbon guest molecules. Five hydrate structures were investigated: empty, propane, isobutane, ethane-methane, and propane-methane sII hydrates. The computed IR spectra are in good agreement with available experimental and theoretical results. The OH stretching frequencies were found to increase, while the H-bond stretching and H₂O libration frequencies decreased with an increase in guest size and cage occupancy and with a decrease in pressure. The H₂O bending vibrations are relatively independent of guest size, cage occupancy, pressure, temperature, and crystal structure. The guest vibrational modes, especially the bending modes, also have minimal pressure dependence. We have also provided more quantitative evidence that gas hydrate material properties are defined by their hydrogen bond properties, by linking H-bond strength to Young's modulus. The results and ensuing vibrational analysis presented in this paper are a valuable contribution to the ongoing efforts into developing more accurate gas hydrate identification and characterization methods in the laboratory, in industry/nature, and even in outer space.

Quantum approaches to vibrational dynamics and spectroscopy: is ease of interpretation sacrificed as rigor increases?

The subject of this Perspective is quantum approaches, beyond the harmonic approximation, to vibrational dynamics and IR spectroscopy.

Retracted Article: Effect of temperature and large guest molecules on the C–H symmetric stretching vibrational frequencies of methane in structure H and I clathrate hydrates

Large molecules such as 2-methylbutane (C₅H₁₂) or 2,2-dimethylbutane (C₆H₁₄) form structure H (sH) hydrates with methane (CH₄) as a help gas. In this study, the Raman spectra of the C–H symmetric stretch region of CH₄ enclathrated within various sH hydrates and structure I CH₄ hydrates were analyzed in the temperature range 83–183 K. Thermal expansions of these sH hydrate samples were also measured using powder X-ray diffraction. Symmetric stretch vibrational frequencies of CH₄ in host water cages increased because of varying temperature, and the sizes of the host water cages also increased; variation of CH₄ in small cages was less than in larger cages. Comparing the variations of the C–H symmetric stretching frequencies of CH₄ in gas hydrates with varying pressure and temperature, we suggest that the observed trend is caused by thermal vibrations of the CH₄ molecule in water cages.

Temperature effects on C–H symmetric stretching frequencies of CH₄ in water cages of sI and sH clathrate hydrates were clarified.

Evaluation of hydrogen bond networks in cellulose Iβ and II crystals using density functional theory and Car-Parrinello molecular dynamics

Crystal models of cellulose Iβ and II, which contain various hydrogen bonding (HB) networks, were analyzed using density functional theory and Car-Parrinello molecular dynamics (CPMD) simulations. From the CPMD trajectories, the power spectra of the velocity correlation functions of hydroxyl groups involved in hydrogen bonds were calculated. For the Iβ allomorph, HB network A, which is dominant according to the neutron diffraction data, was stable, and the power spectrum represented the essential features of the experimental IR spectra. In contrast, network B, which is a minor structure, was unstable because its hydroxymethyl groups reoriented during the CPMD simulation, yielding a different crystal structure to that determined by experiments. For the II allomorph, a HB network A is proposed based on diffraction data, whereas molecular modeling identifies an alternative network B. Our simulations showed that the interaction energies of the cellulose II (B) model are slightly more favorable than model II(A). However, the evaluation of the free energy should be waited for the accurate determination from the energy point of view. For the IR calculation, cellulose II (B) model reproduces the spectra better than model II (A).

Energy benchmarks for methane-water systems from quantum Monte Carlo and second-order Møller-Plesset calculations

The quantum Monte Carlo (QMC) technique is used to generate accurate energy benchmarks for methane-water clusters containing a single methane monomer and up to 20 water monomers. The benchmarks for each type of cluster are computed for a set of geometries drawn from molecular dynamics simulations. The accuracy of QMC is expected to be comparable with that of coupled-cluster calculations, and this is confirmed by comparisons for the CH4-H2O dimer. The benchmarks are used to assess the accuracy of the second-order Møller-Plesset (MP2) approximation close to the complete basis-set limit. A recently developed embedded many-body technique is shown to give an efficient procedure for computing basis-set converged MP2 energies for the large clusters. It is found that MP2 values for the methane binding energies and the cohesive energies of the water clusters without methane are in close agreement with the QMC benchmarks, but the agreement is aided by partial cancelation between 2-body and beyond-2-body errors of MP2. The embedding approach allows MP2 to be applied without loss of accuracy to the methane hydrate crystal, and it is shown that the resulting methane binding energy and the cohesive energy of the water lattice agree almost exactly with recently reported QMC values.

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.

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.

A quantum chemistry study of natural gas hydrates

The structure and properties of natural gas hydrates containing hydrocarbons, CO₂, and N₂ molecules were studied by using computational quantum chemistry methods via the density functional theory approach. All host cages involved in I, II, and H types structures where filled with hydrocarbons up to pentanes, CO₂ and N₂ molecules, depending on their size, and the structures of these host-guest systems optimized. Structural properties, vibrational spectra, and density of states were analyzed together with results from atoms-in-a-molecule and natural bond orbitals methods. The inclusion of dispersion terms in the used functional plays a vital role for obtaining reliable information, and thus, B97D functional was shown to be useful for these systems. Results showed remarkable interaction energies, not strongly affected by the type of host cage, with molecules tending to be placed at the center of the cavities when host cages and guest molecules cavities are of similar size, but with molecules approaching hexagonal faces for larger cages. Vibrational properties show remarkable features in certain regions, with shiftings rising from host-guest interactions, and useful patterns in the terahertz region rising from water surface vibrations strongly coupled with guest molecules. Likewise, calculations on crystal systems for the I and H types were carried out using a pseudopotential approach combined with Grimme's method to take account of dispersion.