Mesomorphology of clathrate hydrates from molecular ordering.

Clathrate hydrates are crystals formed by guest molecules that stabilize cages of hydrogen-bonded water molecules. Whereas thermodynamic equilibrium is well described via the van der Waals and Platteeuw approach, the increasing concerns with global warming and energy transition require extending the knowledge to non-equilibrium conditions in multiphase, sheared systems, in a multiscale framework. Potential macro-applications concern the storage of carbon dioxide in the form of clathrates, and the reduction of hydrate inhibition additives currently required in hydrocarbon production. We evidence porous mesomorphologies as key to bridging the molecular scales to macro-applications of low solubility guests. We discuss the coupling of molecular ordering with the mesoscales, including (i) the emergence of porous patterns as a combined factor from the walk over the free energy landscape and 3D competitive nucleation and growth and (ii) the role of molecular attachment rates in crystallization-diffusion models that allow predicting the timescale of pore sealing. This is a perspective study that discusses the use of discrete models (molecular dynamics) to build continuum models (phase field models, crystallization laws, and transport phenomena) to predict multiscale manifestations at a feasible computational cost. Several advances in correlated fields (ice, polymers, alloys, and nanoparticles) are discussed in the scenario of clathrate hydrates, as well as the challenges and necessary developments to push the field forward.

Novel approach for designing order parameters of clathrate hydrate structures by graph neural network.

Clathrate hydrates continue to be the focus of active research efforts due to their use in energy resources, transportation, and storage-related applications. Therefore, it is crucial to define their essential characteristics from a molecular standpoint. Understanding molecular structure in particular is crucial because it aids in understanding the mechanisms that lead to the formation or dissociation of clathrate hydrates. In the past, a wide variety of order parameters have been employed to classify and evaluate hydrate structures. An alternative approach to inventing bespoke order parameters is to apply machine learning techniques to automatically generate effective order parameters. In earlier work, we suggested a method for automatically designing novel parameters for ice and liquid water structures with Graph Neural Networks (GNNs). In this work, we use a GNN to implement our method, which can independently produce feature representations of the molecular structures. By using the TeaNet-type model in our method, it is possible to directly learn the molecular geometry and topology. This enables us to build novel parameters without prior knowledge of suitable order parameters for the structure type, discover structural differences, and classify molecular structures with high accuracy. We use this approach to classify the structures of clathrate hydrate structures: sI, sII, and sH. This innovative approach provides an appealing and highly accurate replacement for the traditional order parameters. Furthermore, our method makes clear the process of automatically designing a universal parameter for liquid water, ice, and clathrate hydrate to analyze their structures and phases.

Methane hydrate phase equilibrium considering dissolved methane concentrations and interfacial geometries from molecular simulations.

Natural gas hydrates, mainly existing in permafrost and on the seabed, are expected to be a new energy source with great potential. The exploitation technology of natural gas hydrates is one of the main focuses of hydrate-related studies. In this study, a large-size liquid aqueous solution wrapping a methane hydrate system was established and molecular dynamics simulations were used to investigate the phase equilibrium conditions of methane hydrate at different methane concentrations and interfacial geometries. It is found that the methane concentration of a solution significantly affects the phase equilibrium of methane hydrates. Different methane concentrations at the same temperature and pressure can lead to hydrate formation or decomposition. At the same temperature and pressure, in a system reaching equilibrium, the size of spherical hydrate clusters is coupled to the solution concentration, which is proportional to the Laplace pressure at the solid-liquid interface. Lower solution concentrations reduce the phase equilibrium temperature of methane hydrates at the same pressure; as the concentration increases, the phase equilibrium temperature gradually approaches the actual phase equilibrium temperature. In addition, the interfacial geometry of hydrates affects the thermodynamic stability of hydrates. The spherical hydrate particles have the highest stability for the same volume. Through this study, we provide a stronger foundation to understand the principles driving hydrate formation/dissociation relevant to the exploitation of methane hydrates.

Topological dual and extended relations between networks of clathrate hydrates and Frank-Kasper phases.

Clathrate hydrates are a class of ordered structures that are stabilized via the delicate balance of hydrophobic interactions between water and guest molecules, of which the space-filling network of hydrogen-bonded (H-bonded) water molecules are closely related to tetrahedrally close-packed structures, known as Frank-Kasper (FK) phases. Here we report an alternative way to understand the intricate structures of clathrate hydrates, which unveils the diverse crystalline H-bonded networks that can be generated via assembly of one common building block. In addition to the intrinsic relations and pathways linking these crystals, we further illustrate the rich structural possibilities of clathrate hydrates. Given that the topological dual relations between networks of clathrate hydrates and tetrahedral close-packed structures, the descriptors presented for clathrate hydrates can be directly extended to other ordered materials for a more thorough understanding of their nucleation, phases transition, and co-existence mechanisms.

A Clathrate Hydrate Structure Hidden in Plain Sight.

Clathrate hydrates have diverse crystal structures, and among them, the three (sI, sII, and sH) most prevalent ones cover nearly all known structures, while the norm is to consider other structures only when specific guest molecules are present. Here we report the observation of a hidden clathrate structure: the tetragonal structure (TS-I) in commonly formed gas hydrates, as evidenced from molecular dynamics simulations. We show that when two (or more) sI crystal grains with different growth directions come into contact or when the growth of a sI crystal encounters geometrical frustration, the TS-I results as a cocrystal. We give evidence that TS-I may also play an important role in the combination and/or transition between sI and sII. These results imply that this previously neglected structure may be commonly present whenever sI or sII is formed. This hidden structure must be identified, experimentally and in simulations; confining the possible structures may hinder an in-depth understanding of clathrate hydrates.

Molecular simulations on the stability and dynamics of bulk nanobubbles in aqueous environments.

Nanobubbles have attracted significant attention due to their unexpectedly long lifetimes and stabilities in liquid solutions. However, explanations for the unique properties of nanobubbles at the molecular scale are somewhat controversial. Of special interest is the validity of the Young-Laplace equation in predicting the inner pressure of such bubbles. In this work, large-scale molecular dynamics simulations were performed to study the stability and diffusion of nanobubbles of methane in water. Two types of force field, atomistic and coarse-grained, were used to compare the calculated results. In accordance with predictions from the Young-Laplace equation, it was found that the inner pressure of the nanobubbles increased with decreasing nanobubble size. Consequently, a large pressure difference between the nanobubble and its surroundings resulted in the high solubility of methane molecules in water. The solubility was considered to enable nanobubble stability at exceptionally high pressures. Smaller bubbles were observed to be more mobile via Brownian motion. The calculated diffusion coefficient also showed a strong dependence on the nanobubble size. However, this active mobility of small nanobubbles also triggered a mutable nanobubble shape over time. Nanobubbles were also found to coalesce when they were sufficiently close. A critical distance between two nanobubbles was thus identified to avoid coalescence. These results provide insight into the behavior of nanobubbles in solution and the mechanism of their unique stability while withstanding high inner pressures.

Sixty Years of the van der Waals and Platteeuw Model for Clathrate Hydrates-A Critical Review from Its Statistical Thermodynamic Basis to Its Extensions and Applications.

In light of the 60-year anniversary of the publishing of "Clathrate Solutions" by van der Waals and Platteeuw in 2019, we present a critical review of the famed solid solution model first disclosed in 1959. First, we lay out the groundwork in the 1950s aimed at the development of a phenomenological approach to clathrate modeling. Then we review the statistical thermodynamics fundamentals of the model, considering van der Waals and Platteeuw's earlier works, to obtain a consistent interpretation of the model. We turn our focus to clathrate hydrates and discuss the major contributions that led to the current state-of-the-art of gas hydrate thermodynamic modeling. Finally, we present some of the areas in clathrate thermodynamics that we foresee as the new frontiers in this subject. We expect this review to help newcomers to clathrate science in elucidating some subtle aspects of the model and to intrigue clathrate experts with a fresh look on this well-established solid solution model.

Mechanism for H2 diffusion in sII hydrates by molecular dynamics simulations.

Among the many different types of molecules that form clathrate hydrates, H2 is unique as it can easily diffuse into and out of clathrate cages, a process that involves the physical-chemical interactions between guest (H2) and host (water) molecules, and is unlike any other molecular system. The dynamic and nano-scale process of H2 diffusion into binary structure II hydrates, where the large cages are occupied by larger molecules, was studied using molecular dynamics simulation. As the H2 molecules diffused from one cage to another, two types of diffusion processes were observed: (i) when moving between a pair of large cages, the H2 molecules pass through the central part of the hexagonal rings; (ii) however, when the H2 molecules move from a large cage to a small one, it requires one of the pentagonal rings to partially break, as this allows the H2 molecule to pass through the widened space. While the diffusion of H2 molecules between large cages was found to occur more frequently, the presence of SF6 molecules in the large cages was found to inhibit diffusion. Therefore, in order to attain higher H2 storage capacities in binary hydrates, it is suggested that there is an optimal number of large cages that should be occupied by SF6 molecules.

Propane and Water: The Cooperativity of Unlikely Molecules to Form Clathrate Structures.

Many unanswered questions still exist at the molecular level to understand the nucleation process and mechanism of clathrate hydrates, especially for larger guest molecules that would result in the structure II crystal. Here, we report on molecular dynamics simulations for propane and water to describe the molecular mechanism leading to a structure II system. Through a large number (30) of long (5 µs) and coupled annealing (20 µs) simulations, we detail the prenucleation, nucleation, growth, and annealing of propane clathrate hydrate structures at 250 K and 1800 bar. The results demonstrate the equal importance of the empty and occupied cages in the nucleation of propane hydrates. The critical nucleus size is identified to be eight cages. While separate distinct clusters may exist during the prenucleation period, only one survives to grow beyond the critical nucleus size, with the others remaining subcritical. From the annealing simulations, it is clear that solid rearrangement is a very slow process, and 20 µs is still not long enough to capture long-range ordering resembling the structure II crystal. These results, along with the developed analysis method, have a significant impact in advancing our understanding of the nucleation process for unlike molecules.

Functionalized Nanoparticles for the Dispersion of Gas Hydrates in Slurry Flow.

Gas hydrates are crystals that can form in oil and gas production. Their agglomeration in flowlines may disrupt the normal production. One current strategy of hydrate management is to inject an anti-agglomerant, a type of low-dosage hydrate inhibitor that prevents hydrate agglomeration. Concerns in the use of these chemicals include their toxicity, cost, and environmental impacts. In this study, we exploited functionalized nanoparticles in place of anti-agglomerants to produce hydrate slurry, with the potential benefit of nanoparticles to be more environmentally friendly and conveniently recyclable. We coated 256 nm spherical silica nanoparticles with different hydrophobicity and evaluated their performance for the hydrate dispersion at atmospheric and high pressure. Nanoparticles with moderate hydrophobicity stabilized oil-in-water (O/W) or water-in-oil (W/O) emulsions. Direct visualization of the cyclopentane hydrate formation from the nanoparticle-stabilized emulsions revealed different morphologies of hydrate particles depending on whether the nanoparticles prevented agglomeration. We also measured the apparent viscosity of a hydrate-nanoparticle mixture using a high-pressure rheometer. Nanoparticles with moderate hydrophobicity during hydrate formation slowed the viscosification, reduced the maximum viscosity, increased the water conversion, and ultimately helped to maintain a low steady-state viscosity. Increasing nanoparticle or salt concentrations also improved the gas hydrate dispersion. Our study demonstrated the great potential of using nanoparticles in preventing agglomeration of gas hydrates under realistic pipeline flow conditions.

Cage occupancies, lattice constants, and guest chemical potentials for structure II hydrogen clathrate hydrate from Gibbs ensemble Monte Carlo simulations.

In this paper, equilibrium properties of structure II hydrates of hydrogen were determined from Monte Carlo simulations in the isothermal-isobaric Gibbs ensemble. Water and hydrogen molecules are described by the TIP4P/Ice and Silvera-Goldman models, respectively. The use of the Gibbs ensemble has many key advantages for the simulation of hydrates. By the separation of hydrogen vapor and hydrate phases into their own domains, coupled with transfer moves of hydrogen molecules between domains, cage occupancies were determined. Furthermore, the choice of this ensemble also allows equilibrium lattice constants and guest molecule chemical potentials to be straightforwardly estimated. Results for hydrogen mass fractions indicate reasonable agreement with prior simulation data and theoretical models, while detailed analysis of cage occupancy distributions and neighboring cage pair occupancy combinations gives valuable insight into the behavior of this hydrate at the inter-cage scale. These results will aid in the construction of theoretical models, for which knowledge of the occupancy of neighboring cages is of great importance. In support of previous experimental and theoretical works, we also find evidence of double occupancy of a few small cages inside of the hydrate stability zone, albeit at very high pressures; approximately 0.1% of small cages are doubly occupied at 300 MPa, for temperatures of 225 K and 250 K.

Intrinsic Structural Features of the Human IRE1α Transmembrane Domain Sense Membrane Lipid Saturation.

Activation of inositol-requiring enzyme (IRE1α) is an indispensable step in remedying the cellular stress associated with lipid perturbation in the endoplasmic reticulum (ER) membrane. IRE1α is a single-spanning ER transmembrane protein possessing both kinase and endonuclease functions, and its activation can be fully achieved through the dimerization and/or oligomerization process. How IRE1α senses membrane lipid saturation remains largely unresolved. Using both computational and experimental tools, we systematically investigated the dimerization process of the transmembrane domain (TMD) of IRE1α and found that, with help of the serine 450 residue, the conserved tryptophan 457 residue buttresses the core dimerization interface of IRE1α-TMD. BiFC (bimolecular fluorescence complementation) experiments revealed that mutation on these residues abolished the saturated fatty acid-induced dimerization in the ER membrane and subsequently inactivated IRE1α activity in vivo. Therefore, our results suggest that the structural elements of IRE1α-TMD serve as a key sensor that detects membrane aberrancy.

Analysis of three-phase equilibrium conditions for methane hydrate by isometric-isothermal molecular dynamics simulations.

To develop prediction methods of three-phase equilibrium (coexistence) conditions of methane hydrate by molecular simulations, we examined the use of NVT (isometric-isothermal) molecular dynamics (MD) simulations. NVT MD simulations of coexisting solid hydrate, liquid water, and vapor methane phases were performed at four different temperatures, namely, 285, 290, 295, and 300 K. NVT simulations do not require complex pressure control schemes in multi-phase systems, and the growth or dissociation of the hydrate phase can lead to significant pressure changes in the approach toward equilibrium conditions. We found that the calculated equilibrium pressures tended to be higher than those reported by previous NPT (isobaric-isothermal) simulation studies using the same water model. The deviations of equilibrium conditions from previous simulation studies are mainly attributable to the employed calculation methods of pressure and Lennard-Jones interactions. We monitored the pressure in the methane phase, far from the interfaces with other phases, and confirmed that it was higher than the total pressure of the system calculated by previous studies. This fact clearly highlights the difficulties associated with the pressure calculation and control for multi-phase systems. The treatment of Lennard-Jones interactions without tail corrections in MD simulations also contributes to the overestimation of equilibrium pressure. Although improvements are still required to obtain accurate equilibrium conditions, NVT MD simulations exhibit potential for the prediction of equilibrium conditions of multi-phase systems.

Design Principles for Nanoparticles Enveloped by a Polymer-Tethered Lipid Membrane.

We propose the design for a nanoparticle carrier that combines three existing motifs into a single construct: a liposome is stabilized by anchoring it to an enclosed solid core via extended polymeric tethers that are chemically grafted to the core and physisorb into the surrounding lipid membrane. Such a design would exhibit several enticing properties, among them: (i) the anchoring stabilizes the liposome against a variety of external stresses, while preserving an aqueous compartment between core and membrane; (ii) the interplay of design parameters such as polymer length or grafting density enforces strong constraints on nanoparticle size and hence ensures a high degree of uniformity; and (iii) the physical and chemical characteristics of the individual constituents equip the construct with numerous functionalities that can be exploited in many ways. However, navigating the large parameter space requires a sound prior understanding for how various design features work together, and how this impacts potential pathways for synthesizing and assembling these nanoparticles. In this paper, we examine these connections in detail, using both soft matter theory and computer simulations at all levels of resolution. We thereby derive strong constraints on the experimentally relevant parameter space, and also propose potential equilibrium and nonequilibrium pathways for nanoparticle assembly.

How Properties of Solid Surfaces Modulate the Nucleation of Gas Hydrate.

Molecular dynamics simulations were performed for CO2 dissolved in water near silica surfaces to investigate how the hydrophilicity and crystallinity of solid surfaces modulate the local structure of adjacent molecules and the nucleation of CO2 hydrates. Our simulations reveal that the hydrophilicity of solid surfaces can change the local structure of water molecules and gas distribution near liquid-solid interfaces, and thus alter the mechanism and dynamics of gas hydrate nucleation. Interestingly, we find that hydrate nucleation tends to occur more easily on relatively less hydrophilic surfaces. Different from surface hydrophilicity, surface crystallinity shows a weak effect on the local structure of adjacent water molecules and on gas hydrate nucleation. At the initial stage of gas hydrate growth, however, the structuring of molecules induced by crystalline surfaces are more ordered than that induced by amorphous solid surfaces.

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.

Nucleation rate analysis of methane hydrate from molecular dynamics simulations.

Clathrate hydrates are solid crystalline structures most commonly formed from solutions that have nucleated to form a mixed solid composed of water and gas. Understanding the mechanism of clathrate hydrate nucleation is essential to grasp the fundamental chemistry of these complex structures and their applications. Molecular dynamics (MD) simulation is an ideal method to study nucleation at the molecular level because the size of the critical nucleus and formation rate occur on the nano scale. Various analysis methods for nucleation have been developed through MD to analyze nucleation. In particular, the mean first-passage time (MFPT) and survival probability (SP) methods have proven to be effective in procuring the nucleation rate and critical nucleus size for monatomic systems. This study assesses the MFPT and SP methods, previously used for monatomic systems, when applied to analyzing clathrate hydrate nucleation. Because clathrate hydrate nucleation is relatively difficult to observe in MD simulations (due to its high free energy barrier), these methods have yet to be applied to clathrate hydrate systems. In this study, we have analyzed the nucleation rate and critical nucleus size of methane hydrate using MFPT and SP methods from data generated by MD simulations at 255 K and 50 MPa. MFPT was modified for clathrate hydrate from the original version by adding the maximum likelihood estimate and growth effect term. The nucleation rates calculated by MFPT and SP methods are within 5%, and the critical nucleus size estimated by the MFPT method was 50% higher, than values obtained through other more rigorous but computationally expensive estimates. These methods can also be extended to the analysis of other clathrate hydrates.

Micromechanical cohesion force between gas hydrate particles measured under high pressure and low temperature conditions.

To prevent hydrate plugging conditions in the transportation of oil/gas in multiphase flowlines, one of the key processes to control is the agglomeration/deposition of hydrate particles, which are determined by the cohesive/adhesive forces. Previous studies reporting measurements of the cohesive/adhesive force between hydrate particles used cyclopentane hydrate particles in a low-pressure micromechanical force apparatus. In this study, we report the cohesive forces of particles measured in a new high-pressure micromechanical force (MMF) apparatus for ice particles, mixed (methane/ethane, 74.7:25.3) hydrate particles (Structure II), and carbon dioxide hydrate particles (Structure I). The cohesive forces are measured as a function of the contact time, contact force, temperature, and pressure, and determined from pull-off measurements. For the measurements performed of the gas hydrate particles in the gas phase, the determined cohesive force is about 30-35 mN/m, about 8 times higher than the cohesive force of CyC5 hydrates in the liquid CyC5, which is about 4.3 mN/m. We show from our results that the hydrate structure (sI with CO2 hydrates and sII with CH4/C2H6 hydrates) has no influence on the cohesive force. These results are important in the deposition of a gas-dominated system, where the hydrate particles formed in the liquid phase can then stick to the hydrate deposited in the wall exposed to the gas phase.