Amorphous precursors in the nucleation of clathrate hydrates

Dissociation temperature of gas hydrates through isenthalpic-isobaric molecular dynamics simulations

Molecular simulations are a powerful tool to understand phenomena and obtain properties of gas hydrate systems. The direct coexistence method (DCM) in the NVT or NPT ensembles, the most commonly used method to determine hydrate dissociation temperatures, can be computationally expensive due to the need for several long simulations. Through an extensive set of simulations, we report here the details of the DCM within the NPH (isobaric-isenthalpic) ensemble, which require fewer and shorter trajectories. The dissociation pressure of methane hydrates is obtained for pressures of 4, 8, 15, 30, and 50 MPa. The values are in agreement with other literature simulations and experimental data. The results are further validated with the calculation of the enthalpy of dissociation, with a value of 50 kJ/mol of methane, also in agreement with the literature. The complexity of a multiphase and multicomponent system presents challenges lacking in simpler water/ice systems. These are found to be dependent on energy conservation. The optimal set of parameters to achieve it is also reported, including a smaller time step and the use of double precision, along with an analysis of some factors that could affect the convergence of the method. Although these parameters require more computational cost, the NPH ensemble is successful in providing the dissociation temperature of gas hydrates in fewer simulations than other ensembles and with productions lasting only 500 ns.

Reparameterization of the mW model to accurately predict the experimental phase diagram of methane hydrate

Due to their high computational efficiency, the coarse-grained water models are of particular importance for practical molecular simulations of gas hydrates. In these models, the mW model is successfully used to study many thermodynamics and dynamics of methane hydrate. Yet, despite several decades of intense research, the mW model is still found to overestimate the melting temperature of methane hydrate. We here employ the minimum mean squared error estimation to revisit the key parameter of the mW model, which determines the strength of the tetrahedral angle of the water system. Relying on the free energy calculations, we first estimate the chemical potentials of water in the liquid phase for temperatures at which methane hydrate forms. We then turn to the mean squared error to describe the chemical potential deviation between the mW model and the TIP4P/ice model (the latter could reproduce the experimental phase diagram of methane hydrate). By minimizing the mean squared error, we finally have an optimized parameter for the mW model. In this part, we also discuss the pressure effect on such reparameterization procedure. Moreover, relying on the direct coexistence method, the melting temperature determined using the reparameterized mW model is found to be consistent with the experimental data. This strategy provides a means to improve the coarse-grained model to match the experimental observations for temperatures in the range of interest.

Dissociation line and driving force for nucleation of the nitrogen hydrate from computer simulation. II. Effect of multiple occupancy

In this work, we determine the dissociation line of the nitrogen (N2) hydrate by computer simulation using the TIP4P/Ice model for water and the TraPPE force field for N2. This work is the natural extension of Paper I, in which the dissociation temperature of the N2 hydrate has been obtained at 500, 1000, and 1500 bar [Algaba et al., J. Chem. Phys. 159, 224707 (2023)] using the solubility method and assuming single occupancy. We extend our previous study and determine the dissociation temperature of the N2 hydrate at different pressures, from 500 to 4500 bar, taking into account the single and double occupancy of the N2 molecules in the hydrate structure. We calculate the solubility of N2 in the aqueous solution as a function of temperature when it is in contact with a N2-rich liquid phase and when in contact with the hydrate phase with single and double occupancy via planar interfaces. Both curves intersect at a certain temperature that determines the dissociation temperature at a given pressure. We observe a negligible effect of occupancy on the dissociation temperature. Our findings are in very good agreement with the experimental data taken from the literature. We have also obtained the driving force for the nucleation of the hydrate as a function of temperature and occupancy at several pressures. As in the case of the dissociation line, the effect of occupancy on the driving force for nucleation is negligible. To the best of our knowledge, this is the first time that the effect of the occupancy on the driving force for nucleation of a hydrate that exhibits sII crystallographic structure is studied from computer simulation.

Amorphous aggregates with a very wide size distribution play a central role in crystal nucleation

There is mounting evidence that crystal nucleation from supersaturated solution involves the formation and reorganization of prenucleation clusters, contradicting classical nucleation theory. One of the key unresolved issues pertains to the origin, composition, and structure of these clusters. Here, a range of amino acids and peptides is investigated using light scattering, mass spectrometry, and in situ terahertz Raman spectroscopy, showing that the presence of amorphous aggregates is a general phenomenon in supersaturated solutions. Significantly, these aggregates are found on a vast range of length scales from dimers to 30-mers to the nanometre and even micrometre scale, implying a continuous distribution throughout this range. Larger amorphous aggregates are sites of spontaneous crystal nucleation and act as intermediates for laser-induced crystal nucleation. These results are shown to be consistent with a nonclassical nucleation model in which barrierless (homogeneous) nucleation of amorphous aggregates is followed by the nucleation of crystals from solute-enriched aggregates. This provides a novel perspective on crystal nucleation and the role of nonclassical pathways.

Exploring Porous Flow Behavior of the Decomposed Gas from CH4 Hydrate in Clayey Sediments by Molecular Dynamics Simulation

A fundamental understanding of the fluid flow mechanism during CH4 hydrate dissociation in nanoscale clayey sediments from the molecular perspective can provide invaluable information for macroscale natural gas hydrate (NGH) exploration. In this work, the fluid flow behaviors of the decomposed gas from CH4 hydrate within clayey nanopores under different temperature conditions are revealed by molecular dynamics (MD) simulation. The simulation results indicate that the key influencing factors of gas-water flow in nanoscale clayey sediments include the diffusion and the random migration of gas molecules. The influencing mechanisms of fluid flow in nanopores are closely related with the temperature conditions. Under a low temperature condition, the gas diffusion process is impeded by the secondary hydrate formation, leading to the decline in gas transport velocity within nanopores. However, it is still noteworthy that the gas-water fluid flow channels are not completely blocked by the occurrence of secondary hydrate. Under a high temperature condition, the significant phenomenon of water migration during gas flow is observed, which can be ascribed to the gas-liquid entrainment effect in nanopores of the clayey sediment. These results may provide valuable implications and fundamental evidence for improving gas production efficiency in future field tests of NGH exploitation in marine sediments.

A Molecular Dynamics Study on Xe/Kr Separation Mechanisms Using Crystal Growth Method

The separation of xenon/krypton gas mixtures is a valuable but challenging endeavor in the gas industry due to their similar physical characteristics and closely sized molecules. To address this, we investigated the effectiveness of the hydrate-based gas separation method for mixed Xe-Kr gas via molecular dynamics (MD) simulations. The formation process of hydrates facilitates the encapsulation of guest molecules within hydrate cages, offering a potential strategy for gas separation. Higher temperatures and pressures are advantageous for accelerating the hydrate growth rate. The final occupancy of guest molecules and empty cages within 512, 51264, and all hydrate cages were thoroughly examined. An increase in the pressure and temperature enhanced the occupancy rates of Xe in both 512 and 51264 cages, whereas elevated pressure alone improved the occupancy of Kr in 51264 cages. However, the impact of temperature and pressure on Kr occupancy within 512 cages was found to be minimal. Elevated temperature and pressure resulted in a reduced occupancy of empty cages. Predominantly, 51264 cages were occupied by Xe, whereas Kr showed a propensity to occupy the 512 cages. With increasing simulated pressure, the final occupancy of Xe molecules in all cages rose from 0.37 to 0.41 for simulations at 260 K, while the final occupancy of empty cages decreased from 0.24 to 0.2.

HTR+: a novel algorithm for identifying type and polycrystal of gas hydrates

In this work, the hierarchical topology ring (HTR+) algorithm, an extension of the HTR algorithm, was developed for identifying gas hydrate types, cage structures, and grain boundaries (GBs) within polycrystalline structures. Utilizing molecular dynamics trajectories of polycrystalline hydrates, the accuracy of the HTR+ algorithm is validated in identifying sI, sII and sH hydrate types, hydrate grains, and GBs in multi-hydrate polycrystals, as well as clathrate cages at GBs. Additionally, during the hydrate nucleation and growth processes, clathrate cages, hydrate type, hydrate grains and ice structures are accurately recognized. Significantly, this algorithm demonstrates high efficiency, particularly for large hydrate systems. HTR+ algorithm emerges a powerful tool for identifying micro/mesoscopic structures of gas hydrates, enabling an in-depth understanding of the formation mechanisms and properties of gas hydrates.

Unusual species of methane hydrate detected in nanoporous media using solid state 13C NMR

Methane is considered to be a cubic structure I (CS-I) clathrate hydrate former, although in a number of instances, small amounts of structure II (CS-II) clathrate hydrate have been transiently observed as well. In this work, solid-state magic angle spinning 13C NMR spectra of methane hydrate formed at low temperatures inside silica-based nanoporous materials with pores in the range of 3.8-20.0 nm (CPG-20, Vycor, and MCM-41) show methane in several different environments. In addition to methane encapsulated in the dodecahedral 512 (D) and tetrakaidecahedral 51262 (T) cages typical of the CS-I clathrate hydrate phase, methane guests in pentakaidecahedral 51263 (P) and hexakaidecahedral 51264 (H) cages are also identified, and these appear to be stabilized for extended periods of time. The ratio of methane guests among the D and T cages determined from the line intensities is significantly different from that of bulk CS-I samples and indicates that both CS-I and CS-II are present as the dominant species. This is the first observation of methane in P cages, and the possible structures in which they could be present are discussed. Broad and relatively strong methane peaks, which are also observed in the spectra, can be related to methane dissolved in an amorphous component of water adjacent to the pore walls. Nanoconfinement and interaction with the pore walls clearly have a strong influence on the hydrate formed and may reflect species present in the early stages of hydrate growth.

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.

Three-phase equilibria of hydrates from computer simulation. III. Effect of dispersive interactions in the methane and carbon dioxide hydrates

In this work, the effect of the range of dispersive interactions in determining the three-phase coexistence line of the CO2 and CH4 hydrates has been studied. In particular, the temperature (T3) at which solid hydrate, water, and liquid CO2/gas CH4 coexist has been determined through molecular dynamics simulations using different cutoff values (from 0.9 to 1.6 nm) for dispersive interactions. The T3 of both hydrates has been determined using the direct coexistence simulation technique. Following this method, the three phases in equilibrium are put together in the same simulation box, the pressure is fixed, and simulations are performed at different temperatures T. If the hydrate melts, then T > T3. Conversely, if the hydrate grows, then T < T3. The effect of the cutoff distance on the dissociation temperature has been analyzed at three different pressures for CO2 hydrate: 100, 400, and 1000 bar. Then, we have changed the guest and studied the effect of the cutoff distance on the dissociation temperature of the CH4 hydrate at 400 bar. Moreover, the effect of long-range corrections for dispersive interactions has been analyzed by running simulations with homo- and inhomogeneous corrections and a cutoff value of 0.9 nm. The results obtained in this work highlight that the cutoff distance for the dispersive interactions affects the stability conditions of these hydrates. This effect is enhanced when the pressure is decreased, displacing the T3 about 2-4 K depending on the system and the pressure.

Mechanical properties of amorphous CO2 hydrates: insights from molecular simulations

Understanding physicochemical properties of amorphous gas hydrate systems is of great significance to reveal structural stabilities of polycrystalline gas hydrate systems. Furthermore, amorphous gas hydrates can occur ordinarily in the nucleation events of gas hydrate systems. Herein, the mechanical properties of amorphous carbon dioxide hydrates are examined by means of all-atom classical molecular dynamic simulations. Our molecular simulation results reveal that mechanical strengths of amorphous carbon dioxide hydrates are evidently governed by temperatures, confining pressures, and ratios of water to carbon dioxide molecules. Notably, under compressive loads, amorphous carbon dioxide hydrates firstly exhibit monotonic strain hardening, followed by an interesting distinct phenomenon characterized by a steady flow stress at further large deformation strains. Furthermore, structural evolutions of amorphous carbon dioxide hydrates are analyzed on the basis of the N-Hbond DOP order parameter. These important findings can not only contribute to our understanding of the structural stabilities of amorphous gas hydrate systems, but also help to develop fundamental understandings about grain boundaries of gas hydrate systems.

Comparing brute force to transition path sampling for gas hydrate nucleation with a flat interface: comments on time reversal symmetry

Fluid to solid nucleation is often investigated with the rare event method transition path sampling (TPS). I claim that the inherent irreversibility of solid nucleation, even at stationary conditions, calls into question TPS's applicability for determining solid nucleation mechanisms, especially for pre-critical behavior. Even when applied to a phenomenon which displays time reversal asymmetry like solid nucleation, TPS is a good means of exploring phase space and giving trends in post-critical structure, and its ability to facilitate nucleation rate and free energy calculations remains outstanding. Forward-only splitting and ratcheting methods such as forward flux sampling are more attractive for understanding nucleation mechanisms as they do not require time reversal symmetry, but at low driving forces may suffer from the same limitations as brute force: they may never make it to the first ratchet. Here I briefly summarize the TPS method and gas hydrate nucleation simulation literature, focusing on topics within both to facilitate a comparison of brute force hydrate nucleation to transition path sampling of hydrate nucleation. Perhaps anecdotally, the brute force technique results in more crystalline trajectories despite having higher driving forces than TPS. I maintain this difference is because of the inherent irreversibility of hydrate nucleation, meaning its pre-critical behavior cannot accurately be determined by the melting trajectories that comprise approximately half of the configurations in TPS's path ensemble.

Probing the critical nucleus size in tetrahydrofuran clathrate hydrate formation using surface-anchored nanoparticles

Controlling the formation of clathrate hydrates is crucial for advancing hydrate-based technologies. However, the microscopic mechanism underlying clathrate hydrate formation through nucleation remains poorly elucidated. Specifically, the critical nucleus, theorized as a pivotal step in nucleation, lacks empirical validation. Here, we report uniform nanoparticles, e.g., graphene oxide (GO) nanosheets and gold or silver nanocubes with controlled sizes, as nanoprobes to experimentally measure the size of the critical nucleus of tetrahydrofuran (THF) clathrate hydrate formation. The capability of the nanoparticles in facilitating THF clathrate hydrate nucleation displays generally an abrupt change at a nanoparticle-size-determined specific supercooling. It is revealed that the free-energy barrier shows an abrupt change when the nanoparticles have an approximately the same size as that of the critical nucleus. Thus, it is inferred that THF clathrate hydrate nucleation involves the creation of a critical nucleus with its size being inversely proportional to the supercooling. By proving the existence and determining the supercooling-dependent size of the critical nucleus of the THF clathrate hydrates, this work brings insights in the microscopic pictures of the clathrate hydrate nucleation.

Multiscale Molecular Dynamics Simulations of Ice-Binding Proteins

Ice-binding proteins (IBPs) are a diverse class of proteins that are essential for the survival of organisms in cold conditions. IBPs are diverse in their function and can prevent or promote ice growth and selectively bind to specific crystallographic planes of the growing ice lattice. Moreover, IBPs are widely utilized to modulate ice crystal growth and recrystallization in the food industry and as cryoprotectants to preserve biological matter. A key unresolved aspect of the mode of action is how the ice-binding sites of these proteins distinguish between ice and water and interact with multiple crystal facets of the ice. The use of molecular dynamics (MD) simulation allows us to thoroughly investigate the binding mechanism and energetics of ice-binding proteins, to complement and expand on the mechanistic understandings gained from experiments. In this chapter, we describe a series of molecular dynamics simulation methodologies to investigate the mechanism of action of ice-binding proteins. Specifically, we provide detailed instructions to set up MD simulations to study the binding and interaction of ice-binding proteins using atomistic and coarse-grained simulations.

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.

Carbon dioxide sequestration in natural gas hydrates - effect of flue and noble gases

Clean energy is one of the immediate requirements all over the world to tackle the global energy demands. Natural gas hydrates (NGHs) are one of the proposed alternatives that could be used to extract methane as clean energy and simultaneously sequestrate carbon dioxide. However, the formation of CH4-CO2 mixed hydrates and the first hydrate layer besides the interface reduces the rate of CO2 sequestration and methane extraction in NGHs, and thus, multistep extraction of methane is one of the proposed solutions. We report the atomic level factors that could enhance CO2 sequestration in the newly formed first hydrate layer besides the interface in the presence of flue and noble gases using DFT calculations and molecular dynamics simulations at 250 K and 0.15 kbar. The simulations show the formation of stable dual cages (large-large or small-large) that lead to the formation of a four-caged, Y-shaped cluster (growth synthon) which leads to the formation of a hydrate unit cell in heterogeneous medium. Among the flue and noble gases, only argon forms energetically favorable dual cages with itself and CO2 due to which enhanced CO2 sequestration is observed at different concentrations of Ar and CO2 where the CO2 : Ar (2.5 : 1.5) system shows the best CO2 sequestration in the first layer besides the interface. The results also provide understanding into the previously reported concentration dependent CO2 selectivity in sI hydrates in the presence of third gases (N2 and H2S).

Understanding why constant energy or constant temperature may affect nucleation behavior in MD simulations: A study of gas hydrate nucleation

Molecular dynamics simulations have been widely used in exploring the nucleation behavior of many systems, including gas hydrates. Gas hydrates are ice-like solids in which gas molecules are trapped in water cages. During hydrate formation, a considerable amount of heat is released, and previous work has reported that the choice of temperature control scheme may affect the behavior of hydrate formation. The origins of this effect have remained an open question. To address this question, extensive NVE simulations and thermostatted (NPT and NVT) simulations with different temperature coupling strengths have been performed and compared for systems where a water nanodroplet is immersed in a H2S liquid. Detailed analysis of the hydrate structures and their mechanisms of formation has been carried out. Slower nucleation rates in NVE simulations in comparison to NPT simulations have been observed in agreement with previous studies. Probability distributions for various temperature measures along with their spatial distributions have been examined. Interestingly, a comparison of these temperature distributions reveals a small yet noticeable difference in the widths of the distributions for water. The somewhat reduced fluctuations in the temperature for the water species in the NVE simulations appear to be responsible for reducing the hydrate nucleation rate. We further conjecture that the NVE-impeded nucleation rate may be the result of the finite size of the surroundings (here the liquid H2S portion of the system). Additionally, a local spatial temperature gradient arising from the heat released during hydrate formation could not be detected.

Resolving Temperature-Dependent Hydrate Nucleation Pathway: The Role of "Transition Layer"

Understanding the nucleation of natural gas hydrate (NGH) at different conditions has important implications to NGH recovery and other industrial applications, such as gas storage and separation. Herein, vast numbers of hydrate nucleation events are traced via molecular dynamics (MD) simulations at different degrees of supercooling (or driving forces). Specifically, to precisely characterize a hydrate nucleus from an aqueous system during the MD simulation, we develop an evolutionary order parameter (OP) to recognize the nucleus size and shape. Subsequently, the free energy landscapes of hydrate during nucleation are explored by using the newly developed OP. The results suggest that at 270 K (or 0.92 Tm supercooling, where Tm is the melting point), the near-rounded nucleus prevails during the nucleation, as described from the classical nucleation theory. In contrast, at relatively strong driving forces of 0.85 and 0.88 Tm, nonclassical nucleation events arise. Specifically, the pathway toward an elongated nucleus becomes as important as the pathway toward a near-rounded nucleus. To explain the distinct nucleation phenomena at different supercoolings, a notion of a "transition layer" (or liquid-blob-like layer) is proposed. Here, the transition layer is to describe the interfacial region between the nucleus and aqueous solution, and this layer entails two functionalities: (1) it tends to retain CH4 depending on the degrees of supercooling and (2) it facilitates collision among CH4, which thus promote the incorporation of CH4 into nucleus. Our simulation indicates that compared to the near-rounded nucleus, the transition layer surrounding the elongated nucleus is more evident with the higher collision rate among CH4 molecules. As such, the transition layer tends to promote the elongated nucleus pathway, while offsetting the cost of larger surface free energy associated with the elongated nucleus. At 0.92 Tm, however, the transition layer gradually disappears, and classical nucleation events dominate. Overall, the notion of "transition layer" offers deeper insight into the NGH nucleation at different degrees of supercooling and could be extended to describe other types of hydrate nucleation.

Molecular Dynamics Simulation of the Three-Phase Equilibrium Line of CO2 Hydrate with OPC Water Model

The three-phase coexistence line of the CO2 hydrate was determined using molecular dynamics (MD) simulations. By using the classical and modified Lorentz-Berthelot (LB) parameters, the simulations were carried out at 10 different pressures from 3 to 500 MPa. For the OPC water model, simulations with the classic and the modified LB parameters both showed negative deviations from the experimental values. For the TIP4P/Ice water model, good agreement with experimental equilibrium data can be achieved when the LB parameter is adjusted based on the solubility of CO2 in water. Our results also show that the influence of the water model on the equilibrium prediction is much larger than the CO2 model. Current simulations indicated that the H2O-H2O and H2O-CO2 cross-interactions' parameters might contribute equally to the accurate prediction of T3. According to our simulations, the prediction of T3 values showed relatively higher accuracy while using the combination of TIP4P/Ice water and EPM2 CO2 with modified LB parameter. Furthermore, varied χ values are recommended for accurate T3 estimation over a wide pressure range. The knowledge obtained in this study will be helpful for further accurate MD simulation of the process of CO2/CH4 replacement.

Solubility of carbon dioxide in water: Some useful results for hydrate nucleation

In this paper, the solubility of carbon dioxide (CO2) in water along the isobar of 400 bar is determined by computer simulations using the well-known TIP4P/Ice force field for water and the TraPPE model for CO2. In particular, the solubility of CO2 in water when in contact with the CO2 liquid phase and the solubility of CO2 in water when in contact with the hydrate have been determined. The solubility of CO2 in a liquid-liquid system decreases as the temperature increases. The solubility of CO2 in a hydrate-liquid system increases with temperature. The two curves intersect at a certain temperature that determines the dissociation temperature of the hydrate at 400 bar (T3). We compare the predictions with T3 obtained using the direct coexistence technique in a previous work. The results of both methods agree, and we suggest 290(2) K as the value of T3 for this system using the same cutoff distance for dispersive interactions. We also propose a novel and alternative route to evaluate the change in chemical potential for the formation of hydrates along the isobar. The new approach is based on the use of the solubility curve of CO2 when the aqueous solution is in contact with the hydrate phase. It considers rigorously the non-ideality of the aqueous solution of CO2, providing reliable values for the driving force for nucleation of hydrates in good agreement with other thermodynamic routes used. It is shown that the driving force for hydrate nucleation at 400 bar is larger for the methane hydrate than for the carbon dioxide hydrate when compared at the same supercooling. We have also analyzed and discussed the effect of the cutoff distance of dispersive interactions and the occupancy of CO2 on the driving force for nucleation of the hydrate.

Machine-guided path sampling to discover mechanisms of molecular self-organization

Molecular self-organization driven by concerted many-body interactions produces the ordered structures that define both inanimate and living matter. Here we present an autonomous path sampling algorithm that integrates deep learning and transition path theory to discover the mechanism of molecular self-organization phenomena. The algorithm uses the outcome of newly initiated trajectories to construct, validate and-if needed-update quantitative mechanistic models. Closing the learning cycle, the models guide the sampling to enhance the sampling of rare assembly events. Symbolic regression condenses the learned mechanism into a human-interpretable form in terms of relevant physical observables. Applied to ion association in solution, gas-hydrate crystal formation, polymer folding and membrane-protein assembly, we capture the many-body solvent motions governing the assembly process, identify the variables of classical nucleation theory, uncover the folding mechanism at different levels of resolution and reveal competing assembly pathways. The mechanistic descriptions are transferable across thermodynamic states and chemical space.

Molecular Dynamics Study of Clathrate-like Ordering of Water in Supersaturated Methane Solution at Low Pressure

Using molecular dynamics, the evolution of a metastable solution for "methane + water" was studied for concentrations of 3.36, 6.5, 9.45, 12.2, and 14.8 mol% methane at 270 K and 1 bar during 100 ns. We have found the intriguing behavior of the system containing over 10,000 water molecules: the formation of hydrate-like structures is observed at 6.5 and 9.45 mol% concentrations throughout the entire solution volume. This formation of "blobs" and the following amorphous hydrate were studied. The creation of a metastable methane solution through supersaturation is the key to triggering the collective process of hydrate formation under low pressure. Even the first stage (0-1 ns), before the first fluctuating cavities appear, is a collective process of H-bond network reorganization. The formation of fluctuation cavities appears before steady hydrate growth begins and is associated with a preceding uniform increase in the water molecule's tetrahedrality. Later, the constantly presented hydrate cavities become the foundation for a few independent hydrate nucleation centers, this evolution is consistent with the labile cluster and local structure hypotheses. This new mechanism of hydrogen-bond network reorganization depends on the entropy of the cavity arrangement of the guest molecules in the hydrate lattice and leads to hydrate growth.

Homogeneous nucleation rate of methane hydrate formation under experimental conditions from seeding simulations

In this work, we shall estimate via computer simulations the homogeneous nucleation rate for the methane hydrate at 400 bars for a supercooling of about 35 K. The TIP4P/ICE model and a Lennard-Jones center were used for water and methane, respectively. To estimate the nucleation rate, the seeding technique was employed. Clusters of the methane hydrate of different sizes were inserted into the aqueous phase of a two-phase gas-liquid equilibrium system at 260 K and 400 bars. Using these systems, we determined the size at which the cluster of the hydrate is critical (i.e., it has 50% probability of either growing or melting). Since nucleation rates estimated from the seeding technique are sensitive to the choice of the order parameter used to determine the size of the cluster of the solid, we considered several possibilities. We performed brute force simulations of an aqueous solution of methane in water in which the concentration of methane was several times higher than the equilibrium concentration (i.e., the solution was supersaturated). From brute force runs, we infer the value of the nucleation rate for this system rigorously. Subsequently, seeding runs were carried out for this system, and it was found that only two of the considered order parameters were able to reproduce the value of the nucleation rate obtained from brute force simulations. By using these two order parameters, we estimated the nucleation rate under experimental conditions (400 bars and 260 K) to be of the order of log₁₀ (J/(m³ s)) = -7(5).

Kinetics and Mechanisms of Pressure-Induced Ice Amorphization and Polyamorphic Transitions in a Machine-Learned Coarse-Grained Water Model

Water glasses have attracted considerable attention due to their potential connection to a liquid-liquid transition in supercooled water. Here we use molecular simulations to investigate the formation and phase behavior of water glasses using the machine-learned bond-order parameter (ML-BOP) water model. We produce glasses through hyperquenching of water, pressure-induced amorphization (PIA) of ice, and pressure-induced polyamorphic transformations. We find that PIA of polycrystalline ice occurs at a lower pressure than that of monocrystalline ice and through a different mechanism. The temperature dependence of the amorphization pressure of polycrystalline ice for ML-BOP agrees with that in experiments. We also find that ML-BOP accurately reproduces the density, coordination number, and structural features of low-density (LDA), high-density (HDA), and very high-density (VHDA) amorphous water glasses. ML-BOP accurately reproduces the experimental radial distribution function of LDA but overpredicts the minimum between the first two shells in high-density glasses. We examine the kinetics and mechanism of the transformation between low-density and high-density glasses and find that the sharp nature of these transitions in ML-BOP is similar to that in experiments and all-atom water models with a liquid-liquid transition. Transitions between ML-BOP glasses occur through a spinodal-like mechanism, similar to ice crystallization from LDA. Both glass-to-glass and glass-to-ice transformations have Avrami-Kolmogorov kinetics with exponent n = 1.5 ± 0.2 in experiments and simulations. Importantly, ML-BOP reproduces the competition between crystallization and HDA→LDA transition above the glass transition temperature T_g, and separation of their time scales below T_g, observed also in experiments. These findings demonstrate the ability of ML-BOP to accurately reproduce water properties across various regimes, making it a promising model for addressing the competition between polyamorphic transitions and crystallization in water and solutions.

Homogeneous nucleation of crystalline methane hydrate in molecular dynamics transition paths sampled under realistic conditions

Methane hydrates are important from a scientific and industrial perspective, and form by nucleation and growth from a supersaturated aqueous solution of methane. Molecular simulation is able to shed light on the process of homogeneous nucleation of hydrates, using straightforward molecular dynamics or rare event enhanced sampling techniques with atomistic and coarse grained force fields. In our previous work [Arjun, T. A. Berendsen, and P. G. Bolhuis, Proc. Natl. Acad. Sci. U. S. A. 116, 19305 (2019)], we performed transition path sampling (TPS) simulations using all atom force fields under moderate driving forces at high pressure, which enabled unbiased atomistic insight into the formation of methane hydrates. The supersaturation in these simulations was influenced by the Laplace pressure induced by the spherical gas reservoir. Here, we investigate the effect of removing this influence. Focusing on the supercooled, supersaturated regime to keep the system size tractable, our TPS simulations indicate that nuclei form amorphous structures below roughly 260 K and crystalline sI structures above 260 K. For these temperatures, the average transition path lengths are significantly longer than in our previous study, pushing the boundaries of what can be achieved with TPS. The temperature to observe a critical nucleus of certain size was roughly 20 K lower compared to a spherical reservoir due to the lower concentration of methane in the solution, yielding a reduced driving force. We analyze the TPS results using a model based on classical nucleation theory. The corresponding free energy barriers are estimated and found to be consistent with previous predictions, thus adding to the overall picture of the hydrate formation process.

Dynamic Dissociation Behaviors of sII Hydrates in Liquid Water by Heating: A Molecular Dynamics Simulation Approach

An understanding of the dynamic behavior of subtle hydrate dissociation in the liquid water phase is fundamental for gas production from marine hydrate reservoirs. Molecular dynamics simulations are performed in this study to investigate the dissociation kinetics of pure propane and binary propane + methane sII hydrates in a liquid water environment. The results show that faster hydrate dissociation rates are observed at higher initial temperatures. The hydrate phase dissociates from the cluster surface to the inside in a layer-by-layer manner under the simulation temperature conditions, which is similar to the behavior of sI hydrates and is independent of the hydrate crystal type. Compared to the binary sII hydrate, the pure sII hydrate dissociates more easily under the same initial temperature conditions, which can be attributed to the stabilizing effect of guest molecules in the hydrate cages. The empty cages collapse in one step, in contrast to the two-step pathway induced by the guest-host interaction. In addition, a hydrocarbon phase forms in the binary hydrate dissociation system instead of nanobubbles. These results can provide molecular-level insights into the dynamic mechanism of hydrate dissociation and theoretical guidance for gas recovery by thermal injection from marine hydrate reservoirs.

Molecular Simulation of the Effects of Cyclic Organic Compounds on the Stability of Lccbm Hydrates

CH₄ can be separated from low-concentration coal bed methane (LCCBM) by using the hydrate-based gas separation (HBGS) method. To study the contribution of different cyclic organic compounds to the separation of CH₄ in LCCBM, an LCCBM hydrate model was constructed. Based on the Monte Carlo and molecular dynamics theory, we simulated the effect of three cyclic organic compounds—cyclopentane (CP), cyclopentanone (CP-one), and cyclopentanol (CP-ol)—on the stability of the LCCBM hydrate at P = 2 MPa, various temperatures, and discussed the structural stability of the hydrate in depth in terms of final snapshots, radial distribution function, mean square displacement, diffusion coefficient, and potential energy change. The results showed that for the CH₄-N₂ LCCMM gas mixture, CP showed the best facilitation effect compared to the other two cyclic compounds by maintaining the stability of the LCCBM hydrate well at T = 293 K. The promotion effect of CP-one is between CP and CP-ol, and when the temperature increases to T = 293 K, the oxygen atoms in the water molecule can maintain the essential stability of the hydrate structure, although the orderliness decreases significantly. Moreover, the structure of the hydrate model containing CP-ol is destroyed at T = 293 K, and the eventual escape of CH₄ and N₂ molecules in solution occurs as bubbles. The research results are important for further exploration of the mechanism of action of cyclic promoter molecules with LCCBM hydrate molecules and promoter preferences.

Mixed Hydrate Nucleation: Molecular Mechanisms and Cage Structures

The molecular-level details of the formation of mixed gas hydrates remain elusive despite their significance for a variety of scientific and industrial applications. In this study, extensive molecular simulations have been performed to examine the behavior of CH₄/H₂S mixed hydrate nucleation utilizing two different simulation setups varying in compositions and temperatures. The observed behavior exhibits similar phenomenology across the various systems once differences in nucleation rates and guest uptake are accounted for. We find that CH₄ is always enriched in the hydrate phase while the aqueous phase is enriched in H₂S. Even with H₂S as a minor component (i.e., 10% mole fraction), the system can mirror the overall nucleation kinetics of pure H₂S hydrate systems with CH₄-dominant nuclei. Through analyses of cages and their transitions, nonstandard cages, particularly those with 12 faces (e.g., 5¹⁰6²), have been found to be key intermediate cage types in the early stage of nucleation. Additionally, we present previously unreported cage types comprising heptagonal faces (e.g., 5⁹6²7¹) as having a significant role in the early-stage gas hydrate structural transitions.

Xenon and Krypton Dissolved in Water Form Nanoblobs: No Evidence for Nanobubbles

We demonstrate, experimentally and by molecular dynamics simulations, that krypton and xenon form nanostructured water-gas domains. High pressure was applied to force the inert gases to dissolve in water following Henry's law, then the liquid was depressurized, centrifuged, and inspected by dynamic light scattering. The observed objects have similar sizes and electrical properties to nanobubbles, but we found that they have fairly neutral buoyancy even at high gravitational fields. We posit that the formed nano objects are not bubbles but blobs, unique structures conceived as clathrate-hydrate precursors, thus resolving the so-called Laplace pressure bubble catastrophe.

Effects of ice and supercooled water on the metastability of methane hydrate: DSC analysis and MD simulations

Methane hydrate (MH) has been viewed as a potential abundant clean energy resource worldwide. Its related technologies play important roles in applications of gas and energy storage, flow assurance of natural gas pipelines etc. Unlike the well-researched stability and decomposition of MH at temperatures above 273 K, the metastability of MH below the ice freezing point, i.e. the anomalous slow decomposition out of thermodynamically stable regions, remains to be unravelled. Studies regarding the influences of ice and supercooled water (SW) on the metastable properties of MH led to varied conclusions, i.e. the as-proposed self-preservation effect and metastable MH-SW-gas equilibrium. In this study, a series of DSC experiments were performed to investigate the thermal stability boundaries and the associated metastable behaviours of MH-ice-gas and MH-SW-gas samples in porous medium. The DSC analysis probed accurate thermal stabilities and characterized decomposition behaviors of the samples, contributing to the hypothesis of potential influences from SW and ice on the metastability of MH. MD simulations were also validated and performed. Active guest-host interactions by the SW layers between MH and gas phases were identified, suggesting probable microscopic configurations related to the metastability of the MH-SW-gas system. Indications of the DSC and MD simulation results call for future high-resolution in situ experimental validations.

The performance of OPC water model in prediction of the phase equilibria of methane hydrate

Molecular dynamics (MD) simulations were performed to determine the three-phase coexistence line of sI methane hydrates. The MD simulations were carried out at four different pressures (4, 10, 40 and 100 MPa) by using direct phase coexistence method. In current simulations, water was described by either TIP4P/Ice or OPC models and methane was described as a simple Lennard-Jones (LJ) interaction site. Lorentz-Berthelot combining rules were used to calculate the parameters of the cross interactions. For OPC model, positive deviations from the energetic Lorentz-Berthelot rule were also considered based on the solubility of methane in water. For TIP4P/Ice water model, the obtained three phase coexistence temperatures showed good agreement with experiment data at higher pressures, which is consistent with previous predictions. For OPC water model, simulations using the classic and the modified LB parameters both showed negative deviations to the experimental values. Our results also indicated that the deviation of the T3 prediction by OPC model not much correlated with the predicted melting point of ice. At 4 MPa, the modified OPC model showed outstanding prediction of hydrate equilibrium temperature, even better than the prediction by TIP4P/Ice. The relative higher accuracy in biomolecular MD of OPC model suggests that this model may have a better performance in hydrate MD simulations of biomolecule-based additives.

Simulation of the carbon dioxide hydrate-water interfacial energy

HYPOTHESIS

Carbon dioxide hydrates are ice-like nonstoichiometric inclusion solid compounds with importance to global climate change, and gas transportation and storage. The thermodynamic and kinetic mechanisms that control carbon dioxide nucleation critically depend on hydrate-water interfacial free energy. Only two independent indirect experiments are available in the literature. Interfacial energies show large uncertainties due to the conditions at which experiments are performed. Under these circumstances, we hypothesize that accurate molecular models for water and carbon dioxide combined with computer simulation tools can offer an alternative but complementary way to estimate interfacial energies at coexistence conditions from a molecular perspective.

CALCULATIONS

We have evaluated the interfacial free energy of carbon dioxide hydrates at coexistence conditions (three-phase equilibrium or dissociation line) implementing advanced computational methodologies, including the novel Mold Integration methodology. Our calculations are based on the definition of the interfacial free energy, standard statistical thermodynamic techniques, and the use of the most reliable and used molecular models for water (TIP4P/Ice) and carbon dioxide (TraPPE) available in the literature.

FINDINGS

We find that simulations provide an interfacial energy value, at coexistence conditions, consistent with the experiments from its thermodynamic definition. Our calculations are reliable since are based on the use of two molecular models that accurately predict: (1) The ice-water interfacial free energy; and (2) the dissociation line of carbon dioxide hydrates. Computer simulation predictions provide alternative but reliable estimates of the carbon dioxide interfacial energy. Our pioneering work demonstrates that is possible to predict interfacial energies of hydrates from a truly computational molecular perspective and opens a new door to the determination of free energies of hydrates.

Molecular behavior of hybrid gas hydrate nucleation: separation of soluble H2S from mixed gas

Soluble H₂S widely exists in natural gas or oil potentially corroding oil/gas pipelines. Furthermore, it can affect the hydrate formation condition, resulting in pipeline blockage; the nucleation mechanism from mixed gas including H₂S is still largely unclear. Molecular dynamics simulations were performed to reveal the effects of different initial mixed H₂S/CH₄ compositions on the hydrate nucleation and growth process. The geometric details of the nanobubbles and gas composition in the nanobubbles were analyzed; the size of the nanobubbles was found to decrease from 3.4 nm to 1.4 nm. With the increase in the initial H₂S proportion, the diameter of the nanobubbles decreased; more guest molecules were dissolved in the water, which improved the initial concentration of guest molecules in the water. A multi-site nucleation process was observed, and separate hydrate clusters could grow independently until the simulation box limited their growth due to high local H₂S concentration as a potential nucleation location. When the initial proportion of mixed gas approaches, H₂S preferred to occupy and stabilize the incipient cage. Moreover, 5¹², 4¹5¹⁰6², and 5¹²6² cages accounted for approximately 95% of the first hydrate cage. Nucleation rates were shown to increase from 4.62 × 10²⁴ to 9.438 × 10²⁶ nuclei cm^-3 s^-1. The present high subcooling and H₂S concentration provided a high driving force to promote mixed hydrate nucleation and growth. The proportion of cages occupied by H₂S increased with increasing initial H₂S proportion, but the largest enrichment factor of 1.38 occurred at 10% initial H₂S/CH₄ mixed gas.

Experimental Characterization of Memory Effect, Anomalous Self-Preservation and Ice-Hydrate Competition, during Methane-Hydrates Formation and Dissociation in a Lab-Scale Apparatus

This study explores the process of methane hydrate formation and dissociation in a small-scale confined environment and in the presence of a porous sediment. The research is focused on answering the shortage of information about the intrinsic properties of the hydrate formation and dissociation processes, such as memory effect and anomalous self-preservation, in a lab-scale apparatus. Experiments were carried out consecutively and with the same gas–water mixture. The temperature reached during dissociation was high enough to ensure the complete dissolution of water cages. At the same time, it was sufficiently low to keep the system able to retain the memory of the previous formation of hydrates. Different well-known phenomena were observed and described; memory effect, anomalous self-preservation and competition between ice and hydrates were shown in detail. Experiments confirmed that the memory effect improves the process mainly during the initial nucleation phase, while it does not provide significant changes in the following massive growth phase. Finally, experiments proved that the formation process can be divided in two different steps: the initial intense growth, due to the small difference in local equilibrium conditions, and the subsequent asymptotic growth, which continues until the process is completed.

Atomistic Insights into the Droplet Size Evolution during Self-Microemulsification

Microemulsions have been attracting great attention for their importance in various fields, including nanomaterial fabrication, food industry, drug delivery, and enhanced oil recovery. Atomistic insights into the self-microemulsifying process and the underlying mechanisms are crucial for the design and tuning of the size of microemulsion droplets toward applications. In this work, coarse-grained models were used to investigate the role that droplet sizes played in the preliminary self-microemulsifying process. Time evolution of liquid mixtures consisting of several hundreds of water/surfactant/oil droplets was resolved in large-scale simulations. By monitoring the size variation of the microemulsion droplets in the self-microemulsifying process, the dynamics of diameter distribution of water/surfactant/oil droplets were studied. The underlying mass transport mechanisms responsible for droplet size evolution and stability were elucidated. Specifically, temperature effects on the droplet size were clarified. This work provides the knowledge of the self-microemulsification of water-in-oil microemulsions at the nanoscale. The results are expected to serve as guidelines for practical strategies for preparing a microemulsion system with desirable droplet sizes and properties.

Three-body aggregation of guest molecules as a key step in methane hydrate nucleation and growth

Gas hydrates have an important role in environmental and astrochemistry, as well as in energy materials research. Although it is widely accepted that gas accumulation is an important and necessary process during hydrate nucleation, how guest molecules aggregate remains largely unknown. Here, we have performed molecular dynamics simulations to clarify the nucleation path of methane hydrate. We demonstrated that methane gather with a three-body aggregate pattern corresponding to the free energy minimum of three-methane hydrophobic interaction. Methane molecules fluctuate around one methane which later becomes the central gas molecule, and when several methanes move into the region within 0.8 nm of the potential central methane, they act as directional methane molecules. Two neighbor directional methanes and the potential central methane form a three-body aggregate as a regular triangle with a distance of ~6.7 Å which is well within the range of typical methane-methane distances in hydrates or in solution. We further showed that hydrate nucleation and growth is inextricably linked to three-body aggregates. By forming one, two, and three three-body aggregates, the possibility of hydrate nucleation at the aggregate increases from 3/6, 5/6 to 6/6. The results show three-body aggregation of guest molecules is a key step in gas hydrate formation.

Effect of Cage Occupancy on Stability and Decomposition of Methane Hydrate

Gas hydrates usually contain a certain number of empty cages that will both affect the hydrate stability and reduce the gas storage capacity. In this work, by MD simulations, we found that the hydrate stability is related to the cage occupancy, the empty cage types, and especially the distribution of empty cages. With the decrease of overall occupancy, the stability of hydrate becomes worse. Under the same overall occupancy, the more concentrated the empty cages are, the more unstable the hydrate is and hence the faster it decomposes. The methane molecules may migrate between distorted cages during the decomposition, resulting in a temporary increase in the stability of hydrate. Hydrates with different empty cage distributions show different decomposition mechanisms: when empty cages are concentrated, the melting rate is fast first due to the rapid decomposition of empty cages, but the remaining filled cages will reduce the melting rate; when empty cages are separated on the contrary, the early melting is slow because of the high local occupancy, and the following melting will be accelerated because of the high melting surface area. It indicates that the empty cage distribution plays a controlling role in hydrate decomposition kinetics at different stages.

Molecular Origins of Deformation in Amorphous Methane Hydrates

Water and methane can stay together under low temperature and high pressure in the forms of liquid solutions and crystalline solids. From liquid and gaseous states to crystalline solids or the contrary processes, amorphous methane hydrates can occur in these evolution scenarios. Herein, mechanical properties of amorphous methane hydrates are explored for the first time to bridge the gap between mechanical responses of monocrystalline and polycrystalline methane hydrates. Our results demonstrate that mechanical properties of amorphous methane hydrates are strongly governed by our original proposed order parameter, namely, normalized hydrogen-bond directional order parameter. Followed by this important achievement, a multistep deformation mechanism core is proposed to explain mechanical properties of amorphous methane hydrates. Through an extensive detailed analysis of amorphous methane hydrates, our simulation results not only greatly enlarge our fundamental understanding for mechanical responses of amorphous methane hydrates in geological systems but also offer a fresh perspective in structure-property topics of solid materials in future science and technology.

An extended autoencoder model for reaction coordinate discovery in rare event molecular dynamics datasets

The reaction coordinate (RC) is the principal collective variable or feature that determines the progress along an activated or reactive process. In a molecular simulation using enhanced sampling, a good description of the RC is crucial for generating sufficient statistics. Moreover, the RC provides invaluable atomistic insight into the process under study. The optimal RC is the committor, which represents the likelihood of a system to evolve toward a given state based on the coordinates of all its particles. As the interpretability of such a high dimensional function is low, a more practical approach is to describe the RC by some low-dimensional molecular collective variables or order parameters. While several methods can perform this dimensionality reduction, they usually require a preselection of these low-dimension collective variables (CVs). Here, we propose to automate this dimensionality reduction using an extended autoencoder, which maps the input (many CVs) onto a lower-dimensional latent space, which is subsequently used for the reconstruction of the input as well as the prediction of the committor function. As a consequence, the latent space is optimized for both reconstruction and committor prediction and is likely to yield the best non-linear low-dimensional representation of the committor. We test our extended autoencoder model on simple but nontrivial toy systems, as well as extensive molecular simulation data of methane hydrate nucleation. The extended autoencoder model can effectively extract the underlying mechanism of a reaction, make reliable predictions about the committor of a given configuration, and potentially even generate new paths representative for a reaction.

Design and applications of surfaces that control the accretion of matter

Surfaces that provide control over liquid, solid, or vapor accretion provide an evolutionary advantage to numerous plants, insects, and animals. Synthetic surfaces inspired by these natural surfaces can have a substantial impact on diverse commercial applications. Engineered liquid and solid repellent surfaces are often designed to impart control over a single state of matter, phase, or fouling length scale. However, surfaces used in diverse real-world applications need to effectively control the accrual of matter across multiple phases and fouling length scales. We discuss the surface design strategies aimed at controlling the accretion of different states of matter, particularly those that work across multiple length scales and different foulants. We also highlight notable applications, as well as challenges associated with these designer surfaces' scale-up and commercialization.