Can Amorphous Nuclei Grow Crystalline Clathrates? The Size and Crystallinity of Critical Clathrate Nuclei

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.

A Coordination-Derived Cerium-Based Amorphous-Crystalline Heterostructure with High Electrocatalytic Oxygen Evolution Activity

The rational design of heterogeneous catalysts is crucial for achieving optimal physicochemical properties and high electrochemical activity. However, the development of new amorphous-crystalline heterostructures is significantly more challenging than that of the existing crystalline-crystalline heterostructures. To overcome these issues, a coordination-assisted strategy that can help fabricate an amorphous NiO/crystalline NiCeOx (a-NiO/c-NiCeOx) heterostructure is reported herein. The coordination geometry of the organic ligands plays a pivotal role in permitting the formation of coordination polymers with high Ni contents. This consequently provides an opportunity for enabling the supersaturation of Ni in the NiCeOx structure during annealing, leading to the endogenous spillover of Ni from the depths of NiCeOx to its surface. The resulting heterostructure, featuring strongly coupled amorphous NiO and crystalline NiCeOx, exhibits harmonious interactions in addition to low overpotentials and high catalytic stability in the oxygen evolution reaction (OER). Theoretical calculations prove that the amorphous-crystalline interfaces facilitate charge transfer, which plays a critical role in regulating the local electron density of the Ni sites, thereby promoting the adsorption of oxygen-based intermediates on the Ni sites and lowering the dissociation-related energy barriers. Overall, this study underscores the potential of coordinating different metal ions at the molecular level to advance amorphous-crystalline heterostructure design.

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.

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.

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.

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.

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.

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.

Atomic-Scale Tracking of Dynamic Nucleation and Growth of an Interfacial Lead Nanodroplet

Revealing the evolutional pathway of the nucleation and crystallization of nanostructures at the atomic scale is crucial for understanding the complex growth mechanisms at the early stage of new substances and spices. Real-time discrimination of the atomic mechanism of a nanodroplet transition is still a formidable challenge. Here, taking advantage of the high temporal and spatial resolution of transmission electron microscopy, the detailed growth pathway of Pb nanodroplets at the early stage of nucleation was directly observed by employing electron beams to induce the nucleation, growth, and fusion process of Pb nanodroplets based on PbTiO3 nanowires. Before the nucleation of Pb nanoparticles, the atoms began to precipitate when they were irradiated by electrons, forming a local crystal structure, and then rapidly and completely crystallized. Small nanodroplets maintain high activity and high density and gradually grow and merge into stable crystals. The whole process was recorded and imaged by HRTEM in real time. The growth of Pb nanodroplets advanced through the classical path and instantaneous droplet coalescence. These results provide an atomic-scale insight on the dynamic process of solid/solid interface, which has implications in thin-film growth and advanced nanomanufacturing.

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.

Double Life of Methanol: Experimental Studies and Nonequilibrium Molecular-Dynamics Simulation of Methanol Effects on Methane-Hydrate Nucleation

We have investigated systematically and statistically methanol-concentration effects on methane-hydrate nucleation using both experiment and restrained molecular-dynamics simulation, employing simple observables to achieve an initially homogeneous methane-supersaturated solution particularly favorable for nucleation realization in reasonable simulation times. We observe the pronounced "bifurcated" character of the nucleation rate upon methanol concentration in both experiments and simulation, with promotion at low concentrations and switching to industrially familiar inhibition at higher concentrations. Higher methanol concentrations suppress hydrate growth by in-lattice methanol incorporation, resulting in the formation of "defects", increasing the energy of the nucleus. At low concentrations, on the contrary, the detrimental effect of defects is more than compensated for by the beneficial contribution of CH₃ in easing methane incorporation in the cages or replacing it altogether.

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.

A novel hybrid method for the calculation of methane hydrate-water interfacial tension along the three-phase (hydrate-liquid water-vapor) equilibrium line

We use a novel hybrid method to explore the temperature dependence of the solid-liquid interfacial tension of a system that consists of solid methane hydrate and liquid water. The calculated values along the three-phase (hydrate-liquid water-vapor) equilibrium line are obtained through the combination of available experimental measurements and computational results that are based on approaches at the atomistic scale, including molecular dynamics and Monte Carlo. An extensive comparison with available experimental and computational studies is performed, and a critical assessment and re-evaluation of previously reported data is presented.

Reduced phase stability and faster formation/dissociation kinetics in confined methane hydrate

The mechanisms involved in the formation/dissociation of methane hydrate confined at the nanometer scale are unraveled using advanced molecular modeling techniques combined with a mesoscale thermodynamic approach. Using atom-scale simulations probing coexistence upon confinement and free energy calculations, phase stability of confined methane hydrate is shown to be restricted to a narrower temperature and pressure domain than its bulk counterpart. The melting point depression at a given pressure, which is consistent with available experimental data, is shown to be quantitatively described using the Gibbs-Thomson formalism if used with accurate estimates for the pore/liquid and pore/hydrate interfacial tensions. The metastability barrier upon hydrate formation and dissociation is found to decrease upon confinement, therefore providing a molecular-scale picture for the faster kinetics observed in experiments on confined gas hydrates. By considering different formation mechanisms-bulk homogeneous nucleation, external surface nucleation, and confined nucleation within the porosity-we identify a cross-over in the nucleation process; the critical nucleus formed in the pore corresponds either to a hemispherical cap or to a bridge nucleus depending on temperature, contact angle, and pore size. Using the classical nucleation theory, for both mechanisms, the typical induction time is shown to scale with the pore volume to surface ratio and hence the pore size. These findings for the critical nucleus and nucleation rate associated with such complex transitions provide a means to rationalize and predict methane hydrate formation in any porous media from simple thermodynamic data.

Ranking the Efficiency of Gas Hydrate Anti-agglomerants through Molecular Dynamic Simulations

Using both computational and experimental methods, the capacity of four different surfactant molecules to inhibit the agglomeration of sII hydrate particles was assessed. The computational simulations were carried out using both steered and non-steered molecular dynamics (MD), simulating the coalescence process of a hydrate slab and a water droplet, both covered with surfactant molecules. The surfactants were ranked according to free energy calculations (steered MD) and the number of agglomeration events (non-steered MD). The experimental work was based on rocking cell measurements, determining the minimum effective dose necessary to inhibit agglomeration. Overall, good agreement was obtained between the performance predicted by the simulations and the experimental measurements. Moreover, the simulations allowed us to gain additional insights that are not directly accessible via experiments, such as an analysis of the mass density profiles, the diffusion coefficients, or the orientations of the long tails.

Iterative Cup Overlapping: An Efficient Identification Algorithm for Cage Structures of Amorphous Phase Hydrates

Molecular dynamics studies have revealed that the nucleation pathway of clathrate hydrates involves the evolution from amorphous to crystalline hydrates. In this study, complete cages are further classified into the standard edge-saturated cages (SECs) and nonstandard edge-saturated cages (non-SECs). Centered on studying the structure and evolution of non-SECs and SECs, we propose a novel and efficient algorithm, iterative cup overlapping (ICO), to monitor hydrate nucleation and growth in molecular simulations by identifying SECs and discuss possible causes of the instability of non-SECs. Manipulation of topological information makes it possible for ICO to avoid the repeated searches for identified cages and deduce all SECs with low time costs, improving the efficiency of identification significantly. The accuracy and efficiency of ICO were verified by comparing the identification results with other well-proven algorithms. Furthermore, it was found that non-SECs have short lifetimes and eventually decompose or reorganize into more stable structures. Some evidence suggests that the instability of non-SECs is closely related to the hydrogen-bonding configuration of water-ring aggregations that they contain. The spontaneous evolution of the hydrogen-bonding network into the tetrahedral network may be the main factor that causes the conversion of QWRAs and the evolution of non-SECs.

Rate Prediction for Homogeneous Nucleation of Methane Hydrate at Moderate Supersaturation Using Transition Interface Sampling

The crystallization of methane hydrates via homogeneous nucleation under natural, moderate conditions is of both industrial and scientific relevance, yet still poorly understood. Predicting the nucleation rates at such conditions is notoriously difficult due to high nucleation barriers, and requires, besides an accurate molecular model, enhanced sampling. Here, we apply the transition interface sampling technique, which efficiently computes the exact rate of nucleation by generating ensembles of unbiased dynamical trajectories crossing predefined interfaces located between the stable states. Using an accurate atomistic force field and focusing on specific conditions of 280 K and 500 bar, we compute for nucleation directly into the sI crystal phase at a rate of ∼10^-17 nuclei per nanosecond per simulation volume or ∼10² nuclei per second per cm³, in agreement with consensus estimates for nearby conditions. As this is most likely fortuitous, we discuss the causes of the large differences between our results and previous simulation studies. Our work shows that it is now possible to compute rates for methane hydrates at moderate supersaturation, without relying on any assumptions other than the force field.

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.

Effects of Layer-Charge Distribution of 2:1 Clay Minerals on Methane Hydrate Formation: A Molecular Dynamics Simulation Study

Molecular dynamics simulations were used to investigate the effects of the external surface of a 2:1 clay mineral with different charge amounts and charge locations on CH₄ hydrate formation. The results showed that 5¹², 5¹²6², 5¹²6³, and 5¹²6⁴ were formed away from the clay mineral surface. The surface of the clay mineral with high- and low-charge layers was occupied by Na⁺ to form various distributions of outer- and inner-sphere hydration structures, respectively. The adsorbed Na⁺ on the high-charge layer surface reduced the H₂O activity by disturbing the hydrogen bond network, resulting in low tetrahedral arrangement of H₂O molecules near the layer surface, which inhibited CH₄ hydrate formation. However, more CH₄ molecules were adsorbed onto the vacancy in the Si-O rings of a neutral-charge layer to form semicage structures. Thus, the order parameter of H₂O molecules near this surface indicated that the arrangement of H₂O molecules resulted in a more optimal tetrahedral structure for CH₄ hydrate formation than that near the negatively charged layer surface. Different nucleation mechanisms of the CH₄ hydrate on external surfaces of clay mineral models were observed. For clay minerals with negatively charged layers (i.e., high and low charge), the homogeneous nucleation of the CH₄ hydrate occurred away from the surface. For a clay mineral with a neutral-charge layer, the CH₄ hydrate could nucleate either in the bulk-like solution homogeneously or at the clay mineral-H₂O interface heterogeneously.

Gas hydrates in sustainable chemistry

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

Unbiased atomistic insight in the competing nucleation mechanisms of methane hydrates

Mixtures of methane gas and water can form ice-like solid methane hydrates via homogeneous nucleation at natural, moderate conditions. Understanding the formation of the different hydrate polymorphs, required for improved control of crystallization, is hampered by limited experimental resolution. Direct molecular dynamics simulations could provide insight, but it would require computation times beyond the age of the Universe for a single nucleation event to take place. Yet, the nucleation event itself, while rare, occurs fast. Therefore, we sample and examine ensembles of rare unbiased nucleation trajectories. Detailed analysis shows how selection between competing amorphous and crystalline polymorph formation mechanisms takes place. The conclusions shed light onto the formation of clathrate hydrates.

Methane hydrates have important industrial and climate implications, yet their formation via homogeneous nucleation under natural, moderate conditions is poorly understood. Obtaining such understanding could lead to improved control of crystallization, as well as insight into polymorph selection in general, but is hampered by limited experimental resolution. Direct molecular dynamics simulations using atomistic force fields could provide such insight, but are not feasible for moderate undercooling, due to the rare event nature of nucleation. Instead, we harvest ensembles of the rare unbiased nucleation trajectories by employing transition path sampling. We find that with decreasing undercooling the mechanism shifts from amorphous to crystalline polymorph formation. At intermediate temperature the 2 mechanisms compete. Reaction coordinate analysis reveals the amount of a specific methane cage type is crucial for crystallization, while irrelevant for amorphous solids. Polymorph selection is thus governed by kinetic accessibility of the correct cage type and, moreover, occurs at precritical nucleus sizes, apparently against Ostwald’s step rule. We argue that these results are still in line with classical nucleation theory. Our findings illuminate how selection between competing methane hydrate polymorphs occurs and might generalize to other hydrates and molecular crystal formation.

Free energy of conformational isomers: The case of gapped DNA duplexes

Liquid-crystalline phases in all-DNA systems have been extensively studied in the past and although nematic, cholesteric and columnar mesophases have been observed, the smectic phase remained elusive. Recently, it has been found evidence of a smectic-A ordering in an all-DNA system, where the constituent particles, which are gapped DNA duplexes, resemble chain-sticks. It has been argued that in the smectic-A phase these DNA chain-sticks should be folded as a means to suppress aggregate polydispersity and excluded volume. Nevertheless, if initial crystalline configurations are prepared in silico with gapped DNA duplexes either fully unfolded or fully folded by carrying out computer simulations one can end up with two different phases having at the same concentration and temperature the majority of gapped DNA duplexes either folded or unfolded. This result suggests that these two phases have a small free energy difference, since no transition is observed from one to the other within the simulation time span. In the present manuscript, we assess which of these two phases is thermodynamically stable through a suitable protocol based on thermodynamic integration. Our method is rather general and it can be used to discriminate stable states from metastable ones of comparable free energy.

Characterizing key features in the formation of ice and gas hydrate systems

Crystallization in liquids is critical to a range of important processes occurring in physics, chemistry and life sciences. In this article, we review our efforts towards understanding the crystallization mechanisms, where we focus on theoretical modelling and molecular simulations applied to ice and gas hydrate systems. We discuss the order parameters used to characterize molecular ordering processes and how different order parameters offer different perspectives of the underlying mechanisms of crystallization. With extensive simulations of water and gas hydrate systems, we have revealed unexpected defective structures and demonstrated their important roles in crystallization processes. Nucleation of gas hydrates can in most cases be characterized to take place in a two-step mechanism where the nucleation occurs via intermediate metastable precursors, which gradually reorganizes to a stable crystalline phase. We have examined the potential energy landscapes explored by systems during nucleation, and have shown that these landscapes are rugged and funnel-shaped. These insights provide a new framework for understanding nucleation phenomena that has not been addressed in classical nucleation theory. This article is part of the theme issue 'The physics and chemistry of ice: scaffolding across scales, from the viability of life to the formation of planets'.

Following the nucleation pathway from disordered liquid to gyroid mesophase

Mesophases have order intermediate between liquids and crystals and arise in systems with frustration, such as surfactants, block copolymers, and Janus nanoparticles. The gyroid mesophase contains two interpenetrated, nonintersecting chiral networks that give it properties useful for photonics. It is challenging to nucleate a gyroid from the liquid. Elucidating the reaction coordinate for gyroid nucleation could assist in designing additives that facilitate the formation of the mesophase. However, the complexity of the gyroid structure and the extreme weakness of the first-order liquid to gyroid transition make this a challenging quest. Here, we investigate the pathway and transition states for the nucleation of a gyroid from the liquid in molecular simulations with a mesogenic binary mixture. We find that the gyroid nuclei at the transition states have a large degree of positional disorder and are not compact, consistent with the low surface free energy of the liquid-gyroid interface. A combination of bond-order parameters for the minor component is best to describe the passage from liquid to gyroid, among those we consider. The committor analyses, however, show that this best coordinate is not perfect and suggests that accounting for the relative ordering of the two interpenetrated networks in infant nuclei, as well as for signatures of ordering in the major component of the mesophase, would improve the accuracy of the reaction coordinate for gyroid formation and its use to evaluate nucleation barriers. To our knowledge, this study is the first to investigate the reaction coordinate and critical nuclei for the formation of any mesophase from an amorphous phase.

How Do Surfactants Control the Agglomeration of Clathrate Hydrates?

Clathrate hydrates can spontaneously form under typical conditions found in oil and gas pipelines. The agglomeration of clathrates into large solid masses plugs the pipelines, posing adverse safety, economic, and environmental threats. Surfactants are customarily used to prevent the aggregation of clathrate particles and their coalescence with water droplets. It is generally assumed that a large contact angle between the surfactant-covered clathrate and water is a key predictor of the antiagglomerant performance of the surfactant. Here we use molecular dynamic simulations to investigate the structure and dynamics of surfactant films at the clathrate-oil interface, and their impact on the contact angle and coalescence between water droplets and hydrate particles. In agreement with the experiments, the simulations predict that surfactant-covered clathrate-oil interfaces are oil wet but super-hydrophobic to water. Although the water contact angle determines the driving force for coalescence, we find that a large contact angle is not sufficient to predict good antiagglomerant performance of a surfactant. We conclude that the length of the surfactant molecules, the density of the interfacial film, and the strength of binding of its molecules to the clathrate surface are the main factors in preventing the coalescence and agglomeration of clathrate particles with water droplets in oil. Our analysis provides a molecular foundation to guide the molecular design of effective clathrate antiagglomerants.

The Clathrate-Water Interface Is Oleophilic

The slow nucleation of clathrate hydrates is a central challenge for their use in the storage and transportation of natural gas. Molecules that strongly adsorb to the clathrate-water interface decrease the crystal-water surface tension, lowering the barrier for clathrate nucleation. Surfactants are widely used to promote the nucleation and growth of clathrate hydrates. It has been proposed that these amphiphilic molecules bind to the clathrate surface via hydrogen bonding. However, recent studies reveal that PVCap, an amphiphilic polymer, binds to clathrates through hydrophobic moieties. Here we use molecular dynamic simulations and theory to investigate the mode and strength of binding of surfactants to the clathrate-water interface and their effect on the nucleation rate. We find that the surfactants bind to the clathrate-water interface exclusively through their hydrophobic tails. The binding is strong, driven by the entropy of dehydration of the alkyl chain, as it penetrates empty cavities at the hydrate surface. The hydrophobic attraction of alkyl groups to the clathrate surface also results in strong adsorption of alkanes. We identify two regimes for the binding of surfactants as a function of their density at the hydrate surface, which we interpret to correspond to the two steps of the Langmuir adsorption isotherm observed in experiments. Our results indicate that hydrophobic attraction to the clathrate-water interface is key for the design of soluble additives that promote the nucleation of hydrates. We use the calculated adsorption coefficients to estimate the concentration of sodium dodecyl sulfate (SDS) required to reach nucleation rates for methane hydrate consistent with those measured in experiments. To our knowledge, this study is the first to quantify the effect of surfactant concentration in the nucleation rate of clathrate hydrates.

Free energy landscape and molecular pathways of gas hydrate nucleation

Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p_B histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p_B histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.

Overview: Nucleation of clathrate hydrates

Molecular level knowledge of nucleation and growth of clathrate hydrates is of importance for advancing fundamental understanding on the nature of water and hydrophobic hydrate formers, and their interactions that result in the formation of ice-like solids at temperatures higher than the ice-point. The stochastic nature and the inability to probe the small length and time scales associated with the nucleation process make it very difficult to experimentally determine the molecular level changes that lead to the nucleation event. Conversely, for this reason, there have been increasing efforts to obtain this information using molecular simulations. Accurate knowledge of how and when hydrate structures nucleate will be tremendously beneficial for the development of sustainable hydrate management strategies in oil and gas flowlines, as well as for their application in energy storage and recovery, gas separation, carbon sequestration, seawater desalination, and refrigeration. This article reviews various aspects of hydrate nucleation. First, properties of supercooled water and ice nucleation are reviewed briefly due to their apparent similarity to hydrates. Hydrate nucleation is then reviewed starting from macroscopic observations as obtained from experiments in laboratories and operations in industries, followed by various hydrate nucleation hypotheses and hydrate nucleation driving force calculations based on the classical nucleation theory. Finally, molecular simulations on hydrate nucleation are discussed in detail followed by potential future research directions.

Formation of Methane Hydrate in the Presence of Natural and Synthetic Nanoparticles

Natural gas hydrates occur widely on the ocean-bed and in permafrost regions, and have potential as an untapped energy resource. Their formation and growth, however, poses major problems for the energy sector due to their tendency to block oil and gas pipelines, whereas their melting is viewed as a potential contributor to climate change. Although recent advances have been made in understanding bulk methane hydrate formation, the effect of impurity particles, which are always present under conditions relevant to industry and the environment, remains an open question. Here we present results from neutron scattering experiments and molecular dynamics simulations that show that the formation of methane hydrate is insensitive to the addition of a wide range of impurity particles. Our analysis shows that this is due to the different chemical natures of methane and water, with methane generally excluded from the volume surrounding the nanoparticles. This has important consequences for our understanding of the mechanism of hydrate nucleation and the design of new inhibitor molecules.

Fast methane diffusion at the interface of two clathrate structures

Methane hydrates naturally form on Earth and in the interiors of some icy bodies of the Universe, and are also expected to play a paramount role in future energy and environmental technologies. Here we report experimental observation of an extremely fast methane diffusion at the interface of the two most common clathrate hydrate structures, namely clathrate structures I and II. Methane translational diffusion—measured by quasielastic neutron scattering at 0.8 GPa—is faster than that expected in pure supercritical methane at comparable pressure and temperature. This phenomenon could be an effect of strong confinement or of methane aggregation in the form of micro-nanobubbles at the interface of the two structures. Our results could have implications for understanding the replacement kinetics during sI–sII conversion in gas exchange experiments and for establishing the methane mobility in methane hydrates embedded in the cryosphere of large icy bodies in the Universe.

Methane dynamics at the interface of ice clathrate structures is expected to play a role in phenomena ranging from gas exchange to methane mobility in planetary cryospheres. Here, the authors observe extremely fast methane diffusion at the interface of the two most common clathrate hydrate structures.

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

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

In situ study on atomic mechanism of melting and freezing of single bismuth nanoparticles

Experimental study of the atomic mechanism in melting and freezing processes remains a formidable challenge. We report herein on a unique material system that allows for in situ growth of bismuth nanoparticles from the precursor compound SrBi₂Ta₂O₉ under an electron beam within a high-resolution transmission electron microscope (HRTEM). Simultaneously, the melting and freezing processes within the nanoparticles are triggered and imaged in real time by the HRTEM. The images show atomic-scale evidence for point defect induced melting, and a freezing mechanism mediated by crystallization of an intermediate ordered liquid. During the melting and freezing, the formation of nucleation precursors, nucleation and growth, and the relaxation of the system, are directly observed. Based on these observations, an interaction-relaxation model is developed towards understanding the microscopic mechanism of the phase transitions, highlighting the importance of cooperative multiscale processes.