Molecular dynamics methodology to investigate steady-state heterogeneous crystal growth

Molecular dynamics of the spontaneous generation mechanism of natural gas hydrates during methane nanobubble rupture

Natural gas hydrates have garnered significant attention as a potential new source of alternative energy, and understanding their formation mechanism is of paramount importance for efficient utilization and pipeline transportation. However, there is no consensus among academics on the formation mechanism of natural gas hydrates. In this paper, we propose a method for promoting the rapid formation of natural gas hydrates based on the rupture of methane nanobubbles, which creates local high temperature and pressure to facilitate the mixing of methane and water. The rapid decrease in system temperature and pressure during the process further enhances the formation of gas hydrates. Using molecular dynamics simulations, we theoretically verify the formation of natural gas hydrates. Our results indicate that the instantaneous rupture of methane nanobubbles induced by shock waves leads to a dramatic increase in the local molecular motion velocity around the bubbles. This results in extreme local high temperature and high pressure, leading to complete mixing of methane and water and rapid formation of gas hydrates during the cooling and pressure drop of the mixture. We confirm our findings by analyzing F3-order parameters, F4-order parameters, and water cage statistics.

Non-Equilibrium Modeling of Concentration-Driven processes with Constant Chemical Potential Molecular Dynamics Simulations

ConspectusConcentration-driven processes in solution, i.e., phenomena that are sustained by persistent concentration gradients, such as crystallization and surface adsorption, are fundamental chemical processes. Understanding such phenomena is crucial for countless applications, from pharmaceuticals to biotechnology. Molecular dynamics (MD), both in- and out-of-equilibrium, plays an essential role in the current understanding of concentration-driven processes. Computational costs, however, impose drastic limitations on the accessible scale of simulated systems, hampering the effective study of such phenomena. In particular, due to these size limitations, closed system MD of concentration-driven processes is affected by solution depletion/enrichment that unavoidably impacts the dynamics of the chemical phenomena under study. As a notable example, in simulations of crystallization from solution, the transfer of monomers between the liquid and crystal phases results in a gradual depletion/enrichment of solution concentration, altering the driving force for phase transition. In contrast, this effect is negligible in experiments, given the macroscopic size of the solution volume. Because of these limitations, accurate MD characterization of concentration-driven phenomena has proven to be a long-standing simulation challenge. While disparate equilibrium and nonequilibrium simulation strategies have been proposed to address the study of such processes, the methodologies are in continuous development.In this context, a novel simulation technique named constant chemical potential molecular dynamics (CμMD) was recently proposed. CμMD employs properly designed, concentration-dependent external forces that regulate the flux of solute species between selected subregions of the simulation volume. This enables simulations of systems under a constant chemical drive in an efficient and straightforward way. The CμMD scheme was originally applied to the case of crystal growth from solution and then extended to the simulation of various physicochemical processes, resulting in new variants of the method. This Account illustrates the CμMD method and the key advances enabled by it in the framework of in silico chemistry. We review results obtained in crystallization studies, where CμMD allows growth rate calculations and equilibrium shape predictions, and in adsorption studies, where adsorption thermodynamics on porous or solid surfaces was correctly characterized via CμMD. Furthermore, we will discuss the application of CμMD variants to simulate permeation through porous materials, solution separation, and nucleation upon fixed concentration gradients. While presenting the numerous applications of the method, we provide an original and comprehensive assessment of concentration-driven simulations using CμMD. To this end, we also shed light on the theoretical and technical foundations of CμMD, underlining the novelty and specificity of the method with respect to existing techniques while stressing its current limitations. Overall, the application of CμMD to a diverse range of fields provides new insight into many physicochemical processes, the in silico study of which has been hitherto limited by finite-size effects. In this context, CμMD stands out as a general-purpose method that promises to be an invaluable simulation tool for studying molecular-scale concentration-driven phenomena.

Spotlight onto surfactant-steam-bitumen interfacial behavior via molecular dynamics simulation

Heavy oil and bitumen play a vital role in the global energy supply, and to unlock such resources, thermal methods, e.g., steam injection, are applied. To improve the performance of these methods, different additives, such as air, solvents, and chemicals, can be used. As a subset of chemicals, surfactants are one of the potential additives for steam-based bitumen recovery methods. Molecular interactions between surfactant/steam/bitumen have not been addressed in the literature. This paper investigates molecular interactions between anionic surfactants, steam, and bitumen in high-temperature and high-pressure conditions. For this purpose, a real Athabasca oil sand composition is employed to assess the phase behavior of surfactant/steam/bitumen under in-situ steam-based bitumen recovery. Two different asphaltene architectures, archipelago and Island, are used to examine the effect of asphaltene type on bitumen's interfacial behavior. The influence of having sulfur heteroatoms in a resin structure and a benzene ring's effect in an anionic surfactant structure on surfactant-steam-bitumen interactions are investigated systematically. The outputs are supported by different analyses, including radial distribution functions (RDFs), mean squared displacement (MSD), radius of gyration, self-diffusion coefficient, solvent accessible surface area (SASA), interfacial thickness, and interaction energies. According to MD outputs, adding surfactant molecules to the steam phase improved the interaction energy between steam and bitumen. Moreover, surfactants can significantly improve steam emulsification capability by decreasing the interfacial tension (IFT) between bitumen and the steam phase. Asphaltene architecture has a considerable effect on the interfacial behavior in such systems. This study provides a better and more in-depth understanding of surfactant-steam-bitumen systems and spotlights the interactions between bitumen fractions and surfactant molecules under thermal recovery conditions.

Formation of hot ice caused by carbon nanobrushes. II. Dependency on the radius of nanotubes

Stable crystalline structures of confined water can be different from bulk ice. In Paper I [T. Yagasaki et al., J. Chem. Phys. 151, 064702 (2019)] of this study, it was shown, using molecular dynamics (MD) simulations, that a zeolite-like ice structure forms in nanobrushes consisting of (6,6) carbon nanotubes (CNTs) when the CNTs are located in a triangle arrangement. The melting temperature of the zeolite-like ice structure is much higher than the melting temperature of ice I_h when the distance between the surfaces of CNTs is ∼0.94 nm, which is the best spacing for the bilayer structure of water. In this paper, we perform MD simulations of nanobrushes of CNTs that are different from (6,6) CNTs in radius. Several new porous ice structures form spontaneously in the MD simulations. A stable porous ice forms when the radius of its cavities matches the radius of the CNTs well. All cylindrical porous ice structures found in this study can be decomposed into a small number of structural blocks. We provide a new protocol to classify cylindrical porous ice crystals on the basis of this decomposition.

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'.

Multiple binding modes of a moderate ice-binding protein from a polar microalga

Ice-binding proteins (IBPs) produced by cold-tolerant organisms interact with ice and strongly control crystal growth. The molecular basis for the different magnitudes of activity displayed by various IBPs (moderate and hyperactive) has not yet been clarified. Previous studies questioned whether the moderate activity of some IBPs relies on their weaker binding modus to the ice surface, compared to hyperactive IBPs, rather than relying on binding only to selected faces of the ice crystal. We present the structure of one moderate IBP from the sea-ice diatom Fragilariopsis cylindrus (fcIBP) as determined by X-ray crystallography and investigate the protein's binding modes to the growing ice-water interface using molecular dynamics simulations. The structure of fcIBP is the IBP-1 fold, defined by a discontinuous β-solenoid delimitated by three faces (A, B and C-faces) and braced by an α-helix. The fcIBP structure shows capping loops on both N- and C-terminal parts of the solenoid. We show that the protein adsorbs on both the prism and the basal faces of ice crystals, confirming experimental results. The fcIBP binds irreversibly to the prism face using the loop between the B and the C-faces, involving also the B-face in water immobilization despite its irregular structure. The α-helix attaches the protein to the basal face with a partly reversible modus. Our results suggest that fcIBP has a looser attachment to ice and that this weaker binding modus is the basis to explain the moderate activity of fcIBP.

Adsorption of Kinetic Hydrate Inhibitors on Growing Surfaces: A Molecular Dynamics Study

We investigate the mechanism of a typical kinetic hydrate inhibitor (KHI), polyvinylcaprolactam (PVCap), which has been applied to prevent hydrate plugs from forming in gas pipe lines, using molecular dynamics simulations of crystal growth of ethylene oxide hydrate. Water-soluble ethylene oxide is chosen as a guest species to avoid problems associated with the presence of the gas phase in the simulation cell such as slow crystal growth. A PVCap dodecamer adsorbs irreversibly on the hydrate surface which grows at supercooling of 3 K when the hydrophobic part of two pendent groups are trapped in open cages at the surface. The amide hydrogen bonds make no contribution to the adsorption. PVCap can adsorb on various crystallographic planes of sI hydrate. This is in contrast to antifreeze proteins, each of which prefers a specific plane of ice. The trapped PVCap gives rise to necessarily the concave surface of the hydrate. The crystal growth rate decreases with increasing surface curvature, indicating that the inhibition by PVCap is explained by the Gibbs-Thomson effect.

Carbon dioxide induced bubble formation in a CH4–CO2–H2O ternary system: a molecular dynamics simulation study

The role of carbon dioxide in the formation of gas bubbles in a CH₄–CO₂–H₂O ternary system is studied using molecular dynamics simulations.

The nucleation of gas hydrates near silica surfaces

Understanding the nucleation and crystal growth of gas hydrates near mineral surfaces and in confinement are critical to the methane recovery from gas hydrate reservoirs. In this work, through molecular dynamics simulation studies, we present an exploration of the nucleation behavior of methane hydrates near model hydroxylated silica surfaces. Our simulation results indicate that the nucleation of methane hydrates can initiate from the silica surfaces despite of the structural mismatch of the two solid phases. A layer of intermediate half-cage structures was observed between the gas hydrate and silica surfaces, apparently helping to minimize the free energy penalty. These results have important implications to our understanding of the effects of solid surfaces on hydrate nucleation processes.

Non-Faradaic Energy Storage by Room Temperature Ionic Liquids in Nanoporous Electrodes

The enhancement of non-Faradaic charge and energy density stored by ionic electrolytes in nanostructured electrodes is an intriguing issue of great practical importance for energy storage in electric double layer capacitors. On the basis of extensive molecular dynamics simulations of various carbon-based nanoporous electrodes and room temperature ionic liquid (RTIL) electrolytes, we identify atomistic mechanisms and correlations between electrode/electrolyte structures that lead to capacitance enhancement. In the symmetric electrode setup with nanopores having atomically smooth walls, most RTILs showed up to 50% capacitance increase compared to infinitely wide pore. Extensive simulations using asymmetric electrodes and pores with atomically rough surfaces demonstrated that tuning of electrode nanostructure could lead to further substantial capacitance enhancement. Therefore, the capacitance in nanoporous electrodes can be increased due to a combination of two effects: (i) the screening of ionic interactions by nanopore walls upon electrolyte nanoconfinement, and (ii) the optimization of nanopore structure (volume, surface roughness) to take into account the asymmetry between cation and anion chemical structures.

Molecular insights into clathrate hydrate nucleation at an ice-solution interface

Clathrate hydrates are specific cage-like structures formed by water molecules around a guest molecule. Despite the many studies that have been performed on clathrate hydrates, the actual molecular mechanism of both their homogeneous and heterogeneous nucleation has yet to be fully clarified. Here, by means of molecular simulations, we demonstrate how the interface of hexagonal ice can facilitate the heterogeneous nucleation of methane clathrate hydrate from an aqueous methane solution. Our results indicate an initial accumulation of methane molecules, which promote induction of defective structures, particularly coupled 5-8 ring defects, at the ice surface. Structural fluctuations promoted by these defective motifs assist hydrate cage formation next to the interface. The cage-like structures formed then act as a sink for methane molecules in the solution and enhance the stability and growth of an amorphous nucleus, which can evolve into a hydrate crystal upon annealing. These results are illustrative of how a surface that is structurally incompatible can serve to facilitate heterogeneous nucleation of a new crystalline phase. They should also further our general understanding of the formation of gas hydrates and their critical roles in various industrial and environmental processes, including carbon capture and storage.

Nucleation of gas hydrates within constant energy systems

The early stage of formation of gas hydrates has recently attracted attention as amorphous intermediate gas hydrate structures have been observed, apparently contrary to a classical model of nucleation and some experimental observations. To date, essentially all reported molecular simulations of the nucleation of gas hydrates have been under constant temperature conditions, which does not consider the possible impacts of heat transfer on the nucleation processes. Here we show, using constant energy molecular simulations, that the nuclei at an early stage of the hydrate formation have relatively more crystalline order in comparison with those observed in previous isothermal (NPT or NVT) work. The current work suggests a more transient role for intermediate amorphous structures during hydrate nucleation, thereby providing a stronger link between molecular simulation and experimental observations. Our NVE results nevertheless support the two-step nucleation mechanism proposed in previous simulation studies under constant temperature conditions which features the initial formation of amorphous hydrate-like structures.

Nanopatterning of Electrode Surfaces as a Potential Route to Improve the Energy Density of Electric Double-Layer Capacitors: Insight from Molecular Simulations

Electrostatic double-layer capacitors (EDLCs) with room-temperature ionic liquids (RTILs) as electrolytes are among the most promising energy storage technologies. Utilizing atomistic molecular dynamics simulations, we demonstrate that the capacitance and energy density stored within the electric double layers (EDLs) formed at the electrode-RTIL electrolyte interface can be significantly improved by tuning the nanopatterning of the electrode surface. Significantly increased values and complex dependence of differential capacitance on applied potential were observed for surface patterns having dimensions similar to the ions' dimensions. Electrode surfaces patterned with rough edges promote ion separation in the EDL at lower potentials and therefore result in increased capacitance. The observed trends, which are not accounted for by the current basic EDL theories, provide a potentially new route for optimizing electrode structure for specific electrolytes.

The mobility of water molecules through gas hydrates

Crystal growth simulations of gas hydrates have suggested that hydrate cages may occasionally be occupied by H(2)O rather than guest molecules, leaving interstitial defects within the hydrate crystal. Further inspection of the behavior of these interstitial H(2)O molecules has revealed that they are relatively highly mobile entities within a gas hydrate. In this paper, we report these observations and examine the molecular mechanisms responsible for the transport of these interstitial molecules through hydrate crystals. Four distinct pathways for the H(2)O molecule transport between cages are found, each facilitated by the presence of empty cages. The relative richness of the observed behavior of interstitial defects suggests that interstitial diffusion could be an important mechanism for the mass transport of H(2)O molecules through gas hydrates.

Observation of two-step nucleation in methane hydrates

In this work we show that homogeneous nucleation of methane hydrate can, under appropriate conditions, be a very rapid process, achieved within tens of nanoseconds. In agreement with recent experimental results on different systems, we find that the nucleation of a gas hydrate crystal appears as a two-step process. It starts with the formation of disordered solid-like structures, which will then spontaneously evolve to more recognizable crystalline forms. This previously elusive first-stage state is confirmed to be post-critical in the nucleation process, and is characterized as processing reasonable short-range structure but essentially no long-range order. Its energy, molecular diffusion and local structure reflect a solid-like character, although it does exhibit mobility over longer (tens of ns) timescales. We provide insights into the controversial issue of memory effects in methane hydrates. We show that areas locally richer in methane will nucleate much more readily, and no 'memory' of the crystal is required for fast re-crystallization. We anticipate that much richer polycrystallinity and novel methane hydrate phases could be possible.

Heterogeneous crystal growth of methane hydrate on its sII [001] crystallographic face

This paper presents a systematic molecular simulation study of the heterogeneous crystal growth of methane hydrate sII from supersaturated aqueous methane solutions. The growth of sII hydrate on the [001] crystallographic face is achieved through utilization of a recently proposed methodology, and rates of crystal growth of 1 A/ns were sustained for the molecular models and specific conditions employed in this work. Characteristics of the crystals grown as well as properties and structure of the interface are examined. Water cages with a 5(12)6(3) arrangement, which are improper to both sI and sII structures, are identified during the heterogeneous growth of sII methane hydrate. We show that the growth of a [001] face of sII hydrate can produce an sI crystalline structure, confirming that cross-nucleation of methane hydrate structures is possible. Defects consisting of two methane molecules trapped in large 5(12)6(4) cages and water molecules trapped in small and large cages are observed, where in one instance we have found a large 5(12)6(4) cage containing three water molecules.