A review of clathrate hydrate nucleation, growth and decomposition studied using molecular dynamics simulation

Molecular Dynamics Simulation for the Acidic Compounds Retention Mechanism Study on Octyl-Quaternary Ammonium Mixed-Mode Stationary Phase

With the widespread application of mixed-mode chromatography in separation analysis, it is becoming increasingly important to study its retention mechanism. The retention behavior of acidic compounds on mixed-mode octyl-quaternary ammonium (Sil-C8-QA) columns was investigated by computer simulation. Firstly, the benzoic acid homologues were used as the analytes, and the simulation model was constructed by the Materials Studio. Geometric optimization, annealing and molecular dynamics (MD) simulation of these complexes resulted in optimized conformations. The binding energy, mean square displacement (MSD) and torsion angle distribution generated by MD simulation were then analyzed. The results showed that the more negative binding energy, the greater the MSD and the narrower the torsion angle distribution, indicating that the stationary phase behaves with stronger interaction and retention. The retention behavior of five acidic drugs on the Sil-C8-QA column was then successfully explained by simulation. Acidic drugs are more retentive on the mixed-mode column due to the more substantial interaction brought by the reversed-phase/ion-exchange mixed-mode mechanism compared to other single-mode columns. This simulation method is expected to provide ideas for studying the separation mechanism and predicting the retention behavior of more complex samples.

Liquid-liquid biopolymers aqueous solution segregative phase separation in food: From fundamentals to applications-A review

As a result of the spontaneous movement of molecules, liquid-liquid biopolymer segregative phase separation takes place in an aqueous solution. The efficacy of this type of separation can be optimized under conditions where variables such as pH, temperature, and molecular concentrations have minimal impact on its dynamics. Recently, interest in the applications of biopolymers and their segregative phase separation-associated molecular stratification has increased, particularly in the food industry, where these methods permit the purification of specific particles and the embedding of microcapsules. The present review offers a comprehensive examination of the theoretical mechanisms that regulate the liquid-liquid biopolymers aqueous solution segregative phase separation, the factors that may exert an impact on this procedure, and the importance of this particular separation method in the context of food science. These discussion points also address existing difficulties and future possibilities related to the use of segregative phase separation in food applications. This highlights the potential for the design of novel functional foods and the enhancement of food properties.

Stochastic Cellular Automata Modeling of CO2 Hydrate Growth and Morphology

Carbon dioxide (CO₂) hydrates are important in a diverse range of applications and technologies in the environmental and energy fields. The development of such technologies relies on fundamental understanding, which necessitates not only experimental but also computational studies of the growth behavior of CO₂ hydrates and the factors affecting their crystal morphology. As experimental observations show that the morphology of CO₂ hydrate particles differs depending on growth conditions, a detailed understanding of the relation between the hydrate structure and growth conditions would be helpful. To this end, this work adopts a modeling approach based on hybrid probabilistic cellular automata to investigate variations in CO₂ hydrate crystal morphology during hydrate growth from stagnant liquid water presaturated with CO₂. The model, which uses free energy density profiles as inputs, correlates the variations in growth morphology to the system subcooling ΔT, i.e., the temperature deficiency from the triple CO₂-hydrate-water equilibrium temperature under a given pressure, and properties of the growing hydrate-water interface, such as surface tension and curvature. The model predicts that when ΔT is large, parabolic needle-like or dendrite crystals emerge from planar fronts that deform and lose stability. In agreement with chemical diffusion-limited growth, the position of such planar fronts versus time follows a power law. In contrast, the tips of the emerging parabolic crystals steadily grow in proportion to time. The modeling framework is computationally fast and produces complex growth morphology phenomena under diffusion-controlled growth from simple, easy-to-implement rules, opening the way for employing it in multiscale modeling of gas hydrates.

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 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.