The effect of the water/methane interface on methane hydrate cages: The potential of mean force and cage lifetimes

Pressure-regulated rotational guests in nano-confined spaces suppress heat transport in methane hydrates

Materials with low lattice thermal conductivity are essential for various heat-related applications like thermoelectrics, and usual approaches for achieving this rely on specific crystalline structures. Here, we report a strategy for thermal conductivity reduction and regulation via guest rotational dynamics and their couplings with lattice vibrations. By applying pressure to manipulate rotational states, we find the intensified rotor-lattice couplings of compressed methane hydrate MH-III can trigger strong phonon scatterings and phonon localizations, enabling an almost three-fold suppression of thermal conductivity. Besides, the disorder in methane rotational dynamics results in anharmonic interactions and nonlinear pressure-dependent heat transport. The overall guest rotational dynamics and heat conduction changes can be flexibly regulated by the rotor-lattice coupling strength. We further underscore that this reduction mechanism can be extended to a wide range of systems with different structures. The results demonstrate a potentially universal method for reducing or controlling heat transport by developing a hybrid system with tailored molecular rotors.

Dual-Comb Gas Sensor Integrated with a Neural Network-Based Spectral Decoupling Algorithm of Overlapped Spectra for Gas Mixture Sensing

Cross-interference among absorptions severely affects the ability to achieve accurate gas concentration retrieval through gas molecular specificity. In this study, a novel dual gas sensor was proposed to separate methane and water absorbance from the blended spectra of their mixture in the mid-infrared (MIR) band by employing a neural network algorithm. To address the scarcity of experimental data, the neural network was trained over a simulated data set constructed with the same distribution as the experimental ones. The system takes advantages of the broadband spectra to provide high-quality comb data and allows the neural network to establish an accurate spectral decoupling function. In addition, a feature absorption peak screening mechanism was proposed to achieve more accurate concentration retrieval, which avoids the prediction error introduced by interrogating the only peak of the separated spectra. The promising results of the systematic evaluation have demonstrated the feasibility of our methods in practical detections.

Acoustic-propagation properties of methane clathrate hydrates from non-equilibrium molecular dynamics

Given methane hydrates' importance in marine sediments, as well as the widespread use of seabed acoustic-signaling methods in oil and gas exploration, the elastic characterization of these materials is particularly relevant. A greater understanding of the properties governing phonon, sound, and acoustic propagation would help to better classify methane-hydrate deposits, aiding in their discovery. Recently, we have published a new nonequilibrium molecular-dynamics (NEMD) methodology to recreate longitudinal and transverse perturbations, observing their propagation through a crystalline lattice by various metrics, to study the underlying S- and P-wave velocities (achieving excellent agreement with experiment) [Melgar et al., J. Phys. Chem. 122(5), 3006-3013 (2018); ibid.150, 084101 (2019)]. Here, we apply these NEMD methods to methane-clathrate systems to study acoustic-propagation characteristics, as well as the lattice elastic behavior. In so doing, we determine S- and P-wave velocities in excellent accord with experiment; we also ascertain the allowable magnitude range of acoustic perturbation and establish a threshold for lattice breakup and hydrate decomposition. Interestingly, upon dissociation, we observe the formation of methane nanobubbles, which agrees with previous studies on the microscopic fundamentals of hydrate dissociation by various means.

Magnetic-field effects on methane-hydrate kinetics and potential geophysical implications: Insights from non-equilibrium molecular dynamics

We have conducted non-equilibrium molecular-dynamics (NEMD) simulation to show that externally-applied magnetic fields, including their reversals in direction, have important effects on gas-release dynamics from methane hydrates. In particular, we apply fluctuation-dissipation analysis in the guise of Onsager's hypothesis to study hydrate kinetics at lower applied-field intensities, including temporary hydrate destabilisation in the wake of field-polarity switch; we scale down to the lowest practicable field intensities, of the order of 1 T. We conjecture, that these NEMD-based findings, particularly those involving polarity switch, may have ramifications for superchron-related Earth's magnetic-field polarity swaps affecting methane release into the geosphere, although a good deal of further work would be needed to provide a more definitive causal link.

What are the key factors governing the nucleation of CO2 hydrate?

Microsecond molecular dynamics simulations were performed to provide molecular insights into the nucleation of CO₂ hydrate. The adsorption of sufficient CO₂ molecules around CO₂ hydration shells is revealed to be crucial to effectively stabilize the hydrogen bonds formed therein, catalyzing the hydration shells into hydrate cages and inducing the nucleation. Moreover, a high aqueous CO₂ concentration is found to be another key factor governing the nucleation of CO₂ hydrate, and only above a critical concentration can the nucleation of CO₂ hydrate occur. The 4¹5¹⁰6² cages, with size similar to the CO₂ hydration shell and an elliptical space closely matching a linear CO₂ molecule, play a dominant role in initiating the nucleation and remain the most abundant. The incipient CO₂ hydrate is rather amorphous due to the abundance of metastable cages (mostly 4¹5¹⁰6²).

A Theoretical Study of the Hydration of Methane, from the Aqueous Solution to the sI Hydrate-Liquid Water-Gas Coexistence

Monte Carlo and molecular dynamics simulations were done with three recent water models TIP4P/2005 (Transferable Intermolecular Potential with 4 Points/2005), TIP4P/Ice (Transferable Intermolecular Potential with 4 Points/ Ice) and TIP4Q (Transferable Intermolecular Potential with 4 charges) combined with two models for methane: an all-atom one OPLS-AA (Optimal Parametrization for the Liquid State) and a united-atom one (UA); a correction for the C–O interaction was applied to the latter and used in a third set of simulations. The models were validated by comparison to experimental values of the free energy of hydration at 280, 300, 330 and 370 K, all under a pressure of 1 bar, and to the experimental radial distribution functions at 277, 283 and 291 K, under a pressure of 145 bar. Regardless of the combination rules used for σ_C,O, good agreement was found, except when the correction to the UA model was applied. Thus, further simulations of the sI hydrate were performed with the united-atom model to compare the thermal expansivity to the experiment. A final set of simulations was done with the UA methane model and the three water models, to study the sI hydrate-liquid water-gas coexistence at 80, 230 and 400 bar. The melting temperatures were compared to the experimental values. The results show the need to perform simulations with various different models to attain a reliable and robust molecular image of the systems of interest.

Effects of thermodynamic inhibitors on the dissociation of methane hydrate: a molecular dynamics study

We investigate the effects of methanol and NaCl, which are known as thermodynamic hydrate inhibitors, on the dissociation kinetics of methane hydrate in aqueous solutions by using molecular dynamics simulations. It is shown that the dissociation rate is not constant but changes with time. The dissociation rate in the initial stage is increased by methanol whereas it is decreased by NaCl. This difference arises from the opposite effects of the two thermodynamic inhibitors on the hydration free energy of methane. The dissociation rate of methane hydrate is increased by the formation of methane bubbles in the aqueous phase because the bubbles absorb surrounding methane molecules. It is found that both methanol and NaCl facilitate the bubble formation. However, their mechanisms are completely different from each other. The presence of ions enhances the hydrophobic interactions between methane molecules. In addition, the ions in the solution cause a highly non-uniform distribution of dissolved methane molecules. These two effects result in the easy formation of bubbles in the NaCl solution. In contrast, methanol assists the bubble formation because of its amphiphilic character.

A Monte Carlo simulation study of methane clathrate hydrates confined in slit-shaped pores

Monte Carlo simulations are used to study the structure, stability, and dissociation mechanisms of methane hydrate crystals inside carbon-like slit-shaped pores. The simulation conditions used mimic experimental studies of the dissociation of methane and propane hydrates in mesoporous silica gels (Handa, Y. P.; Stupin, D. J. Phys. Chem. 1992, 96, 8599). Simulations are performed under conditions of fixed methane pressure and fixed water loading, with the temperature increased in steps, with long equilibrations at each temperature. The initial structures of the confined hydrates are taken to be bulk-like, and pore widths chosen to accommodate integer or half-integer numbers of hydrate unit cells. Density profiles and orientational order parameter profiles are obtained and used to understand the structural changes associated with hydrate dissociation. Three different common water models, SPC/E, TIP4P, and TIP4P/2005, are used and the results compared. For water modeled using either the TIP4P or TIP4P/2005 potentials, dissociation temperatures are depressed proportionally to the inverse pore width, as predicted by the macroscopic Gibbs-Thomson equation. This behavior is observed for pores small enough that only half-cages of the clathrate structure are present. Experimental work has verified Gibbs-Thomson behavior for pores as small as 2 nm (Seshadri, K.; Wilder, J. W.; Smith, D. H. J. Phys. Chem. B 2001, 105, 2627); micropores of the size studied here have not yet been studied by experiment. Interestingly, the dissociation of hydrates modeled using the SPC/E water potential does not display the predicted pore-size dependence, and the dissociation mechanisms in this model seem to be quite different than those in the TIP4P-type models. In the SPC/E hydrates, with increasing temperature, cage dissocation occurs before methane desorption. In TIP4P-type hydrates, these processes occur either at the same temperature (to within the resolution of this study) or with dissociation occurring at higher temperatures than desorption. These simulations show that a variety of interesting clathrate structures and phase behaviors may be accessed in suitably designed microporous materials, with potentially useful applications in gas storage or separations.

Nanobubbles and micropancakes: gaseous domains on immersed substrates

Surface nanobubbles and micropancakes are two recent discoveries in interfacial physics. They are nanoscopic gaseous domains that form at the solid/liquid interface. The fundamental interest focuses on the fact that they are surprisingly stable to dissolution, lasting for at least 10-11 orders of magnitude longer than the classical expectation. So far, many articles have been published that describe various different nucleation methods and 'ideal' systems and experimental techniques for nanobubble research, and we are now at the stage where we can begin to investigate the fundamental questions in detail. In this topical review, we summarize the current state of research in the field and give an overview of the partial answers that have been proposed or that can be inferred to date. We relate nanobubbles and micropancakes, and we try to build a framework within which nucleation may be understood. We also discuss evidence for and against different aspects of nanobubble stability, as well as suggesting what still needs to be done to obtain a full understanding.

Microsecond simulations of spontaneous methane hydrate nucleation and growth

Despite the industrial implications and worldwide abundance of gas hydrates, the formation mechanism of these compounds remains poorly understood. We report direct molecular dynamics simulations of the spontaneous nucleation and growth of methane hydrate. The multiple-microsecond trajectories offer detailed insight into the process of hydrate nucleation. Cooperative organization is observed to lead to methane adsorption onto planar faces of water and the fluctuating formation and dissociation of early hydrate cages. The early cages are mostly face-sharing partial small cages, favoring structure II; however, larger cages subsequently appear as a result of steric constraints and thermodynamic preference for the structure I phase. The resulting structure after nucleation and growth is a combination of the two dominant types of hydrate crystals (structure I and structure II), which are linked by uncommon 5(12)6(3) cages that facilitate structure coexistence without an energetically unfavorable interface.

Surface activity of amphiphilic helical beta-peptides from molecular dynamics simulation

The surface activity of beta-peptides is investigated using molecular simulations. The type and display of hydrophobic and hydrophilic groups on helical beta-peptides is varied systematically. Peptides with 2/3 hydrophobic groups are found to be surface active, and to adopt an orientation parallel to the air-water interface. For select beta-peptides, we also determine the potential of mean force required to bring a peptide to the air-water interface. Facially amphiphilic helices with 2/3 hydrophobic groups are found to exhibit the lowest free energy of adsorption. The adsorption process is driven by a favorable energetic term and opposed by negative entropic changes. The temperature dependence of adsorption is also investigated; facially amphiphilic helices are found to adopt orientations that are largely independent of temperature, while nonfacially amphiphilic helices sample a broader range of interfacial orientations at elevated temperatures. The thermodynamics of adsorption of beta-peptides is compared to that of 1-octanol, a well-known surfactant, and ovispirin, a naturally occurring antimicrobial peptide. It is found that the essential difference lies in the sign of the entropy of adsorption, which is negative for beta- and alpha-peptides and positive for traditional surfactants such as octanol.

The human gene for vascular endothelial growth factor. Multiple protein forms are encoded through alternative exon splicing

Vascular endothelial growth factor (VEGF) is an apparently endothelial cell-specific mitogen that is structurally related to platelet-derived growth factor. By Northern blot and protein analyses, we show that VEGF is produced by cultured vascular smooth muscle cells. Analysis of VEGF transcripts in these cells by polymerase chain reaction and cDNA cloning revealed three different forms of the VEGF coding region, as had been reported in HL60 cells. The three forms of the human VEGF protein chain predicted from these coding regions are 189, 165, and 121 amino acids in length. Comparison of cDNA nucleotide sequences with sequences derived from human VEGF genomic clones indicates that the VEGF gene is split among eight exons and that the various VEGF coding region forms arise from this gene by alternative splicing: the 165-amino-acid form of the protein is missing the residues encoded by exon 6, whereas the 121-amino-acid form is missing the residues encoded by exons 6 and 7. Analysis of the VEGF gene promoter region revealed a single major transcription start, which lies near a cluster of potential Sp1 factor binding sites. The promoter region also contains several potential binding sites for the transcription factors AP-1 and AP-2; consistent with the presence of these sites, Northern blot analysis demonstrated that the level of VEGF transcripts is elevated in cultured vascular smooth muscle cells after treatment with the phorbol ester 12-O-tetradecanoyl-phorbol-13-acetate.