A potential model for the study of ices and amorphous water: TIP4P/Ice

On the role of intermolecular vibrational motions for ice polymorphs. III. Mode characteristics associated with negative thermal expansion

Low-pressure ice forms, such as hexagonal and cubic ice, expand on cooling below temperature 60 K. This negative thermal expansivity has been explored in terms of phonon frequency modulation with varying volume and attributed to the negative Grüneisen parameters unique mostly to tetrahedrally coordinated substances. However, an underlying mechanism for the negative Grüneisen parameters has not been known except some schematic analyses. We investigate in this study the characteristics of the intermolecular vibrational modes whose Grüneisen parameters are negative by examining the individual vibrational modes rigorously. It is found that the low frequency modes below 100 cm^-1, which we explicitly show are mostly bending motions of three hydrogen-bonded molecules, necessarily accompany elongation of the hydrogen bond length at peak amplitudes compared with that at the equilibrium position in executing the vibrational motions. The elongation gives rise to a decrease in the repulsive interaction while an increase in the Coulombic one. The decrease in the repulsive interaction is relaxed substantially by expansion due to its steep slope against molecular separation compared with the sluggish increase in the Coulombic one, and therefore, the negative Grüneisen parameters are obtainable. This scenario is tested against some variants of cubic ice with various water potential models. It is demonstrated that four interaction-site models are suitable to describe the intermolecular vibrations and the thermal expansivity because of the moderate tendency to favor the tetrahedral coordination.

Advances in the study of supercooled water

In this review, we report recent progress in the field of supercooled water. Due to its uniqueness, water presents numerous anomalies with respect to most simple liquids, showing polyamorphism both in the liquid and in the glassy state. We first describe the thermodynamic scenarios hypothesized for the supercooled region and in particular among them the liquid-liquid critical point scenario that has so far received more experimental evidence. We then review the most recent structural indicators, the two-state model picture of water, and the importance of cooperative effects related to the fact that water is a hydrogen-bonded network liquid. We show throughout the review that water's peculiar properties come into play also when water is in solution, confined, and close to biological molecules. Concerning dynamics, upon mild supercooling water behaves as a fragile glass former following the mode coupling theory, and it turns into a strong glass former upon further cooling. Connections between the slow dynamics and the thermodynamics are discussed. The translational relaxation times of density fluctuations show in fact the fragile-to-strong crossover connected to the thermodynamics arising from the existence of two liquids. When considering also rotations, additional crossovers come to play. Mobility-viscosity decoupling is also discussed in supercooled water and aqueous solutions. Finally, the polyamorphism of glassy water is considered through experimental and simulation results both in bulk and in salty aqueous solutions. Grains and grain boundaries are also discussed.

Hyperactive Antifreeze Proteins Promote Ice Growth before Binding to It

The antifreeze mechanism of antifreeze proteins (AFPs) evolved by organisms has been widely studied. However, detailed knowledge of the synergy between AFPs and ice crystals still remains fragmentary. In the present contribution, the cooperative effect of the hyperactive insect antifreeze protein TmAFP and ice crystals on the interfacial water during the entire process of inhibiting ice growth is systematically investigated at the atomic level and compared with its low activity mutant and a nonantifreeze protein. The results indicate a significant synergy between TmAFP and ice crystals, which enables the TmAFP to promote the ice growth before adsorbing on the surfaces of the ice crystals, while the mutant and the nonantifreeze protein cannot promote the ice growth due to the lack of this synergy. When TmAFP approaches the ice surface, the interfacial water is induced by both the AFP and the ice crystals to form the anchored clathrate motif, which binds TmAFP to the ice surface, resulting in a local increase in the curvature of the ice surface, thereby inhibiting the growth of ice. In this study, three stages, namely, promotion, adsorption, and inhibition, are observed in the complete process of TmAFP inhibiting ice growth, and the synergistic mechanism between protein and ice crystals is revealed. The results are helpful for the design of antifreeze proteins and bioinspired antifreeze materials with superior performance.

On the anomalous homogeneity of hydrogen-disordered ice and its origin

Pauling's successful estimation of the residual entropy of hydrogen-disordered ice was based on the homogeneity of the binding energy of individual water molecules in ice. However, it has not been explained why the binding energies are homogeneous although the pair interaction energy of hydrogen-bonded dimers distributes widely. Here, we provide a rationale for this phenomenon. The topological constraints imposed by the ice rules, in which water molecules form directed cyclic paths of hydrogen bonds, cancel out the variability of local interactions. We also show that the cancellation mechanism does not work due to some imperfect cyclic paths on the surface of ice. Such water molecules do not enjoy homogeneity in the bulk state and suffer from a wide spectrum in the binding energy.

Structure of High-Pressure Supercooled and Glassy Water

We numerically investigate the structure of deep supercooled and glassy water under pressure, covering the range of densities corresponding to the experimentally produced high- and very-high-density amorphous phases. At T=188  K, a continuous increase in density is observed on varying pressure from 2.5 to 13 kbar, with no signs of first-order transitions. Exploiting a recently proposed approach to the analysis of the radial distribution function-based on topological properties of the hydrogen-bond network-we are able to identify well-defined local geometries that involve pairs of molecules separated by multiple hydrogen bonds, specific to the high- and very-high-density structures.

Modulating Water Slip Using Atomic-Scale Defects: Friction on Realistic Hexagonal Boron Nitride Surfaces

Atomic-scale defects are ubiquitous in nanomaterials, yet their role in modulating fluid flow is inadequately understood. Hexagonal boron nitride (hBN) is an important two-dimensional material with applications in desalination and osmotic power. Although pristine hBN offers higher friction to the flow of water than graphene, we show here that certain defects can enhance water slippage on hBN. Using classical molecular dynamics simulations assisted by quantum-mechanical density functional theory, we compute the friction coefficient of water on hBN containing various vacancies (B, N, BN, B₂N, and B₃N) and the Stone-Wales defect. By investigating two defect concentrations, we obtain friction coefficients ranging from 0.4 to 2.6 times that of pristine hBN, leading to a maximum water slip length of 18.1 nm on hBN with a N vacancy or a Stone-Wales defect. Our work informs the use of defects to tune water flow and reveals defective hBN as an alternative high-slip surface to graphene.

Detailed Analysis of the Ice Surface after Binding of an Insect Antifreeze Protein and Correlation with the Gibbs-Thomson Equation

Antifreeze proteins (AFPs) are able to influence the ice crystal growth and the recrystallization process due to the Gibbs-Thomson effect. The binding of the AFP leads to the formation of a curved ice surface and it is generally assumed that there is a critical radius between the proteins on the ice surface that determines the maximal thermal hysteresis. Up to now, this critical radius has not yet been proven beyond doubt or only in poor agreement with the Gibbs-Thomson equation. Using molecular dynamics (MD) simulations, the resulting three-dimensional surface structure is analyzed and the location of the critical radius is identified. Our results demonstrate that the correct analysis of the geometry of the ice surface is extremely important and cannot be guessed upfront a simulation. In contrary to earlier expectations from the literature, we could show that the critical radius is not located directly between the adsorbed proteins. In addition, we showed that the minimum temperature at which the system does not freeze is in very good agreement with the value calculated with the Gibbs-Thomson equation at the critical radius, as long as dynamic system conditions are taken into account. This proves on the one hand that the Gibbs-Thomson effect is the basis of thermal hysteresis and that MD simulations are suitable for the prediction of the melting point depression.

Interfacial study of clathrates confined in reversed silica pores

Storing methane in clathrates is one of the most promising alternatives for transporting natural gas (NG) as it offers similar gas densities to liquefied and compressed NG while offering lower safety risks. However, the practical use of clathrates is limited given the extremely low temperatures and high pressures necessary to form these structures. Therefore, it has been suggested to confine clathrates in nanoporous materials, as this can facilitate clathrate's formation conditions while preserving its CH4 volumetric storage. Yet, the choice of nanoporous materials to be employed as the clathrate growing platform is still rather arbitrary. Herein, we tackle this challenge in a systematic way by computationally exploring the stability of clathrates confined in alkyl-grafted silica materials with different pore sizes, ligand densities and ligand types. Based on our findings, we are able to propose key design criteria for nanoporous materials favoring the stability of a neighbouring clathrate phase, namely large pore sizes, high ligand densities, and smooth pore walls. We hope that the atomistic insight provided in this work will guide and facilitate the development of new nanomaterials designed to promote the formation of clathrates.

Mechanical Instability of Methane Hydrate-Mineral Interface Systems

Massive methane hydrates occur on sediment matrices in nature. Therefore, sediment-based methane hydrate systems play an essential role in the society and hydrate community, including energy resources, global climate changes, and geohazards. However, a fundamental understanding of mechanical properties of methane hydrate-mineral interface systems is largely limited due to insufficient experimental techniques. Herein, by using large-scale molecular simulations, we show that the mechanical properties of methane hydrate-mineral (silica, kaolinite, and Wyoming-type montmorillonite) interface systems are strongly dictated by the chemical components of sedimentary minerals that determine interfacial microstructures between methane hydrates and minerals. The tensile strengths of hydrate-mineral systems are found to decrease following the order of Wyoming-type montmorillonite- > silica- > kaolinite-based methane hydrate systems, all of which show a brittle failure at the interface between methane hydrates and minerals under tension. In contrast, upon compression, methane hydrates decompose into water and methane molecules, resulting from a large strain-induced mechanical instability. In particular, the failure of Wyoming-type montmorillonite-based methane hydrate systems under compression is characterized by a sudden decrease in the compressive stress at a strain of around 0.23, distinguishing it from those of silica- and kaolinite-based methane hydrate systems under compression. Our findings thus provide a molecular insight into the potential mechanisms of mechanical instability of gas hydrate-bearing sediment systems on Earth.

The microscopic mechanism of bulk melting of ice

We study the initial stages of homogeneous melting of a hexagonal ice crystal at coexistence and at moderate superheating. Our trajectory-based computer simulation approach provides a comprehensive picture of the events that lead to melting, from the initial accumulation of 5+7 defects, via the formation of L-D and interstitial-vacancy pairs, to the formation of a liquid nucleus. Of the different types of defects that we observe to be involved in melting, a particular kind of 5+7 type defect (type 5) plays a prominent role as it often forms prior to the formation of the initial liquid nucleus and close to the site where the nucleus forms. Hence, like other solids, ice homogeneously melts via the prior accumulation of defects.

Systematic Comparison of the Structural and Dynamic Properties of Commonly Used Water Models for Molecular Dynamics Simulations

Water is a unique solvent that is ubiquitous in biology and present in a variety of solutions, mixtures, and materials settings. It therefore forms the basis for all molecular dynamics simulations of biological phenomena, as well as for many chemical, industrial, and materials investigations. Over the years, many water models have been developed, and it remains a challenge to find a single water model that accurately reproduces all experimental properties of water simultaneously. Here, we report a comprehensive comparison of structural and dynamic properties of 30 commonly used 3-point, 4-point, 5-point, and polarizable water models simulated using consistent settings and analysis methods. For the properties of density, coordination number, surface tension, dielectric constant, self-diffusion coefficient, and solvation free energy of methane, models published within the past two decades consistently show better agreement with experimental values compared to models published earlier, albeit with some notable exceptions. However, no single model reproduced all experimental values exactly, highlighting the need to carefully choose a water model for a particular study, depending on the phenomena of interest. Finally, machine learning algorithms quantified the relationship between the water model force field parameters and the resulting bulk properties, providing insight into the parameter-property relationship and illustrating the challenges of developing a water model that can accurately reproduce all properties of water simultaneously.

Nanopores in Atomically Thin 2D Nanosheets Limit Aqueous Single-Stranded DNA Transport

Nanopores in 2D materials are highly desirable for DNA sequencing, yet achieving single-stranded DNA (ssDNA) transport through them is challenging. Using density functional theory calculations and molecular dynamics simulations we show that ssDNA transport through a pore in monolayer hexagonal boron nitride (h-BN) is marked by a basic nanomechanical conflict. It arises from the notably inhomogeneous flexural rigidity of ssDNA and causes high friction via transient DNA desorption costs exacerbated by solvation effects. For a similarly sized pore in bilayer h-BN, its self-passivated atomically smooth edge enables continuous ssDNA transport. Our findings shed light on the fundamental physics of biopolymer transport through pores in 2D materials.

Structural investigation of three distinct amorphous forms of Ar hydrate

Three amorphous forms of Ar hydrate were produced using the crystalline clathrate hydrate Ar·6.5H₂O (structure II, Fd3̄m, a ≈ 17.1 Å) as a precursor and structurally characterized by a combination of isotope substitution (³⁶Ar) neutron diffraction and molecular dynamics (MD) simulations. The first form followed from the pressure-induced amorphization of the precursor at 1.5 GPa at 95 K and the second from isobaric annealing at 2 GPa and subsequent cooling back to 95 K. In analogy to amorphous ice, these amorphs are termed high-density amorphous (HDA) and very-high-density amorphous (VHDA), respectively. The third amorph (recovered amorphous, RA) was obtained when recovering VHDA to ambient pressure (at 95 K). The three amorphs have distinctly different structures. In HDA the distinction of the original two crystallographically different Ar guests is maintained as differently dense Ar–water hydration structures, which expresses itself in a split first diffraction peak in the neutron structure factor function. Relaxation of the local water structure during annealing produces a homogeneous hydration environment around Ar, which is accompanied with a densification by about 3%. Upon pressure release the homogeneous amorphous structure undergoes expansion by about 21%. Both VHDA and RA can be considered frozen solutions of immiscible Ar and water in which in average 15 and 11 water molecules, respectively, coordinate Ar out to 4 Å. The local water structures of HDA and VHDA Ar hydrates show some analogy to those of the corresponding amorphous ices, featuring H₂O molecules in 5- and 6-fold coordination with neighboring molecules. However, they are considerably less dense. Most similarity is seen between RA and low density amorphous ice (LDA), which both feature strictly 4-coordinated H₂O networks. It is inferred that, depending on the kind of clathrate structure and occupancy of cages, amorphous states produced from clathrate hydrates display variable local water structures.

Three amorphous forms of Ar clathrate hydrate (pressure-amorphized, annealed and recovered) were characterized by isotope substitution (³⁶Ar) neutron diffraction and molecular dynamics and their local coordinations analyzed and compared to pure ice.

Correlating Antiagglomerant Performance with Gas Hydrate Cohesion

Although inhibiting hydrate formation in hydrocarbon-water systems is paramount in preventing pipe blockage in hydrocarbon transport systems, the molecular mechanisms responsible for antiagglomerant (AA) performance are not completely understood. To better understand why macroscopic performance is affected by apparently small changes in the AA molecular structure, we perform molecular dynamics simulations. We quantify the cohesion energy between two gas hydrate nanoparticles dispersed in liquid hydrocarbons in the presence of different AAs, and we achieve excellent agreement against experimental data obtained at high pressure using the micromechanical force apparatus. This suggests that the proposed simulation approach could provide a screening method for predicting, in silico, the performance of new molecules designed to manage hydrates in flow assurance. Our results suggest that entropy and free energy of solvation of AAs, combined in some cases with the molecular orientation at hydrate-oil interfaces, are descriptors that could be used to predict performance, should the results presented here be reproduced for other systems as well. These insights could help speed up the design of new AAs and guide future experiments.

Temperature-dependent kinetic pathways of heterogeneous ice nucleation competing between classical and non-classical nucleation

Ice nucleation on the surface plays a vital role in diverse areas, ranging from physics and cryobiology to atmospheric science. Compared to ice nucleation in the bulk, the water-surface interactions present in heterogeneous ice nucleation complicate the nucleation process, making heterogeneous ice nucleation less comprehended, especially the relationship between the kinetics and the structures of the critical ice nucleus. Here we combine Markov State Models and transition path theory to elucidate the ensemble pathways of heterogeneous ice nucleation. Our Markov State Models reveal that the classical one-step and non-classical two-step nucleation pathways can surprisingly co-exist with comparable fluxes at T = 230 K. Interestingly, we find that the disordered mixing of rhombic and hexagonal ice leads to a favorable configurational entropy that stabilizes the critical nucleus, facilitating the non-classical pathway. In contrast, the favorable energetics promotes the formation of hexagonal ice, resulting in the classical pathway. Furthermore, we discover that, at elevated temperatures, the nucleation process prefers to proceed via the classical pathway, as opposed to the non-classical pathway, since the potential energy contributions override the configurational entropy compensation. This study provides insights into the mechanisms of heterogeneous ice nucleation and sheds light on the rational designs to control crystallization processes.

Dynamical crossover and its connection to the Widom line in supercooled TIP4P/Ice water

We perform molecular dynamics simulations with the TIP4P/Ice water model to characterize the relationship between dynamics and thermodynamics of liquid water in the supercooled region. We calculate the relevant properties of the phase diagram, and we find that TIP4P/Ice presents a retracing line of density maxima, similar to what was previously found for atomistic water models and models of other tetrahedral liquids. For this model, a liquid-liquid critical point between a high-density liquid and a low-density liquid was recently found. We compute the lines of the maxima of isothermal compressibility and the minima of the coefficient of thermal expansion in the one phase region, and we show that these lines point to the liquid-liquid critical point while collapsing on the Widom line. This line is the line of the maxima of correlation length that emanates from a second order critical point in the one phase region. Supercooled water was found to follow mode coupling theory and to undergo a transition from a fragile to a strong behavior right at the crossing of the Widom line. We find here that this phenomenology also happens for TIP4P/Ice. Our results appear, therefore, to be a general characteristic of supercooled water, which does not depend on the interaction potential used, and they reinforce the idea that the dynamical crossover from a region where the relaxation mechanism is dominated by cage relaxation to a region where cages are frozen and hopping dominates is correlated in water to a phase transition between a high-density liquid and a low-density liquid.

Formation of porous ice frameworks at room temperature

Bulk crystalline ices with ultralow densities have been demonstrated to be thermodynamically metastable at negative pressures. However, the direct formation of these bulk porous ices from liquid water at negative pressures is extremely challenging. Inspired by approaches toward porous media based on host-guest chemistry, such as metal-organic frameworks and covalent organic frameworks, we herein demonstrate via molecular dynamics simulations that a class of ultralow-density porous ices with upright channels can be formed spontaneously from liquid water at 300 K with the assistance of carbon nanotube arrays. We refer to these porous ice polymorphs as water oxygen-vertex frameworks (WOFs). Notably, our simulations revealed that the liquid-WOF phase transition is first-order and occurs at room temperature. All the WOFs exhibited the unique structural feature that they can be regarded as assemblies of nanoribbons of hexagonal bilayer ice (2D ice I) at their armchair or zigzag edges. Based on density functional theory calculations, a comprehensive phase diagram of the WOFs was constructed considering both the thermodynamic and thermal stabilities of the porous ices at negative pressures. Like other types of porous media, these WOFs may be applicable to gas storage, purification, and separation. Moreover, these biocompatible porous ice networks may be exploited as medical-related carriers.

A high-accuracy machine-learning water model for exploring water nanocluster structures

Water, the most important molecule on the Earth, possesses many essential and unique physical properties that are far from completely understood, partly due to serious difficulties in identifying the precise microscopic structures of water. Hence, identifying the structures of water nanoclusters is a fundamental and challenging issue for studies on the relationship between the macroscopic physical properties of water and its microscopic structures. For large-scale simulations (at the level of nm and ns) of water nanoclusters, a calculation method with simultaneous accuracy at the level of quantum chemistry and efficiency at the level of an empirical potential method is in great demand. Herein, a machine-learning (ML) water model was utilized to explore the microscopic structural features at different length scales for water nanoclusters with a size up to several nm. The ML water model can be employed to efficiently predict the structures of water nanoclusters with a similar accuracy to that of density functional theory and with substantially lower computational resource demands. To validate the low-lying structure search results with experimental spectral results, an ML water model combined with velocity autocorrelation function analysis was used to simulate the vibrational spectra of water nanoclusters with up to thousands of water molecules. By comparing the simulated and experimentally recorded vibrational spectra, the atomic structures determined by a simulation based on the ML water model are all verified. To demonstrate its ability to represent water's structural evolution at large length and time scales, the ML water model was employed to model the structural evolution during the crystal-liquid transition, and the phase transition temperatures of water clusters with different sizes were precisely predicted. The ML water model provides an efficient theoretical calculation tool for exploring the structures and physical properties of water and their relationships, especially for clusters with relatively large sizes and processes with relatively long durations.

Effect of interfacial dipole on heterogeneous ice nucleation

In this work, we performed molecular dynamics simulations of ice nucleation on a rigid surface model of cubic zinc blende structure with different surface dipole strength and orientation. Our results show that, although substrates are excellently lattice-matched to cubic ice, ice nucleation merely occurred as the interfacial water molecules (IWs) show identical or similar orientations to that of water molecules in cubic ice. Free energy landscapes revealed that, as substrates have non-suitable dipole strength/orientation, there exist large free energy barriers for rotating dipole IWs to the right orientation to trigger ice formation. This study stresses that, beyond the traditional view of lattice match and the similarity of lattice length between the substrate and new-formed crystal, the similarity between molecular orientations of interfacial component and component in the specific new-formed crystalline face is also critical for promoting ice nucleation.

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.

Field-Dependent Dehydration and Optimal Ionic Escape Paths for C2N Membranes

Most analytic theories describing electrostatically driven ion transport through water-filled nanopores assume that the corresponding permeation barriers are bias-independent. While this assumption may hold for sufficiently wide pores under infinitely small bias, transport through subnanometer pores under finite bias is difficult to interpret analytically. Given recent advances in subnanometer pore fabrication and the rapid progress in detailed computer simulations, it is important to identify and understand the specific field-induced phenomena arising during ion transport. Here we consider an atomistic model of electrostatically driven ion permeation through subnanoporous C2N membranes. We analyze probability distributions of ionic escape trajectories and show that the optimal escape path switches between two different configurations depending on the bias magnitude. We identify two distinct mechanisms contributing to field-induced changes in transport-opposing barriers: a weak one arising from field-induced ion dehydration and a strong one due to the field-induced asymmetry of the hydration shells. The simulated current-voltage characteristics are compared with the solution of the 1D Nernst-Planck model. Finally, we show that the deviation of simulated currents from analytic estimates for large fields is consistent with the field-induced barriers and the observed changes in the optimal ion escape path.

Classical nucleation theory of ice nucleation: Second-order corrections to thermodynamic parameters

Accurately estimating the nucleation rate is crucial in studying ice nucleation and ice-promoting and anti-freeze strategies. In classical nucleation theory, estimates of the ice nucleation rate are very sensitive to thermodynamic parameters, such as the chemical potential difference between water and ice Δμ and the ice-water interfacial free energy γ. However, even today, there are still many contradictions and approximations when estimating these thermodynamic parameters, introducing a large uncertainty in any estimate of the ice nucleation rate. Starting from basic concepts for a general solid-liquid crystallization system, we expand the Gibbs-Thomson equation to second order and derive second-order analytical formulas for Δμ, γ, and the nucleation barrier ΔG*, which are used in molecular dynamics simulations. These formulas describe well the temperature dependence of these thermodynamic parameters. This may be a new method of estimating Δμ, γ, and ΔG*.

Phase Diagram of a Deep Potential Water Model

Using the Deep Potential methodology, we construct a model that reproduces accurately the potential energy surface of the SCAN approximation of density functional theory for water, from low temperature and pressure to about 2400 K and 50 GPa, excluding the vapor stability region. The computational efficiency of the model makes it possible to predict its phase diagram using molecular dynamics. Satisfactory overall agreement with experimental results is obtained. The fluid phases, molecular and ionic, and all the stable ice polymorphs, ordered and disordered, are predicted correctly, with the exception of ice III and XV that are stable in experiments, but metastable in the model. The evolution of the atomic dynamics upon heating, as ice VII transforms first into ice VII^{''} and then into an ionic fluid, reveals that molecular dissociation and breaking of the ice rules coexist with strong covalent fluctuations, explaining why only partial ionization was inferred in experiments.

Molecular Simulations of CO2/CH4, CO2/N2 and N2/CH4 Binary Mixed Hydrates

Abstract

Grand canonical Monte Carlo simulations were performed to study the occupancy of structure I multicomponent gas hydrates by CO2/CH4, CO2/N2, and N2/CH4 binary gas mixtures with various compositions at a temperature of 270 K and pressures up to 70 atm. The presence of nitrogen in the gas mixture allows for an increase of both the hydrate framework selectivity to CO2 and the amount of carbon dioxide encapsulated in hydrate cages, as compared to the CO2/CH4 hydrate. Despite the selectivity to CH4 molecules demonstrated by N2/CH4 hydrate, nitrogen can compete with methane if the gas mixture contains at least 70% of N2.

Universal Nucleation Behavior of Sheared Systems

Using molecular simulations and a modified classical nucleation theory, we study the nucleation, under flow, of a variety of liquids: different water models, Lennard-Jones, and hard sphere colloids. Our approach enables us to analyze a wide range of shear rates inaccessible to brute-force simulations. Our results reveal that the variation of the nucleation rate with shear is universal. A simplified version of the theory successfully captures the nonmonotonic temperature dependence of the nucleation behavior, which is shown to originate from the violation of the Stokes-Einstein relation.

Structural and topological changes across the liquid-liquid transition in water

It has recently been shown that the TIP4P/Ice model of water can be studied numerically in metastable equilibrium at and below its liquid-liquid critical temperature. We report here simulations along a subcritical isotherm, for which two liquid states with the same pressure and temperature but different density can be equilibrated. This allows for a clear visualization of the structural changes taking place across the transition. We specifically focus on how the topological properties of the H-bond network change across the liquid-liquid transition. Our results demonstrate that the structure of the high-density liquid, characterized by the existence of interstitial molecules and commonly explained in terms of the collapse of the second neighbor shell, actually originates from the folding back of long rings, bringing pairs of molecules separated by several hydrogen-bonds close by in space.

A minimalistic cyclic ice-binding peptide from phage display

Developing molecules that emulate the properties of naturally occurring ice-binding proteins (IBPs) is a daunting challenge. Rather than relying on the (limited) existing structure-property relationships that have been established for IBPs, here we report the use of phage display for the identification of short peptide mimics of IBPs. To this end, an ice-affinity selection protocol is developed, which enables the selection of a cyclic ice-binding peptide containing just 14 amino acids. Mutational analysis identifies three residues, Asp8, Thr10 and Thr14, which are found to be essential for ice binding. Molecular dynamics simulations reveal that the side chain of Thr10 hydrophobically binds to ice revealing a potential mechanism. To demonstrate the biotechnological potential of this peptide, it is expressed as a fusion ('Ice-Tag') with mCherry and used to purify proteins directly from cell lysate.

Phase Equilibrium of Water with Hexagonal and Cubic Ice Using the SCAN Functional

Machine learning models are rapidly becoming widely used to simulate complex physicochemical phenomena with ab initio accuracy. Here, we use one such model as well as direct density functional theory (DFT) calculations to investigate the phase equilibrium of water, hexagonal ice (Ih), and cubic ice (Ic), with an eye toward studying ice nucleation. The machine learning model is based on deep neural networks and has been trained on DFT data obtained using the SCAN exchange and correlation functional. We use this model to drive enhanced sampling simulations aimed at calculating a number of complex properties that are out of reach of DFT-driven simulations and then employ an appropriate reweighting procedure to compute the corresponding properties for the SCAN functional. This approach allows us to calculate the melting temperature of both ice polymorphs, the driving force for nucleation, the heat of fusion, the densities at the melting temperature, the relative stability of ices Ih and Ic, and other properties. We find a correct qualitative prediction of all properties of interest. In some cases, quantitative agreement with experiment is better than for state-of-the-art semiempirical potentials for water. Our results also show that SCAN correctly predicts that ice Ih is more stable than ice Ic.

Methane Clathrate Formation is Catalyzed and Kinetically Inhibited by the Same Molecule: Two Facets of Methanol

Here, we perform molecular dynamics simulations to provide atomic-level insights into the dual roles of methanol in enhancing and delaying the rate of methane clathrate hydrate nucleation. Consistent with experiments, we find that methanol slows clathrate hydrate nucleation above 250 K but promotes clathrate formation at temperatures below 250 K. We show that this behavior can be rationalized by the unusual temperature dependence of the methane-methanol interaction in an aqueous solution, which emerges due to the hydrophobic effect. In addition to its antifreeze properties at temperatures above 250 K, methanol competes with water to interact with methane prior to the formation of clathrate nuclei. Below 250 K, methanol encourages water to occupy the space between methane molecules favoring clathrate formation and it may additionally promote water mobility.

Homogenous nucleation rate of CO2 hydrates using transition interface sampling

Carbon dioxide and water can form solid clathrate structures in which water cages encapsulate the gas molecules. Such hydrates have sparked much interest due to their possible application in CO₂ sequestration. How the solid structure forms exactly from the liquid phase via a homogenous nucleation process is still poorly understood. This nucleation event is rare on the molecular timescale even under moderate undercooling or supersaturation conditions because of the large free energy barrier toward crystallization, rendering a brute force simulation of hydrate nucleation unfeasible for moderate undercooling or supersaturation. Here, we perform transition interface sampling simulations to quantify the homogenous nucleation rate for CO₂ hydrate formation using accurate atomistic force fields at 500 bars for three different temperatures between 260 and 273 K. Collecting more than 100 000 pathways comprising roughly two milliseconds of simulation time, we computed a nucleation rate in the amorphous phase of ∼10²¹ nuclei s^-1 cm^-3 for a temperature of 260 K and a rate of ∼10¹² nuclei s^-1 cm^-3 for a temperature of 265 K. For a temperature of 273 K, we find that the hydrate forms an sI crystalline phase with a rate of order of ∼10¹ nuclei s^-1 cm^-3. We compare these rates to classical nucleation theory estimates as well as experiments, and to nucleation rate estimates for methane hydrates and discuss possible causes of the observed differences. Our findings shed light on the kinetics of this important clathrate and should assist in future hydrate formation investigation.

Liquid Water and Interfacial, Cubic, and Hexagonal Ice Classification through Eclipsed and Staggered Conformation Template Matching

We propose a novel method based on template matching for the recognition of liquid water, cubic ice (ice I_c), hexagonal ice (ice I_h), clathrate hydrates, and different interfacial structures in atomistic and coarse-grained simulations of water and ice. The two template matrices represent staggered and eclipsed conformations, which are the building blocks of hexagonal and cubic ice and clathrate crystals. The algorithm is rotationally invariant and highly robust against imperfections in the ice structure, and its sensitivity for recognizing ice-like structures can be tuned for different applications. Unlike most other algorithms, it can discriminate between cubic, hexagonal, clathrate, mixed, and other interfacial ice types and is therefore well suited to study complex systems and heterogeneous ice nucleation.

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.

Is Ice Nucleation by Organic Crystals Nonclassical? An Assessment of the Monolayer Hypothesis of Ice Nucleation

Potent ice nucleating organic crystals display an increase in nucleation efficiency with pressure and memory effect after pressurization that set them apart from inorganic nucleants. These characteristics were proposed to arise from an ordered water monolayer at the organic-water interface. It was interpreted that ordering of the monolayer is the limiting step for ice nucleation on organic crystals, rendering their mechanism of nucleation nonclassical. Despite the importance of organics in atmospheric ice nucleation, that explanation has never been investigated. Here we elucidate the structure of interfacial water and its role in ice nucleation at ambient pressure on phloroglucinol dihydrate, the paradigmatic example of outstanding ice nucleating organic crystal, using molecular simulations. The simulations confirm the existence of an interfacial monolayer that orders on cooling and becomes fully ordered upon ice formation. The monolayer does not resemble any ice face but seamlessly connects the distinct hydrogen-bonding orders of ice and the organic surface. Although large ordered patches develop in the monolayer before ice nucleates, we find that the critical step is the formation of the ice crystallite, indicating that the mechanism is classical. We predict that the fully ordered, crystalline monolayer nucleates ice above -2 °C and could be responsible for the exceptional ice nucleation by the organic crystal at high pressures. The lifetime of the fully ordered monolayer around 0 °C, however, is too short to account for the memory effect reported in the experiments. The latter could arise from an increase in the melting temperature of ice confined by strongly ice-binding surfaces.

Molecular insights on poly(N-isopropylacrylamide) coil-to-globule transition induced by pressure

By using extensive all-atom molecular dynamics simulations of an atactic linear polymer chain, we provide microscopic insights into poly(N-isopropylacrylamide) (PNIPAM) coil-to-globule transition addressing the roles played by both temperature and pressure. We detect a coil-to-globule transition up to large pressures, showing a reentrant behavior of the critical temperature with increasing pressure in agreement with experimental observations. Furthermore, again confirming the experimental findings, we report the existence at high pressures of a new kind of globular state. It is characterized by a more structured hydration shell that is closer to PNIPAM hydrophobic domains, as compared to the globular state observed at atmospheric pressure. Our results highlight that temperature and pressure induce a PNIPAM coil-to-globule transition through different molecular mechanisms, opening the way for a systematic use of both thermodynamic variables to tune the location of the transition and the properties of the associated swollen/collapsed states.

The atomistic details of the ice recrystallisation inhibition activity of PVA

Understanding the ice recrystallisation inhibition (IRI) activity of antifreeze biomimetics is crucial to the development of the next generation of cryoprotectants. In this work, we bring together molecular dynamics simulations and quantitative experimental measurements to unravel the microscopic origins of the IRI activity of poly(vinyl)alcohol (PVA)-the most potent of biomimetic IRI agents. Contrary to the emerging consensus, we find that PVA does not require a "lattice matching" to ice in order to display IRI activity: instead, it is the effective volume of PVA and its contact area with the ice surface which dictates its IRI strength. We also find that entropic contributions may play a role in the ice-PVA interaction and we demonstrate that small block co-polymers (up to now thought to be IRI-inactive) might display significant IRI potential. This work clarifies the atomistic details of the IRI activity of PVA and provides novel guidelines for the rational design of cryoprotectants.

Homogeneous Freezing of Water Using Microfluidics

The homogeneous freezing of water is important in the formation of ice in clouds, but there remains a great deal of variability in the representation of the homogeneous freezing of water in the literature. The development of new instrumentation, such as droplet microfluidic platforms, may help to constrain our understanding of the kinetics of homogeneous freezing via the analysis of monodisperse, size-selected water droplets in temporally and spatially controlled environments. Here, we evaluate droplet freezing data obtained using the Lab-on-a-Chip Nucleation by Immersed Particle Instrument (LOC-NIPI), in which droplets are generated and frozen in continuous flow. This high-throughput method was used to analyse over 16,000 water droplets (86 μm diameter) across three experimental runs, generating data with high precision and reproducibility that has largely been unrepresented in the microfluidic literature. Using this data, a new LOC-NIPI parameterisation of the volume nucleation rate coefficient (JV(T)) was determined in the temperature region of -35.1 to -36.9 °C, covering a greater JV(T) compared to most other microfluidic techniques thanks to the number of droplets analysed. Comparison to recent theory suggests inconsistencies in the theoretical representation, further implying that microfluidics could be used to inform on changes to parameterisations. By applying classical nucleation theory (CNT) to our JV(T) data, we have gone a step further than other microfluidic homogeneous freezing examples by calculating the stacking-disordered ice-supercooled water interfacial energy, estimated to be 22.5 ± 0.7 mJ m-2, again finding inconsistencies when compared to theoretical predictions. Further, we briefly review and compile all available microfluidic homogeneous freezing data in the literature, finding that the LOC-NIPI and other microfluidically generated data compare well with commonly used non-microfluidic datasets, but have generally been obtained with greater ease and with higher numbers of monodisperse droplets.

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.