GenIce-core: Efficient algorithm for generation of hydrogen-disordered ice structures.

Ice is different from ordinary crystals because it contains randomness, which means that statistical treatment based on ensemble averaging is essential. Ice structures are constrained by topological rules known as the ice rules, which give them unique anomalous properties. These properties become more apparent when the system size is large. For this reason, there is a need to produce a large number of sufficiently large crystals that are homogeneously random and satisfy the ice rules. We have developed an algorithm to quickly generate ice structures containing ions and defects. This algorithm is provided as an independent software module that can be incorporated into crystal structure generation software. By doing so, it becomes possible to simulate ice crystals on a previously impossible scale.

Cage occupancies of CH4, CO2, and Xe hydrates: Mean field theory and grandcanonical Monte Carlo simulations.

We propose a statistical mechanical theory for the thermodynamic stability of clathrate hydrates, considering the influence of the guest-guest interaction on the occupancies of the cages. A mean field approximation is developed to examine the magnitude of the influence. Our new method works remarkably well, which is manifested by two sorts of grandcanonical Monte Carlo (GCMC) simulations. One is full GCMC, and the other is designed in the present study for clathrate hydrates, called lattice-GCMC, in which each guest can be adsorbed at one of the centers of the cage. In the latter simulation, only the guest-guest interaction is explicitly treated, incorporating the host-guest interaction into the free energy of the cage occupation without other guests. Critical phenomena for guest species, such as large density fluctuations, are observed when the temperature is low or the guest-guest interaction is strong.

Efficiency and energy balance for substitution of CH4 in clathrate hydrates with CO2 under multiple-phase coexisting conditions.

Many experimental and theoretical studies on CH4-CO2 hydrates have been performed aiming at the extraction of CH4 as a relatively clean energy resource and concurrent sequestration of CO2. However, vague or insufficient characterization of the environmental conditions prevents us from a comprehensive understanding of even equilibrium properties of CH4-CO2 hydrates for this substitution. We propose possible reaction schemes for the substitution, paying special attention to the coexisting phases, the aqueous and/or the fluid, where CO2 is supplied from and CH4 is transferred to. We address the two schemes for the substitution operating in three-phase and two-phase coexistence. Advantages and efficiencies of extracting CH4 in the individual scheme are estimated from the chemical potentials of all the components in all the phases involved in the substitution on the basis of a statistical mechanical theory developed recently. It is found that although substitution is feasible in the three-phase coexistence, its working window in temperature-pressure space is much narrower compared to the two-phase coexistence condition. Despite that the substitution normally generates only a small amount of heat, a large endothermic substitution is suggested in the medium pressure range, caused by the vaporization of liquid CO2 due to mixing with a small amount of the released CH4. This study provides the first theoretical framework toward the practical use of hydrates replacing CH4 with CO2 and serves as a basis for quantitative planning.

On the phase behaviors of CH4-CO2 binary clathrate hydrates: Two-phase and three-phase coexistences.

We develop a statistical mechanical theory on clathrate hydrates in order to explore the phase behaviors of clathrate hydrates containing two kinds of guest species and apply it to CH4-CO2 binary hydrates. The two boundaries separating water and hydrate and hydrate and guest fluid mixtures are estimated, which are extended to the lower temperature and the higher pressure region far distant from the three-phase coexisting conditions. The chemical potentials of individual guest components can be calculated from free energies of cage occupations, which are available from intermolecular interactions between host water and guest molecules. This allows us to derive all thermodynamic properties pertinent to the phase behaviors in the whole space of thermodynamic variables of temperature, pressure, and guest compositions. It is found that the phase boundaries of CH4-CO2 binary hydrates with water and with fluid mixtures locate between simple CH4 and CO2 hydrates, but the composition ratios of CH4 guests in hydrates are disproportional to those in fluid mixtures. Such differences arise from the affinities of each guest species to the large and small cages of CS-I hydrates and significantly affect occupation of each cage type, which results in a deviation of the guest composition in hydrates from that in fluid on the two-phase equilibrium conditions. The present method provides a basis for the evaluation of the efficiency of the guest CH4 replacement to CO2 at the thermodynamic limit.

On the role of intermolecular vibrational motions for ice polymorphs. IV. Anisotropy in the thermal expansivity and the nonaffine deformation for ice IX and III.

We explore anisotropic properties in the thermal expansivities of hydrogen-ordered ice IX and its hydrogen-disordered counterpart, ice III. The free energies of these ice forms are calculated to obtain the lattice constants for the tetragonal unit cell and the thermal expansivities at various thermodynamic conditions in the framework of quasi-harmonic approximation, taking account of their anisotropic nature. The thermal expansivities are also examined by applying a thermodynamic relation that connects them with the Grüneisen parameters and the elastic compliances. Both calculations suggest that ice III and IX exhibit a negative thermal expansion along the a-axis but have a positive one along the c-axis at low temperatures. It is found that nonaffine deformation in the variation of the lattice constant beyond affine transformation (the Born approximation) is essential in the theoretical calculation of the thermal properties of ice III and IX. We also find that the nonaffine deformation is described by the shift of the minimum energy positions in the potential manifold of hydrogen-ordered ice along a limited number of the normal mode coordinates, which is irrelevant to the system size. These modes become unstable against an applied strain, so that the potential minimum moves along those normal coordinates away from that of the affine-transformed structure. The unstable modes are all symmetry-preserving modes, and the space-group symmetry is an invariant under displacement along either of those normal coordinates. The number of the unstable modes in ice IX is 8 while it is 1 in another hydrogen-ordered ice VIII.

Enhanced generation of active oxygen species induced by O3 fine bubble formation and its application to organic compound degradation.

By using O3 fine bubbles that promote the mass transfer of O3 to the liquid phase and the conversion of the dissolved O3 into active oxygen species with a high oxidation potential, an improved liquid-phase oxidation technique was developed to accelerate the degradation of an organic compound at a constant O3 flow rate. By the use of a dielectric-barrier-discharge reactor, O2 was converted into O3 at an O2 flow rate of 0.56 mmol/(L·min), with 5 mol% O2-to-O3 conversion. Using a self-supporting bubble generator, O3 bubbles with an average diameter (dbbl) of 50 µm were continuously supplied into a solution in TBA (OH• scavenger) at 303 K, and the TBA being degraded. For comparison, O3 bubbles with dbbl values of 200-5000 µm were obtained using a dispersing-type generator. It was found that the minimization of bubble diameter accelerated both O3 dissolution, as a consequence of the increase in the gas-liquid interfacial area and the residence time of the bubbles, and enhanced OH• generation, because of the increase in contact probability between dissolved O3 and OH- at the minute gas-liquid interfaces, caused by the accumulation of OH- around the fine bubble surfaces. To ascertain the influence on organic compound degradation of the improved oxidation potential, bisphenol A, as a model compound, was degraded by O3 bubble injection at different dbbl values. Sequentially, the high OH• selectivity obtained by minimizing the bubble diameter can effectively achieve the rapid degradation of organic compounds and intermediates under a constant O3 flow rate.

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.

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.

Novel Algorithm to Generate Hydrogen-Disordered Ice Structures.

We propose an efficient algorithm for generating hydrogen-disordered ice networks utilizing graph theory and the topological characteristic of the network. The computational efficiency with the new algorithm is much higher than the conventional ones developed by Rahman and Stillinger and Buch et al. The difference in the computational time between our algorithm and either of the two conventional ones increases with increasing the system size.

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 Ih 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.

Molecular dynamics study of grain boundaries and triple junctions in ice.

We perform classical molecular dynamics simulations of polycrystalline ice at 250 K using the TIP4P/Ice model. The structures of polycrystalline ice are prepared by growing ice particles in supercooled water. An order parameter developed recently is used to characterize local structures in terms of the liquid-liquid phase transition scenario. It is shown that the grain boundaries and triple junctions in ice are structurally similar to low-density liquid water in which most water molecules form four hydrogen bonds and the O-O-O angles deviate from the tetrahedral angle of 109.47°. The thickness of the grain boundaries is ∼1 nm. The diffusion coefficient of water molecules along the grain boundaries calculated in this study, 5.0 × 10-13 m2 s-1, is in good agreement with experimental data. The diffusion along the triple junctions is 3.4 times faster than that along the grain boundaries. We model the grain size dependence of diffusivity of water molecules in polycrystalline ice using the simulation results and find that the impact of the grain boundaries and the triple junctions on the diffusivity is negligible for typical polycrystalline ice samples having grain sizes of the order of millimeters. We also demonstrate that the properties of the grain boundaries are quite different from those of the ice/vapor interface at the same temperature: the quasi-liquid layer at the ice/vapor interface is similar to high-density liquid water and the diffusion coefficient along the ice/vapor interface is two orders of magnitude larger than that along the grain boundaries.

Lennard-Jones Parameters Determined to Reproduce the Solubility of NaCl and KCl in SPC/E, TIP3P, and TIP4P/2005 Water.

Most classical nonpolarizable ion potential models underestimate the solubility values of NaCl and KCl in water significantly. We determine Lennard-Jones parameters of Na+, K+, and Cl- that reproduce the solubility as well as the hydration free energy in dilute aqueous solutions for three water potential models, SPC/E, TIP3P, and TIP4P/2005. The ion-oxygen distance in the solution and the cation-anion distance in salt are also considered in the parametrization. In addition to the target properties, the hydration enthalpy, hydration entropy, self-diffusion coefficient, coordination number, lattice energy, enthalpy of solution, density, viscosity, and number of contact ion pairs are calculated for comparison with 17 frequently used or recently developed ion potential models. The overall performance of each ion model is represented by a global score using a scheme that was originally developed for comparison of water potential models. The global score is better for our models than for the other 17 models not only because of the quite good prediction for the solubility but also because of the relatively small deviation from the experimental value for many of the other properties.

On the role of intermolecular vibrational motions for ice polymorphs. II. Atomic vibrational amplitudes and localization of phonons in ordered and disordered ices.

We investigate the vibrational amplitudes and the degree of the phonon localization in 19 ice forms, both crystalline and amorphous, by a quasi-harmonic approximation with a reliable classical intermolecular interaction model for water. The amplitude in the low pressure ices increases with compression, while the opposite trend is observed in the medium and high pressure ices. The amplitude of the oxygen atom does not differ from that of hydrogen in low pressure ices apart from the contribution from the zero-point vibrations. This is accounted for by the coherent but opposite phase motions in the mixed translational and rotational vibrations. A decoupling of translation-dominant and rotation-dominant motions significantly reduces the vibrational amplitudes in any ice form. The amplitudes in ice III are found to be much larger than any other crystalline ice form. In order to investigate the vibrational mode characteristics, the moment ratio of the atomic displacements for individual phonon modes, called the inverse participation ratio, is calculated and the degree of the phonon localization in crystalline and amorphous ices is discussed. It is found that the phonon modes in the hydrogen-ordered ice forms are remarkably spread over the entire crystal having propagative or diffusive characteristic, while many localized modes appear at the edges of the vibrational bands, called dissipative modes, in the hydrogen-disordered counterparts. The degree of localization is little pronounced in low density amorphous and high density amorphous due to disordering of oxygen atoms.

On the role of intermolecular vibrational motions for ice polymorphs I: Volumetric properties of crystalline and amorphous ices.

Intermolecular vibrations and volumetric properties are investigated using the quasiharmonic approximation with the TIP4P/2005, TIP4P/Ice, and SPC/E potential models for most of the known crystalline and amorphous ice forms that have hydrogen-disordering. The ice forms examined here cover low pressure ices (hexagonal and cubic ice I, XVI, and hypothetical dtc ice), medium pressure ices (III, IV, V, VI, XII, hydrogen-disordered variant of ice II), and high pressure ice (VII) as well as the low density and the high density amorphous forms. We focus on the thermal expansivities and the isothermal compressibilities in the low temperature regime over a wide range of pressures calculated via the intermolecular vibrational free energies. Negative thermal expansivity appears only in the low pressure ice forms. The sign of the thermal expansivity is elucidated in terms of the mode Grüneisen parameters of the low frequency intermolecular vibrational motions. Although the band structure for the low frequency region of the vibrational density of state in the medium pressure ice has a close resemblance to that in the low pressure ice, its response against volume variation is opposite. We reveal that the mixing of translational and rotational motions in the low frequency modes plays a crucial role in the appearance of the negative thermal expansivity in the low pressure ice forms. The medium pressure ices can be further divided into two groups in terms of the hydrogen-bond network flexibility, which is manifested in the properties on the molecular rearrangement against volume variation, notably the isothermal compressibility.

A Bayesian approach for identification of ice Ih, ice Ic, high density, and low density liquid water with a torsional order parameter.

An order parameter is proposed to classify the local structures of liquid and solid water. The order parameter, which is calculated from the O-O-O-O dihedral angles, can distinguish ice Ih, ice Ic, high density, and low density liquid water. Three coloring schemes are proposed to visualize each of the coexisting phases in a system using the order parameter on the basis of Bayesian decision theory. The schemes are applied to a molecular dynamics trajectory in which ice nucleation occurs following spontaneous liquid-liquid separation in the deeply supercooled region as a demonstration.

Liquid-liquid separation of aqueous solutions: A molecular dynamics study.

In the liquid-liquid phase transition scenario, supercooled water separates into the high density liquid (HDL) and low density liquid (LDL) phases at temperatures lower than the second critical point. We investigate the effects of hydrophilic and hydrophobic solutes on the liquid-liquid phase transition using molecular dynamics simulations. It is found that a supercooled aqueous NaCl solution separates into solute-rich HDL and solute-poor LDL parts at low pressures. By contrast, a supercooled aqueous Ne solution separates into solute-rich LDL and solute-poor HDL parts at high pressures. Both the solutes increase the high temperature limit of the liquid-liquid separation. The degree of separation is quantified using the local density of solute particles to determine the liquid-liquid coexistence region in the pressure-temperature phase diagram. The effects of NaCl and Ne on the phase diagram of supercooled water are explained in terms of preferential solvation of ions in HDL and that of small hydrophobic particles in LDL, respectively.

Phase diagram of ice polymorphs under negative pressure considering the limits of mechanical stability.

Thermodynamic and mechanical stabilities of various ultralow-density ices are examined using computer simulations to construct the phase diagram of ice under negative pressure. Some ultralow-density ices, which were predicted to be thermodynamically metastable under negative pressures on the basis of the quasi-harmonic approximation, can exist only in a narrow pressure range at very low temperatures because they are mechanically fragile due to the large distortion in the hydrogen bonding network. By contrast, relatively dense ices such as ice Ih and ice XVI withstand large negative pressure. Consequently, various ices appear one after another in the phase diagram. The phase diagram of ice under negative pressure exhibits a different complexity from that of positive pressure because of the mechanical instability.

On the phase behaviors of hydrocarbon and noble gas clathrate hydrates: Dissociation pressures, phase diagram, occupancies, and equilibrium with aqueous solution.

We apply a statistical mechanical theory on clathrate hydrates to an exploration of the phase behaviors of hydrocarbon and noble gas clathrate hydrates. Two- and three-phase coexisting conditions in the whole space of thermodynamic variables (temperature, pressure, and composition) are evaluated only from intermolecular interactions for water and guest species. The occupancy of guest molecules in various types of cages is also calculated. We find that a small difference in the guest size gives rise to a rich variety of phase behaviors, notably for the shape of the two-phase boundary and the occupancy. Ethane clathrate hydrate is found to exhibit the most drastic and intriguing features in various properties arising from its non-stoichiometry. We investigate the phase behaviors of clathrate hydrate in terms of the partial molar quantities derived from the chemical potentials of guest and water. Our method also allows exploring the aqueous solution of an apolar guest molecule in the low temperature and high pressure regime coexisting with the corresponding clathrate hydrate for which the free guest fluid phase is substituted at high temperatures. It is shown that the temperature dependence of methane solubility in liquid water in the presence of clathrate hydrate is opposite to that being in equilibrium with the methane fluid without clathrate hydrate. This phenomenon is elucidated by a substantial decrease in the chemical potential of methane from the hydrate/guest boundary to the hydrate/water.

Phase Diagrams of TIP4P/2005, SPC/E, and TIP5P Water at High Pressure.

We investigate high-pressure ice phases using molecular dynamics simulations. Spontaneous nucleation of a new crystalline solid, named ice T2, is observed in a simulation of TIP4P/2005 water at 260 K and 3.3 GPa. The phase diagram of ices VI, VII, T2, and recently reported two other hypothetical ices, ice R and ice T, is determined using the direct coexistence method and the Clausius-Clapeyron equation for TIP4P/2005, SPC/E, and TIP5P water. It is found that there exists at least one pressure region in which a hypothetical ice phase is the most stable at ambient temperature with those models. Although the hypothetical ices may be metastable in reality, these ices could be of great importance toward a comprehensive understanding of the phase behaviors of water including many metastable ice polymorphs settled in the hidden area of T- P space. The unit cell of ice T2 is tetragonal with a space group of I41/ acd and it contains 152 water molecules. This is probably the most entangled structure among crystals which have been found in nucleation simulations without bias.

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.