Free-energy calculation of structure-H hydrates

A molecular-dynamics (MD) simulation of structure-H hydrates was performed under constant pressure and temperature with 6120 TIP4P water molecules, 900 OPLS-UA methane molecules, and 180 large molecular guest substance (LMGS) molecules. The LMGS molecules were represented in the form of a one-site Lennard-Jones (LJ) model using the LJ parameters sigma and epsilon. In order to clarify the thermodynamic stability of structure-H hydrates, we calculated the free-energy difference, changing on the sigma and epsilon only of the LMGS molecules. In this simulation, stable crystals of structure-H hydrates and a minimum value of DeltaG were obtained at sigma approximately 6.2 A and large values of epsilon. All simulations were performed using the special-purpose computer hardware MDGRAPE-2.     

Molecular dynamics study of structure H clathrate hydrates of methane and large guest molecules

Methane storage in structure H (sH) clathrate hydrates is attractive due to the relatively higher stability of sH as compared to structure I methane hydrate. The additional stability is gained without losing a significant amount of gas storage density as happens in the case of structure II (sII) methane clathrate. Our previous work has showed that the selection of a specific large molecule guest substance (LMGS) as the sH hydrate former is critical in obtaining the optimum conditions for crystallization kinetics, hydrate stability, and methane content. In this work, molecular dynamics simulations are employed to provide further insight regarding the dependence of methane occupancy on the type of the LMGS and pressure. Moreover, the preference of methane molecules to occupy the small (5(12)) or medium (4(3)5(6)6(3)) cages and the minimum cage occupancy required to maintain sH clathrate mechanical stability are examined. We found that thermodynamically, methane occupancy depends on pressure but not on the nature of the LMGS. The experimentally observed differences in methane occupancy for different LMGS may be attributed to the differences in crystallization kinetics and/or the nonequilibrium conditions during the formation. It is also predicted that full methane occupancies in both small and medium clathrate cages are preferred at higher pressures but these cages are not fully occupied at lower pressures. It was found that both small and medium cages are equally favored for occupancy by methane guests and at the same methane content, the system suffers a free energy penalty if only one type of cage is occupied. The simulations confirm the instability of the hydrate when the small and medium cages are empty. Hydrate decomposition was observed when less than 40% of the small and medium cages are occupied.     

Molecular dynamics simulation for studying the stability of structure H clathrate-hydrates of argon and large guest molecules

The aim of present paper is to study the stability of (argon + large guest molecules) structure H clathrate-hydrates by using molecular dynamics simulations and with employing the COMPASS force field to consider the molecular interactions. The simulations are performed by embedding the structure H clathrate-hydrates in a simulation cell under isobaric-isothermal (NPT) conditions. The obtained equilibrium lattice parameters are compared with the experimental data, where a good consistency is observed. The results show that the size and dipole moment of the guest molecules enclosed in the hydrate cages play the main role in the interactions between the guest molecules and the water molecules, which constitute the surrounding walls of the hydrate cage and these interactions would stabilize the hydrate structure. The characteristics of the clathrate-hydrate structure are analyzed by evaluating the radial distribution function, where the agreement between the results obtained in this work and other similar theoretical and experimental investigations validates the simulation procedure and related interpretations.     

A powerful computational crystallography method to study ice polymorphism

Classical molecular dynamics (MD) simulations are employed as a tool to investigate structural properties of ice crystals under several temperature and pressure conditions. All ice crystal phases are analyzed by means of a computational protocol based on a clustering approach following standard MD simulations. The MD simulations are performed by using a recently published classical interaction potential for oxygen and hydrogen in bulk water, derived from neutron scattering data, able to successfully describe complex phenomena such as proton hopping and bond formation/breaking. The present study demonstrates the ability of the interaction potential model to well describe most ice structures found in the phase diagram of water and to estimate the relative stability of 16 known phases through a cluster analysis of simulated powder diagrams of polymorphs obtained from MD simulations. The proposed computational protocol is suited for automated crystal structure identification.     

Structure and decompression melting of a novel, high-pressure nanoconfined 2-D ice

Molecular dynamics (MD) simulations of water confined in nanospaces between layers of talc (system composition Mg(3)Si(4)O(10)(OH)(2) + 2H(2)O) at 300 K and pressures of approximately 0.45 GPa show the presence of a novel 2-D ice structure, and the simulation results at lower pressures provide insight into the mechanisms of its decompression melting. Talc is hydrophobic at ambient pressure and temperature, but weak hydrogen bonding between the talc surface and the water molecules plays an important role in stabilizing the hydrated structure at high pressure. The simulation results suggest that experimentally accessible elevated pressures may cause formation of a wide range of previously unknown water structures in nanoconfinement. In the talc 2-D ice, each water molecule is coordinated by six O(b) atoms of one basal siloxane sheet and three water molecules. The water molecules are arranged in a buckled hexagonal array in the a-b crystallographic plane with two sublayers along [001]. Each H(2)O molecule has four H-bonds, accepting one from the talc OH group and one from another water molecule and donating one to an O(b) and one to another water molecule. In plan view, the molecules are arranged in six-member rings reflecting the substrate talc structure. Decompression melting occurs by migration of water molecules to interstitial sites in the centers of six-member rings and eventual formation of separate empty and water-filled regions.     

Hydrate kinetics study in the presence of nonaqueous liquid by nuclear magnetic resonance spectroscopy and imaging

The dynamics of methane hydrate growth and decomposition were studied by nuclear magnetic resonance (NMR) spectroscopy and imaging (MRI). Three well-known large molecule guest substances (LMGS) were used as structure H hydrate formers: 2,2-dimethylbutane (NH), methylcyclohexane (MCH), tert-butyl methyl ether (TBME). In addition, the impact of a non-hydrate former (n-heptane/nC7) was studied. The methane diffusion and hydrate growth were monitored by recording the 2H NMR spectra at 253 K and approximately 4.5 MPa for 20 h. The results revealed that methane diffuses faster in TBME and NH, slower in nC7, and slowest in MCH. The TBME system gives the fastest hydrate formation kinetics followed by NH, MCH, and nC7. The conversion of water into hydrate was also observed. The imaging study showed that TBME has a strong affinity toward ice, which is not the case for the NH and MCH systems. The degree of ice packing was also found to affect the LMGS distribution between ice particles. Highly packed ice increases the mass transfer resistance and hence limits the contact between LMGS and ice. It was also found that "temperature ramping" above the ice point improves the conversion significantly. Finally, hydrates were found to dissociate quickly within the first hour at atmospheric pressure and subsequently at a much slower rate. Methane dissolved in LMGS was also seen. The residual methane in hydrate phase and dissolved in LMGS phase explain the faster kinetics during hydrate re-formation.     

The effect of aqueous solutions of trimethylamine-N-oxide on pressure induced modifications of hydrophobic interactions

To understand the mechanism of protein protection by the osmolyte trimethylamine-N-oxide (TMAO) at high pressure, using molecular dynamics (MD) simulations, solvation of hydrophobic group is probed in aqueous solutions of TMAO over a wide range of pressures relevant to protein denaturation. The hydrophobic solute considered in this study is neopentane which is a considerably large molecule. The concentrations of TMAO range from 0 to 4 M and for each TMAO concentration, simulations are performed at five different pressures ranging from 1 atm to 8000 atm. Potentials of mean force are calculated and the relative stability of solvent-separated state over the associated state of hydrophobic solute are estimated. Results suggest that high pressure reduces association of hydrophobic solutes. From computations of site-site radial distribution function followed by analysis of coordination number, it is found that water molecules are tightly packed around the nonpolar particle at high pressure and the hydration number increases with increasing pressure. On the other hand, neopentane interacts preferentially with TMAO over water and although hydration of neopentane reduces in presence of this osmolyte, TMAO does not show any tendency to prevent the pressure-induced dispersion of neopentane moieties. It is also observed that TMAO molecules prefer a side-on orientation near the neopentane surface, allowing its oxygen atom to form favorable hydrogen bonds with water while maintaining some hydrophobic contacts with neopentane. Analysis of hydrogen-bond properties and solvation characteristics of TMAO reveals that TMAO can form hydrogen bonds with water and it reduces the identical nearest neighbor water molecules caused by high hydrostatic pressures. Moreover, TMAO enhances life-time of water-water hydrogen bonds and makes these hydrogen bonds more attractive. Implication of these results for counteracting effect of TMAO against protein denaturation at high pressures are discussed.     

NMR studies of carbon dioxide and methane self-diffusion in ZIF-8 at elevated gas pressures

Self-diffusion measurements with methane and carbon dioxide adsorbed in the Zeolitic Imidazolate Framework-8 (ZIF-8) were performed by ¹H and ¹³C pulsed field gradient nuclear magnetic resonance (PFG NMR). The experiments were conducted at 298 K and variable pressures of 7 to 15 bar in the gas phase above the ZIF-8 bed. Via known adsorption isotherms these pressures were converted to loadings of the adsorbed molecules. The self-diffusion coefficients of carbon dioxide measured by PFG NMR are found to be independent of loading. They are in good agreement with results from molecular dynamic (MD) simulations and resume the trend previously found by IR microscopy at lower loadings. Methane diffuses in ZIF-8 only slightly slower than carbon dioxide. Its experimentally obtained self-diffusion coefficients are about a factor of two smaller than the corresponding values determined by MD simulations using flexible frameworks.     

添加氧影响下低压金刚石生长的条件

采用非平衡热力学耦合模型研究金刚石在CO-H₂、CO-O₂-H₂体系中的生长情况,计算不同氧含量下的金刚石生长相图,固定氧氢比考察压力变化对金刚石生长区的影响,讨论了不同氧氢含量对金刚石生长区的影响。与经典的平衡热力学理论计算所得的相图不同,本文的相图均有金刚石生长区,可以很好地解释低压下金刚石在气相中的生长,还可以用于指导低压金刚石生长的实验研究。     

Thermodynamic properties of benzene under shock conditions

We present in this paper a thermodynamic analysis of benzene properties under shock conditions as given by molecular dynamics (MD) simulations. Reactive MD simulations of benzene predict a decomposition threshold corresponding to the flection point on the experimental Hugoniot curve. A polymerlike carbonated structure is observed for pressures above this threshold, but the calculated Hugoniot curve is in disagreement with the experimental one at high pressure. On the contrary, a system consisting of a diamond cluster in hydrogen gas leads to a correct prediction of the pressure on the Hugoniot curves. The central question is then linked to the kinetics of the transition between the polymerlike structure and the diamond cluster.     

Fluid phase stability and equilibrium calculations in binary mixtures: Part II: Application to single-point calculations and the construction of phase diagrams

The methodology presented in Part I of this work is applied to a large number of pressure–temperature flash calculations, and to the automated construction of constant temperature pressure–composition phase diagrams, and constant pressure temperature–composition phase diagrams for binary mixtures modeled with an augmented van der Waals equation of state. An automated prototype implementation of the algorithm is developed for this purpose. We follow the classification of Scott and van Konynenburg [R.L. Scott, P.H. van Konynenburg, Discuss. Faraday Soc. 49 (1970) 87] and present phase diagrams corresponding to non-azeotropic mixtures of the five main types of fluid phase behavior (I–V), studying in detail representative diagrams at constant pressure and constant temperature. Special attention is given to the solution of numerically problematic equilibrium regions, such as those close to three-phase equilibria where metastable and unstable critical points can also be found. Of the order of 10⁴ flash calculations at varying temperatures and pressures, and for different intermolecular parameters of the components in the mixture, have been carried out. The algorithm provides the correct stable equilibrium state for all of the points considered. Despite the fact that our implementation is not optimised for performance, we find that the algorithm identifies the stable solution in difficult regions of the phase space without any penalty in terms of computational time, when compared to simpler regions.     

Application of the cell potential method to predict phase equilibria of multicomponent gas hydrate systems

We present the application of a mathematical method reported earlier by which the van der Waals-Platteeuw statistical mechanical model with the Lennard-Jones and Devonshire approximation can be posed as an integral equation with the unknown function being the intermolecular potential between the guest molecules and the host molecules. This method allows us to solve for the potential directly for hydrates for which the Langmuir constants are computed, either from experimental data or from ab initio data. Given the assumptions made in the van der Waals-Platteeuw model with the spherical-cell approximation, there are an infinite number of solutions; however, the only solution without cusps is a unique central-well solution in which the potential is at a finite minimum at the center to the cage. From this central-well solution, we have found the potential well depths and volumes of negative energy for 16 single-component hydrate systems: ethane (C2H6), cyclopropane (C3H6), methane (CH4), argon (Ar), and chlorodifluoromethane (R-22) in structure I; and ethane (C2H6), cyclopropane (C3H6), propane (C3H8), isobutane (C4H10), methane (CH4), argon (Ar), trichlorofluoromethane (R-11), dichlorodifluoromethane (R-12), bromotrifluoromethane (R-13B1), chloroform (CHCl3), and 1,1,1,2-tetrafluoroethane (R-134a) in structure II. This method and the calculated cell potentials were validated by predicting existing mixed hydrate phase equilibrium data without any fitting parameters and calculating mixture phase diagrams for methane, ethane, isobutane, and cyclopropane mixtures. Several structural transitions that have been determined experimentally as well as some structural transitions that have not been examined experimentally were also predicted. In the methane-cyclopropane hydrate system, a structural transition from structure I to structure II and back to structure I is predicted to occur outside of the known structure II range for the cyclopropane hydrate. Quintuple (L(w)-sI-sII-L(hc)-V) points have been predicted for the ethane-propane-water (277.3 K, 12.28 bar, and x(eth,waterfree) = 0.676) and ethane-isobutane-water (274.7 K, 7.18 bar, and x(eth,waterfree) = 0.81) systems.     

Searching for nanostructures of the cubic mesophase of liquid crystal molecules, BABH8

Nanostructures of a thermotropic cubic phase forming liquid crystal compound, 1,2-bis-[4-n-octyloxy-benzoyl]-hydrazine was studied by molecular dynamics (MD) simulations. A model for its cubic phase structure was proposed, which was constructed from the building unit of a locally orientational ordered "bundle" consistent with the cell parameter and the space group (Ia3d) from the recent x-ray results. Stability of the model structure was studied by multinanosecond MD simulations. A periodic nanostructure with 2.6 nm periodicity [coincides with the Ia3d (211) reflection] was kept up to 60 ns in the reduced pressure simulation which realizes the experimental value of density. However, the calculated fourth-rank order parameter shows that the simulated final state above does not have cubic orientational symmetry but rather isotropic symmetry.     

Equations of states for an ionic liquid under high pressure: A molecular dynamics simulation study

The high-pressure dependence of density given by empirical equation of states (EoS) for the ionic liquid 1-butyl-3-methylimidazolium trifluoromethanesulfonate (or triflate), [C₄C₁im][TfO], is compared with results obtained by molecular dynamics (MD) simulations. Two EoS proposed for [C₄C₁im][TfO] in the pressure range of tens of MPa, which give very different densities when extrapolated to pressures beyond the original experiments, are compared with a group contribution model (GCM). The MD simulations provide support that one of the empirical EoS and the GCM is valid in the pressure range of hundreds of MPa. As an alternative to these EoS that are based on modified Tait equations, it is shown that a perturbed hard-sphere EoS based on the Carnahan–Starling–van der Waals equation also fits the densities calculated by MD simulations of [C₄C₁im][TfO] up to ∼1.0 GPa.     

Structure, energetics, and dynamics of water adsorbed on the muscovite (001) surface: a molecular dynamics simulation

Molecular dynamics (MD) computer simulations of liquid water adsorbed on the muscovite (001) surface provide a greatly increased, atomistically detailed understanding of surface-related effects on the spatial variation in the structural and orientational ordering, hydrogen bond (H-bond) organization, and local density of H2O molecules at this important model phyllosilicate surface. MD simulations at constant temperature and volume (statistical NVT ensemble) were performed for a series of model systems consisting of a two-layer muscovite slab (representing 8 crystallographic surface unit cells of the substrate) and 0 to 319 adsorbed H2O molecules, probing the atomistic structure and dynamics of surface aqueous films up to 3 nm in thickness. The results do not demonstrate a completely liquid-like behavior, as otherwise suggested from the interpretation of X-ray reflectivity measurements and earlier Monte Carlo simulations. Instead, a more structurally and orientationally restricted behavior of surface H2O molecules is observed, and this structural ordering extends to larger distances from the surface than previously expected. Even at the largest surface water coverage studied, over 20% of H2O molecules are associated with specific adsorption sites, and another 50% maintain strongly preferred orientations relative to the surface. This partially ordered structure is also different from the well-ordered 2-dimensional ice-like structure predicted by ab initio MD simulations for a system with a complete monolayer water coverage. However, consistent with these ab initio results, our simulations do predict that a full molecular monolayer surface water coverage represents a relatively stable surface structure in terms of the lowest diffusional mobility of H2O molecules along the surface. Calculated energies of water adsorption are in good agreement with available experimental data.     

High-pressure study of adamantane: variable shape simulations up to 26 GPa

We report simulations of adamantane by carefully combining ab initio and empirical approaches to enable simulations with internal degrees of freedom on crystalline adamantane up to a pressure of 26 GPa. Two sets of simulations, assuming the adamantane molecule as a rigid (RB) and flexible body (FB), have been carried out as a function of pressure up to 26 GPa to understand changes in the crystal structure as well as molecular structure. The flexible body simulations have been performed by including 6 lowest frequency internal modes (obtained from DFT calculations performed with Gaussian98) out of the total of 72. The calculated variation in c/a and V/V(0) from the RB and FB calculations as a function of pressure have been compared with the experimental curve. Other relevant thermodynamic and structural properties reported are the radial distribution functions, deviation in the position of a given type of atom with respect to its position at standard pressure, delta(s), cell parameters, volume, and energy. With an increase in pressure, three additional peaks are seen to develop gradually at three different pressures in the center of mass (com)-com radial distribution function (rdf). We attribute these changes to structural transformations (probably second-order phase transitions) which is consistent with the three phase transitions reported by Vijayakumar et al. for adamantane in the pressure range of 1 atm-15 GPa. Our simulations also show that these additional peaks in the rdf's are associated with the differences between opposite and parallel spin neighbors of Greig and Pawley as well as the crystallographic directional dependence of intermolecular distances in the first three shells of the neighbors. Also, the structural quantities from the RB calculation show considerable deviation from the FB calculation for pressures greater than 5 GPa, which suggests that the rigid body assumption for molecules may not be valid above this pressure.     

Methane adsorption and diffusion in a model nanoporous carbon: an atomistic simulation study

A constricted slit model was introduced to improve, one step further, the performance of the simple slit model in prediction of the adsorption and diffusion behavior of simple molecules in the nanoporous carbons (NPCs). The grand canonical Monte Carlo (GCMC) and molecular dynamics (MD) simulations are performed to study the adsorption and diffusion behavior of methane within the constricted slit models. The models are called slit-1, 2, and 3 with constriction heights 5, 7, and 9 Å respectively. For comparison, we used the slit-0 name for the simple slit without constriction. Adsorption results show that at low pressures, the constriction increases the adsorbed amount irrespective of its height. Slit-2 with a constriction height as a molecular diameter has the greatest heat of adsorption and has highest loading at pressures up to 3,000 kPa. At high pressures, when all pores are filled, the adsorption trend is in line with the pore volumes of slits where slit-0 with higher pore volume is dominant. The density profiles in the models were calculated and examined. The spatial distribution of adsorbed methane molecules was examined by various radial distribution functions calculated by MD. Also, MD simulation results show that the diffusion coefficient of methane decreases in constricted slits. The calculated diffusion coefficients in slit-2 in the direction of the constriction are one order of magnitude smaller than the calculated one in the simple slit model but it is far from the experimental values in the NPCs.     

Equilibrium surface properties of lipid mixtures of retinal,phosphatidylcholine and fatty acid derivatives at the air/water interface

The miscibilities of phosphatidylcholine, retinal and saturated fatty acid derivatives in surface phases at the air/water interface are investigated on the basis of the thermodynamic two-dimensional phase rule. The latter is applied to the ‘collapse’ pressure and the equilibrium surface pressure characteristics of binary lipid monolayers or spread amphiphilic mixtures, respectively. The equilibrium surface pressures (ESPs), at which insoluble lipid monolayers are in equilibrium with three-dimensional lipid phases, are determined by spreading of single-component or binary solutions of lipids in organic solvent up to supersaturation at the air/water interface. The kinetics of establishment of steady surface pressure values at supersaturation is followed depending on the nature of the lipid samples. ESPs and ‘collapse’ pressures of mixtures of dilaur-oylphosphatidylcholine (DLPC), all-trans retinal (t-R) and lauric acid (LA) are studied at various lipid molar ratios. The compositional phase diagrams of the ESPs and ‘collapse’ pressures, obtained at a constant temperature, indicate that the interfacial miscibilities of both DLPC and t-R and DLPC and LA are non-ideal. Owing to its ‘bulky’ molecular structure and the tendency towards self-aggregation, dominated by intermolecular π-π interactions, the t-R component could be accommodated in the hydrophobic portion of the phospholipid membrane at mole fractions less than 0.5. The accommodation of the other neutral, rod-like fatty acid component in the DLPC matrix is probably favoured by the formation of intermolecular hydrogen bonding. Phase separation between DLPC and LA is evident from the thermodynamic results at high LA mole fractions (> 0.75) in the surface mixtures.     

Methanation of CO over nickel: Mechanism and kinetics at high H2/CO ratios

The CO methanation reaction over nickel was studied at low CO concentrations and at hydrogen pressures slightly above ambient pressure. The kinetics of this reaction is well described by a first-order expression with CO dissociation at the nickel surface as the rate-determining step. At very low CO concentrations, adsorption of CO molecules and H atoms compete for the sites at the surface, whereas the coverage of CO is close to unity at higher CO pressures. The ratio of the equilibrium constants for CO and H atom adsorption, K(CO)/K(H), was obtained from the rate of CO methanation at various CO concentrations. K(H) was determined independently from temperature programmed adsorption/desorption of hydrogen to be K(H) = 7.7 x 10(-4) (bar(-0.5)) exp[43 (kJ/mol)/RT] and hence the equilibrium constants for adsorption of CO molecules may be calculated to be K(CO) = 3 x 10(-7) (bar(-1)) exp[122 (kJ/mol)/RT]. Furthermore, the rate of dissociation of CO at the catalyst surface was determined to be 5 x 10(9) (s(-1)) exp[-96.7 (kJ/mol)/RT] assuming that 5% of the surface nickel atoms are active for CO dissociation. The results are compared to equilibrium and rate constants reported in the literature.