Lívia B. Pártay

A new method for determining the interfacial molecules and characterizing the surface roughness in computer simulations. Application to the liquid–vapor interface of water

A new method is presented to identify the truly interfacial molecules at fluid/fluid interfaces seen at molecular resolution, a situation that regularly occurs in computer simulations. In the new method, the surface is scanned by moving a probe sphere of a given radius along a large set of test lines that are perpendicular to the plane of the interface. The molecules that are hit by the probe spheres are regarded as interfacial ones, and the position of the test spheres when they are in contact with the interfacial molecules give an estimate of the surface. The dependence of the method on various parameters, in particular, on the size of the probe sphere is discussed in detail. Based on the list of molecules identified as truly interfacial ones, two measures of the molecular scale roughness of the surface are proposed. The bivariate distribution of the lateral and normal distances of two points of the interface provides a full description of the molecular scale morphology of the surface in a statistical sense. For practical purposes two parameters related to the dependence of the average normal distance of two surface points on their lateral distance can be used. These two parameters correspond to the frequency and amplitude of the surface roughness, respectively. The new method is applied for the analysis of the molecular level structure of the liquid–vapor interface of water. As an immediate result of the application of the new method it is shown that the orientational preferences of the interfacial water molecules depend only on the local curvature of the interface, and hence the molecules located at wells of concave curvature of the rippled surface prefer the same orientations as waters located at the surface of small apolar solutes. The vast majority of the truly interfacial molecules are found to form a strongly percolating two‐dimensional hydrogen bonded network at the surface, whereas no percolation is observed within the second molecular layer beyond the surface.

Diffusive nested sampling

We introduce a general Monte Carlo method based on Nested Sampling (NS), for sampling complex probability distributions and estimating the normalising constant. The method uses one or more particles, which explore a mixture of nested probability distributions, each successive distribution occupying ∼e−1 times the enclosed prior mass of the previous distribution. While NS technically requires independent generation of particles, Markov Chain Monte Carlo (MCMC) exploration fits naturally into this technique. We illustrate the new method on a test problem and find that it can achieve four times the accuracy of classic MCMC-based Nested Sampling, for the same computational effort; equivalent to a factor of 16 speedup. An additional benefit is that more samples and a more accurate evidence value can be obtained simply by continuing the run for longer, as in standard MCMC.

Properties of free surface of water-methanol mixtures. Analysis of the truly interfacial molecular layer in computer simulation.

Molecular dynamics simulations of the vapor-liquid interface of water-methanol mixtures of five different compositions were performed on the canonical (N,V,T) ensemble at 298 K. In addition, the vapor-liquid interface of the two neat systems was simulated, as well. The obtained configurations were analyzed by means of the novel identification of truly interfacial molecules method, which provides a full list of the molecules that are right at the surface (i.e., at the boundary of the two phases). The molecular level roughness of the surface, the adsorption of the methanol molecules at the surface layer, the orientation of the surface molecules, the residence time of the molecules at the surface layer, as well as the surface aggregation of the molecules were analyzed in detail. Both the frequency and the amplitude of the surface roughness were found to become larger with an increasing methanol content. This effect was found to be stronger for the amplitude, which falls in the range of 2-4 A, depending on the composition of the system. Methanol was found to be adsorbed at the surface layer, being preferentially at the humps of the molecularly rough surface. Surface methanol prefers to orient in such a way that the O-CH(3) bond remains perpendicular to the macroscopic plane of the surface, pointing the methyl group to the vapor phase. The main orientational preference of the water molecules is to lie parallel to the surface. Methanol was found to remain considerably longer at the surface layer of the mixed systems than water. Thus, contrary to the fact that the residence times of the two molecules were found to be rather similar to each other at the surface of their neat liquids, the residence time of the methanol molecules was an order of magnitude larger than that of water molecules at the surface of their mixtures. A strong lateral microscopic segregation of the molecules was observed at the surface layer; the minor component of the system (irrespective of whether it was water or methanol) was found to form two-dimensional aggregates, leaving the rest of the surface empty for the major component. The effect of the vicinity of the vapor phase on the properties of the molecules was found to vanish very quickly: the composition of the second layer as well as the properties of the molecules of this layer (e.g., dynamics and orientation) did not differ considerably from those in the bulk liquid phase.

Line of percolation in supercritical water

The percolation transition of the hydrogen-bonded clusters of molecules is investigated in supercritical water by Monte Carlo computer simulations. Simulations have been performed at four thermodynamic state points located above the supercritical extension of the vapor-liquid coexistence curve on the p-T phase diagram and at four state points located below this curve. It is found in a temperature range of a few hundred Kelvin that the extension of the vapor-liquid coexistence curve separates the supercritical thermodynamic states in which the water molecules form infinite hydrogen-bonded clusters from those in which the hydrogen-bonded clusters are isolated oligomers. However, the difference between the size of the hydrogen-bonded clusters at thermodynamic states located at the two sides of the extension of the coexistence curve is found to decrease with increasing temperature, and the present results suggest that this difference is likely to vanish at high enough temperatures.

Efficient Sampling of Atomic Configurational Spaces

We describe a method to explore the configurational phase space of chemical systems. It is based on the nested sampling algorithm recently proposed by Skilling (AIP Conf. Proc. 2004, 395; J. Bayesian Anal. 2006, 1, 833) and allows us to explore the entire potential energy surface (PES) efficiently in an unbiased way. The algorithm has two parameters which directly control the trade-off between the resolution with which the space is explored and the computational cost. We demonstrate the use of nested sampling on Lennard-Jones (LJ) clusters. Nested sampling provides a straightforward approximation for the partition function; thus, evaluating expectation values of arbitrary smooth operators at arbitrary temperatures becomes a simple postprocessing step. Access to absolute free energies allows us to determine the temperature-density phase diagram for LJ cluster stability. Even for relatively small clusters, the efficiency gain over parallel tempering in calculating the heat capacity is an order of magnitude or more. Furthermore, by analyzing the topology of the resulting samples, we are able to visualize the PES in a new and illuminating way. We identify a discretely valued order parameter with basins and suprabasins of the PES, allowing a straightforward and unambiguous definition of macroscopic states of an atomistic system and the evaluation of the associated free energies.

Molecular level properties of the free water surface and different organic liquid/water interfaces, as seen from ITIM analysis of computer simulation results

Molecular dynamics simulations of the interface of water with four different apolar phases, namely water vapour, liquid carbon tetrachloride, liquid dichloromethane (DCM) and liquid dichloroethane (DCE) are performed on the canonical ensemble at 298 K. The resulting configurations are analysed using the novel method of identification of the truly interfacial molecules (ITIM). Properties of the first three molecular layers of the liquid phases (e.g. width, spacing, roughness, extent of the in-layer hydrogen bonding network) as well as of the molecules constituting these layers (e.g., dynamics, orientation) are investigated in detail. In the analyses, particular attention is paid to the effect of the polarity of the non-aqueous phase and to the length scale of the effect of the vicinity of the interface on the various properties of the molecules. The obtained results show that increasing polarity of the non-aqueous phase leads to the narrowing of the interface, in spite of the fact that, at the same time, the truly interfacial layer of water gets somewhat broader. The influence of the nearby interface is found to extend only to the first molecular layer in many respects. This result is attributed to the larger space available for the truly interfacial than for the non-interfacial molecules (as the shapes of the two liquid surfaces are largely independent of each other, resulting in the presence of voids between the two phases), and to the fact that the hydrogen bonding interaction of the truly interfacial water molecules with other waters is hindered in the direction of the interface.

Molecular level structure of the liquid/liquid interface. Molecular dynamics simulation and ITIM analysis of the water-CCl4 system

The molecular level properties of the liquid/liquid interface between water and CCl(4) are analysed in detail on the basis of molecular dynamics computer simulation. This analysis requires a full list of the molecules that are right at the interface in both phases. Such a list can be provided by the novel method for identifying truly interfacial molecules (ITIM). The full list of the truly interfacial molecules various properties (e.g., width, molecular level roughness) of the interface can be meaningfully analysed. The residence time of the molecules at the interface, the percolation of the water molecules at the interfacial layer as well as in the second layer beneath the surface, the preferred orientations of the interfacial water molecules and the dependence of these orientational preferences on the local curvature of the interface are also analysed and discussed in detail.

Structural and thermodynamic properties of different phases of supercooled liquid water

Computer simulation results are reported for a realistic polarizable potential model of water in the supercooled region. Three states, corresponding to the low density amorphous ice, high density amorphous ice, and very high density amorphous ice phases are chosen for the analyses. These states are located close to the liquid-liquid coexistence lines already shown to exist for the considered model. Thermodynamic and structural quantities are calculated, in order to characterize the properties of the three phases. The results point out the increasing relevance of the interstitial neighbors, which clearly appear in going from the low to the very high density amorphous phases. The interstitial neighbors are found to be, at the same time, also distant neighbors along the hydrogen bonded network of the molecules. The role of these interstitial neighbors has been discussed in connection with the interpretation of recent neutron scattering measurements. The structural properties of the systems are characterized by looking at the angular distribution of neighboring molecules, volume and face area distribution of the Voronoi polyhedra, and order parameters. The cumulative analysis of all the corresponding results confirms the assumption that a close similarity between the structural arrangement of molecules in the three explored amorphous phases and that of the ice polymorphs I(h), III, and VI exists.

A grand canonical Monte-Carlo simulation study of water adsorption on a model soot particle

The grand canonical Monte-Carlo (GCMC) method is used to simulate the adsorption of water molecules on a spherical soot particle. Soot is modelled by graphite-type layers arranged in an onion-like structure. The calculated water adsorption isotherm at 298 K exhibits two plateaus, corresponding to the filling of the internal core of the soot particle and to the three-dimensional condensation of the water molecules around it, respectively. Moreover, no wetting of the external soot surface is evidenced. The results of these simulations can help in interpreting experimental isotherms of water adsorbed on aircraft soot.

Counterion binding in the aqueous solutions of bile acid salts, as studied by computer simulation methods.

We investigate the structural and dynamical properties of counterion binding in sodium cholate and sodium deoxycholate micelles at three different concentration, namely, 30, 90, and 300 mM, by means of molecular dynamics simulations at the atomistic level. The obtained results can resolve a long-standing, apparent contradiction between different experiments that reported discordant values for the degree of counterion binding. Namely, our results suggest that certain experimental techniques, such as freezing point depression, are only sensitive to the contact counterions, and hence, the degree of contact binding of the counterions is measured. On the other hand, in experiments employing, e.g., electrode potential or nuclear magnetic resonance measurements, the solvent-separated counterions also contribute to the signal detected, and hence, the counterions that are measured as bound ones do include the solvent-separated counterions as well.