Eva G. Noya

Determination of phase diagrams via computer simulation: methodology and applications to water, electrolytes and proteins

In this review we focus on the determination of phase diagrams by computer simulation, with particular attention to the fluid–solid and solid–solid equilibria. The methodology to compute the free energy of solid phases will be discussed. In particular, the Einstein crystal and Einstein molecule methodologies are described in a comprehensive way. It is shown that both methodologies yield the same free energies and that free energies of solid phases present noticeable finite size effects. In fact, this is the case for hard spheres in the solid phase. Finite size corrections can be introduced, although in an approximate way, to correct for the dependence of the free energy on the size of the system. The computation of free energies of solid phases can be extended to molecular fluids. The procedure to compute free energies of solid phases of water (ices) will be described in detail. The free energies of ices Ih, II, III, IV, V, VI, VII, VIII, IX, XI and XII will be presented for the SPC/E and TIP4P models of water. Initial coexistence points leading to the determination of the phase diagram of water for these two models will be provided. Other methods to estimate the melting point of a solid, such as the direct fluid–solid coexistence or simulations of the free surface of the solid, will be discussed. It will be shown that the melting points of ice Ih for several water models, obtained from free energy calculations, direct coexistence simulations and free surface simulations agree within their statistical uncertainty. Phase diagram calculations can indeed help to improve potential models of molecular fluids. For instance, for water, the potential model TIP4P/2005 can be regarded as an improved version of TIP4P. Here we will review some recent work on the phase diagram of the simplest ionic model, the restricted primitive model. Although originally devised to describe ionic liquids, the model is becoming quite popular to describe the behavior of charged colloids. Moreover, the possibility of obtaining fluid–solid equilibria for simple protein models will be discussed. In these primitive models, the protein is described by a spherical potential with certain anisotropic bonding sites (patchy sites). (Some figures in this article are in colour only in the electronic version)

Reversible self-assembly of patchy particles into monodisperse icosahedral clusters

We systematically study the design of simple patchy sphere models that reversibly self-assemble into monodisperse icosahedral clusters. We find that the optimal patch width is a compromise between structural specificity (the patches must be narrow enough to energetically select the desired clusters) and kinetic accessibility (they must be sufficiently wide to avoid kinetic traps). Similarly, for good yields the temperature must be low enough for the clusters to be thermodynamically stable, but the clusters must also have enough thermal energy to allow incorrectly formed bonds to be broken. Ordered clusters can form through a number of different dynamic pathways, including direct nucleation and indirect pathways involving large disordered intermediates. The latter pathway is related to a reentrant liquid-to-gas transition that occurs for intermediate patch widths upon lowering the temperature. We also find that the assembly process is robust to inaccurate patch placement up to a certain threshold and that it is possible to replace the five discrete patches with a single ring patch with no significant loss in yield.

Anomalies in water as obtained from computer simulations of the TIP4P/2005 model: density maxima, and density, isothermal compressibility and heat capacity minima

The so-called thermodynamic anomalies of water form an integral part of the peculiar behaviour of this both important and ubiquitous molecule. In this paper our aim is to establish whether the recently proposed TIP4P/2005 model is capable of reproducing a number of these anomalies. Using molecular dynamics simulations we investigate both the maximum in density and the minimum in the isothermal compressibility along a number of isobars. It is shown that the model correctly describes the decrease in the temperature of the density maximum with increasing pressure. At atmospheric pressure the model exhibits an additional minimum in density at a temperature of about 200K, in good agreement with recent experimental work on super-cooled confined water. The model also presents a minimum in the isothermal compressibility close to 310K. We have also investigated the atmospheric pressure isobar for three other water models; the SPC/E and TIP4P models also present a minimum in the isothermal compressibility, although at a considerably lower temperature than the experimental one. For the temperature range considered no such minimum is found for the TIP5P model.

Revisiting the Frenkel-Ladd method to compute the free energy of solids: The Einstein molecule approach

In this paper a new method to evaluate the free energy of solids is proposed. The method can be regarded as a variant of the method proposed by Frenkel and Ladd [J. Chem. Phys. 81, 3188 (1984)]. The main equations of the method can be derived in a simple way. The method can be easily implemented within a Monte Carlo program. We have applied the method to determine the free energy of hard spheres in the solid phase for several system sizes. The obtained free energies agree within the numerical uncertainty with those obtained by Polson et al. [J. Chem. Phys. 112, 5339 (2000)]. The fluid-solid equilibria has been determined for several system sizes and compared to the values published previously by Wilding and Bruce [Phys. Rev. Lett. 85, 5138 (2000)] using the phase switch methodology. It is shown that both the free energies and the coexistence pressures present a strong size dependence and that the results obtained from free energy calculations agree with those obtained using the phase switch method, which constitutes a cross-check of both methodologies. From the results of this work we estimate the coexistence pressure of the fluid-solid transition of hard spheres in the thermodynamic limit to be p*=11.54(4), which is slightly lower than the classical value of Hoover and Ree (p*=11.70) [J. Chem. Phys. 49, 3609 (1968)]. Taking into account the strong size dependence of the free energy of the solid phase, we propose to introduce finite size corrections, which allow us to estimate approximately the free energy of the solid phase in the thermodynamic limit from the known value of the free energy of the solid phase with N molecules. We have also determined the free energy of a Lennard-Jones solid by using both the methodology of this work and the finite size correction. It is shown how a relatively good estimate of the free energy of the system in the thermodynamic limit is obtained even from the free energy of a relatively small system.

Phase diagram of model anisotropic particles with octahedral symmetry

The phase diagram for a system of model anisotropic particles with six attractive patches in an octahedral arrangement has been computed. This model for a relatively narrow value of the patch width where the lowest-energy configuration of the system is a simple cubic crystal. At this value of the patch width, there is no stable vapor-liquid phase separation, and there are three other crystalline phases in addition to the simple cubic crystal that is most stable at low pressure. First, at moderate pressures, it is more favorable to form a body-centered-cubic crystal, which can be viewed as two interpenetrating, and almost noninteracting, simple cubic lattices. Second, at high pressures and low temperatures, an orientationally ordered face-centered-cubic structure becomes favorable. Finally, at high temperatures a face-centered-cubic plastic crystal is the most stable solid phase.

The stability of a crystal with diamond structure for patchy particles with tetrahedral symmetry

The phase diagram of model anisotropic particles with four attractive patches in a tetrahedral arrangement has been computed at two different values of the range of the potential, with the aim of investigating the conditions under which a diamond crystal can be formed. We find that the diamond phase is never stable for our longer-ranged potential. At low temperatures and pressures, the fluid freezes into a body-centered-cubic solid that can be viewed as two interpenetrating diamond lattices with a weak interaction between the two sublattices. Upon compression, an orientationally ordered face-centered-cubic crystal becomes more stable than the body-centered-cubic crystal, and at higher temperatures, a plastic face-centered-cubic phase is stabilized by the increased entropy due to orientational disorder. A similar phase diagram is found for the shorter-ranged potential, but at low temperatures and pressures, we also find a region over which the diamond phase is thermodynamically favored over the body-centered-cubic phase. The higher vibrational entropy of the diamond structure with respect to the body-centered-cubic solid explains why it is stable even though the enthalpy of the latter phase is lower. Some preliminary studies on the growth of the diamond structure starting from a crystal seed were performed. Even though the diamond phase is never thermodynamically stable for the longer-ranged model, direct coexistence simulations of the interface between the fluid and the body-centered-cubic crystal and between the fluid and the diamond crystal show that at sufficiently low pressures, it is quite probable that in both cases the solid grows into a diamond crystal, albeit involving some defects. These results highlight the importance of kinetic effects in the formation of diamond crystals in systems of patchy particles.

Determination of the melting point of hard spheres from direct coexistence simulation methods

We consider the computation of the coexistence pressure of the liquid-solid transition of a system of hard spheres from direct simulation of the inhomogeneous system formed from liquid and solid phases separated by an interface. Monte Carlo simulations of the interfacial system are performed in three different ensembles. In a first approach, a series of simulations is carried out in the isothermal-isobaric ensemble, where the solid is allowed to relax to its equilibrium crystalline structure, thus avoiding the appearance of artificial stress in the system. Here, the total volume of the system fluctuates due to changes in the three dimensions of the simulation box. In a second approach, we consider simulations of the inhomogeneous system in an isothermal-isobaric ensemble where the normal pressure, as well as the area of the (planar) fluid-solid interface, are kept constant. Now, the total volume of the system fluctuates due to changes in the longitudinal dimension of the simulation box. In both approaches, the coexistence pressure is estimated by monitoring the evolution of the density along several simulations carried out at different pressures. Both routes are seen to provide consistent values of the fluid-solid coexistence pressure, p=11.54(4)k(B)T/sigma(3), which indicates that the error introduced by the use of the standard constant-pressure ensemble for this particular problem is small, provided the systems are sufficiently large. An additional simulation of the interfacial system is conducted in a canonical ensemble where the dimensions of the simulation box are allowed to change subject to the constraint that the total volume is kept fixed. In this approach, the coexistence pressure corresponds to the normal component of the pressure tensor, which can be computed as an appropriate ensemble average in a single simulation. This route yields a value of p=11.54(4)k(B)T/sigma(3). We conclude that the results obtained for the coexistence pressure from direct simulations of the liquid and solid phases in coexistence using different ensembles are mutually consistent and are in excellent agreement with the values obtained from free energy calculations.

Heat capacity of water : a signature of nuclear quantum effects

In this note we present results for the heat capacity at constant pressure for the TIP4PQ/2005 model, as obtained from path-integral simulations. The model does a rather good job of describing both the heat capacity of ice I(h) and of liquid water. Classical simulations using the TIP4P/2005, TIP3P, TIP4P, TIP4P-Ew, simple point charge/extended, and TIP5P models are unable to reproduce the heat capacity of water. Given that classical simulations do not satisfy the third law of thermodynamics, one would expect such a failure at low temperatures. However, it seems that for water, nuclear quantum effects influence the heat capacities all the way up to room temperature. The failure of classical simulations to reproduce C(p) points to the necessity of incorporating nuclear quantum effects to describe this property accurately.

Quantum contributions in the ice phases: The path to a new empirical model for water—TIP4PQ/2005

With a view to a better understanding of the influence of atomic quantum delocalization effects on the phase behavior of water, path integral simulations have been undertaken for almost all of the known ice phases using the TIP4P/2005 model in conjunction with the rigid rotor propagator proposed by Muser and Berne [Phys. Rev. Lett. 77, 2638 (1996)]. The quantum contributions then being known, a new empirical model of water is developed (TIP4PQ/2005) which reproduces, to a good degree, a number of the physical properties of the ice phases, for example, densities, structure, and relative stabilities.

Structural transitions in the 309-atom magic number Lennard-Jones cluster.

The thermal behavior of the 309-atom Lennard-Jones cluster, whose structure is a complete Mackay icosahedron, has been studied by parallel tempering Monte Carlo simulations. Surprisingly for a magic number cluster, the heat capacity shows a very pronounced peak before melting, which is attributed to several coincident structural transformation processes. The main transformation is somewhat akin to surface roughening and involves a cooperative condensation of vacancies and adatoms that leads to the formation of pits and islands one or two layers thick on the Mackay icosahedron. The second transition in order of importance involves a whole scale transformation of the cluster structure and leads to a diverse set of twinned structures that are assemblies of face-centered-cubic tetrahedra with six atoms along their edges, i.e., one atom more than the edges of the 20 tetrahedra that make up the 309-atom Mackay icosahedron. A surface reconstruction of the icosahedron from a Mackay to an anti-Mackay overlayer is also observed, but with a lower probability.