Molecular dynamics investigation of the pressure induced B1 to B2 phase transitions of RbBr

Deciphering the molecular mechanism of water boiling at heterogeneous interfaces

Water boiling control evolution of natural geothermal systems is widely exploited in industrial processes due to the unique non-linear thermophysical behavior. Even though the properties of water both in the liquid and gas state have been extensively studied experimentally and by numerical simulations, there is still a fundamental knowledge gap in understanding the mechanism of the heterogeneous nucleate boiling controlling evaporation and condensation. In this study, the molecular mechanism of bubble nucleation at the hydrophilic and hydrophobic solid-water interface was determined by performing unbiased molecular dynamics simulations using the transition path sampling scheme. Analyzing the liquid to vapor transition path, the initiation of small void cavities (vapor bubbles nuclei) and their subsequent merging mechanism, leading to successively growing vacuum domains (vapor phase), has been elucidated. The molecular mechanism and the boiling nucleation sites' location are strongly dependent on the solid surface hydrophobicity and hydrophilicity. Then simulations reveal the impact of the surface functionality on the adsorbed thin water molecules film structuring and the location of high probability nucleation sites. Our findings provide molecular-scale insights into the computational aided design of new novel materials for more efficient heat removal and rationalizing the damage mechanisms.

Exploring the Mechanisms of Reactions in Solution from Transition Path Sampling Molecular Dynamics Simulations

Recent advances in molecular dynamics simulations of rare reaction events and aggregation processes are reviewed. Therein the central focus is dedicated to employing the transition path sampling method to study reactions in solution. We describe systematic approaches for generating initial transition pathways and efficient strategies for computationally feasible exploration of further transition routes. The unprejudiced study of reaction mechanisms is illustrated for reactions in aqueous solution and other complex systems. Transition path sampling allows very detailed investigation of solvent effects. Apart from stabilization of reactant, transition, or product state ensembles, this also includes the role of the solvent as a heat bath and as a putative reaction partner. The latter issue is of particular importance for reactions in aqueous solutions, which involve proton-transfer steps that may be assisted by water molecules via the Grotthuss mechanism.

Molecular dynamic simulations of ocular tablet dissolution

Small tablets for implantation into the subconjunctival space in the eye are being developed to inhibit scarring after glaucoma filtration surgery (GFS). There is a need to evaluate drug dissolution at the molecular level to determine how the chemical structure of the active may correlate with dissolution in the nonsink conditions of the conjunctival space. We conducted molecular dynamics simulations to study the dissolution process of tablets derived from two drugs that can inhibit fibrosis after GFS, 5-fluorouracil (5-FU) and the matrix metalloprotease inhibitor (MMPi), ilomastat. The dissolution was simulated in the presence of simple point charge (SPC) water molecules, and the liquid turnover of the aqueous humor in the subconjunctival space was simulated by removal of the dissolved drug molecules at regular intervals and replacement by new water molecules. At the end of the simulation, the total molecular solvent accessible surface area of 5-FU tablets increased by 60 times more than that of ilomastat as a result of tablet swelling and release of molecules into solution. The tablet dissolution pattern shown in our molecular dynamic simulations tends to correlate with experimental release profiles. This work indicates that a series of molecular dynamic simulations can be used to predict the influence of the molecular properties of a drug on its dissolution profile and could be useful during preformulation where sufficient amounts of the drug are not always available to perform dissolution studies.

Atomistic Mechanisms of Phase Separation and Formation of Solid Solutions: Model Studies of NaCl, NaCl−NaF, and Na(Cl1-xBrx) Crystallization from the Melt

The crystallization of sodium chloride from its melt and mixtures with other sodium halides is investigated by means of transition path sampling molecular dynamics simulations. From this we explore the nucleation mechanisms of both the solidification and the melting process at the atomistic level of detail. By incorporation of impurities the nucleation picture of the eutectic mixtures changes considerably. Doping the NaCl crystal with fluoride ions, we observed the substitutional defects to act as favored nucleation centers for the melting transition. This phenomenon plays a critical role during the solidification process of NaCl-NaF melts of low NaF concentration and is demonstrated to account for the segregation of fluoride ions. While NaCl-NaF corresponds to a eutectic system, we also investigated NaCl-NaBr mixtures. The bromide ions were observed to behave very similarly to chloride ions. As a consequence, no phase separation occurs and Na(Cl1-xBrx) solid solutions are formed. At the example of these two prototypes we demonstrate the study of the atomistic mechanisms related to phase separation processes and solid solution formation during the nucleation and growth of crystals from multinary melts.

Generation of initial trajectories for transition path sampling of chemical reactions with ab initio molecular dynamics

Transition path sampling is an innovative method for focusing a molecular dynamics simulation on a reactive event. Although transition path sampling methods can generate an ensemble of reactive trajectories, an initial reactive trajectory must be generated by some other means. In this paper, the authors have evaluated three methods for generating initial reactive trajectories for transition path sampling with ab initio molecular dynamics. The authors have tested each of these methods on a set of chemical reactions involving the breaking and making of covalent bonds: the 1,2-hydrogen elimination in the borane-ammonia adduct, a tautomerization, and the Claisen rearrangement. The first method is to initiate trajectories from the potential energy transition state, which was effective for all reactions in the test set. Assigning atomic velocities found using normal mode analysis greatly improved the success of this method. The second method uses a high temperature molecular dynamics simulation and then iteratively reduces the total energy of the simulation until a low temperature reactive trajectory is found. This was effective in generating a low temperature trajectory from an initial trajectory run at 3000 K of the tautomerization reaction, although it failed for the other two. The third uses an orbital based bias potential to find a reactive trajectory and uses this trajectory to initiate an unbiased trajectory. The authors found that a highest occupied molecular orbital-lowest unoccupied molecular orbital bias could be used to find a reactive trajectory for the Claisen rearrangement, although it failed for the other two reactions. These techniques will help make it practical to use transition path sampling to study chemical reaction mechanisms that involve bond breaking and forming.

Competing Evaporation and Condensation Processes during the Boiling of Methane

The atomistic mechanism of the boiling of methane is explored from molecular dynamics simulations. The liquid --> vapor transition is initiated by local density fluctuations resulting in a nanometer-sized domain that exhibits both liquid and vapor characteristics. Though the rates of evaporation and condensation events increase dramatically in this area, the overall balance exhibits only a marginal net rate of evaporation. Growth of the precritical domain leads to the nucleation of a vapor phase in which isolated methane molecules are confined by a liquid-vapor interface. After crossing the transition state, the system experiences progressive destabilization of the liquid phase and the evaporation processes clearly outnumber the condensation events.

Mechanisms and Nucleation Characteristics of the Pressure-Induced B1−B2 Transition in Potassium Halides: A Question of Ion Hardness and Softness

The transformation of potassium bromide from the B1 to the high-pressure B2 structure type is investigated by means of molecular dynamics simulations and compared to previous studies of KF and KCl. The underlying simulation scheme is based on the transition path sampling approach, which allows an unbiased investigation of the phase transition and offers a unique perspective for studying the involved mechanisms at the atomistic level of detail. Our analysis reveals identical mechanisms for the overall transition in KF, KCl, and KBr, but rather dissimilar characteristics of the nucleation and growth of phases. The transformation of KCl may be initiated by both K+ and Cl- ion displacement, exhibiting no preference for either species. However, for KF and KBr, we identified a clear favoring of column-wise F- and K+ displacement, respectively. Such tendencies have important implications on the morphogenesis of the phase nuclei and account for the observation of short-ranged coexisting nucleation centers, resulting in the formation of nanosized twin domains separated by mirror planes on completion of the transition. On the basis of a systematic study of potassium halides, we present a conclusive explanation for the observed nucleation characteristics, which is expected to be of general relevance to pressure-induced phase transitions in ionic compounds.

Unprejudiced identification of reaction mechanisms from biased transition path sampling

A method for unprejudiced investigation of reaction mechanisms from molecular-dynamics simulations is presented. It combines the transition path sampling approach with a biasing strategy, which (a) allows optimization of transition paths crossing an energy minimum of the transition state surface. The bias is then used to (b) find reaction pathways, which follow different mechanistic routes. In the first step the manifold of similar trajectories that correspond to the same mechanism is reduced to a single characteristic dynamical path. Our method then allows a systematic search for further reaction mechanisms and the related energy barriers. It is illustrated at the example of a single particle in a two-dimensional potential and of the rather complex process of the pressure-induced insertion of a helium atom into a C60 buckyball molecule.

How does water boil?

Insight into the boiling of water is obtained from molecular dynamics simulations. The process is initiated by the spontaneous formation of small vacuum cavities in liquid water. By themselves, these defects are very short lived. If, however, several cavities occur at close distances, they are likely to merge into larger vacuum holes. At the liquid-vapor interfaces, single or small groups of water molecules tend to leave the liquid surface. Once the system is propagated beyond the transition state, these evaporation events outnumber the competing reintegration into the hydrogen-bonded network.