Consensus on the solubility of NaCl in water from computer simulations using the chemical potential route

Addressing hysteresis and slow equilibration issues in cavity-based calculation of chemical potentials

In this paper, we explore the strengths and weaknesses of a cavity-based method to calculate the excess chemical potential of a large molecular solute in a dense liquid solvent. Use of the cavity alleviates some technical problems associated with the appearance of (integrable) divergences in the integrand during alchemical particle growth. The excess chemical potential calculated using the cavity-based method should be independent of the cavity attributes. However, the performance of the method (equilibration time and the robustness) does depend on the cavity attributes. To illustrate the importance of a suitable choice of the cavity attributes, we calculate the partition coefficient of pyrene in toluene and heptane using a coarse-grained model. We find that a poor choice for the functional form of the cavity may lead to hysteresis between growth and shrinkage of the cavity. Somewhat unexpectedly, we find that, by allowing the cavity to move as a pseudo-particle within the simulation box, the decay time of fluctuations in the integrand of the thermodynamic integration can be reduced by an order of magnitude, thereby increasing the statistical accuracy of the calculation.

Optical-Spectrometry-Based Method for Immunosuppressant Medicine Level Detection in Aqueous Solutions

In this paper, an investigation into detecting immunosuppressive medicine in aqueous solutions using a spectrometry-based technique is described. Using optical transmissive spectrometry, absorbance measurements in the spectra range from 250 nm to 1000 nm were carried out for different cyclosporine A (CsA) concentrations in aqueous solutions. The experiment was conducted for samples both with and without interferent substances—glucose and sodium chloride. Using a dedicated algorithm, the measured data was analyzed and a high correlation coefficient R² = 0.8647 was achieved. The experiment showed that the described technique allowed for the detection of various CsA concentration levels in a selective, label-free and simple way. This method could be used in medicine, veterinary medicine and laboratory diagnostics.

Computational methodology for solubility prediction: Application to the sparingly soluble solutes

The solubility of a crystalline substance in the solution can be estimated from its absolute solid free energy and excess solvation free energy. Here, we present a numerical method, which enables convenient solubility estimation of general molecular crystals at arbitrary thermodynamic conditions where solid and solution can coexist. The methodology is based on standard alchemical free energy methods, such as thermodynamic integration and free energy perturbation, and consists of two parts: (1) systematic extension of the Einstein crystal method to calculate the absolute solid free energies of molecular crystals at arbitrary temperatures and pressures and (2) a flexible cavity method that can yield accurate estimates of the excess solvation free energies. As an illustration, via classical Molecular Dynamic simulations, we show that our approach can predict the solubility of OPLS-AA-based (Optimized Potentials for Liquid Simulations All Atomic) naphthalene in SPC (Simple Point Charge) water in good agreement with experimental data at various temperatures and pressures. Because the procedure is simple and general and only makes use of readily available open-source software, the methodology should provide a powerful tool for universal solubility prediction.

Biomolecular Simulations under Realistic Macroscopic Salt Conditions

Biomolecular simulations are typically performed in an aqueous environment where the number of ions remains fixed for the duration of the simulation, generally with either a minimally neutralizing ion environment or a number of salt pairs intended to match the macroscopic salt concentration. In contrast, real biomolecules experience local ion environments where the salt concentration is dynamic and may differ from bulk. The degree of salt concentration variability and average deviation from the macroscopic concentration remains, as yet, unknown. Here, we describe the theory and implementation of a Monte Carlo osmostat that can be added to explicit solvent molecular dynamics or Monte Carlo simulations to sample from a semigrand canonical ensemble in which the number of salt pairs fluctuates dynamically during the simulation. The osmostat reproduces the correct equilibrium statistics for a simulation volume that can exchange ions with a large reservoir at a defined macroscopic salt concentration. To achieve useful Monte Carlo acceptance rates, the method makes use of nonequilibrium candidate Monte Carlo (NCMC) moves in which monovalent ions and water molecules are alchemically transmuted using short nonequilibrium trajectories, with a modified Metropolis-Hastings criterion ensuring correct equilibrium statistics for an ( Δμ, N, p, T) ensemble to achieve a ∼1046× boost in acceptance rates. We demonstrate how typical protein (DHFR and the tyrosine kinase Src) and nucleic acid (Drew-Dickerson B-DNA dodecamer) systems exhibit salt concentration distributions that significantly differ from fixed-salt bulk simulations and display fluctuations that are on the same order of magnitude as the average.

Ion dissolution mechanism and kinetics at kink sites on NaCl surfaces

Desolvation barriers are present for solute-solvent exchange events, such as ligand binding to an enzyme active site, during protein folding, and at battery electrodes. For solution-grown crystals, desolvation at kink sites can be the rate-limiting step for growth. However, desolvation and the associated kinetic barriers are poorly understood. In this work, we use rare-event simulation techniques to investigate attachment/detachment events at kink sites of a NaCl crystal in water. We elucidate the desolvation mechanism and present an optimized reaction coordinate, which involves one solute collective variable and one solvent collective variable. The attachment/detachment pathways for Na⁺ and Cl^- are qualitatively similar, with quantitative differences that we attribute to different ion sizes and solvent coordination. The attachment barriers primarily result from kink site desolvation, while detachment barriers largely result from breaking ion-crystal bonds. We compute ion detachment rates from kink sites and compare with results from an independent study. We anticipate that the reaction coordinate and desolvation mechanism identified in this work may be applicable to other alkali halides.

Solubility prediction from first principles: a density of states approach

Solubility is a fundamental property of widespread significance. Its accurate prediction remains a major challenge. We present a novel, efficient approach to solubility prediction for molecules over a range of conditions based on density of states.

Density Fluctuation in Aqueous Solutions and Molecular Origin of Salting-Out Effect for CO2

Using molecular dynamics simulation, we studied the density fluctuations and cavity formation probabilities in aqueous solutions and their effect on the hydration of CO₂. With increasing salt concentration, we report an increased probability of observing a larger than the average number of species in the probe volume. Our energetic analyses indicate that the van der Waals and electrostatic interactions between CO₂ and aqueous solutions become more favorable with increasing salt concentration, favoring the solubility of CO₂ (salting in). However, due to the decreasing number of cavities forming when salt concentration is increased, the solubility of CO₂ decreases. The formation of cavities was found to be the primary control on the dissolution of gas, and is responsible for the observed CO₂ salting-out effect. Our results provide the fundamental understanding of the density fluctuation in aqueous solutions and the molecular origin of the salting-out effect for real gas.

Phase Diagram of TIP4P/2005 Water at High Pressure

We report a new ice phase that forms spontaneously at the interface between ice VII and liquid water in molecular dynamics simulations of TIP4P/2005 water. The new phase is structurally quite similar to an ice phase originally found to be a precursor in the course of the homogeneous nucleation of ice VII in liquid water. A part of the water molecules in these ice phases can rotate easily because the number of hydrogen bonds in them is less than four, and thus they can be regarded as partial plastic phases. A rough estimate suggests that these phases are thermodynamically more stable than either ice VI or ice VII for 3 GPa < P < 18 GPa at T = 300 K. Although the partial plastic phases would be metastable states at any point in the phase diagram of real water, they might be realized experimentally with the aid of dopants and/or solid surfaces.

Role of Salt, Pressure, and Water Activity on Homogeneous Ice Nucleation

Pure water can be substantially supercooled below the melting temperature without transforming into ice. The achievable supercooling can be enhanced by adding solutes or by applying hydrostatic pressure. Avoiding ice formation is of great importance in the cryopreservation of food or biological samples. In this Letter, we investigate the similarity between the effects of pressure and salt on ice formation using a combination of state-of-the-art simulation techniques. We find that both hinder ice formation by increasing the energetic cost of creating the ice-fluid interface. Moreover, we examine the widely accepted proposal that the ice nucleation rate for different pressures and solute concentrations can be mapped through the activity of water [ Koop , L. ; Tsias , P. Nature , 2000 , 406 , 611 ]. We show that such a proposal is not consistent with the nucleation rates predicted in our simulations because it does not include all parameters affecting ice nucleation. Therefore, even though salt and pressure have a qualitatively similar effect on ice formation, they cannot be quantitatively mapped onto one another.

Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database

Solvation free energies can now be calculated precisely from molecular simulations, providing a valuable test of the energy functions underlying these simulations. Here, we briefly review "alchemical" approaches for calculating the solvation free energies of small, neutral organic molecules from molecular simulations, and illustrate by applying them to calculate aqueous solvation free energies (hydration free energies). These approaches use a non-physical pathway to compute free energy differences from a simulation or set of simulations and appear to be a particularly robust and general-purpose approach for this task. We also present an update (version 0.5) to our FreeSolv database of experimental and calculated hydration free energies of neutral compounds and provide input files in formats for several simulation packages. This revision to FreeSolv provides calculated values generated with a single protocol and software version, rather than the heterogeneous protocols used in the prior version of the database. We also further update the database to provide calculated enthalpies and entropies of hydration and some experimental enthalpies and entropies, as well as electrostatic and nonpolar components of solvation free energies.

Crystal structures of model lithium halides in bulk phase and in clusters

We employ lattice energy calculations and molecular dynamics simulations to compare the stability of wurtzite and rock salt crystal structures of four lithium halides (LiF, LiCl, LiBr, and LiI) modeled using the Tosi-Fumi and Joung-Cheatham potentials, which are models frequently used in simulation studies. Both infinite crystals and finite clusters are considered. For the Tosi-Fumi model, we find that all four salts prefer the wurtzite structure both at 0 K and at finite temperatures, in disagreement with experiments, where rock salt is the stable structure and wurtzite exists as a metastable state. For Joung-Cheatham potentials, rock salt is more stable for LiF and LiCl, but the wurtzite structure is preferred by LiBr and LiI. It is clear that the available lithium halide force fields need improvement to bring them into better accord with the experiment. Finite-size clusters that are more stable as rock salt in the bulk phase tend to solidify as small rock salt crystals. However, small clusters of salts that prefer the wurtzite structure as bulk crystals tend to form structures that have hexagonal motifs, but are not finite-size wurtzite crystals. We show that small wurtzite structures are unstable due to the presence of a dipole and rearrange into more stable, size-dependent structures. We also show that entropic contributions can act in favor of the wurtzite structure at higher temperatures. The possible relevance of our results for simulation studies of crystal nucleation from melts and/or aqueous solutions is discussed.

Birth of NaCl Crystals: Insights from Molecular Simulations

Molecular dynamics simulations are used to investigate the factors that influence the nucleation of NaCl crystals in a supersaturated aqueous solution. We describe a methodology for detecting solidlike NaCl clusters (potential nuclei) and following their evolution in time until they achieve nucleation (which is very rare) or dissolve back into solution. Through an analysis of cluster lifetimes and multiple nucleation events, we demonstrate that cluster size is not the only property that influences cluster stability and the probability of achieving nucleation. We introduce a parameter called cluster crystallinity, which is a measure of the solidlike order in a particular cluster. We show that cluster order (as measured by this parameter) has a strong influence on the lifetime and nucleation probability of clusters of equal sizes, with the lifetime and probability of nucleation increasing with increasing crystallinity. These observations remain true for clusters as small as six ions, showing that the structural factors are important even at the earliest stages of crystal birth.