TIP3P Water Research Articles

Morse potential parameters of dissipative particle dynamics force fields for non-polarizable water models

The Morse potential parameters compatible with dissipative particle dynamics (DPD) for water are determined by the Ornstein-Zernike (OZ) equation with the hyper-netted chain (HNC) closure. The present study verifies that the HNC approximation is accurate for a DPD system described by the soft repulsive and Morse potentials. Firstly, we demonstrate that the modified form of the Morse potential is necessary for the numerical solution of the OZ/HNC equations. Subsequently, the Morse potential parameters for mimicking SPCE, TIP3P, TIP4P, and TIP5P water models within the DPD framework are determined by mapping the radial distribution function (RDF) in the HNC approximation to those of all-atom simulations. The first-peak positions and heights of the center-of-mass RDFs for all-atom water models are successfully reproduced by DPD simulations using the determined parameters. The OZ/HNC results for the RDFs and pressures, calculated for the obtained water models, are in satisfactory agreement with the DPD results. Moreover, we investigate how the addition of the Morse potential term to the solute-solvent interaction manifests itself in the solution properties. Major effects of the Morse potential are found in the solute-solvent RDF and the potential of mean force (PMF) between a pair of solutes. We discuss the molecular mechanism underlying the effects induced by the Morse potential in detail.

Effect of coarse graining in water models for the study of kinetics and mechanisms of clathrate hydrates nucleation and growth.

Clathrate hydrates are crystalline inclusion compounds wherein a water framework encages small guest atoms/molecules within its cavities. Among the others, methane clathrates are the largest fossil fuel resource still available. They can also be used to safely transport gases and can also form spontaneously under suitable conditions plugging pipelines. Understanding the crystallization mechanism is very important, and given the impossibility of experimentally identifying the atomistic path, simulations played an important role in this field. Given the large computational cost of these simulations, in addition to all-atom force fields, scientists considered coarse-grained water models. Here, we have investigated the effect of coarse-graining, as implemented in the water model mW, on the crystallization characteristics of methane clathrate in comparison with the all-atom TIP4P force field. Our analyses revealed that although the characteristics directly depending on the energetics of the water models are well reproduced, dynamical properties are off by the orders of magnitude. Being crystallization a non-equilibrium process, the altered kinetics of the process results in different characteristics of crystalline nuclei. Both TIP4P and mW water models produce methane clathrate nuclei with some amount of the less stable (in the given thermodynamic conditions) structure II phase and an excess of pentagonal dodecahedral cages over the tetrakaidecahedral ones regarding the ideal ratio in structure I. However, the dependence of this excess on the methane concentration in solution is higher with the former water model, whereas with the latter, the methane concentration in solution dependence is reduced and within the statistical error.

Implementation of solvation free energy framework to predict the vapor-liquid equilibrium behaviors for the water–hydrazine and ethanol–water azeotropic systems

An azeotrope is a special vapor–liquid equilibrium in which the composition of two coexisting phases is equal. Due to its strong deviation from the Raoult’s law, it poses a great challenge to the simple distillation process and the understanding of fundamental molecular mechanisms. In this study, we calculated the coupling work of solute species based on the solvation free energy framework to predict the vapor–liquid equilibrium (VLE) behavior and azeotrope point of mixtures. Two prototypical binary mixtures: the negative water-hydrazine and positive ethanol–water azeotrope were investigated using molecular dynamic simulations and the OPLS-AA force field. All the simulations were performed with the TIP3P water model, because it has a good capability to represent enthalpy properties. The molecular models of hydrazine and ethanol have been re-parameterized to reproduce the density and solvation free energy properties of pure substance. Using free energy perturbation simulation, the coupling work of each substance was studied against liquid mixture composition. The coupling work is also translated to x-y or T-x-y phase diagrams for comparison with available experimental data. The tendency of two azeotropes is that the more volatile components experience the less pronounced coupling work changes in their local environments as the azeotropes form. The coupling work is also divided into van der Waals and Coulomb contributions to investigate the interactions between particles. Lithium Chloride was investigated as an entrainer for the separation of ethanol–water system. The coupling works of binary mixtures were calculated at different salt concentrations to study the salt-out effect for the violate species and salt-in effect for the less violate species. By adding LiCl, it was found that the azeotrope point was efficiently eliminated at a salinity 0.05 mol fraction at 1 bar. All the results show that the simulation methodology of coupling work are reliable for calculating the liquid–vapor equilibrium behavior. This method is also valuable for selecting and designing new extractants for distillation process.

Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans.

In computational studies of glycosaminoglycans (GAGs), a group of anionic, periodic linear polysaccharides, so far there has been very little discussion about the role of solvent models in the molecular dynamics simulations of these molecules. Predominantly, the TIP3P water model is commonly used as one of the most popular explicit water models in general. However, there are numerous alternative explicit and implicit water models that are neglected in the computational research of GAGs. Since solvent-mediated interactions are particularly important for GAG dynamic and structural properties, it would be of great interest for the GAG community to establish the solvent model that is suited the best in terms of the quality of theoretically obtained GAG parameters and, at the same time, would be reasonably demanding in terms of computational resources required. In this study, heparin (HP) was simulated using five implicit and six explicit solvent models with the aim to find out how different solvent models influence HP's molecular descriptors in the molecular dynamics simulations. Here, we initiate the search for the most appropriate solvent representation for GAG systems and we hope to encourage other groups to contribute to this highly relevant subject.

Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-Guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation.

Host-guest binding, despite the relatively simple structural and chemical features of individual components, still poses a challenge in computational modelling. The extreme underperformance of standard end-point methods in host-guest binding makes them practically useless. In the current work, we explore a potentially promising modification of the three-trajectory realization. The alteration couples the binding-induced structural reorganization into free energy estimation and suffers from dramatic fluctuations in internal energies in protein-ligand situations. Fortunately, the relatively small size of host-guest systems minimizes the magnitude of internal fluctuations and makes the three-trajectory realization practically suitable. Due to the incorporation of intra-molecular interactions in free energy estimation, a strong dependence on the force field parameters could be incurred. Thus, a term-specific investigation of transferable GAFF derivatives is presented, and noticeable differences in many aspects are identified between commonly applied GAFF and GAFF2. These force-field differences lead to different dynamic behaviors of the macrocyclic host, which ultimately would influence the end-point sampling and binding thermodynamics. Therefore, the three-trajectory end-point free energy calculations are performed with both GAFF versions. Additionally, due to the noticeable differences between host dynamics under GAFF and GAFF2, we add additional benchmarks of the single-trajectory end-point calculations. When only the ranks of binding affinities are pursued, the three-trajectory realization performs very well, comparable to and even better than the regressed PBSA_E scoring function and the dielectric constant-variable regime. With the GAFF parameter set, the TIP3P water in explicit solvent sampling and either PB or GB implicit solvent model in free energy estimation, the predictive power of the three-trajectory realization in ranking calculations surpasses all existing end-point methods on this dataset. We further combine the three-trajectory realization with another promising modified end-point regime of varying the interior dielectric constant. The combined regime does not incur sizable improvements for ranks and deviations from experiment exhibit non-monotonic variations.

Thermodynamics and transport properties of valine and cysteine peptides in water

The study of thermodynamic and transport properties of amino acids gives access to knowledge about interactions between distinct molecules necessary to understand a variety of biological processes. In this work, we have performed molecular dynamics simulations of valine and cysteine peptides with lengths of (n) = 1, 2, 4, 8 & 16 monomers in an aqueous environment to estimate the solvation free energy and diffusion coefficients. We modeled our system using OPLS-AA parameter sets and TIP3P water at 310 K temperature. Solvation free energy of both the peptides have been reported using two thermodynamic integration (TI) based methods: TI and TI-CUBIC. The solvation free energy of both the peptides increases with the chain length. The estimated values using both methods are in good agreement with a statistical error of < 3%. The solvent accessible surface area (SASA) of solutes and hydrogen bonds between solute and solvent have also been presented to get more insights on solvation processes. The increase in solvation energy of both peptides with chain length is further corroborated by increase in the number of hydrogen bond (between peptide and water) and SASA with the chain length. In addition, the self diffusion coefficient of both solute and solvent along with their binary diffusion coefficient have been estimated for both the peptides. Furthermore, the effect of chain length on solvation free energy as well as diffusion coefficients have been studied.

Comparison of classical and ab initio simulations of hydronium and aqueous proton transfer.

Proton transfer represents the simplest chemical reaction, yet it is still typically not accounted for in standard biomolecular simulations. Here we compare an ab initio molecular dynamics (MD) simulation trajectory of an excess proton in water to classical MD trajectories of hydronium in TIP3P water. We characterize the structural differences between them and correlate these with the energy gap upon instant proton transfer, which is much higher in the classical simulations. One structural difference is in the tilt angle of the waters that accept an h-bond from hydronium, which is too large in TIP3P. This can be largely alleviated by use of the TIP5P model, whose lone pairs orient the water molecule properly. Other discrepancies include a lower number of h-bonds and a less favorable second solvation shell geometry in classical MD, which is likely due to lack of polarization. The identification of these structural differences paves the way toward classical MD simulations that can more closely mimic ab initio trajectories. We also present efforts to develop a classical model for hydroxide that reproduces ab initio solvation structure and proton transfer mechanism.

Exploring the structural conformations of amyloid-beta oligomers on self-assembled monolayers and in water under confinement, a molecular dynamics study.

Alzheimer's disease (AD) is a devastating neurological disorder, affecting millions of people worldwide. The aggregation of amyloid-beta (Aβ) peptides and the intermediate protein tau into amyloid fibrils is believed to be a critical event in the pathogenesis of AD. Amyloid fibrils represent the endpoints of aggregation, and it is widely believed that their precursors—the soluble oligomers—are the more important neurotoxins. However, there is limited structural information available on Aβ oligomers. Although atomic force microscopy (AFM) is a widely-used method employed to study the conformation of Aβ oligomers, the resolution of AFM is limited and unable to discern atomistic structural features. Here, we construct a self-assembled monolayer (SAM), mimicking the surface properties of mica (used in AFM), with varying surface charge densities. Then, we apply the enhanced sampling algorithm REST2 (replica exchange with solute tempering) from the NAMD package, to efficiently sample the protein conformations on the SAM surface. Our simulations have resulted in cross β-sheet formation between Aβ monomers, similar to that observed experimentally. In particular, we find that residues 17-21 and 35-40 are involved in β-sheet formation, the former of which has been observed in the Aβ fibril structure. We also observe the prominence of the intramolecular Asp23-Lys28 salt bridge, which has been found to play a significant role in the formation of Aβ fibrils. Further, we notice that an asymmetric charge distribution on the SAM surface tends to result in greater β-sheet formation. Our simulations of Aβ monomers in TIP4P water, confined using a harmonic wall, similarly result in cross β-sheet formation among the monomers. Confinement has been found to increase the conformational stability of proteins, suggesting the possibility of Aβ formation in the crowded environment of the cell.

The rigidization of water dynamics around proteins: A molecular dynamics study.

The interaction between a solvated protein and its solvent is a rich area of biophysics that has yet to be fully explored. While a wealth of research suggests that the dynamics of a protein are intimately related to the dynamics of its surrounding solvent, the degree and the intensity of this modulation has not been fully quantified. To elucidate this phenomenon, we modeled multiple protein structures of various sizes and shapes in an explicit TIP4P-2005 water solvent. Motivated by past findings which related it to the α-relaxation process of the intermediate scattering function, the Debye-Waller factor u2 was used to characterize the local mobility of the protein and the water atoms. In all the solvated protein systems considered, we observed the presence of two regimes of water behavior: the hydration layer and the bulk. Aligning with previous findings in THz microscopy, the hydration layer had a thickness on the order of 1 nm. Moreover, as seen before in studies of the interfacial region of glass-forming and crystalline inorganic materials, the interfacial water u2 exponentially approached the bulk water u2 over the length of the hydration shell. Among all the water molecules in the hydration shell, the u2's obeyed a -distribution. The right tails in these distributions were associated with pockets of fast-moving water molecules clustered near the positively-charged regions of the protein surface. Put together, these in silica findings lend credence to Karplus’ analogy between the dynamics of solvated proteins and inorganic nanoparticles.

Extending the applicability of popular force fields for describing water/metal interfaces: application to water/Pd(111)

We propose a new method for constructing a polarizable classical force field using data obtained from QM and QM/MM calculations to account for the charge redistribution at the water/metal interface. The induced charge effects are described by adding dipoles to the system topology following the Rod Model (Iori, F, et al J. Comput. Chem.2009, 30, 1465). Furthermore, the force field uses the TIP3P water model, and its functional form is compatible with popular force fields such as AMBER, CHARMM, GROMOS, OPLS-AA, CVFF and IFF. The proposed model was evaluated and validated for water/Pd(111) systems. We tuned the model parameters to reproduce a few critical water/Pd(111) geometries and energies obtained from DFT calculations using both PBE and a non-local van der Waals xc-functional. Our model can reproduce the hexagonal ice layer for the Pd(111)/water systems typically present in low-temperature experiments, in agreement with information available from the literature. Additionally, the model can also reproduce the experimental metal-water interfacial tension at room temperature.

Enhanced thermophysical properties of water-based single and hybrid metallic nanofluids: Insights from Equilibrium Molecular Dynamics

The effect of single (Cu or Ag) and hybrid (Cu+Ag) metallic nanoparticles on the thermophysical properties, namely viscosity and thermal conductivity of water-based nanofluids, has been studied using Equilibrium Molecular dynamics (EMD) simulation. The TIP3P (three-site transferrable intermolecular potential) water model has been chosen. The interaction of water molecules has been modelled by the Lennard-Jones (L J) potential in combination with Coulomb potential. The embedded-atom (EAM) potential method has been used for hybrid (Cu and Ag) atom interaction. Simulation has been performed at 303 K and atmospheric pressure using the Berendsen algorithm under NVT (constant number, constant volume, and constant temperature) ensemble with production steps of 2 ns and integral step of 1fs. Interestingly, nanofluids containing one metallic nanoparticle (Cu or Ag) have lower thermal conductivity and viscosity than nanofluids having hybrid metallic nanoparticles with the same volume fraction.

SpiDec: Computing binodals and interfacial tension of biomolecular condensates from simulations of spinodal decomposition

Phase separation of intrinsically disordered proteins (IDPs) is a phenomenon associated with many essential cellular processes, but a robust method to compute the binodal from molecular dynamics simulations of IDPs modeled at the all-atom level in explicit solvent is still elusive, due to the difficulty in preparing a suitable initial dense configuration and in achieving phase equilibration. Here we present SpiDec as such a method, based on spontaneous phase separation via spinodal decomposition that produces a dense slab when the system is initiated at a homogeneous, low density. After illustrating the method on four model systems, we apply SpiDec to a tetrapeptide modeled at the all-atom level and solvated in TIP3P water. The concentrations in the dense and dilute phases agree qualitatively with experimental results and point to binodals as a sensitive property for force-field parameterization. SpiDec may prove useful for the accurate determination of the phase equilibrium of IDPs.

Extraction of Dielectric Permittivity from Atomistic Molecular Dynamics Simulations and Microwave Measurements.

The design of new biotechnology depends on the prediction and measurement of the electrical properties of biomolecules. The dielectric permittivity, in particular, is highly important for the design of microwave systems for diagnostics, yet this property is rarely explicitly targeted during the development of biomolecular force fields for molecular dynamics (MD) simulations. In order to explore the ability of existing force fields to reproduce the frequency-dependent permittivity, we carried out MD simulations of various aqueous solutions, including pure water, isopropyl alcohol, alanine, and the protein ubiquitin. The TIP3P, TIP4P, TIP4P/ε, and SWM4-NDP water models were used along with the CHARMM36m and Drude protein force fields. An experimental setup using a truncated coaxial line was created to measure the permittivity of the same solutions to check for measure-model agreement. We found that one of the nonpolarizable force fields (TIP4P/ε + CHARMM36m) and the polarizable force fields (SWM4-NDP + Drude) closely agree with experimental results. This demonstrates the strength of the tuned TIP4P/ε water model, as well as the physical validity of polarizable force fields in capturing dielectric permittivity. This represents an important step toward the predictive design of biosensors.

The Performance of Different Water Models on the Structure and Function of Cytochrome P450 Enzymes.

Modeling approaches and modern simulations to investigate the biomolecular structure and function rely on various methods. Since water molecules play a crucial role in all sorts of chemistry, the accurate modeling of water molecules is vital for such simulations. In cytochrome P450 (CYP450), in particular, water molecules play a key role in forming active oxidant that ultimately performs oxidation and metabolism. In the present study, we have highlighted the behavior of the three most widely used water models─TIP3P, SPC/E, and OPC─for three different CYP450 enzymes─CYP450BM3, CYP450OleT, and CYP450BSβ─during MD simulations and QM/MM calculations. We studied the various properties, such as RMSD, RMSF, H-bond, water occupancy, and hydrogen atom transfer (HAT), using QM/MM calculations and compared them for all three water models. Our study shows that the stabilities of the enzyme complexes are well maintained in all three water models. However, the OPC water model performs well for the polar active sites, that is, in CYP450OleT and CYP450BSβ, while the TIP3P water model is superior for the hydrophobic site, such as CYP450BM3.

Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions.

Proper balance between protein-protein and protein-water interactions is vital for atomistic molecular dynamics (MD) simulations of globular proteins as well as intrinsically disordered proteins (IDPs). The overestimation of protein-protein interactions tends to make IDPs more compact than those in experiments. Likewise, multiple proteins in crowded solutions are aggregated with each other too strongly. To optimize the balance, Lennard-Jones (LJ) interactions between protein and water are often increased about 10% (with a scaling parameter, λ = 1.1) from the existing force fields. Here, we explore the optimal scaling parameter of protein-water LJ interactions for CHARMM36m in conjunction with the modified TIP3P water model, by performing enhanced sampling MD simulations of several peptides in dilute solutions and conventional MD simulations of globular proteins in dilute and crowded solutions. In our simulations, 10% increase of protein-water LJ interaction for the CHARMM36m cannot maintain stability of a small helical peptide, (AAQAA)3 in a dilute solution and only a small modification of protein-water LJ interaction up to the 3% increase (λ = 1.03) is allowed. The modified protein-water interactions are applicable to other peptides and globular proteins in dilute solutions without changing thermodynamic properties from the original CHARMM36m. However, it has a great impact on the diffusive properties of proteins in crowded solutions, avoiding the formation of too sticky protein-protein interactions.

Dynamics of Topology-dependent Water Purification by Siliceous Zeolite Membranes

• Simulated the effect of topology and pore size of zeolites on water purification. • Compared porous LTA, FAU, and MFI zeolites in purification of Cl - , Pb 2+ , and Co 2+ . • Tersoff and Lennard-Jones hybrid force fields, and TIP3P water models were used. • Applying PMF in MD simulation, the efficiency of zeolite membranes was conceptualized. • Applying a long time of 15 ns, heavy metal ions behaved differently in rejection. The efficiency of pollutant rejection (PR, %) and water purification of the zeolite membranes is highly dependent on their topology, i.e., porosity and chemical composition. Nevertheless, mechanisms controlling such a physicochemical phenomenon have been limitedly discussed. Herein, we provide insights into the physics and dynamics of water purification by zeolite nanosheets in terms of topological variables. The molecular dynamics (MD) simulation pictured the molecular-lever water purification having heavy metal ions (Co 2+ and Pb 2+ ) as typical water contaminants. Three siliceous zeolites having different topologies, i.e., LTA, FAU, and MFI zeolites, were positioned in the simulation space. MD simulation was served under pressure and temperature of 24 MPa and 300 K, respectively, applying the Canonical ensemble (NVT) condition. The intermolecular interactions between contaminant ions, zeolite, and graphene were tracked by hybridizing Tersoff and Lenard-Jones potentials, while the TIP3P model of the CHARMM force field was used to simulate water dynamics. The LAMMPS software and Visual Molecular Dynamics (VMD) were used to collect data and graphics over 15 ns, with early 5 ns devoted to reaching equilibrium. Interestingly, we demonstrated by the aid of potential of the mean force (PMF) pollutant ions which encounter the zeolite pores smaller than their kinetic diameter consume more energy for permeation across the membrane, -reason why LTA appeared selective against Pb 2+ , Co 2+ , and Cl - ions, with PR of 40, 60, and 100%, respectively. The absolute water flux values were monitored, and LTA and FAU fluxes were ∼ 50% higher than MFI zeolite, but 5 ns after equilibrium, LTA flux was overtaken sharply by the simulation because of the larger pore size. Overall, the electrostatic forces showed absolute control over the purification but were governed by the zeolite topology.

Molecular Dynamics Investigation of Clustering in Aqueous Glycine Solutions.

Recent experiments with undersaturated aqueous glycine solutions have repeatedly exhibited the presence of giant liquid-like clusters or nanodroplets around 100 nm in diameter. These nanodroplets re-appear even after careful efforts for their removal and purification of the glycine solution. The composition of these clusters is not clear, although it has been suggested that they are mainly composed of glycine, a small and very soluble amino acid. To gain insights into this phenomenon, we study the aggregation of glycine in aqueous solutions at concentrations below the experimental solubility limit using large-scale molecular dynamics simulations under ambient conditions. Three protonation states of glycine (zwitterion = GLZ, anion = GLA, and cation = GLC) are simulated using molecular force fields based on the 1.14*CM1A partial charge scheme, which incorporates the OPLS all-atom force field and TIP3P water. When initiated from dispersed states, we find that giant clusters do not form in our simulations unless salt impurities are present. Moreover, if simulations are initiated from giant cluster states, we find that they tend to dissolve in the absence of salt impurities. Therefore, the simulation results provide little support for the possibility that the giant clusters seen in experiments are composed purely of glycine (and water). Considering that strenuous efforts are made in experiments to remove impurities such as salt, we propose that the giant clusters observed might instead result from the aggregation of reaction products of aqueous glycine, such as diketopiperazine or other oligoglycines which may be difficult to separate from glycine using conventional methods, or their co-aggregation with glycine.

Discovery of novel Glutaminase allosteric inhibitors through drug repurposing and comparative MMGB/PBSA and molecular dynamics simulation

GLS1 enzymes (Glutaminase C (GAC) and kidney-type Glutaminase (KGA)) are gaining prominence as a target for tumor treatment including lung, breast, kidney, prostate, and colorectal. To date, several medicinal chemistry studies are being conducted to develop new and effective inhibitors against GLS1 enzymes. Telaglenastat, a drug that targets the allosteric site of GLS1, has undergone clinical trials for the first time for the therapy of solid tumors and hematological malignancies. A comprehensive computational investigation is performed to get insights into the inhibition mechanism of the Telaglenastat. Some novel inhibitors are also proposed against GLS1 enzymes using the drug repurposing approach using 2D-fingerprinting virtual screening method against 2.4 million compounds, application of pharmacokinetics, Molecular Docking, and Molecular Dynamic (MD) Simulations. A TIP3P water box of 10 Å was defined to solvate both enzymes to improve MD simulation reliability. The dynamics results were validated further by the MMGB/PBSA binding free energy method, RDF, and AFD analysis. Results of these computational analysis revealed a stable binding affinity of Telaglenastat, as well as an FDA approved drug Astemizole (IC50 ∼ 0.9 nM) and a novel para position oriented methoxy group containing Chembridge compound (Chem-64284604) that provides an effective inhibitory action against GAC and KGA.

A Coupled EXAFS-Molecular Dynamics Study on PuO2+ and NpO2+ Hydration: The Importance of Electron Correlation in Force-Field Building.

The physicochemical properties of the monovalent actinyl cations, PuO2+ and NpO2+, in water have been studied by means of classical molecular dynamic simulations. A specific set of cation-water intermolecular potentials based on ab initio potential energy surfaces has been built on the basis of the hydrated ion concept. The TIP4P water model was adopted. Given the paramagnetic character of these actinyls, the cation–water interaction energies were computed from highly correlated wave functions using the NEVPT2 method. It is shown that the multideterminantal character of the wave function has a relevant effect on the main distances of the hydrated molecular cations. Several structural, dynamical, and energetic properties of the aqueous solutions have been obtained and analyzed. Structural RDF analysis gives An–Oyl distances of 1.82 and 1.84 Å and An–O(water) distances of 2.51 and 2.53 Å for PuO2+ and NpO2+ in water, respectively. Experimental EXAFS spectra from dilute aqueous solutions of PuO2+ and NpO2+ are revisited and analyzed, assuming tetra- and pentahydration of the actinyl cations. Simulated EXAFS spectra have been computed from the snapshots of the MD simulations. Good agreement with the experimental information available is found. The global analysis leads us to conclude that both PuO2+ and NpO2+ cations in water are stable pentahydrated aqua ions.

Homogeneous nucleation in supercooled liquid water. Determination of ice germ size and activation energy barrier in Molecular Dynamics simulations

ABSTRACT Homogeneous freezing nucleation occurs in supercooled liquid water by the formation of critical-sized ice embryos. Molecular Dynamics simulations were performed ‘sowing’ a solid embryo into liquid and monitoring the subsequent system evolution. The size of critical ice embryos and the activation energy barrier associated with the incorporation of molecules into the germ were estimated using the TIP5P-E water model for three different temperatures: 237, 240 and 244 K. The results show how MD simulations provide reliable outcomes for the study of both parameters.