Water Force Field Research Articles

Solubility of Methane and Carbon Dioxide in the Aqueous Phase of the Ternary (Methane + Carbon Dioxide + Water) Mixture: Experimental Measurements and Molecular Dynamics Simulations

New experimental measurements (at 10 MPa and 323.15 K) and molecular dynamics (MD) simulations (at 10 MPa and 323.15 K, 50 MPa and 344.25 K, and 50 MPa and 375.5 K) are reported in order to measure/predict the aqueous solubilities of the ternary methane–carbon dioxide–water system under two-phase (vapor–liquid) equilibrium conditions. The TIP4P/ice, TraPPE-UA, and OPLS-UA force fields for water, carbon dioxide, and methane, respectively, are used, according to the modifications introduced in the recent study by Michalis et al. (Phys. Chem. Chem. Phys., 2016, 18, 23538–23548) for the binary methane–carbon dioxide hydrate. The MD calculated values for the solubility are in good agreement with the newly available experimental measurements. The molecular dynamics simulations clearly indicate that the solubility of each gas decreases by the addition of the other gas. The particular conclusion is in excellent agreement with the conclusion obtained from the new experimental measurements reported in the current s...

Towards Realistic Models of Lung Surfactant - MD Simulations with Improved Water and Ion Force Fields

Towards Realistic Models of Lung Surfactant - MD Simulations with Improved Water and Ion Force Fields

NMR Relaxation and Molecular Dynamics Simulations of Side Chain Dynamics in Proteins

Molecular dynamics (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation experiments have become increasingly powerful to study protein dynamics at atomic resolution due to steady improvements in physical models and computation power. Good agreement between generalized Lipari-Szabo (S2NH) order parameters derived from experiment and simulation is now observed for the backbone dynamics of a number of proteins. Unfortunately, the agreement for side chains, as e.g. probed by S2CH3 for methyl-containing side chains, is much poorer. In this work we discuss several issues with methyl side chains that need to be addressed to close the gap between NMR and MD. Accounting for protein tumbling is one very important factor to obtain a good agreement. In our hands, the application of improved water force fields with an appropriate way of including anisotropic overall protein tumbling improves the prediction of experimentally measured dynamic observables by MD simulations. We demonstrate these aspects for T4 lysozyme as a representative example. Our results guide the way for extracting from the NMR relaxation data the most accurate parameters that describe protein side chain dynamics and report on conformational entropy. Additionally, we reparametrized side chain dihedral angle energy barriers for methyl rotation in the Amber99SB∗-ILDN force field. We demonstrate that this leads to a much more realistic dynamics of methyl groups and is another important feature to close the gap between spectral densities from NMR relaxation and MD simulation.

The Water-Alkane Interface at Various NaCl Salt Concentrations: A Molecular Dynamics Study of the Readily Available Force Fields

In this study, classical molecular dynamic simulations have been used to examine the molecular properties of the water-alkane interface at various NaCl salt concentrations (up to 3.0 mol/kg). A variety of different force field combinations have been compared against experimental surface/interfacial tension values for the water-vapour, decane-vapour and water-decane interfaces. Six different force fields for water (SPC, SPC/E, TIP3P, TIP3Pcharmm, TIP4P & TIP4P2005), and three further force fields for alkane (TraPPE-UA, CGenFF & OPLS) have been compared to experimental data. CGenFF, OPLS-AA and TraPPE-UA all accurately reproduce the interfacial properties of decane. The TIP4P2005 (four-point) water model is shown to be the most accurate water model for predicting the interfacial properties of water. The SPC/E water model is the best three-point parameterisation of water for this purpose. The CGenFF and TraPPE parameterisations of oil accurately reproduce the interfacial tension with water using either the TIP4P2005 or SPC/E water model. The salinity dependence on surface/interfacial tension is accurately captured using the Smith & Dang parameterisation of NaCl. We observe that the Smith & Dang model slightly overestimates the surface/interfacial tensions at higher salinities (>1.5 mol/kg). This is ascribed to an overestimation of the ion exclusion at the interface.

Evaluation and Optimization of Interface Force Fields for Water on Gold Surfaces.

The structure and dynamics of water at gold surfaces are important for a variety of applications, including lab on a chip and electrowetting. Classical molecular dynamics (MD) simulations are frequently used to investigate systems with water-gold interfaces, such as biomacromolecules in gold nanoparticle dispersions, but the accuracy of the simulations depends on the suitability of the force field. Density functional theory (DFT) calculations of a water molecule on gold were used as a benchmark to assess force field accuracy. It was found that Lennard-Jones potentials did not reproduce the DFT water-gold configurational energy landscape, whereas the softer Morse and Buckingham potentials allowed for a more accurate representation. MD simulations with different force fields exhibited rather different structural and dynamic properties of water on a gold surface. This emphasizes the need for experimental data and further effort on the validation of a realistic force field for water-gold interactions.

Molecular dynamics simulation of hydrated Na-montmorillonite with inorganic salts addition at high temperature and high pressure

The swelling behaviors of Na-montmorillonite (Na-Mt) in non-ambient environment have been the subject of considerable speculation due to the difficulties associated with their study. Inorganic salts are often used to minimize clay mineral hydration. The influence of inorganic salts addition (NaCl, CaCl2, KCl) on the hydration of Na-Mt at high temperature and high pressure (HTHP) was investigated by molecular dynamics simulation at 6GPa and different temperatures (200, 300, 400, 500 and 600K) in an isobaric isothermal ensemble (NPT). Water model and force field used in the clay-water system are SPC/E model and universal force field (UFF), respectively. The results show that after adding inorganic salts into Na-Mt, the mobility of the interlayer species increases, and the hydration shell of the interlayer cations decreases with a rise in temperature. The influence of temperature on the diffusion of water molecules is much greater than that of the ions present in the interlayer. Temperature increase and hydration degree play an important role on the diffusion behavior of the interlayer species. The size, valence, mass and hydration energy of cations present between the layers affect the structure of Na-Mt interlayer. The inorganic salts are able to inhibit the hydration of Na-Mt by reducing the mobility of the interlayer species and the basal spacing. After analyzing the effect of each salt on Na-Mt, it was found that, the most stable state of Na-Mt at HTHP is achieved with KCl addition, compared with NaCl and CaCl2. It is expected the results obtained from this study would help to understand the inhibition effect of inorganic salts on Na-Mt, and predict the swelling of Na-Mt at HTHP.

Second-Generation ReaxFF Water Force Field: Improvements in the Description of Water Density and OH-Anion Diffusion.

Hydronium (H3O+) and hydroxide (OH-) ions have anomalously large diffusion constants in aqueous solutions due to their combination of vehicular and Grotthuss hopping diffusion mechanisms. An improvement of the ReaxFF reactive water force field on the basis of our first-generation water force field (water-2010) is presented to describe the proton transfer (PT) mechanisms of H3O+ and OH- in water. Molecular dynamics simulation studies with the water-2017 force field support the Eigen-Zundel-Eigen mechanism for PT in acidic aqueous solution and reproduce the hypercoordinated solvation structure of the OH- in a basic environment. In particular, it predicts the correct order of the diffusion constants of H2O, H3O+, and OH- and their values are in agreement with the experimental data. Another interesting observation is that the diffusion constants of H3O+ and OH- are close to each other at high concentration due to the strong correlation between OH- ions in basic aqueous solution. On the basis of our results, it is shown that ReaxFF provides a novel approach to study the complex acid-base chemical reactions in aqueous solution with any pH value.

Thermodynamics and Kinetics of Nucleobase Stacking Oligomerization Revealed by Molecular Dynamics Simulations.

The aggregation of N6N9-dimethyladenine in aqueous solution into stacked oligomers represents an important model system for oligomerization processes. Molecular dynamics simulations allowed us to extract statistically converged stacking thermodynamics as well as converged association and dissociation kinetics. The simulations confirm an oligomerization mechanism according to a random isodesmic stacking model without significant cooperative effects. Multiple oligomerization and dissociation events were used to characterize stacking and unstacking processes and intermediate states in atomic detail. Standard three-point rigid body water force field models lead to significantly accelerated dynamics and an underestimation of enthalpic and entropic contributions. The fully flexible SPCFW water model yielded close agreement with the experimental equilibrium constant, entropy contribution, and, importantly, kinetic observables. In addition, the performance of several other water models was systematically tested in stacking dimerization simulations indicating that the realistic prediction of thermodynamics and kinetics will likely benefit from the use of flexible water models.

Free energy functionals for polarization fluctuations: Pekar factor revisited.

The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. Within dielectric continuum models, this separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom. The main qualitative prediction of Pekar's perspective is a significant, by about a factor of two, drop of the nuclear solvation free energy compared to the total (electronic plus nuclear) free energy of solvation. The Pekar factor enters the solvent reorganization energy of electron transfer reactions and is a significant mechanistic parameter accounting for the solvent effect on electron transfer. Here, we study the separation of the fast and slow polarization modes in polar molecular liquids (polarizable dipolar liquids and polarizable water force fields) without relying on the continuum approximation. We derive the nonlocal free energy functional and use atomistic numerical simulations to obtain nonlocal, reciprocal space electronic and nuclear susceptibilities. A consistent transition to the continuum limit is introduced by extrapolating the results of finite-size numerical simulation to zero wavevector. The continuum nuclear susceptibility extracted from the simulations is numerically close to the Pekar factor. However, we derive a new functionality involving the static and high-frequency dielectric constants. The main distinction of our approach from the traditional theories is found in the solvation free energy due to the nuclear polarization: the anticipated significant drop of its magnitude with increasing liquid polarizability does not occur. The reorganization energy of electron transfer is either nearly constant with increasing the solvent polarizability and the corresponding high-frequency dielectric constant (polarizable dipolar liquids) or actually noticeably increases (polarizable force fields of water).

A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions.

We present a refined version of the polarizable Martini water model - coined refPOL - designed specifically for the use with long-range electrostatics. The refPOL model improves the agreement with the experimentally measured dielectric constant and the mass density of water at room temperature compared to the original polarizable Martini water force field when particle mesh Ewald electrostatics are employed. Our study reveals that the model remains applicable with various commonly used settings for the non-bonded interactions, including reaction field electrostatics. The oil/water partitioning behavior of uncharged Martini bead types is thoroughly investigated: Lennard-Jones interactions between the refPOL model and the remaining Martini beads are adjusted to reproduce the hydration free energies obtained with the original polarizable water model, while free energies of solvation in apolar media remain unchanged. The cross-interactions with charged bead types are parameterized to agree with the experimentally observed area per lipid of a fully solvated dipalmitoylphosphatidylcholine bilayer. We additionally verify the model by analyzing the potentials of mean force between different sample pairs in refPOL water and comparing the results to reference data obtained using the original polarizable Martini water model as well as fully atomistic simulations. Based on the results, we suggest to replace the original polarizable Martini water model with the new refPOL model for future applications.

Rate theory on water exchange in aqueous uranyl ion

We report a classical rate theory approach to predict the exchange mechanism that occurs between water and aqueous uranyl ion. Using our water and ion-water polarizable force field and molecular dynamics techniques, we computed the potentials of mean force for the uranyl ion-water pair as a function of different pressures at ambient temperature. These potentials of mean force were used to calculate rate constants using transition rate theory; the transmission coefficients also were examined using the reactive flux method and Grote-Hynes approach. The computed activation volumes are positive; thus, the mechanism of this particular water-exchange is a dissociative process.

Using Force Matching To Determine Reactive Force Fields for Water under Extreme Thermodynamic Conditions.

We present a method for the creation of classical force fields for water under dissociative thermodynamic conditions by force matching to molecular dynamics trajectories from Kohn-Sham density functional theory (DFT). We apply our method to liquid water under dissociative conditions, where molecular lifetimes are less than 1 ps, and superionic water, where hydrogen ions diffuse at liquid-like rates through an oxygen lattice. We find that, in general, our new models are capable of accurately reproducing the structural and dynamic properties computed from DFT, as well as the molecular concentrations and lifetimes. Overall, our force-matching approach presents a relatively simple way to create classical reactive force fields for a single thermodynamic state point that largely retains the accuracy of DFT while having the potential to access experimental time and length scales.

Molecular Dynamics Study of Combustion Reactions in a Supercritical Environment. Part 1: Carbon Dioxide and Water Force Field Parameters Refitting and Critical Isotherms of Binary Mixtures

The oxy-fuel–carbon dioxide combustion process is expected to drastically increase the energy efficiency and enable easy carbon sequestration. In this technology, the combustion products (carbon dioxide and water) are used to control the temperature and nitrogen is excluded from the combustion chamber, so that nitrogen oxide pollutants do not form. Therefore, in oxy-combustion, carbon dioxide and water are present in large concentrations in their transcritical state and may play an important role in kinetics. The computational chemistry methods may assist in understanding these effects, and molecular dynamics with a reactive force field (ReaxFF) seems to be a suitable tool for such a study. Here, we investigate applicability of the ReaxFF to describe the critical phenomena in carbon dioxide and water and find that several non-bonding parameters need adjustment. We report the new parameter set, capable of reproducing the critical temperatures and pressures. The critical isotherms of CO2/H2O binary mixtures...

Diffusion in Homogeneous and in Inhomogeneous Media: A New Unified Approach.

We propose a new method to calculate the diffusion coefficient within molecular dynamics simulations for either homogeneous or inhomogeneous fluids. We formulate such method by solving analytically the Smoluchowski equation for a linear potential of mean force within a thin layer with absorbing boundary conditions. The bulk, or homogeneous, fluid diffusion emerges as a particular case in this approach. We apply this method to bulk liquid water at atmospheric pressure and different temperatures using the SPC/E water force field. We show that our method gives results as accurate as the traditional Einstein-Smoluchowski method, avoiding the fitting procedure required in the traditional method. We also apply this method for molten sodium chloride showing its applicability for multicomponent systems. The water vapor-liquid interface is studied as an example of an inhomogeneous system. We calculate all the components of the diffusion tensor at the interface. We observe the same anisotropy between the perpendicular and the parallel components at the interface as it has been noted in the literature. We also calculate the perpendicular self-diffusion coefficient of methane near the calcite surface showing that this coefficient is much lower than the parallel diffusion coefficients. We believe that this new unified approach is a very promising technique for both bulk and confined media.

To Polarize or Not to Polarize? Charge-on-Spring versus KBFF Models for Water and Methanol Bulk and Vapor-Liquid Interfacial Mixtures.

Simulations of water and methanol mixtures using polarizable force fields (FFs) for methanol (COS/M and CPC) and water (COS/G2) were performed and compared to experiment and also to a nonpolarizable methanol (KBFF) model with SPC/E water in an effort to quantify the importance of explicit electronic polarization effects in bulk liquid mixtures and vapor-liquid interfaces. The bulk liquid mixture properties studied included the center of mass radial distribution functions, Kirkwood-Buff integrals (KBIs), volumetric properties, isothermal compressibility, enthalpy of mixing, dielectric constant, and diffusion coefficients. The vapor-liquid interface properties investigated included the relative surface probability distributions, surface tension, excess surface adsorption, preferred surface molecule orientations, and the surface dipole. None of the three FFs tested here was clearly superior for all of the properties examined. All the force fields typically reproduced the correct trends with composition for both the bulk and interfacial system properties; the differences between the force fields were primarily quantitative. The overall results suggest that the polarizable FFs are not, at the present stage of development, inherently better able to reproduce the studied bulk and interfacial properties-despite the added degree of explicit transferability that is, by definition, built into the polarizable models. Indeed, the specific parametrization of the FF appears to be just as important as the class of FF.

Lattice constants of pure methane and carbon dioxide hydrates at low temperatures. Implementing quantum corrections to classical molecular dynamics studies.

We introduce a simple correction to the calculation of the lattice constants of fully occupied structure sI methane or carbon dioxide pure hydrates that are obtained from classical molecular dynamics simulations using the TIP4PQ/2005 water force field. The obtained corrected lattice constants are subsequently used in order to obtain isobaric thermal expansion coefficients of the pure gas hydrates that exhibit a trend that is significantly closer to the experimental behavior than previously reported classical molecular dynamics studies.

Molecular hydrogen solvated in water--A computational study.

The aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H2 molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the H2 molecule without major structural distortions and two-dimensional, radial-angular distribution functions indicate that as opposed to strictly tangential, the orientation of these water molecules is such that the solute is solvated with one of the free electron pairs of H2O. The calculated self-diffusion coefficient of H2(aq) agrees very well with experimental results and the time dependence of mean square displacement suggests the presence of caging on a time scale corresponding to hydrogen bond network vibrations in liquid water. Orientational correlation function of H2 experiences an extremely short-scale decay, making the H2-H2O interaction potential essentially isotropic by virtue of rotational averaging. The inclusion of explicit polarizability in the model allows for the calculation of Raman spectra that agree very well with available experimental data on H2(aq) under differing pressure conditions, including accurate reproduction of the experimentally noted trends with solute pressure or concentration.

Free energy of ion hydration: Interface susceptibility and scaling with the ion size.

Free energy of solvation of a spherical ion in a force-field water is studied by numerical simulations. The focus is on the linear solvation susceptibility connecting the linear response solvation free energy to the squared ion charge. Spherical hard-sphere solutes, hard-sphere ions, and Kihara solutes (Lennard-Jones modified hard-sphere core) are studied here. The scaling of the solvation susceptibility with the solute size significantly deviates from the Born equation. Using empirical offset corrections of the solute size (or the position of the first peak of the solute-solvent distribution function) do not improve the agreement with simulations. We advance a new perspective on the problem by deriving an exact relation for the radial susceptibility function of the interface. This function yields an effective cavity radius in the Born equation calculated from the solute-solvent radial distribution function. We find that the perspective of the local response, assuming significant alteration of the solvent structure by the solute, is preferable compared to the homogeneous approximation assuming intact solvent structure around the solute. The model finds a simple explanation of the asymmetry of hydration between anions and cations in denser water shells around anions and smaller cavity radii arising from the solute-solvent density profiles.

A modified two-state empirical valence bond model for proton transport in aqueous solutions.

A detailed analysis of the proton solvation structure and transport properties in aqueous solutions is performed using classical molecular dynamics simulations. A refined two-state empirical valence bond (aTS-EVB) method, which is based on the EVB model of Walbran and Kornyshev and the anharmonic water force field, is developed in order to describe efficiently excess proton transport via the Grotthuss mechanism. The new aTS-EVB model clearly satisfies the requirement for simpler and faster calculation, because of the simplicity of the two-state EVB algorithm, while providing a better description of diffusive dynamics of the excess proton and water in comparison with the previous two-state EVB models, which significantly improves agreement with the available experimental data. The results of activation energies for the excess proton and water calculated between 300 and 340 K (the temperature range used in this study) are also found to be in good agreement with the corresponding experimental data.

Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering.

Following a previous report on a coarse-grained protein model in implicit solvent, we applied simulated tempering (ST) with on-the-fly Helmholtz free energy (weight factors) determination to the folding or aggregation of seven proteins with the CHARMM, OPLS, and AMBER protein, and the SPC and TIP3P water force fields. For efficiency and reliability, we also performed replica exchange molecular dynamics (REMD) simulations on the alanine di- and deca-peptide, and the dimer of the Aβ16-22 Alzheimer's fragment, and used experimental data and previous simulation results on the chignolin, beta3s, Trp-cage, and WW domain peptides of 10-37 amino acids. The sampling with ST is found to be more efficient than with REMD for a much lower CPU cost. Starting from unfolded or extended conformations, the WW domain and the Trp-cage peptide fold to their NMR structures with a backbone RMSD of 2.0 and 1 Å. Remarkably, the ST simulation explores transient non-native topologies for Trp-cage that have been rarely discussed by other simulations. Our ST simulations also show that the CHARMM22* force field has limitations in describing accurately the beta3s peptide. Taken together, these results open the door to the study of the configurations of single proteins, protein aggregates, and any molecular systems at atomic details in explicit solvent using a single normal CPU. They also demonstrate that our ST scheme can be used with any force field ranging from quantum mechanics to coarse-grain and atomistic.