Water Force Field Research Articles

Water adsorption in hydrophilic zeolites: experiment and simulation

We have measured experimental adsorption isotherms of water in zeolite LTA4A, and studied the regeneration process by performing subsequent adsorption cycles after degassing at different temperatures. We observed incomplete desorption at low temperatures, and cation rearrangement at successive adsorption cycles. We also developed a new molecular simulation force field able to reproduce experimental adsorption isotherms in the range of temperatures between 273 K and 374 K. Small deviations observed at high pressures are attributed to the change in the water dipole moment at high loadings. The force field correctly describes the preferential adsorption sites of water at different pressures. We tested the influence of the zeolite structure, framework flexibility, and cation mobility when considering adsorption and diffusion of water. Finally, we performed checks on force field transferability between different hydrophilic zeolite types, concluding that classical, non-polarizable water force fields are not transferable.

Extension of Brownian Dynamics for Studying Blockers of Ion Channels

We present new Brownian dynamics techniques for studying blockers of ion channels. By treating the channel as a fixed body, simulating the blocker molecules using rigid bodies, and using an implicit water force field with explicit ions, we are able to carry out fast simulations that can be used to investigate the dynamics of block and unblock, deduce binding modes, and calculate binding affinities. We test our program using the NavAb bacterial sodium channel, whose structure was recently solved (Payandeh et al. Nature, 2011, 475, 353-358) in conjunction with the μ-conotoxin PIIIA blocker. We derive an ohmic current-voltage relationship for channel permeation, calculate potentials of mean force for blocker unbinding, and deduce multiple binding modes for the blocker. Our results are shown to be compatible with other computational and experimental results. Finally, we discuss future improvements such as the inclusion of flexible side chains. After these improvements are carried out, we anticipate our program will be an extremely useful new tool that could be used to help develop new drugs to treat a range of ion-channel related diseases.

Ab initio parameterization of an all-atom polarizable and dissociable force field for water

A novel all-atom, dissociative, and polarizable force field for water is presented. The force field is parameterized based on forces, stresses, and energies obtained form ab initio calculations of liquid water at ambient conditions. The accuracy of the force field is tested by calculating structural and dynamical properties of liquid water and the energetics of small water clusters. The transferability of the force field to dissociated states is studied by considering the solvation of a proton and the ionization of water at extreme conditions of pressure and temperature. In the case of the solvated proton, the force field properly describes the presence of both Eigen and Zundel configurations. In the case of the pressure-induced ice VIII/ice X transition and the temperature-induced transition to a superionic phase, the force field is found to describe accurately the proton symmetrization and the melting of the proton sublattice, respectively.

Vibrational Spectra of Phosphate Ions in Aqueous Solution Probed by First-Principles Molecular Dynamics

We have carried out "first-principles" Born-Oppenheimer molecular dynamics (BOMD) simulations of the phosphate ions H₂PO₄⁻ and HPO₄²⁻ in liquid water and have calculated their IR spectra by Fourier transform techniques from the trajectories. IR bands were assigned by a so-called "generalized normal coordinate analysis". The effects of including Hartree-Fock (HF) exchange into the density functional theory (DFT) computation of forces were studied by comparing results obtained with the well-known BP, BLYP, and B3LYP functionals. The neglect of dispersion in the functionals was empirically corrected. The inclusion of HF exchange turned out to yield dramatically improved and, thus, quite accurate descriptions of the IR spectra observed for H₂PO₄⁻ and HPO₄²⁻ in aqueous solution. An analysis of earlier computational results (Klähn, M. et al. J. Phys. Chem. A 2004, 108, 6186-6194) on these vibrational spectra, which had been obtained in a hybrid setting combining a BP description of the respective phosphate with a simple molecular mechanics (MM) model of its aqueous environment, revealed three different sources of error, (i) the BP force field of the phosphates is much too soft and would have required a substantial scaling of frequencies, (ii) the oversimplified water force field entailed incorrect solvation structures and, thus, qualitatively wrong patterns of solvatochromic band shifts, and (iii) quantitative frequency computations additionally required the inclusion of HF exchange. Thus, the results of the B3LYP BOMD simulations do not only characterize physical properties like the IR spectra or the solvation structures of the phosphate systems but also provide clues for the future design of simplified but nevertheless reasonably accurate DFT/MM methods applicable to phosphates.

Study of effect of water vapor and mechanical strain on thermal conductivity of zinc oxide using the ReaxFF reactive force field

We present a study of the effect of strain on the thermal conductivity of the zinc oxide using ReaxFF reactive force field. Effect of water vapor on failure stress of zinc oxide has also been carried out. Force fields for zinc oxide and water have already been developed by Raymand et al. [1–3]. The thermal conductivity calculations were carried out using the Transient Non-Equilibrium Molecular Dynamics (T-NEMD) described by Bharathi and van Duin [4].For a zinc oxide nanowire, the effect of different values of mechanical strain – 0%, 2%, 6% and 10% (in the absence of water) on thermal conductivity is studied. No significant change in thermal conductivity is observed as the nanowire is stretched up to 6% strain (∼5W/mK) and is in good agreement with the results presented by Kulkarni and Zhou (Average value ∼5.5W/mK) [6]. The conductivity drops by 30% when the wire is stretched to 10% of its length. However, in contrast to the observations by Kulkarni et al. [7], no phase change is observed in our simulations.The effect of water vapor (system density – 1.04, 1.09, 1.18 and 1.24kg/m3) on the failure stress of zinc oxide nanowire is evaluated. The studies on effect water vapor on failure indicate that the failure stress drops from 14.25GPa in the absence of water vapor to 12.0GPa (−15.8%) for water vapor density of 1.24kg/m3. Significant hysteresis is observed with increasing water vapor density.As a practical application of T-NEMD, results from work on the sintering of zinc oxide nanoparticles in water vapor are reported.

Fitting properties from density functional theory based molecular dynamics simulations to parameterize a rigid water force field

In the quest towards coarse-grained potentials and new water models, we present an extension of the force matching technique to parameterize an all-atom force field for rigid water. The methodology presented here allows to improve the matching procedure by first optimizing the weighting exponents present in the objective function. A new gauge for unambiguously evaluating the quality of the fit has been introduced; it is based on the root mean square difference of the distributions of target properties between reference data and fitted potentials. Four rigid water models have been parameterized; the matching procedure has been used to assess the role of the ghost atom in TIP4P-like models and of electrostatic damping. In the former case, burying the negative charge inside the molecule allows to fit better the torques. In the latter, since short-range interactions are damped, a better fit of the forces is obtained. Overall, the best performing model is the one with a ghost atom and with electrostatic damping. The approach shown in this paper is of general validity and could be applied to any matching algorithm and to any level of coarse graining, also for non-rigid molecules.

Comparison of selected polarizable and nonpolarizable water models in molecular dynamics simulations of ice Ih

We present a molecular dynamics simulation study in which we determined the melting point of ice I(h) for the polarizable SWM4-NDP water model (Lamoureux et al., Chem. Phys. Lett., 2006, 418, 245-249) and compared the performance of several popular water force fields, both polarizable and nonpolarizable, in terms of melting temperature, stability and orientational structuring of ice. The simulations yield the melting temperature of SWM4-NDP ice as low as T(m) = 185 ± 10 K, despite the quadrupole moment of a SWM4-NDP water molecule being close to the experimental gas phase value. The results thus show that the dependence of T(m) on the molecular quadrupole, observed for the three- and four-site water models, is generally lost if polarization is explicitly included. The study also shows that adding polarizability to a planar three-charge water model increases orientational disorder in hexagonal ice. In addition, analysis of the tetrahedral order in bulk ice reveals a correlation between the pre-existing degree of orientational disorder in ice simulated using different polarizable and nonpolarizable models and the melting temperature of the models. Our findings thus suggest some new considerations regarding the role of polarization forces in a crystalline solid that may guide future development of reliable polarizable water models for ice.

Aqueous halide potentials from force matching of Car–Parrinello data

Recently many various research groups have devoted a huge effort to develop a realistic classical force field for ions in water. The parametrization techniques used could be gathered into two classes: (i) fit of the ab initio potential energy surface for clusters at gas phase, and (ii) fit of experimental properties. For both classes of force fields, a high level of accuracy has been achieved, which has led to important improvements in the modeling of ion–water systems. In this paper a new, complementary, approach is proposed to overcome the limitations and to get a deeper insight into the atomistic description of ion–water interactions. We use the recently developed force matching method to parametrize classical halide–water force fields for three different water models. Here we discuss both methodological issues and the level of agreement between the results obtained using this method to Car–Parrinello simulation results.

A Refined MS-EVB Model for Proton Transport in Aqueous Environments

In order to improve the description of proton mobility in aqueous environments, a revised multistate empirical valence bond model (aMS-EVB3) is developed. The new aMS-EVB3 model is built upon an anharmonic water force field (aSPC/Fw) in which the OH bond potential is described through a quartic approximation to a Morse potential. First, it is shown that the aSPC/Fw anharmonic water model provides an accurate description of water at ambient conditions and reproduces the available experimental data for several structural, thermodynamic, and dynamical properties. Second, it is shown that, when applied to the study of proton solvation and transport in bulk water, the new aMS-EVB3 model accurately describes the solvation structure around the excess proton. Importantly, the new aMS-EVB3 model predicts a significantly larger proton diffusion coefficient than previous models, which largely improves the agreement with the available experimental data.

Approaching post-Hartree–Fock quality potential energy surfaces with simple pair-wise expressions: parameterising point-charge-based force fields for liquid water using the adaptive force matching method

This article summarises the adaptive force matching (AFM) method recently developed by the Wang group. The AFM method is capable of parameterising force fields in the condensed phase by fitting electronic structure forces obtained through quantum mechanics/molecular mechanics (QM/MM) calculations. The AFM method utilises an iterative procedure to ensure good sampling and high-quality MM models for QM/MM calculations. By fitting forces directly in the condensed phase, simple pair-wise additive potentials parameterised following AFM can account for many-body effects implicitly. The AFM method provides a mechanism for judging the effectiveness of force field terms and the quality and transferability of the final force field. Realising the limitation of simple potentials, AFM emphasises fitting problem-specific force fields instead of a universal force field. This article provides a demonstration using the recently developed density functional theory/supplemental potential method to provide reference forces to parameterise a four-site point-charge model, BLYPSP-4F, for liquid water in the temperature range from 0 to 40°C. No experimental information was used for the development of BLYPSP-4F the model is found to satisfactorily reproduce experimental properties.

Molecular Simulation of Aqueous Electrolyte Solubility. 2. Osmotic Ensemble Monte Carlo Methodology for Free Energy and Solubility Calculations and Application to NaCl

We present a new and computationally efficient methodology using osmotic ensemble Monte Carlo (OEMC) simulation to calculate chemical potential-concentration curves and the solubility of aqueous electrolytes. The method avoids calculations for the solid phase, incorporating readily available data from thermochemical tables that are based on well-defined reference states. It performs simulations of the aqueous solution at a fixed number of water molecules, pressure, temperature, and specified overall electrolyte chemical potential. Insertion/deletion of ions to/from the system is implemented using fractional ions, which are coupled to the system via a coupling parameter λ that varies between 0 (no interaction between the fractional ions and the other particles in the system) and 1 (full interaction between the fractional ions and the other particles of the system). Transitions between λ-states are accepted with a probability following from the osmotic ensemble partition function. Biasing weights associated with the λ-states are used in order to efficiently realize transitions between them; these are determined by means of the Wang-Landau method. We also propose a novel scaling procedure for λ, which can be used for both nonpolarizable and polarizable models of aqueous electrolyte systems. The approach is readily extended to involve other solvents, multiple electrolytes, and species complexation reactions. The method is illustrated for NaCl, using SPC/E water and several force field models for NaCl from the literature, and the results are compared with experiment at ambient conditions. Good agreement is obtained for the chemical potential-concentration curve and the solubility prediction is reasonable. Future improvements to the predictions will require improved force field models.

The Ice−Vapor Interface and the Melting Point of Ice Ih for the Polarizable POL3 Water Model

We use molecular dynamics simulations to determine the melting point of ice I(h) for the polarizable POL3 water force field (Dang, L. X. J. Chem. Phys.1992, 97, 2659). Simulations are performed on a slab of ice I(h) with two free surfaces at several different temperatures. The analysis of the time evolution of the total energy in the course of the simulations at the set of temperatures yields the melting point of the POL3 model to be T(m) = 180 ± 10 K. Moreover, the results of the simulations show that the degree of hydrogen-bond disorder occurring in the bulk of POL3 ice is larger (at the corresponding degree of undercooling) than in ice modeled by nonpolarizable water models. These results demonstrate that the POL3 water force field is rather a poor model for studying ice and ice-liquid or ice-vapor interfaces. While a number of polarizable water models have been developed over the past years, little is known about their performance in simulations of supercooled water and ice. This study thus highlights the need for testing of the existing polarizable water models over a broad range of temperatures, pressures, and phases, and developing a new polarizable water force field, reliable over larger areas of the phase diagram.

Limiting diffusion coefficients of ionic liquids in water and methanol: a combined experimental and molecular dynamics study

Mutual diffusion coefficients D(12) of the ionic liquids 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([C(2)MIM][NTf(2)]) and [C(4)MIM][NTf(2)] in highly diluted solutions of water and methanol have been measured at different temperatures between 288 K and 313 K using the Taylor dispersion technique. Tracer diffusion coefficients of the two cations [C(2)MIM](+) and [C(4)MIM](+) as well as the anion [NTf(2)](-) in these solutions have been obtained by molecular dynamics (MD) simulations. For our simulations we used well established force fields for the solvents water and methanol and a recently developed force field for imidazolium-based ionic liquid [C(n)MIM][NTf(2)]. Mutual diffusion coefficients D(12) have been calculated from the tracer diffusion coefficients using the Nernst-Hartley equation strictly valid only at low ionic concentration. The agreement between the diffusion coefficients reported in the literature, the experimental data obtained in this work and the MD results is excellent.

Improving the force matching algorithm: Application to a simple point charge flexible model of water

In the last years the force matching algorithm has appeared to be a promising method for deriving next generation classical force fields. Recently it has been successfully utilized to parameterize new water models based on pairwise potentials. In this contribution we will present a refined version of the method which has been applied to parameterize a new force field for flexible water. Static and dynamical properties of the new water model reproduce fairly well the ab initio results. This enriched version of the method could possibly be applied to produce a fully flexible force field for any molecular systems where intramolecular motion plays a central role.

Molecular dynamics simulations of aqueous ions at the liquid–vapor interface accelerated using graphics processors

Molecular dynamics (MD) simulations are a vital tool in chemical research, as they are able to provide an atomistic view of chemical systems and processes that is not obtainable through experiment. However, large-scale MD simulations require access to multicore clusters or supercomputers that are not always available to all researchers. Recently, scientists have returned to exploring the power of graphics processing units (GPUs) for various applications, such as MD, enabled by the recent advances in hardware and integrated programming interfaces such as NVIDIA's CUDA platform. One area of particular interest within the context of chemical applications is that of aqueous interfaces, the salt solutions of which have found application as model systems for studying atmospheric process as well as physical behaviors such as the Hoffmeister effect. Here, we present results of GPU-accelerated simulations of the liquid-vapor interface of aqueous sodium iodide solutions. Analysis of various properties, such as density and surface tension, demonstrates that our model is consistent with previous studies of similar systems. In particular, we find that the current combination of water and ion force fields coupled with the ability to simulate surfaces of differing area enabled by GPU hardware is able to reproduce the experimental trend of increasing salt solution surface tension relative to pure water. In terms of performance, our GPU implementation performs equivalent to CHARMM running on 21 CPUs. Finally, we address possible issues with the accuracy of MD simulaions caused by nonstandard single-precision arithmetic implemented on current GPUs.

Relationship between population of the fibril-prone conformation in the monomeric state and oligomer formation times of peptides: Insights from all-atom simulations

Despite much progress in understanding the aggregation process of biomolecules, the factors that govern its rates have not been fully understood. This problem is of particular importance since many conformational diseases such as Alzheimer, Parkinson, and type-II diabetes are associated with the protein oligomerization. Having performed all-atom simulations with explicit water and various force fields for two short peptides KFFE and NNQQ, we show that their oligomer formation times are strongly correlated with the population of the fibril-prone conformation in the monomeric state. The larger the population the faster the aggregation process. Our result not only suggests that this quantity plays a key role in the self-assembly of polypeptide chains but also opens a new way to understand the fibrillogenesis of biomolecules at the monomeric level. The nature of oligomer ordering of NNQQ is studied in detail.

A Coarse-Grained Model Based on Morse Potential for Water and n-Alkanes.

In order to extend the time and distance scales of molecular dynamics simulations, it is essential to create accurate coarse-grained force fields, in which each particle contains several atoms. Coarse-grained force fields that utilize the Lennard-Jones potential form for pairwise nonbonded interactions have been shown to suffer from serious inaccuracy, notably with respect to describing the behavior of water. In this paper, we describe a coarse-grained force field for water, in which each particle contains four water molecules, based on the Morse potential form. By molecular dynamics simulations, we show that our force field closely replicates important water properties. We also describe a Morse potential force field for alkanes and a simulation method for alkanes in which individual particles may have variable size, providing flexibility in constructing complex molecules comprised partly or solely of alkane groups. We find that, in addition to being more accurate, the Morse potential also provides the ability to take larger time steps than the Lennard-Jones, because the short distance repulsion potential profile is less steep. We suggest that the Morse potential form should be considered as an alternative for the Lennard-Jones form for coarse-grained molecular dynamics simulations.

Molecular dynamics simulations of nonpolarizable inorganic salt solution interfaces: NaCl, NaBr, and NaI in transferable intermolecular potential 4-point with charge dependent polarizability (TIP4P-QDP) water.

We present molecular dynamics simulations of the liquid-vapor interface of 1M salt solutions of nonpolarizable NaCl, NaBr, and NaI in polarizable transferable intermolecular potential 4-point with charge dependent polarizability water [B. A. Bauer et al., J. Chem. Theory Comput. 5, 359 (2009)]; this water model accommodates increased solvent polarizability (relative to the condensed phase) in the interfacial and vapor regions. We employ fixed-charge ion models developed in conjunction with the TIP4P-QDP water model to reproduce ab initio ion-water binding energies and ion-water distances for isolated ion-water pairs. The transferability of these ion models to the condensed phase was validated with hydration free energies computed using thermodynamic integration (TI) and appropriate energy corrections. Density profiles of Cl(-), Br(-), and I(-) exhibit charge layering in the interfacial region; anions and cation interfacial probabilities show marked localization, with the anions penetrating further toward the vapor than the cations. Importantly, in none of the cases studied do anions favor the outermost regions of the interface; there is always an aqueous region between the anions and vapor phase. Observed interfacial charge layering is independent of the strength of anion-cation interactions as manifest in anion-cation contact ion pair peaks and solvent separated ion pair peaks; by artificially modulating the strength of anion-cation interactions (independent of their interactions with solvent), we find little dependence on charge layering particularly for the larger iodide anion. The present results reiterate the widely held view of the importance of solvent and ion polarizability in mediating specific anion surface segregation effects. Moreover, due to the higher parametrized polarizability of the TIP4P-QDP condensed phase {1.31 A(3) for TIP4P-QDP versus 1.1 A(3) (TIP4P-FQ) and 0.87 A(3) (POL3) [Ponder and Case, Adv. Protein Chem. 66, 27 (2003)]} based on ab initio calculations of the condensed-phase polarizability reduction in liquid water, the present simulations highlight the role of water polarizability in inducing water molecular dipole moments parallel to the interface normal (and within the interfacial region) so as to favorably oppose the macrodipole generated by the separation of anion and cation charge. Since the TIP4P-QDP water polarizability approaches that of the experimental vapor phase value for water, the present results suggest a fundamental role of solvent polarizability in accommodating the large spatial dipole generated by the separation of ion charges. The present results draw further attention to the question of what exact value of condensed phase water polarizability to incorporate in classical polarizable water force fields.

Molecular Dynamics Simulation of Phospholipid Bilayers and Monolayers Using a Polarizable Force Field

The assumptions that underlie empirical force field models based on fixed molecular charge densities become questionable in the strongly heterogeneous electrostatic environment of bilayer membranes. Membranes contain regions that are polar (bulk water) highly charged (zwitterionic lipid head groups) and decidedly non-polar (hydrocarbon core). Using a recently developed polarizable Drude oscillator force field for lipids and water we present a study that illustrates the significant role played by electronic polarization effects in the electrostatic modeling of a phospholipid membrane. Specifically, we show that the inclusion of such many-body polarization effects can bring macroscopic electrostatic properties into quantitative precision with experimental observation.

A Coarse-Grained Model Based on Morse Potential for Water and N-Alkanes

In order to extend the time and distance scales of molecular dynamics simulations, it is essential to create accurate coarse-grained force fields, in which each particle contains several atoms. Coarse-grained force fields that utilize the Lennard-Jones potential form for pair-wise non-bonded interactions have been shown to suffer from serious inaccuracy, notably with respect to describing the behavior of water. In this paper we describe a coarse-grained force field for water, in which each particle contains four water molecules, based on the Morse potential form. By molecular dynamics simulations we show that our CSJ force field closely replicates important water properties. We also describe a Morse potential force field for alkanes and a simulation method for alkanes in which individual particles may have variable size, providing flexibility in constructing complex molecules comprised partly or solely of alkane groups. We find that in addition to being more accurate, the Morse potential also provides the ability to take larger time steps than the Lennard-Jones, because the short distance repulsion potential profile is less steep. The Morse potential is implemented in Gromacs, using a rapid table look-up capability available in that simulation package. The table look-up is about 20% slower per time step than the standard Lennard-Jones, but is more than compensated for by the longer time step possible, so that overall simulation times are shorter when using the Morse potential. We suggest that the Morse potential form should be considered as an alternative for the Lennard-Jones form for coarse-grained molecular dynamics simulations. We are working on coarse-grained force fields for amphipathic molecules and for ions, and will provide a progress report on that work in this presentation.