Simple Point Charge Water Model Research Articles

Reactive force field potential with shielded long-range Coulomb interaction: Application to graphene–water capacitors

Electrode–electrolyte interfacial properties characterize the functioning of electrochemical devices, and reactive molecular dynamics simulations, using reactive force fields (ReaxFF) and charge equilibration (QEq) techniques, are classical atomistic methods for investigating the processes that govern the device properties. However, the numerical implementation of ReaxFF and QEq treats Coulomb interaction with a short-distance cutoff for computational speed, thereby limiting interactions among atoms to a domain containing only their neighbor lists. Excluding long-distance Coulomb interactions makes the description of electrostatics in large-scale systems intractable. We apply Ewald sum in the extension of ReaxFF to include long-range Coulomb (LRC) interactions and investigate the effect of the inclusion on the electrostatic and capacitive properties of graphene–water interfaces at different applied potentials in comparison with the original ReaxFF. The study shows that with the inclusion of long-range Coulomb, the capacitance amounts to 4.9 ± 0.2 μF cm−2 compared with 4.4 ± 0.2 μF cm−2 predicted by the original ReaxFF [with short-range Coulomb (SRC)]; thus, indicating that SRC underestimates the capacitance of water between graphene walls by 12% when compared with the 5.0 μF cm−2 predicted with the extended simple point charge (SPC/E) water model. Thus, the results indicate that LRC ReaxFF/QEq have the ability and advantage to model electrochemical processes at a more realistic Coulomb interaction description and foster the processing of the details about the operation of electrochemical devices than the SRC.

COMPARATIVE CHAINS DYNAMICS OF TRIOSEPHOSPHATE ISOMERASE INVESTIGATED BY MOLECULAR DYNAMICS SIMULATION

Triosephosphate isomerase is an enzyme which catalyzes the inter-conversion between glyceraldehyde-3-phosphate and dihydroxyacetone phosphate in the fifth step of the glycolytic pathway. In this study, molecular dynamics simulation technique was employed to investigate the dynamics of the two monomer chains of triosephosphate isomerase of trypanosoma brucei brucei (TbTIM) using GROMACS 2016.04 software. The MD simulation of the x-ray structure of TbTIM was performed using the GROMOS 9643a1 force field and simple point charge water model under isothermal-isobaric condition with periodic boundary conditions imposed on x, y, z directions. The Root Mean Square Deviation (RMSD) Root Mean Square fluctuation (RMSF), Radius of Gyration (ROG), Solvent accessible surface area (SASA) and hydrogen bonds were computed. The RMSD values indicate that chain-B shows transition between two conformational states with higher RMSD value of 0.45 nm when compared to chain-A with RMSD of 0.27 nm. The RMSF values indicates that residues of loop 6 (residues 166 to 177) have the highest fluctuations in both chains compared to other residues with chain-A having higher fluctuations peak. The ROG values of chain-A varies from 1.675 nm to 1.761 nm while that of chain-B varies from 2.480 nm to 2.590 nm implying that chain-A is more compact during the simulation than chain-B. The SASA values indicates that chain-B has more contact with solvent than chain-A. 160 hydrogen bonds were found which indicates the stability of the protein during the simulation. From the RMSD, ROG, SASA values, it is evident that chain-B of triosephosphate isomerase of trypanosoma bruceibrucei displayed greater structural dynamics than chain-A during the MD simulation.

On the Choice of Different Water Model in Molecular Dynamics Simulations of Nanopore Transport Phenomena.

The water transport through nanoporous multilayered graphene at 300k is investigated using molecular dynamics (MD) simulation with different water models in this study. We used functionalized and non-functionalized membranes along with five different 3-point rigid water models: SPC (simple point charge), SPC/E (extended simple point charge), TIP3P-FB (transferable intermolecular potential with 3 points-Force Balance), TIP3P-EW (transferable intermolecular potential with 3 points with Ewald summation) and OPC3 (3-point optimal point charge) water models. Based on our simulations with two water reservoirs and a porous multilayered graphene membrane in-between them, it is evident that the water transport varies significantly depending on the water model used, which is in good agreement with previous works. This study contributes to the selection of a water model for molecular dynamics simulations of water transport through multilayered porous graphene.

Diffusion coefficient and solvation free energy of sucrose in water: a molecular dynamics study

In this work, we have carried out Molecular Dynamics Simulation technique to study the diffusion coefficients, radial distribution functions and solvation free energy of sucrose (C12H22O11) at different temperatures ranging from 298.15 K to 318.15 K. We have taken 2 molecules of sucrose in 1343 molecules of extended simple point charge (SPC/E) water model. The self-diffusion coefficients are obtained by applying linear best fit to the mean squaredisplacement (MSD) plot and binary diffusion coefficients are obtained by using Darken’s relation. Arrhenius equation has been used to show a linear relationship between natural logarithm of binary diffusion coefficient and reciprocal of temperature. The structural analysis of the solution has been carried out with the help of radial distribution functions (RDFs) of its constituents. The solvation free energy of sucrose is studied at 300 K by using free energy perturbation method like Bennett Acceptance Ratio (BAR). The results of binary diffusion coefficients obtained from this simulation work agree very well with the previously reported experimental data.

Molecular dynamics simulations of Lithium Fluoride aqueous solutions: Effects of ion concentration on the structural and dynamical properties at T=300 K

Lithium fluoride aqueous system play an important role in a variety of chemical engineering, energy, biochemistry and environmental processes. Lithium salts are also widely used in conventional electrolytes for making lithium-ion batteries. Computer simulation of lithium in fluoride aqueous solution has an important tool in understanding the structural and dynamical characteristics of ionic complexes. In this investigation, the structural and dynamical properties of supersatured LiF systems have been studied by molecular dynamics simulations at different molalities range from 0.05 up to 2.00 mol.Kg-1 using extended simple point charge (SPC/E) water model and the ions which are modeled as charged Lennard-Jones particles. Molecular dynamics simulations return highly complex data. The cartesian positions of each atom of lithium chloride aqueous solution are recorded at every time step of the trajectory. Therefore, the analysis of data requires to calculate the radial distribution functions (RDFs) describing the structure of the hydration shells around the ions in solutions and the hydration number. The structural properties of the water and Li+ and F- ions, such as the coordination number, interparticle distance, self-diffusion coefficient and dielectric constant are strongly depending on the molality and chemical nature of counterions.

When do short-range atomistic machine-learning models fall short?

We explore the role of long-range interactions in atomistic machine-learning models by analyzing the effects on fitting accuracy, isolated cluster properties, and bulk thermodynamic properties. Such models have become increasingly popular in molecular simulations given their ability to learn highly complex and multi-dimensional interactions within a local environment; however, many of them fundamentally lack a description of explicit long-range interactions. In order to provide a well-defined benchmark system with precisely known pairwise interactions, we chose as the reference model a flexible version of the Extended Simple Point Charge (SPC/E) water model. Our analysis shows that while local representations are sufficient for predictions of the condensed liquid phase, the short-range nature of machine-learning models falls short in representing cluster and vapor phase properties. These findings provide an improved understanding of the role of long-range interactions in machine learning models and the regimes where they are necessary.

Diffusion of oxytocin in water: a molecular dynamics study

Classical molecular dynamics simulation is performed to estimate the diffusion coefficient of oxytocin in water at different temperatures, 288 K, 300 K, 313 K, 323 K, using GROningen Machine for Chemical Simulations (GROMOCS). The simulation is carried out using GROMOS43A1 force field and extended simple point charge (SPC/E) water model. The stability of the system is evaluated from energy profile of potential and kinetic energy, which assures well equilibrated molecular system. The self-diffusion coefficient of oxytocin and water is obtained from Einstein’s relation and binary diffusion coefficient is obtained from Darken’s relation. As temperature increases the diffusion coefficient also increases as per expectation. The diffusion coefficients of water from the present calculations agree well with the previously reported values, within the 10% of deviation. Furthermore, the activation energy has been studied using Arrhenius Plot.
 BIBECHANA 18 (2021) 108-117

Wetting Properties of the CO2-Water-Calcite System via Molecular Simulations: Shape and Size Effects.

Assessment of the risks and environmental impacts of carbon geosequestration requires knowledge about the wetting behavior of mineral surfaces in the presence of CO2 and the pore fluids. In this context, the interfacial tension (IFT) between CO2 and the aqueous fluid and the contact angle, θ, with the pore mineral surfaces are the two key parameters that control the capillary pressure in the pores of the candidate host rock. Knowledge of these two parameters and their dependence on the local conditions of pressure, temperature, and salinity is essential for the correct prediction of structural and residual trapping. We have performed classical molecular dynamics simulations to predict the CO2-water IFT and the CO2-water-calcite contact angle. The IFT results are consistent with previous simulations, where simple point charge water models have been shown to underestimate the water surface tension, thus affecting the simulated IFT values. When combined with the EPM2 CO2 model, the SPC/Fw water model indeed underestimates the IFT in the low-pressure region at all temperatures studied. On the other hand, at high pressure and low temperature, the IFT is overestimated by ∼5 mN/m. Literature data regarding the CO2/water/calcite contact angle on calcite are contradictory. Using our new set of force field parameters, we performed NVT simulations at 323 K and 20 MPa to calculate the contact angle of a water droplet on the calcite {10.4} surface in a CO2 atmosphere. We performed simulations for both spherical and cylindrical droplet configurations for different initial radii to study the size dependence of the water contact angle on calcite in the presence of CO2. Our results suggest that the contact angle of a cylindrical droplet, is independent of droplet size, for droplets with a radius of 50 Å or more. On the contrary, spherical droplets make a contact angle that is strongly influenced by their size. At the largest size explored in this study, both spherical and cylindrical droplets converge to the same contact angle, 38°, indicating that calcite is strongly wetted by water.

Systematic Design-of-Experiments, factorial-design approaches for tuning simple empirical water models

ABSTRACT Using systematic Design-of-Experiments, factorial-design approaches, we identify how five variables (site charge, sigma, epsilon, OH bond length and HOH bond angle) affect the diffusivity and radial distribution function accuracy within the framework of the Simple Point Charge water model. From this (by a full-functional DoX-effects model), we glean response equations for the effects of these systematic variations on both estimation of site-site radial distribution functions, in addition to self-diffusivities, allowing scope to estimate more precisely optimal parameters for use in tailored force-fields for particular purposes (e.g. improved fidelity towards particular desired structural or dynamical properties). To this end, the diffusivity error was reduced from an initial value of 35.2–0.64%, whilst the radial distribution function was more difficult to improve, with a reduction in error of 2.83%.

Compatibility of GROMOS-Derived Atomic Parameters for Lipopolysaccharide Membranes with the SPC/E Water Model and Alternative Long-Range Electrostatic Treatments Using Single Nonbonded Cutoff and Atom-Based Charge Schemes

Recent developments of GROMACS v.2016 ceased to support methodological approaches used in the development and validation of the GROMOS force field. We investigated the performance of a previously developed extension of the GROMOS force field for lipopolysaccharides to reproduce the structural dynamics of bacterial outer membrane (OM) using a single cutoff for nonbonded interactions and atom-based charge truncation. We further compared this setup for use with reaction field (RF) or particle mesh Ewald (PME) approximations in the presence of simple point charge (SPC) and extended simple point charge (SPC/E) water models. We find that the OM structural dynamics is well conserved in all simulated conditions, reproducing the available experimental data within the measurement uncertainty. The SPC/E model induces a small increase in OM fluidity, and when combined with the RF correction, shows a decrease in water orientation at the membrane surface. The present simulations support the compatibility of the GROMOS-derived lipopolysaccharide (LPS) parameters for use with single cutoff and atom-based charge schemes, either with RF or PME approximations, in GROMACS v.2016. Both SPC and SPC/E water models are suitable for use, but usage of SPC/E combined with the reaction field correction needs to be further investigated.

All-atom computations with irreversible Markov chains.

We apply the irreversible event-chain Monte Carlo (ECMC) algorithm to the simulation of dense all-atom systems with long-range Coulomb interactions. ECMC is event-driven and exactly samples the Boltzmann distribution. It neither uses time-step approximations nor spatial cutoffs on the range of the interaction potentials. Most importantly, it need not evaluate the total Coulomb potential and thus circumvents the major computational bottleneck of traditional approaches. It only requires the derivatives of the two-particle Coulomb potential, for which we discuss mutually consistent choices. ECMC breaks up the total interaction potential into factors. For particle systems made up of neutral dipolar molecules, we demonstrate the superior performance of dipole-dipole factors that do not decompose the Coulomb potential beyond the two-molecule level. We demonstrate that these long-range factors can nevertheless lead to local lifting schemes, where subsequently moved particles are mostly close to each other. For the simple point-charge water model with flexible molecules (SPC/Fw), which combines the long-ranged intermolecular Coulomb potential with hydrogen-oxygen bond-length vibrations, a flexible hydrogen-oxygen-hydrogen bond angle, and Lennard-Jones oxygen-oxygen potentials, we break up the potential into factors containing between two and six particles. For this all-atom liquid-water model, we demonstrate that the computational complexity of ECMC scales very well with the system size. This is achieved in a pure particle-particle framework, without the interpolating mesh required for the efficient implementation of other modern Coulomb algorithms. Finally, we discuss prospects and challenges for ECMC and outline several future applications.

Specific Cation Effects on SCN- in Bulk Solution and at the Air-Water Interface.

The large and sparsely hydrated thiocyanate anion, SCN-, plays a prominent role in the study of specific ion effects in biological, colloid, and atmospheric chemistry due to its extreme position in the Hofmeister series. Using atomistic modeling of aqueous SCN- solutions, we provide novel insight at the molecular scale into the experimentally observed differences in ion pairing, clustering, reorientation dynamics, mutual diffusion, and solubility between the sodium, Na+, and the potassium, K+, salt. Compared to KSCN, NaSCN has a less pronounced tendency to ion pairing; nevertheless, at high salt concentrations, we observe a strong attraction between Na+ cations and the nitrogen end of SCN-, resulting in larger and more closely packed ion clusters. To accurately model aqueous SCN- solutions in computer simulations, we develop a thermodynamically consistent force field rooted in quantum-chemical calculations and refined using the Kirkwood-Buff theory. The force field is compatible with the extended simple point charge and three-point optimal point charge classical water models and reproduces experimental activity derivatives and air-water surface tension for a wide range of salt concentrations.

Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration.

The absolute intrinsic hydration free energy GH+,wat◦ of the proton, the surface electric potential jump χwat◦ upon entering bulk water, and the absolute redox potential VH+,wat◦ of the reference hydrogen electrode are cornerstone quantities for formulating single-ion thermodynamics on absolute scales. They can be easily calculated from each other but remain fundamentally elusive, i.e., they cannot be determined experimentally without invoking some extra-thermodynamic assumption (ETA). The Born model provides a natural framework to formulate such an assumption (Born ETA), as it automatically factors out the contribution of crossing the water surface from the hydration free energy. However, this model describes the short-range solvation inaccurately and relies on the choice of arbitrary ion-size parameters. In the present study, both shortcomings are alleviated by performing first-principle calculations of the hydration free energies of the sodium (Na+) and potassium (K+) ions. The calculations rely on thermodynamic integration based on quantum-mechanical molecular-mechanical (QM/MM) molecular dynamics (MD) simulations involving the ion and 2000 water molecules. The ion and its first hydration shell are described using a correlated ab initio method, namely resolution-of-identity second-order Møller-Plesset perturbation (RIMP2). The next hydration shells are described using the extended simple point charge water model (SPC/E). The hydration free energy is first calculated at the MM level and subsequently increased by a quantization term accounting for the transformation to a QM/MM description. It is also corrected for finite-size, approximate-electrostatics, and potential-summation errors, as well as standard-state definition. These computationally intensive simulations provide accurate first-principle estimates for GH+,wat◦, χwat◦, and VH+,wat◦, reported with statistical errors based on a confidence interval of 99%. The values obtained from the independent Na+ and K+ simulations are in excellent agreement. In particular, the difference between the two hydration free energies, which is not an elusive quantity, is 73.9 ± 5.4 kJ mol-1 (K+ minus Na+), to be compared with the experimental value of 71.7 ± 2.8 kJ mol-1. The calculated values of GH+,wat◦, χwat◦, and VH+,wat◦ (-1096.7 ± 6.1 kJ mol-1, 0.10 ± 0.10 V, and 4.32 ± 0.06 V, respectively, averaging over the two ions) are also in remarkable agreement with the values recommended by Reif and Hünenberger based on a thorough analysis of the experimental literature (-1100 ± 5 kJ mol-1, 0.13 ± 0.10 V, and 4.28 ± 0.13 V, respectively). The QM/MM MD simulations are also shown to provide an accurate description of the hydration structure, dynamics, and energetics.

Forward flux sampling calculation of homogeneous nucleation rates from aqueous NaCl solutions.

We used molecular dynamics simulations and the path sampling technique known as forward flux sampling to study homogeneous nucleation of NaCl crystals from supersaturated aqueous solutions at 298 K and 1 bar. Nucleation rates were obtained for a range of salt concentrations for the Joung-Cheatham NaCl force field combined with the Extended Simple Point Charge (SPC/E) water model. The calculated nucleation rates are significantly lower than the available experimental measurements. The estimates for the nucleation rates in this work do not rely on classical nucleation theory, but the pathways observed in the simulations suggest that the nucleation process is better described by classical nucleation theory than an alternative interpretation based on Ostwald's step rule, in contrast to some prior simulations of related models. In addition to the size of NaCl nucleus, we find that the crystallinity of a nascent cluster plays an important role in the nucleation process. Nuclei with high crystallinity were found to have higher growth probability and longer lifetimes, possibly because they are less exposed to hydration water.

Molecular dynamics simulation of nanomanipulation based on AFM in liquid ambient

Environmental factor is one of the most fundamental parameters in analyzing nanorobots and nanoassemblies. This study focuses on analyzing the manipulation process in a liquid environment using molecular dynamics simulation method. For this purpose, extended simple point-charge water model has been used to model an aqueous media. The effects of different conditions such as substrate material, submerging, electrical charge, and adhesion have been investigated on the manipulation force. In the water media, performing the manipulation process can reduce the manipulation force and increase the possibility of manipulation on the substrates with high adhesion. The manipulation results illustrate that these forces have extremum values in dry (vacuum) and partially submerged nanomanipulations. When the manipulation is carried out in the aqueous media, the interaction of nanoparticle and substrate reduces and leads to decrease the damage of targeted nanoparticle. The RMS criterion confirms this result. The results indicate the adhesion and attraction forces between the tip and nanoparticle reduce in the aqueous media. This reason leads to occur no pulling mode manipulation in the water. Due to dipolar property of water molecules, charge plays a significant role in the manipulation for aqueous ambient. The comparison of manipulation results by charged and chargeless tip shows a larger manipulation force while the charged tip is used.

Temperature-dependent solubilities and mean ionic activity coefficients of alkali halides in water from molecular dynamics simulations.

The mean ionic activity coefficients of aqueous KCl, NaF, NaI, and NaCl solutions of varying concentrations have been obtained from molecular dynamics simulations following a recently developed methodology based on gradual insertions of salt molecules [Z. Mester and A. Z. Panagiotopoulos, J. Chem. Phys. 142, 044507 (2015)]. The non-polarizable ion models of Weerasinghe and Smith [J. Chem. Phys. 119, 11342 (2003)], Gee et al. [J. Chem. Theory Comput. 7, 1369 (2011)], Reiser et al. [J. Chem. Phys. 140, 044504 (2014)], and Joung and Cheatham [J. Phys. Chem. B 112, 9020 (2008)] were used along with the extended simple point charge (SPC/E) water model [Berendsen et al., J. Phys. Chem. 91, 6269 (1987)] in the simulations. In addition to the chemical potentials in solution used to obtain the activity coefficients, we also calculated the chemical potentials of salt crystals and used them to obtain the solubility of these alkali halide models in SPC/E water. The models of Weerasinghe and Smith [J. Chem. Phys. 119, 11342 (2003)] and Gee et al. [J. Chem. Theory Comput. 7, 1369 (2011)] provide excellent predictions of the mean ionic activity coefficients at 298.15 K and 1 bar, but significantly underpredict or overpredict the solubilities. The other two models generally predicted the mean ionic activity coefficients only qualitatively. With the exception of NaF for which the solubility is significantly overpredicted, the model of Joung and Cheatham predicts salt solubilities that are approximately 40%-60% of the experimental values. The models of Reiser et al. [J. Chem. Phys. 140, 044504 (2014)] make good predictions for the NaCl and NaI solubilities, but significantly underpredict the solubilities for KCl and NaF. We also tested the transferability of the models to temperatures much higher than were used to parametrize them by performing simulations for NaCl at 373.15 K and 1 bar, and at 473.15 K and 15.5 bar. All models overpredict the drop in the values of mean ionic activity coefficients with increased temperature seen in experiments. The present results, together with earlier calculations for a number of models for NaCl aqueous solutions at 298.15 K, point to the strong need for development of improved intermolecular potential models for classical simulations of electrolyte solutions.

Structural and energetic effects of the use of polarisable water to solvate proteins

Using a non-polarisable model (simple-point-charge (SPC)) for liquid water and two polarisable water models (COS/G2, COS/D), the effect of introducing molecular polarisability into the solvent upon protein structure and energetics is investigated for eight proteins, hen egg-white lysozyme (HEWL), major cold shock protein (CspA), protein G (GP), chorismate mutase (CM), the C-terminal domain of the ribosomal protein L7/L12 (RB), the amino terminal domain of phage 434 repressor (GRP), a 12-residue β-hairpin (DNV) and the GCN trigger peptide (GTP), using MD simulation, one 50 ns simulation and four additional 20 ns simulations for each protein and each water model. The differences in overall structural and energetic properties of the proteins induced by the three different water models are small, except for the amino-terminal domain of phage 434 repressor (GRP). The polarisable COS/G2 water model induces a slightly stronger interaction with the proteins modelled using the GROMOS 54A7 force field than the non-polarisable SPC water model, while for the polarisable COS/D water model the opposite effect is observed.

General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of 15N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S2) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S2) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S2 values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S2 parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S2 calculated from the experimental NMR relaxation measurements, in a site-specific manner.

Interfacial thermal resistance of Cu–SWCNT nanowire in water

The conduction along the radial direction of CuNW–SWCNT nanocomposite surrounded with water is examined. Due to its simplicity and adaptability, a simple point-charge water model is implemented. Using the Nose–Hoover thermostat, the copper core is kept at a uniform temperature as a heat source, and a circular edge layer of water is kept at a lower temperature as a heat sink in order to impose a radial temperature distribution. The thermal boundary resistance was predicted as 0.1732 × 10 −8 m 2 K/W at the interface of CuNW–water, 3.16 × 10 −8 m 2 K/W at the interface of SWCNT–water, and 0.743 × 10 −8 m 2 K/W at the interface of (CuNW–SWCNT)–water.

Adaptive Resolution Simulation of MARTINI Solvents.

We present adaptive resolution molecular dynamics simulations of aqueous and apolar solvents using coarse-grained molecular models that are compatible with the MARTINI force field. As representatives of both classes of solvents we have chosen liquid water and butane, respectively, at ambient temperature. The solvent molecules change their resolution back and forth between the atomistic and coarse-grained representations according to their positions in the system. The difficulties that arise from coupling to a coarse-grained model with a multimolecule mapping, for example, 4-to-1 mapping in the case of the Simple Point Charge (SPC) and MARTINI water models, could be successfully circumvented by using bundled water models. We demonstrate that the presented multiscale approach faithfully reproduces the structural and dynamical properties computed by reference fully atomistic molecular dynamics simulations. Our approach is general and can be used with any atomistic force field to be linked with the MARTINI force field.