Molecular dynamics simulations of rigid and flexible water models: Temperature dependence of viscosity

Computational Modeling: Up-to-Date Approaches and Cutting-Edge Applications from Clusters, Nanostructures to Bulk Systems

The contributions in this special theme collection, in honor to Prof. P. Villarreal, cover a broad variety of computational methodologies and experimental techniques, containing studies on gas phase, clusters and condensed phase systems.

Exploration of the Existence Forms and Patterns of Dissolved Oxygen Molecules in Water

The structure of liquid water is primarily composed of three-dimensional networks of water clusters formed by hydrogen bonds, and dissolved oxygen is one of the most important indicators for assessing water quality. In this work, distilled water with different concentration of dissolved oxygen were prepared, and a clear negative correlation between the size of water clusters and dissolved oxygen concentration was observed. Besides, a phenomenon of rapid absorption and release of oxygen at the water interfaces was unveiled, suggesting that oxygen molecules predominantly exist at the interfaces of water clusters. Oxygen molecules can move rapidly through the interfaces among water clusters, allowing dissolved oxygen to quickly reach a saturation level at certain partial pressure of oxygen and temperature. Further exploration into the mechanism by molecular dynamics simulations of oxygen and water clusters found that oxygen molecules can only exist stably at the interfaces among water clusters. A semi-empirical formula relating the average number of water molecules in a cluster (n) to 17O NMR half-peak width (W) was summarized: n = 0.1 W + 0.85. These findings provide a foundation for exploring the structure and properties of water.

Accuracy of TIP4P/2005 and SPC/Fw Water Models

Water is used as the main solvent in model systems containing bioorganic molecules. Choosing the right water model is an important step in the study of the biophysical and biochemical processes that occur in cells. In the present work, we perform molecular dynamics simulations using two distinct force fields for water: the rigid model TIP4P/2005, where only intermolecular interactions are considered, and the flexible model SPC/Fw, where intramolecular interactions are also taken into account. The simulations aim to determine the effect of the inclusion of intramolecular interactions on the accuracy of calculated properties of bulk water (density and thermal expansion coefficient, self-diffusion coefficients, shear viscosity, radial distribution functions, and dielectric constant), as compared to experimental results, over a temperature range between 250 and 370 K. We find that the results of the rigid model present the smallest deviations relative to experiments for most of the calculated quantities, except for the shear viscosity of supercooled water and the water dielectric constant, where the flexible model presents better agreement with experiments.

Modeling Zeta Potential for Nanoparticles in Solution: Water Flexibility Matters

Nonequilibrium molecular dynamics simulations were performed to study the electrokinetic properties of five mainstream TIPxP water models (namely, TIP3P-FB, TIP3Pm, TIP4P-FB, TIP4P-Ew, and TIP4P/2005) in NaCl aqueous solutions in the presence of a negatively charged TiO₂ surface. The impact of solvent flexibility and system geometry on the electro-osmotic (EO) mobility and flow direction was systematically assessed and compared. We found that lack of water flexibility decelerates the forward EO flow of aqueous solutions at moderate (0.15 M) or high (0.30 M) NaCl concentrations, in some special cases to such an extent that EO flow reversal occurs. Zeta potential (ZP) values were then determined from the bulk EO mobilities using the Helmholtz-Smoluchowski formula. The straight comparison against available experimental data strongly suggests that water flexibility improves the ZP determination of NaCl solutions adjacent to a realistic TiO₂ surface under neutral pH conditions.

Simulating a flexible water model as rigid: Best practices and lessons learned

Two ways to create rigid versions of flexible models are explored. The rigid model can assume the Model's Geometry (MG) as if the molecule is not interacting with any other molecules or the ensemble averaged geometry (EG) under a particular thermodynamic condition. Although the MG model is more straightforward to create, it leads to relatively poor performance. The EG model behaves similarly to the corresponding flexible model (the FL model) and, in some cases, agrees even better with experiments. While the difference between the EG and the FL models is mostly a result of flexibility, the MG and EG models have different dipole moments as a result of an effective induction in the condensed phase. For the three water models studied, the property that shows the most difference is the temperature dependence of density. The MG version of the water model by adaptive force matching for ice and liquid does not possess a temperature of maximum density, which is attributed to a downshift of the putative liquid-liquid phase transition line, leading to the hypothesized second critical point of liquid water to manifest at negative pressure. A new three-phase coexistence method for determining the melting temperature of ice is also presented.

A Facile Strategy to Prepare Small Water Clusters via Interacting with Functional Molecules

Although small water clusters (SWCs) are important in many research fields, efficient methods of preparing SWCs are still rarely reported, which is mainly due to the lack of related materials and understanding of the molecular interaction mechanisms. In this study, a series of functional molecules were added in water to obtain small water cluster systems. The decreasing rate of the half-peak width in a sodium dodecyl sulfate (SDS)–water system reaches ≈20% at 0.05 mM from ¹⁷O nuclear magnetic resonance (NMR) results. Based on density functional theory (DFT) and molecular dynamics (MD) simulation calculation, it can be concluded that functional molecules with stronger negative electrostatic potential (ESP) and higher hydrophilicity have a stronger ability to destroy big water clusters. Notably, the concentrations of our selected molecule systems are one to two magnitudes lower than that of previous reports. This study provides a promising way to optimize aqueous systems in various fields such as oilfield development, protein stability, and metal anti-corrosion.

Comparison of atomic force microscopy force curve and solvation structure studied by integral equation theory

Atomic force microscopy can observe structures of liquids (solvents) on solid surfaces as oscillating force curves. The oscillation originates from the solvation force, which is affected by the interaction between the probe, substrate, and solvents. To investigate the effects of the interactions on the force curve, we calculated the force curves by integral equation theory with various probe and substrate conditions. The probe solvophilicity affected the force curves more than the substrate solvophilicity in our calculation, and its reason is qualitatively explained by the amount of the desolvated solvents. We evaluated the probes and parameters in terms of the qualitative estimation of the number density distribution of the solvent on the wall. The negative of the force curve's derivative with respect to the surface separation reflected the number density distribution better than the force curve. This parameter is based on the method that is proposed previously by Amano et al. [Phys. Chem. Chem. Phys. 18, 15534 (2016)]. The normalized frequency shift can also be used for the qualitative estimation of the number density distribution if the cantilever amplitude is small. Solvophobic probes reflected the number density distribution better than the solvophilic probes. Solvophilic probes resulted in larger oscillation amplitudes than solvophobic probes and are suitable for measurements with a high S/N ratio.

Ab-initio molecular dynamics and hybrid explicit-implicit solvation model for aqueous and nonaqueous solvents: GFP chromophore in water and methanol solution as case study

Solute-solvent interactions are proxies for understanding how the electronic density of a chromophore interacts with the environment in a more exhaustive way. The subtle balance between polarization, electrostatic, and non-bonded interactions need to be accurately described to obtain good agreement between simulations and experiments. First principles approaches providing accurate configurational sampling through molecular dynamics may be a suitable choice to describe solvent effects on solute chemical-physical properties and spectroscopic features, such as optical absorption of dyes. In this context, accurate energy potentials, obtained by hybrid implicit/explicit solvation methods along with employing nonperiodic boundary conditions, are required to represent bulk solvent around a large solute-solvent cluster. In this work, a novel strategy to simulate methanol solutions is proposed combining ab initio molecular dynamics, a hybrid implicit/explicit flexible solvent model, nonperiodic boundary conditions, and time dependent density functional theory. As case study, the robustness of the proposed protocol has been gauged by investigating the microsolvation and electronic absorption of the anionic green fluorescent protein chromophore in methanol and aqueous solution. Satisfactory results are obtained, reproducing the microsolvation layout of the chromophore and, as a consequence, the experimental trends shown by the optical absorption in different solvents.

Rheology of Water Flows Confined between Multilayer Graphene Walls

Water confined by hydrophilic materials shows unique transport properties compared to bulk water, thereby offering new opportunities for the development of nanofluidic devices. Recent experimental and numerical studies showed that nanoconfined water undergoes liquid- to solid-phase-like transitions depending on the degree of confinement. In the case of water confined by graphene layers, the van der Waals forces are known to deform the graphene layers, whose bending leads to further nonuniform confinement effects. Despite the extensive studies of nanoconfined water under equilibrium conditions, the interplay between the confinement and rheological water properties, such as viscosity, slip length, and normal stress differences under shear flow conditions, is poorly understood. The current investigation uses a validated all-atom nonequilibrium molecular dynamics model to simultaneously analyze the continuum transport and atomistic structural properties of water in a slit between two moving graphene walls under Couette flow conditions. A range of different slit widths and velocity strain rates are considered. It is shown that under subnanometer confinement, water loses the rotational symmetry of a Newtonian fluid. Under such conditions, water transforms into ice, where the atomistic structure is completely insensitive to the applied shear force and behaves like a frozen slab sliding between the graphene walls. This leads to the shear viscosity increase, although it is not as dramatic as the normal force increase that contributes to the increased friction force reported in previous experimental studies. On the other end of the spectrum, for flows at large velocity strain rates in moderate to large slits between the graphene walls, water is in the liquid state and reveals shear thinning behavior. In this case, water exhibits a constant slip length on the wall, which is typical of liquids in the vicinity of hydrophobic surfaces.

Bulk viscosity of liquid noble gases

An equation of state for the bulk viscosity of liquid noble gases is proposed. On the basis of dedicated equilibrium molecular dynamics simulations, a multi-mode relaxation ansatz is used to obtain precise bulk viscosity data over a wide range of liquid states. From this dataset, the equation of state emerges as a two-parametric power function with both parameters showing a conspicuous saturation behavior over temperature. After passing a temperature threshold, the bulk viscosity is found to vary significantly over density, a behavior that resembles the frequency response of a one pole low-pass filter. The proposed equation of state is in good agreement with available experimental sound attenuation data.

Structural, Thermodynamic, and Transport Properties of Aqueous Reline and Ethaline Solutions from Molecular Dynamics Simulations

Deep eutectic solvents (DESs) are a new generation of green solvents, which are considered an environmentally friendly alternative to ionic liquids and volatile organic compounds. The addition of controlled amounts of water to DESs has a significant effect on their microscopic structure and thus on their thermodynamic and transport properties. In this way, DESs can be modified, leading to solvents with improved characteristics. In this work, molecular dynamics (MD) simulations are performed to obtain a better understanding of the relation between the microscopic structure, molecular interactions, and thermophysical properties of aqueous reline and ethaline solutions at temperatures ranging from 303.15 to 363.15 K. For both reline and ethaline solutions, the hydrogen bond (HB) networks disappear with increasing mass fraction of water, and the intensity of radial distribution function (RDF) peaks decreases. For a mass fraction of water of 40%, most of the HBs between the compounds of reline and ethaline are broken, and DESs are fully dissolved in water. Consequently, a monotonic decrease in viscosities and an increase in self-diffusion coefficients are observed. Ionic conductivities show a nonmonotonic behavior with increasing water content. Up to 60% water mass fraction, the ionic conductivities increase with increasing water content. A further increase in the mass fraction of water decreases conductivities. For all studied systems, the HB network and the peaks of RDFs show relatively small changes for water mass fractions below 5% and beyond 40%. The MD results show that viscosities decrease with temperature, while diffusivities and ionic conductivities increase. The effect of the temperature on the structure of DES-water mixtures is negligible.

Optimizing Nonbonded Interactions of the OPLS Force Field for Aqueous Solutions of Carbohydrates: How to Capture Both Thermodynamics and Dynamics

Knowledge on thermodynamic and transport properties of aqueous solutions of carbohydrates is of great interest for process and product design in the food, pharmaceutical, and biotechnological industries. Molecular simulation is a powerful tool to calculate these properties, but current classical force fields cannot provide accurate estimates for all properties of interest. The poor performance of the force fields is mainly observed for concentrated solutions, where solute–solute interactions are overestimated. In this study, we propose a method to refine force fields, such that solute–solute interactions are more accurately described. The OPLS force field combined with the SPC/Fw water model is used as a basis. We scale the nonbonded interaction parameters of sucrose, a disaccharide. The scaling factors are chosen in such a way that experimental thermodynamic and transport properties of aqueous solutions of sucrose are accurately reproduced. Using a scaling factor of 0.8 for Lennard-Jones energy parameters (ϵ) and a scaling factor of 0.95 for partial atomic charges (q), we find excellent agreement between experiments and computed liquid densities, thermodynamic factors, shear viscosities, self-diffusion coefficients, and Fick (mutual) diffusion coefficients. The transferability of these optimum scaling factors to other carbohydrates is verified by computing thermodynamic and transport properties of aqueous solutions of d-glucose, a monosaccharide. The good agreement between computed properties and experiments suggests that the scaled interaction parameters are transferable to other carbohydrates, especially for concentrated solutions.

Breakdown of the Stokes–Einstein water transport through narrow hydrophobic nanotubes

As water density is increased inside narrow hydrophobic nanotubes, the viscosity shows a huge increase associated with a small increase in the diffusion, which violates the Stokes–Einstein relation.

Parameterization and optimization of the menthol force field for molecular dynamics simulations

Menthol’s various biological properties render it a useful component for medical and cosmetological applications, while its three centers of asymmetry mean that it can be used in a range of organic reactions. Menthol-substituted ionic liquids (ILs) have been found to exhibit promising antimicrobial and antielectrostatic properties, as well as being useful in organic catalysis and biochemical studies. However, so far, a force field designed and validated specifically for the menthol molecule has not been constructed. In the present work, the validation and optimization of force field parameters with regard to the ability to reproduce the macroscopic properties of menthol is presented. The set of optimized potentials for liquid simulations all atom (OPLS-AA) compatible parameters was tested and carefully tuned. The refinement of parameters included fitting of partial atomic charges, optimization of Lennard-Jones parameters, and recalculation of the dihedral angle parameters needed to reproduce quantum energy profiles. To validate the force field, a variety of physicochemical properties were calculated for liquid menthol. Both thermodynamic and kinetic properties were taken into account, including density, surface tension, enthalpy of vaporization, and shear viscosity. The obtained force field was proven to accurately reproduce the properties of the investigated compound while being fully compatible with the OPLS-AA force field.

Passage of TBP–uranyl complexes from aqueous–organic interface to the organic phase: insights from molecular dynamics simulation

Water/organic interface representing TBP orientation for neutral versus acidic interface and occurrence of UO₂²⁺–TBP–NO₃⁻ species in various stoichiometry.