Thermalized Drude Oscillators with the LAMMPS Molecular Dynamics Simulator

Molecular transport enhancement in pure metallic carbon nanotube porins

Nanofluidic channels impose extreme confinement on water and ions, giving rise to unusual transport phenomena strongly dependent on the interactions at the channel-wall interface. Yet how the electronic properties of the nanofluidic channels influence transport efficiency remains largely unexplored. Here we measure transport through the inner pores of sub-1 nm metallic and semiconducting carbon nanotube porins. We find that water and proton transport are enhanced in metallic nanotubes over semiconducting nanotubes, whereas ion transport is largely insensitive to the nanotube bandgap value. Molecular simulations using polarizable force fields highlight the contributions of the anisotropic polarizability tensor of the carbon nanotubes to the ion-nanotube interactions and the water friction coefficient. We also describe the origin of the proton transport enhancement in metallic nanotubes using deep neural network molecular dynamics simulations. These results emphasize the complex role of the electronic properties of nanofluidic channels in modulating transport under extreme nanoscale confinement.

Sodium Triflate Water-in-Salt Electrolytes in Advanced Battery Applications: A First-Principles-Based Molecular Dynamics Study

Offering a compelling combination of safety and cost-effectiveness, water-in-salt (WiS) electrolytes have emerged as promising frontiers in energy storage technology. Still, there is a strong demand for research and development efforts to make these electrolytes ripe for commercialization. Here, we present a first-principles-based molecular dynamics (MD) study addressing in detail the properties of a sodium triflate WiS electrolyte for Na-ion batteries. We have developed a workflow based on a machine learning (ML) potential derived from ab initio MD simulations. As ML potentials are typically restricted to the interpolation of the data points of the training set and have hardly any predictive properties, we subsequently optimize a classical force field based on physics principles to ensure broad applicability and high performance. Performing and analyzing detailed MD simulations, we identify several very promising properties of the sodium triflate as a WiS electrolyte but also indicate some potential stability challenges associated with its use as a battery electrolyte.

Understanding electrochemical interfaces through comparing experimental and computational charge density-potential curves

Electrode-electrolyte interfaces play a decisive role in electrochemical charge accumulation and transfer processes. Theoretical modelling of these interfaces is critical to decipher the microscopic details of such phenomena. Different force field-based molecular dynamics protocols are compared here in a view to connect calculated and experimental charge density-potential relationships. Platinum-aqueous electrolyte interfaces are taken as a model. The potential of using experimental charge density-potential curves to transform cell voltage into electrode potential in force-field molecular dynamics simulations, and the need for that purpose of developing simulation protocols that can accurately calculate the double-layer capacitance, are discussed.

How Do Deep Eutectic Solvents Form Porous Liquids? The Example of Methyltriphenylphosphonium Bromide: Glycerol and ZIF-8

Porous liquids are new materials that provide permanent porosity in the liquid phase through the dispersion of nanoporous solid particles in a bulky solvent. Herein, we aim at understanding how new sustainable solvents such as deep eutectic solvent (DES) can be used to form porous stable suspensions for the capture of gases of interest for sustainable chemistry. The properties of an ionic DES, methyltriphenylphosphonium bromide/glycerol in a 1:3 molar composition, and its behavior at the interface with a metal-organic framework (MOF), ZIF-8, are here investigated by polarizable molecular dynamics simulations. The structural and dynamic properties of the DES are analyzed in the bulk liquid and in the interfacial regions with the MOF, namely, in the accessible cavities exposed at the surface. The porosity of the suspension is maintained, and it is caused not only by the Coulomb cohesive energy between cations and anions, which prevents the small anions from entering the pores, but also by the glycerol molecules not penetrating the small aperture of the ZIF-8 structure. This was further verified by simulating a system composed of glycerol and ZIF-8. Simulations with CO2 show its partition between the DES and the MOF, with higher concentrations registered in the MOF cavities.

Water Electric Field Induced Modulation of the Wetting of Hexagonal Boron Nitride: Insights from Multiscale Modeling of Many-Body Polarization

Understanding the behavior of water contacting two-dimensional materials, such as hexagonal boron nitride (hBN), is important in practical applications, including seawater desalination and energy harvesting. Water, being a polar solvent, can strongly polarize the hBN surface via the electric fields that it generates. However, there is a lack of molecular-level understanding about the role of polarization effects at the hBN/water interface, including its effect on the wetting properties of water. In this study, we develop a theoretical framework that introduces an all-atomistic polarizable force field to accurately model the interactions of water molecules with hBN surfaces. The force field is then utilized to self-consistently describe the water-induced polarization of hBN using the classical Drude oscillator model, including predicting the hBN-water binding energies which are found to be in excellent agreement with diffusion Monte Carlo (DMC) predictions. By carrying out molecular dynamics (MD) simulations, we demonstrate that the polarizable force field yields a water contact angle on multilayered hBN which is in close agreement with the recent experimentally reported values. Conversely, an implicit modeling of the hBN-water polarization energy utilizing a Lennard-Jones (LJ) potential, a commonly utilized approximation in previous MD simulation studies, leads to a considerably lower water contact angle. This difference in the predicted contact angles is attributed to the significant energy-entropy compensation resulting from the incorporation of polarization effects at the hBN-water interface. Our work highlights the importance of self-consistently modeling the hBN-water polarization energy and offers insights into the wetting-related interfacial phenomena of water on polarizable materials.

The effect of monomer polarizability on the stability and salt partitioning in model coacervates

Coacervation of charged polymer chains has been a topic of major interest in both polymer and biological sciences, as it is a subset of a phenomenon called liquid-liquid phase separation (LLPS). In this process the polymer-rich phase separates from the polymer-lean supernatant while still maintaining its liquid-like properties. LLPS has been shown to play a crucial role in cellular homeostasis by driving the formation of membraneless organelles. It also has the potential to be harnessed to aid in novel therapeutical applications. Recent studies have demonstrated that there is no one simple mechanism which drives LLPS, which is instead a result of the combined effect of electrostatic, dipolar, hydrophobic, and other weak interactions. Using coarse-grained polymer simulations we investigate the relatively unexplored effects of monomer polarizability and spatially varying dielectric constant on LLPS propensity, and these factors affect the properties of the resulting condensates. In order to produce spatial variations in the dielectric constant, all our simulations include explicit solvent and counterions. We demonstrate that polarizability has only a minor effect on the bulk behaviour of the condensates but plays a major role when ion partitioning and microstructure are considered. We observe that the major contribution comes from the nature of the neutral blocks as endowing them with an induced dipole changes their character from hydrophobic to hydrophilic. We hypothesize that the results of this work can aid in guiding future studies concerned with LLPS by providing a general framework and by highlighting important factors which influence LLPS.

Molecular Modeling of Water-in-Salt Electrolytes: A Comprehensive Analysis of Polarization Effects and Force Field Parameters in Molecular Dynamics Simulations

Accurate modeling of highly concentrated aqueous solutions, such as water-in-salt (WiS) electrolytes in battery applications, requires proper consideration of polarization contributions to atomic interactions. Within the force field molecular dynamics (MD) simulations, the atomic polarization can be accounted for at various levels. Nonpolarizable force fields implicitly account for polarization effects by incorporating them into their van der Waals interaction parameters. They can additionally mimic electron polarization within a mean-field approximation through ionic charge scaling. Alternatively, explicit polarization description methods, such as the Drude oscillator model, can be selectively applied to either a subset of polarizable atoms or all polarizable atoms to enhance simulation accuracy. The trade-off between simulation accuracy and computational efficiency highlights the importance of determining an optimal level of accounting for atomic polarization. In this study, we analyze different approaches to include polarization effects in MD simulations of WiS electrolytes, with an example of a Na-OTF solution. These approaches range from a nonpolarizable to a fully polarizable force field. After careful examination of computational costs, simulation stability, and feasibility of controlling the electrolyte properties, we identify an efficient combination of force fields: the Drude polarizable force field for salt ions and non-polarizable models for water. This cost-effective combination is sufficiently flexible to reproduce a broad range of electrolyte properties, while ensuring simulation stability over a relatively wide range of force field parameters. Furthermore, we conduct a thorough evaluation of the influence of various force field parameters on both the simulation results and technical requirements, with the aim of establishing a general framework for force field optimization and facilitating parametrization of similar systems.

Influence of pH on the self-assembly of diphenylalanine peptides: molecular insights from coarse-grained simulations

Nanostructures fabricated from peptide self-assemblies are attracting increasing attention owing to their possible applications in biology and nanotechnology. A known example is an aromatic dipeptide (diphenylalanine, FF) which is extracted from Alzheimer's β-amyloid polypeptide as the core recognition motif for molecular self-assembly. Many studies have been carried out to organize FF peptides into various functional ordered nanostructures. For potential applications of self-assembled FF-based nanomaterials, it becomes important to consider some influencing factors (e.g., solvents, peptide concentrations, pH, temperature, etc.) on the self-assembly process. Among these factors, the effect of pH on the self-assembly process of FF peptides into assembled nanostructures through simulation studies is the main focus of the present work. In the current study, we have investigated the assembly pathway of 1000 FF peptides and qualitatively evaluated the morphological changes of FF-based nanostructures at different pH values by performing extensive coarse-grained molecular dynamics (CG-MD) simulations. Structural analyses suggest that FF peptides can spontaneously assemble into nanotubes with different shapes under acidic, neutral and basic conditions. Based on the analysis of FF nanostructure formation pathways in different pH solutions, the self-assembly of the nanotube involves the aggregation of molecules to form a bilayer, the curling of a bilayer to form a vesicle and the transformation of a vesicle into a tubular structure. It is noted that a flat hollow columnar structure is observed as a special intermediate state during the transformation process of a vesicle-like to a tube-like structure. Energetic analysis suggests that the aggregation of FF peptides is driven by the vdW interactions but the aggregation shape is mainly affected by the electrostatic interactions. Overall, this study provides further understanding of the self-assembly behavior of aromatic short peptide derivatives in different pH solutions.

MD-Ligand-Receptor: A High-Performance Computing Tool for Characterizing Ligand-Receptor Binding Interactions in Molecular Dynamics Trajectories

Molecular dynamics simulation is a widely employed computational technique for studying the dynamic behavior of molecular systems over time. By simulating macromolecular biological systems consisting of a drug, a receptor and a solvated environment with thousands of water molecules, MD allows for realistic ligand-receptor binding interactions (lrbi) to be studied. In this study, we present MD-ligand-receptor (MDLR), a state-of-the-art software designed to explore the intricate interactions between ligands and receptors over time using molecular dynamics trajectories. Unlike traditional static analysis tools, MDLR goes beyond simply taking a snapshot of ligand-receptor binding interactions (lrbi), uncovering long-lasting molecular interactions and predicting the time-dependent inhibitory activity of specific drugs. With MDLR, researchers can gain insights into the dynamic behavior of complex ligand-receptor systems. Our pipeline is optimized for high-performance computing, capable of efficiently processing vast molecular dynamics trajectories on multicore Linux servers or even multinode HPC clusters. In the latter case, MDLR allows the user to analyze large trajectories in a very short time. To facilitate the exploration and visualization of lrbi, we provide an intuitive Python notebook (Jupyter), which allows users to examine and interpret the results through various graphical representations.

Impact of the inner solute structure on the electrostatic mean-field and strong-coupling regimes of macromolecular interactions

The structural diversity of the solute molecules involved in biomolecular processes necessitates the characterization of the forces between charged macromolecules beyond the point-ion description. From the field-theoretic partition function of an electrolyte confined between two anionic membranes, we derive a contact-value identity valid for general intramolecular solute structure and electrostatic coupling strength. In the electrostatic mean-field regime, the inner charge spread of the solute particles is shown to induce the twofold enhancement of the short-range Poisson-Boltzmann level membrane repulsion and a longer-range depletion attraction. Our contact theorem indicates that the twofold repulsion enhancement by solute size is equally present in the opposite strong-coupling regime of linear and spherical solute molecules. Upon the inclusion of the dielectric contrast between the electrolyte and the interacting membranes, the emerging polarization forces substantially amplify the solute specificity of the macromolecular interactions. Namely, the finite size of the dumbbell-like solute particles composed of similar terminal charges weakens the intermembrane repulsion. However, the extended structure of the solute molecules carrying opposite elementary charges such as ionized atoms and zwitterionic molecules enhances the membrane repulsion by several factors. We also show that these polarization forces can extend the range of the solute structure effects up to intermembrane distances exceeding the solute size by an order of magnitude. This radical alteration of the intermembrane interactions by the salt structure identifies the solute specificity as a key ingredient of the thermodynamic stability in colloidal systems.

Symmetrized Drude Oscillator Force Fields Improve Numerical Performance of Polarizable Molecular Dynamics

Drude oscillator potentials are a popular and computationally efficient class of polarizable models that represent each polarizable atom as a positively charged Drude core harmonically bound to a negatively charged Drude shell. We show that existing force fields that place all non-Coulomb forces on the Drude core and none on the shell inadvertently couple the dipole to non-Coulombic forces. This introduces errors where interactions with neutral particles can erroneously induce atomic polarization, leading to spurious polarizations in the absence of an electric field, exacerbating violations of equipartition in the employed Carr-Parinello scheme. A suitable symmetrization of the interaction potential that correctly splits the force between the Drude core and shell can correct this shortcoming, improving the stability and numerical performance of Drude oscillator-based simulations. The symmetrization procedure is straightforward and only requires the rescaling of a few force field parameters.

Charge Transport in Water-NaCl Electrolytes with Molecular Dynamics Simulations

A systematic description of microscopic mechanisms is necessary to understand mass transport in solid and liquid electrolytes. From Molecular Dynamics (MD) simulations, transport properties can be computed and provide a detailed view of the molecular and ionic motions. In this work, ionic conductivity and transport numbers in electrolyte systems are computed from equilibrium and nonequilibrium MD simulations. Results from the two methods are compared with experimental results, and we discuss the significance of the frame of reference when determining and comparing transport numbers. Two ways of computing ionic conductivity from equilibrium simulations are presented: the Nernst-Einstein approximation or the Onsager coefficients. The Onsager coefficients take ionic correlations into account and are found to be more suitable for concentrated electrolytes. Main features and differences between equilibrium and nonequilibrium simulations are discussed, and some potential anomalies and critical pitfalls of using nonequilibrium molecular dynamics to determine transport properties are highlighted.

Structural elucidation of polydopamine facilitated by ionic liquid solvation

Minimal understanding of the formation mechanism and structure of polydopamine (pDA) and its natural analogue, eumelanin, impedes the practical application of these versatile polymers and limits our knowledge of the origin of melanoma. The lack of conclusive structural evidence stems from the insolubility of these materials, which has spawned significantly diverse suggestions of pDA's structure in the literature. We discovered that pDA is soluble in certain ionic liquids. Using these ionic liquids (ILs) as solvents, we present an experimental methodology to solvate pDA, enabling us to identify pDA's chemical structure. The resolved pDA structure consists of self-assembled supramolecular aggregates that contribute to the increasing complexity of the polymer. The underlying molecular energetics of pDA solvation and a macroscopic picture of the disruption of the aggregates using IL solvents have been investigated, along with studies of the aggregation mechanism in water.

How Does Electronic Polarizability or Scaled-Charge Affect the Interfacial Properties of Room Temperature Ionic Liquids?

The room temperature ionic liquid (RTIL) air-liquid interface plays an important role in many applications. Herein, we present molecular dynamics simulation results for the air-liquid interface of a common RTIL, 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide, [C4mim][NTf2]. To elucidate the effects of electronic polarizability and scaled-charge ions on the properties of the RTIL air-liquid interface, we employ three different kinds of force fields: a nonpolarizable force field (FF) with united ion charges (FixQ), a nonpolarizable FF with scaled-charge by 0.8 (ScaleQ), and a polarizable FF (Drude). To identify whether the ions reside at the interface or not, the method of identification of the truly interfacial molecules is used. The structural and dynamical properties in the interfacial, subinterfacial, and central layers are evaluated. In general for bulk liquids, the FixQ model predicts too-ordered structures and too-sluggish dynamics, while the ScaleQ model can serve as a simple cure. However, the ScaleQ model cannot reproduce the results of the Drude model at the interface, due to an inappropriate scaled-down charge near the interface.

Breakdown of the Nernst-Einstein relation in carbon nanotube porins

For over 100 years, the Nernst-Einstein relation has linked a charged particle's electrophoretic mobility and diffusion coefficient. Here we report experimental measurements of diffusion and electromigration of K⁺ ions in narrow 0.8-nm-diameter single-walled carbon nanotube porins (CNTPs) and demonstrate that the Nernst-Einstein relation in these channels breaks down by more than three orders of magnitude. Molecular dynamics simulations using polarizable force fields show that K⁺ ion diffusion in CNTPs in the presence of a single-file water chain is three orders of magnitude slower than bulk diffusion. Intriguingly, the simulations also reveal a disintegration of the water chain upon application of electric fields, resulting in the formation of distinct K⁺-water clusters, which then traverse the CNTP at high velocity. Finally, we show that although individual ion-water clusters still obey the Nernst-Einstein relation, the overall relation breaks down because of two distinct mechanisms for ion diffusion and electromigration.

Flexibility is the key to tuning the transport properties of fluorinated imide-based ionic liquids

Ionic liquids are becoming increasingly popular for practical applications such as biomass processing and lithium-ion batteries. However, identifying ionic liquids with optimal properties for specific applications by trial and error is extremely inefficient since there are a vast number of potential candidate ions. Here we combine experimental and computational techniques to determine how the interplay of fluorination, flexibility and mass affects the transport properties of ionic liquids with the popular imide anion. We observe that fluorination and flexibility have a large impact on properties such as viscosity, whereas the influence of mass is negligible. Using targeted modifications, we show that conformational flexibility provides a significant contribution to the success of fluorination as a design element. Contrary to conventional wisdom, fluorination by itself is thus not a guarantor for beneficial properties such as low viscosity.

Molecular Dynamics Simulation Study of the Far-Infrared Spectrum of a Deep Eutectic Solvent

Deep eutectic solvents (DESs) are similar to ionic liquids (IL) in terms of physicochemical properties and technical uses. In ILs, far-infrared (FIR) spectroscopy has been utilized to reveal ionic interactions and even to produce a signature of the strengthening of the cation-anion hydrogen bond. However, for the situation of the DES, where the mixing of a salt and a molecular species makes the interplay between multiple intermolecular interactions even more complex, a full investigation of FIR spectra is still absent. In this work, the FIR spectrum of the DES, often referred to as ethaline, which is a 1:2 mixture of choline chloride and ethylene glycol, is calculated using classical molecular dynamics (MD) simulations and compared to experimental data. To explore the induced dipole effect on the computed FIR spectrum, MD simulations were run with both nonpolarizable and polarizable models. The calculation satisfactorily reproduces the position of the peak at ∼110 cm^-1 and the bandwidth seen in the experimental FIR spectrum of ethaline. The MD simulations show that the charge current is the most important contributor to the FIR spectrum, but the cross-correlation between the charge current and dipole reorientation also plays a role in the polarizable model. The dynamics of the chloride-ethylene glycol correlation span a wide frequency range, with a maximum at ∼150 cm^-1, but it participates as a direct mechanism only in the charge current-dipole reorientation cross-term. Anion correlations, whose dynamics are regulated via correlation with both ethylene glycol and choline, make the most significant contribution to the charge current mechanism. The MD simulations were also utilized to investigate the effect on the FIR spectrum of adding water to the DES and switching to a 1:1 composition.

Recent Developments in Polarizable Molecular Dynamics Simulations of Electrolyte Solutions

Polarizable molecular dynamics simulations are a fast progressing field in the scientific research of ionic liquids. The fundamentals of polarizable simulations, as well as their application to ionic liquids, were summarized in a review [Bedrov, D.; Piquemal, J.-P.; Borodin, O.; MacKerell, Jr., A. D.; Roux, B.; Schröder, C. Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields. Chem. Rev. 2019, 119, 7940–7995] in 2019. Since then, new methods to treat intermolecular interaction of induced dipoles in these highly charged systems were developed. This concerns the damping of these interactions and additional charge transfer as well as the prediction of ionic materials with ultrahigh refractive indices. In addition to the progress of the polarizable force fields, also thermostats and barostats for polarizable simulations evolved recently.

DLPGEN: Preparing Molecular Dynamics Simulations with Support for Polarizable Force Fields

Preparing input files for molecular dynamics (MD) simulations can be a tedious task, particularly if different MD programs need to be used. Most simulation packages are accompanied by applications that handle this task, and, in some cases, software to perform interconversion between MD programs can be found. However, the conversion between different types of files is not always foolproof or the force field may not be fully supported, as quite often observed with polarization models. This work describes the program DLPGEN, which produces input files for the MD programs GROMACS, CHARMM, DL_POLY, and LAMMPS. The program can prepare polarizable force fields using a self-consistent field approach or with a dual thermostat-extended Lagrangian model. For GROMACS, a new polarization scheme suitable for the simulation of molecules containing more than one virtual particle is described. Results obtained for ethanol in the liquid state revealed that the system configurational energy, liquid density, and self-diffusion coefficient obtained with GROMACS are in good agreement with the data found with LAMMPS and CHARMM. In the case of DL_POLY, a problem with the Shells temperature control was found, suggesting that this program may not be suitable for the simulation of molecules containing multiple Drude particles.

Does Explicit Polarizability Improve Molecular Dynamics Predictions of Glass Transition Temperatures of Ionic Liquids?

Molecular dynamics simulations are used for predictions of the glass transition temperatures for a test set of five aprotic ionic liquids. Glass transitions are localized with the trend-shift method, analyzing volumetric and transport properties of bulk amorphous phases. A classical nonpolarizable all-atom OPLS force-field model developed by Canongia Lopes and Pádua (CL&P) is employed as a starting level of theory for all calculations. Alternative approaches of charge scaling and the Drude oscillator model, accounting for atomic polarizability either implicitly or explicitly, respectively, are used to investigate the sensitivity of the glass transition temperatures to induction effects. The former nonpolarizable model overestimates the glass transition temperature by tens of Kelvins (37 K on average). The charge-scaling technique yields a significant improvement, and the best estimations were achieved using polarizable simulations with the Drude model, which yielded an average deviation of 11 K. Although the volumetric data usually exhibit a lesser trend shift upon vitrification, their lower statistical uncertainty enables to predict the glass transition temperature with lower uncertainty than the ionic self-diffusivities, the temperature dependence of which is usually more scattered. Additional analyses of the simulated data were also performed, revealing that the Drude model predicts lower densities for most subcooled liquids but higher densities for the glasses than the original CL&P, and that the Drude model also invokes some longer-range organization of the subcooled liquid, greatly impacting the temperature trend of ionic self-diffusivities in the low-temperature region.

Charge transfer and polarisability in ionic liquids: a case study

The practical use of ionic liquids (ILs) is benefiting from a growing understanding of the underpinning structural and dynamic properties, facilitated through classical molecular dynamics (MD) simulations. The predictive and explanatory power of a classical MD simulation is inextricably linked to the underlying force field. A key aspect of the forcefield for ILs is the ability to recover charge based interactions. Our focus in this paper is on the description and recovery of charge transfer and polarisability effects, demonstrated through MD simulations of the widely used 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide [C₄C₁im][NTf₂] IL. We study the charge distributions generated by a range of ab initio methods, and present an interpolation method for determining atom-wise scaled partial charges. Two novel methods for determining the mean field (total) charge transfer from anion to cation are presented. The impact of using different charge models and different partial charge scaling (unscaled, uniformly scaled, atom-wise scaled) are compared to fully polarisable simulations. We study a range of Drude particle explicitly polarisable potentials and shed light on the performance of current approaches to counter known problems. It is demonstrated that small changes in the charge description and MD methodology can have a significant impact; biasing some properties, while leaving others unaffected within the structural and dynamic domains.

An automated framework for high-throughput predictions of NMR chemical shifts within liquid solutions

Identifying stable speciation in multi-component liquid solutions is fundamentally important to areas from electrochemistry to organic chemistry and biomolecular systems. Here we introduce a fully automated, high-throughput computational framework for the accurate prediction of stable species in liquid solutions by computing the nuclear magnetic resonance (NMR) chemical shifts. The framework automatically extracts and categorizes hundreds of thousands of atomic clusters from classical molecular dynamics simulations, identifies the most stable species in solution and calculates their NMR chemical shifts via density functional theory calculations. Additionally, the framework creates a database of computed chemical shifts for liquid solutions across a wide chemical and parameter space. We compare our computational results to experimental measurements for magnesium bis(trifluoromethanesulfonyl)imide Mg(TFSI)2 salt in dimethoxyethane solvent. Our analysis of the Mg2+ solvation structural evolutions reveals key factors that influence the accuracy of NMR chemical shift predictions in liquid solutions. Furthermore, we show how the framework reduces the performance of over 300 13C and 600 1H density functional theory chemical shift predictions to a single submission procedure.

Fine-Tuning the Polarizable CL&Pol Force Field for the Deep Eutectic Solvent Ethaline

Polarizable force fields are gradually becoming a common choice for ionic soft matter, in particular, for molecular dynamics (MD) simulations of ionic liquids (ILs) and deep eutectic solvents (DESs). The CL&Pol force field introduced in 2019 is the first general, transferable, and polarizable force field for MD simulations of different types of DESs. The original formulation contains, however, some problems that appear in simulations of ethaline and may also have a broader impact. First, the originally proposed atomic diameter parameters are unbalanced, resulting in too weak interactions between the chlorides and the hydroxyl groups of the ethylene glycol molecules. This, in turn, causes an artificial phase separation in long simulations. Second, there is an overpolarization of chlorides due to strong induced dipoles that give rise to the presence of peaks and antipeaks at very low q-vector values (2.4 nm^-1) in the partial components of the structure factors. In physical terms, this is equivalent to overestimated spatial nanoscale heterogeneity. To correct these problems, we adjusted the chloride-hydroxyl radial distribution functions against ab initio data and then extended the use of the Tang-Toennis damping function for the chlorides' induced dipoles. These adjustments correct the problems without losing the robustness of the CL&Pol force field. The results were also compared with the nonpolarizable version, the CL&P force field. We expect that the corrections will facilitate reliable use of the CL&Pol force field for other types of DESs.

CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

Explicit treatment of electronic polarizability in empirical force fields (FFs) represents an extension over a traditional additive or pairwise FF and provides a more realistic model of the variations in electronic structure in condensed phase, macromolecular simulations. To facilitate utilization of the polarizable FF based on the classical Drude oscillator model, Drude Prepper has been developed in CHARMM-GUI. Drude Prepper ingests additive CHARMM protein structures file (PSF) and pre-equilibrated coordinates in CHARMM, PDB, or NAMD format, from which the molecular components of the system are identified. These include all residues and patches connecting those residues along with water, ions, and other solute molecules. This information is then used to construct the Drude FF-based PSF using molecular generation capabilities in CHARMM, followed by minimization and equilibration. In addition, inputs are generated for molecular dynamics (MD) simulations using CHARMM, GROMACS, NAMD, and OpenMM. Validation of the Drude Prepper protocol and inputs is performed through conversion and MD simulations of various heterogeneous systems that include proteins, nucleic acids, lipids, polysaccharides, and atomic ions using the aforementioned simulation packages. Stable simulations are obtained in all studied systems, including 5 μs simulation of ubiquitin, verifying the integrity of the generated Drude PSFs. In addition, the ability of the Drude FF to model variations in electronic structure is shown through dipole moment analysis in selected systems. The capabilities and availability of Drude Prepper in CHARMM-GUI is anticipated to greatly facilitate the application of the Drude FF to a range of condensed phase, macromolecular systems.

Microscale modelling of dielectrophoresis assembly processes

This work presents a microscale approach for simulating the dielectrophoresis assembly of polarizable particles under an external electric field. The model is shown to capture interesting dynamical and topological features, such as the formation of chains of particles and their incipient aggregation into hierarchical structures. A quantitative characterization in terms of the number and size of these structures is also discussed. This computational model could represent a viable numerical tool to study the mechanical properties of particle-based hierarchical materials and suggest new strategies for enhancing their design and manufacture. This article is part of the theme issue 'Progress in mesoscale methods for fluid dynamics simulation'.

Does Explicit Polarizability Improve Simulations of Phase Behavior of Ionic Liquids?

Molecular dynamics simulations are performed for a test set of 20 aprotic ionic liquids to investigate whether including an explicit polarizability model in the force field leads to higher accuracy and reliability of the calculated phase behavior properties, especially the enthalpy of fusion. A classical nonpolarizable all-atom optimized potentials for liquid simulations (OPLS) force-field model developed by Canongia Lopes and Pádua (CL&P) serves as a reference level of theory. Polarizability is included either in the form of Drude oscillators, resulting in the CL&P-D models, or in the framework of the atomic multipole optimized energetics for biomolecular application (AMOEBA) force field with polarizable atomic sites. Benchmarking of the calculated fusion enthalpy values against the experimental data reveals that overall the nonpolarizable CL&P model and polarizable CL&P-D models perform similarly with average deviations of about 30%. However, fusion enthalpies from the CL&P-D models exhibit a stronger correlation with their experimental counterparts. The least successful predictions are interestingly obtained from AMOEBA (deviation ca. 60%), which may indicate that a reparametrization of this force-field model is needed to achieve improved predictions of the fusion enthalpy. In general, all FF models tend to underestimate the fusion enthalpies. In addition, quantum chemical calculations are used to compute the electronic cohesive energies of the crystalline phases of the ionic liquids and of the interaction energies within the ion pair. Significant positive correlations are found between the fusion enthalpy and the cohesive energies. The character of the present anions predetermines the magnitude of individual mechanistic components of the interaction energy and related enthalpic and cohesive properties.

Systematic Comparison of the Structural and Dynamic Properties of Commonly Used Water Models for Molecular Dynamics Simulations

Water is a unique solvent that is ubiquitous in biology and present in a variety of solutions, mixtures, and materials settings. It therefore forms the basis for all molecular dynamics simulations of biological phenomena, as well as for many chemical, industrial, and materials investigations. Over the years, many water models have been developed, and it remains a challenge to find a single water model that accurately reproduces all experimental properties of water simultaneously. Here, we report a comprehensive comparison of structural and dynamic properties of 30 commonly used 3-point, 4-point, 5-point, and polarizable water models simulated using consistent settings and analysis methods. For the properties of density, coordination number, surface tension, dielectric constant, self-diffusion coefficient, and solvation free energy of methane, models published within the past two decades consistently show better agreement with experimental values compared to models published earlier, albeit with some notable exceptions. However, no single model reproduced all experimental values exactly, highlighting the need to carefully choose a water model for a particular study, depending on the phenomena of interest. Finally, machine learning algorithms quantified the relationship between the water model force field parameters and the resulting bulk properties, providing insight into the parameter-property relationship and illustrating the challenges of developing a water model that can accurately reproduce all properties of water simultaneously.

Extension of the CL&Pol Polarizable Force Field to Electrolytes, Protic Ionic Liquids, and Deep Eutectic Solvents

The polarizable CL&Pol force field presented in our previous study, Transferable, Polarizable Force Field for Ionic Liquids (J. Chem. Theory Comput. 2019, 15, 5858, DOI: http://doi.org/10.1021/acs.jctc.9b0068910.1021/acs.jctc.9b00689), is extended to electrolytes, protic ionic liquids (PIL), deep eutectic solvents (DES), and glycols. These systems are problematic in polarizable simulations because they contain either small, highly charged ions or strong hydrogen bonds, which cause trajectory instabilities due to the pull exerted on the induced dipoles. We use a Tang-Toennies (TT) function to dampen, or smear, the interactions between charges and induced dipole at a short range involving small, highly charged atoms (such as hydrogen or lithium), thus preventing the "polarization catastrophe". The new force field gives stable trajectories and is validated through comparison with experimental data on density, viscosity, and ion diffusion coefficients of liquid systems of the above-mentioned classes. The results also shed light on the hydrogen-bonding pattern in ethylammonium nitrate, a PIL, for which the literature contains conflicting views. We describe the implementation of the TT damping function, of the temperature-grouped Nosé-Hoover thermostat for polarizable molecular dynamics (MD) and of the periodic perturbation method for viscosity evaluation from non-equilibrium trajectories in the LAMMPS MD code. The main result of this work is the wider applicability of the CL&Pol polarizable force field to new, important classes of fluids, achieving robust trajectories and a good description of equilibrium and transport properties in challenging systems. The fragment-based approach of CL&Pol will allow ready extension to a wide variety of PILs, DES, and electrolytes.

Uncovering a Universal Molecular Mechanism of Salt Ion Adsorption at Solid/Water Interfaces

Solid/water interfaces, in which salt ions come in close proximity to solids, are ubiquitous in nature. Because water is a polar solvent and salt ions are charged, a long-standing puzzle involving solid/water interfaces is how do the electric fields exerted by the salt ions and the interfacial water molecules polarize the charge distribution in the solid and how does this polarization, in turn, influence ion adsorption at any solid/water interface. Here, using state-of-the-art polarizable force fields derived from quantum chemical simulations, we perform all-atomistic molecular dynamics simulations to investigate the adsorption of various ions comprising the well-known Hofmeister series at the graphene/water interface, including comparing with available experimental data. Our findings reveal that, in vacuum, the ionic electric field-induced polarization of graphene results in a significantly large graphene-ion polarization energy, which drives all salt ions to adsorb to graphene. On the contrary, in the presence of water molecules, we show that the ions and the water molecules exert waves of molecular electric fields on graphene which destructively interfere with each other. This remarkable phenomenon is shown to cause a water-mediated screening of more than 85% of the graphene-ion polarization energy. Finally, by investigating superhydrophilic and superhydrophobic model surfaces, we demonstrate that this phenomenon occurs universally at all solid/water interfaces and results in a significant weakening of the ion-solid interactions, such that ion specific effects are governed primarily by a competition between the ion-water and water-water interactions, irrespective of the nature of the solid/water interface.

Methylguanidinium at the Air/Water Interface: A Simulation Study with the Drude Polarizable Force Field

Methylguanidinium is an important molecular ion, which also serves as the model compound for the arginine side chain. We studied the structure and dynamics of the methylguanidium ion at the air/water interface by molecular dynamics simulations employing the Drude polarizable force field. We found out that methylguanidinium accumulated at the interface, with a majority adopting tilted conformations. We also demonstrated that methylguanidinium and guanidinium ions had different preference toward the air/water interface. Detailed analysis of induced dipole moments showed how ions adjusted their charge distribution at the interface and revealed how the anisotropy in molecular polarizability impacted the orientation of molecular ions. Our results illustrate the importance of explicitly including the electronic polarization effects in modeling interfacial properties.

Next-Generation Accurate, Transferable, and Polarizable Potentials for Material Simulations

PHAHST (potentials with high accuracy, high speed, and transferability) intermolecular potential energy functions have been developed from first principles for H₂, N₂, the noble gases, and a metal-organic material, HKUST-1. The potentials are designed from the outset to be transferable to heterogeneous environments including porous materials, interfaces, and material simulations. This is accomplished by theoretically justified choices for all functional forms, parameters, and mixing rules, including explicit polarization in every environment and fitting to high quality electronic structure calculations using methods that are tractable for real systems. The models have been validated in neat systems by comparison to second virial coefficients and bulk pressure-density isotherms. For inhomogeneous applications, our main target, comparisons are presented to previously published experimental studies on the metal-organic material HKUST-1 including adsorption, isosteric heats of adsorption, binding site locations, and binding site energies. A systematic prescription is provided for developing compatible potentials for additional small molecules and materials. The resulting models are recommended for use in complex heterogeneous simulations where existing potentials may be inadequate.

SEM-Drude Model for the Accurate and Efficient Simulation of MgCl2-KCl Mixtures in the Condensed Phase

There is a long history of models that to different extents reproduce structural and dynamical properties of high-temperature molten salts. Whereas rigid ion models can work fairly well for some of the monovalent salts, polarizability is fundamentally important when small divalent or multivalent cations are combined with significantly polarizable anions such as Cl^- to form networked liquids that display a first sharp diffraction peak. There are excellent polarizable ion models (PIMs) for these systems, but there has been little success with the less expensive Core-Shell type models, which are often described as unwieldy or difficult to fit. In this article, we present the Sharma-Emerson-Margulis (SEM)-Drude model for MgCl₂/KCl mixtures that with the same ingredients used in the latest and most accurate PIM models overcome the aforementioned obstacles at significantly less computational cost; structural and dynamical properties are for all practical purposes very similar to what we obtain from the PIM but typical simulations can be more than 30 times faster. This has allowed us not only to expand our recent studies on the temperature and composition dependence of intermediate range order in MgCl₂/KCl mixtures but also to access transport properties that were simply too costly to properly sample in our recently published studies.

Ordered Solvents and Ionic Liquids Can Be Harnessed for Electrostatic Catalysis

Herein, we employ classical molecular dynamics simulations using the Drude oscillator-based polarizable force field, quantum chemical calculations, and ONIOM multiscale calculations to study (a) how an external field orders the solvent environment in a chemical reaction and then (b) whether in the absence of this same applied field the ordered solvent environment alone can electrostatically catalyze a chemical reaction when compared with the corresponding disordered solvent. Our results show that a 0.2 V/Å external electric field, which is below the threshold for bond breaking of solvent molecules, leads to significant ordering of bulk methanol solvent and the ionic liquid [EMIM][BF₄]. Importantly, in the absence of this same field, the ordered solvent lowers the activation energy of the hydrogen-transfer reaction of o-alkylphenyl ketones in excess of 20 kcal/mol when the solvent is methanol and by over 30 kcal/mol for [EMIM][BF₄]. Even a 0.1 V/Å external field has effects of ca. 10 and 20 kcal/mol, respectively. This work suggests a possible strategy for scaling electrostatic catalysis by applying a pulsed external field to the reaction medium to maintain solvent ordering while allowing the reaction to proceed largely in the absence of an external field.

Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields

The water-octanol partition coefficient is an important physicochemical property for small molecule drug design. Here, we report our participation in the SAMPL6 logP prediction challenge with free energy perturbation (FEP) calculations in the water phase and in the 1-octanol phase using Drude polarizable force fields. Root mean square error (RMSE) and mean absolute error (MAE) of our prediction are equal to 1.85 and 1.25 logP units. The errors are not evenly distributed. Out of eleven SAMPL6 solutes, FEP/Drude performed very badly on three molecules (deviations all larger than 2 logP units) but good on the remaining eight (deviations all less than 1 logP unit). We find while FEP converges well within one nanosecond in water, simulations in 1-octanol need much longer simulation time and possibly more independent runs for sampling. We also find out that 1-octanol, albeit being a non-polar solvent, still polarizes solute molecules and forms stable hydrogen bonds with them. At the end, we attempt to reweight FEP trajectories with QM/Drude calculations and discuss possible caveats in our simulation setup.

Sodium diffusion in ionic liquid-based electrolytes for Na-ion batteries: the effect of polarizable force fields

Understanding the transport of sodium ions in ionic liquids is the key to design novel electrolyte materials for sodium-ion batteries.

Effect of an external electric field on the dynamics and intramolecular structures of ions in an ionic liquid

Simulations of the ionic liquid 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide in an external electric field have been performed using a Drude particle polarizable force field. The structure of the ions has been analyzed, with close attention paid to the configurations of the ions. The "charge arm" concept is used to explain certain changes of these configurations that would be difficult to rationalize otherwise, e.g., trans → cis isomerization of the bis(trifluoromethylsulfonyl)imide anion and extension of the alkyl chain of the cation. It has also been shown that the ions orient themselves so that their charge arms align with and stretch out along the field, and these effects occur at lower external electric field strengths than cause a change in the inherent diffusion of the ions. The dynamics of the system parallel and perpendicular to the field were analyzed, and it was found that the applied field affected the diffusion normal to the field. This is explained as a secondary effect of a change in the ion cage formed by the surrounding counterions of a given ion in the ionic liquid. The breakdown of the ion cages was rationalized by correlating changes to the inherent diffusion of the ions with other changes to the diffusion and bulk structure of the liquid, as well as considering the average forces on the ions compared to the force the ions would be expected to experience in an electric field. Parallel to the field, a drift was observed at every electric field studied. In electric fields with no changes to the ion cage structure, the relationship between the drift and electric field was found to be linear, becoming nonlinear as the ion cage structure breaks down.

Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields

Many applications in chemistry, biology, and energy storage/conversion research rely on molecular simulations to provide fundamental insight into structural and transport properties of materials with high ionic concentrations. Whether the system is comprised entirely of ions, like ionic liquids, or is a mixture of a polar solvent with a salt, e.g., liquid electrolytes for battery applications, the presence of ions in these materials results in strong local electric fields polarizing solvent molecules and large ions. To predict properties of such systems from molecular simulations often requires either explicit or mean-field inclusion of the influence of polarization on electrostatic interactions. In this manuscript, we review the pros and cons of different treatments of polarization ranging from the mean-field approaches to the most popular explicit polarization models in molecular dynamics simulations of ionic materials. For each method, we discuss their advantages and disadvantages and emphasize key assumptions as well as their adjustable parameters. Strategies for the development of polarizable models are presented with a specific focus on extracting atomic polarizabilities. Finally, we compare simulations using polarizable and nonpolarizable models for several classes of ionic systems, discussing the underlying physics that each approach includes or ignores, implications for implementation and computational efficiency, and the accuracy of properties predicted by these methods compared to experiments.

A molecular contact theory for simulating polarization: application to dielectric constant prediction

Microscopic polarization in liquids, which is challenging to account for intuitively and quantitatively, can impact the behavior of liquids in numerous ways and thus is ubiquitous in a broad range of domains and applications. To overcome this challenge, in this work, a molecular contact theory was proposed as a proxy to simulate microscopic polarization in liquids. In particular, molecular surfaces from implicit solvation models were used to predict both the dipole moment of individual molecules and mutual orientations arising from contacts between molecules. Then, the calculated dipole moments and orientations were combined in an analytical coupling, which allowed for the prediction of effective (polarized) dipole moments for all distinct species in the liquid. As a proof-of-concept, the model focused on predicting the dielectric constant and was tested on 420 pure liquids, 269 binary organic mixtures (3792 individual compositions) and 46 aqueous mixtures (704 individual compositions). The model proved to be flexible enough to reach an unprecedented satisfactory mean relative error of about 16-22% and a classification accuracy of 84-90% within four meaningful classes of weak, low average, high average and strong dielectric constants. The method also proved to be computationally very efficient, with calculation times ranging from a few seconds to about ten minutes on a personal computer with a single CPU. This success demonstrates that much of the microscopic polarization concept can be satisfactorily described based on a simple molecular contact theory. Moreover, the new model for dielectric constants provides a useful alternative to computationally expensive molecular dynamics simulations for large scale virtual screenings in chemical engineering and material sciences.