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Towards molecular simulations that are transparent, reproducible, usable by others, and extensible (TRUE)

Published in Molecular Physics, 2020

Abstract: Systems composed of soft matter (e.g. liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges, requiring time and/or ensemble-averaged data to be collected over long simulation trajectories for property evaluation. Performing a molecular simulation of a soft matter system involves multiple steps, which have traditionally been performed by researchers in a ‘bespoke’ fashion, resulting in many published soft matter simulations not being reproducible based on the information provided in the publications. To address the issue of reproducibility and to provide tools for computational screening, we have been developing the open-source Molecular Simulation and Design Framework (MoSDeF) software suite. In this paper, we propose a set of principles to create Transparent, Reproducible, Usable by others, and Extensible (TRUE) molecular simulations. MoSDeF facilitates the publication and dissemination of TRUE simulations by automating many of the critical steps in molecular simulation, thus enhancing their reproducibilitya. We provide several examples of TRUE molecular simulations: All of the steps involved in creating, running and extracting properties from the simulations are distributed on open-source platforms (within MoSDeF and on GitHub), thus meeting the definition of TRUE simulations.

Identifying Water–Anion Correlated Motion in Aqueous Solutions through Van Hove Functions

Published in The Journal of Physical Chemistry Letters, 2019

Abstract: Electrolyte solutions are ubiquitous in materials in daily use and in biological systems. However, the understanding of their molecular and ionic dynamics, particularly those of their correlated motions, are elusive despite extensive experimental, theoretical, and numerical studies. Here we report the real-space observations of the molecular/ionic-correlated dynamics of aqueous salt (NaCl, NaBr, and NaI) solutions using the Van Hove functions obtained by high-resolution inelastic X-ray scattering measurement and molecular dynamics simulation. Our results directly depict the distance-dependent dynamics of aqueous salt solutions on the picosecond time scale and identify the changes in the anion–water correlations. This study demonstrates the capability of the real-space Van Hove function analysis to describe the local correlated dynamics in aqueous salt solutions.

Ion Pairing Controls Physical Properties of Ionic Liquid-Solvent Mixtures

Published in The Journal of Physical Chemistry B, 2019

Abstract: The dissolution of room temperature ionic liquids (RTILs) in organic solvents has been shown to enhance ion dynamics. We previously used molecular dynamics (MD) simulations to study the ionic liquid ([BMIM+][Tf2N–]) in 22 unique solvents over a wide range of concentrations. By screening over a large parameter space, we reached several conclusions: (1) ion diffusivity increases monotonically as a function of increasing ionic liquid composition, (2) pure solvent diffusivity strongly correlates with ion diffusivity, and (3) conductivity predicted by the Nernst–Einstein (NE) equation has a maximum at intermediate compositions of ionic liquid. Building off this work, we now utilize the same parameter space to study the structure of ([BMIM+][Tf2N–]) solvated in organic solvents. We explore ion correlations through a number of structural and thermodynamic properties, including liquid densities, pair correlation functions, ion pairing and ion caging lifetimes, and free energy calculations. Through these analyses, we find that some solvents are much more effective at screening ion–ion interactions than others and that these differences impact the ion dynamics in these mixtures. In general, the strong pairing of ionic liquids negatively impacts transport properties, but some solvents can robustly screen these interactions, resulting in greatly enhanced ion dynamics. These results uncover trends connecting ionic liquid structure to transport, which can help in the design of new electrolytes for energy storage devices, such as electrical double layer capacitors and batteries.

Formalizing atom-typing and the dissemination of force fields with foyer

Published in Computational Materials Science, 2019

Abstract: A key component to enhancing reproducibility in the molecular simulation community is reducing ambiguity in the parameterization of molecular models used to perform a study. Ambiguity in molecular models often stems from inadequate usage documentation of molecular force fields and the fact that force fields are not typically disseminated in a format that is directly usable by software. Specifically, the lack of a generally applicable scheme for the annotation of the rules of a particular force field and a general purpose tool for performing automated parameterization (i.e., atom-typing) based on these rules, may lead to errors in model parameterization that are not easily identified. Here, we present Foyer, an open-source Python tool that enables users to define and apply force field atom-typing rules in a format that is both human- and machine-readable and provides a framework for force field dissemination, thus eliminating ambiguity in atom-typing and improving reproducibility. Foyer defines force fields in an XML format, where SMARTS strings are used to define the chemical context of a particular atom type and “overrides” are used to set rule precedence, rather than a rigid hierarchical scheme. Herein we describe the underlying methodology and force field annotation scheme of the Foyer software, demonstrate its application in several use-cases, and discuss specific aspects of the Foyer approach that are designed to improve reproducibility.

Scalable Screening of Soft Matter: A Case Study of Mixtures of Ionic Liquids and Organic Solvents

Published in The Journal of Physical Chemistry B, 2019

Abstract: Room temperature ionic liquids (RTILs) are a class of organic salts that are liquid at room temperature. Their physiochemical properties, including low vapor pressure and wide electrochemical stability window, have driven their use as electrolytes in many electrochemical applications, however, their slow transport properties can hinder their performance. This issue is often mitigated by solvating ionic liquids in neutral organic solvents. To date, however, solvent interactions have only been explored for a small number of solvents, particularly acetonitrile and propylene carbonate, at only a few compositions. In this work, we use molecular dynamics simulations in the context of a computational screening approach to study mixtures of ionic liquids in many different solvents at a range of concentrations. Building on prior work, we again find that ionic liquid diffusivity increases monotonically with greater solvent concentration. In contrast to a prior conclusion, we find that pure solvent diffusivity, not …

Humidity Exposure Enhances Microscopic Mobility in a Room-Temperature Ionic Liquid in MXene

Published in The Journal of Physical Chemistry C, 2018

Abstract: Present and future electrochemical devices employing advanced electrode and electrolyte materials are expected to operate in diverse environments, where they are exposed to variable conditions, such as changing humidity levels. Such conditions can possibly alter the microscopic mechanisms that influence the electrochemical performance. Here, using quasi-elastic neutron scattering and molecular dynamics simulations, we investigate the influence of humidity exposure on a room-temperature ionic liquid, [EMIm+][Tf2N−], in Ti3C2Tx MXene. Absorbed water enhances the microscopic mobility of confined [EMIm+][Tf2N−], even though the ionic liquid itself is not very hygroscopic. The absorbed water molecules predominantly reside on the termination groups of the more hydrophilic MXene layers, thereby displacing the ions from the surface and facilitating their motions in the MXene matrix.

An Atomistic Carbide-Derived Carbon Model Generated Using ReaxFF-Based Quenched Molecular Dynamics

Published in C, 2017

Abstract: We report a novel atomistic model of carbide-derived carbons (CDCs), which are nanoporous carbons with high specific surface areas, synthesis-dependent degrees of graphitization, and well-ordered, tunable porosities. These properties make CDCs viable substrates in several energy-relevant applications, such as gas storage media, electrochemical capacitors, and catalytic supports. These materials are heterogenous, non-ideal structures and include several important parameters that govern their performance. Therefore, a realistic model of the CDC structure is needed in order to study these systems and their nanoscale and macroscale properties with molecular simulation. We report the use of the ReaxFF reactive force field in a quenched molecular dynamics routine to generate atomistic CDC models. The pair distribution function, pore size distribution, and adsorptive properties of this model are reported and corroborated with experimental data. Simulations demonstrate that compressing the system after quenching changes the pore size distribution to better match the experimental target. Ring size distributions of this model demonstrate the prevalence of non-hexagonal carbon rings in CDCs. These effects may contrast the properties of CDCs against those of activated carbons with similar pore size distributions and explain higher energy densities of CDC-based supercapacitors. View Full-Text

Influence of humidity on performance and microscopic dynamics of an ionic liquid in supercapacitor

Published in Physical Review Materials, 2017

Abstract: We investigated the influence of water molecules on the diffusion, dynamics, and electrosorption of a room temperature ionic liquid (RTIL), [BMIm+][Tf2N−], confined in carbide-derived carbon with a bimodal nanoporosity. Water molecules in pores improved power densities and rate handling abilities of these materials in supercapacitor electrode configurations. We measured the water-dependent microscopic dynamics of the RTIL cations using quasielastic neutron scatting (QENS). The ionic liquid demonstrated greater mobility with increasing water uptake, facilitated by the nanoporous carbon environment, up to a well-defined saturation point. We concluded that water molecules displaced RTIL ions attached to the pore surfaces and improved the diffusivity of the displaced cations. This effect consequently increased capacitance and rate handling of the electrolyte in water-containing pores. Our findings suggest the possible effect of immiscible co-solvents on energy and power densities of energy storage devices, as well as the operating viability of nonaqueous supercapacitor electrolytes in humid environments.

Computational Insights into Materials and Interfaces for Capacitive Energy Storage

Published in Advanced Science, 2017

Abstract: Supercapacitors such as electric double‐layer capacitors (EDLCs) and pseudocapacitors are becoming increasingly important in the field of electrical energy storage. Theoretical study of energy storage in EDLCs focuses on solving for the electric double‐layer structure in different electrode geometries and electrolyte components, which can be achieved by molecular simulations such as classical molecular dynamics (MD), classical density functional theory (classical DFT), and Monte‐Carlo (MC) methods. In recent years, combining first‐principles and classical simulations to investigate the carbon‐based EDLCs has shed light on the importance of quantum capacitance in graphene‐like 2D systems. More recently, the development of joint density functional theory (JDFT) enables self‐consistent electronic‐structure calculation for an electrode being solvated by an electrolyte. In contrast with the large amount of theoretical and computational effort on EDLCs, theoretical understanding of pseudocapacitance is very limited. In this review, we first introduce popular modeling methods and then focus on several important aspects of EDLCs including nanoconfinement, quantum capacitance, dielectric screening, and novel 2D electrode design; we also briefly touch upon pseudocapactive mechanism in RuO2. We summarize and conclude with an outlook for the future of materials simulation and design for capacitive energy storage.

Solvent Polarity Governs Ion Interactions and Transport in a Solvated Room-Temperature Ionic Liquid

Published in The Journal of Physical Chemistry Letters, 2016

Abstract: We explore the influence of the solvent dipole moment on cation− anion interactions and transport in 1-butyl-3-methyl-imidazolium bis- (trifluoromethylsulfonyl), [BMIM+][Tf2N−]. Free energy profiles derived from atomistic molecular dynamics (MD) simulations show a correlation of the cation− anion separation and the equilibrium depth of the potential of mean force with the dipole moment of the solvent. Correlations of the ion diffusivity with the dipole moment and the concentration of the solvent were further demonstrated by classical MD simulations. Quasi-elastic neutron scattering experiments with deuterated solvents reveal a complex picture of nanophase separation into the ionic liquid-rich and solvent-rich phases. The experiment corroborates the trend of concentration- and dipole moment-dependent enhancement of ion mobility by the solvent, as suggested by the simulations. Despite the considerable structural complexity of ionic liquid−solvent mixtures, we can rationalize and generalize the trends governing ionic transport in these complex electrolytes.

Relationship between pore size and reversible and irreversible immobilization of ionic liquid electrolytes in porous carbon under applied electric potential

Published in Applied Physics Letters, 2016

Abstract: Transport of electrolytes in nanoporous carbon-based electrodes largely defines the function and performance of energy storage devices. Using molecular dynamics simulation and quasielastic neu- tron scattering, we investigate the microscopic dynamics of a prototypical ionic liquid electrolyte, [emim][Tf2N], under applied electric potential in carbon materials with 6.7 nm and 1.5 nm pores. The simulations demonstrate the formation of dense layers of counter-ions near the charged surfa- ces, which is reversible when the polarity is reversed. In the experiment, the ions immobilized near the surface manifest themselves in the elastic scattering signal. The experimentally observed ion immobilization near the wall is fully reversible as a function of the applied electric potential in the 6.7 nm, but not in the 1.5 nm nanopores. In the latter case, remarkably, the first application of the electric potential leads to apparently irreversible immobilization of cations or anions, depending on the polarity, near the carbon pore walls. This unexpectedly demonstrates that in carbon electrode materials with the small pores, which are optimal for energy storage applications, the polarity of the electrical potential applied for the first time after the introduction of an ionic liquid electrolyte may define the decoration of the small pore walls with ions for prolonged periods of time and possi- bly for the lifetime of the electrode.