CDFTPY: A python package for performing classical density functional theory calculations for molecular liquids
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Valiev, Marat (ORCID:0000000161271988)↗
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Development and application of hybrid AIMD/cDFT simulations for atomic-to-mesoscale chemistry
Many important chemical processes involve reactivity and dynamics in complex solutions. Gaining a fundamental understanding of these reaction mechanisms is a challenging goal that requires advanced computational and experimental approaches. However, important techniques such as molecular simulation have limitations in terms of scales of time, length, and system complexity. Furthermore, among the currently available solvation models, there are very few designed to describe the interaction between the molecular scale and the mesoscale. To help address this challenge, here, we establish a novel hybrid approach that couples first-principles plane-wave density functional theory with classical density functional theory (cDFT). In this approach, a region of interest described by ab initio molecular dynamics (AIMD) interacts with the surrounding medium described using cDFT to arrive at a self-consistent ground state. cDFT is a robust but efficient mesoscopic approach to accurate thermodynamics of bulk electrolyte solutions over a wide concentration range (up to 2M concentrations). Benchmarking against commonly used continuum models of solvation, such as SMD, as well as experiments, demonstrates that our hybrid AIMD–cDFT method is able to produce reasonable solvation energies for a variety of molecules and ions. With this model, we also examined the solvent effects on a prototype S N 2 reaction of the nucleophilic attack of a chloride ion on methyl chloride in the solution. The resulting reaction pathway profile and the solution phase barrier agree well with experiment, showing that our AIMD/cDFT hybrid approach can provide insight into the specific role of the solvent on the reaction coordinate.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Ionic Liquid Mixture Expands the Potential Window and Capacitance of a Supercapacitor in Tandem
Mixing room temperature ionic liquids (RTIL) may optimize electrolyte properties for the better performance of electrical double layer capacitors (EDLCs). To understand the composition effects, we theoretically investigate the potential window, interfacial structure, capacitance, and energy density of RTIL mixtures consisting of one common cation and two anions of different sizes. A combination of quantum density functional theory (QDFT) and classical density functional theory (CDFT) calculations indicates that the electrolyte composition has significant effects on the EDL structure and potential of zero charge, thereby altering the integral capacitance and electrochemical potential window. The two quantities can be optimized together to achieve the best EDLC performance.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Chemical bond effects in classical site density functional theory of inhomogeneous molecular liquids
Intra-molecular interactions or chemical bonds represent one of the main distinguishing characteristic of molecular fluids. Development of accurate and practical methods to treat these effects is one of the long standing problems in classical site density functional theory (SDFT). One particular instance when these issues become particularly severe is the case of classical interactions potentials with auxiliary sites or dummy atoms. In this situation current SDFT implementations, such as three-dimensional reference interaction site model (3D-RISM), lead to nonphysical results. We re-examine this issue in this work using our recent reformulation of SDFT. We put forward a simple practical solution to this problem, and illustrate its utility for the case of spherical solutes in diatomic liquids.
Chuev, Gennady N.↗
Flow effects on silicate dissolution and ion transport at an aqueous interface
Combination of the classical density functional theory with kinetics modeling and the Navier–Stokes equation enables a quantitative description of the convoluted effects of fluid flow, surface reactions, interfacial structure and mass transport.
Lian, Cheng↗
Silk Flexible Electronics: From Bombyx mori Silk Ag Nanoclusters Hybrid Materials to Mesoscopic Memristors and Synaptic Emulators
Functionalization of flexible materials based on mesoscopic reconstruction is a key strategy in fabricating biocompatible flexible electronics. This work is to acquire new mesoscopic bioelectronic hybrid materials of silk fibroin (SF)-Ag nanoclusters (AgNCs@BSA; BSA: bovine serum albumin), which enhance significantly the performance of silk memristors. It is to build AgNCs@BSA into SF mesoscopic networks by templated ß-crystallization. Atomic force microscopy potential probing indicates that AgNCs@BSA serve as electronic potential wells that change completely the transport behavior of charge particles within the SF films. This leads to significant enhancement in the switching speed (˜10 ns), very good switching stability, extremely low set/reset voltages (0.3/-0.18 V) of SF meso-hybrid memristors, compared with the original and other organic memristors, and displays unique synapse characteristics and the capability of synapse learning. Classical density functional theory Poisson–Nernst–Planck simulations indicate that the enhanced performance is subject to the low potential paths interconnecting the AgNCs@BSA, which guide charges' transport (Ag+) and deposition in SF films.
Shi, Chenyang↗
Simultaneous Adsorption and Incorporation of Sr 2+ at the Barite (001)–Water Interface
Ionically-bonded minerals are ubiquitous and play a determinative role in controlling the mobility of toxic metals in natural environments. However, little is known about the mechanism of ion uptake by these mineral surfaces. In this study, the sorption of strontium ions (Sr 2+ ) to the barite (001) – water interface was studied using a combination of synchrotron x-ray scattering and three types of computational simulations (density functional theory, classical molecular dynamics (CMD), and CMD-metadynamics). In situ resonant anomalous X-ray reflectivity (RAXR) revealed that Sr 2+ adsorbed on the barite surface as inner-sphere surface complexes and was incorporated within the outermost barite atomic layers. Density functional theory combined with classical molecular dynamics simulations confirmed the thermodynamic stability of these species, demonstrating almost equal magnitudes in the free energy of sorption between these species. Metadynamics simulations showed a more detailed feature in the free energy landscape for metal adsorption where adsorbed Sr 2+ are stabilized in as many as four distinct inner-sphere sites and additional outer-sphere sites that are more diffuse and less energetically favorable than the inner-sphere sites. Additionally, the energy barriers among those inner-sphere sites were significantly lower compared with those for constituent cation Ba 2+ , implying fast exchange among adsorbed Sr 2+ species. The Sr 2+ uptake measured by RAXR followed a Frumkin isotherm defined with an apparent free energy of sorption, Δ≈ G Sr -22 kJ/mol, and an effective attractive interaction constant, γ ≈ -4.5 kJ/mol, between sorbed Sr 2+ . While the observed free energy can be mostly explained by the Helmholtz free energy of adsorption for Sr 2+ , ΔF Sr = -15.3 kJ/mol, the origin of the sorbate – sorbate correlation could not be fully described by our computational work. Together, these experimental and computational results demonstrate the complexity of Sr 2+ adsorption behavior at the barite (001) surface.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Theoretical prediction of crystallization kinetics of a supercooled Lennard-Jones fluid
The first order curvature correction to the crystal-liquid interfacial free energy is calculated using a theoretical model based on the interfacial excess thermodynamic properties. The correction parameter (δ), which is analogous to the Tolman length at a liquid-vapor interface, is found to be 0.48 ± 0.05 for a Lennard-Jones (LJ) fluid. We show that this curvature correction is crucial in predicting the nucleation barrier when the size of the crystal nucleus is small. The thermodynamic driving force (Δμ) corresponding to available simulated nucleation conditions is also calculated by combining the simulated data with a classical density functional theory. In this study, we show that the classical nucleation theory is capable of predicting the nucleation barrier with excellent agreement to the simulated results when the curvature correction to the interfacial free energy is accounted for.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Enhancing the capacitive performance of microporous materials with protic ionic liquids
Classical density functional theory (cDFT) is used to investigate the electrosorption of protic ionic liquids in porous electrodes within the framework of a coarse-grained model. The purpose of this study is to clarify the capacitive behavior of protic ionic liquids in confined geometry. Previous studies have indicated that thermodynamic properties (e.g., capacitance, phase behavior and ionic conductivity) are influenced by the composition of the acid-base system and show asymmetry between acid dominant versus base dominant compositions. Here, we find that the electric double layer capacitance can be significantly improved by using protic ionic liquids compared to its aprotic counterpart through optimization of the mixture composition (i.e., the ratio of acid to base). We demonstrate the influence of pore size and applied voltage on the capacitance performance of protic ionic liquids and provide insight into microscopic understanding of ion and solvent distributions inside micropores.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Electric double layer capacitance for ionic liquids in nanoporous electrodes: Effects of pore size and ion composition
The energy density of an electric double layer (EDL) capacitor, a type of supercapacitor, depends on the ion distribution within the micropores of electrodes that are typically made of amorphous carbon. By using coarse-grained models and the classical density functional theory, we investigate the distributions of ionic species among different idealized nanopores in contact with an asymmetric ionic liquid mixture and the effects of the bulk electrolyte composition on capacitive energy storage. We find that a charged pore is always small-ion selective, provided all ions have the same valence and similar non-electrostatic interactions. While small ions enhance both the EDL capacitance and the accessibility of micropores, an ionic mixture containing ions of different sizes may yield a capacitance higher than those corresponding to pure ionic liquids. Furthermore, the increased capacitance may be attributed to more efficient ion packing near the charged surface. At certain conditions, the improvement is on a par with the anomalous capacitance rise for pure ionic liquids in electrodes with ultranarrow pores.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A hybrid, coupled approach for modeling charged fluids from the nano to the mesoscale
Here, we develop and demonstrate a new, hybrid simulation approach for charged fluids, which combines the accuracy of the nonlocal, classical density functional theory (cDFT) with the efficiency of the Poisson–Nernst–Planck (PNP) equations. The approach is motivated by the fact that the more accurate description of the physics in the cDFT model is required only near the charged surfaces, while away from these regions the PNP equations provide an acceptable representation of the ionic system. We formulate the hybrid approach in two stages. The first stage defines a coupled hybrid model in which the PNP and cDFT equations act independently on two overlapping domains, subject to suitable interface coupling conditions. At the second stage we apply the principles of the alternating Schwarz method to the hybrid model by using the interface conditions to define the appropriate boundary conditions and volume constraints exchanged between the PNP and the cDFT subdomains. Numerical examples with two representative examples of ionic systems demonstrate the numerical properties of the method and its potential to reduce the computational cost of a full cDFT calculation, while retaining the accuracy of the latter near the charged surfaces.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Impurity effects on ionic-liquid-based supercapacitors
Small amounts of an impurity may affect the key properties of an ionic liquid and such effects can be dramatically amplified when the electrolyte is under confinement. Here the classical density functional theory is employed to investigate the impurity effects on the microscopic structure and the performance of ionic-liquid-based electrical double-layer capacitors, also known as supercapacitors. Using a primitive model for ionic species, we study the effects of an impurity on the double layer structure and the integral capacitance of a room temperature ionic liquid in model electrode pores and find that an impurity strongly binding to the surface of a porous electrode can significantly alter the electric double layer structure and dampen the oscillatory dependence of the capacitance with the pore size of the electrode. Meanwhile, a strong affinity of the impurity with the ionic species affects the dependence of the integral capacitance on the pore size. Up to 30% increase in the integral capacitance can be achieved even at a very low impurity bulk concentration. By comparing with an ionic liquid mixture containing modified ionic species, we find that the cooperative effect of the bounded impurities is mainly responsible for the significant enhancement of the supercapacitor performance.
25 ENERGY STORAGE↗
Molecular-based analysis of nanoparticle solvation: Classical density functional approach
Proper statistical mechanics understanding of nanoparticle solvation processes requires an accurate description of the molecular structure of the solvent. Achieving this goal with standard molecular dynamics (MD) simulation methods is challenging due to large length scales. An alternative approach to this problem can be formulated using classical density functional theory (cDFT), where a full configurational description of the positions of all the atoms is replaced by collective atomic site densities in the molecule. Using an example of the negatively charged silica-like system in an aqueous polar environment represented by a two-site water model, we demonstrate here that cDFT can reproduce MD data at a fraction of the computational cost. An important implication of this result is the ability to understand how the solvent molecular features may affect the system’s properties at the macroscopic scale. A concrete example highlighted in this work is the analysis of nanoparticle interactions with sizes of up to 100 nm in diameter.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Molecular Theory of Hydration at Different Temperatures
Solvation plays an important role in diverse chemical processes ranging from reaction kinetics to molecular recognition, solubility, and phase separations. Despite a long-history of theoretical exploration, quantitative prediction of solvation remains a theoretical challenge without relying on the macroscopic properties of the solvent as an input. Here we present a molecular density functional theory that provides a self-consistent description of the solvation structure and thermodynamic properties of small organic molecules in liquid water at different temperatures. Based on the solute configuration and force-field parameters generated from first-principles calculations, the theoretical predictions are found in good agreement with experimental data for the hydration free energies of 197 organic molecules in a temperature range from 0 to 40 °C. In addition to calibration with experimental results, the theoretical predictions are compared with recent molecular dynamics simulations for the hydration of five highly explosive nitrotoluenes. Lastly, this work demonstrates the potential of the classical density functional theory for high-throughput prediction of solvation properties over a broad range of temperatures.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Revisiting the Growth Mechanism of Hierarchical Semiconductor Nanostructures: The Role of Secondary Nucleation in Branch Formation
Although advances in synthesizing hierarchical semiconductor materials, there have been few studies on the fundamental nucleation mechanisms to explain the origins of such complex structures. Resolving these nucleation and growth pathways is very difficult and time consuming, but is critical for developing predictive synthetic capabilities for the synthesis and applications of new materials. In this paper, we use state-of-the-art in-situ liquid phase scanning electron microscopy (SEM) and high-resolution transmission electron microscopy in combination of classical Density Functional Theory (cDFT) to study the nucleation of highly-branched wurtzite ZnO nanostructures via a facile, room temperature aqueous synthesis route. Using a range of precursor concentrations, we systematically vary their hierarchical organization. In situ liquid phase SEM demonstrates that all branches form through secondary nucleation and grow by classical processes. Neither random aggregation nor oriented attachment is observed. cDFT results imply the morphological evolution with increasing [Zn 2+ ] arises from an interplay between rising thermodynamic driving force, which promotes branch number and variability of orientation, and increasing barriers to interfacial transport due to ion correlation forces that alter the anisotropic kinetics of growth. Finally, these findings provide a quantitative picture of branching that sets to rest past controversies and advances efforts to decipher growth mechanisms of hierarchical structures in real solution environments.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Thermodynamic Route to Efficient Prediction of Gas Diffusivity in Nanoporous Materials
We report an efficient computational procedure for rapid and accurate prediction of the self-diffusivity of gas molecules in nanoporous materials by implementing the transition state theory for intercage hopping at infinite dilution with the string method in conjunction with the excess-entropy scaling for predicting gas diffusion coefficients at finite loadings. The theoretical procedure has been calibrated with molecular dynamics simulations for the diffusion coefficients of methane and hydrogen gases in representative nanoporous materials including metal organic frameworks and zeolites. Combined with the classical density functional theory for calculating the excess entropy of gas molecules in micropores, the theoretical procedure enables efficient computation of both thermodynamic and transport properties important for design and screening of nanostructured materials for gas storage and separation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Ion Correlation Effects in Salt-Doped Block Copolymers
Here, we apply classical density functional theory to study how salt changes the microphase morphology of diblock copolymers. Polymers are freely jointed and one monomer type favorably interacts with ions, to account for the selective solvation that arises from different dielectric constants of the microphases. By including correlations from liquid state theory of an unbound reference fluid, the theory can treat chain behavior, microphase separation, ion correlations, and preferential solvation, at same coarse grained level. We show good agreement with molecular dynamics simulations.
36 MATERIALS SCIENCE↗
Effective Electrostatic Interactions Between Two Overall Neutral Surfaces with Quenched Charge Heterogeneity Over Atomic Length Scale
Using Monte Carlo results as a reference, a classical density functional theory (CDFT) is shown to reliably predict the forces between two heterogeneously charged surfaces immersed in an electrolyte solution, whereas the Poisson–Boltzmann (PB) theory is demonstrated to deteriorate obviously for the same system even if the system parameters considered fall within the validity range of the PB theory in the homogeneously charged surfaces. By applying the tested CDFT, we study the effective electrostatic potential of mean force (EPMF) between two face–face planar and hard surfaces of zero net charge on which positive and negative charges are separated and considered to present as discontinuous spots on the inside edges of the two surfaces. Main conclusions are summarized as follows: (i) strength of the EPMF in the surface charge separation case is very sensitively and positively correlated with the surface charge separation level and valency of the salt ion. Particularly, the charge separation level and the salt ion valency have a synergistic effect, which makes high limit of the EPMF strength in the surface charge separation case significantly go beyond that of the ideal homogeneously charged surface counterpart at average surface charge density similar to the average surface positive or negative charge density in the charge separation case. (ii) The surface charge distribution patterns mainly influence sign of the EPMF: symmetrical and asymmetrical patterns induce repulsive and attractive (at small distances) EPMF, respectively; but with low valency salt ions and low charge separation level the opposite may be the case. With simultaneous presence of both higher valency cation and anion, the EPMF can be repulsive at intermediate distances for asymmetrical patterns. (iii) Salt ion size has a significant impact, which makes the EPMF tend to become more and more repulsive with the ion diameter regardless of the surface charge distribution patterns and the valency of the salt ion; whereas if the 1:1 type electrolyte and the symmetrical patterns are considered, then the opposite may be the case. All of these findings can be explained self-consistently from several perspectives: an excess adsorption of the salt ions (induced by the surface charge separation) serving to raise the osmotic pressure between the plates, configuration fine-tuning in the thinner ion adsorption layer driven by the energy decrease principle, direct Coulombic interactions operating between charged objects on the two face-to-face plates involved, and net charge strength in the ion adsorption layer responsible for the net electrostatic repulsion.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗