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↗
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.↗
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↗
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↗
Boost of the Bio-memristor Performance for Artificial Electronic Synapses by Surface Reconstruction
Biomaterial-based memristors (bio-memristors) are often adopted to emulate biological synapse functions and applied to construct neural computing networks in brain-inspired chip systems. However, the randomness of conductive filament formation in bio-memristors inhibits their switching performance by causing the dispersion of the device-switching parameters. In this case, a facile porous silk fibroin (p-SF) memristor was obtained through a protein surface reconstruction strategy, in which the size of the hole can be adjusted by the density of hybrid nanoseeds. Here, the porous SF memristors exhibit greatly enhanced electrical characteristics, including uniform I-V cycles, centralized distribution of the switching voltages, and both high and low resistances, compared to devices without pores. The results of three-dimensional (3D) simulations based on classical density functional theory (cDFT) suggest that the reconstructed pores in the SF layers guide the formation and fracture of Ag filaments under an electric field and enhance the overall conductivity by separating Ag + ion and electron diffusion pathways. Ag + ions are predicted to preferentially diffuse through pores, whereas electrons diffuse through the SF network. Interestingly, the device conductance can be bidirectionally modulated gradually by positive and negative voltages, can faithfully simulate short-term and long-term plasticity, and can even realize the triplet-spike-timing-dependent plasticity (triplet-STDP) rule, which can be used for pattern recognition in biological systems. The simulation results reveal that a memristor network of this type has an accuracy of ~95.78% in memory learning and the capability of pattern learning. This work provides a facile technology route to improve the performance of bionic-material memristors.
36 MATERIALS SCIENCE↗
Diffusion-to-Imbibition Transition in Water Sorption in Nanoporous Media: Theoretical Studies
The ability to predict multiphase fluid transport in nanoporous rocks such as shales is critical for many geoscience applications, for example unconventional hydrocarbon production, geologic carbon sequestration, and nuclear waste disposal. When the pore sizes approach nanoscales, the impact of the molecular interaction forces between fluids and solids becomes increasingly important. These forces can alter macroscopic fluid phase behavior and control transport. Recent experimental studies have shown that capillary condensation and subsequent imbibition of liquid water can occur in hydrophilic nanoporous media even if the vapor phase is at a critical relative humidity (rhcrit) well below vapor saturation. This study presents a theoretical investigation of the processes controlling adsorption, capillary condensation and imbibition in nanoporous media, using the square-gradient classical density functional theory. The proposed theoretical model explicitly includes the relevant interaction forces among fluids and solids in macroscopic porous media. Application of the model to a relative-humidity-controlled water adsorption experiment is presented to demonstrate the impact of water-pore wall attractive forces on multiphase water behavior in a hydrophilic silicon nanoporous medium. Here, the model represents well the measured time-dependent evolution of the water imbibition front inside the nanoporous medium and also explains the diffusion-like water transport regimes observed at rh < rh crit and the imbibition-like flow regimes observed at rh > rh crit . The study furthermore gives an insight on hysteresis phenomenon in adsorption and desorption isotherms.
58 GEOSCIENCES↗
Wettability of ultra-small pores of carbon electrodes by size-asymmetric ionic fluids
Recently, we studied the phase behavior of ionic fluids under confinement using the classical density functional theory within the framework of the restricted primitive model. Additionally, the theoretical results indicate that narrowing the pore size may lead to a drastic reduction in the electric double layer capacitance, while increasing the surface electrical potential would improve the ionic accessibility of micropores. In this work, we extend the theoretical investigation to systems containing size-asymmetric electrolytes that may exhibit a vapor-liquid like phase transition in the bulk phase. The effects of pore size and surface electric potential on the phase diagram and microscopic structures of the confined electrolytes were studied over a broad range of parameters. We found that decreasing the pore size or increasing the surface potential could destabilize the liquid phase in micropores, and capillary evaporation could occur regardless of the size asymmetry between cations and anions. Compared to that in a symmetric ionic system, the vapor-liquid phase separation is more likely to take place as the size asymmetry becomes more pronounced. The phase transition would alter the “accessibility” of ions to micropores and lead to coexisting micropores with different surface charge densities as identified by Monte Carlo simulation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Demystifying the Stern layer at a metal–electrolyte interface: Local dielectric constant, specific ion adsorption, and partial charge transfer
Electric double layer (EDL) represents one of the most basic concepts in electrochemistry and is pertinent to diverse engineering applications ranging from electrocatalysis to energy storage. Whereas phenomenological and coarse-grained models have been long established to describe ionic distributions in the diffuse layer, a faithful prediction of the physicochemical properties of the electrode–electrolyte interface from a molecular perspective remains a daunting challenge. In this work, we investigate the charging behavior of an Ag (111) electrode in NaF aqueous solutions leveraging experimental results and theoretical calculations based on the classical density functional theory for ion distributions in the diffuse layer and on the joint density functional theory (JDFT) for the electronic structure. When the Ag electrode is applied with a negative voltage, the surface charge density can be reasonably described by assuming a neutral Stern layer with the dielectric constant dependent on the local electric field as predicted by the Kirkwood equation. However, the specific adsorption of F− ions must be considered when the electrode is positively charged and the fluoride adsorption can be attributed to both physical and chemical interactions. Qualitatively, F− binding and partial charge transfer are supported by JDFT calculations, which predict an increased binding energy as the voltage increases. Our findings shed insight on the molecular characteristics of the Stern layer and the charge behavior of adsorbed species not specified by conventional EDL models.
Wang, Xuepeng (ORCID:0000000285704546)↗
Effect of surface properties and polymer chain length on polymer adsorption in solution
In polymer nanoparticle composites (PNCs) with attractive interactions between nanoparticles (NPs) and polymers, a bound layer of the polymer forms on the NP surface, with significant effects on the macroscopic properties of the PNCs. The adsorption and wetting behaviors of polymer solutions in the presence of a solid surface are critical to the fabrication process of PNCs. In this study, we use both classical density functional theory (cDFT) and molecular dynamics (MD) simulations to study dilute and semi-dilute solutions of short polymer chains near a solid surface. Using cDFT, we calculate the equilibrium properties of polymer solutions near a flat surface while varying the solvent quality, surface–fluid interactions, and the polymer chain lengths to investigate their effects on the polymer adsorption and wetting transitions. Using MD simulations, we simulate polymer solutions near solid surfaces with three different curvatures (a flat surface and NPs with two radii) to study the static conformation of the polymer bound layer near the surface and the dynamic chain adsorption process. Additionally, we find that the bulk polymer concentration at which the wetting transition in the poor solvent system occurs is not affected by the difference in surface–fluid interactions; however, a threshold value of surface–fluid interaction is needed to observe the wetting transition. We also find that with good solvent, increasing the chain length or the difference in the surface–polymer interaction relative to the surface–solvent interaction increases the surface coverage of polymer segments and independent chains for all surface curvatures. Finally, we demonstrate that the polymer segmental adsorption times are heavily influenced only by the surface–fluid interactions, although polymers desorb more quickly from highly curved surfaces.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The Effect of Topology on Phase Behavior under Confinement
This work studies how morphology (i.e., the shape of a structure) and topology (i.e., how different structures are connected) influence wall adsorption and capillary condensation under tight confinement. Numerical simulations based on classical density functional theory (cDFT) are run for a wide variety of geometries using both hard-sphere and Lennard-Jones fluids. These cDFT computations are compared to results obtained using the Minkowski functionals. It is found that the Minkowski functionals can provide a good description of the behavior of Lennard-Jones fluids down to small system sizes. In addition, through decomposition of the free energy, the Minkowski functionals provide a good framework to better understand what are the dominant contributions to the phase behavior of a system. Lastly, while studying the phase envelope shift as a function of the Minkowski functionals it is found that topology has a different effect depending on whether the phase transition under consideration is a continuous or a discrete (first-order) transition.
42 ENGINEERING↗
Water–Hydrocarbon Interactions in Anionic Pyrene Monohydrate
Interactions between water and polycyclic aromatic hydrocarbons are essential in many aspects of chemistry, from interstellar and atmospheric processes to interfacial hydrophobicity and wetting phenomena. Despite their growing importance, the intermolecular potentials of the water-hydrocarbon interactions are underdeveloped compared to water-water potentials, and there are similarly few experimental probes that are sensitive to the details of the water-hydrocarbon potential. We present a combined experimental and computational study of anionic pyrene monohydrate, one of the simplest water/hydrocarbon clusters. The action spectrum in the OH region of the mass-selected cluster ion provides a rigorous benchmark for intermolecular potentials and computational methodologies. We identify missing intermolecular interactions and shortcomings in conventional dynamics calculations by comparing experimental data to density functional theory and classical molecular dynamics calculations. Kinetic trapping is prevalent, even for one water molecule and one pyrene molecule, leading to slow equilibration in conventional molecular dynamics calculations, even on nanosecond timescales and at low temperatures (50 K). At constant energy, temperature fluctuations for the pair of molecules are substantial. Immersing the system in a bath of soft spheres and employing parallel tempering alleviates kinetic trapping and dampens temperature fluctuations, bringing the system closer to the thermodynamic limit. With such augmented sampling, a simple, flexible water model reproduces the linewidth and the asymmetric broadening of the symmetric OH stretching mode, which we assign to spectral diffusion. In the OH stretching region, dynamics calculations predict a more intense antisymmetric peak than experiments observe but do not predict the bimodal split symmetric peak that the experiments show. Furthermore, our work suggests that electronic polarization, missing in the empirical force field, is responsible for the first discrepancy and that quantum nuclear effects, captured neither in density functional theory nor in classical dynamics, may be responsible for the second.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex
The entry of the SARS-CoV-2, a causative agent of COVID-19, into human host cells is mediated by the SARS-CoV-2 spike (S) glycoprotein, which critically depends on the formation of complexes involving the spike protein receptor-binding domain (RBD) and the human cellular membrane receptor angiotensin-converting enzyme 2 (hACE2). Using classical site density functional theory (SDFT) and structural bioinformatics methods, we investigate binding and conformational properties of these complexes and study the overlooked role of water-mediated interactions. Analysis of the three-dimensional reference interaction site model (3DRISM) of SDFT indicates that water mediated interactions in the form of additional water bridges strongly increases the binding between SARS-CoV-2 spike protein and hACE2 compared to SARS-CoV-1-hACE2 complex. By analyzing structures of SARS-CoV-2 and SARS-CoV-1, we find that the homotrimer SARS-CoV-2 S receptor-binding domain (RBD) has expanded in size, indicating large conformational change relative to SARS-CoV-1 S protein. Protomer with the up-conformational form of RBD, which binds with hACE2, exhibits stronger intermolecular interactions at the RBD-ACE2 interface, with differential distributions and the inclusion of specific H-bonds in the CoV-2 complex. Further interface analysis has shown that interfacial water promotes and stabilizes the formation of CoV-2/hACE2 complex. This interaction causes a significant structural rigidification of the spike protein, favoring proteolytic processing of the S protein for the fusion of the viral and cellular membrane. Moreover, conformational dynamics simulations of RBD motions in SARS-CoV-2 and SARS-CoV-1 point to the role in modification of the RBD dynamics and their impact on infectivity.
3DRISM↗
Mode-Selective Vibrational Energy Transfer Dynamics in 1,3,5-Trinitroperhydro-1,3,5-triazine (RDX) Thin Films
The coupling of inter- and intramolecular vibrations plays a critical role in initiating chemistry during the shock-to-detonation transition in energetic materials. In this work, we report on the subpicosecond to subnanosecond vibrational energy transfer (VET) dynamics of the solid energetic material 1,3,5-trinitroperhydro-1,3,5-triazine (RDX) by using broadband, ultrafast infrared transient absorption spectroscopy. Experiments reveal VET occurring on three distinct time scales: subpicosecond, 5 ps, and 200 ps. The ultrafast appearance of signal at all probed modes in the mid-infrared suggests strong anharmonic coupling of all vibrations in the solid, whereas the long-lived evolution demonstrates that VET is incomplete, and thus thermal equilibrium is not attained, even on the 100 ps time scale. Density functional theory and classical molecular dynamics simulations provide valuable insights into the experimental observations, revealing compression-insensitive time scales for the initial VET dynamics of high-frequency vibrations and drastically extended relaxation times for low-frequency phonon modes under lattice compression. Mode selectivity of the longest dynamics suggests coupling of the N–N and axial NO2 stretching modes with the long-lived, excited phonon bath.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Electronic structure, magnetic properties, spin orientation, and doping effect in Mn 3 Si 2 Te 6
The layered material Mn 3 Si 2 Te 6 , with alternating stacking honeycomb and triangular layers, is attracting considerable attention due to its rich physical properties. Here, in this study, using density functional theory and classical Monte Carlo (MC) methods, we systematically study this system with the 3d 5 electronic configuration. Near the Fermi level, the states are mainly contributed by Te 5p orbitals hybridized with Mn 3d orbitals, resembling a charge-transfer system. Furthermore, the spin orientations of the ferrimagnetic (FiM) ground state display different conductive behaviors when along the ab plane or out-of-plane directions: insulating vs metallic states. The energy difference between the FiM [110] insulating and FiM [001] metallic phases is very small (~0.71 meV/Mn) . Changing the angle θ of spin orientation from in-plane to out-of-plane directions, the band gaps of this system are gradually reduced, leading to an insulator-metal transition, resulting in an enhanced electrical conductivity, related to the colossal angular magnetoresistance (MR) effect. Although the three main magnetic couplings were found to be antiferromagnetic, overall the ground state is FiM. In addition, we also constructed the magnetic phase diagram using the classical XY spin model studied with the MC method. Three magnetic phases were obtained, including antiferromagnetic order, noncollinear spin patterns, and FiM order. Moreover, we also investigated the Se and Ge doping into the Mn 3 Si 2 Te 6 system: the FiM state has the lowest energy among the magnetic candidates for both Se- and Ge-doped cases. The magnetic anisotropy energy (MAE) decreases in the Se-doped case because the Mn orbital moment is reduced as the doping x increases. Due to the small spin-orbit-coupling effect of Se, the insulator-metal transition caused by the spin orientation disappears in the Se-doped case, resulting in an insulating phase in the FiM [001] phase. This causes a reduced colossal angular MR. However, both the MAE and the band gap of the Ge-doped case do not change much with increasing doping x . Our results for Mn 3 Si 2 Te 6 could provide guidance to experimentalists and theorists working on this system or related materials.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Cellular Phosphate Sensing and Anion Binding by an Azacrown‐Calixpyrrole Hybrid
A hybrid receptor-sensor for anions originating from the merging of positively charged ammonium moieties for electrostatic attraction/stronger binding of azacrowns with directionality of calixpyrrole hydrogen bond donors for selectivity is investigated. As demonstrated this hybrid receptor-sensor shows a remarkable selectivity for orthophosphate even in the presence of other phosphates and anions found in cellular materials (K assoc H 2 PO 4 − >H 2 P 2 O 7 2− >AMP − ≫ADP 2− or ATP 3− over halides, nitrate, or hydrogen sulfate; all Na + salts in water) but also cellular polyphosphate or phospholipids. This selectivity is harnessed in a real-time monitoring of cell lysis by lysozyme, which releases orthophosphate and other phosphates and anions from the cells. This sensitive (LOD 0.4 μM) fluorescence-based microscale method compares favorably with the state-of-the-art techniques but can easily be practiced in a high-throughput screening (HTS) manner. The anion binding and selectivity in aqueous solutions were investigated by NMR and put in context with phosphate binding of the parent calix[4]pyrrole. The microscopic understanding of anion binding by the hybrid receptor was then obtained from a combination of density functional theory (DFT), classical molecular dynamics (MD) with explicit water solvation, and ab initio MD (AIMD) simulations. Correlating the NMR and fluorescence binding data with studies of solvation of the receptor, phosphate anion, and the resulting complex confirms the binding is largely driven by entropic component (TΔS) associated with receptor and anion desolvation.
Anions↗
Exploring the Role of Inorganic and Organic Interfaces on CO 2 and CH 4 Partitioning: Case Study of Silica, Illite, Calcite, and Kerogen Nanopores on Gas Adsorption and Nanoscale Transport Behaviors
The adsorption, partitioning, and diffusion of CO 2 and CH 4 in organic–inorganic pores composed of kerogen with silica, illite, or calcite are studied using density functional theory and classical molecular dynamics simulations. The adsorption and partitioning behavior of CO 2 and CH 4 molecules is found to be a function of chemistry of the solid interface, pore size, and surface area. CO 2 molecules are preferentially adsorbed compared to CH 4 molecules on silica, illite, calcite, and kerogen surfaces due to significant contributions of electrostatic interactions with the atoms of the associated surfaces. CO 2 and CH 4 molecules display higher adsorption energy on calcite and silica compared to those on illite and kerogen because of enhanced interactions with the positively charged calcium ions on the calcite surface and the hydroxyl group (-OH) on the silica surface. Enhanced internal nanopores and the availability of adsorption active sites in illite and kerogen matrices aid in higher partitioning of the gas molecules into these pores. CO 2 has a significant influence on the clustering and swelling of kerogen fragments compared to CH 4 . Higher CO 2 adsorption on inorganic and kerogen surfaces results in lower overall self-diffusivities compared to CH 4 . This study illustrates surface and pore size controls on the adsorption, partitioning, and self-diffusivities of CO 2 and CH 4 at conditions relevant for subsurface energy applications. The chemistry of the surfaces along with the availability of internal pores and active adsorption sites influences the adsorption behavior of gases. Our results suggest that CO 2 stored in depleted gas reservoirs may preferentially inhabit nanoconfined pores.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The joint automated repository for various integrated simulations (JARVIS) for data-driven materials design
The Joint Automated Repository for Various Integrated Simulations (JARVIS) is an integrated infrastructure to accelerate materials discovery and design using density functional theory (DFT), classical force-fields (FF), and machine learning (ML) techniques. JARVIS is motivated by the Materials Genome Initiative (MGI) principles of developing open-access databases and tools to reduce the cost and development time of materials discovery, optimization, and deployment. The major features of JARVIS are: JARVIS-DFT, JARVIS-FF, JARVIS-ML, and JARVIS-tools. To date, JARVIS consists of ≈40,000 materials and ≈1 million calculated properties in JARVIS-DFT, ≈500 materials and ≈110 force-fields in JARVIS-FF, and ≈25 ML models for material-property predictions in JARVIS-ML, all of which are continuously expanding. JARVIS-tools provides scripts and workflows for running and analyzing various simulations. We compare our computational data to experiments or high-fidelity computational methods wherever applicable to evaluate error/uncertainty in predictions. In addition to the existing workflows, the infrastructure can support a wide variety of other technologically important applications as part of the data-driven materials design paradigm. The JARVIS datasets and tools are publicly available at the website: https://jarvis.nist.gov .
36 MATERIALS SCIENCE↗