In situ investigation of water on MXene interfaces.

A continuum of water populations can exist in nanoscale layered materials, which impacts transport phenomena relevant for separation, adsorption, and charge storage processes. Quantification and direct interrogation of water structure and organization are important in order to design materials with molecular-level control for emerging energy and water applications. Through combining molecular simulations with ambient-pressure X-ray photoelectron spectroscopy, X-ray diffraction, and diffuse reflectance infrared Fourier transform spectroscopy, we directly probe hydration mechanisms at confined and nonconfined regions in nanolayered transition-metal carbide materials. Hydrophobic (K+) cations decrease water mobility within the confined interlayer and accelerate water removal at nonconfined surfaces. Hydrophilic cations (Li+) increase water mobility within the confined interlayer and decrease water-removal rates at nonconfined surfaces. Solutes, rather than the surface terminating groups, are shown to be more impactful on the kinetics of water adsorption and desorption. Calculations from grand canonical molecular dynamics demonstrate that hydrophilic cations (Li+) actively aid in water adsorption at MXene interfaces. In contrast, hydrophobic cations (K+) weakly interact with water, leading to higher degrees of water ordering (orientation) and faster removal at elevated temperatures.

MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC.

MoSDeF-GOMC is a python interface for the Monte Carlo software GOMC to the Molecular Simulation Design Framework (MoSDeF) ecosystem. MoSDeF-GOMC automates the process of generating initial coordinates, assigning force field parameters, and writing coordinate (PDB), connectivity (PSF), force field parameter, and simulation control files. The software lowers entry barriers for novice users while allowing advanced users to create complex workflows that encapsulate simulation setup, execution, and data analysis in a single script. All relevant simulation parameters are encoded within the workflow, ensuring reproducible simulations. MoSDeF-GOMC's capabilities are illustrated through a number of examples, including prediction of the adsorption isotherm for CO2 in IRMOF-1, free energies of hydration for neon and radon over a broad temperature range, and the vapor-liquid coexistence curve of a four-component surrogate for the jet fuel S-8. The MoSDeF-GOMC software is available on GitHub at https://github.com/GOMC-WSU/MoSDeF-GOMC.

Investigation of Multilayered Structures of Ionic Liquids on Graphite and Platinum Using Atomic Force Microscopy and Molecular Simulations.

The molecular-level orientation and structure of ionic liquids (ILs) at liquid-solid interfaces are significantly different than in the bulk. The interfacial ordering influences both IL properties, such as dielectric constants and viscosity, and their efficacy in devices, such as fuel cells and electrical capacitors. Here, we report the layered structures of four ILs on unbiased, highly ordered pyrolytic graphite (HOPG) and Pt(111) surfaces, as determined by atomic force microscopy. The ILs investigated are 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([emim][Tf2N]), 1-ethyl-3-methylimidazolium perfluorobutylsulfonate ([emim][C4F9SO3]), 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene bis(trifluoromethylsulfonyl)imide ([MTBD][Tf2N]), and 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene perfluorobutylsulfonate ([MTBD][C4F9SO3]). Molecular dynamics simulations provide complementary information on the position and orientation of the ions. These ILs form a cation layer at the IL-solid interface, followed by a layer of anions. [Emim]+ and [MTBD]+ have similar orientations at the surface, but [MTBD]+ forms a thinner layer compared to [emim]+ on both HOPG and Pt(111). In addition, [Tf2N]- shows stronger interactions with Pt(111) surfaces than [C4F9SO3]-.

High-throughput screening of tribological properties of monolayer films using molecular dynamics and machine learning.

Monolayer films have shown promise as a lubricating layer to reduce friction and wear of mechanical devices with separations on the nanoscale. These films have a vast design space with many tunable properties that can affect their tribological effectiveness. For example, terminal group chemistry, film composition, and backbone chemistry can all lead to films with significantly different tribological properties. This design space, however, is very difficult to explore without a combinatorial approach and an automatable, reproducible, and extensible workflow to screen for promising candidate films. Using the Molecular Simulation Design Framework (MoSDeF), a combinatorial screening study was performed to explore 9747 unique monolayer films (116 964 total simulations) and a machine learning (ML) model using a random forest regressor, an ensemble learning technique, to explore the role of terminal group chemistry and its effect on tribological effectiveness. The most promising films were found to contain small terminal groups such as cyano and ethylene. The ML model was subsequently applied to screen terminal group candidates identified from the ChEMBL small molecule library. Approximately 193 131 unique film candidates were screened with approximately a five order of magnitude speed-up in analysis compared to simulation alone. The ML model was thus able to be used as a predictive tool to greatly speed up the initial screening of promising candidate films for future simulation studies, suggesting that computational screening in combination with ML can greatly increase the throughput in combinatorial approaches to generate in silico data and then train ML models in a controlled, self-consistent fashion.

MoSDeF Cassandra: A complete Python interface for the Cassandra Monte Carlo software.

We introduce a new Python interface for the Cassandra Monte Carlo software, molecular simulation design framework (MoSDeF) Cassandra. MoSDeF Cassandra provides a simplified user interface, offers broader interoperability with other molecular simulation codes, enables the construction of programmatic and reproducible molecular simulation workflows, and builds the infrastructure necessary for high-throughput Monte Carlo studies. Many of the capabilities of MoSDeF Cassandra are enabled via tight integration with MoSDeF. We discuss the motivation and design of MoSDeF Cassandra and proceed to demonstrate both simple use-cases and more complex workflows, including adsorption in porous media and a combined molecular dynamics - Monte Carlo workflow for computing lateral diffusivity in graphene slit pores. The examples presented herein demonstrate how even relatively complex simulation workflows can be reduced to, at most, a few files of Python code that can be version-controlled and shared with other researchers. We believe this paradigm will enable more rapid research advances and represents the future of molecular simulations.

A mathematical model for Escherichia coli chemotaxis to competing stimuli.

Chemotactic bacteria sense and respond to temporal and spatial gradients of chemical cues in their surroundings. This phenomenon plays a critical role in many microbial processes such as groundwater bioremediation, microbially enhanced oil recovery, nitrogen fixation in legumes, and pathogenesis of the disease. Chemical heterogeneity in these natural systems may produce numerous competing signals from various directions. Predicting the migration behavior of bacterial populations under such conditions is necessary for designing effective treatment schemes. In this study, experimental studies and mathematical models are reported for the chemotactic response of Escherichia coli to a combination of attractant (α-methylaspartate) and repellent (NiCl2 ), which bind to the same transmembrane receptor complex. The model describes the binding of chemoeffectors and phosphorylation of the kinase in the signal transduction mechanism. Chemotactic parameters of E. coli (signaling efficiency σ , stimuli sensitivity coefficient γ , and repellent sensitivity coefficient κ ) were determined by fitting the model with experimental results for individual stimuli. Interestingly, our model naturally identifies NiCl2 as a repellent for κ>1 . The model is capable of describing quantitatively the response to the individual attractant and repellent, and correctly predicts the change in direction of bacterial population migration for competing stimuli with a twofold increase in repellent concentration.

Integral equation theory for mixtures of spherical and patchy colloids. 2. Numerical results.

Thermodynamic properties and structure of binary mixtures of patchy and spherical colloids are studied using a recently developed theory [Y. V. Kalyuzhnyi, et al., Soft Matter, 2020, 16, 3456]. The theory is based on a solution of the multidensity Ornstein-Zernike equation and provides completely analytical expressions for the structure factors of these systems and for all their major thermodynamical quantities. The considered mixtures are made up of particles of different size and with a different number of patches. A set of molecular simulation data has been generated to enable a systematic comparison and to access thus accuracy of the theoretical predictions. In general, the predictions of the theory appear to be in good agreement with computer simulation data. For the models with a lower number of patches (np = 1, 2) the theoretical results show very good accuracy. Less accurate are the predictions for the four-patch versions of the model. While theoretical results for the radial distribution functions are, generally, relatively accurate for all the models, results for thermodynamics deteriorate with increasing concentration of the spherical colloids. Possible ways to improve the theory are briefly outlined.

Integral equation theory for a mixture of spherical and patchy colloids: analytical description.

An analytic theory for the structure and thermodynamics of two-component mixtures of patchy and spherical colloids is developed. The theory is based on an analytical solution of the multidensity Ornstein-Zernike equation supplemented by the associative Percus-Yevick closure relations. We derive closed-form analytic expressions for the partial structure factors and thermodynamic properties using the energy route for the model with arbitrary number of patches and any hard-sphere size ratio of the particles. To assess the accuracy of the theoretical predictions we compare them against existing and newly generated set of computer simulation data. In our numerical calculations we consider the model with equal hard-sphere sizes and one patch. Very good agreement between results of the theory and simulation for the pair correlation functions, excess internal energy and pressure is observed for almost all values of the system density, temperature and composition studied. Only in the region of low concentrations of spherical colloids the theoretical results become less accurate.

Investigating Alkylsilane Monolayer Tribology at a Single-Asperity Contact with Molecular Dynamics Simulation.

Chemisorbed monolayer films are known to possess favorable characteristics for nanoscale lubrication of micro- and nanoelectromechanical systems (MEMS/NEMS). Prior studies have shown that the friction observed for monolayer-coated surfaces features a strong dependence on the geometry of contact. Specifically, tip-like geometries have been shown to penetrate into monolayer films, inducing defects in the monolayer chains and leading to plowing mechanisms during shear, which result in higher coefficients of friction (COF) than those observed for planar geometries. In this work, we use molecular dynamics simulations to examine the tribology of model silica single-asperity contacts under shear with monolayer-coated substrates featuring various film densities. It is observed that lower monolayer densities lead to reduced COFs, in contrast to results for planar systems where COF is found to be nearly independent of monolayer density. This is attributed to a liquid-like response to shear, whereby fewer defects are imparted in monolayer chains from the asperity, and chains are easily displaced by the tip as a result of the higher free volume. This transition in the mechanism of molecular plowing suggests that liquid-like films should provide favorable lubrication at single-asperity contacts.

Melting upon cooling and freezing upon heating: fluid-solid phase diagram for Svejk-Hasek model of dimerizing hard spheres.

A simple model of dimerizing hard spheres with highly nontrivial fluid-solid phase behavior is proposed and studied using the recently proposed resummed thermodynamic perturbation theory for central force (RTPT-CF) associating potentials. The phase diagram has the fluid branch of the fluid-solid coexistence curve located at temperatures lower than those of the solid branch. This unusual behavior is related to the strong dependence of the system excluded volume on the temperature, which for the model at hand decreases with increasing temperature. This effect can be also seen for a wide family of fluid models with an effective interaction that combines short range attraction and repulsion at a larger distance. We expect that for sufficiently high repulsive barrier, such systems may show similar phase behavior.

Influence of Surface Morphology on the Shear-Induced Wear of Alkylsilane Monolayers: Molecular Dynamics Study.

Chemisorbed alkylsilane monolayer coatings have been shown to possess favorable lubrication properties; however, film degradation prevents the widespread use of these materials as lubricants in micro- and nanoelectromechanical systems (MEMS/NEMS). In this work, molecular dynamics (MD) simulations are used to provide insight into the conditions that promote the degradation and wear of these materials. This is achieved through removal of interfacial chain-substrate bonds during shear and the examination of the mobility of the resulting free, unbound chains. Specific focus is given to the effects of surface morphology, which has been shown previously to strongly influence frictional forces in monolayer systems. In-plane order of chain attachments is shown to lead to pressure-induced orientational ordering of monolayers, promoting film stability. This behavior is lost as nonideality is introduced into the substrate and chain patterning on the surface becomes disordered. The presence of surface roughness is found to reduce film stability, with localization of wear observed for chain attachment sites nearest the interface of contact. The influence of substrate nonideality on monolayer degradation is shown to diminish as chain length is increased.

Enhancing graphene capacitance by nitrogen: effects of doping configuration and concentration.

Recent experiments have shown that nitrogen doping enhances capacitance in carbon electrode supercapacitors. However, a detailed study of the effect of N-doping on capacitance is still lacking. In this paper, we study the doping concentration and the configuration effect on the electric double-layer (EDL) capacitance, quantum capacitance, and total capacitance. It is found that pyridinic and graphitic nitrogens can increase the total capacitance by increasing quantum capacitance, but pyrrolic configuration limits the total capacitance due to its much lower quantum capacitance than the other two configurations. We also find that, unlike the graphitic and pyridinic nitrogens, the pyrrolic configuration's quantum capacitance does not depend on the nitrogen concentration, which may explain why some capacitance versus voltage measurements of N-doped graphene exhibit a V-shaped curve similar to that of undoped graphene. Our investigation provides a deeper understanding of the capacitance enhancement of the N-doping effect in carbon electrodes and suggests a potentially effective way to optimize the capacitance by controlling the type of N-doping.

Molecular mechanics of the cooperative adsorption of a Pro-Hyp-Gly tripeptide on a hydroxylated rutile TiO2(110) surface mediated by calcium ions.

The interaction of amino acids with inorganic materials at interfaces plays an important role in enhancing the biocompatibility of titanium-based alloys. The adsorption of a tripeptide, i.e. Pro-Hyp-Gly, on the hydroxylated rutile TiO2(110) surface was investigated by the MD simulations. The changes in free energy during the adsorption of both the tripeptide and calcium ions were calculated by using the PMF method in order to obtain the adsorption strength. The results suggested that the adsorption of the tripeptide on the TiO2 surface through the carboxyl groups in glycine residues can be more stable compared with other binding conformations. Special attention was focused on the cooperative adsorption of the tripeptide with the assistance of calcium ions. Calcium ions preferred to absorb at the tetradentate or monodentate sites on the negatively charged TiO2 surface. As a result of the strong attraction between the carboxyl group and calcium ions, the tripeptide can be pulled down to the surface by following the trajectory of the calcium ions, forming an indirect interaction with a sandwich structure of peptide-cation-TiO2. However, this indirect interaction could eventually transform to the direct adsorption of the tripeptide on the TiO2 surface with higher binding energy. The results may help to interpret the adsorption of peptides on inorganic materials in aqueous solution with ions.

A DFT study of water adsorption on rutile TiO2 (110) surface: The effects of surface steps.

The associative and dissociative adsorption of water molecules at low-coverage situations on rutile TiO2 (110) surface with step defects was investigated by the density functional theory calculations. Structural optimization of the hydroxylated/hydrated configurations at step edges along the 11̄1 crystal directions and the dynamic process of water dissociation were discussed to get a better description of the water/TiO2 interface. Our results indicate that steps on the TiO2 (110) surface could be an active site for water dissociation. The results of geometry optimization suggest that the stability of hydroxylated configuration is largely dependent on the locations of the H species and the recombination of water molecules from hydroxyls is observed in the fully hydroxylated condition. However, these hydroxyls can be stabilized by the associatively absorbed water nearby by forming competitive intermolecular hydrogen bonds. The dynamics of water dissociation and hydrogen diffusion were studied by the first principles molecular dynamics simulation and our results suggest that the hydrogen released by water dissociation can be transferred among the adsorbates, such as the unsaturated oxygen atoms-H2O-hydroxyl (TiO-H2O-OH) complex at step edges, or gradually diffuses to the bulk water system in the form of hydronium (H3O(+)) at higher water coverage.

A computational study of dicationic ionic liquids/CO2 interfaces.

Recent studies on CO2 capture using dicationic ionic liquids (DILs) demonstrated that DILs are promising absorbents for CO2 uptake especially compared with monocationic ionic liquids (MILs) analogues, in which each cation carries single positive charge in contrast to two unit charges of a dication. However, DILs/CO2 interfacial properties at the molecular level are still unknown. This work investigated the CO2 absorption properties of representative DILs, 1-alkyl-3-dimethylimidazolium bis(trifluoromethylsulfonyl)imide, [Cn(mim)2](Tf2N)2 (n = 3, 6, 12), using molecular dynamics (MD) simulations. The higher interfacial CO2 density at DIL than that at MIL interfaces suggests the increased CO2 interaction sites in DILs. The interfacial CO2 density also exhibits an alkyl chain length dependence which decreases with the elongation of alkyl chain and proportionally correlates with the content of fluorine atoms at interfaces. Different alkyl chain orientations in DILs were illustrated in contrast to those of MILs; both DILs and CO2 inside DILs exhibit lower diffusivity than MILs, in agreement with the stronger cation-anion binding energy of DILs. Moreover, DILs show a lower H2O and N2 uptake from flue gas compared with MILs, implicating the higher CO2/H2O and CO2/N2 selectivity.

Molecular dynamics study of alkylsilane monolayers on realistic amorphous silica surfaces.

Interfacial properties of n-alkylsilane monolayers on silica have been investigated with molecular dynamics simulations using both reactive and classical (i.e., nonreactive) force fields. A synthesis mimetic simulation (SMS) procedure using the reactive force field ReaxFF has been developed to mimic the experimental processing of silicon wafers involved in the preparation of alkylsilane monolayers; in the SMS procedure, amorphous silica surfaces are generated and exposed to hydrogen peroxide (H2O2) to create a hydroxide surface layer. Alkylsilane monolayers are then assembled on these surfaces, and their behavior is studied. To investigate the impact of the SMS procedure on monolayer properties, simulations have also been performed using more idealized monolayers assembled on crystalline surfaces and non-H2O2-processed amorphous surfaces. The simulations reported here demonstrate that processing-induced silica surface roughness plays a key role in the structure and frictional performance of monolayers. Furthermore, ignoring these effects results in a significant underestimation of the coefficient of friction and an overestimation of the orientational ordering of the monolayers.

Tunable transition from hydration to monomer-supported lubrication in zwitterionic monolayers revealed by molecular dynamics simulation.

The tribology of 2-methacryloyloxyethyl phosphorylcholine monolayers in water is studied using molecular dynamics simulations. Our results show two distinct shear regimes where the first is dominated by hydration lubrication, exhibiting near zero friction coefficients, and the second by chain-chain interactions, resembling monomer-supported lubrication. These results provide insight into the hydration lubrication mechanism - a phenomena thought to underlie the extremely efficient lubrication provided by surfaces functionalized with polyzwitterionic polymer brushes and the mammalian synovial joint.

Thickness-dependent structural arrangement in nano-confined imidazolium-based ionic liquid films.

A fundamental understanding of interfacial processes in nano-confined ionic liquids is crucial to increase the performance of modern energy storage devices. It is well-known that interfaces between electrodes and ionic liquids exhibit structures distinct from that of the bulk liquid. Following the recent interest in these systems, we studied the structure of thin ionic liquid films confined in flexible uncharged carbon nano-pores by using fully-atomistic molecular dynamics simulations. We show that the interfacial ions self-assemble into a closely-packed chequerboard-like pattern, formed by both cations and anions in direct contact with the pore wall, and that within this structure we find changes dependent on the thickness of the confined films. At low coverages a dense layer is formed in which both the imidazolium-ring and its alkyl-tail lie parallel to the pore wall. With increasing coverage the alkyl-chains reorient perpendicular to the surface, making space for additional ions until a densified highly ordered layer is formed. This wall-induced self-patterning into interfacial layers with significantly higher than bulk density is consistent with recent experimental and theoretical studies of similar systems. This work reveals additional molecular-level details on the effect of the film-thickness on the structure and density of the ionic liquid.

Examination of the phase transition behavior of nano-confined fluids by statistical temperature molecular dynamics.

The fluid-solid phase transition behavior of nano-confined Lennard-Jones fluids as a function of temperature and degree of nanoconfinement has been studied via statistical temperature molecular dynamics (STMD). The STMD method allows the direct calculation of the density of states and thus the heat capacity with high efficiency. The fluids are simulated between parallel solid surfaces with varying pore sizes, wall-fluid interaction energies, and registry of the walls. The fluid-solid phase transition behavior has been characterized through determination of the heat capacity. The results show that for pores of ideal-spacing, the order-disorder transition temperature (T(ODT)) is reduced as the pore size increases until values consistent with that seen in a bulk system. Also, as the interaction between the wall and fluid is reduced, T(ODT) is reduced due to weak constraints from the wall. However, for non-ideal spacing pores, quite different behavior is obtained, e.g., generally T(ODT) are largely reduced, and T(ODT) is decreased as the wall constraint becomes larger. For unaligned walls (i.e., whose lattices are not in registry), the fluid-solid transition is also detected as T is reduced, indicating non-ideality in orientation of the walls does not impact the formation of a solid, but results in a slight change in T(ODT) compared to the perfectly aligned systems. The STMD method is demonstrated to be a robust way for probing the phase transitions of nanoconfined fluids systematically, enabling the future examination of the phase transition behavior of more complex fluids.

Examining the aggregation behavior of polymer grafted nanoparticles using molecular simulation and theory.

Grafting polymers to nanoparticles is one approach used to control and enhance the structure and properties of nanomaterials. However, predicting the aggregation behavior of tethered nanoparticles (TNPs) is a somewhat trial and error process as a result of the large number of possible polymer tethers, nanoparticles, and solvent species that can be studied. With the main goal of understanding how to control the dispersion and aggregation of TNP systems, molecular simulations and the hetero-statistical associating fluid theory for potentials of variable range have been used to calculate the fluid phase equilibrium of TNPs in both vacuum and in simple solvents under a wide range of conditions. The role of graft length, graft density, and solvent interactions is examined and trends established. Additionally, the fluid distribution ratio (k value) is used to study the solubility of TNPs in industrially relevant solvents including carbon dioxide, nitrogen, propane, and ethylene.