Theory and Simulations of Ionic Liquids in Nanoconfinement.

Room-temperature ionic liquids (RTILs) have exciting properties such as nonvolatility, large electrochemical windows, and remarkable variety, drawing much interest in energy storage, gating, electrocatalysis, tunable lubrication, and other applications. Confined RTILs appear in various situations, for instance, in pores of nanostructured electrodes of supercapacitors and batteries, as such electrodes increase the contact area with RTILs and enhance the total capacitance and stored energy, between crossed cylinders in surface force balance experiments, between a tip and a sample in atomic force microscopy, and between sliding surfaces in tribology experiments, where RTILs act as lubricants. The properties and functioning of RTILs in confinement, especially nanoconfinement, result in fascinating structural and dynamic phenomena, including layering, overscreening and crowding, nanoscale capillary freezing, quantized and electrotunable friction, and superionic state. This review offers a comprehensive analysis of the fundamental physical phenomena controlling the properties of such systems and the current state-of-the-art theoretical and simulation approaches developed for their description. We discuss these approaches sequentially by increasing atomistic complexity, paying particular attention to new physical phenomena emerging in nanoscale confinement. This review covers theoretical models, most of which are based on mapping the problems on pertinent statistical mechanics models with exact analytical solutions, allowing systematic analysis and new physical insights to develop more easily. We also describe a classical density functional theory, which offers a reliable and computationally inexpensive tool to account for some microscopic details and correlations that simplified models often fail to consider. Molecular simulations play a vital role in studying confined ionic liquids, enabling deep microscopic insights otherwise unavailable to researchers. We describe the basics of various simulation approaches and discuss their challenges and applicability to specific problems, focusing on RTIL structure in cylindrical and slit confinement and how it relates to friction and capacitive and dynamic properties of confined ions.

Size Sensitivity of Metabolite Diffusion in Macromolecular Crowds.

Metabolites play crucial roles in cellular processes, yet their diffusion in the densely packed interiors of cells remains poorly understood, compounded by conflicting reports in existing studies. Here, we employ pulsed-gradient stimulated-echo NMR and Brownian/Stokesian dynamics simulations to elucidate the behavior of nano- and subnanometer-sized tracers in crowded environments. Using Ficoll as a crowder, we observe a linear decrease in tracer diffusivity with increasing occupied volume fraction, persisting─somewhat surprisingly─up to volume fractions of 30-40%. While simulations suggest a linear correlation between diffusivity slowdown and particle size, experimental findings hint at a more intricate relationship, possibly influenced by Ficoll's porosity. Simulations and numerical calculations of tracer diffusivity in the E. coli cytoplasm show a nonlinear yet monotonic diffusion slowdown with particle size. We discuss our results in the context of nanoviscosity and discrepancies with existing studies.

Electrolytes in conducting nanopores: Revisiting constant charge and constant potential simulations.

Simulating electrolyte-electrode systems poses challenges due to the need to account for the electrode's response to ion movements in order to maintain a constant electrode potential, which slows down the simulations. To circumvent this, computationally more efficient constant charge (CC) simulations are sometimes employed. However, the accuracy of CC simulations in capturing the behavior of electrolyte-electrode systems remains unclear, especially for microporous electrodes. Herein, we consider electrolyte-filled slit nanopores and systematically analyze the in-pore ion structure and diffusivity using CC and constant potential simulations. Our results indicate that CC simulations provide comparable pore occupancies at high bulk ion densities and for highly charged pores, but they fail to accurately describe the ion structure and dynamics, particularly in quasi-2D (single-layer) pores and at low ion densities. We attribute these results to the superionic state emerging in conducting nanoconfinement and its interplay with excluded volume interactions.

Crowding-Regulated Binding of Divalent Biomolecules.

Macromolecular crowding affects biophysical processes as diverse as diffusion, gene expression, cell growth, and senescence. Yet, there is no comprehensive understanding of how crowding affects reactions, particularly multivalent binding. Herein, we use scaled particle theory and develop a molecular simulation method to investigate the binding of monovalent to divalent biomolecules. We find that crowding can increase or reduce cooperativity-the extent to which the binding of a second molecule is enhanced after binding a first molecule-by orders of magnitude, depending on the sizes of the involved molecular complexes. Cooperativity generally increases when a divalent molecule swells and then shrinks upon binding two ligands. Our calculations also reveal that, in some cases, crowding enables binding that does not occur otherwise. As an immunological example, we consider immunoglobulin G-antigen binding and show that crowding enhances its cooperativity in bulk but reduces it when an immunoglobulin G binds antigens on a surface.

Solvent Effects on Structure and Screening in Confined Electrolytes.

Using classical density functional theory, we investigate the influence of solvent on the structure and ionic screening of electrolytes under slit confinement and in contact with a reservoir. We consider a symmetric electrolyte with implicit and explicit solvent models and find that spatially resolving solvent molecules is essential for the ion structure at confining walls, excess ion adsorption, and the pressure exerted on the walls. Despite this, we observe only moderate differences in the period of oscillations of the pressure with the slit width and virtually coinciding decay lengths as functions of the scaling variable σ_{ion}/λ_{D}, where σ_{ion} is the ion diameter and λ_{D} the Debye length. Moreover, in the electrostatic-dominated regime, this scaling behavior is practically independent of the relative permittivity and its dependence on the ion concentration. In contrast, the crossover to the hard-core-dominated regime depends sensitively on all three factors.

A screening of results on the decay length in concentrated electrolytes.

Screening of electrostatic interactions in room-temperature ionic liquids and concentrated electrolytes has recently attracted much attention as surface force balance experiments have suggested the emergence of unanticipated anomalously large screening lengths at high ion concentrations. Termed underscreening, this effect was ascribed to the bulk properties of concentrated ionic systems. However, underscreening under experimentally relevant conditions is not predicted by classical theories and challenges our understanding of electrostatic correlations. Despite the enormous effort in performing large-scale simulations and new theoretical investigations, the origin of the anomalously long-range screening length remains elusive. This contribution briefly summarises the experimental, analytical and simulation results on ionic screening and the scaling behaviour of screening lengths. We then present an atomistic simulation approach that accounts for the solvent and ion exchange with a reservoir. We find that classical density functional theory (DFT) for concentrated electrolytes under confinement reproduces ion adsorption at charged interfaces surprisingly well. With DFT, we study confined electrolytes using implicit and explicit solvent models and the dependence on the solvent's dielectric properties. Our results demonstrate how the absence vs. presence of solvent particles and their discrete nature affect the short and long-range screening in concentrated ionic systems.

How macromolecules softness affects diffusion under crowding.

Diffusion in a macromolecularly crowded environment is essential for many intracellular processes, from metabolism and catalysis to gene transcription and translation. So far, theoretical and experimental work has focused on anomalous subdiffusion, and the effects of interactions, shapes, and composition, while the compactness or softness of macromolecules has received less attention. Herein, we use Brownian dynamics simulations to study how the softness of crowders affects macromolecular diffusion. We find that in most cases, soft crowders slow down the diffusion less effectively than hard crowders like Ficoll. For instance, at a 30% occupied volume fraction, the diffusion in Ficoll70 is about 20% slower than in soft crowders of the same size. However, our simulations indicate that elongated macromolecules, such as double-stranded DNA pieces, can diffuse comparably or even faster in hard crowders. We relate these effects to the volume excluded by soft and hard crowders to different tracers. Our results show that the softness and shape of macromolecules are crucial factors determining diffusion under crowding, relevant to diverse intracellular environments.

Conformation-changing enzymes and macromolecular crowding.

We study how crowding affects the activity and catalysis-enhanced diffusion of enzymes and passive tracers by employing a fluctuating-dumbbell model of conformation-changing enzymes. Our Brownian dynamics simulations reveal that the diffusion of enzymes depends qualitatively on the type of crowding. If only enzymes are present in the system, the catalysis-induced enhancement of the enzyme diffusion - somewhat counter-intuitively - increases with crowding, while it decreases if crowding is due to inert particles. For the tracers, the diffusion enhancement increases with increasing the enzyme concentration. We also show how the enzyme activity is reduced by crowding and propose a simple expression to describe this reduction. Our results highlight subtle effects at play concerning enzymatic activity and macromolecular transport in crowded systems, such as, e.g., the interior of living cells.

Capacitive energy storage in single-file pores: Exactly solvable models and simulations.

Understanding charge storage in low-dimensional electrodes is crucial for developing novel ecologically friendly devices for capacitive energy storage and conversion and water desalination. Exactly solvable models allow in-depth analyses and essential physical insights into the charging mechanisms. So far, however, such analytical approaches have been mainly limited to lattice models. Herein, we develop a versatile, exactly solvable, one-dimensional off-lattice model for charging single-file pores. Unlike the lattice model, this model shows an excellent quantitative agreement with three-dimensional Monte Carlo simulations. With analytical calculations and simulations, we show that the differential capacitance can be bell-shaped (one peak), camel-shaped (two peaks), or have four peaks. Transformations between these capacitance shapes can be induced by changing pore ionophilicity, by changing cation-anion size asymmetry, or by adding solvent. We find that the camel-shaped capacitance, characteristic of dilute electrolytes, appears for strongly ionophilic pores with high ion densities, which we relate to charging mechanisms specific to narrow pores. We also derive a large-voltage asymptotic expression for the capacitance, showing that the capacitance decays to zero as the inverse square of the voltage, C ∼ u-2. This dependence follows from hard-core interactions and is not captured by the lattice model.

Ionic screening in bulk and under confinement.

Recent experiments have shown that the repulsive force between atomically flat, like-charged surfaces confining room-temperature ionic liquids or concentrated electrolytes exhibits an anomalously large decay length. In our previous publication [J. Zeman, S. Kondrat, and C. Holm, Chem. Commun. 56, 15635 (2020)], we showed by means of extremely large-scale molecular dynamics simulations that this so-called underscreening effect might not be a feature of bulk electrolytes. Herein, we corroborate these findings by providing additional results with more detailed analyses and expand our investigations to ionic liquids under confinement. Unlike in bulk systems, where screening lengths are computed from the decay of interionic potentials of mean force, we extract such data in confined systems from cumulative charge distributions. At high concentrations, our simulations show increasing screening lengths with increasing electrolyte concentration, consistent with classical liquid state theories. However, our analyses demonstrate that-also for confined systems-there is no anomalously large screening length. As expected, the screening lengths determined for ionic liquids under confinement are in good quantitative agreement with the screening lengths of the same ionic systems in bulk. In addition, we show that some theoretical models used in the literature to relate the measured screening lengths to other observables are inapplicable to highly concentrated electrolytes.

Bridging transitions and capillary forces for colloids in a slit.

Capillary bridges can form between colloids immersed in a two-phase fluid, e.g., in a binary liquid mixture, if the surface of the colloids prefers the species other than the one favored in the bulk liquid. Here, we study the formation of liquid bridges induced by confining colloids to a slit, with the slit walls having a preference opposite to the one of the colloid surface. Using mean field theory, we show that there is a line of first-order phase transitions between the bridge and the no-bridge states, which ends at a critical point. By decreasing the slit width, this critical point is shifted toward smaller separations between the colloids. However, at very small separations and far from criticality, we observe only a minor influence of the slit width on the location of the transition. Monte Carlo simulations of the Ising model, which mimics incompressible binary liquid mixtures, confirm the occurrence of the bridging transitions, as manifested by the appearance of "spinodal" regions where both bridge and no-bridge configurations are stable or metastable. Interestingly, we find that there is no such spinodal region in the case of small colloids, but we observe a sharpening of the transition when the colloid size increases. In addition, we demonstrate that the capillary force acting between the colloids can depend sensitively on the slit width and varies drastically with temperature, thus achieving strengths orders of magnitude higher than at criticality of the fluid.

Brownian dynamics assessment of enhanced diffusion exhibited by 'fluctuating-dumbbell enzymes'.

Recent experiments have reported that diffusion of enzymes can be enhanced in the presence of their substrates. Using a fluctuating dumbbell model of enzymes, it has been argued that such an enhancement can be rationalized by the reduction of the enzyme size and by the suppression of the hydrodynamically coupled conformational fluctuations, induced by binding a substrate or an inhibitor to the enzyme [Nano Lett. 2017, 17, 4415]. Herein, we critically examine these expectations via extensive Brownian dynamics simulations of a similar model. The numerical results show that neither of the two mechanisms can cause an enhancement comparable to that reported experimentally, unless very large, physically counter-intuitive, enzyme deformations are invoked.

Superionic liquids in conducting nanoslits: A variety of phase transitions and ensuing charging behavior.

We develop a theory of charge storage in ultranarrow slitlike pores of nanostructured electrodes. Our analysis is based on the Blume-Capel model in an external field, which we solve analytically on a Bethe lattice. The obtained solutions allow us to explore the complete phase diagram of confined ionic liquids in terms of the key parameters characterizing the system, such as pore ionophilicity, interionic interaction energy, and voltage. The phase diagram includes the lines of first- and second-order, direct and re-entrant phase transitions, which are manifested by singularities in the corresponding capacitance-voltage plots. Testing our predictions experimentally requires monodisperse, conducting ultranarrow slit pores, to permit only one layer of ions, and thick pore walls, to prevent interionic interactions across the pore walls. However, some qualitative features, which distinguish the behavior of ionophilic and ionophobic pores and their underlying physics, may emerge in future experimental studies of more complex electrode structures.

Nonadditive interactions and phase transitions in strongly confined colloidal systems.

The behaviour of colloids can be controlled effectively by tuning the solvent-mediated interactions among them. An extensively studied example is the temperature-induced aggregation of suspended colloids close to the consolute point of their binary solvent. Here, using mean field theory and Monte Carlo simulations, we study the behaviour of colloids confined to a narrow slit containing a nearly-critical binary liquid mixture. We found that the effective interactions in this system are highly non-additive. In particular, the effective interactions among the colloids can be a few times stronger than the corresponding sum of the effective pair potentials. Inter alia, this non-additivity manifests itself in the phase behaviour of confined colloids, which depends sensitively on the slit width and temperature. In addition, we demonstrate the possibility of a first-order bridging transition between colloids confined to a slit and suspended in a phase-separated fluid well below the critical point of the solvent and at its critical composition in the bulk. This transition is accompanied by a remarkably large hysteresis loop, in which the force between the colloids varies by two orders of magnitude.

The effect of finite pore length on ion structure and charging.

Nanoporous supercapacitors play an important role in modern energy storage systems, and their modeling is essential to predict and optimize the charging behaviour. Two classes of models have been developed that consist of finite and infinitely long pores. Here, we show that although both types of models predict qualitatively consistent results, there are important differences emerging due to the finite pore length. In particular, we find that the ion density inside a finite pore is not constant, but increases linearly from the pore entrance to the pore end, where the ions form a strongly layered structure. This hinders a direct quantitative comparison between the two models. In addition, we show that although the ion density between the electrodes changes appreciably with the applied potential, this change has a minor effect on charging. Our simulations also reveal a complex charging behaviour, which is adsorption-driven at high voltages, but it is dominated either by co-ion desorption or by adsorption of both types of ions at low voltages, depending on the ion concentration.

Discrete-continuous reaction-diffusion model with mobile point-like sources and sinks.

In many applications in soft and biological physics, there are multiple time and length scales involved but often with a distinct separation between them. For instance, in enzyme kinetics, enzymes are relatively large, move slowly and their copy numbers are typically small, while the metabolites (being transformed by these enzymes) are often present in abundance, are small in size and diffuse fast. It seems thus natural to apply different techniques to different time and length levels and couple them. Here we explore this possibility by constructing a stochastic-deterministic discrete-continuous reaction-diffusion model with mobile sources and sinks. Such an approach allows in particular to separate different sources of stochasticity. We demonstrate its application by modelling enzyme-catalysed reactions with freely diffusing enzymes and a heterogeneous source of metabolites. Our calculations suggest that using a higher amount of less active enzymes, as compared to fewer more active enzymes, reduces the metabolite pool size and correspondingly the lag time, giving rise to a faster response to external stimuli. The methodology presented can be extended to more complex systems and offers exciting possibilities for studying problems where spatial heterogeneities, stochasticity or discreteness play a role.

Accelerating charging dynamics in subnanometre pores.

Supercapacitors have exceptional power density and cyclability but smaller energy density than batteries. Their energy density can be increased using ionic liquids and electrodes with subnanometre pores, but this tends to reduce their power density and compromise the key advantage of supercapacitors. To help address this issue through material optimization, here we unravel the mechanisms of charging subnanometre pores with ionic liquids using molecular dynamics simulations, navigated by a phenomenological model. We show that charging of ionophilic pores is a diffusive process, often accompanied by overfilling followed by de-filling. In sharp contrast to conventional expectations, charging is fast because ion diffusion during charging can be an order of magnitude faster than in the bulk, and charging itself is accelerated by the onset of collective modes. Further acceleration can be achieved using ionophobic pores by eliminating overfilling/de-filling and thus leading to charging behaviour qualitatively different from that in conventional, ionophilic pores.

The effect of composition on diffusion of macromolecules in a crowded environment.

We study diffusion of macromolecules in a crowded cytoplasm-like environment, focusing on its dependence on composition and its crossover to the anomalous subdiffusion. The crossover and the diffusion itself depend on both the volume fraction and the relative concentration of macromolecules. In accordance with previous theoretical and experimental studies, diffusion slows down when the volume fraction increases. Contrary to expectations, however, the diffusion is also strongly dependent on the molecular composition. The crossover time decreases and diffusion slows down when the smaller macromolecules start to dominate. Interestingly, diffusion is faster in a cytoplasm-like (more polydisperse) system than it is in a two-component system, at comparable packing fractions, or even when the cytoplasm packing fraction is larger.

Dynamics of Ion Transport in Ionic Liquids.

A gap in understanding the link between continuum theories of ion transport in ionic liquids and the underlying microscopic dynamics has hindered the development of frameworks for transport phenomena in these concentrated electrolytes. Here, we construct a continuum theory for ion transport in ionic liquids by coarse graining a simple exclusion process of interacting particles on a lattice. The resulting dynamical equations can be written as a gradient flow with a mobility matrix that vanishes at high densities. This form of the mobility matrix gives rise to a charging behavior that is different to the one known for electrolytic solutions, but which agrees qualitatively with the phenomenology observed in experiments and simulations.

Single-file charge storage in conducting nanopores.

Charging of a conducting tubular nanopore in a nanostructured electrode is treated using an exactly solvable 1D lattice model, including ion correlations screened by ion-image interactions. Analytical expressions are obtained for the accumulated charge and capacitance as a function of voltage. They show that the mechanism of charge storage, and the qualitative form of the capacitance-voltage curve, are sensitive to how favorable it is for ions to occupy the unpolarized pore, and the pore radius. Qualitative predictions of the theory are corroborated by Monte Carlo simulations. These results highlight the effect of ion affinity to unpolarized pores on the charge and energy storage in supercapacitors. Furthermore, they suggest that the question of the occupancy of unpolarized pores could be answered by measuring the capacitance-voltage dependence.